Going back to png

plugins/Alavi/README.rst

@@ -17,7 +17,7 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. by the `update_README.py` script.
 
-.. image:: tree_dependency.pdf
+.. image:: tree_dependency.png
 
 * `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
 

plugins/CAS_SD/README.rst

@@ -17,7 +17,7 @@ Documentation
   Undocumented
 
 
-`h_apply_cas_sd <http://github.com/LCPQ/quantum_package/tree/master/src/CAS_SD/H_apply.irp.f_shell_16#L406>`_
+`h_apply_cas_sd <http://github.com/LCPQ/quantum_package/tree/master/src/CAS_SD/H_apply.irp.f_shell_16#L408>`_
   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.
 
@@ -28,41 +28,41 @@ Documentation
   Assume N_int is already provided.
 
 
-`h_apply_cas_sd_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CAS_SD/H_apply.irp.f_shell_16#L263>`_
+`h_apply_cas_sd_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CAS_SD/H_apply.irp.f_shell_16#L264>`_
   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/src/CAS_SD/H_apply.irp.f_shell_16#L1842>`_
+`h_apply_cas_sd_pt2 <http://github.com/LCPQ/quantum_package/tree/master/src/CAS_SD/H_apply.irp.f_shell_16#L1848>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cas_sd_pt2_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CAS_SD/H_apply.irp.f_shell_16#L1358>`_
+`h_apply_cas_sd_pt2_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CAS_SD/H_apply.irp.f_shell_16#L1362>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cas_sd_pt2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CAS_SD/H_apply.irp.f_shell_16#L1661>`_
+`h_apply_cas_sd_pt2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CAS_SD/H_apply.irp.f_shell_16#L1666>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cas_sd_selected <http://github.com/LCPQ/quantum_package/tree/master/src/CAS_SD/H_apply.irp.f_shell_16#L1112>`_
+`h_apply_cas_sd_selected <http://github.com/LCPQ/quantum_package/tree/master/src/CAS_SD/H_apply.irp.f_shell_16#L1116>`_
   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/src/CAS_SD/H_apply.irp.f_shell_16#L594>`_
+`h_apply_cas_sd_selected_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CAS_SD/H_apply.irp.f_shell_16#L596>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cas_sd_selected_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CAS_SD/H_apply.irp.f_shell_16#L917>`_
+`h_apply_cas_sd_selected_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CAS_SD/H_apply.irp.f_shell_16#L920>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.

plugins/CID/.gitignore

@@ -6,7 +6,6 @@ tags
 irpf90.make
 Makefile
 Makefile.depend
-build.ninja
 .ninja_log
 .ninja_deps
 ezfio_interface.irp.f

plugins/CID/README.rst

@@ -30,7 +30,7 @@ Documentation
   Undocumented
 
 
-`h_apply_cid <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_8#L406>`_
+`h_apply_cid <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_8#L408>`_
   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.
 
@@ -41,7 +41,7 @@ Documentation
   Assume N_int is already provided.
 
 
-`h_apply_cid_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_8#L263>`_
+`h_apply_cid_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_8#L264>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
@@ -51,143 +51,143 @@ Documentation
   Undocumented
 
 
-`h_apply_cisd_selection_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L1283>`_
+`h_apply_cisd_selection_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L1287>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_delta_rho_one_point_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L765>`_
+`h_apply_cisd_selection_delta_rho_one_point_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L767>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_delta_rho_one_point_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L1088>`_
+`h_apply_cisd_selection_delta_rho_one_point_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L1091>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_dipole_moment_z <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L6631>`_
+`h_apply_cisd_selection_dipole_moment_z <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L6649>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_dipole_moment_z_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L6113>`_
+`h_apply_cisd_selection_dipole_moment_z_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L6129>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_dipole_moment_z_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L6436>`_
+`h_apply_cisd_selection_dipole_moment_z_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L6453>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L5103>`_
+`h_apply_cisd_selection_epstein_nesbet <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L5117>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_epstein_nesbet_2x2 <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L5867>`_
+`h_apply_cisd_selection_epstein_nesbet_2x2 <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L5883>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_epstein_nesbet_2x2_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L5349>`_
+`h_apply_cisd_selection_epstein_nesbet_2x2_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L5363>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_2x2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L5672>`_
+`h_apply_cisd_selection_epstein_nesbet_2x2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L5687>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L4585>`_
+`h_apply_cisd_selection_epstein_nesbet_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L4597>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L4908>`_
+`h_apply_cisd_selection_epstein_nesbet_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L4921>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L4339>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L4351>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L3821>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L3831>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L4144>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L4155>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_no_projected <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L3575>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2_no_projected <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L3585>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_no_projected_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L3057>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2_no_projected_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L3065>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_no_projected_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L3380>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2_no_projected_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L3389>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_projected <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L2811>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2_projected <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L2819>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_projected_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L2293>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2_projected_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L2299>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_projected_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L2616>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2_projected_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L2623>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_h_core <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L2047>`_
+`h_apply_cisd_selection_h_core <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L2053>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_h_core_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L1529>`_
+`h_apply_cisd_selection_h_core_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L1533>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_h_core_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L1852>`_
+`h_apply_cisd_selection_h_core_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L1857>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_moller_plesset <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L519>`_
+`h_apply_cisd_selection_moller_plesset <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L521>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
@@ -198,7 +198,7 @@ Documentation
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_moller_plesset_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L324>`_
+`h_apply_cisd_selection_moller_plesset_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_10#L325>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.

