Metadata-Version: 2.1
Name: kinbot
Version: 2.1.1
Summary: Automated reaction kinetics for gas-phase species
Author-email: Judit Zádor <jzador@sandia.gov>, Ruben Vande Vijver <ruben.vandevijver@ugent.be>, Carles Martí <cmartia@sandia.gov>, Amanda Dewyer <adewyer@sandia.gov>
Maintainer-email: Judit Zádor <jzador@sandia.gov>, Carles Martí <cmartia@sandia.gov>
License: BSD 3-Clause License
        
        Copyright (c) 2018, zadorlab
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Project-URL: homepage, https://github.com/zadorlab/KinBot
Project-URL: documentation, https://github.com/zadorlab/KinBot/wiki
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: Natural Language :: English
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Topic :: Scientific/Engineering :: Chemistry
Requires-Python: >=3.8
Description-Content-Type: text/markdown
Provides-Extra: plot
License-File: LICENSE

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# KinBot: Automated reaction pathway search for gas-phase molecules

<p>
    <img src="https://raw.githubusercontent.com/zadorlab/KinBot/master/graphics/kinbot_logo_V2.png" width="220" height="240" />
</p>

## Description
This repository contains the KinBot code version 2.0,
a tool for automatically searching for reactions on the potential energy surface.

If you are using this tool in scientific publications, please reference the following publications:

* Ruben Van de Vijver, Judit Zádor: KinBot: _Automated stationary point search on potential energy surfaces_, Comp. Phys. Comm., **2019**, 248, 106947. https://doi.org/10.1016/j.cpc.2019.106947
* Judit Zádor, Carles Martí, Ruben Van de Vijver, Sommer L. Johansen, Yoona Yang, Hope A. Michelsen, Habib N. Najm: _Automated reaction kinetics of gas-phase organic species over multiwell potential energy surfaces_, J. Phys. Chem. A, **2023**, 127, 565–588. https://doi.org/10.1021/acs.jpca.2c06558

We appreciate if you send us the DOI of your published paper that used KinBot, so we can feature it here below.

## How to Install

KinBot is installed with `pip`, either from the PyPI repo or by first cloning this github repo and then install it locally.

### PyPI

    pip install kinbot

> **Note**
>  KinBot only works with Python >= 3.8.

### From Github

If you want to have the very last version of KinBot without waiting for a 
release or you want to modify KinBot acccording to your needs you can clone the project 
from github:

    git clone git@github.com:zadorlab/KinBot.git

and then, from within the KinBot directory produced after cloning, type:

    pip install .
 
> **Note**
> If you want to modify KinBot yourself it's better to fork the project 
> into your own repository and then clone it.

## How to Run
To run KinBot (which will only explore one well), make an input file (e.g. input.json) and run:

    kinbot input.json

To run a full PES search, make an input file (e.g. input.json) and run:

    pes input.json

You can find additional command line arguments in the manual. 

## Documentation
See [wiki](https://github.com/zadorlab/KinBot/wiki).

## List of files in this project
See [list](https://github.com/zadorlab/KinBot/wiki/KinBot-file-structure).

## Authors
* Judit Zádor (jzador@sandia.gov)
* Ruben Van de Vijver (Ruben.VandeVijver@UGent.be)
* Amanda Dewyer
* Carles Martí (cmartia@sandia.gov)

