Merge branch 'development' of magit1.mpie.de:damask/DAMASK into miscImprovements
This commit is contained in:
Martin Diehl
commit
b1d714581c
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@ -2,7 +2,7 @@
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# usage: source DAMASK_env.sh
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if [ "$OSTYPE" == "linux-gnu" ] || [ "$OSTYPE" == 'linux' ]; then
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DAMASK_ROOT=$(readlink -f "`dirname $BASH_SOURCE`")
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DAMASK_ROOT=$(python -c "import os,sys; print(os.path.realpath(os.path.expanduser(sys.argv[1])))" "`dirname $BASH_SOURCE`")
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else
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[[ "${BASH_SOURCE::1}" == "/" ]] && BASE="" || BASE="`pwd`/"
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STAT=$(stat "`dirname $BASE$BASH_SOURCE`")
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@ -18,11 +18,11 @@ fi
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SOLVER=`which DAMASK_spectral 2>/dev/null`
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if [ "x$SOLVER" == "x" ]; then
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export SOLVER='Not found!'
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SOLVER='Not found!'
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fi
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PROCESSING=`which postResults 2>/dev/null`
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if [ "x$PROCESSING" == "x" ]; then
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export PROCESSING='Not found!'
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PROCESSING='Not found!'
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fi
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# according to http://software.intel.com/en-us/forums/topic/501500
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@ -55,7 +55,8 @@ if [ ! -z "$PS1" ]; then
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echo "Multithreading DAMASK_NUM_THREADS=$DAMASK_NUM_THREADS"
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if [ "x$PETSC_DIR" != "x" ]; then
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echo "PETSc location $PETSC_DIR"
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[[ `readlink -f $PETSC_DIR` == $PETSC_DIR ]] || echo " ~~> "`readlink -f $PETSC_DIR`
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[[ `python -c "import os,sys; print(os.path.realpath(os.path.expanduser(sys.argv[1])))" "$PETSC_DIR"` == $PETSC_DIR ]] \
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|| echo " ~~> "`python -c "import os,sys; print(os.path.realpath(os.path.expanduser(sys.argv[1])))" "$PETSC_DIR"`
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fi
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[[ "x$PETSC_ARCH" != "x" ]] && echo "PETSc architecture $PETSC_ARCH"
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echo "MSC.Marc/Mentat $MSC_ROOT"
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@ -13,7 +13,8 @@ program DAMASK_spectral
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pInt, &
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pLongInt, &
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pReal, &
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tol_math_check
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tol_math_check, &
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dNeq
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use DAMASK_interface, only: &
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DAMASK_interface_init, &
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loadCaseFile, &
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@ -147,7 +148,9 @@ program DAMASK_spectral
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MPI_file_seek, &
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MPI_file_get_position, &
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MPI_file_write, &
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MPI_allreduce
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MPI_abort, &
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MPI_allreduce, &
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PETScFinalize
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!--------------------------------------------------------------------------------------------------
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! init DAMASK (all modules)
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@ -339,7 +342,7 @@ program DAMASK_spectral
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reshape(spread(tol_math_check,1,9),[ 3,3]))&
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.or. abs(math_det33(loadCases(currentLoadCase)%rotation)) > &
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1.0_pReal + tol_math_check) errorID = 846_pInt ! given rotation matrix contains strain
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if (any(loadCases(currentLoadCase)%rotation /= math_I3)) &
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if (any(dNeq(loadCases(currentLoadCase)%rotation, math_I3))) &
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write(6,'(2x,a,/,3(3(3x,f12.7,1x)/))',advance='no') 'rotation of loadframe:',&
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math_transpose33(loadCases(currentLoadCase)%rotation)
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if (loadCases(currentLoadCase)%time < 0.0_pReal) errorID = 834_pInt ! negative time increment
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@ -423,17 +426,21 @@ program DAMASK_spectral
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!--------------------------------------------------------------------------------------------------
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! prepare MPI parallel out (including opening of file)
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allocate(outputSize(worldsize), source = 0_MPI_OFFSET_KIND)
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outputSize(worldrank+1) = int(size(materialpoint_results)*pReal,MPI_OFFSET_KIND)
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outputSize(worldrank+1) = size(materialpoint_results,kind=MPI_OFFSET_KIND)*int(pReal,MPI_OFFSET_KIND)
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call MPI_allreduce(MPI_IN_PLACE,outputSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process
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if(ierr /=0_pInt) call IO_error(894_pInt, ext_msg='MPI_allreduce')
