Source code for pymatgen.analysis.chemenv.connectivity.connectivity_finder

from pymatgen.analysis.chemenv.connectivity.structure_connectivity import StructureConnectivity
import logging
import numpy as np

__author__ = "David Waroquiers"
__copyright__ = "Copyright 2012, The Materials Project"
__credits__ = "Geoffroy Hautier"
__version__ = "1.0"
__maintainer__ = "David Waroquiers"
__email__ = "david.waroquiers@gmail.com"
__date__ = "June 25, 2019"


[docs]class ConnectivityFinder(object): """ Main class used to find the structure connectivity of a structure """ def __init__(self, multiple_environments_choice=None): """ Constructor for the ConnectivityFinder. :param multiple_environments_choice: defines the procedure to apply when the environment of a given site is described as a "mix" of more than one coordination environments. """ self.setup_parameters(multiple_environments_choice=multiple_environments_choice)
[docs] def get_structure_connectivity(self, light_structure_environments): """ Get the structure connectivity from the coordination environments provided as an input. :param light_structure_environments: LightStructureEnvironments with the relevant coordination environments in the structure :return: a StructureConnectivity object describing the connectivity of the environments in the structure """ logging.info('Setup of structure connectivity graph') structure_connectivity = StructureConnectivity(light_structure_environments) structure_connectivity.add_sites() for isite, site in enumerate(light_structure_environments.structure): site_neighbors_sets = light_structure_environments.neighbors_sets[isite] if site_neighbors_sets is None: continue if len(site_neighbors_sets) > 1: if self.multiple_environments_choice is None: raise ValueError('Local environment of site {:d} is a mix and ' 'nothing is asked about it'.format(isite)) elif self.multiple_environments_choice == 'TAKE_HIGHEST_FRACTION': imax = np.argmax([ee['ce_fraction'] for ee in light_structure_environments.coordination_environments[isite]]) print('IMAX {:d}'.format(imax)) site_neighbors_set = site_neighbors_sets[imax] else: raise RuntimeError('Should not be here') else: site_neighbors_set = site_neighbors_sets[0] structure_connectivity.add_bonds(isite, site_neighbors_set) return structure_connectivity
[docs] def setup_parameters(self, multiple_environments_choice): """ Setup of the parameters for the connectivity finder. """ if multiple_environments_choice is not None: if multiple_environments_choice not in ['TAKE_HIGHEST_FRACTION']: raise ValueError('Option "{}" for multiple_environments_choice is ' 'not allowed'.format(self.multiple_environments_choice)) self.multiple_environments_choice = multiple_environments_choice