GKMC – Graph Kinetic Monte Carlo

A simulator of intramolecular and unimolecular reactions within a molecule represented by a graph. Developed for the study of scrambling of PAHs as a mechanism for deuterium storage.^[1]

Features

• Rejection-free kinetic Monte Carlo using Gillespie's direct method with:
  • Graph-based molecular representation with GraphML loading, aliphatic site identification, and isotope scrambling and dissociation reactions.
  • JSON input and rate-file schemas with validation (see Preparing your simulation).
  • RRKM rate-table parsing, validation, and energy-dependent rate lookup.
  • Reproducible per iteration random seeds.
  • Local and Slurm parallel simulation execution through run_simulation.
  • JSON output including the final molecule, elapsed time, reaction counts, and aliphatic-substituent analysis.
• RRKM-theory-based reaction-rate calculation with JSON rate-file output.
• Web app to generate GraphML input files.

You can find the full changelog in the release notes.