kinbot 2.2.1__tar.gz → 2.2.2__tar.gz

{kinbot-2.2.1 → kinbot-2.2.2}/KinBot.egg-info/PKG-INFO

@@ -1,13 +1,14 @@
 Metadata-Version: 2.1
 Name: kinbot
-Version: 2.2.1
+Version: 2.2.2
 Summary: Automated reaction kinetics for gas-phase species
-Author-email: Judit Zádor <jzador@sandia.gov>, Ruben Vande Vijver <ruben.vandevijver@ugent.be>, Carles Martí <cmartia@sandia.gov>, Amanda Dewyer <adewyer@sandia.gov>
-Maintainer-email: Judit Zádor <jzador@sandia.gov>, Carles Martí <cmartia@sandia.gov>
+Author-email: Judit Zádor <jzador@sandia.gov>, Ruben Van de Vijver <ruben.vandevijver@ugent.be>, Carles Martí <cmartia@sandia.gov>, Clément Soulié <csoulie@sandia.gov>, Amanda Dewyer <adewyer@sandia.gov>
+Maintainer-email: Judit Zádor <jzador@sandia.gov>, Clément Soulié <csoulie@sandia.gov>
 License: BSD 3-Clause License
         
-        Copyright (c) 2018, zadorlab
-        All rights reserved.
+        Copyright (c) 2018, National Technology & Engineering Solutions of Sandia,
+        LLC (NTESS). Under the terms of Contract DE-NA0003525 with NTESS,
+        the U.S. Government retains certain rights in this software
         
         Redistribution and use in source and binary forms, with or without
         modification, are permitted provided that the following conditions are met:
@@ -41,14 +42,20 @@ Classifier: Intended Audience :: Science/Research
 Classifier: Natural Language :: English
 Classifier: License :: OSI Approved :: BSD License
 Classifier: Operating System :: OS Independent
-Classifier: Programming Language :: Python :: 3.8
-Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Topic :: Scientific/Engineering :: Chemistry
-Requires-Python: >=3.8
+Requires-Python: >=3.10
 Description-Content-Type: text/markdown
-Provides-Extra: plot
 License-File: LICENSE
+Requires-Dist: numpy<2.0,>=1.17.0
+Requires-Dist: ase<3.23,>=3.19
+Requires-Dist: networkx
+Requires-Dist: rmsd>=1.5.1
+Requires-Dist: sella
+Provides-Extra: plot
+Requires-Dist: matplotlib; extra == "plot"
+Requires-Dist: pyvis; extra == "plot"
+Requires-Dist: rdkit; extra == "plot"
 
 [![Gitter chat](https://badges.gitter.im/gitterHQ/gitter.png)](https://gitter.im/zadorlab/KinBot)
 
@@ -59,14 +66,37 @@ License-File: LICENSE
 </p>
 
 ## Description
-This repository contains the KinBot code version 2.0,
+This repository contains the KinBot code version 2.2.1,
 a tool for automatically searching for reactions on the potential energy surface.
 
 If you are using this tool in scientific publications, please reference the following publications:
 
 * Ruben Van de Vijver, Judit Zádor: KinBot: _Automated stationary point search on potential energy surfaces_, Comp. Phys. Comm., **2019**, 248, 106947. https://doi.org/10.1016/j.cpc.2019.106947
+```
+@article{Vijver2020,
+   author = {Van de Vijver, Ruben and Z\'ador, Judit},
+   title = {KinBot: Automated stationary point search on potential energy surfaces},
+   journal = {Comput. Phys. Commun.},
+   volume = {248},
+   pages = {106947},
+   year = {2020},
+   type = {Journal Article}
+}
+```
 * Judit Zádor, Carles Martí, Ruben Van de Vijver, Sommer L. Johansen, Yoona Yang, Hope A. Michelsen, Habib N. Najm: _Automated reaction kinetics of gas-phase organic species over multiwell potential energy surfaces_, J. Phys. Chem. A, **2023**, 127, 565–588. https://doi.org/10.1021/acs.jpca.2c06558
 
+```
+@article{Zador2022,
+   author = {Z\'ador, Judit and Mart\'i, Carles and Van de Vijver, Ruben and Johansen, Sommer L. and Yang, Yoona and Michelsen, Hope A. and Najm, Habib N.},
+   title = {Automated reaction kinetics of gas-phase organic species over multiwell potential energy surfaces},
+   journal = {J. Phys. Chem. A},
+   volume = {127},
+   pages = {565-588},
+   year = {2023},
+   type = {Journal Article}
+}
+```
+
 We appreciate if you send us the DOI of your published paper that used KinBot, so we can feature it here below.
 
 ## How to Install
@@ -78,7 +108,7 @@ KinBot can be installed both in three different ways, from the PyPI index (`pip
     pip install kinbot
 
 > **Note**
->  KinBot only works with Python >= 3.8.
+>  KinBot only works with Python >= 3.10.
 
 ### conda-forge
 
@@ -112,18 +142,28 @@ 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 [wiki](https://github.com/zadorlab/KinBot/wiki).
+See the [wiki](https://github.com/zadorlab/KinBot/wiki) for keywords, and our [tutorial](https://hackmd.io/@jzador/kinbot_workshop_2023#/) for a more hands-on introduction to the code.
 
