def test_utilities():
eps = 1e-5
atoms = Icosahedron('Cu', 3)
atoms.numbers[[0, 13, 15, 16, 18, 19, 21, 22, 24, 25, 27, 28, 30]] = 79
atoms.center(vacuum=0.0)
atoms.calc = EMT()
with FIRE(atoms, logfile=None) as opt:
opt.run(fmax=0.05)
rmax = 8.
nbins = 5
rdf, dists = get_rdf(atoms, rmax, nbins)
calc_dists = np.arange(rmax / (2 * nbins), rmax, rmax / nbins)
assert all(abs(dists - calc_dists) < eps)
calc_rdf = [0., 0.84408157, 0.398689, 0.23748934, 0.15398546]
assert all(abs(rdf - calc_rdf) < eps)
dm = atoms.get_all_distances()
s = np.zeros(5)
for c in [(29, 29), (29, 79), (79, 29), (79, 79)]:
inv_norm = len(np.where(atoms.numbers == c[0])[0]) / len(atoms)
s += get_rdf(atoms, rmax, nbins, elements=c,
distance_matrix=dm, no_dists=True) * inv_norm
assert all(abs(s - calc_rdf) < eps)
AuAu = get_rdf(atoms, rmax, nbins, elements=(79, 79),
distance_matrix=dm, no_dists=True)
assert all(abs(AuAu[-2:] - [0.12126445, 0.]) < eps)
bulk = L1_2(['Au', 'Cu'], size=(3, 3, 3), latticeconstant=2 * np.sqrt(2))
rdf = get_rdf(bulk, 4.2, 5)[0]
calc_rdf = [0., 0., 1.43905094, 0.36948605, 1.34468694]
assert all(abs(rdf - calc_rdf) < eps)
def make_ico(sym):
atoms = Icosahedron(sym, 4)
atoms.center(vacuum=4.0)
return atoms