Merge remote-tracking branch 'origin/development' into export_DAMASK_to_DREAM3D
This commit is contained in:
Martin Diehl
commit
b5e34e7949
|
|
@ -2,7 +2,7 @@ name: Grid and Mesh Solver
|
||||||
on: [push]
|
on: [push]
|
||||||
|
|
||||||
env:
|
env:
|
||||||
PETSC_VERSION: '3.18.4'
|
PETSC_VERSION: '3.20.1'
|
||||||
HOMEBREW_NO_ANALYTICS: 'ON' # Make Homebrew installation a little quicker
|
HOMEBREW_NO_ANALYTICS: 'ON' # Make Homebrew installation a little quicker
|
||||||
HOMEBREW_NO_AUTO_UPDATE: 'ON'
|
HOMEBREW_NO_AUTO_UPDATE: 'ON'
|
||||||
HOMEBREW_NO_BOTTLE_SOURCE_FALLBACK: 'ON'
|
HOMEBREW_NO_BOTTLE_SOURCE_FALLBACK: 'ON'
|
||||||
|
|
@ -17,7 +17,7 @@ jobs:
|
||||||
|
|
||||||
strategy:
|
strategy:
|
||||||
matrix:
|
matrix:
|
||||||
gcc_v: [9, 10, 11, 12]
|
gcc_v: [9, 10, 11, 12, 13]
|
||||||
fail-fast: false
|
fail-fast: false
|
||||||
|
|
||||||
env:
|
env:
|
||||||
|
|
@ -47,7 +47,7 @@ jobs:
|
||||||
- name: PETSc - Download
|
- name: PETSc - Download
|
||||||
if: steps.petsc-download.outputs.cache-hit != 'true'
|
if: steps.petsc-download.outputs.cache-hit != 'true'
|
||||||
run: |
|
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
|
- name: PETSc - Prepare
|
||||||
run: |
|
run: |
|
||||||
|
|
@ -88,31 +88,22 @@ jobs:
|
||||||
|
|
||||||
intel:
|
intel:
|
||||||
|
|
||||||
runs-on: [ubuntu-22.04]
|
runs-on: ubuntu-22.04
|
||||||
|
container:
|
||||||
|
image: intel/oneapi-hpckit:latest
|
||||||
|
|
||||||
strategy:
|
strategy:
|
||||||
matrix:
|
|
||||||
intel_v: [classic, llvm] # Variant of Intel compilers
|
|
||||||
fail-fast: false
|
fail-fast: false
|
||||||
|
|
||||||
env:
|
|
||||||
INTEL_V: ${{ matrix.intel_v }}
|
|
||||||
|
|
||||||
steps:
|
steps:
|
||||||
- uses: actions/checkout@v3
|
- uses: actions/checkout@v3
|
||||||
|
|
||||||
- name: Intel - Install
|
- name: Intel - Install
|
||||||
run: |
|
run: |
|
||||||
wget -q https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB
|
apt-get update --allow-insecure-repositories
|
||||||
sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB
|
apt-get install --allow-unauthenticated -y \
|
||||||
rm GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB
|
cmake build-essential autoconf libtool \
|
||||||
echo "deb https://apt.repos.intel.com/oneapi all main" | sudo tee /etc/apt/sources.list.d/oneAPI.list
|
zlib1g-dev
|
||||||
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
|
|
||||||
printenv >> $GITHUB_ENV
|
printenv >> $GITHUB_ENV
|
||||||
|
|
||||||
- name: PETSc - Cache download
|
- name: PETSc - Cache download
|
||||||
|
|
@ -125,15 +116,15 @@ jobs:
|
||||||
- name: PETSc - Download
|
- name: PETSc - Download
|
||||||
if: steps.petsc-download.outputs.cache-hit != 'true'
|
if: steps.petsc-download.outputs.cache-hit != 'true'
|
||||||
run: |
|
run: |
|
||||||
wget -q https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-${PETSC_VERSION}.tar.gz -P download
|
wget -q https://web.cels.anl.gov/projects/petsc/download/release-snapshots/petsc-${PETSC_VERSION}.tar.gz -P download
|
||||||
|
|
||||||
- name: PETSc - Prepare
|
- name: PETSc - Prepare
|
||||||
run: |
|
run: |
|
||||||
tar -xf download/petsc-${PETSC_VERSION}.tar.gz -C .
|
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
|
./petsc-${PETSC_VERSION}/config/BuildSystem/config/package.py
|
||||||
export PETSC_DIR=${PWD}/petsc-${PETSC_VERSION}
|
export PETSC_DIR=${PWD}/petsc-${PETSC_VERSION}
|
||||||
export PETSC_ARCH=intel-${INTEL_V}
|
export PETSC_ARCH=intel
|
||||||
printenv >> $GITHUB_ENV
|
printenv >> $GITHUB_ENV
|
||||||
|
|
||||||
- name: PETSc - Cache installation
|
- name: PETSc - Cache installation
|
||||||
|
|
@ -141,21 +132,9 @@ jobs:
|
||||||
uses: actions/cache@v3
|
uses: actions/cache@v3
|
||||||
with:
|
with:
|
||||||
path: petsc-${{ env.PETSC_VERSION }}
|
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)
|
- name: PETSc - Install
|
||||||
if: contains( matrix.intel_v, 'classic')
|
|
||||||
run: |
|
|
||||||
cd petsc-${PETSC_VERSION}
|
|
||||||
./configure \
|
|
||||||
--with-fc='mpiifort -fc=ifort -diag-disable=10441' \
|
|
||||||
--with-cc='mpiicc -cc=icc -diag-disable=10441' \
|
|
||||||
--with-cxx='mpiicpc -cxx=icpc -diag-disable=10441' \
|
|
||||||
--download-fftw --download-hdf5 --download-hdf5-fortran-bindings=1 --download-zlib
|
|
||||||
make all
|
|
||||||
|
|
||||||
- name: PETSc - Install (LLVM)
|
|
||||||
if: contains( matrix.intel_v, 'llvm')
|
|
||||||
run: |
|
run: |
|
||||||
cd petsc-${PETSC_VERSION}
|
cd petsc-${PETSC_VERSION}
|
||||||
./configure \
|
./configure \
|
||||||
|
|
@ -166,7 +145,6 @@ jobs:
|
||||||
make all
|
make all
|
||||||
|
|
||||||
- name: DAMASK - Compile
|
- name: DAMASK - Compile
|
||||||
if: contains( matrix.intel_v, 'classic')
|
|
||||||
run: |
|
run: |
|
||||||
cmake -B build/grid -DDAMASK_SOLVER=grid -DCMAKE_INSTALL_PREFIX=${PWD}
|
cmake -B build/grid -DDAMASK_SOLVER=grid -DCMAKE_INSTALL_PREFIX=${PWD}
|
||||||
cmake --build build/grid --parallel
|
cmake --build build/grid --parallel
|
||||||
|
|
@ -175,18 +153,6 @@ jobs:
|
||||||
cmake --build build/mesh --parallel
|
cmake --build build/mesh --parallel
|
||||||
cmake --install build/mesh
|
cmake --install build/mesh
|
||||||
|
|
||||||
# ifx has issue with openMP
|
|
||||||
# https://community.intel.com/t5/Intel-Fortran-Compiler/ifx-ICE-and-SEGFAULT/m-p/1459877
|
|
||||||
- name: DAMASK - Compile
|
|
||||||
if: contains( matrix.intel_v, 'llvm')
|
|
||||||
run: |
|
|
||||||
cmake -B build/grid -DDAMASK_SOLVER=grid -DCMAKE_INSTALL_PREFIX=${PWD} -DOPENMP=OFF
|
|
||||||
cmake --build build/grid --parallel
|
|
||||||
cmake --install build/grid
|
|
||||||
cmake -B build/mesh -DDAMASK_SOLVER=mesh -DCMAKE_INSTALL_PREFIX=${PWD} -DOPENMP=OFF
|
|
||||||
cmake --build build/mesh --parallel
|
|
||||||
cmake --install build/mesh
|
|
||||||
|
|
||||||
- name: DAMASK - Run
|
- name: DAMASK - Run
|
||||||
run: |
|
run: |
|
||||||
./bin/DAMASK_grid -l tensionX.yaml -g 20grains16x16x16.vti -m material.yaml -w examples/grid
|
./bin/DAMASK_grid -l tensionX.yaml -g 20grains16x16x16.vti -m material.yaml -w examples/grid
|
||||||
|
|
|
||||||
|
|
@ -9,7 +9,7 @@ jobs:
|
||||||
|
|
||||||
strategy:
|
strategy:
|
||||||
matrix:
|
matrix:
|
||||||
python-version: ['3.8', '3.9', '3.10', '3.11']
|
python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
|
||||||
os: [ubuntu-latest, macos-latest, windows-latest]
|
os: [ubuntu-latest, macos-latest, windows-latest]
|
||||||
fail-fast: false
|
fail-fast: false
|
||||||
|
|
||||||
|
|
|
||||||
|
|
@ -47,7 +47,7 @@ variables:
|
||||||
PETSC_INTELLLVM: "Libraries/PETSc/3.16.3/oneAPI-2022.0.1-IntelMPI-2021.5.0"
|
PETSC_INTELLLVM: "Libraries/PETSc/3.16.3/oneAPI-2022.0.1-IntelMPI-2021.5.0"
|
||||||
PETSC_INTEL: "Libraries/PETSc/3.16.5/Intel-2022.0.1-IntelMPI-2021.5.0"
|
PETSC_INTEL: "Libraries/PETSc/3.16.5/Intel-2022.0.1-IntelMPI-2021.5.0"
|
||||||
# ++++++++++++ MSC Marc +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|
# ++++++++++++ MSC Marc +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|
||||||
MSC: "FEM/MSC/2023.1"
|
MSC: "FEM/MSC/2023.3"
|
||||||
IntelMarc: "Compiler/Intel/19.1.2 Libraries/IMKL/2020"
|
IntelMarc: "Compiler/Intel/19.1.2 Libraries/IMKL/2020"
|
||||||
HDF5Marc: "HDF5/1.12.2/Intel-19.1.2"
|
HDF5Marc: "HDF5/1.12.2/Intel-19.1.2"
|
||||||
|
|
||||||
|
|
|
||||||
|
|
@ -130,7 +130,10 @@ set(CMAKE_Fortran_FLAGS_${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 ${PETSC_EXTERNAL_LIB} -lz")
|
set(CMAKE_Fortran_LINK_EXECUTABLE "${CMAKE_Fortran_LINK_EXECUTABLE} <OBJECTS> -o <TARGET> <LINK_LIBRARIES> -L${PETSC_LIBRARY_DIRS} -lpetsc ${PETSC_EXTERNAL_LIB} -lz")
|
||||||
|
|
||||||
if(fYAML_FOUND STREQUAL "1")
|
if(fYAML_FOUND STREQUAL "1")
|
||||||
set(CMAKE_Fortran_LINK_EXECUTABLE "${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)
|
add_definitions(-DFYAML)
|
||||||
pkg_get_variable(fYAML_INCLUDE_DIR libfyaml includedir) # fYAML_INCLUDE_DIRS and fYAML_CFLAGS are not working
|
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}")
|
set(CMAKE_C_FLAGS_${CMAKE_BUILD_TYPE} "${CMAKE_C_FLAGS_${CMAKE_BUILD_TYPE}} -I${fYAML_INCLUDE_DIR}")
|
||||||
|
|
|
||||||
|
|
@ -88,7 +88,7 @@ done
|
||||||
secondLevel "Details on $DEFAULT_PYTHON:"
|
secondLevel "Details on $DEFAULT_PYTHON:"
|
||||||
echo $(ls -la $(which $DEFAULT_PYTHON))
|
echo $(ls -la $(which $DEFAULT_PYTHON))
|
||||||
for MODULE in numpy scipy pandas matplotlib yaml h5py;do
|
for MODULE in numpy scipy pandas matplotlib yaml h5py;do
|
||||||
thirdLevel $module
|
thirdLevel $MODULE
|
||||||
$DEFAULT_PYTHON -c "import $MODULE; \
|
$DEFAULT_PYTHON -c "import $MODULE; \
|
||||||
print('Version: {}'.format($MODULE.__version__)); \
|
print('Version: {}'.format($MODULE.__version__)); \
|
||||||
print('Location: {}'.format($MODULE.__file__))"
|
print('Location: {}'.format($MODULE.__file__))"
|
||||||
|
|
|
||||||
2
PRIVATE
2
PRIVATE
|
|
@ -1 +1 @@
|
||||||
Subproject commit 9d2a98d72d9bf547dd697124cb795cf6a9668d30
|
Subproject commit bc2c8e3b8f405fdda0d69a2900d9b94c7cc0936f
|
||||||
24
README.md
24
README.md
|
|
@ -1,6 +1,23 @@
|
||||||
# DAMASK - The Düsseldorf Advanced Material Simulation Kit
|
# 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
|
## Contact Information
|
||||||
|
|
||||||
|
|
@ -8,8 +25,3 @@ Max-Planck-Institut für Eisenforschung GmbH
|
||||||
Max-Planck-Str. 1
|
Max-Planck-Str. 1
|
||||||
40237 Düsseldorf
|
40237 Düsseldorf
|
||||||
Germany
|
Germany
|
||||||
|
|
||||||
damask@mpie.de
|
|
||||||
https://damask.mpie.de
|
|
||||||
https://git.damask.mpie.de
|
|
||||||
|
|
||||||
|
|
|
||||||
|
|
@ -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
