Merge pull request #23 from LCPQ/master

README

plugins/CAS_SD/README.rst

@@ -118,101 +118,101 @@ Documentation
   Undocumented
 
 
-`h_apply_cas_sd <http://github.com/LCPQ/quantum_package/tree/master/plugins/CAS_SD/H_apply.irp.f_shell_22#L537>`_
+h_apply_cas_sd
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cas_sd_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CAS_SD/H_apply.irp.f_shell_22#L3>`_
+h_apply_cas_sd_diexc
   Undocumented
 
 
-`h_apply_cas_sd_diexcorg <http://github.com/LCPQ/quantum_package/tree/master/plugins/CAS_SD/H_apply.irp.f_shell_22#L119>`_
+h_apply_cas_sd_diexcorg
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cas_sd_diexcp <http://github.com/LCPQ/quantum_package/tree/master/plugins/CAS_SD/H_apply.irp.f_shell_22#L96>`_
+h_apply_cas_sd_diexcp
   Undocumented
 
 
-`h_apply_cas_sd_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CAS_SD/H_apply.irp.f_shell_22#L387>`_
+h_apply_cas_sd_monoexc
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cas_sd_pt2 <http://github.com/LCPQ/quantum_package/tree/master/plugins/CAS_SD/H_apply.irp.f_shell_22#L3175>`_
+h_apply_cas_sd_pt2
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cas_sd_pt2_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CAS_SD/H_apply.irp.f_shell_22#L2540>`_
+h_apply_cas_sd_pt2_diexc
   Undocumented
 
 
-`h_apply_cas_sd_pt2_diexcorg <http://github.com/LCPQ/quantum_package/tree/master/plugins/CAS_SD/H_apply.irp.f_shell_22#L2678>`_
+h_apply_cas_sd_pt2_diexcorg
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cas_sd_pt2_diexcp <http://github.com/LCPQ/quantum_package/tree/master/plugins/CAS_SD/H_apply.irp.f_shell_22#L2644>`_
+h_apply_cas_sd_pt2_diexcp
   Undocumented
 
 
-`h_apply_cas_sd_pt2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CAS_SD/H_apply.irp.f_shell_22#L2987>`_
+h_apply_cas_sd_pt2_monoexc
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cas_sd_selected <http://github.com/LCPQ/quantum_package/tree/master/plugins/CAS_SD/H_apply.irp.f_shell_22#L2291>`_
+h_apply_cas_sd_selected
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cas_sd_selected_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CAS_SD/H_apply.irp.f_shell_22#L1620>`_
+h_apply_cas_sd_selected_diexc
   Undocumented
 
 
-`h_apply_cas_sd_selected_diexcorg <http://github.com/LCPQ/quantum_package/tree/master/plugins/CAS_SD/H_apply.irp.f_shell_22#L1760>`_
+h_apply_cas_sd_selected_diexcorg
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cas_sd_selected_diexcp <http://github.com/LCPQ/quantum_package/tree/master/plugins/CAS_SD/H_apply.irp.f_shell_22#L1725>`_
+h_apply_cas_sd_selected_diexcp
   Undocumented
 
 
-`h_apply_cas_sd_selected_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CAS_SD/H_apply.irp.f_shell_22#L2089>`_
+h_apply_cas_sd_selected_monoexc
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cas_sd_selected_no_skip <http://github.com/LCPQ/quantum_package/tree/master/plugins/CAS_SD/H_apply.irp.f_shell_22#L1399>`_
+h_apply_cas_sd_selected_no_skip
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cas_sd_selected_no_skip_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CAS_SD/H_apply.irp.f_shell_22#L728>`_
+h_apply_cas_sd_selected_no_skip_diexc
   Undocumented
 
 
-`h_apply_cas_sd_selected_no_skip_diexcorg <http://github.com/LCPQ/quantum_package/tree/master/plugins/CAS_SD/H_apply.irp.f_shell_22#L868>`_
+h_apply_cas_sd_selected_no_skip_diexcorg
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cas_sd_selected_no_skip_diexcp <http://github.com/LCPQ/quantum_package/tree/master/plugins/CAS_SD/H_apply.irp.f_shell_22#L833>`_
+h_apply_cas_sd_selected_no_skip_diexcp
   Undocumented
 
 
-`h_apply_cas_sd_selected_no_skip_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CAS_SD/H_apply.irp.f_shell_22#L1197>`_
+h_apply_cas_sd_selected_no_skip_monoexc
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.

plugins/CID/README.rst

@@ -203,3 +203,48 @@ Documentation
   particles.
   Assume N_int is already provided.
 
