/usr/lib/python2.7/dist-packages/ase/structure.py is in python-ase 3.9.1.4567-3.
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"""Atomic structure.
This mudule contains helper functions for setting up nanotubes and
graphene nanoribbons."""
import warnings
from math import sqrt
import numpy as np
from ase.atoms import Atoms, string2symbols
from ase.data import covalent_radii
from ase.utils import gcd
def nanotube(n, m, length=1, bond=1.42, symbol='C', verbose=False):
if n < m:
m, n = n, m
sign = -1
else:
sign = 1
nk = 6000
sq3 = sqrt(3.0)
a = sq3 * bond
l2 = n * n + m * m + n * m
l = sqrt(l2)
nd = gcd(n, m)
if (n - m) % (3 * nd) == 0:
ndr = 3 * nd
else:
ndr = nd
nr = (2 * m + n) / ndr
ns = -(2 * n + m) / ndr
nn = 2 * l2 / ndr
ichk = 0
if nr == 0:
n60 = 1
else:
n60 = nr * 4
absn = abs(n60)
nnp = []
nnq = []
for i in range(-absn, absn + 1):
for j in range(-absn, absn + 1):
j2 = nr * j - ns * i
if j2 == 1:
j1 = m * i - n * j
if j1 > 0 and j1 < nn:
ichk += 1
nnp.append(i)
nnq.append(j)
if ichk == 0:
raise RuntimeError('not found p, q strange!!')
if ichk >= 2:
raise RuntimeError('more than 1 pair p, q strange!!')
nnnp = nnp[0]
nnnq = nnq[0]
if verbose:
print('the symmetry vector is', nnnp, nnnq)
lp = nnnp * nnnp + nnnq * nnnq + nnnp * nnnq
r = a * sqrt(lp)
c = a * l
t = sq3 * c / ndr
if 2 * nn > nk:
raise RuntimeError('parameter nk is too small!')
rs = c / (2.0 * np.pi)
if verbose:
print('radius=', rs, t)
q1 = np.arctan((sq3 * m) / (2 * n + m))
q2 = np.arctan((sq3 * nnnq) / (2 * nnnp + nnnq))
q3 = q1 - q2
q4 = 2.0 * np.pi / nn
q5 = bond * np.cos((np.pi / 6.0) - q1) / c * 2.0 * np.pi
h1 = abs(t) / abs(np.sin(q3))
h2 = bond * np.sin((np.pi / 6.0) - q1)
ii = 0
x, y, z = [], [], []
for i in range(nn):
x1, y1, z1 = 0, 0, 0
k = np.floor(i * abs(r) / h1)
x1 = rs * np.cos(i * q4)
y1 = rs * np.sin(i * q4)
z1 = (i * abs(r) - k * h1) * np.sin(q3)
kk2 = abs(np.floor((z1 + 0.0001) / t))
if z1 >= t - 0.0001:
z1 -= t * kk2
elif z1 < 0:
z1 += t * kk2
ii += 1
x.append(x1)
y.append(y1)
z.append(z1)
z3 = (i * abs(r) - k * h1) * np.sin(q3) - h2
ii += 1
if z3 >= 0 and z3 < t:
x2 = rs * np.cos(i * q4 + q5)
y2 = rs * np.sin(i * q4 + q5)
z2 = (i * abs(r) - k * h1) * np.sin(q3) - h2
x.append(x2)
y.append(y2)
z.append(z2)
else:
x2 = rs * np.cos(i * q4 + q5)
y2 = rs * np.sin(i * q4 + q5)
z2 = (i * abs(r) - (k + 1) * h1) * np.sin(q3) - h2
kk = abs(np.floor(z2 / t))
if z2 >= t - 0.0001:
z2 -= t * kk
elif z2 < 0:
z2 += t * kk
x.append(x2)
y.append(y2)
z.append(z2)
ntotal = 2 * nn
X = []
for i in range(ntotal):
X.append([x[i], y[i], sign * z[i]])
if length > 1:
xx = X[:]
for mnp in range(2, length + 1):
for i in range(len(xx)):
X.append(xx[i][:2] + [xx[i][2] + (mnp - 1) * t])
TransVec = t
NumAtom = ntotal * length
Diameter = rs * 2
ChiralAngle = np.arctan((sq3 * n) / (2 * m + n)) / (np.pi * 180)
cell = [Diameter * 2, Diameter * 2, length * t]
atoms = Atoms(symbol + str(NumAtom), positions=X, cell=cell,
pbc=[False, False, True])
atoms.center()
if verbose:
print('translation vector =', TransVec)
print('diameter = ', Diameter)
print('chiral angle = ', ChiralAngle)
return atoms
def graphene_nanoribbon(n, m, type='zigzag', saturated=False, C_H=1.09,
C_C=1.42, vacuum=2.5, magnetic=None, initial_mag=1.12,
sheet=False, main_element='C', saturate_element='H',
vacc=None):
"""Create a graphene nanoribbon.
