diff --git a/beaker-notebooks/sisso-metal-nonmetal.bkr b/beaker-notebooks/sisso-metal-nonmetal.bkr
index 2c785730d53d7a709a7b7a82117244d690035e30..c9c9237038e9fd3d63f109ba1492be68e0f04631 100644
--- a/beaker-notebooks/sisso-metal-nonmetal.bkr
+++ b/beaker-notebooks/sisso-metal-nonmetal.bkr
@@ -107,7 +107,7 @@
" 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>",
- " <span class=\"nomad--last-updated\" data-version=\"v1.0.0\">[Last updated: October 20, 2017]</span>",
+ " <span class=\"nomad--last-updated\" data-version=\"v1.0.0\">[Last updated: November 9, 2017]</span>",
" </p>",
"</div>",
"",
@@ -124,11 +124,11 @@
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+ "height": 368,
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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 the metal-insulator classification of elements and binary systems</h3>\n <p class=\"nomad--description\">\n created by:\n Emre Ahmetcik<sup>1</sup>,\n Angelo Ziletti<sup> 1</sup>,\n Runhai Ouyang<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 20, 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"
+ "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 the metal-insulator classification of elements and binary systems</h3>\n <p class=\"nomad--description\">\n created by:\n Emre Ahmetcik<sup>1</sup>,\n Angelo Ziletti<sup> 1</sup>,\n Runhai Ouyang<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: November 9, 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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@@ -141,12 +141,12 @@
"body": [
"### Introduction ",
"",
- "This tutorial shows how to find descriptive parameters (short formulas) for the classification of materials properties. As an example we adress the classification of elements and binary systems into metals and non metals using experimental data extracted from the SpringerMaterials data base. The method is based on the algorithm sure independence screening and sparsifying operator (SISSO), that enables to search for optimal descriptor by scanning huge feature spaces.",
+ "This tutorial shows how to find descriptive parameters (short formulas) for the classification of materials properties. As an example, we address the classification of elemental and binary systems A$_x$B$_y$ into metals and non metals using experimental data extracted from the SpringerMaterials data base. The method is based on the algorithm <u>s</u>ure <i><u>i</u>ndependence <u>s</u>creening and <u>s</u>parsifying <u>o</u>perator</i> (SISSO), which enables to search for optimal descriptors by scanning huge feature spaces. ",
" <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=\"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> .",
"</div>",
- " 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.",
+ " Click first <b>Reference settings</b> and afterwards <b>RUN</b> to reproduce the results from this publication; click <b>Background</b> for an explanation of the approach; or, modify <b>Settings</b> to produce your own results.",
"",
"<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."
],
@@ -166,11 +166,19 @@
" </div>",
" <div class=\"modal-body modal-credits-body\">",
"",
- " <p>We present a tool for predicting the metal-insulator classification of elements and binary systems, by using a set of descriptive parameters (a descriptor) based on free-atom data of the atomic species constituting the elemental/binary materials as well as a unit cell dependentent packing parameter (the normalized ratio between the volume of spherical atoms and the unit cell). The data is extracted from the <a href=\" http://materials.springer.com/\">SpringerMaterials</a> data base. 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. In this tutorial an $\\ell_0$-optimization is used as the sparsifying operator. The method is described in:",
