> ## Documentation Index
> Fetch the complete documentation index at: https://docs.claviscage.app/llms.txt
> Use this file to discover all available pages before exploring further.

# CHILL+ Classification

> Classify and visualize ice, hydrate, interfacial, and liquid water environments

# CHILL+ Classification

CHILL+ classifies each cage-forming water molecule by its local orientational environment. It complements cage-finding methods such as TRACE: TRACE reports closed cage topology, while CHILL+ shows where ordered ice-like and hydrate-like water environments occur throughout the system.

## Structure Classes

Clavis reports six classes:

| Class                   | Interpretation                                          |
| ----------------------- | ------------------------------------------------------- |
| **Other / liquid**      | Water without a recognized ordered local environment    |
| **Hexagonal ice**       | Ice Ih-like local order                                 |
| **Cubic ice**           | Ice Ic-like local order                                 |
| **Interfacial ice**     | Water at an ice/liquid or imperfect ice boundary        |
| **Gas hydrate**         | Hydrate-like local order                                |
| **Interfacial hydrate** | Water at a hydrate/liquid or imperfect hydrate boundary |

The result panel reports the count and fraction of waters in every class. Use these values as a structural descriptor, not as a substitute for checking the trajectory, force field, thermodynamic state, and cage topology.

## Run CHILL+

1. Load a structure or select a trajectory frame.
2. Open **ANALYZE** and choose **CHILL+**.
3. Run the current-frame analysis.
4. Inspect the class counts, 3D colors, and classified-water network in **RESULTS**.

Only recognized cage-forming water residues participate in classification. Guest molecules, ions, surfactants, slabs, and other non-water residues remain ordinary scene geometry.

## 3D Visualization

When analysis completes, Clavis switches the water visualization to CHILL+ class colors and draws the classified O–O neighbor network. The result controls provide:

* **HYDRATE ONLY**, **ICE ONLY**, and **SHOW ALL** quick filters
* Per-class visibility checkboxes
* Network width and opacity controls
* Per-class network colors or one color override
* H-bond visibility, width, and opacity controls alongside CHILL+

CHILL+ class filtering applies only to classified water atoms. Changing the visibility, atom size, bond size, opacity, color, or render style of a non-water residue channel such as `SDS` or `NA` does not turn CHILL+ off or invalidate its water classification.

<Info>
  H-bonds and the CHILL+ network can be displayed together. They are separate overlays: the CHILL+ network represents the classifier's O–O neighbor lattice, while the H-bond overlay uses the active H-bond cutoff and angular criterion.
</Info>

<Info>
  CHILL+ visualization is preserved in path-traced output: classified oxygen colors, complete-water class filtering, non-water residues, and the classified O–O network are passed to the path-traced scene. For very large systems, begin with a 256–640 px, 64-sample GPU render because path tracing still has to construct and sample a multi-million-triangle scene.
</Info>

## Trajectory Behavior

For native GROMACS and mapped LAMMPS sessions, select CHILL+ and use the trajectory range card's **Start**, **End**, and **Step** values. The range action classifies those exact frames, plots the six class fractions, and exports the one-based frame labels to CSV. In-memory multi-frame GRO still uses a bounded sample of up to 40 evenly spaced frames across the full trajectory. The separate large-GRO streaming worker is not yet included in the CHILL+ sweep.

When you move to another frame while CHILL+ visualization is active, Clavis refreshes the classification for the displayed frame. It preserves your class filters and network styling, but does not reuse a result whose frame identity no longer matches. Rapid native GROMACS navigation keeps the newest frame request and discards superseded requests without presenting them as runtime failures.

## Interpreting Results

* Compare class fractions over time rather than relying on a single frame.
* Use TRACE or another cage topology method when you need explicit cage counts and cage types.
* Inspect interfacial classes near growth, dissociation, material, or guest boundaries.
* Confirm that water residue names are recognized before treating a low classified fraction as a physical result.

## Related Guides

* [Hydrogen Bonds](/analysis/hydrogen-bonds)
* [TRACE Cage Detection](/analysis/trace)
* [Visualization Controls](/getting-started/visualization)
* [Layer Management](/getting-started/layers)