kinbot 2.2.4__tar.gz → 2.3.0__tar.gz

{kinbot-2.2.4/KinBot.egg-info → kinbot-2.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: kinbot
-Version: 2.2.4
+Version: 2.3.0
 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>
@@ -42,20 +42,26 @@ Classifier: Intended Audience :: Science/Research
 Classifier: Natural Language :: English
 Classifier: License :: OSI Approved :: BSD License
 Classifier: Operating System :: OS Independent
-Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Classifier: Topic :: Scientific/Engineering :: Chemistry
-Requires-Python: >=3.10
+Requires-Python: >=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: numpy>=1.17.0
-Requires-Dist: ase<3.22,>=3.19
+Requires-Dist: ase>=3.26
 Requires-Dist: networkx
 Requires-Dist: rmsd>=1.5.1
-Requires-Dist: sella
+Requires-Dist: sella>=2.5.0
 Provides-Extra: plot
 Requires-Dist: matplotlib; extra == "plot"
 Requires-Dist: pyvis; extra == "plot"
 Requires-Dist: rdkit; extra == "plot"
+Provides-Extra: fc
+Requires-Dist: fairchem-core>=2.0; extra == "fc"
+Requires-Dist: scipy>=1.15; extra == "fc"
+Dynamic: license-file
 
 [![Gitter chat](https://badges.gitter.im/gitterHQ/gitter.png)](https://gitter.im/zadorlab/KinBot)
 
@@ -108,7 +114,7 @@ KinBot can be installed both in three different ways, from the PyPI index (`pip
     pip install kinbot
 
 > **Note**
->  KinBot only works with Python >= 3.10.
+>  KinBot only works with Python >= 3.11.
 
 ### conda-forge
 
@@ -142,7 +148,7 @@ To run a full PES search, make an input file (e.g. input.json) and run:
 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.
+See the [wiki](https://github.com/zadorlab/KinBot/wiki) for keywords, and our [tutorial](https://hackmd.io/@jzador/ry1DSsEyyx#/) 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).
@@ -155,28 +161,33 @@ See [list](https://github.com/zadorlab/KinBot/wiki/KinBot-file-structure).
 * Clément Soulié (csoulie@sandia.gov)
 
