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Merge pull request #99 from TApplencourt/master

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Fix path error in doc and graphiz dependancy
This commit is contained in:
Thomas Applencourt 2015-07-28 17:38:35 +02:00
commit 5e8a106d85
24 changed files with 934 additions and 744 deletions
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2
configure vendored
View File

@ -451,7 +451,7 @@ def create_ninja_and_rc(l_installed):
'export IRPF90={0}'.format(path_irpf90),
'export NINJA={0}'.format(path_ninja),
'export QP_PYTHON={0}'.format(":".join(l_python)), "",
'export PYTHONPATH="${QP_PYTHON}":"${PYTHONPATH}"',
'export PYTHONPATH="${QP_EZFIO}":"${QP_PYTHON}":"${PYTHONPATH}"',
'export PATH="${QP_PYTHON}":"${QP_ROOT}"/bin:"${QP_ROOT}"/ocaml:"${PATH}"',
'export LD_LIBRARY_PATH="${QP_ROOT}"/lib:"${LD_LIBRARY_PATH}"',
'export LIBRARY_PATH="${QP_ROOT}"/lib:"${LIBRARY_PATH}"', "",

1
plugins/Full_CI/.gitignore vendored
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@ -22,7 +22,6 @@ Properties
Pseudo
Selectors_full
Utils
exc_degree
ezfio_interface.irp.f
full_ci
full_ci_no_skip

307
plugins/Full_CI/README.rst
View File

@ -4,164 +4,165 @@ Full_CI Module
Performs a perturbatively selected Full-CI.
Documentation
=============
.. Do not edit this section. It was auto-generated from the
.. 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>`_
Undocumented
`h_apply_fci <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L521>`_
Calls H_apply on the HF determinant and selects all connected single and double
excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
`h_apply_fci_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L1>`_
Generate all double excitations of key_in using the bit masks of holes and
particles.
Assume N_int is already provided.
`h_apply_fci_mono <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L2720>`_
Calls H_apply on the HF determinant and selects all connected single and double
excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
`h_apply_fci_mono_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L2198>`_
Generate all double excitations of key_in using the bit masks of holes and
particles.
Assume N_int is already provided.
`h_apply_fci_mono_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L2522>`_
Generate all single excitations of key_in using the bit masks of holes and
particles.
Assume N_int is already provided.
`h_apply_fci_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L325>`_
Generate all single excitations of key_in using the bit masks of holes and
particles.
Assume N_int is already provided.
`h_apply_fci_no_skip <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L1980>`_
Calls H_apply on the HF determinant and selects all connected single and double
excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
`h_apply_fci_no_skip_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L1460>`_
Generate all double excitations of key_in using the bit masks of holes and
particles.
Assume N_int is already provided.
`h_apply_fci_no_skip_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L1784>`_
Generate all single excitations of key_in using the bit masks of holes and
particles.
Assume N_int is already provided.
`h_apply_fci_pt2 <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L1253>`_
Calls H_apply on the HF determinant and selects all connected single and double
excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
`h_apply_fci_pt2_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L767>`_
Generate all double excitations of key_in using the bit masks of holes and
particles.
Assume N_int is already provided.
`h_apply_fci_pt2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L1071>`_
Generate all single excitations of key_in using the bit masks of holes and
particles.
Assume N_int is already provided.
`h_apply_pt2_mono_delta_rho <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L4222>`_
Calls H_apply on the HF determinant and selects all connected single and double
excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
`h_apply_pt2_mono_delta_rho_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L3734>`_
Generate all double excitations of key_in using the bit masks of holes and
particles.
Assume N_int is already provided.
`h_apply_pt2_mono_delta_rho_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L4038>`_
Generate all single excitations of key_in using the bit masks of holes and
particles.
Assume N_int is already provided.
`h_apply_pt2_mono_di_delta_rho <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L5681>`_
Calls H_apply on the HF determinant and selects all connected single and double
excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
`h_apply_pt2_mono_di_delta_rho_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L5195>`_
Generate all double excitations of key_in using the bit masks of holes and
particles.
Assume N_int is already provided.
`h_apply_pt2_mono_di_delta_rho_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L5499>`_
Generate all single excitations of key_in using the bit masks of holes and
particles.
Assume N_int is already provided.
`h_apply_select_mono_delta_rho <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L3488>`_
Calls H_apply on the HF determinant and selects all connected single and double
excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
`h_apply_select_mono_delta_rho_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L2966>`_
Generate all double excitations of key_in using the bit masks of holes and
particles.
Assume N_int is already provided.
`h_apply_select_mono_delta_rho_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L3290>`_
Generate all single excitations of key_in using the bit masks of holes and
particles.
Assume N_int is already provided.
`h_apply_select_mono_di_delta_rho <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L4949>`_
Calls H_apply on the HF determinant and selects all connected single and double
excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
`h_apply_select_mono_di_delta_rho_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L4429>`_
Generate all double excitations of key_in using the bit masks of holes and
particles.
Assume N_int is already provided.
`h_apply_select_mono_di_delta_rho_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L4753>`_
Generate all single excitations of key_in using the bit masks of holes and
particles.
Assume N_int is already provided.
`var_pt2_ratio_run <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/var_pt2_ratio.irp.f#L1>`_
Undocumented
Needed Modules
==============
.. Do not edit this section. It was auto-generated from the
.. Do not edit this section It was auto-generated
.. by the `update_README.py` script.
.. image:: tree_dependency.png
* `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
* `Generators_full <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full>`_
* `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation>`_
* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/plugins/Selectors_full>`_
* `Generators_full <http://github.com/LCPQ/quantum_package/tree/master/plugins/Generators_full>`_
Documentation
=============
.. Do not edit this section It was auto-generated
.. by the `update_README.py` script.
`full_ci <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/full_ci_no_skip.irp.f#L1>`_
Undocumented
`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
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/plugins/Full_CI/H_apply.irp.f_shell_43#L1>`_
Generate all double excitations of key_in using the bit masks of holes and
particles.
Assume N_int is already provided.
`h_apply_fci_mono <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
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/plugins/Full_CI/H_apply.irp.f_shell_43#L2198>`_
Generate all double excitations of key_in using the bit masks of holes and
particles.
Assume N_int is already provided.
`h_apply_fci_mono_monoexc <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
particles.
Assume N_int is already provided.
`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
particles.
Assume N_int is already provided.
`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
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/plugins/Full_CI/H_apply.irp.f_shell_43#L1460>`_
Generate all double excitations of key_in using the bit masks of holes and
particles.
Assume N_int is already provided.
`h_apply_fci_no_skip_monoexc <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
particles.
Assume N_int is already provided.
`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
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/plugins/Full_CI/H_apply.irp.f_shell_43#L767>`_
Generate all double excitations of key_in using the bit masks of holes and
particles.
Assume N_int is already provided.
`h_apply_fci_pt2_monoexc <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
particles.
Assume N_int is already provided.
`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
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/plugins/Full_CI/H_apply.irp.f_shell_43#L3734>`_
Generate all double excitations of key_in using the bit masks of holes and
particles.
Assume N_int is already provided.
`h_apply_pt2_mono_delta_rho_monoexc <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
particles.
Assume N_int is already provided.
`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
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/plugins/Full_CI/H_apply.irp.f_shell_43#L5195>`_
Generate all double excitations of key_in using the bit masks of holes and
particles.
Assume N_int is already provided.
`h_apply_pt2_mono_di_delta_rho_monoexc <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
particles.
Assume N_int is already provided.
`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
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/plugins/Full_CI/H_apply.irp.f_shell_43#L2966>`_
Generate all double excitations of key_in using the bit masks of holes and
particles.
Assume N_int is already provided.
`h_apply_select_mono_delta_rho_monoexc <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
particles.
Assume N_int is already provided.
`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
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/plugins/Full_CI/H_apply.irp.f_shell_43#L4429>`_
Generate all double excitations of key_in using the bit masks of holes and
particles.
Assume N_int is already provided.
`h_apply_select_mono_di_delta_rho_monoexc <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
particles.
Assume N_int is already provided.
`var_pt2_ratio_run <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/var_pt2_ratio.irp.f#L1>`_
Undocumented