plugins/CID_SC2_selected/README.rst

@@ -12,7 +12,7 @@ Documentation
   Undocumented
 
 
-`h_apply_pt2 <http://github.com/LCPQ/quantum_package/tree/master/src/CID_SC2_selected/H_apply.irp.f_shell_9#L487>`_
+`h_apply_pt2 <http://github.com/LCPQ/quantum_package/tree/master/src/CID_SC2_selected/H_apply.irp.f_shell_9#L489>`_
   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.
 
@@ -23,7 +23,7 @@ Documentation
   Assume N_int is already provided.
 
 
-`h_apply_pt2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_SC2_selected/H_apply.irp.f_shell_9#L306>`_
+`h_apply_pt2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_SC2_selected/H_apply.irp.f_shell_9#L307>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.

plugins/CID_selected/.gitignore

@@ -6,7 +6,6 @@ tags
 irpf90.make
 Makefile
 Makefile.depend
-build.ninja
 .ninja_log
 .ninja_deps
 ezfio_interface.irp.f

plugins/CID_selected/README.rst

@@ -12,143 +12,143 @@ Documentation
   Undocumented
 
 
-`h_apply_cisd_selection_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L1283>`_
+`h_apply_cisd_selection_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L1287>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_delta_rho_one_point_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L765>`_
+`h_apply_cisd_selection_delta_rho_one_point_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L767>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_delta_rho_one_point_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L1088>`_
+`h_apply_cisd_selection_delta_rho_one_point_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L1091>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_dipole_moment_z <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L6631>`_
+`h_apply_cisd_selection_dipole_moment_z <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L6649>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_dipole_moment_z_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L6113>`_
+`h_apply_cisd_selection_dipole_moment_z_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L6129>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_dipole_moment_z_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L6436>`_
+`h_apply_cisd_selection_dipole_moment_z_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L6453>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L5103>`_
+`h_apply_cisd_selection_epstein_nesbet <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L5117>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_epstein_nesbet_2x2 <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L5867>`_
+`h_apply_cisd_selection_epstein_nesbet_2x2 <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L5883>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_epstein_nesbet_2x2_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L5349>`_
+`h_apply_cisd_selection_epstein_nesbet_2x2_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L5363>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_2x2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L5672>`_
+`h_apply_cisd_selection_epstein_nesbet_2x2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L5687>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L4585>`_
+`h_apply_cisd_selection_epstein_nesbet_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L4597>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L4908>`_
+`h_apply_cisd_selection_epstein_nesbet_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L4921>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L4339>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L4351>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L3821>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L3831>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L4144>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L4155>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_no_projected <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L3575>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2_no_projected <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L3585>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_no_projected_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L3057>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2_no_projected_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L3065>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_no_projected_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L3380>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2_no_projected_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L3389>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_projected <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L2811>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2_projected <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L2819>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_projected_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L2293>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2_projected_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L2299>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_projected_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L2616>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2_projected_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L2623>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_h_core <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L2047>`_
+`h_apply_cisd_selection_h_core <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L2053>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_h_core_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L1529>`_
+`h_apply_cisd_selection_h_core_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L1533>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_h_core_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L1852>`_
+`h_apply_cisd_selection_h_core_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L1857>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_moller_plesset <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L519>`_
+`h_apply_cisd_selection_moller_plesset <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L521>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
@@ -159,7 +159,7 @@ Documentation
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_moller_plesset_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L324>`_
+`h_apply_cisd_selection_moller_plesset_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f_shell_10#L325>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.

plugins/CIS/README.rst

@@ -17,7 +17,7 @@ Documentation
   Undocumented
 
 
-`h_apply_cis <http://github.com/LCPQ/quantum_package/tree/master/src/CIS/H_apply.irp.f_shell_8#L406>`_
+`h_apply_cis <http://github.com/LCPQ/quantum_package/tree/master/src/CIS/H_apply.irp.f_shell_8#L408>`_
   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.
 