+ " <p>We present a tool for predicting the metal-insulator classification of elemental and binary systems, by using a set of descriptive parameters (a descriptor) based on free-atom data of the atomic species constituting the elemental/binary materials as well as a unit cell dependentent packing parameter (the normalized ratio between the volume of spherical atoms and the unit cell). The data is extracted from the <a href=\" http://materials.springer.com/\">SpringerMaterials</a> data base. 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. In this tutorial an $\\ell_0$-optimization is used as the sparsifying operator. 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=\" https://arxiv.org/abs/1710.03319\">https://arxiv.org/abs/1710.03319</a> (2017). <br>",
"</div>",
+ "By running the tutorial with the reference settings ( click <b>Reference settings</b> , then <b>RUN</b>) the results of this publication can be recovered. In particular, by clicking on “View interactive 2D plot”, an interactive classification map (a chart where metals and non metals are separated into different regions of a low-dimensional representation, here two dimensional) will be opened in a new tab, similar to the following ( Fig. 3. (a) in <a href=\" https://arxiv.org/abs/1710.03319\">https://arxiv.org/abs/1710.03319</a>):",
+ "<center>",
+ "<figure>",
+ "<img src=\"/user/SISSO-binaries-metal-nonmetal.png\" style=\"width:60%;height:60%\" >",
+ "<figcaption>An almost perfect classification (99.2\\%) of metal/non metal for 363 materials (299 binaries and 64 elements (A=B)). Symbols: $\\chi$ Pauling electronegativity, $IE$ ionization energy, $x$ atomic composition, $\\sum V_{\\text{ atom}}/V_{\\text{ cell}}$ packing factor. Red circles, blue squares, and open blue squares represent metals, non-metals, and the three erroneously characterized non-metals, respectively.</figcaption>",
+ "<figure>",
+ "</center>",
"</p>",
+ "",
"<p>SISSO($\\ell_0$) for classification seeks in an iterative approach for that desriptor in whose space the overlap between class domains is minimal, where a class domain is represented by the convex hull of the training data. In the first iteration, a number $k$ of features is collected which seperate the convex hulls best. The feature with the lowest domain overlap is simply the 1D descriptor. In the next iteration, a new set of $k$ features is selected, now as those seperating the unclassified data from the first iteration best. The 2D descriptor is the pair of features that yield the smallest overlap region, among all possible pairs contained in the union of the sets selected in this and the first iteration. In each next iteration new set of $k$ features is extracted as those that separate the unclassified data from the previous step best. The $n$D descriptor is the $n$-tuple of features that yield the smallest convex hull overlap regions, among all possible $n$-tuples contained in the union of the sets obtained in each new iteration and all the previous iterations. ",
"</p>",
"",
@@ -258,6 +266,21 @@
" e.style.display = 'block';",
" b.style.display = 'inline';",
"};",
+ " ",
+ "var settings_for_paper = function(){",
+ " document.getElementById('n_comb').value=\"3\";",
+ " document.getElementById('n_sis').value=\"3700\";",
+ " var ids = [\"+\", \"-\", \"|-|\", \"*\", \"/\", \"^-1\", \"^2\", \"^3\", \"sqrt\", \"exp\", \"exp-\", \"log\", \"SCD\", \"IE\", \"Xp\", \"x\", \"IPF\"];",
+ " var ids_unchecked = [\"exp-\", \"SCD\"];",
+ " for (i=0;i<ids.length;i++){",
+ " if (ids_unchecked.includes(ids[i])) {",
+ " document.getElementById(ids[i]).checked = false;",
+ " } else {",
+ " document.getElementById(ids[i]).checked = true;",
+ " }",
+ " }",
+ "};",
+ " ",
"var getFeatures = function() {",
" beaker.selected_feature_list = [];",
" $('#lasso_features_select input:checkbox').each(function () {",
@@ -303,95 +326,16 @@
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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>"
- },
- "elapsedTime": 0
- },
- "evaluatorReader": true,
- "lineCount": 59
- },
- {
- "id": "codePjdM5h",
- "type": "code",
- "evaluator": "HTML",
- "input": {
- "body": [
- "<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.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>"
- ],
- "hidden": true
- },
- "output": {
