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DAMASK_EICMD
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Merge branch 'development' of magit1.mpie.de:damask/DAMASK into development

This commit is contained in:
Jennifer Nastola 2016-09-22 15:34:28 +02:00
parent a0567e8642 0f636bf6c3
commit f8901220ab
48 changed files with 1043 additions and 906 deletions
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2
DAMASK_env.zsh
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@ -41,7 +41,7 @@ if [ ! -z "$PS1" ]; then
echo Max-Planck-Institut für Eisenforschung GmbH, Düsseldorf echo Max-Planck-Institut für Eisenforschung GmbH, Düsseldorf
echo https://damask.mpie.de echo https://damask.mpie.de
echo echo
echo Using environment with ... echo "Using environment with ..."
echo "DAMASK $DAMASK_ROOT" echo "DAMASK $DAMASK_ROOT"
echo "Spectral Solver $SOLVER" echo "Spectral Solver $SOLVER"
echo "Post Processing $PROCESSING" echo "Post Processing $PROCESSING"

2
VERSION
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@ -1 +1 @@
v2.0.1-5-g920cf2c v2.0.1-132-g1180c8b

53
code/DAMASK_spectral.f90
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@ -150,17 +150,16 @@ program DAMASK_spectral
MPI_file_get_position, & MPI_file_get_position, &
MPI_file_write, & MPI_file_write, &
MPI_abort, & MPI_abort, &
MPI_finalize, &
MPI_allreduce, & MPI_allreduce, &
PETScFinalize PETScFinalize
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
! init DAMASK (all modules) ! init DAMASK (all modules)
call CPFEM_initAll(el = 1_pInt, ip = 1_pInt) call CPFEM_initAll(el = 1_pInt, ip = 1_pInt)
mainProcess: if (worldrank == 0) then
write(6,'(/,a)') ' <<<+- DAMASK_spectral init -+>>>' write(6,'(/,a)') ' <<<+- DAMASK_spectral init -+>>>'
write(6,'(a15,a)') ' Current time: ',IO_timeStamp() write(6,'(a15,a)') ' Current time: ',IO_timeStamp()
#include "compilation_info.f90" #include "compilation_info.f90"
endif mainProcess
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
! initialize field solver information ! initialize field solver information
@ -199,14 +198,14 @@ program DAMASK_spectral
allocate(loadCases(i)%ID(nActiveFields)) allocate(loadCases(i)%ID(nActiveFields))
field = 1 field = 1
loadCases(i)%ID(field) = FIELD_MECH_ID ! mechanical active by default loadCases(i)%ID(field) = FIELD_MECH_ID ! mechanical active by default
if (any(thermal_type == THERMAL_conduction_ID)) then ! thermal field active thermalActive: if (any(thermal_type == THERMAL_conduction_ID)) then
field = field + 1 field = field + 1
loadCases(i)%ID(field) = FIELD_THERMAL_ID loadCases(i)%ID(field) = FIELD_THERMAL_ID
endif endif thermalActive
if (any(damage_type == DAMAGE_nonlocal_ID)) then ! damage field active damageActive: if (any(damage_type == DAMAGE_nonlocal_ID)) then
field = field + 1 field = field + 1
loadCases(i)%ID(field) = FIELD_DAMAGE_ID loadCases(i)%ID(field) = FIELD_DAMAGE_ID
endif endif damageActive
enddo enddo
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
@ -232,8 +231,6 @@ program DAMASK_spectral
endif endif
do j = 1_pInt, 9_pInt do j = 1_pInt, 9_pInt
temp_maskVector(j) = IO_stringValue(line,chunkPos,i+j) /= '*' ! true if not a * temp_maskVector(j) = IO_stringValue(line,chunkPos,i+j) /= '*' ! true if not a *
enddo
do j = 1_pInt,9_pInt
if (temp_maskVector(j)) temp_valueVector(j) = IO_floatValue(line,chunkPos,i+j) ! read value where applicable if (temp_maskVector(j)) temp_valueVector(j) = IO_floatValue(line,chunkPos,i+j) ! read value where applicable
enddo enddo
loadCases(currentLoadCase)%deformation%maskLogical = & ! logical mask in 3x3 notation loadCases(currentLoadCase)%deformation%maskLogical = & ! logical mask in 3x3 notation
@ -245,8 +242,6 @@ program DAMASK_spectral
temp_valueVector = 0.0_pReal temp_valueVector = 0.0_pReal
do j = 1_pInt, 9_pInt do j = 1_pInt, 9_pInt
temp_maskVector(j) = IO_stringValue(line,chunkPos,i+j) /= '*' ! true if not an asterisk temp_maskVector(j) = IO_stringValue(line,chunkPos,i+j) /= '*' ! true if not an asterisk
enddo
do j = 1_pInt,9_pInt
if (temp_maskVector(j)) temp_valueVector(j) = IO_floatValue(line,chunkPos,i+j) ! read value where applicable if (temp_maskVector(j)) temp_valueVector(j) = IO_floatValue(line,chunkPos,i+j) ! read value where applicable
enddo enddo
loadCases(currentLoadCase)%P%maskLogical = transpose(reshape(temp_maskVector,[ 3,3])) loadCases(currentLoadCase)%P%maskLogical = transpose(reshape(temp_maskVector,[ 3,3]))
@ -303,14 +298,14 @@ program DAMASK_spectral
write(6,'(1x,a,i6)') 'load case: ', currentLoadCase write(6,'(1x,a,i6)') 'load case: ', currentLoadCase
if (.not. loadCases(currentLoadCase)%followFormerTrajectory) & if (.not. loadCases(currentLoadCase)%followFormerTrajectory) &
write(6,'(2x,a)') 'drop guessing along trajectory' write(6,'(2x,a)') 'drop guessing along trajectory'
if (loadCases(currentLoadCase)%deformation%myType=='l') then if (loadCases(currentLoadCase)%deformation%myType == 'l') then
do j = 1_pInt, 3_pInt do j = 1_pInt, 3_pInt
if (any(loadCases(currentLoadCase)%deformation%maskLogical(j,1:3) .eqv. .true.) .and. & if (any(loadCases(currentLoadCase)%deformation%maskLogical(j,1:3) .eqv. .true.) .and. &
any(loadCases(currentLoadCase)%deformation%maskLogical(j,1:3) .eqv. .false.)) & any(loadCases(currentLoadCase)%deformation%maskLogical(j,1:3) .eqv. .false.)) &
errorID = 832_pInt ! each row should be either fully or not at all defined errorID = 832_pInt ! each row should be either fully or not at all defined
enddo enddo
write(6,'(2x,a)') 'velocity gradient:' write(6,'(2x,a)') 'velocity gradient:'
else if (loadCases(currentLoadCase)%deformation%myType=='f') then else if (loadCases(currentLoadCase)%deformation%myType == 'f') then
write(6,'(2x,a)') 'deformation gradient at end of load case:' write(6,'(2x,a)') 'deformation gradient at end of load case:'
else else
write(6,'(2x,a)') 'deformation gradient rate:' write(6,'(2x,a)') 'deformation gradient rate:'
@ -339,7 +334,7 @@ program DAMASK_spectral
enddo; write(6,'(/)',advance='no') enddo; write(6,'(/)',advance='no')
enddo enddo
if (any(abs(math_mul33x33(loadCases(currentLoadCase)%rotation, & if (any(abs(math_mul33x33(loadCases(currentLoadCase)%rotation, &
math_transpose33(loadCases(currentLoadCase)%rotation))-math_I3) >& math_transpose33(loadCases(currentLoadCase)%rotation))-math_I3) > &
reshape(spread(tol_math_check,1,9),[ 3,3]))& reshape(spread(tol_math_check,1,9),[ 3,3]))&
.or. abs(math_det33(loadCases(currentLoadCase)%rotation)) > & .or. abs(math_det33(loadCases(currentLoadCase)%rotation)) > &
1.0_pReal + tol_math_check) errorID = 846_pInt ! given rotation matrix contains strain 1.0_pReal + tol_math_check) errorID = 846_pInt ! given rotation matrix contains strain
@ -379,7 +374,7 @@ program DAMASK_spectral
call Polarisation_init call Polarisation_init
case default case default
call IO_error(error_ID = 891, ext_msg = trim(spectral_solver)) call IO_error(error_ID = 891_pInt, ext_msg = trim(spectral_solver))
end select end select
@ -429,29 +424,30 @@ program DAMASK_spectral
allocate(outputSize(worldsize), source = 0_MPI_OFFSET_KIND) allocate(outputSize(worldsize), source = 0_MPI_OFFSET_KIND)
outputSize(worldrank+1) = size(materialpoint_results,kind=MPI_OFFSET_KIND)*int(pReal,MPI_OFFSET_KIND) outputSize(worldrank+1) = size(materialpoint_results,kind=MPI_OFFSET_KIND)*int(pReal,MPI_OFFSET_KIND)
call MPI_allreduce(MPI_IN_PLACE,outputSize,worldsize,MPI_LONG,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process call MPI_allreduce(MPI_IN_PLACE,outputSize,worldsize,MPI_LONG,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process
if(ierr /=0_pInt) call IO_error(894_pInt, ext_msg='MPI_allreduce') if (ierr /= 0_pInt) call IO_error(error_ID=894_pInt, ext_msg='MPI_allreduce')
call MPI_file_open(PETSC_COMM_WORLD, & call MPI_file_open(PETSC_COMM_WORLD, &
trim(getSolverWorkingDirectoryName())//trim(getSolverJobName())//'.spectralOut', & trim(getSolverWorkingDirectoryName())//trim(getSolverJobName())//'.spectralOut', &
MPI_MODE_WRONLY + MPI_MODE_APPEND, & MPI_MODE_WRONLY + MPI_MODE_APPEND, &
MPI_INFO_NULL, & MPI_INFO_NULL, &
resUnit, & resUnit, &
ierr) ierr)
if(ierr /=0_pInt) call IO_error(894_pInt, ext_msg='MPI_file_open') if (ierr /= 0_pInt) call IO_error(error_ID=894_pInt, ext_msg='MPI_file_open')
call MPI_file_get_position(resUnit,fileOffset,ierr) ! get offset from header call MPI_file_get_position(resUnit,fileOffset,ierr) ! get offset from header
if(ierr /=0_pInt) call IO_error(894_pInt, ext_msg='MPI_file_get_position') if (ierr /= 0_pInt) call IO_error(error_ID=894_pInt, ext_msg='MPI_file_get_position')
fileOffset = fileOffset + sum(outputSize(1:worldrank)) ! offset of my process in file (header + processes before me) fileOffset = fileOffset + sum(outputSize(1:worldrank)) ! offset of my process in file (header + processes before me)
call MPI_file_seek (resUnit,fileOffset,MPI_SEEK_SET,ierr) call MPI_file_seek (resUnit,fileOffset,MPI_SEEK_SET,ierr)
if(ierr /=0_pInt) call IO_error(894_pInt, ext_msg='MPI_file_seek') if (ierr /= 0_pInt) call IO_error(error_ID=894_pInt, ext_msg='MPI_file_seek')
if (.not. appendToOutFile) then ! if not restarting, write 0th increment if (.not. appendToOutFile) then ! if not restarting, write 0th increment
do i=1, size(materialpoint_results,3)/(maxByteOut/(materialpoint_sizeResults*pReal))+1 ! slice the output of my process in chunks not exceeding the limit for one output do i = 1, size(materialpoint_results,3)/(maxByteOut/(materialpoint_sizeResults*pReal))+1 ! slice the output of my process in chunks not exceeding the limit for one output
outputIndex=int([(i-1_pInt)*((maxRealOut)/materialpoint_sizeResults)+1_pInt, & outputIndex = int([(i-1_pInt)*((maxRealOut)/materialpoint_sizeResults)+1_pInt, &
min(i*((maxRealOut)/materialpoint_sizeResults),size(materialpoint_results,3))],pLongInt) min(i*((maxRealOut)/materialpoint_sizeResults),size(materialpoint_results,3))],pLongInt)
call MPI_file_write(resUnit,reshape(materialpoint_results(:,:,outputIndex(1):outputIndex(2)),& call MPI_file_write(resUnit, &
reshape(materialpoint_results(:,:,outputIndex(1):outputIndex(2)), &
[(outputIndex(2)-outputIndex(1)+1)*materialpoint_sizeResults]), & [(outputIndex(2)-outputIndex(1)+1)*materialpoint_sizeResults]), &
(outputIndex(2)-outputIndex(1)+1)*materialpoint_sizeResults,& (outputIndex(2)-outputIndex(1)+1)*materialpoint_sizeResults, &
MPI_DOUBLE, MPI_STATUS_IGNORE, ierr) MPI_DOUBLE, MPI_STATUS_IGNORE, ierr)
if(ierr /=0_pInt) call IO_error(894_pInt, ext_msg='MPI_file_write') if (ierr /= 0_pInt) call IO_error(error_ID=894_pInt, ext_msg='MPI_file_write')
enddo enddo
fileOffset = fileOffset + sum(outputSize) ! forward to current file position fileOffset = fileOffset + sum(outputSize) ! forward to current file position
if (worldrank == 0) & if (worldrank == 0) &
@ -490,7 +486,7 @@ program DAMASK_spectral
endif endif
timeinc = timeinc / 2.0_pReal**real(cutBackLevel,pReal) ! depending on cut back level, decrease time step timeinc = timeinc / 2.0_pReal**real(cutBackLevel,pReal) ! depending on cut back level, decrease time step
forwarding: if(totalIncsCounter >= restartInc) then forwarding: if (totalIncsCounter >= restartInc) then
stepFraction = 0_pInt stepFraction = 0_pInt
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
@ -596,7 +592,7 @@ program DAMASK_spectral
guess,timeinc,timeIncOld,remainingLoadCaseTime) guess,timeinc,timeIncOld,remainingLoadCaseTime)
end select end select
if(.not. solres(field)%converged) exit ! no solution found if (.not. solres(field)%converged) exit ! no solution found
enddo enddo
stagIter = stagIter + 1_pInt stagIter = stagIter + 1_pInt
stagIterate = stagIter < stagItMax .and. & stagIterate = stagIter < stagItMax .and. &
@ -711,6 +707,13 @@ program DAMASK_spectral
call PETScFinalize(ierr); CHKERRQ(ierr) call PETScFinalize(ierr); CHKERRQ(ierr)
#ifdef _OPENMP
call MPI_finalize(i)
if (i /= 0_pInt) then
call IO_error(error_ID=894, el=i, ext_msg="Finalize()")
endif
#endif
if (notConvergedCounter > 0_pInt) call quit(3_pInt) ! error if some are not converged if (notConvergedCounter > 0_pInt) call quit(3_pInt) ! error if some are not converged
call quit(0_pInt) ! no complains ;) call quit(0_pInt) ! no complains ;)

2
code/FEsolving.f90
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@ -60,8 +60,6 @@ subroutine FE_init
IO_warning, & IO_warning, &
IO_timeStamp IO_timeStamp
use DAMASK_interface use DAMASK_interface
use numerics, only: &
worldrank
implicit none implicit none
#if defined(Marc4DAMASK) || defined(Abaqus) #if defined(Marc4DAMASK) || defined(Abaqus)

3
code/IO.f90
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@ -129,6 +129,7 @@ recursive function IO_read(fileUnit,reset) result(line)
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
! normal case ! normal case
if (input == '') return ! regular line if (input == '') return ! regular line
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
! recursion case ! recursion case
if (stack >= 10_pInt) call IO_error(104_pInt,ext_msg=input) ! recursion limit reached if (stack >= 10_pInt) call IO_error(104_pInt,ext_msg=input) ! recursion limit reached
@ -141,7 +142,7 @@ recursive function IO_read(fileUnit,reset) result(line)
pathOn(stack) = path(1:scan(path,SEP,.true.))//input ! glue include to current file's dir pathOn(stack) = path(1:scan(path,SEP,.true.))//input ! glue include to current file's dir
endif endif
open(newunit=unitOn(stack),iostat=myStat,file=pathOn(stack)) ! open included file open(newunit=unitOn(stack),iostat=myStat,file=pathOn(stack),action='read') ! open included file
if (myStat /= 0_pInt) call IO_error(100_pInt,el=myStat,ext_msg=pathOn(stack)) if (myStat /= 0_pInt) call IO_error(100_pInt,el=myStat,ext_msg=pathOn(stack))
line = IO_read(fileUnit) line = IO_read(fileUnit)

