PydSEAMSlib

pydseams

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())

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.

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.

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MIT.

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pydseamslib 2.6.0

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