Source code for sknano.generators._swnt_bundle_generator
# -*- coding: utf-8 -*-
"""
==============================================================================
SWNT Bundle Generator (:mod:`sknano.generators._swnt_bundle_generator`)
==============================================================================
.. currentmodule:: sknano.generators._swnt_bundle_generator
"""
from __future__ import absolute_import, division, print_function, \
unicode_literals
__docformat__ = 'restructuredtext en'
from sknano.core import pluralize
from sknano.structures import SWNTBundle
from ._swnt_generator import SWNTGenerator
from ._mixins import NanotubeBundleGeneratorMixin
__all__ = ['SWNTBundleGenerator']
[docs]class SWNTBundleGenerator(NanotubeBundleGeneratorMixin, SWNTBundle,
SWNTGenerator):
"""Class for generating nanotube bundles.
.. versionadded:: 0.2.4
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**.
vdw_spacing : float, optional
van der Waals distance between nearest neighbor tubes
.. versionadded:: 0.2.5
bundle_packing : {'hcp', 'ccp'}, optional
Packing arrangement of nanotubes bundles.
If `bundle_packing` is `None`, then it will be determined by the
`bundle_geometry` parameter if `bundle_geometry` is not `None`.
If both `bundle_packing` and `bundle_geometry` are `None`, then
`bundle_packing` defaults to `hcp`.
.. versionadded:: 0.2.5
bundle_geometry : {'triangle', 'hexagon', 'square', 'rectangle'}, optional
Force a specific geometry on the nanotube bundle boundaries.
.. versionadded:: 0.2.5
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.
.. versionadded:: 0.2.5
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.
.. versionadded:: 0.2.6
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
Examples
--------
Using the `SWNTBundleGenerator` class, you can generate structure
data for nanotube *bundles* with either cubic close packed (ccp) or
hexagonal close packed (hcp) arrangement of nanotubes. The bundle
packing arrangement is set using the `bundle_packing` parameter.
You can also enforce a specific
`bundle geometry` which will try and build the nanotube bundle such
that it "fits inside" the boundaries of a specified geometric shape.
This allows you to generate **hcp** bundles that are trianglar,
hexagonal, or rectangular in shape, as some of the examples below
illustrate.
To start, let's generate an hcp bundle of
:math:`C_{\\mathrm{h}} = (10, 5)` SWCNTs and cell count
:math:`n_x=10, n_y=3, n_z=5`.
>>> from sknano.generators import SWNTBundleGenerator
>>> SWCNTbundle = SWNTBundleGenerator(n=10, m=5, nx=10, ny=3, nz=5)
>>> SWCNTbundle.save_data()
The rendered structure looks like:
.. image:: /images/1005_hcp_10cellsx3cellsx5cells-01.png
Now let's generate a nice hexagon bundle, 3 tubes wide, with
:math:`C_{\\mathrm{h}} = (6, 5)`.
>>> SWCNTbundle = SWNTBundleGenerator(n=6, m=5, nz=5,
... bundle_geometry='hexagon')
>>> SWCNTbundle.save_data()
which looks like:
.. image:: /images/0605_hcp_7tube_hexagon-01.png
Remember, all of the :meth:`~SWNTBundleGenerator.save_data`
methods allow you to rotate the structure data before saving:
>>> SWCNTbundle.save_data(fname='0605_hcp_7tube_hexagon_rot-30deg.xyz',
... rot_axis='z', rotation_angle=30)
.. image:: /images/0605_hcp_7tube_hexagon_rot-30deg-01.png
Now, just because we can, let's make a big ass hexagon bundle with
:math:`C_{\\mathrm{h}} = (10, 0)`.
>>> BIGASSHEXABUN = SWNTBundleGenerator(10, 0, nx=25, ny=25, nz=1,
... bundle_geometry='hexagon')
>>> BIGASSHEXABUN.save_data()
Take a look at the 469 :math:`(10, 0)` unit cells in this big ass bundle!
.. image:: /images/1000_hcp_469tube_hexagon-01.png
Lastly, here's a look at a bundle generated with cubic close packed
bundle arrangement:
>>> SWCNTbundle = SWNTBundleGenerator(10, 10, nx=3, ny=3, nz=5,
... bundle_packing='ccp')
>>> SWCNTbundle.save_data()
The rendered `ccp` structure looks like:
.. image:: /images/1010_ccp_3cellsx3cellsx5cells-01.png
"""
def __init__(self, autogen=True, **kwargs):
super(SWNTBundleGenerator, self).__init__(autogen=False, **kwargs)
if autogen:
super(SWNTBundleGenerator, self).generate_unit_cell()
self.generate_structure_data()
[docs] def generate_structure_data(self):
"""Generate structure data."""
super(SWNTBundleGenerator, self).generate_structure_data()
super(SWNTBundleGenerator, self).generate_bundle()
[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))
packing = '{}cp'.format(self.bundle_packing[0])
#Ntubes = ''.join(('{}'.format(self._Ntubes),
# pluralize('tube', self._Ntubes)))
Ntube = '{}tube'.format(self.Ntubes)
fname_wordlist = None
if self.bundle_geometry is None:
nx = ''.join(('{}'.format(self.nx),
pluralize('cell', self.nx)))
ny = ''.join(('{}'.format(self.ny),
pluralize('cell', self.ny)))
if self._assert_integer_nz:
nz = ''.join(('{}'.format(self.nz),
pluralize('cell', self.nz)))
else:
nz = ''.join(('{:.2f}'.format(self.nz),
pluralize('cell', self.nz)))
cells = 'x'.join((nx, ny, nz))
fname_wordlist = (chirality, packing, cells)
else:
fname_wordlist = \
(chirality, packing, Ntube, self.bundle_geometry)
fname = '_'.join(fname_wordlist)
super(SWNTBundleGenerator, 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=center_CM,
savecopy=savecopy, **kwargs)