kinbot 2.2.2__tar.gz → 2.2.4__tar.gz

kinbot-2.2.4/KinBot.egg-info/PKG-INFO

@@ -0,0 +1,191 @@
+Metadata-Version: 2.2
+Name: kinbot
+Version: 2.2.4
+Summary: Automated reaction kinetics for gas-phase species
+Author-email: Judit Zádor <jzador@sandia.gov>, Ruben Van de Vijver <ruben.vandevijver@ugent.be>, Carles Martí <cmartia@sandia.gov>, Clément Soulié <csoulie@sandia.gov>, Amanda Dewyer <adewyer@sandia.gov>
+Maintainer-email: Judit Zádor <jzador@sandia.gov>, Clément Soulié <csoulie@sandia.gov>
+License: BSD 3-Clause License
+        
+        Copyright (c) 2018, 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
+        
+        Redistribution and use in source and binary forms, with or without
+        modification, are permitted provided that the following conditions are met:
+        
+        * Redistributions of source code must retain the above copyright notice, this
+          list of conditions and the following disclaimer.
+        
+        * Redistributions in binary form must reproduce the above copyright notice,
+          this list of conditions and the following disclaimer in the documentation
+          and/or other materials provided with the distribution.
+        
+        * Neither the name of the copyright holder nor the names of its
+          contributors may be used to endorse or promote products derived from
+          this software without specific prior written permission.
+        
+        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+        AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+        IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+        DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+        FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+        DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+        SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+        CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+        OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+        OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+        
+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 :: 3.10
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.17.0
+Requires-Dist: ase<3.22,>=3.19
+Requires-Dist: networkx
+Requires-Dist: rmsd>=1.5.1
+Requires-Dist: sella
+Provides-Extra: plot
+Requires-Dist: matplotlib; extra == "plot"
+Requires-Dist: pyvis; extra == "plot"
+Requires-Dist: rdkit; extra == "plot"
+
+[![Gitter chat](https://badges.gitter.im/gitterHQ/gitter.png)](https://gitter.im/zadorlab/KinBot)
+
+# KinBot: Automated Reaction Kinetics of Gas-Phase Organic Species over Multiwell Potential Energy Surfaces
+
+<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 2.2.1,
+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
+```
+@article{Vijver2020,
+   author = {Van de Vijver, Ruben and Z\'ador, Judit},
+   title = {KinBot: Automated stationary point search on potential energy surfaces},
+   journal = {Comput. Phys. Commun.},
+   volume = {248},
+   pages = {106947},
+   year = {2020},
+   type = {Journal Article}
+}
+```
+* 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
+
+```
+@article{Zador2022,
+   author = {Z\'ador, Judit and Mart\'i, Carles and Van de Vijver, Ruben and Johansen, Sommer L. and Yang, Yoona and Michelsen, Hope A. and Najm, Habib N.},
+   title = {Automated reaction kinetics of gas-phase organic species over multiwell potential energy surfaces},
+   journal = {J. Phys. Chem. A},
+   volume = {127},
+   pages = {565-588},
+   year = {2023},
+   type = {Journal Article}
+}
+```
+
+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 can be installed both in three different ways, from the PyPI index (`pip install`), from the conda-forge repo (`conda install`) or by cloning this github repo and then install it locally.
+
+### PyPI
+
+    pip install kinbot
+
+> **Note**
+>  KinBot only works with Python >= 3.10.
+
+### conda-forge
+
+    conda install -c conda-forge kinbot
+
+### 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 -e .
+ 
+> **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 a single-well exploration of KinBot, 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 the [wiki](https://github.com/zadorlab/KinBot/wiki) for keywords, and our [tutorial](https://hackmd.io/@jzador/kinbot_workshop_2023#/) for a more hands-on introduction to the code.
