from ase.atoms import Atoms
from ase.data import covalent_radii
from ase.neighborlist import NeighborList
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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)]
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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
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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
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def split_bond(atoms, index1, index2, **kwargs):
"""Split atoms by a bond specified by indices
index1: index of first atom
index2: index of second atom
kwargs: kwargs transferred to connected_atoms
Returns two Atoms objects
"""
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], **kwargs)
atoms_copy = atoms.copy()
del atoms_copy[index1]
atoms2 = connected_atoms(atoms_copy, index2 - shift[1], **kwargs)
return atoms1, atoms2