Difference between revisions of "AutoMeKin"

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(→‎News)
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==News==
 
==News==
 
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]].
 
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">
 
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  <head>
 
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      <meta charset="utf-8">
 
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      <title>Reaction network visualization</title>
 
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        <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>
 
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        <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>
 
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        <script type="text/javascript">
 
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            Bokeh.set_log_level("info");
 
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        </script>
 
−
        <script type="text/javascript">
 
−
            (function(root, factory) {
 
−
                    factory(root["Bokeh"]);
 
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                })(this, function(Bokeh) {
 
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                  var define;
 
−
                  return (function outer(modules, entry) {
 
−
                  if (Bokeh != null) {
 
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                    return Bokeh.register_plugin(modules, entry);
 
−
                  } else {
 
−
                    throw new Error("Cannot find Bokeh. You have to load it prior to loading plugins.");
 
−
                  }
 
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                })
 
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                ({
 
−
                  "custom/main": function(require, module, exports) {
 
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                    var models = {
 
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                      "JSMol": require("custom/jsmol_bokeh_extension.jsmol.js_mol").JSMol
 
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                    };
 
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                    require("base").register_models(models);
 
−
                    module.exports = models;
 
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                  },
 
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                  "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;
 
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                    Object.defineProperty(o, k2, { enumerable: true, get: function() { return m[k]; } });
 
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                }) : (function(o, m, k, k2) {
 
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                    if (k2 === undefined) k2 = k;
 
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                    o[k2] = m[k];
 
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                }));
 
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                var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
 
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                    Object.defineProperty(o, "default", { enumerable: true, value: v });
 
−
                }) : function(o, v) {
 
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                    o["default"] = v;
 
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                });
 
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                var __importStar = (this && this.__importStar) || function (mod) {
 
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                    if (mod && mod.__esModule) return mod;
 
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                    var result = {};
 
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                    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
 
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                    __setModuleDefault(result, mod);
 
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                    return result;
 
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                };
 
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                Object.defineProperty(exports, "__esModule", { value: true });
 
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                exports.JSMol = exports.JSMolView = void 0;
 
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                // These "require" lines are similar to python "import" statements
 
−
                const layout_dom_1 = require("models/layouts/layout_dom");
 
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                const layout_1 = require("core/layout");
 
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                const p = __importStar(require("core/properties"));
 
−
                // This defines some default options for JSmol
 
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                // See https://gist.github.com/jhjensen2/4701339 for more details.
 
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                const INFO = {
 
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                    height: "100%",
 
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                    width: "100%",
 
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                    serverURL: "https://chemapps.stolaf.edu/jmol/jsmol/php/jsmol.php",
 
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                    use: "HTML5",
 
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                    j2sPath: "https://chemapps.stolaf.edu/jmol/jsmol/j2s",
 
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                    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.
 
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                //
 
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                // 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();
 
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                        //script.onreadystatechange = (script.onload = () => this._init())
 
−
                        //script.onreadystatechange = script.onload
 
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                        document.querySelector("head").appendChild(script);
 
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                    }
 
−
                    _init() {
 
−
                        // Create a new Jmol applet using the JSmol.js API. This assumes JSmol.js
 
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                        // has already been loaded.
 
−
                        // Models will be able to specify and load external scripts automatically.
 
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                        //
 
−
                        // 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, () => {
 
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                            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";
 
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                        // 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>
 
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−
     
 
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<style>
 
−
.bk-root .bk-btn-default {
 
−
font-size: 1.2vh;
 
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}
 
−
.bk-root .bk-input {
 
−
font-size: 1.2vh;
 
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padding-bottom: 5px;
 
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padding-top: 5px;
 
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}
 
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.bk-root .bk {
 
−
font-size: 1.2vh;
 
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}
 
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.bk-root .bk-clearfix{
 
−
padding-bottom: 0.8vh;
 
−
}
 
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</style>
 
−
 
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  </head>
 
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  <body>
 
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−
     
 
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              <div class="bk-root" id="3c780241-42fe-478b-8b7d-bb4e3e9dfbe4" data-root-id="1159"></div>
 
