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.