Merge pull request #1 from LCPQ/master

Update before merge

.gitignore

@@ -1,15 +1,8 @@
 quantum_package.rc
-EZFIO/
-irpf90/
-EMSL_Basis/
-ninja/
-bin/
-*.log
 quantum_package_static.tar.gz
-resultsFile
-opam_installer.sh
-*.mod
-*.p
 build.ninja
 .ninja_log
 .ninja_deps
+bin/
+lib/
+config/qp_create_ninja.pickle

install/.gitignore

@@ -0,0 +1,10 @@
+config/qp_create_ninja.pickle
+Downloads
+_build
+docopt
+emsl
+EZFIO
+irpf90
+resultsFile
+zlib
+build.ninja

plugins/CAS_SD/.gitignore

@@ -1,32 +1,31 @@
-#
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
-# Do not modify this file. Add your ignored files to the gitignore
-# (without the dot at the beginning) file.
-#
 IRPF90_temp
 IRPF90_man
-irpf90.make
-tags
-Makefile.depend
 irpf90_entities
+tags
+irpf90.make
+Makefile
+Makefile.depend
 build.ninja
 .ninja_log
 .ninja_deps
-Pseudo
+ezfio_interface.irp.f
-Integrals_Monoelec
+Ezfio_files
-Generators_CAS
-Bitmask
-Integrals_Bielec
-AOs
-Selectors_full
-MOs
-Hartree_Fock
 Perturbation
 Determinants
-Electrons
 Utils
-Properties
+Integrals_Monoelec
-Nuclei
+MO_Basis
+Selectors_full
+Integrals_Bielec
+Pseudo
+Bitmask
+Generators_CAS
+AO_Basis
+Electrons
 MOGuess
-Ezfio_files
+Nuclei
+Hartree_Fock
+Properties
 cas_sd_selected
 cas_sd

plugins/CID/.gitignore

@@ -1,30 +1,29 @@
-#
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
-# Do not modify this file. Add your ignored files to the gitignore
-# (without the dot at the beginning) file.
-#
 IRPF90_temp
 IRPF90_man
-irpf90.make
-tags
-Makefile.depend
 irpf90_entities
+tags
+irpf90.make
+Makefile
+Makefile.depend
 build.ninja
 .ninja_log
 .ninja_deps
-Pseudo
+ezfio_interface.irp.f
-Integrals_Monoelec
-Bitmask
-Integrals_Bielec
-AOs
-Selectors_full
-MOs
-Hartree_Fock
-Determinants
-Electrons
-Utils
-Nuclei
-MOGuess
-SingleRefMethod
 Ezfio_files
+Determinants
+Integrals_Monoelec
+MO_Basis
+Selectors_full
+Utils
+Pseudo
+AO_Basis
+Bitmask
+SingleRefMethod
+Electrons
+MOGuess
+Nuclei
+Hartree_Fock
+Integrals_Bielec
 cid
 cid_lapack

plugins/CID/H_apply.irp.f

@@ -1,9 +1,9 @@
-! Generates subroutine H_apply_cisd
+! Generates subroutine H_apply_cid
 ! ----------------------------------
 
 BEGIN_SHELL [ /usr/bin/env python ]
 from generate_h_apply import H_apply
-H = H_apply("cisd",do_double_exc=True,do_mono_exc=False)
+H = H_apply("cid",do_double_exc=True,do_mono_exc=False)
 print H
 END_SHELL
 

plugins/CID/README.rst

@@ -1,7 +1,7 @@
-CISD
+CID
 ====
 
-This is a test directory which builds a CISD by setting the follwoing rules:
+This is a test directory which builds a CID by setting the follwoing rules:
 
 * The only generator determinant is the Hartee-Fock (single-reference method)
 * All generated determinants are included in the wave function (no perturbative
@@ -26,22 +26,179 @@ Documentation
 .. Do not edit this section. It was auto-generated from the
 .. by the `update_README.py` script.
 
-`cisd <http://github.com/LCPQ/quantum_package/tree/master/src/CID/cid_lapack.irp.f#L1>`_
+`cid <http://github.com/LCPQ/quantum_package/tree/master/src/CID/cid_lapack.irp.f#L1>`_
   Undocumented
 
 
-`h_apply_cisd <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#L406>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cisd_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_8#L1>`_
+`h_apply_cid_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f_shell_8#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_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#L263>`_
+  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 <http://github.com/LCPQ/quantum_package/tree/master/src/CID/H_apply.irp.f#L13>`_
+  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>`_
+  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>`_
+  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>`_
+  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>`_
+  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>`_
+  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>`_
+  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>`_
+  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>`_
+  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>`_
+  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>`_
+  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>`_
+  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>`_
+  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>`_
+  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>`_
+  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>`_
+  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>`_
+  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>`_
+  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>`_
+  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>`_
+  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>`_
+  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>`_
+  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>`_
+  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>`_
+  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>`_
+  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>`_
+  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/CID/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/CID/H_apply.irp.f_shell_10#L324>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.