Creates a graphene nanoribbon in the x-z plane, with the nanoribbon
running along the z axis.
Parameters:
n: int
The width of the nanoribbon.
m: int
The length of the nanoribbon.
type: str
The orientation of the ribbon. Must be either 'zigzag'
or 'armchair'.
saturated: bool
If true, hydrogen atoms are placed along the edge.
C_H: float
Carbon-hydrogen bond length. Default: 1.09 Angstrom.
C_C: float
Carbon-carbon bond length. Default: 1.42 Angstrom.
vacuum: float
Amount of vacuum added to both sides. Default 2.5 Angstrom.
magnetic: bool
Make the edges magnetic.
initial_mag: float
Magnitude of magnetic moment if magnetic=True.
sheet: bool
If true, make an infinite sheet instead of a ribbon.
"""
if vacc is not None:
warnings.warn('Use vacuum=%f' % (0.5 * vacc))
vacuum = 0.5 * vacc
assert vacuum > 0
b = sqrt(3) * C_C / 4
arm_unit = Atoms(main_element + '4',
pbc=(1, 0, 1),
cell=[4 * b, 2 * vacuum, 3 * C_C])
arm_unit.positions = [[0, 0, 0],
[b * 2, 0, C_C / 2.],
[b * 2, 0, 3 * C_C / 2.],
[0, 0, 2 * C_C]]
zz_unit = Atoms(main_element + '2',
pbc=(1, 0, 1),
cell=[3 * C_C / 2.0, 2 * vacuum, b * 4])
zz_unit.positions = [[0, 0, 0],
[C_C / 2.0, 0, b * 2]]
atoms = Atoms()
if sheet:
vacuum2 = 0.0
else:
vacuum2 = vacuum
if type == 'zigzag':
edge_index0 = np.arange(m) * 2 + 1
edge_index1 = (n - 1) * m * 2 + np.arange(m) * 2
if magnetic:
mms = np.zeros(m * n * 2)
for i in edge_index0:
mms[i] = initial_mag
for i in edge_index1:
mms[i] = -initial_mag
for i in range(n):
layer = zz_unit.repeat((1, 1, m))
layer.positions[:, 0] -= 3 * C_C / 2 * i
if i % 2 == 1:
layer.positions[:, 2] += 2 * b
layer[-1].position[2] -= b * 4 * m
atoms += layer
if magnetic:
atoms.set_initial_magnetic_moments(mms)
if saturated:
H_atoms0 = Atoms(saturate_element + str(m))
H_atoms0.positions = atoms[edge_index0].positions
H_atoms0.positions[:, 0] += C_H
H_atoms1 = Atoms(saturate_element + str(m))
H_atoms1.positions = atoms[edge_index1].positions
H_atoms1.positions[:, 0] -= C_H
atoms += H_atoms0 + H_atoms1
atoms.cell = [n * 3 * C_C / 2 + 2 * vacuum2, 2 * vacuum, m * 4 * b]
elif type == 'armchair':
for i in range(n):
layer = arm_unit.repeat((1, 1, m))
layer.positions[:, 0] -= 4 * b * i
atoms += layer
if saturated:
arm_right_saturation = Atoms(saturate_element + '2', pbc=(1, 0, 1),
cell=[4 * b, 2 * vacuum, 3 * C_C])
arm_right_saturation.positions = [
[- sqrt(3) / 2 * C_H, 0, C_H * 0.5],
[- sqrt(3) / 2 * C_H, 0, 2 * C_C - C_H * 0.5]]
arm_left_saturation = Atoms(saturate_element + '2', pbc=(1, 0, 1),
cell=[4 * b, 2 * vacuum, 3 * C_C])
arm_left_saturation.positions = [
[b * 2 + sqrt(3) / 2 * C_H, 0, C_C / 2 - C_H * 0.5],
[b * 2 + sqrt(3) / 2 * C_H, 0, 3 * C_C / 2.0 + C_H * 0.5]]
arm_right_saturation.positions[:, 0] -= 4 * b * (n - 1)
atoms += arm_right_saturation.repeat((1, 1, m))
atoms += arm_left_saturation.repeat((1, 1, m))
atoms.cell = [b * 4 * n + 2 * vacuum2, 2 * vacuum, 3 * C_C * m]
atoms.center()
atoms.set_pbc([sheet, False, True])
return atoms
def molecule(name, data=None, **kwargs):
"""Create formula base on data. If data is None assume G2 set.
