Difference between revisions of "AutoMeKin"

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{{warning}} All content from this page has been transferred to a [https://github.com/emartineznunez/AutoMeKin [[File:gh.jpg|40px|link=]] repository], and this site will no longer receive support.
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== Introduction ==
 
== Introduction ==
 
<div style="column-count:2;-moz-column-count:2;-webkit-column-count:2">
 
<div style="column-count:2;-moz-column-count:2;-webkit-column-count:2">
 
[[File:Automekin.png|center]]
 
[[File:Automekin.png|center]]
 
AutoMeKin (formerly ''tsscds'') has been designed to discover reaction mechanisms in an automated fashion. Transition states are located using MD simulations and Graph Theory algorithms. Monte Carlo simulations afford kinetic results. The only input is a starting structure in XYZ format. The method is described in these two publications: [http://onlinelibrary.wiley.com/doi/10.1002/jcc.23790/abstract 1]
 
AutoMeKin (formerly ''tsscds'') has been designed to discover reaction mechanisms in an automated fashion. Transition states are located using MD simulations and Graph Theory algorithms. Monte Carlo simulations afford kinetic results. The only input is a starting structure in XYZ format. The method is described in these two publications: [http://onlinelibrary.wiley.com/doi/10.1002/jcc.23790/abstract 1]
[http://pubs.rsc.org/en/content/articlelanding/2015/cp/c5cp02175h#!divAbstract 2]. At present [http://openmopac.net/ MOPAC2016], [https://www.entos.info/ Entos Qcore] and Gaussian 09 (G09) are interfaced with AutoMeKin. The program has been tested on the following Linux distros: CentOS 7, Red Hat Enterprise Linux and Ubuntu 16.04.3 LTS.
+
[http://pubs.rsc.org/en/content/articlelanding/2015/cp/c5cp02175h#!divAbstract 2]. At present [http://openmopac.net/ MOPAC2016], [https://www.entos.ai/qcore/documentation/ Entos Qcore] and Gaussian (G09/G16) are interfaced with AutoMeKin. The program has been tested on the following Linux distros: CentOS 7, Red Hat Enterprise Linux and Ubuntu 20.04 LTS.
 +
 
 +
To give you a flavor of the capabilities of the program you can try our [http://rxnkin.usc.es/amk/ web interface] or [https://colab.research.google.com/github/emartineznunez/AutoMeKin/blob/main/AutoMeKin.ipynb Google Colab]
  
To give you a flavor of the capabilities of the program you can try our [http://rxnkin.usc.es/amk/ web interface]
 
  
  
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</div>
 
</div>
  
== Authors==
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== Developers team==
George L. Barnes, David R. Glowacki, Sabine Kopec, Emilio Martinez-Nunez, Daniel Pelaez-Ruiz, Aurelio Rodriguez, Roberto Rodriguez-Fernandez, Robin J. Shannon, James J. P. Stewart, Pablo G. Tahoces and Saulo A. Vazquez
+
'''Emilio Martinez-Nunez''', George L. Barnes, Carles Bo, Diego Garay-Ruiz, David R. Glowacki, Sabine Kopec, Daniel Pelaez-Ruiz, Aurelio Rodriguez, Roberto Rodriguez-Fernandez, Robin J. Shannon, James J. P. Stewart, Pablo G. Tahoces and Saulo A. Vazquez
  
 
'''Address'''<br />
 
'''Address'''<br />
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MIT License
 
MIT License
  
Copyright (C) 2020 George L. Barnes, David R. Glowacki, Sabine Kopec,
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Copyright (C) 2021 AutoMeKin
Emilio Martinez-Nunez, Daniel Pelaez-Ruiz, Aurelio Rodriguez,
 
Roberto Rodriguez-Fernandez, Robin J. Shannon, James J. P. Stewart,
 
Pablo G. Tahoces and Saulo A. Vazquez
 
  
 
Permission is hereby granted, free of charge, to any person obtaining a copy
 
Permission is hereby granted, free of charge, to any person obtaining a copy
Line 51: Line 52:
  