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data 'model FRQS'\n5\nfrq = -1949.30 cm-1 \nC -0.3115 -0.469 0 0 0.033400 0.050400 0.000000\nO 0.935099 -0.469 0 0 -0.025100 -0.035800 0.000000\nO -0.794898 0.680099 0 0 -0.023300 -0.037000 0.000000\nH 1.1494 0.850298 0 0 -0.035800 0.424500 0.000000\nH 0.3382 1.3891 0 0 0.405200 0.131600 0.000000\n5\nfrq = 777.70 cm-1 \nC -0.3115 -0.469 0 0 0.000000 0.000000 0.112000\nO 0.935099 -0.469 0 0 0.000000 0.000000 -0.065900\nO -0.794898 0.680099 0 0 0.000000 0.000000 -0.065900\nH 1.1494 0.850298 0 0 0.000000 0.000000 0.378100\nH 0.3382 1.3891 0 0 0.000000 0.000000 0.378100\n5\nfrq = 861.40 cm-1 \nC -0.3115 -0.469 0 0 -0.025600 0.017000 0.000000\nO 0.935099 -0.469 0 0 0.008700 0.042500 0.000000\nO -0.794898 0.680099 0 0 -0.035800 -0.024500 0.000000\nH 1.1494 0.850298 0 0 0.367800 -0.243800 0.000000\nH 0.3382 1.3891 0 0 0.367400 -0.244500 0.000000\n5\nfrq = 895.40 cm-1 \nC -0.3115 -0.469 0 0 -0.093900 -0.141400 0.000000\nO 0.935099 -0.469 0 0 -0.126600 0.146500 0.000000\nO -0.794898 0.680099 0 0 0.184200 -0.059900 0.000000\nH 1.1494 0.850298 0 0 0.001700 0.221500 0.000000\nH 0.3382 1.3891 0 0 0.203500 0.087500 0.000000\n5\nfrq = 1136.40 cm-1 \nC -0.3115 -0.469 0 0 0.000000 0.000000 0.000000\nO 0.935099 -0.469 0 0 0.000000 0.000000 0.014300\nO -0.794898 0.680099 0 0 0.000000 0.000000 -0.014300\nH 1.1494 0.850298 0 0 0.000000 0.000000 -0.485700\nH 0.3382 1.3891 0 0 0.000000 0.000000 0.485700\n5\nfrq = 1577.90 cm-1 \nC -0.3115 -0.469 0 0 0.111700 0.168200 0.000000\nO 0.935099 -0.469 0 0 -0.122700 0.008100 0.000000\nO -0.794898 0.680099 0 0 0.055000 -0.109900 0.000000\nH 1.1494 0.850298 0 0 -0.005000 -0.276100 0.000000\nH 0.3382 1.3891 0 0 -0.252500 -0.111600 0.000000\n5\nfrq = 1608.90 cm-1 \nC -0.3115 -0.469 0 0 0.234700 -0.155900 0.000000\nO 0.935099 -0.469 0 0 -0.131500 0.009500 0.000000\nO -0.794898 0.680099 0 0 -0.059700 0.117600 0.000000\nH 1.1494 0.850298 0 0 0.216900 0.067700 0.000000\nH 0.3382 1.3891 0 0 0.021700 -0.226200 0.000000\n5\nfrq = 2040.00 cm-1 \nC -0.3115 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0.000000 0.000000 0.044600\nH 0.4048 -1.5715 0 0 0.000000 0.000000 0.759301\nH -0.4169 1.5559 0.0001 0 0.000000 0.000000 0.061900\n5\nfrq = 496.20 cm-1 \nC -0.2036 -0.3962 0 0 -0.081900 -0.140500 0.000000\nO 1.0655 -0.3962 0 0 -0.081100 0.124900 0.000000\nO -0.911899 0.694699 0 0 0.108200 -0.007300 0.000000\nH 0.4048 -1.5715 0 0 0.100200 -0.017300 0.000000\nH -0.4169 1.5559 0.0001 0 0.445100 -0.175100 0.000000\n5\nfrq = 641.80 cm-1 \nC -0.2036 -0.3962 0 0 0.000000 0.000000 0.066300\nO 1.0655 -0.3962 0 0 0.000000 0.000000 -0.034800\nO -0.911899 0.694699 0 0 0.000000 0.000000 -0.067400\nH 0.4048 -1.5715 0 0 0.000000 0.000000 0.145900\nH -0.4169 1.5559 0.0001 0 0.000000 0.000000 0.685703\n5\nfrq = 1064.40 cm-1 \nC -0.2036 -0.3962 0 0 0.013100 -0.028000 0.000000\nO 1.0655 -0.3962 0 0 0.073900 -0.022300 0.000000\nO -0.911899 0.694699 0 0 -0.127500 0.060700 0.000000\nH 0.4048 -1.5715 0 0 0.072800 -0.007000 0.000000\nH -0.4169 1.5559 0.0001 0 0.622302 -0.267800 0.000000\n5\nfrq = 1342.00 cm-1 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-0.041400 0.000000\nH 0.4048 -1.5715 0 0 0.011900 0.013300 0.000000\nH -0.4169 1.5559 0.0001 0 0.349700 0.845800 0.000000\nend 'model FRQS'","load data 'model FRQS'\n5\nfrq = -2928.30 cm-1 \nC 0.008 -0.221 0 0 0.008500 -0.056500 0.000000\nO 1.1831 -0.221 0 0 0.006600 0.008600 0.000000\nO -1.0411 0.5156 0 0 -0.028300 -0.007000 0.000000\nH -1.5835 -0.698202 0 0 -0.094400 0.540899 0.000000\nH -0.764698 -1.3442 0 0 0.337700 0.105600 0.000000\n5\nfrq = 451.40 cm-1 \nC 0.008 -0.221 0 0 0.000000 0.000000 0.207300\nO 1.1831 -0.221 0 0 0.000000 0.000000 -0.083000\nO -1.0411 0.5156 0 0 0.000000 0.000000 -0.029900\nH -1.5835 -0.698202 0 0 0.000000 0.000000 -0.641601\nH -0.764698 -1.3442 0 0 0.000000 0.000000 -0.038200\n5\nfrq = 587.20 cm-1 \nC 0.008 -0.221 0 0 0.090300 0.258300 0.000000\nO 1.1831 -0.221 0 0 0.095500 -0.161800 0.000000\nO -1.0411 0.5156 0 0 -0.183600 -0.040100 0.000000\nH -1.5835 -0.698202 0 0 0.082800 0.008000 0.000000\nH -0.764698 -1.3442 0 0 0.239400 0.119200 0.000000\n5\nfrq = 904.50 cm-1 \nC 0.008 -0.221 0 0 -0.032700 -0.018100 0.000000\nO 1.1831 -0.221 0 0 -0.027100 -0.015300 0.000000\nO -1.0411 0.5156 0 0 0.000800 0.049400 0.000000\nH -1.5835 -0.698202 0 0 0.331000 -0.213700 0.000000\nH -0.764698 -1.3442 0 0 0.475300 -0.111200 0.000000\n5\nfrq = 997.80 cm-1 \nC 0.008 -0.221 0 0 0.000000 0.000000 -0.075400\nO 1.1831 -0.221 0 0 0.000000 0.000000 0.017000\nO -1.0411 0.5156 0 0 0.000000 0.000000 0.032200\nH -1.5835 -0.698202 0 0 0.000000 0.000000 -0.378900\nH -0.764698 -1.3442 0 0 0.000000 0.000000 0.496400\n5\nfrq = 1345.80 cm-1 \nC 0.008 -0.221 0 0 0.009300 -0.173300 0.000000\nO 1.1831 -0.221 0 0 0.167300 0.014200 0.000000\nO -1.0411 0.5156 0 0 -0.159100 0.134600 0.000000\nH -1.5835 -0.698202 0 0 -0.004100 -0.189100 0.000000\nH -0.764698 -1.3442 0 0 -0.237400 -0.108600 0.000000\n5\nfrq = 1946.90 cm-1 \nC 0.008 -0.221 0 0 -0.100200 0.006300 0.000000\nO 1.1831 -0.221 0 0 0.058300 -0.002100 0.000000\nO -1.0411 0.5156 0 0 0.025200 -0.010600 0.000000\nH -1.5835 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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 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].

Revision as of 17:07, 1 December 2021

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 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.

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


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

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

AutoMeKin can be used through our web interface.

News

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, available through the autoinstaller.

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).

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