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Code Issues Releases Wiki Activity

Fix error in doc path

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Thomas Applencourt 2015-07-28 17:31:54 +02:00
parent 1c35435ea6
commit 006c28f4ee
8 changed files with 169 additions and 152 deletions
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58
plugins/Full_CI/README.rst
View File

@ -13,9 +13,9 @@ Needed Modules
.. image:: tree_dependency.png .. image:: tree_dependency.png
* `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_ * `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation>`_
* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_ * `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/plugins/Selectors_full>`_
* `Generators_full <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full>`_ * `Generators_full <http://github.com/LCPQ/quantum_package/tree/master/plugins/Generators_full>`_
Documentation Documentation
============= =============
@ -23,146 +23,146 @@ Documentation
.. by the `update_README.py` script. .. by the `update_README.py` script.
`full_ci <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/full_ci_no_skip.irp.f#L1>`_ `full_ci <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/full_ci_no_skip.irp.f#L1>`_
Undocumented Undocumented
`h_apply_fci <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L521>`_ `h_apply_fci <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L521>`_
Calls H_apply on the HF determinant and selects all connected single and double 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. excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
`h_apply_fci_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L1>`_ `h_apply_fci_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L1>`_
Generate all double excitations of key_in using the bit masks of holes and Generate all double excitations of key_in using the bit masks of holes and
particles. particles.
Assume N_int is already provided. Assume N_int is already provided.
`h_apply_fci_mono <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L2720>`_ `h_apply_fci_mono <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L2720>`_
Calls H_apply on the HF determinant and selects all connected single and double 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. excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
`h_apply_fci_mono_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L2198>`_ `h_apply_fci_mono_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L2198>`_
Generate all double excitations of key_in using the bit masks of holes and Generate all double excitations of key_in using the bit masks of holes and
particles. particles.
Assume N_int is already provided. Assume N_int is already provided.
`h_apply_fci_mono_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L2522>`_ `h_apply_fci_mono_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L2522>`_
Generate all single excitations of key_in using the bit masks of holes and Generate all single excitations of key_in using the bit masks of holes and
particles. particles.
Assume N_int is already provided. Assume N_int is already provided.
`h_apply_fci_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L325>`_ `h_apply_fci_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L325>`_
Generate all single excitations of key_in using the bit masks of holes and Generate all single excitations of key_in using the bit masks of holes and
particles. particles.
Assume N_int is already provided. Assume N_int is already provided.
`h_apply_fci_no_skip <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L1980>`_ `h_apply_fci_no_skip <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L1980>`_
Calls H_apply on the HF determinant and selects all connected single and double 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. excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
`h_apply_fci_no_skip_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L1460>`_ `h_apply_fci_no_skip_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L1460>`_
Generate all double excitations of key_in using the bit masks of holes and Generate all double excitations of key_in using the bit masks of holes and
particles. particles.
Assume N_int is already provided. Assume N_int is already provided.
`h_apply_fci_no_skip_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L1784>`_ `h_apply_fci_no_skip_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L1784>`_
Generate all single excitations of key_in using the bit masks of holes and Generate all single excitations of key_in using the bit masks of holes and
particles. particles.
Assume N_int is already provided. Assume N_int is already provided.
`h_apply_fci_pt2 <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L1253>`_ `h_apply_fci_pt2 <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L1253>`_
Calls H_apply on the HF determinant and selects all connected single and double 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. excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
`h_apply_fci_pt2_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L767>`_ `h_apply_fci_pt2_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L767>`_
Generate all double excitations of key_in using the bit masks of holes and Generate all double excitations of key_in using the bit masks of holes and
particles. particles.
Assume N_int is already provided. Assume N_int is already provided.
`h_apply_fci_pt2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L1071>`_ `h_apply_fci_pt2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L1071>`_
Generate all single excitations of key_in using the bit masks of holes and Generate all single excitations of key_in using the bit masks of holes and
particles. particles.
Assume N_int is already provided. Assume N_int is already provided.
`h_apply_pt2_mono_delta_rho <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L4222>`_ `h_apply_pt2_mono_delta_rho <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L4222>`_
Calls H_apply on the HF determinant and selects all connected single and double 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. excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
`h_apply_pt2_mono_delta_rho_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L3734>`_ `h_apply_pt2_mono_delta_rho_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L3734>`_
Generate all double excitations of key_in using the bit masks of holes and Generate all double excitations of key_in using the bit masks of holes and
particles. particles.
Assume N_int is already provided. Assume N_int is already provided.
`h_apply_pt2_mono_delta_rho_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L4038>`_ `h_apply_pt2_mono_delta_rho_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L4038>`_
Generate all single excitations of key_in using the bit masks of holes and Generate all single excitations of key_in using the bit masks of holes and
particles. particles.
Assume N_int is already provided. Assume N_int is already provided.
`h_apply_pt2_mono_di_delta_rho <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L5681>`_ `h_apply_pt2_mono_di_delta_rho <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L5681>`_
Calls H_apply on the HF determinant and selects all connected single and double 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. excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
`h_apply_pt2_mono_di_delta_rho_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L5195>`_ `h_apply_pt2_mono_di_delta_rho_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L5195>`_
Generate all double excitations of key_in using the bit masks of holes and Generate all double excitations of key_in using the bit masks of holes and
particles. particles.
Assume N_int is already provided. Assume N_int is already provided.
`h_apply_pt2_mono_di_delta_rho_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L5499>`_ `h_apply_pt2_mono_di_delta_rho_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L5499>`_
Generate all single excitations of key_in using the bit masks of holes and Generate all single excitations of key_in using the bit masks of holes and
particles. particles.
Assume N_int is already provided. Assume N_int is already provided.
`h_apply_select_mono_delta_rho <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L3488>`_ `h_apply_select_mono_delta_rho <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L3488>`_
Calls H_apply on the HF determinant and selects all connected single and double 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. excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
`h_apply_select_mono_delta_rho_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L2966>`_ `h_apply_select_mono_delta_rho_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L2966>`_
Generate all double excitations of key_in using the bit masks of holes and Generate all double excitations of key_in using the bit masks of holes and
particles. particles.
Assume N_int is already provided. Assume N_int is already provided.
`h_apply_select_mono_delta_rho_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L3290>`_ `h_apply_select_mono_delta_rho_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L3290>`_
Generate all single excitations of key_in using the bit masks of holes and Generate all single excitations of key_in using the bit masks of holes and
particles. particles.
Assume N_int is already provided. Assume N_int is already provided.
`h_apply_select_mono_di_delta_rho <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L4949>`_ `h_apply_select_mono_di_delta_rho <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L4949>`_
Calls H_apply on the HF determinant and selects all connected single and double 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. excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
`h_apply_select_mono_di_delta_rho_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L4429>`_ `h_apply_select_mono_di_delta_rho_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L4429>`_
Generate all double excitations of key_in using the bit masks of holes and Generate all double excitations of key_in using the bit masks of holes and
particles. particles.
Assume N_int is already provided. Assume N_int is already provided.
`h_apply_select_mono_di_delta_rho_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L4753>`_ `h_apply_select_mono_di_delta_rho_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L4753>`_
Generate all single excitations of key_in using the bit masks of holes and Generate all single excitations of key_in using the bit masks of holes and
particles. particles.
Assume N_int is already provided. Assume N_int is already provided.
`var_pt2_ratio_run <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/var_pt2_ratio.irp.f#L1>`_ `var_pt2_ratio_run <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/var_pt2_ratio.irp.f#L1>`_
Undocumented Undocumented

