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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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52
INSTALL.rst
View File

@ -25,8 +25,8 @@ sets all the environment variables required for the normal operation of the
Running this script will also tell you which external dependencies are missing
and need to be installed.
When all dependencies have been installed, ( the :command:`configure` will tell you)
source the :file:`quantum_package.rc` in order to load all environment variables and compile the |QP|.
When all dependencies have been installed, ( the :command:`configure` will tell you)
source the :file:`quantum_package.rc` in order to load all environment variables and compile the |QP|.
Requirements
@ -36,14 +36,14 @@ Requirements
- Fortran compiler : GNU Fortran, Intel Fortran or IBM XL Fortran
- `GNU make`_
- `Autoconf`_
- `Python`_ > 2.6
- `Python`_ > 3.0
- |IRPF90| : Fortran code generator
- |EZFIO| : Easy Fortran Input/Output library generator
- |BLAS| and |LAPACK|
- `Zlib`_
- |ZeroMQ| : networking library
- `GMP <https://gmplib.org/>`_ : Gnu Multiple Precision Arithmetic Library
- |OCaml| compiler with |OPAM| package manager
- |OCaml| compiler with |OPAM| package manager
- `Bubblewrap <https://github.com/projectatomic/bubblewrap>`_ : Sandboxing tool required by Opam
- `libcap <https://git.kernel.org/pub/scm/linux/kernel/git/morgan/libcap.git>`_ : POSIX capabilities required by Bubblewrap
- |Ninja| : a parallel build system
@ -83,29 +83,29 @@ spack install quantum_package
Using the :command:`configure` executable
-----------------------------------------
The :command:`configure` executable can help you in installing the minimal dependencies you will need to compile the |QP|.
The command is to be used as follows:
The :command:`configure` executable can help you in installing the minimal dependencies you will need to compile the |QP|.
The command is to be used as follows:
.. code:: bash
./configure --install <package>
The following packages are supported by the :command:`configure` installer:
The following packages are supported by the :command:`configure` installer:
* ninja
* irpf90
* zeromq
* ninja
* irpf90
* zeromq
* f77zmq
* gmp
* libcap
* bwrap
* ocaml ( :math:`\approx` 10 minutes)
* ezfio
* docopt
* resultsFile
* ezfio
* docopt
* resultsFile
* bats
Example:
Example:
.. code:: bash
@ -124,7 +124,7 @@ Example:
If the :command:`configure` executable fails to install a specific dependency
-----------------------------------------------------------------------------
If the :command:`configure` executable does not succeed to install a specific dependency,
If the :command:`configure` executable does not succeed to install a specific dependency,
there are some proposition of how to download and install the minimal dependencies to compile and use the |QP|.
@ -149,13 +149,13 @@ IRPF90
------
*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
python2 -m pip install --user irpf90
python3 -m pip install --user irpf90
Otherwise,
@ -329,26 +329,26 @@ OCaml
`<https://raw.githubusercontent.com/ocaml/opam/master/shell/install.sh>`_
and move it in the :file:`${QP_ROOT}/external` directory
* If you use OCaml only with the |qp|, you can install the OPAM directory
* If you use OCaml only with the |qp|, you can install the OPAM directory
containing the compiler and all the installed libraries in the
:file:`${QP_ROOT}/external` directory as
.. code:: bash
export OPAMROOT=${QP_ROOT}/external/opam
* Run the installer
.. code:: bash
echo ${QP_ROOT}/bin
${QP_ROOT}/external/opam_installer.sh --no-backup --fresh
The :command:`opam` command can be installed in the :file:`${QP_ROOT}/bin`
directory. To do this, take the output of ``echo ${QP_ROOT}/bin`` and
use it as an answer to where :command:`opam` should be installed.
* Install the OCaml compiler
@ -387,11 +387,11 @@ Docopt
*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
python2 -m pip install --user docopt
python3 -m pip install --user docopt
Otherwise,
@ -408,11 +408,11 @@ resultsFile
*resultsFile* is a Python package to extract data from output files of quantum chemistry
codes.
If you have *pip* for Python2, you can do
If you have *pip* for Python3, you can do
.. 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 -*-
"""
@ -12,7 +12,7 @@ Usage:
"""
from __future__ import print_function
import sys
import os
import subprocess

