kinbot 2.1.1__tar.gz → 2.2.2__tar.gz

{kinbot-2.1.1 → kinbot-2.2.2/KinBot.egg-info}/PKG-INFO

@@ -1,13 +1,14 @@
 Metadata-Version: 2.1
 Name: kinbot
-Version: 2.1.1
+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:
@@ -41,44 +42,77 @@ 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)
 
-# KinBot: Automated reaction pathway search for gas-phase molecules
+# KinBot: Automated Reaction Kinetics of Gas-Phase Organic Species over Multiwell Potential Energy Surfaces
 
 <p>
     <img src="https://raw.githubusercontent.com/zadorlab/KinBot/master/graphics/kinbot_logo_V2.png" width="220" height="240" />
 </p>
 
 ## Description
-This repository contains the KinBot code version 2.0,
+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
 
-KinBot is installed with `pip`, either from the PyPI repo or by first cloning this github repo and then install it locally.
+KinBot can be installed both in three different ways, from the PyPI index (`pip install`), from the conda-forge repo (`conda install`) or by cloning this github repo and then install it locally.
 
 ### PyPI
 
     pip install kinbot
 
 > **Note**
->  KinBot only works with Python >= 3.8.
+>  KinBot only works with Python >= 3.10.
+
+### conda-forge
+
+    conda install -c conda-forge kinbot
 
 ### From Github
 
@@ -90,14 +124,14 @@ from github:
 
 and then, from within the KinBot directory produced after cloning, type:
 
-    pip install .
+    pip install -e .
  
 > **Note**
 > If you want to modify KinBot yourself it's better to fork the project 
 > into your own repository and then clone it.
 
 ## How to Run
-To run KinBot (which will only explore one well), make an input file (e.g. input.json) and run:
+To run a single-well exploration of KinBot, make an input file (e.g. input.json) and run:
 
     kinbot input.json
 
@@ -108,20 +142,31 @@ 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
-* 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**, ASAP. https://pubs.acs.org/doi/full/10.1021/acs.jpca.2c08035  
+* Almeida, T. G., Martí, C., Kurtén, T., Zádor, J., Johansen, S. L.: _Theoretical analysis of the OH-Initiated atmospheric oxidation reactions of imidazole_. Phys. Chem. Chem. Phys., **2024** 26 23570-23587. https://doi.org/10.1039/D4CP02103G
+* Yuan, E. C.-Y., Kumar, A., Guan, X., Hermes, E. D., Rosen, A. S., Zádor, J., Head-Gordon, T., Blau, S. M.: _Analytical ab initio Hessian from a Deep Learning Potential for Transition State Optimization_. Nat. Comm., **2024** 
+* Doner, A. C., Zádor, J., Rotavera, B.: _Stereoisomer-dependent rate coefficients and reaction mechanisms of 2-ethyloxetanylperoxy radicals_. Proc. Combust. Inst., **2024**, 40, 105578. https://doi.org/10.1016/j.proci.2024.105578
+* Hansen, N. A, Price, T. D., Filardi, L. R., Gurses, S. M., Zhou, W., Hansen, N., Osborn, D. L. Zádor, J., Kronawitter, C. X.: _The photoionization of methoxymethanol: Fingerprinting a reactive C2 oxygenate in a complex reactive mixture_. J. Chem. Phys., **2024**, 160, 124306. https://doi.org/10.1063/5.0197827 
+* Martí, C., Devereux, C., Najm, H. N., Zádor, J.: _Evaluation of rate coefficients in the gas-phase using a machine learned potential_. J. Phys. Chem. A, **2024**, 128, 1958–1971. https://doi.org/10.1021/acs.jpca.3c07872 
+* Lang, J., Foley, C. D., Thawoos, S., Behzadfar, A., Liu, Y., Zádor, J., Suits, A. G.: _Reaction dynamics of S(3P) with 1,3-butadiene and isoprene: Crossed beam scattering, low temperature flow experiments, and high-level electronic structure calculations_. Farad. Discuss., **2024**, 251, 550-572. https://doi.org/10.1039/D4FD00009A 
+* Wang, D., Tian, Z.-Y., Zheng, Z.-H., Li, W., Wu, L.-N., Kuang, J.-J., Yang, J.-Z.: _Experimental and modeling study of the n, n-dimethylformamide pyrolysis at atmospheric pressure_. Combust. Flame, **2024**, 260, 113240. https://doi.org/10.1016/j.combustflame.2023.113240
+* Doner, A. C., Zádor, J., Rotavera, B.: _Unimolecular reactions of 2,4-dimethyloxetanyl radicals._ J. Phys. Chem A, **2023**, 127, 2591–2600 https://doi.org/10.1021/acs.jpca.2c08290
+* Li, H., Lang, J., Foley, C. D., Zádor, J., Suits, A. G.: _Sulfur (3P) reaction with conjugated dienes gives cyclization to thiophenes under single collision conditions._ J. Phys. Chem. Letters, **2023**, 14, 7611–7617. https://doi.org/10.1021/acs.jpclett.3c01953
+* Martí, C., Michelsen, H. A., Najm, H. N., Zádor, J.: _Comprehensive kinetics on the C7H7 potential energy surface under combustion conditions._ J. Phys. Chem. A, **2023**, 127, 1941–1959. https://pubs.acs.org/doi/full/10.1021/acs.jpca.2c08035  
 * Zádor, J, Martí, C., Van de Vijver, R., Johansen, S. L., Yang, Y., Michelsen, H. A., Najm, H. N.: _Automated reaction kinetics of gas-phase organic species over multiwell potential energy surfaces._ J. Phys. Chem. A, **2023**, 127, 565–588. https://doi.org/10.1021/acs.jpca.2c06558
+* Lockwood, K. S., Ahmed, S. F., Huq, N. A., Stutzman, S. C., Foust, T. D., Labbe, N. J.: _Advances in predictive chemistry enable a multi-scale rational design approach for biofuels with advantaged properties_ Sustainable Energy Fuels, **2022**, 6, 5371-5383. https://doi.org/10.1039/D2SE00773H 
 * Takahashi, L., Yoshida, S., Fujima, J., Oikawa, H., Takahashi, K.: _Unveiling the reaction pathways of hydrocarbons via experiments, computations and data science._ Phys. Chem. Chem. Phys., **2022**, 24, 29841-29849. https://pubs.rsc.org/en/content/articlelanding/2022/CP/D2CP04499D
 * Doner, A. C., Zádor, J., Rotavera, B.: _Stereoisomer-dependent unimolecular kinetics of 2,4-dimethyloxetane peroxy radicals._ Faraday Discuss., **2022**, 238, 295-319. https://doi.org/10.1039/D2FD00029F
 * Ramasesha, K., Savee, J. D., Zádor, J., Osborn, D. L.: _A New Pathway for Intersystem Crossing: Unexpected Products in the O(3P) + Cyclopentene Reaction._ J. Phys. Chem. A, **2021**, 125 9785-9801. https://doi.org/10.1021/acs.jpca.1c05817

