Realy fix the readme... Maybe to mush

scripts/compilation/create_ninja_build.py

@@ -681,10 +681,11 @@ if __name__ == "__main__":
         l_string += ninja_irpf90_make_build(module_to_compile, l_children,
                                             d_irp)
 
-        # ~#~#~#~#~#~#~#~ #
+        # ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
-        # d o t _ t r e e #
+        # d o t _ t r e e  & r e a d  m e #
-        # ~#~#~#~#~#~#~#~ #
+        # ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
         l_string += ninja_dot_tree_build(module_to_compile)
+        l_string += ninja_readme_build(module_to_compile)
 
     # ~#~#~#~#~#~#~ #
     #  b i n a r y  #
@@ -693,7 +694,6 @@ if __name__ == "__main__":
 
         l_string += ninja_binaries_build(module_to_compile, l_children,
                                          d_binaries_production)
-        l_string += ninja_readme_build(module_to_compile)
 
     with open(join(QPACKAGE_ROOT, "build.ninja"), "w+") as f:
         f.write("\n".join(l_string))

src/AOs/README.rst

@@ -34,121 +34,148 @@ Needed Modules
 ==============
 
 .. Do not edit this section. It was auto-generated from the
-.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
+.. by the `update_README.py` script.
 
-.. image:: tree_dependancy.png
+.. image:: tree_dependency.png
 
 * `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
-* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
 
 Documentation
 =============
 
 .. Do not edit this section. It was auto-generated from the
-.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
+.. by the `update_README.py` script.
-
-`ao_overlap <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/ao_overlap.irp.f#L1>`_
-  Overlap between atomic basis functions:
-  :math:`\int \chi_i(r) \chi_j(r) dr)`
-
-`ao_overlap_abs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/ao_overlap.irp.f#L65>`_
-  Overlap between absolute value of atomic basis functions:
-  :math:`\int |\chi_i(r)| |\chi_j(r)| dr)`
-
-`ao_overlap_x <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/ao_overlap.irp.f#L2>`_
-  Overlap between atomic basis functions:
-  :math:`\int \chi_i(r) \chi_j(r) dr)`
-
-`ao_overlap_y <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/ao_overlap.irp.f#L3>`_
-  Overlap between atomic basis functions:
-  :math:`\int \chi_i(r) \chi_j(r) dr)`
-
-`ao_overlap_z <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/ao_overlap.irp.f#L4>`_
-  Overlap between atomic basis functions:
-  :math:`\int \chi_i(r) \chi_j(r) dr)`
 
 `ao_coef <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L62>`_
   AO Coefficients, read from input. Those should not be used directly, as
   the MOs are expressed on the basis of **normalized** AOs.
 
+
 `ao_coef_normalized <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L84>`_
   Coefficients including the AO normalization
 
+
 `ao_coef_normalized_ordered <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L107>`_
   Sorted primitives to accelerate 4 index MO transformation
 
+
 `ao_coef_normalized_ordered_transp <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L133>`_
   Transposed ao_coef_normalized_ordered
 
+
 `ao_expo <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L41>`_
   AO Exponents read from input
 
+
 `ao_expo_ordered <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L108>`_
   Sorted primitives to accelerate 4 index MO transformation
 
+
 `ao_expo_ordered_transp <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L147>`_
   Transposed ao_expo_ordered
 
+
 `ao_l <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L162>`_
   ao_l = l value of the AO: a+b+c in x^a y^b z^c
 
+
 `ao_l_char <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L163>`_
   ao_l = l value of the AO: a+b+c in x^a y^b z^c
 
+
 `ao_l_char_space <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L311>`_
   Undocumented
 
+
 `ao_md5 <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L403>`_
   MD5 key characteristic of the AO basis
 
+
 `ao_nucl <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L209>`_
   Index of the nuclei on which the ao is centered
 
+
 `ao_num <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L1>`_
   Number of atomic orbitals
 
+
 `ao_num_align <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L2>`_
   Number of atomic orbitals
 
+
+`ao_overlap <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/ao_overlap.irp.f#L1>`_
+  Overlap between atomic basis functions:
+  :math:`\int \chi_i(r) \chi_j(r) dr)`
+
+
+`ao_overlap_abs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/ao_overlap.irp.f#L65>`_
+  Overlap between absolute value of atomic basis functions:
+  :math:`\int |\chi_i(r)| |\chi_j(r)| dr)`
+
+
+`ao_overlap_x <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/ao_overlap.irp.f#L2>`_
+  Overlap between atomic basis functions:
+  :math:`\int \chi_i(r) \chi_j(r) dr)`
+
+
+`ao_overlap_y <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/ao_overlap.irp.f#L3>`_
+  Overlap between atomic basis functions:
+  :math:`\int \chi_i(r) \chi_j(r) dr)`
+
+
+`ao_overlap_z <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/ao_overlap.irp.f#L4>`_
+  Overlap between atomic basis functions:
+  :math:`\int \chi_i(r) \chi_j(r) dr)`
+
+
 `ao_power <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L19>`_
   Powers of x,y and z read from input
 
+
 `ao_prim_num <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L177>`_
   Number of primitives per atomic orbital
 
+
 `ao_prim_num_max <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L199>`_
   Undocumented
 
+
 `ao_prim_num_max_align <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L200>`_
   Undocumented
 
+
 `l_to_charater <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L218>`_
   character corresponding to the "L" value of an AO orbital
 
+
 `n_aos_max <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L231>`_
   Number of AOs per atom
 
+
+`n_pt_max_i_x <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/dimensions_integrals.irp.f#L2>`_
+  Undocumented
+
+
+`n_pt_max_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/dimensions_integrals.irp.f#L1>`_
+  Undocumented
+
+
 `nucl_aos <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L244>`_
   List of AOs attached on each atom
 
+
 `nucl_list_shell_aos <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L262>`_
   Index of the shell type Aos and of the corresponding Aos
   Per convention, for P,D,F and G AOs, we take the index
   of the AO with the the corresponding power in the "X" axis
 
+
 `nucl_n_aos <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L230>`_
   Number of AOs per atom
 
+
 `nucl_num_shell_aos <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L263>`_
   Index of the shell type Aos and of the corresponding Aos
   Per convention, for P,D,F and G AOs, we take the index
   of the AO with the the corresponding power in the "X" axis
 
-`n_pt_max_i_x <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/dimensions_integrals.irp.f#L2>`_
-  Undocumented
-
-`n_pt_max_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/dimensions_integrals.irp.f#L1>`_
-  Undocumented
-
-
-

src/Bitmask/README.rst

@@ -38,9 +38,9 @@ Needed Modules
 ==============
 
 .. Do not edit this section. It was auto-generated from the
-.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
+.. by the `update_README.py` script.
 
-.. image:: tree_dependancy.png
+.. image:: tree_dependency.png
 
 * `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
 
@@ -48,32 +48,42 @@ Documentation
 =============
 
 .. Do not edit this section. It was auto-generated from the
-.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
+.. by the `update_README.py` script.
 
-`is_a_two_holes_two_particles <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmask_cas_routines.irp.f#L206>`_
+`bitstring_to_hexa <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks_routines.irp.f#L98>`_
-  Undocumented
+  Transform a bit string to a string in hexadecimal format for printing
 
-`number_of_holes <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmask_cas_routines.irp.f#L1>`_
-  Undocumented
 
-`number_of_holes_verbose <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmask_cas_routines.irp.f#L394>`_
+`bitstring_to_list <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks_routines.irp.f#L1>`_
-  Undocumented
+  Gives the inidices(+1) of the bits set to 1 in the bit string
 
-`number_of_particles <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmask_cas_routines.irp.f#L103>`_
-  Undocumented
 
-`number_of_particles_verbose <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmask_cas_routines.irp.f#L422>`_
+`bitstring_to_str <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks_routines.irp.f#L65>`_
-  Undocumented
+  Transform a bit string to a string for printing
+
 
 `cas_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L173>`_
   Bitmasks for CAS reference determinants. (N_int, alpha/beta, CAS reference)
 
+
 `cis_ijkl_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L32>`_
   Bitmask to include all possible single excitations from Hartree-Fock
 
+
+`debug_det <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks_routines.irp.f#L120>`_
+  Subroutine to print the content of a determinant in '+-' notation and
+  hexadecimal representation.
+
+
+`debug_spindet <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks_routines.irp.f#L155>`_
+  Subroutine to print the content of a determinant in '+-' notation and
+  hexadecimal representation.
+
+
 `full_ijkl_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L12>`_
   Bitmask to include all possible MOs
 
+
 `generators_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L100>`_
   Bitmasks for generator determinants.
   (N_int, alpha/beta, hole/particle, generator).
@@ -93,56 +103,68 @@ Documentation
   * 6 : particle for 2nd exc of double
   .br
 
+
 `hf_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L44>`_
   Hartree Fock bit mask
 
+
 `i_bitmask_gen <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L211>`_
   Current bitmask for the generators
 
+
 `inact_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L193>`_
   Bitmasks for the inactive orbitals that are excited in post CAS method
 
-`n_cas_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L143>`_
-  Number of bitmasks for CAS
 
-`n_generators_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L70>`_
+`is_a_two_holes_two_particles <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmask_cas_routines.irp.f#L206>`_
-  Number of bitmasks for generators
+  Undocumented
 
-`n_int <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L3>`_
-  Number of 64-bit integers needed to represent determinants as binary strings
-
-`ref_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L62>`_
-  Reference bit mask, used in Slater rules, chosen as Hartree-Fock bitmask
-
-`virt_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L194>`_
-  Bitmasks for the inactive orbitals that are excited in post CAS method
-
-`bitstring_to_hexa <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks_routines.irp.f#L98>`_
-  Transform a bit string to a string in hexadecimal format for printing
-
-`bitstring_to_list <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks_routines.irp.f#L1>`_
-  Gives the inidices(+1) of the bits set to 1 in the bit string
-
-`bitstring_to_str <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks_routines.irp.f#L65>`_
-  Transform a bit string to a string for printing
-
-`debug_det <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks_routines.irp.f#L120>`_
-  Subroutine to print the content of a determinant in '+-' notation and
-  hexadecimal representation.
-
-`debug_spindet <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks_routines.irp.f#L155>`_
-  Subroutine to print the content of a determinant in '+-' notation and
-  hexadecimal representation.
 
 `list_to_bitstring <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks_routines.irp.f#L29>`_
   Returns the physical string "string(N_int,2)" from the array of
   occupations "list(N_int*bit_kind_size,2)
 
+
+`n_cas_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L143>`_
+  Number of bitmasks for CAS
+
+
+`n_generators_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L70>`_
+  Number of bitmasks for generators
+
+
+`n_int <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L3>`_
+  Number of 64-bit integers needed to represent determinants as binary strings
+
+
+`number_of_holes <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmask_cas_routines.irp.f#L1>`_
+  Undocumented
+
+
+`number_of_holes_verbose <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmask_cas_routines.irp.f#L394>`_
+  Undocumented
+
+
+`number_of_particles <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmask_cas_routines.irp.f#L103>`_
+  Undocumented
+
+
+`number_of_particles_verbose <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmask_cas_routines.irp.f#L422>`_
+  Undocumented
+
+
 `print_det <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks_routines.irp.f#L138>`_
   Subroutine to print the content of a determinant using the '+-' notation
 
+
 `print_spindet <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks_routines.irp.f#L171>`_
   Subroutine to print the content of a determinant using the '+-' notation
 
 
+`ref_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L62>`_
+  Reference bit mask, used in Slater rules, chosen as Hartree-Fock bitmask
+
+
+`virt_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L194>`_
+  Bitmasks for the inactive orbitals that are excited in post CAS method
 

src/CID/README.rst

@@ -13,9 +13,9 @@ Needed Modules
 ==============
 
 .. Do not edit this section. It was auto-generated from the
-.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
+.. by the `update_README.py` script.
 
-.. image:: tree_dependancy.png
+.. image:: tree_dependency.png
 
 * `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
 * `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod>`_
@@ -24,10 +24,25 @@ Documentation
 =============
 
 .. Do not edit this section. It was auto-generated from the
-.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
+.. by the `update_README.py` script.
 
 `cisd <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>`_
+  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>`_
+  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>`_
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
 

src/CID_selected/README.rst

@@ -6,23 +6,175 @@ Documentation
 =============
 
 .. Do not edit this section. It was auto-generated from the
-.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
+.. by the `update_README.py` script.
-
-`h_apply_cisd_selection <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected/H_apply.irp.f#L13>`_
-  Undocumented
 
 `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
+
+
+`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>`_
+  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>`_
+  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>`_
+  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>`_
+  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>`_
+  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>`_
+  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>`_
+  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>`_
+  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>`_
+  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>`_
+  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>`_
+  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>`_
+  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>`_
+  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>`_
+  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>`_
+  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>`_
+  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>`_
+  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>`_
+  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>`_
+  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>`_
+  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>`_
+  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>`_
+  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>`_
+  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>`_
+  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>`_
+  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_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/CID_selected/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.
 
 Needed Modules
 ==============
 
 .. Do not edit this section. It was auto-generated from the
-.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
+.. by the `update_README.py` script.
 
-.. image:: tree_dependancy.png
+.. image:: tree_dependency.png
 
 * `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
 * `CID <http://github.com/LCPQ/quantum_package/tree/master/src/CID>`_

src/CISD/README.rst

@@ -13,9 +13,9 @@ Needed Modules
 ==============
 
 .. Do not edit this section. It was auto-generated from the
-.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
+.. by the `update_README.py` script.
 
-.. image:: tree_dependancy.png
+.. image:: tree_dependency.png
 
 * `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
 * `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod>`_
@@ -24,10 +24,25 @@ Documentation
 =============
 
 .. Do not edit this section. It was auto-generated from the
-.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
+.. by the `update_README.py` script.
 
 `cisd <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/cisd_lapack.irp.f#L1>`_
   Undocumented
 
 
+`h_apply_cisd <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/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/CISD/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/CISD/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.
 

src/CISD_selected/README.rst

@@ -6,23 +6,175 @@ Documentation
 =============
 
 .. Do not edit this section. It was auto-generated from the
-.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
+.. by the `update_README.py` script.
-
-`h_apply_cisd_selection <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f#L13>`_
-  Undocumented
 
 `cisd <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/cisd_selection.irp.f#L1>`_
   Undocumented
 
 
+`h_apply_cisd_selection <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/H_apply.irp.f#L13>`_
+  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#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/CISD_selected/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/CISD_selected/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/CISD_selected/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/CISD_selected/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/CISD_selected/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/CISD_selected/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/CISD_selected/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/CISD_selected/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/CISD_selected/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/CISD_selected/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/CISD_selected/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/CISD_selected/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/CISD_selected/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/CISD_selected/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/CISD_selected/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/CISD_selected/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/CISD_selected/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/CISD_selected/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/CISD_selected/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/CISD_selected/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/CISD_selected/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/CISD_selected/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/CISD_selected/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/CISD_selected/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/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#L324>`_
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
 
 Needed Modules
 ==============
 
 .. Do not edit this section. It was auto-generated from the
-.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
+.. by the `update_README.py` script.
 
