diff --git a/beaker-notebooks/Embedding.bkr b/beaker-notebooks/Embedding.bkr
index b8fa97cffcbc5c72dfd10593a74f33390a91212a..be4f5a372b667f4aa8c43fd3880aa87add1d9ee3 100644
--- a/beaker-notebooks/Embedding.bkr
+++ b/beaker-notebooks/Embedding.bkr
@@ -373,18 +373,44 @@
"output": {
"selectedType": "BeakerDisplay",
"outputArrived": true,
- "elapsedTime": 0,
+ "elapsedTime": 1,
"state": {},
"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 getEmbedMethod();\n getStandardize();\n getUnits();\n beaker.evaluate(\"lasso_cell\"); // evaluate cells with tag \"lasso_cell\"\n // view_result()\n};\nvar reset_lasso = function(){\n beaker.evaluate(\"lasso_gui\");\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};\n \nvar getUnits = function() {\n beaker.units = $(\"#units_select\").val();\n};\n \nvar getEmbedMethod = function() {\n beaker.embed_method = \"pca\";\n $('#embed_method_selector input:radio').each(function () {\n if(this.checked )\n beaker.embed_method = this.value;\n });\n};\n \nvar getStandardize = function() {\n beaker.standardize = \"yes\";\n $('#standardize input:radio').each(function () {\n if(this.checked )\n beaker.standardize = this.value;\n });\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</script>\n<style type=\"text/css\">\n label {\n font-size: 18px;\n }\n .lasso_control{\n font-size: 18px;\n } \n.lasso_form_group input {\n width: 15px;\n height: 15px;\n padding: 0;\n margin:0;\n padding-right:5px; \n vertical-align: bottom;\n top: -1px;\n} \n .lasso_selection_description{\n padding: 10px 15px;\n }\n</style>\n<div class=\"lasso_control\">\n <div class=\"row\">\n <p class=\"lasso_selection_description\"><b>Primary features </b>\n (hover the mouse pointer 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_homo\" type=\"checkbox\"> <span title=\"Energy of highest occupied molecular orbital\"><i>E</i> <sub>HOMO</sub></span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-2\"> <input value=\"atomic_lumo\" type=\"checkbox\"> <span title=\"Energy of lowest unoccupied molecular orbital\"> <i>E</i> <sub>LUMO</sub> </span> </label>\n \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=\"atomic_number_valence_electrons\" type=\"checkbox\"> <span title=\"Number of valence electrons\"> <i>Z</i><sub>val</sub> </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 the dimer\"> <i>d</i> <sub>dimer</sub> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"atomic_electronic_binding_energy_dimer\" type=\"checkbox\"> <span title=\"Binding energy of the dimer\"> <i>E</i> <sub>b</sub> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"atomic_homo_lumo_diff\" type=\"checkbox\"> <span title=\"HOMO-LUMO gap of the dimer\"> Δ<i>E</i><sub>HL</sub> </span> </label>\n \n<!--- <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"Es/sqrt(Zval)\" > \n <span title=\"Energy of the valence s orbital(s) divided by the square root of the number of valence electrons. [Phys. Rev. B 85, 104104 (2012)]\"> <i>E</i><sub>s</sub>/sqrt(<i>Z</i> <sub>val</sub>) </span> </label>\n <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"Ep/sqrt(Zval)\" > \n <span title=\"Energy of the valence p orbital(s) divided by the square root of the number of valence electrons. [Phys. Rev. B 85, 104104 (2012)]\"> <i>E</i><sub>p</sub>/sqrt(<i>Z</i> <sub>val</sub>) </span> </label>\n--> \n </div>\n </form>\n </div> <!-- End of row-->\n \n <br>\n <div class=\"row\"> <!