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)