Merge OK

.travis.yml

@@ -1,17 +1,28 @@
-sudo: true
+#sudo: true
-#
+#before_script:
-#cache:
+#  - sudo apt-get update -q
-#  directories:
+#  - sudo apt-get install gfortran liblapack-dev gcc
-#  - $HOME/.opam/
+#  - sudo apt-get install graphviz
+
+sudo: false
+
+addons:
+  apt:
+    packages:
+    - gfortran
+    - gcc
+    - liblapack-dev
+    - graphviz
+
+cache:
+  directories:
+  - $HOME/.opam/
 
 language: python
 python:
     - "2.6"
 
-before_script:
+
-  - sudo apt-get update -q
-  - sudo apt-get install gfortran liblapack-dev gcc
-  - sudo apt-get install graphviz
 
 script: 
   - ./configure  --production ./config/gfortran.cfg

README.md

@@ -160,4 +160,17 @@ size: 1
 type: Strictly_negative_float
 doc: Calculated HF energy
 interface: ezfio
-```
+```
+
+#FAQ
+
+### Error: ezfio_* is already defined.
+
+#### Why ?
+
+You have two or more ezfio configuration file for the same variable. Check in `$QP_ROOT/install/config/`
+
+#### Fix
+
+    - rm $QP_ROOT/install/EZFIO/config/*
+    - ninja 

configure

@@ -63,7 +63,8 @@ d_dependency = {
     "gcc": [],
     "python": [],
     "ninja": ["gcc", "python"],
-    "make": []
+    "make": [],
+    "p_graphviz": ["python"]
 }
 
 from collections import namedtuple
@@ -128,10 +129,15 @@ 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

@@ -7,4 +7,5 @@ EZFIO
 irpf90
 resultsFile
 zlib
-build.ninja
+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 $QP_ROOT/scripts/module/module_handler.py 
+.ninja_deps
+.ninja_log
+AO_Basis
+Bitmask
+Determinants
+Electrons
+Ezfio_files
+IRPF90_man
+IRPF90_temp
+Integrals_Bielec
+Integrals_Monoelec
+MO_Basis
+Makefile
+Makefile.depend
+Nuclei
+Pseudo
+Utils
+alavi_graph
+ezfio_interface.irp.f
+irpf90.make
+irpf90_entities
+tags

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/CID/.gitignore

@@ -1,29 +1,28 @@
-# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
+# Automatically created by $QP_ROOT/scripts/module/module_handler.py 
-IRPF90_temp
-IRPF90_man
-irpf90_entities
-tags
-irpf90.make
-Makefile
-Makefile.depend
-build.ninja
-.ninja_log
 .ninja_deps
-ezfio_interface.irp.f
+.ninja_log
-Ezfio_files
-Determinants
-Integrals_Monoelec
-MO_Basis
-Selectors_full
-Utils
-Pseudo
 AO_Basis
 Bitmask
-SingleRefMethod
+Determinants
 Electrons
-MOGuess
+Ezfio_files
-Nuclei
 Hartree_Fock
+IRPF90_man
+IRPF90_temp
 Integrals_Bielec
+Integrals_Monoelec
+MOGuess
+MO_Basis
+Makefile
+Makefile.depend
+Nuclei
+Pseudo
+Selectors_full
+SingleRefMethod
+Utils
 cid
-cid_lapack
+cid_lapack
+ezfio_interface.irp.f
+irpf90.make
+irpf90_entities
+tags

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

@@ -1,32 +1,31 @@
-# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
+# Automatically created by $QP_ROOT/scripts/module/module_handler.py 
-IRPF90_temp
+.ninja_deps
+.ninja_log
+AO_Basis
+Bitmask
+CID
+CID_selected
+Determinants
+Electrons
+Ezfio_files
+Hartree_Fock
 IRPF90_man
-irpf90_entities
+IRPF90_temp
-tags
+Integrals_Bielec
-irpf90.make
+Integrals_Monoelec
+MOGuess
+MO_Basis
 Makefile
 Makefile.depend
-build.ninja
+Nuclei
-.ninja_log
-.ninja_deps
-ezfio_interface.irp.f
-Ezfio_files
 Perturbation
-Determinants
+Properties
-Integrals_Monoelec
+Pseudo
-MO_Basis
 Selectors_full
 SingleRefMethod
 Utils
-CID
+cid_sc2_selection
-Pseudo
+ezfio_interface.irp.f
-Properties
+irpf90.make
-Bitmask
+irpf90_entities
-AO_Basis
+tags
-Electrons
-MOGuess
-CID_selected
-Nuclei
-Hartree_Fock
-Integrals_Bielec
-cid_sc2_selection

