Merge branch 'dev' of github.com:QuantumPackage/qp2 into dev

INSTALL.rst

@@ -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) 
+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|. 
+source the :file:`quantum_package.rc` in order to load all environment variables and compile the |QP|.
 
 
 Requirements
@@ -36,7 +36,7 @@ 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|
@@ -44,7 +44,7 @@ Requirements
 - `GNU Patch`_
 - |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
@@ -74,29 +74,29 @@ Help for installing external dependencies
 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:`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 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 
+* ninja
-* irpf90 
+* irpf90
-* zeromq 
+* zeromq
 * f77zmq
 * gmp
 * libcap
 * bwrap
 * ocaml  ( :math:`\approx` 10 minutes)
-* ezfio 
+* ezfio
-* docopt 
+* docopt
-* resultsFile 
+* resultsFile
 * bats
 
-Example: 
+Example:
 
 .. code:: bash
 
@@ -115,7 +115,7 @@ 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|.
 
 
@@ -140,7 +140,7 @@ IRPF90
 ------
 
 *IRPF90* is a Fortran code generator for programming using the Implicit Reference
-to Parameters (IRP) method. 
+to Parameters (IRP) method.
 
 * Download the latest version of IRPF90
   here : `<https://gitlab.com/scemama/irpf90/-/archive/v1.7.2/irpf90-v1.7.2.tar.gz>`_ and move
@@ -312,26 +312,26 @@ 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
 
@@ -370,11 +370,11 @@ 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
 
-   pip2 install --user docopt
+   python3 -m pip install --user docopt
 
 Otherwise,
 

bin/qp_basis

@@ -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

bin/qp_convert_output_to_ezfio

@@ -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_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)
         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)
+    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
 
     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).""")
 

bin/qp_name

@@ -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("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"]
         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)
 
 
 

bin/qp_plugins

@@ -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("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):
@@ -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("Created plugin:")
-        print path, '\n'
+        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("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)
-        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("    [ OK ]")
-        print ""
+        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("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:
                 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("Removing plugins:")
-        print l_name_to_remove
+        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)

bin/qp_reset

@@ -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

bin/qp_set_frozen_core

@@ -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:

bin/qp_set_frozen_large_core

@@ -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:

bin/qp_test

@@ -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("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)
 
 
@@ -54,11 +54,11 @@ def main(arguments):
     os.chdir(QP_TESTS)
 
     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"]:
             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:

config/ifort_avx.cfg

@@ -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
 #################

config/ifort_avx_mpi.cfg

@@ -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

config/ifort_debug.cfg

@@ -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

config/ifort_epyc.cfg

@@ -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
-

config/ifort_mpi.cfg

@@ -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

configure

@@ -1,4 +1,4 @@
-#!/bin/bash 
+#!/bin/bash
 #
 # Quantum Package configuration script
 #
@@ -15,20 +15,20 @@ unset CCXX
 export CC=gcc
 
 
-# When updating version, update also etc files
+# /!\ When updating version, update also etc files
 
+EZFIO_TGZ="EZFIO.2.0.2.tar.gz"
 BATS_URL="https://github.com/bats-core/bats-core/archive/v1.1.0.tar.gz"
 BUBBLE_URL="https://github.com/projectatomic/bubblewrap/releases/download/v0.3.3/bubblewrap-0.3.3.tar.xz"
 DOCOPT_URL="https://github.com/docopt/docopt/archive/0.6.2.tar.gz"
 BSE_URL="https://github.com/MolSSI-BSE/basis_set_exchange/archive/v0.8.11.tar.gz"
-EZFIO_URL="https://gitlab.com/scemama/EZFIO/-/archive/v1.6.1/EZFIO-v1.6.1.tar.gz"
 F77ZMQ_URL="https://github.com/scemama/f77_zmq/archive/v4.2.5.tar.gz"
 GMP_URL="ftp://ftp.gnu.org/gnu/gmp/gmp-6.1.2.tar.bz2"
-IRPF90_URL="https://gitlab.com/scemama/irpf90/-/archive/v1.7.6/irpf90-v1.7.6.tar.gz"
+IRPF90_URL="https://gitlab.com/scemama/irpf90/-/archive/v2.0.0/irpf90-v2.0.0.tar.gz"
 LIBCAP_URL="https://git.kernel.org/pub/scm/linux/kernel/git/morgan/libcap.git/snapshot/libcap-2.25.tar.gz"
 NINJA_URL="https://github.com/ninja-build/ninja/releases/download/v1.8.2/ninja-linux.zip"
 OCAML_URL="https://raw.githubusercontent.com/ocaml/opam/master/shell/install.sh"
-RESULTS_URL="https://gitlab.com/scemama/resultsFile/-/archive/v1.0/resultsFile-v1.0.tar.gz"
+RESULTS_URL="https://gitlab.com/scemama/resultsFile/-/archive/v2.0/resultsFile-v2.0.tar.gz"
 ZEROMQ_URL="https://github.com/zeromq/libzmq/releases/download/v4.2.5/zeromq-4.2.5.tar.gz"
 ZLIB_URL="https://www.zlib.net/zlib-1.2.11.tar.gz"
 
@@ -45,7 +45,7 @@ Usage:
 
 Options:
   -c, --config=<file>      Define a COMPILATION configuration file,
-                           in "${QP_ROOT}/config/". 
+                           in "${QP_ROOT}/config/".
   -h, --help               Print the HELP message
   -i, --install=<package>  INSTALL <package>. Use at your OWN RISK:
                            no support will be provided for the installation of
@@ -73,7 +73,7 @@ function execute () {
     while read -r line; do
       echo "  " $line
       _command+="${line} ;"
-    done 
+    done
     sleep 1
     echo ""
     printf "\e[0;94m"
@@ -87,7 +87,7 @@ OCAML_PACKAGES="ocamlbuild cryptokit zmq sexplib ppx_sexp_conv ppx_deriving geto
 
 while true ; do
     case "$1" in
-        -c|--config) 
+        -c|--config)
             case "$2" in
                 "") help ; break;;
                 *) if [[ -f $2 ]] ; then
@@ -96,15 +96,15 @@ while true ; do
                       error "error: configuration file $2 not found."
                       exit 1
                    fi
-            esac 
+            esac
             shift 2;;
         -i|--install)
             case "$2" in
                 "") help ; break;;
                 *) PACKAGES="${PACKAGE} $2"
-            esac 
+            esac
             shift 2;;
-        -h|-help|--help) 
+        -h|-help|--help)
             help
             exit 0;;
         --) shift ; break ;;
@@ -154,7 +154,7 @@ function find_exe() {
 }
 
 function find_python_lib() {
-        python2 -c "import $1" &> /dev/null && echo "$1" || not_found
+        python3 -c "import $1" &> /dev/null && echo "$1" || not_found
 }
 
 function find_lib() {
@@ -178,6 +178,19 @@ function find_dir() {
 }
 
 
+# Extract EZFIO if needed
+EZFIO=$(find_dir "${QP_ROOT}"/external/ezfio)
+if [[ ${EZFIO} = $(not_found) ]] ; then
+            execute << EOF
+              cd "\${QP_ROOT}"/external
+              tar --gunzip --extract --file ${EZFIO_TGZ}
+              rm -rf ezfio
+              mv EZFIO ezfio
+EOF
+fi
+
+
+
 if [[ "${PACKAGES}.x" != ".x" ]] ; then
         printf "\e[0;31m"
         echo ""
@@ -224,7 +237,7 @@ EOF
               ./configure --prefix=$QP_ROOT && make -j 8
               make install
 EOF
-    
+
     elif [[ ${PACKAGE} = libcap ]] ; then
 
             download ${LIBCAP_URL} "${QP_ROOT}"/external/libcap.tar.gz
@@ -259,12 +272,14 @@ EOF
               cd irpf90-*
               make
 EOF
-    
+
 
     elif [[ ${PACKAGE} = zeromq ]] ; then
 
             download ${ZEROMQ_URL} "${QP_ROOT}"/external/zeromq.tar.gz
             execute << EOF
+              export CC=gcc
+              export CXX=g++
               cd "\${QP_ROOT}"/external
               tar --gunzip --extract --file zeromq.tar.gz
               rm zeromq.tar.gz
@@ -290,7 +305,7 @@ EOF
               cp f77_zmq_free.h "\${QP_ROOT}"/include
 EOF
 
