223031012
/
DAMASK_EICMD
mirror of https://github.com/achalhp/DAMASK_EICMD.git
1
0
Fork 0
Code Issues Projects Releases Wiki Activity

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

This commit is contained in:
Martin Diehl 2016-04-25 12:35:31 +02:00
parent ce99a071c2 43e74f00cf
commit dadf840c95
62 changed files with 188001 additions and 190901 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

9
.gitattributes vendored Normal file
View File

@ -0,0 +1,9 @@
# from https://help.github.com/articles/dealing-with-line-endings/
#
# always use LF, even if the files are edited on windows, they need to be compiled/used on unix
* text eol=lf
# Denote all files that are truly binary and should not be modified.
*.png binary
*.jpg binary
*.cae binary

9
DAMASK_env.sh
View File

@ -2,7 +2,7 @@
# usage: source DAMASK_env.sh
if [ "$OSTYPE" == "linux-gnu" ] || [ "$OSTYPE" == 'linux' ]; then
DAMASK_ROOT=$(readlink -f "`dirname $BASH_SOURCE`")
DAMASK_ROOT=$(python -c "import os,sys; print(os.path.realpath(os.path.expanduser(sys.argv[1])))" "`dirname $BASH_SOURCE`")
else
[[ "${BASH_SOURCE::1}" == "/" ]] && BASE="" || BASE="`pwd`/"
STAT=$(stat "`dirname $BASE$BASH_SOURCE`")
@ -18,11 +18,11 @@ fi
SOLVER=`which DAMASK_spectral 2>/dev/null`
if [ "x$SOLVER" == "x" ]; then
export SOLVER='Not found!'
SOLVER='Not found!'
fi
PROCESSING=`which postResults 2>/dev/null`
if [ "x$PROCESSING" == "x" ]; then
export PROCESSING='Not found!'
PROCESSING='Not found!'
fi
# according to http://software.intel.com/en-us/forums/topic/501500
@ -55,7 +55,8 @@ if [ ! -z "$PS1" ]; then
echo "Multithreading DAMASK_NUM_THREADS=$DAMASK_NUM_THREADS"
if [ "x$PETSC_DIR" != "x" ]; then
echo "PETSc location $PETSC_DIR"
[[ `readlink -f $PETSC_DIR` == $PETSC_DIR ]] || echo " ~~> "`readlink -f $PETSC_DIR`
[[ `python -c "import os,sys; print(os.path.realpath(os.path.expanduser(sys.argv[1])))" "$PETSC_DIR"` == $PETSC_DIR ]] \
|| echo " ~~> "`python -c "import os,sys; print(os.path.realpath(os.path.expanduser(sys.argv[1])))" "$PETSC_DIR"`
fi
[[ "x$PETSC_ARCH" != "x" ]] && echo "PETSc architecture $PETSC_ARCH"
echo "MSC.Marc/Mentat $MSC_ROOT"

2
VERSION
View File

@ -1 +1 @@
v2.0.0-43-ge39441f
v2.0.0-160-g26f437b

8
code/.gitattributes vendored Normal file
View File

@ -0,0 +1,8 @@
# from https://help.github.com/articles/dealing-with-line-endings/
#
# always use LF, even if the files are edited on windows, they need to be compiled/used on unix
* text eol=lf
# Denote all files that are truly binary and should not be modified.
*.png binary
*.jpg binary

24
code/DAMASK_spectral.f90
View File

@ -13,7 +13,8 @@ program DAMASK_spectral
pInt, &
pLongInt, &
pReal, &
tol_math_check
tol_math_check, &
dNeq
use DAMASK_interface, only: &
DAMASK_interface_init, &
loadCaseFile, &
@ -147,7 +148,9 @@ program DAMASK_spectral
MPI_file_seek, &
MPI_file_get_position, &
MPI_file_write, &
MPI_allreduce
MPI_abort, &
MPI_allreduce, &
PETScFinalize
!--------------------------------------------------------------------------------------------------
! init DAMASK (all modules)
@ -339,7 +342,7 @@ program DAMASK_spectral
reshape(spread(tol_math_check,1,9),[ 3,3]))&
.or. abs(math_det33(loadCases(currentLoadCase)%rotation)) > &
1.0_pReal + tol_math_check) errorID = 846_pInt ! given rotation matrix contains strain
if (any(loadCases(currentLoadCase)%rotation /= math_I3)) &
if (any(dNeq(loadCases(currentLoadCase)%rotation, math_I3))) &
write(6,'(2x,a,/,3(3(3x,f12.7,1x)/))',advance='no') 'rotation of loadframe:',&
math_transpose33(loadCases(currentLoadCase)%rotation)
if (loadCases(currentLoadCase)%time < 0.0_pReal) errorID = 834_pInt ! negative time increment
@ -423,17 +426,21 @@ program DAMASK_spectral
!--------------------------------------------------------------------------------------------------
! prepare MPI parallel out (including opening of file)
allocate(outputSize(worldsize), source = 0_MPI_OFFSET_KIND)
outputSize(worldrank+1) = int(size(materialpoint_results)*pReal,MPI_OFFSET_KIND)
call MPI_allreduce(MPI_IN_PLACE,outputSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process
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
if(ierr /=0_pInt) call IO_error(894_pInt, ext_msg='MPI_allreduce')
call MPI_file_open(PETSC_COMM_WORLD, &
trim(getSolverWorkingDirectoryName())//trim(getSolverJobName())//'.spectralOut', &
MPI_MODE_WRONLY + MPI_MODE_APPEND, &
MPI_INFO_NULL, &
resUnit, &
ierr)
if(ierr /=0_pInt) call IO_error(894_pInt, ext_msg='MPI_file_open')
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')
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)
if(ierr /=0_pInt) call IO_error(894_pInt, ext_msg='MPI_file_seek')
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
@ -443,6 +450,7 @@ program DAMASK_spectral
[(outputIndex(2)-outputIndex(1)+1)*materialpoint_sizeResults]), &
(outputIndex(2)-outputIndex(1)+1)*materialpoint_sizeResults,&
MPI_DOUBLE, MPI_STATUS_IGNORE, ierr)
if(ierr /=0_pInt) call IO_error(894_pInt, ext_msg='MPI_file_write')
enddo
fileOffset = fileOffset + sum(outputSize) ! forward to current file position
if (worldrank == 0) &
@ -643,13 +651,15 @@ program DAMASK_spectral
write(6,'(1/,a)') ' ... writing results to file ......................................'
call materialpoint_postResults()
call MPI_file_seek (resUnit,fileOffset,MPI_SEEK_SET,ierr)
if(ierr /=0_pInt) call IO_error(894_pInt, ext_msg='MPI_file_seek')
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)*((maxByteOut/pReal)/materialpoint_sizeResults)+1_pInt, &
outputIndex=int([(i-1_pInt)*((maxByteOut/pReal)/materialpoint_sizeResults)+1_pInt, &
min(i*((maxByteOut/pReal)/materialpoint_sizeResults),size(materialpoint_results,3))],pLongInt)
call MPI_file_write(resUnit,reshape(materialpoint_results(:,:,outputIndex(1):outputIndex(2)),&
[(outputIndex(2)-outputIndex(1)+1)*materialpoint_sizeResults]), &
(outputIndex(2)-outputIndex(1)+1)*materialpoint_sizeResults,&
MPI_DOUBLE, MPI_STATUS_IGNORE, ierr)
if(ierr /=0_pInt) call IO_error(894_pInt, ext_msg='MPI_file_write')
enddo
fileOffset = fileOffset + sum(outputSize) ! forward to current file position
endif
@ -698,7 +708,7 @@ program DAMASK_spectral
enddo
call utilities_destroy()
call PetscFinalize(ierr); CHKERRQ(ierr)
call PETScFinalize(ierr); CHKERRQ(ierr)
if (notConvergedCounter > 0_pInt) call quit(3_pInt) ! error if some are not converged
call quit(0_pInt) ! no complains ;)

547
code/IO.f90
View File

@ -6,10 +6,6 @@
!> @brief input/output functions, partly depending on chosen solver
!--------------------------------------------------------------------------------------------------
module IO
#ifdef HDF
use hdf5, only: &
HID_T
#endif
use prec, only: &
pInt, &
pReal
@ -18,22 +14,8 @@ module IO
private
character(len=5), parameter, public :: &
IO_EOF = '#EOF#' !< end of file string
#ifdef HDF
integer(HID_T), public, protected :: tempCoordinates, tempResults
integer(HID_T), private :: resultsFile, tempFile
integer(pInt), private :: currentInc
#endif
public :: &
#ifdef HDF
HDF5_mappingConstitutive, &
HDF5_mappingHomogenization, &
HDF5_mappingCells, &
HDF5_addGroup ,&
HDF5_forwardResults, &
HDF5_addScalarDataset, &
IO_formatIntToString ,&
#endif
IO_init, &
IO_read, &
IO_checkAndRewind, &
@ -117,9 +99,6 @@ subroutine IO_init
#include "compilation_info.f90"
endif mainProcess
#ifdef HDF
call HDF5_createJobFile
#endif
end subroutine IO_init
@ -1669,7 +1648,9 @@ subroutine IO_error(error_ID,el,ip,g,ext_msg)
msg = 'unknown filter type selected'
case (893_pInt)
msg = 'PETSc: SNES_DIVERGED_FNORM_NAN'
case (894_pInt)
msg = 'MPI error'
!-------------------------------------------------------------------------------------------------
! error messages related to parsing of Abaqus input file
case (900_pInt)
@ -1942,526 +1923,4 @@ recursive function abaqus_assembleInputFile(unit1,unit2) result(createSuccess)
end function abaqus_assembleInputFile
#endif
#ifdef HDF
!--------------------------------------------------------------------------------------------------
!> @brief creates and initializes HDF5 output files
!--------------------------------------------------------------------------------------------------
subroutine HDF5_createJobFile
use hdf5
use DAMASK_interface, only: &
getSolverWorkingDirectoryName, &
getSolverJobName
implicit none
integer :: hdferr
integer(SIZE_T) :: typeSize
character(len=1024) :: path
integer(HID_T) :: prp_id
integer(SIZE_T), parameter :: increment = 104857600 ! increase temp file in memory in 100MB steps
!--------------------------------------------------------------------------------------------------
! initialize HDF5 library and check if integer and float type size match
call h5open_f(hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_createJobFile: h5open_f')
call h5tget_size_f(H5T_NATIVE_INTEGER,typeSize, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_createJobFile: h5tget_size_f (int)')
if (int(pInt,SIZE_T)/=typeSize) call IO_error(0_pInt,ext_msg='pInt does not match H5T_NATIVE_INTEGER')
call h5tget_size_f(H5T_NATIVE_DOUBLE,typeSize, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_createJobFile: h5tget_size_f (double)')
if (int(pReal,SIZE_T)/=typeSize) call IO_error(0_pInt,ext_msg='pReal does not match H5T_NATIVE_DOUBLE')
!--------------------------------------------------------------------------------------------------
! open file
path = trim(getSolverWorkingDirectoryName())//trim(getSolverJobName())//'.'//'DAMASKout'
call h5fcreate_f(path,H5F_ACC_TRUNC_F,resultsFile,hdferr)
if (hdferr < 0) call IO_error(100_pInt,ext_msg=path)
call HDF5_addStringAttribute(resultsFile,'createdBy','$Id$')
!--------------------------------------------------------------------------------------------------
! open temp file
path = trim(getSolverWorkingDirectoryName())//trim(getSolverJobName())//'.'//'DAMASKoutTemp'
call h5pcreate_f(H5P_FILE_ACCESS_F, prp_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_createJobFile: h5pcreate_f')
call h5pset_fapl_core_f(prp_id, increment, .false., hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_createJobFile: h5pset_fapl_core_f')
call h5fcreate_f(path,H5F_ACC_TRUNC_F,tempFile,hdferr)
if (hdferr < 0) call IO_error(100_pInt,ext_msg=path)
!--------------------------------------------------------------------------------------------------
! create mapping groups in out file
call HDF5_closeGroup(HDF5_addGroup("mapping"))
call HDF5_closeGroup(HDF5_addGroup("results"))
call HDF5_closeGroup(HDF5_addGroup("coordinates"))
!--------------------------------------------------------------------------------------------------
! create results group in temp file
tempResults = HDF5_addGroup("results",tempFile)
tempCoordinates = HDF5_addGroup("coordinates",tempFile)
end subroutine HDF5_createJobFile
!--------------------------------------------------------------------------------------------------
!> @brief creates and initializes HDF5 output file
!--------------------------------------------------------------------------------------------------
subroutine HDF5_closeJobFile()
use hdf5
implicit none
integer :: hdferr
call h5fclose_f(resultsFile,hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_closeJobFile: h5fclose_f')
end subroutine HDF5_closeJobFile
!--------------------------------------------------------------------------------------------------
!> @brief adds a new group to the results file, or if loc is present at the given location
!--------------------------------------------------------------------------------------------------
integer(HID_T) function HDF5_addGroup(path,loc)
use hdf5
implicit none
character(len=*), intent(in) :: path
integer(HID_T), intent(in),optional :: loc
integer :: hdferr
if (present(loc)) then
call h5gcreate_f(loc, trim(path), HDF5_addGroup, hdferr)
else
call h5gcreate_f(resultsFile, trim(path), HDF5_addGroup, hdferr)
endif
if (hdferr < 0) call IO_error(1_pInt,ext_msg = 'HDF5_addGroup: h5gcreate_f ('//trim(path)//' )')
end function HDF5_addGroup
!--------------------------------------------------------------------------------------------------
!> @brief adds a new group to the results file
!--------------------------------------------------------------------------------------------------
integer(HID_T) function HDF5_openGroup(path)
use hdf5
implicit none
character(len=*), intent(in) :: path
integer :: hdferr
call h5gopen_f(resultsFile, trim(path), HDF5_openGroup, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg = 'HDF5_openGroup: h5gopen_f ('//trim(path)//' )')
end function HDF5_openGroup
!--------------------------------------------------------------------------------------------------
!> @brief closes a group
!--------------------------------------------------------------------------------------------------
subroutine HDF5_closeGroup(ID)
use hdf5
implicit none
integer(HID_T), intent(in) :: ID
integer :: hdferr
call h5gclose_f(ID, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg = 'HDF5_closeGroup: h5gclose_f')
end subroutine HDF5_closeGroup
!--------------------------------------------------------------------------------------------------
!> @brief adds a new group to the results file
!--------------------------------------------------------------------------------------------------
subroutine HDF5_addStringAttribute(entity,attrLabel,attrValue)
use hdf5
implicit none
integer(HID_T), intent(in) :: entity
character(len=*), intent(in) :: attrLabel, attrValue
integer :: hdferr
integer(HID_T) :: attr_id, space_id, type_id
call h5screate_f(H5S_SCALAR_F,space_id,hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_addStringAttribute: h5screate_f')
call h5tcopy_f(H5T_NATIVE_CHARACTER, type_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_addStringAttribute: h5tcopy_f')
call h5tset_size_f(type_id, int(len(trim(attrValue)),HSIZE_T), hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_addStringAttribute: h5tset_size_f')
call h5acreate_f(entity, trim(attrLabel),type_id,space_id,attr_id,hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_addStringAttribute: h5acreate_f')
call h5awrite_f(attr_id, type_id, trim(attrValue), int([1],HSIZE_T), hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_addStringAttribute: h5awrite_f')
call h5aclose_f(attr_id,hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_addStringAttribute: h5aclose_f')
call h5sclose_f(space_id,hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_addStringAttribute: h5sclose_f')
end subroutine HDF5_addStringAttribute
!--------------------------------------------------------------------------------------------------
!> @brief adds the unique mapping from spatial position and constituent ID to results
!--------------------------------------------------------------------------------------------------
subroutine HDF5_mappingConstitutive(mapping)
use hdf5
implicit none
integer(pInt), intent(in), dimension(:,:,:) :: mapping
integer :: hdferr, NmatPoints,Nconstituents
integer(HID_T) :: mapping_id, dtype_id, dset_id, space_id,instance_id,position_id
Nconstituents=size(mapping,1)
NmatPoints=size(mapping,2)
mapping_ID = HDF5_openGroup("mapping")
!--------------------------------------------------------------------------------------------------
! create dataspace
call h5screate_simple_f(2, int([Nconstituents,NmatPoints],HSIZE_T), space_id, hdferr, &
int([Nconstituents,NmatPoints],HSIZE_T))
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingConstitutive')
!--------------------------------------------------------------------------------------------------
! compound type
call h5tcreate_f(H5T_COMPOUND_F, 6_SIZE_T, dtype_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingConstitutive: h5tcreate_f dtype_id')
call h5tinsert_f(dtype_id, "Constitutive Instance", 0_SIZE_T, H5T_STD_U16LE, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingConstitutive: h5tinsert_f 0')
call h5tinsert_f(dtype_id, "Position in Instance Results", 2_SIZE_T, H5T_STD_U32LE, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingConstitutive: h5tinsert_f 2')
!--------------------------------------------------------------------------------------------------
! create Dataset
call h5dcreate_f(mapping_id, "Constitutive", dtype_id, space_id, dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingConstitutive')
!--------------------------------------------------------------------------------------------------
! Create memory types (one compound datatype for each member)
call h5tcreate_f(H5T_COMPOUND_F, int(pInt,SIZE_T), instance_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingConstitutive: h5tcreate_f instance_id')
call h5tinsert_f(instance_id, "Constitutive Instance", 0_SIZE_T, H5T_NATIVE_INTEGER, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingConstitutive: h5tinsert_f instance_id')
call h5tcreate_f(H5T_COMPOUND_F, int(pInt,SIZE_T), position_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingConstitutive: h5tcreate_f position_id')
call h5tinsert_f(position_id, "Position in Instance Results", 0_SIZE_T, H5T_NATIVE_INTEGER, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingConstitutive: h5tinsert_f position_id')
!--------------------------------------------------------------------------------------------------
! write data by fields in the datatype. Fields order is not important.
call h5dwrite_f(dset_id, position_id, mapping(1:Nconstituents,1:NmatPoints,1), &
int([Nconstituents, NmatPoints],HSIZE_T), hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingConstitutive: h5dwrite_f position_id')
call h5dwrite_f(dset_id, instance_id, mapping(1:Nconstituents,1:NmatPoints,2), &
int([Nconstituents, NmatPoints],HSIZE_T), hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingConstitutive: h5dwrite_f instance_id')
!--------------------------------------------------------------------------------------------------
!close types, dataspaces
call h5tclose_f(dtype_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingConstitutive: h5tclose_f dtype_id')
call h5tclose_f(position_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingConstitutive: h5tclose_f position_id')
call h5tclose_f(instance_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingConstitutive: h5tclose_f instance_id')
call h5dclose_f(dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingConstitutive: h5dclose_f')
call h5sclose_f(space_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingConstitutive: h5sclose_f')
call HDF5_closeGroup(mapping_ID)
end subroutine HDF5_mappingConstitutive
!--------------------------------------------------------------------------------------------------
!> @brief adds the unique mapping from spatial position and constituent ID to results
!--------------------------------------------------------------------------------------------------
subroutine HDF5_mappingCrystallite(mapping)
use hdf5
implicit none
integer(pInt), intent(in), dimension(:,:,:) :: mapping
integer :: hdferr, NmatPoints,Nconstituents
integer(HID_T) :: mapping_id, dtype_id, dset_id, space_id,instance_id,position_id
Nconstituents=size(mapping,1)
NmatPoints=size(mapping,2)
mapping_ID = HDF5_openGroup("mapping")
!--------------------------------------------------------------------------------------------------
! create dataspace
call h5screate_simple_f(2, int([Nconstituents,NmatPoints],HSIZE_T), space_id, hdferr, &
int([Nconstituents,NmatPoints],HSIZE_T))
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCrystallite')
!--------------------------------------------------------------------------------------------------
! compound type
call h5tcreate_f(H5T_COMPOUND_F, 6_SIZE_T, dtype_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCrystallite: h5tcreate_f dtype_id')
call h5tinsert_f(dtype_id, "Crystallite Instance", 0_SIZE_T, H5T_STD_U16LE, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCrystallite: h5tinsert_f 0')
call h5tinsert_f(dtype_id, "Position in Instance Results", 2_SIZE_T, H5T_STD_U32LE, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCrystallite: h5tinsert_f 2')
!--------------------------------------------------------------------------------------------------
! create Dataset
call h5dcreate_f(mapping_id, "Crystallite", dtype_id, space_id, dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCrystallite')
!--------------------------------------------------------------------------------------------------
! Create memory types (one compound datatype for each member)
call h5tcreate_f(H5T_COMPOUND_F, int(pInt,SIZE_T), instance_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCrystallite: h5tcreate_f instance_id')
call h5tinsert_f(instance_id, "Crystallite Instance", 0_SIZE_T, H5T_NATIVE_INTEGER, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCrystallite: h5tinsert_f instance_id')
call h5tcreate_f(H5T_COMPOUND_F, int(pInt,SIZE_T), position_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCrystallite: h5tcreate_f position_id')
call h5tinsert_f(position_id, "Position in Instance Results", 0_SIZE_T, H5T_NATIVE_INTEGER, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCrystallite: h5tinsert_f position_id')
!--------------------------------------------------------------------------------------------------
! write data by fields in the datatype. Fields order is not important.
call h5dwrite_f(dset_id, position_id, mapping(1:Nconstituents,1:NmatPoints,1), &
int([Nconstituents, NmatPoints],HSIZE_T), hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCrystallite: h5dwrite_f position_id')
call h5dwrite_f(dset_id, instance_id, mapping(1:Nconstituents,1:NmatPoints,2), &
int([Nconstituents, NmatPoints],HSIZE_T), hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCrystallite: h5dwrite_f instance_id')
!--------------------------------------------------------------------------------------------------
!close types, dataspaces
call h5tclose_f(dtype_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCrystallite: h5tclose_f dtype_id')
call h5tclose_f(position_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCrystallite: h5tclose_f position_id')
call h5tclose_f(instance_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCrystallite: h5tclose_f instance_id')
call h5dclose_f(dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCrystallite: h5dclose_f')
call h5sclose_f(space_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCrystallite: h5sclose_f')
call HDF5_closeGroup(mapping_ID)
end subroutine HDF5_mappingCrystallite
!--------------------------------------------------------------------------------------------------
!> @brief adds the unique mapping from spatial position to results
!--------------------------------------------------------------------------------------------------
subroutine HDF5_mappingHomogenization(mapping)
use hdf5
implicit none
integer(pInt), intent(in), dimension(:,:) :: mapping
integer :: hdferr, NmatPoints
integer(HID_T) :: mapping_id, dtype_id, dset_id, space_id,instance_id,position_id,elem_id,ip_id
NmatPoints=size(mapping,1)
mapping_ID = HDF5_openGroup("mapping")
!--------------------------------------------------------------------------------------------------
! create dataspace
call h5screate_simple_f(1, int([NmatPoints],HSIZE_T), space_id, hdferr, &
int([NmatPoints],HSIZE_T))
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomogenization')
!--------------------------------------------------------------------------------------------------
! compound type
call h5tcreate_f(H5T_COMPOUND_F, 11_SIZE_T, dtype_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomogenization: h5tcreate_f dtype_id')
call h5tinsert_f(dtype_id, "Homogenization Instance", 0_SIZE_T, H5T_STD_U16LE, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomogenization: h5tinsert_f 0')
call h5tinsert_f(dtype_id, "Position in Instance Results", 2_SIZE_T, H5T_STD_U32LE, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomogenization: h5tinsert_f 2')
call h5tinsert_f(dtype_id, "Element Number", 6_SIZE_T, H5T_STD_U32LE, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomogenization: h5tinsert_f 6')
call h5tinsert_f(dtype_id, "Material Point Number", 10_SIZE_T, H5T_STD_U8LE, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomogenization: h5tinsert_f 10')
!--------------------------------------------------------------------------------------------------
! create Dataset
call h5dcreate_f(mapping_id, "Homogenization", dtype_id, space_id, dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomogenization')
!--------------------------------------------------------------------------------------------------
! Create memory types (one compound datatype for each member)
call h5tcreate_f(H5T_COMPOUND_F, int(pInt,SIZE_T), instance_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomogenization: h5tcreate_f instance_id')
call h5tinsert_f(instance_id, "Homogenization Instance", 0_SIZE_T, H5T_NATIVE_INTEGER, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomogenization: h5tinsert_f instance_id')
call h5tcreate_f(H5T_COMPOUND_F, int(pInt,SIZE_T), position_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomogenization: h5tcreate_f position_id')
call h5tinsert_f(position_id, "Position in Instance Results", 0_SIZE_T, H5T_NATIVE_INTEGER, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomogenization: h5tinsert_f position_id')
call h5tcreate_f(H5T_COMPOUND_F, int(pInt,SIZE_T), elem_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomogenization: h5tcreate_f elem_id')
call h5tinsert_f(elem_id, "Element Number", 0_SIZE_T, H5T_NATIVE_INTEGER, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomogenization: h5tinsert_f elem_id')
call h5tcreate_f(H5T_COMPOUND_F, int(pInt,SIZE_T), ip_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomogenization: h5tcreate_f ip_id')
call h5tinsert_f(ip_id, "Material Point Number", 0_SIZE_T, H5T_NATIVE_INTEGER, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomogenization: h5tinsert_f ip_id')
!--------------------------------------------------------------------------------------------------
! write data by fields in the datatype. Fields order is not important.
call h5dwrite_f(dset_id, position_id, mapping(1:NmatPoints,1), &
int([NmatPoints],HSIZE_T), hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomogenization: h5dwrite_f position_id')
call h5dwrite_f(dset_id, instance_id, mapping(1:NmatPoints,2), &
int([NmatPoints],HSIZE_T), hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomogenization: h5dwrite_f position_id')
call h5dwrite_f(dset_id, elem_id, mapping(1:NmatPoints,3), &
int([NmatPoints],HSIZE_T), hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomogenization: h5dwrite_f elem_id')
call h5dwrite_f(dset_id, ip_id, mapping(1:NmatPoints,4), &
int([NmatPoints],HSIZE_T), hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomogenization: h5dwrite_f ip_id')
!--------------------------------------------------------------------------------------------------
!close types, dataspaces
call h5tclose_f(dtype_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomogenization: h5tclose_f dtype_id')
call h5tclose_f(position_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomogenization: h5tclose_f position_id')
call h5tclose_f(instance_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomogenization: h5tclose_f instance_id')
call h5tclose_f(ip_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomogenization: h5tclose_f ip_id')
call h5tclose_f(elem_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomogenization: h5tclose_f elem_id')
call h5dclose_f(dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomogenization: h5dclose_f')
call h5sclose_f(space_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomogenization: h5sclose_f')
call HDF5_closeGroup(mapping_ID)
end subroutine HDF5_mappingHomogenization
!--------------------------------------------------------------------------------------------------
!> @brief adds the unique cell to node mapping
!--------------------------------------------------------------------------------------------------
subroutine HDF5_mappingCells(mapping)
use hdf5
implicit none
integer(pInt), intent(in), dimension(:) :: mapping
integer :: hdferr, Nnodes
integer(HID_T) :: mapping_id, dset_id, space_id
Nnodes=size(mapping)
mapping_ID = HDF5_openGroup("mapping")
!--------------------------------------------------------------------------------------------------
! create dataspace
call h5screate_simple_f(1, int([Nnodes],HSIZE_T), space_id, hdferr, &
int([Nnodes],HSIZE_T))
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCells: h5screate_simple_f')
!--------------------------------------------------------------------------------------------------
! create Dataset
call h5dcreate_f(mapping_id, "Cell",H5T_NATIVE_INTEGER, space_id, dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCells')
!--------------------------------------------------------------------------------------------------
! write data by fields in the datatype. Fields order is not important.
call h5dwrite_f(dset_id, H5T_NATIVE_INTEGER, mapping, int([Nnodes],HSIZE_T), hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCells: h5dwrite_f instance_id')
!--------------------------------------------------------------------------------------------------
!close types, dataspaces
call h5dclose_f(dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingConstitutive: h5dclose_f')
call h5sclose_f(space_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingConstitutive: h5sclose_f')
call HDF5_closeGroup(mapping_ID)
end subroutine HDF5_mappingCells
!--------------------------------------------------------------------------------------------------
!> @brief creates a new scalar dataset in the given group location
!--------------------------------------------------------------------------------------------------
subroutine HDF5_addScalarDataset(group,nnodes,label,SIunit)
use hdf5
implicit none
integer(HID_T), intent(in) :: group
integer(pInt), intent(in) :: nnodes
character(len=*), intent(in) :: SIunit,label
integer :: hdferr
integer(HID_T) :: dset_id, space_id
!--------------------------------------------------------------------------------------------------
! create dataspace
call h5screate_simple_f(1, int([Nnodes],HSIZE_T), space_id, hdferr, &
int([Nnodes],HSIZE_T))
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addScalarDataset: h5screate_simple_f')
!--------------------------------------------------------------------------------------------------
! create Dataset
call h5dcreate_f(group, trim(label),H5T_NATIVE_DOUBLE, space_id, dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addScalarDataset: h5dcreate_f')
call HDF5_addStringAttribute(dset_id,'unit',trim(SIunit))
!--------------------------------------------------------------------------------------------------
!close types, dataspaces
call h5dclose_f(dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addScalarDataset: h5dclose_f')
call h5sclose_f(space_id, hdferr)
end subroutine HDF5_addScalarDataset
!--------------------------------------------------------------------------------------------------
!> @brief returns nicely formatted string of integer value
!--------------------------------------------------------------------------------------------------
function IO_formatIntToString(myInt)
implicit none
integer(pInt), intent(in) :: myInt
character(len=1_pInt + int(log10(real(myInt)),pInt)) :: IO_formatIntToString
write(IO_formatIntToString,'('//IO_intOut(myInt)//')') myInt
end function
!--------------------------------------------------------------------------------------------------
!> @brief copies the current temp results to the actual results file
!--------------------------------------------------------------------------------------------------
subroutine HDF5_forwardResults
use hdf5
implicit none
integer :: hdferr
integer(HID_T) :: new_loc_id
new_loc_id = HDF5_openGroup("results")
currentInc = currentInc + 1_pInt
call h5ocopy_f(tempFile, 'results', new_loc_id,dst_name=IO_formatIntToString(currentInc), hdferr=hdferr)
if (hdferr < 0_pInt) call IO_error(1_pInt,ext_msg='HDF5_forwardResults: h5ocopy_f')
call HDF5_closeGroup(new_loc_id)
end subroutine HDF5_forwardResults
#endif
end module IO

