=================== 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 <../tutorials/bulk-ice.rst>`_. Bond graph ---------- ``seams cages --graph`` chooses the bond graph those rings are found on: .. table:: +---------------+-------------------------------------------------------+ | 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.