def __init__(
self,
n=6,
parameters=DEFAULT,
):
atoms = Atoms([])
C_C = 1.42
C_H = 1.09
main_element = 'C'
saturate_element = 'H'
vacuum = 10
m = 1
b = np.sqrt(3) * C_C / 4
zz_unit = Atoms(main_element + '2',
pbc=(0, 1, 1),
cell=[2 * vacuum, 3 * C_C / 2.0, b * 4])
zz_unit.positions = [[0, 0, 0],
[0, C_C / 2.0, b * 2]]
edge_index0 = np.arange(m) * 2 + 1
edge_index1 = (n - 1) * m * 2 + np.arange(m) * 2
for i in range(n):
layer = zz_unit.repeat((1, 1, m))
layer.positions[:, 1] -= 3 * C_C / 2 * i
if i % 2 == 1:
layer.positions[:, 2] += 2 * b
layer[-1].position[2] -= b * 4 * m
atoms += layer
H_atoms0 = Atoms(saturate_element + str(m))
H_atoms0.positions = atoms[edge_index0].positions
H_atoms0.positions[:, 1] += C_H
H_atoms1 = Atoms(saturate_element + str(m))
H_atoms1.positions = atoms[edge_index1].positions
H_atoms1.positions[:, 1] -= C_H
atoms += H_atoms0 + H_atoms1
atoms.cell = [2 * vacuum, n * 3 * C_C / 2 + 2 * vacuum, m * 4 * b]
atoms.set_pbc([False, False, True])
center = atoms.positions.mean(axis=0)
center[0] = 0
center[2] = 0
atoms.translate(-center)
Crystal1D.__init__(
self,
atoms,
parameters=parameters,
)
def __init__(
self,
n=7,
parameters=DEFAULT,
):
atoms = Atoms([])
C_C = 1.42
C_H = 1.09
main_element = 'C'
saturate_element = 'H'
vacuum = 10
b = np.sqrt(3) * C_C / 4
arm_unit = Atoms(main_element + '2',
pbc=(1, 0, 1),
cell=[
[2 * vacuum, 0, 0 ],
[0, 2 * b, 1.5*C_C],
[0, 0, 3 * C_C ],])
arm_unit.positions = [[0, 0, -1.5*C_C],
[0, 0, -0.5*C_C]]
core_atoms = arm_unit.repeat((1, n, 1))
h_positions=np.array([
[0, -np.sqrt(3) / 2 * C_H, - C_H * 0.5],
[0, -np.sqrt(3) / 2 * C_H, C_H * 0.5],
])
atoms = Atoms(
saturate_element + '2',
cell= core_atoms.get_cell(),
)
atoms.positions = core_atoms[:2].positions + h_positions
atoms += core_atoms
last_hydrogens = Atoms(
saturate_element + '2',
)
h_positions[:, 1] *= -1
last_hydrogens.positions = core_atoms[-2:].positions + h_positions
atoms += last_hydrogens
atoms.cell = [b * 2 * n + 2 * vacuum, 2 * vacuum, 3 * C_C]
atoms.set_pbc([False, False, True])
atoms.wrap()
atoms.translate((0, -b*float(n-1), 0))
Crystal1D.__init__(
self,
atoms,
parameters=parameters,
)
def __init__(self):
atoms = Atoms(
[
Atom('H', ( 0.0, 2.4 ,1.2, )),
Atom('C', ( 0.0, 1.4 ,1.2, )),
Atom('C', ( 0.0, 0.7 ,0.0, )),
Atom('C', ( 0.0,-0.7 ,0.0, )),
Atom('C', ( 0.0,-1.4 ,1.2, )),
Atom('H', ( 0.0,-2.4 ,1.2, )),
],
cell=(10, 16.00, 2.41),
pbc=[False, False, True],
)
Crystal1D.__init__(self, atoms)