## Papers using KinBot
* Martí, C., Michelsen, H. A., Najm, H. N., Zádor, J.: _Comprehensive kinetics on the C7H7 potential energy surface under combustion conditions._ J. Phys. Chem. A, **2023**, ASAP. https://pubs.acs.org/doi/full/10.1021/acs.jpca.2c08035  
* 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 species over multiwell potential energy surfaces._ J. Phys. Chem. A, **2023**, 127, 565–588. https://doi.org/10.1021/acs.jpca.2c06558
* Takahashi, L., Yoshida, S., Fujima, J., Oikawa, H., Takahashi, K.: _Unveiling the reaction pathways of hydrocarbons via experiments, computations and data science._ Phys. Chem. Chem. Phys., **2022**, 24, 29841-29849. https://pubs.rsc.org/en/content/articlelanding/2022/CP/D2CP04499D
* Doner, A. C., Zádor, J., Rotavera, B.: _Stereoisomer-dependent unimolecular kinetics of 2,4-dimethyloxetane peroxy radicals._ Faraday Discuss., **2022**, 238, 295-319. https://doi.org/10.1039/D2FD00029F
* Ramasesha, K., Savee, J. D., Zádor, J., Osborn, D. L.: _A New Pathway for Intersystem Crossing: Unexpected Products in the O(3P) + Cyclopentene Reaction._ J. Phys. Chem. A, **2021**, 125 9785-9801. https://doi.org/10.1021/acs.jpca.1c05817
* Rogers, C. O, Lockwood, K. S., Nguyen, Q. L. D., Labbe, N. J.: _Diol isomer revealed as a source of methyl ketene from propionic acid unimolecular decomposition._ Int. J. Chem. Kinet., **2021**, 53, 1272–1284. https://doi.org/10.1002/kin.21532
* Lockwood, K. S., Labbe, N. J.: _Insights on keto-hydroperoxide formation from O2 addition to the beta-tetrahydrofuran radical._ Proceedings of the Combustion Institute, **2021**, 38, 1, 533. https://doi.org/10.1016/j.proci.2020.06.357
* Sheps, L., Dewyer, A. L., Demireva, M., and Zádor, J.: _Quantitative Detection of Products and Radical Intermediates in Low-Temperature Oxidation of Cyclopentane._ J. Phys. Chem. A **2021**, 125, 20, 4467. https://doi.org/10.1021/acs.jpca.1c02001
* Zhang, J., Vermeire, F., Van de Vijver, R., Herbinet, O.; Battin-Leclerc, F., Reyniers, M.-F., Van Geem, K. M.: _Detailed experimental and kinetic modeling study of 3-carene pyrolysis._ Int. J. Chem. Kinet., **2020**, 52, 785-795. https://doi.org/10.1002/kin.21400
* 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
* Joshi, S. P., Seal, P., Pekkanen, T. T., Timonen, R. S., Eskola, A. J.: _Direct Kinetic Measurements and Master Equation Modelling of the Unimolecular Decomposition of Resonantly-Stabilized CH2CHCHC(O)OCH3 Radical and an Upper Limit Determination for CH2CHCHC(O)OCH3+O2 Reaction._ Z. Phys. Chem., **2020**, 234, 1251. https://doi.org/10.1515/zpch-2020-1612


Older Version of KinBot:
* Van de Vijver, R., Van Geem, K. M., Marin, G. B., Zádor, J.: _Decomposition and isomerization of 1-pentanol radicals and the pyrolysis of 1-pentanol._ Combustion and Flame, **2018,** 196, 500. https://doi.org/10.1016/j.combustflame.2018.05.011
* Grambow, C. A., Jamal, A., Li, Y.-P., Green, W. H., Zádor, J., Suleimanov, Y. V.: _Unimolecular reaction pathways of a g-ketohydroperoxide from combined application of automated reaction discovery methods._ J. Am. Chem. Soc., 2018, 140, 1035. https://doi.org/10.1021/jacs.7b11009
* Rotavera, B., Savee, J. D., Antonov, I. O., Caravan, R. L., Sheps, L., Osborn, D. L., Zádor, J., Taatjes, C. A.: _Influence of oxygenation in cyclic hydrocarbons on chain-termination reactions from R + O2: tetrahydropyran and cyclohexane._ Proceedings of the Combustion Institute, **2017,** 36, 597. https://doi.org/10.1016/j.proci.2016.05.020
* Antonov, I. O., Zádor, J., Rotavera, B., Papajak, E., Osborn, D. L., Taatjes, C. A., Sheps, L.: _Pressure-Dependent Competition among Reaction Pathways from First- and Second-O2 Additions in the Low-Temperature Oxidation of Tetrahydrofuran._ J. Phys. Chem. A, **2016,** 120 6582. https://doi.org/10.1021/acs.jpca.6b05411
* Antonov, I. O., Kwok, J., Zádor, J., Sheps, L.: OH + 2-butene: A combined experimental and theoretical study in the 300-800 K temperature range. J. Phys. Chem. A, **2015,** 119, 7742. https://doi.org/10.1021/acs.jpca.5b01012
* Zádor, J., Miller, J.A.: _Adventures on the C3H5O potential energy surface: OH + propyne, OH + allene and related reactions._ Proceedings of the Combustion Institute, **2015,** 35, 181. https://doi.org/10.1016/j.proci.2014.05.103
* Rotavera, B., Zádor, J., Welz, O., Sheps, L., Scheer, A.M., Savee, J.D., Ali, M.A., Lee, T.S., Simmons, B.A., Osborn, D.L., Violi, A., Taatjes, C.A.: _Photoionization mass spectrometric measurements of initial reaction pathways in low-temperature oxidation of 2,5-dimethylhexane._ J. Phys. Chem. A, **2014,** 44, 10188. https://doi.org/10.1021/jp507811d

## Acknowledgement
This research was supported by the Exascale Computing Project (ECP), Project Number: 17-SC-20-SC, a collaborative effort of two DOE organizations, the Office of Science and the National Nuclear Security Administration, responsible for the planning and preparation of a capable exascale ecosystem including software, applications, hardware, advanced system engineering, and early test bed platforms to support the nation's exascale computing imperative. RVdV was also supported by the AITSTME project as part of the Predictive Theory and Modeling component of the Materials Genome Initiative. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology and Engineering Solutions of Sandia, LLC., a wholly owned subsidiary of Honeywell International, Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525. 
