pairlist

Fast neighbor (pair) lists for particles under periodic boundary conditions.

Given coordinates and a cutoff, it yields index pairs ((i, j)) whose distance is below the threshold. Internally it uses a cell-list algorithm with an optional C extension.

version 1.0.1

Install

pip install pairlist

Quick start

No external data files are required—only NumPy.

import numpy as np
import pairlist as pl

N = 500
cell = np.eye(3) * 20.0                         # 20 × 20 × 20 box
pos = np.random.default_rng(0).random((N, 3))    # fractional coordinates

for i, j, r in pl.pairs_iter(pos, maxdist=3.0, cell=cell):
    # i, j: particle indices; r: distance in the same unit as cell
    print(i, j, r)

Absolute coordinates work the same way if you set fractional=False:

pos_abs = pos @ cell
for i, j, r in pl.pairs_iter(
    pos_abs, maxdist=3.0, cell=cell, fractional=False
):
    ...

Pairs between two sets of points:

pos_A = np.random.default_rng(1).random((100, 3))
pos_B = np.random.default_rng(2).random((200, 3))
for i, j, r in pl.pairs_iter(pos_A, maxdist=3.0, cell=cell, pos2=pos_B):
    ...

API reference: pairlist.html

Demo: draw neighbor bonds

demo

Particles in a periodic box; lines are pairs within the cutoff (colored by distance; minimum-image segments). Regenerate with:

python samples/demo_bonds.py -o benchmark/demo.png

Minimal version:

import numpy as np
import matplotlib.pyplot as plt
import pairlist as pl

rng = np.random.default_rng(0)
cell = np.eye(3) * 10.0
pos = rng.random((80, 3))
xyz = pos @ cell

fig, ax = plt.subplots(figsize=(5, 5))
ax.scatter(xyz[:, 0], xyz[:, 1], s=12, zorder=2)
for i, j, _ in pl.pairs_iter(pos, maxdist=2.0, cell=cell):
    ax.plot(
        [xyz[i, 0], xyz[j, 0]],
        [xyz[i, 1], xyz[j, 1]],
        color="0.6",
        lw=0.6,
        zorder=1,
    )
ax.set_aspect("equal")
ax.set_title("pairs within cutoff (xy projection)")
plt.show()

Benchmark

Cell lists vs. naive (O(N^2)) and other methods:

benchmark.ipynb

benchmark

C / other languages

The core cell-list routines are also available as a small C library (csource/pairlist.h, libpairlist.a). See the header for the API.

Optional: GenIce samples

The scripts under samples/ (RDF, hydrogen-bond graph, …) read Gromacs-style coordinates. You can generate an example box with GenIce:

genice2 CRN1 -r 2 2 2 > CRN1x222.gro
python samples/RDF_pairlist.py < CRN1x222.gro

Or simply make test if GenIce is installed.

Requirements

python
numpy

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Release history Release notifications | RSS feed

This release

1.0.1

Aug 16, 2026

1.0.0

Jul 25, 2026

0.6.4

Feb 12, 2026

0.6.3

Jan 9, 2026

0.6.2

Dec 1, 2025

0.6.1

Dec 1, 2025

0.6

Feb 8, 2025

0.5.1.3

Apr 3, 2024

0.5.1.2

Dec 11, 2023

0.5.1.1

Dec 11, 2023

0.5.1

Dec 11, 2023

0.5

Dec 11, 2023

0.3.2

Nov 27, 2023

0.3.1

Oct 26, 2023

0.3.0.2

Oct 24, 2023

0.3.0.1

Sep 2, 2023

0.2.12.4

Mar 12, 2022

0.2.12.3

Mar 12, 2022

0.2.12.2

Mar 12, 2022

0.2.12

Feb 27, 2022

0.2.11.3

Jun 25, 2021

0.2.11.1

Mar 24, 2021

0.2.11

Mar 24, 2021

0.2.10.2

Mar 20, 2021

0.2.10.1

Jun 6, 2020

0.2.10

Jun 6, 2020

0.2.9

Sep 7, 2019

0.2.8

Sep 6, 2019

0.2.7

Aug 23, 2019

0.2.6

Jun 25, 2018

0.2.5

Jun 25, 2018

0.2.4

May 14, 2018

0.2.3

May 7, 2018

0.2.2

Apr 6, 2018

0.2

Apr 5, 2018

0.1.8

Apr 3, 2018

0.1.6

Apr 3, 2018

0.1.4

Apr 2, 2018

0.1.3

Apr 2, 2018

0.1

Apr 2, 2018

pairlist 1.0.1

pairlist

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