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Merge branch 'dev' into features_spack

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Anthony Scemama 2020-03-18 11:46:46 +01:00
commit 3fb7c6e48e
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14
INSTALL.rst
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@ -36,7 +36,7 @@ Requirements
- Fortran compiler : GNU Fortran, Intel Fortran or IBM XL Fortran - Fortran compiler : GNU Fortran, Intel Fortran or IBM XL Fortran
- `GNU make`_ - `GNU make`_
- `Autoconf`_ - `Autoconf`_
- `Python`_ > 2.6 - `Python`_ > 3.0
- |IRPF90| : Fortran code generator - |IRPF90| : Fortran code generator
- |EZFIO| : Easy Fortran Input/Output library generator - |EZFIO| : Easy Fortran Input/Output library generator
- |BLAS| and |LAPACK| - |BLAS| and |LAPACK|
@ -151,11 +151,11 @@ IRPF90
*IRPF90* is a Fortran code generator for programming using the Implicit Reference *IRPF90* is a Fortran code generator for programming using the Implicit Reference
to Parameters (IRP) method. to Parameters (IRP) method.
If you have *pip* for Python2, you can do If you have *pip* for Python3, you can do
.. code:: bash .. code:: bash
python2 -m pip install --user irpf90 python3 -m pip install --user irpf90
Otherwise, Otherwise,
@ -387,11 +387,11 @@ Docopt
*Docopt* is a Python package defining a command-line interface description language. *Docopt* is a Python package defining a command-line interface description language.
If you have *pip* for Python2, you can do If you have *pip* for Python3, you can do
.. code:: bash .. code:: bash
python2 -m pip install --user docopt python3 -m pip install --user docopt
Otherwise, Otherwise,
@ -408,11 +408,11 @@ resultsFile
*resultsFile* is a Python package to extract data from output files of quantum chemistry *resultsFile* is a Python package to extract data from output files of quantum chemistry
codes. codes.
If you have *pip* for Python2, you can do If you have *pip* for Python3, you can do
.. code:: bash .. code:: bash
python2 -m pip install --user resultsFile python3 -m pip install --user resultsFile

4
bin/qp_basis
View File

@ -1,4 +1,4 @@
#!/usr/bin/env python2 #!/usr/bin/env python3
# -*- coding: utf-8 -*- # -*- coding: utf-8 -*-
""" """
@ -12,7 +12,7 @@ Usage:
""" """
from __future__ import print_function
import sys import sys
import os import os
import subprocess import subprocess

54
bin/qp_convert_output_to_ezfio
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@ -1,4 +1,4 @@
#!/usr/bin/env python2 #!/usr/bin/env python3
""" """
convert output of GAMESS/GAU$$IAN to ezfio convert output of GAMESS/GAU$$IAN to ezfio
@ -22,7 +22,7 @@ try:
QP_ROOT = os.environ["QP_ROOT"] QP_ROOT = os.environ["QP_ROOT"]
QP_EZFIO = os.environ["QP_EZFIO"] QP_EZFIO = os.environ["QP_EZFIO"]
except KeyError: except KeyError:
print "Error: QP_ROOT environment variable not found." print("Error: QP_ROOT environment variable not found.")
sys.exit(1) sys.exit(1)
else: else:
sys.path = [QP_EZFIO + "/Python", sys.path = [QP_EZFIO + "/Python",
@ -30,10 +30,11 @@ else:
QP_ROOT + "/install", QP_ROOT + "/install",
QP_ROOT + "/scripts"] + sys.path QP_ROOT + "/scripts"] + sys.path
from resultsFile import *
try: try:
from resultsFile import * from resultsFile import *
except: except:
print "Error: resultsFile Python library not installed" print("Error: resultsFile Python library not installed")
sys.exit(1) sys.exit(1)
@ -48,17 +49,17 @@ def write_ezfio(res, filename):
# |_ | _ _ _|_ ._ _ ._ _ # |_ | _ _ _|_ ._ _ ._ _
# |_ | (/_ (_ |_ | (_) | | _> # |_ | (/_ (_ |_ | (_) | | _>
# #
print "Electrons\t...\t", print("Electrons\t...\t", end=' ')
ezfio.set_electrons_elec_alpha_num(res.num_alpha) ezfio.set_electrons_elec_alpha_num(res.num_alpha)
ezfio.set_electrons_elec_beta_num(res.num_beta) ezfio.set_electrons_elec_beta_num(res.num_beta)
print "OK" print("OK")
# #
# |\ | _ | _ o # |\ | _ | _ o
# | \| |_| (_ | (/_ | # | \| |_| (_ | (/_ |
# #
print "Nuclei\t\t...\t", print("Nuclei\t\t...\t", end=' ')
# ~#~#~#~ # # ~#~#~#~ #
# I n i t # # I n i t #
# ~#~#~#~ # # ~#~#~#~ #
@ -93,24 +94,23 @@ def write_ezfio(res, filename):
# Transformt H1 into H # Transformt H1 into H
import re import re
p = re.compile(ur'(\d*)$') p = re.compile(r'(\d*)$')
label = [p.sub("", x.name).capitalize() for x in res.geometry] label = [p.sub("", x.name).capitalize() for x in res.geometry]
ezfio.set_nuclei_nucl_label(label) ezfio.set_nuclei_nucl_label(label)
ezfio.set_nuclei_nucl_coord(coord_x + coord_y + coord_z) ezfio.set_nuclei_nucl_coord(coord_x + coord_y + coord_z)
print "OK" print("OK")
# _ # _
# /\ _ _ |_) _. _ o _ # /\ _ _ |_) _. _ o _
# /--\ (_) _> |_) (_| _> | _> # /--\ (_) _> |_) (_| _> | _>
# #
print "AOS\t\t...\t", print("AOS\t\t...\t", end=' ')
# ~#~#~#~ # # ~#~#~#~ #
# I n i t # # I n i t #
# ~#~#~#~ # # ~#~#~#~ #
import string
at = [] at = []
num_prim = [] num_prim = []
power_x = [] power_x = []
@ -131,9 +131,9 @@ def write_ezfio(res, filename):
at.append(i + 1) at.append(i + 1)
num_prim.append(len(b.prim)) num_prim.append(len(b.prim))
s = b.sym s = b.sym
power_x.append(string.count(s, "x")) power_x.append(str.count(s, "x"))
power_y.append(string.count(s, "y")) power_y.append(str.count(s, "y"))
power_z.append(string.count(s, "z")) power_z.append(str.count(s, "z"))
coefficient.append(b.coef) coefficient.append(b.coef)
exponent.append([p.expo for p in b.prim]) exponent.append([p.expo for p in b.prim])
@ -175,14 +175,14 @@ def write_ezfio(res, filename):
ezfio.set_ao_basis_ao_expo(expo) ezfio.set_ao_basis_ao_expo(expo)
ezfio.set_ao_basis_ao_basis("Read by resultsFile") ezfio.set_ao_basis_ao_basis("Read by resultsFile")
print "OK" print("OK")
# _ # _
# |\/| _ _ |_) _. _ o _ # |\/| _ _ |_) _. _ o _
# | | (_) _> |_) (_| _> | _> # | | (_) _> |_) (_| _> | _>
# #
print "MOS\t\t...\t", print("MOS\t\t...\t", end=' ')
# ~#~#~#~ # # ~#~#~#~ #
# I n i t # # I n i t #
# ~#~#~#~ # # ~#~#~#~ #
@ -205,9 +205,9 @@ def write_ezfio(res, filename):
virtual = [] virtual = []
active = [(allMOs[i].eigenvalue, i) for i in range(len(allMOs))] active = [(allMOs[i].eigenvalue, i) for i in range(len(allMOs))]
closed = map(lambda x: x[1], closed) closed = [x[1] for x in closed]
active = map(lambda x: x[1], active) active = [x[1] for x in active]
virtual = map(lambda x: x[1], virtual) virtual = [x[1] for x in virtual]
MOindices = closed + active + virtual MOindices = closed + active + virtual
MOs = [] MOs = []
@ -223,7 +223,7 @@ def write_ezfio(res, filename):
MOmap[i] = MOindices.index(i) MOmap[i] = MOindices.index(i)
energies = [] energies = []
for i in xrange(mo_num): for i in range(mo_num):
energies.append(MOs[i].eigenvalue) energies.append(MOs[i].eigenvalue)
if res.occ_num is not None: if res.occ_num is not None:
@ -237,11 +237,11 @@ def write_ezfio(res, filename):
MoMatrix = [] MoMatrix = []
sym0 = [i.sym for i in res.mo_sets[MO_type]] sym0 = [i.sym for i in res.mo_sets[MO_type]]
sym = [i.sym for i in res.mo_sets[MO_type]] sym = [i.sym for i in res.mo_sets[MO_type]]
for i in xrange(len(sym)): for i in range(len(sym)):
sym[MOmap[i]] = sym0[i] sym[MOmap[i]] = sym0[i]
MoMatrix = [] MoMatrix = []
for i in xrange(len(MOs)): for i in range(len(MOs)):
m = MOs[i] m = MOs[i]
for coef in m.vector: for coef in m.vector:
MoMatrix.append(coef) MoMatrix.append(coef)
@ -256,10 +256,10 @@ def write_ezfio(res, filename):
ezfio.set_mo_basis_mo_num(mo_num) ezfio.set_mo_basis_mo_num(mo_num)
ezfio.set_mo_basis_mo_occ(OccNum) ezfio.set_mo_basis_mo_occ(OccNum)
ezfio.set_mo_basis_mo_coef(MoMatrix) ezfio.set_mo_basis_mo_coef(MoMatrix)
print "OK" print("OK")
print "Pseudos\t\t...\t", print("Pseudos\t\t...\t", end=' ')
try: try:
lmax = 0 lmax = 0
nucl_charge_remove = [] nucl_charge_remove = []
@ -327,7 +327,7 @@ def write_ezfio(res, filename):
else: else:
ezfio.set_pseudo_do_pseudo(True) ezfio.set_pseudo_do_pseudo(True)
print "OK" print("OK")
@ -354,15 +354,15 @@ if __name__ == '__main__':
except: except:
raise raise
else: else:
print FILE, 'recognized as', str(RES_FILE).split('.')[-1].split()[0] print(FILE, 'recognized as', str(RES_FILE).split('.')[-1].split()[0])
write_ezfio(RES_FILE, EZFIO_FILE) write_ezfio(RES_FILE, EZFIO_FILE)
sys.stdout.flush() sys.stdout.flush()
if os.system("qp_run save_ortho_mos "+EZFIO_FILE) != 0: if os.system("qp_run save_ortho_mos "+EZFIO_FILE) != 0:
print """Warning: You need to run print("""Warning: You need to run
qp run save_ortho_mos qp run save_ortho_mos
to be sure your MOs will be orthogonal, which is not the case when to be sure your MOs will be orthogonal, which is not the case when
the MOs are read from output files (not enough precision in output).""" the MOs are read from output files (not enough precision in output).""")