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

@@ -1,31 +1,30 @@
-# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
+# Automatically created by $QP_ROOT/scripts/module/module_handler.py 
-IRPF90_temp
-IRPF90_man
-irpf90_entities
-tags
-irpf90.make
-Makefile
-Makefile.depend
-build.ninja
-.ninja_log
 .ninja_deps
-ezfio_interface.irp.f
+.ninja_log
-Ezfio_files
-Perturbation
-Determinants
-Utils
-Integrals_Monoelec
-MO_Basis
-Selectors_full
-Integrals_Bielec
-CID
-Pseudo
 AO_Basis
 Bitmask
-SingleRefMethod
+CID
+Determinants
 Electrons
-MOGuess
+Ezfio_files
-Nuclei
 Hartree_Fock
+IRPF90_man
+IRPF90_temp
+Integrals_Bielec
+Integrals_Monoelec
+MOGuess
+MO_Basis
+Makefile
+Makefile.depend
+Nuclei
+Perturbation
 Properties
-cid_selection
+Pseudo
+Selectors_full
+SingleRefMethod
+Utils
+cid_selection
+ezfio_interface.irp.f
+irpf90.make
+irpf90_entities
+tags

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

@@ -1,29 +1,28 @@
-# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
+# Automatically created by $QP_ROOT/scripts/module/module_handler.py 
-IRPF90_temp
-IRPF90_man
-irpf90_entities
-tags
-irpf90.make
-Makefile
-Makefile.depend
-build.ninja
-.ninja_log
 .ninja_deps
-ezfio_interface.irp.f
+.ninja_log
-Ezfio_files
-Determinants
-Integrals_Monoelec
-MO_Basis
-Selectors_full
-Utils
-Pseudo
 AO_Basis
 Bitmask
-SingleRefMethod
+Determinants
 Electrons
-MOGuess
+Ezfio_files
-Nuclei
 Hartree_Fock
+IRPF90_man
+IRPF90_temp
 Integrals_Bielec
+Integrals_Monoelec
+MOGuess
+MO_Basis
+Makefile
+Makefile.depend
+Nuclei
+Pseudo
+Selectors_full
+SingleRefMethod
+Utils
+cis
+ezfio_interface.irp.f
+irpf90.make
+irpf90_entities
 super_ci
-cis
+tags

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

@@ -1,29 +1,28 @@
-# Automatically created by /home/giner/quantum_package/scripts/module/module_handler.py 
+# Automatically created by $QP_ROOT/scripts/module/module_handler.py 
-IRPF90_temp
-IRPF90_man
-irpf90_entities
-tags
-irpf90.make
-Makefile
-Makefile.depend
-build.ninja
-.ninja_log
 .ninja_deps
-ezfio_interface.irp.f
+.ninja_log
-Ezfio_files
-Determinants
-Integrals_Monoelec
-MO_Basis
-Selectors_full
-Utils
-Pseudo
 AO_Basis
 Bitmask
-SingleRefMethod
+Determinants
 Electrons
-MOGuess
+Ezfio_files
-Nuclei
 Hartree_Fock
+IRPF90_man
+IRPF90_temp
 Integrals_Bielec
+Integrals_Monoelec
+MOGuess
+MO_Basis
+Makefile
+Makefile.depend
+Nuclei
+Pseudo
+Selectors_full
+SingleRefMethod
+Utils
+cisd
 cisd_lapack
-cisd
+ezfio_interface.irp.f
+irpf90.make
+irpf90_entities
+tags

