Merge pull request #15 from LCPQ/master

Merge with Manu

.gitignore

@@ -1,15 +1,8 @@
 quantum_package.rc
-EZFIO/
-irpf90/
-EMSL_Basis/
-ninja/
-bin/
-*.log
 quantum_package_static.tar.gz
-resultsFile
-opam_installer.sh
-*.mod
-*.p
 build.ninja
 .ninja_log
-.ninja_deps
+.ninja_deps
+bin/
+lib/
+config/qp_create_ninja.pickle

README.md

@@ -138,6 +138,8 @@ Optional:
     size: <str>         The size information.
                             (by default is one)
                             Example : 1, =sum(ao_num); (ao_num,3)
+                            ATTENTION : The module and the value are separed by a "." not a "_".
+                            For exemple (determinants.n_det)
     ezfio_name: <str>   The name for the EZFIO lib
                              (by default is <provider_name>)
     ezfio_dir: <str>    Will be the folder of EZFIO.

config/ifort.cfg

@@ -57,6 +57,6 @@ FCFLAGS : -xSSE2 -C  -fpe0
 #################
 #
 [OPENMP]
-FC           : -fopenmp
+FC           : -openmp
 IRPF90_FLAGS : --openmp
 

configure

@@ -158,7 +158,7 @@ def check_output(*popenargs, **kwargs):
     >>> check_output(['/usr/bin/python', '--version'])
     Python 2.6.2
     """
-    process = subprocess.Popen(stdout=subprocess.PIPE, *popenargs, **kwargs)
+    process = subprocess.Popen(stdout=subprocess.PIPE,stderr=subprocess.PIPE, *popenargs, **kwargs)
     output, unused_err = process.communicate()
     retcode = process.poll()
     if retcode:
@@ -190,7 +190,7 @@ def checking(d_dependency):
 
     def check_availability(binary):
         """
-        If avalabie return the path who can can't find the
+        If avalable return the path who can find the
         binary else return 0
         """
 
@@ -198,7 +198,19 @@ def checking(d_dependency):
             check_python()
 
         try:
-            return check_output(["which", binary])
+            a = check_output(["which", binary])
+
+            if binary == "irpf90":
+                version = check_output("irpf90 -v".split()).strip()
+
+                from distutils.version import LooseVersion
+                if LooseVersion(version) < LooseVersion("1.6.7"):
+                    return 0
+                else:
+                    return a
+
+            return a
+
         except subprocess.CalledProcessError:
             default_path = d_info[binary].default_path
             if os.path.exists(default_path):
@@ -208,7 +220,7 @@ def checking(d_dependency):
 
     def get_list_descendant(d_dependency, l_installed, l_needed):
         """
-        Descendant – a node reachable by repeated proceeding from parent to child.
+        Descendant : a node reachable by repeated proceeding from parent to child.
         """
         d_need_genealogy = dict()
 
@@ -265,7 +277,7 @@ def installation(l_install_descendant):
     def create_rule_ninja():
 
         l_rules = [
-            "rule download", "  command = wget ${url} -O ${out} -o /dev/null",
+            "rule download", "  command = wget --no-check-certificate ${url} -O ${out} -o /dev/null",
             "  description = Downloading ${descr}", ""
         ]
 
@@ -423,8 +435,8 @@ def create_ninja_and_rc(l_installed):
         'export IRPF90={0}'.format(find_path("irpf90", l_installed)),
         'export NINJA={0}'.format(find_path("ninja", l_installed)),
         'export QP_PYTHON={0}'.format(":".join(l_python)), "",
-        'export PYTHONPATH="${PYTHONPATH}":"${QP_PYTHON}"',
+        'export PYTHONPATH="${QP_PYTHON}":"${PYTHONPATH}"',
-        'export PATH="${PATH}":"${QP_PYTHON}":"${QP_ROOT}"/bin:"${QP_ROOT}"/ocaml',
+        'export PATH="${QP_PYTHON}":"${QP_ROOT}"/bin:"${QP_ROOT}"/ocaml:"${PATH}"',
         'export LD_LIBRARY_PATH="${QP_ROOT}"/lib:"${LD_LIBRARY_PATH}"',
         'export LIBRARY_PATH="${QP_ROOT}"/lib:"${LIBRARY_PATH}"', ""
         'source ${HOME}/.opam/opam-init/init.sh > /dev/null 2> /dev/null || true',

install/.gitignore

@@ -0,0 +1,10 @@
+config/qp_create_ninja.pickle
+Downloads
+_build
+docopt
+emsl
+EZFIO
+irpf90
+resultsFile
+zlib
+build.ninja

install/scripts/check_irp_version.sh

@@ -0,0 +1,25 @@
+#!/bin/bash
+# This script should be included
+
+# pro:
+# 
+# solid way to compare fancy version strings:
+# support any length of sub-parts (ie: 1.3alpha.2.dev2 > 1.1 ?)
+# support alpha-betical sort (ie: 1.alpha < 1.beta2)
+# support big size version (ie: 1.10003939209329320932 > 1.2039209378273789273 ?)
+# can easily be modified to support n arguments. (leaved as an exercise ;) )
+# usually very usefull with 3 arguments: (ie: 1.2 < my_version < 2.7 )
+# cons:
+# 
+# uses a lot of various calls to different programs. So it's not that efficient.
+# uses a pretty recent version of sort and it might not be available on your system. (check with man sort)
+
+function version_gt() { test "$(echo "$@" | tr " " "\n" | sort -V | tail -n 1)" == "$1"; }
+
+irp_cur_version=`irpf90 -v`
+irp_need_version=1.6.7
+
+if version_gt $irp_cur_version $irp_need_version; then
+    echo "OK"
+fi
+echo "FAIL"

install/scripts/install_irpf90.sh

@@ -13,8 +13,16 @@ function _install()
   [[ -x ./irpf90/bin/irpf90 ]] || return 1
   [[ -x ./irpf90/bin/irpman ]] || return 1
   rm -rf -- ../bin/irpf90 ../bin/irpman
-  echo 'exec ${QP_ROOT}/install/irpf90/bin/irpf90 $@' > ../bin/irpf90 || return 1
+  cat << EOF > ../bin/irpf90 || return 1
-  echo 'exec ${QP_ROOT}/install/irpf90/bin/irpman $@' > ../bin/irpman || return 1
+#!/bin/bash
+exec \${QP_ROOT}/install/irpf90/bin/irpf90 \$@
+EOF
+
+  
+  cat << EOF > ../bin/irpman || return 1
+#!/bin/bash
+exec \${QP_ROOT}/install/irpf90/bin/irpman \$@
+EOF
   chmod +x ../bin/irpf90 ../bin/irpman || return 1
   return 0
 }

plugins/All_singles/README.rst

@@ -0,0 +1,4 @@
+==================
+All_singles Module
+==================
+

plugins/CAS_SD/.gitignore

@@ -1,32 +1,31 @@
-#
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
-# Do not modify this file. Add your ignored files to the gitignore
-# (without the dot at the beginning) file.
-#
 IRPF90_temp
 IRPF90_man
-irpf90.make
-tags
-Makefile.depend
 irpf90_entities
+tags
+irpf90.make
+Makefile
+Makefile.depend
 build.ninja
 .ninja_log
 .ninja_deps
-Pseudo
+ezfio_interface.irp.f
-Integrals_Monoelec
+Ezfio_files
-Generators_CAS
-Bitmask
-Integrals_Bielec
-AOs
-Selectors_full
-MOs
-Hartree_Fock
 Perturbation
 Determinants
-Electrons
 Utils
-Properties
+Integrals_Monoelec
-Nuclei
+MO_Basis
+Selectors_full
+Integrals_Bielec
+Pseudo
+Bitmask
+Generators_CAS
+AO_Basis
+Electrons
 MOGuess
-Ezfio_files
+Nuclei
+Hartree_Fock
+Properties
 cas_sd_selected
-cas_sd
+cas_sd

plugins/CAS_SD/README.rst

@@ -34,24 +34,24 @@ Documentation
   Assume N_int is already provided.
 
 
-`h_apply_cas_sd_pt2 <http://github.com/LCPQ/quantum_package/tree/master/src/CAS_SD/H_apply.irp.f_shell_16#L1842>`_
+`h_apply_cas_sd_pt2 <http://github.com/LCPQ/quantum_package/tree/master/src/CAS_SD/H_apply.irp.f_shell_16#L1892>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cas_sd_pt2_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CAS_SD/H_apply.irp.f_shell_16#L1358>`_
+`h_apply_cas_sd_pt2_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CAS_SD/H_apply.irp.f_shell_16#L1383>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cas_sd_pt2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CAS_SD/H_apply.irp.f_shell_16#L1661>`_
+`h_apply_cas_sd_pt2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CAS_SD/H_apply.irp.f_shell_16#L1701>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cas_sd_selected <http://github.com/LCPQ/quantum_package/tree/master/src/CAS_SD/H_apply.irp.f_shell_16#L1112>`_
+`h_apply_cas_sd_selected <http://github.com/LCPQ/quantum_package/tree/master/src/CAS_SD/H_apply.irp.f_shell_16#L1137>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
@@ -62,7 +62,7 @@ Documentation
   Assume N_int is already provided.
 
 
-`h_apply_cas_sd_selected_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CAS_SD/H_apply.irp.f_shell_16#L917>`_
+`h_apply_cas_sd_selected_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CAS_SD/H_apply.irp.f_shell_16#L932>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.

plugins/CID/.gitignore

@@ -1,30 +1,29 @@
-#
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
-# Do not modify this file. Add your ignored files to the gitignore
-# (without the dot at the beginning) file.
-#
 IRPF90_temp
 IRPF90_man
-irpf90.make
-tags
-Makefile.depend
 irpf90_entities
+tags
+irpf90.make
+Makefile
+Makefile.depend
 build.ninja
 .ninja_log
 .ninja_deps
-Pseudo
+ezfio_interface.irp.f
-Integrals_Monoelec
-Bitmask
-Integrals_Bielec
-AOs
-Selectors_full
-MOs
-Hartree_Fock
-Determinants
-Electrons
-Utils
-Nuclei
-MOGuess
-SingleRefMethod
 Ezfio_files
+Determinants
+Integrals_Monoelec
+MO_Basis
+Selectors_full
+Utils
+Pseudo
+AO_Basis
+Bitmask
+SingleRefMethod
+Electrons
+MOGuess
+Nuclei
+Hartree_Fock
+Integrals_Bielec
 cid
-cid_lapack
+cid_lapack

plugins/CID/H_apply.irp.f

@@ -1,9 +1,9 @@
-! Generates subroutine H_apply_cisd
+! Generates subroutine H_apply_cid
 ! ----------------------------------
 
 BEGIN_SHELL [ /usr/bin/env python ]
 from generate_h_apply import H_apply
-H = H_apply("cisd",do_double_exc=True,do_mono_exc=False)
+H = H_apply("cid",do_double_exc=True,do_mono_exc=False)
 print H
 END_SHELL
 

plugins/CID/README.rst

@@ -1,7 +1,7 @@
-CISD
+CID
 ====
 
-This is a test directory which builds a CISD by setting the follwoing rules:
+This is a test directory which builds a CID by setting the follwoing rules:
 
 * The only generator determinant is the Hartee-Fock (single-reference method)
 * All generated determinants are included in the wave function (no perturbative
@@ -26,22 +26,179 @@ Documentation
 .. Do not edit this section. It was auto-generated from the
 .. by the `update_README.py` script.
 
