Ice and clathrate labels

You label one frame two ways. CHILL+ reads a staggered or eclipsed star. A cage signature counts closed polyhedra of a given ring census. The runnable copy is docs/tutorials/test_ice_and_clathrate.py. Python is pip install pydseamslib. The import is pydseams.

The mixed TIP4P frame

input/traj/exampleTraj.lammpstrj has 750 atoms and 250 oxygens (LAMMPS type 2).

import pydseams as ds

frame = ds.read("input/traj/exampleTraj.lammpstrj", atom_type=2)
print(frame.chill_plus())
print(frame.cages())

Frame.chill_plus uses the cutoff neighbour list. IceCounts(interClathrate=12, water=238). CageScore(n_ih=0, n_ic=0, n_water=250).

seams chill-plus on the same file uses the mutual four-neighbour list and prints clathrate 1 interClathrate 7 water 242. The cage score matches the CLI. The CHILL+ histogram does not match the CLI.

Cubic ice and an sI cage

input/traj/mW_cubic.lammpstrj frame 1 is 4096 mW sites. Both the cutoff list and the mutual four-neighbour list label every site cubic, and every site sits in a double-diamond cage.

input/traj/genice_sI.lammpstrj with cages_by_signature("512") returns 2 cages and 40 vertices.

The default face-edge window is 2.65,3.15 in the coordinate units of the file. These dumps are angstroms, and that window covers the oxygen-oxygen contacts of the reference cells. Set edge to the heavy-atom contact range of the model, and widen it for a compressed cell or a guest that stretches a cage. A nanometre file uses 0.265,0.315. none turns the window off: every ring the neighbour list already accepted can be a face, and the cage bound is the face census alone. On sI, sII, the sI 2×2×2 cell and the sII 10×10×10 cell the default and none return the same cages.

found = frame.cages_by_signature("512")
found = frame.cages_by_signature("512", edge="none")
found = frame.cages_by_signature("512", edge="2.4,3.4")

local dseams = require("dseams")
local found = dseams.cages_by_signature(frame, "512")
found = dseams.cages_by_signature(frame, "512", {edge = "none"})
found = dseams.cages_by_signature(frame, "512", {edge = "2.4,3.4"})

The CLI spelling is --cage-edge and SEAMS_CAGE_EDGE. The C spelling is seams_frame_signature_edge; a null edge string keeps the default.