From 4a627161d57b8acd47f5b04558ef92f4b36fcac1 Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Fri, 16 Sep 2016 03:23:59 +0200 Subject: [PATCH] clarified fixed expression --- DAMASK_env.zsh | 99 +++++++++++++----------------- processing/pre/geom_grainGrowth.py | 7 +-- 2 files changed, 46 insertions(+), 60 deletions(-) diff --git a/DAMASK_env.zsh b/DAMASK_env.zsh index 3bbab82df..730993bf8 100644 --- a/DAMASK_env.zsh +++ b/DAMASK_env.zsh @@ -1,87 +1,74 @@ -# sets up an environment for DAMASK on zsh -# usage: source DAMASK_env.zsh +# sets up an environment for DAMASK on bash +# usage: source DAMASK_env.sh -DAMASK_ROOT=${0:a:h} - -# defining set() allows to source the same file for tcsh and zsh, with and without space around = -set() { - export $1$2$3 - } -source $DAMASK_ROOT/CONFIG -unset -f set - -# add DAMASK_BIN if present but not yet in $PATH -MATCH=`echo ":$PATH:" | grep $DAMASK_BIN:` -if [[ ( "x$DAMASK_BIN" != "x" ) && ( "x$MATCH" = "x" ) ]]; then - export PATH=$DAMASK_BIN:$PATH +if [ "$OSTYPE" = "linux-gnu" ] || [ "$OSTYPE" = 'linux' ]; then + DAMASK_ROOT=$(readlink -f "`dirname ${(%):-%N}`") +else + print 'Not done yet' fi +[[ -f $HOME/.damask/damask.conf ]] && source $HOME/.damask/damask.conf || source /etc/damask.conf + +# if DAMASK_BIN is present and not in $PATH, add it +#if [[ [[ "x$DAMASK_BIN" != "x" ]] && ! `echo ":$PATH:" | grep $DAMASK_BIN:` ]]; then + export PATH=$DAMASK_BIN:$PATH +#fi + SOLVER=`which DAMASK_spectral 2>/dev/null` +if [ "x$SOLVER" = "x" ]; then + export SOLVER='Not found!' +fi PROCESSING=`which postResults 2>/dev/null` -if [ "x$DAMASK_NUM_THREADS" = "x" ]; then - DAMASK_NUM_THREADS=1 +if [ "x$PROCESSING" = "x" ]; then + export PROCESSING='Not found!' fi # according to http://software.intel.com/en-us/forums/topic/501500 # this seems to make sense for the stack size -if [ "`which free 2>/dev/null`" != "free not found" ]; then - freeMem=`free -k | grep -E '(Mem|Speicher):' | awk '{print $4;}'` - - # http://superuser.com/questions/220059/what-parameters-has-ulimit - ulimit -s `expr $freeMem / $DAMASK_NUM_THREADS / 2` 2>/dev/null # maximum stack size (kB) - ulimit -d `expr $freeMem / 2` 2>/dev/null # maximum heap size (kB) -fi -ulimit -v unlimited 2>/dev/null # maximum virtual memory size +#FREE=`which free 2>/dev/null` +#if [ "x$FREE" != "x" ]; then +# freeMem=`free -k | grep -E '(Mem|Speicher):' | awk '{print $4;}'` +# heap=`expr $freeMem / 2` +# stack=`expr $freeMem / 2` +# +# # http://superuser.com/questions/220059/what-parameters-has-ulimit +# ulimit -s $stack 2>/dev/null # maximum stack size (kB) +# ulimit -d $heap 2>/dev/null # maximum heap size (kB) +#fi +#ulimit -c 2000 2>/dev/null # core file size (512-byte blocks) +#ulimit -v unlimited 2>/dev/null # maximum virtual memory size ulimit -m unlimited 2>/dev/null # maximum physical memory size # disable output in case of scp if [ ! -z "$PS1" ]; then echo - echo Düsseldorf Advanced Materials Simulation Kit --- DAMASK - echo Max-Planck-Institut für Eisenforschung GmbH, Düsseldorf - echo https://damask.mpie.de + echo Düsseldorf Advanced Materials Simulation Kit - DAMASK + echo Max-Planck-Institut für Eisenforschung, Düsseldorf + echo http://damask.mpie.de echo - echo "Using environment with ..." + echo Using environment with ... echo "DAMASK $DAMASK_ROOT" - echo "Spectral Solver $SOLVER" - echo "Post Processing $PROCESSING" + [[ "x$SOLVER" != "x" ]] && echo "Spectral Solver $SOLVER" + [[ "x$PROCESSING" != "x" ]] && echo "Post Processing $PROCESSING" echo "Multithreading DAMASK_NUM_THREADS=$DAMASK_NUM_THREADS" if [ "x$PETSC_DIR" != "x" ]; then echo "PETSc location $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") + [[ `readlink -f $PETSC_DIR` == $PETSC_DIR ]] || echo " ~~> "`readlink -f $PETSC_DIR` fi - [[ "x$PETSC_ARCH" == "x" ]] \ - || echo "PETSc architecture $PETSC_ARCH" + [[ "x$PETSC_ARCH" != "x" ]] && echo "PETSc architecture $PETSC_ARCH" echo "MSC.Marc/Mentat $MSC_ROOT" echo - echo -n "heap size " - [[ "$(ulimit -d)" == "unlimited" ]] \ - && echo "unlimited" \ - || echo $(python -c \ - "import math; \ - size=$(( 1024*$(ulimit -d) )); \ - print('{:.4g} {}'.format(size / (1 << ((int(math.log(size,2) / 10) if size else 0) * 10)), \ - ['bytes','KiB','MiB','GiB','TiB','EiB','ZiB'][int(math.log(size,2) / 10) if size else 0]))") - echo -n "stack size " - [[ "$(ulimit -s)" == "unlimited" ]] \ - && echo "unlimited" \ - || echo $(python -c \ - "import math; \ - size=$(( 1024*$(ulimit -s) )); \ - print('{:.4g} {}'.format(size / (1 << ((int(math.log(size,2) / 10) if size else 0) * 10)), \ - ['bytes','KiB','MiB','GiB','TiB','EiB','ZiB'][int(math.log(size,2) / 10) if size else 0]))") + echo -n "heap size/MiB "; echo "`ulimit -d`/1024" | bc + echo -n "stack size/MiB "; echo "`ulimit -s`/1024" | bc fi export DAMASK_NUM_THREADS export PYTHONPATH=$DAMASK_ROOT/lib:$PYTHONPATH -for var in BASE STAT SOLVER PROCESSING FREE DAMASK_BIN MATCH; do +for var in BASE STAT SOLVER PROCESSING FREE; do unset "${var}" done -for var in DAMASK MSC; do +for var in DAMASK IMKL ACML LAPACK MSC FFTW HDF5; do unset "${var}_ROOT" done -for var in ABAQUS MARC; do - unset "${var}_VERSION" -done + diff --git a/processing/pre/geom_grainGrowth.py b/processing/pre/geom_grainGrowth.py index 95c67fb28..ac7af9e85 100755 --- a/processing/pre/geom_grainGrowth.py +++ b/processing/pre/geom_grainGrowth.py @@ -99,16 +99,15 @@ for name in filenames: for smoothIter in xrange(options.N): - boundary = np.zeros(microstructure.shape) + interfaceEnergy = np.zeros(microstructure.shape) for i in (-1,0,1): for j in (-1,0,1): for k in (-1,0,1): # assign interfacial energy to all voxels that have a differing neighbor (in Moore neighborhood) - boundary = np.maximum(boundary, + interfaceEnergy = np.maximum(interfaceEnergy, interfacialEnergy(microstructure,np.roll(np.roll(np.roll( microstructure,i,axis=0), j,axis=1), k,axis=2))) - interfaceEnergy = boundary - + # periodically extend interfacial energy array by half a grid size in positive and negative directions periodic_interfaceEnergy = np.tile(interfaceEnergy,(3,3,3))[grid[0]/2:-grid[0]/2, grid[1]/2:-grid[1]/2,