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. Frame.monolayer_rings writes polygonRingAnalysis output and reads coverage back.

Python¶

from pydseams import Frame

frame = Frame.from_file("dump-6-320-310.lammpstrj")
print(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. max_depth defaults to 4.

Lua¶

dseams.core.ringAnalysis is a compiled registration, not a require("dseams") helper. The 1.x scripts under example_lua/monolayer/ depend on CLI-injected globals. Use Frame.monolayer_rings for the supported library workflow.

Howto: confined ice.

References¶

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