Difference between revisions of "AutoMeKin"

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==Web interface==
 
==Web interface==
 
AutoMeKin can be used through our [http://rxnkin.usc.es/amk/ web interface] (only MOPAC2016 calculations).
 
AutoMeKin can be used through our [http://rxnkin.usc.es/amk/ web interface] (only MOPAC2016 calculations).
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<html lang="en">
 
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  <head>
 
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      <meta charset="utf-8">
 
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      <title>slider.py example</title>
 
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        <link rel="stylesheet" href="https://cdn.pydata.org/bokeh/release/bokeh-1.0.2.min.css" type="text/css" />
 
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        <link rel="stylesheet" href="https://cdn.pydata.org/bokeh/release/bokeh-widgets-1.0.2.min.css" type="text/css" />
 
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        <script type="text/javascript" src="https://cdn.pydata.org/bokeh/release/bokeh-1.0.2.min.js"></script>
 
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        <script type="text/javascript" src="https://cdn.pydata.org/bokeh/release/bokeh-widgets-1.0.2.min.js"></script>
 
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        <script type="text/javascript">
 
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            Bokeh.set_log_level("info");
 
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        </script>
 
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  </head>
 
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              <div class="bk-root" id="538a509d-e6cd-4f11-ae0b-0cc81abe235e"></div>
 
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        <script type="application/json" id="1124">
 
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          {"12fcf5fa-eb2b-4212-b695-52540d1bde88":{"roots":{"references":[{"attributes":{"children":[{"id":"1044","type":"Slider"}]},"id":"1048","type":"WidgetBox"},{"attributes":{"children":[{"id":"1046","type":"WidgetBox"},{"id":"1047","type":"WidgetBox"},{"id":"1048","type":"WidgetBox"},{"id":"1049","type":"WidgetBox"}]},"id":"1050","type":"Column"},{"attributes":{"children":[{"id":"1002","subtype":"Figure","type":"Plot"},{"id":"1050","type":"Column"}]},"id":"1051","type":"Row"},{"attributes":{"plot":null,"text":""},"id":"1053","type":"Title"},{"attributes":{},"id":"1055","type":"BasicTickFormatter"},{"attributes":{},"id":"1057","type":"BasicTickFormatter"},{"attributes":{},"id":"1058","type":"Selection"},{"attributes":{},"id":"1059","type":"UnionRenderers"},{"attributes":{"line_alpha":0.1,"line_color":"#1f77b4","line_width":3,"x":{"field":"x"},"y":{"field":"y"}},"id":"1038","type":"Line"},{"attributes":{"data_source":{"id":"1001","type":"ColumnDataSource"},"glyph":{"id":"1037","type":"Line"},"hover_glyph":null,"muted_glyph":null,"nonselection_glyph":{"id":"1038","type":"Line"},"selection_glyph":null,"view":{"id":"1040","type":"CDSView"}},"id":"1039","type":"GlyphRenderer"},{"attributes":{"plot":{"id":"1002","subtype":"Figure","type":"Plot"},"ticker":{"id":"1012","type":"BasicTicker"}},"id":"1015","type":"Grid"},{"attributes":{"formatter":{"id":"1057","type":"BasicTickFormatter"},"plot":{"id":"1002","subtype":"Figure","type":"Plot"},"ticker":{"id":"1017","type":"BasicTicker"}},"id":"1016","type":"LinearAxis"},{"attributes":{},"id":"1017","type":"BasicTicker"},{"attributes":{"line_alpha":0.6,"line_color":"#1f77b4","line_width":3,"x":{"field":"x"},"y":{"field":"y"}},"id":"1037","type":"Line"},{"attributes":{},"id":"1012","type":"BasicTicker"},{"attributes":{"callback":{"id":"1041","type":"CustomJS"},"end":10,"start":0.1,"step":0.1,"title":"Frequency","value":1},"id":"1043","type":"Slider"},{"attributes":{"callback":{"id":"1041","type":"CustomJS"},"end":10,"start":0.1,"step":0.1,"title":"Amplitude","value":1},"id":"1042","type":"Slider"},{"attributes":{"args":{"amp":{"id":"1042","type":"Slider"},"freq":{"id":"1043","type":"Slider"},"offset":{"id":"1045","type":"Slider"},"phase":{"id":"1044","type":"Slider"},"source":{"id":"1001","type":"ColumnDataSource"}},"code":"\n    var data = source.data;\n    var A = amp.value;\n    var k = freq.value;\n    var phi = phase.value;\n    var B = offset.value;\n    var x = data['x']\n    var y = data['y']\n    for (var i = 0; i &lt; x.length; i++) {\n        y[i] = B + A*Math.sin(k*x[i]+phi);\n    }\n    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","dtype":"float64","shape":[500]}},"selected":{"id":"1058","type":"Selection"},"selection_policy":{"id":"1059","type":"UnionRenderers"}},"id":"1001","type":"ColumnDataSource"}],"root_ids":["1051"]},"title":"Bokeh Application","version":"1.0.2"}}
 
−
        </script>
 
−
        <script type="text/javascript">
 
−
          (function() {
 
−
            var fn = function() {
 
−
              Bokeh.safely(function() {
 
−
                (function(root) {
 
−
                  function embed_document(root) {
 
−
                   
 
−
                  var docs_json = document.getElementById('1124').textContent;
 
−
                  var render_items = [{"docid":"12fcf5fa-eb2b-4212-b695-52540d1bde88","roots":{"1051":"538a509d-e6cd-4f11-ae0b-0cc81abe235e"}}];
 
−
                  root.Bokeh.embed.embed_items(docs_json, render_items);
 
−
               
 
−
                  }
 
−
                  if (root.Bokeh !== undefined) {
 
−
                    embed_document(root);
 
−
                  } else {
 
−
                    var attempts = 0;
 
−
                    var timer = setInterval(function(root) {
 
−
                      if (root.Bokeh !== undefined) {
 
−
                        embed_document(root);
 
−
                        clearInterval(timer);
 
−
                      }
 
−
                      attempts++;
 
−
                      if (attempts > 100) {
 
−
                        console.log("Bokeh: ERROR: Unable to run BokehJS code because BokehJS library is missing");
 
−
                        clearInterval(timer);
 
−
                      }
 
−
                    }, 10, root)
 
−
                  }
 
−
                })(window);
 
−
              });
 
−
            };
 
−
            if (document.readyState != "loading") fn();
 
−
            else document.addEventListener("DOMContentLoaded", fn);
 
−
          })();
 
−
        </script>
 
−
   
 
−
  </body>
 
−
 
 
−
</html>
 

Revision as of 08:20, 19 April 2019

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

MIT License

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

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.

Download source code & tutorial

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

Install the code

To install the code read the 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:

  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

Changelog

Latest revision: 340
04/18/2019 MIT license
04/17/2019 The label of 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).

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