Fix error in doc path
This commit is contained in:
Thomas Applencourt
parent
1c35435ea6
commit
006c28f4ee
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@ -13,9 +13,9 @@ Needed Modules
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.. image:: tree_dependency.png
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* `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
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* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
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* `Generators_full <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full>`_
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* `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation>`_
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* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/plugins/Selectors_full>`_
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* `Generators_full <http://github.com/LCPQ/quantum_package/tree/master/plugins/Generators_full>`_
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Documentation
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=============
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@ -23,146 +23,146 @@ Documentation
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.. by the `update_README.py` script.
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`full_ci <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/full_ci_no_skip.irp.f#L1>`_
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`full_ci <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/full_ci_no_skip.irp.f#L1>`_
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Undocumented
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`h_apply_fci <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L521>`_
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`h_apply_fci <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L521>`_
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Calls H_apply on the HF determinant and selects all connected single and double
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excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
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`h_apply_fci_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L1>`_
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`h_apply_fci_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L1>`_
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Generate all double excitations of key_in using the bit masks of holes and
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particles.
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Assume N_int is already provided.
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`h_apply_fci_mono <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L2720>`_
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`h_apply_fci_mono <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L2720>`_
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Calls H_apply on the HF determinant and selects all connected single and double
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excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
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`h_apply_fci_mono_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L2198>`_
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`h_apply_fci_mono_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L2198>`_
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Generate all double excitations of key_in using the bit masks of holes and
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particles.
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Assume N_int is already provided.
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`h_apply_fci_mono_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L2522>`_
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`h_apply_fci_mono_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L2522>`_
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Generate all single excitations of key_in using the bit masks of holes and
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particles.
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Assume N_int is already provided.
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`h_apply_fci_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L325>`_
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`h_apply_fci_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L325>`_
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Generate all single excitations of key_in using the bit masks of holes and
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particles.
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Assume N_int is already provided.
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`h_apply_fci_no_skip <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L1980>`_
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`h_apply_fci_no_skip <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L1980>`_
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Calls H_apply on the HF determinant and selects all connected single and double
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excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
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`h_apply_fci_no_skip_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L1460>`_
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`h_apply_fci_no_skip_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L1460>`_
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Generate all double excitations of key_in using the bit masks of holes and
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particles.
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Assume N_int is already provided.
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`h_apply_fci_no_skip_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L1784>`_
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`h_apply_fci_no_skip_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L1784>`_
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Generate all single excitations of key_in using the bit masks of holes and
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particles.
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Assume N_int is already provided.
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`h_apply_fci_pt2 <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L1253>`_
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`h_apply_fci_pt2 <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L1253>`_
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Calls H_apply on the HF determinant and selects all connected single and double
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excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
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`h_apply_fci_pt2_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L767>`_
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`h_apply_fci_pt2_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L767>`_
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Generate all double excitations of key_in using the bit masks of holes and
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particles.
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Assume N_int is already provided.
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`h_apply_fci_pt2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L1071>`_
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`h_apply_fci_pt2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L1071>`_
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Generate all single excitations of key_in using the bit masks of holes and
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particles.
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Assume N_int is already provided.
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`h_apply_pt2_mono_delta_rho <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L4222>`_
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`h_apply_pt2_mono_delta_rho <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L4222>`_
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Calls H_apply on the HF determinant and selects all connected single and double
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excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
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`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>`_
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`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>`_
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Generate all double excitations of key_in using the bit masks of holes and
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particles.
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Assume N_int is already provided.
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`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>`_
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`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>`_
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Generate all single excitations of key_in using the bit masks of holes and
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particles.
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Assume N_int is already provided.
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`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>`_
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`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>`_
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Calls H_apply on the HF determinant and selects all connected single and double
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excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
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`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>`_
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`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>`_
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Generate all double excitations of key_in using the bit masks of holes and
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particles.
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Assume N_int is already provided.
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`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>`_
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`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>`_
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Generate all single excitations of key_in using the bit masks of holes and
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particles.
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Assume N_int is already provided.
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`h_apply_select_mono_delta_rho <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L3488>`_
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`h_apply_select_mono_delta_rho <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L3488>`_
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Calls H_apply on the HF determinant and selects all connected single and double
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excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
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`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>`_
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`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>`_
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Generate all double excitations of key_in using the bit masks of holes and
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particles.
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Assume N_int is already provided.
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`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>`_
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`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>`_
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Generate all single excitations of key_in using the bit masks of holes and
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particles.
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Assume N_int is already provided.
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`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>`_
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`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>`_
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Calls H_apply on the HF determinant and selects all connected single and double
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excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
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`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>`_
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`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>`_
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Generate all double excitations of key_in using the bit masks of holes and
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particles.
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Assume N_int is already provided.
