Source code for sknano.generators._swnt_generator

# -*- coding: utf-8 -*-
"""
===============================================================================
SWNT structure generator (:mod:`sknano.generators._swnt_generator`)
===============================================================================

.. currentmodule:: sknano.generators._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

__docformat__ = 'restructuredtext en'

import numpy as np

from sknano.core import pluralize
from sknano.core.math import Point
from sknano.structures import SWNT
from sknano.core.geometric_regions import Cuboid
from ._base import GeneratorBase

__all__ = ['SWNTGenerator']


[docs]class SWNTGenerator(GeneratorBase, SWNT): """Class for generating :class:`SWNT` structures. Parameters ---------- *Ch : {:class:`python:tuple` or :class:`python:int`\ s} Either a 2-tuple of integers (i.e., *Ch = [(n, m)]) or 2 integers (i.e., *Ch = [n, m]) specifying the chiral indices of the nanotube chiral vector :math:`\\mathbf{C}_h = n\\mathbf{a}_1 + m\\mathbf{a}_2 = (n, m)`. nz : :class:`python:int`, optional Number of repeat unit cells in the :math:`z` direction, along the *length* of the nanotube. 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**. Lz : float, optional Length of nanotube in units of **nanometers**. Overrides the `nz` value. .. versionadded:: 0.2.5 tube_length : float, optional Length of nanotube in units of **nanometers**. Overrides the `nz` value. .. deprecated:: 0.2.5 Use `Lz` instead 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 -------- First, load the :class:`~sknano.generators.SWNTGenerator` class. >>> from sknano.generators import SWNTGenerator Now let's generate a :math:`\\mathbf{C}_{\\mathrm{h}} = (10, 5)` :class:`SWNT` unit cell. >>> swnt = SWNTGenerator((10, 5)) >>> swnt.save(fname='10,5_unit_cell.xyz') >>> # note that there are two other alternative, but equivalent >>> # means of passing arguments to SWNTGenerator constructor: >>> # SWNTGenerator(10, 5) and SWNTGenerator(n=10, m=5) Here's a nice ray traced rendering of the generated :math:`(10, 5)` :class:`SWNT` unit cell. .. image:: /images/10,5_unit_cell-01.png """
[docs] def generate(self): """Generate structure data.""" super().generate() if self.L0 is not None and self.fix_Lz: Lz_cutoff = 10 * self.L0 + 1 region_bounds = Cuboid(pmin=Point([-np.inf, -np.inf, 0]), pmax=Point([np.inf, np.inf, Lz_cutoff])) self.atoms.clip_bounds(region_bounds)
@classmethod
[docs] def generate_fname(cls, n=None, m=None, nz=None, fix_Lz=False, **kwargs):
chirality = '{}{}'.format('{}'.format(n).zfill(2), '{}'.format(m).zfill(2)) nz_fmtstr = '{:.2f}' if fix_Lz else '{:.0f}' nz = ''.join((nz_fmtstr.format(nz), pluralize('cell', nz))) fname_wordlist = (chirality, nz) 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, nz=self.nz, fix_Lz=self.fix_Lz) super().save(fname=fname, outpath=outpath, structure_format=structure_format, center_centroid=center_centroid, **kwargs)