def test_get_scaled_positions(self):
basis_Mg = CrystalStructure("Mg",
bravais_basis="fcc",
lattice_constant=4.2)
self.assertTrue(
np.array_equal(basis_Mg.scaled_positions,
basis_Mg.get_scaled_positions()))
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())
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)
struct = CrystalStructure(elements='Fe', lattice_constants=2.85, bravais_basis='bcc').repeat(10)
neigh = struct.get_neighbors()
self.assertAlmostEqual(np.absolute(neigh.distances-np.linalg.norm(neigh.vecs, axis=-1)).max(), 0)
self.assertAlmostEqual(neigh.vecs[neigh.shells==1].sum(), 0)
self.assertAlmostEqual(neigh.vecs[0, neigh.shells[0]==1].sum(), 0)
struct = CrystalStructure(elements='Fe', lattice_constants=2.85, bravais_basis='bcc')
neigh = struct.get_neighbors()
self.assertAlmostEqual(neigh.vecs[neigh.shells==1].sum(), 0)
struct = CrystalStructure(elements='Al', lattice_constants=4.04, bravais_basis='bcc').repeat(10)
neigh = struct.get_neighbors()
self.assertAlmostEqual(np.absolute(neigh.distances-np.linalg.norm(neigh.vecs, axis=-1)).max(), 0)
self.assertAlmostEqual(neigh.vecs[neigh.shells==1].sum(), 0)
self.assertAlmostEqual(neigh.vecs[0, neigh.shells[0]==1].sum(), 0)
struct = CrystalStructure(elements='Al', lattice_constants=4.04, bravais_basis='bcc')
neigh = struct.get_neighbors()
self.assertAlmostEqual(np.absolute(neigh.distances-np.linalg.norm(neigh.vecs, axis=-1)).max(), 0)
self.assertAlmostEqual(neigh.vecs[neigh.shells==1].sum(), 0)
with self.assertRaises(ValueError):
struct.get_neighbors(num_neighbors=0)