Difference between revisions of "AutoMeKin"

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== Introduction ==
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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.
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<div style="column-count:2;-moz-column-count:2;-webkit-column-count:2">
 
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[[File:Automekin.png|center]]
 
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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]
 
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[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 09 (G09) 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.
 
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To give you a flavor of the capabilities of the program you can try our [http://rxnkin.usc.es/amk/ web interface]
 
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[[File:Web.png|center]]
 
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</div>
 
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== Developers team==
 
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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
 
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'''Address'''<br />
 
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Departamento de Química Física, Facultade de Química, Avda. das Ciencias s/n, 15782 Santiago de Compostela, SPAIN<br />
 
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[mailto:emilio.nunez@usc.es email me]
 
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==License==
 
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MIT License
 
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Copyright (C) 2021 AutoMeKin
 
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Permission is hereby granted, free of charge, to any person obtaining a copy
 
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of this software and associated documentation files (the "Software"), to deal
 
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in the Software without restriction, including without limitation the rights
 
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 
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copies of the Software, and to permit persons to whom the Software is
 
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furnished to do so, subject to the following conditions:
 
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The above copyright notice and this permission notice shall be included in all
 
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copies or substantial portions of the Software.
 
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 
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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.
 
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==Install the code==
 
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To install the code follow the [[Installation instructions]]
 
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==Tutorial==
 
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Download [[Media:tutorial2021.pdf| tutorial ]]<br />
 
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==Program execution==
 
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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:
 
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<code>module load amk/2021</code>
 
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To run the low-level calculations use:
 
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<code>nohup llcalcs.sh molecule.dat ntasks niter runningtasks >llcalcs.log 2>&1 &</code>
 
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where:<br />
 
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<code>molecule</code> is  the name of your molecule<br />
 
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<code>ntasks</code> is the number of tasks<br />
 
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<code>niter</code> is the number of iterations<br />
 
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<code>runningtasks</code> is the number of simultaneous tasks
 
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To run the high-level calculations use:
 
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<code>nohup hlcalcs.sh molecule.dat runningtasks >hlcalcs.log 2>&1 &</code>
 
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For more details, follow the instructions given in the [[Media:Tutorial2020.pdf| tutorial ]]
 
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==Reference==
 
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If you use '''AutoMeKin''', please cite the following publications:
 
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<ol start="1">
 
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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>
 
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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>
 
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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>
 
−
</ol>
 
−
 
 
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If you use the older version '''tsscds''', please cite, instead of ref 1 above, the following one:
 
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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>]
 
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==Works that employ AutoMeKin==
 
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The following works employ AutoMeKin: [[Works]]
 
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==Changelog==
 
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Consult the [[Latest changes]]
 
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==Web interface==
 
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AutoMeKin can be used through our [http://rxnkin.usc.es/amk/ web interface].
 
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==News==
 
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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, available through the [[Installation instructions#Auto installer| autoinstaller]].
 
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<html lang="en">
 
−
 
 
−
  <head>
 
−
   
 
−
      <meta charset="utf-8">
 
−
      <title>Reaction network visualization</title>
 
−
     
 
−
     
 
−
       
 
−
         
 
−
       
 
−
       
 
−
         
 
−
        <script type="text/javascript" src="https://cdn.bokeh.org/bokeh/release/bokeh-2.3.3.min.js" integrity="sha384-dM3QQsP+wXdHg42wTqW85BjZQdLNNIXqlPw/BgKoExPmTG7ZLML4EGqLMfqHT6ON" crossorigin="anonymous"></script>
 
−
        <script type="text/javascript" src="https://cdn.bokeh.org/bokeh/release/bokeh-widgets-2.3.3.min.js" integrity="sha384-3QTqdz9LyAm2i0sG5XTePsHec3UHWwVsrOL68SYRoAXsafvfAyqtQ+h440+qIBhS" crossorigin="anonymous"></script>
 
−
        <script type="text/javascript">
 
−
            Bokeh.set_log_level("info");
 
−
        </script>
 
−
        <script type="text/javascript">
 
−
            (function(root, factory) {
 
−
                    factory(root["Bokeh"]);
 
−
                })(this, function(Bokeh) {
 
−
                  var define;
 
−
                  return (function outer(modules, entry) {
 
−
                  if (Bokeh != null) {
 
−
                    return Bokeh.register_plugin(modules, entry);
 