113
code/Makefile
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@ -257,10 +257,10 @@ COMPILE_OPTIONS_gfortran :=-DDAMASKVERSION=\"${DAMASKVERSION}\"\
#-Wunsafe-loop-optimizations: warn if the loop cannot be optimized due to nontrivial assumptions. #-Wunsafe-loop-optimizations: warn if the loop cannot be optimized due to nontrivial assumptions.
#-Wstrict-overflow: #-Wstrict-overflow:
DEBUG_OPTIONS_gfortran :=-g\ DEBUG_OPTIONS_gfortran :=-g \
-fbacktrace\ -fbacktrace \
-fdump-core\ -fdump-core \
-fcheck=all\ -fcheck=all \
-ffpe-trap=invalid,zero,overflow -ffpe-trap=invalid,zero,overflow
################################################################################################### ###################################################################################################
@ -300,37 +300,60 @@ COMPILE =$(OPENMP_FLAG_$(F90)) $(STANDARD_CHECK_$(F90)) $(OPTIMIZATION_$
COMPILE_MAXOPTI =$(OPENMP_FLAG_$(F90)) $(STANDARD_CHECK_$(F90)) $(OPTIMIZATION_$(MAXOPTI)_$(F90)) $(COMPILE_OPTIONS_$(F90)) $(INCLUDE_DIRS) $(PRECISION_$(F90)) COMPILE_MAXOPTI =$(OPENMP_FLAG_$(F90)) $(STANDARD_CHECK_$(F90)) $(OPTIMIZATION_$(MAXOPTI)_$(F90)) $(COMPILE_OPTIONS_$(F90)) $(INCLUDE_DIRS) $(PRECISION_$(F90))
################################################################################################### ###################################################################################################
SOURCE_FILES = \ SOURCE_FILES = \
source_thermal_dissipation.o source_thermal_externalheat.o \ source_thermal_dissipation.o \
source_damage_isoBrittle.o source_damage_isoDuctile.o source_damage_anisoBrittle.o source_damage_anisoDuctile.o \ source_thermal_externalheat.o \
source_vacancy_phenoplasticity.o source_vacancy_irradiation.o source_vacancy_thermalfluc.o source_damage_isoBrittle.o \
source_damage_isoDuctile.o \
source_damage_anisoBrittle.o \
source_damage_anisoDuctile.o \
source_vacancy_phenoplasticity.o \
source_vacancy_irradiation.o \
source_vacancy_thermalfluc.o
KINEMATICS_FILES = \ KINEMATICS_FILES = \
kinematics_cleavage_opening.o kinematics_slipplane_opening.o \ kinematics_cleavage_opening.o \
kinematics_slipplane_opening.o \
kinematics_thermal_expansion.o \ kinematics_thermal_expansion.o \
kinematics_vacancy_strain.o kinematics_hydrogen_strain.o kinematics_vacancy_strain.o \
kinematics_hydrogen_strain.o
PLASTIC_FILES = \ PLASTIC_FILES = \
plastic_dislotwin.o plastic_disloUCLA.o plastic_isotropic.o \ plastic_dislotwin.o \
plastic_phenopowerlaw.o plastic_titanmod.o plastic_nonlocal.o plastic_none.o \ plastic_disloUCLA.o \
plastic_isotropic.o \
plastic_phenopowerlaw.o \
plastic_titanmod.o \
plastic_nonlocal.o \
plastic_none.o \
plastic_phenoplus.o plastic_phenoplus.o
THERMAL_FILES = \ THERMAL_FILES = \
thermal_isothermal.o thermal_adiabatic.o thermal_conduction.o thermal_isothermal.o \
thermal_adiabatic.o \
thermal_conduction.o
DAMAGE_FILES = \ DAMAGE_FILES = \
damage_none.o damage_local.o damage_nonlocal.o damage_none.o \
damage_local.o \
damage_nonlocal.o
VACANCYFLUX_FILES = \ VACANCYFLUX_FILES = \
vacancyflux_isoconc.o vacancyflux_isochempot.o vacancyflux_cahnhilliard.o vacancyflux_isoconc.o \
vacancyflux_isochempot.o \
vacancyflux_cahnhilliard.o
POROSITY_FILES = \ POROSITY_FILES = \
porosity_none.o porosity_phasefield.o porosity_none.o \
porosity_phasefield.o
HYDROGENFLUX_FILES = \ HYDROGENFLUX_FILES = \
hydrogenflux_isoconc.o hydrogenflux_cahnhilliard.o hydrogenflux_isoconc.o \
hydrogenflux_cahnhilliard.o
HOMOGENIZATION_FILES = \ HOMOGENIZATION_FILES = \
homogenization_RGC.o homogenization_isostrain.o homogenization_none.o homogenization_RGC.o \
homogenization_isostrain.o \
homogenization_none.o
##################### #####################
# Spectral Solver # Spectral Solver
@ -351,11 +374,28 @@ DAMASK_spectral.o: INTERFACENAME := spectral_interface.f90
SPECTRAL_SOLVER_FILES = spectral_mech_AL.o spectral_mech_Basic.o spectral_mech_Polarisation.o \ SPECTRAL_SOLVER_FILES = spectral_mech_AL.o spectral_mech_Basic.o spectral_mech_Polarisation.o \
spectral_thermal.o spectral_damage.o spectral_thermal.o spectral_damage.o
SPECTRAL_FILES = C_routines.o system_routines.o prec.o DAMASK_interface.o IO.o numerics.o debug.o math.o \ SPECTRAL_FILES = C_routines.o \
FEsolving.o mesh.o material.o lattice.o \ system_routines.o \
$(SOURCE_FILES) $(KINEMATICS_FILES) $(PLASTIC_FILES) constitutive.o \ prec.o \
DAMASK_interface.o \
IO.o \
numerics.o \
debug.o \
math.o \
FEsolving.o \
mesh.o \
material.o \
lattice.o \
$(SOURCE_FILES) \
$(KINEMATICS_FILES) \
$(PLASTIC_FILES) \
constitutive.o \
crystallite.o \ crystallite.o \
$(THERMAL_FILES) $(DAMAGE_FILES) $(VACANCYFLUX_FILES) $(HYDROGENFLUX_FILES) $(POROSITY_FILES) \ $(THERMAL_FILES) \
$(DAMAGE_FILES) \
$(VACANCYFLUX_FILES) \
$(HYDROGENFLUX_FILES) \
$(POROSITY_FILES) \
$(HOMOGENIZATION_FILES) homogenization.o \ $(HOMOGENIZATION_FILES) homogenization.o \
CPFEM2.o \ CPFEM2.o \
spectral_utilities.o \ spectral_utilities.o \
@ -401,14 +441,31 @@ DAMASK_FEM.exe: INCLUDE_DIRS += -I./
FEM_SOLVER_FILES = FEM_mech.o FEM_thermal.o FEM_damage.o FEM_vacancyflux.o FEM_porosity.o FEM_hydrogenflux.o FEM_SOLVER_FILES = FEM_mech.o FEM_thermal.o FEM_damage.o FEM_vacancyflux.o FEM_porosity.o FEM_hydrogenflux.o
FEM_FILES = prec.o DAMASK_interface.o FEZoo.o IO.o numerics.o debug.o math.o \ FEM_FILES = prec.o \
FEsolving.o mesh.o material.o lattice.o \ DAMASK_interface.o \
$(SOURCE_FILES) $(KINEMATICS_FILES) $(PLASTIC_FILES) constitutive.o \ FEZoo.o \
IO.o \
numerics.o \
debug.o \
math.o \
FEsolving.o \
mesh.o \
material.o \
lattice.o \
$(SOURCE_FILES) \
$(KINEMATICS_FILES) \
$(PLASTIC_FILES) \
constitutive.o \
crystallite.o \ crystallite.o \
$(THERMAL_FILES) $(DAMAGE_FILES) $(VACANCYFLUX_FILES) $(HYDROGENFLUX_FILES) $(POROSITY_FILES) \ $(THERMAL_FILES) \
$(DAMAGE_FILES) \
$(VACANCYFLUX_FILES) \
$(HYDROGENFLUX_FILES) \
$(POROSITY_FILES) \
$(HOMOGENIZATION_FILES) homogenization.o \ $(HOMOGENIZATION_FILES) homogenization.o \
CPFEM.o \ CPFEM.o \
FEM_utilities.o $(FEM_SOLVER_FILES) FEM_utilities.o \
$(FEM_SOLVER_FILES)
DAMASK_FEM.exe: DAMASK_FEM_driver.o DAMASK_FEM.exe: DAMASK_FEM_driver.o
$(PREFIX) $(LINKERNAME) $(OPENMP_FLAG_$(F90)) $(LINK_OPTIONS_$(F90)) $(STANDARD_CHECK_$(F90)) $(OPTIMIZATION_$(MAXOPTI)_$(F90)) \ $(PREFIX) $(LINKERNAME) $(OPENMP_FLAG_$(F90)) $(LINK_OPTIONS_$(F90)) $(STANDARD_CHECK_$(F90)) $(OPTIMIZATION_$(MAXOPTI)_$(F90)) \
@ -658,8 +715,8 @@ tidy:
@rm -rf *.inst.f90 # for instrumentation @rm -rf *.inst.f90 # for instrumentation
@rm -rf *.pomp.f90 # for instrumentation @rm -rf *.pomp.f90 # for instrumentation
@rm -rf *.pp.f90 # for instrumentation @rm -rf *.pp.f90 # for instrumentation
@rm -rf *.pdb # for instrumnentation @rm -rf *.pdb # for instrumentation
@rm -rf *.opari.inc # for instrumnentation @rm -rf *.opari.inc # for instrumentation
.PHONY: cleanDAMASK .PHONY: cleanDAMASK
cleanDAMASK: cleanDAMASK:

33
code/debug.f90
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@ -104,7 +104,6 @@ contains
subroutine debug_init subroutine debug_init
use, intrinsic :: iso_fortran_env ! to get compiler_version and compiler_options (at least for gfortran 4.6 at the moment) use, intrinsic :: iso_fortran_env ! to get compiler_version and compiler_options (at least for gfortran 4.6 at the moment)
use numerics, only: & use numerics, only: &
worldrank, &
nStress, & nStress, &
nState, & nState, &
nCryst, & nCryst, &
@ -130,36 +129,16 @@ subroutine debug_init
integer(pInt), allocatable, dimension(:) :: chunkPos integer(pInt), allocatable, dimension(:) :: chunkPos
character(len=65536) :: tag, line character(len=65536) :: tag, line
mainProcess: if (worldrank == 0) then
write(6,'(/,a)') ' <<<+- debug init -+>>>' write(6,'(/,a)') ' <<<+- debug init -+>>>'
write(6,'(a15,a)') ' Current time: ',IO_timeStamp() write(6,'(a15,a)') ' Current time: ',IO_timeStamp()
#include "compilation_info.f90" #include "compilation_info.f90"
endif mainProcess
if (allocated(debug_StressLoopLpDistribution)) & allocate(debug_StressLoopLpDistribution(nStress+1,2), source=0_pInt)
deallocate(debug_StressLoopLpDistribution) allocate(debug_StressLoopLiDistribution(nStress+1,2), source=0_pInt)
allocate(debug_StressLoopLpDistribution(nStress+1,2)) allocate(debug_StateLoopDistribution(nState+1,2), source=0_pInt)
debug_StressLoopLpDistribution = 0_pInt allocate(debug_CrystalliteLoopDistribution(nCryst+1), source=0_pInt)
if (allocated(debug_StressLoopLiDistribution)) & allocate(debug_MaterialpointStateLoopDistribution(nMPstate), source=0_pInt)
deallocate(debug_StressLoopLiDistribution) allocate(debug_MaterialpointLoopDistribution(nHomog+1), source=0_pInt)
allocate(debug_StressLoopLiDistribution(nStress+1,2))
debug_StressLoopLiDistribution = 0_pInt
if (allocated(debug_StateLoopDistribution)) &
deallocate(debug_StateLoopDistribution)
allocate(debug_StateLoopDistribution(nState+1,2))
debug_StateLoopDistribution = 0_pInt
if (allocated(debug_CrystalliteLoopDistribution)) &
deallocate(debug_CrystalliteLoopDistribution)
allocate(debug_CrystalliteLoopDistribution(nCryst+1))
debug_CrystalliteLoopDistribution = 0_pInt
if (allocated(debug_MaterialpointStateLoopDistribution)) &
deallocate(debug_MaterialpointStateLoopDistribution)
allocate(debug_MaterialpointStateLoopDistribution(nMPstate))
debug_MaterialpointStateLoopDistribution = 0_pInt
if (allocated(debug_MaterialpointLoopDistribution)) &
deallocate(debug_MaterialpointLoopDistribution)
allocate(debug_MaterialpointLoopDistribution(nHomog+1))
debug_MaterialpointLoopDistribution = 0_pInt
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
! try to open the config file ! try to open the config file

4
code/math.f90
View File

@ -158,7 +158,8 @@ module math
math_areaTriangle, & math_areaTriangle, &
math_rotate_forward33, & math_rotate_forward33, &
math_rotate_backward33, & math_rotate_backward33, &
math_rotate_forward3333 math_rotate_forward3333, &
math_limit
private :: & private :: &
math_partition, & math_partition, &
halton, & halton, &
@ -178,7 +179,6 @@ subroutine math_init
use, intrinsic :: iso_fortran_env ! to get compiler_version and compiler_options (at least for gfortran 4.6 at the moment) use, intrinsic :: iso_fortran_env ! to get compiler_version and compiler_options (at least for gfortran 4.6 at the moment)
use prec, only: tol_math_check use prec, only: tol_math_check
use numerics, only: & use numerics, only: &
worldrank, &
fixedSeed fixedSeed
use IO, only: IO_error, IO_timeStamp use IO, only: IO_error, IO_timeStamp

13
code/mesh.f90
View File

@ -481,6 +481,7 @@ subroutine mesh_init(ip,el)
#endif #endif
#ifdef Spectral #ifdef Spectral
IO_open_file, & IO_open_file, &
IO_error, &
#else #else
IO_open_InputFile, & IO_open_InputFile, &
#endif #endif
@ -507,7 +508,8 @@ subroutine mesh_init(ip,el)
implicit none implicit none
#ifdef Spectral #ifdef Spectral
integer(C_INTPTR_T) :: gridMPI(3), alloc_local, local_K, local_K_offset integer(C_INTPTR_T) :: devNull, local_K, local_K_offset
integer :: ierr, worldsize
#endif #endif
integer(pInt), parameter :: FILEUNIT = 222_pInt integer(pInt), parameter :: FILEUNIT = 222_pInt
integer(pInt), intent(in) :: el, ip integer(pInt), intent(in) :: el, ip
@ -547,10 +549,13 @@ subroutine mesh_init(ip,el)
call IO_open_file(FILEUNIT,geometryFile) ! parse info from geometry file... call IO_open_file(FILEUNIT,geometryFile) ! parse info from geometry file...
if (myDebug) write(6,'(a)') ' Opened geometry file'; flush(6) if (myDebug) write(6,'(a)') ' Opened geometry file'; flush(6)
grid = mesh_spectral_getGrid(fileUnit) grid = mesh_spectral_getGrid(fileUnit)
call MPI_comm_size(MPI_COMM_WORLD, worldsize, ierr)
if(ierr /=0_pInt) call IO_error(894_pInt, ext_msg='MPI_comm_size')
if(worldsize>grid(3)) call IO_error(894_pInt, ext_msg='number of processes exceeds grid(3)')
geomSize = mesh_spectral_getSize(fileUnit) geomSize = mesh_spectral_getSize(fileUnit)
gridMPI = int(grid,C_INTPTR_T) devNull = fftw_mpi_local_size_3d(int(grid(3),C_INTPTR_T),int(grid(2),C_INTPTR_T),&
alloc_local = fftw_mpi_local_size_3d(gridMPI(3), gridMPI(2), gridMPI(1)/2 +1, & int(grid(1),C_INTPTR_T)/2+1,MPI_COMM_WORLD,local_K,local_K_offset)
MPI_COMM_WORLD, local_K, local_K_offset)
grid3 = int(local_K,pInt) grid3 = int(local_K,pInt)
grid3Offset = int(local_K_offset,pInt) grid3Offset = int(local_K_offset,pInt)
size3 = geomSize(3)*real(grid3,pReal) /real(grid(3),pReal) size3 = geomSize(3)*real(grid3,pReal) /real(grid(3),pReal)

2
code/plastic_nonlocal.f90
View File

@ -1115,7 +1115,7 @@ allocate(nonSchmidProjection(3,3,4,maxTotalNslip,maxNinstances),
initializeInstances: do phase = 1_pInt, size(phase_plasticity) initializeInstances: do phase = 1_pInt, size(phase_plasticity)
NofMyPhase=count(material_phase==phase) NofMyPhase=count(material_phase==phase)
myPhase2: if (phase_plasticity(phase) == PLASTICITY_NONLOCAL_ID .and. NofMyPhase/=0) then myPhase2: if (phase_plasticity(phase) == PLASTICITY_NONLOCAL_ID) then
instance = phase_plasticityInstance(phase) instance = phase_plasticityInstance(phase)
!*** Inverse lookup of my slip system family and the slip system in lattice !*** Inverse lookup of my slip system family and the slip system in lattice

2
code/prec.f90
View File

@ -81,7 +81,7 @@ module prec
nTwin = 0_pInt, & nTwin = 0_pInt, &
nTrans = 0_pInt nTrans = 0_pInt
logical :: & logical :: &
nonlocal = .false. !< absolute tolerance for state integration nonlocal = .false.
real(pReal), pointer, dimension(:,:), contiguous :: & real(pReal), pointer, dimension(:,:), contiguous :: &
slipRate, & !< slip rate slipRate, & !< slip rate
accumulatedSlip !< accumulated plastic slip accumulatedSlip !< accumulated plastic slip

11
code/spectral_interface.f90
View File

@ -57,7 +57,8 @@ subroutine DAMASK_interface_init()
integer :: & integer :: &
i, & i, &
threadLevel, & threadLevel, &
worldrank = 0 worldrank = 0, &
worldsize = 0
integer, allocatable, dimension(:) :: & integer, allocatable, dimension(:) :: &
chunkPos chunkPos
integer, dimension(8) :: & integer, dimension(8) :: &
@ -66,6 +67,7 @@ subroutine DAMASK_interface_init()
external :: & external :: &
quit,& quit,&
MPI_Comm_rank,& MPI_Comm_rank,&
MPI_Comm_size,&
PETScInitialize, & PETScInitialize, &
MPI_Init_Thread, & MPI_Init_Thread, &
MPI_abort MPI_abort
@ -77,17 +79,17 @@ subroutine DAMASK_interface_init()
#ifdef _OPENMP #ifdef _OPENMP
call MPI_Init_Thread(MPI_THREAD_FUNNELED,threadLevel,ierr);CHKERRQ(ierr) ! in case of OpenMP, don't rely on PETScInitialize doing MPI init call MPI_Init_Thread(MPI_THREAD_FUNNELED,threadLevel,ierr);CHKERRQ(ierr) ! in case of OpenMP, don't rely on PETScInitialize doing MPI init
if (threadLevel<MPI_THREAD_FUNNELED) then if (threadLevel<MPI_THREAD_FUNNELED) then
write(6,'(a)') 'MPI library does not support OpenMP' write(6,'(a)') ' MPI library does not support OpenMP'
call quit(1_pInt) call quit(1_pInt)
endif endif
#endif #endif
call PetscInitialize(PETSC_NULL_CHARACTER,ierr) ! according to PETSc manual, that should be the first line in the code call PetscInitialize(PETSC_NULL_CHARACTER,ierr) ! according to PETSc manual, that should be the first line in the code
CHKERRQ(ierr) ! this is a macro definition, it is case sensitive CHKERRQ(ierr) ! this is a macro definition, it is case sensitive
call MPI_Comm_rank(PETSC_COMM_WORLD,worldrank,ierr);CHKERRQ(ierr) call MPI_Comm_rank(PETSC_COMM_WORLD,worldrank,ierr);CHKERRQ(ierr)
call MPI_Comm_size(MPI_COMM_WORLD, worldsize, ierr);CHKERRQ(ierr)
mainProcess: if (worldrank == 0) then mainProcess: if (worldrank == 0) then
if (output_unit /= 6) then if (output_unit /= 6) then
write(output_unit,'(a)') 'STDOUT != 6' write(output_unit,'(a)') ' STDOUT != 6'
call quit(1_pInt) call quit(1_pInt)
endif endif
else mainProcess else mainProcess
@ -104,6 +106,7 @@ subroutine DAMASK_interface_init()
write(6,'(a,2(i2.2,a),i2.2)') ' Time: ',dateAndTime(5),':',& write(6,'(a,2(i2.2,a),i2.2)') ' Time: ',dateAndTime(5),':',&
dateAndTime(6),':',& dateAndTime(6),':',&
dateAndTime(7) dateAndTime(7)
write(6,'(/,a,i4.1)') ' MPI processes: ',worldsize
write(6,'(/,a)') ' <<<+- DAMASK_interface init -+>>>' write(6,'(/,a)') ' <<<+- DAMASK_interface init -+>>>'
#include "compilation_info.f90" #include "compilation_info.f90"

2
code/spectral_thermal.f90
View File

@ -245,7 +245,7 @@ type(tSolutionState) function spectral_thermal_solution(guess,timeinc,timeinc_ol
if (worldrank == 0) then if (worldrank == 0) then
if (spectral_thermal_solution%converged) & if (spectral_thermal_solution%converged) &
write(6,'(/,a)') ' ... thermal conduction converged ..................................' write(6,'(/,a)') ' ... thermal conduction converged ..................................'
write(6,'(/,a,f8.4,2x,f8.4,2x,f8.4,/)',advance='no') ' Minimum|Maximum|Delta Temperature = ',& write(6,'(/,a,f8.4,2x,f8.4,2x,f8.4,/)',advance='no') ' Minimum|Maximum|Delta Temperature / K = ',&
minTemperature, maxTemperature, stagNorm minTemperature, maxTemperature, stagNorm
write(6,'(/,a)') ' ===========================================================================' write(6,'(/,a)') ' ==========================================================================='
flush(6) flush(6)