+Needed Modules
+==============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
+.. image:: tree_dependency.png
+
+* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/plugins/Selectors_full>`_
+* `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/plugins/SingleRefMethod>`_
+
+Documentation
+=============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
+`cid <http://github.com/LCPQ/quantum_package/tree/master/plugins/CID/cid_lapack.irp.f#L1>`_
+  Undocumented
+
+
+h_apply_cid
+  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_cid_diexc
+  Undocumented
+
+
+h_apply_cid_diexcorg
+  Generate all double excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+h_apply_cid_diexcp
+  Undocumented
+
+
+h_apply_cid_monoexc
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+

plugins/CISD/README.rst

@@ -59,18 +59,26 @@ Documentation
 .. by the `update_README.py` script.
 
 
-`h_apply_cisd <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD/H_apply.irp.f_shell_8#L414>`_
+h_apply_cisd
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD/H_apply.irp.f_shell_8#L1>`_
+h_apply_cisd_diexc
+  Undocumented
+
+
+h_apply_cisd_diexcorg
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD/H_apply.irp.f_shell_8#L269>`_
+h_apply_cisd_diexcp
+  Undocumented
+
+
+h_apply_cisd_monoexc
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.

plugins/CISD_SC2_selected/README.rst

@@ -72,3 +72,122 @@ Needed Modules
 
 * `CISD_selected <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected>`_
 
+Needed Modules
+==============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
+.. image:: tree_dependency.png
+
+* `CISD_selected <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected>`_
+
+Documentation
+=============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
+`cisd_sc2_selected <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_SC2_selected/cisd_sc2_selection.irp.f#L1>`_
+  Undocumented
+
+
+h_apply_cisd
+  Calls H_apply on the HF determinant and selects all connected single and double
+  excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
+
+
+h_apply_cisd_diexc
+  Undocumented
+
+
+h_apply_cisd_diexcorg
+  Generate all double excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+h_apply_cisd_diexcp
+  Undocumented
+
+
+h_apply_cisd_monoexc
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+h_apply_pt2
+  Calls H_apply on the HF determinant and selects all connected single and double
+  excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
+
+
+h_apply_pt2_diexc
+  Undocumented
+
+
+h_apply_pt2_diexcorg
+  Generate all double excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+h_apply_pt2_diexcp
+  Undocumented
+
+
+h_apply_pt2_en_sc2
+  Calls H_apply on the HF determinant and selects all connected single and double
+  excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
+
+
+h_apply_pt2_en_sc2_diexc
+  Undocumented
+
+
+h_apply_pt2_en_sc2_diexcorg
+  Generate all double excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+h_apply_pt2_en_sc2_diexcp
+  Undocumented
+
+
+h_apply_pt2_en_sc2_monoexc
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+h_apply_pt2_monoexc
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+h_apply_sc2_selected
+  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_sc2_selected_diexc
+  Undocumented
+
+
+h_apply_sc2_selected_diexcorg
+  Generate all double excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+h_apply_sc2_selected_diexcp
+  Undocumented
+
+
+h_apply_sc2_selected_monoexc
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+

plugins/CISD_selected/README.rst

@@ -196,22 +196,26 @@ Documentation
 .. by the `update_README.py` script.
 
 
-`cisd <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/cisd_selection.irp.f#L1>`_
+h_apply_cisd
-  Undocumented
-
-
-`h_apply_cisd <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_8#L414>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_8#L1>`_
+h_apply_cisd_diexc
+  Undocumented
+
+
+h_apply_cisd_diexcorg
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_8#L269>`_
+h_apply_cisd_diexcp
+  Undocumented
+
+
+h_apply_cisd_monoexc
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
@@ -221,154 +225,226 @@ Documentation
   Undocumented
 
