pymatgen.analysis.chemenv.connectivity.connectivity_finder — pymatgen 2020.7.3 documentation

# 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