68
code/spectral_utilities.f90
View File

@ -172,8 +172,7 @@ subroutine utilities_init()
memory_efficient, & memory_efficient, &
petsc_defaultOptions, & petsc_defaultOptions, &
petsc_options, & petsc_options, &
divergence_correction, & divergence_correction
worldrank
use debug, only: & use debug, only: &
debug_level, & debug_level, &
debug_SPECTRAL, & debug_SPECTRAL, &
@ -212,11 +211,9 @@ subroutine utilities_init()
vecSize = 3_C_INTPTR_T, & vecSize = 3_C_INTPTR_T, &
tensorSize = 9_C_INTPTR_T tensorSize = 9_C_INTPTR_T
mainProcess: if (worldrank == 0) then
write(6,'(/,a)') ' <<<+- spectral_utilities init -+>>>' write(6,'(/,a)') ' <<<+- spectral_utilities init -+>>>'
write(6,'(a15,a)') ' Current time: ',IO_timeStamp() write(6,'(a15,a)') ' Current time: ',IO_timeStamp()
#include "compilation_info.f90" #include "compilation_info.f90"
endif mainProcess
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
! set debugging parameters ! set debugging parameters
@ -224,11 +221,11 @@ subroutine utilities_init()
debugRotation = iand(debug_level(debug_SPECTRAL),debug_SPECTRALROTATION) /= 0 debugRotation = iand(debug_level(debug_SPECTRAL),debug_SPECTRALROTATION) /= 0
debugPETSc = iand(debug_level(debug_SPECTRAL),debug_SPECTRALPETSC) /= 0 debugPETSc = iand(debug_level(debug_SPECTRAL),debug_SPECTRALPETSC) /= 0
if(debugPETSc .and. worldrank == 0_pInt) write(6,'(3(/,a),/)') & if(debugPETSc) write(6,'(3(/,a),/)') &
' Initializing PETSc with debug options: ', & ' Initializing PETSc with debug options: ', &
trim(PETScDebug), & trim(PETScDebug), &
' add more using the PETSc_Options keyword in numerics.config ' ' add more using the PETSc_Options keyword in numerics.config '; flush(6)
flush(6)
call PetscOptionsClear(ierr); CHKERRQ(ierr) call PetscOptionsClear(ierr); CHKERRQ(ierr)
if(debugPETSc) call PetscOptionsInsertString(trim(PETSCDEBUG),ierr); CHKERRQ(ierr) if(debugPETSc) call PetscOptionsInsertString(trim(PETSCDEBUG),ierr); CHKERRQ(ierr)
call PetscOptionsInsertString(trim(petsc_defaultOptions),ierr); CHKERRQ(ierr) call PetscOptionsInsertString(trim(petsc_defaultOptions),ierr); CHKERRQ(ierr)
@ -237,10 +234,8 @@ subroutine utilities_init()
grid1Red = grid(1)/2_pInt + 1_pInt grid1Red = grid(1)/2_pInt + 1_pInt
wgt = 1.0/real(product(grid),pReal) wgt = 1.0/real(product(grid),pReal)
if (worldrank == 0) then
write(6,'(a,3(i12 ))') ' grid a b c: ', grid write(6,'(a,3(i12 ))') ' grid a b c: ', grid
write(6,'(a,3(es12.5))') ' size x y z: ', geomSize write(6,'(a,3(es12.5))') ' size x y z: ', geomSize
endif
select case (spectral_derivative) select case (spectral_derivative)
case ('continuous') ! default, no weighting case ('continuous') ! default, no weighting
@ -342,8 +337,7 @@ subroutine utilities_init()
if (pReal /= C_DOUBLE .or. pInt /= C_INT) call IO_error(0_pInt,ext_msg='Fortran to C') ! check for correct precision in C if (pReal /= C_DOUBLE .or. pInt /= C_INT) call IO_error(0_pInt,ext_msg='Fortran to C') ! check for correct precision in C
call fftw_set_timelimit(fftw_timelimit) ! set timelimit for plan creation call fftw_set_timelimit(fftw_timelimit) ! set timelimit for plan creation
if (debugGeneral .and. worldrank == 0_pInt) write(6,'(/,a)') ' FFTW initialized' if (debugGeneral) write(6,'(/,a)') ' FFTW initialized'; flush(6)
flush(6)
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
! calculation of discrete angular frequencies, ordered as in FFTW (wrap around) ! calculation of discrete angular frequencies, ordered as in FFTW (wrap around)
@ -527,8 +521,6 @@ subroutine utilities_fourierGammaConvolution(fieldAim)
use math, only: & use math, only: &
math_det33, & math_det33, &
math_invert math_invert
use numerics, only: &
worldrank
use mesh, only: & use mesh, only: &
grid3, & grid3, &
grid, & grid, &
@ -545,10 +537,8 @@ subroutine utilities_fourierGammaConvolution(fieldAim)
logical :: err logical :: err
if (worldrank == 0_pInt) then
write(6,'(/,a)') ' ... doing gamma convolution ...............................................' write(6,'(/,a)') ' ... doing gamma convolution ...............................................'
flush(6) flush(6)
endif
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
! do the actual spectral method calculation (mechanical equilibrium) ! do the actual spectral method calculation (mechanical equilibrium)
@ -624,8 +614,6 @@ end subroutine utilities_fourierGreenConvolution
real(pReal) function utilities_divergenceRMS() real(pReal) function utilities_divergenceRMS()
use IO, only: & use IO, only: &
IO_error IO_error
use numerics, only: &
worldrank
use mesh, only: & use mesh, only: &
geomSize, & geomSize, &
grid, & grid, &
@ -638,10 +626,9 @@ real(pReal) function utilities_divergenceRMS()
external :: & external :: &
MPI_Allreduce MPI_Allreduce
if (worldrank == 0_pInt) then
write(6,'(/,a)') ' ... calculating divergence ................................................' write(6,'(/,a)') ' ... calculating divergence ................................................'
flush(6) flush(6)
endif
rescaledGeom = cmplx(geomSize/scaledGeomSize,0.0_pReal) rescaledGeom = cmplx(geomSize/scaledGeomSize,0.0_pReal)
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
@ -680,8 +667,6 @@ end function utilities_divergenceRMS
real(pReal) function utilities_curlRMS() real(pReal) function utilities_curlRMS()
use IO, only: & use IO, only: &
IO_error IO_error
use numerics, only: &
worldrank
use mesh, only: & use mesh, only: &
geomSize, & geomSize, &
grid, & grid, &
@ -693,13 +678,11 @@ real(pReal) function utilities_curlRMS()
complex(pReal), dimension(3) :: rescaledGeom complex(pReal), dimension(3) :: rescaledGeom
external :: & external :: &
MPI_Reduce, &
MPI_Allreduce MPI_Allreduce
if (worldrank == 0_pInt) then
write(6,'(/,a)') ' ... calculating curl ......................................................' write(6,'(/,a)') ' ... calculating curl ......................................................'
flush(6) flush(6)
endif
rescaledGeom = cmplx(geomSize/scaledGeomSize,0.0_pReal) rescaledGeom = cmplx(geomSize/scaledGeomSize,0.0_pReal)
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
@ -757,8 +740,6 @@ function utilities_maskedCompliance(rot_BC,mask_stress,C)
prec_isNaN prec_isNaN
use IO, only: & use IO, only: &
IO_error IO_error
use numerics, only: &
worldrank
use math, only: & use math, only: &
math_Plain3333to99, & math_Plain3333to99, &
math_plain99to3333, & math_plain99to3333, &
@ -790,7 +771,7 @@ function utilities_maskedCompliance(rot_BC,mask_stress,C)
allocate (sTimesC(size_reduced,size_reduced), source =0.0_pReal) allocate (sTimesC(size_reduced,size_reduced), source =0.0_pReal)
temp99_Real = math_Plain3333to99(math_rotate_forward3333(C,rot_BC)) temp99_Real = math_Plain3333to99(math_rotate_forward3333(C,rot_BC))
if(debugGeneral .and. worldrank == 0_pInt) then if(debugGeneral) then
write(6,'(/,a)') ' ... updating masked compliance ............................................' write(6,'(/,a)') ' ... updating masked compliance ............................................'
write(6,'(/,a,/,9(9(2x,f12.7,1x)/))',advance='no') ' Stiffness C (load) / GPa =',& write(6,'(/,a,/,9(9(2x,f12.7,1x)/))',advance='no') ' Stiffness C (load) / GPa =',&
transpose(temp99_Real)/1.e9_pReal transpose(temp99_Real)/1.e9_pReal
@ -831,7 +812,7 @@ function utilities_maskedCompliance(rot_BC,mask_stress,C)
if(m/=n .and. abs(sTimesC(m,n)) > (0.0_pReal + 10.0e-12_pReal)) errmatinv = .true. ! off diagonal elements of S*C should be 0 if(m/=n .and. abs(sTimesC(m,n)) > (0.0_pReal + 10.0e-12_pReal)) errmatinv = .true. ! off diagonal elements of S*C should be 0
enddo enddo
enddo enddo
if((debugGeneral .or. errmatinv) .and. (worldrank == 0_pInt)) then ! report if(debugGeneral .or. errmatinv) then
write(formatString, '(I16.16)') size_reduced write(formatString, '(I16.16)') size_reduced
formatString = '(/,a,/,'//trim(formatString)//'('//trim(formatString)//'(2x,es9.2,1x)/))' formatString = '(/,a,/,'//trim(formatString)//'('//trim(formatString)//'(2x,es9.2,1x)/))'
write(6,trim(formatString),advance='no') ' C * S (load) ', & write(6,trim(formatString),advance='no') ' C * S (load) ', &
@ -845,7 +826,7 @@ function utilities_maskedCompliance(rot_BC,mask_stress,C)
else else
temp99_real = 0.0_pReal temp99_real = 0.0_pReal
endif endif
if(debugGeneral .and. worldrank == 0_pInt) & ! report if(debugGeneral) &
write(6,'(/,a,/,9(9(2x,f12.7,1x)/),/)',advance='no') ' Masked Compliance (load) * GPa =', & write(6,'(/,a,/,9(9(2x,f12.7,1x)/),/)',advance='no') ' Masked Compliance (load) * GPa =', &
transpose(temp99_Real*1.e9_pReal) transpose(temp99_Real*1.e9_pReal)
flush(6) flush(6)
@ -938,15 +919,11 @@ end subroutine utilities_fourierTensorDivergence
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
subroutine utilities_constitutiveResponse(F_lastInc,F,timeinc, & subroutine utilities_constitutiveResponse(F_lastInc,F,timeinc, &
P,C_volAvg,C_minmaxAvg,P_av,forwardData,rotation_BC) P,C_volAvg,C_minmaxAvg,P_av,forwardData,rotation_BC)
use prec, only: &
dNeq
use IO, only: & use IO, only: &
IO_error IO_error
use debug, only: & use debug, only: &
debug_reset, & debug_reset, &
debug_info debug_info
use numerics, only: &
worldrank
use math, only: & use math, only: &
math_transpose33, & math_transpose33, &
math_rotate_forward33, & math_rotate_forward33, &
@ -984,26 +961,18 @@ subroutine utilities_constitutiveResponse(F_lastInc,F,timeinc, &
real(pReal), dimension(3,3,3,3) :: max_dPdF, min_dPdF real(pReal), dimension(3,3,3,3) :: max_dPdF, min_dPdF
real(pReal) :: max_dPdF_norm, min_dPdF_norm, defgradDetMin, defgradDetMax, defgradDet real(pReal) :: max_dPdF_norm, min_dPdF_norm, defgradDetMin, defgradDetMax, defgradDet
external :: &
MPI_Reduce, &
MPI_Allreduce
if (worldrank == 0_pInt) then
write(6,'(/,a)') ' ... evaluating constitutive response ......................................' write(6,'(/,a)') ' ... evaluating constitutive response ......................................'
flush(6) flush(6)
endif
age = .False. age = .False.
if (forwardData) then ! aging results if (forwardData) then ! aging results
age = .True. age = .True.
materialpoint_F0 = reshape(F_lastInc, [3,3,1,product(grid(1:2))*grid3]) materialpoint_F0 = reshape(F_lastInc, [3,3,1,product(grid(1:2))*grid3])
endif endif
if (cutBack) then ! restore saved variables if (cutBack) age = .False. ! restore saved variables
age = .False.
endif
materialpoint_F = reshape(F,[3,3,1,product(grid(1:2))*grid3]) materialpoint_F = reshape(F,[3,3,1,product(grid(1:2))*grid3])
call debug_reset() call debug_reset() ! this has no effect on rank >0
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
! calculate bounds of det(F) and report ! calculate bounds of det(F) and report
@ -1015,16 +984,11 @@ subroutine utilities_constitutiveResponse(F_lastInc,F,timeinc, &
defgradDetMax = max(defgradDetMax,defgradDet) defgradDetMax = max(defgradDetMax,defgradDet)
defgradDetMin = min(defgradDetMin,defgradDet) defgradDetMin = min(defgradDetMin,defgradDet)
end do end do
call MPI_reduce(MPI_IN_PLACE,defgradDetMax,1,MPI_DOUBLE,MPI_MAX,0,PETSC_COMM_WORLD,ierr)
if(ierr /=0_pInt) call IO_error(894_pInt, ext_msg='MPI_Allreduce max')
call MPI_reduce(MPI_IN_PLACE,defgradDetMin,1,MPI_DOUBLE,MPI_MIN,0,PETSC_COMM_WORLD,ierr)
if(ierr /=0_pInt) call IO_error(894_pInt, ext_msg='MPI_Allreduce min')
if (worldrank == 0_pInt) then
write(6,'(a,1x,es11.4)') ' max determinant of deformation =', defgradDetMax write(6,'(a,1x,es11.4)') ' max determinant of deformation =', defgradDetMax
write(6,'(a,1x,es11.4)') ' min determinant of deformation =', defgradDetMin write(6,'(a,1x,es11.4)') ' min determinant of deformation =', defgradDetMin
flush(6) flush(6)
endif endif
endif
call CPFEM_general(age,timeinc) call CPFEM_general(age,timeinc)
@ -1053,7 +1017,7 @@ subroutine utilities_constitutiveResponse(F_lastInc,F,timeinc, &
call MPI_Allreduce(MPI_IN_PLACE,C_volAvg,81,MPI_DOUBLE,MPI_SUM,PETSC_COMM_WORLD,ierr) call MPI_Allreduce(MPI_IN_PLACE,C_volAvg,81,MPI_DOUBLE,MPI_SUM,PETSC_COMM_WORLD,ierr)
call debug_info() call debug_info() ! this has no effect on rank >0
restartWrite = .false. ! reset restartWrite status restartWrite = .false. ! reset restartWrite status
cutBack = .false. ! reset cutBack status cutBack = .false. ! reset cutBack status
@ -1061,15 +1025,13 @@ subroutine utilities_constitutiveResponse(F_lastInc,F,timeinc, &
P = reshape(materialpoint_P, [3,3,grid(1),grid(2),grid3]) P = reshape(materialpoint_P, [3,3,grid(1),grid(2),grid3])
P_av = sum(sum(sum(P,dim=5),dim=4),dim=3) * wgt ! average of P P_av = sum(sum(sum(P,dim=5),dim=4),dim=3) * wgt ! average of P
call MPI_Allreduce(MPI_IN_PLACE,P_av,9,MPI_DOUBLE,MPI_SUM,PETSC_COMM_WORLD,ierr) call MPI_Allreduce(MPI_IN_PLACE,P_av,9,MPI_DOUBLE,MPI_SUM,PETSC_COMM_WORLD,ierr)
if (debugRotation .and. worldrank == 0_pInt) & if (debugRotation) &
write(6,'(/,a,/,3(3(2x,f12.4,1x)/))',advance='no') ' Piola--Kirchhoff stress (lab) / MPa =',& write(6,'(/,a,/,3(3(2x,f12.4,1x)/))',advance='no') ' Piola--Kirchhoff stress (lab) / MPa =',&
math_transpose33(P_av)*1.e-6_pReal math_transpose33(P_av)*1.e-6_pReal
P_av = math_rotate_forward33(P_av,rotation_BC) P_av = math_rotate_forward33(P_av,rotation_BC)
if (worldrank == 0_pInt) then
write(6,'(/,a,/,3(3(2x,f12.4,1x)/))',advance='no') ' Piola--Kirchhoff stress / MPa =',& write(6,'(/,a,/,3(3(2x,f12.4,1x)/))',advance='no') ' Piola--Kirchhoff stress / MPa =',&
math_transpose33(P_av)*1.e-6_pReal math_transpose33(P_av)*1.e-6_pReal
flush(6) flush(6)
endif
end subroutine utilities_constitutiveResponse end subroutine utilities_constitutiveResponse

22
examples/ConfigFiles/Phase_Phenopowerlaw_BCC-Ferrite.config
View File

@ -1,7 +1,8 @@
# Tasan et.al. 2015 Acta Materalia # Tasan et.al. 2015 Acta Materalia
# Tasan et.al. 2015 International Journal of Plasticity # Tasan et.al. 2015 International Journal of Plasticity
# Diehl et.al. 2015 Meccanica # Diehl et.al. 2015 Meccanica
[BCC_Ferrite] [BCC-Ferrite]
elasticity hooke elasticity hooke
plasticity phenopowerlaw plasticity phenopowerlaw
@ -13,23 +14,12 @@ c12 135.5e9
c44 118.0e9 c44 118.0e9
gdot0_slip 0.001 gdot0_slip 0.001
n_slip 20 n_slip 20
tau0_slip 95.e6 97.e6 0 0 # per family, optimization long simplex 109 tau0_slip 95.e6 97.e6 # per family, optimization long simplex 109
tausat_slip 222.e6 412.7e6 0 0 # per family, optimization long simplex 109 tausat_slip 222.e6 412.7e6 # per family, optimization long simplex 109
gdot0_twin 0.001 h0_slipslip 1000.0e6
n_twin 20
tau0_twin 31.0e6 # per family
s_pr 0 # push-up factor for slip saturation due to twinning
twin_b 0
twin_c 0
twin_d 0
twin_e 0
h0_slipslip 1000.0e6 # opti
h0_twinslip 0
h0_twintwin 0
interaction_slipslip 1 1 1.4 1.4 1.4 1.4 interaction_slipslip 1 1 1.4 1.4 1.4 1.4
interaction_sliptwin 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 interaction_sliptwin 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
interaction_twinslip 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 interaction_twinslip 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
interaction_twintwin 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 interaction_twintwin 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
w0_slip 2.0 # opti w0_slip 2.0
atol_resistance 1
(output) totalshear (output) totalshear

21
examples/ConfigFiles/Phase_Phenopowerlaw_BCC-Martensite.config
View File

@ -1,9 +1,11 @@
# Tasan et.al. 2015 Acta Materalia # Tasan et.al. 2015 Acta Materalia
# Tasan et.al. 2015 International Journal of Plasticity # Tasan et.al. 2015 International Journal of Plasticity
# Diehl et.al. 2015 Meccanica # Diehl et.al. 2015 Meccanica
[BCC_Martensite] [BCC-Martensite]
plasticity phenopowerlaw
elasticity hooke elasticity hooke
plasticity phenopowerlaw
lattice_structure bcc lattice_structure bcc
Nslip 12 12 # per family Nslip 12 12 # per family
Ntwin 0 # per family Ntwin 0 # per family
@ -12,23 +14,12 @@ c12 242.4e9
c44 211.1e9 c44 211.1e9
gdot0_slip 0.001 gdot0_slip 0.001
n_slip 20 n_slip 20
tau0_slip 405.8e6 456.7e6 0 0 # per family tau0_slip 405.8e6 456.7e6 # per family
tausat_slip 872.9e6 971.2e6 0 0 # per family tausat_slip 872.9e6 971.2e6 # per family
gdot0_twin 0.001
n_twin 20
tau0_twin 31.0e6 # per family
s_pr 0 # push-up factor for slip saturation due to twinning
twin_b 0
twin_c 0
twin_d 0
twin_e 0
h0_slipslip 563.0e9 h0_slipslip 563.0e9
h0_twinslip 0
h0_twintwin 0
interaction_slipslip 1 1 1.4 1.4 1.4 1.4 interaction_slipslip 1 1 1.4 1.4 1.4 1.4
interaction_sliptwin 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 interaction_sliptwin 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
interaction_twinslip 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 interaction_twinslip 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
interaction_twintwin 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 interaction_twintwin 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
w0_slip 2.0 w0_slip 2.0
atol_resistance 1
(output) totalshear (output) totalshear

12
examples/SpectralMethod/Makefile
View File

@ -1,12 +0,0 @@
include ${PETSC_DIR}/${PETSC_ARCH}/lib/petsc/conf/variables
include ${PETSC_DIR}/${PETSC_ARCH}/lib/petsc/conf/rules
run16x16x16:
-@${MPIEXEC} -n 2 DAMASK_spectral -l tensionX.load -g 20grains16x16x16.geom
run32x32x32:
-@${MPIEXEC} -n 4 DAMASK_spectral -l tensionX.load -g 20grains32x32x32.geom
run64x64x64:
-@${MPIEXEC} -n 8 DAMASK_spectral -l tensionX.load -g 20grains64x64x64.geom

56
installation/symlink_Code.py
View File

@ -11,7 +11,15 @@ bin_link = { \
], ],
} }
MarcReleases =[2011,2012,2013,2013.1,2014,2014.2,2015] MarcReleases =[ \
'2011',
'2012',
'2013',
'2013.1',
'2014',
'2014.2',
'2015',
]
damaskEnv = damask.Environment() damaskEnv = damask.Environment()
baseDir = damaskEnv.relPath('code/') baseDir = damaskEnv.relPath('code/')
@ -20,27 +28,41 @@ binDir = damaskEnv.options['DAMASK_BIN']
if not os.path.isdir(binDir): if not os.path.isdir(binDir):
os.mkdir(binDir) os.mkdir(binDir)
for dir in bin_link: sys.stdout.write('\nsymbolic linking...\n')
for file in bin_link[dir]:
src = os.path.abspath(os.path.join(baseDir,dir,file))
if os.path.exists(src):
sym_link = os.path.abspath(os.path.join(binDir,\
{True: dir,
False:os.path.splitext(file)[0]}[file == '']))
if os.path.lexists(sym_link): os.remove(sym_link)
os.symlink(src,sym_link)
sys.stdout.write(sym_link+' -> '+src+'\n')
for subDir in bin_link:
theDir = os.path.abspath(os.path.join(baseDir,subDir))
sys.stdout.write('\n'+binDir+' ->\n'+theDir+damask.util.deemph(' ...')+'\n')
for theFile in bin_link[subDir]:
theName,theExt = os.path.splitext(theFile)
src = os.path.abspath(os.path.join(theDir,theFile))
for version in MarcReleases:
src = os.path.abspath(os.path.join(baseDir,'DAMASK_marc.f90'))
if os.path.exists(src): if os.path.exists(src):
sym_link = os.path.abspath(os.path.join(baseDir,'DAMASK_marc'+str(version)+'.f90')) sym_link = os.path.abspath(os.path.join(binDir,subDir if theFile == '' else theName))
if os.path.lexists(sym_link): if os.path.lexists(sym_link):
os.remove(sym_link) os.remove(sym_link)
sys.stdout.write(sym_link) output = theName+damask.util.deemph(theExt)
else: else:
sys.stdout.write(damask.util.emph(sym_link)) output = damask.util.emph(theName)+damask.util.deemph(theExt)
sys.stdout.write(damask.util.deemph('... ')+output+'\n')
os.symlink(src,sym_link) os.symlink(src,sym_link)
sys.stdout.write(' -> '+src+'\n')
sys.stdout.write('\nMSC.Marc versioning...\n\n')
theMaster = 'DAMASK_marc.f90'
for version in MarcReleases:
src = os.path.abspath(os.path.join(baseDir,theMaster))
if os.path.exists(src):
sym_link = os.path.abspath(os.path.join(baseDir,'DAMASK_marc{}.f90'.format(version)))
if os.path.lexists(sym_link):
os.remove(sym_link)
output = version
else:
output = damask.util.emph(version)
sys.stdout.write(' '+output+'\n')
os.symlink(theMaster,sym_link)

