Open Access Publications
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Open access publications by faculty, staff, postdocs, and graduate students from the Delaware Energy Institute.
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Browsing Open Access Publications by Author "Kasiraju, Sashank"
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Item CKineticsDB─An Extensible and FAIR Data Management Framework and Datahub for Multiscale Modeling in Heterogeneous Catalysis(Journal of Chemical Information and Modeling, 2023-07-24) Lambor, Siddhant M.; Kasiraju, Sashank; Vlachos, Dionisios G.A great advantage of computational research is its reproducibility and reusability. However, an enormous amount of computational research data in heterogeneous catalysis is barricaded due to logistical limitations. Sufficient provenance and characterization of data and computational environment, with uniform organization and easy accessibility, can allow the development of software tools for integration across the multiscale modeling workflow. Here, we develop the Chemical Kinetics Database, CKineticsDB, a state-of-the-art datahub for multiscale modeling, designed to be compliant with the FAIR guiding principles for scientific data management. CKineticsDB utilizes a MongoDB back-end for extensibility and adaptation to varying data formats, with a referencing-based data model to reduce redundancy in storage. We have developed a Python software program for data processing operations and with built-in features to extract data for common applications. CKineticsDB evaluates the incoming data for quality and uniformity, retains curated information from simulations, enables accurate regeneration of publication results, optimizes storage, and allows the selective retrieval of files based on domain-relevant catalyst and simulation parameters. CKineticsDB provides data from multiple scales of theory (ab initio calculations, thermochemistry, and microkinetic models) to accelerate the development of new reaction pathways, kinetic analysis of reaction mechanisms, and catalysis discovery, along with several data-driven applications. Abstract Graphic available at: https://doi.org/10.1021/acs.jcim.3c00123Item OpenMKM: An Open-Source C++ Multiscale Modeling Simulator for Homogeneous and Heterogeneous Catalytic Reactions(Journal of Chemical Information and Modeling, 2023-06-12) Medasani, Bharat; Kasiraju, Sashank; Vlachos, Dionisios G.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.