 
Download [[Media:tutorial2021.pdf| tutorial ]]<br />
 
Download [[Media:tutorial2021.pdf| tutorial ]]<br />
 +
 +
The tutorial can be more easily followed executing the example:
 +
 +
<code>https://colab.research.google.com/github/emartineznunez/AutoMeKin/blob/main/AutoMeKin.ipynb</code>
  
 
==Program execution==
 
==Program execution==
Unless you donwloaded the singularity container (in that case skip this step), to start using any of the scripts of the program, load the amk/20XX module:
+
Unless you donwloaded the singularity container (in that case skip this step), to start using any of the scripts of the program, load the amk/2021 module:
  
<code>module load amk/20XX</code>
+
<code>module load amk/2021</code>
  
 
To run the low-level calculations use:
 
To run the low-level calculations use:
Line 73: Line 78:
 
For more details, follow the instructions given in the [[Media:Tutorial2020.pdf| tutorial ]]
 
For more details, follow the instructions given in the [[Media:Tutorial2020.pdf| tutorial ]]
  
==References and citations==
+
==Reference==
These four publications must be cited in any work presenting results obtained with our software:
+
If you use '''AutoMeKin''', please cite the following publications:
<div style="column-count:2;-moz-column-count:2;-webkit-column-count:2">
 
  
 
<ol start="1">
 
<ol start="1">
<li>[http://onlinelibrary.wiley.com/doi/10.1002/jcc.23790/abstract <span style="font-size:100%">E. Martínez-Núñez J. Comput. Chem. 2015, 36, 222</span>]</li>
+
<li>[https://onlinelibrary.wiley.com/doi/full/10.1002/jcc.26734 <span style="font-size:100%">E Martínez-Nuñez, G.L. Barnes, D.R. Glowacki, S. Kopec, D. Pelaez, A. Rodriguez, R. Rodriguez-Fernandez, R.J. Shannon, J.J.P. Stewart, P.G. Tahoces, S.A. Vazquez, J. Comput. Chem. 2021, 42, 2036</span>]</li>
<li>[http://pubs.rsc.org/en/content/articlelanding/2015/cp/c5cp02175h#!divAbstract <span style="font-size:100%">E. Martínez-Núñez Phys. Chem. Chem. Phys. 2015,17, 14912</span>]</li>
+
<li>[http://onlinelibrary.wiley.com/doi/10.1002/jcc.23790/abstract <span style="font-size:100%">E. Martínez-Núñez, J. Comput. Chem. 2015, 36, 222</span>]</li>
<li>[https://onlinelibrary.wiley.com/doi/full/10.1002/jcc.25370 <span style="font-size:100%">A. Rodriguez, R. Rodriguez-Fernandez, S.A. Vazquez, G.L. Barnes, J.J.P. Stewart, E Martínez-Nuñez, J. Comput. Chem. 2018, 39, 1922</span>]</li>
+
<li>[http://pubs.rsc.org/en/content/articlelanding/2015/cp/c5cp02175h#!divAbstract <span style="font-size:100%">E. Martínez-Núñez, Phys. Chem. Chem. Phys. 2015,17, 14912</span>]</li>
 
<li>[http://OpenMOPAC.net <span style="font-size:100%">J. J. P. Stewart, MOPAC2016, Stewart Computational Chemistry: Colorado Springs, CO, USA, HTTP://OpenMOPAC.net, 2016.</span>]</li>
 
<li>[http://OpenMOPAC.net <span style="font-size:100%">J. J. P. Stewart, MOPAC2016, Stewart Computational Chemistry: Colorado Springs, CO, USA, HTTP://OpenMOPAC.net, 2016.</span>]</li>
 
</ol>
 
</ol>
</div>
 
  
Publications using AutoMeKin:
+
If you use the older version '''tsscds''', please cite, instead of ref 1 above, the following one:
<div style="column-count:2;-moz-column-count:2;-webkit-column-count:2">
+
 