-- Start of row-->\n <p class=\"lasso_selection_description\"><b>Units of measurement: </b> \n <select id=\"units_select\">\n <option value=\"eV_angstrom\"> [energy]=eV; [length]=angstrom</option>\n <option value=\"J_m\"> [energy]=J; [length]=m</option>\n <option value=\"kcal/mol_angstrom\"> [energy]=kcal/mol; [length]=angstrom</option>\n </select> </p>\n </div><!-- End of row-->\n \n <br>\n <div class=\"row\"> <!-- Start of second row-->\n <div class=\"lasso_form_group\">\n <p class=\"lasso_selection_description\"><b>Embedding methods:</b> </p>\n <div id=\"embed_method_selector\">\n <label class=\"col-xs-4 col-md-4 col-lg-4\"><input name=\"inlineRadioOptions\" id=\"inlineRadio1\" value=\"pca\" checked=\"\" type=\"radio\"> Principal Compenent Analysis (PCA) [<a href=\"https://en.wikipedia.org/wiki/Principal_component_analysis\" target=\"_blank\">more info</a>]</label>\n <label class=\"col-xs-4 col-md-4 col-lg-4\"><input name=\"inlineRadioOptions\" id=\"inlineRadio2\" value=\"mds\" type=\"radio\"> Multidimensional scaling (MDS) [<a href=\"https://en.wikipedia.org/wiki/Multidimensional_scaling\" target=\"_blank\">more info</a>]</label>\n <label class=\"col-xs-4 col-md-4 col-lg-4\"><input name=\"inlineRadioOptions\" id=\"inlineRadio3\" value=\"tsne_pca\" type=\"radio\"> t-Distributed Stochastic Neighbor Embedding (t-SNE) [<a href=\"https://en.wikipedia.org/wiki/T-distributed_stochastic_neighbor_embedding\" target=\"_blank\">more info</a>]</label>\n </div> \n </div>\n </div><!-- End of row--> \n <div class=\"row\"> <!-- Start of second row-->\n <div class=\"lasso_form_group\">\n <p class=\"lasso_selection_description\"><b>Scale data to unit-variance:</b>\n (data are centered around the mean in any case) [<a href=\"https://en.wikipedia.org/wiki/Feature_scaling\" target=\"_blank\">more info</a>]</p>\n <div id=\"standardize\">\n <label class=\"col-xs-4 col-md-4 col-lg-4\"><input name=\"inlineRadioOptionsStandardize\" id=\"inlineRadio4\" value=\"True\" checked=\"\" type=\"radio\"> yes </label>\n <label class=\"col-xs-4 col-md-4 col-lg-4\"><input name=\"inlineRadioOptionsStandardize\" id=\"inlineRadio5\" value=\"False\" type=\"radio\"> no </label>\n </div> \n </div>\n </div><!-- End of row--> \n <br>\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 TWO-DIMENSIONAL EMBEDDING</button>\n <button class=\"btn btn-default\" onclick=\"reset_lasso()\">RESET</button>\n <label title=\"This button becomes active when the run is finished. By clicking it, an interactive structural-similarity plot will be opened\"> <a href=\"#\" target=\"_blank\" class=\"btn btn-primary disabled\" id=\"lasso_result_button\">View interactive 2D scatter plot</a> </label>\n</div> <!-- End of lasso_control -->\n"
},
- "height": 553
+ "height": 529
},
"evaluatorReader": true,
"lineCount": 137
},
+ {
+ "id": "codecuLX9f",
+ "type": "code",
+ "evaluator": "HTML",
+ "input": {
+ "body": [
+ "<p style=\"text-align: left; color: #aa3311; font-weight: 900; font-size: 18pt;\"> Note:</p>",
+ "<p style=\"text-align: left; color: #aa3311; font-weight: 400; font-size: 12pt;\"> you will automatically generate atomic descriptors, select an <i>optimal two-dimensional representation</i>, and produce a <i>fully-interactive plot</i> of your results. <br>",
+ "Please understand that the whole procedure may take a few moments.</p>"
+ ],
+ "hidden": true
+ },
+ "output": {
+ "state": {},
+ "result": {
+ "type": "BeakerDisplay",
+ "innertype": "Html",
+ "object": "<script>\nvar beaker = bkHelper.getBeakerObject().beakerObj;\n</script>\n<p style=\"text-align: left; color: #aa3311; font-weight: 900; font-size: 18pt;\"> Note:</p>\n<p style=\"text-align: left; color: #aa3311; font-weight: 400; font-size: 12pt;\"> you will automatically generate atomic descriptors, select an <i>optimal two-dimensional representation</i>, and produce a <i>fully-interactive plot</i> of your results. <br>\nPlease understand that the whole procedure may take a few moments.</p>"