@@ -28,7 +28,7 @@ Documentation
   Assume N_int is already provided.
 
 
-`h_apply_cis_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CIS/H_apply.irp.f_shell_8#L263>`_
+`h_apply_cis_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CIS/H_apply.irp.f_shell_8#L264>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.

plugins/CISD/.gitignore

@@ -6,7 +6,6 @@ tags
 irpf90.make
 Makefile
 Makefile.depend
-build.ninja
 .ninja_log
 .ninja_deps
 ezfio_interface.irp.f

plugins/CISD/README.rst

@@ -26,7 +26,7 @@ Documentation
 .. Do not edit this section. It was auto-generated from the
 .. by the `update_README.py` script.
 
-`h_apply_cisd <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_8#L406>`_
+`h_apply_cisd <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_8#L408>`_
   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.
 
@@ -37,7 +37,7 @@ Documentation
   Assume N_int is already provided.
 
 
-`h_apply_cisd_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_8#L263>`_
+`h_apply_cisd_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_8#L264>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
@@ -47,154 +47,154 @@ Documentation
   Undocumented
 
 
-`h_apply_cisd_selection_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L6067>`_
+`h_apply_cisd_selection_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L1287>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_delta_rho_one_point_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L5524>`_
+`h_apply_cisd_selection_delta_rho_one_point_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L767>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_delta_rho_one_point_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L5862>`_
+`h_apply_cisd_selection_delta_rho_one_point_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L1091>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_dipole_moment_z <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L6856>`_
+`h_apply_cisd_selection_dipole_moment_z <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L6649>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_dipole_moment_z_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L6313>`_
+`h_apply_cisd_selection_dipole_moment_z_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L6129>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_dipole_moment_z_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L6651>`_
+`h_apply_cisd_selection_dipole_moment_z_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L6453>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L1333>`_
+`h_apply_cisd_selection_epstein_nesbet <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L5117>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_epstein_nesbet_2x2 <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L2122>`_
+`h_apply_cisd_selection_epstein_nesbet_2x2 <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L5883>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_epstein_nesbet_2x2_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L1579>`_
+`h_apply_cisd_selection_epstein_nesbet_2x2_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L5363>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_2x2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L1917>`_
+`h_apply_cisd_selection_epstein_nesbet_2x2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L5687>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L790>`_
+`h_apply_cisd_selection_epstein_nesbet_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L4597>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L1128>`_
+`h_apply_cisd_selection_epstein_nesbet_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L4921>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L4489>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L4351>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L3946>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L3831>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L4284>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L4155>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_no_projected <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L3700>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2_no_projected <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L3585>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_no_projected_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L3157>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2_no_projected_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L3065>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_no_projected_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L3495>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2_no_projected_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L3389>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_projected <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L2911>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2_projected <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L2819>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_projected_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L2368>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2_projected_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L2299>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_projected_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L2706>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2_projected_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L2623>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_h_core <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L544>`_
+`h_apply_cisd_selection_h_core <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L2053>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_h_core_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L1>`_
+`h_apply_cisd_selection_h_core_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L1533>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_h_core_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L339>`_
+`h_apply_cisd_selection_h_core_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L1857>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_moller_plesset <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L5278>`_
+`h_apply_cisd_selection_moller_plesset <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L521>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_moller_plesset_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L4735>`_
+`h_apply_cisd_selection_moller_plesset_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L1>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_moller_plesset_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L5073>`_
+`h_apply_cisd_selection_moller_plesset_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_10#L325>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.