+
+## 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 
+* Amanda Dewyer
+* Carles Martí
+* Clément Soulié (csoulie@sandia.gov)
+
+## Papers using KinBot
+1. Hansen, N., Gaiser, N., Bierkandt, T., Oßwald, P., Köhler, M., Zádor, J., Hemberger, P.: _Identification of dihydropentalenes as products of the molecular-weight growth reaction of cyclopentadienyl plus propargyl_. J. Phys. Chem. A, **2025** 129 1714-1725. https://doi.org/10.1021/acs.jpca.4c06549
+2. Almeida, T. G., Martí, C., Kurtén, T., Zádor, J., Johansen, S. L.: _Theoretical analysis of the OH-Initiated atmospheric oxidation reactions of imidazole_. Phys. Chem. Chem. Phys., **2024** 26 23570-23587. https://doi.org/10.1039/D4CP02103G
+3. Yuan, E. C.-Y., Kumar, A., Guan, X., Hermes, E. D., Rosen, A. S., Zádor, J., Head-Gordon, T., Blau, S. M.: _Analytical ab initio Hessian from a Deep Learning Potential for Transition State Optimization_. Nat. Comm., **2024** 15 8865. https://doi.org/10.1038/s41467-024-52481-5
+4. Doner, A. C., Zádor, J., Rotavera, B.: _Stereoisomer-dependent rate coefficients and reaction mechanisms of 2-ethyloxetanylperoxy radicals_. Proc. Combust. Inst., **2024**, 40, 105578. https://doi.org/10.1016/j.proci.2024.105578
+5. Hansen, N. A, Price, T. D., Filardi, L. R., Gurses, S. M., Zhou, W., Hansen, N., Osborn, D. L. Zádor, J., Kronawitter, C. X.: _The photoionization of methoxymethanol: Fingerprinting a reactive C2 oxygenate in a complex reactive mixture_. J. Chem. Phys., **2024**, 160, 124306. https://doi.org/10.1063/5.0197827
+6. Martí, C., Devereux, C., Najm, H. N., Zádor, J.: _Evaluation of rate coefficients in the gas-phase using a machine learned potential_. J. Phys. Chem. A, **2024**, 128, 1958–1971. https://doi.org/10.1021/acs.jpca.3c07872
+7. Lang, J., Foley, C. D., Thawoos, S., Behzadfar, A., Liu, Y., Zádor, J., Suits, A. G.: _Reaction dynamics of S(3P) with 1,3-butadiene and isoprene: Crossed beam scattering, low temperature flow experiments, and high-level electronic structure calculations_. Farad. Discuss., **2024**, 251, 550-572. https://doi.org/10.1039/D4FD00009A
+8. Wang, D., Tian, Z.-Y., Zheng, Z.-H., Li, W., Wu, L.-N., Kuang, J.-J., Yang, J.-Z.: _Experimental and modeling study of the n, n-dimethylformamide pyrolysis at atmospheric pressure_. Combust. Flame, **2024**, 260, 113240. https://doi.org/10.1016/j.combustflame.2023.113240
+9. Doner, A. C., Zádor, J., Rotavera, B.: _Unimolecular reactions of 2,4-dimethyloxetanyl radicals._ J. Phys. Chem A, **2023**, 127, 2591–2600 https://doi.org/10.1021/acs.jpca.2c08290
+10. Li, H., Lang, J., Foley, C. D., Zádor, J., Suits, A. G.: _Sulfur (3P) reaction with conjugated dienes gives cyclization to thiophenes under single collision conditions._ J. Phys. Chem. Letters, **2023**, 14, 7611–7617. https://doi.org/10.1021/acs.jpclett.3c01953
+11. 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**, 127, 1941–1959. https://pubs.acs.org/doi/full/10.1021/acs.jpca.2c08035
+12. 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
+13. Lockwood, K. S., Ahmed, S. F., Huq, N. A., Stutzman, S. C., Foust, T. D., Labbe, N. J.: _Advances in predictive chemistry enable a multi-scale rational design approach for biofuels with advantaged properties_ Sustainable Energy Fuels, **2022**, 6, 5371-5383. https://doi.org/10.1039/D2SE00773H
+14. 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
+15. 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
+16. 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
+17. 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
+18. 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
+19. 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
+20. 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
+21. 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
+22. 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:
+1. 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
+2. 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
+3. 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
+4. 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
+5. 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
+6. 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
+7. 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. 

