mirror of
https://github.com/QuantumPackage/qp2.git
synced 2024-11-07 05:53:37 +01:00
commit
01a77edd36
4
bin/python
Executable file
4
bin/python
Executable file
@ -0,0 +1,4 @@
|
||||
#!/bin/bash
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|
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exec python3 $@
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|
@ -127,6 +127,7 @@ def main(arguments):
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l_repository = list(d_tmp.keys())
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if l_repository == []:
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l_result = []
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l_plugins = []
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else:
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m_instance = ModuleHandler(l_repository)
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l_plugins = [module for module in m_instance.l_module]
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|
3
bin/qpsh
3
bin/qpsh
@ -1,6 +1,7 @@
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#!/bin/bash
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export QP_ROOT=$(dirname "$(readlink -f "$0")")/..
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REALPATH=$( cd "$(dirname "$0")" ; pwd -P )
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export QP_ROOT=${REALPATH}/..
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bash --init-file <(cat << EOF
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[[ -f /etc/bashrc ]] && source /etc/bashrc
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|
22
bin/zcat
Executable file
22
bin/zcat
Executable file
@ -0,0 +1,22 @@
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#!/bin/bash
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# On Darwin: try gzcat if available, otherwise use Python
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if [[ $(uname -s) = Darwin ]] ; then
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which gzcat &> /dev/null
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if [[ $? -eq 0 ]] ; then
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exec gzcat $@
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else
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exec python3 << EOF
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import sys
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import gzip
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with gzip.open("$1", "rt") as f:
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print(f.read())
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EOF
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fi
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else
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command=$(which -a zcat | grep -v 'qp2/bin/' | head -1)
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exec $command $@
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fi
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|
@ -10,7 +10,7 @@
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#
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#
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[COMMON]
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FC : gfortran -g -ffree-line-length-none -I . -fPIC -march=native
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FC : gfortran -g -ffree-line-length-none -I . -fPIC -march=native -std=legacy
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LAPACK_LIB : -lblas -llapack
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IRPF90 : irpf90
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IRPF90_FLAGS : --ninja --align=32 --assert -DSET_NESTED
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|
@ -13,7 +13,7 @@
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#
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#
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[COMMON]
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FC : gfortran -g -ffree-line-length-none -I . -fPIC -march=native
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FC : gfortran -g -ffree-line-length-none -I . -fPIC -march=native -std=legacy
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LAPACK_LIB : -larmpl_lp64_mp
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IRPF90 : irpf90
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IRPF90_FLAGS : --ninja --align=32 --assert -DSET_NESTED
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|
@ -10,7 +10,7 @@
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#
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#
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[COMMON]
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FC : gfortran -ffree-line-length-none -I . -mavx -g -fPIC
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FC : gfortran -ffree-line-length-none -I . -mavx -g -fPIC -std=legacy
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LAPACK_LIB : -llapack -lblas
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IRPF90 : irpf90
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IRPF90_FLAGS : --ninja --align=32 -DSET_NESTED
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|
@ -10,7 +10,7 @@
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#
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#
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[COMMON]
|
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FC : gfortran -g -ffree-line-length-none -I . -fPIC
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FC : gfortran -g -ffree-line-length-none -I . -fPIC -std=legacy
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LAPACK_LIB : -lblas -llapack
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IRPF90 : irpf90
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IRPF90_FLAGS : --ninja --align=32 --assert -DSET_NESTED
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|
62
config/gfortran_macos.cfg
Normal file
62
config/gfortran_macos.cfg
Normal file
@ -0,0 +1,62 @@
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# Common flags
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##############
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#
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# -ffree-line-length-none : Needed for IRPF90 which produces long lines
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# -lblas -llapack : Link with libblas and liblapack libraries provided by the system
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# -I . : Include the curent directory (Mandatory)
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#
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# --ninja : Allow the utilisation of ninja. (Mandatory)
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# --align=32 : Align all provided arrays on a 32-byte boundary
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#
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#
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[COMMON]
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FC : gfortran -ffree-line-length-none -I . -g -fPIC -std=legacy
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LAPACK_LIB : -llapack -lblas
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IRPF90 : irpf90
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IRPF90_FLAGS : --ninja --align=32 -DSET_NESTED -DMACOS
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|
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# Global options
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################
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#
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# 1 : Activate
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# 0 : Deactivate
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#
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[OPTION]
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MODE : OPT ; [ OPT | PROFILE | DEBUG ] : Chooses the section below
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CACHE : 0 ; Enable cache_compile.py
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OPENMP : 1 ; Append OpenMP flags
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|
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# Optimization flags
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####################
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#
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# -Ofast : Disregard strict standards compliance. Enables all -O3 optimizations.
