Ice nanotube prisms

Figshare: Quasi-1D Nanotube LAMMPS Trajectory (dump-240-square.lammpstrj, 750 TIP4P/2005 waters in a smooth (13,0) tube at 240 K). Tetragonal prism blocks.

The seams CLI has no prism command. Use a front end.

Python

import pydseams as ds

frame = ds.read("dump-240-square.lammpstrj")
frame.find_prisms(output_dir="output/")

Lua

The 1.x scripts live under example_lua/iceNanotube/ in yodaStruct. The library call is require("dseams") plus the prism helper in that tree, not yodaStruct -c.

Howto: confined ice.

References

  1. The confined-ice topological criterion in the 2020 d-SEAMS paper, doi:10.1021/acs.jcim.0c00031.