-`cisd <http://github.com/LCPQ/quantum_package/tree/master/src/CID/cid_lapack.irp.f#L1>`_
+`cid <http://github.com/LCPQ/quantum_package/tree/master/src/CID/cid_lapack.irp.f#L1>`_
   Undocumented
 
 
-`h_apply_cisd <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_8#L406>`_
+`h_apply_cid <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_8#L406>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_8#L1>`_
+`h_apply_cid_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_8#L1>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_8#L263>`_
+`h_apply_cid_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_8#L263>`_
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_cisd_selection <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f#L13>`_
+  Undocumented
+
+
+`h_apply_cisd_selection_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L1283>`_
+  Calls H_apply on the HF determinant and selects all connected single and double
+  excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
+
+
+`h_apply_cisd_selection_delta_rho_one_point_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L765>`_
+  Generate all double excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_cisd_selection_delta_rho_one_point_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L1088>`_
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_cisd_selection_dipole_moment_z <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L6631>`_
+  Calls H_apply on the HF determinant and selects all connected single and double
+  excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
+
+
+`h_apply_cisd_selection_dipole_moment_z_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L6113>`_
+  Generate all double excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_cisd_selection_dipole_moment_z_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L6436>`_
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_cisd_selection_epstein_nesbet <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L5103>`_
+  Calls H_apply on the HF determinant and selects all connected single and double
+  excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
+
+
+`h_apply_cisd_selection_epstein_nesbet_2x2 <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L5867>`_
+  Calls H_apply on the HF determinant and selects all connected single and double
+  excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
+
+
+`h_apply_cisd_selection_epstein_nesbet_2x2_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L5349>`_
+  Generate all double excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_cisd_selection_epstein_nesbet_2x2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L5672>`_
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_cisd_selection_epstein_nesbet_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L4585>`_
+  Generate all double excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_cisd_selection_epstein_nesbet_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L4908>`_
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_cisd_selection_epstein_nesbet_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L4339>`_
+  Calls H_apply on the HF determinant and selects all connected single and double
+  excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
+
+
+`h_apply_cisd_selection_epstein_nesbet_sc2_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L3821>`_
+  Generate all double excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_cisd_selection_epstein_nesbet_sc2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L4144>`_
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_cisd_selection_epstein_nesbet_sc2_no_projected <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L3575>`_
+  Calls H_apply on the HF determinant and selects all connected single and double
+  excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
+
+
+`h_apply_cisd_selection_epstein_nesbet_sc2_no_projected_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L3057>`_
+  Generate all double excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_cisd_selection_epstein_nesbet_sc2_no_projected_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L3380>`_
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_cisd_selection_epstein_nesbet_sc2_projected <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L2811>`_
+  Calls H_apply on the HF determinant and selects all connected single and double
+  excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
+
+
+`h_apply_cisd_selection_epstein_nesbet_sc2_projected_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L2293>`_
+  Generate all double excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_cisd_selection_epstein_nesbet_sc2_projected_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L2616>`_
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_cisd_selection_h_core <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L2047>`_
+  Calls H_apply on the HF determinant and selects all connected single and double
+  excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
+
+
+`h_apply_cisd_selection_h_core_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L1529>`_
+  Generate all double excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_cisd_selection_h_core_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L1852>`_
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_cisd_selection_moller_plesset <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L519>`_
+  Calls H_apply on the HF determinant and selects all connected single and double
+  excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
+
+
+`h_apply_cisd_selection_moller_plesset_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L1>`_
+  Generate all double excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_cisd_selection_moller_plesset_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L324>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.

plugins/CID/cid.irp.f

@@ -1,4 +1,4 @@
-program cisd
+program cid
   implicit none
   integer :: i
 
@@ -6,7 +6,7 @@ program cisd
   print *,  'N_states = ', N_states
   N_det = 1
   touch psi_det psi_coef N_det
-  call H_apply_cisd
+  call H_apply_cid
   print *,  'N_det = ', N_det
   do i = 1,N_states
    print *,  'energy  = ',CI_energy(i) 

plugins/CID/cid_lapack.irp.f

@@ -1,4 +1,4 @@
-program cisd
+program cid
   implicit none
   integer :: i
 
@@ -6,7 +6,7 @@ program cisd
   touch diag_algorithm
   print *,   'HF      = ', HF_energy
   print *,  'N_states = ', N_states
-  call H_apply_cisd
+  call H_apply_cid
   print *,  'N_det = ', N_det
   do i = 1,N_states
    print *,  'energy  = ',CI_energy(i) 

plugins/CID_SC2_selected/.gitignore

@@ -1,35 +1,32 @@
-#
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
-# Do not modify this file. Add your ignored files to the gitignore
-# (without the dot at the beginning) file.
-#
 IRPF90_temp
 IRPF90_man
-irpf90.make
-tags
-Makefile.depend
 irpf90_entities
+tags
+irpf90.make
+Makefile
+Makefile.depend
 build.ninja
 .ninja_log
 .ninja_deps
-CID_selected
+ezfio_interface.irp.f
-Pseudo
-Integrals_Monoelec
-Bitmask
-CID
-Integrals_Bielec
-CISD_selected
-AOs
-Selectors_full
-MOs
-Hartree_Fock
-Perturbation
-CISD
-Determinants
-Electrons
-Utils
-Properties
-Nuclei
-MOGuess
-SingleRefMethod
 Ezfio_files
-cid_sc2_selection
+Perturbation
+Determinants
+Integrals_Monoelec
+MO_Basis
+Selectors_full
+SingleRefMethod
+Utils
+CID
+Pseudo
+Properties
+Bitmask
+AO_Basis
+Electrons
+MOGuess
+CID_selected
+Nuclei
+Hartree_Fock
+Integrals_Bielec
+cid_sc2_selection

plugins/CID_selected/.gitignore

@@ -1,33 +1,31 @@
-#
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
-# Do not modify this file. Add your ignored files to the gitignore
-# (without the dot at the beginning) file.
-#
 IRPF90_temp
 IRPF90_man
-irpf90.make
-tags
-Makefile.depend
 irpf90_entities
+tags
+irpf90.make
+Makefile
+Makefile.depend
 build.ninja
 .ninja_log
 .ninja_deps
-Pseudo
+ezfio_interface.irp.f
-Integrals_Monoelec
-Bitmask
-CID
-Integrals_Bielec
-AOs
-Selectors_full
-MOs
-Hartree_Fock
-Perturbation
-CISD
-Determinants
-Electrons
-Utils
-Properties
-Nuclei
-MOGuess
-SingleRefMethod
 Ezfio_files
-cid_selection
+Perturbation
+Determinants
+Utils
+Integrals_Monoelec
+MO_Basis
+Selectors_full
+Integrals_Bielec
+CID
+Pseudo
+AO_Basis
+Bitmask
+SingleRefMethod
+Electrons
+MOGuess
+Nuclei
+Hartree_Fock
+Properties
+cid_selection

plugins/CID_selected/README.rst

@@ -8,10 +8,6 @@ Documentation
 .. Do not edit this section. It was auto-generated from the
 .. by the `update_README.py` script.
 
-`cisd <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/cid_selection.irp.f#L1>`_
-  Undocumented
-
-
 `h_apply_cisd_selection <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f#L13>`_
   Undocumented
 

plugins/CIS/.gitignore

@@ -1,30 +1,29 @@
-#
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
-# Do not modify this file. Add your ignored files to the gitignore
-# (without the dot at the beginning) file.
-#
 IRPF90_temp
 IRPF90_man
-irpf90.make
-tags
-Makefile.depend
 irpf90_entities
+tags
+irpf90.make
+Makefile
+Makefile.depend
 build.ninja
 .ninja_log
 .ninja_deps
-Pseudo
+ezfio_interface.irp.f
-Integrals_Monoelec
-Bitmask
-Integrals_Bielec
-AOs
-Selectors_full
-MOs
-Hartree_Fock
-Determinants
-Electrons
-Utils
-Nuclei
-MOGuess
-SingleRefMethod
 Ezfio_files
+Determinants
+Integrals_Monoelec
+MO_Basis
+Selectors_full
+Utils
+Pseudo
+AO_Basis
+Bitmask
+SingleRefMethod
+Electrons
+MOGuess
+Nuclei
+Hartree_Fock
+Integrals_Bielec
 super_ci
-cis
+cis

plugins/CISD/.gitignore

@@ -1,30 +1,29 @@
-#
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
-# Do not modify this file. Add your ignored files to the gitignore
-# (without the dot at the beginning) file.
-#
 IRPF90_temp
 IRPF90_man
-irpf90.make
-tags
-Makefile.depend
 irpf90_entities
+tags
+irpf90.make
+Makefile
+Makefile.depend
 build.ninja
 .ninja_log
 .ninja_deps
-Pseudo
+ezfio_interface.irp.f
-Integrals_Monoelec
-Bitmask
-Integrals_Bielec
-AOs
-Selectors_full
-MOs
-Hartree_Fock
-Determinants
-Electrons
-Utils
-Nuclei
-MOGuess
-SingleRefMethod
 Ezfio_files
+Determinants
+Integrals_Monoelec
+MO_Basis
+Selectors_full
+Utils
+Pseudo
+AO_Basis
+Bitmask
+SingleRefMethod
+Electrons
+MOGuess
+Nuclei
+Hartree_Fock
+Integrals_Bielec
 cisd_lapack
-cisd
+cisd

plugins/CISD/README.rst

@@ -26,10 +26,6 @@ Documentation
 .. Do not edit this section. It was auto-generated from the
 .. by the `update_README.py` script.
 
-`cisd <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/cisd_lapack.irp.f#L1>`_
-  Undocumented
-
-
 `h_apply_cisd <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_8#L406>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
@@ -46,3 +42,160 @@ Documentation
   particles.
   Assume N_int is already provided.
 
+
+`h_apply_cisd_selection <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f#L13>`_
+  Undocumented
+
+
+`h_apply_cisd_selection_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L6067>`_
+  Calls H_apply on the HF determinant and selects all connected single and double
+  excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
+
+
+`h_apply_cisd_selection_delta_rho_one_point_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L5524>`_
+  Generate all double excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_cisd_selection_delta_rho_one_point_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L5862>`_
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_cisd_selection_dipole_moment_z <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L6856>`_
+  Calls H_apply on the HF determinant and selects all connected single and double
+  excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
+
+
+`h_apply_cisd_selection_dipole_moment_z_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L6313>`_
+  Generate all double excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_cisd_selection_dipole_moment_z_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L6651>`_
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_cisd_selection_epstein_nesbet <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L1333>`_
+  Calls H_apply on the HF determinant and selects all connected single and double
+  excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
+
+
+`h_apply_cisd_selection_epstein_nesbet_2x2 <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L2122>`_
+  Calls H_apply on the HF determinant and selects all connected single and double
+  excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
+
+
+`h_apply_cisd_selection_epstein_nesbet_2x2_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L1579>`_
+  Generate all double excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_cisd_selection_epstein_nesbet_2x2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L1917>`_
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_cisd_selection_epstein_nesbet_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L790>`_
+  Generate all double excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_cisd_selection_epstein_nesbet_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L1128>`_
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_cisd_selection_epstein_nesbet_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L4489>`_
+  Calls H_apply on the HF determinant and selects all connected single and double
+  excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
+
+
+`h_apply_cisd_selection_epstein_nesbet_sc2_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L3946>`_
+  Generate all double excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_cisd_selection_epstein_nesbet_sc2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L4284>`_
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_cisd_selection_epstein_nesbet_sc2_no_projected <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L3700>`_
+  Calls H_apply on the HF determinant and selects all connected single and double
+  excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
+
+
+`h_apply_cisd_selection_epstein_nesbet_sc2_no_projected_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L3157>`_
+  Generate all double excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_cisd_selection_epstein_nesbet_sc2_no_projected_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L3495>`_
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_cisd_selection_epstein_nesbet_sc2_projected <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L2911>`_
+  Calls H_apply on the HF determinant and selects all connected single and double
+  excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
+
+
+`h_apply_cisd_selection_epstein_nesbet_sc2_projected_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L2368>`_
+  Generate all double excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_cisd_selection_epstein_nesbet_sc2_projected_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L2706>`_
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_cisd_selection_h_core <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L544>`_
+  Calls H_apply on the HF determinant and selects all connected single and double
+  excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
+
+
+`h_apply_cisd_selection_h_core_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L1>`_
+  Generate all double excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_cisd_selection_h_core_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L339>`_
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_cisd_selection_moller_plesset <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L5278>`_
+  Calls H_apply on the HF determinant and selects all connected single and double
+  excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
+
+
+`h_apply_cisd_selection_moller_plesset_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L4735>`_
+  Generate all double excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_cisd_selection_moller_plesset_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L5073>`_
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+

plugins/CISD_SC2_selected/README.rst

@@ -12,41 +12,41 @@ Documentation
   Undocumented
 
 
-`h_apply_pt2 <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_SC2_selected/H_apply.irp.f_shell_17#L1253>`_
+`h_apply_pt2 <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_SC2_selected/H_apply.irp.f_shell_17#L1303>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_pt2_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_SC2_selected/H_apply.irp.f_shell_17#L767>`_
+`h_apply_pt2_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_SC2_selected/H_apply.irp.f_shell_17#L792>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_pt2_en_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_SC2_selected/H_apply.irp.f_shell_17#L1946>`_
+`h_apply_pt2_en_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_SC2_selected/H_apply.irp.f_shell_17#L2021>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_pt2_en_sc2_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_SC2_selected/H_apply.irp.f_shell_17#L1460>`_
+`h_apply_pt2_en_sc2_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_SC2_selected/H_apply.irp.f_shell_17#L1510>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_pt2_en_sc2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_SC2_selected/H_apply.irp.f_shell_17#L1765>`_
+`h_apply_pt2_en_sc2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_SC2_selected/H_apply.irp.f_shell_17#L1830>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_pt2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_SC2_selected/H_apply.irp.f_shell_17#L1072>`_
+`h_apply_pt2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_SC2_selected/H_apply.irp.f_shell_17#L1112>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_sc2_selected <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_SC2_selected/H_apply.irp.f_shell_17#L521>`_
+`h_apply_sc2_selected <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_SC2_selected/H_apply.irp.f_shell_17#L546>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
@@ -57,7 +57,7 @@ Documentation
   Assume N_int is already provided.
 