 ## Papers using KinBot
-1. Hansen, N., Gaiser, N., Bierkandt, T., Oßwald, P., Köhler, M., Zádor, J., Hemberger, P.: _Identification of dihydropentalenes as products of the molecular-weight growth reaction of cyclopentadienyl plus propargyl_. J. Phys. Chem. A, **2025** 129 1714-1725. https://doi.org/10.1021/acs.jpca.4c06549
-2. Almeida, T. G., Martí, C., Kurtén, T., Zádor, J., Johansen, S. L.: _Theoretical analysis of the OH-Initiated atmospheric oxidation reactions of imidazole_. Phys. Chem. Chem. Phys., **2024** 26 23570-23587. https://doi.org/10.1039/D4CP02103G
-3. Yuan, E. C.-Y., Kumar, A., Guan, X., Hermes, E. D., Rosen, A. S., Zádor, J., Head-Gordon, T., Blau, S. M.: _Analytical ab initio Hessian from a Deep Learning Potential for Transition State Optimization_. Nat. Comm., **2024** 15 8865. https://doi.org/10.1038/s41467-024-52481-5
-4. Doner, A. C., Zádor, J., Rotavera, B.: _Stereoisomer-dependent rate coefficients and reaction mechanisms of 2-ethyloxetanylperoxy radicals_. Proc. Combust. Inst., **2024**, 40, 105578. https://doi.org/10.1016/j.proci.2024.105578
-5. Hansen, N. A, Price, T. D., Filardi, L. R., Gurses, S. M., Zhou, W., Hansen, N., Osborn, D. L. Zádor, J., Kronawitter, C. X.: _The photoionization of methoxymethanol: Fingerprinting a reactive C2 oxygenate in a complex reactive mixture_. J. Chem. Phys., **2024**, 160, 124306. https://doi.org/10.1063/5.0197827
-6. Martí, C., Devereux, C., Najm, H. N., Zádor, J.: _Evaluation of rate coefficients in the gas-phase using a machine learned potential_. J. Phys. Chem. A, **2024**, 128, 1958–1971. https://doi.org/10.1021/acs.jpca.3c07872
-7. Lang, J., Foley, C. D., Thawoos, S., Behzadfar, A., Liu, Y., Zádor, J., Suits, A. G.: _Reaction dynamics of S(3P) with 1,3-butadiene and isoprene: Crossed beam scattering, low temperature flow experiments, and high-level electronic structure calculations_. Farad. Discuss., **2024**, 251, 550-572. https://doi.org/10.1039/D4FD00009A
-8. Wang, D., Tian, Z.-Y., Zheng, Z.-H., Li, W., Wu, L.-N., Kuang, J.-J., Yang, J.-Z.: _Experimental and modeling study of the n, n-dimethylformamide pyrolysis at atmospheric pressure_. Combust. Flame, **2024**, 260, 113240. https://doi.org/10.1016/j.combustflame.2023.113240
-9. Doner, A. C., Zádor, J., Rotavera, B.: _Unimolecular reactions of 2,4-dimethyloxetanyl radicals._ J. Phys. Chem A, **2023**, 127, 2591–2600 https://doi.org/10.1021/acs.jpca.2c08290
-10. Li, H., Lang, J., Foley, C. D., Zádor, J., Suits, A. G.: _Sulfur (3P) reaction with conjugated dienes gives cyclization to thiophenes under single collision conditions._ J. Phys. Chem. Letters, **2023**, 14, 7611–7617. https://doi.org/10.1021/acs.jpclett.3c01953
-11. Martí, C., Michelsen, H. A., Najm, H. N., Zádor, J.: _Comprehensive kinetics on the C7H7 potential energy surface under combustion conditions._ J. Phys. Chem. A, **2023**, 127, 1941–1959. https://pubs.acs.org/doi/full/10.1021/acs.jpca.2c08035
-12. Zádor, J, Martí, C., Van de Vijver, R., Johansen, S. L., Yang, Y., Michelsen, H. A., Najm, H. N.: _Automated reaction kinetics of gas-phase organic species over multiwell potential energy surfaces._ J. Phys. Chem. A, **2023**, 127, 565–588. https://doi.org/10.1021/acs.jpca.2c06558
-13. Lockwood, K. S., Ahmed, S. F., Huq, N. A., Stutzman, S. C., Foust, T. D., Labbe, N. J.: _Advances in predictive chemistry enable a multi-scale rational design approach for biofuels with advantaged properties_ Sustainable Energy Fuels, **2022**, 6, 5371-5383. https://doi.org/10.1039/D2SE00773H
-14. Takahashi, L., Yoshida, S., Fujima, J., Oikawa, H., Takahashi, K.: _Unveiling the reaction pathways of hydrocarbons via experiments, computations and data science._ Phys. Chem. Chem. Phys., **2022**, 24, 29841-29849. https://pubs.rsc.org/en/content/articlelanding/2022/CP/D2CP04499D
-15. Doner, A. C., Zádor, J., Rotavera, B.: _Stereoisomer-dependent unimolecular kinetics of 2,4-dimethyloxetane peroxy radicals._ Faraday Discuss., **2022**, 238, 295-319. https://doi.org/10.1039/D2FD00029F
-16. Ramasesha, K., Savee, J. D., Zádor, J., Osborn, D. L.: _A New Pathway for Intersystem Crossing: Unexpected Products in the O(3P) + Cyclopentene Reaction._ J. Phys. Chem. A, **2021**, 125 9785-9801. https://doi.org/10.1021/acs.jpca.1c05817
