Merge remote-tracking branch 'origin/development' into export_DAMASK_to_DREAM3D

This commit is contained in:
Martin Diehl 2023-12-04 22:37:05 +01:00
commit b5e34e7949
174 changed files with 6550 additions and 1297 deletions

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@ -2,7 +2,7 @@ name: Grid and Mesh Solver
on: [push]
env:
PETSC_VERSION: '3.18.4'
PETSC_VERSION: '3.20.1'
HOMEBREW_NO_ANALYTICS: 'ON' # Make Homebrew installation a little quicker
HOMEBREW_NO_AUTO_UPDATE: 'ON'
HOMEBREW_NO_BOTTLE_SOURCE_FALLBACK: 'ON'
@ -17,7 +17,7 @@ jobs:
strategy:
matrix:
gcc_v: [9, 10, 11, 12]
gcc_v: [9, 10, 11, 12, 13]
fail-fast: false
env:
@ -47,7 +47,7 @@ jobs:
- name: PETSc - Download
if: steps.petsc-download.outputs.cache-hit != 'true'
run: |
wget -q https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-${PETSC_VERSION}.tar.gz -P download
wget -q https://web.cels.anl.gov/projects/petsc/download/release-snapshots/petsc-${PETSC_VERSION}.tar.gz -P download
- name: PETSc - Prepare
run: |
@ -88,31 +88,22 @@ jobs:
intel:
runs-on: [ubuntu-22.04]
runs-on: ubuntu-22.04
container:
image: intel/oneapi-hpckit:latest
strategy:
matrix:
intel_v: [classic, llvm] # Variant of Intel compilers
fail-fast: false
env:
INTEL_V: ${{ matrix.intel_v }}
steps:
- uses: actions/checkout@v3
- name: Intel - Install
run: |
wget -q https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB
sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB
rm GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB
echo "deb https://apt.repos.intel.com/oneapi all main" | sudo tee /etc/apt/sources.list.d/oneAPI.list
sudo apt-get update
sudo apt-get install \
intel-basekit \
intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic intel-oneapi-compiler-fortran \
intel-oneapi-openmp intel-oneapi-mkl-devel
source /opt/intel/oneapi/setvars.sh
apt-get update --allow-insecure-repositories
apt-get install --allow-unauthenticated -y \
cmake build-essential autoconf libtool \
zlib1g-dev
printenv >> $GITHUB_ENV
- name: PETSc - Cache download
@ -125,15 +116,15 @@ jobs:
- name: PETSc - Download
if: steps.petsc-download.outputs.cache-hit != 'true'
run: |
wget -q https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-${PETSC_VERSION}.tar.gz -P download
wget -q https://web.cels.anl.gov/projects/petsc/download/release-snapshots/petsc-${PETSC_VERSION}.tar.gz -P download
- name: PETSc - Prepare
run: |
tar -xf download/petsc-${PETSC_VERSION}.tar.gz -C .
sed -i "1719s/if not os.path.isfile(os.path.join(self.packageDir,'configure')):/if True:/g" \
sed -i "1805s/if not os.path.isfile(os.path.join(self.packageDir,self.configureName)):/if True:/g" \
./petsc-${PETSC_VERSION}/config/BuildSystem/config/package.py
export PETSC_DIR=${PWD}/petsc-${PETSC_VERSION}
export PETSC_ARCH=intel-${INTEL_V}
export PETSC_ARCH=intel
printenv >> $GITHUB_ENV
- name: PETSc - Cache installation
@ -141,21 +132,9 @@ jobs:
uses: actions/cache@v3
with:
path: petsc-${{ env.PETSC_VERSION }}
key: petsc-${{ env.PETSC_VERSION }}-intel-${{ matrix.intel_v }}-${{ hashFiles('**/petscversion.h') }}
key: petsc-${{ env.PETSC_VERSION }}-intel-${{ hashFiles('**/petscversion.h') }}
- name: PETSc - Install (classic)
if: contains( matrix.intel_v, 'classic')
run: |
cd petsc-${PETSC_VERSION}
./configure \
--with-fc='mpiifort -fc=ifort -diag-disable=10441' \
--with-cc='mpiicc -cc=icc -diag-disable=10441' \
--with-cxx='mpiicpc -cxx=icpc -diag-disable=10441' \
--download-fftw --download-hdf5 --download-hdf5-fortran-bindings=1 --download-zlib
make all
- name: PETSc - Install (LLVM)
if: contains( matrix.intel_v, 'llvm')
- name: PETSc - Install
run: |
cd petsc-${PETSC_VERSION}
./configure \
@ -166,7 +145,6 @@ jobs:
make all
- name: DAMASK - Compile
if: contains( matrix.intel_v, 'classic')
run: |
cmake -B build/grid -DDAMASK_SOLVER=grid -DCMAKE_INSTALL_PREFIX=${PWD}
cmake --build build/grid --parallel
@ -175,18 +153,6 @@ jobs:
cmake --build build/mesh --parallel
cmake --install build/mesh
# ifx has issue with openMP
# https://community.intel.com/t5/Intel-Fortran-Compiler/ifx-ICE-and-SEGFAULT/m-p/1459877
- name: DAMASK - Compile
if: contains( matrix.intel_v, 'llvm')
run: |
cmake -B build/grid -DDAMASK_SOLVER=grid -DCMAKE_INSTALL_PREFIX=${PWD} -DOPENMP=OFF
cmake --build build/grid --parallel
cmake --install build/grid
cmake -B build/mesh -DDAMASK_SOLVER=mesh -DCMAKE_INSTALL_PREFIX=${PWD} -DOPENMP=OFF
cmake --build build/mesh --parallel
cmake --install build/mesh
- name: DAMASK - Run
run: |
./bin/DAMASK_grid -l tensionX.yaml -g 20grains16x16x16.vti -m material.yaml -w examples/grid

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@ -9,7 +9,7 @@ jobs:
strategy:
matrix:
python-version: ['3.8', '3.9', '3.10', '3.11']
python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
os: [ubuntu-latest, macos-latest, windows-latest]
fail-fast: false

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@ -47,7 +47,7 @@ variables:
PETSC_INTELLLVM: "Libraries/PETSc/3.16.3/oneAPI-2022.0.1-IntelMPI-2021.5.0"
PETSC_INTEL: "Libraries/PETSc/3.16.5/Intel-2022.0.1-IntelMPI-2021.5.0"
# ++++++++++++ MSC Marc +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
MSC: "FEM/MSC/2023.1"
MSC: "FEM/MSC/2023.3"
IntelMarc: "Compiler/Intel/19.1.2 Libraries/IMKL/2020"
HDF5Marc: "HDF5/1.12.2/Intel-19.1.2"

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@ -130,7 +130,10 @@ set(CMAKE_Fortran_FLAGS_${CMAKE_BUILD_TYPE} "${CMAKE_Fortran_FLAGS_${CMAKE_BUILD
set(CMAKE_Fortran_LINK_EXECUTABLE "${CMAKE_Fortran_LINK_EXECUTABLE} <OBJECTS> -o <TARGET> <LINK_LIBRARIES> -L${PETSC_LIBRARY_DIRS} -lpetsc ${PETSC_EXTERNAL_LIB} -lz")
if(fYAML_FOUND STREQUAL "1")
set(CMAKE_Fortran_LINK_EXECUTABLE "${CMAKE_Fortran_LINK_EXECUTABLE} -L${fYAML_LIBRARY_DIRS} -l${fYAML_LIBRARIES}")
set(CMAKE_Fortran_LINK_EXECUTABLE "${CMAKE_Fortran_LINK_EXECUTABLE} -L${fYAML_LIBRARY_DIRS}")
foreach(fYAML_LIBRARY ${fYAML_LIBRARIES})
set(CMAKE_Fortran_LINK_EXECUTABLE "${CMAKE_Fortran_LINK_EXECUTABLE} -L${fYAML_LIBRARY_DIRS} -l${fYAML_LIBRARY}")
endforeach()
add_definitions(-DFYAML)
pkg_get_variable(fYAML_INCLUDE_DIR libfyaml includedir) # fYAML_INCLUDE_DIRS and fYAML_CFLAGS are not working
set(CMAKE_C_FLAGS_${CMAKE_BUILD_TYPE} "${CMAKE_C_FLAGS_${CMAKE_BUILD_TYPE}} -I${fYAML_INCLUDE_DIR}")

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@ -88,7 +88,7 @@ done
secondLevel "Details on $DEFAULT_PYTHON:"
echo $(ls -la $(which $DEFAULT_PYTHON))
for MODULE in numpy scipy pandas matplotlib yaml h5py;do
thirdLevel $module
thirdLevel $MODULE
$DEFAULT_PYTHON -c "import $MODULE; \
print('Version: {}'.format($MODULE.__version__)); \
print('Location: {}'.format($MODULE.__file__))"

@ -1 +1 @@
Subproject commit 9d2a98d72d9bf547dd697124cb795cf6a9668d30
Subproject commit bc2c8e3b8f405fdda0d69a2900d9b94c7cc0936f

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@ -1,6 +1,23 @@
# DAMASK - The Düsseldorf Advanced Material Simulation Kit
Visit [damask.mpie.de](https://damask.mpie.de) for installation and usage instructions
- Usage, installation, and support: https://damask.mpie.de
- Code development: https://git.damask.mpie.de
- General inquiries: damask@mpie.de
## Repository Locations
### [git.damask.mpie.de](https://git.damask.mpie.de)
All code development is centralized in the principal DAMASK code repository hosted at [git.damask.mpie.de](https://git.damask.mpie.de).
Access to this GitLab instance requires registration and is granted to anyone with an interest in actively supporting the development of DAMASK.
### [github.com](https://github.com)
GitHub hosts the publicly accessible, but read-only, mirror of the principal DAMASK code repository and replicates its three top-level branches from [git.damask.mpie.de](https://git.damask.mpie.de).
The site is primarily meant to provide a forum for [Discussions](https://github.com/eisenforschung/DAMASK/discussions) and [Issues](https://github.com/eisenforschung/DAMASK/issues).
## Contact Information
@ -8,8 +25,3 @@ Max-Planck-Institut für Eisenforschung GmbH
Max-Planck-Str. 1
40237 Düsseldorf
Germany
damask@mpie.de
https://damask.mpie.de
https://git.damask.mpie.de

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@ -1 +1 @@
3.0.0-alpha7-880-g3644fe586
3.0.0-alpha8-67-g9f8ecd44b

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@ -0,0 +1,21 @@
type: Hooke
references:
- R.A. Ayres et al.,
Journal of Applied Physics 46:1526-1530, 1975,
https://doi.org/10.1063/1.321804,
fit to Table IV (T_min=100K, T_max=300K)
C_11: 524.6e+9
C_11,T: -5.783e+07
C_11,T^2: -1.355e+05
C_12: 219.0e+9
C_12,T: 1.940e+07
C_12,T^2: 7.634e+04
C_44: 168.7e+9
C_44,T: -2.048e+07
C_44,T^2: -5.478e+04
T_ref: 293.15

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@ -0,0 +1,21 @@
type: Hooke
references:
- R.A. Ayres et al.,
Journal of Applied Physics 46:1526-1530, 1975,
https://doi.org/10.1063/1.321804,
fit to Table IV (T_min=100K, T_max=300K)
C_11: 535.1e+9
C_11,T: -6.459e+07
C_11,T^2: -1.664e+05
C_12: 216.1e+9
C_12,T: 2.357e+07
C_12,T^2: 5.186e+04
C_44: 161.1e+9
C_44,T: -1.498e+07
C_44,T^2: -3.234e+04
T_ref: 293.15

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@ -0,0 +1,49 @@
---
+++
@@ -6,18 +6,27 @@
DIR=$1
user=$3
program=$4
+usernoext=$user
+usernoext=`dirname $usernoext`/`$BASENAME $usernoext .f`
+usernoext=`dirname $usernoext`/`$BASENAME $usernoext .F`
+usernoext=`dirname $usernoext`/`$BASENAME $usernoext .for`
+usernoext=`dirname $usernoext`/`$BASENAME $usernoext .f90`
+
+# add BLAS options for linking
+ BLAS="%BLAS%"
+
. $DIR/tools/include
DIRJOB=$2
cd $DIRJOB
-echo "Compiling and linking user subroutine $user.f on host `hostname`"
+echo "Compiling and linking user subroutine $user on host `hostname`"
echo "program: $program"
- $FORTRAN $user.f || \
+ $DFORTHIGHMP $user || \
{
- echo "$0: compile failed for $user.f"
+ echo "$0: compile failed for $user"
exit 1
}
/bin/rm $program 2>/dev/null
- userobj=$user.o
+ userobj=$usernoext.o
$LOAD ${program} $DIR/lib/main.o\
@@ -33,9 +42,13 @@
$TKLIBS \
$MRCLIBS \
$METISLIBS \
+ $BLAS \
$SYSLIBS || \
{
- echo "$0: link failed for $user.o on host `hostname`"
+ echo "$0: link failed for $usernoext.o on host `hostname`"
exit 1
}
/bin/rm $userobj
+ /bin/rm $DIRJOB/*.mod
+ /bin/rm $DIRJOB/*.smod
+ /bin/rm $DIRJOB/*_genmod.f90

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@ -0,0 +1,49 @@
---
+++
@@ -6,18 +6,27 @@
DIR=$1
user=$3
program=$4
+usernoext=$user
+usernoext=`dirname $usernoext`/`$BASENAME $usernoext .f`
+usernoext=`dirname $usernoext`/`$BASENAME $usernoext .F`
+usernoext=`dirname $usernoext`/`$BASENAME $usernoext .for`
+usernoext=`dirname $usernoext`/`$BASENAME $usernoext .f90`
+
+# add BLAS options for linking
+ BLAS="%BLAS%"
+
. $DIR/tools/include
DIRJOB=$2
cd $DIRJOB
-echo "Compiling and linking user subroutine $user.f on host `hostname`"
+echo "Compiling and linking user subroutine $user on host `hostname`"
echo "program: $program"
- $FORTRAN $user.f || \
+ $DFORTRANLOWMP $user || \
{
- echo "$0: compile failed for $user.f"
+ echo "$0: compile failed for $user"
exit 1
}
/bin/rm $program 2>/dev/null
- userobj=$user.o
+ userobj=$usernoext.o
$LOAD ${program} $DIR/lib/main.o\
@@ -33,9 +42,13 @@
$TKLIBS \
$MRCLIBS \
$METISLIBS \
+ $BLAS \
$SYSLIBS || \
{
- echo "$0: link failed for $user.o on host `hostname`"
+ echo "$0: link failed for $usernoext.o on host `hostname`"
exit 1
}
/bin/rm $userobj
+ /bin/rm $DIRJOB/*.mod
+ /bin/rm $DIRJOB/*.smod
+ /bin/rm $DIRJOB/*_genmod.f90

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@ -0,0 +1,49 @@
---
+++
@@ -6,18 +6,27 @@
DIR=$1
user=$3
program=$4
+usernoext=$user
+usernoext=`dirname $usernoext`/`$BASENAME $usernoext .f`
+usernoext=`dirname $usernoext`/`$BASENAME $usernoext .F`
+usernoext=`dirname $usernoext`/`$BASENAME $usernoext .for`
+usernoext=`dirname $usernoext`/`$BASENAME $usernoext .f90`
+
+# add BLAS options for linking
+ BLAS="%BLAS%"
+
. $DIR/tools/include
DIRJOB=$2
cd $DIRJOB
-echo "Compiling and linking user subroutine $user.f on host `hostname`"
+echo "Compiling and linking user subroutine $user on host `hostname`"
echo "program: $program"
- $FORTRAN $user.f || \
+ $DFORTRANMP $user || \
{
- echo "$0: compile failed for $user.f"
+ echo "$0: compile failed for $user"
exit 1
}
/bin/rm $program 2>/dev/null
- userobj=$user.o
+ userobj=$usernoext.o
$LOAD ${program} $DIR/lib/main.o\
@@ -33,9 +42,13 @@
$TKLIBS \
$MRCLIBS \
$METISLIBS \
+ $BLAS \
$SYSLIBS || \
{
- echo "$0: link failed for $user.o on host `hostname`"
+ echo "$0: link failed for $usernoext.o on host `hostname`"
exit 1
}
/bin/rm $userobj
+ /bin/rm $DIRJOB/*.mod
+ /bin/rm $DIRJOB/*.smod
+ /bin/rm $DIRJOB/*_genmod.f90

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@ -0,0 +1,75 @@
---
+++
@@ -172,6 +178,15 @@
MARC_COSIM_LIB="$MSCCOSIM_HOME/CoSim$MSCCOSIM_VERSION/Dcosim$MSCCOSIM_VERSION/lib"
fi
+# DAMASK uses the HDF5 compiler wrapper around the Intel compiler
+H5FC=$(h5fc -shlib -show)
+if [[ "$H5FC" == *"$dir is"* ]]; then
+ H5FC=$(echo $(echo "$H5FC" | tail -n1) | sed -e "s/\-shlib/-fPIC -qopenmp/g")
+ H5FC=${H5FC%-lmpifort*}
+fi
+HDF5_LIB=${H5FC//*ifort/}
+FCOMP="$H5FC"
+
# AEM
if test "$MARCDLLOUTDIR" = ""; then
DLLOUTDIR="$MARC_LIB"
@@ -599,7 +609,7 @@
PROFILE=" $PROFILE -pg"
fi
-FORT_OPT="-c -assume byterecl -safe-cray-ptr -mp1 -WB -fp-model source"
+FORT_OPT="-c -implicitnone -stand f18 -standard-semantics -assume nostd_mod_proc_name -safe-cray-ptr -mp1 -WB -fp-model source"
if test "$MTHREAD" = "OPENMP"
then
FORT_OPT=" $FORT_OPT -qopenmp"
@@ -612,7 +621,7 @@
FORT_OPT=" $FORT_OPT -save -zero"
fi
if test "$MARCHDF_HDF" = "HDF"; then
- FORT_OPT="$FORT_OPT -DMARCHDF_HDF=$MARCHDF_HDF $HDF_INCLUDE"
+ FORT_OPT="$FORT_OPT -DMARCHDF=$MARCHDF_HDF"
fi
FORTLOW="$FCOMP $FORT_OPT $PROFILE -O0 $I8FFLAGS -I$MARC_SOURCE/common \
@@ -626,6 +635,29 @@
# for compiling free form f90 files. high opt, integer(4)
FORTF90="$FCOMP -c -O3"
+# determine DAMASK version
+if test -n "$DAMASK_USER"; then
+ DAMASKROOT=`dirname $DAMASK_USER`/../..
+ read DAMASKVERSION < $DAMASKROOT/VERSION
+ DAMASKVERSION="'"$DAMASKVERSION"'"
+else
+ DAMASKVERSION="'N/A'"
+fi
+
+# DAMASK compiler calls
+DFORTLOWMP="$FCOMP -c -O0 -qno-offload -implicitnone -stand f18 -standard-semantics -assume nostd_mod_proc_name -safe-cray-ptr $PROFILE -zero -mp1 -WB $I8FFLAGS -I$MARC_SOURCE/common \
+ -fpp -ftz -diag-disable 5268 -warn declarations -warn general -warn usage -warn interfaces -warn ignore_loc -warn alignments -DMARC4DAMASK=2023.2 -DDAMASKVERSION=$DAMASKVERSION \
+ -qopenmp -qopenmp-threadprivate=compat\
+ $MUMPS_INCLUDE $I8DEFINES -DLinux -DLINUX -DLinux_intel $FDEFINES $DDM $SOLVERFLAGS -I$KDTREE2_MOD -I$MARC_MOD"
+DFORTRANMP="$FCOMP -c -O1 -qno-offload -implicitnone -stand f18 -standard-semantics -assume nostd_mod_proc_name -safe-cray-ptr $PROFILE -zero -mp1 -WB $I8FFLAGS -I$MARC_SOURCE/common \
+ -fpp -ftz -diag-disable 5268 -warn declarations -warn general -warn usage -warn interfaces -warn ignore_loc -warn alignments -DMARC4DAMASK=2023.2 -DDAMASKVERSION=$DAMASKVERSION \
+ -qopenmp -qopenmp-threadprivate=compat\
+ $MUMPS_INCLUDE $I8DEFINES -DLinux -DLINUX -DLinux_intel $FDEFINES $DDM $SOLVERFLAGS -I$KDTREE2_MOD -I$MARC_MOD"
+DFORTHIGHMP="$FCOMP -c -O3 -qno-offload -implicitnone -stand f18 -standard-semantics -assume nostd_mod_proc_name -safe-cray-ptr $PROFILE -zero -mp1 -WB $I8FFLAGS -I$MARC_SOURCE/common \
+ -fpp -ftz -diag-disable 5268 -warn declarations -warn general -warn usage -warn interfaces -warn ignore_loc -warn alignments -DMARC4DAMASK=2023.2 -DDAMASKVERSION=$DAMASKVERSION \
+ -qopenmp -qopenmp-threadprivate=compat\
+ $MUMPS_INCLUDE $I8DEFINES -DLinux -DLINUX -DLinux_intel $FDEFINES $DDM $SOLVERFLAGS -I$KDTREE2_MOD -I$MARC_MOD"
+
if test "$MARCDEBUG" = "ON"
then
FORTLOW="$FCOMP $FORT_OPT $PROFILE $I8FFLAGS -I$MARC_SOURCE/common \
@@ -783,7 +815,7 @@
SOLVERLIBS="${BCSSOLVERLIBS} ${VKISOLVERLIBS} ${CASISOLVERLIBS} ${MF2SOLVERLIBS} \
-L$MARC_MKL \
- $MARC_LIB/blas_src.a ${ACSI_LIB}/ACSI_MarcLib.a $KDTREE2_LIB/libkdtree2.a $MARC_LIB/libtetmeshinterface.a $MARC_LIB/libcaefatigueinterface.a -L$MARC_LIB -lmkl_blacs_intelmpi_ilp64 -lmkl_scalapack_ilp64 -lmkl_intel_ilp64 -lmkl_intel_thread -lmkl_core -liomp5 -ltetmesh -ltetadapt -lmeshgems -lmg-tetra -lmeshgems_stubs -lCATMshMesherCore -lCATMshCVMforCSM -lmg-hybrid -lmg-cadsurf -lmg-hexa $HDF_LIBS $SOLVER2LIBS $RTREE_LIB/librtree_lib.a $SFGEO_LIB/libgeo_lib.a"
+ $MARC_LIB/blas_src.a ${ACSI_LIB}/ACSI_MarcLib.a $KDTREE2_LIB/libkdtree2.a $MARC_LIB/libtetmeshinterface.a $MARC_LIB/libcaefatigueinterface.a -L$MARC_LIB -lmkl_blacs_intelmpi_ilp64 -lmkl_scalapack_ilp64 -lmkl_intel_ilp64 -lmkl_intel_thread -lmkl_core -liomp5 -ltetmesh -ltetadapt -lmeshgems -lmg-tetra -lmeshgems_stubs -lCATMshMesherCore -lCATMshCVMforCSM -lmg-hybrid -lmg-cadsurf -lmg-hexa $HDF5_LIB $SOLVER2LIBS $RTREE_LIB/librtree_lib.a $SFGEO_LIB/libgeo_lib.a"
SOLVERLIBS_DLL=${SOLVERLIBS}
if test "$AEM_DLL" -eq 1