77
plugins/Generators_full/README.rst
View File

@ -5,42 +5,10 @@ Generators_full Module
All the determinants of the wave function are generators. In this way, the Full CI
space is explored.
Documentation
=============
.. Do not edit this section. It was auto-generated from the
.. by the `update_README.py` script.
`degree_max_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full/generators.irp.f#L43>`_
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>`_
For Single reference wave functions, the number of generators is 1 : the
Hartree-Fock determinant
`psi_coef_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full/generators.irp.f#L26>`_
For Single reference wave functions, the generator is the
Hartree-Fock determinant
`psi_det_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full/generators.irp.f#L25>`_
For Single reference wave functions, the generator is the
Hartree-Fock determinant
`select_max <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full/generators.irp.f#L66>`_
Memo to skip useless selectors
`size_select_max <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full/generators.irp.f#L58>`_
Size of the select_max array
Needed Modules
==============
.. Do not edit this section. It was auto-generated from the
.. Do not edit this section It was auto-generated
.. by the `update_README.py` script.
.. image:: tree_dependency.png
@ -48,3 +16,46 @@ Needed Modules
* `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
Needed Modules
==============
.. Do not edit this section It was auto-generated
.. by the `update_README.py` script.
.. 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/plugins/Hartree_Fock>`_
Documentation
=============
.. Do not edit this section It was auto-generated
.. by the `update_README.py` script.
`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
`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
Hartree-Fock determinant
`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
Hartree-Fock determinant
`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
Hartree-Fock determinant
`select_max <http://github.com/LCPQ/quantum_package/tree/master/plugins/Generators_full/generators.irp.f#L66>`_
Memo to skip useless selectors
`size_select_max <http://github.com/LCPQ/quantum_package/tree/master/plugins/Generators_full/generators.irp.f#L58>`_
Size of the select_max array

