AutoMeKin

Automated Reaction Mechanisms and Kinetics (AutoMeKin)

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. 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 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 Emilio Martinez-Nunez, Aurelio Rodriguez, Roberto Rodriguez-Fernandez, Saulo Vazquez-Rodriguez, George L. Barnes and James J. P. Stewart

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/.

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

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:

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

News

Use threads=1 in your input file (see the tutorial) to avoid multhreading in MOPAC calculations for much better performance