 
-`h_apply_sc2_selected_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_SC2_selected/H_apply.irp.f_shell_17#L326>`_
+`h_apply_sc2_selected_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_SC2_selected/H_apply.irp.f_shell_17#L341>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.

plugins/CISD_selected/README.rst

@@ -8,162 +8,158 @@ Documentation
 .. Do not edit this section. It was auto-generated from the
 .. by the `update_README.py` script.
 
-`cisd <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/cisd_selection.irp.f#L1>`_
-  Undocumented
-
-
 `h_apply_cisd_selection <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f#L13>`_
   Undocumented
 
 
-`h_apply_cisd_selection_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L1283>`_
+`h_apply_cisd_selection_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L6067>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_delta_rho_one_point_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L765>`_
+`h_apply_cisd_selection_delta_rho_one_point_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L5524>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_delta_rho_one_point_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L1088>`_
+`h_apply_cisd_selection_delta_rho_one_point_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L5862>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_dipole_moment_z <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L6631>`_
+`h_apply_cisd_selection_dipole_moment_z <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L6856>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_dipole_moment_z_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L6113>`_
+`h_apply_cisd_selection_dipole_moment_z_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L6313>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_dipole_moment_z_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L6436>`_
+`h_apply_cisd_selection_dipole_moment_z_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L6651>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L5103>`_
+`h_apply_cisd_selection_epstein_nesbet <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L1333>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_epstein_nesbet_2x2 <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L5867>`_
+`h_apply_cisd_selection_epstein_nesbet_2x2 <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L2122>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_epstein_nesbet_2x2_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L5349>`_
+`h_apply_cisd_selection_epstein_nesbet_2x2_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L1579>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_2x2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L5672>`_
+`h_apply_cisd_selection_epstein_nesbet_2x2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L1917>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L4585>`_
+`h_apply_cisd_selection_epstein_nesbet_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L790>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L4908>`_
+`h_apply_cisd_selection_epstein_nesbet_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L1128>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L4339>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L4489>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L3821>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L3946>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L4144>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L4284>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_no_projected <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L3575>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2_no_projected <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L3700>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_no_projected_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L3057>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2_no_projected_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L3157>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_no_projected_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L3380>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2_no_projected_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L3495>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_projected <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L2811>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2_projected <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L2911>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_projected_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L2293>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2_projected_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L2368>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_projected_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L2616>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2_projected_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L2706>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_h_core <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L2047>`_
+`h_apply_cisd_selection_h_core <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L544>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_h_core_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L1529>`_
+`h_apply_cisd_selection_h_core_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L1>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_h_core_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L1852>`_
+`h_apply_cisd_selection_h_core_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L339>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_moller_plesset <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L519>`_
+`h_apply_cisd_selection_moller_plesset <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L5278>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_moller_plesset_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L1>`_
+`h_apply_cisd_selection_moller_plesset_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L4735>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_moller_plesset_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L324>`_
+`h_apply_cisd_selection_moller_plesset_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L5073>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.

plugins/DDCI_selected/.gitignore

@@ -1,31 +1,30 @@
-#
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
-# Do not modify this file. Add your ignored files to the gitignore
-# (without the dot at the beginning) file.
-#
 IRPF90_temp
 IRPF90_man
-irpf90.make
-tags
-Makefile.depend
 irpf90_entities
+tags
+irpf90.make
+Makefile
+Makefile.depend
 build.ninja
 .ninja_log
 .ninja_deps
-Pseudo
+ezfio_interface.irp.f
-Integrals_Monoelec
+Ezfio_files
-Generators_CAS
-Bitmask
-Integrals_Bielec
-AOs
-Selectors_full
-MOs
-Hartree_Fock
 Perturbation
 Determinants
-Electrons
 Utils
-Properties
+Integrals_Monoelec
-Nuclei
+MO_Basis
+Selectors_full
+Integrals_Bielec
+Pseudo
+Bitmask
+Generators_CAS
+AO_Basis
+Electrons
 MOGuess
-Ezfio_files
+Nuclei
-ddci
+Hartree_Fock
+Properties
+ddci

plugins/DDCI_selected/README.rst

@@ -12,24 +12,24 @@ Documentation
   Undocumented
 
 
-`h_apply_ddci_pt2 <http://github.com/LCPQ/quantum_package/tree/master/src/DDCI_selected/H_apply.irp.f_shell_15#L1267>`_
+`h_apply_ddci_pt2 <http://github.com/LCPQ/quantum_package/tree/master/src/DDCI_selected/H_apply.irp.f_shell_15#L1341>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_ddci_pt2_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/DDCI_selected/H_apply.irp.f_shell_15#L774>`_
+`h_apply_ddci_pt2_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/DDCI_selected/H_apply.irp.f_shell_15#L811>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_ddci_pt2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/DDCI_selected/H_apply.irp.f_shell_15#L1083>`_
+`h_apply_ddci_pt2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/DDCI_selected/H_apply.irp.f_shell_15#L1143>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_ddci_selection <http://github.com/LCPQ/quantum_package/tree/master/src/DDCI_selected/H_apply.irp.f_shell_15#L528>`_
+`h_apply_ddci_selection <http://github.com/LCPQ/quantum_package/tree/master/src/DDCI_selected/H_apply.irp.f_shell_15#L565>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
@@ -40,7 +40,7 @@ Documentation
   Assume N_int is already provided.
 
 
-`h_apply_ddci_selection_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/DDCI_selected/H_apply.irp.f_shell_15#L330>`_
+`h_apply_ddci_selection_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/DDCI_selected/H_apply.irp.f_shell_15#L353>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.

plugins/FCIdump/.gitignore

@@ -1,25 +1,24 @@
-#
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
-# Do not modify this file. Add your ignored files to the gitignore
-# (without the dot at the beginning) file.
-#
 IRPF90_temp
 IRPF90_man
-irpf90.make
-tags
-Makefile.depend
 irpf90_entities
+tags
+irpf90.make
+Makefile
+Makefile.depend
 build.ninja
 .ninja_log
 .ninja_deps
-Pseudo
+ezfio_interface.irp.f
-Integrals_Monoelec
-Bitmask
-Integrals_Bielec
-AOs
-MOs
-Determinants
-Electrons
-Utils
-Nuclei
 Ezfio_files
-fcidump
+Determinants
+Integrals_Monoelec
+MO_Basis
+Utils
+Pseudo
+Bitmask
+AO_Basis
+Electrons
+Nuclei
+Integrals_Bielec
+fcidump

plugins/Full_CI/.gitignore

@@ -1,34 +1,33 @@
-#
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
-# Do not modify this file. Add your ignored files to the gitignore
-# (without the dot at the beginning) file.
-#
 IRPF90_temp
 IRPF90_man
-irpf90.make
-tags
-Makefile.depend
 irpf90_entities
+tags
+irpf90.make
+Makefile
+Makefile.depend
 build.ninja
 .ninja_log
 .ninja_deps
-Generators_full
+ezfio_interface.irp.f
-Pseudo
+Ezfio_files
-Integrals_Monoelec
-Bitmask
-Integrals_Bielec
-AOs
-Selectors_full
-MOs
-Hartree_Fock
 Perturbation
 Determinants
-Electrons
 Utils
-Properties
+Integrals_Monoelec
-Nuclei
+MO_Basis
+Selectors_full
+Integrals_Bielec
+Pseudo
+Generators_full
+Bitmask
+AO_Basis
+Electrons
 MOGuess
-Ezfio_files
+Nuclei
+Hartree_Fock
+Properties
 target_pt2
 full_ci
 var_pt2_ratio
-full_ci_no_skip
+full_ci_no_skip

plugins/Full_CI/README.rst

@@ -14,7 +14,7 @@ Documentation
   Undocumented
 
 
-`h_apply_fci <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L519>`_
+`h_apply_fci <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L544>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
@@ -25,126 +25,126 @@ Documentation
   Assume N_int is already provided.
 
 
-`h_apply_fci_mono <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L2712>`_
+`h_apply_fci_mono <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L2812>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_fci_mono_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L2192>`_
+`h_apply_fci_mono_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L2267>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_fci_mono_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L2515>`_
+`h_apply_fci_mono_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L2605>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_fci_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L324>`_
+`h_apply_fci_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L339>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_fci_no_skip <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L1974>`_
+`h_apply_fci_no_skip <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L2049>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_fci_no_skip_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L1456>`_
+`h_apply_fci_no_skip_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L1506>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_fci_no_skip_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L1779>`_
+`h_apply_fci_no_skip_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L1844>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_fci_pt2 <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L1249>`_
+`h_apply_fci_pt2 <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L1299>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_fci_pt2_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L765>`_
+`h_apply_fci_pt2_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L790>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_fci_pt2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L1068>`_
+`h_apply_fci_pt2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L1108>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_pt2_mono_delta_rho <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L4210>`_
+`h_apply_pt2_mono_delta_rho <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L4360>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_pt2_mono_delta_rho_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L3724>`_
+`h_apply_pt2_mono_delta_rho_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L3849>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_pt2_mono_delta_rho_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L4027>`_
+`h_apply_pt2_mono_delta_rho_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L4167>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_pt2_mono_di_delta_rho <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L5665>`_
+`h_apply_pt2_mono_di_delta_rho <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L5865>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_pt2_mono_di_delta_rho_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L5181>`_
+`h_apply_pt2_mono_di_delta_rho_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L5356>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_pt2_mono_di_delta_rho_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L5484>`_
+`h_apply_pt2_mono_di_delta_rho_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L5674>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_select_mono_delta_rho <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L3478>`_
+`h_apply_select_mono_delta_rho <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L3603>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_select_mono_delta_rho_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L2958>`_
+`h_apply_select_mono_delta_rho_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L3058>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_select_mono_delta_rho_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L3281>`_
+`h_apply_select_mono_delta_rho_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L3396>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_select_mono_di_delta_rho <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L4935>`_
+`h_apply_select_mono_di_delta_rho <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L5110>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_select_mono_di_delta_rho_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L4417>`_
+`h_apply_select_mono_di_delta_rho_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L4567>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_select_mono_di_delta_rho_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L4740>`_
+`h_apply_select_mono_di_delta_rho_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L4905>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.

plugins/Full_CI/full_ci.irp.f

@@ -28,6 +28,7 @@ program full_ci
     print *,  '-----'
   endif
   double precision :: i_H_psi_array(N_states),diag_H_mat_elem,h,i_O1_psi_array(N_states)
+  double precision :: E_CI_before(N_states)
   if(read_wf)then
    call i_H_psi(psi_det(1,1,N_det),psi_det,psi_coef,N_int,N_det,psi_det_size,N_states,i_H_psi_array)
    h = diag_H_mat_elem(psi_det(1,1,N_det),N_int)
@@ -38,6 +39,7 @@ program full_ci
 
   integer :: n_det_before
   print*,'Beginning the selection ...'
+  E_CI_before = CI_energy
   do while (N_det < N_det_max.and.maxval(abs(pt2(1:N_st))) > pt2_max)
     n_det_before = N_det
     call H_apply_FCI(pt2, norm_pert, H_pert_diag,  N_st)
@@ -57,12 +59,13 @@ program full_ci
     if(n_det_before == N_det)then
      selection_criterion = selection_criterion * 0.5d0
     endif
-    print *,  'N_det    = ', N_det
+    print *,  'N_det          = ', N_det
-    print *,  'N_states = ', N_states
+    print *,  'N_states       = ', N_states
-    print *,  'PT2      = ', pt2
+    print *,  'PT2            = ', pt2
-    print *,  'E        = ', CI_energy
+    print *,  'E              = ', CI_energy
-    print *,  'E+PT2    = ', CI_energy+pt2
+    print *,  'E(before)+PT2  = ', E_CI_before+pt2
     print *,  '-----'
+    E_CI_before = CI_energy
     call ezfio_set_full_ci_energy(CI_energy)
     if (abort_all) then
       exit

plugins/Full_CI/full_ci_no_skip.irp.f

@@ -28,6 +28,7 @@ program full_ci
     print *,  '-----'
   endif
   double precision :: i_H_psi_array(N_states),diag_H_mat_elem,h,i_O1_psi_array(N_states)
+  double precision :: E_CI_before(N_states)
   if(read_wf)then
    call i_H_psi(psi_det(1,1,N_det),psi_det,psi_coef,N_int,N_det,psi_det_size,N_states,i_H_psi_array)
    h = diag_H_mat_elem(psi_det(1,1,N_det),N_int)
@@ -38,6 +39,7 @@ program full_ci
 
   integer :: n_det_before
   print*,'Beginning the selection ...'
+  E_CI_before = CI_energy
   do while (N_det < N_det_max.and.maxval(abs(pt2(1:N_st))) > pt2_max)
     n_det_before = N_det
     call H_apply_FCI_no_skip(pt2, norm_pert, H_pert_diag,  N_st)
@@ -61,8 +63,9 @@ program full_ci
     print *,  'N_states = ', N_states
     print *,  'PT2      = ', pt2
     print *,  'E        = ', CI_energy
-    print *,  'E+PT2    = ', CI_energy+pt2
+    print *,  'E+PT2    = ', E_CI_before+pt2
     print *,  '-----'
+    E_CI_before = CI_energy
     call ezfio_set_full_ci_energy(CI_energy)
     if (abort_all) then
       exit
@@ -73,6 +76,7 @@ program full_ci
    call diagonalize_CI
    if(do_pt2_end)then
     print*,'Last iteration only to compute the PT2'
+!   print*,'The thres'
     threshold_selectors = 1.d0
     threshold_generators = 0.999d0
     call H_apply_FCI_PT2(pt2, norm_pert, H_pert_diag,  N_st)