 ## List of files in this project
 See [list](https://github.com/zadorlab/KinBot/wiki/KinBot-file-structure).
 
 ## Authors
 * Judit Zádor (jzador@sandia.gov)
-* Ruben Van de Vijver (Ruben.VandeVijver@UGent.be)
+* Ruben Van de Vijver 
 * Amanda Dewyer
-* Carles Martí (cmartia@sandia.gov)
+* Carles Martí
+* Clément Soulié (csoulie@sandia.gov)
 
 ## Papers using KinBot
+* Almeida, T. G., Martí, C., Kurtén, T., Zádor, J., Johansen, S. L.: _Theoretical analysis of the OH-Initiated atmospheric oxidation reactions of imidazole_. Phys. Chem. Chem. Phys., **2024** 26 23570-23587. https://doi.org/10.1039/D4CP02103G
+* Yuan, E. C.-Y., Kumar, A., Guan, X., Hermes, E. D., Rosen, A. S., Zádor, J., Head-Gordon, T., Blau, S. M.: _Analytical ab initio Hessian from a Deep Learning Potential for Transition State Optimization_. Nat. Comm., **2024** 
+* Doner, A. C., Zádor, J., Rotavera, B.: _Stereoisomer-dependent rate coefficients and reaction mechanisms of 2-ethyloxetanylperoxy radicals_. Proc. Combust. Inst., **2024**, 40, 105578. https://doi.org/10.1016/j.proci.2024.105578
+* Hansen, N. A, Price, T. D., Filardi, L. R., Gurses, S. M., Zhou, W., Hansen, N., Osborn, D. L. Zádor, J., Kronawitter, C. X.: _The photoionization of methoxymethanol: Fingerprinting a reactive C2 oxygenate in a complex reactive mixture_. J. Chem. Phys., **2024**, 160, 124306. https://doi.org/10.1063/5.0197827 
+* Martí, C., Devereux, C., Najm, H. N., Zádor, J.: _Evaluation of rate coefficients in the gas-phase using a machine learned potential_. J. Phys. Chem. A, **2024**, 128, 1958–1971. https://doi.org/10.1021/acs.jpca.3c07872 
+* Lang, J., Foley, C. D., Thawoos, S., Behzadfar, A., Liu, Y., Zádor, J., Suits, A. G.: _Reaction dynamics of S(3P) with 1,3-butadiene and isoprene: Crossed beam scattering, low temperature flow experiments, and high-level electronic structure calculations_. Farad. Discuss., **2024**, 251, 550-572. https://doi.org/10.1039/D4FD00009A 
+* Wang, D., Tian, Z.-Y., Zheng, Z.-H., Li, W., Wu, L.-N., Kuang, J.-J., Yang, J.-Z.: _Experimental and modeling study of the n, n-dimethylformamide pyrolysis at atmospheric pressure_. Combust. Flame, **2024**, 260, 113240. https://doi.org/10.1016/j.combustflame.2023.113240
+* Doner, A. C., Zádor, J., Rotavera, B.: _Unimolecular reactions of 2,4-dimethyloxetanyl radicals._ J. Phys. Chem A, **2023**, 127, 2591–2600 https://doi.org/10.1021/acs.jpca.2c08290
+* Li, H., Lang, J., Foley, C. D., Zádor, J., Suits, A. G.: _Sulfur (3P) reaction with conjugated dienes gives cyclization to thiophenes under single collision conditions._ J. Phys. Chem. Letters, **2023**, 14, 7611–7617. https://doi.org/10.1021/acs.jpclett.3c01953
 * Martí, C., Michelsen, H. A., Najm, H. N., Zádor, J.: _Comprehensive kinetics on the C7H7 potential energy surface under combustion conditions._ J. Phys. Chem. A, **2023**, 127, 1941–1959. https://pubs.acs.org/doi/full/10.1021/acs.jpca.2c08035  
 * Zádor, J, Martí, C., Van de Vijver, R., Johansen, S. L., Yang, Y., Michelsen, H. A., Najm, H. N.: _Automated reaction kinetics of gas-phase organic species over multiwell potential energy surfaces._ J. Phys. Chem. A, **2023**, 127, 565–588. https://doi.org/10.1021/acs.jpca.2c06558
 * Lockwood, K. S., Ahmed, S. F., Huq, N. A., Stutzman, S. C., Foust, T. D., Labbe, N. J.: _Advances in predictive chemistry enable a multi-scale rational design approach for biofuels with advantaged properties_ Sustainable Energy Fuels, **2022**, 6, 5371-5383. https://doi.org/10.1039/D2SE00773H 

