Difference between revisions of "AutoMeKin"

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MIT License
 
MIT License
  
Copyright (C) 2018 George L. Barnes, David R. Glowacki, Sabine Kopec,  
+
Copyright (C) 2020 George L. Barnes, David R. Glowacki, Sabine Kopec,  
 
Emilio Martinez-Nunez, Daniel Pelaez-Ruiz, Aurelio Rodriguez,  
 
Emilio Martinez-Nunez, Daniel Pelaez-Ruiz, Aurelio Rodriguez,  
 
oberto Rodriguez-Fernandez, Robin J. Shannon, James J. P. Stewart,  
 
oberto Rodriguez-Fernandez, Robin J. Shannon, James J. P. Stewart,  
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==Downloads==
 
==Downloads==
 +
'''2020 version'''
 +
 +
Download [[Media:tutorial2020.pdf| tutorial2020 ]]<br />
 +
The 2020 version can be [[Media:amk-SOURCE-2020.tar.gz| downloaded here ]]<br />
 +
It can also be cloned from:
 +
[[File:github2.png|90px|link=https://github.com/emartineznunez/AutoMeKin2020]]
 +
 
'''2018 version'''
 
'''2018 version'''
  
Download the [[Media:amk_tutorial.pdf| tutorial ]]<br />
+
Download [[Media:amk_tutorial.pdf| tutorial2018 ]]<br />
The most recent version of AutoMeKin can be [[Media:amk-SOURCE-2018rev.tar.gz| downloaded here ]]<br />
+
The 2018 version can be [[Media:amk-SOURCE-2018rev.tar.gz| downloaded here ]]<br />
A stable (but maybe not up-to-date) version can also be cloned from:<br />
+
It can also be cloned from:
 
[[File:github2.png|90px|link=https://github.com/emartineznunez/AutoMeKin]]
 
[[File:github2.png|90px|link=https://github.com/emartineznunez/AutoMeKin]]
 
'''2020 version'''
 
 
[[File:github2.png|90px|link=https://github.com/emartineznunez/AutoMeKin2020]]
 
  
 
==Install the code==
 
==Install the code==
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==Program execution==
 
==Program execution==
To start using any of the scripts of the program, load the amk/2018 module:
+
To start using any of the scripts of the program, load the amk/20XX module:
  
<code>module load amk/2018</code>
+
<code>module load amk/20XX</code>
  
 
To run the low-level calculations use:
 
To run the low-level calculations use:
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</ol>
 
</ol>
 
</div>
 
</div>
 +
 
Publications using AutoMeKin:
 
Publications using AutoMeKin:
 
<div style="column-count:2;-moz-column-count:2;-webkit-column-count:2">
 
<div style="column-count:2;-moz-column-count:2;-webkit-column-count:2">
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==News==
 
==News==
The improvements briefly described below will be available in AutoMeKin2020.
+
The improvements briefly described below are available in AutoMeKin2020.
  
 
AutoMeKin has been interfaced with BXDE to enhance its efficiency ([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>]).
 
AutoMeKin has been interfaced with BXDE to enhance its efficiency ([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>]).

Revision as of 11:22, 21 January 2020

Introduction

Automekin.png

AutoMeKin (formerly tsscds) has been designed to discover reaction mechanisms in an automated fashion. Transition states are located using MD simulations and Graph Theory algorithms. Monte Carlo simulations afford kinetic results. The only input is a starting structure in XYZ format. The method is described in these two publications: 1 2. At present MOPAC2016 and Gaussian 09 (G09) are interfaced with AutoMeKin. The program has been tested on the following Linux distros: CentOS 7, Red Hat Enterprise Linux and Ubuntu 16.04.3 LTS.

To give you a flavor of the capabilities of the program you can try our web interface


Web.png

Authors

George L. Barnes, David R. Glowacki, Sabine Kopec, Emilio Martinez-Nunez, Daniel Pelaez-Ruiz, Aurelio Rodriguez, Roberto Rodriguez-Fernandez, Robin J. Shannon, James J. P. Stewart, Pablo G. Tahoces and Saulo A. Vazquez

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

License

MIT License

Copyright (C) 2020 George L. Barnes, David R. Glowacki, Sabine Kopec, Emilio Martinez-Nunez, Daniel Pelaez-Ruiz, Aurelio Rodriguez, oberto Rodriguez-Fernandez, Robin J. Shannon, James J. P. Stewart, Pablo G. Tahoces and Saulo A. Vazquez

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

Downloads

2020 version

Download tutorial2020
The 2020 version can be downloaded here
It can also be cloned from: 90px

2018 version

Download tutorial2018
The 2018 version can be downloaded here
It can also be cloned from: 90px

Install the code

To install the code read the Installation instructions

Program execution

To start using any of the scripts of the program, load the amk/20XX module:

module load amk/20XX

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 publications 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.

Publications using AutoMeKin:

  1. A. Esteban et al. Tetrahedron (2019), doi: https://doi.org/10.1016/j.tet.2019.130764
  2. R. A. Jara-Toro et al. ChemSystemsChem doi: 10.1002/syst.201900024
  3. R. Panades-Barrueta et al. Frontiers in Chemistry 2019, 7, 576
  4. S. Kopec et al. Int. J. Quantum Chem. 2019, 119, e26008
  5. V. Macaluso et al. J. Phys. Chem. A 2019, 123, 3685-3696
  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

Consult the Latest changes

Web interface

AutoMeKin can be used through our web interface.

News

The improvements briefly described below are available in AutoMeKin2020.

AutoMeKin has been interfaced with BXDE to enhance its efficiency ( R. A. Jara-Toro et al. ChemSystemsChem doi: 10.1002/syst.201900024).

The method has also been recently generalized in a collaboration with Dani Pelaez and co-workers to study van der Waals structures ( S. Kopec et al. Int. J. Quantum Chem. 2019, 119, e26008 ) and also to generate sum-of-products PESs for quantum dynamics ( R. Panades-Barrueta et al. Frontiers in Chemistry 2019, 7, 576).

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