54
bin/qp_convert_output_to_ezfio
View File

@ -1,4 +1,4 @@
#!/usr/bin/env python2
#!/usr/bin/env python3
"""
convert output of GAMESS/GAU$$IAN to ezfio
@ -22,7 +22,7 @@ try:
QP_ROOT = os.environ["QP_ROOT"]
QP_EZFIO = os.environ["QP_EZFIO"]
except KeyError:
print "Error: QP_ROOT environment variable not found."
print("Error: QP_ROOT environment variable not found.")
sys.exit(1)
else:
sys.path = [QP_EZFIO + "/Python",
@ -30,10 +30,11 @@ else:
QP_ROOT + "/install",
QP_ROOT + "/scripts"] + sys.path
from resultsFile import *
try:
from resultsFile import *
except:
print "Error: resultsFile Python library not installed"
print("Error: resultsFile Python library not installed")
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_beta_num(res.num_beta)
print "OK"
print("OK")
#
# |\ | _ | _ o
# | \| |_| (_ | (/_ |
#
print "Nuclei\t\t...\t",
print("Nuclei\t\t...\t", end=' ')
# ~#~#~#~ #
# I n i t #
# ~#~#~#~ #
@ -93,24 +94,23 @@ def write_ezfio(res, filename):
# Transformt H1 into H
import re
p = re.compile(ur'(\d*)$')
p = re.compile(r'(\d*)$')
label = [p.sub("", x.name).capitalize() for x in res.geometry]
ezfio.set_nuclei_nucl_label(label)
ezfio.set_nuclei_nucl_coord(coord_x + coord_y + coord_z)
print "OK"
print("OK")
# _
# /\ _ _ |_) _. _ o _
# /--\ (_) _> |_) (_| _> | _>
#
print "AOS\t\t...\t",
print("AOS\t\t...\t", end=' ')
# ~#~#~#~ #
# I n i t #
# ~#~#~#~ #
import string
at = []
num_prim = []
power_x = []
@ -131,9 +131,9 @@ def write_ezfio(res, filename):
at.append(i + 1)
num_prim.append(len(b.prim))
s = b.sym
power_x.append(string.count(s, "x"))
power_y.append(string.count(s, "y"))
power_z.append(string.count(s, "z"))
power_x.append(str.count(s, "x"))
power_y.append(str.count(s, "y"))
power_z.append(str.count(s, "z"))
coefficient.append(b.coef)
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_basis("Read by resultsFile")
print "OK"
print("OK")
# _
# |\/| _ _ |_) _. _ o _
# | | (_) _> |_) (_| _> | _>
#
print "MOS\t\t...\t",
print("MOS\t\t...\t", end=' ')
# ~#~#~#~ #
# I n i t #
# ~#~#~#~ #
@ -205,9 +205,9 @@ def write_ezfio(res, filename):
virtual = []
active = [(allMOs[i].eigenvalue, i) for i in range(len(allMOs))]
closed = map(lambda x: x[1], closed)
active = map(lambda x: x[1], active)
virtual = map(lambda x: x[1], virtual)
closed = [x[1] for x in closed]
active = [x[1] for x in active]
virtual = [x[1] for x in virtual]
MOindices = closed + active + virtual
MOs = []
@ -223,7 +223,7 @@ def write_ezfio(res, filename):
MOmap[i] = MOindices.index(i)
energies = []
for i in xrange(mo_num):
for i in range(mo_num):
energies.append(MOs[i].eigenvalue)
if res.occ_num is not None:
@ -237,11 +237,11 @@ def write_ezfio(res, filename):
MoMatrix = []
sym0 = [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]
MoMatrix = []
for i in xrange(len(MOs)):
for i in range(len(MOs)):
m = MOs[i]
for coef in m.vector:
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_occ(OccNum)
ezfio.set_mo_basis_mo_coef(MoMatrix)
print "OK"
print("OK")
print "Pseudos\t\t...\t",
print("Pseudos\t\t...\t", end=' ')
try:
lmax = 0
nucl_charge_remove = []
@ -327,7 +327,7 @@ def write_ezfio(res, filename):
else:
ezfio.set_pseudo_do_pseudo(True)
print "OK"
print("OK")
@ -354,15 +354,15 @@ if __name__ == '__main__':
except:
raise
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)
sys.stdout.flush()
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
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
@ -30,7 +30,7 @@ try:
from docopt import docopt
from qp_path import QP_SRC, QP_ROOT
except ImportError:
print "source .quantum_package.rc"
print("source .quantum_package.rc")
raise
@ -38,7 +38,7 @@ def main(arguments):
"""Main function"""
# Check that name exist in */IRPF90_man
print "Checking that name exists..."
print("Checking that name exists...")
all_modules = os.listdir(QP_SRC)
f = arguments["<name>"]+".l"
@ -52,21 +52,21 @@ def main(arguments):
if found: break
if not found:
print "Error:"
print "The variable/subroutine/function \""+arguments["<name>"] \
+ "\" was not found in the sources."
print "Did you compile the code at the root?"
print "Continue? [y/N] ",
print("Error:")
print("The variable/subroutine/function \""+arguments["<name>"] \
+ "\" was not found in the sources.")
print("Did you compile the code at the root?")
print("Continue? [y/N] ", end=' ')
cont = sys.stdin.read(1).strip() in ["y", "Y"]
if not cont:
print "Aborted"
print("Aborted")
sys.exit(1)
# Now search in all the files
if arguments["--rename"]:
print "Replacing..."
print("Replacing...")
else:
print "Searching..."
print("Searching...")
name = re.compile(r"\b"+arguments["<name>"]+r"\b", re.IGNORECASE)
@ -84,15 +84,15 @@ def main(arguments):
with open(filename, "r") as f:
f_in = f.read()
if name.search(f_in):
print filename
print(filename)
if arguments["--rename"]:
f_new = name.sub(arguments["--rename"], f_in)
with open(filename, "w") as f:
f.write(f_new)
print "Done"
print("Done")
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 -*-
"""
Usage:
@ -43,9 +43,9 @@ try:
from module_handler import get_l_module_descendant
from qp_path import QP_SRC, QP_PLUGINS, QP_DATA, QP_ROOT
except ImportError:
print "Please check if you have sourced the ${QP_ROOT}/quantum_package.rc"
print "(`source ${QP_ROOT}/quantum_package.rc`)"
print sys.exit(1)
print("Please check if you have sourced the ${QP_ROOT}/quantum_package.rc")
print("(`source ${QP_ROOT}/quantum_package.rc`)")
print(sys.exit(1))
def save_new_module(path, l_child):
@ -58,7 +58,7 @@ def save_new_module(path, l_child):
try:
os.makedirs(path)
except OSError:
print "The module ({0}) already exists...".format(path)
print("The module ({0}) already exists...".format(path))
sys.exit(1)
with open(os.path.join(path, "NEED"), "w") as f:
@ -105,7 +105,7 @@ def main(arguments):
if arguments["list"]:
if arguments["--repositories"]:
for repo in get_repositories():
print repo
print(repo)
else:
# Search in QP_PLUGINS all directories with a NEED file
@ -121,7 +121,7 @@ def main(arguments):
for (x, y) in l_tmp:
d_tmp[x] = y
repo_of_plugin[y] = x.replace(QP_PLUGINS+'/','')
l_repository = d_tmp.keys()
l_repository = list(d_tmp.keys())
if l_repository == []:
l_result = []
else:
@ -142,7 +142,7 @@ def main(arguments):
l_result = [f for f in l_plugins if f not in l_installed]
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"]:
@ -159,29 +159,29 @@ def main(arguments):
path = os.path.join(QP_PLUGINS, repository, name)
print "Created plugin:"
print path, '\n'
print("Created plugin:")
print(path, '\n')
for children in l_children:
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)
print "Needed modules:"
print l_children, '\n'
print("Needed modules:")
print(l_children, '\n')
print "This corresponds to using the following modules:"
print l_children + m_instance.l_descendant_unique(l_children), '\n'
print("This corresponds to using the following modules:")
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)
print l_child_reduce, '\n'
print(l_child_reduce, '\n')
print "Installation",
print("Installation", end=' ')
save_new_module(path, l_child_reduce)
print " [ OK ]"
print ""
print(" [ OK ]")
print("")
arguments["create"] = False
arguments["install"] = True
main(arguments)
@ -228,7 +228,7 @@ def main(arguments):
for (x, y) in [os.path.split(f) for f in l_tmp]:
d_repo_of_plugin[y] = x
d_repo[x] = None
l_repository = d_repo.keys()
l_repository = list(d_repo.keys())
d_plugin = get_dict_child(l_repository)
@ -236,7 +236,7 @@ def main(arguments):
d_child.update(d_plugin)
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
l_name = [normalize_case[name.lower()] for name in arguments["<name>"]]
@ -244,7 +244,7 @@ def main(arguments):
for name in l_name:
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)
@ -252,10 +252,10 @@ def main(arguments):
if l_module_to_cp:
print "Required dependencies:"
print l_module_to_cp
print("Required dependencies:")
print(l_module_to_cp)
print "Installation...",
print("Installation...", end=' ')
for module_to_cp in l_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])
os.chdir(wd)
except OSError:
print "The src directory is broken. Please remove %s" % des
print("The src directory is broken. Please remove %s" % des)
raise
subprocess.check_call(["qp_create_ninja", "update"])
print "[ OK ]"
print("[ OK ]")
elif arguments["uninstall"]:
@ -285,17 +285,17 @@ def main(arguments):
l_failed = [name for name in l_name if name not in d_local]
if l_failed:
print "Plugins not installed:"
print("Plugins not installed:")
for name in sorted(l_failed):
print "%s" % name
print("%s" % name)
sys.exit(1)
l_name_to_remove = l_name + \
[module for module in m_instance.l_module \
for name in l_name if name in d_descendant[module]]
print "Removing plugins:"
print l_name_to_remove
print("Removing plugins:")
print(l_name_to_remove)
for module in set(l_name_to_remove):
@ -310,7 +310,7 @@ def main(arguments):
try:
os.unlink(os.path.join(QP_SRC, module))
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"]:
@ -321,7 +321,7 @@ def main(arguments):
l_repositories = get_repositories()
for repo in l_repositories:
print "Updating ", repo
print("Updating ", repo)
os.chdir(os.path.join(QP_PLUGINS,repo))
git_cmd=["git", "pull"]
subprocess.check_call(git_cmd)

