Sort gitignore to avoid stupid conflicts

config/ifort.cfg

@@ -18,7 +18,7 @@ IRPF90_FLAGS : --ninja --align=32
 # 0 : Deactivate
 # 
 [OPTION]
-MODE    : DEBUG      ; [ OPT | PROFILE | DEBUG ] : Chooses the section below
+MODE    : OPT        ; [ OPT | PROFILE | DEBUG ] : Chooses the section below
 CACHE   : 1          ; Enable cache_compile.py
 OPENMP  : 1          ; Append OpenMP flags
 

plugins/CAS_SD/.gitignore

@@ -1,31 +1,30 @@
-# Automatically created by /home/scemama/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
-.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
-cas_sd_selected_no_skip
+Pseudo
+Selectors_full
+Utils
 cas_sd
 cas_sd_selected
+ezfio_interface.irp.f
+irpf90.make
+irpf90_entities
+tags

plugins/CAS_SD/README.rst

@@ -13,11 +13,11 @@ 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/CAS_SD/cas_sd_selected_no_skip.irp.f#L1>`_
+`full_ci <http://github.com/LCPQ/quantum_package/tree/master/src/CAS_SD/cas_sd_selected.irp.f#L1>`_
   Undocumented
 
 
-`h_apply_cas_sd <http://github.com/LCPQ/quantum_package/tree/master/src/CAS_SD/H_apply.irp.f_shell_16#L408>`_
+`h_apply_cas_sd <http://github.com/LCPQ/quantum_package/tree/master/src/CAS_SD/H_apply.irp.f_shell_22#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.
 
@@ -28,58 +28,58 @@ Documentation
   Assume N_int is already provided.
 
 
-`h_apply_cas_sd_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CAS_SD/H_apply.irp.f_shell_16#L264>`_
+`h_apply_cas_sd_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CAS_SD/H_apply.irp.f_shell_22#L264>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cas_sd_pt2 <http://github.com/LCPQ/quantum_package/tree/master/src/CAS_SD/H_apply.irp.f_shell_16#L1848>`_
+`h_apply_cas_sd_pt2 <http://github.com/LCPQ/quantum_package/tree/master/src/CAS_SD/H_apply.irp.f_shell_22#L2586>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cas_sd_pt2_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CAS_SD/H_apply.irp.f_shell_16#L1362>`_
+`h_apply_cas_sd_pt2_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CAS_SD/H_apply.irp.f_shell_22#L2100>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cas_sd_pt2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CAS_SD/H_apply.irp.f_shell_16#L1666>`_
+`h_apply_cas_sd_pt2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CAS_SD/H_apply.irp.f_shell_22#L2404>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cas_sd_selected <http://github.com/LCPQ/quantum_package/tree/master/src/CAS_SD/H_apply.irp.f_shell_16#L1116>`_
+`h_apply_cas_sd_selected <http://github.com/LCPQ/quantum_package/tree/master/src/CAS_SD/H_apply.irp.f_shell_22#L1854>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cas_sd_selected_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CAS_SD/H_apply.irp.f_shell_16#L596>`_
+`h_apply_cas_sd_selected_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CAS_SD/H_apply.irp.f_shell_22#L1334>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cas_sd_selected_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CAS_SD/H_apply.irp.f_shell_16#L920>`_
+`h_apply_cas_sd_selected_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CAS_SD/H_apply.irp.f_shell_22#L1658>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cas_sd_selected_no_skip <http://github.com/LCPQ/quantum_package/tree/master/src/CAS_SD/H_apply.irp.f_shell_22#L1112>`_
+`h_apply_cas_sd_selected_no_skip <http://github.com/LCPQ/quantum_package/tree/master/src/CAS_SD/H_apply.irp.f_shell_22#L1116>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cas_sd_selected_no_skip_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CAS_SD/H_apply.irp.f_shell_22#L594>`_
+`h_apply_cas_sd_selected_no_skip_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CAS_SD/H_apply.irp.f_shell_22#L596>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cas_sd_selected_no_skip_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CAS_SD/H_apply.irp.f_shell_22#L917>`_
+`h_apply_cas_sd_selected_no_skip_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CAS_SD/H_apply.irp.f_shell_22#L920>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.

