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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

67
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:'
@ -319,12 +314,12 @@ program DAMASK_spectral
if(loadCases(currentLoadCase)%deformation%maskLogical(i,j)) then if(loadCases(currentLoadCase)%deformation%maskLogical(i,j)) then
write(6,'(2x,f12.7)',advance='no') loadCases(currentLoadCase)%deformation%values(i,j) write(6,'(2x,f12.7)',advance='no') loadCases(currentLoadCase)%deformation%values(i,j)
else else
write(6,'(2x,12a)',advance='no') ' * ' write(6,'(2x,12a)',advance='no') ' * '
endif endif
enddo; write(6,'(/)',advance='no') enddo; write(6,'(/)',advance='no')
enddo enddo
if (any(loadCases(currentLoadCase)%P%maskLogical .eqv. & if (any(loadCases(currentLoadCase)%P%maskLogical .eqv. &
loadCases(currentLoadCase)%deformation%maskLogical)) errorID = 831_pInt ! exclusive or masking only loadCases(currentLoadCase)%deformation%maskLogical)) errorID = 831_pInt ! exclusive or masking only
if (any(loadCases(currentLoadCase)%P%maskLogical .and. & if (any(loadCases(currentLoadCase)%P%maskLogical .and. &
transpose(loadCases(currentLoadCase)%P%maskLogical) .and. & transpose(loadCases(currentLoadCase)%P%maskLogical) .and. &
reshape([ .false.,.true.,.true.,.true.,.false.,.true.,.true.,.true.,.false.],[ 3,3]))) & reshape([ .false.,.true.,.true.,.true.,.false.,.true.,.true.,.true.,.false.],[ 3,3]))) &
@ -334,12 +329,12 @@ program DAMASK_spectral
if(loadCases(currentLoadCase)%P%maskLogical(i,j)) then if(loadCases(currentLoadCase)%P%maskLogical(i,j)) then
write(6,'(2x,f12.7)',advance='no') loadCases(currentLoadCase)%P%values(i,j)*1e-9_pReal write(6,'(2x,f12.7)',advance='no') loadCases(currentLoadCase)%P%values(i,j)*1e-9_pReal
else else
write(6,'(2x,12a)',advance='no') ' * ' write(6,'(2x,12a)',advance='no') ' * '
endif endif
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, &
[(outputIndex(2)-outputIndex(1)+1)*materialpoint_sizeResults]), & 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, &
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:

41
code/debug.f90
View File

@ -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, &
@ -130,47 +129,27 @@ 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
line = '' line = ''
fileExists: if(IO_open_file_stat(FILEUNIT,debug_configFile)) then fileExists: if(IO_open_file_stat(FILEUNIT,debug_configFile)) then
do while (trim(line) /= IO_EOF) ! read thru sections of phase part do while (trim(line) /= IO_EOF) ! read thru sections of phase part
line = IO_read(FILEUNIT) line = IO_read(FILEUNIT)
if (IO_isBlank(line)) cycle ! skip empty lines if (IO_isBlank(line)) cycle ! skip empty lines
chunkPos = IO_stringPos(line) chunkPos = IO_stringPos(line)
tag = IO_lc(IO_stringValue(line,chunkPos,1_pInt)) ! extract key tag = IO_lc(IO_stringValue(line,chunkPos,1_pInt)) ! extract key
select case(tag) select case(tag)
case ('element','e','el') case ('element','e','el')
debug_e = IO_intValue(line,chunkPos,2_pInt) debug_e = IO_intValue(line,chunkPos,2_pInt)

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)

104
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, &
@ -974,7 +951,7 @@ subroutine utilities_constitutiveResponse(F_lastInc,F,timeinc, &
real(pReal),intent(out), dimension(3,3,3,3) :: C_volAvg, C_minmaxAvg !< average stiffness real(pReal),intent(out), dimension(3,3,3,3) :: C_volAvg, C_minmaxAvg !< average stiffness
real(pReal),intent(out), dimension(3,3) :: P_av !< average PK stress real(pReal),intent(out), dimension(3,3) :: P_av !< average PK stress
real(pReal),intent(out), dimension(3,3,grid(1),grid(2),grid3) :: P !< PK stress real(pReal),intent(out), dimension(3,3,grid(1),grid(2),grid3) :: P !< PK stress
logical :: & logical :: &
age age
@ -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 :: & write(6,'(/,a)') ' ... evaluating constitutive response ......................................'
MPI_Reduce, & flush(6)
MPI_Allreduce
if (worldrank == 0_pInt) then
write(6,'(/,a)') ' ... evaluating constitutive response ......................................'
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
@ -1015,15 +984,10 @@ 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') write(6,'(a,1x,es11.4)') ' max determinant of deformation =', defgradDetMax
call MPI_reduce(MPI_IN_PLACE,defgradDetMin,1,MPI_DOUBLE,MPI_MIN,0,PETSC_COMM_WORLD,ierr) write(6,'(a,1x,es11.4)') ' min determinant of deformation =', defgradDetMin
if(ierr /=0_pInt) call IO_error(894_pInt, ext_msg='MPI_Allreduce min') flush(6)
if (worldrank == 0_pInt) then
write(6,'(a,1x,es11.4)') ' max determinant of deformation =', defgradDetMax
write(6,'(a,1x,es11.4)') ' min determinant of deformation =', defgradDetMin
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