 
-`h_apply_cisd_selection_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L5931>`_
+h_apply_cisd_selection_delta_rho_one_point
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_delta_rho_one_point_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L5405>`_
+h_apply_cisd_selection_delta_rho_one_point_diexc
+  Undocumented
+
+
+h_apply_cisd_selection_delta_rho_one_point_diexcorg
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_delta_rho_one_point_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L5734>`_
+h_apply_cisd_selection_delta_rho_one_point_diexcp
+  Undocumented
+
+
+h_apply_cisd_selection_delta_rho_one_point_monoexc
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_dipole_moment_z <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L5159>`_
+h_apply_cisd_selection_dipole_moment_z
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_dipole_moment_z_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L4633>`_
+h_apply_cisd_selection_dipole_moment_z_diexc
+  Undocumented
+
+
+h_apply_cisd_selection_dipole_moment_z_diexcorg
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_dipole_moment_z_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L4962>`_
+h_apply_cisd_selection_dipole_moment_z_diexcp
+  Undocumented
+
+
+h_apply_cisd_selection_dipole_moment_z_monoexc
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L3615>`_
+h_apply_cisd_selection_epstein_nesbet
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_epstein_nesbet_2x2 <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L4387>`_
+h_apply_cisd_selection_epstein_nesbet_2x2
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_epstein_nesbet_2x2_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L3861>`_
+h_apply_cisd_selection_epstein_nesbet_2x2_diexc
+  Undocumented
+
+
+h_apply_cisd_selection_epstein_nesbet_2x2_diexcorg
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_2x2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L4190>`_
+h_apply_cisd_selection_epstein_nesbet_2x2_diexcp
+  Undocumented
+
+
+h_apply_cisd_selection_epstein_nesbet_2x2_monoexc
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L3089>`_
+h_apply_cisd_selection_epstein_nesbet_diexc
+  Undocumented
+
+
+h_apply_cisd_selection_epstein_nesbet_diexcorg
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L3418>`_
+h_apply_cisd_selection_epstein_nesbet_diexcp
+  Undocumented
+
+
+h_apply_cisd_selection_epstein_nesbet_monoexc
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2 <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L2843>`_
+h_apply_cisd_selection_epstein_nesbet_sc2
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L2317>`_
+h_apply_cisd_selection_epstein_nesbet_sc2_diexc
+  Undocumented
+
+
+h_apply_cisd_selection_epstein_nesbet_sc2_diexcorg
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L2646>`_
+h_apply_cisd_selection_epstein_nesbet_sc2_diexcp
+  Undocumented
+
+
+h_apply_cisd_selection_epstein_nesbet_sc2_monoexc
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_no_projected <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L2071>`_
+h_apply_cisd_selection_epstein_nesbet_sc2_no_projected
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_no_projected_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L1545>`_
+h_apply_cisd_selection_epstein_nesbet_sc2_no_projected_diexc
+  Undocumented
+
+
+h_apply_cisd_selection_epstein_nesbet_sc2_no_projected_diexcorg
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_no_projected_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L1874>`_
+h_apply_cisd_selection_epstein_nesbet_sc2_no_projected_diexcp
+  Undocumented
+
+
+h_apply_cisd_selection_epstein_nesbet_sc2_no_projected_monoexc
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_projected <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L1299>`_
+h_apply_cisd_selection_epstein_nesbet_sc2_projected
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_projected_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L773>`_
+h_apply_cisd_selection_epstein_nesbet_sc2_projected_diexc
+  Undocumented
+
+
+h_apply_cisd_selection_epstein_nesbet_sc2_projected_diexcorg
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_projected_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L1102>`_
+h_apply_cisd_selection_epstein_nesbet_sc2_projected_diexcp
+  Undocumented
+
+
+h_apply_cisd_selection_epstein_nesbet_sc2_projected_monoexc
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_h_core <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L527>`_
+h_apply_cisd_selection_h_core
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_h_core_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L1>`_
+h_apply_cisd_selection_h_core_diexc
+  Undocumented
+
+
+h_apply_cisd_selection_h_core_diexcorg
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_h_core_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L330>`_
+h_apply_cisd_selection_h_core_diexcp
+  Undocumented
+
+
+h_apply_cisd_selection_h_core_monoexc
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_moller_plesset <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L6703>`_
+h_apply_cisd_selection_moller_plesset
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_moller_plesset_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L6177>`_
+h_apply_cisd_selection_moller_plesset_diexc
+  Undocumented
+
+
+h_apply_cisd_selection_moller_plesset_diexcorg
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_moller_plesset_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L6506>`_
+h_apply_cisd_selection_moller_plesset_diexcp
+  Undocumented
+
+
+h_apply_cisd_selection_moller_plesset_monoexc
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.

plugins/DDCI_selected/README.rst

@@ -57,3 +57,74 @@ Needed Modules
 * `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
 * `Generators_CAS <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_CAS>`_
 