{kinbot-2.2.1 → kinbot-2.2.2}/KinBot.egg-info/SOURCES.txt

@@ -16,6 +16,7 @@ kinbot/conformers.py
 kinbot/constants.py
 kinbot/exceptions.py
 kinbot/find_motif.py
+kinbot/fragments.py
 kinbot/frequencies.py
 kinbot/geometry.py
 kinbot/hindered_rotors.py
@@ -31,6 +32,8 @@ kinbot/orca.py
 kinbot/parameters.py
 kinbot/pes.py
 kinbot/postprocess.py
+kinbot/pp_settings.py
+kinbot/pp_tables.py
 kinbot/qc.py
 kinbot/reac_General.py
 kinbot/reac_family.py
@@ -44,6 +47,8 @@ kinbot/symmetry.py
 kinbot/thread_kinbot.py
 kinbot/uncertaintyAnalysis.py
 kinbot/utils.py
+kinbot/vrc_tst_scan.py
+kinbot/vrc_tst_surfaces.py
 kinbot/zmatrix.py
 kinbot.egg-info/PKG-INFO
 kinbot.egg-info/SOURCES.txt
@@ -55,6 +60,7 @@ kinbot/ase_modules/__init__.py
 kinbot/ase_modules/constraints.py
 kinbot/ase_modules/calculators/__init__.py
 kinbot/ase_modules/calculators/gaussian.py
+kinbot/ase_modules/calculators/nn_pes.py
 kinbot/ase_modules/calculators/qchem.py
 kinbot/ase_modules/io/__init__.py
 kinbot/ase_modules/io/formats.py
@@ -114,6 +120,7 @@ kinbot/tpl/ase_gauss_opt_well.tpl.py
 kinbot/tpl/ase_gauss_ring_conf.tpl.py
 kinbot/tpl/ase_gauss_ts_end.tpl.py
 kinbot/tpl/ase_gauss_ts_search.tpl.py
+kinbot/tpl/ase_gauss_vts.tpl.py
 kinbot/tpl/ase_nwchem_freq_well.tpl.py
 kinbot/tpl/ase_nwchem_irc.tpl.py
 kinbot/tpl/ase_nwchem_opt_well.tpl.py
@@ -131,6 +138,7 @@ kinbot/tpl/ase_sella_opt_well.tpl.py
 kinbot/tpl/ase_sella_ring_conf.tpl.py
 kinbot/tpl/ase_sella_ts_end.tpl.py
 kinbot/tpl/ase_sella_ts_search.tpl.py
+kinbot/tpl/ase_sella_vts.tpl.py
 kinbot/tpl/local_molpro.tpl
 kinbot/tpl/mess_2tst.tpl
 kinbot/tpl/mess_atom.tpl
@@ -146,6 +154,7 @@ kinbot/tpl/mess_fragment_OH.tpl
 kinbot/tpl/mess_freerotor.tpl
 kinbot/tpl/mess_header.tpl
 kinbot/tpl/mess_hinderedrotor.tpl
+kinbot/tpl/mess_hinderedrotorgeom.tpl
 kinbot/tpl/mess_outerrrho.tpl
 kinbot/tpl/mess_pst.tpl
 kinbot/tpl/mess_pstfragment.tpl
@@ -157,6 +166,8 @@ kinbot/tpl/mess_variational.tpl
 kinbot/tpl/mess_well.tpl
 kinbot/tpl/mess_well_union.tpl
 kinbot/tpl/molpro.tpl
+kinbot/tpl/molpro_ts_search.tpl.py
+kinbot/tpl/molpro_vts.tpl
 kinbot/tpl/pbs.tpl
 kinbot/tpl/pbs_mesmer.tpl
 kinbot/tpl/pbs_mess.tpl
@@ -164,6 +175,11 @@ kinbot/tpl/pbs_mess_uq.tpl
 kinbot/tpl/pbs_molpro.tpl
 kinbot/tpl/pbs_python.tpl
 kinbot/tpl/pesviewer.inp.tpl
+kinbot/tpl/rotdPy.tpl
+kinbot/tpl/rotdPy_1d_corr.tpl
+kinbot/tpl/rotdPy_calc.tpl
+kinbot/tpl/rotdPy_frag.tpl
+kinbot/tpl/rotdPy_surf.tpl
 kinbot/tpl/slurm.tpl
 kinbot/tpl/slurm_mesmer.tpl
 kinbot/tpl/slurm_mess.tpl

{kinbot-2.2.1 → kinbot-2.2.2}/KinBot.egg-info/requires.txt

@@ -1,7 +1,8 @@
-numpy>=1.17.0
-ase>=3.19
+numpy<2.0,>=1.17.0
+ase<3.23,>=3.19
 networkx
 rmsd>=1.5.1
+sella
 
 [plot]
 matplotlib

{kinbot-2.2.1 → kinbot-2.2.2}/KinBot.egg-info/top_level.txt

@@ -1,3 +1,6 @@
+build
 examples
 kinbot
+reactions
 tests
+tpl

{kinbot-2.2.1 → kinbot-2.2.2}/LICENSE

@@ -1,7 +1,8 @@
 BSD 3-Clause License
 
-Copyright (c) 2018, zadorlab
-All rights reserved.
+Copyright (c) 2018, National Technology & Engineering Solutions of Sandia,
+LLC (NTESS). Under the terms of Contract DE-NA0003525 with NTESS,
+the U.S. Government retains certain rights in this software
 
 Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions are met:

{kinbot-2.2.1 → kinbot-2.2.2}/PKG-INFO

@@ -1,13 +1,14 @@
 Metadata-Version: 2.1
 Name: kinbot
-Version: 2.2.1
+Version: 2.2.2
 Summary: Automated reaction kinetics for gas-phase species
-Author-email: Judit Zádor <jzador@sandia.gov>, Ruben Vande Vijver <ruben.vandevijver@ugent.be>, Carles Martí <cmartia@sandia.gov>, Amanda Dewyer <adewyer@sandia.gov>
-Maintainer-email: Judit Zádor <jzador@sandia.gov>, Carles Martí <cmartia@sandia.gov>
+Author-email: Judit Zádor <jzador@sandia.gov>, Ruben Van de Vijver <ruben.vandevijver@ugent.be>, Carles Martí <cmartia@sandia.gov>, Clément Soulié <csoulie@sandia.gov>, Amanda Dewyer <adewyer@sandia.gov>
+Maintainer-email: Judit Zádor <jzador@sandia.gov>, Clément Soulié <csoulie@sandia.gov>
 License: BSD 3-Clause License
         
-        Copyright (c) 2018, zadorlab
-        All rights reserved.
+        Copyright (c) 2018, National Technology & Engineering Solutions of Sandia,
+        LLC (NTESS). Under the terms of Contract DE-NA0003525 with NTESS,
+        the U.S. Government retains certain rights in this software
         
         Redistribution and use in source and binary forms, with or without
         modification, are permitted provided that the following conditions are met:
@@ -41,14 +42,20 @@ Classifier: Intended Audience :: Science/Research
 Classifier: Natural Language :: English
 Classifier: License :: OSI Approved :: BSD License
 Classifier: Operating System :: OS Independent
-Classifier: Programming Language :: Python :: 3.8
-Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Topic :: Scientific/Engineering :: Chemistry
-Requires-Python: >=3.8
+Requires-Python: >=3.10
 Description-Content-Type: text/markdown
-Provides-Extra: plot
 License-File: LICENSE
+Requires-Dist: numpy<2.0,>=1.17.0
+Requires-Dist: ase<3.23,>=3.19
+Requires-Dist: networkx
+Requires-Dist: rmsd>=1.5.1
+Requires-Dist: sella
+Provides-Extra: plot
+Requires-Dist: matplotlib; extra == "plot"
+Requires-Dist: pyvis; extra == "plot"
+Requires-Dist: rdkit; extra == "plot"
 
 [![Gitter chat](https://badges.gitter.im/gitterHQ/gitter.png)](https://gitter.im/zadorlab/KinBot)
 
@@ -59,14 +66,37 @@ License-File: LICENSE
 </p>
 
 ## Description
-This repository contains the KinBot code version 2.0,
+This repository contains the KinBot code version 2.2.1,
 a tool for automatically searching for reactions on the potential energy surface.
 
 If you are using this tool in scientific publications, please reference the following publications:
 
 * Ruben Van de Vijver, Judit Zádor: KinBot: _Automated stationary point search on potential energy surfaces_, Comp. Phys. Comm., **2019**, 248, 106947. https://doi.org/10.1016/j.cpc.2019.106947
+```
+@article{Vijver2020,
+   author = {Van de Vijver, Ruben and Z\'ador, Judit},
+   title = {KinBot: Automated stationary point search on potential energy surfaces},
+   journal = {Comput. Phys. Commun.},
+   volume = {248},
+   pages = {106947},
+   year = {2020},
+   type = {Journal Article}
+}
+```
 * Judit Zádor, Carles Martí, Ruben Van de Vijver, Sommer L. Johansen, Yoona Yang, Hope A. Michelsen, Habib N. Najm: _Automated reaction kinetics of gas-phase organic species over multiwell potential energy surfaces_, J. Phys. Chem. A, **2023**, 127, 565–588. https://doi.org/10.1021/acs.jpca.2c06558
 
+```
+@article{Zador2022,
+   author = {Z\'ador, Judit and Mart\'i, Carles and Van de Vijver, Ruben and Johansen, Sommer L. and Yang, Yoona and Michelsen, Hope A. and Najm, Habib N.},
+   title = {Automated reaction kinetics of gas-phase organic species over multiwell potential energy surfaces},
+   journal = {J. Phys. Chem. A},
+   volume = {127},
+   pages = {565-588},
+   year = {2023},
+   type = {Journal Article}
+}
+```
+
 We appreciate if you send us the DOI of your published paper that used KinBot, so we can feature it here below.
 
 ## How to Install
@@ -78,7 +108,7 @@ KinBot can be installed both in three different ways, from the PyPI index (`pip
     pip install kinbot
 
 > **Note**
->  KinBot only works with Python >= 3.8.
+>  KinBot only works with Python >= 3.10.
 
 ### conda-forge
 
@@ -112,18 +142,28 @@ 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 [wiki](https://github.com/zadorlab/KinBot/wiki).
+See the [wiki](https://github.com/zadorlab/KinBot/wiki) for keywords, and our [tutorial](https://hackmd.io/@jzador/kinbot_workshop_2023#/) for a more hands-on introduction to the code.
 
