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 ._nanotube_bundle_generator import NanotubeBundleGeneratorBase
__all__ = ['SWNTBundleGenerator']
[docs]class SWNTBundleGenerator(NanotubeBundleGeneratorBase, SWNTGenerator,
SWNTBundle):
"""Class for generating nanotube bundles.
.. versionadded:: 0.2.4
Parameters
----------
*Ch : {:class:`python:tuple` or :class:`python:int`\ s}
Either a 2-tuple of ints or 2 integers giving the chiral indices
of 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.
basis : {:class:`python:list`}, optional
List of :class:`python:str`\ s of element symbols or atomic number
of the two atom basis (default: ['C', 'C'])
.. versionadded:: 0.3.10
element1, element2 : {str, int}, optional
Element symbol or atomic number of basis
:class:`~sknano.core.Atom` 1 and 2
.. deprecated:: 0.3.10
Use `basis` instead
bond : float, optional
:math:`\\mathrm{a}_{\\mathrm{CC}} =` distance between
nearest neighbor atoms. Must be in units of **Angstroms**.
vdw_radius : float, optional
van der Waals radius of nanotube atoms
.. 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
Lz : float, optional
length of bundle in :math:`z` dimension in **nanometers**.
Overrides `nz` value.
.. 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 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()
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()
which looks like:
.. image:: /images/0605_hcp_7tube_hexagon-01.png
Remember, all of the :meth:`~SWNTBundleGenerator.save`
methods allow you to rotate the structure data before saving:
>>> SWCNTbundle.save(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)`.
>>> big_hexagonal_bundle = SWNTBundleGenerator(10, 0, nx=25, ny=25, nz=1,
... bundle_geometry='hexagon')
>>> big_hexagonal_bundle.save()
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()
The rendered `ccp` structure looks like:
.. image:: /images/1010_ccp_3cellsx3cellsx5cells-01.png
"""
@classmethod
[docs] def generate_fname(cls, n=None, m=None, nx=None, ny=None, nz=None,
fix_Lz=False, Ntubes=None, bundle_geometry=None,
bundle_packing=None, **kwargs):
chirality = '{}{}'.format('{}'.format(n).zfill(2),
'{}'.format(m).zfill(2))
packing = '{}cp'.format(bundle_packing[0])
Ntube = '{}tube'.format(Ntubes)
fname_wordlist = None
if bundle_geometry is None:
nx = ''.join(('{}'.format(nx),
pluralize('cell', nx)))
ny = ''.join(('{}'.format(ny),
pluralize('cell', ny)))
nz_fmtstr = '{:.2f}' if fix_Lz else '{:.0f}'
nz = ''.join((nz_fmtstr.format(nz), pluralize('cell', nz)))
cells = 'x'.join((nx, ny, nz))
fname_wordlist = (chirality, packing, cells)
else:
fname_wordlist = \
(chirality, packing, Ntube, bundle_geometry)
fname = '_'.join(fname_wordlist)
return fname
[docs] def save(self, fname=None, outpath=None, structure_format=None,
center_centroid=True, **kwargs):
"""Save structure data.
See :meth:`~sknano.generators.GeneratorBase.save` method
for documentation.
"""
if fname is None:
fname = self.generate_fname(n=self.n, m=self.m,
nx=self.nx, ny=self.ny, nz=self.nz,
fix_Lz=self.fix_Lz,
Ntubes=self.Ntubes,
bundle_geometry=self.bundle_geometry,
bundle_packing=self.bundle_packing)
super().save(fname=fname, outpath=outpath,
structure_format=structure_format,
center_centroid=center_centroid, **kwargs)