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msspec_python3
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Work on continuous integration 

* Started port of the previous CI.bash
* Also fix bug in spec.f (stdout was closed so nothing appeared on screen
  at the second call to libspec)
* Work on test suite
  - utils to create clusters are tested
  - PED calculator for polar and azimutal scans are tested
This commit is contained in:
Sylvain Tricot 2019-11-20 18:14:00 +01:00
parent d167bd9f75
commit 4807474889
14 changed files with 497 additions and 29 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

1
.gitignore vendored
View File

@ -2,3 +2,4 @@ __pycache__
*.py[cod]
*.so
*.bak
package/

176
CI/CI.bash Normal file
View File

@ -0,0 +1,176 @@
#!/bin/bash
SCRIPT_NAME=$(basename $0)
TOPLEVEL=$(git rev-parse --show-toplevel)
VERSION=$(git describe|sed 's/-\([[:digit:]]\+\)-.*/\.post\1/')
(return 0 2>/dev/null) && sourced=1 || sourced=0
pythonpath_prepend() {
if [ -d "$1" ]; then
PYTHONPATH=${PYTHONPATH//":$1:"/:} #delete all instances in the middle
PYTHONPATH=${PYTHONPATH/%":$1"/} #delete any instance at the end
PYTHONPATH=${PYTHONPATH/#"$1:"/} #delete any instance at the beginning
PYTHONPATH="$1${PYTHONPATH:+":$PYTHONPATH"}" #prepend $1 or if $PATH is empty set to $1
export PYTHONPATH
fi
}
# Setup or upgrade the Python virtual environment
setup_virtualenv(){
VENV_PATH="$1"
virtualenv --python=python3 --system-site-packages "$VENV_PATH"
source "$VENV_PATH/bin/activate"
pip install --upgrade pip
pip install --upgrade numpy ase h5py lxml pint terminaltables pycairo
pip install --upgrade sphinx
status=$?
deactivate
[ $status -eq 0 ] || exit 1
}
activate_msspec_python3_virtualenv() {
VENV_PATH="$1"
# do not activate virtualenv if already activated
if [ x"${VIRTUAL_ENV}" == x ]; then
# We are not in a virtualenv
if [ x"${VENV_PATH}" != x ]; then
# activate the specified venv
export MSSPEC_ROOT="${TOPLEVEL}"
pythonpath_prepend "$MSSPEC_ROOT/src"
#PYTHONPATH="$PYTHONPATH":"$MSSPEC_ROOT"/src
source "$VENV_PATH/bin/activate"
else
# error
echo "Error: No venv specified!!"
fi
else
# We are in a virtualenv so load only variables
export MSSPEC_ROOT="${TOPLEVEL}"
pythonpath_prepend "$MSSPEC_ROOT/src"
fi
}
make_pymsspec_package() {
echo "Running setuptools for pymsspec, please wait... "
VERSION=$(get_package_version)
DEST=${TOPLEVEL}/install_resources/packages/${VERSION}
mkdir -p $DEST
cd ${TOPLEVEL}/src/python/pymsspec && python setup.py sdist 2>&1 > /dev/null
cp ${TOPLEVEL}/src/python/pymsspec/dist/pymsspec-${VERSION}.tar.gz ${DEST}/
rm -rf ${TOPLEVEL}/src/python/pymsspec/{*.egg-info,dist}
}
make_pybinding() {
echo "Creating Python library for Fortran code, please wait... "
activate_msspec_python3_virtualenv
cd ${TOPLEVEL}/src/ && make pybinding
}
make_selfex() {
echo "Creating the self-extractible setup program... "
VERSION=$(get_package_version)
DEST=${TOPLEVEL}/install_resources/packages/${VERSION}
LICENSE="${TOPLEVEL}/src/CI/license.txt"
REQUIREMENTS="${TOPLEVEL}/src/CI/requirements"
SETUPFILE="MsSpec-${VERSION}.setup"
MAKESELF=${TOPLEVEL}/src/CI/makeself/makeself.sh
#pip freeze > "${REQUIREMENTS}"
mkdir -p $DEST
cp "${TOPLEVEL}/src/CI/install.sh" "${DEST}"
chmod u+x "${DEST}/install.sh"
cp "${TOPLEVEL}/src/CI/uninstall.sh" "${DEST}"
cp "${TOPLEVEL}/src/CI/msspec" "${DEST}"
cp "${TOPLEVEL}/src/CI/requirements" "${DEST}"
cp "${TOPLEVEL}/src/CI/distro-requirements" "${DEST}"
get_makeself
cd "${DEST}/../" && ${MAKESELF} --license ${LICENSE} --quiet ${VERSION} ${SETUPFILE} "MsSpec - pymsspec" ./install.sh
rm -rf ${SETUPFILE}.bak
rm -rf "${DEST}"
#rm -rf "${REQUIREMENTS}"
}
make_pdf() {
DEST=${TOPLEVEL}/package
mkdir -p ${DEST}
# first activate the virtual environment
activate_msspec_python3_virtualenv
# then build the documentation.
cd "${TOPLEVEL}/doc"
make --no-print-directory latexpdf || exit 1
# remove previous pdf
rm -rf "${DEST}"/*.pdf
# copy the produced pdf file to the final location
cp "build/latex/MsSpec-python.pdf" "${TOPLEVEL}/package/MsSpec-${VERSION}.pdf"
}
make_html () {
make_pdf
# first activate the virtual environment
activate_msspec_python3_virtualenv
# then build the documentation.
cd "${TOPLEVEL}/doc"
make --no-print-directory html || exit 1
}
make_tests() {
echo "generate results for unit tests..."
activate_msspec_python3_virtualenv
python -c "from msspec.tests import create_tests_results; create_tests_results()"
}
create_package() {
VENV_PATH="$1"
source "$VENV_PATH/bin/activate"
#update_version
#make_tests
#make_pdf
#make_pymsspec_package
#make_msspecgui_package
#make_fortran_package
#make_selfex
#cleanup
deactivate
}
cleanup() {
echo "cleaning up..."
# remove results.txt file
python -c "from msspec.tests import delete_results_file; delete_results_file()"
VERSION=$(get_package_version)
rm -f ${TOPLEVEL}/guide/MsSpec-${VERSION}.pdf
}
show_help () {
echo "Usage: $SCRIPT_NAME [OPTIONS]"
echo "List of possible options:"
echo " -i Initialize a Python virtual environnment in FOLDER"
echo " -d Build the html documentation within the Python "
echo " virtual environnment in FOLDER"
}
if [ "$sourced" == 0 ]; then
while getopts "hi:dt" option; do
case $option in
i) setup_virtualenv "$OPTARG"
;;
d) make_html
;;
t) make_tests
;;
h) show_help
;;
*) show_help
;;
esac
done
fi