-    
+
     elif [[ ${PACKAGE} = ocaml ]] ; then
 
             download ${OCAML_URL} "${QP_ROOT}"/external/opam_installer.sh
@@ -303,7 +318,7 @@ EOF
                         rm -rf ${HOME}/.opam
                 fi
                 export OPAMROOT=${HOME}/.opam
-                cat << EOF | bash ${QP_ROOT}/external/opam_installer.sh --no-backup 
+                cat << EOF | bash ${QP_ROOT}/external/opam_installer.sh --no-backup
 ${QP_ROOT}/bin
 
 
@@ -313,8 +328,8 @@ EOF
                 rm ${QP_ROOT}/external/opam_installer.sh
 #                source ${OPAMROOT}/opam-init/init.sh > /dev/null 2> /dev/null || true
 #
-#                opam switch create ocaml-base-compiler.4.07.1
+#                opam switch create ocaml-base-compiler.4.10.0
-                opam init --verbose --yes --compiler=4.07.1 --disable-sandboxing
+                opam init --verbose --yes --compiler=4.10.0 --disable-sandboxing
 
                 eval $(opam env)
                 opam install -y ${OCAML_PACKAGES}  || exit 1
@@ -323,37 +338,25 @@ EOF
                 # Conventional commands
                 execute << EOF
                   chmod +x "${QP_ROOT}"/external/opam_installer.sh
-                  "${QP_ROOT}"/external/opam_installer.sh --no-backup 
+                  "${QP_ROOT}"/external/opam_installer.sh --no-backup
 EOF
                 execute << EOF
                   rm --force ${QP_ROOT}/bin/opam
                   export OPAMROOT=${OPAMROOT:-${QP_ROOT}/external/opam}
                   echo ${QP_ROOT}/bin \
-                  | sh ${QP_ROOT}/external/opam_installer.sh 
+                  | sh ${QP_ROOT}/external/opam_installer.sh
 EOF
                 rm ${QP_ROOT}/external/opam_installer.sh
 #                source ${OPAMROOT}/opam-init/init.sh > /dev/null 2> /dev/null || true
-#                opam switch create ocaml-base-compiler.4.07.1     || exit 1
+#                opam switch create ocaml-base-compiler.4.10.0     || exit 1
 
-                opam init --verbose --yes --compiler=4.07.1 --disable-sandboxing
+                opam init --verbose --yes --compiler=4.10.0 --disable-sandboxing
                 eval $(opam env)
                 execute << EOF
                   opam install -y \${OCAML_PACKAGES}  || exit 1
 EOF
             fi
 
-            
-    elif [[ ${PACKAGE} = ezfio ]] ; then
-
-            download ${EZFIO_URL} "${QP_ROOT}"/external/ezfio.tar.gz
-            execute << EOF
-              cd "\${QP_ROOT}"/external
-              tar --gunzip --extract --file ezfio.tar.gz
-              rm -f ezfio.tar.gz
-              rm -rf ezfio
-              mv EZFIO-* ezfio
-EOF
-
 
     elif [[ ${PACKAGE} = bse ]] ; then
 
@@ -375,13 +378,13 @@ EOF
               make && make install
 EOF
 
-            
+
     elif [[ ${PACKAGE} = docopt ]] ; then
 
             download ${DOCOPT_URL} "${QP_ROOT}"/external/docopt.tar.gz
             execute << EOF
               cd "\${QP_ROOT}"/external
-              tar --gunzip --extract --file docopt.tar.gz 
+              tar --gunzip --extract --file docopt.tar.gz
               mv docopt-*/docopt.py "\${QP_ROOT}/external/Python"
               rm --recursive --force -- docopt-*/ docopt.tar.gz
 EOF
@@ -392,7 +395,7 @@ EOF
             download ${RESULTS_URL} "${QP_ROOT}"/external/resultsFile.tar.gz
             execute << EOF
               cd "\${QP_ROOT}"/external
-              tar --gunzip --extract --file resultsFile.tar.gz 
+              tar --gunzip --extract --file resultsFile.tar.gz
               mv resultsFile-*/resultsFile "\${QP_ROOT}/external/Python/"
               rm --recursive --force resultsFile-* resultsFile.tar.gz
 EOF
@@ -402,7 +405,7 @@ EOF
             download ${BATS_URL} "${QP_ROOT}"/external/bats.tar.gz
             execute << EOF
               cd "\${QP_ROOT}"/external
-              tar -zxf bats.tar.gz 
+              tar -zxf bats.tar.gz
               ( cd bats-core-1.1.0/ ; ./install.sh \${QP_ROOT})
               rm --recursive --force -- bats-core-1.1.0 \  "\${QP_ROOT}"/external/bats.tar.gz
 EOF
@@ -468,12 +471,6 @@ if [[ ${OCAML} = $(not_found) ]] ; then
         fail
 fi
 
-EZFIO=$(find_dir "${QP_ROOT}"/external/ezfio)
-if [[ ${EZFIO} = $(not_found) ]] ; then
-        error "EZFIO (ezfio) is not installed."
-        fail
-fi
-
 ZLIB=$(find_lib -lz)
 if [[ ${ZLIB} = $(not_found) ]] ; then
         error "Zlib (zlib) is not installed."
@@ -520,15 +517,15 @@ fi
 
 if [[ -f ${QP_ROOT}/build.ninja ]] ; then
   [[ -z ${TRAVIS} ]] && echo "You can now run ./bin/qpsh to enter in the QP shell mode :)"
-else 
+else
       echo ""
       echo "${QP_ROOT}/build.ninja does not exist,"
       echo "you need to specify the COMPILATION configuration file."
-      echo "See  ./configure --help  for more details." 
+      echo "See  ./configure --help  for more details."
       echo ""
 fi
 
 exit 0
-    
+
 
 

docs/Makefile

@@ -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).

docs/source/auto_generate.py

@@ -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():

etc/irpf90.rc

@@ -1,7 +1,7 @@
 # Configuration of IRPF90 package
 
 # Set the path of IRPF90 here:
-export IRPF90_PATH=${QP_ROOT}/external/irpf90-v1.7.6
+export IRPF90_PATH=${QP_ROOT}/external/irpf90-v2.0.0
 export PATH=${PATH}:${IRPF90_PATH}/bin
 
 export IRPF90=${IRPF90_PATH}/bin/irpf90
@@ -10,10 +10,10 @@ 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"
-  
+
 

etc/paths.rc

@@ -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)
 
 

external/Python/.gitignore

@@ -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/

ocaml/qp_tunnel.ml

@@ -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

ocaml/qptypes_generator.ml

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

scripts/compilation/cache_compile.py

@@ -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)')
+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)
 
 tmpdir_root = os.environ.get("TMPDIR", failobj="/dev/shm")

scripts/compilation/qp_create_ninja

@@ -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,
+        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 += [""]
@@ -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,
+        l_string += ["build {0}: build_ezfio_config {1}".format(*list(map(comp_path,(file_create,
-                                                                file_source)))]
+                                                                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_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:
         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())
 
 
     # ~#~#~#~#~#~#~#~#~#~#~#~ #

scripts/compilation/read_compilation_cfg.py

@@ -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, "FC"))
-    print get_compilation_option(pwd_cfg, "FCFLAGS")
+    print(get_compilation_option(pwd_cfg, "FCFLAGS"))

scripts/ezfio_interface/ei_handler.py

@@ -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 = 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 #
@@ -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("{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)
         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"]:

scripts/ezfio_interface/ezfio_generate_ocaml.py

@@ -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))

scripts/ezfio_interface/ezfio_generate_provider.py

@@ -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()

scripts/generate_h_apply.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python2
+#!/usr/bin/env python3
 
 import os
 
@@ -105,7 +105,6 @@ 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"] = """
@@ -156,7 +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
 

scripts/hello.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python2
+#!/usr/bin/env python3
 