5
code/Makefile
View File

@ -309,7 +309,7 @@ KINEMATICS_FILES = \
kinematics_vacancy_strain.o kinematics_hydrogen_strain.o
PLASTIC_FILES = \
plastic_dislotwin.o plastic_disloUCLA.o plastic_isotropic.o plastic_j2.o \
plastic_dislotwin.o plastic_disloUCLA.o plastic_isotropic.o \
plastic_phenopowerlaw.o plastic_titanmod.o plastic_nonlocal.o plastic_none.o \
plastic_phenoplus.o
@ -579,9 +579,6 @@ plastic_phenoplus.o: plastic_phenoplus.f90 \
plastic_isotropic.o: plastic_isotropic.f90 \
lattice.o
plastic_j2.o: plastic_j2.f90 \
lattice.o
plastic_none.o: plastic_none.f90 \
lattice.o
ifeq "$(F90)" "gfortran"

1
code/commercialFEM_fileList.f90
View File

@ -28,7 +28,6 @@
#include "kinematics_hydrogen_strain.f90"
#include "plastic_none.f90"
#include "plastic_isotropic.f90"
#include "plastic_j2.f90"
#include "plastic_phenopowerlaw.f90"
#include "plastic_phenoplus.f90"
#include "plastic_titanmod.f90"

28
code/constitutive.f90
View File

@ -69,7 +69,6 @@ subroutine constitutive_init()
ELASTICITY_hooke_ID, &
PLASTICITY_none_ID, &
PLASTICITY_isotropic_ID, &
PLASTICITY_j2_ID, &
PLASTICITY_phenopowerlaw_ID, &
PLASTICITY_phenoplus_ID, &
PLASTICITY_dislotwin_ID, &
@ -93,7 +92,6 @@ subroutine constitutive_init()
ELASTICITY_HOOKE_label, &
PLASTICITY_NONE_label, &
PLASTICITY_ISOTROPIC_label, &
PLASTICITY_J2_label, &
PLASTICITY_PHENOPOWERLAW_label, &
PLASTICITY_PHENOPLUS_label, &
PLASTICITY_DISLOTWIN_label, &
@ -114,7 +112,6 @@ subroutine constitutive_init()
use plastic_none
use plastic_isotropic
use plastic_j2
use plastic_phenopowerlaw
use plastic_phenoplus
use plastic_dislotwin
@ -160,7 +157,6 @@ subroutine constitutive_init()
! parse plasticities from config file
if (any(phase_plasticity == PLASTICITY_NONE_ID)) call plastic_none_init
if (any(phase_plasticity == PLASTICITY_ISOTROPIC_ID)) call plastic_isotropic_init(FILEUNIT)
if (any(phase_plasticity == PLASTICITY_J2_ID)) call plastic_j2_init(FILEUNIT)
if (any(phase_plasticity == PLASTICITY_PHENOPOWERLAW_ID)) call plastic_phenopowerlaw_init(FILEUNIT)
if (any(phase_plasticity == PLASTICITY_PHENOPLUS_ID)) call plastic_phenoplus_init(FILEUNIT)
if (any(phase_plasticity == PLASTICITY_DISLOTWIN_ID)) call plastic_dislotwin_init(FILEUNIT)
@ -217,11 +213,6 @@ subroutine constitutive_init()
thisNoutput => plastic_isotropic_Noutput
thisOutput => plastic_isotropic_output
thisSize => plastic_isotropic_sizePostResult
case (PLASTICITY_J2_ID) plasticityType
outputName = PLASTICITY_J2_label
thisNoutput => plastic_j2_Noutput
thisOutput => plastic_j2_output
thisSize => plastic_j2_sizePostResult
case (PLASTICITY_PHENOPOWERLAW_ID) plasticityType
outputName = PLASTICITY_PHENOPOWERLAW_label
thisNoutput => plastic_phenopowerlaw_Noutput
@ -408,8 +399,6 @@ function constitutive_homogenizedC(ipc,ip,el)
plastic_titanmod_homogenizedC
use plastic_dislotwin, only: &
plastic_dislotwin_homogenizedC
use plastic_disloucla, only: &
plastic_disloucla_homogenizedC
use lattice, only: &
lattice_C66
@ -423,8 +412,6 @@ function constitutive_homogenizedC(ipc,ip,el)
plasticityType: select case (phase_plasticity(material_phase(ipc,ip,el)))
case (PLASTICITY_DISLOTWIN_ID) plasticityType
constitutive_homogenizedC = plastic_dislotwin_homogenizedC(ipc,ip,el)
case (PLASTICITY_DISLOUCLA_ID) plasticityType
constitutive_homogenizedC = plastic_disloucla_homogenizedC(ipc,ip,el)
case (PLASTICITY_TITANMOD_ID) plasticityType
constitutive_homogenizedC = plastic_titanmod_homogenizedC (ipc,ip,el)
case default plasticityType
@ -513,7 +500,6 @@ subroutine constitutive_LpAndItsTangent(Lp, dLp_dTstar3333, dLp_dFi3333, Tstar_v
thermalMapping, &
PLASTICITY_NONE_ID, &
PLASTICITY_ISOTROPIC_ID, &
PLASTICITY_J2_ID, &
PLASTICITY_PHENOPOWERLAW_ID, &
PLASTICITY_PHENOPLUS_ID, &
PLASTICITY_DISLOTWIN_ID, &
@ -522,8 +508,6 @@ subroutine constitutive_LpAndItsTangent(Lp, dLp_dTstar3333, dLp_dFi3333, Tstar_v
PLASTICITY_NONLOCAL_ID
use plastic_isotropic, only: &
plastic_isotropic_LpAndItsTangent
use plastic_j2, only: &
plastic_j2_LpAndItsTangent
use plastic_phenopowerlaw, only: &
plastic_phenopowerlaw_LpAndItsTangent
use plastic_phenoplus, only: &
@ -574,8 +558,6 @@ subroutine constitutive_LpAndItsTangent(Lp, dLp_dTstar3333, dLp_dFi3333, Tstar_v
dLp_dMstar = 0.0_pReal
case (PLASTICITY_ISOTROPIC_ID) plasticityType
call plastic_isotropic_LpAndItsTangent(Lp,dLp_dMstar,Mstar_v,ipc,ip,el)
case (PLASTICITY_J2_ID) plasticityType
call plastic_j2_LpAndItsTangent(Lp,dLp_dMstar,Mstar_v,ipc,ip,el)
case (PLASTICITY_PHENOPOWERLAW_ID) plasticityType
call plastic_phenopowerlaw_LpAndItsTangent(Lp,dLp_dMstar,Mstar_v,ipc,ip,el)
case (PLASTICITY_PHENOPLUS_ID) plasticityType
@ -903,7 +885,6 @@ subroutine constitutive_collectDotState(Tstar_v, FeArray, FpArray, subdt, subfra
homogenization_maxNgrains, &
PLASTICITY_none_ID, &
PLASTICITY_isotropic_ID, &
PLASTICITY_j2_ID, &
PLASTICITY_phenopowerlaw_ID, &
PLASTICITY_phenoplus_ID, &
PLASTICITY_dislotwin_ID, &
@ -916,8 +897,6 @@ subroutine constitutive_collectDotState(Tstar_v, FeArray, FpArray, subdt, subfra
SOURCE_thermal_externalheat_ID
use plastic_isotropic, only: &
plastic_isotropic_dotState
use plastic_j2, only: &
plastic_j2_dotState
use plastic_phenopowerlaw, only: &
plastic_phenopowerlaw_dotState
use plastic_phenoplus, only: &
@ -971,8 +950,6 @@ subroutine constitutive_collectDotState(Tstar_v, FeArray, FpArray, subdt, subfra
plasticityType: select case (phase_plasticity(material_phase(ipc,ip,el)))
case (PLASTICITY_ISOTROPIC_ID) plasticityType
call plastic_isotropic_dotState (Tstar_v,ipc,ip,el)
case (PLASTICITY_J2_ID) plasticityType
call plastic_j2_dotState (Tstar_v,ipc,ip,el)
case (PLASTICITY_PHENOPOWERLAW_ID) plasticityType
call plastic_phenopowerlaw_dotState(Tstar_v,ipc,ip,el)
case (PLASTICITY_PHENOPLUS_ID) plasticityType
@ -1117,7 +1094,6 @@ function constitutive_postResults(Tstar_v, FeArray, ipc, ip, el)
homogenization_maxNgrains, &
PLASTICITY_NONE_ID, &
PLASTICITY_ISOTROPIC_ID, &
PLASTICITY_J2_ID, &
PLASTICITY_PHENOPOWERLAW_ID, &
PLASTICITY_PHENOPLUS_ID, &
PLASTICITY_DISLOTWIN_ID, &
@ -1130,8 +1106,6 @@ function constitutive_postResults(Tstar_v, FeArray, ipc, ip, el)
SOURCE_damage_anisoDuctile_ID
use plastic_isotropic, only: &
plastic_isotropic_postResults
use plastic_j2, only: &
plastic_j2_postResults
use plastic_phenopowerlaw, only: &
plastic_phenopowerlaw_postResults
use plastic_phenoplus, only: &
@ -1185,8 +1159,6 @@ function constitutive_postResults(Tstar_v, FeArray, ipc, ip, el)
constitutive_postResults(startPos:endPos) = plastic_titanmod_postResults(ipc,ip,el)
case (PLASTICITY_ISOTROPIC_ID) plasticityType
constitutive_postResults(startPos:endPos) = plastic_isotropic_postResults(Tstar_v,ipc,ip,el)
case (PLASTICITY_J2_ID) plasticityType
constitutive_postResults(startPos:endPos) = plastic_j2_postResults(Tstar_v,ipc,ip,el)
case (PLASTICITY_PHENOPOWERLAW_ID) plasticityType
constitutive_postResults(startPos:endPos) = &
plastic_phenopowerlaw_postResults(Tstar_v,ipc,ip,el)

23
code/homogenization.f90
View File

@ -71,12 +71,6 @@ contains
!> @brief module initialization
!--------------------------------------------------------------------------------------------------
subroutine homogenization_init
#ifdef HDF
use hdf5, only: &
HID_T
use IO, only : &
HDF5_mappingHomogenization
#endif
use, intrinsic :: iso_fortran_env ! to get compiler_version and compiler_options (at least for gfortran 4.6 at the moment)
use math, only: &
math_I3
@ -131,12 +125,6 @@ subroutine homogenization_init
character(len=64), dimension(:,:), pointer :: thisOutput
character(len=32) :: outputName !< name of output, intermediate fix until HDF5 output is ready
logical :: knownHomogenization, knownThermal, knownDamage, knownVacancyflux, knownPorosity, knownHydrogenflux
#ifdef HDF
integer(pInt), dimension(:,:), allocatable :: mapping
integer(pInt), dimension(:), allocatable :: InstancePosition
allocate(mapping(mesh_ncpelems,4),source=0_pInt)
allocate(InstancePosition(material_Nhomogenization),source=0_pInt)
#endif
!--------------------------------------------------------------------------------------------------
@ -396,17 +384,6 @@ subroutine homogenization_init
!--------------------------------------------------------------------------------------------------
! allocate and initialize global state and postresutls variables
#ifdef HDF
elementLooping: do e = 1,mesh_NcpElems
myInstance = homogenization_typeInstance(mesh_element(3,e))
IpLooping: do i = 1,FE_Nips(FE_geomtype(mesh_element(2,e)))
InstancePosition(myInstance) = InstancePosition(myInstance)+1_pInt
mapping(e,1:4) = [instancePosition(myinstance),myinstance,e,i]
enddo IpLooping
enddo elementLooping
call HDF5_mappingHomogenization(mapping)
#endif
homogenization_maxSizePostResults = 0_pInt
thermal_maxSizePostResults = 0_pInt
damage_maxSizePostResults = 0_pInt

27
code/material.f90
View File

@ -24,7 +24,6 @@ module material
ELASTICITY_hooke_label = 'hooke', &
PLASTICITY_none_label = 'none', &
PLASTICITY_isotropic_label = 'isotropic', &
PLASTICITY_j2_label = 'j2', &
PLASTICITY_phenopowerlaw_label = 'phenopowerlaw', &
PLASTICITY_phenoplus_label = 'phenoplus', &
PLASTICITY_dislotwin_label = 'dislotwin', &
@ -74,7 +73,6 @@ module material
enumerator :: PLASTICITY_undefined_ID, &
PLASTICITY_none_ID, &
PLASTICITY_isotropic_ID, &
PLASTICITY_j2_ID, &
PLASTICITY_phenopowerlaw_ID, &
PLASTICITY_phenoplus_ID, &
PLASTICITY_dislotwin_ID, &
@ -313,7 +311,6 @@ module material
ELASTICITY_hooke_ID ,&
PLASTICITY_none_ID, &
PLASTICITY_isotropic_ID, &
PLASTICITY_J2_ID, &
PLASTICITY_phenopowerlaw_ID, &
PLASTICITY_phenoplus_ID, &
PLASTICITY_dislotwin_ID, &
@ -351,9 +348,6 @@ module material
HYDROGENFLUX_cahnhilliard_ID, &
HOMOGENIZATION_none_ID, &
HOMOGENIZATION_isostrain_ID, &
#ifdef HDF
material_NconstituentsPhase, &
#endif
HOMOGENIZATION_RGC_ID
private :: &
@ -982,8 +976,6 @@ subroutine material_parsePhase(fileUnit,myPart)
phase_plasticity(section) = PLASTICITY_NONE_ID
case (PLASTICITY_ISOTROPIC_label)
phase_plasticity(section) = PLASTICITY_ISOTROPIC_ID
case (PLASTICITY_J2_label)
phase_plasticity(section) = PLASTICITY_J2_ID
case (PLASTICITY_PHENOPOWERLAW_label)
phase_plasticity(section) = PLASTICITY_PHENOPOWERLAW_ID
case (PLASTICITY_PHENOPLUS_label)
@ -1280,7 +1272,7 @@ subroutine material_populateGrains
integer(pInt) :: t,e,i,g,j,m,c,r,homog,micro,sgn,hme, myDebug, &
phaseID,textureID,dGrains,myNgrains,myNorientations,myNconstituents, &
grain,constituentGrain,ipGrain,symExtension, ip
real(pReal) :: extreme,rnd
real(pReal) :: deviation,extreme,rnd
integer(pInt), dimension (:,:), allocatable :: Nelems ! counts number of elements in homog, micro array
type(p_intvec), dimension (:,:), allocatable :: elemsOfHomogMicro ! lists element number in homog, micro array
@ -1407,8 +1399,11 @@ subroutine material_populateGrains
extreme = 0.0_pReal
t = 0_pInt
do i = 1_pInt,myNconstituents ! find largest deviator
if (real(sgn,pReal)*log(NgrainsOfConstituent(i)/myNgrains/microstructure_fraction(i,micro)) > extreme) then
extreme = real(sgn,pReal)*log(NgrainsOfConstituent(i)/myNgrains/microstructure_fraction(i,micro))
deviation = real(sgn,pReal)*log( microstructure_fraction(i,micro) / &
!-------------------------------- &
(real(NgrainsOfConstituent(i),pReal)/real(myNgrains,pReal) ) )
if (deviation > extreme) then
extreme = deviation
t = i
endif
enddo
@ -1600,14 +1595,4 @@ subroutine material_populateGrains
end subroutine material_populateGrains
#ifdef HDF
integer(pInt) pure function material_NconstituentsPhase(matID)
implicit none
integer(pInt), intent(in) :: matID
material_NconstituentsPhase = count(microstructure_phase == matID)
end function
#endif
end module material

16
code/mesh.f90
View File

@ -4525,17 +4525,9 @@ subroutine mesh_write_cellGeom
VTK_geo, &
VTK_con, &
VTK_end
#ifdef HDF
use IO, only: &
HDF5_mappingCells
#endif
implicit none
integer(I4P), dimension(1:mesh_Ncells) :: celltype
integer(I4P), dimension(mesh_Ncells*(1_pInt+FE_maxNcellnodesPerCell)) :: cellconnection
#ifdef HDF
integer(pInt), dimension(mesh_Ncells*FE_maxNcellnodesPerCell) :: cellconnectionHDF5
integer(pInt) :: j2=0_pInt
#endif
integer(I4P):: error
integer(I4P):: g, c, e, CellID, i, j
@ -4550,16 +4542,8 @@ subroutine mesh_write_cellGeom
cellconnection(j+1_pInt:j+FE_NcellnodesPerCell(c)+1_pInt) &
= [FE_NcellnodesPerCell(c),mesh_cell(1:FE_NcellnodesPerCell(c),i,e)-1_pInt] ! number of cellnodes per cell & list of global cellnode IDs belnging to this cell (cellnode counting starts at 0)
j = j + FE_NcellnodesPerCell(c) + 1_pInt
#ifdef HDF
cellconnectionHDF5(j2+1_pInt:j2+FE_NcellnodesPerCell(c)) &
= mesh_cell(1:FE_NcellnodesPerCell(c),i,e)-1_pInt
j2=j2 + FE_ncellnodesPerCell(c)
#endif
enddo
enddo
#ifdef HDF
call HDF5_mappingCells(cellconnectionHDF5(1:j2))
#endif
error=VTK_ini(output_format = 'ASCII', &
title=trim(getSolverJobName())//' cell mesh', &

823
code/plastic_disloUCLA.f90
View File

File diff suppressed because it is too large Load Diff

90
code/plastic_isotropic.f90
View File

@ -7,14 +7,10 @@
!! untextured polycrystal
!--------------------------------------------------------------------------------------------------
module plastic_isotropic
#ifdef HDF
use hdf5, only: &
HID_T
#endif
use prec, only: &
pReal,&
pInt
pInt, &
DAMASK_NaN
implicit none
private
@ -40,20 +36,20 @@ module plastic_isotropic
integer(kind(undefined_ID)), allocatable, dimension(:) :: &
outputID
real(pReal) :: &
fTaylor, &
tau0, &
gdot0, &
n, &
h0, &
h0_slopeLnRate=0.0_pReal, &
tausat, &
a, &
aTolFlowstress, &
aTolShear , &
tausat_SinhFitA=0.0_pReal, &
tausat_SinhFitB=0.0_pReal, &
tausat_SinhFitC=0.0_pReal, &
tausat_SinhFitD=0.0_pReal
fTaylor = DAMASK_NaN, &
tau0 = DAMASK_NaN, &
gdot0 = DAMASK_NaN, &
n = DAMASK_NaN, &
h0 = DAMASK_NaN, &
h0_slopeLnRate = 0.0_pReal, &
tausat = DAMASK_NaN, &
a = DAMASK_NaN, &
aTolFlowstress = 1.0_pReal, &
aTolShear = 1.0e-6_pReal, &
tausat_SinhFitA= 0.0_pReal, &
tausat_SinhFitB= 0.0_pReal, &
tausat_SinhFitC= 0.0_pReal, &
tausat_SinhFitD= 0.0_pReal
logical :: &
dilatation = .false.
end type
@ -143,9 +139,10 @@ subroutine plastic_isotropic_init(fileUnit)
sizeDeltaState
character(len=65536) :: &
tag = '', &
outputtag = '', &
line = '', &
extmsg = ''
character(len=64) :: &
outputtag = ''
integer(pInt) :: NipcMyPhase
mainProcess: if (worldrank == 0) then
@ -385,8 +382,7 @@ subroutine plastic_isotropic_LpAndItsTangent(Lp,dLp_dTstar99,Tstar_v,ipc,ip,el)
math_mul33xx33, &
math_transpose33
use material, only: &
phaseAt, phasememberAt, &
plasticState, &
phasememberAt, &
material_phase, &
phase_plasticityInstance
@ -416,7 +412,7 @@ subroutine plastic_isotropic_LpAndItsTangent(Lp,dLp_dTstar99,Tstar_v,ipc,ip,el)
k, l, m, n
of = phasememberAt(ipc,ip,el) ! phasememberAt should be tackled by material and be renamed to material_phasemember
instance = phase_plasticityInstance(phaseAt(ipc,ip,el)) ! "phaseAt" equivalent to "material_phase" !!
instance = phase_plasticityInstance(material_phase(ipc,ip,el))
Tstar_dev_33 = math_deviatoric33(math_Mandel6to33(Tstar_v)) ! deviatoric part of 2nd Piola-Kirchhoff stress
squarenorm_Tstar_dev = math_mul33xx33(Tstar_dev_33,Tstar_dev_33)
@ -467,14 +463,14 @@ subroutine plastic_isotropic_LiAndItsTangent(Li,dLi_dTstar_3333,Tstar_v,ipc,ip,e
math_mul33xx33
use material, only: &
phasememberAt, &
plasticState, &
material_phase, &
phase_plasticityInstance
implicit none
real(pReal), dimension(3,3), intent(out) :: &
Li !< plastic velocity gradient
real(pReal), dimension(3,3,3,3), intent(out) :: &
dLi_dTstar_3333 !< derivative of Li with respect to Tstar as 4th order tensor
real(pReal), dimension(6), intent(in) :: &
Tstar_v !< 2nd Piola Kirchhoff stress tensor in Mandel notation
integer(pInt), intent(in) :: &
@ -484,9 +480,7 @@ subroutine plastic_isotropic_LiAndItsTangent(Li,dLi_dTstar_3333,Tstar_v,ipc,ip,e
real(pReal), dimension(3,3) :: &
Tstar_sph_33 !< sphiatoric part of the 2nd Piola Kirchhoff stress tensor as 2nd order tensor
real(pReal), dimension(3,3,3,3), intent(out) :: &
dLi_dTstar_3333 !< derivative of Li with respect to Tstar as 4th order tensor
real(pReal) :: &
real(pReal) :: &
gamma_dot, & !< strainrate
norm_Tstar_sph, & !< euclidean norm of Tstar_sph
squarenorm_Tstar_sph !< square of the euclidean norm of Tstar_sph
@ -501,28 +495,26 @@ subroutine plastic_isotropic_LiAndItsTangent(Li,dLi_dTstar_3333,Tstar_v,ipc,ip,e
squarenorm_Tstar_sph = math_mul33xx33(Tstar_sph_33,Tstar_sph_33)
norm_Tstar_sph = sqrt(squarenorm_Tstar_sph)
if (param(instance)%dilatation) then
if (norm_Tstar_sph <= 0.0_pReal) then ! Tstar == 0 --> both Li and dLi_dTstar are zero
Li = 0.0_pReal
dLi_dTstar_3333 = 0.0_pReal
else
gamma_dot = param(instance)%gdot0 &
* (sqrt(1.5_pReal) * norm_Tstar_sph / param(instance)%fTaylor / state(instance)%flowstress(of) ) &
**param(instance)%n
if (param(instance)%dilatation .and. norm_Tstar_sph > 0.0_pReal) then ! Tstar == 0 or J2 plascitiy --> both Li and dLi_dTstar are zero
gamma_dot = param(instance)%gdot0 &
* (sqrt(1.5_pReal) * norm_Tstar_sph / param(instance)%fTaylor / state(instance)%flowstress(of) ) &
**param(instance)%n
Li = Tstar_sph_33/norm_Tstar_sph * gamma_dot/param(instance)%fTaylor
Li = Tstar_sph_33/norm_Tstar_sph * gamma_dot/param(instance)%fTaylor
!--------------------------------------------------------------------------------------------------
! Calculation of the tangent of Li
forall (k=1_pInt:3_pInt,l=1_pInt:3_pInt,m=1_pInt:3_pInt,n=1_pInt:3_pInt) &
dLi_dTstar_3333(k,l,m,n) = (param(instance)%n-1.0_pReal) * &
Tstar_sph_33(k,l)*Tstar_sph_33(m,n) / squarenorm_Tstar_sph
forall (k=1_pInt:3_pInt,l=1_pInt:3_pInt) &
dLi_dTstar_3333(k,l,k,l) = dLi_dTstar_3333(k,l,k,l) + 1.0_pReal
!--------------------------------------------------------------------------------------------------
! Calculation of the tangent of Li
forall (k=1_pInt:3_pInt,l=1_pInt:3_pInt,m=1_pInt:3_pInt,n=1_pInt:3_pInt) &
dLi_dTstar_3333(k,l,m,n) = (param(instance)%n-1.0_pReal) * &
Tstar_sph_33(k,l)*Tstar_sph_33(m,n) / squarenorm_Tstar_sph
forall (k=1_pInt:3_pInt,l=1_pInt:3_pInt) &
dLi_dTstar_3333(k,l,k,l) = dLi_dTstar_3333(k,l,k,l) + 1.0_pReal
dLi_dTstar_3333 = gamma_dot / param(instance)%fTaylor * &
dLi_dTstar_3333 / norm_Tstar_sph
endif
dLi_dTstar_3333 = gamma_dot / param(instance)%fTaylor * &
dLi_dTstar_3333 / norm_Tstar_sph
else
Li = 0.0_pReal
dLi_dTstar_3333 = 0.0_pReal
endif
end subroutine plastic_isotropic_LiAndItsTangent
@ -536,7 +528,6 @@ subroutine plastic_isotropic_dotState(Tstar_v,ipc,ip,el)
math_mul6x6
use material, only: &
phasememberAt, &
plasticState, &
material_phase, &
phase_plasticityInstance
@ -615,7 +606,6 @@ function plastic_isotropic_postResults(Tstar_v,ipc,ip,el)
math_mul6x6
use material, only: &
material_phase, &
plasticState, &
phasememberAt, &
phase_plasticityInstance

