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
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:
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
1 maintainer
Metadata
1 maintainer
Release files for pairlist 1.0.1
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| pairlist-1.0.1.tar.gz | 17.5 kB | Details |
Built distributions (wheels)
Total release size: 752.3 kB
Release files / pairlist-1.0.1.tar.gz
| Download URL | pairlist-1.0.1.tar.gz |
|---|---|
| Size | 17.5 kB |
| Tags | Source |
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Release files / pairlist-1.0.1-cp314-cp314-win_amd64.whl
| Download URL | pairlist-1.0.1-cp314-cp314-win_amd64.whl |
|---|---|
| Size | 24.3 kB |
| Tags | CPython 3.14 Windows x86-64 |
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Release files / pairlist-1.0.1-cp314-cp314-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl
| Download URL | pairlist-1.0.1-cp314-cp314-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl |
|---|---|
| Size | 79.5 kB |
| Tags | CPython 3.14 Linux glibc 2.28+ x86-64 Linux glibc 2.5+ x86-64 |
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Release files / pairlist-1.0.1-cp314-cp314-macosx_11_0_arm64.whl
| Download URL | pairlist-1.0.1-cp314-cp314-macosx_11_0_arm64.whl |
|---|---|
| Size | 20.5 kB |
| Tags | CPython 3.14 macOS 11.0+ ARM64 |
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| Download URL | pairlist-1.0.1-cp313-cp313-win_amd64.whl |
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| Size | 23.6 kB |
| Tags | CPython 3.13 Windows x86-64 |
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| Size | 79.4 kB |
| Tags | CPython 3.13 Linux glibc 2.28+ x86-64 Linux glibc 2.5+ x86-64 |
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| Download URL | pairlist-1.0.1-cp313-cp313-macosx_11_0_arm64.whl |
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| Size | 20.5 kB |
| Tags | CPython 3.13 macOS 11.0+ ARM64 |
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| Download URL | pairlist-1.0.1-cp312-cp312-win_amd64.whl |
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| Download URL | pairlist-1.0.1-cp312-cp312-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl |
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| Size | 79.3 kB |
| Tags | CPython 3.12 Linux glibc 2.28+ x86-64 Linux glibc 2.5+ x86-64 |
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