-.. image:: tree_dependancy.png
+.. image:: tree_dependency.png
 
 * `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
 * `CISD <http://github.com/LCPQ/quantum_package/tree/master/src/CISD>`_

src/DensityFit/README.rst

@@ -8,62 +8,74 @@ Documentation
 =============
 
 .. Do not edit this section. It was auto-generated from the
-.. NEEDED_MODULES file.
+.. by the `update_README.py` script.
 
 `aux_basis_coef <http://github.com/LCPQ/quantum_package/tree/master/src/DensityFit/aux_basis.irp.f#L94>`_
   Exponents and coefficients of the auxiliary basis
 
+
 `aux_basis_coef_transp <http://github.com/LCPQ/quantum_package/tree/master/src/DensityFit/aux_basis.irp.f#L37>`_
   Exponents of the auxiliary basis
 
+
 `aux_basis_expo <http://github.com/LCPQ/quantum_package/tree/master/src/DensityFit/aux_basis.irp.f#L93>`_
   Exponents and coefficients of the auxiliary basis
 
+
 `aux_basis_expo_transp <http://github.com/LCPQ/quantum_package/tree/master/src/DensityFit/aux_basis.irp.f#L36>`_
   Exponents of the auxiliary basis
 
-`aux_basis_idx <http://github.com/LCPQ/quantum_package/tree/master/src/DensityFit/aux_basis.irp.f#L20>`_
-  aux_basis_idx(k) -> i,j
-
-`aux_basis_nucl <http://github.com/LCPQ/quantum_package/tree/master/src/DensityFit/aux_basis.irp.f#L40>`_
-  Exponents of the auxiliary basis
-
-`aux_basis_num <http://github.com/LCPQ/quantum_package/tree/master/src/DensityFit/aux_basis.irp.f#L2>`_
-  Number of auxiliary basis functions
-
-`aux_basis_num_8 <http://github.com/LCPQ/quantum_package/tree/master/src/DensityFit/aux_basis.irp.f#L3>`_
-  Number of auxiliary basis functions
-
-`aux_basis_num_sqrt <http://github.com/LCPQ/quantum_package/tree/master/src/DensityFit/aux_basis.irp.f#L1>`_
-  Number of auxiliary basis functions
-
-`aux_basis_overlap_matrix <http://github.com/LCPQ/quantum_package/tree/master/src/DensityFit/aux_basis.irp.f#L69>`_
-  Auxiliary basis set
-
-`aux_basis_power <http://github.com/LCPQ/quantum_package/tree/master/src/DensityFit/aux_basis.irp.f#L39>`_
-  Exponents of the auxiliary basis
-
-`aux_basis_prim_num <http://github.com/LCPQ/quantum_package/tree/master/src/DensityFit/aux_basis.irp.f#L38>`_
-  Exponents of the auxiliary basis
-
-`aux_basis_prim_num_max <http://github.com/LCPQ/quantum_package/tree/master/src/DensityFit/aux_basis.irp.f#L111>`_
-  = ao_prim_num_max
-
-`save_aux_basis <http://github.com/LCPQ/quantum_package/tree/master/src/DensityFit/aux_basis.irp.f#L120>`_
-  Undocumented
 
 `aux_basis_four_overlap <http://github.com/LCPQ/quantum_package/tree/master/src/DensityFit/overlap.irp.f#L1>`_
   \int \chi_i(r) \chi_j(r) \chi_k(r) \chi_l(r) dr
 
 
+`aux_basis_idx <http://github.com/LCPQ/quantum_package/tree/master/src/DensityFit/aux_basis.irp.f#L20>`_
+  aux_basis_idx(k) -> i,j
+
+
+`aux_basis_nucl <http://github.com/LCPQ/quantum_package/tree/master/src/DensityFit/aux_basis.irp.f#L40>`_
+  Exponents of the auxiliary basis
+
+
+`aux_basis_num <http://github.com/LCPQ/quantum_package/tree/master/src/DensityFit/aux_basis.irp.f#L2>`_
+  Number of auxiliary basis functions
+
+
+`aux_basis_num_8 <http://github.com/LCPQ/quantum_package/tree/master/src/DensityFit/aux_basis.irp.f#L3>`_
+  Number of auxiliary basis functions
+
+
+`aux_basis_num_sqrt <http://github.com/LCPQ/quantum_package/tree/master/src/DensityFit/aux_basis.irp.f#L1>`_
+  Number of auxiliary basis functions
+
+
+`aux_basis_overlap_matrix <http://github.com/LCPQ/quantum_package/tree/master/src/DensityFit/aux_basis.irp.f#L69>`_
+  Auxiliary basis set
+
+
+`aux_basis_power <http://github.com/LCPQ/quantum_package/tree/master/src/DensityFit/aux_basis.irp.f#L39>`_
+  Exponents of the auxiliary basis
+
+
+`aux_basis_prim_num <http://github.com/LCPQ/quantum_package/tree/master/src/DensityFit/aux_basis.irp.f#L38>`_
+  Exponents of the auxiliary basis
+
+
+`aux_basis_prim_num_max <http://github.com/LCPQ/quantum_package/tree/master/src/DensityFit/aux_basis.irp.f#L111>`_
+  = ao_prim_num_max
+
+
+`save_aux_basis <http://github.com/LCPQ/quantum_package/tree/master/src/DensityFit/aux_basis.irp.f#L120>`_
+  Undocumented
 
 Needed Modules
 ==============
 
 .. Do not edit this section. It was auto-generated from the
-.. NEEDED_MODULES file.
+.. by the `update_README.py` script.
 
-.. image:: tree_dependancy.png
+.. image:: tree_dependency.png
 
 * `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
 * `Pseudo <http://github.com/LCPQ/quantum_package/tree/master/src/Pseudo>`_

src/Electrons/README.rst

@@ -22,9 +22,9 @@ Needed Modules
 ==============
 
 .. Do not edit this section. It was auto-generated from the
-.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
+.. by the `update_README.py` script.
 
-.. image:: tree_dependancy.png
+.. image:: tree_dependency.png
 
 * `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
 
@@ -32,19 +32,20 @@ Documentation
 =============
 
 .. Do not edit this section. It was auto-generated from the
-.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
+.. by the `update_README.py` script.
 
 `elec_alpha_num <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons/electrons.irp.f#L1>`_
   Numbers of alpha ("up") , beta ("down") and total electrons
 
+
 `elec_beta_num <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons/electrons.irp.f#L2>`_
   Numbers of alpha ("up") , beta ("down") and total electrons
 
+
 `elec_num <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons/electrons.irp.f#L3>`_
   Numbers of alpha ("up") , beta ("down") and total electrons
 
+
 `elec_num_tab <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons/electrons.irp.f#L4>`_
   Numbers of alpha ("up") , beta ("down") and total electrons
 
-
-

src/Ezfio_files/README.rst

@@ -9,12 +9,13 @@ Documentation
 =============
 
 .. Do not edit this section. It was auto-generated from the
-.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
+.. 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
@@ -28,24 +29,180 @@ Documentation
   'x' : READ/WRITE, FORMATTED
   .br
 
+
+`output_aos <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L1>`_
+  Output file for AOs
+
+
+`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_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_cis <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L121>`_
+  Output file for CIS
+
+
+`output_cisd <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L141>`_
+  Output file for CISD
+
+
+`output_cisd_sc2_selected <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L161>`_
+  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#L181>`_
+  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
 
+
+`output_ddci_selected <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L201>`_
+  Output file for DDCI_selected
+
+
+`output_densityfit <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L221>`_
+  Output file for DensityFit
+
+
+`output_densitymatrix <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L241>`_
+  Output file for DensityMatrix
+
+
+`output_determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L261>`_
+  Output file for Determinants
+
+
+`output_electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L281>`_
+  Output file for Electrons
+
+
+`output_ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L301>`_
+  Output file for Ezfio_files
+
+
+`output_fcidump <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L321>`_
+  Output file for FCIdump
+
+
+`output_full_ci <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L341>`_
+  Output file for Full_CI
+
+
+`output_generators_cas <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L361>`_
+  Output file for Generators_CAS
+
+
+`output_generators_full <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L381>`_
+  Output file for Generators_full
+
+
+`output_generators_restart <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L401>`_
+  Output file for Generators_restart
+
+
+`output_hartree_fock <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L421>`_
+  Output file for Hartree_Fock
+
+
+`output_integrals_bielec <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L441>`_
+  Output file for Integrals_Bielec
+
+
+`output_integrals_monoelec <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L461>`_
+  Output file for Integrals_Monoelec
+
+
+`output_moguess <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L481>`_
+  Output file for MOGuess
+
+
+`output_molden <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L501>`_
+  Output file for Molden
+
+
+`output_mos <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L521>`_
+  Output file for MOs
+
+
+`output_mp2 <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L541>`_
+  Output file for MP2
+
+
+`output_mrcc <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L561>`_
+  Output file for MRCC
+
+
+`output_nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L581>`_
+  Output file for Nuclei
+
+
+`output_perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L601>`_
+  Output file for Perturbation
+
+
+`output_properties <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L621>`_
+  Output file for Properties
+
+
+`output_pseudo <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L641>`_
+  Output file for Pseudo
+
+
+`output_qmcchem <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L661>`_
+  Output file for QmcChem
+
+
+`output_selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L681>`_
+  Output file for Selectors_full
+
+
+`output_selectors_no_sorted <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L701>`_
+  Output file for Selectors_no_sorted
+
+
+`output_singlerefmethod <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L721>`_
+  Output file for SingleRefMethod
+
+
+`output_utils <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L741>`_
+  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/Generators_CAS/README.rst

@@ -16,34 +16,36 @@ Documentation
 =============
 
 .. Do not edit this section. It was auto-generated from the
-.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
+.. by the `update_README.py` script.
 
 `n_det_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_CAS/generators.irp.f#L3>`_
   Number of generator detetrminants
 
+
 `psi_coef_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_CAS/generators.irp.f#L35>`_
   For Single reference wave functions, the generator is the
   Hartree-Fock determinant
 
+
 `psi_det_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_CAS/generators.irp.f#L34>`_
   For Single reference wave functions, the generator is the
   Hartree-Fock determinant
 
+
 `select_max <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_CAS/generators.irp.f#L78>`_
   Memo to skip useless selectors
 
+
 `size_select_max <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_CAS/generators.irp.f#L70>`_
   Size of the select_max array
 
-
-
 Needed Modules
 ==============
 
 .. Do not edit this section. It was auto-generated from the
-.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
+.. by the `update_README.py` script.
 
-.. image:: tree_dependancy.png
+.. image:: tree_dependency.png
 
 * `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
 

src/Generators_full/README.rst

@@ -9,38 +9,41 @@ Documentation
 =============
 
 .. Do not edit this section. It was auto-generated from the
-.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
+.. by the `update_README.py` script.
 
 `degree_max_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full/generators.irp.f#L43>`_
   Max degree of excitation (respect to HF) of the generators
 
+
 `n_det_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full/generators.irp.f#L3>`_
   For Single reference wave functions, the number of generators is 1 : the
   Hartree-Fock determinant
 
+
 `psi_coef_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full/generators.irp.f#L26>`_
   For Single reference wave functions, the generator is the
   Hartree-Fock determinant
 
+
 `psi_det_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full/generators.irp.f#L25>`_
   For Single reference wave functions, the generator is the
   Hartree-Fock determinant
 
+
 `select_max <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full/generators.irp.f#L66>`_
   Memo to skip useless selectors
 
+
 `size_select_max <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full/generators.irp.f#L58>`_
   Size of the select_max array
 
-
-
 Needed Modules
 ==============
 
 .. Do not edit this section. It was auto-generated from the
-.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
+.. by the `update_README.py` script.
 
-.. image:: tree_dependancy.png
+.. image:: tree_dependency.png
 
 * `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
 * `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_

src/Generators_restart/README.rst

@@ -2,3 +2,40 @@
 Generators_restart Module
 =========================
 
+Documentation
+=============
+
+.. Do not edit this section. It was auto-generated from the
+.. by the `update_README.py` script.
+
+`n_det_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_restart/generators.irp.f#L3>`_
+  Read the wave function
+
+
+`psi_coef_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_restart/generators.irp.f#L21>`_
+  read wf
+  .br
+
+
+`psi_det_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_restart/generators.irp.f#L20>`_
+  read wf
+  .br
+
+
+`select_max <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_restart/generators.irp.f#L52>`_
+  Memo to skip useless selectors
+
+
+`size_select_max <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_restart/generators.irp.f#L44>`_
+  Size of the select_max array
+
+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>`_
+

src/Hartree_Fock/README.rst

@@ -8,9 +8,9 @@ Needed Modules
 ==============
 
 .. Do not edit this section. It was auto-generated from the
-.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
+.. by the `update_README.py` script.
 
-.. image:: tree_dependancy.png
+.. image:: tree_dependency.png
 
 * `Integrals_Bielec <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec>`_
 * `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
@@ -19,29 +19,58 @@ Documentation
 =============
 
 .. Do not edit this section. It was auto-generated from the
-.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
+.. by the `update_README.py` script.
 
