This package is for generating atom coordinate files to initialize structures in atomistic simulations of nanowires.
It's written to work with the read_data command in LAMMPS. However, output files can be visualized directly in OVITO (free version works OK) or VMD (for example). The format of the file corresponds to what's called xyz in the LAMMPS docs. This is just a text file listing every atom as well as its type, coordinates, and velocity.
Download or clone
git clone https://github.com/araghukas/nwlattice.git
Navigate to the nwlattice directory, which contains setup.py, then
pip install .
Import the nanowire type of interest and instantiate it. Then call the write_points(file_path=None) instance method. If file_path is not specified, this will write a file at './TypeName_structure.data', with 'TypeName' substituted for the actual class name. The resulting file can be imported directly by LAMMPS using, say,
read_data ./TypeName_structure.data
to initialize atom locations and the simulation cell dimensions.
For a summary describing the nanowire classes, import the get_info(type_name=None) method:
from nwlattice import get_info
Calling get_info without specifying type_name will print doc information for all implemented nanowire classes.
If you're after a data file representing, say, atoms in a GaAs nanowire that is 10 nm wide and 300 nm long, run something like:
from nwlattice.nw import ZBPristine111
scale = 5.6531 # GaAs lattice constant @ 300K (in Angstroms)
wire = ZBPristine111(scale, width=100, length=3000)
wire.write_points("~/Desktop/my_GaAs_nanowire.data")
Keep in mind that the number of atoms in the nanowire scales with the square of the width, so the output files (being uncompressed text) can quickly become several GB in size. However file sizes should be manageable for dimensions suitable to MD.
The argument set scale, width, and length is enough to instantiate the simplest nanowire classes. Other classes may additionally require period or fraction to be specified, if applicable. For example, a faceted twinning nanowire can be instantiated using
wire = ZBTwinFaceted(5.6531, 100, 3000, 30)
where the arguments specify scale, width, length, and period, respectively.
See the class docstrings in nwlattice/nw.py or use the get_info method mentioned above for instructions on instantiating with integer atom-wise dimension parameters.
Note that because the lattice is discrete, input dimensions such as width, length, and period will be approximated in general. The actual resulting dimensions are stored in the size attribute of each instance.
actual_scale = wire.size.scale
actual_width = wire.size.width
actual_length = wire.size.length
actial_period = wire.size.period # error for not periodic nanowire types
actual_area = wire.size.area
Please note that this project is a work in progress. Use at your own risk.