Muse

Mixture builder for simulation environments

Build amorphous solids and liquid mixtures from relaxed solid-state structures on Materials Project using Packmol and machine learning interatomic potentials.

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Features

• 🧱 Structure generation — Build binary/multicomponent amorphous mixtures from Materials Project crystal structures
• ⚖️ Density equilibration — Run NVT → NPT molecular dynamics to compute equilibrium densities
• 📊 Thermodynamic analysis — Plot binary mixing diagrams with Redlich–Kister fits
• 📁 Trajectory I/O — Convert pymatgen trajectories to extended XYZ format
• 🖥️ HPC integration — Submit SLURM batch jobs programmatically

Installation

pipuvFrom source

pip install muse-xtal

uv pip install muse-xtal

git clone https://github.com/chiang-yuan/muse.git
cd muse
pip install -e ".[dev]"

Optional extras

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

# Development tools
pip install "muse-xtal[dev]"

Prerequisites

• Packmol must be installed and on your PATH
• A Materials Project API key set as the MP_API_KEY environment variable

Quick example

from muse.transforms.mixture import mix_number

atoms = mix_number(
    recipe={"NaCl": 3, "KCl": 1},
    tolerance=2.0,
    scale=1.05,
    seed=42,
)
print(atoms)

Citation

If you use Muse in your research, please cite:

@software{chiang2023muse,
    title  = {muse},
    author = {Yuan Chiang},
    year   = {2023},
    url    = {https://github.com/chiang-yuan/muse}
}