 ## List of files in this project
 See [list](https://github.com/zadorlab/KinBot/wiki/KinBot-file-structure).
 
 ## Authors
 * Judit Zádor (jzador@sandia.gov)
-* Ruben Van de Vijver (Ruben.VandeVijver@UGent.be)
+* Ruben Van de Vijver 
 * Amanda Dewyer
-* Carles Martí (cmartia@sandia.gov)
+* Carles Martí
+* Clément Soulié (csoulie@sandia.gov)
 
 ## Papers using KinBot
+* Almeida, T. G., Martí, C., Kurtén, T., Zádor, J., Johansen, S. L.: _Theoretical analysis of the OH-Initiated atmospheric oxidation reactions of imidazole_. Phys. Chem. Chem. Phys., **2024** 26 23570-23587. https://doi.org/10.1039/D4CP02103G
+* Yuan, E. C.-Y., Kumar, A., Guan, X., Hermes, E. D., Rosen, A. S., Zádor, J., Head-Gordon, T., Blau, S. M.: _Analytical ab initio Hessian from a Deep Learning Potential for Transition State Optimization_. Nat. Comm., **2024** 
+* Doner, A. C., Zádor, J., Rotavera, B.: _Stereoisomer-dependent rate coefficients and reaction mechanisms of 2-ethyloxetanylperoxy radicals_. Proc. Combust. Inst., **2024**, 40, 105578. https://doi.org/10.1016/j.proci.2024.105578
+* Hansen, N. A, Price, T. D., Filardi, L. R., Gurses, S. M., Zhou, W., Hansen, N., Osborn, D. L. Zádor, J., Kronawitter, C. X.: _The photoionization of methoxymethanol: Fingerprinting a reactive C2 oxygenate in a complex reactive mixture_. J. Chem. Phys., **2024**, 160, 124306. https://doi.org/10.1063/5.0197827 
+* Martí, C., Devereux, C., Najm, H. N., Zádor, J.: _Evaluation of rate coefficients in the gas-phase using a machine learned potential_. J. Phys. Chem. A, **2024**, 128, 1958–1971. https://doi.org/10.1021/acs.jpca.3c07872 
+* Lang, J., Foley, C. D., Thawoos, S., Behzadfar, A., Liu, Y., Zádor, J., Suits, A. G.: _Reaction dynamics of S(3P) with 1,3-butadiene and isoprene: Crossed beam scattering, low temperature flow experiments, and high-level electronic structure calculations_. Farad. Discuss., **2024**, 251, 550-572. https://doi.org/10.1039/D4FD00009A 
+* Wang, D., Tian, Z.-Y., Zheng, Z.-H., Li, W., Wu, L.-N., Kuang, J.-J., Yang, J.-Z.: _Experimental and modeling study of the n, n-dimethylformamide pyrolysis at atmospheric pressure_. Combust. Flame, **2024**, 260, 113240. https://doi.org/10.1016/j.combustflame.2023.113240
+* Doner, A. C., Zádor, J., Rotavera, B.: _Unimolecular reactions of 2,4-dimethyloxetanyl radicals._ J. Phys. Chem A, **2023**, 127, 2591–2600 https://doi.org/10.1021/acs.jpca.2c08290
+* Li, H., Lang, J., Foley, C. D., Zádor, J., Suits, A. G.: _Sulfur (3P) reaction with conjugated dienes gives cyclization to thiophenes under single collision conditions._ J. Phys. Chem. Letters, **2023**, 14, 7611–7617. https://doi.org/10.1021/acs.jpclett.3c01953
 * Martí, C., Michelsen, H. A., Najm, H. N., Zádor, J.: _Comprehensive kinetics on the C7H7 potential energy surface under combustion conditions._ J. Phys. Chem. A, **2023**, 127, 1941–1959. https://pubs.acs.org/doi/full/10.1021/acs.jpca.2c08035  
 * Zádor, J, Martí, C., Van de Vijver, R., Johansen, S. L., Yang, Y., Michelsen, H. A., Najm, H. N.: _Automated reaction kinetics of gas-phase organic species over multiwell potential energy surfaces._ J. Phys. Chem. A, **2023**, 127, 565–588. https://doi.org/10.1021/acs.jpca.2c06558
 * Lockwood, K. S., Ahmed, S. F., Huq, N. A., Stutzman, S. C., Foust, T. D., Labbe, N. J.: _Advances in predictive chemistry enable a multi-scale rational design approach for biofuels with advantaged properties_ Sustainable Energy Fuels, **2022**, 6, 5371-5383. https://doi.org/10.1039/D2SE00773H 

{kinbot-2.2.1 → kinbot-2.2.2}/README.md

@@ -7,14 +7,37 @@
 </p>
 
 ## Description
-This repository contains the KinBot code version 2.0,
+This repository contains the KinBot code version 2.2.1,
 a tool for automatically searching for reactions on the potential energy surface.
 
 If you are using this tool in scientific publications, please reference the following publications:
 
 * Ruben Van de Vijver, Judit Zádor: KinBot: _Automated stationary point search on potential energy surfaces_, Comp. Phys. Comm., **2019**, 248, 106947. https://doi.org/10.1016/j.cpc.2019.106947
+```
+@article{Vijver2020,
+   author = {Van de Vijver, Ruben and Z\'ador, Judit},
+   title = {KinBot: Automated stationary point search on potential energy surfaces},
+   journal = {Comput. Phys. Commun.},
+   volume = {248},
+   pages = {106947},
+   year = {2020},
+   type = {Journal Article}
+}
+```
 * Judit Zádor, Carles Martí, Ruben Van de Vijver, Sommer L. Johansen, Yoona Yang, Hope A. Michelsen, Habib N. Najm: _Automated reaction kinetics of gas-phase organic species over multiwell potential energy surfaces_, J. Phys. Chem. A, **2023**, 127, 565–588. https://doi.org/10.1021/acs.jpca.2c06558
 