plugins/CID/cid.irp.f

@@ -1,4 +1,4 @@
-program cisd
+program cid
   implicit none
   integer :: i
 
@@ -6,7 +6,7 @@ program cisd
   print *,  'N_states = ', N_states
   N_det = 1
   touch psi_det psi_coef N_det
-  call H_apply_cisd
+  call H_apply_cid
   print *,  'N_det = ', N_det
   do i = 1,N_states
    print *,  'energy  = ',CI_energy(i) 

plugins/CID/cid_lapack.irp.f

@@ -1,4 +1,4 @@
-program cisd
+program cid
   implicit none
   integer :: i
 
@@ -6,7 +6,7 @@ program cisd
   touch diag_algorithm
   print *,   'HF      = ', HF_energy
   print *,  'N_states = ', N_states
-  call H_apply_cisd
+  call H_apply_cid
   print *,  'N_det = ', N_det
   do i = 1,N_states
    print *,  'energy  = ',CI_energy(i) 

plugins/CID_SC2_selected/.gitignore

@@ -1,35 +1,32 @@
-#
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
-# Do not modify this file. Add your ignored files to the gitignore
-# (without the dot at the beginning) file.
-#
 IRPF90_temp
 IRPF90_man
-irpf90.make
-tags
-Makefile.depend
 irpf90_entities
+tags
+irpf90.make
+Makefile
+Makefile.depend
 build.ninja
 .ninja_log
 .ninja_deps
-CID_selected
+ezfio_interface.irp.f
-Pseudo
-Integrals_Monoelec
-Bitmask
-CID
-Integrals_Bielec
-CISD_selected
-AOs
-Selectors_full
-MOs
-Hartree_Fock
-Perturbation
-CISD
-Determinants
-Electrons
-Utils
-Properties
-Nuclei
-MOGuess
-SingleRefMethod
 Ezfio_files
+Perturbation
+Determinants
+Integrals_Monoelec
+MO_Basis
+Selectors_full
+SingleRefMethod
+Utils
+CID
+Pseudo
+Properties
+Bitmask
+AO_Basis
+Electrons
+MOGuess
+CID_selected
+Nuclei
+Hartree_Fock
+Integrals_Bielec
 cid_sc2_selection

plugins/CID_selected/.gitignore

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

plugins/CID_selected/README.rst

@@ -8,10 +8,6 @@ Documentation
 .. Do not edit this section. It was auto-generated from the
 .. by the `update_README.py` script.
 
-`cisd <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/cid_selection.irp.f#L1>`_
-  Undocumented
-
-
 `h_apply_cisd_selection <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f#L13>`_
   Undocumented
 

plugins/CIS/.gitignore

@@ -1,30 +1,29 @@
-#
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
-# Do not modify this file. Add your ignored files to the gitignore
-# (without the dot at the beginning) file.
-#
 IRPF90_temp
 IRPF90_man
-irpf90.make
-tags
-Makefile.depend
 irpf90_entities
+tags
+irpf90.make
+Makefile
+Makefile.depend
 build.ninja
 .ninja_log
 .ninja_deps
-Pseudo
+ezfio_interface.irp.f
-Integrals_Monoelec
-Bitmask
-Integrals_Bielec
-AOs
-Selectors_full
-MOs
-Hartree_Fock
-Determinants
-Electrons
-Utils
-Nuclei
-MOGuess
-SingleRefMethod
 Ezfio_files
+Determinants
+Integrals_Monoelec
+MO_Basis
+Selectors_full
+Utils
+Pseudo
+AO_Basis
+Bitmask
+SingleRefMethod
+Electrons
+MOGuess
+Nuclei
+Hartree_Fock
+Integrals_Bielec
 super_ci
 cis

plugins/CISD/.gitignore

@@ -1,30 +1,29 @@
-#
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
-# Do not modify this file. Add your ignored files to the gitignore
-# (without the dot at the beginning) file.
-#
 IRPF90_temp
 IRPF90_man
-irpf90.make
-tags
-Makefile.depend
 irpf90_entities
+tags
+irpf90.make
+Makefile
+Makefile.depend
 build.ninja
 .ninja_log
 .ninja_deps
-Pseudo
+ezfio_interface.irp.f
-Integrals_Monoelec
-Bitmask
-Integrals_Bielec
-AOs
-Selectors_full
-MOs
-Hartree_Fock
-Determinants
-Electrons
-Utils
-Nuclei
-MOGuess
-SingleRefMethod
 Ezfio_files
+Determinants
+Integrals_Monoelec
+MO_Basis
+Selectors_full
+Utils
+Pseudo
+AO_Basis
+Bitmask
+SingleRefMethod
+Electrons
+MOGuess
+Nuclei
+Hartree_Fock
+Integrals_Bielec
 cisd_lapack
 cisd

plugins/DDCI_selected/.gitignore

@@ -1,31 +1,30 @@
-#
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
-# Do not modify this file. Add your ignored files to the gitignore
-# (without the dot at the beginning) file.
-#
 IRPF90_temp
 IRPF90_man
-irpf90.make
-tags
-Makefile.depend
 irpf90_entities
+tags
+irpf90.make
+Makefile
+Makefile.depend
 build.ninja
 .ninja_log
 .ninja_deps
-Pseudo
+ezfio_interface.irp.f
-Integrals_Monoelec
+Ezfio_files
-Generators_CAS
-Bitmask
-Integrals_Bielec
-AOs
-Selectors_full
-MOs
-Hartree_Fock
 Perturbation
 Determinants
-Electrons
 Utils
-Properties
+Integrals_Monoelec
-Nuclei
+MO_Basis
+Selectors_full
+Integrals_Bielec
+Pseudo
+Bitmask
+Generators_CAS
+AO_Basis
+Electrons
 MOGuess
-Ezfio_files
+Nuclei
+Hartree_Fock
+Properties
 ddci

