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| − | == Description of the software ==
| + | {{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 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 MOPAC2016 and Gaussian 09 (G09).
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| − | 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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| − | [http://pubs.rsc.org/en/content/articlelanding/2015/cp/c5cp02175h#!divAbstract 2]
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| − | Users are encouraged to read the [http://forge.cesga.es/frs/?group_id=77&release_id=21 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).
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| − | 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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| − | == Authors==
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| − | 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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| − | '''Address'''<br />
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| − | Departamento de Química Física, Facultade de Química, Avda. das Ciencias s/n, 15782 Santiago de Compostela, SPAIN<br />
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| − | [mailto:emilio.nunez@usc.es email me]
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| − | ==License==
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| − | A computer program for finding reaction mechanisms and solving the kinetics. 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
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| − | This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or any later version.
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| − | This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
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| − | You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.
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| − | ==Download source code & tutorial==
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| − | Both, the source code and tutorial can be downloaded from the following [http://forge.cesga.es/frs/?group_id=77&release_id=21 link]
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| − | ==Install the code==
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| − | Follow this link: [[Installation instructions]]
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| − | ==Program execution==
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| − | To start using any of the scripts of the program, you have to load tsscds/2018 module:
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| − | <code>module load tsscds/2018</code>
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| − | To run the low-level calculations use:
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| − | <code>nohup llcalcs.sh molecule.dat ntasks niter runningtasks >llcalcs.log 2>&1 &</code>
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| − | where:<br />
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| − | <code>molecule</code> is the name of your molecule<br />
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| − | <code>ntasks</code> is the number of tasks<br />
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| − | <code>niter</code> is the number of iterations<br />
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| − | <code>runningtasks</code> is the number of simultaneous tasks
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| − | To run the high-level calculations use:
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| − | <code>nohup hlcalcs.sh molecule.dat runningtasks >hlcalcs.log 2>&1 &</code>
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| − | For more details, follow the instructions given in the [http://forge.cesga.es/frs/?group_id=77&release_id=21 tutorial]
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| − | ==References and citations==
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| − | These four papers must be cited in any work presenting results obtained with our software:
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| − | <div style="column-count:2;-moz-column-count:2;-webkit-column-count:2">
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| − | <ol start="1">
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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>
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| − | <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>[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>
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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>
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| − | </div>
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| − | Additional references:
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| − | <div style="column-count:2;-moz-column-count:2;-webkit-column-count:2">
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| − | <ol start="5">
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| − | <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 (ASAP)</span>]</li>
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| − | <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>
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| − | <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>
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| − | <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>
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| − | <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>
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| − | <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>
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| − | <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>
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| − | <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>
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| − | <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>
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| − | <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>
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| − | </ol>
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| − | </div>
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| − | ==Changelog==
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| − | {| class="wikitable"
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| − | !colspan="6"|Latest revision: 334
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| − | |-
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| − | |04/15/2019
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| − | |A bug in get_energy_g09_MP2.sh was corrected
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| − | |-
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| − | |04/01/2019
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| − | |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
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| − | |-
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| − | |03/01/2019
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| − | |A bug in the kmc.f90 source file was corrected
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| − | |}
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| − | ==Web interface==
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| − | AutoMeKin can be used through our [http://rxnkin.usc.es/amk/ web interface] (only MOPAC2016 calculations).
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repository, and this site will no longer receive support.
