kinbot 2.2.2__tar.gz → 2.2.3__tar.gz

{kinbot-2.2.2 → kinbot-2.2.3}/KinBot.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: kinbot
-Version: 2.2.2
+Version: 2.2.3
 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>
@@ -47,8 +47,8 @@ Classifier: Topic :: Scientific/Engineering :: Chemistry
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: numpy<2.0,>=1.17.0
-Requires-Dist: ase<3.23,>=3.19
+Requires-Dist: numpy>=1.17.0
+Requires-Dist: ase>=3.19
 Requires-Dist: networkx
 Requires-Dist: rmsd>=1.5.1
 Requires-Dist: sella
@@ -155,37 +155,36 @@ See [list](https://github.com/zadorlab/KinBot/wiki/KinBot-file-structure).
 * Clément Soulié (csoulie@sandia.gov)
 
 ## Papers using KinBot
-* 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
-* 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** 
-* 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
-* 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 
-* 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 
-* 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 
-* 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
-* 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
-* 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
-* 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  
-* 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
-* 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 
-* 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
-
+1. 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
+2. 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**
+3. 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
+4. 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
+5. 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
+6. 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
+7. 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
+8. 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
+9. 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
+10. 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
+11. 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
+12. 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
+13. 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
+14. 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
+15. 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
+16. 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
+17. 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
+18. 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
+19. 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
+20. 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
+21. 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
+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-2.2.3}/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>=3.19
 networkx
 rmsd>=1.5.1
 sella

{kinbot-2.2.2 → kinbot-2.2.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: kinbot
-Version: 2.2.2
+Version: 2.2.3
 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>
@@ -47,8 +47,8 @@ Classifier: Topic :: Scientific/Engineering :: Chemistry
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: numpy<2.0,>=1.17.0
-Requires-Dist: ase<3.23,>=3.19
+Requires-Dist: numpy>=1.17.0
+Requires-Dist: ase>=3.19
 Requires-Dist: networkx
 Requires-Dist: rmsd>=1.5.1
 Requires-Dist: sella
@@ -155,37 +155,36 @@ See [list](https://github.com/zadorlab/KinBot/wiki/KinBot-file-structure).
 * Clément Soulié (csoulie@sandia.gov)
 
 ## Papers using KinBot
-* 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
-* 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** 
-* 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
-* 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 
-* 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 
-* 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 
-* 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
-* 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
-* 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
-* 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  
-* 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
-* 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 
-* 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
-
+1. 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
+2. 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**
+3. 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
+4. 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
+5. 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
+6. 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
+7. 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
+8. 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
+9. 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
+10. 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
+11. 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
+12. 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
+13. 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
+14. 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
+15. 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
+16. 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
+17. 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
+18. 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
+19. 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
+20. 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
+21. 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
+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-2.2.3/README.md

@@ -0,0 +1,131 @@
+[![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. 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
+2. 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**
+3. 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
+4. 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
+5. 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
+6. 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
+7. 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
+8. 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
+9. 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
+10. 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
+11. 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
+12. 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
+13. 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
+14. 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
+15. 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
+16. 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
+17. 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
+18. 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
+19. 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
+20. 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
+21. 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-2.2.3}/kinbot/find_motif.py

@@ -7,13 +7,14 @@ def start_motif(motif, natom, bond, atom, allover, eqv):
     chain = [-999] * natom
     nsteps = -1
     motifset = []
+    mask = []  # to mask new patterns that allow eqv atoms in some cases
     find_motif(motif, visit, chain, nsteps, 0, -1,
-               motifset, allover, natom, bond, atom, eqv)
+               motifset, allover, natom, bond, atom, eqv, mask, True)
     return motifset
 
 
 def find_motif(motif, visit, chain, nsteps, current,
-               previous, motifset, allover, natom, bond, atom, eqv):
+               previous, motifset, allover, natom, bond, atom, eqv, mask, mask_current):
     """
     This recursive function finds a specific motif in the structure.
     FIXIT - the comments here
@@ -28,6 +29,7 @@ def find_motif(motif, visit, chain, nsteps, current,
     allover < 0: all-over path-finding mode
     allover = > 0: only atom 'allover' is used for the search
     eqv: array for equvivalent atoms
+    mask: mask irregulara patterns that contain equivalent atoms
     """
     if nsteps == -1:
         nsteps = 0
@@ -37,13 +39,14 @@ def find_motif(motif, visit, chain, nsteps, current,
                 current = i
                 visit = [0] * natom
                 chain = [-999] * natom
+                mask_current = True
                 find_motif(motif, visit, chain, nsteps, current, previous,
-                           motifset, allover, natom, bond, atom, eqv)
+                           motifset, allover, natom, bond, atom, eqv, mask, mask_current)
         else:
             current = allover
             visit = [0] * natom
             find_motif(motif, visit, chain, nsteps, current, previous,
-                       motifset, allover, natom, bond, atom, eqv)
+                       motifset, allover, natom, bond, atom, eqv, mask, mask_current)
 
