Classify a dump

You have a LAMMPS water dump and want counts. Flags and the full surface live on seams CLI. Measured numbers for the in-tree mixed frame live in the mixed TIP4P tutorial.

One frame

seams read FILE
seams chill-plus FILE --cutoff 3.5 --type 2
seams cages FILE --type 2
seams rdf FILE --type 2 --cutoff 10

chill is the original CHILL rule. chill-plus is CHILL+. chill_plus is a CLI alias of chill-plus.

Type

--type 0 (default) guesses type 2 then type 1. Mixed water dumps in this tree use type 2 oxygen. Single-site mW dumps use type 1. A mixed-type dump that is not that guess needs --type I; see Ionic-liquid dumps. --type is that load filter, not the neighbour mask. AgI, kaolinite, INP and brine dumps keep substrate and ions out of the four neighbours with --water-types (OW LAMMPS types). That flag loads the mixed frame and scores ice on those types only.

seams chill-plus FILE --water-types 1
seams cages FILE --graph seeded --water-types 1
seams ions FILE --ion-types 3,4 --water-types 1

--family defaults to waterIce. chill / chill-plus / cages refuse every other family. A triclinic dump uses the stored tilt; see Sheared cells.

seams chill-plus FILE --type 2
seams cages input/traj/mW_cubic.lammpstrj --type 1

Frame range

Frames are 1-based. --last is inclusive. --jobs walks the range via forEachLammpsFrame (--jobs 1 is serial).

seams chill-plus FILE --frame 1 --last 10 --jobs 4

Bond graph for cages

seams cages FILE --graph seeded
seams cages FILE --graph seeded --complete
seams cages FILE --graph cutoff --cutoff 3.5
seams cages FILE --graph knn -k 4
seams cages FILE --graph knn-union -k 4

seeded is the CLI default: mutual four-nearest seeds, union completions. --complete then runs ring::ringAdjacentCompletion on those labels. On a perfect cubic crystal the four graphs coincide.

Features of this binary

seams --features