 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")
 
 
 

scripts/module/module_handler.py

@@ -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("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)
 
     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(
+                print("Check NEED for {0}".format(
-                    module_name)
+                    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("{0} is not a valid module. Abort".format(module))
-            print "No NEED in it"
+            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"]:
 

scripts/perturbation.py

@@ -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)

scripts/utility/get_groups

@@ -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("Group\t", group, "\nn\t", n)
-    print "\n     \tIrred     \tOperation"
+    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("%8.5f "%(data[i][j]), end=' ') 
-    print "\n"
+    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)
 

scripts/utility/qp_bitmasks.py

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

scripts/utility/qp_path.py

@@ -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"]

src/cipsi/cipsi.irp.f

@@ -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

src/cipsi/energy.irp.f

@@ -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

src/cipsi/selection.irp.f

@@ -13,7 +13,7 @@ END_PROVIDER
 BEGIN_PROVIDER [ double precision, variance_match_weight, (N_states) ]
  implicit none
  BEGIN_DOC
- ! Weights adjusted along the selection to make the variances 
+ ! Weights adjusted along the selection to make the variances
  ! of each state coincide.
  END_DOC
  variance_match_weight(:) = 1.d0
@@ -46,10 +46,10 @@ subroutine update_pt2_and_variance_weights(pt2, variance, norm, N_st)
     i_iter = 1
   endif
 
-  dt = 4.d0 
+  dt = 4.d0
 
   do k=1,N_st
-    rpt2(k) = pt2(k)/(1.d0 + norm(k))                                                     
+    rpt2(k) = pt2(k)/(1.d0 + norm(k))
   enddo
 
   avg = sum(rpt2(1:N_st)) / dble(N_st)
@@ -90,7 +90,7 @@ BEGIN_PROVIDER [ double precision, selection_weight, (N_states) ]
 
      case (1)
       print *,  'Using 1/c_max^2 weight in selection'
-      selection_weight(1:N_states) = c0_weight(1:N_states) 
+      selection_weight(1:N_states) = c0_weight(1:N_states)
 
      case (2)
       print *,  'Using pt2-matching weight in selection'
@@ -114,7 +114,7 @@ BEGIN_PROVIDER [ double precision, selection_weight, (N_states) ]
       print *, '# var weight ', real(variance_match_weight(:),4)
 
      case (6)
-      print *,  'Using CI coefficient-based selection' 
+      print *,  'Using CI coefficient-based selection'
       selection_weight(1:N_states) = c0_weight(1:N_states)
 
      case (7)
@@ -289,34 +289,34 @@ subroutine select_singles_and_doubles(i_generator,hole_mask,particle_mask,fock_d
 
   monoAdo = .true.
   monoBdo = .true.
-  
+
-  
+
   do k=1,N_int
     hole    (k,1) = iand(psi_det_generators(k,1,i_generator), hole_mask(k,1))
     hole    (k,2) = iand(psi_det_generators(k,2,i_generator), hole_mask(k,2))
     particle(k,1) = iand(not(psi_det_generators(k,1,i_generator)), particle_mask(k,1))
     particle(k,2) = iand(not(psi_det_generators(k,2,i_generator)), particle_mask(k,2))
   enddo
-  
+
-  
+
   integer                        :: N_holes(2), N_particles(2)
   integer                        :: hole_list(N_int*bit_kind_size,2)
   integer                        :: particle_list(N_int*bit_kind_size,2)
-  
+
   call bitstring_to_list_ab(hole    , hole_list    , N_holes    , N_int)
   call bitstring_to_list_ab(particle, particle_list, N_particles, N_int)
-  
+
   integer                        :: l_a, nmax, idx
   integer, allocatable           :: indices(:), exc_degree(:), iorder(:)
   allocate (indices(N_det),                                          &
       exc_degree(max(N_det_alpha_unique,N_det_beta_unique)))
-  
+
   k=1
   do i=1,N_det_alpha_unique
     call get_excitation_degree_spin(psi_det_alpha_unique(1,i),       &
         psi_det_generators(1,1,i_generator), exc_degree(i), N_int)
   enddo
-  
+
   do j=1,N_det_beta_unique
     call get_excitation_degree_spin(psi_det_beta_unique(1,j),        &
         psi_det_generators(1,2,i_generator), nt, N_int)
@@ -332,12 +332,12 @@ subroutine select_singles_and_doubles(i_generator,hole_mask,particle_mask,fock_d
       endif
     enddo
   enddo
-  
+
   do i=1,N_det_beta_unique
     call get_excitation_degree_spin(psi_det_beta_unique(1,i),        &
         psi_det_generators(1,2,i_generator), exc_degree(i), N_int)
   enddo
-  
+
   do j=1,N_det_alpha_unique
     call get_excitation_degree_spin(psi_det_alpha_unique(1,j),       &
         psi_det_generators(1,1,i_generator), nt, N_int)
@@ -356,7 +356,7 @@ subroutine select_singles_and_doubles(i_generator,hole_mask,particle_mask,fock_d
       endif
     enddo
   enddo
-  
+
   deallocate(exc_degree)
   nmax=k-1
 
@@ -366,18 +366,18 @@ subroutine select_singles_and_doubles(i_generator,hole_mask,particle_mask,fock_d
   enddo
   call isort(indices,iorder,nmax)
   deallocate(iorder)
-  
+
   ! Start with 32 elements. Size will double along with the filtering.
   allocate(preinteresting(0:32), prefullinteresting(0:32),     &
       interesting(0:32), fullinteresting(0:32))
   preinteresting(:) = 0
   prefullinteresting(:) = 0
-  
+
   do i=1,N_int
     negMask(i,1) = not(psi_det_generators(i,1,i_generator))
     negMask(i,2) = not(psi_det_generators(i,2,i_generator))
   end do
-  
+
   do k=1,nmax
     i = indices(k)
     mobMask(1,1) = iand(negMask(1,1), psi_det_sorted(1,1,i))
@@ -388,10 +388,10 @@ subroutine select_singles_and_doubles(i_generator,hole_mask,particle_mask,fock_d
       mobMask(j,2) = iand(negMask(j,2), psi_det_sorted(j,2,i))
       nt = nt + popcnt(mobMask(j, 1)) + popcnt(mobMask(j, 2))
     end do
-    
+
     if(nt <= 4) then
       if(i <= N_det_selectors) then
-        sze = preinteresting(0) 
+        sze = preinteresting(0)
         if (sze+1 == size(preinteresting)) then
           allocate (tmp_array(0:sze))
           tmp_array(0:sze) = preinteresting(0:sze)
@@ -403,7 +403,7 @@ subroutine select_singles_and_doubles(i_generator,hole_mask,particle_mask,fock_d
         preinteresting(0) = sze+1
         preinteresting(sze+1) = i
       else if(nt <= 2) then
-        sze = prefullinteresting(0) 
+        sze = prefullinteresting(0)
         if (sze+1 == size(prefullinteresting)) then
           allocate (tmp_array(0:sze))
           tmp_array(0:sze) = prefullinteresting(0:sze)
@@ -422,17 +422,17 @@ subroutine select_singles_and_doubles(i_generator,hole_mask,particle_mask,fock_d
 !  !$OMP CRITICAL
 !  print *,  'Step1: ', i_generator, preinteresting(0)
 !  !$OMP END CRITICAL
-    
+
   allocate(banned(mo_num, mo_num,2), bannedOrb(mo_num, 2))
   allocate (mat(N_states, mo_num, mo_num))
   maskInd = -1
-  
+
   integer                        :: nb_count, maskInd_save
   logical                        :: monoBdo_save
   logical                        :: found
   do s1=1,2
     do i1=N_holes(s1),1,-1   ! Generate low excitations first
-      
+
       found = .False.
       monoBdo_save = monoBdo
       maskInd_save = maskInd
@@ -447,21 +447,21 @@ subroutine select_singles_and_doubles(i_generator,hole_mask,particle_mask,fock_d
         enddo
         if(s1 /= s2) monoBdo = .false.
       enddo
-      
+
       if (.not.found) cycle
       monoBdo = monoBdo_save
       maskInd = maskInd_save
-      
+
       h1 = hole_list(i1,s1)
       call apply_hole(psi_det_generators(1,1,i_generator), s1,h1, pmask, ok, N_int)
-      
+
       negMask = not(pmask)
-      
+
       interesting(0) = 0
       fullinteresting(0) = 0
-      
+
       do ii=1,preinteresting(0)
-        i = preinteresting(ii) 
+        i = preinteresting(ii)
         select case (N_int)
           case (1)
             mobMask(1,1) = iand(negMask(1,1), psi_det_sorted(1,1,i))
@@ -515,9 +515,9 @@ subroutine select_singles_and_doubles(i_generator,hole_mask,particle_mask,fock_d
               endif
             end do
         end select
-        
+
         if(nt <= 4) then
-          sze = interesting(0) 
+          sze = interesting(0)
           if (sze+1 == size(interesting)) then
             allocate (tmp_array(0:sze))
             tmp_array(0:sze) = interesting(0:sze)
@@ -529,7 +529,7 @@ subroutine select_singles_and_doubles(i_generator,hole_mask,particle_mask,fock_d
           interesting(0) = sze+1
           interesting(sze+1) = i
           if(nt <= 2) then
-            sze = fullinteresting(0) 
+            sze = fullinteresting(0)
             if (sze+1 == size(fullinteresting)) then
               allocate (tmp_array(0:sze))
               tmp_array(0:sze) = fullinteresting(0:sze)
@@ -542,9 +542,9 @@ subroutine select_singles_and_doubles(i_generator,hole_mask,particle_mask,fock_d
             fullinteresting(sze+1) = i
           end if
         end if
-        
+
       end do
-      
+
       do ii=1,prefullinteresting(0)
         i = prefullinteresting(ii)
         nt = 0
@@ -560,7 +560,7 @@ subroutine select_singles_and_doubles(i_generator,hole_mask,particle_mask,fock_d
         end do
 