|
||||||
|
|
@ -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
|
||||||
|
|
@ -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
|
||||||
|
|
@ -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
|
||||||
|
|
@ -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 $DIRJOB/*_genmod.f90
|
||||||
|
|
@ -0,0 +1,75 @@
|
||||||
|
---
|
||||||
|
+++
|
||||||
|
@@ -172,6 +178,15 @@
|
||||||
|
MARC_COSIM_LIB="$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 "$AEM_DLL" -eq 1
|
||||||
|
|
@ -0,0 +1,517 @@
|
||||||
|
---
|
||||||
|
+++
|
||||||
|
@@ -136,6 +136,11 @@
|
||||||
|
# is created. For job running in the background, the log #
|
||||||
|
# file is always created. Default is "yes" #
|
||||||
|
##############################################################################
|
||||||
|
+# remove all Mentat paths from LD_LIBRARY_PATH
|
||||||
|
+LD_LIBRARY_PATH=:$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 $rmdll = yes;then
|
||||||
|
|
@ -0,0 +1,517 @@
|
||||||
|
---
|
||||||
|
+++
|
||||||
|
@@ -136,6 +136,11 @@
|
||||||
|
# is created. For job running in the background, the log #
|
||||||
|
# file is always created. Default is "yes" #
|
||||||
|
##############################################################################
|
||||||
|
+# remove all Mentat paths from LD_LIBRARY_PATH
|
||||||
|
+LD_LIBRARY_PATH=:$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 $rmdll = yes;then
|
||||||
|
|
@ -0,0 +1,517 @@
|
||||||
|
---
|
||||||
|
+++
|
||||||
|
@@ -136,6 +136,11 @@
|
||||||
|
# is created. For job running in the background, the log #
|
||||||
|
# file is always created. Default is "yes" #
|
||||||
|
##############################################################################
|
||||||
|
+# remove all Mentat paths from LD_LIBRARY_PATH
|
||||||
|
+LD_LIBRARY_PATH=:$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 $rmdll = yes;then
|
||||||
|
|
@ -0,0 +1,24 @@
|
||||||
|
---
|
||||||
|
+++
|
||||||
|
@@ -1,18 +1,5 @@
|
||||||
|
#!/bin/sh
|
||||||
|
-# This script opens a window running an editor. The default window is an
|
||||||
|
-# xterm, and the default editor is vi. These may be customized.
|
||||||
|
+# This script opens a window running an editor.
|
||||||
|
+# The command to invoke the editor is specified during DAMASK installation
|
||||||
|
|
||||||
|
-dir=
|
||||||
|
-for d in /usr/bin /usr/bin/X11; do
|
||||||
|
- if test -x "$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% $*
|
||||||
|
|
@ -0,0 +1,38 @@
|
||||||
|
---
|
||||||
|
+++
|
||||||
|
@@ -63,10 +63,10 @@
|
||||||
|
if [ "$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 $gpu
|
||||||
|
|
@ -0,0 +1,38 @@
|
||||||
|
---
|
||||||
|
+++
|
||||||
|
@@ -63,10 +63,10 @@
|
||||||
|
if [ "$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 $gpu
|
||||||
|
|
@ -0,0 +1,38 @@
|
||||||
|
---
|
||||||
|
+++
|
||||||
|
@@ -63,10 +63,10 @@
|
||||||
|
if [ "$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
|
||||||
|
|
@ -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 {
|
||||||
|
|
||||||
|
|
@ -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
|
||||||
|
|
@ -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
|
||||||
|
|
@ -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 $DIRJOB/*_genmod.f90
|
||||||
|
|
@ -0,0 +1,75 @@
|
||||||
|
---
|
||||||
|
+++
|
||||||
|
@@ -172,6 +178,15 @@
|
||||||
|
MARC_COSIM_LIB="$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 "$AEM_DLL" -eq 1
|
||||||
|
|
@ -0,0 +1,477 @@
|
||||||
|
---
|
||||||
|
+++
|
||||||
|
@@ -136,6 +136,11 @@
|
||||||
|
# is created. For job running in the background, the log #
|
||||||
|
# file is always created. Default is "yes" #
|
||||||
|
##############################################################################
|
||||||
|
+# remove all Mentat paths from LD_LIBRARY_PATH
|
||||||
|
+LD_LIBRARY_PATH=:$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 $rmdll = yes;then
|
||||||
|
|
@ -0,0 +1,477 @@
|
||||||
|
---
|
||||||
|
+++
|
||||||
|
@@ -136,6 +136,11 @@
|
||||||
|
# is created. For job running in the background, the log #
|
||||||
|
# file is always created. Default is "yes" #
|
||||||
|
##############################################################################
|
||||||
|
+# remove all Mentat paths from LD_LIBRARY_PATH
|
||||||
|
+LD_LIBRARY_PATH=:$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 $rmdll = yes;then
|
||||||
|
|
@ -0,0 +1,477 @@
|
||||||
|
---
|
||||||
|
+++
|
||||||
|
@@ -136,6 +136,11 @@
|
||||||
|
# is created. For job running in the background, the log #
|
||||||
|
# file is always created. Default is "yes" #
|
||||||
|
##############################################################################
|
||||||
|
+# remove all Mentat paths from LD_LIBRARY_PATH
|
||||||
|
+LD_LIBRARY_PATH=:$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 $rmdll = yes;then
|
||||||
|
|
@ -0,0 +1,24 @@
|
||||||
|
---
|
||||||
|
+++
|
||||||
|
@@ -1,18 +1,5 @@
|
||||||
|
#!/bin/sh
|
||||||
|
-# This script opens a window running an editor. The default window is an
|
||||||
|
-# xterm, and the default editor is vi. These may be customized.
|
||||||
|
+# This script opens a window running an editor.
|
||||||
|
+# The command to invoke the editor is specified during DAMASK installation
|
||||||
|
|
||||||
|
-dir=
|
||||||
|
-for d in /usr/bin /usr/bin/X11; do
|
||||||
|
- if test -x "$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% $*
|
||||||
|
|
@ -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
|
||||||
|
|
@ -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
|
||||||
|
|
@ -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
|
||||||
|
|
@ -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 {
|
||||||
|
|
||||||
|
|
@ -65,13 +65,13 @@ def mesh(r,d):
|
||||||
return [
|
return [
|
||||||
"*add_nodes",
|
"*add_nodes",
|
||||||
"%f %f %f"%(0.0,0.0,0.0),
|
"%f %f %f"%(0.0,0.0,0.0),
|
||||||
"%f %f %f"%(0.0,0.0,d[2]),
|
"%f %f %f"%(d[0],0.0,0.0),
|
||||||
"%f %f %f"%(0.0,d[1],d[2]),
|
"%f %f %f"%(d[0],d[1],0.0),
|
||||||
"%f %f %f"%(0.0,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"%(0.0,0.0,d[2]),
|
||||||
"%f %f %f"%(-d[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"%(d[0],d[1],d[2]),
|
||||||
"%f %f %f"%(-d[0],d[1],0.0),
|
"%f %f %f"%(0.0,d[1],d[2]),
|
||||||
"*add_elements",
|
"*add_elements",
|
||||||
"1",
|
"1",
|
||||||
"2",
|
"2",
|
||||||
|
|
@ -82,19 +82,17 @@ def mesh(r,d):
|
||||||
"7",
|
"7",
|
||||||
"8",
|
"8",
|
||||||
"*sub_divisions",
|
"*sub_divisions",
|
||||||
"%i %i %i"%(r[2],r[1],r[0]),
|
"%i %i %i"%(r[0],r[1],r[2]),
|
||||||
"*subdivide_elements",
|
"*subdivide_elements",
|
||||||
"all_existing",
|
"all_existing",
|
||||||
"*set_sweep_tolerance",
|
"*set_sweep_tolerance",
|
||||||
"%f"%(float(min(d))/max(r)/2.0),
|
"%f"%(float(min(d))/max(r)/2.0),
|
||||||
"*sweep_all",
|
"*sweep_all",
|
||||||
"*renumber_all",
|
"*remove_unused_nodes",
|
||||||
"*set_move_scale_factor x -1",
|
"*set_renumber_direction",
|
||||||
"*move_elements",
|
"%i %i %i"%(1,r[0],r[0]*r[1]),
|
||||||
"all_existing",
|
"*renumber_elements_directed",
|
||||||
"*flip_elements",
|
"*renumber_nodes_directed",
|
||||||
"all_existing",
|
|
||||||
"*fill_view",
|
|
||||||
]
|
]
|
||||||
|
|
||||||
|
|
||||||
|
|
@ -142,8 +140,7 @@ def initial_conditions(material):
|
||||||
cmds = [\
|
cmds = [\
|
||||||
"*new_icond",
|
"*new_icond",
|
||||||
"*icond_name _temperature",
|
"*icond_name _temperature",
|
||||||
"*icond_type state_variable",
|
"*icond_type elem_temperature_state",
|
||||||
"*icond_param_value state_var_id 1",
|
|
||||||
"*icond_dof_value var 300",
|
"*icond_dof_value var 300",
|
||||||
"*add_icond_elements",
|
"*add_icond_elements",
|
||||||
"all_existing",
|
"all_existing",
|
||||||
|
|
@ -153,9 +150,9 @@ def initial_conditions(material):
|
||||||
cmds.append([\
|
cmds.append([\
|
||||||
"*new_icond",
|
"*new_icond",
|
||||||
"*icond_name material_%i"%(grain+1),
|
"*icond_name material_%i"%(grain+1),
|
||||||
"*icond_type state_variable",
|
"*icond_type elem_user_state",
|
||||||
"*icond_param_value state_var_id 2",
|
"*icond_param_value state_var_id 2",
|
||||||
"*icond_dof_value var %i"%(grain+1),
|
"*icond_dof_value var %i"%(grain),
|
||||||
"*add_icond_elements",
|
"*add_icond_elements",
|
||||||
elementList,
|
elementList,
|
||||||
"#",
|
"#",
|
||||||
|
|
@ -196,7 +193,7 @@ if filenames == []: filenames = [None]
|
||||||
for name in filenames:
|
for name in filenames:
|
||||||
print(script_name+': '+name)
|
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')
|
material = geom.material.flatten(order='F')
|
||||||
|
|
||||||
cmds = [\
|
cmds = [\
|
||||||
|
|
@ -209,6 +206,7 @@ for name in filenames:
|
||||||
'*show_model',
|
'*show_model',
|
||||||
'*redraw',
|
'*redraw',
|
||||||
'*draw_automatic',
|
'*draw_automatic',
|
||||||
|
'*fill_view',
|
||||||
]
|
]
|
||||||
|
|
||||||
output_locals = {}
|
output_locals = {}
|
||||||
|
|
|
||||||
|
|
@ -26,5 +26,5 @@ from ._vtk import VTK # noqa
|
||||||
from ._config import Config # noqa
|
from ._config import Config # noqa
|
||||||
from ._configmaterial import ConfigMaterial # noqa
|
from ._configmaterial import ConfigMaterial # noqa
|
||||||
from ._loadcasegrid import LoadcaseGrid # noqa
|
from ._loadcasegrid import LoadcaseGrid # noqa
|
||||||
from ._grid import Grid # noqa
|
from ._geomgrid import GeomGrid # noqa
|
||||||
from ._result import Result # noqa
|
from ._result import Result # noqa
|
||||||
|
|
|
||||||
|
|
@ -296,7 +296,7 @@ class Colormap(mpl.colors.ListedColormap):
|
||||||
RGBA image of shaded data.
