Merge branch 'release/0.1.0'

configure

@@ -61,7 +61,8 @@ d_dependency = {
     "gcc": [],
     "python": [],
     "ninja": ["gcc", "python"],
-    "make": []
+    "make": [],
+    "p_graphviz": ["python"]
 }
 
 from collections import namedtuple
@@ -126,10 +127,15 @@ ezfio = Info(
     description=' EZFIO',
     default_path=join(QP_ROOT_INSTALL, "EZFIO"))
 
+p_graphviz = Info(
+    url='https://github.com/xflr6/graphviz/archive/master.tar.gz',
+    description=' Python library for graphviz',
+    default_path=join(QP_ROOT_INSTALL, "p_graphviz"))
+
 d_info = dict()
 
 for m in ["ocaml", "m4", "curl", "zlib", "path", "irpf90", "docopt",
-          "resultsFile", "ninja", "emsl", "ezfio"]:
+          "resultsFile", "ninja", "emsl", "ezfio", "p_graphviz"]:
     exec ("d_info['{0}']={0}".format(m))
 
 

install/.gitignore

@@ -8,3 +8,4 @@ irpf90
 resultsFile
 zlib
 build.ninja
+p_graphviz

install/scripts/install_p_graphviz.sh

@@ -0,0 +1,10 @@
+#!/bin/bash -x
+
+TARGET=p_graphviz
+
+function _install()
+{
+  cp -R ${BUILD} . || exit 1
+}
+
+source scripts/build.sh

plugins/Alavi/.gitignore

@@ -0,0 +1,23 @@
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
+IRPF90_temp
+IRPF90_man
+irpf90_entities
+tags
+irpf90.make
+Makefile
+Makefile.depend
+.ninja_log
+.ninja_deps
+ezfio_interface.irp.f
+Ezfio_files
+Determinants
+Integrals_Monoelec
+MO_Basis
+Utils
+Pseudo
+Bitmask
+AO_Basis
+Electrons
+Nuclei
+Integrals_Bielec
+alavi_graph

plugins/Alavi/NEEDED_CHILDREN_MODULES

@@ -0,0 +1 @@
+Determinants

plugins/Alavi/README.rst

@@ -0,0 +1,23 @@
+=====
+alavi
+=====
+
+Documentation
+=============
+
+.. Do not edit this section. It was auto-generated from the
+.. by the `update_README.py` script.
+
+`alavi_graph <http://github.com/LCPQ/quantum_package/tree/master/src/Alavi/alavi_graph.irp.f#L1>`_
+  Undocumented
+
+Needed Modules
+==============
+
+.. Do not edit this section. It was auto-generated from the
+.. by the `update_README.py` script.
+
+.. image:: tree_dependency.png
+
+* `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
+

plugins/Alavi/alavi_graph.irp.f

@@ -0,0 +1,28 @@
+program alavi_graph
+  implicit none
+  integer :: exc(0:2,2,2),h1,p1,h2,p2,s1,s2
+  double precision :: phase
+
+  read_wf = .True.
+  touch read_wf
+
+  integer :: k,degree
+  double precision :: hii
+
+  do k=1,N_det
+      call get_excitation_degree(psi_det(1,1,1),psi_det(1,1,k),degree,N_int)
+      call  i_H_j(psi_det(1,1,k),psi_det(1,1,k),N_int,hii) 
+      print*, k,abs(psi_coef(k,1)), hii,degree
+
+!      if (degree == 2) then
+!      	call get_excitation(psi_det(1,1,1),psi_det(1,1,k),exc,degree,phase,N_int)
+!      	call decode_exc(exc,degree,h1,p1,h2,p2,s1,s2)
+!		print*, h1,h2,hii, abs(psi_coef(k,1))
+!      endif
+!      
+
+
+  enddo
+end
+
+!plot "test.dat" u (abs($2)):(abs($3)):4  w p palette

plugins/All_singles/README.rst

@@ -1,4 +0,0 @@
-==================
-All_singles Module
-==================
-

plugins/CAS_SD/.gitignore

@@ -1,4 +1,4 @@
-# Automatically created by /home/scemama/quantum_package/scripts/module/module_handler.py 
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
 IRPF90_temp
 IRPF90_man
 irpf90_entities