+Needed Modules
+==============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
+.. image:: tree_dependency.png
+
+* `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation>`_
+* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/plugins/Selectors_full>`_
+* `Generators_CAS <http://github.com/LCPQ/quantum_package/tree/master/plugins/Generators_CAS>`_
+
+Documentation
+=============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
+`ddci <http://github.com/LCPQ/quantum_package/tree/master/plugins/DDCI_selected/ddci.irp.f#L1>`_
+  Undocumented
+
+
+h_apply_ddci_pt2
+  Calls H_apply on the HF determinant and selects all connected single and double
+  excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
+
+
+h_apply_ddci_pt2_diexc
+  Undocumented
+
+
+h_apply_ddci_pt2_diexcorg
+  Generate all double excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+h_apply_ddci_pt2_diexcp
+  Undocumented
+
+
+h_apply_ddci_pt2_monoexc
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+h_apply_ddci_selection
+  Calls H_apply on the HF determinant and selects all connected single and double
+  excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
+
+
+h_apply_ddci_selection_diexc
+  Undocumented
+
+
+h_apply_ddci_selection_diexcorg
+  Generate all double excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+h_apply_ddci_selection_diexcp
+  Undocumented
+
+
+h_apply_ddci_selection_monoexc
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+

plugins/Full_CI/.gitignore

@@ -0,0 +1,32 @@
+# Automatically created by $QP_ROOT/scripts/module/module_handler.py 
+.ninja_deps
+.ninja_log
+AO_Basis
+Bitmask
+Determinants
+Electrons
+Ezfio_files
+Generators_full
+Hartree_Fock
+IRPF90_man
+IRPF90_temp
+Integrals_Bielec
+Integrals_Monoelec
+MOGuess
+MO_Basis
+Makefile
+Makefile.depend
+Nuclei
+Perturbation
+Properties
+Pseudo
+Selectors_full
+Utils
+ezfio_interface.irp.f
+full_ci
+full_ci_no_skip
+irpf90.make
+irpf90_entities
+tags
+target_pt2
+var_pt2_ratio

plugins/Full_CI/README.rst

@@ -23,209 +23,205 @@ Documentation
 .. by the `update_README.py` script.
 
 
-`e_curve <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/e_curve.irp.f#L1>`_
-  Undocumented
-
-
 `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#L674>`_
+h_apply_fci
   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#L3>`_
+h_apply_fci_diexc
   Undocumented
 
 
-`h_apply_fci_diexcorg <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L143>`_
+h_apply_fci_diexcorg
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_fci_diexcp <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L108>`_
+h_apply_fci_diexcp
   Undocumented
 
 
-`h_apply_fci_mono <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L3333>`_
+h_apply_fci_mono
   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#L2660>`_
+h_apply_fci_mono_diexc
   Undocumented
 
 
-`h_apply_fci_mono_diexcorg <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L2800>`_
+h_apply_fci_mono_diexcorg
   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_diexcp <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L2765>`_
+h_apply_fci_mono_diexcp
   Undocumented
 
 
-`h_apply_fci_mono_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L3129>`_
+h_apply_fci_mono_monoexc
   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#L472>`_
+h_apply_fci_monoexc
   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#L2439>`_
+h_apply_fci_no_skip
   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#L1768>`_
+h_apply_fci_no_skip_diexc
   Undocumented
 
 
-`h_apply_fci_no_skip_diexcorg <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L1908>`_
+h_apply_fci_no_skip_diexcorg
   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_diexcp <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L1873>`_
+h_apply_fci_no_skip_diexcp
   Undocumented
 
 
-`h_apply_fci_no_skip_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L2237>`_
+h_apply_fci_no_skip_monoexc
   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#L1558>`_
+h_apply_fci_pt2
   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#L923>`_
+h_apply_fci_pt2_diexc
   Undocumented
 
 
-`h_apply_fci_pt2_diexcorg <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L1061>`_
+h_apply_fci_pt2_diexcorg
   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_diexcp <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L1027>`_
+h_apply_fci_pt2_diexcp
   Undocumented
 
 
-`h_apply_fci_pt2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L1370>`_
+h_apply_fci_pt2_monoexc
   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#L5141>`_
+h_apply_pt2_mono_delta_rho
   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#L4504>`_
+h_apply_pt2_mono_delta_rho_diexc
   Undocumented
 
 
-`h_apply_pt2_mono_delta_rho_diexcorg <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L4642>`_
+h_apply_pt2_mono_delta_rho_diexcorg
   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_diexcp <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L4608>`_
+h_apply_pt2_mono_delta_rho_diexcp
   Undocumented
 
 
-`h_apply_pt2_mono_delta_rho_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L4951>`_
+h_apply_pt2_mono_delta_rho_monoexc
   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#L6906>`_
+h_apply_pt2_mono_di_delta_rho
   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#L6271>`_
+h_apply_pt2_mono_di_delta_rho_diexc
   Undocumented
 
 
-`h_apply_pt2_mono_di_delta_rho_diexcorg <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L6409>`_
+h_apply_pt2_mono_di_delta_rho_diexcorg
   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_diexcp <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L6375>`_
+h_apply_pt2_mono_di_delta_rho_diexcp
   Undocumented
 
