qp2/docs/source/modules/mo_basis.rst

.. _module_mo_basis: 
 
.. program:: mo_basis 
 
.. default-role:: option 
 
========
mo_basis
========

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 functions.

The current set of |MOs| 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 :file:`mo_basis` directory of the |EZFIO| database
is copied in the :file:`save` directory, named by the current `mo_label`. All
this is done with the script named :file:`save_current_mos.sh` in the
:file:`$QP_ROOT/scripts` directory.



 
 
 
EZFIO parameters 
---------------- 
 
.. option:: mo_num
 
    Total number of |MOs|
 
 
.. option:: mo_coef
 
    Coefficient of the i-th |AO| on the j-th |MO|
 
 
.. option:: mo_label
 
    Label characterizing the MOS (Local, Canonical, Natural, *etc*)
 
 
.. option:: mo_occ
 
    |MO| occupation numbers
 
 
.. option:: mo_class
 
    [ Core | Inactive | Active | Virtual | Deleted ], as defined by :ref:`qp_set_mo_class`
 
 
.. option:: ao_md5
 
    MD5 checksum characterizing the |AO| basis set.
 
 
 
Providers 
--------- 
 
.. c:var:: mo_coef


    File : :file:`mo_basis/mos.irp.f`

    .. code:: fortran

        double precision, allocatable	:: mo_coef	(ao_num,mo_num)


    Molecular orbital coefficients on |AO| basis set
    
    mo_coef(i,j) = coefficient of the i-th |AO| on the jth mo
    
    mo_label : Label characterizing the MOS (local, canonical, natural, etc)

    Needs:

    .. hlist::
       :columns: 3

       * :c:data:`ao_num`
       * :c:data:`ao_ortho_canonical_coef`
       * :c:data:`ezfio_filename`
       * :c:data:`mo_num`
       * :c:data:`mpi_master`

    Needed by:

    .. hlist::
       :columns: 3

       * :c:data:`eigenvectors_fock_matrix_mo`
       * :c:data:`fock_matrix_mo_alpha`
       * :c:data:`fock_matrix_mo_beta`
       * :c:data:`fps_spf_matrix_mo`
       * :c:data:`mo_coef_in_ao_ortho_basis`
       * :c:data:`mo_coef_transp`
       * :c:data:`mo_dipole_x`
       * :c:data:`mo_integrals_n_e`
       * :c:data:`mo_integrals_n_e_per_atom`
       * :c:data:`mo_kinetic_integrals`
       * :c:data:`mo_overlap`
       * :c:data:`mo_pseudo_integrals`
       * :c:data:`mo_spread_x`
       * :c:data:`mo_two_e_int_erf_jj_from_ao`
       * :c:data:`mo_two_e_integral_jj_from_ao`
       * :c:data:`mo_two_e_integrals_erf_in_map`
       * :c:data:`mo_two_e_integrals_in_map`
       * :c:data:`mo_two_e_integrals_vv_from_ao`
       * :c:data:`one_e_dm_ao_alpha`
       * :c:data:`one_e_spin_density_ao`
       * :c:data:`psi_det`
       * :c:data:`s_mo_coef`
       * :c:data:`scf_density_matrix_ao_alpha`
       * :c:data:`scf_density_matrix_ao_beta`

 
.. c:var:: mo_coef_begin_iteration


    File : :file:`mo_basis/track_orb.irp.f`

    .. code:: fortran

        double precision, allocatable	:: mo_coef_begin_iteration	(ao_num,mo_num)


    Void provider to store the coefficients of the |MO| basis at the beginning of the SCF iteration
    
    Usefull to track some orbitals

    Needs:

    .. hlist::
       :columns: 3

       * :c:data:`ao_num`
       * :c:data:`mo_num`


 
.. c:var:: mo_coef_in_ao_ortho_basis


    File : :file:`mo_basis/mos.irp.f`

    .. code:: fortran

        double precision, allocatable	:: mo_coef_in_ao_ortho_basis	(ao_num,mo_num)


    |MO| coefficients in orthogonalized |AO| basis
    
    :math:`C^{-1}.C_{mo}` 

    Needs:

    .. hlist::
       :columns: 3

       * :c:data:`ao_num`
       * :c:data:`ao_ortho_canonical_coef_inv`
       * :c:data:`mo_coef`
       * :c:data:`mo_num`


 
.. c:var:: mo_coef_transp


    File : :file:`mo_basis/mos.irp.f`

    .. code:: fortran

        double precision, allocatable	:: mo_coef_transp	(mo_num,ao_num)


    |MO| coefficients on |AO| basis set

    Needs:

    .. hlist::
       :columns: 3

       * :c:data:`ao_num`
       * :c:data:`mo_coef`
       * :c:data:`mo_num`

    Needed by:

    .. hlist::
       :columns: 3

       * :c:data:`mo_two_e_int_erf_jj_from_ao`
       * :c:data:`mo_two_e_integral_jj_from_ao`
       * :c:data:`mo_two_e_integrals_erf_in_map`
       * :c:data:`mo_two_e_integrals_in_map`
       * :c:data:`mo_two_e_integrals_vv_from_ao`

 
.. c:var:: mo_label


    File : :file:`mo_basis/mos.irp.f`

    .. code:: fortran

        character*(64)	:: mo_label	


    |MO| coefficients on |AO| basis set
    
    mo_coef(i,j) = coefficient of the i-th |AO| on the j-th |MO|
    
    mo_label : Label characterizing the |MOs| (local, canonical, natural, etc)

    Needs:

    .. hlist::
       :columns: 3

       * :c:data:`ezfio_filename`
       * :c:data:`mpi_master`

    Needed by:

    .. hlist::
       :columns: 3

       * :c:data:`n_det`
       * :c:data:`psi_coef`
       * :c:data:`psi_det`

 
.. c:var:: mo_num


    File : :file:`mo_basis/mos.irp.f`

    .. code:: fortran

        integer	:: mo_num	


    Number of MOs

    Needs:

    .. hlist::
       :columns: 3

       * :c:data:`ao_ortho_canonical_coef`
       * :c:data:`ezfio_filename`
       * :c:data:`mpi_master`

    Needed by:

    .. hlist::
       :columns: 3

       * :c:data:`ao_ortho_canonical_nucl_elec_integrals`
       * :c:data:`ao_ortho_lowdin_nucl_elec_integrals`
       * :c:data:`big_array_coulomb_integrals`
       * :c:data:`core_fock_operator`
       * :c:data:`core_fock_operator_erf`
       * :c:data:`data_one_e_dm_alpha_mo`
       * :c:data:`data_one_e_dm_beta_mo`
       * :c:data:`eigenvectors_fock_matrix_mo`
       * :c:data:`fock_matrix_ao`
       * :c:data:`fock_matrix_mo`
       * :c:data:`fock_matrix_mo_alpha`
       * :c:data:`fock_matrix_mo_beta`
       * :c:data:`fock_operator_closed_shell_ref_bitmask`
       * :c:data:`fock_wee_closed_shell`
       * :c:data:`fps_spf_matrix_mo`
       * :c:data:`full_ijkl_bitmask`
       * :c:data:`int_erf_3_index`
       * :c:data:`list_core_inact_act`
       * :c:data:`list_inact`
       * :c:data:`mo_class`
       * :c:data:`mo_coef`
       * :c:data:`mo_coef_begin_iteration`
       * :c:data:`mo_coef_in_ao_ortho_basis`
       * :c:data:`mo_coef_transp`
       * :c:data:`mo_dipole_x`
       * :c:data:`mo_integrals_cache_min`
       * :c:data:`mo_integrals_erf_cache_min`
       * :c:data:`mo_integrals_erf_map`
       * :c:data:`mo_integrals_map`
       * :c:data:`mo_integrals_n_e`
       * :c:data:`mo_integrals_n_e_per_atom`
       * :c:data:`mo_kinetic_integrals`
       * :c:data:`mo_occ`
       * :c:data:`mo_one_e_integrals`
       * :c:data:`mo_overlap`
       * :c:data:`mo_pseudo_integrals`
       * :c:data:`mo_spread_x`
       * :c:data:`mo_two_e_int_erf_jj`
       * :c:data:`mo_two_e_int_erf_jj_from_ao`
       * :c:data:`mo_two_e_integral_jj_from_ao`
       * :c:data:`mo_two_e_integrals_erf_in_map`
       * :c:data:`mo_two_e_integrals_in_map`
       * :c:data:`mo_two_e_integrals_jj`
       * :c:data:`mo_two_e_integrals_vv_from_ao`
       * :c:data:`n_core_orb`
       * :c:data:`n_int`
       * :c:data:`one_e_dm_ao_alpha`
       * :c:data:`one_e_dm_dagger_mo_spin_index`
       * :c:data:`one_e_dm_mo`
       * :c:data:`one_e_dm_mo_alpha`
       * :c:data:`one_e_dm_mo_alpha_average`
       * :c:data:`one_e_dm_mo_diff`
       * :c:data:`one_e_dm_mo_spin_index`
       * :c:data:`one_e_spin_density_ao`
       * :c:data:`one_e_spin_density_mo`
       * :c:data:`psi_energy_h_core`
       * :c:data:`s_mo_coef`
       * :c:data:`singles_alpha_csc_idx`
       * :c:data:`singles_beta_csc_idx`

