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                    "    <h2> <img id=\"nomad\" src=\"https://nomad-coe.eu/uploads/nomad/images/NOMAD_Logo2.png\" height=\"100\" alt=\"NOMAD Logo\">  NOMAD Analytics Toolkit   ",
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                    "  </div>",
                    "    <h3>Predicting energy differences between crystal structures: (Meta-)stability of octet-binary compounds</h3>",
                    "    <p class=\"nomad--description\">",
                    "      created by:",
                    " Angelo Ziletti<sup> 1</sup>,",
                    " Emre Ahmetcik<sup>1</sup>,",
                    " Runhai Ouyang<sup>1</sup>,",
                    " Ankit Kariryaa<sup>1</sup>, ",
                    " Fawzi R. Mohamed<sup>1</sup>,",
                    " Luca Ghiringhelli<sup>1</sup>,",
                    " and Matthias Scheffler<sup>1</sup> <br><br>",
                    "   ",
                    "      <sup>1</sup> Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, D-14195 Berlin, Germany <br>",
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                    "      <span class=\"nomad--last-updated\" data-version=\"v1.0.0\">[Last updated: October 16, 2017]</span>",
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                    "    </p>",
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                    ""
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                    "object": "<script>\nvar beaker = bkHelper.getBeakerObject().beakerObj;\n</script>\n<div id=\"teaser\" style=\"background-color: rgba(149,170,79, 1.0); background-position:  right center; background-size: 200px; background-repeat: no-repeat; \n    padding-top: 20px;\n    padding-right: 10px;\n    padding-bottom: 50px;\n    padding-left: 80px;\"> \n\n  <div class=\"nomad--header\">\n   <div style=\"text-align:center\">\n    <h2> <img id=\"nomad\" src=\"https://nomad-coe.eu/uploads/nomad/images/NOMAD_Logo2.png\" alt=\"NOMAD Logo\" height=\"100\">  NOMAD Analytics Toolkit   \n  <img id=\"nomad\" src=\"https://www.nomad-coe.eu/uploads/nomad/backgrounds/head_big-data_analytics_2.png\" alt=\"NOMAD Logo\" height=\"80\"> </h2>\n  </div>\n    <h3>Predicting energy differences between crystal structures: (Meta-)stability of octet-binary compounds</h3>\n    <p class=\"nomad--description\">\n      created by:\n Angelo Ziletti<sup> 1</sup>,\n Emre Ahmetcik<sup>1</sup>,\n Runhai Ouyang<sup>1</sup>,\n Ankit Kariryaa<sup>1</sup>, \n Fawzi R. Mohamed<sup>1</sup>,\n Luca Ghiringhelli<sup>1</sup>,\n and Matthias Scheffler<sup>1</sup> <br><br>\n   \n      <sup>1</sup> Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, D-14195 Berlin, Germany <br>\n      <span class=\"nomad--last-updated\" data-version=\"v1.0.0\">[Last updated: October 16, 2017]</span>\n    </p>\n</div>\n\n</div>  \n\n<div style=\"text-align: right;\">\n<a href=\"https://analytics-toolkit.nomad-coe.eu/home/\" class=\"btn btn-primary\" style=\"font-size:larger;\">Back to Analytics Home</a> \n<a href=\"https://www.nomad-coe.eu/\" class=\"btn btn-primary\" style=\"font-size:larger;\">Back to NOMAD CoE Home</a> \n</div>\n"
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            "id": "markdownKOPYxK",
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            "body": [
                "### Introduction ",
                "",
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                "This tutorial shows how to find descriptive parameters (short formulas) that predict the crystal structure (here, rocksalt (RS), zincblende (ZB), CsCl, NiAs or CrB), using the example of octet binary compounds. It is based on the algorithm sure independence screening and sparsifying operator (SISSO), that enables to search for optimal descriptor by scanning huge feature spaces.",
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                "  <div style=\"padding: 1ex; margin-top: 1ex; margin-bottom: 1ex; border-style: dotted; border-width: 1pt; border-color: blue; border-radius: 3px;\">",
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                "R. Ouyang, S. Curtarolo, E. Ahmetcik, L. M. Ghiringhelli, and M. Scheffler: <span style=\"font-style: italic;\">SISSO: a compressed-sensing method for systematically identifying efficient physical models of materials properties, </span> <a href=\"https://arxiv.org/abs/1710.03319\">https://arxiv.org/abs/1710.03319</a> (2017). <br>",
                "You can download the code <a href=\"https://github.com/rouyang2017/SISSO\">here</a> .",
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                "</div>",
                "With the default settings, the method reproduces the same results from:",
                "<div style=\"padding: 1ex; margin-top: 1ex; margin-bottom: 1ex; border-style: dotted; border-width: 1pt; border-color: blue; border-radius: 3px;\">",
                "L. M. Ghiringhelli, J. Vybiral, S. V. Levchenko, C. Draxl, M. Scheffler: <span style=\"font-style: italic;\">Big Data of Materials Science: Critical Role of the Descriptor</span>,  Phys. Rev. Lett. 114, 105503 (2015) <a href=\"http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.114.105503\">[PDF]</a>,",
                "</div>",
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                "that were obtained by applying the <a href=\"http://analytics-toolkit.nomad-coe.eu/tutorial-LASSO_L0\">[LASSO+L0 algorithm]</a>. Click on <b>Run</b> below to reproduce results from this publication; click <b>Background</b> for an explanation of the approach; or, modify <b>Settings</b> to produce your own results.",
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                "",
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                "<b> Idea: </b> Starting from simple physical quantities (\"building blocks\", here properties of the constituent free atoms such as orbital radii), millions (or billions) of candidate formulas are generated by applying arithmetic operations combining building blocks, for example forming sums and products of them. These candidate formulas constitute the so-called \"feature space\". Then a feature selection method (SISSO) is used to select only a few of these formulas that explain the data."
