Skip to content

Commit

Permalink
Merge pull request #100 from mvdebolskiy/megan-fates-pr-follow-up
Browse files Browse the repository at this point in the history 
Megan fates pr follow up
  • Loading branch information
@mvdebolskiy
mvdebolskiy authored Jan 15, 2025
2 parents ca5cddb + 3a977f6 commit ce6b973
Show file tree
Hide file tree
Showing 7 changed files with 63 additions and 37 deletions.
1 change: 1 addition & 0 deletions bld/namelist_files/namelist_defaults_drydep.xml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -25,6 +25,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).

<megan_specifier>'ISOP = isoprene', 'C10H16 = pinene_a + carene_3 + thujene_a', 'CH3OH = methanol', 'C2H5OH = ethanol', 'CH2O = formaldehyde', 'CH3CHO = acetaldehyde', 'CH3COOH = acetic_acid', 'CH3COCH3 = acetone'</megan_specifier>

<megan_factors_file phys="clm6_0" use_fates=".true." >atm/cam/chem/trop_mozart/emis/megan21_emis_factors_78pft_c20161108.nc</megan_factors_file>
<megan_factors_file phys="clm6_0" >atm/cam/chem/trop_mozart/emis/megan21_emis_factors_78pft_c20161108.nc</megan_factors_file>
<megan_factors_file phys="clm5_1" >atm/cam/chem/trop_mozart/emis/megan21_emis_factors_78pft_c20161108.nc</megan_factors_file>
<megan_factors_file phys="clm5_0" >atm/cam/chem/trop_mozart/emis/megan21_emis_factors_78pft_c20161108.nc</megan_factors_file>
Expand Down
4 changes: 0 additions & 4 deletions cime_config/testdefs/testmods_dirs/clm/FatesColdMeganSatPhen/user_nl_clm
View file

This file was deleted.

57 changes: 36 additions & 21 deletions src/biogeochem/VOCEmissionMod.F90
View file
Original file line number Diff line number Diff line change
Expand Up @@ -92,7 +92,7 @@ subroutine Init(this, bounds)

if ( shr_megan_mechcomps_n > 0) then
if (use_fates) then
if (.not. use_fates_nocomp) then
if (.not. use_fates_nocomp) then ! SP implies NOCOMP is on.
call endrun( msg='ERROR: MEGAN currently only works with when FATES is in SP and/or NOCOMP mode '//&
errMsg(sourcefile, __LINE__))
end if
Expand Down Expand Up @@ -417,6 +417,7 @@ subroutine VOCEmission (bounds, num_soilp, filter_soilp, &
! !USES:
use subgridAveMod , only : p2g
use clm_varctl , only : use_fates
use GridcellType , only : grc
!
! !ARGUMENTS:
type(bounds_type) , intent(in) :: bounds
Expand Down Expand Up @@ -452,7 +453,9 @@ subroutine VOCEmission (bounds, num_soilp, filter_soilp, &
real(r8) :: par240_sha ! temporary

integer :: class_num, n_meg_comps, imech, imeg, ii
integer :: patchpft ! to transfer FATES PFT space into CLM PFT space.
integer :: l_pft_itype(bounds%begp:bounds%endp) ! local index of pft type
! that corresponds to pfts on megan factors
! for BGC it will be 1 to 1 with pftcon%itype(p)
character(len=16) :: mech_name
type(shr_megan_megcomp_t), pointer :: meg_cmp
real(r8) :: cp, alpha, Eopt, topt ! for history output
Expand Down Expand Up @@ -499,7 +502,6 @@ subroutine VOCEmission (bounds, num_soilp, filter_soilp, &
fsun240 => canopystate_inst%fsun240_patch , & ! Input: [real(r8) (:) ] sunlit fraction of canopy last 240 hrs
elai => canopystate_inst%elai_patch , & ! Input: [real(r8) (:) ] one-sided leaf area index with burying by snow
elai240 => canopystate_inst%elai240_patch , & ! Input: [real(r8) (:) ] one-sided leaf area index with burying by snow last 240 hrs
ci_fates => canopystate_inst%ci_patch , & !Input: [real(r8) (:) ] FATES-calculated internalleaf ci
cisun_z => photosyns_inst%cisun_z_patch , & ! Input: [real(r8) (:,:) ] sunlit intracellular CO2 (Pa)
cisha_z => photosyns_inst%cisha_z_patch , & ! Input: [real(r8) (:,:) ] shaded intracellular CO2 (Pa)

