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0
mirror of https://github.com/LCPQ/quantum_package synced 2024-12-22 12:23:48 +01:00

Merge branch 'master' of https://github.com/TApplencourt/quantum_package into TApplencourt-master

Conflicts:
	install/scripts/install_ocaml.sh
	testing_no_regression/unit_test.py
This commit is contained in:
Anthony Scemama 2016-01-04 10:18:09 +01:00
commit adc95a3678
13 changed files with 137 additions and 445 deletions

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@ -22,12 +22,10 @@ language: python
python:
- "2.6"
script:
- ./configure --production ./config/gfortran.cfg
- source ./quantum_package.rc
- qp_install_module.py install Full_CI Hartree_Fock CAS_SD MRCC_CASSD
- qp_module.py install Full_CI Hartree_Fock CAS_SD MRCC_CASSD
- ninja
- cd ocaml ; make ; cd -
- cd testing_no_regression ; ./unit_test.py
- cd test ; bats bats/qp.bats

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@ -18,6 +18,9 @@ For more information, you can visit the [wiki of the project](http://github.com/
* Python >= 2.6
* GNU make
* Bash
* Blast/Lapack
* unzip
* g++ (For ninja)
## Standard installation
@ -51,19 +54,17 @@ This file contains all the environment variables needed by the quantum package b
### Optional) Add some new module
Usage: qp_install_module.py list (--installed|--avalaible-local|--avalaible-remote)
qp_install_module.py install <name>...
qp_install_module.py create -n <name> [<children_module>...]
qp_install_module.py download -n <name> [<path_folder>...]
Usage: qp_module.py list (--installed|--avalaible-local|--avalaible-remote)
qp_module.py install <name>...
qp_module.py create -n <name> [<children_module>...]
qp_module.py download -n <name> [<path_folder>...]
For exemple you can type :
`qp_install_module.py install Full_CI`
`qp_module.py install Full_CI`
### 3) Compiling the fortran
ninja
Just type `ninja` if you are in `$QP_ROOT` (or `ninja -f $QP_ROOT/build.ninja`
elsewhere). The compilation will take approximately 3 min.
Just type `ninja` if you are in `$QP_ROOT` (or `ninja -f $QP_ROOT/build.ninja` elsewhere). The compilation will take approximately 3 min.
If you have set the `--developement` flag in a specific module you can go in
the corresponding module directory and run `ninja` to build only this module.

15
configure vendored
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@ -69,7 +69,8 @@ d_dependency = {
"python": [],
"ninja": ["g++", "python"],
"make": [],
"p_graphviz": ["python"]
"p_graphviz": ["python"],
"bats": []
}
from collections import namedtuple
@ -149,11 +150,16 @@ p_graphviz = Info(
description=' Python library for graphviz',
default_path=join(QP_ROOT_INSTALL, "p_graphviz"))
bats = Info(
url='https://github.com/sstephenson/bats/archive/master.tar.gz',
description=' Bash Automated Testing System',
default_path=join(QP_ROOT_INSTALL, "bats"))
d_info = dict()
for m in ["ocaml", "m4", "curl", "zlib", "patch", "irpf90", "docopt",
"resultsFile", "ninja", "emsl", "ezfio", "p_graphviz",
"zeromq", "f77zmq" ]:
"zeromq", "f77zmq","bats" ]:
exec ("d_info['{0}']={0}".format(m))
@ -478,7 +484,7 @@ def create_ninja_and_rc(l_installed):
'export IRPF90={0}'.format(path_irpf90.replace(QP_ROOT,"${QP_ROOT}")),
'export NINJA={0}'.format(path_ninja.replace(QP_ROOT,"${QP_ROOT}")),
'export QP_PYTHON={0}'.format(":".join(l_python)), "",
'export PYTHONPATH="${QP_EZFIO}":"${QP_PYTHON}":"${PYTHONPATH}"',
'export PYTHONPATH="${QP_EZFIO}/Python":"${QP_PYTHON}":"${PYTHONPATH}"',
'export PATH="${QP_PYTHON}":"${QP_ROOT}"/bin:"${QP_ROOT}"/ocaml:"${PATH}"',
'export LD_LIBRARY_PATH="${QP_ROOT}"/lib:"${LD_LIBRARY_PATH}"',
'export LIBRARY_PATH="${QP_ROOT}"/lib:"${LIBRARY_PATH}"', "",
@ -531,7 +537,8 @@ def recommendation():
print " ninja"
print " make -C ocaml"
print ""
print "PS : For more info on compiling the code, read the COMPILE_RUN.md file."
print "You can install more plugin with the qp_install command"
print "PS : For more info on compiling the code, read the README.md"
if __name__ == '__main__':

