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CHILL+ on a cubic lattice

Figshare: CHILL LAMMPS Trajectory (mW_cubic.lammpstrj, 4096 type-1 mW sites of ice Ic). CHILL+ labels every site cubic on that lattice. nucleation.lammpstrj is a different figshare deposit.

The 1.x driver (yodaStruct -c, conf.yaml, lua_inputs/) is gone. Use seams, pydseams, or require("dseams").

CLI

seams read mW_cubic.lammpstrj --type 1
seams chill mW_cubic.lammpstrj --cutoff 3.5 --type 1
seams chill-plus mW_cubic.lammpstrj --cutoff 3.5 --type 1

Counts print to stdout (cubic, hexagonal, water, interfacial, clathrate, interClathrate, reCubic, reHex, unclassified). chill_plus is an accepted alias of chill-plus.

Python

ds.read is a suffix-dispatch alias of Frame.from_file for LAMMPS dumps. New examples use the constructor.

from pydseams import Frame

frame = Frame.from_file("mW_cubic.lammpstrj", atom_type=1)
print(frame.chill_plus())

ASE and raw arrays use the other constructors:

from pydseams import Frame

frame = Frame.from_ase(atoms)                 # default select="O"
frame = Frame.from_arrays(positions, cell, numbers=[1, 1, 1, 1])

Lua

local dseams = require("dseams")
local cloud = dseams.read("mW_cubic.lammpstrj", {type = 1})
print(dseams.chill_plus(cloud, {cutoff = 3.5}))

Books: seams CLI, pydseams, dseams.

References

  1. Nguyen, A. H.; Molinero, V. J. Phys. Chem. B 2015, 119, 9369. doi:10.1021/jp510289t