Difference between revisions of "AutoMeKin"

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== Description of the software ==
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== Introduction ==
AutoMeKin (formerly known as ''tsscds'') is a computer program that has been designed to discover reaction mechanisms and solve the kinetics in an automated fashion. AutoMeKin obtains transition state guess structures from trajectory simulations of the highly vibrationally excited species. From the obtained TS structures, minima and product fragments are determined following the intrinsic reaction coordinate. Finally, having determined the stationary points, the reaction network is constructed and the kinetics is solved. The program is interfaced with [http://openmopac.net/ MOPAC2016] and Gaussian 09 (G09).
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<div style="column-count:2;-moz-column-count:2;-webkit-column-count:2">
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[[File:Automekin.png|center]]
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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.ai/qcore/documentation/ 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.
  
Details of the method are described in these two publications: [http://onlinelibrary.wiley.com/doi/10.1002/jcc.23790/abstract 1]
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To give you a flavor of the capabilities of the program you can try our [http://rxnkin.usc.es/amk/ web interface]
[http://pubs.rsc.org/en/content/articlelanding/2015/cp/c5cp02175h#!divAbstract 2]
 
  
Users are encouraged to read the [[Media:amk_tutorial.pdf| tutorial]], which is thought to guide you through the various steps necessary to predict reaction mechanisms and kinetics of unimolecular decompositions. To facilitate the presentation, we consider, as an example, the decomposition of formic acid (FA).
 
  
The program has been tested on the following Linux distros: CentOS 7, Red Hat Enterprise Linux and Ubuntu 16.04.3 LTS
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[[File:Web.png|center]]
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 +
</div>
  
 
== Authors==
 
== Authors==
George L. Barnes, Sabine Kopec, Daniel Peláez, Aurelio Rodríguez, Roberto Rodríguez-Fernández, James J. P. Stewart, Pablo Tahoces, Saulo A. Vázquez and Emilio Martínez-Núñez
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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
  
 
'''Address'''<br />
 
'''Address'''<br />
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MIT License
 
MIT License
  
Copyright (C) 2018  George L. Barnes, Sabine Kopec, Daniel Peláez, Aurelio Rodríguez, Roberto Rodríguez-Fernández, James J. P. Stewart, Pablo Tahoces, Saulo A. Vázquez and Emilio Martínez-Núñez
+
Copyright (C) 2021 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
  
 
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
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SOFTWARE.
 
SOFTWARE.
  
==Downloads==
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==Install the code==
Download the [[Media:amk_tutorial.pdf| tutorial ]]<br />
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To install the code follow the [[Installation instructions]]
The most recent version of AutoMeKin can be [[Media:amk-SOURCE-2018rev.tar.gz| downloaded here ]]<br />
 
A stable (but maybe not up-to-date) version can also be cloned from:<br />
 
[[File:github2.png|90px|link=https://github.com/emartineznunez/AutoMeKin]]
 
  
==Install the code==
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==Tutorial==
To install the code read the [[Installation instructions]]
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 +
Download [[Media:tutorial2021.pdf| tutorial ]]<br />
  
 
==Program execution==
 
==Program execution==
To start using any of the scripts of the program, load the amk/2018 module:
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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/2018</code>
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<code>module load amk/2021</code>
  
 
To run the low-level calculations use:
 
To run the low-level calculations use:
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<code>nohup hlcalcs.sh molecule.dat runningtasks >hlcalcs.log 2>&1 &</code>
 
<code>nohup hlcalcs.sh molecule.dat runningtasks >hlcalcs.log 2>&1 &</code>
  
For more details, follow the instructions given in the [[Media:amk_tutorial.pdf| tutorial ]]
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For more details, follow the instructions given in the [[Media:Tutorial2020.pdf| tutorial ]]
  
==References and citations==
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==Reference==
These four publications must be cited in any work presenting results obtained with our software:
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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">
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<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>
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Publications using AutoMeKin:
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==Works that employ AutoMeKin==
<div style="column-count:2;-moz-column-count:2;-webkit-column-count:2">
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<ol start="5">
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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==
{| class="wikitable"
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Consult the [[Latest changes]]
!colspan="6"|Latest revision: 362
 
|-
 
|07/09/2019
 
|if name of working dir is too long, name--->wrkdir
 
|-
 
|06/30/2019
 
|amk acronym replaces old tsscds acronym
 
|-
 
|04/18/2019
 
|MIT license
 
|-
 
|04/17/2019
 
|The label of the starting min in the kmc simulations is in tsdirll/KMC/starting_minimum
 
|-
 
|04/15/2019
 
|A bug in get_energy_g09_MP2.sh was corrected
 
|-
 
|04/01/2019
 
|threads=1 has been added to the input files in the examples folder. The use of this keyword is highly recommented to avoid multhreading in MOPAC calculations for much better performance
 
|-
 
|03/01/2019
 
|A bug in the kmc.f90 source file was corrected
 
|}
 
  
 
==Web interface==
 
==Web interface==
AutoMeKin can be used through our [http://rxnkin.usc.es/amk/ web interface] (only MOPAC2016 calculations).
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AutoMeKin can be used through our [http://rxnkin.usc.es/amk/ web interface].
  
 
==News==
 
==News==
<html lang="en"> 
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The improvements briefly described below are available in AutoMeKin2021.
  <head>
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<blockquote class="twitter-tweet" data-lang="es"><p lang="en" dir="ltr">vdW‐TSSCDS—An automated and global procedure for the computation of stationary points on intermolecular potential energy surfaces - Kopec -  - International Journal of Quantum Chemistry - Wiley Online Library <a href="https://t.co/f5caCQv37s">https://t.co/f5caCQv37s</a></p>&mdash; Emilio Martinez-Nunez (@emilio_nune) <a href="https://twitter.com/emilio_nune/status/1151464285660430336?ref_src=twsrc%5Etfw">17 de julio de 2019</a></blockquote>
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From revision 1096, AutoMeKin includes barrierless channels. However, these channels are not considered in the kinetics.
<script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
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</html>
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AutoMeKin has been interfaced with [https://www.entos.info/ 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>]).
 +
 
 +
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 [[Main_Page]]
 
Return to [[Main_Page]]

Revision as of 05:35, 23 July 2021

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 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.

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


Web.png

Authors

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

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 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

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

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-Núñez J. Comput. Chem. 2015, 36, 222
  2. E. Martínez-Núñez Phys. Chem. Chem. Phys. 2015,17, 14912
  3. A. Rodriguez, R. Rodriguez-Fernandez, S.A. Vazquez, G.L. Barnes, J.J.P. Stewart, E Martínez-Nuñez, J. Comput. Chem. 2018, 39, 1922
  4. J. J. P. Stewart, MOPAC2016, Stewart Computational Chemistry: Colorado Springs, CO, USA, HTTP://OpenMOPAC.net, 2016.

Works that employ AutoMeKin

The following works employ AutoMeKin: Works

Changelog

Consult the Latest changes

Web interface

AutoMeKin can be used through our web interface.

News

The improvements briefly described below are available in AutoMeKin2021.

From revision 1096, AutoMeKin 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