Expand Down Expand Up @@ -531,11 +533,29 @@ subroutine VOCEmission (bounds, num_soilp, filter_soilp, &
! initialize variables which get passed to the atmosphere
vocflx(bounds%begp:bounds%endp,:) = 0._r8
vocflx_tot(bounds%begp:bounds%endp) = 0._r8

do imeg=1,shr_megan_megcomps_n
meg_out(imeg)%flux_out(bounds%begp:bounds%endp) = 0._r8
enddo


! Get local pft types:
! this has to be done earlier, so if use_fates, we locally know what is not bare ground
! voc_pft_index comes from fates-internal mapping between pft's in megan_factors_file and fates pfts
l_pft_itype(bounds%begp:bounds%endp) = 0
if (use_fates) then
do fp = 1,num_soilp
p = filter_soilp(fp)
if (patch%is_fates(p)) then
l_pft_itype(p) = canopystate_inst%voc_pftindex_patch(p)
endif
end do
else
do fp = 1,num_soilp
p = filter_soilp(fp)
l_pft_itype(p) = patch%itype(p)
end do
end if

! Begin loop over points
!_______________________________________________________________________________
do fp = 1,num_soilp
Expand All @@ -551,7 +571,7 @@ subroutine VOCEmission (bounds, num_soilp, filter_soilp, &
vocflx_meg(:) = 0._r8

! calculate VOC emissions for non-bare ground Patches
if (patch%itype(p) > 0) then
if (l_pft_itype(p) > 0) then
gamma=0._r8

! Calculate PAR: multiply w/m2 by 4.6 to get umol/m2/s for par (added 8/14/02)
Expand Down Expand Up @@ -583,16 +603,10 @@ subroutine VOCEmission (bounds, num_soilp, filter_soilp, &

! set emis factor
! if specified, set EF for isoprene with mapped values
if(use_fates)then
patchpft = canopystate_inst%voc_pftindex_patch(p)
else
patchpft = patch%itype(p)
endif

if ( trim(meg_cmp%name) == 'isoprene' .and. shr_megan_mapped_emisfctrs) then
epsilon = get_map_EF(patchpft,g, vocemis_inst)
epsilon = get_map_EF(l_pft_itype(p),g, vocemis_inst)
else
epsilon = meg_cmp%emis_factors(patchpft)
epsilon = meg_cmp%emis_factors(l_pft_itype(p))
end if


Expand All @@ -604,20 +618,21 @@ subroutine VOCEmission (bounds, num_soilp, filter_soilp, &

! Activity factor for T
gamma_t = get_gamma_T(t_veg240(p), t_veg24(p),t_veg(p), ct1(class_num), ct2(class_num),&
betaT(class_num),LDF(class_num), Ceo(class_num), Eopt, topt, patchpft)
betaT(class_num),LDF(class_num), Ceo(class_num), Eopt, topt, l_pft_itype(p))

! Activity factor for Leaf Age
gamma_a = get_gamma_A(patchpft, elai240(p),elai(p),class_num)
gamma_a = get_gamma_A(l_pft_itype(p), elai240(p),elai(p),class_num)