14
plugins/Generators_full/README.rst
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@ -25,7 +25,7 @@ Needed Modules
.. image:: tree_dependency.png .. image:: tree_dependency.png
* `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_ * `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_ * `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock>`_
Documentation Documentation
============= =============
@ -33,29 +33,29 @@ Documentation
.. by the `update_README.py` script. .. by the `update_README.py` script.
`degree_max_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full/generators.irp.f#L43>`_ `degree_max_generators <http://github.com/LCPQ/quantum_package/tree/master/plugins/Generators_full/generators.irp.f#L43>`_
Max degree of excitation (respect to HF) of the generators Max degree of excitation (respect to HF) of the generators
`n_det_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full/generators.irp.f#L3>`_ `n_det_generators <http://github.com/LCPQ/quantum_package/tree/master/plugins/Generators_full/generators.irp.f#L3>`_
For Single reference wave functions, the number of generators is 1 : the For Single reference wave functions, the number of generators is 1 : the
Hartree-Fock determinant Hartree-Fock determinant
`psi_coef_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full/generators.irp.f#L26>`_ `psi_coef_generators <http://github.com/LCPQ/quantum_package/tree/master/plugins/Generators_full/generators.irp.f#L26>`_
For Single reference wave functions, the generator is the For Single reference wave functions, the generator is the
Hartree-Fock determinant Hartree-Fock determinant
`psi_det_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full/generators.irp.f#L25>`_ `psi_det_generators <http://github.com/LCPQ/quantum_package/tree/master/plugins/Generators_full/generators.irp.f#L25>`_
For Single reference wave functions, the generator is the For Single reference wave functions, the generator is the
Hartree-Fock determinant Hartree-Fock determinant
`select_max <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full/generators.irp.f#L66>`_ `select_max <http://github.com/LCPQ/quantum_package/tree/master/plugins/Generators_full/generators.irp.f#L66>`_
Memo to skip useless selectors Memo to skip useless selectors
`size_select_max <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full/generators.irp.f#L58>`_ `size_select_max <http://github.com/LCPQ/quantum_package/tree/master/plugins/Generators_full/generators.irp.f#L58>`_
Size of the select_max array Size of the select_max array

