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.. | ||
.gitignore | ||
ao_ortho_canonical.irp.f | ||
cholesky_mo.irp.f | ||
EZFIO.cfg | ||
mo_overlap.irp.f | ||
mo_permutation.irp.f | ||
mos.irp.f | ||
NEEDED_CHILDREN_MODULES | ||
print_aos.irp.f | ||
print_mo_in_space.irp.f | ||
README.rst | ||
rotate_mos.irp.f | ||
swap_mos.irp.f | ||
tree_dependency.png | ||
utils.irp.f |
========== MOs Module ========== Molecular orbitals are expressed as .. math:: \phi_k({\bf r}) = \sum_i C_{ik} \chi_k({\bf r}) where :math:`\chi_k` are *normalized* atomic basis set. The current set of molecular orbitals has a label ``mo_label``. When the orbitals are modified, the label should also be updated to keep everything consistent. When saving the MOs, the ``mo_basis`` directory of the EZFIO file is copied in the ``save`` directory, named by the current ``mo_label``. All this is done with the script named ``save_current_mos.sh`` in the ``scripts`` directory. Assumptions =========== .. Do not edit this section. It was auto-generated from the .. NEEDED_MODULES_CHILDREN file by the `update_README.py` script. ASSUMPTONS ========== * The AO basis functions are normalized. 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>`_ * `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>`_ * `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_ Documentation ============= .. Do not edit this section It was auto-generated .. by the `update_README.py` script. `ao_cart_to_sphe_coef <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis/ao_ortho_canonical.irp.f#L1>`_ matrix of the coefficients of the mos generated by the orthonormalization by the S^{-1/2} canonical transformation of the aos ao_cart_to_sphe_coef(i,j) = coefficient of the ith ao on the jth ao_ortho_canonical orbital `ao_cart_to_sphe_inv <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis/ao_ortho_canonical.irp.f#L73>`_ AO_cart_to_sphe_coef^(-1) `ao_cart_to_sphe_num <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis/ao_ortho_canonical.irp.f#L2>`_ matrix of the coefficients of the mos generated by the orthonormalization by the S^{-1/2} canonical transformation of the aos ao_cart_to_sphe_coef(i,j) = coefficient of the ith ao on the jth ao_ortho_canonical orbital `ao_cart_to_sphe_overlap <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis/ao_ortho_canonical.irp.f#L51>`_ AO overlap matrix in the spherical basis set `ao_ortho_canonical_coef <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis/ao_ortho_canonical.irp.f#L85>`_ matrix of the coefficients of the mos generated by the orthonormalization by the S^{-1/2} canonical transformation of the aos ao_ortho_canonical_coef(i,j) = coefficient of the ith ao on the jth ao_ortho_canonical orbital `ao_ortho_canonical_num <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis/ao_ortho_canonical.irp.f#L86>`_ matrix of the coefficients of the mos generated by the orthonormalization by the S^{-1/2} canonical transformation of the aos ao_ortho_canonical_coef(i,j) = coefficient of the ith ao on the jth ao_ortho_canonical orbital `ao_ortho_canonical_overlap <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis/ao_ortho_canonical.irp.f#L130>`_ overlap matrix of the ao_ortho_canonical. Expected to be the Identity `ao_to_mo <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis/mos.irp.f#L144>`_ Transform A from the AO basis to the MO basis `cholesky_mo <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis/cholesky_mo.irp.f#L1>`_ Cholesky decomposition of AO Density matrix to generate MOs `mix_mo_jk <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis/mos.irp.f#L228>`_ subroutine that rotates the jth MO with the kth MO to give two new MO's that are '+' = 1/sqrt(2) (|j> + |k>) '-' = 1/sqrt(2) (|j> - |k>) by convention, the '+' MO is in the lower index (min(j,k)) by convention, the '-' MO is in the greater index (max(j,k)) `mo_as_eigvectors_of_mo_matrix <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis/utils.irp.f#L47>`_ Undocumented `mo_as_eigvectors_of_mo_matrix_sort_by_observable <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis/utils.irp.f#L150>`_ Undocumented `mo_as_svd_vectors_of_mo_matrix <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis/utils.irp.f#L103>`_ Undocumented `mo_coef <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis/mos.irp.f#L29>`_ Molecular orbital coefficients on AO basis set mo_coef(i,j) = coefficient of the ith ao on the jth mo mo_label : Label characterizing the MOS (local, canonical, natural, etc) `mo_coef_transp <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis/mos.irp.f#L89>`_ Molecular orbital coefficients on AO basis set `mo_density_matrix <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis/cholesky_mo.irp.f#L44>`_ Density matrix in MO basis `mo_density_matrix_virtual <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis/cholesky_mo.irp.f#L64>`_ Density matrix in MO basis (virtual MOs) `mo_label <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis/mos.irp.f#L71>`_ Molecular orbital coefficients on AO basis set mo_coef(i,j) = coefficient of the ith ao on the jth mo mo_label : Label characterizing the MOS (local, canonical, natural, etc) `mo_occ <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis/mos.irp.f#L120>`_ MO occupation numbers `mo_overlap <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis/mo_overlap.irp.f#L2>`_ Undocumented `mo_sort_by_observable <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis/utils.irp.f#L232>`_ Undocumented `mo_to_ao <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis/mos.irp.f#L170>`_ Transform A from the MO basis to the AO basis `mo_to_ao_no_overlap <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis/mos.irp.f#L202>`_ Transform A from the MO basis to the S^-1 AO basis `mo_tot_num <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis/mos.irp.f#L1>`_ Total number of molecular orbitals and the size of the keys corresponding `mo_tot_num_align <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis/mos.irp.f#L19>`_ Aligned variable for dimensioning of arrays `s_mo_coef <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis/mos.irp.f#L107>`_ Product S.C where S is the overlap matrix in the AO basis and C the mo_coef matrix. `save_mos <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis/utils.irp.f#L1>`_ Undocumented `save_mos_truncated <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis/utils.irp.f#L24>`_ Undocumented `swap_mos <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis/swap_mos.irp.f#L1>`_ Undocumented