{kinbot-2.2.2 → kinbot-2.2.4}/KinBot.egg-info/requires.txt

@@ -1,5 +1,5 @@
-numpy<2.0,>=1.17.0
-ase<3.23,>=3.19
+numpy>=1.17.0
+ase<3.22,>=3.19
 networkx
 rmsd>=1.5.1
 sella

kinbot-2.2.4/PKG-INFO

@@ -0,0 +1,191 @@
+Metadata-Version: 2.2
+Name: kinbot
+Version: 2.2.4
+Summary: Automated reaction kinetics for gas-phase species
+Author-email: Judit Zádor <jzador@sandia.gov>, Ruben Van de Vijver <ruben.vandevijver@ugent.be>, Carles Martí <cmartia@sandia.gov>, Clément Soulié <csoulie@sandia.gov>, Amanda Dewyer <adewyer@sandia.gov>
+Maintainer-email: Judit Zádor <jzador@sandia.gov>, Clément Soulié <csoulie@sandia.gov>
+License: BSD 3-Clause License
+        
+        Copyright (c) 2018, 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
+        
+        Redistribution and use in source and binary forms, with or without
+        modification, are permitted provided that the following conditions are met:
+        
+        * Redistributions of source code must retain the above copyright notice, this
+          list of conditions and the following disclaimer.
+        
+        * Redistributions in binary form must reproduce the above copyright notice,
+          this list of conditions and the following disclaimer in the documentation
+          and/or other materials provided with the distribution.
+        
+        * Neither the name of the copyright holder nor the names of its
+          contributors may be used to endorse or promote products derived from
+          this software without specific prior written permission.
+        
+        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+        AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+        IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+        DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+        FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+        DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+        SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+        CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+        OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+        OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+        
+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 :: 3.10
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.17.0
+Requires-Dist: ase<3.22,>=3.19
+Requires-Dist: networkx
+Requires-Dist: rmsd>=1.5.1
+Requires-Dist: sella
+Provides-Extra: plot
+Requires-Dist: matplotlib; extra == "plot"
+Requires-Dist: pyvis; extra == "plot"
+Requires-Dist: rdkit; extra == "plot"
+
+[![Gitter chat](https://badges.gitter.im/gitterHQ/gitter.png)](https://gitter.im/zadorlab/KinBot)
+
+# KinBot: Automated Reaction Kinetics of Gas-Phase Organic Species over Multiwell Potential Energy Surfaces
+
+<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 2.2.1,
+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
+```
+@article{Vijver2020,
+   author = {Van de Vijver, Ruben and Z\'ador, Judit},
+   title = {KinBot: Automated stationary point search on potential energy surfaces},
+   journal = {Comput. Phys. Commun.},
+   volume = {248},
+   pages = {106947},
+   year = {2020},
+   type = {Journal Article}
+}
+```
+* 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
+
+```
+@article{Zador2022,
+   author = {Z\'ador, Judit and Mart\'i, Carles and Van de Vijver, Ruben and Johansen, Sommer L. and Yang, Yoona and Michelsen, Hope A. and Najm, Habib N.},
+   title = {Automated reaction kinetics of gas-phase organic species over multiwell potential energy surfaces},
+   journal = {J. Phys. Chem. A},
+   volume = {127},
+   pages = {565-588},
+   year = {2023},
+   type = {Journal Article}
+}
+```
+
+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 can be installed both in three different ways, from the PyPI index (`pip install`), from the conda-forge repo (`conda install`) or by cloning this github repo and then install it locally.
+
+### PyPI
+
+    pip install kinbot
+
+> **Note**
+>  KinBot only works with Python >= 3.10.
+
+### conda-forge
+
+    conda install -c conda-forge kinbot
+
+### 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 -e .
+ 
+> **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 a single-well exploration of KinBot, 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 the [wiki](https://github.com/zadorlab/KinBot/wiki) for keywords, and our [tutorial](https://hackmd.io/@jzador/kinbot_workshop_2023#/) for a more hands-on introduction to the code.
