From 1c35435ea6517dab553c128fd7a4fdcc91032f35 Mon Sep 17 00:00:00 2001 From: Thomas Applencourt Date: Tue, 28 Jul 2015 17:18:45 +0200 Subject: [PATCH] Fixing doc in double --- plugins/Full_CI/README.rst | 160 ------ plugins/Generators_full/README.rst | 32 -- plugins/Hartree_Fock/README.rst | 138 ----- plugins/Perturbation/README.rst | 283 ---------- plugins/Properties/README.rst | 140 ----- plugins/Selectors_full/README.rst | 173 ------ scripts/module/qp_update_readme.py | 14 +- src/AO_Basis/README.rst | 138 ----- src/Bitmask/README.rst | 124 ---- src/Determinants/README.rst | 876 ----------------------------- src/Electrons/README.rst | 21 - src/Integrals_Bielec/README.rst | 281 --------- src/Integrals_Monoelec/README.rst | 267 --------- src/MOGuess/README.rst | 29 - src/MO_Basis/README.rst | 91 --- src/Nuclei/README.rst | 71 --- src/Pseudo/README.rst | 53 -- src/Utils/README.rst | 630 --------------------- 18 files changed, 7 insertions(+), 3514 deletions(-) diff --git a/plugins/Full_CI/README.rst b/plugins/Full_CI/README.rst index 8debefdb..913fd972 100644 --- a/plugins/Full_CI/README.rst +++ b/plugins/Full_CI/README.rst @@ -4,166 +4,6 @@ Full_CI Module Performs a perturbatively selected Full-CI. -Needed Modules -============== - -.. Do not edit this section It was auto-generated -.. by the `update_README.py` script. - -.. image:: tree_dependency.png - -* `Perturbation `_ -* `Selectors_full `_ -* `Generators_full `_ - -Documentation -============= - -.. Do not edit this section It was auto-generated -.. by the `update_README.py` script. - -`full_ci `_ - Undocumented - - -`h_apply_fci `_ - 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_fci_diexc `_ - Generate all double excitations of key_in using the bit masks of holes and - particles. - Assume N_int is already provided. - - -`h_apply_fci_mono `_ - 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_fci_mono_diexc `_ - Generate all double excitations of key_in using the bit masks of holes and - particles. - Assume N_int is already provided. - - -`h_apply_fci_mono_monoexc `_ - Generate all single excitations of key_in using the bit masks of holes and - particles. - Assume N_int is already provided. - - -`h_apply_fci_monoexc `_ - Generate all single excitations of key_in using the bit masks of holes and - particles. - Assume N_int is already provided. - - -`h_apply_fci_no_skip `_ - 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_fci_no_skip_diexc `_ - Generate all double excitations of key_in using the bit masks of holes and - particles. - Assume N_int is already provided. - - -`h_apply_fci_no_skip_monoexc `_ - Generate all single excitations of key_in using the bit masks of holes and - particles. - Assume N_int is already provided. - - -`h_apply_fci_pt2 `_ - 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_fci_pt2_diexc `_ - Generate all double excitations of key_in using the bit masks of holes and - particles. - Assume N_int is already provided. - - -`h_apply_fci_pt2_monoexc `_ - Generate all single excitations of key_in using the bit masks of holes and - particles. - Assume N_int is already provided. - - -`h_apply_pt2_mono_delta_rho `_ - Calls H_apply on the HF determinant and selects all connected single and double - excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script. - - -`h_apply_pt2_mono_delta_rho_diexc `_ - Generate all double excitations of key_in using the bit masks of holes and - particles. - Assume N_int is already provided. - - -`h_apply_pt2_mono_delta_rho_monoexc `_ - Generate all single excitations of key_in using the bit masks of holes and - particles. - Assume N_int is already provided. - - -`h_apply_pt2_mono_di_delta_rho `_ - Calls H_apply on the HF determinant and selects all connected single and double - excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script. - - -`h_apply_pt2_mono_di_delta_rho_diexc `_ - Generate all double excitations of key_in using the bit masks of holes and - particles. - Assume N_int is already provided. - - -`h_apply_pt2_mono_di_delta_rho_monoexc `_ - Generate all single excitations of key_in using the bit masks of holes and - particles. - Assume N_int is already provided. - - -`h_apply_select_mono_delta_rho `_ - 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_select_mono_delta_rho_diexc `_ - Generate all double excitations of key_in using the