def test1():
print('generating graphene structure')
graphene = GrapheneGenerator(armchair_edge_length=5,
zigzag_edge_length=5)
lattice = graphene.lattice
print('graphene.bounds:\n{}'.format(graphene.bounds))
print('graphene.centroid:\n{}'.format(graphene.centroid))
print('graphene.lattice:\n{}'.format(lattice))
print('graphene.lattice.a1:\n{}'.format(lattice.a1))
print('graphene.lattice.a2:\n{}'.format(lattice.a2))
print('graphene.lattice.a3:\n{}'.format(lattice.a3))
print('graphene.lattice.orientation_matrix:\n{}'.format(
lattice.orientation_matrix))
print('rotating graphene')
graphene.rotate(angle=-np.pi/2, axis='x')
print('graphene.bounds:\n{}'.format(graphene.bounds))
print('graphene.centroid:\n{}'.format(graphene.centroid))
print('graphene.lattice:\n{}'.format(lattice))
print('graphene.lattice.a1:\n{}'.format(lattice.a1))
print('graphene.lattice.a2:\n{}'.format(lattice.a2))
print('graphene.lattice.a3:\n{}'.format(lattice.a3))
print('graphene.lattice.orientation_matrix:\n{}'.format(
lattice.orientation_matrix))
assert_true(np.allclose(lattice.angles, 3 * [90.0]))
lattice_region = Cuboid(pmax=lattice.lengths)
# lattice_region = Parallelepiped(u=lattice.a * xhat,
# v=lattice.b * yhat,
# w=lattice.c * zhat)
assert_equal(lattice_region.a, lattice.a)
assert_equal(lattice_region.b, lattice.b)
assert_equal(lattice_region.c, lattice.c)
print('lattice_region:\n{}'.format(lattice_region))
print('lattice_region.centroid:\n{}'.format(lattice_region.centroid))
print('\nrotating lattice_region')
lattice_region.rotate(transform_matrix=lattice.orientation_matrix)
# assert_equal(lattice_region.a, lattice.a)
# assert_equal(lattice_region.b, lattice.b)
# assert_equal(lattice_region.c, lattice.c)
print('lattice_region:\n{}'.format(lattice_region))
print('lattice_region.centroid:\n{}'.format(lattice_region.centroid))
print('\ncentering lattice_region on graphene centroid')
tvec = Vector(Point(graphene.centroid) - lattice_region.centroid)
lattice_region.translate(tvec)
# assert_equal(lattice_region.a, lattice.a)
# assert_equal(lattice_region.b, lattice.b)
# assert_equal(lattice_region.c, lattice.c)
print('lattice_region:\n{}'.format(lattice_region))
print('lattice_region.centroid:\n{}'.format(lattice_region.centroid))
bounding_box = generate_bounding_box(from_lattice=lattice,
center=graphene.centroid,
verbose=True)
print('bounding_box:\n{}'.format(bounding_box))
assert_equal(bounding_box, lattice_region)
print('lattice_region.lengths: {}, {}, {}'.format(
lattice_region.a, lattice_region.b, lattice_region.c))
def test1():
print('generating graphene structure')
graphene = GrapheneGenerator(armchair_edge_length=5, zigzag_edge_length=5)
lattice = graphene.lattice
print('graphene.bounds:\n{}'.format(graphene.bounds))
print('graphene.centroid:\n{}'.format(graphene.centroid))
print('graphene.lattice:\n{}'.format(lattice))
print('graphene.lattice.a1:\n{}'.format(lattice.a1))
print('graphene.lattice.a2:\n{}'.format(lattice.a2))
print('graphene.lattice.a3:\n{}'.format(lattice.a3))
print('graphene.lattice.orientation_matrix:\n{}'.format(
lattice.orientation_matrix))
print('rotating graphene')
graphene.rotate(angle=-np.pi / 2, axis='x')
print('graphene.bounds:\n{}'.format(graphene.bounds))
print('graphene.centroid:\n{}'.format(graphene.centroid))
print('graphene.lattice:\n{}'.format(lattice))
print('graphene.lattice.a1:\n{}'.format(lattice.a1))
print('graphene.lattice.a2:\n{}'.format(lattice.a2))
print('graphene.lattice.a3:\n{}'.format(lattice.a3))
print('graphene.lattice.orientation_matrix:\n{}'.format(
lattice.orientation_matrix))
assert_true(np.allclose(lattice.angles, 3 * [90.0]))
lattice_region = Cuboid(pmax=lattice.lengths)
# lattice_region = Parallelepiped(u=lattice.a * xhat,
# v=lattice.b * yhat,
# w=lattice.c * zhat)
assert_equal(lattice_region.a, lattice.a)
assert_equal(lattice_region.b, lattice.b)
assert_equal(lattice_region.c, lattice.c)
print('lattice_region:\n{}'.format(lattice_region))
print('lattice_region.centroid:\n{}'.format(lattice_region.centroid))
print('\nrotating lattice_region')
lattice_region.rotate(transform_matrix=lattice.orientation_matrix)
# assert_equal(lattice_region.a, lattice.a)
# assert_equal(lattice_region.b, lattice.b)
# assert_equal(lattice_region.c, lattice.c)
print('lattice_region:\n{}'.format(lattice_region))
print('lattice_region.centroid:\n{}'.format(lattice_region.centroid))
print('\ncentering lattice_region on graphene centroid')
tvec = Vector(Point(graphene.centroid) - lattice_region.centroid)
lattice_region.translate(tvec)
# assert_equal(lattice_region.a, lattice.a)
# assert_equal(lattice_region.b, lattice.b)
# assert_equal(lattice_region.c, lattice.c)
print('lattice_region:\n{}'.format(lattice_region))
print('lattice_region.centroid:\n{}'.format(lattice_region.centroid))
bounding_box = generate_bounding_box(from_lattice=lattice,
center=graphene.centroid,
verbose=True)
print('bounding_box:\n{}'.format(bounding_box))
assert_equal(bounding_box, lattice_region)
print('lattice_region.lengths: {}, {}, {}'.format(lattice_region.a,
lattice_region.b,
lattice_region.c))
def test2():
graphene = GrapheneGenerator(armchair_edge_length=5,
zigzag_edge_length=5)
graphene.rotate(angle=-np.pi/2, axis='x')
lattice = graphene.lattice
bounding_box1 = Cuboid()
bounding_box2 = Cuboid()
lattice_region1 = Cuboid(pmax=lattice.lengths)
bounding_box1.pmin = lattice_region1.pmin
bounding_box1.pmax = lattice_region1.pmax
a, b, c = lattice.lengths
cos_alpha, cos_beta, cos_gamma = np.cos(np.radians(lattice.angles))
lx = a
xy = b * cos_gamma
xz = c * cos_beta
ly = np.sqrt(b ** 2 - xy ** 2)
yz = (b * c * cos_alpha - xy * xz) / ly
lz = np.sqrt(c ** 2 - xz ** 2 - yz ** 2)
lattice_region2 = \
Parallelepiped(u=Vector(lattice.ortho_matrix[:, 0].A.flatten()),
v=Vector(lattice.ortho_matrix[:, 1].A.flatten()),
w=Vector(lattice.ortho_matrix[:, 2].A.flatten()))
xlo, ylo, zlo = lattice_region2.o
print('xy={}, xz={}, yz={}'.format(xy, xz, yz))
print('lx={}, ly={}, lz={}'.format(lx, ly, lz))
print('xlo={}, ylo={}, zlo={}'.format(xlo, ylo, zlo))
xlo_bound = xlo + min(0.0, xy, xz, xy + xz)
xhi_bound = xlo + lx + max(0.0, xy, xz, xy + xz)
ylo_bound = ylo + min(0.0, yz)
yhi_bound = ylo + ly + max(0.0, yz)
zlo_bound = zlo
zhi_bound = zlo + lz
bounding_box2.pmin = [xlo_bound, ylo_bound, zlo_bound]
bounding_box2.pmax = [xhi_bound, yhi_bound, zhi_bound]
print(bounding_box1)
print(bounding_box2)
[bounding_box.rotate(transform_matrix=lattice.orientation_matrix)
for bounding_box in (bounding_box1, bounding_box2)]
[bounding_box.translate(Vector(Point(graphene.centroid) -
bounding_box.centroid))
for bounding_box in (bounding_box1, bounding_box2)]
[assert_true(bounding_box.pmin <= bounding_box.pmax) for bounding_box
in (bounding_box1, bounding_box2)]
assert_equal(bounding_box1, bounding_box2)
print(bounding_box1)
print(bounding_box2)
def test8(self):
generator = \
GrapheneGenerator.from_conventional_cell(armchair_edge_length=2,
zigzag_edge_length=2,
nlayers=3)
generator.save(fname='2nmx2nm_3layer_conventional_cell_graphene.data')
self.tmpdata.append(generator.fname)
def test8(self):
generator = \
GrapheneGenerator.from_conventional_cell(armchair_edge_length=2,
zigzag_edge_length=2,
nlayers=3)
generator.save(fname='2nmx2nm_3layer_conventional_cell_graphene.data')
self.tmpdata.append(generator.fname)
def test3(self):
generator = \
GrapheneGenerator.from_conventional_cell(armchair_edge_length=2,
zigzag_edge_length=2)
generator.atoms.update_attrs()
# generator.save(deepcopy=False)
generator.save(fname='2nmx2nm_1layer_conventional_cell_graphene-2.xyz',
deepcopy=False)
self.tmpdata.append(generator.fname)
def test3(self):
generator = \
GrapheneGenerator.from_conventional_cell(armchair_edge_length=2,
zigzag_edge_length=2)
generator.atoms.update_attrs()
# generator.save(deepcopy=False)
generator.save(fname='2nmx2nm_1layer_conventional_cell_graphene-2.xyz',
deepcopy=False)
self.tmpdata.append(generator.fname)
def test9(self):
generator = \
GrapheneGenerator.from_primitive_cell(edge_length=2, nlayers=3)
generator.save(fname='2nm_3layer_primitive_cell_graphene.data')
self.tmpdata.append(generator.fname)
def test5(self):
generator = \
GrapheneGenerator.from_primitive_cell(edge_length=2)
generator.save(fname='2nm_1layer_primitive_cell_graphene-2.xyz')
self.tmpdata.append(generator.fname)
def test1(self):
generator = GrapheneGenerator(armchair_edge_length=2,
zigzag_edge_length=2)
generator.save()
self.tmpdata.append(generator.fname)
def test9(self):
generator = \
GrapheneGenerator.from_primitive_cell(edge_length=2, nlayers=3)
generator.save(fname='2nm_3layer_primitive_cell_graphene.data')
self.tmpdata.append(generator.fname)
def test5(self):
generator = \
GrapheneGenerator.from_primitive_cell(edge_length=2)
generator.save(fname='2nm_1layer_primitive_cell_graphene-2.xyz')
self.tmpdata.append(generator.fname)
def test1(self):
generator = GrapheneGenerator(armchair_edge_length=2,
zigzag_edge_length=2)
generator.save()
self.tmpdata.append(generator.fname)
def test2():
graphene = GrapheneGenerator(armchair_edge_length=5, zigzag_edge_length=5)
graphene.rotate(angle=-np.pi / 2, axis='x')
lattice = graphene.lattice
bounding_box1 = Cuboid()
bounding_box2 = Cuboid()
lattice_region1 = Cuboid(pmax=lattice.lengths)
bounding_box1.pmin = lattice_region1.pmin
bounding_box1.pmax = lattice_region1.pmax
a, b, c = lattice.lengths
cos_alpha, cos_beta, cos_gamma = np.cos(np.radians(lattice.angles))
lx = a
xy = b * cos_gamma
xz = c * cos_beta
ly = np.sqrt(b**2 - xy**2)
yz = (b * c * cos_alpha - xy * xz) / ly
lz = np.sqrt(c**2 - xz**2 - yz**2)
lattice_region2 = \
Parallelepiped(u=Vector(lattice.ortho_matrix[:, 0].A.flatten()),
v=Vector(lattice.ortho_matrix[:, 1].A.flatten()),
w=Vector(lattice.ortho_matrix[:, 2].A.flatten()))
xlo, ylo, zlo = lattice_region2.o
print('xy={}, xz={}, yz={}'.format(xy, xz, yz))
print('lx={}, ly={}, lz={}'.format(lx, ly, lz))
print('xlo={}, ylo={}, zlo={}'.format(xlo, ylo, zlo))
xlo_bound = xlo + min(0.0, xy, xz, xy + xz)
xhi_bound = xlo + lx + max(0.0, xy, xz, xy + xz)
ylo_bound = ylo + min(0.0, yz)
yhi_bound = ylo + ly + max(0.0, yz)
zlo_bound = zlo
zhi_bound = zlo + lz
bounding_box2.pmin = [xlo_bound, ylo_bound, zlo_bound]
bounding_box2.pmax = [xhi_bound, yhi_bound, zhi_bound]
print(bounding_box1)
print(bounding_box2)
[
bounding_box.rotate(transform_matrix=lattice.orientation_matrix)
for bounding_box in (bounding_box1, bounding_box2)
]
[
bounding_box.translate(
Vector(Point(graphene.centroid) - bounding_box.centroid))
for bounding_box in (bounding_box1, bounding_box2)
]
[
assert_true(bounding_box.pmin <= bounding_box.pmax)
for bounding_box in (bounding_box1, bounding_box2)
]
assert_equal(bounding_box1, bounding_box2)
print(bounding_box1)
print(bounding_box2)