11
Makefile
View File

@ -8,7 +8,11 @@ SETUPFILE:=pymsspec-$(VERSION).setup
clean:
@rm -rf *.setup
@echo "Cleaning all..."
@find ./src -type f -name '*.pyc' -exec rm {} +
@find ./src -type d -name '__pycache__' -exec rm -r {} +
+$(MAKE) -C src/ clean
+$(MAKE) -C doc/ clean
version:
@python ./CI/update_version.py
@ -16,9 +20,8 @@ version:
purge: clean
@echo "Purging all..."
@find ./src -type f -name '*.pyc' -exec rm {} +
@find ./src -type d -name '__pycache__' -exec rm -r {} +
+$(MAKE) -C src/ clean
@rm -rf *.setup
+$(MAKE) -C src/ purge
selfex: purge
@echo "Creating the self-extractible setup program... "

4
src/Makefile
View File

@ -16,3 +16,7 @@ clean:
@rm -rf dist
@rm -rf *.egg*
purge: clean
+$(MAKE) -C msspec/spec/fortran purge
+$(MAKE) -C msspec/phagen/fortran purge

1
src/install.sh
View File

@ -1,6 +1,7 @@
#!/bin/bash
# vim: set ts=4 sw=4 sts noet mouse=a fdm=indent:
SCRIPT_NAME=$(basename "$0")
PYTHON=python3
VERSION=$(cat ./msspec/version.py|cut -d\" -f2)
DEFAULT_DEST="${HOME}/.local/share"

24
src/msspec/calculator.py
View File

@ -68,14 +68,14 @@ from terminaltables.ascii_table import AsciiTable
try:
MSSPEC_ROOT = os.environ['MSSPEC_ROOT']
except KeyError:
cfg = Config()
MSSPEC_ROOT = cfg.get('path')
#try:
# MSSPEC_ROOT = os.environ['MSSPEC_ROOT']
#except KeyError:
# cfg = Config()
# MSSPEC_ROOT = cfg.get('path')
if MSSPEC_ROOT == str(None):
raise NameError('No path to the MsSpec distribution found !!')
#if MSSPEC_ROOT == str(None):
# raise NameError('No path to the MsSpec distribution found !!')
@ -185,7 +185,7 @@ class _MSCALCULATOR(Calculator):
LOGGER.debug(' create a space dedicated to the calculation')
########################################################################
self.init_folder = os.getcwd()
self.msspec_folder = os.path.join(MSSPEC_ROOT)
#self.msspec_folder = os.path.join(MSSPEC_ROOT)
self.tmp_folder = os.path.abspath(folder)
LOGGER.debug(' folder: \'%s\'', self.tmp_folder)
if not os.path.exists(self.tmp_folder):
@ -195,7 +195,7 @@ class _MSCALCULATOR(Calculator):
#copyfile(os.path.join(self.msspec_folder, 'ase', 'Makefile'),
# os.path.join(self.tmp_folder, 'Makefile'))
os.chdir(self.tmp_folder)
#os.chdir(self.tmp_folder)
inv = cor = 'NO'
if algorithm == 'expansion':
@ -225,8 +225,8 @@ class _MSCALCULATOR(Calculator):
calctype_spectro = self.spec_parameters.get_parameter('calctype_spectro')
calctype_spectro = calctype_spectro.value
self._make_opts = (MSSPEC_ROOT, calctype_spectro, inv, cor,
spin, sorb, self.tmp_folder)
#self._make_opts = (MSSPEC_ROOT, calctype_spectro, inv, cor,
# spin, sorb, self.tmp_folder)
# Initialize the working environment
#self._make('init')
@ -306,6 +306,7 @@ class _MSCALCULATOR(Calculator):
os.rename('fort.10', 'cluster.clu')
os.rename('fort.35', 'tmatrix.tl')
os.rename('fort.55', 'tmatrix.rad')
os.chdir(self.init_folder)
def run_spec(self):
@ -366,6 +367,7 @@ class _MSCALCULATOR(Calculator):
t1 = time.time()
self.resources['spec_time'] = t1 - t0
os.chdir(self.init_folder)
def get_tmatrix(self):
LOGGER.info("Getting the TMatrix...")