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/.gitignore

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

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/.gitignore

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

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/.gitignore

@@ -1,33 +1,31 @@
-#
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
-# Do not modify this file. Add your ignored files to the gitignore
-# (without the dot at the beginning) file.
-#
 IRPF90_temp
 IRPF90_man
-irpf90.make
-tags
-Makefile.depend
 irpf90_entities
-build.ninja
+tags
+irpf90.make
+Makefile
+Makefile.depend
 .ninja_log
 .ninja_deps
-Pseudo
+ezfio_interface.irp.f
-Integrals_Monoelec
-Bitmask
-Integrals_Bielec
-CISD_selected
-AOs
-Selectors_full
-MOs
-Hartree_Fock
-Perturbation
-CISD
-Determinants
-Electrons
-Utils
-Properties
-Nuclei
-MOGuess
-SingleRefMethod
 Ezfio_files
+Perturbation
+Determinants
+Integrals_Monoelec
+MO_Basis
+Selectors_full
+SingleRefMethod
+Utils
+Pseudo
+Properties
+Bitmask
+AO_Basis
+Electrons
+CISD_selected
+MOGuess
+CISD
+Nuclei
+Hartree_Fock
+Integrals_Bielec
 cisd_sc2_selection

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

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

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/DensityMatrix/NEEDED_CHILDREN_MODULES

@@ -0,0 +1 @@
+Bitmask

plugins/FCIdump/.gitignore

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

plugins/Generators_full/README.rst

@@ -43,7 +43,7 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. by the `update_README.py` script.
 
-.. image:: tree_dependency.png
+.. image:: tree_dependency.pdf
 
 * `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
 * `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_

plugins/Hartree_Fock/.gitignore

@@ -21,5 +21,4 @@ MOGuess
 Nuclei
 Utils
 Huckel_guess
-test
 SCF

plugins/Hartree_Fock/README.rst

@@ -29,16 +29,6 @@ Documentation
   Alpha Fock matrix in AO basis set
 
 
-`big <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/test.irp.f#L1>`_
-  Produce `Huckel` MO orbital
-  output:  mo_basis.mo_tot_num mo_basis.mo_label mo_basis.ao_md5 mo_basis.mo_coef mo_basis.mo_occ
-  Produce `Hartree_Fock` MO orbital
-  output: mo_basis.mo_tot_num mo_basis.mo_label mo_basis.ao_md5 mo_basis.mo_coef mo_basis.mo_occ
-  output: hartree_fock.energy
-  input: mo_basis.mo_coef
-  Run SCF calculation
-
-
 `create_guess <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/SCF.irp.f#L13>`_
   Create an MO guess if no MOs are present in the EZFIO directory
 

plugins/MP2/.gitignore

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

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/.gitignore

@@ -1,4 +1,4 @@
-# Automatically created by /home/scemama/quantum_package/scripts/module/module_handler.py 
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
 IRPF90_temp
 IRPF90_man
 irpf90_entities

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>`_
+`lambda_mrcc <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L1>`_
-  cm/<Psi_0|H|D_m>
+  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>`_
+`lambda_pert <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L2>`_
-  cm/<Psi_0|H|D_m>
+  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/MRCC/mrcc_utils.irp.f

@@ -17,7 +17,6 @@ do i=1,N_det_non_cas
    lambda_mrcc(k,i) = psi_non_cas_coef(i,k)/ihpsi(k)
     if (dabs(ihpsi(k)).le.1.d-3) then
       lambda_mrcc(k,i) = 1.d0 / (psi_cas_energy_diagonalized(k)-hii)
-      icount_manu = icount_manu+1
       cycle
     endif
    enddo

plugins/Perturbation/README.rst

@@ -356,7 +356,7 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. by the `update_README.py` script.
 
-.. image:: tree_dependency.png
+.. image:: tree_dependency.pdf
 
 * `Properties <http://github.com/LCPQ/quantum_package/tree/master/src/Properties>`_
 * `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_

plugins/Properties/README.rst

@@ -148,7 +148,7 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. by the `update_README.py` script.
 
-.. image:: tree_dependency.png
+.. image:: tree_dependency.pdf
 
 * `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
 

plugins/QmcChem/.gitignore

@@ -1,4 +1,4 @@
-# Automatically created by /home/scemama/quantum_package/scripts/module/module_handler.py 
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
 IRPF90_temp
 IRPF90_man
 irpf90_entities

plugins/Selectors_full/README.rst

@@ -181,7 +181,7 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. by the `update_README.py` script.
 
