Source code for icet.core.cluster_counts

This module provides the ClusterCounts class.

from collections import OrderedDict
from _icet import ClusterCounts as _ClusterCounts
from _icet import Cluster
from ase import Atoms
from icet.core.orbit_list import OrbitList
from icet import Structure
from .local_orbit_list_generator import LocalOrbitListGenerator

[docs]class ClusterCounts(_ClusterCounts): """ Provides an interface for inspecting cluster counts. Parameters ---------- orbit_list : icet.OrbitList orbit list for a primitive structure structure : ase.Atoms supercell of the structure that `orbit_list` is based on Attributes ---------- cluster_counts : OrderedDict keys are representative clusters (icet Cluster objects) for all distinct orbits in the orbit list, values are dicts where the key is the chemical symbols of the species in a cluster, and the value is the number of counts of such clusters, e.g., {('Au', 'Ag'): 3, ('Au', 'Au'): 5}. """ def __init__(self, orbit_list: OrbitList, structure: Atoms): self._orbit_list = orbit_list self._structure = Structure.from_atoms(structure) # call (base) C++ constructor _ClusterCounts.__init__(self) self.cluster_counts = self._count_clusters() def _count_clusters(self, keep_order_intact=False, permute_sites=True): """ Counts all clusters in a structure by finding their local orbit list. Parameters ---------- keep_order_intact : bool if true the order in the cluster will be sorted permute_sites : bool if true will permute the sites so they are in the symmetrically equivalent order as the representative sites """ local_orbit_list_generator = LocalOrbitListGenerator( self._orbit_list, self._structure) for i in range( local_orbit_list_generator.get_number_of_unique_offsets()): self.count_orbit_list( self._structure, local_orbit_list_generator.generate_local_orbit_list(i), keep_order_intact, permute_sites) sorted_cluster_counts = \ OrderedDict(sorted(self.get_cluster_counts().items())) return sorted_cluster_counts def __str__(self): """ String representation of ClusterCounts object that provides an overview of the clusters (cluster, chemical symbol, and count). """ tuplets = {1: 'Singlet', 2: 'Pair', 3: 'Triplet', 4: 'Quadruplet', 5: 'Pentuplet'} width = 60 s = ['{s:=^{n}}'.format(s=' Cluster Counts ', n=width)] first = True for cluster, counts in self.cluster_counts.items(): if not first: s += [''] else: first = False # Add a description of the orbit to the string tuplet_type = tuplets.get(len(cluster.sites), '{}-tuplet'.format(len(cluster.sites))) s += ['{}: {} {:} {:.4f}' .format(tuplet_type, cluster.sites, cluster.distances, cluster.radius)] # Print the actual counts together with the species they refer to for chemical_symbols, count in counts.items(): t = ['{:3} '.format(el) for el in chemical_symbols] s += ['{} {}'.format(''.join(t), count)] s += [''.center(width, '=')] return '\n'.join(s) def __getitem__(self, key): """ Returns cluster count (Cluster object and dict with counts) for a ClusterCounts object. Parameters ---------- key : int or icet.Cluster if int, return the key-th counts; if Cluster, return the counts belonging to that cluster """ if isinstance(key, int): return list(self.cluster_counts.values())[key] elif isinstance(key, Cluster): return self.cluster_counts[key]