One task, four fronts

The task is CHILL+ on frame 1 of input/traj/mW_cubic.lammpstrj, LAMMPS type 1. The result is 4096 cubic sites. docs/tutorials/test_cross_language.py runs the fronts.

language	call	cubic
CLI	seams chill-plus input/traj/mW_cubic.lammpstrj --type 1 --frame 1	4096
Python	pydseams.read(path, atom_type=1).chill_plus().cubic	4096
R	sum(chill_plus(read_frame(path, type=1L))$name = “cubic”)=	4096
Julia	chill_plus(read_frame(path; type=1)).counts["cubic"]	4096

Python is pip install pydseamslib. The import is pydseams. import pydseamslib is the same package. The package name the d-SEAMS paper should use is pydseamslib. R is bindings/r/dseams. Julia is bindings/julia/Dseams and calls libseams_lang with ccall.

Every front defaults to the cutoff neighbour list (graph = "cutoff", pairs closer than cutoff, 3.5 Å). graph = "mutual" is the mutual four-nearest list with candidates inside cutoff + 1.5, under the same name on every front. On this lattice the two lists label the same sites cubic. On the mixed TIP4P dump (input/traj/exampleTraj.lammpstrj, type 2) they do not:

front	mutual-list call
CLI	seams chill-plus FILE --type 2 --graph mutual
Python	frame.chill_plus(graph”mutual”)=
R	chill_plus(frame, graph = "mutual")
Julia	chill_plus(frame; graph = "mutual")

The cutoff list gives 12 interClathrate and 238 water. The mutual list gives 1 clathrate, 7 interClathrate, and 242 water.

A cage signature takes the same face-edge window on every front. The default is 2.65,3.15 in the coordinate units of the file. none leaves the cage bound to the face census.

front	call
CLI	seams cages FILE --signature 512 --cage-edge none
Python	frame.cages_by_signature("512", edge”none”)=
Lua	dseams.cages_by_signature(frame, "512", {edge = "none"})
C	seams_frame_signature_edge(frame, 3.5, 1, "cutoff", "512", "none", &n_cages, &n_atoms)

A null C edge string keeps the default. Set the window to the heavy-atom contact range of the model. Widen it for a compressed cell or a guest that stretches a cage. A nanometre file uses 0.265,0.315.

tests/chill_plus_fronts.py (Meson test chill_plus_fronts_agree) runs all four fronts on that dump with both lists. It checks the histograms on all four and the per-atom labels on Python, R, and Julia. The Python front needs a pydseamslib whose chill_plus takes graph.