38
installation/symlink_Processing.py
View File

@ -13,23 +13,47 @@ if not os.path.isdir(binDir):
os.mkdir(binDir) os.mkdir(binDir)
#define ToDo list #define ToDo list
processing_subDirs = ['pre','post','misc',] processing_subDirs = ['pre',
processing_extensions = ['.py','.sh',] 'post',
'misc',
]
processing_extensions = ['.py',
'.sh',
]
sys.stdout.write('\nsymbolic linking...\n')
for subDir in processing_subDirs: for subDir in processing_subDirs:
theDir = os.path.abspath(os.path.join(baseDir,subDir)) theDir = os.path.abspath(os.path.join(baseDir,subDir))
sys.stdout.write('\n'+binDir+' ->\n'+theDir+damask.util.deemph(' ...')+'\n')
for theFile in os.listdir(theDir): for theFile in os.listdir(theDir):
if os.path.splitext(theFile)[1] in processing_extensions: # only consider files with proper extensions theName,theExt = os.path.splitext(theFile)
if theExt in processing_extensions: # only consider files with proper extensions
src = os.path.abspath(os.path.join(theDir,theFile)) src = os.path.abspath(os.path.join(theDir,theFile))
sym_link = os.path.abspath(os.path.join(binDir,os.path.splitext(theFile)[0])) sym_link = os.path.abspath(os.path.join(binDir,theName))
if os.path.lexists(sym_link): if os.path.lexists(sym_link):
os.remove(sym_link) os.remove(sym_link)
sys.stdout.write(sym_link) output = theName+damask.util.deemph(theExt)
else: else:
sys.stdout.write(damask.util.emph(sym_link)) output = damask.util.emph(theName)+damask.util.deemph(theExt)
sys.stdout.write(damask.util.deemph('... ')+output+'\n')
os.symlink(src,sym_link) os.symlink(src,sym_link)
sys.stdout.write(' -> '+src+'\n')
sys.stdout.write('\npruning broken links...\n')
brokenLinks = 0
for filename in os.listdir(binDir):
path = os.path.join(binDir,filename)
if os.path.islink(path) and not os.path.exists(path):
sys.stdout.write(' '+damask.util.delete(path)+'\n')
os.remove(path)
brokenLinks += 1
sys.stdout.write(('none.' if brokenLinks == 0 else '')+'\n')

42
lib/damask/asciitable.py
View File

@ -3,6 +3,14 @@
import os,sys import os,sys
import numpy as np import numpy as np
# ------------------------------------------------------------------
# python 3 has no unicode object, this ensures that the code works on Python 2&3
try:
test=isinstance('test', unicode)
except(NameError):
unicode=str
# ------------------------------------------------------------------
class ASCIItable(): class ASCIItable():
"""Read and write to ASCII tables""" """Read and write to ASCII tables"""
@ -158,12 +166,12 @@ class ASCIItable():
if self.__IO__['labeled']: # table features labels if self.__IO__['labeled']: # table features labels
self.info = [self.__IO__['in'].readline().strip() for i in xrange(1,int(m.group(1)))] self.info = [self.__IO__['in'].readline().strip() for i in range(1,int(m.group(1)))]
self.tags = shlex.split(self.__IO__['in'].readline()) # store tags found in last line self.tags = shlex.split(self.__IO__['in'].readline()) # store tags found in last line
else: else:
self.info = [self.__IO__['in'].readline().strip() for i in xrange(0,int(m.group(1)))] # all header is info ... self.info = [self.__IO__['in'].readline().strip() for i in range(0,int(m.group(1)))] # all header is info ...
else: # other table format else: # other table format
try: try:
@ -224,11 +232,11 @@ class ASCIItable():
extra_header = [] extra_header = []
for header in self.info: for header in self.info:
headitems = map(str.lower,header.split()) headitems = list(map(str.lower,header.split()))
if len(headitems) == 0: continue # skip blank lines if len(headitems) == 0: continue # skip blank lines
if headitems[0] in mappings.keys(): if headitems[0] in list(mappings.keys()):
if headitems[0] in identifiers.keys(): if headitems[0] in list(identifiers.keys()):
for i in xrange(len(identifiers[headitems[0]])): for i in range(len(identifiers[headitems[0]])):
info[headitems[0]][i] = \ info[headitems[0]][i] = \
mappings[headitems[0]](headitems[headitems.index(identifiers[headitems[0]][i])+1]) mappings[headitems[0]](headitems[headitems.index(identifiers[headitems[0]][i])+1])
else: else:
@ -415,9 +423,9 @@ class ASCIItable():
start = self.label_index(labels) start = self.label_index(labels)
dim = self.label_dimension(labels) dim = self.label_dimension(labels)
return np.hstack(map(lambda c: xrange(c[0],c[0]+c[1]), zip(start,dim))) \ return np.hstack([range(c[0],c[0]+c[1]) for c in zip(start,dim)]) \
if isinstance(labels, Iterable) and not isinstance(labels, str) \ if isinstance(labels, Iterable) and not isinstance(labels, str) \
else xrange(start,start+dim) else range(start,start+dim)
# ------------------------------------------------------------------ # ------------------------------------------------------------------
def info_append(self, def info_append(self,
@ -447,7 +455,7 @@ class ASCIItable():
def data_skipLines(self, def data_skipLines(self,
count): count):
"""wind forward by count number of lines""" """wind forward by count number of lines"""
for i in xrange(count): for i in range(count):
alive = self.data_read() alive = self.data_read()
return alive return alive
@ -501,10 +509,10 @@ class ASCIItable():
columns = [] columns = []
for i,(c,d) in enumerate(zip(indices[present],dimensions[present])): # for all valid labels ... for i,(c,d) in enumerate(zip(indices[present],dimensions[present])): # for all valid labels ...
# ... transparently add all components unless column referenced by number or with explicit dimension # ... transparently add all components unless column referenced by number or with explicit dimension
columns += range(c,c + \ columns += list(range(c,c + \
(d if str(c) != str(labels[present[i]]) else \ (d if str(c) != str(labels[present[i]]) else \
1)) 1)))
use = np.array(columns) use = np.array(columns) if len(columns) > 0 else None
self.tags = list(np.array(self.tags)[use]) # update labels with valid subset self.tags = list(np.array(self.tags)[use]) # update labels with valid subset
@ -530,7 +538,7 @@ class ASCIItable():
"""write whole numpy array data""" """write whole numpy array data"""
for row in self.data: for row in self.data:
try: try:
output = [fmt % value for value in row] if fmt else map(repr,row) output = [fmt % value for value in row] if fmt else list(map(repr,row))
except: except:
output = [fmt % row] if fmt else [repr(row)] output = [fmt % row] if fmt else [repr(row)]
@ -555,7 +563,7 @@ class ASCIItable():
try: try:
idx = self.label_index(where) idx = self.label_index(where)
if len(self.data) <= idx: if len(self.data) <= idx:
self.data_append(['n/a' for i in xrange(idx+1-len(self.data))]) # grow data if too short self.data_append(['n/a' for i in range(idx+1-len(self.data))]) # grow data if too short
self.data[idx] = str(what) self.data[idx] = str(what)
except(ValueError): except(ValueError):
pass pass
@ -568,7 +576,7 @@ class ASCIItable():
# ------------------------------------------------------------------ # ------------------------------------------------------------------
def data_asFloat(self): def data_asFloat(self):
return map(self._transliterateToFloat,self.data) return list(map(self._transliterateToFloat,self.data))
@ -590,8 +598,8 @@ class ASCIItable():
if len(items) > 2: if len(items) > 2:
if items[1].lower() == 'of': items = np.ones(datatype(items[0]))*datatype(items[2]) if items[1].lower() == 'of': items = np.ones(datatype(items[0]))*datatype(items[2])
elif items[1].lower() == 'to': items = np.arange(datatype(items[0]),1+datatype(items[2])) elif items[1].lower() == 'to': items = np.arange(datatype(items[0]),1+datatype(items[2]))
else: items = map(datatype,items) else: items = list(map(datatype,items))
else: items = map(datatype,items) else: items = list(map(datatype,items))
s = min(len(items), N-i) # prevent overflow of microstructure array s = min(len(items), N-i) # prevent overflow of microstructure array
microstructure[i:i+s] = items[:s] microstructure[i:i+s] = items[:s]

24
lib/damask/colormaps.py
View File

@ -33,7 +33,7 @@ class Color():
} }
model = model.upper() model = model.upper()
if model not in self.__transforms__.keys(): model = 'RGB' if model not in list(self.__transforms__.keys()): model = 'RGB'
if model == 'RGB' and max(color) > 1.0: # are we RGB255 ? if model == 'RGB' and max(color) > 1.0: # are we RGB255 ?
for i in range(3): for i in range(3):
color[i] /= 255.0 # rescale to RGB color[i] /= 255.0 # rescale to RGB
@ -62,7 +62,7 @@ class Color():
# ------------------------------------------------------------------ # ------------------------------------------------------------------
def convertTo(self,toModel = 'RGB'): def convertTo(self,toModel = 'RGB'):
toModel = toModel.upper() toModel = toModel.upper()
if toModel not in self.__transforms__.keys(): return if toModel not in list(self.__transforms__.keys()): return
sourcePos = self.__transforms__[self.model]['index'] sourcePos = self.__transforms__[self.model]['index']
targetPos = self.__transforms__[toModel]['index'] targetPos = self.__transforms__[toModel]['index']
@ -139,7 +139,7 @@ class Color():
HSL[0] = HSL[0]*60.0 # scaling to 360 might be dangerous for small values HSL[0] = HSL[0]*60.0 # scaling to 360 might be dangerous for small values
if (HSL[0] < 0.0): if (HSL[0] < 0.0):
HSL[0] = HSL[0] + 360.0 HSL[0] = HSL[0] + 360.0
for i in xrange(2): for i in range(2):
HSL[i+1] = min(HSL[i+1],1.0) HSL[i+1] = min(HSL[i+1],1.0)
HSL[i+1] = max(HSL[i+1],0.0) HSL[i+1] = max(HSL[i+1],0.0)
@ -164,11 +164,11 @@ class Color():
[0.212671,0.715160,0.072169], [0.212671,0.715160,0.072169],
[0.019334,0.119193,0.950227]]) [0.019334,0.119193,0.950227]])
for i in xrange(3): for i in range(3):
if (self.color[i] > 0.04045): RGB_lin[i] = ((self.color[i]+0.0555)/1.0555)**2.4 if (self.color[i] > 0.04045): RGB_lin[i] = ((self.color[i]+0.0555)/1.0555)**2.4
else: RGB_lin[i] = self.color[i] /12.92 else: RGB_lin[i] = self.color[i] /12.92
XYZ = np.dot(convert,RGB_lin) XYZ = np.dot(convert,RGB_lin)
for i in xrange(3): for i in range(3):
XYZ[i] = max(XYZ[i],0.0) XYZ[i] = max(XYZ[i],0.0)
@ -193,10 +193,10 @@ class Color():
RGB_lin = np.dot(convert,self.color) RGB_lin = np.dot(convert,self.color)
RGB = np.zeros(3,'d') RGB = np.zeros(3,'d')
for i in xrange(3): for i in range(3):
if (RGB_lin[i] > 0.0031308): RGB[i] = ((RGB_lin[i])**(1.0/2.4))*1.0555-0.0555 if (RGB_lin[i] > 0.0031308): RGB[i] = ((RGB_lin[i])**(1.0/2.4))*1.0555-0.0555
else: RGB[i] = RGB_lin[i] *12.92 else: RGB[i] = RGB_lin[i] *12.92
for i in xrange(3): for i in range(3):
RGB[i] = min(RGB[i],1.0) RGB[i] = min(RGB[i],1.0)
RGB[i] = max(RGB[i],0.0) RGB[i] = max(RGB[i],0.0)
@ -225,7 +225,7 @@ class Color():
XYZ[0] = XYZ[1] + self.color[1]/ 500.0 XYZ[0] = XYZ[1] + self.color[1]/ 500.0
XYZ[2] = XYZ[1] - self.color[2]/ 200.0 XYZ[2] = XYZ[1] - self.color[2]/ 200.0
for i in xrange(len(XYZ)): for i in range(len(XYZ)):
if (XYZ[i] > 6./29. ): XYZ[i] = XYZ[i]**3. if (XYZ[i] > 6./29. ): XYZ[i] = XYZ[i]**3.
else: XYZ[i] = 108./841. * (XYZ[i] - 4./29.) else: XYZ[i] = 108./841. * (XYZ[i] - 4./29.)
@ -245,7 +245,7 @@ class Color():
ref_white = np.array([.95047, 1.00000, 1.08883],'d') # Observer = 2, Illuminant = D65 ref_white = np.array([.95047, 1.00000, 1.08883],'d') # Observer = 2, Illuminant = D65
XYZ = self.color/ref_white XYZ = self.color/ref_white
for i in xrange(len(XYZ)): for i in range(len(XYZ)):
if (XYZ[i] > 216./24389 ): XYZ[i] = XYZ[i]**(1.0/3.0) if (XYZ[i] > 216./24389 ): XYZ[i] = XYZ[i]**(1.0/3.0)
else: XYZ[i] = (841./108. * XYZ[i]) + 16.0/116.0 else: XYZ[i] = (841./108. * XYZ[i]) + 16.0/116.0
@ -451,7 +451,7 @@ class Colormap():
""" """
format = format.lower() # consistent comparison basis format = format.lower() # consistent comparison basis
frac = 0.5*(np.array(crop) + 1.0) # rescale crop range to fractions frac = 0.5*(np.array(crop) + 1.0) # rescale crop range to fractions
colors = [self.color(float(i)/(steps-1)*(frac[1]-frac[0])+frac[0]).expressAs(model).color for i in xrange(steps)] colors = [self.color(float(i)/(steps-1)*(frac[1]-frac[0])+frac[0]).expressAs(model).color for i in range(steps)]
if format == 'paraview': if format == 'paraview':
colormap = ['[\n {{\n "ColorSpace" : "RGB", "Name" : "{}",\n "RGBPoints" : ['.format(name)] \ colormap = ['[\n {{\n "ColorSpace" : "RGB", "Name" : "{}",\n "RGBPoints" : ['.format(name)] \
+ [' {:4d},{:8.6f},{:8.6f},{:8.6f},'.format(i,color[0],color[1],color[2],) + [' {:4d},{:8.6f},{:8.6f},{:8.6f},'.format(i,color[0],color[1],color[2],)
@ -461,7 +461,7 @@ class Colormap():
elif format == 'gmsh': elif format == 'gmsh':
colormap = ['View.ColorTable = {'] \ colormap = ['View.ColorTable = {'] \
+ [',\n'.join(['{%s}'%(','.join(map(lambda x:str(x*255.0),color))) for color in colors])] \ + [',\n'.join(['{%s}'%(','.join([str(x*255.0) for x in color])) for color in colors])] \
+ ['}'] + ['}']
elif format == 'gom': elif format == 'gom':
@ -469,7 +469,7 @@ class Colormap():
+ ' 9 ' + str(name) \ + ' 9 ' + str(name) \
+ ' 0 1 0 3 0 0 -1 9 \ 0 0 0 255 255 255 0 0 255 ' \ + ' 0 1 0 3 0 0 -1 9 \ 0 0 0 255 255 255 0 0 255 ' \
+ '30 NO_UNIT 1 1 64 64 64 255 1 0 0 0 0 0 0 3 0 ' + str(len(colors)) \ + '30 NO_UNIT 1 1 64 64 64 255 1 0 0 0 0 0 0 3 0 ' + str(len(colors)) \
+ ' '.join([' 0 %s 255 1'%(' '.join(map(lambda x:str(int(x*255.0)),color))) for color in reversed(colors)])] + ' '.join([' 0 %s 255 1'%(' '.join([str(int(x*255.0)) for x in color])) for color in reversed(colors)])]
elif format == 'raw': elif format == 'raw':
colormap = ['\t'.join(map(str,color)) for color in colors] colormap = ['\t'.join(map(str,color)) for color in colors]

8
lib/damask/config/material.py
View File

@ -19,7 +19,7 @@ class Section():
self.parameters[key] = data[key] self.parameters[key] = data[key]
if '__order__' not in self.parameters: if '__order__' not in self.parameters:
self.parameters['__order__'] = self.parameters.keys() self.parameters['__order__'] = list(self.parameters.keys())
if part.lower() in classes: if part.lower() in classes:
self.__class__ = classes[part.lower()] self.__class__ = classes[part.lower()]
self.__init__(data) self.__init__(data)
@ -61,11 +61,11 @@ class Texture(Section):
def add_component(self,theType,properties): def add_component(self,theType,properties):
if 'scatter' not in map(str.lower,properties.keys()): if 'scatter' not in list(map(str.lower,list(properties.keys()))):
scatter = 0.0 scatter = 0.0
else: else:
scatter = properties['scatter'] scatter = properties['scatter']
if 'fraction' not in map(str.lower,properties.keys()): if 'fraction' not in list(map(str.lower,list(properties.keys()))):
fraction = 1.0 fraction = 1.0
else: else:
fraction = properties['fraction'] fraction = properties['fraction']
@ -227,7 +227,7 @@ class Material():
"""Experimental! Needs expansion to multi-constituent microstructures...""" """Experimental! Needs expansion to multi-constituent microstructures..."""
microstructure = Microstructure() microstructure = Microstructure()
# make keys lower case (http://stackoverflow.com/questions/764235/dictionary-to-lowercase-in-python) # make keys lower case (http://stackoverflow.com/questions/764235/dictionary-to-lowercase-in-python)
components=dict((k.lower(), v) for k,v in components.iteritems()) components=dict((k.lower(), v) for k,v in components.items())
for key in ['phase','texture','fraction','crystallite']: for key in ['phase','texture','fraction','crystallite']:
if type(components[key]) is not list: if type(components[key]) is not list:

6
lib/damask/environment.py
View File

@ -1,6 +1,6 @@
# -*- coding: UTF-8 no BOM -*- # -*- coding: UTF-8 no BOM -*-
import os,subprocess,shlex,re,string import os,subprocess,shlex,re
class Environment(): class Environment():
__slots__ = [ \ __slots__ = [ \
@ -22,7 +22,7 @@ class Environment():
for line in configFile: for line in configFile:
l = re.sub('^set ', '', line).strip() # remove "set" (tcsh) when setting variables l = re.sub('^set ', '', line).strip() # remove "set" (tcsh) when setting variables
if l and not l.startswith('#'): if l and not l.startswith('#'):
items = map(string.strip,l.split('=')) items = re.split(r'\s*=\s*',l)
if len(items) == 2: if len(items) == 2:
self.options[items[0].upper()] = \ self.options[items[0].upper()] = \
re.sub('\$\{*DAMASK_ROOT\}*',self.rootDir(),os.path.expandvars(items[1])) # expand all shell variables and DAMASK_ROOT re.sub('\$\{*DAMASK_ROOT\}*',self.rootDir(),os.path.expandvars(items[1])) # expand all shell variables and DAMASK_ROOT
@ -35,7 +35,7 @@ class Environment():
try: try:
cmd = """ ssh mulicense2 "/Stat_Flexlm | grep 'Users of %s: ' | cut -d' ' -f7,13" """%software cmd = """ ssh mulicense2 "/Stat_Flexlm | grep 'Users of %s: ' | cut -d' ' -f7,13" """%software
process = subprocess.Popen(shlex.split(cmd),stdout = subprocess.PIPE,stderr = subprocess.PIPE) process = subprocess.Popen(shlex.split(cmd),stdout = subprocess.PIPE,stderr = subprocess.PIPE)
licenses = map(int, process.stdout.readline().split()) licenses = list(map(int, process.stdout.readline().split()))
try: try:
if licenses[0]-licenses[1] >= Nneeded: if licenses[0]-licenses[1] >= Nneeded:
return 0 return 0

2
lib/damask/geometry/geometry.py
View File

@ -15,7 +15,7 @@ class Geometry():
'spectral': damask.geometry.Spectral, 'spectral': damask.geometry.Spectral,
'marc': damask.geometry.Marc, 'marc': damask.geometry.Marc,
} }
if solver.lower() in solverClass.keys(): if solver.lower() in list(solverClass.keys()):
self.__class__=solverClass[solver.lower()] self.__class__=solverClass[solver.lower()]
self.__init__() self.__init__()

