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| − | == Automated Reaction Mechanisms and Kinetics (AutoMeKin)==
| + | {{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 has been designed to discover reaction mechanisms and solve the kinetics in an automated fashion, using chemical dynamics simulations. AutoMeKin obtains 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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| − | 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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| − | 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<br /> 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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| − | ==[http://forge.cesga.es/frs/?group_id=77&release_id=21 Download source code & tutorial]==
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| − | ==License==
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| − | A computer program for finding reaction mechanisms and solving the kinetics.<br />
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| − | Copyright (C) 2018 Emilio Martinez-Nunez, Aurelio Rodriguez, Roberto<br />
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| − | Rodriguez-Fernandez, Saulo Vazquez-Rodriguez, George L. Barnes and<br />
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| − | James J. P. Stewart<br />
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| − | This program is free software: you can redistribute it and/or modify<br />
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| − | it under the terms of the GNU General Public License as published by<br />
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| − | the Free Software Foundation, either version 3 of the License, or<br />
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| − | any later version.<br />
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| − | This program is distributed in the hope that it will be useful,<br />
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| − | but WITHOUT ANY WARRANTY; without even the implied warranty of<br />
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| − | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the<br />
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| − | GNU General Public License for more details.<br />
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| − | You should have received a copy of the GNU General Public License<br />
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| − | along with this program. If not, see http://www.gnu.org/licenses/.<br />
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| − | ==[[Installation instructions]]==
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| − | ==[[Program execution]]==
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| − | ==[[References and citations]]==
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| − | ==[[Changelog]]==
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| − | ==News==
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| − | Use threads=1 in your input file (see the tutorial) to avoid multhreading in MOPAC calculations for much better performance
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repository, and this site will no longer receive support.
