OVITO Python modifier to find n-th shell nearest neighbors.
Project description
NShellFinder
Ovito Python modifier to find the n-th coordination shell neighbors.
Utilisation
Here is an example on how to find the indices of nearest neighbors -- cluster by shells up to certain cutoff -- for the fcc crystal structure. The scrip can be found in the examples/
folder.
from ovito.io import import_file
from NshellFinder import NshellFinder
pipeline = import_file("fcc.dump")
mod = NshellFinder(crystal_structure="fcc", cutoff=18.2)
pipeline.modifiers.append(mod)
data = pipeline.compute()
neighbor_indices_per_shell = data.attributes["Neighbor indices per shell"]
# (number of nearest neighbor shells up to cutoff, number of atoms, number of nearest neighbors in the shell)
first_nn = neighbor_indices_per_shell[0] # (number of atoms, 12 first nearest neigbors)
second_nn = neighbor_indices_per_shell[1] # (number of atoms, 6 second nearest neighbors)
Installation
For a standalone Python package or Conda environment, please use:
pip install --user NshellFinder
For OVITO PRO built-in Python interpreter, please use:
ovitos -m pip install --user NshellFinder
If you want to install the lastest git commit, please replace NshellFinder
by git+https://github.com/killiansheriff/NshellFinder.git
.
Contact
If any questions, feel free to contact me (ksheriff at mit dot edu).
References & Citing
If you use this repository in your work, please cite:
@article{TBD,
title={TBD},
author={Sheriff, Killian and Cao, Yifan and Freitas, Rodrigo},
journal={arXiv preprint TBD},
year={2024}
}
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