Merge branch 'LargeFiles' into development
This commit is contained in:
Martin Diehl
commit
fafedd5cd6
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@ -53,8 +53,10 @@ if [ ! -z "$PS1" ]; then
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[[ "x$SOLVER" != "x" ]] && echo "Spectral Solver $SOLVER"
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[[ "x$PROCESSING" != "x" ]] && echo "Post Processing $PROCESSING"
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echo "Multithreading DAMASK_NUM_THREADS=$DAMASK_NUM_THREADS"
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[[ "x$PETSC_DIR" != "x" ]] && echo "PETSc location $PETSC_DIR" && \
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[[ `readlink -f $PETSC_DIR` == $PETSC_DIR ]] || echo " ~~> "`readlink -f $PETSC_DIR`
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if [ "x$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 $PETSC_DIR`
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fi
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[[ "x$PETSC_ARCH" != "x" ]] && echo "PETSc architecture $PETSC_ARCH"
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echo "MSC.Marc/Mentat $MSC_ROOT"
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echo
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@ -51,8 +51,10 @@ if [ ! -z "$PS1" ]; then
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[[ "x$SOLVER" != "x" ]] && echo "Spectral Solver $SOLVER"
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[[ "x$PROCESSING" != "x" ]] && echo "Post Processing $PROCESSING"
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echo "Multithreading DAMASK_NUM_THREADS=$DAMASK_NUM_THREADS"
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[[ "x$PETSC_DIR" != "x" ]] && echo "PETSc location $PETSC_DIR" && \
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[[ `readlink -f $PETSC_DIR` == $PETSC_DIR ]] || echo " ~~> "`readlink -f $PETSC_DIR`
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if [ "x$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 $PETSC_DIR`
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fi
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[[ "x$PETSC_ARCH" != "x" ]] && echo "PETSc architecture $PETSC_ARCH"
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echo "MSC.Marc/Mentat $MSC_ROOT"
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echo
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@ -1 +1,2 @@
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DAMASK_marc*.f90
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quit__genmod.f90
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@ -59,8 +59,6 @@ program DAMASK_spectral
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materialpoint_sizeResults, &
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materialpoint_results, &
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materialpoint_postResults
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use material, only: &
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thermal_type, &
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damage_type, &
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@ -439,14 +437,14 @@ program DAMASK_spectral
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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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outputIndex=[(i-1)*((maxByteOut/pReal)/materialpoint_sizeResults)+1, &
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min(i*((maxByteOut/pReal)/materialpoint_sizeResults),size(materialpoint_results,3))]
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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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call MPI_file_write(resUnit,reshape(materialpoint_results(:,:,outputIndex(1):outputIndex(2)),&
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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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fileOffset = fileOffset + sum(outputSize) ! forward to current file position
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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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write(6,'(1/,a)') ' ... writing initial configuration to file ........................'
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endif
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@ -646,14 +644,14 @@ program DAMASK_spectral
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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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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=[(i-1)*maxByteOut/pReal/materialpoint_sizeResults+1, &
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min(i*maxByteOut/pReal/materialpoint_sizeResults,size(materialpoint_results,3))]
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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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call MPI_file_write(resUnit,reshape(materialpoint_results(:,:,outputIndex(1):outputIndex(2)),&
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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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fileOffset = fileOffset + sum(outputSize) ! forward to current file position
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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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if( loadCases(currentLoadCase)%restartFrequency > 0_pInt .and. & ! at frequency of writing restart information set restart parameter for FEsolving
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mod(inc,loadCases(currentLoadCase)%restartFrequency) == 0_pInt) then ! first call to CPFEM_general will write?
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@ -0,0 +1 @@
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core.so
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@ -1,100 +0,0 @@
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#!/usr/bin/env python
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# -*- coding: UTF-8 no BOM -*-
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import os,sys,numpy as np
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from optparse import OptionParser
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import damask
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scriptName = os.path.splitext(os.path.basename(__file__))[0]
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scriptID = ' '.join([scriptName,damask.version])
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# --------------------------------------------------------------------
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# MAIN
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# --------------------------------------------------------------------
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parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
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Add Quaternions based on Crystal Frame Coordinates.
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""", version = scriptID)
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parser.add_option('-f','--frame',
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dest='frame', nargs=4, type='string', metavar='<string string string string>',
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help='heading of columns containing b* vector components and three frame vectors in that order')
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parser.add_option('-s','--symmetry',
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dest='crysym', nargs=1,type='string',metavar='<string>',
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help='crystal symmetry definition')
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parser.set_defaults(frame = None)
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(options,filenames) = parser.parse_args()
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if options.frame is None:
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parser.error('no data column specified...')
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datainfo = {'len':4,
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'label':[]
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}
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if options.frame is not None: datainfo['label'] += options.frame
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# --- loop over input files -------------------------------------------------------------------------
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if filenames == []: filenames = [None]
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for name in filenames:
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try:
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table = damask.ASCIItable(name = name,
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buffered = False)
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except: continue
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damask.util.report(scriptName,name)
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table.head_read() # read ASCII header info
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# --------------- figure out columns to process ---------------------------------------------------
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active = []
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column = {}
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for label in datainfo['label']:
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key = '1_'+label if datainfo['len'] > 1 else label # non-special labels have to start with '1_'
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if key in table.labels:
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active.append(label)
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column[label] = table.labels.index(key) # remember columns of requested data
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else:
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damask.util.croak('column %s not found...'%label)
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# ------------------------------------------ assemble header ---------------------------------------
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table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
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table.labels_append(['Q_%i'%(i+1) for i in xrange(4)]) # extend ASCII header with new labels [1 real, 3 imaginary components]
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table.head_write()
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# ------------------------------------------ process data ------------------------------------------
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outputAlive = True
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while outputAlive and table.data_read(): # read next data line of ASCII table
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vec = np.zeros([4,3])
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for i,label in enumerate(active):
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vec[i,:] = np.array(table.data[column[label]:
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column[label]+3])
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if sys.argv[1:][6]=='hexagonal': # Ensure Input matrix is orthogonal
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M=np.dot(vec[0,:],vec[2,:])
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vec[1,:]=vec[1,:]/np.linalg.norm(vec[1,:])
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vec[2,:]=M*(vec[0,:]/np.linalg.norm(vec[0,:]))
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vec[3,:]=vec[3,:]/np.linalg.norm(vec[3,:])
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else:
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vec[1,:]=vec[1,:]/np.linalg.norm(vec[1,:])
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vec[2,:]=vec[2,:]/np.linalg.norm(vec[2,:])
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vec[3,:]=vec[3,:]/np.linalg.norm(vec[3,:])
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Ori=damask.Orientation(matrix=vec[1:,:],symmetry=sys.argv[1:][6])
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table.data_append(np.asarray(Ori.asQuaternion()))
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outputAlive = table.data_write() # output processed line
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# ------------------------------------------ output result -----------------------------------------
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outputAlive and table.output_flush() # just in case of buffered ASCII table
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table.close() # close ASCII tables
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