def apply_transformation(self, structure, matrix):
"""
Make a supercell of structure using matrix
Args:
structure (Slab): Slab to make supercell of
matrix (3x3 np.ndarray): supercell matrix
Returns:
(Slab) The supercell of structure
"""
modified_substrate_structure = structure.copy()
# Apply scaling
modified_substrate_structure.make_supercell(matrix)
# Reduce vectors
new_lattice = modified_substrate_structure.lattice.matrix.copy()
new_lattice[:2, :] = reduce_vectors(
*modified_substrate_structure.lattice.matrix[:2, :])
modified_substrate_structure = Slab(
lattice=Lattice(new_lattice),
species=modified_substrate_structure.species,
coords=modified_substrate_structure.cart_coords,
miller_index=modified_substrate_structure.miller_index,
oriented_unit_cell=modified_substrate_structure.oriented_unit_cell,
shift=modified_substrate_structure.shift,
scale_factor=modified_substrate_structure.scale_factor,
coords_are_cartesian=True,
energy=modified_substrate_structure.energy,
reorient_lattice=modified_substrate_structure.reorient_lattice,
to_unit_cell=True)
return modified_substrate_structure
def runTest(self):
# Film VO2
film = SpacegroupAnalyzer(self.get_structure("VO2"),
symprec=0.1).get_conventional_standard_structure()
# Substrate TiO2
substrate = SpacegroupAnalyzer(self.get_structure("TiO2"),
symprec=0.1).get_conventional_standard_structure()
z = ZSLGenerator(film, substrate)
self.assertAlmostEqual(fast_norm([3, 2, 1]), 3.7416573867739413)
self.assertArrayEqual(reduce_vectors([1, 0, 0], [2, 2, 0]),
[[1, 0, 0], [0, 2, 0]])
self.assertEqual(vec_area([1, 0, 0], [0, 2, 0]),
2)
self.assertArrayEqual(list(get_factors(18)), [1, 2, 3, 6, 9, 18])
self.assertTrue(z.is_same_vectors([[1.01, 0, 0], [0, 2, 0]],
[[1, 0, 0], [0, 2.01, 0]]))
self.assertFalse(z.is_same_vectors([[1.01, 2, 0], [0, 2, 0]],
[[1, 0, 0], [0, 2.01, 0]]))
matches = list(z.generate())
self.assertEqual(len(matches), 82)
def get_shear_reduced_slab(slab):
"""
Reduce the vectors of the slab plane according to the algorithm in
substrate_analyzer, then make a new Slab with a Lattice with those
reduced vectors.
Args:
slab (Slab): Slab to reduce
Returns:
Slab object of identical structure to the input slab
but rduced in-plane lattice vectors
"""
original_vectors = [slab.lattice.matrix[0], slab.lattice.matrix[1]]
reduced_vectors = reduce_vectors(slab.lattice.matrix[0],
slab.lattice.matrix[1])
new_lattice = Lattice(
[reduced_vectors[0], reduced_vectors[1], slab.lattice.matrix[2]])
return Slab(lattice=new_lattice,
species=slab.species,
coords=slab.cart_coords,
miller_index=slab.miller_index,
oriented_unit_cell=slab.oriented_unit_cell,
shift=slab.shift,
scale_factor=slab.scale_factor,
coords_are_cartesian=True,
energy=slab.energy,
reorient_lattice=slab.reorient_lattice,
to_unit_cell=True)
def runTest(self):
# Film VO2
film = SpacegroupAnalyzer(
self.get_structure("VO2"),
symprec=0.1).get_conventional_standard_structure()
# Substrate TiO2
substrate = SpacegroupAnalyzer(
self.get_structure("TiO2"),
symprec=0.1).get_conventional_standard_structure()
z = ZSLGenerator()
self.assertAlmostEqual(fast_norm([3, 2, 1]), 3.7416573867739413)
self.assertArrayEqual(reduce_vectors([1, 0, 0], [2, 2, 0]),
[[1, 0, 0], [0, 2, 0]])
self.assertEqual(vec_area([1, 0, 0], [0, 2, 0]), 2)
self.assertArrayEqual(list(get_factors(18)), [1, 2, 3, 6, 9, 18])
self.assertTrue(
z.is_same_vectors([[1.01, 0, 0], [0, 2, 0]],
[[1, 0, 0], [0, 2.01, 0]]))
self.assertFalse(
z.is_same_vectors([[1.01, 2, 0], [0, 2, 0]],
[[1, 0, 0], [0, 2.01, 0]]))
matches = list(z.generate(film, substrate))
self.assertEqual(len(matches), 82)