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call MPI_file_open(PETSC_COMM_WORLD, &
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trim(getSolverWorkingDirectoryName())//trim(getSolverJobName())//'.spectralOut', &
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MPI_MODE_WRONLY + MPI_MODE_APPEND, &
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MPI_INFO_NULL, &
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resUnit, &
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ierr)
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if(ierr /=0_pInt) call IO_error(894_pInt, ext_msg='MPI_file_open')
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call MPI_file_get_position(resUnit,fileOffset,ierr) ! get offset from header
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if(ierr /=0_pInt) call IO_error(894_pInt, ext_msg='MPI_file_get_position')
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fileOffset = fileOffset + sum(outputSize(1:worldrank)) ! offset of my process in file (header + processes before me)
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call MPI_file_seek (resUnit,fileOffset,MPI_SEEK_SET,ierr)
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if(ierr /=0_pInt) call IO_error(894_pInt, ext_msg='MPI_file_seek')
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if (.not. appendToOutFile) then ! if not restarting, write 0th increment
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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
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@ -443,6 +450,7 @@ program DAMASK_spectral
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[(outputIndex(2)-outputIndex(1)+1)*materialpoint_sizeResults]), &
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(outputIndex(2)-outputIndex(1)+1)*materialpoint_sizeResults,&
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MPI_DOUBLE, MPI_STATUS_IGNORE, ierr)
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if(ierr /=0_pInt) call IO_error(894_pInt, ext_msg='MPI_file_write')
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enddo
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fileOffset = fileOffset + sum(outputSize) ! forward to current file position
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if (worldrank == 0) &
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@ -643,6 +651,7 @@ program DAMASK_spectral
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write(6,'(1/,a)') ' ... writing results to file ......................................'
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call materialpoint_postResults()
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call MPI_file_seek (resUnit,fileOffset,MPI_SEEK_SET,ierr)
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if(ierr /=0_pInt) call IO_error(894_pInt, ext_msg='MPI_file_seek')
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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
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outputIndex=int([(i-1_pInt)*((maxByteOut/pReal)/materialpoint_sizeResults)+1_pInt, &
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min(i*((maxByteOut/pReal)/materialpoint_sizeResults),size(materialpoint_results,3))],pLongInt)
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@ -650,6 +659,7 @@ program DAMASK_spectral
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[(outputIndex(2)-outputIndex(1)+1)*materialpoint_sizeResults]), &
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(outputIndex(2)-outputIndex(1)+1)*materialpoint_sizeResults,&
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MPI_DOUBLE, MPI_STATUS_IGNORE, ierr)
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if(ierr /=0_pInt) call IO_error(894_pInt, ext_msg='MPI_file_write')
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enddo
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fileOffset = fileOffset + sum(outputSize) ! forward to current file position
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endif
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@ -698,7 +708,7 @@ program DAMASK_spectral
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enddo
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call utilities_destroy()
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call PetscFinalize(ierr); CHKERRQ(ierr)
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call PETScFinalize(ierr); CHKERRQ(ierr)
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if (notConvergedCounter > 0_pInt) call quit(3_pInt) ! error if some are not converged
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call quit(0_pInt) ! no complains ;)
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@ -1669,6 +1669,8 @@ subroutine IO_error(error_ID,el,ip,g,ext_msg)
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msg = 'unknown filter type selected'
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case (893_pInt)
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msg = 'PETSc: SNES_DIVERGED_FNORM_NAN'
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case (894_pInt)
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msg = 'MPI error'
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!-------------------------------------------------------------------------------------------------
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! error messages related to parsing of Abaqus input file
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@ -1280,7 +1280,7 @@ subroutine material_populateGrains
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integer(pInt) :: t,e,i,g,j,m,c,r,homog,micro,sgn,hme, myDebug, &
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phaseID,textureID,dGrains,myNgrains,myNorientations,myNconstituents, &
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grain,constituentGrain,ipGrain,symExtension, ip
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real(pReal) :: extreme,rnd
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real(pReal) :: deviation,extreme,rnd
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integer(pInt), dimension (:,:), allocatable :: Nelems ! counts number of elements in homog, micro array
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type(p_intvec), dimension (:,:), allocatable :: elemsOfHomogMicro ! lists element number in homog, micro array
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@ -1407,8 +1407,11 @@ subroutine material_populateGrains
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extreme = 0.0_pReal
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t = 0_pInt