1
bin/qp_reset
View File

@ -95,6 +95,7 @@ qp set_file $ezfio
if [[ $dets -eq 1 ]] ; then
rm --force -- ${ezfio}/determinants/n_det
rm --force -- ${ezfio}/determinants/psi_{det,coef}.gz
rm --force -- ${ezfio}/determinants/psi_{det,coef}_qp_edit.gz
fi
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:
import qp_path
except ImportError:
print "source .quantum_package.rc"
print("source .quantum_package.rc")
raise
from docopt import docopt
@ -102,7 +102,7 @@ def main(arguments):
mo_num = ezfio.mo_basis_mo_num
if arguments["--query"]:
print n_frozen
print(n_frozen)
sys.exit(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:
import qp_path
except ImportError:
print "source .quantum_package.rc"
print("source .quantum_package.rc")
raise
from docopt import docopt
@ -62,7 +62,7 @@ def main(arguments):
mo_num = ezfio.mo_basis_mo_num
if arguments["--query"]:
print n_frozen
print(n_frozen)
sys.exit(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 -*-
"""
@ -21,8 +21,8 @@ try:
from docopt import docopt
from qp_path import QP_SRC, QP_TESTS
except ImportError:
print "Please check if you have sourced the ${QP_ROOT}/quantum_package.rc"
print "(`source ${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`)")
sys.exit(1)
@ -54,11 +54,11 @@ def main(arguments):
os.chdir(QP_TESTS)
for bats_file in l_bats:
print ""
print "-~-~-~-~-~-~"
print ""
print "Running tests for %s"%(bats_file)
print ""
print("")
print("-~-~-~-~-~-~")
print("")
print("Running tests for %s"%(bats_file))
print("")
if arguments["-v"]:
p = None
if arguments["TEST"]:
@ -66,7 +66,7 @@ def main(arguments):
else:
test = ""
try:
os.system(test+" python2 bats_to_sh.py "+bats_file+
os.system(test+" python3 bats_to_sh.py "+bats_file+
"| bash")
except:
if p:

8
config/ifort_avx.cfg
View File

@ -9,14 +9,14 @@
FC : ifort -fpic
LAPACK_LIB : -mkl=parallel
IRPF90 : irpf90
IRPF90_FLAGS : --ninja --align=32
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
@ -32,14 +32,14 @@ OPENMP : 1 ; Append OpenMP flags
#
[OPT]
FC : -traceback
FCFLAGS : -xAVX -O2 -ip -ftz -g
FCFLAGS : -mavx -axAVX -O2 -ip -ftz -g
# Profiling flags
#################
#
[PROFILE]
FC : -p -g
FCFLAGS : -xSSE4.2 -O2 -ip -ftz
FCFLAGS : -xSSE4.2 -O2 -ip -ftz
# Debugging flags
#################

8
config/ifort_avx_mpi.cfg
View File

@ -9,14 +9,14 @@
FC : mpiifort -fpic
LAPACK_LIB : -mkl=parallel
IRPF90 : irpf90
IRPF90_FLAGS : --ninja --align=32 -DMPI
IRPF90_FLAGS : --ninja --align=32 -DMPI
# Global options
################
#
# 1 : Activate
# 0 : Deactivate
#
#
[OPTION]
MODE : OPT ; [ OPT | PROFILE | DEBUG ] : Chooses the section below
CACHE : 0 ; Enable cache_compile.py
@ -31,14 +31,14 @@ OPENMP : 1 ; Append OpenMP flags
# -ftz : Flushes denormal results to zero
#
[OPT]
FCFLAGS : -march=corei7-avx -O2 -ip -ftz -g -traceback
FCFLAGS : -mavx -axAVX -O2 -ip -ftz -g -traceback
# Profiling flags
#################
#
[PROFILE]
FC : -p -g
FCFLAGS : -march=corei7 -O2 -ip -ftz
FCFLAGS : -march=corei7 -O2 -ip -ftz
# Debugging flags

8
config/ifort_debug.cfg
View File

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

8
config/ifort_mpi.cfg
View File

@ -9,14 +9,14 @@
FC : mpiifort -fpic
LAPACK_LIB : -mkl=parallel
IRPF90 : irpf90
IRPF90_FLAGS : --ninja --align=32 -DMPI
IRPF90_FLAGS : --ninja --align=32 -DMPI
# Global options
################
#
# 1 : Activate
# 0 : Deactivate
#
#
[OPTION]
MODE : OPT ; [ OPT | PROFILE | DEBUG ] : Chooses the section below
CACHE : 0 ; Enable cache_compile.py
@ -31,14 +31,14 @@ OPENMP : 1 ; Append OpenMP flags
# -ftz : Flushes denormal results to zero
#
[OPT]
FCFLAGS : -xSSE4.2 -O2 -ip -ftz -g -traceback
FCFLAGS : -msse4.2 -O2 -ip -ftz -g -traceback
# Profiling flags
#################
#
[PROFILE]
FC : -p -g
FCFLAGS : -xSSE4.2 -O2 -ip -ftz
FCFLAGS : -msse4.2 -O2 -ip -ftz
# Debugging flags