−
                  } else {
 
−
                    throw new Error("Cannot find Bokeh. You have to load it prior to loading plugins.");
 
−
                  }
 
−
                })
 
−
                ({
 
−
                  "custom/main": function(require, module, exports) {
 
−
                    var models = {
 
−
                      "JSMol": require("custom/jsmol_bokeh_extension.jsmol.js_mol").JSMol
 
−
                    };
 
−
                    require("base").register_models(models);
 
−
                    module.exports = models;
 
−
                  },
 
−
                  "custom/jsmol_bokeh_extension.jsmol.js_mol": function(require, module, exports) {
 
−
                "use strict";
 
−
                var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
 
−
                    if (k2 === undefined) k2 = k;
 
−
                    Object.defineProperty(o, k2, { enumerable: true, get: function() { return m[k]; } });
 
−
                }) : (function(o, m, k, k2) {
 
−
                    if (k2 === undefined) k2 = k;
 
−
                    o[k2] = m[k];
 
−
                }));
 
−
                var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
 
−
                    Object.defineProperty(o, "default", { enumerable: true, value: v });
 
−
                }) : function(o, v) {
 
−
                    o["default"] = v;
 
−
                });
 
−
                var __importStar = (this && this.__importStar) || function (mod) {
 
−
                    if (mod && mod.__esModule) return mod;
 
−
                    var result = {};
 
−
                    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
 
−
                    __setModuleDefault(result, mod);
 
−
                    return result;
 
−
                };
 
−
                Object.defineProperty(exports, "__esModule", { value: true });
 
−
                exports.JSMol = exports.JSMolView = void 0;
 
−
                // These "require" lines are similar to python "import" statements
 
−
                const layout_dom_1 = require("models/layouts/layout_dom");
 
−
                const layout_1 = require("core/layout");
 
−
                const p = __importStar(require("core/properties"));
 
−
                // This defines some default options for JSmol
 
−
                // See https://gist.github.com/jhjensen2/4701339 for more details.
 
−
                const INFO = {
 
−
                    height: "100%",
 
−
                    width: "100%",
 
−
                    serverURL: "https://chemapps.stolaf.edu/jmol/jsmol/php/jsmol.php",
 
−
                    use: "HTML5",
 
−
                    j2sPath: "https://chemapps.stolaf.edu/jmol/jsmol/j2s",
 
−
                    script: "background black;load https://dev-www.materialscloud.org/cofs/api/v2/cifs/febd2d02-5690-4a07-9013-505c9a06bc5b/content/download",
 
−
                };
 
−
                // To create custom model extensions that will render on to the HTML canvas
 
−
                // or into the DOM, we must create a View subclass for the model.
 
−
                //
 
−
                // In this case we will subclass from the existing BokehJS ``LayoutDOMView``
 
−
                class JSMolView extends layout_dom_1.LayoutDOMView {
 
−
                    initialize() {
 
−
                        super.initialize();
 
−
                        var url = this.model.js_url;
 
−
                        if (!url) {
 
−
                            url = "https://chemapps.stolaf.edu/jmol/jsmol/JSmol.min.js";
 
−
                        }
 
−
                        const script = document.createElement('script');
 
−
                        script.src = url;
 
−
                        script.async = false;
 
−
                        script.onload = () => this._init();
 
−
                        //script.onreadystatechange = (script.onload = () => this._init())
 
−
                        //script.onreadystatechange = script.onload
 
−
                        document.querySelector("head").appendChild(script);
 
−
                    }
 
−
                    _init() {
 
−
                        // Create a new Jmol applet using the JSmol.js API. This assumes JSmol.js
 
−
                        // has already been loaded.
 
−
                        // Models will be able to specify and load external scripts automatically.
 
−
                        //
 
−
                        // BokehJS Views create <div> elements by default, accessible as this.el.
 