2
src/msspec/iodata.py
View File

@ -67,7 +67,7 @@ from distutils.version import StrictVersion, LooseVersion
import sys
#sys.path.append('../../MsSpecGui/msspecgui/msspec/gui')
from .msspecgui.msspec.gui.clusterviewer import ClusterViewer
from msspec.msspecgui.msspec.gui.clusterviewer import ClusterViewer
def cols2matrix(x, y, z, nx=88*1+1, ny=360*1+1):
# mix the values of existing theta and new theta and return the

5
src/msspec/phagen/fortran/Makefile
View File

@ -6,7 +6,7 @@ objects_src := phagen_scf.f
objects := $(patsubst %.f,%.o, $(objects_src))
.PHONY: clean pybinding
.PHONY: clean purge pybinding
pybinding: libphagen.so
@ -24,5 +24,8 @@ $(objects): $(objects_src)
clean:
@echo "cleaning..."
rm -rf *.so *.o *.mod
purge: clean
@echo "Purging..."
rm -rf ../*.so

9
src/msspec/spec/fortran/Makefile
View File

@ -8,7 +8,7 @@ OPTS := -g -Wall -Wextra -Warray-temporaries -Wconversion -fbacktrace -ffree-lin
EXE=prog
.PHONY: clean pybinding
.PHONY: clean purge pybinding
pybinding: libspec.so
@ -33,6 +33,9 @@ $(objects): $(objects_src)
clean:
@echo "cleaning..."
@rm -rf *.so *.o *.mod $(EXE)
@rm -rf ../*.so
@rm -rf *.so *.o *.mod
purge: clean
@echo "Purging..."
@rm -rf $(EXE)
@rm -rf ../*.so