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                "<div class=\"modal fade\" id=\"modal-credits\" tabindex=\"-1\" role=\"dialog\" aria-labelledby=\"modal-credits\">",
                "  <div class=\"modal-dialog\" role=\"document\">",
                "    <div class=\"modal-content\">",
                "      <div class=\"modal-header\">",
                "        <button type=\"button\" class=\"close\" data-dismiss=\"modal\" aria-label=\"Close\"><span aria-hidden=\"true\">×</span></button>",
                "        <h1 class=\"modal-title\" id=\"modal-credits-label\">Background</h1>",
                "        <hr>",
                "      </div>",
                "      <div class=\"modal-body modal-credits-body\">",
                "",
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                "    <p>We present a tool for predicting the crystal structure of octet binary compounds, by using a set of descriptive parameters (a descriptor) based on free-atom data of the atomic species constituting the binary material. We apply a newly developed method: sure independence screening and sparsifying operator (SISSO), that allows to find an optimal descriptor in a huge feature space containing billions of features &#167;. In this tutorial an $\\ell_0$-optimization is used as the sparsifying operator.",
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                "The method is described in:",
                "<div style=\"padding: 1ex; margin-top: 1ex; margin-bottom: 1ex; border-style: dotted; border-width: 1pt; border-color: blue; border-radius: 3px;\">",
                "R. Ouyang, S. Curtarolo, E. Ahmetcik, L. M. Ghiringhelli, and M. Scheffler: <span style=\"font-style: italic;\">SISSO: a compressed-sensing method for systematically identifying efficient physical models of materials properties, </span> <a href=\"http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.114.105503\">https://arxiv.org/abs/1710.03319</a> (2017). <br>",
                "</div>",
                "</p>",
                " ",
                "<p>SISSO($\\ell_0$) works iteratively. In the first iteration, a number k of features is collected that have the largest correlation (scalar product) with the property vector. The feature with the largest correlation is simply the 1D descriptor. Next, a residual is constructed as the error made at the first iteration. A new set of k features is now selected as those having the largest  correlation with the residual. The 2D descriptor is the pair of features that yield the smallest fitting error upon least square regression, among all possible pairs contained in the union of the sets selected in this and the first iteration. In each next iteration a new residual is constructed as the error made in the previous iteration, then a new set of k features is extracted as those that have largest correlation with each new residual. The nD descriptor is the n-tuple of features that yield the smallest fitting error upon least square regression, among all possible n-tuples contained in the union of the sets obtained in each new iteration and all the previous iterations. If k=1 the method collapses to the so-called orthogonal matching pursuit.",
                "</p>",
                "",
                "        <p>The prediction of the ground-state structure for binary compounds from a simple descriptor has a notable history in materials science [1-7], where descriptors were designed by chemically/physically-inspired intuition. The tool presented here allows for the machine-learning-aided automatic discovery of a descriptor and a model for the prediction of the difference in energy between a selected pair of structures for 82 octet binary materials.</p>",
                "",
                "",
                "        <p> By running the tutorial with the default setting, the (RS vs. ZB) results of the <a href=\"http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.114.105503\" target=\"_blank\">PRL 2015</a> identified by the LASSO+$\\ell_0$ method can be recovered.</p>",
                "",
                "<p>&#167; The same task is also addressed in the tutorial <a href=\"http://analytics-toolkit.nomad-coe.eu/tutorial-LASSO_L0\">\"[Predicting energy differences between different crystal structures I: large feature space]\"</a>, where an alternative method, LASSO+$\\ell_0$, is used to find an optimal descriptor in a moderately large feature space. LASSO+$\\ell_0$ was introduced in [<a href=\"http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.114.105503\" target=\"_blank\">PRL 2015</a>] and SISSO($\\ell_0$) was introduced more recently in order to cope with much larger and highly correlated feature spaces.</p>",
                "",
                "        <p>References:</p>",
                "        <ol>",
                "          <li>J. A. van Vechten, Phys. Rev. 182, 891 (1969).</li>",
                "          <li>J. C. Phillips, Rev. Mod. Phys. 42, 317 (1970).</li>",
                "          <li>J. John and A. N. Bloch, Phys. Rev. Lett. 33, 1095 (1974).</li>",
                "          <li>J. R. Chelikowsky and J. C. Phillips, Phys. Rev. B 17, 2453 (1978).</li>",
                "          <li>A. Zunger, Phys. Rev. B 22, 5839 (1980).</li>",
                "          <li>D. G. Pettifor, Solid State Commun. 51, 31 (1984).</li>",
                "          <li>Y. Saad, D. Gao, T. Ngo, S. Bobbitt, J. R. Chelikowsky, and W. Andreoni, Phys. Rev. B 85, 104104 (2012).</li>",
                "        </ol>      ",
                "        ",
                "        ",
                "      ",
                "      </div>",
                "      <div class=\"modal-footer\">",
                "        <button type=\"button\" class=\"btn btn-default\" data-dismiss=\"modal\" style=\"font-size:larger;\">Close</button>",
                "      </div>",
                "    </div>",
                "  </div>",
                "</div>",
                "",
                "<div class=\"modal fade\" id=\"modal-instructions\" tabindex=\"-1\" role=\"dialog\" aria-labelledby=\"modal-instructions\">",
                "  <div class=\"modal-dialog\" role=\"document\">",
                "    <div class=\"modal-content\">",
                "      <div class=\"modal-header\">",
                "        <button type=\"button\" class=\"close\" data-dismiss=\"modal\" aria-label=\"Close\"><span aria-hidden=\"true\">×</span></button>",
                "        <h1 class=\"modal-title\" id=\"modal-instructions-label\">Instructions</h1>",
                "        <hr>",
                "      </div>",
                "      <div class=\"modal-body modal-instruction-body\">",
                "        ",
                "   <p>In this example, you can run a compressed-sensing based algorithm for finding the optimal descriptor and model that predicts the difference in energy between crystal structures (here, zincblende vs. rocksalt, CsCl, NiAs or CrB structure). </p>",
                "",
                "<p>The descriptor is selected out of a large number of candidates constructed as functions of basic input features, the primary features. </p>",
                "",
                "<p>By clicking <b>Settings</b> you can select the structure pair of interest (either RS/ZB, CsCl/ZB, NiAs/ZB or CrB/ZB), the primary features as well as which kind of unary and binary operations are allowed during feature space construction from the checklist below. Moreover the dimension of the output energies (kcal/mol or eV) and the following three parameters of the SISSO($\\ell_0$) algorithm can be specified: ",
                "        <ul>",
                "          <li>Number of iterations for the construction for the feature space: How often the selected operations are applied to build the feature space. At each step the operations are applied on all features created until the current step. </li>",
                "          <li>Maximum dimension of optimal descriptor: Number of SIS iterations.</li>",
                "          <li>Number of collected features per SIS iteration.</li>",
                "        </ul>    ",
                "            ",
                "  ",
                "<p>        After the preferred settings have been adjusted, click <b>RUN</b> for performing the calculations (loading the values of the primary features, creation of the feature space, and optimization via SISSO($\\ell_0$)). </p>",
                "",
                "During the run, a brief summary is printed out below the <b>RUN</b> button. At the end of the run: ",
                "  <ul>",
                "  <li> the solution (machine-learned descriptor, model, and its performance in terms of training error) is printed out underneath starting from the one-dimensional solution to the selected maximum dimensionality and</li>",
                "<li> the “View interactive 2D scatter plot” button unlocks. By clicking this button, the scatter plot with the two-dimensional descriptor appears in a separate tab. If a descriptor dimensionality greater than two was selected, the scatter plot displays the two-dimensional descriptor.</li>",