plugins/FCIdump/.gitignore

@@ -1,25 +1,24 @@
-#
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
-# Do not modify this file. Add your ignored files to the gitignore
-# (without the dot at the beginning) file.
-#
 IRPF90_temp
 IRPF90_man
-irpf90.make
-tags
-Makefile.depend
 irpf90_entities
+tags
+irpf90.make
+Makefile
+Makefile.depend
 build.ninja
 .ninja_log
 .ninja_deps
-Pseudo
+ezfio_interface.irp.f
-Integrals_Monoelec
-Bitmask
-Integrals_Bielec
-AOs
-MOs
-Determinants
-Electrons
-Utils
-Nuclei
 Ezfio_files
+Determinants
+Integrals_Monoelec
+MO_Basis
+Utils
+Pseudo
+Bitmask
+AO_Basis
+Electrons
+Nuclei
+Integrals_Bielec
 fcidump

plugins/Full_CI/.gitignore

@@ -1,33 +1,32 @@
-#
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
-# Do not modify this file. Add your ignored files to the gitignore
-# (without the dot at the beginning) file.
-#
 IRPF90_temp
 IRPF90_man
-irpf90.make
-tags
-Makefile.depend
 irpf90_entities
+tags
+irpf90.make
+Makefile
+Makefile.depend
 build.ninja
 .ninja_log
 .ninja_deps
-Generators_full
+ezfio_interface.irp.f
-Pseudo
+Ezfio_files
-Integrals_Monoelec
-Bitmask
-Integrals_Bielec
-AOs
-Selectors_full
-MOs
-Hartree_Fock
 Perturbation
 Determinants
-Electrons
 Utils
-Properties
+Integrals_Monoelec
-Nuclei
+MO_Basis
+Selectors_full
+Integrals_Bielec
+Pseudo
+Generators_full
+Bitmask
+AO_Basis
+Electrons
 MOGuess
-Ezfio_files
+Nuclei
+Hartree_Fock
+Properties
 target_pt2
 full_ci
 var_pt2_ratio

plugins/Generators_CAS/.gitignore

@@ -1,13 +1,23 @@
-#
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
-# Do not modify this file. Add your ignored files to the gitignore
-# (without the dot at the beginning) file.
-#
 IRPF90_temp
 IRPF90_man
-irpf90.make
-tags
-Makefile.depend
 irpf90_entities
+tags
+irpf90.make
+Makefile
+Makefile.depend
 build.ninja
 .ninja_log
 .ninja_deps
+ezfio_interface.irp.f
+Ezfio_files
+Determinants
+Integrals_Monoelec
+MO_Basis
+Utils
+Pseudo
+Bitmask
+AO_Basis
+Electrons
+Nuclei
+Integrals_Bielec

plugins/Generators_full/.gitignore

@@ -1,13 +1,25 @@
-#
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
-# Do not modify this file. Add your ignored files to the gitignore
-# (without the dot at the beginning) file.
-#
 IRPF90_temp
 IRPF90_man
-irpf90.make
-tags
-Makefile.depend
 irpf90_entities
+tags
+irpf90.make
+Makefile
+Makefile.depend
 build.ninja
 .ninja_log
 .ninja_deps
+ezfio_interface.irp.f
+Ezfio_files
+Determinants
+Integrals_Monoelec
+MO_Basis
+Utils
+Pseudo
+Bitmask
+AO_Basis
+Electrons
+MOGuess
+Nuclei
+Hartree_Fock
+Integrals_Bielec

plugins/Hartree_Fock/.gitignore

@@ -1,26 +1,25 @@
-#
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
-# Do not modify this file. Add your ignored files to the gitignore
-# (without the dot at the beginning) file.
-#
 IRPF90_temp
 IRPF90_man
-irpf90.make
-tags
-Makefile.depend
 irpf90_entities
+tags
+irpf90.make
+Makefile
+Makefile.depend
 build.ninja
 .ninja_log
 .ninja_deps
-Pseudo
+ezfio_interface.irp.f
-Integrals_Monoelec
-Bitmask
-Integrals_Bielec
-AOs
-MOs
-Electrons
-Utils
-Nuclei
-MOGuess
 Ezfio_files
+Integrals_Monoelec
+MO_Basis
+Integrals_Bielec
+Pseudo
+Bitmask
+AO_Basis
+Electrons
+MOGuess
+Nuclei
+Utils
 Huckel_guess
 SCF

plugins/MP2/.gitignore

@@ -1,31 +1,30 @@
-#
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
-# Do not modify this file. Add your ignored files to the gitignore
-# (without the dot at the beginning) file.
-#
 IRPF90_temp
 IRPF90_man
-irpf90.make
-tags
-Makefile.depend
 irpf90_entities
+tags
+irpf90.make
+Makefile
+Makefile.depend
 build.ninja
 .ninja_log
 .ninja_deps
-Pseudo
+ezfio_interface.irp.f
-Integrals_Monoelec
+Ezfio_files
-Bitmask
-Integrals_Bielec
-AOs
-Selectors_full
-MOs
-Hartree_Fock
 Perturbation
 Determinants
-Electrons
 Utils
-Properties
+Integrals_Monoelec
-Nuclei
+MO_Basis
-MOGuess
+Selectors_full
+Integrals_Bielec
+Pseudo
+AO_Basis
+Bitmask
 SingleRefMethod
-Ezfio_files
+Electrons
+MOGuess
+Nuclei
+Hartree_Fock
+Properties
 mp2