 
.. c:var:: mo_occ


    File : :file:`mo_basis/mos.irp.f`

    .. code:: fortran

        double precision, allocatable	:: mo_occ	(mo_num)


    |MO| occupation numbers

    Needs:

    .. hlist::
       :columns: 3

       * :c:data:`elec_alpha_num`
       * :c:data:`elec_beta_num`
       * :c:data:`ezfio_filename`
       * :c:data:`mo_num`
       * :c:data:`mpi_master`


 
 
Subroutines / functions 
----------------------- 
 
.. c:function:: ao_ortho_cano_to_ao:


    File : :file:`mo_basis/mos.irp.f`

    .. code:: fortran

        subroutine ao_ortho_cano_to_ao(A_ao,LDA_ao,A,LDA)


    Transform A from the |AO| basis to the orthogonal |AO| basis
    
    $C^{-1}.A_{ao}.C^{\dagger-1}$

    Needs:

    .. hlist::
       :columns: 3

       * :c:data:`ao_num`
       * :c:data:`ao_ortho_canonical_coef_inv`

    Calls:

    .. hlist::
       :columns: 3

       * :c:func:`dgemm`

 
.. c:function:: ao_to_mo:


    File : :file:`mo_basis/mos.irp.f`

    .. code:: fortran

        subroutine ao_to_mo(A_ao,LDA_ao,A_mo,LDA_mo)


    Transform A from the |AO| basis to the |MO| basis
    
    $C^\dagger.A_{ao}.C$

    Needs:

    .. hlist::
       :columns: 3

       * :c:data:`ao_num`
       * :c:data:`mo_num`
       * :c:data:`mo_coef`

    Called by:

    .. hlist::
       :columns: 3

       * :c:data:`fock_matrix_mo_alpha`
       * :c:data:`fock_matrix_mo_beta`
       * :c:data:`fps_spf_matrix_mo`
       * :c:data:`mo_dipole_x`
       * :c:data:`mo_integrals_n_e`
       * :c:data:`mo_integrals_n_e_per_atom`
       * :c:data:`mo_kinetic_integrals`
       * :c:data:`mo_pseudo_integrals`
       * :c:data:`mo_spread_x`

    Calls:

    .. hlist::
       :columns: 3

       * :c:func:`dgemm`

 
.. c:function:: give_all_mos_and_grad_and_lapl_at_r:


    File : :file:`mo_basis/mos_in_r.irp.f`

    .. code:: fortran

        subroutine give_all_mos_and_grad_and_lapl_at_r(r,mos_array,mos_grad_array,mos_lapl_array)