28
bin/qp_name
View File

@ -1,4 +1,4 @@
#!/usr/bin/env python2 #!/usr/bin/env python3
""" """
Displays the names of all the files in which the provider/subroutine/function Displays the names of all the files in which the provider/subroutine/function
@ -30,7 +30,7 @@ try:
from docopt import docopt from docopt import docopt
from qp_path import QP_SRC, QP_ROOT from qp_path import QP_SRC, QP_ROOT
except ImportError: except ImportError:
print "source .quantum_package.rc" print("source .quantum_package.rc")
raise raise
@ -38,7 +38,7 @@ def main(arguments):
"""Main function""" """Main function"""
# Check that name exist in */IRPF90_man # Check that name exist in */IRPF90_man
print "Checking that name exists..." print("Checking that name exists...")
all_modules = os.listdir(QP_SRC) all_modules = os.listdir(QP_SRC)
f = arguments["<name>"]+".l" f = arguments["<name>"]+".l"
@ -52,21 +52,21 @@ def main(arguments):
if found: break if found: break
if not found: if not found:
print "Error:" print("Error:")
print "The variable/subroutine/function \""+arguments["<name>"] \ print("The variable/subroutine/function \""+arguments["<name>"] \
+ "\" was not found in the sources." + "\" was not found in the sources.")
print "Did you compile the code at the root?" print("Did you compile the code at the root?")
print "Continue? [y/N] ", print("Continue? [y/N] ", end=' ')
cont = sys.stdin.read(1).strip() in ["y", "Y"] cont = sys.stdin.read(1).strip() in ["y", "Y"]
if not cont: if not cont:
print "Aborted" print("Aborted")
sys.exit(1) sys.exit(1)
# Now search in all the files # Now search in all the files
if arguments["--rename"]: if arguments["--rename"]:
print "Replacing..." print("Replacing...")
else: else:
print "Searching..." print("Searching...")
name = re.compile(r"\b"+arguments["<name>"]+r"\b", re.IGNORECASE) name = re.compile(r"\b"+arguments["<name>"]+r"\b", re.IGNORECASE)
@ -84,15 +84,15 @@ def main(arguments):
with open(filename, "r") as f: with open(filename, "r") as f:
f_in = f.read() f_in = f.read()
if name.search(f_in): if name.search(f_in):
print filename print(filename)
if arguments["--rename"]: if arguments["--rename"]:
f_new = name.sub(arguments["--rename"], f_in) f_new = name.sub(arguments["--rename"], f_in)
with open(filename, "w") as f: with open(filename, "w") as f:
f.write(f_new) f.write(f_new)
print "Done" print("Done")
with open(os.path.join(QP_ROOT, "REPLACE"), 'a') as f: with open(os.path.join(QP_ROOT, "REPLACE"), 'a') as f:
print >>f, "qp_name "+" ".join(sys.argv[1:]) print("qp_name "+" ".join(sys.argv[1:]), file=f)

68
bin/qp_plugins
View File

@ -1,4 +1,4 @@
#!/usr/bin/env python2 #!/usr/bin/env python3
# -*- coding: utf-8 -*- # -*- coding: utf-8 -*-
""" """
Usage: Usage:
@ -43,9 +43,9 @@ try:
from module_handler import get_l_module_descendant from module_handler import get_l_module_descendant
from qp_path import QP_SRC, QP_PLUGINS, QP_DATA, QP_ROOT from qp_path import QP_SRC, QP_PLUGINS, QP_DATA, QP_ROOT
except ImportError: except ImportError:
print "Please check if you have sourced the ${QP_ROOT}/quantum_package.rc" print("Please check if you have sourced the ${QP_ROOT}/quantum_package.rc")
print "(`source ${QP_ROOT}/quantum_package.rc`)" print("(`source ${QP_ROOT}/quantum_package.rc`)")
print sys.exit(1) print(sys.exit(1))
def save_new_module(path, l_child): def save_new_module(path, l_child):
@ -58,7 +58,7 @@ def save_new_module(path, l_child):
try: try:
os.makedirs(path) os.makedirs(path)
except OSError: except OSError:
print "The module ({0}) already exists...".format(path) print("The module ({0}) already exists...".format(path))
sys.exit(1) sys.exit(1)
with open(os.path.join(path, "NEED"), "w") as f: with open(os.path.join(path, "NEED"), "w") as f:
@ -105,7 +105,7 @@ def main(arguments):
if arguments["list"]: if arguments["list"]:
if arguments["--repositories"]: if arguments["--repositories"]:
for repo in get_repositories(): for repo in get_repositories():
print repo print(repo)
else: else:
# Search in QP_PLUGINS all directories with a NEED file # Search in QP_PLUGINS all directories with a NEED file
@ -121,7 +121,7 @@ def main(arguments):
for (x, y) in l_tmp: for (x, y) in l_tmp:
d_tmp[x] = y d_tmp[x] = y
repo_of_plugin[y] = x.replace(QP_PLUGINS+'/','') repo_of_plugin[y] = x.replace(QP_PLUGINS+'/','')
l_repository = d_tmp.keys() l_repository = list(d_tmp.keys())
if l_repository == []: if l_repository == []:
l_result = [] l_result = []
else: else:
@ -142,7 +142,7 @@ def main(arguments):
l_result = [f for f in l_plugins if f not in l_installed] l_result = [f for f in l_plugins if f not in l_installed]
for module in sorted(l_result): for module in sorted(l_result):
print "%-30s %-30s"%(module, repo_of_plugin[module]) print("%-30s %-30s"%(module, repo_of_plugin[module]))
if arguments["create"]: if arguments["create"]:
@ -159,29 +159,29 @@ def main(arguments):
path = os.path.join(QP_PLUGINS, repository, name) path = os.path.join(QP_PLUGINS, repository, name)
print "Created plugin:" print("Created plugin:")
print path, '\n' print(path, '\n')
for children in l_children: for children in l_children:
if children not in m_instance.dict_descendant: if children not in m_instance.dict_descendant:
print "Error: {0} is not a valid module.".format(children) print("Error: {0} is not a valid module.".format(children))
sys.exit(1) sys.exit(1)
print "Needed modules:" print("Needed modules:")
print l_children, '\n' print(l_children, '\n')
print "This corresponds to using the following modules:" print("This corresponds to using the following modules:")
print l_children + m_instance.l_descendant_unique(l_children), '\n' print(l_children + m_instance.l_descendant_unique(l_children), '\n')
print "Which is reduced to:" print("Which is reduced to:")
l_child_reduce = m_instance.l_reduce_tree(l_children) l_child_reduce = m_instance.l_reduce_tree(l_children)
print l_child_reduce, '\n' print(l_child_reduce, '\n')
print "Installation", print("Installation", end=' ')
save_new_module(path, l_child_reduce) save_new_module(path, l_child_reduce)
print " [ OK ]" print(" [ OK ]")
print "" print("")
arguments["create"] = False arguments["create"] = False
arguments["install"] = True arguments["install"] = True
main(arguments) main(arguments)
@ -228,7 +228,7 @@ def main(arguments):
for (x, y) in [os.path.split(f) for f in l_tmp]: for (x, y) in [os.path.split(f) for f in l_tmp]:
d_repo_of_plugin[y] = x d_repo_of_plugin[y] = x
d_repo[x] = None d_repo[x] = None
l_repository = d_repo.keys() l_repository = list(d_repo.keys())
d_plugin = get_dict_child(l_repository) d_plugin = get_dict_child(l_repository)
@ -236,7 +236,7 @@ def main(arguments):
d_child.update(d_plugin) d_child.update(d_plugin)
normalize_case = {} normalize_case = {}
for name in d_local.keys() + d_plugin.keys(): for name in list(d_local.keys()) + list(d_plugin.keys()):
normalize_case[name.lower()] = name normalize_case[name.lower()] = name
l_name = [normalize_case[name.lower()] for name in arguments["<name>"]] l_name = [normalize_case[name.lower()] for name in arguments["<name>"]]
@ -244,7 +244,7 @@ def main(arguments):
for name in l_name: for name in l_name:
if name in d_local: if name in d_local:
print "{0} Is already installed".format(name) print("{0} Is already installed".format(name))
l_module_descendant = get_l_module_descendant(d_child, l_name) l_module_descendant = get_l_module_descendant(d_child, l_name)
@ -252,10 +252,10 @@ def main(arguments):
if l_module_to_cp: if l_module_to_cp:
print "Required dependencies:" print("Required dependencies:")
print l_module_to_cp print(l_module_to_cp)
print "Installation...", print("Installation...", end=' ')
for module_to_cp in l_module_to_cp: for module_to_cp in l_module_to_cp:
src = os.path.join(d_repo_of_plugin[module_to_cp], module_to_cp) src = os.path.join(d_repo_of_plugin[module_to_cp], module_to_cp)
@ -269,10 +269,10 @@ def main(arguments):
subprocess.check_call([install]) subprocess.check_call([install])
os.chdir(wd) os.chdir(wd)
except OSError: except OSError:
print "The src directory is broken. Please remove %s" % des print("The src directory is broken. Please remove %s" % des)
raise raise
subprocess.check_call(["qp_create_ninja", "update"]) subprocess.check_call(["qp_create_ninja", "update"])
print "[ OK ]" print("[ OK ]")
elif arguments["uninstall"]: elif arguments["uninstall"]:
@ -285,17 +285,17 @@ def main(arguments):
l_failed = [name for name in l_name if name not in d_local] l_failed = [name for name in l_name if name not in d_local]
if l_failed: if l_failed:
print "Plugins not installed:" print("Plugins not installed:")
for name in sorted(l_failed): for name in sorted(l_failed):
print "%s" % name print("%s" % name)
sys.exit(1) sys.exit(1)
l_name_to_remove = l_name + \ l_name_to_remove = l_name + \
[module for module in m_instance.l_module \ [module for module in m_instance.l_module \
for name in l_name if name in d_descendant[module]] for name in l_name if name in d_descendant[module]]
print "Removing plugins:" print("Removing plugins:")
print l_name_to_remove print(l_name_to_remove)
for module in set(l_name_to_remove): for module in set(l_name_to_remove):
@ -310,7 +310,7 @@ def main(arguments):
try: try:
os.unlink(os.path.join(QP_SRC, module)) os.unlink(os.path.join(QP_SRC, module))
except OSError: except OSError:
print "%s is a core module which can't be removed" % module print("%s is a core module which can't be removed" % module)
elif arguments["update"]: elif arguments["update"]:
@ -321,7 +321,7 @@ def main(arguments):
l_repositories = get_repositories() l_repositories = get_repositories()
for repo in l_repositories: for repo in l_repositories:
print "Updating ", repo print("Updating ", repo)
os.chdir(os.path.join(QP_PLUGINS,repo)) os.chdir(os.path.join(QP_PLUGINS,repo))
git_cmd=["git", "pull"] git_cmd=["git", "pull"]
subprocess.check_call(git_cmd) subprocess.check_call(git_cmd)

1
bin/qp_reset
View File

@ -95,6 +95,7 @@ qp set_file $ezfio
if [[ $dets -eq 1 ]] ; then if [[ $dets -eq 1 ]] ; then
rm --force -- ${ezfio}/determinants/n_det rm --force -- ${ezfio}/determinants/n_det
rm --force -- ${ezfio}/determinants/psi_{det,coef}.gz rm --force -- ${ezfio}/determinants/psi_{det,coef}.gz
rm --force -- ${ezfio}/determinants/psi_{det,coef}_qp_edit.gz
fi fi
if [[ $mos -eq 1 ]] ; then if [[ $mos -eq 1 ]] ; then

6
bin/qp_set_frozen_core
View File

@ -1,4 +1,4 @@
#!/usr/bin/env python2 #!/usr/bin/env python3
""" """
@ -49,7 +49,7 @@ import os.path
try: try:
import qp_path import qp_path
except ImportError: except ImportError:
print "source .quantum_package.rc" print("source .quantum_package.rc")
raise raise
from docopt import docopt from docopt import docopt
@ -102,7 +102,7 @@ def main(arguments):
mo_num = ezfio.mo_basis_mo_num mo_num = ezfio.mo_basis_mo_num
if arguments["--query"]: if arguments["--query"]:
print n_frozen print(n_frozen)
sys.exit(0) sys.exit(0)
if n_frozen == 0: if n_frozen == 0:

