adds EMgetKAM program

orientation averaging needs to be verified.

NamelistTemplates/EMgetKAM.template

@@ -0,0 +1,10 @@
+ &getKAM
+! min and max values to use for KAM map [degrees]; anything outside this range will be set to zero
+ kamrange = 0.0, 5.0,
+! orientation average (0 for no, integer otherwise; default 0)
+ orav = 20,
+! name of input dot product HDF5 file [relative to EMdatapathname]
+ dotproductfile = 'undefined',
+! name of tiff output file for KAM map [relative to EMdatapathname]
+ kamtiff = 'undefined',
+ /

Source/DictionaryIndexing/CMakeLists.txt

@@ -88,6 +88,15 @@ if(EMsoftOO_ENABLE_HDF5_SUPPORT)
                       INCLUDE_DIRS ${EMsoftOOLib_BINARY_DIR}
                       )
 
+  Add_EMsoftOO_Executable(TARGET EMgetKAM
+                      SOURCES ${APP_DIR}/EMgetKAM.f90 
+                      LINK_LIBRARIES ${EXE_LINK_LIBRARIES} 
+                      TEMPLATE ${TMPLT_DIR}/EMgetKAM.template 
+                      SOLUTION_FOLDER EMsoftOOPublic/DictionaryIndexing
+                      INSTALL_PROGRAM TRUE
+                      INCLUDE_DIRS ${EMsoftOOLib_BINARY_DIR}
+                      )
+
   Add_EMsoftOO_Executable(TARGET EMgetCTF
                       SOURCES ${APP_DIR}/EMgetCTF.f90 
                       LINK_LIBRARIES ${EXE_LINK_LIBRARIES} 

Source/DictionaryIndexing/EMgetKAM.f90

@@ -0,0 +1,59 @@
+! ###################################################################
+! Copyright (c) 2016-2024, Marc De Graef Research Group/Carnegie Mellon University
+! All rights reserved.
+!
+! Redistribution and use in source and binary forms, with or without modification, are 
+! permitted provided that the following conditions are met:
+!
+!     - Redistributions of source code must retain the above copyright notice, this list 
+!        of conditions and the following disclaimer.
+!     - Redistributions in binary form must reproduce the above copyright notice, this 
+!        list of conditions and the following disclaimer in the documentation and/or 
+!        other materials provided with the distribution.
+!     - Neither the names of Marc De Graef, Carnegie Mellon University nor the names 
+!        of its contributors may be used to endorse or promote products derived from 
+!        this software without specific prior written permission.
+!
+! THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 
+! AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 
+! IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE 
+! ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE 
+! LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL 
+! DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR 
+! SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER 
+! CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, 
+! OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE 
+! USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+! ###################################################################
+
+program EMgetKAM
+  !! author: MDG
+  !! version: 1.0 
+  !! date: 01/24/20
+  !!
+  !! 
+
+use mod_kinds
+use mod_global
+use mod_EMsoft
+use mod_KAM
+use stringconstants
+
+IMPLICIT NONE
+
+character(fnlen)                :: progname = 'EMgetKAM.f90'
+character(fnlen)                :: progdesc = 'Program to compute Kernel Average Misorientation maps'
+
+type(EMsoft_T)                  :: EMsoft
+type(KAM_T)                     :: KAM 
+
+! print the EMsoft header and handle any command line arguments  
+EMsoft = EMsoft_T( progname, progdesc, tpl = (/ 84 /) )
+
+! deal with the namelist stuff
+KAM = KAM_T(EMsoft%nmldeffile)
+
+! perform the computations
+call KAM%KAM(EMsoft, progname)
+
+end program EMgetKAM

Source/EMsoftOOLib/CMakeLists.txt

@@ -176,6 +176,7 @@ set(EMsoftOOLib_SRCS
   ${EMsoftOOLib_SOURCE_DIR}/program_mods/mod_SphInx.f90
   ${EMsoftOOLib_SOURCE_DIR}/program_mods/mod_4DEBSD.f90
   ${EMsoftOOLib_SOURCE_DIR}/program_mods/mod_ppEBSD.f90 
+  ${EMsoftOOLib_SOURCE_DIR}/program_mods/mod_KAM.f90 
 
   ${EMsoftOOLib_Additional_SRCS}
 )

Source/EMsoftOOLib/mod_rotations.f90

@@ -188,8 +188,8 @@ module mod_rotations
 
 ! we use a private parameter and a pair of get/set methods to control the precision (single or double);
 ! by default, all rotation operations are performed in double precision
-logical :: rotdoubleprecision = .TRUE.
-public :: setRotationPrecision, getRotationPrecision, toRadians, toDegrees, cvtoRadians, cvtoDegrees, &
+logical :: rotdoubleprecision = .TRUE., checkvalidity = .FALSE.
+public :: setRotationPrecision, setCheckValidity, getRotationPrecision, toRadians, toDegrees, cvtoRadians, cvtoDegrees, &
           RodriguesProduct, quat_average
 
 interface quat_average
@@ -2784,6 +2784,8 @@ recursive function r_check_(self) result(res)
 