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# It also enables optimizations that are not valid
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# for all standard-compliant programs. It turns on
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# -ffast-math and the Fortran-specific
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# -fno-protect-parens and -fstack-arrays.
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[OPT]
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FCFLAGS : -Ofast -march=native
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|
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# Profiling flags
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#################
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#
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[PROFILE]
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FC : -p -g
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FCFLAGS : -Ofast
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|
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# Debugging flags
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#################
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#
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# -fcheck=all : Checks uninitialized variables, array subscripts, etc...
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# -g : Extra debugging information
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#
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[DEBUG]
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FCFLAGS : -fcheck=all -g
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|
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# OpenMP flags
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#################
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#
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[OPENMP]
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FC : -fopenmp
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IRPF90_FLAGS : --openmp
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|
@ -10,7 +10,7 @@
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#
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#
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[COMMON]
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FC : mpif90 -ffree-line-length-none -I . -g -fPIC
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FC : mpif90 -ffree-line-length-none -I . -g -fPIC -std=legacy
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LAPACK_LIB : -lblas -llapack
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IRPF90 : irpf90
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IRPF90_FLAGS : --ninja --align=32 -DMPI -DSET_NESTED
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|
@ -10,7 +10,7 @@
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#
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#
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[COMMON]
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FC : gfortran -g -ffree-line-length-none -I . -fPIC -march=native
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FC : gfortran -g -ffree-line-length-none -I . -fPIC -march=native -std=legacy
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LAPACK_LIB : -lopenblas
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IRPF90 : irpf90
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IRPF90_FLAGS : --ninja --align=32 --assert -DSET_NESTED
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|
7
configure
vendored
7
configure
vendored
@ -19,7 +19,11 @@ git submodule init
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git submodule update
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# Update ARM or x86 dependencies
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ARCHITECTURE=$(uname -m)
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SYSTEM=$(uname -s)
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if [[ $SYSTEM = "Linux" ]] ; then
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SYSTEM=""
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fi
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ARCHITECTURE=$(uname -m)$SYSTEM
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cd ${QP_ROOT}/external/qp2-dependencies
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git checkout master
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git pull
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@ -275,6 +279,7 @@ EOF
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cd "\${QP_ROOT}"/external
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tar --gunzip --extract --file qp2-dependencies/zeromq-4.2.5.tar.gz
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cd zeromq-*
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[[ "${SYSTEM}" = "Darwin" ]] && ./autogen.sh
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./configure --prefix="\$QP_ROOT" --without-libsodium --enable-libunwind=no
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make -j 8
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make install
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|
@ -32,7 +32,7 @@ export PYTHONPATH=$(qp_prepend_export "PYTHONPATH" "${QP_EZFIO}/Python":"${QP_PY
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export PATH=$(qp_prepend_export "PATH" "${QP_PYTHON}":"${QP_ROOT}"/bin:"${QP_ROOT}"/ocaml)
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export LD_LIBRARY_PATH=$(qp_prepend_export "LD_LIBRARY_PATH" "${QP_ROOT}"/lib)
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export LD_LIBRARY_PATH=$(qp_prepend_export "LD_LIBRARY_PATH" "${QP_ROOT}"/lib:"${QP_ROOT}"/lib64)
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export LIBRARY_PATH=$(qp_prepend_export "LIBRARY_PATH" "${QP_ROOT}"/lib:"${QP_ROOT}"/lib64)
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|
2
external/irpf90
vendored
2
external/irpf90
vendored
@ -1 +1 @@
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Subproject commit 0007f72f677fe7d61c5e1ed461882cb239517102
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Subproject commit 4ab1b175fc7ed0d96c1912f13dc53579b24157a6