! Activity factor for CO2 (only for isoprene)
if (trim(meg_cmp%name) == 'isoprene') then
co2_ppmv = 1.e6_r8*forc_pco2(g)/forc_pbot(c)
if(use_fates)then
gamma_c = get_gamma_C(ci_fates(p),ci_fates(p),forc_pbot(c),fsun(p), co2_ppmv)
else
gamma_c = get_gamma_C(cisun_z(p,1),cisha_z(p,1),forc_pbot(c),fsun(p), co2_ppmv)
gamma_c = get_gamma_C(cisun_z(p,1),cisha_z(p,1),forc_pbot(c),fsun(p), co2_ppmv)
! Check of valid intercellular co2 pressure values.
if (debug .and. (cisha_z(p,1) < 0.0_r8 .or. cisun_z(p,1) < 0.0_r8)) then
write(iulog,*) 'WARNINIG at ', __FILE__,__LINE__
write(iulog,*) 'Invalid intercellular co2 pressure (sunlit, shaded), gamma_c: ',cisun_z(p,1),cisha_z(p,1), gamma_c
write(iulog,*) 'Lat,Lon, voc patch type ',grc%latdeg(g),grc%londeg(g), l_pft_itype(p)
endif

else
gamma_c = 1._r8
end if
Expand Down
13 changes: 7 additions & 6 deletions src/biogeophys/BalanceCheckMod.F90
View file
Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@ module BalanceCheckMod
use decompMod , only : subgrid_level_gridcell, subgrid_level_column, subgrid_level_patch
use abortutils , only : endrun
use clm_varctl , only : iulog
use clm_varctl , only : use_fates_planthydro
use clm_varctl , only : use_fates_planthydro, use_fates
use clm_varpar , only : nlevsoi
use atm2lndType , only : atm2lnd_type
use EnergyFluxType , only : energyflux_type
Expand Down Expand Up @@ -952,14 +952,15 @@ subroutine BalanceCheck( bounds, &

errsol_max_val = maxval( abs(errsol(bounds%begp:bounds%endp)), mask = (errsol(bounds%begp:bounds%endp) /= spval) )

if ((errsol_max_val > energy_warning_thresh) .and. (DAnstep > skip_steps)) then
if ((errsol_max_val > energy_warning_thresh) .and. (DAnstep > skip_steps) ) then

indexp = maxloc( abs(errsol(bounds%begp:bounds%endp)), 1 , mask = (errsol(bounds%begp:bounds%endp) /= spval) ) + bounds%begp -1
indexg = patch%gridcell(indexp)
write(iulog,*)'WARNING:: BalanceCheck, solar radiation balance error (W/m2)'
write(iulog,*)'nstep = ',nstep
write(iulog,*)'errsol = ',errsol(indexp)

if (.not. use_fates) then
write(iulog,*)'WARNING:: BalanceCheck, solar radiation balance error (W/m2)'
write(iulog,*)'nstep = ',nstep
write(iulog,*)'errsol = ',errsol(indexp)
endif
if (errsol_max_val > error_thresh) then
write(iulog,*)'CTSM is stopping because errsol > ', error_thresh, ' W/m2'
write(iulog,*)'fsa = ',fsa(indexp)
Expand Down
3 changes: 1 addition & 2 deletions src/biogeophys/CanopyFluxesMod.F90
View file
Original file line number Diff line number Diff line change
Expand Up @@ -1111,9 +1111,8 @@ subroutine CanopyFluxes(bounds, num_exposedvegp, filter_exposedvegp,
vpd(p) = max((svpts(p) - eah(p)), 50._r8) * 0.001_r8

