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== Description of the software ==
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{{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 MOPAC2016 and Gaussian 09 (G09).
 
  
Details of the method are described in these two publications: [http://onlinelibrary.wiley.com/doi/10.1002/jcc.23790/abstract 1]
 
[http://pubs.rsc.org/en/content/articlelanding/2015/cp/c5cp02175h#!divAbstract 2]
 
  
Users are encouraged to read the [http://forge.cesga.es/frs/?group_id=77&release_id=21 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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== Introduction ==
 +
<div style="column-count:2;-moz-column-count:2;-webkit-column-count:2">
 +
[[File:Automekin.png|center]]
 +
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: [http://onlinelibrary.wiley.com/doi/10.1002/jcc.23790/abstract 1]
 +
[http://pubs.rsc.org/en/content/articlelanding/2015/cp/c5cp02175h#!divAbstract 2]. At present [http://openmopac.net/ MOPAC2016], [https://www.entos.ai/qcore/documentation/ Entos Qcore] and Gaussian (G09/G16) are interfaced with AutoMeKin. The program has been tested on the following Linux distros: CentOS 7, Red Hat Enterprise Linux and Ubuntu 20.04 LTS.
 +
 
 +
To give you a flavor of the capabilities of the program you can try our [http://rxnkin.usc.es/amk/ web interface] or [https://colab.research.google.com/github/emartineznunez/AutoMeKin/blob/main/AutoMeKin.ipynb Google Colab]
 +
 
 +
 
 +
 
 +
[[File:Web.png|center]]
  
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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</div>
  
== Authors==
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== Developers team==
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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'''Emilio Martinez-Nunez''', George L. Barnes, Carles Bo, Diego Garay-Ruiz, David R. Glowacki, Sabine Kopec, Daniel Pelaez-Ruiz, Aurelio Rodriguez, Roberto Rodriguez-Fernandez, Robin J. Shannon, James J. P. Stewart, Pablo G. Tahoces and Saulo A. Vazquez
  
 
'''Address'''<br />
 
'''Address'''<br />
Line 17: Line 24:
  
 
==License==
 
==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
+
MIT License
  
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.
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Copyright (C) 2021 AutoMeKin
  
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.
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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:
  
You should have received a copy of the GNU General Public License along with this program.  If not, see http://www.gnu.org/licenses/.
+
The above copyright notice and this permission notice shall be included in all
 +
copies or substantial portions of the Software.
  
==Download source code & tutorial==
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
Both, the source code and tutorial can be downloaded from the following [http://forge.cesga.es/frs/?group_id=77&release_id=21 link]
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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.
  
 
==Install the code==
 
==Install the code==
Follow this link: [[Installation instructions]]
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To install the code follow the [[Installation instructions]]
 +
 
 +
==Tutorial==
 +
 
 +
Download [[Media:tutorial2021.pdf| tutorial ]]<br />
 +
 
 +
The tutorial can be more easily followed executing the example:
 +
 
 +
<code>https://colab.research.google.com/github/emartineznunez/AutoMeKin/blob/main/AutoMeKin.ipynb</code>
  
 
==Program execution==
 
==Program execution==
To start using any of the scripts of the program, you have to load tsscds/2018 module:
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Unless you donwloaded the singularity container (in that case skip this step), to start using any of the scripts of the program, load the amk/2021 module:
  
<code>module load tsscds/2018</code>
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<code>module load amk/2021</code>
  
 
To run the low-level calculations use:
 
To run the low-level calculations use:
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<code>nohup hlcalcs.sh molecule.dat runningtasks >hlcalcs.log 2>&1 &</code>
 
<code>nohup hlcalcs.sh molecule.dat runningtasks >hlcalcs.log 2>&1 &</code>
  
For more details, follow the instructions given in the [http://forge.cesga.es/frs/?group_id=77&release_id=21 tutorial]
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For more details, follow the instructions given in the [[Media:Tutorial2020.pdf| tutorial ]]
  
==References and citations==
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==Reference==
These four papers must be cited in any work presenting results obtained with our software:
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If you use '''AutoMeKin''', please cite the following publications:
<div style="column-count:2;-moz-column-count:2;-webkit-column-count:2">
 
  
 
<ol start="1">
 
<ol start="1">
<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>[https://onlinelibrary.wiley.com/doi/full/10.1002/jcc.26734 <span style="font-size:100%">E Martínez-Nuñez, G.L. Barnes, D.R. Glowacki, S. Kopec, D. Pelaez, A. Rodriguez, R. Rodriguez-Fernandez, R.J. Shannon, J.J.P. Stewart, P.G. Tahoces, S.A. Vazquez, J. Comput. Chem. 2021, 42, 2036</span>]</li>
<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>[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>
<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://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>
 
<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>
 
<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>
 
</ol>
 
</ol>
</div>
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Additional references:
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If you use the older version '''tsscds''', please cite, instead of ref 1 above, the following one:
<div style="column-count:2;-moz-column-count:2;-webkit-column-count:2">
+
 
<ol start="5">
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[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>[https://pubs.acs.org/doi/10.1021/acs.jpca.9b01779 <span style="font-size:100%">V. Macaluso et al. J. Phys. Chem. A 2019 (ASAP)</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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==Works that employ AutoMeKin==
<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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The following works employ AutoMeKin: [[Works]]
<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>
 
<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>
 
<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>
 
<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>
 
<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>
 
<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>
 
</ol>
 
</div>
 
  
 