bit masks of holes and - particles. - Assume N_int is already provided. - - -`h_apply_select_mono_delta_rho_monoexc `_ - Generate all single excitations of key_in using the bit masks of holes and - particles. - Assume N_int is already provided. - - -`h_apply_select_mono_di_delta_rho `_ - 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_select_mono_di_delta_rho_diexc `_ - Generate all double excitations of key_in using the bit masks of holes and - particles. - Assume N_int is already provided. - - -`h_apply_select_mono_di_delta_rho_monoexc `_ - Generate all single excitations of key_in using the bit masks of holes and - particles. - Assume N_int is already provided. - - -`var_pt2_ratio_run `_ - Undocumented Needed Modules ============== diff --git a/plugins/Generators_full/README.rst b/plugins/Generators_full/README.rst index 6c5890c0..12acdabb 100644 --- a/plugins/Generators_full/README.rst +++ b/plugins/Generators_full/README.rst @@ -16,38 +16,6 @@ Needed Modules * `Determinants `_ * `Hartree_Fock `_ -Documentation -============= - -.. Do not edit this section It was auto-generated -.. 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 diff --git a/plugins/Hartree_Fock/README.rst b/plugins/Hartree_Fock/README.rst index 18c0b3ec..a1da75e1 100644 --- a/plugins/Hartree_Fock/README.rst +++ b/plugins/Hartree_Fock/README.rst @@ -15,144 +15,6 @@ Needed Modules * `Integrals_Bielec `_ * `MOGuess `_ -Documentation -============= - -.. Do not edit this section It was auto-generated -.. 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 - .br - | F-K | F + K/2 | F | - |---------------------------------| - | F + K/2 | F | F - K/2 | - |---------------------------------| - | F | F - K/2 | F + K | - .br - F = 1/2 (Fa + Fb) - .br - K = Fb - Fa - .br - - -`fock_matrix_mo `_ - Fock matrix on the MO basis. - For open shells, the ROHF Fock Matrix is - .br - | F-K | F + K/2 | F | - |---------------------------------| - | F + K/2 | F | F - K/2 | - |---------------------------------| - | F | F - K/2 | F + K | - .br - F = 1/2 (Fa + Fb) - .br - K = Fb - Fa - .br - - -`fock_mo_to_ao `_ - Undocumented - - -`guess `_ - Undocumented - - -`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 - - -`hf_energy `_ - Hartree-Fock energy - - -`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 `_ - Produce `Hartree_Fock` MO orbital - output: mo_basis.mo_tot_num mo_basis.mo_label mo_basis.ao_md5 mo_basis.mo_coef mo_basis.mo_occ - output: hartree_fock.energy - optional: mo_basis.mo_coef - - -`thresh_scf `_ - Threshold on the convergence of the Hartree Fock energy - Needed Modules ============== .. Do not edit this section It was auto-generated diff --git a/plugins/Perturbation/README.rst b/plugins/Perturbation/README.rst index a23b8fe9..e9aafe82 100644 --- a/plugins/Perturbation/README.rst +++ b/plugins/Perturbation/README.rst @@ -78,289 +78,6 @@ Needed Modules * `Properties `_ * `Hartree_Fock `_ -Documentation -============= - -.. Do not edit this section It was auto-generated -.. by the `update_README.py` script. - -`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, 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_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 - .br - for the various N_st states. - .br - c_pert(i) = /( E(i) - ) - .br - e_2_pert(i) = ^2/( E(i) - ) - .br - - -`pt2_epstein_nesbet_2x2 `_ - compute the Epstein-Nesbet 2x2 diagonalization coefficient and energetic contribution - .br - for the various N_st states. - .br - e_2_pert(i) = 0.5 * (( - E(i) ) - sqrt( ( - E(i)) ^2 + 4 ^2 ) - .br - 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 - 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_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 - - -`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. - - -`repeat_all_e_corr `_ - Undocumented - - -`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 diff --git a/plugins/Properties/README.rst b/plugins/Properties/README.rst index 7af3f5c7..0be70c6c 100644 --- a/plugins/Properties/README.rst +++ b/plugins/Properties/README.rst @@ -12,146 +12,6 @@ Needed Modules * `Determinants `_ -Documentation -============= - -.. Do not edit this section It was auto-generated -.. 