3
configure vendored
View File

@ -3,7 +3,7 @@
# 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

2
docs/Makefile
View File

@ -14,7 +14,7 @@ help:
.PHONY: help Makefile 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
# "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
from __future__ import print_function
import os
import sys
import ConfigParser
import configparser
from module_handler import get_binaries
@ -27,7 +27,7 @@ def generate_modules(abs_module, entities):
EZFIO = os.path.join(abs_module,'EZFIO.cfg')
if os.path.exists(EZFIO):
rst += ["", "EZFIO parameters", "----------------", ""]
config_file = ConfigParser.ConfigParser()
config_file = configparser.ConfigParser()
with open(EZFIO, 'r') as f:
config_file.readfp(f)
for section in config_file.sections():

4
etc/irpf90.rc
View File

@ -18,10 +18,10 @@ function source_if_exists() {
if [[ -f $1 ]]; then
cd $(dirname $1) ; source $(basename $1) ; cd -
fi &> /dev/null
}
}
source ${QP_ROOT}/etc/autocomplete.rc
source_if_exists "${IRPF90_PATH}/irpman-completions.bash"

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:"${QP_ROOT}"/lib64)
export C_INCLUDE_PATH=$(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." ;
arg=Without_arg; } ;
{ short='v' ; long="verbose" ; opt=Optional ;
doc="Prints the transfer speed." ;
arg=Without_arg; } ;
anonymous
"(EZFIO_DIR|ADDRESS)"
Mandatory
@ -150,45 +146,6 @@ let () =
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 =
match req_or_sub with

9
ocaml/qptypes_generator.ml
View File

@ -219,22 +219,19 @@ module Perturbation : sig
end = struct
type t =
| EN
| Barycentric
| Variance
| HF
| SOP
[@@deriving sexp]
let to_string = function
| EN -> \"EN\"
| Variance -> \"Variance\"
| Barycentric -> \"Barycentric\"
| HF -> \"HF\"
| SOP -> \"SOP\"
let of_string s =
match (String.lowercase_ascii s) with
| \"sop\" -> SOP
| \"en\" -> EN
| \"variance\" -> Variance
| \"barycentric\" -> Barycentric
| \"hf\" -> HF
| _ -> raise (Invalid_argument (\"Wrong Perturbation type : \"^s))
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
and is the .o is asked a second time, retur it
@ -13,9 +13,9 @@ import re
import shutil
import subprocess
r = re.compile(ur'-c\s+(\S+\.[fF]90)\s+-o\s+(\S+\.o)')
p = re.compile(ur'-I IRPF90_temp/\S*\s+')
mod = re.compile(ur'module\s+(?P<mod>\S+).+end\s?module\s+(?P=mod)?',
r = re.compile(r'-c\s+(\S+\.[fF]90)\s+-o\s+(\S+\.o)')
p = re.compile(r'-I IRPF90_temp/\S*\s+')
mod = re.compile(r'module\s+(?P<mod>\S+).+end\s?module\s+(?P=mod)?',
re.MULTILINE | re.IGNORECASE)
tmpdir_root = os.environ.get("TMPDIR", failobj="/dev/shm")