577
code/plastic_j2.f90
View File

@ -1,577 +0,0 @@
!--------------------------------------------------------------------------------------------------
!> @author Franz Roters, Max-Planck-Institut für Eisenforschung GmbH
!> @author Philip Eisenlohr, Max-Planck-Institut für Eisenforschung GmbH
!> @brief material subroutine for isotropic (J2) plasticity
!> @details Isotropic (J2) Plasticity which resembles the phenopowerlaw plasticity without
!! resolving the stress on the slip systems. Will give the response of phenopowerlaw for an
!! untextured polycrystal
!--------------------------------------------------------------------------------------------------
module plastic_j2
#ifdef HDF
use hdf5, only: &
HID_T
#endif
use prec, only: &
pReal,&
pInt
implicit none
private
integer(pInt), dimension(:), allocatable, public, protected :: &
plastic_j2_sizePostResults !< cumulative size of post results
integer(pInt), dimension(:,:), allocatable, target, public :: &
plastic_j2_sizePostResult !< size of each post result output
character(len=64), dimension(:,:), allocatable, target, public :: &
plastic_j2_output !< name of each post result output
integer(pInt), dimension(:), allocatable, target, public :: &
plastic_j2_Noutput !< number of outputs per instance
real(pReal), dimension(:), allocatable, private :: &
plastic_j2_fTaylor, & !< Taylor factor
plastic_j2_tau0, & !< initial plastic stress
plastic_j2_gdot0, & !< reference velocity
plastic_j2_n, & !< Visco-plastic parameter
!--------------------------------------------------------------------------------------------------
! h0 as function of h0 = A + B log (gammadot)
plastic_j2_h0, &
plastic_j2_h0_slopeLnRate, &
plastic_j2_tausat, & !< final plastic stress
plastic_j2_a, &
plastic_j2_aTolResistance, &
plastic_j2_aTolShear, &
!--------------------------------------------------------------------------------------------------
! tausat += (asinh((gammadot / SinhFitA)**(1 / SinhFitD)))**(1 / SinhFitC) / (SinhFitB * (gammadot / gammadot0)**(1/n))
plastic_j2_tausat_SinhFitA, & !< fitting parameter for normalized strain rate vs. stress function
plastic_j2_tausat_SinhFitB, & !< fitting parameter for normalized strain rate vs. stress function
plastic_j2_tausat_SinhFitC, & !< fitting parameter for normalized strain rate vs. stress function
plastic_j2_tausat_SinhFitD !< fitting parameter for normalized strain rate vs. stress function
enum, bind(c)
enumerator :: undefined_ID, &
flowstress_ID, &
strainrate_ID
end enum
integer(kind(undefined_ID)), dimension(:,:), allocatable, private :: &
plastic_j2_outputID !< ID of each post result output
#ifdef HDF
type plastic_j2_tOutput
real(pReal), dimension(:), allocatable, private :: &
flowstress, &
strainrate
logical :: flowstressActive = .false., strainrateActive = .false. ! if we can write the output block wise, this is not needed anymore because we can do an if(allocated(xxx))
end type plastic_j2_tOutput
type(plastic_j2_tOutput), allocatable, dimension(:) :: plastic_j2_Output2
integer(HID_T), allocatable, dimension(:) :: outID
#endif
public :: &
plastic_j2_init, &
plastic_j2_LpAndItsTangent, &
plastic_j2_dotState, &
plastic_j2_postResults
contains
!--------------------------------------------------------------------------------------------------
!> @brief module initialization
!> @details reads in material parameters, allocates arrays, and does sanity checks
!--------------------------------------------------------------------------------------------------
subroutine plastic_j2_init(fileUnit)
use, intrinsic :: iso_fortran_env ! to get compiler_version and compiler_options (at least for gfortran 4.6 at the moment)
#ifdef HDF
use hdf5
#endif
use debug, only: &
debug_level, &
debug_constitutive, &
debug_levelBasic
use numerics, only: &
analyticJaco, &
worldrank, &
numerics_integrator
use math, only: &
math_Mandel3333to66, &
math_Voigt66to3333
use IO, only: &
IO_read, &
IO_lc, &
IO_getTag, &
IO_isBlank, &
IO_stringPos, &
IO_stringValue, &
IO_floatValue, &
IO_error, &
IO_timeStamp, &
#ifdef HDF
tempResults, &
HDF5_addGroup, &
HDF5_addScalarDataset,&
#endif
IO_EOF
use material, only: &
phase_plasticity, &
phase_plasticityInstance, &
phase_Noutput, &
PLASTICITY_J2_label, &
PLASTICITY_J2_ID, &
material_phase, &
plasticState, &
MATERIAL_partPhase
use lattice
implicit none
integer(pInt), intent(in) :: fileUnit
integer(pInt), allocatable, dimension(:) :: chunkPos
integer(pInt) :: &
o, &
phase, &
maxNinstance, &
instance, &
mySize, &
sizeDotState, &
sizeState, &
sizeDeltaState
character(len=65536) :: &
tag = '', &
line = ''
integer(pInt) :: NofMyPhase
#ifdef HDF
character(len=5) :: &
str1
integer(HID_T) :: ID,ID2,ID4
#endif
mainProcess: if (worldrank == 0) then
write(6,'(/,a)') ' <<<+- constitutive_'//PLASTICITY_J2_label//' init -+>>>'
write(6,'(a15,a)') ' Current time: ',IO_timeStamp()
#include "compilation_info.f90"
endif mainProcess
maxNinstance = int(count(phase_plasticity == PLASTICITY_J2_ID),pInt)
if (maxNinstance == 0_pInt) return
if (iand(debug_level(debug_constitutive),debug_levelBasic) /= 0_pInt) &
write(6,'(a16,1x,i5,/)') '# instances:',maxNinstance
#ifdef HDF
allocate(plastic_j2_Output2(maxNinstance))
allocate(outID(maxNinstance))
#endif
allocate(plastic_j2_sizePostResults(maxNinstance), source=0_pInt)
allocate(plastic_j2_sizePostResult(maxval(phase_Noutput), maxNinstance),source=0_pInt)
allocate(plastic_j2_output(maxval(phase_Noutput), maxNinstance))
plastic_j2_output = ''
allocate(plastic_j2_outputID(maxval(phase_Noutput),maxNinstance), source=undefined_ID)
allocate(plastic_j2_Noutput(maxNinstance), source=0_pInt)
allocate(plastic_j2_fTaylor(maxNinstance), source=0.0_pReal)
allocate(plastic_j2_tau0(maxNinstance), source=0.0_pReal)
allocate(plastic_j2_gdot0(maxNinstance), source=0.0_pReal)
allocate(plastic_j2_n(maxNinstance), source=0.0_pReal)
allocate(plastic_j2_h0(maxNinstance), source=0.0_pReal)
allocate(plastic_j2_h0_slopeLnRate(maxNinstance), source=0.0_pReal)
allocate(plastic_j2_tausat(maxNinstance), source=0.0_pReal)
allocate(plastic_j2_a(maxNinstance), source=0.0_pReal)
allocate(plastic_j2_aTolResistance(maxNinstance), source=0.0_pReal)
allocate(plastic_j2_aTolShear (maxNinstance), source=0.0_pReal)
allocate(plastic_j2_tausat_SinhFitA(maxNinstance), source=0.0_pReal)
allocate(plastic_j2_tausat_SinhFitB(maxNinstance), source=0.0_pReal)
allocate(plastic_j2_tausat_SinhFitC(maxNinstance), source=0.0_pReal)
allocate(plastic_j2_tausat_SinhFitD(maxNinstance), source=0.0_pReal)
rewind(fileUnit)
phase = 0_pInt
do while (trim(line) /= IO_EOF .and. IO_lc(IO_getTag(line,'<','>')) /= material_partPhase) ! wind forward to <phase>
line = IO_read(fileUnit)
enddo
parsingFile: do while (trim(line) /= IO_EOF) ! read through sections of phase part
line = IO_read(fileUnit)
if (IO_isBlank(line)) cycle ! skip empty lines
if (IO_getTag(line,'<','>') /= '') then ! stop at next part
line = IO_read(fileUnit, .true.) ! reset IO_read
exit
endif
if (IO_getTag(line,'[',']') /= '') then ! next section
phase = phase + 1_pInt ! advance section counter
if (phase_plasticity(phase) == PLASTICITY_J2_ID) then
instance = phase_plasticityInstance(phase)
#ifdef HDF
outID(instance)=HDF5_addGroup(str1,tempResults)
#endif
endif
cycle ! skip to next line
endif
if (phase > 0_pInt ) then; if (phase_plasticity(phase) == PLASTICITY_J2_ID) then ! one of my phases. Do not short-circuit here (.and. between if-statements), it's not safe in Fortran
instance = phase_plasticityInstance(phase) ! which instance of my plasticity is present phase
chunkPos = IO_stringPos(line)
tag = IO_lc(IO_stringValue(line,chunkPos,1_pInt)) ! extract key
select case(tag)
case ('(output)')
select case(IO_lc(IO_stringValue(line,chunkPos,2_pInt)))
case ('flowstress')
plastic_j2_Noutput(instance) = plastic_j2_Noutput(instance) + 1_pInt
plastic_j2_outputID(plastic_j2_Noutput(instance),instance) = flowstress_ID
plastic_j2_output(plastic_j2_Noutput(instance),instance) = &
IO_lc(IO_stringValue(line,chunkPos,2_pInt))
#ifdef HDF
call HDF5_addScalarDataset(outID(instance),myConstituents,'flowstress','MPa')
allocate(plastic_j2_Output2(instance)%flowstress(myConstituents))
plastic_j2_Output2(instance)%flowstressActive = .true.
#endif
case ('strainrate')
plastic_j2_Noutput(instance) = plastic_j2_Noutput(instance) + 1_pInt
plastic_j2_outputID(plastic_j2_Noutput(instance),instance) = strainrate_ID
plastic_j2_output(plastic_j2_Noutput(instance),instance) = &
IO_lc(IO_stringValue(line,chunkPos,2_pInt))
#ifdef HDF
call HDF5_addScalarDataset(outID(instance),myConstituents,'strainrate','1/s')
allocate(plastic_j2_Output2(instance)%strainrate(myConstituents))
plastic_j2_Output2(instance)%strainrateActive = .true.
#endif
case default
end select
case ('tau0')
plastic_j2_tau0(instance) = IO_floatValue(line,chunkPos,2_pInt)
if (plastic_j2_tau0(instance) < 0.0_pReal) &
call IO_error(211_pInt,ext_msg=trim(tag)//' ('//PLASTICITY_J2_label//')')
case ('gdot0')
plastic_j2_gdot0(instance) = IO_floatValue(line,chunkPos,2_pInt)
if (plastic_j2_gdot0(instance) <= 0.0_pReal) &
call IO_error(211_pInt,ext_msg=trim(tag)//' ('//PLASTICITY_J2_label//')')
case ('n')
plastic_j2_n(instance) = IO_floatValue(line,chunkPos,2_pInt)
if (plastic_j2_n(instance) <= 0.0_pReal) &
call IO_error(211_pInt,ext_msg=trim(tag)//' ('//PLASTICITY_J2_label//')')
case ('h0')
plastic_j2_h0(instance) = IO_floatValue(line,chunkPos,2_pInt)
case ('h0_slope','slopelnrate')
plastic_j2_h0_slopeLnRate(instance) = IO_floatValue(line,chunkPos,2_pInt)
case ('tausat')
plastic_j2_tausat(instance) = IO_floatValue(line,chunkPos,2_pInt)
if (plastic_j2_tausat(instance) <= 0.0_pReal) &
call IO_error(211_pInt,ext_msg=trim(tag)//' ('//PLASTICITY_J2_label//')')
case ('tausat_sinhfita')
plastic_j2_tausat_SinhFitA(instance) = IO_floatValue(line,chunkPos,2_pInt)
case ('tausat_sinhfitb')
plastic_j2_tausat_SinhFitB(instance) = IO_floatValue(line,chunkPos,2_pInt)
case ('tausat_sinhfitc')
plastic_j2_tausat_SinhFitC(instance) = IO_floatValue(line,chunkPos,2_pInt)
case ('tausat_sinhfitd')
plastic_j2_tausat_SinhFitD(instance) = IO_floatValue(line,chunkPos,2_pInt)
case ('a', 'w0')
plastic_j2_a(instance) = IO_floatValue(line,chunkPos,2_pInt)
if (plastic_j2_a(instance) <= 0.0_pReal) &
call IO_error(211_pInt,ext_msg=trim(tag)//' ('//PLASTICITY_J2_label//')')
case ('taylorfactor')
plastic_j2_fTaylor(instance) = IO_floatValue(line,chunkPos,2_pInt)
if (plastic_j2_fTaylor(instance) <= 0.0_pReal) &
call IO_error(211_pInt,ext_msg=trim(tag)//' ('//PLASTICITY_J2_label//')')
case ('atol_resistance')
plastic_j2_aTolResistance(instance) = IO_floatValue(line,chunkPos,2_pInt)
if (plastic_j2_aTolResistance(instance) <= 0.0_pReal) &
call IO_error(211_pInt,ext_msg=trim(tag)//' ('//PLASTICITY_J2_label//')')
case ('atol_shear')
plastic_j2_aTolShear(instance) = IO_floatValue(line,chunkPos,2_pInt)
case default
end select
endif; endif
enddo parsingFile
initializeInstances: do phase = 1_pInt, size(phase_plasticity)
myPhase: if (phase_plasticity(phase) == PLASTICITY_j2_ID) then
NofMyPhase=count(material_phase==phase)
instance = phase_plasticityInstance(phase)
!--------------------------------------------------------------------------------------------------
! sanity checks
if (plastic_j2_aTolShear(instance) <= 0.0_pReal) &
plastic_j2_aTolShear(instance) = 1.0e-6_pReal ! default absolute tolerance 1e-6
!--------------------------------------------------------------------------------------------------
! Determine size of postResults array
outputsLoop: do o = 1_pInt,plastic_j2_Noutput(instance)
select case(plastic_j2_outputID(o,instance))
case(flowstress_ID,strainrate_ID)
mySize = 1_pInt
case default
end select
outputFound: if (mySize > 0_pInt) then
plastic_j2_sizePostResult(o,instance) = mySize
plastic_j2_sizePostResults(instance) = &
plastic_j2_sizePostResults(instance) + mySize
endif outputFound
enddo outputsLoop
!--------------------------------------------------------------------------------------------------
! allocate state arrays
sizeState = 2_pInt
sizeDotState = sizeState
sizeDeltaState = 0_pInt
plasticState(phase)%sizeState = sizeState
plasticState(phase)%sizeDotState = sizeDotState
plasticState(phase)%sizeDeltaState = sizeDeltaState
plasticState(phase)%sizePostResults = plastic_j2_sizePostResults(instance)
plasticState(phase)%nSlip = 1
plasticState(phase)%nTwin = 0
plasticState(phase)%nTrans= 0
allocate(plasticState(phase)%aTolState ( sizeState))
plasticState(phase)%aTolState(1) = plastic_j2_aTolResistance(instance)
plasticState(phase)%aTolState(2) = plastic_j2_aTolShear(instance)
allocate(plasticState(phase)%state0 ( sizeState,NofMyPhase))
plasticState(phase)%state0(1,1:NofMyPhase) = plastic_j2_tau0(instance)
plasticState(phase)%state0(2,1:NofMyPhase) = 0.0_pReal
allocate(plasticState(phase)%partionedState0 ( sizeState,NofMyPhase),source=0.0_pReal)
allocate(plasticState(phase)%subState0 ( sizeState,NofMyPhase),source=0.0_pReal)
allocate(plasticState(phase)%state ( sizeState,NofMyPhase),source=0.0_pReal)
allocate(plasticState(phase)%dotState (sizeDotState,NofMyPhase),source=0.0_pReal)
allocate(plasticState(phase)%deltaState (sizeDeltaState,NofMyPhase),source=0.0_pReal)
if (.not. analyticJaco) then
allocate(plasticState(phase)%state_backup ( sizeState,NofMyPhase),source=0.0_pReal)
allocate(plasticState(phase)%dotState_backup (sizeDotState,NofMyPhase),source=0.0_pReal)
endif
if (any(numerics_integrator == 1_pInt)) then
allocate(plasticState(phase)%previousDotState (sizeDotState,NofMyPhase),source=0.0_pReal)
allocate(plasticState(phase)%previousDotState2(sizeDotState,NofMyPhase),source=0.0_pReal)
endif
if (any(numerics_integrator == 4_pInt)) &
allocate(plasticState(phase)%RK4dotState (sizeDotState,NofMyPhase),source=0.0_pReal)
if (any(numerics_integrator == 5_pInt)) &
allocate(plasticState(phase)%RKCK45dotState (6,sizeDotState,NofMyPhase),source=0.0_pReal)
plasticState(phase)%slipRate => plasticState(phase)%dotState(2:2,1:NofMyPhase)
plasticState(phase)%accumulatedSlip => plasticState(phase)%state (2:2,1:NofMyPhase)
endif myPhase
enddo initializeInstances
end subroutine plastic_j2_init
!--------------------------------------------------------------------------------------------------
!> @brief calculates plastic velocity gradient and its tangent
!--------------------------------------------------------------------------------------------------
subroutine plastic_j2_LpAndItsTangent(Lp,dLp_dTstar99,Tstar_v,ipc,ip,el)
use math, only: &
math_mul6x6, &
math_Mandel6to33, &
math_Plain3333to99, &
math_deviatoric33, &
math_mul33xx33
use material, only: &
phaseAt, phasememberAt, &
plasticState, &
material_phase, &
phase_plasticityInstance
implicit none
real(pReal), dimension(3,3), intent(out) :: &
Lp !< plastic velocity gradient
real(pReal), dimension(9,9), intent(out) :: &
dLp_dTstar99 !< derivative of Lp with respect to 2nd Piola Kirchhoff stress
real(pReal), dimension(6), intent(in) :: &
Tstar_v !< 2nd Piola Kirchhoff stress tensor in Mandel notation
integer(pInt), intent(in) :: &
ipc, & !< component-ID of integration point
ip, & !< integration point
el !< element
real(pReal), dimension(3,3) :: &
Tstar_dev_33 !< deviatoric part of the 2nd Piola Kirchhoff stress tensor as 2nd order tensor
real(pReal), dimension(3,3,3,3) :: &
dLp_dTstar_3333 !< derivative of Lp with respect to Tstar as 4th order tensor
real(pReal) :: &
gamma_dot, & !< strainrate
norm_Tstar_dev, & !< euclidean norm of Tstar_dev
squarenorm_Tstar_dev !< square of the euclidean norm of Tstar_dev
integer(pInt) :: &
instance, &
k, l, m, n
instance = phase_plasticityInstance(material_phase(ipc,ip,el))
Tstar_dev_33 = math_deviatoric33(math_Mandel6to33(Tstar_v)) ! deviatoric part of 2nd Piola-Kirchhoff stress
squarenorm_Tstar_dev = math_mul33xx33(Tstar_dev_33,Tstar_dev_33)
norm_Tstar_dev = sqrt(squarenorm_Tstar_dev)
if (norm_Tstar_dev <= 0.0_pReal) then ! Tstar == 0 --> both Lp and dLp_dTstar are zero
Lp = 0.0_pReal
dLp_dTstar99 = 0.0_pReal
else
gamma_dot = plastic_j2_gdot0(instance) &
* (sqrt(1.5_pReal) * norm_Tstar_dev / (plastic_j2_fTaylor(instance) * &
plasticState(phaseAt(ipc,ip,el))%state(1,phasememberAt(ipc,ip,el)))) &
**plastic_j2_n(instance)
Lp = Tstar_dev_33/norm_Tstar_dev * gamma_dot/plastic_j2_fTaylor(instance)
!--------------------------------------------------------------------------------------------------
! Calculation of the tangent of Lp
forall (k=1_pInt:3_pInt,l=1_pInt:3_pInt,m=1_pInt:3_pInt,n=1_pInt:3_pInt) &
dLp_dTstar_3333(k,l,m,n) = (plastic_j2_n(instance)-1.0_pReal) * &
Tstar_dev_33(k,l)*Tstar_dev_33(m,n) / squarenorm_Tstar_dev
forall (k=1_pInt:3_pInt,l=1_pInt:3_pInt) &
dLp_dTstar_3333(k,l,k,l) = dLp_dTstar_3333(k,l,k,l) + 1.0_pReal
forall (k=1_pInt:3_pInt,m=1_pInt:3_pInt) &
dLp_dTstar_3333(k,k,m,m) = dLp_dTstar_3333(k,k,m,m) - 1.0_pReal/3.0_pReal
dLp_dTstar99 = math_Plain3333to99(gamma_dot / plastic_j2_fTaylor(instance) * &
dLp_dTstar_3333 / norm_Tstar_dev)
end if
end subroutine plastic_j2_LpAndItsTangent
!--------------------------------------------------------------------------------------------------
!> @brief calculates the rate of change of microstructure
!--------------------------------------------------------------------------------------------------
subroutine plastic_j2_dotState(Tstar_v,ipc,ip,el)
use math, only: &
math_mul6x6
use material, only: &
phaseAt, phasememberAt, &
plasticState, &
material_phase, &
phase_plasticityInstance
implicit none
real(pReal), dimension(6), intent(in):: &
Tstar_v !< 2nd Piola Kirchhoff stress tensor in Mandel notation
integer(pInt), intent(in) :: &
ipc, & !< component-ID of integration point
ip, & !< integration point
el !< element
real(pReal), dimension(6) :: &
Tstar_dev_v !< deviatoric part of the 2nd Piola Kirchhoff stress tensor in Mandel notation
real(pReal) :: &
gamma_dot, & !< strainrate
hardening, & !< hardening coefficient
saturation, & !< saturation resistance
norm_Tstar_dev !< euclidean norm of Tstar_dev
integer(pInt) :: &
instance, & !< instance of my instance (unique number of my constitutive model)
of, & !< shortcut notation for offset position in state array
ph !< shortcut notation for phase ID (unique number of all phases, regardless of constitutive model)
of = phasememberAt(ipc,ip,el)
ph = phaseAt(ipc,ip,el)
instance = phase_plasticityInstance(material_phase(ipc,ip,el))
!--------------------------------------------------------------------------------------------------
! norm of deviatoric part of 2nd Piola-Kirchhoff stress
Tstar_dev_v(1:3) = Tstar_v(1:3) - sum(Tstar_v(1:3))/3.0_pReal
Tstar_dev_v(4:6) = Tstar_v(4:6)
norm_Tstar_dev = sqrt(math_mul6x6(Tstar_dev_v,Tstar_dev_v))
!--------------------------------------------------------------------------------------------------
! strain rate
gamma_dot = plastic_j2_gdot0(instance) * ( sqrt(1.5_pReal) * norm_Tstar_dev &
/ &!-----------------------------------------------------------------------------------
(plastic_j2_fTaylor(instance)*plasticState(ph)%state(1,of)) )**plastic_j2_n(instance)
!--------------------------------------------------------------------------------------------------
! hardening coefficient
if (abs(gamma_dot) > 1e-12_pReal) then
if (abs(plastic_j2_tausat_SinhFitA(instance)) <= tiny(0.0_pReal)) then
saturation = plastic_j2_tausat(instance)
else
saturation = ( plastic_j2_tausat(instance) &
+ ( log( ( gamma_dot / plastic_j2_tausat_SinhFitA(instance)&
)**(1.0_pReal / plastic_j2_tausat_SinhFitD(instance))&
+ sqrt( ( gamma_dot / plastic_j2_tausat_SinhFitA(instance) &
)**(2.0_pReal / plastic_j2_tausat_SinhFitD(instance)) &
+ 1.0_pReal ) &
) & ! asinh(K) = ln(K + sqrt(K^2 +1))
)**(1.0_pReal / plastic_j2_tausat_SinhFitC(instance)) &
/ ( plastic_j2_tausat_SinhFitB(instance) &
* (gamma_dot / plastic_j2_gdot0(instance))**(1.0_pReal / plastic_j2_n(instance)) &
) &
)
endif
hardening = ( plastic_j2_h0(instance) + plastic_j2_h0_slopeLnRate(instance) * log(gamma_dot) ) &
* abs( 1.0_pReal - plasticState(ph)%state(1,of)/saturation )**plastic_j2_a(instance) &
* sign(1.0_pReal, 1.0_pReal - plasticState(ph)%state(1,of)/saturation)
else
hardening = 0.0_pReal
endif
plasticState(ph)%dotState(1,of) = hardening * gamma_dot
plasticState(ph)%dotState(2,of) = gamma_dot
end subroutine plastic_j2_dotState
!--------------------------------------------------------------------------------------------------
!> @brief return array of constitutive results
!--------------------------------------------------------------------------------------------------
function plastic_j2_postResults(Tstar_v,ipc,ip,el)
use math, only: &
math_mul6x6
use material, only: &
material_phase, &
plasticState, &
phaseAt, phasememberAt, &
phase_plasticityInstance
implicit none
real(pReal), dimension(6), intent(in) :: &
Tstar_v !< 2nd Piola Kirchhoff stress tensor in Mandel notation
integer(pInt), intent(in) :: &
ipc, & !< component-ID of integration point
ip, & !< integration point
el !< element
real(pReal), dimension(plastic_j2_sizePostResults(phase_plasticityInstance(material_phase(ipc,ip,el)))) :: &
plastic_j2_postResults
real(pReal), dimension(6) :: &
Tstar_dev_v ! deviatoric part of the 2nd Piola Kirchhoff stress tensor in Mandel notation
real(pReal) :: &
norm_Tstar_dev ! euclidean norm of Tstar_dev
integer(pInt) :: &
instance, & !< instance of my instance (unique number of my constitutive model)
of, & !< shortcut notation for offset position in state array
ph, & !< shortcut notation for phase ID (unique number of all phases, regardless of constitutive model)
c, &
o
of = phasememberAt(ipc,ip,el)
ph = phaseAt(ipc,ip,el)
instance = phase_plasticityInstance(material_phase(ipc,ip,el))
!--------------------------------------------------------------------------------------------------
! calculate deviatoric part of 2nd Piola-Kirchhoff stress and its norm
Tstar_dev_v(1:3) = Tstar_v(1:3) - sum(Tstar_v(1:3))/3.0_pReal
Tstar_dev_v(4:6) = Tstar_v(4:6)
norm_Tstar_dev = sqrt(math_mul6x6(Tstar_dev_v,Tstar_dev_v))
c = 0_pInt
plastic_j2_postResults = 0.0_pReal
outputsLoop: do o = 1_pInt,plastic_j2_Noutput(instance)
select case(plastic_j2_outputID(o,instance))
case (flowstress_ID)
plastic_j2_postResults(c+1_pInt) = plasticState(ph)%state(1,of)
c = c + 1_pInt
case (strainrate_ID)
plastic_j2_postResults(c+1_pInt) = &
plastic_j2_gdot0(instance) * ( sqrt(1.5_pReal) * norm_Tstar_dev &
/ &!----------------------------------------------------------------------------------
(plastic_j2_fTaylor(instance) * plasticState(ph)%state(1,of)) ) ** plastic_j2_n(instance)
c = c + 1_pInt
end select
enddo outputsLoop
end function plastic_j2_postResults
end module plastic_j2

4
code/prec.f90
View File

@ -113,7 +113,9 @@ module prec
public :: &
prec_init, &
prec_isNaN
prec_isNaN, &
dEq, &
dNeq
contains

37
config/Phase_DisloKMC_Tungsten.config
View File

@ -1,37 +0,0 @@
### $Id$ ###
[Tungsten]
elasticity hooke
plasticity dislokmc
### Material parameters ###
lattice_structure bcc
C11 523.0e9 # From Marinica et al. Journal of Physics: Condensed Matter(2013)
C12 202.0e9
C44 161.0e9
grainsize 2.0e-5 # Average grain size [m] 2.0e-5
SolidSolutionStrength 0.0 # Strength due to elements in solid solution
### Dislocation glide parameters ###
#per family
Nslip 12 0
slipburgers 2.72e-10 # Burgers vector of slip system [m]
rhoedge0 1.0e12 # Initial edge dislocation density [m/m**3]
rhoedgedip0 1.0 # Initial edged dipole dislocation density [m/m**3]
Qedge 2.725e-19 # Activation energy for dislocation glide [J]
v0 3560.3 # Initial glide velocity [m/s](kmC)
p_slip 0.16 # p-exponent in glide velocity
q_slip 1.00 # q-exponent in glide velocity
u_slip 2.47 # u-exponent of stress pre-factor (kmC)
s_slip 0.97 # self hardening in glide velocity (kmC)
tau_peierls 2.03e9 # peierls stress [Pa]
#hardening
dipoleformationfactor 0 # to have hardening due to dipole formation off
CLambdaSlip 10.0 # Adj. parameter controlling dislocation mean free path
D0 4.0e-5 # Vacancy diffusion prefactor [m**2/s]
Qsd 4.5e-19 # Activation energy for climb [J]
Catomicvolume 1.0 # Adj. parameter controlling the atomic volume [in b]
Cedgedipmindistance 1.0 # Adj. parameter controlling the minimum dipole distance [in b]
interaction_slipslip 0.2 0.11 0.19 0.15 0.11 0.17

2
config/Phase_J2_AluminumIsotropic.config → config/Phase_Isotropic_AluminumIsotropic.config
View File

@ -3,7 +3,7 @@
# Kuo, J. C., Mikrostrukturmechanik von Bikristallen mit Kippkorngrenzen. Shaker-Verlag 2004. http://edoc.mpg.de/204079
elasticity hooke
plasticity j2
plasticity isotropic
(output) flowstress
(output) strainrate

373258
config/rollingTexture.linearODF
View File

File diff suppressed because it is too large Load Diff

4
installation/symlink_Processing.py
View File

@ -21,13 +21,13 @@ if not os.path.isdir(binDir):
#define ToDo list
processing_subDirs = ['pre','post','misc',]
processing_extensions = ['.py',]
processing_extensions = ['.py','.sh',]
for subDir in processing_subDirs:
theDir = os.path.abspath(os.path.join(baseDir,subDir))
for theFile in os.listdir(theDir):
if os.path.splitext(theFile)[1] in processing_extensions: # omit anything not fitting our script extensions (skip .py.bak, .py~, and the like)
if os.path.splitext(theFile)[1] in processing_extensions: # only consider files with proper extensions
src = os.path.abspath(os.path.join(theDir,theFile))
sym_link = os.path.abspath(os.path.join(binDir,os.path.splitext(theFile)[0]))

