Quickstart

Install

pip install pydseams
pip install 'pydseams[ase]'
pip install 'pydseams[solvis]'

pydseams is the package. The [ase] extra pulls ASE for from_ase / to_ase. The [solvis] extra pulls ASE plus solvis-tools for to_solvis.

With pixi, add the PyPI package:

pixi add --pypi pydseams

Requires Python 3.12+. Wheels are the CPython 3.12 limited ABI (one abi3 wheel per platform). A wheel already links the engine; do not compile yoda to use the package.

import pydseamslib is a compatibility alias of pydseams.

From a PydSEAMSlib checkout:

nix build
nix develop

nix build produces the pydseams package. nix develop is the dev shell (pytest, hypothesis).

The full extra table is in the Install pydseams how-to.

Classify a frame

import pydseams as ds

frame = ds.read("water.lammpstrj")   # also .xyz, .pdb, .gro, .dcd, .con
print(frame.chill_plus())
print(frame.cages())

ds.read picks the engine reader from the suffix and returns a Frame. chill_plus and cages do not write files.

yoda is the compiled module. _core and cyoda are aliases of yoda. Helpers (Frame, read, ASE, solvis) stay in Python.

ASE Atoms: ds.from_ase(atoms). See the Classify ASE Atoms how-to. A worked mixed ice-water dump is the Tutorial: Classify ice tutorial.