Main changes from GenIce2
- Command line
- Option syntax is unified; hierarchical options and YAML config files (
-Y / --config) replace many GenIce2-style flags.
- Polarization control uses
pol_loop_1 and pol_loop_2 (replacing depol_loop).
- Package and entry points are
genice3 (PyPI: genice3); plugin groups use the genice3.* namespaces.
- API
- Python API redesigned around
GenIce3 and DependencyEngine: specify what you need and dependent quantities recompute automatically.
- Embed protonic defects (H₃O⁺, OH⁻) and Bjerrum topological defects from Python (see the API examples in the manual).
- Setter-style configuration and expanded notebooks/examples (
API.ipynb, examples/api/).
- Algorithm and core
- Ice-rule and depolarization logic delegated to genice-core (≥1.6.0); GenIce3 focuses on unit cells, guests, ions, and exporters.
- Reactive pipeline:
@reactive properties and explicit dependency tracking replace ad-hoc recalculation.
- Unit cells and structures
- Lattice plugins moved to
genice3.unitcell; many GenIce2 structures ported with identity comparison tests.
- CIF-derived unit cells branch on whether hydrogen positions are supplied;
partial_order removed.
- New or updated structures include auxiliary ices,
YKD, ice21 (and aliases), and cylindrical prism ice (API).
- Clathrates, ions, and defects
- Cage assessment: GenIce2’s
--assess_cages removed — use exporter cage_survey (JSON). Default max cage ring count is 16 (override via exporter options).
- Spot ions use
-A / -C (spot anion/cation; not the old cage-assessment flag). Group guests and spot-cation cage reporting extended; unit-cell ion suboptions (e.g. --group) in YAML.
- Exporters and visualization
- Built-in and plugin exporters (GROMACS, CIF, LAMMPS, yaplot, plotly, py3Dmol, etc.); format functions and option parsing refined.
- Optional Web API (
genice3-web) with client examples and tests.
- Documentation and tooling
- Manual on GitHub Pages; plugin tables and citations generated from the repo (
make docs, make README.md).
- For a narrative of the GenIce3 development period and compatibility notes, see RELEASE_NOTE.md in the repository.
Example — cage survey (formerly --assess_cages):
genice3 CS2 -e cage_survey > cages.json