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@ -0,0 +1,517 @@
---
+++
@@ -136,6 +136,11 @@
# is created. For job running in the background, the log #
# file is always created. Default is "yes" #
##############################################################################
+# remove all Mentat paths from LD_LIBRARY_PATH
+LD_LIBRARY_PATH=:$LD_LIBRARY_PATH:
+LD_LIBRARY_PATH=${LD_LIBRARY_PATH//+([!(:)])mentat2023.2+([!(:)])/:}
+LD_LIBRARY_PATH=${LD_LIBRARY_PATH//+([(:)])/:}
+LD_LIBRARY_PATH=${LD_LIBRARY_PATH#:}; LD_LIBRARY_PATH=${LD_LIBRARY_PATH%:}
# set DIR to the directory in which this script is
REALCOM="`/bin/ls -l $0 |awk '{ print $NF; }'`"
DIR=`dirname $REALCOM`
@@ -302,7 +307,23 @@
. "$DIR/getarch"
+
+# getting user subroutine file name
+found=0
+for i in "$@"; do
+ if test $found = 1; then
+ DAMASK_USER=$i
+ found=0
+ fi
+ case $i in
+ -u* | -U*)
+ found=1
+ ;;
+ esac
+done
+# sourcing include_linux64 (needs DAMASK_USER to be set)
. $MARC_INCLUDE
+
#
#
@@ -405,7 +426,7 @@
did=
vid=
user=
-usersubname=
+usernoext=
objs=
qid=background
cpu=
@@ -676,50 +697,19 @@
esac
;;
-u* | -U*)
- user=`dirname $value`/`$BASENAME $value .f`
- usersubname=$user
- basefile=`$BASENAME $value`
- if test ${basefile##*.} = f
- then
- user=`dirname $value`/`$BASENAME $value .f`
- usersubname=$user.f
- elif test ${basefile##*.} = F
- then
- user=`dirname $value`/`$BASENAME $value .F`
- usersubname=$user.F
- elif test ${basefile##*.} = f90
- then
- user=`dirname $value`/`$BASENAME $value .f90`
- usersubname=$user.f90
- elif test ${basefile##*.} = F90
- then
- user=`dirname $value`/`$BASENAME $value .F90`
- usersubname=$user.F90
- fi
+ user=$value
case $user in
\/*)
;;
*)
user=`pwd`/$user
- usersubname=`pwd`/$usersubname
;;
esac
- if test ! -f $usersubname
- then
- if test -f $usersubname.f
- then
- usersubname=$usersubname.f
- elif test -f $usersubname.F
- then
- usersubname=$usersubname.F
- elif test -f $usersubname.f90
- then
- usersubname=$usersubname.f90
- elif test -f $usersubname.F90
- then
- usersubname=$usersubname.F90
- fi
- fi
+ usernoext=$user
+ usernoext=`dirname $usernoext`/`$BASENAME $usernoext .f`
+ usernoext=`dirname $usernoext`/`$BASENAME $usernoext .F`
+ usernoext=`dirname $usernoext`/`$BASENAME $usernoext .for`
+ usernoext=`dirname $usernoext`/`$BASENAME $usernoext .f90`
;;
-obj | -OBJ)
objs="$value"
@@ -1207,12 +1197,12 @@
fi
fi
fi
- if test "$usersubname"
+ if test "$user"
then
- if test ! -f $usersubname
+ if test ! -f $user
then
error="$error
-user subroutine file $usersubname not accessible"
+user subroutine file $user not accessible"
fi
fi
if test "$objs"
@@ -1531,7 +1521,7 @@
Marc shared lib : $progdll
Version type : $mode
Job ID : $DIRJID/$jid$extra_job_info
-User subroutine name : $usersubname
+User subroutine name : $user
User objects/libs : $objs
Restart file job ID : $rid
Substructure file ID : $sid
@@ -1564,7 +1554,7 @@
Marc shared lib : $progdll
Version type : $mode
Job ID : $DIRJID/$jid$extra_job_info
-User subroutine name : $usersubname
+User subroutine name : $user
User objects/libs : $objs
Restart file job ID : $rid
Substructure file ID : $sid
@@ -1687,7 +1677,7 @@
;;
esac
fi
- $ECHO "User subroutine name ($usersubname)? $ECHOTXT"
+ $ECHO "User subroutine name ($user)? $ECHOTXT"
read value
if test "$value"
then
@@ -1696,50 +1686,19 @@
user=
;;
*)
- user=`dirname $value`/`$BASENAME $value .f`
- usersubname=$user
- basefile=`$BASENAME $value`
- if test ${basefile##*.} = f
- then
- user=`dirname $value`/`$BASENAME $value .f`
- usersubname=$user.f
- elif test ${basefile##*.} = F
- then
- user=`dirname $value`/`$BASENAME $value .F`
- usersubname=$user.F
- elif test ${basefile##*.} = f90
- then
- user=`dirname $value`/`$BASENAME $value .f90`
- usersubname=$user.f90
- elif test ${basefile##*.} = F90
- then
- user=`dirname $value`/`$BASENAME $value .F90`
- usersubname=$user.F90
- fi
+ user=$value
case $user in
\/*)
;;
*)
user=`pwd`/$user
- usersubname=`pwd`/$usersubname
;;
esac
- if test ! -f $usersubname
- then
- if test -f $usersubname.f
- then
- usersubname=$usersubname.f
- elif test -f $usersubname.F
- then
- usersubname=$usersubname.F
- elif test -f $usersubname.f90
- then
- usersubname=$usersubname.f90
- elif test -f $usersubname.F90
- then
- usersubname=$usersubname.F90
- fi
- fi
+ usernoext=$user
+ usernoext=`dirname $usernoext`/`$BASENAME $usernoext .f`
+ usernoext=`dirname $usernoext`/`$BASENAME $usernoext .F`
+ usernoext=`dirname $usernoext`/`$BASENAME $usernoext .for`
+ usernoext=`dirname $usernoext`/`$BASENAME $usernoext .f90`
;;
esac
fi
@@ -2274,11 +2233,12 @@
#
# user subroutine used
#
+# add DAMASK options for linking
+ DAMASK="-lstdc++"
if test "$user"
then
-# program=$user.marc
- program=$DIRJOB/`$BASENAME $user .f`.marc
+ program=$usernoext.marc
case $program in
\/* | \.\/*)
bd=
@@ -2391,7 +2351,7 @@
fi
if test "$user"
then
- execpath=$DIRJOB/`$BASENAME $user .f`.marc
+ execpath=$usernoext.marc
usersub=1
fi
export execpath
@@ -3274,44 +3234,27 @@
echo
if test "$user"
then
- userobj=$DIRJOB/`$BASENAME $user .f`.o
- basefile=`$BASENAME $usersubname`
- if test ${basefile##*.} = f
- then
- usersub=$DIRJOB/`$BASENAME $user .f`.F
- ln -sf "$user.f" "$usersub"
- else
- usersub=$usersubname
- fi
-
+ userobj=$usernoext.o
fi
cat > $jid.runmarcscript << END4
if test "$user"
then
- if test ${basefile##*.} = f
- then
- ln -sf "$user.f" "$usersub"
- fi
if test $MACHINENAME = "CRAY"
then
- $FORTRAN $usersub || \
+ $DFORTHIGHMP $user || \
{
- echo "$0: compile failed for $user.f"
+ echo "$0: compile failed for $user"
exit 1
}
/bin/rm $program 2>/dev/null
else
- $FORTRAN $usersub -o $userobj || \
+ $DFORTHIGHMP $user -o $userobj || \
{
- echo "$0: compile failed for $user.f"
+ echo "$0: compile failed for $user"
exit 1
}
/bin/rm $program 2>/dev/null
fi
- if test ${basefile##*.} = f
- then
- /bin/rm -f "$usersub"
- fi
fi
@@ -3332,6 +3275,7 @@
$TKLIBS \
$MRCLIBS \
$METISLIBS \
+ $DAMASK \
$SFLIB \
$OPENSSL_LIB \
$SYSLIBS \
@@ -3345,6 +3289,9 @@
prgsav=yes
fi
/bin/rm $userobj 2>/dev/null
+/bin/rm $DIRJOB/*.mod 2>/dev/null
+/bin/rm $DIRJOB/*.smod 2>/dev/null
+/bin/rm $DIRJOB/*_genmod.f90 2>/dev/null
#
# run marc
@@ -3391,7 +3338,7 @@
fi
else
if test $cpdll = yes; then
- filename=`basename $usersubname .f`
+ filename=$usernoext
/bin/cp $DIRJOB/$marcdll $DIRJOB/${filename}_$marcdll 2>/dev/null
fi
if test $rmdll = yes
@@ -3557,7 +3504,7 @@
# first copy over the user sub if local directories
if test ${dirstatus[$counter]} = "local"
then
- $RCP $user.f $i:$DIR1/
+ $RCP $user $i:$DIR1/
fi
# do the compilation on the other machine
if test ${dirstatus[$counter]} = "shared"
@@ -3570,21 +3517,21 @@
remoteuser=$DIR1/`$BASENAME $user`
$RSH $i /bin/rm $remoteprog 2> /dev/null
echo
- $RSH $i $DIR2/tools/comp_user $DIR2 $DIR1 $remoteuser $remoteprog
+ $RSH $i $DIR2/tools/comp_damask_hmp $DIR2 $DIR1 $remoteuser $remoteprog
# check if successful, the new executable should be there
line=`$RSH $i /bin/ls $remoteprog 2> /dev/null`
if test "$line"
then
echo compilation and linking successful on host $i
else
- echo "$0: compile failed for $user.f on host $i"
+ echo "$0: compile failed for $user on host $i"
echo " $PRODUCT Exit number 3"
exit 1
fi
# remove the user subroutine on remote machine
if test ${dirstatus[$counter]} = "local"
then
- $RSH $i /bin/rm $remoteuser.f 2> /dev/null
+ $RSH $i /bin/rm $remoteuser 2> /dev/null
fi
fi
fi
@@ -3594,39 +3541,27 @@
if test "$userhost"
then
echo
- echo "Compiling and linking user subroutine $user.f on host `hostname`"
- fi
- userobj=$DIRJOB/`$BASENAME $user .f`.o
- basefile=`$BASENAME $usersubname`
- if test ${basefile##*.} = f
- then
- usersub=$DIRJOB/`$BASENAME $user .f`.F
- ln -sf "$user.f" "$usersub"
- else
- usersub=$usersubname
+ echo "Compiling and linking user subroutine $user on host `hostname`"
fi
+ userobj=$usernoext.o
if test $MACHINENAME = "CRAY"
then
- $FORTRAN $usersub || \
+ $DFORTHIGHMP $user || \
{
- echo "$0: compile failed for $user.f"
+ echo "$0: compile failed for $user"
echo " $PRODUCT Exit number 3"
exit 1
}
/bin/rm $program 2>/dev/null
else
- $FORTRAN $usersub -o $userobj || \
+ $DFORTHIGHMP $user -o $userobj || \
{
- echo "$0: compile failed for $user.f"
+ echo "$0: compile failed for $user"
echo " $PRODUCT Exit number 3"
exit 1
}
/bin/rm $program 2>/dev/null
fi
- if test ${basefile##*.} = f
- then
- /bin/rm -f "$usersub"
- fi
fi # if test $user
@@ -3647,6 +3582,7 @@
$TKLIBS \
$MRCLIBS \
$METISLIBS \
+ $DAMASK \
$SFLIB \
$OPENSSL_LIB \
$SYSLIBS \
@@ -3688,6 +3624,9 @@
prgsav=yes
fi # if test $link
/bin/rm $userobj 2>/dev/null
+/bin/rm $DIRJOB/*.mod 2>/dev/null
+/bin/rm $DIRJOB/*.smod 2>/dev/null
+/bin/rm $DIRJOB/*_genmod.f90 2>/dev/null
#
# run marc
@@ -3781,7 +3720,7 @@
else
#dllrun >0
if test $cpdll = yes; then
- filename=`basename $usersubname .f`
+ filename=$usernoext
/bin/cp $DIRJOB/$marcdll $DIRJOB/${filename}_$marcdll 2>/dev/null
fi
if test $rmdll = yes;then
@@ -3906,7 +3845,7 @@
# first copy over the user sub if local directories
if test ${dirstatus[$counter]} = "local"
then
- $RCP $user.f $i:$DIR1/
+ $RCP $user $i:$DIR1/
fi
# do the compilation on the other machine
if test ${dirstatus[$counter]} = "shared"
@@ -3919,20 +3858,20 @@
remoteuser=$DIR1/`$BASENAME $user`
$RSH $i /bin/rm $remoteprog 2> /dev/null
echo
- $RSH $i $DIR2/tools/comp_user $DIR2 $DIR1 $remoteuser $remoteprog
+ $RSH $i $DIR2/tools/comp_damask_hmp $DIR2 $DIR1 $remoteuser $remoteprog
# check if successful, the new executable should be there
line=`$RSH $i /bin/ls $remoteprog 2> /dev/null`
if test "$line"
then
echo compilation and linking successful on host $i
else
- echo "$0: compile failed for $user.f on host $i"
+ echo "$0: compile failed for $user on host $i"
exit 1
fi
# remove the user subroutine on remote machine
if test ${dirstatus[$counter]} = "local"
then
- $RSH $i /bin/rm $remoteuser.f 2> /dev/null
+ $RSH $i /bin/rm $remoteuser 2> /dev/null
fi
fi
fi
@@ -3942,37 +3881,25 @@
if test "$userhost"
then
echo
- echo "Compiling and linking user subroutine $user.f on host `hostname`"
- fi
- userobj=$DIRJOB/`$BASENAME $user .f`.o
- basefile=`$BASENAME $usersubname`
- if test ${basefile##*.} = f
- then
- usersub=$DIRJOB/`$BASENAME $user .f`.F
- ln -sf "$user.f" "$usersub"
- else
- usersub=$usersubname
+ echo "Compiling and linking user subroutine $user on host `hostname`"
fi
+ userobj=$usernoext.o
if test $MACHINENAME = "CRAY"
then
- $FORTRAN $usersub || \
+ $DFORTHIGHMP $user || \
{
- echo "$0: compile failed for $user.f"
+ echo "$0: compile failed for $user"
exit 1
}
/bin/rm $program 2>/dev/null
else
- $FORTRAN $usersub -o $userobj || \
+ $DFORTHIGHMP $user -o $userobj || \
{
- echo "$0: compile failed for $user.f"
+ echo "$0: compile failed for $user"
exit 1
}
/bin/rm $program 2>/dev/null
fi
- if test ${basefile##*.} = f
- then
- /bin/rm -f "$usersub"
- fi
fi # if test $user
@@ -3993,6 +3920,7 @@
$TKLIBS \
$MRCLIBS \
$METISLIBS \
+ $DAMASK \
$SFLIB \
$OPENSSL_LIB \
$SYSLIBS \
@@ -4033,7 +3961,9 @@
prgsav=yes
fi # if test $link
/bin/rm $userobj 2>/dev/null
-
+/bin/rm $DIRJOB/*.mod 2>/dev/null
+/bin/rm $DIRJOB/*.smod 2>/dev/null
+/bin/rm $DIRJOB/*_genmod.f90 2>/dev/null
# done if no job id given
if test -z "$jid"
then
@@ -4152,7 +4082,7 @@
else
#dllrun >0
if test $cpdll = yes; then
- filename=`basename $usersubname .f`
+ filename=$usernoext
/bin/cp $DIRJOB/$marcdll $DIRJOB/${filename}_$marcdll 2>/dev/null
fi
if test $rmdll = yes;then

View File

@ -0,0 +1,517 @@
---
+++
@@ -136,6 +136,11 @@
# is created. For job running in the background, the log #
# file is always created. Default is "yes" #
##############################################################################
+# remove all Mentat paths from LD_LIBRARY_PATH
+LD_LIBRARY_PATH=:$LD_LIBRARY_PATH:
+LD_LIBRARY_PATH=${LD_LIBRARY_PATH//+([!(:)])mentat2023.2+([!(:)])/:}
+LD_LIBRARY_PATH=${LD_LIBRARY_PATH//+([(:)])/:}
+LD_LIBRARY_PATH=${LD_LIBRARY_PATH#:}; LD_LIBRARY_PATH=${LD_LIBRARY_PATH%:}
# set DIR to the directory in which this script is
REALCOM="`/bin/ls -l $0 |awk '{ print $NF; }'`"
DIR=`dirname $REALCOM`
@@ -302,7 +307,23 @@
. "$DIR/getarch"
+
+# getting user subroutine file name
+found=0
+for i in "$@"; do
+ if test $found = 1; then
+ DAMASK_USER=$i
+ found=0
+ fi
+ case $i in
+ -u* | -U*)
+ found=1
+ ;;
+ esac
+done
+# sourcing include_linux64 (needs DAMASK_USER to be set)
. $MARC_INCLUDE
+
#
#
@@ -405,7 +426,7 @@
did=
vid=
user=
-usersubname=
+usernoext=
objs=
qid=background
cpu=
@@ -676,50 +697,19 @@
esac
;;
-u* | -U*)
- user=`dirname $value`/`$BASENAME $value .f`
- usersubname=$user
- basefile=`$BASENAME $value`
- if test ${basefile##*.} = f
- then
- user=`dirname $value`/`$BASENAME $value .f`
- usersubname=$user.f
- elif test ${basefile##*.} = F
- then
- user=`dirname $value`/`$BASENAME $value .F`
- usersubname=$user.F
- elif test ${basefile##*.} = f90
- then
- user=`dirname $value`/`$BASENAME $value .f90`
- usersubname=$user.f90
- elif test ${basefile##*.} = F90
- then
- user=`dirname $value`/`$BASENAME $value .F90`
- usersubname=$user.F90
- fi
+ user=$value
case $user in
\/*)
;;
*)
user=`pwd`/$user
- usersubname=`pwd`/$usersubname
;;
esac
- if test ! -f $usersubname
- then
- if test -f $usersubname.f
- then
- usersubname=$usersubname.f
- elif test -f $usersubname.F
- then
- usersubname=$usersubname.F
- elif test -f $usersubname.f90
- then
- usersubname=$usersubname.f90
- elif test -f $usersubname.F90
- then
- usersubname=$usersubname.F90
- fi
- fi
+ usernoext=$user
+ usernoext=`dirname $usernoext`/`$BASENAME $usernoext .f`
+ usernoext=`dirname $usernoext`/`$BASENAME $usernoext .F`
+ usernoext=`dirname $usernoext`/`$BASENAME $usernoext .for`
+ usernoext=`dirname $usernoext`/`$BASENAME $usernoext .f90`
;;
-obj | -OBJ)
objs="$value"
@@ -1207,12 +1197,12 @@
fi
fi
fi
- if test "$usersubname"
+ if test "$user"
then
- if test ! -f $usersubname
+ if test ! -f $user
then
error="$error
-user subroutine file $usersubname not accessible"
+user subroutine file $user not accessible"
fi
fi
if test "$objs"
@@ -1531,7 +1521,7 @@
Marc shared lib : $progdll
Version type : $mode
Job ID : $DIRJID/$jid$extra_job_info
-User subroutine name : $usersubname
+User subroutine name : $user
User objects/libs : $objs
Restart file job ID : $rid
Substructure file ID : $sid
@@ -1564,7 +1554,7 @@
Marc shared lib : $progdll
Version type : $mode
Job ID : $DIRJID/$jid$extra_job_info
-User subroutine name : $usersubname
+User subroutine name : $user
User objects/libs : $objs
Restart file job ID : $rid
Substructure file ID : $sid
@@ -1687,7 +1677,7 @@
;;
esac
fi
- $ECHO "User subroutine name ($usersubname)? $ECHOTXT"
+ $ECHO "User subroutine name ($user)? $ECHOTXT"
read value
if test "$value"
then
@@ -1696,50 +1686,19 @@
user=
;;
*)
- user=`dirname $value`/`$BASENAME $value .f`
- usersubname=$user
- basefile=`$BASENAME $value`
- if test ${basefile##*.} = f
- then
- user=`dirname $value`/`$BASENAME $value .f`
- usersubname=$user.f
- elif test ${basefile##*.} = F
- then
- user=`dirname $value`/`$BASENAME $value .F`
- usersubname=$user.F
- elif test ${basefile##*.} = f90
- then
- user=`dirname $value`/`$BASENAME $value .f90`
- usersubname=$user.f90
- elif test ${basefile##*.} = F90
- then
- user=`dirname $value`/`$BASENAME $value .F90`
- usersubname=$user.F90
- fi
+ user=$value
case $user in
\/*)
;;
*)
user=`pwd`/$user
- usersubname=`pwd`/$usersubname
;;
esac
- if test ! -f $usersubname
- then
- if test -f $usersubname.f
- then
- usersubname=$usersubname.f
- elif test -f $usersubname.F
- then
- usersubname=$usersubname.F
- elif test -f $usersubname.f90
- then
- usersubname=$usersubname.f90
- elif test -f $usersubname.F90
- then
- usersubname=$usersubname.F90
- fi
- fi
+ usernoext=$user
+ usernoext=`dirname $usernoext`/`$BASENAME $usernoext .f`
+ usernoext=`dirname $usernoext`/`$BASENAME $usernoext .F`
+ usernoext=`dirname $usernoext`/`$BASENAME $usernoext .for`
+ usernoext=`dirname $usernoext`/`$BASENAME $usernoext .f90`
;;
esac
fi
@@ -2274,11 +2233,12 @@
#
# user subroutine used
#
+# add DAMASK options for linking
+ DAMASK="-lstdc++"
if test "$user"
then
-# program=$user.marc
- program=$DIRJOB/`$BASENAME $user .f`.marc
+ program=$usernoext.marc
case $program in
\/* | \.\/*)
bd=
@@ -2391,7 +2351,7 @@
fi
if test "$user"
then
- execpath=$DIRJOB/`$BASENAME $user .f`.marc
+ execpath=$usernoext.marc
usersub=1
fi
export execpath
@@ -3274,44 +3234,27 @@
echo
if test "$user"
then
- userobj=$DIRJOB/`$BASENAME $user .f`.o
- basefile=`$BASENAME $usersubname`
- if test ${basefile##*.} = f
- then
- usersub=$DIRJOB/`$BASENAME $user .f`.F
- ln -sf "$user.f" "$usersub"
- else
- usersub=$usersubname
- fi
-
+ userobj=$usernoext.o
fi
cat > $jid.runmarcscript << END4
if test "$user"
then
- if test ${basefile##*.} = f
- then
- ln -sf "$user.f" "$usersub"
- fi
if test $MACHINENAME = "CRAY"
then
- $FORTRAN $usersub || \
+ $DFORTLOWMP $user || \
{
- echo "$0: compile failed for $user.f"
+ echo "$0: compile failed for $user"
exit 1
}
/bin/rm $program 2>/dev/null
else
- $FORTRAN $usersub -o $userobj || \
+ $DFORTLOWMP $user -o $userobj || \
{
- echo "$0: compile failed for $user.f"
+ echo "$0: compile failed for $user"
exit 1
}
/bin/rm $program 2>/dev/null
fi
- if test ${basefile##*.} = f
- then
- /bin/rm -f "$usersub"
- fi
fi
@@ -3332,6 +3275,7 @@
$TKLIBS \
$MRCLIBS \
$METISLIBS \
+ $DAMASK \
$SFLIB \
$OPENSSL_LIB \
$SYSLIBS \
@@ -3345,6 +3289,9 @@
prgsav=yes
fi
/bin/rm $userobj 2>/dev/null
+/bin/rm $DIRJOB/*.mod 2>/dev/null
+/bin/rm $DIRJOB/*.smod 2>/dev/null
+/bin/rm $DIRJOB/*_genmod.f90 2>/dev/null
#
# run marc
@@ -3391,7 +3338,7 @@
fi
else
if test $cpdll = yes; then
- filename=`basename $usersubname .f`
+ filename=$usernoext
/bin/cp $DIRJOB/$marcdll $DIRJOB/${filename}_$marcdll 2>/dev/null
fi
if test $rmdll = yes
@@ -3557,7 +3504,7 @@
# first copy over the user sub if local directories
if test ${dirstatus[$counter]} = "local"
then
- $RCP $user.f $i:$DIR1/
+ $RCP $user $i:$DIR1/
fi
# do the compilation on the other machine
if test ${dirstatus[$counter]} = "shared"
@@ -3570,21 +3517,21 @@
remoteuser=$DIR1/`$BASENAME $user`
$RSH $i /bin/rm $remoteprog 2> /dev/null
echo
- $RSH $i $DIR2/tools/comp_user $DIR2 $DIR1 $remoteuser $remoteprog
+ $RSH $i $DIR2/tools/comp_damask_lmp $DIR2 $DIR1 $remoteuser $remoteprog
# check if successful, the new executable should be there
line=`$RSH $i /bin/ls $remoteprog 2> /dev/null`
if test "$line"
then
echo compilation and linking successful on host $i
else
- echo "$0: compile failed for $user.f on host $i"
+ echo "$0: compile failed for $user on host $i"
echo " $PRODUCT Exit number 3"
exit 1
fi
# remove the user subroutine on remote machine
if test ${dirstatus[$counter]} = "local"
then
- $RSH $i /bin/rm $remoteuser.f 2> /dev/null
+ $RSH $i /bin/rm $remoteuser 2> /dev/null
fi
fi
fi
@@ -3594,39 +3541,27 @@
if test "$userhost"
then
echo
- echo "Compiling and linking user subroutine $user.f on host `hostname`"
- fi
- userobj=$DIRJOB/`$BASENAME $user .f`.o
- basefile=`$BASENAME $usersubname`
- if test ${basefile##*.} = f
- then
- usersub=$DIRJOB/`$BASENAME $user .f`.F
- ln -sf "$user.f" "$usersub"
- else
- usersub=$usersubname
+ echo "Compiling and linking user subroutine $user on host `hostname`"
fi
+ userobj=$usernoext.o
if test $MACHINENAME = "CRAY"
then
- $FORTRAN $usersub || \
+ $DFORTLOWMP $user || \
{
- echo "$0: compile failed for $user.f"
+ echo "$0: compile failed for $user"
echo " $PRODUCT Exit number 3"
exit 1
}
/bin/rm $program 2>/dev/null
else
- $FORTRAN $usersub -o $userobj || \
+ $DFORTLOWMP $user -o $userobj || \
{
- echo "$0: compile failed for $user.f"
+ echo "$0: compile failed for $user"
echo " $PRODUCT Exit number 3"
exit 1
}
/bin/rm $program 2>/dev/null
fi
- if test ${basefile##*.} = f
- then
- /bin/rm -f "$usersub"
- fi
fi # if test $user
@@ -3647,6 +3582,7 @@
$TKLIBS \
$MRCLIBS \
$METISLIBS \
+ $DAMASK \
$SFLIB \
$OPENSSL_LIB \
$SYSLIBS \
@@ -3688,6 +3624,9 @@
prgsav=yes
fi # if test $link
/bin/rm $userobj 2>/dev/null
+/bin/rm $DIRJOB/*.mod 2>/dev/null
+/bin/rm $DIRJOB/*.smod 2>/dev/null
+/bin/rm $DIRJOB/*_genmod.f90 2>/dev/null
#
# run marc
@@ -3781,7 +3720,7 @@
else
#dllrun >0
if test $cpdll = yes; then
- filename=`basename $usersubname .f`
+ filename=$usernoext
/bin/cp $DIRJOB/$marcdll $DIRJOB/${filename}_$marcdll 2>/dev/null
fi
if test $rmdll = yes;then
@@ -3906,7 +3845,7 @@
# first copy over the user sub if local directories
if test ${dirstatus[$counter]} = "local"
then
- $RCP $user.f $i:$DIR1/
+ $RCP $user $i:$DIR1/
fi
# do the compilation on the other machine
if test ${dirstatus[$counter]} = "shared"
@@ -3919,20 +3858,20 @@
remoteuser=$DIR1/`$BASENAME $user`
$RSH $i /bin/rm $remoteprog 2> /dev/null
echo
- $RSH $i $DIR2/tools/comp_user $DIR2 $DIR1 $remoteuser $remoteprog
+ $RSH $i $DIR2/tools/comp_damask_lmp $DIR2 $DIR1 $remoteuser $remoteprog
# check if successful, the new executable should be there
line=`$RSH $i /bin/ls $remoteprog 2> /dev/null`
if test "$line"
then
echo compilation and linking successful on host $i
else
- echo "$0: compile failed for $user.f on host $i"
+ echo "$0: compile failed for $user on host $i"
exit 1
fi
# remove the user subroutine on remote machine
if test ${dirstatus[$counter]} = "local"
then
- $RSH $i /bin/rm $remoteuser.f 2> /dev/null
+ $RSH $i /bin/rm $remoteuser 2> /dev/null
fi
fi
fi
@@ -3942,37 +3881,25 @@
if test "$userhost"
then
echo
- echo "Compiling and linking user subroutine $user.f on host `hostname`"
- fi
- userobj=$DIRJOB/`$BASENAME $user .f`.o
- basefile=`$BASENAME $usersubname`
- if test ${basefile##*.} = f
- then
- usersub=$DIRJOB/`$BASENAME $user .f`.F
- ln -sf "$user.f" "$usersub"
- else
- usersub=$usersubname
+ echo "Compiling and linking user subroutine $user on host `hostname`"
fi
+ userobj=$usernoext.o
if test $MACHINENAME = "CRAY"
then
- $FORTRAN $usersub || \
+ $DFORTLOWMP $user || \
{
- echo "$0: compile failed for $user.f"
+ echo "$0: compile failed for $user"
exit 1
}
/bin/rm $program 2>/dev/null
else
- $FORTRAN $usersub -o $userobj || \
+ $DFORTLOWMP $user -o $userobj || \
{
- echo "$0: compile failed for $user.f"
+ echo "$0: compile failed for $user"
exit 1
}
/bin/rm $program 2>/dev/null
fi
- if test ${basefile##*.} = f
- then
- /bin/rm -f "$usersub"
- fi
fi # if test $user
@@ -3993,6 +3920,7 @@
$TKLIBS \
$MRCLIBS \
$METISLIBS \
+ $DAMASK \
$SFLIB \
$OPENSSL_LIB \
$SYSLIBS \
@@ -4033,7 +3961,9 @@
prgsav=yes
fi # if test $link
/bin/rm $userobj 2>/dev/null
-
+/bin/rm $DIRJOB/*.mod 2>/dev/null
+/bin/rm $DIRJOB/*.smod 2>/dev/null
+/bin/rm $DIRJOB/*_genmod.f90 2>/dev/null
# done if no job id given
if test -z "$jid"
then
@@ -4152,7 +4082,7 @@
else
#dllrun >0
if test $cpdll = yes; then
- filename=`basename $usersubname .f`
+ filename=$usernoext
/bin/cp $DIRJOB/$marcdll $DIRJOB/${filename}_$marcdll 2>/dev/null
fi
if test $rmdll = yes;then