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#L5867>`_
+`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#L5349>`_
+`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#L5672>`_
+`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#L6631>`_
+`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#L6113>`_
+`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#L6436>`_
+`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#L1283>`_
+`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#L2047>`_
+`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#L1529>`_
+`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#L1852>`_
+`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#L765>`_
+`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#L1088>`_
+`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#L4339>`_
+`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#L3821>`_
+`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#L4144>`_
+`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#L3575>`_
+`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#L3057>`_
+`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#L3380>`_
+`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#L2811>`_
+`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#L2293>`_
+`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#L2616>`_
+`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#L519>`_
+`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#L324>`_
+`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#L5103>`_
+`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#L4585>`_
+`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#L4908>`_
+`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

@@ -1,32 +1,31 @@
-# Automatically created by /home/giner/quantum_package/scripts/module/module_handler.py 
+# Automatically created by $QP_ROOT/scripts/module/module_handler.py 
-IRPF90_temp
+.ninja_deps
+.ninja_log
+AO_Basis
+Bitmask
+CISD
+CISD_selected
+Determinants
+Electrons
+Ezfio_files
+Hartree_Fock
 IRPF90_man
-irpf90_entities
+IRPF90_temp
-tags
+Integrals_Bielec
-irpf90.make
+Integrals_Monoelec
+MOGuess
+MO_Basis
 Makefile
 Makefile.depend
-build.ninja
+Nuclei
-.ninja_log
-.ninja_deps
-ezfio_interface.irp.f
-Ezfio_files
 Perturbation
-Determinants
+Properties
-Integrals_Monoelec
+Pseudo
-MO_Basis
 Selectors_full
 SingleRefMethod
 Utils
-Pseudo
+cisd_sc2_selection
-Properties
+ezfio_interface.irp.f
-Bitmask
+irpf90.make
-AO_Basis
+irpf90_entities
-Electrons
+tags
-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#L1253>`_
+`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#L767>`_
+`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#L1946>`_
+`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#L1460>`_
+`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#L1765>`_
+`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#L1072>`_
+`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#L521>`_
+`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#L326>`_
+`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

@@ -1,31 +1,30 @@
-# Automatically created by /home/giner/quantum_package/scripts/module/module_handler.py 
+# Automatically created by $QP_ROOT/scripts/module/module_handler.py 
-IRPF90_temp
-IRPF90_man
-irpf90_entities
-tags
-irpf90.make
-Makefile
-Makefile.depend
-build.ninja
-.ninja_log
 .ninja_deps
-ezfio_interface.irp.f
+.ninja_log
-Ezfio_files
-Perturbation
-Determinants
-Utils
-Integrals_Monoelec
-MO_Basis
-Selectors_full
-Integrals_Bielec
-Pseudo
 AO_Basis
 Bitmask
-SingleRefMethod
-Electrons
-MOGuess
 CISD
-Nuclei
+Determinants
+Electrons
+Ezfio_files
 Hartree_Fock
+IRPF90_man
+IRPF90_temp
+Integrals_Bielec
+Integrals_Monoelec
+MOGuess
+MO_Basis
+Makefile
+Makefile.depend
+Nuclei
+Perturbation
 Properties
-cisd_selection
+Pseudo
+Selectors_full
+SingleRefMethod
+Utils
+cisd_selection
+ezfio_interface.irp.f
+irpf90.make
+irpf90_entities
+tags

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#L5867>`_
+`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#L5349>`_
+`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#L5672>`_
+`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#L6631>`_
+`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#L6113>`_
+`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#L6436>`_
+`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#L1283>`_
+`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#L2047>`_
+`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#L1529>`_
+`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#L1852>`_
+`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#L765>`_
+`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#L1088>`_
+`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#L4339>`_
+`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#L3821>`_
+`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#L4144>`_
+`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#L3575>`_
+`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#L3057>`_
+`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#L3380>`_
+`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#L2811>`_
+`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#L2293>`_
+`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#L2616>`_
+`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#L519>`_
+`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#L324>`_
+`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#L5103>`_
+`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#L4585>`_
+`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#L4908>`_
+`h_apply_cisd_selection_moller_plesset_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f_shell_10#L325>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.