                "</ul>",
                "<p>Note: the scatter plot remains active even if another run is performed, which enables the output of several sets of input parameters to be compared.</p>",
                "           ",
                "      </div>",
                "      <div class=\"modal-footer\">",
                "        <button type=\"button\" class=\"btn btn-default\" data-dismiss=\"modal\" style=\"font-size:larger;\">Close</button>",
                "      </div>",
                "    </div>",
                "  </div>",
                "</div>"
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                    "<script>",
                    "var run_lasso = function() {",
                    "  $(\"#lasso_result_button\").removeClass(\"active\").addClass(\"disabled\");",
                    "  getFeatures();",
                    "  getOperators();",
                    "  beaker.max_dim = $(\"#lasso_max_dim_selector\").val();",
                    "  beaker.structures_diff = $(\"#lasso_structures_diff\").val();",
                    "  beaker.n_comb = $(\"#n_comb\").val();",
                    "  beaker.n_sis = $(\"#n_sis\").val();",
                    "  beaker.units = $(\"#units_select\").val();",
                    "  beaker.evaluate(\"calc_cell\"); // evaluate cells with tag \"lasso_cell\"",
                    " // view_result()",
                    "};",
                    "var reset_lasso = function(){",
                    "  beaker.evaluate(\"lasso-settings-cell\");",
                    "  var e = document.getElementById('lasso-hidden-settings-div');",
                    "  var b = document.getElementById('lasso-hidden-settings-button');",
                    "  e.style.display = 'block';",
                    "  b.style.display = 'inline';",
                    "};",
                    "var getFeatures = function() {",
                    "    beaker.selected_feature_list = [];",
                    "    $('#lasso_features_select input:checkbox').each(function () {",
                    "        if(this.checked )",
                    "          beaker.selected_feature_list.push(this.value);",
                    "    });",
                    "};",
                    "var getOperators = function() {",
                    "    beaker.allowed_operations = [];",
                    "    $('#lasso_operators_select input:checkbox').each(function () {",
                    "        if(this.checked )",
                    "          beaker.allowed_operations.push(this.value);",
                    "    });",
                    "};  ",
                    "",
                    "var toggle_settings = function(){",
                    "  var e = document.getElementById('lasso-hidden-settings-div');",
                    "  var b = document.getElementById('lasso-hidden-settings-button');",
                    "  if(e.style.display == 'block'){",
                    "    e.style.display = 'none';",
                    "    b.style.display = 'none';",
                    "  }",
                    "  else{",
                    "    e.style.display = 'block';",
                    "    b.style.display = 'inline';",
                    "  }",
                    "};",
                    "beaker.view_result = function(result_link) {",
                    "//   beaker.evaluate(\"lasso_viewer_result\").then(function(x) {",
                    "    $(\"#lasso_result_button\").attr(\"href\", result_link);",
                    "//   }); ",
                    "  $(\"#lasso_result_button\").removeClass(\"disabled\").addClass(\"active\");",
                    "}",
                    "",
                    "</script>",
                    "",
                    "",
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                    "<button type=\"button\" class=\"btn btn-default\" data-toggle=\"modal\" data-target=\"#modal-credits\" style=\"font-size:larger;\">Background</button>",
                    "<button type=\"button\" class=\"btn btn-info\" data-toggle=\"modal\" data-target=\"#modal-instructions\" style=\"font-size:larger;\">Read usage instructions</button>"
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                ],
                "hidden": true
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            },
            "output": {
                "state": {},
                "result": {
                    "type": "BeakerDisplay",
                    "innertype": "Html",
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                    "object": "<script>\nvar beaker = bkHelper.getBeakerObject().beakerObj;\n</script>\n<script>\nvar run_lasso = function() {\n  $(\"#lasso_result_button\").removeClass(\"active\").addClass(\"disabled\");\n  getFeatures();\n  getOperators();\n  beaker.max_dim = $(\"#lasso_max_dim_selector\").val();\n  beaker.structures_diff = $(\"#lasso_structures_diff\").val();\n  beaker.n_comb = $(\"#n_comb\").val();\n  beaker.n_sis = $(\"#n_sis\").val();\n  beaker.units = $(\"#units_select\").val();\n  beaker.evaluate(\"calc_cell\"); // evaluate cells with tag \"lasso_cell\"\n // view_result()\n};\nvar reset_lasso = function(){\n  beaker.evaluate(\"lasso-settings-cell\");\n  var e = document.getElementById('lasso-hidden-settings-div');\n  var b = document.getElementById('lasso-hidden-settings-button');\n  e.style.display = 'block';\n  b.style.display = 'inline';\n};\nvar getFeatures = function() {\n    beaker.selected_feature_list = [];\n    $('#lasso_features_select input:checkbox').each(function () {\n        if(this.checked )\n          beaker.selected_feature_list.push(this.value);\n    });\n};\nvar getOperators = function() {\n    beaker.allowed_operations = [];\n    $('#lasso_operators_select input:checkbox').each(function () {\n        if(this.checked )\n          beaker.allowed_operations.push(this.value);\n    });\n};  \n\nvar toggle_settings = function(){\n  var e = document.getElementById('lasso-hidden-settings-div');\n  var b = document.getElementById('lasso-hidden-settings-button');\n  if(e.style.display == 'block'){\n    e.style.display = 'none';\n    b.style.display = 'none';\n  }\n  else{\n    e.style.display = 'block';\n    b.style.display = 'inline';\n  }\n};\nbeaker.view_result = function(result_link) {\n//   beaker.evaluate(\"lasso_viewer_result\").then(function(x) {\n    $(\"#lasso_result_button\").attr(\"href\", result_link);\n//   }); \n  $(\"#lasso_result_button\").removeClass(\"disabled\").addClass(\"active\");\n}\n\n</script>\n\n\n<button type=\"button\" class=\"btn btn-default\" data-toggle=\"modal\" data-target=\"#modal-credits\" style=\"font-size:larger;\">Background</button>\n<button type=\"button\" class=\"btn btn-info\" data-toggle=\"modal\" data-target=\"#modal-instructions\" style=\"font-size:larger;\">Read usage instructions</button>"
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                },
                "selectedType": "BeakerDisplay",
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                "elapsedTime": 0,
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                "height": 80
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            },
            "evaluatorReader": true,
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            "lineCount": 59
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        },
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        {
            "id": "codePjdM5h",
            "type": "code",
            "evaluator": "HTML",
            "input": {
                "body": [
                    "<script>",
                    "var run_lasso = function() {",
                    "  $(\"#lasso_result_button\").removeClass(\"active\").addClass(\"disabled\");",
                    "  getFeatures();",
                    "  getOperators();",
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                    "  beaker.max_dim = $(\"#lasso_max_dim_selector\").val();",
                    "  beaker.structures_diff = $(\"#lasso_structures_diff\").val();",
                    "  beaker.n_comb = $(\"#n_comb\").val();",
                    "  beaker.n_sis = $(\"#n_sis\").val();",
                    "  beaker.evaluate(\"calc_cell\"); // evaluate cells with tag \"lasso_cell\"",
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                    " // view_result()",
                    "};",
                    "var reset_lasso = function(){",
                    "  beaker.evaluate(\"lasso-settings-cell\");",
                    "  var e = document.getElementById('lasso-hidden-settings-div');",
                    "  var b = document.getElementById('lasso-hidden-settings-button');",
                    "  e.style.display = 'block';",
                    "  b.style.display = 'inline';",
                    "};",
                    "var getFeatures = function() {",
                    "    beaker.selected_feature_list = [];",
                    "    $('#lasso_features_select input:checkbox').each(function () {",