29
lib/damask/orientation.py
View File

@ -154,7 +154,7 @@ class Quaternion:
def __div__(self, other): def __div__(self, other):
"""division""" """division"""
if isinstance(other, (int,float,long)): if isinstance(other, (int,float)):
w = self.w / other w = self.w / other
x = self.x / other x = self.x / other
y = self.y / other y = self.y / other
@ -165,7 +165,7 @@ class Quaternion:
def __idiv__(self, other): def __idiv__(self, other):
"""in place division""" """in place division"""
if isinstance(other, (int,float,long)): if isinstance(other, (int,float)):
self.w /= other self.w /= other
self.x /= other self.x /= other
self.y /= other self.y /= other
@ -556,7 +556,7 @@ class Symmetry:
def __init__(self, symmetry = None): def __init__(self, symmetry = None):
"""lattice with given symmetry, defaults to None""" """lattice with given symmetry, defaults to None"""
if isinstance(symmetry, basestring) and symmetry.lower() in Symmetry.lattices: if isinstance(symmetry, str) and symmetry.lower() in Symmetry.lattices:
self.lattice = symmetry.lower() self.lattice = symmetry.lower()
else: else:
self.lattice = None self.lattice = None
@ -653,8 +653,8 @@ class Symmetry:
[ 1.0,0.0,0.0,0.0 ], [ 1.0,0.0,0.0,0.0 ],
] ]
return map(Quaternion, return list(map(Quaternion,
np.array(symQuats)[np.atleast_1d(np.array(who)) if who != [] else xrange(len(symQuats))]) np.array(symQuats)[np.atleast_1d(np.array(who)) if who != [] else range(len(symQuats))]))
def equivalentQuaternions(self, def equivalentQuaternions(self,
@ -891,8 +891,7 @@ class Orientation:
def equivalentOrientations(self, def equivalentOrientations(self,
who = []): who = []):
return map(lambda q: Orientation(quaternion = q, symmetry = self.symmetry.lattice), return [Orientation(quaternion = q, symmetry = self.symmetry.lattice) for q in self.equivalentQuaternions(who)]
self.equivalentQuaternions(who))
def reduced(self): def reduced(self):
"""Transform orientation to fall into fundamental zone according to symmetry""" """Transform orientation to fall into fundamental zone according to symmetry"""
@ -921,7 +920,7 @@ class Orientation:
for i,sA in enumerate(mySymQs): for i,sA in enumerate(mySymQs):
for j,sB in enumerate(otherSymQs): for j,sB in enumerate(otherSymQs):
theQ = sA.conjugated()*misQ*sB theQ = sA.conjugated()*misQ*sB
for k in xrange(2): for k in range(2):
theQ.conjugate() theQ.conjugate()
breaker = self.symmetry.inFZ(theQ) \ breaker = self.symmetry.inFZ(theQ) \
and (not SST or other.symmetry.inDisorientationSST(theQ)) and (not SST or other.symmetry.inDisorientationSST(theQ))
@ -996,11 +995,17 @@ class Orientation:
relationModel, relationModel,
direction, direction,
targetSymmetry = None): targetSymmetry = None):
"""
orientation relationship
positive number: fcc --> bcc
negative number: bcc --> fcc
"""
if relationModel not in ['KS','GT','GTdash','NW','Pitsch','Bain']: return None if relationModel not in ['KS','GT','GTdash','NW','Pitsch','Bain']: return None
if int(direction) == 0: return None if int(direction) == 0: return None
# KS from S. Morito et al./Journal of Alloys and Compounds 5775 (2013) S587-S592 DOES THIS PAPER EXISTS? # KS from S. Morito et al./Journal of Alloys and Compounds 5775 (2013) S587-S592
# for KS rotation matrices also check K. Kitahara et al./Acta Materialia 54 (2006) 1279-1288
# GT from Y. He et al./Journal of Applied Crystallography (2006). 39, 72-81 # GT from Y. He et al./Journal of Applied Crystallography (2006). 39, 72-81
# GT' from Y. He et al./Journal of Applied Crystallography (2006). 39, 72-81 # GT' from Y. He et al./Journal of Applied Crystallography (2006). 39, 72-81
# NW from H. Kitahara et al./Materials Characterization 54 (2005) 378-386 # NW from H. Kitahara et al./Materials Characterization 54 (2005) 378-386
@ -1227,14 +1232,14 @@ class Orientation:
myPlane /= np.linalg.norm(myPlane) myPlane /= np.linalg.norm(myPlane)
myNormal = [float(i) for i in normals[relationModel][variant,me]] # map(float, planes[...]) does not work in python 3 myNormal = [float(i) for i in normals[relationModel][variant,me]] # map(float, planes[...]) does not work in python 3
myNormal /= np.linalg.norm(myNormal) myNormal /= np.linalg.norm(myNormal)
myMatrix = np.array([myPlane,myNormal,np.cross(myPlane,myNormal)]) myMatrix = np.array([myNormal,np.cross(myPlane,myNormal),myPlane]).T
otherPlane = [float(i) for i in planes[relationModel][variant,other]] # map(float, planes[...]) does not work in python 3 otherPlane = [float(i) for i in planes[relationModel][variant,other]] # map(float, planes[...]) does not work in python 3
otherPlane /= np.linalg.norm(otherPlane) otherPlane /= np.linalg.norm(otherPlane)
otherNormal = [float(i) for i in normals[relationModel][variant,other]] # map(float, planes[...]) does not work in python 3 otherNormal = [float(i) for i in normals[relationModel][variant,other]] # map(float, planes[...]) does not work in python 3
otherNormal /= np.linalg.norm(otherNormal) otherNormal /= np.linalg.norm(otherNormal)
otherMatrix = np.array([otherPlane,otherNormal,np.cross(otherPlane,otherNormal)]) otherMatrix = np.array([otherNormal,np.cross(otherPlane,otherNormal),otherPlane]).T
rot=np.dot(otherMatrix.T,myMatrix) rot=np.dot(otherMatrix,myMatrix.T)
return Orientation(matrix=np.dot(rot,self.asMatrix())) # no symmetry information ?? return Orientation(matrix=np.dot(rot,self.asMatrix())) # no symmetry information ??

12
lib/damask/result.py
View File

@ -1,8 +1,6 @@
# -*- coding: UTF-8 no BOM -*- # -*- coding: UTF-8 no BOM -*-
import numpy as np import numpy as np
#import sys
try: try:
import h5py import h5py
@ -19,19 +17,19 @@ class Result():
def __init__(self,resultsFile): def __init__(self,resultsFile):
self.data=h5py.File(resultsFile,"r") self.data=h5py.File(resultsFile,"r")
self.Npoints=self.data.attrs['Number of Materialpoints'] self.Npoints=self.data.attrs['Number of Materialpoints']
print("Opened "+resultsFile+" with %i points"%self.Npoints) print("Opened {} with {} points".format(resultsFile,self.Npoints))
def getCrystallite(self,labels,inc,constituent=1,points=None): def getCrystallite(self,labels,inc,constituent=1,points=None):
if points is None: points = np.array(np.array(xrange(self.Npoints))) if points is None: points = np.array(np.array(range(self.Npoints)))
results = {} results = {}
mapping=self.data['mapping/crystallite'] mapping=self.data['mapping/crystallite']
for instance in self.data['increments/%s/crystallite/'%inc]: for instance in self.data['increments/%s/crystallite/'%inc]:
dsets = self.data['increments/%s/crystallite/%s'%(inc,instance)].keys() dsets = list(self.data['increments/%s/crystallite/%s'%(inc,instance)].keys())
for label in labels: for label in labels:
if label in dsets and label not in results: if label in dsets and label not in results:
shape = np.shape(self.data['increments/%s/crystallite/%s/%s'%(inc,instance,label)])[1:] shape = np.shape(self.data['increments/%s/crystallite/%s/%s'%(inc,instance,label)])[1:]
results[label] = np.nan*np.ones(np.array((self.Npoints,)+shape)) results[label] = np.nan*np.ones(np.array((self.Npoints,)+shape))
for myPoint in xrange(len(points)): for myPoint in range(len(points)):
matPoint = points[myPoint] matPoint = points[myPoint]
pos = mapping[matPoint,constituent-1] pos = mapping[matPoint,constituent-1]
if pos[0] != 0: if pos[0] != 0:
@ -41,5 +39,3 @@ class Result():
except: except:
pass pass
return results return results

4
lib/damask/solver/marc.py
View File

@ -25,7 +25,7 @@ class Marc(Solver):
MSCpath = damask.environment.Environment().options['MSC_ROOT'] MSCpath = damask.environment.Environment().options['MSC_ROOT']
for release,subdirs in sorted(self.releases.items(),reverse=True): for release,subdirs in sorted(list(self.releases.items()),reverse=True):
for subdir in subdirs: for subdir in subdirs:
path = '%s/mentat%s/shlib/%s'%(MSCpath,release,subdir) path = '%s/mentat%s/shlib/%s'%(MSCpath,release,subdir)
if os.path.exists(path): return release if os.path.exists(path): return release
@ -40,7 +40,7 @@ class Marc(Solver):
MSCpath = damask.environment.Environment().options['MSC_ROOT'] MSCpath = damask.environment.Environment().options['MSC_ROOT']
if len(releases) == 0: releases = self.releases.keys() if len(releases) == 0: releases = list(self.releases.keys())
if type(releases) is not list: releases = [releases] if type(releases) is not list: releases = [releases]
for release in sorted(releases,reverse=True): for release in sorted(releases,reverse=True):
if release not in self.releases: continue if release not in self.releases: continue

2
lib/damask/solver/solver.py
View File

@ -15,7 +15,7 @@ class Solver():
'spectral': damask.solver.Spectral, 'spectral': damask.solver.Spectral,
'marc': damask.solver.Marc, 'marc': damask.solver.Marc,
} }
if solver.lower() in solverClass.keys(): if solver.lower() in list(solverClass.keys()):
self.__class__=solverClass[solver.lower()] self.__class__=solverClass[solver.lower()]
self.__init__() self.__init__()

239
lib/damask/test/test.py
View File

@ -17,92 +17,96 @@ class Test():
variants = [] variants = []
def __init__(self,test_description): def __init__(self, **kwargs):
defaults = {'description': '',
'keep': False,
'accept': False,
'updateRequest': False,
}
for arg in defaults.keys():
setattr(self,arg,kwargs.get(arg) if kwargs.get(arg) else defaults[arg])
logger = logging.getLogger()
logger.setLevel(0)
fh = logging.FileHandler('test.log') # create file handler which logs even debug messages fh = logging.FileHandler('test.log') # create file handler which logs even debug messages
fh.setLevel(logging.DEBUG) fh.setLevel(logging.DEBUG)
full = logging.Formatter('%(asctime)s - %(levelname)s: \n%(message)s') fh.setFormatter(logging.Formatter('%(asctime)s - %(levelname)s: \n%(message)s'))
fh.setFormatter(full)
ch = logging.StreamHandler(stream=sys.stdout) # create console handler with a higher log level ch = logging.StreamHandler(stream=sys.stdout) # create console handler with a higher log level
ch.setLevel(logging.INFO) ch.setLevel(logging.INFO)
# create formatter and add it to the handlers ch.setFormatter(logging.Formatter('%(message)s'))
plain = logging.Formatter('%(message)s')
ch.setFormatter(plain) logger = logging.getLogger()
# add the handlers to the logger
logger.addHandler(fh) logger.addHandler(fh)
logger.addHandler(ch) logger.addHandler(ch)
logger.setLevel(0)
logging.info('\n'.join(['+'*40,
'-'*40,
'| '+self.description,
'-'*40,
]))
logging.info('!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n\n' \
+'----------------------------------------------------------------\n' \
+'| '+test_description+'\n' \
+'----------------------------------------------------------------')
self.dirBase = os.path.dirname(os.path.realpath(sys.modules[self.__class__.__module__].__file__)) self.dirBase = os.path.dirname(os.path.realpath(sys.modules[self.__class__.__module__].__file__))
self.parser = OptionParser(
description = test_description+' (using class: {})'.format(damask.version), self.parser = OptionParser(description = '{} (Test class version: {})'.format(self.description,damask.version),
usage='./test.py [options]') usage = './test.py [options]')
self.updateRequested = False self.parser.add_option("-k", "--keep",
self.parser.add_option("-d", "--debug", action="store_true",\ action = "store_true",
dest="debug",\ dest = "keep",
help="debug run, don't calculate but use existing results") help = "keep current results, just run postprocessing")
self.parser.add_option("-p", "--pass", action="store_true",\ self.parser.add_option("--ok", "--accept",
dest="accept",\ action = "store_true",
help="calculate results but always consider test as successfull") dest = "accept",
self.parser.set_defaults(debug=False, help = "calculate results but always consider test as successfull")
accept=False)
self.parser.set_defaults(keep = self.keep,
accept = self.accept,
update = self.updateRequest,
)
def execute(self): def execute(self):
"""Run all variants and report first failure.""" """Run all variants and report first failure."""
if self.options.debug: if not self.options.keep:
for variant in xrange(len(self.variants)): if not self.feasible(): return -1
try:
self.postprocess(variant)
if not self.compare(variant):
return variant+1 # return culprit
except Exception as e :
logging.critical('\nWARNING:\n {}\n'.format(e))
return variant+1 # return culprit
return 0
else:
if not self.testPossible(): return -1
self.clean() self.clean()
self.prepareAll() self.prepareAll()
for variant in xrange(len(self.variants)):
for variant,name in enumerate(self.variants):
try: try:
if not self.options.keep:
self.prepare(variant) self.prepare(variant)
self.run(variant) self.run(variant)
self.postprocess(variant) self.postprocess(variant)
if self.updateRequested: # update requested
self.update(variant) if self.options.update:
if self.update(variant) != 0: logging.critical('update for "{}" failed.'.format(name))
elif not (self.options.accept or self.compare(variant)): # no update, do comparison elif not (self.options.accept or self.compare(variant)): # no update, do comparison
return variant+1 # return culprit return variant+1 # return culprit
except Exception as e : except Exception as e :
logging.critical('\nWARNING:\n {}\n'.format(e)) logging.critical('exception during variant execution: {}'.format(e))
return variant+1 # return culprit return variant+1 # return culprit
return 0 return 0
def testPossible(self): def feasible(self):
"""Check if test is possible or not (e.g. no license available).""" """Check whether test is possible or not (e.g. no license available)."""
return True return True
def clean(self): def clean(self):
"""Delete directory tree containing current results.""" """Delete directory tree containing current results."""
status = True
try: try:
shutil.rmtree(self.dirCurrent()) shutil.rmtree(self.dirCurrent())
except: except:
logging.warning('removal of directory "{}" not possible...'.format(self.dirCurrent())) logging.warning('removal of directory "{}" not possible...'.format(self.dirCurrent()))
status = status and False
try: try:
os.mkdir(self.dirCurrent()) os.mkdir(self.dirCurrent())
return True
except: except:
logging.critical('creation of directory "{}" failed...'.format(self.dirCurrent())) logging.critical('creation of directory "{}" failed.'.format(self.dirCurrent()))
status = status and False return False
return status
def prepareAll(self): def prepareAll(self):
"""Do all necessary preparations for the whole test""" """Do all necessary preparations for the whole test"""
@ -130,8 +134,8 @@ class Test():
def update(self,variant): def update(self,variant):
"""Update reference with current results.""" """Update reference with current results."""
logging.debug('Update not necessary') logging.critical('update not supported.')
return True return 1
def dirReference(self): def dirReference(self):
@ -178,7 +182,7 @@ class Test():
""" """
if not B or len(B) == 0: B = A if not B or len(B) == 0: B = A
for source,target in zip(map(mapA,A),map(mapB,B)): for source,target in zip(list(map(mapA,A)),list(map(mapB,B))):
try: try:
shutil.copy2(source,target) shutil.copy2(source,target)
except: except:
@ -301,26 +305,26 @@ class Test():
# check if comparison is possible and determine lenght of columns # check if comparison is possible and determine lenght of columns
if len(headings0) == len(headings1) == len(normHeadings): if len(headings0) == len(headings1) == len(normHeadings):
dataLength = len(headings0) dataLength = len(headings0)
length = [1 for i in xrange(dataLength)] length = [1 for i in range(dataLength)]
shape = [[] for i in xrange(dataLength)] shape = [[] for i in range(dataLength)]
data = [[] for i in xrange(dataLength)] data = [[] for i in range(dataLength)]
maxError = [0.0 for i in xrange(dataLength)] maxError = [0.0 for i in range(dataLength)]
absTol = [absoluteTolerance for i in xrange(dataLength)] absTol = [absoluteTolerance for i in range(dataLength)]
column = [[1 for i in xrange(dataLength)] for j in xrange(2)] column = [[1 for i in range(dataLength)] for j in range(2)]
norm = [[] for i in xrange(dataLength)] norm = [[] for i in range(dataLength)]
normLength = [1 for i in xrange(dataLength)] normLength = [1 for i in range(dataLength)]
normShape = [[] for i in xrange(dataLength)] normShape = [[] for i in range(dataLength)]
normColumn = [1 for i in xrange(dataLength)] normColumn = [1 for i in range(dataLength)]
for i in xrange(dataLength): for i in range(dataLength):
if headings0[i]['shape'] != headings1[i]['shape']: if headings0[i]['shape'] != headings1[i]['shape']:
raise Exception('shape mismatch between {} and {} '.format(headings0[i]['label'],headings1[i]['label'])) raise Exception('shape mismatch between {} and {} '.format(headings0[i]['label'],headings1[i]['label']))
shape[i] = headings0[i]['shape'] shape[i] = headings0[i]['shape']
for j in xrange(np.shape(shape[i])[0]): for j in range(np.shape(shape[i])[0]):
length[i] *= shape[i][j] length[i] *= shape[i][j]
normShape[i] = normHeadings[i]['shape'] normShape[i] = normHeadings[i]['shape']
for j in xrange(np.shape(normShape[i])[0]): for j in range(np.shape(normShape[i])[0]):
normLength[i] *= normShape[i][j] normLength[i] *= normShape[i][j]
else: else:
raise Exception('trying to compare {} with {} normed by {} data sets'.format(len(headings0), raise Exception('trying to compare {} with {} normed by {} data sets'.format(len(headings0),
@ -332,7 +336,7 @@ class Test():
table1 = damask.ASCIItable(name=file1,readonly=True) table1 = damask.ASCIItable(name=file1,readonly=True)
table1.head_read() table1.head_read()
for i in xrange(dataLength): for i in range(dataLength):
key0 = ('1_' if length[i]>1 else '') + headings0[i]['label'] key0 = ('1_' if length[i]>1 else '') + headings0[i]['label']
key1 = ('1_' if length[i]>1 else '') + headings1[i]['label'] key1 = ('1_' if length[i]>1 else '') + headings1[i]['label']
normKey = ('1_' if normLength[i]>1 else '') + normHeadings[i]['label'] normKey = ('1_' if normLength[i]>1 else '') + normHeadings[i]['label']
@ -350,7 +354,7 @@ class Test():
line0 = 0 line0 = 0
while table0.data_read(): # read next data line of ASCII table while table0.data_read(): # read next data line of ASCII table
if line0 not in skipLines: if line0 not in skipLines:
for i in xrange(dataLength): for i in range(dataLength):
myData = np.array(map(float,table0.data[column[0][i]:\ myData = np.array(map(float,table0.data[column[0][i]:\
column[0][i]+length[i]]),'d') column[0][i]+length[i]]),'d')
normData = np.array(map(float,table0.data[normColumn[i]:\ normData = np.array(map(float,table0.data[normColumn[i]:\
@ -362,11 +366,11 @@ class Test():
norm[i] = np.append(norm[i],np.linalg.norm(np.reshape(normData,normShape[i]),normType)) norm[i] = np.append(norm[i],np.linalg.norm(np.reshape(normData,normShape[i]),normType))
line0 += 1 line0 += 1
for i in xrange(dataLength): for i in range(dataLength):
if not perLine: norm[i] = [np.max(norm[i]) for j in xrange(line0-len(skipLines))] if not perLine: norm[i] = [np.max(norm[i]) for j in xrange(line0-len(skipLines))]
data[i] = np.reshape(data[i],[line0-len(skipLines),length[i]]) data[i] = np.reshape(data[i],[line0-len(skipLines),length[i]])
if any(norm[i]) == 0.0 or absTol[i]: if any(norm[i]) == 0.0 or absTol[i]:
norm[i] = [1.0 for j in xrange(line0-len(skipLines))] norm[i] = [1.0 for j in range(line0-len(skipLines))]
absTol[i] = True absTol[i] = True
if perLine: if perLine:
logging.warning('At least one norm of {} in 1. table is 0.0, using absolute tolerance'.format(headings0[i]['label'])) logging.warning('At least one norm of {} in 1. table is 0.0, using absolute tolerance'.format(headings0[i]['label']))
@ -376,7 +380,7 @@ class Test():
line1 = 0 line1 = 0
while table1.data_read(): # read next data line of ASCII table while table1.data_read(): # read next data line of ASCII table
if line1 not in skipLines: if line1 not in skipLines:
for i in xrange(dataLength): for i in range(dataLength):
myData = np.array(map(float,table1.data[column[1][i]:\ myData = np.array(map(float,table1.data[column[1][i]:\
column[1][i]+length[i]]),'d') column[1][i]+length[i]]),'d')
maxError[i] = max(maxError[i],np.linalg.norm(np.reshape(myData-data[i][line1-len(skipLines),:],shape[i]))/ maxError[i] = max(maxError[i],np.linalg.norm(np.reshape(myData-data[i][line1-len(skipLines),:],shape[i]))/
@ -386,7 +390,7 @@ class Test():
if (line0 != line1): raise Exception('found {} lines in 1. table but {} in 2. table'.format(line0,line1)) if (line0 != line1): raise Exception('found {} lines in 1. table but {} in 2. table'.format(line0,line1))
logging.info(' ********') logging.info(' ********')
for i in xrange(dataLength): for i in range(dataLength):
if absTol[i]: if absTol[i]:
logging.info(' * maximum absolute error {} between {} and {}'.format(maxError[i], logging.info(' * maximum absolute error {} between {} and {}'.format(maxError[i],
headings0[i]['label'], headings0[i]['label'],
@ -424,7 +428,7 @@ class Test():
if column is None: columns[i] = tables[i].labels(raw = True) # if no column is given, read all if column is None: columns[i] = tables[i].labels(raw = True) # if no column is given, read all
logging.info('comparing ASCIItables statistically') logging.info('comparing ASCIItables statistically')
for i in xrange(len(columns)): for i in range(len(columns)):
columns[i] = columns[0] if not columns[i] else \ columns[i] = columns[0] if not columns[i] else \
([columns[i]] if not (isinstance(columns[i], Iterable) and not isinstance(columns[i], str)) else \ ([columns[i]] if not (isinstance(columns[i], Iterable) and not isinstance(columns[i], str)) else \
columns[i] columns[i]
@ -440,7 +444,7 @@ class Test():
table.close() table.close()
for i in xrange(1,len(data)): for i in range(1,len(data)):
delta = data[i]-data[i-1] delta = data[i]-data[i-1]
normBy = (np.abs(data[i]) + np.abs(data[i-1]))*0.5 normBy = (np.abs(data[i]) + np.abs(data[i-1]))*0.5
normedDelta = np.where(normBy>preFilter,delta/normBy,0.0) normedDelta = np.where(normBy>preFilter,delta/normBy,0.0)
@ -458,17 +462,13 @@ class Test():
columns = [None], # list of list of column labels (per file) columns = [None], # list of list of column labels (per file)
rtol = 1e-5, rtol = 1e-5,
atol = 1e-8, atol = 1e-8,
preFilter = -1.0,
postFilter = -1.0,
debug = False): debug = False):
""" """compare multiple tables with np.allclose"""
compare tables with np.allclose
threshold can be used to ignore small values (a negative number disables this feature)
"""
if not (isinstance(files, Iterable) and not isinstance(files, str)): # check whether list of files is requested if not (isinstance(files, Iterable) and not isinstance(files, str)): # check whether list of files is requested
files = [str(files)] files = [str(files)]
if len(files) < 2: return True # single table is always close to itself...
tables = [damask.ASCIItable(name = filename,readonly = True) for filename in files] tables = [damask.ASCIItable(name = filename,readonly = True) for filename in files]
for table in tables: for table in tables:
table.head_read() table.head_read()
@ -477,47 +477,50 @@ class Test():
columns = columns[:len(files)] # truncate to same length as files columns = columns[:len(files)] # truncate to same length as files
for i,column in enumerate(columns): for i,column in enumerate(columns):
if column is None: columns[i] = tables[i].labels(raw = True) # if no column is given, read all if column is None: columns[i] = tables[i].labels(raw = False) # if no column is given, use all
logging.info('comparing ASCIItables') logging.info('comparing ASCIItables')
for i in xrange(len(columns)): for i in range(len(columns)):
columns[i] = columns[0] if not columns[i] else \ columns[i] = columns[0] if not columns[i] else \
([columns[i]] if not (isinstance(columns[i], Iterable) and not isinstance(columns[i], str)) else \ ([columns[i]] if not (isinstance(columns[i], Iterable) and not isinstance(columns[i], str)) else \
columns[i] columns[i]
) )
logging.info(files[i]+':'+','.join(columns[i])) logging.info(files[i]+': '+','.join(columns[i]))
if len(files) < 2: return True # single table is always close to itself... dimensions = tables[0].label_dimension(columns[0]) # width of each requested column
maximum = np.zeros_like(columns[0],dtype=float) # one magnitude per column entry
data = [] # list of feature table extracted from each file (ASCII table)
maximum = np.zeros(len(columns[0]),dtype='f') for i,(table,labels) in enumerate(zip(tables,columns)):
data = [] if np.any(dimensions != table.label_dimension(labels)): # check data object consistency
for table,labels in zip(tables,columns): logging.critical('Table {} differs in data layout.'.format(files[i]))
table.data_readArray(labels) return False
data.append(np.where(np.abs(table.data)<preFilter,np.zeros_like(table.data),table.data)) table.data_readArray(labels) # read data, ...
maximum += np.abs(table.data).max(axis=0) data.append(table.data) # ... store, ...
table.close() table.close() # ... close
maximum /= len(tables) for j,label in enumerate(labels): # iterate over object labels
maximum = np.where(maximum >0.0, maximum, 1) # avoid div by zero for empty columns maximum[j] = np.maximum(\
for i in xrange(len(data)): maximum[j],
data[i] /= maximum np.amax(np.linalg.norm(table.data[:,table.label_indexrange(label)],
axis=1))
) # find maximum Euclidean norm across rows
mask = np.zeros_like(table.data,dtype='bool') maximum = np.where(maximum > 0.0, maximum, 1.0) # avoid div by zero for zero columns
maximum = np.repeat(maximum,dimensions) # spread maximum over columns of each object
for table in data: for i in range(len(data)):
mask |= np.where(np.abs(table)<postFilter,True,False) # mask out (all) tiny values data[i] /= maximum # normalize each table
if debug:
logging.debug(str(maximum))
allclose = np.absolute(data[0]-data[1]) <= (atol + rtol*np.absolute(data[1]))
for ok,valA,valB in zip(allclose,data[0],data[1]):
logging.debug('{}:\n{}\n{}'.format(ok,valA,valB))
allclose = True # start optimistic allclose = True # start optimistic
for i in xrange(1,len(data)): for i in range(1,len(data)):
if debug: allclose &= np.allclose(data[i-1],data[i],rtol,atol) # accumulate "pessimism"
t0 = np.where(mask,0.0,data[i-1])
t1 = np.where(mask,0.0,data[i ])
j = np.argmin(np.abs(t1)*rtol+atol-np.abs(t0-t1))
logging.info('{:f}'.format(np.amax(np.abs(t0-t1)/(np.abs(t1)*rtol+atol))))
logging.info('{:f} {:f}'.format((t0*maximum).flatten()[j],(t1*maximum).flatten()[j]))
allclose &= np.allclose(np.where(mask,0.0,data[i-1]),
np.where(mask,0.0,data[i ]),rtol,atol) # accumulate "pessimism"
return allclose return allclose
@ -545,14 +548,16 @@ class Test():
def report_Success(self,culprit): def report_Success(self,culprit):
ret = culprit
if culprit == 0: if culprit == 0:
logging.critical(('The test' if len(self.variants) == 1 else 'All {} tests'.format(len(self.variants))) + ' passed') msg = 'The test passed' if len(self.variants) == 1 \
logging.critical('\n!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n') else 'All {} tests passed.'.format(len(self.variants))
return 0 elif culprit == -1:
if culprit == -1: msg = 'Warning: Could not start test...'
logging.warning('Warning: Could not start test') ret = 0
return 0
else: else:
logging.critical(' ********\n * Test {} failed...\n ********'.format(culprit)) msg = ' * Test "{}" failed.'.format(self.variants[culprit-1])
logging.critical('\n!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n')
return culprit logging.critical('\n'.join(['*'*40,msg,'*'*40]) + '\n')
return ret

