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import numpy.random as random
import numpy as np
from ase import Atoms
from ase.neighborlist import NeighborList
from ase.build import bulk
atoms = Atoms(numbers=range(10),
cell=[(0.2, 1.2, 1.4),
(1.4, 0.1, 1.6),
(1.3, 2.0, -0.1)])
atoms.set_scaled_positions(3 * random.random((10, 3)) - 1)
def count(nl, atoms):
c = np.zeros(len(atoms), int)
R = atoms.get_positions()
cell = atoms.get_cell()
d = 0.0
for a in range(len(atoms)):
i, offsets = nl.get_neighbors(a)
for j in i:
c[j] += 1
c[a] += len(i)
d += (((R[i] + np.dot(offsets, cell) - R[a])**2).sum(1)**0.5).sum()
return d, c
for sorted in [False, True]:
for p1 in range(2):
for p2 in range(2):
for p3 in range(2):
print(p1, p2, p3)
atoms.set_pbc((p1, p2, p3))
nl = NeighborList(atoms.numbers * 0.2 + 0.5,
skin=0.0, sorted=sorted)
nl.update(atoms)
d, c = count(nl, atoms)
atoms2 = atoms.repeat((p1 + 1, p2 + 1, p3 + 1))
nl2 = NeighborList(atoms2.numbers * 0.2 + 0.5,
skin=0.0, sorted=sorted)
nl2.update(atoms2)
d2, c2 = count(nl2, atoms2)
c2.shape = (-1, 10)
dd = d * (p1 + 1) * (p2 + 1) * (p3 + 1) - d2
print(dd)
print(c2 - c)
assert abs(dd) < 1e-10
assert not (c2 - c).any()
h2 = Atoms('H2', positions=[(0, 0, 0), (0, 0, 1)])
nl = NeighborList([0.5, 0.5], skin=0.1, sorted=True, self_interaction=False)
assert nl.update(h2)
assert not nl.update(h2)
assert (nl.get_neighbors(0)[0] == [1]).all()
h2[1].z += 0.09
assert not nl.update(h2)
assert (nl.get_neighbors(0)[0] == [1]).all()
h2[1].z += 0.09
assert nl.update(h2)
assert (nl.get_neighbors(0)[0] == []).all()
assert nl.nupdates == 2
x = bulk('X', 'fcc', a=2**0.5)
print(x)
nl = NeighborList([0.5], skin=0.01, bothways=True, self_interaction=False)
nl.update(x)
assert len(nl.get_neighbors(0)[0]) == 12
nl = NeighborList([0.5] * 27, skin=0.01, bothways=True, self_interaction=False)
nl.update(x * (3, 3, 3))
for a in range(27):
assert len(nl.get_neighbors(a)[0]) == 12
assert not np.any(nl.get_neighbors(13)[1])
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