 
-`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#L6718>`_
+h_apply_pt2_mono_di_delta_rho_monoexc
   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#L4255>`_
+h_apply_select_mono_delta_rho
   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#L3582>`_
+h_apply_select_mono_delta_rho_diexc
   Undocumented
 
 
-`h_apply_select_mono_delta_rho_diexcorg <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L3722>`_
+h_apply_select_mono_delta_rho_diexcorg
   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_diexcp <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L3687>`_
+h_apply_select_mono_delta_rho_diexcp
   Undocumented
 
 
-`h_apply_select_mono_delta_rho_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L4051>`_
+h_apply_select_mono_delta_rho_monoexc
   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#L6022>`_
+h_apply_select_mono_di_delta_rho
   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#L5351>`_
+h_apply_select_mono_di_delta_rho_diexc
   Undocumented
 
 
-`h_apply_select_mono_di_delta_rho_diexcorg <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L5491>`_
+h_apply_select_mono_di_delta_rho_diexcorg
   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_diexcp <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L5456>`_
+h_apply_select_mono_di_delta_rho_diexcp
   Undocumented
 
 
-`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#L5820>`_
+h_apply_select_mono_di_delta_rho_monoexc
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.

plugins/Hartree_Fock/.gitignore

@@ -21,5 +21,4 @@ Utils
 ezfio_interface.irp.f
 irpf90.make
 irpf90_entities
-simple_SCF
 tags

plugins/Hartree_Fock/README.rst

@@ -161,10 +161,6 @@ Documentation
   optional: mo_basis.mo_coef
 
 
-`simple_scf <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/simple_SCF.irp.f#L1>`_
-  Undocumented
-
-
 `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/MP2/README.rst

@@ -40,3 +40,49 @@ Needed Modules
 * `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
 * `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod>`_
 
+Needed Modules
+==============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
+.. image:: tree_dependency.png
+
+* `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation>`_
+* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/plugins/Selectors_full>`_
+* `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/plugins/SingleRefMethod>`_
+
+Documentation
+=============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
+h_apply_mp2
+  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_mp2_diexc
+  Undocumented
+
+
+h_apply_mp2_diexcorg
+  Generate all double excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+h_apply_mp2_diexcp
+  Undocumented
+
+
+h_apply_mp2_monoexc
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`mp2 <http://github.com/LCPQ/quantum_package/tree/master/plugins/MP2/mp2.irp.f#L1>`_
+  Undocumented
+

plugins/MRCC_Utils/README.rst

@@ -283,26 +283,26 @@ Documentation
   Undocumented
 
 
-`h_apply_mrcc <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/H_apply.irp.f_shell_27#L553>`_
+h_apply_mrcc
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_mrcc_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/H_apply.irp.f_shell_27#L3>`_
+h_apply_mrcc_diexc
   Undocumented
 
 
-`h_apply_mrcc_diexcorg <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/H_apply.irp.f_shell_27#L127>`_
+h_apply_mrcc_diexcorg
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_mrcc_diexcp <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/H_apply.irp.f_shell_27#L100>`_
+h_apply_mrcc_diexcp
   Undocumented
 
 
-`h_apply_mrcc_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/H_apply.irp.f_shell_27#L399>`_
+h_apply_mrcc_monoexc
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.

plugins/Molden/README.rst

@@ -38,3 +38,39 @@ Needed Modules
 * `MO_Basis <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis>`_
 * `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
+
+* `MO_Basis <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis>`_
+* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
+
+Documentation
+=============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
+`print_mos <http://github.com/LCPQ/quantum_package/tree/master/plugins/Molden/print_mo.irp.f#L1>`_
+  Undocumented
+
+
+`write_ao_basis <http://github.com/LCPQ/quantum_package/tree/master/plugins/Molden/print_mo.irp.f#L63>`_
+  Undocumented
+
+
+`write_geometry <http://github.com/LCPQ/quantum_package/tree/master/plugins/Molden/print_mo.irp.f#L45>`_
+  Undocumented
+
+
+`write_intro_gamess <http://github.com/LCPQ/quantum_package/tree/master/plugins/Molden/print_mo.irp.f#L26>`_
+  Undocumented
+
+
+`write_mo_basis <http://github.com/LCPQ/quantum_package/tree/master/plugins/Molden/print_mo.irp.f#L112>`_
+  Undocumented
+