69
plugins/Hartree_Fock/README.rst
View File

@ -7,9 +7,20 @@ From the 140 molecules of the G2 set, only LiO, ONa don't converge well.
Needed Modules
==============
.. Do not edit this section. It was auto-generated from the
.. Do not edit this section It was auto-generated
.. by the `update_README.py` script.
.. image:: tree_dependency.png
* `Integrals_Bielec <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec>`_
* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
Needed Modules
==============
.. Do not edit this section It was auto-generated
.. by the `update_README.py` script.
.. image:: tree_dependency.png
* `Integrals_Bielec <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec>`_
@ -17,61 +28,61 @@ Needed Modules
Documentation
=============
.. Do not edit this section. It was auto-generated from the
.. Do not edit this section It was auto-generated
.. 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
`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
`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
`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
`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_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
with all the electrons in the RHF determinant
diagonal_Fock_matrix_mo_sum(i) = sum_{j=1, N_elec} 2 J_ij -K_ij
`eigenvectors_fock_matrix_mo <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
`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
`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_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
@ -87,7 +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
@ -103,53 +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

113
plugins/Perturbation/README.rst
View File

@ -67,115 +67,137 @@ Assumptions
pt2_....
Documentation
=============
Needed Modules
==============
.. Do not edit this section. It was auto-generated from the
.. Do not edit this section It was auto-generated
.. by the `update_README.py` script.
`do_pt2_end <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/ezfio_interface.irp.f#L6>`_
.. 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>`_
Needed Modules
==============
.. Do not edit this section It was auto-generated
.. by the `update_README.py` script.
.. image:: tree_dependency.png
* `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
=============
.. Do not edit this section It was auto-generated
.. by the `update_README.py` script.
`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.
@ -196,7 +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.
@ -217,7 +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.
@ -228,7 +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.
@ -239,7 +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
@ -250,7 +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,
@ -274,7 +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,
@ -298,7 +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.
@ -309,12 +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.
@ -325,39 +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
Needed Modules
==============
.. Do not edit this section. It was auto-generated from the
.. by the `update_README.py` script.
.. 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>`_

84
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View File

@ -2,47 +2,67 @@
Properties Module
=================
Documentation
=============
Needed Modules
==============
.. Do not edit this section. It was auto-generated from the
.. Do not edit this section It was auto-generated
.. 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>`_
.. image:: tree_dependency.png
* `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
Needed Modules
==============
.. Do not edit this section It was auto-generated
.. by the `update_README.py` script.
.. image:: tree_dependency.png
* `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
Documentation
=============
.. Do not edit this section It was auto-generated
.. by the `update_README.py` script.
`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)
@ -56,99 +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
Needed Modules
==============
.. Do not edit this section. It was auto-generated from the
.. by the `update_README.py` script.
.. image:: tree_dependency.png
* `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_

359
plugins/Selectors_full/README.rst
View File

@ -2,183 +2,10 @@
Selectors_full Module
=====================
Documentation
=============
.. Do not edit this section. It was auto-generated from the
.. 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>`_
energy of correlation per determinant respect to the Hartree Fock determinant
.br
for the all the double excitations in the selectors determinants
.br
E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> is a double excitation
.br
E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
.br
coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
`delta_e_per_selector <http://github.com/LCPQ/quantum_package/tree/master/src/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
.br
E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> is a double excitation
.br
E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
.br
coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
`double_index_selectors <http://github.com/LCPQ/quantum_package/tree/master/src/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
.br
double_index_selectors = list of the index of the double excitations
.br
n_double_selectors = number of double excitations in the selectors determinants
`e_corr_double_only <http://github.com/LCPQ/quantum_package/tree/master/src/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
.br
E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> is a double excitation
.br
E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
.br
coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
`e_corr_per_selectors <http://github.com/LCPQ/quantum_package/tree/master/src/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
.br
E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> is a double excitation
.br
E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
.br
coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
`e_corr_second_order <http://github.com/LCPQ/quantum_package/tree/master/src/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
.br
E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> is a double excitation
.br
E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
.br
coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
`exc_degree_per_selectors <http://github.com/LCPQ/quantum_package/tree/master/src/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
.br
double_index_selectors = list of the index of the double excitations
.br
n_double_selectors = number of double excitations in the selectors determinants
`i_h_hf_per_selectors <http://github.com/LCPQ/quantum_package/tree/master/src/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
.br
E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> is a double excitation
.br
E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
.br
coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
`inv_selectors_coef_hf <http://github.com/LCPQ/quantum_package/tree/master/src/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
.br
E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> is a double excitation
.br
E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
.br
coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
`inv_selectors_coef_hf_squared <http://github.com/LCPQ/quantum_package/tree/master/src/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
.br
E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> is a double excitation
.br
E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
.br
coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
`n_det_selectors <http://github.com/LCPQ/quantum_package/tree/master/src/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>`_
degree of excitation respect to Hartree Fock for the wave function
.br
for the all the selectors determinants
.br
double_index_selectors = list of the index of the double excitations
.br
n_double_selectors = number of double excitations in the selectors determinants
`psi_selectors <http://github.com/LCPQ/quantum_package/tree/master/src/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>`_
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>`_
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>`_
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>`_
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>`_
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>`_
Undocumented
Needed Modules
==============
.. Do not edit this section. It was auto-generated from the
.. Do not edit this section It was auto-generated
.. by the `update_README.py` script.
.. image:: tree_dependency.png
@ -186,3 +13,187 @@ Needed Modules
* `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
Needed Modules
==============
.. Do not edit this section It was auto-generated
.. by the `update_README.py` script.
.. 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/plugins/Hartree_Fock>`_
Documentation
=============
.. Do not edit this section It was auto-generated
.. by the `update_README.py` script.
`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
.br
E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> is a double excitation
.br
E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
.br
coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
`delta_e_per_selector <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
.br
E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> is a double excitation
.br
E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
.br
coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
`double_index_selectors <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
.br
double_index_selectors = list of the index of the double excitations
.br
n_double_selectors = number of double excitations in the selectors determinants
`e_corr_double_only <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
.br
E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> is a double excitation
.br
E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
.br
coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
`e_corr_per_selectors <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
.br
E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> is a double excitation
.br
E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
.br
coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
`e_corr_second_order <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
.br
E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> is a double excitation
.br
E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
.br
coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
`exc_degree_per_selectors <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
.br
double_index_selectors = list of the index of the double excitations
.br
n_double_selectors = number of double excitations in the selectors determinants
`i_h_hf_per_selectors <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
.br
E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> is a double excitation
.br
E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
.br
coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
`inv_selectors_coef_hf <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
.br
E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> is a double excitation
.br
E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
.br
coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
`inv_selectors_coef_hf_squared <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
.br
E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> is a double excitation
.br
E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
.br
coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
`n_det_selectors <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/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
.br
double_index_selectors = list of the index of the double excitations
.br
n_double_selectors = number of double excitations in the selectors determinants
`psi_selectors <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/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/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/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/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/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/plugins/Selectors_full/selectors.irp.f#L3>`_
Undocumented

