Corrected bug with missing README files

plugins/Perturbation/README.rst

@@ -85,92 +85,92 @@ Documentation
   Undocumented
 
 
-`perturb_buffer_by_mono_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L161>`_
+`perturb_buffer_by_mono_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L791>`_
   Applly pertubration ``delta_rho_one_point`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_by_mono_dipole_moment_z <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L896>`_
+`perturb_buffer_by_mono_dipole_moment_z <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L686>`_
   Applly pertubration ``dipole_moment_z`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_by_mono_epstein_nesbet <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L686>`_
+`perturb_buffer_by_mono_epstein_nesbet <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L476>`_
   Applly pertubration ``epstein_nesbet`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_by_mono_epstein_nesbet_2x2 <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L791>`_
+`perturb_buffer_by_mono_epstein_nesbet_2x2 <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L581>`_
   Applly pertubration ``epstein_nesbet_2x2`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_by_mono_epstein_nesbet_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L581>`_
+`perturb_buffer_by_mono_epstein_nesbet_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L371>`_
   Applly pertubration ``epstein_nesbet_sc2`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_by_mono_epstein_nesbet_sc2_no_projected <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L476>`_
+`perturb_buffer_by_mono_epstein_nesbet_sc2_no_projected <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L266>`_
   Applly pertubration ``epstein_nesbet_sc2_no_projected`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_by_mono_epstein_nesbet_sc2_projected <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L371>`_
+`perturb_buffer_by_mono_epstein_nesbet_sc2_projected <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L161>`_
   Applly pertubration ``epstein_nesbet_sc2_projected`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_by_mono_h_core <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L266>`_
+`perturb_buffer_by_mono_h_core <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L56>`_
   Applly pertubration ``h_core`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_by_mono_moller_plesset <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L56>`_
+`perturb_buffer_by_mono_moller_plesset <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L896>`_
   Applly pertubration ``moller_plesset`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L110>`_
+`perturb_buffer_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L740>`_
   Applly pertubration ``delta_rho_one_point`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_dipole_moment_z <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L845>`_
+`perturb_buffer_dipole_moment_z <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L635>`_
   Applly pertubration ``dipole_moment_z`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_epstein_nesbet <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L635>`_
+`perturb_buffer_epstein_nesbet <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L425>`_
   Applly pertubration ``epstein_nesbet`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_epstein_nesbet_2x2 <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L740>`_
+`perturb_buffer_epstein_nesbet_2x2 <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L530>`_
   Applly pertubration ``epstein_nesbet_2x2`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_epstein_nesbet_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L530>`_
+`perturb_buffer_epstein_nesbet_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L320>`_
   Applly pertubration ``epstein_nesbet_sc2`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_epstein_nesbet_sc2_no_projected <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L425>`_
+`perturb_buffer_epstein_nesbet_sc2_no_projected <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L215>`_
   Applly pertubration ``epstein_nesbet_sc2_no_projected`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_epstein_nesbet_sc2_projected <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L320>`_
+`perturb_buffer_epstein_nesbet_sc2_projected <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L110>`_
   Applly pertubration ``epstein_nesbet_sc2_projected`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_h_core <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L215>`_
+`perturb_buffer_h_core <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L5>`_
   Applly pertubration ``h_core`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_moller_plesset <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L5>`_
+`perturb_buffer_moller_plesset <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L845>`_
   Applly pertubration ``moller_plesset`` to the buffer of determinants generated in the H_apply
   routine.
 

plugins/Psiref_Utils/README.rst

@@ -13,3 +13,82 @@ Documentation
 .. Do not edit this section. It was auto-generated from the
 .. by the `update_README.py` script.
 