View File

@ -0,0 +1,517 @@
---
+++
@@ -136,6 +136,11 @@
# is created. For job running in the background, the log #
# file is always created. Default is "yes" #
##############################################################################
+# remove all Mentat paths from LD_LIBRARY_PATH
+LD_LIBRARY_PATH=:$LD_LIBRARY_PATH:
+LD_LIBRARY_PATH=${LD_LIBRARY_PATH//+([!(:)])mentat2023.2+([!(:)])/:}
+LD_LIBRARY_PATH=${LD_LIBRARY_PATH//+([(:)])/:}
+LD_LIBRARY_PATH=${LD_LIBRARY_PATH#:}; LD_LIBRARY_PATH=${LD_LIBRARY_PATH%:}
# set DIR to the directory in which this script is
REALCOM="`/bin/ls -l $0 |awk '{ print $NF; }'`"
DIR=`dirname $REALCOM`
@@ -302,7 +307,23 @@
. "$DIR/getarch"
+
+# getting user subroutine file name
+found=0
+for i in "$@"; do
+ if test $found = 1; then
+ DAMASK_USER=$i
+ found=0
+ fi
+ case $i in
+ -u* | -U*)
+ found=1
+ ;;
+ esac
+done
+# sourcing include_linux64 (needs DAMASK_USER to be set)
. $MARC_INCLUDE
+
#
#
@@ -405,7 +426,7 @@
did=
vid=
user=
-usersubname=
+usernoext=
objs=
qid=background
cpu=
@@ -676,50 +697,19 @@
esac
;;
-u* | -U*)
- user=`dirname $value`/`$BASENAME $value .f`
- usersubname=$user
- basefile=`$BASENAME $value`
- if test ${basefile##*.} = f
- then
- user=`dirname $value`/`$BASENAME $value .f`
- usersubname=$user.f
- elif test ${basefile##*.} = F
- then
- user=`dirname $value`/`$BASENAME $value .F`
- usersubname=$user.F
- elif test ${basefile##*.} = f90
- then
- user=`dirname $value`/`$BASENAME $value .f90`
- usersubname=$user.f90
- elif test ${basefile##*.} = F90
- then
- user=`dirname $value`/`$BASENAME $value .F90`
- usersubname=$user.F90
- fi
+ user=$value
case $user in
\/*)
;;
*)
user=`pwd`/$user
- usersubname=`pwd`/$usersubname
;;
esac
- if test ! -f $usersubname
- then
- if test -f $usersubname.f
- then
- usersubname=$usersubname.f
- elif test -f $usersubname.F
- then
- usersubname=$usersubname.F
- elif test -f $usersubname.f90
- then
- usersubname=$usersubname.f90
- elif test -f $usersubname.F90
- then
- usersubname=$usersubname.F90
- fi
- fi
+ usernoext=$user
+ usernoext=`dirname $usernoext`/`$BASENAME $usernoext .f`
+ usernoext=`dirname $usernoext`/`$BASENAME $usernoext .F`
+ usernoext=`dirname $usernoext`/`$BASENAME $usernoext .for`
+ usernoext=`dirname $usernoext`/`$BASENAME $usernoext .f90`
;;
-obj | -OBJ)
objs="$value"
@@ -1207,12 +1197,12 @@
fi
fi
fi
- if test "$usersubname"
+ if test "$user"
then
- if test ! -f $usersubname
+ if test ! -f $user
then
error="$error
-user subroutine file $usersubname not accessible"
+user subroutine file $user not accessible"
fi
fi
if test "$objs"
@@ -1531,7 +1521,7 @@
Marc shared lib : $progdll
Version type : $mode
Job ID : $DIRJID/$jid$extra_job_info
-User subroutine name : $usersubname
+User subroutine name : $user
User objects/libs : $objs
Restart file job ID : $rid
Substructure file ID : $sid
@@ -1564,7 +1554,7 @@
Marc shared lib : $progdll
Version type : $mode
Job ID : $DIRJID/$jid$extra_job_info
-User subroutine name : $usersubname
+User subroutine name : $user
User objects/libs : $objs
Restart file job ID : $rid
Substructure file ID : $sid
@@ -1687,7 +1677,7 @@
;;
esac
fi
- $ECHO "User subroutine name ($usersubname)? $ECHOTXT"
+ $ECHO "User subroutine name ($user)? $ECHOTXT"
read value
if test "$value"
then
@@ -1696,50 +1686,19 @@
user=
;;
*)
- user=`dirname $value`/`$BASENAME $value .f`
- usersubname=$user
- basefile=`$BASENAME $value`
- if test ${basefile##*.} = f
- then
- user=`dirname $value`/`$BASENAME $value .f`
- usersubname=$user.f
- elif test ${basefile##*.} = F
- then
- user=`dirname $value`/`$BASENAME $value .F`
- usersubname=$user.F
- elif test ${basefile##*.} = f90
- then
- user=`dirname $value`/`$BASENAME $value .f90`
- usersubname=$user.f90
- elif test ${basefile##*.} = F90
- then
- user=`dirname $value`/`$BASENAME $value .F90`
- usersubname=$user.F90
- fi
+ user=$value
case $user in
\/*)
;;
*)
user=`pwd`/$user
- usersubname=`pwd`/$usersubname
;;
esac
- if test ! -f $usersubname
- then
- if test -f $usersubname.f
- then
- usersubname=$usersubname.f
- elif test -f $usersubname.F
- then
- usersubname=$usersubname.F
- elif test -f $usersubname.f90
- then
- usersubname=$usersubname.f90
- elif test -f $usersubname.F90
- then
- usersubname=$usersubname.F90
- fi
- fi
+ usernoext=$user
+ usernoext=`dirname $usernoext`/`$BASENAME $usernoext .f`
+ usernoext=`dirname $usernoext`/`$BASENAME $usernoext .F`
+ usernoext=`dirname $usernoext`/`$BASENAME $usernoext .for`
+ usernoext=`dirname $usernoext`/`$BASENAME $usernoext .f90`
;;
esac
fi
@@ -2274,11 +2233,12 @@
#
# user subroutine used
#
+# add DAMASK options for linking
+ DAMASK="-lstdc++"
if test "$user"
then
-# program=$user.marc
- program=$DIRJOB/`$BASENAME $user .f`.marc
+ program=$usernoext.marc
case $program in
\/* | \.\/*)
bd=
@@ -2391,7 +2351,7 @@
fi
if test "$user"
then
- execpath=$DIRJOB/`$BASENAME $user .f`.marc
+ execpath=$usernoext.marc
usersub=1
fi
export execpath
@@ -3274,44 +3234,27 @@
echo
if test "$user"
then
- userobj=$DIRJOB/`$BASENAME $user .f`.o
- basefile=`$BASENAME $usersubname`
- if test ${basefile##*.} = f
- then
- usersub=$DIRJOB/`$BASENAME $user .f`.F
- ln -sf "$user.f" "$usersub"
- else
- usersub=$usersubname
- fi
-
+ userobj=$usernoext.o
fi
cat > $jid.runmarcscript << END4
if test "$user"
then
- if test ${basefile##*.} = f
- then
- ln -sf "$user.f" "$usersub"
- fi
if test $MACHINENAME = "CRAY"
then
- $FORTRAN $usersub || \
+ $DFORTRANMP $user || \
{
- echo "$0: compile failed for $user.f"
+ echo "$0: compile failed for $user"
exit 1
}
/bin/rm $program 2>/dev/null
else
- $FORTRAN $usersub -o $userobj || \
+ $DFORTRANMP $user -o $userobj || \
{
- echo "$0: compile failed for $user.f"
+ echo "$0: compile failed for $user"
exit 1
}
/bin/rm $program 2>/dev/null
fi
- if test ${basefile##*.} = f
- then
- /bin/rm -f "$usersub"
- fi
fi
@@ -3332,6 +3275,7 @@
$TKLIBS \
$MRCLIBS \
$METISLIBS \
+ $DAMASK \
$SFLIB \
$OPENSSL_LIB \
$SYSLIBS \
@@ -3345,6 +3289,9 @@
prgsav=yes
fi
/bin/rm $userobj 2>/dev/null
+/bin/rm $DIRJOB/*.mod 2>/dev/null
+/bin/rm $DIRJOB/*.smod 2>/dev/null
+/bin/rm $DIRJOB/*_genmod.f90 2>/dev/null
#
# run marc
@@ -3391,7 +3338,7 @@
fi
else
if test $cpdll = yes; then
- filename=`basename $usersubname .f`
+ filename=$usernoext
/bin/cp $DIRJOB/$marcdll $DIRJOB/${filename}_$marcdll 2>/dev/null
fi
if test $rmdll = yes
@@ -3557,7 +3504,7 @@
# first copy over the user sub if local directories
if test ${dirstatus[$counter]} = "local"
then
- $RCP $user.f $i:$DIR1/
+ $RCP $user $i:$DIR1/
fi
# do the compilation on the other machine
if test ${dirstatus[$counter]} = "shared"
@@ -3570,21 +3517,21 @@
remoteuser=$DIR1/`$BASENAME $user`
$RSH $i /bin/rm $remoteprog 2> /dev/null
echo
- $RSH $i $DIR2/tools/comp_user $DIR2 $DIR1 $remoteuser $remoteprog
+ $RSH $i $DIR2/tools/comp_damask_mp $DIR2 $DIR1 $remoteuser $remoteprog
# check if successful, the new executable should be there
line=`$RSH $i /bin/ls $remoteprog 2> /dev/null`
if test "$line"
then
echo compilation and linking successful on host $i
else
- echo "$0: compile failed for $user.f on host $i"
+ echo "$0: compile failed for $user on host $i"
echo " $PRODUCT Exit number 3"
exit 1
fi
# remove the user subroutine on remote machine
if test ${dirstatus[$counter]} = "local"
then
- $RSH $i /bin/rm $remoteuser.f 2> /dev/null
+ $RSH $i /bin/rm $remoteuser 2> /dev/null
fi
fi
fi
@@ -3594,39 +3541,27 @@
if test "$userhost"
then
echo
- echo "Compiling and linking user subroutine $user.f on host `hostname`"
- fi
- userobj=$DIRJOB/`$BASENAME $user .f`.o
- basefile=`$BASENAME $usersubname`
- if test ${basefile##*.} = f
- then
- usersub=$DIRJOB/`$BASENAME $user .f`.F
- ln -sf "$user.f" "$usersub"
- else
- usersub=$usersubname
+ echo "Compiling and linking user subroutine $user on host `hostname`"
fi
+ userobj=$usernoext.o
if test $MACHINENAME = "CRAY"
then
- $FORTRAN $usersub || \
+ $DFORTRANMP $user || \
{
- echo "$0: compile failed for $user.f"
+ echo "$0: compile failed for $user"
echo " $PRODUCT Exit number 3"
exit 1
}
/bin/rm $program 2>/dev/null
else
- $FORTRAN $usersub -o $userobj || \
+ $DFORTRANMP $user -o $userobj || \
{
- echo "$0: compile failed for $user.f"
+ echo "$0: compile failed for $user"
echo " $PRODUCT Exit number 3"
exit 1
}
/bin/rm $program 2>/dev/null
fi
- if test ${basefile##*.} = f
- then
- /bin/rm -f "$usersub"
- fi
fi # if test $user
@@ -3647,6 +3582,7 @@
$TKLIBS \
$MRCLIBS \
$METISLIBS \
+ $DAMASK \
$SFLIB \
$OPENSSL_LIB \
$SYSLIBS \
@@ -3688,6 +3624,9 @@
prgsav=yes
fi # if test $link
/bin/rm $userobj 2>/dev/null
+/bin/rm $DIRJOB/*.mod 2>/dev/null
+/bin/rm $DIRJOB/*.smod 2>/dev/null
+/bin/rm $DIRJOB/*_genmod.f90 2>/dev/null
#
# run marc
@@ -3781,7 +3720,7 @@
else
#dllrun >0
if test $cpdll = yes; then
- filename=`basename $usersubname .f`
+ filename=$usernoext
/bin/cp $DIRJOB/$marcdll $DIRJOB/${filename}_$marcdll 2>/dev/null
fi
if test $rmdll = yes;then
@@ -3906,7 +3845,7 @@
# first copy over the user sub if local directories
if test ${dirstatus[$counter]} = "local"
then
- $RCP $user.f $i:$DIR1/
+ $RCP $user $i:$DIR1/
fi
# do the compilation on the other machine
if test ${dirstatus[$counter]} = "shared"
@@ -3919,20 +3858,20 @@
remoteuser=$DIR1/`$BASENAME $user`
$RSH $i /bin/rm $remoteprog 2> /dev/null
echo
- $RSH $i $DIR2/tools/comp_user $DIR2 $DIR1 $remoteuser $remoteprog
+ $RSH $i $DIR2/tools/comp_damask_mp $DIR2 $DIR1 $remoteuser $remoteprog
# check if successful, the new executable should be there
line=`$RSH $i /bin/ls $remoteprog 2> /dev/null`
if test "$line"
then
echo compilation and linking successful on host $i
else
- echo "$0: compile failed for $user.f on host $i"
+ echo "$0: compile failed for $user on host $i"
exit 1
fi
# remove the user subroutine on remote machine
if test ${dirstatus[$counter]} = "local"
then
- $RSH $i /bin/rm $remoteuser.f 2> /dev/null
+ $RSH $i /bin/rm $remoteuser 2> /dev/null
fi
fi
fi
@@ -3942,37 +3881,25 @@
if test "$userhost"
then
echo
- echo "Compiling and linking user subroutine $user.f on host `hostname`"
- fi
- userobj=$DIRJOB/`$BASENAME $user .f`.o
- basefile=`$BASENAME $usersubname`
- if test ${basefile##*.} = f
- then
- usersub=$DIRJOB/`$BASENAME $user .f`.F
- ln -sf "$user.f" "$usersub"
- else
- usersub=$usersubname
+ echo "Compiling and linking user subroutine $user on host `hostname`"
fi
+ userobj=$usernoext.o
if test $MACHINENAME = "CRAY"
then
- $FORTRAN $usersub || \
+ $DFORTRANMP $user || \
{
- echo "$0: compile failed for $user.f"
+ echo "$0: compile failed for $user"
exit 1
}
/bin/rm $program 2>/dev/null
else
- $FORTRAN $usersub -o $userobj || \
+ $DFORTRANMP $user -o $userobj || \
{
- echo "$0: compile failed for $user.f"
+ echo "$0: compile failed for $user"
exit 1
}
/bin/rm $program 2>/dev/null
fi
- if test ${basefile##*.} = f
- then
- /bin/rm -f "$usersub"
- fi
fi # if test $user
@@ -3993,6 +3920,7 @@
$TKLIBS \
$MRCLIBS \
$METISLIBS \
+ $DAMASK \
$SFLIB \
$OPENSSL_LIB \
$SYSLIBS \
@@ -4033,7 +3961,9 @@
prgsav=yes
fi # if test $link
/bin/rm $userobj 2>/dev/null
-
+/bin/rm $DIRJOB/*.mod 2>/dev/null
+/bin/rm $DIRJOB/*.smod 2>/dev/null
+/bin/rm $DIRJOB/*_genmod.f90 2>/dev/null
# done if no job id given
if test -z "$jid"
then
@@ -4152,7 +4082,7 @@
else
#dllrun >0
if test $cpdll = yes; then
- filename=`basename $usersubname .f`
+ filename=$usernoext
/bin/cp $DIRJOB/$marcdll $DIRJOB/${filename}_$marcdll 2>/dev/null
fi
if test $rmdll = yes;then

View File

@ -0,0 +1,24 @@
---
+++
@@ -1,18 +1,5 @@
#!/bin/sh
-# This script opens a window running an editor. The default window is an
-# xterm, and the default editor is vi. These may be customized.
+# This script opens a window running an editor.
+# The command to invoke the editor is specified during DAMASK installation
-dir=
-for d in /usr/bin /usr/bin/X11; do
- if test -x "$d/xterm"; then
- dir="$d"
- break
- fi
-done
-
-if test -z "$dir"; then
- echo "$0: Could not find xterm"
- exit 1
-fi
-
-"$dir/xterm" -T "vi $*" -n "vi $*" -e vi $*
+%EDITOR% $*

View File

View File

View File

View File

@ -0,0 +1,38 @@
---
+++
@@ -63,10 +63,10 @@
if [ "$slv" != "" -a "$slv" != "marc" -a "$slv" != "datfit" ]; then
slv="-iam sfm"
fi
-if [ "$slv" == "marc" ]; then
+if [ "$slv" = "marc" ]; then
slv=""
fi
-if [ "$slv" == "datfit" ]; then
+if [ "$slv" = "datfit" ]; then
slv="-iam datfit"
fi
@@ -91,6 +91,7 @@
srcfile="-u $srcfile -save y"
;;
runsaved)
+ srcfile=${srcfile%.*}".marc"
srcfile="-prog $srcfile"
;;
esac
@@ -189,12 +190,12 @@
unset PYTHONPATH
if [ "$doe_first" = "-" ]; then # submit of regular Marc job
- "${DIR}/tools/run_marc" $slv -j $job -v n -b y $nprocds $nprocd \
+ "${DIR}/tools/run_damask_hmp" $slv -j $job -v n -b y $nprocds $nprocd \
$srcfile $restart $postfile $viewfactorsfile $hostfile \
$compat $copy_datfile $copy_postfile $scr_dir $dcoup \
$assem_recov_nthread $nthread $nsolver $mode $gpu > /dev/null 2>&1
else # submit of a DoE Marc job
- "${DIR}/tools/run_marc" $slv -j $job -v n -b n $nprocds $nprocd \
+ "${DIR}/tools/run_damask_hmp" $slv -j $job -v n -b n $nprocds $nprocd \
$srcfile $restart $postfile $viewfactorsfile $hostfile \
$compat $copy_datfile $copy_postfile $scr_dir $dcoup \
$assem_recov_nthread $nthread $nsolver $mode $gpu

View File

@ -0,0 +1,38 @@
---
+++
@@ -63,10 +63,10 @@
if [ "$slv" != "" -a "$slv" != "marc" -a "$slv" != "datfit" ]; then
slv="-iam sfm"
fi
-if [ "$slv" == "marc" ]; then
+if [ "$slv" = "marc" ]; then
slv=""
fi
-if [ "$slv" == "datfit" ]; then
+if [ "$slv" = "datfit" ]; then
slv="-iam datfit"
fi
@@ -91,6 +91,7 @@
srcfile="-u $srcfile -save y"
;;
runsaved)
+ srcfile=${srcfile%.*}".marc"
srcfile="-prog $srcfile"
;;
esac
@@ -189,12 +190,12 @@
unset PYTHONPATH
if [ "$doe_first" = "-" ]; then # submit of regular Marc job
- "${DIR}/tools/run_marc" $slv -j $job -v n -b y $nprocds $nprocd \
+ "${DIR}/tools/run_damask_mp" $slv -j $job -v n -b y $nprocds $nprocd \
$srcfile $restart $postfile $viewfactorsfile $hostfile \
$compat $copy_datfile $copy_postfile $scr_dir $dcoup \
$assem_recov_nthread $nthread $nsolver $mode $gpu > /dev/null 2>&1
else # submit of a DoE Marc job
- "${DIR}/tools/run_marc" $slv -j $job -v n -b n $nprocds $nprocd \
+ "${DIR}/tools/run_damask_mp" $slv -j $job -v n -b n $nprocds $nprocd \
$srcfile $restart $postfile $viewfactorsfile $hostfile \
$compat $copy_datfile $copy_postfile $scr_dir $dcoup \
$assem_recov_nthread $nthread $nsolver $mode $gpu

View File

@ -0,0 +1,38 @@
---
+++
@@ -63,10 +63,10 @@
if [ "$slv" != "" -a "$slv" != "marc" -a "$slv" != "datfit" ]; then
slv="-iam sfm"
fi
-if [ "$slv" == "marc" ]; then
+if [ "$slv" = "marc" ]; then
slv=""
fi
-if [ "$slv" == "datfit" ]; then
+if [ "$slv" = "datfit" ]; then
slv="-iam datfit"
fi
@@ -91,6 +91,7 @@
srcfile="-u $srcfile -save y"
;;
runsaved)
+ srcfile=${srcfile%.*}".marc"
srcfile="-prog $srcfile"
;;
esac
@@ -189,12 +190,12 @@
unset PYTHONPATH
if [ "$doe_first" = "-" ]; then # submit of regular Marc job
- "${DIR}/tools/run_marc" $slv -j $job -v n -b y $nprocds $nprocd \
+ "${DIR}/tools/run_damask_lmp" $slv -j $job -v n -b y $nprocds $nprocd \
$srcfile $restart $postfile $viewfactorsfile $hostfile \
$compat $copy_datfile $copy_postfile $scr_dir $dcoup \
$assem_recov_nthread $nthread $nsolver $mode $gpu > /dev/null 2>&1
else # submit of a DoE Marc job
- "${DIR}/tools/run_marc" $slv -j $job -v n -b n $nprocds $nprocd \
+ "${DIR}/tools/run_damask_lmp" $slv -j $job -v n -b n $nprocds $nprocd \
$srcfile $restart $postfile $viewfactorsfile $hostfile \
$compat $copy_datfile $copy_postfile $scr_dir $dcoup \
$assem_recov_nthread $nthread $nsolver $mode $gpu

View File

@ -0,0 +1,158 @@
---
+++
@@ -362,11 +362,18 @@
}
button {
position +25 =
- size 25 4
+ size 18 4
text "ADVANCED JOB SUBMISSION"
help "job_run#Job Submission And Control"
popmenu job_submit_adv_pm
}
+ button {
+ position +18 =
+ size 7 4
+ text "DAMASK"
+ help "damask_run#Job Submission And Control"
+ popmenu damask
+ }
button {
position 0 +4
size 16 4
@@ -1307,6 +1314,135 @@
}
+#--------------------------------------------------------------------------------------------------
+popmenu damask {
+
+#ifdef QT_MENTAT
+ text "DAMASK.MPIE.DE"
+#endif
+
+ group {
+#ifndef QT_MENTAT
+ label {
+ position 0 0
+ size 50 4
+ text "DAMASK.MPIE.DE"
+ }
+#endif
+
+ label {
+ position 1 6
+ size 13 6
+ text "Optimzation"
+ border_width 1
+ border_color black
+ }
+
+ label {
+ position +13 =
+ size 20 6
+ text "write Input"
+ border_width 1
+ border_color black
+ }
+
+ label {
+ position +18 =
+ size 30 6
+ text "do not write Inp."
+ border_width 1
+ border_color black
+ }
+
+ label {
+ position -32 +6
+ size 12 6
+ text "O3 / OpenMP"
+ border_width 1
+ border_color black
+ }
+
+ popdown {
+ position +12 =
+ size 20 6
+ text "Submit"
+ command "*submit_job 4 *monitor_job"
+ }
+
+ popdown {
+ position +20 =
+ size 20 6
+ text "Execute"
+ command "*execute_job 4 *monitor_job"
+ }
+
+ label {
+ position -32 +6
+ size 12 6
+ text "O1 / OpenMP"
+ border_width 1
+ border_color black
+ }
+
+ popdown {
+ position +12 =
+ size 20 6
+ text "Submit"
+ command "*submit_job 5 *monitor_job"
+ }
+
+ popdown {
+ position +20 =
+ size 20 6
+ text "Execute"
+ command "*execute_job 5 *monitor_job"
+ }
+
+ label {
+ position -32 +6
+ size 12 6
+ text "O0 / OpenMP"
+ border_width 1
+ border_color black
+ }
+
+ popdown {
+ position +12 =
+ size 20 6
+ text "Submit"
+ command "*submit_job 6 *monitor_job"
+ }
+
+ popdown {
+ position +20 =
+ size 20 6
+ text "Execute"
+ command "*execute_job 6 *monitor_job"
+ }
+
+ popdown {
+ position 19 +8
+ size 12 8
+ text "CANCEL"
+ }
+}
+
+ window {
+ parent mentat
+ origin 38 8
+#ifdef DCOM
+ size 50 100
+#else
+ size 50 94
+#endif
+ background_color body
+ border_width 1
+ border_color border
+ buffering single
+ }
+ mode permanent
+}
+
#--------------------------------------------------------------------------------------------------
popmenu job_exit_msg_pm {

View File

@ -0,0 +1,49 @@
---
+++
@@ -6,18 +6,27 @@
DIR=$1
user=$3
program=$4
+usernoext=$user
+usernoext=`dirname $usernoext`/`$BASENAME $usernoext .f`
+usernoext=`dirname $usernoext`/`$BASENAME $usernoext .F`
+usernoext=`dirname $usernoext`/`$BASENAME $usernoext .for`
+usernoext=`dirname $usernoext`/`$BASENAME $usernoext .f90`
+
+# add BLAS options for linking
+ BLAS="%BLAS%"
+
. $DIR/tools/include
DIRJOB=$2
cd $DIRJOB
-echo "Compiling and linking user subroutine $user.f on host `hostname`"
+echo "Compiling and linking user subroutine $user on host `hostname`"
echo "program: $program"
- $FORTRAN $user.f || \
+ $DFORTHIGHMP $user || \
{
- echo "$0: compile failed for $user.f"
+ echo "$0: compile failed for $user"
exit 1
}
/bin/rm $program 2>/dev/null
- userobj=$user.o
+ userobj=$usernoext.o
$LOAD ${program} $DIR/lib/main.o\
@@ -33,9 +42,13 @@
$TKLIBS \
$MRCLIBS \
$METISLIBS \
+ $BLAS \
$SYSLIBS || \
{
- echo "$0: link failed for $user.o on host `hostname`"
+ echo "$0: link failed for $usernoext.o on host `hostname`"
exit 1
}
/bin/rm $userobj
+ /bin/rm $DIRJOB/*.mod
+ /bin/rm $DIRJOB/*.smod
+ /bin/rm $DIRJOB/*_genmod.f90