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`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>`_
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`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>`_
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Generate all single excitations of key_in using the bit masks of holes and
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particles.
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Assume N_int is already provided.
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`var_pt2_ratio_run <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/var_pt2_ratio.irp.f#L1>`_
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`var_pt2_ratio_run <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/var_pt2_ratio.irp.f#L1>`_
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Undocumented
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@ -25,7 +25,7 @@ Needed Modules
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.. image:: tree_dependency.png
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* `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
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* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
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* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock>`_
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Documentation
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=============
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@ -33,29 +33,29 @@ Documentation
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.. by the `update_README.py` script.
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`degree_max_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full/generators.irp.f#L43>`_
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`degree_max_generators <http://github.com/LCPQ/quantum_package/tree/master/plugins/Generators_full/generators.irp.f#L43>`_
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Max degree of excitation (respect to HF) of the generators
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`n_det_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full/generators.irp.f#L3>`_
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`n_det_generators <http://github.com/LCPQ/quantum_package/tree/master/plugins/Generators_full/generators.irp.f#L3>`_
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For Single reference wave functions, the number of generators is 1 : the
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Hartree-Fock determinant
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`psi_coef_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full/generators.irp.f#L26>`_
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`psi_coef_generators <http://github.com/LCPQ/quantum_package/tree/master/plugins/Generators_full/generators.irp.f#L26>`_
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For Single reference wave functions, the generator is the
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Hartree-Fock determinant
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`psi_det_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full/generators.irp.f#L25>`_
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`psi_det_generators <http://github.com/LCPQ/quantum_package/tree/master/plugins/Generators_full/generators.irp.f#L25>`_
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For Single reference wave functions, the generator is the
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Hartree-Fock determinant
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`select_max <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full/generators.irp.f#L66>`_
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`select_max <http://github.com/LCPQ/quantum_package/tree/master/plugins/Generators_full/generators.irp.f#L66>`_
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Memo to skip useless selectors
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`size_select_max <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full/generators.irp.f#L58>`_
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`size_select_max <http://github.com/LCPQ/quantum_package/tree/master/plugins/Generators_full/generators.irp.f#L58>`_
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Size of the select_max array
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@ -32,57 +32,57 @@ Documentation
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.. by the `update_README.py` script.
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`ao_bi_elec_integral_alpha <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L102>`_
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`ao_bi_elec_integral_alpha <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/Fock_matrix.irp.f#L102>`_
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Alpha Fock matrix in AO basis set
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`ao_bi_elec_integral_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L103>`_
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`ao_bi_elec_integral_beta <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/Fock_matrix.irp.f#L103>`_
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Alpha Fock matrix in AO basis set
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`create_guess <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/SCF.irp.f#L13>`_
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`create_guess <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/SCF.irp.f#L13>`_
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Create an MO guess if no MOs are present in the EZFIO directory
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`damping_scf <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/damping_SCF.irp.f#L1>`_
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`damping_scf <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/damping_SCF.irp.f#L1>`_
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Undocumented
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`diagonal_fock_matrix_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/diagonalize_fock.irp.f#L1>`_
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`diagonal_fock_matrix_mo <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/diagonalize_fock.irp.f#L1>`_
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Diagonal Fock matrix in the MO basis
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`diagonal_fock_matrix_mo_sum <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/diagonalize_fock.irp.f#L67>`_
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`diagonal_fock_matrix_mo_sum <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/diagonalize_fock.irp.f#L67>`_
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diagonal element of the fock matrix calculated as the sum over all the interactions
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with all the electrons in the RHF determinant
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diagonal_Fock_matrix_mo_sum(i) = sum_{j=1, N_elec} 2 J_ij -K_ij
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`eigenvectors_fock_matrix_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/diagonalize_fock.irp.f#L2>`_
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`eigenvectors_fock_matrix_mo <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/diagonalize_fock.irp.f#L2>`_
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Diagonal Fock matrix in the MO basis
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`fock_matrix_alpha_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L83>`_
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`fock_matrix_alpha_ao <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/Fock_matrix.irp.f#L83>`_
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Alpha Fock matrix in AO basis set
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`fock_matrix_alpha_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L231>`_
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`fock_matrix_alpha_mo <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/Fock_matrix.irp.f#L231>`_
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Fock matrix on the MO basis
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|
||||
`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_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
|
||||
|
||||
|
||||
`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_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.
|
||||
For open shells, the ROHF Fock Matrix is
|
||||
.br
|
||||
|
|
@ -98,7 +98,7 @@ Documentation
|
|||
.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.
