Merge pull request #21 from LCPQ/master

Merge with Manu

configure

@@ -71,7 +71,7 @@ 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',
@@ -180,6 +180,8 @@ 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
 
@@ -224,7 +226,7 @@ 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
@@ -341,9 +343,9 @@ _|_ | | _>  |_ (_| | | (_|  |_ | (_) | |
         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 +453,7 @@ 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}"', "",

plugins/Full_CI/.gitignore

@@ -22,7 +22,6 @@ Properties
 Pseudo
 Selectors_full
 Utils
-exc_degree
 ezfio_interface.irp.f
 full_ci
 full_ci_no_skip

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#L521>`_
+  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#L2720>`_
+  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#L2198>`_
+  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#L2522>`_
+  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#L325>`_
+  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#L1980>`_
+  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#L1460>`_
+  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#L1784>`_
+  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#L1253>`_
+  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#L767>`_
+  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#L1071>`_
+  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#L4222>`_
+  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#L3734>`_
+  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#L4038>`_
+  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#L5681>`_
+  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#L5195>`_
+  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#L5499>`_
+  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#L3488>`_
+  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#L2966>`_
+  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#L3290>`_
+  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#L4949>`_
+  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#L4429>`_
+  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#L4753>`_
+  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_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/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#L161>`_
   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#L896>`_
   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#L686>`_
   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#L791>`_
   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#L581>`_
   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#L476>`_
   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#L371>`_
   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#L266>`_
   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#L56>`_
   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#L110>`_
   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#L845>`_
   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#L635>`_
   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#L740>`_
   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#L530>`_
   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#L425>`_
   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#L320>`_
   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#L215>`_
   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#L5>`_
   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/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
+

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/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()

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>`_
@@ -39,15 +50,11 @@ 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
-
-
-`abs_psi_coef_max <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L451>`_
   Max and min values of the coefficients
 
 

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/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_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.
 
-