kinbot 2.2.3__tar.gz → 2.2.4a0__tar.gz

{kinbot-2.2.3 → kinbot-2.2.4a0}/KinBot.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: kinbot
-Version: 2.2.3
+Version: 2.2.4a0
 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>
@@ -48,7 +48,7 @@ Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: numpy>=1.17.0
-Requires-Dist: ase>=3.19
+Requires-Dist: ase<3.23,>=3.19
 Requires-Dist: networkx
 Requires-Dist: rmsd>=1.5.1
 Requires-Dist: sella
@@ -155,27 +155,28 @@ See [list](https://github.com/zadorlab/KinBot/wiki/KinBot-file-structure).
 * 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
+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

{kinbot-2.2.3 → kinbot-2.2.4a0}/KinBot.egg-info/requires.txt

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

{kinbot-2.2.3 → kinbot-2.2.4a0}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: kinbot
-Version: 2.2.3
+Version: 2.2.4a0
 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>
@@ -48,7 +48,7 @@ Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: numpy>=1.17.0
-Requires-Dist: ase>=3.19
+Requires-Dist: ase<3.23,>=3.19
 Requires-Dist: networkx
 Requires-Dist: rmsd>=1.5.1
 Requires-Dist: sella
@@ -155,27 +155,28 @@ See [list](https://github.com/zadorlab/KinBot/wiki/KinBot-file-structure).
 * 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
+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

{kinbot-2.2.3 → kinbot-2.2.4a0}/README.md

@@ -96,27 +96,28 @@ See [list](https://github.com/zadorlab/KinBot/wiki/KinBot-file-structure).
 * 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
+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

{kinbot-2.2.3 → kinbot-2.2.4a0}/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-2.2.3 → kinbot-2.2.4a0}/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-2.2.3 → kinbot-2.2.4a0}/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

{kinbot-2.2.3 → kinbot-2.2.4a0}/kinbot/fragments.py

@@ -129,17 +129,6 @@ class Fragment(StationaryPoint):
         self.geom: NDArray[Any] = np.subtract(self.geom,
                                               self.atoms.get_center_of_mass())
 
-    def get_chemical_formula(self) -> str:
-        """Create the string of element in the order of the coordinates
-
-        Returns:
-            str: chemical elements
-        """
-        all_elem: str = ""
-        for elem in self.atoms:
-            all_elem += f"{elem}"
-        return all_elem
-
     def get_pp_on_com(self) -> list[float]:
         """Return the coordinate of the center of mass
         of the fragment
@@ -182,7 +171,7 @@ class Fragment(StationaryPoint):
         orientation_vect: NDArray[float32] = self.get_pp_orientation(
             index=index)
         coord = (
-            orientation_vect * 
+            orientation_vect *
             dist_from_ra*constants.BOHRtoANGSTROM +
             self.geom[index]).tolist()
         pp_dist = np.full(
@@ -193,11 +182,26 @@ class Fragment(StationaryPoint):
 
     def get_pp_orientation(self,
                            index: int) -> NDArray[float32]:
+        """Create a list of orientation vectors for all
+        pivot points.
+
+        Args:
+            index (int): index of atom in fragment's geometry
+                         from which the orientation starts.
+
+        Raises:
+            NotImplementedError: _description_
+            NotImplementedError: _description_
+
+        Returns:
+            NDArray[float32]: _description_
+        """
         if str(index) in self.orient:
             return self.orient[str(index)]
         orient: NDArray[float32] = np.array([[0, 0, 0]], dtype=float32)
         # if self.par['pp_orient'] == 'geometric':
         # element = self.atom[index]
+        # DETECT THE CONNECTIVITY
         nconnect = 0
         ndouble = 0
         ntriple = 0

{kinbot-2.2.3 → kinbot-2.2.4a0}/kinbot/geometry.py

@@ -247,12 +247,13 @@ def translate_and_rotate(cart, i, j):
                        [2.*(bd+ac),   2.*(cd-ab),   aa+dd-bb-cc]])
         for i in range(len(cart)):
             cart[i] = np.dot(rot_matrix, cart[i])
-            
+
         if cart[j][2] < 0:
                 cart *= -1.
 
     return cart
 
+
 def rotation_matrix(axis, theta):
     """
     Return the rotation matrix associated with counterclockwise rotation about
@@ -375,16 +376,17 @@ def equal_geom(orig_spec, new_spec, cutoff):
     """
     