|
||||
For open shells, the ROHF Fock Matrix is
|
||||
.br
|
||||
|
|
@ -114,53 +114,53 @@ Documentation
|
|||
.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
|
||||
|
||||
|
||||
`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
|
||||
|
||||
|
||||
`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
|
||||
|
||||
|
||||
`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
|
||||
|
||||
|
||||
`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
|
||||
|
||||
|
||||
`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
|
||||
|
||||
|
||||
`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
|
||||
|
||||
|
||||
`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 ]
|
||||
|
||||
|
||||
`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
|
||||
|
||||
|
||||
`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
|
||||
|
||||
|
||||
`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
|
||||
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 <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
|
||||
|
||||
|
|
|
|||
|
|
@ -86,8 +86,8 @@ Needed Modules
|
|||
|
||||
.. image:: tree_dependency.png
|
||||
|
||||
* `Properties <http://github.com/LCPQ/quantum_package/tree/master/src/Properties>`_
|
||||
* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
|
||||
* `Properties <http://github.com/LCPQ/quantum_package/tree/master/plugins/Properties>`_
|
||||
* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock>`_
|
||||
|
||||
Documentation
|
||||
=============
|
||||
|
|
@ -95,109 +95,109 @@ Documentation
|
|||
.. 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
|
||||
|
||||
|
||||
`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
|
||||
|
||||
|
||||
`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
|
||||
|
||||
|
||||
`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
|
||||
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
|
||||
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
|
||||
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
|
||||
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
|
||||
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
|
||||
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
|
||||
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
|
||||
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
|
||||
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
|
||||
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
|
||||
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
|
||||
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
|
||||
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
|
||||
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
|
||||
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
|
||||
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
|
||||
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
|
||||
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
|
||||
.br
|
||||
for the various n_st states, at various level of theory.
|
||||
|
|
@ -218,7 +218,7 @@ Documentation
|
|||
.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
|
||||
.br
|
||||
for the various n_st states, at various level of theory.
|
||||
|
|
@ -239,7 +239,7 @@ Documentation
|
|||
.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
|
||||
.br
|
||||
for the various N_st states.
|
||||
|
|
@ -250,7 +250,7 @@ Documentation
|
|||
.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
|
||||
.br
|
||||
for the various N_st states.
|
||||
|
|
@ -261,7 +261,7 @@ Documentation
|
|||
.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
|
||||
.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 <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
|
||||
.br
|
||||
for the various N_st states,
|
||||
|
|
@ -296,7 +296,7 @@ Documentation
|
|||
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
|
||||
.br
|
||||
for the various N_st states,
|
||||
|
|
@ -320,7 +320,7 @@ Documentation
|
|||
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
|
||||
.br
|
||||
for the various N_st states.
|
||||
|
|
@ -331,12 +331,12 @@ Documentation
|
|||
.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
|
||||
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
|
||||
.br
|
||||
for the various n_st states.
|
||||
|
|
@ -347,28 +347,28 @@ Documentation
|
|||
.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
|
||||
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
|
||||
|
||||
|
||||
`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.
|
||||
|
||||
|
||||
`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.
|
||||
|
||||
|
||||
`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.
|
||||
|
||||
|
||||
`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)
|
||||
is equal to var_pt2_ratio
|
||||
|
||||
|
|
|
|||
|
|
@ -28,41 +28,41 @@ Documentation
|
|||
.. 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
|
||||
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
|
||||
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(2) = <psi_det|Y|psi_det>
|
||||
average_position(3) = <psi_det|Z|psi_det>
|
||||
|
||||
|
||||
`average_spread <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/properties.irp.f#L27>`_
|
||||
`average_spread <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(2) = <psi_det|Y^2|psi_det>
|
||||
average_spread(3) = <psi_det|Z^2|psi_det>
|
||||
|
||||
|
||||
`delta_z <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/delta_rho.irp.f#L4>`_
|
||||
`delta_z <http://github.com/LCPQ/quantum_package/tree/master/plugins/Properties/delta_rho.irp.f#L4>`_
|
||||
Undocumented
|
||||
|
||||
|
||||
`diag_o1_mat_elem <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/slater_rules_mono_electronic.irp.f#L91>`_
|
||||
`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>
|
||||
|
||||
|
||||
`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>
|
||||
|
||||
|
||||
`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
|
||||
.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 <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
|
||||
whom integrals on the MO basis are stored in "array"
|
||||
and with the density is stored in "density"
|
||||
|
||||
|
||||
`i_o1_j <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/slater_rules_mono_electronic.irp.f#L1>`_
|
||||
`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
|
||||
and O1 is a ONE BODY OPERATOR
|
||||
array is the array of the mono electronic operator
|
||||