         if(nt <= 2) then
-          sze = fullinteresting(0) 
+          sze = fullinteresting(0)
           if (sze+1 == size(fullinteresting)) then
             allocate (tmp_array(0:sze))
             tmp_array(0:sze) = fullinteresting(0:sze)
@@ -577,7 +577,7 @@ subroutine select_singles_and_doubles(i_generator,hole_mask,particle_mask,fock_d
       allocate (fullminilist (N_int, 2, fullinteresting(0)), &
                     minilist (N_int, 2,     interesting(0)) )
       if(pert_2rdm)then
-        allocate(coef_fullminilist_rev(N_states,fullinteresting(0))) 
+        allocate(coef_fullminilist_rev(N_states,fullinteresting(0)))
         do i=1,fullinteresting(0)
           do j = 1, N_states
             coef_fullminilist_rev(j,i) = psi_coef_sorted(fullinteresting(i),j)
@@ -588,7 +588,7 @@ subroutine select_singles_and_doubles(i_generator,hole_mask,particle_mask,fock_d
       do i=1,fullinteresting(0)
         fullminilist(1:N_int,1:2,i) = psi_det_sorted(1:N_int,1:2,fullinteresting(i))
       enddo
-      
+
       do i=1,interesting(0)
         minilist(1:N_int,1:2,i) = psi_det_sorted(1:N_int,1:2,interesting(i))
       enddo
@@ -624,21 +624,21 @@ subroutine select_singles_and_doubles(i_generator,hole_mask,particle_mask,fock_d
               monoAdo = .false.
             end if
           end if
-          
+
           maskInd = maskInd + 1
           if(mod(maskInd, csubset) == (subset-1)) then
-            
+
             call spot_isinwf(mask, fullminilist, i_generator, fullinteresting(0), banned, fullMatch, fullinteresting)
             if(fullMatch) cycle
 ! !$OMP CRITICAL
 !  print *,  'Step3: ', i_generator, h1, interesting(0)
 ! !$OMP END CRITICAL
-            
+
             call splash_pq(mask, sp, minilist, i_generator, interesting(0), bannedOrb, banned, mat, interesting)
-            
+
             if(.not.pert_2rdm)then
              call fill_buffer_double(i_generator, sp, h1, h2, bannedOrb, banned, fock_diag_tmp, E0, pt2, variance, norm, mat, buf)
-            else 
+            else
              call fill_buffer_double_rdm(i_generator, sp, h1, h2, bannedOrb, banned, fock_diag_tmp, E0, pt2, variance, norm, mat, buf,fullminilist, coef_fullminilist_rev, fullinteresting(0))
             endif
           end if
@@ -682,7 +682,7 @@ subroutine fill_buffer_double(i_generator, sp, h1, h2, bannedOrb, banned, fock_d
   double precision, allocatable :: values(:)
   integer, allocatable          :: keys(:,:)
   integer                       :: nkeys
-  
+
 
   if(sp == 3) then
     s1 = 1
@@ -712,7 +712,7 @@ subroutine fill_buffer_double(i_generator, sp, h1, h2, bannedOrb, banned, fock_d
 ! to a determinant of the future. In that case, the determinant will be
 ! detected as already generated when generating in the future with a
 ! double excitation.
-!     
+!
 !      if (.not.do_singles) then
 !        if ((h1 == p1) .or. (h2 == p2)) then
 !          cycle
@@ -783,6 +783,8 @@ subroutine fill_buffer_double(i_generator, sp, h1, h2, bannedOrb, banned, fock_d
         norm(istate) = norm(istate) + coef * coef
 
 !!!DEBUG
+!        pt2(istate) = pt2(istate) - e_pert + alpha_h_psi**2/delta_E
+!
 !        integer :: k
 !        double precision :: alpha_h_psi_2,hij
 !        alpha_h_psi_2 = 0.d0
@@ -792,7 +794,7 @@ subroutine fill_buffer_double(i_generator, sp, h1, h2, bannedOrb, banned, fock_d
 !        enddo
 !        if(dabs(alpha_h_psi_2 - alpha_h_psi).gt.1.d-12)then
 !         call debug_det(psi_det_generators(1,1,i_generator),N_int)
-!         call debug_det(det,N_int)                                                                                        
+!         call debug_det(det,N_int)
 !         print*,'alpha_h_psi,alpha_h_psi_2 = ',alpha_h_psi,alpha_h_psi_2
 !         stop
 !        endif
@@ -816,7 +818,7 @@ subroutine fill_buffer_double(i_generator, sp, h1, h2, bannedOrb, banned, fock_d
 
 
       if(pseudo_sym)then
-        if(dabs(mat(1, p1, p2)).lt.thresh_sym)then 
+        if(dabs(mat(1, p1, p2)).lt.thresh_sym)then
           w = 0.d0
         endif
       endif
@@ -857,7 +859,7 @@ subroutine splash_pq(mask, sp, det, i_gen, N_sel, bannedOrb, banned, mat, intere
     negMask(i,2) = not(mask(i,2))
   end do
 