     # check if all original bonds are still very close to the original lenghts
-    for i in range(orig_spec.natom-1):
+    for i in range(orig_spec.natom - 1):
         for j in range(i + 1, orig_spec.natom):
-            if orig_spec.maxbond[i][j] > 0:
+            if orig_spec.bond[i][j] > 0:  # this includes the reaction bond for TS as well
                 orig_dist = np.linalg.norm(orig_spec.geom[i] - orig_spec.geom[j])
                 new_dist = np.linalg.norm(new_spec.geom[i] - new_spec.geom[j])
                 if np.abs(new_dist - orig_dist) / orig_dist > cutoff:
                     return 0
-    # for saddles, test if any unwanted new bonds are formed 
+    # for saddles
     if orig_spec.wellorts == 1:
-        for i in range(orig_spec.natom-1):
+        # test if any unwanted new bonds are formed 
+        for i in range(orig_spec.natom - 1):
             for j in range(i + 1, orig_spec.natom):
                 if new_spec.bond[i][j] > 0 and orig_spec.bond[i][j] == 0:
                     return 0

{kinbot-2.2.3 → kinbot-2.2.4a0}/kinbot/hindered_rotors.py

@@ -106,7 +106,7 @@ class HIR:
                         success = -1
                     else:
                         # check if all the bond lenghts are within
-                        # 15% or the original bond lengths
+                        # 15% of the original bond lengths
                         temp = StationaryPoint('temp',
                                                self.species.charge,
                                                self.species.mult,
@@ -154,12 +154,15 @@ class HIR:
                     continue
                 energies = self.hir_energies[rotor]
                 if abs(energies[0] - self.species.energy) * constants.AUtoKCAL > 0.1:
-                    logger.warning('\t0 angle rotor has a different energy than '
+                    logger.warning(f'\t0 angle rotor for rotor {rotor} has a different energy than '
                                    'the optimized structure for '
-                                   f'{self.species.chemid}. This might be '
+                                   f'{self.species.name} ({energies[0]} vs {self.species.energy}).')
+                    logger.warning('This might be '
                                    'caused by an SCF convergence issue. '
                                    'Hindered rotors are disabled for this '
                                    'stationary point.')
+                    logger.warning(rotor)
+                    logger.warning(energies)
                     self.hir_status = [[1 for ai in ri] for ri in self.hir_status]
                     return 0
                 # energies taken if status = 0, successful geom check or normal gauss termination

{kinbot-2.2.3 → kinbot-2.2.4a0}/kinbot/kb.py

@@ -41,7 +41,7 @@ def main():
     input_file = masterpar.input_file
     # set up the logging environment
     if par['verbose']:
-        logger = config_log('KinBot', 'debug')
+        logger = config_log('KinBot', level='debug')
 