|
RGBA image of shaded data.
|
||||||
|
|
||||||
"""
|
"""
|
||||||
mask = np.logical_not(np.isnan(field) if gap is None else \
|
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)
|
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 \
|
l,r = (field[mask].min(),field[mask].max()) if bounds is None else \
|
||||||
|
|
@ -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
|
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
|
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(
|
return Image.fromarray(
|
||||||
(np.dstack((
|
(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)
|
mask.astype(float)
|
||||||
)
|
)
|
||||||
)*255
|
)*255
|
||||||
|
|
|
||||||
|
|
@ -144,7 +144,7 @@ class ConfigMaterial(Config):
|
||||||
|
|
||||||
Notes
|
Notes
|
||||||
-----
|
-----
|
||||||
damask.Grid.load_DREAM3D gives the corresponding geometry for
|
damask.GeomGrid.load_DREAM3D gives the corresponding geometry for
|
||||||
the grid solver.
|
the grid solver.
|
||||||
|
|
||||||
For cell-wise data, only unique combinations of
|
For cell-wise data, only unique combinations of
|
||||||
|
|
|
||||||
|
|
@ -6,7 +6,8 @@ from ._typehints import FloatSequence, CrystalFamily, BravaisLattice, CrystalKin
|
||||||
from . import util
|
from . import util
|
||||||
from . import Rotation
|
from . import Rotation
|
||||||
|
|
||||||
lattice_symmetries: Dict[BravaisLattice, CrystalFamily] = {
|
|
||||||
|
lattice_symmetries: Dict[Optional[BravaisLattice], CrystalFamily] = {
|
||||||
'aP': 'triclinic',
|
'aP': 'triclinic',
|
||||||
|
|
||||||
'mP': 'monoclinic',
|
'mP': 'monoclinic',
|
||||||
|
|
@ -27,63 +28,60 @@ lattice_symmetries: Dict[BravaisLattice, CrystalFamily] = {
|
||||||
'cF': 'cubic',
|
'cF': 'cubic',
|
||||||
}
|
}
|
||||||
|
|
||||||
orientation_relationships: Dict[str, Dict[BravaisLattice,np.ndarray]] = {
|
orientation_relationships: Dict[str, Dict[str,List[np.ndarray]]] = {
|
||||||
'KS': {
|
'KS': { # https://doi.org/10.1016/j.jallcom.2012.02.004
|
||||||
'cF': np.array([
|
'cF-->cI' : [
|
||||||
[[-1, 0, 1],[ 1, 1, 1]],
|
np.repeat(np.array([
|
||||||
[[-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]],
|
|
||||||
[[ 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,-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]],
|
||||||
[[ 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, 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]],
|
||||||
[[ 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]],
|
||||||
],dtype=float),
|
],dtype=float),
|
||||||
'cI': np.array([
|
2,axis=0),
|
||||||
[[-1,-1, 1],[ 0, 1, 1]],
|
np.tile(np.array([[[-1,-1, 1],[ 0, 1, 1]],
|
||||||
[[-1, 1,-1],[ 0, 1, 1]],
|
[[-1, 1,-1],[ 0, 1, 1]]],dtype=float),
|
||||||
[[-1,-1, 1],[ 0, 1, 1]],
|
(12,1,1)),
|
||||||
[[-1, 1,-1],[ 0, 1, 1]],
|
],
|
||||||
[[-1,-1, 1],[ 0, 1, 1]],
|
'cI-->cF' : [
|
||||||
[[-1, 1,-1],[ 0, 1, 1]],
|
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],[ 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],[ 1, 0, 1]],
|
||||||
[[-1, 1,-1],[ 0, 1, 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],[ 0, 1, 1]],
|
[[ 1,-1, 1],[ 1, 0,-1]],
|
||||||
[[-1, 1,-1],[ 0, 1, 1]],
|
|
||||||
[[-1,-1, 1],[ 0, 1, 1]],
|
[[ 1,-1, 1],[ 1, 1, 0]],
|
||||||
[[-1, 1,-1],[ 0, 1, 1]],
|
[[ 1,-1,-1],[ 1, 1, 0]],
|
||||||
[[-1,-1, 1],[ 0, 1, 1]],
|
|
||||||
[[-1, 1,-1],[ 0, 1, 1]],
|
[[ 1, 1, 1],[ 1,-1, 0]],
|
||||||
[[-1,-1, 1],[ 0, 1, 1]],
|
[[ 1, 1,-1],[ 1,-1, 0]],
|
||||||
[[-1, 1,-1],[ 0, 1, 1]],
|
|
||||||
],dtype=float),
|
],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': {
|
'GT': { # https://doi.org/10.1107/S0021889805038276
|
||||||
'cF': np.array([
|
'cF-->cI' : [
|
||||||
|
np.array([
|
||||||
[[ -5,-12, 17],[ 1, 1, 1]],
|
[[ -5,-12, 17],[ 1, 1, 1]],
|
||||||
[[ 17, -5,-12],[ 1, 1, 1]],
|
[[ 17, -5,-12],[ 1, 1, 1]],
|
||||||
[[-12, 17, -5],[ 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]],
|
[[ 12, -5,-17],[ 1, -1, 1]],
|
||||||
[[-17,-12, 5],[ 1, -1, 1]],
|
[[-17,-12, 5],[ 1, -1, 1]],
|
||||||
],dtype=float),
|
],dtype=float),
|
||||||
'cI': np.array([
|
np.array([
|
||||||
[[-17, -7, 17],[ 1, 0, 1]],
|
[[-17, -7, 17],[ 1, 0, 1]],
|
||||||
[[ 17,-17, -7],[ 1, 1, 0]],
|
[[ 17,-17, -7],[ 1, 1, 0]],
|
||||||
[[ -7, 17,-17],[ 0, 1, 1]],
|
[[ -7, 17,-17],[ 0, 1, 1]],
|
||||||
|
|
@ -135,9 +133,65 @@ orientation_relationships: Dict[str, Dict[BravaisLattice,np.ndarray]] = {
|
||||||
[[ 7,-17,-17],[ 0, -1, 1]],
|
[[ 7,-17,-17],[ 0, -1, 1]],
|
||||||
[[-17, -7, 17],[ 1, 0, 1]],
|
[[-17, -7, 17],[ 1, 0, 1]],
|
||||||
],dtype=float),
|
],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': {
|
'GT_prime': { # https://doi.org/10.1107/S0021889805038276
|
||||||
'cF' : np.array([
|
'cF-->cI' : [
|
||||||
|
np.array([
|
||||||
[[ 0, 1, -1],[ 7, 17, 17]],
|
[[ 0, 1, -1],[ 7, 17, 17]],
|
||||||
[[ -1, 0, 1],[ 17, 7, 17]],
|
[[ -1, 0, 1],[ 17, 7, 17]],
|
||||||
[[ 1, -1, 0],[ 17, 17, 7]],
|
[[ 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, 0, -1],[-17, 7,-17]],
|
||||||
[[ 1, 1, 0],[-17, 17, -7]],
|
[[ 1, 1, 0],[-17, 17, -7]],
|
||||||
],dtype=float),
|
],dtype=float),
|
||||||
'cI' : np.array([
|
np.array([
|
||||||
[[ 1, 1, -1],[ 12, 5, 17]],
|
[[ 1, 1, -1],[ 12, 5, 17]],
|
||||||
[[ -1, 1, 1],[ 17, 12, 5]],
|
[[ -1, 1, 1],[ 17, 12, 5]],
|
||||||
[[ 1, -1, 1],[ 5, 17, 12]],
|
[[ 1, -1, 1],[ 5, 17, 12]],
|
||||||
|
|
@ -189,112 +243,189 @@ orientation_relationships: Dict[str, Dict[BravaisLattice,np.ndarray]] = {
|
||||||
[[ 1, -1, -1],[ -5, 12,-17]],
|
[[ 1, -1, -1],[ -5, 12,-17]],
|
||||||
[[ 1, 1, -1],[-17, 5,-12]],
|
[[ 1, 1, -1],[-17, 5,-12]],
|
||||||
],dtype=float),
|
],dtype=float),
|
||||||
|
],
|
||||||
|
'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),
|
||||||
|
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),
|
||||||
|
],
|
||||||
},
|
},
|
||||||
'NW': {
|
'NW': { # https://doi.org/10.1016/j.matchar.2004.12.015
|
||||||
'cF' : np.array([
|
'cF-->cI' : [
|
||||||
|
np.array([
|
||||||
[[ 2,-1,-1],[ 1, 1, 1]],
|
[[ 2,-1,-1],[ 1, 1, 1]],
|
||||||
[[-1, 2,-1],[ 1, 1, 1]],
|
[[-1, 2,-1],[ 1, 1, 1]],
|
||||||
[[-1,-1, 2],[ 1, 1, 1]],
|
[[-1,-1, 2],[ 1, 1, 1]],
|
||||||
|
|
||||||
[[-2,-1,-1],[-1, 1, 1]],
|
[[-2,-1,-1],[-1, 1, 1]],
|
||||||
[[ 1, 2,-1],[-1, 1, 1]],
|
[[ 1, 2,-1],[-1, 1, 1]],
|
||||||
[[ 1,-1, 2],[-1, 1, 1]],
|
[[ 1,-1, 2],[-1, 1, 1]],
|
||||||
|
|
||||||
[[ 2, 1,-1],[ 1,-1, 1]],
|
[[ 2, 1,-1],[ 1,-1, 1]],
|
||||||
[[-1,-2,-1],[ 1,-1, 1]],
|
[[-1,-2,-1],[ 1,-1, 1]],
|
||||||
[[-1, 1, 2],[ 1,-1, 1]],
|
[[-1, 1, 2],[ 1,-1, 1]],
|
||||||
[[ 2, -1, 1],[ -1, -1, 1]],
|
|
||||||
[[ -1, 2, 1],[ -1, -1, 1]],
|
[[ 2,-1, 1],[ 1, 1,-1]],
|
||||||
[[ -1, -1, -2],[ -1, -1, 1]],
|
[[-1, 2, 1],[ 1, 1,-1]],
|
||||||
|
[[-1,-1,-2],[ 1, 1,-1]],
|
||||||
],dtype=float),
|
],dtype=float),
|
||||||
'cI' : np.array([
|
np.broadcast_to(np.array([[ 0,-1, 1],[ 0, 1, 1]],dtype=float),
|
||||||
[[ 0, -1, 1],[ 0, 1, 1]],
|
(12,2,3)),
|
||||||
[[ 0, -1, 1],[ 0, 1, 1]],
|
],
|
||||||
[[ 0, -1, 1],[ 0, 1, 1]],
|
'cI-->cF' : [
|
||||||
[[ 0, -1, 1],[ 0, 1, 1]],
|
np.repeat(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]],