    Needs:

    .. hlist::
       :columns: 3

       * :c:data:`ao_num`
       * :c:data:`mo_num`
       * :c:data:`mo_coef`

    Calls:

    .. hlist::
       :columns: 3

       * :c:func:`give_all_aos_and_grad_and_lapl_at_r`

 
.. c:function:: give_all_mos_and_grad_at_r:


    File : :file:`mo_basis/mos_in_r.irp.f`

    .. code:: fortran

        subroutine give_all_mos_and_grad_at_r(r,mos_array,mos_grad_array)



    Needs:

    .. hlist::
       :columns: 3

       * :c:data:`ao_num`
       * :c:data:`mo_num`
       * :c:data:`mo_coef`

    Calls:

    .. hlist::
       :columns: 3

       * :c:func:`give_all_aos_and_grad_at_r`

 
.. c:function:: give_all_mos_at_r:


    File : :file:`mo_basis/mos_in_r.irp.f`

    .. code:: fortran

        subroutine give_all_mos_at_r(r,mos_array)



    Needs:

    .. hlist::
       :columns: 3

       * :c:data:`ao_num`
       * :c:data:`mo_num`
       * :c:data:`mo_coef_transp`

    Calls:

    .. hlist::
       :columns: 3

       * :c:func:`dgemv`
       * :c:func:`give_all_aos_at_r`

 
.. c:function:: initialize_mo_coef_begin_iteration:


    File : :file:`mo_basis/track_orb.irp.f`

    .. code:: fortran

        subroutine initialize_mo_coef_begin_iteration


    
    Initialize :c:data:`mo_coef_begin_iteration` to the current :c:data:`mo_coef`

    Needs:

    .. hlist::
       :columns: 3

       * :c:data:`mo_coef_begin_iteration`
       * :c:data:`mo_coef`

    Called by:

    .. hlist::
       :columns: 3

       * :c:func:`damping_scf`
       * :c:func:`roothaan_hall_scf`

 
.. c:function:: mix_mo_jk:


    File : :file:`mo_basis/mos.irp.f`

    .. code:: fortran

        subroutine mix_mo_jk(j,k)


    Rotates the j-th |MO| with the k-th |MO| to give two new |MOs| that are
    
    * $+ = \frac{1}{\sqrt{2}} ( | j\rangle +  | k\rangle)$
    
    * $- = \frac{1}{\sqrt{2}} ( | j\rangle -  | k\rangle)$
    
    by convention, the '+' |MO| is in the lowest  index (min(j,k))
    by convention, the '-' |MO| is in the highest index (max(j,k))

    Needs:

    .. hlist::
       :columns: 3

       * :c:data:`ao_num`
       * :c:data:`mo_coef`

 
.. c:function:: mo_as_eigvectors_of_mo_matrix:


    File : :file:`mo_basis/utils.irp.f`

    .. code:: fortran

        subroutine mo_as_eigvectors_of_mo_matrix(matrix,n,m,label,sign,output)



    Needs:

    .. hlist::
       :columns: 3

       * :c:data:`mo_label`
       * :c:data:`ao_num`
       * :c:data:`mo_num`
       * :c:data:`mo_coef`

    Called by:

    .. hlist::
       :columns: 3

       * :c:func:`create_guess`
       * :c:func:`damping_scf`
       * :c:func:`hcore_guess`
       * :c:func:`roothaan_hall_scf`

    Calls:

    .. hlist::
       :columns: 3

       * :c:func:`dgemm`
       * :c:func:`lapack_diag`
       * :c:func:`write_time`

 
.. c:function:: mo_as_svd_vectors_of_mo_matrix:


    File : :file:`mo_basis/utils.irp.f`

    .. code:: fortran

        subroutine mo_as_svd_vectors_of_mo_matrix(matrix,lda,m,n,label)



    Needs:

    .. hlist::
       :columns: 3

       * :c:data:`mo_label`
       * :c:data:`ao_num`
       * :c:data:`mo_num`
       * :c:data:`mo_coef`