-.. image:: tree_dependency.png
+.. image:: tree_dependency.pdf
 
 * `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
 * `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_

plugins/loc_cele/.gitignore

@@ -0,0 +1,18 @@
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
+IRPF90_temp
+IRPF90_man
+irpf90_entities
+tags
+irpf90.make
+Makefile
+Makefile.depend
+.ninja_log
+.ninja_deps
+ezfio_interface.irp.f
+Ezfio_files
+MO_Basis
+Utils
+AO_Basis
+Electrons
+Nuclei
+loc_cele

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.png")
+    tree = join(path_module.abs, "tree_dependency.png")
 
     l_string = ["build {0}: build_readme {1} {2} {3}".format(path_readme,
                                                              tags,
@@ -663,31 +663,24 @@ 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}".format(path_module.rel,
+    l_string += ["build module_{0}: phony {1} {2} {3}".format(path_module.rel,
-                                                      " ".join(l_abs_bin)), ""]
+                                                              " ".join(l_abs_bin),
+                                                              path_readme,
+                                                              path_png
+                                                              ), ""]
 
     return l_string
 
 
-#
-# |\/|  _   _|     |  _
-# |  | (_) (_| |_| | (/_
-#
-def create_module_ninja():
-    """
-    In a module create a build.ninja
-    """
-
-    l_string = ["rule all:"]
-    return l_string
-
-
 # ___
 #  | ._ _   _     _|  _  ._   _  ._   _|  _  ._   _ o  _   _
 #  | | (/_ (/_   (_| (/_ |_) (/_ | | (_| (/_ | | (_ | (/_ _>
@@ -760,7 +753,7 @@ def create_build_ninja_module(path_module):
         f.write("\n".join(l_string))
 
 
-def create_build_ninja_global(l_module):
+def create_build_ninja_global():
 
     l_string = ["rule update_build_ninja_root",
                 "   command = {0} update".format(__file__),
@@ -772,7 +765,7 @@ def create_build_ninja_global(l_module):
                  ""]
 
     l_string += ["rule make_clean",
-                 "  command = module_handler.py clean {0}".format(" ".join([m.rel for m in l_module])),
+                 "  command = module_handler.py clean --all",
                  "  description = Cleaning all modules", ""]
 
     l_string += ["build dummy_target: update_build_ninja_root",
@@ -869,14 +862,7 @@ if __name__ == "__main__":
     dict_root = module_instance.dict_root
     dict_root_path = dict_module_genelogy_path(dict_root)
 
-    l_module = d_genealogy_path.keys()
+    l_all_module = d_genealogy_path.keys()
-
-    for module in l_module:
-        # ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
-        # d o t _ t r e e  & r e a d  m e #
-        # ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
-        l_string += ninja_dot_tree_build(module, l_module)
-        l_string += ninja_readme_build(module, d_irp, dict_root_path)
 
     # ~#~#~#~#~#~#~#~#~#~#~#~#~ #
     # M o d u l e _ t o _ i r p #
@@ -884,15 +870,47 @@ if __name__ == "__main__":
 
     if arguments["--production"]:
 
-        d_binaries = get_dict_binaries(l_module, mode="production")
+        d_binaries = get_dict_binaries(l_all_module, mode="production")
         l_module = d_binaries.keys()
 
     elif arguments["--development"]:
 
-        d_binaries = get_dict_binaries(l_module, mode="development")
+        d_binaries = get_dict_binaries(l_all_module, mode="development")
         l_module = d_binaries.keys()
 
-    create_build_ninja_global(l_module)
+        for module in l_all_module:
+            # ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
+            # d o t _ t r e e  & r e a d  m e #
+            # ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
+            l_string += ninja_dot_tree_build(module, l_all_module)
+            l_string += ninja_readme_build(module, d_irp, dict_root_path)
+
+    # ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
+    # C h e c k _ c o h e r e n c y #
+    # ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
+
+    for module in dict_root_path.values():
+
+        if module not in d_binaries:
+            l_msg = ["{0} is a root module but he do not containt a main file",
+                     "Is intolerable !",
+                     "You need a main file:",
+                     "- Create it in {0}",
+                     "- Or delete {0} `qp_install_module.py uninstall {0}`"
+                     "- Or install a module who need {0} with a main "]
+
+            print "\n".join(l_msg).format(module)
+            sys.exit(1)
+
+    # ~#~#~#~#~#~#~#~#~#~#~#~ #
+    # G l o b a l _ b u i l d #
+    # ~#~#~#~#~#~#~#~#~#~#~#~ #
+
+    create_build_ninja_global()
+
+    # ~#~#~#~#~#~#~#~#~#~#~#~ #
+    # C r e a t e _ r u l e s #
+    # ~#~#~#~#~#~#~#~#~#~#~#~ #
 
     for module_to_compile in l_module:
 
