def __init__(self, bond=aCC, a=3 * aCC, b=np.sqrt(3) * aCC, c=2 * r_CC_vdw,
basis=4 * ['C'],
coords=[[0, 0, 0], [aCC, 0, 0],
[3 / 2 * aCC, np.sqrt(3) / 2 * aCC, 0],
[5 / 2 * aCC, np.sqrt(3) / 2 * aCC, 0]],
cartesian=True):
lattice = Crystal3DLattice.orthorhombic(a, b, c)
super().__init__(lattice, basis, coords, cartesian)
def generate_unit_cell(self):
"""Generate the nanotube unit cell."""
eps = 0.01
e1 = self.element1
e2 = self.element2
N = self.N
T = self.T
rt = self.rt
psi, tau, dpsi, dtau = self.unit_cell_symmetry_params
a = compute_Ch(self.n, self.m, bond=self.bond)
b = self.layer_spacing
c = compute_T(self.n, self.m, bond=self.bond, length=True)
lattice = Crystal3DLattice.orthorhombic(a, b, c)
basis = Atoms()
if self.verbose:
print('dpsi: {}'.format(dpsi))
print('dtau: {}\n'.format(dtau))
for i in range(N):
for j, element in enumerate((e1, e2), start=1):
theta = i * psi
h = i * tau
if j == 2:
theta += dpsi
h -= dtau
x = rt * theta
z = h
while z > T - eps:
z -= T
if z < 0:
z += T
xs, ys, zs = \
lattice.cartesian_to_fractional([x, 0, z])
if self.wrap_coords:
xs, ys, zs = \
lattice.wrap_fractional_coordinate([xs, ys, zs])
if self.debug:
print('i={}: x, z = ({:.6f}, {:.6f})'.format(i, x, z))
atom = Atom(element, lattice=lattice, xs=xs, ys=ys, zs=zs)
atom.rezero()
if self.verbose:
print('Basis Atom:\n{}'.format(atom))
basis.append(atom)
self.unit_cell = UnitCell(lattice=lattice, basis=basis)
def __init__(self,
bond=aCC,
a=3 * aCC,
b=np.sqrt(3) * aCC,
c=2 * r_CC_vdw,
basis=4 * ['C'],
coords=[[0, 0, 0], [aCC, 0, 0],
[3 / 2 * aCC, np.sqrt(3) / 2 * aCC, 0],
[5 / 2 * aCC, np.sqrt(3) / 2 * aCC, 0]],
cartesian=True):
lattice = Crystal3DLattice.orthorhombic(a, b, c)
super().__init__(lattice, basis, coords, cartesian)