-  do i=1, N_sel 
+  do i=1, N_sel
     if (interesting(i) < 0) then
       stop 'prefetch interesting(i) and det(i)'
     endif
@@ -1210,7 +1212,7 @@ subroutine get_d1(gen, phasemask, bannedOrb, banned, mat, mask, h, p, sp, coefs)
         endif
       end if
 !    enddo
-!      
+!
       putj = p2
 !    do puti=1,mo_num !HOT
       if(.not. banned(putj,puti,bant)) then
@@ -1573,15 +1575,15 @@ subroutine get_d0_reference(gen, phasemask, bannedOrb, banned, mat, mask, h, p,
   double precision, intent(in) :: coefs(N_states)
   double precision, intent(inout) :: mat(N_states, mo_num, mo_num)
   integer, intent(in) :: h(0:2,2), p(0:4,2), sp
-  
+
   integer :: i, j, s, h1, h2, p1, p2, puti, putj
   double precision :: hij, phase
   double precision, external :: get_phase_bi, mo_two_e_integral
   logical :: ok
-  
+
   integer :: bant
   bant = 1
-  
+
 
   if(sp == 3) then ! AB
     h1 = p(1,1)
@@ -1619,7 +1621,7 @@ subroutine get_d0_reference(gen, phasemask, bannedOrb, banned, mat, mask, h, p,
       end do
     end do
   end if
-end 
+end
 
 subroutine get_d1_reference(gen, phasemask, bannedOrb, banned, mat, mask, h, p, sp, coefs)
   use bitmasks
@@ -1639,27 +1641,27 @@ subroutine get_d1_reference(gen, phasemask, bannedOrb, banned, mat, mask, h, p,
   logical, allocatable           :: lbanned(:,:)
   integer                        :: puti, putj, ma, mi, s1, s2, i, i1, i2, j
   integer                        :: hfix, pfix, h1, h2, p1, p2, ib
-  
+
   integer, parameter             :: turn2(2) = (/2,1/)
   integer, parameter             :: turn3(2,3) = reshape((/2,3,  1,3, 1,2/), (/2,3/))
-  
+
   integer                        :: bant
-  
+
-  
+
   allocate (lbanned(mo_num, 2))
   lbanned = bannedOrb
-    
+
   do i=1, p(0,1)
     lbanned(p(i,1), 1) = .true.
   end do
   do i=1, p(0,2)
     lbanned(p(i,2), 2) = .true.
   end do
-  
+
   ma = 1
   if(p(0,2) >= 2) ma = 2
   mi = turn2(ma)
-  
+
   bant = 1
 
   if(sp == 3) then
@@ -1682,7 +1684,7 @@ subroutine get_d1_reference(gen, phasemask, bannedOrb, banned, mat, mask, h, p,
         tmp_row(1:N_states,putj) += hij * coefs(1:N_states)
       end do
 
-      if(ma == 1) then           
+      if(ma == 1) then
         mat(1:N_states,1:mo_num,puti) += tmp_row(1:N_states,1:mo_num)
       else
         mat(1:N_states,puti,1:mo_num) += tmp_row(1:N_states,1:mo_num)
@@ -1701,14 +1703,14 @@ subroutine get_d1_reference(gen, phasemask, bannedOrb, banned, mat, mask, h, p,
         hij = mo_two_e_integral(p2,pfix,hfix,puti) * get_phase_bi(phasemask, ma, mi, hfix, p2, puti, pfix, N_int)
         tmp_row(:,puti) += hij * coefs(:)
       end if
-      
+
       putj = p2
       if(.not. banned(putj,puti,bant)) then
         hij = mo_two_e_integral(p1,pfix,hfix,puti) * get_phase_bi(phasemask, ma, mi, hfix, p1, puti, pfix, N_int)
         tmp_row2(:,puti) += hij * coefs(:)
       end if
     end do
-    
+
     if(mi == 1) then
       mat(:,:,p1) += tmp_row(:,:)
       mat(:,:,p2) += tmp_row2(:,:)
@@ -1752,7 +1754,7 @@ subroutine get_d1_reference(gen, phasemask, bannedOrb, banned, mat, mask, h, p,
           hij = mo_two_e_integral(pfix, p1, hfix, puti) * get_phase_bi(phasemask, mi, ma, hfix, pfix, puti, p1, N_int)
           tmp_row(:,puti) += hij * coefs(:)
         end if
-        
+
         putj = p1
         if(.not. banned(puti,putj,1)) then
           hij = mo_two_e_integral(pfix, p2, hfix, puti) * get_phase_bi(phasemask, mi, ma, hfix, pfix, puti, p2, N_int)
@@ -1788,7 +1790,7 @@ subroutine get_d1_reference(gen, phasemask, bannedOrb, banned, mat, mask, h, p,
         mat(:, p1, p2) += coefs(:) * hij
       end do
     end do
-end 
+end
 
 subroutine get_d2_reference(gen, phasemask, bannedOrb, banned, mat, mask, h, p, sp, coefs)
   use bitmasks
@@ -1800,30 +1802,30 @@ subroutine get_d2_reference(gen, phasemask, bannedOrb, banned, mat, mask, h, p,
   double precision, intent(in) :: coefs(N_states)
   double precision, intent(inout) :: mat(N_states, mo_num, mo_num)
   integer, intent(in) :: h(0:2,2), p(0:4,2), sp
-  
+
   double precision, external :: get_phase_bi, mo_two_e_integral
-  
+
   integer :: i, j, tip, ma, mi, puti, putj
   integer :: h1, h2, p1, p2, i1, i2
   double precision :: hij, phase
-  
+
   integer, parameter:: turn2d(2,3,4) = reshape((/0,0, 0,0, 0,0,  3,4, 0,0, 0,0,  2,4, 1,4, 0,0,  2,3, 1,3, 1,2 /), (/2,3,4/))
   integer, parameter :: turn2(2) = (/2, 1/)
   integer, parameter :: turn3(2,3) = reshape((/2,3,  1,3, 1,2/), (/2,3/))
-  
+
   integer :: bant
   bant = 1
 
   tip = p(0,1) * p(0,2)
-  
+
   ma = sp
   if(p(0,1) > p(0,2)) ma = 1
   if(p(0,1) < p(0,2)) ma = 2
   mi = mod(ma, 2) + 1
-  
+
   if(sp == 3) then
     if(ma == 2) bant = 2
-    
+
     if(tip == 3) then
       puti = p(1, mi)
       do i = 1, 3
@@ -1835,7 +1837,7 @@ subroutine get_d2_reference(gen, phasemask, bannedOrb, banned, mat, mask, h, p,
         p2 = p(i2, ma)
         h1 = h(1, ma)
         h2 = h(2, ma)
-        
+
         hij = (mo_two_e_integral(p1, p2, h1, h2) - mo_two_e_integral(p2,p1, h1, h2)) * get_phase_bi(phasemask, ma, ma, h1, p1, h2, p2, N_int)
         if(ma == 1) then
           mat(:, putj, puti) += coefs(:) * hij
@@ -1851,10 +1853,10 @@ subroutine get_d2_reference(gen, phasemask, bannedOrb, banned, mat, mask, h, p,
         p2 = p(turn2(j), 2)
         do i = 1,2
           puti = p(i, 1)
-          
+
           if(banned(puti,putj,bant)) cycle
           p1 = p(turn2(i), 1)
-          
+
           hij = mo_two_e_integral(p1, p2, h1, h2) * get_phase_bi(phasemask, 1, 2, h1, p1, h2, p2,N_int)
           mat(:, puti, putj) += coefs(:) * hij
         end do
@@ -1870,7 +1872,7 @@ subroutine get_d2_reference(gen, phasemask, bannedOrb, banned, mat, mask, h, p,
       do j=i+1,4
         putj = p(j, ma)
         if(banned(puti,putj,1)) cycle
-        
+
         i1 = turn2d(1, i, j)
         i2 = turn2d(2, i, j)
         p1 = p(i1, ma)
@@ -1888,7 +1890,7 @@ subroutine get_d2_reference(gen, phasemask, bannedOrb, banned, mat, mask, h, p,
         putj = p(turn3(2,i), ma)
         if(banned(puti,putj,1)) cycle
         p2 = p(i, ma)
-        
+
         hij = mo_two_e_integral(p1, p2, h1, h2) * get_phase_bi(phasemask, mi, ma, h1, p1, h2, p2,N_int)
         mat(:, min(puti, putj), max(puti, putj)) += coefs(:) * hij
       end do
@@ -1905,6 +1907,6 @@ subroutine get_d2_reference(gen, phasemask, bannedOrb, banned, mat, mask, h, p,
       end if
     end if
   end if
-end 
+end
 
