emle._orca_parser

The orca_parser module provides a parser for ORCA output files. This is an internal module used by the emle-analyze and emle-train scripts to load simulation output prior to performing error analysis or training.

class emle._orca_parser.ORCAParser(filename, decompose=False, alpha=False)[source]

Parses ORCA gas phase calculations and corresponding HORTON outputs. Optionally, extract molecular dipolar polarizability (needed for EMLE training) and does energy decomposition analysis for embedding energy. The latter requires additional calculation in presence of point charges and electrostatic potential of the gas phase system at the positions of the point charges).

Constructor.

Parameters:

  • filename (str) –

    Tarball with ORCA and HORTON outputs:
    ”.h5”:

    HORTON output.

    ”.vac.orca”:

    ORCA output for gas phase calculation. If alpha=True, must contain molecular dipolar polarizability tensor as well.

    The following files are required if decompose=True:
    ”.pc.orca”:

    ORCA output for calculation with point charges (PC).

    ”.pc”:

    Charges and positions of the point charges (the ones used for .pc.orca calculation).

    ”.vpot”:

    Output of orca_vpot, electrostatic potential of gas phase system at the positions of the point charges.

    ”.h5”:

    HORTON output.

    ”.vac.orca”:

    ORCA output for gas phase calculation. If alpha=True, must contain molecular dipolar polarizability tensor as well.

    All files must have numeric names (same number for the same structure).

  • decompose (bool) – Whether to do energy decomposition analysis

  • alpha (bool) – Whether to extract molecular dipolar polarizability tensor

Notes

Once the files are parsed the following attributes are available:
z:

(N_MOLS, MAX_N_ATOMS) atomic indices.

xyz:

(N_MOLS, MAX_N_ATOMS, 3) positions of atoms

mbis:

a dictionary with MBIS properties (s, q_core, q_val, mu)

alpha:

(N_MOLS, 3, 3) array of molecular dipolar polarizability tensors (alpha=True)

E:

total embedding energies (decompose=True)

E_static:

static embedding energies (decompose=True)

E_induced:

induced embedding energies (decompose=True)