Merge branch 'master' of lpqlx139:quantum_package

configure

@@ -7,15 +7,16 @@ Usage: configure <config_file> (--production | --development)
 
 Options:
 
-    config_file   A config file with all the information for the compilation
+    config_file   A config file with all the information for compiling.
                   Example config_files are given in config/
 
-   --production   You can only compile all the modules with this flag,
+   --production   You can only compile **all** the modules with this flag,
-                  but the compilation will be lighting fast
+                  but it will compile lighting fast.
+
+   --development  this will create a build.ninja for each directory which 
+                  contains a binary. In a second step you may compile them
+                  individually if you like.
 
-   --development  It will create a build.ninja for each directory
-                  who contains a binary, than you can compile then
-                  individualy if you want
 
 Examples:
 
@@ -71,7 +72,7 @@ from collections import namedtuple
 
 Info = namedtuple("Info", ["url", "description", "default_path"])
 
-path_github = {"head": "http://github.com/", "tail": "archive/master.tar.gz"}
+path_github = {"head": "http://github.com", "tail": "archive/master.tar.gz"}
 
 ocaml = Info(
     url='http://raw.github.com/ocaml/opam/master/shell/opam_installer.sh',
@@ -163,7 +164,7 @@ def find_path(bin_, l_installed, var_for_qp_root=False):
 # | |_| | | (_  |_ | (_) | |
 #
 def check_output(*popenargs, **kwargs):
-    """Run command with arguments and return its output as a byte string.
+    """Run command with arguments and return its output as a string.
 
     Backported from Python 2.7 as it's implemented as pure python on stdlib.
 
@@ -180,6 +181,8 @@ def check_output(*popenargs, **kwargs):
             cmd = popenargs[0]
         error = subprocess.CalledProcessError(retcode, cmd)
         error.output = output
+#        print output
+#        print unused_err
         raise error
     return output
 
@@ -187,7 +190,7 @@ def check_output(*popenargs, **kwargs):
 def checking(d_dependency):
     """
     For each key in d_dependency check if it
-    it avalabie or not
+    is avalabie or not
     """
 
     def check_python():
@@ -203,8 +206,8 @@ def checking(d_dependency):
 
     def check_availability(binary):
         """
-        If avalable return the path who can find the
+        If avalable return the path where the binary 
-        binary else return 0
+        can be found, else return 0
         """
 
         if binary == "python":
@@ -224,7 +227,7 @@ def checking(d_dependency):
 
             return a
 
-        except subprocess.CalledProcessError:
+        except (OSError,subprocess.CalledProcessError):
             default_path = d_info[binary].default_path
             if os.path.exists(default_path):
                 return default_path
@@ -252,7 +255,7 @@ def checking(d_dependency):
 
     """
 
-    print "Checking what you need to install and what is it avalaible"
+    print "Checking what you need to install and what is avalaible"
     print ""
     l_installed = dict()
     l_needed = []
@@ -325,7 +328,7 @@ _|_ | | _>  |_ (_| | | (_|  |_ | (_) | |
     d_print = {
         "install_ninja": "Install ninja...",
         "build": "Creating build.ninja...",
-        "install": "Installing the dependency through ninja..."
+        "install": "Installing the dependencies with Ninja..."
     }
 
     length = max(map(len, d_print.values()))
@@ -341,9 +344,9 @@ _|_ | | _>  |_ (_| | | (_|  |_ | (_) | |
         extension = splitext(url)[1]
         path_archive = "Downloads/{0}{1}".format("ninja", extension)
 
-        l_cmd = ["cd install &&",
+        l_cmd = ["set -x ;", "cd install &&",
-                 "wget {0} -O {1} -o /dev/null &&".format(url, path_archive),
+                 "wget {0} -O {1} &&".format(url, path_archive),
-                 "./scripts/install_ninja.sh 2> /dev/null &&", "cd -"]
+                 "./scripts/install_ninja.sh &&", "cd -"]
 
         try:
             check_output(" ".join(l_cmd), shell=True)
@@ -451,7 +454,7 @@ def create_ninja_and_rc(l_installed):
         'export IRPF90={0}'.format(path_irpf90),
         'export NINJA={0}'.format(path_ninja),
         'export QP_PYTHON={0}'.format(":".join(l_python)), "",
-        'export PYTHONPATH="${QP_PYTHON}":"${PYTHONPATH}"',
+        'export PYTHONPATH="${QP_EZFIO}":"${QP_PYTHON}":"${PYTHONPATH}"',
         'export PATH="${QP_PYTHON}":"${QP_ROOT}"/bin:"${QP_ROOT}"/ocaml:"${PATH}"',
         'export LD_LIBRARY_PATH="${QP_ROOT}"/lib:"${LD_LIBRARY_PATH}"',
         'export LIBRARY_PATH="${QP_ROOT}"/lib:"${LIBRARY_PATH}"', "",
@@ -484,7 +487,7 @@ def create_ninja_and_rc(l_installed):
             subprocess.check_call(" ".join(l), shell=True,stderr=dnull)
     except:
         print "[ FAIL ]"
-        print "Check the valididy of the config file provided ({0})".format(sys.argv[1])
+        print "Check the validity of the config file provided ({0})".format(sys.argv[1])
         print "Exit..."
         sys.exit(1)
 
@@ -496,6 +499,11 @@ def recommendation():
     path = join(QP_ROOT, "quantum_package.rc")
     print "Now :"
     print "   source {0}".format(path)
+    print ""
+    print "Then, install the modules you want to install using :"
+    print "    qp_install_module.py "
+    print ""
+    print "Finally :"
     print "   ninja"
     print "   make -C ocaml"
     print ""

ocaml/qp_create_ezfio_from_xyz.ml

@@ -14,7 +14,7 @@ let spec =
   +> flag "m" (optional_with_default 1 int)
      ~doc:"int Spin multiplicity (2S+1) of the molecule. Default is 1."
   +> flag "p" no_arg
-     ~doc:"Using pseudopotentials"
+     ~doc:" Using pseudopotentials"
   +> anon ("xyz_file" %: string)
 ;;
 

plugins/CAS_SD/README.rst

@@ -96,3 +96,92 @@ Needed Modules
 * `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
 * `Generators_CAS <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_CAS>`_
 
+Needed Modules
+==============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
+.. image:: tree_dependency.png
+
+* `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation>`_
+* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/plugins/Selectors_full>`_
+* `Generators_CAS <http://github.com/LCPQ/quantum_package/tree/master/plugins/Generators_CAS>`_
+
+Documentation
+=============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
+`full_ci <http://github.com/LCPQ/quantum_package/tree/master/plugins/CAS_SD/cas_sd_selected.irp.f#L1>`_
+  Undocumented
+
+
+`h_apply_cas_sd <http://github.com/LCPQ/quantum_package/tree/master/plugins/CAS_SD/H_apply.irp.f_shell_22#L414>`_
+  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_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CAS_SD/H_apply.irp.f_shell_22#L1>`_
+  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_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CAS_SD/H_apply.irp.f_shell_22#L269>`_
+  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_pt2 <http://github.com/LCPQ/quantum_package/tree/master/plugins/CAS_SD/H_apply.irp.f_shell_22#L2610>`_
+  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/plugins/CAS_SD/H_apply.irp.f_shell_22#L2118>`_
+  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/plugins/CAS_SD/H_apply.irp.f_shell_22#L2427>`_
+  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/plugins/CAS_SD/H_apply.irp.f_shell_22#L1872>`_
+  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_selected_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CAS_SD/H_apply.irp.f_shell_22#L1346>`_
+  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_selected_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CAS_SD/H_apply.irp.f_shell_22#L1675>`_
+  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_no_skip <http://github.com/LCPQ/quantum_package/tree/master/plugins/CAS_SD/H_apply.irp.f_shell_22#L1128>`_
+  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_selected_no_skip_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CAS_SD/H_apply.irp.f_shell_22#L602>`_
+  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_selected_no_skip_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CAS_SD/H_apply.irp.f_shell_22#L931>`_
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+

plugins/CIS/README.rst

@@ -48,3 +48,44 @@ Needed Modules
 * `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
 * `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod>`_
 
+Needed Modules
+==============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
+.. image:: tree_dependency.png
+
+* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/plugins/Selectors_full>`_
+* `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/plugins/SingleRefMethod>`_
+
+Documentation
+=============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
+`cis <http://github.com/LCPQ/quantum_package/tree/master/plugins/CIS/super_ci.irp.f#L1>`_
+  Undocumented
+
+
+`h_apply_cis <http://github.com/LCPQ/quantum_package/tree/master/plugins/CIS/H_apply.irp.f_shell_8#L414>`_
+  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_cis_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CIS/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_cis_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CIS/H_apply.irp.f_shell_8#L269>`_
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`super_ci <http://github.com/LCPQ/quantum_package/tree/master/plugins/CIS/super_ci.irp.f#L9>`_
+  Undocumented
+

plugins/CISD/.gitignore

@@ -20,7 +20,6 @@ Pseudo
 Selectors_full
 SingleRefMethod
 Utils
-cisd
 cisd_lapack
 ezfio_interface.irp.f
 irpf90.make

plugins/CISD/README.rst

@@ -42,3 +42,36 @@ Documentation
   particles.
   Assume N_int is already provided.
 
+Needed Modules
+==============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
+.. image:: tree_dependency.png
+
+* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/plugins/Selectors_full>`_
+* `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/plugins/SingleRefMethod>`_
+
+Documentation
+=============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
+`h_apply_cisd <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD/H_apply.irp.f_shell_8#L414>`_
+  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/plugins/CISD/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/plugins/CISD/H_apply.irp.f_shell_8#L269>`_
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+

plugins/CISD/cisd.irp.f

@@ -14,6 +14,7 @@ program cisd
   enddo
 
   call save_wavefunction
+  call ezfio_set_cisd_energy(CI_energy(1))
 ! call CISD_SC2(psi_det,psi_coef,eigvalues,size(psi_coef,1),N_det,N_states,N_int)
 ! do i = 1, N_states
 !  print*,'eigvalues(i) = ',eigvalues(i)

plugins/CISD_selected/.gitignore

@@ -23,7 +23,6 @@ Pseudo
 Selectors_full
 SingleRefMethod
 Utils
-cisd_selection
 ezfio_interface.irp.f
 irpf90.make
 irpf90_entities

plugins/CISD_selected/README.rst

@@ -179,3 +179,197 @@ Needed Modules
 * `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
 * `CISD <http://github.com/LCPQ/quantum_package/tree/master/src/CISD>`_
 
+Needed Modules
+==============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
+.. image:: tree_dependency.png
+
+* `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation>`_
+* `CISD <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD>`_
+
+Documentation
+=============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
+`cisd <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/cisd_selection.irp.f#L1>`_
+  Undocumented
+
+
+`h_apply_cisd <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_8#L414>`_
+  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/plugins/CISD_selected/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/plugins/CISD_selected/H_apply.irp.f_shell_8#L269>`_
+  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/plugins/CISD_selected/H_apply.irp.f#L13>`_
+  Undocumented
+
+
+`h_apply_cisd_selection_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L5931>`_
+  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/plugins/CISD_selected/H_apply.irp.f_shell_10#L5405>`_
+  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/plugins/CISD_selected/H_apply.irp.f_shell_10#L5734>`_
+  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/plugins/CISD_selected/H_apply.irp.f_shell_10#L5159>`_
+  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/plugins/CISD_selected/H_apply.irp.f_shell_10#L4633>`_
+  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/plugins/CISD_selected/H_apply.irp.f_shell_10#L4962>`_
+  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/plugins/CISD_selected/H_apply.irp.f_shell_10#L3615>`_
+  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/plugins/CISD_selected/H_apply.irp.f_shell_10#L4387>`_
+  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/plugins/CISD_selected/H_apply.irp.f_shell_10#L3861>`_
+  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/plugins/CISD_selected/H_apply.irp.f_shell_10#L4190>`_
+  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/plugins/CISD_selected/H_apply.irp.f_shell_10#L3089>`_
+  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/plugins/CISD_selected/H_apply.irp.f_shell_10#L3418>`_
+  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/plugins/CISD_selected/H_apply.irp.f_shell_10#L2843>`_
+  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/plugins/CISD_selected/H_apply.irp.f_shell_10#L2317>`_
+  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/plugins/CISD_selected/H_apply.irp.f_shell_10#L2646>`_
+  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/plugins/CISD_selected/H_apply.irp.f_shell_10#L2071>`_
+  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/plugins/CISD_selected/H_apply.irp.f_shell_10#L1545>`_
+  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/plugins/CISD_selected/H_apply.irp.f_shell_10#L1874>`_
+  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/plugins/CISD_selected/H_apply.irp.f_shell_10#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_cisd_selection_epstein_nesbet_sc2_projected_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L773>`_
+  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/plugins/CISD_selected/H_apply.irp.f_shell_10#L1102>`_
+  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/plugins/CISD_selected/H_apply.irp.f_shell_10#L527>`_
+  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/plugins/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/plugins/CISD_selected/H_apply.irp.f_shell_10#L330>`_
+  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/plugins/CISD_selected/H_apply.irp.f_shell_10#L6703>`_
+  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/plugins/CISD_selected/H_apply.irp.f_shell_10#L6177>`_
+  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/plugins/CISD_selected/H_apply.irp.f_shell_10#L6506>`_
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+

plugins/CISD_selected/cisd_selection.irp.f

@@ -43,4 +43,6 @@ program cisd
   call diagonalize_CI
   deallocate(pt2,norm_pert,H_pert_diag)
     call save_wavefunction
+  call ezfio_set_cisd_energy(CI_energy)
+  call ezfio_set_cisd_energy_pt2(CI_energy+pt2)
 end

plugins/FCIdump/.gitignore

@@ -1,23 +1,23 @@
-# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
+# Automatically created by $QP_ROOT/scripts/module/module_handler.py 
-IRPF90_temp
-IRPF90_man
-irpf90_entities
-tags
-irpf90.make
-Makefile
-Makefile.depend
-.ninja_log
 .ninja_deps
-ezfio_interface.irp.f
+.ninja_log
-Ezfio_files
+AO_Basis
+Bitmask
 Determinants
+Electrons
+Ezfio_files
+IRPF90_man
+IRPF90_temp
+Integrals_Bielec
 Integrals_Monoelec
 MO_Basis
-Utils
+Makefile
-Pseudo
+Makefile.depend
-Bitmask
-AO_Basis
-Electrons
 Nuclei
-Integrals_Bielec
+Pseudo
-fcidump
+Utils
+ezfio_interface.irp.f
+fcidump
+irpf90.make
+irpf90_entities
+tags

plugins/FCIdump/README.rst

@@ -23,3 +23,22 @@ Needed Modules
 
 * `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
 
+Needed Modules
+==============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
+.. image:: tree_dependency.png
+
+* `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
+
+Documentation
+=============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
+`fcidump <http://github.com/LCPQ/quantum_package/tree/master/plugins/FCIdump/fcidump.irp.f#L1>`_
+  Undocumented
+

plugins/Full_CI/README.rst

@@ -4,164 +4,165 @@ Full_CI Module
 
 Performs a perturbatively selected Full-CI.
 
-Documentation
-=============
-
-.. Do not edit this section. It was auto-generated from the
-.. by the `update_README.py` script.
-
-`full_ci <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/full_ci_no_skip.irp.f#L1>`_
-  Undocumented
-
-
-`h_apply_fci <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L527>`_
-  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_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L1>`_
-  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 <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L2744>`_
-  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#L2216>`_
-  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#L2545>`_
-  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#L330>`_
-  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#L1998>`_
-  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#L1472>`_
-  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#L1801>`_
-  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#L1265>`_
-  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#L773>`_
-  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#L1082>`_
-  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#L4258>`_
-  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#L3764>`_
-  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#L4073>`_
-  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#L5729>`_
-  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#L5237>`_
-  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#L5546>`_
-  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#L3518>`_
-  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#L2990>`_
-  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#L3319>`_
-  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#L4991>`_
-  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#L4465>`_
-  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#L4794>`_
-  Generate all single excitations of key_in using the bit masks of holes and
-  particles.
-  Assume N_int is already provided.
-
-
-`var_pt2_ratio_run <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/var_pt2_ratio.irp.f#L1>`_
-  Undocumented
 
 Needed Modules
 ==============
-
+.. Do not edit this section It was auto-generated
-.. Do not edit this section. It was auto-generated from the
 .. by the `update_README.py` script.
 
+
 .. image:: tree_dependency.png
 
-* `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
+* `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation>`_
-* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
+* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/plugins/Selectors_full>`_
-* `Generators_full <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full>`_
+* `Generators_full <http://github.com/LCPQ/quantum_package/tree/master/plugins/Generators_full>`_
+
+Documentation
+=============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
+`full_ci <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/full_ci_no_skip.irp.f#L1>`_
+  Undocumented
+
+
+`h_apply_fci <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L527>`_
+  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_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L1>`_
+  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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L2744>`_
+  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/plugins/Full_CI/H_apply.irp.f_shell_43#L2216>`_
+  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/plugins/Full_CI/H_apply.irp.f_shell_43#L2545>`_
+  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/plugins/Full_CI/H_apply.irp.f_shell_43#L330>`_
+  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/plugins/Full_CI/H_apply.irp.f_shell_43#L1998>`_
+  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/plugins/Full_CI/H_apply.irp.f_shell_43#L1472>`_
+  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/plugins/Full_CI/H_apply.irp.f_shell_43#L1801>`_
+  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/plugins/Full_CI/H_apply.irp.f_shell_43#L1265>`_
+  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/plugins/Full_CI/H_apply.irp.f_shell_43#L773>`_
+  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/plugins/Full_CI/H_apply.irp.f_shell_43#L1082>`_
+  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/plugins/Full_CI/H_apply.irp.f_shell_43#L4258>`_
+  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/plugins/Full_CI/H_apply.irp.f_shell_43#L3764>`_
+  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/plugins/Full_CI/H_apply.irp.f_shell_43#L4073>`_
+  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/plugins/Full_CI/H_apply.irp.f_shell_43#L5729>`_
+  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/plugins/Full_CI/H_apply.irp.f_shell_43#L5237>`_
+  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/plugins/Full_CI/H_apply.irp.f_shell_43#L5546>`_
+  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/plugins/Full_CI/H_apply.irp.f_shell_43#L3518>`_
+  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/plugins/Full_CI/H_apply.irp.f_shell_43#L2990>`_
+  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/plugins/Full_CI/H_apply.irp.f_shell_43#L3319>`_
+  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/plugins/Full_CI/H_apply.irp.f_shell_43#L4991>`_
+  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/plugins/Full_CI/H_apply.irp.f_shell_43#L4465>`_
+  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/plugins/Full_CI/H_apply.irp.f_shell_43#L4794>`_
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`var_pt2_ratio_run <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/var_pt2_ratio.irp.f#L1>`_
+  Undocumented
 

plugins/Generators_CAS/README.rst

@@ -49,3 +49,40 @@ Needed Modules
 
 * `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
 
+Needed Modules
+==============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
+.. image:: tree_dependency.png
+
+* `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
+
+Documentation
+=============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
+`n_det_generators <http://github.com/LCPQ/quantum_package/tree/master/plugins/Generators_CAS/generators.irp.f#L3>`_
+  Number of generator detetrminants
+
+
+`psi_coef_generators <http://github.com/LCPQ/quantum_package/tree/master/plugins/Generators_CAS/generators.irp.f#L35>`_
+  For Single reference wave functions, the generator is the
+  Hartree-Fock determinant
+
+
+`psi_det_generators <http://github.com/LCPQ/quantum_package/tree/master/plugins/Generators_CAS/generators.irp.f#L34>`_
+  For Single reference wave functions, the generator is the
+  Hartree-Fock determinant
+
+
+`select_max <http://github.com/LCPQ/quantum_package/tree/master/plugins/Generators_CAS/generators.irp.f#L78>`_
+  Memo to skip useless selectors
+
+
+`size_select_max <http://github.com/LCPQ/quantum_package/tree/master/plugins/Generators_CAS/generators.irp.f#L70>`_
+  Size of the select_max array
+

plugins/Generators_full/README.rst

@@ -5,42 +5,10 @@ Generators_full Module
 All the determinants of the wave function are generators. In this way, the Full CI
 space is explored.
 
-Documentation
-=============
-
-.. Do not edit this section. It was auto-generated from the
-.. by the `update_README.py` script.
-
-`degree_max_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full/generators.irp.f#L43>`_
-  Max degree of excitation (respect to HF) of the generators
-
-
-`n_det_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full/generators.irp.f#L3>`_
-  For Single reference wave functions, the number of generators is 1 : the
-  Hartree-Fock determinant
-
-
-`psi_coef_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full/generators.irp.f#L26>`_
-  For Single reference wave functions, the generator is the
-  Hartree-Fock determinant
-
-
-`psi_det_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full/generators.irp.f#L25>`_
-  For Single reference wave functions, the generator is the
-  Hartree-Fock determinant
-
-
-`select_max <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full/generators.irp.f#L66>`_
-  Memo to skip useless selectors
-
-
-`size_select_max <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full/generators.irp.f#L58>`_
-  Size of the select_max array
-
 Needed Modules
 ==============
 
-.. Do not edit this section. It was auto-generated from the
+.. Do not edit this section It was auto-generated
 .. by the `update_README.py` script.
 
