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.

Released versions live in CHANGELOG.md (Keep a Changelog). Unreleased notes are files under changelog.d/. The cut is towncrier build --version X.Y.Z.

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. A file with more than one element symbol gives each symbol its own c_type, and the cutoff graph contains like and unlike pairs. Pass periodic=False for a molecule so pairs are not wrapped across the bounding span. atom_type is the species single-type ice routines still receive. pydseams.band.band_rows names the pairs that enter or leave that graph from one frame to the next. 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 3.11+. CPython 3.11 has a version-specific wheel. Python 3.12 and newer use 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.