| Name | Application | extension | water | solute | HB | suboptions | remarks |
|---|---|---|---|---|---|---|---|
_KG |
Kirkwood G(r) | Statistical test suite 2: Calculate G(r) for checking long-range disorder in molecular orientations. | |||||
_pol |
Polarization | none | Calculate the polarization of the ice. | ||||
cage_survey |
JSON | .json | none | none | none | Cage positions and types (fractional coords, labels, faces). Replaces -A/–assess_cages. Optional :max_cage_rings N (max rings per cage, default 16). | |
cif |
CIF | .cif | Atomic positions | Atomic positions | none | Experimental | |
g, gromacs |
Gromacs | .gro | Atomic positions | Atomic positions | none | water_model: 3site, 4site, 6site, tip4p, etc. (water model name). | Default format. |
lammps, lmp |
LAMMPS | .lammps | Atomic positions | Atomic positions | none | water_model: 3site, 4site, 6site, tip4p, etc. (water model name). | Yet to be verified. |
plotly |
Plotly | .html | Atomic positions | Atomic positions | o | type: full, digraph, fixed, frame, graph (plot layout). | Interactive 3D visualization. |
py, python |
Python unitcell plugin | .py | none | none | graph | name: optional label stored in desc (e.g. match the saved .py stem); omit when redirecting stdout—nothing is invented by default. | Outputs a unitcell plugin where the supercell becomes the new unit cell; desc documents base plugin, replication matrix, and invoking CLI when available. |
y, yaplot |
Yaplot | .yap | Atomic positions | Atomic positions | o | H: radius of H atom (numeric). | It renders molecular configurations and the HB network. |
A GenIce3-compatible plugin genice3-mdanalysis is available; it provides an exporter for MDAnalysis and the many formats it supports. See genice3-mdanalysis. Plugins lists other prepared/planned plugins.
You can add custom output formats by placing exporter plugins in an exporter directory under the current working directory.
GenIce3 does not use the old GenIce2-style fixed “seven stages”. The pipeline is reactive: which steps run is determined automatically from the Dependency graph. You request outputs (e.g. coordinates, cage list); the engine runs only the tasks required to produce them. Exporter plugins register hooks that run when their inputs become available.