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do i = 1_pInt,myNconstituents ! find largest deviator
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if (real(sgn,pReal)*log(NgrainsOfConstituent(i)/myNgrains/microstructure_fraction(i,micro)) > extreme) then
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extreme = real(sgn,pReal)*log(NgrainsOfConstituent(i)/myNgrains/microstructure_fraction(i,micro))
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deviation = real(sgn,pReal)*log( microstructure_fraction(i,micro) / &
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!-------------------------------- &
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(real(NgrainsOfConstituent(i),pReal)/real(myNgrains,pReal) ) )
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if (deviation > extreme) then
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extreme = deviation
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t = i
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endif
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enddo
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@ -113,7 +113,9 @@ module prec
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public :: &
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prec_init, &
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prec_isNaN
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prec_isNaN, &
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dEq, &
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dNeq
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contains
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@ -40,12 +40,12 @@ class ASCIItable():
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self.__IO__['in'] = name
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try:
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self.__IO__['out'] = (open(outname,'w') if (not os.path.isfile(outname) \
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or os.access( outname, os.W_OK) \
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) \
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and (not self.__IO__['inPlace'] \
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or not os.path.isfile(name) \
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or os.access( name, os.W_OK) \
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self.__IO__['out'] = (open(outname,'w') if (not os.path.isfile(outname) or
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os.access( outname, os.W_OK)
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) and
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(not self.__IO__['inPlace'] or
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not os.path.isfile(name) or
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os.access( name, os.W_OK)
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) else None) if outname else sys.stdout
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except TypeError:
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self.__IO__['out'] = outname
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@ -272,7 +272,7 @@ class ASCIItable():
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for label in labels:
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if label is not None:
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try:
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idx.append(int(label)) # column given as integer number?
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idx.append(int(label)-1) # column given as integer number?
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except ValueError:
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try:
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idx.append(self.labels.index(label)) # locate string in label list
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@ -283,7 +283,7 @@ class ASCIItable():
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idx.append(-1) # not found...
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else:
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try:
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idx = int(labels)
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idx = int(labels)-1 # offset for python array indexing
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except ValueError:
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try:
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idx = self.labels.index(labels)
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@ -293,7 +293,7 @@ class ASCIItable():
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except ValueError:
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idx = None if labels is None else -1
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return np.array(idx) if isinstance(idx,list) else idx
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return np.array(idx) if isinstance(idx,Iterable) else idx
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# ------------------------------------------------------------------
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def label_dimension(self,
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@ -312,7 +312,7 @@ class ASCIItable():
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if label is not None:
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myDim = -1
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try: # column given as number?
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idx = int(label)
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idx = int(label)-1
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myDim = 1 # if found has at least dimension 1
|
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if self.labels[idx].startswith('1_'): # column has multidim indicator?
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while idx+myDim < len(self.labels) and self.labels[idx+myDim].startswith("%i_"%(myDim+1)):
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@ -331,7 +331,7 @@ class ASCIItable():
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dim = -1 # assume invalid label
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idx = -1
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try: # column given as number?
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idx = int(labels)
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idx = int(labels)-1
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dim = 1 # if found has at least dimension 1
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if self.labels[idx].startswith('1_'): # column has multidim indicator?
