muse-xtal 0.2.0

Build amorphous solids and liquid mixtures from Materials Project structures using Packmol and machine learning interatomic potentials

Muse

Muse (Mixture builder for simulation environments) is a Python package for rapidly building amorphous solids and liquid mixtures from relaxed solid-state structures on Materials Project. It uses Packmol for packing molecules into simulation cells and supports density equilibration through molecular dynamics with machine learning interatomic potentials (MLIPs), especially universal interatomic potentials (UIPs) such as MACE and CHGNet.

Features

• Structure generation — Build binary/multicomponent amorphous mixtures from Materials Project crystal structures via mix_number and mix_cell
• Density equilibration — Run NVT → NPT molecular dynamics workflows to compute equilibrium densities with DensityCalc
• Thermodynamic analysis — Plot binary mixing enthalpy (G–x), density–composition, and excess volume diagrams with Redlich–Kister fits
• Trajectory I/O — Convert pymatgen trajectories to extended XYZ format
• HPC integration — Submit SLURM batch jobs programmatically

Installation

pip install muse-xtal

Optional extras

# MACE calculator support
pip install "muse-xtal[mace]"

# Development tools (ruff, pytest)
pip install "muse-xtal[dev]"

# Documentation building
pip install "muse-xtal[docs]"

Prerequisites

Muse requires Packmol to be installed and available on your PATH. You can compile it from source:

bash scripts/install-packmol.sh

You also need a Materials Project API key set as the MP_API_KEY environment variable (or in a .env file).

Quick Start

from muse.transforms.mixture import mix_number

# Build a NaCl–KCl mixture (3:1 ratio, ~20 atoms)
atoms = mix_number(
    recipe={"NaCl": 3, "KCl": 1},
    tolerance=2.0,
    scale=1.05,
    seed=42,
)
print(atoms)  # Atoms object ready for simulation

Density equilibration with MACE

import numpy as np
from ase import units
from mace.calculators import MACECalculator
from muse.calcs.density import DensityCalc

calc = MACECalculator(model_paths="path/to/model", device="cpu")

density_calc = DensityCalc(
    calculator=calc,
    optimizer="FIRE",
    steps=500,
    mask=np.eye(3),
    rtol=1e-3,
    atol=5e-4,
)

results = density_calc.calc(
    atoms=atoms,
    temperature=1100,  # K
    externalstress=0.0,  # eV/ų
)
print(f"Density: {results['mass_density']:.4f} amu/ų")

Documentation

Full documentation is available at chiang-yuan.github.io/muse.

Citation

If you use Muse in your research, please cite:

@software{chiang2023muse,
  author    = {Chiang, Yuan},
  title     = {muse-xtal},
  version   = {0.2.0},
  year      = {2023},
  doi       = {10.5281/zenodo.10369245},
  url       = {https://github.com/chiang-yuan/muse}
}

Contributing

Contributions are welcome! See CONTRIBUTING.md for guidelines.

License

This project is licensed under the MIT License — see LICENSE for details.