User Guide

Getted Started

• Installation
  • Install via conda
  • Install via pip
  • Install via uv
  • Docker images
• Supported trajectory formats
  • LAMMPS dump files
  • XYZ files
  • LAMMPS ReaxFF bonds file
• Analysis
  • Oversized connected components
• Generated files
  • Web page
  • Data file
  • Species file
  • Molecule file
  • Molecule timeline file
  • Route file
  • Reaction files
  • Reaction event file
  • Reaction matrix file
  • Reaction network
• Optional HDF5 timeline (schema 1.0)
  • Why validation is part of the format
  • Meaning of time and identity
  • Versioned file contract
  • Compact Python reading
  • Validation and semantic comparison
  • Publication and resource behavior
• GUI version
• FAQ
  • Can ReacNetGenerator process my trajectory?
  • Out of memory (OOM)

Advanced

• Build ReacNetGenerator
  • Installing via pip
  • Building a conda package
  • Building a Docker Image
• Enable HMM filter
• Command line interface
  • Named Arguments
  • Explicit output directory
• Python interface
  • Running the ReacNetGenerator
  • Calculate rate constants
  • Explicit output directory