55
scripts/compilation/qp_create_ninja.py
View File

@ -23,12 +23,11 @@ except ImportError:
"..",
"..",
"quantum_package.rc"))
print """
Error:
source %s
""" % f
print "\n".join(["", "Error:", "source %s" % f, ""])
sys.exit(1)
# __
# /__ | _ |_ _. | _. ._ o _. |_ | _ _
# \_| | (_) |_) (_| | \/ (_| | | (_| |_) | (/_ _>
@ -516,7 +515,7 @@ def ninja_readme_rule():
For not dealted the readme when ninja -t clean and the generator option
"""
l_string = ["rule build_readme",
" command = cd $module_abs ; update_README.py $module_root",
" command = qp_update_readme.py $module_abs --root_module $module_root",
" description = update_README $module_rel",
" generator = 1", ""]
@ -552,7 +551,8 @@ def ninja_readme_build(path_module, d_irp, dict_root_path):
# /
def get_binaries(path_module):
"""
Return the list of binaries (Path= namedtuple('Path', ['abs', 'rel']) for a module
Return the list of binaries
(Path= namedtuple('Path', ['abs', 'rel']) for a module
"""
import subprocess
@ -666,20 +666,26 @@ def ninja_binaries_build(path_module, l_children, d_binaries):
# s t r i n g #
# ~#~#~#~#~#~ #
path_readme = os.path.join(path_module.abs, "README.rst")
path_png = os.path.join(path_module.abs, "tree_dependency.png")
l_string = ["build {0}: build_binaries {1} {2}".format(" ".join(l_abs_bin),
EZFIO_LIB,
ninja_module_path),
" module_abs = {0}".format(path_module.abs),
" module_rel = {0}".format(path_module.rel), ""]
l_string += ["build module_{0}: phony {1} {2} {3}".format(path_module.rel,
return l_string
def ninja_module_build(path_module, d_binaries):
l_abs_bin = [binary.abs for binary in d_binaries[path_module]]
path_readme = os.path.join(path_module.abs, "README.rst")
path_png = os.path.join(path_module.abs, "tree_dependency.png")
l_string = ["build module_{0}: phony {1} {2} {3}".format(path_module.rel,
" ".join(l_abs_bin),
path_readme,
path_png
), ""]
path_png), ""]
return l_string
@ -723,7 +729,7 @@ def ninja_dot_tree_build(path_module, l_module):
# |\/| _ _| | _
# | | (_) (_| |_| | (/_
#
def create_build_ninja_module(path_module):
def save_subninja_file(path_module):
l_string = ["builddir = {0}".format(os.path.dirname(ROOT_BUILD_NINJA)),
""]
@ -732,17 +738,19 @@ def create_build_ninja_module(path_module):
""]
l_string += ["rule make_local_binaries",
" command = ninja -f {0} module_{1}".format(
ROOT_BUILD_NINJA, path_module.rel), " pool = console",
" command = ninja -f {0} module_{1}".format(ROOT_BUILD_NINJA, path_module.rel),
" pool = console",
" description = Compile only {0}".format(path_module.rel),
""]
l_string += ["rule make_all_binaries",
" command = ninja -f {0}".format(ROOT_BUILD_NINJA),
" pool = console", " description = Compiling all modules",
" pool = console",
" description = Compiling all modules",
""]
l_string += ["rule make_clean", " command = module_handler.py clean {0}".format(path_module.rel),
l_string += ["rule make_clean",
" command = module_handler.py clean {0}".format(path_module.rel),
" description = Cleaning module {0}".format(path_module.rel),
""]
@ -766,7 +774,7 @@ def create_build_ninja_global():
" command = {0} update".format(__file__),
""]
l_string += ["rule make_all_binaries",
l_string += ["rule make_all",
" command = ninja -f {0}".format(ROOT_BUILD_NINJA),
" pool = console", " description = Compiling all modules",
""]
@ -777,7 +785,7 @@ def create_build_ninja_global():
l_string += ["build dummy_target: update_build_ninja_root",
"",
"build all: make_all_binaries dummy_target",
"build all: make_all dummy_target",
"default all",
"",
"build clean: make_clean dummy_target",
@ -921,9 +929,6 @@ if __name__ == "__main__":
for module_to_compile in l_module:
if arguments["--development"]:
create_build_ninja_module(module_to_compile)
# ~#~#~#~#~#~#~#~ #
# S y m l i n k #
# ~#~#~#~#~#~#~#~ #
@ -941,9 +946,15 @@ if __name__ == "__main__":
l_string += ninja_binaries_build(module_to_compile, l_children,
d_binaries)
if arguments["--development"]:
l_string += ninja_module_build(module_to_compile, d_binaries)
l_string += ninja_gitignore_build(module_to_compile, d_binaries,
l_symlink)
save_subninja_file(module_to_compile)
# ~#~#~#~#~ #
# S a v e s #
# ~#~#~#~#~ #