plugins/MRCC/.gitignore

@@ -1,31 +1,30 @@
-#
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
-# Do not modify this file. Add your ignored files to the gitignore
-# (without the dot at the beginning) file.
-#
 IRPF90_temp
 IRPF90_man
-irpf90.make
-tags
-Makefile.depend
 irpf90_entities
+tags
+irpf90.make
+Makefile
+Makefile.depend
 build.ninja
 .ninja_log
 .ninja_deps
-Generators_full
+ezfio_interface.irp.f
-Pseudo
+Ezfio_files
-Integrals_Monoelec
-Bitmask
-Integrals_Bielec
-AOs
-Selectors_full
-MOs
-Hartree_Fock
 Perturbation
 Determinants
-Electrons
 Utils
-Properties
+Integrals_Monoelec
-Nuclei
+MO_Basis
+Selectors_full
+Integrals_Bielec
+Pseudo
+Generators_full
+Bitmask
+AO_Basis
+Electrons
 MOGuess
-Ezfio_files
+Nuclei
+Hartree_Fock
+Properties
 mrcc

plugins/Perturbation/.gitignore

@@ -1,13 +1,26 @@
-#
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
-# Do not modify this file. Add your ignored files to the gitignore
-# (without the dot at the beginning) file.
-#
 IRPF90_temp
 IRPF90_man
-irpf90.make
-tags
-Makefile.depend
 irpf90_entities
+tags
+irpf90.make
+Makefile
+Makefile.depend
 build.ninja
 .ninja_log
 .ninja_deps
+ezfio_interface.irp.f
+Ezfio_files
+Determinants
+Integrals_Monoelec
+MO_Basis
+Utils
+Pseudo
+Properties
+Bitmask
+AO_Basis
+Electrons
+MOGuess
+Nuclei
+Hartree_Fock
+Integrals_Bielec

plugins/Properties/.gitignore

@@ -1,13 +1,23 @@
-#
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
-# Do not modify this file. Add your ignored files to the gitignore
-# (without the dot at the beginning) file.
-#
 IRPF90_temp
 IRPF90_man
-irpf90.make
-tags
-Makefile.depend
 irpf90_entities
+tags
+irpf90.make
+Makefile
+Makefile.depend
 build.ninja
 .ninja_log
 .ninja_deps
+ezfio_interface.irp.f
+Ezfio_files
+Determinants
+Integrals_Monoelec
+MO_Basis
+Utils
+Pseudo
+Bitmask
+AO_Basis
+Electrons
+Nuclei
+Integrals_Bielec

plugins/Selectors_full/.gitignore

@@ -1,13 +1,25 @@
-#
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
-# Do not modify this file. Add your ignored files to the gitignore
-# (without the dot at the beginning) file.
-#
 IRPF90_temp
 IRPF90_man
-irpf90.make
-tags
-Makefile.depend
 irpf90_entities
+tags
+irpf90.make
+Makefile
+Makefile.depend
 build.ninja
 .ninja_log
 .ninja_deps
+ezfio_interface.irp.f
+Ezfio_files
+Determinants
+Integrals_Monoelec
+MO_Basis
+Utils
+Pseudo
+Bitmask
+AO_Basis
+Electrons
+MOGuess
+Nuclei
+Hartree_Fock
+Integrals_Bielec

plugins/SingleRefMethod/.gitignore

@@ -1,13 +1,19 @@
-#
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
-# Do not modify this file. Add your ignored files to the gitignore
-# (without the dot at the beginning) file.
-#
 IRPF90_temp
 IRPF90_man
-irpf90.make
-tags
-Makefile.depend
 irpf90_entities
+tags
+irpf90.make
+Makefile
+Makefile.depend
 build.ninja
 .ninja_log
 .ninja_deps
+ezfio_interface.irp.f
+Ezfio_files
+MO_Basis
+Utils
+Bitmask
+AO_Basis
+Electrons
+Nuclei

scripts/compilation/qp_create_ninja.py

@@ -257,7 +257,7 @@ def ninja_ezfio_rule():
 
     install_lib_ezfio = join(QP_ROOT, 'install', 'EZFIO', "lib", "libezfio.a")
     l_cmd = ["cd {0}".format(QP_EZFIO)] + l_flag
-    l_cmd += ["ninja && ln -sf {0} {1}".format(install_lib_ezfio, EZFIO_LIB)]
+    l_cmd += ["rm -f make.config ; ninja && ln -sf {0} {1}".format(install_lib_ezfio, EZFIO_LIB)]
 
     l_string = ["rule build_ezfio",
                 "   command = {0}".format(" ; ".join(l_cmd)),
@@ -320,6 +320,37 @@ def ninja_symlink_build(path_module, l_symlink):
     return l_string
 