 `ao_bi_elec_integral_alpha <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L102>`_
   Alpha Fock matrix in AO basis set
 
+
 `ao_bi_elec_integral_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L103>`_
   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 an MO guess if no MOs are present in the EZFIO directory
+
+
+`damping_scf <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/damping_SCF.irp.f#L1>`_
+  Undocumented
+
+
+`diagonal_fock_matrix_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/diagonalize_fock.irp.f#L1>`_
+  Diagonal Fock matrix in the MO basis
+
+
+`diagonal_fock_matrix_mo_sum <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/diagonalize_fock.irp.f#L67>`_
+  diagonal element of the fock matrix calculated as the sum over all the interactions
+  with all the electrons in the RHF determinant
+  diagonal_Fock_matrix_mo_sum(i) = sum_{j=1, N_elec} 2 J_ij -K_ij
+
+
+`eigenvectors_fock_matrix_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/diagonalize_fock.irp.f#L2>`_
+  Diagonal Fock matrix in the MO basis
+
+
 `fock_matrix_alpha_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L83>`_
   Alpha Fock matrix in AO basis set
 
+
 `fock_matrix_alpha_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L231>`_
   Fock matrix on the MO basis
 
+
 `fock_matrix_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L289>`_
   Fock matrix in AO basis set
 
+
 `fock_matrix_beta_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L84>`_
   Alpha Fock matrix in AO basis set
 
+
 `fock_matrix_beta_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L251>`_
   Fock matrix on the MO basis
 
+
 `fock_matrix_diag_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L2>`_
   Fock matrix on the MO basis.
   For open shells, the ROHF Fock Matrix is
@@ -57,6 +86,7 @@ Documentation
   K = Fb - Fa
   .br
 
+
 `fock_matrix_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L1>`_
   Fock matrix on the MO basis.
   For open shells, the ROHF Fock Matrix is
@@ -72,49 +102,51 @@ Documentation
   K = Fb - Fa
   .br
 
+
 `fock_mo_to_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L332>`_
   Undocumented
 
-`hf_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L270>`_
-  Hartree-Fock energy
-
-`hf_density_matrix_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/HF_density_matrix_ao.irp.f#L27>`_
-  S^-1 Density matrix in the AO basis S^-1
-
-`hf_density_matrix_ao_alpha <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/HF_density_matrix_ao.irp.f#L1>`_
-  S^-1 x Alpha density matrix in the AO basis x S^-1
-
-`hf_density_matrix_ao_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/HF_density_matrix_ao.irp.f#L14>`_
-  S^-1 Beta density matrix in the AO basis x S^-1
 
 `guess <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Huckel_guess.irp.f#L1>`_
   Undocumented
 
-`create_guess <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/SCF.irp.f#L8>`_
-  Create an MO guess if no MOs are present in the EZFIO directory
 
-`run <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/SCF.irp.f#L33>`_
+`hf_density_matrix_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/HF_density_matrix_ao.irp.f#L27>`_
-  Run SCF calculation
+  S^-1 Density matrix in the AO basis S^-1
 
-`scf <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/SCF.irp.f#L2>`_
-  Undocumented
 
-`damping_scf <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/damping_SCF.irp.f#L1>`_
+`hf_density_matrix_ao_alpha <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/HF_density_matrix_ao.irp.f#L1>`_
-  Undocumented
+  S^-1 x Alpha density matrix in the AO basis x S^-1
 
-`diagonal_fock_matrix_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/diagonalize_fock.irp.f#L1>`_
-  Diagonal Fock matrix in the MO basis
 
-`diagonal_fock_matrix_mo_sum <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/diagonalize_fock.irp.f#L67>`_
+`hf_density_matrix_ao_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/HF_density_matrix_ao.irp.f#L14>`_
-  diagonal element of the fock matrix calculated as the sum over all the interactions
+  S^-1 Beta density matrix in the AO basis x S^-1
-  with all the electrons in the RHF determinant
+
-  diagonal_Fock_matrix_mo_sum(i) = sum_{j=1, N_elec} 2 J_ij -K_ij
+
+`hf_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L270>`_
+  Hartree-Fock energy
 
-`eigenvectors_fock_matrix_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/diagonalize_fock.irp.f#L2>`_
-  Diagonal Fock matrix in the MO basis
 
 `huckel_guess <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/huckel.irp.f#L1>`_
   Build the MOs using the extended Huckel model
 
 
+`mo_guess_type <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/ezfio_interface.irp.f#L28>`_
+  Initial MO guess. Can be [ Huckel | HCore ]
+
+
+`n_it_scf_max <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/ezfio_interface.irp.f#L6>`_
+  Maximum number of SCF iterations
+
+
+`run <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/SCF.irp.f#L33>`_
+  Run SCF calculation
+
+
+`scf <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/SCF.irp.f#L2>`_
+  Undocumented
+
+
+`thresh_scf <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/ezfio_interface.irp.f#L46>`_
+  Threshold on the convergence of the Hartree Fock energy
 

src/Integrals_Bielec/README.rst

@@ -14,41 +14,94 @@ Needed Modules
 ==============
 
 .. Do not edit this section. It was auto-generated from the
-.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
+.. by the `update_README.py` script.
 
-.. image:: tree_dependancy.png
+.. image:: tree_dependency.png
 
 * `Pseudo <http://github.com/LCPQ/quantum_package/tree/master/src/Pseudo>`_
-* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
 * `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
 
 Documentation
 =============
 
 .. Do not edit this section. It was auto-generated from the
-.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
+.. by the `update_README.py` script.
+
+`add_integrals_to_map <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/mo_bi_integrals.irp.f#L42>`_
+  Adds integrals to tha MO map according to some bitmask
+
 
 `ao_bielec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L1>`_
   integral of the AO basis <ik|jl> or (ij|kl)
   i(r1) j(r1) 1/r12 k(r2) l(r2)
 
+
 `ao_bielec_integral_schwartz <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L489>`_
   Needed to compute Schwartz inequalities
 
+
 `ao_bielec_integral_schwartz_accel <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L107>`_
   integral of the AO basis <ik|jl> or (ij|kl)
   i(r1) j(r1) 1/r12 k(r2) l(r2)
 
+
 `ao_bielec_integrals_in_map <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L322>`_
   Map of Atomic integrals
   i(r1) j(r2) 1/r12 k(r1) l(r2)
 
+
+`ao_integrals_map <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f#L6>`_
+  AO integrals
+
+
+`ao_integrals_threshold <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ezfio_interface.irp.f#L46>`_
+  If |<pq|rs>| < ao_integrals_threshold then <pq|rs> is zero
+
+
 `ao_l4 <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L279>`_
   Computes the product of l values of i,j,k,and l
 
+
+`bielec_integrals_index <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f#L19>`_
+  Undocumented
+
+
+`bielec_integrals_index_reverse <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f#L36>`_
+  Undocumented
+
+
+`clear_ao_map <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f#L223>`_
+  Frees the memory of the AO map
+
+
+`clear_mo_map <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f#L399>`_
+  Frees the memory of the MO map
+
+
 `compute_ao_bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L290>`_
   Compute AO 1/r12 integrals for all i and fixed j,k,l
 
+
+`disk_access_ao_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ezfio_interface.irp.f#L28>`_
+  Read/Write AO integrals from/to disk [ Write | Read | None ]
+
+
+`disk_access_mo_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ezfio_interface.irp.f#L68>`_
+  Read/Write MO integrals from/to disk [ Write | Read | None ]
+
+
+`do_direct_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ezfio_interface.irp.f#L6>`_
+  Compute integrals on the fly
+
+
+`dump_ao_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f_template_547#L3>`_
+  Save to disk the $ao integrals
+
+
+`dump_mo_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f_template_547#L140>`_
+  Save to disk the $ao integrals
+
+
 `eri <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L652>`_
   ATOMIC PRIMTIVE bielectronic integral between the 4 primitives ::
   primitive_1 = x1**(a_x) y1**(a_y) z1**(a_z) exp(-alpha * r1**2)
@@ -56,165 +109,196 @@ Documentation
   primitive_3 = x2**(c_x) y2**(c_y) z2**(c_z) exp(-delta * r2**2)
   primitive_4 = x2**(d_x) y2**(d_y) z2**(d_z) exp(- gama * r2**2)
 
-`general_primitive_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L514>`_
-  Computes the integral <pq|rs> where p,q,r,s are Gaussian primitives
-
-`give_polynom_mult_center_x <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L850>`_
-  subroutine that returns the explicit polynom in term of the "t"
-  variable of the following polynomw :
-  I_x1(a_x, d_x,p,q) * I_x1(a_y, d_y,p,q) * I_x1(a_z, d_z,p,q)
-
-`i_x1_new <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L771>`_
-  recursive function involved in the bielectronic integral
-
-`i_x1_pol_mult <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L913>`_
-  recursive function involved in the bielectronic integral
-
-`i_x1_pol_mult_a1 <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L1033>`_
-  recursive function involved in the bielectronic integral
-
-`i_x1_pol_mult_a2 <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L1087>`_
-  recursive function involved in the bielectronic integral
-
-`i_x1_pol_mult_recurs <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L947>`_
-  recursive function involved in the bielectronic integral
-
-`i_x2_new <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L806>`_
-  recursive function involved in the bielectronic integral
-
-`i_x2_pol_mult <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L1149>`_
-  recursive function involved in the bielectronic integral
-
-`integrale_new <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L697>`_
-  calculate the integral of the polynom ::
-  I_x1(a_x+b_x, c_x+d_x,p,q) * I_x1(a_y+b_y, c_y+d_y,p,q) * I_x1(a_z+b_z, c_z+d_z,p,q)
-  between ( 0 ; 1)
-
-`n_pt_sup <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L836>`_
-  Returns the upper boundary of the degree of the polynomial involved in the
-  bielctronic integral :
-  Ix(a_x,b_x,c_x,d_x) * Iy(a_y,b_y,c_y,d_y) * Iz(a_z,b_z,c_z,d_z)
 
 `gauleg <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/gauss_legendre.irp.f#L29>`_
   Gauss-Legendre
 
+
 `gauleg_t2 <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/gauss_legendre.irp.f#L10>`_
   t_w(i,1,k) = w(i)
   t_w(i,2,k) = t(i)
 
+
 `gauleg_w <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/gauss_legendre.irp.f#L11>`_
   t_w(i,1,k) = w(i)
   t_w(i,2,k) = t(i)
 
-`n_pt_max_integrals_16 <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/gauss_legendre.irp.f#L1>`_
-  Aligned n_pt_max_integrals
 
-`ao_integrals_map <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f#L6>`_
+`general_primitive_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L514>`_
-  AO integrals
+  Computes the integral <pq|rs> where p,q,r,s are Gaussian primitives
 
-`bielec_integrals_index <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f#L19>`_
-  Undocumented
-
-`bielec_integrals_index_reverse <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f#L36>`_
-  Undocumented
-
-`clear_ao_map <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f#L223>`_
-  Frees the memory of the AO map
-
-`clear_mo_map <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f#L399>`_
-  Frees the memory of the MO map
 
 `get_ao_bielec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f#L113>`_
   Gets one AO bi-electronic integral from the AO map
 
+
 `get_ao_bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f#L137>`_
   Gets multiple AO bi-electronic integral from the AO map .
   All i are retrieved for j,k,l fixed.
 
+
 `get_ao_bielec_integrals_non_zero <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f#L172>`_
   Gets multiple AO bi-electronic integral from the AO map .
   All non-zero i are retrieved for j,k,l fixed.
 
+
 `get_ao_map_size <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f#L214>`_
   Returns the number of elements in the AO map
 
+
 `get_mo_bielec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f#L281>`_
   Returns one integral <ij|kl> in the MO basis
 
+
 `get_mo_bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f#L310>`_
   Returns multiple integrals <ij|kl> in the MO basis, all
   i for j,k,l fixed.
 
+
 `get_mo_bielec_integrals_existing_ik <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f#L341>`_
   Returns multiple integrals <ij|kl> in the MO basis, all
   i(1)j(1) 1/r12 k(2)l(2)
   i for j,k,l fixed.
 
+
 `get_mo_map_size <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f#L391>`_
   Return the number of elements in the MO map
 
+
+`give_polynom_mult_center_x <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L850>`_
+  subroutine that returns the explicit polynom in term of the "t"
+  variable of the following polynomw :
+  I_x1(a_x, d_x,p,q) * I_x1(a_y, d_y,p,q) * I_x1(a_z, d_z,p,q)
+
+
+`i_x1_new <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L771>`_
+  recursive function involved in the bielectronic integral
+
+
+`i_x1_pol_mult <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L913>`_
+  recursive function involved in the bielectronic integral
+
+
+`i_x1_pol_mult_a1 <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L1033>`_
+  recursive function involved in the bielectronic integral
+
+
+`i_x1_pol_mult_a2 <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L1087>`_
+  recursive function involved in the bielectronic integral
+
+
+`i_x1_pol_mult_recurs <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L947>`_
+  recursive function involved in the bielectronic integral
+
+
+`i_x2_new <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L806>`_
+  recursive function involved in the bielectronic integral
+
+
+`i_x2_pol_mult <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L1149>`_
+  recursive function involved in the bielectronic integral
+
+
 `insert_into_ao_integrals_map <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f#L250>`_
   Create new entry into AO map
 
+
 `insert_into_mo_integrals_map <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f#L265>`_
   Create new entry into MO map, or accumulate in an existing entry
 
+
+`integrale_new <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L697>`_
+  calculate the integral of the polynom ::
+  I_x1(a_x+b_x, c_x+d_x,p,q) * I_x1(a_y+b_y, c_y+d_y,p,q) * I_x1(a_z+b_z, c_z+d_z,p,q)
+  between ( 0 ; 1)
+
+
+`load_ao_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f_template_547#L89>`_
+  Read from disk the $ao integrals
+
+
+`load_mo_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f_template_547#L226>`_
+  Read from disk the $ao integrals
+
+
 `mo_bielec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f#L298>`_
   Returns one integral <ij|kl> in the MO basis
 
-`mo_integrals_map <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f#L237>`_
-  MO integrals
-
-`add_integrals_to_map <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/mo_bi_integrals.irp.f#L42>`_
-  Adds integrals to tha MO map according to some bitmask
 
 `mo_bielec_integral_jj <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/mo_bi_integrals.irp.f#L465>`_
   mo_bielec_integral_jj(i,j) = J_ij
   mo_bielec_integral_jj_exchange(i,j) = K_ij
   mo_bielec_integral_jj_anti(i,j) = J_ij - K_ij
 
+
 `mo_bielec_integral_jj_anti <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/mo_bi_integrals.irp.f#L467>`_
   mo_bielec_integral_jj(i,j) = J_ij
   mo_bielec_integral_jj_exchange(i,j) = K_ij
   mo_bielec_integral_jj_anti(i,j) = J_ij - K_ij
 
+
 `mo_bielec_integral_jj_anti_from_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/mo_bi_integrals.irp.f#L327>`_
   mo_bielec_integral_jj_from_ao(i,j) = J_ij
   mo_bielec_integral_jj_exchange_from_ao(i,j) = J_ij
   mo_bielec_integral_jj_anti_from_ao(i,j) = J_ij - K_ij
 
+
 `mo_bielec_integral_jj_exchange <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/mo_bi_integrals.irp.f#L466>`_
   mo_bielec_integral_jj(i,j) = J_ij
   mo_bielec_integral_jj_exchange(i,j) = K_ij
   mo_bielec_integral_jj_anti(i,j) = J_ij - K_ij
 
+
 `mo_bielec_integral_jj_exchange_from_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/mo_bi_integrals.irp.f#L326>`_
   mo_bielec_integral_jj_from_ao(i,j) = J_ij
   mo_bielec_integral_jj_exchange_from_ao(i,j) = J_ij
   mo_bielec_integral_jj_anti_from_ao(i,j) = J_ij - K_ij
 
+
 `mo_bielec_integral_jj_from_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/mo_bi_integrals.irp.f#L325>`_
   mo_bielec_integral_jj_from_ao(i,j) = J_ij
   mo_bielec_integral_jj_exchange_from_ao(i,j) = J_ij
   mo_bielec_integral_jj_anti_from_ao(i,j) = J_ij - K_ij
 
+
 `mo_bielec_integrals_in_map <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/mo_bi_integrals.irp.f#L22>`_
   If True, the map of MO bielectronic integrals is provided
 
+
 `mo_bielec_integrals_index <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/mo_bi_integrals.irp.f#L1>`_
   Computes an unique index for i,j,k,l integrals
 
+
+`mo_integrals_map <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f#L237>`_
+  MO integrals
+
+
+`mo_integrals_threshold <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ezfio_interface.irp.f#L86>`_
+  If |<ij|kl>| < ao_integrals_threshold then <pq|rs> is zero
+
+
+`n_pt_max_integrals_16 <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/gauss_legendre.irp.f#L1>`_
+  Aligned n_pt_max_integrals
+
+
+`n_pt_sup <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L836>`_
+  Returns the upper boundary of the degree of the polynomial involved in the
+  bielctronic integral :
+  Ix(a_x,b_x,c_x,d_x) * Iy(a_y,b_y,c_y,d_y) * Iz(a_z,b_z,c_z,d_z)
+
+
 `read_ao_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/read_write.irp.f#L1>`_
   One level of abstraction for disk_access_ao_integrals and disk_access_mo_integrals
 
+
 `read_mo_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/read_write.irp.f#L2>`_
   One level of abstraction for disk_access_ao_integrals and disk_access_mo_integrals
 
+
 `write_ao_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/read_write.irp.f#L3>`_
   One level of abstraction for disk_access_ao_integrals and disk_access_mo_integrals
 
+
 `write_mo_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/read_write.irp.f#L4>`_
   One level of abstraction for disk_access_ao_integrals and disk_access_mo_integrals
 
-
-

src/Integrals_Monoelec/README.rst

@@ -2,9 +2,9 @@ Needed Modules
 ==============
 
 .. Do not edit this section. It was auto-generated from the
-.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
+.. by the `update_README.py` script.
 