27
scripts/module/module_handler.py
View File

@ -23,16 +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
# Canot cache for namedtuple are not hashable
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"))
@ -180,13 +183,7 @@ class ModuleHandler():
basename = "tree_dependency"
path = '{0}.png'.format(basename)
# Init
try:
from graphviz import Digraph
except:
with open(path, 'a'):
os.utime(path, None)
return
all_ready_done = []
@ -209,7 +206,14 @@ class ModuleHandler():
graph.node(module, fontcolor="red")
draw_module_edge(module, d_ref[module])
# Try to render the png
# If not just touch it
try:
graph.render(cleanup=True)
except:
with open(path, 'a'):
os.utime(path, None)
return
if __name__ == '__main__':
@ -289,4 +293,3 @@ if __name__ == '__main__':
l_text = l_dir + l_file + l_symlink + l_exe
l_text.sort()
f.write("\n".join(l_text))

9
scripts/module/qp_install_module.py
View File

@ -22,7 +22,7 @@ try:
from docopt import docopt
from module_handler import ModuleHandler, get_dict_child
from module_handler import get_l_module_descendant
from update_README import Doc_key, Needed_key
from qp_update_readme import D_KEY
from qp_path import QP_SRC, QP_PLUGINS, QP_ROOT
except ImportError:
print "Please check if you have sourced the .quantum_package.rc"
@ -56,8 +56,8 @@ def save_new_module(path, l_child):
with open(os.path.join(path, "README.rst"), "w") as f:
f.write(header + "\n")
f.write(Doc_key + "\n")
f.write(Needed_key + "\n")
f.write(D_KEY["needed_module"])
f.write(D_KEY["documentation"])
if __name__ == '__main__':
@ -108,8 +108,9 @@ if __name__ == '__main__':
save_new_module(path, l_child_reduce)
print " [ OK ]"
print "If this was a plugins, you can install it normaly. Type:"
print "You can now install it normaly. Type:"
print "` {0} install {1} `".format(os.path.basename(__file__), name)
print "And don't forgot to add this to the git if you want"
elif arguments["download"]:
pass