    Calls:

    .. hlist::
       :columns: 3

       * :c:func:`dgemm`
       * :c:func:`svd`
       * :c:func:`write_time`

 
.. c:function:: mo_as_svd_vectors_of_mo_matrix_eig:


    File : :file:`mo_basis/utils.irp.f`

    .. code:: fortran

        subroutine mo_as_svd_vectors_of_mo_matrix_eig(matrix,lda,m,n,eig,label)



    Needs:

    .. hlist::
       :columns: 3

       * :c:data:`mo_label`
       * :c:data:`ao_num`
       * :c:data:`mo_num`
       * :c:data:`mo_coef`

    Called by:

    .. hlist::
       :columns: 3

       * :c:func:`set_natural_mos`

    Calls:

    .. hlist::
       :columns: 3

       * :c:func:`dgemm`
       * :c:func:`svd`
       * :c:func:`write_time`

 
.. c:function:: reorder_core_orb:


    File : :file:`mo_basis/track_orb.irp.f`

    .. code:: fortran

        subroutine reorder_core_orb


    routines that takes the current :c:data:`mo_coef` and reorder the core orbitals (see :c:data:`list_core` and :c:data:`n_core_orb`) according to the overlap with :c:data:`mo_coef_begin_iteration`

    Needs:

    .. hlist::
       :columns: 3

       * :c:data:`mo_num`
       * :c:data:`mo_coef_begin_iteration`
       * :c:data:`mo_coef`
       * :c:data:`ao_overlap`
       * :c:data:`n_core_orb`
       * :c:data:`ao_num`
       * :c:data:`list_inact`

    Called by:

    .. hlist::
       :columns: 3

       * :c:func:`damping_scf`
       * :c:func:`roothaan_hall_scf`

    Calls:

    .. hlist::
       :columns: 3

       * :c:func:`dsort`

 
.. c:function:: save_mos:


    File : :file:`mo_basis/utils.irp.f`

    .. code:: fortran

        subroutine save_mos



    Needs:

    .. hlist::
       :columns: 3

       * :c:data:`mo_occ`
       * :c:data:`ao_md5`
       * :c:data:`ezfio_filename`
       * :c:data:`mo_num`
       * :c:data:`mo_coef`
       * :c:data:`ao_num`
       * :c:data:`mo_label`

    Called by:

    .. hlist::
       :columns: 3

       * :c:func:`damping_scf`
       * :c:func:`hcore_guess`
       * :c:func:`huckel_guess`
       * :c:func:`roothaan_hall_scf`
       * :c:func:`save_natural_mos`
       * :c:func:`save_ortho_mos`

    Calls:

    .. hlist::
       :columns: 3

       * :c:func:`ezfio_set_mo_basis_ao_md5`
       * :c:func:`ezfio_set_mo_basis_mo_coef`
       * :c:func:`ezfio_set_mo_basis_mo_label`
       * :c:func:`ezfio_set_mo_basis_mo_num`
       * :c:func:`ezfio_set_mo_basis_mo_occ`
       * :c:func:`system`

 
.. c:function:: save_mos_truncated:


    File : :file:`mo_basis/utils.irp.f`

    .. code:: fortran

        subroutine save_mos_truncated(n)



    Needs:

    .. hlist::
       :columns: 3

       * :c:data:`mo_occ`
       * :c:data:`ao_md5`
       * :c:data:`ezfio_filename`
       * :c:data:`mo_coef`
       * :c:data:`ao_num`
       * :c:data:`mo_label`

    Calls:

    .. hlist::
       :columns: 3

       * :c:func:`ezfio_set_mo_basis_ao_md5`
       * :c:func:`ezfio_set_mo_basis_mo_coef`
       * :c:func:`ezfio_set_mo_basis_mo_label`
       * :c:func:`ezfio_set_mo_basis_mo_num`
       * :c:func:`ezfio_set_mo_basis_mo_occ`
       * :c:func:`system`