 .. image:: tree_dependency.png
@@ -48,3 +16,46 @@ Needed Modules
 * `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
 * `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
 
+Needed Modules
+==============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
+.. image:: tree_dependency.png
+
+* `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
+* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock>`_
+
+Documentation
+=============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
+`degree_max_generators <http://github.com/LCPQ/quantum_package/tree/master/plugins/Generators_full/generators.irp.f#L43>`_
+  Max degree of excitation (respect to HF) of the generators
+
+
+`n_det_generators <http://github.com/LCPQ/quantum_package/tree/master/plugins/Generators_full/generators.irp.f#L3>`_
+  For Single reference wave functions, the number of generators is 1 : the
+  Hartree-Fock determinant
+
+
+`psi_coef_generators <http://github.com/LCPQ/quantum_package/tree/master/plugins/Generators_full/generators.irp.f#L26>`_
+  For Single reference wave functions, the generator is the
+  Hartree-Fock determinant
+
+
+`psi_det_generators <http://github.com/LCPQ/quantum_package/tree/master/plugins/Generators_full/generators.irp.f#L25>`_
+  For Single reference wave functions, the generator is the
+  Hartree-Fock determinant
+
+
+`select_max <http://github.com/LCPQ/quantum_package/tree/master/plugins/Generators_full/generators.irp.f#L66>`_
+  Memo to skip useless selectors
+
+
+`size_select_max <http://github.com/LCPQ/quantum_package/tree/master/plugins/Generators_full/generators.irp.f#L58>`_
+  Size of the select_max array
+

plugins/Hartree_Fock/README.rst

@@ -7,9 +7,20 @@ From the 140 molecules of the G2 set, only LiO, ONa don't converge well.
 Needed Modules
 ==============
 
-.. Do not edit this section. It was auto-generated from the
+.. Do not edit this section It was auto-generated
 .. by the `update_README.py` script.
 
+.. image:: tree_dependency.png
+
+* `Integrals_Bielec <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec>`_
+* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
+
+Needed Modules
+==============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
 .. image:: tree_dependency.png
 
 * `Integrals_Bielec <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec>`_
@@ -17,61 +28,61 @@ Needed Modules
 
 Documentation
 =============
-
+.. Do not edit this section It was auto-generated
-.. Do not edit this section. It was auto-generated from the
 .. by the `update_README.py` script.
 
-`ao_bi_elec_integral_alpha <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L102>`_
+
+`ao_bi_elec_integral_alpha <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/Fock_matrix.irp.f#L102>`_
   Alpha Fock matrix in AO basis set
 
 
-`ao_bi_elec_integral_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L103>`_
+`ao_bi_elec_integral_beta <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/Fock_matrix.irp.f#L103>`_
   Alpha Fock matrix in AO basis set
 
 
-`create_guess <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/SCF.irp.f#L13>`_
+`create_guess <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/SCF.irp.f#L13>`_
   Create an MO guess if no MOs are present in the EZFIO directory
 
 
-`damping_scf <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/damping_SCF.irp.f#L1>`_
+`damping_scf <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/damping_SCF.irp.f#L1>`_
   Undocumented
 
 
-`diagonal_fock_matrix_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/diagonalize_fock.irp.f#L1>`_
+`diagonal_fock_matrix_mo <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/diagonalize_fock.irp.f#L1>`_
   Diagonal Fock matrix in the MO basis
 
 
-`diagonal_fock_matrix_mo_sum <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/diagonalize_fock.irp.f#L67>`_
+`diagonal_fock_matrix_mo_sum <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/diagonalize_fock.irp.f#L67>`_
   diagonal element of the fock matrix calculated as the sum over all the interactions
   with all the electrons in the RHF determinant
   diagonal_Fock_matrix_mo_sum(i) = sum_{j=1, N_elec} 2 J_ij -K_ij
 
 
-`eigenvectors_fock_matrix_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/diagonalize_fock.irp.f#L2>`_
+`eigenvectors_fock_matrix_mo <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/diagonalize_fock.irp.f#L2>`_
   Diagonal Fock matrix in the MO basis
 
 
-`fock_matrix_alpha_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L83>`_
+`fock_matrix_alpha_ao <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/Fock_matrix.irp.f#L83>`_
   Alpha Fock matrix in AO basis set
 
 
-`fock_matrix_alpha_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L231>`_
+`fock_matrix_alpha_mo <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/Fock_matrix.irp.f#L231>`_
   Fock matrix on the MO basis
 
 
-`fock_matrix_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L289>`_
+`fock_matrix_ao <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/Fock_matrix.irp.f#L289>`_
   Fock matrix in AO basis set
 
 
-`fock_matrix_beta_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L84>`_
+`fock_matrix_beta_ao <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/Fock_matrix.irp.f#L84>`_
   Alpha Fock matrix in AO basis set
 
 
-`fock_matrix_beta_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L251>`_
+`fock_matrix_beta_mo <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/Fock_matrix.irp.f#L251>`_
   Fock matrix on the MO basis
 
 
-`fock_matrix_diag_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L2>`_
+`fock_matrix_diag_mo <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/Fock_matrix.irp.f#L2>`_
   Fock matrix on the MO basis.
   For open shells, the ROHF Fock Matrix is
   .br
@@ -87,7 +98,7 @@ Documentation
   .br
 
 
-`fock_matrix_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L1>`_
+`fock_matrix_mo <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/Fock_matrix.irp.f#L1>`_
   Fock matrix on the MO basis.
   For open shells, the ROHF Fock Matrix is
   .br
@@ -103,53 +114,53 @@ Documentation
   .br
 
 
-`fock_mo_to_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L332>`_
+`fock_mo_to_ao <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/Fock_matrix.irp.f#L332>`_
   Undocumented
 
 
-`guess <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Huckel_guess.irp.f#L1>`_
+`guess <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/Huckel_guess.irp.f#L1>`_
   Undocumented
 
 
-`hf_density_matrix_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/HF_density_matrix_ao.irp.f#L27>`_
+`hf_density_matrix_ao <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/HF_density_matrix_ao.irp.f#L27>`_
   S^-1 Density matrix in the AO basis S^-1
 
 
-`hf_density_matrix_ao_alpha <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/HF_density_matrix_ao.irp.f#L1>`_
+`hf_density_matrix_ao_alpha <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/HF_density_matrix_ao.irp.f#L1>`_
   S^-1 x Alpha density matrix in the AO basis x S^-1
 
 
-`hf_density_matrix_ao_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/HF_density_matrix_ao.irp.f#L14>`_
+`hf_density_matrix_ao_beta <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/HF_density_matrix_ao.irp.f#L14>`_
   S^-1 Beta density matrix in the AO basis x S^-1
 
 
-`hf_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L270>`_
+`hf_energy <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/Fock_matrix.irp.f#L270>`_
   Hartree-Fock energy
 
 
-`huckel_guess <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/huckel.irp.f#L1>`_
+`huckel_guess <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/huckel.irp.f#L1>`_
   Build the MOs using the extended Huckel model
 
 
-`mo_guess_type <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/ezfio_interface.irp.f#L28>`_
+`mo_guess_type <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/ezfio_interface.irp.f#L28>`_
   Initial MO guess. Can be [ Huckel | HCore ]
 
 
-`n_it_scf_max <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/ezfio_interface.irp.f#L6>`_
+`n_it_scf_max <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/ezfio_interface.irp.f#L6>`_
   Maximum number of SCF iterations
 
 
-`run <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/SCF.irp.f#L38>`_
+`run <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/SCF.irp.f#L38>`_
   Run SCF calculation
 
 
-`scf <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/SCF.irp.f#L1>`_
+`scf <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/SCF.irp.f#L1>`_
   Produce `Hartree_Fock` MO orbital
   output: mo_basis.mo_tot_num mo_basis.mo_label mo_basis.ao_md5 mo_basis.mo_coef mo_basis.mo_occ
   output: hartree_fock.energy
   optional: mo_basis.mo_coef
 
 
-`thresh_scf <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/ezfio_interface.irp.f#L46>`_
+`thresh_scf <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/ezfio_interface.irp.f#L46>`_
   Threshold on the convergence of the Hartree Fock energy
 

plugins/MRCC_CASSD/.gitignore

@@ -14,7 +14,7 @@ Integrals_Bielec
 Integrals_Monoelec
 MOGuess
 MO_Basis
-MRCC_Utils_new
+MRCC_Utils
 Makefile
 Makefile.depend
 Nuclei

plugins/MRCC_CASSD/NEEDED_CHILDREN_MODULES

@@ -1 +1 @@
-Perturbation Selectors_full Generators_full Psiref_CAS MRCC_Utils_new
+Perturbation Selectors_full Generators_full Psiref_CAS MRCC_Utils

plugins/MRCC_CASSD/README.rst

@@ -16,7 +16,7 @@ Needed Modules
 * `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
 * `Generators_full <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full>`_
 * `Psiref_CAS <http://github.com/LCPQ/quantum_package/tree/master/src/Psiref_CAS>`_
-* `MRCC_Utils_new <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC_Utils_new>`_
+* `MRCC_Utils <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC_Utils>`_
 
 Documentation
 =============
@@ -31,3 +31,30 @@ Documentation
 `print_cas_coefs <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC_CASSD/mrcc_cassd.irp.f#L11>`_
   Undocumented
 
+Needed Modules
+==============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
+.. image:: tree_dependency.png
+
+* `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation>`_
+* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/plugins/Selectors_full>`_
+* `Generators_full <http://github.com/LCPQ/quantum_package/tree/master/plugins/Generators_full>`_
+* `Psiref_CAS <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_CAS>`_
+* `MRCC_Utils <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils>`_
+
+Documentation
+=============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
+`mrcc <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_CASSD/mrcc_cassd.irp.f#L1>`_
+  Undocumented
+
+
+`print_cas_coefs <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_CASSD/mrcc_cassd.irp.f#L11>`_
+  Undocumented
+

plugins/MRCC_Utils/README.rst

@@ -21,19 +21,19 @@ Documentation
 .. Do not edit this section. It was auto-generated from the
 .. by the `update_README.py` script.
 
-`ci_eigenvectors_dressed <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC_Utils/mrcc_utils.irp.f#L76>`_
+`ci_eigenvectors_dressed <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC_Utils/mrcc_utils.irp.f#L166>`_
   Eigenvectors/values of the CI matrix
 
 
-`ci_eigenvectors_s2_dressed <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC_Utils/mrcc_utils.irp.f#L77>`_
+`ci_eigenvectors_s2_dressed <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC_Utils/mrcc_utils.irp.f#L167>`_
   Eigenvectors/values of the CI matrix
 
 
-`ci_electronic_energy_dressed <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC_Utils/mrcc_utils.irp.f#L75>`_
+`ci_electronic_energy_dressed <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC_Utils/mrcc_utils.irp.f#L165>`_
   Eigenvectors/values of the CI matrix
 
 
-`ci_energy_dressed <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC_Utils/mrcc_utils.irp.f#L142>`_
+`ci_energy_dressed <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC_Utils/mrcc_utils.irp.f#L232>`_
   N_states lowest eigenvalues of the dressed CI matrix
 
 
@@ -77,15 +77,15 @@ Documentation
   Initial guess vectors are not necessarily orthonormal
 
 
-`delta_ii <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC_Utils/mrcc_utils.irp.f#L39>`_
+`delta_ii <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC_Utils/mrcc_utils.irp.f#L104>`_
   Dressing matrix in N_det basis
 
 
-`delta_ij <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC_Utils/mrcc_utils.irp.f#L38>`_
+`delta_ij <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC_Utils/mrcc_utils.irp.f#L103>`_
   Dressing matrix in N_det basis
 
 
-`diagonalize_ci_dressed <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC_Utils/mrcc_utils.irp.f#L157>`_
+`diagonalize_ci_dressed <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC_Utils/mrcc_utils.irp.f#L247>`_
   Replace the coefficients of the CI states by the coefficients of the
   eigenstates of the CI matrix
 
@@ -111,7 +111,7 @@ Documentation
   Assume N_int is already provided.
 
 
-`h_matrix_dressed <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC_Utils/mrcc_utils.irp.f#L50>`_
+`h_matrix_dressed <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC_Utils/mrcc_utils.irp.f#L140>`_
   Dressed H with Delta_ij
 
 
@@ -123,11 +123,15 @@ Documentation
   H_jj : array of <j|H|j>
 
 
-`lambda_mrcc <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC_Utils/mrcc_utils.irp.f#L1>`_
+`lambda_mrcc <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC_Utils/mrcc_utils.irp.f#L5>`_
   cm/<Psi_0|H|D_m> or perturbative 1/Delta_E(m)
 
 
-`lambda_pert <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC_Utils/mrcc_utils.irp.f#L2>`_
+`lambda_mrcc_tmp <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC_Utils/mrcc_utils.irp.f#L81>`_
+  Undocumented
+
+
+`lambda_pert <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC_Utils/mrcc_utils.irp.f#L6>`_
   cm/<Psi_0|H|D_m> or perturbative 1/Delta_E(m)
 
 
@@ -143,6 +147,14 @@ Documentation
   Undocumented
 
 
+`oscillations <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC_Utils/mrcc_utils.irp.f#L86>`_
+  Undocumented
+
+
+`pert_determinants <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC_Utils/mrcc_utils.irp.f#L1>`_
+  Undocumented
+
+
 `psi_ref_lock <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC_Utils/mrcc_dress.irp.f#L3>`_
   Locks on ref determinants to fill delta_ij
 
@@ -151,6 +163,795 @@ Documentation
   Undocumented
 
 
-`set_generators_bitmasks_as_holes_and_particles <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC_Utils/mrcc_general.irp.f#L39>`_
+`set_generators_bitmasks_as_holes_and_particles <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC_Utils/mrcc_general.irp.f#L69>`_
   Undocumented
 