47
scripts/compilation/qp_create_ninja
View File

@ -1,4 +1,4 @@
#!/usr/bin/env python2
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Usage: qp_create_ninja create <config_file> (--development | --production)
@ -24,7 +24,7 @@ except ImportError:
"..",
"quantum_package.rc"))
print "\n".join(["", "Error:", "source %s" % f, ""])
print("\n".join(["", "Error:", "source %s" % f, ""]))
sys.exit(1)
# Compress path
@ -124,7 +124,7 @@ def dict_module_genelogy_path(d_module_genelogy):
d_module_genelogy
"""
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)
p = Path(module_abs, module_rel)
@ -235,11 +235,11 @@ def ninja_ezfio_cfg_build(l_util):
"""
l_string = []
for m in l_util.itervalues():
for m in l_util.values():
str_ = "build {1} {2}: build_ezfio_interface {0}"
l_string += [str_.format(*map(comp_path,(m.ez_cfg.abs, m.ez_interface.abs,
m.ez_config.abs)))]
l_string += [str_.format(*list(map(comp_path,(m.ez_cfg.abs, m.ez_interface.abs,
m.ez_config.abs))))]
l_string += [" sub_module = {0}".format(comp_path(m.ez_module.abs))]
l_string += [""]
@ -257,8 +257,8 @@ def ninja_ezfio_config_build(l_ezfio_config):
file_source = m.path_in_module
file_create = m.path_in_ezfio
l_string += ["build {0}: build_ezfio_config {1}".format(*map(comp_path,(file_create,
file_source)))]
l_string += ["build {0}: build_ezfio_config {1}".format(*list(map(comp_path,(file_create,
file_source))))]
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_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)))
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:
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
@ -360,7 +360,7 @@ def ninja_gitignore_build(path_module, d_binaries, l_symlink):
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,
" ".join(l_b))
@ -420,9 +420,9 @@ def get_file_dependency(d_info_module):
"""
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"]:
values = [join(module.abs, o) for o in values]
if key in ["l_obj"]:
@ -431,7 +431,7 @@ def get_file_dependency(d_info_module):
d_irp[module][key] = values
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"]:
values = [join(module.abs, children.rel, o)
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 #
# ~#~#~#~#~#~#~#~#~#~ #
l_depend = map(comp_path,d_irp[path_module]["l_depend"])
l_src = map(comp_path,d_irp[path_module]["l_src"])
l_obj = map(comp_path,d_irp[path_module]["l_obj"])
l_template = map(comp_path,d_irp[path_module]["l_template"])
l_depend = list(map(comp_path,d_irp[path_module]["l_depend"]))
l_src = list(map(comp_path,d_irp[path_module]["l_src"]))
l_obj = list(map(comp_path,d_irp[path_module]["l_obj"]))
l_template = list(map(comp_path,d_irp[path_module]["l_template"]))
if l_needed_molule:
l_symlink = ["l_symlink_{0}".format(path_module.rel)]
@ -511,7 +511,7 @@ def ninja_irpf90_make_build(path_module, l_needed_molule, d_irp):
# N i n j a _ b u i l d #
# ~#~#~#~#~#~#~#~#~#~#~ #
l_include_dir = ["-I {0}".format(m.rel) for m in l_needed_molule]
l_include_dir = ["-I {0}".format(m.rel) for m in l_needed_molule]
l_string = [
"build {0}: build_irpf90.ninja {1}".format(str_creation, str_depend),
@ -544,6 +544,7 @@ def get_binaries(path_module):
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
stdout, stderr = process.communicate()
stdout = stdout.decode()
except OSError:
return []
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")
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 #
@ -658,7 +659,7 @@ def ninja_binaries_build(path_module, l_children, 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")
@ -829,14 +830,14 @@ if __name__ == "__main__":
dict_root = module_instance.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 #
# ~#~#~#~#~#~#~#~#~#~#~#~#~ #
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 -*-
import os, sys
import ConfigParser
import configparser
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
"""
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)
config = ConfigParser.ConfigParser()
config = configparser.ConfigParser(inline_comment_prefixes=(';','#'))
config.read(pwd_cfg)
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:
try:
l.extend(config.get(section, flag_name).split())
except ConfigParser.NoOptionError:
except configparser.NoOptionError:
pass
return " ".join(l)
@ -43,5 +43,5 @@ if __name__ == '__main__':
qpackage_root = os.environ['QP_ROOT']
pwd_cfg = os.path.join(qpackage_root, "config/ifort_gpi2.cfg")
print get_compilation_option(pwd_cfg, "FC")
print get_compilation_option(pwd_cfg, "FCFLAGS")
print(get_compilation_option(pwd_cfg, "FC"))
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 -*-
"""
Welcome to the ei_handler.
@ -72,7 +72,7 @@ import sys
import os
import os.path
import ConfigParser
import configparser
from collections import defaultdict
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 #
# ~#~#~#~#~#~#~#~#~#~#~ #
config_file = ConfigParser.ConfigParser()
config_file.readfp(open(module_obj.path))
config_file = configparser.ConfigParser()
config_file.read_file(open(module_obj.path))
# ~#~#~#~#~#~#~#~#~ #
# F i l l _ d i c t #
@ -229,7 +229,7 @@ def get_dict_config_file(module_obj):
def error(o, p, c):
"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():
# pvd = provider
@ -245,13 +245,13 @@ def get_dict_config_file(module_obj):
# Check if type is avalaible
try:
type_ = config_file.get(section, "type").strip()
except ConfigParser.NoOptionError:
except configparser.NoOptionError:
error("type", pvd, module_obj.path)
sys.exit(1)
if type_ not in type_dict:
print "{0} not avalaible. Choose in:".format(type_).strip()
print ", ".join(sorted([i for i in type_dict]))
print("{0} not avalaible. Choose in:".format(type_).strip())
print(", ".join(sorted([i for i in type_dict])))
sys.exit(1)
else:
d[pvd]["type"] = type_dict[type_]
@ -259,18 +259,18 @@ def get_dict_config_file(module_obj):
# Fill the dict with REQUIRED information
try:
d[pvd]["doc"] = config_file.get(section, "doc")
except ConfigParser.NoOptionError:
except configparser.NoOptionError:
error("doc", pvd, module_obj.path)
sys.exit(1)
try:
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)
sys.exit(1)
else:
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)
else:
d[pvd]["interface"] = interface
@ -279,7 +279,7 @@ def get_dict_config_file(module_obj):
for option in l_info_optional:
try:
d[pvd][option] = config_file.get(section, option).lower()
except ConfigParser.NoOptionError:
except configparser.NoOptionError:
if option in d_default:
d[pvd][option] = d_default[option]
@ -287,7 +287,7 @@ def get_dict_config_file(module_obj):
try:
default_raw = config_file.get(section, "default")
except ConfigParser.NoOptionError:
except configparser.NoOptionError:
if "ocaml" in d[pvd]["interface"]:
error("default", pvd, module_obj.path)
sys.exit(1)
@ -322,7 +322,7 @@ def create_ezfio_provider(dict_ezfio_cfg):
dict_code_provider = dict()
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"]:
ez_p.set_type(dict_info['type'].fortran)
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),
"\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)
@ -381,22 +381,22 @@ def create_ezfio_stuff(dict_ezfio_cfg, config_or_default="config"):
def size_format_to_ezfio(size_raw):
"""
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
If the value are between parenthses -> do nothing; return
If the values are between parenthses -> do nothing; return
"""
size_raw = str(size_raw)
if size_raw.startswith('='):
size_convert = size_raw.replace('.', '_')
else:
size_raw = provider_info["size"].translate(None, "()")
size_raw = provider_info["size"].translate(str.maketrans("","","()"))
size_raw = size_raw.replace('.', '_')
a_size_raw = []
for dim in size_raw.split(","):
try:
(begin, end) = map(str.strip, dim.split(":"))
(begin, end) = list(map(str.strip, dim.split(":")))
except ValueError:
a_size_raw.append(dim)
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_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_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
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):
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
else:
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
name_raw = provider_info["ezfio_name"].lower()
@ -532,7 +532,7 @@ def create_ocaml_input(dict_ezfio_cfg, module_lower):
l_type = []
l_doc = []
for k, v in dict_ezfio_cfg.iteritems():
for k, v in dict_ezfio_cfg.items():
if "ocaml" in v['interface']:
l_ezfio_name.append(v['ezfio_name'])
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:
continue
@ -655,7 +655,7 @@ def get_l_module_with_auto_generate_ocaml_lower():
l_module_lower = []
import re
p = re.compile(ur'interface:.*ocaml')
p = re.compile(r'interface:.*ocaml')
for f in l_folder:
path = "{0}/{1}/EZFIO.cfg".format(QP_SRC, f)
@ -782,7 +782,7 @@ if __name__ == "__main__":
#
if arguments["list_supported_types"]:
for i in sorted(get_type_dict()):
print i
print(i)
sys.exit(0)
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
OCaml templates needed by qp_edit
@ -17,12 +17,12 @@ class EZFIO_ocaml(object):
def __init__(self, **kwargs):
for k, v in kwargs.iteritems():
for k, v in kwargs.items():
try:
exec "self.{0} = {1}".format(k, v)
exec("self.{0} = {1}".format(k, v))
except NameError:
exec "self.{0} = '{1}'".format(k, v)
exec("self.{0} = '{1}'".format(k, v))
@property
def Ocaml_type(self):
@ -39,7 +39,7 @@ class EZFIO_ocaml(object):
def check_if_init(self, l_arg, name):
for i in l_arg:
try:
exec "self.{0}".format(i)
exec("self.{0}".format(i))
except AttributeError:
msg = "You need to provide a '{0}' for creating {1}"
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"
__date__ = "jeudi 26 mars 2015, 12:49:35 (UTC+0100)"
@ -88,7 +88,7 @@ END_PROVIDER
def __init__(self):
self.values = "type doc name ezfio_dir ezfio_name write output".split()
for v in self.values:
exec "self.{0} = None".format(v)
exec("self.{0} = None".format(v))
def __repr__(self):
self.set_write()
@ -96,7 +96,7 @@ END_PROVIDER
for v in self.values:
if not v:
msg = "Error : %s is not set in EZFIO.cfg" % (v)
print >>sys.stderr, msg
print(msg, file=sys.stderr)
sys.exit(1)
if "size" not in self.__dict__:
self.__dict__["size"] = ""
@ -167,7 +167,7 @@ def test_module():
T.set_ezfio_dir("Hartree_Fock")
T.set_ezfio_name("thresh_SCF")
T.set_output("output_Hartree_Fock")
print T
print(T)
if __name__ == '__main__':
test_module()