|
[[ 1, 0,-1],[ 1, 0, 1]],
|
||||||
[[ 0, -1, 1],[ 0, 1, 1]],
|
[[ 1, 0, 1],[ 1, 0,-1]],
|
||||||
[[ 0, -1, 1],[ 0, 1, 1]],
|
[[ 1,-1, 0],[ 1, 1, 0]],
|
||||||
[[ 0, -1, 1],[ 0, 1, 1]],
|
[[ 1, 1, 0],[ 1,-1, 0]],
|
||||||
[[ 0, -1, 1],[ 0, 1, 1]],
|
|
||||||
[[ 0, -1, 1],[ 0, 1, 1]],
|
|
||||||
],dtype=float),
|
],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': {
|
'Pitsch': { # https://doi.org/10.1080/14786435908238253
|
||||||
'cF' : np.array([
|
'cF-->cI' : [
|
||||||
[[ 1, 0, 1],[ 0, 1, 0]],
|
np.repeat(np.array([
|
||||||
[[ 1, 1, 0],[ 0, 0, 1]],
|
|
||||||
[[ 0, 1, 1],[ 1, 0, 0]],
|
[[ 0, 1, 1],[ 1, 0, 0]],
|
||||||
[[ 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]],
|
|
||||||
[[ 0, 1, 1],[ 1, 0, 0]],
|
|
||||||
[[ 1, 0, 1],[ 0, 1, 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]],
|
||||||
|
[[ 1,-1, 0],[ 0, 0, 1]],
|
||||||
],dtype=float),
|
],dtype=float),
|
||||||
'cI' : np.array([
|
2,axis=0),
|
||||||
[[ 1, -1, 1],[ -1, 0, 1]],
|
np.tile(np.array([
|
||||||
[[ 1, 1, -1],[ 1, -1, 0]],
|
[[ 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],[ 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, -1, 0]],
|
[[ 1, 1, 1],[ 1, 0,-1]],
|
||||||
[[ 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, 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, 0]],
|
||||||
],dtype=float),
|
],dtype=float),
|
||||||
|
np.broadcast_to(np.array([[ 1, 1, 0],[ 0, 0, 1]],dtype=float),
|
||||||
|
(12,2,3)),
|
||||||
|
],
|
||||||
},
|
},
|
||||||
'Bain': {
|
'Bain': { # https://doi.org/10.1107/S0021889805038276
|
||||||
'cF' : np.array([
|
'cF-->cI' : [
|
||||||
|
np.array([
|
||||||
[[ 0, 1, 0],[ 1, 0, 0]],
|
[[ 0, 1, 0],[ 1, 0, 0]],
|
||||||
[[ 0, 0, 1],[ 0, 1, 0]],
|
[[ 0, 0, 1],[ 0, 1, 0]],
|
||||||
[[ 1, 0, 0],[ 0, 0, 1]],
|
[[ 1, 0, 0],[ 0, 0, 1]],
|
||||||
],dtype=float),
|
],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]],
|
[[ 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),
|
],dtype=float),
|
||||||
|
np.broadcast_to(np.array([[ 1, 0, 0],[ 0, 0, 1]],dtype=float),
|
||||||
|
(3,2,3)),
|
||||||
|
]
|
||||||
},
|
},
|
||||||
'Burgers' : {
|
'Burgers' : { # https://doi.org/10.1016/S0031-8914(34)80244-3
|
||||||
'cI' : np.array([
|
'cI-->hP' : [
|
||||||
[[ -1, 1, 1],[ 1, 1, 0]],
|
np.array([
|
||||||
[[ -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, 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, 0]],
|
[[ 1, 1,-1],[ 1,-1, 0]],
|
||||||
|
],dtype=float),
|
||||||
[[ 1, 1, -1],[ 1, 0, 1]],
|
np.broadcast_to(np.array([[ 2,-1,-1, 0],[ 0, 0, 0, 1]],dtype=float),
|
||||||
[[ -1, 1, 1],[ 1, 0, 1]],
|
(12,2,4)),
|
||||||
[[ 1, 1, 1],[ -1, 0, 1]],
|
],
|
||||||
[[ 1, -1, 1],[ -1, 0, 1]],
|
'hP-->cI' : [
|
||||||
|
np.repeat(np.array([
|
||||||
[[ -1, 1, -1],[ 0, 1, 1]],
|
[[ 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]],
|
||||||
[[ -1, 1, 1],[ 0, -1, 1]],
|
[[-1, 1,-1],[ 0, 1, 1]],
|
||||||
[[ 1, 1, 1],[ 0, -1, 1]],
|
|
||||||
],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]],
|
|
||||||
],dtype=float),
|
],dtype=float),
|
||||||
|
(3,1,1)),
|
||||||
|
]
|
||||||
},
|
},
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
@ -428,20 +559,20 @@ class Crystal():
|
||||||
Crystal to check for equality.
|
Crystal to check for equality.
|
||||||
|
|
||||||
"""
|
"""
|
||||||
return NotImplemented if not isinstance(other, Crystal) else \
|
return (NotImplemented if not isinstance(other, Crystal) else
|
||||||
self.lattice == other.lattice and \
|
self.lattice == other.lattice and
|
||||||
self.parameters == other.parameters and \
|
self.parameters == other.parameters and
|
||||||
self.family == other.family
|
self.family == other.family) # type: ignore
|
||||||
|
|
||||||
@property
|
@property
|
||||||
def parameters(self):
|
def parameters(self) -> Optional[Tuple]:
|
||||||
"""Return lattice parameters a, b, c, alpha, beta, gamma."""
|
"""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
|
@property
|
||||||
def immutable(self):
|
def immutable(self) -> Dict[str, float]:
|
||||||
"""Return immutable lattice parameters."""
|
"""Return immutable lattice parameters."""
|
||||||
_immutable = {
|
_immutable: Dict[CrystalFamily, Dict[str,float]] = {
|
||||||
'cubic': {
|
'cubic': {
|
||||||
'b': 1.0,
|
'b': 1.0,
|
||||||
'c': 1.0,
|
'c': 1.0,
|
||||||
|
|
@ -476,9 +607,9 @@ class Crystal():
|
||||||
|
|
||||||
|
|
||||||
@property
|
@property
|
||||||
def orientation_relationships(self):
|
def orientation_relationships(self) -> List[str]:
|
||||||
"""Return labels of orientation relationships."""
|
"""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
|
@property
|
||||||
|
|
@ -671,9 +802,9 @@ class Crystal():
|
||||||
|
|
||||||
|
|
||||||
@property
|
@property
|
||||||
def lattice_points(self):
|
def lattice_points(self) -> np.ndarray:
|
||||||
"""Return lattice points."""
|
"""Return lattice points."""
|
||||||
_lattice_points = {
|
_lattice_points: Dict[str, List] = {
|
||||||
'P': [
|
'P': [
|
||||||
],
|
],
|
||||||
'S': [
|
'S': [
|
||||||
|
|
@ -694,8 +825,8 @@ class Crystal():
|
||||||
|
|
||||||
if self.lattice is None: raise KeyError('no lattice type specified')
|
if self.lattice is None: raise KeyError('no lattice type specified')
|
||||||
return np.array([[0,0,0]]
|
return np.array([[0,0,0]]
|
||||||
+ _lattice_points.get(self.lattice if self.lattice == 'hP' else \
|
+ _lattice_points.get(self.lattice if self.lattice == 'hP' else
|
||||||
self.lattice[-1],None),dtype=float)
|
self.lattice[-1],[]),dtype=float)
|
||||||
|
|
||||||
def to_lattice(self, *,
|
def to_lattice(self, *,
|
||||||
direction: Optional[FloatSequence] = None,
|
direction: Optional[FloatSequence] = None,
|
||||||
|
|
@ -753,7 +884,7 @@ class Crystal():
|
||||||
Crystal frame vector (reciprocal space) of Titanium along (1,0,0) plane normal:
|
Crystal frame vector (reciprocal space) of Titanium along (1,0,0) plane normal:
|
||||||
|
|
||||||
>>> import damask
|
>>> 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))
|
>>> Ti.to_frame(hkl=(1, 0, 0))
|
||||||
array([ 3.38983051e+09, 1.95711956e+09, -4.15134508e-07])
|
array([ 3.38983051e+09, 1.95711956e+09, -4.15134508e-07])
|
||||||
|
|
||||||
|
|
@ -782,7 +913,7 @@ class Crystal():
|
||||||
Directions and planes of deformation mode families.
|
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': {
|
'cF': {
|
||||||
'slip': [np.array([
|
'slip': [np.array([
|
||||||
[ 0,+1,-1, +1,+1,+1],
|
[ 0,+1,-1, +1,+1,+1],
|
||||||
|
|
@ -1025,7 +1156,8 @@ class Crystal():
|
||||||
|
|
||||||
|
|
||||||
def relation_operations(self,
|
def relation_operations(self,
|
||||||
model: str) -> Tuple[BravaisLattice, Rotation]:
|
model: str,
|
||||||
|
target = None) -> Tuple[BravaisLattice, Rotation]:
|
||||||
"""
|
"""
|
||||||
Crystallographic orientation relationships for phase transformations.
|
Crystallographic orientation relationships for phase transformations.
|
||||||
|
|
||||||
|
|
@ -1033,6 +1165,10 @@ class Crystal():
|
||||||
----------
|
----------
|
||||||
model : str
|
model : str
|
||||||
Name of orientation relationship.