−
                        // if no info dict provided, use reasonable default
 
−
                        if (!this.model.info) {
 
−
                            this.model.info = INFO;
 
−
                        }
 
−
                        // disable usage tracker - this conflicts with cross-site-scripting policies when served over https
 
−
                        delete Jmol._tracker;
 
−
                        // returns html + assigns applet object to "jmolApplet0" variable
 
−
                        var html = Jmol.getAppletHtml("jmolApplet0", this.model.info);
 
−
                        this._applet = jmolApplet0;
 
−
                        this.el.innerHTML = html;
 
−
                        // avoid creating a "deferred" applet
 
−
                        // https://sourceforge.net/p/jsmol/discussion/general/thread/48083aa7///10a6/bc1c
 
−
                        this._applet._cover(false);
 
−
                        // Set a listener so that when the Bokeh script input changes it is executed
 
−
                        this.connect(this.model.script_source.properties.data.change, () => {
 
−
                            console.log("Script source changed");
 
−
                            Jmol.script(this._applet, this.model.script_source.get_column('script')[0]);
 
−
                        });
 
−
                    }
 
−
                    get child_models() {
 
−
                        return [];
 
−
                    }
 
−
                    _update_layout() {
 
−
                        this.layout = new layout_1.LayoutItem();
 
−
                        this.layout.set_sizing(this.box_sizing());
 
−
                    }
 
−
                }
 
−
                exports.JSMolView = JSMolView;
 
−
                JSMolView.__name__ = "JSMolView";
 
−
                class JSMol extends layout_dom_1.LayoutDOM {
 
−
                    constructor(attrs) {
 
−
                        super(attrs);
 
−
                    }
 
−
                    static initClass() {
 
−
                        // The ``type`` class attribute should generally match exactly the name
 
−
                        // of the corresponding Python class.
 
−
                        this.prototype.type = "JSMol";
 
−
                        // This is usually boilerplate. In some cases there may not be a view.
 
−
                        this.prototype.default_view = JSMolView;
 
−
                        // The define block adds corresponding "properties" to the JS model. These
 
−
                        // should basically line up 1-1 with the Python model class. Most property
 
−
                        // types have counterparts, e.g. ``bokeh.core.properties.String`` will be
 
−
                        // ``p.String`` in the JS implementation. Where the JS type system is not yet
 
−
                        // as rich, you can use ``p.Any`` as a "wildcard" property type.
 
−
                        this.define({
 
−
                            script_source: [p.Instance],
 
−
                            info: [p.Any],
 
−
                            js_url: [p.String],
 
−
                        });
 
−
                    }
 
−
                }
 
−
                exports.JSMol = JSMol;
 
−
                JSMol.__name__ = "JSMol";
 
−
                JSMol.initClass();
 
−
                //# sourceMappingURL=jsmol.py:JSMol.js.map
 
−
                }
 
−
                }, "custom/main");
 
−
                ;
 
−
                });
 
−
 
 
−
        </script>
 
−
       
 
−
     
 
−
     
 
−
<style>
 
−
.bk-root .bk-btn-default {
 
−
font-size: 1.2vh;
 
−
}
 
−
.bk-root .bk-input {
 
−
font-size: 1.2vh;
 
−
padding-bottom: 5px;
 
−
padding-top: 5px;
 
−
}
 
−
.bk-root .bk {
 
−
font-size: 1.2vh;
 
−
}
 
−
.bk-root .bk-clearfix{
 
−
padding-bottom: 0.8vh;
 
−
}
 
−
</style>
 
−
 
−
   
 
−
  </head>
 
−
 
 
−
 
 
−
  <body>
 
−
   
 
−
     
 
−
       
 
−
         
 
−
         
 
−
           
 
−
              <div class="bk-root" id="3c780241-42fe-478b-8b7d-bb4e3e9dfbe4" data-root-id="1159"></div>
 