                    "        if(this.checked )",
                    "          beaker.selected_feature_list.push(this.value);",
                    "    });",
                    "};",
                    "var getOperators = function() {",
                    "    beaker.allowed_operations = [];",
                    "    $('#lasso_operators_select input:checkbox').each(function () {",
                    "        if(this.checked )",
                    "          beaker.allowed_operations.push(this.value);",
                    "    });",
                    "};  ",
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                    "",
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                    "var toggle_settings = function(){",
                    "  var e = document.getElementById('lasso-hidden-settings-div');",
                    "  var b = document.getElementById('lasso-hidden-settings-button');",
                    "  if(e.style.display == 'block'){",
                    "    e.style.display = 'none';",
                    "    b.style.display = 'none';",
                    "  }",
                    "  else{",
                    "    e.style.display = 'block';",
                    "    b.style.display = 'inline';",
                    "  }",
                    "};",
                    "beaker.view_result = function(result_link) {",
                    "//   beaker.evaluate(\"lasso_viewer_result\").then(function(x) {",
                    "    $(\"#lasso_result_button\").attr(\"href\", result_link);",
                    "//   }); ",
                    "  $(\"#lasso_result_button\").removeClass(\"disabled\").addClass(\"active\");",
                    "}",
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                    "",
                    "",
                    "",
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                    "</script>"
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                ],
                "hidden": true
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            },
            "output": {
                "state": {},
                "result": {
                    "type": "BeakerDisplay",
                    "innertype": "Html",
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                    "object": "<script>\nvar beaker = bkHelper.getBeakerObject().beakerObj;\n</script>\n<script>\nvar run_lasso = function() {\n  $(\"#lasso_result_button\").removeClass(\"active\").addClass(\"disabled\");\n  getFeatures();\n  getOperators();\n  beaker.max_dim = $(\"#lasso_max_dim_selector\").val();\n  beaker.structures_diff = $(\"#lasso_structures_diff\").val();\n  beaker.n_comb = $(\"#n_comb\").val();\n  beaker.n_sis = $(\"#n_sis\").val();\n  beaker.evaluate(\"calc_cell\"); // evaluate cells with tag \"lasso_cell\"\n // view_result()\n};\nvar reset_lasso = function(){\n  beaker.evaluate(\"lasso-settings-cell\");\n  var e = document.getElementById('lasso-hidden-settings-div');\n  var b = document.getElementById('lasso-hidden-settings-button');\n  e.style.display = 'block';\n  b.style.display = 'inline';\n};\nvar getFeatures = function() {\n    beaker.selected_feature_list = [];\n    $('#lasso_features_select input:checkbox').each(function () {\n        if(this.checked )\n          beaker.selected_feature_list.push(this.value);\n    });\n};\nvar getOperators = function() {\n    beaker.allowed_operations = [];\n    $('#lasso_operators_select input:checkbox').each(function () {\n        if(this.checked )\n          beaker.allowed_operations.push(this.value);\n    });\n};  \n\nvar toggle_settings = function(){\n  var e = document.getElementById('lasso-hidden-settings-div');\n  var b = document.getElementById('lasso-hidden-settings-button');\n  if(e.style.display == 'block'){\n    e.style.display = 'none';\n    b.style.display = 'none';\n  }\n  else{\n    e.style.display = 'block';\n    b.style.display = 'inline';\n  }\n};\nbeaker.view_result = function(result_link) {\n//   beaker.evaluate(\"lasso_viewer_result\").then(function(x) {\n    $(\"#lasso_result_button\").attr(\"href\", result_link);\n//   }); \n  $(\"#lasso_result_button\").removeClass(\"disabled\").addClass(\"active\");\n}\n\n\n\n</script>"
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                },
                "selectedType": "BeakerDisplay",
                "elapsedTime": 0,
                "height": 50
            },
            "evaluatorReader": true,
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            "lineCount": 56
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        },
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        {
            "id": "lasso-settings-cell",
            "type": "code",
            "evaluator": "HTML",
            "input": {
                "body": [
                    "<style type=\"text/css\">",
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                    "  .lasso_control{",
                    "    margin-left: 10px;",
                    "  }",
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                    "</style>",
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                    "<div class=\"lasso_control\" id=\"lasso-hidden-settings-div\"> ",
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                    "  <div class=\"row\"> <!-- Start of third row-->",
                    "  <p class=\"lasso_selection_description\"><b>Relative stability (energy difference between two structures): </b> ",
                    "  <select id='lasso_structures_diff'>",
                    "    <option value=\"0\" >RS-ZB</option>",
                    "    <option value=\"1\">CsCl-ZB</option>",
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                    "    <option value=\"2\">NiAs-ZB</option>",
                    "    <option value=\"3\">CrB-ZB</option>",
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                    "  </select> </p>",
                    "  </div><!-- End of row--> ",
                    "  ",
                    "  ",
                    "  ",
                    "  <div class=\"row\">",
                    "    <p class=\"lasso_selection_description\"><b>Primary features </b>",
                    "  (hover the mouse",
                    "pointer over the feature names to see a full description):</p>",
                    "    <form id=\"lasso_features_select\">",
                    "      <div class=\"lasso_form_group\">",
                    "         <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"atomic_ionization_potential\" CHECKED > <span title=\"Atomic ionization potential\"><i>IP</i> </span></label>",
                    "         <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"atomic_electron_affinity\" CHECKED > <span title=\"Atomic electron affinity\"> <i>EA</i></span></label>",
                    "         <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"atomic_rs_max\" CHECKED > <span title=\"Radius at which the radial probability density of the valence s orbital is maximum\"> <i>r</i><sub>s</sub>  </span> </label>",
                    "         <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"atomic_rp_max\" CHECKED > <span title=\"Radius at which the radial probability density of the valence p orbital is maximum\"> <i>r</i><sub>p</sub>  </span> </label>",
                    "         <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"atomic_rd_max\" CHECKED > <span title=\"Radius at which the radial probability density of the valence d orbital is maximum\"> <i>r</i><sub>d</sub>  </span> </label>",
                    "         <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"atomic_number\" > <span title=\"Atomic number\"> <i>Z</i>  </span> </label>",
                    "         <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"period\" > <span title=\"Period (in the periodic table)\"> <i>n</i> <sub>period</sub>  </span> </label>",
                    "         <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"atomic_r_by_2_dimer\" > <span title=\"Bond length of atomA-atomA dimer\"> <i>d</i> <sup>AA</sup> </span> </label>",
                    "",
                    "        ",
                    "      </div>",
                    "    </form>",
                    "  </div>  <!-- End of row-->",
                    "  <div class=\"row\"> <!-- Start of second row-->",
                    "    <p class=\"lasso_selection_description\"><b>Allowed operations:</b> <br>",
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                    "  Given features x and y, apply these operations for feature space construction:</p>",
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                    "    <form id=\"lasso_operators_select\">",
                    "      <div class=\"lasso_form_group\">",
                    "        <label class =\"col-xs-4 col-md-4 col-lg-1\"> <input type=\"checkbox\" value=\"+\" CHECKED > x+y  </label>",
