minimage

Minimum-image convention for a periodic parallelepiped.

linkcell walks k-nearest neighbours. vesin builds cutoff pair lists. Both need the same wrap: fold through H, pick one image, never the self image. This crate is that wrap. Cell holds the 3x3 lattice and a dump-cell origin. Constructors accept LAMMPS bounds plus xy, xz, yz tilts, a CON lattice or length-angle box, an ASE-style 3x3 cell, and a vesin box.

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

Docs (orgmode first, HTML export): lode-org.github.io/minimage. Org catalog: lode-org.github.io.

Install

Rust:

cargo add minimage

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

pip install minimage

import minimage

cell = minimage.Cell.ortho(10.0, 10.0, 10.0)
assert abs(cell.dist2([0.2, 0.0, 0.0], [9.4, 0.0, 0.0]) - 0.64) < 1e-12

Meson

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

As a wrap, Meson exposes minimage_dep:

[wrap-git]
url = https://github.com/lode-org/minimage.git
revision = v0.1.4
depth = 1

[provide]
minimage = minimage_dep

minimage_dep = dependency('minimage', fallback: ['minimage', 'minimage_dep'])

CMake

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

find_package(minimage 0.1 REQUIRED)
target_link_libraries(app PRIVATE minimage::minimage)

pkg-config

pkg-config --cflags --libs minimage

Rust

use minimage::{dist2_many, reduce_pairs, Cell};

let sim = Cell::ortho(10.0, 10.0, 10.0)?;
let sheared = Cell::from_lammps_bounds(
    15.0, 8.660254037844386, 10.0, 5.0, 0.0, 0.0, 0.0, 0.0, 0.0,
)?;
let left = [0.2, 0.0, 0.0];
let right = [9.4, 0.0, 0.0];
assert!((sim.dist2(left, right) - 0.64).abs() < 1e-12);

let qs = [[9.4, 0.0, 0.0], [1.0, 0.0, 0.0]];
let mut out = [0.0; 2];
dist2_many(&sim, left, &qs, &mut out)?;

let pairs = [[0, 1], [0, 0], [0, 1]];
let mut kept = Vec::new();
reduce_pairs(&pairs, &mut kept)?;
assert_eq!(kept, vec![[0, 1]]);

Cell::from_ase, Cell::from_con, Cell::from_con_box, and Cell::from_vesin take the same row-major 3x3 lattice. Displacement is the wrapped vector from p to q.

License

MIT. See LICENSE.