plugins/Generators_CAS/.gitignore

@@ -1,13 +1,23 @@
-#
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
-# Do not modify this file. Add your ignored files to the gitignore
-# (without the dot at the beginning) file.
-#
 IRPF90_temp
 IRPF90_man
-irpf90.make
-tags
-Makefile.depend
 irpf90_entities
+tags
+irpf90.make
+Makefile
+Makefile.depend
 build.ninja
 .ninja_log
 .ninja_deps
+ezfio_interface.irp.f
+Ezfio_files
+Determinants
+Integrals_Monoelec
+MO_Basis
+Utils
+Pseudo
+Bitmask
+AO_Basis
+Electrons
+Nuclei
+Integrals_Bielec

plugins/Generators_full/.gitignore

@@ -1,13 +1,25 @@
-#
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
-# Do not modify this file. Add your ignored files to the gitignore
-# (without the dot at the beginning) file.
-#
 IRPF90_temp
 IRPF90_man
-irpf90.make
-tags
-Makefile.depend
 irpf90_entities
+tags
+irpf90.make
+Makefile
+Makefile.depend
 build.ninja
 .ninja_log
 .ninja_deps
+ezfio_interface.irp.f
+Ezfio_files
+Determinants
+Integrals_Monoelec
+MO_Basis
+Utils
+Pseudo
+Bitmask
+AO_Basis
+Electrons
+MOGuess
+Nuclei
+Hartree_Fock
+Integrals_Bielec

plugins/Generators_restart/README.rst

@@ -2,40 +2,3 @@
 Generators_restart Module
 =========================
 
-Documentation
-=============
-
-.. Do not edit this section. It was auto-generated from the
-.. by the `update_README.py` script.
-
-`n_det_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_restart/generators.irp.f#L3>`_
-  Read the wave function
-
-
-`psi_coef_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_restart/generators.irp.f#L21>`_
-  read wf
-  .br
-
-
-`psi_det_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_restart/generators.irp.f#L20>`_
-  read wf
-  .br
-
-
-`select_max <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_restart/generators.irp.f#L52>`_
-  Memo to skip useless selectors
-
-
-`size_select_max <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_restart/generators.irp.f#L44>`_
-  Size of the select_max array
-
-Needed Modules
-==============
-
-.. Do not edit this section. It was auto-generated from the
-.. by the `update_README.py` script.
-
-.. image:: tree_dependency.png
-
-* `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
-

plugins/Hartree_Fock/.gitignore

@@ -1,26 +1,25 @@
-#
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
-# Do not modify this file. Add your ignored files to the gitignore
-# (without the dot at the beginning) file.
-#
 IRPF90_temp
 IRPF90_man
-irpf90.make
-tags
-Makefile.depend
 irpf90_entities
+tags
+irpf90.make
+Makefile
+Makefile.depend
 build.ninja
 .ninja_log
 .ninja_deps
-Pseudo
+ezfio_interface.irp.f
-Integrals_Monoelec
-Bitmask
-Integrals_Bielec
-AOs
-MOs
-Electrons
-Utils
-Nuclei
-MOGuess
 Ezfio_files
+Integrals_Monoelec
+MO_Basis
+Integrals_Bielec
+Pseudo
+Bitmask
+AO_Basis
+Electrons
+MOGuess
+Nuclei
+Utils
 Huckel_guess
-SCF
+SCF

plugins/MP2/.gitignore

@@ -1,31 +1,30 @@
-#
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
-# Do not modify this file. Add your ignored files to the gitignore
-# (without the dot at the beginning) file.
-#
 IRPF90_temp
 IRPF90_man
-irpf90.make
-tags
-Makefile.depend
 irpf90_entities
+tags
+irpf90.make
+Makefile
+Makefile.depend
 build.ninja
 .ninja_log
 .ninja_deps
-Pseudo
+ezfio_interface.irp.f
-Integrals_Monoelec
+Ezfio_files
-Bitmask
-Integrals_Bielec
-AOs
-Selectors_full
-MOs
-Hartree_Fock
 Perturbation
 Determinants
-Electrons
 Utils
-Properties
+Integrals_Monoelec
-Nuclei
+MO_Basis
-MOGuess
+Selectors_full
+Integrals_Bielec
+Pseudo
+AO_Basis
+Bitmask
 SingleRefMethod
-Ezfio_files
+Electrons
-mp2
+MOGuess
+Nuclei
+Hartree_Fock
+Properties
+mp2

plugins/MRCC/.gitignore

@@ -1,31 +1,30 @@
-#
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
-# Do not modify this file. Add your ignored files to the gitignore
-# (without the dot at the beginning) file.
-#
 IRPF90_temp
 IRPF90_man
-irpf90.make
-tags
-Makefile.depend
 irpf90_entities
+tags
+irpf90.make
+Makefile
+Makefile.depend
 build.ninja
 .ninja_log
 .ninja_deps
-Generators_full
+ezfio_interface.irp.f
-Pseudo
+Ezfio_files
-Integrals_Monoelec
-Bitmask
-Integrals_Bielec
-AOs
-Selectors_full
-MOs
-Hartree_Fock
 Perturbation
 Determinants
-Electrons
 Utils
-Properties
+Integrals_Monoelec
-Nuclei
+MO_Basis
+Selectors_full
+Integrals_Bielec
+Pseudo
+Generators_full
+Bitmask
+AO_Basis
+Electrons
 MOGuess
-Ezfio_files
+Nuclei
-mrcc
+Hartree_Fock
+Properties
+mrcc

plugins/MRCC/mrcc_utils.irp.f

@@ -1,21 +1,32 @@
 
 BEGIN_PROVIDER [ double precision, lambda_mrcc, (N_states,psi_det_size) ]
+&BEGIN_PROVIDER [ double precision, lambda_pert, (N_states,psi_det_size) ] 
  implicit none
  BEGIN_DOC
  ! cm/<Psi_0|H|D_m>
  END_DOC
  integer :: i,k
- double precision :: ihpsi(N_states)
+ double precision :: ihpsi(N_states), hij(N_states) 
- do i=1,N_det_non_cas
+ 
+do i=1,N_det_non_cas
    call i_h_psi(psi_non_cas(1,1,i), psi_cas, psi_cas_coef, N_int, N_det_cas, &
      size(psi_cas_coef,1), n_states, ihpsi)
-   double precision :: hij
+   call i_h_j(psi_non_cas(1,1,i),psi_non_cas(1,1,i),N_int,hij)
    do k=1,N_states
-     if (dabs(ihpsi(k)) > 1.d-5) then
+   lambda_pert(k,i) = 1d0 / (CI_electronic_energy(k)-hij(k))
-       lambda_mrcc(k,i) = psi_non_cas_coef(i,k)/ihpsi(k)
+   lambda_mrcc(k,i) = psi_non_cas_coef(i,k)/ihpsi(k)
-       lambda_mrcc(k,i) = min( lambda_mrcc (k,i),0.d0 )
+     if ((lambda_mrcc(k,i)/lambda_pert(k,i))<0.d0 .or. (lambda_mrcc(k,i)/lambda_pert(k,i))>4.d0) then
+       lambda_mrcc(k,i) = lambda_pert(k,i)
      else
-       lambda_mrcc(k,i) = 0.d0
+       if ((lambda_mrcc(k,i)/lambda_pert(k,i))<0.1d0 .or. (lambda_mrcc(k,i)/lambda_pert(k,i))>=0d0) then
+       lambda_mrcc(k,i) = lambda_mrcc(k,i)*((cos((lambda_mrcc(k,i)/lambda_pert(k,i))*3.141592653589793d0/0.1d0+3.141592653589793d0)+1d0)/2.d0) &
+                          + lambda_pert(k,i)*(1.d0-((cos((lambda_mrcc(k,i)/lambda_pert(k,i))*3.141592653589793d0/0.1d0+3.141592653589793d0)+1.d0)/2.d0))
+       elseif ((lambda_mrcc(k,i)/lambda_pert(k,i))<=4.0d0 .or. (lambda_mrcc(k,i)/lambda_pert(k,i))>2.0d0) then
+       lambda_mrcc(k,i) = lambda_mrcc(k,i)*(1.d0-(cos(abs(2.d0-(lambda_mrcc(k,i)/lambda_pert(k,i)))*3.141592653589793d0/2.0d0+3.141592653589793d0)+1.d0)/2d0) &
+                          + lambda_pert(k,i)*((cos(abs(2.d0-(lambda_mrcc(k,i)/lambda_pert(k,i)))*3.141592653589793d0/2.0d0+3.141592653589793d0)+1.d0)/2.d0)
+       else
+       lambda_mrcc(k,i) = lambda_mrcc(k,i)
+       endif
      endif
    enddo
  enddo
@@ -23,6 +34,8 @@ END_PROVIDER
 
 
 
+
+
 BEGIN_PROVIDER [ character*(32), dressing_type ]
  implicit none
  BEGIN_DOC

plugins/Molden/NEEDED_CHILDREN_MODULES

@@ -1 +1 @@
-MOs Utils
+MO_Basis Utils

plugins/Molden/README.rst

@@ -35,6 +35,6 @@ Needed Modules
 
 .. image:: tree_dependency.png
 
-* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
+* `MO_Basis <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis>`_
 * `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
 

plugins/Perturbation/.gitignore

@@ -1,13 +1,26 @@
-#
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
-# Do not modify this file. Add your ignored files to the gitignore
-# (without the dot at the beginning) file.
-#
 IRPF90_temp
 IRPF90_man
-irpf90.make
-tags
-Makefile.depend
 irpf90_entities
+tags
+irpf90.make
+Makefile
+Makefile.depend
 build.ninja
 .ninja_log
 .ninja_deps
+ezfio_interface.irp.f
+Ezfio_files
+Determinants
+Integrals_Monoelec
+MO_Basis
+Utils
+Pseudo
+Properties
+Bitmask
+AO_Basis
+Electrons
+MOGuess
+Nuclei
+Hartree_Fock
+Integrals_Bielec

plugins/Perturbation/README.rst

@@ -85,7 +85,7 @@ Documentation
   Undocumented
 
 
-`perturb_buffer_by_mono_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L161>`_
+`perturb_buffer_by_mono_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L791>`_
   Applly pertubration ``delta_rho_one_point`` to the buffer of determinants generated in the H_apply
   routine.
 
@@ -95,12 +95,12 @@ Documentation
   routine.
 
 
-`perturb_buffer_by_mono_epstein_nesbet <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L686>`_
+`perturb_buffer_by_mono_epstein_nesbet <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L161>`_
   Applly pertubration ``epstein_nesbet`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_by_mono_epstein_nesbet_2x2 <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L791>`_
+`perturb_buffer_by_mono_epstein_nesbet_2x2 <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L266>`_
   Applly pertubration ``epstein_nesbet_2x2`` to the buffer of determinants generated in the H_apply
   routine.
 
@@ -120,17 +120,17 @@ Documentation
   routine.
 
 
-`perturb_buffer_by_mono_h_core <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L266>`_
+`perturb_buffer_by_mono_h_core <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L56>`_
   Applly pertubration ``h_core`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_by_mono_moller_plesset <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L56>`_
+`perturb_buffer_by_mono_moller_plesset <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L686>`_
   Applly pertubration ``moller_plesset`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L110>`_
+`perturb_buffer_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L740>`_
   Applly pertubration ``delta_rho_one_point`` to the buffer of determinants generated in the H_apply
   routine.
 
@@ -140,12 +140,12 @@ Documentation
   routine.
 
 
-`perturb_buffer_epstein_nesbet <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L635>`_
+`perturb_buffer_epstein_nesbet <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L110>`_
   Applly pertubration ``epstein_nesbet`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_epstein_nesbet_2x2 <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L740>`_
+`perturb_buffer_epstein_nesbet_2x2 <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L215>`_
   Applly pertubration ``epstein_nesbet_2x2`` to the buffer of determinants generated in the H_apply
   routine.
 
@@ -165,12 +165,12 @@ Documentation
   routine.
 