{kinbot-2.1.1/kinbot.egg-info → kinbot-2.2.2/KinBot.egg-info}/SOURCES.txt

@@ -1,6 +1,12 @@
 LICENSE
 README.md
 pyproject.toml
+KinBot.egg-info/PKG-INFO
+KinBot.egg-info/SOURCES.txt
+KinBot.egg-info/dependency_links.txt
+KinBot.egg-info/entry_points.txt
+KinBot.egg-info/requires.txt
+KinBot.egg-info/top_level.txt
 kinbot/__init__.py
 kinbot/bfgs.py
 kinbot/bond_combinations.py
@@ -10,6 +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
@@ -25,6 +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
@@ -38,6 +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
@@ -49,6 +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
@@ -80,6 +92,7 @@ kinbot/reactions/reac_Retro_Ene.py
 kinbot/reactions/reac_abstraction.py
 kinbot/reactions/reac_barrierless_saddle.py
 kinbot/reactions/reac_beta_delta.py
+kinbot/reactions/reac_bimol_disproportionation_R.py
 kinbot/reactions/reac_birad_recombination_F.py
 kinbot/reactions/reac_birad_recombination_R.py
 kinbot/reactions/reac_combinatorial.py
@@ -107,6 +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
@@ -118,6 +132,13 @@ kinbot/tpl/ase_qchem_irc.tpl.py
 kinbot/tpl/ase_qchem_opt_well.tpl.py
 kinbot/tpl/ase_qchem_ts_end.tpl.py
 kinbot/tpl/ase_qchem_ts_search.tpl.py
+kinbot/tpl/ase_sella_hir.tpl.py
+kinbot/tpl/ase_sella_irc.tpl.py
+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
@@ -133,6 +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
@@ -144,6 +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
@@ -151,6 +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-2.1.1/kinbot.egg-info → 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-2.1.1/kinbot.egg-info → kinbot-2.2.2/KinBot.egg-info}/top_level.txt

@@ -1,3 +1,4 @@
+build
 examples
 kinbot
 reactions

{kinbot-2.1.1 → 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-2.1.1/kinbot.egg-info → kinbot-2.2.2}/PKG-INFO