+```
+@article{Zador2022,
+   author = {Z\'ador, Judit and Mart\'i, Carles and Van de Vijver, Ruben and Johansen, Sommer L. and Yang, Yoona and Michelsen, Hope A. and Najm, Habib N.},
+   title = {Automated reaction kinetics of gas-phase organic species over multiwell potential energy surfaces},
+   journal = {J. Phys. Chem. A},
+   volume = {127},
+   pages = {565-588},
+   year = {2023},
+   type = {Journal Article}
+}
+```
+
 We appreciate if you send us the DOI of your published paper that used KinBot, so we can feature it here below.
 
 ## How to Install
@@ -26,7 +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 >= 3.8.
+>  KinBot only works with Python >= 3.10.
 
 ### conda-forge
 
@@ -60,18 +83,28 @@ 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 [wiki](https://github.com/zadorlab/KinBot/wiki).
+See the [wiki](https://github.com/zadorlab/KinBot/wiki) for keywords, and our [tutorial](https://hackmd.io/@jzador/kinbot_workshop_2023#/) for a more hands-on introduction to the code.
 
 ## List of files in this project
 See [list](https://github.com/zadorlab/KinBot/wiki/KinBot-file-structure).
 
 ## Authors
 * Judit Zádor (jzador@sandia.gov)
-* Ruben Van de Vijver (Ruben.VandeVijver@UGent.be)
+* Ruben Van de Vijver 
 * Amanda Dewyer
-* Carles Martí (cmartia@sandia.gov)
+* Carles Martí
+* Clément Soulié (csoulie@sandia.gov)
 
 ## Papers using KinBot
+* Almeida, T. G., Martí, C., Kurtén, T., Zádor, J., Johansen, S. L.: _Theoretical analysis of the OH-Initiated atmospheric oxidation reactions of imidazole_. Phys. Chem. Chem. Phys., **2024** 26 23570-23587. https://doi.org/10.1039/D4CP02103G
+* Yuan, E. C.-Y., Kumar, A., Guan, X., Hermes, E. D., Rosen, A. S., Zádor, J., Head-Gordon, T., Blau, S. M.: _Analytical ab initio Hessian from a Deep Learning Potential for Transition State Optimization_. Nat. Comm., **2024** 
+* Doner, A. C., Zádor, J., Rotavera, B.: _Stereoisomer-dependent rate coefficients and reaction mechanisms of 2-ethyloxetanylperoxy radicals_. Proc. Combust. Inst., **2024**, 40, 105578. https://doi.org/10.1016/j.proci.2024.105578
+* Hansen, N. A, Price, T. D., Filardi, L. R., Gurses, S. M., Zhou, W., Hansen, N., Osborn, D. L. Zádor, J., Kronawitter, C. X.: _The photoionization of methoxymethanol: Fingerprinting a reactive C2 oxygenate in a complex reactive mixture_. J. Chem. Phys., **2024**, 160, 124306. https://doi.org/10.1063/5.0197827 
+* Martí, C., Devereux, C., Najm, H. N., Zádor, J.: _Evaluation of rate coefficients in the gas-phase using a machine learned potential_. J. Phys. Chem. A, **2024**, 128, 1958–1971. https://doi.org/10.1021/acs.jpca.3c07872 
+* Lang, J., Foley, C. D., Thawoos, S., Behzadfar, A., Liu, Y., Zádor, J., Suits, A. G.: _Reaction dynamics of S(3P) with 1,3-butadiene and isoprene: Crossed beam scattering, low temperature flow experiments, and high-level electronic structure calculations_. Farad. Discuss., **2024**, 251, 550-572. https://doi.org/10.1039/D4FD00009A 
+* Wang, D., Tian, Z.-Y., Zheng, Z.-H., Li, W., Wu, L.-N., Kuang, J.-J., Yang, J.-Z.: _Experimental and modeling study of the n, n-dimethylformamide pyrolysis at atmospheric pressure_. Combust. Flame, **2024**, 260, 113240. https://doi.org/10.1016/j.combustflame.2023.113240
+* Doner, A. C., Zádor, J., Rotavera, B.: _Unimolecular reactions of 2,4-dimethyloxetanyl radicals._ J. Phys. Chem A, **2023**, 127, 2591–2600 https://doi.org/10.1021/acs.jpca.2c08290
+* Li, H., Lang, J., Foley, C. D., Zádor, J., Suits, A. G.: _Sulfur (3P) reaction with conjugated dienes gives cyclization to thiophenes under single collision conditions._ J. Phys. Chem. Letters, **2023**, 14, 7611–7617. https://doi.org/10.1021/acs.jpclett.3c01953
 * Martí, C., Michelsen, H. A., Najm, H. N., Zádor, J.: _Comprehensive kinetics on the C7H7 potential energy surface under combustion conditions._ J. Phys. Chem. A, **2023**, 127, 1941–1959. https://pubs.acs.org/doi/full/10.1021/acs.jpca.2c08035  
 * Zádor, J, Martí, C., Van de Vijver, R., Johansen, S. L., Yang, Y., Michelsen, H. A., Najm, H. N.: _Automated reaction kinetics of gas-phase organic species over multiwell potential energy surfaces._ J. Phys. Chem. A, **2023**, 127, 565–588. https://doi.org/10.1021/acs.jpca.2c06558
 * Lockwood, K. S., Ahmed, S. F., Huq, N. A., Stutzman, S. C., Foust, T. D., Labbe, N. J.: _Advances in predictive chemistry enable a multi-scale rational design approach for biofuels with advantaged properties_ Sustainable Energy Fuels, **2022**, 6, 5371-5383. https://doi.org/10.1039/D2SE00773H 