 
-`perturb_buffer_h_core <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L215>`_
+`perturb_buffer_h_core <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L5>`_
   Applly pertubration ``h_core`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_moller_plesset <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L5>`_
+`perturb_buffer_moller_plesset <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L635>`_
   Applly pertubration ``moller_plesset`` to the buffer of determinants generated in the H_apply
   routine.
 

plugins/Properties/.gitignore

@@ -1,13 +1,23 @@
-#
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
-# Do not modify this file. Add your ignored files to the gitignore
-# (without the dot at the beginning) file.
-#
 IRPF90_temp
 IRPF90_man
-irpf90.make
-tags
-Makefile.depend
 irpf90_entities
+tags
+irpf90.make
+Makefile
+Makefile.depend
 build.ninja
 .ninja_log
 .ninja_deps
+ezfio_interface.irp.f
+Ezfio_files
+Determinants
+Integrals_Monoelec
+MO_Basis
+Utils
+Pseudo
+Bitmask
+AO_Basis
+Electrons
+Nuclei
+Integrals_Bielec

plugins/Selectors_full/.gitignore

@@ -1,13 +1,25 @@
-#
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
-# Do not modify this file. Add your ignored files to the gitignore
-# (without the dot at the beginning) file.
-#
 IRPF90_temp
 IRPF90_man
-irpf90.make
-tags
-Makefile.depend
 irpf90_entities
+tags
+irpf90.make
+Makefile
+Makefile.depend
 build.ninja
 .ninja_log
 .ninja_deps
+ezfio_interface.irp.f
+Ezfio_files
+Determinants
+Integrals_Monoelec
+MO_Basis
+Utils
+Pseudo
+Bitmask
+AO_Basis
+Electrons
+MOGuess
+Nuclei
+Hartree_Fock
+Integrals_Bielec

plugins/SingleRefMethod/.gitignore

@@ -1,13 +1,19 @@
-#
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
-# Do not modify this file. Add your ignored files to the gitignore
-# (without the dot at the beginning) file.
-#
 IRPF90_temp
 IRPF90_man
-irpf90.make
-tags
-Makefile.depend
 irpf90_entities
+tags
+irpf90.make
+Makefile
+Makefile.depend
 build.ninja
 .ninja_log
 .ninja_deps
+ezfio_interface.irp.f
+Ezfio_files
+MO_Basis
+Utils
+Bitmask
+AO_Basis
+Electrons
+Nuclei

scripts/compilation/cache_compile.py

@@ -18,9 +18,8 @@ p = re.compile(ur'-I IRPF90_temp/\S*\s+')
 mod = re.compile(ur'module\s+(?P<mod>\S+).+end\s?module\s+(?P=mod)?',
                  re.MULTILINE | re.IGNORECASE)
 
-tmpdir_root = os.environ.get("TMPDIR",failobj="/dev/shm")
+tmpdir_root = os.environ.get("TMPDIR", failobj="/dev/shm")
-TMPDIR = os.path.join(tmpdir_root,os.environ["USER"],"qp_compiler") 
+TMPDIR = os.path.join(tmpdir_root, os.environ["USER"], "qp_compiler")
-
 
 
 def return_filename_to_cache(command):

scripts/compilation/qp_create_ninja.py

@@ -257,7 +257,7 @@ def ninja_ezfio_rule():
 
     install_lib_ezfio = join(QP_ROOT, 'install', 'EZFIO', "lib", "libezfio.a")
     l_cmd = ["cd {0}".format(QP_EZFIO)] + l_flag
-    l_cmd += ["ninja && ln -sf {0} {1}".format(install_lib_ezfio, EZFIO_LIB)]
+    l_cmd += ["rm -f make.config ; ninja && ln -sf {0} {1}".format(install_lib_ezfio, EZFIO_LIB)]
 
     l_string = ["rule build_ezfio",
                 "   command = {0}".format(" ; ".join(l_cmd)),
@@ -320,6 +320,37 @@ def ninja_symlink_build(path_module, l_symlink):
     return l_string
 
 
+#
+#    _  o _|_ o  _  ._   _  ._ _
+# o (_| |  |_ | (_| | | (_) | (/_
+#    _|          _|
+def ninja_gitignore_rule():
+    """
+    Return the command to create the gitignore
+    """
+    return ["rule build_gitignore",
+            "  command = module_handler.py create_git_ignore $module_rel",
+            "  description = Create gitignore for $module_rel", ""]
+
+
+def ninja_gitignore_build(path_module, l_symlink, d_binaries):
+    """
+    """
+
+    path_gitignore = join(path_module.abs, ".gitignore")
+
+    l_b = [i.abs for i in d_binaries[path_module]]
+    l_sym = [i.destination for i in l_symlink]
+
+    l_string = ["build {0}: build_gitignore {1} || {2}".format(path_gitignore,
+                                                               " ".join(l_b),
+                                                               " ".join(l_sym)),
+                "   module_rel = {0}".format(path_module.rel),
+                ""]
+
+    return l_string
+
+
 #           _  _   _
 # o ._ ._ _|_ (_| / \   ._ _   _. |   _
 # | |  |_) |    | \_/ o | | | (_| |< (/_
@@ -474,21 +505,25 @@ def ninja_readme_rule():
     For not dealted the readme when ninja -t clean and the generator option
     """
     l_string = ["rule build_readme",
-                "   command = cd $module_abs ; update_README.py",
+                "   command = cd $module_abs ; update_README.py $module_root",
+                "   description = update_README $module_rel",
                 "   generator = 1", ""]
 
     return l_string
 
 
-def ninja_readme_build(path_module):
+def ninja_readme_build(path_module, d_irp, dict_root_path):
     """
     Rule for creation the readme
     """
-    path_irp_man = join(path_module.abs, "irpf90.make")
     path_readme = join(path_module.abs, "README.rst")
+    root_module = dict_root_path[module]
+
+    l_depend = d_irp[path_module]["l_depend"] + [join(root_module.abs, "tags")]
 
     l_string = ["build {0}: build_readme {1}".format(path_readme,
-                                                     path_irp_man),
+                                                     " ".join(l_depend)),
+                "   module_root = {0}".format(root_module.abs),
                 "   module_abs = {0}".format(path_module.abs),
                 "   module_rel = {0}".format(path_module.rel), ""]
 
@@ -533,7 +568,7 @@ def get_dict_binaries(l_module, mode="production"):
     Example : The module Full_CI can produce the binary SCF
     so you dont need to compile at all the module Hartree-Fock
 
-    But you need to change the path acordingle
+    But you need to change the path acordingly
     Full_CI/Hartree-Fock/SCF
     """
     d_binaries = defaultdict(list)
@@ -664,10 +699,11 @@ def ninja_dot_tree_rule():
     return l_string
 
 
-def ninja_dot_tree_build(path_module):
+def ninja_dot_tree_build(path_module, l_module):
 
     path_tree = join(path_module.abs, "tree_dependency.png")
-    l_string = ["build {0}: build_dot_tree".format(path_tree),
+    l_dep = [join(path.abs, "NEEDED_CHILDREN_MODULES") for path in l_module]
+    l_string = ["build {0}: build_dot_tree {1}".format(path_tree, " ".join(l_dep)),
                 "   module_abs = {0}".format(path_module.abs),
                 "   module_rel = {0}".format(path_module.rel), ""]
 
@@ -695,7 +731,7 @@ def create_build_ninja_module(path_module):
                  "  pool = console", "  description = Compile all the module",
                  ""]
 
-    l_string += ["rule make_clean", "  command = clean_modules.sh",
+    l_string += ["rule make_clean", "  command = module_handler.py clean {0}".format(path_module.rel),
                  "  description = Cleaning module {0}".format(path_module.rel),
                  ""]
 
@@ -711,7 +747,7 @@ def create_build_ninja_module(path_module):
         f.write("\n".join(l_string))
 
 
-def create_build_ninja_global():
+def create_build_ninja_global(l_module):
 
     l_string = ["rule update_build_ninja_root",
                 "   command = {0} update".format(__file__),
@@ -723,7 +759,7 @@ def create_build_ninja_global():
                  ""]
 
     l_string += ["rule make_clean",
-                 "  command = cd {0} ; clean_modules.sh *".format(QP_SRC),
+                 "  command = module_handler.py clean {0}".format(" ".join([m.rel for m in l_module])),
                  "  description = Cleaning all modules", ""]
 
     l_string += ["build dummy_target: update_build_ninja_root",
@@ -782,6 +818,7 @@ if __name__ == "__main__":
 
     l_string += ninja_irpf90_make_rule()
     l_string += ninja_readme_rule()
+    l_string += ninja_gitignore_rule()
 
     l_string += ninja_binaries_rule()
 
@@ -816,8 +853,18 @@ if __name__ == "__main__":
     d_genealogy_path = dict_module_genelogy_path(d_genealogy)
     d_irp = get_file_dependency(d_genealogy_path)
 
+    dict_root = module_instance.dict_root
+    dict_root_path = dict_module_genelogy_path(dict_root)
+
     l_module = d_genealogy_path.keys()
 
+    for module in l_module:
+        # ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
+        # d o t _ t r e e  & r e a d  m e #
+        # ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
+        l_string += ninja_dot_tree_build(module, l_module)
+        l_string += ninja_readme_build(module, d_irp, dict_root_path)
+
     # ~#~#~#~#~#~#~#~#~#~#~#~#~ #
     # M o d u l e _ t o _ i r p #
     # ~#~#~#~#~#~#~#~#~#~#~#~#~ #
@@ -832,7 +879,7 @@ if __name__ == "__main__":
         d_binaries = get_dict_binaries(l_module, mode="development")
         l_module = d_binaries.keys()
 
-    create_build_ninja_global()
+    create_build_ninja_global(l_module)
 
     for module_to_compile in l_module:
 
@@ -853,15 +900,11 @@ if __name__ == "__main__":
         l_string += ninja_irpf90_make_build(module_to_compile, l_children,
                                             d_irp)
 
-        # ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
-        # d o t _ t r e e  & r e a d  m e #
-        # ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
-        l_string += ninja_dot_tree_build(module_to_compile)
-        l_string += ninja_readme_build(module_to_compile)
-
         l_string += ninja_binaries_build(module_to_compile, l_children,
                                          d_binaries)
 
+        l_string += ninja_gitignore_build(module_to_compile, l_symlink, d_binaries)
+
     with open(join(QP_ROOT, "config", "build.ninja"), "w+") as f:
         f.write(header)
         f.write("\n".join(l_string))

scripts/ezfio_interface/ei_handler.py

@@ -44,6 +44,8 @@ Optional:
     size: <str>         The size information.
                             (by default is one)
                             Example : 1, =sum(ao_num); (ao_num,3)
+                            ATTENTION : The module and the value are separed by a "." not a "_".
+                            For exemple (determinants.n_det)
     ezfio_name: <str>   The name for the EZFIO lib
                              (by default is <provider_name>)
     ezfio_dir: <str>    Will be the folder of EZFIO.
@@ -131,7 +133,7 @@ def get_type_dict():
     fancy_type['bool'] = Type(None, "bool", "logical")
 
     fancy_type['character*(32)'] = Type(None, "string", "character*(32)")
-    fancy_type['character*(64)'] = Type(None, "string", "character*(68)")
+    fancy_type['character*(64)'] = Type(None, "string", "character*(64)")
     fancy_type['character*(256)'] = Type(None, "string", "character*(256)")
 
     # ~#~#~#~#~#~#~#~ #
@@ -228,6 +230,8 @@ def get_dict_config_file(module_obj):
         # pvd = provider
         pvd = section.lower()
 
+        d[pvd]["module"] = module_obj
+
         # Create the dictionary who containt the value per default
         d_default = {"ezfio_name": pvd,
                      "ezfio_dir": module_obj.lower,
@@ -255,7 +259,7 @@ def get_dict_config_file(module_obj):
             sys.exit(1)
 
         try:
-            interface = map(str.lower, config_file.get(section, "interface").split(","))
+            interface = [i.lower().strip() for i in config_file.get(section, "interface").split(",")]
         except ConfigParser.NoOptionError:
             error("doc", pvd, module_obj.path)
             sys.exit(1)
@@ -317,7 +321,7 @@ def create_ezfio_provider(dict_ezfio_cfg):
             ez_p.set_doc(dict_info['doc'])
             ez_p.set_ezfio_dir(dict_info['ezfio_dir'])
             ez_p.set_ezfio_name(dict_info['ezfio_name'])
-            ez_p.set_output("output_%s" % dict_info['ezfio_dir'])
+            ez_p.set_output("output_%s" % dict_info['module'].lower)
 
             # (nuclei.nucl_num,pseudo.klocmax) => (nucl_num,klocmax)
             ez_p.set_size(re.sub(r'\w+\.', "", dict_info['size']))

scripts/generate_h_apply.py

@@ -277,7 +277,7 @@ class H_apply(object):
           do k=1,N_st
             norm_psi(k) = norm_psi(k) + psi_coef_generators(i_generator,k)*psi_coef_generators(i_generator,k)
 !            delta_pt2(k) = 0.d0
-!            pt2_old(k) = 0.d0
+             pt2_old(k) = 0.d0
 !            pt2(k) = select_max(i_generator)
           enddo
           !$ call omp_unset_lock(lck)

scripts/module/clean_modules.sh

@@ -1,37 +0,0 @@
-#!/bin/bash 
-#
-# Cleans a module directory 
-
-if [[ -z ${QP_ROOT} ]]
-then
-  print "The QP_ROOT environment variable is not set."
-  print "Please reload the quantum_package.rc file."
-  exit -1
-fi
-source ${QP_ROOT}/scripts/qp_include.sh
-
-function do_clean()
-{
-  rm -rf -- \
-    IRPF90_temp IRPF90_man \
-    $(module_handler.py print_descendant) include \
-    ezfio_interface.irp.f irpf90.make irpf90_entities tags $(ls_exe) *.mod
-}
-
-if [[ -z $1 ]]
-then
-  check_current_dir_is_module
-  do_clean
-else
-  check_current_dir_is_src
-  for i in $@
-  do
-    if [[ -d $i ]]
-    then
-       cd $i
-       do_clean
-       cd $OLDPWD
-    fi
-  done
-fi
-

scripts/module/module_handler.py

@@ -1,13 +1,13 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 """
-Create the NEEDED_MODULE
+Module utilitary
-    aka the genealogy (children module, subchildren module and so on),
-of a NEEDED_CHILDREN_MODULES file
 
 Usage:
-    module_handler.py print_descendant      [<NEEDED_CHILDREN_MODULES>]
+    module_handler.py print_descendant      [<module_name>...]
-    module_handler.py create_png            [<NEEDED_CHILDREN_MODULES>]
+    module_handler.py create_png            [<module_name>...]
+    module_handler.py clean                 [<module_name>...]
+    module_handler.py create_git_ignore     [<module_name>...]
 