53
lib/damask/asciitable.py
View File

@ -25,7 +25,7 @@ class ASCIItable():
readonly = False, # no reading from file
):
self.__IO__ = {'output': [],
'buffered': buffered,
'buffered': buffered,
'labeled': labeled, # header contains labels
'labels': [], # labels according to file info
'readBuffer': [], # buffer to hold non-advancing reads
@ -35,18 +35,18 @@ class ASCIItable():
self.__IO__['inPlace'] = not outname and name and not readonly
if self.__IO__['inPlace']: outname = name + self.tmpext # transparently create tmp file
try:
self.__IO__['in'] = (open( name,'r') if os.access( name, os.R_OK) else None) if name else sys.stdin
self.__IO__['in'] = (open( name,'r') if os.access( name, os.R_OK) else None) if name else sys.stdin
except TypeError:
self.__IO__['in'] = name
try:
self.__IO__['out'] = (open(outname,'w') if (not os.path.isfile(outname) \
or os.access( outname, os.W_OK) \
) \
and (not self.__IO__['inPlace'] \
or not os.path.isfile(name) \
or os.access( name, os.W_OK) \
) else None) if outname else sys.stdout
self.__IO__['out'] = (open(outname,'w') if (not os.path.isfile(outname) or
os.access( outname, os.W_OK)
) and
(not self.__IO__['inPlace'] or
not os.path.isfile(name) or
os.access( name, os.W_OK)
) else None) if outname else sys.stdout
except TypeError:
self.__IO__['out'] = outname
@ -66,6 +66,14 @@ class ASCIItable():
except:
return 0.0
# ------------------------------------------------------------------
def _removeCRLF(self,
string):
try:
return string.replace('\n','').replace('\r','')
except:
return string
# ------------------------------------------------------------------
def close(self,
dismiss = False):
@ -243,9 +251,9 @@ class ASCIItable():
try:
for item in what: self.labels_append(item)
except:
self.labels += [str(what)]
self.labels += [self._removeCRLF(str(what))]
else:
self.labels += [what]
self.labels += [self._removeCRLF(what)]
self.__IO__['labeled'] = True # switch on processing (in particular writing) of labels
if reset: self.__IO__['labels'] = list(self.labels) # subsequent data_read uses current labels as data size
@ -272,7 +280,7 @@ class ASCIItable():
for label in labels:
if label is not None:
try:
idx.append(int(label)) # column given as integer number?
idx.append(int(label)-1) # column given as integer number?
except ValueError:
try:
idx.append(self.labels.index(label)) # locate string in label list
@ -283,7 +291,7 @@ class ASCIItable():
idx.append(-1) # not found...
else:
try:
idx = int(labels)
idx = int(labels)-1 # offset for python array indexing
except ValueError:
try:
idx = self.labels.index(labels)
@ -293,7 +301,7 @@ class ASCIItable():
except ValueError:
idx = None if labels is None else -1
return np.array(idx) if isinstance(idx,list) else idx
return np.array(idx) if isinstance(idx,Iterable) else idx
# ------------------------------------------------------------------
def label_dimension(self,
@ -312,7 +320,7 @@ class ASCIItable():
if label is not None:
myDim = -1
try: # column given as number?
idx = int(label)
idx = int(label)-1
myDim = 1 # if found has at least dimension 1
if self.labels[idx].startswith('1_'): # column has multidim indicator?
while idx+myDim < len(self.labels) and self.labels[idx+myDim].startswith("%i_"%(myDim+1)):
@ -331,7 +339,7 @@ class ASCIItable():
dim = -1 # assume invalid label
idx = -1
try: # column given as number?
idx = int(labels)
idx = int(labels)-1
dim = 1 # if found has at least dimension 1
if self.labels[idx].startswith('1_'): # column has multidim indicator?
while idx+dim < len(self.labels) and self.labels[idx+dim].startswith("%i_"%(dim+1)):
@ -345,7 +353,7 @@ class ASCIItable():
while idx+dim < len(self.labels) and self.labels[idx+dim].startswith("%i_"%(dim+1)):
dim += 1 # keep adding while going through object
return np.array(dim) if isinstance(dim,list) else dim
return np.array(dim) if isinstance(dim,Iterable) else dim
# ------------------------------------------------------------------
def label_indexrange(self,
@ -361,9 +369,10 @@ class ASCIItable():
start = self.label_index(labels)
dim = self.label_dimension(labels)
return map(lambda a,b: xrange(a,a+b), zip(start,dim)) if isinstance(labels, Iterable) and not isinstance(labels, str) \
else xrange(start,start+dim)
return np.hstack(map(lambda c: xrange(c[0],c[0]+c[1]), zip(start,dim))) \
if isinstance(labels, Iterable) and not isinstance(labels, str) \
else xrange(start,start+dim)
# ------------------------------------------------------------------
def info_append(self,
what):
@ -372,9 +381,9 @@ class ASCIItable():
try:
for item in what: self.info_append(item)
except:
self.info += [str(what)]
self.info += [self._removeCRLF(str(what))]
else:
self.info += [what]
self.info += [self._removeCRLF(what)]
# ------------------------------------------------------------------
def info_clear(self):

14
lib/damask/util.py
View File

@ -53,6 +53,20 @@ def report(who,what):
"""reports script and file name"""
croak( (emph(who) if who else '') + (': '+what if what else '') )
# -----------------------------
def report_geom(info,
what = ['grid','size','origin','homogenization','microstructures']):
"""reports (selected) geometry information"""
output = {
'grid' : 'grid a b c: {}'.format(' x '.join(map(str,info['grid' ]))),
'size' : 'size x y z: {}'.format(' x '.join(map(str,info['size' ]))),
'origin' : 'origin x y z: {}'.format(' : '.join(map(str,info['origin']))),
'homogenization' : 'homogenization: {}'.format(info['homogenization']),
'microstructures' : 'microstructures: {}'.format(info['microstructures']),
}
for item in what: croak(output[item.lower()])
# -----------------------------
def emph(what):
"""emphasizes string on screen"""

BIN
misc/DAMASK QR-Code.png
View File

Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 80 KiB

After

Width:  |  Height:  |  Size: 34 KiB

61
processing/post/addCauchyX.py
View File

@ -1,61 +0,0 @@
#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
import os,string,h5py
import numpy as np
from optparse import OptionParser
import damask
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
Add column(s) containing Cauchy stress based on given column(s) of
deformation gradient and first Piola--Kirchhoff stress.
""" + string.replace('$Id$','\n','\\n')
)
parser.add_option('-f','--defgrad', dest='defgrad', \
help='heading of columns containing deformation gradient [%default]')
parser.add_option('-p','--stress', dest='stress', \
help='heading of columns containing first Piola--Kirchhoff stress [%default]')
parser.add_option('-o','--output', dest='output', \
help='group containing requested data [%default]')
parser.set_defaults(defgrad = 'f')
parser.set_defaults(stress = 'p')
parser.set_defaults(output = 'crystallite')
(options,filenames) = parser.parse_args()
if options.defgrad is None or options.stress is None or options.output is None:
parser.error('missing data column...')
# ------------------------------------------ setup file handles ---------------------------------------
files = []
for name in filenames:
if os.path.exists(name):
files.append({'name':name, 'file':h5py.File(name,"a")})
# ------------------------------------------ loop over input files ------------------------------------
for myFile in files:
print(myFile['name'])
# ------------------------------------------ loop over increments -------------------------------------
for inc in myFile['file']['increments'].keys():
print("Current Increment: "+inc)
for instance in myFile['file']['increments/'+inc+'/'+options.output].keys():
dsets = myFile['file']['increments/'+inc+'/'+options.output+'/'+instance].keys()
if (options.defgrad in dsets and options.stress in dsets):
defgrad = myFile['file']['increments/'+inc+'/'+options.output+'/'+instance+'/'+options.defgrad]
stress = myFile['file']['increments/'+inc+'/'+options.output+'/'+instance+'/'+options.stress]
cauchy=np.zeros(np.shape(stress),'f')
for p in range(stress.shape[0]):
cauchy[p,...] = 1.0/np.linalg.det(defgrad[p,...])*np.dot(stress[p,...],defgrad[p,...].T) # [Cauchy] = (1/det(F)) * [P].[F_transpose]
cauchyFile = myFile['file']['increments/'+inc+'/'+options.output+'/'+instance].create_dataset('cauchy', data=cauchy)
cauchyFile.attrs['units'] = 'Pa'

2
processing/post/addCompatibilityMismatch.py
View File

@ -36,7 +36,7 @@ parser.add_option('--no-volume','-v',
dest = 'volume',
action = 'store_false',
help = 'omit volume mismatch')
parser.set_defaults(coords = 'ipinitialcoord',
parser.set_defaults(coords = 'pos',
defgrad = 'f',
shape = True,
volume = True,

10
processing/post/addCurl.py
View File

@ -71,18 +71,18 @@ Deals with both vector- and tensor-valued fields.
parser.add_option('-c','--coordinates',
dest = 'coords',
type = 'string', metavar='string',
help = 'column heading for coordinates [%default]')
type = 'string', metavar = 'string',
help = 'column label of coordinates [%default]')
parser.add_option('-v','--vector',
dest = 'vector',
action = 'extend', metavar = '<string LIST>',
help = 'heading of columns containing vector field values')
help = 'column label(s) of vector field values')
parser.add_option('-t','--tensor',
dest = 'tensor',
action = 'extend', metavar = '<string LIST>',
help = 'heading of columns containing tensor field values')
help = 'column label(s) of tensor field values')
parser.set_defaults(coords = 'ipinitialcoord',
parser.set_defaults(coords = 'pos',
)
(options,filenames) = parser.parse_args()

164
processing/post/addDeformedConfiguration.py
View File

@ -1,164 +0,0 @@
#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
import os,sys,math
import numpy as np
from optparse import OptionParser
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
#--------------------------------------------------------------------------------------------------
def deformedCoordsFFT(F,undeformed=False):
wgt = 1.0/grid.prod()
integrator = np.array([0.+1.j,0.+1.j,0.+1.j],'c16') * size/ 2.0 / math.pi
step = size/grid
F_fourier = np.fft.rfftn(F,axes=(0,1,2))
coords_fourier = np.zeros(F_fourier.shape[0:4],'c16')
if undeformed:
Favg=np.eye(3)
else:
Favg=np.real(F_fourier[0,0,0,:,:])*wgt
#--------------------------------------------------------------------------------------------------
# integration in Fourier space
k_s = np.zeros([3],'i')
for i in xrange(grid[2]):
k_s[2] = i
if(i > grid[2]//2 ): k_s[2] = k_s[2] - grid[2]
for j in xrange(grid[1]):
k_s[1] = j
if(j > grid[1]//2 ): k_s[1] = k_s[1] - grid[1]
for k in xrange(grid[0]//2+1):
k_s[0] = k
for m in xrange(3):
coords_fourier[i,j,k,m] = sum(F_fourier[i,j,k,m,0:3]*k_s*integrator)
if (any(k_s != 0)):
coords_fourier[i,j,k,0:3] /= -sum(k_s*k_s)
#--------------------------------------------------------------------------------------------------
# add average to scaled fluctuation and put (0,0,0) on (0,0,0)
coords = np.fft.irfftn(coords_fourier,F.shape[0:3],axes=(0,1,2))
offset_coords = np.dot(F[0,0,0,:,:],step/2.0) - scaling*coords[0,0,0,0:3]
for z in xrange(grid[2]):
for y in xrange(grid[1]):
for x in xrange(grid[0]):
coords[z,y,x,0:3] = scaling*coords[z,y,x,0:3] \
+ offset_coords \
+ np.dot(Favg,step*np.array([x,y,z]))
return coords
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options file[s]', description = """
Add deformed configuration of given initial coordinates.
Operates on periodic three-dimensional x,y,z-ordered data sets.
""", version = scriptID)
parser.add_option('-f', '--defgrad',dest='defgrad', metavar = 'string',
help='heading of deformation gradient columns [%default]')
parser.add_option('--reference', dest='undeformed', action='store_true',
help='map results to reference (undeformed) average configuration [%default]')
parser.add_option('--scaling', dest='scaling', action='extend', metavar = '<float LIST>',
help='scaling of fluctuation')
parser.add_option('-u', '--unitlength', dest='unitlength', type='float', metavar = 'float',
help='set unit length for 2D model [%default]')
parser.add_option('--coordinates', dest='coords', metavar='string',
help='column heading for coordinates [%default]')
parser.set_defaults(defgrad = 'f')
parser.set_defaults(coords = 'ipinitialcoord')
parser.set_defaults(scaling = [])
parser.set_defaults(undeformed = False)
parser.set_defaults(unitlength = 0.0)
(options,filenames) = parser.parse_args()
options.scaling += [1.0 for i in xrange(max(0,3-len(options.scaling)))]
scaling = map(float, options.scaling)
# --- 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)
# ------------------------------------------ read header ------------------------------------------
table.head_read()
# ------------------------------------------ sanity checks ----------------------------------------
errors = []
remarks = []
if table.label_dimension(options.coords) != 3: errors.append('coordinates {} are not a vector.'.format(options.coords))
else: colCoord = table.label_index(options.coords)
if table.label_dimension(options.defgrad) != 9: errors.append('deformation gradient {} is not a tensor.'.format(options.defgrad))
else: colF = table.label_index(options.defgrad)
if remarks != []: damask.util.croak(remarks)
if errors != []:
damask.util.croak(errors)
table.close(dismiss = True)
continue
# --------------- figure out size and grid ---------------------------------------------------------
table.data_readArray()
coords = [np.unique(table.data[:,colCoord+i]) for i in xrange(3)]
mincorner = np.array(map(min,coords))
maxcorner = np.array(map(max,coords))
grid = np.array(map(len,coords),'i')
size = grid/np.maximum(np.ones(3,'d'), grid-1.0) * (maxcorner-mincorner) # size from edge to edge = dim * n/(n-1)
size = np.where(grid > 1, size, min(size[grid > 1]/grid[grid > 1])) # spacing for grid==1 set to smallest among other spacings
N = grid.prod()
if N != len(table.data): errors.append('data count {} does not match grid {}x{}x{}.'.format(N,*grid))
if errors != []:
damask.util.croak(errors)
table.close(dismiss = True)
continue
# ------------------------------------------ assemble header ---------------------------------------
table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
for coord in xrange(3):
label = '{}_{}_{}'.format(coord+1,options.defgrad,options.coords)
if np.any(scaling) != 1.0: label+='_{}_{}_{}'.format(scaling)
if options.undeformed: label+='_undeformed'
table.labels_append([label]) # extend ASCII header with new labels
table.head_write()
# ------------------------------------------ read deformation gradient field -----------------------
centroids = deformedCoordsFFT(table.data[:,colF:colF+9].reshape(grid[2],grid[1],grid[0],3,3),
options.undeformed)
# ------------------------------------------ process data ------------------------------------------
table.data_rewind()
for z in xrange(grid[2]):
for y in xrange(grid[1]):
for x in xrange(grid[0]):
table.data_read()
table.data_append(list(centroids[z,y,x,:]))
table.data_write()
# ------------------------------------------ output finalization -----------------------------------
table.close() # close ASCII tables

221
processing/post/addDisplacement.py Executable file
View File

@ -0,0 +1,221 @@
#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
import os,sys,math
import numpy as np
import scipy.ndimage
from optparse import OptionParser
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
#--------------------------------------------------------------------------------------------------
def cell2node(cellData,grid):
nodeData = 0.0
datalen = np.array(cellData.shape[3:]).prod()
for i in xrange(datalen):
node = scipy.ndimage.convolve(cellData.reshape(tuple(grid)+(datalen,))[...,i],
np.ones((2,2,2))/8., # 2x2x2 neighborhood of cells
mode = 'wrap',
origin = -1, # offset to have cell origin as center
) # now averaged at cell origins
node = np.append(node,node[np.newaxis,0,:,:,...],axis=0) # wrap along z
node = np.append(node,node[:,0,np.newaxis,:,...],axis=1) # wrap along y
node = np.append(node,node[:,:,0,np.newaxis,...],axis=2) # wrap along x
nodeData = node[...,np.newaxis] if i==0 else np.concatenate((nodeData,node[...,np.newaxis]),axis=-1)
return nodeData
#--------------------------------------------------------------------------------------------------
def displacementAvgFFT(F,grid,size,nodal=False,transformed=False):
"""calculate average cell center (or nodal) displacement for deformation gradient field specified in each grid cell"""
if nodal:
x, y, z = np.meshgrid(np.linspace(0,size[0],1+grid[0]),
np.linspace(0,size[1],1+grid[1]),
np.linspace(0,size[2],1+grid[2]),
indexing = 'ij')
else:
x, y, z = np.meshgrid(np.linspace(0,size[0],grid[0],endpoint=False),
np.linspace(0,size[1],grid[1],endpoint=False),
np.linspace(0,size[2],grid[2],endpoint=False),
indexing = 'ij')
origCoords = np.concatenate((z[:,:,:,None],y[:,:,:,None],x[:,:,:,None]),axis = 3)
F_fourier = F if transformed else np.fft.rfftn(F,axes=(0,1,2)) # transform or use provided data
Favg = np.real(F_fourier[0,0,0,:,:])/grid.prod() # take zero freq for average
avgDisplacement = np.einsum('ml,ijkl->ijkm',Favg-np.eye(3),origCoords) # dX = Favg.X
return avgDisplacement
#--------------------------------------------------------------------------------------------------
def displacementFluctFFT(F,grid,size,nodal=False,transformed=False):
"""calculate cell center (or nodal) displacement for deformation gradient field specified in each grid cell"""
integrator = 0.5j * size / math.pi
kk, kj, ki = np.meshgrid(np.where(np.arange(grid[2])>grid[2]//2,np.arange(grid[2])-grid[2],np.arange(grid[2])),
np.where(np.arange(grid[1])>grid[1]//2,np.arange(grid[1])-grid[1],np.arange(grid[1])),
np.arange(grid[0]//2+1),
indexing = 'ij')
k_s = np.concatenate((ki[:,:,:,None],kj[:,:,:,None],kk[:,:,:,None]),axis = 3)
k_sSquared = np.einsum('...l,...l',k_s,k_s)
k_sSquared[0,0,0] = 1.0 # ignore global average frequency
#--------------------------------------------------------------------------------------------------
# integration in Fourier space
displacement_fourier = -np.einsum('ijkml,ijkl,l->ijkm',
F if transformed else np.fft.rfftn(F,axes=(0,1,2)),
k_s,
integrator,
) / k_sSquared[...,np.newaxis]
#--------------------------------------------------------------------------------------------------
# backtransformation to real space
displacement = np.fft.irfftn(displacement_fourier,grid,axes=(0,1,2))
return cell2node(displacement,grid) if nodal else displacement
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options file[s]', description = """
Add displacments resulting from deformation gradient field.
Operates on periodic three-dimensional x,y,z-ordered data sets.
Outputs at cell centers or cell nodes (into separate file).
""", version = scriptID)
parser.add_option('-f',
'--defgrad',
dest = 'defgrad',
metavar = 'string',
help = 'column label of deformation gradient [%default]')
parser.add_option('-p',
'--pos', '--position',
dest = 'coords',
metavar = 'string',
help = 'label of coordinates [%default]')
parser.add_option('--nodal',
dest = 'nodal',
action = 'store_true',
help = 'output nodal (instad of cell-centered) displacements')
parser.set_defaults(defgrad = 'f',
coords = 'pos',
nodal = False,
)
(options,filenames) = parser.parse_args()
# --- loop over input files -------------------------------------------------------------------------
if filenames == []: filenames = [None]
for name in filenames:
try: table = damask.ASCIItable(name = name,
outname = (os.path.splitext(name)[0] +
'_nodal' +
os.path.splitext(name)[1]) if (options.nodal and name) else None,
buffered = False)
except: continue
damask.util.report(scriptName,name)
# ------------------------------------------ read header ------------------------------------------
table.head_read()
# ------------------------------------------ sanity checks ----------------------------------------
errors = []
remarks = []
if table.label_dimension(options.defgrad) != 9:
errors.append('deformation gradient "{}" is not a 3x3 tensor.'.format(options.defgrad))
coordDim = table.label_dimension(options.coords)
if not 3 >= coordDim >= 1:
errors.append('coordinates "{}" need to have one, two, or three dimensions.'.format(options.coords))
elif coordDim < 3:
remarks.append('appending {} dimension{} to coordinates "{}"...'.format(3-coordDim,
's' if coordDim < 2 else '',
options.coords))
if remarks != []: damask.util.croak(remarks)
if errors != []:
damask.util.croak(errors)
table.close(dismiss=True)
continue
# --------------- figure out size and grid ---------------------------------------------------------
table.data_readArray([options.defgrad,options.coords])
table.data_rewind()
if len(table.data.shape) < 2: table.data.shape += (1,) # expand to 2D shape
if table.data[:,9:].shape[1] < 3:
table.data = np.hstack((table.data,
np.zeros((table.data.shape[0],
3-table.data[:,9:].shape[1]),dtype='f'))) # fill coords up to 3D with zeros
coords = [np.unique(table.data[:,9+i]) for i in xrange(3)]
mincorner = np.array(map(min,coords))
maxcorner = np.array(map(max,coords))
grid = np.array(map(len,coords),'i')
size = grid/np.maximum(np.ones(3,'d'), grid-1.0) * (maxcorner-mincorner) # size from edge to edge = dim * n/(n-1)
size = np.where(grid > 1, size, min(size[grid > 1]/grid[grid > 1])) # spacing for grid==1 set to smallest among other spacings
N = grid.prod()
if N != len(table.data): errors.append('data count {} does not match grid {}x{}x{}.'.format(N,*grid))
if errors != []:
damask.util.croak(errors)
table.close(dismiss = True)
continue
# ------------------------------------------ process data ------------------------------------------
F_fourier = np.fft.rfftn(table.data[:,:9].reshape(grid[2],grid[1],grid[0],3,3),axes=(0,1,2)) # perform transform only once...
displacement = displacementFluctFFT(F_fourier,grid,size,options.nodal,transformed=True)
avgDisplacement = displacementAvgFFT (F_fourier,grid,size,options.nodal,transformed=True)
# ------------------------------------------ assemble header ---------------------------------------
if options.nodal:
table.info_clear()
table.labels_clear()
table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
table.labels_append((['{}_pos' .format(i+1) for i in xrange(3)] if options.nodal else []) +
['{}_avg({}).{}' .format(i+1,options.defgrad,options.coords) for i in xrange(3)] +
['{}_fluct({}).{}'.format(i+1,options.defgrad,options.coords) for i in xrange(3)] )
table.head_write()
# ------------------------------------------ output data -------------------------------------------
zrange = np.linspace(0,size[2],1+grid[2]) if options.nodal else xrange(grid[2])
yrange = np.linspace(0,size[1],1+grid[1]) if options.nodal else xrange(grid[1])
xrange = np.linspace(0,size[0],1+grid[0]) if options.nodal else xrange(grid[0])
for i,z in enumerate(zrange):
for j,y in enumerate(yrange):
for k,x in enumerate(xrange):
if options.nodal: table.data_clear()
else: table.data_read()
table.data_append([x,y,z] if options.nodal else [])
table.data_append(list(avgDisplacement[i,j,k,:]))
table.data_append(list( displacement[i,j,k,:]))
table.data_write()
# ------------------------------------------ output finalization -----------------------------------
table.close() # close ASCII tables

8
processing/post/addDivergence.py
View File

@ -58,17 +58,17 @@ Deals with both vector- and tensor-valued fields.
parser.add_option('-c','--coordinates',
dest = 'coords',
type = 'string', metavar = 'string',
help = 'column heading for coordinates [%default]')
help = 'column label of coordinates [%default]')
parser.add_option('-v','--vector',
dest = 'vector',
action = 'extend', metavar = '<string LIST>',
help = 'heading of columns containing vector field values')
help = 'column label(s) of vector field values')
parser.add_option('-t','--tensor',
dest = 'tensor',
action = 'extend', metavar = '<string LIST>',
help = 'heading of columns containing tensor field values')
help = 'column label(s) of tensor field values')
parser.set_defaults(coords = 'ipinitialcoord',
parser.set_defaults(coords = 'pos',
)
(options,filenames) = parser.parse_args()

74
processing/post/addEuclideanDistance.py
View File

@ -88,20 +88,32 @@ Add column(s) containing Euclidean distance to grain structural features: bounda
""", version = scriptID)
parser.add_option('-c','--coordinates', dest='coords', metavar='string',
help='column heading for coordinates [%default]')
parser.add_option('-i','--identifier', dest='id', metavar = 'string',
help='heading of column containing grain identifier [%default]')
parser.add_option('-t','--type', dest = 'type', action = 'extend', metavar = '<string LIST>',
help = 'feature type {%s} '%(', '.join(map(lambda x:'/'.join(x['names']),features))) )
parser.add_option('-n','--neighborhood',dest='neighborhood', choices = neighborhoods.keys(), metavar = 'string',
help = 'type of neighborhood [neumann] {%s}'%(', '.join(neighborhoods.keys())))
parser.add_option('-s', '--scale', dest = 'scale', type = 'float', metavar='float',
parser.add_option('-p',
'--pos', '--position',
dest = 'coords', metavar = 'string',
help = 'label of coordinates [%default]')
parser.add_option('-i',
'--id', '--identifier',
dest = 'id', metavar = 'string',
help='label of grain identifier [%default]')
parser.add_option('-t',
'--type',
dest = 'type', action = 'extend', metavar = '<string LIST>',
help = 'feature type {{{}}} '.format(', '.join(map(lambda x:'/'.join(x['names']),features))) )
parser.add_option('-n',
'--neighborhood',
dest = 'neighborhood', choices = neighborhoods.keys(), metavar = 'string',
help = 'neighborhood type [neumann] {{{}}}'.format(', '.join(neighborhoods.keys())))
parser.add_option('-s',
'--scale',
dest = 'scale', type = 'float', metavar = 'float',
help = 'voxel size [%default]')
parser.set_defaults(coords = 'ipinitialcoord')
parser.set_defaults(id = 'texture')
parser.set_defaults(neighborhood = 'neumann')
parser.set_defaults(scale = 1.0)
parser.set_defaults(coords = 'pos',
id = 'texture',
neighborhood = 'neumann',
scale = 1.0,
)
(options,filenames) = parser.parse_args()
@ -110,7 +122,7 @@ if options.type is None:
if not set(options.type).issubset(set(list(itertools.chain(*map(lambda x: x['names'],features))))):
parser.error('type must be chosen from (%s).'%(', '.join(map(lambda x:'|'.join(x['names']),features))) )
if 'biplane' in options.type and 'boundary' in options.type:
parser.error("only one from aliases 'biplane' and 'boundary' possible.")
parser.error('only one from aliases "biplane" and "boundary" possible.')
feature_list = []
for i,feature in enumerate(features):
@ -125,10 +137,8 @@ for i,feature in enumerate(features):
if filenames == []: filenames = [None]
for name in filenames:
try:
table = damask.ASCIItable(name = name, buffered = False)
except:
continue
try: table = damask.ASCIItable(name = name, buffered = False)
except: continue
damask.util.report(scriptName,name)
# ------------------------------------------ read header ------------------------------------------
@ -141,9 +151,11 @@ for name in filenames:
remarks = []
column = {}
if table.label_dimension(options.coords) != 3: errors.append('coordinates {} are not a vector.'.format(options.coords))
coordDim = table.label_dimension(options.coords)
if not 3 >= coordDim >= 1:
errors.append('coordinates "{}" need to have one, two, or three dimensions.'.format(options.coords))
else: coordCol = table.label_index(options.coords)
if table.label_dimension(options.id) != 1: errors.append('grain identifier {} not found.'.format(options.id))
else: idCol = table.label_index(options.id)
@ -164,18 +176,18 @@ for name in filenames:
table.data_readArray()
coords = [{},{},{}]
for i in xrange(len(table.data)):
for j in xrange(3):
coords[j][str(table.data[i,coordCol+j])] = True
grid = np.array(map(len,coords),'i')
size = grid/np.maximum(np.ones(3,'d'),grid-1.0)* \
np.array([max(map(float,coords[0].keys()))-min(map(float,coords[0].keys())),\
max(map(float,coords[1].keys()))-min(map(float,coords[1].keys())),\
max(map(float,coords[2].keys()))-min(map(float,coords[2].keys())),\
],'d') # size from bounding box, corrected for cell-centeredness
coords = [np.unique(table.data[:,coordCol+i]) for i in xrange(coordDim)]
mincorner = np.array(map(min,coords))
maxcorner = np.array(map(max,coords))
grid = np.array(map(len,coords)+[1]*(3-len(coords)),'i')
size = np.where(grid > 1, size, min(size[grid > 1]/grid[grid > 1])) # spacing for grid==1 set to smallest among other spacings
N = grid.prod()
if N != len(table.data): errors.append('data count {} does not match grid {}.'.format(N,'x'.join(map(str,grid))))
if errors != []:
damask.util.croak(errors)
table.close(dismiss = True)
continue
# ------------------------------------------ process value field -----------------------------------

14
processing/post/addGradient.py
View File

@ -9,7 +9,9 @@ import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
#--------------------------------------------------------------------------------------------------
def gradFFT(geomdim,field):
grid = np.array(np.shape(field)[2::-1])
N = grid.prod() # field size
n = np.array(np.shape(field)[3:]).prod() # data size
@ -17,7 +19,7 @@ def gradFFT(geomdim,field):
elif n == 1: dataType = 'scalar'
field_fourier = np.fft.fftpack.rfftn(field,axes=(0,1,2))
grad_fourier = np.zeros(field_fourier.shape+(3,),'c16')
grad_fourier = np.zeros(field_fourier.shape+(3,),'c16')
# differentiation in Fourier space
k_s = np.zeros([3],'i')
@ -61,17 +63,17 @@ Deals with both vector- and scalar fields.
parser.add_option('-c','--coordinates',
dest = 'coords',
type = 'string', metavar='string',
help = 'column heading for coordinates [%default]')
help = 'column label of coordinates [%default]')
parser.add_option('-v','--vector',
dest = 'vector',
action = 'extend', metavar = '<string LIST>',
help = 'heading of columns containing vector field values')
help = 'column label(s) of vector field values')
parser.add_option('-s','--scalar',
dest = 'scalar',
action = 'extend', metavar = '<string LIST>',
help = 'heading of columns containing scalar field values')
help = 'column label(s) of scalar field values')
parser.set_defaults(coords = 'ipinitialcoord',
parser.set_defaults(coords = 'pos',
)
(options,filenames) = parser.parse_args()
@ -96,7 +98,7 @@ for name in filenames:
items = {
'scalar': {'dim': 1, 'shape': [1], 'labels':options.scalar, 'active':[], 'column': []},
'vector': {'dim': 3, 'shape': [3], 'labels':options.vector, 'active':[], 'column': []},
'vector': {'dim': 3, 'shape': [3], 'labels':options.vector, 'active':[], 'column': []},
}
errors = []
remarks = []