@@ -1,13 +1,14 @@
 Metadata-Version: 2.1
 Name: kinbot
-Version: 2.1.1
+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:
@@ -41,44 +42,77 @@ 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)
 
-# KinBot: Automated reaction pathway search for gas-phase molecules
+# KinBot: Automated Reaction Kinetics of Gas-Phase Organic Species over Multiwell Potential Energy Surfaces
 
 <p>
     <img src="https://raw.githubusercontent.com/zadorlab/KinBot/master/graphics/kinbot_logo_V2.png" width="220" height="240" />
 </p>
 
 ## Description
-This repository contains the KinBot code version 2.0,
+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
 
-KinBot is installed with `pip`, either from the PyPI repo or by first cloning this github repo and then install it locally.
+KinBot can be installed both in three different ways, from the PyPI index (`pip install`), from the conda-forge repo (`conda install`) or by cloning this github repo and then install it locally.
 
 ### PyPI
 
     pip install kinbot
 
 > **Note**
->  KinBot only works with Python >= 3.8.
+>  KinBot only works with Python >= 3.10.
+
+### conda-forge
+
+    conda install -c conda-forge kinbot
 
 ### From Github
 
@@ -90,14 +124,14 @@ from github:
 
 and then, from within the KinBot directory produced after cloning, type:
 
-    pip install .
+    pip install -e .
  
 > **Note**
 > If you want to modify KinBot yourself it's better to fork the project 
 > into your own repository and then clone it.
 
 ## How to Run
-To run KinBot (which will only explore one well), make an input file (e.g. input.json) and run:
+To run a single-well exploration of KinBot, make an input file (e.g. input.json) and run:
 
     kinbot input.json
 
@@ -108,20 +142,31 @@ 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
-* 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**, ASAP. https://pubs.acs.org/doi/full/10.1021/acs.jpca.2c08035  
+* Almeida, T. G., Martí, C., Kurtén, T., Zádor, J., Johansen, S. L.: _Theoretical analysis of the OH-Initiated atmospheric oxidation reactions of imidazole_. Phys. Chem. Chem. Phys., **2024** 26 23570-23587. https://doi.org/10.1039/D4CP02103G
+* Yuan, E. C.-Y., Kumar, A., Guan, X., Hermes, E. D., Rosen, A. S., Zádor, J., Head-Gordon, T., Blau, S. M.: _Analytical ab initio Hessian from a Deep Learning Potential for Transition State Optimization_. Nat. Comm., **2024** 
+* Doner, A. C., Zádor, J., Rotavera, B.: _Stereoisomer-dependent rate coefficients and reaction mechanisms of 2-ethyloxetanylperoxy radicals_. Proc. Combust. Inst., **2024**, 40, 105578. https://doi.org/10.1016/j.proci.2024.105578
+* Hansen, N. A, Price, T. D., Filardi, L. R., Gurses, S. M., Zhou, W., Hansen, N., Osborn, D. L. Zádor, J., Kronawitter, C. X.: _The photoionization of methoxymethanol: Fingerprinting a reactive C2 oxygenate in a complex reactive mixture_. J. Chem. Phys., **2024**, 160, 124306. https://doi.org/10.1063/5.0197827 
+* Martí, C., Devereux, C., Najm, H. N., Zádor, J.: _Evaluation of rate coefficients in the gas-phase using a machine learned potential_. J. Phys. Chem. A, **2024**, 128, 1958–1971. https://doi.org/10.1021/acs.jpca.3c07872 
+* Lang, J., Foley, C. D., Thawoos, S., Behzadfar, A., Liu, Y., Zádor, J., Suits, A. G.: _Reaction dynamics of S(3P) with 1,3-butadiene and isoprene: Crossed beam scattering, low temperature flow experiments, and high-level electronic structure calculations_. Farad. Discuss., **2024**, 251, 550-572. https://doi.org/10.1039/D4FD00009A 
+* Wang, D., Tian, Z.-Y., Zheng, Z.-H., Li, W., Wu, L.-N., Kuang, J.-J., Yang, J.-Z.: _Experimental and modeling study of the n, n-dimethylformamide pyrolysis at atmospheric pressure_. Combust. Flame, **2024**, 260, 113240. https://doi.org/10.1016/j.combustflame.2023.113240
+* Doner, A. C., Zádor, J., Rotavera, B.: _Unimolecular reactions of 2,4-dimethyloxetanyl radicals._ J. Phys. Chem A, **2023**, 127, 2591–2600 https://doi.org/10.1021/acs.jpca.2c08290
+* Li, H., Lang, J., Foley, C. D., Zádor, J., Suits, A. G.: _Sulfur (3P) reaction with conjugated dienes gives cyclization to thiophenes under single collision conditions._ J. Phys. Chem. Letters, **2023**, 14, 7611–7617. https://doi.org/10.1021/acs.jpclett.3c01953
+* Martí, C., Michelsen, H. A., Najm, H. N., Zádor, J.: _Comprehensive kinetics on the C7H7 potential energy surface under combustion conditions._ J. Phys. Chem. A, **2023**, 127, 1941–1959. https://pubs.acs.org/doi/full/10.1021/acs.jpca.2c08035  
 * Zádor, J, Martí, C., Van de Vijver, R., Johansen, S. L., Yang, Y., Michelsen, H. A., Najm, H. N.: _Automated reaction kinetics of gas-phase organic species over multiwell potential energy surfaces._ J. Phys. Chem. A, **2023**, 127, 565–588. https://doi.org/10.1021/acs.jpca.2c06558
+* Lockwood, K. S., Ahmed, S. F., Huq, N. A., Stutzman, S. C., Foust, T. D., Labbe, N. J.: _Advances in predictive chemistry enable a multi-scale rational design approach for biofuels with advantaged properties_ Sustainable Energy Fuels, **2022**, 6, 5371-5383. https://doi.org/10.1039/D2SE00773H 
 * Takahashi, L., Yoshida, S., Fujima, J., Oikawa, H., Takahashi, K.: _Unveiling the reaction pathways of hydrocarbons via experiments, computations and data science._ Phys. Chem. Chem. Phys., **2022**, 24, 29841-29849. https://pubs.rsc.org/en/content/articlelanding/2022/CP/D2CP04499D
 * Doner, A. C., Zádor, J., Rotavera, B.: _Stereoisomer-dependent unimolecular kinetics of 2,4-dimethyloxetane peroxy radicals._ Faraday Discuss., **2022**, 238, 295-319. https://doi.org/10.1039/D2FD00029F
 * Ramasesha, K., Savee, J. D., Zádor, J., Osborn, D. L.: _A New Pathway for Intersystem Crossing: Unexpected Products in the O(3P) + Cyclopentene Reaction._ J. Phys. Chem. A, **2021**, 125 9785-9801. https://doi.org/10.1021/acs.jpca.1c05817