 
+#
+#    _  o _|_ o  _  ._   _  ._ _
+# o (_| |  |_ | (_| | | (_) | (/_
+#    _|          _|
+def ninja_gitignore_rule():
+    """
+    Return the command to create the gitignore
+    """
+    return ["rule build_gitignore",
+            "  command = module_handler.py create_git_ignore $module_rel",
+            "  description = Create gitignore for $module_rel", ""]
+
+
+def ninja_gitignore_build(path_module, l_symlink, d_binaries):
+    """
+    """
+
+    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} || {2}".format(path_gitignore,
+                                                               " ".join(l_b),
+                                                               " ".join(l_sym)),
+                "   module_rel = {0}".format(path_module.rel),
+                ""]
+
+    return l_string
+
+
 #           _  _   _
 # o ._ ._ _|_ (_| / \   ._ _   _. |   _
 # | |  |_) |    | \_/ o | | | (_| |< (/_
@@ -700,7 +731,7 @@ def create_build_ninja_module(path_module):
                  "  pool = console", "  description = Compile all the module",
                  ""]
 
-    l_string += ["rule make_clean", "  command = clean_modules.sh",
+    l_string += ["rule make_clean", "  command = module_handler.py clean {0}".format(path_module.rel),
                  "  description = Cleaning module {0}".format(path_module.rel),
                  ""]
 
@@ -787,6 +818,7 @@ if __name__ == "__main__":
 
     l_string += ninja_irpf90_make_rule()
     l_string += ninja_readme_rule()
+    l_string += ninja_gitignore_rule()
 
     l_string += ninja_binaries_rule()
 
@@ -871,6 +903,8 @@ if __name__ == "__main__":
         l_string += ninja_binaries_build(module_to_compile, l_children,
                                          d_binaries)
 
+        l_string += ninja_gitignore_build(module_to_compile, l_symlink, d_binaries)
+
     with open(join(QP_ROOT, "config", "build.ninja"), "w+") as f:
         f.write(header)
         f.write("\n".join(l_string))

scripts/module/clean_modules.sh

@@ -1,37 +0,0 @@
-#!/bin/bash 
-#
-# Cleans a module directory 
-
-if [[ -z ${QP_ROOT} ]]
-then
-  print "The QP_ROOT environment variable is not set."
-  print "Please reload the quantum_package.rc file."
-  exit -1
-fi
-source ${QP_ROOT}/scripts/qp_include.sh
-
-function do_clean()
-{
-  rm -rf -- \
-    IRPF90_temp IRPF90_man \
-    $(module_handler.py print_descendant) include \
-    ezfio_interface.irp.f irpf90.make irpf90_entities tags $(ls_exe) *.mod
-}
-
-if [[ -z $1 ]]
-then
-  check_current_dir_is_module
-  do_clean
-else
-  check_current_dir_is_src
-  for i in $@
-  do
-    if [[ -d $i ]]
-    then
-       cd $i
-       do_clean
-       cd $OLDPWD
-    fi
-  done
-fi
-

scripts/module/module_handler.py

@@ -7,6 +7,7 @@ Usage:
     module_handler.py print_descendant      [<module_name>...]
     module_handler.py create_png            [<module_name>...]
     module_handler.py clean                 [<module_name>...]
+    module_handler.py create_git_ignore     [<module_name>...]
 
 Options:
     print_descendant         Print the genealogy of the NEEDED_CHILDREN_MODULES
@@ -18,6 +19,7 @@ Options:
 import os
 import sys
 import os.path
+import shutil
 
 try:
     from docopt import docopt
@@ -34,6 +36,10 @@ def is_module(path_module):
                                        "NEEDED_CHILDREN_MODULES"))
 
 
+def is_exe(fpath):
+    return os.path.isfile(fpath) and os.access(fpath, os.X_OK)
+
+
 def get_dict_child(l_root_abs=None):
     """Loop over MODULE in  QP_ROOT/src, open all the NEEDED_CHILDREN_MODULES
     and create a dict[MODULE] = [sub module needed, ...]
@@ -227,37 +233,48 @@ if __name__ == '__main__':
     if arguments["create_png"]:
         m.create_png(l_module)
 
-    if arguments["clean"]:
+    if arguments["clean"] or arguments["create_git_ignore"]:
+
+        l_dir = ['IRPF90_temp', 'IRPF90_man']
+        l_file = ["irpf90_entities", "tags", "irpf90.make",
+                  "Makefile", "Makefile.depend",
+                  "build.ninja", ".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))]
 
-            import shutil
+            if arguments["clean"]:
-
+                for f in l_dir:
-            for f in ['IRPF90_temp', 'IRPF90_man']:
                     try:
                         shutil.rmtree(os.path.join(module_abs, f))
                     except:
                         pass
 
-            for symlink in m.l_descendant_unique([module]):
+                for symlink in l_symlink:
                     try:
-                    os.unlink(os.path.join(module_abs,symlink))
+                        os.unlink(os.path.join(module_abs, symlink))
                     except:
                         pass
 
-            for f in ["irpf90_entities", "tags", "irpf90.make", "Makefile"]:
+                for f in l_file:
-                try:
-                    os.remove(os.path.join(module_abs,f))
-                except:
-                    pass
-
-            for f in os.listdir(module_abs):
-
-                def is_exe(fpath):
-                    return os.path.isfile(fpath) and os.access(fpath, os.X_OK)
-
-                if is_exe(f):
                     try:
                         os.remove(os.path.join(module_abs, f))
                     except:
                         pass
+
+                for f in l_exe:
+
+                    try:
+                        os.remove(os.path.join(module_abs, f))
+                    except:
+                        pass
+
+            if arguments["create_git_ignore"]:
+                path = os.path.join(module_abs, ".gitignore")
+
+                with open(path, "w+") as f:
+                    f.write("# Automatically created by {0} \n".format(__file__))
+                    f.write("\n".join(l_dir + l_file + l_symlink + l_exe))

scripts/module/qp_install_module.py

@@ -5,12 +5,12 @@ 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|--avalaible-local)
+       qp_install_module.py list (--installed | --available-local)
        qp_install_module.py uninstall <name>... [--and_ancestor]
 