-.. image:: tree_dependancy.png
+.. image:: tree_dependency.png
 
 * `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
 * `Pseudo <http://github.com/LCPQ/quantum_package/tree/master/src/Pseudo>`_
@@ -13,17 +13,7 @@ Documentation
 =============
 
 .. Do not edit this section. It was auto-generated from the
-.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
+.. by the `update_README.py` script.
-
-`ao_mono_elec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/ao_mono_ints.irp.f#L1>`_
-  array of the mono electronic hamiltonian on the AOs basis
-  : sum of the kinetic and nuclear electronic potential
-
-`check_ortho <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/check_orthonormality.irp.f#L1>`_
-  Undocumented
-
-`do_print <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/check_orthonormality.irp.f#L11>`_
-  Undocumented
 
 `ao_deriv2_x <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/kin_ao_ints.irp.f#L1>`_
   second derivatives matrix elements in the ao basis
@@ -31,198 +21,258 @@ Documentation
   .br
   {\tt ao_deriv2_x} = \langle \chi_i(x,y,z) \frac{\partial^2}{\partial x^2} |\chi_j (x,y,z) \rangle
 
+
 `ao_deriv2_y <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/kin_ao_ints.irp.f#L2>`_
   second derivatives matrix elements in the ao basis
   .. math::
   .br
   {\tt ao_deriv2_x} = \langle \chi_i(x,y,z) \frac{\partial^2}{\partial x^2} |\chi_j (x,y,z) \rangle
 
+
 `ao_deriv2_z <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/kin_ao_ints.irp.f#L3>`_
   second derivatives matrix elements in the ao basis
   .. math::
   .br
   {\tt ao_deriv2_x} = \langle \chi_i(x,y,z) \frac{\partial^2}{\partial x^2} |\chi_j (x,y,z) \rangle
 
-`ao_kinetic_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/kin_ao_ints.irp.f#L125>`_
-  array of the priminitve basis kinetic integrals
-  \langle \chi_i |\hat{T}| \chi_j \rangle
-
-`mo_kinetic_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/kin_mo_ints.irp.f#L1>`_
-  Undocumented
-
-`mo_mono_elec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/mo_mono_ints.irp.f#L1>`_
-  array of the mono electronic hamiltonian on the MOs basis
-  : sum of the kinetic and nuclear electronic potential
-
-`orthonormalize_mos <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/orthonormalize.irp.f#L1>`_
-  Undocumented
-
-`ao_nucl_elec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/pot_ao_ints.irp.f#L1>`_
-  interaction nuclear electron
-
-`ao_nucl_elec_integral_per_atom <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/pot_ao_ints.irp.f#L72>`_
-  ao_nucl_elec_integral_per_atom(i,j,k) = -<AO(i)|1/|r-Rk|AO(j)>
-  where Rk is the geometry of the kth atom
-
-`give_polynom_mult_center_mono_elec <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/pot_ao_ints.irp.f#L218>`_
-  Undocumented
-
-`i_x1_pol_mult_mono_elec <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/pot_ao_ints.irp.f#L346>`_
-  Undocumented
-
-`i_x2_pol_mult_mono_elec <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/pot_ao_ints.irp.f#L417>`_
-  Undocumented
-
-`int_gaus_pol <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/pot_ao_ints.irp.f#L488>`_
-  Undocumented
-
-`nai_pol_mult <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/pot_ao_ints.irp.f#L139>`_
-  Undocumented
-
-`v_e_n <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/pot_ao_ints.irp.f#L469>`_
-  Undocumented
-
-`v_phi <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/pot_ao_ints.irp.f#L533>`_
-  Undocumented
-
-`v_r <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/pot_ao_ints.irp.f#L517>`_
-  Undocumented
-
-`v_theta <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/pot_ao_ints.irp.f#L546>`_
-  Undocumented
-
-`wallis <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/pot_ao_ints.irp.f#L562>`_
-  Undocumented
-
-`ao_pseudo_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/pot_ao_pseudo_ints.irp.f#L1>`_
-  Pseudo-potential
-
-`ao_pseudo_integral_local <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/pot_ao_pseudo_ints.irp.f#L15>`_
-  Local pseudo-potential
-
-`ao_pseudo_integral_non_local <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/pot_ao_pseudo_ints.irp.f#L121>`_
-  Local pseudo-potential
-
-`mo_nucl_elec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/pot_mo_ints.irp.f#L1>`_
-  interaction nuclear electron on the MO basis
-
-`mo_nucl_elec_integral_per_atom <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/pot_mo_ints.irp.f#L30>`_
-  mo_nucl_elec_integral_per_atom(i,j,k) = -<MO(i)|1/|r-Rk|MO(j)>
-  where Rk is the geometry of the kth atom
-
-`mo_pseudo_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/pot_mo_pseudo_ints.irp.f#L1>`_
-  interaction nuclear electron on the MO basis
-
-`save_ortho_mos <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/save_ortho_mos.irp.f#L1>`_
-  Undocumented
 
 `ao_deriv_1_x <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/spread_dipole_ao.irp.f#L148>`_
   array of the integrals of AO_i * d/dx  AO_j
   array of the integrals of AO_i * d/dy  AO_j
   array of the integrals of AO_i * d/dz  AO_j
 
+
 `ao_deriv_1_y <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/spread_dipole_ao.irp.f#L149>`_
   array of the integrals of AO_i * d/dx  AO_j
   array of the integrals of AO_i * d/dy  AO_j
   array of the integrals of AO_i * d/dz  AO_j
 
+
 `ao_deriv_1_z <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/spread_dipole_ao.irp.f#L150>`_
   array of the integrals of AO_i * d/dx  AO_j
   array of the integrals of AO_i * d/dy  AO_j
   array of the integrals of AO_i * d/dz  AO_j
 
+
 `ao_dipole_x <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/spread_dipole_ao.irp.f#L75>`_
   array of the integrals of AO_i * x AO_j
   array of the integrals of AO_i * y AO_j
   array of the integrals of AO_i * z AO_j
 
+
 `ao_dipole_y <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/spread_dipole_ao.irp.f#L76>`_
   array of the integrals of AO_i * x AO_j
   array of the integrals of AO_i * y AO_j
   array of the integrals of AO_i * z AO_j
 
+
 `ao_dipole_z <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/spread_dipole_ao.irp.f#L77>`_
   array of the integrals of AO_i * x AO_j
   array of the integrals of AO_i * y AO_j
   array of the integrals of AO_i * z AO_j
 
+
+`ao_kinetic_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/kin_ao_ints.irp.f#L125>`_
+  array of the priminitve basis kinetic integrals
+  \langle \chi_i |\hat{T}| \chi_j \rangle
+
+
+`ao_mono_elec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/ao_mono_ints.irp.f#L1>`_
+  array of the mono electronic hamiltonian on the AOs basis
+  : sum of the kinetic and nuclear electronic potential
+
+
+`ao_nucl_elec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/pot_ao_ints.irp.f#L1>`_
+  interaction nuclear electron
+
+
+`ao_nucl_elec_integral_per_atom <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/pot_ao_ints.irp.f#L72>`_
+  ao_nucl_elec_integral_per_atom(i,j,k) = -<AO(i)|1/|r-Rk|AO(j)>
+  where Rk is the geometry of the kth atom
+
+
+`ao_pseudo_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/pot_ao_pseudo_ints.irp.f#L1>`_
+  Pseudo-potential
+
+
+`ao_pseudo_integral_local <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/pot_ao_pseudo_ints.irp.f#L15>`_
+  Local pseudo-potential
+
+
+`ao_pseudo_integral_non_local <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/pot_ao_pseudo_ints.irp.f#L121>`_
+  Local pseudo-potential
+
+
 `ao_spread_x <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/spread_dipole_ao.irp.f#L1>`_
   array of the integrals of AO_i * x^2 AO_j
   array of the integrals of AO_i * y^2 AO_j
   array of the integrals of AO_i * z^2 AO_j
 
+
 `ao_spread_y <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/spread_dipole_ao.irp.f#L2>`_
   array of the integrals of AO_i * x^2 AO_j
   array of the integrals of AO_i * y^2 AO_j
   array of the integrals of AO_i * z^2 AO_j
 
+
 `ao_spread_z <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/spread_dipole_ao.irp.f#L3>`_
   array of the integrals of AO_i * x^2 AO_j
   array of the integrals of AO_i * y^2 AO_j
   array of the integrals of AO_i * z^2 AO_j
 
-`overlap_bourrin_deriv_x <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/spread_dipole_ao.irp.f#L365>`_
+
+`check_ortho <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/check_orthonormality.irp.f#L1>`_
   Undocumented
 
-`overlap_bourrin_dipole <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/spread_dipole_ao.irp.f#L318>`_
+
+`do_print <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/check_orthonormality.irp.f#L11>`_
   Undocumented
 
-`overlap_bourrin_spread <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/spread_dipole_ao.irp.f#L265>`_
+
+`give_polynom_mult_center_mono_elec <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/pot_ao_ints.irp.f#L218>`_
   Undocumented
 
-`overlap_bourrin_x <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/spread_dipole_ao.irp.f#L380>`_
+
+`i_x1_pol_mult_mono_elec <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/pot_ao_ints.irp.f#L346>`_
   Undocumented
 
-`overlap_bourrin_x_abs <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/spread_dipole_ao.irp.f#L226>`_
+
+`i_x2_pol_mult_mono_elec <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/pot_ao_ints.irp.f#L417>`_
   Undocumented
 
-`power <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/spread_dipole_ao.irp.f#L310>`_
+
+`int_gaus_pol <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/pot_ao_ints.irp.f#L488>`_
   Undocumented
 
+
 `mo_deriv_1_x <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/spread_dipole_mo.irp.f#L69>`_
   array of the integrals of MO_i * d/dx  MO_j
   array of the integrals of MO_i * d/dy  MO_j
   array of the integrals of MO_i * d/dz  MO_j
 
+
 `mo_deriv_1_y <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/spread_dipole_mo.irp.f#L70>`_
   array of the integrals of MO_i * d/dx  MO_j
   array of the integrals of MO_i * d/dy  MO_j
   array of the integrals of MO_i * d/dz  MO_j
 
+
 `mo_deriv_1_z <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/spread_dipole_mo.irp.f#L71>`_
   array of the integrals of MO_i * d/dx  MO_j
   array of the integrals of MO_i * d/dy  MO_j
   array of the integrals of MO_i * d/dz  MO_j
 
+
 `mo_dipole_x <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/spread_dipole_mo.irp.f#L1>`_
   array of the integrals of MO_i * x MO_j
   array of the integrals of MO_i * y MO_j
   array of the integrals of MO_i * z MO_j
 
+
 `mo_dipole_y <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/spread_dipole_mo.irp.f#L2>`_
   array of the integrals of MO_i * x MO_j
   array of the integrals of MO_i * y MO_j
   array of the integrals of MO_i * z MO_j
 
+
 `mo_dipole_z <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/spread_dipole_mo.irp.f#L3>`_
   array of the integrals of MO_i * x MO_j
   array of the integrals of MO_i * y MO_j
   array of the integrals of MO_i * z MO_j
 
+
+`mo_kinetic_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/kin_mo_ints.irp.f#L1>`_
+  Undocumented
+
+
+`mo_mono_elec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/mo_mono_ints.irp.f#L1>`_
+  array of the mono electronic hamiltonian on the MOs basis
+  : sum of the kinetic and nuclear electronic potential
+
+
+`mo_nucl_elec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/pot_mo_ints.irp.f#L1>`_
+  interaction nuclear electron on the MO basis
+
+
+`mo_nucl_elec_integral_per_atom <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/pot_mo_ints.irp.f#L30>`_
+  mo_nucl_elec_integral_per_atom(i,j,k) = -<MO(i)|1/|r-Rk|MO(j)>
+  where Rk is the geometry of the kth atom
+
+
+`mo_pseudo_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/pot_mo_pseudo_ints.irp.f#L1>`_
+  interaction nuclear electron on the MO basis
+
+
 `mo_spread_x <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/spread_dipole_mo.irp.f#L36>`_
   array of the integrals of MO_i * x^2 MO_j
   array of the integrals of MO_i * y^2 MO_j
   array of the integrals of MO_i * z^2 MO_j
 
+
 `mo_spread_y <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/spread_dipole_mo.irp.f#L37>`_
   array of the integrals of MO_i * x^2 MO_j
   array of the integrals of MO_i * y^2 MO_j
   array of the integrals of MO_i * z^2 MO_j
 
+
 `mo_spread_z <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/spread_dipole_mo.irp.f#L38>`_
   array of the integrals of MO_i * x^2 MO_j
   array of the integrals of MO_i * y^2 MO_j
   array of the integrals of MO_i * z^2 MO_j
 
 
+`nai_pol_mult <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/pot_ao_ints.irp.f#L139>`_
+  Undocumented
+
+
+`orthonormalize_mos <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/orthonormalize.irp.f#L1>`_
+  Undocumented
+
+
+`overlap_bourrin_deriv_x <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/spread_dipole_ao.irp.f#L365>`_
+  Undocumented
+
+
+`overlap_bourrin_dipole <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/spread_dipole_ao.irp.f#L318>`_
+  Undocumented
+
+
+`overlap_bourrin_spread <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/spread_dipole_ao.irp.f#L265>`_
+  Undocumented
+
+
+`overlap_bourrin_x <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/spread_dipole_ao.irp.f#L380>`_
+  Undocumented
+
+
+`overlap_bourrin_x_abs <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/spread_dipole_ao.irp.f#L226>`_
+  Undocumented
+
+
+`power <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/spread_dipole_ao.irp.f#L310>`_
+  Undocumented
+
+
+`save_ortho_mos <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/save_ortho_mos.irp.f#L1>`_
+  Undocumented
+
+
+`v_e_n <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/pot_ao_ints.irp.f#L469>`_
+  Undocumented
+
+
+`v_phi <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/pot_ao_ints.irp.f#L533>`_
+  Undocumented
+
+
+`v_r <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/pot_ao_ints.irp.f#L517>`_
+  Undocumented
+
+
+`v_theta <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/pot_ao_ints.irp.f#L546>`_
+  Undocumented
+
+
+`wallis <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/pot_ao_ints.irp.f#L562>`_
+  Undocumented
 

src/MOGuess/README.rst

@@ -6,9 +6,9 @@ Needed Modules
 ==============
 
 .. Do not edit this section. It was auto-generated from the
-.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
+.. by the `update_README.py` script.
 
