AutoMeKin

Description of the software

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).

Details of the method are described in these two publications: 1 2

Users are encouraged to read the 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).

The program has been tested 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, Pablo Tahoces, Saulo A. Vázquez and Emilio Martínez-Núñez

Address
Departamento de Química Física, Facultade de Química, Avda. das Ciencias s/n, 15782 Santiago de Compostela, SPAIN
email me

License

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

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.

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.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.

Download source code & tutorial

Both, the source code and tutorial can be downloaded from the following link

Install the code

Follow this link: Installation instructions

Program execution

To start using any of the scripts of the program, you have to load tsscds/2018 module:

module load tsscds/2018

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

References and citations

These four papers must be cited in any work presenting results obtained with our software:

1. E. Martínez-Núñez J. Comput. Chem. 2015, 36, 222
2. E. Martínez-Núñez Phys. Chem. Chem. Phys. 2015,17, 14912
3. A. Rodriguez, R. Rodriguez-Fernandez, S.A. Vazquez, G.L. Barnes, J.J.P. Stewart, E Martínez-Nuñez, J. Comput. Chem. 2018, 39, 1922
4. J. J. P. Stewart, MOPAC2016, Stewart Computational Chemistry: Colorado Springs, CO, USA, HTTP://OpenMOPAC.net, 2016.

Additional references:

5. V. Macaluso et al. J. Phys. Chem. A 2019 (ASAP)
6. S. A. Vázquez et al. Molecules 2018, 23, 3156
7. A. Rodríguez et al. J. Comput. Chem. 2018, 39, 1922-1930
8. D. Ferro-Costas et al. J. Phys. Chem. A 2018, 122, 4790-4800
9. Y. Fenard et al. Combust. Flame. 2018, 191, 252-269
10. M. J. Wilhelm et al. ApJ. 2017, 849, 15
11. J. A. Varela et al. Chem. Sci 2017, 8, 3843-3851
12. E. Rossich-Molina et al. Phys. Chem. Chem. Phys. 2016, 18, 22712-22718
13. R. Pérez-Soto et al. Phys. Chem. Chem. Phys. 2016, 18, 5019-5026
14. S. A. Vázquez and E. Martínez-Núñez, Phys. Chem. Chem. Phys. 2015, 17, 6948-6955

Changelog

Latest revision: 337
04/17/2019	The starting min in the kmc simulations is in tsdirll/KMC/starting_minimum
04/15/2019	A bug in get_energy_g09_MP2.sh was corrected
04/01/2019	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
03/01/2019	A bug in the kmc.f90 source file was corrected

Web interface

AutoMeKin can be used through our web interface (only MOPAC2016 calculations).