plugins/Casino/.gitignore

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

plugins/DDCI_selected/.gitignore

@@ -1,30 +1,29 @@
-# Automatically created by /home/giner/quantum_package/scripts/module/module_handler.py 
+# Automatically created by $QP_ROOT/scripts/module/module_handler.py 
-IRPF90_temp
+.ninja_deps
+.ninja_log
+AO_Basis
+Bitmask
+Determinants
+Electrons
+Ezfio_files
+Generators_CAS
+Hartree_Fock
 IRPF90_man
-irpf90_entities
+IRPF90_temp
-tags
+Integrals_Bielec
-irpf90.make
+Integrals_Monoelec
+MOGuess
+MO_Basis
 Makefile
 Makefile.depend
-build.ninja
-.ninja_log
-.ninja_deps
-ezfio_interface.irp.f
-Ezfio_files
-Perturbation
-Determinants
-Utils
-Integrals_Monoelec
-MO_Basis
-Selectors_full
-Integrals_Bielec
-Pseudo
-Bitmask
-Generators_CAS
-AO_Basis
-Electrons
-MOGuess
 Nuclei
-Hartree_Fock
+Perturbation
 Properties
-ddci
+Pseudo
+Selectors_full
+Utils
+ddci
+ezfio_interface.irp.f
+irpf90.make
+irpf90_entities
+tags

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#L1267>`_
+`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#L774>`_
+`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#L1083>`_
+`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#L528>`_
+`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#L330>`_
+`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/Full_CI/.gitignore

@@ -22,6 +22,7 @@ Properties
 Pseudo
 Selectors_full
 Utils
+exc_degree
 ezfio_interface.irp.f
 full_ci
 full_ci_no_skip

plugins/Hartree_Fock/README.rst

@@ -29,7 +29,7 @@ Documentation
   Alpha Fock matrix in AO basis set
 
 
-`create_guess <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/SCF.irp.f#L8>`_
+`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
 
 
@@ -139,12 +139,15 @@ Documentation
   Maximum number of SCF iterations
 
 
-`run <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/SCF.irp.f#L33>`_
+`run <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/SCF.irp.f#L38>`_
   Run SCF calculation
 
 
-`scf <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/SCF.irp.f#L2>`_
+`scf <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/SCF.irp.f#L1>`_
-  Undocumented
+  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
+  optional: mo_basis.mo_coef
 
 
 `thresh_scf <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/ezfio_interface.irp.f#L46>`_

plugins/Hartree_Fock/SCF.irp.f

@@ -1,5 +1,10 @@
-
 program scf
+  BEGIN_DOC
+! 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
+! optional: mo_basis.mo_coef
+  END_DOC
   call create_guess
   call orthonormalize_mos
   call run

plugins/Hartree_Fock/huckel.irp.f

@@ -12,15 +12,17 @@ subroutine huckel_guess
   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)
+                                     size(mo_mono_elec_integral,1),  &
+                                     size(mo_mono_elec_integral,2),label)
   TOUCH mo_coef
 
   c = 0.5d0 * 1.75d0
+
   do j=1,ao_num
     do i=1,ao_num
-      if (i/=j) then
+      if (i.ne.j) then
         Fock_matrix_ao(i,j) = c*ao_overlap(i,j)*(ao_mono_elec_integral(i,i) + &
-           ao_mono_elec_integral(j,j))
+                                                 ao_mono_elec_integral(j,j))
       else
         Fock_matrix_ao(i,j) = Fock_matrix_alpha_ao(i,j)
       endif

plugins/MP2/.gitignore

@@ -1,30 +1,29 @@
-# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
+# Automatically created by $QP_ROOT/scripts/module/module_handler.py 
-IRPF90_temp
-IRPF90_man
-irpf90_entities
-tags
-irpf90.make
-Makefile
-Makefile.depend
-build.ninja
-.ninja_log
 .ninja_deps
-ezfio_interface.irp.f
+.ninja_log
-Ezfio_files
-Perturbation
-Determinants
-Utils
-Integrals_Monoelec
-MO_Basis
-Selectors_full
-Integrals_Bielec
-Pseudo
 AO_Basis
 Bitmask
-SingleRefMethod
+Determinants
 Electrons
-MOGuess
+Ezfio_files
-Nuclei
 Hartree_Fock
+IRPF90_man
+IRPF90_temp
+Integrals_Bielec
+Integrals_Monoelec
+MOGuess
+MO_Basis
+Makefile
+Makefile.depend
+Nuclei
+Perturbation
 Properties
-mp2
+Pseudo
+Selectors_full
+SingleRefMethod
+Utils
+ezfio_interface.irp.f
+irpf90.make
+irpf90_entities
+mp2
+tags

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/Perturbation/README.rst

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

plugins/QmcChem/.gitignore

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

plugins/loc_cele/.gitignore

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

plugins/loc_cele/README.rst

@@ -8,7 +8,7 @@ Documentation
   This program performs a localization of the active orbitals
   of a CASSCF wavefunction, reading the orbitals from a RASORB
   file of molcas.
-  id1=max number of MO in a given symmetry.
+  id1=max is the number of MO in a given symmetry.
 
