Source code for sknano.scripts.nanogen
# -*- coding: utf-8 -*-
#!/usr/bin/env python
"""
====================================================
Command line script (:mod:`sknano.scripts.nanogen`)
====================================================
CLI to :mod:`sknano.generators` tools.
.. currentmodule:: sknano.scripts.nanogen
This module allows for easy structure generation from the command line.
.. seealso::
:class:`~sknano.generators.GrapheneGenerator`
:class:`~sknano.generators.BilayerGrapheneGenerator`
:class:`~sknano.generators.UnrolledSWNTGenerator`
:class:`~sknano.generators.SWNTGenerator`
:class:`~sknano.generators.SWNTBundleGenerator`
:class:`~sknano.generators.MWNTGenerator`
:class:`~sknano.generators.MWNTBundleGenerator`
.. code-block:: python
> nanogen --help
usage: nanogen [-h] [--element1 ELEMENT1] [--element2 ELEMENT2]
[--bond BOND] [--fname FNAME]
[--structure-format {data,xyz}] [--verbose]
{graphene,BLG,swnt,unrolled_swnt,mwnt,swnt_bundle,
mwnt_bundle}
...
optional arguments:
-h, --help show this help message and exit
--element1 ELEMENT1 element symbol or atomic number of basis atom 1
(default: C)
--element2 ELEMENT2 element symbol or atomic number of basis atom 2
(default: C)
--bond BOND Bond length between nearest neighbor atoms. Must
in units of Angstroms. (default: 1.42)
--fname FNAME structure file name
--structure-format {data,xyz}
structure file format (default: xyz)
--verbose verbose output
--debug debug output
sub-commands:
{graphene,BLG,swnt,unrolled_swnt,mwnt,swnt_bundle,mwnt_bundle}
.. autofunction:: nanogen
Examples
--------
The following command generates a graphene sheet 10 nm long by 1 nm wide
with an armchair edge pattern along its length and saves the data in the
LAMMPS data format.::
> nanogen --structure-format data graphene 10 1 --edge AC
This command will generate a :math:`(20, 0)` SWNT, 5 unit cells
long and saves the data in `xyz` format.::
> nanogen swnt -n 20 -m 0 --nz 5
Notes
-----
The :mod:`nanogen` script calls the :func:`~sknano.scripts.nanogen.nanogen`
function and neither the script nor the function allow for generating
multiple structures per call. It's easy to do this using the scripting
capabilities of the shell or from within an interactive Python session.
For example, if you have a list of chiralities that you want structure data
for, you can do something like this from within an interactive session::
>>> from sknano.structures import generate_Ch_list
>>> from sknano.generators import SWNTGenerator
>>> # Generate your list of (n, m) chiralities
>>> Ch_list = generate_Ch_list(ni=5, nf=25, mi=0, mf=25, handedness='right')
>>> for n, m in Ch_list:
... SWNTGenerator(n=n, m=m).save_data(structure_format='data')
"""
from __future__ import absolute_import, division, print_function
__docformat__ = 'restructuredtext en'
import argparse
import importlib
import sys
from sknano.core.refdata import CCbond, dVDW
from sknano.version import short_version as version
__all__ = ['nanogen']
def argparser():
parser = argparse.ArgumentParser()
parser.add_argument(
'--element1', default='C', help='element symbol or atomic number of '
'basis atom 1 (default: %(default)s)')
parser.add_argument(
'--element2', default='C', help='element symbol or atomic number of '
'basis atom 2 (default: %(default)s)')
parser.add_argument(
'--bond', type=float, default=CCbond, help='Bond length between '
'nearest neighbor atoms. Must in units of Angstroms. '
'(default: %(default)s)')
parser.add_argument('--fname', help='structure file name')
parser.add_argument(
'--structure-format', default='xyz', choices=('data', 'xyz'),
help='structure file format (default: %(default)s)')
parser.add_argument(
'--verbose', action='store_true', help='verbose output')
parser.add_argument(
'--debug', action='store_true', help='debug output')
parser.add_argument('--version', action='version',
version='%(prog)s {}'.format(version),
help="show %(prog)s's version number and exit")
subparsers = parser.add_subparsers(title='sub-commands')
graphene_parent_parser = argparse.ArgumentParser(add_help=False)
graphene_parent_parser.add_argument(
'length', type=float, help='length of graphene sheet in '
'**nanometers**')
graphene_parent_parser.add_argument(
'width', type=float, help='width of graphene sheet in **nanometers** ')
graphene_parent_parser.add_argument(
'--edge', choices=('AC', 'ZZ'), help='chirality along the '
'**length** of sheet. If `None`, then one will chosen at random. '
'(default: %(default)s)')
graphene_parent_parser.add_argument(
'--layer-spacing', type=float, default=3.35, help='distance between '
'layers in **Angstroms**. (default: %(default)s)')
graphene_parent_parser.add_argument(