6
bin/qp_set_frozen_large_core
View File

@ -1,4 +1,4 @@
#!/usr/bin/env python2 #!/usr/bin/env python3
""" """
@ -23,7 +23,7 @@ import os.path
try: try:
import qp_path import qp_path
except ImportError: except ImportError:
print "source .quantum_package.rc" print("source .quantum_package.rc")
raise raise
from docopt import docopt from docopt import docopt
@ -62,7 +62,7 @@ def main(arguments):
mo_num = ezfio.mo_basis_mo_num mo_num = ezfio.mo_basis_mo_num
if arguments["--query"]: if arguments["--query"]:
print n_frozen print(n_frozen)
sys.exit(0) sys.exit(0)
if n_frozen == 0: if n_frozen == 0:

18
bin/qp_test
View File

@ -1,4 +1,4 @@
#!/usr/bin/env python2 #!/usr/bin/env python3
# -*- coding: utf-8 -*- # -*- coding: utf-8 -*-
""" """
@ -21,8 +21,8 @@ try:
from docopt import docopt from docopt import docopt
from qp_path import QP_SRC, QP_TESTS from qp_path import QP_SRC, QP_TESTS
except ImportError: except ImportError:
print "Please check if you have sourced the ${QP_ROOT}/quantum_package.rc" print("Please check if you have sourced the ${QP_ROOT}/quantum_package.rc")
print "(`source ${QP_ROOT}/quantum_package.rc`)" print("(`source ${QP_ROOT}/quantum_package.rc`)")
sys.exit(1) sys.exit(1)
@ -54,11 +54,11 @@ def main(arguments):
os.chdir(QP_TESTS) os.chdir(QP_TESTS)
for bats_file in l_bats: for bats_file in l_bats:
print "" print("")
print "-~-~-~-~-~-~" print("-~-~-~-~-~-~")
print "" print("")
print "Running tests for %s"%(bats_file) print("Running tests for %s"%(bats_file))
print "" print("")
if arguments["-v"]: if arguments["-v"]:
p = None p = None
if arguments["TEST"]: if arguments["TEST"]:
@ -66,7 +66,7 @@ def main(arguments):
else: else:
test = "" test = ""
try: try:
os.system(test+" python2 bats_to_sh.py "+bats_file+ os.system(test+" python3 bats_to_sh.py "+bats_file+
"| bash") "| bash")
except: except:
if p: if p:

2
config/ifort_avx.cfg
View File

@ -32,7 +32,7 @@ OPENMP : 1 ; Append OpenMP flags
# #
[OPT] [OPT]
FC : -traceback FC : -traceback
FCFLAGS : -xAVX -O2 -ip -ftz -g FCFLAGS : -mavx -axAVX -O2 -ip -ftz -g
# Profiling flags # Profiling flags
################# #################

2
config/ifort_avx_mpi.cfg
View File

@ -31,7 +31,7 @@ OPENMP : 1 ; Append OpenMP flags
# -ftz : Flushes denormal results to zero # -ftz : Flushes denormal results to zero
# #
[OPT] [OPT]
FCFLAGS : -march=corei7-avx -O2 -ip -ftz -g -traceback FCFLAGS : -mavx -axAVX -O2 -ip -ftz -g -traceback
# Profiling flags # Profiling flags
################# #################

8
config/ifort_debug.cfg
View File

@ -32,7 +32,7 @@ OPENMP : 1 ; Append OpenMP flags
# #
[OPT] [OPT]
FC : -traceback FC : -traceback
FCFLAGS : -xSSE4.2 -O2 -ip -ftz -g FCFLAGS : -msse4.2 -O2 -ip -ftz -g
# Profiling flags # Profiling flags
@ -40,7 +40,7 @@ FCFLAGS : -xSSE4.2 -O2 -ip -ftz -g
# #
[PROFILE] [PROFILE]
FC : -p -g FC : -p -g
FCFLAGS : -xSSE4.2 -O2 -ip -ftz FCFLAGS : -msse4.2 -O2 -ip -ftz
# Debugging flags # Debugging flags
@ -50,11 +50,11 @@ FCFLAGS : -xSSE4.2 -O2 -ip -ftz
# -fpe0 : All floating point exaceptions # -fpe0 : All floating point exaceptions
# -C : Checks uninitialized variables, array subscripts, etc... # -C : Checks uninitialized variables, array subscripts, etc...
# -g : Extra debugging information # -g : Extra debugging information
# -xSSE2 : Valgrind needs a very simple x86 executable # -msse4.2 : Valgrind needs a very simple x86 executable
# #
[DEBUG] [DEBUG]
FC : -g -traceback FC : -g -traceback
FCFLAGS : -xSSE4.2 -C -fpe0 -implicitnone FCFLAGS : -msse4.2 -C -fpe0 -implicitnone
# OpenMP flags # OpenMP flags

63
config/ifort_epyc.cfg
View File

@ -1,63 +0,0 @@
# Common flags
##############
#
# -mkl=[parallel|sequential] : Use the MKL library
# --ninja : Allow the utilisation of ninja. It is mandatory !
# --align=32 : Align all provided arrays on a 32-byte boundary
#
[COMMON]
FC : ifort -fpic
LAPACK_LIB : -mkl=parallel
IRPF90 : irpf90
IRPF90_FLAGS : --ninja --align=32
# Global options
################
#
# 1 : Activate
# 0 : Deactivate
#
[OPTION]
MODE : OPT ; [ OPT | PROFILE | DEBUG ] : Chooses the section below
CACHE : 0 ; Enable cache_compile.py
OPENMP : 1 ; Append OpenMP flags
# Optimization flags
####################
#
# -xHost : Compile a binary optimized for the current architecture
# -O2 : O3 not better than O2.
# -ip : Inter-procedural optimizations
# -ftz : Flushes denormal results to zero
#
[OPT]
FC : -traceback
FCFLAGS : -march=core-avx2 -O2 -ip -ftz -g
# Profiling flags
#################
#
[PROFILE]
FC : -p -g
FCFLAGS : -march=core-avx2 -O2 -ip -ftz
# Debugging flags
#################
#
# -traceback : Activate backtrace on runtime
# -fpe0 : All floating point exaceptions
# -C : Checks uninitialized variables, array subscripts, etc...
# -g : Extra debugging information
# -xSSE2 : Valgrind needs a very simple x86 executable
#
[DEBUG]
FC : -g -traceback
FCFLAGS : -xSSE2 -C -fpe0 -implicitnone
# OpenMP flags
#################
#
[OPENMP]
FC : -qopenmp
IRPF90_FLAGS : --openmp

4
config/ifort_mpi.cfg
View File

@ -31,14 +31,14 @@ OPENMP : 1 ; Append OpenMP flags
# -ftz : Flushes denormal results to zero # -ftz : Flushes denormal results to zero
# #
[OPT] [OPT]
FCFLAGS : -xSSE4.2 -O2 -ip -ftz -g -traceback FCFLAGS : -msse4.2 -O2 -ip -ftz -g -traceback
# Profiling flags # Profiling flags
################# #################
# #
[PROFILE] [PROFILE]
FC : -p -g FC : -p -g
FCFLAGS : -xSSE4.2 -O2 -ip -ftz FCFLAGS : -msse4.2 -O2 -ip -ftz
# Debugging flags # Debugging flags

3
configure vendored
View File

@ -3,7 +3,7 @@
# Quantum Package configuration script # Quantum Package configuration script
# #
EZFIO_TGZ="EZFIO.1.6.2.tar.gz" EZFIO_TGZ="EZFIO.2.0.2.tar.gz"
@ -315,3 +315,4 @@ fi
exit 0 exit 0

2
docs/Makefile
View File

@ -14,7 +14,7 @@ help:
.PHONY: help Makefile auto .PHONY: help Makefile auto
auto: auto:
cd source ; python2 auto_generate.py cd source ; python3 auto_generate.py
# Catch-all target: route all unknown targets to Sphinx using the new # Catch-all target: route all unknown targets to Sphinx using the new
# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). # "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).

6
docs/source/auto_generate.py
View File

@ -1,9 +1,9 @@
#!/usr/bin/env python2 #!/usr/bin/env python2
from __future__ import print_function
import os import os
import sys import sys
import ConfigParser import configparser
from module_handler import get_binaries from module_handler import get_binaries
@ -27,7 +27,7 @@ def generate_modules(abs_module, entities):
EZFIO = os.path.join(abs_module,'EZFIO.cfg') EZFIO = os.path.join(abs_module,'EZFIO.cfg')
if os.path.exists(EZFIO): if os.path.exists(EZFIO):
rst += ["", "EZFIO parameters", "----------------", ""] rst += ["", "EZFIO parameters", "----------------", ""]
config_file = ConfigParser.ConfigParser() config_file = configparser.ConfigParser()
with open(EZFIO, 'r') as f: with open(EZFIO, 'r') as f:
config_file.readfp(f) config_file.readfp(f)
for section in config_file.sections(): for section in config_file.sections():

1
etc/paths.rc
View File

@ -38,5 +38,6 @@ export LD_LIBRARY_PATH=$(qp_prepend_export "LD_LIBRARY_PATH" "${QP_ROOT}"/lib)
export LIBRARY_PATH=$(qp_prepend_export "LIBRARY_PATH" "${QP_ROOT}"/lib:"${QP_ROOT}"/lib64) export LIBRARY_PATH=$(qp_prepend_export "LIBRARY_PATH" "${QP_ROOT}"/lib:"${QP_ROOT}"/lib64)
export C_INCLUDE_PATH=$(qp_prepend_export "C_INCLUDE_PATH" "${QP_ROOT}"/include) export C_INCLUDE_PATH=$(qp_prepend_export "C_INCLUDE_PATH" "${QP_ROOT}"/include)
export CPATH=$(qp_prepend_export "CPATH" "${QP_ROOT}"/include)

BIN
external/EZFIO.1.6.2.tar.gz vendored
View File

Binary file not shown.

BIN
external/EZFIO.2.0.2.tar.gz vendored Normal file
View File

Binary file not shown.