                    "        <label class =\"col-xs-4 col-md-4 col-lg-1\"> <input type=\"checkbox\" value=\"-\" > x-y  </label>",
                    "        <label class =\"col-xs-4 col-md-4 col-lg-1\"> <input type=\"checkbox\" value=\"|-|\" CHECKED > |x-y|  </label>",
                    "        <label class =\"col-xs-4 col-md-4 col-lg-1\"> <input type=\"checkbox\" value=\"*\" > x &middot y  </label>",
                    "        <label class =\"col-xs-4 col-md-4 col-lg-1\"> <input type=\"checkbox\" value=\"/\" CHECKED > x/y  </label>",
                    "        <label class =\"col-xs-4 col-md-4 col-lg-1\"> <input type=\"checkbox\" value=\"^-1\" > x^(-1)  </label>",
                    "        <label class =\"col-xs-4 col-md-4 col-lg-1\"> <input type=\"checkbox\" value=\"^2\" CHECKED > x^2  </label>",
                    "        <label class =\"col-xs-4 col-md-4 col-lg-1\"> <input type=\"checkbox\" value=\"^3\" > x^3  </label>",
                    "        <label class =\"col-xs-4 col-md-4 col-lg-1\"> <input type=\"checkbox\" value=\"sqrt\" > &radic;<span style=\"text-decoration: overline\">x</span>  </label>",
                    "        <label class =\"col-xs-4 col-md-4 col-lg-1\"> <input type=\"checkbox\" value=\"exp\" CHECKED > exp(x)  </label>",
                    "        <label class =\"col-xs-4 col-md-4 col-lg-1\"> <input type=\"checkbox\" value=\"exp-\" > exp(-x)  </label>",
                    "        <label class =\"col-xs-4 col-md-4 col-lg-1\"> <input type=\"checkbox\" value=\"log\" > log(x)  </label>",
                    "        <label class =\"col-xs-4 col-md-4 col-lg-1\"> <input type=\"checkbox\" value=\"SCD\" >  <span title=\"Standard Cauchy distribution\"> SCD  </span> </label>",
                    "      </div>",
                    "    </form>",
                    "  </div>  <!-- End of row-->",
                    "  <div class=\"row\"> <!-- Start of third row-->",
                    "    <p class=\"lasso_selection_description\"><b>Number of iterations for the construction for the feature space: </b> ",
                    "  <select id='n_comb'>",
                    "    <option value=\"1\" > 1</option>",
                    "    <option value=\"2 \" selected=\"selected\"> 2</option>",
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                    "    <option value=\"3\" > 3</option>",
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                    "  </select> ",
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                    "      <br> The required computational resources scale exponentially with the <b>Number of iterations for the construction for the feature space</b>.</p>",
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                    "   ",
                    "  <p class=\"lasso_selection_description\"><b>Optimal descriptor maximum dimension (number of SIS iterations): </b> ",
                    "  <select id='lasso_max_dim_selector'>",
                    "    <option value=\"2\" > 2D</option>",
                    "    <option value=\"3\" > 3D</option>",
                    "    <option value=\"4\" > 4D</option>",
                    "    <option value=\"5\" > 5D</option>",
                    "  </select> </p>",
                    "  <p class=\"lasso_selection_description\"><b>Number of collected features per SIS iteration: </b> ",
                    "  <input type=\"number\" name=\"quantity\" id=\"n_sis\" min=\"1\" max=\"1658\" value=\"10\" step=\"100\"> </p>",
                    "",
                    "  </div><!-- End of row-->",
                    "  <div class=\"row\"> <!-- Start of forth row-->",
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                    "  <p class=\"lasso_selection_description\"><b>Units of measurement: </b>",
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                    "  <select id='units_select'>",
                    "    <option value=\"eV_angstrom\" > [energy]=eV;&nbsp;&nbsp;[length]=angstrom</option>",
                    "    <option value=\"kcal/mol_angstrom\" > [energy]=kcal/mol;&nbsp;&nbsp;[length]=angstrom</option>",
                    "  </select> </p>",
                    "  </div><!-- End of row-->",
                    "<!-- <span title=''> <img src=\"http://images.clipartpanda.com/question-purzen_Icon_with_question_mark_Vector_Clipart.png\" style=\"height: 30px; width: 30px;\"> </span> -->",
                    "<!--   <button class=\"btn btn-default\" onclick='run_lasso()'>RUN LASSO+L0</button> -->",
                    "<!--   <button class=\"btn btn-default\" onclick='reset_lasso()'>RESET</button> -->",
                    "<!--   <label title=\"This button becomes active when the",
                    "run is finished. By clicking it, an interactive plot of the first 2",
                    "dimensions of the optimized descriptor will be opened\"> ",
                    "  <a href=\"#\" target=\"_blank\" class=\"btn btn-primary disabled\" id=\"lasso_result_button\" >View interactive 2D scatter plot</a> </label> -->",
                    "</div>"
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                ],
                "hidden": true
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            },
            "output": {
                "state": {},
                "result": {
                    "type": "BeakerDisplay",
                    "innertype": "Html",
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                    "object": "<script>\nvar beaker = bkHelper.getBeakerObject().beakerObj;\n</script>\n<style type=\"text/css\">\n  .lasso_control{\n    margin-left: 10px;\n  }\n</style>\n<div class=\"lasso_control\" id=\"lasso-hidden-settings-div\"> \n  <div class=\"row\"> <!-- Start of third row-->\n  <p class=\"lasso_selection_description\"><b>Relative stability (energy difference between two structures): </b> \n  <select id=\"lasso_structures_diff\">\n    <option value=\"0\">RS-ZB</option>\n    <option value=\"1\">CsCl-ZB</option>\n    <option value=\"2\">NiAs-ZB</option>\n    <option value=\"3\">CrB-ZB</option>\n  </select> </p>\n  </div><!-- End of row--> \n  \n  \n  \n  <div class=\"row\">\n    <p class=\"lasso_selection_description\"><b>Primary features </b>\n  (hover the mouse\npointer over the feature names to see a full description):</p>\n    <form id=\"lasso_features_select\">\n      <div class=\"lasso_form_group\">\n         <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"atomic_ionization_potential\" checked=\"\" type=\"checkbox\"> <span title=\"Atomic ionization potential\"><i>IP</i> </span></label>\n         <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"atomic_electron_affinity\" checked=\"\" type=\"checkbox\"> <span title=\"Atomic electron affinity\"> <i>EA</i></span></label>\n         <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"atomic_rs_max\" checked=\"\" type=\"checkbox\"> <span title=\"Radius at which the radial probability density of the valence s orbital is maximum\"> <i>r</i><sub>s</sub>  </span> </label>\n         <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"atomic_rp_max\" checked=\"\" type=\"checkbox\"> <span title=\"Radius at which the radial probability density of the valence p orbital is maximum\"> <i>r</i><sub>p</sub>  </span> </label>\n         <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"atomic_rd_max\" checked=\"\" type=\"checkbox\"> <span title=\"Radius at which the radial probability density of the valence d orbital is maximum\"> <i>r</i><sub>d</sub>  </span> </label>\n         <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"atomic_number\" type=\"checkbox\"> <span title=\"Atomic number\"> <i>Z</i>  </span> </label>\n         <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"period\" type=\"checkbox\"> <span title=\"Period (in the periodic table)\"> <i>n</i> <sub>period</sub>  </span> </label>\n         <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"atomic_r_by_2_dimer\" type=\"checkbox\"> <span title=\"Bond length of atomA-atomA dimer\"> <i>d</i> <sup>AA</sup> </span> </label>\n\n        \n      </div>\n    </form>\n  </div>  <!-- End of row-->\n  <div class=\"row\"> <!-- Start of second row-->\n    <p class=\"lasso_selection_description\"><b>Allowed operations:</b> <br>\n  Given features x and y, apply these operations for feature space construction:</p>\n    <form id=\"lasso_operators_select\">\n      <div class=\"lasso_form_group\">\n        <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"+\" checked=\"\" type=\"checkbox\"> x+y  </label>\n        <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"-\" type=\"checkbox\"> x-y  </label>\n        <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"|-|\" checked=\"\" type=\"checkbox\"> |x-y|  </label>\n        <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"*\" type=\"checkbox\"> x · y  </label>\n        <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"/\" checked=\"\" type=\"checkbox\"> x/y  </label>\n        <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"^-1\" type=\"checkbox\"> x^(-1)  </label>\n        <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"^2\" checked=\"\" type=\"checkbox\"> x^2  </label>\n        <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"^3\" type=\"checkbox\"> x^3  </label>\n        <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"sqrt\" type=\"checkbox\"> √<span style=\"text-decoration: overline\">x</span>  </label>\n        <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"exp\" checked=\"\" type=\"checkbox\"> exp(x)  </label>\n        <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"exp-\" type=\"checkbox\"> exp(-x)  </label>\n        <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"log\" type=\"checkbox\"> log(x)  </label>\n        <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"SCD\" type=\"checkbox\">  <span title=\"Standard Cauchy distribution\"> SCD  </span> </label>\n      </div>\n    </form>\n  </div>  <!