FAQ

How do I install the engine?

Install the engine. pixi or nix build.

Where is Python?

PydSEAMSlib. pip install pydseamslib. import pydseams. import pydseamslib is an alias. The compiled module is yoda.

Where is Lua / Fennel?

yodaStruct. require("dseams"). require("yoda") still resolves to that table. There is no yodaStruct executable.

Why do CHILL+ and cages disagree?

They answer different questions. CHILL+ versus cages.

What does --graph seeded mean?

Mutual four-nearest seeds, union completions. It is the CLI default for cages only.

Which --type do I pass?

Mixed water dumps in this tree: type 2 oxygen. Single-site mW dumps: type 1. Default 0 guesses type 2 then type 1. Any other mixed-type dump (ionic liquid, solvent plus solute) needs the integer type of the species you want; see Ionic-liquid dumps.

How does a sheared dump box work?

The dump stores bound spans plus optional xy, xz, yz. Those spans are not edge lengths. The engine recovers H. See Sheared cells.

Why is chemfiles disabled on nix build?

chemfiles is not in the flake closure. The default pixi lock enables it.

How do I turn colors off?

NO_COLOR. FORCE_COLOR forces them on.

Does seams walk a trajectory?

Yes: --frame N --last M --jobs J via forEachLammpsFrame. --jobs 1 is serial.

How do I view a classified dump?

solvis, through pydseamslib[solvis] (frame.to_solvis()). That is the viewer for this release. See View a classified frame. OVITO still opens the LAMMPS text the engine writes; it is not the documented path.

How do I cite this?

Citation. The preferred citation is the 2020 JCIM paper.