Repositories

d-SEAMS 2 is not a monolith. The classifier is one C++ library. Neighbour search is linkcell. Each language ships its own package against that library.

repository

product

role

seams-core

libyodaLib, seams

C++ engine and CLI

PydSEAMSlib

pydseams

Python helpers on yoda

yodaStruct

dseams

Lua/Fennel library

linkcell

lc_*

Periodic linked-cell k-nearest neighbours

The front ends take seams-core as a Meson subproject (static library) or as a flake input. They do not vendor a second engine.

A language binding that lived in the engine tree would force every C++ user to take that language’s toolchain, and every wheel or rock to rebuild the same library. Splitting the repos keeps the Catch2 suite, the seams CLI, and the optional backends on one Meson project, while Python and Lua version and release on their own schedules.

        flowchart TB
  subgraph engine["seams-core"]
    LIB[libyodaLib]
    CLI[seams CLI]
  end
  subgraph fronts["Front ends"]
    PY[pydseams Frame]
    LUA["require(\"dseams\")"]
  end
  LC[linkcell]
  DUMP[LAMMPS / XYZ / chemfiles / con] --> LIB
  LC --> LIB
  LIB --> CLI
  LIB --> PY
  LIB --> LUA

Why yoda

The 2020 product was a single executable named yodaStruct. That binary is gone. The compiled C++ surface kept the name so existing registrations stay findable: the Python module is pydseams.yoda (_core and cyoda are aliases of yoda). Lua helpers are require("dseams"); require("yoda") still resolves to that table. There is no yodaStruct executable in any of the three repositories.

Builds

  • Nix flake: nix build / nix develop in each repo. Optional wrap-git backends stay off unless nixpkgs already provides them.

  • pixi: locked conda-forge toolchain in seams-core.

  • Wheels: cibuildwheel on PydSEAMSlib, CPython 3.12 limited ABI.

The 2020 CMake Nix derivation of yodaStruct is gone. -Dwith_python=true and -Dwith_lua=enabled are Meson errors that name PydSEAMSlib and yodaStruct.

Ice score and the CHILL+ star

Two classifiers live in libyodaLib. They answer different questions and they do not imply each other. The argument is CHILL+ versus cages.

seams cages --graph chooses the bond graph the six-rings are found on: cutoff, knn, knn-union, or seeded (CLI default). On a perfect cubic crystal the four graphs coincide. On a mixed nucleation dump they do not.