ATOMic Order-to-Disorder Engine
Generate atomistic supercells across the full order-to-disorder spectrum (amorphous, short- and medium-range order, nanocrystalline, and single crystal) at any size, by seeding Voronoi grains and refining them into physically realistic structures with a machine-learning potential (MACE-MP0) or a fast spring-network quench.
Silicon, liquid → nanocrystalline. See Static Examples → Silicon.
Overview¶
atomode builds periodic supercells across the order-to-disorder spectrum by seeding Voronoi grains and refining them into physically realistic structures, either with a fast spring-network (FIRE) quench or with the MACE-MP0 machine-learning potential for near-DFT accuracy. Grain size and density set the local order, from a single amorphous network up to large, well-aligned crystallites. Pair (g2) and rooted three-body (g3) distributions are provided to characterize the result.
Key features:
Rapidly generate structures from liquid to nanocrystalline with a single call
Voronoi grain construction with per-species-pair bond topology
Interactive g3 distribution widgets for Jupyter (Three.js + anywidget)
Self-contained HTML exporters for trajectories, g3 heatmaps, and multi-cell overviews
Rotating MP4 / GIF movie export for publication figures
Works with any crystal structure (Si, SiC, oxides, metals, etc.)
Refining generated structures¶
atomode generates the initial supercell; a separate relaxation step turns it into a physically realistic structure. Two worked pipelines are documented, in order of accuracy:
MACE-MP0 refinement (recommended) — relax with a universal machine-learning potential. Near-DFT accuracy, minutes per ~5000-atom cell on a laptop CPU.
Fast FIRE refinement — the built-in spring-network FIRE quench. Orders of magnitude faster than MACE at reduced accuracy, and the only option that stays practical at 100³ Å and larger. Optionally calibrate the springs against MACE with one call (
shell.calibrate_to_mace()) — Morse anharmonicity, per-pair stiffness, and the hard-core wall are measured from the MACE potential on the reference crystal, improving accuracy at zero extra relaxation cost.