-- End of row-->\n  <div class=\"row\"> <!-- Start of third row-->\n    <p class=\"lasso_selection_description\"><b>Number of iterations for the construction for the feature space: </b> \n  <select id=\"n_comb\">\n    <option value=\"1\"> 1</option>\n    <option value=\"2 \" selected=\"selected\"> 2</option>\n    <option value=\"3\"> 3</option>\n  </select> \n      <br> The required computational resources scale exponentially with the <b>Number of iterations for the construction for the feature space</b>.</p>\n   \n  <p class=\"lasso_selection_description\"><b>Optimal descriptor maximum dimension (number of SIS iterations): </b> \n  <select id=\"lasso_max_dim_selector\">\n    <option value=\"2\"> 2D</option>\n    <option value=\"3\"> 3D</option>\n    <option value=\"4\"> 4D</option>\n    <option value=\"5\"> 5D</option>\n  </select> </p>\n  <p class=\"lasso_selection_description\"><b>Number of collected features per SIS iteration: </b> \n  <input name=\"quantity\" id=\"n_sis\" min=\"1\" max=\"1658\" value=\"10\" step=\"100\" type=\"number\"> </p>\n\n  </div><!-- End of row-->\n  <div class=\"row\"> <!-- Start of forth row-->\n  <p class=\"lasso_selection_description\"><b>Units of measurement: </b>\n  <select id=\"units_select\">\n    <option value=\"eV_angstrom\"> [energy]=eV;&nbsp;&nbsp;[length]=angstrom</option>\n    <option value=\"kcal/mol_angstrom\"> [energy]=kcal/mol;&nbsp;&nbsp;[length]=angstrom</option>\n  </select> </p>\n  </div><!-- End of row-->\n<!-- <span title=''> <img src=\"http://images.clipartpanda.com/question-purzen_Icon_with_question_mark_Vector_Clipart.png\" style=\"height: 30px; width: 30px;\"> </span> -->\n<!--   <button class=\"btn btn-default\" onclick='run_lasso()'>RUN LASSO+L0</button> -->\n<!--   <button class=\"btn btn-default\" onclick='reset_lasso()'>RESET</button> -->\n<!--   <label title=\"This button becomes active when the\nrun is finished. By clicking it, an interactive plot of the first 2\ndimensions of the optimized descriptor will be opened\"> \n  <a href=\"#\" target=\"_blank\" class=\"btn btn-primary disabled\" id=\"lasso_result_button\" >View interactive 2D scatter plot</a> </label> -->\n</div>"
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                },
                "selectedType": "BeakerDisplay",
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                "elapsedTime": 0,
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                "height": 528
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            },
            "evaluatorReader": true,
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            "lineCount": 93,
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            "tags": "lasso-settings"
        },
        {
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            "id": "code4TqlnK",
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            "type": "code",
            "evaluator": "HTML",
            "input": {
                "body": [
                    "<div class=\"lasso_control\">",
                    "",
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                    "<button type=\"button\" class=\"btn btn-info\" style=\"font-size:larger; color: #ffffff; font-weight: bold;\" onclick='run_lasso()'>RUN</button>",
                    "",
                    "<button type=\"button\" class=\"btn btn-default\" style=\"font-size:larger;\" onclick='reset_lasso()' >Reset</button>",
                    "",
                    "<label title=\"This button becomes active when the",
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                    "run is finished. By clicking it, an interactive plot of the first 2",
                    "dimensions of the optimized descriptor will be opened\"> ",
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                    "<a href=\"#\" target=\"_blank\" class=\"btn btn-primary disabled\" style=\"font-size:larger;\" id=\"lasso_result_button\" >View interactive 2D scatter plot</a> </label>",
                    "  </div>"
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                ],
                "hidden": true
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            },
            "output": {
                "state": {},
                "result": {
                    "type": "BeakerDisplay",
                    "innertype": "Html",
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                    "object": "<script>\nvar beaker = bkHelper.getBeakerObject().beakerObj;\n</script>\n<div class=\"lasso_control\">\n\n<button type=\"button\" class=\"btn btn-info\" style=\"font-size:larger; color: #ffffff; font-weight: bold;\" onclick=\"run_lasso()\">RUN</button>\n\n<button type=\"button\" class=\"btn btn-default\" style=\"font-size:larger;\" onclick=\"reset_lasso()\">Reset</button>\n\n<label title=\"This button becomes active when the\nrun is finished. By clicking it, an interactive plot of the first 2\ndimensions of the optimized descriptor will be opened\"> \n<a href=\"#\" target=\"_blank\" class=\"btn btn-primary disabled\" style=\"font-size:larger;\" id=\"lasso_result_button\">View interactive 2D scatter plot</a> </label>\n  </div>"
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                },
                "selectedType": "BeakerDisplay",
                "elapsedTime": 0,
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                "height": 84
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            "evaluatorReader": true,
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            "lineCount": 11
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        },
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        {
            "id": "code0sZSEt",
            "type": "code",
            "evaluator": "HTML",
            "input": {
                "body": [
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                    "<p style=\"text-align: left; color: #aa3311; font-weight: 900; font-size: 20pt;\"> Note</p>",
                    "<p style=\"text-align: left; color: #aa3311; font-weight: 400; font-size: 16pt;\"> You will automatically generate atomic descriptors, select an <i>optimal combination</i> among <i>millions or billions</i> of candidates, and produce a <i>fully-interactive plot</i> of your results. <br>",
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                    "With the Default settings you will reproduce our publication cited above.  <br>",
                    "Please understand that the whole procedure may take a few moments.</p>"
                ],
                "hidden": true
            },
            "output": {
                "state": {},
                "result": {
                    "type": "BeakerDisplay",
                    "innertype": "Html",
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                    "object": "<script>\nvar beaker = bkHelper.getBeakerObject().beakerObj;\n</script>\n<p style=\"text-align: left; color: #aa3311; font-weight: 900; font-size: 20pt;\"> Note</p>\n<p style=\"text-align: left; color: #aa3311; font-weight: 400; font-size: 16pt;\"> You will automatically generate atomic descriptors, select an <i>optimal combination</i> among <i>millions or billions</i> of candidates, and produce a <i>fully-interactive plot</i> of your results. <br>\nWith the Default settings you will reproduce our publication cited above.  <br>\nPlease understand that the whole procedure may take a few moments.</p>"
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                },
                "selectedType": "BeakerDisplay",
                "elapsedTime": 0,
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                "height": 261
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            },
            "evaluatorReader": true,
            "lineCount": 4
        },
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        {
            "id": "codemBpYu9",
            "type": "code",
            "evaluator": "IPython",
            "input": {
                "body": [
                    "import random",
                    "import string",