 Needed Modules
 ==============

scripts/compilation/qp_create_ninja.py

@@ -19,11 +19,14 @@ try:
     from read_compilation_cfg import get_compilation_option
     from docopt import docopt
 except ImportError:
-    f = os.path.realpath(os.path.join(os.path.dirname(__file__),"..","..","quantum_package.rc"))
+    f = os.path.realpath(os.path.join(os.path.dirname(__file__),
+                                      "..",
+                                      "..",
+                                      "quantum_package.rc"))
     print """
 Error:
  source %s
-"""%f
+""" % f
     sys.exit(1)
 
 #  __
@@ -83,7 +86,9 @@ def ninja_create_env_variable(pwd_config_file):
     FC, FCFLAGS, IRPF90, IRPF90_FLAGS
     The env variable is usefull for the generation of EZFIO, and IRPF90
     """
-    l_string = []
+    l_string = ["builddir = {0}".format(os.path.dirname(ROOT_BUILD_NINJA)),
+                ""]
+
     for flag in ["FC", "FCFLAGS", "IRPF90", "IRPF90_FLAGS"]:
         str_ = "{0} = {1}".format(flag, get_compilation_option(pwd_config_file,
                                                                flag))
@@ -311,8 +316,11 @@ def ninja_symlink_build(path_module, l_symlink):
     if not l_symlink:
         return []
 
-    l_string = ["build l_symlink_{0} : phony {1}".format(
+    l_folder = [s.destination for s in l_symlink]
-        path_module.rel, " ".join([s.destination for s in l_symlink])), ""]
+
+    l_string = ["build l_symlink_{0} : phony {1}".format(path_module.rel,
+                                                         " ".join(l_folder)),
+                ""]
 
     for symlink in l_symlink:
         l_string += ["build {0}: build_symlink {1}".format(symlink.destination,
@@ -334,20 +342,22 @@ def ninja_gitignore_rule():
             "  description = Create gitignore for $module_rel", ""]
 
 
-def ninja_gitignore_build(path_module, d_binaries):
+def ninja_gitignore_build(path_module, d_binaries, l_symlink):
     """
     """
 
     path_gitignore = join(path_module.abs, ".gitignore")
 
     l_b = [i.abs for i in d_binaries[path_module]]
-    l_sym = [i.destination for i in l_symlink]
 
-    l_string = ["build {0}: build_gitignore {1} || l_symlink_{2}".format(path_gitignore,
+    root = "build {0}: build_gitignore {1}".format(path_gitignore,
-                                                                         " ".join(l_b),
+                                                   " ".join(l_b))
-                                                                         path_module.rel),
+    if l_symlink:
-                "   module_rel = {0}".format(path_module.rel),
+        l_string = ["{0} || l_symlink_{1}".format(root, path_module.rel)]
-                ""]
+    else:
+        l_string = ["{0}".format(root)]
+
+    l_string.extend(("   module_rel = {0}".format(path_module.rel), ""))
 
     return l_string
 
@@ -523,7 +533,7 @@ 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,
@@ -656,31 +666,24 @@ 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  _   _
 #  | | (/_ (/_   (_| (/_ |_) (/_ | | (_| (/_ | | (_ | (/_ _>
@@ -721,11 +724,13 @@ def ninja_dot_tree_build(path_module, l_module):
 # |  | (_) (_| |_| | (/_
 #
 def create_build_ninja_module(path_module):
-
+    l_string = ["builddir = {0}".format(os.path.dirname(ROOT_BUILD_NINJA)),
-    l_string = ["rule update_build_ninja_root",
-                "   command = {0} update".format(__file__),
                 ""]
 
