Paper figures¶

The 2020 JCIM figures are drawn from figshare project 73545. This page is the same calls on the dumps that are in the tree. The runnable copy is docs/tutorials/test_paper_figures.py. Python is pip install pydseamslib.

figure	dump in this tree	call	result
cubic ice, CHILL+	`mW_cubic.lammpstrj` frame 1, type 1	`chill_plus()`	4096 cubic
cubic ice, cages	the same frame	`cages()`	`n_ic` 4096
sI 5^12 cages	`genice_sI.lammpstrj`, type 1	`cages_by_signature("512")`	2 cages, 40 atoms
mixed frame	`exampleTraj.lammpstrj`, type 2	cutoff CHILL+ versus cages	12 interfacial clathrate, no complete cage

The R and Julia fronts also report 4096 cubic on the first row. They call libseams_lang with the mutual four-neighbour list. On this lattice that list and the cutoff list agree.

The nucleation, nanotube, monolayer, and in-plane RDF figures need the figshare dumps. Point the same functions at those files.

import pydseams as ds

ice = ds.read("input/traj/mW_cubic.lammpstrj", frame=1, atom_type=1)
print(ice.chill_plus().cubic, ice.cages().n_ic)

guest = ds.read("input/traj/genice_sI.lammpstrj", atom_type=1)
print(len(guest.cages_by_signature("512")))