                    "import os",
                    "import __builtin__",
                    "__builtin__.isBeaker = True",
                    "",
                    "dict_feat = {",
                    "    'period':['period(A)','period(B)'],",
                    "    'atomic_number':['Z(A)', 'Z(B)'],",
                    "    'atomic_r_by_2_dimer':['d(A)', 'd(B)'],",
                    "    'atomic_ionization_potential':['IP(A)', 'IP(B)'],",
                    "    'atomic_electron_affinity':['EA(A)', 'EA(B)'],",
                    "    'atomic_rs_max':['r_s(A)', 'r_s(B)'],",
                    "    'atomic_rp_max':['r_p(A)', 'r_p(B)'],",
                    "    'atomic_rd_max':['r_d(A)', 'r_d(B)']",
                    "}",
                    "",
                    "feature_list = [f for f_li in beaker.selected_feature_list for f in dict_feat[f_li]]",
                    "",
                    "random_name = 'AA_'+''.join(random.SystemRandom().choice(string.ascii_uppercase + string.digits) for _ in range(20))",
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                    "kube_namespace = os.environ.get('KUBE_NAMESPACE','default')",
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                    "IP = 'sisso-img.%s.svc.cluster.local' %kube_namespace",
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                    "PORT = 22",
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                    "### Settings",
                    "#1) Local paths",
                    "Local_paths = {",
                    "    'local_path' : '/home/beaker/',",
                    "    'SIS_input_folder_name' : random_name,",
                    "}",
                    "",
                    "#2) for ssh connection",
                    "Remote_run = {",
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                    "    'mpi_command':'mpirun -np 5',",
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                    "    'remote_path' : '/home/tutorial/',",
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                    "    'SIS_code_path' : '/home/tutorial/src/',",
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                    "    'hostname' : IP,",
                    "    'port' : PORT,",
                    "    'username' : 'tutorial',",
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                    "    'key_file' : \"/home/keys/4Sofj9D3I1kc03E39k1fIPO9w9A03N5Z\"",
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                    "}",
                    "",
                    "#3) SIS parameters",
                    "Parameters = {",
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                    "    'rung' :int(beaker.n_comb),",
                    "    'opset' : beaker.allowed_operations,",
                    "    'desc_dim' : int(beaker.max_dim),",
                    "    'subs_sis' : int(beaker.n_sis),",
                    "    'ptype': 'quanti'",
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                    "}",
                    "sis_control = {'local_paths':Local_paths, 'remote_run':Remote_run, 'parameters':Parameters}",
                    "",
                    "",
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                    "",
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                    ""
                ],
                "hidden": true
            },
            "output": {
                "state": {},
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                "selectedType": "Results",
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                "pluginName": "IPython",
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                "shellId": "62DB60DEBBBE4180B24CAB69D52EE574",
                "elapsedTime": 1617
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            },
            "evaluatorReader": true,
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            "lineCount": 70,
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            "tags": "calc_cell"
        },
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        {
            "id": "code75Jsw6",
            "type": "code",
            "evaluator": "IPython",
            "input": {
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                    "]",
                    ""
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                ],
                "hidden": true
            },
            "output": {
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                "state": {},
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                "selectedType": "BeakerDisplay",
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                "pluginName": "IPython",
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                "shellId": "62DB60DEBBBE4180B24CAB69D52EE574",
                "elapsedTime": 519
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            },
            "evaluatorReader": true,
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            "lineCount": 427,
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            "tags": "calc_cell"
        },
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        {
            "id": "codeLARUgI",
            "type": "code",
            "evaluator": "IPython",
            "input": {
                "body": [
                    "from nomad_sim.wrappers import get_json_list, calc_descriptor ",
                    "from nomad_sim.wrappers import calc_model, calc_embedding, plot",
                    "from nomad_sim.utils_crystals import create_supercell",
                    "from nomad_sim.utils_crystals import create_vacancies",
                    "from nomad_sim.utils_crystals import random_displace_atoms",
                    "from nomad_sim.utils_crystals import substitute_atoms",
                    "from nomad_sim.descriptors import XrayDiffraction",
                    "from nomad_sim.utils_crystals import create_supercell",
                    "",
                    "# hack to change to local/Beaker mode in all files in the packages",
                    "# DEPRECATED",
                    "import __builtin__",
                    "__builtin__.isBeaker = True",
                    "",
                    "import hashlib",
                    "",
                    "import sys, os",
                    "import pandas as pd",
                    "import numpy as np",
                    "import json",
                    "",
                    "",
                    "# define paths",
                    "tmp_folder = '/home/beaker/.beaker/v1/web/tmp/'",
                    "control_file = '/home/beaker/.beaker/v1/web/tmp/control.json'",
                    "data_folder='/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT'",
                    "data_folder='/parsed/prod-017/FhiAimsParser2.0.0/RdUzye8EKmv-z4LGNHGTSk8S3S1WY'",
                    "lookup_file = '/home/beaker/.beaker/v1/web/tmp/lookup.dat'",
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                    "collection_path = '/home/beaker/test/nomad_sim/data_zcrs/ExtendedBinaries_Dimers_Atoms_new.json'",
                    "path_to_collection = '/home/beaker/test/nomad_sim/data_zcrs/ExtendedBinaries_Dimers_Atoms_new.json'",
                    "",
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                    "",
                    "",
                    "",
                    "",
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                    "structures_diff =  ['RS-ZB', 'CsCl-ZB', 'NiAs-ZB', 'CrB-ZB'][int(beaker.structures_diff)]",
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                    " ",
                    "if structures_diff == 'RS-ZB':",
                    "    spacegroup_tuples = [(225, 221), (216, 227)]",
                    "    json_list = json_list_RS + json_list_ZB",
                    "    legend_title='Reference E(RS)-E(ZB)'",
                    "    target_name='E(RS)-E(ZB)'",
                    "elif structures_diff == 'CsCl-ZB':",
                    "    spacegroup_tuples = [(229, 221), (216, 227)]",
                    "    json_list = json_list_CsCl + json_list_ZB",
                    "    legend_title='Reference E(CsCl)-E(ZB)'",
                    "    target_name='E(CsCl)-E(ZB)'",
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                    "elif structures_diff == 'NiAs-ZB':",
                    "    spacegroup_tuples = [(194, 1), (216, 227)]",
                    "    json_list = json_list_NiAs + json_list_ZB",
                    "    legend_title='Reference E(NiAs)-E(ZB)'",
                    "    target_name='E(NiAs)-E(ZB)'",
                    "elif structures_diff == 'CrB-ZB':",
                    "    spacegroup_tuples = [(63, 139), (216, 227)]",
                    "    json_list = json_list_CrB + json_list_ZB",
                    "    legend_title='Reference E(CrB)-E(ZB)'",
                    "    target_name='E(CrB)-E(ZB)'",