52
plugins/Hartree_Fock/README.rst
View File

@ -32,57 +32,57 @@ Documentation
.. by the `update_README.py` script. .. by the `update_README.py` script.
`ao_bi_elec_integral_alpha <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L102>`_ `ao_bi_elec_integral_alpha <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/Fock_matrix.irp.f#L102>`_
Alpha Fock matrix in AO basis set Alpha Fock matrix in AO basis set
`ao_bi_elec_integral_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L103>`_ `ao_bi_elec_integral_beta <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/Fock_matrix.irp.f#L103>`_
Alpha Fock matrix in AO basis set Alpha Fock matrix in AO basis set
`create_guess <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/SCF.irp.f#L13>`_ `create_guess <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/SCF.irp.f#L13>`_
Create an MO guess if no MOs are present in the EZFIO directory Create an MO guess if no MOs are present in the EZFIO directory
`damping_scf <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/damping_SCF.irp.f#L1>`_ `damping_scf <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/damping_SCF.irp.f#L1>`_
Undocumented Undocumented
`diagonal_fock_matrix_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/diagonalize_fock.irp.f#L1>`_ `diagonal_fock_matrix_mo <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/diagonalize_fock.irp.f#L1>`_
Diagonal Fock matrix in the MO basis Diagonal Fock matrix in the MO basis
`diagonal_fock_matrix_mo_sum <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/diagonalize_fock.irp.f#L67>`_ `diagonal_fock_matrix_mo_sum <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/diagonalize_fock.irp.f#L67>`_
diagonal element of the fock matrix calculated as the sum over all the interactions diagonal element of the fock matrix calculated as the sum over all the interactions
with all the electrons in the RHF determinant with all the electrons in the RHF determinant
diagonal_Fock_matrix_mo_sum(i) = sum_{j=1, N_elec} 2 J_ij -K_ij diagonal_Fock_matrix_mo_sum(i) = sum_{j=1, N_elec} 2 J_ij -K_ij
`eigenvectors_fock_matrix_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/diagonalize_fock.irp.f#L2>`_ `eigenvectors_fock_matrix_mo <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/diagonalize_fock.irp.f#L2>`_
Diagonal Fock matrix in the MO basis Diagonal Fock matrix in the MO basis
`fock_matrix_alpha_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L83>`_ `fock_matrix_alpha_ao <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/Fock_matrix.irp.f#L83>`_
Alpha Fock matrix in AO basis set Alpha Fock matrix in AO basis set
`fock_matrix_alpha_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L231>`_ `fock_matrix_alpha_mo <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/Fock_matrix.irp.f#L231>`_
Fock matrix on the MO basis Fock matrix on the MO basis
`fock_matrix_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L289>`_ `fock_matrix_ao <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/Fock_matrix.irp.f#L289>`_
Fock matrix in AO basis set Fock matrix in AO basis set
`fock_matrix_beta_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L84>`_ `fock_matrix_beta_ao <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/Fock_matrix.irp.f#L84>`_
Alpha Fock matrix in AO basis set Alpha Fock matrix in AO basis set
`fock_matrix_beta_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L251>`_ `fock_matrix_beta_mo <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/Fock_matrix.irp.f#L251>`_
Fock matrix on the MO basis Fock matrix on the MO basis
`fock_matrix_diag_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L2>`_ `fock_matrix_diag_mo <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/Fock_matrix.irp.f#L2>`_
Fock matrix on the MO basis. Fock matrix on the MO basis.
For open shells, the ROHF Fock Matrix is For open shells, the ROHF Fock Matrix is
.br .br
@ -98,7 +98,7 @@ Documentation
.br .br
`fock_matrix_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L1>`_ `fock_matrix_mo <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/Fock_matrix.irp.f#L1>`_
Fock matrix on the MO basis. Fock matrix on the MO basis.
For open shells, the ROHF Fock Matrix is For open shells, the ROHF Fock Matrix is
.br .br
@ -114,53 +114,53 @@ Documentation
.br .br
`fock_mo_to_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L332>`_ `fock_mo_to_ao <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/Fock_matrix.irp.f#L332>`_
Undocumented Undocumented
`guess <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Huckel_guess.irp.f#L1>`_ `guess <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/Huckel_guess.irp.f#L1>`_
Undocumented Undocumented
`hf_density_matrix_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/HF_density_matrix_ao.irp.f#L27>`_ `hf_density_matrix_ao <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/HF_density_matrix_ao.irp.f#L27>`_
S^-1 Density matrix in the AO basis S^-1 S^-1 Density matrix in the AO basis S^-1
`hf_density_matrix_ao_alpha <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/HF_density_matrix_ao.irp.f#L1>`_ `hf_density_matrix_ao_alpha <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/HF_density_matrix_ao.irp.f#L1>`_
S^-1 x Alpha density matrix in the AO basis x S^-1 S^-1 x Alpha density matrix in the AO basis x S^-1
`hf_density_matrix_ao_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/HF_density_matrix_ao.irp.f#L14>`_ `hf_density_matrix_ao_beta <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/HF_density_matrix_ao.irp.f#L14>`_
S^-1 Beta density matrix in the AO basis x S^-1 S^-1 Beta density matrix in the AO basis x S^-1
`hf_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L270>`_ `hf_energy <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/Fock_matrix.irp.f#L270>`_
Hartree-Fock energy Hartree-Fock energy
`huckel_guess <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/huckel.irp.f#L1>`_ `huckel_guess <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/huckel.irp.f#L1>`_
Build the MOs using the extended Huckel model Build the MOs using the extended Huckel model
`mo_guess_type <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/ezfio_interface.irp.f#L28>`_ `mo_guess_type <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/ezfio_interface.irp.f#L28>`_
Initial MO guess. Can be [ Huckel | HCore ] Initial MO guess. Can be [ Huckel | HCore ]
`n_it_scf_max <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/ezfio_interface.irp.f#L6>`_ `n_it_scf_max <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/ezfio_interface.irp.f#L6>`_
Maximum number of SCF iterations Maximum number of SCF iterations
`run <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/SCF.irp.f#L38>`_ `run <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/SCF.irp.f#L38>`_
Run SCF calculation Run SCF calculation
`scf <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/SCF.irp.f#L1>`_ `scf <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/SCF.irp.f#L1>`_
Produce `Hartree_Fock` MO orbital 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: 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 output: hartree_fock.energy
optional: mo_basis.mo_coef optional: mo_basis.mo_coef
`thresh_scf <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/ezfio_interface.irp.f#L46>`_ `thresh_scf <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/ezfio_interface.irp.f#L46>`_
Threshold on the convergence of the Hartree Fock energy Threshold on the convergence of the Hartree Fock energy