-17. Rogers, C. O, Lockwood, K. S., Nguyen, Q. L. D., Labbe, N. J.: _Diol isomer revealed as a source of methyl ketene from propionic acid unimolecular decomposition._ Int. J. Chem. Kinet., **2021**, 53, 1272–1284. https://doi.org/10.1002/kin.21532
-18. Lockwood, K. S., Labbe, N. J.: _Insights on keto-hydroperoxide formation from O2 addition to the beta-tetrahydrofuran radical._ Proceedings of the Combustion Institute, **2021**, 38, 1, 533. https://doi.org/10.1016/j.proci.2020.06.357
-19. Sheps, L., Dewyer, A. L., Demireva, M., and Zádor, J.: _Quantitative Detection of Products and Radical Intermediates in Low-Temperature Oxidation of Cyclopentane._ J. Phys. Chem. A **2021**, 125, 20, 4467. https://doi.org/10.1021/acs.jpca.1c02001
-20. Zhang, J., Vermeire, F., Van de Vijver, R., Herbinet, O.; Battin-Leclerc, F., Reyniers, M.-F., Van Geem, K. M.: _Detailed experimental and kinetic modeling study of 3-carene pyrolysis._ Int. J. Chem. Kinet., **2020**, 52, 785-795. https://doi.org/10.1002/kin.21400
-21. Van de Vijver, R., Zádor, J.: _KinBot: Automated stationary point search on potential energy surfaces._ Computer Physics Communications, **2020**, 248, 106947. https://doi.org/10.1016/j.cpc.2019.106947
-22. Joshi, S. P., Seal, P., Pekkanen, T. T., Timonen, R. S., Eskola, A. J.: _Direct Kinetic Measurements and Master Equation Modelling of the Unimolecular Decomposition of Resonantly-Stabilized CH2CHCHC(O)OCH3 Radical and an Upper Limit Determination for CH2CHCHC(O)OCH3+O2 Reaction._ Z. Phys. Chem., **2020**, 234, 1251. https://doi.org/10.1515/zpch-2020-1612
+1.	Kjaersgaard, A., Zádor J., Zwier, T. S., Shiels, O.J., Sheps, L.: _Measurement of the CH3SCH2O2 -> CH2SCH2OOH rate coefficient and mass spectrometric characterization of hydroperoxymethyl thioformate (HPMTF) at T = 400 – 550 K._ J. Phys. Chem. A, **2025** accepted. https://doi.org/10.1021/acs.jpca.5c06279
+2. Shiels, O. J., Kjaersgaard, A., Zádor, J., Sheps, L.: _Low-temperature autooxidation of cyclopentanone and 3-pentanone: The critical role of competing radical chain-branching and chain inhibiting pathways._ Phys. Chem. Chem. Phys., **2025** accepted. https://doi.org/10.1039/D5CP03403E
+3. Osborn, D. L., Samanta, B. R., Soulié, C., Reisler, H., Zádor, J.: _Chemistry of sugar formation in the gas phase: Following the activated aldehyde_. J. Am. Chem. Soc., **2025** 147, 32468–32479. https://doi.org/10.1021/jacs.5c05357
+4. 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
+5. Wang, Z.-M., Wang, D., Mansy, A. E., Tian, Z.-Y.: _Pyrolysis and kinetic modeling investigation of 1-methoxy-2-propanol_. Combust. Flame, **2025**, 271, 113804. https://doi.org/10.1016/j.combustflame.2024.113804
+6. 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
+7. 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
+8. 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
+9. 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
+10. 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
+11. 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
+12. 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
+13. Wang, D. Dai, W.-K., Tian, Z.-Y., Liu, Y.-W., Wang, Z.-M., Wu, L.-N., Kuang, J.-J., Wang ,Q.-P., Xu, Q., Wang, Z.-D.: _Theoretical and experimental study on the pyrolysis of N-methylpyrrolidone_. J Anal Appl Pyrolysis, **2024**, 183, 106751. https://doi.org/10.1016/j.jaap.2024.106751
+14. 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
+15. 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
+16. 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
+17. 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
+18. 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
+19. 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
+20. 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
+21. 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
+22. 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
+23. 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
+24. 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
+25. 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
+26. 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
+27. 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-2.2.4 → kinbot-2.3.0}/README.md

