walk_compare¶

tests/walk_compare walks a LAMMPS dump and prints one row per frame. Each row has four-neighbour star (CHILL+) counts, cage membership on the same cutoff graph, and the seeded assignment on the mutual and union four-nearest graphs, with the largest ice cluster of each score. Cage flags are hexagonal cage (HC) and double-diamond cage (DDC).

The walk_compare binary is a Meson executable. pixi run setup && pixi run build (-Dwith_tests=true) writes bbdir/tests/walk_compare. A Nix develop tree writes the same name under the Meson build directory. Catch2 does not run this binary.

Inputs¶

walk_compare TRAJ [lastFrame] [atomType] [stride]

argument	default	meaning
`TRAJ`	required	LAMMPS dump path
`lastFrame`	all frames	inclusive 1-based cap; `0` or a value at or above the dump length walks every frame
`atomType`	`1`	LAMMPS type kept by `sinp::readLammpsTrjO`
`stride`	`1`	frame step; a non-positive value becomes `1`

Missing TRAJ exits 2 with a usage line. A dump with no frames exits 1.

Neighbour knobs are hard-wired:

knob	value
cutoff	`3.5`
k-NN candidate cutoff	`5.5`
`k`	`4`

seededCageAffiliation is called with the completion flag left at its default, false. See Ring-adjacent completion.

Columns¶

Stdout opens with two comments: the dump path with nframes, last, and stride, then the column names. Each later line is twenty integers.

column	source
`frame`	1-based dump index
`nop`	atoms kept of `atomType`
`chill_cubic`	CHILL+ cubic (and reCubic)
`chill_hex`	CHILL+ hexagonal (and reHex)
`chill_interfacial`	CHILL+ interfacial
`chill_clathrate`	CHILL+ clathrate
`chill_interclathrate`	CHILL+ interClathrate
`chill_water`	every other CHILL+ label
`chill_ice`	cubic plus hexagonal (Nguyen and Molinero bulk ice; interfacial is not ice)
`chill_max`	largest `chill_ice` component on the cutoff graph
`chill_clus`	number of those components
`cut_ice`	atoms in an HC- or DDC-affiliated six-ring on the cutoff graph
`cut_max`	largest `cut_ice` component on the cutoff graph
`cut_clus`	number of those components
`seed_ih`	seeded HC and not DDC
`seed_ic`	seeded DDC and not HC
`seed_both`	seeded HC and DDC
`seed_ice`	`seed_ih + seed_ic + seed_both`
`seed_max`	largest `seed_ice` component on the union four-nearest graph
`seed_clus`	number of those components

Those twenty integers split into star counts, cutoff-graph cage counts (cut_*), and seeded counts (seed_*). The star counts and cut_* share the cutoff neighbour list (nneigh::neighListO at 3.5). The seed_* columns use nneigh::kNearestNeighbourPair (k=4, candidate cutoff 5.5): mutual seeds, union completions. Cluster walks are connected components of the flagged atoms on that same index graph. A frame with nop 0 prints the frame index and nineteen zeros.

Example¶

bbdir/tests/walk_compare input/traj/exampleTraj.lammpstrj 1 2

That walks frame 1, type 2 (TIP4P oxygen in the in-tree mixed dump). Add a fourth argument to stride a long trajectory.