+    l_string += ["rule update_build_ninja_root",
+                 "   command = {0} update".format(__file__),
+                 ""]
+
     l_string += ["rule make_local_binaries",
                  "   command = ninja -f {0} module_{1}".format(
                      ROOT_BUILD_NINJA, path_module.rel), "   pool = console",
@@ -753,7 +758,9 @@ 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 = ["builddir = {0}".format(os.path.dirname(ROOT_BUILD_NINJA)),
+                ""]
 
     l_string = ["rule update_build_ninja_root",
                 "   command = {0} update".format(__file__),
@@ -765,7 +772,7 @@ 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",
@@ -862,14 +869,7 @@ 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 #
@@ -877,15 +877,47 @@ 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.rel)
+            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:
 
@@ -909,8 +941,13 @@ if __name__ == "__main__":
         l_string += ninja_binaries_build(module_to_compile, l_children,
                                          d_binaries)
 
-        l_string += ninja_gitignore_build(module_to_compile, d_binaries)
+        l_string += ninja_gitignore_build(module_to_compile, d_binaries,
+                                          l_symlink)
 
-    with open(join(QP_ROOT, "config", "build.ninja"), "w+") as f:
+    # ~#~#~#~#~ #
+    # S a v e s #
+    # ~#~#~#~#~ #
+
+    with open(ROOT_BUILD_NINJA, "w+") as f:
         f.write(header)
         f.write("\n".join(l_string))

scripts/ezfio_interface/ei_handler.py

@@ -86,6 +86,7 @@ from os.path import isdir, join, exists
 from qp_path import QP_ROOT, QP_SRC, QP_OCAML, QP_EZFIO
 
 Type = namedtuple('Type', 'fancy ocaml fortran')
+Module = namedtuple('Module', 'path lower')
 
 
 def is_bool(str_):
@@ -789,8 +790,6 @@ if __name__ == "__main__":
 
     l_module_with_ezfio = []
 
-    Module = namedtuple('Module', 'path lower')
-
     for f in l_module:
         path = join(QP_SRC, f, "EZFIO.cfg")
         if exists(path):

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:
@@ -32,8 +32,7 @@ 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"))
 
 
@@ -84,15 +83,15 @@ 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)
 
@@ -110,7 +109,8 @@ 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
 
@@ -124,11 +124,12 @@ class ModuleHandler():
         d_child = self.dict_child
 
         for module_name in d_child:
-            try :
+            try:
                 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
@@ -147,7 +148,9 @@ 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
 
@@ -174,8 +177,17 @@ class ModuleHandler():
     def create_png(self, l_module):
         """Create the png of the dependency tree for a l_module"""
 
+        basename = "tree_dependency"
+        path = '{0}.png'.format(basename)
+
         # Init
-        import pydot
+        try:
+            from graphviz import Digraph
+        except:
+            with open(path, 'a'):
+                os.utime(path, None)
+            return
+
         all_ready_done = []
 
         def draw_module_edge(module, l_children):
@@ -184,39 +196,31 @@ 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)
 
-        path = '{0}.png'.format("tree_dependency")
+        graph = Digraph(comment=l_module, format="png", filename=basename)
-
-        # Init
-        try:
-            graph = pydot.Dot(graph_type='digraph')
-        except:
-            with open(path, 'a'):
-                os.utime(path, None)
-            return
-
         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:
@@ -241,14 +245,15 @@ 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

@@ -1,12 +1,12 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 """
-Usage: 
+Usage:
        qp_install_module.py create -n <name> [<children_module>...]
        qp_install_module.py download -n <name> [<path_folder>...]
        qp_install_module.py install <name>...
        qp_install_module.py list (--installed | --available-local)
-       qp_install_module.py uninstall <name>... [--and_ancestor]
+       qp_install_module.py uninstall <name>...
 