 res = 1
 
+if (checkvalidity.eqv..TRUE.) then
+
 if (rotdoubleprecision) then
   if (self%rd(4).lt.0.D0) then
      call Message%printMessage('rotations:r_check: Rodrigues-Frank vector has negative length')
@@ -2799,6 +2801,7 @@ recursive function r_check_(self) result(res)
   self%r(1:3) = self%r(1:3) / r
   res = 0
 end if
+end if 
 
 end function r_check_
 
@@ -2826,6 +2829,8 @@ recursive function s_check_(self) result(res)
 
 res = 1
 
+if (checkvalidity.eqv..TRUE.) then
+
 if (rotdoubleprecision) then
   rd = sqrt(sum(self%sd*self%sd))
   if (rd.gt.(1.D0+epsd)) then
@@ -2839,6 +2844,7 @@ recursive function s_check_(self) result(res)
   endif
   res = 0
 end if
+end if 
 
 end function s_check_
 
@@ -2867,6 +2873,8 @@ recursive function o_check_(self) result(res)
 
 res = 1
 
+if (checkvalidity.eqv..TRUE.) then
+
 if (rotdoubleprecision) then
   ! compute the determinant (must be +1)
   detd = self%od(1,1)*self%od(2,2)*self%od(3,3) + self%od(1,2)*self%od(2,3)*self%od(3,1) + &
@@ -2904,6 +2912,7 @@ recursive function o_check_(self) result(res)
   endif
   res = 0
 end if
+end if 
 
 end function o_check_
 
@@ -2928,6 +2937,9 @@ recursive function h_check_(self) result(res)
 real(kind=dbl)             :: rd
 
 res = 1
+
+if (checkvalidity.eqv..TRUE.) then
+
 if (rotdoubleprecision) then
   rd = sqrt(sum(self%hd*self%hd))
   if (rd.gt.LPs%R1) then
@@ -2941,6 +2953,7 @@ recursive function h_check_(self) result(res)
   endif
   res = 0
 end if
+end if 
 
 end function h_check_
 
@@ -2968,6 +2981,8 @@ recursive function a_check_(self) result(res)
 
 res = 1
 
+if (checkvalidity.eqv..TRUE.) then
+
 if (rotdoubleprecision) then
   rd = sqrt(sum(self%ad(1:3)*self%ad(1:3)))
   if ((self%ad(4).lt.0.D0).or.(self%ad(4).gt.cPi)) then
@@ -2987,6 +3002,7 @@ recursive function a_check_(self) result(res)
   endif
   res = 0
 end if
+end if 
 
 end function a_check_
 
@@ -3014,6 +3030,9 @@ recursive function v_check_(self) result(res)
 
 res = 1
 
+if (checkvalidity.eqv..TRUE.) then
+
+
 if (rotdoubleprecision) then
   rd = sqrt(sum(self%vd*self%vd))
   write (*,*) rd, cPi, rd-cPi
@@ -3028,6 +3047,7 @@ recursive function v_check_(self) result(res)
   endif
   res = 0
 end if
+end if 
 
 end function v_check_
 
@@ -3053,6 +3073,9 @@ recursive function c_check_(self) result(res)
 
 res = 1
 
+if (checkvalidity.eqv..TRUE.) then
+
+
 if (rotdoubleprecision) then
   rd = maxval(abs(self%cd))
   if (rd.gt.LPs%ap/2.D0) then
@@ -3066,6 +3089,7 @@ recursive function c_check_(self) result(res)
   endif
   res = 0
 end if
+end if 
 
 end function c_check_
 
@@ -3089,6 +3113,9 @@ recursive function e_check_(self) result(res)
 
 res = 1
 
+if (checkvalidity.eqv..TRUE.) then
+
+
 if (rotdoubleprecision) then
   if ((self%ed(1).lt.0.D0).or.(self%ed(1).gt.(2.D0*cPi))) then
      call Message%printMessage('rotations:e_check: phi1 Euler angle outside of valid range [0,2pi]')
@@ -3112,6 +3139,7 @@ recursive function e_check_(self) result(res)
   endif
   res = 0
 end if
+end if 
 
 end function e_check_
 
@@ -3138,6 +3166,8 @@ recursive function q_check_(self) result(res)
 
 res = 1
 
+if (checkvalidity.eqv..TRUE.) then
+
 if (rotdoubleprecision) then
   rd = dsqrt(sum(self%qd*self%qd))
   self%qd = self%qd/rd
@@ -3147,7 +3177,7 @@ recursive function q_check_(self) result(res)
   self%q = self%q/r
   res = 0
 end if
-
+end if 
 end function q_check_
 
 !--------------------------------------------------------------------------
@@ -6099,6 +6129,18 @@ recursive function qe_(self) result(e)
 
 end function qe_
 
+!------------------------------------------
+subroutine setCheckValidity(c)
+!DEC$ ATTRIBUTES DLLEXPORT :: setCheckValidity
+
+IMPLICIT NONE
+
+logical, INTENT(IN)    :: c
+
+checkvalidity = c 
+
+end subroutine setCheckValidity
+
 !------------------------------------------
 subroutine setRotationPrecision(c)
 !DEC$ ATTRIBUTES DLLEXPORT :: setRotationPrecision