plugins/CISD_SC2_selected/README.rst

@@ -12,41 +12,41 @@ Documentation
   Undocumented
 
 
-`h_apply_pt2 <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_SC2_selected/H_apply.irp.f_shell_17#L1303>`_
+`h_apply_pt2 <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_SC2_selected/H_apply.irp.f_shell_17#L1257>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_pt2_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_SC2_selected/H_apply.irp.f_shell_17#L792>`_
+`h_apply_pt2_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_SC2_selected/H_apply.irp.f_shell_17#L769>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_pt2_en_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_SC2_selected/H_apply.irp.f_shell_17#L2021>`_
+`h_apply_pt2_en_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_SC2_selected/H_apply.irp.f_shell_17#L1952>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_pt2_en_sc2_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_SC2_selected/H_apply.irp.f_shell_17#L1510>`_
+`h_apply_pt2_en_sc2_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_SC2_selected/H_apply.irp.f_shell_17#L1464>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_pt2_en_sc2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_SC2_selected/H_apply.irp.f_shell_17#L1830>`_
+`h_apply_pt2_en_sc2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_SC2_selected/H_apply.irp.f_shell_17#L1770>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_pt2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_SC2_selected/H_apply.irp.f_shell_17#L1112>`_
+`h_apply_pt2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_SC2_selected/H_apply.irp.f_shell_17#L1075>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_sc2_selected <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_SC2_selected/H_apply.irp.f_shell_17#L546>`_
+`h_apply_sc2_selected <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_SC2_selected/H_apply.irp.f_shell_17#L523>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
@@ -57,7 +57,7 @@ Documentation
   Assume N_int is already provided.
 
 
-`h_apply_sc2_selected_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_SC2_selected/H_apply.irp.f_shell_17#L341>`_
+`h_apply_sc2_selected_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_SC2_selected/H_apply.irp.f_shell_17#L327>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.

plugins/CISD_selected/.gitignore

@@ -1,32 +1,30 @@
-#
-# Do not modify this file. Add your ignored files to the gitignore
-# (without the dot at the beginning) file.
-#
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
 IRPF90_temp
 IRPF90_man
-irpf90.make
-tags
-Makefile.depend
 irpf90_entities
-build.ninja
+tags
+irpf90.make
+Makefile
+Makefile.depend
 .ninja_log
 .ninja_deps
-Pseudo
-Integrals_Monoelec
-Bitmask
-Integrals_Bielec
-AOs
-Selectors_full
-MOs
-Hartree_Fock
-Perturbation
-CISD
-Determinants
-Electrons
-Utils
-Properties
-Nuclei
-MOGuess
-SingleRefMethod
+ezfio_interface.irp.f
 Ezfio_files
-cisd_selection
+Perturbation
+Determinants
+Utils
+Integrals_Monoelec
+MO_Basis
+Selectors_full
+Integrals_Bielec
+Pseudo
+AO_Basis
+Bitmask
+SingleRefMethod
+Electrons
+MOGuess
+CISD
+Nuclei
+Hartree_Fock
+Properties
+cisd_selection

plugins/CISD_selected/README.rst

@@ -12,154 +12,154 @@ Documentation
   Undocumented
 
 
-`h_apply_cisd_selection_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L6067>`_
+`h_apply_cisd_selection_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L1287>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_delta_rho_one_point_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L5524>`_
+`h_apply_cisd_selection_delta_rho_one_point_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L767>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_delta_rho_one_point_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L5862>`_
+`h_apply_cisd_selection_delta_rho_one_point_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L1091>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_dipole_moment_z <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L6856>`_
+`h_apply_cisd_selection_dipole_moment_z <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L6649>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_dipole_moment_z_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L6313>`_
+`h_apply_cisd_selection_dipole_moment_z_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L6129>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_dipole_moment_z_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L6651>`_
+`h_apply_cisd_selection_dipole_moment_z_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L6453>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L1333>`_
+`h_apply_cisd_selection_epstein_nesbet <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L5117>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_epstein_nesbet_2x2 <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L2122>`_
+`h_apply_cisd_selection_epstein_nesbet_2x2 <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L5883>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_epstein_nesbet_2x2_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L1579>`_
+`h_apply_cisd_selection_epstein_nesbet_2x2_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L5363>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_2x2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L1917>`_
+`h_apply_cisd_selection_epstein_nesbet_2x2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L5687>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L790>`_
+`h_apply_cisd_selection_epstein_nesbet_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L4597>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L1128>`_
+`h_apply_cisd_selection_epstein_nesbet_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L4921>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L4489>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L4351>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L3946>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L3831>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L4284>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L4155>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_no_projected <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L3700>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2_no_projected <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L3585>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_no_projected_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L3157>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2_no_projected_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L3065>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_no_projected_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L3495>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2_no_projected_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L3389>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_projected <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L2911>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2_projected <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L2819>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_projected_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L2368>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2_projected_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L2299>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_epstein_nesbet_sc2_projected_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L2706>`_
+`h_apply_cisd_selection_epstein_nesbet_sc2_projected_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L2623>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_h_core <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L544>`_
+`h_apply_cisd_selection_h_core <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L2053>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_h_core_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L1>`_
+`h_apply_cisd_selection_h_core_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L1533>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_h_core_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L339>`_
+`h_apply_cisd_selection_h_core_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L1857>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_moller_plesset <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L5278>`_
+`h_apply_cisd_selection_moller_plesset <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L521>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_selection_moller_plesset_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L4735>`_
+`h_apply_cisd_selection_moller_plesset_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L1>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cisd_selection_moller_plesset_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L5073>`_
+`h_apply_cisd_selection_moller_plesset_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L325>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.