205
scripts/module/qp_update_readme.py Executable file
View File

@ -0,0 +1,205 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Updates the README.rst of a module
Usage:
qp_update_readme.py [<module_path>...] [--root_module=<module_path>]
Options:
path_readme: All the absolute path you want to update.
By default is the cwd
--root_module: Is the path of the root module who containt the tags file.
By default is the cwd
"""
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`)"
print sys.exit(1)
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",
".. by the `update_README.py` script."])
return "{0}\n{1}\n{2}\n".format(str_, "=" * len(str_), warning)
D_KEY = {"needed_module": header_format("Needed Modules"),
"documentation": header_format("Documentation")}
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):
"""Read the README.rst file and split it in strings:
* The documentation
* The needed modules
The result is given as a list of strings
"""
sentinel = "@@$%&@@"
for path_readme in l_module_readme:
with open(os.path.join(path_readme, "README.rst"), 'r') as f:
data = f.read()
# Place sentinels
for v in D_KEY.values():
data = data.replace(v, sentinel + v)
# Now Split data using the sentinels
d_readme[path_readme] = {"human": data.split(sentinel)[0]}
def update_needed(d_readme):
"""Read the NEEDED_CHILDREN_MODULES file, and replace the data with it.
Create the links to the GitHub pages."""
header_image = ".. image:: tree_dependency.png"
for path in d_readme:
with open(os.path.join(path, 'NEEDED_CHILDREN_MODULES'), 'r') as f:
modules = f.read()
if modules.strip():
l_module = ['* `{0} <{1}>`_'.format(name, get_url(name))
for name in modules.split()]
l_module_section = [D_KEY["needed_module"], '',
header_image, '',
'\n'.join(l_module), '', '']
else:
l_module_section = ""
d_readme[path]["needed_module"] = "\n".join(l_module_section)
def extract_doc(root_module, provider):
"""Extracts the documentation contained in IRPF90_man file"""
path = os.path.join(root_module, "IRPF90_man/%s.l" % (provider))
with open(path, 'r') as f:
l_line = f.readlines()
result = []
inside = False
for line in l_line:
if not inside:
inside = line.startswith(".SH Description")
else:
if line.startswith(".SH"):
break
result.append(" {0}".format(line.strip()))
if not result:
result = [" Undocumented"]
return "\n".join(result) + "\n"
def update_documentation(d_readmen, root_module):
"""Reads the BEGIN_DOC ... END_DOC blocks and builds the documentation"""
IRP_info = namedtuple('IRP_info', ["module", "file", "provider", "line"])
# If the file does not exist, don't do anything
path = os.path.join(root_module, "tags")
with open(path, 'r') as f:
dump = f.readlines()
d_info = defaultdict(list)
for i in dump:
# i =
# output_cpu_time_0 Ezfio_files/output.irp.f 2
provider, irp_file_raw, ligne = i.split()
for path in d_readme:
if root_module == path and "/" not in irp_file_raw:
d_info[path].append(IRP_info(os.path.basename(path),
irp_file_raw,
provider,
ligne))
elif "/" in irp_file_raw and os.path.dirname(irp_file_raw) in path:
module, irp_file = os.path.split(irp_file_raw)
d_info[path].append(IRP_info(module, irp_file, provider, ligne))
for path in d_readme:
l_doc = []
for irp in d_info[path]:
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),
doc,
""]
l_doc_section = [D_KEY["documentation"], '',
"\n".join(l_doc)]
d_readme[path]["documentation"] = "\n".join(l_doc_section)
if __name__ == '__main__':
arguments = docopt(__doc__)
if arguments["--root_module"]:
root_module = os.path.realpath(arguments["--root_module"])
else:
root_module = os.getcwd()
if not arguments["<module_path>"]:
l_module_readme = [os.path.join(os.getcwd())]
else:
l_module_readme = arguments["<module_path>"]
# d[Path] ={humain, needed_module, documentation}
d_readme = defaultdict(dict)
try:
fetch_splitted_data(d_readme, l_module_readme)
except IOError:
print l_module_readme, "is not a module and/or",
print "have not a `README.rst` file inside"
print "Abort..."
sys.exit(1)
update_needed(d_readme)
update_documentation(d_readme, root_module)
for path, d in d_readme.iteritems():
with open(os.path.join(path, "README.rst"), 'w') as f:
for k in ["human",
"needed_module",
"documentation"]:
f.write(d[k])

188
scripts/module/update_README.py
View File

@ -1,188 +0,0 @@
#!/usr/bin/env python
"""Updates the README.rst file as the include directive is disabled on GitHub."""
__date__ = "Thu Apr 3 23:06:18 CEST 2014"
__author__ = "Anthony Scemama<scemama@irsamc.ups-tlse.fr> & TApplencourt "
README = "README.rst"
Assum_key = "Assumptions\n===========\n"
Needed_key = "Needed Modules\n==============\n"
Doc_key = "Documentation\n=============\n"
Sentinel = "@@$%&@@"
URL = "http://github.com/LCPQ/quantum_package/tree/master/src/"
import os
import subprocess
from collections import namedtuple
import sys
"""
NEED to call in a module
First arg can be the root parent
"""
try:
ROOT_module = os.path.realpath(sys.argv[1])
except:
ROOT_module = os.getcwd()
if ROOT_module != os.getcwd():
change = True
else:
change = False
MODULE_NAME = os.path.basename(os.getcwd())
header = """
.. Do not edit this section. It was auto-generated from the
.. by the `update_README.py` script.
"""
def fetch_splitted_data():
"""Read the README.rst file and split it in strings:
* The documentation
* The needed modules
The result is given as a list of strings
"""
with open(README, 'r') as f:
data = f.read()
# Place sentinels
data = data.replace(Doc_key, Sentinel + Doc_key)
data = data.replace(Needed_key, Sentinel + Needed_key)
# Now Split data using the sentinels
result = data.split(Sentinel)
return result
def update_needed(data):
"""Read the NEEDED_CHILDREN_MODULES file, and replace the data with it.
Create the links to the GitHub pages."""
with open('NEEDED_CHILDREN_MODULES', 'r') as f:
modules = f.read()
header_image = ".. image:: tree_dependency.png\n\n"
if modules.strip():
modules = ['* `{0} <{1}>`_'.format(name, os.path.join(URL, name))
for name in modules.split()]
modules = "\n".join(modules)
modules = Needed_key + header + header_image + modules + '\n\n'
has_modules = False
for i in range(len(data)):
if data[i].startswith(Needed_key):
has_modules = True
data[i] = modules
if not has_modules:
data.append(modules)
return data
def extract_doc(item):
"""Extracts the documentation contained in IRPF90_man file"""
path = os.path.join(ROOT_module, "IRPF90_man/%s.l" % (item))
with open(path, 'r') as f:
l_line = f.readlines()
result = []
inside = False
for line in l_line:
if not inside:
inside = line.startswith(".SH Description")
else:
if line.startswith(".SH"):
break
result.append(" {0}".format(line.strip()))
if not result:
result = [" Undocumented"]
return "\n".join(result) + '\n'
def update_documentation(data):
"""Reads the BEGIN_DOC ... END_DOC blocks and builds the documentation"""
IRP_info = namedtuple('IRP_info', ["name", "file", "line"])
# If the file does not exist, don't do anything
path = os.path.join(ROOT_module, "tags")
with open(path, 'r') as f:
dump = f.readlines()
l_info = []
for i in dump:
name, f, ligne = i.split()
if not change and "/" not in i:
l_info.append(IRP_info(name, f, ligne))
elif change and MODULE_NAME in i:
l_info.append(IRP_info(name, f.split("/")[-1], ligne))
l_line = []
for irp in l_info:
url = os.path.join(URL, MODULE_NAME, irp.file)
doc = extract_doc(irp.name)
l_line += ["`{0} <{1}#L{2}>`_".format(irp.name, url, irp.line), doc,
""]
documentation = Doc_key + header + "\n".join(l_line)
has_doc = False
for i in range(len(data)):
if data[i].startswith(Doc_key):
has_doc = True
data[i] = documentation
if not has_doc:
data.append(documentation)
return data
def git_add():
"""Executes:
git add README.rst
throw an error if git is not precent"""
try:
# pipe output to /dev/null for silence
null = open("/dev/null", "w")
subprocess.Popen("git add README.rst", stdout=null, stderr=null)
null.close()
except OSError:
raise
def main():
data = fetch_splitted_data()
data = update_documentation(data)
data = update_needed(data)
output = ''.join(data)
with open(README, 'w') as f:
f.write(output)
try:
git_add()
except OSError:
pass
if __name__ == '__main__':
main()