 

src/cis/20.cis.bats

@@ -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

src/cis/h_apply.irp.f

@@ -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
 

src/cisd/h_apply.irp.f

@@ -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
 

src/davidson/diagonalize_ci.irp.f

@@ -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
+         do j=1,N_det
-            ! Select at least n_states states with S^2 values closed to "expected_s2"
+           ! 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
+           if(dabs(s2_eigvalues(j)-expected_s2).le.0.5d0)then
-              i_state +=1
+             i_state +=1
-              index_good_state_array(i_state) = j
+             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
              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,&
+       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
        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)

src/density_for_dft/EZFIO.cfg

@@ -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: 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
 default: full_density
 
 [normalize_dm]
 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
 default: True

src/determinants/EZFIO.cfg

@@ -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

src/determinants/h_apply.irp.f

@@ -342,139 +342,3 @@ subroutine fill_H_apply_buffer_no_selection(n_selected,det_buffer,Nint,iproc)
   call omp_unset_lock(H_apply_buffer_lock(1,iproc))
 end
 
-subroutine push_pt2(zmq_socket_push,pt2,norm_pert,H_pert_diag,i_generator,N_st,task_id)
-  use f77_zmq
-  implicit none
-  BEGIN_DOC
-! Push |PT2| calculation to the collector
-  END_DOC
-  integer(ZMQ_PTR), intent(in)   :: zmq_socket_push
-  integer, intent(in)            :: N_st, i_generator
-  double precision, intent(in)   :: pt2(N_st), norm_pert(N_st), H_pert_diag(N_st)
-  integer, intent(in)            :: task_id
-  integer :: rc
-
-  rc = f77_zmq_send( zmq_socket_push, 1, 4, ZMQ_SNDMORE)
-  if (rc /= 4) then
-    print *, irp_here,  'f77_zmq_send( zmq_socket_push, 1, 4, ZMQ_SNDMORE)'
-    stop 'error'
-  endif
-
-  rc = f77_zmq_send( zmq_socket_push, pt2, 8*N_st, ZMQ_SNDMORE)
-  if (rc /= 8*N_st) then
-    print *, irp_here,  'f77_zmq_send( zmq_socket_push, pt2, 8*N_st, ZMQ_SNDMORE)'
-    stop 'error'
-  endif
-
-  rc = f77_zmq_send( zmq_socket_push, norm_pert, 8*N_st, ZMQ_SNDMORE)
-  if (rc /= 8*N_st) then
-    print *, irp_here,  'f77_zmq_send( zmq_socket_push, norm_pert, 8*N_st, ZMQ_SNDMORE)'
-    stop 'error'
-  endif
-
-  rc = f77_zmq_send( zmq_socket_push, H_pert_diag, 8*N_st, ZMQ_SNDMORE)
-  if (rc /= 8*N_st) then
-    print *, irp_here,  'f77_zmq_send( zmq_socket_push, H_pert_diag, 8*N_st, ZMQ_SNDMORE)'
-    stop 'error'
-  endif
-
-  rc = f77_zmq_send( zmq_socket_push, i_generator, 4, ZMQ_SNDMORE)
-  if (rc /= 4) then
-    print *, irp_here,  'f77_zmq_send( zmq_socket_push, i_generator, 4, 0)'
-    stop 'error'
-  endif
-
-  rc = f77_zmq_send( zmq_socket_push, task_id, 4, 0)
-  if (rc /= 4) then
-    print *, irp_here,  'f77_zmq_send( zmq_socket_push, task_id, 4, 0)'
-    stop 'error'
-  endif
-
-! Activate if zmq_socket_push is a REQ
-IRP_IF ZMQ_PUSH
-IRP_ELSE
-  integer :: idummy
-  rc = f77_zmq_recv( zmq_socket_push, idummy, 4, 0)
-  if (rc /= 4) then
-    print *, irp_here, 'f77_zmq_send( zmq_socket_push, idummy, 4, 0)'
-    stop 'error'
-  endif
-IRP_ENDIF
-
-end
-
-subroutine pull_pt2(zmq_socket_pull,pt2,norm_pert,H_pert_diag,i_generator,N_st,n,task_id)
-  use f77_zmq
-  implicit none
-  BEGIN_DOC
-! Pull |PT2| calculation in the collector
-  END_DOC
-  integer(ZMQ_PTR), intent(in)   :: zmq_socket_pull
-  integer, intent(in)            :: N_st
-  double precision, intent(out)  :: pt2(N_st), norm_pert(N_st), H_pert_diag(N_st)
-  integer, intent(out)           :: task_id
-  integer, intent(out)           :: n, i_generator
-  integer                        :: rc
-
-  n=0
-  rc = f77_zmq_recv( zmq_socket_pull, n, 4, 0)
-  if (rc == -1) then
-    n=9
-    return
-  endif
-  if (rc /= 4) then
-    print *, irp_here,  'f77_zmq_recv( zmq_socket_pull, n, 4, 0)'
-    stop 'error'
-  endif
-
-  if (n > 0) then
-
-    rc = f77_zmq_recv( zmq_socket_pull, pt2(1), 8*N_st, 0)
-    if (rc /= 8*N_st) then
-      print *,  ''
-      print *,  ''
-      print *,  ''
-      print *, irp_here,  'f77_zmq_recv( zmq_socket_pull, pt2(1) , 8*N_st, 0)'
-      print *,  rc
-      stop 'error'
-    endif
-
-    rc = f77_zmq_recv( zmq_socket_pull, norm_pert(1), 8*N_st, 0)
-    if (rc /= 8*N_st) then
-      print *, irp_here,  'f77_zmq_recv( zmq_socket_pull, norm_pert(1,1), 8*N_st)'
-      stop 'error'
-    endif
-
-    rc = f77_zmq_recv( zmq_socket_pull, H_pert_diag(1), 8*N_st, 0)
-    if (rc /= 8*N_st) then
-      print *, irp_here,  'f77_zmq_recv( zmq_socket_pull, H_pert_diag(1,1), 8*N_st)'
-      stop 'error'
-    endif
-
-    rc = f77_zmq_recv( zmq_socket_pull, i_generator, 4, 0)
-    if (rc /= 4) then
-      print *, irp_here,  'f77_zmq_recv( zmq_socket_pull, i_generator, 4, 0)'
-      stop 'error'
-    endif
-
-    rc = f77_zmq_recv( zmq_socket_pull, task_id, 4, 0)
-    if (rc /= 4) then
-      print *, irp_here,  'f77_zmq_recv( zmq_socket_pull, task_id, 4, 0)'
-      stop 'error'
-    endif
-
-  endif
-
-! Activate if zmq_socket_pull is a REP
-IRP_IF ZMQ_PUSH
-IRP_ELSE
-  rc = f77_zmq_send( zmq_socket_pull, 0, 4, 0)
-  if (rc /= 4) then
-    print *, irp_here,  'f77_zmq_send( zmq_socket_pull, 0, 4, 0)'
-    stop 'error'
-  endif
-IRP_ENDIF
-
-end
-
-

src/determinants/h_apply.template.f

@@ -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)