kinbot-2.2.2/kinbot/ase_modules/calculators/nn_pes.py

@@ -0,0 +1,220 @@
+import os
+from pathlib import Path
+import warnings
+
+import numpy as np
+import torch
+from ase import Atoms
+from ase.calculators.calculator import Calculator, all_changes
+
+from util import util_path
+from util.data import data
+import util.nn.pes_compNet_multifid as pes
+from util.sfi import daev
+
+os.environ['KMP_DUPLICATE_LIB_OK']='True'
+
+
+class Nn_surr(Calculator):
+    implemented_properties = ['energy', 'forces']
+
+    def __init__(self, fname, restart=None, ignore_bad_restart_file=False, 
+                 label='surrogate', atoms=None, tnsr=False, **kwargs):
+        Calculator.__init__(self, restart=restart, 
+                            ignore_bad_restart_file=ignore_bad_restart_file, 
+                            label=label,
+                            atoms=atoms, tnsr=tnsr, **kwargs)
+        if isinstance(fname, list) and fname.__len__() > 1:
+            self.multinn = True
+        else:
+            self.multinn = False
+        self.surrogate = Nnpes_calc(fname, self.multinn)
+        self.tnsr = tnsr
+    
+    def calculate(self, atoms=None, properties=['energy', 'forces'], 
+                  system_changes=all_changes, loaddb=None, args=None, xid=None):
+        Calculator.calculate(self, atoms, properties, system_changes)
+        if 'forces' in properties:
+            favail = True
+        else:
+            favail = False
+
+        xyzd = [[[s for s in atoms.symbols], np.array(atoms.positions)]]
+        self.surrogate.dpes.aev_from_xyz(xyzd, 32, 8, 8, [4.6,3.1], False, 
+                                         self.surrogate.myaev)
+        self.surrogate.nforce = self.surrogate.dpes.full_symb_data[0].__len__() * 3
+
+        if self.multinn:
+            energy, Estd, E_hf = self.surrogate.eval()
+            if favail:
+                force, Fstd, force_ind = self.surrogate.evalforce()
+        else:
+            energy = self.surrogate.eval()[0][0]
+            Estd = torch.tensor(0.)
+            if favail:
+                force = self.surrogate.evalforce()
+                Fstd = torch.tensor(0.)
+
+        if self.tnsr:
+            self.results['energy'] = energy
+            self.results['energy_std'] = Estd
+            if self.multinn:
+                self.results['all_energies'] = E_hf
+            if favail:
+                self.results['forces'] = force.view(-1, 3)
+                self.results['forces_std'] = Fstd
+                if self.multinn:
+                    self.results['all_forces'] = force_ind
+        else:
+            self.results['energy'] = float(energy)
+            self.results['energy_std'] = Estd.detach().numpy()
+            if self.multinn:
+                self.results['all_energies'] = E_hf.detach().numpy()
+            if favail:
+                self.results['forces'] = np.reshape(force.detach().numpy(), 
+                                                    (-1, 3))
+                self.results['forces_std'] = Fstd.detach().numpy()
+                if self.multinn:
+                    self.results['all_forces'] = force_ind.detach().numpy()
+
+
+class My_args():
+
+    def __init__(self, nntype, model_name, fid):
+        self.nntype = [nntype]
+        if model_name is None:
+            self.load_model = False
+        else:
+            if isinstance(model_name, list):
+                self.load_model_name = model_name
+            else:
+                self.load_model_name = [model_name]
+        self.fid = [fid]
+        self.nw = True
+        self.savepth = None
+        self.savepth_pars = None
+        self.device = torch.device('cpu')
+
+class Nnpes_calc():
+
+    def __init__(self, fname, multinn=False):
+        self.dpes = data.Data_pes(['C', 'H'])
+        self.myaev = self.dpes.prep_aev()
+        if multinn:
+            self.nmodel = fname.__len__()
+            options = [My_args('Comp', fnm, 'hfonly') for fnm in fname]
+            self.dpes.device = options[0].device
+            self.nn_pes = [pes.prep_model(True, opts, load_opt=False) 
+                           for opts in options]
+        else:
+            self.nmodel = 1
+            options = My_args('Comp', fname, 'hfonly')
+            self.dpes.device = options.device
+            self.nn_pes = pes.prep_model(True, options, load_opt=False)