==Changelog==
 
==Changelog==
{| class="wikitable"
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Consult the [[Latest changes]]
!colspan="6"|Latest revision: 337
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|-
+
==Web interface and Google Colab==
|04/17/2019
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AutoMeKin can be used through our [http://rxnkin.usc.es/amk/ web interface].
|The label of the starting min in the kmc simulations is in tsdirll/KMC/starting_minimum
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|-
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The tutorial example (formic acid) can be easily tested on Google Colab using this link:
|04/15/2019
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|A bug in get_energy_g09_MP2.sh was corrected
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<code>https://colab.research.google.com/github/emartineznunez/AutoMeKin/blob/main/AutoMeKin.ipynb</code>
|-
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|04/01/2019
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==News==
|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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AutoMeKin is now interfaced with Gaussian 16 (from rev. 1131)
|-
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|03/01/2019
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The Python library [https://github.com/dgarayr/amk_tools '''amk-tools'''] can be employed to read, process and visualize reaction networks generated by AutoMeKin and is available in the latest singularity container (and through our web interface). Here is the paper describing the new tool: [https://pubs.acs.org/doi/10.1021/acsphyschemau.1c00051 <span style="font-size:100%"> Garay-Ruiz et al. ACS Phys. Chem. Au 2022]
|A bug in the kmc.f90 source file was corrected
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|}
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AutoMekin got the [https://geqc.rseq.org/emilio-martinez-nunez-and-mireia-via-nadal-recieve-the-geqc-rseq-2021-methodology-development-prize/ GEQC-RSEQ 2021 Methodology Development Prize].
 +
 
 +
AutoMeKin now includes '''barrierless channels'''. However, these channels are not considered in the kinetics.
 +
 
 +
AutoMeKin has been interfaced with [https://www.entos.ai/qcore/documentation/ '''Entos Qcore'''].
 +
 
 +
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>]).
 +
 
 +
The method has also been recently generalized in a collaboration with Dani Pelaez and co-workers to study '''van der Waals structures''' ([https://onlinelibrary.wiley.com/doi/abs/10.1002/qua.26008 <span style="font-size:100%"> S. Kopec et al. Int. J. Quantum Chem. 2019, 119, e26008 </span>]) and also to generate sum-of-products PESs for quantum dynamics ([https://www.frontiersin.org/articles/10.3389/fchem.2019.00576/full <span style="font-size:100%"> R. Panades-Barrueta et al. Frontiers in Chemistry 2019, 7, 576</span>]).
 +
 
 +
Return to [[#toc|Contents]]
  
==Web interface==
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Return to [[Main_Page]]
AutoMeKin can be used through our [http://rxnkin.usc.es/amk/ web interface] (only MOPAC2016 calculations).<br>
 
While we finish setting up the Web interface you can get a username and password by sending a message to [mailto:emilio.nunez@usc.es Emilio Martinez-Nunez]
 

Revision as of 06:48, 11 February 2024

All content from this page has been transferred to a gh.jpg repository, and this site will no longer receive support.


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, Entos Qcore and Gaussian (G09/G16) are interfaced with AutoMeKin. The program has been tested on the following Linux distros: CentOS 7, Red Hat Enterprise Linux and Ubuntu 20.04 LTS.

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


Web.png

Developers team

Emilio Martinez-Nunez, George L. Barnes, Carles Bo, Diego Garay-Ruiz, David R. Glowacki, Sabine Kopec, 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) 2021 AutoMeKin

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.

Install the code

To install the code follow the Installation instructions

Tutorial

Download tutorial

The tutorial can be more easily followed executing the example:

https://colab.research.google.com/github/emartineznunez/AutoMeKin/blob/main/AutoMeKin.ipynb

Program execution

Unless you donwloaded the singularity container (in that case skip this step), to start using any of the scripts of the program, load the amk/2021 module:

module load amk/2021

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

Reference

If you use AutoMeKin, please cite the following publications:

  1. E Martínez-Nuñez, G.L. Barnes, D.R. Glowacki, S. Kopec, D. Pelaez, A. Rodriguez, R. Rodriguez-Fernandez, R.J. Shannon, J.J.P. Stewart, P.G. Tahoces, S.A. Vazquez, J. Comput. Chem. 2021, 42, 2036
  2. E. Martínez-Núñez, J. Comput. Chem. 2015, 36, 222
  3. E. Martínez-Núñez, Phys. Chem. Chem. Phys. 2015,17, 14912
  4. J. J. P. Stewart, MOPAC2016, Stewart Computational Chemistry: Colorado Springs, CO, USA, HTTP://OpenMOPAC.net, 2016.

If you use the older version tsscds, please cite, instead of ref 1 above, the following one:

A. Rodriguez, R. Rodriguez-Fernandez, S.A. Vazquez, G.L. Barnes, J.J.P. Stewart, E Martínez-Nuñez, J. Comput. Chem. 2018, 39, 1922

Works that employ AutoMeKin

The following works employ AutoMeKin: Works

Changelog

Consult the Latest changes

Web interface and Google Colab

AutoMeKin can be used through our web interface.

The tutorial example (formic acid) can be easily tested on Google Colab using this link:

https://colab.research.google.com/github/emartineznunez/AutoMeKin/blob/main/AutoMeKin.ipynb

News

AutoMeKin is now interfaced with Gaussian 16 (from rev. 1131)

The Python library amk-tools can be employed to read, process and visualize reaction networks generated by AutoMeKin and is available in the latest singularity container (and through our web interface). Here is the paper describing the new tool: Garay-Ruiz et al. ACS Phys. Chem. Au 2022

AutoMekin got the GEQC-RSEQ 2021 Methodology Development Prize.

AutoMeKin now includes barrierless channels. However, these channels are not considered in the kinetics.

AutoMeKin has been interfaced with Entos Qcore.

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).

Return to Contents

Return to Main_Page