 
 Options:
-    list: List all the module avalaible
+    list: List all the module available
     create: Create a new module
 """
 
@@ -22,7 +22,7 @@ try:
     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_ROOT, QP_SRC, QP_PLUGINS
+    from qp_path import QP_SRC, QP_PLUGINS
 
 except ImportError:
     print "source .quantum_package.rc"
@@ -66,7 +66,7 @@ if __name__ == '__main__':
 
         if arguments["--installed"]:
             l_repository = [QP_SRC]
-        elif arguments["--avalaible-local"]:
+        elif arguments["--available-local"]:
             l_repository = [QP_PLUGINS]
 
         m_instance = ModuleHandler(l_repository)
@@ -87,7 +87,7 @@ if __name__ == '__main__':
         for children in l_children:
             if children not in m_instance.dict_descendant:
                 print "This module ({0}) is not a valide module.".format(children)
-                print "Run `list` flag for the list of module avalaible"
+                print "Run `list` flag for the list of module available"
                 print "Maybe you need to install some module first"
                 print "Aborting..."
                 sys.exit(1)

scripts/qp_include.sh

@@ -1,78 +0,0 @@
-#!/bin/bash
-#
-# Useful functions in all scripts
-
-# Make a list unique
-function unique_list()
-{
-  for d in $@
-  do
-    echo $d
-  done | sort | uniq
-}
-
-function check_current_dir_is_src()
-{
-  if [[ "${PWD}" == "${QP_ROOT}/src" ]]
-  then
-     return 0
-  else
-     echo "Current directory should be \$QP_ROOT/src"
-     exit -1
-  fi
-}
-
-function check_current_dir_is_module()
-{
-  # If the prefix ${QP_ROOT}/src/ can be removed from $PWD, it means that
-  # $PWD is somewhere below ${QP_ROOT}/src/ so it is a module.
-  # If the prefix ${QP_ROOT}/src/ can not be removed from $PWD, then
-  # "${PWD##${QP_ROOT}/src/}" == "$PWD".
-
-  if [[ "${PWD##${QP_ROOT}/src/}" != "$PWD" ]]
-  then
-     return 0
-  else
-     echo "You are not in a submodule"
-     exit -1
-  fi
-}
-
-# List of executables in the current directory
-function ls_exe()
-{
-  find . -perm /u+x -type f
-}
-
-function asksure() {
-  echo -n $@ "(Y/N) "
-  answer=w
-  while [[ $answer != [YyNn] ]]
-  do
-     read answer
-     [[ $answer = [Yy] ]] && retval=0 || retval=1
-  done
-  return $retval
-}
-
-function error()
-{
-  echo "-------------------- Error --------------------"
-  printf "$@\n"
-  echo "-----------------------------------------------"
-  exit -1
-}
-
-if [[ -z ${DEBUG} ]]
-then
-  function info ()
-  {
-    :
-  }
-else
-  function info ()
-  {
-    echo "$@"
-  }
-fi
-

src/.gitignore

@@ -1,2 +1,25 @@
-Makefile.config
+CAS_SD
-ezfio_interface.irp.f
+CID
+CID_SC2_selected
+CID_selected
+CIS
+CISD
+CISD_SC2_selected
+CISD_selected
+DDCI_selected
+DensityMatrix
+FCIdump
+Full_CI
+Generators_CAS
+Generators_full
+Generators_restart
+Hartree_Fock
+Molden
+MP2
+MRCC
+Perturbation
+Properties
+QmcChem
+Selectors_full
+Selectors_no_sorted
+SingleRefMethod

src/AO_Basis/.gitignore

@@ -1,13 +1,15 @@
-#
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
-# Do not modify this file. Add your ignored files to the gitignore
-# (without the dot at the beginning) file.
-#
 IRPF90_temp
 IRPF90_man
-irpf90.make
-tags
-Makefile.depend
 irpf90_entities
+tags
+irpf90.make
+Makefile
+Makefile.depend
 build.ninja
 .ninja_log
 .ninja_deps
+ezfio_interface.irp.f
+Nuclei
+Ezfio_files
+Utils

src/Bitmask/.gitignore

@@ -1,13 +1,18 @@
-#
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
-# Do not modify this file. Add your ignored files to the gitignore
-# (without the dot at the beginning) file.
-#
 IRPF90_temp
 IRPF90_man
-irpf90.make
-tags
-Makefile.depend
 irpf90_entities
+tags
+irpf90.make
+Makefile
+Makefile.depend
 build.ninja
 .ninja_log
 .ninja_deps
+ezfio_interface.irp.f
+Ezfio_files
+MO_Basis
+Utils
+AO_Basis
+Electrons
+Nuclei

