From 2ecacdd18e1e8bc8b43554c7cb6263400ae607f8 Mon Sep 17 00:00:00 2001 From: Thomas Applencourt Date: Thu, 4 Jun 2015 12:15:54 +0200 Subject: [PATCH] Realy fix the readme... Maybe to mush --- scripts/compilation/create_ninja_build.py | 8 +- src/AOs/README.rst | 91 ++- src/Bitmask/README.rst | 106 ++- src/CID/README.rst | 21 +- src/CID_selected/README.rst | 164 +++- src/CISD/README.rst | 21 +- src/CISD_selected/README.rst | 164 +++- src/DensityFit/README.rst | 76 +- src/Determinants/README.rst | 906 +++++++++++++--------- src/Electrons/README.rst | 11 +- src/Ezfio_files/README.rst | 163 +++- src/Generators_CAS/README.rst | 12 +- src/Generators_full/README.rst | 13 +- src/Generators_restart/README.rst | 37 + src/Hartree_Fock/README.rst | 92 ++- src/Integrals_Bielec/README.rst | 212 +++-- src/Integrals_Monoelec/README.rst | 232 +++--- src/MOGuess/README.rst | 19 +- src/MOs/README.rst | 82 +- src/Nuclei/README.rst | 21 +- src/Perturbation/README.rst | 253 +++++- src/Properties/README.rst | 150 ++++ src/Pseudo/README.rst | 4 +- src/Selectors_full/README.rst | 32 +- src/Selectors_no_sorted/README.rst | 183 +++++ src/SingleRefMethod/README.rst | 26 +- src/Utils/README.rst | 662 ++++++++++++---- 27 files changed, 2815 insertions(+), 946 deletions(-) diff --git a/scripts/compilation/create_ninja_build.py b/scripts/compilation/create_ninja_build.py index 9b8bea7c..47de8120 100755 --- a/scripts/compilation/create_ninja_build.py +++ b/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)) diff --git a/src/AOs/README.rst b/src/AOs/README.rst index d98ff003..a2f39f8d 100644 --- a/src/AOs/README.rst +++ b/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 `_ -* `Utils `_ Documentation ============= .. Do not edit this section. It was auto-generated from the -.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script. - -`ao_overlap `_ - Overlap between atomic basis functions: - :math:`\int \chi_i(r) \chi_j(r) dr)` - -`ao_overlap_abs `_ - Overlap between absolute value of atomic basis functions: - :math:`\int |\chi_i(r)| |\chi_j(r)| dr)` - -`ao_overlap_x `_ - Overlap between atomic basis functions: - :math:`\int \chi_i(r) \chi_j(r) dr)` - -`ao_overlap_y `_ - Overlap between atomic basis functions: - :math:`\int \chi_i(r) \chi_j(r) dr)` - -`ao_overlap_z `_ - Overlap between atomic basis functions: - :math:`\int \chi_i(r) \chi_j(r) dr)` +.. by the `update_README.py` script. `ao_coef `_ 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 `_ Coefficients including the AO normalization + `ao_coef_normalized_ordered `_ Sorted primitives to accelerate 4 index MO transformation + `ao_coef_normalized_ordered_transp `_ Transposed ao_coef_normalized_ordered + `ao_expo `_ AO Exponents read from input + `ao_expo_ordered `_ Sorted primitives to accelerate 4 index MO transformation + `ao_expo_ordered_transp `_ Transposed ao_expo_ordered + `ao_l `_ ao_l = l value of the AO: a+b+c in x^a y^b z^c + `ao_l_char `_ ao_l = l value of the AO: a+b+c in x^a y^b z^c + `ao_l_char_space `_ Undocumented + `ao_md5 `_ MD5 key characteristic of the AO basis + `ao_nucl `_ Index of the nuclei on which the ao is centered + `ao_num `_ Number of atomic orbitals + `ao_num_align `_ Number of atomic orbitals + +`ao_overlap `_ + Overlap between atomic basis functions: + :math:`\int \chi_i(r) \chi_j(r) dr)` + + +`ao_overlap_abs `_ + Overlap between absolute value of atomic basis functions: + :math:`\int |\chi_i(r)| |\chi_j(r)| dr)` + + +`ao_overlap_x `_ + Overlap between atomic basis functions: + :math:`\int \chi_i(r) \chi_j(r) dr)` + + +`ao_overlap_y `_ + Overlap between atomic basis functions: + :math:`\int \chi_i(r) \chi_j(r) dr)` + + +`ao_overlap_z `_ + Overlap between atomic basis functions: + :math:`\int \chi_i(r) \chi_j(r) dr)` + + `ao_power `_ Powers of x,y and z read from input + `ao_prim_num `_ Number of primitives per atomic orbital + `ao_prim_num_max `_ Undocumented + `ao_prim_num_max_align `_ Undocumented + `l_to_charater `_ character corresponding to the "L" value of an AO orbital + `n_aos_max `_ Number of AOs per atom + +`n_pt_max_i_x `_ + Undocumented + + +`n_pt_max_integrals `_ + Undocumented + + `nucl_aos `_ List of AOs attached on each atom + `nucl_list_shell_aos `_ 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 `_ Number of AOs per atom + `nucl_num_shell_aos `_ 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 `_ - Undocumented - -`n_pt_max_integrals `_ - Undocumented - - - diff --git a/src/Bitmask/README.rst b/src/Bitmask/README.rst index de1d09f5..ae339939 100644 --- a/src/Bitmask/README.rst +++ b/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 `_ @@ -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 `_ - Undocumented +`bitstring_to_hexa `_ + Transform a bit string to a string in hexadecimal format for printing -`number_of_holes `_ - Undocumented -`number_of_holes_verbose `_ - Undocumented +`bitstring_to_list `_ + Gives the inidices(+1) of the bits set to 1 in the bit string -`number_of_particles `_ - Undocumented -`number_of_particles_verbose `_ - Undocumented +`bitstring_to_str `_ + Transform a bit string to a string for printing + `cas_bitmask `_ Bitmasks for CAS reference determinants. (N_int, alpha/beta, CAS reference) + `cis_ijkl_bitmask `_ Bitmask to include all possible single excitations from Hartree-Fock + +`debug_det `_ + Subroutine to print the content of a determinant in '+-' notation and + hexadecimal representation. + + +`debug_spindet `_ + Subroutine to print the content of a determinant in '+-' notation and + hexadecimal representation. + + `full_ijkl_bitmask `_ Bitmask to include all possible MOs + `generators_bitmask `_ 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 `_ Hartree Fock bit mask + `i_bitmask_gen `_ Current bitmask for the generators + `inact_bitmask `_ Bitmasks for the inactive orbitals that are excited in post CAS method -`n_cas_bitmask `_ - Number of bitmasks for CAS -`n_generators_bitmask `_ - Number of bitmasks for generators +`is_a_two_holes_two_particles `_ + Undocumented -`n_int `_ - Number of 64-bit integers needed to represent determinants as binary strings - -`ref_bitmask `_ - Reference bit mask, used in Slater rules, chosen as Hartree-Fock bitmask - -`virt_bitmask `_ - Bitmasks for the inactive orbitals that are excited in post CAS method - -`bitstring_to_hexa `_ - Transform a bit string to a string in hexadecimal format for printing - -`bitstring_to_list `_ - Gives the inidices(+1) of the bits set to 1 in the bit string - -`bitstring_to_str `_ - Transform a bit string to a string for printing - -`debug_det `_ - Subroutine to print the content of a determinant in '+-' notation and - hexadecimal representation. - -`debug_spindet `_ - Subroutine to print the content of a determinant in '+-' notation and - hexadecimal representation. `list_to_bitstring `_ Returns the physical string "string(N_int,2)" from the array of occupations "list(N_int*bit_kind_size,2) + +`n_cas_bitmask `_ + Number of bitmasks for CAS + + +`n_generators_bitmask `_ + Number of bitmasks for generators + + +`n_int `_ + Number of 64-bit integers needed to represent determinants as binary strings + + +`number_of_holes `_ + Undocumented + + +`number_of_holes_verbose `_ + Undocumented + + +`number_of_particles `_ + Undocumented + + +`number_of_particles_verbose `_ + Undocumented + + `print_det `_ Subroutine to print the content of a determinant using the '+-' notation + `print_spindet `_ Subroutine to print the content of a determinant using the '+-' notation +`ref_bitmask `_ + Reference bit mask, used in Slater rules, chosen as Hartree-Fock bitmask + + +`virt_bitmask `_ + Bitmasks for the inactive orbitals that are excited in post CAS method diff --git a/src/CID/README.rst b/src/CID/README.rst index 7f7b9913..326546f5 100644 --- a/src/CID/README.rst +++ b/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 `_ * `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 `_ Undocumented +`h_apply_cisd `_ + 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 `_ + 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 `_ + Generate all single excitations of key_in using the bit masks of holes and + particles. + Assume N_int is already provided. diff --git a/src/CID_selected/README.rst b/src/CID_selected/README.rst index a304f085..ad309857 100644 --- a/src/CID_selected/README.rst +++ b/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. - -`h_apply_cisd_selection `_ - Undocumented +.. by the `update_README.py` script. `cisd `_ Undocumented +`h_apply_cisd_selection `_ + Undocumented + + +`h_apply_cisd_selection_delta_rho_one_point `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ * `CID `_ diff --git a/src/CISD/README.rst b/src/CISD/README.rst index 9ed22089..412f0aad 100644 --- a/src/CISD/README.rst +++ b/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 `_ * `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 `_ Undocumented +`h_apply_cisd `_ + 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 `_ + 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 `_ + Generate all single excitations of key_in using the bit masks of holes and + particles. + Assume N_int is already provided. diff --git a/src/CISD_selected/README.rst b/src/CISD_selected/README.rst index a13a40ca..230df80c 100644 --- a/src/CISD_selected/README.rst +++ b/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. - -`h_apply_cisd_selection `_ - Undocumented +.. by the `update_README.py` script. `cisd `_ Undocumented +`h_apply_cisd_selection `_ + Undocumented + + +`h_apply_cisd_selection_delta_rho_one_point `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ * `CISD `_ diff --git a/src/DensityFit/README.rst b/src/DensityFit/README.rst index 9d3c4d9b..9687dec6 100644 --- a/src/DensityFit/README.rst +++ b/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 `_ Exponents and coefficients of the auxiliary basis + `aux_basis_coef_transp `_ Exponents of the auxiliary basis + `aux_basis_expo `_ Exponents and coefficients of the auxiliary basis + `aux_basis_expo_transp `_ Exponents of the auxiliary basis -`aux_basis_idx `_ - aux_basis_idx(k) -> i,j - -`aux_basis_nucl `_ - Exponents of the auxiliary basis - -`aux_basis_num `_ - Number of auxiliary basis functions - -`aux_basis_num_8 `_ - Number of auxiliary basis functions - -`aux_basis_num_sqrt `_ - Number of auxiliary basis functions - -`aux_basis_overlap_matrix `_ - Auxiliary basis set - -`aux_basis_power `_ - Exponents of the auxiliary basis - -`aux_basis_prim_num `_ - Exponents of the auxiliary basis - -`aux_basis_prim_num_max `_ - = ao_prim_num_max - -`save_aux_basis `_ - Undocumented `aux_basis_four_overlap `_ \int \chi_i(r) \chi_j(r) \chi_k(r) \chi_l(r) dr +`aux_basis_idx `_ + aux_basis_idx(k) -> i,j + + +`aux_basis_nucl `_ + Exponents of the auxiliary basis + + +`aux_basis_num `_ + Number of auxiliary basis functions + + +`aux_basis_num_8 `_ + Number of auxiliary basis functions + + +`aux_basis_num_sqrt `_ + Number of auxiliary basis functions + + +`aux_basis_overlap_matrix `_ + Auxiliary basis set + + +`aux_basis_power `_ + Exponents of the auxiliary basis + + +`aux_basis_prim_num `_ + Exponents of the auxiliary basis + + +`aux_basis_prim_num_max `_ + = ao_prim_num_max + + +`save_aux_basis `_ + 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 `_ * `Pseudo `_ diff --git a/src/Determinants/README.rst b/src/Determinants/README.rst index 9bf75ee3..34392b7a 100644 --- a/src/Determinants/README.rst +++ b/src/Determinants/README.rst @@ -30,9 +30,9 @@ 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 `_ * `Integrals_Bielec `_ @@ -41,29 +41,67 @@ 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. -`copy_h_apply_buffer_to_wf `_ - Copies the H_apply buffer to psi_coef. - After calling this subroutine, N_det, psi_det and psi_coef need to be touched +`a_operator `_ + Needed for diag_H_mat_elem -`fill_h_apply_buffer_no_selection `_ - Fill the H_apply buffer with determiants for CISD -`h_apply_buffer_allocated `_ - Buffer of determinants/coefficients/perturbative energy for H_apply. - Uninitialized. Filled by H_apply subroutines. +`ac_operator `_ + Needed for diag_H_mat_elem -`h_apply_buffer_lock `_ - Buffer of determinants/coefficients/perturbative energy for H_apply. - Uninitialized. Filled by H_apply subroutines. -`remove_duplicates_in_psi_det `_ - Removes duplicate determinants in the wave function. +`apply_mono `_ + Undocumented + + +`bi_elec_ref_bitmask_energy `_ + Energy of the reference bitmask used in Slater rules + + +`ci_eigenvectors `_ + Eigenvectors/values of the CI matrix + + +`ci_eigenvectors_mono `_ + Eigenvectors/values of the CI matrix + + +`ci_eigenvectors_s2 `_ + Eigenvectors/values of the CI matrix + + +`ci_eigenvectors_s2_mono `_ + Eigenvectors/values of the CI matrix + + +`ci_electronic_energy `_ + Eigenvectors/values of the CI matrix + + +`ci_electronic_energy_mono `_ + Eigenvectors/values of the CI matrix + + +`ci_energy `_ + N_states lowest eigenvalues of the CI matrix + + +`ci_sc2_eigenvectors `_ + Eigenvectors/values of the CI matrix + + +`ci_sc2_electronic_energy `_ + Eigenvectors/values of the CI matrix + + +`ci_sc2_energy `_ + N_states_diag lowest eigenvalues of the CI matrix + + +`cisd `_ + Undocumented -`resize_h_apply_buffer `_ - Resizes the H_apply buffer of proc iproc. The buffer lock should - be set before calling this function. `cisd_sc2 `_ CISD+SC2 method :: take off all the disconnected terms of a CISD (selected or not) @@ -81,38 +119,32 @@ Documentation .br Initial guess vectors are not necessarily orthonormal + `connected_to_ref `_ Undocumented + `connected_to_ref_by_mono `_ Undocumented -`det_search_key `_ - Return an integer*8 corresponding to a determinant index for searching -`get_index_in_psi_det_sorted_bit `_ - Returns the index of the determinant in the ``psi_det_sorted_bit`` array +`copy_h_apply_buffer_to_wf `_ + Copies the H_apply buffer to psi_coef. + After calling this subroutine, N_det, psi_det and psi_coef need to be touched -`is_in_wavefunction `_ - True if the determinant ``det`` is in the wave function -`occ_pattern_search_key `_ - Return an integer*8 corresponding to a determinant index for searching +`create_wf_of_psi_svd_matrix `_ + Matrix of wf coefficients. Outer product of alpha and beta determinants -`do_mono_excitation `_ - Apply the mono excitation operator : a^{dager}_(i_particle) a_(i_hole) of spin = ispin - on key_in - ispin = 1 == alpha - ispin = 2 == beta - i_ok = 1 == the excitation is possible - i_ok = -1 == the excitation is not possible `davidson_converged `_ True if the Davidson algorithm is converged + `davidson_criterion `_ Can be : [ energy | residual | both | wall_time | cpu_time | iterations ] + `davidson_diag `_ Davidson diagonalization. .br @@ -131,6 +163,7 @@ Documentation .br Initial guess vectors are not necessarily orthonormal + `davidson_diag_hjj `_ Davidson diagonalization with specific diagonal elements of the H matrix .br @@ -151,140 +184,74 @@ Documentation .br Initial guess vectors are not necessarily orthonormal + `davidson_iter_max `_ Max number of Davidson iterations + `davidson_sze_max `_ Max number of Davidson sizes + `davidson_threshold `_ Can be : [ energy | residual | both | wall_time | cpu_time | iterations ] -`one_body_dm_mo `_ - One-body density matrix -`one_body_dm_mo_alpha `_ - Alpha and beta one-body density matrix for each state +`decode_exc `_ + Decodes the exc arrays returned by get_excitation. + h1,h2 : Holes + p1,p2 : Particles + s1,s2 : Spins (1:alpha, 2:beta) + degree : Degree of excitation -`one_body_dm_mo_beta `_ - Alpha and beta one-body density matrix for each state -`one_body_single_double_dm_mo_alpha `_ - Alpha and beta one-body density matrix for each state +`det_connections `_ + Build connection proxy between determinants -`one_body_single_double_dm_mo_beta `_ - Alpha and beta one-body density matrix for each state -`one_body_spin_density_mo `_ - rho(alpha) - rho(beta) +`det_search_key `_ + Return an integer*8 corresponding to a determinant index for searching -`save_natural_mos `_ - Save natural orbitals, obtained by diagonalization of the one-body density matrix in the MO basis - -`set_natural_mos `_ - Set natural orbitals, obtained by diagonalization of the one-body density matrix in the MO basis - -`state_average_weight `_ - Weights in the state-average calculation of the density matrix `det_svd `_ Computes the SVD of the Alpha x Beta determinant coefficient matrix -`filter_3_highest_electrons `_ - Returns a determinant with only the 3 highest electrons -`int_of_3_highest_electrons `_ - Returns an integer*8 as : - .br - |_<--- 21 bits ---><--- 21 bits ---><--- 21 bits --->| - .br - |0<--- i1 ---><--- i2 ---><--- i3 --->| - .br - It encodes the value of the indices of the 3 highest MOs - in descending order - .br +`det_to_occ_pattern `_ + Transform a determinant to an occupation pattern -`max_degree_exc `_ - Maximum degree of excitation in the wf -`n_det `_ - Number of determinants in the wave function +`diag_algorithm `_ + Diagonalization algorithm (Davidson or Lapack) -`psi_average_norm_contrib `_ - Contribution of determinants to the state-averaged density -`psi_average_norm_contrib_sorted `_ - Wave function sorted by determinants contribution to the norm (state-averaged) +`diag_h_mat_elem `_ + Computes -`psi_coef `_ - The wave function coefficients. Initialized with Hartree-Fock if the EZFIO file - is empty -`psi_coef_sorted `_ - Wave function sorted by determinants contribution to the norm (state-averaged) +`diagonalize_ci `_ + Replace the coefficients of the CI states by the coefficients of the + eigenstates of the CI matrix -`psi_coef_sorted_ab `_ - Determinants on which we apply . - 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_coef_sorted_bit `_ - Determinants on which we apply for perturbation. - They are sorted by determinants interpreted as integers. Useful - to accelerate the search of a random determinant in the wave - function. +`diagonalize_ci_mono `_ + Replace the coefficients of the CI states by the coefficients of the + eigenstates of the CI matrix -`psi_det `_ - The wave function determinants. Initialized with Hartree-Fock if the EZFIO file - is empty -`psi_det_size `_ - Size of the psi_det/psi_coef arrays +`diagonalize_ci_sc2 `_ + Replace the coefficients of the CI states_diag by the coefficients of the + eigenstates of the CI matrix -`psi_det_sorted `_ - Wave function sorted by determinants contribution to the norm (state-averaged) -`psi_det_sorted_ab `_ - Determinants on which we apply . - 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. +`do_mono_excitation `_ + Apply the mono excitation operator : a^{dager}_(i_particle) a_(i_hole) of spin = ispin + on key_in + ispin = 1 == alpha + ispin = 2 == beta + i_ok = 1 == the excitation is possible + i_ok = -1 == the excitation is not possible -`psi_det_sorted_bit `_ - Determinants on which we apply for perturbation. - They are sorted by determinants interpreted as integers. Useful - to accelerate the search of a random determinant in the wave - function. - -`psi_det_sorted_next_ab `_ - Determinants on which we apply . - 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. - -`read_dets `_ - Reads the determinants from the EZFIO file - -`save_wavefunction `_ - Save the wave function into the EZFIO file - -`save_wavefunction_general `_ - Save the wave function into the EZFIO file - -`save_wavefunction_unsorted `_ - Save the wave function into the EZFIO file - -`sort_dets_by_3_highest_electrons `_ - Determinants on which we apply . - 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. - -`sort_dets_by_det_search_key `_ - Determinants are sorted are sorted according to their det_search_key. - Useful to accelerate the search of a random determinant in the wave - function. `double_exc_bitmask `_ double_exc_bitmask(:,1,i) is the bitmask for holes of excitation 1 @@ -293,67 +260,18 @@ Documentation double_exc_bitmask(:,4,i) is the bitmask for particles of excitation 2 for a given couple of hole/particle excitations i. -`n_double_exc_bitmasks `_ - Number of double excitation bitmasks -`n_single_exc_bitmasks `_ - Number of single excitation bitmasks +`expected_s2 `_ + Expected value of S2 : S*(S+1) -`single_exc_bitmask `_ - single_exc_bitmask(:,1,i) is the bitmask for holes - single_exc_bitmask(:,2,i) is the bitmask for particles - for a given couple of hole/particle excitations i. -`ci_eigenvectors `_ - Eigenvectors/values of the CI matrix +`fill_h_apply_buffer_no_selection `_ + Fill the H_apply buffer with determiants for CISD -`ci_eigenvectors_s2 `_ - Eigenvectors/values of the CI matrix -`ci_electronic_energy `_ - Eigenvectors/values of the CI matrix +`filter_3_highest_electrons `_ + Returns a determinant with only the 3 highest electrons -`ci_energy `_ - N_states lowest eigenvalues of the CI matrix - -`diag_algorithm `_ - Diagonalization algorithm (Davidson or Lapack) - -`diagonalize_ci `_ - Replace the coefficients of the CI states by the coefficients of the - eigenstates of the CI matrix - -`ci_sc2_eigenvectors `_ - Eigenvectors/values of the CI matrix - -`ci_sc2_electronic_energy `_ - Eigenvectors/values of the CI matrix - -`ci_sc2_energy `_ - N_states_diag lowest eigenvalues of the CI matrix - -`diagonalize_ci_sc2 `_ - Replace the coefficients of the CI states_diag by the coefficients of the - eigenstates of the CI matrix - -`threshold_convergence_sc2 `_ - convergence of the correlation energy of SC2 iterations - -`ci_eigenvectors_mono `_ - Eigenvectors/values of the CI matrix - -`ci_eigenvectors_s2_mono `_ - Eigenvectors/values of the CI matrix - -`ci_electronic_energy_mono `_ - Eigenvectors/values of the CI matrix - -`diagonalize_ci_mono `_ - Replace the coefficients of the CI states by the coefficients of the - eigenstates of the CI matrix - -`apply_mono `_ - Undocumented `filter_connected `_ Filters out the determinants that are not connected by H @@ -366,6 +284,7 @@ Documentation .br idx(0) is the number of determinants that interact with key1 + `filter_connected_davidson `_ Filters out the determinants that are not connected by H returns the array idx which contains the index of the @@ -375,6 +294,7 @@ Documentation idx(0) is the number of determinants that interact with key1 key1 should come from psi_det_sorted_ab. + `filter_connected_i_h_psi0 `_ returns the array idx which contains the index of the .br @@ -384,6 +304,7 @@ Documentation .br idx(0) is the number of determinants that interact with key1 + `filter_connected_i_h_psi0_sc2 `_ standard filter_connected_i_H_psi but returns in addition .br @@ -395,6 +316,7 @@ Documentation .br to repeat the excitations + `filter_connected_sorted_ab `_ Filters out the determinants that are not connected by H returns the array idx which contains the index of the @@ -404,174 +326,69 @@ Documentation .br Determinants are taken from the psi_det_sorted_ab array -`put_gess `_ - Undocumented -`det_to_occ_pattern `_ - Transform a determinant to an occupation pattern +`generate_all_alpha_beta_det_products `_ + Create a wave function from all possible alpha x beta determinants -`make_s2_eigenfunction `_ - Undocumented - -`n_occ_pattern `_ - array of the occ_pattern present in the wf - psi_occ_pattern(:,1,j) = jth occ_pattern of the wave function : represent all the single occupation - psi_occ_pattern(:,2,j) = jth occ_pattern of the wave function : represent all the double occupation - -`occ_pattern_to_dets `_ - Generate all possible determinants for a give occ_pattern - -`occ_pattern_to_dets_size `_ - Number of possible determinants for a given occ_pattern - -`psi_occ_pattern `_ - array of the occ_pattern present in the wf - psi_occ_pattern(:,1,j) = jth occ_pattern of the wave function : represent all the single occupation - psi_occ_pattern(:,2,j) = jth occ_pattern of the wave function : represent all the double occupation - -`rec_occ_pattern_to_dets `_ - Undocumented - -`n_states_diag `_ - Number of states to consider for the diagonalization - -`pouet `_ - Undocumented - -`routine `_ - Undocumented - -`idx_cas `_ - CAS wave function, defined from the application of the CAS bitmask on the - determinants. idx_cas gives the indice of the CAS determinant in psi_det. - -`idx_non_cas `_ - Set of determinants which are not part of the CAS, defined from the application - of the CAS bitmask on the determinants. - idx_non_cas gives the indice of the determinant in psi_det. - -`n_det_cas `_ - CAS wave function, defined from the application of the CAS bitmask on the - determinants. idx_cas gives the indice of the CAS determinant in psi_det. - -`n_det_non_cas `_ - Set of determinants which are not part of the CAS, defined from the application - of the CAS bitmask on the determinants. - idx_non_cas gives the indice of the determinant in psi_det. - -`psi_cas `_ - CAS wave function, defined from the application of the CAS bitmask on the - determinants. idx_cas gives the indice of the CAS determinant in psi_det. - -`psi_cas_coef `_ - CAS wave function, defined from the application of the CAS bitmask on the - determinants. idx_cas gives the indice of the CAS determinant in psi_det. - -`psi_cas_coef_sorted_bit `_ - CAS determinants sorted to accelerate the search of a random determinant in the wave - function. - -`psi_cas_sorted_bit `_ - CAS determinants sorted to accelerate the search of a random determinant in the wave - function. - -`psi_non_cas `_ - Set of determinants which are not part of the CAS, defined from the application - of the CAS bitmask on the determinants. - idx_non_cas gives the indice of the determinant in psi_det. - -`psi_non_cas_coef `_ - Set of determinants which are not part of the CAS, defined from the application - of the CAS bitmask on the determinants. - idx_non_cas gives the indice of the determinant in psi_det. - -`psi_non_cas_coef_sorted_bit `_ - CAS determinants sorted to accelerate the search of a random determinant in the wave - function. - -`psi_non_cas_sorted_bit `_ - CAS determinants sorted to accelerate the search of a random determinant in the wave - function. - -`bi_elec_ref_bitmask_energy `_ - Energy of the reference bitmask used in Slater rules - -`kinetic_ref_bitmask_energy `_ - Energy of the reference bitmask used in Slater rules - -`mono_elec_ref_bitmask_energy `_ - Energy of the reference bitmask used in Slater rules - -`nucl_elec_ref_bitmask_energy `_ - Energy of the reference bitmask used in Slater rules - -`ref_bitmask_energy `_ - Energy of the reference bitmask used in Slater rules - -`expected_s2 `_ - Expected value of S2 : S*(S+1) - -`get_s2 `_ - Returns - -`get_s2_u0 `_ - Undocumented - -`s2_values `_ - array of the averaged values of the S^2 operator on the various states - -`s_z `_ - z component of the Spin - -`s_z2_sz `_ - z component of the Spin - -`prog_save_casino `_ - Undocumented - -`save_casino `_ - Undocumented - -`save_natorb `_ - Undocumented - -`a_operator `_ - Needed for diag_H_mat_elem - -`ac_operator `_ - Needed for diag_H_mat_elem - -`decode_exc `_ - Decodes the exc arrays returned by get_excitation. - h1,h2 : Holes - p1,p2 : Particles - s1,s2 : Spins (1:alpha, 2:beta) - degree : Degree of excitation - -`det_connections `_ - Build connection proxy between determinants - -`diag_h_mat_elem `_ - Computes `get_double_excitation `_ Returns the two excitation operators between two doubly excited determinants and the phase + `get_excitation `_ Returns the excitation operators between two determinants and the phase + `get_excitation_degree `_ Returns the excitation degree between two determinants + `get_excitation_degree_vector `_ Applies get_excitation_degree to an array of determinants + +`get_index_in_psi_det_alpha_unique `_ + Returns the index of the determinant in the ``psi_det_alpha_unique`` array + + +`get_index_in_psi_det_beta_unique `_ + Returns the index of the determinant in the ``psi_det_beta_unique`` array + + +`get_index_in_psi_det_sorted_bit `_ + Returns the index of the determinant in the ``psi_det_sorted_bit`` array + + `get_mono_excitation `_ Returns the excitation operator between two singly excited determinants and the phase + `get_occ_from_key `_ Returns a list of occupation numbers from a bitstring + +`get_s2 `_ + Returns + + +`get_s2_u0 `_ + Undocumented + + +`h_apply_buffer_allocated `_ + Buffer of determinants/coefficients/perturbative energy for H_apply. + Uninitialized. Filled by H_apply subroutines. + + +`h_apply_buffer_lock `_ + Buffer of determinants/coefficients/perturbative energy for H_apply. + Uninitialized. Filled by H_apply subroutines. + + +`h_matrix_all_dets `_ + H matrix on the basis of the slater determinants defined by psi_det + + `h_u_0 `_ Computes v_0 = H|u_0> .br @@ -579,15 +396,19 @@ Documentation .br H_jj : array of + `i_h_j `_ Returns where i and j are determinants + `i_h_j_verbose `_ Returns where i and j are determinants + `i_h_psi `_ for the various Nstates + `i_h_psi_sc2 `_ for the various Nstate .br @@ -601,6 +422,7 @@ Documentation .br to repeat the excitations + `i_h_psi_sc2_verbose `_ for the various Nstate .br @@ -614,62 +436,440 @@ Documentation .br to repeat the excitations + `i_h_psi_sec_ord `_ for the various Nstates + +`idx_cas `_ + CAS wave function, defined from the application of the CAS bitmask on the + determinants. idx_cas gives the indice of the CAS determinant in psi_det. + + +`idx_non_cas `_ + Set of determinants which are not part of the CAS, defined from the application + of the CAS bitmask on the determinants. + idx_non_cas gives the indice of the determinant in psi_det. + + +`int_of_3_highest_electrons `_ + Returns an integer*8 as : + .br + |_<--- 21 bits ---><--- 21 bits ---><--- 21 bits --->| + .br + |0<--- i1 ---><--- i2 ---><--- i3 --->| + .br + It encodes the value of the indices of the 3 highest MOs + in descending order + .br + + +`is_in_wavefunction `_ + True if the determinant ``det`` is in the wave function + + +`kinetic_ref_bitmask_energy `_ + Energy of the reference bitmask used in Slater rules + + +`make_s2_eigenfunction `_ + Undocumented + + +`max_degree_exc `_ + Maximum degree of excitation in the wf + + +`mono_elec_ref_bitmask_energy `_ + Energy of the reference bitmask used in Slater rules + + `n_con_int `_ Number of integers to represent the connections between determinants -`create_wf_of_psi_svd_matrix `_ - Matrix of wf coefficients. Outer product of alpha and beta determinants -`generate_all_alpha_beta_det_products `_ - Create a wave function from all possible alpha x beta determinants +`n_det `_ + Number of determinants in the wave function -`get_index_in_psi_det_alpha_unique `_ - Returns the index of the determinant in the ``psi_det_alpha_unique`` array -`get_index_in_psi_det_beta_unique `_ - Returns the index of the determinant in the ``psi_det_beta_unique`` array +`n_det_alpha_unique `_ + Unique alpha determinants + + +`n_det_beta_unique `_ + Unique beta determinants + + +`n_det_cas `_ + CAS wave function, defined from the application of the CAS bitmask on the + determinants. idx_cas gives the indice of the CAS determinant in psi_det. + + +`n_det_max `_ + Max number of determinants in the wave function + + +`n_det_max_jacobi `_ + Maximum number of determinants diagonalized by Jacobi + + +`n_det_max_property `_ + Max number of determinants in the wave function when you select for a given property + + +`n_det_non_cas `_ + Set of determinants which are not part of the CAS, defined from the application + of the CAS bitmask on the determinants. + idx_non_cas gives the indice of the determinant in psi_det. + + +`n_double_exc_bitmasks `_ + Number of double excitation bitmasks + + +`n_occ_pattern `_ + array of the occ_pattern present in the wf + psi_occ_pattern(:,1,j) = jth occ_pattern of the wave function : represent all the single occupation + psi_occ_pattern(:,2,j) = jth occ_pattern of the wave function : represent all the double occupation + + +`n_single_exc_bitmasks `_ + Number of single excitation bitmasks + + +`n_states `_ + Number of states to consider + + +`n_states_diag `_ + Number of states to consider for the diagonalization + + +`nucl_elec_ref_bitmask_energy `_ + Energy of the reference bitmask used in Slater rules + + +`occ_pattern_search_key `_ + Return an integer*8 corresponding to a determinant index for searching + + +`occ_pattern_to_dets `_ + Generate all possible determinants for a give occ_pattern + + +`occ_pattern_to_dets_size `_ + Number of possible determinants for a given occ_pattern + + +`one_body_dm_mo `_ + One-body density matrix + + +`one_body_dm_mo_alpha `_ + Alpha and beta one-body density matrix for each state + + +`one_body_dm_mo_beta `_ + Alpha and beta one-body density matrix for each state + + +`one_body_single_double_dm_mo_alpha `_ + Alpha and beta one-body density matrix for each state + + +`one_body_single_double_dm_mo_beta `_ + Alpha and beta one-body density matrix for each state + + +`one_body_spin_density_mo `_ + rho(alpha) - rho(beta) + + +`only_single_double_dm `_ + If true, The One body DM is calculated with ignoring the Double<->Doubles extra diag elements + + +`pouet `_ + Undocumented + + +`prog_save_casino `_ + Undocumented + + +`psi_average_norm_contrib `_ + Contribution of determinants to the state-averaged density + + +`psi_average_norm_contrib_sorted `_ + Wave function sorted by determinants contribution to the norm (state-averaged) + + +`psi_cas `_ + CAS wave function, defined from the application of the CAS bitmask on the + determinants. idx_cas gives the indice of the CAS determinant in psi_det. + + +`psi_cas_coef `_ + CAS wave function, defined from the application of the CAS bitmask on the + determinants. idx_cas gives the indice of the CAS determinant in psi_det. + + +`psi_cas_coef_sorted_bit `_ + CAS determinants sorted to accelerate the search of a random determinant in the wave + function. + + +`psi_cas_sorted_bit `_ + CAS determinants sorted to accelerate the search of a random determinant in the wave + function. + + +`psi_coef `_ + The wave function coefficients. Initialized with Hartree-Fock if the EZFIO file + is empty + + +`psi_coef_sorted `_ + Wave function sorted by determinants contribution to the norm (state-averaged) + + +`psi_coef_sorted_ab `_ + Determinants on which we apply . + 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_coef_sorted_bit `_ + Determinants on which we apply for perturbation. + They are sorted by determinants interpreted as integers. Useful + to accelerate the search of a random determinant in the wave + function. + + +`psi_det `_ + The wave function determinants. Initialized with Hartree-Fock if the EZFIO file + is empty + `psi_det_alpha `_ List of alpha determinants of psi_det + +`psi_det_alpha_unique `_ + Unique alpha determinants + + `psi_det_beta `_ List of beta determinants of psi_det + +`psi_det_beta_unique `_ + Unique beta determinants + + +`psi_det_size `_ + Size of the psi_det/psi_coef arrays + + +`psi_det_sorted `_ + Wave function sorted by determinants contribution to the norm (state-averaged) + + +`psi_det_sorted_ab `_ + Determinants on which we apply . + 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_det_sorted_bit `_ + Determinants on which we apply for perturbation. + They are sorted by determinants interpreted as integers. Useful + to accelerate the search of a random determinant in the wave + function. + + +`psi_det_sorted_next_ab `_ + Determinants on which we apply . + 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_non_cas `_ + Set of determinants which are not part of the CAS, defined from the application + of the CAS bitmask on the determinants. + idx_non_cas gives the indice of the determinant in psi_det. + + +`psi_non_cas_coef `_ + Set of determinants which are not part of the CAS, defined from the application + of the CAS bitmask on the determinants. + idx_non_cas gives the indice of the determinant in psi_det. + + +`psi_non_cas_coef_sorted_bit `_ + CAS determinants sorted to accelerate the search of a random determinant in the wave + function. + + +`psi_non_cas_sorted_bit `_ + CAS determinants sorted to accelerate the search of a random determinant in the wave + function. + + +`psi_occ_pattern `_ + array of the occ_pattern present in the wf + psi_occ_pattern(:,1,j) = jth occ_pattern of the wave function : represent all the single occupation + psi_occ_pattern(:,2,j) = jth occ_pattern of the wave function : represent all the double occupation + + `psi_svd_alpha `_ SVD wave function + `psi_svd_beta `_ SVD wave function + `psi_svd_coefs `_ SVD wave function + `psi_svd_matrix `_ Matrix of wf coefficients. Outer product of alpha and beta determinants + `psi_svd_matrix_columns `_ Matrix of wf coefficients. Outer product of alpha and beta determinants + `psi_svd_matrix_rows `_ Matrix of wf coefficients. Outer product of alpha and beta determinants + `psi_svd_matrix_values `_ Matrix of wf coefficients. Outer product of alpha and beta determinants + +`put_gess `_ + Undocumented + + +`read_dets `_ + Reads the determinants from the EZFIO file + + +`read_wf `_ + If true, read the wave function from the EZFIO file + + +`rec_occ_pattern_to_dets `_ + Undocumented + + +`ref_bitmask_energy `_ + Energy of the reference bitmask used in Slater rules + + +`remove_duplicates_in_psi_det `_ + Removes duplicate determinants in the wave function. + + +`resize_h_apply_buffer `_ + Resizes the H_apply buffer of proc iproc. The buffer lock should + be set before calling this function. + + +`routine `_ + Undocumented + + +`s2_eig `_ + Force the wave function to be an eigenfunction of S^2 + + +`s2_values `_ + array of the averaged values of the S^2 operator on the various states + + +`s_z `_ + z component of the Spin + + +`s_z2_sz `_ + z component of the Spin + + +`save_casino `_ + Undocumented + + +`save_natorb `_ + Undocumented + + +`save_natural_mos `_ + Save natural orbitals, obtained by diagonalization of the one-body density matrix in the MO basis + + +`save_wavefunction `_ + Save the wave function into the EZFIO file + + +`save_wavefunction_general `_ + Save the wave function into the EZFIO file + + +`save_wavefunction_unsorted `_ + Save the wave function into the EZFIO file + + +`set_natural_mos `_ + Set natural orbitals, obtained by diagonalization of the one-body density matrix in the MO basis + + +`single_exc_bitmask `_ + single_exc_bitmask(:,1,i) is the bitmask for holes + single_exc_bitmask(:,2,i) is the bitmask for particles + for a given couple of hole/particle excitations i. + + +`sort_dets_by_3_highest_electrons `_ + Determinants on which we apply . + 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. + + +`sort_dets_by_det_search_key `_ + Determinants are sorted are sorted according to their det_search_key. + Useful to accelerate the search of a random determinant in the wave + function. + + `spin_det_search_key `_ Return an integer*8 corresponding to a determinant index for searching + +`state_average_weight `_ + Weights in the state-average calculation of the density matrix + + +`threshold_convergence_sc2 `_ + convergence of the correlation energy of SC2 iterations + + +`threshold_generators `_ + Thresholds on generators (fraction of the norm) + + +`threshold_selectors `_ + Thresholds on selectors (fraction of the norm) + + `write_spindeterminants `_ Undocumented -`cisd `_ - Undocumented - -`h_matrix_all_dets `_ - H matrix on the basis of the slater determinants defined by psi_det - - - diff --git a/src/Electrons/README.rst b/src/Electrons/README.rst index b0293762..ecbcf9c4 100644 --- a/src/Electrons/README.rst +++ b/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 `_ @@ -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 `_ Numbers of alpha ("up") , beta ("down") and total electrons + `elec_beta_num `_ Numbers of alpha ("up") , beta ("down") and total electrons + `elec_num `_ Numbers of alpha ("up") , beta ("down") and total electrons + `elec_num_tab `_ Numbers of alpha ("up") , beta ("down") and total electrons - - diff --git a/src/Ezfio_files/README.rst b/src/Ezfio_files/README.rst index 50de3483..db63d6c8 100644 --- a/src/Ezfio_files/README.rst +++ b/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 `_ 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 `_ :f: file name @@ -28,24 +29,180 @@ Documentation 'x' : READ/WRITE, FORMATTED .br + +`output_aos `_ + Output file for AOs + + +`output_bitmask `_ + Output file for Bitmask + + +`output_cas_sd `_ + Output file for CAS_SD + + +`output_cid `_ + Output file for CID + + +`output_cid_sc2_selected `_ + Output file for CID_SC2_selected + + +`output_cid_selected `_ + Output file for CID_selected + + +`output_cis `_ + Output file for CIS + + +`output_cisd `_ + Output file for CISD + + +`output_cisd_sc2_selected `_ + Output file for CISD_SC2_selected + + +`output_cisd_selected `_ + Output file for CISD_selected + + `output_cpu_time_0 `_ Initial CPU and wall times when printing in the output files + +`output_ddci_selected `_ + Output file for DDCI_selected + + +`output_densityfit `_ + Output file for DensityFit + + +`output_densitymatrix `_ + Output file for DensityMatrix + + +`output_determinants `_ + Output file for Determinants + + +`output_electrons `_ + Output file for Electrons + + +`output_ezfio_files `_ + Output file for Ezfio_files + + +`output_fcidump `_ + Output file for FCIdump + + +`output_full_ci `_ + Output file for Full_CI + + +`output_generators_cas `_ + Output file for Generators_CAS + + +`output_generators_full `_ + Output file for Generators_full + + +`output_generators_restart `_ + Output file for Generators_restart + + +`output_hartree_fock `_ + Output file for Hartree_Fock + + +`output_integrals_bielec `_ + Output file for Integrals_Bielec + + +`output_integrals_monoelec `_ + Output file for Integrals_Monoelec + + +`output_moguess `_ + Output file for MOGuess + + +`output_molden `_ + Output file for Molden + + +`output_mos `_ + Output file for MOs + + +`output_mp2 `_ + Output file for MP2 + + +`output_mrcc `_ + Output file for MRCC + + +`output_nuclei `_ + Output file for Nuclei + + +`output_perturbation `_ + Output file for Perturbation + + +`output_properties `_ + Output file for Properties + + +`output_pseudo `_ + Output file for Pseudo + + +`output_qmcchem `_ + Output file for QmcChem + + +`output_selectors_full `_ + Output file for Selectors_full + + +`output_selectors_no_sorted `_ + Output file for Selectors_no_sorted + + +`output_singlerefmethod `_ + Output file for SingleRefMethod + + +`output_utils `_ + Output file for Utils + + `output_wall_time_0 `_ Initial CPU and wall times when printing in the output files + `write_bool `_ Write an logical value in output + `write_double `_ Write a double precision value in output + `write_int `_ Write an integer value in output + `write_time `_ Write a time stamp in the output for chronological reconstruction - - diff --git a/src/Generators_CAS/README.rst b/src/Generators_CAS/README.rst index aeb6b73d..9a361c8b 100644 --- a/src/Generators_CAS/README.rst +++ b/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 `_ Number of generator detetrminants + `psi_coef_generators `_ For Single reference wave functions, the generator is the Hartree-Fock determinant + `psi_det_generators `_ For Single reference wave functions, the generator is the Hartree-Fock determinant + `select_max `_ Memo to skip useless selectors + `size_select_max `_ 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 `_ diff --git a/src/Generators_full/README.rst b/src/Generators_full/README.rst index 6325b143..dc6965e8 100644 --- a/src/Generators_full/README.rst +++ b/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 `_ Max degree of excitation (respect to HF) of the generators + `n_det_generators `_ For Single reference wave functions, the number of generators is 1 : the Hartree-Fock determinant + `psi_coef_generators `_ For Single reference wave functions, the generator is the Hartree-Fock determinant + `psi_det_generators `_ For Single reference wave functions, the generator is the Hartree-Fock determinant + `select_max `_ Memo to skip useless selectors + `size_select_max `_ 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 `_ * `Hartree_Fock `_ diff --git a/src/Generators_restart/README.rst b/src/Generators_restart/README.rst index e7ab7045..2a476a1a 100644 --- a/src/Generators_restart/README.rst +++ b/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 `_ + Read the wave function + + +`psi_coef_generators `_ + read wf + .br + + +`psi_det_generators `_ + read wf + .br + + +`select_max `_ + Memo to skip useless selectors + + +`size_select_max `_ + 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 `_ + diff --git a/src/Hartree_Fock/README.rst b/src/Hartree_Fock/README.rst index 7b17fb78..4dacf17c 100644 --- a/src/Hartree_Fock/README.rst +++ b/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 `_ * `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 `_ Alpha Fock matrix in AO basis set + `ao_bi_elec_integral_beta `_ Alpha Fock matrix in AO basis set + +`create_guess `_ + Create an MO guess if no MOs are present in the EZFIO directory + + +`damping_scf `_ + Undocumented + + +`diagonal_fock_matrix_mo `_ + Diagonal Fock matrix in the MO basis + + +`diagonal_fock_matrix_mo_sum `_ + 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 `_ + Diagonal Fock matrix in the MO basis + + `fock_matrix_alpha_ao `_ Alpha Fock matrix in AO basis set + `fock_matrix_alpha_mo `_ Fock matrix on the MO basis + `fock_matrix_ao `_ Fock matrix in AO basis set + `fock_matrix_beta_ao `_ Alpha Fock matrix in AO basis set + `fock_matrix_beta_mo `_ Fock matrix on the MO basis + `fock_matrix_diag_mo `_ 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 `_ 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 `_ Undocumented -`hf_energy `_ - Hartree-Fock energy - -`hf_density_matrix_ao `_ - S^-1 Density matrix in the AO basis S^-1 - -`hf_density_matrix_ao_alpha `_ - S^-1 x Alpha density matrix in the AO basis x S^-1 - -`hf_density_matrix_ao_beta `_ - S^-1 Beta density matrix in the AO basis x S^-1 `guess `_ Undocumented -`create_guess `_ - Create an MO guess if no MOs are present in the EZFIO directory -`run `_ - Run SCF calculation +`hf_density_matrix_ao `_ + S^-1 Density matrix in the AO basis S^-1 -`scf `_ - Undocumented -`damping_scf `_ - Undocumented +`hf_density_matrix_ao_alpha `_ + S^-1 x Alpha density matrix in the AO basis x S^-1 -`diagonal_fock_matrix_mo `_ - Diagonal Fock matrix in the MO basis -`diagonal_fock_matrix_mo_sum `_ - 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 +`hf_density_matrix_ao_beta `_ + S^-1 Beta density matrix in the AO basis x S^-1 + + +`hf_energy `_ + Hartree-Fock energy -`eigenvectors_fock_matrix_mo `_ - Diagonal Fock matrix in the MO basis `huckel_guess `_ Build the MOs using the extended Huckel model +`mo_guess_type `_ + Initial MO guess. Can be [ Huckel | HCore ] + + +`n_it_scf_max `_ + Maximum number of SCF iterations + + +`run `_ + Run SCF calculation + + +`scf `_ + Undocumented + + +`thresh_scf `_ + Threshold on the convergence of the Hartree Fock energy diff --git a/src/Integrals_Bielec/README.rst b/src/Integrals_Bielec/README.rst index 4ed5c09b..eed456c4 100644 --- a/src/Integrals_Bielec/README.rst +++ b/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 `_ -* `MOs `_ * `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 `_ + Adds integrals to tha MO map according to some bitmask + `ao_bielec_integral `_ integral of the AO basis or (ij|kl) i(r1) j(r1) 1/r12 k(r2) l(r2) + `ao_bielec_integral_schwartz `_ Needed to compute Schwartz inequalities + `ao_bielec_integral_schwartz_accel `_ integral of the AO basis or (ij|kl) i(r1) j(r1) 1/r12 k(r2) l(r2) + `ao_bielec_integrals_in_map `_ Map of Atomic integrals i(r1) j(r2) 1/r12 k(r1) l(r2) + +`ao_integrals_map `_ + AO integrals + + +`ao_integrals_threshold `_ + If || < ao_integrals_threshold then is zero + + `ao_l4 `_ Computes the product of l values of i,j,k,and l + +`bielec_integrals_index `_ + Undocumented + + +`bielec_integrals_index_reverse `_ + Undocumented + + +`clear_ao_map `_ + Frees the memory of the AO map + + +`clear_mo_map `_ + Frees the memory of the MO map + + `compute_ao_bielec_integrals `_ Compute AO 1/r12 integrals for all i and fixed j,k,l + +`disk_access_ao_integrals `_ + Read/Write AO integrals from/to disk [ Write | Read | None ] + + +`disk_access_mo_integrals `_ + Read/Write MO integrals from/to disk [ Write | Read | None ] + + +`do_direct_integrals `_ + Compute integrals on the fly + + +`dump_ao_integrals `_ + Save to disk the $ao integrals + + +`dump_mo_integrals `_ + Save to disk the $ao integrals + + `eri `_ 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 `_ - Computes the integral where p,q,r,s are Gaussian primitives - -`give_polynom_mult_center_x `_ - 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 `_ - recursive function involved in the bielectronic integral - -`i_x1_pol_mult `_ - recursive function involved in the bielectronic integral - -`i_x1_pol_mult_a1 `_ - recursive function involved in the bielectronic integral - -`i_x1_pol_mult_a2 `_ - recursive function involved in the bielectronic integral - -`i_x1_pol_mult_recurs `_ - recursive function involved in the bielectronic integral - -`i_x2_new `_ - recursive function involved in the bielectronic integral - -`i_x2_pol_mult `_ - recursive function involved in the bielectronic integral - -`integrale_new `_ - 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 `_ - 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 `_ Gauss-Legendre + `gauleg_t2 `_ t_w(i,1,k) = w(i) t_w(i,2,k) = t(i) + `gauleg_w `_ t_w(i,1,k) = w(i) t_w(i,2,k) = t(i) -`n_pt_max_integrals_16 `_ - Aligned n_pt_max_integrals -`ao_integrals_map `_ - AO integrals +`general_primitive_integral `_ + Computes the integral where p,q,r,s are Gaussian primitives -`bielec_integrals_index `_ - Undocumented - -`bielec_integrals_index_reverse `_ - Undocumented - -`clear_ao_map `_ - Frees the memory of the AO map - -`clear_mo_map `_ - Frees the memory of the MO map `get_ao_bielec_integral `_ Gets one AO bi-electronic integral from the AO map + `get_ao_bielec_integrals `_ 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 `_ 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 `_ Returns the number of elements in the AO map + `get_mo_bielec_integral `_ Returns one integral in the MO basis + `get_mo_bielec_integrals `_ Returns multiple integrals in the MO basis, all i for j,k,l fixed. + `get_mo_bielec_integrals_existing_ik `_ Returns multiple integrals 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 `_ Return the number of elements in the MO map + +`give_polynom_mult_center_x `_ + 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 `_ + recursive function involved in the bielectronic integral + + +`i_x1_pol_mult `_ + recursive function involved in the bielectronic integral + + +`i_x1_pol_mult_a1 `_ + recursive function involved in the bielectronic integral + + +`i_x1_pol_mult_a2 `_ + recursive function involved in the bielectronic integral + + +`i_x1_pol_mult_recurs `_ + recursive function involved in the bielectronic integral + + +`i_x2_new `_ + recursive function involved in the bielectronic integral + + +`i_x2_pol_mult `_ + recursive function involved in the bielectronic integral + + `insert_into_ao_integrals_map `_ Create new entry into AO map + `insert_into_mo_integrals_map `_ Create new entry into MO map, or accumulate in an existing entry + +`integrale_new `_ + 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 `_ + Read from disk the $ao integrals + + +`load_mo_integrals `_ + Read from disk the $ao integrals + + `mo_bielec_integral `_ Returns one integral in the MO basis -`mo_integrals_map `_ - MO integrals - -`add_integrals_to_map `_ - Adds integrals to tha MO map according to some bitmask `mo_bielec_integral_jj `_ 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 `_ 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 `_ 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 `_ 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 `_ 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 `_ 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 `_ If True, the map of MO bielectronic integrals is provided + `mo_bielec_integrals_index `_ Computes an unique index for i,j,k,l integrals + +`mo_integrals_map `_ + MO integrals + + +`mo_integrals_threshold `_ + If || < ao_integrals_threshold then is zero + + +`n_pt_max_integrals_16 `_ + Aligned n_pt_max_integrals + + +`n_pt_sup `_ + 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 `_ One level of abstraction for disk_access_ao_integrals and disk_access_mo_integrals + `read_mo_integrals `_ One level of abstraction for disk_access_ao_integrals and disk_access_mo_integrals + `write_ao_integrals `_ One level of abstraction for disk_access_ao_integrals and disk_access_mo_integrals + `write_mo_integrals `_ One level of abstraction for disk_access_ao_integrals and disk_access_mo_integrals - - diff --git a/src/Integrals_Monoelec/README.rst b/src/Integrals_Monoelec/README.rst index 720929ef..1a6ed8f1 100644 --- a/src/Integrals_Monoelec/README.rst +++ b/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 `_ * `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. - -`ao_mono_elec_integral `_ - array of the mono electronic hamiltonian on the AOs basis - : sum of the kinetic and nuclear electronic potential - -`check_ortho `_ - Undocumented - -`do_print `_ - Undocumented +.. by the `update_README.py` script. `ao_deriv2_x `_ 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 `_ 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 `_ 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 `_ - array of the priminitve basis kinetic integrals - \langle \chi_i |\hat{T}| \chi_j \rangle - -`mo_kinetic_integral `_ - Undocumented - -`mo_mono_elec_integral `_ - array of the mono electronic hamiltonian on the MOs basis - : sum of the kinetic and nuclear electronic potential - -`orthonormalize_mos `_ - Undocumented - -`ao_nucl_elec_integral `_ - interaction nuclear electron - -`ao_nucl_elec_integral_per_atom `_ - ao_nucl_elec_integral_per_atom(i,j,k) = - - where Rk is the geometry of the kth atom - -`give_polynom_mult_center_mono_elec `_ - Undocumented - -`i_x1_pol_mult_mono_elec `_ - Undocumented - -`i_x2_pol_mult_mono_elec `_ - Undocumented - -`int_gaus_pol `_ - Undocumented - -`nai_pol_mult `_ - Undocumented - -`v_e_n `_ - Undocumented - -`v_phi `_ - Undocumented - -`v_r `_ - Undocumented - -`v_theta `_ - Undocumented - -`wallis `_ - Undocumented - -`ao_pseudo_integral `_ - Pseudo-potential - -`ao_pseudo_integral_local `_ - Local pseudo-potential - -`ao_pseudo_integral_non_local `_ - Local pseudo-potential - -`mo_nucl_elec_integral `_ - interaction nuclear electron on the MO basis - -`mo_nucl_elec_integral_per_atom `_ - mo_nucl_elec_integral_per_atom(i,j,k) = - - where Rk is the geometry of the kth atom - -`mo_pseudo_integral `_ - interaction nuclear electron on the MO basis - -`save_ortho_mos `_ - Undocumented `ao_deriv_1_x `_ 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 `_ 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 `_ 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 `_ 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 `_ 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 `_ 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 `_ + array of the priminitve basis kinetic integrals + \langle \chi_i |\hat{T}| \chi_j \rangle + + +`ao_mono_elec_integral `_ + array of the mono electronic hamiltonian on the AOs basis + : sum of the kinetic and nuclear electronic potential + + +`ao_nucl_elec_integral `_ + interaction nuclear electron + + +`ao_nucl_elec_integral_per_atom `_ + ao_nucl_elec_integral_per_atom(i,j,k) = - + where Rk is the geometry of the kth atom + + +`ao_pseudo_integral `_ + Pseudo-potential + + +`ao_pseudo_integral_local `_ + Local pseudo-potential + + +`ao_pseudo_integral_non_local `_ + Local pseudo-potential + + `ao_spread_x `_ 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 `_ 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 `_ 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 `_ + +`check_ortho `_ Undocumented -`overlap_bourrin_dipole `_ + +`do_print `_ Undocumented -`overlap_bourrin_spread `_ + +`give_polynom_mult_center_mono_elec `_ Undocumented -`overlap_bourrin_x `_ + +`i_x1_pol_mult_mono_elec `_ Undocumented -`overlap_bourrin_x_abs `_ + +`i_x2_pol_mult_mono_elec `_ Undocumented -`power `_ + +`int_gaus_pol `_ Undocumented + `mo_deriv_1_x `_ 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 `_ 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 `_ 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 `_ 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 `_ 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 `_ 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 `_ + Undocumented + + +`mo_mono_elec_integral `_ + array of the mono electronic hamiltonian on the MOs basis + : sum of the kinetic and nuclear electronic potential + + +`mo_nucl_elec_integral `_ + interaction nuclear electron on the MO basis + + +`mo_nucl_elec_integral_per_atom `_ + mo_nucl_elec_integral_per_atom(i,j,k) = - + where Rk is the geometry of the kth atom + + +`mo_pseudo_integral `_ + interaction nuclear electron on the MO basis + + `mo_spread_x `_ 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 `_ 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 `_ 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 `_ + Undocumented + + +`orthonormalize_mos `_ + Undocumented + + +`overlap_bourrin_deriv_x `_ + Undocumented + + +`overlap_bourrin_dipole `_ + Undocumented + + +`overlap_bourrin_spread `_ + Undocumented + + +`overlap_bourrin_x `_ + Undocumented + + +`overlap_bourrin_x_abs `_ + Undocumented + + +`power `_ + Undocumented + + +`save_ortho_mos `_ + Undocumented + + +`v_e_n `_ + Undocumented + + +`v_phi `_ + Undocumented + + +`v_r `_ + Undocumented + + +`v_theta `_ + Undocumented + + +`wallis `_ + Undocumented diff --git a/src/MOGuess/README.rst b/src/MOGuess/README.rst index f10941cc..03ae8c15 100644 --- a/src/MOGuess/README.rst +++ b/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 `_ @@ -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. - -`h_core_guess `_ - Undocumented +.. by the `update_README.py` script. `ao_ortho_lowdin_coef `_ 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 `_ - overlap matrix of the ao_ortho_lowdin - supposed to be the Identity `ao_ortho_lowdin_nucl_elec_integral `_ Undocumented +`ao_ortho_lowdin_overlap `_ + overlap matrix of the ao_ortho_lowdin + supposed to be the Identity + + +`h_core_guess `_ + Undocumented diff --git a/src/MOs/README.rst b/src/MOs/README.rst index f84702c9..784ac176 100644 --- a/src/MOs/README.rst +++ b/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 `_ * `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 `_ + Transform A from the AO basis to the MO basis + `cholesky_mo `_ Cholesky decomposition of AO Density matrix to generate MOs -`mo_density_matrix `_ - Density matrix in MO basis - -`mo_density_matrix_virtual `_ - Density matrix in MO basis (virtual MOs) - -`mo_overlap `_ - Undocumented - -`ao_to_mo `_ - Transform A from the AO basis to the MO basis `mix_mo_jk `_ 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 `_ + Undocumented + + +`mo_as_eigvectors_of_mo_matrix_sort_by_observable `_ + Undocumented + + `mo_coef `_ 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 `_ Molecular orbital coefficients on AO basis set + +`mo_density_matrix `_ + Density matrix in MO basis + + +`mo_density_matrix_virtual `_ + Density matrix in MO basis (virtual MOs) + + `mo_label `_ 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 `_ MO occupation numbers -`mo_to_ao `_ - Transform A from the MO basis to the AO basis -`mo_to_ao_no_overlap `_ - Transform A from the MO basis to the S^-1 AO basis - -`mo_tot_num `_ - Total number of molecular orbitals and the size of the keys corresponding - -`mo_tot_num_align `_ - Aligned variable for dimensioning of arrays - -`s_mo_coef `_ - 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 `_ +`mo_overlap `_ Undocumented -`mo_as_eigvectors_of_mo_matrix_sort_by_observable `_ - Undocumented `mo_sort_by_observable `_ Undocumented + +`mo_to_ao `_ + Transform A from the MO basis to the AO basis + + +`mo_to_ao_no_overlap `_ + Transform A from the MO basis to the S^-1 AO basis + + +`mo_tot_num `_ + Total number of molecular orbitals and the size of the keys corresponding + + +`mo_tot_num_align `_ + Aligned variable for dimensioning of arrays + + +`s_mo_coef `_ + Product S.C where S is the overlap matrix in the AO basis and C the mo_coef matrix. + + `save_mos `_ Undocumented - - diff --git a/src/Nuclei/README.rst b/src/Nuclei/README.rst index 0b2ae381..e96fd490 100644 --- a/src/Nuclei/README.rst +++ b/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 `_ * `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 `_ Array of the name of element, sorted by nuclear charge (integer) + `nucl_charge `_ Nuclear charges + `nucl_coord `_ Nuclear coordinates in the format (:, {x,y,z}) + `nucl_coord_transp `_ Transposed array of nucl_coord + `nucl_dist `_ nucl_dist : Nucleus-nucleus distances nucl_dist_2 : Nucleus-nucleus distances squared nucl_dist_vec : Nucleus-nucleus distances vectors + `nucl_dist_2 `_ nucl_dist : Nucleus-nucleus distances nucl_dist_2 : Nucleus-nucleus distances squared nucl_dist_vec : Nucleus-nucleus distances vectors + `nucl_dist_vec_x `_ nucl_dist : Nucleus-nucleus distances nucl_dist_2 : Nucleus-nucleus distances squared nucl_dist_vec : Nucleus-nucleus distances vectors + `nucl_dist_vec_y `_ nucl_dist : Nucleus-nucleus distances nucl_dist_2 : Nucleus-nucleus distances squared nucl_dist_vec : Nucleus-nucleus distances vectors + `nucl_dist_vec_z `_ nucl_dist : Nucleus-nucleus distances nucl_dist_2 : Nucleus-nucleus distances squared nucl_dist_vec : Nucleus-nucleus distances vectors + `nucl_label `_ Nuclear labels + `nucl_num `_ Number of nuclei + `nucl_num_aligned `_ Number of nuclei + `nuclear_repulsion `_ Nuclear repulsion energy + `positive_charge_barycentre `_ Centroid of the positive charges - - diff --git a/src/Perturbation/README.rst b/src/Perturbation/README.rst index 74625c91..9162e94b 100644 --- a/src/Perturbation/README.rst +++ b/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 `_ - compute the standard Moller-Plesset perturbative first order coefficient and second order energetic contribution +`do_pt2_end `_ + If true, compute the PT2 at the end of the selection + + +`fill_h_apply_buffer_selection `_ + Fill the H_apply buffer with determiants for the selection + + +`max_exc_pert `_ + Undocumented + + +`perturb_buffer_by_mono_delta_rho_one_point `_ + Applly pertubration ``delta_rho_one_point`` to the buffer of determinants generated in the H_apply + routine. + + +`perturb_buffer_by_mono_dipole_moment_z `_ + Applly pertubration ``dipole_moment_z`` to the buffer of determinants generated in the H_apply + routine. + + +`perturb_buffer_by_mono_epstein_nesbet `_ + Applly pertubration ``epstein_nesbet`` to the buffer of determinants generated in the H_apply + routine. + + +`perturb_buffer_by_mono_epstein_nesbet_2x2 `_ + Applly pertubration ``epstein_nesbet_2x2`` to the buffer of determinants generated in the H_apply + routine. + + +`perturb_buffer_by_mono_epstein_nesbet_sc2 `_ + 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 `_ + 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 `_ + Applly pertubration ``epstein_nesbet_sc2_projected`` to the buffer of determinants generated in the H_apply + routine. + + +`perturb_buffer_by_mono_h_core `_ + Applly pertubration ``h_core`` to the buffer of determinants generated in the H_apply + routine. + + +`perturb_buffer_by_mono_moller_plesset `_ + Applly pertubration ``moller_plesset`` to the buffer of determinants generated in the H_apply + routine. + + +`perturb_buffer_delta_rho_one_point `_ + Applly pertubration ``delta_rho_one_point`` to the buffer of determinants generated in the H_apply + routine. + + +`perturb_buffer_dipole_moment_z `_ + Applly pertubration ``dipole_moment_z`` to the buffer of determinants generated in the H_apply + routine. + + +`perturb_buffer_epstein_nesbet `_ + Applly pertubration ``epstein_nesbet`` to the buffer of determinants generated in the H_apply + routine. + + +`perturb_buffer_epstein_nesbet_2x2 `_ + Applly pertubration ``epstein_nesbet_2x2`` to the buffer of determinants generated in the H_apply + routine. + + +`perturb_buffer_epstein_nesbet_sc2 `_ + Applly pertubration ``epstein_nesbet_sc2`` to the buffer of determinants generated in the H_apply + routine. + + +`perturb_buffer_epstein_nesbet_sc2_no_projected `_ + Applly pertubration ``epstein_nesbet_sc2_no_projected`` to the buffer of determinants generated in the H_apply + routine. + + +`perturb_buffer_epstein_nesbet_sc2_projected `_ + Applly pertubration ``epstein_nesbet_sc2_projected`` to the buffer of determinants generated in the H_apply + routine. + + +`perturb_buffer_h_core `_ + Applly pertubration ``h_core`` to the buffer of determinants generated in the H_apply + routine. + + +`perturb_buffer_moller_plesset `_ + Applly pertubration ``moller_plesset`` to the buffer of determinants generated in the H_apply + routine. + + +`pt2_delta_rho_one_point `_ + 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) = /(difference of orbital energies) + c_pert(i) = /( - ) .br - e_2_pert(i) = ^2/(difference of orbital energies) + e_2_pert(i) = c_pert(i) * .br + H_pert_diag(i) = c_pert(i)^2 * + .br + To get the contribution of the first order : + .br + = sum(over i) e_2_pert(i) + .br + To get the contribution of the diagonal elements of the second order : + .br + [ + + sum(over i) H_pert_diag(i) ] / [1. + sum(over i) c_pert(i) **2] + .br + + +`pt2_dipole_moment_z `_ + 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) = /( - ) + .br + e_2_pert(i) = c_pert(i) * + .br + H_pert_diag(i) = c_pert(i)^2 * + .br + To get the contribution of the first order : + .br + = sum(over i) e_2_pert(i) + .br + To get the contribution of the diagonal elements of the second order : + .br + [ + + sum(over i) H_pert_diag(i) ] / [1. + sum(over i) c_pert(i) **2] + .br + `pt2_epstein_nesbet `_ compute the standard Epstein-Nesbet perturbative first order coefficient and second order energetic contribution @@ -93,7 +227,8 @@ Documentation e_2_pert(i) = ^2/( E(i) - ) .br -`pt2_epstein_nesbet_2x2 `_ + +`pt2_epstein_nesbet_2x2 `_ 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)/ .br + +`pt2_epstein_nesbet_sc2 `_ + 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) = /( E(i) - ) + .br + e_2_pert(i) = ^2/( E(i) - ) + .br + + +`pt2_epstein_nesbet_sc2_no_projected `_ + 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 = ^2/(Delta_E) + .br + and also the purely projected contribution + .br + H_pert_diag = c_pert + + `pt2_epstein_nesbet_sc2_projected `_ compute the Epstein-Nesbet perturbative first order coefficient and second order energetic contribution .br @@ -126,43 +297,67 @@ Documentation .br H_pert_diag = c_pert -`repeat_all_e_corr `_ - Undocumented -`fill_h_apply_buffer_selection `_ - Fill the H_apply buffer with determiants for the selection +`pt2_h_core `_ + 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) = /( E(i) - ) + .br + e_2_pert(i) = ^2/( E(i) - ) + .br -`remove_small_contributions `_ + +`pt2_max `_ + The selection process stops when the largest PT2 (for all the state) is lower + than pt2_max in absolute value + + +`pt2_moller_plesset `_ + 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) = /(difference of orbital energies) + .br + e_2_pert(i) = ^2/(difference of orbital energies) + .br + + +`remove_small_contributions `_ Remove determinants with small contributions. N_states is assumed to be provided. -`selection_criterion `_ - Threshold to select determinants. Set by selection routines. -`selection_criterion_factor `_ - Threshold to select determinants. Set by selection routines. +`repeat_all_e_corr `_ + Undocumented -`selection_criterion_min `_ + +`selection_criterion `_ Threshold to select determinants. Set by selection routines. +`selection_criterion_factor `_ + Threshold to select determinants. Set by selection routines. + + +`selection_criterion_min `_ + Threshold to select determinants. Set by selection routines. + + +`var_pt2_ratio `_ + 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 `_ -* `BiInts `_ -* `Bitmask `_ -* `Dets `_ -* `Electrons `_ -* `Ezfio_files `_ +.. image:: tree_dependency.png + +* `Properties `_ * `Hartree_Fock `_ -* `MonoInts `_ -* `MOs `_ -* `Nuclei `_ -* `Output `_ -* `Utils `_ diff --git a/src/Properties/README.rst b/src/Properties/README.rst index 34565220..5e5ab1cc 100644 --- a/src/Properties/README.rst +++ b/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 `_ + 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 `_ + 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 `_ + average_position(1) = + average_position(2) = + average_position(3) = + + +`average_spread `_ + average_spread(1) = + average_spread(2) = + average_spread(3) = + + +`delta_z `_ + Undocumented + + +`diag_o1_mat_elem `_ + Computes + + +`diag_o1_mat_elem_alpha_beta `_ + Computes + + +`filter_connected_mono `_ + 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 `_ + 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 `_ + Returns 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 `_ + Returns 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 `_ + 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 `_ + 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 `_ + fortran unit for the writing of the integrated delta_rho + + +`integrated_delta_rho_all_points `_ + .br + integrated_rho(alpha,z) - integrated_rho(beta,z) for all the z points + chosen + .br + + +`integrated_delta_rho_one_point `_ + .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 `_ + .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 `_ + Undocumented + + +`test_average_value `_ + Undocumented + + +`test_average_value_alpha_beta `_ + Undocumented + + +`test_dm `_ + Undocumented + + +`z_max `_ + Undocumented + + +`z_min `_ + Undocumented + + +`z_one_point `_ + 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 `_ + diff --git a/src/Pseudo/README.rst b/src/Pseudo/README.rst index f52f15a7..84a555da 100644 --- a/src/Pseudo/README.rst +++ b/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 `_ Using pseudo potential integral of not diff --git a/src/Selectors_full/README.rst b/src/Selectors_full/README.rst index f9b14e33..33cbaf16 100644 --- a/src/Selectors_full/README.rst +++ b/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 `_ 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 `_ 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 `_ 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 `_ 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 `_ 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 `_ 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 `_ 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 `_ 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 `_ 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 `_ 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 `_ + For Single reference wave functions, the number of selectors is 1 : the + Hartree-Fock determinant + + `n_double_selectors `_ 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 `_ - For Single reference wave functions, the number of selectors is 1 : the - Hartree-Fock determinant `psi_selectors `_ Determinants on which we apply for perturbation. + `psi_selectors_ab `_ Determinants on which we apply . 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 `_ Determinants on which we apply for perturbation. + `psi_selectors_coef_ab `_ Determinants on which we apply . 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 `_ Diagonal elements of the H matrix for each selectors + `psi_selectors_next_ab `_ Determinants on which we apply . 