+
+## 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 
+* Amanda Dewyer
+* Carles Martí
+* Clément Soulié (csoulie@sandia.gov)
+
+## Papers using KinBot
+1. Hansen, N., Gaiser, N., Bierkandt, T., Oßwald, P., Köhler, M., Zádor, J., Hemberger, P.: _Identification of dihydropentalenes as products of the molecular-weight growth reaction of cyclopentadienyl plus propargyl_. J. Phys. Chem. A, **2025** 129 1714-1725. https://doi.org/10.1021/acs.jpca.4c06549
+2. Almeida, T. G., Martí, C., Kurtén, T., Zádor, J., Johansen, S. L.: _Theoretical analysis of the OH-Initiated atmospheric oxidation reactions of imidazole_. Phys. Chem. Chem. Phys., **2024** 26 23570-23587. https://doi.org/10.1039/D4CP02103G
+3. Yuan, E. C.-Y., Kumar, A., Guan, X., Hermes, E. D., Rosen, A. S., Zádor, J., Head-Gordon, T., Blau, S. M.: _Analytical ab initio Hessian from a Deep Learning Potential for Transition State Optimization_. Nat. Comm., **2024** 15 8865. https://doi.org/10.1038/s41467-024-52481-5
+4. Doner, A. C., Zádor, J., Rotavera, B.: _Stereoisomer-dependent rate coefficients and reaction mechanisms of 2-ethyloxetanylperoxy radicals_. Proc. Combust. Inst., **2024**, 40, 105578. https://doi.org/10.1016/j.proci.2024.105578
+5. Hansen, N. A, Price, T. D., Filardi, L. R., Gurses, S. M., Zhou, W., Hansen, N., Osborn, D. L. Zádor, J., Kronawitter, C. X.: _The photoionization of methoxymethanol: Fingerprinting a reactive C2 oxygenate in a complex reactive mixture_. J. Chem. Phys., **2024**, 160, 124306. https://doi.org/10.1063/5.0197827
+6. Martí, C., Devereux, C., Najm, H. N., Zádor, J.: _Evaluation of rate coefficients in the gas-phase using a machine learned potential_. J. Phys. Chem. A, **2024**, 128, 1958–1971. https://doi.org/10.1021/acs.jpca.3c07872
+7. Lang, J., Foley, C. D., Thawoos, S., Behzadfar, A., Liu, Y., Zádor, J., Suits, A. G.: _Reaction dynamics of S(3P) with 1,3-butadiene and isoprene: Crossed beam scattering, low temperature flow experiments, and high-level electronic structure calculations_. Farad. Discuss., **2024**, 251, 550-572. https://doi.org/10.1039/D4FD00009A
+8. Wang, D., Tian, Z.-Y., Zheng, Z.-H., Li, W., Wu, L.-N., Kuang, J.-J., Yang, J.-Z.: _Experimental and modeling study of the n, n-dimethylformamide pyrolysis at atmospheric pressure_. Combust. Flame, **2024**, 260, 113240. https://doi.org/10.1016/j.combustflame.2023.113240
+9. Doner, A. C., Zádor, J., Rotavera, B.: _Unimolecular reactions of 2,4-dimethyloxetanyl radicals._ J. Phys. Chem A, **2023**, 127, 2591–2600 https://doi.org/10.1021/acs.jpca.2c08290
+10. Li, H., Lang, J., Foley, C. D., Zádor, J., Suits, A. G.: _Sulfur (3P) reaction with conjugated dienes gives cyclization to thiophenes under single collision conditions._ J. Phys. Chem. Letters, **2023**, 14, 7611–7617. https://doi.org/10.1021/acs.jpclett.3c01953
+11. 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**, 127, 1941–1959. https://pubs.acs.org/doi/full/10.1021/acs.jpca.2c08035
+12. 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
+13. Lockwood, K. S., Ahmed, S. F., Huq, N. A., Stutzman, S. C., Foust, T. D., Labbe, N. J.: _Advances in predictive chemistry enable a multi-scale rational design approach for biofuels with advantaged properties_ Sustainable Energy Fuels, **2022**, 6, 5371-5383. https://doi.org/10.1039/D2SE00773H
+14. 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
+15. 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
+16. 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
+17. 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
+18. 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
+19. 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
+20. 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
+21. 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
+22. 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:
+1. 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
+2. 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
+3. 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
+4. 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
+5. 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
+6. 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
+7. 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. 