161
processing/post/addGrainID.py
View File

@ -5,7 +5,6 @@ import numpy as np
import damask
from optparse import OptionParser
from scipy import spatial
from collections import defaultdict
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
@ -16,53 +15,61 @@ Add grain index based on similiarity of crystal lattice orientation.
""", version = scriptID)
parser.add_option('-r', '--radius',
parser.add_option('-r',
'--radius',
dest = 'radius',
type = 'float', metavar = 'float',
help = 'search radius')
parser.add_option('-d', '--disorientation',
parser.add_option('-d',
'--disorientation',
dest = 'disorientation',
type = 'float', metavar = 'float',
help = 'disorientation threshold per grain [%default] (degrees)')
parser.add_option('-s', '--symmetry',
help = 'disorientation threshold in degrees [%default]')
parser.add_option('-s',
'--symmetry',
dest = 'symmetry',
type = 'string', metavar = 'string',
help = 'crystal symmetry [%default]')
parser.add_option('-e', '--eulers',
parser.add_option('-e',
'--eulers',
dest = 'eulers',
type = 'string', metavar = 'string',
help = 'Euler angles')
parser.add_option( '--degrees',
help = 'label of Euler angles')
parser.add_option('--degrees',
dest = 'degrees',
action = 'store_true',
help = 'Euler angles are given in degrees [%default]')
parser.add_option('-m', '--matrix',
parser.add_option('-m',
'--matrix',
dest = 'matrix',
type = 'string', metavar = 'string',
help = 'orientation matrix')
help = 'label of orientation matrix')
parser.add_option('-a',
dest = 'a',
type = 'string', metavar = 'string',
help = 'crystal frame a vector')
help = 'label of crystal frame a vector')
parser.add_option('-b',
dest = 'b',
type = 'string', metavar = 'string',
help = 'crystal frame b vector')
help = 'label of crystal frame b vector')
parser.add_option('-c',
dest = 'c',
type = 'string', metavar = 'string',
help = 'crystal frame c vector')
parser.add_option('-q', '--quaternion',
help = 'label of crystal frame c vector')
parser.add_option('-q',
'--quaternion',
dest = 'quaternion',
type = 'string', metavar = 'string',
help = 'quaternion')
parser.add_option('-p', '--position',
dest = 'coords',
help = 'label of quaternion')
parser.add_option('-p',
'--pos', '--position',
dest = 'pos',
type = 'string', metavar = 'string',
help = 'spatial position of voxel [%default]')
help = 'label of coordinates [%default]')
parser.set_defaults(symmetry = 'cubic',
coords = 'pos',
parser.set_defaults(disorientation = 5,
symmetry = 'cubic',
pos = 'pos',
degrees = False,
)
@ -86,17 +93,16 @@ if np.sum(input) != 1: parser.error('needs exactly one input format.')
(options.matrix,9,'matrix'),
(options.quaternion,4,'quaternion'),
][np.where(input)[0][0]] # select input label that was requested
toRadians = np.pi/180.0 if options.degrees else 1.0 # rescale degrees to radians
cos_disorientation = np.cos(options.disorientation/2.*toRadians)
toRadians = np.pi/180.0 if options.degrees else 1.0 # rescale degrees to radians
cos_disorientation = np.cos(np.radians(options.disorientation/2.)) # cos of half the disorientation angle
# --- loop over input files -------------------------------------------------------------------------
if filenames == []: filenames = [None]
for name in filenames:
try:
table = damask.ASCIItable(name = name,
buffered = False)
try: table = damask.ASCIItable(name = name,
buffered = False)
except: continue
damask.util.report(scriptName,name)
@ -109,8 +115,10 @@ for name in filenames:
errors = []
remarks = []
if table.label_dimension(options.coords) != 3: errors.append('coordinates {} are not a vector.'.format(options.coords))
if not np.all(table.label_dimension(label) == dim): errors.append('input {} does not have dimension {}.'.format(label,dim))
if not 3 >= table.label_dimension(options.pos) >= 1:
errors.append('coordinates "{}" need to have one, two, or three dimensions.'.format(options.pos))
if not np.all(table.label_dimension(label) == dim):
errors.append('input "{}" does not have dimension {}.'.format(label,dim))
else: column = table.label_index(label)
if remarks != []: damask.util.croak(remarks)
@ -122,8 +130,10 @@ for name in filenames:
# ------------------------------------------ assemble header ---------------------------------------
table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
table.labels_append('grainID_{}@{}'.format(label,
options.disorientation if options.degrees else np.degrees(options.disorientation))) # report orientation source and disorientation in degrees
table.labels_append('grainID_{}@{:g}'.format('+'.join(label)
if isinstance(label, (list,tuple))
else label,
options.disorientation)) # report orientation source and disorientation
table.head_write()
# ------------------------------------------ process data ------------------------------------------
@ -137,7 +147,7 @@ for name in filenames:
bg.set_message('reading positions...')
table.data_readArray(options.coords) # read position vectors
table.data_readArray(options.pos) # read position vectors
grainID = -np.ones(len(table.data),dtype=int)
start = tick = time.clock()
@ -162,7 +172,7 @@ for name in filenames:
time_delta = (time.clock()-tick) * (len(grainID) - p) / p
bg.set_message('(%02i:%02i:%02i) processing point %i of %i (grain count %i)...'\
%(time_delta//3600,time_delta%3600//60,time_delta%60,p,len(grainID),len(orientations)))
%(time_delta//3600,time_delta%3600//60,time_delta%60,p,len(grainID),np.count_nonzero(memberCounts)))
if inputtype == 'eulers':
o = damask.Orientation(Eulers = np.array(map(float,table.data[column:column+3]))*toRadians,
@ -179,84 +189,51 @@ for name in filenames:
o = damask.Orientation(quaternion = np.array(map(float,table.data[column:column+4])),
symmetry = options.symmetry).reduced()
matched = False
matched = False
alreadyChecked = {}
candidates = []
bestDisorientation = damask.Quaternion([0,0,0,1]) # initialize to 180 deg rotation as worst case
# check against last matched needs to be really picky. best would be to exclude jumps across the poke (checking distance between last and me?)
# when walking through neighborhood first check whether grainID of that point has already been tested, if yes, skip!
if matchedID != -1: # has matched before?
matched = (o.quaternion.conjugated() * orientations[matchedID].quaternion).w > cos_disorientation
if not matched:
alreadyChecked = {}
bestDisorientation = damask.Quaternion([0,0,0,1]) # initialize to 180 deg rotation as worst case
for i in kdtree.query_ball_point(kdtree.data[p],options.radius): # check all neighboring points
gID = grainID[i]
if gID != -1 and gID not in alreadyChecked: # indexed point belonging to a grain not yet tested?
alreadyChecked[gID] = True # remember not to check again
disorientation = o.disorientation(orientations[gID],SST = False)[0] # compare against other orientation
if disorientation.quaternion.w > cos_disorientation and \
disorientation.quaternion.w >= bestDisorientation.w: # within threshold and betterthan current best?
for i in kdtree.query_ball_point(kdtree.data[p],options.radius): # check all neighboring points
gID = grainID[i]
if gID != -1 and gID not in alreadyChecked: # indexed point belonging to a grain not yet tested?
alreadyChecked[gID] = True # remember not to check again
disorientation = o.disorientation(orientations[gID],SST = False)[0] # compare against other orientation
if disorientation.quaternion.w > cos_disorientation: # within threshold ...
candidates.append(gID) # remember as potential candidate
if disorientation.quaternion.w >= bestDisorientation.w: # ... and better than current best?
matched = True
matchedID = gID # remember that grain
bestDisorientation = disorientation.quaternion
if not matched: # no match -> new grain found
memberCounts += [1] # start new membership counter
if matched: # did match existing grain
memberCounts[matchedID] += 1
if len(candidates) > 1: # ambiguity in grain identification?
largestGrain = sorted(candidates,key=lambda x:memberCounts[x])[-1] # find largest among potential candidate grains
matchedID = largestGrain
for c in [c for c in candidates if c != largestGrain]: # loop over smaller candidates
memberCounts[largestGrain] += memberCounts[c] # reassign member count of smaller to largest
memberCounts[c] = 0
grainID = np.where(np.in1d(grainID,candidates), largestGrain, grainID) # relabel grid points of smaller candidates as largest one
else: # no match -> new grain found
orientations += [o] # initialize with current orientation
memberCounts += [1] # start new membership counter
matchedID = g
g += 1 # increment grain counter
else: # did match existing grain
memberCounts[matchedID] += 1
grainID[p] = matchedID # remember grain index assigned to point
p += 1 # increment point
bg.set_message('identifying similar orientations among {} grains...'.format(len(orientations)))
memberCounts = np.array(memberCounts)
similarOrientations = [[] for i in xrange(len(orientations))]
for i,orientation in enumerate(orientations[:-1]): # compare each identified orientation...
for j in xrange(i+1,len(orientations)): # ...against all others that were defined afterwards
if orientation.disorientation(orientations[j],SST = False)[0].quaternion.w > cos_disorientation: # similar orientations in both grainIDs?
similarOrientations[i].append(j) # remember in upper triangle...
similarOrientations[j].append(i) # ...and lower triangle of matrix
if similarOrientations[i] != []:
bg.set_message('grainID {} is as: {}'.format(i,' '.join(map(str,similarOrientations[i]))))
stillShifting = True
while stillShifting:
stillShifting = False
tick = time.clock()
for p,gID in enumerate(grainID): # walk through all points
if p > 0 and p % 1000 == 0:
time_delta = (time.clock()-tick) * (len(grainID) - p) / p
bg.set_message('(%02i:%02i:%02i) shifting ID of point %i out of %i (grain count %i)...'
%(time_delta//3600,time_delta%3600//60,time_delta%60,p,len(grainID),len(orientations)))
if similarOrientations[gID] != []: # orientation of my grainID is similar to someone else?
similarNeighbors = defaultdict(int) # frequency of neighboring grainIDs sharing my orientation
for i in kdtree.query_ball_point(kdtree.data[p],options.radius): # check all neighboring point
if grainID[i] in similarOrientations[gID]: # neighboring point shares my orientation?
similarNeighbors[grainID[i]] += 1 # remember its grainID
if similarNeighbors != {}: # found similar orientation(s) in neighborhood
candidates = np.array([gID]+similarNeighbors.keys()) # possible replacement grainIDs for me
grainID[p] = candidates[np.argsort(memberCounts[candidates])[-1]] # adopt ID that is most frequent in overall dataset
memberCounts[gID] -= 1 # my former ID loses one fellow
memberCounts[grainID[p]] += 1 # my new ID gains one fellow
bg.set_message('{}:{} --> {}'.format(p,gID,grainID[p])) # report switch of grainID
stillShifting = True
grainIDs = np.where(np.array(memberCounts) > 0)[0] # identify "live" grain identifiers
packingMap = dict(zip(list(grainIDs),range(len(grainIDs)))) # map to condense into consecutive IDs
table.data_rewind()
outputAlive = True
p = 0
while outputAlive and table.data_read(): # read next data line of ASCII table
table.data_append(1+grainID[p]) # add grain ID
table.data_append(1+packingMap[grainID[p]]) # add (condensed) grain ID
outputAlive = table.data_write() # output processed line
p += 1

56
processing/post/addInfo.py Executable file
View File

@ -0,0 +1,56 @@
#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
import os
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 = """
Add info lines to ASCIItable header.
""", version = scriptID)
parser.add_option('-i',
'--info',
dest = 'info', action = 'extend', metavar = '<string LIST>',
help = 'items to add')
parser.set_defaults(info = [],
)
(options,filenames) = parser.parse_args()
# --- 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)
# ------------------------------------------ assemble header ---------------------------------------
table.head_read()
table.info_append(options.info)
table.head_write()
# ------------------------------------------ pass through data -------------------------------------
outputAlive = True
while outputAlive and table.data_read(): # read next data line of ASCII table
outputAlive = table.data_write() # output processed line
# ------------------------------------------ output finalization -----------------------------------
table.close() # close ASCII tables

4
processing/post/addSchmidfactors.py
View File

@ -239,7 +239,9 @@ for name in filenames:
# ------------------------------------------ assemble header ---------------------------------------
table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
table.labels_append(['{id}_S[{direction[0]:.1g}_{direction[1]:.1g}_{direction[2]:.1g}]({normal[0]:.1g}_{normal[1]:.1g}_{normal[2]:.1g})'\
table.labels_append(['{id}_'
'S[{direction[0]:.1g}_{direction[1]:.1g}_{direction[2]:.1g}]'
'({normal[0]:.1g}_{normal[1]:.1g}_{normal[2]:.1g})'\
.format( id = i+1,
normal = theNormal,
direction = theDirection,

15
processing/post/averageDown.py
View File

@ -22,7 +22,7 @@ Average each data block of size 'packing' into single values thus reducing the f
parser.add_option('-c','--coordinates',
dest = 'coords',
type = 'string', metavar = 'string',
help = 'column heading for coordinates [%default]')
help = 'column label of coordinates [%default]')
parser.add_option('-p','--packing',
dest = 'packing',
type = 'int', nargs = 3, metavar = 'int int int',
@ -39,7 +39,7 @@ parser.add_option('-s', '--size',
dest = 'size',
type = 'float', nargs = 3, metavar = 'float float float',
help = 'size in x,y,z [autodetect]')
parser.set_defaults(coords = 'ipinitialcoord',
parser.set_defaults(coords = 'pos',
packing = (2,2,2),
shift = (0,0,0),
grid = (0,0,0),
@ -59,11 +59,10 @@ if any(shift != 0): prefix += 'shift{:+}{:+}{:+}_'.format(*shift)
if filenames == []: filenames = [None]
for name in filenames:
try:
table = damask.ASCIItable(name = name,
outname = os.path.join(os.path.dirname(name),
prefix+os.path.basename(name)) if name else name,
buffered = False)
try: table = damask.ASCIItable(name = name,
outname = os.path.join(os.path.dirname(name),
prefix+os.path.basename(name)) if name else name,
buffered = False)
except: continue
damask.util.report(scriptName,name)
@ -75,7 +74,6 @@ for name in filenames:
errors = []
remarks = []
colCoord = None
if table.label_dimension(options.coords) != 3: errors.append('coordinates {} are not a vector.'.format(options.coords))
else: colCoord = table.label_index(options.coords)
@ -86,7 +84,6 @@ for name in filenames:
table.close(dismiss = True)
continue
# ------------------------------------------ assemble header ---------------------------------------
table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))

12
processing/post/averageTable.py
View File

@ -37,10 +37,14 @@ if options.label is None:
if filenames == []: filenames = [None]
for name in filenames:
try:
table = damask.ASCIItable(name = name,
outname = options.label+'_averaged_'+name if name else name,
buffered = False)
damask.util.croak(name)
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)

97
processing/post/blowUp.py
View File

@ -19,84 +19,83 @@ to resolution*packing.
""", version = scriptID)
parser.add_option('-c','--coordinates', dest='coords', metavar='string',
help='column heading for coordinates [%default]')
parser.add_option('-p','--packing', dest='packing', type='int', nargs=3, metavar='int int int',
help='dimension of packed group [%default]')
parser.add_option('-g','--grid', dest='resolution', type='int', nargs=3, metavar='int int int',
help='resolution in x,y,z [autodetect]')
parser.add_option('-s','--size', dest='dimension', type='float', nargs=3, metavar='int int int',
help='dimension in x,y,z [autodetect]')
parser.set_defaults(coords = 'ipinitialcoord')
parser.set_defaults(packing = (2,2,2))
parser.set_defaults(grid = (0,0,0))
parser.set_defaults(size = (0.0,0.0,0.0))
parser.add_option('-c','--coordinates',
dest = 'coords', metavar = 'string',
help = 'column label of coordinates [%default]')
parser.add_option('-p','--packing',
dest = 'packing', type = 'int', nargs = 3, metavar = 'int int int',
help = 'dimension of packed group [%default]')
parser.add_option('-g','--grid',
dest = 'resolution', type = 'int', nargs = 3, metavar = 'int int int',
help = 'resolution in x,y,z [autodetect]')
parser.add_option('-s','--size',
dest = 'dimension', type = 'float', nargs = 3, metavar = 'int int int',
help = 'dimension in x,y,z [autodetect]')
parser.set_defaults(coords = 'pos',
packing = (2,2,2),
grid = (0,0,0),
size = (0.0,0.0,0.0),
)
(options,filenames) = parser.parse_args()
options.packing = np.array(options.packing)
prefix = 'blowUp%ix%ix%i_'%(options.packing[0],options.packing[1],options.packing[2])
prefix = 'blowUp{}x{}x{}_'.format(*options.packing)
# --- loop over input files -------------------------------------------------------------------------
if filenames == []: filenames = [None]
for name in filenames:
try:
table = damask.ASCIItable(name = name,
outname = os.path.join(os.path.dirname(name),
prefix+ \
os.path.basename(name)) if name else name,
buffered = False)
try: table = damask.ASCIItable(name = name,
outname = os.path.join(os.path.dirname(name),
prefix+os.path.basename(name)) if name else name,
buffered = False)
except: continue
damask.util.report(scriptName,name)
# ------------------------------------------ read header ------------------------------------------
table.head_read()
errors = []
# ------------------------------------------ sanity checks ----------------------------------------
if table.label_dimension(options.coords) != 3:
damask.util.croak('coordinates {} are not a vector.'.format(options.coords))
errors = []
remarks = []
if table.label_dimension(options.coords) != 3: errors.append('coordinates {} are not a vector.'.format(options.coords))
else: colCoord = table.label_index(options.coords)
colElem = table.label_index('elem')
if remarks != []: damask.util.croak(remarks)
if errors != []:
damask.util.croak(errors)
table.close(dismiss = True)
continue
else:
coordCol = table.label_index(options.coords)
# ------------------------------------------ assemble header --------------------------------------
table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
# --------------- figure out size and grid ---------------------------------------------------------
table.data_readArray()
coords = [{},{},{}]
for i in xrange(len(table.data)):
for j in xrange(3):
coords[j][str(table.data[i,coordCol+j])] = True
grid = np.array(map(len,coords),'i')
size = grid/np.maximum(np.ones(3,'d'),grid-1.0)* \
np.array([max(map(float,coords[0].keys()))-min(map(float,coords[0].keys())),\
max(map(float,coords[1].keys()))-min(map(float,coords[1].keys())),\
max(map(float,coords[2].keys()))-min(map(float,coords[2].keys())),\
],'d') # size from bounding box, corrected for cell-centeredness
size = np.where(grid > 1, size, min(size[grid > 1]/grid[grid > 1])) # spacing for grid==1 set to smallest among other spacings
table.data_readArray(options.coords)
table.data_rewind()
coords = [np.unique(table.data[:,i]) for i in xrange(3)]
mincorner = np.array(map(min,coords))
maxcorner = np.array(map(max,coords))
grid = np.array(map(len,coords),'i')
size = grid/np.maximum(np.ones(3,'d'), grid-1.0) * (maxcorner-mincorner) # size from edge to edge = dim * n/(n-1)
size = np.where(grid > 1, size, min(size[grid > 1]/grid[grid > 1])) # spacing for grid==1 set to smallest among other spacings
packing = np.array(options.packing,'i')
outSize = grid*packing
# ------------------------------------------ assemble header ---------------------------------------
# ------------------------------------------ assemble header --------------------------------------
table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
table.head_write()
# ------------------------------------------ process data -------------------------------------------
table.data_rewind()
data = np.zeros(outSize.tolist()+[len(table.labels)])
p = np.zeros(3,'i')
@ -107,15 +106,15 @@ for name in filenames:
table.data_read()
data[d[0]:d[0]+packing[0],
d[1]:d[1]+packing[1],
d[2]:d[2]+packing[2],
d[2]:d[2]+packing[2],
: ] = np.tile(np.array(table.data_asFloat(),'d'),packing.tolist()+[1]) # tile to match blowUp voxel size
elementSize = size/grid/packing
elem = 1
for c in xrange(outSize[2]):
for b in xrange(outSize[1]):
for a in xrange(outSize[0]):
data[a,b,c,coordCol:coordCol+3] = [a+0.5,b+0.5,c+0.5]*elementSize
data[a,b,c,table.label_index('elem')] = elem
data[a,b,c,colCoord:colCoord+3] = [a+0.5,b+0.5,c+0.5]*elementSize
if colElem != -1: data[a,b,c,colElem] = elem
table.data = data[a,b,c,:].tolist()
outputAlive = table.data_write() # output processed line
elem += 1

142
processing/post/histogram.py Executable file
View File

@ -0,0 +1,142 @@
#!/usr/bin/env python
# -*- 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 = """
Generate histogram of N bins in given data range.
""", version = scriptID)
parser.add_option('-d','--data',
dest = 'data',
type = 'string', metavar = 'string',
help = 'column heading for data')
parser.add_option('-w','--weights',
dest = 'weights',
type = 'string', metavar = 'string',
help = 'column heading for weights')
parser.add_option('--range',
dest = 'range',
type = 'float', nargs = 2, metavar = 'float float',
help = 'data range of histogram [min - max]')
parser.add_option('-N',
dest = 'N',
type = 'int', metavar = 'int',
help = 'number of bins')
parser.add_option('--density',
dest = 'density',
action = 'store_true',
help = 'report probability density')
parser.add_option('--logarithmic',
dest = 'log',
action = 'store_true',
help = 'logarithmically spaced bins')
parser.set_defaults(data = None,
weights = None,
range = None,
N = None,
density = False,
log = False,
)
(options,filenames) = parser.parse_args()
if not options.data: parser.error('no data specified.')
if not options.N: parser.error('no bin number specified.')
if options.log:
def forward(x):
return np.log(x)
def reverse(x):
return np.exp(x)
else:
def forward(x):
return x
def reverse(x):
return x
# --- loop over input files ------------------------------------------------------------------------
if filenames == []: filenames = [None]
for name in filenames:
try: table = damask.ASCIItable(name = name,
buffered = False,
readonly = True)
except: continue
damask.util.report(scriptName,name)
# ------------------------------------------ read header ------------------------------------------
table.head_read()
# ------------------------------------------ sanity checks ----------------------------------------
errors = []
remarks = []
if table.label_dimension(options.data) != 1: errors.append('data {} are not scalar.'.format(options.data))
if options.weights and \
table.label_dimension(options.data) != 1: errors.append('weights {} are not scalar.'.format(options.weights))
if remarks != []: damask.util.croak(remarks)
if errors != []:
damask.util.croak(errors)
table.close(dismiss = True)
continue
# --------------- read data ----------------------------------------------------------------
table.data_readArray([options.data,options.weights])
# --------------- auto range ---------------------------------------------------------------
if options.range is None:
rangeMin,rangeMax = min(table.data[:,0]),max(table.data[:,0])
else:
rangeMin,rangeMax = min(options.range),max(options.range)
# --------------- bin data ----------------------------------------------------------------
count,edges = np.histogram(table.data[:,0],
bins = reverse(forward(rangeMin) + np.arange(options.N+1) *
(forward(rangeMax)-forward(rangeMin))/options.N),
range = (rangeMin,rangeMax),
weights = None if options.weights is None else table.data[:,1],
density = options.density,
)
bincenter = reverse(forward(rangeMin) + (0.5+np.arange(options.N)) *
(forward(rangeMax)-forward(rangeMin))/options.N) # determine center of bins
# ------------------------------------------ assemble header ---------------------------------------
table.info_clear()
table.info_append([scriptID + '\t' + ' '.join(sys.argv[1:]),
scriptID + ':\t' +
'data range {} -- {}'.format(rangeMin,rangeMax) +
(' (log)' if options.log else ''),
])
table.labels_clear()
table.labels_append(['bincenter','count'])
table.head_write()
# ------------------------------------------ output result -----------------------------------------
table.data = np.squeeze(np.dstack((bincenter,count)))
table.data_writeArray()
# ------------------------------------------ output finalization -----------------------------------
table.close() # close ASCII tables

144
processing/post/marc_deformedGeometry.py
View File

@ -1,144 +0,0 @@
#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
import os,sys,shutil
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 FUNCTION STARTS HERE
# -----------------------------
# --- input parsing
parser = OptionParser(usage='%prog [options] resultfile', description = """
Create vtk files for the (deformed) geometry that belongs to a .t16 (MSC.Marc) results file.
""", version = scriptID)
parser.add_option('-d','--dir', dest='dir', \
help='name of subdirectory to hold output [%default]')
parser.add_option('-r','--range', dest='range', type='int', nargs=3, \
help='range of positions (or increments) to output (start, end, step) [all]')
parser.add_option('--increments', action='store_true', dest='getIncrements', \
help='switch to increment range [%default]')
parser.add_option('-t','--type', dest='type', type='choice', choices=['ipbased','nodebased'], \
help='processed geometry type [ipbased and nodebased]')
parser.set_defaults(dir = 'vtk')
parser.set_defaults(getIncrements= False)
(options, files) = parser.parse_args()
# --- basic sanity checks
if files == []:
parser.print_help()
parser.error('no file specified...')
filename = os.path.splitext(files[0])[0]
if not os.path.exists(filename+'.t16'):
parser.print_help()
parser.error('invalid file "%s" specified...'%filename+'.t16')
if not options.type :
options.type = ['nodebased', 'ipbased']
else:
options.type = [options.type]
# --- more sanity checks
sys.path.append(damask.solver.Marc().libraryPath('../../'))
try:
import py_post
except:
print('error: no valid Mentat release found')
sys.exit(-1)
# --------------------------- open results file and initialize mesh ----------
p = py_post.post_open(filename+'.t16')
p.moveto(0)
Nnodes = p.nodes()
Nincrements = p.increments() - 1 # t16 contains one "virtual" increment (at 0)
if damask.core.mesh.mesh_init_postprocessing(filename+'.mesh') > 0:
print('error: init not successful')
sys.exit(-1)
Ncellnodes = damask.core.mesh.mesh_get_Ncellnodes()
unitlength = damask.core.mesh.mesh_get_unitlength()
# --------------------------- create output dir --------------------------------
dirname = os.path.abspath(os.path.join(os.path.dirname(filename),options.dir))
if not os.path.isdir(dirname):
os.mkdir(dirname,0755)
# --------------------------- get positions --------------------------------
incAtPosition = {}
positionOfInc = {}
for position in range(Nincrements):
p.moveto(position+1)
incAtPosition[position] = p.increment # remember "real" increment at this position
positionOfInc[p.increment] = position # remember position of "real" increment
if not options.range:
options.getIncrements = False
locations = range(Nincrements) # process all positions
else:
options.range = list(options.range) # convert to list
if options.getIncrements:
locations = [positionOfInc[x] for x in range(options.range[0],options.range[1]+1,options.range[2])
if x in positionOfInc]
else:
locations = range( max(0,options.range[0]),
min(Nincrements,options.range[1]+1),
options.range[2] )
increments = [incAtPosition[x] for x in locations] # build list of increments to process
# --------------------------- loop over positions --------------------------------
for incCount,position in enumerate(locations): # walk through locations
p.moveto(position+1) # wind to correct position
# --- get displacements
node_displacement = [[0,0,0] for i in range(Nnodes)]
for n in range(Nnodes):
if p.node_displacements():
node_displacement[n] = map(lambda x:x*unitlength,list(p.node_displacement(n)))
c = damask.core.mesh.mesh_build_cellnodes(np.array(node_displacement).T,Ncellnodes)
cellnode_displacement = [[c[i][n] for i in range(3)] for n in range(Ncellnodes)]
# --- append displacements to corresponding files
for geomtype in options.type:
outFilename = eval('"'+eval("'%%s_%%s_inc%%0%ii.vtk'%(math.log10(max(increments+[1]))+1)")\
+'"%(dirname + os.sep + os.path.split(filename)[1],geomtype,increments[incCount])')
print outFilename
shutil.copyfile('%s_%s.vtk'%(filename,geomtype),outFilename)
with open(outFilename,'a') as myfile:
myfile.write("POINT_DATA %i\n"%{'nodebased':Nnodes,'ipbased':Ncellnodes}[geomtype])
myfile.write("VECTORS displacement double\n")
coordinates = {'nodebased':node_displacement,'ipbased':cellnode_displacement}[geomtype]
for n in range({'nodebased':Nnodes,'ipbased':Ncellnodes}[geomtype]):
myfile.write("%.8e %.8e %.8e\n"%(coordinates[n][0],coordinates[n][1],coordinates[n][2]))
# --------------------------- DONE --------------------------------