 Options:
     print_descendant         Print the genealogy of the NEEDED_CHILDREN_MODULES
@@ -19,16 +19,27 @@ Options:
 import os
 import sys
 import os.path
-from collections import namedtuple
+import shutil
 
 try:
     from docopt import docopt
+    from qp_path import QP_SRC
 except ImportError:
     print "source .quantum_package.rc"
     raise
 
 
 # Canot cache for namedtuple are not hashable
+def is_module(path_module):
+    return os.path.isfile(os.path.join(QP_SRC,
+                                       path_module,
+                                       "NEEDED_CHILDREN_MODULES"))
+
+
+def is_exe(fpath):
+    return os.path.isfile(fpath) and os.access(fpath, os.X_OK)
+
+
 def get_dict_child(l_root_abs=None):
     """Loop over MODULE in  QP_ROOT/src, open all the NEEDED_CHILDREN_MODULES
     and create a dict[MODULE] = [sub module needed, ...]
@@ -36,8 +47,7 @@ def get_dict_child(l_root_abs=None):
     d_ref = dict()
 
     if not l_root_abs:
-        qp_root = os.environ['QP_ROOT']
+        l_root_abs = [QP_SRC]
-        l_root_abs = [os.path.join(qp_root, 'src')]
 
     for root_abs in l_root_abs:
         for module_rel in os.listdir(root_abs):
@@ -201,19 +211,70 @@ if __name__ == '__main__':
 
     arguments = docopt(__doc__)
 
-    if not arguments['<NEEDED_CHILDREN_MODULES>']:
+    if not arguments['<module_name>']:
         dir_ = os.getcwd()
+        l_module = [os.path.basename(dir_)]
     else:
-        path_file = os.path.abspath(arguments['<NEEDED_CHILDREN_MODULES>'])
+        l_module = arguments['<module_name>']
-        path_file = os.path.expanduser(path_file)
+
-        path_file = os.path.expandvars(path_file)
+    for module in l_module:
-        dir_ = os.path.dirname(path_file)
+        if not is_module(module):
+            print "{0} is not a volide module. Abort".format(module)
+            print "No NEEDED_CHILDREN_MODULES in it"
+            sys.exit(1)
 
-    path_file = os.path.basename(dir_)
     m = ModuleHandler()
 
     if arguments['print_descendant']:
-        print " ".join(sorted(m.l_module))
+
+        for module in l_module:
+            print " ".join(sorted(m.l_descendant_unique([module])))
 
     if arguments["create_png"]:
-        m.create_png([path_file])
+        m.create_png(l_module)
+
+    if arguments["clean"] or arguments["create_git_ignore"]:
+
+        l_dir = ['IRPF90_temp', 'IRPF90_man']
+        l_file = ["irpf90_entities", "tags", "irpf90.make",
+                  "Makefile", "Makefile.depend",
+                  "build.ninja", ".ninja_log", ".ninja_deps",
+                  "ezfio_interface.irp.f"]
+
+        for module in l_module:
+            module_abs = os.path.realpath(os.path.join(QP_SRC, module))
+            l_symlink = m.l_descendant_unique([module])
+            l_exe = [f for f in os.listdir(module_abs) if is_exe(os.path.join(module_abs,f))]
+
+            if arguments["clean"]:
+                for f in l_dir:
+                    try:
+                        shutil.rmtree(os.path.join(module_abs, f))
+                    except:
+                        pass
+
+                for symlink in l_symlink:
+                    try:
+                        os.unlink(os.path.join(module_abs, symlink))
+                    except:
+                        pass
+
+                for f in l_file:
+                    try:
+                        os.remove(os.path.join(module_abs, f))
+                    except:
+                        pass
+
+                for f in l_exe:
+
+                    try:
+                        os.remove(os.path.join(module_abs, f))
+                    except:
+                        pass
+
+            if arguments["create_git_ignore"]:
+                path = os.path.join(module_abs, ".gitignore")
+
+                with open(path, "w+") as f:
+                    f.write("# Automatically created by {0} \n".format(__file__))
+                    f.write("\n".join(l_dir + l_file + l_symlink + l_exe))

scripts/module/qp_install_module.py

@@ -5,12 +5,12 @@ Usage:
        qp_install_module.py create -n <name> [<children_module>...]
        qp_install_module.py download -n <name> [<path_folder>...]
        qp_install_module.py install <name>...
-       qp_install_module.py list (--installed|--avalaible-local|--avalaible-remote)
+       qp_install_module.py list (--installed | --available-local)
-       qp_install_module.py uninstall <name>...
+       qp_install_module.py uninstall <name>... [--and_ancestor]
 
 
 Options:
-    list: List all the module avalaible
+    list: List all the module available
     create: Create a new module
 """
 
@@ -22,6 +22,8 @@ try:
     from module_handler import ModuleHandler, get_dict_child
     from module_handler import get_l_module_descendant
     from update_README import Doc_key, Needed_key
+    from qp_path import QP_SRC, QP_PLUGINS
+
 except ImportError:
     print "source .quantum_package.rc"
     raise
@@ -59,15 +61,13 @@ def save_new_module(path, l_child):
 
 if __name__ == '__main__':
     arguments = docopt(__doc__)
-    qp_root_src = os.path.join(os.environ['QP_ROOT'], "src")
-    qp_root_plugin = os.path.join(os.environ['QP_ROOT'], "plugins")
 
     if arguments["list"]:
 
         if arguments["--installed"]:
-            l_repository = [qp_root_src]
+            l_repository = [QP_SRC]
-        if arguments["--avalaible-local"]:
+        elif arguments["--available-local"]:
-            l_repository = [qp_root_plugin]
+            l_repository = [QP_PLUGINS]
 
         m_instance = ModuleHandler(l_repository)
 
@@ -75,11 +75,11 @@ if __name__ == '__main__':
             print "* {0}".format(module)
 
     elif arguments["create"]:
-        m_instance = ModuleHandler([qp_root_src])
+        m_instance = ModuleHandler([QP_SRC])
 
         l_children = arguments["<children_module>"]
 
-        path = os.path.join(qp_root_src, arguments["<name>"])
+        path = os.path.join(QP_SRC, arguments["<name>"])
 
         print "You will create the module:"
         print path
@@ -87,7 +87,8 @@ if __name__ == '__main__':
         for children in l_children:
             if children not in m_instance.dict_descendant:
                 print "This module ({0}) is not a valide module.".format(children)
-                print "Run `list` flag for the list of module avalaible"
+                print "Run `list` flag for the list of module available"
+                print "Maybe you need to install some module first"
                 print "Aborting..."
                 sys.exit(1)
 
@@ -104,7 +105,7 @@ if __name__ == '__main__':
 
     elif arguments["download"]:
         pass
-#        d_local = get_dict_child([qp_root_src])
+#        d_local = get_dict_child([QP_SRC])
 #        d_remote = get_dict_child(arguments["<path_folder>"])
 #
 #        d_child = d_local.copy()
@@ -119,8 +120,8 @@ if __name__ == '__main__':
 
     elif arguments["install"]:
 
-        d_local = get_dict_child([qp_root_src])
+        d_local = get_dict_child([QP_SRC])
-        d_plugin = get_dict_child([qp_root_plugin])
+        d_plugin = get_dict_child([QP_PLUGINS])
 
         d_child = d_local.copy()
         d_child.update(d_plugin)
@@ -143,31 +144,43 @@ if __name__ == '__main__':
             print "Installation...",
 
             for module_to_cp in l_module_to_cp:
-                    src = os.path.join(qp_root_plugin, module_to_cp)
+                    src = os.path.join(QP_PLUGINS, module_to_cp)
-                    des = os.path.join(qp_root_src, module_to_cp)
+                    des = os.path.join(QP_SRC, module_to_cp)
                     try:
                         os.symlink(src, des)
                     except OSError:
-                        print "Your src directory is broken. Please remove %s"%des
+                        print "Your src directory is broken. Please remove %s" % des
                         raise
             print "Done"
             print "You can now compile as usual"
 
     elif arguments["uninstall"]:
 
-        d_local = get_dict_child([qp_root_src])
+        m_instance = ModuleHandler([QP_SRC])
+        d_descendant = m_instance.dict_descendant
+
+        d_local = get_dict_child([QP_SRC])
         l_name = arguments["<name>"]
 
-        l_failed = [ name for name in l_name if name not in d_local ]
+        l_failed = [name for name in l_name if name not in d_local]
         if l_failed:
             print "Modules not installed:"
             for name in sorted(l_failed):
-                print "* %s"%name
+                print "* %s" % name
             sys.exit(1)
         else:
+            if arguments["--and_ancestor"]:
+
+                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 "You will remove all of:"
+                print l_name_to_remove
+
+            else:
+                l_name_to_remove = l_name
+
             def unlink(x):
                 try:
-                    os.unlink(os.path.join(qp_root_src,x))
+                    os.unlink(os.path.join(QP_SRC, x))
                 except OSError:
-                    print "%s is a core module which can not be renmoved"%x
+                    print "%s is a core module which can not be renmoved" % x
-            map(unlink,l_name) 
+            map(unlink, l_name_to_remove)

scripts/module/update_README.py

@@ -13,6 +13,24 @@ URL = "http://github.com/LCPQ/quantum_package/tree/master/src/"
 import os
 import subprocess
 from collections import namedtuple
+import sys
+
+"""
+NEED to call in a module
+First arg can be the root parent
+"""
+try:
+    ROOT_module = os.path.realpath(sys.argv[1])
+except:
+    ROOT_module = os.getcwd()
+
+if ROOT_module != os.getcwd():
+    change = True
+else:
+    change = False
+
+MODULE_NAME = os.path.basename(os.getcwd())
+
 
 header = """
 .. Do not edit this section. It was auto-generated from the
@@ -71,7 +89,8 @@ def update_needed(data):
 def extract_doc(item):
     """Extracts the documentation contained in IRPF90_man file"""
 
-    with open("IRPF90_man/%s.l" % (item), 'r') as f:
+    path = os.path.join(ROOT_module, "IRPF90_man/%s.l" % (item))
+    with open(path, 'r') as f:
         l_line = f.readlines()
 
     result = []
@@ -97,15 +116,24 @@ def update_documentation(data):
 