46
external/Python/.gitignore vendored
View File

@ -0,0 +1,46 @@
# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
# C extensions
*.so
# Distribution / packaging
.Python
env/
build/
develop-eggs/
dist/
downloads/
eggs/
# PyInstaller
# Usually these files are written by a python script from a template
# before PyInstaller builds the exe, so as to inject date/other infos into it.
*.manifest
*.spec
# Installer logs
pip-log.txt
pip-delete-this-directory.txt
# Unit test / coverage reports
htmlcov/
.tox/
.coverage
.cache
nosetests.xml
coverage.xml
# Translations
*.mo
*.pot
# Django stuff:
*.log
# Sphinx documentation
docs/_build/
# PyBuilder
target/

43
ocaml/qp_tunnel.ml
View File

@ -21,10 +21,6 @@ let () =
doc="Downloads the EZFIO directory." ; doc="Downloads the EZFIO directory." ;
arg=Without_arg; } ; arg=Without_arg; } ;
{ short='v' ; long="verbose" ; opt=Optional ;
doc="Prints the transfer speed." ;
arg=Without_arg; } ;
anonymous anonymous
"(EZFIO_DIR|ADDRESS)" "(EZFIO_DIR|ADDRESS)"
Mandatory Mandatory
@ -150,45 +146,6 @@ let () =
Zmq.Socket.subscribe socket_in ""; Zmq.Socket.subscribe socket_in "";
(*
let action =
if verbose then
begin
match req_or_sub with
| REQ -> (fun () ->
let msg =
Zmq.Socket.recv_all socket_in
in
let t0 = Unix.gettimeofday () in
Zmq.Socket.send_all socket_out msg;
let in_size =
float_of_int ( List.fold_left (fun accu x -> accu + String.length x) 0 msg )
/. 8192. /. 1024.
in
let msg =
Zmq.Socket.recv_all socket_out
in
let t1 = Unix.gettimeofday () in
Zmq.Socket.send_all socket_in msg;
let in_time = t1 -. t0 in
in_time_sum := !in_time_sum +. in_time;
in_size_sum := !in_size_sum +. in_size;
Printf.printf " %16.2f MiB/s -- %16.2f MiB/s\n%!" (in_size /. in_time) (!in_size_sum /. !in_time_sum);
)
| SUB -> (fun () ->
Zmq.Socket.recv_all socket_in |> Zmq.Socket.send_all socket_out)
end
else
begin
match req_or_sub with
| REQ -> (fun () ->
Zmq.Socket.recv_all socket_in |> Zmq.Socket.send_all socket_out;
Zmq.Socket.recv_all socket_out |> Zmq.Socket.send_all socket_in )
| SUB -> (fun () ->
Zmq.Socket.recv_all socket_in |> Zmq.Socket.send_all socket_out)
end
in
*)
let action_in = let action_in =
match req_or_sub with match req_or_sub with

9
ocaml/qptypes_generator.ml
View File

@ -219,22 +219,19 @@ module Perturbation : sig
end = struct end = struct
type t = type t =
| EN | EN
| Barycentric | HF
| Variance
| SOP | SOP
[@@deriving sexp] [@@deriving sexp]
let to_string = function let to_string = function
| EN -> \"EN\" | EN -> \"EN\"
| Variance -> \"Variance\" | HF -> \"HF\"
| Barycentric -> \"Barycentric\"
| SOP -> \"SOP\" | SOP -> \"SOP\"
let of_string s = let of_string s =
match (String.lowercase_ascii s) with match (String.lowercase_ascii s) with
| \"sop\" -> SOP | \"sop\" -> SOP
| \"en\" -> EN | \"en\" -> EN
| \"variance\" -> Variance | \"hf\" -> HF
| \"barycentric\" -> Barycentric
| _ -> raise (Invalid_argument (\"Wrong Perturbation type : \"^s)) | _ -> raise (Invalid_argument (\"Wrong Perturbation type : \"^s))
end end
" "

8
scripts/compilation/cache_compile.py
View File

@ -1,4 +1,4 @@
#!/usr/bin/env python2 #!/usr/bin/env python3
""" """
Save the .o from a .f90 Save the .o from a .f90
and is the .o is asked a second time, retur it and is the .o is asked a second time, retur it
@ -13,9 +13,9 @@ import re
import shutil import shutil
import subprocess import subprocess
r = re.compile(ur'-c\s+(\S+\.[fF]90)\s+-o\s+(\S+\.o)') r = re.compile(r'-c\s+(\S+\.[fF]90)\s+-o\s+(\S+\.o)')
p = re.compile(ur'-I IRPF90_temp/\S*\s+') p = re.compile(r'-I IRPF90_temp/\S*\s+')
mod = re.compile(ur'module\s+(?P<mod>\S+).+end\s?module\s+(?P=mod)?', mod = re.compile(r'module\s+(?P<mod>\S+).+end\s?module\s+(?P=mod)?',
re.MULTILINE | re.IGNORECASE) re.MULTILINE | re.IGNORECASE)
tmpdir_root = os.environ.get("TMPDIR", failobj="/dev/shm") tmpdir_root = os.environ.get("TMPDIR", failobj="/dev/shm")

45
scripts/compilation/qp_create_ninja
View File

@ -1,4 +1,4 @@
#!/usr/bin/env python2 #!/usr/bin/env python3
# -*- coding: utf-8 -*- # -*- coding: utf-8 -*-
""" """
Usage: qp_create_ninja create <config_file> (--development | --production) Usage: qp_create_ninja create <config_file> (--development | --production)
@ -24,7 +24,7 @@ except ImportError:
"..", "..",
"quantum_package.rc")) "quantum_package.rc"))
print "\n".join(["", "Error:", "source %s" % f, ""]) print("\n".join(["", "Error:", "source %s" % f, ""]))
sys.exit(1) sys.exit(1)
# Compress path # Compress path
@ -124,7 +124,7 @@ def dict_module_genelogy_path(d_module_genelogy):
d_module_genelogy d_module_genelogy
""" """
d = dict() d = dict()
for module_rel, l_children_rel in d_module_genelogy.iteritems(): for module_rel, l_children_rel in d_module_genelogy.items():
module_abs = real_join(QP_SRC, module_rel) module_abs = real_join(QP_SRC, module_rel)
p = Path(module_abs, module_rel) p = Path(module_abs, module_rel)
@ -235,11 +235,11 @@ def ninja_ezfio_cfg_build(l_util):
""" """
l_string = [] l_string = []
for m in l_util.itervalues(): for m in l_util.values():
str_ = "build {1} {2}: build_ezfio_interface {0}" str_ = "build {1} {2}: build_ezfio_interface {0}"
l_string += [str_.format(*map(comp_path,(m.ez_cfg.abs, m.ez_interface.abs, l_string += [str_.format(*list(map(comp_path,(m.ez_cfg.abs, m.ez_interface.abs,
m.ez_config.abs)))] m.ez_config.abs))))]
l_string += [" sub_module = {0}".format(comp_path(m.ez_module.abs))] l_string += [" sub_module = {0}".format(comp_path(m.ez_module.abs))]
l_string += [""] l_string += [""]
@ -257,8 +257,8 @@ def ninja_ezfio_config_build(l_ezfio_config):
file_source = m.path_in_module file_source = m.path_in_module
file_create = m.path_in_ezfio file_create = m.path_in_ezfio
l_string += ["build {0}: build_ezfio_config {1}".format(*map(comp_path,(file_create, l_string += ["build {0}: build_ezfio_config {1}".format(*list(map(comp_path,(file_create,
file_source)))] file_source))))]
l_string += [""] l_string += [""]
return l_string return l_string
@ -291,7 +291,7 @@ def ninja_ezfio_build(l_ezfio_config, l_util):
""" """
l_ezfio_config = [i.path_in_ezfio for i in l_ezfio_config] l_ezfio_config = [i.path_in_ezfio for i in l_ezfio_config]
l_ezfio_from_cfg = [i.ez_config.abs for i in l_util.itervalues()] l_ezfio_from_cfg = [i.ez_config.abs for i in l_util.values()]
str_ = " ".join(map(comp_path,(l_ezfio_config + l_ezfio_from_cfg))) str_ = " ".join(map(comp_path,(l_ezfio_config + l_ezfio_from_cfg)))
l_string = ["build {0}: build_ezfio {1}".format(EZFIO_LIB, str_), ""] l_string = ["build {0}: build_ezfio {1}".format(EZFIO_LIB, str_), ""]
@ -335,7 +335,7 @@ def ninja_symlink_build(path_module, l_symlink):
""] ""]
for symlink in l_symlink: for symlink in l_symlink:
l_string += ["build {0}: build_symlink {1}".format(*map(comp_path,(symlink.destination, symlink.source))), ""] l_string += ["build {0}: build_symlink {1}".format(*list(map(comp_path,(symlink.destination, symlink.source)))), ""]
return l_string return l_string
@ -360,7 +360,7 @@ def ninja_gitignore_build(path_module, d_binaries, l_symlink):
path_gitignore = comp_path(join(path_module.abs, ".gitignore")) path_gitignore = comp_path(join(path_module.abs, ".gitignore"))
l_b = map(comp_path,[i.abs for i in d_binaries[path_module]]) l_b = list(map(comp_path,[i.abs for i in d_binaries[path_module]]))
root = "build {0}: build_gitignore {1}".format(path_gitignore, root = "build {0}: build_gitignore {1}".format(path_gitignore,
" ".join(l_b)) " ".join(l_b))
@ -420,9 +420,9 @@ def get_file_dependency(d_info_module):
""" """
d_irp = defaultdict(dict) d_irp = defaultdict(dict)
for module, l_children in d_info_module.iteritems(): for module, l_children in d_info_module.items():
for key, values in get_l_file_for_module(module).iteritems(): for key, values in get_l_file_for_module(module).items():
if key in ["l_src"]: if key in ["l_src"]:
values = [join(module.abs, o) for o in values] values = [join(module.abs, o) for o in values]
if key in ["l_obj"]: if key in ["l_obj"]:
@ -431,7 +431,7 @@ def get_file_dependency(d_info_module):
d_irp[module][key] = values d_irp[module][key] = values
for children in l_children: for children in l_children:
for key, values in get_l_file_for_module(children).iteritems(): for key, values in get_l_file_for_module(children).items():
if key in ["l_src"]: if key in ["l_src"]:
values = [join(module.abs, children.rel, o) values = [join(module.abs, children.rel, o)
for o in values] for o in values]
@ -495,10 +495,10 @@ def ninja_irpf90_make_build(path_module, l_needed_molule, d_irp):
# D e p e n d a n c y # # D e p e n d a n c y #
# ~#~#~#~#~#~#~#~#~#~ # # ~#~#~#~#~#~#~#~#~#~ #
l_depend = map(comp_path,d_irp[path_module]["l_depend"]) l_depend = list(map(comp_path,d_irp[path_module]["l_depend"]))
l_src = map(comp_path,d_irp[path_module]["l_src"]) l_src = list(map(comp_path,d_irp[path_module]["l_src"]))
l_obj = map(comp_path,d_irp[path_module]["l_obj"]) l_obj = list(map(comp_path,d_irp[path_module]["l_obj"]))
l_template = map(comp_path,d_irp[path_module]["l_template"]) l_template = list(map(comp_path,d_irp[path_module]["l_template"]))
if l_needed_molule: if l_needed_molule:
l_symlink = ["l_symlink_{0}".format(path_module.rel)] l_symlink = ["l_symlink_{0}".format(path_module.rel)]
@ -544,6 +544,7 @@ def get_binaries(path_module):
stdout=subprocess.PIPE, stdout=subprocess.PIPE,
stderr=subprocess.PIPE) stderr=subprocess.PIPE)
stdout, stderr = process.communicate() stdout, stderr = process.communicate()
stdout = stdout.decode()
except OSError: except OSError:
return [] return []
else: else:
@ -641,7 +642,7 @@ def ninja_binaries_build(path_module, l_children, d_binaries):
# ~#~#~ # # ~#~#~ #
ninja_module_path = join(comp_path(path_module.abs), "IRPF90_temp/build.ninja") ninja_module_path = join(comp_path(path_module.abs), "IRPF90_temp/build.ninja")
l_abs_bin = map(comp_path,[binary.abs for binary in d_binaries[path_module]]) l_abs_bin = list(map(comp_path,[binary.abs for binary in d_binaries[path_module]]))
# ~#~#~#~#~#~ # # ~#~#~#~#~#~ #
# s t r i n g # # s t r i n g #
@ -658,7 +659,7 @@ def ninja_binaries_build(path_module, l_children, d_binaries):
def ninja_module_build(path_module, d_binaries): def ninja_module_build(path_module, d_binaries):
l_abs_bin = map(comp_path,[binary.abs for binary in d_binaries[path_module]]) l_abs_bin = list(map(comp_path,[binary.abs for binary in d_binaries[path_module]]))
path_readme = os.path.join(comp_path(path_module.abs), "README.rst") path_readme = os.path.join(comp_path(path_module.abs), "README.rst")
@ -829,14 +830,14 @@ if __name__ == "__main__":
dict_root = module_instance.dict_root dict_root = module_instance.dict_root
dict_root_path = dict_module_genelogy_path(dict_root) dict_root_path = dict_module_genelogy_path(dict_root)
l_all_module = d_genealogy_path.keys() l_all_module = list(d_genealogy_path.keys())
# ~#~#~#~#~#~#~#~#~#~#~#~#~ # # ~#~#~#~#~#~#~#~#~#~#~#~#~ #
# M o d u l e _ t o _ i r p # # M o d u l e _ t o _ i r p #
# ~#~#~#~#~#~#~#~#~#~#~#~#~ # # ~#~#~#~#~#~#~#~#~#~#~#~#~ #
d_binaries = get_dict_binaries(l_all_module, mode="development") d_binaries = get_dict_binaries(l_all_module, mode="development")
l_module = d_binaries.keys() l_module = list(d_binaries.keys())
# ~#~#~#~#~#~#~#~#~#~#~#~ # # ~#~#~#~#~#~#~#~#~#~#~#~ #