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 diff --git a/plugins/Selectors_full/README.rst b/plugins/Selectors_full/README.rst index 1fe14576..e90ee6c2 100644 --- a/plugins/Selectors_full/README.rst +++ b/plugins/Selectors_full/README.rst @@ -13,179 +13,6 @@ Needed Modules * `Determinants `_ * `Hartree_Fock `_ -Documentation -============= - -.. Do not edit this section It was auto-generated -.. 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 diff --git a/scripts/module/qp_update_readme.py b/scripts/module/qp_update_readme.py index 4c681d82..eef1b699 100755 --- a/scripts/module/qp_update_readme.py +++ b/scripts/module/qp_update_readme.py @@ -37,11 +37,8 @@ D_KEY = {"needed_module": header_format("Needed Modules"), URL = "http://github.com/LCPQ/quantum_package/tree/master/src" -# d[Path] ={humain, needed_module, documentation} -d_readme = defaultdict(dict) - -def fetch_splitted_data(l_module_readme): +def fetch_splitted_data(d_readme, l_module_readme): """Read the README.rst file and split it in strings: * The documentation * The needed modules @@ -110,7 +107,7 @@ def extract_doc(root_module, provider): return "\n".join(result) + "\n" -def update_documentation(root_module, d_readme): +def update_documentation(d_readmen, root_module): """Reads the BEGIN_DOC ... END_DOC blocks and builds the documentation""" IRP_info = namedtuple('IRP_info', ["module", "file", "provider", "line"]) @@ -171,8 +168,11 @@ if __name__ == '__main__': else: l_module_readme = arguments[""] + # d[Path] ={humain, needed_module, documentation} + d_readme = defaultdict(dict) + try: - fetch_splitted_data(l_module_readme) + fetch_splitted_data(d_readme, l_module_readme) except IOError: print l_module_readme, "is not a module and/or", print "have not a `README.rst` file inside" @@ -180,7 +180,7 @@ if __name__ == '__main__': sys.exit(1) update_needed(d_readme) - update_documentation(root_module, d_readme) + update_documentation(d_readme, root_module) for path, d in d_readme.iteritems(): diff --git a/src/AO_Basis/README.rst b/src/AO_Basis/README.rst index 6a8d0add..e0a487fe 100644 --- a/src/AO_Basis/README.rst +++ b/src/AO_Basis/README.rst @@ -40,144 +40,6 @@ Needed Modules * `Nuclei `_ -Documentation -============= - -.. Do not edit this section It was auto-generated -.. 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 `_ - expo for each primitive of each ao_basis - - -`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 ao - - -`ao_num_align `_ - Number of atomic orbitals align - - -`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 `_ - power for each dimension for each ao_basis - - -`ao_prim_num `_ - Number of primitives per atomic orbital - - -`ao_prim_num_max `_ - Undocumented - - -`ao_prim_num_max_align `_ - Number of primitives per atomic orbital aligned - - -`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 - Needed Modules ============== .. Do not edit this section It was auto-generated diff --git a/src/Bitmask/README.rst b/src/Bitmask/README.rst index bf041e66..6f3696b4 100644 --- a/src/Bitmask/README.rst +++ b/src/Bitmask/README.rst @@ -44,130 +44,6 @@ Needed Modules * `MO_Basis `_ -Documentation -============= - -.. Do not edit this section It was auto-generated -.. by the `update_README.py` script. - -`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 - - -`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). - .br - 3rd index is : - .br - * 1 : hole for single exc - .br - * 2 : particle for single exc - .br - * 3 : hole for 1st exc of double - .br - * 4 : particle for 1st exc of double - .br - * 5 : hole for 2nd exc of double - .br - * 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 - - -`is_a_two_holes_two_particles `_ - Undocumented - - -`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 - Needed Modules ============== .. Do not edit this section It was auto-generated diff --git a/src/Determinants/README.rst b/src/Determinants/README.rst index ac97074c..1c114a19 100644 --- a/src/Determinants/README.rst +++ b/src/Determinants/README.rst @@ -37,882 +37,6 @@ Needed Modules * `Integrals_Monoelec `_ * `Integrals_Bielec `_ -Documentation -============= - -.. Do not edit this section It was auto-generated -.. by the `update_README.py` script. - -`a_operator `_ - Needed for diag_H_mat_elem - - -`abs_psi_coef_max `_ - Max and min values of the coefficients - - -`abs_psi_coef_min `_ - Max and min values of the coefficients - - -`ac_operator `_ - Needed for diag_H_mat_elem - - -`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 - - -`cisd_sc2 `_ - CISD+SC2 method :: take off all the disconnected terms of a CISD (selected or not) - .br - dets_in : bitmasks corresponding to determinants - .br - u_in : guess coefficients on the various states. Overwritten - on exit - .br - dim_in : leftmost dimension of u_in - .br - sze : Number of determinants - .br - N_st : Number of eigenstates - .br - Initial guess vectors are not necessarily orthonormal - - -`connected_to_ref `_ - Undocumented - - -`connected_to_ref_by_mono `_ - Undocumented - - -`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 - - -`create_wf_of_psi_svd_matrix `_ - Matrix of wf coefficients. Outer product of alpha and beta determinants - - -`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 - dets_in : bitmasks corresponding to determinants - .br - u_in : guess coefficients on the various states. Overwritten - on exit - .br - dim_in : leftmost dimension of u_in - .br - sze : Number of determinants - .br - N_st : Number of eigenstates - .br - iunit : Unit number for the I/O - .br - Initial guess vectors are not necessarily orthonormal - - -`davidson_diag_hjj `_ - Davidson diagonalization with specific diagonal elements of the H matrix - .br - H_jj : specific diagonal H matrix elements to diagonalize de Davidson - .br - dets_in : bitmasks corresponding to determinants - .br - u_in : guess coefficients on the various states. Overwritten - on exit - .br - dim_in : leftmost dimension of u_in - .br - sze : Number of determinants - .br - N_st : Number of eigenstates - .br - iunit : Unit for the I/O - .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 ] - - -`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_coef `_ - det_coef - - -`det_connections `_ - Build connection proxy between determinants - - -`det_num `_ - det_num - - -`det_occ `_ - det_occ - - -`det_search_key `_ - Return an integer*8 corresponding to a determinant index for searching - - -`det_svd `_ - Computes the SVD of the Alpha x Beta determinant coefficient matrix - - -`det_to_occ_pattern `_ - Transform a determinant to an occupation pattern - - -`diag_algorithm `_ - Diagonalization algorithm (Davidson or Lapack) - - -`diag_h_mat_elem `_ - Computes - - -`diagonalize_ci `_ - Replace the coefficients of the CI states by the coefficients of the - eigenstates of the CI matrix - - -`diagonalize_ci_mono `_ - Replace the coefficients of the CI states by the coefficients of the - eigenstates 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 - - -`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 - - -`double_exc_bitmask `_ - double_exc_bitmask(:,1,i) is the bitmask for holes of excitation 1 - double_exc_bitmask(:,2,i) is the bitmask for particles of excitation 1 - double_exc_bitmask(:,3,i) is the bitmask for holes of excitation 2 - double_exc_bitmask(:,4,i) is the bitmask for particles of excitation 2 - for a given couple of hole/particle excitations i. - - -`expected_s2 `_ - Expected value of S2 : S*(S+1) - - -`fill_h_apply_buffer_no_selection `_ - Fill the H_apply buffer with determiants for CISD - - -`filter_3_highest_electrons `_ - Returns a determinant with only the 3 highest electrons - - -`filter_connected `_ - Filters out the determinants that are not connected by H - .br - returns the array idx which contains the index of the - .br - determinants in the array key1 that interact - .br - via the H operator with key2. - .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 - determinants in the array key1 that interact - via the H operator with key2. - .br - 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 - determinants in the array key1 that interact - .br - via the H operator with key2. - .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 - the array of the index of the non connected determinants to key1 - .br - in order to know what double excitation can be repeated on key1 - .br - idx_repeat(0) is the number of determinants that can be used - .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 - determinants in the array key1 that interact - via the H operator with key2. - idx(0) is the number of determinants that interact with key1 - .br - Determinants are taken from the psi_det_sorted_ab array - - -`generate_all_alpha_beta_det_products `_ - Create a wave function from all possible alpha x beta determinants - - -`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 - - -`get_s2_u0_old `_ - 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_matrix_cas `_ - Undocumented - - -`h_u_0 `_ - Computes v_0 = H|u_0> - .br - n : number of determinants - .