kwargs currently not used. """
if data is None:
from ase.data.g2 import data
if name not in data.keys():
raise NotImplementedError('%s not in data.' % (name))
args = {}
dct = data[name]
for k in ['symbols', 'positions', 'numbers', 'tags', 'masses',
'magmoms', 'charges', 'info']:
if k in dct:
args[k] = dct[k]
args.update(kwargs) # kwargs overwrites data
return Atoms(**args)
def estimate_lattice_constant(name, crystalstructure, covera):
from ase.lattice import bulk
atoms = bulk(name, crystalstructure, 1.0, covera)
v0 = atoms.get_volume()
v = 0.0
for Z in atoms.get_atomic_numbers():
r = covalent_radii[Z]
v += 4 * np.pi / 3 * r**3 * 1.5
return (v / v0)**(1.0 / 3)
def _orthorhombic_bulk(name, x, a, covera=None):
if x == 'fcc':
b = a / sqrt(2)
atoms = Atoms(2 * name, cell=(b, b, a), pbc=True,
scaled_positions=[(0, 0, 0), (0.5, 0.5, 0.5)])
elif x == 'bcc':
atoms = Atoms(2 * name, cell=(a, a, a), pbc=True,
scaled_positions=[(0, 0, 0), (0.5, 0.5, 0.5)])
elif x == 'hcp':
atoms = Atoms(4 * name,
cell=(a, a * sqrt(3), covera * a),
scaled_positions=[(0, 0, 0),
(0.5, 0.5, 0),
(0.5, 1.0 / 6.0, 0.5),
(0, 2.0 / 3.0, 0.5)],
pbc=True)
elif x == 'diamond':
atoms = _orthorhombic_bulk(2 * name, 'zincblende', a)
elif x == 'zincblende':
s1, s2 = string2symbols(name)
b = a / sqrt(2)
atoms = Atoms(2 * name, cell=(b, b, a), pbc=True,
scaled_positions=[(0, 0, 0), (0.5, 0, 0.25),
(0.5, 0.5, 0.5), (0, 0.5, 0.75)])
elif x == 'rocksalt':
s1, s2 = string2symbols(name)
b = a / sqrt(2)
atoms = Atoms(2 * name, cell=(b, b, a), pbc=True,
scaled_positions=[(0, 0, 0), (0.5, 0.5, 0),
(0.5, 0.5, 0.5), (0, 0, 0.5)])
else:
raise RuntimeError
return atoms
def _cubic_bulk(name, x, a):
if x == 'fcc':
atoms = Atoms(4 * name, cell=(a, a, a), pbc=True,
scaled_positions=[(0, 0, 0), (0, 0.5, 0.5),
(0.5, 0, 0.5), (0.5, 0.5, 0)])
elif x == 'diamond':
atoms = _cubic_bulk(2 * name, 'zincblende', a)
elif x == 'zincblende':
atoms = Atoms(4 * name, cell=(a, a, a), pbc=True,
scaled_positions=[(0, 0, 0), (0.25, 0.25, 0.25),
(0, 0.5, 0.5), (0.25, 0.75, 0.75),
(0.5, 0, 0.5), (0.75, 0.25, 0.75),
(0.5, 0.5, 0), (0.75, 0.75, 0.25)])
elif x == 'rocksalt':
atoms = Atoms(4 * name, cell=(a, a, a), pbc=True,
scaled_positions=[(0, 0, 0), (0.5, 0, 0),
(0, 0.5, 0.5), (0.5, 0.5, 0.5),
(0.5, 0, 0.5), (0, 0, 0.5),
(0.5, 0.5, 0), (0, 0.5, 0)])
else:
raise RuntimeError
return atoms
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