|
@ -11,7 +11,11 @@ fi
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cd ${QP_ROOT}/data
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rm -f executables
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if [[ "$(uname -s)" = "Darwin" ]] ; then
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EXES=$(find -L ${QP_ROOT}/src -maxdepth 2 -depth -perm +111 -type f | grep -e "${QP_ROOT}/src/[^/]*/[^/]*$" |sort )
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else
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EXES=$(find -L ${QP_ROOT}/src -maxdepth 2 -depth -executable -type f | grep -e "${QP_ROOT}/src/[^/]*/[^/]*$" |sort )
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fi
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for EXE in $EXES
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do
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|
@ -53,7 +53,6 @@ function run {
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@test "B-B" {
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qp set_file b2_stretched.ezfio
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run b2_stretched.zmt 1 0 6-31g
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}
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|
@ -33,6 +33,8 @@ BEGIN_PROVIDER [ character*(1024), ezfio_filename ]
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call ezfio_set_file(ezfio_filename)
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IRP_IF MACOS
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IRP_ELSE
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! Adjust out-of-memory killer flag such that the current process will be
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! killed first by the OOM killer, allowing compute nodes to survive
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integer :: getpid
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@ -40,6 +42,7 @@ BEGIN_PROVIDER [ character*(1024), ezfio_filename ]
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write(pidc,*) getpid()
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write(command,*) 'echo 15 > /proc//'//trim(adjustl(pidc))//'/oom_adj'
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call system(command)
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IRP_ENDIF
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PROVIDE file_lock
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|
@ -39,7 +39,7 @@ rm -rf $EZFIO
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qp create_ezfio -b def2-svp hcn.xyz -o $EZFIO
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qp run scf
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mv hcn_charges.xyz ${EZFIO}_point_charges.xyz
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python write_pt_charges.py ${EZFIO}
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python3 write_pt_charges.py ${EZFIO}
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qp set nuclei point_charges True
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qp run scf | tee ${EZFIO}.pt_charges.out
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energy="$(ezfio get hartree_fock energy)"
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|
@ -9,25 +9,27 @@ subroutine mo_two_e_integrals_erf_index(i,j,k,l,i1)
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integer(key_kind) :: p,q,r,s,i2
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p = min(i,k)
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r = max(i,k)
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p = p+ishft(r*r-r,-1)
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p = p+shiftr(r*r-r,1)
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q = min(j,l)
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s = max(j,l)
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q = q+ishft(s*s-s,-1)
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q = q+shiftr(s*s-s,1)
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i1 = min(p,q)
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i2 = max(p,q)
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i1 = i1+ishft(i2*i2-i2,-1)
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i1 = i1+shiftr(i2*i2-i2,1)
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end
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|
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|
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BEGIN_PROVIDER [ logical, mo_two_e_integrals_erf_in_map ]
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use map_module
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implicit none
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integer(bit_kind) :: mask_ijkl(N_int,4)
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integer(bit_kind) :: mask_ijk(N_int,3)
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|
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BEGIN_DOC
|
||||
! If True, the map of MO two-electron integrals is provided
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END_DOC
|
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integer(bit_kind) :: mask_ijkl(N_int,4)
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integer(bit_kind) :: mask_ijk(N_int,3)
|
||||
double precision :: cpu_1, cpu_2, wall_1, wall_2
|
||||
|
||||
PROVIDE mo_class
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|
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real :: map_mb
|
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|
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|
@ -128,7 +128,7 @@
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BEGIN_PROVIDER [double precision, mu_average_prov, (N_states)]
|
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implicit none
|
||||
BEGIN_DOC
|
||||
! average value of mu(r) weighted with the total one-e density and divised by the number of electrons
|
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! average value of mu(r) weighted with the total one-e density and divided by the number of electrons
|
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!
|
||||
! !!!!!! WARNING !!!!!! if no_core_density == .True. then all contributions from the core orbitals
|
||||
!