on the MO basis
|
||||
|
||||
|
||||
`i_o1_j_alpha_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/slater_rules_mono_electronic.irp.f#L158>`_
|
||||
`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
|
||||
and O1 is a ONE BODY OPERATOR
|
||||
array is the array of the mono electronic operator
|
||||
on the MO basis
|
||||
|
||||
|
||||
`i_o1_psi <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/slater_rules_mono_electronic.irp.f#L52>`_
|
||||
`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
|
||||
and O1 is a ONE BODY OPERATOR
|
||||
array is the array of the mono electronic operator
|
||||
on the MO basis
|
||||
|
||||
|
||||
`i_o1_psi_alpha_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/slater_rules_mono_electronic.irp.f#L119>`_
|
||||
`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
|
||||
and O1 is a ONE BODY OPERATOR
|
||||
array is the array of the mono electronic operator
|
||||
on the MO basis
|
||||
|
||||
|
||||
`i_unit_integrated_delta_rho <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/delta_rho.irp.f#L118>`_
|
||||
`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
|
||||
|
||||
|
||||
`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
|
||||
integrated_rho(alpha,z) - integrated_rho(beta,z) for all the z points
|
||||
chosen
|
||||
.br
|
||||
|
||||
|
||||
`integrated_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/delta_rho.irp.f#L212>`_
|
||||
`integrated_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/plugins/Properties/delta_rho.irp.f#L212>`_
|
||||
.br
|
||||
integral (x,y) and (z,z+delta_z) of rho(alpha) - rho(beta)
|
||||
on the MO basis
|
||||
.br
|
||||
|
||||
|
||||
`mo_integrated_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/delta_rho.irp.f#L184>`_
|
||||
`mo_integrated_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/plugins/Properties/delta_rho.irp.f#L184>`_
|
||||
.br
|
||||
array of the integrals needed of integrated_rho(alpha,z) - integrated_rho(beta,z) for z = z_one_point
|
||||
on the MO basis
|
||||
.br
|
||||
|
||||
|
||||
`n_z_pts <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/delta_rho.irp.f#L1>`_
|
||||
`n_z_pts <http://github.com/LCPQ/quantum_package/tree/master/plugins/Properties/delta_rho.irp.f#L1>`_
|
||||
Undocumented
|
||||
|
||||
|
||||
`test_average_value <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/routines_test.irp.f#L3>`_
|
||||
`test_average_value <http://github.com/LCPQ/quantum_package/tree/master/plugins/Properties/routines_test.irp.f#L3>`_
|
||||
Undocumented
|
||||
|
||||
|
||||
`test_average_value_alpha_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/routines_test.irp.f#L25>`_
|
||||
`test_average_value_alpha_beta <http://github.com/LCPQ/quantum_package/tree/master/plugins/Properties/routines_test.irp.f#L25>`_
|
||||
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
|
||||
|
||||
|
||||
`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
|
||||
|
||||
|
||||
`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
|
||||
|
||||
|
||||
`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
|
||||
|
||||
|
|
|
|||
|
|
@ -22,7 +22,7 @@ Needed Modules
|
|||
.. image:: tree_dependency.png
|
||||
|
||||
* `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
|
||||
* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
|
||||
* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock>`_
|
||||
|
||||
Documentation
|
||||
=============
|
||||
|
|
@ -30,7 +30,7 @@ Documentation
|
|||
.. 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
|
||||
.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 <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
|
||||
.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 <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
|
||||
.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 <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
|
||||
.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 <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
|
||||
.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 <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
|
||||
.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 <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
|
||||
.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 <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
|
||||
.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 <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
|
||||
.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 <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
|
||||
.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 <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
|
||||
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
|
||||
.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 <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.
|
||||
|
||||
|
||||
`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>.
|
||||
They are sorted by the 3 highest electrons in the alpha part,
|
||||
then by the 3 highest electrons in the beta part to accelerate
|
||||
the research of connected determinants.
|
||||
|
||||
|
||||
`psi_selectors_coef <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L31>`_
|
||||
`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.
|
||||
|
||||
|
||||
`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>.
|
||||
They are sorted by the 3 highest electrons in the alpha part,
|
||||
then by the 3 highest electrons in the beta part to accelerate
|
||||
the research of connected determinants.
|
||||
|
||||
|
||||
`psi_selectors_diag_h_mat <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L51>`_
|
||||
`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
|
||||
|
||||
|
||||
`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>.
|
||||
They are sorted by the 3 highest electrons in the alpha part,
|
||||
then by the 3 highest electrons in the beta part to accelerate
|
||||
the research of connected determinants.
|
||||
|
||||
|
||||
`psi_selectors_size <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L3>`_
|
||||
`psi_selectors_size <http://github.com/LCPQ/quantum_package/tree/master/plugins/Selectors_full/selectors.irp.f#L3>`_
|
||||
Undocumented
|
||||
|
||||
|
|
|
|||
|
|
@ -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"))
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -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),
|
||||
|
|
|
|||
Loading…
Reference in New Issue