13
install/scripts/install_bats.sh Executable file
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@ -0,0 +1,13 @@
#!/bin/bash -x
TARGET=bats
function _install()
{
cp -R ${BUILD} . || exit 1
cd ../bin
ln -s ../install/${TARGET}/libexec/bats . || return 1
cd -
}
source scripts/build.sh

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@ -12,9 +12,18 @@ export C_INCLUDE_PATH="${QP_ROOT}"/lib:"${C_INCLUDE_PATH}"
export LIBRARY_PATH="${QP_ROOT}"/lib:"${LIBRARY_PATH}"
export LD_LIBRARY_PATH="${QP_ROOT}"/lib:"${LD_LIBRARY_PATH}"
declare -i i
i=$(gcc -dumpversion | cut -d '.' -f 1)
if [[ i -lt 4 ]]
# return 0 if program version is equal or greater than check version
check_version()
{
local version=$1 check=$2
local winner=$(echo -e "$version\n$check" | sed '/^$/d' | sort -nr | head -1)
[[ "$winner" = "$version" ]] && return 0
return 1
}
i=$(gcc -dumpversion)
if check_version i 4.6
then
echo "GCC version $(gcc -dumpversion) too old. GCC >= 4.6 required."
exit 1

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@ -911,7 +911,7 @@ if __name__ == "__main__":
if module not in d_binaries:
l_msg = ["{0} is a root module but does not contain a main file.",
"- Create it in {0}",
"- Or delete {0} `qp_install_module.py uninstall {0}`",
"- Or delete {0} `qp_module.py uninstall {0}`",
"- Or install a module that needs {0} with a main "]
print "\n".join(l_msg).format(module.rel)

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@ -2,13 +2,11 @@
# -*- coding: utf-8 -*-
"""
Usage:
qp_install_module.py create -n <name> [<children_modules>...]
qp_install_module.py download -n <name> [<path_folder>...]
qp_install_module.py install <name>...
qp_install_module.py list (--installed | --available-local)
qp_install_module.py uninstall <name>...
qp_module.py create -n <name> [<children_modules>...]
qp_module.py download -n <name> [<path_folder>...]
qp_module.py install <name>...
qp_module.py list (--installed | --available-local)
qp_module.py uninstall <name>
Options:
list: List all the modules available
create: Create a new module

