Changelog

All notable changes to the software will be documented in this file.

The format is based on Keep a Changelog 1.1.0, and the project adheres to Semantic Versioning 2.0.0.

Unreleased

Updated RRKM CLI to include output directory.
Updated RRKM to use new DFT directory structure.
Add source code and input details to JSON output, move main results into "results".

Extend JSON output to including the final molecule, elapsed time, reaction counts, and aliphatic-substituent analysis.

Graph-based molecular representation with GraphML loading, aliphatic site identification, and isotope scrambling and dissociation reactions.
JSON input and rate-file schemas with validation.
RRKM rate-table parsing, validation, and energy-dependent rate lookup.
Rejection-free kinetic Monte Carlo using Gillespie's direct method.
Reproducible per iteration random seeds.
Local and Slurm parallel simulation execution through run_simulation.
Bulk JSON output containing molecule configuration and elapsed time.
Rice-Rammsperger-Kassel-Marcus (RRKM) theory based reaction rate calculation tool with JSON rate-file output.
Documentation using Documenter.jl that is deployed on Codeberg Pages.