View File

@ -0,0 +1,49 @@
---
+++
@@ -6,18 +6,27 @@
DIR=$1
user=$3
program=$4
+usernoext=$user
+usernoext=`dirname $usernoext`/`$BASENAME $usernoext .f`
+usernoext=`dirname $usernoext`/`$BASENAME $usernoext .F`
+usernoext=`dirname $usernoext`/`$BASENAME $usernoext .for`
+usernoext=`dirname $usernoext`/`$BASENAME $usernoext .f90`
+
+# add BLAS options for linking
+ BLAS="%BLAS%"
+
. $DIR/tools/include
DIRJOB=$2
cd $DIRJOB
-echo "Compiling and linking user subroutine $user.f on host `hostname`"
+echo "Compiling and linking user subroutine $user on host `hostname`"
echo "program: $program"
- $FORTRAN $user.f || \
+ $DFORTRANLOWMP $user || \
{
- echo "$0: compile failed for $user.f"
+ echo "$0: compile failed for $user"
exit 1
}
/bin/rm $program 2>/dev/null
- userobj=$user.o
+ userobj=$usernoext.o
$LOAD ${program} $DIR/lib/main.o\
@@ -33,9 +42,13 @@
$TKLIBS \
$MRCLIBS \
$METISLIBS \
+ $BLAS \
$SYSLIBS || \
{
- echo "$0: link failed for $user.o on host `hostname`"
+ echo "$0: link failed for $usernoext.o on host `hostname`"
exit 1
}
/bin/rm $userobj
+ /bin/rm $DIRJOB/*.mod
+ /bin/rm $DIRJOB/*.smod
+ /bin/rm $DIRJOB/*_genmod.f90

View File

@ -0,0 +1,49 @@
---
+++
@@ -6,18 +6,27 @@
DIR=$1
user=$3
program=$4
+usernoext=$user
+usernoext=`dirname $usernoext`/`$BASENAME $usernoext .f`
+usernoext=`dirname $usernoext`/`$BASENAME $usernoext .F`
+usernoext=`dirname $usernoext`/`$BASENAME $usernoext .for`
+usernoext=`dirname $usernoext`/`$BASENAME $usernoext .f90`
+
+# add BLAS options for linking
+ BLAS="%BLAS%"
+
. $DIR/tools/include
DIRJOB=$2
cd $DIRJOB
-echo "Compiling and linking user subroutine $user.f on host `hostname`"
+echo "Compiling and linking user subroutine $user on host `hostname`"
echo "program: $program"
- $FORTRAN $user.f || \
+ $DFORTRANMP $user || \
{
- echo "$0: compile failed for $user.f"
+ echo "$0: compile failed for $user"
exit 1
}
/bin/rm $program 2>/dev/null
- userobj=$user.o
+ userobj=$usernoext.o
$LOAD ${program} $DIR/lib/main.o\
@@ -33,9 +42,13 @@
$TKLIBS \
$MRCLIBS \
$METISLIBS \
+ $BLAS \
$SYSLIBS || \
{
- echo "$0: link failed for $user.o on host `hostname`"
+ echo "$0: link failed for $usernoext.o on host `hostname`"
exit 1
}
/bin/rm $userobj
+ /bin/rm $DIRJOB/*.mod
+ /bin/rm $DIRJOB/*.smod
+ /bin/rm $DIRJOB/*_genmod.f90

View File

@ -0,0 +1,75 @@
---
+++
@@ -172,6 +178,15 @@
MARC_COSIM_LIB="$MSCCOSIM_HOME/CoSim$MSCCOSIM_VERSION/Dcosim$MSCCOSIM_VERSION/lib"
fi
+# DAMASK uses the HDF5 compiler wrapper around the Intel compiler
+H5FC=$(h5fc -shlib -show)
+if [[ "$H5FC" == *"$dir is"* ]]; then
+ H5FC=$(echo $(echo "$H5FC" | tail -n1) | sed -e "s/\-shlib/-fPIC -qopenmp/g")
+ H5FC=${H5FC%-lmpifort*}
+fi
+HDF5_LIB=${H5FC//*ifort/}
+FCOMP="$H5FC"
+
# AEM
if test "$MARCDLLOUTDIR" = ""; then
DLLOUTDIR="$MARC_LIB"
@@ -599,7 +609,7 @@
PROFILE=" $PROFILE -pg"
fi
-FORT_OPT="-c -assume byterecl -safe-cray-ptr -mp1 -WB -fp-model source"
+FORT_OPT="-c -implicitnone -stand f18 -standard-semantics -assume nostd_mod_proc_name -safe-cray-ptr -mp1 -WB -fp-model source"
if test "$MTHREAD" = "OPENMP"
then
FORT_OPT=" $FORT_OPT -qopenmp"
@@ -612,7 +621,7 @@
FORT_OPT=" $FORT_OPT -save -zero"
fi
if test "$MARCHDF_HDF" = "HDF"; then
- FORT_OPT="$FORT_OPT -DMARCHDF_HDF=$MARCHDF_HDF $HDF_INCLUDE"
+ FORT_OPT="$FORT_OPT -DMARCHDF=$MARCHDF_HDF"
fi
FORTLOW="$FCOMP $FORT_OPT $PROFILE -O0 $I8FFLAGS -I$MARC_SOURCE/common \
@@ -626,6 +635,29 @@
# for compiling free form f90 files. high opt, integer(4)
FORTF90="$FCOMP -c -O3"
+# determine DAMASK version
+if test -n "$DAMASK_USER"; then
+ DAMASKROOT=`dirname $DAMASK_USER`/../..
+ read DAMASKVERSION < $DAMASKROOT/VERSION
+ DAMASKVERSION="'"$DAMASKVERSION"'"
+else
+ DAMASKVERSION="'N/A'"
+fi
+
+# DAMASK compiler calls
+DFORTLOWMP="$FCOMP -c -O0 -qno-offload -implicitnone -stand f18 -standard-semantics -assume nostd_mod_proc_name -safe-cray-ptr $PROFILE -zero -mp1 -WB $I8FFLAGS -I$MARC_SOURCE/common \
+ -fpp -ftz -diag-disable 5268 -warn declarations -warn general -warn usage -warn interfaces -warn ignore_loc -warn alignments -DMARC4DAMASK=2023.3 -DDAMASKVERSION=$DAMASKVERSION \
+ -qopenmp -qopenmp-threadprivate=compat\
+ $MUMPS_INCLUDE $I8DEFINES -DLinux -DLINUX -DLinux_intel $FDEFINES $DDM $SOLVERFLAGS -I$KDTREE2_MOD -I$MARC_MOD"
+DFORTRANMP="$FCOMP -c -O1 -qno-offload -implicitnone -stand f18 -standard-semantics -assume nostd_mod_proc_name -safe-cray-ptr $PROFILE -zero -mp1 -WB $I8FFLAGS -I$MARC_SOURCE/common \
+ -fpp -ftz -diag-disable 5268 -warn declarations -warn general -warn usage -warn interfaces -warn ignore_loc -warn alignments -DMARC4DAMASK=2023.3 -DDAMASKVERSION=$DAMASKVERSION \
+ -qopenmp -qopenmp-threadprivate=compat\
+ $MUMPS_INCLUDE $I8DEFINES -DLinux -DLINUX -DLinux_intel $FDEFINES $DDM $SOLVERFLAGS -I$KDTREE2_MOD -I$MARC_MOD"
+DFORTHIGHMP="$FCOMP -c -O3 -qno-offload -implicitnone -stand f18 -standard-semantics -assume nostd_mod_proc_name -safe-cray-ptr $PROFILE -zero -mp1 -WB $I8FFLAGS -I$MARC_SOURCE/common \
+ -fpp -ftz -diag-disable 5268 -warn declarations -warn general -warn usage -warn interfaces -warn ignore_loc -warn alignments -DMARC4DAMASK=2023.3 -DDAMASKVERSION=$DAMASKVERSION \
+ -qopenmp -qopenmp-threadprivate=compat\
+ $MUMPS_INCLUDE $I8DEFINES -DLinux -DLINUX -DLinux_intel $FDEFINES $DDM $SOLVERFLAGS -I$KDTREE2_MOD -I$MARC_MOD"
+
if test "$MARCDEBUG" = "ON"
then
FORTLOW="$FCOMP $FORT_OPT $PROFILE $I8FFLAGS -I$MARC_SOURCE/common \
@@ -783,7 +815,7 @@
SOLVERLIBS="${BCSSOLVERLIBS} ${VKISOLVERLIBS} ${CASISOLVERLIBS} ${MF2SOLVERLIBS} \
-L$MARC_MKL \
- $MARC_LIB/blas_src.a ${ACSI_LIB}/ACSI_MarcLib.a $KDTREE2_LIB/libkdtree2.a $MARC_LIB/libtetmeshinterface.a $MARC_LIB/libcaefatigueinterface.a -L$MARC_LIB -lmkl_blacs_intelmpi_ilp64 -lmkl_scalapack_ilp64 -lmkl_intel_ilp64 -lmkl_intel_thread -lmkl_core -liomp5 -ltetmesh -ltetadapt -lmeshgems -lmg-tetra -lmeshgems_stubs -lCATMshMesherCore -lCATMshCVMforCSM -lmg-hybrid -lmg-cadsurf -lmg-hexa $HDF_LIBS $SOLVER2LIBS $RTREE_LIB/librtree_lib.a $SFGEO_LIB/libgeo_lib.a"
+ $MARC_LIB/blas_src.a ${ACSI_LIB}/ACSI_MarcLib.a $KDTREE2_LIB/libkdtree2.a $MARC_LIB/libtetmeshinterface.a $MARC_LIB/libcaefatigueinterface.a -L$MARC_LIB -lmkl_blacs_intelmpi_ilp64 -lmkl_scalapack_ilp64 -lmkl_intel_ilp64 -lmkl_intel_thread -lmkl_core -liomp5 -ltetmesh -ltetadapt -lmeshgems -lmg-tetra -lmeshgems_stubs -lCATMshMesherCore -lCATMshCVMforCSM -lmg-hybrid -lmg-cadsurf -lmg-hexa $HDF5_LIB $SOLVER2LIBS $RTREE_LIB/librtree_lib.a $SFGEO_LIB/libgeo_lib.a"
SOLVERLIBS_DLL=${SOLVERLIBS}
if test "$AEM_DLL" -eq 1

View File

@ -0,0 +1,477 @@
---
+++
@@ -136,6 +136,11 @@
# is created. For job running in the background, the log #
# file is always created. Default is "yes" #
##############################################################################
+# remove all Mentat paths from LD_LIBRARY_PATH
+LD_LIBRARY_PATH=:$LD_LIBRARY_PATH:
+LD_LIBRARY_PATH=${LD_LIBRARY_PATH//+([!(:)])mentat2023.3+([!(:)])/:}
+LD_LIBRARY_PATH=${LD_LIBRARY_PATH//+([(:)])/:}
+LD_LIBRARY_PATH=${LD_LIBRARY_PATH#:}; LD_LIBRARY_PATH=${LD_LIBRARY_PATH%:}
# set DIR to the directory in which this script is
REALCOM="`/bin/ls -l $0 |awk '{ print $NF; }'`"
DIR=`dirname $REALCOM`
@@ -303,7 +308,23 @@
. "$DIR/getarch"
+
+# getting user subroutine file name
+found=0
+for i in "$@"; do
+ if test $found = 1; then
+ DAMASK_USER=$i
+ found=0
+ fi
+ case $i in
+ -u* | -U*)
+ found=1
+ ;;
+ esac
+done
+# sourcing include_linux64 (needs DAMASK_USER to be set)
. $MARC_INCLUDE
+
#
#
@@ -406,7 +427,7 @@
did=
vid=
user=
-usersubname=
+usernoext=
objs=
qid=background
cpu=
@@ -677,50 +698,19 @@
esac
;;
-u* | -U*)
- user=`dirname $value`/`$BASENAME $value .f`
- usersubname=$user
- basefile=`$BASENAME $value`
- if test ${basefile##*.} = f
- then
- user=`dirname $value`/`$BASENAME $value .f`
- usersubname=$user.f
- elif test ${basefile##*.} = F
- then
- user=`dirname $value`/`$BASENAME $value .F`
- usersubname=$user.F
- elif test ${basefile##*.} = f90
- then
- user=`dirname $value`/`$BASENAME $value .f90`
- usersubname=$user.f90
- elif test ${basefile##*.} = F90
- then
- user=`dirname $value`/`$BASENAME $value .F90`
- usersubname=$user.F90
- fi
+ user=$value
case $user in
\/*)
;;
*)
user=`pwd`/$user
- usersubname=`pwd`/$usersubname
;;
esac
- if test ! -f $usersubname
- then
- if test -f $usersubname.f
- then
- usersubname=$usersubname.f
- elif test -f $usersubname.F
- then
- usersubname=$usersubname.F
- elif test -f $usersubname.f90
- then
- usersubname=$usersubname.f90
- elif test -f $usersubname.F90
- then
- usersubname=$usersubname.F90
- fi
- fi
+ usernoext=$user
+ usernoext=`dirname $usernoext`/`$BASENAME $usernoext .f`
+ usernoext=`dirname $usernoext`/`$BASENAME $usernoext .F`
+ usernoext=`dirname $usernoext`/`$BASENAME $usernoext .for`
+ usernoext=`dirname $usernoext`/`$BASENAME $usernoext .f90`
;;
-obj | -OBJ)
objs="$value"
@@ -1208,12 +1198,12 @@
fi
fi
fi
- if test "$usersubname"
+ if test "$user"
then
- if test ! -f $usersubname
+ if test ! -f $user
then
error="$error
-user subroutine file $usersubname not accessible"
+user subroutine file $user not accessible"
fi
fi
if test "$objs"
@@ -1532,7 +1522,7 @@
Marc shared lib : $progdll
Version type : $mode
Job ID : $DIRJID/$jid$extra_job_info
-User subroutine name : $usersubname
+User subroutine name : $user
User objects/libs : $objs
Restart file job ID : $rid
Substructure file ID : $sid
@@ -1565,7 +1555,7 @@
Marc shared lib : $progdll
Version type : $mode
Job ID : $DIRJID/$jid$extra_job_info
-User subroutine name : $usersubname
+User subroutine name : $user
User objects/libs : $objs
Restart file job ID : $rid
Substructure file ID : $sid
@@ -1688,7 +1678,7 @@
;;
esac
fi
- $ECHO "User subroutine name ($usersubname)? $ECHOTXT"
+ $ECHO "User subroutine name ($user)? $ECHOTXT"
read value
if test "$value"
then
@@ -1697,50 +1687,19 @@
user=
;;
*)
- user=`dirname $value`/`$BASENAME $value .f`
- usersubname=$user
- basefile=`$BASENAME $value`
- if test ${basefile##*.} = f
- then
- user=`dirname $value`/`$BASENAME $value .f`
- usersubname=$user.f
- elif test ${basefile##*.} = F
- then
- user=`dirname $value`/`$BASENAME $value .F`
- usersubname=$user.F
- elif test ${basefile##*.} = f90
- then
- user=`dirname $value`/`$BASENAME $value .f90`
- usersubname=$user.f90
- elif test ${basefile##*.} = F90
- then
- user=`dirname $value`/`$BASENAME $value .F90`
- usersubname=$user.F90
- fi
+ user=$value
case $user in
\/*)
;;
*)
user=`pwd`/$user
- usersubname=`pwd`/$usersubname
;;
esac
- if test ! -f $usersubname
- then
- if test -f $usersubname.f
- then
- usersubname=$usersubname.f
- elif test -f $usersubname.F
- then
- usersubname=$usersubname.F
- elif test -f $usersubname.f90
- then
- usersubname=$usersubname.f90
- elif test -f $usersubname.F90
- then
- usersubname=$usersubname.F90
- fi
- fi
+ usernoext=$user
+ usernoext=`dirname $usernoext`/`$BASENAME $usernoext .f`
+ usernoext=`dirname $usernoext`/`$BASENAME $usernoext .F`
+ usernoext=`dirname $usernoext`/`$BASENAME $usernoext .for`
+ usernoext=`dirname $usernoext`/`$BASENAME $usernoext .f90`
;;
esac
fi
@@ -2275,11 +2234,12 @@
#
# user subroutine used
#
+# add DAMASK options for linking
+ DAMASK="-lstdc++"
if test "$user"
then
-# program=$user.marc
- program=$DIRJOB/`$BASENAME $user .f`.marc
+ program=$usernoext.marc
case $program in
\/* | \.\/*)
bd=
@@ -2392,7 +2352,7 @@
fi
if test "$user"
then
- execpath=$DIRJOB/`$BASENAME $user .f`.marc
+ execpath=$usernoext.marc
usersub=1
fi
export execpath
@@ -3275,33 +3235,16 @@
echo
if test "$user"
then
- userobj=$DIRJOB/`$BASENAME $user .f`.o
- basefile=`$BASENAME $usersubname`
- if test ${basefile##*.} = f
- then
- usersub=$DIRJOB/`$BASENAME $user .f`.F
- ln -sf "$user.f" "$usersub"
- else
- usersub=$usersubname
- fi
-
+ userobj=$usernoext.o
fi
cat > $jid.runmarcscript << END4
if test "$user"
then
- if test ${basefile##*.} = f
- then
- ln -sf "$user.f" "$usersub"
- fi
- $FORTRAN $usersub -o $userobj || \
+ $DFORTHIGHMP $user -o $userobj || \
{
- echo "$0: compile failed for $usersubname"
+ echo "$0: compile failed for $user"
exit 1
}
/bin/rm $program 2>/dev/null
- if test ${basefile##*.} = f
- then
- /bin/rm -f "$usersub"
- fi
fi
@@ -3323,6 +3266,7 @@
$TKLIBS \
$MRCLIBS \
$METISLIBS \
+ $DAMASK \
$SFLIB \
$OPENSSL_LIB \
$SYSLIBS \
@@ -3336,6 +3280,9 @@
prgsav=yes
fi
/bin/rm $userobj 2>/dev/null
+/bin/rm $DIRJOB/*.mod 2>/dev/null
+/bin/rm $DIRJOB/*.smod 2>/dev/null
+/bin/rm $DIRJOB/*_genmod.f90 2>/dev/null
#
# run marc
@@ -3383,7 +3330,7 @@
fi
else
if test $cpdll = yes; then
- filename=`basename $usersubname .f`
+ filename=$usernoext
/bin/cp $DIRJOB/$marcdll $DIRJOB/${filename}_$marcdll 2>/dev/null
fi
if test $rmdll = yes
@@ -3549,7 +3496,7 @@
# first copy over the user sub if local directories
if test ${dirstatus[$counter]} = "local"
then
- $RCP $user.f $i:$DIR1/
+ $RCP $user $i:$DIR1/
fi
# do the compilation on the other machine
if test ${dirstatus[$counter]} = "shared"
@@ -3562,21 +3509,21 @@
remoteuser=$DIR1/`$BASENAME $user`
$RSH $i /bin/rm $remoteprog 2> /dev/null
echo
- $RSH $i $DIR2/tools/comp_user $DIR2 $DIR1 $remoteuser $remoteprog
+ $RSH $i $DIR2/tools/comp_damask_hmp $DIR2 $DIR1 $remoteuser $remoteprog
# check if successful, the new executable should be there
line=`$RSH $i /bin/ls $remoteprog 2> /dev/null`
if test "$line"
then
echo compilation and linking successful on host $i
else
- echo "$0: compile failed for $usersubname on host $i"
+ echo "$0: compile failed for $user on host $i"
echo " $PRODUCT Exit number 3"
exit 1
fi
# remove the user subroutine on remote machine
if test ${dirstatus[$counter]} = "local"
then
- $RSH $i /bin/rm $remoteuser.f 2> /dev/null
+ $RSH $i /bin/rm $remoteuser 2> /dev/null
fi
fi
fi
@@ -3586,27 +3533,15 @@
if test "$userhost"
then
echo
- echo "Compiling and linking user subroutine $user.f on host `hostname`"
- fi
- userobj=$DIRJOB/`$BASENAME $user .f`.o
- basefile=`$BASENAME $usersubname`
- if test ${basefile##*.} = f
- then
- usersub=$DIRJOB/`$BASENAME $user .f`.F
- ln -sf "$user.f" "$usersub"
- else
- usersub=$usersubname
+ echo "Compiling and linking user subroutine $user on host `hostname`"
fi
+ userobj=$usernoext.o
- $FORTRAN $usersub -o $userobj || \
+ $DFORTHIGHMP $user -o $userobj || \
{
- echo "$0: compile failed for $usersubname"
+ echo "$0: compile failed for $user"
echo " $PRODUCT Exit number 3"
exit 1
}
/bin/rm $program 2>/dev/null
- if test ${basefile##*.} = f
- then
- /bin/rm -f "$usersub"
- fi
fi # if test $user
@@ -3628,6 +3563,7 @@
$TKLIBS \
$MRCLIBS \
$METISLIBS \
+ $DAMASK \
$SFLIB \
$OPENSSL_LIB \
$SYSLIBS \
@@ -3669,6 +3605,9 @@
prgsav=yes
fi # if test $link
/bin/rm $userobj 2>/dev/null
+/bin/rm $DIRJOB/*.mod 2>/dev/null
+/bin/rm $DIRJOB/*.smod 2>/dev/null
+/bin/rm $DIRJOB/*_genmod.f90 2>/dev/null
#
# run marc
@@ -3763,7 +3702,7 @@
else
#dllrun >0
if test $cpdll = yes; then
- filename=`basename $usersubname .f`
+ filename=$usernoext
/bin/cp $DIRJOB/$marcdll $DIRJOB/${filename}_$marcdll 2>/dev/null
fi
if test $rmdll = yes;then
@@ -3888,7 +3827,7 @@
# first copy over the user sub if local directories
if test ${dirstatus[$counter]} = "local"
then
- $RCP $user.f $i:$DIR1/
+ $RCP $user $i:$DIR1/
fi
# do the compilation on the other machine
if test ${dirstatus[$counter]} = "shared"
@@ -3901,20 +3840,20 @@
remoteuser=$DIR1/`$BASENAME $user`
$RSH $i /bin/rm $remoteprog 2> /dev/null
echo
- $RSH $i $DIR2/tools/comp_user $DIR2 $DIR1 $remoteuser $remoteprog
+ $RSH $i $DIR2/tools/comp_damask_hmp $DIR2 $DIR1 $remoteuser $remoteprog
# check if successful, the new executable should be there
line=`$RSH $i /bin/ls $remoteprog 2> /dev/null`
if test "$line"
then
echo compilation and linking successful on host $i
else
- echo "$0: compile failed for $usersubname on host $i"
+ echo "$0: compile failed for $user on host $i"
exit 1
fi
# remove the user subroutine on remote machine
if test ${dirstatus[$counter]} = "local"
then
- $RSH $i /bin/rm $remoteuser.f 2> /dev/null
+ $RSH $i /bin/rm $remoteuser 2> /dev/null
fi
fi
fi
@@ -3924,26 +3863,14 @@
if test "$userhost"
then
echo
- echo "Compiling and linking user subroutine $user.f on host `hostname`"
- fi
- userobj=$DIRJOB/`$BASENAME $user .f`.o
- basefile=`$BASENAME $usersubname`
- if test ${basefile##*.} = f
- then
- usersub=$DIRJOB/`$BASENAME $user .f`.F
- ln -sf "$user.f" "$usersub"
- else
- usersub=$usersubname
+ echo "Compiling and linking user subroutine $user on host `hostname`"
fi
+ userobj=$usernoext.o
- $FORTRAN $usersub -o $userobj || \
+ $DFORTHIGHMP $user -o $userobj || \
{
- echo "$0: compile failed for $usersubname"
+ echo "$0: compile failed for $user"
exit 1
}
/bin/rm $program 2>/dev/null
- if test ${basefile##*.} = f
- then
- /bin/rm -f "$usersub"
- fi
fi # if test $user
@@ -3965,6 +3892,7 @@
$TKLIBS \
$MRCLIBS \
$METISLIBS \
+ $DAMASK \
$SFLIB \
$OPENSSL_LIB \
$SYSLIBS \
@@ -4005,7 +3933,9 @@
prgsav=yes
fi # if test $link
/bin/rm $userobj 2>/dev/null
-
+/bin/rm $DIRJOB/*.mod 2>/dev/null
+/bin/rm $DIRJOB/*.smod 2>/dev/null
+/bin/rm $DIRJOB/*_genmod.f90 2>/dev/null
# done if no job id given
if test -z "$jid"
then
@@ -4125,7 +4055,7 @@
else
#dllrun >0
if test $cpdll = yes; then
- filename=`basename $usersubname .f`
+ filename=$usernoext
/bin/cp $DIRJOB/$marcdll $DIRJOB/${filename}_$marcdll 2>/dev/null
fi
if test $rmdll = yes;then