<ol start="5">
+
[https://onlinelibrary.wiley.com/doi/full/10.1002/jcc.25370 <span style="font-size:100%">A. Rodriguez, R. Rodriguez-Fernandez, S.A. Vazquez, G.L. Barnes, J.J.P. Stewart, E Martínez-Nuñez, J. Comput. Chem. 2018, 39, 1922</span>]
<li>[https://www.sciencedirect.com/science/article/pii/S0040402019311573 <span style="font-size:100%"> A. Esteban et al. Tetrahedron 2020, 76, 130764</span>]</li>
+
 
<li>[https://onlinelibrary.wiley.com/doi/full/10.1002/syst.201900024 <span style="font-size:100%"> R. A. Jara-Toro et al. ChemSystemsChem 2020, 2, e1900024</span>]</li>
+
==Works that employ AutoMeKin==
<li>[https://www.frontiersin.org/articles/10.3389/fchem.2019.00576/full <span style="font-size:100%"> R. Panades-Barrueta et al. Frontiers in Chemistry 2019, 7, 576</span>]</li>
+
 
<li>[https://onlinelibrary.wiley.com/doi/abs/10.1002/qua.26008 <span style="font-size:100%"> S. Kopec et al. Int. J. Quantum Chem. 2019, 119, e26008 </span>]</li>
+
The following works employ AutoMeKin: [[Works]]
<li>[https://pubs.acs.org/doi/10.1021/acs.jpca.9b01779 <span style="font-size:100%">V. Macaluso et al. J. Phys. Chem. A 2019, 123, 3685-3696</span>]</li>
 
<li>[https://www.mdpi.com/1420-3049/23/12/3156 <span style="font-size:100%">S. A. Vázquez et al. Molecules 2018, 23, 3156</span>]</li>
 
<li>[https://onlinelibrary.wiley.com/doi/full/10.1002/jcc.25370 <span style="font-size:100%">A. Rodríguez et al. J. Comput. Chem. 2018, 39, 1922-1930</span>]</li>
 
<li>[https://pubs.acs.org/doi/10.1021/acs.jpca.8b02949 <span style="font-size:100%">D. Ferro-Costas et al. J. Phys. Chem. A 2018, 122, 4790-4800</span>]</li>
 
<li>[https://www.sciencedirect.com/science/article/pii/S0010218018300105 <span style="font-size:100%">Y. Fenard et al. Combust. Flame. 2018, 191, 252-269</span>]</li>
 
<li>[http://iopscience.iop.org/article/10.3847/1538-4357/aa8ea7/meta <span style="font-size:100%">M. J. Wilhelm et al. ApJ. 2017, 849, 15</span>]</li>
 
<li>[http://pubs.rsc.org/en/content/articlelanding/2017/sc/c7sc00549k#!divAbstract <span style="font-size:100%">J. A. Varela et al. Chem. Sci 2017, 8, 3843-3851</span>]</li>
 
<li>[http://pubs.rsc.org/-/content/articlelanding/2016/cp/c6cp01657j#!divAbstract <span style="font-size:100%">E. Rossich-Molina et al. Phys. Chem. Chem. Phys. 2016, 18, 22712-22718</span>]</li>
 
<li>[http://pubs.rsc.org/en/content/articlelanding/2016/cp/c5cp07759a#!divAbstract <span style="font-size:100%">R. Pérez-Soto et al. Phys. Chem. Chem. Phys. 2016, 18, 5019-5026</span>]</li>
 
<li>[http://pubs.rsc.org/en/content/articlelanding/2015/cp/c4cp05626d#!divAbstract <span style="font-size:100%">S. A. Vázquez and E. Martínez-Núñez, Phys. Chem. Chem. Phys. 2015, 17, 6948-6955</span>]</li>
 
</ol>
 
</div>
 
  
 
==Changelog==
 
==Changelog==
 
Consult the [[Latest changes]]
 
Consult the [[Latest changes]]
  
==Web interface==
+
==Web interface and Google Colab==
 
AutoMeKin can be used through our [http://rxnkin.usc.es/amk/ web interface].
 
