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== Description of the software ==
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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.
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 reaction mechanisms and kinetics from MD simulations, Graph Theory algorithms and Kinetic Monte Carlo. The user only needs to provide a starting structure of the system. So far, the electronic structure programs interfaced with AutoMeKin are [http://openmopac.net/ MOPAC2016] and Gaussian 09 (G09).
 
 
 
[[File:Web.png]]
 
 
 
Details of the method are 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]
 
 
 
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
 
 
 
== 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
 
 
 
'''Address'''<br />
 
Departamento de Química Física, Facultade de Química, Avda. das Ciencias s/n, 15782 Santiago de Compostela, SPAIN<br />
 
[mailto:emilio.nunez@usc.es email me]
 
 
 
==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
 
 
 
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.
 
 
 
==Downloads==
 
Download the [[Media:amk_tutorial.pdf| tutorial ]]<br />
 
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==
 
To install the code read the [[Installation instructions]]
 
 
 
==Program execution==
 
To start using any of the scripts of the program, load the amk/2018 module:
 
 
 
<code>module load amk/2018</code>
 
 
 
To run the low-level calculations use:
 
 
 
<code>nohup llcalcs.sh molecule.dat ntasks niter runningtasks >llcalcs.log 2>&1 &</code>
 
 
 
where:<br />
 
<code>molecule</code> is  the name of your molecule<br />
 
<code>ntasks</code> is the number of tasks<br />
 
<code>niter</code> is the number of iterations<br />
 
<code>runningtasks</code> is the number of simultaneous tasks
 
 
 
To run the high-level calculations use:
 
 
 
<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 ]]
 
 
 
==References and citations==
 
These four publications must be cited in any work presenting results obtained with our software:
 
<div style="column-count:2;-moz-column-count:2;-webkit-column-count:2">
 
 
 
<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>[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>[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://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>
 
</div>
 
Publications using AutoMeKin:
 
<div style="column-count:2;-moz-column-count:2;-webkit-column-count:2">
 
<ol start="5">
 
<li>[https://www.sciencedirect.com/science/article/pii/S0040402019311573 <span style="font-size:100%"> A. Esteban et al. Tetrahedron (2019), doi: https://doi.org/10.1016/j.tet.2019.130764</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 doi: 10.1002/syst.201900024</span>]</li>
 
<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>
 
<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==
 
Consult the [[Latest changes]]
 
 
 
==Web interface==
 
AutoMeKin can be used through our [http://rxnkin.usc.es/amk/ web interface].
 
 
 
==News==
 
AutoMeKin has been interfaced with BXDE to enhance its efficiency.
 
The method has also been recently generalized in a collaboration with Dani Pelaez and co-workers to study van der Waals structures and also to generate sum-of-products PESs for quantum dynamics.
 
 
 
<html lang="en"> 
 
 
 
<iframe src="https://www.facebook.com/plugins/post.php?href=https%3A%2F%2Fwww.facebook.com%2Femilio.martineznunez%2Fposts%2F10158821119149008&width=500" width="500" height="463" style="border:none;overflow:hidden" scrolling="no" frameborder="0" allowTransparency="true" allow="encrypted-media"></iframe>
 
 
 
 
 
<iframe src="https://www.facebook.com/plugins/post.php?href=https%3A%2F%2Fwww.facebook.com%2Femilio.martineznunez%2Fposts%2F10158519314634008&width=500" width="500" height="462" style="border:none;overflow:hidden" scrolling="no" frameborder="0" allowTransparency="true" allow="encrypted-media"></iframe>
 
 
 
 
 
 
 
<iframe src="https://www.facebook.com/plugins/post.php?href=https%3A%2F%2Fwww.facebook.com%2Femilio.martineznunez%2Fposts%2F10158567272429008&width=500" width="500" height="463" style="border:none;overflow:hidden" scrolling="no" frameborder="0" allowTransparency="true" allow="encrypted-media"></iframe>
 
 
 
</html>
 
 
 
 
 
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Latest revision as of 15:32, 17 July 2024

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