plugins/Full_CI/.gitignore

@@ -1,32 +1,32 @@
-# Automatically created by /home/scemama/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_full
+Hartree_Fock
 IRPF90_man
-irpf90_entities
+IRPF90_temp
-tags
+Integrals_Bielec
-irpf90.make
+Integrals_Monoelec
+MOGuess
+MO_Basis
 Makefile
 Makefile.depend
-.ninja_log
-.ninja_deps
-ezfio_interface.irp.f
-Ezfio_files
-Perturbation
-Determinants
-Utils
-Integrals_Monoelec
-MO_Basis
-Selectors_full
-Integrals_Bielec
-Pseudo
-Generators_full
-Bitmask
-AO_Basis
-Electrons
-MOGuess
 Nuclei
-Hartree_Fock
+Perturbation
 Properties
-var_pt2_ratio
+Pseudo
-target_pt2
+Selectors_full
+Utils
+ezfio_interface.irp.f
 full_ci
 full_ci_no_skip
+irpf90.make
+irpf90_entities
+tags
+target_pt2
+var_pt2_ratio

plugins/Hartree_Fock/.gitignore

@@ -1,24 +1,24 @@
-# Automatically created by /home/scemama/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
+Electrons
+Ezfio_files
+Huckel_guess
 IRPF90_man
-irpf90_entities
+IRPF90_temp
-tags
+Integrals_Bielec
-irpf90.make
+Integrals_Monoelec
+MOGuess
+MO_Basis
 Makefile
 Makefile.depend
-.ninja_log
-.ninja_deps
-ezfio_interface.irp.f
-Ezfio_files
-Integrals_Monoelec
-MO_Basis
-Integrals_Bielec
-Pseudo
-Bitmask
-AO_Basis
-Electrons
-MOGuess
 Nuclei
-Utils
+Pseudo
 SCF
-Huckel_guess
+Utils
+ezfio_interface.irp.f
+irpf90.make
+irpf90_entities
+tags

plugins/MRCC/.gitignore

@@ -1,29 +1,29 @@
-# Automatically created by /home/scemama/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_full
+Hartree_Fock
 IRPF90_man
-irpf90_entities
+IRPF90_temp
-tags
+Integrals_Bielec
-irpf90.make
+Integrals_Monoelec
+MOGuess
+MO_Basis
 Makefile
 Makefile.depend
-.ninja_log
-.ninja_deps
-ezfio_interface.irp.f
-Ezfio_files
-Perturbation
-Determinants
-Utils
-Integrals_Monoelec
-MO_Basis
-Selectors_full
-Integrals_Bielec
-Pseudo
-Generators_full
-Bitmask
-AO_Basis
-Electrons
-MOGuess
 Nuclei
-Hartree_Fock
+Perturbation
 Properties
+Pseudo
+Selectors_full
+Utils
+ezfio_interface.irp.f
+irpf90.make
+irpf90_entities
 mrcc
+tags

plugins/MRCC/README.rst

@@ -20,23 +20,23 @@ Documentation
 .. Do not edit this section. It was auto-generated from the
 .. by the `update_README.py` script.
 
-`ci_eigenvectors_dressed <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L93>`_
+`ci_eigenvectors_dressed <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L76>`_
   Eigenvectors/values of the CI matrix
 
 
-`ci_eigenvectors_s2_dressed <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L94>`_
+`ci_eigenvectors_s2_dressed <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L77>`_
   Eigenvectors/values of the CI matrix
 
 
-`ci_electronic_energy_dressed <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L92>`_
+`ci_electronic_energy_dressed <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L75>`_
   Eigenvectors/values of the CI matrix
 
 
-`ci_energy_dressed <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L159>`_
+`ci_energy_dressed <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L142>`_
   N_states lowest eigenvalues of the dressed CI matrix
 
 
-`davidson_diag_hjj_mrcc <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/davidson.irp.f#L51>`_
+`davidson_diag_hjj_mrcc <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/davidson.irp.f#L56>`_
   Davidson diagonalization with specific diagonal elements of the H matrix
   .br
   H_jj : specific diagonal H matrix elements to diagonalize de Davidson
@@ -76,66 +76,45 @@ Documentation
   Initial guess vectors are not necessarily orthonormal
 