@@ -49,7 +49,7 @@ KinBot can be installed both in three different ways, from the PyPI index (`pip
     pip install kinbot
 
 > **Note**
->  KinBot only works with Python >= 3.10.
+>  KinBot only works with Python >= 3.11.
 
 ### conda-forge
 
@@ -83,7 +83,7 @@ To run a full PES search, make an input file (e.g. input.json) and run:
 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.
+See the [wiki](https://github.com/zadorlab/KinBot/wiki) for keywords, and our [tutorial](https://hackmd.io/@jzador/ry1DSsEyyx#/) 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).
@@ -96,28 +96,33 @@ See [list](https://github.com/zadorlab/KinBot/wiki/KinBot-file-structure).
 * Clément Soulié (csoulie@sandia.gov)
 
 ## Papers using KinBot
-1. Hansen, N., Gaiser, N., Bierkandt, T., Oßwald, P., Köhler, M., Zádor, J., Hemberger, P.: _Identification of dihydropentalenes as products of the molecular-weight growth reaction of cyclopentadienyl plus propargyl_. J. Phys. Chem. A, **2025** 129 1714-1725. https://doi.org/10.1021/acs.jpca.4c06549
-2. Almeida, T. G., Martí, C., Kurtén, T., Zádor, J., Johansen, S. L.: _Theoretical analysis of the OH-Initiated atmospheric oxidation reactions of imidazole_. Phys. Chem. Chem. Phys., **2024** 26 23570-23587. https://doi.org/10.1039/D4CP02103G
-3. Yuan, E. C.-Y., Kumar, A., Guan, X., Hermes, E. D., Rosen, A. S., Zádor, J., Head-Gordon, T., Blau, S. M.: _Analytical ab initio Hessian from a Deep Learning Potential for Transition State Optimization_. Nat. Comm., **2024** 15 8865. https://doi.org/10.1038/s41467-024-52481-5
-4. Doner, A. C., Zádor, J., Rotavera, B.: _Stereoisomer-dependent rate coefficients and reaction mechanisms of 2-ethyloxetanylperoxy radicals_. Proc. Combust. Inst., **2024**, 40, 105578. https://doi.org/10.1016/j.proci.2024.105578
-5. Hansen, N. A, Price, T. D., Filardi, L. R., Gurses, S. M., Zhou, W., Hansen, N., Osborn, D. L. Zádor, J., Kronawitter, C. X.: _The photoionization of methoxymethanol: Fingerprinting a reactive C2 oxygenate in a complex reactive mixture_. J. Chem. Phys., **2024**, 160, 124306. https://doi.org/10.1063/5.0197827
-6. Martí, C., Devereux, C., Najm, H. N., Zádor, J.: _Evaluation of rate coefficients in the gas-phase using a machine learned potential_. J. Phys. Chem. A, **2024**, 128, 1958–1971. https://doi.org/10.1021/acs.jpca.3c07872
-7. Lang, J., Foley, C. D., Thawoos, S., Behzadfar, A., Liu, Y., Zádor, J., Suits, A. G.: _Reaction dynamics of S(3P) with 1,3-butadiene and isoprene: Crossed beam scattering, low temperature flow experiments, and high-level electronic structure calculations_. Farad. Discuss., **2024**, 251, 550-572. https://doi.org/10.1039/D4FD00009A
-8. Wang, D., Tian, Z.-Y., Zheng, Z.-H., Li, W., Wu, L.-N., Kuang, J.-J., Yang, J.-Z.: _Experimental and modeling study of the n, n-dimethylformamide pyrolysis at atmospheric pressure_. Combust. Flame, **2024**, 260, 113240. https://doi.org/10.1016/j.combustflame.2023.113240
-9. Doner, A. C., Zádor, J., Rotavera, B.: _Unimolecular reactions of 2,4-dimethyloxetanyl radicals._ J. Phys. Chem A, **2023**, 127, 2591–2600 https://doi.org/10.1021/acs.jpca.2c08290
-10. Li, H., Lang, J., Foley, C. D., Zádor, J., Suits, A. G.: _Sulfur (3P) reaction with conjugated dienes gives cyclization to thiophenes under single collision conditions._ J. Phys. Chem. Letters, **2023**, 14, 7611–7617. https://doi.org/10.1021/acs.jpclett.3c01953
-11. Martí, C., Michelsen, H. A., Najm, H. N., Zádor, J.: _Comprehensive kinetics on the C7H7 potential energy surface under combustion conditions._ J. Phys. Chem. A, **2023**, 127, 1941–1959. https://pubs.acs.org/doi/full/10.1021/acs.jpca.2c08035
-12. Zádor, J, Martí, C., Van de Vijver, R., Johansen, S. L., Yang, Y., Michelsen, H. A., Najm, H. N.: _Automated reaction kinetics of gas-phase organic species over multiwell potential energy surfaces._ J. Phys. Chem. A, **2023**, 127, 565–588. https://doi.org/10.1021/acs.jpca.2c06558
-13. Lockwood, K. S., Ahmed, S. F., Huq, N. A., Stutzman, S. C., Foust, T. D., Labbe, N. J.: _Advances in predictive chemistry enable a multi-scale rational design approach for biofuels with advantaged properties_ Sustainable Energy Fuels, **2022**, 6, 5371-5383. https://doi.org/10.1039/D2SE00773H
-14. Takahashi, L., Yoshida, S., Fujima, J., Oikawa, H., Takahashi, K.: _Unveiling the reaction pathways of hydrocarbons via experiments, computations and data science._ Phys. Chem. Chem. Phys., **2022**, 24, 29841-29849. https://pubs.rsc.org/en/content/articlelanding/2022/CP/D2CP04499D
-15. Doner, A. C., Zádor, J., Rotavera, B.: _Stereoisomer-dependent unimolecular kinetics of 2,4-dimethyloxetane peroxy radicals._ Faraday Discuss., **2022**, 238, 295-319. https://doi.org/10.1039/D2FD00029F
