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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 [http://openmopac.net/ 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 [[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).
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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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| − | MIT License
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| − | 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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| − | Permission is hereby granted, free of charge, to any person obtaining a copy
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| − | of this software and associated documentation files (the "Software"), to deal
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| − | in the Software without restriction, including without limitation the rights
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| − | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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| − | copies of the Software, and to permit persons to whom the Software is
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| − | furnished to do so, subject to the following conditions:
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| − | The above copyright notice and this permission notice shall be included in all
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| − | copies or substantial portions of the Software.
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| − | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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| − | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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| − | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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| − | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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| − | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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| − | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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| − | SOFTWARE.
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| − | ==Downloads==
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| − | Download the [[Media:amk_tutorial.pdf| tutorial ]]<br />
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| − | The most recent version of AutoMeKin can be [[Media:amk-SOURCE-2018rev.tar.gz| downloaded here ]]<br />
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| − | A stable (but maybe not up-to-date) version can also be cloned from:<br />
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| − | [[File:github2.png|90px|link=https://github.com/emartineznunez/AutoMeKin]] | |
| − | | |
| − | ==Install the code==
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| − | To install the code read the [[Installation instructions]]
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| − | ==Program execution==
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| − | To start using any of the scripts of the program, load the amk/2018 module:
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| − | <code>module load amk/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 [[Media:amk_tutorial.pdf| tutorial ]]
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| − | ==References and citations==
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| − | These four publications 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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| − | Publications using AutoMeKin:
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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://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>
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| − | <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 7:576 doi: 10.3389/fchem.2019.00576</span>]</li>
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| − | <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;e26008 (https://doi.org/10.1002/qua.26008)</span>]</li>
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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, 123, 3685-3696</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: 366
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| − | |-
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| − | |09/16/2019
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| − | |pdfs are now generated also in FINAL_HL
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| − | |-
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| − | |07/09/2019
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| − | |if name of working dir is too long, name--->wrkdir
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| − | |-
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| − | |06/30/2019
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| − | |amk acronym replaces old tsscds acronym
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| − | |-
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| − | |04/18/2019
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| − | |MIT license
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| − | |-
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| − | |04/17/2019
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| − | |The label of the starting min in the kmc simulations is in tsdirll/KMC/starting_minimum
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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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| − | ==News==
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| − | AutoMeKin has been interfaced with BXDE to enhance its efficiency.
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| − | 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.
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