View File

@ -0,0 +1,477 @@
---
+++
@@ -136,6 +136,11 @@
# is created. For job running in the background, the log #
# file is always created. Default is "yes" #
##############################################################################
+# remove all Mentat paths from LD_LIBRARY_PATH
+LD_LIBRARY_PATH=:$LD_LIBRARY_PATH:
+LD_LIBRARY_PATH=${LD_LIBRARY_PATH//+([!(:)])mentat2023.3+([!(:)])/:}
+LD_LIBRARY_PATH=${LD_LIBRARY_PATH//+([(:)])/:}
+LD_LIBRARY_PATH=${LD_LIBRARY_PATH#:}; LD_LIBRARY_PATH=${LD_LIBRARY_PATH%:}
# set DIR to the directory in which this script is
REALCOM="`/bin/ls -l $0 |awk '{ print $NF; }'`"
DIR=`dirname $REALCOM`
@@ -303,7 +308,23 @@
. "$DIR/getarch"
+
+# getting user subroutine file name
+found=0
+for i in "$@"; do
+ if test $found = 1; then
+ DAMASK_USER=$i
+ found=0
+ fi
+ case $i in
+ -u* | -U*)
+ found=1
+ ;;
+ esac
+done
+# sourcing include_linux64 (needs DAMASK_USER to be set)
. $MARC_INCLUDE
+
#
#
@@ -406,7 +427,7 @@
did=
vid=
user=
-usersubname=
+usernoext=
objs=
qid=background
cpu=
@@ -677,50 +698,19 @@
esac
;;
-u* | -U*)
- user=`dirname $value`/`$BASENAME $value .f`
- usersubname=$user
- basefile=`$BASENAME $value`
- if test ${basefile##*.} = f
- then
- user=`dirname $value`/`$BASENAME $value .f`
- usersubname=$user.f
- elif test ${basefile##*.} = F
- then
- user=`dirname $value`/`$BASENAME $value .F`
- usersubname=$user.F
- elif test ${basefile##*.} = f90
- then
- user=`dirname $value`/`$BASENAME $value .f90`
- usersubname=$user.f90
- elif test ${basefile##*.} = F90
- then
- user=`dirname $value`/`$BASENAME $value .F90`
- usersubname=$user.F90
- fi
+ user=$value
case $user in
\/*)
;;
*)
user=`pwd`/$user
- usersubname=`pwd`/$usersubname
;;
esac
- if test ! -f $usersubname
- then
- if test -f $usersubname.f
- then
- usersubname=$usersubname.f
- elif test -f $usersubname.F
- then
- usersubname=$usersubname.F
- elif test -f $usersubname.f90
- then
- usersubname=$usersubname.f90
- elif test -f $usersubname.F90
- then
- usersubname=$usersubname.F90
- fi
- fi
+ usernoext=$user
+ usernoext=`dirname $usernoext`/`$BASENAME $usernoext .f`
+ usernoext=`dirname $usernoext`/`$BASENAME $usernoext .F`
+ usernoext=`dirname $usernoext`/`$BASENAME $usernoext .for`
+ usernoext=`dirname $usernoext`/`$BASENAME $usernoext .f90`
;;
-obj | -OBJ)
objs="$value"
@@ -1208,12 +1198,12 @@
fi
fi
fi
- if test "$usersubname"
+ if test "$user"
then
- if test ! -f $usersubname
+ if test ! -f $user
then
error="$error
-user subroutine file $usersubname not accessible"
+user subroutine file $user not accessible"
fi
fi
if test "$objs"
@@ -1532,7 +1522,7 @@
Marc shared lib : $progdll
Version type : $mode
Job ID : $DIRJID/$jid$extra_job_info
-User subroutine name : $usersubname
+User subroutine name : $user
User objects/libs : $objs
Restart file job ID : $rid
Substructure file ID : $sid
@@ -1565,7 +1555,7 @@
Marc shared lib : $progdll
Version type : $mode
Job ID : $DIRJID/$jid$extra_job_info
-User subroutine name : $usersubname
+User subroutine name : $user
User objects/libs : $objs
Restart file job ID : $rid
Substructure file ID : $sid
@@ -1688,7 +1678,7 @@
;;
esac
fi
- $ECHO "User subroutine name ($usersubname)? $ECHOTXT"
+ $ECHO "User subroutine name ($user)? $ECHOTXT"
read value
if test "$value"
then
@@ -1697,50 +1687,19 @@
user=
;;
*)
- user=`dirname $value`/`$BASENAME $value .f`
- usersubname=$user
- basefile=`$BASENAME $value`
- if test ${basefile##*.} = f
- then
- user=`dirname $value`/`$BASENAME $value .f`
- usersubname=$user.f
- elif test ${basefile##*.} = F
- then
- user=`dirname $value`/`$BASENAME $value .F`
- usersubname=$user.F
- elif test ${basefile##*.} = f90
- then
- user=`dirname $value`/`$BASENAME $value .f90`
- usersubname=$user.f90
- elif test ${basefile##*.} = F90
- then
- user=`dirname $value`/`$BASENAME $value .F90`
- usersubname=$user.F90
- fi
+ user=$value
case $user in
\/*)
;;
*)
user=`pwd`/$user
- usersubname=`pwd`/$usersubname
;;
esac
- if test ! -f $usersubname
- then
- if test -f $usersubname.f
- then
- usersubname=$usersubname.f
- elif test -f $usersubname.F
- then
- usersubname=$usersubname.F
- elif test -f $usersubname.f90
- then
- usersubname=$usersubname.f90
- elif test -f $usersubname.F90
- then
- usersubname=$usersubname.F90
- fi
- fi
+ usernoext=$user
+ usernoext=`dirname $usernoext`/`$BASENAME $usernoext .f`
+ usernoext=`dirname $usernoext`/`$BASENAME $usernoext .F`
+ usernoext=`dirname $usernoext`/`$BASENAME $usernoext .for`
+ usernoext=`dirname $usernoext`/`$BASENAME $usernoext .f90`
;;
esac
fi
@@ -2275,11 +2234,12 @@
#
# user subroutine used
#
+# add DAMASK options for linking
+ DAMASK="-lstdc++"
if test "$user"
then
-# program=$user.marc
- program=$DIRJOB/`$BASENAME $user .f`.marc
+ program=$usernoext.marc
case $program in
\/* | \.\/*)
bd=
@@ -2392,7 +2352,7 @@
fi
if test "$user"
then
- execpath=$DIRJOB/`$BASENAME $user .f`.marc
+ execpath=$usernoext.marc
usersub=1
fi
export execpath
@@ -3275,33 +3235,16 @@
echo
if test "$user"
then
- userobj=$DIRJOB/`$BASENAME $user .f`.o
- basefile=`$BASENAME $usersubname`
- if test ${basefile##*.} = f
- then
- usersub=$DIRJOB/`$BASENAME $user .f`.F
- ln -sf "$user.f" "$usersub"
- else
- usersub=$usersubname
- fi
-
+ userobj=$usernoext.o
fi
cat > $jid.runmarcscript << END4
if test "$user"
then
- if test ${basefile##*.} = f
- then
- ln -sf "$user.f" "$usersub"
- fi
- $FORTRAN $usersub -o $userobj || \
+ $DFORTLOWMP $user -o $userobj || \
{
- echo "$0: compile failed for $usersubname"
+ echo "$0: compile failed for $user"
exit 1
}
/bin/rm $program 2>/dev/null
- if test ${basefile##*.} = f
- then
- /bin/rm -f "$usersub"
- fi
fi
@@ -3323,6 +3266,7 @@
$TKLIBS \
$MRCLIBS \
$METISLIBS \
+ $DAMASK \
$SFLIB \
$OPENSSL_LIB \
$SYSLIBS \
@@ -3336,6 +3280,9 @@
prgsav=yes
fi
/bin/rm $userobj 2>/dev/null
+/bin/rm $DIRJOB/*.mod 2>/dev/null
+/bin/rm $DIRJOB/*.smod 2>/dev/null
+/bin/rm $DIRJOB/*_genmod.f90 2>/dev/null
#
# run marc
@@ -3383,7 +3330,7 @@
fi
else
if test $cpdll = yes; then
- filename=`basename $usersubname .f`
+ filename=$usernoext
/bin/cp $DIRJOB/$marcdll $DIRJOB/${filename}_$marcdll 2>/dev/null
fi
if test $rmdll = yes
@@ -3549,7 +3496,7 @@
# first copy over the user sub if local directories
if test ${dirstatus[$counter]} = "local"
then
- $RCP $user.f $i:$DIR1/
+ $RCP $user $i:$DIR1/
fi
# do the compilation on the other machine
if test ${dirstatus[$counter]} = "shared"
@@ -3562,21 +3509,21 @@
remoteuser=$DIR1/`$BASENAME $user`
$RSH $i /bin/rm $remoteprog 2> /dev/null
echo
- $RSH $i $DIR2/tools/comp_user $DIR2 $DIR1 $remoteuser $remoteprog
+ $RSH $i $DIR2/tools/comp_damask_lmp $DIR2 $DIR1 $remoteuser $remoteprog
# check if successful, the new executable should be there
line=`$RSH $i /bin/ls $remoteprog 2> /dev/null`
if test "$line"
then
echo compilation and linking successful on host $i
else
- echo "$0: compile failed for $usersubname on host $i"
+ echo "$0: compile failed for $user on host $i"
echo " $PRODUCT Exit number 3"
exit 1
fi
# remove the user subroutine on remote machine
if test ${dirstatus[$counter]} = "local"
then
- $RSH $i /bin/rm $remoteuser.f 2> /dev/null
+ $RSH $i /bin/rm $remoteuser 2> /dev/null
fi
fi
fi
@@ -3586,27 +3533,15 @@
if test "$userhost"
then
echo
- echo "Compiling and linking user subroutine $user.f on host `hostname`"
- fi
- userobj=$DIRJOB/`$BASENAME $user .f`.o
- basefile=`$BASENAME $usersubname`
- if test ${basefile##*.} = f
- then
- usersub=$DIRJOB/`$BASENAME $user .f`.F
- ln -sf "$user.f" "$usersub"
- else
- usersub=$usersubname
+ echo "Compiling and linking user subroutine $user on host `hostname`"
fi
+ userobj=$usernoext.o
- $FORTRAN $usersub -o $userobj || \
+ $DFORTLOWMP $user -o $userobj || \
{
- echo "$0: compile failed for $usersubname"
+ echo "$0: compile failed for $user"
echo " $PRODUCT Exit number 3"
exit 1
}
/bin/rm $program 2>/dev/null
- if test ${basefile##*.} = f
- then
- /bin/rm -f "$usersub"
- fi
fi # if test $user
@@ -3628,6 +3563,7 @@
$TKLIBS \
$MRCLIBS \
$METISLIBS \
+ $DAMASK \
$SFLIB \
$OPENSSL_LIB \
$SYSLIBS \
@@ -3669,6 +3605,9 @@
prgsav=yes
fi # if test $link
/bin/rm $userobj 2>/dev/null
+/bin/rm $DIRJOB/*.mod 2>/dev/null
+/bin/rm $DIRJOB/*.smod 2>/dev/null
+/bin/rm $DIRJOB/*_genmod.f90 2>/dev/null
#
# run marc
@@ -3763,7 +3702,7 @@
else
#dllrun >0
if test $cpdll = yes; then
- filename=`basename $usersubname .f`
+ filename=$usernoext
/bin/cp $DIRJOB/$marcdll $DIRJOB/${filename}_$marcdll 2>/dev/null
fi
if test $rmdll = yes;then
@@ -3888,7 +3827,7 @@
# first copy over the user sub if local directories
if test ${dirstatus[$counter]} = "local"
then
- $RCP $user.f $i:$DIR1/
+ $RCP $user $i:$DIR1/
fi
# do the compilation on the other machine
if test ${dirstatus[$counter]} = "shared"
@@ -3901,20 +3840,20 @@
remoteuser=$DIR1/`$BASENAME $user`
$RSH $i /bin/rm $remoteprog 2> /dev/null
echo
- $RSH $i $DIR2/tools/comp_user $DIR2 $DIR1 $remoteuser $remoteprog
+ $RSH $i $DIR2/tools/comp_damask_lmp $DIR2 $DIR1 $remoteuser $remoteprog
# check if successful, the new executable should be there
line=`$RSH $i /bin/ls $remoteprog 2> /dev/null`
if test "$line"
then
echo compilation and linking successful on host $i
else
- echo "$0: compile failed for $usersubname on host $i"
+ echo "$0: compile failed for $user on host $i"
exit 1
fi
# remove the user subroutine on remote machine
if test ${dirstatus[$counter]} = "local"
then
- $RSH $i /bin/rm $remoteuser.f 2> /dev/null
+ $RSH $i /bin/rm $remoteuser 2> /dev/null
fi
fi
fi
@@ -3924,26 +3863,14 @@
if test "$userhost"
then
echo
- echo "Compiling and linking user subroutine $user.f on host `hostname`"
- fi
- userobj=$DIRJOB/`$BASENAME $user .f`.o
- basefile=`$BASENAME $usersubname`
- if test ${basefile##*.} = f
- then
- usersub=$DIRJOB/`$BASENAME $user .f`.F
- ln -sf "$user.f" "$usersub"
- else
- usersub=$usersubname
+ echo "Compiling and linking user subroutine $user on host `hostname`"
fi
+ userobj=$usernoext.o
- $FORTRAN $usersub -o $userobj || \
+ $DFORTLOWMP $user -o $userobj || \
{
- echo "$0: compile failed for $usersubname"
+ echo "$0: compile failed for $user"
exit 1
}
/bin/rm $program 2>/dev/null
- if test ${basefile##*.} = f
- then
- /bin/rm -f "$usersub"
- fi
fi # if test $user
@@ -3965,6 +3892,7 @@
$TKLIBS \
$MRCLIBS \
$METISLIBS \
+ $DAMASK \
$SFLIB \
$OPENSSL_LIB \
$SYSLIBS \
@@ -4005,7 +3933,9 @@
prgsav=yes
fi # if test $link
/bin/rm $userobj 2>/dev/null
-
+/bin/rm $DIRJOB/*.mod 2>/dev/null
+/bin/rm $DIRJOB/*.smod 2>/dev/null
+/bin/rm $DIRJOB/*_genmod.f90 2>/dev/null
# done if no job id given
if test -z "$jid"
then
@@ -4125,7 +4055,7 @@
else
#dllrun >0
if test $cpdll = yes; then
- filename=`basename $usersubname .f`
+ filename=$usernoext
/bin/cp $DIRJOB/$marcdll $DIRJOB/${filename}_$marcdll 2>/dev/null
fi
if test $rmdll = yes;then

View File

@ -0,0 +1,477 @@
---
+++
@@ -136,6 +136,11 @@
# is created. For job running in the background, the log #
# file is always created. Default is "yes" #
##############################################################################
+# remove all Mentat paths from LD_LIBRARY_PATH
+LD_LIBRARY_PATH=:$LD_LIBRARY_PATH:
+LD_LIBRARY_PATH=${LD_LIBRARY_PATH//+([!(:)])mentat2023.3+([!(:)])/:}
+LD_LIBRARY_PATH=${LD_LIBRARY_PATH//+([(:)])/:}
+LD_LIBRARY_PATH=${LD_LIBRARY_PATH#:}; LD_LIBRARY_PATH=${LD_LIBRARY_PATH%:}
# set DIR to the directory in which this script is
REALCOM="`/bin/ls -l $0 |awk '{ print $NF; }'`"
DIR=`dirname $REALCOM`
@@ -303,7 +308,23 @@
. "$DIR/getarch"
+
+# getting user subroutine file name
+found=0
+for i in "$@"; do
+ if test $found = 1; then
+ DAMASK_USER=$i
+ found=0
+ fi
+ case $i in
+ -u* | -U*)
+ found=1
+ ;;
+ esac
+done
+# sourcing include_linux64 (needs DAMASK_USER to be set)
. $MARC_INCLUDE
+
#
#
@@ -406,7 +427,7 @@
did=
vid=
user=
-usersubname=
+usernoext=
objs=
qid=background
cpu=
@@ -677,50 +698,19 @@
esac
;;
-u* | -U*)
- user=`dirname $value`/`$BASENAME $value .f`
- usersubname=$user
- basefile=`$BASENAME $value`
- if test ${basefile##*.} = f
- then
- user=`dirname $value`/`$BASENAME $value .f`
- usersubname=$user.f
- elif test ${basefile##*.} = F
- then
- user=`dirname $value`/`$BASENAME $value .F`
- usersubname=$user.F
- elif test ${basefile##*.} = f90
- then
- user=`dirname $value`/`$BASENAME $value .f90`
- usersubname=$user.f90
- elif test ${basefile##*.} = F90
- then
- user=`dirname $value`/`$BASENAME $value .F90`
- usersubname=$user.F90
- fi
+ user=$value
case $user in
\/*)
;;
*)
user=`pwd`/$user
- usersubname=`pwd`/$usersubname
;;
esac
- if test ! -f $usersubname
- then
- if test -f $usersubname.f
- then
- usersubname=$usersubname.f
- elif test -f $usersubname.F
- then
- usersubname=$usersubname.F
- elif test -f $usersubname.f90
- then
- usersubname=$usersubname.f90
- elif test -f $usersubname.F90
- then
- usersubname=$usersubname.F90
- fi
- fi
+ usernoext=$user
+ usernoext=`dirname $usernoext`/`$BASENAME $usernoext .f`
+ usernoext=`dirname $usernoext`/`$BASENAME $usernoext .F`
+ usernoext=`dirname $usernoext`/`$BASENAME $usernoext .for`
+ usernoext=`dirname $usernoext`/`$BASENAME $usernoext .f90`
;;
-obj | -OBJ)
objs="$value"
@@ -1208,12 +1198,12 @@
fi
fi
fi
- if test "$usersubname"
+ if test "$user"
then
- if test ! -f $usersubname
+ if test ! -f $user
then
error="$error
-user subroutine file $usersubname not accessible"
+user subroutine file $user not accessible"
fi
fi
if test "$objs"
@@ -1532,7 +1522,7 @@
Marc shared lib : $progdll
Version type : $mode
Job ID : $DIRJID/$jid$extra_job_info
-User subroutine name : $usersubname
+User subroutine name : $user
User objects/libs : $objs
Restart file job ID : $rid
Substructure file ID : $sid
@@ -1565,7 +1555,7 @@
Marc shared lib : $progdll
Version type : $mode
Job ID : $DIRJID/$jid$extra_job_info
-User subroutine name : $usersubname
+User subroutine name : $user
User objects/libs : $objs
Restart file job ID : $rid
Substructure file ID : $sid
@@ -1688,7 +1678,7 @@
;;
esac
fi
- $ECHO "User subroutine name ($usersubname)? $ECHOTXT"
+ $ECHO "User subroutine name ($user)? $ECHOTXT"
read value
if test "$value"
then
@@ -1697,50 +1687,19 @@
user=
;;
*)
- user=`dirname $value`/`$BASENAME $value .f`
- usersubname=$user
- basefile=`$BASENAME $value`
- if test ${basefile##*.} = f
- then
- user=`dirname $value`/`$BASENAME $value .f`
- usersubname=$user.f
- elif test ${basefile##*.} = F
- then
- user=`dirname $value`/`$BASENAME $value .F`
- usersubname=$user.F
- elif test ${basefile##*.} = f90
- then
- user=`dirname $value`/`$BASENAME $value .f90`
- usersubname=$user.f90
- elif test ${basefile##*.} = F90
- then
- user=`dirname $value`/`$BASENAME $value .F90`
- usersubname=$user.F90
- fi
+ user=$value
case $user in
\/*)
;;
*)
user=`pwd`/$user
- usersubname=`pwd`/$usersubname
;;
esac
- if test ! -f $usersubname
- then
- if test -f $usersubname.f
- then
- usersubname=$usersubname.f
- elif test -f $usersubname.F
- then
- usersubname=$usersubname.F
- elif test -f $usersubname.f90
- then
- usersubname=$usersubname.f90
- elif test -f $usersubname.F90
- then
- usersubname=$usersubname.F90
- fi
- fi
+ usernoext=$user
+ usernoext=`dirname $usernoext`/`$BASENAME $usernoext .f`
+ usernoext=`dirname $usernoext`/`$BASENAME $usernoext .F`
+ usernoext=`dirname $usernoext`/`$BASENAME $usernoext .for`
+ usernoext=`dirname $usernoext`/`$BASENAME $usernoext .f90`
;;
esac
fi
@@ -2275,11 +2234,12 @@
#
# user subroutine used
#
+# add DAMASK options for linking
+ DAMASK="-lstdc++"
if test "$user"
then
-# program=$user.marc
- program=$DIRJOB/`$BASENAME $user .f`.marc
+ program=$usernoext.marc
case $program in
\/* | \.\/*)
bd=
@@ -2392,7 +2352,7 @@
fi
if test "$user"
then
- execpath=$DIRJOB/`$BASENAME $user .f`.marc
+ execpath=$usernoext.marc
usersub=1
fi
export execpath
@@ -3275,33 +3235,16 @@
echo
if test "$user"
then
- userobj=$DIRJOB/`$BASENAME $user .f`.o
- basefile=`$BASENAME $usersubname`
- if test ${basefile##*.} = f
- then
- usersub=$DIRJOB/`$BASENAME $user .f`.F
- ln -sf "$user.f" "$usersub"
- else
- usersub=$usersubname
- fi
-
+ userobj=$usernoext.o
fi
cat > $jid.runmarcscript << END4
if test "$user"
then
- if test ${basefile##*.} = f
- then
- ln -sf "$user.f" "$usersub"
- fi
- $FORTRAN $usersub -o $userobj || \
+ $DFORTRANMP $user -o $userobj || \
{
- echo "$0: compile failed for $usersubname"
+ echo "$0: compile failed for $user"
exit 1
}
/bin/rm $program 2>/dev/null
- if test ${basefile##*.} = f
- then
- /bin/rm -f "$usersub"
- fi
fi
@@ -3323,6 +3266,7 @@
$TKLIBS \
$MRCLIBS \
$METISLIBS \
+ $DAMASK \
$SFLIB \
$OPENSSL_LIB \
$SYSLIBS \
@@ -3336,6 +3280,9 @@
prgsav=yes
fi
/bin/rm $userobj 2>/dev/null
+/bin/rm $DIRJOB/*.mod 2>/dev/null
+/bin/rm $DIRJOB/*.smod 2>/dev/null
+/bin/rm $DIRJOB/*_genmod.f90 2>/dev/null
#
# run marc
@@ -3383,7 +3330,7 @@
fi
else
if test $cpdll = yes; then
- filename=`basename $usersubname .f`
+ filename=$usernoext
/bin/cp $DIRJOB/$marcdll $DIRJOB/${filename}_$marcdll 2>/dev/null
fi
if test $rmdll = yes
@@ -3549,7 +3496,7 @@
# first copy over the user sub if local directories
if test ${dirstatus[$counter]} = "local"
then
- $RCP $user.f $i:$DIR1/
+ $RCP $user $i:$DIR1/
fi
# do the compilation on the other machine
if test ${dirstatus[$counter]} = "shared"
@@ -3562,21 +3509,21 @@
remoteuser=$DIR1/`$BASENAME $user`
$RSH $i /bin/rm $remoteprog 2> /dev/null
echo
- $RSH $i $DIR2/tools/comp_user $DIR2 $DIR1 $remoteuser $remoteprog
+ $RSH $i $DIR2/tools/comp_damask_mp $DIR2 $DIR1 $remoteuser $remoteprog
# check if successful, the new executable should be there
line=`$RSH $i /bin/ls $remoteprog 2> /dev/null`
if test "$line"
then
echo compilation and linking successful on host $i
else
- echo "$0: compile failed for $usersubname on host $i"
+ echo "$0: compile failed for $user on host $i"
echo " $PRODUCT Exit number 3"
exit 1
fi
# remove the user subroutine on remote machine
if test ${dirstatus[$counter]} = "local"
then
- $RSH $i /bin/rm $remoteuser.f 2> /dev/null
+ $RSH $i /bin/rm $remoteuser 2> /dev/null
fi
fi
fi
@@ -3586,27 +3533,15 @@
if test "$userhost"
then
echo
- echo "Compiling and linking user subroutine $user.f on host `hostname`"
- fi
- userobj=$DIRJOB/`$BASENAME $user .f`.o
- basefile=`$BASENAME $usersubname`
- if test ${basefile##*.} = f
- then
- usersub=$DIRJOB/`$BASENAME $user .f`.F
- ln -sf "$user.f" "$usersub"
- else
- usersub=$usersubname
+ echo "Compiling and linking user subroutine $user on host `hostname`"
fi
+ userobj=$usernoext.o
- $FORTRAN $usersub -o $userobj || \
+ $DFORTRANMP $user -o $userobj || \
{
- echo "$0: compile failed for $usersubname"
+ echo "$0: compile failed for $user"
echo " $PRODUCT Exit number 3"
exit 1
}
/bin/rm $program 2>/dev/null
- if test ${basefile##*.} = f
- then
- /bin/rm -f "$usersub"
- fi
fi # if test $user
@@ -3628,6 +3563,7 @@
$TKLIBS \
$MRCLIBS \
$METISLIBS \
+ $DAMASK \
$SFLIB \
$OPENSSL_LIB \
$SYSLIBS \
@@ -3669,6 +3605,9 @@
prgsav=yes
fi # if test $link
/bin/rm $userobj 2>/dev/null
+/bin/rm $DIRJOB/*.mod 2>/dev/null
+/bin/rm $DIRJOB/*.smod 2>/dev/null
+/bin/rm $DIRJOB/*_genmod.f90 2>/dev/null
#
# run marc
@@ -3763,7 +3702,7 @@
else
#dllrun >0
if test $cpdll = yes; then
- filename=`basename $usersubname .f`
+ filename=$usernoext
/bin/cp $DIRJOB/$marcdll $DIRJOB/${filename}_$marcdll 2>/dev/null
fi
if test $rmdll = yes;then
@@ -3888,7 +3827,7 @@
# first copy over the user sub if local directories
if test ${dirstatus[$counter]} = "local"
then
- $RCP $user.f $i:$DIR1/
+ $RCP $user $i:$DIR1/
fi
# do the compilation on the other machine
if test ${dirstatus[$counter]} = "shared"
@@ -3901,20 +3840,20 @@
remoteuser=$DIR1/`$BASENAME $user`
$RSH $i /bin/rm $remoteprog 2> /dev/null
echo
- $RSH $i $DIR2/tools/comp_user $DIR2 $DIR1 $remoteuser $remoteprog
+ $RSH $i $DIR2/tools/comp_damask_mp $DIR2 $DIR1 $remoteuser $remoteprog
# check if successful, the new executable should be there
line=`$RSH $i /bin/ls $remoteprog 2> /dev/null`
if test "$line"
then
echo compilation and linking successful on host $i
else
- echo "$0: compile failed for $usersubname on host $i"
+ echo "$0: compile failed for $user on host $i"
exit 1
fi
# remove the user subroutine on remote machine
if test ${dirstatus[$counter]} = "local"
then
- $RSH $i /bin/rm $remoteuser.f 2> /dev/null
+ $RSH $i /bin/rm $remoteuser 2> /dev/null
fi
fi
fi
@@ -3924,26 +3863,14 @@
if test "$userhost"
then
echo
- echo "Compiling and linking user subroutine $user.f on host `hostname`"
- fi
- userobj=$DIRJOB/`$BASENAME $user .f`.o
- basefile=`$BASENAME $usersubname`
- if test ${basefile##*.} = f
- then
- usersub=$DIRJOB/`$BASENAME $user .f`.F
- ln -sf "$user.f" "$usersub"
- else
- usersub=$usersubname
+ echo "Compiling and linking user subroutine $user on host `hostname`"
fi
+ userobj=$usernoext.o
- $FORTRAN $usersub -o $userobj || \
+ $DFORTRANMP $user -o $userobj || \
{
- echo "$0: compile failed for $usersubname"
+ echo "$0: compile failed for $user"
exit 1
}
/bin/rm $program 2>/dev/null
- if test ${basefile##*.} = f
- then
- /bin/rm -f "$usersub"
- fi
fi # if test $user
@@ -3965,6 +3892,7 @@
$TKLIBS \
$MRCLIBS \
$METISLIBS \
+ $DAMASK \
$SFLIB \
$OPENSSL_LIB \
$SYSLIBS \
@@ -4005,7 +3933,9 @@
prgsav=yes
fi # if test $link
/bin/rm $userobj 2>/dev/null
-
+/bin/rm $DIRJOB/*.mod 2>/dev/null
+/bin/rm $DIRJOB/*.smod 2>/dev/null
+/bin/rm $DIRJOB/*_genmod.f90 2>/dev/null
# done if no job id given
if test -z "$jid"
then
@@ -4125,7 +4055,7 @@
else
#dllrun >0
if test $cpdll = yes; then
- filename=`basename $usersubname .f`
+ filename=$usernoext
/bin/cp $DIRJOB/$marcdll $DIRJOB/${filename}_$marcdll 2>/dev/null
fi
if test $rmdll = yes;then