'--stacking-order', choices=('AA', 'AB'), default='AB',
help='Stacking order of graphene layers (default: %(default)s)')
graphene_parser = \
subparsers.add_parser('graphene', parents=[graphene_parent_parser])
graphene_parser.add_argument('--nlayers', type=int, default=1,
help='Number of graphene layers. '
'(default: %(default)s)')
graphene_parser.set_defaults(generator_class='GrapheneGenerator')
bilayer_graphene_parser = \
subparsers.add_parser('bilayer_graphene',
parents=[graphene_parent_parser])
bilayer_graphene_parser.add_argument(
'--layer-rotation-angle', type=float, help='Rotation angle of second '
'layer in **degrees.** (default: %(default)s)')
bilayer_graphene_parser.set_defaults(
generator_class='BilayerGrapheneGenerator')
nanotube_parent_parser = argparse.ArgumentParser(add_help=False)
nanotube_parent_parser_group = \
nanotube_parent_parser.add_mutually_exclusive_group()
nanotube_parent_parser_group.add_argument(
'--nz', type=int, default=1,
help='Number of repeat unit cells along `z` axis '
'(default: %(default)s)')
nanotube_parent_parser_group.add_argument(
'--Lz', type=float, default=None,
help='Length of nanotube along `z` axis in **nanometers**. '
'(default: %(default)s)')
nanotube_parent_parser.add_argument(
'--fix-Lz', action='store_true', help='Generate the nanotube with '
'length as close to the specified `Lz` as possible. If `True`, then '
'non integer `nz` cells are permitted. (default: ' '%(default)s)')
swnt_parent_parser = argparse.ArgumentParser(add_help=False)
swnt_parent_parser.add_argument('-n', type=int, default=10,
help='Chiral index `n` '
'(default: %(default)s)')
swnt_parent_parser.add_argument('-m', type=int, default=10,
help='Chiral index `m` '
'(default: %(default)s)')
mwnt_parent_parser = argparse.ArgumentParser(add_help=False)
swnt_parser = \
subparsers.add_parser('swnt', parents=[swnt_parent_parser,
nanotube_parent_parser])
swnt_parser.set_defaults(generator_class='SWNTGenerator')
unrolled_swnt_parser = \
subparsers.add_parser('unrolled_swnt',
parents=[swnt_parent_parser,
nanotube_parent_parser])
unrolled_swnt_parser_group = \
unrolled_swnt_parser.add_mutually_exclusive_group()
unrolled_swnt_parser_group.add_argument(
'--nx', type=int, default=1,
help='Number of repeat unit cells along `x` axis '
'(default: %(default)s)')
unrolled_swnt_parser_group.add_argument(
'--Lx', type=float, default=None,
help='Length of unrolled nanotube along `x` axis in **nanometers**. '
'(default: %(default)s)')
unrolled_swnt_parser.add_argument(
'--fix-Lx', action='store_true', help='Generate the nanotube with '
'length as close to the specified `Lx` as possible. If `True`, then '
'non integer `nx` cells are permitted. (default: ' '%(default)s)')
unrolled_swnt_parser.set_defaults(generator_class='UnrolledSWNTGenerator')
mwnt_parser = \
subparsers.add_parser('mwnt', parents=[nanotube_parent_parser])
mwnt_parser.set_defaults(generator_class='MWNTGenerator')
bundle_parent_parser = argparse.ArgumentParser(add_help=False)
bundle_parent_parser.add_argument('--nx', type=int, default=1,
help='Number of repeat unit cells '
'along `x` axis (default: %(default)s)')
bundle_parent_parser.add_argument('--ny', type=int, default=1,
help='Number of repeat unit cells '
'along `y` axis (default: %(default)s)')
swnt_bundle_parser = \
subparsers.add_parser('swnt_bundle', parents=[swnt_parent_parser,
bundle_parent_parser])
swnt_bundle_parser.add_argument(
'--vdw-spacing', type=float, default=dVDW, help='van der Waals '
'distance between nearest neighbor tubes (default: %(default)s)')
swnt_bundle_parser.set_defaults(generator_class='SWNTBundleGenerator')
mwnt_bundle_parser = \
subparsers.add_parser('mwnt_bundle', parents=[mwnt_parent_parser,
bundle_parent_parser])
mwnt_bundle_parser.set_defaults(generator_class='MWNTBundleGenerator')
return parser
[docs]def nanogen(generator_class=None, element1='C', element2='C', bond=CCbond,
fname=None, structure_format='xyz', **kwargs):
"""Generate nano-structure data.
Parameters
----------
generator_class : str
nano-structure generator class
element1 : str, optional
element symbol or atomic number of basis atom 1
element2 : str, optional
element symbol or atomic number of basis atom 2
bond : float, optional
element1-element2 bond length in ``units``
fname : str, optional
structure file name
structure_format : str, optional
output file format
"""
generator = getattr(importlib.import_module('sknano.generators'),
generator_class)
generator(**kwargs).save_data(fname=fname,
structure_format=structure_format)
def main():
args = argparser().parse_args()
if hasattr(args, 'generator_class'):
nanogen(**vars(args))
else:
argparser().print_help()
if __name__ == '__main__':
sys.exit(main())