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 `_ 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 `_ * `Hartree_Fock `_ diff --git a/src/Selectors_no_sorted/README.rst b/src/Selectors_no_sorted/README.rst index 79b78499..361b5845 100644 --- a/src/Selectors_no_sorted/README.rst +++ b/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 `_ + 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) = * 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 `_ + 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) = * 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 `_ + 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 `_ + 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) = * 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 `_ + 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) = * 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 `_ + 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) = * 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 `_ + 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 `_ + 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) = * 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 `_ + 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) = * 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 `_ + 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) = * 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 `_ + For Single reference wave functions, the number of selectors is 1 : the + Hartree-Fock determinant + + +`n_double_selectors `_ + 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 `_ + Determinants on which we apply for perturbation. + + +`psi_selectors_ab `_ + Determinants on which we apply . + 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 `_ + Determinants on which we apply for perturbation. + + +`psi_selectors_coef_ab `_ + Determinants on which we apply . + 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 `_ + Diagonal elements of the H matrix for each selectors + + +`psi_selectors_next_ab `_ + Determinants on which we apply . + 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 `_ + 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 `_ + diff --git a/src/SingleRefMethod/README.rst b/src/SingleRefMethod/README.rst index 837f5635..1295f24f 100644 --- a/src/SingleRefMethod/README.rst +++ b/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 `_ For Single reference wave functions, the number of generators is 1 : the Hartree-Fock determinant -`psi_generators `_ + +`psi_coef_generators `_ For Single reference wave functions, the generator is the Hartree-Fock determinant -`select_max `_ + +`psi_det_generators `_ + For Single reference wave functions, the generator is the + Hartree-Fock determinant + + +`select_max `_ Memo to skip useless selectors +`size_select_max `_ + 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 `_ * `Bitmask `_ -* `Electrons `_ -* `Ezfio_files `_ -* `MOs `_ -* `Nuclei `_ -* `Output `_ -* `Utils `_ diff --git a/src/Utils/README.rst b/src/Utils/README.rst index ebf30e97..104705a4 100644 --- a/src/Utils/README.rst +++ b/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 `_ + Undocumented + + +`abort_all `_ + If True, all the calculation is aborted + + +`abort_here `_ + If True, all the calculation is aborted + + +`add_poly `_ + Add two polynomials + D(t) =! D(t) +( B(t)+C(t)) + + +`add_poly_multiply `_ + Add a polynomial multiplied by a constant + D(t) =! D(t) +( cst * B(t)) + + +`align_double `_ + Compute 1st dimension such that it is aligned for vectorization. + `apply_rotation `_ Apply the rotation found by find_rotation + +`approx_dble `_ + Undocumented + + +`b_coef `_ + Undocumented + + +`binom `_ + Binomial coefficients + + +`binom_func `_ + .. math :: + .br + \frac{i!}{j!(i-j)!} + .br + + +`binom_transp `_ + Binomial coefficients + + +`catch_signal `_ + What to do on Ctrl-C. If two Ctrl-C are pressed within 1 sec, the calculation if aborted. + + +`dble_fact `_ + Undocumented + + +`dble_fact_even `_ + n!! + + +`dble_fact_odd `_ + n!! + + +`dble_logfact `_ + n!! + + +`ddfact2 `_ + Undocumented + + +`dset_order `_ + 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 `_ + 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 `_ + Sort array x(isize). + iorder in input should be (1,2,3,...,isize), and in output + contains the new order of the elements. + + +`erf0 `_ + Undocumented + + +`f_integral `_ + function that calculates the following integral + \int_{\-infty}^{+\infty} x^n \exp(-p x^2) dx + + +`fact `_ + n! + + +`fact_inv `_ + 1/n! + + `find_rotation `_ Find A.C = B + +`gammln `_ + Undocumented + + +`gammp `_ + Undocumented + + +`gaussian_product `_ + 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 `_ + 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 `_ + Undocumented + + `get_pseudo_inverse `_ Find C = A^-1 + +`give_explicit_poly_and_gaussian `_ + 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 `_ + 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 `_ + 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 `_ + Undocumented + + +`heap_dsort `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + Hermite polynomial + + +`i2radix_sort `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 1/i + + +`iradix_sort `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ + 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 `_ Diagonalize matrix H .br @@ -29,6 +430,7 @@ Documentation eigvectors(i,j) = where i is the basis function and psi_j is the j th eigenvector .br + `lapack_diag_s2 `_ Diagonalize matrix H .br @@ -39,6 +441,7 @@ Documentation eigvectors(i,j) = where i is the basis function and psi_j is the j th eigenvector .br + `lapack_diagd `_ Diagonalize matrix H .br @@ -49,6 +452,7 @@ Documentation eigvectors(i,j) = where i is the basis function and psi_j is the j th eigenvector .br + `lapack_partial_diag `_ Diagonalize matrix H .br @@ -59,6 +463,25 @@ Documentation eigvectors(i,j) = where i is the basis function and psi_j is the j th eigenvector .br + +`logfact `_ + n! + + +`multiply_poly `_ + Multiply two polynomials + D(t) =! D(t) +( B(t)*C(t)) + + +`normalize `_ + Normalizes vector u + u is expected to be aligned in memory. + + +`nproc `_ + Number of current OpenMP threads + + `ortho_lowdin `_ 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 `_ - Undocumented - -`abort_all `_ - If True, all the calculation is aborted - -`abort_here `_ - If True, all the calculation is aborted - -`catch_signal `_ - What to do on Ctrl-C. If two Ctrl-C are pressed within 1 sec, the calculation if aborted. - -`trap_signals `_ - What to do when a signal is caught. Here, trap Ctrl-C and call the control_C subroutine. - -`add_poly `_ - Add two polynomials - D(t) =! D(t) +( B(t)+C(t)) - -`add_poly_multiply `_ - Add a polynomial multiplied by a constant - D(t) =! D(t) +( cst * B(t)) - -`f_integral `_ - function that calculates the following integral - \int_{\-infty}^{+\infty} x^n \exp(-p x^2) dx - -`gaussian_product `_ - 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 `_ - 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 `_ - 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 `_ - 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 `_ - 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 `_ - Hermite polynomial - -`multiply_poly `_ - Multiply two polynomials - D(t) =! D(t) +( B(t)*C(t)) - -`recentered_poly2 `_ - Recenter two polynomials - -`rint `_ - .. math:: - .br - \int_0^1 dx \exp(-p x^2) x^n - .br - -`rint1 `_ - Standard version of rint - -`rint_large_n `_ - Version of rint for large values of n - -`rint_sum `_ - Needed for the calculation of two-electron integrals. - -`a_coef `_ - Undocumented - -`b_coef `_ - Undocumented - -`ddfact2 `_ - Undocumented - -`erf0 `_ - Undocumented - -`gammln `_ - Undocumented - -`gammp `_ - Undocumented - -`gcf `_ - Undocumented - -`gser `_ - Undocumented - -`rinteg `_ - Undocumented - -`rintgauss `_ - Undocumented - -`sabpartial `_ - Undocumented `overlap_a_b_c `_ Undocumented + `overlap_gaussian_x `_ .. 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 `_ .. math:: .br @@ -209,97 +518,120 @@ Documentation S = S_x S_y S_z .br + `overlap_x_abs `_ .. 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 `_ Current status for displaying progress bars. Global variable. + `progress_bar `_ Current status for displaying progress bars. Global variable. + `progress_timeout `_ Current status for displaying progress bars. Global variable. + `progress_title `_ Current status for displaying progress bars. Global variable. + `progress_value `_ Current status for displaying progress bars. Global variable. + +`recentered_poly2 `_ + Recenter two polynomials + + +`rint `_ + .. math:: + .br + \int_0^1 dx \exp(-p x^2) x^n + .br + + +`rint1 `_ + Standard version of rint + + +`rint_large_n `_ + Version of rint for large values of n + + +`rint_sum `_ + Needed for the calculation of two-electron integrals. + + +`rinteg `_ + Undocumented + + +`rintgauss `_ + Undocumented + + `run_progress `_ Display a progress bar with documentation of what is happening + +`sabpartial `_ + Undocumented + + +`set_order `_ + 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 `_ + 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 `_ + Undocumented + + +`sort `_ + 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 `_ Starts the progress bar + `stop_progress `_ Stop the progress bar -`align_double `_ - Compute 1st dimension such that it is aligned for vectorization. -`approx_dble `_ - Undocumented +`trap_signals `_ + What to do when a signal is caught. Here, trap Ctrl-C and call the control_C subroutine. -`binom `_ - Binomial coefficients - -`binom_func `_ - .. math :: - .br - \frac{i!}{j!(i-j)!} - .br - -`binom_transp `_ - Binomial coefficients - -`dble_fact `_ - Undocumented - -`dble_fact_even `_ - n!! - -`dble_fact_odd `_ - n!! - -`dble_logfact `_ - n!! - -`fact `_ - n! - -`fact_inv `_ - 1/n! - -`inv_int `_ - 1/i - -`logfact `_ - n! - -`normalize `_ - Normalizes vector u - u is expected to be aligned in memory. - -`nproc `_ - Number of current OpenMP threads `u_dot_u `_ Compute + `u_dot_v `_ Compute + `wall_time `_ The equivalent of cpu_time, but for the wall time. + `write_git_log `_ Write the last git commit in file iunit. - -