+Needed Modules
+==============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
+.. image:: tree_dependency.png
+
+* `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation>`_
+* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/plugins/Selectors_full>`_
+* `Generators_full <http://github.com/LCPQ/quantum_package/tree/master/plugins/Generators_full>`_
+* `Psiref_Utils <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils>`_
+
+Documentation
+=============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
+`a_coef <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/need.irp.f#L252>`_
+  Undocumented
+
+
+`abort_all <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/abort.irp.f#L1>`_
+  If True, all the calculation is aborted
+
+
+`abort_here <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/abort.irp.f#L11>`_
+  If True, all the calculation is aborted
+
+
+`add_poly <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/integration.irp.f#L306>`_
+  Add two polynomials
+  D(t) =! D(t) +( B(t)+C(t))
+
+
+`add_poly_multiply <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/integration.irp.f#L334>`_
+  Add a polynomial multiplied by a constant
+  D(t) =! D(t) +( cst * B(t))
+
+
+`align_double <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/util.irp.f#L48>`_
+  Compute 1st dimension such that it is aligned for vectorization.
+
+
+`apply_rotation <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/LinearAlgebra.irp.f#L168>`_
+  Apply the rotation found by find_rotation
+
+
+`approx_dble <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/util.irp.f#L380>`_
+  Undocumented
+
+
+`b_coef <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/need.irp.f#L257>`_
+  Undocumented
+
+
+`binom <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/util.irp.f#L31>`_
+  Binomial coefficients
+
+
+`binom_func <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/util.irp.f#L1>`_
+  .. math                       ::
+  .br
+  \frac{i!}{j!(i-j)!}
+  .br
+
+
+`binom_transp <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/util.irp.f#L32>`_
+  Binomial coefficients
+
+
+`catch_signal <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/abort.irp.f#L30>`_
+  What to do on Ctrl-C. If two Ctrl-C are pressed within 1 sec, the calculation if aborted.
+
+
+`ci_eigenvectors_dressed <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/mrcc_utils.irp.f#L166>`_
+  Eigenvectors/values of the CI matrix
+
+
+`ci_eigenvectors_s2_dressed <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/mrcc_utils.irp.f#L167>`_
+  Eigenvectors/values of the CI matrix
+
+
+`ci_electronic_energy_dressed <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/mrcc_utils.irp.f#L165>`_
+  Eigenvectors/values of the CI matrix
+
+
+`ci_energy_dressed <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/mrcc_utils.irp.f#L232>`_
+  N_states lowest eigenvalues of the dressed CI matrix
+
+
+`davidson_diag_hjj_mrcc <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/davidson.irp.f#L56>`_
+  Davidson diagonalization with specific diagonal elements of the H matrix
+  .br
+  H_jj : specific diagonal H matrix elements to diagonalize de Davidson
+  .br
+  dets_in : bitmasks corresponding to determinants
+  .br
+  u_in : guess coefficients on the various states. Overwritten
+  on exit
+  .br
+  dim_in : leftmost dimension of u_in
+  .br
+  sze : Number of determinants
+  .br
+  N_st : Number of eigenstates
+  .br
+  iunit : Unit for the I/O
+  .br
+  Initial guess vectors are not necessarily orthonormal
+
+
+`davidson_diag_mrcc <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/davidson.irp.f#L1>`_
+  Davidson diagonalization.
+  .br
+  dets_in : bitmasks corresponding to determinants
+  .br
+  u_in : guess coefficients on the various states. Overwritten
+  on exit
+  .br
+  dim_in : leftmost dimension of u_in
+  .br
+  sze : Number of determinants
+  .br
+  N_st : Number of eigenstates
+  .br
+  iunit : Unit number for the I/O
+  .br
+  Initial guess vectors are not necessarily orthonormal
+
+
+`dble_fact <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/util.irp.f#L138>`_
+  Undocumented
+
+
+`dble_fact_even <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/util.irp.f#L155>`_
+  n!!
+
+
+`dble_fact_odd <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/util.irp.f#L176>`_
+  n!!
+
+
+`dble_logfact <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/util.irp.f#L210>`_
+  n!!
+
+
+`ddfact2 <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/need.irp.f#L243>`_
+  Undocumented
+
+
+`delta_ii <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/mrcc_utils.irp.f#L104>`_
+  Dressing matrix in N_det basis
+
+
+`delta_ij <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/mrcc_utils.irp.f#L103>`_
+  Dressing matrix in N_det basis
+
+
+`diagonalize_ci_dressed <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/mrcc_utils.irp.f#L247>`_
+  Replace the coefficients of the CI states by the coefficients of the
+  eigenstates of the CI matrix
+
+
+`dset_order <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/sort.irp.f_template_216#L27>`_
+  array A has already been sorted, and iorder has contains the new order of
+  elements of A. This subroutine changes the order of x to match the new order of A.
+
+
+`dset_order_big <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/sort.irp.f_template_283#L94>`_
+  array A has already been sorted, and iorder has contains the new order of
+  elements of A. This subroutine changes the order of x to match the new order of A.
+  This is a version for very large arrays where the indices need
+  to be in integer*8 format
+
+
+`dsort <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/sort.irp.f_template_184#L339>`_
+  Sort array x(isize).
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+
+
+`erf0 <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/need.irp.f#L105>`_
+  Undocumented
+
+
+`f_integral <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/integration.irp.f#L408>`_
+  function that calculates the following integral
+  \int_{\-infty}^{+\infty} x^n \exp(-p x^2) dx
+
+
+`fact <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/util.irp.f#L63>`_
+  n!
+
+
+`fact_inv <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/util.irp.f#L125>`_
+  1/n!
+
+
+`find_rotation <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/LinearAlgebra.irp.f#L149>`_
+  Find A.C = B
+
+
+`find_triples_and_quadruples <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/mrcc_dress.irp.f#L206>`_
+  Undocumented
+
+
+`gammln <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/need.irp.f#L271>`_
+  Undocumented
+
+
+`gammp <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/need.irp.f#L133>`_
+  Undocumented
+
+
+`gaussian_product <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/integration.irp.f#L184>`_
+  Gaussian product in 1D.
+  e^{-a (x-x_A)^2} e^{-b (x-x_B)^2} = K_{ab}^x e^{-p (x-x_P)^2}
+
+
+`gaussian_product_x <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/integration.irp.f#L226>`_
+  Gaussian product in 1D.
+  e^{-a (x-x_A)^2} e^{-b (x-x_B)^2} = K_{ab}^x e^{-p (x-x_P)^2}
+
+
+`gcf <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/need.irp.f#L211>`_
+  Undocumented
+
+
+`get_pseudo_inverse <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/LinearAlgebra.irp.f#L95>`_
+  Find C = A^-1
+
+
+`give_explicit_poly_and_gaussian <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/integration.irp.f#L46>`_
+  Transforms the product of
+  (x-x_A)^a(1) (x-x_B)^b(1) (x-x_A)^a(2) (y-y_B)^b(2) (z-z_A)^a(3) (z-z_B)^b(3) exp(-(r-A)^2 alpha) exp(-(r-B)^2 beta)
+  into
+  fact_k * [ sum (l_x = 0,i_order(1)) P_new(l_x,1) * (x-P_center(1))^l_x ] exp (- p (x-P_center(1))^2 )
+  * [ sum (l_y = 0,i_order(2)) P_new(l_y,2) * (y-P_center(2))^l_y ] exp (- p (y-P_center(2))^2 )
+  * [ sum (l_z = 0,i_order(3)) P_new(l_z,3) * (z-P_center(3))^l_z ] exp (- p (z-P_center(3))^2 )
+
+
+`give_explicit_poly_and_gaussian_double <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/integration.irp.f#L122>`_
+  Transforms the product of
+  (x-x_A)^a(1) (x-x_B)^b(1) (x-x_A)^a(2) (y-y_B)^b(2) (z-z_A)^a(3) (z-z_B)^b(3)
+  exp(-(r-A)^2 alpha) exp(-(r-B)^2 beta) exp(-(r-Nucl_center)^2 gama
+  .br
+  into
+  fact_k * [ sum (l_x = 0,i_order(1)) P_new(l_x,1) * (x-P_center(1))^l_x ] exp (- p (x-P_center(1))^2 )
+  * [ sum (l_y = 0,i_order(2)) P_new(l_y,2) * (y-P_center(2))^l_y ] exp (- p (y-P_center(2))^2 )
+  * [ sum (l_z = 0,i_order(3)) P_new(l_z,3) * (z-P_center(3))^l_z ] exp (- p (z-P_center(3))^2 )
+
+
+`give_explicit_poly_and_gaussian_x <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/integration.irp.f#L1>`_
+  Transform the product of
+  (x-x_A)^a(1) (x-x_B)^b(1) (x-x_A)^a(2) (y-y_B)^b(2) (z-z_A)^a(3) (z-z_B)^b(3) exp(-(r-A)^2 alpha) exp(-(r-B)^2 beta)
+  into
+  fact_k  (x-x_P)^iorder(1)  (y-y_P)^iorder(2)  (z-z_P)^iorder(3) exp(-p(r-P)^2)
+
+
+`gser <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/need.irp.f#L167>`_
+  Undocumented
+
+
+`h_apply_mrcc <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/H_apply.irp.f_shell_27#L422>`_
+  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_mrcc_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/H_apply.irp.f_shell_27#L1>`_
+  Generate all double excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_mrcc_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/H_apply.irp.f_shell_27#L273>`_
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_matrix_dressed <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/mrcc_utils.irp.f#L140>`_
+  Dressed H with Delta_ij
+
+
+`h_u_0_mrcc <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/davidson.irp.f#L360>`_
+  Computes v_0 = H|u_0>
+  .br
+  n : number of determinants
+  .br
+  H_jj : array of <j|H|j>
+
+
+`heap_dsort <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/sort.irp.f_template_184#L210>`_
+  Sort array x(isize) using the heap sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+
+
+`heap_dsort_big <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/sort.irp.f_template_184#L273>`_
+  Sort array x(isize) using the heap sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+  This is a version for very large arrays where the indices need
+  to be in integer*8 format
+
+
+`heap_i2sort <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/sort.irp.f_template_184#L744>`_
+  Sort array x(isize) using the heap sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+
+
+`heap_i2sort_big <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/sort.irp.f_template_184#L807>`_
+  Sort array x(isize) using the heap sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+  This is a version for very large arrays where the indices need
+  to be in integer*8 format
+
+
+`heap_i8sort <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/sort.irp.f_template_184#L566>`_
+  Sort array x(isize) using the heap sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+
+
+`heap_i8sort_big <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/sort.irp.f_template_184#L629>`_
+  Sort array x(isize) using the heap sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+  This is a version for very large arrays where the indices need
+  to be in integer*8 format
+
+
+`heap_isort <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/sort.irp.f_template_184#L388>`_
+  Sort array x(isize) using the heap sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+
+
+`heap_isort_big <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/sort.irp.f_template_184#L451>`_
+  Sort array x(isize) using the heap sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+  This is a version for very large arrays where the indices need
+  to be in integer*8 format
+
+
+`heap_sort <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/sort.irp.f_template_184#L32>`_
+  Sort array x(isize) using the heap sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+
+
+`heap_sort_big <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/sort.irp.f_template_184#L95>`_
+  Sort array x(isize) using the heap sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+  This is a version for very large arrays where the indices need
+  to be in integer*8 format
+
+
+`hermite <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/integration.irp.f#L540>`_
+  Hermite polynomial
+
+
+`i2radix_sort <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/sort.irp.f_template_450#L323>`_
+  Sort integer array x(isize) using the radix sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+  iradix should be -1 in input.
+
+
+`i2set_order <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/sort.irp.f_template_216#L102>`_
+  array A has already been sorted, and iorder has contains the new order of
+  elements of A. This subroutine changes the order of x to match the new order of A.
+
+
+`i2set_order_big <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/sort.irp.f_template_283#L271>`_
+  array A has already been sorted, and iorder has contains the new order of
+  elements of A. This subroutine changes the order of x to match the new order of A.
+  This is a version for very large arrays where the indices need
+  to be in integer*8 format
+
+
+`i2sort <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/sort.irp.f_template_184#L873>`_
+  Sort array x(isize).
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+
+
+`i8radix_sort <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/sort.irp.f_template_450#L163>`_
+  Sort integer array x(isize) using the radix sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+  iradix should be -1 in input.
+
+
+`i8radix_sort_big <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/sort.irp.f_template_450#L643>`_
+  Sort integer array x(isize) using the radix sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+  iradix should be -1 in input.
+
+
+`i8set_order <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/sort.irp.f_template_216#L77>`_
+  array A has already been sorted, and iorder has contains the new order of
+  elements of A. This subroutine changes the order of x to match the new order of A.
+
+
+`i8set_order_big <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/sort.irp.f_template_283#L212>`_
+  array A has already been sorted, and iorder has contains the new order of
+  elements of A. This subroutine changes the order of x to match the new order of A.
+  This is a version for very large arrays where the indices need
+  to be in integer*8 format
+
+
+`i8sort <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/sort.irp.f_template_184#L695>`_
+  Sort array x(isize).
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+
+
+`insertion_dsort <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/sort.irp.f_template_184#L180>`_
+  Sort array x(isize) using the insertion sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+
+
+`insertion_dsort_big <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/sort.irp.f_template_283#L61>`_
+  Sort array x(isize) using the insertion sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+  This is a version for very large arrays where the indices need
+  to be in integer*8 format
+
+
+`insertion_i2sort <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/sort.irp.f_template_184#L714>`_
+  Sort array x(isize) using the insertion sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+
+
+`insertion_i2sort_big <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/sort.irp.f_template_283#L238>`_
+  Sort array x(isize) using the insertion sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+  This is a version for very large arrays where the indices need
+  to be in integer*8 format
+
+
+`insertion_i8sort <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/sort.irp.f_template_184#L536>`_
+  Sort array x(isize) using the insertion sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+
+
+`insertion_i8sort_big <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/sort.irp.f_template_283#L179>`_
+  Sort array x(isize) using the insertion sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+  This is a version for very large arrays where the indices need
+  to be in integer*8 format
+
+
+`insertion_isort <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/sort.irp.f_template_184#L358>`_
+  Sort array x(isize) using the insertion sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+
+
+`insertion_isort_big <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/sort.irp.f_template_283#L120>`_
+  Sort array x(isize) using the insertion sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+  This is a version for very large arrays where the indices need
+  to be in integer*8 format
+
+
+`insertion_sort <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/sort.irp.f_template_184#L2>`_
+  Sort array x(isize) using the insertion sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+
+
+`insertion_sort_big <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/sort.irp.f_template_283#L2>`_
+  Sort array x(isize) using the insertion sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+  This is a version for very large arrays where the indices need
+  to be in integer*8 format
+
+
+`inv_int <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/util.irp.f#L257>`_
+  1/i
+
+
+`iradix_sort <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/sort.irp.f_template_450#L3>`_
+  Sort integer array x(isize) using the radix sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+  iradix should be -1 in input.
+
+
+`iradix_sort_big <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/sort.irp.f_template_450#L483>`_
+  Sort integer array x(isize) using the radix sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+  iradix should be -1 in input.
+
+
+`iset_order <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/sort.irp.f_template_216#L52>`_
+  array A has already been sorted, and iorder has contains the new order of
+  elements of A. This subroutine changes the order of x to match the new order of A.
+
+
+`iset_order_big <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/sort.irp.f_template_283#L153>`_
+  array A has already been sorted, and iorder has contains the new order of
+  elements of A. This subroutine changes the order of x to match the new order of A.
+  This is a version for very large arrays where the indices need
+  to be in integer*8 format
+
+
+`isort <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/sort.irp.f_template_184#L517>`_
+  Sort array x(isize).
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+
+
+`lambda_mrcc <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/mrcc_utils.irp.f#L5>`_
+  cm/<Psi_0|H|D_m> or perturbative 1/Delta_E(m)
+
+
+`lambda_mrcc_tmp <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/mrcc_utils.irp.f#L81>`_
+  Undocumented
+
+
+`lambda_pert <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/mrcc_utils.irp.f#L6>`_
+  cm/<Psi_0|H|D_m> or perturbative 1/Delta_E(m)
+
+
+`lapack_diag <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/LinearAlgebra.irp.f#L247>`_
+  Diagonalize matrix H
+  .br
+  H is untouched between input and ouptut
+  .br
+  eigevalues(i) = ith lowest eigenvalue of the H matrix
+  .br
+  eigvectors(i,j) = <i|psi_j> where i is the basis function and psi_j is the j th eigenvector
+  .br
+
+
+`lapack_diag_s2 <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/LinearAlgebra.irp.f#L310>`_
+  Diagonalize matrix H
+  .br
+  H is untouched between input and ouptut
+  .br
+  eigevalues(i) = ith lowest eigenvalue of the H matrix
+  .br
+  eigvectors(i,j) = <i|psi_j> where i is the basis function and psi_j is the j th eigenvector
+  .br
+
+
+`lapack_diagd <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/LinearAlgebra.irp.f#L180>`_
+  Diagonalize matrix H
+  .br
+  H is untouched between input and ouptut
+  .br
+  eigevalues(i) = ith lowest eigenvalue of the H matrix
+  .br
+  eigvectors(i,j) = <i|psi_j> where i is the basis function and psi_j is the j th eigenvector
+  .br
+
+
+`lapack_partial_diag <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/LinearAlgebra.irp.f#L376>`_
+  Diagonalize matrix H
+  .br
+  H is untouched between input and ouptut
+  .br
+  eigevalues(i) = ith lowest eigenvalue of the H matrix
+  .br
+  eigvectors(i,j) = <i|psi_j> where i is the basis function and psi_j is the j th eigenvector
+  .br
+
+
+`logfact <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/util.irp.f#L93>`_
+  n!
+
+
+`mrcc_dress <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/mrcc_dress.irp.f#L15>`_
+  Undocumented
+
+
+`mrcc_dress_simple <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/mrcc_dress.irp.f#L160>`_
+  Undocumented
+
+
+`mrcc_iterations <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/mrcc_general.irp.f#L7>`_
+  Undocumented
+
+
+`multiply_poly <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/integration.irp.f#L264>`_
+  Multiply two polynomials
+  D(t) =! D(t) +( B(t)*C(t))
+
+
+`normalize <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/util.irp.f#L356>`_
+  Normalizes vector u
+  u is expected to be aligned in memory.
+
+
+`nproc <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/util.irp.f#L283>`_
+  Number of current OpenMP threads
+
+
+`ortho_lowdin <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/LinearAlgebra.irp.f#L1>`_
+  Compute C_new=C_old.S^-1/2 canonical orthogonalization.
+  .br
+  overlap : overlap matrix
+  .br
+  LDA : leftmost dimension of overlap array
+  .br
+  N : Overlap matrix is NxN (array is (LDA,N) )
+  .br
+  C : Coefficients of the vectors to orthogonalize. On exit,
+  orthogonal vectors
+  .br
+  LDC : leftmost dimension of C
+  .br
+  m : Coefficients matrix is MxN, ( array is (LDC,N) )
+  .br
+
+
+`oscillations <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/mrcc_utils.irp.f#L86>`_
+  Undocumented
+
+
+`overlap_a_b_c <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/one_e_integration.irp.f#L35>`_
+  Undocumented
+
+
+`overlap_gaussian_x <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/one_e_integration.irp.f#L1>`_
+  .. math::
+  .br
+  \sum_{-infty}^{+infty} (x-A_x)^ax (x-B_x)^bx exp(-alpha(x-A_x)^2) exp(-beta(x-B_X)^2) dx
+  .br
+
+
+`overlap_gaussian_xyz <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/one_e_integration.irp.f#L113>`_
+  .. math::
+  .br
+  S_x = \int (x-A_x)^{a_x} exp(-\alpha(x-A_x)^2)  (x-B_x)^{b_x} exp(-beta(x-B_x)^2) dx \\
+  S = S_x S_y S_z
+  .br
+
+
+`overlap_x_abs <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/one_e_integration.irp.f#L175>`_
+  .. math                      ::
+  .br
+  \int_{-infty}^{+infty} (x-A_center)^(power_A) * (x-B_center)^power_B * exp(-alpha(x-A_center)^2) * exp(-beta(x-B_center)^2) dx
+  .br
+
+
+`pert_determinants <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/mrcc_utils.irp.f#L1>`_
+  Undocumented
+
+
+`progress_active <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/progress.irp.f#L29>`_
+  Current status for displaying progress bars. Global variable.
+
+
+`progress_bar <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/progress.irp.f#L27>`_
+  Current status for displaying progress bars. Global variable.
+
+
+`progress_timeout <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/progress.irp.f#L28>`_
+  Current status for displaying progress bars. Global variable.
+
+
+`progress_title <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/progress.irp.f#L31>`_
+  Current status for displaying progress bars. Global variable.
+
+
+`progress_value <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/progress.irp.f#L30>`_
+  Current status for displaying progress bars. Global variable.
+
+
+`psi_ref_lock <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/mrcc_dress.irp.f#L3>`_
+  Locks on ref determinants to fill delta_ij
+
+
+`recentered_poly2 <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/integration.irp.f#L363>`_
+  Recenter two polynomials
+
+
+`rint <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/integration.irp.f#L436>`_
+  .. math::
+  .br
+  \int_0^1 dx \exp(-p x^2) x^n
+  .br
+
+
+`rint1 <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/integration.irp.f#L596>`_
+  Standard version of rint
+
+
+`rint_large_n <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/integration.irp.f#L565>`_
+  Version of rint for large values of n
+
+
+`rint_sum <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/integration.irp.f#L484>`_
+  Needed for the calculation of two-electron integrals.
+
+
+`rinteg <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/need.irp.f#L47>`_
+  Undocumented
+
+
+`rintgauss <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/need.irp.f#L31>`_
+  Undocumented
+
+
+`run_mrcc <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/mrcc_general.irp.f#L1>`_
+  Undocumented
+
+
+`run_progress <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/progress.irp.f#L45>`_
+  Display a progress bar with documentation of what is happening
+
+
+`sabpartial <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/need.irp.f#L2>`_
+  Undocumented
+
+
+`set_generators_bitmasks_as_holes_and_particles <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/mrcc_general.irp.f#L69>`_
+  Undocumented
+
+
+`set_order <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/sort.irp.f_template_216#L2>`_
+  array A has already been sorted, and iorder has contains the new order of
+  elements of A. This subroutine changes the order of x to match the new order of A.
+
+
+`set_order_big <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/sort.irp.f_template_283#L35>`_
+  array A has already been sorted, and iorder has contains the new order of
+  elements of A. This subroutine changes the order of x to match the new order of A.
+  This is a version for very large arrays where the indices need
+  to be in integer*8 format
+
+
+`set_zero_extra_diag <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/LinearAlgebra.irp.f#L433>`_
+  Undocumented
+
+
+`sort <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/sort.irp.f_template_184#L161>`_
+  Sort array x(isize).
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+
+
+`start_progress <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/progress.irp.f#L1>`_
+  Starts the progress bar
+
+
+`stop_progress <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/progress.irp.f#L19>`_
+  Stop the progress bar
+
+
+`trap_signals <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/abort.irp.f#L19>`_
+  What to do when a signal is caught. Here, trap Ctrl-C and call the control_C subroutine.
+
+
+`u_dot_u <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/util.irp.f#L325>`_
+  Compute <u|u>
+
+
+`u_dot_v <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/util.irp.f#L299>`_
+  Compute <u|v>
+
+
+`wall_time <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/util.irp.f#L268>`_
+  The equivalent of cpu_time, but for the wall time.
+
+
+`write_git_log <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/util.irp.f#L243>`_
+  Write the last git commit in file iunit.
+

plugins/MRCC_Utils/mrcc_general.irp.f

@@ -10,11 +10,14 @@ subroutine mrcc_iterations
   integer :: i,j
 
   double precision :: E_new, E_old, delta_e
-  integer :: iteration
+  integer :: iteration,i_oscillations
+  double precision :: E_past(4)
   E_new = 0.d0
   delta_E = 1.d0
   iteration = 0
-  do while (delta_E > 100.d0*davidson_threshold)
+  j = 1
+  i_oscillations = 0
+  do while (delta_E > 1.d-7)
     iteration += 1
     print *,  '===========================' 
     print *,  'MRCC Iteration', iteration
@@ -25,10 +28,37 @@ subroutine mrcc_iterations
     call diagonalize_ci_dressed
     E_new = sum(ci_energy_dressed)
     delta_E = dabs(E_new - E_old)
-    if (iteration > 20) then
+
-      exit
+    E_past(j) = E_new
+    j +=1
+    if(j>4)then
+     j=1
+    endif
+    if(iteration > 4) then 
+     if(delta_E > 1.d-10)then
+      if(dabs(E_past(1) - E_past(3)) .le. delta_E .and. dabs(E_past(2) - E_past(4)).le. delta_E)then 
+       print*,'OSCILLATIONS !!!'
+       oscillations = .True.
+       i_oscillations +=1
+       lambda_mrcc_tmp = lambda_mrcc
+      endif
+     endif
     endif
     call save_wavefunction
+!   if (i_oscillations > 5) then
+!    exit
+!   endif
+    if (iteration > 200) then
+      exit
+    endif
+    print*,'------------'
+    print*,'VECTOR'
+    do i = 1, N_det_ref
+     print*,''
+     print*,'psi_ref_coef(i,1) = ',psi_ref_coef(i,1)
+     print*,'delta_ii(i,1)     = ',delta_ii(i,1)
+    enddo
+    print*,'------------'
   enddo
   call write_double(6,ci_energy_dressed(1),"Final MRCC energy")
   call ezfio_set_mrcc_cassd_energy(ci_energy_dressed(1))

plugins/MRCC_Utils/mrcc_utils.irp.f

@@ -1,29 +1,94 @@
+ BEGIN_PROVIDER [integer, pert_determinants, (N_states, psi_det_size) ]
+ END_PROVIDER 
+
+
  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> or perturbative 1/Delta_E(m)
  END_DOC
- integer :: i,k
+ integer :: i,k,j
- double precision               :: ihpsi(N_states), hii
+ double precision               :: ihpsi(N_states), hii,delta_e_eff,ihpsi_current(N_states),hij
+ integer :: i_ok,i_pert,i_pert_count
+ i_ok = 0
+
+ double precision :: phase_restart(N_states),tmp
+ do k = 1, N_states
+  phase_restart(k) = dsign(1.d0,psi_ref_coef_restart(1,k)/psi_ref_coef(1,k))
+ enddo
+ i_pert_count = 0
  
  do i=1,N_det_non_ref
-   call i_h_psi(psi_non_ref(1,1,i), psi_ref, psi_ref_coef, N_int, N_det_ref,&
+   call i_h_psi(psi_non_ref(1,1,i), psi_ref_restart, psi_ref_coef_restart, N_int, N_det_ref,&
-       size(psi_ref_coef,1), n_states, ihpsi)
+       size(psi_ref_coef_restart,1), n_states, ihpsi)
-   call i_h_j(psi_non_ref(1,1,i),psi_non_ref(1,1,i),N_int,hii)
+   call i_H_j(psi_non_ref(1,1,i),psi_non_ref(1,1,i),N_int,hii)
    do k=1,N_states
      lambda_pert(k,i) = 1.d0 / (psi_ref_energy_diagonalized(k)-hii)
-     if (dabs(ihpsi(k)).le.1.d-3) then
+     call i_h_psi(psi_non_ref(1,1,i), psi_ref, psi_ref_coef, N_int, N_det_ref,size(psi_ref_coef,1), n_states, ihpsi_current)
+     tmp = psi_non_ref_coef(i,k)/ihpsi_current(k)
+     i_pert = 1
+     if((ihpsi(k) * lambda_pert(k,i))/psi_non_ref_coef_restart(i,k) .ge. 0.5d0 & 
+        .and. (ihpsi(k) * lambda_pert(k,i))/psi_non_ref_coef_restart(i,k) > 0.d0 )then  ! test on the first order coefficient
+      i_pert = 0
+     endif
+     do j = 1, N_det_ref
+      call i_H_j(psi_non_ref(1,1,i),psi_ref(1,1,j),N_int,hij)
+      if(dabs(hij * tmp).ge.0.5d0)then
+       i_pert_count +=1
+       i_pert = 1
+       exit
+      endif
+     enddo
+     if( i_pert == 1)then
+      pert_determinants(k,i) = i_pert
+     endif
+     if(pert_determinants(k,i) == 1)then
+       i_ok +=1
        lambda_mrcc(k,i) = lambda_pert(k,i)
      else
-       lambda_mrcc(k,i) = psi_non_ref_coef(i,k)/ihpsi(k)
+       lambda_mrcc(k,i) = psi_non_ref_coef(i,k)/ihpsi_current(k)
      endif
    enddo
  enddo
+!if(oscillations)then
+! print*,'AVERAGING the lambda_mrcc with those of the previous iterations'
+! do i = 1, N_det_non_ref
+!  do k = 1, N_states
+
+!   double precision :: tmp
+!   tmp = lambda_mrcc(k,i)
+!   lambda_mrcc(k,i) += lambda_mrcc_tmp(k,i)
+!   lambda_mrcc(k,i) = lambda_mrcc(k,i) * 0.5d0
+!   if(dabs(tmp - lambda_mrcc(k,i)).ge.1.d-9)then
+!   print*,''
+!   print*,'i = ',i
+!   print*,'psi_non_ref_coef(i,k) = ',psi_non_ref_coef(i,k)
+!   print*,'lambda_mrcc(k,i)     = ',lambda_mrcc(k,i)
+!   print*,'                 tmp = ',tmp
+!   endif
+!  enddo
+! enddo
+!endif
+ print*,'N_det_non_ref = ',N_det_non_ref
+ print*,'Number of Perturbatively treated determinants = ',i_ok
+ print*,'i_pert_count = ',i_pert_count
+ print*,'psi_coef_ref_ratio = ',psi_ref_coef(2,1)/psi_ref_coef(1,1)
 