-16. Ramasesha, K., Savee, J. D., Zádor, J., Osborn, D. L.: _A New Pathway for Intersystem Crossing: Unexpected Products in the O(3P) + Cyclopentene Reaction._ J. Phys. Chem. A, **2021**, 125 9785-9801. https://doi.org/10.1021/acs.jpca.1c05817
-17. Rogers, C. O, Lockwood, K. S., Nguyen, Q. L. D., Labbe, N. J.: _Diol isomer revealed as a source of methyl ketene from propionic acid unimolecular decomposition._ Int. J. Chem. Kinet., **2021**, 53, 1272–1284. https://doi.org/10.1002/kin.21532
-18. Lockwood, K. S., Labbe, N. J.: _Insights on keto-hydroperoxide formation from O2 addition to the beta-tetrahydrofuran radical._ Proceedings of the Combustion Institute, **2021**, 38, 1, 533. https://doi.org/10.1016/j.proci.2020.06.357
-19. Sheps, L., Dewyer, A. L., Demireva, M., and Zádor, J.: _Quantitative Detection of Products and Radical Intermediates in Low-Temperature Oxidation of Cyclopentane._ J. Phys. Chem. A **2021**, 125, 20, 4467. https://doi.org/10.1021/acs.jpca.1c02001
-20. Zhang, J., Vermeire, F., Van de Vijver, R., Herbinet, O.; Battin-Leclerc, F., Reyniers, M.-F., Van Geem, K. M.: _Detailed experimental and kinetic modeling study of 3-carene pyrolysis._ Int. J. Chem. Kinet., **2020**, 52, 785-795. https://doi.org/10.1002/kin.21400
-21. Van de Vijver, R., Zádor, J.: _KinBot: Automated stationary point search on potential energy surfaces._ Computer Physics Communications, **2020**, 248, 106947. https://doi.org/10.1016/j.cpc.2019.106947
-22. Joshi, S. P., Seal, P., Pekkanen, T. T., Timonen, R. S., Eskola, A. J.: _Direct Kinetic Measurements and Master Equation Modelling of the Unimolecular Decomposition of Resonantly-Stabilized CH2CHCHC(O)OCH3 Radical and an Upper Limit Determination for CH2CHCHC(O)OCH3+O2 Reaction._ Z. Phys. Chem., **2020**, 234, 1251. https://doi.org/10.1515/zpch-2020-1612
+1.	Kjaersgaard, A., Zádor J., Zwier, T. S., Shiels, O.J., Sheps, L.: _Measurement of the CH3SCH2O2 -> CH2SCH2OOH rate coefficient and mass spectrometric characterization of hydroperoxymethyl thioformate (HPMTF) at T = 400 – 550 K._ J. Phys. Chem. A, **2025** accepted. https://doi.org/10.1021/acs.jpca.5c06279
+2. Shiels, O. J., Kjaersgaard, A., Zádor, J., Sheps, L.: _Low-temperature autooxidation of cyclopentanone and 3-pentanone: The critical role of competing radical chain-branching and chain inhibiting pathways._ Phys. Chem. Chem. Phys., **2025** accepted. https://doi.org/10.1039/D5CP03403E
+3. Osborn, D. L., Samanta, B. R., Soulié, C., Reisler, H., Zádor, J.: _Chemistry of sugar formation in the gas phase: Following the activated aldehyde_. J. Am. Chem. Soc., **2025** 147, 32468–32479. https://doi.org/10.1021/jacs.5c05357
+4. 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
+5. Wang, Z.-M., Wang, D., Mansy, A. E., Tian, Z.-Y.: _Pyrolysis and kinetic modeling investigation of 1-methoxy-2-propanol_. Combust. Flame, **2025**, 271, 113804. https://doi.org/10.1016/j.combustflame.2024.113804
+6. 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
+7. 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
+8. 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
+9. 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
+10. 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
+11. 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
+12. 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
+13. Wang, D. Dai, W.-K., Tian, Z.-Y., Liu, Y.-W., Wang, Z.-M., Wu, L.-N., Kuang, J.-J., Wang ,Q.-P., Xu, Q., Wang, Z.-D.: _Theoretical and experimental study on the pyrolysis of N-methylpyrrolidone_. J Anal Appl Pyrolysis, **2024**, 183, 106751. https://doi.org/10.1016/j.jaap.2024.106751
+14. 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
+15. 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
+16. 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
+17. 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
+18. 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
+19. 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
+20. 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
+21. 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
+22. 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
+23. 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
+24. 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
+25. 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
+26. 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
+27. 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-2.2.4 → kinbot-2.3.0}/kinbot/ase_modules/calculators/gaussian.py