-.. image:: tree_dependancy.png
+.. image:: tree_dependency.png
 
 * `Integrals_Monoelec <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec>`_
 
@@ -16,22 +16,23 @@ Documentation
 =============
 
 .. Do not edit this section. It was auto-generated from the
-.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
+.. by the `update_README.py` script.
-
-`h_core_guess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess/H_CORE_guess.irp.f#L1>`_
-  Undocumented
 
 `ao_ortho_lowdin_coef <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess/mo_ortho_lowdin.irp.f#L2>`_
   matrix of the coefficients of the mos generated by the
   orthonormalization by the S^{-1/2} canonical transformation of the aos
   ao_ortho_lowdin_coef(i,j) = coefficient of the ith ao on the jth ao_ortho_lowdin orbital
 
-`ao_ortho_lowdin_overlap <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess/mo_ortho_lowdin.irp.f#L26>`_
-  overlap matrix of the ao_ortho_lowdin
-  supposed to be the Identity
 
 `ao_ortho_lowdin_nucl_elec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess/pot_mo_ortho_lowdin_ints.irp.f#L1>`_
   Undocumented
 
 
+`ao_ortho_lowdin_overlap <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess/mo_ortho_lowdin.irp.f#L26>`_
+  overlap matrix of the ao_ortho_lowdin
+  supposed to be the Identity
+
+
+`h_core_guess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess/H_CORE_guess.irp.f#L1>`_
+  Undocumented
 

src/MOs/README.rst

@@ -34,9 +34,9 @@ Needed Modules
 ==============
 
 .. Do not edit this section. It was auto-generated from the
-.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
+.. by the `update_README.py` script.
 
-.. image:: tree_dependancy.png
+.. image:: tree_dependency.png
 
 * `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
 * `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
@@ -45,23 +45,16 @@ Documentation
 =============
 
 .. Do not edit this section. It was auto-generated from the
-.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
+.. by the `update_README.py` script.
+
+`ao_to_mo <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L126>`_
+  Transform A from the AO basis to the MO basis
+
 
 `cholesky_mo <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/cholesky_mo.irp.f#L1>`_
   Cholesky decomposition of AO Density matrix to
   generate MOs
 
-`mo_density_matrix <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/cholesky_mo.irp.f#L44>`_
-  Density matrix in MO basis
-
-`mo_density_matrix_virtual <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/cholesky_mo.irp.f#L64>`_
-  Density matrix in MO basis (virtual MOs)
-
-`mo_overlap <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mo_overlap.irp.f#L2>`_
-  Undocumented
-
-`ao_to_mo <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L126>`_
-  Transform A from the AO basis to the MO basis
 
 `mix_mo_jk <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L210>`_
   subroutine that rotates the jth MO with the kth MO
@@ -71,48 +64,71 @@ Documentation
   by convention, the '+' MO is in the lower index (min(j,k))
   by convention, the '-' MO is in the greater index (max(j,k))
 
+
+`mo_as_eigvectors_of_mo_matrix <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/utils.irp.f#L24>`_
+  Undocumented
+
+
+`mo_as_eigvectors_of_mo_matrix_sort_by_observable <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/utils.irp.f#L62>`_
+  Undocumented
+
+
 `mo_coef <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L28>`_
   Molecular orbital coefficients on AO basis set
   mo_coef(i,j) = coefficient of the ith ao on the jth mo
   mo_label : Label characterizing the MOS (local, canonical, natural, etc)
 
+
 `mo_coef_transp <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L71>`_
   Molecular orbital coefficients on AO basis set
 
+
+`mo_density_matrix <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/cholesky_mo.irp.f#L44>`_
+  Density matrix in MO basis
+
+
+`mo_density_matrix_virtual <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/cholesky_mo.irp.f#L64>`_
+  Density matrix in MO basis (virtual MOs)
+
+
 `mo_label <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L29>`_
   Molecular orbital coefficients on AO basis set
   mo_coef(i,j) = coefficient of the ith ao on the jth mo
   mo_label : Label characterizing the MOS (local, canonical, natural, etc)
 
+
 `mo_occ <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L102>`_
   MO occupation numbers
 
-`mo_to_ao <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L152>`_
-  Transform A from the MO basis to the AO basis
 
-`mo_to_ao_no_overlap <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L184>`_
+`mo_overlap <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mo_overlap.irp.f#L2>`_
-  Transform A from the MO basis to the S^-1 AO basis
-
-`mo_tot_num <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L1>`_
-  Total number of molecular orbitals and the size of the keys corresponding
-
-`mo_tot_num_align <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L18>`_
-  Aligned variable for dimensioning of arrays
-
-`s_mo_coef <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L89>`_
-  Product S.C where S is the overlap matrix in the AO basis and C the mo_coef matrix.
-
-`mo_as_eigvectors_of_mo_matrix <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/utils.irp.f#L24>`_
   Undocumented
 
-`mo_as_eigvectors_of_mo_matrix_sort_by_observable <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/utils.irp.f#L62>`_
-  Undocumented
 
 `mo_sort_by_observable <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/utils.irp.f#L144>`_
   Undocumented
 
+
+`mo_to_ao <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L152>`_
+  Transform A from the MO basis to the AO basis
+
+
+`mo_to_ao_no_overlap <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L184>`_
+  Transform A from the MO basis to the S^-1 AO basis
+
+
+`mo_tot_num <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L1>`_
+  Total number of molecular orbitals and the size of the keys corresponding
+
+
+`mo_tot_num_align <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L18>`_
+  Aligned variable for dimensioning of arrays
+
+
+`s_mo_coef <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L89>`_
+  Product S.C where S is the overlap matrix in the AO basis and C the mo_coef matrix.
+
+
 `save_mos <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/utils.irp.f#L1>`_
   Undocumented
 
-
-

src/Nuclei/README.rst

@@ -10,9 +10,9 @@ Needed Modules
 ==============
 
 .. Do not edit this section. It was auto-generated from the
-.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
+.. by the `update_README.py` script.
 
-.. image:: tree_dependancy.png
+.. image:: tree_dependency.png
 
 * `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
 * `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
@@ -21,59 +21,70 @@ Documentation
 =============
 
 .. Do not edit this section. It was auto-generated from the
-.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
+.. by the `update_README.py` script.
 
 `element_name <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L215>`_
   Array of the name of element, sorted by nuclear charge (integer)
 
+
 `nucl_charge <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L23>`_
   Nuclear charges
 
+
 `nucl_coord <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L55>`_
   Nuclear coordinates in the format (:, {x,y,z})
 
+
 `nucl_coord_transp <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L110>`_
   Transposed array of nucl_coord
 
+
 `nucl_dist <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L129>`_
   nucl_dist     : Nucleus-nucleus distances
   nucl_dist_2   : Nucleus-nucleus distances squared
   nucl_dist_vec : Nucleus-nucleus distances vectors
 
+
 `nucl_dist_2 <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L125>`_
   nucl_dist     : Nucleus-nucleus distances
   nucl_dist_2   : Nucleus-nucleus distances squared
   nucl_dist_vec : Nucleus-nucleus distances vectors
 
+
 `nucl_dist_vec_x <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L126>`_
   nucl_dist     : Nucleus-nucleus distances
   nucl_dist_2   : Nucleus-nucleus distances squared
   nucl_dist_vec : Nucleus-nucleus distances vectors
 
+
 `nucl_dist_vec_y <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L127>`_
   nucl_dist     : Nucleus-nucleus distances
   nucl_dist_2   : Nucleus-nucleus distances squared
   nucl_dist_vec : Nucleus-nucleus distances vectors
 
+
 `nucl_dist_vec_z <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L128>`_
   nucl_dist     : Nucleus-nucleus distances
   nucl_dist_2   : Nucleus-nucleus distances squared
   nucl_dist_vec : Nucleus-nucleus distances vectors
 
+
 `nucl_label <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L41>`_
   Nuclear labels
 
+
 `nucl_num <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L1>`_
   Number of nuclei
 
+
 `nucl_num_aligned <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L2>`_
   Number of nuclei
 
+
 `nuclear_repulsion <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L187>`_
   Nuclear repulsion energy
 
+
 `positive_charge_barycentre <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L171>`_
   Centroid of the positive charges
 
-
-

src/Perturbation/README.rst

@@ -71,17 +71,151 @@ Documentation
 =============
 
 .. Do not edit this section. It was auto-generated from the
-.. NEEDED_MODULES file.
+.. by the `update_README.py` script.
 
-`pt2_moller_plesset <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/Moller_plesset.irp.f#L1>`_
+`do_pt2_end <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/ezfio_interface.irp.f#L6>`_
-  compute the standard Moller-Plesset perturbative first order coefficient and second order energetic contribution
+  If true, compute the PT2 at the end of the selection
+
+
+`fill_h_apply_buffer_selection <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/selection.irp.f#L1>`_
+  Fill the H_apply buffer with determiants for the selection
+
+
+`max_exc_pert <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/exc_max.irp.f#L1>`_
+  Undocumented
+
+
+`perturb_buffer_by_mono_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L161>`_
+  Applly pertubration ``delta_rho_one_point`` to the buffer of determinants generated in the H_apply
+  routine.
+
+
+`perturb_buffer_by_mono_dipole_moment_z <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L896>`_
+  Applly pertubration ``dipole_moment_z`` to the buffer of determinants generated in the H_apply
+  routine.
+
+
+`perturb_buffer_by_mono_epstein_nesbet <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L686>`_
+  Applly pertubration ``epstein_nesbet`` to the buffer of determinants generated in the H_apply
+  routine.
+
+
+`perturb_buffer_by_mono_epstein_nesbet_2x2 <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L791>`_
+  Applly pertubration ``epstein_nesbet_2x2`` to the buffer of determinants generated in the H_apply
+  routine.
+
+
+`perturb_buffer_by_mono_epstein_nesbet_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L581>`_
+  Applly pertubration ``epstein_nesbet_sc2`` to the buffer of determinants generated in the H_apply
+  routine.
+
+
+`perturb_buffer_by_mono_epstein_nesbet_sc2_no_projected <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L476>`_
+  Applly pertubration ``epstein_nesbet_sc2_no_projected`` to the buffer of determinants generated in the H_apply
+  routine.
+
+
+`perturb_buffer_by_mono_epstein_nesbet_sc2_projected <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L371>`_
+  Applly pertubration ``epstein_nesbet_sc2_projected`` to the buffer of determinants generated in the H_apply
+  routine.
+
+
+`perturb_buffer_by_mono_h_core <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L266>`_
+  Applly pertubration ``h_core`` to the buffer of determinants generated in the H_apply
+  routine.
+
+
+`perturb_buffer_by_mono_moller_plesset <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L56>`_
+  Applly pertubration ``moller_plesset`` to the buffer of determinants generated in the H_apply
+  routine.
+
+
+`perturb_buffer_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L110>`_
+  Applly pertubration ``delta_rho_one_point`` to the buffer of determinants generated in the H_apply
+  routine.
+
+
+`perturb_buffer_dipole_moment_z <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L845>`_
+  Applly pertubration ``dipole_moment_z`` to the buffer of determinants generated in the H_apply
+  routine.
+
+
+`perturb_buffer_epstein_nesbet <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L635>`_
+  Applly pertubration ``epstein_nesbet`` to the buffer of determinants generated in the H_apply
+  routine.
+
+
+`perturb_buffer_epstein_nesbet_2x2 <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L740>`_
+  Applly pertubration ``epstein_nesbet_2x2`` to the buffer of determinants generated in the H_apply
+  routine.
+
+
+`perturb_buffer_epstein_nesbet_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L530>`_
+  Applly pertubration ``epstein_nesbet_sc2`` to the buffer of determinants generated in the H_apply
+  routine.
+
+
+`perturb_buffer_epstein_nesbet_sc2_no_projected <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L425>`_
+  Applly pertubration ``epstein_nesbet_sc2_no_projected`` to the buffer of determinants generated in the H_apply
+  routine.
+
+
+`perturb_buffer_epstein_nesbet_sc2_projected <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L320>`_
+  Applly pertubration ``epstein_nesbet_sc2_projected`` to the buffer of determinants generated in the H_apply
+  routine.
+
+
+`perturb_buffer_h_core <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L215>`_
+  Applly pertubration ``h_core`` to the buffer of determinants generated in the H_apply
+  routine.
+
+
+`perturb_buffer_moller_plesset <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L5>`_
+  Applly pertubration ``moller_plesset`` to the buffer of determinants generated in the H_apply
+  routine.
+
+
+`pt2_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/delta_rho_perturbation.irp.f#L1>`_
+  compute the perturbatibe contribution to the Integrated Spin density at z = z_one point of one determinant
   .br
-  for the various n_st states.
+  for the various n_st states, at various level of theory.
   .br
-  c_pert(i) = <psi(i)|H|det_pert>/(difference of orbital energies)
+  c_pert(i) = <psi(i)|H|det_pert>/(<psi(i)|H|psi(i)> - <det_pert|H|det_pert>)
   .br
-  e_2_pert(i) = <psi(i)|H|det_pert>^2/(difference of orbital energies)
+  e_2_pert(i) = c_pert(i) * <det_pert|O|psi(i)>
   .br
+  H_pert_diag(i) = c_pert(i)^2 * <det_pert|O|det_pert>
+  .br
+  To get the contribution of the first order :
+  .br
+  <O_1> = sum(over i)  e_2_pert(i)
+  .br
+  To get the contribution of the diagonal elements of the second order :
+  .br
+  [ <O_0> + <O_1> + sum(over i)  H_pert_diag(i) ] / [1. + sum(over i) c_pert(i) **2]
+  .br
+
+
+`pt2_dipole_moment_z <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/dipole_moment.irp.f#L1>`_
+  compute the perturbatibe contribution to the dipole moment of one determinant
+  .br
+  for the various n_st states, at various level of theory.
+  .br
+  c_pert(i) = <psi(i)|H|det_pert>/(<psi(i)|H|psi(i)> - <det_pert|H|det_pert>)
+  .br
+  e_2_pert(i) = c_pert(i) * <det_pert|Z|psi(i)>
+  .br
+  H_pert_diag(i) = c_pert(i)^2 * <det_pert|Z|det_pert>
+  .br
+  To get the contribution of the first order :
+  .br
+  <Z_1> = sum(over i)  e_2_pert(i)
+  .br
+  To get the contribution of the diagonal elements of the second order :
+  .br
+  [ <Z_0> + <Z_1> + sum(over i)  H_pert_diag(i) ] / [1. + sum(over i) c_pert(i) **2]
+  .br
+
 
 `pt2_epstein_nesbet <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/epstein_nesbet.irp.f#L1>`_
   compute the standard Epstein-Nesbet perturbative first order coefficient and second order energetic contribution
@@ -93,7 +227,8 @@ Documentation
   e_2_pert(i) = <psi(i)|H|det_pert>^2/( E(i) - <det_pert|H|det_pert> )
   .br
 
