Central Variables

In ORBKIT, all central variables are extracted from quantum chemistry outputs (cf. orbkit.read) and organized within the class 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)	(Natoms, 3)
qc.geo_spec	numpy.ndarray (dtype= str)	(Natoms, 3)
qc.ao_spec	list of dict	“pnum”, “atom”, “type”, “coeffs”, (“exp_list”)
qc.ao_spherical	list of tuple	(Nspherical AOs, 2)
qc.mo_spec	list of dict	“energy”, “occ_num”, “sym”, “coeffs”

qc.geo_info:

• Contains information about the atoms and is only required for the creation of the output file.
• The three columns correspond to
  1. Atom symbol
  2. Atom number (according to the input file)
  3. Nuclear charge (if present in the input file)

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:

• 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_primitives, 2)
  • “pnum”
    • Number of number of primitives (int)
  • “exp_list” (optional)
    • Exponents \((l_x,l_y,l_z)\) 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:  

• 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:

• 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_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 orbkit.qcinfo.QCinfo class possess additional members which are not of importance for the computations done by ORBKIT.