78
plugins/Perturbation/README.rst
View File

@ -86,8 +86,8 @@ Needed Modules
.. image:: tree_dependency.png .. image:: tree_dependency.png
* `Properties <http://github.com/LCPQ/quantum_package/tree/master/src/Properties>`_ * `Properties <http://github.com/LCPQ/quantum_package/tree/master/plugins/Properties>`_
* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_ * `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock>`_
Documentation Documentation
============= =============
@ -95,109 +95,109 @@ Documentation
.. by the `update_README.py` script. .. by the `update_README.py` script.
`do_pt2_end <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/ezfio_interface.irp.f#L6>`_ `do_pt2_end <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/ezfio_interface.irp.f#L6>`_
If true, compute the PT2 at the end of the selection If true, compute the PT2 at the end of the selection
`fill_h_apply_buffer_selection <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/selection.irp.f#L1>`_ `fill_h_apply_buffer_selection <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/selection.irp.f#L1>`_
Fill the H_apply buffer with determiants for the selection Fill the H_apply buffer with determiants for the selection
`max_exc_pert <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/exc_max.irp.f#L1>`_ `max_exc_pert <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/exc_max.irp.f#L1>`_
Undocumented Undocumented
`perturb_buffer_by_mono_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L161>`_ `perturb_buffer_by_mono_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L161>`_
Applly pertubration ``delta_rho_one_point`` to the buffer of determinants generated in the H_apply Applly pertubration ``delta_rho_one_point`` to the buffer of determinants generated in the H_apply
routine. routine.
`perturb_buffer_by_mono_dipole_moment_z <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L896>`_ `perturb_buffer_by_mono_dipole_moment_z <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L896>`_
Applly pertubration ``dipole_moment_z`` to the buffer of determinants generated in the H_apply Applly pertubration ``dipole_moment_z`` to the buffer of determinants generated in the H_apply
routine. routine.
`perturb_buffer_by_mono_epstein_nesbet <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L686>`_ `perturb_buffer_by_mono_epstein_nesbet <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L686>`_
Applly pertubration ``epstein_nesbet`` to the buffer of determinants generated in the H_apply Applly pertubration ``epstein_nesbet`` to the buffer of determinants generated in the H_apply
routine. routine.
`perturb_buffer_by_mono_epstein_nesbet_2x2 <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L791>`_ `perturb_buffer_by_mono_epstein_nesbet_2x2 <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L791>`_
Applly pertubration ``epstein_nesbet_2x2`` to the buffer of determinants generated in the H_apply Applly pertubration ``epstein_nesbet_2x2`` to the buffer of determinants generated in the H_apply
routine. routine.
`perturb_buffer_by_mono_epstein_nesbet_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L581>`_ `perturb_buffer_by_mono_epstein_nesbet_sc2 <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L581>`_
Applly pertubration ``epstein_nesbet_sc2`` to the buffer of determinants generated in the H_apply Applly pertubration ``epstein_nesbet_sc2`` to the buffer of determinants generated in the H_apply
routine. routine.
`perturb_buffer_by_mono_epstein_nesbet_sc2_no_projected <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L476>`_ `perturb_buffer_by_mono_epstein_nesbet_sc2_no_projected <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L476>`_
Applly pertubration ``epstein_nesbet_sc2_no_projected`` to the buffer of determinants generated in the H_apply Applly pertubration ``epstein_nesbet_sc2_no_projected`` to the buffer of determinants generated in the H_apply
routine. routine.
`perturb_buffer_by_mono_epstein_nesbet_sc2_projected <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L371>`_ `perturb_buffer_by_mono_epstein_nesbet_sc2_projected <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L371>`_
Applly pertubration ``epstein_nesbet_sc2_projected`` to the buffer of determinants generated in the H_apply Applly pertubration ``epstein_nesbet_sc2_projected`` to the buffer of determinants generated in the H_apply
routine. routine.
`perturb_buffer_by_mono_h_core <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L266>`_ `perturb_buffer_by_mono_h_core <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L266>`_
Applly pertubration ``h_core`` to the buffer of determinants generated in the H_apply Applly pertubration ``h_core`` to the buffer of determinants generated in the H_apply
routine. routine.
`perturb_buffer_by_mono_moller_plesset <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L56>`_ `perturb_buffer_by_mono_moller_plesset <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L56>`_
Applly pertubration ``moller_plesset`` to the buffer of determinants generated in the H_apply Applly pertubration ``moller_plesset`` to the buffer of determinants generated in the H_apply
routine. routine.
`perturb_buffer_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L110>`_ `perturb_buffer_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L110>`_
Applly pertubration ``delta_rho_one_point`` to the buffer of determinants generated in the H_apply Applly pertubration ``delta_rho_one_point`` to the buffer of determinants generated in the H_apply
routine. routine.
`perturb_buffer_dipole_moment_z <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L845>`_ `perturb_buffer_dipole_moment_z <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L845>`_
Applly pertubration ``dipole_moment_z`` to the buffer of determinants generated in the H_apply Applly pertubration ``dipole_moment_z`` to the buffer of determinants generated in the H_apply
routine. routine.
`perturb_buffer_epstein_nesbet <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L635>`_ `perturb_buffer_epstein_nesbet <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L635>`_
Applly pertubration ``epstein_nesbet`` to the buffer of determinants generated in the H_apply Applly pertubration ``epstein_nesbet`` to the buffer of determinants generated in the H_apply
routine. routine.
`perturb_buffer_epstein_nesbet_2x2 <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L740>`_ `perturb_buffer_epstein_nesbet_2x2 <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L740>`_
Applly pertubration ``epstein_nesbet_2x2`` to the buffer of determinants generated in the H_apply Applly pertubration ``epstein_nesbet_2x2`` to the buffer of determinants generated in the H_apply
routine. routine.
`perturb_buffer_epstein_nesbet_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L530>`_ `perturb_buffer_epstein_nesbet_sc2 <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L530>`_
Applly pertubration ``epstein_nesbet_sc2`` to the buffer of determinants generated in the H_apply Applly pertubration ``epstein_nesbet_sc2`` to the buffer of determinants generated in the H_apply
routine. routine.
`perturb_buffer_epstein_nesbet_sc2_no_projected <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L425>`_ `perturb_buffer_epstein_nesbet_sc2_no_projected <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L425>`_
Applly pertubration ``epstein_nesbet_sc2_no_projected`` to the buffer of determinants generated in the H_apply Applly pertubration ``epstein_nesbet_sc2_no_projected`` to the buffer of determinants generated in the H_apply
routine. routine.
`perturb_buffer_epstein_nesbet_sc2_projected <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L320>`_ `perturb_buffer_epstein_nesbet_sc2_projected <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L320>`_
Applly pertubration ``epstein_nesbet_sc2_projected`` to the buffer of determinants generated in the H_apply Applly pertubration ``epstein_nesbet_sc2_projected`` to the buffer of determinants generated in the H_apply
routine. routine.