View File

@ -0,0 +1,24 @@
---
+++
@@ -1,18 +1,5 @@
#!/bin/sh
-# This script opens a window running an editor. The default window is an
-# xterm, and the default editor is vi. These may be customized.
+# This script opens a window running an editor.
+# The command to invoke the editor is specified during DAMASK installation
-dir=
-for d in /usr/bin /usr/bin/X11; do
- if test -x "$d/xterm"; then
- dir="$d"
- break
- fi
-done
-
-if test -z "$dir"; then
- echo "$0: Could not find xterm"
- exit 1
-fi
-
-"$dir/xterm" -T "vi $*" -n "vi $*" -e vi $*
+%EDITOR% $*

View File

View File

View File

View File

@ -0,0 +1,25 @@
---
+++
@@ -91,6 +91,7 @@
srcfile="-u $srcfile -save y"
;;
runsaved)
+ srcfile=${srcfile%.*}".marc"
srcfile="-prog $srcfile"
;;
esac
@@ -189,12 +190,12 @@
unset PYTHONPATH
if [ "$doe_first" = "-" ]; then # submit of regular Marc job
- "${DIR}/tools/run_marc" $slv -j $job -v n -b y $nprocds $nprocd \
+ "${DIR}/tools/run_damask_hmp" $slv -j $job -v n -b y $nprocds $nprocd \
$srcfile $restart $postfile $viewfactorsfile $hostfile \
$compat $copy_datfile $copy_postfile $scr_dir $dcoup \
$assem_recov_nthread $nthread $nsolver $mode $gpu > /dev/null 2>&1
else # submit of a DoE Marc job
- "${DIR}/tools/run_marc" $slv -j $job -v n -b n $nprocds $nprocd \
+ "${DIR}/tools/run_damask_hmp" $slv -j $job -v n -b n $nprocds $nprocd \
$srcfile $restart $postfile $viewfactorsfile $hostfile \
$compat $copy_datfile $copy_postfile $scr_dir $dcoup \
$assem_recov_nthread $nthread $nsolver $mode $gpu

View File

@ -0,0 +1,25 @@
---
+++
@@ -91,6 +91,7 @@
srcfile="-u $srcfile -save y"
;;
runsaved)
+ srcfile=${srcfile%.*}".marc"
srcfile="-prog $srcfile"
;;
esac
@@ -189,12 +190,12 @@
unset PYTHONPATH
if [ "$doe_first" = "-" ]; then # submit of regular Marc job
- "${DIR}/tools/run_marc" $slv -j $job -v n -b y $nprocds $nprocd \
+ "${DIR}/tools/run_damask_mp" $slv -j $job -v n -b y $nprocds $nprocd \
$srcfile $restart $postfile $viewfactorsfile $hostfile \
$compat $copy_datfile $copy_postfile $scr_dir $dcoup \
$assem_recov_nthread $nthread $nsolver $mode $gpu > /dev/null 2>&1
else # submit of a DoE Marc job
- "${DIR}/tools/run_marc" $slv -j $job -v n -b n $nprocds $nprocd \
+ "${DIR}/tools/run_damask_mp" $slv -j $job -v n -b n $nprocds $nprocd \
$srcfile $restart $postfile $viewfactorsfile $hostfile \
$compat $copy_datfile $copy_postfile $scr_dir $dcoup \
$assem_recov_nthread $nthread $nsolver $mode $gpu

View File

@ -0,0 +1,25 @@
---
+++
@@ -91,6 +91,7 @@
srcfile="-u $srcfile -save y"
;;
runsaved)
+ srcfile=${srcfile%.*}".marc"
srcfile="-prog $srcfile"
;;
esac
@@ -189,12 +190,12 @@
unset PYTHONPATH
if [ "$doe_first" = "-" ]; then # submit of regular Marc job
- "${DIR}/tools/run_marc" $slv -j $job -v n -b y $nprocds $nprocd \
+ "${DIR}/tools/run_damask_lmp" $slv -j $job -v n -b y $nprocds $nprocd \
$srcfile $restart $postfile $viewfactorsfile $hostfile \
$compat $copy_datfile $copy_postfile $scr_dir $dcoup \
$assem_recov_nthread $nthread $nsolver $mode $gpu > /dev/null 2>&1
else # submit of a DoE Marc job
- "${DIR}/tools/run_marc" $slv -j $job -v n -b n $nprocds $nprocd \
+ "${DIR}/tools/run_damask_lmp" $slv -j $job -v n -b n $nprocds $nprocd \
$srcfile $restart $postfile $viewfactorsfile $hostfile \
$compat $copy_datfile $copy_postfile $scr_dir $dcoup \
$assem_recov_nthread $nthread $nsolver $mode $gpu

View File

@ -0,0 +1,158 @@
---
+++
@@ -362,11 +362,18 @@
}
button {
position +25 =
- size 25 4
+ size 18 4
text "ADVANCED JOB SUBMISSION"
help "job_run#Job Submission And Control"
popmenu job_submit_adv_pm
}
+ button {
+ position +18 =
+ size 7 4
+ text "DAMASK"
+ help "damask_run#Job Submission And Control"
+ popmenu damask
+ }
button {
position 0 +4
size 16 4
@@ -1307,6 +1314,135 @@
}
+#--------------------------------------------------------------------------------------------------
+popmenu damask {
+
+#ifdef QT_MENTAT
+ text "DAMASK.MPIE.DE"
+#endif
+
+ group {
+#ifndef QT_MENTAT
+ label {
+ position 0 0
+ size 50 4
+ text "DAMASK.MPIE.DE"
+ }
+#endif
+
+ label {
+ position 1 6
+ size 13 6
+ text "Optimzation"
+ border_width 1
+ border_color black
+ }
+
+ label {
+ position +13 =
+ size 20 6
+ text "write Input"
+ border_width 1
+ border_color black
+ }
+
+ label {
+ position +18 =
+ size 30 6
+ text "do not write Inp."
+ border_width 1
+ border_color black
+ }
+
+ label {
+ position -32 +6
+ size 12 6
+ text "O3 / OpenMP"
+ border_width 1
+ border_color black
+ }
+
+ popdown {
+ position +12 =
+ size 20 6
+ text "Submit"
+ command "*submit_job 4 *monitor_job"
+ }
+
+ popdown {
+ position +20 =
+ size 20 6
+ text "Execute"
+ command "*execute_job 4 *monitor_job"
+ }
+
+ label {
+ position -32 +6
+ size 12 6
+ text "O1 / OpenMP"
+ border_width 1
+ border_color black
+ }
+
+ popdown {
+ position +12 =
+ size 20 6
+ text "Submit"
+ command "*submit_job 5 *monitor_job"
+ }
+
+ popdown {
+ position +20 =
+ size 20 6
+ text "Execute"
+ command "*execute_job 5 *monitor_job"
+ }
+
+ label {
+ position -32 +6
+ size 12 6
+ text "O0 / OpenMP"
+ border_width 1
+ border_color black
+ }
+
+ popdown {
+ position +12 =
+ size 20 6
+ text "Submit"
+ command "*submit_job 6 *monitor_job"
+ }
+
+ popdown {
+ position +20 =
+ size 20 6
+ text "Execute"
+ command "*execute_job 6 *monitor_job"
+ }
+
+ popdown {
+ position 19 +8
+ size 12 8
+ text "CANCEL"
+ }
+}
+
+ window {
+ parent mentat
+ origin 38 8
+#ifdef DCOM
+ size 50 100
+#else
+ size 50 94
+#endif
+ background_color body
+ border_width 1
+ border_color border
+ buffering single
+ }
+ mode permanent
+}
+
#--------------------------------------------------------------------------------------------------
popmenu job_exit_msg_pm {

View File

@ -65,13 +65,13 @@ def mesh(r,d):
return [
"*add_nodes",
"%f %f %f"%(0.0,0.0,0.0),
"%f %f %f"%(0.0,0.0,d[2]),
"%f %f %f"%(0.0,d[1],d[2]),
"%f %f %f"%(d[0],0.0,0.0),
"%f %f %f"%(d[0],d[1],0.0),
"%f %f %f"%(0.0,d[1],0.0),
"%f %f %f"%(-d[0],0.0,0.0),
"%f %f %f"%(-d[0],0.0,d[2]),
"%f %f %f"%(-d[0],d[1],d[2]),
"%f %f %f"%(-d[0],d[1],0.0),
"%f %f %f"%(0.0,0.0,d[2]),
"%f %f %f"%(d[0],0.0,d[2]),
"%f %f %f"%(d[0],d[1],d[2]),
"%f %f %f"%(0.0,d[1],d[2]),
"*add_elements",
"1",
"2",
@ -82,19 +82,17 @@ def mesh(r,d):
"7",
"8",
"*sub_divisions",
"%i %i %i"%(r[2],r[1],r[0]),
"%i %i %i"%(r[0],r[1],r[2]),
"*subdivide_elements",
"all_existing",
"*set_sweep_tolerance",
"%f"%(float(min(d))/max(r)/2.0),
"*sweep_all",
"*renumber_all",
"*set_move_scale_factor x -1",
"*move_elements",
"all_existing",
"*flip_elements",
"all_existing",
"*fill_view",
"*remove_unused_nodes",
"*set_renumber_direction",
"%i %i %i"%(1,r[0],r[0]*r[1]),
"*renumber_elements_directed",
"*renumber_nodes_directed",
]
@ -142,8 +140,7 @@ def initial_conditions(material):
cmds = [\
"*new_icond",
"*icond_name _temperature",
"*icond_type state_variable",
"*icond_param_value state_var_id 1",
"*icond_type elem_temperature_state",
"*icond_dof_value var 300",
"*add_icond_elements",
"all_existing",
@ -153,9 +150,9 @@ def initial_conditions(material):
cmds.append([\
"*new_icond",
"*icond_name material_%i"%(grain+1),
"*icond_type state_variable",
"*icond_type elem_user_state",
"*icond_param_value state_var_id 2",
"*icond_dof_value var %i"%(grain+1),
"*icond_dof_value var %i"%(grain),
"*add_icond_elements",
elementList,
"#",
@ -196,7 +193,7 @@ if filenames == []: filenames = [None]
for name in filenames:
print(script_name+': '+name)
geom = damask.Grid.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
geom = damask.GeomGrid.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
material = geom.material.flatten(order='F')
cmds = [\
@ -209,6 +206,7 @@ for name in filenames:
'*show_model',
'*redraw',
'*draw_automatic',
'*fill_view',
]
output_locals = {}

View File

@ -26,5 +26,5 @@ from ._vtk import VTK # noqa
from ._config import Config # noqa
from ._configmaterial import ConfigMaterial # noqa
from ._loadcasegrid import LoadcaseGrid # noqa
from ._grid import Grid # noqa
from ._geomgrid import GeomGrid # noqa
from ._result import Result # noqa

View File

@ -296,8 +296,8 @@ class Colormap(mpl.colors.ListedColormap):
RGBA image of shaded data.
"""
mask = np.logical_not(np.isnan(field) if gap is None else \
np.logical_or (np.isnan(field), field == gap)) # mask NaN (and gap if present)
mask = np.logical_not(np.isnan(field) if gap is None else
np.logical_or(np.isnan(field), field == gap)) # mask NaN (and gap if present)
l,r = (field[mask].min(),field[mask].max()) if bounds is None else \
(bounds[0],bounds[1])
@ -305,9 +305,11 @@ class Colormap(mpl.colors.ListedColormap):
if abs(delta := r-l) * 1e8 <= (avg := 0.5*abs(r+l)): # delta is similar to numerical noise
l,r = (l-0.5*avg*np.sign(delta),r+0.5*avg*np.sign(delta)) # extend range to have actual data centered within
field_ = np.nan_to_num(field, nan=(l+r)/2, posinf=r, neginf=l)
return Image.fromarray(
(np.dstack((
self.colors[(np.round(np.clip((field-l)/delta,0.0,1.0)*(self.N-1))).astype(np.uint16),:3],
self.colors[np.round(np.clip((field_-l)/(r-l),0.0,1.0)*(self.N-1)).astype(np.uint16),:3],
mask.astype(float)
)
)*255

View File

@ -144,7 +144,7 @@ class ConfigMaterial(Config):
Notes
-----
damask.Grid.load_DREAM3D gives the corresponding geometry for
damask.GeomGrid.load_DREAM3D gives the corresponding geometry for
the grid solver.
For cell-wise data, only unique combinations of