|
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|
@ -99,6 +99,7 @@ subroutine grad1_j12_mu(r1, r2, grad)
|
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stop
|
||||
|
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endif
|
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grad = -grad
|
||||
|
||||
return
|
||||
end subroutine grad1_j12_mu
|
||||
@ -486,6 +487,13 @@ subroutine mu_r_val_and_grad(r1, r2, mu_val, mu_der)
|
||||
!!!!!!!!! rho1,rho2,rho1+rho2
|
||||
call get_all_rho_grad_rho(r1,r2,rho1,rho2,grad_rho1)
|
||||
rho_tot = rho1 + rho2
|
||||
! if(rho_tot.lt.1.d-10)rho_tot = 1.d-10
|
||||
if(rho_tot.lt.1.d-10)then
|
||||
mu_val = mu_erf
|
||||
mu_der = 0.d0
|
||||
return
|
||||
endif
|
||||
|
||||
if(rho_tot.lt.1.d-10)rho_tot = 1.d-10
|
||||
inv_rho_tot = 1.d0/rho_tot
|
||||
! f(rho) = mu_r_ct * rho**beta_rho_power + mu_erf
|
||||
@ -506,18 +514,26 @@ subroutine mu_r_val_and_grad(r1, r2, mu_val, mu_der)
|
||||
! d/dx1 f[rho(r1)] = [0.5 alpha / sqrt(rho(r1)) ] (d rho(r1) / dx1)
|
||||
!
|
||||
! d/dx1 (rho(r1) f[rho(r1)] = rho(r1) * d/dx1 f[rho(r1)] + f[rho(r1)] * d/dx1 rho(r1)
|
||||
|
||||
!!!!!!!!! rho1,rho2,rho1+rho2
|
||||
call get_all_rho_grad_rho(r1,r2,rho1,rho2,grad_rho1)
|
||||
rho_tot = rho1 + rho2
|
||||
! if(rho_tot.lt.1.d-10)rho_tot = 1.d-10
|
||||
if(rho_tot.lt.1.d-10)then
|
||||
mu_val = mu_erf
|
||||
mu_der = 0.d0
|
||||
return
|
||||
endif
|
||||
|
||||
if(rho_tot.lt.1.d-10)rho_tot = 1.d-10
|
||||
inv_rho_tot = 1.d0/rho_tot
|
||||
! f(rho) = mu_r_ct * rho**beta_rho_power + mu_erf
|
||||
call get_all_f_rho_simple(rho1,rho2,mu_r_ct,mu_erf,beta_rho_power,f_rho1,d_drho_f_rho1,f_rho2)
|
||||
! f(rho) = (mu_r_ct* rho)**beta_rho_power * erf(zeta_erf_mu_of_r * rho) + mu_eff * (1 - erf(zeta_erf_mu_of_r*rho))
|
||||
call get_all_f_rho_erf(rho1,rho2,mu_r_ct,beta_rho_power,mu_erf,zeta_erf_mu_of_r,f_rho1,d_drho_f_rho1,f_rho2)
|
||||
d_dx1_f_rho1(1:3) = d_drho_f_rho1 * grad_rho1(1:3)
|
||||
d_dx_rho_f_rho(1:3) = rho1 * d_dx1_f_rho1(1:3) + f_rho1 * grad_rho1(1:3)
|
||||
mu_val = 0.5d0 * ( f_rho1 + f_rho2)
|
||||
mu_der(1:3) = d_dx_rho_f_rho(1:3)
|
||||
nume = rho1 * f_rho1 + rho2 * f_rho2
|
||||
mu_val = nume * inv_rho_tot
|
||||
mu_der(1:3) = inv_rho_tot*inv_rho_tot * (rho_tot * d_dx_rho_f_rho(1:3) - grad_rho1(1:3) * nume)
|
||||
|
||||
else
|
||||
print *, ' j1b_type = ', j1b_type, 'not implemented yet'
|
||||
stop
|
||||
@ -676,8 +692,17 @@ subroutine get_all_f_rho_simple(rho1,rho2,alpha,mu0,beta,f_rho1,d_drho_f_rho1,f_
|
||||
double precision, intent(in) :: rho1,rho2,alpha,mu0,beta
|
||||
double precision, intent(out):: f_rho1,d_drho_f_rho1,f_rho2
|
||||
double precision :: tmp
|
||||
if(rho1.lt.1.d-10)then
|
||||
f_rho1 = 0.d0
|
||||
d_drho_f_rho1 = 0.d0
|
||||
else
|
||||
call f_mu_and_deriv_mu_simple(rho1,alpha,mu0,beta,f_rho1,d_drho_f_rho1)
|
||||
endif
|
||||
if(rho2.lt.1.d-10)then
|
||||
f_rho2 = 0.d0
|
||||
else
|
||||
call f_mu_and_deriv_mu_simple(rho2,alpha,mu0,beta,f_rho2,tmp)
|
||||
endif
|
||||
end
|
||||
|
||||
subroutine f_mu_and_deriv_mu_simple(rho,alpha,mu0,beta,f_mu,d_drho_f_mu)
|
||||
@ -691,10 +716,53 @@ subroutine f_mu_and_deriv_mu_simple(rho,alpha,mu0,beta,f_mu,d_drho_f_mu)
|
||||
END_DOC
|
||||
double precision, intent(in) :: rho,alpha,mu0,beta
|
||||
double precision, intent(out) :: f_mu,d_drho_f_mu
|
||||
f_mu = alpha * (rho)**beta + mu0
|
||||
d_drho_f_mu = alpha * beta * rho**(beta-1.d0)
|
||||
f_mu = alpha**beta * (rho)**beta + mu0
|
||||
d_drho_f_mu = alpha**beta * beta * rho**(beta-1.d0)
|
||||
|
||||
end
|
||||
|
||||
! ---
|
||||
|
||||
subroutine f_mu_and_deriv_mu_erf(rho,alpha,zeta,mu0,beta,f_mu,d_drho_f_mu)
|
||||
implicit none
|
||||
include 'constants.include.F'
|
||||
BEGIN_DOC
|
||||
! function giving mu as a function of rho
|
||||
!