275
src/msspec/spec/fortran/modules.f
View File

@ -11,6 +11,9 @@ C=======================================================================
CONTAINS
SUBROUTINE ALLOC_ADSORB()
USE DIM_MOD
IF (ALLOCATED(ADS)) THEN
DEALLOCATE(ADS)
ENDIF
ALLOCATE(ADS(3,900))
END SUBROUTINE ALLOC_ADSORB
END MODULE ADSORB_MOD
@ -37,8 +40,17 @@ C=======================================================================
CONTAINS
SUBROUTINE ALLOC_APPROX()
USE DIM_MOD
IF (ALLOCATED(RTHFWD)) THEN
DEALLOCATE(RTHFWD)
ENDIF
ALLOCATE(RTHFWD(NATP_M))
IF (ALLOCATED(IBWD)) THEN
DEALLOCATE(IBWD)
ENDIF
ALLOCATE(IBWD(NATP_M))
IF (ALLOCATED(RTHBWD)) THEN
DEALLOCATE(RTHBWD)
ENDIF
ALLOCATE(RTHBWD(NATP_M))
END SUBROUTINE ALLOC_APPROX
END MODULE APPROX_MOD
@ -55,8 +67,17 @@ C=======================================================================
CONTAINS
SUBROUTINE ALLOC_ATOMS()
USE DIM_MOD
IF (ALLOCATED(VALZ)) THEN
DEALLOCATE(VALZ)
ENDIF
ALLOCATE(VALZ(NATCLU_M))
IF (ALLOCATED(NZAT)) THEN
DEALLOCATE(NZAT)
ENDIF
ALLOCATE(NZAT(NATCLU_M))
IF (ALLOCATED(CHEM)) THEN
DEALLOCATE(CHEM)
ENDIF
ALLOCATE(CHEM(NATCLU_M))
END SUBROUTINE ALLOC_ATOMS
END MODULE ATOMS_MOD
@ -70,7 +91,13 @@ C=======================================================================
CONTAINS
SUBROUTINE ALLOC_AUGER()
USE DIM_MOD
IF (ALLOCATED(NLIN_A)) THEN
DEALLOCATE(NLIN_A)
ENDIF
ALLOCATE(NLIN_A(0:20))
IF (ALLOCATED(L_BOUNDS)) THEN
DEALLOCATE(L_BOUNDS)
ENDIF
ALLOCATE(L_BOUNDS(0:20,2))
END SUBROUTINE ALLOC_AUGER
END MODULE AUGER_MOD
@ -83,7 +110,13 @@ C=======================================================================
CONTAINS
SUBROUTINE ALLOC_BASES()
USE DIM_MOD
IF (ALLOCATED(ATBAS)) THEN
DEALLOCATE(ATBAS)
ENDIF
ALLOCATE(ATBAS(3*NATP_M))
IF (ALLOCATED(VECBAS)) THEN
DEALLOCATE(VECBAS)
ENDIF
ALLOCATE(VECBAS(9))
END SUBROUTINE ALLOC_BASES
END MODULE BASES_MOD
@ -100,10 +133,25 @@ C=======================================================================
CONTAINS
SUBROUTINE ALLOC_CLUSLIM()
USE DIM_MOD
IF (ALLOCATED(X_MAX)) THEN
DEALLOCATE(X_MAX)
ENDIF
ALLOCATE(X_MAX(NATCLU_M))
IF (ALLOCATED(X_MIN)) THEN
DEALLOCATE(X_MIN)
ENDIF
ALLOCATE(X_MIN(NATCLU_M))
IF (ALLOCATED(Y_MAX)) THEN
DEALLOCATE(Y_MAX)
ENDIF
ALLOCATE(Y_MAX(NATCLU_M))
IF (ALLOCATED(Y_MIN)) THEN
DEALLOCATE(Y_MIN)
ENDIF
ALLOCATE(Y_MIN(NATCLU_M))
IF (ALLOCATED(VAL)) THEN
DEALLOCATE(VAL)
ENDIF
ALLOCATE(VAL(NATCLU_M))
END SUBROUTINE ALLOC_CLUSLIM
END MODULE CLUSLIM_MOD
@ -121,10 +169,25 @@ C=======================================================================
CONTAINS
SUBROUTINE ALLOC_COOR()
USE DIM_MOD
IF (ALLOCATED(NATYP)) THEN
DEALLOCATE(NATYP)
ENDIF
ALLOCATE(NATYP(NATM))
IF (ALLOCATED(NCHTYP)) THEN
DEALLOCATE(NCHTYP)
ENDIF
ALLOCATE(NCHTYP(NATP_M))
IF (ALLOCATED(NCORR)) THEN
DEALLOCATE(NCORR)
ENDIF
ALLOCATE(NCORR(NAT_EQ_M,NATP_M))
IF (ALLOCATED(INEW_AT)) THEN
DEALLOCATE(INEW_AT)
ENDIF
ALLOCATE(INEW_AT(NATCLU_M))
IF (ALLOCATED(SYM_AT)) THEN
DEALLOCATE(SYM_AT)
ENDIF
ALLOCATE(SYM_AT(3,NATCLU_M))
END SUBROUTINE ALLOC_COOR
END MODULE COOR_MOD
@ -142,6 +205,9 @@ C=======================================================================
CONTAINS
SUBROUTINE ALLOC_DEBWAL()
USE DIM_MOD
IF (ALLOCATED(UJ2)) THEN
DEALLOCATE(UJ2)
ENDIF
ALLOCATE(UJ2(NATM))
END SUBROUTINE ALLOC_DEBWAL
END MODULE DEBWAL_MOD
@ -153,6 +219,9 @@ C=======================================================================
CONTAINS
SUBROUTINE ALLOC_INDAT()
USE DIM_MOD
IF (ALLOCATED(INDATA)) THEN
DEALLOCATE(INDATA)
ENDIF
ALLOCATE(INDATA(100))
END SUBROUTINE ALLOC_INDAT
END MODULE INDAT_MOD
@ -280,6 +349,9 @@ C=======================================================================
CONTAINS
SUBROUTINE ALLOC_MASSAT()
USE DIM_MOD
IF (ALLOCATED(XMT)) THEN
DEALLOCATE(XMT)
ENDIF
ALLOCATE(XMT(NATM))
END SUBROUTINE ALLOC_MASSAT
END MODULE MASSAT_MOD
@ -296,6 +368,9 @@ C=======================================================================
CONTAINS
SUBROUTINE ALLOC_MILLER()
USE DIM_MOD
IF (ALLOCATED(IVN)) THEN
DEALLOCATE(IVN)