82
test/bats/qp.bats Normal file
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@ -0,0 +1,82 @@
#!/usr/bin/env bats
# float number comparison
# Compare two number ($1, $2) with a given precision ($3)
# If the number are not equal, the exit is 1 else is 0
# So we strip the "-", is the abs value of the poor
function eq() {
awk -v n1=${1#-} -v n2=${2#-} -v p=$3 'BEGIN{ if ((n1-n2)^2 < p^2) exit 0; exit 1}'
}
#: "${QP_ROOT?Pls set your quantum_package.rc}"
source ${QP_ROOT}/install/EZFIO/Bash/ezfio.sh
TEST_DIR=${QP_ROOT}/test/work/
mkdir -p ${TEST_DIR}
cd ${TEST_DIR}
@test "init HBO STO-3G" {
cp ${QP_ROOT}/test/input/HBO.xyz .
qp_create_ezfio_from_xyz -b "STO-3G" HBO.xyz
qp_edit -c HBO.ezfio
}
@test "hartree fock HBO STO-3G" {
run init HBO STO-3G
ezfio set_file HBO.ezfio
ezfio hartree_fock thresh_scf 1E-5
qp_run SCF HBO.ezfio
# Check energy
energy="$(ezfio get hartree_fock energy)"
eq $energy -98.8251985622549 1E-5
}
@test "full ci HBO STO-3G" {
run init HBO STO-3G
ezfio set_file HBO.ezfio
ezfio set perturbation do_pt2_end 1
ezfio set determinants n_det_max 1000
qp_run full_ci HBO.ezfio
energy="$(ezfio get full_ci energy)"
eq $energy -98.9649618899175 1E-2
energy_pt2="$(ezfio get full_ci energy_pt2)"
eq $energy_pt2 -98.966228232164 1E-5
}
@test "cas_sd_selected HBO STO-3G" {
run hartree fock HBO STO-3G
ezfio set_file HBO.ezfio
ezfio set perturbation do_pt2_end 0
ezfio set determinants n_det_max 1000
qp_set_mo_class HBO.ezfio -core "[1-2]" -inact "[3-5]" -act "[6-9]" -virt "[10-11]"
qp_run cas_sd_selected HBO.ezfio
# Check energy
energy="$(ezfio get cas_sd energy)"
eq $energy -98.9646946027433 1E-5
}
@test "mrcc_cassd HBO STO-3G" {
run cas_sd_selected fock HBO STO-3G
ezfio set_file HBO.ezfio
ezfio set determinants threshold_generators 1
ezfio set determinants read_wf 1
qp_run mrcc_cassd HBO.ezfio
# Check energy
energy="$(ezfio get mrcc_cassd energy)"
eq $energy -98.9653606184686 1E-5
}
@test "script conversion HBO.out" {
cp ${QP_ROOT}/test/input/HBO.out .
qp_convert_output_to_ezfio.py HBO.out
qp_edit -c HBO.out.ezfio
qp_run SCF HBO.out.ezfio
ezfio set_file HBO.out.ezfio
energy="$(ezfio get hartree_fock energy)"
eq $energy -100.01858225534 1E-5
}

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@ -1,5 +0,0 @@
3
SO2 Geo: Experiment Mult: 1 symmetry: 32
O 0.0 1.2371 0.7215
O 0.0 -1.2371 0.7215
S 0.0 0.0 0.0

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@ -1,7 +0,0 @@
5
methane molecule (in ångströms)
C 0.000000 0.000000 0.000000
H 0.000000 0.000000 1.089000
H 1.026719 0.000000 -0.363000
H -0.513360 -0.889165 -0.363000
H -0.513360 0.889165 -0.363000