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 - returns in addition - .br - the array of the index of the non connected determinants to key1 - .br - in order to know what double excitation can be repeated on key1 - .br - idx_repeat(0) is the number of determinants that can be used - .br - to repeat the excitations - - -`i_h_psi_sc2_verbose `_ - for the various Nstate - .br - returns in addition - .br - the array of the index of the non connected determinants to key1 - .br - in order to know what double excitation can be repeated on key1 - .br - idx_repeat(0) is the number of determinants that can be used - .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 - - -`n_det `_ - Number of determinants in the wave function - - -`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 - - -`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_energy `_ - Undocumented - - -`psi_cas_energy_diagonalized `_ - Undocumented - - -`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_cas_diagonalized `_ - Undocumented - - -`psi_coef_max `_ - Max and min values of the coefficients - - -`psi_coef_min `_ - Max and min values of the coefficients - - -`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_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 - Needed Modules ============== .. Do not edit this section It was auto-generated diff --git a/src/Electrons/README.rst b/src/Electrons/README.rst index 2bc9f70d..d1c342b5 100644 --- a/src/Electrons/README.rst +++ b/src/Electrons/README.rst @@ -28,27 +28,6 @@ Needed Modules * `Ezfio_files `_ -Documentation -============= - -.. Do not edit this section It was auto-generated -.. by the `update_README.py` script. - -`elec_alpha_num `_ - Numbers of electrons alpha ("up") - - -`elec_beta_num `_ - Numbers of electrons beta ("down") - - -`elec_num `_ - Numbers of alpha ("up") , beta ("down") and total electrons - - -`elec_num_tab `_ - Numbers of alpha ("up") , beta ("down") and total electrons - Needed Modules ============== .. Do not edit this section It was auto-generated diff --git a/src/Integrals_Bielec/README.rst b/src/Integrals_Bielec/README.rst index 054a6720..b71d9c0d 100644 --- a/src/Integrals_Bielec/README.rst +++ b/src/Integrals_Bielec/README.rst @@ -21,287 +21,6 @@ Needed Modules * `Pseudo `_ * `Bitmask `_ -Documentation -============= - -.. Do not edit this section It was auto-generated -.. 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) - primitive_2 = x1**(b_x) y1**(b_y) z1**(b_z) exp(- beta * r1**2) - 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) - - -`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) - - -`general_primitive_integral `_ - Computes the integral where p,q,r,s are Gaussian primitives - - -`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_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 - Needed Modules ============== .. Do not edit this section It was auto-generated diff --git a/src/Integrals_Monoelec/README.rst b/src/Integrals_Monoelec/README.rst index dbdd753b..13aceb0e 100644 --- a/src/Integrals_Monoelec/README.rst +++ b/src/Integrals_Monoelec/README.rst @@ -9,273 +9,6 @@ Needed Modules * `MO_Basis `_ * `Pseudo `_ -Documentation -============= - -.. Do not edit this section It was auto-generated -.. by the `update_README.py` script. - -`ao_deriv2_x `_ - 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_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_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 - - -`check_ortho `_ - Undocumented - - -`do_print `_ - Undocumented - - -`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 - - -`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 - Needed Modules ============== .. Do not edit this section It was auto-generated diff --git a/src/MOGuess/README.rst b/src/MOGuess/README.rst index a2d58aec..86f352a9 100644 --- a/src/MOGuess/README.rst +++ b/src/MOGuess/README.rst @@ -12,35 +12,6 @@ Needed Modules * `Integrals_Monoelec `_ -Documentation -============= - -.. Do not edit this section It was auto-generated -.. 