pymatgen.core.molecular_orbitals module

This module implements a MolecularOrbital class to represent band character in solids. Usefull for predicting PDOS character from structural information.

class MolecularOrbitals(formula)

Bases: object

Represents the character of bands in a solid. The input is a chemical formula, since no structural characteristics are taken into account.

The band character of a crystal emerges from the atomic orbitals of the constituant ions, hybridization/covalent bonds, and the spin-orbit interaction (ex: Fe2O3). Right now the orbitals are only built from the uncharged atomic species. Functionality can be improved by: 1) calculate charged ion orbital energies 2) incorportate the coordination enviornment to account for covalant bonds

The atomic orbital energies are stored in pymatgen.core.periodic_table.JSON

>>> MOs = MolecularOrbitals('SrTiO3')
>>> MOs.band_edges
{'HOMO':['O','2p',-0.338381], 'LUMO':['Ti','3d',-0.17001], 'metal':False}

Parameters

• formula as a string. formula must have integer subscripts (chemical) –

• Ex – ‘SrTiO3’

composition

the composition as a dictionary. Ex: {‘Sr’: 1, ‘Ti’: 1, ‘O’, 3}

elements

the dictionary keys for the composition

elec_neg

the maximum pairwise electronegetivity difference

aos

the consituant atomic orbitals for each element as a dictionary

band_edges

dictionary containing the highest occupied molecular orbital (HOMO), lowest unocupied molecular orbital (LUMO), and whether the material is predicted to be a metal

aos_as_list()

Returns

A list of atomic orbitals, sorted from lowest to highest energy.

The orbitals energies in eV are represented as

[[‘O’, ‘1s’, -18.758245], [‘O’, ‘2s’, -0.871362], [‘O’, ‘2p’, -0.338381]]

Data is obtained from https://www.nist.gov/pml/data/atomic-reference-data-electronic-structure-calculations

max_electronegativity()

Returns

The maximum pairwise electronegativity difference.

obtain_band_edges()

Fill up the atomic orbitals with available electrons. :returns: HOMO, LUMO, and whether it’s a metal.