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Title: KinBot: Automated stationary point search on potential energy surfaces

Abstract

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 productsmore » 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.« less

Authors:
 [1];  [1]
  1. Sandia National Lab. (SNL-CA), Livermore, CA (United States)
Publication Date:
Research Org.:
Sandia National Lab. (SNL-CA), Livermore, CA (United States)
Sponsoring Org.:
USDOE National Nuclear Security Administration (NNSA)
OSTI Identifier:
1574477
Report Number(s):
SAND-2019-13005J
Journal ID: ISSN 0010-4655; 680834
Grant/Contract Number:  
AC04-94AL85000; NA0003525
Resource Type:
Accepted Manuscript
Journal Name:
Computer Physics Communications
Additional Journal Information:
Journal Name: Computer Physics Communications; Journal ID: ISSN 0010-4655
Publisher:
Elsevier
Country of Publication:
United States
Language:
English
Subject:
Automation; Potential energy surface; Temperature and pressure dependent rate; coefficients

Citation Formats

Van de Vijver, Ruben, and Zádor, Judit. KinBot: Automated stationary point search on potential energy surfaces. United States: N. p., 2019. Web. doi:10.1016/j.cpc.2019.106947.
Van de Vijver, Ruben, & Zádor, Judit. KinBot: Automated stationary point search on potential energy surfaces. United States. doi:10.1016/j.cpc.2019.106947.
Van de Vijver, Ruben, and Zádor, Judit. Fri . "KinBot: Automated stationary point search on potential energy surfaces". United States. doi:10.1016/j.cpc.2019.106947.
@article{osti_1574477,
title = {KinBot: Automated stationary point search on potential energy surfaces},
author = {Van de Vijver, Ruben and Zádor, Judit},
abstractNote = {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},
journal = {Computer Physics Communications},
number = ,
volume = ,
place = {United States},
year = {2019},
month = {10}
}

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This content will become publicly available on October 4, 2020
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