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_nucl_elec_integral `_ - Undocumented - - -`ao_ortho_lowdin_overlap `_ - overlap matrix of the ao_ortho_lowdin - supposed to be the Identity - - -`h_core_guess `_ - Produce `H_core` MO orbital - output: mo_basis.mo_tot_num mo_basis.mo_label mo_basis.ao_md5 mo_basis.mo_coef mo_basis.mo_occ - - -`hcore_guess `_ - Produce `H_core` MO orbital - Needed Modules ============== .. Do not edit this section It was auto-generated diff --git a/src/MO_Basis/README.rst b/src/MO_Basis/README.rst index 361ef96f..87df08b1 100644 --- a/src/MO_Basis/README.rst +++ b/src/MO_Basis/README.rst @@ -41,97 +41,6 @@ Needed Modules * `AO_Basis `_ * `Electrons `_ -Documentation -============= - -.. Do not edit this section It was auto-generated -.. 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 - - -`mix_mo_jk `_ - subroutine that rotates the jth MO with the kth MO - to give two new MO's that are - '+' = 1/sqrt(2) (|j> + |k>) - '-' = 1/sqrt(2) (|j> - |k>) - 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_overlap `_ - 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 - Needed Modules ============== .. Do not edit this section It was auto-generated diff --git a/src/Nuclei/README.rst b/src/Nuclei/README.rst index 032c9963..bf7e6f52 100644 --- a/src/Nuclei/README.rst +++ b/src/Nuclei/README.rst @@ -17,77 +17,6 @@ Needed Modules * `Ezfio_files `_ * `Utils `_ -Documentation -============= - -.. Do not edit this section It was auto-generated -.. 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 algined - - -`nuclear_repulsion `_ - Nuclear repulsion energy - - -`positive_charge_barycentre `_ - Centroid of the positive charges - Needed Modules ============== .. Do not edit this section It was auto-generated diff --git a/src/Pseudo/README.rst b/src/Pseudo/README.rst index 60023235..062a9465 100644 --- a/src/Pseudo/README.rst +++ b/src/Pseudo/README.rst @@ -12,59 +12,6 @@ Needed Modules * `Nuclei `_ -Documentation -============= - -.. Do not edit this section It was auto-generated -.. by the `update_README.py` script. - -`do_pseudo `_ - Using pseudo potential integral of not - - -`pseudo_dz_k `_ - test - - -`pseudo_dz_kl `_ - test - - -`pseudo_grid_rmax `_ - R_maxof the QMC grid - - -`pseudo_grid_size `_ - Nb of points of the QMC grid - - -`pseudo_klocmax `_ - test - - -`pseudo_kmax `_ - test - - -`pseudo_lmax `_ - test - - -`pseudo_n_k `_ - test - - -`pseudo_n_kl `_ - test - - -`pseudo_v_k `_ - test - - -`pseudo_v_kl `_ - test - Needed Modules ============== .. Do not edit this section It was auto-generated diff --git a/src/Utils/README.rst b/src/Utils/README.rst index 5c271c93..e3c36e71 100644 --- a/src/Utils/README.rst +++ b/src/Utils/README.rst @@ -4,636 +4,6 @@ Utils Module Contains general purpose utilities. -Documentation -============= - -.. Do not edit this section It was auto-generated -.. 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 - H is untouched between input and ouptut - .br - eigevalues(i) = ith lowest eigenvalue of the H matrix - .br - 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 - H is untouched between input and ouptut - .br - eigevalues(i) = ith lowest eigenvalue of the H matrix - .br - eigvectors(i,j) = where i is the basis function and psi_j is the j th eigenvector - .br - - -`lapack_diagd `_ - Diagonalize matrix H - .br - H is untouched between input and ouptut - .br - eigevalues(i) = ith lowest eigenvalue of the H matrix - .br - 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 - H is untouched between input and ouptut - .br - eigevalues(i) = ith lowest eigenvalue of the H matrix - .br - 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 - overlap : overlap matrix - .br - LDA : leftmost dimension of overlap array - .br - N : Overlap matrix is NxN (array is (LDA,N) ) - .br - C : Coefficients of the vectors to orthogonalize. On exit, - orthogonal vectors - .br - LDC : leftmost dimension of C - .br - m : Coefficients matrix is MxN, ( array is (LDC,N) ) - .br - - -`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 - S_x = \int (x-A_x)^{a_x} exp(-\alpha(x-A_x)^2) (x-B_x)^{b_x} exp(-beta(x-B_x)^2) dx \\ - 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 - - -`trap_signals `_ - What to do when a signal is caught. Here, trap Ctrl-C and call the control_C subroutine. - - -`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. - Documentation ============= .. Do not edit this section It was auto-generated