pymatgen.io.cp2k.utils module

Utility functions for assisting with cp2k IO

get_aux_basis(basis_type, default_basis_type='cFIT')[source]

Get auxiliary basis info for a list of species.

Parameters
  • basis_type (dict) –

    dict of auxiliary basis sets to use. i.e: basis_type = {‘Si’: ‘cFIT’, ‘O’: ‘cpFIT’}. Basis type needs to exist for that species.

    Basis types:

    FIT cFIT pFIT cpFIT GTH-def2 aug-{FIT,cFIT,pFIT,cpFIT, GTH-def2}

  • default_basis_type (str) –

get_basis_and_potential(species, d, cardinality='DZVP', functional='PBE')[source]

Given a specie and a potential/basis type, this function accesses the available basis sets and potentials. Generally, the GTH potentials are used with the GTH basis sets.

Parameters
  • species – (list) list of species for which to get the potential/basis strings

  • d – (dict) a dictionary specifying how bases and/or potentials should be assigned to species E.g. {‘Si’: {‘cardinality’: ‘DZVP’, ‘sr’: True}, ‘O’: {‘cardinality’: ‘TZVP’}}

  • functional – (str) functional type. Default: ‘PBE’

  • basis_type – (str) the basis set type. Default: ‘MOLOPT’

  • cardinality – (str) basis set cardinality. Default: ‘DZVP’

Returns

{‘potential’: potential, ‘basis’: basis}…}

Return type

(dict) of the form {‘specie’

get_unique_site_indices(structure)[source]

Get unique site indices for a structure according to site properties. Whatever site-property has the most unique values is used for indexing.

For example, if you have magnetic CoO with half Co atoms having a positive moment, and the other half having a negative moment. Then this function will create a dict of sites for Co_1, Co_2, O.

This creates unique sites, based on site properties, but does not have anything to do with turning those site properties into CP2K input parameters.

natural_keys(text)[source]

Sort text by numbers coming after an underscore with natural number convention, Ex: [file_1, file_12, file_2] becomes [file_1, file_2, file_12]