Changelog

The C++ engine is this repository. Python is pydseams (PydSEAMSlib). Lua is require("dseams") (yodaStruct).

Unreleased

The C++ API in the book is Doxygen via doxyrest (api/index), the same path as rgpot. The hand function tables are gone.

2.2.5

subprojects/linkcell.wrap is v0.2.4. A static libyodaLib.a no longer passes liblinkcell.so to ar. Wrap consumers link the static archive. Dump doubles parse with strtod on Apple libc++.

2.2.4

Periodic k-nearest graphs via d-SEAMS/linkcell v0.2.2. kNearestNeighbourList / kNearestNeighbourPair write packed n*k nominations. Mutual and union come from one walk. The LAMMPS dump box is bound spans plus xy, xz, yz; periodicDistSq recovers H. Empty frames no longer abort the walker.

Docs orgmode covers the seams CLI, the Nix flake, and the three-repo split.

2.2.3

The seams CLI uses Argum. Help, errors, ice-type counts, and --features are colorized. NO_COLOR turns the colors off.

2.2.2

The compiled Python surface is pydseams.yoda. _core remains an alias.

2.2.1

• Flake package for libyodaLib and seams (Meson, not the CMake-era yodaStruct derivation).

• Live LAMMPS dump session (nLammpsFrames, forEachLammpsFrame): seams --frame N --last M --jobs J.

• BondGraph at runtime: cutoff, knn, knn-union. seams cages --graph adds seeded.

• LAMMPS readers bind xu~/~yu~/~zu and xs~/~ys~/~zs when x y z are absent.

2.2.0

seams CLI: read, chill, chill-plus, cages. This is the engine command line.

2.1.2

Removed CMake-era Nix entrypoints that still named the product yodaStruct. Build with pixi or nix build.

2.1.1

CHILL interfacial walk uses the same four-neighbour star as c_ij. Atoms without four recorded bonds go to water. Seeded affiliation floods HC and DDC separately.

2.1.0

The C++ engine is this repository. Front ends are not.

• The yodaStruct Lua/Fennel CLI moved to https://github.com/d-SEAMS/yodaStruct . -Dwith_lua=enabled is an error that names that repository.

• Python bindings remain in https://github.com/d-SEAMS/PydSEAMSlib (moved in 2.0.1).

• C++ getCorrel / getIceType family and reclassifyWater return void.

2.0.1

Python bindings moved to PydSEAMSlib. This repository is the C++ engine.

2.0.0

Meson replaces CMake. License is MIT. Optional vesin neighbour lists, Highway SIMD, chemfiles, and readcon-core. Catch2 suite for the engine.

1.0.0

Initial release. See Goswami et al., J. Chem. Inf. Model. 2020, 60, 2169-2177.