`perturb_buffer_h_core <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L215>`_ `perturb_buffer_h_core <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L215>`_
Applly pertubration ``h_core`` to the buffer of determinants generated in the H_apply Applly pertubration ``h_core`` to the buffer of determinants generated in the H_apply
routine. routine.
`perturb_buffer_moller_plesset <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L5>`_ `perturb_buffer_moller_plesset <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L5>`_
Applly pertubration ``moller_plesset`` to the buffer of determinants generated in the H_apply Applly pertubration ``moller_plesset`` to the buffer of determinants generated in the H_apply
routine. routine.
`pt2_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/delta_rho_perturbation.irp.f#L1>`_ `pt2_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/delta_rho_perturbation.irp.f#L1>`_
compute the perturbatibe contribution to the Integrated Spin density at z = z_one point of one determinant compute the perturbatibe contribution to the Integrated Spin density at z = z_one point of one determinant
.br .br
for the various n_st states, at various level of theory. for the various n_st states, at various level of theory.
@ -218,7 +218,7 @@ Documentation
.br .br
`pt2_dipole_moment_z <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/dipole_moment.irp.f#L1>`_ `pt2_dipole_moment_z <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/dipole_moment.irp.f#L1>`_
compute the perturbatibe contribution to the dipole moment of one determinant compute the perturbatibe contribution to the dipole moment of one determinant
.br .br
for the various n_st states, at various level of theory. for the various n_st states, at various level of theory.
@ -239,7 +239,7 @@ Documentation
.br .br
`pt2_epstein_nesbet <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/epstein_nesbet.irp.f#L1>`_ `pt2_epstein_nesbet <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/epstein_nesbet.irp.f#L1>`_
compute the standard Epstein-Nesbet perturbative first order coefficient and second order energetic contribution compute the standard Epstein-Nesbet perturbative first order coefficient and second order energetic contribution
.br .br
for the various N_st states. for the various N_st states.
@ -250,7 +250,7 @@ Documentation
.br .br
`pt2_epstein_nesbet_2x2 <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/epstein_nesbet.irp.f#L45>`_ `pt2_epstein_nesbet_2x2 <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/epstein_nesbet.irp.f#L45>`_
compute the Epstein-Nesbet 2x2 diagonalization coefficient and energetic contribution compute the Epstein-Nesbet 2x2 diagonalization coefficient and energetic contribution
.br .br
for the various N_st states. for the various N_st states.
@ -261,7 +261,7 @@ Documentation
.br .br
`pt2_epstein_nesbet_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/pert_sc2.irp.f#L186>`_ `pt2_epstein_nesbet_sc2 <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/pert_sc2.irp.f#L186>`_
compute the standard Epstein-Nesbet perturbative first order coefficient and second order energetic contribution compute the standard Epstein-Nesbet perturbative first order coefficient and second order energetic contribution
.br .br
for the various N_st states, but with the CISD_SC2 energies and coefficients for the various N_st states, but with the CISD_SC2 energies and coefficients
@ -272,7 +272,7 @@ Documentation
.br .br
`pt2_epstein_nesbet_sc2_no_projected <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/pert_sc2.irp.f#L87>`_ `pt2_epstein_nesbet_sc2_no_projected <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/pert_sc2.irp.f#L87>`_
compute the Epstein-Nesbet perturbative first order coefficient and second order energetic contribution compute the Epstein-Nesbet perturbative first order coefficient and second order energetic contribution
.br .br
for the various N_st states, for the various N_st states,
@ -296,7 +296,7 @@ Documentation
H_pert_diag = <HF|H|det_pert> c_pert H_pert_diag = <HF|H|det_pert> c_pert
`pt2_epstein_nesbet_sc2_projected <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/pert_sc2.irp.f#L2>`_ `pt2_epstein_nesbet_sc2_projected <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/pert_sc2.irp.f#L2>`_
compute the Epstein-Nesbet perturbative first order coefficient and second order energetic contribution compute the Epstein-Nesbet perturbative first order coefficient and second order energetic contribution
.br .br
for the various N_st states, for the various N_st states,
@ -320,7 +320,7 @@ Documentation
H_pert_diag = <HF|H|det_pert> c_pert H_pert_diag = <HF|H|det_pert> c_pert
`pt2_h_core <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/pert_single.irp.f#L1>`_ `pt2_h_core <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/pert_single.irp.f#L1>`_
compute the standard Epstein-Nesbet perturbative first order coefficient and second order energetic contribution compute the standard Epstein-Nesbet perturbative first order coefficient and second order energetic contribution
.br .br
for the various N_st states. for the various N_st states.
@ -331,12 +331,12 @@ Documentation
.br .br
`pt2_max <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/ezfio_interface.irp.f#L28>`_ `pt2_max <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/ezfio_interface.irp.f#L28>`_
The selection process stops when the largest PT2 (for all the state) is lower The selection process stops when the largest PT2 (for all the state) is lower
than pt2_max in absolute value than pt2_max in absolute value
`pt2_moller_plesset <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/Moller_plesset.irp.f#L1>`_ `pt2_moller_plesset <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/Moller_plesset.irp.f#L1>`_
compute the standard Moller-Plesset perturbative first order coefficient and second order energetic contribution compute the standard Moller-Plesset perturbative first order coefficient and second order energetic contribution
.br .br
for the various n_st states. for the various n_st states.
@ -347,28 +347,28 @@ Documentation
.br .br
`remove_small_contributions <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/selection.irp.f#L87>`_ `remove_small_contributions <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/selection.irp.f#L87>`_
Remove determinants with small contributions. N_states is assumed to be Remove determinants with small contributions. N_states is assumed to be
provided. provided.
`repeat_all_e_corr <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/pert_sc2.irp.f#L156>`_ `repeat_all_e_corr <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/pert_sc2.irp.f#L156>`_
Undocumented Undocumented
`selection_criterion <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/selection.irp.f#L74>`_ `selection_criterion <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/selection.irp.f#L74>`_
Threshold to select determinants. Set by selection routines. Threshold to select determinants. Set by selection routines.
`selection_criterion_factor <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/selection.irp.f#L76>`_ `selection_criterion_factor <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/selection.irp.f#L76>`_
Threshold to select determinants. Set by selection routines. Threshold to select determinants. Set by selection routines.
`selection_criterion_min <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/selection.irp.f#L75>`_ `selection_criterion_min <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/selection.irp.f#L75>`_
Threshold to select determinants. Set by selection routines. Threshold to select determinants. Set by selection routines.
`var_pt2_ratio <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/ezfio_interface.irp.f#L51>`_ `var_pt2_ratio <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/ezfio_interface.irp.f#L51>`_
The selection process stops when the energy ratio variational/(variational+PT2) The selection process stops when the energy ratio variational/(variational+PT2)
is equal to var_pt2_ratio is equal to var_pt2_ratio

