Monolayer square ice

Figshare: Monolayer LAMMPS Trajectory (dump-6-320-310.lammpstrj, fMSI on cooling 320 K to 310 K). Four-membered primitive rings.

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

Python

import pydseams as ds

frame = ds.read("dump-6-320-310.lammpstrj")
frame.monolayer_rings(output_dir="output/", sheet_area=1.0)

Pass the sheet area for the system you downloaded. The engine does not guess it.

Lua

The library call is require("dseams") plus dseams.core.ringAnalysis. The 1.x scripts under example_lua/monolayer/ still use the 2020 globals; rewrite them. Do not run yodaStruct -c.

Howto: confined ice.

References

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