src/Determinants/.gitignore

@@ -1,32 +1,30 @@
-#
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
-# Do not modify this file. Add your ignored files to the gitignore
-# (without the dot at the beginning) file.
-#
 IRPF90_temp
 IRPF90_man
-irpf90.make
-tags
-Makefile.depend
 irpf90_entities
+tags
+irpf90.make
+Makefile
+Makefile.depend
 build.ninja
 .ninja_log
 .ninja_deps
-Pseudo
+ezfio_interface.irp.f
-Integrals_Monoelec
-Bitmask
-Integrals_Bielec
-AOs
-MOs
-Electrons
-Utils
-Nuclei
 Ezfio_files
+Integrals_Monoelec
+MO_Basis
+Utils
+Pseudo
+Bitmask
+AO_Basis
+Electrons
+Nuclei
+Integrals_Bielec
 guess_triplet
 guess_singlet
 truncate_wf
 save_natorb
-save_for_qmcchem
+program_initial_determinants
-program_beginer_determinants
 save_for_casino
 det_svd
 guess_doublet

src/Determinants/EZFIO.cfg

@@ -68,8 +68,8 @@ doc: bit_kind
 type: Bit_kind
 
 [mo_label]
-interface: ezfio,provider
+interface: ezfio
-doc: o_label
+doc: mo_label
 type: character*(64)
 
 [n_det]

src/Determinants/README.rst

@@ -213,11 +213,11 @@ Documentation
   Build connection proxy between determinants
 
 
-`det_num <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/ezfio_interface.irp.f#L266>`_
+`det_num <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/ezfio_interface.irp.f#L248>`_
   det_num
 
 
-`det_occ <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/ezfio_interface.irp.f#L244>`_
+`det_occ <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/ezfio_interface.irp.f#L226>`_
   det_occ
 
 
@@ -525,7 +525,7 @@ Documentation
   Maximum number of determinants diagonalized by Jacobi
 
 
-`n_det_max_property <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/ezfio_interface.irp.f#L310>`_
+`n_det_max_property <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/ezfio_interface.irp.f#L292>`_
   Max number of determinants in the wave function when you select for a given property
 
 
@@ -874,7 +874,7 @@ Documentation
   convergence of the correlation energy of SC2 iterations
 
 
-`threshold_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/ezfio_interface.irp.f#L288>`_
+`threshold_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/ezfio_interface.irp.f#L270>`_
   Thresholds on generators (fraction of the norm)
 
 

src/Electrons/.gitignore

@@ -1,13 +1,13 @@
-#
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
-# Do not modify this file. Add your ignored files to the gitignore
-# (without the dot at the beginning) file.
-#
 IRPF90_temp
 IRPF90_man
-irpf90.make
-tags
-Makefile.depend
 irpf90_entities
+tags
+irpf90.make
+Makefile
+Makefile.depend
 build.ninja
 .ninja_log
 .ninja_deps
+ezfio_interface.irp.f
+Ezfio_files

src/Ezfio_files/.gitignore

@@ -1,13 +1,12 @@
-#
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
-# Do not modify this file. Add your ignored files to the gitignore
-# (without the dot at the beginning) file.
-#
 IRPF90_temp
 IRPF90_man
-irpf90.make
-tags
-Makefile.depend
 irpf90_entities
+tags
+irpf90.make
+Makefile
+Makefile.depend
 build.ninja
 .ninja_log
 .ninja_deps
+ezfio_interface.irp.f

src/Ezfio_files/README.rst

@@ -38,71 +38,95 @@ Documentation
   Output file for Bitmask
 
 
+`output_cas_sd <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L41>`_
+  Output file for CAS_SD
+
+
+`output_cid <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L61>`_
+  Output file for CID
+
+
+`output_cid_sc2_selected <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L81>`_
+  Output file for CID_SC2_selected
+
+
+`output_cid_selected <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L101>`_
+  Output file for CID_selected
+
+
 `output_cpu_time_0 <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f#L2>`_
   Initial CPU and wall times when printing in the output files
 
 
-`output_determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L41>`_
+`output_determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L121>`_
   Output file for Determinants
 
 
-`output_electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L61>`_
+`output_electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L141>`_
   Output file for Electrons
 
 
-`output_ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L81>`_
+`output_ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L161>`_
   Output file for Ezfio_files
 
 
-`output_full_ci <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L101>`_
+`output_generators_cas <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L181>`_
-  Output file for Full_CI
+  Output file for Generators_CAS
 
 
-`output_generators_full <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L121>`_
+`output_generators_full <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L201>`_
   Output file for Generators_full
 
 
-`output_hartree_fock <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L141>`_
+`output_hartree_fock <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L221>`_
   Output file for Hartree_Fock
 
 
-`output_integrals_bielec <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L161>`_
+`output_integrals_bielec <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L241>`_
   Output file for Integrals_Bielec
 
 
-`output_integrals_monoelec <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L181>`_
+`output_integrals_monoelec <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L261>`_
   Output file for Integrals_Monoelec
 
 
-`output_mo_basis <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L201>`_
+`output_mo_basis <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L281>`_
   Output file for MO_Basis
 
 
-`output_moguess <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L221>`_
+`output_moguess <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L301>`_
   Output file for MOGuess
 
 
-`output_nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L241>`_
+`output_mrcc <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L321>`_
+  Output file for MRCC
+
+
+`output_nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L341>`_
   Output file for Nuclei
 
 
-`output_perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L261>`_
+`output_perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L361>`_
   Output file for Perturbation
 
 
-`output_properties <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L281>`_
+`output_properties <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L381>`_
   Output file for Properties
 
 
-`output_pseudo <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L301>`_
+`output_pseudo <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L401>`_
   Output file for Pseudo
 
 
-`output_selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L321>`_
+`output_selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L421>`_
   Output file for Selectors_full
 