48
plugins/Properties/README.rst
View File

@ -28,41 +28,41 @@ Documentation
.. by the `update_README.py` script. .. by the `update_README.py` script.
`ao_integrated_delta_rho_all_points <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/delta_rho.irp.f#L61>`_ `ao_integrated_delta_rho_all_points <http://github.com/LCPQ/quantum_package/tree/master/plugins/Properties/delta_rho.irp.f#L61>`_
array of the overlap in x,y between the AO function and integrated between [z,z+dz] in the z axis 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) for all the z points that are given (N_z_pts)
`ao_integrated_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/delta_rho.irp.f#L130>`_ `ao_integrated_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/plugins/Properties/delta_rho.irp.f#L130>`_
array of the overlap in x,y between the AO function and integrated between [z,z+dz] in the z axis 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 for one specific z point
`average_position <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/properties.irp.f#L1>`_ `average_position <http://github.com/LCPQ/quantum_package/tree/master/plugins/Properties/properties.irp.f#L1>`_
average_position(1) = <psi_det|X|psi_det> average_position(1) = <psi_det|X|psi_det>
average_position(2) = <psi_det|Y|psi_det> average_position(2) = <psi_det|Y|psi_det>
average_position(3) = <psi_det|Z|psi_det> average_position(3) = <psi_det|Z|psi_det>
`average_spread <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/properties.irp.f#L27>`_ `average_spread <http://github.com/LCPQ/quantum_package/tree/master/plugins/Properties/properties.irp.f#L27>`_
average_spread(1) = <psi_det|X^2|psi_det> average_spread(1) = <psi_det|X^2|psi_det>
average_spread(2) = <psi_det|Y^2|psi_det> average_spread(2) = <psi_det|Y^2|psi_det>
average_spread(3) = <psi_det|Z^2|psi_det> average_spread(3) = <psi_det|Z^2|psi_det>
`delta_z <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/delta_rho.irp.f#L4>`_ `delta_z <http://github.com/LCPQ/quantum_package/tree/master/plugins/Properties/delta_rho.irp.f#L4>`_
Undocumented Undocumented
`diag_o1_mat_elem <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/slater_rules_mono_electronic.irp.f#L91>`_ `diag_o1_mat_elem <http://github.com/LCPQ/quantum_package/tree/master/plugins/Properties/slater_rules_mono_electronic.irp.f#L91>`_
Computes <i|O1|i> Computes <i|O1|i>
`diag_o1_mat_elem_alpha_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/slater_rules_mono_electronic.irp.f#L210>`_ `diag_o1_mat_elem_alpha_beta <http://github.com/LCPQ/quantum_package/tree/master/plugins/Properties/slater_rules_mono_electronic.irp.f#L210>`_
Computes <i|O1(alpha) -O1(beta)|i> Computes <i|O1(alpha) -O1(beta)|i>
`filter_connected_mono <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/slater_rules_mono_electronic.irp.f#L240>`_ `filter_connected_mono <http://github.com/LCPQ/quantum_package/tree/master/plugins/Properties/slater_rules_mono_electronic.irp.f#L240>`_
Filters out the determinants that are not connected through PURE Filters out the determinants that are not connected through PURE
.br .br
MONO EXCITATIONS OPERATORS (a^{\dagger}j a_i) MONO EXCITATIONS OPERATORS (a^{\dagger}j a_i)
@ -76,89 +76,89 @@ Documentation
idx(0) is the number of determinants that interact with key1 idx(0) is the number of determinants that interact with key1
`get_average <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/average.irp.f#L1>`_ `get_average <http://github.com/LCPQ/quantum_package/tree/master/plugins/Properties/average.irp.f#L1>`_
computes the average value of a pure MONO ELECTRONIC OPERATOR computes the average value of a pure MONO ELECTRONIC OPERATOR
whom integrals on the MO basis are stored in "array" whom integrals on the MO basis are stored in "array"
and with the density is stored in "density" and with the density is stored in "density"
`i_o1_j <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/slater_rules_mono_electronic.irp.f#L1>`_ `i_o1_j <http://github.com/LCPQ/quantum_package/tree/master/plugins/Properties/slater_rules_mono_electronic.irp.f#L1>`_
Returns <i|O1|j> where i and j are determinants Returns <i|O1|j> where i and j are determinants
and O1 is a ONE BODY OPERATOR and O1 is a ONE BODY OPERATOR
array is the array of the mono electronic operator array is the array of the mono electronic operator
on the MO basis on the MO basis
`i_o1_j_alpha_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/slater_rules_mono_electronic.irp.f#L158>`_ `i_o1_j_alpha_beta <http://github.com/LCPQ/quantum_package/tree/master/plugins/Properties/slater_rules_mono_electronic.irp.f#L158>`_
Returns <i|O1(alpha) - O1(beta)|j> where i and j are determinants Returns <i|O1(alpha) - O1(beta)|j> where i and j are determinants
and O1 is a ONE BODY OPERATOR and O1 is a ONE BODY OPERATOR
array is the array of the mono electronic operator array is the array of the mono electronic operator
on the MO basis on the MO basis
`i_o1_psi <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/slater_rules_mono_electronic.irp.f#L52>`_ `i_o1_psi <http://github.com/LCPQ/quantum_package/tree/master/plugins/Properties/slater_rules_mono_electronic.irp.f#L52>`_
<key|O1|psi> for the various Nstates <key|O1|psi> for the various Nstates
and O1 is a ONE BODY OPERATOR and O1 is a ONE BODY OPERATOR
array is the array of the mono electronic operator array is the array of the mono electronic operator
on the MO basis on the MO basis
`i_o1_psi_alpha_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/slater_rules_mono_electronic.irp.f#L119>`_ `i_o1_psi_alpha_beta <http://github.com/LCPQ/quantum_package/tree/master/plugins/Properties/slater_rules_mono_electronic.irp.f#L119>`_
<key|O1(alpha) - O1(beta)|psi> for the various Nstates <key|O1(alpha) - O1(beta)|psi> for the various Nstates
and O1 is a ONE BODY OPERATOR and O1 is a ONE BODY OPERATOR
array is the array of the mono electronic operator array is the array of the mono electronic operator
on the MO basis on the MO basis
`i_unit_integrated_delta_rho <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/delta_rho.irp.f#L118>`_ `i_unit_integrated_delta_rho <http://github.com/LCPQ/quantum_package/tree/master/plugins/Properties/delta_rho.irp.f#L118>`_
fortran unit for the writing of the integrated delta_rho fortran unit for the writing of the integrated delta_rho
`integrated_delta_rho_all_points <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/delta_rho.irp.f#L15>`_ `integrated_delta_rho_all_points <http://github.com/LCPQ/quantum_package/tree/master/plugins/Properties/delta_rho.irp.f#L15>`_
.br .br
integrated_rho(alpha,z) - integrated_rho(beta,z) for all the z points integrated_rho(alpha,z) - integrated_rho(beta,z) for all the z points
chosen chosen
.br .br
`integrated_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/delta_rho.irp.f#L212>`_ `integrated_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/plugins/Properties/delta_rho.irp.f#L212>`_
.br .br
integral (x,y) and (z,z+delta_z) of rho(alpha) - rho(beta) integral (x,y) and (z,z+delta_z) of rho(alpha) - rho(beta)
on the MO basis on the MO basis
.br .br
`mo_integrated_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/delta_rho.irp.f#L184>`_ `mo_integrated_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/plugins/Properties/delta_rho.irp.f#L184>`_
.br .br
array of the integrals needed of integrated_rho(alpha,z) - integrated_rho(beta,z) for z = z_one_point array of the integrals needed of integrated_rho(alpha,z) - integrated_rho(beta,z) for z = z_one_point
on the MO basis on the MO basis
.br .br
`n_z_pts <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/delta_rho.irp.f#L1>`_ `n_z_pts <http://github.com/LCPQ/quantum_package/tree/master/plugins/Properties/delta_rho.irp.f#L1>`_
Undocumented Undocumented
`test_average_value <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/routines_test.irp.f#L3>`_ `test_average_value <http://github.com/LCPQ/quantum_package/tree/master/plugins/Properties/routines_test.irp.f#L3>`_
Undocumented Undocumented
`test_average_value_alpha_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/routines_test.irp.f#L25>`_ `test_average_value_alpha_beta <http://github.com/LCPQ/quantum_package/tree/master/plugins/Properties/routines_test.irp.f#L25>`_
Undocumented Undocumented
`test_dm <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/routines_test.irp.f#L56>`_ `test_dm <http://github.com/LCPQ/quantum_package/tree/master/plugins/Properties/routines_test.irp.f#L56>`_
Undocumented Undocumented
`z_max <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/delta_rho.irp.f#L3>`_ `z_max <http://github.com/LCPQ/quantum_package/tree/master/plugins/Properties/delta_rho.irp.f#L3>`_
Undocumented Undocumented
`z_min <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/delta_rho.irp.f#L2>`_ `z_min <http://github.com/LCPQ/quantum_package/tree/master/plugins/Properties/delta_rho.irp.f#L2>`_
Undocumented Undocumented
`z_one_point <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/ezfio_interface.irp.f#L6>`_ `z_one_point <http://github.com/LCPQ/quantum_package/tree/master/plugins/Properties/ezfio_interface.irp.f#L6>`_
z point on which the integrated delta rho is calculated z point on which the integrated delta rho is calculated

