def get_aligned_lattices(slab_sub, slab_2d, max_area=200,
max_mismatch=0.05,
max_angle_diff=1, r1r2_tol=0.2):
"""
given the 2 slab structures and the alignment paramters, return
slab structures with lattices that are aligned with respect to each
other
"""
# get the matching substrate and 2D material lattices
uv_substrate, uv_mat2d = get_matching_lattices(slab_sub, slab_2d,
max_area=max_area,
max_mismatch=max_mismatch,
max_angle_diff=max_angle_diff,
r1r2_tol=r1r2_tol)
if not uv_substrate and not uv_mat2d:
print("no matching u and v, trying adjusting the parameters")
sys.exit()
substrate = Structure.from_sites(slab_sub)
mat2d = Structure.from_sites(slab_2d)
# map the intial slabs to the newly found matching lattices
substrate_latt = Lattice(np.array(
[
uv_substrate[0][:],
uv_substrate[1][:],
substrate.lattice.matrix[2, :]
]))
# to avoid numerical issues with find_mapping
mat2d_fake_c = mat2d.lattice.matrix[2, :] / np.linalg.norm(mat2d.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(
[
mat2d.lattice.matrix[0, :],
mat2d.lattice.matrix[1, :],
mat2d_fake_c
]))
_, __, scell = substrate.lattice.find_mapping(substrate_latt,
ltol=0.05,
atol=1)
scell[2] = np.array([0, 0, 1])
substrate.make_supercell(scell)
_, __, scell = mat2d_latt_fake.find_mapping(mat2d_latt,
ltol=0.05,
atol=1)
scell[2] = np.array([0, 0, 1])
mat2d.make_supercell(scell)
# modify the substrate lattice so that the 2d material can be
# grafted on top of it
lmap = Lattice(np.array(
[
substrate.lattice.matrix[0, :],
substrate.lattice.matrix[1, :],
mat2d.lattice.matrix[2, :]
]))
mat2d.modify_lattice(lmap)
return substrate, mat2d
def get_aligned_lattices(slab_sub,
slab_2d,
max_area=200,
max_mismatch=0.05,
max_angle_diff=1,
r1r2_tol=0.2):
"""
given the 2 slab structures and the alignment paramters, return
slab structures with lattices that are aligned with respect to each
other
"""
# get the matching substrate and 2D material lattices
uv_substrate, uv_mat2d = get_matching_lattices(
slab_sub,
slab_2d,
max_area=max_area,
max_mismatch=max_mismatch,
max_angle_diff=max_angle_diff,
r1r2_tol=r1r2_tol)
if not uv_substrate and not uv_mat2d:
print("no matching u and v, trying adjusting the parameters")
sys.exit()
substrate = Structure.from_sites(slab_sub)
mat2d = Structure.from_sites(slab_2d)
# map the intial slabs to the newly found matching lattices
substrate_latt = Lattice(
np.array([
uv_substrate[0][:], uv_substrate[1][:],
substrate.lattice.matrix[2, :]
]))
# to avoid numerical issues with find_mapping
mat2d_fake_c = mat2d.lattice.matrix[2, :] / np.linalg.norm(
mat2d.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([
mat2d.lattice.matrix[0, :], mat2d.lattice.matrix[1, :],
mat2d_fake_c
]))
_, __, scell = substrate.lattice.find_mapping(substrate_latt,
ltol=0.05,
atol=1)
scell[2] = np.array([0, 0, 1])
substrate.make_supercell(scell)
_, __, scell = mat2d_latt_fake.find_mapping(mat2d_latt, ltol=0.05, atol=1)
scell[2] = np.array([0, 0, 1])
mat2d.make_supercell(scell)
# modify the substrate lattice so that the 2d material can be
# grafted on top of it
lmap = Lattice(
np.array([
substrate.lattice.matrix[0, :], substrate.lattice.matrix[1, :],
mat2d.lattice.matrix[2, :]
]))
mat2d.modify_lattice(lmap)
return substrate, mat2d
def test_find_mapping(self):
m = np.array([[0.1, 0.2, 0.3], [-0.1, 0.2, 0.7], [0.6, 0.9, 0.2]])
latt = Lattice(m)
op = SymmOp.from_origin_axis_angle([0, 0, 0], [2, 3, 3], 35)
rot = op.rotation_matrix
scale = np.array([[1, 1, 0], [0, 1, 0], [0, 0, 1]])
latt2 = Lattice(np.dot(rot, np.dot(scale, m).T).T)
(latt, rot, scale2) = latt2.find_mapping(latt)
self.assertAlmostEqual(abs(np.linalg.det(rot)), 1)
self.assertTrue(np.allclose(scale2, scale) or
np.allclose(scale2, -scale))
def test_find_mapping(self):
m = np.array([[0.1, 0.2, 0.3], [-0.1, 0.2, 0.7], [0.6, 0.9, 0.2]])
latt = Lattice(m)
op = SymmOp.from_origin_axis_angle([0, 0, 0], [2, 3, 3], 35)
rot = op.rotation_matrix
scale = np.array([[1, 1, 0], [0, 1, 0], [0, 0, 1]])
latt2 = Lattice(np.dot(rot, np.dot(scale, m).T).T)
(latt, rot, scale2) = latt2.find_mapping(latt)
self.assertAlmostEqual(abs(np.linalg.det(rot)), 1)
self.assertTrue(
np.allclose(scale2, scale) or np.allclose(scale2, -scale))
def test_find_mapping(self):
m = np.array([[0.1, 0.2, 0.3], [-0.1, 0.2, 0.7], [0.6, 0.9, 0.2]])
latt = Lattice(m)
op = SymmOp.from_origin_axis_angle([0, 0, 0], [2, 3, 3], 35)
rot = op.rotation_matrix
scale = np.array([[1, 1, 0], [0, 1, 0], [0, 0, 1]])
latt2 = Lattice(np.dot(rot, np.dot(scale, m).T).T)
(aligned_out, rot_out, scale_out) = latt2.find_mapping(latt)
self.assertAlmostEqual(abs(np.linalg.det(rot)), 1)
rotated = SymmOp.from_rotation_and_translation(rot_out).operate_multi(latt.matrix)
self.assertArrayAlmostEqual(rotated, aligned_out.matrix)
self.assertArrayAlmostEqual(np.dot(scale_out, latt2.matrix), aligned_out.matrix)
self.assertArrayAlmostEqual(aligned_out.parameters, latt.parameters)
self.assertFalse(np.allclose(aligned_out.parameters, latt2.parameters))
def test_find_mapping(self):
m = np.array([[0.1, 0.2, 0.3], [-0.1, 0.2, 0.7], [0.6, 0.9, 0.2]])
latt = Lattice(m)
op = SymmOp.from_origin_axis_angle([0, 0, 0], [2, 3, 3], 35)
rot = op.rotation_matrix
scale = np.array([[1, 1, 0], [0, 1, 0], [0, 0, 1]])
latt2 = Lattice(np.dot(rot, np.dot(scale, m).T).T)
(aligned_out, rot_out, scale_out) = latt2.find_mapping(latt)
self.assertAlmostEqual(abs(np.linalg.det(rot)), 1)
rotated = SymmOp.from_rotation_and_translation(rot_out).operate_multi(latt.matrix)
self.assertArrayAlmostEqual(rotated, aligned_out.matrix)
self.assertArrayAlmostEqual(np.dot(scale_out, latt2.matrix), aligned_out.matrix)
self.assertArrayAlmostEqual(aligned_out.lengths_and_angles, latt.lengths_and_angles)
self.assertFalse(np.allclose(aligned_out.lengths_and_angles,
latt2.lengths_and_angles))
def process_sys(
slab_sub,
slab_2d,
uv_substrate,
uv_mat2d,
):
"""
"""
#| - process_sys
substrate = Structure.from_sites(slab_sub)
mat2d = Structure.from_sites(slab_2d)
# map the intial slabs to the newly found matching lattices
substrate_latt = Lattice(
np.array(
[
uv_substrate[0][:],
uv_substrate[1][:],
substrate.lattice.matrix[2, :]
]
)
)
# to avoid numerical issues with find_mapping
mat2d_fake_c = mat2d.lattice.matrix[2, :] / np.linalg.norm(
mat2d.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(
[
mat2d.lattice.matrix[0, :],
mat2d.lattice.matrix[1, :],
mat2d_fake_c
]
)
)
_, __, scell = substrate.lattice.find_mapping(substrate_latt,
ltol=0.05,
atol=1)
scell[2] = np.array([0, 0, 1])
substrate.make_supercell(scell)
_, __, scell = mat2d_latt_fake.find_mapping(mat2d_latt,
ltol=0.05,
atol=1)
scell[2] = np.array([0, 0, 1])
mat2d.make_supercell(scell)
# modify the substrate lattice so that the 2d material can be
# grafted on top of it
lmap = Lattice(
np.array(
[
substrate.lattice.matrix[0, :],
substrate.lattice.matrix[1, :],
mat2d.lattice.matrix[2, :]
]
)
)
mat2d.modify_lattice(lmap)
return(substrate, mat2d)
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