−
           
 
−
         
 
−
       
 
−
     
 
−
     
 
−
        <script type="application/json" id="1703">
 
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          {"f436dc99-c491-4996-b7ca-3e1293247474":{"defs":[],"roots":{"references":[{"attributes":{"formatter":{"id":"1250"},"major_label_policy":{"id":"1249"},"ticker":{"id":"1171"},"visible":false},"id":"1170","type":"LinearAxis"},{"attributes":{"axis_label":"E (kcal/mol)","axis_label_text_font":"Arial","axis_label_text_font_size":"1.5vh","axis_label_text_font_style":"bold","formatter":{"id":"1253"},"major_label_policy":{"id":"1252"},"major_label_text_font_size":"1.2vh","ticker":{"id":"1175"}},"id":"1174","type":"LinearAxis"},{"attributes":{},"id":"1282","type":"UnionRenderers"},{"attributes":{"data":{"elab":["-8.3","58.2","-37.6"],"lab":["MIN1","TS10","PR2"],"x":{"__ndarray__":"AAAAAAAA4D8AAAAAAAAEQAAAAAAAABJA","dtype":"float64","order":"little","shape":[3]},"y":[-8.323520999999985,58.154156,-37.60977]},"selected":{"id":"1275"},"selection_policy":{"id":"1276"}},"id":"1216","type":"ColumnDataSource"},{"attributes":{},"id":"1171","type":"BasicTicker"},{"attributes":{"axis":{"id":"1170"},"ticker":null},"id":"1173","type":"Grid"},{"attributes":{"text":"Reaction network visualization","text_font_size":"1.5vh"},"id":"1005","type":"Title"},{"attributes":{},"id":"1256","type":"Selection"},{"attributes":{"axis":{"id":"1174"},"dimension":1,"ticker":null},"id":"1177","type":"Grid"},{"attributes":{},"id":"1257","type":"UnionRenderers"},{"attributes":{},"id":"1269","type":"Selection"},{"attributes":{},"id":"1175","type":"BasicTicker"},{"attributes":{},"id":"1270","type":"UnionRenderers"},{"attributes":{},"id":"1258","type":"Selection"},{"attributes":{},"id":"1179","type":"WheelZoomTool"},{"attributes":{},"id":"1178","type":"PanTool"},{"attributes":{},"id":"1259","type":"UnionRenderers"},{"attributes":{"overlay":{"id":"1183"}},"id":"1180","type":"BoxZoomTool"},{"attributes":{},"id":"1181","type":"ResetTool"},{"attributes":{},"id":"1182","type":"SaveTool"},{"attributes":{"args":{"prof":{"id":"1161"},"thrbox":{"id":"1137"}},"code":"\n\t\t// graph - bokeh graph for the network view, use to fetch node and edge renderers\n\t\t// prof - bokeh figure for the profiles, thrbox - textbox for threshold energy\n\t\tvar thr = parseFloat(thrbox.value)\n\t\tvar range = {min: thr, max: thr}\n\t\tfunction overThreshold(element){\n\t\t\treturn element &gt; thr\n\t\t}\n\t\tvar Nlines = prof.renderers.length/2\n\t\tfor (let i = 0 ; i &lt; Nlines ; i++){\n\t\t\tconst index = 2*i\n\t\t\tvar current_data = prof.renderers[index].data_source\n\t\t\tvar energies = current_data.data[\"y\"]\n\t\t\t//hide if anything is above the threshold\n\t\t\tif (energies.some(overThreshold)){\n\t\t\t\tprof.renderers[index].visible = false\n\t\t\t\tprof.renderers[index+1].visible = false\n\t\t\t\t// labels are also duplicated: first tag, then energy.\n\t\t\t\tprof.center[index+2].visible = false\n\t\t\t\tprof.center[index+3].visible = false\n\t\t\t} \n\t\t}\n\t\t"},"id":"1228","type":"CustomJS"},{"attributes":{"args":{"prof":{"id":"1161"},"state":[false]},"code":"\n\t// show ENERGY labels for the profile\n\t// prof - bokeh profile for figures, state - counter for the inner state\n\tstate[0] = !state[0]\n\tvar Nlines = prof.renderers.length/2\n\tfor (let i = 0 ; i &lt; Nlines ; i++){\n\t\t// show or hide for ODD ii values (energy label) AND only for visible renderers\n\t\tvar jj = 2*i + 1\n\t\tif (prof.renderers[jj-1].visible == true){\n\t\t\tprof.center[jj+2].visible = state[0]\n\t\t} \n\t}\n\t"},"id":"1229","type":"CustomJS"},{"attributes":{"align":"center","height":100,"text":"(Click an