14
scripts/compilation/read_compilation_cfg.py
View File

@ -1,8 +1,8 @@
#!/usr/bin/env python2 #!/usr/bin/env python3
# -*- coding: utf-8 -*- # -*- coding: utf-8 -*-
import os, sys import os, sys
import ConfigParser import configparser
def get_l_option_section(config): def get_l_option_section(config):
@ -17,10 +17,10 @@ def get_compilation_option(pwd_cfg, flag_name):
Return the flag compilation of a compile.cfg located in pwd_cfg Return the flag compilation of a compile.cfg located in pwd_cfg
""" """
if not os.path.isfile(pwd_cfg): if not os.path.isfile(pwd_cfg):
print "Configuration file %s not found"%(pwd_cfg) print("Configuration file %s not found"%(pwd_cfg))
sys.exit(1) sys.exit(1)
config = ConfigParser.ConfigParser() config = configparser.ConfigParser(inline_comment_prefixes=(';','#'))
config.read(pwd_cfg) config.read(pwd_cfg)
if flag_name == "FC" and config.getboolean("OPTION","CACHE"): if flag_name == "FC" and config.getboolean("OPTION","CACHE"):
@ -33,7 +33,7 @@ def get_compilation_option(pwd_cfg, flag_name):
for section in ["COMMON"] + l_option_section: for section in ["COMMON"] + l_option_section:
try: try:
l.extend(config.get(section, flag_name).split()) l.extend(config.get(section, flag_name).split())
except ConfigParser.NoOptionError: except configparser.NoOptionError:
pass pass
return " ".join(l) return " ".join(l)
@ -43,5 +43,5 @@ if __name__ == '__main__':
qpackage_root = os.environ['QP_ROOT'] qpackage_root = os.environ['QP_ROOT']
pwd_cfg = os.path.join(qpackage_root, "config/ifort_gpi2.cfg") pwd_cfg = os.path.join(qpackage_root, "config/ifort_gpi2.cfg")
print get_compilation_option(pwd_cfg, "FC") print(get_compilation_option(pwd_cfg, "FC"))
print get_compilation_option(pwd_cfg, "FCFLAGS") print(get_compilation_option(pwd_cfg, "FCFLAGS"))

54
scripts/ezfio_interface/ei_handler.py
View File

@ -1,4 +1,4 @@
#!/usr/bin/env python2 #!/usr/bin/env python3
# -*- coding: utf-8 -*- # -*- coding: utf-8 -*-
""" """
Welcome to the ei_handler. Welcome to the ei_handler.
@ -72,7 +72,7 @@ import sys
import os import os
import os.path import os.path
import ConfigParser import configparser
from collections import defaultdict from collections import defaultdict
from collections import namedtuple from collections import namedtuple
@ -220,8 +220,8 @@ def get_dict_config_file(module_obj):
# L o a d _ C o n f i g # # L o a d _ C o n f i g #
# ~#~#~#~#~#~#~#~#~#~#~ # # ~#~#~#~#~#~#~#~#~#~#~ #
config_file = ConfigParser.ConfigParser() config_file = configparser.ConfigParser()
config_file.readfp(open(module_obj.path)) config_file.read_file(open(module_obj.path))
# ~#~#~#~#~#~#~#~#~ # # ~#~#~#~#~#~#~#~#~ #
# F i l l _ d i c t # # F i l l _ d i c t #
@ -229,7 +229,7 @@ def get_dict_config_file(module_obj):
def error(o, p, c): def error(o, p, c):
"o option ; p provider_name ;c module_obj.path" "o option ; p provider_name ;c module_obj.path"
print "You need a {0} for {1} in {2}".format(o, p, c) print("You need a {0} for {1} in {2}".format(o, p, c))
for section in config_file.sections(): for section in config_file.sections():
# pvd = provider # pvd = provider
@ -245,13 +245,13 @@ def get_dict_config_file(module_obj):
# Check if type is avalaible # Check if type is avalaible
try: try:
type_ = config_file.get(section, "type").strip() type_ = config_file.get(section, "type").strip()
except ConfigParser.NoOptionError: except configparser.NoOptionError:
error("type", pvd, module_obj.path) error("type", pvd, module_obj.path)
sys.exit(1) sys.exit(1)
if type_ not in type_dict: if type_ not in type_dict:
print "{0} not avalaible. Choose in:".format(type_).strip() print("{0} not avalaible. Choose in:".format(type_).strip())
print ", ".join(sorted([i for i in type_dict])) print(", ".join(sorted([i for i in type_dict])))
sys.exit(1) sys.exit(1)
else: else:
d[pvd]["type"] = type_dict[type_] d[pvd]["type"] = type_dict[type_]
@ -259,18 +259,18 @@ def get_dict_config_file(module_obj):
# Fill the dict with REQUIRED information # Fill the dict with REQUIRED information
try: try:
d[pvd]["doc"] = config_file.get(section, "doc") d[pvd]["doc"] = config_file.get(section, "doc")
except ConfigParser.NoOptionError: except configparser.NoOptionError:
error("doc", pvd, module_obj.path) error("doc", pvd, module_obj.path)
sys.exit(1) sys.exit(1)
try: try:
interface = [i.lower().strip() for i in config_file.get(section, "interface").split(",")] interface = [i.lower().strip() for i in config_file.get(section, "interface").split(",")]
except ConfigParser.NoOptionError: except configparser.NoOptionError:
error("doc", pvd, module_obj.path) error("doc", pvd, module_obj.path)
sys.exit(1) sys.exit(1)
else: else:
if not any(i in ["ezfio", "provider", "ocaml"] for i in interface): if not any(i in ["ezfio", "provider", "ocaml"] for i in interface):
print "Bad keyword for interface for {0}".format(pvd) print("Bad keyword for interface for {0}".format(pvd))
sys.exit(1) sys.exit(1)
else: else:
d[pvd]["interface"] = interface d[pvd]["interface"] = interface
@ -279,7 +279,7 @@ def get_dict_config_file(module_obj):
for option in l_info_optional: for option in l_info_optional:
try: try:
d[pvd][option] = config_file.get(section, option).lower() d[pvd][option] = config_file.get(section, option).lower()
except ConfigParser.NoOptionError: except configparser.NoOptionError:
if option in d_default: if option in d_default:
d[pvd][option] = d_default[option] d[pvd][option] = d_default[option]
@ -287,7 +287,7 @@ def get_dict_config_file(module_obj):
try: try:
default_raw = config_file.get(section, "default") default_raw = config_file.get(section, "default")
except ConfigParser.NoOptionError: except configparser.NoOptionError:
if "ocaml" in d[pvd]["interface"]: if "ocaml" in d[pvd]["interface"]:
error("default", pvd, module_obj.path) error("default", pvd, module_obj.path)
sys.exit(1) sys.exit(1)
@ -322,7 +322,7 @@ def create_ezfio_provider(dict_ezfio_cfg):
dict_code_provider = dict() dict_code_provider = dict()
ez_p = EZFIO_Provider() ez_p = EZFIO_Provider()
for provider_name, dict_info in dict_ezfio_cfg.iteritems(): for provider_name, dict_info in dict_ezfio_cfg.items():
if "provider" in dict_info["interface"]: if "provider" in dict_info["interface"]:
ez_p.set_type(dict_info['type'].fortran) ez_p.set_type(dict_info['type'].fortran)
ez_p.set_name(provider_name) ez_p.set_name(provider_name)
@ -364,7 +364,7 @@ def save_ezfio_provider(path_head, dict_code_provider):
"! from file {0}/EZFIO.cfg".format(path_head), "! from file {0}/EZFIO.cfg".format(path_head),
"\n"] "\n"]
l_output += [code for code in dict_code_provider.values()] l_output += [code for code in list(dict_code_provider.values())]
output = "\n".join(l_output) output = "\n".join(l_output)
@ -381,22 +381,22 @@ def create_ezfio_stuff(dict_ezfio_cfg, config_or_default="config"):
def size_format_to_ezfio(size_raw): def size_format_to_ezfio(size_raw):
""" """
If size_raw == "=" is a formula -> do nothing; return If size_raw == "=" is a formula -> do nothing; return
Else convert the born of a multidimential array Else convert the range of a multidimential array
(12,begin:end) into (12,begin+end+1) for example (12,begin:end) into (12,begin+end+1) for example
If the value are between parenthses -> do nothing; return If the values are between parenthses -> do nothing; return
""" """
size_raw = str(size_raw) size_raw = str(size_raw)
if size_raw.startswith('='): if size_raw.startswith('='):
size_convert = size_raw.replace('.', '_') size_convert = size_raw.replace('.', '_')
else: else:
size_raw = provider_info["size"].translate(None, "()") size_raw = provider_info["size"].translate(str.maketrans("","","()"))
size_raw = size_raw.replace('.', '_') size_raw = size_raw.replace('.', '_')
a_size_raw = [] a_size_raw = []
for dim in size_raw.split(","): for dim in size_raw.split(","):
try: try:
(begin, end) = map(str.strip, dim.split(":")) (begin, end) = list(map(str.strip, dim.split(":")))
except ValueError: except ValueError:
a_size_raw.append(dim) a_size_raw.append(dim)
else: else:
@ -423,7 +423,7 @@ def create_ezfio_stuff(dict_ezfio_cfg, config_or_default="config"):
lenmax_name = max([len(i) for i in dict_ezfio_cfg]) lenmax_name = max([len(i) for i in dict_ezfio_cfg])
lenmax_type = max([len(i["type"].fortran) lenmax_type = max([len(i["type"].fortran)
for i in dict_ezfio_cfg.values()]) for i in list(dict_ezfio_cfg.values())])
str_name_format = create_format_string(lenmax_name + 2) str_name_format = create_format_string(lenmax_name + 2)
str_type_format = create_format_string(lenmax_type + 2) str_type_format = create_format_string(lenmax_type + 2)
@ -433,15 +433,15 @@ def create_ezfio_stuff(dict_ezfio_cfg, config_or_default="config"):
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~# # # ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~# #
# Checking is many ezfio_dir provided # Checking is many ezfio_dir provided
l_ezfio_dir = [d['ezfio_dir'] for d in dict_ezfio_cfg.values()] l_ezfio_dir = [d['ezfio_dir'] for d in list(dict_ezfio_cfg.values())]
if not l_ezfio_dir.count(l_ezfio_dir[0]) == len(l_ezfio_dir): if not l_ezfio_dir.count(l_ezfio_dir[0]) == len(l_ezfio_dir):
print >> sys.stderr, "You have many ezfio_dir. Not supported yet" print("You have many ezfio_dir. Not supported yet", file=sys.stderr)
raise TypeError raise TypeError
else: else:
result = [l_ezfio_dir[0]] result = [l_ezfio_dir[0]]
for provider_name, provider_info in sorted(dict_ezfio_cfg.iteritems()): for provider_name, provider_info in sorted(dict_ezfio_cfg.items()):
# Get the value from dict # Get the value from dict
name_raw = provider_info["ezfio_name"].lower() name_raw = provider_info["ezfio_name"].lower()
@ -532,7 +532,7 @@ def create_ocaml_input(dict_ezfio_cfg, module_lower):
l_type = [] l_type = []
l_doc = [] l_doc = []
for k, v in dict_ezfio_cfg.iteritems(): for k, v in dict_ezfio_cfg.items():
if "ocaml" in v['interface']: if "ocaml" in v['interface']:
l_ezfio_name.append(v['ezfio_name']) l_ezfio_name.append(v['ezfio_name'])
l_type.append(v["type"]) l_type.append(v["type"])
@ -580,7 +580,7 @@ def create_ocaml_input(dict_ezfio_cfg, module_lower):
'(* =~=~=~==~=~~=~=~=~=~=~=~=~ *)', '(* =~=~=~==~=~~=~=~=~=~=~=~=~ *)',
""] ""]
for provider_name, d_val in sorted(dict_ezfio_cfg.iteritems()): for provider_name, d_val in sorted(dict_ezfio_cfg.items()):
if 'default' not in d_val: if 'default' not in d_val:
continue continue
@ -655,7 +655,7 @@ def get_l_module_with_auto_generate_ocaml_lower():
l_module_lower = [] l_module_lower = []
import re import re
p = re.compile(ur'interface:.*ocaml') p = re.compile(r'interface:.*ocaml')
for f in l_folder: for f in l_folder:
path = "{0}/{1}/EZFIO.cfg".format(QP_SRC, f) path = "{0}/{1}/EZFIO.cfg".format(QP_SRC, f)
@ -782,7 +782,7 @@ if __name__ == "__main__":
# #
if arguments["list_supported_types"]: if arguments["list_supported_types"]:
for i in sorted(get_type_dict()): for i in sorted(get_type_dict()):
print i print(i)
sys.exit(0) sys.exit(0)
if arguments["ocaml_global"]: if arguments["ocaml_global"]:

