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

seams cages nucleation.lammpstrj --type 2

Add --graph knn / knn-union / seeded when the bond graph is not the cutoff list.

Python

import pydseams as ds

frame = ds.read("nucleation.lammpstrj")
print(frame.cages())

Lua

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

Books: seams cages, pydseams.

References

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