kinbot-2.2.4/README.md

@@ -0,0 +1,132 @@
+[![Gitter chat](https://badges.gitter.im/gitterHQ/gitter.png)](https://gitter.im/zadorlab/KinBot)
+
+# KinBot: Automated Reaction Kinetics of Gas-Phase Organic Species over Multiwell Potential Energy Surfaces
+
+<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 2.2.1,
+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
+```
+@article{Vijver2020,
+   author = {Van de Vijver, Ruben and Z\'ador, Judit},
+   title = {KinBot: Automated stationary point search on potential energy surfaces},
+   journal = {Comput. Phys. Commun.},
+   volume = {248},
+   pages = {106947},
+   year = {2020},
+   type = {Journal Article}
+}
+```
+* 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
+
+```
+@article{Zador2022,
+   author = {Z\'ador, Judit and Mart\'i, Carles and Van de Vijver, Ruben and Johansen, Sommer L. and Yang, Yoona and Michelsen, Hope A. and Najm, Habib N.},
+   title = {Automated reaction kinetics of gas-phase organic species over multiwell potential energy surfaces},
+   journal = {J. Phys. Chem. A},
+   volume = {127},
+   pages = {565-588},
+   year = {2023},
+   type = {Journal Article}
+}
+```
+
+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 can be installed both in three different ways, from the PyPI index (`pip install`), from the conda-forge repo (`conda install`) or by cloning this github repo and then install it locally.
+
+### PyPI
+
+    pip install kinbot
+
+> **Note**
+>  KinBot only works with Python >= 3.10.
+
+### conda-forge
+
+    conda install -c conda-forge kinbot
+
+### 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 -e .
+ 
+> **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 a single-well exploration of KinBot, 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 the [wiki](https://github.com/zadorlab/KinBot/wiki) for keywords, and our [tutorial](https://hackmd.io/@jzador/kinbot_workshop_2023#/) for a more hands-on introduction to the code.
+
+## 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 
+* Amanda Dewyer
+* Carles Martí
+* Clément Soulié (csoulie@sandia.gov)
+
+## Papers using KinBot
+1. Hansen, N., Gaiser, N., Bierkandt, T., Oßwald, P., Köhler, M., Zádor, J., Hemberger, P.: _Identification of dihydropentalenes as products of the molecular-weight growth reaction of cyclopentadienyl plus propargyl_. J. Phys. Chem. A, **2025** 129 1714-1725. https://doi.org/10.1021/acs.jpca.4c06549
+2. Almeida, T. G., Martí, C., Kurtén, T., Zádor, J., Johansen, S. L.: _Theoretical analysis of the OH-Initiated atmospheric oxidation reactions of imidazole_. Phys. Chem. Chem. Phys., **2024** 26 23570-23587. https://doi.org/10.1039/D4CP02103G
+3. Yuan, E. C.-Y., Kumar, A., Guan, X., Hermes, E. D., Rosen, A. S., Zádor, J., Head-Gordon, T., Blau, S. M.: _Analytical ab initio Hessian from a Deep Learning Potential for Transition State Optimization_. Nat. Comm., **2024** 15 8865. https://doi.org/10.1038/s41467-024-52481-5
+4. Doner, A. C., Zádor, J., Rotavera, B.: _Stereoisomer-dependent rate coefficients and reaction mechanisms of 2-ethyloxetanylperoxy radicals_. Proc. Combust. Inst., **2024**, 40, 105578. https://doi.org/10.1016/j.proci.2024.105578
+5. Hansen, N. A, Price, T. D., Filardi, L. R., Gurses, S. M., Zhou, W., Hansen, N., Osborn, D. L. Zádor, J., Kronawitter, C. X.: _The photoionization of methoxymethanol: Fingerprinting a reactive C2 oxygenate in a complex reactive mixture_. J. Chem. Phys., **2024**, 160, 124306. https://doi.org/10.1063/5.0197827
+6. Martí, C., Devereux, C., Najm, H. N., Zádor, J.: _Evaluation of rate coefficients in the gas-phase using a machine learned potential_. J. Phys. Chem. A, **2024**, 128, 1958–1971. https://doi.org/10.1021/acs.jpca.3c07872
+7. Lang, J., Foley, C. D., Thawoos, S., Behzadfar, A., Liu, Y., Zádor, J., Suits, A. G.: _Reaction dynamics of S(3P) with 1,3-butadiene and isoprene: Crossed beam scattering, low temperature flow experiments, and high-level electronic structure calculations_. Farad. Discuss., **2024**, 251, 550-572. https://doi.org/10.1039/D4FD00009A
+8. Wang, D., Tian, Z.-Y., Zheng, Z.-H., Li, W., Wu, L.-N., Kuang, J.-J., Yang, J.-Z.: _Experimental and modeling study of the n, n-dimethylformamide pyrolysis at atmospheric pressure_. Combust. Flame, **2024**, 260, 113240. https://doi.org/10.1016/j.combustflame.2023.113240
+9. Doner, A. C., Zádor, J., Rotavera, B.: _Unimolecular reactions of 2,4-dimethyloxetanyl radicals._ J. Phys. Chem A, **2023**, 127, 2591–2600 https://doi.org/10.1021/acs.jpca.2c08290
+10. Li, H., Lang, J., Foley, C. D., Zádor, J., Suits, A. G.: _Sulfur (3P) reaction with conjugated dienes gives cyclization to thiophenes under single collision conditions._ J. Phys. Chem. Letters, **2023**, 14, 7611–7617. https://doi.org/10.1021/acs.jpclett.3c01953
+11. 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**, 127, 1941–1959. https://pubs.acs.org/doi/full/10.1021/acs.jpca.2c08035
+12. 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
+13. Lockwood, K. S., Ahmed, S. F., Huq, N. A., Stutzman, S. C., Foust, T. D., Labbe, N. J.: _Advances in predictive chemistry enable a multi-scale rational design approach for biofuels with advantaged properties_ Sustainable Energy Fuels, **2022**, 6, 5371-5383. https://doi.org/10.1039/D2SE00773H
+14. 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
+15. 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
+16. 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
+17. 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
+18. 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
+19. 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
+20. 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
+21. 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
+22. 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:
+1. 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
+2. 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
+3. 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
+4. 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
+5. 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
+6. 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
+7. 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. 