 
 Options:
@@ -16,15 +16,16 @@ Options:
 
 import sys
 import os
+import subprocess
 
 try:
     from docopt import docopt
     from module_handler import ModuleHandler, get_dict_child
     from module_handler import get_l_module_descendant
     from update_README import Doc_key, Needed_key
-    from qp_path import QP_SRC, QP_PLUGINS
+    from qp_path import QP_SRC, QP_PLUGINS, QP_ROOT
 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)
 
@@ -79,7 +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
@@ -101,9 +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])
@@ -152,8 +159,15 @@ if __name__ == '__main__':
                     except OSError:
                         print "Your src directory is broken. Please remove %s" % des
                         raise
-            print "Done"
+            try:
+                subprocess.check_call(["qp_create_ninja.py", "update"])
+            except:
+                raise
+
+            print "[ OK ]"
             print "You can now compile as usual"
+            print "`cd {0} ; ninja` for exemple".format(QP_ROOT)
+            print " or --in developement mode-- you can cd in a directory and compile here"
 
     elif arguments["uninstall"]:
 
@@ -164,24 +178,28 @@ if __name__ == '__main__':
         l_name = arguments["<name>"]
 
         l_failed = [name for name in l_name if name not in d_local]
+
         if l_failed:
             print "Modules not installed:"
             for name in sorted(l_failed):
                 print "* %s" % name
             sys.exit(1)
-        else:
-            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]]
+        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:
+        print "You will remove all of:"
-                l_name_to_remove = l_name
+        print l_name_to_remove
 
-            def unlink(x):
+        for module in set(l_name_to_remove):
-                try:
+
-                    os.unlink(os.path.join(QP_SRC, x))
+            try:
-                except OSError:
+                subprocess.check_call(["module_handler.py", "clean", module])
-                    print "%s is a core module which can not be renmoved" % x
+            except:
-            map(unlink, l_name_to_remove)
+                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" % module

src/.gitignore

@@ -23,4 +23,6 @@ QmcChem
 Selectors_full
 Selectors_no_sorted
 SingleRefMethod
-Casino
+Casino
+loc_cele
+Alavi

src/Determinants/README.rst

@@ -141,7 +141,7 @@ Documentation
   After calling this subroutine, N_det, psi_det and psi_coef need to be touched
 
 
-`create_wf_of_psi_svd_matrix <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L484>`_
+`create_wf_of_psi_svd_matrix <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L416>`_
   Matrix of wf coefficients. Outer product of alpha and beta determinants
 
 
@@ -347,7 +347,7 @@ Documentation
   Determinants are taken from the psi_det_sorted_ab array
 
 
-`generate_all_alpha_beta_det_products <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L539>`_
+`generate_all_alpha_beta_det_products <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L471>`_
   Create a wave function from all possible alpha x beta determinants
 
 
@@ -367,11 +367,11 @@ Documentation
   Applies get_excitation_degree to an array of determinants
 
 
-`get_index_in_psi_det_alpha_unique <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L140>`_
+`get_index_in_psi_det_alpha_unique <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L141>`_
   Returns the index of the determinant in the ``psi_det_alpha_unique`` array
 
 
-`get_index_in_psi_det_beta_unique <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L222>`_
+`get_index_in_psi_det_beta_unique <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L223>`_
   Returns the index of the determinant in the ``psi_det_beta_unique`` array
 
 
@@ -520,11 +520,11 @@ Documentation
   Number of determinants in the wave function
 
 
-`n_det_alpha_unique <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f_template_135#L4>`_
+`n_det_alpha_unique <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f_template_136#L4>`_
   Unique alpha determinants
 
 
-`n_det_beta_unique <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f_template_135#L80>`_
+`n_det_beta_unique <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f_template_136#L80>`_
   Unique beta determinants
 
 
@@ -697,19 +697,19 @@ Documentation
   is empty
 
 
-`psi_det_alpha <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L26>`_
+`psi_det_alpha <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L27>`_
   List of alpha determinants of psi_det
 
 
-`psi_det_alpha_unique <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f_template_135#L3>`_
+`psi_det_alpha_unique <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f_template_136#L3>`_
   Unique alpha determinants
 
 
-`psi_det_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L40>`_
+`psi_det_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L41>`_
   List of beta determinants of psi_det
 
 
-`psi_det_beta_unique <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f_template_135#L79>`_
+`psi_det_beta_unique <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f_template_136#L79>`_
   Unique beta determinants
 
 
@@ -770,31 +770,31 @@ Documentation
   psi_occ_pattern(:,2,j) = jth occ_pattern of the wave function : represent all the double occupation
 
