linkcell

Periodic linked-cell k-nearest neighbour search for molecular simulations.

vesin builds cutoff pair lists. nanoflann builds Euclidean KD-trees without a minimum-image convention. This crate is the piece those two leave open: the linked-cell walk of Allen and Tildesley (Computer Simulation of Liquids), a k-heap per source, shells expanded until the k-th neighbour cannot sit outside the visited cube. The optional gpulite path runs that walk on a CUDA device (linkcell::gpu::Workspace); pair lists stay on the device.

It is a LODE library. The Rust crate is the implementation. The C ABI (lc_*) is the hourglass waist, the same shape as readcon-core. C++ is a RAII header over that ABI.

Install

Rust:

cargo add linkcell

C and C++ consumers take the staticlib (--features capi, on by default) plus include/linkcell.h or include/linkcell.hpp. Meson, CMake, and pkg-config all install that archive and those headers.

Python takes the same search through DLPack (dlpk). Any __dlpack__() object (numpy, torch, jax, cupy) is a valid xyz / cell, on any device. A CUDA xyz stays on device; a CUDA cell is inverted on device. torch.from_dlpack consumes (indices, dist2). Wheels: one CPython 3.12 limited-ABI (abi3) artifact per platform, and one free-threaded set (cp314t; PyO3 0.29 needs 3.14+ for t).

pip install linkcell

import numpy as np
import linkcell

xyz = np.array([[0.2, 0.0, 0.0], [9.4, 0.0, 0.0]], dtype=np.float64)
cell = np.array([10.0, 10.0, 10.0], dtype=np.float64)
nn, d2 = linkcell.knearest(xyz, cell, 1)
nn = np.from_dlpack(nn)

Meson

meson setup build
meson compile -C build
meson install -C build

As a wrap, Meson exposes linkcell_dep:

[wrap-git]
url = https://github.com/d-SEAMS/linkcell.git
revision = v0.3.2
depth = 1

[provide]
linkcell = linkcell_dep

linkcell_dep = dependency('linkcell', fallback: ['linkcell', 'linkcell_dep'])

CMake

cmake -B build -DCMAKE_INSTALL_PREFIX=$PREFIX
cmake --build build
cmake --install build

find_package(linkcell 0.3 REQUIRED)
target_link_libraries(app PRIVATE linkcell::linkcell)

In the same build tree the target is linkcell::linkcell.

pkg-config

pkg-config --cflags --libs linkcell

Both Meson and CMake write linkcell.pc (Libs includes the Rust sysroot: pthread, dl, m on Linux).

Rust

use linkcell::{knearest, Cell};

let sim = Cell::ortho(10.0, 10.0, 10.0)?;
let sheared = Cell::from_vectors(
    [10.0, 0.0, 0.0],
    [5.0, 8.66, 0.0],
    [0.0, 0.0, 10.0],
    [0.0, 0.0, 0.0],
)?;
let xyz = [[0.0, 0.0, 0.0], [1.0, 0.0, 0.0]];
let rows = knearest(&xyz, &sim, 1, None, None)?;
assert_eq!(rows[0].indices, vec![1]);

mask[i] == false removes a point as both a source and a candidate. cell_hint is the target cell edge; None uses 3.0 in the box units.

C

#include "linkcell.h"

double xyz[] = {0.0, 0.0, 0.0, 1.0, 0.0, 0.0};
lc_cell box = lc_cell_ortho(10.0, 10.0, 10.0);
int out[2];
if (lc_knearest(xyz, 2, &box, 1, NULL, 0.0, out) != 0) {
  return 1;
}

n and k are size_t. out has length n * k. Unused slots are -1. Neighbours of source i are out[i*k + 0 ..], nearest first.

C++

#include "linkcell.hpp"

const linkcell::Cell box = linkcell::Cell::ortho(10.0, 10.0, 10.0);
const double xyz[] = {0.0, 0.0, 0.0, 1.0, 0.0, 0.0};
const linkcell::Neighbours nn = linkcell::knearest(xyz, 2, box, 1);

nn owns the packed n * k buffer. Unused slots are -1. nn.neighbour(i, j) is the j-th neighbour of i. Failure throws linkcell::Error.

The optional device walk reads occupancy from the environment: LINKCELL_TPP (threads per particle) and LINKCELL_BLOCK (CUDA block size). Unset, the library picks a pair that maximises particles per block under the device thread and 48 KiB shared-memory limits. d-SEAMS writes the same keys from SEAMS_CONFIG / seams --tpp.

Docs

Quadrant	Page
Tutorial	Two points
How-to	Embed from C, Embed from C++, pkg-config
Reference	C ABI, Algorithm
Explanation	MIC and cells

Rust API: docs.rs/linkcell. Map: docs/index.md.

Design

The cell is a general parallelepiped: three lattice vectors plus an origin. Orthorhombic boxes are Cell::ortho / lc_cell_ortho. Binning is in fractional space, so a sheared dump is not treated as orthogonal.
Points fold into the primary cell once. Each source then walks Chebyshev shells of neighbour cells. Pair distances are a Cartesian subtract plus that cell's lattice translation (dist2_shifted and lattice_shift), the vesin / LAMMPS ghost construction. Orthorhombic boxes use three independent wraps and skip the two Hinv matvecs.
One lattice shift per unique cell is wrong unless every wrap of that cell is visited. The walk visits integer cell offsets, so each wrap of a bin is a separate visit.
The search does not take a cutoff. A cell-size hint only sets the bin width. Shells grow until the k-heap is exact.
vesin remains the right library for a cutoff pair list.

License

MIT

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