26
examples/ConfigFiles/Phase_Phenopowerlaw_BCC-Ferrite.config
View File

@ -1,35 +1,25 @@
# 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
lattice_structure bcc lattice_structure bcc
Nslip 12 12 # per family Nslip 12 12 # per family
Ntwin 0 # per family Ntwin 0 # per family
c11 233.3e9 c11 233.3e9
c12 135.5e9 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

25
examples/ConfigFiles/Phase_Phenopowerlaw_BCC-Martensite.config
View File

@ -1,34 +1,25 @@
# 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
c11 417.4e9 c11 417.4e9
c12 242.4e9 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))
if os.path.exists(src):
sym_link = os.path.abspath(os.path.join(binDir,subDir if theFile == '' else theName))
if os.path.lexists(sym_link):
os.remove(sym_link)
output = theName+damask.util.deemph(theExt)
else:
output = damask.util.emph(theName)+damask.util.deemph(theExt)
sys.stdout.write(damask.util.deemph('... ')+output+'\n')
os.symlink(src,sym_link)
sys.stdout.write('\nMSC.Marc versioning...\n\n')
theMaster = 'DAMASK_marc.f90'
for version in MarcReleases: for version in MarcReleases:
src = os.path.abspath(os.path.join(baseDir,'DAMASK_marc.f90')) src = os.path.abspath(os.path.join(baseDir,theMaster))
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(baseDir,'DAMASK_marc{}.f90'.format(version)))
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 = version
else: else:
sys.stdout.write(damask.util.emph(sym_link)) output = damask.util.emph(version)
os.symlink(src,sym_link) sys.stdout.write(' '+output+'\n')
sys.stdout.write(' -> '+src+'\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__()

269
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])
fh = logging.FileHandler('test.log') # create file handler which logs even debug messages
fh.setLevel(logging.DEBUG)
fh.setFormatter(logging.Formatter('%(asctime)s - %(levelname)s: \n%(message)s'))
ch = logging.StreamHandler(stream=sys.stdout) # create console handler with a higher log level
ch.setLevel(logging.INFO)
ch.setFormatter(logging.Formatter('%(message)s'))
logger = logging.getLogger() logger = logging.getLogger()
logger.setLevel(0)
fh = logging.FileHandler('test.log') # create file handler which logs even debug messages
fh.setLevel(logging.DEBUG)
full = 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.setLevel(logging.INFO)
# create formatter and add it to the handlers
plain = logging.Formatter('%(message)s')
ch.setFormatter(plain)
# 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)):
try: for variant,name in enumerate(self.variants):
try:
if not self.options.keep:
self.prepare(variant) self.prepare(variant)
self.run(variant) self.run(variant)
self.postprocess(variant)
if self.updateRequested: # update requested
self.update(variant)
elif not (self.options.accept or self.compare(variant)): # no update, do comparison
return variant+1 # return culprit
except Exception as e :
logging.critical('\nWARNING:\n {}\n'.format(e))
return variant+1 # return culprit
return 0
def testPossible(self): self.postprocess(variant)
"""Check if test is possible or not (e.g. no license available)."""
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
return variant+1 # return culprit
except Exception as e :
logging.critical('exception during variant execution: {}'.format(e))
return variant+1 # return culprit
return 0
def feasible(self):
"""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']))
@ -376,9 +380,9 @@ 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]))/
norm[i][line1-len(skipLines)]) norm[i][line1-len(skipLines)])
line1 +=1 line1 +=1
@ -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)
@ -454,21 +458,17 @@ class Test():
def compare_Tables(self, def compare_Tables(self,
files = [None,None], # list of file names files = [None,None], # list of file names
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, debug = False):
postFilter = -1.0, """compare multiple tables with np.allclose"""
debug = False):
"""
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 -----------------------------------------------------------------------------