element)"},"id":"1133","type":"Div"},{"attributes":{},"id":"1271","type":"Selection"},{"attributes":{},"id":"1272","type":"UnionRenderers"},{"attributes":{"callback":{"id":"1229"},"description":"Show energy labels","icon":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAgAAAAICAIAAABLbSncAAAAKklEQVR4nGP8//8/AzbAwsDAcPLkSTRRc3NzFjgLTY4JqzlQozBNo65RAAfvDWESs4jlAAAAAElFTkSuQmCC"},"id":"1230","type":"CustomAction"},{"attributes":{},"id":"1273","type":"Selection"},{"attributes":{"align":"center","disabled":true,"icon":null,"js_event_callbacks":{"button_click":[{"id":"1228"}]},"label":"Energy filter","max_width":120},"id":"1136","type":"Button"},{"attributes":{},"id":"1252","type":"AllLabels"},{"attributes":{},"id":"1253","type":"BasicTickFormatter"},{"attributes":{},"id":"1274","type":"UnionRenderers"},{"attributes":{},"id":"1260","type":"Selection"},{"attributes":{"js_property_callbacks":{"change:indices":[{"id":"1138"}]}},"id":"1147","type":"Selection"},{"attributes":{"align":"center","disabled":true,"icon":null,"js_event_callbacks":{"menu_item_click":[{"id":"1142"}]},"label":"Normal modes","max_width":400,"menu":[["No vibr. loaded","None"],null]},"id":"1131","type":"Dropdown"},{"attributes":{"align":"center","disabled":true,"icon":null,"js_event_callbacks":{"button_click":[{"id":"1227"}]},"label":"Molec. filter","max_width":120},"id":"1134","type":"Button"},{"attributes":{},"id":"1261","type":"UnionRenderers"},{"attributes":{},"id":"1275","type":"Selection"},{"attributes":{"align":"center","width":300},"id":"1132","type":"Spacer"},{"attributes":{"name":"ENERGYLABELS","source":{"id":"1219"},"text":{"field":"elab"},"text_font_size":{"value":"1.4vh"},"visible":false,"x":{"field":"x"},"x_offset":{"value":-1},"y":{"field":"y"},"y_offset":{"value":-20}},"id":"1220","type":"LabelSet"},{"attributes":{},"id":"1276","type":"UnionRenderers"},{"attributes":{"args":{"graph":{"id":"1033"},"source":{"id":"1125"},"textField":{"id":"1133"}},"code":"\n\t\t// from graph, we fetch nrend - node renderer, erend - edgerenderer\n\t\t//source - source object for JSMol\n\t\tvar nrend = graph.node_renderer.data_source\n\t\tvar erend = graph.edge_renderer.data_source\n\t\tif (cb_obj.indices.length) {\n\t\t\tvar ninds = nrend.selected.indices\n\t\t\tvar einds = erend.selected.indices\n\t\t\tif (ninds.length) {\n\t\t\t\tvar rend = nrend\n\t\t\t} else {\n\t\t\t\tvar rend = erend\n\t\t\t}\n\t\t\tvar ndx = rend.selected.indices[0]\n\t\t\tvar model = rend.data[\"model\"][ndx]\n\t\t\tif (model == null){\n\t\t\t\t// clear view if no model is available\n\t\t\t\tmodel = \"backbone only ; backbone off\"\n\t\t\t}\n\t\t\tvar molname = rend.data[\"name\"][ndx]\n\t\t\ttextField.text = \"&lt;font size=+1&gt;&lt;b&gt;\" + molname + \"&lt;/b&gt;&lt;/font&gt;\"\n\t\t\tsource.data[\"script\"] = [model]\n\t\t\tsource.properties.data.change.emit()\n\t\t}\n\t\t"},"id":"1138","type":"CustomJS"},{"attributes":{"data":{"elab":["-8.3","58.2","-37.6"],"lab":["MIN1","TS10","PR2"],"x":{"__ndarray__":"AAAAAAAA4D8AAAAAAAAEQAAAAAAAABJA","dtype":"float64","order":"little","shape":[3]},"y":[-8.323520999999985,58.154156,-37.60977]},"selected":{"id":"1277"},"selection_policy":{"id":"1278"}},"id":"1219","type":"ColumnDataSource"},{"attributes":{"align":"center","value":"58.15","width":240},"id":"1137","type":"TextInput"},{"attributes":{"end":1.2,"start":-1.2},"id":"1003","type":"Range1d"},{"attributes":{},"id":"1277","type":"Selection"},{"attributes":{"align":"center","js_property_callbacks":{"change:active":[{"id":"1226"}]},"labels":["Show