ENDIF
ALLOCATE(IVN(3))
END SUBROUTINE ALLOC_MILLER
END MODULE MILLER_MOD
@ -350,6 +425,9 @@ C=======================================================================
CONTAINS
SUBROUTINE ALLOC_RELADS()
USE DIM_MOD
IF (ALLOCATED(PCRELA)) THEN
DEALLOCATE(PCRELA)
ENDIF
ALLOCATE(PCRELA(3))
END SUBROUTINE ALLOC_RELADS
END MODULE RELADS_MOD
@ -365,6 +443,9 @@ C=======================================================================
CONTAINS
SUBROUTINE ALLOC_RELAX()
USE DIM_MOD
IF (ALLOCATED(PCREL)) THEN
DEALLOCATE(PCREL)
ENDIF
ALLOCATE(PCREL(10))
END SUBROUTINE ALLOC_RELAX
END MODULE RELAX_MOD
@ -429,10 +510,25 @@ C=======================================================================
CONTAINS
SUBROUTINE ALLOC_TRANS()
USE DIM_MOD
IF (ALLOCATED(DLT)) THEN
DEALLOCATE(DLT)
ENDIF
ALLOCATE(DLT(NE_M,NATM,0:18,2))
IF (ALLOCATED(TL)) THEN
DEALLOCATE(TL)
ENDIF
ALLOCATE(TL(0:NT_M,4,NATM,NE_M))
IF (ALLOCATED(VK)) THEN
DEALLOCATE(VK)
ENDIF
ALLOCATE(VK(NE_M))
IF (ALLOCATED(VK2)) THEN
DEALLOCATE(VK2)
ENDIF
ALLOCATE(VK2(NE_M))
IF (ALLOCATED(LMAX)) THEN
DEALLOCATE(LMAX)
ENDIF
ALLOCATE(LMAX(NATM,NE_M))
END SUBROUTINE ALLOC_TRANS
END MODULE TRANS_MOD
@ -450,10 +546,25 @@ C=======================================================================
CONTAINS
SUBROUTINE ALLOC_TL_AED()
USE DIM_MOD
IF (ALLOCATED(DLT_A)) THEN
DEALLOCATE(DLT_A)
ENDIF
ALLOCATE(DLT_A(NE_M,NATM,0:18,2))
IF (ALLOCATED(TL_A)) THEN
DEALLOCATE(TL_A)
ENDIF
ALLOCATE(TL_A(0:NT_M,4,NATM,NE_M))
IF (ALLOCATED(VK_A)) THEN
DEALLOCATE(VK_A)
ENDIF
ALLOCATE(VK_A(NE_M))
IF (ALLOCATED(VK2_A)) THEN
DEALLOCATE(VK2_A)
ENDIF
ALLOCATE(VK2_A(NE_M))
IF (ALLOCATED(LMAX_A)) THEN
DEALLOCATE(LMAX_A)
ENDIF
ALLOCATE(LMAX_A(NATM,NE_M))
END SUBROUTINE ALLOC_TL_AED
END MODULE TL_AED_MOD
@ -502,6 +613,9 @@ C=======================================================================
CONTAINS
SUBROUTINE ALLOC_TYPEM()
USE DIM_MOD
IF (ALLOCATED(IEMET)) THEN
DEALLOCATE(IEMET)
ENDIF
ALLOCATE(IEMET(NEMET_M))
END SUBROUTINE ALLOC_TYPEM
END MODULE TYPEM_MOD
@ -532,6 +646,9 @@ C=======================================================================
CONTAINS
SUBROUTINE ALLOC_VALIN()
USE DIM_MOD
IF (ALLOCATED(NONVOL)) THEN
DEALLOCATE(NONVOL)
ENDIF
ALLOCATE(NONVOL(100))
END SUBROUTINE ALLOC_VALIN
END MODULE VALIN_MOD
@ -544,7 +661,13 @@ C=======================================================================
CONTAINS
SUBROUTINE ALLOC_XMRHO()
USE DIM_MOD
IF (ALLOCATED(XMAT)) THEN
DEALLOCATE(XMAT)
ENDIF
ALLOCATE(XMAT(0:99))
IF (ALLOCATED(RHOAT)) THEN
DEALLOCATE(RHOAT)
ENDIF
ALLOCATE(RHOAT(0:99))
END SUBROUTINE ALLOC_XMRHO
END MODULE XMRHO_MOD
@ -570,8 +693,17 @@ C=======================================================================
CONTAINS
SUBROUTINE ALLOC_VECSYS()
USE DIM_MOD
IF (ALLOCATED(ASYS)) THEN
DEALLOCATE(ASYS)
ENDIF
ALLOCATE(ASYS(3))
IF (ALLOCATED(BSYS)) THEN
DEALLOCATE(BSYS)
ENDIF
ALLOCATE(BSYS(3))
IF (ALLOCATED(CSYS)) THEN
DEALLOCATE(CSYS)
ENDIF
ALLOCATE(CSYS(3))
END SUBROUTINE ALLOC_VECSYS
END MODULE VECSYS_MOD
@ -583,6 +715,9 @@ C=======================================================================
CONTAINS
SUBROUTINE ALLOC_VIBRAT()
USE DIM_MOD
IF (ALLOCATED(I_FREE)) THEN
DEALLOCATE(I_FREE)
ENDIF
ALLOCATE(I_FREE(NATP_M))
END SUBROUTINE ALLOC_VIBRAT
END MODULE VIBRAT_MOD
@ -594,6 +729,9 @@ C=======================================================================
CONTAINS
SUBROUTINE ALLOC_COEFRLM()
USE DIM_MOD
IF (ALLOCATED(CF)) THEN
DEALLOCATE(CF)
ENDIF
ALLOCATE(CF(0:2*NL_M-2,0:2*NL_M-2,0:2*NL_M-2))
END SUBROUTINE ALLOC_COEFRLM
END MODULE COEFRLM_MOD
@ -605,6 +743,9 @@ C=======================================================================
CONTAINS
SUBROUTINE ALLOC_EXPROT()
USE DIM_MOD
IF (ALLOCATED(EXPR)) THEN
DEALLOCATE(EXPR)
ENDIF
ALLOCATE(EXPR(0:2*NL_M-2,0:2*NL_M-2))
END SUBROUTINE ALLOC_EXPROT
END MODULE EXPROT_MOD
@ -616,6 +757,9 @@ C=======================================================================
CONTAINS
SUBROUTINE ALLOC_EXPFAC()
USE DIM_MOD
IF (ALLOCATED(EXPF)) THEN
DEALLOCATE(EXPF)
ENDIF
ALLOCATE(EXPF(0:2*NL_M-2,0:2*NL_M-2))
END SUBROUTINE ALLOC_EXPFAC
END MODULE EXPFAC_MOD
@ -627,6 +771,9 @@ C=======================================================================
CONTAINS
SUBROUTINE ALLOC_LOGAMAD()
USE DIM_MOD
IF (ALLOCATED(GLD)) THEN
DEALLOCATE(GLD)
ENDIF
ALLOCATE(GLD(0:N_GAUNT,2))
END SUBROUTINE ALLOC_LOGAMAD
END MODULE LOGAMAD_MOD
@ -638,6 +785,9 @@ C=======================================================================
CONTAINS
SUBROUTINE ALLOC_EXPFAC2()
USE DIM_MOD
IF (ALLOCATED(EXPF2)) THEN
DEALLOCATE(EXPF2)
ENDIF
ALLOCATE(EXPF2(0:2*NL_M-2,0:2*NL_M-2))
END SUBROUTINE ALLOC_EXPFAC2
END MODULE EXPFAC2_MOD
@ -649,6 +799,9 @@ C=======================================================================
CONTAINS
SUBROUTINE ALLOC_FACTSQ()
USE DIM_MOD
IF (ALLOCATED(FSQ)) THEN
DEALLOCATE(FSQ)
ENDIF
ALLOCATE(FSQ(0:2*NL_M-2))
END SUBROUTINE ALLOC_FACTSQ
END MODULE FACTSQ_MOD
@ -715,7 +868,13 @@ C=======================================================================
CONTAINS
SUBROUTINE ALLOC_VALIN_AV()
USE DIM_MOD
IF (ALLOCATED(TH_0)) THEN
DEALLOCATE(TH_0)
ENDIF
ALLOCATE(TH_0(NTH_M))
IF (ALLOCATED(PH_0)) THEN
DEALLOCATE(PH_0)
ENDIF
ALLOCATE(PH_0(NPH_M))
END SUBROUTINE ALLOC_VALIN_AV
END MODULE VALIN_AV_MOD
@ -797,6 +956,9 @@ C=======================================================================
CONTAINS
SUBROUTINE ALLOC_C_G()
USE DIM_MOD
IF (ALLOCATED(CG)) THEN
DEALLOCATE(CG)
ENDIF
ALLOCATE(CG(-LI_M:LI_M+1,2,2))
END SUBROUTINE ALLOC_C_G
END MODULE C_G_MOD
@ -808,8 +970,11 @@ C=======================================================================
CONTAINS
SUBROUTINE ALLOC_C_G_A()
USE DIM_MOD
ALLOCATE(CGA(0:NCG_M,-NCG_M:NCG_M,0:NCG_M,-NCG_M:NCG_M,0:2*NCG
&_M))
IF (ALLOCATED(CGA)) THEN
DEALLOCATE(CGA)
ENDIF
ALLOCATE(CGA(0:NCG_M,-NCG_M:NCG_M,0:NCG_M,-NCG_M:NCG_M,0:
& 2*NCG_M))
END SUBROUTINE ALLOC_C_G_A
END MODULE C_G_A_MOD
@ -820,6 +985,9 @@ C=======================================================================
CONTAINS
SUBROUTINE ALLOC_C_G_M()
USE DIM_MOD
IF (ALLOCATED(CG_S)) THEN
DEALLOCATE(CG_S)
ENDIF
ALLOCATE(CG_S(2,2,2))
END SUBROUTINE ALLOC_C_G_M
END MODULE C_G_M_MOD
@ -831,6 +999,9 @@ C=======================================================================
CONTAINS
SUBROUTINE ALLOC_DEXPFAC2()
USE DIM_MOD
IF (ALLOCATED(DEXPF2)) THEN
DEALLOCATE(DEXPF2)
ENDIF
ALLOCATE(DEXPF2(0:2*NL_M-2,0:2*NL_M-2))
END SUBROUTINE ALLOC_DEXPFAC2
END MODULE DEXPFAC2_MOD
@ -842,6 +1013,9 @@ C=======================================================================
CONTAINS
SUBROUTINE ALLOC_DFACTSQ()
USE DIM_MOD
IF (ALLOCATED(DFSQ)) THEN
DEALLOCATE(DFSQ)
ENDIF
ALLOCATE(DFSQ(0:2*NL_M-2))
END SUBROUTINE ALLOC_DFACTSQ
END MODULE DFACTSQ_MOD
@ -912,7 +1086,13 @@ C=======================================================================
CONTAINS
SUBROUTINE ALLOC_LINLBD()
USE DIM_MOD
IF (ALLOCATED(LBD)) THEN
DEALLOCATE(LBD)
ENDIF
ALLOCATE(LBD(-N_MU_M:N_MU_M,0:N_NU_M))
IF (ALLOCATED(NUMAX)) THEN
DEALLOCATE(NUMAX)
ENDIF
ALLOCATE(NUMAX(NATP_M))
END SUBROUTINE ALLOC_LINLBD
END MODULE LINLBD_MOD
@ -952,6 +1132,9 @@ C=======================================================================
CONTAINS
SUBROUTINE ALLOC_RA()
USE DIM_MOD
IF (ALLOCATED(N_RA)) THEN
DEALLOCATE(N_RA)
ENDIF
ALLOCATE(N_RA(NATP_M))
END SUBROUTINE ALLOC_RA
END MODULE RA_MOD
@ -963,6 +1146,9 @@ C=======================================================================
CONTAINS
SUBROUTINE ALLOC_SPECTRUM()
USE DIM_MOD
IF (ALLOCATED(I_SPECTRUM)) THEN
DEALLOCATE(I_SPECTRUM)
ENDIF
ALLOCATE(I_SPECTRUM(NE_M))
END SUBROUTINE ALLOC_SPECTRUM
END MODULE SPECTRUM_MOD
@ -979,9 +1165,21 @@ C=======================================================================
CONTAINS
SUBROUTINE ALLOC_DIRECT()
USE DIM_MOD
IF (ALLOCATED(DIRANA)) THEN
DEALLOCATE(DIRANA)
ENDIF
ALLOCATE(DIRANA(3,49))
IF (ALLOCATED(ANADIR)) THEN
DEALLOCATE(ANADIR)
ENDIF
ALLOCATE(ANADIR(3,49))
IF (ALLOCATED(THETAR)) THEN
DEALLOCATE(THETAR)
ENDIF
ALLOCATE(THETAR(49))
IF (ALLOCATED(PHIR)) THEN
DEALLOCATE(PHIR)
ENDIF
ALLOCATE(PHIR(49))
END SUBROUTINE ALLOC_DIRECT
END MODULE DIRECT_MOD
@ -998,9 +1196,21 @@ C=======================================================================
CONTAINS
SUBROUTINE ALLOC_DIRECT_A()
USE DIM_MOD
IF (ALLOCATED(DIRANA_A)) THEN
DEALLOCATE(DIRANA_A)
ENDIF
ALLOCATE(DIRANA_A(3,49))
IF (ALLOCATED(ANADIR_A)) THEN
DEALLOCATE(ANADIR_A)
ENDIF
ALLOCATE(ANADIR_A(3,49))
IF (ALLOCATED(THETAR_A)) THEN
DEALLOCATE(THETAR_A)
ENDIF
ALLOCATE(THETAR_A(49))
IF (ALLOCATED(PHIR_A)) THEN
DEALLOCATE(PHIR_A)
ENDIF
ALLOCATE(PHIR_A(49))
END SUBROUTINE ALLOC_DIRECT_A
END MODULE DIRECT_A_MOD
@ -1016,9 +1226,21 @@ C=======================================================================
CONTAINS
SUBROUTINE ALLOC_PATH()
USE DIM_MOD
IF (ALLOCATED(NPATH)) THEN
DEALLOCATE(NPATH)
ENDIF
ALLOCATE(NPATH(0:NDIF_M))
IF (ALLOCATED(NPATH2)) THEN
DEALLOCATE(NPATH2)
ENDIF
ALLOCATE(NPATH2(0:NDIF_M))
IF (ALLOCATED(NPMA)) THEN
DEALLOCATE(NPMA)
ENDIF
ALLOCATE(NPMA(0:NDIF_M))
IF (ALLOCATED(NPMI)) THEN
DEALLOCATE(NPMI)
ENDIF
ALLOCATE(NPMI(0:NDIF_M))
END SUBROUTINE ALLOC_PATH
END MODULE PATH_MOD
@ -1030,6 +1252,9 @@ C=======================================================================
CONTAINS
SUBROUTINE ALLOC_ROT()
USE DIM_MOD
IF (ALLOCATED(RLM01)) THEN
DEALLOCATE(RLM01)
ENDIF
ALLOCATE(RLM01(1-NL_M:NL_M-1,1-NL_M:NL_M-1,0:NL_M-1))
END SUBROUTINE ALLOC_ROT
END MODULE ROT_MOD
@ -1043,7 +1268,13 @@ C=======================================================================
CONTAINS
SUBROUTINE ALLOC_TESTPA()
USE DIM_MOD
IF (ALLOCATED(IT)) THEN
DEALLOCATE(IT)
ENDIF
ALLOCATE(IT(0:NDIF_M))
IF (ALLOCATED(IN)) THEN
DEALLOCATE(IN)
ENDIF
ALLOCATE(IN(0:NDIF_M))
END SUBROUTINE ALLOC_TESTPA
END MODULE TESTPA_MOD
@ -1067,6 +1298,9 @@ C=======================================================================
CONTAINS
SUBROUTINE ALLOC_TLDW()
USE DIM_MOD
IF (ALLOCATED(TLT)) THEN
DEALLOCATE(TLT)
ENDIF
ALLOCATE(TLT(0:NT_M,4,NATM,NE_M))
END SUBROUTINE ALLOC_TLDW
END MODULE TLDW_MOD
@ -1080,8 +1314,17 @@ C=======================================================================
CONTAINS
SUBROUTINE ALLOC_VARIA()
USE DIM_MOD
IF (ALLOCATED(CEX)) THEN
DEALLOCATE(CEX)
ENDIF
ALLOCATE(CEX(0:NDIF_M))
IF (ALLOCATED(CEXDW)) THEN
DEALLOCATE(CEXDW)
ENDIF
ALLOCATE(CEXDW(0:NDIF_M))
IF (ALLOCATED(DW)) THEN
DEALLOCATE(DW)
ENDIF
ALLOCATE(DW(0:NDIF_M))
END SUBROUTINE ALLOC_VARIA
END MODULE VARIA_MOD
@ -1094,6 +1337,9 @@ C=======================================================================
SUBROUTINE ALLOC_LBD()
USE DIM_MOD
INTEGER I, J
IF (ALLOCATED(LBDM)) THEN
DEALLOCATE(LBDM)
ENDIF
ALLOCATE(LBDM(2,NDIF_M))
DO I=1,NDIF_M
DO J=1,2
@ -1110,6 +1356,9 @@ C=======================================================================
CONTAINS
SUBROUTINE ALLOC_SCATMAT()
USE DIM_MOD
IF (ALLOCATED(F21)) THEN
DEALLOCATE(F21)
ENDIF
ALLOCATE(F21(NSPIN2_M,NLAMBDA_M,NLAMBDA_M,NDIF_M))
END SUBROUTINE ALLOC_SCATMAT
END MODULE SCATMAT_MOD
@ -1123,7 +1372,13 @@ C=======================================================================
CONTAINS
SUBROUTINE ALLOC_EXTREM()
USE DIM_MOD
IF (ALLOCATED(FMIN)) THEN
DEALLOCATE(FMIN)
ENDIF
ALLOCATE(FMIN(0:NDIF_M))
IF (ALLOCATED(FMAX)) THEN
DEALLOCATE(FMAX)
ENDIF
ALLOCATE(FMAX(0:NDIF_M))
END SUBROUTINE ALLOC_EXTREM
END MODULE EXTREM_MOD
@ -1139,11 +1394,25 @@ C=======================================================================
CONTAINS
SUBROUTINE ALLOC_PRINTP()
USE DIM_MOD
INTEGER I,J
IF (ALLOCATED(FMN)) THEN
DEALLOCATE(FMN)
ENDIF
ALLOCATE(FMN(NPATH_M))
IF (ALLOCATED(PATH)) THEN
DEALLOCATE(PATH)
ENDIF
ALLOCATE(PATH(NPATH_M))
IF (ALLOCATED(DMN)) THEN
DEALLOCATE(DMN)
ENDIF
ALLOCATE(DMN(NPATH_M))
IF (ALLOCATED(JON)) THEN
DEALLOCATE(JON)
ENDIF
ALLOCATE(JON(NPATH_M))
IF (ALLOCATED(JPON)) THEN
DEALLOCATE(JPON)
ENDIF
ALLOCATE(JPON(NPATH_M,NDIF_M))
END SUBROUTINE ALLOC_PRINTP
END MODULE PRINTP_MOD

