KinBot is a Python code that automatically characterizes kinetically important stationary points on reactive potential energy surfaces and arranges the results into a form that lends itself easily to master equation calculations. This version of KinBot tackles C, H, O and S atom containing species and unimolecular (isomerization or dissociation) reactions. KinBot iteratively changes the geometry of the reactant to obtain initial guesses for reactive saddle points defined by KinBot’s reaction types, which are then optimized by a third-party quantum chemistry package. KinBot verifies the connectivity of the saddle points with the reactant and identifies the products through intrinsic reaction coordinate calculations. Here, new calculations can be automatically spawned from the products to obtain complete potential energy surfaces. The utilities of KinBot include conformer searches, projected frequency and hindered rotor calculations, and the automatic determination of the rotational symmetry numbers. Input files for popular RRKM master equation codes are automatically built, enabling an automated workflow all the way to the calculation of pressure and temperature dependent rate coefficients. Four examples are as follows: (i) [1,3]-sigmatropic H-migration reactions of unsaturated hydrocarbons and oxygenates are calculated to assess the relative importance of suprafacial and antrafacial reactions. (ii) Saddle points on three products of gamma-valerolactone thermal decomposition are studied and compared to literature potential energy surfaces. (iii) The previously published propene+OH reaction is reproduced to show the capability of building an entire potential energy surface. (iv) All species up to C4 in the Aramco Mech 2.0 are subjected to a KinBot search.
Van de Vijver, Ruben and Zádor, Judit. "KinBot: Automated stationary point search on potential energy surfaces." Computer Physics Communications, vol. 248, no. C, Oct. 2019. https://doi.org/10.1016/j.cpc.2019.106947
Van de Vijver, Ruben, & Zádor, Judit (2019). KinBot: Automated stationary point search on potential energy surfaces. Computer Physics Communications, 248(C). https://doi.org/10.1016/j.cpc.2019.106947
Van de Vijver, Ruben, and Zádor, Judit, "KinBot: Automated stationary point search on potential energy surfaces," Computer Physics Communications 248, no. C (2019), https://doi.org/10.1016/j.cpc.2019.106947
@article{osti_1574477,
author = {Van de Vijver, Ruben and Zádor, Judit},
title = {KinBot: Automated stationary point search on potential energy surfaces},
annote = {KinBot is a Python code that automatically characterizes kinetically important stationary points on reactive potential energy surfaces and arranges the results into a form that lends itself easily to master equation calculations. This version of KinBot tackles C, H, O and S atom containing species and unimolecular (isomerization or dissociation) reactions. KinBot iteratively changes the geometry of the reactant to obtain initial guesses for reactive saddle points defined by KinBot’s reaction types, which are then optimized by a third-party quantum chemistry package. KinBot verifies the connectivity of the saddle points with the reactant and identifies the products through intrinsic reaction coordinate calculations. Here, new calculations can be automatically spawned from the products to obtain complete potential energy surfaces. The utilities of KinBot include conformer searches, projected frequency and hindered rotor calculations, and the automatic determination of the rotational symmetry numbers. Input files for popular RRKM master equation codes are automatically built, enabling an automated workflow all the way to the calculation of pressure and temperature dependent rate coefficients. Four examples are as follows: (i) [1,3]-sigmatropic H-migration reactions of unsaturated hydrocarbons and oxygenates are calculated to assess the relative importance of suprafacial and antrafacial reactions. (ii) Saddle points on three products of gamma-valerolactone thermal decomposition are studied and compared to literature potential energy surfaces. (iii) The previously published propene+OH reaction is reproduced to show the capability of building an entire potential energy surface. (iv) All species up to C4 in the Aramco Mech 2.0 are subjected to a KinBot search.},
doi = {10.1016/j.cpc.2019.106947},
url = {https://www.osti.gov/biblio/1574477},
journal = {Computer Physics Communications},
issn = {ISSN 0010-4655},
number = {C},
volume = {248},
place = {United States},
publisher = {Elsevier},
year = {2019},
month = {10}}