58
lib/damask/util.py
View File

@ -20,6 +20,7 @@ class bcolors:
FAIL = '\033[91m' FAIL = '\033[91m'
ENDC = '\033[0m' ENDC = '\033[0m'
BOLD = '\033[1m' BOLD = '\033[1m'
DIM = '\033[2m'
UNDERLINE = '\033[4m' UNDERLINE = '\033[4m'
def disable(self): def disable(self):
@ -40,7 +41,7 @@ def srepr(arg,glue = '\n'):
hasattr(arg, "__getitem__") or hasattr(arg, "__getitem__") or
hasattr(arg, "__iter__")): hasattr(arg, "__iter__")):
return glue.join(srepr(x) for x in arg) return glue.join(srepr(x) for x in arg)
return arg if isinstance(arg,basestring) else repr(arg) return arg if isinstance(arg,str) else repr(arg)
# ----------------------------- # -----------------------------
def croak(what, newline = True): def croak(what, newline = True):
@ -70,9 +71,19 @@ def report_geom(info,
# ----------------------------- # -----------------------------
def emph(what): def emph(what):
"""emphasizes string on screen""" """boldens string"""
return bcolors.BOLD+srepr(what)+bcolors.ENDC return bcolors.BOLD+srepr(what)+bcolors.ENDC
# -----------------------------
def deemph(what):
"""dims string"""
return bcolors.DIM+srepr(what)+bcolors.ENDC
# -----------------------------
def delete(what):
"""dims string"""
return bcolors.DIM+srepr(what)+bcolors.ENDC
# ----------------------------- # -----------------------------
def execute(cmd, def execute(cmd,
streamIn = None, streamIn = None,
@ -137,29 +148,22 @@ class extendableOption(Option):
class backgroundMessage(threading.Thread): class backgroundMessage(threading.Thread):
"""reporting with animation to indicate progress""" """reporting with animation to indicate progress"""
choices = {'bounce': ['_', 'o', 'O', u'\u00B0', choices = {'bounce': ['_', 'o', 'O', '°', '‾', '‾', '°', 'O', 'o', '_'],
u'\u203e',u'\u203e',u'\u00B0','O','o','_'], 'spin': ['◜', '◝', '◞', '◟'],
'spin': [u'\u25dc',u'\u25dd',u'\u25de',u'\u25df'], 'circle': ['◴', '◵', '◶', '◷'],
'circle': [u'\u25f4',u'\u25f5',u'\u25f6',u'\u25f7'], 'hexagon': ['⬢', '⬣'],
'hexagon': [u'\u2b22',u'\u2b23'], 'square': ['▖', '▘', '▝', '▗'],
'square': [u'\u2596',u'\u2598',u'\u259d',u'\u2597'], 'triangle': ['ᐊ', 'ᐊ', 'ᐃ', 'ᐅ', 'ᐅ', 'ᐃ'],
'triangle': [u'\u140a',u'\u140a',u'\u1403',u'\u1405',u'\u1405',u'\u1403'], 'amoeba': ['▖', '▏', '▘', '▔', '▝', '▕', '▗', '▂'],
'amoeba': [u'\u2596',u'\u258f',u'\u2598',u'\u2594',u'\u259d',u'\u2595', 'beat': ['▁', '▂', '▃', '▅', '▆', '▇', '▇', '▆', '▅', '▃', '▂'],
u'\u2597',u'\u2582'], 'prison': ['ᚋ', 'ᚌ', 'ᚍ', 'ᚏ', 'ᚎ', 'ᚍ', 'ᚌ', 'ᚋ'],
'beat': [u'\u2581',u'\u2582',u'\u2583',u'\u2585',u'\u2586',u'\u2587', 'breath': ['ᚐ', 'ᚑ', 'ᚒ', 'ᚓ', 'ᚔ', 'ᚓ', 'ᚒ', 'ᚑ', 'ᚐ'],
u'\u2587',u'\u2586',u'\u2585',u'\u2583',u'\u2582',], 'pulse': ['·', '•', '●', '●', '•'],
'prison': [u'\u168b',u'\u168c',u'\u168d',u'\u168f',u'\u168e',u'\u168d', 'ant': ['⠁', '⠂', '⠐', '⠠', '⠄', '⡀', '⢀', '⠠', '⠄', '⠂', '⠐', '⠈'],
u'\u168c',u'\u168b',], 'juggle': ['꜈', '꜉', '꜊', '꜋', '꜌', '꜑', '꜐', '꜏', '꜍'],
'breath': [u'\u1690',u'\u1691',u'\u1692',u'\u1693',u'\u1694',u'\u1693', # 'wobbler': ['▁', '◣', '▏', '◤', '▔', '◥', '▕', '◢'],
u'\u1692',u'\u1691',u'\u1690',], 'grout': ['▁', '▏', '▔', '▕'],
'pulse': [u'·',u'•',u'\u25cf',u'\u25cf',u'•',], 'partner': ['⚬', '⚭', '⚮', '⚯', '⚮', '⚭'],
'ant': [u'\u2801',u'\u2802',u'\u2810',u'\u2820',u'\u2804',u'\u2840',
u'\u2880',u'\u2820',u'\u2804',u'\u2802',u'\u2810',u'\u2808'],
'juggle': [u'\ua708',u'\ua709',u'\ua70a',u'\ua70b',u'\ua70c',u'\ua711',
u'\ua710',u'\ua70f',u'\ua70d',],
# 'wobbler': [u'\u2581',u'\u25e3',u'\u258f',u'\u25e4',u'\u2594',u'\u25e5',u'\u2595',u'\u25e2',],
'grout': [u'\u2581',u'\u258f',u'\u2594',u'\u2595',],
'partner': [u'\u26ac',u'\u26ad',u'\u26ae',u'\u26af',u'\u26ae',u'\u26ad',],
'classic': ['-', '\\', '|', '/',], 'classic': ['-', '\\', '|', '/',],
} }
@ -171,7 +175,7 @@ class backgroundMessage(threading.Thread):
self.new_message = '' self.new_message = ''
self.counter = 0 self.counter = 0
self.gap = ' ' self.gap = ' '
self.symbols = self.choices[symbol if symbol in self.choices else random.choice(self.choices.keys())] self.symbols = self.choices[symbol if symbol in self.choices else random.choice(list(self.choices.keys()))]
self.waittime = wait self.waittime = wait
def __quit__(self): def __quit__(self):
@ -200,7 +204,7 @@ class backgroundMessage(threading.Thread):
def print_message(self): def print_message(self):
length = len(self.symbols[self.counter] + self.gap + self.message) length = len(self.symbols[self.counter] + self.gap + self.message)
sys.stderr.write(chr(8)*length + ' '*length + chr(8)*length + \ sys.stderr.write(chr(8)*length + ' '*length + chr(8)*length + \
self.symbols[self.counter].encode('utf-8') + self.gap + self.new_message) # delete former and print new message self.symbols[self.counter] + self.gap + self.new_message) # delete former and print new message
sys.stderr.flush() sys.stderr.flush()
self.message = self.new_message self.message = self.new_message

2
processing/misc/OIMgrainFile_toTable.py
View File

@ -12,7 +12,7 @@ scriptID = ' '.join([scriptName,damask.version])
# MAIN # MAIN
#-------------------------------------------------------------------------------------------------- #--------------------------------------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """ parser = OptionParser(option_class=damask.extendableOption, usage='%prog [file[s]]', description = """
Adds header to OIM grain file to make it accesible as ASCII table Adds header to OIM grain file to make it accesible as ASCII table
""", version = scriptID) """, version = scriptID)

4
processing/misc/ang_toTable.py
View File

@ -13,7 +13,7 @@ scriptID = ' '.join([scriptName,damask.version])
# MAIN # MAIN
#-------------------------------------------------------------------------------------------------- #--------------------------------------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog [geomfile[s]]', description = """ parser = OptionParser(option_class=damask.extendableOption, usage='%prog [angfile[s]]', description = """
Convert TSL/EDAX *.ang file to ASCIItable Convert TSL/EDAX *.ang file to ASCIItable
""", version = scriptID) """, version = scriptID)
@ -30,7 +30,7 @@ for name in filenames:
outname = os.path.splitext(name)[0]+'.txt' if name else name, outname = os.path.splitext(name)[0]+'.txt' if name else name,
buffered = False, labeled = False) buffered = False, labeled = False)
except: continue except: continue
table.croak('\033[1m'+scriptName+'\033[0m'+(': '+name if name else '')) damask.util.report(scriptName,name)
# --- interpret header ----------------------------------------------------------------------------- # --- interpret header -----------------------------------------------------------------------------

14
processing/post/addMapped.py
View File

@ -2,6 +2,7 @@
# -*- coding: UTF-8 no BOM -*- # -*- coding: UTF-8 no BOM -*-
import os,sys import os,sys
import numpy as np
from optparse import OptionParser from optparse import OptionParser
import damask import damask
@ -28,7 +29,7 @@ parser.add_option('-o','--offset',
parser.add_option('-l','--label', parser.add_option('-l','--label',
dest = 'label', dest = 'label',
action = 'extend', metavar = '<string LIST>', action = 'extend', metavar = '<string LIST>',
help='heading of column(s) to be mapped') help='column label(s) to be mapped')
parser.add_option('-a','--asciitable', parser.add_option('-a','--asciitable',
dest = 'asciitable', dest = 'asciitable',
type = 'string', metavar = 'string', type = 'string', metavar = 'string',
@ -49,12 +50,13 @@ if options.map is None:
if options.asciitable is not None and os.path.isfile(options.asciitable): if options.asciitable is not None and os.path.isfile(options.asciitable):
mappedTable = damask.ASCIItable(name = options.asciitable, mappedTable = damask.ASCIItable(name = options.asciitable,
buffered = False, readonly = True) buffered = False,
readonly = True)
mappedTable.head_read() # read ASCII header info of mapped table mappedTable.head_read() # read ASCII header info of mapped table
missing_labels = mappedTable.data_readArray(options.label) missing_labels = mappedTable.data_readArray(options.label)
if len(missing_labels) > 0: if len(missing_labels) > 0:
mappedTable.croak('column{} {} not found...'.format('s' if len(missing_labels) > 1 else '',', '.join(missing_labels))) damask.util.croak('column{} {} not found...'.format('s' if len(missing_labels) > 1 else '',', '.join(missing_labels)))
else: else:
parser.error('no mapped ASCIItable given.') parser.error('no mapped ASCIItable given.')
@ -64,8 +66,7 @@ else:
if filenames == []: filenames = [None] if filenames == []: filenames = [None]
for name in filenames: for name in filenames:
try: try: table = damask.ASCIItable(name = name,
table = damask.ASCIItable(name = name,
buffered = False) buffered = False)
except: continue except: continue
damask.util.report(scriptName,name) damask.util.report(scriptName,name)
@ -96,7 +97,10 @@ for name in filenames:
outputAlive = True outputAlive = True
while outputAlive and table.data_read(): # read next data line of ASCII table while outputAlive and table.data_read(): # read next data line of ASCII table
try:
table.data_append(mappedTable.data[int(round(float(table.data[mappedColumn])))+options.offset-1]) # add all mapped data types table.data_append(mappedTable.data[int(round(float(table.data[mappedColumn])))+options.offset-1]) # add all mapped data types
except IndexError:
table.data_append(np.nan*np.ones_like(mappedTable.data[0]))
outputAlive = table.data_write() # output processed line outputAlive = table.data_write() # output processed line
# ------------------------------------------ output finalization ----------------------------------- # ------------------------------------------ output finalization -----------------------------------

3
processing/post/addOrientations.py
View File

@ -69,7 +69,8 @@ parser.add_option('-q', '--quaternion',
parser.set_defaults(output = [], parser.set_defaults(output = [],
symmetry = damask.Symmetry.lattices[-1], symmetry = damask.Symmetry.lattices[-1],
rotation = (0.,1.,1.,1.), # no rotation about 1,1,1 labrotation = (0.,1.,1.,1.), # no rotation about 1,1,1
crystalrotation = (0.,1.,1.,1.), # no rotation about 1,1,1
degrees = False, degrees = False,
) )

1
processing/post/addSchmidfactors.py
View File

@ -167,7 +167,6 @@ force = np.array(options.force)
force /= np.linalg.norm(force) force /= np.linalg.norm(force)
if options.normal: if options.normal:
damask.util.croak('got normal')
normal = np.array(options.normal) normal = np.array(options.normal)
normal /= np.linalg.norm(normal) normal /= np.linalg.norm(normal)
if abs(np.dot(force,normal)) > 1e-3: if abs(np.dot(force,normal)) > 1e-3:

1
processing/post/addSpectralDecomposition.py
View File

@ -78,6 +78,7 @@ for name in filenames:
for type, data in items.iteritems(): for type, data in items.iteritems():
for column in data['column']: for column in data['column']:
(u,v) = np.linalg.eigh(np.array(map(float,table.data[column:column+data['dim']])).reshape(data['shape'])) (u,v) = np.linalg.eigh(np.array(map(float,table.data[column:column+data['dim']])).reshape(data['shape']))
if np.dot(np.cross(v[:,0], v[:,1]), v[:,2]) < 0.0 : v[:, 2] *= -1.0 # ensure right-handed coordinate system
table.data_append(list(u)) table.data_append(list(u))
table.data_append(list(v.transpose().reshape(data['dim']))) table.data_append(list(v.transpose().reshape(data['dim'])))
outputAlive = table.data_write() # output processed line outputAlive = table.data_write() # output processed line

82
processing/post/averageTable.py
View File

@ -1,82 +0,0 @@
#!/usr/bin/env python2.7
# -*- coding: UTF-8 no BOM -*-
import os,sys
import numpy as np
from optparse import OptionParser
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
Replace all rows for which column 'label' has identical values by a single row containing their average.
Output table will contain as many rows as there are different (unique) values in the grouping column.
Examples:
For grain averaged values, replace all rows of particular 'texture' with a single row containing their average.
""", version = scriptID)
parser.add_option('-l','--label',
dest = 'label',
type = 'string', metavar = 'string',
help = 'column label for grouping rows')
(options,filenames) = parser.parse_args()
if options.label is None:
parser.error('no grouping column specified.')
# --- loop over input files -------------------------------------------------------------------------
if filenames == []: filenames = [None]
for name in filenames:
try: table = damask.ASCIItable(name = name,
outname = os.path.join(
os.path.split(name)[0],
options.label+'_averaged_'+os.path.split(name)[1]
) if name else name,
buffered = False)
except: continue
damask.util.report(scriptName,name)
# ------------------------------------------ sanity checks ---------------------------------------
table.head_read()
if table.label_dimension(options.label) != 1:
damask.util.croak('column {} is not of scalar dimension.'.format(options.label))
table.close(dismiss = True) # close ASCIItable and remove empty file
continue
# ------------------------------------------ assemble info ---------------------------------------
table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
table.head_write()
# ------------------------------------------ process data --------------------------------
table.data_readArray()
rows,cols = table.data.shape
table.data = table.data[np.lexsort([table.data[:,table.label_index(options.label)]])]
values,index = np.unique(table.data[:,table.label_index(options.label)], return_index = True)
index = np.append(index,rows)
avgTable = np.empty((len(values), cols))
for j in xrange(cols) :
for i in xrange(len(values)) :
avgTable[i,j] = np.average(table.data[index[i]:index[i+1],j])
table.data = avgTable
# ------------------------------------------ output result -------------------------------
table.data_writeArray()
table.close() # close ASCII table