plugins/Perturbation/README.rst

@@ -107,156 +107,92 @@ Documentation
   Undocumented
 
 
-`perturb_buffer_by_mono_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L791>`_
+perturb_buffer_by_mono_delta_rho_one_point
   Applly pertubration ``delta_rho_one_point`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-<<<<<<< HEAD
+perturb_buffer_by_mono_dipole_moment_z
-`perturb_buffer_by_mono_dipole_moment_z <http://github.com/LCPQ/quantum_package/tree/master/plugins/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#L266>`_
->>>>>>> 2d3ba8003b05cb406674cc93a9bfc917d94db7fc
   Applly pertubration ``dipole_moment_z`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-<<<<<<< HEAD
+perturb_buffer_by_mono_epstein_nesbet
-`perturb_buffer_by_mono_epstein_nesbet <http://github.com/LCPQ/quantum_package/tree/master/plugins/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#L371>`_
->>>>>>> 2d3ba8003b05cb406674cc93a9bfc917d94db7fc
   Applly pertubration ``epstein_nesbet`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-<<<<<<< HEAD
+perturb_buffer_by_mono_epstein_nesbet_2x2
-`perturb_buffer_by_mono_epstein_nesbet_2x2 <http://github.com/LCPQ/quantum_package/tree/master/plugins/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#L476>`_
->>>>>>> 2d3ba8003b05cb406674cc93a9bfc917d94db7fc
   Applly pertubration ``epstein_nesbet_2x2`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-<<<<<<< HEAD
+perturb_buffer_by_mono_epstein_nesbet_sc2
-`perturb_buffer_by_mono_epstein_nesbet_sc2 <http://github.com/LCPQ/quantum_package/tree/master/plugins/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#L791>`_
->>>>>>> 2d3ba8003b05cb406674cc93a9bfc917d94db7fc
   Applly pertubration ``epstein_nesbet_sc2`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-<<<<<<< HEAD
+perturb_buffer_by_mono_epstein_nesbet_sc2_no_projected
-`perturb_buffer_by_mono_epstein_nesbet_sc2_no_projected <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L266>`_
-=======
-`perturb_buffer_by_mono_epstein_nesbet_sc2_no_projected <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L686>`_
->>>>>>> 2d3ba8003b05cb406674cc93a9bfc917d94db7fc
   Applly pertubration ``epstein_nesbet_sc2_no_projected`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-<<<<<<< HEAD
+perturb_buffer_by_mono_epstein_nesbet_sc2_projected
-`perturb_buffer_by_mono_epstein_nesbet_sc2_projected <http://github.com/LCPQ/quantum_package/tree/master/plugins/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#L581>`_
->>>>>>> 2d3ba8003b05cb406674cc93a9bfc917d94db7fc
   Applly pertubration ``epstein_nesbet_sc2_projected`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-<<<<<<< HEAD
+perturb_buffer_by_mono_h_core
-`perturb_buffer_by_mono_h_core <http://github.com/LCPQ/quantum_package/tree/master/plugins/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#L896>`_
->>>>>>> 2d3ba8003b05cb406674cc93a9bfc917d94db7fc
   Applly pertubration ``h_core`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-<<<<<<< HEAD
+perturb_buffer_by_mono_moller_plesset
-`perturb_buffer_by_mono_moller_plesset <http://github.com/LCPQ/quantum_package/tree/master/plugins/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>`_
->>>>>>> 2d3ba8003b05cb406674cc93a9bfc917d94db7fc
   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/plugins/Perturbation/perturbation.irp.f_shell_13#L740>`_
+perturb_buffer_delta_rho_one_point
   Applly pertubration ``delta_rho_one_point`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-<<<<<<< HEAD
+perturb_buffer_dipole_moment_z
-`perturb_buffer_dipole_moment_z <http://github.com/LCPQ/quantum_package/tree/master/plugins/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#L215>`_
->>>>>>> 2d3ba8003b05cb406674cc93a9bfc917d94db7fc
   Applly pertubration ``dipole_moment_z`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-<<<<<<< HEAD
+perturb_buffer_epstein_nesbet
-`perturb_buffer_epstein_nesbet <http://github.com/LCPQ/quantum_package/tree/master/plugins/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#L320>`_
->>>>>>> 2d3ba8003b05cb406674cc93a9bfc917d94db7fc
   Applly pertubration ``epstein_nesbet`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-<<<<<<< HEAD
+perturb_buffer_epstein_nesbet_2x2
-`perturb_buffer_epstein_nesbet_2x2 <http://github.com/LCPQ/quantum_package/tree/master/plugins/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#L425>`_
->>>>>>> 2d3ba8003b05cb406674cc93a9bfc917d94db7fc
   Applly pertubration ``epstein_nesbet_2x2`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-<<<<<<< HEAD
+perturb_buffer_epstein_nesbet_sc2
-`perturb_buffer_epstein_nesbet_sc2 <http://github.com/LCPQ/quantum_package/tree/master/plugins/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#L740>`_
->>>>>>> 2d3ba8003b05cb406674cc93a9bfc917d94db7fc
   Applly pertubration ``epstein_nesbet_sc2`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-<<<<<<< HEAD
+perturb_buffer_epstein_nesbet_sc2_no_projected
-`perturb_buffer_epstein_nesbet_sc2_no_projected <http://github.com/LCPQ/quantum_package/tree/master/plugins/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#L635>`_
->>>>>>> 2d3ba8003b05cb406674cc93a9bfc917d94db7fc
   Applly pertubration ``epstein_nesbet_sc2_no_projected`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-<<<<<<< HEAD
+perturb_buffer_epstein_nesbet_sc2_projected
-`perturb_buffer_epstein_nesbet_sc2_projected <http://github.com/LCPQ/quantum_package/tree/master/plugins/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#L530>`_
->>>>>>> 2d3ba8003b05cb406674cc93a9bfc917d94db7fc
   Applly pertubration ``epstein_nesbet_sc2_projected`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-<<<<<<< HEAD
+perturb_buffer_h_core
-`perturb_buffer_h_core <http://github.com/LCPQ/quantum_package/tree/master/plugins/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#L845>`_
->>>>>>> 2d3ba8003b05cb406674cc93a9bfc917d94db7fc
   Applly pertubration ``h_core`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-<<<<<<< HEAD
+perturb_buffer_moller_plesset
-`perturb_buffer_moller_plesset <http://github.com/LCPQ/quantum_package/tree/master/plugins/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>`_
->>>>>>> 2d3ba8003b05cb406674cc93a9bfc917d94db7fc
   Applly pertubration ``moller_plesset`` to the buffer of determinants generated in the H_apply
   routine.
 