     # If the file does not exist, don't do anything
 
-    with open('tags', 'r') as f:
+    path = os.path.join(ROOT_module, "tags")
-        l_info = [IRP_info(*i.split()) for i in f.readlines()
+
-                  if "/" not in i.split()[1]]
+    with open(path, 'r') as f:
+        dump = f.readlines()
+
+    l_info = []
+    for i in dump:
+        name, f, ligne = i.split()
+
+        if not change and "/" not in i:
+            l_info.append(IRP_info(name, f, ligne))
+        elif change and MODULE_NAME in i:
+            l_info.append(IRP_info(name, f.split("/")[-1], ligne))
 
     l_line = []
-    module_name = os.path.basename(os.getcwd())
 
     for irp in l_info:
-        url = os.path.join(URL, module_name, irp.file)
+        url = os.path.join(URL, MODULE_NAME, irp.file)
         doc = extract_doc(irp.name)
 
         l_line += ["`{0} <{1}#L{2}>`_".format(irp.name, url, irp.line), doc,

scripts/qp_include.sh

@@ -1,78 +0,0 @@
-#!/bin/bash
-#
-# Useful functions in all scripts
-
-# Make a list unique
-function unique_list()
-{
-  for d in $@
-  do
-    echo $d
-  done | sort | uniq
-}
-
-function check_current_dir_is_src()
-{
-  if [[ "${PWD}" == "${QP_ROOT}/src" ]]
-  then
-     return 0
-  else
-     echo "Current directory should be \$QP_ROOT/src"
-     exit -1
-  fi
-}
-
-function check_current_dir_is_module()
-{
-  # If the prefix ${QP_ROOT}/src/ can be removed from $PWD, it means that
-  # $PWD is somewhere below ${QP_ROOT}/src/ so it is a module.
-  # If the prefix ${QP_ROOT}/src/ can not be removed from $PWD, then
-  # "${PWD##${QP_ROOT}/src/}" == "$PWD".
-
-  if [[ "${PWD##${QP_ROOT}/src/}" != "$PWD" ]]
-  then
-     return 0
-  else
-     echo "You are not in a submodule"
-     exit -1
-  fi
-}
-
-# List of executables in the current directory
-function ls_exe()
-{
-  find . -perm /u+x -type f
-}
-
-function asksure() {
-  echo -n $@ "(Y/N) "
-  answer=w
-  while [[ $answer != [YyNn] ]]
-  do
-     read answer
-     [[ $answer = [Yy] ]] && retval=0 || retval=1
-  done
-  return $retval
-}
-
-function error()
-{
-  echo "-------------------- Error --------------------"
-  printf "$@\n"
-  echo "-----------------------------------------------"
-  exit -1
-}
-
-if [[ -z ${DEBUG} ]]
-then
-  function info ()
-  {
-    :
-  }
-else
-  function info ()
-  {
-    echo "$@"
-  }
-fi
-

scripts/utility/qp_path.py

@@ -11,5 +11,6 @@ except:
     sys.exit(1)
 else:
     QP_SRC = os.path.join(QP_ROOT, "src")
+    QP_PLUGINS = os.path.join(QP_ROOT, "plugins")
     QP_EZFIO = os.path.join(QP_ROOT, "install", "EZFIO")
     QP_OCAML = os.path.join(QP_ROOT, "ocaml")

src/.gitignore

@@ -1,2 +1,25 @@
-Makefile.config
+CAS_SD
-ezfio_interface.irp.f
+CID
+CID_SC2_selected
+CID_selected
+CIS
+CISD
+CISD_SC2_selected
+CISD_selected
+DDCI_selected
+DensityMatrix
+FCIdump
+Full_CI
+Generators_CAS
+Generators_full
+Generators_restart
+Hartree_Fock
+Molden
+MP2
+MRCC
+Perturbation
+Properties
+QmcChem
+Selectors_full
+Selectors_no_sorted
+SingleRefMethod

src/AO_Basis/.gitignore

@@ -0,0 +1,15 @@
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
+IRPF90_temp
+IRPF90_man
+irpf90_entities
+tags
+irpf90.make
+Makefile
+Makefile.depend
+build.ninja
+.ninja_log
+.ninja_deps
+ezfio_interface.irp.f
+Nuclei
+Ezfio_files
+Utils

src/AO_Basis/README.rst

@@ -46,135 +46,135 @@ Documentation
 .. Do not edit this section. It was auto-generated from the
 .. by the `update_README.py` script.
 
-`ao_coef <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L62>`_
+`ao_coef <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L62>`_
   AO Coefficients, read from input. Those should not be used directly, as
   the MOs are expressed on the basis of **normalized** AOs.
 
 
-`ao_coef_normalized <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L84>`_
+`ao_coef_normalized <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L84>`_
   Coefficients including the AO normalization
 
 
-`ao_coef_normalized_ordered <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L107>`_
+`ao_coef_normalized_ordered <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L107>`_
   Sorted primitives to accelerate 4 index MO transformation
 
 
-`ao_coef_normalized_ordered_transp <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L133>`_
+`ao_coef_normalized_ordered_transp <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L133>`_
   Transposed ao_coef_normalized_ordered
 
 
-`ao_expo <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L41>`_
+`ao_expo <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L41>`_
   AO Exponents read from input
 
 
-`ao_expo_ordered <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L108>`_
+`ao_expo_ordered <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L108>`_
   Sorted primitives to accelerate 4 index MO transformation
 
 
-`ao_expo_ordered_transp <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L147>`_
+`ao_expo_ordered_transp <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L147>`_
   Transposed ao_expo_ordered
 
 
-`ao_l <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L162>`_
+`ao_l <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L162>`_
   ao_l = l value of the AO: a+b+c in x^a y^b z^c
 
 
-`ao_l_char <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L163>`_
+`ao_l_char <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L163>`_
   ao_l = l value of the AO: a+b+c in x^a y^b z^c
 
 
-`ao_l_char_space <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L311>`_
+`ao_l_char_space <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L311>`_
   Undocumented
 
 
-`ao_md5 <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L403>`_
+`ao_md5 <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L403>`_
   MD5 key characteristic of the AO basis
 
 
-`ao_nucl <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L209>`_
+`ao_nucl <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L209>`_
   Index of the nuclei on which the ao is centered
 
 
-`ao_num <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L1>`_
+`ao_num <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L1>`_
   Number of atomic orbitals
 
 
-`ao_num_align <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L2>`_
+`ao_num_align <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L2>`_
   Number of atomic orbitals
 
 
-`ao_overlap <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/ao_overlap.irp.f#L1>`_
+`ao_overlap <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/ao_overlap.irp.f#L1>`_
   Overlap between atomic basis functions:
   :math:`\int \chi_i(r) \chi_j(r) dr)`
 
 
-`ao_overlap_abs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/ao_overlap.irp.f#L65>`_
+`ao_overlap_abs <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/ao_overlap.irp.f#L65>`_
   Overlap between absolute value of atomic basis functions:
   :math:`\int |\chi_i(r)| |\chi_j(r)| dr)`
 
 
-`ao_overlap_x <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/ao_overlap.irp.f#L2>`_
+`ao_overlap_x <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/ao_overlap.irp.f#L2>`_
   Overlap between atomic basis functions:
   :math:`\int \chi_i(r) \chi_j(r) dr)`
 
 
-`ao_overlap_y <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/ao_overlap.irp.f#L3>`_
+`ao_overlap_y <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/ao_overlap.irp.f#L3>`_
   Overlap between atomic basis functions:
   :math:`\int \chi_i(r) \chi_j(r) dr)`
 
 
-`ao_overlap_z <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/ao_overlap.irp.f#L4>`_
+`ao_overlap_z <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/ao_overlap.irp.f#L4>`_
   Overlap between atomic basis functions:
   :math:`\int \chi_i(r) \chi_j(r) dr)`
 
 
-`ao_power <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L19>`_
+`ao_power <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L19>`_
   Powers of x,y and z read from input
 
 
-`ao_prim_num <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L177>`_
+`ao_prim_num <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L177>`_
   Number of primitives per atomic orbital
 
 
-`ao_prim_num_max <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L199>`_
+`ao_prim_num_max <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L199>`_
   Undocumented
 
 
-`ao_prim_num_max_align <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L200>`_
+`ao_prim_num_max_align <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L200>`_
   Undocumented
 
 
-`l_to_charater <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L218>`_
+`l_to_charater <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L218>`_
   character corresponding to the "L" value of an AO orbital
 
 
-`n_aos_max <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L231>`_
+`n_aos_max <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L231>`_
   Number of AOs per atom
 
 
-`n_pt_max_i_x <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/dimensions_integrals.irp.f#L2>`_
+`n_pt_max_i_x <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/dimensions_integrals.irp.f#L2>`_
   Undocumented
 
 
-`n_pt_max_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/dimensions_integrals.irp.f#L1>`_
+`n_pt_max_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/dimensions_integrals.irp.f#L1>`_
   Undocumented
 
 
-`nucl_aos <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L244>`_
+`nucl_aos <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L244>`_
   List of AOs attached on each atom
 
 
-`nucl_list_shell_aos <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L262>`_
+`nucl_list_shell_aos <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L262>`_
   Index of the shell type Aos and of the corresponding Aos
   Per convention, for P,D,F and G AOs, we take the index
   of the AO with the the corresponding power in the "X" axis
 
 
-`nucl_n_aos <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L230>`_
+`nucl_n_aos <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L230>`_
   Number of AOs per atom
 
 
-`nucl_num_shell_aos <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L263>`_
+`nucl_num_shell_aos <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L263>`_
   Index of the shell type Aos and of the corresponding Aos
   Per convention, for P,D,F and G AOs, we take the index
   of the AO with the the corresponding power in the "X" axis

src/AOs/.gitignore

@@ -1,13 +0,0 @@
-#
-# Do not modify this file. Add your ignored files to the gitignore
-# (without the dot at the beginning) file.
-#
-IRPF90_temp
-IRPF90_man
-irpf90.make
-tags
-Makefile.depend
-irpf90_entities
-build.ninja
-.ninja_log
-.ninja_deps

src/Bitmask/.gitignore

@@ -1,13 +1,18 @@
-#
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
-# Do not modify this file. Add your ignored files to the gitignore
-# (without the dot at the beginning) file.
-#
 IRPF90_temp
 IRPF90_man
-irpf90.make
-tags
-Makefile.depend
 irpf90_entities
+tags
+irpf90.make
+Makefile
+Makefile.depend
 build.ninja
 .ninja_log
 .ninja_deps
+ezfio_interface.irp.f
+Ezfio_files
+MO_Basis
+Utils
+AO_Basis
+Electrons
+Nuclei

src/Bitmask/NEEDED_CHILDREN_MODULES

@@ -1 +1 @@
-MOs
+MO_Basis

src/Bitmask/README.rst

@@ -42,7 +42,7 @@ Needed Modules
 
 .. image:: tree_dependency.png
 
-* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
+* `MO_Basis <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis>`_
 
 Documentation
 =============

src/Determinants/.gitignore

@@ -1,32 +1,30 @@
-#
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
-# Do not modify this file. Add your ignored files to the gitignore
-# (without the dot at the beginning) file.
-#
 IRPF90_temp
 IRPF90_man
-irpf90.make
-tags
-Makefile.depend
 irpf90_entities
+tags
+irpf90.make
+Makefile
+Makefile.depend
 build.ninja
 .ninja_log
 .ninja_deps
-Pseudo
+ezfio_interface.irp.f
-Integrals_Monoelec
-Bitmask
-Integrals_Bielec
-AOs
-MOs
-Electrons
-Utils
-Nuclei
 Ezfio_files
+Integrals_Monoelec
+MO_Basis
+Utils
+Pseudo
+Bitmask
+AO_Basis
+Electrons
+Nuclei
+Integrals_Bielec
 guess_triplet
 guess_singlet
 truncate_wf
 save_natorb
-save_for_qmcchem
+program_initial_determinants
-program_beginer_determinants
 save_for_casino
 det_svd
-guess_doublet
+guess_doublet

src/Determinants/EZFIO.cfg

@@ -55,58 +55,58 @@ default:        0.999
 [n_states_diag]
 type: integer
 doc: n_states_diag
-interface: ezfio, provider
+interface: ezfio,provider
 
 [n_int]
-interface: ezfio, provider
+interface: ezfio
 doc: n_int
 type: N_int_number
 
 [bit_kind]
-interface: ezfio, provider
+interface: ezfio
 doc: bit_kind
 type: Bit_kind
 
 [mo_label]
-interface: ezfio, provider
+interface: ezfio
-doc: o_label
+doc: mo_label
 type: character*(64)
 
 [n_det]
-interface: ezfio, provider
+interface: ezfio
 doc: n_det
 type: integer
 
 [psi_coef]
-interface: ezfio, provider
+interface: ezfio
 doc: psi_coef
 type: double precision 
 size: (determinants.n_det,determinants.n_states)
 
 [psi_det]
-interface: ezfio, provider
+interface: ezfio
 doc: psi_det
 type: integer*8
 size: (determinants.n_int*determinants.bit_kind/8,2,determinants.n_det)
 
 [det_num]
-interface: ezfio, provider
+interface: ezfio,provider
 doc: det_num
 type: integer
 
 [det_occ]
-interface: ezfio, provider
+interface: ezfio,provider
 doc: det_occ
 type: integer          
 size:  (electrons.elec_alpha_num,determinants.det_num,2)
 
 [det_coef]
-interface: ezfio, provider
+interface: ezfio,provider
 doc: det_coef
 type: double precision 
 size:  (determinants.det_num)
 
 [expected_s2]
-interface: ezfio, provider
+interface: ezfio,provider
 doc: expcted_s2
 type: double precision 

src/Determinants/README.rst

@@ -205,10 +205,22 @@ Documentation
   degree : Degree of excitation
 
 
+`det_coef <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/ezfio_interface.irp.f#L138>`_
+  det_coef
+
+
 `det_connections <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/slater_rules.irp.f#L1139>`_
   Build connection proxy between determinants
 
 
+`det_num <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/ezfio_interface.irp.f#L248>`_
+  det_num
+
+
+`det_occ <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/ezfio_interface.irp.f#L226>`_
+  det_occ
+
+
 `det_search_key <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/connected_to_ref.irp.f#L1>`_
   Return an integer*8 corresponding to a determinant index for searching
 
@@ -505,15 +517,15 @@ Documentation
   determinants. idx_cas gives the indice of the CAS determinant in psi_det.
 