plugins/Casino/README.rst

@@ -21,7 +21,7 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. by the `update_README.py` script.
 
-.. image:: tree_dependency.pdf
+.. image:: tree_dependency.png
 
 * `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
 

plugins/DDCI_selected/README.rst

@@ -8,28 +8,28 @@ Documentation
 .. Do not edit this section. It was auto-generated from the
 .. by the `update_README.py` script.
 
-`full_ci <http://github.com/LCPQ/quantum_package/tree/master/src/DDCI_selected/ddci.irp.f#L1>`_
+`ddci <http://github.com/LCPQ/quantum_package/tree/master/src/DDCI_selected/ddci.irp.f#L1>`_
   Undocumented
 
 
-`h_apply_ddci_pt2 <http://github.com/LCPQ/quantum_package/tree/master/src/DDCI_selected/H_apply.irp.f_shell_15#L1341>`_
+`h_apply_ddci_pt2 <http://github.com/LCPQ/quantum_package/tree/master/src/DDCI_selected/H_apply.irp.f_shell_15#L1271>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_ddci_pt2_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/DDCI_selected/H_apply.irp.f_shell_15#L811>`_
+`h_apply_ddci_pt2_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/DDCI_selected/H_apply.irp.f_shell_15#L776>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_ddci_pt2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/DDCI_selected/H_apply.irp.f_shell_15#L1143>`_
+`h_apply_ddci_pt2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/DDCI_selected/H_apply.irp.f_shell_15#L1086>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_ddci_selection <http://github.com/LCPQ/quantum_package/tree/master/src/DDCI_selected/H_apply.irp.f_shell_15#L565>`_
+`h_apply_ddci_selection <http://github.com/LCPQ/quantum_package/tree/master/src/DDCI_selected/H_apply.irp.f_shell_15#L530>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
@@ -40,7 +40,7 @@ Documentation
   Assume N_int is already provided.
 
 
-`h_apply_ddci_selection_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/DDCI_selected/H_apply.irp.f_shell_15#L353>`_
+`h_apply_ddci_selection_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/DDCI_selected/H_apply.irp.f_shell_15#L331>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.

plugins/Full_CI/README.rst

@@ -159,7 +159,7 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. by the `update_README.py` script.
 
-.. image:: tree_dependency.pdf
+.. image:: tree_dependency.png
 
 * `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
 * `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_

plugins/Hartree_Fock/README.rst

@@ -10,7 +10,7 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. by the `update_README.py` script.
 
-.. image:: tree_dependency.pdf
+.. image:: tree_dependency.png
 
 * `Integrals_Bielec <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec>`_
 * `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_

plugins/MP2/README.rst

@@ -8,7 +8,7 @@ Documentation
 .. Do not edit this section. It was auto-generated from the
 .. by the `update_README.py` script.
 
-`h_apply_mp2 <http://github.com/LCPQ/quantum_package/tree/master/src/MP2/H_apply.irp.f_shell_9#L485>`_
+`h_apply_mp2 <http://github.com/LCPQ/quantum_package/tree/master/src/MP2/H_apply.irp.f_shell_9#L487>`_
   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.
 
@@ -19,7 +19,7 @@ Documentation
   Assume N_int is already provided.
 
 
-`h_apply_mp2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/MP2/H_apply.irp.f_shell_9#L304>`_
+`h_apply_mp2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/MP2/H_apply.irp.f_shell_9#L305>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.

plugins/MRCC/README.rst

@@ -20,19 +20,19 @@ Documentation
 .. Do not edit this section. It was auto-generated from the
 .. by the `update_README.py` script.
 