plugins/QmcChem/.gitignore

@@ -16,11 +16,9 @@ Makefile.depend
 Nuclei
 Pseudo
 Utils
-e_curve_qmc
 ezfio_interface.irp.f
 irpf90.make
 irpf90_entities
 save_for_qmcchem
 tags
-target_pt2_qmc
+target_pt2_qmc
-test

plugins/QmcChem/README.rst

@@ -70,7 +70,7 @@ Documentation
   Compute an energy when a threshold is applied
 
 
-`e_curve <http://github.com/LCPQ/quantum_package/tree/master/plugins/QmcChem/test.irp.f#L1>`_
+`e_curve <http://github.com/LCPQ/quantum_package/tree/master/plugins/QmcChem/target_pt2_qmc.irp.f#L1>`_
   Undocumented
 
 

plugins/loc_cele/README.rst

@@ -20,3 +20,25 @@ Needed Modules
 
 * `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
+.. by the `update_README.py` script.
+
+
+`loc_rasorb <http://github.com/LCPQ/quantum_package/tree/master/plugins/loc_cele/loc_cele.irp.f#L1>`_
+  This program performs a localization of the active orbitals
+  of a CASSCF wavefunction, reading the orbitals from a RASORB
+  file of molcas.
+  id1=max is the number of MO in a given symmetry.
+

plugins/loc_cele/loc_cele.irp.f

@@ -280,7 +280,7 @@
 
       enddo !big loop over symmetry
 
-      10 format (4E18.12)
+      10 format (4E20.12)
 
 
 !  Now we copyt the newcmo into the mo_coef

scripts/module/qp_update_readme.py

@@ -44,7 +44,7 @@ def get_url(path_module_rel):
     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)
+        print "{0} Is not a valid module nor plugin".format(path_module_rel)
         sys.exit(1)
 
     return os.path.join(url, path_module_rel)
@@ -155,13 +155,18 @@ def update_documentation(d_readmen, root_module):
         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),
+            if ".irp.f_shell_" in irp.file:
-                      doc,
+                print irp.file
-                      ""]
+                l_doc += ["{0}".format(irp.provider),
+                          doc,
+                          ""]
+            else:
+                l_doc += ["`{0} <{1}#L{2}>`_".format(irp.provider, url, irp.line),
+                          doc,
+                          ""]
 
         l_doc_section = [D_KEY["documentation"], '',
                          "\n".join(l_doc)]
@@ -196,8 +201,8 @@ if __name__ == '__main__':
         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 "has not a `README.rst` file inside"
-        print "Abort..."
+        print "Aborting..."
         sys.exit(1)
 
     update_needed(d_readme)

src/Determinants/README.rst

@@ -314,21 +314,7 @@ Documentation
   to repeat the excitations
 
 
-<<<<<<< HEAD
-`filter_connected_sorted_ab <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/filter_connected.irp.f#L101>`_
-  Filters out the determinants that are not connected by H
-  returns the array idx which contains the index of the
-  determinants in the array key1 that interact
-  via the H operator with key2.
-  idx(0) is the number of determinants that interact with key1
-  .br
-  Determinants are taken from the psi_det_sorted_ab array
-
-
 `generate_all_alpha_beta_det_products <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L500>`_
-=======
-`generate_all_alpha_beta_det_products <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L472>`_
->>>>>>> 2d3ba8003b05cb406674cc93a9bfc917d94db7fc
   Create a wave function from all possible alpha x beta determinants
 
