Vesin: fast neighbor lists for atomistic systems

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Vesin is a C library that computes neighbor lists for atomistic system, and tries to be fast and easy to use. We also provide a Python package to call the C library.

Installation

To use the code from Python, you can install it with pip:

pip install git+https://github.com/luthaf/vesin

See the documentation 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:

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:

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 for more information on how to use the code from C or C++.

Benchmarks

You can find below benchmark result for increasingly large diamond supercells, on Apple M1 Max CPU. You can run this benchmark on your system with the script at benchmarks/benchmark.py.

License

Vesin is is distributed under the 3 clauses BSD license. By contributing to this code, you agree to distribute your contributions under the same license.