-`ci_eigenvectors_dressed <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L92>`_
+`ci_eigenvectors_dressed <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L94>`_
   Eigenvectors/values of the CI matrix
 
 
-`ci_eigenvectors_s2_dressed <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L93>`_
+`ci_eigenvectors_s2_dressed <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L95>`_
   Eigenvectors/values of the CI matrix
 
 
-`ci_electronic_energy_dressed <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L91>`_
+`ci_electronic_energy_dressed <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L93>`_
   Eigenvectors/values of the CI matrix
 
 
-`ci_energy_dressed <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L158>`_
+`ci_energy_dressed <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L160>`_
   N_states lowest eigenvalues of the dressed CI matrix
 
 
@@ -76,45 +76,45 @@ Documentation
   Initial guess vectors are not necessarily orthonormal
 
 
-`delta_ij <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L56>`_
+`delta_ij <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L48>`_
   Dressing matrix in N_det basis
 
 
-`delta_ij_non_cas <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L47>`_
+`delta_ij_non_cas <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L39>`_
   Dressing matrix in SD basis
 
 
-`diagonalize_ci_dressed <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L173>`_
+`diagonalize_ci_dressed <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L175>`_
   Replace the coefficients of the CI states by the coefficients of the
   eigenstates of the CI matrix
 
 
-`dressing_type <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L39>`_
+`dressing_type <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L31>`_
   [ Simple | MRCC ]
 
 
-`find_triples_and_quadruples <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_dress.irp.f#L202>`_
+`find_triples_and_quadruples <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_dress.irp.f#L206>`_
   Undocumented
 
 
-`h_apply_mrcc <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/H_apply.irp.f_shell_31#L986>`_
+`h_apply_mrcc <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/H_apply.irp.f_shell_31#L990>`_
   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/src/MRCC/H_apply.irp.f_shell_31#L575>`_
+`h_apply_mrcc_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/H_apply.irp.f_shell_31#L577>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_mrcc_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/H_apply.irp.f_shell_31#L840>`_
+`h_apply_mrcc_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/H_apply.irp.f_shell_31#L843>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_mrcc_simple <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/H_apply.irp.f_shell_31#L412>`_
+`h_apply_mrcc_simple <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/H_apply.irp.f_shell_31#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.
 
@@ -125,13 +125,13 @@ Documentation
   Assume N_int is already provided.
 
 
-`h_apply_mrcc_simple_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/H_apply.irp.f_shell_31#L266>`_
+`h_apply_mrcc_simple_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/H_apply.irp.f_shell_31#L267>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_matrix_dressed <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L76>`_
+`h_matrix_dressed <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L78>`_
   Dressed H with Delta_ij
 
 
@@ -143,12 +143,12 @@ Documentation
   H_jj : array of <j|H|j>
 
 
-`lambda_mrcc <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L2>`_
-  cm/<Psi_0|H|D_m>
+`lambda_mrcc <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L1>`_
+  cm/<Psi_0|H|D_m> or perturbative 1/Delta_E(m)
 
 
-`lambda_pert <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L3>`_
-  cm/<Psi_0|H|D_m>
+`lambda_pert <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L2>`_
+  cm/<Psi_0|H|D_m> or perturbative 1/Delta_E(m)
 
 
 `mrcc <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc.irp.f#L1>`_
@@ -159,7 +159,7 @@ Documentation
   Undocumented
 
 
-`mrcc_dress_simple <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_dress.irp.f#L156>`_
+`mrcc_dress_simple <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_dress.irp.f#L160>`_
   Undocumented
 
 

plugins/Molden/README.rst

@@ -33,7 +33,7 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. by the `update_README.py` script.
 
-.. image:: tree_dependency.pdf
+.. 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>`_

plugins/loc_cele/README.rst

@@ -16,7 +16,7 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. by the `update_README.py` script.
 
