GenIce3
GenIce3 Manual
GenIce3 is a Swiss army knife to generate hydrogen-disordered ice structures (and related systems such as clathrate hydrates). You provide a unit cell name, optional replication and options (guests, ions, exporters), and GenIce3 produces atomic coordinates in formats suitable for molecular dynamics or visualization.
Quick start: genice3 1h > ice.gro
Documentation
| Section | Description |
|---|---|
| Getting started | Installation, requirements, demo, what’s new in GenIce3 |
| CLI reference | Command-line usage and options |
| Basics | Generating ice, supercells, seed, density |
| Clathrate hydrates | Guest molecules, cage types, occupancy |
| Doping and defects | Ions (CLI), H₃O⁺/OH⁻ and Bjerrum defects (API) |
| Output formats | Exporters (GROMACS, CIF, LAMMPS, etc.) and generation stages |
| Unit cells | Table of unit cell symbols (1h, 4, CS2, CIF, …) |
| Water models | Built-in water models (exporter water_model suboption) |
| Guest molecules | Built-in guest molecules for clathrates |
| Plugins | Extra PyPI plugins and custom unit cell / exporter / molecule plugins |
| Changes from GenIce2 | Cage survey and other changes |
| Citation | How to cite GenIce |
| Contribute | How to contribute |
| License | MIT License |
API examples
The API examples show how to use GenIce3 from Python with embedded sample code (basic usage, CIF I/O, doping, guest occupancy, polarization, unit cell extension, topological defects).
For AI assistants
A concise, structured overview of GenIce3 for AI/LLM systems that need to explain the project to users: For AI assistants.