View File

@ -6,7 +6,8 @@ from ._typehints import FloatSequence, CrystalFamily, BravaisLattice, CrystalKin
from . import util
from . import Rotation
lattice_symmetries: Dict[BravaisLattice, CrystalFamily] = {
lattice_symmetries: Dict[Optional[BravaisLattice], CrystalFamily] = {
'aP': 'triclinic',
'mP': 'monoclinic',
@ -27,63 +28,60 @@ lattice_symmetries: Dict[BravaisLattice, CrystalFamily] = {
'cF': 'cubic',
}
orientation_relationships: Dict[str, Dict[BravaisLattice,np.ndarray]] = {
'KS': {
'cF': np.array([
[[-1, 0, 1],[ 1, 1, 1]],
orientation_relationships: Dict[str, Dict[str,List[np.ndarray]]] = {
'KS': { # https://doi.org/10.1016/j.jallcom.2012.02.004
'cF-->cI' : [
np.repeat(np.array([
[[-1, 0, 1],[ 1, 1, 1]],
[[ 0, 1,-1],[ 1, 1, 1]],
[[ 0, 1,-1],[ 1, 1, 1]],
[[ 1,-1, 0],[ 1, 1, 1]],
[[ 1,-1, 0],[ 1, 1, 1]],
[[ 1, 0,-1],[ 1,-1, 1]],
[[ 1, 0,-1],[ 1,-1, 1]],
[[-1,-1, 0],[ 1,-1, 1]],
[[-1,-1, 0],[ 1,-1, 1]],
[[ 0, 1, 1],[ 1,-1, 1]],
[[ 0, 1, 1],[ 1,-1, 1]],
[[ 0,-1, 1],[-1, 1, 1]],
[[ 0,-1, 1],[-1, 1, 1]],
[[-1, 0,-1],[-1, 1, 1]],
[[-1, 0,-1],[-1, 1, 1]],
[[ 1, 1, 0],[-1, 1, 1]],
[[ 1, 1, 0],[-1, 1, 1]],
[[-1, 1, 0],[ 1, 1,-1]],
[[-1, 1, 0],[ 1, 1,-1]],
[[ 0,-1,-1],[ 1, 1,-1]],
[[ 0,-1,-1],[ 1, 1,-1]],
[[ 1, 0, 1],[ 1, 1,-1]],
[[ 1, 0, 1],[ 1, 1,-1]],
],dtype=float),
'cI': np.array([
[[-1,-1, 1],[ 0, 1, 1]],
[[-1, 1,-1],[ 0, 1, 1]],
[[-1,-1, 1],[ 0, 1, 1]],
[[-1, 1,-1],[ 0, 1, 1]],
[[-1,-1, 1],[ 0, 1, 1]],
[[-1, 1,-1],[ 0, 1, 1]],
[[-1,-1, 1],[ 0, 1, 1]],
[[-1, 1,-1],[ 0, 1, 1]],
[[-1,-1, 1],[ 0, 1, 1]],
[[-1, 1,-1],[ 0, 1, 1]],
[[-1,-1, 1],[ 0, 1, 1]],
[[-1, 1,-1],[ 0, 1, 1]],
[[-1,-1, 1],[ 0, 1, 1]],
[[-1, 1,-1],[ 0, 1, 1]],
[[-1,-1, 1],[ 0, 1, 1]],
[[-1, 1,-1],[ 0, 1, 1]],
[[-1,-1, 1],[ 0, 1, 1]],
[[-1, 1,-1],[ 0, 1, 1]],
[[-1,-1, 1],[ 0, 1, 1]],
[[-1, 1,-1],[ 0, 1, 1]],
[[-1,-1, 1],[ 0, 1, 1]],
[[-1, 1,-1],[ 0, 1, 1]],
[[-1,-1, 1],[ 0, 1, 1]],
[[-1, 1,-1],[ 0, 1, 1]],
2,axis=0),
np.tile(np.array([[[-1,-1, 1],[ 0, 1, 1]],
[[-1, 1,-1],[ 0, 1, 1]]],dtype=float),
(12,1,1)),
],
'cI-->cF' : [
np.repeat(np.array([
[[ 1, 1,-1],[ 0, 1, 1]],
[[ 1,-1, 1],[ 0, 1, 1]],
[[ 1, 1, 1],[ 0, 1,-1]],
[[-1, 1, 1],[ 0, 1,-1]],
[[ 1, 1,-1],[ 1, 0, 1]],
[[ 1,-1,-1],[ 1, 0, 1]],
[[ 1, 1, 1],[ 1, 0,-1]],
[[ 1,-1, 1],[ 1, 0,-1]],
[[ 1,-1, 1],[ 1, 1, 0]],
[[ 1,-1,-1],[ 1, 1, 0]],
[[ 1, 1, 1],[ 1,-1, 0]],
[[ 1, 1,-1],[ 1,-1, 0]],
],dtype=float),
2,axis=0),
np.tile(np.array([[[ 0, 1,-1],[ 1, 1, 1]],
[[ 0,-1, 1],[ 1, 1, 1]]],dtype=float),
(12,1,1)),
],
},
'GT': {
'cF': np.array([
'GT': { # https://doi.org/10.1107/S0021889805038276
'cF-->cI' : [
np.array([
[[ -5,-12, 17],[ 1, 1, 1]],
[[ 17, -5,-12],[ 1, 1, 1]],
[[-12, 17, -5],[ 1, 1, 1]],
@ -109,7 +107,7 @@ orientation_relationships: Dict[str, Dict[BravaisLattice,np.ndarray]] = {
[[ 12, -5,-17],[ 1, -1, 1]],
[[-17,-12, 5],[ 1, -1, 1]],
],dtype=float),
'cI': np.array([
np.array([
[[-17, -7, 17],[ 1, 0, 1]],
[[ 17,-17, -7],[ 1, 1, 0]],
[[ -7, 17,-17],[ 0, 1, 1]],
@ -135,9 +133,65 @@ orientation_relationships: Dict[str, Dict[BravaisLattice,np.ndarray]] = {
[[ 7,-17,-17],[ 0, -1, 1]],
[[-17, -7, 17],[ 1, 0, 1]],
],dtype=float),
],
'cI-->cF' : [
np.array([
[[-17, -7, 17],[ 1, 0, 1]],
[[ 17,-17, -7],[ 1, 1, 0]],
[[ -7, 17,-17],[ 0, 1, 1]],
[[ 17, 7, 17],[ -1, 0, 1]],
[[-17, 17, -7],[ -1, -1, 0]],
[[ 7,-17,-17],[ 0, -1, 1]],
[[-17, 7,-17],[ -1, 0, 1]],
[[ 17, 17, 7],[ -1, 1, 0]],
[[ -7,-17, 17],[ 0, 1, 1]],
[[ 17, -7,-17],[ 1, 0, 1]],
[[-17,-17, 7],[ 1, -1, 0]],
[[ 7, 17, 17],[ 0, -1, 1]],
[[-17, 17, -7],[ 1, 1, 0]],
[[ -7,-17, 17],[ 0, 1, 1]],
[[ 17, -7,-17],[ 1, 0, 1]],
[[ 17,-17, -7],[ -1, -1, 0]],
[[ 7, 17, 17],[ 0, -1, 1]],
[[-17, 7,-17],[ -1, 0, 1]],
[[-17,-17, 7],[ -1, 1, 0]],
[[ -7, 17,-17],[ 0, 1, 1]],
[[ 17, 7, 17],[ -1, 0, 1]],
[[ 17, 17, 7],[ 1, -1, 0]],
[[ 7,-17,-17],[ 0, -1, 1]],
[[-17, -7, 17],[ 1, 0, 1]],
],dtype=float),
np.array([
[[ -5,-12, 17],[ 1, 1, 1]],
[[ 17, -5,-12],[ 1, 1, 1]],
[[-12, 17, -5],[ 1, 1, 1]],
[[ 5, 12, 17],[ -1, -1, 1]],
[[-17, 5,-12],[ -1, -1, 1]],
[[ 12,-17, -5],[ -1, -1, 1]],
[[ -5, 12,-17],[ -1, 1, 1]],
[[ 17, 5, 12],[ -1, 1, 1]],
[[-12,-17, 5],[ -1, 1, 1]],
[[ 5,-12,-17],[ 1, -1, 1]],
[[-17, -5, 12],[ 1, -1, 1]],
[[ 12, 17, 5],[ 1, -1, 1]],
[[ -5, 17,-12],[ 1, 1, 1]],
[[-12, -5, 17],[ 1, 1, 1]],
[[ 17,-12, -5],[ 1, 1, 1]],
[[ 5,-17,-12],[ -1, -1, 1]],
[[ 12, 5, 17],[ -1, -1, 1]],
[[-17, 12, -5],[ -1, -1, 1]],
[[ -5,-17, 12],[ -1, 1, 1]],
[[-12, 5,-17],[ -1, 1, 1]],
[[ 17, 12, 5],[ -1, 1, 1]],
[[ 5, 17, 12],[ 1, -1, 1]],
[[ 12, -5,-17],[ 1, -1, 1]],
[[-17,-12, 5],[ 1, -1, 1]],
],dtype=float),
],
},
'GT_prime': {
'cF' : np.array([
'GT_prime': { # https://doi.org/10.1107/S0021889805038276
'cF-->cI' : [
np.array([
[[ 0, 1, -1],[ 7, 17, 17]],
[[ -1, 0, 1],[ 17, 7, 17]],
[[ 1, -1, 0],[ 17, 17, 7]],
@ -163,7 +217,7 @@ orientation_relationships: Dict[str, Dict[BravaisLattice,np.ndarray]] = {
[[ 1, 0, -1],[-17, 7,-17]],
[[ 1, 1, 0],[-17, 17, -7]],
],dtype=float),
'cI' : np.array([
np.array([
[[ 1, 1, -1],[ 12, 5, 17]],
[[ -1, 1, 1],[ 17, 12, 5]],
[[ 1, -1, 1],[ 5, 17, 12]],
@ -189,114 +243,191 @@ orientation_relationships: Dict[str, Dict[BravaisLattice,np.ndarray]] = {
[[ 1, -1, -1],[ -5, 12,-17]],
[[ 1, 1, -1],[-17, 5,-12]],
],dtype=float),
},
'NW': {
'cF' : np.array([
[[ 2, -1, -1],[ 1, 1, 1]],
[[ -1, 2, -1],[ 1, 1, 1]],
[[ -1, -1, 2],[ 1, 1, 1]],
[[ -2, -1, -1],[ -1, 1, 1]],
[[ 1, 2, -1],[ -1, 1, 1]],
[[ 1, -1, 2],[ -1, 1, 1]],
[[ 2, 1, -1],[ 1, -1, 1]],
[[ -1, -2, -1],[ 1, -1, 1]],
[[ -1, 1, 2],[ 1, -1, 1]],
[[ 2, -1, 1],[ -1, -1, 1]],
[[ -1, 2, 1],[ -1, -1, 1]],
[[ -1, -1, -2],[ -1, -1, 1]],
],
'cI-->cF' : [
np.array([
[[ 1, 1, -1],[ 12, 5, 17]],
[[ -1, 1, 1],[ 17, 12, 5]],
[[ 1, -1, 1],[ 5, 17, 12]],
[[ -1, -1, -1],[-12, -5, 17]],
[[ 1, -1, 1],[-17,-12, 5]],
[[ 1, -1, -1],[ -5,-17, 12]],
[[ -1, 1, -1],[ 12, -5,-17]],
[[ 1, 1, 1],[ 17,-12, -5]],
[[ -1, -1, 1],[ 5,-17,-12]],
[[ 1, -1, -1],[-12, 5,-17]],
[[ -1, -1, 1],[-17, 12, -5]],
[[ -1, -1, -1],[ -5, 17,-12]],
[[ 1, -1, 1],[ 12, 17, 5]],
[[ 1, 1, -1],[ 5, 12, 17]],
[[ -1, 1, 1],[ 17, 5, 12]],
[[ -1, 1, 1],[-12,-17, 5]],
[[ -1, -1, -1],[ -5,-12, 17]],
[[ -1, 1, -1],[-17, -5, 12]],
[[ -1, -1, 1],[ 12,-17, -5]],
[[ -1, 1, -1],[ 5,-12,-17]],
[[ 1, 1, 1],[ 17, -5,-12]],
[[ 1, 1, 1],[-12, 17, -5]],
[[ 1, -1, -1],[ -5, 12,-17]],
[[ 1, 1, -1],[-17, 5,-12]],
],dtype=float),
'cI' : np.array([
[[ 0, -1, 1],[ 0, 1, 1]],
[[ 0, -1, 1],[ 0, 1, 1]],
[[ 0, -1, 1],[ 0, 1, 1]],
[[ 0, -1, 1],[ 0, 1, 1]],
[[ 0, -1, 1],[ 0, 1, 1]],
[[ 0, -1, 1],[ 0, 1, 1]],
[[ 0, -1, 1],[ 0, 1, 1]],
[[ 0, -1, 1],[ 0, 1, 1]],
[[ 0, -1, 1],[ 0, 1, 1]],
[[ 0, -1, 1],[ 0, 1, 1]],
[[ 0, -1, 1],[ 0, 1, 1]],
[[ 0, -1, 1],[ 0, 1, 1]],
np.array([
[[ 0, 1, -1],[ 7, 17, 17]],
[[ -1, 0, 1],[ 17, 7, 17]],
[[ 1, -1, 0],[ 17, 17, 7]],
[[ 0, -1, -1],[ -7,-17, 17]],
[[ 1, 0, 1],[-17, -7, 17]],
[[ 1, -1, 0],[-17,-17, 7]],
[[ 0, 1, -1],[ 7,-17,-17]],
[[ 1, 0, 1],[ 17, -7,-17]],
[[ -1, -1, 0],[ 17,-17, -7]],
[[ 0, -1, -1],[ -7, 17,-17]],
[[ -1, 0, 1],[-17, 7,-17]],
[[ -1, -1, 0],[-17, 17, -7]],
[[ 0, -1, 1],[ 7, 17, 17]],
[[ 1, 0, -1],[ 17, 7, 17]],
[[ -1, 1, 0],[ 17, 17, 7]],
[[ 0, 1, 1],[ -7,-17, 17]],
[[ -1, 0, -1],[-17, -7, 17]],
[[ -1, 1, 0],[-17,-17, 7]],
[[ 0, -1, 1],[ 7,-17,-17]],
[[ -1, 0, -1],[ 17, -7,-17]],
[[ 1, 1, 0],[ 17,-17, -7]],
[[ 0, 1, 1],[ -7, 17,-17]],
[[ 1, 0, -1],[-17, 7,-17]],
[[ 1, 1, 0],[-17, 17, -7]],
],dtype=float),
],
},
'Pitsch': {
'cF' : np.array([
[[ 1, 0, 1],[ 0, 1, 0]],
[[ 1, 1, 0],[ 0, 0, 1]],
[[ 0, 1, 1],[ 1, 0, 0]],
[[ 0, 1, -1],[ 1, 0, 0]],
[[ -1, 0, 1],[ 0, 1, 0]],
[[ 1, -1, 0],[ 0, 0, 1]],
[[ 1, 0, -1],[ 0, 1, 0]],
[[ -1, 1, 0],[ 0, 0, 1]],
[[ 0, -1, 1],[ 1, 0, 0]],
'NW': { # https://doi.org/10.1016/j.matchar.2004.12.015
'cF-->cI' : [
np.array([
[[ 2,-1,-1],[ 1, 1, 1]],
[[-1, 2,-1],[ 1, 1, 1]],
[[-1,-1, 2],[ 1, 1, 1]],
[[-2,-1,-1],[-1, 1, 1]],
[[ 1, 2,-1],[-1, 1, 1]],
[[ 1,-1, 2],[-1, 1, 1]],
[[ 2, 1,-1],[ 1,-1, 1]],
[[-1,-2,-1],[ 1,-1, 1]],
[[-1, 1, 2],[ 1,-1, 1]],
[[ 2,-1, 1],[ 1, 1,-1]],
[[-1, 2, 1],[ 1, 1,-1]],
[[-1,-1,-2],[ 1, 1,-1]],
],dtype=float),
np.broadcast_to(np.array([[ 0,-1, 1],[ 0, 1, 1]],dtype=float),
(12,2,3)),
],
'cI-->cF' : [
np.repeat(np.array([
[[ 0, 1,-1],[ 0, 1, 1]],
[[ 0, 1, 1],[ 0, 1,-1]],
[[ 1, 0,-1],[ 1, 0, 1]],
[[ 1, 0, 1],[ 1, 0,-1]],
[[ 1,-1, 0],[ 1, 1, 0]],
[[ 1, 1, 0],[ 1,-1, 0]],
],dtype=float),
2,axis=0),
np.tile(np.array([
[[ 2,-1,-1],[ 1, 1, 1]],
[[-2, 1, 1],[ 1, 1, 1]],
],dtype=float),
(6,1,1)),
],
},
'Pitsch': { # https://doi.org/10.1080/14786435908238253
'cF-->cI' : [
np.repeat(np.array([
[[ 0, 1, 1],[ 1, 0, 0]],
[[ 0, 1,-1],[ 1, 0, 0]],
[[ 1, 0, 1],[ 0, 1, 0]],
[[ 1, 0,-1],[ 0, 1, 0]],
[[ 1, 1, 0],[ 0, 0, 1]],
[[ 1,-1, 0],[ 0, 0, 1]],
],dtype=float),
'cI' : np.array([
[[ 1, -1, 1],[ -1, 0, 1]],
[[ 1, 1, -1],[ 1, -1, 0]],
[[ -1, 1, 1],[ 0, 1, -1]],
[[ -1, 1, -1],[ 0, -1, -1]],
[[ -1, -1, 1],[ -1, 0, -1]],
[[ 1, -1, -1],[ -1, -1, 0]],
[[ 1, -1, -1],[ -1, 0, -1]],
[[ -1, 1, -1],[ -1, -1, 0]],
[[ -1, -1, 1],[ 0, -1, -1]],
[[ -1, 1, 1],[ 0, -1, 1]],
[[ 1, -1, 1],[ 1, 0, -1]],
[[ 1, 1, -1],[ -1, 1, 0]],
2,axis=0),
np.tile(np.array([
[[ 1, 1,-1],[ 0, 1, 1]],
[[-1, 1,-1],[ 0, 1, 1]],
],dtype=float),
(6,1,1)),
],
'cI-->cF' : [
np.array([
[[ 1, 1,-1],[ 0, 1, 1]],
[[ 1,-1, 1],[ 0, 1, 1]],
[[ 1, 1, 1],[ 0, 1,-1]],
[[-1, 1, 1],[ 0, 1,-1]],
[[ 1, 1,-1],[ 1, 0, 1]],
[[ 1,-1,-1],[ 1, 0, 1]],
[[ 1, 1, 1],[ 1, 0,-1]],
[[ 1,-1, 1],[ 1, 0,-1]],
[[ 1,-1, 1],[ 1, 1, 0]],
[[ 1,-1,-1],[ 1, 1, 0]],
[[ 1, 1, 1],[ 1,-1, 0]],
[[ 1, 1,-1],[ 1,-1, 0]],
],dtype=float),
np.broadcast_to(np.array([[ 1, 1, 0],[ 0, 0, 1]],dtype=float),
(12,2,3)),
],
},
'Bain': {
'cF' : np.array([
'Bain': { # https://doi.org/10.1107/S0021889805038276
'cF-->cI' : [
np.array([
[[ 0, 1, 0],[ 1, 0, 0]],
[[ 0, 0, 1],[ 0, 1, 0]],
[[ 1, 0, 0],[ 0, 0, 1]],
],dtype=float),
'cI' : np.array([
np.broadcast_to(np.array([[ 1, 1, 0],[ 0, 0, 1]],dtype=float),
(3,2,3)),
],
'cI-->cF' : [
np.array([
[[ 0, 1, 1],[ 1, 0, 0]],
[[ 1, 0, 1],[ 0, 1, 0]],
[[ 1, 1, 0],[ 0, 0, 1]],
],dtype=float),
np.broadcast_to(np.array([[ 1, 0, 0],[ 0, 0, 1]],dtype=float),
(3,2,3)),
]
},
'Burgers' : {
'cI' : np.array([
[[ -1, 1, 1],[ 1, 1, 0]],
[[ -1, 1, -1],[ 1, 1, 0]],
[[ 1, 1, 1],[ 1, -1, 0]],
[[ 1, 1, -1],[ 1, -1, 0]],
[[ 1, 1, -1],[ 1, 0, 1]],
[[ -1, 1, 1],[ 1, 0, 1]],
[[ 1, 1, 1],[ -1, 0, 1]],
[[ 1, -1, 1],[ -1, 0, 1]],
[[ -1, 1, -1],[ 0, 1, 1]],
[[ 1, 1, -1],[ 0, 1, 1]],
[[ -1, 1, 1],[ 0, -1, 1]],
[[ 1, 1, 1],[ 0, -1, 1]],
'Burgers' : { # https://doi.org/10.1016/S0031-8914(34)80244-3
'cI-->hP' : [
np.array([
[[ 1, 1,-1],[ 0, 1, 1]],
[[ 1,-1, 1],[ 0, 1, 1]],
[[ 1, 1, 1],[ 0, 1,-1]],
[[-1, 1, 1],[ 0, 1,-1]],
[[ 1, 1,-1],[ 1, 0, 1]],
[[ 1,-1,-1],[ 1, 0, 1]],
[[ 1, 1, 1],[ 1, 0,-1]],
[[ 1,-1, 1],[ 1, 0,-1]],
[[ 1,-1, 1],[ 1, 1, 0]],
[[ 1,-1,-1],[ 1, 1, 0]],
[[ 1, 1, 1],[ 1,-1, 0]],
[[ 1, 1,-1],[ 1,-1, 0]],
],dtype=float),
'hP' : np.array([
[[ -1, 2, -1, 0],[ 0, 0, 0, 1]],
[[ -1, -1, 2, 0],[ 0, 0, 0, 1]],
[[ -1, 2, -1, 0],[ 0, 0, 0, 1]],
[[ -1, -1, 2, 0],[ 0, 0, 0, 1]],
[[ -1, 2, -1, 0],[ 0, 0, 0, 1]],
[[ -1, -1, 2, 0],[ 0, 0, 0, 1]],
[[ -1, 2, -1, 0],[ 0, 0, 0, 1]],
[[ -1, -1, 2, 0],[ 0, 0, 0, 1]],
[[ -1, 2, -1, 0],[ 0, 0, 0, 1]],
[[ -1, -1, 2, 0],[ 0, 0, 0, 1]],
[[ -1, 2, -1, 0],[ 0, 0, 0, 1]],
[[ -1, -1, 2, 0],[ 0, 0, 0, 1]],
np.broadcast_to(np.array([[ 2,-1,-1, 0],[ 0, 0, 0, 1]],dtype=float),
(12,2,4)),
],
'hP-->cI' : [
np.repeat(np.array([
[[ 2,-1,-1, 0],[ 0, 0, 0, 1]],
[[-1, 2,-1, 0],[ 0, 0, 0, 1]],
[[-1,-1, 2, 0],[ 0, 0, 0, 1]],
],dtype=float),
2,axis=0),
np.tile(np.array([
[[ 1, 1,-1],[ 0, 1, 1]],
[[-1, 1,-1],[ 0, 1, 1]],
],dtype=float),
(3,1,1)),
]
},
}
}
class Crystal():
"""
@ -428,20 +559,20 @@ class Crystal():
Crystal to check for equality.
"""
return NotImplemented if not isinstance(other, Crystal) else \
self.lattice == other.lattice and \
self.parameters == other.parameters and \
self.family == other.family
return (NotImplemented if not isinstance(other, Crystal) else
self.lattice == other.lattice and
self.parameters == other.parameters and
self.family == other.family) # type: ignore
@property
def parameters(self):
def parameters(self) -> Optional[Tuple]:
"""Return lattice parameters a, b, c, alpha, beta, gamma."""
if hasattr(self,'a'): return (self.a,self.b,self.c,self.alpha,self.beta,self.gamma)
return (self.a,self.b,self.c,self.alpha,self.beta,self.gamma) if hasattr(self,'a') else None
@property
def immutable(self):
def immutable(self) -> Dict[str, float]:
"""Return immutable lattice parameters."""
_immutable = {
_immutable: Dict[CrystalFamily, Dict[str,float]] = {
'cubic': {
'b': 1.0,
'c': 1.0,
@ -476,9 +607,9 @@ class Crystal():
@property
def orientation_relationships(self):
def orientation_relationships(self) -> List[str]:
"""Return labels of orientation relationships."""
return [k for k,v in orientation_relationships.items() if self.lattice in v]
return [k for k,v in orientation_relationships.items() if np.any([m.startswith(str(self.lattice)) for m in v])]
@property
@ -671,9 +802,9 @@ class Crystal():
@property
def lattice_points(self):
def lattice_points(self) -> np.ndarray:
"""Return lattice points."""
_lattice_points = {
_lattice_points: Dict[str, List] = {
'P': [
],
'S': [
@ -694,8 +825,8 @@ class Crystal():
if self.lattice is None: raise KeyError('no lattice type specified')
return np.array([[0,0,0]]
+ _lattice_points.get(self.lattice if self.lattice == 'hP' else \
self.lattice[-1],None),dtype=float)
+ _lattice_points.get(self.lattice if self.lattice == 'hP' else
self.lattice[-1],[]),dtype=float)
def to_lattice(self, *,
direction: Optional[FloatSequence] = None,
@ -753,7 +884,7 @@ class Crystal():
Crystal frame vector (reciprocal space) of Titanium along (1,0,0) plane normal:
>>> import damask
>>> Ti = damask.Crystal(lattice='hP', a=0.295e-9, c=0.469e-9)
>>> Ti = damask.Crystal(lattice='hP', a=295e-12, c=469e-12)
>>> Ti.to_frame(hkl=(1, 0, 0))
array([ 3.38983051e+09, 1.95711956e+09, -4.15134508e-07])
@ -782,7 +913,7 @@ class Crystal():
Directions and planes of deformation mode families.
"""
_kinematics: Dict[BravaisLattice, Dict[CrystalKinematics, List[np.ndarray]]] = {
_kinematics: Dict[Optional[BravaisLattice], Dict[CrystalKinematics, List[np.ndarray]]] = {
'cF': {
'slip': [np.array([
[ 0,+1,-1, +1,+1,+1],
@ -1025,7 +1156,8 @@ class Crystal():
def relation_operations(self,
model: str) -> Tuple[BravaisLattice, Rotation]:
model: str,
target = None) -> Tuple[BravaisLattice, Rotation]:
"""
Crystallographic orientation relationships for phase transformations.
@ -1033,6 +1165,10 @@ class Crystal():
----------
model : str
Name of orientation relationship.
target : Crystal, optional
Crystal to transform to.
Providing this parameter allows specification of non-standard lattice parameters.
Default is inferred from selected model and uses standard lattice parameters.
Returns
-------
@ -1057,20 +1193,27 @@ class Crystal():
https://doi.org/10.1016/j.actamat.2004.11.021
"""
my_relationships = {k:v for k,v in orientation_relationships.items() if self.lattice in v}
if model not in my_relationships:
m_l: BravaisLattice
o_l: BravaisLattice
if model not in self.orientation_relationships:
raise KeyError(f'unknown orientation relationship "{model}"')
r = my_relationships[model]
sl = self.lattice
ol = (set(r)-{sl}).pop()
m = r[sl]
o = r[ol]
sep = '-->'
search = self.lattice+sep+('' if target is None else target.lattice) # type: ignore
transform = [t for t in orientation_relationships[model].keys() if t.startswith(search)] # type: ignore
p_,_p = np.zeros(m.shape[:-1]+(3,)),np.zeros(o.shape[:-1]+(3,))
p_[...,0,:] = m[...,0,:] if m.shape[-1] == 3 else util.Bravais_to_Miller(uvtw=m[...,0,0:4])
p_[...,1,:] = m[...,1,:] if m.shape[-1] == 3 else util.Bravais_to_Miller(hkil=m[...,1,0:4])
_p[...,0,:] = o[...,0,:] if o.shape[-1] == 3 else util.Bravais_to_Miller(uvtw=o[...,0,0:4])
_p[...,1,:] = o[...,1,:] if o.shape[-1] == 3 else util.Bravais_to_Miller(hkil=o[...,1,0:4])
if len(transform) != 1:
raise ValueError(f'invalid target lattice "{search.split(sep)[1]}"')
return (ol,Rotation.from_parallel(p_,_p))
m_l,o_l = transform[0].split(sep) # type: ignore
m_p,o_p = orientation_relationships[model][m_l+sep+o_l]
other = Crystal(lattice=o_l) if target is None else target
m_p = np.stack((self.to_frame(uvw=m_p[:,0] if len(m_p[0,0])==3 else util.Bravais_to_Miller(uvtw=m_p[:,0])),
self.to_frame(hkl=m_p[:,1] if len(m_p[0,1])==3 else util.Bravais_to_Miller(hkil=m_p[:,1]))),
axis=1)
o_p = np.stack((other.to_frame(uvw=o_p[:,0] if len(o_p[0,0])==3 else util.Bravais_to_Miller(uvtw=o_p[:,0])),
other.to_frame(hkl=o_p[:,1] if len(o_p[0,1])==3 else util.Bravais_to_Miller(hkil=o_p[:,1]))),
axis=1)
return (o_l,Rotation.from_parallel(a=m_p,b=o_p))