- "state": {},
- "selectedType": "BeakerDisplay",
- "height": 50,
+ "height": 81,
"result": {
"type": "BeakerDisplay",
"innertype": "Html",
- "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>"
+ "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};\n \nvar settings_for_paper = function(){\n document.getElementById('n_comb').value=\"3\";\n document.getElementById('n_sis').value=\"3700\";\n var ids = [\"+\", \"-\", \"|-|\", \"*\", \"/\", \"^-1\", \"^2\", \"^3\", \"sqrt\", \"exp\", \"exp-\", \"log\", \"SCD\", \"IE\", \"Xp\", \"x\", \"IPF\"];\n var ids_unchecked = [\"exp-\", \"SCD\"];\n for (i=0;i<ids.length;i++){\n if (ids_unchecked.includes(ids[i])) {\n document.getElementById(ids[i]).checked = false;\n } else {\n document.getElementById(ids[i]).checked = true;\n }\n }\n};\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>"
},
"elapsedTime": 0
},
"evaluatorReader": true,
- "lineCount": 56
+ "lineCount": 74
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{
"id": "lasso-settings-cell",
@@ -411,10 +355,10 @@
"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=\"IE\" CHECKED > <span title=\"Atomic ionization energy\"><i>IE</i> </span></label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"Xp\" CHECKED > <span title=\"Pauling electronegativity\"> <i>χ</i><sub>p</sub></span></label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"x\" CHECKED > <span title=\"Atomic composition\"> <i>x</i> </span> </label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"IPF\" CHECKED > <span title=\"Inverse packing factor: Vcell/Σ Vatom\"> <i>IPF</i> </span> </label>",
+ " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"IE\" id=\"IE\" CHECKED > <span title=\"Atomic ionization energy\"><i>IE</i> </span></label>",
+ " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"Xp\" id=\"Xp\" CHECKED > <span title=\"Pauling electronegativity\"> <i>χ</i><sub>p</sub></span></label>",
+ " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"x\" id=\"x\" CHECKED > <span title=\"Atomic composition\"> <i>x</i> </span> </label>",
+ " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"IPF\" id=\"IPF\" CHECKED > <span title=\"Inverse packing factor (IPF): Vcell/Σ Vatom\"> Inverse packing factor </span> </label>",
" </div>",
" </form>",
" </div> <!-- End of row-->",
@@ -423,19 +367,19 @@
" Given features x and y, apply these operations for feature space construction:</p>",
" <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=\"-\" CHECKED > 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=\"*\" CHECKED > 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=\"^-1\" CHECKED > 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\" CHECKED > x^3 </label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-1\"> <input type=\"checkbox\" value=\"sqrt\" CHECKED > √<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\" CHECKED > 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>",
+ " <label class =\"col-xs-4 col-md-4 col-lg-1\"> <input type=\"checkbox\" value=\"+\" id=\"+\" CHECKED > x+y </label>",
+ " <label class =\"col-xs-4 col-md-4 col-lg-1\"> <input type=\"checkbox\" value=\"-\" id=\"-\" CHECKED > x-y </label>",
+ " <label class =\"col-xs-4 col-md-4 col-lg-1\"> <input type=\"checkbox\" value=\"|-|\" id=\"|-|\" CHECKED > |x-y| </label>",
+ " <label class =\"col-xs-4 col-md-4 col-lg-1\"> <input type=\"checkbox\" value=\"*\" id=\"*\" CHECKED > x · y </label>",
+ " <label class =\"col-xs-4 col-md-4 col-lg-1\"> <input type=\"checkbox\" value=\"/\" id=\"/\" CHECKED > x/y </label>",
+ " <label class =\"col-xs-4 col-md-4 col-lg-1\"> <input type=\"checkbox\" value=\"^-1\" id=\"^-1\" CHECKED > x^(-1) </label>",
+ " <label class =\"col-xs-4 col-md-4 col-lg-1\"> <input type=\"checkbox\" value=\"^2\" id=\"^2\" CHECKED > x^2 </label>",
+ " <label class =\"col-xs-4 col-md-4 col-lg-1\"> <input type=\"checkbox\" value=\"^3\" id=\"^3\" CHECKED > x^3 </label>",
+ " <label class =\"col-xs-4 col-md-4 col-lg-1\"> <input type=\"checkbox\" value=\"sqrt\" id=\"sqrt\" CHECKED > √<span style=\"text-decoration: overline\">x</span> </label>",