10
scripts/ezfio_interface/ezfio_generate_ocaml.py
View File

@ -1,4 +1,4 @@
#!/usr/bin/env python2 #!/usr/bin/env python3
""" """
This program generates all the This program generates all the
OCaml templates needed by qp_edit OCaml templates needed by qp_edit
@ -17,12 +17,12 @@ class EZFIO_ocaml(object):
def __init__(self, **kwargs): def __init__(self, **kwargs):
for k, v in kwargs.iteritems(): for k, v in kwargs.items():
try: try:
exec "self.{0} = {1}".format(k, v) exec("self.{0} = {1}".format(k, v))
except NameError: except NameError:
exec "self.{0} = '{1}'".format(k, v) exec("self.{0} = '{1}'".format(k, v))
@property @property
def Ocaml_type(self): def Ocaml_type(self):
@ -39,7 +39,7 @@ class EZFIO_ocaml(object):
def check_if_init(self, l_arg, name): def check_if_init(self, l_arg, name):
for i in l_arg: for i in l_arg:
try: try:
exec "self.{0}".format(i) exec("self.{0}".format(i))
except AttributeError: except AttributeError:
msg = "You need to provide a '{0}' for creating {1}" msg = "You need to provide a '{0}' for creating {1}"
raise KeyError(msg.format(i, name)) raise KeyError(msg.format(i, name))

8
scripts/ezfio_interface/ezfio_generate_provider.py
View File

@ -1,4 +1,4 @@
#!/usr/bin/env python2 #!/usr/bin/env python3
__author__ = "Applencourt PEP8" __author__ = "Applencourt PEP8"
__date__ = "jeudi 26 mars 2015, 12:49:35 (UTC+0100)" __date__ = "jeudi 26 mars 2015, 12:49:35 (UTC+0100)"
@ -88,7 +88,7 @@ END_PROVIDER
def __init__(self): def __init__(self):
self.values = "type doc name ezfio_dir ezfio_name write output".split() self.values = "type doc name ezfio_dir ezfio_name write output".split()
for v in self.values: for v in self.values:
exec "self.{0} = None".format(v) exec("self.{0} = None".format(v))
def __repr__(self): def __repr__(self):
self.set_write() self.set_write()
@ -96,7 +96,7 @@ END_PROVIDER
for v in self.values: for v in self.values:
if not v: if not v:
msg = "Error : %s is not set in EZFIO.cfg" % (v) msg = "Error : %s is not set in EZFIO.cfg" % (v)
print >>sys.stderr, msg print(msg, file=sys.stderr)
sys.exit(1) sys.exit(1)
if "size" not in self.__dict__: if "size" not in self.__dict__:
self.__dict__["size"] = "" self.__dict__["size"] = ""
@ -167,7 +167,7 @@ def test_module():
T.set_ezfio_dir("Hartree_Fock") T.set_ezfio_dir("Hartree_Fock")
T.set_ezfio_name("thresh_SCF") T.set_ezfio_name("thresh_SCF")
T.set_output("output_Hartree_Fock") T.set_output("output_Hartree_Fock")
print T print(T)
if __name__ == '__main__': if __name__ == '__main__':
test_module() test_module()

10
scripts/generate_h_apply.py
View File

@ -1,4 +1,4 @@
#!/usr/bin/env python2 #!/usr/bin/env python3
import os import os
@ -11,6 +11,7 @@ declarations
decls_main decls_main
deinit_thread deinit_thread
init_main init_main
filter_integrals
filter2p filter2p
filter2h2p_double filter2h2p_double
filter2h2p_single filter2h2p_single
@ -104,6 +105,11 @@ class H_apply(object):
s["do_mono_excitations"] = d[do_mono_exc] s["do_mono_excitations"] = d[do_mono_exc]
s["do_double_excitations"] = d[do_double_exc] s["do_double_excitations"] = d[do_double_exc]
s["keys_work"] += "call fill_H_apply_buffer_no_selection(key_idx,keys_out,N_int,iproc)" s["keys_work"] += "call fill_H_apply_buffer_no_selection(key_idx,keys_out,N_int,iproc)"
s["filter_integrals"] = "array_pairs = .True."
if SingleRef:
s["filter_integrals"] = """
call get_mo_bielec_integrals_existing_ik(i_a,j_a,mo_num,array_pairs,mo_integrals_map)
"""
s["generate_psi_guess"] = """ s["generate_psi_guess"] = """
! Sort H_jj to find the N_states lowest states ! Sort H_jj to find the N_states lowest states
@ -149,7 +155,7 @@ class H_apply(object):
def __repr__(self): def __repr__(self):
buffer = self.template buffer = self.template
for key,value in self.data.items(): for key,value in list(self.data.items()):
buffer = buffer.replace('$'+key, value) buffer = buffer.replace('$'+key, value)
return buffer return buffer

6
scripts/hello.py
View File

@ -1,4 +1,4 @@
#!/usr/bin/env python2 #!/usr/bin/env python3
import random import random
@ -131,8 +131,8 @@ _ __ `/___ __ \__ ___/__ __ \
""" ] """ ]
print random.choice(hello) print(random.choice(hello))
print "\n -- Quantum Package Shell --\n" print("\n -- Quantum Package Shell --\n")

27
scripts/module/module_handler.py
View File

@ -1,4 +1,4 @@
#!/usr/bin/env python2 #!/usr/bin/env python3
# -*- coding: utf-8 -*- # -*- coding: utf-8 -*-
""" """
Module utilitary Module utilitary
@ -25,7 +25,7 @@ try:
from docopt import docopt from docopt import docopt
from qp_path import QP_SRC, QP_ROOT, QP_PLUGINS, QP_EZFIO from qp_path import QP_SRC, QP_ROOT, QP_PLUGINS, QP_EZFIO
except ImportError: except ImportError:
print "source .quantum_package.rc" print("source .quantum_package.rc")
raise raise
@ -50,6 +50,7 @@ def get_binaries(path_module):
stdout=subprocess.PIPE, stdout=subprocess.PIPE,
stderr=subprocess.PIPE) stderr=subprocess.PIPE)
stdout, stderr = process.communicate() stdout, stderr = process.communicate()
stdout = stdout.decode()
except OSError: except OSError:
return [] return []
else: else:
@ -106,9 +107,9 @@ def get_l_module_descendant(d_child, l_module):
try: try:
l.extend(get_l_module_descendant(d_child, d_child[module])) l.extend(get_l_module_descendant(d_child, d_child[module]))
except KeyError: except KeyError:
print >> sys.stderr, "Error: " print("Error: ", file=sys.stderr)
print >> sys.stderr, "`{0}` is not a submodule".format(module) print("`{0}` is not a submodule".format(module), file=sys.stderr)
print >> sys.stderr, "Check the typo (spelling, case, '/', etc.) " print("Check the typo (spelling, case, '/', etc.) ", file=sys.stderr)
sys.exit(1) sys.exit(1)
return list(set(l)) return list(set(l))
@ -120,7 +121,7 @@ class ModuleHandler():
@property @property
def l_module(self): def l_module(self):
return self.dict_child.keys() return list(self.dict_child.keys())
@property @property
def dict_parent(self): def dict_parent(self):
@ -132,7 +133,7 @@ class ModuleHandler():
d = {} d = {}
for module_name in d_child: for module_name in d_child:
d[module_name] = [i for i in d_child.keys() d[module_name] = [i for i in list(d_child.keys())
if module_name in d_child[i]] if module_name in d_child[i]]
return d return d
@ -151,8 +152,8 @@ class ModuleHandler():
d[module_name] = get_l_module_descendant(d_child, d[module_name] = get_l_module_descendant(d_child,
d_child[module_name]) d_child[module_name])
except KeyError: except KeyError:
print "Check NEED for {0}".format( print("Check NEED for {0}".format(
module_name) module_name))
sys.exit(1) sys.exit(1)
return d return d
@ -185,7 +186,7 @@ class ModuleHandler():
for e in d_desc[module]: for e in d_desc[module]:
d[e] = 1 d[e] = 1
return d.keys() return list(d.keys())
def l_reduce_tree(self, l_module): def l_reduce_tree(self, l_module):
"""For a list of module in input return only the root""" """For a list of module in input return only the root"""
@ -218,8 +219,8 @@ if __name__ == '__main__':
for module in l_module: for module in l_module:
if not is_module(module): if not is_module(module):
print "{0} is not a valid module. Abort".format(module) print("{0} is not a valid module. Abort".format(module))
print "No NEED in it" print("No NEED in it")
sys.exit(1) sys.exit(1)
m = ModuleHandler() m = ModuleHandler()
@ -227,7 +228,7 @@ if __name__ == '__main__':
if arguments['print_descendant']: if arguments['print_descendant']:
for module in l_module: for module in l_module:
print " ".join(sorted(m.l_descendant_unique([module]))) print(" ".join(sorted(m.l_descendant_unique([module]))))
if arguments["clean"]: if arguments["clean"]:

