Source code for ase.build.connected

from ase.atoms import Atoms
from ase.data import covalent_radii
from ase.neighborlist import NeighborList


[docs]def connected_atoms(atoms, index, dmax=None, scale=1.5): """Find all atoms connected to atoms[index] and return them.""" return atoms[connected_indices(atoms, index, dmax, scale)]
[docs]def connected_indices(atoms, index, dmax=None, scale=1.5): """Find atoms connected to atoms[index] and return their indices. If dmax is not None: Atoms are defined to be connected if they are nearer than dmax to each other. If dmax is None: Atoms are defined to be connected if they are nearer than the sum of their covalent radii * scale to each other. """ if index < 0: index = len(atoms) + index # set neighbor lists if dmax is None: # define neighbors according to covalent radii radii = scale * covalent_radii[atoms.get_atomic_numbers()] else: # define neighbors according to distance radii = [0.5 * dmax] * len(atoms) nl = NeighborList(radii, skin=0, self_interaction=False, bothways=True) nl.update(atoms) connected = [index] + list(nl.get_neighbors(index)[0]) isolated = False while not isolated: isolated = True for i in connected: for j in nl.get_neighbors(i)[0]: if j not in connected: connected.append(j) isolated = False return connected
[docs]def separate(atoms, **kwargs): """Split atoms into separated entities Returns: List of Atoms object that connected_indices calls connected. """ indices = list(range(len(atoms))) separated = [] while indices: my_indcs = connected_indices(atoms, indices[0], **kwargs) separated.append(Atoms(cell=atoms.cell, pbc=atoms.pbc)) for i in my_indcs: separated[-1].append(atoms[i]) del indices[indices.index(i)] return separated
[docs]def split_bond(atoms, index1, index2): """Split atoms by a bond specified by indices""" assert index1 != index2 if index2 > index1: shift = 0, 1 else: shift = 1, 0 atoms_copy = atoms.copy() del atoms_copy[index2] atoms1 = connected_atoms(atoms_copy, index1 - shift[0]) atoms_copy = atoms.copy() del atoms_copy[index1] atoms2 = connected_atoms(atoms_copy, index2 - shift[1]) return atoms1, atoms2