CHILL+ versus cages¶

Two classifiers live in libyodaLib. They answer different questions and they do not imply each other.

Four-neighbour star¶

CHILL and CHILL+ (seams chill / seams chill-plus, chill::getCorrelPlus / getIceTypePlus) look at the four-neighbour star. They compute bond-order correlations c_ij on the four nearest neighbours of each oxygen (or each mW site) and label the atom cubic, hexagonal, interfacial, clathrate, or water from the staggered and eclipsed pattern of that star.

A molecule is cubic or hexagonal when its four bonds look like ice, even if those neighbours do not close a cage.

CHILL+: Nguyen and Molinero, J. Phys. Chem. B 2015 (10.1021/jp510289t). CHILL: Moore et al., Phys. Chem. Chem. Phys. 2010.

Cage membership¶

The ice score (seams cages, ring::seededCageAffiliation by default) is cage membership. A molecule in a hexagonal cage (HC) is ice Ih. A molecule in a double-diamond cage (DDC) is ice Ic. A molecule in neither is water. The cages are assembled from six-membered primitive rings on a chosen bond graph, not from the four-neighbour star.

This is topological unit matching (TUM). The methods paper is the 2020 JCIM article (see Citation).

Why they disagree¶

A configuration can agree exactly on the closed star of a vertex (same induced graph, same coordinates on those five atoms) and still disagree on that vertex’s cage label, because the cage predicates read a larger neighbourhood of six-rings. The Catch2 suite encodes that fact: cage membership is not a function of the four-neighbour star.

On the in-tree mixed TIP4P dump (input/traj/exampleTraj.lammpstrj), CHILL+ reports 12 interfacial clathrate and 238 water. Seeded cages report zero HC and zero DDC. A three-eclipsed star is not cage membership. Walk through the commands in the mixed TIP4P tutorial.

Bond graph¶

seams cages --graph chooses the bond graph those rings are found on:

value	graph
`cutoff`	pairs inside the distance cutoff
`knn`	mutual k-nearest (default `k=4`)
`knn-union`	union k-nearest (completion graph of the seeded rule)
`seeded`	mutual seeds, union completions (CLI default)

On a perfect cubic crystal the four graphs coincide. On a mixed nucleation dump they do not have to.