lammps-md-tools 0.1.0

Small, dependency-light command-line tools for working with LAMMPS data/trajectory files.

lammps-md-tools

Small, dependency-light command-line tools for working with LAMMPS data/trajectory files.

This project is intentionally tiny:

• minimal dependencies
• deterministic behavior (good for automation/agents)
• clear input/output contracts

Install / run

Run without installing (recommended)

Using uvx (from Astral's uv):

uvx --from lammps-md-tools lammps-fix-box --help

Install into an environment

python -m pip install -U lammps-md-tools

Commands

lammps-fix-box

Rewrite the box bounds in a LAMMPS data file to match a cubic box length L.

Typical use case: tools that convert XYZ -> LAMMPS data may leave default bounds (e.g. 0..100 Å) that do not match the actual packing box.

# rewrite bounds to 0..L and wrap atoms into the box
lammps-fix-box --in input.data --out output.boxfix.data --L 60.69 --wrap

# use a different origin (origin..origin+L)
lammps-fix-box --in input.data --out output.data --L 60.69 --origin -30.345

What it does

• Rewrites header lines like xlo xhi, ylo yhi, zlo zhi to origin..origin+L.
• If a xy xz yz tilt line is present, it is rewritten to 0 0 0 xy xz yz.
• If --wrap is passed, wraps x y z coordinates into [lo, hi).

Assumptions / limitations

• Assumes a common LAMMPS data layout with an Atoms section containing at least: atom-ID atom-type x y z [extra...]
• It does not try to interpret/repair bonds, angles, velocities, etc.

Development

Build (wheel + sdist):

python -m pip install -U build
python -m build

License

MIT (see LICENSE).