Changelog

v3.1.1 (2026-04)

All changes in this release by @Yi5817.

Fixed

  • Fix NaN bug in cgenarris crystal generation (3366fbb).

Changed

  • Add git-tag-based release versioning with setuptools-scm.

Documentation

  • Improve installation documentation (45237f6).

CI / Chores

  • Add GitHub Actions release workflow with release-drafter and GitHub Release asset uploads.

v3.1.0 (2026-03)

All changes in this release by @Yi5817.

Highlights

Genarris v3.1.0 brings GPU-accelerated batch optimization, a full Sphinx documentation site, serial DFT execution, YAML configuration migration, and bug fixes.

Added

  • AIMNet2 energy – AIMNet2 MLIP support for molecular crystal energies (9082ef6, c92063d).

  • Task registry – centralised TaskSpec-based task registration with instance IDs, replacing ad-hoc task dispatch (74f5247, e884843).

  • GPU worker/feeder pattern – asynchronous GPU worker pool for parallel MLIP energy and force evaluations (f7a65ad).

  • Batch optimization with GPU mode – GPU worker/feeder support during geometry optimization (d6b77cb).

  • Serial DFT mode – run DFT calculations serially when MPI parallelism is not available or desired (9906837).

  • Deduplication task – duplicate crystal removal task integrated into the workflow pipeline (7effd58, 9958b69).

  • AP clustering worker limit – max_ap_workers parameter to cap Affinity Propagation memory usage (eb9cf84).

  • Feature descriptor cleanup – automatic removal of intermediate feature descriptor files after clustering (0883c8c).

  • Random seed support – reproducible runs via a configurable random seed (5130987).

  • Sphinx documentation site – full documentation with MyST Markdown, Furo theme, configuration reference, API docs, quickstart guide, case studies, and GitHub Pages deployment (dc0ff5e, a25b9fa).

  • Additional geometry optimization tasks registered in the task system (1274390).

Changed

  • JSON → YAML configuration – migrated all configuration from JSON to YAML with updated package data inclusion (dcc0c67).

  • Logger refactor – updated logger throughout the codebase (9c4335d).

  • StructureMatcher settings – updated tolerance settings for more reliable structure matching (fdd3756).

  • Python version requirement – bumped minimum Python to 3.10 (eb35644).

  • MC volume estimator – performance-optimized Monte Carlo volume estimation (a684c0d).

  • Symmetry rigid press tolerance – tolerance value for symmetry-aware rigid body pressure optimization (c11a002).

  • Project metadata – updated pyproject.toml dependencies, build requirements, and license format (a9e24f1, 9f32eec).

  • License – updated LICENSE file (301a8ea, 34150e6).

Fixed

  • SWIG ≥ 4.4 compatibility – avoid compilation errors from wrapper files generated with newer SWIG versions (81b4392, fd6bf13).

  • mpi4py headers – include mpi4py headers in SWIG options for correct compilation (d7333c0).

  • Hydrogen bond acceptor – recognise R-O-H oxygen as a hydrogen bond acceptor (f7b2066).

  • Unit cell volume std key – correct configuration key for unit cell volume standard deviation (409740a).

  • AP clustering default – remove incorrect default value for clusters_tol in APCluster (9d39b60).

  • Structure writing – improved logic for writing optimised structures to disk (6ff3a7c).

  • Moment of inertia – correct axis handling in moment of inertia calculations (8c2c82d).

  • Experimental structure check – validate experimental reference structure in config before use (97dd275).

  • Docstring indentation – fix indentation issues in module docstrings (ec8b174).

  • cgenarris docs inclusion – remove docs inclusion for cgenarris that caused build errors (43d61d9).

Documentation

  • Comprehensive configuration reference (master, workflow, energy, generation, clustering, selection, descriptor, optimisers, rigid press, deduplication, experimental) (a25b9fa).

  • DFT execution modes documentation (serial vs MPI-parallel) (7491e6d).

  • Installation instructions including pybind11 and mpi4py (92ad061, 2e2647e, 61ff130).

  • Quickstart guide (498b1cc).

  • Citation and references pages (b37fb57, 8240237, b38892f).

  • Updated README with badges, features, and usage instructions (146f18c, 30fbcb7, a0524b2, fac45d0).

CI / Chores

  • GitHub Pages deployment workflow for documentation (98e1bf2, 3f87de3).

  • Updated cgenarris submodule (d160851, 6f9fd47).

v3.0.0 (2025-07)

All changes in this release by @Yi5817.

Highlights

Initial public release of Genarris v3.

Added

  • CLI & workflow orchestration – gnrs CLI entry point with YAML-driven workflow engine for end-to-end crystal structure prediction (35a9e2a, 4960fb8).

  • UMA energy – Universal Materials Accelerator (UMA) MLIP support (cf23bb6, 43cab58).

  • pandas<=2.3 as optional dependency (cddeb16).

  • Black linting GitHub Action (89599c5).

Changed

  • Simplified MPI compiler detection and build configuration (350a4e3).

  • Updated pyproject.toml dependencies and build setup (a279dd4, 10663ec).

  • Removed requirements.txt in favour of pyproject.toml (7a37709).

Fixed

  • Unified logger name to genarris (db6f382).

  • Safe get with False default for debug_mode (0b17a0a).