PydSEAMSlib

Python bindings for the d-SEAMS C++ engine (seams-core).

This repository is the Python package pydseams. The C++ engine and seams CLI live in seams-core. Lua/Fennel is dseams in yodaStruct. Neighbour search is linkcell. Do not grow a second engine here. import pydseamslib still works.

pip install pydseamslib
pip install 'pydseamslib[ase]'      # ASE Atoms
pip install 'pydseamslib[solvis]'   # solvis / PyVista

Nix flake:

nix build
nix develop

Docs: docs/orgmode/ (ox-rst) and docs/source/ (Shibuya). Site: https://d-seams.github.io/PydSEAMSlib/.

import pydseams as ds

frame = ds.read("water.lammpstrj")   # also .xyz, .pdb, .gro, .dcd, .con
print(frame.chill_plus())
print(frame.cages())
print(frame.density(bins=100, axis="z"))

mixed = ds.read("ions.lammpstrj", all_atoms=True, atom_type=1)
sites = ds.yoda.parseSiteSpec("1=polar,2=apolar")
print(mixed.domain(sites, ds.yoda.Kind.polar))

ions = ds.yoda.parseSiteSpec("1=cationHead,2=anion")
print(mixed.pairs(ions))

frame = ds.from_ase(atoms)
atoms = frame.to_ase()
system = frame.to_solvis()           # optional extra

ds.read picks the engine reader from the suffix. yoda is the compiled surface. Helpers (Frame, io, ASE, solvis) stay in Python. _core and cyoda still name the same module.

Frame.density, Frame.pairs, and Frame.domain expose the same site-resolved density, ion-pair, and connected-domain analyses as the CLI. Use ds.read(..., all_atoms=True) when a site analysis needs every LAMMPS type; atom_type still selects the species used by neighbour and ice methods. ASE adapters accept nonsingular cells periodic in all three directions and preserve cell orientation and displacement on roundtrip. Hydrogen donors use an ASE mol-id array when present and periodic nearest-atom ownership otherwise. All-atom ASE imports (select=None) use cutoff bonding; hydrogen-bond topology requires a heavy-atom selection such as select="O".

Cutoff, frame, and k follow the same twelve-factor table as seams: SEAMS_CONFIG or ./seams.env, then the environment, then the function argument. pydseams.config is the reader.

Primary author: Ruhila S. The project started as PSF GSoC 2023 (pyseams).

Requires Python 3.12+. Wheels are built against the CPython 3.12 stable ABI (one abi3 wheel per platform). Free-threaded CPython has no limited ABI and is not a target.

License

MIT.