| Name | NshellFinder JSON |
| Version |
0.0.5
JSON |
| download |
| home_page | |
| Summary | OVITO Python modifier to find n-th shell nearest neighbors. |
| upload_time | 2024-03-13 23:24:01 |
| maintainer | |
| docs_url | None |
| author | |
| requires_python | >=3.7 |
| license | MIT License |
| keywords |
ovito
python-modifier
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# 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.
```python
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:
```bash
pip install --user NshellFinder
```
For *OVITO PRO* built-in Python interpreter, please use:
```bash
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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"description": "# NShellFinder\n  \n\nOvito Python modifier to find the n-th coordination shell neighbors. \n\n## Utilisation \nHere 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. \n\n```python\nfrom ovito.io import import_file\nfrom NshellFinder import NshellFinder\n\npipeline = import_file(\"fcc.dump\")\nmod = NshellFinder(crystal_structure=\"fcc\", cutoff=18.2)\npipeline.modifiers.append(mod)\ndata = pipeline.compute()\n\nneighbor_indices_per_shell = data.attributes[\"Neighbor indices per shell\"]\n# (number of nearest neighbor shells up to cutoff, number of atoms, number of nearest neighbors in the shell)\n\nfirst_nn = neighbor_indices_per_shell[0] # (number of atoms, 12 first nearest neigbors)\nsecond_nn = neighbor_indices_per_shell[1] # (number of atoms, 6 second nearest neighbors)\n```\n\n\n## Installation\nFor a standalone Python package or Conda environment, please use:\n```bash\npip install --user NshellFinder\n```\n\nFor *OVITO PRO* built-in Python interpreter, please use:\n```bash\novitos -m pip install --user NshellFinder\n```\n\nIf you want to install the lastest git commit, please replace ``NshellFinder`` by ``git+https://github.com/killiansheriff/NshellFinder.git``.\n\n## Contact\nIf any questions, feel free to contact me (ksheriff at mit dot edu).\n\n## References & Citing \nIf you use this repository in your work, please cite:\n\n```\n@article{TBD,\n title={TBD},\n author={Sheriff, Killian and Cao, Yifan and Freitas, Rodrigo},\n journal={arXiv preprint TBD},\n year={2024}\n}\n```\n",
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