 
-`n_det_max <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/ezfio_interface.irp.f#L28>`_
+`n_det_max <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/ezfio_interface.irp.f#L50>`_
   Max number of determinants in the wave function
 
 
-`n_det_max_jacobi <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/ezfio_interface.irp.f#L72>`_
+`n_det_max_jacobi <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/ezfio_interface.irp.f#L94>`_
   Maximum number of determinants diagonalized by Jacobi
 
 
-`n_det_max_property <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/ezfio_interface.irp.f#L182>`_
+`n_det_max_property <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/ezfio_interface.irp.f#L292>`_
   Max number of determinants in the wave function when you select for a given property
 
 
@@ -537,7 +549,7 @@ Documentation
   Number of single excitation bitmasks
 
 
-`n_states <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/ezfio_interface.irp.f#L50>`_
+`n_states <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/ezfio_interface.irp.f#L72>`_
   Number of states to consider
 
 
@@ -585,7 +597,7 @@ Documentation
   rho(alpha) - rho(beta)
 
 
-`only_single_double_dm <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/ezfio_interface.irp.f#L116>`_
+`only_single_double_dm <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/ezfio_interface.irp.f#L182>`_
   If true, The One body DM is calculated with ignoring the Double<->Doubles extra diag elements
 
 
@@ -762,7 +774,7 @@ Documentation
   Reads the determinants from the EZFIO file
 
 
-`read_wf <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/ezfio_interface.irp.f#L94>`_
+`read_wf <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/ezfio_interface.irp.f#L160>`_
   If true, read the wave function from the EZFIO file
 
 
@@ -787,7 +799,7 @@ Documentation
   Undocumented
 
 
-`s2_eig <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/ezfio_interface.irp.f#L138>`_
+`s2_eig <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/ezfio_interface.irp.f#L116>`_
   Force the wave function to be an eigenfunction of S^2
 
 
@@ -862,7 +874,7 @@ Documentation
   convergence of the correlation energy of SC2 iterations
 
 
-`threshold_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/ezfio_interface.irp.f#L160>`_
+`threshold_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/ezfio_interface.irp.f#L270>`_
   Thresholds on generators (fraction of the norm)
 
 

src/Determinants/diagonalize_CI.irp.f

@@ -52,6 +52,10 @@ END_PROVIDER
     
     call davidson_diag(psi_det,CI_eigenvectors,CI_electronic_energy, &
         size(CI_eigenvectors,1),N_det,N_states_diag,N_int,output_determinants)
+    do j=1,N_states_diag
+      call get_s2_u0(psi_det,CI_eigenvectors(1,j),N_det,size(CI_eigenvectors,1),CI_eigenvectors_s2(j))
+    enddo
+
     
   else if (diag_algorithm == "Lapack") then
     
@@ -69,7 +73,8 @@ END_PROVIDER
     if (s2_eig) then
       i_state = 0
       do j=1,N_det
-        call get_s2_u0(psi_det,eigenvectors(1,j),N_det,N_det,s2)
+        call get_s2_u0(psi_det,eigenvectors(1,j),N_det,size(eigenvectors,1),s2)
+        print*,'s2 = ',s2
         if(dabs(s2-expected_s2).le.0.3d0)then
         i_state += 1
         do i=1,N_det

src/Determinants/s2.irp.f

@@ -1,4 +1,4 @@
-subroutine get_s2(key_i,key_j,phase,Nint)
+subroutine get_s2(key_i,key_j,s2,Nint)
  implicit none
  use bitmasks
  BEGIN_DOC
@@ -7,21 +7,21 @@ subroutine get_s2(key_i,key_j,phase,Nint)
  integer, intent(in)  :: Nint
  integer(bit_kind), intent(in)  :: key_i(Nint,2)
  integer(bit_kind), intent(in)  :: key_j(Nint,2)
- double precision, intent(out) :: phase
+ double precision, intent(out) :: s2
  integer :: exc(0:2,2,2)
  integer :: degree
  double precision :: phase_spsm
  integer :: nup, i
 
- phase = 0.d0
+ s2 = 0.d0
  !$FORCEINLINE
  call get_excitation_degree(key_i,key_j,degree,Nint)
  select case (degree)
    case(2)
-     call get_double_excitation(key_i,key_j,exc,phase_spsm,Nint)
+     call get_double_excitation(key_j,key_i,exc,phase_spsm,Nint)
      if (exc(0,1,1) == 1) then   ! Mono alpha + mono-beta
        if ( (exc(1,1,1) == exc(1,2,2)).and.(exc(1,1,2) == exc(1,2,1)) ) then
-         phase =  -phase_spsm
+         s2 =  -phase_spsm
        endif
      endif
    case(0)
@@ -29,7 +29,7 @@ subroutine get_s2(key_i,key_j,phase,Nint)
       do i=1,Nint
         nup += popcnt(iand(xor(key_i(i,1),key_i(i,2)),key_i(i,1)))
       enddo
-      phase = dble(nup)
+      s2 = dble(nup)
    end select
 end
 
@@ -72,7 +72,7 @@ BEGIN_PROVIDER [ double precision, s2_values, (N_states) ]
  integer :: i
  double precision :: s2
  do i = 1, N_states
-  call get_s2_u0(psi_det,psi_coef(1,i),n_det,psi_det_size,s2)
+  call get_s2_u0(psi_det,psi_coef(1,i),n_det,size(psi_coef,1),s2)
   s2_values(i) = s2
  enddo
 
@@ -89,18 +89,32 @@ subroutine get_s2_u0(psi_keys_tmp,psi_coefs_tmp,n,nmax,s2)
  integer :: i,j,l
  double precision :: s2_tmp
  s2 = 0.d0
+!print*,'IN get_s2_u0'
+!print*,'n,nmax = ',n,nmax
+ double precision :: accu
+ accu = 0.d0
+ do i = 1,n
+  accu += psi_coefs_tmp(i) * psi_coefs_tmp(i)
+! print*,'psi_coef = ',psi_coefs_tmp(i)
+ enddo
+!print*,'accu = ',accu
+!print*,''
  !$OMP PARALLEL DO DEFAULT(NONE) &
- !$OMP PRIVATE(i,j,s2_tmp) SHARED(n,psi_coefs_tmp,psi_keys_tmp,N_int) &
+ !$OMP PRIVATE(i,j,s2_tmp) SHARED(n,psi_coefs_tmp,psi_keys_tmp,N_int) REDUCTION(+:s2) SCHEDULE(dynamic) 
- !$OMP REDUCTION(+:s2) SCHEDULE(dynamic)
  do i=1,n
-   call get_s2(psi_keys_tmp(1,1,i),psi_keys_tmp(1,1,i),s2_tmp,N_int)
-   s2 += psi_coefs_tmp(i)*psi_coefs_tmp(i)*s2_tmp
    do j=i+1,n
      call get_s2(psi_keys_tmp(1,1,i),psi_keys_tmp(1,1,j),s2_tmp,N_int)
      s2 += (psi_coefs_tmp(i)+psi_coefs_tmp(i))*psi_coefs_tmp(j)*s2_tmp
+!    s2 = s2 + 2.d0 * psi_coefs_tmp(i)*psi_coefs_tmp(j)*s2_tmp
    enddo
  enddo
  !$OMP END PARALLEL DO
+ do i=1,n
+   call get_s2(psi_keys_tmp(1,1,i),psi_keys_tmp(1,1,i),s2_tmp,N_int)
+   s2 += psi_coefs_tmp(i)*psi_coefs_tmp(i)*s2_tmp
+ enddo
  s2 +=  S_z2_Sz
+!print*,'s2 = ',s2
+!print*,''
 end
 

src/Electrons/.gitignore

@@ -1,13 +1,13 @@
-#
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
-# Do not modify this file. Add your ignored files to the gitignore
-# (without the dot at the beginning) file.
-#
 IRPF90_temp
 IRPF90_man
-irpf90.make
-tags
-Makefile.depend
 irpf90_entities
+tags
+irpf90.make
+Makefile
+Makefile.depend
 build.ninja
 .ninja_log
 .ninja_deps
+ezfio_interface.irp.f
+Ezfio_files

src/Ezfio_files/.gitignore

@@ -1,13 +1,12 @@
-#
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
-# Do not modify this file. Add your ignored files to the gitignore
-# (without the dot at the beginning) file.
-#
 IRPF90_temp
 IRPF90_man
-irpf90.make
-tags
-Makefile.depend
 irpf90_entities
+tags
+irpf90.make
+Makefile
+Makefile.depend
 build.ninja
 .ninja_log
 .ninja_deps
+ezfio_interface.irp.f

src/Ezfio_files/README.rst

@@ -30,8 +30,8 @@ Documentation
   .br
 
 
-`output_aos <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L1>`_
+`output_ao_basis <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L1>`_
-  Output file for AOs
+  Output file for AO_Basis
 
 
 `output_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L21>`_
@@ -54,135 +54,79 @@ Documentation
   Output file for CID_selected
 
 
-`output_cis <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L121>`_
-  Output file for CIS
-
-
-`output_cisd <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L141>`_
-  Output file for CISD
-
-
-`output_cisd_sc2_selected <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L161>`_
-  Output file for CISD_SC2_selected
-
-
-`output_cisd_selected <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L181>`_
-  Output file for CISD_selected
-
-
 `output_cpu_time_0 <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f#L2>`_
   Initial CPU and wall times when printing in the output files
 
 
-`output_ddci_selected <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L201>`_
+`output_determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L121>`_
-  Output file for DDCI_selected
-
-
-`output_densityfit <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L221>`_
-  Output file for DensityFit
-
-
-`output_densitymatrix <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L241>`_
-  Output file for DensityMatrix
-
-
-`output_determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L261>`_
   Output file for Determinants
 
 
-`output_electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L281>`_
+`output_electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L141>`_
   Output file for Electrons
 
 
-`output_ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L301>`_
+`output_ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L161>`_
   Output file for Ezfio_files
 
 
-`output_fcidump <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L321>`_
+`output_generators_cas <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L181>`_
-  Output file for FCIdump
-
-
-`output_full_ci <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L341>`_
-  Output file for Full_CI
-
-
-`output_generators_cas <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L361>`_
   Output file for Generators_CAS
 
 
-`output_generators_full <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L381>`_
+`output_generators_full <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L201>`_
   Output file for Generators_full
 
 
-`output_generators_restart <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L401>`_
+`output_hartree_fock <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L221>`_
-  Output file for Generators_restart
-
-
-`output_hartree_fock <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L421>`_
   Output file for Hartree_Fock
 
 
-`output_integrals_bielec <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L441>`_
+`output_integrals_bielec <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L241>`_
   Output file for Integrals_Bielec
 
 
-`output_integrals_monoelec <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L461>`_
+`output_integrals_monoelec <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L261>`_
   Output file for Integrals_Monoelec
 
 
-`output_moguess <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L481>`_
+`output_mo_basis <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L281>`_
+  Output file for MO_Basis
+
+
+`output_moguess <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L301>`_
   Output file for MOGuess
 
 
-`output_molden <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L501>`_
+`output_mrcc <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L321>`_
-  Output file for Molden
-
-
-`output_mos <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L521>`_
-  Output file for MOs
-
-
-`output_mp2 <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L541>`_
-  Output file for MP2
-
-
-`output_mrcc <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L561>`_
   Output file for MRCC
 
 
-`output_nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L581>`_
+`output_nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L341>`_
   Output file for Nuclei
 
 
-`output_perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L601>`_
+`output_perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L361>`_
   Output file for Perturbation
 
 
-`output_properties <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L621>`_
+`output_properties <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L381>`_
   Output file for Properties
 
 
-`output_pseudo <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L641>`_
+`output_pseudo <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L401>`_
   Output file for Pseudo
 
 
-`output_qmcchem <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L661>`_
+`output_selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L421>`_
-  Output file for QmcChem
-
-
-`output_selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L681>`_
   Output file for Selectors_full
 
 
-`output_selectors_no_sorted <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L701>`_
+`output_singlerefmethod <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L441>`_
-  Output file for Selectors_no_sorted
-
-
-`output_singlerefmethod <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L721>`_
   Output file for SingleRefMethod
 
 
-`output_utils <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L741>`_
+`output_utils <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L461>`_
   Output file for Utils
 
 

src/Integrals_Bielec/.gitignore

@@ -1,13 +1,20 @@
-#
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
-# Do not modify this file. Add your ignored files to the gitignore
-# (without the dot at the beginning) file.
-#
 IRPF90_temp
 IRPF90_man
-irpf90.make
-tags
-Makefile.depend
 irpf90_entities
+tags
+irpf90.make
+Makefile
+Makefile.depend
 build.ninja
 .ninja_log
 .ninja_deps
+ezfio_interface.irp.f
+Ezfio_files
+MO_Basis
+Utils
+Pseudo
+Bitmask
+AO_Basis
+Electrons
+Nuclei