src/determinants/h_apply_zmq.template.f

@@ -1,289 +0,0 @@
-subroutine $subroutine($params_main)
-  implicit none
-  use omp_lib
-  use bitmasks
-  use f77_zmq
-  BEGIN_DOC
-  ! Calls H_apply on the |HF| determinant and selects all connected single and double
-  ! excitations (of the same symmetry). Auto-generated by the :file:`generate_h_apply` script.
-  END_DOC
-
-  $decls_main
-
-  integer                        :: i
-  integer                        :: i_generator
-  double precision               :: wall_0, wall_1
-  integer(bit_kind), allocatable :: mask(:,:,:)
-  integer                        :: ispin, k
-  integer                        :: rc
-  character*(512)                :: task
-  double precision, allocatable  :: fock_diag_tmp(:,:)
-
-  $initialization
-  PROVIDE H_apply_buffer_allocated mo_two_e_integrals_in_map psi_det_generators psi_coef_generators
-
-  integer(ZMQ_PTR), external     :: new_zmq_pair_socket
-  integer(ZMQ_PTR)               :: zmq_socket_pair, zmq_socket_pull
-
-  integer(ZMQ_PTR) :: zmq_to_qp_run_socket
-  double precision, allocatable :: pt2_generators(:,:), norm_pert_generators(:,:)
-  double precision, allocatable :: H_pert_diag_generators(:,:)
-  double precision              :: energy(N_st)
-
-  call new_parallel_job(zmq_to_qp_run_socket,zmq_socket_pull,'$subroutine')
-  zmq_socket_pair = new_zmq_pair_socket(.True.)
-
-  integer, external              :: zmq_put_psi
-  integer, external              :: zmq_put_N_det_generators
-  integer, external              :: zmq_put_N_det_selectors
-  integer, external              :: zmq_put_dvector
-
-  if (zmq_put_psi(zmq_to_qp_run_socket,1) == -1) then
-    stop 'Unable to put psi on ZMQ server'
-  endif
-  if (zmq_put_N_det_generators(zmq_to_qp_run_socket, 1) == -1) then
-    stop 'Unable to put N_det_generators on ZMQ server'
-  endif
-  if (zmq_put_N_det_selectors(zmq_to_qp_run_socket, 1) == -1) then
-    stop 'Unable to put N_det_selectors on ZMQ server'
-  endif
-  if (zmq_put_dvector(zmq_to_qp_run_socket,1,'energy',energy,size(energy)) == -1) then
-    stop 'Unable to put energy on ZMQ server'
-  endif
-
-  do i_generator=1,N_det_generators
-    $skip
-    write(task,*) i_generator
-    integer, external :: add_task_to_taskserver
-    if (add_task_to_taskserver(zmq_to_qp_run_socket,trim(task)) == -1) then
-      stop 'Unable to add task to taskserver'
-    endif
-  enddo
-
-  allocate ( pt2_generators(N_states,N_det_generators), &
-       norm_pert_generators(N_states,N_det_generators), &
-     H_pert_diag_generators(N_states,N_det_generators) )
-
-  PROVIDE nproc N_states
-  !$OMP PARALLEL DEFAULT(NONE) &
-  !$OMP PRIVATE(i) &
-  !$OMP SHARED(zmq_socket_pair,N_states, pt2_generators, norm_pert_generators, H_pert_diag_generators, n, task_id, i_generator,zmq_socket_pull)  &
-  !$OMP num_threads(nproc+1)
-      i = omp_get_thread_num()
-      if (i == 0) then
-        call  $subroutine_collector(zmq_socket_pull)
-        integer :: n, task_id
-        call pull_pt2(zmq_socket_pair, pt2_generators, norm_pert_generators, H_pert_diag_generators, i_generator, size(pt2_generators), n, task_id)
-      else
-        call $subroutine_slave_inproc(i)
-      endif
-  !$OMP END PARALLEL
-
-
-  call end_zmq_pair_socket(zmq_socket_pair)
-  call end_parallel_job(zmq_to_qp_run_socket,zmq_socket_pull,'$subroutine')
-
-
-  $copy_buffer
-  $generate_psi_guess
-
-  deallocate ( pt2_generators, norm_pert_generators, H_pert_diag_generators)
-end
-
-subroutine $subroutine_slave_tcp(iproc)
-  implicit none
-  integer, intent(in) :: iproc
-  BEGIN_DOC
-! Computes a buffer over the network
-  END_DOC
-  call $subroutine_slave(0,iproc)
-end
-
-subroutine $subroutine_slave_inproc(iproc)
-  implicit none
-  integer, intent(in) :: iproc
-  BEGIN_DOC
-! Computes a buffer using threads
-  END_DOC
-  call $subroutine_slave(1,iproc)
-end
-
-
-subroutine $subroutine_slave(thread, iproc)
-  implicit none
-  use omp_lib
-  use bitmasks
-  use f77_zmq
-  integer, intent(in)            :: thread
-  BEGIN_DOC
-  ! Calls H_apply on the HF determinant and selects all connected single and double
-  ! excitations (of the same symmetry). Auto-generated by the :file:`generate_h_apply` script.
-  END_DOC
-
-  integer, intent(in)            :: iproc
-  integer                        :: i_generator
-  double precision               :: wall_0, wall_1
-  integer(bit_kind), allocatable :: mask(:,:,:)
-  integer                        :: ispin, k
-  double precision, allocatable  :: fock_diag_tmp(:,:)
-  double precision, allocatable  :: pt2(:), norm_pert(:), H_pert_diag(:)
-
-  integer                        :: worker_id, task_id, rc, N_st
-  character*(512)                :: task
-  integer(ZMQ_PTR),external      :: new_zmq_to_qp_run_socket
-  integer(ZMQ_PTR)               :: zmq_to_qp_run_socket
-  integer(ZMQ_PTR),external      :: new_zmq_push_socket
-  integer(ZMQ_PTR)               :: zmq_socket_push
-
-  zmq_to_qp_run_socket = new_zmq_to_qp_run_socket()
-
-  integer, external              :: connect_to_taskserver
-  if (connect_to_taskserver(zmq_to_qp_run_socket,worker_id,thread) == -1) then
-    call end_zmq_to_qp_run_socket(zmq_to_qp_run_socket)
-    return
-  endif
-
-  zmq_socket_push = new_zmq_push_socket(thread)
-
-  N_st = N_states
-  allocate( pt2(N_st), norm_pert(N_st), H_pert_diag(N_st), &
-            mask(N_int,2,6), fock_diag_tmp(2,mo_num+1) )
-
-  do
-    integer, external :: get_task_from_taskserver
-    if (get_task_from_taskserver(zmq_to_qp_run_socket,worker_id, task_id, task) == -1) then
-      exit
-    endif
-    if (task_id == 0) exit
-    read(task,*) i_generator
-
-    ! Compute diagonal of the Fock matrix
-    call build_fock_tmp(fock_diag_tmp,psi_det_generators(1,1,i_generator),N_int)
-
-    pt2 = 0.d0
-    norm_pert = 0.d0
-    H_pert_diag = 0.d0
-
-    ! Create bit masks for holes and particles
-    do ispin=1,2
-      do k=1,N_int
-        mask(k,ispin,s_hole) =                                      &
-            iand(generators_bitmask(k,ispin,s_hole,i_bitmask_gen),  &
-            psi_det_generators(k,ispin,i_generator) )
-        mask(k,ispin,s_part) =                                      &
-            iand(generators_bitmask(k,ispin,s_part,i_bitmask_gen),  &
-            not(psi_det_generators(k,ispin,i_generator)) )
-        mask(k,ispin,d_hole1) =                                      &
-            iand(generators_bitmask(k,ispin,d_hole1,i_bitmask_gen),  &
-            psi_det_generators(k,ispin,i_generator) )
-        mask(k,ispin,d_part1) =                                      &
-            iand(generators_bitmask(k,ispin,d_part1,i_bitmask_gen),  &
-            not(psi_det_generators(k,ispin,i_generator)) )
-        mask(k,ispin,d_hole2) =                                      &
-            iand(generators_bitmask(k,ispin,d_hole2,i_bitmask_gen),  &
-            psi_det_generators(k,ispin,i_generator) )
-        mask(k,ispin,d_part2) =                                      &
-            iand(generators_bitmask(k,ispin,d_part2,i_bitmask_gen),  &
-            not (psi_det_generators(k,ispin,i_generator)) )
-      enddo
-    enddo
-
-    if($do_double_excitations)then
-      call $subroutine_diexc(psi_det_generators(1,1,i_generator),    &
-        psi_det_generators(1,1,1),                                   &
-        mask(1,1,d_hole1), mask(1,1,d_part1),                        &
-        mask(1,1,d_hole2), mask(1,1,d_part2),                        &
-        fock_diag_tmp, i_generator, iproc $params_post)
-    endif
-    if($do_mono_excitations)then
-      call $subroutine_monoexc(psi_det_generators(1,1,i_generator),  &
-        mask(1,1,s_hole ), mask(1,1,s_part ),                        &
-        fock_diag_tmp, i_generator, iproc $params_post)
-    endif
-
-    integer, external :: task_done_to_taskserver
-    if (task_done_to_taskserver(zmq_to_qp_run_socket, worker_id, task_id) == -1) then
-        print *,  irp_here, ': Unable to send task_done'
-    endif
-    call push_pt2(zmq_socket_push,pt2,norm_pert,H_pert_diag,i_generator,N_st,task_id)
-
-  enddo
-
-  deallocate( mask, fock_diag_tmp, pt2, norm_pert, H_pert_diag )
-
-
-  integer, external              :: disconnect_from_taskserver
-  if (disconnect_from_taskserver(zmq_to_qp_run_socket,worker_id) == -1) then
-    continue
-  endif
-  call end_zmq_push_socket(zmq_socket_push,thread)
-  call end_zmq_to_qp_run_socket(zmq_to_qp_run_socket)
-
-end
-
-subroutine $subroutine_collector(zmq_socket_pull)
-  use f77_zmq
-  implicit none
-  BEGIN_DOC
-! Collects results from the selection in an array of generators
-  END_DOC
-
-  integer :: k, rc
-
-  integer(ZMQ_PTR), external     :: new_zmq_pull_socket
-  integer(ZMQ_PTR), intent(in)   :: zmq_socket_pull
-  integer*8                      :: control, accu
-  integer                        :: n, more, task_id, i_generator
-
-  integer(ZMQ_PTR),external      :: new_zmq_to_qp_run_socket
-  integer(ZMQ_PTR)               :: zmq_to_qp_run_socket
-
-  zmq_to_qp_run_socket = new_zmq_to_qp_run_socket()
-
-  double precision, allocatable :: pt2(:), norm_pert(:), H_pert_diag(:)
-  double precision, allocatable :: pt2_result(:,:), norm_pert_result(:,:), H_pert_diag_result(:,:)
-  allocate (pt2(N_states), norm_pert(N_states), H_pert_diag(N_states))
-  allocate (pt2_result(N_states,N_det_generators), norm_pert_result(N_states,N_det_generators), &
-            H_pert_diag_result(N_states,N_det_generators))
-
-  pt2_result = 0.d0
-  norm_pert_result = 0.d0
-  H_pert_diag_result = 0.d0
-  accu = 0_8
-  more = 1
-  do while (more == 1)
-
-    call pull_pt2(zmq_socket_pull, pt2, norm_pert, H_pert_diag, i_generator, N_states, n, task_id)
-    if (n > 0) then
-      do k=1,N_states
-        pt2_result(k,i_generator) = pt2(k)
-        norm_pert_result(k,i_generator) = norm_pert(k)
-        H_pert_diag_result(k,i_generator) = H_pert_diag(k)
-      enddo
-      accu = accu + 1_8
-      integer, external :: zmq_delete_task
-      if (zmq_delete_task(zmq_to_qp_run_socket,zmq_socket_pull,task_id,more) == -1) then
-        stop 'Unable to delete task'
-      endif
-    endif
-
-  enddo
-
-  call end_zmq_to_qp_run_socket(zmq_to_qp_run_socket)
-
-
-  integer(ZMQ_PTR), external     :: new_zmq_pair_socket
-  integer(ZMQ_PTR)               :: socket_result
-
-  socket_result = new_zmq_pair_socket(.False.)
-
-  call push_pt2(socket_result, pt2_result, norm_pert_result, H_pert_diag_result, i_generator, &
-     N_states*N_det_generators,0)
-
-  deallocate (pt2, norm_pert, H_pert_diag, pt2_result, norm_pert_result, H_pert_diag_result)
-
-  call end_zmq_pair_socket(socket_result)
-
-end
-
-