profile"],"max_height":100,"max_width":120},"id":"1135","type":"CheckboxGroup"},{"attributes":{"below":[{"id":"1013"}],"center":[{"id":"1016"},{"id":"1020"},{"id":"1082"},{"id":"1085"}],"left":[{"id":"1017"}],"renderers":[{"id":"1033"}],"title":{"id":"1005"},"toolbar":{"id":"1027"},"toolbar_location":"above","width":800,"x_range":{"id":"1002"},"x_scale":{"id":"1009"},"y_range":{"id":"1003"},"y_scale":{"id":"1011"}},"id":"1004","subtype":"Figure","type":"Plot"},{"attributes":{},"id":"1278","type":"UnionRenderers"},{"attributes":{},"id":"1022","type":"WheelZoomTool"},{"attributes":{"data":{"script":[]},"selected":{"id":"1260"},"selection_policy":{"id":"1261"}},"id":"1125","type":"ColumnDataSource"},{"attributes":{},"id":"1021","type":"PanTool"},{"attributes":{"args":{"graph":{"id":"1033"},"menu":{"id":"1131"},"source":{"id":"1125"},"textField":{"id":"1133"}},"code":"\n\t\t// from graph, we fetch nrend - node renderer, erend - edgerenderer, \n\t\t// source - source object for JSMol, menu - dropdown menu to change vibrations\n\t\tvar nrend = graph.node_renderer.data_source\n\t\tvar erend = graph.edge_renderer.data_source\n\t\t\n\t\tvar ninds = nrend.selected.indices\n\t\tvar einds = erend.selected.indices\n\t\tif (ninds.length) {\n\t\t\tvar rend = nrend\n\t\t} else {\n\t\t\tvar rend = erend\n\t\t}\n\t\tvar ndx = rend.selected.indices[0]\n\t\tvar vibr_models = rend.data[\"vibr_models\"][ndx]\n\t\tif (vibr_models.length){\n\t\t\tsource.data[\"current_model\"] = [vibr_models]\n\t\t\tsource.data[\"script\"] = [vibr_models + \"; vibration on ; vibration scale 0.25\"]\n\t\t\tsource.data[\"current_mol\"] = rend.data[\"name\"][ndx]\n\t\t\t// and also populate the normal mode dropdown: get the frequencies and assign them to menu\n\t\t\t// we must pass indices as strings for it to work, add 1 to match model numbering\n\t\t\tmenu.disabled = false\n\t\t\tvar freqlist = rend.data[\"frequencies\"][ndx].split(\";\")\n\t\t\tvar menulist = freqlist.map(function (frq,ii) {return [frq+\" cm-1\",(ii+1).toString()]})\n\t\t\tmenu.menu = menulist\n\t\t\tvar nw_label = \"Normal modes (\" + source.data[\"current_mol\"] + \")\"\n\t\t\tmenu.label = nw_label\n\t\t\t// modify text element using the BASE frequency\n\t\t\tvar molname = source.data[\"current_mol\"]\n\t\t\tvar frqval = freqlist[0].toString().trim() + \" cm-1\"\n\t\t\ttextField.text = \"&lt;font size=+1&gt;&lt;b&gt;\" + molname + \" (\" + frqval + \")\" + \"&lt;/b&gt;&lt;/font&gt;\"\n\t\t}\n\t\n\t\tsource.properties.data.change.emit()\n\t\t"},"id":"1139","type":"CustomJS"},{"attributes":{"js_property_callbacks":{"change:indices":[{"id":"1138"}]}},"id":"1152","type":"Selection"},{"attributes":{"args":{"button":{"id":"1128"},"graph":{"id":"1033"},"source":{"id":"1125"}},"code":"\n\t\t// from graph, we fetch nrend - node renderer, erend - edgerenderer\n\t\t// source - source object for JSMol, button - button object\n\t\tvar nrend = graph.node_renderer.data_source\n\t\tvar erend = graph.edge_renderer.data_source\n\n\t\tvar ninds = nrend.selected.indices\n\t\tvar einds = erend.selected.indices\n\t\tif (ninds.length) {\n\t\t\tvar rend = nrend\n\t\t} else {\n\t\t\tvar rend = erend\n\t\t}\n\t\tvar ndx = rend.selected.indices[0]\n\t\tvar geo = rend.data[\"geometry\"][ndx]\n\t\tvar name = rend.data[\"name\"][ndx]\n\t\tvar orig_label = button.label\n\t\t// use a function to apply setTimeout and recover original label\n\t\tfunction recover_label(button,orig_label){\n\t\t\tbutton.label = orig_label\n\t\t}\t\n\n\t\tif (geo.length){\n\t\t\tnavigator.clipboard.writeText([geo])\n\t\t\tbutton.label = \"Copied \" + name + \"!