Bulk HC / DDC cages¶

Figshare: Nucleation LAMMPS Trajectory (4096 mW waters after crystallization). Hexagonal cages (HC), double-diamond cages (DDC), and mixed rings sit on the ice cluster.

seams cages is the 2.x replacement for the 1.x bulkTopologicalCriterion Lua script.

CLI¶

--graph defaults to seeded. --complete turns on ring-adjacent completion of that seeded assignment.

seams cages nucleation.lammpstrj --type 2 --graph seeded --complete

Other bond graphs: --graph cutoff, --graph knn, --graph knn-union. -k (default 4) applies to knn, knn-union, and seeded.

Stdout is nop N graph KIND hexagonal IH cubic IC water W. Hexagonal is HC (Ih), cubic is DDC (Ic), water is neither.

Python¶

Frame.cages defaults to the seeded construction. ring_adjacent=True is the same completion as --complete.

from pydseams import Frame

frame = Frame.from_file("nucleation.lammpstrj", atom_type=2)
print(frame.cages(ring_adjacent=True))
print(frame.seeded_affiliation(ring_adjacent=True))

cages(seeded=False) is cutoff-graph affiliation on this frame's six-rings. IceFeaturizer turns ring-adjacent completion on by default.

Lua¶

local dseams = require("dseams")
local cloud = dseams.read("nucleation.lammpstrj", {type = 2})
print(dseams.cages(cloud, {type = 2, complete = true}))

dseams.cages always uses the seeded pair of k-nearest graphs. o.type defaults to 1. read keeps the LAMMPS type, so a type-2 cloud still needs type = 2 or the k-nearest graphs stay empty. complete fills the last vertex of a six-ring whose other vertices carry a label.

Books: seams cages, pydseams.

References¶

1. Haji-Akbari, A.; Debenedetti, P. G. Proc. Natl. Acad. Sci. 2015, 112, 10582. doi:10.1073/pnas.1509267112