|
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
|
Returns
|
||||||
-------
|
-------
|
||||||
|
|
@ -1057,20 +1193,27 @@ class Crystal():
|
||||||
https://doi.org/10.1016/j.actamat.2004.11.021
|
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}
|
m_l: BravaisLattice
|
||||||
if model not in my_relationships:
|
o_l: BravaisLattice
|
||||||
|
|
||||||
|
if model not in self.orientation_relationships:
|
||||||
raise KeyError(f'unknown orientation relationship "{model}"')
|
raise KeyError(f'unknown orientation relationship "{model}"')
|
||||||
r = my_relationships[model]
|
|
||||||
|
|
||||||
sl = self.lattice
|
sep = '-->'
|
||||||
ol = (set(r)-{sl}).pop()
|
search = self.lattice+sep+('' if target is None else target.lattice) # type: ignore
|
||||||
m = r[sl]
|
transform = [t for t in orientation_relationships[model].keys() if t.startswith(search)] # type: ignore
|
||||||
o = r[ol]
|
|
||||||
|
|
||||||
p_,_p = np.zeros(m.shape[:-1]+(3,)),np.zeros(o.shape[:-1]+(3,))
|
if len(transform) != 1:
|
||||||
p_[...,0,:] = m[...,0,:] if m.shape[-1] == 3 else util.Bravais_to_Miller(uvtw=m[...,0,0:4])
|
raise ValueError(f'invalid target lattice "{search.split(sep)[1]}"')
|
||||||
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])
|
|
||||||
|
|
||||||
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))
|
||||||
|
|
|
||||||
|
|
@ -28,7 +28,7 @@ def numba_njit_wrapper(**kwargs):
|
||||||
return (lambda function: nb.njit(function) if nb else function)
|
return (lambda function: nb.njit(function) if nb else function)
|
||||||
|
|
||||||
|
|
||||||
class Grid:
|
class GeomGrid:
|
||||||
"""
|
"""
|
||||||
Geometry definition for grid solvers.
|
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 []))
|
]+(['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).
|
Return deepcopy(self).
|
||||||
|
|
||||||
|
|
@ -110,11 +110,11 @@ class Grid:
|
||||||
|
|
||||||
Parameters
|
Parameters
|
||||||
----------
|
----------
|
||||||
other : damask.Grid
|
other : damask.GeomGrid
|
||||||
Grid to compare self against.
|
GeomGrid to compare self against.
|
||||||
|
|
||||||
"""
|
"""
|
||||||
if not isinstance(other, Grid):
|
if not isinstance(other, GeomGrid):
|
||||||
return NotImplemented
|
return NotImplemented
|
||||||
return bool( np.allclose(other.size,self.size)
|
return bool( np.allclose(other.size,self.size)
|
||||||
and np.allclose(other.origin,self.origin)
|
and np.allclose(other.origin,self.origin)
|
||||||
|
|
@ -197,38 +197,84 @@ class Grid:
|
||||||
|
|
||||||
|
|
||||||
@staticmethod
|
@staticmethod
|
||||||
def load(fname: Union[str, Path]) -> 'Grid':
|
def _load(fname: Union[str, Path], label: str) -> 'GeomGrid':
|
||||||
"""
|
"""
|
||||||
Load from VTK ImageData file.
|
Load from VTK ImageData file.
|
||||||
|
|
||||||
Parameters
|
Parameters
|
||||||
----------
|
----------
|
||||||
fname : str or pathlib.Path
|
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.
|
Valid extension is .vti, which will be appended if not given.
|
||||||
|
label : str
|
||||||
|
Label of the dataset containing the material IDs.
|
||||||
|
|
||||||
Returns
|
Returns
|
||||||
-------
|
-------
|
||||||
loaded : damask.Grid
|
loaded : damask.GeomGrid
|
||||||
Grid-based geometry from file.
|
GeomGrid-based geometry from file.
|
||||||
|
|
||||||
"""
|
"""
|
||||||
v = VTK.load(fname if str(fname).endswith('.vti') else str(fname)+'.vti')
|
v = VTK.load(fname if str(fname).endswith('.vti') else str(fname)+'.vti')
|
||||||
cells = np.array(v.vtk_data.GetDimensions())-1
|
cells = np.array(v.vtk_data.GetDimensions())-1
|
||||||
bbox = np.array(v.vtk_data.GetBounds()).reshape(3,2).T
|
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],
|
size = bbox[1] - bbox[0],
|
||||||
origin = bbox[0],
|
origin = bbox[0],
|
||||||
initial_conditions = ic,
|
initial_conditions = ic,
|
||||||
comments = v.comments,
|
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
|
@typing.no_type_check
|
||||||
@staticmethod
|
@staticmethod
|
||||||
def load_ASCII(fname)-> 'Grid':
|
def load_ASCII(fname)-> 'GeomGrid':
|
||||||
"""
|
"""
|
||||||
Load from geom file.
|
Load from geom file.
|
||||||
|
|
||||||
|
|
@ -242,8 +288,8 @@ class Grid:
|
||||||
|
|
||||||
Returns
|
Returns
|
||||||
-------
|
-------
|
||||||
loaded : damask.Grid
|
loaded : damask.GeomGrid
|
||||||
Grid-based geometry from file.
|
GeomGrid-based geometry from file.
|
||||||
|
|
||||||
"""
|
"""
|
||||||
warnings.warn('Support for ASCII-based geom format will be removed in DAMASK 3.0.0', DeprecationWarning,2)
|
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
|
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)
|
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,
|
size = size,
|
||||||
origin = origin,
|
origin = origin,
|
||||||
comments = comments)
|
comments = comments,
|
||||||
|
)
|
||||||
|
|
||||||
|
|
||||||
@staticmethod
|
@staticmethod
|
||||||
def load_Neper(fname: Union[str, Path]) -> 'Grid':
|
def load_Neper(fname: Union[str, Path]) -> 'GeomGrid':
|
||||||
"""
|
"""
|
||||||
Load from Neper VTK file.
|
Load from Neper VTK file.
|
||||||
|
|
||||||
|
|
@ -314,8 +361,8 @@ class Grid:
|
||||||
|
|
||||||
Returns
|
Returns
|
||||||
-------
|
-------
|
||||||
loaded : damask.Grid
|
loaded : damask.GeomGrid
|
||||||
Grid-based geometry from file.
|
GeomGrid-based geometry from file.
|
||||||
|
|
||||||
Notes
|
Notes
|
||||||
-----
|
-----
|
||||||
|
|
@ -330,7 +377,7 @@ class Grid:
|
||||||
>>> N_grains = 20
|
>>> N_grains = 20
|
||||||
>>> cells = (32,32,32)
|
>>> 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.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
|
cells: 32 × 32 × 32
|
||||||
size: 1.0 × 1.0 × 1.0 m³
|
size: 1.0 × 1.0 × 1.0 m³
|
||||||
origin: 0.0 0.0 0.0 m
|
origin: 0.0 0.0 0.0 m
|
||||||
|
|
@ -341,10 +388,10 @@ class Grid:
|
||||||
cells = np.array(v.vtk_data.GetDimensions())-1
|
cells = np.array(v.vtk_data.GetDimensions())-1
|
||||||
bbox = np.array(v.vtk_data.GetBounds()).reshape(3,2).T
|
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],
|
size = bbox[1] - bbox[0],
|
||||||
origin = 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,
|
cell_data: Optional[str] = None,
|
||||||
phases: str = 'Phases',
|
phases: str = 'Phases',
|
||||||
Euler_angles: str = 'EulerAngles',
|
Euler_angles: str = 'EulerAngles',
|
||||||
base_group: Optional[str] = None) -> 'Grid':
|
base_group: Optional[str] = None) -> 'GeomGrid':
|
||||||
"""
|
"""
|
||||||
Load DREAM.3D (HDF5) file.
|
Load DREAM.3D (HDF5) file.
|
||||||
|
|
||||||
|
|
@ -389,8 +436,8 @@ class Grid:
|
||||||
|
|
||||||
Returns
|
Returns
|
||||||
-------
|
-------
|
||||||
loaded : damask.Grid
|
loaded : damask.GeomGrid
|
||||||
Grid-based geometry from file.
|
GeomGrid-based geometry from file.
|
||||||
|
|
||||||
Notes
|
Notes
|
||||||
-----
|
-----
|
||||||
|
|
@ -418,17 +465,17 @@ class Grid:
|
||||||
else:
|
else:
|
||||||
ma = f['/'.join([b,c,feature_IDs])][()].flatten()
|
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,
|
size = size,
|
||||||
origin = origin,
|
origin = origin,
|
||||||
comments = util.execution_stamp('Grid','load_DREAM3D'),
|
comments = util.execution_stamp('GeomGrid','load_DREAM3D'),
|
||||||
)
|
)
|
||||||
|
|
||||||
|
|
||||||
@staticmethod
|
@staticmethod
|
||||||
def from_table(table: Table,
|
def from_table(table: Table,
|
||||||
coordinates: str,
|
coordinates: str,
|
||||||
labels: Union[str, Sequence[str]]) -> 'Grid':
|
labels: Union[str, Sequence[str]]) -> 'GeomGrid':
|
||||||
"""
|
"""
|
||||||
Create grid from ASCII table.
|
Create grid from ASCII table.
|
||||||
|
|
||||||
|
|
@ -445,8 +492,8 @@ class Grid:
|
||||||
|
|
||||||
Returns
|
Returns
|
||||||
-------
|
-------
|
||||||
new : damask.Grid
|
new : damask.GeomGrid
|
||||||
Grid-based geometry from values in table.
|
GeomGrid-based geometry from values in table.
|
||||||
|
|
||||||
"""
|
"""
|
||||||
cells,size,origin = grid_filters.cellsSizeOrigin_coordinates0_point(table.get(coordinates))
|
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 \
|
ma = np.arange(cells.prod()) if len(unique) == cells.prod() else \
|
||||||
np.arange(unique.size)[np.argsort(pd.unique(unique_inverse))][unique_inverse]
|
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,
|
size = size,
|
||||||
origin = origin,
|
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)
|
size : sequence of float, len (3)
|
||||||
Edge lengths of the grid in meter.
|
Edge lengths of the grid in meter.
|
||||||
seeds : numpy.ndarray of float, shape (:,3)
|
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 : 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 : sequence of int, len (seeds.shape[0]), optional
|
||||||
Material ID of the seeds.
|
Material ID of the seeds.
|
||||||
Defaults to None, in which case materials are consecutively numbered.
|
Defaults to None, in which case materials are consecutively numbered.
|
||||||
|
|
@ -498,8 +547,8 @@ class Grid:
|
||||||
|
|
||||||
Returns
|
Returns
|
||||||
-------
|
-------
|
||||||
new : damask.Grid
|
new : damask.GeomGrid
|
||||||
Grid-based geometry from tessellation.
|
GeomGrid-based geometry from tessellation.
|
||||||
|
|
||||||
"""
|
"""
|
||||||
weights_p: FloatSequence
|
weights_p: FloatSequence
|
||||||
|
|
@ -515,16 +564,16 @@ class Grid:
|
||||||
coords = grid_filters.coordinates0_point(cells,size).reshape(-1,3)
|
coords = grid_filters.coordinates0_point(cells,size).reshape(-1,3)
|
||||||
|
|
||||||
pool = mp.Pool(int(os.environ.get('OMP_NUM_THREADS',4)))
|
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.close()
|
||||||
pool.join()
|
pool.join()
|
||||||
material_ = np.array(result.get()).reshape(cells)
|
material_ = np.array(result.get()).reshape(cells)
|
||||||
|
|
||||||
if periodic: material_ %= len(weights)
|
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,
|
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,
|
size: FloatSequence,
|
||||||
seeds: np.ndarray,
|
seeds: np.ndarray,
|
||||||
material: Optional[IntSequence] = None,
|
material: Optional[IntSequence] = None,
|
||||||
periodic: bool = True) -> 'Grid':
|
periodic: bool = True) -> 'GeomGrid':
|
||||||
"""
|
"""
|
||||||
Create grid from Voronoi tessellation.
|
Create grid from Voronoi tessellation.
