Difference between revisions of "AutoMeKin"
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| − | + | == **Transition State Search Using Chemical Dynamics Simulations** == | |
| − | + | %color=red% (03/18/2019) Use threads=1 in your input file (see the tutorial) to avoid multhreading in MOPAC calculations for much better performance%% | |
| − | + | [Download code (tsscds-SOURCE-2018rev1.tar.gz) & tutorial (tutorial_tsscds.pdf) | http://forge.cesga.es/frs/?group_id=77&release_id=21]\\ | |
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| − | == | + | [[License]] |
| − | + | ||
| + | [[Installation instructions]] | ||
| + | |||
| + | [[Running the test]] | ||
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| + | [[Program execution]] | ||
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| + | [[How to cite the program]] | ||
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| + | [[Research]] | ||
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| + | 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. | ||
| + | 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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| + | [[Image:pr2.png]] | ||
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| + | Details of the method are described in these two publications: [1 | http://onlinelibrary.wiley.com/doi/10.1002/jcc.23790/abstract] | ||
| + | [2 | http://pubs.rsc.org/en/content/articlelanding/2015/cp/c5cp02175h#!divAbstract] | ||
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| + | 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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| + | 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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| + | == Authors: == | ||
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| + | 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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| + | Departamento de Química Física\\ | ||
| + | Facultade de Química\\ | ||
| + | Avda. das Ciencias s/n\\ | ||
| + | 15782 Santiago de Compostela, SPAIN\\ | ||
| + | [mailto: emilio.nunez@usc.es] | ||
Revision as of 16:48, 12 April 2019
**Transition State Search Using Chemical Dynamics Simulations**
%color=red% (03/18/2019) Use threads=1 in your input file (see the tutorial) to avoid multhreading in MOPAC calculations for much better performance%%
[Download code (tsscds-SOURCE-2018rev1.tar.gz) & tutorial (tutorial_tsscds.pdf) | http://forge.cesga.es/frs/?group_id=77&release_id=21]\\
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. The program is interfaced with MOPAC2016 and Gaussian 09 (G09), but work is in progress to incorporate more electronic structure programs.\\
Details of the method are described in these two publications: [1 | http://onlinelibrary.wiley.com/doi/10.1002/jcc.23790/abstract] [2 | http://pubs.rsc.org/en/content/articlelanding/2015/cp/c5cp02175h#!divAbstract]
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).\\
The program has been tested so far 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, Saulo A. Vázquez and //Emilio Martínez-Núñez//\\
Departamento de Química Física\\ Facultade de Química\\ Avda. das Ciencias s/n\\ 15782 Santiago de Compostela, SPAIN\\ [mailto: emilio.nunez@usc.es]
