Skip to main content

OVITO Python modifier to find n-th shell nearest neighbors.

Project description

NShellFinder

PyPI Version PyPI Downloads tests

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}
}

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

NshellFinder-0.0.5.tar.gz (4.4 kB view details)

Uploaded Source

Built Distribution

NshellFinder-0.0.5-py3-none-any.whl (4.8 kB view details)

Uploaded Python 3

File details

Details for the file NshellFinder-0.0.5.tar.gz.

File metadata

  • Download URL: NshellFinder-0.0.5.tar.gz
  • Upload date:
  • Size: 4.4 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/5.0.0 CPython/3.9.18

File hashes

Hashes for NshellFinder-0.0.5.tar.gz
Algorithm Hash digest
SHA256 02b5fa023765f8c692e5e772277d134e241429b1f7209e392763a133bb109688
MD5 edef901b8daf802ee02c17cd1e38b674
BLAKE2b-256 6ae01f5f3f55e2306ea73abcaffd89e95953d05f6f105d9d416810f0e1039708

See more details on using hashes here.

File details

Details for the file NshellFinder-0.0.5-py3-none-any.whl.

File metadata

File hashes

Hashes for NshellFinder-0.0.5-py3-none-any.whl
Algorithm Hash digest
SHA256 3c3671886b274007073c42b198a2bf312d1eef3d4cf3a4499598bb8d3a001722
MD5 fc83d481799045cd75935f269c8574ac
BLAKE2b-256 1389f161538f90f6d9d1f0daa3cb7c7a8e472e1bebb858813888360f0e3dfcc2

See more details on using hashes here.

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page