|
||||||
|
|
||||||
|
|
@ -544,7 +593,8 @@ class Grid:
|
||||||
size : sequence of float, len (3)
|
size : sequence of float, len (3)
|
||||||
Edge lengths of the grid in meter.
|
Edge lengths of the grid in meter.
|
||||||
seeds : numpy.ndarray of float, shape (:,3)
|
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 : sequence of int, len (seeds.shape[0]), optional
|
||||||
Material ID of the seeds.
|
Material ID of the seeds.
|
||||||
Defaults to None, in which case materials are consecutively numbered.
|
Defaults to None, in which case materials are consecutively numbered.
|
||||||
|
|
@ -553,8 +603,8 @@ class Grid:
|
||||||
|
|
||||||
Returns
|
Returns
|
||||||
-------
|
-------
|
||||||
new : damask.Grid
|
new : damask.GeomGrid
|
||||||
Grid-based geometry from tessellation.
|
GeomGrid-based geometry from tessellation.
|
||||||
|
|
||||||
"""
|
"""
|
||||||
coords = grid_filters.coordinates0_point(cells,size).reshape(-1,3)
|
coords = grid_filters.coordinates0_point(cells,size).reshape(-1,3)
|
||||||
|
|
@ -565,9 +615,9 @@ class Grid:
|
||||||
except TypeError:
|
except TypeError:
|
||||||
material_ = tree.query(coords, n_jobs = int(os.environ.get('OMP_NUM_THREADS',4)))[1] # scipy <1.6
|
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,
|
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,
|
surface: str,
|
||||||
threshold: float = 0.0,
|
threshold: float = 0.0,
|
||||||
periods: int = 1,
|
periods: int = 1,
|
||||||
materials: IntSequence = (0,1)) -> 'Grid':
|
materials: IntSequence = (0,1)) -> 'GeomGrid':
|
||||||
"""
|
"""
|
||||||
Create grid from definition of triply-periodic minimal surface.
|
Create grid from definition of triply-periodic minimal surface.
|
||||||
|
|
||||||
|
|
@ -640,8 +690,8 @@ class Grid:
|
||||||
|
|
||||||
Returns
|
Returns
|
||||||
-------
|
-------
|
||||||
new : damask.Grid
|
new : damask.GeomGrid
|
||||||
Grid-based geometry from definition of minimal surface.
|
GeomGrid-based geometry from definition of minimal surface.
|
||||||
|
|
||||||
Notes
|
Notes
|
||||||
-----
|
-----
|
||||||
|
|
@ -676,7 +726,7 @@ class Grid:
|
||||||
|
|
||||||
>>> import numpy as np
|
>>> import numpy as np
|
||||||
>>> import damask
|
>>> 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
|
cells : 64 × 64 × 64
|
||||||
size : 0.0001 × 0.0001 × 0.0001 m³
|
size : 0.0001 × 0.0001 × 0.0001 m³
|
||||||
origin: 0.0 0.0 0.0 m
|
origin: 0.0 0.0 0.0 m
|
||||||
|
|
@ -686,7 +736,7 @@ class Grid:
|
||||||
|
|
||||||
>>> import numpy as np
|
>>> import numpy as np
|
||||||
>>> import damask
|
>>> 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))
|
... 'Neovius',materials=(1,5))
|
||||||
cells : 80 × 80 × 80
|
cells : 80 × 80 × 80
|
||||||
size : 0.0005 × 0.0005 × 0.0005 m³
|
size : 0.0005 × 0.0005 × 0.0005 m³
|
||||||
|
|
@ -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[1])+0.5)/cells[1],
|
||||||
periods*2.0*np.pi*(np.arange(cells[2])+0.5)/cells[2],
|
periods*2.0*np.pi*(np.arange(cells[2])+0.5)/cells[2],
|
||||||
indexing='ij',sparse=True)
|
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,
|
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,
|
def canvas(self,
|
||||||
cells: Optional[IntSequence] = None,
|
cells: Optional[IntSequence] = None,
|
||||||
offset: Optional[IntSequence] = None,
|
offset: Optional[IntSequence] = None,
|
||||||
fill: Optional[int] = None) -> 'Grid':
|
fill: Optional[int] = None) -> 'GeomGrid':
|
||||||
"""
|
"""
|
||||||
Crop or enlarge/pad grid.
|
Crop or enlarge/pad grid.
|
||||||
|
|
||||||
|
|
@ -795,7 +845,7 @@ class Grid:
|
||||||
|
|
||||||
Returns
|
Returns
|
||||||
-------
|
-------
|
||||||
updated : damask.Grid
|
updated : damask.GeomGrid
|
||||||
Updated grid-based geometry.
|
Updated grid-based geometry.
|
||||||
|
|
||||||
Examples
|
Examples
|
||||||
|
|
@ -804,7 +854,7 @@ class Grid:
|
||||||
|
|
||||||
>>> import numpy as np
|
>>> import numpy as np
|
||||||
>>> import damask
|
>>> 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])
|
>>> g.canvas([32,32,16],[0,0,16])
|
||||||
cells: 32 × 32 × 16
|
cells: 32 × 32 × 16
|
||||||
size: 0.001 × 0.001 × 0.0005 m³
|
size: 0.001 × 0.001 × 0.0005 m³
|
||||||
|
|
@ -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]]
|
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),
|
size = self.size/self.cells*np.asarray(canvas.shape),
|
||||||
origin = self.origin+offset_*self.size/self.cells,
|
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,
|
def mirror(self,
|
||||||
directions: Sequence[str],
|
directions: Sequence[str],
|
||||||
reflect: bool = False) -> 'Grid':
|
reflect: bool = False) -> 'GeomGrid':
|
||||||
"""
|
"""
|
||||||
Mirror grid along given directions.
|
Mirror grid along given directions.
|
||||||
|
|
||||||
|
|
@ -846,7 +896,7 @@ class Grid:
|
||||||
|
|
||||||
Returns
|
Returns
|
||||||
-------
|
-------
|
||||||
updated : damask.Grid
|
updated : damask.GeomGrid
|
||||||
Updated grid-based geometry.
|
Updated grid-based geometry.
|
||||||
|
|
||||||
Examples
|
Examples
|
||||||
|
|
@ -855,7 +905,7 @@ class Grid:
|
||||||
|
|
||||||
>>> import numpy as np
|
>>> import numpy as np
|
||||||
>>> import damask
|
>>> 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
|
cells: 4 × 5 × 6
|
||||||
size: 1.0 × 1.0 × 1.0 m³
|
size: 1.0 × 1.0 × 1.0 m³
|
||||||
origin: 0.0 0.0 0.0 m
|
origin: 0.0 0.0 0.0 m
|
||||||
|
|
@ -893,15 +943,15 @@ class Grid:
|
||||||
if 'z' in directions:
|
if 'z' in directions:
|
||||||
mat = np.concatenate([mat,mat[:,:,limits[0]:limits[1]:-1]],2)
|
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),
|
size = self.size/self.cells*np.asarray(mat.shape),
|
||||||
origin = self.origin,
|
origin = self.origin,
|
||||||
comments = self.comments+[util.execution_stamp('Grid','mirror')],
|
comments = self.comments+[util.execution_stamp('GeomGrid','mirror')],
|
||||||
)
|
)
|
||||||
|
|
||||||
|
|
||||||
def flip(self,
|
def flip(self,
|
||||||
directions: Sequence[str]) -> 'Grid':
|
directions: Sequence[str]) -> 'GeomGrid':
|
||||||
"""
|
"""
|
||||||
Flip grid along given directions.
|
Flip grid along given directions.
|
||||||
|
|
||||||
|
|
@ -912,7 +962,7 @@ class Grid:
|
||||||
|
|
||||||
Returns
|
Returns
|
||||||
-------
|
-------
|
||||||
updated : damask.Grid
|
updated : damask.GeomGrid
|
||||||
Updated grid-based geometry.
|
Updated grid-based geometry.
|
||||||
|
|
||||||
Examples
|
Examples
|
||||||
|
|
@ -921,7 +971,7 @@ class Grid:
|
||||||
|
|
||||||
>>> import numpy as np
|
>>> import numpy as np
|
||||||
>>> import damask
|
>>> 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
|
cells: 4 × 5 × 6
|
||||||
size: 1.0 × 1.0 × 1.0 m³
|
size: 1.0 × 1.0 × 1.0 m³
|
||||||
origin: 0.0 0.0 0.0 m
|
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])
|
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,
|
size = self.size,
|
||||||
origin = self.origin,
|
origin = self.origin,
|
||||||
comments = self.comments+[util.execution_stamp('Grid','flip')],
|
comments = self.comments+[util.execution_stamp('GeomGrid','flip')],
|
||||||
)
|
)
|
||||||
|
|
||||||
|
|
||||||
def rotate(self,
|
def rotate(self,
|
||||||
R: Rotation,
|
R: Rotation,
|
||||||
fill: Optional[int] = None) -> 'Grid':
|
fill: Optional[int] = None) -> 'GeomGrid':
|
||||||
"""
|
"""
|
||||||
Rotate grid (possibly extending its bounding box).
|
Rotate grid (possibly extending its bounding box).
|
||||||
|
|
||||||
|
|
@ -963,7 +1013,7 @@ class Grid:
|
||||||
|
|
||||||
Returns
|
Returns
|
||||||
-------
|
-------
|
||||||
updated : damask.Grid
|
updated : damask.GeomGrid
|
||||||
Updated grid-based geometry.
|
Updated grid-based geometry.
|
||||||
|
|
||||||
Examples
|
Examples
|
||||||
|
|
@ -972,7 +1022,7 @@ class Grid:
|
||||||
|
|
||||||
>>> import numpy as np
|
>>> import numpy as np
|
||||||
>>> import damask
|
>>> 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
|
cells: 4 × 5 × 6
|
||||||
size: 1.0 × 1.0 × 1.0 m³
|
size: 1.0 × 1.0 × 1.0 m³
|
||||||
origin: 0.0 0.0 0.0 m
|
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
|
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),
|
size = self.size/self.cells*np.asarray(material.shape),
|
||||||
origin = origin,
|
origin = origin,
|
||||||
comments = self.comments+[util.execution_stamp('Grid','rotate')],
|
comments = self.comments+[util.execution_stamp('GeomGrid','rotate')],
|
||||||
)
|
)
|
||||||
|
|
||||||
|
|
||||||
def scale(self,
|
def scale(self,
|
||||||
cells: IntSequence) -> 'Grid':
|
cells: IntSequence) -> 'GeomGrid':
|
||||||
"""
|
"""
|
||||||
Scale grid to new cell counts.
|
Scale grid to new cell counts.
|
||||||
|
|
||||||
|
|
@ -1013,7 +1063,7 @@ class Grid:
|
||||||
|
|
||||||
Returns
|
Returns
|
||||||
-------
|
-------
|
||||||
updated : damask.Grid
|
updated : damask.GeomGrid
|
||||||
Updated grid-based geometry.
|
Updated grid-based geometry.
