def test_get_neighborhood_single(self):
struct = CrystalStructure(elements='Al',
lattice_constants=4,
bravais_basis='fcc')
neigh = struct.get_neighborhood(np.random.random(3), cutoff_radius=3)
distances = neigh.distances.copy()
neigh.allow_ragged = False
self.assertTrue(np.array_equal(neigh.distances, distances))
neigh.allow_ragged = True
self.assertTrue(np.array_equal(neigh.distances, distances))
neigh.allow_ragged = False
self.assertTrue(np.array_equal(neigh.distances, distances))
def test_get_neighborhood(self):
struct = CrystalStructure(elements='Al',
lattice_constants=4,
bravais_basis='fcc')
struct.positions += 0.01 * (
2 * np.random.random(struct.positions.shape) - 1)
struct = struct.center_coordinates_in_unit_cell()
positions = np.random.random((2, 3)).dot(struct.cell)
neigh = struct.get_neighborhood(positions)
positions = np.random.random((2, 3)).dot(struct.cell)
new_neigh = neigh.get_neighborhood(positions)
self.assertTrue(
np.array_equal(new_neigh.distances,
neigh.get_distances(positions)))
self.assertTrue(
np.array_equal(new_neigh.vecs, neigh.get_vectors(positions)))
self.assertTrue(
np.array_equal(new_neigh.indices, neigh.get_indices(positions)))