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"


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)

    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

    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