16
src/AO_Basis/README.rst
View File

@ -33,19 +33,29 @@ Assumptions
Needed Modules
==============
.. Do not edit this section. It was auto-generated from the
.. Do not edit this section It was auto-generated
.. by the `update_README.py` script.
.. image:: tree_dependency.png
* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
Needed Modules
==============
.. Do not edit this section It was auto-generated
.. by the `update_README.py` script.
.. image:: tree_dependency.png
* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
Documentation
=============
.. Do not edit this section. It was auto-generated from the
.. Do not edit this section It was auto-generated
.. by the `update_README.py` script.
`ao_coef <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/ezfio_interface.irp.f#L24>`_
AO Coefficients, read from input. Those should not be used directly, as the MOs are expressed on the basis of **normalized** AOs.

16
src/Bitmask/README.rst
View File

@ -37,19 +37,29 @@ Assumptions
Needed Modules
==============
.. Do not edit this section. It was auto-generated from the
.. Do not edit this section It was auto-generated
.. by the `update_README.py` script.
.. image:: tree_dependency.png
* `MO_Basis <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis>`_
Needed Modules
==============
.. Do not edit this section It was auto-generated
.. by the `update_README.py` script.
.. image:: tree_dependency.png
* `MO_Basis <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis>`_
Documentation
=============
.. Do not edit this section. It was auto-generated from the
.. Do not edit this section It was auto-generated
.. by the `update_README.py` script.
`bitstring_to_hexa <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks_routines.irp.f#L98>`_
Transform a bit string to a string in hexadecimal format for printing

17
src/Determinants/README.rst
View File

@ -29,9 +29,20 @@ Assumptions
Needed Modules
==============
.. Do not edit this section. It was auto-generated from the
.. Do not edit this section It was auto-generated
.. by the `update_README.py` script.
.. image:: tree_dependency.png
* `Integrals_Monoelec <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec>`_
* `Integrals_Bielec <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec>`_
Needed Modules
==============
.. Do not edit this section It was auto-generated
.. by the `update_README.py` script.
.. image:: tree_dependency.png
* `Integrals_Monoelec <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec>`_
@ -39,10 +50,10 @@ Needed Modules
Documentation
=============
.. Do not edit this section. It was auto-generated from the
.. Do not edit this section It was auto-generated
.. by the `update_README.py` script.
`a_operator <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/slater_rules.irp.f#L962>`_
Needed for diag_H_mat_elem

16
src/Electrons/README.rst
View File

@ -21,19 +21,29 @@ Assumptions
Needed Modules
==============
.. Do not edit this section. It was auto-generated from the
.. Do not edit this section It was auto-generated
.. by the `update_README.py` script.
.. image:: tree_dependency.png
* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
Needed Modules
==============
.. Do not edit this section It was auto-generated
.. by the `update_README.py` script.
.. image:: tree_dependency.png
* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
Documentation
=============
.. Do not edit this section. It was auto-generated from the
.. Do not edit this section It was auto-generated
.. by the `update_README.py` script.
`elec_alpha_num <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons/ezfio_interface.irp.f#L28>`_
Numbers of electrons alpha ("up")