|
||||||
|
|
||||||
Examples
|
Examples
|
||||||
|
|
@ -1022,7 +1072,7 @@ class Grid:
|
||||||
|
|
||||||
>>> import numpy as np
|
>>> import numpy as np
|
||||||
>>> import damask
|
>>> 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
|
cells: 32 × 32 × 32
|
||||||
size: 0.0001 × 0.0001 × 0.0001 m³
|
size: 0.0001 × 0.0001 × 0.0001 m³
|
||||||
origin: 0.0 0.0 0.0 m
|
origin: 0.0 0.0 0.0 m
|
||||||
|
|
@ -1040,28 +1090,28 @@ class Grid:
|
||||||
points=orig,method='nearest',bounds_error=False,fill_value=None)
|
points=orig,method='nearest',bounds_error=False,fill_value=None)
|
||||||
new = grid_filters.coordinates0_point(cells,self.size,self.origin)
|
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,
|
size = self.size,
|
||||||
origin = self.origin,
|
origin = self.origin,
|
||||||
initial_conditions = {k: interpolator(values=v)(new)
|
initial_conditions = {k: interpolator(values=v)(new)
|
||||||
for k,v in self.initial_conditions.items()},
|
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,
|
def assemble(self,
|
||||||
idx: np.ndarray) -> 'Grid':
|
idx: np.ndarray) -> 'GeomGrid':
|
||||||
"""
|
"""
|
||||||
Assemble new grid from index map.
|
Assemble new grid from index map.
|
||||||
|
|
||||||
Parameters
|
Parameters
|
||||||
----------
|
----------
|
||||||
idx : numpy.ndarray of int, shape (:,:,:) or (:,:,:,3)
|
idx : numpy.ndarray of int, shape (:,:,:) or (:,:,:,3)
|
||||||
Grid of flat indices or coordinate indices.
|
GeomGrid of flat indices or coordinate indices.
|
||||||
|
|
||||||
Returns
|
Returns
|
||||||
-------
|
-------
|
||||||
updated : damask.Grid
|
updated : damask.GeomGrid
|
||||||
Updated grid-based geometry.
|
Updated grid-based geometry.
|
||||||
Cell count of resulting grid matches shape of index map.
|
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')
|
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()}
|
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,
|
size = self.size,
|
||||||
origin = self.origin,
|
origin = self.origin,
|
||||||
initial_conditions = ic,
|
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.
|
Renumber sorted material indices as 0,...,N-1.
|
||||||
|
|
||||||
Returns
|
Returns
|
||||||
-------
|
-------
|
||||||
updated : damask.Grid
|
updated : damask.GeomGrid
|
||||||
Updated grid-based geometry.
|
Updated grid-based geometry.
|
||||||
|
|
||||||
"""
|
"""
|
||||||
_,renumbered = np.unique(self.material,return_inverse=True)
|
_,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,
|
size = self.size,
|
||||||
origin = self.origin,
|
origin = self.origin,
|
||||||
initial_conditions = self.initial_conditions,
|
initial_conditions = self.initial_conditions,
|
||||||
comments = self.comments+[util.execution_stamp('Grid','renumber')],
|
comments = self.comments+[util.execution_stamp('GeomGrid','renumber')],
|
||||||
)
|
)
|
||||||
|
|
||||||
|
|
||||||
def substitute(self,
|
def substitute(self,
|
||||||
from_material: Union[int,IntSequence],
|
from_material: Union[int,IntSequence],
|
||||||
to_material: Union[int,IntSequence]) -> 'Grid':
|
to_material: Union[int,IntSequence]) -> 'GeomGrid':
|
||||||
"""
|
"""
|
||||||
Substitute material indices.
|
Substitute material indices.
|
||||||
|
|
||||||
|
|
@ -1113,7 +1163,7 @@ class Grid:
|
||||||
|
|
||||||
Returns
|
Returns
|
||||||
-------
|
-------
|
||||||
updated : damask.Grid
|
updated : damask.GeomGrid
|
||||||
Updated grid-based geometry.
|
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
|
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
|
material[self.material==f] = t
|
||||||
|
|
||||||
return Grid(material = material,
|
return GeomGrid(material = material,
|
||||||
size = self.size,
|
size = self.size,
|
||||||
origin = self.origin,
|
origin = self.origin,
|
||||||
initial_conditions = self.initial_conditions,
|
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).
|
Sort material indices such that min(material ID) is located at (0,0,0).
|
||||||
|
|
||||||
Returns
|
Returns
|
||||||
-------
|
-------
|
||||||
updated : damask.Grid
|
updated : damask.GeomGrid
|
||||||
Updated grid-based geometry.
|
Updated grid-based geometry.
|
||||||
|
|
||||||
"""
|
"""
|
||||||
|
|
@ -1145,11 +1195,11 @@ class Grid:
|
||||||
sort_idx = np.argsort(from_ma)
|
sort_idx = np.argsort(from_ma)
|
||||||
ma = np.unique(a)[sort_idx][np.searchsorted(from_ma,a,sorter = sort_idx)]
|
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,
|
size = self.size,
|
||||||
origin = self.origin,
|
origin = self.origin,
|
||||||
initial_conditions = self.initial_conditions,
|
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,
|
selection: Optional[IntSequence] = None,
|
||||||
invert_selection: bool = False,
|
invert_selection: bool = False,
|
||||||
periodic: bool = True,
|
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.
|
Smooth grid by selecting most frequent material ID within given stencil at each location.
|
||||||
|
|
||||||
|
|
@ -1179,7 +1229,7 @@ class Grid:
|
||||||
|
|
||||||
Returns
|
Returns
|
||||||
-------
|
-------
|
||||||
updated : damask.Grid
|
updated : damask.GeomGrid
|
||||||
Updated grid-based geometry.
|
Updated grid-based geometry.
|
||||||
|
|
||||||
Notes
|
Notes
|
||||||
|
|
@ -1213,11 +1263,11 @@ class Grid:
|
||||||
mode='wrap' if periodic else 'nearest',
|
mode='wrap' if periodic else 'nearest',
|
||||||
extra_keywords=dict(selection=selection_,rng=rng),
|
extra_keywords=dict(selection=selection_,rng=rng),
|
||||||
).astype(self.material.dtype)
|
).astype(self.material.dtype)
|
||||||
return Grid(material = material,
|
return GeomGrid(material = material,
|
||||||
size = self.size,
|
size = self.size,
|
||||||
origin = self.origin,
|
origin = self.origin,
|
||||||
initial_conditions = self.initial_conditions,
|
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,
|
fill: Optional[int] = None,
|
||||||
R: Rotation = Rotation(),
|
R: Rotation = Rotation(),
|
||||||
inverse: bool = False,
|
inverse: bool = False,
|
||||||
periodic: bool = True) -> 'Grid':
|
periodic: bool = True) -> 'GeomGrid':
|
||||||
"""
|
"""
|
||||||
Insert a primitive geometric object at a given position.
|
Insert a primitive geometric object at a given position.
|
||||||
|
|
||||||
|
|
@ -1258,7 +1308,7 @@ class Grid:
|
||||||
|
|
||||||
Returns
|
Returns
|
||||||
-------
|
-------
|
||||||
updated : damask.Grid
|
updated : damask.GeomGrid
|
||||||
Updated grid-based geometry.
|
Updated grid-based geometry.
|
||||||
|
|
||||||
Examples
|
Examples
|
||||||
|
|
@ -1267,7 +1317,7 @@ class Grid:
|
||||||
|
|
||||||
>>> import numpy as np
|
>>> import numpy as np
|
||||||
>>> import damask
|
>>> 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)
|
>>> g.add_primitive(np.ones(3)*5e-5,np.ones(3)*5e-5,1)
|
||||||
cells : 64 × 64 × 64
|
cells : 64 × 64 × 64
|
||||||
size : 0.0001 × 0.0001 × 0.0001 m³
|
size : 0.0001 × 0.0001 × 0.0001 m³
|
||||||
|
|
@ -1278,7 +1328,7 @@ class Grid:
|
||||||
|
|
||||||
>>> import numpy as np
|
>>> import numpy as np
|
||||||
>>> import damask
|
>>> 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)
|
>>> g.add_primitive(np.ones(3,int)*32,np.zeros(3),np.inf)
|
||||||
cells : 64 × 64 × 64
|
cells : 64 × 64 × 64
|
||||||
size : 0.0001 × 0.0001 × 0.0001 m³
|
size : 0.0001 × 0.0001 × 0.0001 m³
|
||||||
|
|
@ -1304,13 +1354,13 @@ class Grid:
|
||||||
if periodic: # translate back to center
|
if periodic: # translate back to center
|
||||||
mask = np.roll(mask,((c/self.size-0.5)*self.cells).round().astype(np.int64),(0,1,2))
|
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,
|
self.material,
|
||||||
np.nanmax(self.material)+1 if fill is None else fill),
|
np.nanmax(self.material)+1 if fill is None else fill),
|
||||||
size = self.size,
|
size = self.size,
|
||||||
origin = self.origin,
|
origin = self.origin,
|
||||||
initial_conditions = self.initial_conditions,
|
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,
|
offset: Optional[int] = None,
|
||||||
selection: Optional[IntSequence] = None,
|
selection: Optional[IntSequence] = None,
|
||||||
invert_selection: bool = False,
|
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.
|
Offset material ID of points in the vicinity of selected (or just other) material IDs.
|
||||||
|
|
||||||
|
|
@ -1345,7 +1395,7 @@ class Grid:
|
||||||
|
|
||||||
Returns
|
Returns
|
||||||
-------
|
-------
|
||||||
updated : damask.Grid
|
updated : damask.GeomGrid
|
||||||
Updated grid-based geometry.
|
Updated grid-based geometry.
|
||||||
|
|
||||||
"""
|
"""
|
||||||
|
|
@ -1377,11 +1427,11 @@ class Grid:
|
||||||
extra_keywords=dict(selection=selection_),
|
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,
|
size = self.size,
|
||||||
origin = self.origin,
|
origin = self.origin,
|
||||||
initial_conditions = self.initial_conditions,
|
initial_conditions = self.initial_conditions,
|
||||||
comments = self.comments+[util.execution_stamp('Grid','vicinity_offset')],
|
comments = self.comments+[util.execution_stamp('GeomGrid','vicinity_offset')],
|
||||||
)
|
)
|
||||||
|
|
||||||
|
|
||||||
|
|
@ -240,13 +240,6 @@ class Orientation(Rotation,Crystal):
|
||||||
return self.copy(Rotation(self.quaternion)*Rotation(other.quaternion))
|
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
|
@classmethod
|
||||||
@util.extend_docstring(Rotation.from_quaternion,
|
@util.extend_docstring(Rotation.from_quaternion,
|
||||||
adopted_parameters=Crystal.__init__)
|
adopted_parameters=Crystal.__init__)
|
||||||
|
|
@ -282,6 +275,13 @@ class Orientation(Rotation,Crystal):
|
||||||
def from_matrix(cls, **kwargs) -> 'Orientation':
|
def from_matrix(cls, **kwargs) -> 'Orientation':
|
||||||
return cls(**kwargs)
|
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
|
@classmethod
|
||||||
@util.extend_docstring(Rotation.from_Rodrigues_vector,
|
@util.extend_docstring(Rotation.from_Rodrigues_vector,
|
||||||
adopted_parameters=Crystal.__init__)
|
adopted_parameters=Crystal.__init__)
|
||||||
|
|
@ -303,6 +303,20 @@ class Orientation(Rotation,Crystal):
|
||||||
def from_cubochoric(cls, **kwargs) -> 'Orientation':
|
def from_cubochoric(cls, **kwargs) -> 'Orientation':
|
||||||
return cls(**kwargs)
|
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
|
@classmethod
|
||||||
@util.extend_docstring(Rotation.from_spherical_component,
|
@util.extend_docstring(Rotation.from_spherical_component,
|
||||||
adopted_parameters=Crystal.__init__)
|
adopted_parameters=Crystal.__init__)
|
||||||
|
|
@ -325,7 +339,7 @@ class Orientation(Rotation,Crystal):
|
||||||
hkl: FloatSequence,
|
hkl: FloatSequence,
|
||||||
**kwargs) -> 'Orientation':
|
**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
|
Parameters
|
||||||
----------
|
----------
|
||||||
|
|
@ -855,7 +869,8 @@ class Orientation(Rotation,Crystal):
|
||||||
|
|
||||||
|
|
||||||
def related(self: MyType,
|
def related(self: MyType,
|
||||||
model: str) -> MyType:
|
model: str,
|
||||||
|
target = None) -> MyType:
|
||||||
"""
|
"""
|
||||||
All orientations related to self by given relationship model.