 
-`psi_svd_alpha <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L579>`_
+`psi_svd_alpha <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L511>`_
   SVD wave function
 
 
-`psi_svd_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L580>`_
+`psi_svd_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L512>`_
   SVD wave function
 
 
-`psi_svd_coefs <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L581>`_
+`psi_svd_coefs <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L513>`_
   SVD wave function
 
 
-`psi_svd_matrix <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L468>`_
+`psi_svd_matrix <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L400>`_
   Matrix of wf coefficients. Outer product of alpha and beta determinants
 
 
-`psi_svd_matrix_columns <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L408>`_
+`psi_svd_matrix_columns <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L362>`_
   Matrix of wf coefficients. Outer product of alpha and beta determinants
 
 
-`psi_svd_matrix_rows <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L407>`_
+`psi_svd_matrix_rows <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L361>`_
   Matrix of wf coefficients. Outer product of alpha and beta determinants
 
 
-`psi_svd_matrix_values <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L406>`_
+`psi_svd_matrix_values <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L360>`_
   Matrix of wf coefficients. Outer product of alpha and beta determinants
 
 
@@ -910,6 +910,6 @@ Documentation
   Thresholds on selectors (fraction of the norm)
 
 
-`write_spindeterminants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L304>`_
+`write_spindeterminants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L305>`_
   Undocumented
 

src/Ezfio_files/.gitignore

@@ -9,4 +9,5 @@ Makefile.depend
 build.ninja
 .ninja_log
 .ninja_deps
-ezfio_interface.irp.f
+ezfio_interface.irp.f
+README.rst

src/Ezfio_files/README.rst

@@ -1,160 +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 ``QPACKAGE_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_cas_sd <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L41>`_
-  Output file for CAS_SD
-
-
-`output_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_cas <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L141>`_
-  Output file for Generators_CAS
-
-
-`output_generators_full <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L161>`_
-  Output file for Generators_full
-
-
-`output_hartree_fock <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L181>`_
-  Output file for Hartree_Fock
-
-
-`output_integrals_bielec <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L201>`_
-  Output file for Integrals_Bielec
-
-
-`output_integrals_monoelec <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L221>`_
-  Output file for Integrals_Monoelec
-
-
-`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_mrcc_cassd <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L281>`_
-  Output file for MRCC_CASSD
-
-
-`output_mrcc_utils <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L301>`_
-  Output file for MRCC_Utils
-
-
-`output_nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L321>`_
-  Output file for Nuclei
-
-
-`output_perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L341>`_
-  Output file for Perturbation
-
-
-`output_properties <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L361>`_
-  Output file for Properties
-
-
-`output_pseudo <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L381>`_
-  Output file for Pseudo
-
-
-`output_psiref_cas <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L401>`_
-  Output file for Psiref_CAS
-
-
-`output_psiref_threshold <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L421>`_
-  Output file for Psiref_threshold
-
-
-`output_psiref_utils <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L441>`_
-  Output file for Psiref_Utils
-
-
-`output_qmcchem <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L461>`_
-  Output file for QmcChem
-
-
-`output_selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L481>`_
-  Output file for Selectors_full
-
-
-`output_utils <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L501>`_
-  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.irp.f

@@ -1,11 +1,16 @@
 program H_CORE_guess
+  BEGIN_DOC
+! Produce `H_core` MO orbital 
+! output:  mo_basis.mo_tot_num mo_basis.mo_label mo_basis.ao_md5 mo_basis.mo_coef mo_basis.mo_occ
+  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)
+                                     size(mo_mono_elec_integral,1),  &
+                                     size(mo_mono_elec_integral,2),label)
   print *,  'save mos'
   call save_mos
   

src/MOGuess/README.rst

@@ -34,5 +34,10 @@ Documentation
 
 
 `h_core_guess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess/H_CORE_guess.irp.f#L1>`_
-  Undocumented
+  Produce `H_core` MO orbital
+  output:  mo_basis.mo_tot_num mo_basis.mo_label mo_basis.ao_md5 mo_basis.mo_coef mo_basis.mo_occ
+
+
+`hcore_guess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess/h_core_guess_routine.irp.f#L1>`_
+  Produce `H_core` MO orbital
 

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