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Pynta

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pynta is an automated workflow code to enable the calculation of thermochemistry and rate coefficients for reactions involving metallic surfaces.

The pynta code is designed to automatically characterize chemical reactions relevant to heterogeneous catalysis. In particular, it spawns and processes a large number of ab initio quantum chemistry calculations to study gas-phase reactions on crystal facets. It is designed to run both on local clusters and on petascale and upcoming exascale machines.

Pynta generates initial guesses for all gas phase species and adsorbates on the surface accounting for the symmetry of the surface. These guesses are then optimized and frequencies are calculated for the unique resulting geometries. Based on the provided reaction semi-atom mappings the adsorbate are placed on the surface and perturbed in many unique ways to generate transition state guesses, the best guesses are optimized and vibrational frequencies and IRCs are generated for unique successfully optimized transition states. This information can then be processed to generate thermochemistry and rate coefficients for the adsorbates and reactions that can be used in microkinetic models.

Pynta is designed to work with the workflow code Fireworks, which provides users with significant flexiblity in running Pynta.

Pynta Documentation

Instructions on how to install and run Pynta are available in the documentation here.

Acknowledgments

Please cite our paper if you are using Pynta:

Matthew S. Johnson, Maciej Gierada, Eric D. Hermes, David H. Bross, Khachik Sargsyan, Habib N. Najm, and Judit Zádor Journal of Chemical Information and Modeling 2023 63 (16), 5153-5168 https://doi.org/10.1021/acs.jcim.3c00948

@article{Johnson2023,
   author = {Johnson, Matthew S. and Gierada, Maciej and Hermes, Eric D. and Bross, David H. and Sargsyan, Khachik and Najm, Habib N. and Zádor, Judit},
   title = {Pynta─An Automated Workflow for Calculation of Surface and Gas–Surface Kinetics},
   journal = {Journal of Chemical Information and Modeling},
   volume = {63},
   number = {16},
   pages = {5153-5168},
   note = {doi: 10.1021/acs.jcim.3c00948},
   ISSN = {1549-9596},
   DOI = {10.1021/acs.jcim.3c00948},
   url = {https://doi.org/10.1021/acs.jcim.3c00948},
   year = {2023},
   type = {Journal Article}
}

Copyright Notice

For five (5) years from 1/19/2021 the United States Government is granted for itself and others acting on its behalf a paid-up, nonexclusive, irrevocable worldwide license in this data to reproduce, prepare derivative works, and perform publicly and display publicly, by or on behalf of the Government. There is provision for the possible extension of the term of this license. Subsequent to that period or any extension granted, the United States Government is granted for itself and others acting on its behalf a paid-up, nonexclusive, irrevocable worldwide license in this data to reproduce, prepare derivative works, distribute copies to the public, perform publicly and display publicly, and to permit others to do so. The specific term of the license can be identified by inquiry made to National Technology and Engineering Solutions of Sandia, LLC or DOE.

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Any licensee of this software has the obligation and responsibility to abide by the applicable export control laws, regulations, and general prohibitions relating to the export of technical data. Failure to obtain an export control license or other authority from the Government may result in criminal liability under U.S. laws.

License Notice

Copyright 2021 National Technology & Engineering Solutions of Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with NTESS, the U.S. Government retains certain rights in this software.