RMG User’s Guide

For any questions related to RMG and its usage and installation, please post an issue at https://github.com/ReactionMechanismGenerator/RMG-Py/issues and the RMG developers will get back to you as soon as we can. You can also search for your problem on the issues page to see if there are already solutions in development. Alternatively, you can email us at rmg_dev@mit.edu.

• 1. Introduction
  • 1.1. License
• 2. Overview of Features
• 3. Installation
  • 3.1. Recommended Install: Docker
  • 3.2. Alternative Install: Binary Installation Using Anaconda
  • 3.3. Developer Install: Installation from Source
  • 3.4. Archive of Unsupported Installation Methods
  • 3.5. Dependencies
• 4. Creating Input Files
  • 4.1. Syntax
  • 4.2. Datasources
  • 4.3. List of species
  • 4.4. Forbidden Structures
  • 4.5. Reaction System
  • 4.6. Simulator Tolerances
  • 4.7. Model Tolerances
  • 4.8. On the fly Quantum Calculations
  • 4.9. Machine Learning-based Thermo Estimation
  • 4.10. Pressure Dependence
  • 4.11. Uncertainty Analysis
  • 4.12. Miscellaneous Options
  • 4.13. Species Constraints
  • 4.14. Staging
  • 4.15. Restarting from a Seed Mechanism
• 5. Example Input Files
  • 5.1. Ethane pyrolysis (Minimal)
  • 5.2. 1,3-hexadiene pyrolysis
  • 5.3. Commented input file
• 6. Running a Job
  • 6.1. Input flags
  • 6.2. Details on the multiprocessing implementation
  • 6.3. Details on profiling RMG jobs
• 7. Analyzing the Output Files
  • 7.1. The Chemkin Folder
  • 7.2. The Species Folder
  • 7.3. The Pdep Folder
  • 7.4. The Solver Folder
• 8. Guidelines for Building a Model
  • 8.1. Start with a good seed mechanism
  • 8.2. Setting up the right termination criterion
  • 8.3. Restricting the number of carbon atoms, oxygen atoms, and radical sites per species
  • 8.4. Adding key species into the initial condition file
  • 8.5. Starting with a single molecule when generating a model for a mixture
• 9. Standalone Modules
  • 9.1. HTML Chemkin Output
  • 9.2. Model Comparison
  • 9.3. Merging Models
  • 9.4. Generate Reactions
  • 9.5. Simulation and Sensitivity/Uncertainty Analysis
  • 9.6. Generating Flux Diagrams
  • 9.7. Thermo Estimation Module
  • 9.8. Database Scripts
  • 9.9. Standardize Model Species Names
  • 9.10. Isotopes
• 10. Species Representation
  • 10.1. Representing Oxygen
• 11. Group Representation
• 12. Databases
  • 12.1. Introduction
  • 12.2. Thermo Database
  • 12.3. Kinetics Database
  • 12.4. Database Modification
• 13. Thermochemistry Estimation
  • 13.1. Species thermochemistry libraries
  • 13.2. Group contribution methods
  • 13.3. On-the-fly Quantum-chemical calculation of Thermochemical Properties (QMTP)
  • 13.4. Symmetry and Chirality
  • 13.5. References
• 14. Kinetics Estimation
  • 14.1. Priority of Kinetic Databases
  • 14.2. Kinetic Families
• 15. Liquid Phase Systems
  • 15.1. Equation of state
  • 15.2. Solvation thermochemistry
  • 15.3. Diffusion-limited kinetics
  • 15.4. Example liquid-phase input file, no constant species
  • 15.5. Example liquid-phase input file, with constant species
• 16. Heterogeneous Catalysis Systems and Surface Reactions
  • 16.1. Catalyst properties
  • 16.2. Reactor specifications
  • 16.3. Thermochemistry
  • 16.4. Reactions and kinetics
  • 16.5. Coverage Dependence
  • 16.6. Examples
• 17. Frequently Asked Questions
  • 17.1. Introduction
  • 17.2. Installing RMG
  • 17.3. Running RMG
  • 17.4. Miscellaneous
• 18. Release Notes
  • 18.1. RMG-Py Version 3.2.0
  • 18.2. RMG-Database Version 3.2.0
  • 18.3. RMG-Py Version 3.1.0
  • 18.4. RMG-Database Version 3.1.0
  • 18.5. RMG-Py Version 3.0.0
  • 18.6. RMG-database Version 3.0.0
  • 18.7. RMG-Py Version 2.4.1
  • 18.8. RMG-Py Version 2.4.0
  • 18.9. RMG-database Version 2.4.0
  • 18.10. RMG-Py Version 2.3.0
  • 18.11. RMG-database Version 2.3.0
  • 18.12. RMG-Py Version 2.2.1
  • 18.13. RMG-Py Version 2.2.0
  • 18.14. RMG-database Version 2.2.0
  • 18.15. RMG-Py Version 2.1.9
  • 18.16. RMG-database Version 2.1.9
  • 18.17. RMG-Py Version 2.1.8
  • 18.18. RMG-database Version 2.1.8
  • 18.19. RMG-Py Version 2.1.7
  • 18.20. RMG-database Version 2.1.7
  • 18.21. RMG-Py Version 2.1.6
  • 18.22. RMG-database Version 2.1.6
  • 18.23. RMG-Py Version 2.1.5
  • 18.24. RMG-database Version 2.1.5
  • 18.25. RMG-Py Version 2.1.4
  • 18.26. RMG-database Version 2.1.4
  • 18.27. RMG-Py Version 2.1.3
  • 18.28. RMG-database Version 2.1.3
  • 18.29. RMG-Py Version 2.1.2
  • 18.30. RMG-database Version 2.1.2
  • 18.31. RMG-Py Version 2.1.1
  • 18.32. RMG-database Version 2.1.1
  • 18.33. RMG-Py Version 2.1.0
  • 18.34. RMG-database Version 2.1.0
  • 18.35. RMG-Py Version 2.0.0
  • 18.36. RMG-database Version 2.0.0
  • 18.37. RMG-Py Version 1.0.4
  • 18.38. RMG-Py Version 1.0.3
  • 18.39. RMG-Py Version 1.0.2
  • 18.40. RMG-database Version 1.0.2
• 19. Credits
• 20. How to Cite

• Index

• Module Index

• Search Page