clarified fixed expression
This commit is contained in:
Martin Diehl
parent
1180c8bb88
commit
4a627161d5
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@ -1,87 +1,74 @@
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# sets up an environment for DAMASK on zsh
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# usage: source DAMASK_env.zsh
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# sets up an environment for DAMASK on bash
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# usage: source DAMASK_env.sh
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DAMASK_ROOT=${0:a:h}
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# defining set() allows to source the same file for tcsh and zsh, with and without space around =
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set() {
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export $1$2$3
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}
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source $DAMASK_ROOT/CONFIG
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unset -f set
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# add DAMASK_BIN if present but not yet in $PATH
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MATCH=`echo ":$PATH:" | grep $DAMASK_BIN:`
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if [[ ( "x$DAMASK_BIN" != "x" ) && ( "x$MATCH" = "x" ) ]]; then
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export PATH=$DAMASK_BIN:$PATH
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if [ "$OSTYPE" = "linux-gnu" ] || [ "$OSTYPE" = 'linux' ]; then
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DAMASK_ROOT=$(readlink -f "`dirname ${(%):-%N}`")
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else
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print 'Not done yet'
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fi
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[[ -f $HOME/.damask/damask.conf ]] && source $HOME/.damask/damask.conf || source /etc/damask.conf
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# if DAMASK_BIN is present and not in $PATH, add it
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#if [[ [[ "x$DAMASK_BIN" != "x" ]] && ! `echo ":$PATH:" | grep $DAMASK_BIN:` ]]; then
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export PATH=$DAMASK_BIN:$PATH
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#fi
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SOLVER=`which DAMASK_spectral 2>/dev/null`
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if [ "x$SOLVER" = "x" ]; then
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export SOLVER='Not found!'
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fi
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PROCESSING=`which postResults 2>/dev/null`
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if [ "x$DAMASK_NUM_THREADS" = "x" ]; then
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DAMASK_NUM_THREADS=1
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if [ "x$PROCESSING" = "x" ]; then
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export 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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# this seems to make sense for the stack size
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if [ "`which free 2>/dev/null`" != "free not found" ]; then
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freeMem=`free -k | grep -E '(Mem|Speicher):' | awk '{print $4;}'`
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# http://superuser.com/questions/220059/what-parameters-has-ulimit
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ulimit -s `expr $freeMem / $DAMASK_NUM_THREADS / 2` 2>/dev/null # maximum stack size (kB)
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ulimit -d `expr $freeMem / 2` 2>/dev/null # maximum heap size (kB)
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fi
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ulimit -v unlimited 2>/dev/null # maximum virtual memory size
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#FREE=`which free 2>/dev/null`
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#if [ "x$FREE" != "x" ]; then
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# freeMem=`free -k | grep -E '(Mem|Speicher):' | awk '{print $4;}'`
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# heap=`expr $freeMem / 2`
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# stack=`expr $freeMem / 2`
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#
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# # http://superuser.com/questions/220059/what-parameters-has-ulimit
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# ulimit -s $stack 2>/dev/null # maximum stack size (kB)
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# ulimit -d $heap 2>/dev/null # maximum heap size (kB)
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#fi
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#ulimit -c 2000 2>/dev/null # core file size (512-byte blocks)
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#ulimit -v unlimited 2>/dev/null # maximum virtual memory size
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ulimit -m unlimited 2>/dev/null # maximum physical memory size
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# disable output in case of scp
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if [ ! -z "$PS1" ]; then
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echo
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echo Düsseldorf Advanced Materials Simulation Kit --- DAMASK
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echo Max-Planck-Institut für Eisenforschung GmbH, Düsseldorf
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echo https://damask.mpie.de
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echo Düsseldorf Advanced Materials Simulation Kit - DAMASK
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echo Max-Planck-Institut für Eisenforschung, Düsseldorf
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echo http://damask.mpie.de
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echo
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echo "Using environment with ..."
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echo Using environment with ...
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echo "DAMASK $DAMASK_ROOT"
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echo "Spectral Solver $SOLVER"
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echo "Post Processing $PROCESSING"
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[[ "x$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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if [ "x$PETSC_DIR" != "x" ]; then
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echo "PETSc location $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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[[ `readlink -f $PETSC_DIR` == $PETSC_DIR ]] || echo " ~~> "`readlink -f $PETSC_DIR`
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fi
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[[ "x$PETSC_ARCH" == "x" ]] \
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|| echo "PETSc architecture $PETSC_ARCH"
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[[ "x$PETSC_ARCH" != "x" ]] && echo "PETSc architecture $PETSC_ARCH"
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echo "MSC.Marc/Mentat $MSC_ROOT"
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echo
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echo -n "heap size "
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[[ "$(ulimit -d)" == "unlimited" ]] \
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&& echo "unlimited" \
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|| echo $(python -c \
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"import math; \
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size=$(( 1024*$(ulimit -d) )); \
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print('{:.4g} {}'.format(size / (1 << ((int(math.log(size,2) / 10) if size else 0) * 10)), \
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['bytes','KiB','MiB','GiB','TiB','EiB','ZiB'][int(math.log(size,2) / 10) if size else 0]))")
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echo -n "stack size "
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[[ "$(ulimit -s)" == "unlimited" ]] \
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&& echo "unlimited" \
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|| echo $(python -c \
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"import math; \
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size=$(( 1024*$(ulimit -s) )); \
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print('{:.4g} {}'.format(size / (1 << ((int(math.log(size,2) / 10) if size else 0) * 10)), \
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['bytes','KiB','MiB','GiB','TiB','EiB','ZiB'][int(math.log(size,2) / 10) if size else 0]))")
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echo -n "heap size/MiB "; echo "`ulimit -d`/1024" | bc
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echo -n "stack size/MiB "; echo "`ulimit -s`/1024" | bc
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fi
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export DAMASK_NUM_THREADS
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export PYTHONPATH=$DAMASK_ROOT/lib:$PYTHONPATH
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for var in BASE STAT SOLVER PROCESSING FREE DAMASK_BIN MATCH; do
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for var in BASE STAT SOLVER PROCESSING FREE; do
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unset "${var}"
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done
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for var in DAMASK MSC; do
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for var in DAMASK IMKL ACML LAPACK MSC FFTW HDF5; do
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unset "${var}_ROOT"
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done
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for var in ABAQUS MARC; do
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unset "${var}_VERSION"
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done
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@ -99,16 +99,15 @@ for name in filenames:
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for smoothIter in xrange(options.N):
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boundary = np.zeros(microstructure.shape)
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interfaceEnergy = np.zeros(microstructure.shape)
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for i in (-1,0,1):
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for j in (-1,0,1):
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for k in (-1,0,1):
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# assign interfacial energy to all voxels that have a differing neighbor (in Moore neighborhood)
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boundary = np.maximum(boundary,
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interfaceEnergy = np.maximum(interfaceEnergy,
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interfacialEnergy(microstructure,np.roll(np.roll(np.roll(
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microstructure,i,axis=0), j,axis=1), k,axis=2)))
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interfaceEnergy = boundary
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# periodically extend interfacial energy array by half a grid size in positive and negative directions
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periodic_interfaceEnergy = np.tile(interfaceEnergy,(3,3,3))[grid[0]/2:-grid[0]/2,
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grid[1]/2:-grid[1]/2,
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