10
scripts/generate_h_apply.py
View File

@ -1,4 +1,4 @@
#!/usr/bin/env python2
#!/usr/bin/env python3
import os
@ -11,6 +11,7 @@ declarations
decls_main
deinit_thread
init_main
filter_integrals
filter2p
filter2h2p_double
filter2h2p_single
@ -104,6 +105,11 @@ class H_apply(object):
s["do_mono_excitations"] = d[do_mono_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["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"] = """
! Sort H_jj to find the N_states lowest states
@ -149,7 +155,7 @@ class H_apply(object):
def __repr__(self):
buffer = self.template
for key,value in self.data.items():
for key,value in list(self.data.items()):
buffer = buffer.replace('$'+key, value)
return buffer

6
scripts/hello.py
View File

@ -1,4 +1,4 @@
#!/usr/bin/env python2
#!/usr/bin/env python3
import random
@ -131,8 +131,8 @@ _ __ `/___ __ \__ ___/__ __ \
""" ]
print random.choice(hello)
print "\n -- Quantum Package Shell --\n"
print(random.choice(hello))
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 -*-
"""
Module utilitary
@ -25,7 +25,7 @@ try:
from docopt import docopt
from qp_path import QP_SRC, QP_ROOT, QP_PLUGINS, QP_EZFIO
except ImportError:
print "source .quantum_package.rc"
print("source .quantum_package.rc")
raise
@ -50,6 +50,7 @@ def get_binaries(path_module):
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
stdout, stderr = process.communicate()
stdout = stdout.decode()
except OSError:
return []
else:
@ -106,9 +107,9 @@ def get_l_module_descendant(d_child, l_module):
try:
l.extend(get_l_module_descendant(d_child, d_child[module]))
except KeyError:
print >> sys.stderr, "Error: "
print >> sys.stderr, "`{0}` is not a submodule".format(module)
print >> sys.stderr, "Check the typo (spelling, case, '/', etc.) "
print("Error: ", file=sys.stderr)
print("`{0}` is not a submodule".format(module), file=sys.stderr)
print("Check the typo (spelling, case, '/', etc.) ", file=sys.stderr)
sys.exit(1)
return list(set(l))
@ -120,7 +121,7 @@ class ModuleHandler():
@property
def l_module(self):
return self.dict_child.keys()
return list(self.dict_child.keys())
@property
def dict_parent(self):
@ -132,7 +133,7 @@ class ModuleHandler():
d = {}
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]]
return d
@ -151,8 +152,8 @@ class ModuleHandler():
d[module_name] = get_l_module_descendant(d_child,
d_child[module_name])
except KeyError:
print "Check NEED for {0}".format(
module_name)
print("Check NEED for {0}".format(
module_name))
sys.exit(1)
return d
@ -185,7 +186,7 @@ class ModuleHandler():
for e in d_desc[module]:
d[e] = 1
return d.keys()
return list(d.keys())
def l_reduce_tree(self, l_module):
"""For a list of module in input return only the root"""
@ -218,8 +219,8 @@ if __name__ == '__main__':
for module in l_module:
if not is_module(module):
print "{0} is not a valid module. Abort".format(module)
print "No NEED in it"
print("{0} is not a valid module. Abort".format(module))
print("No NEED in it")
sys.exit(1)
m = ModuleHandler()
@ -227,7 +228,7 @@ if __name__ == '__main__':
if arguments['print_descendant']:
for module in l_module:
print " ".join(sorted(m.l_descendant_unique([module])))
print(" ".join(sorted(m.l_descendant_unique([module]))))
if arguments["clean"]:

8
scripts/perturbation.py
View File

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

5
scripts/utility/qp_path.py
View File

@ -1,13 +1,14 @@
#!/usr/bin/env python2
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
import os
import sys
try:
QP_ROOT = os.environ['QP_ROOT']
except:
print "source quantum_package.rc"
print("source quantum_package.rc")
sys.exit(1)
else:
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
to_select = int(sqrt(dble(N_states))*dble(N_det)*selection_factor)
to_select = max(N_states_diag, to_select)
to_select = max(to_select,1)
call ZMQ_selection(to_select, pt2, variance, norm)
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
else if (h0_type == "Barycentric") then
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
pt2_E0_denominator(1:N_states) = psi_energy(1:N_states)
else

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

@ -64,7 +64,7 @@ function run() {
@test "SO" { # 1.9667s 2.91234s
[[ -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