end do

if ( use_fates ) then

call clm_fates%wrap_photosynthesis(nc, bounds, fn, filterp(1:fn), &
svpts(begp:endp), eah(begp:endp), o2(begp:endp), &
co2(begp:endp), rb(begp:endp), dayl_factor(begp:endp), &
Expand Down
2 changes: 0 additions & 2 deletions src/biogeophys/CanopyStateType.F90
View file
Original file line number Diff line number Diff line change
Expand Up @@ -46,7 +46,6 @@ module CanopyStateType
real(r8) , pointer :: hbot_patch (:) ! patch canopy bottom (m)
real(r8) , pointer :: z0m_patch (:) ! patch momentum roughness length (m)
real(r8) , pointer :: displa_patch (:) ! patch displacement height (m)
real(r8) , pointer :: ci_patch (:) ! Internal leaf CO2 concentration for MEGAN
real(r8) , pointer :: fsun_patch (:) ! patch sunlit fraction of canopy
real(r8) , pointer :: fsun24_patch (:) ! patch 24hr average of sunlit fraction of canopy
real(r8) , pointer :: fsun240_patch (:) ! patch 240hr average of sunlit fraction of canopy
Expand Down Expand Up @@ -141,7 +140,6 @@ subroutine InitAllocate(this, bounds)
allocate(this%hbot_patch (begp:endp)) ; this%hbot_patch (:) = nan
allocate(this%z0m_patch (begp:endp)) ; this%z0m_patch (:) = nan
allocate(this%displa_patch (begp:endp)) ; this%displa_patch (:) = nan
allocate(this%ci_patch (begp:endp)) ; this%ci_patch (:) = nan
allocate(this%fsun_patch (begp:endp)) ; this%fsun_patch (:) = nan
allocate(this%fsun24_patch (begp:endp)) ; this%fsun24_patch (:) = nan
allocate(this%fsun240_patch (begp:endp)) ; this%fsun240_patch (:) = nan
Expand Down
20 changes: 18 additions & 2 deletions src/utils/clmfates_interfaceMod.F90
View file
Original file line number Diff line number Diff line change
Expand Up @@ -1616,6 +1616,10 @@ subroutine wrap_update_hlmfates_dyn(this, nc, bounds_clump, &
patch%is_bareground(col%patchi(c)) = .true.
npatch = this%fates(nc)%sites(s)%youngest_patch%patchno

! set voc_pft_index of bareground to 0 explicitly, so the bare ground is properly ignored in VOCEmissionMod
if (patch%is_bareground(col%patchi(c))) then
voc_pftindex(col%patchi(c)) = 0
endif
! Precision errors on the canopy_fraction_pa sum, even small (e-12)
! do exist, and can create potentially negetive bare-soil fractions
! (ie -1e-12 or smaller). Even though this is effectively zero,
Expand Down Expand Up @@ -2578,7 +2582,9 @@ subroutine wrap_photosynthesis(this, nc, bounds, fn, filterp, &
rssha => photosyns_inst%rssha_patch, &
psnsun => photosyns_inst%psnsun_patch, &
psnsha => photosyns_inst%psnsha_patch, &
ci => canopystate_inst%ci_patch)
cisun_z => photosyns_inst%cisun_z_patch, &
cisha_z => photosyns_inst%cisha_z_patch &
)
do s = 1, this%fates(nc)%nsites

c = this%f2hmap(nc)%fcolumn(s)
Expand Down Expand Up @@ -2645,7 +2651,17 @@ subroutine wrap_photosynthesis(this, nc, bounds, fn, filterp, &
this%fates(nc)%bc_in(s)%filter_photo_pa(ifp) = 3
rssun(p) = this%fates(nc)%bc_out(s)%rssun_pa(ifp)
rssha(p) = this%fates(nc)%bc_out(s)%rssha_pa(ifp)
ci(p) = this%fates(nc)%bc_out(s)%ci_pa(ifp)
! this is needed for MEGAN to work with FATES
cisun_z(p,:) = this%fates(nc)%bc_out(s)%ci_pa(ifp)
cisha_z(p,:) = this%fates(nc)%bc_out(s)%ci_pa(ifp)
if (this%fates(nc)%bc_out(s)%ci_pa(ifp) <0.0_r8) then
cisha_z(p,:) = 0.0_r8
cisun_z(p,:) = 0.0_r8
if (debug) then
write(iulog,*) 'WARNING: ci_pa is less than 0: ', this%fates(nc)%bc_out(s)%ci_pa(ifp)
write(iulog,*) 'filter ran photosynthesis s p icp ifp ilter',s,p,icp,ifp
endif
endif
! These fields are marked with a bad-value flag
photosyns_inst%psnsun_patch(p) = spval
photosyns_inst%psnsha_patch(p) = spval
Expand Down

0 comments on commit ce6b973

Please sign in to comment.