 
-`delta_ij <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L47>`_
+`delta_ii <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L39>`_
   Dressing matrix in N_det basis
 
 
-`delta_ij_non_cas <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L38>`_
+`delta_ij <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L38>`_
-  Dressing matrix in SD basis
+  Dressing matrix in N_det basis
 
 
-`diagonalize_ci_dressed <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L174>`_
+`diagonalize_ci_dressed <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L157>`_
   Replace the coefficients of the CI states by the coefficients of the
   eigenstates of the CI matrix
 
 
-`dressing_type <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L30>`_
-  [ Simple | MRCC ]
-
-
 `find_triples_and_quadruples <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_dress.irp.f#L206>`_
   Undocumented
 
 
-`h_apply_mrcc <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/H_apply.irp.f_shell_31#L990>`_
+`h_apply_mrcc <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/H_apply.irp.f_shell_27#L416>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_mrcc_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/H_apply.irp.f_shell_31#L577>`_
+`h_apply_mrcc_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/H_apply.irp.f_shell_27#L1>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_mrcc_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/H_apply.irp.f_shell_31#L843>`_
+`h_apply_mrcc_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/H_apply.irp.f_shell_27#L268>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_mrcc_simple <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/H_apply.irp.f_shell_31#L414>`_
+`h_matrix_dressed <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L50>`_
-  Calls H_apply on the HF determinant and selects all connected single and double
-  excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
-
-
-`h_apply_mrcc_simple_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/H_apply.irp.f_shell_31#L1>`_
-  Generate all double excitations of key_in using the bit masks of holes and
-  particles.
-  Assume N_int is already provided.
-
-
-`h_apply_mrcc_simple_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/H_apply.irp.f_shell_31#L267>`_
-  Generate all single excitations of key_in using the bit masks of holes and
-  particles.
-  Assume N_int is already provided.
-
-
-`h_matrix_dressed <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L77>`_
   Dressed H with Delta_ij
 
 
-`h_u_0_mrcc <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/davidson.irp.f#L355>`_
+`h_u_0_mrcc <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/davidson.irp.f#L360>`_
   Computes v_0 = H|u_0>
   .br
   n : number of determinants

plugins/MRCC/mrcc_utils.irp.f

@@ -43,32 +43,8 @@ END_PROVIDER
  END_DOC
  integer :: i,j,m
  delta_ij = 0.d0
-<<<<<<< HEAD
- if (dressing_type == "MRCC") then
-   call H_apply_mrcc(delta_ij,N_det)
- else if (dressing_type == "Simple") then
-   do m=1,N_states
-     do j=1,N_det_non_cas
-       do i=1,N_det_non_cas
-         delta_ij(idx_non_cas(i),idx_non_cas(j),m) = delta_ij_non_cas(i,j,m)
-       enddo
-     enddo
-   enddo
- endif
- do i = 1, N_det
-   do j = 1, N_det
-     do m = 1, N_states
-       if(isnan(delta_ij(j,i,m)))then
-         delta_ij(j,i,m) = 0.d0
-       endif
-     enddo
-   enddo
- enddo
-
-=======
  delta_ii = 0.d0
  call H_apply_mrcc(delta_ij,delta_ii,N_det_cas,N_det_non_cas)
->>>>>>> 12e81de1c7275076c25c223979f80c8facb506a3
 END_PROVIDER
 
 BEGIN_PROVIDER [ double precision, h_matrix_dressed, (N_det,N_det,N_states) ]

plugins/QmcChem/.gitignore

@@ -1,23 +1,23 @@
-# Automatically created by /home/scemama/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
+Utils
+ezfio_interface.irp.f
+irpf90.make
+irpf90_entities
 save_for_qmcchem
+tags

scripts/compilation/qp_create_ninja.py

@@ -26,6 +26,16 @@ Error:
 """%f
     sys.exit(1)
 