17
src/Integrals_Bielec/README.rst
View File

@ -13,9 +13,20 @@ MO integral, use ``get_mo_bielec_integral(i,j,k,l,mo_integrals_map)`` or
Needed Modules
==============
.. Do not edit this section. It was auto-generated from the
.. Do not edit this section It was auto-generated
.. by the `update_README.py` script.
.. image:: tree_dependency.png
* `Pseudo <http://github.com/LCPQ/quantum_package/tree/master/src/Pseudo>`_
* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
Needed Modules
==============
.. Do not edit this section It was auto-generated
.. by the `update_README.py` script.
.. image:: tree_dependency.png
* `Pseudo <http://github.com/LCPQ/quantum_package/tree/master/src/Pseudo>`_
@ -23,10 +34,10 @@ Needed Modules
Documentation
=============
.. Do not edit this section. It was auto-generated from the
.. Do not edit this section It was auto-generated
.. by the `update_README.py` script.
`add_integrals_to_map <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/mo_bi_integrals.irp.f#L42>`_
Adds integrals to tha MO map according to some bitmask

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src/Integrals_Monoelec/README.rst
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@ -1,9 +1,20 @@
Needed Modules
==============
.. Do not edit this section. It was auto-generated from the
.. Do not edit this section It was auto-generated
.. by the `update_README.py` script.
.. image:: tree_dependency.png
* `MO_Basis <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis>`_
* `Pseudo <http://github.com/LCPQ/quantum_package/tree/master/src/Pseudo>`_
Needed Modules
==============
.. Do not edit this section It was auto-generated
.. by the `update_README.py` script.
.. image:: tree_dependency.png
* `MO_Basis <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis>`_
@ -11,10 +22,10 @@ Needed Modules
Documentation
=============
.. Do not edit this section. It was auto-generated from the
.. Do not edit this section It was auto-generated
.. by the `update_README.py` script.
`ao_deriv2_x <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/kin_ao_ints.irp.f#L1>`_
second derivatives matrix elements in the ao basis
.. math::

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src/MOGuess/README.rst
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@ -5,19 +5,29 @@ MOGuess Module
Needed Modules
==============
.. Do not edit this section. It was auto-generated from the
.. Do not edit this section It was auto-generated
.. by the `update_README.py` script.
.. image:: tree_dependency.png
* `Integrals_Monoelec <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec>`_
Needed Modules
==============
.. Do not edit this section It was auto-generated
.. by the `update_README.py` script.
.. image:: tree_dependency.png
* `Integrals_Monoelec <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec>`_
Documentation
=============
.. Do not edit this section. It was auto-generated from the
.. Do not edit this section It was auto-generated
.. by the `update_README.py` script.
`ao_ortho_lowdin_coef <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess/mo_ortho_lowdin.irp.f#L2>`_
matrix of the coefficients of the mos generated by the
orthonormalization by the S^{-1/2} canonical transformation of the aos

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@ -33,9 +33,20 @@ ASSUMPTONS
Needed Modules
==============
.. Do not edit this section. It was auto-generated from the
.. Do not edit this section It was auto-generated
.. by the `update_README.py` script.
.. image:: tree_dependency.png
* `AO_Basis <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis>`_
* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
Needed Modules
==============
.. Do not edit this section It was auto-generated
.. by the `update_README.py` script.
.. image:: tree_dependency.png
* `AO_Basis <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis>`_
@ -43,10 +54,10 @@ Needed Modules
Documentation
=============
.. Do not edit this section. It was auto-generated from the
.. Do not edit this section It was auto-generated
.. by the `update_README.py` script.
`ao_to_mo <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis/mos.irp.f#L136>`_
Transform A from the AO basis to the MO basis

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@ -9,9 +9,20 @@ The coordinates are expressed in atomic units.
Needed Modules
==============
.. Do not edit this section. It was auto-generated from the
.. Do not edit this section It was auto-generated
.. by the `update_README.py` script.
.. image:: tree_dependency.png
* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
Needed Modules
==============
.. Do not edit this section It was auto-generated
.. by the `update_README.py` script.
.. image:: tree_dependency.png
* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
@ -19,10 +30,10 @@ Needed Modules
Documentation
=============
.. Do not edit this section. It was auto-generated from the
.. Do not edit this section It was auto-generated
.. by the `update_README.py` script.
`element_name <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L172>`_
Array of the name of element, sorted by nuclear charge (integer)

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@ -5,19 +5,29 @@ Pseudo Module
Needed Modules
==============
.. Do not edit this section. It was auto-generated from the
.. Do not edit this section It was auto-generated
.. by the `update_README.py` script.
.. image:: tree_dependency.png
* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
Needed Modules
==============
.. Do not edit this section It was auto-generated
.. by the `update_README.py` script.
.. image:: tree_dependency.png
* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
Documentation
=============
.. Do not edit this section. It was auto-generated from the
.. Do not edit this section It was auto-generated
.. by the `update_README.py` script.
`do_pseudo <http://github.com/LCPQ/quantum_package/tree/master/src/Pseudo/ezfio_interface.irp.f#L248>`_
Using pseudo potential integral of not

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@ -6,10 +6,10 @@ Contains general purpose utilities.
Documentation
=============
.. Do not edit this section. It was auto-generated from the
.. Do not edit this section It was auto-generated
.. by the `update_README.py` script.
`a_coef <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/need.irp.f#L252>`_
Undocumented
@ -634,4 +634,3 @@ Documentation
`write_git_log <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L243>`_
Write the last git commit in file iunit.