\"\n\t\t\tsetTimeout(recover_label,2000,button,orig_label)\n\t\t}\n\t\t"},"id":"1140","type":"CustomJS"},{"attributes":{"data_source":{"id":"1039"},"glyph":{"id":"1038"},"hover_glyph":{"id":"1071"},"muted_glyph":null,"selection_glyph":{"id":"1076"},"view":{"id":"1041"}},"id":"1040","type":"GlyphRenderer"},{"attributes":{"args":{"fig":{"id":"1004"},"graph":{"id":"1033"},"text_input":{"id":"1129"}},"code":"\n\t\t// source - source object for JSMol\n\t\t// pass graph and fetch node and edge renderers\n\t\t// from fig, we modify x_range and y_range. Default plot starts from -1.2 to 1.2,\n\t\tvar nrend = graph.node_renderer.data_source\n\t\tvar erend = graph.edge_renderer.data_source\n\t\tvar layout = graph.layout_provider.graph_layout\n\t\t// fetch the query in the data sources, choosing the appropiate renderer depending on the query\n\t\tvar mol_query = text_input.value\n\t\tif (mol_query.includes(\"TS\")) {\n\t\t\tvar renderer = erend\n\t\t\tvar other_renderer = nrend\n\t\t} else {\n\t\t\tvar renderer = nrend\n\t\t\tvar other_renderer = erend\n\t\t}\n\t\tvar pool_names = renderer.data[\"name\"]\n\t\tvar ndx = pool_names.indexOf(mol_query)\n\t\t// locate positions of the node or of the nodes defining an edge\n\t\tif (mol_query.includes(\"TS\")) {\n\t\t\tvar n1 = renderer.data[\"start\"][ndx]\n\t\t\tvar n2 = renderer.data[\"end\"][ndx]\n\t\t\tvar pos1 = layout[n1]\n\t\t\tvar pos2 = layout[n2]\n\t\t\tvar positions = new Array(2)\n\t\t\tpositions[0] = 0.5*(pos1[0]+pos2[0])\n\t\t\tpositions[1] = 0.5*(pos1[1]+pos2[1])\n\t\t} else {\n\t\t\tvar positions = layout[mol_query]\n\t\t}\n\t\t// returns -1 if element is not present\n\t\tif (ndx &gt;= 0) {\n\t\t\t// clearing other sel. avoids problems for model loading sometimes\n\t\t\tother_renderer.selected.indices = []\n\t\t\trenderer.selected.indices = [ndx]\n\t\t\tfig.x_range.start = positions[0] - 0.5\n\t\t\tfig.x_range.end = positions[0] + 0.5\n\t\t\tfig.y_range.start = positions[1] - 0.5\n\t\t\tfig.y_range.end = positions[1] + 0.5\n\t\t}\n\t\t"},"id":"1141","type":"CustomJS"},{"attributes":{"data":{"form":[null,null,null,null,null,null,null,null,"H2 + CO2","H2 + CO2"],"lab":["MIN1","MIN1","TS9","TS9","MIN3","MIN3","TS8","TS8","PR2","PR2"],"x":{"__ndarray__":"AAAAAAAAAAAAAAAAAADwPwAAAAAAAABAAAAAAAAACEAAAAAAAAAQQAAAAAAAABRAAAAAAAAAGEAAAAAAAAAcQAAAAAAAACBAAAAAAAAAIkA=","dtype":"float64","order":"little","shape":[10]},"y":[-8.323520999999985,-8.323520999999985,53.170985,53.170985,5.312669999999997,5.312669999999997,43.967468999999994,43.967468999999994,-37.60977,-37.60977]},"selected":{"id":"1263"},"selection_policy":{"id":"1264"}},"id":"1190","type":"ColumnDataSource"},{"attributes":{"args":{"menu":{"id":"1131"},"source":{"id":"1125"},"textField":{"id":"1133"}},"code":"\n\t\t// source - source object for JSMol ; menu - dropdown menu object\n\t\tsource.data[\"script\"] = [source.data[\"current_model\"] + \"; vibration on ; vibration scale 0.25 ; model \" + this.item]\n\t\tvar ndx = parseInt(this.item) - 1\n\t\tvar molname = source.data[\"current_mol\"]\n\t\tvar frqval = menu.menu[ndx][0]\n\t\tsource.data[\"current_vibration\"] = 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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].
 
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AutoMeKin now includes '''barrierless channels'''. However, these channels are not considered in the kinetics.
 
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AutoMeKin has been interfaced with [https://www.entos.ai/qcore/documentation/ '''Entos Qcore'''].
 
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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>]).
 
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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>]).
 
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Return to [[#toc|Contents]]
 
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Return to [[Main_Page]]
 

Latest revision as of 15:32, 17 July 2024

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