Software

Software tools developed in our group

Our group develops and maintains several software suites to support our research goals.
All of these tools are made open-source for the benefit of the entire chemical kinetics scientific community. We hope you find them useful.

 

ARC logo
Automated Rate Calculator (ARC)

ARC’s mission is to provide the kinetics community with a well-documented and extensible code base for automatically calculating species thermochemistry and reaction rate coefficients. ARC has many advanced features, yet at its core it is simple: It accepts 2D graph representations of chemical species (i.e., SMILES, InChI, or RMG’s adjacency list), and automatically executes, tracks, and processes relevant electronic structure calculation jobs on user-defined server\s. The principal outputs of ARC are thermodynamic properties (H, S, Cp) and high-pressure limit kinetic rate coefficients of species and reactions of interest.

Source code: https://github.com/ReactionMechanismGenerator/ARC
Documentation: https://reactionmechanismgenerator.github.io/ARC

 

T3

The Tandem Tool (T3)

T3 is a tool for automatically generating refined kinetic models.

The key features are:

  • Convenient: A single universal input file with an equivalent API, controlling all engines.
  • Flexible: Supports all features of RMG and ARC, while maintaining reasonable defaults for simplicity.
  • Structured: All outputs from all iterations are organized in an intuitive folder tree.
  • Easy: Designed to be easy to use and learn.
  • Robust: Captures lower-level exceptions, attempts to troubleshoot.
  • Restartable: Has a convenient restart feature that’s being triggered by identifying existing iteration outputs.

Principal workflow:

T3 circle

Source code: https://github.com/ReactionMechanismGenerator/T3
Documentation: https://reactionmechanismgenerator.github.io/T3

 

TCKDB
Theoretical Chemical Kinetics Database (TCKDB)

The goal of the TCKDB project is to establish a standardized open infrastructure for conveniently storing and attaining theoretical chemical information of relevance for kinetic computations. The TCKDB project aims to (1) create a community-accepted standard for storing electronic structure calculations relevant to chemical kinetic modeling, and (2) allow sharing of and free access to such data for direct use in kinetic computations and modeling. Ultimately, the TCKDB will facilitate efficient workflows by negating the need for repeating the same computational tasks, giving access to fully detailed computations. As a by-product, it will facilitate big-data queries for either direct research or algorithm training purposes (e.g., learning conformational and transition state geometries). Finally, it would also serve as a citable repository that could become the standard when publishing kinetic-relevant electronic structure computations.

This project, lead by our group, is done in collaboration with researchers from the following institutions:

– Argonne National Laboratories
– Georgia University
– Ghent University
– Massachusetts Institute of Technology
– Molecular Scientific Software Institute
– National Renewable Energy Laboratory
– Northeastern University
– Polytechnic University of Milan
– U.S. Army Research Laboratories

Source code: https://github.com/tckdb/TCKDB
Documentation: https://tckdb.github.io/TCKDB/

 

Software tools our group actively contributes to

 

rmg image
Reaction Mechanism Generator (RMG)

RMG is an automatic chemical reaction mechanism generator that constructs kinetic models composed of elementary chemical reaction steps using a general understanding of how molecules react.

Source code (software): https://github.com/ReactionMechanismGenerator/RMG-Py
Source code (database): https://github.com/ReactionMechanismGenerator/RMG-database
Documentation: http://reactionmechanismgenerator.github.io/RMG-Py/users/rmg/index.html
Interactive website: https://rmg.mit.edu/

 

Arkane

Automated Reaction Kinetics and Network Exploration (Arkane)

Arkane is a Statistical Mechanics, Thermodynamics, Transition State Theory, and Master Equation Software. Arkane is used for calculating thermodynamic properties, high-pressure limit rate coefficients, and pressure-dependent rate coefficients from electronic structure computations. It can also explore potential energy surfaces. Arkane is a root module of RMG and they share functionalities, yet it also functions as a standalone software.

Source code: https://github.com/ReactionMechanismGenerator/RMG-Py/tree/master/arkane
Documentation: http://reactionmechanismgenerator.github.io/RMG-Py/users/arkane/index.html