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Merge branch 'master' of github.com:scemama/quantum_package

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This commit is contained in:
Anthony Scemama 2018-12-13 10:26:08 +01:00
commit a9edb4907e
9 changed files with 72 additions and 95 deletions
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1
.travis.yml
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@ -35,5 +35,6 @@ python:
script:
- ./configure --install all --config ./config/travis.cfg
- ./configure --install bats
- source ./quantum_package.rc ; ninja -j 1 -v
- source ./quantum_package.rc ; cd tests ; ./run_tests.sh -v

30
configure vendored
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@ -131,7 +131,7 @@ if [[ "${PACKAGES}.x" != ".x" ]] ; then
fi
if [[ ${PACKAGES} = all ]] ; then
PACKAGES="ninja irpf90 zeromq f77zmq ocaml ezfio emsl docopt resultsFile"
PACKAGES="ninja irpf90 zeromq f77zmq ocaml ezfio emsl docopt resultsFile bats"
fi
@ -220,7 +220,7 @@ EOF
else
# Conventional commands
export OPAMROOT=${OPAMROOT:-${QP_ROOT}/external/opam}
echo ${QP_ROOT}/bin
echo "QP>> Please install it here: " ${QP_ROOT}/bin
${QP_ROOT}/external/opam_installer.sh
fi
rm ${QP_ROOT}/external/opam_installer.sh
@ -276,7 +276,16 @@ EOF
rm -rf resultsFile-master resultsFile.tar.gz
cd "${QP_ROOT}"
elif [[ ${PACKAGE} = bats ]] ; then
cd "${QP_ROOT}"/external
git clone https://github.com/bats-core/bats-core.git
cd bats-core
./install.sh .
ln -s ./bin/bats "${QP_ROOT}"/bin/bats
cd "${QP_ROOT}"
fi
done
@ -300,13 +309,13 @@ fi
F77ZMQ=$(find_lib -lzmq -lf77zmq)
if [[ ${F77ZMQ} = not_found ]] ; then
echo "Fortran binding of ZeroMQ is not installed."
echo "Fortran binding of ZeroMQ (f77zmq) is not installed."
fail
fi
OPAM=$(find_exe opam)
if [[ ${OPAM} = not_found ]] ; then
echo "OPAM package manager is not installed."
echo "OPAM (ocaml) package manager is not installed."
fail
fi
@ -340,9 +349,16 @@ if [[ ${RESULTSFILE} = not_found ]] ; then
fail
fi
echo "All dependencies installed."
echo " ___________________________ "
echo "< All dependencies installed. >"
echo " --------------------------- "
echo " \ ^__^ "
echo " \ (oo)\_______ "
echo " (__)\ )\/\. "
echo " ||----w | "
echo " || || "
if [[ -n $CONFIG ]] ; then

56
docs/applications.rst
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@ -1,56 +0,0 @@
Research made with the Quantum Package
======================================
.. bibliography:: refs.bib
#. :cite:`Loos_2018` A Mountaineering Strategy to Excited States: Highly
Accurate Reference Energies and Benchmarks
#. :cite:`Scemama_2018` Deterministic Construction of Nodal Surfaces within
Quantum Monte Carlo: The Case of FeS
#. :cite:`Scemama_2018.2` Excitation energies from diffusion Monte Carlo using
selected configuration interaction nodes
#. :cite:`Dash_2018` Perturbatively Selected Configuration-Interaction Wave
Functions for Efficient Geometry Optimization in Quantum Monte Carlo
#. :cite:`Garniron_2018` Selected configuration interaction dressed by
perturbation
#. :cite:`Giner_2017` A Jeziorski-Monkhorst fully uncontracted multi-reference
perturbative treatment. I. Principles, second-order versions, and tests on
ground state potential energy curves
#. :cite:`Garniron_2017` Alternative definition of excitation amplitudes in
multi-reference state-specific coupled cluster
#. :cite:`Garniron_2017.2` Hybrid stochastic-deterministic calculation of the
second-order perturbative contribution of multireference perturbation theory
#. :cite:`Giner_2017.2` Orthogonal Valence Bond Hamiltonians incorporating
dynamical correlation effects
#. :cite:`Giner_2016` A simple approach to the state-specific MR-CC using
the intermediate Hamiltonian formalism
#. :cite:`Caffarel_2016` Communication: Toward an improved control of the
fixed-node error in quantum Monte Carlo: The case of the water molecule
#. :cite:`Caffarel_2016.2` Using CIPSI Nodes in Diffusion Monte Carlo
#. :cite:`Giner_2015` Fixed-node diffusion Monte Carlo potential energy curve of
the fluorine molecule F2 using selected configuration interaction trial
wavefunctions
#. :cite:`Scemama_2014` Accurate nonrelativistic ground-state energies of 3d
transition metal atoms
#. :cite:`Caffarel_2014` Spin Density Distribution in Open-Shell Transition
Metal Systems: A Comparative Post-Hartree-Fock, Density Functional Theory,
and Quantum Monte Carlo Study of the CuCl2 Molecule
#. :cite:`Giner_2013` Using perturbatively selected configuration interaction in
quantum Monte Carlo calculations

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2
docs/source/intro/intro.rst
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@ -2,7 +2,7 @@
The |qp|
========
.. image:: /_static/qp.png
.. image:: /_static/qp2.png
:align: center
:width: 200px
:alt: Quantum Package