 END_PROVIDER
 
 
+BEGIN_PROVIDER [ double precision, lambda_mrcc_tmp, (N_states,psi_det_size) ]
+ implicit none
+ lambda_mrcc_tmp = 0.d0
+END_PROVIDER 
+
+BEGIN_PROVIDER [ logical, oscillations ]
+ implicit none
+ oscillations = .False.
+END_PROVIDER 
+
+
 
 
 !BEGIN_PROVIDER [ double precision, delta_ij_non_ref, (N_det_non_ref, N_det_non_ref,N_states) ]
@@ -45,6 +110,31 @@ END_PROVIDER
  delta_ij = 0.d0
  delta_ii = 0.d0
  call H_apply_mrcc(delta_ij,delta_ii,N_det_ref,N_det_non_ref)
+ double precision :: max_delta
+ double precision :: accu
+ integer :: imax,jmax
+ max_delta = 0.d0
+ accu = 0.d0
+ do i = 1, N_det_ref
+  do j = 1, N_det_non_ref
+   accu += psi_non_ref_coef(j,1) * psi_ref_coef(i,1) * delta_ij(i,j,1)
+   if(dabs(delta_ij(i,j,1)).gt.max_delta)then
+    max_delta = dabs(delta_ij(i,j,1))
+    imax = i
+    jmax = j
+   endif
+  enddo
+ enddo
+ print*,''
+ print*,''
+ print*,'<psi| Delta H |psi> = ',accu
+ print*,'MAX VAL OF DRESING = ',delta_ij(imax,jmax,1)
+ print*,'imax,jmax = ',imax,jmax
+ print*,'psi_ref_coef(imax,1)     = ',psi_ref_coef(imax,1)
+ print*,'psi_non_ref_coef(jmax,1) = ',psi_non_ref_coef(jmax,1)
+ do i = 1, N_det_ref
+  print*,'delta_ii(i,1)     = ',delta_ii(i,1)
+ enddo
 END_PROVIDER
 
 BEGIN_PROVIDER [ double precision, h_matrix_dressed, (N_det,N_det,N_states) ]

plugins/Perturbation/README.rst

@@ -67,115 +67,137 @@ Assumptions
     pt2_....
 
 
-Documentation
+Needed Modules
-=============
+==============
 
-.. Do not edit this section. It was auto-generated from the
+.. Do not edit this section It was auto-generated
 .. by the `update_README.py` script.
 
-`do_pt2_end <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/ezfio_interface.irp.f#L6>`_
+.. image:: tree_dependency.png
+
+* `Properties <http://github.com/LCPQ/quantum_package/tree/master/src/Properties>`_
+* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
+
+Needed Modules
+==============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
+.. image:: tree_dependency.png
+
+* `Properties <http://github.com/LCPQ/quantum_package/tree/master/plugins/Properties>`_
+* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock>`_
+
+Documentation
+=============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
+`do_pt2_end <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/ezfio_interface.irp.f#L6>`_
   If true, compute the PT2 at the end of the selection
 
 
-`fill_h_apply_buffer_selection <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/selection.irp.f#L1>`_
+`fill_h_apply_buffer_selection <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/selection.irp.f#L1>`_
   Fill the H_apply buffer with determiants for the selection
 
 
-`max_exc_pert <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/exc_max.irp.f#L1>`_
+`max_exc_pert <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/exc_max.irp.f#L1>`_
   Undocumented
 
 
-`perturb_buffer_by_mono_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L791>`_
+`perturb_buffer_by_mono_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L791>`_
   Applly pertubration ``delta_rho_one_point`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_by_mono_dipole_moment_z <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L686>`_
+`perturb_buffer_by_mono_dipole_moment_z <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L686>`_
   Applly pertubration ``dipole_moment_z`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_by_mono_epstein_nesbet <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L476>`_
+`perturb_buffer_by_mono_epstein_nesbet <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L476>`_
   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#L581>`_
+`perturb_buffer_by_mono_epstein_nesbet_2x2 <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L581>`_
   Applly pertubration ``epstein_nesbet_2x2`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_by_mono_epstein_nesbet_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L371>`_
+`perturb_buffer_by_mono_epstein_nesbet_sc2 <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L371>`_
   Applly pertubration ``epstein_nesbet_sc2`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_by_mono_epstein_nesbet_sc2_no_projected <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L266>`_
+`perturb_buffer_by_mono_epstein_nesbet_sc2_no_projected <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L266>`_
   Applly pertubration ``epstein_nesbet_sc2_no_projected`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_by_mono_epstein_nesbet_sc2_projected <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L161>`_
+`perturb_buffer_by_mono_epstein_nesbet_sc2_projected <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L161>`_
   Applly pertubration ``epstein_nesbet_sc2_projected`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_by_mono_h_core <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L56>`_
+`perturb_buffer_by_mono_h_core <http://github.com/LCPQ/quantum_package/tree/master/plugins/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#L896>`_
+`perturb_buffer_by_mono_moller_plesset <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L896>`_
   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#L740>`_
+`perturb_buffer_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L740>`_
   Applly pertubration ``delta_rho_one_point`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_dipole_moment_z <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L635>`_
+`perturb_buffer_dipole_moment_z <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L635>`_
   Applly pertubration ``dipole_moment_z`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_epstein_nesbet <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L425>`_
+`perturb_buffer_epstein_nesbet <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L425>`_
   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#L530>`_
+`perturb_buffer_epstein_nesbet_2x2 <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L530>`_
   Applly pertubration ``epstein_nesbet_2x2`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_epstein_nesbet_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L320>`_
+`perturb_buffer_epstein_nesbet_sc2 <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L320>`_
   Applly pertubration ``epstein_nesbet_sc2`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_epstein_nesbet_sc2_no_projected <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L215>`_
+`perturb_buffer_epstein_nesbet_sc2_no_projected <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L215>`_
   Applly pertubration ``epstein_nesbet_sc2_no_projected`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_epstein_nesbet_sc2_projected <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L110>`_
+`perturb_buffer_epstein_nesbet_sc2_projected <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L110>`_
   Applly pertubration ``epstein_nesbet_sc2_projected`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_h_core <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L5>`_
+`perturb_buffer_h_core <http://github.com/LCPQ/quantum_package/tree/master/plugins/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#L845>`_
+`perturb_buffer_moller_plesset <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L845>`_
   Applly pertubration ``moller_plesset`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`pt2_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/delta_rho_perturbation.irp.f#L1>`_
+`pt2_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/delta_rho_perturbation.irp.f#L1>`_
   compute the perturbatibe contribution to the Integrated Spin density at z = z_one point of one determinant
   .br
   for the various n_st states, at various level of theory.
@@ -196,7 +218,7 @@ Documentation
   .br
 
 
-`pt2_dipole_moment_z <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/dipole_moment.irp.f#L1>`_
+`pt2_dipole_moment_z <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/dipole_moment.irp.f#L1>`_
   compute the perturbatibe contribution to the dipole moment of one determinant
   .br
   for the various n_st states, at various level of theory.
@@ -217,7 +239,7 @@ Documentation
   .br
 
 
-`pt2_epstein_nesbet <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/epstein_nesbet.irp.f#L1>`_
+`pt2_epstein_nesbet <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/epstein_nesbet.irp.f#L1>`_
   compute the standard Epstein-Nesbet perturbative first order coefficient and second order energetic contribution
   .br
   for the various N_st states.
@@ -228,7 +250,7 @@ Documentation
   .br
 
 
-`pt2_epstein_nesbet_2x2 <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/epstein_nesbet.irp.f#L45>`_
+`pt2_epstein_nesbet_2x2 <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/epstein_nesbet.irp.f#L45>`_
   compute the Epstein-Nesbet 2x2 diagonalization coefficient and energetic contribution
   .br
   for the various N_st states.
@@ -239,7 +261,7 @@ Documentation
   .br
 
 
-`pt2_epstein_nesbet_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/pert_sc2.irp.f#L186>`_
+`pt2_epstein_nesbet_sc2 <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/pert_sc2.irp.f#L186>`_
   compute the standard Epstein-Nesbet perturbative first order coefficient and second order energetic contribution
   .br
   for the various N_st states, but with the CISD_SC2 energies and coefficients
@@ -250,7 +272,7 @@ Documentation
   .br
 
 
-`pt2_epstein_nesbet_sc2_no_projected <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/pert_sc2.irp.f#L87>`_
+`pt2_epstein_nesbet_sc2_no_projected <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/pert_sc2.irp.f#L87>`_
   compute the Epstein-Nesbet perturbative first order coefficient and second order energetic contribution
   .br
   for the various N_st states,
@@ -274,7 +296,7 @@ Documentation
   H_pert_diag = <HF|H|det_pert> c_pert
 
 
-`pt2_epstein_nesbet_sc2_projected <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/pert_sc2.irp.f#L2>`_
+`pt2_epstein_nesbet_sc2_projected <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/pert_sc2.irp.f#L2>`_
   compute the Epstein-Nesbet perturbative first order coefficient and second order energetic contribution
   .br
   for the various N_st states,
@@ -298,7 +320,7 @@ Documentation
   H_pert_diag = <HF|H|det_pert> c_pert
 
 
-`pt2_h_core <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/pert_single.irp.f#L1>`_
+`pt2_h_core <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/pert_single.irp.f#L1>`_
   compute the standard Epstein-Nesbet perturbative first order coefficient and second order energetic contribution
   .br
   for the various N_st states.
@@ -309,12 +331,12 @@ Documentation
   .br
 
 
-`pt2_max <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/ezfio_interface.irp.f#L28>`_
+`pt2_max <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/ezfio_interface.irp.f#L28>`_
   The selection process stops when the largest PT2 (for all the state) is lower
   than pt2_max in absolute value
 
 
-`pt2_moller_plesset <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/Moller_plesset.irp.f#L1>`_
+`pt2_moller_plesset <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/Moller_plesset.irp.f#L1>`_
   compute the standard Moller-Plesset perturbative first order coefficient and second order energetic contribution
   .br
   for the various n_st states.
@@ -325,39 +347,28 @@ Documentation
   .br
 
 
-`remove_small_contributions <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/selection.irp.f#L87>`_
+`remove_small_contributions <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/selection.irp.f#L87>`_
   Remove determinants with small contributions. N_states is assumed to be
   provided.
 
 
-`repeat_all_e_corr <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/pert_sc2.irp.f#L156>`_
+`repeat_all_e_corr <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/pert_sc2.irp.f#L156>`_
   Undocumented
 
 
-`selection_criterion <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/selection.irp.f#L74>`_
+`selection_criterion <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/selection.irp.f#L74>`_
   Threshold to select determinants. Set by selection routines.
 
 
-`selection_criterion_factor <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/selection.irp.f#L76>`_
+`selection_criterion_factor <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/selection.irp.f#L76>`_
   Threshold to select determinants. Set by selection routines.
 
 
-`selection_criterion_min <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/selection.irp.f#L75>`_
+`selection_criterion_min <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/selection.irp.f#L75>`_
   Threshold to select determinants. Set by selection routines.
 
 
-`var_pt2_ratio <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/ezfio_interface.irp.f#L51>`_
+`var_pt2_ratio <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/ezfio_interface.irp.f#L51>`_
   The selection process stops when the energy ratio variational/(variational+PT2)
   is equal to var_pt2_ratio
 
-Needed Modules
-==============
-
-.. Do not edit this section. It was auto-generated from the
-.. by the `update_README.py` script.
-
-.. image:: tree_dependency.png
-
-* `Properties <http://github.com/LCPQ/quantum_package/tree/master/src/Properties>`_
-* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
-

plugins/Properties/README.rst

@@ -2,47 +2,67 @@
 Properties Module
 =================
 
-Documentation
+Needed Modules
-=============
+==============
 
-.. Do not edit this section. It was auto-generated from the
+.. Do not edit this section It was auto-generated
 .. by the `update_README.py` script.
 
-`ao_integrated_delta_rho_all_points <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/delta_rho.irp.f#L61>`_
+.. image:: tree_dependency.png
+
+* `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
+
+Needed Modules
+==============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
+.. image:: tree_dependency.png
+
+* `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
+
+Documentation
+=============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
+`ao_integrated_delta_rho_all_points <http://github.com/LCPQ/quantum_package/tree/master/plugins/Properties/delta_rho.irp.f#L61>`_
   array of the overlap in x,y between the AO function and integrated between [z,z+dz] in the z axis
   for all the z points that are given (N_z_pts)
 
 
-`ao_integrated_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/delta_rho.irp.f#L130>`_
+`ao_integrated_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/plugins/Properties/delta_rho.irp.f#L130>`_
   array of the overlap in x,y between the AO function and integrated between [z,z+dz] in the z axis
   for one specific z point
 
 
-`average_position <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/properties.irp.f#L1>`_
+`average_position <http://github.com/LCPQ/quantum_package/tree/master/plugins/Properties/properties.irp.f#L1>`_
   average_position(1) = <psi_det|X|psi_det>
   average_position(2) = <psi_det|Y|psi_det>
   average_position(3) = <psi_det|Z|psi_det>
 
 
-`average_spread <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/properties.irp.f#L27>`_
+`average_spread <http://github.com/LCPQ/quantum_package/tree/master/plugins/Properties/properties.irp.f#L27>`_
   average_spread(1) = <psi_det|X^2|psi_det>
   average_spread(2) = <psi_det|Y^2|psi_det>
   average_spread(3) = <psi_det|Z^2|psi_det>
 
 
-`delta_z <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/delta_rho.irp.f#L4>`_
+`delta_z <http://github.com/LCPQ/quantum_package/tree/master/plugins/Properties/delta_rho.irp.f#L4>`_
   Undocumented
 
 
-`diag_o1_mat_elem <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/slater_rules_mono_electronic.irp.f#L91>`_
+`diag_o1_mat_elem <http://github.com/LCPQ/quantum_package/tree/master/plugins/Properties/slater_rules_mono_electronic.irp.f#L91>`_
   Computes <i|O1|i>
 
 
-`diag_o1_mat_elem_alpha_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/slater_rules_mono_electronic.irp.f#L210>`_
+`diag_o1_mat_elem_alpha_beta <http://github.com/LCPQ/quantum_package/tree/master/plugins/Properties/slater_rules_mono_electronic.irp.f#L210>`_
   Computes <i|O1(alpha) -O1(beta)|i>
 
 
-`filter_connected_mono <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/slater_rules_mono_electronic.irp.f#L240>`_
+`filter_connected_mono <http://github.com/LCPQ/quantum_package/tree/master/plugins/Properties/slater_rules_mono_electronic.irp.f#L240>`_
   Filters out the determinants that are not connected through PURE
   .br
   MONO EXCITATIONS OPERATORS (a^{\dagger}j a_i)
@@ -56,99 +76,89 @@ Documentation
   idx(0) is the number of determinants that interact with key1
 
 
-`get_average <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/average.irp.f#L1>`_
+`get_average <http://github.com/LCPQ/quantum_package/tree/master/plugins/Properties/average.irp.f#L1>`_
   computes the average value of a pure MONO ELECTRONIC OPERATOR
   whom integrals on the MO basis are stored in "array"
   and with the density is stored in  "density"
 
 
-`i_o1_j <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/slater_rules_mono_electronic.irp.f#L1>`_
+`i_o1_j <http://github.com/LCPQ/quantum_package/tree/master/plugins/Properties/slater_rules_mono_electronic.irp.f#L1>`_
   Returns <i|O1|j> where i and j are determinants
   and O1 is a ONE BODY OPERATOR
   array  is the array of the mono electronic operator
   on the MO basis
 
 
-`i_o1_j_alpha_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/slater_rules_mono_electronic.irp.f#L158>`_
+`i_o1_j_alpha_beta <http://github.com/LCPQ/quantum_package/tree/master/plugins/Properties/slater_rules_mono_electronic.irp.f#L158>`_
   Returns <i|O1(alpha) - O1(beta)|j> where i and j are determinants
   and O1 is a ONE BODY OPERATOR
   array  is the array of the mono electronic operator
   on the MO basis
 
 
-`i_o1_psi <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/slater_rules_mono_electronic.irp.f#L52>`_
+`i_o1_psi <http://github.com/LCPQ/quantum_package/tree/master/plugins/Properties/slater_rules_mono_electronic.irp.f#L52>`_
   <key|O1|psi> for the various Nstates
   and O1 is a ONE BODY OPERATOR
   array  is the array of the mono electronic operator
   on the MO basis
 
 
-`i_o1_psi_alpha_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/slater_rules_mono_electronic.irp.f#L119>`_
+`i_o1_psi_alpha_beta <http://github.com/LCPQ/quantum_package/tree/master/plugins/Properties/slater_rules_mono_electronic.irp.f#L119>`_
   <key|O1(alpha) - O1(beta)|psi> for the various Nstates
   and O1 is a ONE BODY OPERATOR
   array  is the array of the mono electronic operator
   on the MO basis
 
 
-`i_unit_integrated_delta_rho <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/delta_rho.irp.f#L118>`_
+`i_unit_integrated_delta_rho <http://github.com/LCPQ/quantum_package/tree/master/plugins/Properties/delta_rho.irp.f#L118>`_
   fortran unit for the writing of the integrated delta_rho
 
 
-`integrated_delta_rho_all_points <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/delta_rho.irp.f#L15>`_
+`integrated_delta_rho_all_points <http://github.com/LCPQ/quantum_package/tree/master/plugins/Properties/delta_rho.irp.f#L15>`_
   .br
   integrated_rho(alpha,z) - integrated_rho(beta,z) for all the z points
   chosen
   .br
 
 
-`integrated_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/delta_rho.irp.f#L212>`_
+`integrated_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/plugins/Properties/delta_rho.irp.f#L212>`_
   .br
   integral (x,y) and (z,z+delta_z) of rho(alpha) - rho(beta)
   on the MO basis
   .br
 
 
-`mo_integrated_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/delta_rho.irp.f#L184>`_
+`mo_integrated_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/plugins/Properties/delta_rho.irp.f#L184>`_
   .br
   array of the integrals needed of integrated_rho(alpha,z) - integrated_rho(beta,z) for z = z_one_point
   on the MO basis
   .br
 
 
-`n_z_pts <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/delta_rho.irp.f#L1>`_
+`n_z_pts <http://github.com/LCPQ/quantum_package/tree/master/plugins/Properties/delta_rho.irp.f#L1>`_
   Undocumented
 
 
-`test_average_value <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/routines_test.irp.f#L3>`_
+`test_average_value <http://github.com/LCPQ/quantum_package/tree/master/plugins/Properties/routines_test.irp.f#L3>`_
   Undocumented
 
 
-`test_average_value_alpha_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/routines_test.irp.f#L25>`_
+`test_average_value_alpha_beta <http://github.com/LCPQ/quantum_package/tree/master/plugins/Properties/routines_test.irp.f#L25>`_
   Undocumented
 
 
-`test_dm <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/routines_test.irp.f#L56>`_
+`test_dm <http://github.com/LCPQ/quantum_package/tree/master/plugins/Properties/routines_test.irp.f#L56>`_
   Undocumented
 
 
-`z_max <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/delta_rho.irp.f#L3>`_
+`z_max <http://github.com/LCPQ/quantum_package/tree/master/plugins/Properties/delta_rho.irp.f#L3>`_
   Undocumented
 
 
-`z_min <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/delta_rho.irp.f#L2>`_
+`z_min <http://github.com/LCPQ/quantum_package/tree/master/plugins/Properties/delta_rho.irp.f#L2>`_
   Undocumented
 
 
-`z_one_point <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/ezfio_interface.irp.f#L6>`_
+`z_one_point <http://github.com/LCPQ/quantum_package/tree/master/plugins/Properties/ezfio_interface.irp.f#L6>`_
   z point on which the integrated delta rho is calculated
 
-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/Psiref_CAS/README.rst

@@ -31,6 +31,14 @@ Documentation
   CAS wave function, defined from the application of the CAS bitmask on the
   determinants. idx_cas gives the indice of the CAS determinant in psi_det.
 