+ " <label class =\"col-xs-4 col-md-4 col-lg-1\"> <input type=\"checkbox\" value=\"exp\" id=\"exp\" CHECKED > exp(x) </label>",
+ " <label class =\"col-xs-4 col-md-4 col-lg-1\"> <input type=\"checkbox\" value=\"exp-\" id=\"exp-\" > exp(-x) </label>",
+ " <label class =\"col-xs-4 col-md-4 col-lg-1\"> <input type=\"checkbox\" value=\"log\" id=\"log\" CHECKED > log(x) </label>",
+ " <label class =\"col-xs-4 col-md-4 col-lg-1\"> <input type=\"checkbox\" value=\"SCD\" id=\"SCD\" > <span title=\"Standard Cauchy distribution\"> SCD </span> </label>",
" </div> ",
" </form>",
" </div> <!-- End of row-->",
@@ -460,6 +404,10 @@
"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>",
+ "<div class=\"lasso_control\">",
+ "<button type=\"button\" class=\"btn btn-default\" style=\"font-size:larger;\" onclick='settings_for_paper()' title=\"This button sets the settings for reproducing the result of the reference publication.\">Reference settings</button>",
+ " <p style=\"color: red; font-weight: 900; font-size: 15pt; display:inline;\" > WARNING:</p><p style=\"color: red; font-weight: 900; font-size: 11pt; display:inline;\"> with these settings, the calculations will take 40 min.</p>",
"</div>"
],
"hidden": true
@@ -467,16 +415,16 @@
"output": {
"state": {},
"selectedType": "BeakerDisplay",
- "height": 329,
+ "height": 386,
"result": {
"type": "BeakerDisplay",
"innertype": "Html",
- "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\">\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=\"IE\" checked=\"\" type=\"checkbox\"> <span title=\"Atomic ionization energy\"><i>IE</i> </span></label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"Xp\" checked=\"\" type=\"checkbox\"> <span title=\"Pauling electronegativity\"> <i>χ</i><sub>p</sub></span></label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"x\" checked=\"\" type=\"checkbox\"> <span title=\"Atomic composition\"> <i>x</i> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"IPF\" checked=\"\" type=\"checkbox\"> <span title=\"Inverse packing factor: Vcell/Σ Vatom\"> <i>IPF</i> </span> </label>\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=\"-\" checked=\"\" 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=\"*\" checked=\"\" 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\" checked=\"\" 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\" checked=\"\" type=\"checkbox\"> x^3 </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"sqrt\" checked=\"\" 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\" checked=\"\" 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 </p>\n \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=\"3701\" value=\"10\" step=\"100\" type=\"number\"> </p>\n\n </div><!-- End of row-->\n\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>"
+ "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\">\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=\"IE\" id=\"IE\" checked=\"\" type=\"checkbox\"> <span title=\"Atomic ionization energy\"><i>IE</i> </span></label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"Xp\" id=\"Xp\" checked=\"\" type=\"checkbox\"> <span title=\"Pauling electronegativity\"> <i>χ</i><sub>p</sub></span></label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"x\" id=\"x\" checked=\"\" type=\"checkbox\"> <span title=\"Atomic composition\"> <i>x</i> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"IPF\" id=\"IPF\" checked=\"\" type=\"checkbox\"> <span title=\"Inverse packing factor (IPF): Vcell/Σ Vatom\"> Inverse packing factor </span> </label>\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=\"+\" id=\"+\" checked=\"\" type=\"checkbox\"> x+y </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"-\" id=\"-\" checked=\"\" type=\"checkbox\"> x-y </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"|-|\" id=\"|-|\" checked=\"\" type=\"checkbox\"> |x-y| </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"*\" id=\"*\" checked=\"\" type=\"checkbox\"> x · y </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"/\" id=\"/\" checked=\"\" type=\"checkbox\"> x/y </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"^-1\" id=\"^-1\" checked=\"\" type=\"checkbox\"> x^(-1) </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"^2\" id=\"^2\" checked=\"\" type=\"checkbox\"> x^2 </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"^3\" id=\"^3\" checked=\"\" type=\"checkbox\"> x^3 </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"sqrt\" id=\"sqrt\" checked=\"\" 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\" id=\"exp\" checked=\"\" type=\"checkbox\"> exp(x) </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"exp-\" id=\"exp-\" type=\"checkbox\"> exp(-x) </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"log\" id=\"log\" checked=\"\" type=\"checkbox\"> log(x) </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"SCD\" id=\"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 </p>\n \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=\"3701\" value=\"10\" step=\"100\" type=\"number\"> </p>\n\n </div><!-- End of row-->\n\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>\n<div class=\"lasso_control\">\n<button type=\"button\" class=\"btn btn-default\" style=\"font-size:larger;\" onclick=\"settings_for_paper()\" title=\"This button sets the settings for reproducing the result of the reference publication.\">Reference settings</button>\n <p style=\"color: red; font-weight: 900; font-size: 15pt; display:inline;\"> WARNING:</p><p style=\"color: red; font-weight: 900; font-size: 11pt; display:inline;\"> with these settings, the calculations will take 40 min.</p>\n</div>"
},
- "elapsedTime": 1
+ "elapsedTime": 0
},
"evaluatorReader": true,
- "lineCount": 62,
+ "lineCount": 66,
"tags": "lasso-settings"
},
{
@@ -529,7 +477,7 @@
"output": {
"state": {},
"selectedType": "BeakerDisplay",
- "height": 261,
+ "height": 230,
"result": {
"type": "BeakerDisplay",
"innertype": "Html",
@@ -1009,8 +957,8 @@
"output": {
"state": {},
"pluginName": "IPython",
- "shellId": "5F3355B3A3C14E908F48D87B83D3C557",
- "elapsedTime": 333,
+ "shellId": "2A7DBBB3D82248578E9BD1E64633CA91",
+ "elapsedTime": 317,
"selectedType": "Hidden"
},
"evaluatorReader": true,
@@ -1116,7 +1064,7 @@
"results = sis.get_results()",
"Des, D_selected, overlap = results[-1]",
"print \"INFO: Identified descriptor: %s, %s\" %(Des[0], Des[1])",
- "print \"INFO: Number of samples in overlap region: %s\" %overlap"
+ "print \"INFO: Number of samples in the overlap region: %s\" %overlap"
],
"hidden": true
},
@@ -1163,8 +1111,8 @@
"name_html_page = hashlib.sha224(str(parameter_list)).hexdigest()[:16]",
"beaker.viewer_result_5_strucs = name_html_page",
"with open(tmp_folder+'output.log', 'w') as f:",
- " f.write(\"Descriptors: %s,%s \\nNumber of samples in overlap regions: %s\\nallowed_operations : %s\\nselected_feature_list : %s\\n\" ",
- " %(x_axis_label, y_axis_label, overlap,beaker.allowed_operations,selected_feature_list))",
+ " f.write(\"SETTINGS\\nPrimary features: %s \\nAllowed operations : %s\\nNumber of iterations for the construction for the feature space: %s\\nNumber of collected features per SIS iteration: %s\\n\\nOUTPUT\\nDescriptor: %s,%s \\nNumber of samples in the overlap region: %s\" ",
+ " %(selected_feature_list, beaker.allowed_operations, beaker.n_comb, beaker.n_sis, x_axis_label, y_axis_label, overlap))",
"",
"",
"# plot",
@@ -1177,8 +1125,7 @@
" plot_convex_hull=True, is_classification=True,",
" x_axis_label=x_axis_label, y_axis_label=y_axis_label, plot_title=plot_title,",
" tmp_folder=tmp_folder)"
- ],
- "hidden": true
+ ]
},
"output": {
"state": {},
@@ -1237,8 +1184,8 @@
],
"max_dim": null,
"ncomb": "1",
- "n_sis": "201",
- "n_comb": "3",
+ "n_sis": "20",
+ "n_comb": "1",
"viewer_result": "6edb65b9776deeb2",
"structures_diff": null,
"units": "eV_angstrom",
diff --git a/example-data/SISSO/SISSO-binaries-metal-nonmetal.png b/example-data/SISSO/SISSO-binaries-metal-nonmetal.png
new file mode 100644
index 0000000000000000000000000000000000000000..9fecd3703cc6d449e4396962ccde0846e5d5360f
Binary files /dev/null and b/example-data/SISSO/SISSO-binaries-metal-nonmetal.png differ