40
plugins/Selectors_full/README.rst
View File

@ -22,7 +22,7 @@ Needed Modules
.. image:: tree_dependency.png .. image:: tree_dependency.png
* `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_ * `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_ * `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock>`_
Documentation Documentation
============= =============
@ -30,7 +30,7 @@ Documentation
.. by the `update_README.py` script. .. by the `update_README.py` script.
`coef_hf_selector <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L28>`_ `coef_hf_selector <http://github.com/LCPQ/quantum_package/tree/master/plugins/Selectors_full/e_corr_selectors.irp.f#L28>`_
energy of correlation per determinant respect to the Hartree Fock determinant energy of correlation per determinant respect to the Hartree Fock determinant
.br .br
for the all the double excitations in the selectors determinants 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 coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
`delta_e_per_selector <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L33>`_ `delta_e_per_selector <http://github.com/LCPQ/quantum_package/tree/master/plugins/Selectors_full/e_corr_selectors.irp.f#L33>`_
energy of correlation per determinant respect to the Hartree Fock determinant energy of correlation per determinant respect to the Hartree Fock determinant
.br .br
for the all the double excitations in the selectors determinants 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 coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
`double_index_selectors <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L4>`_ `double_index_selectors <http://github.com/LCPQ/quantum_package/tree/master/plugins/Selectors_full/e_corr_selectors.irp.f#L4>`_
degree of excitation respect to Hartree Fock for the wave function degree of excitation respect to Hartree Fock for the wave function
.br .br
for the all the selectors determinants for the all the selectors determinants
@ -64,7 +64,7 @@ Documentation
n_double_selectors = number of double excitations in the selectors determinants n_double_selectors = number of double excitations in the selectors determinants
`e_corr_double_only <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L34>`_ `e_corr_double_only <http://github.com/LCPQ/quantum_package/tree/master/plugins/Selectors_full/e_corr_selectors.irp.f#L34>`_
energy of correlation per determinant respect to the Hartree Fock determinant energy of correlation per determinant respect to the Hartree Fock determinant
.br .br
for the all the double excitations in the selectors determinants 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 coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
`e_corr_per_selectors <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L31>`_ `e_corr_per_selectors <http://github.com/LCPQ/quantum_package/tree/master/plugins/Selectors_full/e_corr_selectors.irp.f#L31>`_
energy of correlation per determinant respect to the Hartree Fock determinant energy of correlation per determinant respect to the Hartree Fock determinant
.br .br
for the all the double excitations in the selectors determinants 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 coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
`e_corr_second_order <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L35>`_ `e_corr_second_order <http://github.com/LCPQ/quantum_package/tree/master/plugins/Selectors_full/e_corr_selectors.irp.f#L35>`_
energy of correlation per determinant respect to the Hartree Fock determinant energy of correlation per determinant respect to the Hartree Fock determinant
.br .br
for the all the double excitations in the selectors determinants 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 coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
`exc_degree_per_selectors <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L3>`_ `exc_degree_per_selectors <http://github.com/LCPQ/quantum_package/tree/master/plugins/Selectors_full/e_corr_selectors.irp.f#L3>`_
degree of excitation respect to Hartree Fock for the wave function degree of excitation respect to Hartree Fock for the wave function
.br .br
for the all the selectors determinants for the all the selectors determinants
@ -110,7 +110,7 @@ Documentation
n_double_selectors = number of double excitations in the selectors determinants n_double_selectors = number of double excitations in the selectors determinants
`i_h_hf_per_selectors <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L32>`_ `i_h_hf_per_selectors <http://github.com/LCPQ/quantum_package/tree/master/plugins/Selectors_full/e_corr_selectors.irp.f#L32>`_
energy of correlation per determinant respect to the Hartree Fock determinant energy of correlation per determinant respect to the Hartree Fock determinant
.br .br
for the all the double excitations in the selectors determinants 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 coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
`inv_selectors_coef_hf <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L29>`_ `inv_selectors_coef_hf <http://github.com/LCPQ/quantum_package/tree/master/plugins/Selectors_full/e_corr_selectors.irp.f#L29>`_
energy of correlation per determinant respect to the Hartree Fock determinant energy of correlation per determinant respect to the Hartree Fock determinant
.br .br
for the all the double excitations in the selectors determinants 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 coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
`inv_selectors_coef_hf_squared <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L30>`_ `inv_selectors_coef_hf_squared <http://github.com/LCPQ/quantum_package/tree/master/plugins/Selectors_full/e_corr_selectors.irp.f#L30>`_
energy of correlation per determinant respect to the Hartree Fock determinant energy of correlation per determinant respect to the Hartree Fock determinant
.br .br
for the all the double excitations in the selectors determinants 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 coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