     if nsteps > -1:
         if nsteps > natom:
@@ -55,9 +58,12 @@ def find_motif(motif, visit, chain, nsteps, current,
             if current in mylist:
                 eqv_list = mylist[:]
                 eqv_list.remove(current)
-        for m in motifset:
+        for mi, m in enumerate(motifset):
+            if mask[mi] == False:
+                continue
             if m[nsteps] in eqv_list:
-                if any([True for i in eqv_list if i in chain]):
+                if any([True for i in eqv_list if i in chain[:nsteps]]):
+                    mask_current = False
                     break
                 return 0
         if visit[current] == 1:
@@ -77,6 +83,7 @@ def find_motif(motif, visit, chain, nsteps, current,
                 motifset.append(chain[:chain.index(-999)])
             else:
                 motifset.append(chain[:])
+            mask.append(mask_current)
             return 0
 
         visit[current] = 1
@@ -86,7 +93,7 @@ def find_motif(motif, visit, chain, nsteps, current,
         for i in range(natom):
             current = i
             find_motif(motif, visit, chain, nsteps, current, previous,
-                       motifset, allover, natom, bond, atom, eqv)
+                       motifset, allover, natom, bond, atom, eqv, mask, mask_current)
             visit[current] = 0
 
         if nsteps > 0:

{kinbot-2.2.2 → kinbot-2.2.3}/kinbot/fragments.py

@@ -1,4 +1,3 @@
-import rmsd
 import os
 from typing import Any
 from kinbot import kb_path
@@ -13,6 +12,7 @@ import logging
 import copy
 import math
 from kinbot.constants import BOHRtoANGSTROM
+from kinbot.utils import reorder_coord
 
 logger = logging.getLogger('KinBot')
 
@@ -68,12 +68,14 @@ class Fragment(StationaryPoint):
         self.geom = np.array(geom)
 
         self.recentre()
-        if abs(np.prod(self.atoms.get_moments_of_inertia())) < 1e-6:
+        self.frag_name: str
+        if len(self.geom) == 1:
+            self.frag_type = 'Monoatomic'
+        elif abs(np.prod(self.atoms.get_moments_of_inertia())) < 1e-6:
             self.frag_type = 'Linear'
         else:
             self.frag_type = 'Nonlinear'
 
-        self.frag_name: str
         Fragment.set_fragnames(self)
 
         super(Fragment, self).__init__(name=self.frag_name,
@@ -550,6 +552,13 @@ class Fragment(StationaryPoint):
             raise TypeError('HOMO mode selected for pivot point orientation, but cubefile is not available.')
         step: NDArray[float32] = np.zeros(3, dtype=float32)
         dim: NDArray[int16] = np.zeros(3, dtype=int16)
+        elements: list[str] = []
+        num2str: dict[str, str] = {
+            '1': 'H',
+            '6': 'C',
+            '7': 'N',
+            '8': 'O',
+            '16': 'S'}
         # Saves info from the header: step size, origin and dimension
         for ln, line in enumerate(cubefile):
             if ln == 2:
@@ -573,8 +582,9 @@ class Fragment(StationaryPoint):
                 continue
             # Save the cube geometry
             elif ln > 5 and ln <= 5 + natm:
-                x, y, z = line.split()[2:]
+                num, _, x, y, z = line.split()
                 cube_geom[ln-6] = np.array([x, y, z], dtype=float32)
+                elements.append(num2str[num])
             elif ln > 5 and len(line.split()) == 2:
                 start: int = ln + 1
                 break
@@ -590,16 +600,20 @@ class Fragment(StationaryPoint):
         xsize = int(ysize*dim[1])
 
         # Change the geom for the one in the cube to ensure same orientation
-        self.geom = cube_geom
+        tmp_atm = Atoms(elements, positions=cube_geom)
+        tmp_stp = StationaryPoint.from_ase_atoms(tmp_atm)
+        tmp_stp.characterize()
+        reorder_coord(self, tmp_stp)
+        self.geom = tmp_stp.geom
         self.recentre()
 
