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 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)
def test_lattice(self):
zsl = ZSLGenerator()
for ib in self.ibs:
interface = ib.interfaces[0]
assert zsl.is_same_vectors(
interface.modified_sub_structure.lattice.matrix[:2],
interface.modified_film_structure.lattice.matrix[:2])
def mismatch_strts(film=[], subs=[]):
z = ZSLGenerator()
matches = list(
z(film.lattice.matrix[:2], subs.lattice.matrix[:2], lowest=True))
info = {}
info["mismatch_u"] = "na"
info["mismatch_v"] = "na"
info["mismatch_angle"] = "na"
info["area1"] = "na"
info["area2"] = "na"
info["film_sl"] = film
info["subs_sl"] = subs
try:
uv1 = matches[0]["sub_sl_vecs"]
uv2 = matches[0]["film_sl_vecs"]
# uv1=[[-8.52917200e+00, 9.12745800e+00, 3.66344517e-17],[1.27937580e+01, 9.12745800e+00, 1.34228735e-15]]
# uv2=[[7.02403800e+00, 1.05360570e+01, 1.07524571e-15],[-1.40480760e+01, 7.02403800e+00, -4.30098283e-16]]
u = np.array(uv1)
v = np.array(uv2)
a1 = u[0]
a2 = u[1]
b1 = v[0]
b2 = v[1]
mismatch_u = np.linalg.norm(b1) / np.linalg.norm(a1) - 1
mismatch_v = np.linalg.norm(b2) / np.linalg.norm(a2) - 1
angle1 = (np.arccos(
np.dot(a1, a2) / np.linalg.norm(a1) / np.linalg.norm(a2)) * 180 /
np.pi)
angle2 = (np.arccos(
np.dot(b1, b2) / np.linalg.norm(b1) / np.linalg.norm(b2)) * 180 /
np.pi)
mismatch_angle = abs(angle1 - angle2)
area1 = np.linalg.norm(np.cross(a1, a2))
area2 = np.linalg.norm(np.cross(b1, b2))
uv_substrate = uv1
uv_mat2d = uv2
substrate_latt = Lattice(
np.array([
uv_substrate[0][:], uv_substrate[1][:],
subs.lattice.matrix[2, :]
]))
# to avoid numerical issues with find_mapping
mat2d_fake_c = (film.lattice.matrix[2, :] /
np.linalg.norm(film.lattice.matrix[2, :]) * 5.0)
mat2d_latt = Lattice(
np.array([uv_mat2d[0][:], uv_mat2d[1][:], mat2d_fake_c]))
mat2d_latt_fake = Lattice(
np.array([
film.lattice.matrix[0, :], film.lattice.matrix[1, :],
mat2d_fake_c
]))
_, __, scell = subs.lattice.find_mapping(substrate_latt,
ltol=0.05,
atol=1)
scell[2] = np.array([0, 0, 1])
subs.make_supercell(scell)
_, __, scell = mat2d_latt_fake.find_mapping(mat2d_latt,
ltol=0.05,
atol=1)
scell[2] = np.array([0, 0, 1])
film.make_supercell(scell)
# modify the substrate lattice so that the 2d material can be
# grafted on top of it
lmap = Lattice(
np.array([
subs.lattice.matrix[0, :],
subs.lattice.matrix[1, :],
film.lattice.matrix[2, :],
]))
film.modify_lattice(lmap)
# print ("film",film)
# print ("subs",subs)
info["mismatch_u"] = mismatch_u
info["mismatch_v"] = mismatch_v
info["mismatch_angle"] = mismatch_angle
info["area1"] = area1
info["area2"] = area2
info["film_sl"] = film
info["subs_sl"] = subs
except:
pass
return info