     # write the license message and the parameters to the log file
     logger.info('Input parameters')

{kinbot-2.2.3 → kinbot-2.2.4a0}/kinbot/molpro.py

@@ -166,23 +166,24 @@ class Molpro:
                     method = " {rhf;wf," + f"{nelectron},{symm},{spin},{self.species.charge}" + "}\n\n"
                     method += " omega=0.2    !range-separation parameter\n"
                     method += " srx=0.222036 !short-range exchange\n"
-                    #method += " {grid,wcut=1d-30,min_nr=[175,250,250,250],max_nr=[175,250,250,250],min_L=[974,974,974,974],max_L=[974,974,974,974]}\n"
+                    # Same as Gaussian fine grid, important for long range
+                    method += " {grid,wcut=1d-30,min_nr=[175,250,250,250],max_nr=[175,250,250,250],min_L=[974,974,974,974],max_L=[974,974,974,974]}\n"
                     method += " {int; ERFLERFC,mu=$omega,srfac=$srx}\n"
                     method += " uks,HYB_GGA_XC_WB97X_D\n"
                 case "wb97xd":
                     method = " {rhf;wf," + f"{nelectron},{symm},{spin},{self.species.charge}" + "}\n\n"
                     method += " omega=0.2    !range-separation parameter\n"
                     method += " srx=0.222036 !short-range exchange\n"
-                    # method += " {grid,wcut=1d-30,min_nr=[175,250,250,250],max_nr=[175,250,250,250],min_L=[974,974,974,974],max_L=[974,974,974,974]}\n"
+                    method += " {grid,wcut=1d-30,min_nr=[175,250,250,250],max_nr=[175,250,250,250],min_L=[974,974,974,974],max_L=[974,974,974,974]}\n"
                     method += " {int; ERFLERFC,mu=$omega,srfac=$srx}\n"
                     method += " ks,HYB_GGA_XC_WB97X_D\n"
                 case "ub3lyp":
                     method = " {rhf;wf," + f"{nelectron},{symm},{spin},{self.species.charge}" + "}\n\n"
-                    # method += " {grid,wcut=1d-30,min_nr=[175,250,250,250],max_nr=[175,250,250,250],min_L=[974,974,974,974],max_L=[974,974,974,974]}\n"
+                    method += " {grid,wcut=1d-30,min_nr=[175,250,250,250],max_nr=[175,250,250,250],min_L=[974,974,974,974],max_L=[974,974,974,974]}\n"
                     method += " uks,HYB_GGA_XC_B3LYP\n"
                 case "b3lyp":
                     method = " {rhf;wf," + f"{nelectron},{symm},{spin},{self.species.charge}" + "}\n\n"
-                    # method += " {grid,wcut=1d-30,min_nr=[175,250,250,250],max_nr=[175,250,250,250],min_L=[974,974,974,974],max_L=[974,974,974,974]}\n"
+                    method += " {grid,wcut=1d-30,min_nr=[175,250,250,250],max_nr=[175,250,250,250],min_L=[974,974,974,974],max_L=[974,974,974,974]}\n"
                     method += " ks,HYB_GGA_XC_B3LYP\n"
                 case _:
                     method += " rhf\n"

{kinbot-2.2.3 → kinbot-2.2.4a0}/kinbot/optimize.py

@@ -282,18 +282,19 @@ class Optimize:
                                         for rotor in range(len(self.species.dihed)):
                                             for ai in range(self.species.hir.nrotation):
                                                 # use a 0.1 kcal/mol cutoff for numerical noise
-                                                if self.species.hir.hir_energies[rotor][ai] < min_en - 1.6E-4:
-                                                    min_en = self.species.hir.hir_energies[rotor][ai]
-                                                    min_rotor = rotor
-                                                    min_ai = ai
+                                                if self.species.hir.hir_status[rotor][ai] == 0:  # do not test for fails
+                                                    if self.species.hir.hir_energies[rotor][ai] < min_en - 1.6E-4:
+                                                        min_en = self.species.hir.hir_energies[rotor][ai]
+                                                        min_rotor = rotor
+                                                        min_ai = ai
                                         if min_rotor > -1:
                                             self.restart += 1
+                                            job = self.log_name(1, hir=1, r=min_rotor, s=min_ai)
+                                            diff = (self.species.hir.hir_energies[min_rotor][0] - 
+                                                    self.species.hir.hir_energies[min_rotor][min_ai]) * constants.AUtoKCAL 
                                             if self.restart < self.par['rotation_restart']:
                                                 # lower energy structure found
-                                                logger.warning(f'Lower energy conformer during HIR for {self.name} for rotor {min_rotor}. Restart #{self.restart}')
-                                                logger.debug('Rotor: ' + str(min_rotor))
-                                                logger.debug('Scan point: ' + str(min_ai))
-                                                job = self.log_name(1, hir=1, r=min_rotor, s=min_ai)
+                                                logger.warning(f'Lower energy conformer during HIR: {job}, diff = {np.round(diff, 2)} kcal/mol. Restart #{self.restart}')
 
                                                 err, self.species.geom = self.qc.get_qc_geom(job, self.species.natom)
                                                 # err, geom = self.qc.get_qc_geom(job, self.species.natom)
@@ -311,7 +312,7 @@ class Optimize:
                                                 self.shigh = -1
                                                 self.shir = -1
                                             else:
-                                                logger.warning(f'Lower energy conformer found, but reached max restart for {self.name}')
+                                                logger.warning(f'Lower energy during HIR: {job}, diff = {np.round(diff, 2)} kcal/mol. Reached max restart for this species.')
                                                 self.shir = 1
                                         else:
                                             self.shir = 1