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
• Generated files
  • Web page
  • Data file
  • Species file
  • Molecule file
  • Route file
  • Reaction files
  • Reaction matrix file
  • Reaction network
• 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
• Python interface
  • Running the ReacNetGenerator
  • Calculate rate constants