-`pt2_epstein_nesbet_2x2 <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/epstein_nesbet.irp.f#L43>`_
+
+`pt2_epstein_nesbet_2x2 <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/epstein_nesbet.irp.f#L45>`_
   compute the Epstein-Nesbet 2x2 diagonalization coefficient and energetic contribution
   .br
   for the various N_st states.
@@ -103,6 +238,42 @@ Documentation
   c_pert(i) = e_2_pert(i)/ <psi(i)|H|det_pert>
   .br
 
+
+`pt2_epstein_nesbet_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/pert_sc2.irp.f#L186>`_
+  compute the standard Epstein-Nesbet perturbative first order coefficient and second order energetic contribution
+  .br
+  for the various N_st states, but with the CISD_SC2 energies and coefficients
+  .br
+  c_pert(i) = <psi(i)|H|det_pert>/( E(i) - <det_pert|H|det_pert> )
+  .br
+  e_2_pert(i) = <psi(i)|H|det_pert>^2/( E(i) - <det_pert|H|det_pert> )
+  .br
+
+
+`pt2_epstein_nesbet_sc2_no_projected <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/pert_sc2.irp.f#L87>`_
+  compute the Epstein-Nesbet perturbative first order coefficient and second order energetic contribution
+  .br
+  for the various N_st states,
+  .br
+  but  with the correction in the denominator
+  .br
+  comming from the interaction of that determinant with all the others determinants
+  .br
+  that can be repeated by repeating all the double excitations
+  .br
+  : you repeat all the correlation energy already taken into account in CI_electronic_energy(1)
+  .br
+  that could be repeated to this determinant.
+  .br
+  In addition, for the perturbative energetic contribution you have the standard second order
+  .br
+  e_2_pert = <psi_i|H|det_pert>^2/(Delta_E)
+  .br
+  and also the purely projected contribution
+  .br
+  H_pert_diag = <HF|H|det_pert> c_pert
+
+
 `pt2_epstein_nesbet_sc2_projected <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/pert_sc2.irp.f#L2>`_
   compute the Epstein-Nesbet perturbative first order coefficient and second order energetic contribution
   .br
@@ -126,43 +297,67 @@ Documentation
   .br
   H_pert_diag = <HF|H|det_pert> c_pert
 
-`repeat_all_e_corr <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/pert_sc2.irp.f#L90>`_
-  Undocumented
 
-`fill_h_apply_buffer_selection <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/selection.irp.f#L1>`_
+`pt2_h_core <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/pert_single.irp.f#L1>`_
-  Fill the H_apply buffer with determiants for the selection
+  compute the standard Epstein-Nesbet perturbative first order coefficient and second order energetic contribution
+  .br
+  for the various N_st states.
+  .br
+  c_pert(i) = <psi(i)|H|det_pert>/( E(i) - <det_pert|H|det_pert> )
+  .br
+  e_2_pert(i) = <psi(i)|H|det_pert>^2/( E(i) - <det_pert|H|det_pert> )
+  .br
 
-`remove_small_contributions <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/selection.irp.f#L84>`_
+
+`pt2_max <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/ezfio_interface.irp.f#L28>`_
+  The selection process stops when the largest PT2 (for all the state) is lower
+  than pt2_max in absolute value
+
+
+`pt2_moller_plesset <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/Moller_plesset.irp.f#L1>`_
+  compute the standard Moller-Plesset perturbative first order coefficient and second order energetic contribution
+  .br
+  for the various n_st states.
+  .br
+  c_pert(i) = <psi(i)|H|det_pert>/(difference of orbital energies)
+  .br
+  e_2_pert(i) = <psi(i)|H|det_pert>^2/(difference of orbital energies)
+  .br
+
+
+`remove_small_contributions <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/selection.irp.f#L87>`_
   Remove determinants with small contributions. N_states is assumed to be
   provided.
 
-`selection_criterion <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/selection.irp.f#L71>`_
-  Threshold to select determinants. Set by selection routines.
 
-`selection_criterion_factor <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/selection.irp.f#L73>`_
+`repeat_all_e_corr <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/pert_sc2.irp.f#L156>`_
-  Threshold to select determinants. Set by selection routines.
+  Undocumented
 
-`selection_criterion_min <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/selection.irp.f#L72>`_
+
+`selection_criterion <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/selection.irp.f#L74>`_
   Threshold to select determinants. Set by selection routines.
 
 
+`selection_criterion_factor <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/selection.irp.f#L76>`_
+  Threshold to select determinants. Set by selection routines.
+
+
+`selection_criterion_min <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/selection.irp.f#L75>`_
+  Threshold to select determinants. Set by selection routines.
+
+
+`var_pt2_ratio <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/ezfio_interface.irp.f#L51>`_
+  The selection process stops when the energy ratio variational/(variational+PT2)
+  is equal to var_pt2_ratio
 
 Needed Modules
 ==============
 
 .. Do not edit this section. It was auto-generated from the
-.. NEEDED_MODULES file.
+.. by the `update_README.py` script.
 
-* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
+.. image:: tree_dependency.png
-* `BiInts <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts>`_
+
-* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
+* `Properties <http://github.com/LCPQ/quantum_package/tree/master/src/Properties>`_
-* `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
-* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
-* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
 * `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
-* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
-* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
-* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
-* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
-* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
 

src/Properties/README.rst

@@ -2,3 +2,153 @@
 Properties Module
 =================
 
+Documentation
+=============
+
+.. Do not edit this section. It was auto-generated from the
+.. by the `update_README.py` script.
+
+`ao_integrated_delta_rho_all_points <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/delta_rho.irp.f#L61>`_
+  array of the overlap in x,y between the AO function and integrated between [z,z+dz] in the z axis
+  for all the z points that are given (N_z_pts)
+
+
+`ao_integrated_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/delta_rho.irp.f#L130>`_
+  array of the overlap in x,y between the AO function and integrated between [z,z+dz] in the z axis
+  for one specific z point
+
+
+`average_position <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/properties.irp.f#L1>`_
+  average_position(1) = <psi_det|X|psi_det>
+  average_position(2) = <psi_det|Y|psi_det>
+  average_position(3) = <psi_det|Z|psi_det>
+
+
+`average_spread <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/properties.irp.f#L27>`_
+  average_spread(1) = <psi_det|X^2|psi_det>
+  average_spread(2) = <psi_det|Y^2|psi_det>
+  average_spread(3) = <psi_det|Z^2|psi_det>
+
+
+`delta_z <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/delta_rho.irp.f#L4>`_
+  Undocumented
+
+
+`diag_o1_mat_elem <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/slater_rules_mono_electronic.irp.f#L91>`_
+  Computes <i|O1|i>
+
+
+`diag_o1_mat_elem_alpha_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/slater_rules_mono_electronic.irp.f#L210>`_
+  Computes <i|O1(alpha) -O1(beta)|i>
+
+
+`filter_connected_mono <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/slater_rules_mono_electronic.irp.f#L240>`_
+  Filters out the determinants that are not connected through PURE
+  .br
+  MONO EXCITATIONS OPERATORS (a^{\dagger}j a_i)
+  .br
+  returns the array idx which contains the index of the
+  .br
+  determinants in the array key1 that interact
+  .br
+  via some PURE MONO EXCITATIONS OPERATORS
+  .br
+  idx(0) is the number of determinants that interact with key1
+
+
+`get_average <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/average.irp.f#L1>`_
+  computes the average value of a pure MONO ELECTRONIC OPERATOR
+  whom integrals on the MO basis are stored in "array"
+  and with the density is stored in  "density"
+
+
+`i_o1_j <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/slater_rules_mono_electronic.irp.f#L1>`_
+  Returns <i|O1|j> where i and j are determinants
+  and O1 is a ONE BODY OPERATOR
+  array  is the array of the mono electronic operator
+  on the MO basis
+
+
+`i_o1_j_alpha_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/slater_rules_mono_electronic.irp.f#L158>`_
+  Returns <i|O1(alpha) - O1(beta)|j> where i and j are determinants
+  and O1 is a ONE BODY OPERATOR
+  array  is the array of the mono electronic operator
+  on the MO basis
+
+
+`i_o1_psi <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/slater_rules_mono_electronic.irp.f#L52>`_
+  <key|O1|psi> for the various Nstates
+  and O1 is a ONE BODY OPERATOR
+  array  is the array of the mono electronic operator
+  on the MO basis
+
+
+`i_o1_psi_alpha_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/slater_rules_mono_electronic.irp.f#L119>`_
+  <key|O1(alpha) - O1(beta)|psi> for the various Nstates
+  and O1 is a ONE BODY OPERATOR
+  array  is the array of the mono electronic operator
+  on the MO basis
+
+
+`i_unit_integrated_delta_rho <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/delta_rho.irp.f#L118>`_
+  fortran unit for the writing of the integrated delta_rho
+
+
+`integrated_delta_rho_all_points <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/delta_rho.irp.f#L15>`_
+  .br
+  integrated_rho(alpha,z) - integrated_rho(beta,z) for all the z points
+  chosen
+  .br
+
+
+`integrated_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/delta_rho.irp.f#L212>`_
+  .br
+  integral (x,y) and (z,z+delta_z) of rho(alpha) - rho(beta)
+  on the MO basis
+  .br
+
+
+`mo_integrated_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/delta_rho.irp.f#L184>`_
+  .br
+  array of the integrals needed of integrated_rho(alpha,z) - integrated_rho(beta,z) for z = z_one_point
+  on the MO basis
+  .br
+
+
+`n_z_pts <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/delta_rho.irp.f#L1>`_
+  Undocumented
+
+
+`test_average_value <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/routines_test.irp.f#L3>`_
+  Undocumented
+
+
+`test_average_value_alpha_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/routines_test.irp.f#L25>`_
+  Undocumented
+
+
+`test_dm <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/routines_test.irp.f#L56>`_
+  Undocumented
+
+
+`z_max <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/delta_rho.irp.f#L3>`_
+  Undocumented
+
+
+`z_min <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/delta_rho.irp.f#L2>`_
+  Undocumented
+
+
+`z_one_point <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/ezfio_interface.irp.f#L6>`_
+  z point on which the integrated delta rho is calculated
+
+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>`_
+

src/Pseudo/README.rst

@@ -6,7 +6,7 @@ Needed Modules
 ==============
 
 .. Do not edit this section. It was auto-generated from the
-.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
+.. by the `update_README.py` script.
 
 .. image:: tree_dependency.png
 
@@ -16,7 +16,7 @@ Documentation
 =============
 
 .. Do not edit this section. It was auto-generated from the
-.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
+.. by the `update_README.py` script.
 
 `do_pseudo <http://github.com/LCPQ/quantum_package/tree/master/src/Pseudo/ezfio_interface.irp.f#L248>`_
   Using pseudo potential integral of not

src/Selectors_full/README.rst

@@ -6,7 +6,7 @@ Documentation
 =============
 
 .. Do not edit this section. It was auto-generated from the
-.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
+.. by the `update_README.py` script.
 
 `coef_hf_selector <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L28>`_
   energy of correlation per determinant respect to the Hartree Fock determinant
@@ -19,6 +19,7 @@ Documentation
   .br
   coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
 
+
 `delta_e_per_selector <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L33>`_
   energy of correlation per determinant respect to the Hartree Fock determinant
   .br
@@ -30,6 +31,7 @@ Documentation
   .br
   coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
 
+
 `double_index_selectors <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L4>`_
   degree of excitation respect to Hartree Fock for the wave function
   .br
@@ -39,6 +41,7 @@ Documentation
   .br
   n_double_selectors = number of double excitations in the selectors determinants
 
+
 `e_corr_double_only <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L34>`_
   energy of correlation per determinant respect to the Hartree Fock determinant
   .br
@@ -50,6 +53,7 @@ Documentation
   .br
   coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
 
+
 `e_corr_per_selectors <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L31>`_
   energy of correlation per determinant respect to the Hartree Fock determinant
   .br
@@ -61,6 +65,7 @@ Documentation
   .br
   coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
 
+
 `e_corr_second_order <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L35>`_
   energy of correlation per determinant respect to the Hartree Fock determinant
   .br
@@ -72,6 +77,7 @@ Documentation
   .br
   coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
 
+
 `exc_degree_per_selectors <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L3>`_
   degree of excitation respect to Hartree Fock for the wave function
   .br
@@ -81,6 +87,7 @@ Documentation
   .br
   n_double_selectors = number of double excitations in the selectors determinants
 
+
 `i_h_hf_per_selectors <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L32>`_
   energy of correlation per determinant respect to the Hartree Fock determinant
   .br
@@ -92,6 +99,7 @@ Documentation
   .br
   coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
 
+
 `inv_selectors_coef_hf <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L29>`_
   energy of correlation per determinant respect to the Hartree Fock determinant
   .br
@@ -103,6 +111,7 @@ Documentation
   .br
   coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
 
+
 `inv_selectors_coef_hf_squared <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L30>`_
   energy of correlation per determinant respect to the Hartree Fock determinant
   .br
@@ -114,6 +123,12 @@ Documentation
   .br
   coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
 
+
+`n_det_selectors <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L8>`_
+  For Single reference wave functions, the number of selectors is 1 : the
+  Hartree-Fock determinant
+
+
 `n_double_selectors <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L5>`_
   degree of excitation respect to Hartree Fock for the wave function
   .br
@@ -123,49 +138,50 @@ Documentation
   .br
   n_double_selectors = number of double excitations in the selectors determinants
 
-`n_det_selectors <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L8>`_
-  For Single reference wave functions, the number of selectors is 1 : the
-  Hartree-Fock determinant
 
 `psi_selectors <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L30>`_
   Determinants on which we apply <i|H|psi> for perturbation.
 
+
 `psi_selectors_ab <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L64>`_
   Determinants on which we apply <i|H|j>.
   They are sorted by the 3 highest electrons in the alpha part,
   then by the 3 highest electrons in the beta part to accelerate
   the research of connected determinants.
 
+
 `psi_selectors_coef <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L31>`_
   Determinants on which we apply <i|H|psi> for perturbation.
 
+
 `psi_selectors_coef_ab <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L65>`_
   Determinants on which we apply <i|H|j>.
   They are sorted by the 3 highest electrons in the alpha part,
   then by the 3 highest electrons in the beta part to accelerate
   the research of connected determinants.
 
+
 `psi_selectors_diag_h_mat <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L51>`_
   Diagonal elements of the H matrix for each selectors
 
+
 `psi_selectors_next_ab <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L66>`_
   Determinants on which we apply <i|H|j>.
   They are sorted by the 3 highest electrons in the alpha part,
   then by the 3 highest electrons in the beta part to accelerate
   the research of connected determinants.
 
+
 `psi_selectors_size <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L3>`_
   Undocumented
 
-
-
 Needed Modules
 ==============
 
 .. Do not edit this section. It was auto-generated from the
-.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
+.. by the `update_README.py` script.
 
