# -*- coding: utf-8 -*-
"""
===============================================================================
MWNT structure generator (:mod:`sknano.generators.mwnt_generator`)
===============================================================================
.. currentmodule:: sknano.generators.mwnt_generator
"""
from __future__ import absolute_import, division, print_function, \
unicode_literals
__docformat__ = 'restructuredtext en'
# import copy
import numpy as np
from sknano.core import pluralize
from sknano.core.math import Point
from sknano.core.structures import MWNT
from sknano.core.geometric_regions import Cuboid
from .base import NanoStructureGenerator
from .nanotube_bundle_generator import NanotubeBundleGeneratorBase
from .swnt_generator import SWNTGenerator
__all__ = ['MWNTGeneratorBase', 'MWNTGenerator']
[docs]class MWNTGeneratorBase(NanoStructureGenerator):
"""Mixin :class:`~sknano.core.structures.MWNT` structure generator."""
[docs] def generate(self, finalize=True):
"""Generate structure data.
.. todo::
Load the diameter and chirality data from file instead of
generating it every time.
"""
self.structure.clear()
for swnt in self.walls:
self.atoms.extend(SWNTGenerator(finalize=False,
**swnt.todict()).atoms)
if finalize:
self.finalize()
[docs]class MWNTGenerator(NanotubeBundleGeneratorBase, MWNTGeneratorBase, MWNT):
"""Class for generating multi-walled nanotubes (MWNT).
.. versionchanged:: 0.4.0
`MWNTGenerator` now generates both *single* MWNTs and
MWNT bundles.
.. versionadded:: 0.2.8
Parameters
----------
Ch_list : :class:`python:list`, optional
(:attr:`~SWNT.n`, :attr:`~SWNT.m`) for each `SWNT` wall in `MWNT`.
Nwalls : int, optional
Number of `SWNT` walls in `MWNT`.
Lz : float, optional
`MWNT` length in **Angstroms**.
min_wall_diameter : float, optional
Minimum `MWNT` wall diameter, in units of **Angstroms**.
max_wall_diameter : float, optional
Maximum `MWNT` wall diameter, in units of **Angstroms**.
max_walls : int, optional
Maximum number of `MWNT` walls.
chiral_types : {None, 'armchair', 'zigzag', 'achiral', 'chiral'}, optional
If `None`, the :attr:`~SWNT.chiral_type` of each `MWNT` walls
will be random and determined by the set of randomly selected
chiral indices (:attr:`~SWNT.n`, :attr:`~SWNT.m`).
wall_spacing : float, optional
Inter-wall spacing in units of **Angstroms**.
Default value is the van der Waals interaction distance of 3.4
Angstroms.
nx, ny : int, optional
Number of repeat unit cells in the :math:`x, y` dimensions.
vdw_radius : float, optional
van der Waals radius of nanotube atoms
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, in units of **Angstroms**.
bundle_packing : {'hcp', 'ccp'}, optional
Packing arrangement of MWNT 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`.
bundle_geometry : {'triangle', 'hexagon', 'square', 'rectangle'}, optional
autogen : bool, optional
if `True`, automatically call
:meth:`~MWNTGenerator.generate`.
verbose : bool, optional
if `True`, show verbose output
Examples
--------
>>> from sknano.generators import MWNTGenerator
>>> MWNTGenerator(Nwalls=5, min_wall_diameter=10, Lz=50).save()
The above command generated a 5 wall, 50 **Angstrom** long `MWNT`.
The only constraints on the `MWNT` wall chiralities were the diameter
constraints imposed by the `min_wall_diameter` parameter,
which set the minimum wall diameter to 10 Angstroms,
as well as the minimum wall-to-wall separation, which
defaults to the van der Waals distance of 3.4 Angstroms.
This `MWNT` chirality may be written as:
:math:`\\mathbf{C}_{\\mathrm{h}} = (8,7)@(17,8)@(9,24)@(27,18)@(22,32)`
Here's a colorful rendering of the generated `MWNT` structure:
.. image:: /images/5wall_mwnt_(8,7)@(17,8)@(9,24)@(27,18)@(22,32)-04.png
In the next example, we generate a `MWNT` bundle.
>>> mwntbundle = MWNTGenerator(Nwalls=5, min_wall_diameter=5, Lz=50,
... bundle_geometry='hexagon')
>>> mwntbundle.save()
.. image:: /images/5wall_mwnt_(1,6)@(11,7)@(18,9)@(31,2)@(41,0)_hcp_7tube_hexagon-perspective_view-01.png
"""
[docs] def finalize(self):
"""Finalize structure data by clipping region bounds if \
:attr:`~MWNT.fix_Lz` is `True`."""
# print('finalizing structure data')
# print('Natoms: {}'.format(self.atoms.Natoms))
if self.fix_Lz:
Lz_cutoff = self.Lz + self.bond
# print('clipping_bounds')
# print(self.atoms.coordinates_bounding_box)
# print('Lz_cutoff: {}'.format(Lz_cutoff))
region_bounds = Cuboid(pmin=Point([-np.inf, -np.inf, 0]),
pmax=Point([np.inf, np.inf, Lz_cutoff]))
self.atoms.clip_bounds(region_bounds)
# print('Natoms: {}'.format(self.atoms.Natoms))
super().finalize()
@classmethod
[docs] def generate_fname(cls, Ch_list=None, Nwalls=None, Ntubes=None, Lz=None,
nx=None, ny=None, nz=None, bundle_geometry=None,
bundle_packing=None, **kwargs):
"""Generate a filename string."""
# Nwalls = '{}wall_mwnt'.format(Nwalls)
fname = '@'.join([str(Ch).replace(' ', '') for Ch in Ch_list])
if nx == ny == 1 and bundle_geometry is None:
return fname
# fname = '_'.join((Nwalls, chiralities))
# return fname
packing = '{}cp'.format(bundle_packing[0])
Ntubes = '{}tube'.format(Ntubes)
nx = ''.join(('{}'.format(nx), pluralize('cell', nx)))
ny = ''.join(('{}'.format(ny), pluralize('cell', ny)))
cells = 'x'.join((nx, ny))
if nz is not None:
nz = ''.join(('{}'.format(nz), pluralize('cell', nz)))
cells = 'x'.join((cells, nz))
else:
cells = 'x'.join((cells, '{:.1f}Å'.format(Lz)))
fname = '_'.join((fname, cells, packing))
if bundle_geometry is not None:
fname = '_'.join((fname, Ntubes, bundle_geometry))
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(Ch_list=self.Ch_list,
Nwalls=self.Nwalls, Ntubes=self.Ntubes,
Lz=self.Lz,
nx=self.nx, ny=self.ny, nz=self.nz,
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)