20
processing/post/binXY.py
View File

@ -20,7 +20,7 @@ Produces a binned grid of two columns from an ASCIItable, i.e. a two-dimensional
parser.add_option('-d','--data', parser.add_option('-d','--data',
dest = 'data', dest = 'data',
type='string', nargs = 2, metavar = 'string string', type = 'string', nargs = 2, metavar = 'string string',
help = 'column labels containing x and y ') help = 'column labels containing x and y ')
parser.add_option('-w','--weight', parser.add_option('-w','--weight',
dest = 'weight', dest = 'weight',
@ -49,15 +49,15 @@ parser.add_option('-z','--zrange',
parser.add_option('-i','--invert', parser.add_option('-i','--invert',
dest = 'invert', dest = 'invert',
action = 'store_true', action = 'store_true',
help = 'invert probability density [%default]') help = 'invert probability density')
parser.add_option('-r','--rownormalize', parser.add_option('-r','--rownormalize',
dest = 'normRow', dest = 'normRow',
action = 'store_true', action = 'store_true',
help = 'normalize probability density in each row [%default]') help = 'normalize probability density in each row')
parser.add_option('-c','--colnormalize', parser.add_option('-c','--colnormalize',
dest = 'normCol', dest = 'normCol',
action = 'store_true', action = 'store_true',
help = 'normalize probability density in each column [%default]') help = 'normalize probability density in each column')
parser.set_defaults(bins = (10,10), parser.set_defaults(bins = (10,10),
type = ('linear','linear','linear'), type = ('linear','linear','linear'),
@ -79,7 +79,8 @@ result = np.zeros((options.bins[0],options.bins[1],3),'f')
if options.data is None: parser.error('no data columns specified.') if options.data is None: parser.error('no data columns specified.')
labels = options.data labels = list(options.data)
if options.weight is not None: labels += [options.weight] # prevent character splitting of single string value if options.weight is not None: labels += [options.weight] # prevent character splitting of single string value
@ -120,11 +121,10 @@ for name in filenames:
delta = minmax[:,1]-minmax[:,0] delta = minmax[:,1]-minmax[:,0]
for i in xrange(len(table.data)): (grid,xedges,yedges) = np.histogram2d(table.data[:,0],table.data[:,1],
x = int(options.bins[0]*(table.data[i,0]-minmax[0,0])/delta[0]) bins=options.bins,
y = int(options.bins[1]*(table.data[i,1]-minmax[1,0])/delta[1]) range=minmax,
if x >= 0 and x < options.bins[0] and y >= 0 and y < options.bins[1]: weights=None if options.weight is None else table.data[:,2])
grid[x,y] += 1. if options.weight is None else table.data[i,2] # count (weighted) occurrences
if options.normCol: if options.normCol:
for x in xrange(options.bins[0]): for x in xrange(options.bins[0]):

131
processing/post/groupTable.py Executable file
View File

@ -0,0 +1,131 @@
#!/usr/bin/env python2.7
# -*- coding: UTF-8 no BOM -*-
import os,sys
import math # noqa
import numpy as np
from optparse import OptionParser, OptionGroup
import damask
#"https://en.wikipedia.org/wiki/Center_of_mass#Systems_with_periodic_boundary_conditions"
def periodicAverage(Points, Box):
theta = (Points/Box[1]) * (2.0*np.pi)
xi = np.cos(theta)
zeta = np.sin(theta)
theta_avg = np.arctan2(-1.0*zeta.mean(), -1.0*xi.mean()) + np.pi
Pmean = Box[1] * theta_avg/(2.0*np.pi)
return Pmean
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
Apply a user-specified function to condense all rows for which column 'label' has identical values into a single row.
Output table will contain as many rows as there are different (unique) values in the grouping column.
Examples:
For grain averaged values, replace all rows of particular 'texture' with a single row containing their average.
""", version = scriptID)
parser.add_option('-l','--label',
dest = 'label',
type = 'string', metavar = 'string',
help = 'column label for grouping rows')
parser.add_option('-f','--function',
dest = 'function',
type = 'string', metavar = 'string',
help = 'mapping function [%default]')
parser.add_option('-a','--all',
dest = 'all',
action = 'store_true',
help = 'apply mapping function also to grouping column')
group = OptionGroup(parser, "periodic averaging", "")
group.add_option('-p','--periodic',
dest = 'periodic',
action = 'store_true',
help = 'calculate average in periodic space defined by periodic length [%default]')
group.add_option('--boundary',
dest = 'boundary', metavar = 'MIN MAX',
type = 'float', nargs = 2,
help = 'define periodic box end points %default')
parser.add_option_group(group)
parser.set_defaults(function = 'np.average',
all = False,
periodic = False,
boundary = [0.0, 1.0])
(options,filenames) = parser.parse_args()
funcModule,funcName = options.function.split('.')
try:
mapFunction = getattr(locals().get(funcModule) or
globals().get(funcModule) or
__import__(funcModule),
funcName)
except:
mapFunction = None
if options.label is None:
parser.error('no grouping column specified.')
if not hasattr(mapFunction,'__call__'):
parser.error('function "{}" is not callable.'.format(options.function))
# --- loop over input files -------------------------------------------------------------------------
if filenames == []: filenames = [None]
for name in filenames:
try: table = damask.ASCIItable(name = name,
buffered = False)
except: continue
damask.util.report(scriptName,name)
# ------------------------------------------ sanity checks ---------------------------------------
table.head_read()
if table.label_dimension(options.label) != 1:
damask.util.croak('column {} is not of scalar dimension.'.format(options.label))
table.close(dismiss = True) # close ASCIItable and remove empty file
continue
else:
grpColumn = table.label_index(options.label)
# ------------------------------------------ assemble info ---------------------------------------
table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
table.head_write()
# ------------------------------------------ process data --------------------------------
table.data_readArray()
rows,cols = table.data.shape
table.data = table.data[np.lexsort([table.data[:,grpColumn]])] # sort data by grpColumn
values,index = np.unique(table.data[:,grpColumn], return_index = True) # unique grpColumn values and their positions
index = np.append(index,rows) # add termination position
grpTable = np.empty((len(values), cols)) # initialize output
for i in xrange(len(values)): # iterate over groups (unique values in grpColumn)
if options.periodic :
grpTable[i] = periodicAverage(table.data[index[i]:index[i+1]],options.boundary) # apply periodicAverage mapping function
else :
grpTable[i] = np.apply_along_axis(mapFunction,0,table.data[index[i]:index[i+1]]) # apply mapping function
if not options.all: grpTable[i,grpColumn] = table.data[index[i],grpColumn] # restore grouping column value
table.data = grpTable
# ------------------------------------------ output result -------------------------------
table.data_writeArray()
table.close() # close ASCII table

79
processing/post/vtk_addPointcloudData.py
View File

@ -5,6 +5,7 @@ import os,vtk
import damask import damask
from collections import defaultdict from collections import defaultdict
from optparse import OptionParser from optparse import OptionParser
from vtk.util import numpy_support
scriptName = os.path.splitext(os.path.basename(__file__))[0] scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version]) scriptID = ' '.join([scriptName,damask.version])
@ -13,10 +14,10 @@ scriptID = ' '.join([scriptName,damask.version])
# MAIN # MAIN
# -------------------------------------------------------------------- # --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """ parser = OptionParser(option_class=damask.extendableOption,
Add scalar and RGB tuples from ASCIItable to existing VTK point cloud (.vtp). usage='%prog options [file[s]]',
description = """Add scalar and RGB tuples from ASCIItable to existing VTK point cloud (.vtp).""",
""", version = scriptID) version = scriptID)
parser.add_option( '--vtk', parser.add_option( '--vtk',
dest = 'vtk', dest = 'vtk',
@ -30,19 +31,20 @@ parser.add_option('-r', '--render',
dest = 'render', dest = 'render',
action = 'store_true', action = 'store_true',
help = 'open output in VTK render window') help = 'open output in VTK render window')
parser.add_option('-s', '--scalar', dest='scalar', action='extend', parser.add_option('-d', '--data',
metavar ='<string LIST>', dest = 'data',
help = 'scalar values')
parser.add_option('-v', '--vector',
dest = 'vector',
action = 'extend', metavar = '<string LIST>', action = 'extend', metavar = '<string LIST>',
help = 'vector value label(s)') help = 'scalar/vector value(s) label(s)')
parser.add_option('-t', '--tensor',
dest = 'tensor',
action = 'extend', metavar = '<string LIST>',
help = 'tensor (3x3) value label(s)')
parser.add_option('-c', '--color', dest='color', action='extend', parser.add_option('-c', '--color', dest='color', action='extend',
metavar ='<string LIST>', metavar ='<string LIST>',
help = 'RGB color tuples') help = 'RGB color tuples')
parser.set_defaults(scalar = [], parser.set_defaults(data = [],
vector = [], tensor = [],
color = [], color = [],
inplace = False, inplace = False,
render = False, render = False,
@ -95,9 +97,9 @@ for name in filenames:
VTKarray = {} VTKarray = {}
active = defaultdict(list) active = defaultdict(list)
for datatype,dimension,label in [['scalar',1,options.scalar], for datatype,dimension,label in [['data',99,options.vector],
['vector',3,options.vector], ['tensor',9,options.tensor],
['color',3,options.color], ['color' ,3,options.color],
]: ]:
for i,dim in enumerate(table.label_dimension(label)): for i,dim in enumerate(table.label_dimension(label)):
me = label[i] me = label[i]
@ -107,46 +109,47 @@ for name in filenames:
remarks.append('adding {} "{}"...'.format(datatype,me)) remarks.append('adding {} "{}"...'.format(datatype,me))
active[datatype].append(me) active[datatype].append(me)
if datatype in ['scalar','vector']: VTKarray[me] = vtk.vtkDoubleArray()
elif datatype == 'color': VTKarray[me] = vtk.vtkUnsignedCharArray()
VTKarray[me].SetNumberOfComponents(dimension)
VTKarray[me].SetName(label[i])
if remarks != []: damask.util.croak(remarks) if remarks != []: damask.util.croak(remarks)
if errors != []: if errors != []:
damask.util.croak(errors) damask.util.croak(errors)
table.close(dismiss = True) table.close(dismiss = True)
continue continue
# ------------------------------------------ process data --------------------------------------- # --------------------------------------- process and add data -----------------------------------
while table.data_read(): # read next data line of ASCII table table.data_readArray([item for sublist in active.values() for item in sublist]) # read all requested data
for datatype,labels in active.items(): # loop over scalar,color for datatype,labels in active.items(): # loop over scalar,color
for me in labels: # loop over all requested items for me in labels: # loop over all requested items
theData = [table.data[i] for i in table.label_indexrange(me)] # read strings VTKtype = vtk.VTK_DOUBLE
if datatype == 'color': VTKarray[me].InsertNextTuple3(*map(lambda x: int(255.*float(x)),theData)) VTKdata = table.data[:, table.label_indexrange(me)].copy() # copy to force contiguous layout
elif datatype == 'vector': VTKarray[me].InsertNextTuple3(*map(float,theData))
elif datatype == 'scalar': VTKarray[me].InsertNextValue(float(theData[0]))
table.input_close() # close input ASCII table
# ------------------------------------------ add data ---------------------------------------
for datatype,labels in active.items(): # loop over scalar,color
if datatype == 'color': if datatype == 'color':
Polydata.GetPointData().SetScalars(VTKarray[active['color'][0]]) VTKtype = vtk.VTK_UNSIGNED_CHAR
Polydata.GetCellData().SetScalars(VTKarray[active['color'][0]]) VTKdata = (VTKdata*255).astype(int) # translate to 0..255 UCHAR
for me in labels: # loop over all requested items elif datatype == 'tensor':
VTKdata[:,1] = VTKdata[:,3] = 0.5*(VTKdata[:,1]+VTKdata[:,3])
VTKdata[:,2] = VTKdata[:,6] = 0.5*(VTKdata[:,2]+VTKdata[:,6])
VTKdata[:,5] = VTKdata[:,7] = 0.5*(VTKdata[:,5]+VTKdata[:,7])
VTKarray[me] = numpy_support.numpy_to_vtk(num_array=VTKdata,deep=True,array_type=VTKtype)
VTKarray[me].SetName(me)
if datatype == 'color':
Polydata.GetPointData().SetScalars(VTKarray[me])
Polydata.GetCellData().SetScalars(VTKarray[me])
else:
Polydata.GetPointData().AddArray(VTKarray[me]) Polydata.GetPointData().AddArray(VTKarray[me])
Polydata.GetCellData().AddArray(VTKarray[me]) Polydata.GetCellData().AddArray(VTKarray[me])
Polydata.Modified()
if vtk.VTK_MAJOR_VERSION <= 5: Polydata.Update() table.input_close() # close input ASCII table
# ------------------------------------------ output result --------------------------------------- # ------------------------------------------ output result ---------------------------------------
Polydata.Modified()
if vtk.VTK_MAJOR_VERSION <= 5: Polydata.Update()
writer = vtk.vtkXMLPolyDataWriter() writer = vtk.vtkXMLPolyDataWriter()
writer.SetDataModeToBinary() writer.SetDataModeToBinary()
writer.SetCompressorTypeToZLib() writer.SetCompressorTypeToZLib()
@ -164,7 +167,7 @@ if options.render:
actor.SetMapper(mapper) actor.SetMapper(mapper)
# Create the graphics structure. The renderer renders into the # Create the graphics structure. The renderer renders into the
# render window. The render window interactor captures mouse events # render window. The render window interactively captures mouse events
# and will perform appropriate camera or actor manipulation # and will perform appropriate camera or actor manipulation
# depending on the nature of the events. # depending on the nature of the events.

55
processing/post/vtk_addRectilinearGridData.py
View File

@ -3,6 +3,7 @@
import os,vtk import os,vtk
import damask import damask
from vtk.util import numpy_support
from collections import defaultdict from collections import defaultdict
from optparse import OptionParser from optparse import OptionParser
@ -30,21 +31,21 @@ parser.add_option('-r', '--render',
dest = 'render', dest = 'render',
action = 'store_true', action = 'store_true',
help = 'open output in VTK render window') help = 'open output in VTK render window')
parser.add_option('-s', '--scalar', parser.add_option('-d', '--data',
dest = 'scalar', dest = 'data',
action = 'extend', metavar = '<string LIST>', action = 'extend', metavar = '<string LIST>',
help = 'scalar value label(s)') help = 'scalar/vector value(s) label(s)')
parser.add_option('-v', '--vector', parser.add_option('-t', '--tensor',
dest = 'vector', dest = 'tensor',
action = 'extend', metavar = '<string LIST>', action = 'extend', metavar = '<string LIST>',
help = 'vector value label(s)') help = 'tensor (3x3) value label(s)')
parser.add_option('-c', '--color', parser.add_option('-c', '--color',
dest = 'color', dest = 'color',
action = 'extend', metavar = '<string LIST>', action = 'extend', metavar = '<string LIST>',
help = 'RGB color tuple label') help = 'RGB color tuple label')
parser.set_defaults(scalar = [], parser.set_defaults(data = [],
vector = [], tensor = [],
color = [], color = [],
inplace = False, inplace = False,
render = False, render = False,
@ -93,9 +94,9 @@ for name in filenames:
VTKarray = {} VTKarray = {}
active = defaultdict(list) active = defaultdict(list)
for datatype,dimension,label in [['scalar',1,options.scalar], for datatype,dimension,label in [['data',99,options.data],
['vector',3,options.vector], ['tensor',9,options.tensor],
['color',3,options.color], ['color' ,3,options.color],
]: ]:
for i,dim in enumerate(table.label_dimension(label)): for i,dim in enumerate(table.label_dimension(label)):
me = label[i] me = label[i]
@ -105,12 +106,6 @@ for name in filenames:
remarks.append('adding {} "{}"...'.format(datatype,me)) remarks.append('adding {} "{}"...'.format(datatype,me))
active[datatype].append(me) active[datatype].append(me)
if datatype in ['scalar','vector']: VTKarray[me] = vtk.vtkDoubleArray()
elif datatype == 'color': VTKarray[me] = vtk.vtkUnsignedCharArray()
VTKarray[me].SetNumberOfComponents(dimension)
VTKarray[me].SetName(label[i])
if remarks != []: damask.util.croak(remarks) if remarks != []: damask.util.croak(remarks)
if errors != []: if errors != []:
damask.util.croak(errors) damask.util.croak(errors)
@ -119,24 +114,30 @@ for name in filenames:
# ------------------------------------------ process data --------------------------------------- # ------------------------------------------ process data ---------------------------------------
datacount = 0 table.data_readArray([item for sublist in active.values() for item in sublist]) # read all requested data
while table.data_read(): # read next data line of ASCII table
datacount += 1 # count data lines
for datatype,labels in active.items(): # loop over scalar,color for datatype,labels in active.items(): # loop over scalar,color
for me in labels: # loop over all requested items for me in labels: # loop over all requested items
theData = [table.data[i] for i in table.label_indexrange(me)] # read strings VTKtype = vtk.VTK_DOUBLE
if datatype == 'color': VTKarray[me].InsertNextTuple3(*map(lambda x: int(255.*float(x)),theData)) VTKdata = table.data[:, table.label_indexrange(me)].copy() # copy to force contiguous layout
elif datatype == 'vector': VTKarray[me].InsertNextTuple3(*map(float,theData))
elif datatype == 'scalar': VTKarray[me].InsertNextValue(float(theData[0])) if datatype == 'color':
VTKtype = vtk.VTK_UNSIGNED_CHAR
VTKdata = (VTKdata*255).astype(int) # translate to 0..255 UCHAR
elif datatype == 'tensor':
VTKdata[:,1] = VTKdata[:,3] = 0.5*(VTKdata[:,1]+VTKdata[:,3])
VTKdata[:,2] = VTKdata[:,6] = 0.5*(VTKdata[:,2]+VTKdata[:,6])
VTKdata[:,5] = VTKdata[:,7] = 0.5*(VTKdata[:,5]+VTKdata[:,7])
VTKarray[me] = numpy_support.numpy_to_vtk(num_array=VTKdata,deep=True,array_type=VTKtype)
VTKarray[me].SetName(me)
table.close() # close input ASCII table table.close() # close input ASCII table
# ------------------------------------------ add data --------------------------------------- # ------------------------------------------ add data ---------------------------------------
if datacount == Npoints: mode = 'point' if len(table.data) == Npoints: mode = 'point'
elif datacount == Ncells: mode = 'cell' elif len(table.data) == Ncells: mode = 'cell'
else: else:
damask.util.croak('Data count is incompatible with grid...') damask.util.croak('Data count is incompatible with grid...')
continue continue

4
processing/post/vtk_rectilinearGrid.py
View File

@ -79,9 +79,9 @@ for name in filenames:
coords = [np.unique(table.data[:,i]) for i in xrange(3)] coords = [np.unique(table.data[:,i]) for i in xrange(3)]
if options.mode == 'cell': if options.mode == 'cell':
coords = [0.5 * np.array([3.0 * coords[i][0] - coords[i][0 + len(coords[i]) > 1]] + \ coords = [0.5 * np.array([3.0 * coords[i][0] - coords[i][0 + int(len(coords[i]) > 1)]] + \
[coords[i][j-1] + coords[i][j] for j in xrange(1,len(coords[i]))] + \ [coords[i][j-1] + coords[i][j] for j in xrange(1,len(coords[i]))] + \
[3.0 * coords[i][-1] - coords[i][-1 - (len(coords[i]) > 1)]]) for i in xrange(3)] [3.0 * coords[i][-1] - coords[i][-1 - int(len(coords[i]) > 1)]]) for i in xrange(3)]
grid = np.array(map(len,coords),'i') grid = np.array(map(len,coords),'i')
N = grid.prod() if options.mode == 'point' else (grid-1).prod() N = grid.prod() if options.mode == 'point' else (grid-1).prod()