@@ -919,6 +937,10 @@ if __name__ == "__main__":
         l_string += ninja_gitignore_build(module_to_compile, d_binaries,
                                           l_symlink)
 
+    # ~#~#~#~#~ #
+    # S a v e s #
+    # ~#~#~#~#~ #
+
     with open(join(QP_ROOT, "config", "build.ninja"), "w+") as f:
         f.write(header)
         f.write("\n".join(l_string))

scripts/module/module_handler.py

@@ -6,7 +6,7 @@ Module utilitary
 Usage:
     module_handler.py print_descendant      [<module_name>...]
     module_handler.py create_png            [<module_name>...]
-    module_handler.py clean                 [<module_name>...]
+    module_handler.py clean                 [ --all | <module_name>...]
     module_handler.py create_git_ignore     [<module_name>...]
 
 Options:
@@ -31,8 +31,7 @@ except ImportError:
 
 # Canot cache for namedtuple are not hashable
 def is_module(path_module):
-    return os.path.isfile(os.path.join(QP_SRC,
+    return os.path.isfile(os.path.join(QP_SRC, path_module,
-                                       path_module,
                                        "NEEDED_CHILDREN_MODULES"))
 
 
@@ -83,15 +82,15 @@ def get_l_module_descendant(d_child, l_module):
             try:
                 l.extend(get_l_module_descendant(d_child, d_child[module]))
             except KeyError:
-                print >> sys.stderr, "`{0}` not submodule".format(module)
+                print >> sys.stderr, "Error: "
-                print >> sys.stderr, "Check the corresponding NEEDED_CHILDREN_MODULES"
+                print >> sys.stderr, "`{0}` is not a submodule".format(module)
-                raise
+                print >> sys.stderr, "Check the typo (orthograph, case, '/', etc.) "
+                sys.exit(1)
 
     return list(set(l))
 
 
 class ModuleHandler():
-
     def __init__(self, l_root_abs=None):
         self.dict_child = get_dict_child(l_root_abs)
 
@@ -109,7 +108,8 @@ class ModuleHandler():
         d = {}
 
         for module_name in d_child:
-            d[module_name] = [i for i in d_child.keys() if module_name in d_child[i]]
+            d[module_name] = [i for i in d_child.keys()
+                              if module_name in d_child[i]]
 
         return d
 
@@ -127,7 +127,8 @@ class ModuleHandler():
                 d[module_name] = get_l_module_descendant(d_child,
                                                          d_child[module_name])
             except KeyError:
-                print "Check NEEDED_CHILDREN_MODULES for {0}".format(module_name)
+                print "Check NEEDED_CHILDREN_MODULES for {0}".format(
+                    module_name)
                 sys.exit(1)
 
         return d
@@ -146,7 +147,9 @@ class ModuleHandler():
         dict_root = {}
 
         for module in l_all_module:
-            dict_root[module] = [ p for p in l_all_module if module in [p] + d_desc[p] and not d_asc[p]][0]
+            dict_root[module] = [p for p in l_all_module
+                                 if module in [p] + d_desc[p] and not d_asc[p]
+                                 ][0]
 
         return dict_root
 
@@ -173,11 +176,12 @@ 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:
-            import pydot
+            from graphviz import Digraph
         except:
             with open(path, 'a'):
                 os.utime(path, None)
@@ -191,30 +195,31 @@ class ModuleHandler():
             if module not in all_ready_done:
                 for children in l_children:
                     # Add Edge
-                    edge = pydot.Edge(module, children)
+                    graph.edge(module, children)
-                    graph.add_edge(edge)
                     # Recurs
                     draw_module_edge(children, d_ref[children])
                 all_ready_done.append(module)
 
-        graph = pydot.Dot(graph_type='digraph')
+        graph = Digraph(comment=l_module, format="png", filename=basename)
         d_ref = self.dict_child
 
