From 006c28f4ee65798746ddd88f1d8fc9778acb3b7e Mon Sep 17 00:00:00 2001 From: Thomas Applencourt Date: Tue, 28 Jul 2015 17:31:54 +0200 Subject: [PATCH] Fix error in doc path --- plugins/Full_CI/README.rst | 58 +++++++++++----------- plugins/Generators_full/README.rst | 14 +++--- plugins/Hartree_Fock/README.rst | 52 ++++++++++---------- plugins/Perturbation/README.rst | 78 +++++++++++++++--------------- plugins/Properties/README.rst | 48 +++++++++--------- plugins/Selectors_full/README.rst | 40 +++++++-------- scripts/module/module_handler.py | 12 +++-- scripts/module/qp_update_readme.py | 19 ++++++-- 8 files changed, 169 insertions(+), 152 deletions(-) diff --git a/plugins/Full_CI/README.rst b/plugins/Full_CI/README.rst index 913fd972..1af26ae6 100644 --- a/plugins/Full_CI/README.rst +++ b/plugins/Full_CI/README.rst @@ -13,9 +13,9 @@ Needed Modules .. image:: tree_dependency.png -* `Perturbation `_ -* `Selectors_full `_ -* `Generators_full `_ +* `Perturbation `_ +* `Selectors_full `_ +* `Generators_full `_ Documentation ============= @@ -23,146 +23,146 @@ Documentation .. by the `update_README.py` script. -`full_ci `_ +`full_ci `_ Undocumented -`h_apply_fci `_ +`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 `_ +`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 `_ +`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 `_ +`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 `_ +`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 `_ +`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 `_ +`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 `_ +`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 `_ +`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 `_ +`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 `_ +`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 `_ +`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 `_ +`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 `_ +`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 `_ +`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 `_ +`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 `_ +`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 `_ +`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 `_ +`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 `_ +`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 `_ +`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 `_ +`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 `_ +`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 `_ +`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 `_ +`var_pt2_ratio_run `_ Undocumented diff --git a/plugins/Generators_full/README.rst b/plugins/Generators_full/README.rst index 12acdabb..c30193a2 100644 --- a/plugins/Generators_full/README.rst +++ b/plugins/Generators_full/README.rst @@ -25,7 +25,7 @@ Needed Modules .. image:: tree_dependency.png * `Determinants `_ -* `Hartree_Fock `_ +* `Hartree_Fock `_ Documentation ============= @@ -33,29 +33,29 @@ Documentation .. by the `update_README.py` script. -`degree_max_generators `_ +`degree_max_generators `_ Max degree of excitation (respect to HF) of the generators -`n_det_generators `_ +`n_det_generators `_ For Single reference wave functions, the number of generators is 1 : the Hartree-Fock determinant -`psi_coef_generators `_ +`psi_coef_generators `_ For Single reference wave functions, the generator is the Hartree-Fock determinant -`psi_det_generators `_ +`psi_det_generators `_ For Single reference wave functions, the generator is the Hartree-Fock determinant -`select_max `_ +`select_max `_ Memo to skip useless selectors -`size_select_max `_ +`size_select_max `_ Size of the select_max array diff --git a/plugins/Hartree_Fock/README.rst b/plugins/Hartree_Fock/README.rst index a1da75e1..345285ec 100644 --- a/plugins/Hartree_Fock/README.rst +++ b/plugins/Hartree_Fock/README.rst @@ -32,57 +32,57 @@ Documentation .. by the `update_README.py` script. -`ao_bi_elec_integral_alpha `_ +`ao_bi_elec_integral_alpha `_ Alpha Fock matrix in AO basis set -`ao_bi_elec_integral_beta `_ +`ao_bi_elec_integral_beta `_ Alpha Fock matrix in AO basis set -`create_guess `_ +`create_guess `_ Create an MO guess if no MOs are present in the EZFIO directory -`damping_scf `_ +`damping_scf `_ Undocumented -`diagonal_fock_matrix_mo `_ +`diagonal_fock_matrix_mo `_ Diagonal Fock matrix in the MO basis -`diagonal_fock_matrix_mo_sum `_ +`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 `_ +`eigenvectors_fock_matrix_mo `_ Diagonal Fock matrix in the MO basis -`fock_matrix_alpha_ao `_ +`fock_matrix_alpha_ao `_ Alpha Fock matrix in AO basis set -`fock_matrix_alpha_mo `_ +`fock_matrix_alpha_mo `_ Fock matrix on the MO basis -`fock_matrix_ao `_ +`fock_matrix_ao `_ Fock matrix in AO basis set -`fock_matrix_beta_ao `_ +`fock_matrix_beta_ao `_ Alpha Fock matrix in AO basis set -`fock_matrix_beta_mo `_ +`fock_matrix_beta_mo `_ Fock matrix on the MO basis -`fock_matrix_diag_mo `_ +`fock_matrix_diag_mo `_ Fock matrix on the MO basis. For open shells, the ROHF Fock Matrix is .br @@ -98,7 +98,7 @@ Documentation .br -`fock_matrix_mo `_ +`fock_matrix_mo `_ Fock matrix on the MO basis. For open shells, the ROHF Fock Matrix is .br @@ -114,53 +114,53 @@ Documentation .br -`fock_mo_to_ao `_ +`fock_mo_to_ao `_ Undocumented -`guess `_ +`guess `_ Undocumented -`hf_density_matrix_ao `_ +`hf_density_matrix_ao `_ S^-1 Density matrix in the AO basis S^-1 -`hf_density_matrix_ao_alpha `_ +`hf_density_matrix_ao_alpha `_ S^-1 x Alpha density matrix in the AO basis x S^-1 -`hf_density_matrix_ao_beta `_ +`hf_density_matrix_ao_beta `_ S^-1 Beta density matrix in the AO basis x S^-1 -`hf_energy `_ +`hf_energy `_ Hartree-Fock energy -`huckel_guess `_ +`huckel_guess `_ Build the MOs using the extended Huckel model -`mo_guess_type `_ +`mo_guess_type `_ Initial MO guess. Can be [ Huckel | HCore ] -`n_it_scf_max `_ +`n_it_scf_max `_ Maximum number of SCF iterations -`run `_ +`run `_ Run SCF calculation -`scf `_ +`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 `_ +`thresh_scf `_ Threshold on the convergence of the Hartree Fock energy diff --git a/plugins/Perturbation/README.rst b/plugins/Perturbation/README.rst index e9aafe82..3f77b2a2 100644 --- a/plugins/Perturbation/README.rst +++ b/plugins/Perturbation/README.rst @@ -86,8 +86,8 @@ Needed Modules .. image:: tree_dependency.png -* `Properties `_ -* `Hartree_Fock `_ +* `Properties `_ +* `Hartree_Fock `_ Documentation ============= @@ -95,109 +95,109 @@ Documentation .. by the `update_README.py` script. -`do_pt2_end `_ +`do_pt2_end `_ If true, compute the PT2 at the end of the selection -`fill_h_apply_buffer_selection `_ +`fill_h_apply_buffer_selection `_ Fill the H_apply buffer with determiants for the selection -`max_exc_pert `_ +`max_exc_pert `_ Undocumented -`perturb_buffer_by_mono_delta_rho_one_point `_ +`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 `_ +`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 `_ +`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 `_ +`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 `_ +`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 `_ +`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 `_ +`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 `_ +`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 `_ +`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 `_ +`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 `_ +`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 `_ +`perturb_buffer_epstein_nesbet `_ Applly pertubration ``epstein_nesbet`` to the buffer of determinants generated in the H_apply routine. -`perturb_buffer_epstein_nesbet_2x2 `_ +`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 `_ +`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 `_ +`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 `_ +`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 `_ +`perturb_buffer_h_core `_ Applly pertubration ``h_core`` to the buffer of determinants generated in the H_apply routine. -`perturb_buffer_moller_plesset `_ +`perturb_buffer_moller_plesset `_ Applly pertubration ``moller_plesset`` to the buffer of determinants generated in the H_apply routine. -`pt2_delta_rho_one_point `_ +`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. @@ -218,7 +218,7 @@ Documentation .br -`pt2_dipole_moment_z `_ +`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. @@ -239,7 +239,7 @@ Documentation .br -`pt2_epstein_nesbet `_ +`pt2_epstein_nesbet `_ compute the standard Epstein-Nesbet perturbative first order coefficient and second order energetic contribution .br for the various N_st states. @@ -250,7 +250,7 @@ Documentation .