#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
====================================================
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.FullereneGenerator`
:class:`~sknano.generators.GrapheneGenerator`
:class:`~sknano.generators.BilayerGrapheneGenerator`
:class:`~sknano.generators.UnrolledSWNTGenerator`
:class:`~sknano.generators.SWNTGenerator`
:class:`~sknano.generators.MWNTGenerator`
:class:`~sknano.generators.LayeredStructureGenerator`
.. code-block:: sh
> nanogen --help
usage: nanogen [-h] [--fname FNAME] [--structure-format {data,xyz}]
[--debug] [--verbose] [--version]
{fullerene,graphene,bilayer_graphene,unrolled_swnt,swnt,mwnt,layered_structure}
...
optional arguments:
-h, --help show this help message and exit
--fname FNAME structure file name
--structure-format {data,xyz}
structure file format (default: xyz)
--debug debug output
--verbose verbose output
--version show nanogen's version number and exit
sub-commands:
{fullerene,graphene,bilayer_graphene,unrolled_swnt,swnt,mwnt,layered_structure}
.. autofunction:: nanogen
Examples
--------
The following command generates a graphene sheet with a 10 Å long
armchair edge and 1 Å long zigzag edge and saves the data in the
LAMMPS data format.::
> nanogen --structure-format data graphene 10 1
This command will generate a :math:`(20, 0)` SWNT, 5 unit cells
long and saves the data in `xyz` format.::
> nanogen swnt --Ch 20 0 --nz 5
"""
from __future__ import absolute_import, division, print_function, \
unicode_literals
__docformat__ = 'restructuredtext en'
import argparse
import importlib
import sys
from sknano.core.refdata import aCC, element_data
# from sknano.core.structures import get_chiral_indices_from_str
from .parser import add_default_arguments
_r_CC_vdw = element_data['C']['VanDerWaalsRadius']
__all__ = ['nanogen', 'nanogen_parser']
[docs]def nanogen_parser():
""":mod:`~sknano.scripts.nanogen` script \
:class:`~python:argparse.ArgumentParser`."""
parser = argparse.ArgumentParser()
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_default_arguments(parser)
subparsers = parser.add_subparsers(title='sub-commands')
fullerene_parser = subparsers.add_parser('fullerene')
fullerene_parser.add_argument('N', type=int, help='The N in C_N')
fullerene_parser.set_defaults(generator_class='FullereneGenerator')
nanostructure_parent_parser = argparse.ArgumentParser(add_help=False)
nanostructure_parent_parser.add_argument(
'--basis', type=str, nargs=2, metavar=('ELEMENT1', 'ELEMENT2'),
default=['C', 'C'], help='2 element symbols or atomic numbers of the '
'two atom basis (default: %(default)s)')
nanostructure_parent_parser.add_argument(
'--bond', type=float, default=aCC, help='Bond length between '
'nearest-neighbor atoms. Must be in units of Angstroms. '
'(default: %(default)s)')
graphene_parent_parser = argparse.ArgumentParser(add_help=False)
graphene_parent_parser.add_argument('--layer-spacing', type=float,
default=2*_r_CC_vdw,
help='distance between '
'graphene layers in **Angstroms**. '
'(default: %(default)s)')
graphene_parent_parser.add_argument('--layer-rotation-increment',
type=float,
default=None,
help='Layer rotation angles of '
'each layer in **degrees** '
'(default: %(default)s)')
graphene_parent_parser.add_argument('--layer-rotation-angles', type=list,
default=None,
help='Layer rotation angles of '
'each layer in **degrees** '
'(default: %(default)s)')
graphene_parent_parser.add_argument('--stacking-order', default='AB',
choices=('AA', 'AB'),
help='Stacking order of graphene '
'layers (default: %(default)s)')
graphene_parser = \
subparsers.add_parser('graphene', parents=[nanostructure_parent_parser,
graphene_parent_parser])
graphene_parser.add_argument('--nlayers', type=int, default=1,
help='Number of graphene layers. '
'(default: %(default)s)')
graphene_subparsers = \
graphene_parser.add_subparsers(title='graphene sub-commands')
primitive_cell_graphene_parser = \
graphene_subparsers.add_parser('from_primitive_cell')
primitive_cell_graphene_parser.add_argument(
'--edge-length', type=float, default=10,
help='graphene edge length in **Angstroms**')
primitive_cell_graphene_parser.set_defaults(
generator_class='PrimitiveCellGrapheneGenerator')
conventional_cell_graphene_parser = \
graphene_subparsers.add_parser('from_conventional_cell')
conventional_cell_graphene_parser.add_argument(
