CODES
KinBot allows the user go from a single structure all the way to a master equation.
Primary developers: Judit Zádor, Ruben Van de Vijver, Carles Martí
To read more about it:
Zádor, J., Martí, C., Van de Vijver, R., Johansen, S. L., Yang, Y., Michelsen, H. A., Najm, H. N., Automated reaction kinetics of gas-phase organic molecules. Journal of Physical Chemistry A Feature Article, 2023 127 565–588. https://doi.org/10.1021/acs.jpca.2c06558
Van de Vijver, R., Zádor, J.: KinBot: Automated stationary point search on potential energy surfaces. Computer Physics Communications, 2020 248 106947. https://doi.org/10.1016/j.cpc.2019.106947
Pynta allows the user go from a simpe reaction representation of a surface reaction all the way to rate coefficients to be used in a microkinetic model.
Primary developers: Matthew S. Johnson, Shinae Kim, Maciej Gierada, Eric D. Hermes
To read more about it:
Johnson, M. S., Gierada, M., Hermes, E. D., Bross, D. H., Sargsyan, K., Najm, H. N., Zádor, J.: Pynta - An automated workflow for calculation of surface and gas-surface kinetics. J. Chem. Inf. Model., 2023 63 5153–5168. https://doi.org/10.1021/acs.jcim.3c00948
Johnson, M. S., Bross, D. H., Zádor, J.: Resolving the coverage dependence of surface reaction kinetics with machine learning and automated quantum chemistry workflows. J. Phys. Chem. C, 2025 129 7, 3469–3482. https://doi.org/10.1021/acs.jpcc.4c06636
Sella is a utility to find saddle points in molecular systems and for materials. It is also a good minimizer, can follow IRCs, and has a range of constrained optimization features.
Primary developer: Eric D. Hermes
To read more about it:
Hermes, E. D., Sagsyan, K., Najm, H. N., Zádor, J.: Sella, an open-source automation-friendly molecular saddle point optimizer. Journal of Chemical Theory and Computation, 2022 18 6974–6988. https://pubs.acs.org/doi/10.1021/acs.jctc.2c00395
Hermes, E. D., Sagsyan, K., Najm, H. N., Zádor, J.: A geodesic approach to internal coordinate optimization. The Journal of Chemical Physics, 2021 155 094105. https://doi.org/10.1063/5.0060146
Hermes, E., Sargsyan, K., Najm, H. N., Zádor, J.: Accelerated saddle point refinement through full exploitation of partial Hessian diagonalization. Journal of Chemical Theory and Computation, 2019 15 6536-6549. https://doi.org/10.1021/acs.jctc.9b00869
PESViewer, originally developed by Ruben Van de Vijver, is a utility to visualize reaction pathways on complex potential energy surfaces. It works as a postprocessor for KinBot.
Primary developers: Ruben Van de Vijver, Judit Zádor, Carles Martí
Visit the github site to see examples.