+            #print('SAE energies: ', self.nn_pes.sae_energies)
+
+    def eval(self, indvout=False):
+        idl = list(range(0, self.dpes.ndat))
+        self.dpes.prep_data(idl)
+        self.dpes.indvout = indvout
+        self.dpes.ymax = np.max([y[-1] for y in self.dpes.xdat])
+        self.dpes.ymin = np.min([y[-1] for y in self.dpes.xdat])
+        self.dpes.xb = [[xt.requires_grad_() for xt in self.dpes.xb[b]] 
+                        for b in range(self.dpes.nbt)]
+        if self.nmodel == 1:
+            self.E_lf, self.E_hf = self.nn_pes.eval_dl(self.dpes)
+            E_pred = self.E_hf
+            return E_pred
+        else:
+            self.E_hf = torch.empty((self.dpes.ndat, self.nmodel))
+            for i in range(self.nmodel):
+                E_lf, E_hf = self.nn_pes[i].eval_dl(self.dpes)
+                self.E_hf[:, i] = E_hf.reshape(-1)
+            E_pred = torch.mean(self.E_hf)
+            Estd = torch.std(self.E_hf, 1)
+            return E_pred, Estd, self.E_hf
+
+    def evalgrad(self):
+        if self.nmodel == 1:
+            dEdxyz = daev.cal_dEdxyz_dl(self.dpes, self.E_hf)[0]
+            return dEdxyz
+        else:
+            dEdxyz = torch.empty((self.dpes.ndat, self.nmodel, self.nforce))
+            for i in range(self.nmodel):
+                tmp = daev.cal_dEdxyz_dl(self.dpes, self.E_hf[:, i])[0]
+                dEdxyz[:, i] = tmp
+            gmean = torch.mean(dEdxyz, 1).reshape(-1)
+            gstd  = torch.std(dEdxyz, 1).reshape(-1)
+            return gmean, gstd, dEdxyz
+
+    def evalforce(self):
+        if self.nmodel == 1:
+            gradient = self.evalgrad()
+            return -gradient
+        else:
+            gmean, gstd, dEdxyz = self.evalgrad()
+            return -gmean, gstd, -dEdxyz
+
+
+def main():
+    # set default pytorch as double precision
+    torch.set_default_dtype(torch.float64)
+
+    torch.set_printoptions(precision=12)
+
+    home = str(Path.home())
+
+    nn1 = home+'/mls/util/models/AL/C5H5-2b2IRC1ts_full/run1-1/C5H5_lf_reddb_2w2IRC1ts_20k_rand0-29540.pt'
+    nn2 = home+'/mls/util/models/AL/C5H5-2b2IRC1ts_full/run1-1/C5H5_lf_reddb_2w2IRC1ts_20k_rand1-29260.pt'
+    nn3 = home+'/mls/util/models/AL/C5H5-2b2IRC1ts_full/run1-1/C5H5_lf_reddb_2w2IRC1ts_20k_rand2-29115.pt'
+    nn4 = home+'/mls/util/models/AL/C5H5-2b2IRC1ts_full/run1-1/C5H5_lf_reddb_2w2IRC1ts_20k_rand3-0005.pt'
+    nn5 = home+'/mls/util/models/AL/C5H5-2b2IRC1ts_full/run1-1/C5H5_lf_reddb_2w2IRC1ts_20k_rand4-2500.pt'
+
+    # import glob
+    # fn_nn = glob.glob('../../models/AL/C5H5-2b2IRC1ts_smallset/run0/*')
+    # fn_nn = ['comp-0010.pt', 'comp-0010.pt']
+
+    fn_nn = [nn1, nn2, nn3, nn4, nn5]
+
+
+    #atoms = Atoms(['C', 'H', 'C'],
+    #              [(1.734285, 1.257951, 0.130304), 
+    #               (3.016641, 1.515035, 0.130976), 
+    #               (1.617565, -0.19116, -0.177416)])
+
+    xyz_db = [[
+        ['C', 'H', 'C'],
+        np.array([[1.734285, 1.257951, 0.130304], 
+                  [3.016641, 1.515035, 0.130976], 
+                  [1.617565, -0.19116, -0.177416]])
+    ]]
+
+    # simple test
+    for nn in fn_nn:
+        print("nn:",nn)
+        surr  = Nn_surr(nn,tnsr=False)
+        for xyz in xyz_db:
+            atoms = Atoms(xyz[0], xyz[1])
+            atoms.set_calculator(surr)
+            surr.calculate(atoms)
+            print('System:',atoms)
+            print('Energy:', surr.results['energy'])
+            print('Forces:\n', surr.results['forces'])
+            print('Numerical forces with ASE:\n', 
+                  surr.calculate_numerical_forces(atoms))
+
+    print("avg nn:")
+    surr  = Nn_surr(fn_nn,tnsr=False)
+    for xyz in xyz_db:
+        atoms = Atoms(xyz[0], xyz[1])
+        atoms.set_calculator(surr)
+        surr.calculate(atoms)
+        print('System:',atoms)
+        print('Energy:', surr.results['energy'])
+        print('Forces:\n', surr.results['forces'])
+        print('Numerical forces with ASE:\n', 
+              surr.calculate_numerical_forces(atoms))
+
+
+if __name__ == "__main__":
+    main()

{kinbot-2.2.1 → kinbot-2.2.2}/kinbot/cheminfo.py

@@ -247,3 +247,5 @@ def create_smiles(inchi):
 def create_smi_from_geom(atom, geom):
     inchi = create_inchi_from_geom(atom, geom)
     return create_smiles(inchi)
+
+