Skip to content

seams CLI

The engine command is seams. A positional command and a trajectory file are required. --format text|json applies to every command. JSON emits one object per output frame with schema dseams.cli/v1.

seams --help
seams --version
seams --features

Commands

seams read FILE
seams chill FILE
seams chill-plus FILE
seams cages FILE [--graph seeded --complete --per-atom OUT]
seams cages FILE --signature SPEC [--guest-types T,U --guest-radius R]
seams fingerprint FILE [--hops N --library FILE[,FILE...] --emit-library LABEL --colour-types --per-atom OUT]
seams ions FILE --ion-types I,J [--ion-cutoff ANGSTROM --per-atom OUT]
seams rdf FILE [--types I,J --cutoff ANGSTROM --bins N]
seams cn FILE [--types I,J --cutoff ANGSTROM]
seams hbonds FILE [--type I --htype I --hdist ANGSTROM --hangle DEG --donors]
seams pairs FILE --site SPEC
seams density-z FILE [--type I --axis XYZ --bins N]
seams domains FILE --site SPEC [--subset polar|apolar]

chill_plus is an accepted alias of chill-plus. Ice scores (chill, chill-plus, cages, ions) refuse every --family except waterIce.

Worked flags

seams read input/traj/exampleTraj.lammpstrj
seams chill-plus input/traj/exampleTraj.lammpstrj --cutoff 3.5 --type 2
seams cages input/traj/mW_cubic.lammpstrj --type 1 --graph seeded --complete
seams fingerprint mW_cubic.lammpstrj --type 1 --hops 2 --emit-library Ic
seams ions brine.lammpstrj --type 1 --ion-types 3,4 --ion-cutoff 3.5
seams rdf dump.lammpstrj --types 1,2 --cutoff 10 --bins 100
seams cn dump.lammpstrj --types 1,2 --cutoff 4.5
seams cn dump.lammpstrj --ions --site '1=cationHead,2=anion' --cutoff 6.0
seams hbonds dump.lammpstrj --type 2 --htype 1
seams pairs dump.lammpstrj --site '1=cationHead,2=anion'
seams density-z dump.lammpstrj --type 0 --axis z
seams domains dump.lammpstrj --site '1=cationHead,2=anion' --subset polar

cn --ions is cage degree on ionCloud and needs --site. That is not seams ions. pairs is the mutual-nearest contact-pair count. domains is the largest polar or apolar Stoddard component.

--type 0 on read / chill / cages guesses oxygen (type 2, then type 1). density-z treats 0 as every atom.

Book: seams CLI.