.. _`Central Variables`:

Central Variables
=================

In ORBKIT, all central variables are extracted from quantum chemistry outputs
(cf. :mod:`orbkit.read`) and organized within the class 
:mod:`orbkit.qcinfo.QCinfo`. The corresponding command reads::

  from orbkit import read
  qc = read.main_read('h2o.md',itype='molden')

This class stores all the information required for subsequent
computations and is organized as follows:

+-------------------+-----------------------------------+-----------------------------------------------+
| Member            | Type                              | Shape/Members                                 |
+===================+===================================+===============================================+
| `qc.geo_info`_    | ``numpy.ndarray`` (dtype= ``str``)| (N\ :sub:`atoms`, 3)                          |
+-------------------+-----------------------------------+-----------------------------------------------+
| `qc.geo_spec`_    | ``numpy.ndarray`` (dtype= ``str``)| (N\ :sub:`atoms`, 3)                          |
+-------------------+-----------------------------------+-----------------------------------------------+
| `qc.ao_spec`_     | ``list`` of ``dict``              | "pnum", "atom", "type", "coeffs", ("exp_list")|
+-------------------+-----------------------------------+-----------------------------------------------+
| `qc.ao_spherical`_| ``list`` of ``tuple``             | (N\ :sub:`spherical AOs`, 2)                  |
+-------------------+-----------------------------------+-----------------------------------------------+
| `qc.mo_spec`_     | ``list`` of ``dict``              | "energy", "occ_num", "sym", "coeffs"          |
+-------------------+-----------------------------------+-----------------------------------------------+

.. _`qc.geo_info`:

:qc.geo_info:

  * Contains information about the atoms and is only required for the creation 
    of the output file.
  * The three columns correspond to

    #. Atom symbol
    #. Atom number (according to the input file)
    #. Nuclear charge (if present in the input file)

.. _`qc.geo_spec`:

:qc.geo_spec:

  * Contains the atom positions in units of Bohr radii.
  * The three columns correspond to the *x-*, *y-*, and *z-*\ coordinates.

.. _`qc.ao_spec`:

:qc.ao_spec:

  * Contains all information about the atomic orbitals
  * The number of dictionaries corresponds to the number of contracted Gaussians
  * Members of the dictionaries:  

    * "atom"

      * Atom number (according to the input file, i.e., starting from 1) (``int``)
    * "coeffs"

      * **1st** element exponent and **2nd** element contraction coefficients of 
        the basis functions 
      * ``numpy.ndarray`` (dtype= ``float``) with the shape (N\ :sub:`primitives`, 2)
    * "pnum"

      * Number of number of primitives (``int``)
    * "exp_list" (optional)

      * Exponents :math:`(l_x,l_y,l_z)` of the basis functions 
      * Only present if the order of the exponents deviate from the standard 
        molden order
      * ``list`` of ``tuple``, i.e., ``[(l_x1,l_y1,l_z1), (l_x2,l_y2,l_z2), ...]``


.. _`qc.ao_spherical`:

:qc.ao_spherical:

  * Contains the order of the spherical harmonic basis functions within the
    input file
  * ``list`` of ``tuple``, i.e., ``[(l_1,m_1), (l_2,m_2), ...]`` with
    the angular momentum quantum number ``m`` and the magnetic quantum number 
    ``l``

.. _`qc.mo_spec`:

:qc.mo_spec:

  * Contains all information about the molecular orbitals.
  * The number of dictionaries corresponds to number of molecular orbitals
  * Members of the dictionaries:  

    * "coeffs"

      * Molecular orbital coefficients
      * ``numpy.ndarray`` (dtype= ``float``) with the shape (N\ :sub:`AO`, 1)
    * "energy"

      * Energy of molecular orbital (``float``)
    * "occ_num"

      * Occupation of molecular orbital (``float``)
    * "sym"

      * MOLPRO-like symmetry label of molecular orbital (``str``), e.g., 
        "12.1" or "12.A1"

Besides those central variables, the :mod:`orbkit.qcinfo.QCinfo` class possess 
additional members which are not of importance for the computations done by
ORBKIT.