genice3 3.0b0

A Swiss army knife to generate hydrogen-disordered ice structures.

GenIce3

A Swiss army knife to generate hydrogen-disordered ice structures.

Quick start: Use the unit cell name as the first argument (e.g. 1h for Ice Ih, 4 for Ice IV): genice3 1h > ice.gro

Version 3.0b0

For usage, ice structures, output formats, water models, guest molecules, and the full manual, see the documentation.

New in GenIce3

• Command line: Option syntax unified; options can be read from config files.
• API: Improved API; embed protonic (H₃O⁺, OH⁻) and Bjerrum topological defects via Python.
• Algorithm: Reactive pipeline with DependencyEngine; data generation runs automatically from your specifications.

Demo

Try GenIce3 on Google Colaboratory.

Requirements

• networkx >=2.0.dev20160901144005
• numpy >=2.0
• pairlist >=0.6.4
• cycless >=0.7
• graphstat >=0.3.3
• yaplotlib >=0.1.2
• openpyscad >=0.5.0
• genice-core >=1.3.1
• pyyaml >=6.0
• jinja2 >=3.1.4
• cif2ice (>=0.4.1,<0.5.0)

Installation

GenIce3 is on PyPI. Install with pip:

pip install genice3

Uninstallation

pip uninstall genice3

References

See the manual → References for the full reference list (generated from citations.json).

Citation

If you use GenIce in your work, please cite as in CITATION.cff or:

M. Matsumoto, T. Yagasaki, and H. Tanaka, "GenIce: Hydrogen-Disordered Ice Generator", J. Comput. Chem. 39, 61-64 (2017). DOI: 10.1002/jcc.25077

M. Matsumoto, T. Yagasaki, and H. Tanaka, "GenIce-core: Efficient algorithm for generation of hydrogen-disordered ice structures.", J. Chem. Phys. 160, 094101 (2024). DOI:10.1063/5.0198056

How to contribute

GenIce is developed on GitHub (https://github.com/genice-dev/GenIce3). Feedback, bug fixes, and contributions are welcome.

License

MIT License. See LICENSE for details.