421
processing/post/marc_extractData.py
View File

@ -1,421 +0,0 @@
#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
import os,sys,string,re,time
from optparse import OptionParser, OptionGroup
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
# -----------------------------
def ParseOutputFormat(filename,homogID,crystID,phaseID):
"""parse .output* files in order to get a list of outputs"""
myID = {'Homogenization': homogID,
'Crystallite': crystID,
'Constitutive': phaseID,
}
format = {}
for what in ['Homogenization','Crystallite','Constitutive']:
content = []
format[what] = {'outputs':{},'specials':{'brothers':[]}}
for prefix in ['']+map(str,range(1,17)):
if os.path.exists(prefix+filename+'.output'+what):
try:
file = open(prefix+filename+'.output'+what)
content = file.readlines()
file.close()
break
except:
pass
if content == []: continue # nothing found...
tag = ''
tagID = 0
for line in content:
if re.match("\s*$",line) or re.match("#",line): # skip blank lines and comments
continue
m = re.match("\[(.+)\]",line) # look for block indicator
if m: # next section
tag = m.group(1)
tagID += 1
format[what]['specials']['brothers'].append(tag)
if tag == myID[what] or (myID[what].isdigit() and tagID == int(myID[what])):
format[what]['specials']['_id'] = tagID
format[what]['outputs'] = []
tag = myID[what]
else: # data from section
if tag == myID[what]:
(output,length) = line.split()
output.lower()
if length.isdigit():
length = int(length)
if re.match("\((.+)\)",output): # special data, e.g. (Ngrains)
format[what]['specials'][output] = length
elif length > 0:
format[what]['outputs'].append([output,length])
if '_id' not in format[what]['specials']:
print "\nsection '%s' not found in <%s>"%(myID[what], what)
print '\n'.join(map(lambda x:' [%s]'%x, format[what]['specials']['brothers']))
return format
# -----------------------------
def ParsePostfile(p,filename, outputFormat, legacyFormat):
"""
parse postfile in order to get position and labels of outputs
needs "outputFormat" for mapping of output names to postfile output indices
"""
startVar = {True: 'GrainCount',
False:'HomogenizationCount'}
# --- build statistics
stat = { \
'IndexOfLabel': {}, \
'Title': p.title(), \
'Extrapolation': p.extrapolate, \
'NumberOfIncrements': p.increments() - 1, \
'NumberOfNodes': p.nodes(), \
'NumberOfNodalScalars': p.node_scalars(), \
'LabelOfNodalScalar': [None]*p.node_scalars() , \
'NumberOfElements': p.elements(), \
'NumberOfElementalScalars': p.element_scalars(), \
'LabelOfElementalScalar': [None]*p.element_scalars() , \
'NumberOfElementalTensors': p.element_tensors(), \
'LabelOfElementalTensor': [None]*p.element_tensors(), \
}
# --- find labels
for labelIndex in range(stat['NumberOfNodalScalars']):
label = p.node_scalar_label(labelIndex)
stat['IndexOfLabel'][label] = labelIndex
stat['LabelOfNodalScalar'][labelIndex] = label
for labelIndex in range(stat['NumberOfElementalScalars']):
label = p.element_scalar_label(labelIndex)
stat['IndexOfLabel'][label] = labelIndex
stat['LabelOfElementalScalar'][labelIndex] = label
for labelIndex in range(stat['NumberOfElementalTensors']):
label = p.element_tensor_label(labelIndex)
stat['IndexOfLabel'][label] = labelIndex
stat['LabelOfElementalTensor'][labelIndex] = label
if 'User Defined Variable 1' in stat['IndexOfLabel']: # output format without dedicated names?
stat['IndexOfLabel'][startVar[legacyFormat]] = stat['IndexOfLabel']['User Defined Variable 1'] # adjust first named entry
if startVar[legacyFormat] in stat['IndexOfLabel']: # does the result file contain relevant user defined output at all?
startIndex = stat['IndexOfLabel'][startVar[legacyFormat]]
stat['LabelOfElementalScalar'][startIndex] = startVar[legacyFormat]
# We now have to find a mapping for each output label as defined in the .output* files to the output position in the post file
# Since we know where the user defined outputs start ("startIndex"), we can simply assign increasing indices to the labels
# given in the .output* file
offset = 1
if legacyFormat:
stat['LabelOfElementalScalar'][startIndex + offset] = startVar[not legacyFormat] # add HomogenizationCount as second
offset += 1
for (name,N) in outputFormat['Homogenization']['outputs']:
for i in range(N):
label = {False: '%s'%( name),
True:'%i_%s'%(i+1,name)}[N > 1]
stat['IndexOfLabel'][label] = startIndex + offset
stat['LabelOfElementalScalar'][startIndex + offset] = label
offset += 1
if not legacyFormat:
stat['IndexOfLabel'][startVar[not legacyFormat]] = startIndex + offset
stat['LabelOfElementalScalar'][startIndex + offset] = startVar[not legacyFormat] # add GrainCount
offset += 1
if '(ngrains)' in outputFormat['Homogenization']['specials']:
for grain in range(outputFormat['Homogenization']['specials']['(ngrains)']):
stat['IndexOfLabel']['%i_CrystalliteCount'%(grain+1)] = startIndex + offset # report crystallite count
stat['LabelOfElementalScalar'][startIndex + offset] = '%i_CrystalliteCount'%(grain+1) # add GrainCount
offset += 1
for (name,N) in outputFormat['Crystallite']['outputs']: # add crystallite outputs
for i in range(N):
label = {False: '%i_%s'%(grain+1, name),
True:'%i_%i_%s'%(grain+1,i+1,name)}[N > 1]
stat['IndexOfLabel'][label] = startIndex + offset
stat['LabelOfElementalScalar'][startIndex + offset] = label
offset += 1
stat['IndexOfLabel']['%i_ConstitutiveCount'%(grain+1)] = startIndex + offset # report constitutive count
stat['LabelOfElementalScalar'][startIndex + offset] = '%i_ConstitutiveCount'%(grain+1) # add GrainCount
offset += 1
for (name,N) in outputFormat['Constitutive']['outputs']: # add constitutive outputs
for i in range(N):
label = {False: '%i_%s'%(grain+1, name),
True:'%i_%i_%s'%(grain+1,i+1,name)}[N > 1]
stat['IndexOfLabel'][label] = startIndex + offset
try:
stat['LabelOfElementalScalar'][startIndex + offset] = label
except IndexError:
print 'trying to assign %s at position %i+%i'%(label,startIndex,offset)
sys.exit(1)
offset += 1
return stat
# -----------------------------
def GetIncrementLocations(p,Nincrements,options):
"""get mapping between positions in postfile and increment number"""
incAtPosition = {}
positionOfInc = {}
for position in range(Nincrements):
p.moveto(position+1)
incAtPosition[position] = p.increment # remember "real" increment at this position
positionOfInc[p.increment] = position # remember position of "real" increment
if not options.range:
options.getIncrements = False
locations = range(Nincrements) # process all positions
else:
options.range = list(options.range) # convert to list
if options.getIncrements:
locations = [positionOfInc[x] for x in range(options.range[0],options.range[1]+1,options.range[2])
if x in positionOfInc]
else:
locations = range( max(0,options.range[0]),
min(Nincrements,options.range[1]+1),
options.range[2] )
increments = [incAtPosition[x] for x in locations] # build list of increments to process
return [increments,locations]
# -----------------------------
def SummarizePostfile(stat,where=sys.stdout):
where.write('\n\n')
where.write('title:\t%s'%stat['Title'] + '\n\n')
where.write('extraplation:\t%s'%stat['Extrapolation'] + '\n\n')
where.write('increments:\t%i'%(stat['NumberOfIncrements']) + '\n\n')
where.write('nodes:\t%i'%stat['NumberOfNodes'] + '\n\n')
where.write('elements:\t%i'%stat['NumberOfElements'] + '\n\n')
where.write('nodal scalars:\t%i'%stat['NumberOfNodalScalars'] + '\n\n '\
+'\n '.join(stat['LabelOfNodalScalar']) + '\n\n')
where.write('elemental scalars:\t%i'%stat['NumberOfElementalScalars'] + '\n\n '\
+ '\n '.join(stat['LabelOfElementalScalar']) + '\n\n')
where.write('elemental tensors:\t%i'%stat['NumberOfElementalTensors'] + '\n\n '\
+ '\n '.join(stat['LabelOfElementalTensor']) + '\n\n')
return True
# -----------------------------
def SummarizeOutputfile(format,where=sys.stdout):
where.write('\nUser Defined Outputs')
for what in format.keys():
where.write('\n\n %s:'%what)
for output in format[what]['outputs']:
where.write('\n %s'%output)
return True
# -----------------------------
def writeHeader(myfile,stat,geomtype):
myfile.write('2\theader\n')
myfile.write(string.replace('$Id$','\n','\\n')+
'\t' + ' '.join(sys.argv[1:]) + '\n')
if geomtype == 'nodebased':
myfile.write('node')
for i in range(stat['NumberOfNodalScalars']):
myfile.write('\t%s'%''.join(stat['LabelOfNodalScalar'][i].split()))
elif geomtype == 'ipbased':
myfile.write('elem\tip')
for i in range(stat['NumberOfElementalScalars']):
myfile.write('\t%s'%''.join(stat['LabelOfElementalScalar'][i].split()))
myfile.write('\n')
return True
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
Extract data from a .t16 (MSC.Marc) results file.
""", version = scriptID)
parser.add_option('-i','--info', action='store_true', dest='info', \
help='list contents of resultfile [%default]')
parser.add_option('-l','--legacy', action='store_true', dest='legacy', \
help='legacy user result block (starts with GrainCount) [%default]')
parser.add_option('-d','--dir', dest='dir', \
help='name of subdirectory to hold output [%default]')
parser.add_option('-r','--range', dest='range', type='int', nargs=3, \
help='range of positions (or increments) to output (start, end, step) [all]')
parser.add_option('--increments', action='store_true', dest='getIncrements', \
help='switch to increment range [%default]')
parser.add_option('-t','--type', dest='type', type='choice', choices=['ipbased','nodebased'], \
help='processed geometry type [ipbased and nodebased]')
group_material = OptionGroup(parser,'Material identifier')
group_material.add_option('--homogenization', dest='homog', \
help='homogenization identifier (as string or integer [%default])', metavar='<ID>')
group_material.add_option('--crystallite', dest='cryst', \
help='crystallite identifier (as string or integer [%default])', metavar='<ID>')
group_material.add_option('--phase', dest='phase', \
help='phase identifier (as string or integer [%default])', metavar='<ID>')
parser.add_option_group(group_material)
parser.set_defaults(info = False)
parser.set_defaults(legacy = False)
parser.set_defaults(dir = 'vtk')
parser.set_defaults(getIncrements= False)
parser.set_defaults(homog = '1')
parser.set_defaults(cryst = '1')
parser.set_defaults(phase = '1')
(options, files) = parser.parse_args()
# --- sanity checks
if files == []:
parser.print_help()
parser.error('no file specified...')
filename = os.path.splitext(files[0])[0]
if not os.path.exists(filename+'.t16'):
parser.print_help()
parser.error('invalid file "%s" specified...'%filename+'.t16')
sys.path.append(damask.solver.Marc().libraryPath('../../'))
try:
import py_post
except:
print('error: no valid Mentat release found')
sys.exit(-1)
if not options.type :
options.type = ['nodebased', 'ipbased']
else:
options.type = [options.type]
# --- initialize mesh data
if damask.core.mesh.mesh_init_postprocessing(filename+'.mesh'):
print('error: init not successful')
sys.exit(-1)
# --- check if ip data available for all elements; if not, then .t19 file is required
p = py_post.post_open(filename+'.t16')
asciiFile = False
p.moveto(1)
for e in range(p.elements()):
if not damask.core.mesh.mesh_get_nodeAtIP(str(p.element(e).type),1):
if os.path.exists(filename+'.t19'):
p.close()
p = py_post.post_open(filename+'.t19')
asciiFile = True
break
# --- parse *.output and *.t16 file
outputFormat = ParseOutputFormat(filename,options.homog,options.cryst,options.phase)
p.moveto(1)
p.extrapolation('translate')
stat = ParsePostfile(p,filename,outputFormat,options.legacy)
# --- output info
if options.info:
print '\n\nMentat release %s'%damask.solver.Marc().version('../../')
SummarizePostfile(stat)
SummarizeOutputfile(outputFormat)
sys.exit(0)
# --- create output dir
dirname = os.path.abspath(os.path.join(os.path.dirname(filename),options.dir))
if not os.path.isdir(dirname):
os.mkdir(dirname,0755)
# --- get positions
[increments,locations] = GetIncrementLocations(p,stat['NumberOfIncrements'],options)
# --- loop over positions
time_start = time.time()
for incCount,position in enumerate(locations): # walk through locations
p.moveto(position+1) # wind to correct position
time_delta = (float(len(locations)) / float(incCount+1) - 1.0) * (time.time() - time_start)
sys.stdout.write("\r(%02i:%02i:%02i) processing increment %i of %i..."\
%(time_delta//3600,time_delta%3600//60,time_delta%60,incCount+1,len(locations)))
sys.stdout.flush()
# --- write header
outFilename = {}
for geomtype in options.type:
outFilename[geomtype] = eval('"'+eval("'%%s_%%s_inc%%0%ii.txt'%(math.log10(max(increments+[1]))+1)")\
+'"%(dirname + os.sep + os.path.split(filename)[1],geomtype,increments[incCount])')
with open(outFilename[geomtype],'w') as myfile:
writeHeader(myfile,stat,geomtype)
# --- write node based data
if geomtype == 'nodebased':
for n in range(stat['NumberOfNodes']):
myfile.write(str(n))
for l in range(stat['NumberOfNodalScalars']):
myfile.write('\t'+str(p.node_scalar(n,l)))
myfile.write('\n')
# --- write ip based data
elif geomtype == 'ipbased':
for e in range(stat['NumberOfElements']):
if asciiFile:
print 'ascii postfile not yet supported'
sys.exit(-1)
else:
ipData = [[]]
for l in range(stat['NumberOfElementalScalars']):
data = p.element_scalar(e,l)
for i in range(len(data)): # at least as many nodes as ips
node = damask.core.mesh.mesh_get_nodeAtIP(str(p.element(e).type),i+1) # fortran indexing starts at 1
if not node: break # no more ips
while i >= len(ipData): ipData.append([])
ipData[i].extend([data[node-1].value]) # python indexing starts at 0
for i in range(len(ipData)):
myfile.write('\t'.join(map(str,[e,i]+ipData[i]))+'\n')
p.close()
sys.stdout.write("\n")

7
processing/post/postResults.py
View File

@ -1003,11 +1003,8 @@ fileOpen = False
assembleHeader = True
header = []
standard = ['inc'] + \
{True: ['time'],
False:[]}[options.time] + \
['elem','node','ip','grain'] + \
{True: ['1_nodeinitialcoord','2_nodeinitialcoord','3_nodeinitialcoord'],
False:['1_ipinitialcoord','2_ipinitialcoord','3_ipinitialcoord']}[options.nodalScalar != []]
(['time'] if options.time else []) + \
['elem','node','ip','grain','1_pos','2_pos','3_pos']
# --------------------------- loop over positions --------------------------------

14
processing/post/reLabel.py
View File

@ -1,7 +1,7 @@
#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
import os,sys
import os,sys,re
import damask
from optparse import OptionParser
@ -32,14 +32,17 @@ parser.set_defaults(label = [],
(options,filenames) = parser.parse_args()
pattern = [re.compile('^()(.+)$'), # label pattern for scalar
re.compile('^(\d+_)?(.+)$'), # label pattern for multidimension
]
# --- loop over input files -------------------------------------------------------------------------
if filenames == []: filenames = [None]
for name in filenames:
try:
table = damask.ASCIItable(name = name,
buffered = False)
try: table = damask.ASCIItable(name = name,
buffered = False)
except: continue
damask.util.report(scriptName,name)
@ -63,8 +66,9 @@ for name in filenames:
for i,index in enumerate(indices):
if index == -1: remarks.append('label {} not present...'.format(options.label[i]))
else:
m = pattern[dimensions[i]>1].match(table.labels[index]) # isolate label name
for j in xrange(dimensions[i]):
table.labels[index+j] = table.labels[index+j].replace(options.label[i],options.substitute[i])
table.labels[index+j] = table.labels[index+j].replace(m.group(2),options.substitute[i]) # replace name with substitute
if remarks != []: damask.util.croak(remarks)
if errors != []:

82
processing/post/vtk_addData.py
View File

@ -1,82 +0,0 @@
#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
import os,glob,re
import damask
from optparse import OptionParser
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
# -----------------------------
def findTag(filename,tag):
with open(filename,'r') as myfile:
mypattern = re.compile(str(tag))
for line in myfile:
if mypattern.search(line): return True
return False
# -----------------------------
# MAIN FUNCTION STARTS HERE
# -----------------------------
# --- input parsing
parser = OptionParser(usage='%prog [options] directory', description = """
Add data from an ASCII table to a VTK geometry file.
""", version = scriptID)
parser.add_option('-s','--sub', action='store_true', dest='subdir', \
help='include files in subdirectories [%default]')
parser.set_defaults(subdir = False)
(options, dirname) = parser.parse_args()
# --- sanity checks
if dirname == []:
parser.print_help()
parser.error('no directory specified...')
else:
dirname = os.path.abspath(dirname[0]) # only use first argument
if not os.path.isdir(dirname):
parser.print_help()
parser.error('invalid directory "%s" specified...'%dirname)
# --- loop over "nodebased" and "ipbased" data files and
# copy data to corresponding geometry files
dataSetTag = {'nodebased':'POINT_DATA', 'ipbased':'CELL_DATA'}
for geomtype in ['nodebased','ipbased']:
for vtkfilename in glob.iglob(dirname+os.sep+'*'+geomtype+'*.vtk'):
if not os.path.dirname(vtkfilename) == dirname and not options.subdir: continue # include files in subdir?
datafilename = os.path.splitext(vtkfilename)[0] + '.txt'
if not os.path.exists(datafilename): continue # no corresponding datafile found
# --- read data from datafile
with open(datafilename,'r') as datafile: # open datafile in read mode
table = damask.ASCIItable(fileIn=datafile) # use ASCIItable class to read data file
table.head_read() # read ASCII header info
myData = []
while table.data_read(): # read line in datafile
myData.append(table.data)
myData = zip(*myData) # reorder data: first index now label, not node
# --- append data to vtkfile
with open(vtkfilename,'a') as vtkfile: # open vtkfile in append mode
print vtkfilename
if not findTag(vtkfilename,dataSetTag[geomtype]): # check if data set is already present...
vtkfile.write(dataSetTag[geomtype] + ' %i'%len(myData[0])) # ... if not, write keyword
for idx,label in enumerate(table.labels): # write data
vtkfile.write('\nSCALARS '+label+' double 1\nLOOKUP_TABLE default\n') # all scalar data
vtkfile.write('\n'.join(map(str,myData[idx])))

220
processing/post/vtk_addPointcloudData.py
View File

@ -1,8 +1,9 @@
#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
import os,sys,vtk
import os,vtk
import damask
from collections import defaultdict
from optparse import OptionParser
scriptName = os.path.splitext(os.path.basename(__file__))[0]
@ -17,125 +18,166 @@ Add scalar and RGB tuples from ASCIItable to existing VTK point cloud (.vtp).
""", version = scriptID)
parser.add_option('-v', '--vtk', dest='vtk', \
parser.add_option( '--vtk',
dest = 'vtk',
type = 'string', metavar = 'string',
help = 'VTK file name')
parser.add_option( '--inplace',
dest = 'inplace',
action = 'store_true',
help = 'modify VTK file in-place')
parser.add_option('-r', '--render',
dest = 'render',
action = 'store_true',
help = 'open output in VTK render window')
parser.add_option('-s', '--scalar', dest='scalar', action='extend', \
help = 'scalar values')
parser.add_option('-v', '--vector',
dest = 'vector',
action = 'extend', metavar = '<string LIST>',
help = 'vector value label(s)')
parser.add_option('-c', '--color', dest='color', action='extend', \
help = 'RGB color tuples')
parser.set_defaults(scalar = [])
parser.set_defaults(color = [])
parser.set_defaults(scalar = [],
vector = [],
color = [],
inplace = False,
render = False,
)
(options, filenames) = parser.parse_args()
datainfo = { # list of requested labels per datatype
'scalar': {'len':1,
'label':[]},
'color': {'len':3,
'label':[]},
}
if not options.vtk: parser.error('No VTK file specified.')
if not os.path.exists(options.vtk): parser.error('VTK file does not exist.')
if not os.path.exists(options.vtk):
parser.error('VTK file does not exist'); sys.exit()
if os.path.splitext(options.vtk)[1] == '.vtp':
reader = vtk.vtkXMLPolyDataReader()
reader.SetFileName(options.vtk)
reader.Update()
Polydata = reader.GetOutput()
elif os.path.splitext(options.vtk)[1] == '.vtk':
reader = vtk.vtkGenericDataObjectReader()
reader.SetFileName(options.vtk)
reader.Update()
Polydata = reader.GetPolyDataOutput()
else:
parser.error('Unsupported VTK file type extension.')
reader = vtk.vtkXMLPolyDataReader()
reader.SetFileName(options.vtk)
reader.Update()
Npoints = reader.GetNumberOfPoints()
Ncells = reader.GetNumberOfCells()
Nvertices = reader.GetNumberOfVerts()
Polydata = reader.GetOutput()
Npoints = Polydata.GetNumberOfPoints()
Ncells = Polydata.GetNumberOfCells()
Nvertices = Polydata.GetNumberOfVerts()
if Npoints != Ncells or Npoints != Nvertices:
parser.error('Number of points, cells, and vertices in VTK differ from each other'); sys.exit()
if options.scalar is not None: datainfo['scalar']['label'] += options.scalar
if options.color is not None: datainfo['color']['label'] += options.color
parser.error('Number of points, cells, and vertices in VTK differ from each other.')
# ------------------------------------------ setup file handles ---------------------------------------
damask.util.croak('{}: {} points, {} vertices, and {} cells...'.format(options.vtk,Npoints,Nvertices,Ncells))
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':sys.stderr, 'croak':sys.stderr})
# --- loop over input files -------------------------------------------------------------------------
#--- loop over input files ------------------------------------------------------------------------
for file in files:
if file['name'] != 'STDIN': file['croak'].write('\033[1m'+scriptName+'\033[0m: '+file['name']+'\n')
else: file['croak'].write('\033[1m'+scriptName+'\033[0m\n')
if filenames == []: filenames = [None]
table = damask.ASCIItable(file['input'],file['output'],False) # make unbuffered ASCII_table
table.head_read() # read ASCII header info
for name in filenames:
try: table = damask.ASCIItable(name = name,
buffered = False,
readonly = True)
except: continue
damask.util.report(scriptName, name)
# --------------- figure out columns to process
active = {}
column = {}
# --- interpret header ----------------------------------------------------------------------------
array = {}
table.head_read()
remarks = []
errors = []
VTKarray = {}
active = defaultdict(list)
for datatype,info in datainfo.items():
for label in info['label']:
foundIt = False
for key in ['1_'+label,label]:
if key in table.labels:
foundIt = True
if datatype not in active: active[datatype] = []
if datatype not in column: column[datatype] = {}
if datatype not in array: array[datatype] = {}
active[datatype].append(label)
column[datatype][label] = table.labels.index(key) # remember columns of requested data
if datatype == 'scalar':
array[datatype][label] = vtk.vtkDoubleArray()
array[datatype][label].SetNumberOfComponents(1)
array[datatype][label].SetName(label)
elif datatype == 'color':
array[datatype][label] = vtk.vtkUnsignedCharArray()
array[datatype][label].SetNumberOfComponents(3)
array[datatype][label].SetName(label)
if not foundIt:
file['croak'].write('column %s not found...\n'%label)
for datatype,dimension,label in [['scalar',1,options.scalar],
['vector',3,options.vector],
['color',3,options.color],
]:
for i,dim in enumerate(table.label_dimension(label)):
me = label[i]
if dim == -1: remarks.append('{} "{}" not found...'.format(datatype,me))
elif dim > dimension: remarks.append('"{}" not of dimension {}...'.format(me,dimension))
else:
remarks.append('adding {} "{}"...'.format(datatype,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 errors != []:
damask.util.croak(errors)
table.close(dismiss = True)
continue
# ------------------------------------------ process data ---------------------------------------
while table.data_read(): # read next data line of ASCII table
while table.data_read(): # read next data line of ASCII table
for datatype,labels in active.items(): # loop over scalar,color
for label in labels: # loop over all requested items
theData = table.data[column[datatype][label]:\
column[datatype][label]+datainfo[datatype]['len']] # read strings
if datatype == 'color':
theData = map(lambda x: int(255.*float(x)),theData)
array[datatype][label].InsertNextTuple3(theData[0],theData[1],theData[2],)
elif datatype == 'scalar':
array[datatype][label].InsertNextValue(float(theData[0]))
for datatype,labels in active.items(): # loop over scalar,color
for me in labels: # loop over all requested items
theData = [table.data[i] for i in table.label_indexrange(me)] # read strings
if datatype == 'color': VTKarray[me].InsertNextTuple3(*map(lambda x: int(255.*float(x)),theData))
elif datatype == 'vector': VTKarray[me].InsertNextTuple3(*map(float,theData))
elif datatype == 'scalar': VTKarray[me].InsertNextValue(float(theData[0]))
table.input_close() # close input ASCII table
# ------------------------------------------ add data ---------------------------------------
for datatype,labels in active.items(): # loop over scalar,color
for datatype,labels in active.items(): # loop over scalar,color
if datatype == 'color':
Polydata.GetPointData().SetScalars(array[datatype][labels[0]])
Polydata.GetCellData().SetScalars(array[datatype][labels[0]])
for label in labels: # loop over all requested items
Polydata.GetPointData().AddArray(array[datatype][label])
Polydata.GetCellData().AddArray(array[datatype][label])
Polydata.GetPointData().SetScalars(VTKarray[active['color'][0]])
Polydata.GetCellData().SetScalars(VTKarray[active['color'][0]])
for me in labels: # loop over all requested items
Polydata.GetPointData().AddArray(VTKarray[me])
Polydata.GetCellData().AddArray(VTKarray[me])
Polydata.Modified()
if vtk.VTK_MAJOR_VERSION <= 5:
Polydata.Update()
if vtk.VTK_MAJOR_VERSION <= 5: Polydata.Update()
# ------------------------------------------ output result ---------------------------------------
writer = vtk.vtkXMLPolyDataWriter()
writer.SetDataModeToBinary()
writer.SetCompressorTypeToZLib()
writer.SetFileName(os.path.splitext(options.vtk)[0]+'_added.vtp')
if vtk.VTK_MAJOR_VERSION <= 5:
writer.SetInput(Polydata)
else:
writer.SetInputData(Polydata)
writer.Write()
writer = vtk.vtkXMLPolyDataWriter()
writer.SetDataModeToBinary()
writer.SetCompressorTypeToZLib()
writer.SetFileName(os.path.splitext(options.vtk)[0]+('.vtp' if options.inplace else '_added.vtp'))
if vtk.VTK_MAJOR_VERSION <= 5: writer.SetInput(Polydata)
else: writer.SetInputData(Polydata)
writer.Write()
# ------------------------------------------ render result ---------------------------------------
if options.render:
mapper = vtk.vtkDataSetMapper()
mapper.SetInputData(Polydata)
actor = vtk.vtkActor()
actor.SetMapper(mapper)
# Create the graphics structure. The renderer renders into the
# render window. The render window interactor captures mouse events
# and will perform appropriate camera or actor manipulation
# depending on the nature of the events.
ren = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren)
ren.AddActor(actor)
ren.SetBackground(1, 1, 1)
renWin.SetSize(200, 200)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
iren.Initialize()
renWin.Render()
iren.Start()

34
processing/post/vtk_addRectilinearGridData.py
View File

@ -30,10 +30,6 @@ parser.add_option('-r', '--render',
dest = 'render',
action = 'store_true',
help = 'open output in VTK render window')
parser.add_option('-m', '--mode',
dest = 'mode',
type = 'choice', metavar = 'string', choices = ['cell', 'point'],
help = 'cell-centered or point-centered data')
parser.add_option('-s', '--scalar',
dest = 'scalar',
action = 'extend', metavar = '<string LIST>',
@ -56,7 +52,6 @@ parser.set_defaults(scalar = [],
(options, filenames) = parser.parse_args()
if not options.mode: parser.error('No data mode specified.')
if not options.vtk: parser.error('No VTK file specified.')
if not os.path.exists(options.vtk): parser.error('VTK file does not exist.')
@ -83,9 +78,9 @@ damask.util.croak('{}: {} points and {} cells...'.format(options.vtk,Npoints,Nce
if filenames == []: filenames = [None]
for name in filenames:
try:
table = damask.ASCIItable(name = name,
buffered = False, readonly = True)
try: table = damask.ASCIItable(name = name,
buffered = False,
readonly = True)
except: continue
damask.util.report(scriptName, name)
@ -124,8 +119,11 @@ for name in filenames:
# ------------------------------------------ process data ---------------------------------------
datacount = 0
while table.data_read(): # read next data line of ASCII table
datacount += 1 # count data lines
for datatype,labels in active.items(): # loop over scalar,color
for me in labels: # loop over all requested items
theData = [table.data[i] for i in table.label_indexrange(me)] # read strings
@ -133,15 +131,25 @@ for name in filenames:
elif datatype == 'vector': VTKarray[me].InsertNextTuple3(*map(float,theData))
elif datatype == 'scalar': VTKarray[me].InsertNextValue(float(theData[0]))
table.close() # close input ASCII table
# ------------------------------------------ add data ---------------------------------------
if datacount == Npoints: mode = 'point'
elif datacount == Ncells: mode = 'cell'
else:
damask.util.croak('Data count is incompatible with grid...')
continue
damask.util.croak('{} mode...'.format(mode))
for datatype,labels in active.items(): # loop over scalar,color
if datatype == 'color':
if options.mode == 'cell': rGrid.GetCellData().SetScalars(VTKarray[active['color'][0]])
elif options.mode == 'point': rGrid.GetPointData().SetScalars(VTKarray[active['color'][0]])
if mode == 'cell': rGrid.GetCellData().SetScalars(VTKarray[active['color'][0]])
elif mode == 'point': rGrid.GetPointData().SetScalars(VTKarray[active['color'][0]])
for me in labels: # loop over all requested items
if options.mode == 'cell': rGrid.GetCellData().AddArray(VTKarray[me])
elif options.mode == 'point': rGrid.GetPointData().AddArray(VTKarray[me])
if mode == 'cell': rGrid.GetCellData().AddArray(VTKarray[me])
elif mode == 'point': rGrid.GetPointData().AddArray(VTKarray[me])
rGrid.Modified()
if vtk.VTK_MAJOR_VERSION <= 5: rGrid.Update()

