def test_get_neighbors(self):
struct = CrystalStructure(elements='Fe',
lattice_constants=2.85,
bravais_basis='bcc').repeat(10)
cell = struct.cell.copy()
cell += np.random.random((3, 3)) - 0.5
struct.positions += np.random.random((len(struct), 3)) - 0.5
struct.set_cell(cell, scale_atoms=True)
neigh = struct.get_neighbors()
self.assertAlmostEqual(
np.absolute(neigh.distances -
np.linalg.norm(neigh.vecs, axis=-1)).max(), 0)
myself = np.ones_like(neigh.indices)
myself = myself * np.arange(len(myself))[:, np.newaxis]
dist = struct.get_distances(myself.flatten(),
neigh.indices.flatten(),
mic=True)
self.assertAlmostEqual(
np.absolute(dist - neigh.distances.flatten()).max(), 0)
vecs = struct.get_distances(myself.flatten(),
neigh.indices.flatten(),
mic=True,
vector=True)
self.assertAlmostEqual(
np.absolute(vecs - neigh.vecs.reshape(-1, 3)).max(), 0)
dist = struct.get_scaled_positions()
dist = dist[:, np.newaxis, :] - dist[np.newaxis, :, :]
dist -= np.rint(dist)
dist = np.einsum('nmi,ij->nmj', dist, struct.cell)
dist = np.linalg.norm(dist, axis=-1).flatten()
dist = dist[dist > 0]
self.assertAlmostEqual(neigh.distances.min(), dist.min())
def test_pbc_false(self):
struct = CrystalStructure(elements='Fe',
lattice_constants=2.85,
bravais_basis='bcc').repeat(10)
struct.pbc = False
cell = struct.cell.copy()
cell += np.random.random((3, 3)) - 0.5
struct.set_cell(cell, scale_atoms=True)
neigh = struct.get_neighbors()
self.assertAlmostEqual(
np.absolute(neigh.distances -
np.linalg.norm(neigh.vecs, axis=-1)).max(), 0)
myself = np.ones_like(neigh.indices)
myself = myself * np.arange(len(myself))[:, np.newaxis]
dist = np.linalg.norm(struct.positions[myself] -
struct.positions[neigh.indices],
axis=-1)
self.assertAlmostEqual(np.absolute(dist - neigh.distances).max(), 0)