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                    "    ",
                    "if beaker.units == 'eV_angstrom':",
                    "    energy_unit = 'eV'",
                    "    length_unit = 'angstrom'",
                    "elif beaker.units == 'J_m':",
                    "    energy_unit = 'J'",
                    "    length_unit = 'm'",
                    "elif beaker.units == 'kcal/mol_angstrom':",
                    "    energy_unit = 'kcal/mol'",
                    "    length_unit = 'angstrom'",
                    "",
                    "operations_on_structure = [(create_supercell, {'replicas': [3, 3, 3]})]",
                    "op_list = np.zeros(len(json_list))",
                    "kwargs = {'path_to_collection': path_to_collection,",
                    "          'feature_order_by': 'atomic_mulliken_electronegativity',",
                    "          'energy_unit': energy_unit,",
                    "          'length_unit': length_unit}",
                    "",
                    "",
                    "descriptor = calc_descriptor(",
                    "    desc_type='atomic_features',",
                    "    selected_feature_list=beaker.selected_feature_list,",
                    "    op_list=op_list,",
                    "    operations_on_structure=operations_on_structure,",
                    "    json_list=json_list, tmp_folder=tmp_folder,",
                    "    spacegroup_tuples=spacegroup_tuples,",
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                    "    take_first=False,",
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                    "    **kwargs)",
                    ""
                ],
                "hidden": true
            },
            "output": {
                "state": {},
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                "selectedType": "BeakerDisplay",
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                "pluginName": "IPython",
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                "shellId": "62DB60DEBBBE4180B24CAB69D52EE574",
                "elapsedTime": 6228,
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                "height": 1206
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            },
            "evaluatorReader": true,
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            "lineCount": 86,
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            "tags": "calc_cell"
        },
        {
            "id": "codeo2yP7p",
            "type": "code",
            "evaluator": "IPython",
            "input": {
                "body": [
                    "",
                    "calc_model(method='SIS', desc_type='atomic_features',",
                    "    sis_control=sis_control, allowed_operations = ['+','-','/','|-|','exp','^2'],",
                    "    tmp_folder=tmp_folder, lookup_file=lookup_file, control_file=control_file,",
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                    "    energy_unit=energy_unit, length_unit=length_unit)"
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                ],
                "hidden": true
            },
            "output": {
                "state": {},
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                "selectedType": "BeakerDisplay",
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                "pluginName": "IPython",
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                "shellId": "62DB60DEBBBE4180B24CAB69D52EE574",
                "elapsedTime": 1336,
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                "height": 56
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            },
            "evaluatorReader": true,
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            "lineCount": 5,
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            "tags": "calc_cell"
        },
        {
            "id": "code7NKF5Q",
            "type": "code",
            "evaluator": "IPython",
            "input": {
                "body": [
                    "parameter_list = beaker.selected_feature_list",
                    "parameter_list.append(beaker.allowed_operations)",
                    "name_html_page = hashlib.sha224(str(parameter_list)).hexdigest()[:16]",
                    "",
                    "",
                    "json_list, frame_list, x_list, y_list, target_list, target_pred_list = get_json_list(method='file', data_folder=data_folder,",
                    "    path_to_file=lookup_file, drop_duplicates=False, displace_duplicates=True, predicted_value=True)",
                    "beaker.viewer_result = name_html_page",
                    "",
                    "",
                    "plot_result = plot(name=name_html_page, json_list=json_list, frames='list', frame_list=frame_list, ",
                    "    file_format='NOMAD', clustering_x_list=x_list, clustering_y_list=y_list, target_list=target_list,",
                    "    target_unit=energy_unit, legend_title=legend_title, target_name=target_name,",
                    "    target_pred_list=target_pred_list,",
                    "    plot_title='SIS+L0 structure map',",
                    "    clustering_point_size=12, tmp_folder=tmp_folder, control_file=control_file,",
                    "    op_list=op_list, operations_on_structure=operations_on_structure)"
                ],
                "hidden": true
            },
            "output": {
                "state": {},
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                "selectedType": "BeakerDisplay",
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                "height": 56,
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                "pluginName": "IPython",
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                "shellId": "62DB60DEBBBE4180B24CAB69D52EE574",
                "elapsedTime": 4949
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            },
            "evaluatorReader": true,
            "lineCount": 17,
            "tags": "calc_cell"
        },
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        {
            "id": "codeSiTCyt",
            "type": "code",
            "evaluator": "HTML",
            "input": {
                "body": [
                    "<h3 style=\"margin-top: 0;\">Feedback</h3>",
                    "<p>Want to give feedback?<br /><br />",
                    " <a target=\"_blank\" href=\"https://nomad-forum.rz-berlin.mpg.de\" class=\"btn btn-primary\" style=\"font-size: larger\">Send your feedback to the analytics-toolkit forum</a>",
                    "</p>",
                    "<p>Your comments are invaluable in helping us to provide a user-friendly experience for all!<p>"
                ],
                "hidden": true
            },
            "output": {
                "state": {},
                "selectedType": "BeakerDisplay",
                "elapsedTime": 0,
                "height": 245
            },
            "evaluatorReader": true,
            "lineCount": 5
        },
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        {
            "id": "codeoorGVf",
            "type": "code",
            "evaluator": "JavaScript",
            "input": {
                "body": [
                    "var result_link = '/user/tmp/' + beaker.viewer_result + '.html';",
                    "beaker.view_result(result_link);"
                ],
                "hidden": true
            },
            "output": {
                "state": {},
                "selectedType": "BeakerDisplay",
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                "height": 56,
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                "pluginName": "JavaScript",
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                "elapsedTime": 56
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            },
            "evaluatorReader": true,
            "lineCount": 2,
            "tags": "calc_cell"
        }
    ],
    "namespace": {
        "selected_feature_list": [
            "atomic_ionization_potential",
            "atomic_electron_affinity",
            "atomic_rs_max",
            "atomic_rp_max",
            "atomic_rd_max"
        ],
        "allowed_operations": [
            "+",
            "|-|",
            "/",
            "^2",
            "exp"
        ],
        "max_dim": "2",
        "ncomb": "1",
        "n_sis": "10",
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        "n_comb": "3",
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        "viewer_result": "6edb65b9776deeb2",
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        "structures_diff": "0",
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        "units": "eV_angstrom"
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    },
    "locked": true
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}