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@ -1,404 +0,0 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import unittest
import subprocess
import os
import sys
qpackage_root = os.environ['QP_ROOT']
EZFIO = "{0}/install/EZFIO".format(qpackage_root)
sys.path = [EZFIO + "/Python"] + sys.path
from ezfio import ezfio
from collections import defaultdict
from collections import namedtuple
Energy = namedtuple('Energy', ['without_pseudo', 'with_pseudo'])
# ~#~#~ #
# O p t #
# ~#~#~ #
precision = 5.e-3
# A test get a geo file and a basis file.
# A global dict containt the result for this test
# A test return True or Raise a error !
# More ezfio condition you set, beter it is
# You cannot order the test flow.
# So if you dont whant to remarque on test (for example the HF), set
# a global variable and check for it
global has_hf_alredy
has_hf_alredy = False
global filename_check
def init_folder(geo, basis, mult=1, pseudo=False, ezfio_name=None):
'''
Take a geo in arg (aka a existing geo.xyz in test/)
And create the geo.ezfio with the adeguate basis and multipliciti
DO NOT CHECK IS THE EZFIO FOLDER ALREADY EXIST
'''
if not ezfio_name:
ezfio_name = geo
if pseudo:
cmd = "qp_create_ezfio_from_xyz -b {0} -m {1} {2}.xyz -p -o {3}.ezfio"
else:
cmd = "qp_create_ezfio_from_xyz -b {0} -m {1} {2}.xyz -o {3}.ezfio"
subprocess.check_call([cmd.format(basis, mult, geo, ezfio_name)],
shell=True)
def get_error_message(l_exepected, l_cur):
l_msg = ["Need {0} get {1} error is {2}".format(i, j, abs(i - j))
for i, j in zip(l_exepected, l_cur)]
return "\n" + "\n".join(l_msg)
# _
# / |_ _ _ | o ._ ._ _|_
# \_ | | (/_ (_ |< | | | |_) |_| |_
# |
def check_disk_acess(geo, basis, mult=1):
import uuid
filename = str(uuid.uuid4())
# ~#~#~#~ #
# I n i t #
# ~#~#~#~ #
init_folder(geo, basis, mult, ezfio_name=filename)
ezfio.set_file("{0}.ezfio".format(filename))
# ~#~#~#~#~#~#~#~#~#~#~#~#~ #
# S e t _ p a r a m e t e r #
# ~#~#~#~#~#~#~#~#~#~#~#~#~ #
# Test 1
ezfio.integrals_bielec_disk_access_ao_integrals = "Write"
cmd = "qp_edit -c {0}.ezfio".format(filename)
subprocess.check_call([cmd], shell=True)
# Test 2
ezfio.integrals_bielec_disk_access_ao_integrals = "IculeAcess"
cmd = "qp_edit -c {0}.ezfio".format(filename)
try:
subprocess.check_call([cmd], shell=True)
return_code = False
except subprocess.CalledProcessError:
return_code = True
# ~#~#~#~#~#~#~#~ #
# F i n a l i z e #
# ~#~#~#~#~#~#~#~ #
if return_code:
subprocess.call(["rm -R {0}.ezfio".format(filename)], shell=True)
return return_code
def check_mo_guess(geo, basis, mult=1):
import uuid
filename = str(uuid.uuid4())
# ~#~#~#~ #
# I n i t #
# ~#~#~#~ #
init_folder(geo, basis, mult, ezfio_name=filename)
ezfio.set_file("{0}.ezfio".format(filename))
# ~#~#~#~#~#~#~#~#~#~#~#~#~ #
# S e t _ p a r a m e t e r #
# ~#~#~#~#~#~#~#~#~#~#~#~#~ #
# Test 1
ezfio.hartree_fock_mo_guess_type = "Huckel"
cmd = "qp_edit -c {0}.ezfio".format(filename)
subprocess.check_call([cmd], shell=True)
