def get_atoms_surf():
a = 2.70
c = 1.59 * a
h = 1.85
d = 1.10
slab = Atoms('2Cu', [(0., 0., 0.), (1 / 3., 1 / 3., -0.5 * c)],
tags=(0, 1),
pbc=(1, 1, 0))
slab.set_cell([(a, 0, 0), (a / 2, 3**0.5 * a / 2, 0), (0, 0, 1)])
slab = slab.repeat((4, 4, 1))
mask = [a.tag == 1 for a in slab]
slab.set_constraint(FixAtoms(mask=mask))
return slab
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)