|
||||
! f_mu = (alpha * rho)**zeta * erf(beta * rho) + mu0 * (1 - erf(beta*rho))
|
||||
!
|
||||
! and its derivative with respect to rho d_drho_f_mu
|
||||
!
|
||||
! d_drho_f_mu = 2 beta/sqrt(pi) * exp(-(beta*rho)**2) * ( (alpha*rho)**zeta - mu0)
|
||||
! + alpha * zeta * (alpha *rho)**(zeta-1) * erf(beta*rho)
|
||||
END_DOC
|
||||
double precision, intent(in) :: rho,alpha,mu0,beta,zeta
|
||||
double precision, intent(out) :: f_mu,d_drho_f_mu
|
||||
f_mu = (alpha * rho)**zeta * derf(beta * rho) + mu0 * (1.d0 - derf(beta*rho))
|
||||
d_drho_f_mu = 2.d0 * beta * inv_sq_pi * dexp(-(beta*rho)**2) * ( (alpha*rho)**zeta - mu0) &
|
||||
+ alpha * zeta * (alpha *rho)**(zeta-1) * derf(beta*rho)
|
||||
|
||||
end
|
||||
|
||||
|
||||
subroutine get_all_f_rho_erf(rho1,rho2,alpha,zeta,mu0,beta,f_rho1,d_drho_f_rho1,f_rho2)
|
||||
implicit none
|
||||
BEGIN_DOC
|
||||
! returns the values f(mu(r1)), f(mu(r2)) and d/drho(1) f(mu(r1))
|
||||
! with f_mu = (alpha * rho)**zeta * erf(beta * rho) + mu0 * (1 - erf(beta*rho))
|
||||
END_DOC
|
||||
double precision, intent(in) :: rho1,rho2,alpha,mu0,beta,zeta
|
||||
double precision, intent(out):: f_rho1,d_drho_f_rho1,f_rho2
|
||||
double precision :: tmp
|
||||
if(rho1.lt.1.d-10)then
|
||||
f_rho1 = mu_erf
|
||||
d_drho_f_rho1 = 0.d0
|
||||
else
|
||||
call f_mu_and_deriv_mu_erf(rho1,alpha,zeta,mu0,beta,f_rho1,d_drho_f_rho1)
|
||||
endif
|
||||
if(rho2.lt.1.d-10)then
|
||||
f_rho2 = mu_erf
|
||||
else
|
||||
call f_mu_and_deriv_mu_erf(rho2,alpha,zeta,mu0,beta,f_rho2,tmp)
|
||||
endif
|
||||
end
|
||||
|
@ -13,9 +13,9 @@ subroutine routine_print
|
||||
integer :: i_unit_output,getUnitAndOpen
|
||||
output=trim(ezfio_filename)//'.mu_of_r'
|
||||
i_unit_output = getUnitAndOpen(output,'w')
|
||||
integer :: ipoint,nx
|
||||
double precision :: xmax,xmin,r(3),dx
|
||||
double precision :: mu_val, mu_der(3),dm_a,dm_b,grad
|
||||
integer :: ipoint,nx,i
|
||||
double precision :: xmax,xmin,r(3),dx,sigma
|
||||
double precision :: mu_val, mu_der(3),dm_a,dm_b,grad,grad_dm_a(3), grad_dm_b(3)
|
||||
xmax = 5.D0
|
||||
xmin = -5.D0
|
||||
nx = 10000
|
||||
@ -24,10 +24,15 @@ subroutine routine_print
|
||||
r(1) = xmin
|
||||
do ipoint = 1, nx
|
||||
call mu_r_val_and_grad(r, r, mu_val, mu_der)
|
||||
call dm_dft_alpha_beta_at_r(r,dm_a,dm_b)
|
||||
call density_and_grad_alpha_beta(r,dm_a,dm_b, grad_dm_a, grad_dm_b)
|
||||
sigma = 0.d0