+
+`psi_ref_coef_restart <http://github.com/LCPQ/quantum_package/tree/master/src/Psiref_CAS/psi_ref.irp.f#L30>`_
+  Projection of the CAS wave function on the restart wave function.
+
+
+`psi_ref_restart <http://github.com/LCPQ/quantum_package/tree/master/src/Psiref_CAS/psi_ref.irp.f#L29>`_
+  Projection of the CAS wave function on the restart wave function.
+
 Needed Modules
 ==============
 
@@ -41,3 +49,46 @@ Needed Modules
 
 * `Psiref_Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Psiref_Utils>`_
 
+Needed Modules
+==============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
+.. image:: tree_dependency.png
+
+* `Psiref_Utils <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils>`_
+
+Documentation
+=============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
+`idx_ref <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_CAS/psi_ref.irp.f#L5>`_
+  CAS wave function, defined from the application of the CAS bitmask on the
+  determinants. idx_cas gives the indice of the CAS determinant in psi_det.
+
+
+`n_det_ref <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_CAS/psi_ref.irp.f#L6>`_
+  CAS wave function, defined from the application of the CAS bitmask on the
+  determinants. idx_cas gives the indice of the CAS determinant in psi_det.
+
+
+`psi_ref <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_CAS/psi_ref.irp.f#L3>`_
+  CAS wave function, defined from the application of the CAS bitmask on the
+  determinants. idx_cas gives the indice of the CAS determinant in psi_det.
+
+
+`psi_ref_coef <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_CAS/psi_ref.irp.f#L4>`_
+  CAS wave function, defined from the application of the CAS bitmask on the
+  determinants. idx_cas gives the indice of the CAS determinant in psi_det.
+
+
+`psi_ref_coef_restart <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_CAS/psi_ref.irp.f#L30>`_
+  Projection of the CAS wave function on the restart wave function.
+
+
+`psi_ref_restart <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_CAS/psi_ref.irp.f#L29>`_
+  Projection of the CAS wave function on the restart wave function.
+

plugins/Psiref_CAS/psi_ref.irp.f

@@ -26,3 +26,29 @@ use bitmasks
 
 END_PROVIDER
 
+ BEGIN_PROVIDER [ integer(bit_kind), psi_ref_restart, (N_int,2,psi_det_size) ]
+&BEGIN_PROVIDER [ double precision, psi_ref_coef_restart,  (psi_det_size,n_states) ]
+  implicit none
+  BEGIN_DOC
+  ! Projection of the CAS wave function on the restart wave function. 
+  END_DOC
+  integer :: i,j,k
+  integer, save                  :: ifirst
+
+  if(ifirst == 0)then
+   ifirst = 1
+   do i=1,N_det_ref
+     do k=1,N_int
+       psi_ref_restart(k,1,i) = psi_cas(k,1,i)
+       psi_ref_restart(k,2,i) = psi_cas(k,2,i)
+     enddo
+   enddo
+   do k=1,N_states
+     do i=1,N_det_ref
+       psi_ref_coef_restart(i,k) = psi_cas_coef(i,k)
+     enddo
+   enddo
+  endif
+
+END_PROVIDER
+

plugins/Psiref_Utils/README.rst

@@ -13,11 +13,11 @@ Documentation
 .. Do not edit this section. It was auto-generated from the
 .. by the `update_README.py` script.
 
-`get_index_in_psi_ref_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Psiref_Utils/psi_ref_utils.irp.f#L140>`_
+`get_index_in_psi_ref_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Psiref_Utils/psi_ref_utils.irp.f#L182>`_
   Returns the index of the determinant in the ``psi_ref_sorted_bit`` array
 
 
-`h_matrix_ref <http://github.com/LCPQ/quantum_package/tree/master/src/Psiref_Utils/psi_ref_utils.irp.f#L74>`_
+`h_matrix_ref <http://github.com/LCPQ/quantum_package/tree/master/src/Psiref_Utils/psi_ref_utils.irp.f#L116>`_
   Undocumented
 
 
@@ -42,7 +42,7 @@ Documentation
   idx_non_ref_rev gives the reverse.
 
 
-`is_in_psi_ref <http://github.com/LCPQ/quantum_package/tree/master/src/Psiref_Utils/psi_ref_utils.irp.f#L126>`_
+`is_in_psi_ref <http://github.com/LCPQ/quantum_package/tree/master/src/Psiref_Utils/psi_ref_utils.irp.f#L168>`_
   True if the determinant ``det`` is in the wave function
 
 
@@ -60,7 +60,7 @@ Documentation
   been done going from psi_ref to psi_non_ref
 
 
-`psi_coef_ref_diagonalized <http://github.com/LCPQ/quantum_package/tree/master/src/Psiref_Utils/psi_ref_utils.irp.f#L86>`_
+`psi_coef_ref_diagonalized <http://github.com/LCPQ/quantum_package/tree/master/src/Psiref_Utils/psi_ref_utils.irp.f#L128>`_
   Undocumented
 
 
@@ -78,12 +78,26 @@ Documentation
   idx_non_ref_rev gives the reverse.
 
 
-`psi_non_ref_coef_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Psiref_Utils/psi_ref_utils.irp.f#L62>`_
+`psi_non_ref_coef_restart <http://github.com/LCPQ/quantum_package/tree/master/src/Psiref_Utils/psi_ref_utils.irp.f#L62>`_
+  Set of determinants which are not part of the reference, defined from the application
+  of the reference bitmask on the determinants.
+  idx_non_ref gives the indice of the determinant in psi_det.
+  But this is with respect to the restart wave function.
+
+
+`psi_non_ref_coef_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Psiref_Utils/psi_ref_utils.irp.f#L104>`_
   Reference determinants sorted to accelerate the search of a random determinant in the wave
   function.
 
 
-`psi_non_ref_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Psiref_Utils/psi_ref_utils.irp.f#L61>`_
+`psi_non_ref_restart <http://github.com/LCPQ/quantum_package/tree/master/src/Psiref_Utils/psi_ref_utils.irp.f#L61>`_
+  Set of determinants which are not part of the reference, defined from the application
+  of the reference bitmask on the determinants.
+  idx_non_ref gives the indice of the determinant in psi_det.
+  But this is with respect to the restart wave function.
+
+
+`psi_non_ref_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Psiref_Utils/psi_ref_utils.irp.f#L103>`_
   Reference determinants sorted to accelerate the search of a random determinant in the wave
   function.
 
@@ -93,11 +107,11 @@ Documentation
   function.
 
 
-`psi_ref_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Psiref_Utils/psi_ref_utils.irp.f#L105>`_
+`psi_ref_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Psiref_Utils/psi_ref_utils.irp.f#L147>`_
   Undocumented
 
 
-`psi_ref_energy_diagonalized <http://github.com/LCPQ/quantum_package/tree/master/src/Psiref_Utils/psi_ref_utils.irp.f#L87>`_
+`psi_ref_energy_diagonalized <http://github.com/LCPQ/quantum_package/tree/master/src/Psiref_Utils/psi_ref_utils.irp.f#L129>`_
   Undocumented
 
 
@@ -105,3 +119,740 @@ Documentation
   Reference determinants sorted to accelerate the search of a random determinant in the wave
   function.
 
+Documentation
+=============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
+`a_coef <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/need.irp.f#L252>`_
+  Undocumented
+
+
+`abort_all <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/abort.irp.f#L1>`_
+  If True, all the calculation is aborted
+
+
+`abort_here <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/abort.irp.f#L11>`_
+  If True, all the calculation is aborted
+
+
+`add_poly <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/integration.irp.f#L306>`_
+  Add two polynomials
+  D(t) =! D(t) +( B(t)+C(t))
+
+
+`add_poly_multiply <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/integration.irp.f#L334>`_
+  Add a polynomial multiplied by a constant
+  D(t) =! D(t) +( cst * B(t))
+
+
+`align_double <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/util.irp.f#L48>`_
+  Compute 1st dimension such that it is aligned for vectorization.
+
+
+`apply_rotation <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/LinearAlgebra.irp.f#L168>`_
+  Apply the rotation found by find_rotation
+
+
+`approx_dble <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/util.irp.f#L380>`_
+  Undocumented
+
+
+`b_coef <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/need.irp.f#L257>`_
+  Undocumented
+
+
+`binom <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/util.irp.f#L31>`_
+  Binomial coefficients
+
+
+`binom_func <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/util.irp.f#L1>`_
+  .. math                       ::
+  .br
+  \frac{i!}{j!(i-j)!}
+  .br
+
+
+`binom_transp <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/util.irp.f#L32>`_
+  Binomial coefficients
+
+
+`catch_signal <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/abort.irp.f#L30>`_
+  What to do on Ctrl-C. If two Ctrl-C are pressed within 1 sec, the calculation if aborted.
+
+
+`dble_fact <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/util.irp.f#L138>`_
+  Undocumented
+
+
+`dble_fact_even <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/util.irp.f#L155>`_
+  n!!
+
+
+`dble_fact_odd <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/util.irp.f#L176>`_
+  n!!
+
+
+`dble_logfact <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/util.irp.f#L210>`_
+  n!!
+
+
+`ddfact2 <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/need.irp.f#L243>`_
+  Undocumented
+
+
+`dset_order <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_216#L27>`_
+  array A has already been sorted, and iorder has contains the new order of
+  elements of A. This subroutine changes the order of x to match the new order of A.
+
+
+`dset_order_big <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_283#L94>`_
+  array A has already been sorted, and iorder has contains the new order of
+  elements of A. This subroutine changes the order of x to match the new order of A.
+  This is a version for very large arrays where the indices need
+  to be in integer*8 format
+
+
+`dsort <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_184#L339>`_
+  Sort array x(isize).
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+
+
+`erf0 <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/need.irp.f#L105>`_
+  Undocumented
+
+
+`f_integral <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/integration.irp.f#L408>`_
+  function that calculates the following integral
+  \int_{\-infty}^{+\infty} x^n \exp(-p x^2) dx
+
+
+`fact <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/util.irp.f#L63>`_
+  n!
+
+
+`fact_inv <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/util.irp.f#L125>`_
+  1/n!
+
+
+`find_rotation <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/LinearAlgebra.irp.f#L149>`_
+  Find A.C = B
+
+
+`gammln <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/need.irp.f#L271>`_
+  Undocumented
+
+
+`gammp <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/need.irp.f#L133>`_
+  Undocumented
+
+
+`gaussian_product <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/integration.irp.f#L184>`_
+  Gaussian product in 1D.
+  e^{-a (x-x_A)^2} e^{-b (x-x_B)^2} = K_{ab}^x e^{-p (x-x_P)^2}
+
+
+`gaussian_product_x <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/integration.irp.f#L226>`_
+  Gaussian product in 1D.
+  e^{-a (x-x_A)^2} e^{-b (x-x_B)^2} = K_{ab}^x e^{-p (x-x_P)^2}
+
+
+`gcf <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/need.irp.f#L211>`_
+  Undocumented
+
+
+`get_index_in_psi_ref_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/psi_ref_utils.irp.f#L182>`_
+  Returns the index of the determinant in the ``psi_ref_sorted_bit`` array
+
+
+`get_pseudo_inverse <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/LinearAlgebra.irp.f#L95>`_
+  Find C = A^-1
+
+
+`give_explicit_poly_and_gaussian <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/integration.irp.f#L46>`_
+  Transforms the product of
+  (x-x_A)^a(1) (x-x_B)^b(1) (x-x_A)^a(2) (y-y_B)^b(2) (z-z_A)^a(3) (z-z_B)^b(3) exp(-(r-A)^2 alpha) exp(-(r-B)^2 beta)
+  into
+  fact_k * [ sum (l_x = 0,i_order(1)) P_new(l_x,1) * (x-P_center(1))^l_x ] exp (- p (x-P_center(1))^2 )
+  * [ sum (l_y = 0,i_order(2)) P_new(l_y,2) * (y-P_center(2))^l_y ] exp (- p (y-P_center(2))^2 )
+  * [ sum (l_z = 0,i_order(3)) P_new(l_z,3) * (z-P_center(3))^l_z ] exp (- p (z-P_center(3))^2 )
+
+
+`give_explicit_poly_and_gaussian_double <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/integration.irp.f#L122>`_
+  Transforms the product of
+  (x-x_A)^a(1) (x-x_B)^b(1) (x-x_A)^a(2) (y-y_B)^b(2) (z-z_A)^a(3) (z-z_B)^b(3)
+  exp(-(r-A)^2 alpha) exp(-(r-B)^2 beta) exp(-(r-Nucl_center)^2 gama
+  .br
+  into
+  fact_k * [ sum (l_x = 0,i_order(1)) P_new(l_x,1) * (x-P_center(1))^l_x ] exp (- p (x-P_center(1))^2 )
+  * [ sum (l_y = 0,i_order(2)) P_new(l_y,2) * (y-P_center(2))^l_y ] exp (- p (y-P_center(2))^2 )
+  * [ sum (l_z = 0,i_order(3)) P_new(l_z,3) * (z-P_center(3))^l_z ] exp (- p (z-P_center(3))^2 )
+
+
+`give_explicit_poly_and_gaussian_x <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/integration.irp.f#L1>`_
+  Transform the product of
+  (x-x_A)^a(1) (x-x_B)^b(1) (x-x_A)^a(2) (y-y_B)^b(2) (z-z_A)^a(3) (z-z_B)^b(3) exp(-(r-A)^2 alpha) exp(-(r-B)^2 beta)
+  into
+  fact_k  (x-x_P)^iorder(1)  (y-y_P)^iorder(2)  (z-z_P)^iorder(3) exp(-p(r-P)^2)
+
+
+`gser <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/need.irp.f#L167>`_
+  Undocumented
+
+
+`h_matrix_ref <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/psi_ref_utils.irp.f#L116>`_
+  Undocumented
+
+
+`heap_dsort <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_184#L210>`_
+  Sort array x(isize) using the heap sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+
+
+`heap_dsort_big <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_184#L273>`_
+  Sort array x(isize) using the heap sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+  This is a version for very large arrays where the indices need
+  to be in integer*8 format
+
+
+`heap_i2sort <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_184#L744>`_
+  Sort array x(isize) using the heap sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+
+
+`heap_i2sort_big <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_184#L807>`_
+  Sort array x(isize) using the heap sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+  This is a version for very large arrays where the indices need
+  to be in integer*8 format
+
+
+`heap_i8sort <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_184#L566>`_
+  Sort array x(isize) using the heap sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+
+
+`heap_i8sort_big <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_184#L629>`_
+  Sort array x(isize) using the heap sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+  This is a version for very large arrays where the indices need
+  to be in integer*8 format
+
+
+`heap_isort <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_184#L388>`_
+  Sort array x(isize) using the heap sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+
+
+`heap_isort_big <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_184#L451>`_
+  Sort array x(isize) using the heap sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+  This is a version for very large arrays where the indices need
+  to be in integer*8 format
+
+
+`heap_sort <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_184#L32>`_
+  Sort array x(isize) using the heap sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+
+
+`heap_sort_big <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_184#L95>`_
+  Sort array x(isize) using the heap sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+  This is a version for very large arrays where the indices need
+  to be in integer*8 format
+
+
+`hermite <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/integration.irp.f#L540>`_
+  Hermite polynomial
+
+
+`holes_operators <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/psi_ref_excitations_operators.irp.f#L3>`_
+  holes_operators represents an array of integers where all the holes have
+  been done going from psi_ref to psi_non_ref
+  particles_operators represents an array of integers where all the particles have
+  been done going from psi_ref to psi_non_ref
+
+
+`i2radix_sort <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_450#L323>`_
+  Sort integer array x(isize) using the radix sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+  iradix should be -1 in input.
+
+
+`i2set_order <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_216#L102>`_
+  array A has already been sorted, and iorder has contains the new order of
+  elements of A. This subroutine changes the order of x to match the new order of A.
+
+
+`i2set_order_big <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_283#L271>`_
+  array A has already been sorted, and iorder has contains the new order of
+  elements of A. This subroutine changes the order of x to match the new order of A.
+  This is a version for very large arrays where the indices need
+  to be in integer*8 format
+
+
+`i2sort <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_184#L873>`_
+  Sort array x(isize).
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+
+
+`i8radix_sort <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_450#L163>`_
+  Sort integer array x(isize) using the radix sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+  iradix should be -1 in input.
+
+
+`i8radix_sort_big <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_450#L643>`_
+  Sort integer array x(isize) using the radix sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+  iradix should be -1 in input.
+
+
+`i8set_order <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_216#L77>`_
+  array A has already been sorted, and iorder has contains the new order of
+  elements of A. This subroutine changes the order of x to match the new order of A.
+
+
+`i8set_order_big <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_283#L212>`_
+  array A has already been sorted, and iorder has contains the new order of
+  elements of A. This subroutine changes the order of x to match the new order of A.
+  This is a version for very large arrays where the indices need
+  to be in integer*8 format
+
+
+`i8sort <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_184#L695>`_
+  Sort array x(isize).
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+
+
+`idx_non_ref <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/psi_ref_utils.irp.f#L20>`_
+  Set of determinants which are not part of the reference, defined from the application
+  of the reference bitmask on the determinants.
+  idx_non_ref gives the indice of the determinant in psi_det.
+  idx_non_ref_rev gives the reverse.
+
+
+`idx_non_ref_rev <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/psi_ref_utils.irp.f#L21>`_
+  Set of determinants which are not part of the reference, defined from the application
+  of the reference bitmask on the determinants.
+  idx_non_ref gives the indice of the determinant in psi_det.
+  idx_non_ref_rev gives the reverse.
+
+
+`insertion_dsort <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_184#L180>`_
+  Sort array x(isize) using the insertion sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+
+
+`insertion_dsort_big <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_283#L61>`_
+  Sort array x(isize) using the insertion sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+  This is a version for very large arrays where the indices need
+  to be in integer*8 format
+
+
+`insertion_i2sort <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_184#L714>`_
+  Sort array x(isize) using the insertion sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+
+
+`insertion_i2sort_big <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_283#L238>`_
+  Sort array x(isize) using the insertion sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+  This is a version for very large arrays where the indices need
+  to be in integer*8 format
+
+
+`insertion_i8sort <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_184#L536>`_
+  Sort array x(isize) using the insertion sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+
+
+`insertion_i8sort_big <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_283#L179>`_
+  Sort array x(isize) using the insertion sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+  This is a version for very large arrays where the indices need
+  to be in integer*8 format
+
+
+`insertion_isort <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_184#L358>`_
+  Sort array x(isize) using the insertion sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+
+
+`insertion_isort_big <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_283#L120>`_
+  Sort array x(isize) using the insertion sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+  This is a version for very large arrays where the indices need
+  to be in integer*8 format
+
+
+`insertion_sort <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_184#L2>`_
+  Sort array x(isize) using the insertion sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+
+
+`insertion_sort_big <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_283#L2>`_
+  Sort array x(isize) using the insertion sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+  This is a version for very large arrays where the indices need
+  to be in integer*8 format
+
+
+`inv_int <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/util.irp.f#L257>`_
+  1/i
+
+
+`iradix_sort <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_450#L3>`_
+  Sort integer array x(isize) using the radix sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+  iradix should be -1 in input.
+
+
+`iradix_sort_big <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_450#L483>`_
+  Sort integer array x(isize) using the radix sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+  iradix should be -1 in input.
+
+
+`is_in_psi_ref <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/psi_ref_utils.irp.f#L168>`_
+  True if the determinant ``det`` is in the wave function
+
+
+`iset_order <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_216#L52>`_
+  array A has already been sorted, and iorder has contains the new order of
+  elements of A. This subroutine changes the order of x to match the new order of A.
+
+
+`iset_order_big <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_283#L153>`_
+  array A has already been sorted, and iorder has contains the new order of
+  elements of A. This subroutine changes the order of x to match the new order of A.
+  This is a version for very large arrays where the indices need
+  to be in integer*8 format
+
+
+`isort <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_184#L517>`_
+  Sort array x(isize).
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+
+
+`lapack_diag <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/LinearAlgebra.irp.f#L247>`_
+  Diagonalize matrix H
+  .br
+  H is untouched between input and ouptut
+  .br
+  eigevalues(i) = ith lowest eigenvalue of the H matrix
+  .br
+  eigvectors(i,j) = <i|psi_j> where i is the basis function and psi_j is the j th eigenvector
+  .br
+
+
+`lapack_diag_s2 <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/LinearAlgebra.irp.f#L310>`_
+  Diagonalize matrix H
+  .br
+  H is untouched between input and ouptut
+  .br
+  eigevalues(i) = ith lowest eigenvalue of the H matrix
+  .br
+  eigvectors(i,j) = <i|psi_j> where i is the basis function and psi_j is the j th eigenvector
+  .br
+
+
+`lapack_diagd <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/LinearAlgebra.irp.f#L180>`_
+  Diagonalize matrix H
+  .br
+  H is untouched between input and ouptut
+  .br
+  eigevalues(i) = ith lowest eigenvalue of the H matrix
+  .br
+  eigvectors(i,j) = <i|psi_j> where i is the basis function and psi_j is the j th eigenvector
+  .br
+
+
+`lapack_partial_diag <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/LinearAlgebra.irp.f#L376>`_
+  Diagonalize matrix H
+  .br
+  H is untouched between input and ouptut
+  .br
+  eigevalues(i) = ith lowest eigenvalue of the H matrix
+  .br
+  eigvectors(i,j) = <i|psi_j> where i is the basis function and psi_j is the j th eigenvector
+  .br
+
+
+`logfact <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/util.irp.f#L93>`_
+  n!
+
+
+`multiply_poly <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/integration.irp.f#L264>`_
+  Multiply two polynomials
+  D(t) =! D(t) +( B(t)*C(t))
+
+
+`n_det_non_ref <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/psi_ref_utils.irp.f#L22>`_
+  Set of determinants which are not part of the reference, defined from the application
+  of the reference bitmask on the determinants.
+  idx_non_ref gives the indice of the determinant in psi_det.
+  idx_non_ref_rev gives the reverse.
+
+
+`normalize <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/util.irp.f#L356>`_
+  Normalizes vector u
+  u is expected to be aligned in memory.
+
+
+`nproc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/util.irp.f#L283>`_
+  Number of current OpenMP threads
+
+
+`ortho_lowdin <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/LinearAlgebra.irp.f#L1>`_
+  Compute C_new=C_old.S^-1/2 canonical orthogonalization.
+  .br
+  overlap : overlap matrix
+  .br
+  LDA : leftmost dimension of overlap array
+  .br
+  N : Overlap matrix is NxN (array is (LDA,N) )
+  .br
+  C : Coefficients of the vectors to orthogonalize. On exit,
+  orthogonal vectors
+  .br
+  LDC : leftmost dimension of C
+  .br
+  m : Coefficients matrix is MxN, ( array is (LDC,N) )
+  .br
+
+
+`overlap_a_b_c <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/one_e_integration.irp.f#L35>`_
+  Undocumented
+
+
+`overlap_gaussian_x <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/one_e_integration.irp.f#L1>`_
+  .. math::
+  .br
+  \sum_{-infty}^{+infty} (x-A_x)^ax (x-B_x)^bx exp(-alpha(x-A_x)^2) exp(-beta(x-B_X)^2) dx
+  .br
+
+
+`overlap_gaussian_xyz <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/one_e_integration.irp.f#L113>`_
+  .. math::
+  .br
+  S_x = \int (x-A_x)^{a_x} exp(-\alpha(x-A_x)^2)  (x-B_x)^{b_x} exp(-beta(x-B_x)^2) dx \\
+  S = S_x S_y S_z
+  .br
+
+
+`overlap_x_abs <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/one_e_integration.irp.f#L175>`_
+  .. math                      ::
+  .br
+  \int_{-infty}^{+infty} (x-A_center)^(power_A) * (x-B_center)^power_B * exp(-alpha(x-A_center)^2) * exp(-beta(x-B_center)^2) dx
+  .br
+
+
+`particles_operators <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/psi_ref_excitations_operators.irp.f#L4>`_
+  holes_operators represents an array of integers where all the holes have
+  been done going from psi_ref to psi_non_ref
+  particles_operators represents an array of integers where all the particles have
+  been done going from psi_ref to psi_non_ref
+
+
+`progress_active <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/progress.irp.f#L29>`_
+  Current status for displaying progress bars. Global variable.
+
+
+`progress_bar <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/progress.irp.f#L27>`_
+  Current status for displaying progress bars. Global variable.
+
+
+`progress_timeout <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/progress.irp.f#L28>`_
+  Current status for displaying progress bars. Global variable.
+
+
+`progress_title <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/progress.irp.f#L31>`_
+  Current status for displaying progress bars. Global variable.
+
+
+`progress_value <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/progress.irp.f#L30>`_
+  Current status for displaying progress bars. Global variable.
+
+
+`psi_coef_ref_diagonalized <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/psi_ref_utils.irp.f#L128>`_
+  Undocumented
+
+
+`psi_non_ref <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/psi_ref_utils.irp.f#L18>`_
+  Set of determinants which are not part of the reference, defined from the application
+  of the reference bitmask on the determinants.
+  idx_non_ref gives the indice of the determinant in psi_det.
+  idx_non_ref_rev gives the reverse.
+
+
+`psi_non_ref_coef <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/psi_ref_utils.irp.f#L19>`_
+  Set of determinants which are not part of the reference, defined from the application
+  of the reference bitmask on the determinants.
+  idx_non_ref gives the indice of the determinant in psi_det.
+  idx_non_ref_rev gives the reverse.
+
+
+`psi_non_ref_coef_restart <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/psi_ref_utils.irp.f#L62>`_
+  Set of determinants which are not part of the reference, defined from the application
+  of the reference bitmask on the determinants.
+  idx_non_ref gives the indice of the determinant in psi_det.
+  But this is with respect to the restart wave function.
+
+
+`psi_non_ref_coef_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/psi_ref_utils.irp.f#L104>`_
+  Reference determinants sorted to accelerate the search of a random determinant in the wave
+  function.
+
+
+`psi_non_ref_restart <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/psi_ref_utils.irp.f#L61>`_
+  Set of determinants which are not part of the reference, defined from the application
+  of the reference bitmask on the determinants.
+  idx_non_ref gives the indice of the determinant in psi_det.
+  But this is with respect to the restart wave function.
+
+
+`psi_non_ref_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/psi_ref_utils.irp.f#L103>`_
+  Reference determinants sorted to accelerate the search of a random determinant in the wave
+  function.
+
+
+`psi_ref_coef_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/psi_ref_utils.irp.f#L5>`_
+  Reference determinants sorted to accelerate the search of a random determinant in the wave
+  function.
+
+
+`psi_ref_energy <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/psi_ref_utils.irp.f#L147>`_
+  Undocumented
+
+
+`psi_ref_energy_diagonalized <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/psi_ref_utils.irp.f#L129>`_
+  Undocumented
+
+
+`psi_ref_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/psi_ref_utils.irp.f#L4>`_
+  Reference determinants sorted to accelerate the search of a random determinant in the wave
+  function.
+
+
+`recentered_poly2 <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/integration.irp.f#L363>`_
+  Recenter two polynomials
+
+
+`rint <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/integration.irp.f#L436>`_
+  .. math::
+  .br
+  \int_0^1 dx \exp(-p x^2) x^n
+  .br
+
+
+`rint1 <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/integration.irp.f#L596>`_
+  Standard version of rint
+
+
+`rint_large_n <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/integration.irp.f#L565>`_
+  Version of rint for large values of n
+
+
+`rint_sum <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/integration.irp.f#L484>`_
+  Needed for the calculation of two-electron integrals.
+
+
+`rinteg <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/need.irp.f#L47>`_
+  Undocumented
+
+
+`rintgauss <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/need.irp.f#L31>`_
+  Undocumented
+
+
+`run_progress <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/progress.irp.f#L45>`_
+  Display a progress bar with documentation of what is happening
+
+
+`sabpartial <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/need.irp.f#L2>`_
+  Undocumented
+
+
+`set_order <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_216#L2>`_
+  array A has already been sorted, and iorder has contains the new order of
+  elements of A. This subroutine changes the order of x to match the new order of A.
+
+
+`set_order_big <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_283#L35>`_
+  array A has already been sorted, and iorder has contains the new order of
+  elements of A. This subroutine changes the order of x to match the new order of A.
+  This is a version for very large arrays where the indices need
+  to be in integer*8 format
+
+
+`set_zero_extra_diag <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/LinearAlgebra.irp.f#L433>`_
+  Undocumented
+
+
+`sort <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_184#L161>`_
+  Sort array x(isize).
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+
+
+`start_progress <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/progress.irp.f#L1>`_
+  Starts the progress bar
+
+
+`stop_progress <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/progress.irp.f#L19>`_
+  Stop the progress bar
+
+
+`trap_signals <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/abort.irp.f#L19>`_
+  What to do when a signal is caught. Here, trap Ctrl-C and call the control_C subroutine.
+
+
+`u_dot_u <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/util.irp.f#L325>`_
+  Compute <u|u>
+
+
+`u_dot_v <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/util.irp.f#L299>`_
+  Compute <u|v>
+
+
+`wall_time <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/util.irp.f#L268>`_
+  The equivalent of cpu_time, but for the wall time.
+
+
+`write_git_log <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/util.irp.f#L243>`_
+  Write the last git commit in file iunit.
+