+#  __
+# /__ |  _  |_   _. |       _. ._ o  _. |_  |  _   _
+# \_| | (_) |_) (_| |   \/ (_| |  | (_| |_) | (/_ _>
+#
+
+from qp_path import QP_ROOT, QP_SRC, QP_EZFIO
+
+EZFIO_LIB = join(QP_ROOT, "lib", "libezfio.a")
+ROOT_BUILD_NINJA = join(QP_ROOT, "config", "build.ninja")
+
 header = r"""#
 #  _______                     _____
 #  __  __ \___  _______ _________  /____  ________ ___
@@ -45,17 +55,8 @@ header = r"""#
 # Generated automatically by {0}
 #
 #
-""".format(__file__)
+""".format(__file__).replace(QP_ROOT,"$QP_ROOT")
 
-#  __
-# /__ |  _  |_   _. |       _. ._ o  _. |_  |  _   _
-# \_| | (_) |_) (_| |   \/ (_| |  | (_| |_) | (/_ _>
-#
-
-from qp_path import QP_ROOT, QP_SRC, QP_EZFIO
-
-EZFIO_LIB = join(QP_ROOT, "lib", "libezfio.a")
-ROOT_BUILD_NINJA = join(QP_ROOT, "config", "build.ninja")
 
 #
 # |\ |  _. ._ _   _   _|   _|_     ._  |  _

scripts/module/create_gitignore.sh

@@ -21,15 +21,15 @@ function do_gitingore()
 # Do not modify this file. Add your ignored files to the gitignore
 # (without the dot at the beginning) file.
 #
-IRPF90_temp
-IRPF90_man
-irpf90.make
-tags
-Makefile.depend
-irpf90_entities
 build.ninja
-.ninja_log
+irpf90_entities
+irpf90.make
+IRPF90_man
+IRPF90_temp
+Makefile.depend
 .ninja_deps
+.ninja_log
+tags
 EOF
   
   if [[ -f gitignore ]]
@@ -59,3 +59,6 @@ else
   done
 fi
 
+# Sort the .gitignore to reduce conflict in git merges
+sort .gitignore |uniq > .gitignore.new
+mv .gitignore.new .gitignore

scripts/module/module_handler.py

@@ -24,6 +24,7 @@ import shutil
 try:
     from docopt import docopt
     from qp_path import QP_SRC
+    from qp_path import QP_ROOT
 except ImportError:
     print "source .quantum_package.rc"
     raise
@@ -279,5 +280,8 @@ if __name__ == '__main__':
                 path = os.path.join(module_abs, ".gitignore")
 
                 with open(path, "w+") as f:
-                    f.write("# Automatically created by {0} \n".format(__file__))
+                    f.write("# Automatically created by {0} \n".format(__file__).replace(QP_ROOT,"$QP_ROOT"))
-                    f.write("\n".join(l_dir + l_file + l_symlink + l_exe))
+                    l_text = l_dir + l_file + l_symlink + l_exe
+                    l_text.sort()
+                    f.write("\n".join(l_text))
+

src/Determinants/.gitignore

@@ -1,31 +1,28 @@
-# Automatically created by /home/scemama/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
+AO_Basis
+Bitmask
+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
+Utils
+det_svd
+ezfio_interface.irp.f
+guess_doublet
 guess_singlet
 guess_triplet
-truncate_wf
+irpf90.make
-save_natorb
+irpf90_entities
-guess_doublet
-det_svd
-save_for_casino
 program_initial_determinants
-print_cas_energy
+save_natorb
-print_s2
+tags
+truncate_wf

src/Determinants/README.rst

@@ -213,7 +213,7 @@ Documentation
   Build connection proxy between determinants
 
 
-`det_num <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/ezfio_interface.irp.f#L116>`_
+`det_num <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/ezfio_interface.irp.f#L248>`_
   det_num
 
 
@@ -609,14 +609,6 @@ Documentation
   Undocumented
 
 
-`print_psi_cas <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/print_cas_energy.irp.f#L1>`_
-  Undocumented
-
-
-`prog_save_casino <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/save_for_casino.irp.f#L266>`_
-  Undocumented
-
-
 `psi_average_norm_contrib <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L273>`_
   Contribution of determinants to the state-averaged density
 
@@ -819,7 +811,7 @@ Documentation
   Undocumented
 
 
-`s2_eig <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/ezfio_interface.irp.f#L248>`_
+`s2_eig <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/ezfio_interface.irp.f#L116>`_
   Force the wave function to be an eigenfunction of S^2
 