|
||||
do i = 1,3
|
||||
sigma += grad_dm_a(i)**2
|
||||
enddo
|
||||
sigma=dsqrt(sigma)
|
||||
grad = mu_der(1)**2 + mu_der(2)**2 + mu_der(3)**2
|
||||
grad = dsqrt(grad)
|
||||
write(i_unit_output,'(100(F16.7,X))')r(1),mu_val,dm_a+dm_b,grad
|
||||
write(i_unit_output,'(100(F16.7,X))')r(1),mu_val,dm_a+dm_b,grad,sigma/dm_a
|
||||
r(1) += dx
|
||||
enddo
|
||||
end
|
||||
|
@ -158,13 +158,19 @@ default: 0
|
||||
type: double precision
|
||||
doc: a parameter used to define mu(r)
|
||||
interface: ezfio, provider, ocaml
|
||||
default: 6.203504908994001e-1
|
||||
default: 1.5
|
||||
|
||||
[beta_rho_power]
|
||||
type: double precision
|
||||
doc: a parameter used to define mu(r)
|
||||
interface: ezfio, provider, ocaml
|
||||
default: 0.5
|
||||
default: 0.33333
|
||||
|
||||
[zeta_erf_mu_of_r]
|
||||
type: double precision
|
||||
doc: a parameter used to define mu(r)
|
||||
interface: ezfio, provider, ocaml
|
||||
default: 1.
|
||||
|
||||
[thr_degen_tc]
|
||||
type: Threshold
|
||||
|
@ -13,7 +13,7 @@ subroutine routine
|
||||
output=trim(ezfio_filename)//'.wf_sorted'
|
||||
i_unit_output = getUnitAndOpen(output,'w')
|
||||
do i= 1, N_det
|
||||
write(i_unit_output,*)i,dabs(psi_coef_sorted(i,1))
|
||||
write(i_unit_output,*)i,dabs(psi_coef_sorted(i,1)),dabs(psi_coef_sorted(i,1)/psi_coef_sorted(1,1))
|
||||
enddo
|
||||
|
||||
end
|
||||
|
@ -33,6 +33,8 @@ subroutine resident_memory(value)
|
||||
call usleep(10)
|
||||
|
||||
value = 0.d0
|
||||
IRP_IF MACOS
|
||||
IRP_ELSE
|
||||
iunit = getUnitAndOpen('/proc/self/status','r')
|
||||
do
|
||||
read(iunit,*,err=10,end=20) key, value
|
||||
@ -43,6 +45,7 @@ subroutine resident_memory(value)
|
||||
end do
|
||||
20 continue
|
||||
close(iunit)
|
||||
IRP_ENDIF
|
||||
value = value / (1024.d0*1024.d0)
|
||||
call unlock_io()
|
||||
end function
|
||||
@ -58,6 +61,9 @@ subroutine total_memory(value)
|
||||
double precision, intent(out) :: value
|
||||
|
||||
call lock_io()
|
||||
value = 0.d0
|
||||
IRP_IF MACOS
|
||||
IRP_ELSE
|
||||
iunit = getUnitAndOpen('/proc/self/status','r')
|
||||
do
|
||||
read(iunit,*,err=10,end=20) key, value
|
||||
@ -68,6 +74,7 @@ subroutine total_memory(value)
|
||||
end do
|
||||
20 continue
|
||||
close(iunit)
|
||||
IRP_ENDIF
|
||||
value = value / (1024.d0*1024.d0)
|
||||
call unlock_io()
|
||||
end function
|
||||
|
Loading…
Reference in New Issue
Block a user