106
processing/pre/OIMlinear2linearODF.py
View File

@ -1,106 +0,0 @@
#!/usr/bin/env python2.7
# -*- coding: UTF-8 no BOM -*-
import os,sys
from optparse import OptionParser
import numpy as np
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
sampleSym = { 'Orthotropic' : (90,90,90),
'Triclinic' : (360,180,360)
}
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
Transform the binned texture data from "TSL OIM Analysis" into linear ODF data,
""", version = scriptID)
parser.add_option('-s', '--symmetry', dest='symmetry', choices=sampleSym.keys(),
metavar = 'string',
help='Sample symmetry {%s} [Triclinic]'%(' '.join(sampleSym.keys())))
parser.set_defaults(symmetry = 'Triclinic')
(options,filenames) = parser.parse_args()
#--- setup file handles ---------------------------------------------------------------------------
files = []
if filenames == []:
files.append({'name':'STDIN',
'input':sys.stdin,
'output':sys.stdout,
'croak':sys.stderr,
})
else:
for name in filenames:
if os.path.exists(name):
files.append({'name':name,
'input':open(name),
'output':open(name+'_tmp','w'),
'croak':sys.stdout,
})
#--- loop over input files ------------------------------------------------------------------------
for file in files:
file['croak'].write('\033[1m' + scriptName + '\033[0m: ' + (file['name'] if file['name'] != 'STDIN' else '') + '\n')
while True: # read header (forward and get bin Size)
line = file['input'].readline()
words = line.split()
if len(words)>=3:
if words[1]=='Bin' and words[2]=='Size:': binSize=float(words[3][:-1])
if not line.startswith('#'): break
delta = [sampleSym[options.symmetry][i]/binSize for i in xrange(3)]
nPhi1,nPHI,nPhi2 = map(int,delta)
dPhi1,dPHI,dPhi2 = [sampleSym[options.symmetry][i]/delta[i] for i in xrange(3)]
N = (nPhi1-1)*(nPHI-1)*(nPhi2-1)
ODF = [[[[None] for k in range(nPhi2)] for j in range(nPHI)] for i in range(nPhi1)]
linear = [None]*N
ODF = np.empty([nPhi1,nPHI,nPhi2],'d')
for iPhi1 in range(nPhi1):
for iPHI in range(nPHI):
for iPhi2 in range(nPhi2):
ODF[iPhi1,iPHI,iPhi2] = float(line.split()[3])*0.125 # extract intensity (in column 4) and weight by 1/8
line = file['input'].readline()
for iPhi1 in range(nPhi1-1):
for iPHI in range(nPHI-1):
for iPhi2 in range(nPhi2-1):
linear[iPhi1*(nPHI-1)*(nPhi2-1)+iPHI*(nPhi2-1)+iPhi2] =\
ODF[iPhi1 ,iPHI ,iPhi2 ] +\
ODF[iPhi1 ,iPHI ,iPhi2+1] +\
ODF[iPhi1 ,iPHI+1,iPhi2 ] +\
ODF[iPhi1 ,iPHI+1,iPhi2+1] +\
ODF[iPhi1+1,iPHI ,iPhi2 ] +\
ODF[iPhi1+1,iPHI ,iPhi2+1] +\
ODF[iPhi1+1,iPHI+1,iPhi2 ] +\
ODF[iPhi1+1,iPHI+1,iPhi2+1]
file['output'].write('4 header\n')
file['output'].write('limit phi1 %-6.2f Phi %-6.2f phi2 %-6.2f\n'%sampleSym[options.symmetry])
file['output'].write('delta phi1 %-6.2f Phi %-6.2f phi2 %-6.2f\n'%(dPhi1,dPHI,dPhi2))
file['output'].write('centration cell-centered\n')
file['output'].write('density\n')
for i in range(N):
file['output'].write('%g\n'%(linear[i]))
#--- output finalization --------------------------------------------------------------------------
if file['name'] != 'STDIN':
file['output'].close()
os.rename(file['name']+'_tmp',os.path.splitext(file['name'])[0] +'.linearODF')

6
processing/pre/geom_addPrimitive.py
View File

@ -126,9 +126,9 @@ for name in filenames:
primPos = invRotation*gridpos # rotate back to primitive coordinate system primPos = invRotation*gridpos # rotate back to primitive coordinate system
if np.dot(mask*primPos/dim,mask*primPos/dim) <= 0.25 and \ if np.dot(mask*primPos/dim,mask*primPos/dim) <= 0.25 and \
np.all(abs((1.-mask)*primPos/dim) <= 0.5): # inside ellipsoid and inside box np.all(abs((1.-mask)*primPos/dim) <= 0.5): # inside ellipsoid and inside box
microstructure[(gridpos[0]+options.center[0])%info['grid'][0], microstructure[int((gridpos[0]+options.center[0])%info['grid'][0]),
(gridpos[1]+options.center[1])%info['grid'][1], int((gridpos[1]+options.center[1])%info['grid'][1]),
(gridpos[2]+options.center[2])%info['grid'][2]] = options.fill # assign microstructure index int((gridpos[2]+options.center[2])%info['grid'][2])] = options.fill # assign microstructure index
newInfo['microstructures'] = microstructure.max() newInfo['microstructures'] = microstructure.max()

15
processing/pre/geom_grainGrowth.py
View File

@ -81,17 +81,20 @@ for name in filenames:
periodic_microstructure = np.tile(microstructure,(3,3,3))[grid[0]/2:-grid[0]/2, periodic_microstructure = np.tile(microstructure,(3,3,3))[grid[0]/2:-grid[0]/2,
grid[1]/2:-grid[1]/2, grid[1]/2:-grid[1]/2,
grid[2]/2:-grid[2]/2] # periodically extend the microstructure grid[2]/2:-grid[2]/2] # periodically extend the microstructure
# store a copy the initial microstructure to find locations of immutable indices # store a copy the initial microstructure to find locations of immutable indices
microstructure_original = np.copy(microstructure) microstructure_original = np.copy(microstructure)
X,Y,Z = np.mgrid[0:grid[0],0:grid[1],0:grid[2]] X,Y,Z = np.mgrid[0:grid[0],0:grid[1],0:grid[2]]
# Calculates gaussian weights for simulating 3d diffusion
gauss = np.exp(-(X*X + Y*Y + Z*Z)/(2.0*options.d*options.d))/math.pow(2.0*np.pi*options.d*options.d,1.5) gauss = np.exp(-(X*X + Y*Y + Z*Z)/(2.0*options.d*options.d))/math.pow(2.0*np.pi*options.d*options.d,1.5)
gauss[:,:,grid[2]/2::] = gauss[:,:,round(grid[2]/2.)-1::-1] # trying to cope with uneven (odd) grid size gauss[:,:,grid[2]/2::] = gauss[:,:,int(round(grid[2]/2.))-1::-1] # trying to cope with uneven (odd) grid size
gauss[:,grid[1]/2::,:] = gauss[:,round(grid[1]/2.)-1::-1,:] gauss[:,grid[1]/2::,:] = gauss[:,int(round(grid[1]/2.))-1::-1,:]
gauss[grid[0]/2::,:,:] = gauss[round(grid[0]/2.)-1::-1,:,:] gauss[grid[0]/2::,:,:] = gauss[int(round(grid[0]/2.))-1::-1,:,:]
gauss = np.fft.rfftn(gauss) gauss = np.fft.rfftn(gauss)
interfacialEnergy = lambda A,B: (A*B != 0)*(A != B)*1.0 interfacialEnergy = lambda A,B: (A*B != 0)*(A != B)*1.0 #1.0 if A & B are distinct & nonzero, 0.0 otherwise
struc = ndimage.generate_binary_structure(3,1) # 3D von Neumann neighborhood struc = ndimage.generate_binary_structure(3,1) # 3D von Neumann neighborhood
@ -101,9 +104,11 @@ for name in filenames:
for j in (-1,0,1): for j in (-1,0,1):
for k in (-1,0,1): for k in (-1,0,1):
# assign interfacial energy to all voxels that have a differing neighbor (in Moore neighborhood) # assign interfacial energy to all voxels that have a differing neighbor (in Moore neighborhood)
interfaceEnergy = np.maximum(boundary, boundary = np.maximum(boundary,
interfacialEnergy(microstructure,np.roll(np.roll(np.roll( interfacialEnergy(microstructure,np.roll(np.roll(np.roll(
microstructure,i,axis=0), j,axis=1), k,axis=2))) microstructure,i,axis=0), j,axis=1), k,axis=2)))
interfaceEnergy = boundary
# periodically extend interfacial energy array by half a grid size in positive and negative directions # periodically extend interfacial energy array by half a grid size in positive and negative directions
periodic_interfaceEnergy = np.tile(interfaceEnergy,(3,3,3))[grid[0]/2:-grid[0]/2, periodic_interfaceEnergy = np.tile(interfaceEnergy,(3,3,3))[grid[0]/2:-grid[0]/2,
grid[1]/2:-grid[1]/2, grid[1]/2:-grid[1]/2,

117
processing/pre/geom_mirror.py Executable file
View File

@ -0,0 +1,117 @@
#!/usr/bin/env python2.7
# -*- coding: UTF-8 no BOM -*-
import os,sys,math
import numpy as np
import damask
from optparse import OptionParser
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
#--------------------------------------------------------------------------------------------------
# MAIN
#--------------------------------------------------------------------------------------------------
validDirections = ['x','y','z']
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [geomfile(s)]', description = """
Mirrors spectral geometry description along given directions.
""", version=scriptID)
parser.add_option('-d','--direction',
dest = 'directions',
action = 'extend', metavar = '<string LIST>',
help = "directions in which to mirror {'x','y','z'}")
(options, filenames) = parser.parse_args()
if options.directions is None:
parser.error('no direction given.')
if not set(options.directions).issubset(validDirections):
invalidDirections = [str(e) for e in set(options.directions).difference(validDirections)]
parser.error('invalid directions {}. '.format(*invalidDirections))
# --- loop over input files -------------------------------------------------------------------------
if filenames == []: filenames = [None]
for name in filenames:
try:
table = damask.ASCIItable(name = name,
buffered = False, labeled = False)
except: continue
damask.util.report(scriptName,name)
# --- interpret header ----------------------------------------------------------------------------
table.head_read()
info,extra_header = table.head_getGeom()
damask.util.croak(['grid a b c: %s'%(' x '.join(map(str,info['grid']))),
'size x y z: %s'%(' x '.join(map(str,info['size']))),
'origin x y z: %s'%(' : '.join(map(str,info['origin']))),
'homogenization: %i'%info['homogenization'],
'microstructures: %i'%info['microstructures'],
])
errors = []
if np.any(info['grid'] < 1): errors.append('invalid grid a b c.')
if np.any(info['size'] <= 0.0): errors.append('invalid size x y z.')
if errors != []:
damask.util.croak(errors)
table.close(dismiss = True)
continue
# --- read data ------------------------------------------------------------------------------------
microstructure = table.microstructure_read(info['grid']).reshape(info['grid'],order='F') # read microstructure
if 'z' in options.directions:
microstructure = np.concatenate([microstructure,microstructure[:,:,::-1]],2)
if 'y' in options.directions:
microstructure = np.concatenate([microstructure,microstructure[:,::-1,:]],1)
if 'x' in options.directions:
microstructure = np.concatenate([microstructure,microstructure[::-1,:,:]],0)
# --- do work ------------------------------------------------------------------------------------
newInfo = {
'size': microstructure.shape*info['size']/info['grid'],
'grid': microstructure.shape,
}
# --- report ---------------------------------------------------------------------------------------
remarks = []
if (any(newInfo['grid'] != info['grid'])):
remarks.append('--> grid a b c: %s'%(' x '.join(map(str,newInfo['grid']))))
if (any(newInfo['size'] != info['size'])):
remarks.append('--> size x y z: %s'%(' x '.join(map(str,newInfo['size']))))
if remarks != []: damask.util.croak(remarks)
# --- write header ---------------------------------------------------------------------------------
table.labels_clear()
table.info_clear()
table.info_append([
scriptID + ' ' + ' '.join(sys.argv[1:]),
"grid\ta {grid[0]}\tb {grid[1]}\tc {grid[2]}".format(grid=newInfo['grid']),
"size\tx {size[0]}\ty {size[1]}\tz {size[2]}".format(size=newInfo['size']),
"origin\tx {origin[0]}\ty {origin[1]}\tz {origin[2]}".format(origin=info['origin']),
"homogenization\t{homog}".format(homog=info['homogenization']),
"microstructures\t{microstructures}".format(microstructures=info['microstructures']),
extra_header
])
table.head_write()
# --- write microstructure information ------------------------------------------------------------
formatwidth = int(math.floor(math.log10(microstructure.max())+1))
table.data = microstructure.reshape((newInfo['grid'][0],np.prod(newInfo['grid'][1:])),order='F').transpose()
table.data_writeArray('%%%ii'%(formatwidth),delimiter = ' ')
# --- output finalization --------------------------------------------------------------------------
table.close() # close ASCII table

35
processing/pre/geom_translate.py
View File

@ -30,30 +30,37 @@ parser.add_option('-s', '--substitute',
dest = 'substitute', dest = 'substitute',
action = 'extend', metavar = '<string LIST>', action = 'extend', metavar = '<string LIST>',
help = 'substitutions of microstructure indices from,to,from,to,...') help = 'substitutions of microstructure indices from,to,from,to,...')
parser.add_option('--float',
dest = 'real',
action = 'store_true',
help = 'use float input')
parser.set_defaults(origin = (0.0,0.0,0.0), parser.set_defaults(origin = (0.0,0.0,0.0),
microstructure = 0, microstructure = 0,
substitute = [], substitute = [],
real = False,
) )
(options, filenames) = parser.parse_args() (options, filenames) = parser.parse_args()
datatype = 'f' if options.real else 'i'
sub = {} sub = {}
for i in xrange(len(options.substitute)/2): # split substitution list into "from" -> "to" for i in xrange(len(options.substitute)/2): # split substitution list into "from" -> "to"
sub[int(options.substitute[i*2])] = int(options.substitute[i*2+1]) sub[int(options.substitute[i*2])] = int(options.substitute[i*2+1])
# --- loop over input files ------------------------------------------------------------------------- # --- loop over input files ----------------------------------------------------------------------
if filenames == []: filenames = [None] if filenames == []: filenames = [None]
for name in filenames: for name in filenames:
try: try: table = damask.ASCIItable(name = name,
table = damask.ASCIItable(name = name, buffered = False,
buffered = False, labeled = False) labeled = False)
except: continue except: continue
damask.util.report(scriptName,name) damask.util.report(scriptName,name)
# --- interpret header ---------------------------------------------------------------------------- # --- interpret header ---------------------------------------------------------------------------
table.head_read() table.head_read()
info,extra_header = table.head_getGeom() info,extra_header = table.head_getGeom()
@ -73,9 +80,9 @@ for name in filenames:
table.close(dismiss = True) table.close(dismiss = True)
continue continue
# --- read data ------------------------------------------------------------------------------------ # --- read data ----------------------------------------------------------------------------------
microstructure = table.microstructure_read(info['grid']) # read microstructure microstructure = table.microstructure_read(info['grid'],datatype) # read microstructure
# --- do work ------------------------------------------------------------------------------------ # --- do work ------------------------------------------------------------------------------------
@ -90,9 +97,9 @@ for name in filenames:
substituted += options.microstructure # shift microstructure indices substituted += options.microstructure # shift microstructure indices
newInfo['origin'] = info['origin'] + options.origin newInfo['origin'] = info['origin'] + options.origin
newInfo['microstructures'] = substituted.max() newInfo['microstructures'] = len(np.unique(substituted))
# --- report --------------------------------------------------------------------------------------- # --- report -------------------------------------------------------------------------------------
remarks = [] remarks = []
if (any(newInfo['origin'] != info['origin'])): if (any(newInfo['origin'] != info['origin'])):
@ -101,7 +108,7 @@ for name in filenames:
remarks.append('--> microstructures: %i'%newInfo['microstructures']) remarks.append('--> microstructures: %i'%newInfo['microstructures'])
if remarks != []: damask.util.croak(remarks) if remarks != []: damask.util.croak(remarks)
# --- write header --------------------------------------------------------------------------------- # --- write header -------------------------------------------------------------------------------
table.labels_clear() table.labels_clear()
table.info_clear() table.info_clear()
@ -116,12 +123,12 @@ for name in filenames:
]) ])
table.head_write() table.head_write()
# --- write microstructure information ------------------------------------------------------------ # --- write microstructure information -----------------------------------------------------------
formatwidth = int(math.floor(math.log10(microstructure.max())+1)) format = '%g' if options.real else '%{}i'.format(int(math.floor(math.log10(microstructure.max())+1)))
table.data = substituted.reshape((info['grid'][0],info['grid'][1]*info['grid'][2]),order='F').transpose() table.data = substituted.reshape((info['grid'][0],info['grid'][1]*info['grid'][2]),order='F').transpose()
table.data_writeArray('%%%ii'%(formatwidth),delimiter = ' ') table.data_writeArray(format,delimiter = ' ')
# --- output finalization -------------------------------------------------------------------------- # --- output finalization ------------------------------------------------------------------------
table.close() # close ASCII table table.close() # close ASCII table

29
processing/pre/seeds_fromRandom.py
View File

@ -29,7 +29,7 @@ def kdtree_search(cloud, queryPoints):
# -------------------------------------------------------------------- # --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog [options]', description = """ parser = OptionParser(option_class=damask.extendableOption, usage='%prog [options]', description = """
Distribute given number of points randomly within the three-dimensional cube [0.0,0.0,0.0]--[1.0,1.0,1.0]. Distribute given number of points randomly within (a fraction of) the three-dimensional cube [0.0,0.0,0.0]--[1.0,1.0,1.0].
Reports positions with random crystal orientations in seeds file format to STDOUT. Reports positions with random crystal orientations in seeds file format to STDOUT.
""", version = scriptID) """, version = scriptID)
@ -38,6 +38,11 @@ parser.add_option('-N',
dest = 'N', dest = 'N',
type = 'int', metavar = 'int', type = 'int', metavar = 'int',
help = 'number of seed points [%default]') help = 'number of seed points [%default]')
parser.add_option('-f',
'--fraction',
dest = 'fraction',
type = 'float', nargs = 3, metavar = 'float float float',
help='fractions along x,y,z of unit cube to fill %default')
parser.add_option('-g', parser.add_option('-g',
'--grid', '--grid',
dest = 'grid', dest = 'grid',
@ -86,8 +91,7 @@ group.add_option( '-s',
action = 'store_true', action = 'store_true',
dest = 'selective', dest = 'selective',
help = 'selective picking of seed points from random seed points [%default]') help = 'selective picking of seed points from random seed points [%default]')
group.add_option( '-f', group.add_option( '--force',
'--force',
action = 'store_true', action = 'store_true',
dest = 'force', dest = 'force',
help = 'try selective picking despite large seed point number [%default]') help = 'try selective picking despite large seed point number [%default]')
@ -103,6 +107,7 @@ parser.add_option_group(group)
parser.set_defaults(randomSeed = None, parser.set_defaults(randomSeed = None,
grid = (16,16,16), grid = (16,16,16),
fraction = (1.0,1.0,1.0),
N = 20, N = 20,
weights = False, weights = False,
max = 0.0, max = 0.0,
@ -118,6 +123,7 @@ parser.set_defaults(randomSeed = None,
(options,filenames) = parser.parse_args() (options,filenames) = parser.parse_args()
options.fraction = np.array(options.fraction)
options.grid = np.array(options.grid) options.grid = np.array(options.grid)
gridSize = options.grid.prod() gridSize = options.grid.prod()
@ -160,17 +166,26 @@ for name in filenames:
grainEuler[2,:] *= 360.0 # phi_2 is uniformly distributed grainEuler[2,:] *= 360.0 # phi_2 is uniformly distributed
if not options.selective: if not options.selective:
seeds = np.array([])
seeds = np.zeros((3,options.N),dtype='d') # seed positions array while len(seeds) < options.N:
theSeeds = np.zeros((options.N,3),dtype=float) # seed positions array
gridpoints = random.sample(range(gridSize),options.N) # choose first N from random permutation of grid positions gridpoints = random.sample(range(gridSize),options.N) # choose first N from random permutation of grid positions
seeds[0,:] = (np.mod(gridpoints ,options.grid[0])\ theSeeds[:,0] = (np.mod(gridpoints ,options.grid[0])\
+np.random.random(options.N)) /options.grid[0] +np.random.random(options.N)) /options.grid[0]
seeds[1,:] = (np.mod(gridpoints// options.grid[0] ,options.grid[1])\ theSeeds[:,1] = (np.mod(gridpoints// options.grid[0] ,options.grid[1])\
+np.random.random(options.N)) /options.grid[1] +np.random.random(options.N)) /options.grid[1]
seeds[2,:] = (np.mod(gridpoints//(options.grid[1]*options.grid[0]),options.grid[2])\ theSeeds[:,2] = (np.mod(gridpoints//(options.grid[1]*options.grid[0]),options.grid[2])\
+np.random.random(options.N)) /options.grid[2] +np.random.random(options.N)) /options.grid[2]
goodSeeds = theSeeds[np.all(theSeeds<=options.fraction,axis=1)] # pick seeds within threshold fraction
seeds = goodSeeds if len(seeds) == 0 else np.vstack((seeds,goodSeeds))
if len(seeds) > options.N: seeds = seeds[:min(options.N,len(seeds))]
seeds = seeds.T # switch layout to point index as last index
else: else:
seeds = np.zeros((options.N,3),dtype=float) # seed positions array seeds = np.zeros((options.N,3),dtype=float) # seed positions array