@@ -1,5 +1,6 @@
 import os
 import copy
+import subprocess
 from collections.abc import Iterable
 from shutil import which
 from typing import Dict, Optional
@@ -102,6 +103,21 @@ class Gaussian(FileIOCalculator):
     def __init__(self, *args, label='Gaussian', **kwargs):
         FileIOCalculator.__init__(self, *args, label=label, **kwargs)
 
+    def _initialize_profile(self, command):
+        # KinBot resolves the Gaussian executable dynamically in calculate();
+        # skip ASE's profile/config-file system entirely.
+        return None
+
+    def execute(self):
+        command = self.command.replace('PREFIX', self.prefix)
+        directory = getattr(self, 'directory', '.')
+        proc = subprocess.Popen(command, shell=True, cwd=directory)
+        errorcode = proc.wait()
+        if errorcode:
+            raise RuntimeError(
+                f'Gaussian exited with error code {errorcode} '
+                f'(command: {command})')
+
     def calculate(self, *args, **kwargs):
         gaussians = ('g16', 'g09', 'g03')
         if 'GAUSSIAN' in self.command:

kinbot-2.3.0/kinbot/ase_modules/calculators/orca.py

@@ -0,0 +1,99 @@
+import re
+
+import ase.io.orca as io
+from ase.calculators.genericfileio import (
+    BaseProfile,
+    CalculatorTemplate,
+    GenericFileIOCalculator,
+)
+
+
+def get_version_from_orca_header(orca_header):
+    match = re.search(r'Program Version (\S+)', orca_header, re.M)
+    return match.group(1)
+
+
+class OrcaProfile(BaseProfile):
+    def version(self):
+        # XXX Allow MPI in argv; the version call should not be parallel.
+        from ase.calculators.genericfileio import read_stdout
+        stdout = read_stdout([self.command, "does_not_exist"])
+        return get_version_from_orca_header(stdout)
+
+    def get_calculator_command(self, inputfile):
+        return [inputfile]
+
+
+class OrcaTemplate(CalculatorTemplate):
+    _label = 'orca'
+
+    def __init__(self):
+        super().__init__('orca',
+                         implemented_properties=['energy', 'free_energy',
+                                                 'forces', 'dipole'])
+
+        self.inputname = f'{self._label}.inp'
+        self.outputname = f'{self._label}.out'
+        self.errorname = f'{self._label}.err'
+
+    def execute(self, directory, profile) -> None:
+        profile.run(directory, self.inputname, self.outputname,
+                    errorfile=self.errorname)
+
+    def write_input(self, profile, directory, atoms, parameters, properties):
+        parameters = dict(parameters)
+
+        kw = dict(charge=0, mult=1, orcasimpleinput='B3LYP def2-TZVP',
+                  orcablocks='%pal nprocs 1 end')
+        kw.update(parameters)
+
+        io.write_orca(directory / self.inputname, atoms, kw)
+
+    def read_results(self, directory):
+        return io.read_orca_outputs(directory, directory / self.outputname)
+
+    def load_profile(self, cfg, **kwargs):
+        return OrcaProfile.from_config(cfg, self.name, **kwargs)
+
+class ORCA(GenericFileIOCalculator):
+    """Class for doing ORCA calculations.
+
+    Example:
+
+      calc = ORCA(charge=0, mult=1, orcasimpleinput='B3LYP def2-TZVP',
+        orcablocks='%pal nprocs 16 end')
+    """
+
+    def __init__(self, *, profile=None, directory='.', **kwargs):
+        """Construct ORCA-calculator object.
+
+        Parameters
+        ==========
+        charge: int
+
+        mult: int
+
+        orcasimpleinput : str
+
+        orcablocks: str
+
+
+        Examples
+        ========
+        Use default values:
+
+        >>> from ase.calculators.orca import ORCA
+        >>> h = Atoms(
+        ...     'H',
+        ...     calculator=ORCA(
+        ...         charge=0,
+        ...         mult=1,
+        ...         directory='water',
+        ...         orcasimpleinput='B3LYP def2-TZVP',
+        ...         orcablocks='%pal nprocs 16 end'))
+
+        """
+
+        super().__init__(template=OrcaTemplate(),
+                         profile=profile, directory=directory,
+                         parameters=kwargs)

{kinbot-2.2.4 → kinbot-2.3.0}/kinbot/ase_modules/calculators/qchem.py

@@ -1,3 +1,4 @@
+import subprocess
 import numpy as np
 from ase.calculators.calculator import FileIOCalculator
 import ase.units
@@ -19,35 +20,9 @@ class QChem(FileIOCalculator):
                           'jobtype': None,
                           'charge': 0}
 
-    def __init__(self, restart=None,
-                 ignore_bad_restart_file=FileIOCalculator._deprecated,
-                 label='qchem', scratch=None, np=1, nt=1, pbs=False,
-                 basisfile=None, ecpfile=None, atoms=None, **kwargs):
-        """
-        The scratch directory, number of processor and threads as well as a few
-        other command line options can be set using the arguments explained
-        below. The remaining kwargs are copied as options to the input file.
-        The calculator will convert these options to upper case
-        (Q-Chem standard) when writing the input file.
-
-        scratch: str
-            path of the scratch directory
-        np: int
-            number of processors for the -np command line flag
-        nt: int
-            number of threads for the -nt command line flag
-        pbs: boolean
-            command line flag for pbs scheduler (see Q-Chem manual)
-        basisfile: str
-            path to file containing the basis. Use in combination with
-            basis='gen' keyword argument.
-        ecpfile: str
-            path to file containing the effective core potential. Use in
-            combination with ecp='gen' keyword argument.
-        """
-
-        FileIOCalculator.__init__(self, restart, ignore_bad_restart_file,
-                                  label, atoms, **kwargs)
+    def __init__(self, label='qchem', scratch=None, np=1, nt=1, pbs=False,
+                 basisfile=None, ecpfile=None, **kwargs):
+        FileIOCalculator.__init__(self, label=label, **kwargs)
 