{kinbot-2.2.2 → kinbot-2.2.4}/kinbot/config_log.py

@@ -44,7 +44,10 @@ def config_log(label, mode='kinbot', level='info'):
     @return: The logger object.
     """
     logger = logging.getLogger(label)
-    logger.setLevel(logging.INFO)
+    if level == 'info':
+        logger.setLevel(logging.INFO)
+    elif level == 'debug':
+        logger.setLevel(logging.DEBUG)
     fname = f'{mode}.log'
 
     # Backup previous log

{kinbot-2.2.2 → kinbot-2.2.4}/kinbot/conformers.py

@@ -166,6 +166,9 @@ class Conformers:
     def start_ring_conformer_search(self, index, cart):
         """
         index: number of the conformer
+        In each iteration a given dihedral is changed, and then in the 
+        next one it's fixed and another one is changed, and then two are
+        fixed and the next one is changed, until all are at their desired values
         """
         if self.cyc_conf_index[index] == len(self.cyc_dih_atoms[index]) - 1:
             # this conformer has finished

{kinbot-2.2.2 → kinbot-2.2.4}/kinbot/constants.py

@@ -1,4 +1,5 @@
 from ase import units
+from ase import data
 
 AUtoKCAL = 627.5091809
 AUtoCM = 219474.63068
@@ -19,7 +20,18 @@ CALtoJ = 4.184
 # elements currently in KinBot
 elements = ['C', 'H', 'O', 'N', 'S', 'F', 'Cl', 'Br', 'I']
 
+znumber = {'H': 1}
+znumber['C'] = 6
+znumber['N'] = 7
+znumber['O'] = 8
+znumber['S'] = 16
+znumber['F'] = 9
+znumber['Cl'] = 17
+znumber['Br'] = 35
+znumber['I'] = 53
+
 # standard bond lengths, cutoffs, and oxidation numbers
+
 st_bond = {'CC': 1.5*1.2}
 # st_bond['CO'] = 1.4*1.2 # 1.4*1.54
 st_bond['CO'] = 1.4*1.4
@@ -60,6 +72,21 @@ st_bond['Cl'] = 1
 st_bond['Br'] = 1
 st_bond['I'] = 1
 
+for el1 in elements:
+    for el2 in elements:
+        try:
+            st_bond[f'{el1}{el2}']
+        except KeyError:
+            try:
+                st_bond[f'{el2}{el1}']
+            except KeyError:
+                z1 = znumber[el1]
+                r1 = data.covalent_radii[z1]
+                z2 = znumber[el2]
+                r2 = data.covalent_radii[z2]
+                st_bond[f'{el1}{el2}'] = (r1 + r2) * 1.2 
+#print(st_bond)
+
 mass = {'H': 1}
 mass['C'] = 12
 mass['N'] = 14
@@ -80,16 +107,6 @@ exact_mass['Cl'] = 34.9689
 exact_mass['Br'] = 78.9183
 exact_mass['I'] = 126.904477
 
-znumber = {'H': 1}
-znumber['C'] = 6
-znumber['N'] = 7
-znumber['O'] = 8
-znumber['S'] = 16
-znumber['F'] = 9
-znumber['Cl'] = 17
-znumber['Br'] = 35
-znumber['I'] = 53
-
 # collision parameters
 # Jasper & Miller, C&F 161, 101-110 (2014)
 # data is expected in CHEMKIN format, where