OpenMKM: An Open-Source C++ Multiscale Modeling Simulator for Homogeneous and Heterogeneous Catalytic Reactions
Date
2023-06-12
Journal Title
Journal ISSN
Volume Title
Publisher
Journal of Chemical Information and Modeling
Abstract
Microkinetic modeling is invaluable for coupling “microscale” atomistic data with “macroscale” reactor observables. We introduce an Open-source Microkinetic Modeling (OpenMKM) multiscale mean-field microkinetics modeling toolkit targeting mainly heterogeneous catalytic reactions but applies equally to homogeneous reactions. OpenMKM is a modular, object-oriented, C++ software, built on top of the robust open-source Cantera built mainly for homogeneous reactions. Reaction mechanisms can be input from human-readable files or automatic reaction generators, avoiding tedious work and errors. The governing equations are also built automatically, unlike Matlab and Python manual implementations, providing speed and error-free models. OpenMKM has built-in interfaces with numerical software, SUNDIALS, for solving ordinary differential equations and differential-algebraic equations. Users can choose various ideal reactors and energy balance options, such as isothermal, adiabatic, temperature ramp, and an experimentally measured temperature profile. OpenMKM is tightly integrated with pMuTT for thermochemistry input file generation from density functional theory (DFT), streamlining the workflow from DFT to MKM and eliminating tedious work and human errors. It is also seamlessly integrated with the RenView software for visualizing the reaction pathways and performing the reaction path or flux analysis (RPA). OpenMKM includes local sensitivity analysis (LSA) by solving the augmented system of equations or using the one-at-a-time finite difference (first or second order) method. LSA can identify not only kinetically influential reactions but also species. The software provides two techniques for large reaction mechanisms for which LSA is too expensive to run. One is the Fischer Information Matrix, which is approximate but comes at nearly zero cost. The other is a new method that we term RPA-guided LSA, which is a finite difference-based method but uses RPA to select kinetically relevant reactions instead of exploiting the entire reaction network. Users can quickly set up and conduct microkinetic simulations without writing code. The user inputs are conveniently divided into reactor setup files and thermodynamic and kinetic definition files to set up different reactors. The source code and documentation are openly available at https://github.com/VlachosGroup/openmkm.
Description
This document is the Accepted Manuscript version of a Published Work that appeared in final form in Journal of Chemical Information and Modeling , copyright © 2023 American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see https://doi.org/10.1021/acs.jcim.3c00088. This article will be embargoed until 06/12/2024.
Keywords
Microkinetic Modeling, Multiscale Modeling, Heterogeneous Catalysis, Chemical Kinetics, Reactor Modeling, C++, Open-source, Sensitivity Analysis
Citation
Medasani, Bharat, Sashank Kasiraju, and Dionisios G. Vlachos. “OpenMKM: An Open-Source C++ Multiscale Modeling Simulator for Homogeneous and Heterogeneous Catalytic Reactions.” Journal of Chemical Information and Modeling 63, no. 11 (June 12, 2023): 3377–91. https://doi.org/10.1021/acs.jcim.3c00088.