         # Augment the command by various flags
         if pbs:
@@ -65,6 +40,19 @@ class QChem(FileIOCalculator):
         self.basisfile = basisfile
         self.ecpfile = ecpfile
 
+    def _initialize_profile(self, command):
+        return None
+
+    def execute(self):
+        command = self.command.replace('PREFIX', self.prefix)
+        directory = getattr(self, 'directory', '.')
+        proc = subprocess.Popen(command, shell=True, cwd=directory)
+        errorcode = proc.wait()
+        if errorcode:
+            raise RuntimeError(
+                f'QChem exited with error code {errorcode} '
+                f'(command: {command})')
+
     def read(self, label):
         raise NotImplementedError
 

{kinbot-2.2.4 → kinbot-2.3.0}/kinbot/conformers.py

@@ -436,14 +436,16 @@ class Conformers:
 
                 if all(status):  # if all conformers are invalid, 1 (different) or fail (-1)
                     if self.qc.qc == 'gauss':
-                        ext = 'log'
+                        ext = '.log'
                     elif self.qc.qc == 'qchem':
-                        ext = 'out'
+                        ext = '.out'
                     elif self.qc.qc == 'nn_pes':
-                        ext = 'log'
+                        ext = '.log'
+                    elif self.qc.qc == 'fc' or self.qc.qc == 'orca':
+                        ext = '_sella.log'
                     else:
                         raise NotImplementedError(f'Code {self.qc.qc} not available.')
-                    copyfile(f'{lowest_job}.{ext}', f'conf/{name}_low.{ext}')
+                    copyfile(f'{lowest_job}{ext}', f'conf/{name}_low{ext}')
                     mol = Atoms(symbols=last_row.symbols, positions=last_row.positions)
                     data = {'energy': last_row.data.get('energy'),
                             'frequencies': last_row.data.get('frequencies'),
@@ -555,11 +557,14 @@ class Conformers:
                         copyfile(f'{lowest_job}.log', f'conf/{name}_low.log')
                     elif self.qc.qc == 'qchem':
                         copyfile(f'{lowest_job}.out', f'conf/{name}_low.out')
-                    elif self.qc.qc == 'nn_pes':
+                    elif self.qc.qc == 'nn_pes' or self.qc.qc == 'fc':
                         pass
+                    elif self.qc.qc == 'fc' or self.qc.qc == 'orca':
+                        copyfile(f'{lowest_job}_sella.log', f'conf/{name}_low_sella.log')
                     else:
                         raise NotImplementedError(f'Code {self.qc.qc} not available.')
                     rows = self.db.select(name='{}'.format(lowest_job))
+                    logger.debug(f'Looking at {name} in conformers')
                     for row in rows:
                         row_last = row
                     mol = Atoms(symbols=row_last.symbols, positions=row_last.positions)

{kinbot-2.2.4 → kinbot-2.3.0}/kinbot/constants.py

@@ -6,7 +6,7 @@ AUtoCM = 219474.63068
 CMtoKCAL = 0.0028591
 GHZtoCM = 0.0333564
 EVtoHARTREE = 0.03674932247495664
-MEtoAMU = 1822.8885  # electron mass to atomic mass unit
+MEtoAMU = 1822.8885  # electron mass to be in atomic mass unit
 BOHRtoCM = 5.2917720859E-9  # value taken from the Gaussian website
 BOHRtoANGSTROM = 0.529177
 SPEEDofLIGHTcms = 2.99792458E10  # in cm per s
@@ -112,7 +112,7 @@ exact_mass['I'] = 126.904477
 # data is expected in CHEMKIN format, where
 # sigma is in Angstrom (no need to convert for MESS)
 # epsilon is in epsilon/kB (K), need to be converted to cm-1
-mass['He'] = 4.0
+mass['He'] = 4.002602 # u
 sigma = {'He': 2.715}  # Angstrom
 epsilon = {'He': 11.442}  # e/kB
 
@@ -120,10 +120,19 @@ mass['N2'] = mass['N'] * 2.
 sigma['N2'] = 3.610
 epsilon['N2'] = 97.839
 