-.. image:: tree_dependancy.png
+.. image:: tree_dependency.png
 
 * `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
 * `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_

src/Selectors_no_sorted/README.rst

@@ -2,3 +2,186 @@
 Selectors_no_sorted Module
 ==========================
 
+Documentation
+=============
+
+.. Do not edit this section. It was auto-generated from the
+.. by the `update_README.py` script.
+
+`coef_hf_selector <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_no_sorted/e_corr_selectors.irp.f#L28>`_
+  energy of correlation per determinant respect to the Hartree Fock determinant
+  .br
+  for the all the double excitations in the selectors determinants
+  .br
+  E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> is a double excitation
+  .br
+  E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
+  .br
+  coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
+
+
+`delta_e_per_selector <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_no_sorted/e_corr_selectors.irp.f#L33>`_
+  energy of correlation per determinant respect to the Hartree Fock determinant
+  .br
+  for the all the double excitations in the selectors determinants
+  .br
+  E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> is a double excitation
+  .br
+  E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
+  .br
+  coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
+
+
+`double_index_selectors <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_no_sorted/e_corr_selectors.irp.f#L4>`_
+  degree of excitation respect to Hartree Fock for the wave function
+  .br
+  for the all the selectors determinants
+  .br
+  double_index_selectors = list of the index of the double excitations
+  .br
+  n_double_selectors = number of double excitations in the selectors determinants
+
+
+`e_corr_double_only <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_no_sorted/e_corr_selectors.irp.f#L34>`_
+  energy of correlation per determinant respect to the Hartree Fock determinant
+  .br
+  for the all the double excitations in the selectors determinants
+  .br
+  E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> is a double excitation
+  .br
+  E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
+  .br
+  coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
+
+
+`e_corr_per_selectors <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_no_sorted/e_corr_selectors.irp.f#L31>`_
+  energy of correlation per determinant respect to the Hartree Fock determinant
+  .br
+  for the all the double excitations in the selectors determinants
+  .br
+  E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> is a double excitation
+  .br
+  E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
+  .br
+  coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
+
+
+`e_corr_second_order <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_no_sorted/e_corr_selectors.irp.f#L35>`_
+  energy of correlation per determinant respect to the Hartree Fock determinant
+  .br
+  for the all the double excitations in the selectors determinants
+  .br
+  E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> is a double excitation
+  .br
+  E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
+  .br
+  coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
+
+
+`exc_degree_per_selectors <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_no_sorted/e_corr_selectors.irp.f#L3>`_
+  degree of excitation respect to Hartree Fock for the wave function
+  .br
+  for the all the selectors determinants
+  .br
+  double_index_selectors = list of the index of the double excitations
+  .br
+  n_double_selectors = number of double excitations in the selectors determinants
+
+
+`i_h_hf_per_selectors <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_no_sorted/e_corr_selectors.irp.f#L32>`_
+  energy of correlation per determinant respect to the Hartree Fock determinant
+  .br
+  for the all the double excitations in the selectors determinants
+  .br
+  E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> is a double excitation
+  .br
+  E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
+  .br
+  coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
+
+
+`inv_selectors_coef_hf <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_no_sorted/e_corr_selectors.irp.f#L29>`_
+  energy of correlation per determinant respect to the Hartree Fock determinant
+  .br
+  for the all the double excitations in the selectors determinants
+  .br
+  E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> is a double excitation
+  .br
+  E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
+  .br
+  coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
+
+
+`inv_selectors_coef_hf_squared <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_no_sorted/e_corr_selectors.irp.f#L30>`_
+  energy of correlation per determinant respect to the Hartree Fock determinant
+  .br
+  for the all the double excitations in the selectors determinants
+  .br
+  E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> is a double excitation
+  .br
+  E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
+  .br
+  coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
+
+
+`n_det_selectors <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_no_sorted/selectors.irp.f#L10>`_
+  For Single reference wave functions, the number of selectors is 1 : the
+  Hartree-Fock determinant
+
+
+`n_double_selectors <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_no_sorted/e_corr_selectors.irp.f#L5>`_
+  degree of excitation respect to Hartree Fock for the wave function
+  .br
+  for the all the selectors determinants
+  .br
+  double_index_selectors = list of the index of the double excitations
+  .br
+  n_double_selectors = number of double excitations in the selectors determinants
+
+
+`psi_selectors <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_no_sorted/selectors.irp.f#L26>`_
+  Determinants on which we apply <i|H|psi> for perturbation.
+
+
+`psi_selectors_ab <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_no_sorted/selectors.irp.f#L60>`_
+  Determinants on which we apply <i|H|j>.
+  They are sorted by the 3 highest electrons in the alpha part,
+  then by the 3 highest electrons in the beta part to accelerate
+  the research of connected determinants.
+
+
+`psi_selectors_coef <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_no_sorted/selectors.irp.f#L27>`_
+  Determinants on which we apply <i|H|psi> for perturbation.
+
+
+`psi_selectors_coef_ab <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_no_sorted/selectors.irp.f#L61>`_
+  Determinants on which we apply <i|H|j>.
+  They are sorted by the 3 highest electrons in the alpha part,
+  then by the 3 highest electrons in the beta part to accelerate
+  the research of connected determinants.
+
+
+`psi_selectors_diag_h_mat <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_no_sorted/selectors.irp.f#L47>`_
+  Diagonal elements of the H matrix for each selectors
+
+
+`psi_selectors_next_ab <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_no_sorted/selectors.irp.f#L62>`_
+  Determinants on which we apply <i|H|j>.
+  They are sorted by the 3 highest electrons in the alpha part,
+  then by the 3 highest electrons in the beta part to accelerate
+  the research of connected determinants.
+
+
+`psi_selectors_size <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_no_sorted/selectors.irp.f#L5>`_
+  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>`_
+

src/SingleRefMethod/README.rst

@@ -9,33 +9,37 @@ Documentation
 =============
 
 .. Do not edit this section. It was auto-generated from the
-.. NEEDED_MODULES file.
+.. by the `update_README.py` script.
 
 `n_det_generators <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod/generators.irp.f#L3>`_
   For Single reference wave functions, the number of generators is 1 : the
   Hartree-Fock determinant
 
-`psi_generators <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod/generators.irp.f#L12>`_
+
+`psi_coef_generators <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod/generators.irp.f#L13>`_
   For Single reference wave functions, the generator is the
   Hartree-Fock determinant
 
-`select_max <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod/generators.irp.f#L43>`_
+
+`psi_det_generators <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod/generators.irp.f#L12>`_
+  For Single reference wave functions, the generator is the
+  Hartree-Fock determinant
+
+
+`select_max <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod/generators.irp.f#L41>`_
   Memo to skip useless selectors
 
 
+`size_select_max <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod/generators.irp.f#L49>`_
+  Size of select_max
 
 Needed Modules
 ==============
 
 .. Do not edit this section. It was auto-generated from the
-.. NEEDED_MODULES file.
+.. by the `update_README.py` script.
+
+.. image:: tree_dependency.png
 
-* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
 * `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
-* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
-* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
-* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
-* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
-* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
-* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
 

src/Utils/README.rst

@@ -8,17 +8,418 @@ Documentation
 =============
 
 .. Do not edit this section. It was auto-generated from the
-.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
+.. by the `update_README.py` script.
+
+`a_coef <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/need.irp.f#L252>`_
+  Undocumented
+
+
+`abort_all <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/abort.irp.f#L1>`_
+  If True, all the calculation is aborted
+
+
+`abort_here <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/abort.irp.f#L11>`_
+  If True, all the calculation is aborted
+
+
+`add_poly <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L306>`_
+  Add two polynomials
+  D(t) =! D(t) +( B(t)+C(t))
+
+
+`add_poly_multiply <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L334>`_
+  Add a polynomial multiplied by a constant
+  D(t) =! D(t) +( cst * B(t))
+
+
+`align_double <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L48>`_
+  Compute 1st dimension such that it is aligned for vectorization.
+
 
 `apply_rotation <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L168>`_
   Apply the rotation found by find_rotation
 
+
+`approx_dble <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L380>`_
+  Undocumented
+
+
+`b_coef <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/need.irp.f#L257>`_
+  Undocumented
+
+
+`binom <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L31>`_
+  Binomial coefficients
+
+
+`binom_func <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L1>`_
+  .. math                       ::
+  .br
+  \frac{i!}{j!(i-j)!}
+  .br
+
+
+`binom_transp <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L32>`_
+  Binomial coefficients
+
+
+`catch_signal <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/abort.irp.f#L30>`_
+  What to do on Ctrl-C. If two Ctrl-C are pressed within 1 sec, the calculation if aborted.
+
+
+`dble_fact <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L138>`_
+  Undocumented
+
+
+`dble_fact_even <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L155>`_
+  n!!
+
+
+`dble_fact_odd <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L176>`_
+  n!!
+
+
+`dble_logfact <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L210>`_
+  n!!
+
+
+`ddfact2 <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/need.irp.f#L243>`_
+  Undocumented
+
+
+`dset_order <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/sort.irp.f_template_216#L27>`_
+  array A has already been sorted, and iorder has contains the new order of
+  elements of A. This subroutine changes the order of x to match the new order of A.
+
+
+`dset_order_big <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/sort.irp.f_template_283#L94>`_
+  array A has already been sorted, and iorder has contains the new order of
+  elements of A. This subroutine changes the order of x to match the new order of A.
+  This is a version for very large arrays where the indices need
+  to be in integer*8 format
+
+
+`dsort <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/sort.irp.f_template_184#L339>`_
+  Sort array x(isize).
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+
+
+`erf0 <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/need.irp.f#L105>`_
+  Undocumented
+
+
+`f_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L408>`_
+  function that calculates the following integral
+  \int_{\-infty}^{+\infty} x^n \exp(-p x^2) dx
+
+
+`fact <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L63>`_
+  n!
+
+
+`fact_inv <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L125>`_
+  1/n!
+
+
 `find_rotation <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L149>`_
   Find A.C = B
 
+
+`gammln <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/need.irp.f#L271>`_
+  Undocumented
+
+
+`gammp <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/need.irp.f#L133>`_
+  Undocumented
+
+
+`gaussian_product <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L184>`_
+  Gaussian product in 1D.
+  e^{-a (x-x_A)^2} e^{-b (x-x_B)^2} = K_{ab}^x e^{-p (x-x_P)^2}
+
+
+`gaussian_product_x <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L226>`_
+  Gaussian product in 1D.
+  e^{-a (x-x_A)^2} e^{-b (x-x_B)^2} = K_{ab}^x e^{-p (x-x_P)^2}
+
+
+`gcf <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/need.irp.f#L211>`_
+  Undocumented
+
+
 `get_pseudo_inverse <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L95>`_
   Find C = A^-1
 
+
+`give_explicit_poly_and_gaussian <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L46>`_
+  Transforms the product of
+  (x-x_A)^a(1) (x-x_B)^b(1) (x-x_A)^a(2) (y-y_B)^b(2) (z-z_A)^a(3) (z-z_B)^b(3) exp(-(r-A)^2 alpha) exp(-(r-B)^2 beta)
+  into
+  fact_k * [ sum (l_x = 0,i_order(1)) P_new(l_x,1) * (x-P_center(1))^l_x ] exp (- p (x-P_center(1))^2 )
+  * [ sum (l_y = 0,i_order(2)) P_new(l_y,2) * (y-P_center(2))^l_y ] exp (- p (y-P_center(2))^2 )
+  * [ sum (l_z = 0,i_order(3)) P_new(l_z,3) * (z-P_center(3))^l_z ] exp (- p (z-P_center(3))^2 )
+
+
+`give_explicit_poly_and_gaussian_double <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L122>`_
+  Transforms the product of
+  (x-x_A)^a(1) (x-x_B)^b(1) (x-x_A)^a(2) (y-y_B)^b(2) (z-z_A)^a(3) (z-z_B)^b(3)
+  exp(-(r-A)^2 alpha) exp(-(r-B)^2 beta) exp(-(r-Nucl_center)^2 gama
+  .br
+  into
+  fact_k * [ sum (l_x = 0,i_order(1)) P_new(l_x,1) * (x-P_center(1))^l_x ] exp (- p (x-P_center(1))^2 )
+  * [ sum (l_y = 0,i_order(2)) P_new(l_y,2) * (y-P_center(2))^l_y ] exp (- p (y-P_center(2))^2 )
+  * [ sum (l_z = 0,i_order(3)) P_new(l_z,3) * (z-P_center(3))^l_z ] exp (- p (z-P_center(3))^2 )
+
+
+`give_explicit_poly_and_gaussian_x <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L1>`_
+  Transform the product of
+  (x-x_A)^a(1) (x-x_B)^b(1) (x-x_A)^a(2) (y-y_B)^b(2) (z-z_A)^a(3) (z-z_B)^b(3) exp(-(r-A)^2 alpha) exp(-(r-B)^2 beta)
+  into
+  fact_k  (x-x_P)^iorder(1)  (y-y_P)^iorder(2)  (z-z_P)^iorder(3) exp(-p(r-P)^2)
+
+
+`gser <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/need.irp.f#L167>`_
+  Undocumented
+
+
+`heap_dsort <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/sort.irp.f_template_184#L210>`_
+  Sort array x(isize) using the heap sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+
+
+`heap_dsort_big <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/sort.irp.f_template_184#L273>`_
+  Sort array x(isize) using the heap sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+  This is a version for very large arrays where the indices need
+  to be in integer*8 format
+
+
+`heap_i2sort <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/sort.irp.f_template_184#L744>`_
+  Sort array x(isize) using the heap sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+
+
+`heap_i2sort_big <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/sort.irp.f_template_184#L807>`_
+  Sort array x(isize) using the heap sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+  This is a version for very large arrays where the indices need
+  to be in integer*8 format
+
+
+`heap_i8sort <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/sort.irp.f_template_184#L566>`_
+  Sort array x(isize) using the heap sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+
+
+`heap_i8sort_big <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/sort.irp.f_template_184#L629>`_
+  Sort array x(isize) using the heap sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+  This is a version for very large arrays where the indices need
+  to be in integer*8 format
+
+
+`heap_isort <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/sort.irp.f_template_184#L388>`_
+  Sort array x(isize) using the heap sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+
+
+`heap_isort_big <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/sort.irp.f_template_184#L451>`_
+  Sort array x(isize) using the heap sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+  This is a version for very large arrays where the indices need
+  to be in integer*8 format
+
+
+`heap_sort <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/sort.irp.f_template_184#L32>`_
+  Sort array x(isize) using the heap sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+
+
+`heap_sort_big <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/sort.irp.f_template_184#L95>`_
+  Sort array x(isize) using the heap sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+  This is a version for very large arrays where the indices need
+  to be in integer*8 format
+
+
+`hermite <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L540>`_
+  Hermite polynomial
+
+
+`i2radix_sort <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/sort.irp.f_template_450#L323>`_
+  Sort integer array x(isize) using the radix sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+  iradix should be -1 in input.
+
+
+`i2set_order <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/sort.irp.f_template_216#L102>`_
+  array A has already been sorted, and iorder has contains the new order of
+  elements of A. This subroutine changes the order of x to match the new order of A.
+
+
+`i2set_order_big <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/sort.irp.f_template_283#L271>`_
+  array A has already been sorted, and iorder has contains the new order of
+  elements of A. This subroutine changes the order of x to match the new order of A.
+  This is a version for very large arrays where the indices need
+  to be in integer*8 format
+
+
+`i2sort <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/sort.irp.f_template_184#L873>`_
+  Sort array x(isize).
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+
+
+`i8radix_sort <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/sort.irp.f_template_450#L163>`_
+  Sort integer array x(isize) using the radix sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+  iradix should be -1 in input.
+
+
+`i8radix_sort_big <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/sort.irp.f_template_450#L643>`_
+  Sort integer array x(isize) using the radix sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+  iradix should be -1 in input.
+
+
+`i8set_order <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/sort.irp.f_template_216#L77>`_
+  array A has already been sorted, and iorder has contains the new order of
+  elements of A. This subroutine changes the order of x to match the new order of A.
+
+
+`i8set_order_big <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/sort.irp.f_template_283#L212>`_
+  array A has already been sorted, and iorder has contains the new order of
+  elements of A. This subroutine changes the order of x to match the new order of A.
+  This is a version for very large arrays where the indices need
+  to be in integer*8 format
+
+
+`i8sort <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/sort.irp.f_template_184#L695>`_
+  Sort array x(isize).
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+
+
+`insertion_dsort <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/sort.irp.f_template_184#L180>`_
+  Sort array x(isize) using the insertion sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+
+
+`insertion_dsort_big <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/sort.irp.f_template_283#L61>`_
+  Sort array x(isize) using the insertion sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+  This is a version for very large arrays where the indices need
+  to be in integer*8 format
+
+
+`insertion_i2sort <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/sort.irp.f_template_184#L714>`_
+  Sort array x(isize) using the insertion sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+
+
+`insertion_i2sort_big <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/sort.irp.f_template_283#L238>`_
+  Sort array x(isize) using the insertion sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+  This is a version for very large arrays where the indices need
+  to be in integer*8 format
+
+
+`insertion_i8sort <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/sort.irp.f_template_184#L536>`_
+  Sort array x(isize) using the insertion sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+
+
+`insertion_i8sort_big <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/sort.irp.f_template_283#L179>`_
+  Sort array x(isize) using the insertion sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+  This is a version for very large arrays where the indices need
+  to be in integer*8 format
+
+
+`insertion_isort <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/sort.irp.f_template_184#L358>`_
+  Sort array x(isize) using the insertion sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+
+
+`insertion_isort_big <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/sort.irp.f_template_283#L120>`_
+  Sort array x(isize) using the insertion sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+  This is a version for very large arrays where the indices need
+  to be in integer*8 format
+
+
+`insertion_sort <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/sort.irp.f_template_184#L2>`_
+  Sort array x(isize) using the insertion sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+
+
+`insertion_sort_big <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/sort.irp.f_template_283#L2>`_
+  Sort array x(isize) using the insertion sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+  This is a version for very large arrays where the indices need
+  to be in integer*8 format
+
+
+`inv_int <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L257>`_
+  1/i
+
+
+`iradix_sort <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/sort.irp.f_template_450#L3>`_
+  Sort integer array x(isize) using the radix sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+  iradix should be -1 in input.
+
+
+`iradix_sort_big <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/sort.irp.f_template_450#L483>`_
+  Sort integer array x(isize) using the radix sort algorithm.
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+  iradix should be -1 in input.
+
+
+`iset_order <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/sort.irp.f_template_216#L52>`_
+  array A has already been sorted, and iorder has contains the new order of
+  elements of A. This subroutine changes the order of x to match the new order of A.
+
+
+`iset_order_big <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/sort.irp.f_template_283#L153>`_
+  array A has already been sorted, and iorder has contains the new order of
+  elements of A. This subroutine changes the order of x to match the new order of A.
+  This is a version for very large arrays where the indices need
+  to be in integer*8 format
+
+
+`isort <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/sort.irp.f_template_184#L517>`_
+  Sort array x(isize).
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+
+
 `lapack_diag <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L247>`_
   Diagonalize matrix H
   .br
@@ -29,6 +430,7 @@ Documentation
   eigvectors(i,j) = <i|psi_j> where i is the basis function and psi_j is the j th eigenvector
   .br
 