         # Create all the edge
         for module in l_module:
-            node_a = pydot.Node(module, fontcolor="red")
+            graph.node(module, fontcolor="red")
-            graph.add_node(node_a)
             draw_module_edge(module, d_ref[module])
 
-        # Save
+        graph.render(cleanup=True)
-        graph.write_png(path)
 
 
 if __name__ == '__main__':
 
     arguments = docopt(__doc__)
 
-    if not arguments['<module_name>']:
+    if arguments['--all']:
+        l_module = [f for f in os.listdir(QP_SRC)
+                    if os.path.isdir(os.path.join(QP_SRC, f))]
+
+    elif not arguments['<module_name>']:
         dir_ = os.getcwd()
         l_module = [os.path.basename(dir_)]
     else:
@@ -239,14 +244,15 @@ if __name__ == '__main__':
     if arguments["clean"] or arguments["create_git_ignore"]:
 
         l_dir = ['IRPF90_temp', 'IRPF90_man']
-        l_file = ["irpf90_entities", "tags", "irpf90.make",
+        l_file = ["irpf90_entities", "tags", "irpf90.make", "Makefile",
-                  "Makefile", "Makefile.depend", ".ninja_log", ".ninja_deps",
+                  "Makefile.depend", ".ninja_log", ".ninja_deps",
                   "ezfio_interface.irp.f"]
 
         for module in l_module:
             module_abs = os.path.realpath(os.path.join(QP_SRC, module))
             l_symlink = m.l_descendant_unique([module])
-            l_exe = [f for f in os.listdir(module_abs) if is_exe(os.path.join(module_abs,f))]
+            l_exe = [f for f in os.listdir(module_abs)
+                     if is_exe(os.path.join(module_abs, f))]
 
             if arguments["clean"]:
                 for f in l_dir:

scripts/module/qp_install_module.py

@@ -6,7 +6,7 @@ Usage:
        qp_install_module.py download -n <name> [<path_folder>...]
        qp_install_module.py install <name>...
        qp_install_module.py list (--installed | --available-local)
-       qp_install_module.py uninstall <name>... [--and_ancestor]
+       qp_install_module.py uninstall <name>...
 
 
 Options:
@@ -25,7 +25,7 @@ try:
     from update_README import Doc_key, Needed_key
     from qp_path import QP_SRC, QP_PLUGINS
 except ImportError:
-    print "Please check if you have source the .quantum_package.rc"
+    print "Please check if you have sourced the .quantum_package.rc"
     print "(`source .quantum_package.rc`)"
     print sys.exit(1)
 
@@ -80,7 +80,9 @@ if __name__ == '__main__':
 
         l_children = arguments["<children_module>"]
 
-        path = os.path.join(QP_PLUGINS, arguments["<name>"][0])
+        name = arguments["<name>"][0]
+
+        path = os.path.join(QP_PLUGINS, name)
 
         print "You will create the module:"
         print path
@@ -102,9 +104,13 @@ if __name__ == '__main__':
         print "This can be reduce to:"
         l_child_reduce = m_instance.l_reduce_tree(l_children)
         print l_child_reduce
+        print "Installation",
         save_new_module(path, l_child_reduce)
 
-        print "This was a plugin, you can install it now"
+        print "    [ OK ]"
+        print "If this was a plugins, you can install it normaly. Type:"
+        print "` {0} install {1} `".format(os.path.basename(__file__), name)
+
     elif arguments["download"]:
         pass
 #        d_local = get_dict_child([QP_SRC])
@@ -154,10 +160,10 @@ if __name__ == '__main__':
                         print "Your src directory is broken. Please remove %s" % des
                         raise
             try:
-                import subprocess
                 subprocess.check_call(["qp_create_ninja.py", "update"])
             except:
                 raise
+    
             print "Done"
             print "You can now compile as usual"
 
@@ -177,22 +183,21 @@ if __name__ == '__main__':
                 print "* %s" % name
             sys.exit(1)
 
-        if arguments["--and_ancestor"]:
-
         l_name_to_remove = l_name + [module for module in m_instance.l_module for name in l_name if name in d_descendant[module]]
+
         print "You will remove all of:"
         print l_name_to_remove
-        else:
-            l_name_to_remove = l_name
 
-        for module in l_name_to_remove:
+        for module in set(l_name_to_remove):
 
             try:
                 subprocess.check_call(["module_handler.py", "clean", module])
             except:
                 raise
 