-.. image:: tree_dependency.pdf
+.. image:: tree_dependency.png
 
 * `MO_Basis <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis>`_
 

scripts/compilation/qp_create_ninja.py

@@ -530,7 +530,7 @@ def ninja_readme_build(path_module, d_irp, dict_root_path):
     tags = join(root_module.abs, "tags")
     str_depend = " ".join(d_irp[path_module]["l_depend"])
 
-    tree = join(root_module.abs, "tree_dependency.pdf")
+    tree = join(root_module.abs, "tree_dependency.png")
 
     l_string = ["build {0}: build_readme {1} {2} {3}".format(path_readme,
                                                              tags,
@@ -663,16 +663,20 @@ def ninja_binaries_build(path_module, l_children, d_binaries):
     # s t r i n g #
     # ~#~#~#~#~#~ #
 
+    path_readme = os.path.join(path_module.abs, "README.rst")
+    path_png = os.path.join(path_module.abs, "tree_dependency.png")
+
     l_string = ["build {0}: build_binaries {1} {2}".format(" ".join(l_abs_bin),
                                                            EZFIO_LIB,
                                                            ninja_module_path),
                 "   module_abs = {0}".format(path_module.abs),
                 "   module_rel = {0}".format(path_module.rel), ""]
 
-    l_string += ["build module_{0}: phony {1} {2}".format(path_module.rel,
-                                                          " ".join(l_abs_bin),
-                                                          os.path.join(path_module.abs,"README.rst")),
-                                                           ""]
+    l_string += ["build module_{0}: phony {1} {2} {3}".format(path_module.rel,
+                                                              " ".join(l_abs_bin),
+                                                              path_readme,
+                                                              path_png
+                                                              ), ""]
 
     return l_string
 
@@ -703,7 +707,7 @@ def ninja_dot_tree_rule():
 
 def ninja_dot_tree_build(path_module, l_module):
 
-    path_tree = join(path_module.abs, "tree_dependency.pdf")
+    path_tree = join(path_module.abs, "tree_dependency.png")
     l_dep = [join(path.abs, "NEEDED_CHILDREN_MODULES") for path in l_module]
     l_string = ["build {0}: build_dot_tree {1}".format(path_tree, " ".join(l_dep)),
                 "   module_abs = {0}".format(path_module.abs),

scripts/module/module_handler.py

@@ -176,7 +176,8 @@ class ModuleHandler():
     def create_png(self, l_module):
         """Create the png of the dependency tree for a l_module"""
 
-        path = '{0}.png'.format("tree_dependency")
+        basename = "tree_dependency"
+        path = '{0}.png'.format(basename)
 
         # Init
         try:
@@ -199,7 +200,7 @@ class ModuleHandler():
                     draw_module_edge(children, d_ref[children])
                 all_ready_done.append(module)
 
-        graph = Digraph(comment=l_module)
+        graph = Digraph(comment=l_module, format="png", filename=basename)
         d_ref = self.dict_child
 
         # Create all the edge
@@ -207,7 +208,7 @@ class ModuleHandler():
             graph.node(module, fontcolor="red")
             draw_module_edge(module, d_ref[module])
 
-        graph.render('tree_dependency')
+        graph.render(cleanup=True)
 
 
 if __name__ == '__main__':

scripts/module/qp_install_module.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 """
-Usage: 
+Usage:
        qp_install_module.py create -n <name> [<children_module>...]
        qp_install_module.py download -n <name> [<path_folder>...]
        qp_install_module.py install <name>...

scripts/module/update_README.py

@@ -66,7 +66,7 @@ def update_needed(data):
     with open('NEEDED_CHILDREN_MODULES', 'r') as f:
         modules = f.read()
 
-    header_image = ".. image:: tree_dependency.pdf\n\n"
+    header_image = ".. image:: tree_dependency.png\n\n"
 
     if modules.strip():
         modules = ['* `{0} <{1}>`_'.format(name, os.path.join(URL, name))

src/Determinants/README.rst

@@ -32,7 +32,7 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. by the `update_README.py` script.
 
-.. image:: tree_dependency.pdf
+.. image:: tree_dependency.png
 
 * `Integrals_Monoelec <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec>`_
 * `Integrals_Bielec <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec>`_

src/Integrals_Monoelec/README.rst

@@ -4,7 +4,7 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. by the `update_README.py` script.
 
-.. image:: tree_dependency.pdf
+.. image:: tree_dependency.png
 
 * `MO_Basis <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis>`_
 * `Pseudo <http://github.com/LCPQ/quantum_package/tree/master/src/Pseudo>`_

src/MOGuess/README.rst

@@ -8,7 +8,7 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. by the `update_README.py` script.
 
-.. image:: tree_dependency.pdf
+.. image:: tree_dependency.png
 
 * `Integrals_Monoelec <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec>`_