-mass['Ar'] = 40.
+mass['Ar'] = 39.948 # u
 sigma['Ar'] = 3.462
 epsilon['Ar'] = 127.697
 
+# for Krypton
+# Gábor Rutkai, Monika Thol, Roland Span & Jadran Vrabec (2017) How well
+# does the Lennard-Jones potential represent the thermodynamic properties of noble gases? ,
+# Molecular Physics, 115:9-12, 1104-1121, DOI: 10.1080/00268976.2016.1246760
+
+mass['Kr'] = 83.798 # u
+sigma['Kr'] = 3.6274 # Angstrom
+epsilon['Kr'] = 162.58  # K, e/kB
+
 for e in epsilon:
     epsilon[e] = epsilon[e] * units.kB / units.invcm
 
@@ -135,6 +144,8 @@ qext = {'pbs': '.pbs',
         'slurm': '.sbatch',
         }
 
+mp2_list = ['R_Addition_MultipleBond', 'reac_birad_recombination_R', 
+            'reac_r12_cycloaddition', 'reac_r14_birad_scission']
 
 def main():
     """

{kinbot-2.2.4 → kinbot-2.3.0}/kinbot/fragments.py

@@ -668,21 +668,21 @@ class Fragment(StationaryPoint):
         save_pos = np.arange(0, box_dim[2])
         for ln, line in enumerate(cubefile[start_line:stop_line]):
             nx = int(np.trunc((ln+start_line-start) / xsize))
-            if np.in1d(nx, np.arange(search_origin[0], search_end[0])):
+            if np.isin(nx, np.arange(search_origin[0], search_end[0])):
                 rest_y = (ln+start_line-start) % xsize
                 ny = int(np.trunc(rest_y / ysize))
-                if np.in1d(ny, np.arange(search_origin[1], search_end[1])):
+                if np.isin(ny, np.arange(search_origin[1], search_end[1])):
                     # rest_z goes from 0 to ysize-1
                     rest_z = rest_y % ysize
                     indexes_in_line: NDArray[Any] = np.arange(rest_z*6, rest_z*6+6)
-                    is_in_box: NDArray[bool_] = np.in1d(
+                    is_in_box: NDArray[bool_] = np.isin(
                         indexes_in_line,
                         np.arange(search_origin[2], search_end[2]))
                     zidx_in_box = (
                         indexes_in_line[is_in_box] - search_origin[2]
                         ).tolist()
                     # Boolean mask
-                    where2save = np.in1d(save_pos, zidx_in_box)
+                    where2save = np.isin(save_pos, zidx_in_box)
                     which2save = np.where(is_in_box)[0]
                     if not any(where2save):
                         continue

{kinbot-2.2.4 → kinbot-2.3.0}/kinbot/frequencies.py

@@ -1,8 +1,14 @@
+import os
+import shutil
 import numpy as np
 from ase.data import atomic_numbers, covalent_radii
+from ase import Atoms
+from ase.vibrations import Vibrations
 
 from kinbot import constants
 from kinbot import geometry
+from kinbot.stationary_pt import StationaryPoint
+from kinbot.constants import EVtoHARTREE
 
 
 def get_frequencies(species, hess, geom, checkdist=0, massweighted=False):
@@ -257,3 +263,34 @@ def skip_rotor(name, rot):
         return 0
     elif 'prod' in name:
         return 1
+
+
+def calc_vibrations(mol, label):
+    # this is a frequency calculator when ASE is used
+    mol.calc.label = f'{label}_vib'
+    if 'chk' in mol.calc.parameters:
+        del mol.calc.parameters['chk']
+    # Compute frequencies in a separate temporary directory to avoid 
+    # conflicts accessing the cache in parallel calculations.
+    if not os.path.isdir(f'{label}_vib'):
+        os.mkdir(f'{label}_vib')
+    init_dir = os.getcwd()
+    os.chdir(f'{label}_vib')
+    if os.path.isdir('vib'):
+        shutil.rmtree('vib')
+    vib = Vibrations(mol)
+    try:
+        vib.run()
+        vib.write_jmol()
+        # Use kinbot frequencies to avoid mixing low vib frequencies with 
+        # the values associated with external rotations.
+        _ = vib.get_frequencies()
+        zpe = vib.get_zero_point_energy() * EVtoHARTREE
+        hessian = vib.H / 97.17370087
+        st_pt = StationaryPoint.from_ase_atoms(mol)
+        st_pt.characterize()
+        freqs, _ = get_frequencies(st_pt, hessian, st_pt.geom)
+        os.chdir(init_dir)
+        return freqs, zpe, hessian
+    except:
+        return None, None, None