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while idx+dim < len(self.labels) and self.labels[idx+dim].startswith("%i_"%(dim+1)):
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@ -345,7 +345,7 @@ class ASCIItable():
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while idx+dim < len(self.labels) and self.labels[idx+dim].startswith("%i_"%(dim+1)):
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dim += 1 # keep adding while going through object
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return np.array(dim) if isinstance(dim,list) else dim
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return np.array(dim) if isinstance(dim,Iterable) else dim
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# ------------------------------------------------------------------
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def label_indexrange(self,
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|
|
|
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Binary file not shown.
|
Before Width: | Height: | Size: 80 KiB After Width: | Height: | Size: 34 KiB |
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|
@ -37,9 +37,13 @@ if options.label is None:
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if filenames == []: filenames = [None]
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for name in filenames:
|
||||
try:
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table = damask.ASCIItable(name = name,
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outname = options.label+'_averaged_'+name if name else name,
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damask.util.croak(name)
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|
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try: table = damask.ASCIItable(name = name,
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||||
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)
|
||||
|
|
|
|||
|
|
@ -0,0 +1,142 @@
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|||
#!/usr/bin/env python
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||||
# -*- 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
|
||||
|
|
@ -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
|
||||
|
||||
|
|
@ -32,13 +32,16 @@ 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,
|
||||
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 != []:
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
||||
|
|
@ -109,71 +109,83 @@ 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',
|
||||
|
||||
group = OptionGroup(parser, "Tessellation","")
|
||||
|
||||
group.add_option('-l', '--laguerre',
|
||||
dest = 'laguerre',
|
||||
action = 'store_true',
|
||||
help = 'use Laguerre (weighted Voronoi) tessellation')
|
||||
parser.add_option('--cpus',
|
||||
group.add_option('--cpus',
|
||||
dest = 'cpus',
|
||||
type = 'int', metavar = 'int',
|
||||
help = 'number of parallel processes to use for Laguerre tessellation [%default]')
|
||||
parser.add_option('--nonperiodic',
|
||||
group.add_option('--nonperiodic',
|
||||
dest = 'nonperiodic',
|
||||
action = 'store_true',
|
||||
help = 'use 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', '--position',
|
||||
dest = 'position',
|
||||
type = 'string', metavar = 'string',
|
||||
help = 'column label for seed positions [%default]')
|
||||
group.add_option('-w', '--weight',
|
||||
dest = 'weight',
|
||||
type = 'string', metavar = 'string',
|
||||
help = 'column label for seed weights [%default]')
|
||||
group.add_option('-m', '--microstructure',
|
||||
dest = 'microstructure',
|
||||
type = 'string', metavar = 'string',
|
||||
help = 'column label for seed microstructures [%default]')
|
||||
group.add_option('-e', '--eulers',
|
||||
dest = 'eulers',
|
||||
type = 'string', metavar = 'string',
|
||||
help = 'column label for seed 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(position = 'pos',
|
||||
weight = 'weight',
|
||||
microstructure = 'microstructure',
|
||||
|
|
@ -181,24 +193,18 @@ parser.set_defaults(position = 'pos',
|
|||
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,
|
||||
try: table = damask.ASCIItable(name = name,
|
||||
outname = os.path.splitext(name)[-2]+'.geom' if name else name,
|
||||
buffered = False)
|
||||
except: continue
|
||||
|
|
@ -294,20 +300,11 @@ for name in filenames:
|
|||
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)),
|
||||
'(constituent)\tphase %i\ttexture %s\tfraction 1.0'%(options.phase,str(ID).rjust(formatwidth)),
|
||||
]
|
||||
if hasEulers:
|
||||
config_header += ['<texture>']
|
||||
|
|
|
|||
|
|
@ -48,8 +48,11 @@ parser.add_option('-m', '--microstructure',
|
|||
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 = 'number format of output [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',
|
||||
|
|
@ -70,8 +73,8 @@ group.add_option('--sigma',
|
|||
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',
|
||||
action = 'store_true',
|
||||
|
|
@ -103,6 +106,7 @@ parser.set_defaults(randomSeed = None,
|
|||
force = False,
|
||||
distance = 0.2,
|
||||
numCandidates = 10,
|
||||
format = None,
|
||||
)
|
||||
|
||||
(options,filenames) = parser.parse_args()
|
||||
|
|
@ -215,7 +219,7 @@ for name in filenames:
|
|||
# --- write seeds information ------------------------------------------------------------
|
||||
|
||||
table.data = seeds
|
||||
table.data_writeArray()
|
||||
table.data_writeArray(fmt = options.format)
|
||||
|
||||
# --- output finalization --------------------------------------------------------------------------
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue