LCPQ
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quantum_package
mirror of https://github.com/LCPQ/quantum_package
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QPACKAGE_ROOT => QP_ROOT =D

This commit is contained in:
Thomas Applencourt 2015-06-08 14:49:10 +02:00
parent f26f761b0b
commit e0f360084e
35 changed files with 174 additions and 169 deletions
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2
.travis.yml
View File

@ -10,7 +10,7 @@ before_script:
- sudo apt-get install graphviz
script:
- ./setup_environment.sh --robot
- ./setup_environment.py
- source ./quantum_package.rc
- qp_create_ninja.py --production ./config/gfortran_example.cfg
- ninja

4
install/scripts/install_curl.sh
View File

@ -4,10 +4,10 @@ TARGET=curl
function _install()
{
cd ..
QPACKAGE_ROOT=$PWD
QP_ROOT=$PWD
cd -
cd ${BUILD} || return 1
mv curl.ermine ${QPACKAGE_ROOT}/bin/curl || return 1
mv curl.ermine ${QP_ROOT}/bin/curl || return 1
}
BUILD=_build/${TARGET}

6
install/scripts/install_ezfio.sh
View File

@ -5,12 +5,12 @@ TARGET=ezfio
function _install()
{
cd ..
QPACKAGE_ROOT=$PWD
QP_ROOT=$PWD
cd -
rm -rf ${QPACKAGE_ROOT}/EZFIO
rm -rf ${QP_ROOT}/EZFIO
cd ${BUILD}/config || return 1
cd -
mv ${BUILD} ${QPACKAGE_ROOT}/install/EZFIO || return 1
mv ${BUILD} ${QP_ROOT}/install/EZFIO || return 1
}
source scripts/build.sh

6
install/scripts/install_irpf90.sh
View File

@ -4,7 +4,7 @@ TARGET=irpf90
function _install()
{
cd ..
QPACKAGE_ROOT=$PWD
QP_ROOT=$PWD
cd -
make -C ${BUILD} || return 1
@ -13,8 +13,8 @@ function _install()
[[ -x ./irpf90/bin/irpf90 ]] || return 1
[[ -x ./irpf90/bin/irpman ]] || return 1
rm -rf -- ../bin/irpf90 ../bin/irpman
echo 'exec ${QPACKAGE_ROOT}/install/irpf90/bin/irpf90 $@' > ../bin/irpf90 || return 1
echo 'exec ${QPACKAGE_ROOT}/install/irpf90/bin/irpman $@' > ../bin/irpman || return 1
echo 'exec ${QP_ROOT}/install/irpf90/bin/irpf90 $@' > ../bin/irpf90 || return 1
echo 'exec ${QP_ROOT}/install/irpf90/bin/irpman $@' > ../bin/irpman || return 1
chmod +x ../bin/irpf90 ../bin/irpman || return 1
return 0
}

4
install/scripts/install_m4.sh
View File

@ -5,11 +5,11 @@ TARGET=m4
function _install()
{
cd ..
QPACKAGE_ROOT=$PWD
QP_ROOT=$PWD
cd -
cd ${BUILD}
./configure && make || exit 1
ln -sf ${PWD}/src/m4 ${QPACKAGE_ROOT}/bin || exit 1
ln -sf ${PWD}/src/m4 ${QP_ROOT}/bin || exit 1
}
source scripts/build.sh

16
install/scripts/install_ocaml.sh
View File

@ -11,7 +11,7 @@ then
fi
cd ..
QPACKAGE_ROOT=$PWD
QP_ROOT=$PWD
cd -
cd Downloads || exit 1
@ -22,18 +22,18 @@ then
source ${HOME}/.opam/opam-init/init.sh > /dev/null 2> /dev/null || true
fi
echo N | ./ocaml.sh ${QPACKAGE_ROOT}/bin/ || exit 1
if [[ ! -f ${QPACKAGE_ROOT}/bin/opam ]]
echo N | ./ocaml.sh ${QP_ROOT}/bin/ || exit 1
if [[ ! -f ${QP_ROOT}/bin/opam ]]
then
echo "Installation of OPAM failed"
exit 2
fi
${QPACKAGE_ROOT}/bin/opam config setup -a --dot-profile ${QPACKAGE_ROOT}/qmcchemrc || exit 1
touch ${QPACKAGE_ROOT}/bin/opam
${QP_ROOT}/bin/opam config setup -a --dot-profile ${QP_ROOT}/qmcchemrc || exit 1
touch ${QP_ROOT}/bin/opam
export LD_LIBRARY_PATH=${QPACKAGE_ROOT}/lib:${LD_LIBRARY_PATH}
export LIBRARY_PATH=${QPACKAGE_ROOT}/lib:${LIBRARY_PATH}
export C_INCLUDE_PATH=${QPACKAGE_ROOT}/lib:${C_INCLUDE_PATH}
export LD_LIBRARY_PATH=${QP_ROOT}/lib:${LD_LIBRARY_PATH}
export LIBRARY_PATH=${QP_ROOT}/lib:${LIBRARY_PATH}
export C_INCLUDE_PATH=${QP_ROOT}/lib:${C_INCLUDE_PATH}
opam install ${PACKAGES} || exit 1
rm -f ../_build/ocaml.log
exit 0

6
install/scripts/install_patch.sh
View File

@ -6,13 +6,13 @@ function _install()
{
mkdir ${TARGET}
cd ..
QPACKAGE_ROOT=$PWD
QP_ROOT=$PWD
cd -
cd ${BUILD}
./configure --prefix=${QPACKAGE_ROOT}/install/${TARGET} && make || exit 1
./configure --prefix=${QP_ROOT}/install/${TARGET} && make || exit 1
make install || exit 1
cd -
cp ${TARGET}/bin/${TARGET} ${QPACKAGE_ROOT}/bin || exit 1
cp ${TARGET}/bin/${TARGET} ${QP_ROOT}/bin || exit 1
rm -R -- ${TARGET} || exit 1
}

6
install/scripts/install_zlib.sh
View File

@ -4,13 +4,15 @@ TARGET=zlib
function _install()
{
rm -rf -- ${TARGET}
mkdir ${TARGET} || exit 1
cd ..
QPACKAGE_ROOT=$PWD
QP_ROOT=$PWD
cd -
cd ${BUILD}
./configure && make || exit 1
make install prefix=$QPACKAGE_ROOT/install/${TARGET} || exit 1
make install prefix=$QP_ROOT/install/${TARGET} || exit 1
ln -f $QP_ROOT/install/${TARGET}/lib/libz.so $QP_ROOT/lib || exit 1
}
source scripts/build.sh

2
scripts/compilation/cache_compile.py
View File

@ -104,5 +104,5 @@ if __name__ == '__main__':
try:
cache_utility(command)
except:
except OSError:
process = subprocess.Popen(command, shell=True)

33
scripts/compilation/qp_create_ninja.py
View File

@ -24,11 +24,11 @@ except ImportError:
# \_| | (_) |_) (_| | \/ (_| | | (_| |_) | (/_ _>
#
QPACKAGE_ROOT = os.environ['QPACKAGE_ROOT']
QPACKAGE_ROOT_SRC = join(QPACKAGE_ROOT, 'src')
QPACKAGE_ROOT_EZFIO = join(QPACKAGE_ROOT, 'install', 'EZFIO')
QP_ROOT = os.environ['QP_ROOT']
QP_ROOT_SRC = join(QP_ROOT, 'src')
QP_ROOT_EZFIO = join(QP_ROOT, 'install', 'EZFIO')
EZFIO_LIB = join(QPACKAGE_ROOT_EZFIO, "lib", "libezfio.a")
EZFIO_LIB = join(QP_ROOT, "lib", "libezfio.a")
#
# |\ | _. ._ _ _ _| _|_ ._ | _
@ -75,14 +75,14 @@ def dict_module_genelogy_path(d_module_genelogy):
"""
d = dict()
for module_rel, l_children_rel in d_module_genelogy.iteritems():
module_abs = join(QPACKAGE_ROOT_SRC, module_rel)
module_abs = join(QP_ROOT_SRC, module_rel)
p = Path(module_abs, module_rel)
try:
d[p] = Path(join(QPACKAGE_ROOT_SRC, l_children_rel),
d[p] = Path(join(QP_ROOT_SRC, l_children_rel),
l_children_rel)
except:
d[p] = [Path(join(QPACKAGE_ROOT_SRC, children), children)
d[p] = [Path(join(QP_ROOT_SRC, children), children)
for children in l_children_rel]
return d
@ -99,7 +99,7 @@ def get_l_module_with_ezfio_cfg():
"""
from os import listdir
from os.path import isfile, join
qp_src = QPACKAGE_ROOT_SRC
qp_src = QP_ROOT_SRC
return [join(qp_src, m) for m in listdir(qp_src)
if isfile(join(qp_src, m, "EZFIO.cfg"))]
@ -112,10 +112,10 @@ def get_l_ezfio_config():
l = []
cmd = "{0}/*/*.ezfio_config".format(QPACKAGE_ROOT_SRC)
cmd = "{0}/*/*.ezfio_config".format(QP_ROOT_SRC)
for path_in_module in glob.glob(cmd):
name_lower = os.path.split(path_in_module)[1].lower()
path_in_ezfio = join(QPACKAGE_ROOT_EZFIO, "config", name_lower)
path_in_ezfio = join(QP_ROOT_EZFIO, "config", name_lower)
l.append(EZ_config_path(path_in_module, path_in_ezfio))
return l
@ -146,7 +146,7 @@ def get_children_of_ezfio_cfg(l_module_with_ezfio_cfg):
"""
From a module list of ezfio_cfg return all the stuff create by him
"""
config_folder = join(QPACKAGE_ROOT_EZFIO, "config")
config_folder = join(QP_ROOT_EZFIO, "config")
l_util = dict()
@ -222,8 +222,9 @@ def ninja_ezfio_rule():
l_flag = ["export {0}='${0}'".format(flag)
for flag in ["FC", "FCFLAGS", "IRPF90"]]
l_cmd = ["cd {0}".format(QPACKAGE_ROOT_EZFIO)
] + l_flag + ["ninja"]
l_cmd = ["cd {0}".format(QP_ROOT_EZFIO)
] + l_flag + ["make && ln -f {0} {1}".format(join(QP_ROOT, 'install', 'EZFIO',"lib","libezfio.a"),
EZFIO_LIB)]
l_string = ["rule build_ezfio",
" command = {0}".format(" ; ".join(l_cmd)),
@ -244,7 +245,7 @@ def ninja_ezfio_build(l_ezfio_config, l_util):
str_ = " ".join(l_ezfio_config + l_ezfio_from_cfg)
ezfio_make_config = join(QPACKAGE_ROOT_EZFIO,"make.config")
ezfio_make_config = join(QP_ROOT_EZFIO, "make.config")
l_string = ["build {0} {1}: build_ezfio {2}".format(EZFIO_LIB,
ezfio_make_config,
str_), ""]
@ -261,7 +262,7 @@ def get_source_destination(path_module, l_needed_molule):
Return a list of Sym_link = namedtuple('Sym_link', ['source', 'destination'])
for a module
"""
return [Sym_link(m.abs, join(QPACKAGE_ROOT_SRC, path_module.rel, m.rel))
return [Sym_link(m.abs, join(QP_ROOT_SRC, path_module.rel, m.rel))
for m in l_needed_molule]
@ -704,5 +705,5 @@ if __name__ == "__main__":
l_string += ninja_binaries_build(module_to_compile, l_children,
d_binaries_production)
with open(join(QPACKAGE_ROOT, "build.ninja"), "w+") as f:
with open(join(QP_ROOT, "build.ninja"), "w+") as f:
f.write("\n".join(l_string))

2
scripts/compilation/read_compilation_cfg.py
View File

@ -36,7 +36,7 @@ def get_compilation_option(pwd_cfg, flag_name):
if __name__ == '__main__':
qpackage_root = os.environ['QPACKAGE_ROOT']
qpackage_root = os.environ['QP_ROOT']
pwd_cfg = os.path.join(qpackage_root, "config/gfortran_example.cfg")
print get_compilation_option(pwd_cfg, "FC")

32
scripts/ezfio_interface/ei_handler.py
View File

@ -21,11 +21,11 @@ Options:
(aka all with the `interface: input` parameter)
in `${pwd}`
--ezfio_config Create the `${module_lower}_ezfio_interface_config` in
`${QPACKAGE_ROOT}/EZFIO/config/`
`${QP_ROOT}/EZFIO/config/`
This file is needed by *EZFIO* to create the `libezfio.so`
--ocaml Create the `Input_module.lower.ml` for the *qp_edit*
--ezfio_default Create the `${module_lower}_ezfio_interface_default` in
`${QPACKAGE_ROOT}/data/ezfio_defaults` needed by
`${QP_ROOT}/data/ezfio_defaults` needed by
the ocaml
ocaml_global Create the qp_edit
@ -100,7 +100,7 @@ def get_type_dict():
# ~#~#~#~#~ #
# P i c l e #
# ~#~#~#~#~ #
qpackage_root = os.environ['QPACKAGE_ROOT']
qpackage_root = os.environ['QP_ROOT']
# ~#~#~#~ #
# I n i t #
@ -325,7 +325,7 @@ def save_ezfio_provider(path_head, dict_code_provider):
path = "{0}/ezfio_interface.irp.f".format(path_head)
l_output = ["! DO NOT MODIFY BY HAND",
"! Created by $QPACKAGE_ROOT/scripts/ezfio_interface.py",
"! Created by $QP_ROOT/scripts/ezfio_interface.py",
"! from file {0}/EZFIO.cfg".format(path_head),
"\n"]
@ -452,7 +452,7 @@ def create_ezfio_config(dict_ezfio_cfg):
def save_ezfio_config(module_lower, str_ezfio_config):
"""
Write the str_ezfio_config in
"$QPACKAGE_ROOT/EZFIO/{0}.ezfio_interface_config".format(module_lower)
"$QP_ROOT/EZFIO/{0}.ezfio_interface_config".format(module_lower)
"""
name = "{0}.ezfio_interface_config".format(module_lower)
path = os.path.join(os.environ['QP_EZFIO'], "config", name)
@ -469,11 +469,11 @@ def create_ezfio_default(dict_ezfio_cfg):
def save_ezfio_default(module_lower, str_ezfio_default):
"""
Write the str_ezfio_config in
"$QPACKAGE_ROOT/data/ezfio_defaults/{0}.ezfio_interface_default".format(module_lower)
"$QP_ROOT/data/ezfio_defaults/{0}.ezfio_interface_default".format(module_lower)
"""
root_ezfio_default = "{0}/data/ezfio_defaults/".format(
os.environ['QPACKAGE_ROOT'])
os.environ['QP_ROOT'])
path = "{0}/{1}.ezfio_interface_default".format(root_ezfio_default,
module_lower)
with open(path, "w+") as f:
@ -578,10 +578,10 @@ def create_ocaml_input(dict_ezfio_cfg, module_lower):
def save_ocaml_input(module_lower, str_ocaml_input):
"""
Write the str_ocaml_input in
$QPACKAGE_ROOT/ocaml/Input_{0}.ml".format(module_lower)
$QP_ROOT/ocaml/Input_{0}.ml".format(module_lower)
"""
path = "{0}/ocaml/Input_{1}.ml".format(os.environ['QPACKAGE_ROOT'],
path = "{0}/ocaml/Input_{1}.ml".format(os.environ['QP_ROOT'],
module_lower)
with open(path, "w+") as f:
@ -598,7 +598,7 @@ def get_l_module_with_auto_generate_ocaml_lower():
# I n i t #
# ~#~#~#~ #
mypath = "{0}/src".format(os.environ['QPACKAGE_ROOT'])
mypath = "{0}/src".format(os.environ['QP_ROOT'])
# ~#~#~#~#~#~#~#~ #
# L _ f o l d e r #
@ -639,7 +639,7 @@ def create_ocaml_input_global(l_module_with_auto_generate_ocaml_lower):
from ezfio_generate_ocaml import EZFIO_ocaml
qpackage_root = os.environ['QPACKAGE_ROOT']
qpackage_root = os.environ['QP_ROOT']
path = qpackage_root + "/scripts/ezfio_interface/qp_edit_template"
with open(path, "r") as f:
@ -661,10 +661,10 @@ def create_ocaml_input_global(l_module_with_auto_generate_ocaml_lower):
def save_ocaml_input_auto(str_ocaml_input_global):
"""
Write the str_ocaml_input in
$QPACKAGE_ROOT/ocaml/Input_auto_generated.ml
$QP_ROOT/ocaml/Input_auto_generated.ml
"""
path = "{0}/ocaml/Input_auto_generated.ml".format(os.environ['QPACKAGE_ROOT'])
path = "{0}/ocaml/Input_auto_generated.ml".format(os.environ['QP_ROOT'])
with open(path, "w+") as f:
f.write(str_ocaml_input_global)
@ -673,10 +673,10 @@ def save_ocaml_input_auto(str_ocaml_input_global):
def save_ocaml_qp_edit(str_ocaml_qp_edit):
"""
Write the str_ocaml_qp_edit in
$QPACKAGE_ROOT/ocaml/qp_edit.ml
$QP_ROOT/ocaml/qp_edit.ml
"""
path = "{0}/ocaml/qp_edit.ml".format(os.environ['QPACKAGE_ROOT'])
path = "{0}/ocaml/qp_edit.ml".format(os.environ['QP_ROOT'])
with open(path, "w+") as f:
f.write(str_ocaml_qp_edit)
@ -771,7 +771,7 @@ if __name__ == "__main__":
# G e t _ l _ d i c t _ e z f i o _ c f g #
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~# #
qpackage_root_src = join(os.environ['QPACKAGE_ROOT'], "src")
qpackage_root_src = join(os.environ['QP_ROOT'], "src")
l_module_with_ezfio = []

10
scripts/ezfio_interface/qp_convert_output_to_ezfio.py
View File

@ -24,14 +24,14 @@ from functools import reduce
try:
QPACKAGE_ROOT = os.environ["QPACKAGE_ROOT"]
QP_ROOT = os.environ["QP_ROOT"]
except:
print "Error: QPACKAGE_ROOT environment variable not found."
print "Error: QP_ROOT environment variable not found."
sys.exit(1)
else:
sys.path = [QPACKAGE_ROOT + "/EZFIO/Python",
QPACKAGE_ROOT + "/resultsFile",
QPACKAGE_ROOT + "/scripts"] + sys.path
sys.path = [QP_ROOT + "/EZFIO/Python",
QP_ROOT + "/resultsFile",
QP_ROOT + "/scripts"] + sys.path
# ~#~#~#~#~#~ #
# I m p o r t #

2
scripts/ezfio_interface/qp_edit_template
View File

@ -260,7 +260,7 @@ Edit input data
| Assert_failure (file, line, ch) as e ->
begin
Printf.eprintf "=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-\n\n";
Printf.eprintf "Assert error in file $QPACKAGE_ROOT/ocaml/%s, line %d, character %d\n\n" file line ch;
Printf.eprintf "Assert error in file $QP_ROOT/ocaml/%s, line %d, character %d\n\n" file line ch;
Printf.eprintf "=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-\n\n";
(* restore_backup ezfio_file; *)
raise e

2
scripts/generate_h_apply.py
View File

@ -1,7 +1,7 @@
#!/usr/bin/env python
import os
file = open(os.environ["QPACKAGE_ROOT"]+'/src/Determinants/H_apply.template.f','r')
file = open(os.environ["QP_ROOT"]+'/src/Determinants/H_apply.template.f','r')
template = file.read()
file.close()

6
scripts/get_basis.sh
View File

@ -8,14 +8,14 @@
# Prints in stdout the name of a temporary file containing the basis set.
#
if [[ -z ${QPACKAGE_ROOT} ]]
if [[ -z ${QP_ROOT} ]]
then
print "The QPACKAGE_ROOT environment variable is not set."
print "The QP_ROOT environment variable is not set."
print "Please reload the quantum_package.rc file."
exit -1
fi
export EMSL_API_ROOT="${QPACKAGE_ROOT}"/EMSL_Basis/
export EMSL_API_ROOT="${QP_ROOT}"/install/EMSL_Basis/
export PYTHONPATH="${EMSL_API_ROOT}":${PYTHONPATH}
tmpfile="$1"

42
scripts/make_binary.sh
View File

@ -6,15 +6,15 @@
#
# Check the QPACKAGE_ROOT directory
if [[ -z ${QPACKAGE_ROOT} ]]
# Check the QP_ROOT directory
if [[ -z ${QP_ROOT} ]]
then
echo "The QPACKAGE_ROOT environment variable is not set."
echo "The QP_ROOT environment variable is not set."
echo "Please reload the quantum_package.rc file."
exit 1
fi
cd ${QPACKAGE_ROOT}
cd ${QP_ROOT}
if [[ -f quantum_package.rc \
&& -f README.md \
&& -d src \
@ -35,7 +35,7 @@ fi
# Build all sources
for dir in ${QPACKAGE_ROOT}/{src,ocaml}
for dir in ${QP_ROOT}/{src,ocaml}
do
make -C ${dir}
if [[ $? -ne 0 ]]
@ -46,7 +46,7 @@ done
# Copy the files in the static directory
QPACKAGE_STATIC=${QPACKAGE_ROOT}/quantum_package_static
QPACKAGE_STATIC=${QP_ROOT}/quantum_package_static
function find_libs ()
{
@ -58,7 +58,7 @@ function find_libs ()
function find_exec ()
{
find ${QPACKAGE_ROOT}/$1 -perm /u+x -type f
find ${QP_ROOT}/$1 -perm /u+x -type f
}
@ -111,12 +111,12 @@ cd -
for i in ${FORTRAN_EXEC}
do
i=$(basename $i)
echo $i \$QPACKAGE_ROOT/bin/$i
echo $i \$QP_ROOT/bin/$i
done >> ${QPACKAGE_STATIC}/data/executables
cp ${QPACKAGE_ROOT}/data/ezfio_defaults ${QPACKAGE_STATIC}/data
cp ${QP_ROOT}/data/ezfio_defaults ${QPACKAGE_STATIC}/data
mkdir -p ${QPACKAGE_STATIC}/src/Bitmask
cp ${QPACKAGE_ROOT}/src/Bitmask/bitmasks_module.f90 ${QPACKAGE_STATIC}/src/Bitmask
cp ${QP_ROOT}/src/Bitmask/bitmasks_module.f90 ${QPACKAGE_STATIC}/src/Bitmask
#
echo "Copying dynamic libraries"
@ -143,10 +143,10 @@ cp -- ${QPACKAGE_STATIC}/extra_lib/lib{[gi]omp*,mkl*,lapack*,blas*,z*} ${QPACKAG
echo "Copying EMSL_Basis directory"
# ----------------------------
cp -r -- ${QPACKAGE_ROOT}/EMSL_Basis ${QPACKAGE_STATIC}/
cp -r -- ${QP_ROOT}/EMSL_Basis ${QPACKAGE_STATIC}/
if [[ $? -ne 0 ]] ;
then
echo 'cp -r -- ${QPACKAGE_ROOT}/EMSL_Basis ${QPACKAGE_STATIC}/'
echo 'cp -r -- ${QP_ROOT}/EMSL_Basis ${QPACKAGE_STATIC}/'
exit 1
fi
@ -155,10 +155,10 @@ fi
echo "Copying scripts directory"
# -------------------------
cp -r -- ${QPACKAGE_ROOT}/scripts ${QPACKAGE_STATIC}/
cp -r -- ${QP_ROOT}/scripts ${QPACKAGE_STATIC}/
if [[ $? -ne 0 ]] ;
then
echo 'cp -r -- ${QPACKAGE_ROOT}/scripts ${QPACKAGE_STATIC}/'
echo 'cp -r -- ${QP_ROOT}/scripts ${QPACKAGE_STATIC}/'
exit 1
fi
@ -168,13 +168,13 @@ echo "Creating quantum_package.rc"
# ---------------------------
cat << EOF > ${QPACKAGE_STATIC}/quantum_package.rc
export QPACKAGE_ROOT=\$( cd \$(dirname "\${BASH_SOURCE}") ; pwd -P )
export LD_LIBRARY_PATH="\${QPACKAGE_ROOT}"/lib:\${LD_LIBRARY_PATH}
export LIBRARY_PATH="\${QPACKAGE_ROOT}"/lib:\${LIBRARY_PATH}
export PYTHONPATH="\${QPACKAGE_ROOT}"/scripts:\${PYTHONPATH}
export PATH="\${QPACKAGE_ROOT}"/scripts:\${PATH}
export PATH="\${QPACKAGE_ROOT}"/bin:\${PATH}
export PATH="\${QPACKAGE_ROOT}"/ocaml:\${PATH}
export QP_ROOT=\$( cd \$(dirname "\${BASH_SOURCE}") ; pwd -P )
export LD_LIBRARY_PATH="\${QP_ROOT}"/lib:\${LD_LIBRARY_PATH}
export LIBRARY_PATH="\${QP_ROOT}"/lib:\${LIBRARY_PATH}
export PYTHONPATH="\${QP_ROOT}"/scripts:\${PYTHONPATH}
export PATH="\${QP_ROOT}"/scripts:\${PATH}
export PATH="\${QP_ROOT}"/bin:\${PATH}
export PATH="\${QP_ROOT}"/ocaml:\${PATH}
EOF
#exit 0

6
scripts/module/clean_modules.sh
View File

@ -2,13 +2,13 @@
#
# Cleans a module directory
if [[ -z ${QPACKAGE_ROOT} ]]
if [[ -z ${QP_ROOT} ]]
then
print "The QPACKAGE_ROOT environment variable is not set."
print "The QP_ROOT environment variable is not set."
print "Please reload the quantum_package.rc file."
exit -1
fi
source ${QPACKAGE_ROOT}/scripts/qp_include.sh
source ${QP_ROOT}/scripts/qp_include.sh
function do_clean()
{

10
scripts/module/create_executables_list.sh
View File

@ -2,20 +2,20 @@
#
# Thu Mar 26 01:27:14 CET 2015
if [[ -z ${QPACKAGE_ROOT} ]]
if [[ -z ${QP_ROOT} ]]
then
print "The QPACKAGE_ROOT environment variable is not set."
print "The QP_ROOT environment variable is not set."
print "Please reload the quantum_package.rc file."
exit -1
fi
cd ${QPACKAGE_ROOT}/data
cd ${QP_ROOT}/data
rm -f executables
EXES=$(find ${QPACKAGE_ROOT}/src -perm /u+x -type f | grep -e "${QPACKAGE_ROOT}/src/[^/]*/[^/]*$" |sort )
EXES=$(find ${QP_ROOT}/src -perm /u+x -type f | grep -e "${QP_ROOT}/src/[^/]*/[^/]*$" |sort )
for EXE in $EXES
do
printf "%-30s %s\n" $(basename $EXE) $EXE | sed "s|${QPACKAGE_ROOT}|\$QPACKAGE_ROOT|g" >> executables
printf "%-30s %s\n" $(basename $EXE) $EXE | sed "s|${QP_ROOT}|\$QP_ROOT|g" >> executables
done

6
scripts/module/create_gitignore.sh
View File

@ -5,13 +5,13 @@
# Tue Jan 13 14:18:05 CET 2015
#
if [[ -z ${QPACKAGE_ROOT} ]]
if [[ -z ${QP_ROOT} ]]
then
print "The QPACKAGE_ROOT environment variable is not set."
print "The QP_ROOT environment variable is not set."
print "Please reload the quantum_package.rc file."
exit -1
fi
source ${QPACKAGE_ROOT}/scripts/qp_include.sh
source ${QP_ROOT}/scripts/qp_include.sh
function do_gitingore()

6
scripts/module/module_handler.py
View File

@ -30,13 +30,13 @@ except ImportError:
# Canot cache for namedtuple are not hashable
def get_dict_child():
"""Loop over MODULE in QPACKAGE_ROOT/src, open all the NEEDED_CHILDREN_MODULES
"""Loop over MODULE in QP_ROOT/src, open all the NEEDED_CHILDREN_MODULES
and create a dict[MODULE] = [sub module needed, ...]
"""
d_ref = dict()
qpackage_root = os.environ['QPACKAGE_ROOT']
dir_ = os.path.join(qpackage_root, 'src')
qp_root = os.environ['QP_ROOT']
dir_ = os.path.join(qp_root, 'src')
for o in os.listdir(dir_):

2
scripts/module/qp_install_module.py
View File

@ -61,7 +61,7 @@ if __name__ == '__main__':
elif arguments["create"]:
l_children = arguments["<children_module>"]
qpackage_root = os.environ['QPACKAGE_ROOT']
qpackage_root = os.environ['QP_ROOT']
path = os.path.join(qpackage_root, "src", arguments["<name>"])
print "You will create the module:"

2
scripts/perturbation.py
View File

@ -2,7 +2,7 @@
import os
Pert_dir = os.environ["QPACKAGE_ROOT"]+"/src/Perturbation/"
Pert_dir = os.environ["QP_ROOT"]+"/src/Perturbation/"
perturbations = []

2
scripts/pseudo/put_pseudo_in_ezfio.py
View File

@ -17,7 +17,7 @@ from docopt import docopt
from subprocess import Popen, PIPE
qpackage_root = os.environ['QPACKAGE_ROOT']
qpackage_root = os.environ['QP_ROOT']
EZFIO = "{0}/EZFIO".format(qpackage_root)
sys.path = [EZFIO + "/Python"] + sys.path

14
scripts/qp_include.sh
View File

@ -13,23 +13,23 @@ function unique_list()
function check_current_dir_is_src()
{
if [[ "${PWD}" == "${QPACKAGE_ROOT}/src" ]]
if [[ "${PWD}" == "${QP_ROOT}/src" ]]
then
return 0
else
echo "Current directory should be \$QPACKAGE_ROOT/src"
echo "Current directory should be \$QP_ROOT/src"
exit -1
fi
}
function check_current_dir_is_module()
{
# If the prefix ${QPACKAGE_ROOT}/src/ can be removed from $PWD, it means that
# $PWD is somewhere below ${QPACKAGE_ROOT}/src/ so it is a module.
# If the prefix ${QPACKAGE_ROOT}/src/ can not be removed from $PWD, then
# "${PWD##${QPACKAGE_ROOT}/src/}" == "$PWD".
# If the prefix ${QP_ROOT}/src/ can be removed from $PWD, it means that
# $PWD is somewhere below ${QP_ROOT}/src/ so it is a module.
# If the prefix ${QP_ROOT}/src/ can not be removed from $PWD, then
# "${PWD##${QP_ROOT}/src/}" == "$PWD".
if [[ "${PWD##${QPACKAGE_ROOT}/src/}" != "$PWD" ]]
if [[ "${PWD##${QP_ROOT}/src/}" != "$PWD" ]]
then
return 0
else

2
scripts/qp_set_frozen_core.py
View File

@ -3,7 +3,7 @@
import os
import sys
sys.path = [ os.environ["QPACKAGE_ROOT"]+"/EZFIO/Python" ] + sys.path
sys.path = [ os.environ["QP_ROOT"]+"/EZFIO/Python" ] + sys.path
from ezfio import ezfio
ezfio.set_filename(sys.argv[1])

4
scripts/save_current_mos.sh
View File

@ -4,9 +4,9 @@
# directory, where xxx is the corresponding mo_label.
# Wed Apr 2 14:35:15 CEST 2014
if [[ -z ${QPACKAGE_ROOT} ]]
if [[ -z ${QP_ROOT} ]]
then
print "The QPACKAGE_ROOT environment variable is not set."
print "The QP_ROOT environment variable is not set."
print "Please reload the quantum_package.rc file."
exit -1
fi

16
scripts/upgrade/upgrade_ezfio.sh
View File

@ -3,24 +3,24 @@
# Upgrades the EZFIO library from the web.
# Tue Nov 4 00:53:13 CET 2014
if [[ -z ${QPACKAGE_ROOT} ]]
if [[ -z ${QP_ROOT} ]]
then
print "The QPACKAGE_ROOT environment variable is not set."
print "The QP_ROOT environment variable is not set."
print "Please reload the quantum_package.rc file."
fi
cd -- ${QPACKAGE_ROOT}
mv -- ${QPACKAGE_ROOT}/EZFIO ${QPACKAGE_ROOT}/EZFIO.old
cd -- ${QP_ROOT}
mv -- ${QP_ROOT}/EZFIO ${QP_ROOT}/EZFIO.old
${QPACKAGE_ROOT}/scripts/install/install_ezfio.sh
${QP_ROOT}/scripts/install/install_ezfio.sh
if [[ $? -eq 0 ]]
then
rm -rf -- ${QPACKAGE_ROOT}/EZFIO.old
rm -rf -- ${QP_ROOT}/EZFIO.old
echo "Successfully updated EZFIO"
else
rm -rf -- ${QPACKAGE_ROOT}/EZFIO
mv -- ${QPACKAGE_ROOT}/EZFIO.old ${QPACKAGE_ROOT}/EZFIO
rm -rf -- ${QP_ROOT}/EZFIO
mv -- ${QP_ROOT}/EZFIO.old ${QP_ROOT}/EZFIO
echo "Failed to update EZFIO"
fi

16
scripts/upgrade/upgrade_irpf90.sh
View File

@ -3,23 +3,23 @@
# Upgrades IRPF90 from the web.
# Wed Mar 25 11:41:04 CET 2015
if [[ -z ${QPACKAGE_ROOT} ]]
if [[ -z ${QP_ROOT} ]]
then
print "The QPACKAGE_ROOT environment variable is not set."
print "The QP_ROOT environment variable is not set."
print "Please reload the quantum_package.rc file."
fi
cd -- ${QPACKAGE_ROOT}
mv -f -- ${QPACKAGE_ROOT}/irpf90 ${QPACKAGE_ROOT}/irpf90.old
cd -- ${QP_ROOT}
mv -f -- ${QP_ROOT}/irpf90 ${QP_ROOT}/irpf90.old
${QPACKAGE_ROOT}/scripts/install/install_irpf90.sh
${QP_ROOT}/scripts/install/install_irpf90.sh
if [[ $? -eq 0 ]]
then
rm -rf -- ${QPACKAGE_ROOT}/irpf90.old
rm -rf -- ${QP_ROOT}/irpf90.old
echo "Successfully updated IRPF90"
else
rm -rf -- ${QPACKAGE_ROOT}/irpf90
mv -- ${QPACKAGE_ROOT}/irpf90.old ${QPACKAGE_ROOT}/irpf90
rm -rf -- ${QP_ROOT}/irpf90
mv -- ${QP_ROOT}/irpf90.old ${QP_ROOT}/irpf90
echo "Failed to update IRPF90"
fi

62
setup_environment.py
View File

@ -13,9 +13,9 @@ from os.path import join
# \_| |_ (_) |_) (_| | | | | | (_)
#
QPACKAGE_ROOT = os.getcwd()
QPACKAGE_ROOT_BIN = join(QPACKAGE_ROOT, "bin")
QPACKAGE_ROOT_INSTALL = join(QPACKAGE_ROOT, "install")
QP_ROOT = os.getcwd()
QP_ROOT_BIN = join(QP_ROOT, "bin")
QP_ROOT_INSTALL = join(QP_ROOT, "install")
d_dependancy = {
"ocaml": ["m4", "curl", "zlib", "patch", "gcc"],
@ -42,58 +42,58 @@ path_github = {"head": "http://github.com/", "tail": "archive/master.tar.gz"}
ocaml = Info(
url='http://raw.github.com/ocaml/opam/master/shell/opam_installer.sh',
description=' ocaml',
default_path=join(QPACKAGE_ROOT_BIN, "opam"))
default_path=join(QP_ROOT_BIN, "opam"))
m4 = Info(
url="http://ftp.gnu.org/gnu/m4/m4-latest.tar.gz",
description=" m4",
default_path=join(QPACKAGE_ROOT_BIN, "m4"))
default_path=join(QP_ROOT_BIN, "m4"))
curl = Info(
url="http://qmcchem.ups-tlse.fr/files/scemama/curl-7.30.0.ermine.tar.bz2",
description=" curl",
default_path=join(QPACKAGE_ROOT_BIN, "curl"))
default_path=join(QP_ROOT_BIN, "curl"))
zlib = Info(
url='http://zlib.net/zlib-1.2.8.tar.gz',
description=' zlib',
default_path=join(QPACKAGE_ROOT_INSTALL, "zlib"))
default_path=join(QP_ROOT_INSTALL, "zlib"))
path = Info(
url='ftp://ftp.gnu.org/gnu/patch/patch-2.7.5.tar.gz',
description=' path',
default_path=join(QPACKAGE_ROOT_BIN, "patch"))
default_path=join(QP_ROOT_BIN, "patch"))
irpf90 = Info(
url='{head}/scemama/irpf90/archive/v1.6.5.tar.gz'.format(**path_github),
description=' irpf90',
default_path=join(QPACKAGE_ROOT_BIN, "irpf90"))
default_path=join(QP_ROOT_BIN, "irpf90"))
docopt = Info(
url='{head}/docopt/docopt/{tail}'.format(**path_github),
description=' docop',
default_path=join(QPACKAGE_ROOT_INSTALL, "docopt"))
default_path=join(QP_ROOT_INSTALL, "docopt"))
resultsFile = Info(
url='{head}/LCPQ/resultsFile/{tail}'.format(**path_github),
description=' resultsFile',
default_path=join(QPACKAGE_ROOT_INSTALL, "resultsFile"))
default_path=join(QP_ROOT_INSTALL, "resultsFile"))
ninja = Info(
url='{head}/martine/ninja/{tail}'.format(**path_github),
description=' nina',
default_path=join(QPACKAGE_ROOT_BIN, "ninja"))
default_path=join(QP_ROOT_BIN, "ninja"))
emsl = Info(
url='{head}/LCPQ/EMSL_Basis_Set_Exchange_Local/{tail}'.format(**
path_github),
description=' emsl',
default_path=join(QPACKAGE_ROOT_INSTALL, "emsl"))
default_path=join(QP_ROOT_INSTALL, "emsl"))
ezfio = Info(
url='{head}/LCPQ/EZFIO/{tail}'.format(**path_github),
description=' EZFIO',
default_path=join(QPACKAGE_ROOT_INSTALL, "EZFIO"))
default_path=join(QP_ROOT_INSTALL, "EZFIO"))
d_info = dict()
@ -104,10 +104,10 @@ for m in ["ocaml", "m4", "curl", "zlib", "path", "irpf90", "docopt",
l_need = []
# _
# |_ ._ _ _|_ o _ ._
# | |_| | | (_ |_ | (_) | |
#
# _
# |_ ._ _ _|_ o _ ._
# | |_| | | (_ |_ | (_) | |
#
def check_output(*popenargs, **kwargs):
r"""Run command with arguments and return its output as a byte string.
@ -236,10 +236,10 @@ if "ninja" in l_need_genealogy:
l_cmd = ["cd install;",
"wget {0} -O {1} -o /dev/null ;".format(url, path_archive),
"./scripts/install_ninja.sh;", "cd -"]
"./scripts/install_ninja.sh 2>/dev/null;", "cd -"]
subprocess.check_call(" ".join(l_cmd), shell=True)
l_need_genealogy.remove("ninja")
print """
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
@ -288,7 +288,7 @@ for need in l_need_genealogy:
l_string += l_build
path = join(QPACKAGE_ROOT_INSTALL, "build.ninja")
path = join(QP_ROOT_INSTALL, "build.ninja")
with open(path, "w+") as f:
f.write("\n".join(l_string))
@ -310,9 +310,9 @@ print """
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
"""
python_path = [join(QPACKAGE_ROOT, "scripts"), join(QPACKAGE_ROOT, "install")]
python_path = [join(QP_ROOT, "scripts"), join(QP_ROOT, "install")]
l_python = [join(QPACKAGE_ROOT, "scripts")]
l_python = [join(QP_ROOT, "scripts")]
for dir_ in python_path:
for folder in os.listdir(dir_):
path = join(dir_, folder)
@ -323,25 +323,27 @@ for dir_ in python_path:
def find_path(bin_):
try:
locate = l_installed[bin_]
except:
except KeyError:
locate = d_info[bin_].default_path
return locate
l_rc = [
'export QPACKAGE_ROOT={0}'.format(QPACKAGE_ROOT),
'export QP_ROOT={0}'.format(QP_ROOT),
'export QP_EZFIO={0}'.format(find_path('ezfio')),
'export IRPF90={0}'.format(find_path("irpf90")),
'export NINJA={0}'.format(find_path("ninja")),
'export PYTHONPATH=${{PYTHONPATH}}:{0}'.format(":".join(l_python)), '',
'export PATH=${PATH}:${PYTHONPATH}:"${QPACKAGE_ROOT}"/bin',
'export LD_LIBRARY_PATH="${QPACKAGE_ROOT}"/lib:${LD_LIBRARY_PATH}',
'export LIBRARY_PATH="${QPACKAGE_ROOT}"/lib:${LIBRARY_PATH}', ""
'export QP_PYTHON={0}'.format(":".join(l_python)),
"",
'export PYTHONPATH="${PYTHONPATH}":"${QP_PYTHON}"',
'export PATH="${PATH}":"${QP_PYTHON}":"${QP_ROOT}"/bin',
'export LD_LIBRARY_PATH="${QP_ROOT}"/lib:"${LD_LIBRARY_PATH}"',
'export LIBRARY_PATH="${QP_ROOT}"/lib:"${LIBRARY_PATH}"', ""
'source . ${HOME}/.opam/opam-init/init.sh > /dev/null 2> /dev/null || true',
""
]
path = join(QPACKAGE_ROOT, "quantum_package.rc")
path = join(QP_ROOT, "quantum_package.rc")
with open(path, "w+") as f:
f.write("\n".join(l_rc))

2
src/Ezfio_files/output.irp.f
View File

@ -10,7 +10,7 @@ END_PROVIDER
BEGIN_SHELL [ /bin/bash ]
for NAME in $(\ls -d ${QPACKAGE_ROOT}/src/*/)
for NAME in $(\ls -d ${QP_ROOT}/src/*/)
do
NAME=$(basename ${NAME})
cat << EOF

2
src/MOs/utils.irp.f
View File

@ -3,7 +3,7 @@ subroutine save_mos
double precision, allocatable :: buffer(:,:)
integer :: i,j
call system('$QPACKAGE_ROOT/scripts/save_current_mos.sh '//trim(ezfio_filename))
call system('$QP_ROOT/scripts/save_current_mos.sh '//trim(ezfio_filename))
call ezfio_set_mo_basis_mo_tot_num(mo_tot_num)
call ezfio_set_mo_basis_mo_label(mo_label)

2
src/Perturbation/perturbation.irp.f
View File

@ -2,7 +2,7 @@ BEGIN_SHELL [ /usr/bin/env python ]
from perturbation import perturbations
import os
filename = os.environ["QPACKAGE_ROOT"]+"/src/Perturbation/perturbation.template.f"
filename = os.environ["QP_ROOT"]+"/src/Perturbation/perturbation.template.f"
file = open(filename,'r')
template = file.read()
file.close()

4
src/README.rst
View File

@ -31,7 +31,7 @@ Creating a new module
=====================
Every new module should be created using the interactive ``create_module.sh``
script located in the ``${QPACKAGE_ROOT}/scripts`` directory. This will create
script located in the ``${QP_ROOT}/scripts`` directory. This will create
all the required files with correct templates.
@ -88,7 +88,7 @@ HTML, man, etc.
Creating a shell script
=======================
Shell scripts should be located in the ``${QPACKAGE_ROOT}/scripts`` directory.
Shell scripts should be located in the ``${QP_ROOT}/scripts`` directory.
Relative paths should be avoided as much as possible, and the result of commands
should be always checked. For example, when creating a directory the existence
of the directory has to be checked.

4
testing_no_regression/unit_test.py
View File

@ -5,9 +5,9 @@ import subprocess
import os
import sys
qpackage_root = os.environ['QPACKAGE_ROOT']
qpackage_root = os.environ['QP_ROOT']
EZFIO = "{0}/EZFIO".format(qpackage_root)
EZFIO = "{0}/install/EZFIO".format(qpackage_root)
sys.path = [EZFIO + "/Python"] + sys.path
from ezfio import ezfio