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

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

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

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

40
src/davidson/diagonalize_ci.irp.f
View File

@ -118,22 +118,22 @@ END_PROVIDER
call u_0_S2_u_0(s2_eigvalues,eigenvectors,N_det,psi_det,N_int,&
N_det,size(eigenvectors,1))
if (only_expected_s2) then
do j=1,N_det
! Select at least n_states states with S^2 values closed to "expected_s2"
if(dabs(s2_eigvalues(j)-expected_s2).le.0.5d0)then
i_state +=1
index_good_state_array(i_state) = j
good_state_array(j) = .True.
endif
if(i_state.eq.N_states) then
exit
endif
enddo
else
do j=1,N_det
index_good_state_array(j) = j
do j=1,N_det
! Select at least n_states states with S^2 values closed to "expected_s2"
if(dabs(s2_eigvalues(j)-expected_s2).le.0.5d0)then
i_state +=1
index_good_state_array(i_state) = j
good_state_array(j) = .True.
enddo
endif
if(i_state.eq.N_states) then
exit
endif
enddo
else
do j=1,N_det
index_good_state_array(j) = j
good_state_array(j) = .True.
enddo
endif
if(i_state .ne.0)then
! Fill the first "i_state" states that have a correct S^2 value
@ -163,7 +163,7 @@ END_PROVIDER
print*,'!!!!!!!! WARNING !!!!!!!!!'
print*,' Within the ',N_det,'determinants selected'
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*,' 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'
@ -179,11 +179,11 @@ END_PROVIDER
deallocate(index_good_state_array,good_state_array)
deallocate(s2_eigvalues)
else
call lapack_diag(eigenvalues,eigenvectors, &
call lapack_diag(eigenvalues,eigenvectors, &
H_matrix_all_dets,size(H_matrix_all_dets,1),N_det)
CI_electronic_energy(:) = 0.d0
call u_0_S2_u_0(CI_s2,eigenvectors,N_det,psi_det,N_int,&
min(N_det,N_states_diag),size(eigenvectors,1))
call u_0_S2_u_0(CI_s2,eigenvectors,N_det,psi_det,N_int, &
min(N_det,N_states_diag),size(eigenvectors,1))
! Select the "N_states_diag" states of lowest energy
do j=1,min(N_det,N_states_diag)
do i=1,N_det
@ -213,7 +213,7 @@ subroutine diagonalize_CI
! Replace the coefficients of the |CI| states by the coefficients of the
! eigenstates of the |CI| matrix.
END_DOC
integer :: i,j
integer :: i,j
do j=1,N_states
do i=1,N_det
psi_coef(i,j) = CI_eigenvectors(i,j)

12
src/density_for_dft/EZFIO.cfg
View File

@ -1,25 +1,23 @@
[density_for_dft]
type: character*(32)
doc: Type of density used for DFT calculation. If set to WFT , it uses the density of the wave function stored in (psi_det,psi_coef). If set to input_density it uses the one-body dm stored in aux_quantities/ . If set to damping_rs_dft it uses the damped density between WFT and input_density. In the ks_scf and rs_ks_scf programs, it is set to WFT.
doc: Type of density used for DFT calculation. If set to WFT , it uses the density of the wave function stored in (psi_det,psi_coef). If set to input_density it uses the one-body dm stored in aux_quantities/ . If set to damping_rs_dft it uses the damped density between WFT and input_density. In the ks_scf and rs_ks_scf programs, it is set to WFT.
interface: ezfio, provider, ocaml
default: WFT
default: WFT
[damping_for_rs_dft]
type: double precision
doc: damping factor for the density used in RSFT.
doc: damping factor for the density used in RSFT.
interface: ezfio,provider,ocaml
default: 0.5
[no_core_density]
type: character*(32)
doc: Type of density
doc: if [no_core_dm] then all elements of the density matrix involving at least one orbital set as core are set to zero
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
interface: ezfio, provider, ocaml
default: full_density
[normalize_dm]
type: logical
doc: Type of density
doc: if .True., then you normalize the no_core_dm to elec_alpha_num - n_core_orb and elec_beta_num - n_core_orb
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
interface: ezfio, provider, ocaml
default: True

1
src/determinants/EZFIO.cfg
View File

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

6
src/determinants/h_apply.template.f
View File

@ -243,7 +243,7 @@ subroutine $subroutine_diexcOrg(key_in,key_mask,hole_1,particl_1,hole_2, particl
! Build array of the non-zero integrals of second excitation
$filter_integrals
if (ispin == 1) then
if (ispin == 1) then
integer :: jjj
i=0
@ -285,7 +285,7 @@ subroutine $subroutine_diexcOrg(key_in,key_mask,hole_1,particl_1,hole_2, particl
$only_1h_double
$only_1p_double
$only_2h1p_double
$filter_only_connected_to_hf_double
$filter_only_connected_to_hf_double
key_idx += 1
do k=1,N_int
keys_out(k,1,key_idx) = key(k,1)
@ -497,7 +497,7 @@ subroutine $subroutine_monoexc(key_in, hole_1,particl_1,fock_diag_tmp,i_generato
$filter_only_1h1p_single
$filter_only_1h2p_single
$filter_only_2h2p_single
$filter_only_connected_to_hf_single
$filter_only_connected_to_hf_single
key_idx += 1
do k=1,N_int
keys_out(k,1,key_idx) = hole(k,1)

42
src/dft_one_e/e_xc_general.irp.f
View File

@ -3,8 +3,8 @@ BEGIN_PROVIDER [double precision, energy_x, (N_states)]
BEGIN_DOC
! correlation energies general providers.
END_DOC
BEGIN_SHELL [ /usr/bin/env python2 ]
BEGIN_SHELL [ /usr/bin/env python3 ]
import os
import glob
from qp_path import QP_SRC
@ -13,32 +13,32 @@ os.chdir(funcdir)
functionals = map(lambda x : x.replace(".irp.f",""), glob.glob("*.irp.f"))
prefix = ""
for f in functionals:
print """
print("""
%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 "
print """
print("""
else
print *, 'exchange functional required does not exist ...'
print *, 'exchange_functional ',exchange_functional
stop"""
print "endif"
stop""")
print("endif")
END_SHELL
END_PROVIDER
BEGIN_PROVIDER [double precision, energy_c, (N_states)]
implicit none
BEGIN_DOC
! correlation and exchange energies general providers.
END_DOC
BEGIN_SHELL [ /usr/bin/env python2 ]
BEGIN_SHELL [ /usr/bin/env python3 ]
import os
import glob
from qp_path import QP_SRC
@ -47,19 +47,19 @@ os.chdir(funcdir)
functionals = map(lambda x : x.replace(".irp.f",""), glob.glob("*.irp.f"))
prefix = ""
for f in functionals:
print """
print("""
%sif (trim(correlation_functional) == '%s') then
energy_c = energy_c_%s"""%(prefix, f, f)
energy_c = energy_c_%s"""%(prefix, f, f) )
prefix = "else "
print """
print("""
else
print*, 'Correlation functional required does not exist ...'
print*,'correlation_functional ',correlation_functional
stop"""
print "endif"
stop""")
print("endif")
END_SHELL
END_PROVIDER