18
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.')
@ -64,9 +66,8 @@ 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
table.data_append(mappedTable.data[int(round(float(table.data[mappedColumn])))+options.offset-1]) # add all mapped data types try:
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

89
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,
@ -95,58 +97,59 @@ 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]
if dim == -1: remarks.append('{} "{}" not found...'.format(datatype,me)) if dim == -1: remarks.append('{} "{}" not found...'.format(datatype,me))
elif dim > dimension: remarks.append('"{}" not of dimension {}...'.format(me,dimension)) elif dim > dimension: remarks.append('"{}" not of dimension {}...'.format(me,dimension))
else: else:
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 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])
# ------------------------------------------ add data --------------------------------------- VTKarray[me] = numpy_support.numpy_to_vtk(num_array=VTKdata,deep=True,array_type=VTKtype)
VTKarray[me].SetName(me)
for datatype,labels in active.items(): # loop over scalar,color if datatype == 'color':
if datatype == 'color': Polydata.GetPointData().SetScalars(VTKarray[me])
Polydata.GetPointData().SetScalars(VTKarray[active['color'][0]]) Polydata.GetCellData().SetScalars(VTKarray[me])
Polydata.GetCellData().SetScalars(VTKarray[active['color'][0]]) else:
for me in labels: # loop over all requested items Polydata.GetPointData().AddArray(VTKarray[me])
Polydata.GetPointData().AddArray(VTKarray[me]) Polydata.GetCellData().AddArray(VTKarray[me])
Polydata.GetCellData().AddArray(VTKarray[me])
table.input_close() # close input ASCII table
# ------------------------------------------ output result ---------------------------------------
Polydata.Modified() Polydata.Modified()
if vtk.VTK_MAJOR_VERSION <= 5: Polydata.Update() if vtk.VTK_MAJOR_VERSION <= 5: Polydata.Update()
# ------------------------------------------ output result ---------------------------------------
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.

59
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,
@ -93,24 +94,18 @@ 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]
if dim == -1: remarks.append('{} "{}" not found...'.format(datatype,me)) if dim == -1: remarks.append('{} "{}" not found...'.format(datatype,me))
elif dim > dimension: remarks.append('"{}" not of dimension {}...'.format(me,dimension)) elif dim > dimension: remarks.append('"{}" not of dimension {}...'.format(me,dimension))
else: else:
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 for datatype,labels in active.items(): # loop over scalar,color
for me in labels: # loop over all requested items
VTKtype = vtk.VTK_DOUBLE
VTKdata = table.data[:, table.label_indexrange(me)].copy() # copy to force contiguous layout
datacount += 1 # count data lines if datatype == 'color':
for datatype,labels in active.items(): # loop over scalar,color VTKtype = vtk.VTK_UNSIGNED_CHAR
for me in labels: # loop over all requested items VTKdata = (VTKdata*255).astype(int) # translate to 0..255 UCHAR
theData = [table.data[i] for i in table.label_indexrange(me)] # read strings elif datatype == 'tensor':
if datatype == 'color': VTKarray[me].InsertNextTuple3(*map(lambda x: int(255.*float(x)),theData)) VTKdata[:,1] = VTKdata[:,3] = 0.5*(VTKdata[:,1]+VTKdata[:,3])
elif datatype == 'vector': VTKarray[me].InsertNextTuple3(*map(float,theData)) VTKdata[:,2] = VTKdata[:,6] = 0.5*(VTKdata[:,2]+VTKdata[:,6])
elif datatype == 'scalar': VTKarray[me].InsertNextValue(float(theData[0])) 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

39
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

37
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()
@ -160,16 +166,25 @@ 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:
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 = np.zeros((options.N,3),dtype=float) # seed positions array
+np.random.random(options.N)) /options.grid[0] gridpoints = random.sample(range(gridSize),options.N) # choose first N from random permutation of grid positions
seeds[1,:] = (np.mod(gridpoints// options.grid[0] ,options.grid[1])\
+np.random.random(options.N)) /options.grid[1] theSeeds[:,0] = (np.mod(gridpoints ,options.grid[0])\
seeds[2,:] = (np.mod(gridpoints//(options.grid[1]*options.grid[0]),options.grid[2])\ +np.random.random(options.N)) /options.grid[0]
+np.random.random(options.N)) /options.grid[2] theSeeds[:,1] = (np.mod(gridpoints// options.grid[0] ,options.grid[1])\
+np.random.random(options.N)) /options.grid[1]
theSeeds[:,2] = (np.mod(gridpoints//(options.grid[1]*options.grid[0]),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: