def test2():
lattice = Crystal3DLattice.hexagonal(a=5.0, c=10.0)
cell = UnitCell(lattice=lattice,
basis=['C', 'C'],
coords=[[0, 0, 0], [1 / 2, 1 / 2, 1 / 2]])
print(cell)
print(cell.basis)
def test9():
a = np.sqrt(3) * aCC
latt = Crystal3DLattice(a=a, b=a, c=2 * r_CC_vdw,
alpha=90, beta=90, gamma=120)
print(latt)
hex_latt = \
Crystal3DLattice.hexagonal(a, 2 * r_CC_vdw)
print(hex_latt)
assert_equal(latt, hex_latt)
def test9():
a = np.sqrt(3) * aCC
latt = Crystal3DLattice(a=a,
b=a,
c=2 * r_CC_vdw,
alpha=90,
beta=90,
gamma=120)
print(latt)
hex_latt = \
Crystal3DLattice.hexagonal(a, 2 * r_CC_vdw)
print(hex_latt)
assert_equal(latt, hex_latt)
def test17():
dlattice = Crystal3DLattice.hexagonal(np.sqrt(3) * aCC, r_CC_vdw)
rlattice = dlattice.reciprocal_lattice
assert_true(np.allclose(dlattice.volume ** 2,
np.linalg.det(dlattice.metric_tensor)))
print(dlattice.volume ** 2)
print(np.linalg.det(dlattice.metric_tensor))
print(rlattice.volume ** 2)
print(np.linalg.det(rlattice.metric_tensor))
assert_true(np.allclose(rlattice.volume ** 2,
np.linalg.det(rlattice.metric_tensor)))
print(rlattice.metric_tensor)
print(rlattice.metric_tensor.T)
assert_true(np.allclose(dlattice.volume * rlattice.volume, 1.0))
assert_true(np.allclose(rlattice.metric_tensor * dlattice.metric_tensor.T,
np.asmatrix(np.eye(3))))
def test17():
dlattice = Crystal3DLattice.hexagonal(np.sqrt(3) * aCC, r_CC_vdw)
rlattice = dlattice.reciprocal_lattice
assert_true(
np.allclose(dlattice.volume**2, np.linalg.det(dlattice.metric_tensor)))
print(dlattice.volume**2)
print(np.linalg.det(dlattice.metric_tensor))
print(rlattice.volume**2)
print(np.linalg.det(rlattice.metric_tensor))
assert_true(
np.allclose(rlattice.volume**2, np.linalg.det(rlattice.metric_tensor)))
print(rlattice.metric_tensor)
print(rlattice.metric_tensor.T)
assert_true(np.allclose(dlattice.volume * rlattice.volume, 1.0))
assert_true(
np.allclose(rlattice.metric_tensor * dlattice.metric_tensor.T,
np.asmatrix(np.eye(3))))
def test2():
lattice = Crystal3DLattice.hexagonal(a=5.0, c=10.0)
cell = UnitCell(lattice=lattice, basis=['C', 'C'],
coords=[[0, 0, 0], [1/2, 1/2, 1/2]])
print(cell)
print(cell.basis)
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_dt(self.n, self.m, bond=self.bond) + 2 * self.gutter
c = compute_T(self.n, self.m, bond=self.bond, length=True)
lattice = Crystal3DLattice.hexagonal(a, c)
basis = BasisAtoms()
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 * np.cos(theta)
y = rt * np.sin(theta)
z = h
while z > T - eps:
z -= T
if z < 0:
z += T
xs, ys, zs = \
lattice.cartesian_to_fractional([x, y, z])
if self.wrap_coords:
xs, ys, zs = \
lattice.wrap_fractional_coordinate([xs, ys, zs])
if self.debug:
print('i={}: x, y, z = ({:.6f}, {:.6f}, {:.6f})'.format(
i, x, y, z))
print('xs, ys, zs = ({:.6f}, {:.6f}, {:.6f})'.format(
xs, ys, zs))
# atom = BasisAtom(element, lattice=lattice, x=x, y=y, z=z)
# print('i={}: x, y, z = ({:.6f}, {:.6f}, {:.6f})'.format(
# i, x, y, z))
atom = BasisAtom(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 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_dt(self.n, self.m, bond=self.bond) + 2 * self.gutter
c = compute_T(self.n, self.m, bond=self.bond, length=True)
lattice = Crystal3DLattice.hexagonal(a, c)
basis = BasisAtoms()
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 * np.cos(theta)
y = rt * np.sin(theta)
z = h
while z > T - eps:
z -= T
if z < 0:
z += T
xs, ys, zs = \
lattice.cartesian_to_fractional([x, y, z])
if self.wrap_coords:
xs, ys, zs = \
lattice.wrap_fractional_coordinate([xs, ys, zs])
if self.debug:
print('i={}: x, y, z = ({:.6f}, {:.6f}, {:.6f})'.format(
i, x, y, z))
print('xs, ys, zs = ({:.6f}, {:.6f}, {:.6f})'.format(
xs, ys, zs))
# atom = BasisAtom(element, lattice=lattice, x=x, y=y, z=z)
# print('i={}: x, y, z = ({:.6f}, {:.6f}, {:.6f})'.format(
# i, x, y, z))
atom = BasisAtom(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)