4
src/msspec/spec/fortran/spec.f
View File

@ -1285,7 +1285,7 @@ C
WRITE(IUO1,562)
ENDIF
IF(ISOM.EQ.0) CLOSE(IUO2)
IF((ISOM.EQ.0).AND.(NFICHLEC.NE.1)) CLOSE(IUO1)
C! IF((ISOM.EQ.0).AND.(NFICHLEC.NE.1)) CLOSE(IUO1)
C
C.......... End of the loop on the data files ..........
C
@ -1309,7 +1309,7 @@ c ENDIF
ENDIF
ENDIF
C
IF((ISOM.NE.0).OR.(NFICHLEC.EQ.1)) CLOSE(IUO1)
C! IF((ISOM.NE.0).OR.(NFICHLEC.EQ.1)) CLOSE(IUO1)
IF(ISOM.NE.0) CLOSE(IUO2)
C STOP
GOTO 999

3
src/msspec/tests.py
View File

@ -144,8 +144,9 @@ def create_tests_results():
create_results(tc, 'test_cut_plane')
tc = PEDCopperTestCase()
create_results(tc, 'test_phi_scan')
create_results(tc, 'test_theta_scan')
tc = PEDCopperTestCase()
create_results(tc, 'test_phi_scan')
def delete_results_file():
os.remove(RESULTS_FILENAME)

1
src/setup.py
View File

@ -9,6 +9,7 @@ setup(name='msspec',
include_package_data=True,
packages=find_packages(include='msspec.*'),
install_requires=[
'numpy',
'ase',
'h5py',
'lxml',

8
utils/process.py
View File

@ -266,7 +266,7 @@ class CommonBlockInfo(BaseInfo):
#exit()
else:
if re.match("^[A-HO-Z].*", v.name, re.I):
v.type = "DOUBLE PRECISION"
v.type = "REAL"
else:
v.type = "INTEGER"
@ -808,6 +808,9 @@ def write_modules(infile):
# for each variable with a defined dimension
for variable in variables:
if variable.dimension is not None:
s += f" IF (ALLOCATED({variable.name})) THEN\n"
s += f" DEALLOCATE({variable.name})\n"
s += f" ENDIF\n"
s += f" ALLOCATE({variable})\n"
s += f" END SUBROUTINE ALLOC_{cbi.name.upper()}\n"
@ -832,10 +835,11 @@ def write_modules(infile):
if __name__ == "__main__":
infile = 'spec.f'
infile = 'spec.f.orig'
# write the modules.f file
write_modules(infile)
exit()
fi = FileInfo(filename=infile)