Source code for sknano.generators._unrolled_swnt_generator
# -*- coding: utf-8 -*-
"""
===============================================================================
Unrolled SWNT generator (:mod:`sknano.generators._unrolled_swnt_generator`)
===============================================================================
.. currentmodule:: sknano.generators._unrolled_swnt_generator
.. todo::
Add methods to perform fractional translation and cartesian translation
before structure generation.
.. todo::
Handle different units in output coordinates.
"""
from __future__ import absolute_import, division, print_function, \
unicode_literals
from six.moves import range
__docformat__ = 'restructuredtext en'
import numpy as np
from sknano.core import pluralize
from sknano.core.math import Vector
from sknano.structures import UnrolledSWNT
#from sknano.utils.geometric_shapes import Cuboid
from ._base import Atom, Atoms, GeneratorBase
__all__ = ['UnrolledSWNTGenerator']
[docs]class UnrolledSWNTGenerator(UnrolledSWNT, GeneratorBase):
"""Class for generating unrolled nanotube structures.
.. versionadded:: 0.2.23
Parameters
----------
n, m : int
Chiral indices defining the nanotube chiral vector
:math:`\\mathbf{C}_{h} = n\\mathbf{a}_{1} + m\\mathbf{a}_{2} = (n, m)`.
nx, ny, nz : int, optional
Number of repeat unit cells in the :math:`x, y, z` dimensions
element1, element2 : {str, int}, optional
Element symbol or atomic number of basis
:class:`~sknano.core.Atom` 1 and 2
bond : float, optional
:math:`\\mathrm{a}_{\\mathrm{CC}} =` distance between
nearest neighbor atoms. Must be in units of **Angstroms**.
Lx, Ly, Lz : float, optional
Length of bundle in :math:`x, y, z` dimensions in **nanometers**.
Overrides the :math:`n_x, n_y, n_z` cell values.
fix_Lz : bool, optional
Generate the nanotube with length as close to the specified
:math:`L_z` as possible. If `True`, then
non integer :math:`n_z` cells are permitted.
autogen : bool, optional
if `True`, automatically call
:meth:`~NanotubeGenerator.generate_unit_cell`,
followed by :meth:`~NanotubeGenerator.generate_structure_data`.
verbose : bool, optional
if `True`, show verbose output
Notes
-----
The `UnrolledSWNTGenerator` class generates graphene using the
nanotube unit cell defined by the chiral vector
:math:`\\mathbf{C}_{h} = n\\mathbf{a}_{1} + m\\mathbf{a}_{2} = (n, m)`.
If you want to generate graphene with an armchair or zigzag edge using
`length` and `width` parameters, see the
:class:`~sknano.generators.GrapheneGenerator` class.
.. seealso:: :class:`~sknano.generators.GrapheneGenerator`
Examples
--------
First, load the :class:`~sknano.generators.UnrolledSWNTGenerator`
class.
>>> from sknano.generators import UnrolledSWNTGenerator
Now let's generate an unrolled :math:`\\mathbf{C}_{\\mathrm{h}} = (10, 5)`
SWCNT unit cell.
>>> flatswcnt = UnrolledSWNTGenerator(n=10, m=5)
>>> flatswcnt.save_data()
The rendered structure looks like:
"""
def __init__(self, autogen=True, **kwargs):
super(UnrolledSWNTGenerator, self).__init__(**kwargs)
if autogen:
self.generate_unit_cell()
self.generate_structure_data()
[docs] 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
if self.verbose:
print('dpsi: {}'.format(dpsi))
print('dtau: {}\n'.format(dtau))
self.unit_cell = Atoms()
for i in range(N):
x1 = rt * i * psi
z1 = i * tau
while z1 > T - eps:
z1 -= T
if z1 < 0:
z1 += T
if self.debug:
print('i={}: x1, z1 = ({:.6f}, {:.6f})'.format(
i, x1, z1))
atom1 = Atom(element=e1, x=x1, z=z1)
atom1.rezero()
if self.verbose:
print('Basis Atom 1:\n{}'.format(atom1))
self.unit_cell.append(atom1)
x2 = rt * (i * psi + dpsi)
z2 = i * tau - dtau
while z2 > T - eps:
z2 -= T
if z2 < 0:
z2 += T
if self.debug:
print('i={}: x2, z2 = ({:.6f}, {:.6f})'.format(
i, x2, z2))
atom2 = Atom(element=e2, x=x2, z=z2)
atom2.rezero()
if self.verbose:
print('Basis Atom 2:\n{}'.format(atom2))
self.unit_cell.append(atom2)
[docs] def generate_structure_data(self):
"""Generate structure data."""
#self.atoms = Atoms()
self.structure_data.clear()
for nx in range(self.nx):
for nz in range(int(np.ceil(self.nz))):
dr = Vector([nx * self.Ch, 0.0, nz * self.T])
for uc_atom in self.unit_cell:
nt_atom = Atom(element=uc_atom.symbol)
nt_atom.r = uc_atom.r + dr
self.atoms.append(nt_atom)
[docs] def save_data(self, fname=None, outpath=None, structure_format=None,
rotation_angle=None, rot_axis=None, anchor_point=None,
deg2rad=True, center_CM=True, savecopy=True, **kwargs):
"""Save structure data.
See :meth:`~sknano.generators.GeneratorBase.save_data` method
for documentation.
"""
if fname is None:
chirality = '{}{}'.format('{}'.format(self.n).zfill(2),
'{}'.format(self.m).zfill(2))
nx = '{}' if self._assert_integer_nx else '{:.2f}'
nx = ''.join((nx.format(self.nx), pluralize('cell', self.nx)))
nz = '{}' if self._assert_integer_nz else '{:.2f}'
nz = ''.join((nz.format(self.nz), pluralize('cell', self.nz)))
cells = 'x'.join((nx, nz))
fname_wordlist = (chirality, cells)
fname = 'unrolled_' + '_'.join(fname_wordlist)
if center_CM:
self.atoms.center_CM()
super(UnrolledSWNTGenerator, self).save_data(
fname=fname, outpath=outpath, structure_format=structure_format,
rotation_angle=rotation_angle, rot_axis=rot_axis,
anchor_point=anchor_point, deg2rad=deg2rad, center_CM=False,
savecopy=savecopy, **kwargs)