Update readme

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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/CID/H_apply.irp.f_shell_8#L537>`_
+  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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/CID/H_apply.irp.f_shell_8#L3>`_
+  Undocumented
+
+
+`h_apply_cid_diexcorg <http://github.com/LCPQ/quantum_package/tree/master/plugins/CID/H_apply.irp.f_shell_8#L119>`_
+  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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/CID/H_apply.irp.f_shell_8#L96>`_
+  Undocumented
+
+
+`h_apply_cid_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CID/H_apply.irp.f_shell_8#L387>`_
+  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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD/H_apply.irp.f_shell_8#L537>`_
   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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD/H_apply.irp.f_shell_8#L3>`_
+  Undocumented
+
+
+`h_apply_cisd_diexcorg <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD/H_apply.irp.f_shell_8#L119>`_
   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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD/H_apply.irp.f_shell_8#L96>`_
+  Undocumented
+
+
+`h_apply_cisd_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD/H_apply.irp.f_shell_8#L387>`_
   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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_SC2_selected/H_apply.irp.f_shell_8#L537>`_
+  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_SC2_selected/H_apply.irp.f_shell_8#L3>`_
+  Undocumented
+
+
+`h_apply_cisd_diexcorg <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_SC2_selected/H_apply.irp.f_shell_8#L119>`_
+  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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_SC2_selected/H_apply.irp.f_shell_8#L96>`_
+  Undocumented
+
+
+`h_apply_cisd_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_SC2_selected/H_apply.irp.f_shell_8#L387>`_
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_pt2 <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_SC2_selected/H_apply.irp.f_shell_17#L1562>`_
+  Calls H_apply on the HF determinant and selects all connected single and double
+  excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
+
+
+`h_apply_pt2_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_SC2_selected/H_apply.irp.f_shell_17#L925>`_
+  Undocumented
+
+
+`h_apply_pt2_diexcorg <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_SC2_selected/H_apply.irp.f_shell_17#L1063>`_
+  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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_SC2_selected/H_apply.irp.f_shell_17#L1029>`_
+  Undocumented
+
+
+`h_apply_pt2_en_sc2 <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_SC2_selected/H_apply.irp.f_shell_17#L2409>`_
+  Calls H_apply on the HF determinant and selects all connected single and double
+  excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
+
+
+`h_apply_pt2_en_sc2_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_SC2_selected/H_apply.irp.f_shell_17#L1772>`_
+  Undocumented
+
+
+`h_apply_pt2_en_sc2_diexcorg <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_SC2_selected/H_apply.irp.f_shell_17#L1910>`_
+  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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_SC2_selected/H_apply.irp.f_shell_17#L1876>`_
+  Undocumented
+
+
+`h_apply_pt2_en_sc2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_SC2_selected/H_apply.irp.f_shell_17#L2221>`_
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_pt2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_SC2_selected/H_apply.irp.f_shell_17#L1374>`_
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_sc2_selected <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_SC2_selected/H_apply.irp.f_shell_17#L676>`_
+  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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_SC2_selected/H_apply.irp.f_shell_17#L3>`_
+  Undocumented
+
+
+`h_apply_sc2_selected_diexcorg <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_SC2_selected/H_apply.irp.f_shell_17#L143>`_
+  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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_SC2_selected/H_apply.irp.f_shell_17#L108>`_
+  Undocumented
+
+
+`h_apply_sc2_selected_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_SC2_selected/H_apply.irp.f_shell_17#L474>`_
+  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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_8#L537>`_
-  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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_8#L3>`_
+  Undocumented
+
+
+`h_apply_cisd_diexcorg <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_8#L119>`_
   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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_8#L96>`_
+  Undocumented
+
+
+`h_apply_cisd_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_8#L387>`_
   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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L1594>`_
   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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L923>`_
+  Undocumented
+
+
+`h_apply_cisd_selection_delta_rho_one_point_diexcorg <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L1063>`_
   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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L1028>`_
+  Undocumented
+
+
+`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#L1392>`_
   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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L674>`_
   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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L3>`_
+  Undocumented
+
+
+`h_apply_cisd_selection_dipole_moment_z_diexcorg <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L143>`_
   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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L108>`_
+  Undocumented
+
+
+`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#L472>`_
   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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L2514>`_
   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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L3434>`_
   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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L2763>`_
+  Undocumented
+
+
+`h_apply_cisd_selection_epstein_nesbet_2x2_diexcorg <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L2903>`_
   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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L2868>`_
+  Undocumented
+
+
+`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#L3232>`_
   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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L1843>`_
+  Undocumented
+
+
+`h_apply_cisd_selection_epstein_nesbet_diexcorg <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L1983>`_
   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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L1948>`_
+  Undocumented
+
+
+`h_apply_cisd_selection_epstein_nesbet_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L2312>`_
   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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L8034>`_
   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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L7363>`_
+  Undocumented
+
+
+`h_apply_cisd_selection_epstein_nesbet_sc2_diexcorg <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L7503>`_
   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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L7468>`_
+  Undocumented
+
+
+`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#L7832>`_
   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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L7114>`_
   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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L6443>`_
+  Undocumented
+
+
+`h_apply_cisd_selection_epstein_nesbet_sc2_no_projected_diexcorg <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L6583>`_
   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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L6548>`_
+  Undocumented
+
+
+`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#L6912>`_
   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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L6194>`_
   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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L5523>`_
+  Undocumented
+
+
+`h_apply_cisd_selection_epstein_nesbet_sc2_projected_diexcorg <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L5663>`_
   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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L5628>`_
+  Undocumented
+
+
+`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#L5992>`_
   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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L4354>`_
   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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L3683>`_
+  Undocumented
+
+
+`h_apply_cisd_selection_h_core_diexcorg <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L3823>`_
   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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L3788>`_
+  Undocumented
+
+
+`h_apply_cisd_selection_h_core_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L4152>`_
   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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L5274>`_
   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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L4603>`_
+  Undocumented
+
+
+`h_apply_cisd_selection_moller_plesset_diexcorg <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L4743>`_
   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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L4708>`_
+  Undocumented
+
+
+`h_apply_cisd_selection_moller_plesset_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L5072>`_
   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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/DDCI_selected/H_apply.irp.f_shell_15#L1576>`_
+  Calls H_apply on the HF determinant and selects all connected single and double
+  excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
+
+
+`h_apply_ddci_pt2_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/DDCI_selected/H_apply.irp.f_shell_15#L932>`_
+  Undocumented
+
+
+`h_apply_ddci_pt2_diexcorg <http://github.com/LCPQ/quantum_package/tree/master/plugins/DDCI_selected/H_apply.irp.f_shell_15#L1070>`_
+  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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/DDCI_selected/H_apply.irp.f_shell_15#L1036>`_
+  Undocumented
+
+
+`h_apply_ddci_pt2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/DDCI_selected/H_apply.irp.f_shell_15#L1385>`_
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_ddci_selection <http://github.com/LCPQ/quantum_package/tree/master/plugins/DDCI_selected/H_apply.irp.f_shell_15#L683>`_
+  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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/DDCI_selected/H_apply.irp.f_shell_15#L3>`_
+  Undocumented
+
+
+`h_apply_ddci_selection_diexcorg <http://github.com/LCPQ/quantum_package/tree/master/plugins/DDCI_selected/H_apply.irp.f_shell_15#L143>`_
+  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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/DDCI_selected/H_apply.irp.f_shell_15#L108>`_
+  Undocumented
+
+
+`h_apply_ddci_selection_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/DDCI_selected/H_apply.irp.f_shell_15#L478>`_
+  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