 

src/Ezfio_files/README.rst

@@ -42,18 +42,6 @@ Documentation
   Output file for CAS_SD
 
 
-`output_cisd <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L61>`_
-  Output file for CISD
-
-
-`output_cisd_sc2_selected <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L81>`_
-  Output file for CISD_SC2_selected
-
-
-`output_cisd_selected <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L101>`_
-  Output file for CISD_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
 

src/Integrals_Monoelec/.gitignore

@@ -1,20 +1,20 @@
-# Automatically created by /home/scemama/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
-MO_Basis
-Utils
-Pseudo
 AO_Basis
 Electrons
+Ezfio_files
+IRPF90_man
+IRPF90_temp
+MO_Basis
+Makefile
+Makefile.depend
 Nuclei
-save_ortho_mos
+Pseudo
+Utils
 check_orthonormality
+ezfio_interface.irp.f
+irpf90.make
+irpf90_entities
+save_ortho_mos
+tags

src/MOGuess/.gitignore

@@ -1,20 +1,20 @@
-# Automatically created by /home/scemama/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
-Integrals_Monoelec
-MO_Basis
-Utils
-Pseudo
 AO_Basis
 Electrons
-Nuclei
+Ezfio_files
 H_CORE_guess
+IRPF90_man
+IRPF90_temp
+Integrals_Monoelec
+MO_Basis
+Makefile
+Makefile.depend
+Nuclei
+Pseudo
+Utils
+ezfio_interface.irp.f
+irpf90.make
+irpf90_entities
+tags

src/Nuclei/README.rst

@@ -27,7 +27,7 @@ Documentation
   Array of the name of element, sorted by nuclear charge (integer)
 
 
-`nucl_charge <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/ezfio_interface.irp.f#L28>`_
+`nucl_charge <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/ezfio_interface.irp.f#L24>`_
   Nuclear charges
 
 
@@ -69,11 +69,11 @@ Documentation
   nucl_dist_vec : Nucleus-nucleus distances vectors
 
 
-`nucl_label <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/ezfio_interface.irp.f#L50>`_
+`nucl_label <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/ezfio_interface.irp.f#L6>`_
   Nuclear labels
 
 
-`nucl_num <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/ezfio_interface.irp.f#L6>`_
+`nucl_num <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/ezfio_interface.irp.f#L46>`_
   Number of nuclei
 
 

src/Pseudo/README.rst

@@ -26,7 +26,7 @@ Documentation
   test
 
 
-`pseudo_dz_kl <http://github.com/LCPQ/quantum_package/tree/master/src/Pseudo/ezfio_interface.irp.f#L226>`_
+`pseudo_dz_kl <http://github.com/LCPQ/quantum_package/tree/master/src/Pseudo/ezfio_interface.irp.f#L94>`_
   test
 
 
@@ -42,7 +42,7 @@ Documentation
   test
 
 
-`pseudo_kmax <http://github.com/LCPQ/quantum_package/tree/master/src/Pseudo/ezfio_interface.irp.f#L94>`_
+`pseudo_kmax <http://github.com/LCPQ/quantum_package/tree/master/src/Pseudo/ezfio_interface.irp.f#L72>`_
   test
 
 
@@ -50,7 +50,7 @@ Documentation
   test
 
 
-`pseudo_n_k <http://github.com/LCPQ/quantum_package/tree/master/src/Pseudo/ezfio_interface.irp.f#L72>`_
+`pseudo_n_k <http://github.com/LCPQ/quantum_package/tree/master/src/Pseudo/ezfio_interface.irp.f#L226>`_
   test
 
 

src/Utils/README.rst

@@ -431,7 +431,7 @@ Documentation
   .br
 
 
-`lapack_diag_s2 <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L313>`_
+`lapack_diag_s2 <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L310>`_
   Diagonalize matrix H
   .br
   H is untouched between input and ouptut
@@ -453,7 +453,7 @@ Documentation
   .br
 
 
-`lapack_partial_diag <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L379>`_
+`lapack_partial_diag <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L376>`_
   Diagonalize matrix H
   .br
   H is untouched between input and ouptut
@@ -597,7 +597,7 @@ Documentation
   to be in integer*8 format
 
 
-`set_zero_extra_diag <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L436>`_
+`set_zero_extra_diag <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L433>`_
   Undocumented