{kinbot-2.1.1 → kinbot-2.2.2}/README.md

@@ -1,32 +1,59 @@
 [![Gitter chat](https://badges.gitter.im/gitterHQ/gitter.png)](https://gitter.im/zadorlab/KinBot)
 
-# KinBot: Automated reaction pathway search for gas-phase molecules
+# KinBot: Automated Reaction Kinetics of Gas-Phase Organic Species over Multiwell Potential Energy Surfaces
 
 <p>
     <img src="https://raw.githubusercontent.com/zadorlab/KinBot/master/graphics/kinbot_logo_V2.png" width="220" height="240" />
 </p>
 
 ## Description
-This repository contains the KinBot code version 2.0,
+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
 
-KinBot is installed with `pip`, either from the PyPI repo or by first cloning this github repo and then install it locally.
+KinBot can be installed both in three different ways, from the PyPI index (`pip install`), from the conda-forge repo (`conda install`) or by cloning this github repo and then install it locally.
 
 ### PyPI
 
     pip install kinbot
 
 > **Note**
->  KinBot only works with Python >= 3.8.
+>  KinBot only works with Python >= 3.10.
+
+### conda-forge
+
+    conda install -c conda-forge kinbot
 
 ### From Github
 
@@ -38,14 +65,14 @@ from github:
 
 and then, from within the KinBot directory produced after cloning, type:
 
-    pip install .
+    pip install -e .
  
 > **Note**
 > If you want to modify KinBot yourself it's better to fork the project 
 > into your own repository and then clone it.
 
 ## How to Run
-To run KinBot (which will only explore one well), make an input file (e.g. input.json) and run:
+To run a single-well exploration of KinBot, make an input file (e.g. input.json) and run:
 