src/determinants/occ_pattern.irp.f

@@ -424,7 +424,7 @@ BEGIN_PROVIDER [ double precision, weight_occ_pattern_average, (N_occ_pattern) ]
  enddo
 END_PROVIDER
 
- BEGIN_PROVIDER [ double precision, psi_occ_pattern_sorted, (N_int,2,N_occ_pattern) ]
+ BEGIN_PROVIDER [ integer(bit_kind), psi_occ_pattern_sorted, (N_int,2,N_occ_pattern) ]
 &BEGIN_PROVIDER [ double precision, weight_occ_pattern_average_sorted, (N_occ_pattern) ]
 &BEGIN_PROVIDER [ integer, psi_occ_pattern_sorted_order, (N_occ_pattern) ]
 &BEGIN_PROVIDER [ integer, psi_occ_pattern_sorted_order_reverse, (N_occ_pattern) ]

src/dft_one_e/e_xc_general.irp.f

@@ -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"""
+   stop""")
-print "endif"
+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"""
+   stop""")
-print "endif"
+print("endif")
 
  END_SHELL
- 
+
  END_PROVIDER
 

src/dft_one_e/pot_general.irp.f

@@ -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"""
+   stop""")
-print "endif"
+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"""
+   stop""" )
-print "endif"
+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"""
+   stop""")
-print "endif"
+print("endif")
 
 END_SHELL
- 
+
  END_PROVIDER
 

src/perturbation/perturbation.irp.f

@@ -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

src/perturbation/perturbation.template.f

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

src/scf_utils/diagonalize_fock.irp.f

@@ -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

src/scf_utils/roothaan_hall_scf.irp.f

@@ -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)

src/tools/print_energy.irp.f

@@ -0,0 +1,34 @@
+program print_energy
+ implicit none
+ BEGIN_DOC
+ ! Prints the energy of the wave function stored in the |EZFIO| directory.
+ END_DOC
+
+ ! this has to be done in order to be sure that N_det, psi_det and
+ ! psi_coef_sorted are the wave function stored in the |EZFIO| directory.
+ read_wf = .True.
+ touch read_wf
+ call run
+end
+
+subroutine run
+ implicit none
+ integer :: i
+ double precision :: i_H_psi_array(N_states)
+ double precision :: E(N_states)
+ double precision :: norm(N_states)
+
+ E(:) = nuclear_repulsion
+ norm(:) = 0.d0
+ do i=1,N_det
+  call i_H_psi(psi_det(1,1,i), psi_det, psi_coef, N_int, N_det, &
+               size(psi_coef,1), N_states, i_H_psi_array)
+  norm(:) += psi_coef(i,:)**2
+  E(:) += i_H_psi_array(:) * psi_coef(i,:)
+ enddo
+
+ print *, 'Energy:'
+ do i=1,N_states
+   print *, E(i)/norm(i)
+ enddo
+end

src/tools/print_hamiltonian.irp.f

@@ -0,0 +1,29 @@
+program print_hamiltonian
+ implicit none
+ BEGIN_DOC
+ ! Prints the Hamiltonian matrix defined in the space of determinants
+ ! present in the |EZFIO| directory.
+ END_DOC
+
+ ! this has to be done in order to be sure that N_det, psi_det and
+ ! psi_coef_sorted are the wave function stored in the |EZFIO| directory.
+ read_wf = .True.
+ touch read_wf
+ call run
+end
+
+subroutine run
+ implicit none
+ integer :: i, j
+ double precision :: hij
+
+ do j=1,N_det
+   do i=1,N_det
+     call i_H_j(psi_det(1,1,i), psi_det(1,1,j), N_int, hij)
+     if (dabs(hij) > 1.d-20) then
+       print *, i, j, hij
+     endif
+   enddo
+ enddo
+
+end

src/zmq/f77_zmq_module.f90

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

tests/bats_to_sh.py

@@ -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"))