AutoMeKin can be used through our [http://rxnkin.usc.es/amk/ web interface].
 +
 +
The tutorial example (formic acid) can be easily tested on Google Colab using this link:
 +
 +
<code>https://colab.research.google.com/github/emartineznunez/AutoMeKin/blob/main/AutoMeKin.ipynb</code>
  
 
==News==
 
==News==
The improvements briefly described below are available in AutoMeKin2020.
+
AutoMeKin is now interfaced with Gaussian 16 (from rev. 1131)
 +
 
 +
The Python library [https://github.com/dgarayr/amk_tools '''amk-tools'''] can be employed to read, process and visualize reaction networks generated by AutoMeKin and is available in the latest singularity container (and through our web interface). Here is the paper describing the new tool: [https://pubs.acs.org/doi/10.1021/acsphyschemau.1c00051 <span style="font-size:100%"> Garay-Ruiz et al. ACS Phys. Chem. Au 2022]
 +
 
 +
AutoMekin got the [https://geqc.rseq.org/emilio-martinez-nunez-and-mireia-via-nadal-recieve-the-geqc-rseq-2021-methodology-development-prize/ GEQC-RSEQ 2021 Methodology Development Prize].
 +
 
 +
AutoMeKin now includes '''barrierless channels'''. However, these channels are not considered in the kinetics.
  
AutoMeKin has been interfaced with [https://www.entos.info/ Entos Qcore]
+
AutoMeKin has been interfaced with [https://www.entos.ai/qcore/documentation/ '''Entos Qcore'''].
  
AutoMeKin has been interfaced with BXDE to enhance its efficiency ([https://onlinelibrary.wiley.com/doi/full/10.1002/syst.201900024 <span style="font-size:100%"> R. A. Jara-Toro et al. ChemSystemsChem doi: 10.1002/syst.201900024</span>]).
+
AutoMeKin has been interfaced with '''BXDE''' to enhance its efficiency ([https://onlinelibrary.wiley.com/doi/full/10.1002/syst.201900024 <span style="font-size:100%"> R. A. Jara-Toro et al. ChemSystemsChem doi: 10.1002/syst.201900024</span>]).
  
The method has also been recently generalized in a collaboration with Dani Pelaez and co-workers to study van der Waals structures ([https://onlinelibrary.wiley.com/doi/abs/10.1002/qua.26008 <span style="font-size:100%"> S. Kopec et al. Int. J. Quantum Chem. 2019, 119, e26008 </span>]) and also to generate sum-of-products PESs for quantum dynamics ([https://www.frontiersin.org/articles/10.3389/fchem.2019.00576/full <span style="font-size:100%"> R. Panades-Barrueta et al. Frontiers in Chemistry 2019, 7, 576</span>]).
+
The method has also been recently generalized in a collaboration with Dani Pelaez and co-workers to study '''van der Waals structures''' ([https://onlinelibrary.wiley.com/doi/abs/10.1002/qua.26008 <span style="font-size:100%"> S. Kopec et al. Int. J. Quantum Chem. 2019, 119, e26008 </span>]) and also to generate sum-of-products PESs for quantum dynamics ([https://www.frontiersin.org/articles/10.3389/fchem.2019.00576/full <span style="font-size:100%"> R. Panades-Barrueta et al. Frontiers in Chemistry 2019, 7, 576</span>]).
  
 
Return to [[#toc|Contents]]
 
Return to [[#toc|Contents]]
  
 
Return to [[Main_Page]]
 
Return to [[Main_Page]]

Latest revision as of 06:48, 11 February 2024

All content from this page has been transferred to a gh.jpg repository, and this site will no longer receive support.


Introduction

Automekin.png

AutoMeKin (formerly tsscds) has been designed to discover reaction mechanisms in an automated fashion. Transition states are located using MD simulations and Graph Theory algorithms. Monte Carlo simulations afford kinetic results. The only input is a starting structure in XYZ format. The method is described in these two publications: 1 2. At present MOPAC2016, Entos Qcore and Gaussian (G09/G16) are interfaced with AutoMeKin. The program has been tested on the following Linux distros: CentOS 7, Red Hat Enterprise Linux and Ubuntu 20.04 LTS.