|
All orientations related to self by given relationship model.
|
||||||
|
|
||||||
|
|
@ -863,6 +878,10 @@ class Orientation(Rotation,Crystal):
|
||||||
----------
|
----------
|
||||||
model : str
|
model : str
|
||||||
Orientation relationship model selected from self.orientation_relationships.
|
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
|
Returns
|
||||||
-------
|
-------
|
||||||
|
|
@ -890,11 +909,10 @@ class Orientation(Rotation,Crystal):
|
||||||
[0.924 0.000 0.000 0.383]]
|
[0.924 0.000 0.000 0.383]]
|
||||||
|
|
||||||
"""
|
"""
|
||||||
lattice,o = self.relation_operations(model)
|
lattice,o = self.relation_operations(model,target)
|
||||||
target = Crystal(lattice=lattice)
|
target = Crystal(lattice=lattice) if target is None else target
|
||||||
o = o.broadcast_to(o.shape+self.shape,mode='right')
|
|
||||||
|
|
||||||
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,
|
lattice=lattice,
|
||||||
b = self.b if target.ratio['b'] is None else self.a*target.ratio['b'],
|
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'],
|
c = self.c if target.ratio['c'] is None else self.a*target.ratio['c'],
|
||||||
|
|
|
||||||
|
|
@ -57,6 +57,11 @@ class Table:
|
||||||
|
|
||||||
Test equality of other.
|
Test equality of other.
|
||||||
|
|
||||||
|
Parameters
|
||||||
|
----------
|
||||||
|
other : Table
|
||||||
|
Table to check for equality.
|
||||||
|
|
||||||
"""
|
"""
|
||||||
return NotImplemented if not isinstance(other,Table) else \
|
return NotImplemented if not isinstance(other,Table) else \
|
||||||
self.shapes == other.shapes and self.data.equals(other.data)
|
self.shapes == other.shapes and self.data.equals(other.data)
|
||||||
|
|
|
||||||
|
|
@ -10,8 +10,8 @@ FloatSequence = Union[np.ndarray,Sequence[float]]
|
||||||
IntSequence = Union[np.ndarray,Sequence[int]]
|
IntSequence = Union[np.ndarray,Sequence[int]]
|
||||||
StrSequence = Union[np.ndarray,Sequence[str]]
|
StrSequence = Union[np.ndarray,Sequence[str]]
|
||||||
FileHandle = Union[TextIO, str, Path]
|
FileHandle = Union[TextIO, str, Path]
|
||||||
CrystalFamily = Union[None,Literal['triclinic', 'monoclinic', 'orthorhombic', 'tetragonal', 'hexagonal', 'cubic']]
|
CrystalFamily = Literal['triclinic', 'monoclinic', 'orthorhombic', 'tetragonal', 'hexagonal', 'cubic']
|
||||||
BravaisLattice = Union[None,Literal['aP', 'mP', 'mS', 'oP', 'oS', 'oI', 'oF', 'tP', 'tI', 'hP', 'cP', 'cI', 'cF']]
|
BravaisLattice = Literal['aP', 'mP', 'mS', 'oP', 'oS', 'oI', 'oF', 'tP', 'tI', 'hP', 'cP', 'cI', 'cF']
|
||||||
CrystalKinematics = Literal['slip', 'twin']
|
CrystalKinematics = Literal['slip', 'twin']
|
||||||
NumpyRngSeed = Union[int, IntSequence, np.random.SeedSequence, np.random.Generator]
|
NumpyRngSeed = Union[int, IntSequence, np.random.SeedSequence, np.random.Generator]
|
||||||
# BitGenerator does not exists in older numpy versions
|
# BitGenerator does not exists in older numpy versions
|
||||||
|
|
|
||||||
|
|
@ -457,7 +457,7 @@ class VTK:
|
||||||
data: Union[None, np.ndarray, np.ma.MaskedArray] = None,
|
data: Union[None, np.ndarray, np.ma.MaskedArray] = None,
|
||||||
info: Optional[str] = None,
|
info: Optional[str] = None,
|
||||||
*,
|
*,
|
||||||
table: Optional['Table'] = None):
|
table: Optional['Table'] = None) -> 'VTK':
|
||||||
"""
|
"""
|
||||||
Add new or replace existing point or cell data.
|
Add new or replace existing point or cell data.
|
||||||
|
|
||||||
|
|
@ -534,7 +534,6 @@ class VTK:
|
||||||
else:
|
else:
|
||||||
raise TypeError
|
raise TypeError
|
||||||
|
|
||||||
|
|
||||||
return dup
|
return dup
|
||||||
|
|
||||||
|
|
||||||
|
|
@ -559,20 +558,18 @@ class VTK:
|
||||||
|
|
||||||
"""
|
"""
|
||||||
cell_data = self.vtk_data.GetCellData()
|
cell_data = self.vtk_data.GetCellData()
|
||||||
for a in range(cell_data.GetNumberOfArrays()):
|
if label in [cell_data.GetArrayName(a) for a in range(cell_data.GetNumberOfArrays())]:
|
||||||
if cell_data.GetArrayName(a) == label:
|
|
||||||
try:
|
try:
|
||||||
return vtk_to_numpy(cell_data.GetArray(a))
|
return vtk_to_numpy(cell_data.GetArray(label))
|
||||||
except AttributeError:
|
except AttributeError:
|
||||||
vtk_array = cell_data.GetAbstractArray(a) # string array
|
vtk_array = cell_data.GetAbstractArray(label) # string array
|
||||||
|
|
||||||
point_data = self.vtk_data.GetPointData()
|
point_data = self.vtk_data.GetPointData()
|
||||||
for a in range(point_data.GetNumberOfArrays()):
|
if label in [point_data.GetArrayName(a) for a in range(point_data.GetNumberOfArrays())]:
|
||||||
if point_data.GetArrayName(a) == label:
|
|
||||||
try:
|
try:
|
||||||
return vtk_to_numpy(point_data.GetArray(a))
|
return vtk_to_numpy(point_data.GetArray(label))
|
||||||
except AttributeError:
|
except AttributeError:
|
||||||
vtk_array = point_data.GetAbstractArray(a) # string array
|
vtk_array = point_data.GetAbstractArray(label) # string array
|
||||||
|
|
||||||
try:
|
try:
|
||||||
# string array
|
# string array
|
||||||
|
|
@ -581,6 +578,41 @@ class VTK:
|
||||||
raise KeyError(f'array "{label}" not found')
|
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,
|
def show(self,
|
||||||
label: Optional[str] = None,
|
label: Optional[str] = None,
|
||||||
colormap: Union[Colormap, str] = 'cividis'):
|
colormap: Union[Colormap, str] = 'cividis'):
|
||||||
|
|
|
||||||
|
|
@ -116,7 +116,7 @@ def from_grid(grid,
|
||||||
|
|
||||||
Parameters
|
Parameters
|
||||||
----------
|
----------
|
||||||
grid : damask.Grid
|
grid : damask.GeomGrid
|
||||||
Grid from which the material IDs are used as seeds.
|
Grid from which the material IDs are used as seeds.
|
||||||
selection : (sequence of) int, optional
|
selection : (sequence of) int, optional
|
||||||
Material IDs to consider.
|
Material IDs to consider.
|
||||||
|
|
@ -134,6 +134,12 @@ def from_grid(grid,
|
||||||
coords, materials : numpy.ndarray, shape (:,3); numpy.ndarray, shape (:)
|
coords, materials : numpy.ndarray, shape (:,3); numpy.ndarray, shape (:)
|
||||||
Seed coordinates in 3D space, material IDs.
|
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
|
Examples
|
||||||
--------
|
--------
|
||||||
Recreate seeds from Voronoi tessellation.
|
Recreate seeds from Voronoi tessellation.
|
||||||
|
|
@ -142,7 +148,7 @@ def from_grid(grid,
|
||||||
>>> import scipy.spatial
|
>>> import scipy.spatial
|
||||||
>>> import damask
|
>>> import damask
|
||||||
>>> seeds = damask.seeds.from_random(np.ones(3),29,[128]*3)
|
>>> 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
|
cells: 128 × 128 × 128
|
||||||
size: 1.0 × 1.0 × 1.0 m³
|
size: 1.0 × 1.0 × 1.0 m³
|
||||||
origin: 0.0 0.0 0.0 m
|
origin: 0.0 0.0 0.0 m
|
||||||
|
|
@ -166,8 +172,8 @@ def from_grid(grid,
|
||||||
materials = _np.unique(material[mask])
|
materials = _np.unique(material[mask])
|
||||||
coords_ = _np.zeros((materials.size,3),dtype=float)
|
coords_ = _np.zeros((materials.size,3),dtype=float)
|
||||||
for i,mat in enumerate(materials):
|
for i,mat in enumerate(materials):
|
||||||
pc = (2*_np.pi*coords[material[:,0]==mat,:]-grid.origin)/grid.size
|
pc = 2*_np.pi*coords[material[:,0]==mat,:]/grid.size
|
||||||
coords_[i] = grid.origin + grid.size / 2 / _np.pi * (_np.pi +
|
coords_[i] = grid.size / 2 / _np.pi * (_np.pi +
|
||||||
_np.arctan2(-_np.average(_np.sin(pc),axis=0),
|
_np.arctan2(-_np.average(_np.sin(pc),axis=0),
|
||||||
-_np.average(_np.cos(pc),axis=0))) \
|
-_np.average(_np.cos(pc),axis=0))) \
|
||||||
if periodic else \
|
if periodic else \
|
||||||
|
|
|
||||||
|
|
@ -4,7 +4,7 @@ import re
|
||||||
from pathlib import Path
|
from pathlib import Path
|
||||||
from typing import Literal
|
from typing import Literal
|
||||||
|
|
||||||
_marc_version = '2023.1'
|
_marc_version = '2023.3'
|
||||||
_marc_root = '/opt/msc'
|
_marc_root = '/opt/msc'
|
||||||
_damask_root = str(Path(__file__).parents[3])
|
_damask_root = str(Path(__file__).parents[3])
|
||||||
|
|
||||||
|
|
|
||||||
|
|
@ -1 +1 @@
|
||||||
../Grid/2phase_irregularGrid.dream3d
|
../GeomGrid/2phase_irregularGrid.dream3d
|
||||||
|
|
@ -1 +1 @@
|
||||||
../Grid/2phase_irregularGrid.json
|
../GeomGrid/2phase_irregularGrid.json
|
||||||
|
|
@ -1 +1 @@
|
||||||
../Grid/2phase_irregularGrid.xdmf
|
../GeomGrid/2phase_irregularGrid.xdmf
|
||||||
|
|
@ -1 +1 @@
|
||||||
../Grid/measured.dream3d
|
../GeomGrid/measured.dream3d
|
||||||
|
|
@ -1 +1 @@
|
||||||
../Grid/measured.xdmf
|
../GeomGrid/measured.xdmf
|
||||||
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Reference in New Issue