plugins/Psiref_Utils/psi_ref_utils.irp.f

@@ -58,6 +58,48 @@ END_PROVIDER
  N_det_non_ref = i_non_ref
 END_PROVIDER
 
+ BEGIN_PROVIDER [ integer(bit_kind), psi_non_ref_restart,  (N_int,2,psi_det_size) ]
+&BEGIN_PROVIDER [ double precision, psi_non_ref_coef_restart, (psi_det_size,n_states) ]
+ implicit none
+ BEGIN_DOC
+  ! Set of determinants which are not part of the reference, defined from the application
+  ! of the reference bitmask on the determinants. 
+  ! idx_non_ref gives the indice of the determinant in psi_det.
+  ! But this is with respect to the restart wave function. 
+ END_DOC
+ integer                        :: i_non_ref,j,k
+ integer                        :: degree
+ logical                        :: in_ref
+ integer, save                  :: ifirst = 0
+ if(ifirst==0)then
+  ifirst = 1
+  i_non_ref =0
+  do k=1,N_det
+    in_ref = .False.
+    do j=1,N_det_ref
+      call get_excitation_degree(psi_ref(1,1,j), psi_det(1,1,k), degree, N_int)
+      if (degree == 0) then
+        in_ref = .True.
+        exit
+      endif
+    enddo
+    if (.not.in_ref) then
+      double precision :: hij
+      i_non_ref += 1
+      do j=1,N_int
+        psi_non_ref_restart(j,1,i_non_ref) = psi_det(j,1,k)
+        psi_non_ref_restart(j,2,i_non_ref) = psi_det(j,2,k)
+      enddo
+      do j=1,N_states
+        psi_non_ref_coef_restart(i_non_ref,j) = psi_coef(k,j)
+      enddo
+    endif
+  enddo
+ endif
+END_PROVIDER
+
+
+
  BEGIN_PROVIDER [ integer(bit_kind), psi_non_ref_sorted_bit, (N_int,2,psi_det_size) ]
 &BEGIN_PROVIDER [ double precision, psi_non_ref_coef_sorted_bit, (psi_det_size,N_states) ]
  implicit none

plugins/QmcChem/README.rst

@@ -43,3 +43,44 @@ Needed Modules
 
 * `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
 
+Needed Modules
+==============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
+.. image:: tree_dependency.png
+
+* `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
+
+Documentation
+=============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
+`ao_pseudo_grid <http://github.com/LCPQ/quantum_package/tree/master/plugins/QmcChem/pot_ao_pseudo_ints.irp.f#L2>`_
+  Grid points for f(|r-r_A|) = \int Y_{lm}^{C} (|r-r_C|, \Omega_C) \chi_i^{A} (r-r_A) d\Omega_C
+  .br
+  <img src="http://latex.codecogs.com/gif.latex?f(|r-r_A|)&space;=&space;\int&space;Y_{lm}^{C}&space;(|r-r_C|,&space;\Omega_C)&space;\chi_i^{A}&space;(r-r_A)&space;d\Omega_C"
+  title="f(|r-r_A|) = \int Y_{lm}^{C} (|r-r_C|, \Omega_C) \chi_i^{A} (r-r_A) d\Omega_C" />
+
+
+`mo_pseudo_grid <http://github.com/LCPQ/quantum_package/tree/master/plugins/QmcChem/pot_ao_pseudo_ints.irp.f#L56>`_
+  Grid points for f(|r-r_A|) = \int Y_{lm}^{C} (|r-r_C|, \Omega_C) \phi_i^{A} (r-r_A) d\Omega_C
+  .br
+  <img src="http://latex.codecogs.com/gif.latex?f(|r-r_A|)&space;=&space;\int&space;Y_{lm}^{C}&space;(|r-r_C|,&space;\Omega_C)&space;\chi_i^{A}&space;(r-r_A)&space;d\Omega_C"
+  title="f(|r-r_A|) = \int Y_{lm}^{C} (|r-r_C|, \Omega_C) \chi_i^{A} (r-r_A) d\Omega_C" />
+
+
+`save_for_qmc <http://github.com/LCPQ/quantum_package/tree/master/plugins/QmcChem/save_for_qmcchem.irp.f#L1>`_
+  Undocumented
+
+
+`test_pseudo_grid_ao <http://github.com/LCPQ/quantum_package/tree/master/plugins/QmcChem/pot_ao_pseudo_ints.irp.f#L111>`_
+  Undocumented
+
+
+`write_pseudopotential <http://github.com/LCPQ/quantum_package/tree/master/plugins/QmcChem/pseudo.irp.f#L1>`_
+  Write the pseudo_potential into the EZFIO file
+

plugins/Selectors_full/README.rst

@@ -2,183 +2,10 @@
 Selectors_full Module
 =====================
 
-Documentation
-=============
-
-.. Do not edit this section. It was auto-generated from the
-.. by the `update_README.py` script.
-
-`coef_hf_selector <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L28>`_
-  energy of correlation per determinant respect to the Hartree Fock determinant
-  .br
-  for the all the double excitations in the selectors determinants
-  .br
-  E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> is a double excitation
-  .br
-  E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
-  .br
-  coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
-
-
-`delta_e_per_selector <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L33>`_
-  energy of correlation per determinant respect to the Hartree Fock determinant
-  .br
-  for the all the double excitations in the selectors determinants
-  .br
-  E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> is a double excitation
-  .br
-  E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
-  .br
-  coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
-
-
-`double_index_selectors <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L4>`_
-  degree of excitation respect to Hartree Fock for the wave function
-  .br
-  for the all the selectors determinants
-  .br
-  double_index_selectors = list of the index of the double excitations
-  .br
-  n_double_selectors = number of double excitations in the selectors determinants
-
-
-`e_corr_double_only <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L34>`_
-  energy of correlation per determinant respect to the Hartree Fock determinant
-  .br
-  for the all the double excitations in the selectors determinants
-  .br
-  E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> is a double excitation
-  .br
-  E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
-  .br
-  coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
-
-
-`e_corr_per_selectors <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L31>`_
-  energy of correlation per determinant respect to the Hartree Fock determinant
-  .br
-  for the all the double excitations in the selectors determinants
-  .br
-  E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> is a double excitation
-  .br
-  E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
-  .br
-  coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
-
-
-`e_corr_second_order <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L35>`_
-  energy of correlation per determinant respect to the Hartree Fock determinant
-  .br
-  for the all the double excitations in the selectors determinants
-  .br
-  E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> is a double excitation
-  .br
-  E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
-  .br
-  coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
-
-
-`exc_degree_per_selectors <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L3>`_
-  degree of excitation respect to Hartree Fock for the wave function
-  .br
-  for the all the selectors determinants
-  .br
-  double_index_selectors = list of the index of the double excitations
-  .br
-  n_double_selectors = number of double excitations in the selectors determinants
-
-
-`i_h_hf_per_selectors <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L32>`_
-  energy of correlation per determinant respect to the Hartree Fock determinant
-  .br
-  for the all the double excitations in the selectors determinants
-  .br
-  E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> is a double excitation
-  .br
-  E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
-  .br
-  coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
-
-
-`inv_selectors_coef_hf <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L29>`_
-  energy of correlation per determinant respect to the Hartree Fock determinant
-  .br
-  for the all the double excitations in the selectors determinants
-  .br
-  E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> is a double excitation
-  .br
-  E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
-  .br
-  coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
-
-
-`inv_selectors_coef_hf_squared <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L30>`_
-  energy of correlation per determinant respect to the Hartree Fock determinant
-  .br
-  for the all the double excitations in the selectors determinants
-  .br
-  E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> is a double excitation
-  .br
-  E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
-  .br
-  coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
-
-
-`n_det_selectors <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L8>`_
-  For Single reference wave functions, the number of selectors is 1 : the
-  Hartree-Fock determinant
-
-
-`n_double_selectors <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L5>`_
-  degree of excitation respect to Hartree Fock for the wave function
-  .br
-  for the all the selectors determinants
-  .br
-  double_index_selectors = list of the index of the double excitations
-  .br
-  n_double_selectors = number of double excitations in the selectors determinants
-
-
-`psi_selectors <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L30>`_
-  Determinants on which we apply <i|H|psi> for perturbation.
-
-
-`psi_selectors_ab <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L64>`_
-  Determinants on which we apply <i|H|j>.
-  They are sorted by the 3 highest electrons in the alpha part,
-  then by the 3 highest electrons in the beta part to accelerate
-  the research of connected determinants.
-
-
-`psi_selectors_coef <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L31>`_
-  Determinants on which we apply <i|H|psi> for perturbation.
-
-
-`psi_selectors_coef_ab <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L65>`_
-  Determinants on which we apply <i|H|j>.
-  They are sorted by the 3 highest electrons in the alpha part,
-  then by the 3 highest electrons in the beta part to accelerate
-  the research of connected determinants.
-
-
-`psi_selectors_diag_h_mat <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L51>`_
-  Diagonal elements of the H matrix for each selectors
-
-
-`psi_selectors_next_ab <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L66>`_
-  Determinants on which we apply <i|H|j>.
-  They are sorted by the 3 highest electrons in the alpha part,
-  then by the 3 highest electrons in the beta part to accelerate
-  the research of connected determinants.
-
-
-`psi_selectors_size <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L3>`_
-  Undocumented
-
 Needed Modules
 ==============
 
-.. Do not edit this section. It was auto-generated from the
+.. Do not edit this section It was auto-generated
 .. by the `update_README.py` script.
 
