Source code for catkit.gen.analysis.matching

import networkx as nx
import numpy as np
import ase

[docs]def reactant_indices(R1, R2, P, broken_bond): """Match the indices of a pair of reactants from a product and broken bond. Parameters ---------- R1 : networkx MultiGraph Graph representing reactant 1 R2 : networkx MultiGraph Graph representing reactant 2 P : networkx MultiGraph Graph representing the product broken_bond : list (2,) Indices representing the edge of the product to be removed. Returns ------- pindex: ndarrays (n,) Indices of the product graph sorted by the order of the reactants indices. """ GM = nx.algorithms.isomorphism.GraphMatcher em = nx.algorithms.isomorphism.numerical_edge_match('bonds', 1) nm = nx.algorithms.isomorphism.numerical_node_match('number', 1) Pgraph = P.copy() u, v = broken_bond Pgraph.graph.remove_edge(u, v) Rgraph = R1 + R2 gm = GM(Pgraph.graph, Rgraph.graph, edge_match=em, node_match=nm) gm.is_isomorphic() pindex = np.empty(len(Pgraph), dtype=int) for k, v in gm.mapping.items(): pindex[k] = v return pindex
[docs]def slab_indices(slab0, slab1, mask=None): """Match the indices of similar atoms between two slabs.""" n = len(slab0) if mask is None: mask = np.arange(n) matching = np.arange(n) ipos = slab0.positions[mask] fpos = slab1.positions[mask] d = ase.geometry.get_distances( ipos, fpos, cell=slab0.cell, pbc=slab0.pbc)[1] matching[mask] = np.argmin(d, axis=1) atoms =, matching) return atoms