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. @@ -261,7 +261,7 @@ Documentation .br -`pt2_epstein_nesbet_sc2 `_ +`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 @@ -272,7 +272,7 @@ Documentation .br -`pt2_epstein_nesbet_sc2_no_projected `_ +`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, @@ -296,7 +296,7 @@ Documentation H_pert_diag = c_pert -`pt2_epstein_nesbet_sc2_projected `_ +`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, @@ -320,7 +320,7 @@ Documentation H_pert_diag = c_pert -`pt2_h_core `_ +`pt2_h_core `_ compute the standard Epstein-Nesbet perturbative first order coefficient and second order energetic contribution .br for the various N_st states. @@ -331,12 +331,12 @@ Documentation .br -`pt2_max `_ +`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 `_ +`pt2_moller_plesset `_ compute the standard Moller-Plesset perturbative first order coefficient and second order energetic contribution .br for the various n_st states. @@ -347,28 +347,28 @@ Documentation .br -`remove_small_contributions `_ +`remove_small_contributions `_ Remove determinants with small contributions. N_states is assumed to be provided. -`repeat_all_e_corr `_ +`repeat_all_e_corr `_ Undocumented -`selection_criterion `_ +`selection_criterion `_ Threshold to select determinants. Set by selection routines. -`selection_criterion_factor `_ +`selection_criterion_factor `_ Threshold to select determinants. Set by selection routines. -`selection_criterion_min `_ +`selection_criterion_min `_ Threshold to select determinants. Set by selection routines. -`var_pt2_ratio `_ +`var_pt2_ratio `_ The selection process stops when the energy ratio variational/(variational+PT2) is equal to var_pt2_ratio diff --git a/plugins/Properties/README.rst b/plugins/Properties/README.rst index 0be70c6c..cd92ba14 100644 --- a/plugins/Properties/README.rst +++ b/plugins/Properties/README.rst @@ -28,41 +28,41 @@ Documentation .. by the `update_README.py` script. -`ao_integrated_delta_rho_all_points `_ +`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 `_ +`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 `_ average_position(1) = average_position(2) = average_position(3) = -`average_spread `_ +`average_spread `_ average_spread(1) = average_spread(2) = average_spread(3) = -`delta_z `_ +`delta_z `_ Undocumented -`diag_o1_mat_elem `_ +`diag_o1_mat_elem `_ Computes -`diag_o1_mat_elem_alpha_beta `_ +`diag_o1_mat_elem_alpha_beta `_ Computes -`filter_connected_mono `_ +`filter_connected_mono `_ Filters out the determinants that are not connected through PURE .br MONO EXCITATIONS OPERATORS (a^{\dagger}j a_i) @@ -76,89 +76,89 @@ Documentation idx(0) is the number of determinants that interact with key1 -`get_average `_ +`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 `_ +`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 `_ +`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 `_ +`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 `_ +`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 `_ +`i_unit_integrated_delta_rho `_ fortran unit for the writing of the integrated delta_rho -`integrated_delta_rho_all_points `_ +`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 `_ +`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 `_ +`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 `_ +`n_z_pts `_ Undocumented -`test_average_value `_ +`test_average_value `_ Undocumented -`test_average_value_alpha_beta `_ +`test_average_value_alpha_beta `_ Undocumented -`test_dm `_ +`test_dm `_ Undocumented -`z_max `_ +`z_max `_ Undocumented -`z_min `_ +`z_min `_ Undocumented -`z_one_point `_ +`z_one_point `_ z point on which the integrated delta rho is calculated diff --git a/plugins/Selectors_full/README.rst b/plugins/Selectors_full/README.rst index e90ee6c2..795234b4 100644 --- a/plugins/Selectors_full/README.rst +++ b/plugins/Selectors_full/README.rst @@ -22,7 +22,7 @@ Needed Modules .. image:: tree_dependency.png * `Determinants `_ -* `Hartree_Fock `_ +* `Hartree_Fock `_ Documentation ============= @@ -30,7 +30,7 @@ Documentation .. by the `update_README.py` script. -`coef_hf_selector `_ +`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 @@ -42,7 +42,7 @@ Documentation coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants -`delta_e_per_selector `_ +`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 @@ -54,7 +54,7 @@ Documentation coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants -`double_index_selectors `_ +`double_index_selectors `_ degree of excitation respect to Hartree Fock for the wave function .br for the all the selectors determinants @@ -64,7 +64,7 @@ Documentation n_double_selectors = number of double excitations in the selectors determinants -`e_corr_double_only `_ +`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 @@ -76,7 +76,7 @@ Documentation coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants -`e_corr_per_selectors `_ +`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 @@ -88,7 +88,7 @@ Documentation coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants -`e_corr_second_order `_ +`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 @@ -100,7 +100,7 @@ Documentation coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants -`exc_degree_per_selectors `_ +`exc_degree_per_selectors `_ degree of excitation respect to Hartree Fock for the wave function .br for the all the selectors determinants @@ -110,7 +110,7 @@ Documentation n_double_selectors = number of double excitations in the selectors determinants -`i_h_hf_per_selectors `_ +`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 @@ -122,7 +122,7 @@ Documentation coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants -`inv_selectors_coef_hf `_ +`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 @@ -134,7 +134,7 @@ Documentation coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants -`inv_selectors_coef_hf_squared `_ +`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 @@ -146,12 +146,12 @@ Documentation coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants -`n_det_selectors `_ +`n_det_selectors `_ For Single reference wave functions, the number of selectors is 1 : the Hartree-Fock determinant -`n_double_selectors `_ +`n_double_selectors `_ degree of excitation respect to Hartree Fock for the wave function .br for the all the selectors determinants @@ -161,39 +161,39 @@ Documentation n_double_selectors = number of double excitations in the selectors determinants -`psi_selectors `_ +`psi_selectors `_ Determinants on which we apply for perturbation. -`psi_selectors_ab `_ +`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 `_ +`psi_selectors_coef `_ Determinants on which we apply for perturbation. -`psi_selectors_coef_ab `_ +`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 `_ +`psi_selectors_diag_h_mat `_ Diagonal elements of the H matrix for each selectors -`psi_selectors_next_ab `_ +`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 `_ +`psi_selectors_size `_ Undocumented diff --git a/scripts/module/module_handler.py b/scripts/module/module_handler.py index 08a0b297..1e3546df 100755 --- a/scripts/module/module_handler.py +++ b/scripts/module/module_handler.py @@ -23,15 +23,19 @@ import shutil try: from docopt import docopt - from qp_path import QP_SRC - from qp_path import QP_ROOT + from qp_path import QP_SRC, QP_ROOT, QP_PLUGINS except ImportError: print "source .quantum_package.rc" raise -def is_module(path_module): - return os.path.isfile(os.path.join(QP_SRC, path_module, +def is_module(path_module_rel): + return os.path.isfile(os.path.join(QP_SRC, path_module_rel, + "NEEDED_CHILDREN_MODULES")) + + +def is_plugin(path_module_rel): + return os.path.isfile(os.path.join(QP_PLUGINS, path_module_rel, "NEEDED_CHILDREN_MODULES")) diff --git a/scripts/module/qp_update_readme.py b/scripts/module/qp_update_readme.py index eef1b699..9ff9603b 100755 --- a/scripts/module/qp_update_readme.py +++ b/scripts/module/qp_update_readme.py @@ -16,6 +16,7 @@ import sys try: from docopt import docopt + from module_handler import is_module, is_plugin except: print "Please check if you have sourced the .quantum_package.rc" print "(`source .quantum_package.rc`)" @@ -25,6 +26,7 @@ import os from collections import namedtuple from collections import defaultdict + def header_format(str_): warning = "\n".join([".. Do not edit this section It was auto-generated", @@ -35,7 +37,17 @@ def header_format(str_): D_KEY = {"needed_module": header_format("Needed Modules"), "documentation": header_format("Documentation")} -URL = "http://github.com/LCPQ/quantum_package/tree/master/src" + +def get_url(path_module_rel): + if is_plugin(path_module_rel): + url = "http://github.com/LCPQ/quantum_package/tree/master/plugins" + elif is_module(path_module_rel): + url = "http://github.com/LCPQ/quantum_package/tree/master/src" + else: + print "{0} Is not a valide module nor plugin".format(path_module_rel) + sys.exit(1) + + return os.path.join(url, path_module_rel) def fetch_splitted_data(d_readme, l_module_readme): @@ -72,7 +84,7 @@ def update_needed(d_readme): modules = f.read() if modules.strip(): - l_module = ['* `{0} <{1}>`_'.format(name, os.path.join(URL, name)) + l_module = ['* `{0} <{1}>`_'.format(name, get_url(name)) for name in modules.split()] l_module_section = [D_KEY["needed_module"], '', @@ -143,7 +155,8 @@ def update_documentation(d_readmen, root_module): l_doc = [] for irp in d_info[path]: - url = os.path.join(URL, os.path.basename(path), irp.file) + + url = os.path.join(get_url(os.path.basename(path)), irp.file) doc = extract_doc(root_module, irp.provider) l_doc += ["`{0} <{1}#L{2}>`_".format(irp.provider, url, irp.line),