8
scripts/perturbation.py
View File

@ -1,4 +1,4 @@
#!/usr/bin/env python2 #!/usr/bin/env python3
import os import os
from qp_path import QP_SRC from qp_path import QP_SRC
@ -7,7 +7,7 @@ Pert_dir = os.path.join(QP_SRC,"perturbation")
perturbations = [] perturbations = []
for filename in filter(lambda x: x.endswith(".irp.f"), os.listdir(Pert_dir)): for filename in [x for x in os.listdir(Pert_dir) if x.endswith(".irp.f")]:
filename = os.path.join(Pert_dir,filename) filename = os.path.join(Pert_dir,filename)
file = open(filename,'r') file = open(filename,'r')
@ -22,6 +22,6 @@ for filename in filter(lambda x: x.endswith(".irp.f"), os.listdir(Pert_dir)):
if __name__ == '__main__': if __name__ == '__main__':
print 'Perturbations:' print('Perturbations:')
for k in perturbations: for k in perturbations:
print '* ', k print('* ', k)

26
scripts/utility/get_groups
View File

@ -1,7 +1,7 @@
#!/usr/bin/env python2 #!/usr/bin/env python3
# -*- coding: utf-8 -*- # -*- coding: utf-8 -*-
import urllib import urllib.request, urllib.parse, urllib.error
import sys import sys
from bs4 import BeautifulSoup from bs4 import BeautifulSoup
@ -35,11 +35,11 @@ def clean_up(text):
return False return False
else: else:
return y[0] in irred return y[0] in irred
data = filter(f,data)[:len(irred)] data = list(filter(f,data))[:len(irred)]
for line in data: for line in data:
s = line.replace('*','').split() s = line.replace('*','').split()
l = irred[s[0]] l = irred[s[0]]
data[l] = map(float,s[1:len(irred)+1]) data[l] = list(map(float,s[1:len(irred)+1]))
d = {} d = {}
e = {} e = {}
@ -48,23 +48,23 @@ def clean_up(text):
for k in sop: for k in sop:
e[sop[k]] = k e[sop[k]] = k
n = len(irred) n = len(irred)
print "Group\t", group, "\nn\t", n print("Group\t", group, "\nn\t", n)
print "\n \tIrred \tOperation" print("\n \tIrred \tOperation")
for i in range(n): for i in range(n):
print "%4d \t %s \t %s"%(i+1, d[i].ljust(10), e[i].ljust(10)) print("%4d \t %s \t %s"%(i+1, d[i].ljust(10), e[i].ljust(10)))
print "\nTable\n ", print("\nTable\n ", end=' ')
for j in range(n): for j in range(n):
print "%8s "%(str(j+1).center(8)), print("%8s "%(str(j+1).center(8)), end=' ')
for i in range(n): for i in range(n):
print "\n%4d "%(i+1), print("\n%4d "%(i+1), end=' ')
for j in range(n): for j in range(n):
print "%8.5f "%(data[i][j]), print("%8.5f "%(data[i][j]), end=' ')
print "\n" print("\n")
def main(): def main():
for group in sys.argv[1:]: for group in sys.argv[1:]:
f = urllib.urlopen(address%(group)) f = urllib.request.urlopen(address%(group))
html = f.read().split('\n',1)[1] html = f.read().split('\n',1)[1]
text = clean_up(html) text = clean_up(html)

2
scripts/utility/qp_bitmasks.py
View File

@ -1,4 +1,4 @@
#!/usr/bin/env python2 #!/usr/bin/env python3
BIT_KIND_SIZE=64 BIT_KIND_SIZE=64

5
scripts/utility/qp_path.py
View File

@ -1,13 +1,14 @@
#!/usr/bin/env python2 #!/usr/bin/env python3
# -*- coding: utf-8 -*- # -*- coding: utf-8 -*-
import os import os
import sys import sys
try: try:
QP_ROOT = os.environ['QP_ROOT'] QP_ROOT = os.environ['QP_ROOT']
except: except:
print "source quantum_package.rc" print("source quantum_package.rc")
sys.exit(1) sys.exit(1)
else: else:
QP_EZFIO = os.environ["QP_EZFIO"] QP_EZFIO = os.environ["QP_EZFIO"]

1
src/cipsi/cipsi.irp.f
View File

@ -108,6 +108,7 @@ subroutine run_cipsi
n_det_before = N_det n_det_before = N_det
to_select = int(sqrt(dble(N_states))*dble(N_det)*selection_factor) to_select = int(sqrt(dble(N_states))*dble(N_det)*selection_factor)
to_select = max(N_states_diag, to_select) to_select = max(N_states_diag, to_select)
to_select = max(to_select,1)
call ZMQ_selection(to_select, pt2, variance, norm) call ZMQ_selection(to_select, pt2, variance, norm)
PROVIDE psi_coef PROVIDE psi_coef

2
src/cipsi/energy.irp.f
View File

@ -22,8 +22,6 @@ BEGIN_PROVIDER [ double precision, pt2_E0_denominator, (N_states) ]
enddo enddo
else if (h0_type == "Barycentric") then else if (h0_type == "Barycentric") then
pt2_E0_denominator(1:N_states) = barycentric_electronic_energy(1:N_states) pt2_E0_denominator(1:N_states) = barycentric_electronic_energy(1:N_states)
else if (h0_type == "Variance") then
pt2_E0_denominator(1:N_states) = psi_energy(1:N_states) !1.d0-nuclear_repulsion
else if (h0_type == "SOP") then else if (h0_type == "SOP") then
pt2_E0_denominator(1:N_states) = psi_energy(1:N_states) pt2_E0_denominator(1:N_states) = psi_energy(1:N_states)
else else

2
src/cis/20.cis.bats
View File

@ -64,7 +64,7 @@ function run() {
@test "SO" { # 1.9667s 2.91234s @test "SO" { # 1.9667s 2.91234s
[[ -n $TRAVIS ]] && skip [[ -n $TRAVIS ]] && skip
run so.ezfio -25.7502102903664 -25.586265109319484 -25.582920204099572 run so.ezfio -25.750224071640112 -25.586278842164113 -25.582933929660470
} }
@test "OH" { # 2.201s 2.65573s @test "OH" { # 2.201s 2.65573s

6
src/cis/h_apply.irp.f
View File

@ -1,14 +1,14 @@
! Generates subroutine H_apply_cis ! Generates subroutine H_apply_cis
! -------------------------------- ! --------------------------------
BEGIN_SHELL [ /usr/bin/env python2 ] BEGIN_SHELL [ /usr/bin/env python3 ]
from generate_h_apply import H_apply from generate_h_apply import H_apply
H = H_apply("cis",do_double_exc=False) H = H_apply("cis",do_double_exc=False)
print H print(H)
H = H_apply("cis_sym",do_double_exc=False) H = H_apply("cis_sym",do_double_exc=False)
H.filter_only_connected_to_hf() H.filter_only_connected_to_hf()
print H print(H)
END_SHELL END_SHELL

6
src/cisd/h_apply.irp.f
View File

@ -1,13 +1,13 @@
! Generates subroutine H_apply_cisd ! Generates subroutine H_apply_cisd
! ---------------------------------- ! ----------------------------------
BEGIN_SHELL [ /usr/bin/env python2 ] BEGIN_SHELL [ /usr/bin/env python3 ]
from generate_h_apply import H_apply from generate_h_apply import H_apply
H = H_apply("cisd",do_double_exc=True) H = H_apply("cisd",do_double_exc=True)
print H print(H)
H = H_apply("cisd_sym",do_double_exc=True) H = H_apply("cisd_sym",do_double_exc=True)
H.filter_only_connected_to_hf() H.filter_only_connected_to_hf()
print H print(H)
END_SHELL END_SHELL

4
src/davidson/diagonalize_ci.irp.f
View File

@ -163,7 +163,7 @@ END_PROVIDER
print*,'!!!!!!!! WARNING !!!!!!!!!' print*,'!!!!!!!! WARNING !!!!!!!!!'
print*,' Within the ',N_det,'determinants selected' print*,' Within the ',N_det,'determinants selected'
print*,' and the ',N_states_diag,'states requested' print*,' and the ',N_states_diag,'states requested'
print*,' We did not find any state with S^2 values close to ',expected_s2 print*,' We did not find only states with S^2 values close to ',expected_s2
print*,' We will then set the first N_states eigenvectors of the H matrix' print*,' We will then set the first N_states eigenvectors of the H matrix'
print*,' as the CI_eigenvectors' print*,' as the CI_eigenvectors'
print*,' You should consider more states and maybe ask for s2_eig to be .True. or just enlarge the CI space' print*,' You should consider more states and maybe ask for s2_eig to be .True. or just enlarge the CI space'
@ -182,7 +182,7 @@ END_PROVIDER
call lapack_diag(eigenvalues,eigenvectors, & call lapack_diag(eigenvalues,eigenvectors, &
H_matrix_all_dets,size(H_matrix_all_dets,1),N_det) H_matrix_all_dets,size(H_matrix_all_dets,1),N_det)
CI_electronic_energy(:) = 0.d0 CI_electronic_energy(:) = 0.d0
call u_0_S2_u_0(CI_s2,eigenvectors,N_det,psi_det,N_int,& call u_0_S2_u_0(CI_s2,eigenvectors,N_det,psi_det,N_int, &
min(N_det,N_states_diag),size(eigenvectors,1)) min(N_det,N_states_diag),size(eigenvectors,1))
! Select the "N_states_diag" states of lowest energy ! Select the "N_states_diag" states of lowest energy
do j=1,min(N_det,N_states_diag) do j=1,min(N_det,N_states_diag)

6
src/density_for_dft/EZFIO.cfg
View File

@ -12,14 +12,12 @@ default: 0.5
[no_core_density] [no_core_density]
type: character*(32) type: character*(32)
doc: Type of density doc: Type of density. If [no_core_dm] then all elements of the density matrix involving at least one orbital set as core are set to zero
doc: if [no_core_dm] then all elements of the density matrix involving at least one orbital set as core are set to zero
interface: ezfio, provider, ocaml interface: ezfio, provider, ocaml
default: full_density default: full_density
[normalize_dm] [normalize_dm]
type: logical type: logical
doc: Type of density doc: Type of density. If .True., then you normalize the no_core_dm to elec_alpha_num - n_core_orb and elec_beta_num - n_core_orb
doc: if .True., then you normalize the no_core_dm to elec_alpha_num - n_core_orb and elec_beta_num - n_core_orb
interface: ezfio, provider, ocaml interface: ezfio, provider, ocaml
default: True default: True

1
src/determinants/EZFIO.cfg
View File

@ -76,7 +76,6 @@ type: integer
interface: ezfio interface: ezfio
doc: Number of determinants to print in qp_edit doc: Number of determinants to print in qp_edit
type: integer type: integer
interface: ezfio
[psi_coef] [psi_coef]
interface: ezfio interface: ezfio