 .. image:: tree_dependency.png
@@ -186,3 +13,187 @@ Needed Modules
 * `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
 * `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
 
+Needed Modules
+==============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
+.. image:: tree_dependency.png
+
+* `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
+* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock>`_
+
+Documentation
+=============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
+`coef_hf_selector <http://github.com/LCPQ/quantum_package/tree/master/plugins/Selectors_full/e_corr_selectors.irp.f#L28>`_
+  energy of correlation per determinant respect to the Hartree Fock determinant
+  .br
+  for the all the double excitations in the selectors determinants
+  .br
+  E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> is a double excitation
+  .br
+  E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
+  .br
+  coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
+
+
+`delta_e_per_selector <http://github.com/LCPQ/quantum_package/tree/master/plugins/Selectors_full/e_corr_selectors.irp.f#L33>`_
+  energy of correlation per determinant respect to the Hartree Fock determinant
+  .br
+  for the all the double excitations in the selectors determinants
+  .br
+  E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> is a double excitation
+  .br
+  E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
+  .br
+  coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
+
+
+`double_index_selectors <http://github.com/LCPQ/quantum_package/tree/master/plugins/Selectors_full/e_corr_selectors.irp.f#L4>`_
+  degree of excitation respect to Hartree Fock for the wave function
+  .br
+  for the all the selectors determinants
+  .br
+  double_index_selectors = list of the index of the double excitations
+  .br
+  n_double_selectors = number of double excitations in the selectors determinants
+
+
+`e_corr_double_only <http://github.com/LCPQ/quantum_package/tree/master/plugins/Selectors_full/e_corr_selectors.irp.f#L34>`_
+  energy of correlation per determinant respect to the Hartree Fock determinant
+  .br
+  for the all the double excitations in the selectors determinants
+  .br
+  E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> is a double excitation
+  .br
+  E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
+  .br
+  coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
+
+
+`e_corr_per_selectors <http://github.com/LCPQ/quantum_package/tree/master/plugins/Selectors_full/e_corr_selectors.irp.f#L31>`_
+  energy of correlation per determinant respect to the Hartree Fock determinant
+  .br
+  for the all the double excitations in the selectors determinants
+  .br
+  E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> is a double excitation
+  .br
+  E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
+  .br
+  coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
+
+
+`e_corr_second_order <http://github.com/LCPQ/quantum_package/tree/master/plugins/Selectors_full/e_corr_selectors.irp.f#L35>`_
+  energy of correlation per determinant respect to the Hartree Fock determinant
+  .br
+  for the all the double excitations in the selectors determinants
+  .br
+  E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> is a double excitation
+  .br
+  E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
+  .br
+  coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
+
+
+`exc_degree_per_selectors <http://github.com/LCPQ/quantum_package/tree/master/plugins/Selectors_full/e_corr_selectors.irp.f#L3>`_
+  degree of excitation respect to Hartree Fock for the wave function
+  .br
+  for the all the selectors determinants
+  .br
+  double_index_selectors = list of the index of the double excitations
+  .br
+  n_double_selectors = number of double excitations in the selectors determinants
+
+
+`i_h_hf_per_selectors <http://github.com/LCPQ/quantum_package/tree/master/plugins/Selectors_full/e_corr_selectors.irp.f#L32>`_
+  energy of correlation per determinant respect to the Hartree Fock determinant
+  .br
+  for the all the double excitations in the selectors determinants
+  .br
+  E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> is a double excitation
+  .br
+  E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
+  .br
+  coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
+
+
+`inv_selectors_coef_hf <http://github.com/LCPQ/quantum_package/tree/master/plugins/Selectors_full/e_corr_selectors.irp.f#L29>`_
+  energy of correlation per determinant respect to the Hartree Fock determinant
+  .br
+  for the all the double excitations in the selectors determinants
+  .br
+  E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> is a double excitation
+  .br
+  E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
+  .br
+  coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
+
+
+`inv_selectors_coef_hf_squared <http://github.com/LCPQ/quantum_package/tree/master/plugins/Selectors_full/e_corr_selectors.irp.f#L30>`_
+  energy of correlation per determinant respect to the Hartree Fock determinant
+  .br
+  for the all the double excitations in the selectors determinants
+  .br
+  E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> is a double excitation
+  .br
+  E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
+  .br
+  coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
+
+
+`n_det_selectors <http://github.com/LCPQ/quantum_package/tree/master/plugins/Selectors_full/selectors.irp.f#L8>`_
+  For Single reference wave functions, the number of selectors is 1 : the
+  Hartree-Fock determinant
+
+
+`n_double_selectors <http://github.com/LCPQ/quantum_package/tree/master/plugins/Selectors_full/e_corr_selectors.irp.f#L5>`_
+  degree of excitation respect to Hartree Fock for the wave function
+  .br
+  for the all the selectors determinants
+  .br
+  double_index_selectors = list of the index of the double excitations
+  .br
+  n_double_selectors = number of double excitations in the selectors determinants
+
+
+`psi_selectors <http://github.com/LCPQ/quantum_package/tree/master/plugins/Selectors_full/selectors.irp.f#L30>`_
+  Determinants on which we apply <i|H|psi> for perturbation.
+
+
+`psi_selectors_ab <http://github.com/LCPQ/quantum_package/tree/master/plugins/Selectors_full/selectors.irp.f#L64>`_
+  Determinants on which we apply <i|H|j>.
+  They are sorted by the 3 highest electrons in the alpha part,
+  then by the 3 highest electrons in the beta part to accelerate
+  the research of connected determinants.
+
+
+`psi_selectors_coef <http://github.com/LCPQ/quantum_package/tree/master/plugins/Selectors_full/selectors.irp.f#L31>`_
+  Determinants on which we apply <i|H|psi> for perturbation.
+
+
+`psi_selectors_coef_ab <http://github.com/LCPQ/quantum_package/tree/master/plugins/Selectors_full/selectors.irp.f#L65>`_
+  Determinants on which we apply <i|H|j>.
+  They are sorted by the 3 highest electrons in the alpha part,
+  then by the 3 highest electrons in the beta part to accelerate
+  the research of connected determinants.
+
+
+`psi_selectors_diag_h_mat <http://github.com/LCPQ/quantum_package/tree/master/plugins/Selectors_full/selectors.irp.f#L51>`_
+  Diagonal elements of the H matrix for each selectors
+
+
+`psi_selectors_next_ab <http://github.com/LCPQ/quantum_package/tree/master/plugins/Selectors_full/selectors.irp.f#L66>`_
+  Determinants on which we apply <i|H|j>.
+  They are sorted by the 3 highest electrons in the alpha part,
+  then by the 3 highest electrons in the beta part to accelerate
+  the research of connected determinants.
+
+
+`psi_selectors_size <http://github.com/LCPQ/quantum_package/tree/master/plugins/Selectors_full/selectors.irp.f#L3>`_
+  Undocumented
+

plugins/SingleRefMethod/README.rst

@@ -43,3 +43,41 @@ Needed Modules
 
 * `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
 
+Needed Modules
+==============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
+.. image:: tree_dependency.png
+
+* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
+
+Documentation
+=============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
+`n_det_generators <http://github.com/LCPQ/quantum_package/tree/master/plugins/SingleRefMethod/generators.irp.f#L3>`_
+  For Single reference wave functions, the number of generators is 1 : the
+  Hartree-Fock determinant
+
+
+`psi_coef_generators <http://github.com/LCPQ/quantum_package/tree/master/plugins/SingleRefMethod/generators.irp.f#L13>`_
+  For Single reference wave functions, the generator is the
+  Hartree-Fock determinant
+
+
+`psi_det_generators <http://github.com/LCPQ/quantum_package/tree/master/plugins/SingleRefMethod/generators.irp.f#L12>`_
+  For Single reference wave functions, the generator is the
+  Hartree-Fock determinant
+
+
+`select_max <http://github.com/LCPQ/quantum_package/tree/master/plugins/SingleRefMethod/generators.irp.f#L41>`_
+  Memo to skip useless selectors
+
+
+`size_select_max <http://github.com/LCPQ/quantum_package/tree/master/plugins/SingleRefMethod/generators.irp.f#L49>`_
+  Size of select_max
+

scripts/compilation/qp_create_ninja.py

@@ -23,12 +23,11 @@ except ImportError:
                                       "..",
                                       "..",
                                       "quantum_package.rc"))
-    print """
+
-Error:
+    print "\n".join(["", "Error:", "source %s" % f, ""])
- source %s
-""" % f
     sys.exit(1)
 
+
 #  __
 # /__ |  _  |_   _. |       _. ._ o  _. |_  |  _   _
 # \_| | (_) |_) (_| |   \/ (_| |  | (_| |_) | (/_ _>
@@ -516,7 +515,7 @@ 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 $module_root",
+                "   command = qp_update_readme.py $module_abs --root_module $module_root",
                 "   description = update_README $module_rel",
                 "   generator = 1", ""]
 
@@ -552,7 +551,8 @@ def ninja_readme_build(path_module, d_irp, dict_root_path):
 #                 /
 def get_binaries(path_module):
     """
-    Return the list of binaries (Path= namedtuple('Path', ['abs', 'rel']) for a module
+    Return the list of binaries
+    (Path= namedtuple('Path', ['abs', 'rel']) for a module
     """
     import subprocess
 
@@ -666,20 +666,26 @@ def ninja_binaries_build(path_module, l_children, d_binaries):
     # s t r i n g #
     # ~#~#~#~#~#~ #
 
-    path_readme = os.path.join(path_module.abs, "README.rst")
-    path_png = os.path.join(path_module.abs, "tree_dependency.png")
-
     l_string = ["build {0}: build_binaries {1} {2}".format(" ".join(l_abs_bin),
                                                            EZFIO_LIB,
                                                            ninja_module_path),
                 "   module_abs = {0}".format(path_module.abs),
                 "   module_rel = {0}".format(path_module.rel), ""]
 
-    l_string += ["build module_{0}: phony {1} {2} {3}".format(path_module.rel,
+    return l_string
-                                                              " ".join(l_abs_bin),
+
-                                                              path_readme,
+
-                                                              path_png
+def ninja_module_build(path_module, d_binaries):
-                                                              ), ""]
+
+    l_abs_bin = [binary.abs for binary in d_binaries[path_module]]
+
+    path_readme = os.path.join(path_module.abs, "README.rst")
+    path_png = os.path.join(path_module.abs, "tree_dependency.png")
+
+    l_string = ["build module_{0}: phony {1} {2} {3}".format(path_module.rel,
+                                                             " ".join(l_abs_bin),
+                                                             path_readme,
+                                                             path_png), ""]
 
     return l_string
 
@@ -723,7 +729,7 @@ def ninja_dot_tree_build(path_module, l_module):
 # |\/|  _   _|     |  _
 # |  | (_) (_| |_| | (/_
 #
-def create_build_ninja_module(path_module):
+def save_subninja_file(path_module):
     l_string = ["builddir = {0}".format(os.path.dirname(ROOT_BUILD_NINJA)),
                 ""]
 
@@ -732,17 +738,19 @@ def create_build_ninja_module(path_module):
                  ""]
 
     l_string += ["rule make_local_binaries",
-                 "   command = ninja -f {0} module_{1}".format(
+                 "   command = ninja -f {0} module_{1}".format(ROOT_BUILD_NINJA, path_module.rel),
-                     ROOT_BUILD_NINJA, path_module.rel), "   pool = console",
+                 "   pool = console",
                  "   description = Compile only {0}".format(path_module.rel),
                  ""]
 
     l_string += ["rule make_all_binaries",
                  "  command = ninja -f {0}".format(ROOT_BUILD_NINJA),
-                 "  pool = console", "  description = Compiling all modules",
+                 "  pool = console",
+                 "  description = Compiling all modules",
                  ""]
 
-    l_string += ["rule make_clean", "  command = module_handler.py clean {0}".format(path_module.rel),
+    l_string += ["rule make_clean",
+                 "  command = module_handler.py clean {0}".format(path_module.rel),
                  "  description = Cleaning module {0}".format(path_module.rel),
                  ""]
 
@@ -766,7 +774,7 @@ def create_build_ninja_global():
                 "   command = {0} update".format(__file__),
                 ""]
 
-    l_string += ["rule make_all_binaries",
+    l_string += ["rule make_all",
                  "  command = ninja -f {0}".format(ROOT_BUILD_NINJA),
                  "  pool = console", "  description = Compiling all modules",
                  ""]
@@ -777,7 +785,7 @@ def create_build_ninja_global():
 
     l_string += ["build dummy_target: update_build_ninja_root",
                  "",
-                 "build all: make_all_binaries dummy_target",
+                 "build all: make_all dummy_target",
                  "default all",
                  "",
                  "build clean: make_clean dummy_target",
@@ -919,9 +927,6 @@ if __name__ == "__main__":
 
     for module_to_compile in l_module:
 
-        if arguments["--development"]:
-            create_build_ninja_module(module_to_compile)
-
         # ~#~#~#~#~#~#~#~ #
         #  S y m l i n k  #
         # ~#~#~#~#~#~#~#~ #
@@ -939,8 +944,14 @@ if __name__ == "__main__":
         l_string += ninja_binaries_build(module_to_compile, l_children,
                                          d_binaries)
 
-        l_string += ninja_gitignore_build(module_to_compile, d_binaries,
+        if arguments["--development"]:
-                                          l_symlink)
+
+            l_string += ninja_module_build(module_to_compile, d_binaries)
+
+            l_string += ninja_gitignore_build(module_to_compile, d_binaries,
+                                              l_symlink)
+
+            save_subninja_file(module_to_compile)
 
     # ~#~#~#~#~ #
     # S a v e s #

scripts/get_basis.sh

@@ -8,6 +8,8 @@
 # Prints in stdout the name of a temporary file containing the basis set.
 #
 
+
+
 if [[ -z ${QP_ROOT} ]]
 then
   print "The QP_ROOT environment variable is not set."
@@ -15,6 +17,7 @@ then
   exit -1
 fi
 
+
 export EMSL_API_ROOT="${QP_ROOT}"/install/emsl
 
 tmpfile="$1"

scripts/module/module_handler.py

@@ -23,16 +23,19 @@ import shutil
 
 try:
     from docopt import docopt
-    from qp_path import QP_SRC
+    from qp_path import QP_SRC, QP_ROOT, QP_PLUGINS
-    from qp_path import QP_ROOT
 except ImportError:
     print "source .quantum_package.rc"
     raise
 
 
-# Canot cache for namedtuple are not hashable
+def is_module(path_module_rel):
-def is_module(path_module):
+    return os.path.isfile(os.path.join(QP_SRC, path_module_rel,
-    return os.path.isfile(os.path.join(QP_SRC, path_module,
+                                       "NEEDED_CHILDREN_MODULES"))
+
+
+def is_plugin(path_module_rel):
+    return os.path.isfile(os.path.join(QP_PLUGINS, path_module_rel,
                                        "NEEDED_CHILDREN_MODULES"))
 
 
@@ -180,13 +183,7 @@ class ModuleHandler():
         basename = "tree_dependency"
         path = '{0}.png'.format(basename)
 
-        # Init
+        from graphviz import Digraph
-        try:
-            from graphviz import Digraph
-        except:
-            with open(path, 'a'):
-                os.utime(path, None)
-            return
 
         all_ready_done = []
 
@@ -209,7 +206,14 @@ class ModuleHandler():
             graph.node(module, fontcolor="red")
             draw_module_edge(module, d_ref[module])
 
-        graph.render(cleanup=True)
+        # Try to render the png
+        # If not just touch it
+        try:
+            graph.render(cleanup=True)
+        except:
+            with open(path, 'a'):
+                os.utime(path, None)
+            return
 
 
 if __name__ == '__main__':
@@ -292,4 +296,3 @@ if __name__ == '__main__':
                     l_text = l_dir + l_file + l_symlink + l_exe
                     l_text.sort()
                     f.write("\n".join(l_text))
-

scripts/module/qp_install_module.py

@@ -22,7 +22,7 @@ try:
     from docopt import docopt
     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_update_readme import D_KEY
     from qp_path import QP_SRC, QP_PLUGINS, QP_ROOT
 except ImportError:
     print "Please check if you have sourced the .quantum_package.rc"
@@ -56,8 +56,8 @@ def save_new_module(path, l_child):
 
     with open(os.path.join(path, "README.rst"), "w") as f:
         f.write(header + "\n")
-        f.write(Doc_key + "\n")
+        f.write(D_KEY["needed_module"])
-        f.write(Needed_key + "\n")
+        f.write(D_KEY["documentation"])
 
 
 if __name__ == '__main__':
@@ -108,8 +108,9 @@ if __name__ == '__main__':
         save_new_module(path, l_child_reduce)
 
         print "    [ OK ]"
-        print "If this was a plugins, you can install it normaly. Type:"
+        print "You can now install it normaly. Type:"
         print "` {0} install {1} `".format(os.path.basename(__file__), name)
+        print "And don't forgot to add this to the git if you want"
 
     elif arguments["download"]:
         pass

scripts/module/qp_update_readme.py

@@ -0,0 +1,205 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+"""
+Updates the README.rst of a module
+Usage:
+       qp_update_readme.py [<module_path>...] [--root_module=<module_path>]
+
+Options:
+    path_readme: All the absolute path you want to update.
+                 By default is the cwd
+    --root_module: Is the path of the root module who containt the tags file.
+                   By default is the cwd
+"""
+
+import sys
+
+try:
+    from docopt import docopt
+    from module_handler import is_module, is_plugin
+except:
+    print "Please check if you have sourced the .quantum_package.rc"
+    print "(`source .quantum_package.rc`)"
+    print sys.exit(1)
+
+import os
+from collections import namedtuple
+from collections import defaultdict
+
+
+def header_format(str_):
+
+    warning = "\n".join([".. Do not edit this section It was auto-generated",
+                        ".. by the `update_README.py` script."])
+
+    return "{0}\n{1}\n{2}\n".format(str_, "=" * len(str_), warning)
+
+D_KEY = {"needed_module": header_format("Needed Modules"),
+         "documentation": header_format("Documentation")}
+
+
+def get_url(path_module_rel):
+    if is_plugin(path_module_rel):
+        url = "http://github.com/LCPQ/quantum_package/tree/master/plugins"
+    elif is_module(path_module_rel):
+        url = "http://github.com/LCPQ/quantum_package/tree/master/src"
+    else:
+        print "{0} Is not a valide module nor plugin".format(path_module_rel)
+        sys.exit(1)
+
+    return os.path.join(url, path_module_rel)
+
+
+def fetch_splitted_data(d_readme, l_module_readme):
+    """Read the README.rst file and split it in strings:
+    * The documentation
+    * The needed modules
+    The result is given as a list of strings
+    """
+
+    sentinel = "@@$%&@@"
+
+    for path_readme in l_module_readme:
+        with open(os.path.join(path_readme, "README.rst"), 'r') as f:
+            data = f.read()
+
+        # Place sentinels
+
+        for v in D_KEY.values():
+            data = data.replace(v, sentinel + v)
+
+        # Now Split data using the sentinels
+        d_readme[path_readme] = {"human": data.split(sentinel)[0]}
+
+
+def update_needed(d_readme):
+    """Read the NEEDED_CHILDREN_MODULES file, and replace the data with it.
+    Create the links to the GitHub pages."""
+
+    header_image = ".. image:: tree_dependency.png"
+
+    for path in d_readme:
+
+        with open(os.path.join(path, 'NEEDED_CHILDREN_MODULES'), 'r') as f:
+            modules = f.read()
+
+        if modules.strip():
+            l_module = ['* `{0} <{1}>`_'.format(name, get_url(name))
+                        for name in modules.split()]
+
+            l_module_section = [D_KEY["needed_module"], '',
+                                header_image, '',
+                                '\n'.join(l_module), '', '']
+        else:
+            l_module_section = ""
+
+        d_readme[path]["needed_module"] = "\n".join(l_module_section)
+
+
+def extract_doc(root_module, provider):
+    """Extracts the documentation contained in IRPF90_man file"""
+
+    path = os.path.join(root_module, "IRPF90_man/%s.l" % (provider))
+    with open(path, 'r') as f:
+        l_line = f.readlines()
+
+    result = []
+    inside = False
+    for line in l_line:
+        if not inside:
+            inside = line.startswith(".SH Description")
+        else:
+            if line.startswith(".SH"):
+                break
+            result.append("  {0}".format(line.strip()))
+
+    if not result:
+        result = ["  Undocumented"]
+
+    return "\n".join(result) + "\n"
+
+
+def update_documentation(d_readmen, root_module):
+    """Reads the BEGIN_DOC ... END_DOC blocks and builds the documentation"""
+
+    IRP_info = namedtuple('IRP_info', ["module", "file", "provider", "line"])
+
+    # If the file does not exist, don't do anything
+    path = os.path.join(root_module, "tags")
+
+    with open(path, 'r') as f:
+        dump = f.readlines()
+
+    d_info = defaultdict(list)
+
+    for i in dump:
+        # i =
+        # output_cpu_time_0  Ezfio_files/output.irp.f    2
+        provider, irp_file_raw, ligne = i.split()
+
+        for path in d_readme:
+
+            if root_module == path and "/" not in irp_file_raw:
+                d_info[path].append(IRP_info(os.path.basename(path),
+                                             irp_file_raw,
+                                             provider,
+                                             ligne))
+
+            elif "/" in irp_file_raw and os.path.dirname(irp_file_raw) in path:
+
+                module, irp_file = os.path.split(irp_file_raw)
+                d_info[path].append(IRP_info(module, irp_file, provider, ligne))
+
+    for path in d_readme:
+
+        l_doc = []
+
+        for irp in d_info[path]:
+
+            url = os.path.join(get_url(os.path.basename(path)), irp.file)
+            doc = extract_doc(root_module, irp.provider)
+
+            l_doc += ["`{0} <{1}#L{2}>`_".format(irp.provider, url, irp.line),
+                      doc,
+                      ""]
+
+        l_doc_section = [D_KEY["documentation"], '',
+                         "\n".join(l_doc)]
+
+        d_readme[path]["documentation"] = "\n".join(l_doc_section)
+
+if __name__ == '__main__':
+    arguments = docopt(__doc__)
+
+    if arguments["--root_module"]:
+        root_module = os.path.realpath(arguments["--root_module"])
+    else:
+        root_module = os.getcwd()
+
+    if not arguments["<module_path>"]:
+        l_module_readme = [os.path.join(os.getcwd())]
+    else:
+        l_module_readme = arguments["<module_path>"]
+
+    # d[Path] ={humain, needed_module, documentation}
+    d_readme = defaultdict(dict)
+
+    try:
+        fetch_splitted_data(d_readme, l_module_readme)
+    except IOError:
+        print l_module_readme, "is not a module and/or",
+        print "have not a `README.rst` file inside"
+        print "Abort..."
+        sys.exit(1)
+
+    update_needed(d_readme)
+    update_documentation(d_readme, root_module)
+
+    for path, d in d_readme.iteritems():
+
+        with open(os.path.join(path, "README.rst"), 'w') as f:
+            for k in ["human",
+                      "needed_module",
+                      "documentation"]:
+
+                f.write(d[k])