135
processing/post/vtk_addVoxelcloudData.py
View File

@ -1,135 +0,0 @@
#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
import os,sys,vtk
import damask
from collections import defaultdict
from optparse import OptionParser
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 = """
Add scalar and RGB tuples from ASCIItable to existing VTK voxel cloud (.vtu/.vtk).
""", version = scriptID)
parser.add_option('-v', '--vtk', dest='vtk', \
help = 'VTK file name')
parser.add_option('-s', '--scalar', dest='scalar', action='extend', \
help = 'scalar values')
parser.add_option('-c', '--color', dest='color', action='extend', \
help = 'RGB color tuples')
parser.set_defaults(scalar = [],
color = [],
render = False,
)
(options, filenames) = parser.parse_args()
if options.vtk is None or not os.path.exists(options.vtk):
parser.error('VTK file does not exist')
if os.path.splitext(options.vtk)[1] == '.vtu':
reader = vtk.vtkXMLUnstructuredGridReader()
reader.SetFileName(options.vtk)
reader.Update()
uGrid = reader.GetOutput()
elif os.path.splitext(options.vtk)[1] == '.vtk':
reader = vtk.vtkGenericDataObjectReader()
reader.SetFileName(options.vtk)
reader.Update()
uGrid = reader.GetUnstructuredGridOutput()
else:
parser.error('unsupported VTK file type extension')
Npoints = uGrid.GetNumberOfPoints()
Ncells = uGrid.GetNumberOfCells()
sys.stderr.write('{}: {} points and {} cells...\n'.format(damask.util.emph(options.vtk),Npoints,Ncells))
# --- loop over input files -------------------------------------------------------------------------
if filenames == []: filenames = [None]
for name in filenames:
try:
table = damask.ASCIItable(name = name,
buffered = False, readonly = True)
except: continue
damask.util.croak(damask.util.emph(scriptName)+(': '+name if name else ''))
# --- interpret header ----------------------------------------------------------------------------
table.head_read()
remarks = []
errors = []
VTKarray = {}
active = defaultdict(list)
for datatype,dimension,label in [['scalar',1,options.scalar],
['color',3,options.color],
]:
for i,dim in enumerate(table.label_dimension(label)):
me = label[i]
if dim == -1: remarks.append('{} "{}" not found...'.format(datatype,me))
elif dim > dimension: remarks.append('"{}" not of dimension{}...'.format(me,dimension))
else:
damask.util.croak('adding {} {}'.format(datatype,me))
active[datatype].append(me)
if datatype in ['scalar']:
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 errors != []:
damask.util.croak(errors)
table.close(dismiss=True)
continue
# ------------------------------------------ process 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
theData = [table.data[i] for i in table.label_indexrange(me)] # read strings
if datatype == 'color':
VTKarray[me].InsertNextTuple3(*map(lambda x: int(255.*float(x)),theData))
elif datatype == 'scalar':
VTKarray[me].InsertNextValue(float(theData[0]))
# ------------------------------------------ add data ---------------------------------------
for datatype,labels in active.items(): # loop over scalar,color
if datatype == 'color':
uGrid.GetCellData().SetScalars(VTKarray[active['color'][0]])
for label in labels: # loop over all requested items
uGrid.GetCellData().AddArray(VTKarray[me])
uGrid.Modified()
if vtk.VTK_MAJOR_VERSION <= 5:
uGrid.Update()
# ------------------------------------------ output result ---------------------------------------
writer = vtk.vtkXMLUnstructuredGridWriter()
writer.SetDataModeToBinary()
writer.SetCompressorTypeToZLib()
writer.SetFileName(os.path.splitext(options.vtk)[0]+'_added.vtu')
if vtk.VTK_MAJOR_VERSION <= 5:
writer.SetInput(uGrid)
else:
writer.SetInputData(uGrid)
writer.Write()

31
processing/post/vtk_pointcloud.py
View File

@ -18,12 +18,13 @@ Produce a VTK point cloud dataset based on coordinates given in an ASCIItable.
""", version = scriptID)
parser.add_option('-d', '--deformed',
dest = 'deformed',
parser.add_option('-p',
'--pos', '--position',
dest = 'pos',
type = 'string', metavar = 'string',
help = 'deformed coordinate label [%default]')
help = 'label of coordinates [%default]')
parser.set_defaults(deformed = 'ipdeformedcoord'
parser.set_defaults(pos = 'pos',
)
(options, filenames) = parser.parse_args()
@ -46,9 +47,9 @@ for name in filenames:
errors = []
remarks = []
coordDim = table.label_dimension(options.deformed)
if not 3 >= coordDim >= 1: errors.append('coordinates "{}" need to have one, two, or three dimensions.'.format(options.deformed))
elif coordDim < 3: remarks.append('appending {} dimensions to coordinates "{}"...'.format(3-coordDim,options.deformed))
coordDim = table.label_dimension(options.pos)
if not 3 >= coordDim >= 1: errors.append('coordinates "{}" need to have one, two, or three dimensions.'.format(options.pos))
elif coordDim < 3: remarks.append('appending {} dimensions to coordinates "{}"...'.format(3-coordDim,options.pos))
if remarks != []: damask.util.croak(remarks)
if errors != []:
@ -58,7 +59,7 @@ for name in filenames:
# ------------------------------------------ process data ---------------------------------------
table.data_readArray(options.deformed)
table.data_readArray(options.pos)
if len(table.data.shape) < 2: table.data.shape += (1,) # expand to 2D shape
if table.data.shape[1] < 3:
table.data = np.hstack((table.data,
@ -83,19 +84,21 @@ for name in filenames:
if name:
writer = vtk.vtkXMLPolyDataWriter()
(directory,filename) = os.path.split(name)
writer.SetDataModeToBinary()
writer.SetCompressorTypeToZLib()
writer.SetFileName(os.path.join(directory,os.path.splitext(filename)[0]\
+'.'+writer.GetDefaultFileExtension()))
writer.SetDataModeToBinary()
writer.SetFileName(os.path.join(os.path.split(name)[0],
os.path.splitext(os.path.split(name)[1])[0] +
'.' + writer.GetDefaultFileExtension()))
else:
writer = vtk.vtkDataSetWriter()
writer.WriteToOutputStringOn()
writer.SetHeader('# powered by '+scriptID)
writer.WriteToOutputStringOn()
if vtk.VTK_MAJOR_VERSION <= 5: writer.SetInput(Polydata)
else: writer.SetInputData(Polydata)
writer.Write()
if name is None: sys.stdout.write(writer.GetOutputString()[0:writer.GetOutputStringLength()])
if name is None: sys.stdout.write(writer.GetOutputString()[:writer.GetOutputStringLength()]) # limiting of outputString is fix for vtk <7.0
table.close()

98
processing/post/vtk_rectilinearGrid.py
View File

@ -6,7 +6,6 @@ import numpy as np
import damask
from optparse import OptionParser
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
@ -15,20 +14,29 @@ scriptID = ' '.join([scriptName,damask.version])
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
Create regular voxel grid from points in an ASCIItable.
Create regular voxel grid from points in an ASCIItable (or geom file).
""", version = scriptID)
parser.add_option('-m', '--mode',
parser.add_option('-m',
'--mode',
dest = 'mode',
type = 'choice', choices = ['cell','point'],
help = 'cell-centered or point-centered coordinates ')
parser.add_option('-c', '--coordinates',
dest = 'position',
help = 'cell-centered or point-centered coordinates')
parser.add_option('-p',
'--pos', '--position',
dest = 'pos',
type = 'string', metavar = 'string',
help = 'coordinate label [%default]')
parser.set_defaults(position ='ipinitialcoord',
mode ='cell'
help = 'label of coordinates [%default]')
parser.add_option('-g',
'--geom',
dest = 'geom',
action = 'store_true',
help = 'geom input format')
parser.set_defaults(mode = 'cell',
pos = 'pos',
geom = False,
)
(options, filenames) = parser.parse_args()
@ -38,9 +46,12 @@ parser.set_defaults(position ='ipinitialcoord',
if filenames == []: filenames = [None]
for name in filenames:
try:
table = damask.ASCIItable(name = name,
buffered = False, readonly = True)
isGeom = options.geom or (name is not None and name.endswith('.geom'))
try: table = damask.ASCIItable(name = name,
buffered = False,
labeled = not isGeom,
readonly = True,
)
except: continue
damask.util.report(scriptName,name)
@ -48,10 +59,13 @@ for name in filenames:
table.head_read()
errors = []
if table.label_dimension(options.position) != 3:
errors.append('coordinates {} are not a vector.'.format(options.position))
remarks = []
errors = []
coordDim = 3 if isGeom else table.label_dimension(options.pos)
if not 3 >= coordDim >= 1: errors.append('coordinates "{}" need to have one, two, or three dimensions.'.format(options.pos))
elif coordDim < 3: remarks.append('appending {} dimensions to coordinates "{}"...'.format(3-coordDim,options.pos))
if remarks != []: damask.util.croak(remarks)
if errors != []:
damask.util.croak(errors)
table.close(dismiss=True)
@ -59,17 +73,33 @@ for name in filenames:
# --------------- figure out size and grid ---------------------------------------------------------
table.data_readArray(options.position)
if isGeom:
info,extra_header = table.head_getGeom()
coords = [np.linspace(info['origin'][i],
info['origin'][i]+info['size'][i],
num = info['grid'][i]+1,
endpoint = True,
) for i in xrange(3)]
else:
table.data_readArray(options.pos)
if len(table.data.shape) < 2: table.data.shape += (1,) # expand to 2D shape
if table.data.shape[1] < 3:
table.data = np.hstack((table.data,
np.zeros((table.data.shape[0],
3-table.data.shape[1]),dtype='f'))) # fill coords up to 3D with zeros
coords = [np.unique(table.data[:,i]) for i in xrange(3)]
if options.mode == 'cell':
coords = [0.5 * np.array([3.0 * coords[i][0] - coords[i][0 + len(coords[i]) > 1]] + \
[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)]
grid = np.array(map(len,coords),'i')
N = grid.prod() if options.mode == 'point' else (grid-1).prod()
coords = [np.unique(table.data[:,i]) for i in xrange(3)]
if N != len(table.data): errors.append('data count {} does not match grid {}x{}x{}.'.format(N,*(grid - 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[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)]
grid = np.array(map(len,coords),'i')
N = grid.prod() if options.mode == 'point' or isGeom else (grid-1).prod()
if not isGeom and N != len(table.data):
errors.append('data count {} does not match grid {}x{}x{}.'.format(N,*(grid - (options.mode == 'cell')) ))
if errors != []:
damask.util.croak(errors)
table.close(dismiss = True)
@ -93,24 +123,26 @@ for name in filenames:
rGrid.SetZCoordinates(coordArray[2])
# ------------------------------------------ output result ---------------------------------------
# ------------------------------------------ output result ---------------------------------------
if name:
writer = vtk.vtkXMLRectilinearGridWriter()
(directory,filename) = os.path.split(name)
writer.SetDataModeToBinary()
writer.SetCompressorTypeToZLib()
writer.SetFileName(os.path.join(directory,os.path.splitext(filename)[0] \
+'_{}({})'.format(options.position, options.mode) \
+'.'+writer.GetDefaultFileExtension()))
writer.SetDataModeToBinary()
writer.SetFileName(os.path.join(os.path.split(name)[0],
os.path.splitext(os.path.split(name)[1])[0] +
('' if isGeom else '_{}({})'.format(options.pos, options.mode)) +
'.' + writer.GetDefaultFileExtension()))
else:
writer = vtk.vtkDataSetWriter()
writer.WriteToOutputStringOn()
writer.SetHeader('# powered by '+scriptID)
writer.WriteToOutputStringOn()
if vtk.VTK_MAJOR_VERSION <= 5: writer.SetInput(rGrid)
else: writer.SetInputData(rGrid)
writer.Write()
if name is None: sys.stdout.write(writer.GetOutputString()[0:writer.GetOutputStringLength()])
if name is None: sys.stdout.write(writer.GetOutputString()[:writer.GetOutputStringLength()]) # limiting of outputString is fix for vtk <7.0
table.close()

122
processing/post/vtk_scalars2vectors.py
View File

@ -1,122 +0,0 @@
#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
import os,sys,shutil
import damask
from optparse import OptionParser
import vtk
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 = """
""", version = scriptID)
parser.add_option('-v','--vector', nargs=3, dest='vector', \
help='suffices indicating vector components [%default]')
parser.add_option('-s','--separator', dest='separator', \
help='separator between label and suffix [%default]')
parser.set_defaults(vector = ['x','y','z'])
parser.set_defaults(separator = '.')
(options, filenames) = parser.parse_args()
# --- sanity checks
if filenames == []:
parser.print_help()
parser.error('no file specified...')
for filename in filenames:
if not os.path.isfile(filename):
parser.print_help()
parser.error('invalid file "%s" specified...'%filename)
# --- ITERATE OVER FILES AND PROCESS THEM
for filename in filenames:
sys.stdout.write('read file "%s" ...'%filename)
sys.stdout.flush()
suffix = os.path.splitext(filename)[1]
if suffix == '.vtk':
reader = vtk.vtkUnstructuredGridReader()
reader.ReadAllScalarsOn()
reader.ReadAllVectorsOn()
reader.ReadAllTensorsOn()
elif suffix == '.vtu':
reader = vtk.vtkXMLUnstructuredGridReader()
else:
parser.error('filetype "%s" not supported'%suffix)
reader.SetFileName(filename)
reader.Update()
uGrid = reader.GetOutput()
sys.stdout.write(' done\n')
sys.stdout.flush()
# Read the scalar data
scalarData = {}
scalarsToBeRemoved = []
Nscalars = uGrid.GetCellData().GetNumberOfArrays()
for i in range(Nscalars):
sys.stdout.write("\rread scalar data %d%%" %(100*i/Nscalars))
sys.stdout.flush()
scalarName = uGrid.GetCellData().GetArrayName(i)
if scalarName.split(options.separator)[-1] in options.vector:
label,suffix = scalarName.split(options.separator)
if label not in scalarData:
scalarData[label] = [[],[],[]]
uGrid.GetCellData().SetActiveScalars(scalarName)
scalarData[label][options.vector.index(suffix)] = uGrid.GetCellData().GetScalars(scalarName)
scalarsToBeRemoved.append(scalarName)
for scalarName in scalarsToBeRemoved:
uGrid.GetCellData().RemoveArray(scalarName)
sys.stdout.write('\rread scalar data done\n')
sys.stdout.flush()
# Convert the scalar data to vector data
NscalarData = len(scalarData)
for n,label in enumerate(scalarData):
sys.stdout.write("\rconvert to vector data %d%%" %(100*n/NscalarData))
sys.stdout.flush()
Nvalues = scalarData[label][0].GetNumberOfTuples()
vectorData = vtk.vtkDoubleArray()
vectorData.SetName(label)
vectorData.SetNumberOfComponents(3) # set this before NumberOfTuples !!!
vectorData.SetNumberOfTuples(Nvalues)
for i in range(Nvalues):
for j in range(3):
vectorData.SetComponent(i,j,scalarData[label][j].GetValue(i))
uGrid.GetCellData().AddArray(vectorData)
sys.stdout.write('\rconvert to vector data done\n')
# Write to new vtk file
outfilename = os.path.splitext(filename)[0]+'.vtu'
sys.stdout.write('write to file "%s" ...'%outfilename)
sys.stdout.flush()
writer = vtk.vtkXMLUnstructuredGridWriter()
writer.SetFileName(outfilename+'_tmp')
writer.SetDataModeToAscii()
writer.SetInput(uGrid)
writer.Write()
sys.stdout.write(' done\n')
sys.stdout.flush()
shutil.move(outfilename+'_tmp',outfilename)
# --------------------------- DONE --------------------------------

118
processing/post/vtk_voxelcloud.py
View File

@ -1,118 +0,0 @@
#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
import os,sys,vtk
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 = """
Create hexahedral voxels around points in an ASCIItable.
""", version = scriptID)
parser.add_option('-d', '--deformed',
dest = 'deformed',
type = 'string', metavar = 'string',
help = 'deformed coordinate label [%default]')
parser.add_option('-c','--coordinates',
dest = 'coords',
type = 'string', metavar='string',
help = 'undeformed coordinates label [%default]')
parser.set_defaults(deformed = 'ipdeformedcoord',
coords = 'ipinitialcoord',
)
(options, filenames) = parser.parse_args()
# --- loop over input files -------------------------------------------------------------------------
if filenames == []: filenames = [None]
for name in filenames:
try:
table = damask.ASCIItable(name = name,
buffered = False, readonly = True)
except: continue
damask.util.report(scriptName,name)
# --------------- interprete header -----------------------------------------------------------------
table.head_read()
errors=[]
if table.label_dimension(options.deformed) != 3:
errors.append('columns "{}" have dimension {}'.format(options.deformed,table.label_dimension(options.deformed)))
if table.label_dimension(options.coords) != 3:
errors.append('coordinates {} are not a vector.'.format(options.coords))
table.data_readArray([options.coords,options.deformed])
# --------------- figure out size and grid ---------------------------------------------------------
coords = [{},{},{}]
for i in xrange(len(table.data)):
for j in xrange(3):
coords[j][str(table.data[i,table.label_index(options.coords)+j])] = True
grid = np.array(map(len,coords),'i')
size = grid/np.maximum(np.ones(3,'d'),grid-1.0)* \
np.array([max(map(float,coords[0].keys()))-min(map(float,coords[0].keys())),\
max(map(float,coords[1].keys()))-min(map(float,coords[1].keys())),\
max(map(float,coords[2].keys()))-min(map(float,coords[2].keys())),\
],'d') # size from bounding box, corrected for cell-centeredness
size = np.where(grid > 1, size, min(size[grid > 1]/grid[grid > 1])) # spacing for grid==1 set to smallest among other spacings
# ------------------------------------------ process data ---------------------------------------
hexPoints = np.array([[-1,-1,-1],
[ 1,-1,-1],
[ 1, 1,-1],
[-1, 1,-1],
[-1,-1, 1],
[ 1,-1, 1],
[ 1, 1, 1],
[-1, 1, 1],
])
halfDelta = 0.5*size/grid
Points = vtk.vtkPoints()
Hex = vtk.vtkHexahedron()
uGrid = vtk.vtkUnstructuredGrid()
for p in table.data:
for i,h in enumerate(hexPoints):
pointID = Points.InsertNextPoint(p[table.label_index(options.deformed):table.label_index(options.deformed)+3]+h*halfDelta)
Hex.GetPointIds().SetId(i,pointID)
uGrid.InsertNextCell(Hex.GetCellType(), Hex.GetPointIds())
uGrid.SetPoints(Points)
# ------------------------------------------ output result ---------------------------------------
if name:
writer = vtk.vtkXMLUnstructuredGridWriter()
(directory,filename) = os.path.split(name)
writer.SetDataModeToBinary()
writer.SetCompressorTypeToZLib()
writer.SetFileName(os.path.join(directory,os.path.splitext(filename)[0]\
+'.'+writer.GetDefaultFileExtension()))
else:
writer = vtk.vtkDataSetWriter()
writer.WriteToOutputStringOn()
writer.SetHeader('# powered by '+scriptID)
if vtk.VTK_MAJOR_VERSION <= 5: writer.SetInput(uGrid)
else: writer.SetInputData(uGrid)
writer.Write()
if name is None: sys.stdout.write(writer.GetOutputString()[0:writer.GetOutputStringLength()])
table.close() # close input ASCII table

42
processing/pre/geom_canvas.py
View File

@ -15,25 +15,29 @@ scriptID = ' '.join([scriptName,damask.version])
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
Changes the (three-dimensional) canvas of a spectral geometry description.
Grid can be given as absolute or relative values, e.g. 16 16 16 or 2x 0.5x 32.
""", version = scriptID)
parser.add_option('-g', '--grid',
parser.add_option('-g',
'--grid',
dest = 'grid',
type = 'string', nargs = 3, metavar = ' '.join(['string']*3),
help = 'a,b,c grid of hexahedral box [auto]')
parser.add_option('-o', '--offset',
help = 'a,b,c grid of hexahedral box. [auto]')
parser.add_option('-o',
'--offset',
dest = 'offset',
type = 'int', nargs = 3, metavar = ' '.join(['int']*3),
help = 'a,b,c offset from old to new origin of grid [%default]')
parser.add_option('-f', '--fill',
parser.add_option('-f',
'--fill',
dest = 'fill',
type = 'float', metavar = 'float',
help = '(background) canvas grain index. "0" selects maximum microstructure index + 1 [%default]')
parser.add_option('--float',
dest = 'real',
action = 'store_true',
help = 'input data is float [%default]')
help = 'use float input')
parser.set_defaults(grid = ['0','0','0'],
offset = (0,0,0),
@ -61,13 +65,7 @@ for name in filenames:
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'],
])
damask.util.report_geom(info)
errors = []
if np.any(info['grid'] < 1): errors.append('invalid grid a b c.')
@ -105,7 +103,7 @@ for name in filenames:
translate_y = [i - options.offset[1] for i in yindex]
translate_z = [i - options.offset[2] for i in zindex]
if 0 in map(len,[xindex,yindex,zindex,translate_x,translate_y,translate_z]):
damask.util.croak('Invaldid grid-offset comination')
damask.util.croak('invaldid grid-offset combination.')
table.close(dismiss = True)
continue
microstructure_cropped[min(translate_x):(max(translate_x)+1),\
@ -125,13 +123,13 @@ for name in filenames:
errors = []
if (any(newInfo['grid'] != info['grid'])):
remarks.append('--> grid a b c: %s'%(' x '.join(map(str,newInfo['grid']))))
remarks.append('--> grid a b c: {}'.format(' 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']))))
remarks.append('--> size x y z: {}'.format(' x '.join(map(str,newInfo['size']))))
if (any(newInfo['origin'] != info['origin'])):
remarks.append('--> origin x y z: %s'%(' : '.join(map(str,newInfo['origin']))))
remarks.append('--> origin x y z: {}'.format(' : '.join(map(str,newInfo['origin']))))
if ( newInfo['microstructures'] != info['microstructures']):
remarks.append('--> microstructures: %i'%newInfo['microstructures'])
remarks.append('--> microstructures: {}'.format(newInfo['microstructures']))
if np.any(newInfo['grid'] < 1): errors.append('invalid new grid a b c.')
if np.any(newInfo['size'] <= 0.0): errors.append('invalid new size x y z.')
@ -147,11 +145,11 @@ for name in filenames:
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=newInfo['origin']),
"homogenization\t{homog}".format(homog=info['homogenization']),
"microstructures\t{microstructures}".format(microstructures=newInfo['microstructures']),
"grid\ta {}\tb {}\tc {}".format(*newInfo['grid']),
"size\tx {}\ty {}\tz {}".format(*newInfo['size']),
"origin\tx {}\ty {}\tz {}".format(*newInfo['origin']),
"homogenization\t{}".format(info['homogenization']),
"microstructures\t{}".format(newInfo['microstructures']),
extra_header
])
table.labels_clear()

108
processing/pre/geom_check.py
View File

@ -1,108 +0,0 @@
#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
import os,sys,vtk
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 [file[s]]', description = """
Produce VTK rectilinear mesh of structure data from geom description
""", version = scriptID)
parser.add_option('-m','--nodata',
dest = 'data',
action = 'store_false',
help = 'generate mesh without microstructure index data')
parser.set_defaults(data = True,
)
(options, filenames) = parser.parse_args()
# --- loop over input files -------------------------------------------------------------------------
if filenames == []: filenames = [None]
for name in filenames:
try:
table = damask.ASCIItable(name = name,
buffered = False, labeled = False, readonly = True)
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.')
#--- read microstructure information --------------------------------------------------------------
if options.data:
microstructure,ok = table.microstructure_read(info['grid'],strict = True) # read microstructure
if ok:
structure = vtk.vtkIntArray()
structure.SetName('Microstructures')
for idx in microstructure: structure.InsertNextValue(idx)
else: errors.append('mismatch between data and grid dimension.')
if errors != []:
damask.util.croak(errors)
table.close(dismiss = True)
continue
# --- generate VTK rectilinear grid ---------------------------------------------------------------
grid = vtk.vtkRectilinearGrid()
grid.SetDimensions([x+1 for x in info['grid']])
for i in xrange(3):
temp = vtk.vtkDoubleArray()
temp.SetNumberOfTuples(info['grid'][i]+1)
for j in xrange(info['grid'][i]+1):
temp.InsertTuple1(j,j*info['size'][i]/info['grid'][i]+info['origin'][i])
if i == 0: grid.SetXCoordinates(temp)
elif i == 1: grid.SetYCoordinates(temp)
elif i == 2: grid.SetZCoordinates(temp)
if options.data: grid.GetCellData().AddArray(structure)
# --- write data -----------------------------------------------------------------------------------
if name:
writer = vtk.vtkXMLRectilinearGridWriter()
(directory,filename) = os.path.split(name)
writer.SetDataModeToBinary()
writer.SetCompressorTypeToZLib()
writer.SetFileName(os.path.join(directory,os.path.splitext(filename)[0]+'.'+writer.GetDefaultFileExtension()))
else:
writer = vtk.vtkDataSetWriter()
writer.WriteToOutputStringOn()
writer.SetHeader('# powered by '+scriptID)
if vtk.VTK_MAJOR_VERSION <= 5: writer.SetInput(grid)
else: writer.SetInputData(grid)
writer.Write()
if name is None: sys.stdout.write(writer.GetOutputString()[0:writer.GetOutputStringLength()])
table.close()

15
processing/pre/geom_check.sh Executable file
View File

@ -0,0 +1,15 @@
#!/bin/bash
for geom in "$@"
do
vtk_rectilinearGrid \
--geom $geom
geom_toTable \
< $geom \
| \
vtk_addRectilinearGridData \
--scalar microstructure \
--inplace \
--vtk ${geom%.*}.vtr
done

14
processing/pre/geom_clean.py
View File

@ -6,15 +6,12 @@ import numpy as np
import damask
from scipy import ndimage
from optparse import OptionParser
from collections import defaultdict
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
def mostFrequent(arr):
d = defaultdict(int)
for i in arr: d[i] += 1
return sorted(d.iteritems(), key=lambda x: x[1], reverse=True)[0][0] # return value of most frequent microstructure
return np.argmax(np.bincount(arr))
#--------------------------------------------------------------------------------------------------
@ -43,10 +40,9 @@ parser.set_defaults(stencil = 3,
if filenames == []: filenames = [None]
for name in filenames:
try:
table = damask.ASCIItable(name = name,
buffered = False,
labeled = False)
try: table = damask.ASCIItable(name = name,
buffered = False,
labeled = False)
except: continue
damask.util.report(scriptName,name)
@ -72,7 +68,7 @@ for name in filenames:
# --- read data ------------------------------------------------------------------------------------
microstructure = table.microstructure_read(info['grid']).reshape(info['grid'],order='F') # read microstructure
microstructure = table.microstructure_read(info['grid']).reshape(info['grid'],order='F') # read microstructure
# --- do work ------------------------------------------------------------------------------------

110
processing/pre/geom_fromImage.py
View File

@ -1,110 +0,0 @@
#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
import os,sys,math
import numpy as np
from optparse import OptionParser
from PIL import Image
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 = """
Generate geometry description from (multilayer) images.
Microstructure index is based on gray scale value (1..256).
""", version = scriptID)
parser.add_option('--homogenization',
dest = 'homogenization',
type = 'int', metavar = 'int',
help = 'homogenization index [%default]')
parser.set_defaults(homogenization = 1,
)
(options,filenames) = parser.parse_args()
# --- loop over input files -------------------------------------------------------------------------
if filenames == []: filenames = [None]
for name in filenames:
try:
table = damask.ASCIItable(name = name,
outname = os.path.splitext(name)[0]+'.geom' if name else name,
buffered = False, labeled = False)
except: continue
table.croak('\033[1m'+scriptName+'\033[0m'+(': '+name if name else ''))
# --- read image ------------------------------------------------------------------------------------
img = Image.open(name).convert(mode = 'L') # open and convert to grayscale 8bit
slice = 0
while True:
try:
img.seek(slice) # advance to slice
layer = np.expand_dims(1+np.array(img,dtype = 'uint16'),axis = 0) # read image layer
microstructure = layer if slice == 0 else np.vstack((microstructure,layer)) # noqa
slice += 1 # advance to next slice
except EOFError:
break
# http://docs.scipy.org/doc/scipy/reference/ndimage.html
# http://scipy-lectures.github.io/advanced/image_processing/
info = {
'grid': np.array(microstructure.shape,'i')[::-1],
'size': np.array(microstructure.shape,'d')[::-1],
'origin': np.zeros(3,'d'),
'microstructures': len(np.unique(microstructure)),
'homogenization': options.homogenization,
}
# --- report ---------------------------------------------------------------------------------------
table.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 != []:
table.croak(errors)
table.close(dismiss = True)
continue
# --- write header ---------------------------------------------------------------------------------
table.info_clear()
table.info_append([
scriptID + ' ' + ' '.join(sys.argv[1:]),
"grid\ta {grid[0]}\tb {grid[1]}\tc {grid[2]}".format(grid=info['grid']),
"size\tx {size[0]}\ty {size[1]}\tz {size[2]}".format(size=info['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']),
])
table.labels_clear()
table.head_write()
table.output_flush()
# --- write microstructure information ------------------------------------------------------------
formatwidth = int(math.floor(math.log10(microstructure.max())+1))
table.data = microstructure.reshape((info['grid'][1]*info['grid'][2],info['grid'][0]),order='C')
table.data_writeArray('%%%ii'%(formatwidth),delimiter = ' ')
# --- output finalization --------------------------------------------------------------------------
table.close() # close ASCII table