To give you a flavor of the capabilities of the program you can try our web interface or Google Colab


Web.png

Developers team

Emilio Martinez-Nunez, George L. Barnes, Carles Bo, Diego Garay-Ruiz, David R. Glowacki, Sabine Kopec, Daniel Pelaez-Ruiz, Aurelio Rodriguez, Roberto Rodriguez-Fernandez, Robin J. Shannon, James J. P. Stewart, Pablo G. Tahoces and Saulo A. Vazquez

Address
Departamento de Química Física, Facultade de Química, Avda. das Ciencias s/n, 15782 Santiago de Compostela, SPAIN
email me

License

MIT License

Copyright (C) 2021 AutoMeKin

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

Install the code

To install the code follow the Installation instructions

Tutorial

Download tutorial

The tutorial can be more easily followed executing the example:

https://colab.research.google.com/github/emartineznunez/AutoMeKin/blob/main/AutoMeKin.ipynb

Program execution

Unless you donwloaded the singularity container (in that case skip this step), to start using any of the scripts of the program, load the amk/2021 module:

module load amk/2021

To run the low-level calculations use:

nohup llcalcs.sh molecule.dat ntasks niter runningtasks >llcalcs.log 2>&1 &

where:
molecule is the name of your molecule
ntasks is the number of tasks
niter is the number of iterations
runningtasks is the number of simultaneous tasks

To run the high-level calculations use:

nohup hlcalcs.sh molecule.dat runningtasks >hlcalcs.log 2>&1 &

For more details, follow the instructions given in the tutorial

Reference

If you use AutoMeKin, please cite the following publications:

  1. E Martínez-Nuñez, G.L. Barnes, D.R. Glowacki, S. Kopec, D. Pelaez, A. Rodriguez, R. Rodriguez-Fernandez, R.J. Shannon, J.J.P. Stewart, P.G. Tahoces, S.A. Vazquez, J. Comput. Chem. 2021, 42, 2036
  2. E. Martínez-Núñez, J. Comput. Chem. 2015, 36, 222
  3. E. Martínez-Núñez, Phys. Chem. Chem. Phys. 2015,17, 14912
  4. J. J. P. Stewart, MOPAC2016, Stewart Computational Chemistry: Colorado Springs, CO, USA, HTTP://OpenMOPAC.net, 2016.

If you use the older version tsscds, please cite, instead of ref 1 above, the following one:

A. Rodriguez, R. Rodriguez-Fernandez, S.A. Vazquez, G.L. Barnes, J.J.P. Stewart, E Martínez-Nuñez, J. Comput. Chem. 2018, 39, 1922

Works that employ AutoMeKin

The following works employ AutoMeKin: Works

Changelog

Consult the Latest changes

Web interface and Google Colab

AutoMeKin can be used through our web interface.

The tutorial example (formic acid) can be easily tested on Google Colab using this link:

https://colab.research.google.com/github/emartineznunez/AutoMeKin/blob/main/AutoMeKin.ipynb

News

AutoMeKin is now interfaced with Gaussian 16 (from rev. 1131)

The Python library amk-tools can be employed to read, process and visualize reaction networks generated by AutoMeKin and is available in the latest singularity container (and through our web interface). Here is the paper describing the new tool: Garay-Ruiz et al. ACS Phys. Chem. Au 2022

AutoMekin got the GEQC-RSEQ 2021 Methodology Development Prize.

AutoMeKin now includes barrierless channels. However, these channels are not considered in the kinetics.

AutoMeKin has been interfaced with Entos Qcore.

AutoMeKin has been interfaced with BXDE to enhance its efficiency ( R. A. Jara-Toro et al. ChemSystemsChem doi: 10.1002/syst.201900024).

The method has also been recently generalized in a collaboration with Dani Pelaez and co-workers to study van der Waals structures ( S. Kopec et al. Int. J. Quantum Chem. 2019, 119, e26008 ) and also to generate sum-of-products PESs for quantum dynamics ( R. Panades-Barrueta et al. Frontiers in Chemistry 2019, 7, 576).

Return to Contents

Return to Main_Page