     kinbot input.json
 
@@ -56,20 +83,31 @@ 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
-* 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**, ASAP. https://pubs.acs.org/doi/full/10.1021/acs.jpca.2c08035  
+* Almeida, T. G., Martí, C., Kurtén, T., Zádor, J., Johansen, S. L.: _Theoretical analysis of the OH-Initiated atmospheric oxidation reactions of imidazole_. Phys. Chem. Chem. Phys., **2024** 26 23570-23587. https://doi.org/10.1039/D4CP02103G
+* Yuan, E. C.-Y., Kumar, A., Guan, X., Hermes, E. D., Rosen, A. S., Zádor, J., Head-Gordon, T., Blau, S. M.: _Analytical ab initio Hessian from a Deep Learning Potential for Transition State Optimization_. Nat. Comm., **2024** 
+* Doner, A. C., Zádor, J., Rotavera, B.: _Stereoisomer-dependent rate coefficients and reaction mechanisms of 2-ethyloxetanylperoxy radicals_. Proc. Combust. Inst., **2024**, 40, 105578. https://doi.org/10.1016/j.proci.2024.105578
+* Hansen, N. A, Price, T. D., Filardi, L. R., Gurses, S. M., Zhou, W., Hansen, N., Osborn, D. L. Zádor, J., Kronawitter, C. X.: _The photoionization of methoxymethanol: Fingerprinting a reactive C2 oxygenate in a complex reactive mixture_. J. Chem. Phys., **2024**, 160, 124306. https://doi.org/10.1063/5.0197827 
+* Martí, C., Devereux, C., Najm, H. N., Zádor, J.: _Evaluation of rate coefficients in the gas-phase using a machine learned potential_. J. Phys. Chem. A, **2024**, 128, 1958–1971. https://doi.org/10.1021/acs.jpca.3c07872 
+* Lang, J., Foley, C. D., Thawoos, S., Behzadfar, A., Liu, Y., Zádor, J., Suits, A. G.: _Reaction dynamics of S(3P) with 1,3-butadiene and isoprene: Crossed beam scattering, low temperature flow experiments, and high-level electronic structure calculations_. Farad. Discuss., **2024**, 251, 550-572. https://doi.org/10.1039/D4FD00009A 
+* Wang, D., Tian, Z.-Y., Zheng, Z.-H., Li, W., Wu, L.-N., Kuang, J.-J., Yang, J.-Z.: _Experimental and modeling study of the n, n-dimethylformamide pyrolysis at atmospheric pressure_. Combust. Flame, **2024**, 260, 113240. https://doi.org/10.1016/j.combustflame.2023.113240
+* Doner, A. C., Zádor, J., Rotavera, B.: _Unimolecular reactions of 2,4-dimethyloxetanyl radicals._ J. Phys. Chem A, **2023**, 127, 2591–2600 https://doi.org/10.1021/acs.jpca.2c08290
+* Li, H., Lang, J., Foley, C. D., Zádor, J., Suits, A. G.: _Sulfur (3P) reaction with conjugated dienes gives cyclization to thiophenes under single collision conditions._ J. Phys. Chem. Letters, **2023**, 14, 7611–7617. https://doi.org/10.1021/acs.jpclett.3c01953
+* Martí, C., Michelsen, H. A., Najm, H. N., Zádor, J.: _Comprehensive kinetics on the C7H7 potential energy surface under combustion conditions._ J. Phys. Chem. A, **2023**, 127, 1941–1959. https://pubs.acs.org/doi/full/10.1021/acs.jpca.2c08035  
 * Zádor, J, Martí, C., Van de Vijver, R., Johansen, S. L., Yang, Y., Michelsen, H. A., Najm, H. N.: _Automated reaction kinetics of gas-phase organic species over multiwell potential energy surfaces._ J. Phys. Chem. A, **2023**, 127, 565–588. https://doi.org/10.1021/acs.jpca.2c06558
+* Lockwood, K. S., Ahmed, S. F., Huq, N. A., Stutzman, S. C., Foust, T. D., Labbe, N. J.: _Advances in predictive chemistry enable a multi-scale rational design approach for biofuels with advantaged properties_ Sustainable Energy Fuels, **2022**, 6, 5371-5383. https://doi.org/10.1039/D2SE00773H 
 * Takahashi, L., Yoshida, S., Fujima, J., Oikawa, H., Takahashi, K.: _Unveiling the reaction pathways of hydrocarbons via experiments, computations and data science._ Phys. Chem. Chem. Phys., **2022**, 24, 29841-29849. https://pubs.rsc.org/en/content/articlelanding/2022/CP/D2CP04499D
 * Doner, A. C., Zádor, J., Rotavera, B.: _Stereoisomer-dependent unimolecular kinetics of 2,4-dimethyloxetane peroxy radicals._ Faraday Discuss., **2022**, 238, 295-319. https://doi.org/10.1039/D2FD00029F
 * Ramasesha, K., Savee, J. D., Zádor, J., Osborn, D. L.: _A New Pathway for Intersystem Crossing: Unexpected Products in the O(3P) + Cyclopentene Reaction._ J. Phys. Chem. A, **2021**, 125 9785-9801. https://doi.org/10.1021/acs.jpca.1c05817