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https://github.com/luthaf/vesin
Compute neighbor lists for atomistic systems
https://github.com/luthaf/vesin
Last synced: 4 days ago
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Compute neighbor lists for atomistic systems
- Host: GitHub
- URL: https://github.com/luthaf/vesin
- Owner: Luthaf
- License: bsd-3-clause
- Created: 2024-03-20T15:49:12.000Z (10 months ago)
- Default Branch: main
- Last Pushed: 2024-11-29T17:22:41.000Z (about 2 months ago)
- Last Synced: 2025-01-09T09:12:16.212Z (12 days ago)
- Language: Python
- Homepage: https://luthaf.fr/vesin/
- Size: 480 KB
- Stars: 33
- Watchers: 4
- Forks: 2
- Open Issues: 5
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# Vesin: fast neighbor lists for atomistic systems
[](http://luthaf.fr/vesin/)
| English 🇺🇸/🇬🇧 | Occitan 
| French 🇫🇷 | Arpitan 
| Gallo‑Italic 
| Catalan 
| Spanish 🇪🇸 | Italian 🇮🇹 |
|------------------|----------|-----------|----------|--------------|---------|------------|------------|
| neighbo(u)r | vesin | voisin | vesin | visin | veí | vecino | vicino |
Vesin is a fast and easy to use library computing neighbor lists for atomistic
system. We provide an interface for the following programing languages:
- C (also compatible with C++). The project can be installed and used as a
library with your own build system, or included as a single file and built
directly by your own build system;
- Python;
- TorchScript, with both a C++ and Python interface;
### Installation
To use the code from Python, you can install it with `pip`:
```
pip install vesin
```
See the [documentation](https://luthaf.fr/vesin/latest/index.html#installation)
for more information on how to install the code to use it from C or C++.
### Usage instruction
You can either use the `NeighborList` calculator class:
```py
import numpy as np
from vesin import NeighborList
# positions can be anything compatible with numpy's ndarray
positions = [
(0, 0, 0),
(0, 1.3, 1.3),
]
box = 3.2 * np.eye(3)
calculator = NeighborList(cutoff=4.2, full_list=True)
i, j, S, d = calculator.compute(
points=points,
box=box,
periodic=True,
quantities="ijSd"
)
```
We also provide a function with drop-in compatibility to ASE's neighbor list:
```py
import ase
from vesin import ase_neighbor_list
atoms = ase.Atoms(...)
i, j, S, d = ase_neighbor_list("ijSd", atoms, cutoff=4.2)
```
See the [documentation](https://luthaf.fr/vesin/latest/c-api.html) for more
information on how to use the code from C or C++.
### Benchmarks
You can find below benchmark result computing neighbor lists for increasingly
large diamond supercells, using an AMD 3955WX CPU and an NVIDIA 4070 Ti SUPER
GPU. You can run this benchmark on your system with the script at
`benchmarks/benchmark.py`. Missing points indicate that a specific code could
not run the calculation (for example, NNPOps requires the cell to be twice the
cutoff in size, and can't run with large cutoffs and small cells).
## License
Vesin is is distributed under the [3 clauses BSD license](LICENSE). By
contributing to this code, you agree to distribute your contributions under the
same license.