-        for eq in self.equiv:
-            if index in eq:
-                to_integrate: list[int] = eq
-                break
+        # for eq in self.equiv:
+        #     if index in eq:
+        #         to_integrate: list[int] = eq
+        #         break
 
         # max_integral = -1
-        max_var: float = np.inf
+        # max_var: float = np.inf
         # all_orient = []
         
 

{kinbot-2.2.2 → kinbot-2.2.3}/kinbot/modify_geom.py

@@ -17,7 +17,6 @@ from ase.calculators.singlepoint import SinglePointCalculator
 from ase.calculators.emt import EMT
 from ase.constraints import FixInternals
 from ase.data import atomic_numbers, covalent_radii
-from sella import Sella
 
 from kinbot import bfgs
 from kinbot import constants
@@ -203,7 +202,10 @@ def modify_coordinates(species, name, geom, changes, bond, write_files=0):
             gs += '{}, {:.8f}, {:.8f}, {:.8f}, \n'.format(at, x, y, z)
         logger.debug("For the following initial geometry:\n" + gs)
 
-        opt = bfgs.BFGS()
+        # step_tol=1E-7, grad_tol=1E-7, line_tol=1E-10,
+        # inhess=None, max_step=100, max_lin_step=1000,
+        # use_grad_tol=1, use_step_tol=1
+        opt = bfgs.BFGS(step_tol=1E-12, grad_tol=1E-12)
         x_opt, x_i, g_i = opt.optimize(cost_fct, x0)
 
         new_geom = np.reshape(x_opt, (species.natom, 3))

{kinbot-2.2.2 → kinbot-2.2.3}/kinbot/optimize.py

@@ -416,11 +416,13 @@ class Optimize:
         else:
             names.append(self.name + '_well')
             names.append(self.name + '_well_high')
-            if self.par['high_level'] == 1:
+            if self.par['high_level'] == 1 and \
+               'prod' not in self.species.name:
                 for count in range(self.species.hir.nrotation):
                     for rot_num in range(self.par['nrotation']):
                         names.append('hir/' + self.name + '_hir_' + str(count) + '_' + str(rot_num).zfill(2))
-            if self.par['conformer_search'] == 1:
+            if self.par['conformer_search'] == 1 and \
+               'prod' not in self.species.name:
                 for count in range(self.species.confs.conf):
                     names.append('conf/' + self.name + '_' + str(count).zfill(zf))
                 for count in range(self.species.confs.cyc_conf):

{kinbot-2.2.2 → kinbot-2.2.3}/kinbot/parameters.py

@@ -206,7 +206,7 @@ class Parameters:
             # Basis set to scan bonds in barrierless_saddle family
             'barrierless_saddle_basis_high': '6-31G',
             # for Gaussian, request CalcAll for TS optimization
-            'calcall_ts': 0,
+            'calcall_ts': 1,
             # Quantum chemistry method to use for high-level L2
             'high_level_method': 'M062X',
             # Basis set to use for high-level

{kinbot-2.2.2 → kinbot-2.2.3}/kinbot/pes.py

@@ -1400,7 +1400,7 @@ def create_rotdpy_inputs(par, bless, vdW) -> None:
                                       parent=str(reactant),
                                       mult=pp_info['frags_mult'][frag_num]))
 
-        fragnames = Fragment.get_fragnames()
+        fragnames: list[str] = Fragment.get_fragnames()
 
         # Set the pivot points on each fragments and create the surfaces
         surfaces: list[VRC_TST_Surface] = []

{kinbot-2.2.2 → kinbot-2.2.3}/kinbot/pp_settings.py

@@ -5,7 +5,6 @@ import numpy as np
 from numpy.typing import NDArray
 from ase import Atoms
 
-from kinbot import constants
 from kinbot.fragments import Fragment
 from kinbot.vrc_tst_surfaces import VRC_TST_Surface
 
@@ -220,6 +219,7 @@ def create_surface(dist,
                 info[findex] += 'COM'
                 weights[findex].append(1)
                 reac_weights[findex].append(1)
+                all_pp_dists[findex].append(0.0)
                 continue
             elif pps_dists is None:
                 info[findex] += 'on atom'

{kinbot-2.2.2 → kinbot-2.2.3}/kinbot/reac_family.py

@@ -77,7 +77,7 @@ def carry_out_reaction(rxn, step, command, bimol=0):
                                                        rxn.instance_name, geom, 
                                                        change_starting_zero,
                                                        rxn.species.bond,
-                                                       write_files=1)
+                                                       write_files=0)
         for c in change:
             fix.append(c[:-1])
         change = []