 
@@ -891,13 +877,12 @@ Documentation
   Weights in the state-average calculation of the density matrix
 
 
-<<<<<<< HEAD
-`target_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/ezfio_interface.irp.f#L160>`_
-  Energy that should be obtained when truncating the wave function (optional)
-=======
 `tamiser <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/davidson.irp.f#L91>`_
   Undocumented
->>>>>>> 2d3ba8003b05cb406674cc93a9bfc917d94db7fc
+
+
+`target_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/ezfio_interface.irp.f#L160>`_
+  Energy that should be obtained when truncating the wave function (optional)
 
 
 `threshold_convergence_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/diagonalize_CI_SC2.irp.f#L18>`_

src/Ezfio_files/README.rst

@@ -195,95 +195,147 @@ Documentation
   .br
 
 
-`output_ao_basis <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L1>`_
+output_ao_basis
   Output file for AO_Basis
 
 
-`output_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L21>`_
+output_bitmask
   Output file for Bitmask
 
 
+output_cas_sd
+  Output file for CAS_SD
+
+
+output_cid
+  Output file for CID
+
+
+output_cisd
+  Output file for CISD
+
+
+output_cisd_sc2_selected
+  Output file for CISD_SC2_selected
+
+
+output_cisd_selected
+  Output file for CISD_selected
+
+
 `output_cpu_time_0 <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f#L2>`_
   Initial CPU and wall times when printing in the output files
 
 
-`output_determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L41>`_
+output_ddci_selected
+  Output file for DDCI_selected
+
+
+output_determinants
   Output file for Determinants
 
 
-`output_electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L61>`_
+output_electrons
   Output file for Electrons
 
 
-`output_ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L81>`_
+output_ezfio_files
   Output file for Ezfio_files
 
 
-`output_full_ci <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L101>`_
+output_fcidump
+  Output file for FCIdump
+
+
+output_full_ci
   Output file for Full_CI
 
 
-`output_generators_full <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L121>`_
+output_generators_cas
+  Output file for Generators_CAS
+
+
+output_generators_full
   Output file for Generators_full
 
 
-`output_hartree_fock <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L141>`_
+output_hartree_fock
   Output file for Hartree_Fock
 
 
-`output_integrals_bielec <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L161>`_
+output_integrals_bielec
   Output file for Integrals_Bielec
 
 
-`output_integrals_monoelec <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L181>`_
+output_integrals_monoelec
   Output file for Integrals_Monoelec
 
 
-`output_mo_basis <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L201>`_
+output_loc_cele
+  Output file for loc_cele
+
+
+output_mo_basis
   Output file for MO_Basis
 
 
-`output_moguess <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L221>`_
+output_moguess
   Output file for MOGuess
 
 
-`output_mrcc_cassd <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L241>`_
+output_molden
+  Output file for Molden
+
+
+output_mp2
+  Output file for MP2
+
+
+output_mrcc_cassd
   Output file for MRCC_CASSD
 
 
-`output_mrcc_utils <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L261>`_
+output_mrcc_utils
   Output file for MRCC_Utils
 
 
-`output_nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L281>`_
+output_nuclei
   Output file for Nuclei
 
 
-`output_perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L301>`_
+output_perturbation
   Output file for Perturbation
 
 
-`output_properties <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L321>`_
+output_properties
   Output file for Properties
 
 
-`output_pseudo <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L341>`_
+output_pseudo
   Output file for Pseudo
 
 
-`output_psiref_cas <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L361>`_
+output_psiref_cas
   Output file for Psiref_CAS
 
 
-`output_psiref_utils <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L381>`_
+output_psiref_utils
   Output file for Psiref_Utils
 
 
-`output_selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L401>`_
+output_qmcchem
+  Output file for QmcChem
+
+
+output_selectors_full
   Output file for Selectors_full
 
 
-`output_utils <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L421>`_
+output_singlerefmethod
+  Output file for SingleRefMethod
+
+
+output_utils
   Output file for Utils