Difference between revisions of "AutoMeKin"

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== '''Automated Reaction Mechanisms and Kinetics''' ==
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== Introduction ==
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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.
  
<span style="color: red;">Use threads=1 in your input file (see the tutorial) to avoid multhreading in MOPAC calculations for much better performance</span>
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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://forge.cesga.es/frs/?group_id=77&release_id=21 Download code (tsscds-SOURCE-2018rev1.tar.gz) & tutorial (tutorial_tsscds.pdf) ]
 
  
[[License]]
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[[File:Web.png|center]]
  
[[Installation instructions]]
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</div>
  
[[Running the test]]
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== 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
  
[[Program execution]]
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'''Address'''<br />
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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]
  
[[How to cite the program]]
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==License==
 +
MIT License
  
[[Research]]
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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
  
This program package has been designed to discover reaction mechanisms and solve the kinetics in an automated fashion, using chemical dynamics simulations. The basic idea is to obtain transition state (TS) guess structures from trajectory simulations performed at very high energies or temperatures. From the obtained TS structures, minima and product fragments are determined following the intrinsic reaction coordinate (IRC). Then, with all the stationary points, the reaction network is constructed. Finally, the kinetics is solved using the Kinetic Monte Carlo (KMC) method.
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Permission is hereby granted, free of charge, to any person obtaining a copy
The program is interfaced with MOPAC2016 and Gaussian 09 (G09), but work is in progress to incorporate more electronic structure programs.\\
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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:
  
[[Image:pr2.png]]
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The above copyright notice and this permission notice shall be included in all
 +
copies or substantial portions of the Software.
  
Details of the method are described in these two publications: [1 | http://onlinelibrary.wiley.com/doi/10.1002/jcc.23790/abstract]
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
[2 | http://pubs.rsc.org/en/content/articlelanding/2015/cp/c5cp02175h#!divAbstract]
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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.
  
Users are encouraged to read the tutorial [ (tutorial_tsscds.pdf) | http://forge.cesga.es/frs/?group_id=77&release_id=21], 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).\\
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==Install the code==
 +
To install the code follow the [[Installation instructions]]
  
 +
==Tutorial==
  
 +
Download [[Media:tutorial2021.pdf| tutorial ]]<br />
  
The program has been  tested so far on the following Linux distros: CentOS 7, Red Hat Enterprise Linux and Ubuntu 16.04.3 LTS
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==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:
  
== Authors: ==
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<code>module load amk/2021</code>
  
George L. Barnes, Sabine Kopec, Daniel Peláez, Aurelio Rodríguez, Roberto Rodríguez-Fernández, James J. P. Stewart,  Saulo A. Vázquez and //Emilio Martínez-Núñez//\\
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To run the low-level calculations use:
  
Departamento de Química Física
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<code>nohup llcalcs.sh molecule.dat ntasks niter runningtasks >llcalcs.log 2>&1 &</code>
Facultade de Química
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Avda. das Ciencias s/n
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where:<br />
15782 Santiago de Compostela, SPAIN
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<code>molecule</code> is  the name of your molecule<br />
[mailto: emilio.nunez@usc.es email me]
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<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
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 +
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:Tutorial2020.pdf| tutorial ]]
 +
 
 +
==Reference==
 +
If you use '''AutoMeKin''', please cite the following publications:
 +
 
 +
<ol start="1">
 +
<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>
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<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>
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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>
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</ol>
 +
 
 +
If you use the older version '''tsscds''', please cite, instead of ref 1 above, the following one:
 +
 
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[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>]
 +
 
 +
==Works that employ AutoMeKin==
 +
 
 +
The following works employ AutoMeKin: [[Works]]
 +
 
 +
==Changelog==
 +
Consult the [[Latest changes]]
 +
 
 +
==Web interface==
 +
AutoMeKin can be used through our [http://rxnkin.usc.es/amk/ 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 [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>]).
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Return to [[#toc|Contents]]
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Return to [[Main_Page]]

Latest revision as of 17:51, 16 October 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-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

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