# Test 2
ezfio.hartree_fock_mo_guess_type = "IculeGuess"
cmd = "qp_edit -c {0}.ezfio".format(filename)
try:
subprocess.check_call([cmd], shell=True)
return_code = False
except subprocess.CalledProcessError:
return_code = True
# ~#~#~#~#~#~#~#~ #
# F i n a l i z e #
# ~#~#~#~#~#~#~#~ #
if return_code:
subprocess.call(["rm -R {0}.ezfio".format(filename)], shell=True)
return return_code
# _
# / |_ _ _ | _. | _ _
# \_ | | (/_ (_ |< \/ (_| | |_| (/_ _>
#
def run_hf(geo, basis, mult=1, pseudo=False, remove_after_sucess=True):
"""
Run a simle by default hf
EZFIO path = geo.ezfio
"""
# ~#~#~#~#~#~#~#~#~#~ #
# R e f _ e n e r g y #
# ~#~#~#~#~#~#~#~#~#~ #
ref_energy = defaultdict(defaultdict)
ref_energy["sto-3g"]["methane"] = Energy(-39.7267433402, None)
ref_energy["vdz"]["SO2"] = Energy(None, -41.48912297776174)
# ref_energy["vdz"]["HBO"] = Energy(None, -19.1198231418)
ref_energy["vdz"]["HBO"] = Energy(None, -19.1198254041)
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
# G l o b a l _ v a r i a b l e #
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
global has_hf_alredy
has_hf_alredy = True
# ~#~#~#~ #
# I n i t #
# ~#~#~#~ #
init_folder(geo, basis, mult, pseudo)
ezfio.set_file("{0}.ezfio".format(geo))
# ~#~#~#~#~#~#~#~#~#~#~#~#~ #
# S e t _ p a r a m e t e r #
# ~#~#~#~#~#~#~#~#~#~#~#~#~ #
ezfio.integrals_bielec_direct = False
ezfio.integrals_bielec_threshold_ao = 1.e-15
ezfio.integrals_bielec_disk_access_ao_integrals = "None"
ezfio.integrals_bielec_threshold_mo = 1.e-15
ezfio.integrals_bielec_disk_access_mo_integrals = "None"
ezfio.hartree_fock_mo_guess_type = "Huckel"
ezfio.hartree_fock_thresh_scf = 1.e-10
ezfio.hartree_fock_n_it_scf_max = 100
ezfio.pseudo_do_pseudo = pseudo
# ~#~#~ #
# R u n #
# ~#~#~ #
# cmd = "{0}/Hartree_Fock/SCF {1}.ezfio/".format(QP_src,geo)
cmd = "qp_run SCF {0}.ezfio/".format(geo)
subprocess.check_call([cmd], shell=True)
# ~#~#~#~#~ #
# C h e c k #
# ~#~#~#~#~ #
cur_e = ezfio.get_hartree_fock_energy()
ref_e = ref_energy[basis][geo]
if pseudo:
ref_e = ref_e.with_pseudo
else:
ref_e = ref_e.without_pseudo
if abs(cur_e - ref_e) <= precision:
if remove_after_sucess:
subprocess.call(["rm -R {0}.ezfio".format(geo)], shell=True)
return True
else:
raise ValueError(get_error_message([ref_e], [cur_e]))
def run_full_ci_10k_pt2_end(geo, basis, pseudo):
"""
Run a Full_ci with 10k with the TruePT2
EZFIO path = geo.ezfio
"""
# ~#~#~#~#~#~#~#~#~#~ #
# R e f _ e n e r g y #
# ~#~#~#~#~#~#~#~#~#~ #
ref_energy_var = defaultdict(dict)
ref_energy_pt2 = defaultdict(dict)
ref_energy_var["sto-3g"]["methane"] = Energy(-39.8058687211, None)
ref_energy_pt2["sto-3g"]["methane"] = Energy(-39.8059180427, None)
# ~#~#~#~ #
# I n i t #
# ~#~#~#~ #
ezfio.set_file("{0}.ezfio".format(geo))
# ~#~#~#~#~#~#~#~#~#~#~#~#~ #
# S e t _ p a r a m e t e r #
# ~#~#~#~#~#~#~#~#~#~#~#~#~ #
ezfio.determinants_n_det_max = 10000
ezfio.determinants_n_det_max_jacobi = 10000
ezfio.determinants_n_states = 1
ezfio.determinants_read_wf = 1