 
-`output_utils <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L341>`_
+`output_singlerefmethod <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L441>`_
+  Output file for SingleRefMethod
+
+
+`output_utils <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L461>`_
   Output file for Utils
 
 

src/Integrals_Bielec/.gitignore

@@ -1,13 +1,20 @@
-#
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
-# Do not modify this file. Add your ignored files to the gitignore
-# (without the dot at the beginning) file.
-#
 IRPF90_temp
 IRPF90_man
-irpf90.make
-tags
-Makefile.depend
 irpf90_entities
+tags
+irpf90.make
+Makefile
+Makefile.depend
 build.ninja
 .ninja_log
 .ninja_deps
+ezfio_interface.irp.f
+Ezfio_files
+MO_Basis
+Utils
+Pseudo
+Bitmask
+AO_Basis
+Electrons
+Nuclei

src/Integrals_Monoelec/.gitignore

@@ -1,22 +1,21 @@
-#
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
-# Do not modify this file. Add your ignored files to the gitignore
-# (without the dot at the beginning) file.
-#
 IRPF90_temp
 IRPF90_man
-irpf90.make
-tags
-Makefile.depend
 irpf90_entities
+tags
+irpf90.make
+Makefile
+Makefile.depend
 build.ninja
 .ninja_log
 .ninja_deps
-Pseudo
+ezfio_interface.irp.f
-AOs
-MOs
-Electrons
-Utils
-Nuclei
 Ezfio_files
+MO_Basis
+Utils
+Pseudo
+AO_Basis
+Electrons
+Nuclei
 check_orthonormality
 save_ortho_mos

src/MOGuess/.gitignore

@@ -1,22 +1,21 @@
-#
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
-# Do not modify this file. Add your ignored files to the gitignore
-# (without the dot at the beginning) file.
-#
 IRPF90_temp
 IRPF90_man
-irpf90.make
-tags
-Makefile.depend
 irpf90_entities
+tags
+irpf90.make
+Makefile
+Makefile.depend
 build.ninja
 .ninja_log
 .ninja_deps
-Pseudo
+ezfio_interface.irp.f
-Integrals_Monoelec
-AOs
-MOs
-Electrons
-Utils
-Nuclei
 Ezfio_files
+Integrals_Monoelec
+MO_Basis
+Utils
+Pseudo
+AO_Basis
+Electrons
+Nuclei
 H_CORE_guess

src/MO_Basis/.gitignore

@@ -1,13 +1,17 @@
-#
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
-# Do not modify this file. Add your ignored files to the gitignore
-# (without the dot at the beginning) file.
-#
 IRPF90_temp
 IRPF90_man
-irpf90.make
-tags
-Makefile.depend
 irpf90_entities
+tags
+irpf90.make
+Makefile
+Makefile.depend
 build.ninja
 .ninja_log
 .ninja_deps
+ezfio_interface.irp.f
+Utils
+Nuclei
+AO_Basis
+Electrons
+Ezfio_files

src/MO_Basis/EZFIO.cfg

@@ -2,30 +2,25 @@
 type: integer
 doc: Total number of molecular orbitals and the size of the keys corresponding
 interface: ezfio
-ezfio_dir: mo_basis
 
 [mo_coef]
 type: double precision
 doc: coefficient of the ith ao on the jth mo
 interface: ezfio
 size: (ao_basis.ao_num,mo_basis.mo_tot_num)
-ezfio_dir: mo_basis
 
 [mo_label]
 type: character*(64)
 doc: Label characterizing the MOS (local, canonical, natural, etc)
 interface: ezfio
-ezfio_dir: mo_basis
 
 [mo_occ]
 type: double precision
 doc: MO occupation numbers
 interface: ezfio
 size: (mo_basis.mo_tot_num)
-ezfio_dir: mo_basis
 
 [ao_md5]
 type: character*(32)
 doc: Ao_md5
 interface: ezfio
-ezfio_dir: mo_basis

src/Nuclei/.gitignore

@@ -1,13 +1,14 @@
-#
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
-# Do not modify this file. Add your ignored files to the gitignore
-# (without the dot at the beginning) file.
-#
 IRPF90_temp
 IRPF90_man
-irpf90.make
-tags
-Makefile.depend
 irpf90_entities
+tags
+irpf90.make
+Makefile
+Makefile.depend
 build.ninja
 .ninja_log
 .ninja_deps
+ezfio_interface.irp.f
+Ezfio_files
+Utils

src/Pseudo/.gitignore

@@ -1,13 +1,15 @@
-#
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
-# Do not modify this file. Add your ignored files to the gitignore
-# (without the dot at the beginning) file.
-#
 IRPF90_temp
 IRPF90_man
-irpf90.make
-tags
-Makefile.depend
 irpf90_entities
+tags
+irpf90.make
+Makefile
+Makefile.depend
 build.ninja
 .ninja_log
 .ninja_deps
+ezfio_interface.irp.f
+Nuclei
+Ezfio_files
+Utils

src/Utils/.gitignore

@@ -1,13 +1,12 @@
-#
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
-# Do not modify this file. Add your ignored files to the gitignore
-# (without the dot at the beginning) file.
-#
 IRPF90_temp
 IRPF90_man
-irpf90.make
-tags
-Makefile.depend
 irpf90_entities
+tags
+irpf90.make
+Makefile
+Makefile.depend
 build.ninja
 .ninja_log
 .ninja_deps
+ezfio_interface.irp.f