+        for module in set(l_name_to_remove):
+
             try:
                 os.unlink(os.path.join(QP_SRC, module))
             except OSError:
-                print "%s is a core module which can not be renmoved" % x
+                print "%s is a core module which can not be renmoved" % module

src/.gitignore

@@ -24,3 +24,5 @@ Selectors_full
 Selectors_no_sorted
 SingleRefMethod
 Casino
+loc_cele
+Alavi

src/Ezfio_files/README.rst

@@ -1,140 +0,0 @@
-==================
-Ezfio_files Module
-==================
-
-This modules essentially contains the name of the EZFIO directory in the
-``ezfio_filename`` variable. This is read as the first argument of the
-command-line, or as the ``QP_INPUT`` environment variable.
-Documentation
-=============
-
-.. Do not edit this section. It was auto-generated from the
-.. by the `update_README.py` script.
-
-`ezfio_filename <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/ezfio.irp.f#L1>`_
-  Name of EZFIO file. It is obtained from the QPACKAGE_INPUT environment
-  variable if it is set, or as the 1st argument of the command line.
-
-
-`getunitandopen <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/get_unit_and_open.irp.f#L1>`_
-  :f:
-  file name
-  .br
-  :mode:
-  'R' : READ, UNFORMATTED
-  'W' : WRITE, UNFORMATTED
-  'r' : READ, FORMATTED
-  'w' : WRITE, FORMATTED
-  'a' : APPEND, FORMATTED
-  'x' : READ/WRITE, FORMATTED
-  .br
-
-
-`output_ao_basis <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L1>`_
-  Output file for AO_Basis
-
-
-`output_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L21>`_
-  Output file for Bitmask
-
-
-`output_casino <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L41>`_
-  Output file for Casino
-
-
-`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#L61>`_
-  Output file for Determinants
-
-
-`output_electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L81>`_
-  Output file for Electrons
-
-
-`output_ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L101>`_
-  Output file for Ezfio_files
-
-
-`output_full_ci <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L121>`_
-  Output file for Full_CI
-
-
-`output_generators_full <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L141>`_
-  Output file for Generators_full
-
-
-`output_hartree_fock <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L161>`_
-  Output file for Hartree_Fock
-
-
-`output_integrals_bielec <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L181>`_
-  Output file for Integrals_Bielec
-
-
-`output_integrals_monoelec <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L201>`_
-  Output file for Integrals_Monoelec
-
-
-`output_loc_cele <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L221>`_
-  Output file for loc_cele
-
-
-`output_mo_basis <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L241>`_
-  Output file for MO_Basis
-
-
-`output_moguess <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L261>`_
-  Output file for MOGuess
-
-
-`output_molden <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L281>`_
-  Output file for Molden
-
-
-`output_nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L301>`_
-  Output file for Nuclei
-
-
-`output_perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L321>`_
-  Output file for Perturbation
-
-
-`output_properties <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L341>`_
-  Output file for Properties
-
-
-`output_pseudo <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L361>`_
-  Output file for Pseudo
-
-
-`output_selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L381>`_
-  Output file for Selectors_full
-
-
-`output_utils <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L401>`_
-  Output file for Utils
-
-
-`output_wall_time_0 <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f#L1>`_
-  Initial CPU and wall times when printing in the output files
-
-
-`write_bool <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f#L88>`_
-  Write an logical value in output
-
-
-`write_double <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f#L58>`_
-  Write a double precision value in output
-
-
-`write_int <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f#L73>`_
-  Write an integer value in output
-
-
-`write_time <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f#L42>`_
-  Write a time stamp in the output for chronological reconstruction
-
-

src/MOGuess/h_core_guess_routine.irp.f

@@ -0,0 +1,16 @@
+subroutine hcore_guess
+  BEGIN_DOC
+! Produce `H_core` MO orbital
+  END_DOC
+  implicit none
+  character*(64)                 :: label
+  mo_coef = ao_ortho_lowdin_coef
+  TOUCH mo_coef
+  label = "Guess"
+  call mo_as_eigvectors_of_mo_matrix(mo_mono_elec_integral,          &
+                                     size(mo_mono_elec_integral,1),  &
+                                     size(mo_mono_elec_integral,2),label)
+  print *,  'save mos'
+  call save_mos
+  SOFT_TOUCH mo_coef mo_label
+end