ezfio.determinants_s2_eig = False
ezfio.determinants_threshold_generators = 0.99
ezfio.determinants_threshold_selectors = 0.999
ezfio.perturbation_do_pt2_end = True
ezfio.perturbation_pt2_max = 1.e-4
# ~#~#~ #
# R u n #
# ~#~#~ #
# cmd = "{0}/Full_CI/full_ci {1}.ezfio/".format(QP_src,geo)
cmd = "qp_run full_ci {0}.ezfio/".format(geo)
subprocess.check_call([cmd], shell=True)
# ~#~#~#~#~ #
# C h e c k #
# ~#~#~#~#~ #
cur_var = ezfio.get_full_ci_energy()
cur_pt2 = ezfio.get_full_ci_energy_pt2()
ref_var = ref_energy_var[basis][geo]
ref_pt2 = ref_energy_pt2[basis][geo]
if pseudo:
ref_var = ref_var.with_pseudo
ref_pt2 = ref_pt2.with_pseudo
else:
ref_var = ref_var.without_pseudo
ref_pt2 = ref_pt2.without_pseudo
t = [abs(cur_var - ref_var) <= precision,
abs(cur_pt2 - ref_pt2) <= precision]
if all(t):
return True
else:
raise ValueError(get_error_message([ref_var, ref_pt2],
[cur_var, cur_pt2]))
def hf_then_10k_test(geo, basis, mult=1, pseudo=False):
run_hf(geo, basis, mult, pseudo, remove_after_sucess=False)
try:
run_full_ci_10k_pt2_end(geo, basis, pseudo)
except:
raise
else:
return_code = True
# ~#~#~#~#~#~#~#~ #
# F i n a l i z e #
# ~#~#~#~#~#~#~#~ #
if return_code:
subprocess.call(["rm -R {0}.ezfio".format(geo)], shell=True)
return return_code
# _
# / |_ _ _ | _. ._ _ _ ._ _ ._ _|_
# \_ | | (/_ (_ |< (_| |_) (_ (_) | | \/ (/_ | |_
# | | __
def check_convert(path_out):
'''
Path_out is the out_file
'''
# ~#~#~#~#~#~#~#~#~#~ #
# R e f _ e n e r g y #
# ~#~#~#~#~#~#~#~#~#~ #
ref_energy = defaultdict(dict)
ref_energy["HBO.out"] = -100.0185822589
# ~#~#~#~#~#~#~#~#~#~#~#~#~ #
# S e t _ p a r a m e t e r #
# ~#~#~#~#~#~#~#~#~#~#~#~#~ #
cmd = "qp_convert_output_to_ezfio.py {0}".format(path_out)
subprocess.check_call([cmd], shell=True)
# Test 2
cmd = "qp_edit -c {0}.ezfio".format(path_out)
subprocess.check_call([cmd], shell=True)
cmd = "qp_run SCF {0}.ezfio".format(path_out)
subprocess.check_call([cmd], shell=True)
# ~#~#~#~#~ #
# C h e c k #
# ~#~#~#~#~ #
ezfio.set_file("{0}.ezfio".format(path_out))
cur_e = ezfio.get_hartree_fock_energy()
ref_e = ref_energy[path_out]
if abs(cur_e - ref_e) <= precision:
subprocess.call(["rm -R {0}.ezfio".format(path_out)], shell=True)
return True
else:
raise ValueError(get_error_message([ref_e], [cur_e]))
# ___
# | _ _ _|_
# | (/_ _> |_
#
class ValueTest(unittest.TestCase):
def test_hf_then_full_ci_10k_pt2_end(self):
self.assertTrue(hf_then_10k_test(geo="methane",
basis="sto-3g",
mult=1,
pseudo=False))
def test_hf(self):
self.assertTrue(run_hf(geo="HBO",
basis="vdz",
mult=1,
pseudo=True))
class ConvertTest(unittest.TestCase):
def test_check_convert_hf_energy(self):
self.assertTrue(check_convert("HBO.out"))
class InputTest(unittest.TestCase):
def test_check_disk_acess(self):
self.assertTrue(check_disk_acess(geo="methane",
basis="un-ccemd-ref"))
def test_check_mo_guess(self):
self.assertTrue(check_mo_guess(geo="methane",
basis="maug-cc-pVDZ"))
if __name__ == '__main__':
unittest.main()