+`h_matrix_ref <http://github.com/LCPQ/quantum_package/tree/master/src/Psiref_Utils/psi_ref_utils.irp.f#L70>`_
+  Undocumented
+
+
+`idx_non_ref <http://github.com/LCPQ/quantum_package/tree/master/src/Psiref_Utils/psi_ref_utils.irp.f#L20>`_
+  Set of determinants which are not part of the reference, defined from the application
+  of the reference bitmask on the determinants.
+  idx_non_ref gives the indice of the determinant in psi_det.
+
+
+`idx_ref <http://github.com/LCPQ/quantum_package/tree/master/src/Psiref_Utils/psi_ref.irp.f#L5>`_
+  Reference wave function, defined as determinants with coefficients > 0.05
+  idx_ref gives the indice of the ref determinant in psi_det.
+
+
+`n_det_non_ref <http://github.com/LCPQ/quantum_package/tree/master/src/Psiref_Utils/psi_ref_utils.irp.f#L21>`_
+  Set of determinants which are not part of the reference, defined from the application
+  of the reference bitmask on the determinants.
+  idx_non_ref gives the indice of the determinant in psi_det.
+
+
+`n_det_ref <http://github.com/LCPQ/quantum_package/tree/master/src/Psiref_Utils/psi_ref.irp.f#L6>`_
+  Reference wave function, defined as determinants with coefficients > 0.05
+  idx_ref gives the indice of the ref determinant in psi_det.
+
+
+`psi_coef_ref_diagonalized <http://github.com/LCPQ/quantum_package/tree/master/src/Psiref_Utils/psi_ref_utils.irp.f#L82>`_
+  Undocumented
+
+
+`psi_non_ref <http://github.com/LCPQ/quantum_package/tree/master/src/Psiref_Utils/psi_ref_utils.irp.f#L18>`_
+  Set of determinants which are not part of the reference, defined from the application
+  of the reference bitmask on the determinants.
+  idx_non_ref gives the indice of the determinant in psi_det.
+
+
+`psi_non_ref_coef <http://github.com/LCPQ/quantum_package/tree/master/src/Psiref_Utils/psi_ref_utils.irp.f#L19>`_
+  Set of determinants which are not part of the reference, defined from the application
+  of the reference bitmask on the determinants.
+  idx_non_ref gives the indice of the determinant in psi_det.
+
+
+`psi_non_ref_coef_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Psiref_Utils/psi_ref_utils.irp.f#L58>`_
+  Reference determinants sorted to accelerate the search of a random determinant in the wave
+  function.
+
+
+`psi_non_ref_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Psiref_Utils/psi_ref_utils.irp.f#L57>`_
+  Reference determinants sorted to accelerate the search of a random determinant in the wave
+  function.
+
+
+`psi_ref <http://github.com/LCPQ/quantum_package/tree/master/src/Psiref_Utils/psi_ref.irp.f#L3>`_
+  Reference wave function, defined as determinants with coefficients > 0.05
+  idx_ref gives the indice of the ref determinant in psi_det.
+
+
+`psi_ref_coef <http://github.com/LCPQ/quantum_package/tree/master/src/Psiref_Utils/psi_ref.irp.f#L4>`_
+  Reference wave function, defined as determinants with coefficients > 0.05
+  idx_ref gives the indice of the ref determinant in psi_det.
+
+
+`psi_ref_coef_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Psiref_Utils/psi_ref_utils.irp.f#L5>`_
+  Reference determinants sorted to accelerate the search of a random determinant in the wave
+  function.
+
+
+`psi_ref_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Psiref_Utils/psi_ref_utils.irp.f#L101>`_
+  Undocumented
+
+
+`psi_ref_energy_diagonalized <http://github.com/LCPQ/quantum_package/tree/master/src/Psiref_Utils/psi_ref_utils.irp.f#L83>`_
+  Undocumented
+
+
+`psi_ref_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Psiref_Utils/psi_ref_utils.irp.f#L4>`_
+  Reference determinants sorted to accelerate the search of a random determinant in the wave
+  function.
+

plugins/QmcChem/.gitignore

@@ -20,4 +20,4 @@ ezfio_interface.irp.f
 irpf90.make
 irpf90_entities
 save_for_qmcchem
-tags
+tags

scripts/module/update_README.py

@@ -46,8 +46,11 @@ def fetch_splitted_data():
     The result is given as a list of strings
     """
 
-    with open(README, 'r') as f:
+    try:
-        data = f.read()
+        with open(README, 'r') as f:
+            data = f.read()
+    except IOError:
+      return []
 
     # Place sentinels
     data = data.replace(Doc_key, Sentinel + Doc_key)