`n_det_selectors <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L8>`_ `n_det_selectors <http://github.com/LCPQ/quantum_package/tree/master/plugins/Selectors_full/selectors.irp.f#L8>`_
For Single reference wave functions, the number of selectors is 1 : the For Single reference wave functions, the number of selectors is 1 : the
Hartree-Fock determinant Hartree-Fock determinant
`n_double_selectors <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L5>`_ `n_double_selectors <http://github.com/LCPQ/quantum_package/tree/master/plugins/Selectors_full/e_corr_selectors.irp.f#L5>`_
degree of excitation respect to Hartree Fock for the wave function degree of excitation respect to Hartree Fock for the wave function
.br .br
for the all the selectors determinants for the all the selectors determinants
@ -161,39 +161,39 @@ Documentation
n_double_selectors = number of double excitations in the selectors determinants n_double_selectors = number of double excitations in the selectors determinants
`psi_selectors <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L30>`_ `psi_selectors <http://github.com/LCPQ/quantum_package/tree/master/plugins/Selectors_full/selectors.irp.f#L30>`_
Determinants on which we apply <i|H|psi> for perturbation. Determinants on which we apply <i|H|psi> for perturbation.
`psi_selectors_ab <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L64>`_ `psi_selectors_ab <http://github.com/LCPQ/quantum_package/tree/master/plugins/Selectors_full/selectors.irp.f#L64>`_
Determinants on which we apply <i|H|j>. Determinants on which we apply <i|H|j>.
They are sorted by the 3 highest electrons in the alpha part, They are sorted by the 3 highest electrons in the alpha part,
then by the 3 highest electrons in the beta part to accelerate then by the 3 highest electrons in the beta part to accelerate
the research of connected determinants. the research of connected determinants.
`psi_selectors_coef <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L31>`_ `psi_selectors_coef <http://github.com/LCPQ/quantum_package/tree/master/plugins/Selectors_full/selectors.irp.f#L31>`_
Determinants on which we apply <i|H|psi> for perturbation. Determinants on which we apply <i|H|psi> for perturbation.
`psi_selectors_coef_ab <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L65>`_ `psi_selectors_coef_ab <http://github.com/LCPQ/quantum_package/tree/master/plugins/Selectors_full/selectors.irp.f#L65>`_
Determinants on which we apply <i|H|j>. Determinants on which we apply <i|H|j>.
They are sorted by the 3 highest electrons in the alpha part, They are sorted by the 3 highest electrons in the alpha part,
then by the 3 highest electrons in the beta part to accelerate then by the 3 highest electrons in the beta part to accelerate
the research of connected determinants. the research of connected determinants.
`psi_selectors_diag_h_mat <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L51>`_ `psi_selectors_diag_h_mat <http://github.com/LCPQ/quantum_package/tree/master/plugins/Selectors_full/selectors.irp.f#L51>`_
Diagonal elements of the H matrix for each selectors Diagonal elements of the H matrix for each selectors
`psi_selectors_next_ab <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L66>`_ `psi_selectors_next_ab <http://github.com/LCPQ/quantum_package/tree/master/plugins/Selectors_full/selectors.irp.f#L66>`_
Determinants on which we apply <i|H|j>. Determinants on which we apply <i|H|j>.
They are sorted by the 3 highest electrons in the alpha part, They are sorted by the 3 highest electrons in the alpha part,
then by the 3 highest electrons in the beta part to accelerate then by the 3 highest electrons in the beta part to accelerate
the research of connected determinants. the research of connected determinants.
`psi_selectors_size <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L3>`_ `psi_selectors_size <http://github.com/LCPQ/quantum_package/tree/master/plugins/Selectors_full/selectors.irp.f#L3>`_
Undocumented Undocumented

12
scripts/module/module_handler.py
View File

@ -23,15 +23,19 @@ import shutil
try: try:
from docopt import docopt from docopt import docopt
from qp_path import QP_SRC from qp_path import QP_SRC, QP_ROOT, QP_PLUGINS
from qp_path import QP_ROOT
except ImportError: except ImportError:
print "source .quantum_package.rc" print "source .quantum_package.rc"
raise raise
def is_module(path_module): def is_module(path_module_rel):
return os.path.isfile(os.path.join(QP_SRC, path_module, 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")) "NEEDED_CHILDREN_MODULES"))

19
scripts/module/qp_update_readme.py
View File

@ -16,6 +16,7 @@ import sys
try: try:
from docopt import docopt from docopt import docopt
from module_handler import is_module, is_plugin
except: except:
print "Please check if you have sourced the .quantum_package.rc" print "Please check if you have sourced the .quantum_package.rc"
print "(`source .quantum_package.rc`)" print "(`source .quantum_package.rc`)"
@ -25,6 +26,7 @@ import os
from collections import namedtuple from collections import namedtuple
from collections import defaultdict from collections import defaultdict
def header_format(str_): def header_format(str_):
warning = "\n".join([".. Do not edit this section It was auto-generated", 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"), D_KEY = {"needed_module": header_format("Needed Modules"),
"documentation": header_format("Documentation")} "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): def fetch_splitted_data(d_readme, l_module_readme):
@ -72,7 +84,7 @@ def update_needed(d_readme):
modules = f.read() modules = f.read()
if modules.strip(): 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()] for name in modules.split()]
l_module_section = [D_KEY["needed_module"], '', l_module_section = [D_KEY["needed_module"], '',
@ -143,7 +155,8 @@ def update_documentation(d_readmen, root_module):
l_doc = [] l_doc = []
for irp in d_info[path]: 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) doc = extract_doc(root_module, irp.provider)
l_doc += ["`{0} <{1}#L{2}>`_".format(irp.provider, url, irp.line), l_doc += ["`{0} <{1}#L{2}>`_".format(irp.provider, url, irp.line),