@@ -23,10 +23,6 @@ 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
 

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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/MP2/H_apply.irp.f_shell_9#L638>`_
+  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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/MP2/H_apply.irp.f_shell_9#L3>`_
+  Undocumented
+
+
+`h_apply_mp2_diexcorg <http://github.com/LCPQ/quantum_package/tree/master/plugins/MP2/H_apply.irp.f_shell_9#L141>`_
+  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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/MP2/H_apply.irp.f_shell_9#L107>`_
+  Undocumented
+
+
+`h_apply_mp2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/MP2/H_apply.irp.f_shell_9#L450>`_
+  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/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 <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.
 
 
-<<<<<<< HEAD
+`perturb_buffer_by_mono_dipole_moment_z <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L56>`_
-`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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L266>`_
-`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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L371>`_
-`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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L896>`_
-`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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L791>`_
-`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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L686>`_
-`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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L476>`_
-`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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L581>`_
-`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 <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.
 
 
-<<<<<<< HEAD
+`perturb_buffer_dipole_moment_z <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L5>`_
-`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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L215>`_
-`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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L320>`_
-`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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L845>`_
-`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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L740>`_
-`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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L635>`_
-`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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L425>`_
-`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 <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L530>`_
-`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
-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.
+

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

@@ -203,87 +203,139 @@ Documentation
   Output file for Bitmask
 
 
+`output_cas_sd <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L41>`_
+  Output file for CAS_SD
+
+
+`output_cid <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L61>`_
+  Output file for CID
+
+
+`output_cisd <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L81>`_
+  Output file for CISD
+
+
+`output_cisd_sc2_selected <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L101>`_
+  Output file for CISD_SC2_selected
+
+
+`output_cisd_selected <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L121>`_
+  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 <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L141>`_
+  Output file for DDCI_selected
+
+
+`output_determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L161>`_
   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 <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L181>`_
   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 <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L201>`_
   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 <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L221>`_
+  Output file for FCIdump
+
+
+`output_full_ci <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L241>`_
   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 <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L261>`_
+  Output file for Generators_CAS
+
+
+`output_generators_full <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L281>`_
   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 <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L301>`_
   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 <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L321>`_
   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 <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L341>`_
   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 <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L361>`_
+  Output file for loc_cele
+
+
+`output_mo_basis <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L381>`_
   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 <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L401>`_
   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 <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L421>`_
+  Output file for Molden
+
+
+`output_mp2 <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L441>`_
+  Output file for MP2
+
+
+`output_mrcc_cassd <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L461>`_
   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 <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L481>`_
   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 <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L501>`_
   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 <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L521>`_
   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 <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L541>`_
   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 <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L561>`_
   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 <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L581>`_
   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 <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L601>`_
   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 <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L621>`_
+  Output file for QmcChem
+
+
+`output_selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L641>`_
   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 <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L661>`_
+  Output file for SingleRefMethod
+
+
+`output_utils <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L681>`_
   Output file for Utils