32
docs/source/research.bib
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@ -1,12 +1,12 @@
%%% ARXIV TO BE UPDATED %%%
@article{Giner2018Sep,
author = {Giner, Emmanuel and Pradines, Barth\'{e}l\'{e}my and Fert\'{e}, Anthony and Assaraf, Roland and Savin, Andreas and Toulouse, Julien},
title = {{Curing basis-set convergence of wave-function theory using density-functional theory: a systematically improvable approach}},
journal = {arXiv},
year = {2018},
month = {Sep},
eprint = {1809.01466},
url = {https://arxiv.org/abs/1809.01466}
@article{Loos2018Nov,
author = {Loos, Pierre-Fran{\c{c}}ois and Boggio-Pasqua, Martial and Scemama, Anthony and Caffarel, Michel and Jacquemin, Denis},
title = {{Reference Energies for Double Excitations}},
journal = {arXiv},
year = {2018},
month = {Nov},
pages = {1811.12861},
url = {https://arxiv.org/abs/1811.12861}
}
@article{Flores2018Nov,
@ -15,7 +15,7 @@
journal = {arXiv},
year = {2018},
month = {Nov},
eprint = {1811.00583},
pages = {1811.00583},
url = {https://arxiv.org/abs/1811.00583}
}
@ -25,6 +25,20 @@
%%%% PUBLISHED PAPERS
@article{Giner_2018,
doi = {10.1063/1.5052714},
url = {https://doi.org/10.1063%2F1.5052714},
year = 2018,
month = {nov},
publisher = {{AIP} Publishing},
volume = {149},
number = {19},
pages = {194301},
author = {Emmanuel Giner and Barth{\'{e}}lemy Pradines and Anthony Fert{\'{e}} and Roland Assaraf and Andreas Savin and Julien Toulouse},
title = {Curing basis-set convergence of wave-function theory using density-functional theory: A systematically improvable approach},
journal = {The Journal of Chemical Physics}
}
@article{Giner2018Oct,
author = {Giner, Emmanuel and Tew, David and Garniron, Yann and Alavi, Ali},

6
quantum_package.rc.default
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@ -26,7 +26,11 @@ export LIBRARY_PATH=$(qp_prepend_export "LIBRARY_PATH" "${QP_ROOT}"/lib:"${QP_RO
export C_INCLUDE_PATH=$(qp_prepend_export "C_INCLUDE_PATH" "${QP_ROOT}"/include)
if [[ $SHELL == "/bin/bash" ]] ; then
source ${QP_EZFIO}/Bash/ezfio.sh
if [[ -f ${QP_EZFIO}/Bash/ezfio.sh ]]; then
source ${QP_EZFIO}/Bash/ezfio.sh
else
echo "EZFIO is not installed."
fi
fi
#### END Don't modify

4
scripts/compilation/qp_create_ninja
View File

@ -97,7 +97,9 @@ def ninja_create_env_variable(pwd_config_file):
l_string.append(str_)
lib_lapack = get_compilation_option(pwd_config_file, "LAPACK_LIB")
str_lib = " ".join([LIB, lib_lapack, EZFIO_LIB, ZMQ_LIB])
lib_usr = get_compilation_option(pwd_config_file, "LIB")
str_lib = " ".join([LIB, lib_lapack, EZFIO_LIB, ZMQ_LIB, lib_usr])
l_string.append("LIB = {0} ".format(str_lib))
l_string.append("")

36
scripts/module/qp_module
View File

@ -7,6 +7,7 @@ Usage:
qp_module install <name>...
qp_module list (--installed | --available-local)
qp_module uninstall <name>
Options:
list: List all the modules available
create: Create a new module
@ -15,6 +16,9 @@ Options:
import sys
import os
import subprocess
from os import listdir
from os.path import isdir, join
try:
from docopt import docopt
@ -66,12 +70,11 @@ def save_new_module(path, l_child):
""")
def main(arguments):
if arguments in ["list_installed", "list_plugins"]:
if arguments["list_installed"]:
if arguments["list"]:
if arguments["--installed"]:
l_repository = [QP_SRC]
elif arguments["list_plugins"]:
l_repository = [QP_PLUGINS]
elif arguments["--available-local"]:
l_repository = [join(QP_PLUGINS, f) for f in listdir(QP_PLUGINS) if isdir(join(QP_PLUGINS, f))]
m_instance = ModuleHandler(l_repository)
@ -112,7 +115,6 @@ def main(arguments):
save_new_module(path, l_child_reduce)
print " [ OK ]"
# print "` {0} install {1} `".format(os.path.basename(__file__), name)
print ""
arguments["create"]=False
arguments["install"]=True
@ -121,23 +123,15 @@ def main(arguments):
elif arguments["download"]:
print "Not yet implemented"
pass
# d_local = get_dict_child([QP_SRC])
# d_remote = get_dict_child(arguments["<path_folder>"])
#
# d_child = d_local.copy()
# d_child.update(d_remote)
#
# name = arguments["<name>"]
# l_module_descendant = get_l_module_descendant(d_child, [name])
#
# for module in l_module_descendant:
# if module not in d_local:
# print "you need to install", module
elif arguments["install"]:
# Python 2.6 ...
d_module_location= dict()
d_local = get_dict_child([QP_SRC])
d_plugin = get_dict_child([QP_PLUGINS])
d_plugin = get_dict_child([join(QP_PLUGINS, f) for f in listdir(QP_PLUGINS) if isdir(join(QP_PLUGINS, f))])
d_child = d_local.copy()
d_child.update(d_plugin)
@ -164,7 +158,9 @@ def main(arguments):
print "Installation...",
for module_to_cp in l_module_to_cp:
src = os.path.join(QP_PLUGINS, module_to_cp)
# Find the module. This is ugly. Quick fix, we should refactor
src = [ join(QP_PLUGINS, f, module_to_cp) for f in listdir(QP_PLUGINS) if isdir(join(QP_PLUGINS, f,module_to_cp) ) ][0]
des = os.path.join(QP_SRC, module_to_cp)
try:
os.symlink(src, des)