24
src/dft_one_e/e_xc_general.irp.f
View File

@ -4,7 +4,7 @@ BEGIN_PROVIDER [double precision, energy_x, (N_states)]
! correlation energies general providers. ! correlation energies general providers.
END_DOC END_DOC
BEGIN_SHELL [ /usr/bin/env python2 ] BEGIN_SHELL [ /usr/bin/env python3 ]
import os import os
import glob import glob
from qp_path import QP_SRC from qp_path import QP_SRC
@ -13,16 +13,16 @@ os.chdir(funcdir)
functionals = map(lambda x : x.replace(".irp.f",""), glob.glob("*.irp.f")) functionals = map(lambda x : x.replace(".irp.f",""), glob.glob("*.irp.f"))
prefix = "" prefix = ""
for f in functionals: for f in functionals:
print """ print("""
%sif (trim(exchange_functional) == '%s') then %sif (trim(exchange_functional) == '%s') then
energy_x = (1.d0 - HF_exchange ) * energy_x_%s"""%(prefix, f, f) energy_x = (1.d0 - HF_exchange ) * energy_x_%s"""%(prefix, f, f))
prefix = "else " prefix = "else "
print """ print("""
else else
print *, 'exchange functional required does not exist ...' print *, 'exchange functional required does not exist ...'
print *, 'exchange_functional ',exchange_functional print *, 'exchange_functional ',exchange_functional
stop""" stop""")
print "endif" print("endif")
END_SHELL END_SHELL
@ -38,7 +38,7 @@ print "endif"
! correlation and exchange energies general providers. ! correlation and exchange energies general providers.
END_DOC END_DOC
BEGIN_SHELL [ /usr/bin/env python2 ] BEGIN_SHELL [ /usr/bin/env python3 ]
import os import os
import glob import glob
from qp_path import QP_SRC from qp_path import QP_SRC
@ -47,17 +47,17 @@ os.chdir(funcdir)
functionals = map(lambda x : x.replace(".irp.f",""), glob.glob("*.irp.f")) functionals = map(lambda x : x.replace(".irp.f",""), glob.glob("*.irp.f"))
prefix = "" prefix = ""
for f in functionals: for f in functionals:
print """ print("""
%sif (trim(correlation_functional) == '%s') then %sif (trim(correlation_functional) == '%s') then
energy_c = energy_c_%s"""%(prefix, f, f) energy_c = energy_c_%s"""%(prefix, f, f) )
prefix = "else " prefix = "else "
print """ print("""
else else
print*, 'Correlation functional required does not exist ...' print*, 'Correlation functional required does not exist ...'
print*,'correlation_functional ',correlation_functional print*,'correlation_functional ',correlation_functional
stop""" stop""")
print "endif" print("endif")
END_SHELL END_SHELL

36
src/dft_one_e/pot_general.irp.f
View File

@ -5,7 +5,7 @@
! general providers for the alpha/beta exchange potentials on the AO basis ! general providers for the alpha/beta exchange potentials on the AO basis
END_DOC END_DOC
BEGIN_SHELL [ /usr/bin/env python2 ] BEGIN_SHELL [ /usr/bin/env python3 ]
import os import os
import glob import glob
from qp_path import QP_SRC from qp_path import QP_SRC
@ -15,17 +15,17 @@ functionals = map(lambda x : x.replace(".irp.f",""), glob.glob("*.irp.f"))
prefix = "" prefix = ""
for f in functionals: for f in functionals:
print """ print("""
%sif (trim(exchange_functional) == '%s') then %sif (trim(exchange_functional) == '%s') then
potential_x_alpha_ao = ( 1.d0 - HF_exchange ) * potential_x_alpha_ao_%s potential_x_alpha_ao = ( 1.d0 - HF_exchange ) * potential_x_alpha_ao_%s
potential_x_beta_ao = ( 1.d0 - HF_exchange ) * potential_x_beta_ao_%s"""%(prefix, f, f, f) potential_x_beta_ao = ( 1.d0 - HF_exchange ) * potential_x_beta_ao_%s"""%(prefix, f, f, f) )
prefix = "else " prefix = "else "
print """ print("""
else else
print*, 'exchange functional required does not exist ...' print*, 'exchange functional required does not exist ...'
print*,'exchange_functional ',exchange_functional print*,'exchange_functional ',exchange_functional
stop""" stop""")
print "endif" print("endif")
END_SHELL END_SHELL
@ -41,7 +41,7 @@ print "endif"
! general providers for the alpha/beta correlation potentials on the AO basis ! general providers for the alpha/beta correlation potentials on the AO basis
END_DOC END_DOC
BEGIN_SHELL [ /usr/bin/env python2 ] BEGIN_SHELL [ /usr/bin/env python3 ]
import os import os
import glob import glob
from qp_path import QP_SRC from qp_path import QP_SRC
@ -51,18 +51,18 @@ functionals = map(lambda x : x.replace(".irp.f",""), glob.glob("*.irp.f"))
prefix = "" prefix = ""
for f in functionals: for f in functionals:
print """ print("""
%sif (trim(correlation_functional) == '%s') then %sif (trim(correlation_functional) == '%s') then
potential_c_alpha_ao = potential_c_alpha_ao_%s potential_c_alpha_ao = potential_c_alpha_ao_%s
potential_c_beta_ao = potential_c_beta_ao_%s"""%(prefix, f, f, f) potential_c_beta_ao = potential_c_beta_ao_%s"""%(prefix, f, f, f) )
prefix = "else " prefix = "else "
print """ print("""
else else
print*, 'Correlation functional required does not exist ...' print*, 'Correlation functional required does not exist ...'
print*,'correlation_functional ',correlation_functional print*,'correlation_functional ',correlation_functional
stop""" stop""" )
print "endif" print("endif")
END_SHELL END_SHELL
@ -200,7 +200,7 @@ print "endif"
! general providers for the alpha/beta exchange/correlation potentials on the AO basis ! general providers for the alpha/beta exchange/correlation potentials on the AO basis
END_DOC END_DOC
BEGIN_SHELL [ /usr/bin/env python2 ] BEGIN_SHELL [ /usr/bin/env python3 ]
import os import os
import glob import glob
from qp_path import QP_SRC from qp_path import QP_SRC
@ -210,17 +210,17 @@ functionals = map(lambda x : x.replace(".irp.f",""), glob.glob("*.irp.f"))
prefix = "" prefix = ""
for f in functionals: for f in functionals:
print """ print("""
%sif (trim(exchange_functional) == '%s') then %sif (trim(exchange_functional) == '%s') then
potential_xc_alpha_ao = potential_xc_alpha_ao_%s potential_xc_alpha_ao = potential_xc_alpha_ao_%s
potential_xc_beta_ao = potential_xc_beta_ao_%s"""%(prefix, f, f, f) potential_xc_beta_ao = potential_xc_beta_ao_%s"""%(prefix, f, f, f) )
prefix = "else " prefix = "else "
print """ print("""
else else
print*, 'exchange functional required does not exist ...' print*, 'exchange functional required does not exist ...'
print*,'exchange_functional ',exchange_functional print*,'exchange_functional ',exchange_functional
stop""" stop""")
print "endif" print("endif")
END_SHELL END_SHELL

4
src/perturbation/perturbation.irp.f
View File

@ -1,4 +1,4 @@
BEGIN_SHELL [ /usr/bin/env python2 ] BEGIN_SHELL [ /usr/bin/env python3 ]
from perturbation import perturbations from perturbation import perturbations
import os import os
@ -8,6 +8,6 @@ template = file.read()
file.close() file.close()
for p in perturbations: for p in perturbations:
print template.replace("$PERT",p) print(template.replace("$PERT",p))
END_SHELL END_SHELL

2
src/perturbation/perturbation.template.f
View File

@ -1,4 +1,4 @@
BEGIN_SHELL [ /usr/bin/env python2 ] BEGIN_SHELL [ /usr/bin/env python3 ]
import perturbation import perturbation
END_SHELL END_SHELL

8
src/scf_utils/diagonalize_fock.irp.f
View File

@ -7,11 +7,11 @@ BEGIN_PROVIDER [ double precision, eigenvectors_Fock_matrix_mo, (ao_num,mo_num)
integer :: i,j integer :: i,j
integer :: liwork, lwork, n, info integer :: liwork, lwork, n, info
integer, allocatable :: iwork(:) integer, allocatable :: iwork(:)
double precision, allocatable :: work(:), F(:,:), S(:,:) double precision, allocatable :: work(:), F(:,:), F_save(:,:)
double precision, allocatable :: diag(:) double precision, allocatable :: diag(:)
allocate( F(mo_num,mo_num) ) allocate( F(mo_num,mo_num), F_save(mo_num,mo_num) )
allocate (diag(mo_num) ) allocate (diag(mo_num) )
do j=1,mo_num do j=1,mo_num
@ -51,6 +51,7 @@ BEGIN_PROVIDER [ double precision, eigenvectors_Fock_matrix_mo, (ao_num,mo_num)
lwork = -1 lwork = -1
liwork = -1 liwork = -1
F_save = F
call dsyevd( 'V', 'U', mo_num, F, & call dsyevd( 'V', 'U', mo_num, F, &
size(F,1), diag, work, lwork, iwork, liwork, info) size(F,1), diag, work, lwork, iwork, liwork, info)
@ -71,6 +72,7 @@ BEGIN_PROVIDER [ double precision, eigenvectors_Fock_matrix_mo, (ao_num,mo_num)
if (info /= 0) then if (info /= 0) then
F = F_save
call dsyev( 'V', 'L', mo_num, F, & call dsyev( 'V', 'L', mo_num, F, &
size(F,1), diag, work, lwork, info) size(F,1), diag, work, lwork, info)
@ -83,7 +85,7 @@ BEGIN_PROVIDER [ double precision, eigenvectors_Fock_matrix_mo, (ao_num,mo_num)
call dgemm('N','N',ao_num,mo_num,mo_num, 1.d0, & call dgemm('N','N',ao_num,mo_num,mo_num, 1.d0, &
mo_coef, size(mo_coef,1), F, size(F,1), & mo_coef, size(mo_coef,1), F, size(F,1), &
0.d0, eigenvectors_Fock_matrix_mo, size(eigenvectors_Fock_matrix_mo,1)) 0.d0, eigenvectors_Fock_matrix_mo, size(eigenvectors_Fock_matrix_mo,1))
deallocate(work, F, diag) deallocate(work, F, F_save, diag)
END_PROVIDER END_PROVIDER

1
src/scf_utils/roothaan_hall_scf.irp.f
View File

@ -299,6 +299,7 @@ END_DOC
Fock_matrix_AO_(i,j) = 0.d0 Fock_matrix_AO_(i,j) = 0.d0
enddo enddo
do k=1,dim_DIIS do k=1,dim_DIIS
if (dabs(X_vector_DIIS(k)) < 1.d-10) cycle
do i=1,ao_num do i=1,ao_num
Fock_matrix_AO_(i,j) = Fock_matrix_AO_(i,j) + & Fock_matrix_AO_(i,j) = Fock_matrix_AO_(i,j) + &
X_vector_DIIS(k)*Fock_matrix_DIIS(i,j,dim_DIIS-k+1) X_vector_DIIS(k)*Fock_matrix_DIIS(i,j,dim_DIIS-k+1)

0
src/zmq/f77_zmq.h → src/zmq/f77_zmq_free.h
View File

2
src/zmq/f77_zmq_module.f90
View File

@ -1,4 +1,4 @@
module f77_zmq module f77_zmq
include 'f77_zmq.h' include 'f77_zmq_free.h'
end module end module

8
tests/bats_to_sh.py
View File

@ -1,11 +1,11 @@
#!/usr/bin/env python2 #!/usr/bin/env python3
import sys import sys
with open(sys.argv[1],'r') as f: with open(sys.argv[1],'r') as f:
raw_data = f.read() raw_data = f.read()
print "set -x" print("set -x")
output = [] output = []
inside = False inside = False
@ -25,9 +25,9 @@ for i in raw_data:
level -= 1 level -= 1
output.append(new_i) output.append(new_i)
print "".join(output).replace("@test ", print("".join(output).replace("@test ",
"""[[ -z $BATS_TEST_NUMBER ]] && BATS_TEST_NUMBER=0 || ((++BATS_TEST_NUMBER)) ; """[[ -z $BATS_TEST_NUMBER ]] && BATS_TEST_NUMBER=0 || ((++BATS_TEST_NUMBER)) ;
export BATS_TEST_DESCRIPTION=""").replace("skip","return") export BATS_TEST_DESCRIPTION=""").replace("skip","return"))