94
src/dft_one_e/pot_general.irp.f
View File

@ -4,8 +4,8 @@
BEGIN_DOC
! general providers for the alpha/beta exchange potentials on the AO basis
END_DOC
BEGIN_SHELL [ /usr/bin/env python2 ]
BEGIN_SHELL [ /usr/bin/env python3 ]
import os
import glob
from qp_path import QP_SRC
@ -15,33 +15,33 @@ functionals = map(lambda x : x.replace(".irp.f",""), glob.glob("*.irp.f"))
prefix = ""
for f in functionals:
print """
print("""
%sif (trim(exchange_functional) == '%s') then
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 "
print """
print("""
else
print*, 'exchange functional required does not exist ...'
print*,'exchange_functional ',exchange_functional
stop"""
print "endif"
stop""")
print("endif")
END_SHELL
END_PROVIDER
BEGIN_PROVIDER [double precision, potential_c_alpha_ao,(ao_num,ao_num,N_states)]
&BEGIN_PROVIDER [double precision, potential_c_beta_ao,(ao_num,ao_num,N_states)]
implicit none
BEGIN_DOC
! general providers for the alpha/beta correlation potentials on the AO basis
END_DOC
BEGIN_SHELL [ /usr/bin/env python2 ]
BEGIN_SHELL [ /usr/bin/env python3 ]
import os
import glob
from qp_path import QP_SRC
@ -51,27 +51,27 @@ functionals = map(lambda x : x.replace(".irp.f",""), glob.glob("*.irp.f"))
prefix = ""
for f in functionals:
print """
print("""
%sif (trim(correlation_functional) == '%s') then
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 "
print """
print("""
else
print*, 'Correlation functional required does not exist ...'
print*,'correlation_functional ',correlation_functional
stop"""
print "endif"
stop""" )
print("endif")
END_SHELL
END_PROVIDER
BEGIN_PROVIDER [double precision, potential_x_alpha_mo,(mo_num,mo_num,N_states)]
&BEGIN_PROVIDER [double precision, potential_x_beta_mo ,(mo_num,mo_num,N_states)]
implicit none
@ -86,7 +86,7 @@ print "endif"
potential_x_alpha_mo(1,1,istate), &
size(potential_x_alpha_mo,1) &
)
call ao_to_mo( &
potential_x_beta_ao(1,1,istate), &
size(potential_x_beta_ao,1), &
@ -94,9 +94,9 @@ print "endif"
size(potential_x_beta_mo,1) &
)
enddo
END_PROVIDER
BEGIN_PROVIDER [double precision, potential_c_alpha_mo,(mo_num,mo_num,N_states)]
&BEGIN_PROVIDER [double precision, potential_c_beta_mo, (mo_num,mo_num,N_states)]
implicit none
@ -111,7 +111,7 @@ print "endif"
potential_c_alpha_mo(1,1,istate), &
size(potential_c_alpha_mo,1) &
)
call ao_to_mo( &
potential_c_beta_ao(1,1,istate), &
size(potential_c_beta_ao,1), &
@ -119,7 +119,7 @@ print "endif"
size(potential_c_beta_mo,1) &
)
enddo
END_PROVIDER
@ -147,9 +147,9 @@ print "endif"
enddo
Trace_v_Hxc(istate) = Trace_v_xc(istate) + Trace_v_H(istate)
enddo
END_PROVIDER
BEGIN_PROVIDER [double precision, Trace_v_xc_new, (N_states)]
implicit none
integer :: i,j,istate
@ -166,14 +166,14 @@ print "endif"
enddo
enddo
enddo
END_PROVIDER
BEGIN_PROVIDER [double precision, potential_xc_alpha_mo,(mo_num,mo_num,N_states)]
&BEGIN_PROVIDER [double precision, potential_xc_beta_mo,(mo_num,mo_num,N_states)]
implicit none
integer :: istate
do istate = 1, N_states
call ao_to_mo( &
potential_xc_alpha_ao(1,1,istate), &
@ -181,7 +181,7 @@ print "endif"
potential_xc_alpha_mo(1,1,istate), &
size(potential_xc_alpha_mo,1) &
)
call ao_to_mo( &
potential_xc_beta_ao(1,1,istate), &
size(potential_xc_beta_ao,1), &
@ -189,18 +189,18 @@ print "endif"
size(potential_xc_beta_mo,1) &
)
enddo
END_PROVIDER
BEGIN_PROVIDER [double precision, potential_xc_alpha_ao,(ao_num,ao_num,N_states)]
&BEGIN_PROVIDER [double precision, potential_xc_beta_ao,(ao_num,ao_num,N_states)]
implicit none
BEGIN_DOC
! general providers for the alpha/beta exchange/correlation potentials on the AO basis
END_DOC
BEGIN_SHELL [ /usr/bin/env python2 ]
BEGIN_SHELL [ /usr/bin/env python3 ]
import os
import glob
from qp_path import QP_SRC
@ -210,19 +210,19 @@ functionals = map(lambda x : x.replace(".irp.f",""), glob.glob("*.irp.f"))
prefix = ""
for f in functionals:
print """
print("""
%sif (trim(exchange_functional) == '%s') then
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 "
print """
print("""
else
print*, 'exchange functional required does not exist ...'
print*,'exchange_functional ',exchange_functional
stop"""
print "endif"
stop""")
print("endif")
END_SHELL
END_PROVIDER

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
import os
@ -8,6 +8,6 @@ template = file.read()
file.close()
for p in perturbations:
print template.replace("$PERT",p)
print(template.replace("$PERT",p))
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
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 :: liwork, lwork, n, info
integer, allocatable :: iwork(:)
double precision, allocatable :: work(:), F(:,:), S(:,:)
double precision, allocatable :: work(:), F(:,:), F_save(:,:)
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) )
do j=1,mo_num
@ -51,6 +51,7 @@ BEGIN_PROVIDER [ double precision, eigenvectors_Fock_matrix_mo, (ao_num,mo_num)
lwork = -1
liwork = -1
F_save = F
call dsyevd( 'V', 'U', mo_num, F, &
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
F = F_save
call dsyev( 'V', 'L', mo_num, F, &
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, &
mo_coef, size(mo_coef,1), F, size(F,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

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

@ -299,6 +299,7 @@ END_DOC
Fock_matrix_AO_(i,j) = 0.d0
enddo
do k=1,dim_DIIS
if (dabs(X_vector_DIIS(k)) < 1.d-10) cycle
do i=1,ao_num
Fock_matrix_AO_(i,j) = Fock_matrix_AO_(i,j) + &
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
include 'f77_zmq.h'
include 'f77_zmq_free.h'
end module

8
tests/bats_to_sh.py
View File

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