233
processing/pre/geom_fromVoronoiTessellation.py
View File

@ -4,7 +4,7 @@
import os,sys,math
import numpy as np
import multiprocessing
from optparse import OptionParser
from optparse import OptionParser,OptionGroup
from scipy import spatial
import damask
@ -109,98 +109,112 @@ Generate geometry description and material configuration by standard Voronoi tes
""", version = scriptID)
parser.add_option('-g', '--grid',
dest = 'grid',
type = 'int', nargs = 3, metavar = ' '.join(['int']*3),
help = 'a,b,c grid of hexahedral box [auto]')
parser.add_option('-s', '--size',
dest = 'size',
type = 'float', nargs = 3, metavar=' '.join(['float']*3),
help = 'x,y,z size of hexahedral box [auto]')
parser.add_option('-o', '--origin',
dest = 'origin',
type = 'float', nargs = 3, metavar=' '.join(['float']*3),
help = 'offset from old to new origin of grid')
parser.add_option('-p', '--position',
dest = 'position',
type = 'string', metavar = 'string',
help = 'column label for seed positions [%default]')
parser.add_option('-w', '--weight',
dest = 'weight',
type = 'string', metavar = 'string',
help = 'column label for seed weights [%default]')
parser.add_option('-m', '--microstructure',
dest = 'microstructure',
type = 'string', metavar = 'string',
help = 'column label for seed microstructures [%default]')
parser.add_option('-e', '--eulers',
dest = 'eulers',
type = 'string', metavar = 'string',
help = 'column label for seed Euler angles [%default]')
parser.add_option('--axes',
dest = 'axes',
type = 'string', nargs = 3, metavar = ' '.join(['string']*3),
help = 'orientation coordinate frame in terms of position coordinate frame')
parser.add_option('--homogenization',
dest = 'homogenization',
type = 'int', metavar = 'int',
help = 'homogenization index to be used [%default]')
parser.add_option('--crystallite',
dest = 'crystallite',
type = 'int', metavar = 'int',
help = 'crystallite index to be used [%default]')
parser.add_option('--phase',
dest = 'phase',
type = 'int', metavar = 'int',
help = 'phase index to be used [%default]')
parser.add_option('-r', '--rnd',
dest = 'randomSeed',
type = 'int', metavar='int',
help = 'seed of random number generator for second phase distribution [%default]')
parser.add_option('--secondphase',
dest = 'secondphase',
type = 'float', metavar= 'float',
help = 'volume fraction of randomly distribute second phase [%default]')
parser.add_option('-l', '--laguerre',
dest = 'laguerre',
action = 'store_true',
help = 'use Laguerre (weighted Voronoi) tessellation')
parser.add_option('--cpus',
dest = 'cpus',
type = 'int', metavar = 'int',
help = 'number of parallel processes to use for Laguerre tessellation [%default]')
parser.add_option('--nonperiodic',
dest = 'nonperiodic',
action = 'store_true',
help = 'use nonperiodic tessellation')
parser.set_defaults(position = 'pos',
group = OptionGroup(parser, "Tessellation","")
group.add_option('-l',
'--laguerre',
dest = 'laguerre',
action = 'store_true',
help = 'use Laguerre (weighted Voronoi) tessellation')
group.add_option('--cpus',
dest = 'cpus',
type = 'int', metavar = 'int',
help = 'number of parallel processes to use for Laguerre tessellation [%default]')
group.add_option('--nonperiodic',
dest = 'nonperiodic',
action = 'store_true',
help = 'nonperiodic tessellation')
parser.add_option_group(group)
group = OptionGroup(parser, "Geometry","")
group.add_option('-g',
'--grid',
dest = 'grid',
type = 'int', nargs = 3, metavar = ' '.join(['int']*3),
help = 'a,b,c grid of hexahedral box [auto]')
group.add_option('-s',
'--size',
dest = 'size',
type = 'float', nargs = 3, metavar=' '.join(['float']*3),
help = 'x,y,z size of hexahedral box [auto]')
group.add_option('-o',
'--origin',
dest = 'origin',
type = 'float', nargs = 3, metavar=' '.join(['float']*3),
help = 'origin of grid')
parser.add_option_group(group)
group = OptionGroup(parser, "Seeds","")
group.add_option('-p',
'--pos', '--seedposition',
dest = 'pos',
type = 'string', metavar = 'string',
help = 'label of coordinates [%default]')
group.add_option('-w',
'--weight',
dest = 'weight',
type = 'string', metavar = 'string',
help = 'label of weights [%default]')
group.add_option('-m',
'--microstructure',
dest = 'microstructure',
type = 'string', metavar = 'string',
help = 'label of microstructures [%default]')
group.add_option('-e',
'--eulers',
dest = 'eulers',
type = 'string', metavar = 'string',
help = 'label of Euler angles [%default]')
group.add_option('--axes',
dest = 'axes',
type = 'string', nargs = 3, metavar = ' '.join(['string']*3),
help = 'orientation coordinate frame in terms of position coordinate frame')
parser.add_option_group(group)
group = OptionGroup(parser, "Configuration","")
group.add_option('--homogenization',
dest = 'homogenization',
type = 'int', metavar = 'int',
help = 'homogenization index to be used [%default]')
group.add_option('--crystallite',
dest = 'crystallite',
type = 'int', metavar = 'int',
help = 'crystallite index to be used [%default]')
group.add_option('--phase',
dest = 'phase',
type = 'int', metavar = 'int',
help = 'phase index to be used [%default]')
parser.add_option_group(group)
parser.set_defaults(pos = 'pos',
weight = 'weight',
microstructure = 'microstructure',
eulers = 'eulerangles',
eulers = 'euler',
homogenization = 1,
crystallite = 1,
phase = 1,
secondphase = 0.0,
cpus = 2,
laguerre = False,
nonperiodic = False,
randomSeed = None,
)
(options,filenames) = parser.parse_args()
if options.secondphase > 1.0 or options.secondphase < 0.0:
parser.error('volume fraction of second phase ({}) out of bounds.'.format(options.secondphase))
# --- loop over input files -------------------------------------------------------------------------
if filenames == []: filenames = [None]
for name in filenames:
try:
table = damask.ASCIItable(name = name,
outname = os.path.splitext(name)[-2]+'.geom' if name else name,
buffered = False)
try: table = damask.ASCIItable(name = name,
outname = os.path.splitext(name)[0]+'.geom' if name else name,
buffered = False)
except: continue
damask.util.report(scriptName,name)
@ -232,11 +246,11 @@ for name in filenames:
info['size'][i] = float(info['grid'][i])/max(info['grid']) # normalize to grid
remarks.append('rescaling size {} to {}...'.format({0:'x',1:'y',2:'z'}[i],info['size'][i]))
if table.label_dimension(options.position) != 3:
errors.append('position columns "{}" have dimension {}.'.format(options.position,
table.label_dimension(options.position)))
if table.label_dimension(options.pos) != 3:
errors.append('seed positions "{}" have dimension {}.'.format(options.pos,
table.label_dimension(options.pos)))
else:
labels += [options.position]
labels += [options.pos]
if not hasEulers: remarks.append('missing seed orientations...')
else: labels += [options.eulers]
@ -254,15 +268,14 @@ for name in filenames:
# ------------------------------------------ read seeds ---------------------------------------
table.data_readArray(labels)
coords = table.data[:,table.label_index(options.position):table.label_index(options.position)+3]\
* info['size']
eulers = table.data[:,table.label_index(options.eulers ):table.label_index(options.eulers )+3]\
if hasEulers else np.zeros(3*len(coords))
grains = table.data[:,table.label_index(options.microstructure)].astype('i')\
if hasGrains else 1+np.arange(len(coords))
weights = table.data[:,table.label_index(options.weight)]\
if hasWeights else np.zeros(len(coords))
grainIDs = np.unique(grains).astype('i')
coords = table.data[:,table.label_indexrange(options.pos)] * info['size']
eulers = table.data[:,table.label_indexrange(options.eulers)] if hasEulers \
else np.zeros(3*len(coords))
grains = table.data[:,table.label_indexrange(options.microstructure)].astype('i') if hasGrains \
else 1+np.arange(len(coords))
weights = table.data[:,table.label_indexrange(options.weight)] if hasWeights \
else np.zeros(len(coords))
grainIDs = np.unique(grains).astype('i')
NgrainIDs = len(grainIDs)
# --- tessellate microstructure ------------------------------------------------------------
@ -283,50 +296,38 @@ for name in filenames:
if info['homogenization'] == 0: info['homogenization'] = options.homogenization
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%s'%(info['microstructures'],
(' out of %i'%NgrainIDs if NgrainIDs != info['microstructures'] else '')),
])
damask.util.report_geom(info,['grid','size','origin','homogenization',])
damask.util.croak(['microstructures: {}{}'.format(info['microstructures'],
(' out of {}'.format(NgrainIDs) if NgrainIDs != info['microstructures'] else '')),
])
config_header = []
formatwidth = 1+int(math.log10(NgrainIDs))
phase = options.phase * np.ones(NgrainIDs,'i')
if int(options.secondphase*info['microstructures']) > 0:
phase[0:int(options.secondphase*info['microstructures'])] += 1 # alter fraction 'options.secondphase' of used grainIDs
randomSeed = options.randomSeed if options.randomSeed \
else int(os.urandom(4).encode('hex'), 16) # random seed for second phase
np.random.seed(randomSeed)
np.random.shuffle(phase)
config_header += ['# random seed (phase shuffling): {}'.format(randomSeed)]
config_header += ['<microstructure>']
for i,ID in enumerate(grainIDs):
config_header += ['[Grain%s]'%(str(ID).zfill(formatwidth)),
'crystallite %i'%options.crystallite,
'(constituent)\tphase %i\ttexture %s\tfraction 1.0'%(phase[i],str(ID).rjust(formatwidth)),
config_header += ['[Grain{}]'.format(str(ID).zfill(formatwidth)),
'crystallite {}'.format(options.crystallite),
'(constituent)\tphase {}\ttexture {}\tfraction 1.0'.format(options.phase,str(ID).rjust(formatwidth)),
]
if hasEulers:
config_header += ['<texture>']
for ID in grainIDs:
eulerID = np.nonzero(grains == ID)[0][0] # find first occurrence of this grain id
config_header += ['[Grain%s]'%(str(ID).zfill(formatwidth)),
'(gauss)\tphi1 %g\tPhi %g\tphi2 %g\tscatter 0.0\tfraction 1.0'%tuple(eulers[eulerID])
config_header += ['[Grain{}]'.format(str(ID).zfill(formatwidth)),
'(gauss)\tphi1 {:g}\tPhi {:g}\tphi2 {:g}\tscatter 0.0\tfraction 1.0'.format(*eulers[eulerID])
]
if options.axes is not None: config_header.append('axes\t%s %s %s'%tuple(options.axes))
if options.axes is not None: config_header.append('axes\t{} {} {}'.format(*options.axes))
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=info['grid']),
"size\tx {size[0]}\ty {size[1]}\tz {size[2]}".format(size=info['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']),
"grid\ta {}\tb {}\tc {}".format(*info['grid']),
"size\tx {}\ty {}\tz {}".format(*info['size']),
"origin\tx {}\ty {}\tz {}".format(*info['origin']),
"homogenization\t{}".format(info['homogenization']),
"microstructures\t{}".format(info['microstructures']),
config_header,
])
table.head_write()

25
processing/pre/geom_toTable.py
View File

@ -19,16 +19,18 @@ Translate geom description into ASCIItable containing 1/2/3_pos and microstructu
""", version = scriptID)
parser.add_option('-p','--position',
dest = 'position',
parser.add_option('-p',
'--pos', '--position',
dest = 'pos',
type = 'string', metavar = 'string',
help = 'column label for position [%default]')
parser.add_option('-m','--microstructure',
help = 'label of coordinates [%default]')
parser.add_option('-m',
'--microstructure',
dest = 'microstructure',
type = 'string', metavar = 'string',
help = 'column label for microstructure index [%default]')
help = 'label of microstructure index [%default]')
parser.set_defaults(position = 'pos',
parser.set_defaults(pos = 'pos',
microstructure = 'microstructure',
)
@ -39,10 +41,11 @@ parser.set_defaults(position = 'pos',
if filenames == []: filenames = [None]
for name in filenames:
try:
table = damask.ASCIItable(name = name,
outname = os.path.splitext(name)[0]+'.txt' if name else name,
buffered = False, labeled = False)
try: table = damask.ASCIItable(name = name,
outname = os.path.splitext(name)[0]+'.txt' if name else name,
buffered = False,
labeled = False,
)
except: continue
damask.util.report(scriptName,name)
@ -75,7 +78,7 @@ for name in filenames:
table.info_clear()
table.info_append(extra_header + [scriptID + '\t' + ' '.join(sys.argv[1:])])
table.labels_clear()
table.labels_append(['{}_{}'.format(1+i,options.position) for i in xrange(3)]+[options.microstructure])
table.labels_append(['{}_{}'.format(1+i,options.pos) for i in xrange(3)]+[options.microstructure])
table.head_write()
table.output_flush()

125
processing/pre/seeds_check.py
View File

@ -1,125 +0,0 @@
#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
import os,sys,vtk
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
#--------------------------------------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog [seedsfile[s]]', description = """
Produce VTK point mesh from seeds file
""", version = scriptID)
parser.add_option('-s', '--size',
dest = 'size',
type = 'float', nargs = 3, metavar = 'float float float',
help = 'x,y,z size of hexahedral box [1.0 along largest grid point number]')
parser.add_option('-p','--position',
dest = 'position',
type = 'string', metavar = 'string',
help = 'column label for coordinates [%default]')
parser.set_defaults(size = [0.0,0.0,0.0],
position = 'pos',
)
(options, filenames) = parser.parse_args()
# --- loop over input files -------------------------------------------------------------------------
if filenames == []: filenames = [None]
for name in filenames:
try:
table = damask.ASCIItable(name = name,
buffered = False, readonly = True)
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'],
])
remarks = []
errors = []
if np.any(info['grid'] < 1): remarks.append('invalid grid a b c.')
if np.any(info['size'] <= 0.0) \
and np.all(info['grid'] < 1): errors.append('invalid size x y z.')
else:
for i in xrange(3):
if info['size'][i] <= 0.0: # any invalid size?
info['size'][i] = float(info['grid'][i])/max(info['grid']) # normalize to grid
remarks.append('rescaling size {} to {}...'.format({0:'x',1:'y',2:'z'}[i],info['size'][i]))
if table.label_dimension(options.position) != 3:
errors.append('columns "{}" have dimension {}'.format(options.position,table.label_dimension(options.position)))
if remarks != []: damask.util.croak(remarks)
if errors != []:
damask.util.croak(errors)
table.close(dismiss=True)
continue
labels = ['{dim}_{label}'.format(dim = 1+i,label = options.position) for i in xrange(3)]
hasGrains = table.label_index('microstructure') != -1
labels += ['microstructure'] if hasGrains else []
table.data_readArray(labels) # read ASCIItable columns
coords = table.data[:,:3]*info['size'] # assign coordinates (rescaled to box size)
grain = table.data[:,3].astype('i') if hasGrains else 1+np.arange(len(coords),dtype='i') # assign grains
# --- generate grid --------------------------------------------------------------------------------
grid = vtk.vtkUnstructuredGrid()
pts = vtk.vtkPoints()
# --- process microstructure information -----------------------------------------------------------
IDs = vtk.vtkIntArray()
IDs.SetNumberOfComponents(1)
IDs.SetName("GrainID")
for i,item in enumerate(coords):
IDs.InsertNextValue(grain[i])
pid = pts.InsertNextPoint(item[0:3])
pointIds = vtk.vtkIdList()
pointIds.InsertId(0, pid)
grid.InsertNextCell(1, pointIds)
grid.SetPoints(pts)
grid.GetCellData().AddArray(IDs)
#--- write data -----------------------------------------------------------------------------------
if name:
writer = vtk.vtkXMLRectilinearGridWriter()
(directory,filename) = os.path.split(name)
writer.SetDataModeToBinary()
writer.SetCompressorTypeToZLib()
writer.SetFileName(os.path.join(directory,os.path.splitext(filename)[0]+'.'+writer.GetDefaultFileExtension()))
else:
writer = vtk.vtkDataSetWriter()
writer.WriteToOutputStringOn()
writer.SetHeader('# powered by '+scriptID)
if vtk.VTK_MAJOR_VERSION <= 5: writer.SetInput(grid)
else: writer.SetInputData(grid)
writer.Write()
if name is None: sys.stdout.write(writer.GetOutputString()[0:writer.GetOutputStringLength()])
table.close()

12
processing/pre/seeds_check.sh Executable file
View File

@ -0,0 +1,12 @@
#!/bin/bash
for seeds in "$@"
do
vtk_pointcloud $seeds
vtk_addPointCloudData $seeds \
--scalar microstructure,weight \
--inplace \
--vtk ${seeds%.*}.vtp \
done

51
processing/pre/seeds_fromGeom.py
View File

@ -14,26 +14,30 @@ scriptID = ' '.join([scriptName,damask.version])
#--------------------------------------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
Create seed file taking microstructure indices from given geom file but excluding black-listed grains.
Create seed file taking microstructure indices from given geom file.
Indices can be black-listed or white-listed.
""", version = scriptID)
parser.add_option('-w','--white',
action = 'extend', metavar='<int LIST>',
parser.add_option('-w',
'--white',
action = 'extend', metavar = '<int LIST>',
dest = 'whitelist',
help = 'whitelist of grain IDs')
parser.add_option('-b','--black',
action = 'extend', metavar='<int LIST>',
parser.add_option('-b',
'--black',
action = 'extend', metavar = '<int LIST>',
dest = 'blacklist',
help = 'blacklist of grain IDs')
parser.add_option('-p','--position',
parser.add_option('-p',
'--pos', '--seedposition',
dest = 'position',
type = 'string', metavar = 'string',
help = 'column label for coordinates [%default]')
help = 'label of coordinates [%default]')
parser.set_defaults(whitelist = [],
blacklist = [],
position = 'pos',
pos = 'pos',
)
(options,filenames) = parser.parse_args()
@ -46,25 +50,18 @@ options.blacklist = map(int,options.blacklist)
if filenames == []: filenames = [None]
for name in filenames:
try:
table = damask.ASCIItable(name = name,
outname = os.path.splitext(name)[0]+'.seeds' if name else name,
buffered = False, labeled = False)
except:
continue
try: table = damask.ASCIItable(name = name,
outname = os.path.splitext(name)[0]+'.seeds' if name else 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'],
])
damask.util.report_geom(info)
errors = []
if np.any(info['grid'] < 1): errors.append('invalid grid a b c.')
@ -98,14 +95,14 @@ for name in filenames:
table.info_clear()
table.info_append(extra_header+[
scriptID + ' ' + ' '.join(sys.argv[1:]),
"grid\ta {grid[0]}\tb {grid[1]}\tc {grid[2]}".format(grid=info['grid']),
"size\tx {size[0]}\ty {size[1]}\tz {size[2]}".format(size=info['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']),
"grid\ta {}\tb {}\tc {}".format(*info['grid']),
"size\tx {}\ty {}\tz {}".format(*info['size']),
"origin\tx {}\ty {}\tz {}".format(*info['origin']),
"homogenization\t{}".format(info['homogenization']),
"microstructures\t{}".format(info['microstructures']),
])
table.labels_clear()
table.labels_append(['{dim}_{label}'.format(dim = 1+i,label = options.position) for i in range(3)]+['microstructure'])
table.labels_append(['{dim}_{label}'.format(dim = 1+i,label = options.pos) for i in range(3)]+['microstructure'])
table.head_write()
table.output_flush()

87
processing/pre/seeds_fromRandom.py
View File

@ -34,61 +34,71 @@ Reports positions with random crystal orientations in seeds file format to STDOU
""", version = scriptID)
parser.add_option('-N', dest='N',
parser.add_option('-N',
dest = 'N',
type = 'int', metavar = 'int',
help = 'number of seed points to distribute [%default]')
parser.add_option('-g','--grid',
help = 'number of seed points [%default]')
parser.add_option('-g',
'--grid',
dest = 'grid',
type = 'int', nargs = 3, metavar = 'int int int',
help='min a,b,c grid of hexahedral box %default')
parser.add_option('-m', '--microstructure',
parser.add_option('-m',
'--microstructure',
dest = 'microstructure',
type = 'int', metavar='int',
type = 'int', metavar = 'int',
help = 'first microstructure index [%default]')
parser.add_option('-r', '--rnd',
parser.add_option('-r',
'--rnd',
dest = 'randomSeed', type = 'int', metavar = 'int',
help = 'seed of random number generator [%default]')
parser.add_option('--format',
dest = 'format', type = 'string', metavar = 'string',
help = 'output number format [auto]')
group = OptionGroup(parser, "Laguerre Tessellation Options",
group = OptionGroup(parser, "Laguerre Tessellation",
"Parameters determining shape of weight distribution of seed points"
)
group.add_option('-w', '--weights',
group.add_option( '-w',
'--weights',
action = 'store_true',
dest = 'weights',
help = 'assign random weigts to seed points for Laguerre tessellation [%default]')
group.add_option('--max',
help = 'assign random weights to seed points for Laguerre tessellation [%default]')
group.add_option( '--max',
dest = 'max',
type = 'float', metavar = 'float',
help = 'max of uniform distribution for weights [%default]')
group.add_option('--mean',
group.add_option( '--mean',
dest = 'mean',
type = 'float', metavar = 'float',
help = 'mean of normal distribution for weights [%default]')
group.add_option('--sigma',
dest = 'sigma',
type = 'float', metavar = 'float',
help='standard deviation of normal distribution for weights [%default]')
group.add_option( '--sigma',
dest = 'sigma',
type = 'float', metavar = 'float',
help='standard deviation of normal distribution for weights [%default]')
parser.add_option_group(group)
group = OptionGroup(parser, "Selective Seeding Options",
"More uniform distribution of seed points using Mitchell\'s Best Candidate Algorithm"
group = OptionGroup(parser, "Selective Seeding",
"More uniform distribution of seed points using Mitchell's Best Candidate Algorithm"
)
group.add_option('-s','--selective',
group.add_option( '-s',
'--selective',
action = 'store_true',
dest = 'selective',
help = 'selective picking of seed points from random seed points [%default]')
group.add_option('-f','--force',
group.add_option( '-f',
'--force',
action = 'store_true',
dest = 'force',
help = 'try selective picking despite large seed point number [%default]')
group.add_option('--distance',
dest = 'distance',
type = 'float', metavar = 'float',
help = 'minimum distance to the next neighbor [%default]')
group.add_option('--numCandidates',
dest = 'numCandidates',
type = 'int', metavar = 'int',
help = 'size of point group to select best distance from [%default]')
group.add_option( '--distance',
dest = 'distance',
type = 'float', metavar = 'float',
help = 'minimum distance to next neighbor [%default]')
group.add_option( '--numCandidates',
dest = 'numCandidates',
type = 'int', metavar = 'int',
help = 'size of point group to select best distance from [%default]')
parser.add_option_group(group)
parser.set_defaults(randomSeed = None,
@ -103,6 +113,7 @@ parser.set_defaults(randomSeed = None,
force = False,
distance = 0.2,
numCandidates = 10,
format = None,
)
(options,filenames) = parser.parse_args()
@ -120,11 +131,9 @@ random.seed(options.randomSeed)
if filenames == []: filenames = [None]
for name in filenames:
try:
table = damask.ASCIItable(outname = name,
buffered = False)
except:
continue
try: table = damask.ASCIItable(outname = name,
buffered = False)
except: continue
damask.util.report(scriptName,name)
# --- sanity checks -------------------------------------------------------------------------
@ -132,7 +141,7 @@ for name in filenames:
remarks = []
errors = []
if gridSize == 0:
errors.append('zero grid dimension for %s.'%(', '.join([['a','b','c'][x] for x in np.where(options.grid == 0)[0]])))
errors.append('zero grid dimension for {}.'.format(', '.join([['a','b','c'][x] for x in np.where(options.grid == 0)[0]])))
if options.N > gridSize/10.: errors.append('seed count exceeds 0.1 of grid points.')
if options.selective and 4./3.*math.pi*(options.distance/2.)**3*options.N > 0.5:
(remarks if options.force else errors).append('maximum recommended seed point count for given distance is {}.{}'.
@ -182,10 +191,8 @@ for name in filenames:
seeds = seeds.T # prepare shape for stacking
if options.weights:
if options.max > 0.0:
weights = [np.random.uniform(low = 0, high = options.max, size = options.N)]
else:
weights = [np.random.normal(loc = options.mean, scale = options.sigma, size = options.N)]
weights = [np.random.uniform(low = 0, high = options.max, size = options.N)] if options.max > 0.0 \
else [np.random.normal(loc = options.mean, scale = options.sigma, size = options.N)]
else:
weights = []
seeds = np.transpose(np.vstack(tuple([seeds,
@ -200,13 +207,13 @@ for name in filenames:
table.info_clear()
table.info_append([
scriptID + ' ' + ' '.join(sys.argv[1:]),
"grid\ta {grid[0]}\tb {grid[1]}\tc {grid[2]}".format(grid=options.grid),
"grid\ta {}\tb {}\tc {}".format(*options.grid),
"microstructures\t{}".format(options.N),
"randomSeed\t{}".format(options.randomSeed),
])
table.labels_clear()
table.labels_append( ['{dim}_{label}'.format(dim = 1+k,label = 'pos') for k in xrange(3)] +
['{dim}_{label}'.format(dim = 1+k,label = 'eulerangles') for k in xrange(3)] +
['{dim}_{label}'.format(dim = 1+k,label = 'euler') for k in xrange(3)] +
['microstructure'] +
(['weight'] if options.weights else []))
table.head_write()
@ -215,7 +222,7 @@ for name in filenames:
# --- write seeds information ------------------------------------------------------------
table.data = seeds
table.data_writeArray()
table.data_writeArray(fmt = options.format)
# --- output finalization --------------------------------------------------------------------------

52
processing/pre/seeds_fromTable.py
View File

@ -23,29 +23,38 @@ Examples:
""", version = scriptID)
parser.add_option('-p', '--positions',
dest = 'pos',
type = 'string', metavar = 'string',
help = 'coordinate label [%default]')
parser.add_option('-p',
'--pos', '--seedposition',
dest = 'pos',
type = 'string', metavar = 'string',
help = 'label of coordinates [%default]')
parser.add_option('--boundingbox',
dest = 'box',
type = 'float', nargs = 6, metavar = ' '.join(['float']*6),
help = 'min (x,y,z) and max (x,y,z) coordinates of bounding box [tight]')
parser.add_option('-i', '--index',
dest = 'index',
parser.add_option('-m',
'--microstructure',
dest = 'microstructure',
type = 'string', metavar = 'string',
help = 'microstructure index label [%default]')
parser.add_option('-w','--white',
help = 'label of microstructures [%default]')
parser.add_option('--weight',
dest = 'weight',
type = 'string', metavar = 'string',
help = 'label of weights [%default]')
parser.add_option('-w',
'--white',
dest = 'whitelist',
action = 'extend', metavar = '<int LIST>',
help = 'whitelist of microstructure indices')
parser.add_option('-b','--black',
parser.add_option('-b',
'--black',
dest = 'blacklist',
action = 'extend', metavar = '<int LIST>',
help = 'blacklist of microstructure indices')
parser.set_defaults(pos = 'pos',
index ='microstructure',
parser.set_defaults(pos = 'pos',
microstructure = 'microstructure',
weight = None,
)
(options,filenames) = parser.parse_args()
@ -58,10 +67,9 @@ if options.blacklist is not None: options.blacklist = map(int,options.blacklist)
if filenames == []: filenames = [None]
for name in filenames:
try:
table = damask.ASCIItable(name = name,
outname = os.path.splitext(name)[0]+'.seeds' if name else name,
buffered = False)
try: table = damask.ASCIItable(name = name,
outname = os.path.splitext(name)[0]+'.seeds' if name else name,
buffered = False)
except: continue
damask.util.report(scriptName,name)
@ -69,14 +77,17 @@ for name in filenames:
# ------------------------------------------ sanity checks ---------------------------------------
missing_labels = table.data_readArray([options.pos,options.index])
missing_labels = table.data_readArray([options.pos,options.microstructure] +
([options.weight] if options.weight else []))
errors = []
if len(missing_labels) > 0:
errors.append('column{} {} not found'.format('s' if len(missing_labels) > 1 else '',
', '.join(missing_labels)))
for label, dim in {options.pos: 3,
options.index: 1}.iteritems():
input = {options.pos: 3,
options.microstructure: 1,}
if options.weight: input.update({options.weight: 1})
for label, dim in input.iteritems():
if table.label_dimension(label) != dim:
errors.append('column {} has wrong dimension'.format(label))
@ -113,11 +124,12 @@ for name in filenames:
table.info = [
scriptID,
'size %s'%(' '.join(list(itertools.chain.from_iterable(zip(['x','y','z'],
'size {}'.format(' '.join(list(itertools.chain.from_iterable(zip(['x','y','z'],
map(str,boundingBox[1,:]-boundingBox[0,:])))))),
]
table.labels_clear()
table.labels_append(['1_pos','2_pos','3_pos','microstructure']) # implicitly switching label processing/writing on
table.labels_append(['1_pos','2_pos','3_pos','microstructure'] +
['weight'] if options.weight else []) # implicitly switching label processing/writing on
table.head_write()
# ------------------------------------------ output result ---------------------------------------