scripts/module/update_README.py

@@ -1,191 +0,0 @@
-#!/usr/bin/env python
-"""Updates the README.rst file as the include directive is disabled on GitHub."""
-__date__ = "Thu Apr  3 23:06:18 CEST 2014"
-__author__ = "Anthony Scemama<scemama@irsamc.ups-tlse.fr>  & TApplencourt "
-
-README = "README.rst"
-Assum_key = "Assumptions\n===========\n"
-Needed_key = "Needed Modules\n==============\n"
-Doc_key = "Documentation\n=============\n"
-Sentinel = "@@$%&@@"
-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
-.. by the `update_README.py` script.
-
-"""
-
-
-def fetch_splitted_data():
-    """Read the README.rst file and split it in strings:
-    * The documentation
-    * The needed modules
-    The result is given as a list of strings
-    """
-
-    try:
-        with open(README, 'r') as f:
-            data = f.read()
-    except IOError:
-      return []
-
-    # Place sentinels
-    data = data.replace(Doc_key, Sentinel + Doc_key)
-    data = data.replace(Needed_key, Sentinel + Needed_key)
-
-    # Now Split data using the sentinels
-    result = data.split(Sentinel)
-
-    return result
-
-
-def update_needed(data):
-    """Read the NEEDED_CHILDREN_MODULES file, and replace the data with it.
-    Create the links to the GitHub pages."""
-
-    with open('NEEDED_CHILDREN_MODULES', 'r') as f:
-        modules = f.read()
-
-    header_image = ".. image:: tree_dependency.png\n\n"
-
-    if modules.strip():
-        modules = ['* `{0} <{1}>`_'.format(name, os.path.join(URL, name))
-                   for name in modules.split()]
-        modules = "\n".join(modules)
-        modules = Needed_key + header + header_image + modules + '\n\n'
-
-    has_modules = False
-    for i in range(len(data)):
-        if data[i].startswith(Needed_key):
-            has_modules = True
-            data[i] = modules
-
-    if not has_modules:
-        data.append(modules)
-
-    return data
-
-
-def extract_doc(item):
-    """Extracts the documentation contained in IRPF90_man file"""
-
-    path = os.path.join(ROOT_module, "IRPF90_man/%s.l" % (item))
-    with open(path, 'r') as f:
-        l_line = f.readlines()
-
-    result = []
-    inside = False
-    for line in l_line:
-        if not inside:
-            inside = line.startswith(".SH Description")
-        else:
-            if line.startswith(".SH"):
-                break
-            result.append("  {0}".format(line.strip()))
-
-    if not result:
-        result = ["  Undocumented"]
-
-    return "\n".join(result) + '\n'
-
-
-def update_documentation(data):
-    """Reads the BEGIN_DOC ... END_DOC blocks and builds the documentation"""
-
-    IRP_info = namedtuple('IRP_info', ["name", "file", "line"])
-
-    # If the file does not exist, don't do anything
-
-    path = os.path.join(ROOT_module, "tags")
-
-    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 = []
-
-    for irp in l_info:
-        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,
-                   ""]
-
-    documentation = Doc_key + header + "\n".join(l_line)
-
-    has_doc = False
-    for i in range(len(data)):
-        if data[i].startswith(Doc_key):
-            has_doc = True
-            data[i] = documentation
-
-    if not has_doc:
-        data.append(documentation)
-
-    return data
-
-
-def git_add():
-    """Executes:
-    git add README.rst
-    throw an error if git is not precent"""
-
-    try:
-        # pipe output to /dev/null for silence
-        null = open("/dev/null", "w")
-        subprocess.Popen("git add README.rst", stdout=null, stderr=null)
-        null.close()
-
-    except OSError:
-        raise
-
-
-def main():
-    data = fetch_splitted_data()
-
-    data = update_documentation(data)
-    data = update_needed(data)
-    output = ''.join(data)
-
-    with open(README, 'w') as f:
-        f.write(output)
-
-    try:
-        git_add()
-    except OSError:
-        pass
-
-
-if __name__ == '__main__':
-    main()

scripts/save_current_mos.sh

@@ -4,6 +4,7 @@
 # directory, where xxx is the corresponding mo_label.
 # Wed Apr  2 14:35:15 CEST 2014
 
+
 if [[ -z ${QP_ROOT} ]]
 then
   print "The QP_ROOT environment variable is not set."
@@ -11,40 +12,40 @@ then
   exit -1
 fi
 
-EZFIO=$1
+EZFIO="$1"
 
-if [[ -z ${EZFIO} ]]
+if [[ -z "${EZFIO}" ]]
 then
   echo "Error in $0"
   exit 1
 fi
 
-if [[ ! -f ${EZFIO}/mo_basis/mo_label ]]
+if [[ ! -f "${EZFIO}/mo_basis/mo_label" ]]
 then
   LABEL='no_label'
 else
-  LABEL=$(head -1 ${EZFIO}/mo_basis/mo_label)
+  LABEL=$(head -1 "${EZFIO}/mo_basis/mo_label")
 fi
 
 DESTINATION="save/mo_basis/${LABEL}"
 
-cd ${EZFIO}
+cd "${EZFIO}"
 
 if [[ ! -d save/mo_basis ]]
 then
         mkdir -p save/mo_basis
 fi
 
-BACKUP=${DESTINATION}.old 
+BACKUP="${DESTINATION}.old"
-if [[ -d ${BACKUP} ]]
+if [[ -d "${BACKUP}" ]]
 then
-        rm -rf ${BACKUP}
+        rm -rf "${BACKUP}"
 fi
 
-if [[ -d ${DESTINATION} ]]
+if [[ -d "${DESTINATION}" ]]
 then
-        mv ${DESTINATION} ${BACKUP}
+        mv "${DESTINATION}" "${BACKUP}"
 fi
 
-cp -r mo_basis ${DESTINATION}
+cp -r mo_basis "${DESTINATION}"
 

src/AO_Basis/README.rst

@@ -33,19 +33,29 @@ Assumptions
 Needed Modules
 ==============
 
-.. Do not edit this section. It was auto-generated from the
+.. Do not edit this section It was auto-generated
 .. by the `update_README.py` script.
 
+.. image:: tree_dependency.png
+
+* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
+
+Needed Modules
+==============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
 .. image:: tree_dependency.png
 
 * `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
 
 Documentation
 =============
-
+.. Do not edit this section It was auto-generated
-.. 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/AO_Basis/ezfio_interface.irp.f#L24>`_
   AO Coefficients, read from input. Those should not be used directly, as the MOs are expressed on the basis of **normalized** AOs.
 

src/Bitmask/README.rst

@@ -37,19 +37,29 @@ Assumptions
 Needed Modules
 ==============
 
-.. Do not edit this section. It was auto-generated from the
+.. Do not edit this section It was auto-generated
 .. by the `update_README.py` script.
 
+.. image:: tree_dependency.png
+
+* `MO_Basis <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis>`_
+
+Needed Modules
+==============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
 .. image:: tree_dependency.png
 
 * `MO_Basis <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis>`_
 
 Documentation
 =============
-
+.. Do not edit this section It was auto-generated
-.. Do not edit this section. It was auto-generated from the
 .. by the `update_README.py` script.
 
+
 `bitstring_to_hexa <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks_routines.irp.f#L98>`_
   Transform a bit string to a string in hexadecimal format for printing
 

src/Determinants/README.rst

@@ -29,9 +29,20 @@ Assumptions
 Needed Modules
 ==============
 
-.. Do not edit this section. It was auto-generated from the
+.. Do not edit this section It was auto-generated
 .. by the `update_README.py` script.
 
+.. image:: tree_dependency.png
+
+* `Integrals_Monoelec <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec>`_
+* `Integrals_Bielec <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec>`_
+
+Needed Modules
+==============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
 .. image:: tree_dependency.png
 
 * `Integrals_Monoelec <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec>`_
@@ -39,10 +50,10 @@ Needed Modules
 
 Documentation
 =============
-
+.. Do not edit this section It was auto-generated
-.. Do not edit this section. It was auto-generated from the
 .. by the `update_README.py` script.
 
+
 `a_operator <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/slater_rules.irp.f#L1108>`_
   Needed for diag_H_mat_elem
 

src/Determinants/slater_rules.irp.f

@@ -960,7 +960,7 @@ subroutine get_excitation_degree_vector(key1,key2,degree,Nint,sze,idx)
   integer, intent(out)           :: degree(sze)
   integer, intent(out)           :: idx(0:sze)
   
-  integer                        :: i,l,d
+  integer                        :: i,l,d,m
   
   ASSERT (Nint > 0)
   ASSERT (sze > 0)
@@ -1023,9 +1023,9 @@ subroutine get_excitation_degree_vector(key1,key2,degree,Nint,sze,idx)
     do i=1,sze
       d = 0
       !DEC$ LOOP COUNT MIN(4)
-      do l=1,Nint
+      do m=1,Nint
-        d = d + popcnt(xor( key1(l,1,i), key2(l,1)))                 &
+        d = d + popcnt(xor( key1(m,1,i), key2(m,1)))                 &
-              + popcnt(xor( key1(l,2,i), key2(l,2)))
+              + popcnt(xor( key1(m,2,i), key2(m,2)))
       enddo
       if (d > 4) then
         cycle

src/Electrons/README.rst

@@ -21,19 +21,29 @@ Assumptions
 Needed Modules
 ==============
 
-.. Do not edit this section. It was auto-generated from the
+.. Do not edit this section It was auto-generated
 .. by the `update_README.py` script.
 
+.. image:: tree_dependency.png
+
+* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
+
+Needed Modules
+==============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
 .. image:: tree_dependency.png
 
 * `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
 
 Documentation
 =============
-
+.. Do not edit this section It was auto-generated
-.. Do not edit this section. It was auto-generated from the
 .. by the `update_README.py` script.
 
+
 `elec_alpha_num <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons/ezfio_interface.irp.f#L28>`_
   Numbers of electrons alpha ("up")
 

src/Ezfio_files/README.rst

@@ -170,3 +170,171 @@ Documentation
   Write a time stamp in the output for chronological reconstruction
 
 
+Documentation
+=============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
+`ezfio_filename <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/ezfio.irp.f#L1>`_
+  Name of EZFIO file. It is obtained from the QPACKAGE_INPUT environment
+  variable if it is set, or as the 1st argument of the command line.
+
+
+`getunitandopen <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/get_unit_and_open.irp.f#L1>`_
+  :f:
+  file name
+  .br
+  :mode:
+  'R' : READ, UNFORMATTED
+  'W' : WRITE, UNFORMATTED
+  'r' : READ, FORMATTED
+  'w' : WRITE, FORMATTED
+  'a' : APPEND, FORMATTED
+  'x' : READ/WRITE, FORMATTED
+  .br
+
+
+`output_ao_basis <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L1>`_
+  Output file for AO_Basis
+
+
+`output_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L21>`_
+  Output file for Bitmask
+
+
+`output_cas_sd <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L41>`_
+  Output file for CAS_SD
+
+
+`output_cis <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L61>`_
+  Output file for CIS
+
+
+`output_cisd <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L81>`_
+  Output file for CISD
+
+
+`output_cisd_selected <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L101>`_
+  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_determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L121>`_
+  Output file for Determinants
+
+
+`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#L161>`_
+  Output file for Ezfio_files
+
+
+`output_fcidump <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#L201>`_
+  Output file for Full_CI
+
+
+`output_generators_cas <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L221>`_
+  Output file for Generators_CAS
+
+
+`output_generators_full <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L241>`_
+  Output file for Generators_full
+
+
+`output_hartree_fock <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L261>`_
+  Output file for Hartree_Fock
+
+
+`output_integrals_bielec <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L281>`_
+  Output file for Integrals_Bielec
+
+
+`output_integrals_monoelec <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L301>`_
+  Output file for Integrals_Monoelec
+
+
+`output_mo_basis <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L321>`_
+  Output file for MO_Basis
+
+
+`output_moguess <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L341>`_
+  Output file for MOGuess
+
+
+`output_mrcc_cassd <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L361>`_
+  Output file for MRCC_CASSD
+
+
+`output_mrcc_utils <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L381>`_
+  Output file for MRCC_Utils
+
+
+`output_nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L401>`_
+  Output file for Nuclei
+
+
+`output_perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L421>`_
+  Output file for Perturbation
+
+
+`output_properties <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L441>`_
+  Output file for Properties
+
+
+`output_pseudo <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L461>`_
+  Output file for Pseudo
+
+
+`output_psiref_cas <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L481>`_
+  Output file for Psiref_CAS
+
+
+`output_psiref_utils <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L501>`_
+  Output file for Psiref_Utils
+
+
+`output_qmcchem <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L521>`_
+  Output file for QmcChem
+
+
+`output_selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L541>`_
+  Output file for Selectors_full
+
+
+`output_singlerefmethod <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L561>`_
+  Output file for SingleRefMethod
+
+
+`output_utils <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L581>`_
+  Output file for Utils
+
+
+`output_wall_time_0 <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f#L1>`_
+  Initial CPU and wall times when printing in the output files
+
+
+`write_bool <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f#L88>`_
+  Write an logical value in output
+
+
+`write_double <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f#L58>`_
+  Write a double precision value in output
+
+
+`write_int <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f#L73>`_
+  Write an integer value in output
+
+
+`write_time <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f#L42>`_
+  Write a time stamp in the output for chronological reconstruction
+

src/Integrals_Bielec/README.rst

@@ -13,9 +13,20 @@ MO integral, use ``get_mo_bielec_integral(i,j,k,l,mo_integrals_map)`` or
 Needed Modules
 ==============
 
-.. Do not edit this section. It was auto-generated from the
+.. Do not edit this section It was auto-generated
 .. by the `update_README.py` script.
 
+.. image:: tree_dependency.png
+
+* `Pseudo <http://github.com/LCPQ/quantum_package/tree/master/src/Pseudo>`_
+* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
+
+Needed Modules
+==============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
 .. image:: tree_dependency.png
 
 * `Pseudo <http://github.com/LCPQ/quantum_package/tree/master/src/Pseudo>`_
@@ -23,10 +34,10 @@ Needed Modules
 
 Documentation
 =============
-
+.. Do not edit this section It was auto-generated
-.. Do not edit this section. It was auto-generated from the
 .. by the `update_README.py` script.
 
+
 `add_integrals_to_map <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/mo_bi_integrals.irp.f#L42>`_
   Adds integrals to tha MO map according to some bitmask
 

src/Integrals_Bielec/read_write.irp.f

@@ -20,7 +20,13 @@ implicit none
         read_ao_integrals = .False.
         write_ao_integrals = .False.
 
-    else if (disk_access_mo_integrals.EQ.'Read') then
+    else
+        print *, 'bielec_integrals/disk_access_ao_integrals has a wrong type'
+        stop 1
+
+    endif
+
+    if (disk_access_mo_integrals.EQ.'Read') then
         read_mo_integrals =  .True.
         write_mo_integrals = .False.
 
@@ -33,8 +39,8 @@ implicit none
         write_mo_integrals = .False.
 
     else
-        print *, 'bielec_integrals/disk_acces not of a the good type'
+        print *, 'bielec_integrals/disk_access_mo_integrals has a wrong type'
-        stop "1"
+        stop 1
 
     endif
 

src/Integrals_Monoelec/README.rst

@@ -1,9 +1,20 @@
 Needed Modules
 ==============
 
-.. Do not edit this section. It was auto-generated from the
+.. Do not edit this section It was auto-generated
 .. by the `update_README.py` script.
 
+.. image:: tree_dependency.png
+
+* `MO_Basis <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis>`_
+* `Pseudo <http://github.com/LCPQ/quantum_package/tree/master/src/Pseudo>`_
+
+Needed Modules
+==============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
 .. image:: tree_dependency.png
 
 * `MO_Basis <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis>`_
@@ -11,10 +22,10 @@ Needed Modules
 
 Documentation
 =============
-
+.. Do not edit this section It was auto-generated
-.. Do not edit this section. It was auto-generated from the
 .. by the `update_README.py` script.
 
+
 `ao_deriv2_x <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/kin_ao_ints.irp.f#L1>`_
   second derivatives matrix elements in the ao basis
   .. math::

src/MOGuess/README.rst

@@ -5,19 +5,29 @@ MOGuess Module
 Needed Modules
 ==============
 
-.. Do not edit this section. It was auto-generated from the
+.. Do not edit this section It was auto-generated
 .. by the `update_README.py` script.
 
+.. image:: tree_dependency.png
+
+* `Integrals_Monoelec <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec>`_
+
+Needed Modules
+==============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
 .. image:: tree_dependency.png
 
 * `Integrals_Monoelec <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec>`_
 
 Documentation
 =============
-
+.. Do not edit this section It was auto-generated
-.. Do not edit this section. It was auto-generated from the
 .. by the `update_README.py` script.
 
+
 `ao_ortho_lowdin_coef <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess/mo_ortho_lowdin.irp.f#L2>`_
   matrix of the coefficients of the mos generated by the
   orthonormalization by the S^{-1/2} canonical transformation of the aos

src/MO_Basis/README.rst

@@ -33,9 +33,20 @@ ASSUMPTONS
 Needed Modules
 ==============
 
-.. Do not edit this section. It was auto-generated from the
+.. Do not edit this section It was auto-generated
 .. by the `update_README.py` script.
 
+.. image:: tree_dependency.png
+
+* `AO_Basis <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis>`_
+* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
+
+Needed Modules
+==============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
 .. image:: tree_dependency.png
 
 * `AO_Basis <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis>`_
@@ -43,10 +54,10 @@ Needed Modules
 
 Documentation
 =============
-
+.. Do not edit this section It was auto-generated
-.. Do not edit this section. It was auto-generated from the
 .. by the `update_README.py` script.
 
+
 `ao_to_mo <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis/mos.irp.f#L136>`_
   Transform A from the AO basis to the MO basis
 

src/Nuclei/README.rst

@@ -9,9 +9,20 @@ The coordinates are expressed in atomic units.
 Needed Modules
 ==============
 
-.. Do not edit this section. It was auto-generated from the
+.. Do not edit this section It was auto-generated
 .. by the `update_README.py` script.
 
+.. image:: tree_dependency.png
+
+* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
+* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
+
+Needed Modules
+==============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
 .. image:: tree_dependency.png
 
 * `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
@@ -19,10 +30,10 @@ Needed Modules
 
 Documentation
 =============
-
+.. Do not edit this section It was auto-generated
-.. Do not edit this section. It was auto-generated from the
 .. by the `update_README.py` script.
 
+
 `element_name <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L172>`_
   Array of the name of element, sorted by nuclear charge (integer)
 

src/Pseudo/README.rst

@@ -5,19 +5,29 @@ Pseudo Module
 Needed Modules
 ==============
 
-.. Do not edit this section. It was auto-generated from the
+.. Do not edit this section It was auto-generated
 .. by the `update_README.py` script.
 
+.. image:: tree_dependency.png
+
+* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
+
+Needed Modules
+==============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
 .. image:: tree_dependency.png
 
 * `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
 
 Documentation
 =============
-
+.. Do not edit this section It was auto-generated
-.. Do not edit this section. It was auto-generated from the
 .. by the `update_README.py` script.
 
+
 `do_pseudo <http://github.com/LCPQ/quantum_package/tree/master/src/Pseudo/ezfio_interface.irp.f#L248>`_
   Using pseudo potential integral of not
 

src/Utils/README.rst

@@ -6,10 +6,10 @@ Contains general purpose utilities.
 
 Documentation
 =============
-
+.. Do not edit this section It was auto-generated
-.. Do not edit this section. It was auto-generated from the
 .. by the `update_README.py` script.
 
+
 `a_coef <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/need.irp.f#L252>`_
   Undocumented
 
@@ -634,4 +634,3 @@ Documentation
 `write_git_log <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L243>`_
   Write the last git commit in file iunit.
 
-