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

"""
Environment nodes module.
"""

import abc

from monty.json import MSONable


[docs]class AbstractEnvironmentNode(MSONable): """ Abstract class used to define an environment as a node in a graph. """ COORDINATION_ENVIRONMENT = 0 NUMBER_OF_NEIGHBORING_COORDINATION_ENVIRONMENTS = 1 NUMBER_OF_NEIGHBORING_CES = NUMBER_OF_NEIGHBORING_COORDINATION_ENVIRONMENTS NEIGHBORING_COORDINATION_ENVIRONMENTS = 2 NEIGHBORING_CES = NEIGHBORING_COORDINATION_ENVIRONMENTS NUMBER_OF_LIGANDS_FOR_EACH_NEIGHBORING_COORDINATION_ENVIRONMENT = 3 NUMBER_OF_LIGANDS_FOR_EACH_NEIGHBORING_CE = NUMBER_OF_LIGANDS_FOR_EACH_NEIGHBORING_COORDINATION_ENVIRONMENT LIGANDS_ARRANGEMENT = 4 NEIGHBORS_LIGANDS_ARRANGEMENT = 5 ATOM = 6 CE_NNBCES_NBCES_LIGANDS = -1 DEFAULT_EXTENSIONS = (ATOM, COORDINATION_ENVIRONMENT) def __init__(self, central_site, i_central_site): """ Constructor for the AbstractEnvironmentNode object. Args: central_site (Site or subclass of Site): central site as a pymatgen Site or subclass of Site (e.g. PeriodicSite, ...). i_central_site (int): Index of the central site in the structure. """ self.central_site = central_site self.i_central_site = i_central_site @property def isite(self): """Index of the central site.""" return self.i_central_site def __hash__(self): """Simple hash function based on the hash function of the central site.""" return self.central_site.__hash__() def __eq__(self, other): # When relabelling nodes from a str or int to an EnvironmentNode in-place in a graph (e.g. in a # ConnectedComponent), the comparison should return False when comparing the already relabelled nodes (e.g. as # an EnvironmentNode) with those not yet relabelled (e.g. a str representing the isite). This is useful for # serialization as a json/bson object. return self.__class__ == other.__class__ and self.isite == other.isite def __lt__(self, other): # This simple "Less Than" operator allows to strictly sort environment nodes in a graph. # This is useful (and actually neeeded) in the definition of the cycles but does not have # any real meaning of a "lower value" environment node. return self.isite < other.isite
[docs] def everything_equal(self, other): """Checks equality with respect to another AbstractEnvironmentNode using the index of the central site as well as the central site itself.""" return self.__eq__(other) and self.central_site == other.central_site
@property @abc.abstractmethod def coordination_environment(self): """Coordination environment of this node.""" return @property def ce(self): """Coordination environment of this node.""" return self.coordination_environment @property def mp_symbol(self): """Coordination environment of this node.""" return self.coordination_environment @property def ce_symbol(self): """Coordination environment of this node.""" return self.coordination_environment @property def atom_symbol(self): """Symbol of the atom on the central site.""" return self.central_site.specie.symbol def __str__(self): """String representation of the AbstractEnvironmentNode.""" return "Node #{:d} {} ({})".format(self.isite, self.atom_symbol, self.coordination_environment)
[docs]class EnvironmentNode(AbstractEnvironmentNode): """ Class used to define an environment as a node in a graph. """ def __init__(self, central_site, i_central_site, ce_symbol): """ Constructor for the EnvironmentNode object. Args: central_site (Site or subclass of Site): central site as a pymatgen Site or subclass of Site (e.g. PeriodicSite, ...). i_central_site (int): Index of the central site in the structure. ce_symbol (str): Symbol of the identified environment. """ AbstractEnvironmentNode.__init__(self, central_site, i_central_site) self._ce_symbol = ce_symbol @property def coordination_environment(self): """Coordination environment of this node.""" return self._ce_symbol
[docs] def everything_equal(self, other): """Compare with another environment node. Returns: True if it is equal to the other node, False otherwise. """ return super().everything_equal(other) and self.coordination_environment == other.coordination_environment
# Keep these as they might come in handy later on if we decide to implement specific descriptors # for specific environments # class OctahedralEnvironmentNode(AbstractEnvironmentNode): # # CG = AllCoordinationGeometries().get_geometry_from_mp_symbol('O:6') # # def __init__(self, central_site, i_central_site): # AbstractEnvironmentNode.__init__(self, central_site, i_central_site) # # @property # def coordination_environment(self): # return self.CG.mp_symbol # # # class TetrahedralEnvironmentNode(AbstractEnvironmentNode): # # CG = AllCoordinationGeometries().get_geometry_from_mp_symbol('T:4') # # def __init__(self, central_site, i_central_site): # AbstractEnvironmentNode.__init__(self, central_site, i_central_site) # # @property # def coordination_environment(self): # return self.CG.mp_symbol # # # allowed_environment_nodes = {'O:6': OctahedralEnvironmentNode, # 'T:4': TetrahedralEnvironmentNode}
[docs]def get_environment_node(central_site, i_central_site, ce_symbol): """ Get the EnvironmentNode class or subclass for the given site and symbol. Args: central_site (Site or subclass of Site): Central site of the environment. i_central_site (int): Index of the central site in the structure. ce_symbol: Symbol of the environment. Returns: An EnvironmentNode object. """ return EnvironmentNode(central_site=central_site, i_central_site=i_central_site, ce_symbol=ce_symbol)