'--armchair-edge-length', type=float, default=10,
help='length of graphene armchair edge in **Angstroms**')
conventional_cell_graphene_parser.add_argument(
'--zigzag-edge-length', type=float, default=10,
help='length of graphene zigzag edge in **Angstroms**')
conventional_cell_graphene_parser.set_defaults(
generator_class='ConventionalCellGrapheneGenerator')
# graphene_parser.set_defaults(generator_class='GrapheneGenerator')
bilayer_graphene_parser = \
subparsers.add_parser('bilayer_graphene',
parents=[nanostructure_parent_parser,
graphene_parent_parser])
bilayer_graphene_parser.set_defaults(
generator_class='BilayerGrapheneGenerator')
swnt_parent_parser = argparse.ArgumentParser(add_help=False)
swnt_parent_parser.add_argument('--Ch', type=int, nargs=2,
metavar=('n', 'm'),
default=(5, 0),
help='Chiral indices (`n`, `m`) '
'(default: %(default)s)')
swnt_parent_parser_group = \
swnt_parent_parser.add_mutually_exclusive_group()
swnt_parent_parser_group.add_argument('--nz', type=int, default=1,
help='Number of repeat unit cells '
'along `z` axis '
'(default: %(default)s)')
swnt_parent_parser_group.add_argument('--Lz', type=float, default=None,
help='Length of nanotube along `z` '
'axis in **Angstroms**. '
'(default: %(default)s)')
swnt_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)')
unrolled_swnt_parser = \
subparsers.add_parser('unrolled_swnt',
parents=[nanostructure_parent_parser,
swnt_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 **Angstroms**. '
'(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_parent_parser = argparse.ArgumentParser(add_help=False)
mwnt_parent_parser.add_argument('--Ch', default=None, metavar=('n', 'm'),
type=int, nargs=2, action='append',
help='Use this command multiple times to '
'generate a list of (`n`, `m`) '
'chiralities for each `SWNT` wall in '
'`MWNT` (default: %(default)s)')
mwnt_parent_parser.add_argument('--Nwalls', type=int,
default=3,
help='Number of `SWNT` walls in `MWNT` '
'(default: %(default)s)')
mwnt_parent_parser.add_argument('--Lz', type=float, default=None,
help='Length of nanotube along `z` axis '
'in **Angstroms**. '
'(default: %(default)s)')
mwnt_parent_parser.add_argument('--min-wall-diameter', type=float,
default=None,
help='Minimum `MWNT` wall diameter, in '
'units of **Angstroms** '
'(default: %(default)s)')
mwnt_parent_parser.add_argument('--max-wall-diameter', type=float,
default=None,
help='Maximum `MWNT` wall diameter, in '
'units of **Angstroms** '
'(default: %(default)s)')
mwnt_parent_parser.add_argument('--max-walls', type=int, default=None,
help='Maximum number of `MWNT` walls '
'(default: %(default)s)')
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)')
bundle_parent_parser.add_argument('--vdw-radius', type=float,
default=_r_CC_vdw,
help='van der Waals '
'radius of nanotube atoms '
'(default: %(default)s)')
bundle_parent_parser.add_argument('--bundle-packing',
choices=('hcp', 'ccp'),
default=None,
help='Packing arrangement of nanotube '
'bundles. (default: %(default)s)')
bundle_parent_parser.add_argument('--bundle-geometry',
choices=('hexagon', 'square',
'rectangle', 'triangle'),
default=None,
help='Force a specific geometry on the '
'nanotube bundle boundaries '
'(default: %(default)s)')
swnt_parser = \
subparsers.add_parser('swnt', parents=[nanostructure_parent_parser,
swnt_parent_parser,
bundle_parent_parser])
swnt_parser.set_defaults(generator_class='SWNTGenerator')
mwnt_parser = \
subparsers.add_parser('mwnt', parents=[nanostructure_parent_parser,
mwnt_parent_parser,
bundle_parent_parser])
mwnt_parser.set_defaults(generator_class='MWNTGenerator')
layered_structure_parser = subparsers.add_parser('layered_structure')
layered_structure_parser.add_argument('cfgfile')
layered_structure_parser.set_defaults(
generator_class='LayeredStructureGenerator')
return parser
[docs]def nanogen(generator_class=None, fname=None, structure_format='xyz',
**kwargs):
"""Function for the nanogen script.
Parameters
----------
generator_class : str
nano-structure generator class
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(fname=fname,
structure_format=structure_format)
def main():
args = nanogen_parser().parse_args()
if hasattr(args, 'generator_class'):
nanogen(**vars(args))
else:
nanogen_parser().print_help()
if __name__ == '__main__':
sys.exit(main())