+
 `lapack_diag_s2 <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L310>`_
   Diagonalize matrix H
   .br
@@ -39,6 +441,7 @@ Documentation
   eigvectors(i,j) = <i|psi_j> where i is the basis function and psi_j is the j th eigenvector
   .br
 
+
 `lapack_diagd <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L180>`_
   Diagonalize matrix H
   .br
@@ -49,6 +452,7 @@ Documentation
   eigvectors(i,j) = <i|psi_j> where i is the basis function and psi_j is the j th eigenvector
   .br
 
+
 `lapack_partial_diag <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L376>`_
   Diagonalize matrix H
   .br
@@ -59,6 +463,25 @@ Documentation
   eigvectors(i,j) = <i|psi_j> where i is the basis function and psi_j is the j th eigenvector
   .br
 
+
+`logfact <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L93>`_
+  n!
+
+
+`multiply_poly <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L264>`_
+  Multiply two polynomials
+  D(t) =! D(t) +( B(t)*C(t))
+
+
+`normalize <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L356>`_
+  Normalizes vector u
+  u is expected to be aligned in memory.
+
+
+`nproc <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L283>`_
+  Number of current OpenMP threads
+
+
 `ortho_lowdin <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L1>`_
   Compute C_new=C_old.S^-1/2 canonical orthogonalization.
   .br
@@ -76,132 +499,18 @@ Documentation
   m : Coefficients matrix is MxN, ( array is (LDC,N) )
   .br
 
-`set_zero_extra_diag <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L433>`_
-  Undocumented
-
-`abort_all <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/abort.irp.f#L1>`_
-  If True, all the calculation is aborted
-
-`abort_here <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/abort.irp.f#L11>`_
-  If True, all the calculation is aborted
-
-`catch_signal <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/abort.irp.f#L30>`_
-  What to do on Ctrl-C. If two Ctrl-C are pressed within 1 sec, the calculation if aborted.
-
-`trap_signals <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/abort.irp.f#L19>`_
-  What to do when a signal is caught. Here, trap Ctrl-C and call the control_C subroutine.
-
-`add_poly <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L306>`_
-  Add two polynomials
-  D(t) =! D(t) +( B(t)+C(t))
-
-`add_poly_multiply <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L334>`_
-  Add a polynomial multiplied by a constant
-  D(t) =! D(t) +( cst * B(t))
-
-`f_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L408>`_
-  function that calculates the following integral
-  \int_{\-infty}^{+\infty} x^n \exp(-p x^2) dx
-
-`gaussian_product <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L184>`_
-  Gaussian product in 1D.
-  e^{-a (x-x_A)^2} e^{-b (x-x_B)^2} = K_{ab}^x e^{-p (x-x_P)^2}
-
-`gaussian_product_x <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L226>`_
-  Gaussian product in 1D.
-  e^{-a (x-x_A)^2} e^{-b (x-x_B)^2} = K_{ab}^x e^{-p (x-x_P)^2}
-
-`give_explicit_poly_and_gaussian <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L46>`_
-  Transforms the product of
-  (x-x_A)^a(1) (x-x_B)^b(1) (x-x_A)^a(2) (y-y_B)^b(2) (z-z_A)^a(3) (z-z_B)^b(3) exp(-(r-A)^2 alpha) exp(-(r-B)^2 beta)
-  into
-  fact_k * [ sum (l_x = 0,i_order(1)) P_new(l_x,1) * (x-P_center(1))^l_x ] exp (- p (x-P_center(1))^2 )
-  * [ sum (l_y = 0,i_order(2)) P_new(l_y,2) * (y-P_center(2))^l_y ] exp (- p (y-P_center(2))^2 )
-  * [ sum (l_z = 0,i_order(3)) P_new(l_z,3) * (z-P_center(3))^l_z ] exp (- p (z-P_center(3))^2 )
-
-`give_explicit_poly_and_gaussian_double <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L122>`_
-  Transforms the product of
-  (x-x_A)^a(1) (x-x_B)^b(1) (x-x_A)^a(2) (y-y_B)^b(2) (z-z_A)^a(3) (z-z_B)^b(3)
-  exp(-(r-A)^2 alpha) exp(-(r-B)^2 beta) exp(-(r-Nucl_center)^2 gama
-  .br
-  into
-  fact_k * [ sum (l_x = 0,i_order(1)) P_new(l_x,1) * (x-P_center(1))^l_x ] exp (- p (x-P_center(1))^2 )
-  * [ sum (l_y = 0,i_order(2)) P_new(l_y,2) * (y-P_center(2))^l_y ] exp (- p (y-P_center(2))^2 )
-  * [ sum (l_z = 0,i_order(3)) P_new(l_z,3) * (z-P_center(3))^l_z ] exp (- p (z-P_center(3))^2 )
-
-`give_explicit_poly_and_gaussian_x <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L1>`_
-  Transform the product of
-  (x-x_A)^a(1) (x-x_B)^b(1) (x-x_A)^a(2) (y-y_B)^b(2) (z-z_A)^a(3) (z-z_B)^b(3) exp(-(r-A)^2 alpha) exp(-(r-B)^2 beta)
-  into
-  fact_k  (x-x_P)^iorder(1)  (y-y_P)^iorder(2)  (z-z_P)^iorder(3) exp(-p(r-P)^2)
-
-`hermite <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L540>`_
-  Hermite polynomial
-
-`multiply_poly <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L264>`_
-  Multiply two polynomials
-  D(t) =! D(t) +( B(t)*C(t))
-
-`recentered_poly2 <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L363>`_
-  Recenter two polynomials
-
-`rint <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L436>`_
-  .. math::
-  .br
-  \int_0^1 dx \exp(-p x^2) x^n
-  .br
-
-`rint1 <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L596>`_
-  Standard version of rint
-
-`rint_large_n <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L565>`_
-  Version of rint for large values of n
-
-`rint_sum <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L484>`_
-  Needed for the calculation of two-electron integrals.
-
-`a_coef <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/need.irp.f#L252>`_
-  Undocumented
-
-`b_coef <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/need.irp.f#L257>`_
-  Undocumented
-
-`ddfact2 <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/need.irp.f#L243>`_
-  Undocumented
-
-`erf0 <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/need.irp.f#L105>`_
-  Undocumented
-
-`gammln <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/need.irp.f#L271>`_
-  Undocumented
-
-`gammp <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/need.irp.f#L133>`_
-  Undocumented
-
-`gcf <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/need.irp.f#L211>`_
-  Undocumented
-
-`gser <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/need.irp.f#L167>`_
-  Undocumented
-
-`rinteg <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/need.irp.f#L47>`_
-  Undocumented
-
-`rintgauss <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/need.irp.f#L31>`_
-  Undocumented
-
-`sabpartial <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/need.irp.f#L2>`_
-  Undocumented
 
 `overlap_a_b_c <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/one_e_integration.irp.f#L35>`_
   Undocumented
 
+
 `overlap_gaussian_x <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/one_e_integration.irp.f#L1>`_
   .. math::
   .br
   \sum_{-infty}^{+infty} (x-A_x)^ax (x-B_x)^bx exp(-alpha(x-A_x)^2) exp(-beta(x-B_X)^2) dx
   .br
 
+
 `overlap_gaussian_xyz <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/one_e_integration.irp.f#L113>`_
   .. math::
   .br
@@ -209,97 +518,120 @@ Documentation
   S = S_x S_y S_z
   .br
 
+
 `overlap_x_abs <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/one_e_integration.irp.f#L175>`_
   .. math                      ::
   .br
   \int_{-infty}^{+infty} (x-A_center)^(power_A) * (x-B_center)^power_B * exp(-alpha(x-A_center)^2) * exp(-beta(x-B_center)^2) dx
   .br
 
+
 `progress_active <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/progress.irp.f#L29>`_
   Current status for displaying progress bars. Global variable.
 
+
 `progress_bar <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/progress.irp.f#L27>`_
   Current status for displaying progress bars. Global variable.
 
+
 `progress_timeout <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/progress.irp.f#L28>`_
   Current status for displaying progress bars. Global variable.
 
+
 `progress_title <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/progress.irp.f#L31>`_
   Current status for displaying progress bars. Global variable.
 
+
 `progress_value <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/progress.irp.f#L30>`_
   Current status for displaying progress bars. Global variable.
 
+
+`recentered_poly2 <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L363>`_
+  Recenter two polynomials
+
+
+`rint <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L436>`_
+  .. math::
+  .br
+  \int_0^1 dx \exp(-p x^2) x^n
+  .br
+
+
+`rint1 <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L596>`_
+  Standard version of rint
+
+
+`rint_large_n <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L565>`_
+  Version of rint for large values of n
+
+
+`rint_sum <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L484>`_
+  Needed for the calculation of two-electron integrals.
+
+
+`rinteg <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/need.irp.f#L47>`_
+  Undocumented
+
+
+`rintgauss <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/need.irp.f#L31>`_
+  Undocumented
+
+
 `run_progress <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/progress.irp.f#L45>`_
   Display a progress bar with documentation of what is happening
 
+
+`sabpartial <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/need.irp.f#L2>`_
+  Undocumented
+
+
+`set_order <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/sort.irp.f_template_216#L2>`_
+  array A has already been sorted, and iorder has contains the new order of
+  elements of A. This subroutine changes the order of x to match the new order of A.
+
+
+`set_order_big <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/sort.irp.f_template_283#L35>`_
+  array A has already been sorted, and iorder has contains the new order of
+  elements of A. This subroutine changes the order of x to match the new order of A.
+  This is a version for very large arrays where the indices need
+  to be in integer*8 format
+
+
+`set_zero_extra_diag <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L433>`_
+  Undocumented
+
+
+`sort <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/sort.irp.f_template_184#L161>`_
+  Sort array x(isize).
+  iorder in input should be (1,2,3,...,isize), and in output
+  contains the new order of the elements.
+
+
 `start_progress <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/progress.irp.f#L1>`_
   Starts the progress bar
 
+
 `stop_progress <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/progress.irp.f#L19>`_
   Stop the progress bar
 
-`align_double <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L48>`_
-  Compute 1st dimension such that it is aligned for vectorization.
 
-`approx_dble <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L380>`_
+`trap_signals <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/abort.irp.f#L19>`_
-  Undocumented
+  What to do when a signal is caught. Here, trap Ctrl-C and call the control_C subroutine.
 
-`binom <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L31>`_
-  Binomial coefficients
-
-`binom_func <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L1>`_
-  .. math                       ::
-  .br
-  \frac{i!}{j!(i-j)!}
-  .br
-
-`binom_transp <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L32>`_
-  Binomial coefficients
-
-`dble_fact <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L138>`_
-  Undocumented
-
-`dble_fact_even <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L155>`_
-  n!!
-
-`dble_fact_odd <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L176>`_
-  n!!
-
-`dble_logfact <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L210>`_
-  n!!
-
-`fact <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L63>`_
-  n!
-
-`fact_inv <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L125>`_
-  1/n!
-
-`inv_int <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L257>`_
-  1/i
-
-`logfact <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L93>`_
-  n!
-
-`normalize <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L356>`_
-  Normalizes vector u
-  u is expected to be aligned in memory.
-
-`nproc <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L283>`_
-  Number of current OpenMP threads
 
 `u_dot_u <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L325>`_
   Compute <u|u>
 
+
 `u_dot_v <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L299>`_
   Compute <u|v>
 
+
 `wall_time <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L268>`_
   The equivalent of cpu_time, but for the wall time.
 
+
 `write_git_log <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L243>`_
   Write the last git commit in file iunit.
 
 
-
-