View File

@ -28,7 +28,7 @@ def numba_njit_wrapper(**kwargs):
return (lambda function: nb.njit(function) if nb else function)
class Grid:
class GeomGrid:
"""
Geometry definition for grid solvers.
@ -89,7 +89,7 @@ class Grid:
]+(['initial_conditions:']+[f' - {f}' for f in self.initial_conditions] if self.initial_conditions else []))
def __copy__(self) -> 'Grid':
def __copy__(self) -> 'GeomGrid':
"""
Return deepcopy(self).
@ -110,11 +110,11 @@ class Grid:
Parameters
----------
other : damask.Grid
Grid to compare self against.
other : damask.GeomGrid
GeomGrid to compare self against.
"""
if not isinstance(other, Grid):
if not isinstance(other, GeomGrid):
return NotImplemented
return bool( np.allclose(other.size,self.size)
and np.allclose(other.origin,self.origin)
@ -197,38 +197,84 @@ class Grid:
@staticmethod
def load(fname: Union[str, Path]) -> 'Grid':
def _load(fname: Union[str, Path], label: str) -> 'GeomGrid':
"""
Load from VTK ImageData file.
Parameters
----------
fname : str or pathlib.Path
Grid file to read.
VTK ImageData file to read.
Valid extension is .vti, which will be appended if not given.
label : str
Label of the dataset containing the material IDs.
Returns
-------
loaded : damask.Grid
Grid-based geometry from file.
loaded : damask.GeomGrid
GeomGrid-based geometry from file.
"""
v = VTK.load(fname if str(fname).endswith('.vti') else str(fname)+'.vti')
cells = np.array(v.vtk_data.GetDimensions())-1
bbox = np.array(v.vtk_data.GetBounds()).reshape(3,2).T
ic = {label:v.get(label).reshape(cells,order='F') for label in set(v.labels['Cell Data']) - {'material'}}
ic = {l:v.get(l).reshape(cells,order='F') for l in set(v.labels['Cell Data']) - {label}}
return Grid(material = v.get('material').reshape(cells,order='F'),
return GeomGrid(material = v.get(label).reshape(cells,order='F'),
size = bbox[1] - bbox[0],
origin = bbox[0],
initial_conditions = ic,
comments = v.comments,
)
@staticmethod
def load(fname: Union[str, Path]) -> 'GeomGrid':
"""
Load from VTK ImageData file with material IDs stored as 'material'.
Parameters
----------
fname : str or pathlib.Path
GeomGrid file to read.
Valid extension is .vti, which will be appended if not given.
Returns
-------
loaded : damask.GeomGrid
GeomGrid-based geometry from file.
"""
return GeomGrid._load(fname,'material')
@staticmethod
def load_SPPARKS(fname: Union[str, Path]) -> 'GeomGrid':
"""
Load from SPPARKS VTK dump.
Parameters
----------
fname : str or pathlib.Path
SPPARKS VTK dump file to read.
Valid extension is .vti, which will be appended if not given.
Returns
-------
loaded : damask.GeomGrid
GeomGrid-based geometry from file.
Notes
-----
A SPPARKS VTI dump is equivalent to a DAMASK VTI file,
but stores the materialID information as 'Spin' rather than 'material'.
"""
return GeomGrid._load(fname,'Spin')
@typing.no_type_check
@staticmethod
def load_ASCII(fname)-> 'Grid':
def load_ASCII(fname)-> 'GeomGrid':
"""
Load from geom file.
@ -242,8 +288,8 @@ class Grid:
Returns
-------
loaded : damask.Grid
Grid-based geometry from file.
loaded : damask.GeomGrid
GeomGrid-based geometry from file.
"""
warnings.warn('Support for ASCII-based geom format will be removed in DAMASK 3.0.0', DeprecationWarning,2)
@ -296,14 +342,15 @@ class Grid:
if not np.any(np.mod(material,1) != 0.0): # no float present
material = material.astype(np.int64) - (1 if material.min() > 0 else 0)
return Grid(material = material.reshape(cells,order='F'),
return GeomGrid(material = material.reshape(cells,order='F'),
size = size,
origin = origin,
comments = comments)
comments = comments,
)
@staticmethod
def load_Neper(fname: Union[str, Path]) -> 'Grid':
def load_Neper(fname: Union[str, Path]) -> 'GeomGrid':
"""
Load from Neper VTK file.
@ -314,8 +361,8 @@ class Grid:
Returns
-------
loaded : damask.Grid
Grid-based geometry from file.
loaded : damask.GeomGrid
GeomGrid-based geometry from file.
Notes
-----
@ -330,7 +377,7 @@ class Grid:
>>> N_grains = 20
>>> cells = (32,32,32)
>>> damask.util.run(f'neper -T -n {N_grains} -tesrsize {cells[0]}:{cells[1]}:{cells[2]} -periodicity all -format vtk')
>>> damask.Grid.load_Neper(f'n{N_grains}-id1.vtk').renumber()
>>> damask.GeomGrid.load_Neper(f'n{N_grains}-id1.vtk').renumber()
cells: 32 × 32 × 32
size: 1.0 × 1.0 × 1.0
origin: 0.0 0.0 0.0 m
@ -341,10 +388,10 @@ class Grid:
cells = np.array(v.vtk_data.GetDimensions())-1
bbox = np.array(v.vtk_data.GetBounds()).reshape(3,2).T
return Grid(material = v.get('MaterialId').reshape(cells,order='F').astype('int32',casting='unsafe'),
return GeomGrid(material = v.get('MaterialId').reshape(cells,order='F').astype('int32',casting='unsafe'),
size = bbox[1] - bbox[0],
origin = bbox[0],
comments = util.execution_stamp('Grid','load_Neper'),
comments = util.execution_stamp('GeomGrid','load_Neper'),
)
@ -354,7 +401,7 @@ class Grid:
cell_data: Optional[str] = None,
phases: str = 'Phases',
Euler_angles: str = 'EulerAngles',
base_group: Optional[str] = None) -> 'Grid':
base_group: Optional[str] = None) -> 'GeomGrid':
"""
Load DREAM.3D (HDF5) file.
@ -389,8 +436,8 @@ class Grid:
Returns
-------
loaded : damask.Grid
Grid-based geometry from file.
loaded : damask.GeomGrid
GeomGrid-based geometry from file.
Notes
-----
@ -418,17 +465,17 @@ class Grid:
else:
ma = f['/'.join([b,c,feature_IDs])][()].flatten()
return Grid(material = ma.reshape(cells,order='F'),
return GeomGrid(material = ma.reshape(cells,order='F'),
size = size,
origin = origin,
comments = util.execution_stamp('Grid','load_DREAM3D'),
comments = util.execution_stamp('GeomGrid','load_DREAM3D'),
)
@staticmethod
def from_table(table: Table,
coordinates: str,
labels: Union[str, Sequence[str]]) -> 'Grid':
labels: Union[str, Sequence[str]]) -> 'GeomGrid':
"""
Create grid from ASCII table.
@ -445,8 +492,8 @@ class Grid:
Returns
-------
new : damask.Grid
Grid-based geometry from values in table.
new : damask.GeomGrid
GeomGrid-based geometry from values in table.
"""
cells,size,origin = grid_filters.cellsSizeOrigin_coordinates0_point(table.get(coordinates))
@ -457,10 +504,10 @@ class Grid:
ma = np.arange(cells.prod()) if len(unique) == cells.prod() else \
np.arange(unique.size)[np.argsort(pd.unique(unique_inverse))][unique_inverse]
return Grid(material = ma.reshape(cells,order='F'),
return GeomGrid(material = ma.reshape(cells,order='F'),
size = size,
origin = origin,
comments = util.execution_stamp('Grid','from_table'),
comments = util.execution_stamp('GeomGrid','from_table'),
)
@ -487,9 +534,11 @@ class Grid:
size : sequence of float, len (3)
Edge lengths of the grid in meter.
seeds : numpy.ndarray of float, shape (:,3)
Position of the seed points in meter. All points need to lay within the box.
Position of the seed points in meter. All points need
to lay within the box [(0,0,0),size].
weights : sequence of float, len (seeds.shape[0])
Weights of the seeds. Setting all weights to 1.0 gives a standard Voronoi tessellation.
Weights of the seeds. Setting all weights to 1.0 gives a
standard Voronoi tessellation.
material : sequence of int, len (seeds.shape[0]), optional
Material ID of the seeds.
Defaults to None, in which case materials are consecutively numbered.
@ -498,8 +547,8 @@ class Grid:
Returns
-------
new : damask.Grid
Grid-based geometry from tessellation.
new : damask.GeomGrid
GeomGrid-based geometry from tessellation.
"""
weights_p: FloatSequence
@ -515,16 +564,16 @@ class Grid:
coords = grid_filters.coordinates0_point(cells,size).reshape(-1,3)
pool = mp.Pool(int(os.environ.get('OMP_NUM_THREADS',4)))
result = pool.map_async(partial(Grid._find_closest_seed,seeds_p,weights_p), coords)
result = pool.map_async(partial(GeomGrid._find_closest_seed,seeds_p,weights_p), coords)
pool.close()
pool.join()
material_ = np.array(result.get()).reshape(cells)
if periodic: material_ %= len(weights)
return Grid(material = material_ if material is None else np.array(material)[material_],
return GeomGrid(material = material_ if material is None else np.array(material)[material_],
size = size,
comments = util.execution_stamp('Grid','from_Laguerre_tessellation'),
comments = util.execution_stamp('GeomGrid','from_Laguerre_tessellation'),
)
@ -533,7 +582,7 @@ class Grid:
size: FloatSequence,
seeds: np.ndarray,
material: Optional[IntSequence] = None,
periodic: bool = True) -> 'Grid':
periodic: bool = True) -> 'GeomGrid':
"""
Create grid from Voronoi tessellation.
@ -544,7 +593,8 @@ class Grid:
size : sequence of float, len (3)
Edge lengths of the grid in meter.
seeds : numpy.ndarray of float, shape (:,3)
Position of the seed points in meter. All points need to lay within the box.
Position of the seed points in meter. All points need
to lay within the box [(0,0,0),size].
material : sequence of int, len (seeds.shape[0]), optional
Material ID of the seeds.
Defaults to None, in which case materials are consecutively numbered.
@ -553,8 +603,8 @@ class Grid:
Returns
-------
new : damask.Grid
Grid-based geometry from tessellation.
new : damask.GeomGrid
GeomGrid-based geometry from tessellation.
"""
coords = grid_filters.coordinates0_point(cells,size).reshape(-1,3)
@ -565,9 +615,9 @@ class Grid:
except TypeError:
material_ = tree.query(coords, n_jobs = int(os.environ.get('OMP_NUM_THREADS',4)))[1] # scipy <1.6
return Grid(material = (material_ if material is None else np.array(material)[material_]).reshape(cells),
return GeomGrid(material = (material_ if material is None else np.array(material)[material_]).reshape(cells),
size = size,
comments = util.execution_stamp('Grid','from_Voronoi_tessellation'),
comments = util.execution_stamp('GeomGrid','from_Voronoi_tessellation'),
)
@ -619,7 +669,7 @@ class Grid:
surface: str,
threshold: float = 0.0,
periods: int = 1,
materials: IntSequence = (0,1)) -> 'Grid':
materials: IntSequence = (0,1)) -> 'GeomGrid':
"""
Create grid from definition of triply-periodic minimal surface.
@ -640,8 +690,8 @@ class Grid:
Returns
-------
new : damask.Grid
Grid-based geometry from definition of minimal surface.
new : damask.GeomGrid
GeomGrid-based geometry from definition of minimal surface.
Notes
-----
@ -676,7 +726,7 @@ class Grid:
>>> import numpy as np
>>> import damask
>>> damask.Grid.from_minimal_surface([64]*3,np.ones(3)*1.e-4,'Gyroid')
>>> damask.GeomGrid.from_minimal_surface([64]*3,np.ones(3)*1.e-4,'Gyroid')
cells : 64 × 64 × 64
size : 0.0001 × 0.0001 × 0.0001
origin: 0.0 0.0 0.0 m
@ -686,7 +736,7 @@ class Grid:
>>> import numpy as np
>>> import damask
>>> damask.Grid.from_minimal_surface([80]*3,np.ones(3)*5.e-4,
>>> damask.GeomGrid.from_minimal_surface([80]*3,np.ones(3)*5.e-4,
... 'Neovius',materials=(1,5))
cells : 80 × 80 × 80
size : 0.0005 × 0.0005 × 0.0005
@ -698,9 +748,9 @@ class Grid:
periods*2.0*np.pi*(np.arange(cells[1])+0.5)/cells[1],
periods*2.0*np.pi*(np.arange(cells[2])+0.5)/cells[2],
indexing='ij',sparse=True)
return Grid(material = np.where(threshold < Grid._minimal_surface[surface](x,y,z),materials[1],materials[0]),
return GeomGrid(material = np.where(threshold < GeomGrid._minimal_surface[surface](x,y,z),materials[1],materials[0]),
size = size,
comments = util.execution_stamp('Grid','from_minimal_surface'),
comments = util.execution_stamp('GeomGrid','from_minimal_surface'),
)
@ -778,7 +828,7 @@ class Grid:
def canvas(self,
cells: Optional[IntSequence] = None,
offset: Optional[IntSequence] = None,
fill: Optional[int] = None) -> 'Grid':
fill: Optional[int] = None) -> 'GeomGrid':
"""
Crop or enlarge/pad grid.
@ -795,7 +845,7 @@ class Grid:
Returns
-------
updated : damask.Grid
updated : damask.GeomGrid
Updated grid-based geometry.
Examples
@ -804,7 +854,7 @@ class Grid:
>>> import numpy as np
>>> import damask
>>> g = damask.Grid(np.zeros([32]*3,int),np.ones(3)*1e-3)
>>> g = damask.GeomGrid(np.zeros([32]*3,int),np.ones(3)*1e-3)
>>> g.canvas([32,32,16],[0,0,16])
cells: 32 × 32 × 16
size: 0.001 × 0.001 × 0.0005
@ -824,16 +874,16 @@ class Grid:
canvas[ll[0]:ur[0],ll[1]:ur[1],ll[2]:ur[2]] = self.material[LL[0]:UR[0],LL[1]:UR[1],LL[2]:UR[2]]
return Grid(material = canvas,
return GeomGrid(material = canvas,
size = self.size/self.cells*np.asarray(canvas.shape),
origin = self.origin+offset_*self.size/self.cells,
comments = self.comments+[util.execution_stamp('Grid','canvas')],
comments = self.comments+[util.execution_stamp('GeomGrid','canvas')],
)
def mirror(self,
directions: Sequence[str],
reflect: bool = False) -> 'Grid':
reflect: bool = False) -> 'GeomGrid':
"""
Mirror grid along given directions.
@ -846,7 +896,7 @@ class Grid:
Returns
-------
updated : damask.Grid
updated : damask.GeomGrid
Updated grid-based geometry.
Examples
@ -855,7 +905,7 @@ class Grid:
>>> import numpy as np
>>> import damask
>>> (g := damask.Grid(np.arange(4*5*6).reshape([4,5,6]),np.ones(3)))
>>> (g := damask.GeomGrid(np.arange(4*5*6).reshape([4,5,6]),np.ones(3)))
cells: 4 × 5 × 6
size: 1.0 × 1.0 × 1.0
origin: 0.0 0.0 0.0 m
@ -893,15 +943,15 @@ class Grid:
if 'z' in directions:
mat = np.concatenate([mat,mat[:,:,limits[0]:limits[1]:-1]],2)
return Grid(material = mat,
return GeomGrid(material = mat,
size = self.size/self.cells*np.asarray(mat.shape),
origin = self.origin,
comments = self.comments+[util.execution_stamp('Grid','mirror')],
comments = self.comments+[util.execution_stamp('GeomGrid','mirror')],
)
def flip(self,
directions: Sequence[str]) -> 'Grid':
directions: Sequence[str]) -> 'GeomGrid':
"""
Flip grid along given directions.
@ -912,7 +962,7 @@ class Grid:
Returns
-------
updated : damask.Grid
updated : damask.GeomGrid
Updated grid-based geometry.
Examples
@ -921,7 +971,7 @@ class Grid:
>>> import numpy as np
>>> import damask
>>> (g := damask.Grid(np.arange(4*5*6).reshape([4,5,6]),np.ones(3)))
>>> (g := damask.GeomGrid(np.arange(4*5*6).reshape([4,5,6]),np.ones(3)))
cells: 4 × 5 × 6
size: 1.0 × 1.0 × 1.0
origin: 0.0 0.0 0.0 m
@ -940,16 +990,16 @@ class Grid:
mat = np.flip(self.material, [valid.index(d) for d in directions if d in valid])
return Grid(material = mat,
return GeomGrid(material = mat,
size = self.size,
origin = self.origin,
comments = self.comments+[util.execution_stamp('Grid','flip')],
comments = self.comments+[util.execution_stamp('GeomGrid','flip')],
)
def rotate(self,
R: Rotation,
fill: Optional[int] = None) -> 'Grid':
fill: Optional[int] = None) -> 'GeomGrid':
"""
Rotate grid (possibly extending its bounding box).
@ -963,7 +1013,7 @@ class Grid:
Returns
-------
updated : damask.Grid
updated : damask.GeomGrid
Updated grid-based geometry.
Examples
@ -972,7 +1022,7 @@ class Grid:
>>> import numpy as np
>>> import damask
>>> (g := damask.Grid(np.arange(4*5*6).reshape([4,5,6]),np.ones(3)))
>>> (g := damask.GeomGrid(np.arange(4*5*6).reshape([4,5,6]),np.ones(3)))
cells: 4 × 5 × 6
size: 1.0 × 1.0 × 1.0
origin: 0.0 0.0 0.0 m
@ -994,15 +1044,15 @@ class Grid:
origin = self.origin-(np.asarray(material.shape)-self.cells)*.5 * self.size/self.cells
return Grid(material = material,
return GeomGrid(material = material,
size = self.size/self.cells*np.asarray(material.shape),
origin = origin,
comments = self.comments+[util.execution_stamp('Grid','rotate')],
comments = self.comments+[util.execution_stamp('GeomGrid','rotate')],
)
def scale(self,
cells: IntSequence) -> 'Grid':
cells: IntSequence) -> 'GeomGrid':
"""
Scale grid to new cell counts.
@ -1013,7 +1063,7 @@ class Grid:
Returns
-------
updated : damask.Grid
updated : damask.GeomGrid
Updated grid-based geometry.
Examples
@ -1022,7 +1072,7 @@ class Grid:
>>> import numpy as np
>>> import damask
>>> (g := damask.Grid(np.zeros([32]*3,int),np.ones(3)*1e-4))
>>> (g := damask.GeomGrid(np.zeros([32]*3,int),np.ones(3)*1e-4))
cells: 32 × 32 × 32
size: 0.0001 × 0.0001 × 0.0001
origin: 0.0 0.0 0.0 m
@ -1040,28 +1090,28 @@ class Grid:
points=orig,method='nearest',bounds_error=False,fill_value=None)
new = grid_filters.coordinates0_point(cells,self.size,self.origin)
return Grid(material = interpolator(values=self.material)(new).astype(int),
return GeomGrid(material = interpolator(values=self.material)(new).astype(int),
size = self.size,
origin = self.origin,
initial_conditions = {k: interpolator(values=v)(new)
for k,v in self.initial_conditions.items()},
comments = self.comments+[util.execution_stamp('Grid','scale')],
comments = self.comments+[util.execution_stamp('GeomGrid','scale')],
)
def assemble(self,
idx: np.ndarray) -> 'Grid':
idx: np.ndarray) -> 'GeomGrid':
"""
Assemble new grid from index map.
Parameters
----------
idx : numpy.ndarray of int, shape (:,:,:) or (:,:,:,3)
Grid of flat indices or coordinate indices.
GeomGrid of flat indices or coordinate indices.
Returns
-------
updated : damask.Grid
updated : damask.GeomGrid
Updated grid-based geometry.
Cell count of resulting grid matches shape of index map.
@ -1070,37 +1120,37 @@ class Grid:
flat = (idx if len(idx.shape)==3 else grid_filters.ravel_index(idx)).flatten(order='F')
ic = {k: v.flatten(order='F')[flat].reshape(cells,order='F') for k,v in self.initial_conditions.items()}
return Grid(material = self.material.flatten(order='F')[flat].reshape(cells,order='F'),
return GeomGrid(material = self.material.flatten(order='F')[flat].reshape(cells,order='F'),
size = self.size,
origin = self.origin,
initial_conditions = ic,
comments = self.comments+[util.execution_stamp('Grid','assemble')],
comments = self.comments+[util.execution_stamp('GeomGrid','assemble')],
)
def renumber(self) -> 'Grid':
def renumber(self) -> 'GeomGrid':
"""
Renumber sorted material indices as 0,...,N-1.
Returns
-------
updated : damask.Grid
updated : damask.GeomGrid
Updated grid-based geometry.
"""
_,renumbered = np.unique(self.material,return_inverse=True)
return Grid(material = renumbered.reshape(self.cells),
return GeomGrid(material = renumbered.reshape(self.cells),
size = self.size,
origin = self.origin,
initial_conditions = self.initial_conditions,
comments = self.comments+[util.execution_stamp('Grid','renumber')],
comments = self.comments+[util.execution_stamp('GeomGrid','renumber')],
)
def substitute(self,
from_material: Union[int,IntSequence],
to_material: Union[int,IntSequence]) -> 'Grid':
to_material: Union[int,IntSequence]) -> 'GeomGrid':
"""
Substitute material indices.
@ -1113,7 +1163,7 @@ class Grid:
Returns
-------
updated : damask.Grid
updated : damask.GeomGrid
Updated grid-based geometry.
"""
@ -1122,21 +1172,21 @@ class Grid:
to_material if isinstance(to_material,(Sequence,np.ndarray)) else [to_material]): # ToDo Python 3.10 has strict mode for zip
material[self.material==f] = t
return Grid(material = material,
return GeomGrid(material = material,
size = self.size,
origin = self.origin,
initial_conditions = self.initial_conditions,
comments = self.comments+[util.execution_stamp('Grid','substitute')],
comments = self.comments+[util.execution_stamp('GeomGrid','substitute')],
)
def sort(self) -> 'Grid':
def sort(self) -> 'GeomGrid':
"""
Sort material indices such that min(material ID) is located at (0,0,0).
Returns
-------
updated : damask.Grid
updated : damask.GeomGrid
Updated grid-based geometry.
"""
@ -1145,11 +1195,11 @@ class Grid:
sort_idx = np.argsort(from_ma)
ma = np.unique(a)[sort_idx][np.searchsorted(from_ma,a,sorter = sort_idx)]
return Grid(material = ma.reshape(self.cells,order='F'),
return GeomGrid(material = ma.reshape(self.cells,order='F'),
size = self.size,
origin = self.origin,
initial_conditions = self.initial_conditions,
comments = self.comments+[util.execution_stamp('Grid','sort')],
comments = self.comments+[util.execution_stamp('GeomGrid','sort')],
)
@ -1158,7 +1208,7 @@ class Grid:
selection: Optional[IntSequence] = None,
invert_selection: bool = False,
periodic: bool = True,
rng_seed: Optional[NumpyRngSeed] = None) -> 'Grid':
rng_seed: Optional[NumpyRngSeed] = None) -> 'GeomGrid':
"""
Smooth grid by selecting most frequent material ID within given stencil at each location.
@ -1179,7 +1229,7 @@ class Grid:
Returns
-------
updated : damask.Grid
updated : damask.GeomGrid
Updated grid-based geometry.
Notes
@ -1213,11 +1263,11 @@ class Grid:
mode='wrap' if periodic else 'nearest',
extra_keywords=dict(selection=selection_,rng=rng),
).astype(self.material.dtype)
return Grid(material = material,
return GeomGrid(material = material,
size = self.size,
origin = self.origin,
initial_conditions = self.initial_conditions,
comments = self.comments+[util.execution_stamp('Grid','clean')],
comments = self.comments+[util.execution_stamp('GeomGrid','clean')],
)
@ -1228,7 +1278,7 @@ class Grid:
fill: Optional[int] = None,
R: Rotation = Rotation(),
inverse: bool = False,
periodic: bool = True) -> 'Grid':
periodic: bool = True) -> 'GeomGrid':
"""
Insert a primitive geometric object at a given position.
@ -1258,7 +1308,7 @@ class Grid:
Returns
-------
updated : damask.Grid
updated : damask.GeomGrid
Updated grid-based geometry.
Examples
@ -1267,7 +1317,7 @@ class Grid:
>>> import numpy as np
>>> import damask
>>> g = damask.Grid(np.zeros([64]*3,int), np.ones(3)*1e-4)
>>> g = damask.GeomGrid(np.zeros([64]*3,int), np.ones(3)*1e-4)
>>> g.add_primitive(np.ones(3)*5e-5,np.ones(3)*5e-5,1)
cells : 64 × 64 × 64
size : 0.0001 × 0.0001 × 0.0001
@ -1278,7 +1328,7 @@ class Grid:
>>> import numpy as np
>>> import damask
>>> g = damask.Grid(np.zeros([64]*3,int), np.ones(3)*1e-4)
>>> g = damask.GeomGrid(np.zeros([64]*3,int), np.ones(3)*1e-4)
>>> g.add_primitive(np.ones(3,int)*32,np.zeros(3),np.inf)
cells : 64 × 64 × 64
size : 0.0001 × 0.0001 × 0.0001
@ -1304,13 +1354,13 @@ class Grid:
if periodic: # translate back to center
mask = np.roll(mask,((c/self.size-0.5)*self.cells).round().astype(np.int64),(0,1,2))
return Grid(material = np.where(np.logical_not(mask) if inverse else mask,
return GeomGrid(material = np.where(np.logical_not(mask) if inverse else mask,
self.material,
np.nanmax(self.material)+1 if fill is None else fill),
size = self.size,
origin = self.origin,
initial_conditions = self.initial_conditions,
comments = self.comments+[util.execution_stamp('Grid','add_primitive')],
comments = self.comments+[util.execution_stamp('GeomGrid','add_primitive')],
)
@ -1319,7 +1369,7 @@ class Grid:
offset: Optional[int] = None,
selection: Optional[IntSequence] = None,
invert_selection: bool = False,
periodic: bool = True) -> 'Grid':
periodic: bool = True) -> 'GeomGrid':
"""
Offset material ID of points in the vicinity of selected (or just other) material IDs.
@ -1345,7 +1395,7 @@ class Grid:
Returns
-------
updated : damask.Grid
updated : damask.GeomGrid
Updated grid-based geometry.
"""
@ -1377,11 +1427,11 @@ class Grid:
extra_keywords=dict(selection=selection_),
)
return Grid(material = np.where(mask, self.material + offset_,self.material),
return GeomGrid(material = np.where(mask, self.material + offset_,self.material),
size = self.size,
origin = self.origin,
initial_conditions = self.initial_conditions,
comments = self.comments+[util.execution_stamp('Grid','vicinity_offset')],
comments = self.comments+[util.execution_stamp('GeomGrid','vicinity_offset')],
)

View File

@ -240,13 +240,6 @@ class Orientation(Rotation,Crystal):
return self.copy(Rotation(self.quaternion)*Rotation(other.quaternion))
@classmethod
@util.extend_docstring(Rotation.from_random,
adopted_parameters=Crystal.__init__)
@util.pass_on('rotation', Rotation.from_random, wrapped=__init__)
def from_random(cls, **kwargs) -> 'Orientation':
return cls(**kwargs)
@classmethod
@util.extend_docstring(Rotation.from_quaternion,
adopted_parameters=Crystal.__init__)
@ -282,6 +275,13 @@ class Orientation(Rotation,Crystal):
def from_matrix(cls, **kwargs) -> 'Orientation':
return cls(**kwargs)
@classmethod
@util.extend_docstring(Rotation.from_parallel,
adopted_parameters=Crystal.__init__)
@util.pass_on('rotation', Rotation.from_parallel, wrapped=__init__)
def from_parallel(cls, **kwargs) -> 'Orientation':
return cls(**kwargs)
@classmethod
@util.extend_docstring(Rotation.from_Rodrigues_vector,
adopted_parameters=Crystal.__init__)
@ -303,6 +303,20 @@ class Orientation(Rotation,Crystal):
def from_cubochoric(cls, **kwargs) -> 'Orientation':
return cls(**kwargs)
@classmethod
@util.extend_docstring(Rotation.from_random,
adopted_parameters=Crystal.__init__)
@util.pass_on('rotation', Rotation.from_random, wrapped=__init__)
def from_random(cls, **kwargs) -> 'Orientation':
return cls(**kwargs)
@classmethod
@util.extend_docstring(Rotation.from_ODF,
adopted_parameters=Crystal.__init__)
@util.pass_on('rotation', Rotation.from_ODF, wrapped=__init__)
def from_ODF(cls, **kwargs) -> 'Orientation':
return cls(**kwargs)
@classmethod
@util.extend_docstring(Rotation.from_spherical_component,
adopted_parameters=Crystal.__init__)
@ -325,7 +339,7 @@ class Orientation(Rotation,Crystal):
hkl: FloatSequence,
**kwargs) -> 'Orientation':
"""
Initialize orientation object from two crystallographic directions.
Initialize orientation object from the crystallographic direction and plane parallel to lab x and z, respectively.
Parameters
----------
@ -855,7 +869,8 @@ class Orientation(Rotation,Crystal):
def related(self: MyType,
model: str) -> MyType:
model: str,
target = None) -> MyType:
"""
All orientations related to self by given relationship model.
@ -863,6 +878,10 @@ class Orientation(Rotation,Crystal):
----------
model : str
Orientation relationship model selected from self.orientation_relationships.
target : Crystal, optional
Crystal to transform to.
Providing this parameter allows specification of non-standard lattice parameters.
Default is inferred from selected model and uses standard lattice parameters.
Returns
-------
@ -890,11 +909,10 @@ class Orientation(Rotation,Crystal):
[0.924 0.000 0.000 0.383]]
"""
lattice,o = self.relation_operations(model)
target = Crystal(lattice=lattice)
o = o.broadcast_to(o.shape+self.shape,mode='right')
lattice,o = self.relation_operations(model,target)
target = Crystal(lattice=lattice) if target is None else target
return Orientation(rotation=o*Rotation(self.quaternion).broadcast_to(o.shape,mode='left'),
return Orientation(rotation=o*Rotation(self.quaternion)[np.newaxis,...], # type: ignore
lattice=lattice,
b = self.b if target.ratio['b'] is None else self.a*target.ratio['b'],
c = self.c if target.ratio['c'] is None else self.a*target.ratio['c'],

View File

@ -57,6 +57,11 @@ class Table:
Test equality of other.
Parameters
----------
other : Table
Table to check for equality.
"""
return NotImplemented if not isinstance(other,Table) else \
self.shapes == other.shapes and self.data.equals(other.data)

View File

@ -10,8 +10,8 @@ FloatSequence = Union[np.ndarray,Sequence[float]]
IntSequence = Union[np.ndarray,Sequence[int]]
StrSequence = Union[np.ndarray,Sequence[str]]
FileHandle = Union[TextIO, str, Path]
CrystalFamily = Union[None,Literal['triclinic', 'monoclinic', 'orthorhombic', 'tetragonal', 'hexagonal', 'cubic']]
BravaisLattice = Union[None,Literal['aP', 'mP', 'mS', 'oP', 'oS', 'oI', 'oF', 'tP', 'tI', 'hP', 'cP', 'cI', 'cF']]
CrystalFamily = Literal['triclinic', 'monoclinic', 'orthorhombic', 'tetragonal', 'hexagonal', 'cubic']
BravaisLattice = Literal['aP', 'mP', 'mS', 'oP', 'oS', 'oI', 'oF', 'tP', 'tI', 'hP', 'cP', 'cI', 'cF']
CrystalKinematics = Literal['slip', 'twin']
NumpyRngSeed = Union[int, IntSequence, np.random.SeedSequence, np.random.Generator]
# BitGenerator does not exists in older numpy versions

View File

@ -457,7 +457,7 @@ class VTK:
data: Union[None, np.ndarray, np.ma.MaskedArray] = None,
info: Optional[str] = None,
*,
table: Optional['Table'] = None):
table: Optional['Table'] = None) -> 'VTK':
"""
Add new or replace existing point or cell data.
@ -534,7 +534,6 @@ class VTK:
else:
raise TypeError
return dup
@ -559,20 +558,18 @@ class VTK:
"""
cell_data = self.vtk_data.GetCellData()
for a in range(cell_data.GetNumberOfArrays()):
if cell_data.GetArrayName(a) == label:
if label in [cell_data.GetArrayName(a) for a in range(cell_data.GetNumberOfArrays())]:
try:
return vtk_to_numpy(cell_data.GetArray(a))
return vtk_to_numpy(cell_data.GetArray(label))
except AttributeError:
vtk_array = cell_data.GetAbstractArray(a) # string array
vtk_array = cell_data.GetAbstractArray(label) # string array
point_data = self.vtk_data.GetPointData()
for a in range(point_data.GetNumberOfArrays()):
if point_data.GetArrayName(a) == label:
if label in [point_data.GetArrayName(a) for a in range(point_data.GetNumberOfArrays())]:
try:
return vtk_to_numpy(point_data.GetArray(a))
return vtk_to_numpy(point_data.GetArray(label))
except AttributeError:
vtk_array = point_data.GetAbstractArray(a) # string array
vtk_array = point_data.GetAbstractArray(label) # string array
try:
# string array
@ -581,6 +578,41 @@ class VTK:
raise KeyError(f'array "{label}" not found')
def delete(self,
label: str) -> 'VTK':
"""
Delete either cell or point data.
Cell data takes precedence over point data, i.e. this
function assumes that labels are unique among cell and
point data.
Parameters
----------
label : str
Data label.
Returns
-------
updated : damask.VTK
Updated VTK-based geometry.
"""
dup = self.copy()
cell_data = dup.vtk_data.GetCellData()
if label in [cell_data.GetArrayName(a) for a in range(cell_data.GetNumberOfArrays())]:
dup.vtk_data.GetCellData().RemoveArray(label)
return dup
point_data = self.vtk_data.GetPointData()
if label in [point_data.GetArrayName(a) for a in range(point_data.GetNumberOfArrays())]:
dup.vtk_data.GetPointData().RemoveArray(label)
return dup
raise KeyError(f'array "{label}" not found')
def show(self,
label: Optional[str] = None,
colormap: Union[Colormap, str] = 'cividis'):

View File

@ -116,7 +116,7 @@ def from_grid(grid,
Parameters
----------
grid : damask.Grid
grid : damask.GeomGrid
Grid from which the material IDs are used as seeds.
selection : (sequence of) int, optional
Material IDs to consider.
@ -134,6 +134,12 @@ def from_grid(grid,
coords, materials : numpy.ndarray, shape (:,3); numpy.ndarray, shape (:)
Seed coordinates in 3D space, material IDs.
Notes
-----
The origin is not considered in order to obtain coordinates
in a coordinate system located at the origin. This is expected
by damask.GeomGrid.from_Voronoi_tessellation.
Examples
--------
Recreate seeds from Voronoi tessellation.
@ -142,7 +148,7 @@ def from_grid(grid,
>>> import scipy.spatial
>>> import damask
>>> seeds = damask.seeds.from_random(np.ones(3),29,[128]*3)
>>> (g := damask.Grid.from_Voronoi_tessellation([128]*3,np.ones(3),seeds))
>>> (g := damask.GeomGrid.from_Voronoi_tessellation([128]*3,np.ones(3),seeds))
cells: 128 × 128 × 128
size: 1.0 × 1.0 × 1.0
origin: 0.0 0.0 0.0 m
@ -166,8 +172,8 @@ def from_grid(grid,
materials = _np.unique(material[mask])
coords_ = _np.zeros((materials.size,3),dtype=float)
for i,mat in enumerate(materials):
pc = (2*_np.pi*coords[material[:,0]==mat,:]-grid.origin)/grid.size
coords_[i] = grid.origin + grid.size / 2 / _np.pi * (_np.pi +
pc = 2*_np.pi*coords[material[:,0]==mat,:]/grid.size
coords_[i] = grid.size / 2 / _np.pi * (_np.pi +
_np.arctan2(-_np.average(_np.sin(pc),axis=0),
-_np.average(_np.cos(pc),axis=0))) \
if periodic else \

View File

@ -4,7 +4,7 @@ import re
from pathlib import Path
from typing import Literal
_marc_version = '2023.1'
_marc_version = '2023.3'
_marc_root = '/opt/msc'
_damask_root = str(Path(__file__).parents[3])

View File

@ -1 +1 @@
../Grid/2phase_irregularGrid.dream3d
../GeomGrid/2phase_irregularGrid.dream3d

View File

@ -1 +1 @@
../Grid/2phase_irregularGrid.json
../GeomGrid/2phase_irregularGrid.json

View File

@ -1 +1 @@
../Grid/2phase_irregularGrid.xdmf
../GeomGrid/2phase_irregularGrid.xdmf

View File

@ -1 +1 @@
../Grid/measured.dream3d
../GeomGrid/measured.dream3d

View File

@ -1 +1 @@
../Grid/measured.xdmf
../GeomGrid/measured.xdmf

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