+ },
+ "selectedType": "BeakerDisplay",
+ "elapsedTime": 0,
+ "height": 132
+ },
+ "evaluatorReader": true,
+ "lineCount": 3
+ },
{
"id": "code2uVtKX",
"type": "code",
@@ -436,12 +462,12 @@
"hidden": true
},
"output": {
- "selectedType": "BeakerDisplay",
+ "selectedType": "Results",
"state": {},
"pluginName": "IPython",
- "shellId": "DBE709AF38CB45F29ADDAF47FD4420DD",
+ "shellId": "3C0C9EAD06704422880A63E7DC6B1507",
"height": 103,
- "elapsedTime": 902
+ "elapsedTime": 5100
},
"evaluatorReader": true,
"lineCount": 41,
@@ -549,8 +575,8 @@
"state": {},
"selectedType": "Hidden",
"pluginName": "IPython",
- "shellId": "DBE709AF38CB45F29ADDAF47FD4420DD",
- "elapsedTime": 391
+ "shellId": "3C0C9EAD06704422880A63E7DC6B1507",
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},
"evaluatorReader": true,
"lineCount": 89,
@@ -602,8 +628,8 @@
"state": {},
"selectedType": "Results",
"pluginName": "IPython",
- "shellId": "DBE709AF38CB45F29ADDAF47FD4420DD",
- "elapsedTime": 14863,
+ "shellId": "3C0C9EAD06704422880A63E7DC6B1507",
+ "elapsedTime": 20562,
"height": 166
},
"evaluatorReader": true,
@@ -708,8 +734,8 @@
"state": {},
"selectedType": "Hidden",
"pluginName": "IPython",
- "shellId": "DBE709AF38CB45F29ADDAF47FD4420DD",
- "elapsedTime": 431,
+ "shellId": "3C0C9EAD06704422880A63E7DC6B1507",
+ "elapsedTime": 645,
"height": 78
},
"evaluatorReader": true,
@@ -738,9 +764,9 @@
"state": {},
"selectedType": "Results",
"pluginName": "IPython",
- "shellId": "DBE709AF38CB45F29ADDAF47FD4420DD",
+ "shellId": "3C0C9EAD06704422880A63E7DC6B1507",
"height": 78,
- "elapsedTime": 412
+ "elapsedTime": 690
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"evaluatorReader": true,
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@@ -775,9 +801,9 @@
"state": {},
"selectedType": "Results",
"pluginName": "IPython",
- "shellId": "DBE709AF38CB45F29ADDAF47FD4420DD",
+ "shellId": "3C0C9EAD06704422880A63E7DC6B1507",
"height": 78,
- "elapsedTime": 8127
+ "elapsedTime": 11773
},
"evaluatorReader": true,
"lineCount": 16,
@@ -811,7 +837,7 @@
"pluginName": "JavaScript",
"state": {},
"hidden": true,
- "elapsedTime": 84,
+ "elapsedTime": 92,
"height": 51
},
"evaluatorReader": true,
diff --git a/beaker-notebooks/LASSO_L0.bkr b/beaker-notebooks/LASSO_L0.bkr
index 8f245daf4b6f6adde31b7ed7d14b355659e3c6d1..83c5a201099d8b51bf3320f12959549a08762b61 100644
--- a/beaker-notebooks/LASSO_L0.bkr
+++ b/beaker-notebooks/LASSO_L0.bkr
@@ -67,7 +67,7 @@
},
"selectedType": "BeakerDisplay",
"elapsedTime": 0,
- "height": 316
+ "height": 330
},
"evaluatorReader": true,
"lineCount": 16
@@ -374,7 +374,7 @@
"result": {
"type": "BeakerDisplay",
"innertype": "Html",
- "object": "<script>\nvar beaker = bkHelper.getBeakerObject().beakerObj;\n</script>\n<div class=\"lasso_control\">\n\n <p style=\"margin-top: 1ex;\"></p>\n <button class=\"btn btn-default\" onclick=\"run_lasso()\" style=\"font-weight: bold;\">RUN</button> \n <div style=\"display: none;\" id=\"lasso-hidden-settings-button\"><button class=\"btn btn-default\" onclick=\"reset_lasso()\">RESET</button> </div>\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<div class=\"lasso_control\">\n\n <p style=\"margin-top: 1ex;\"></p>\n <button class=\"btn btn-default\" onclick=\"run_lasso()\" style=\"font-weight: bold;\">RUN</button> \n <div id=\"lasso-hidden-settings-button\"><button class=\"btn btn-default\" onclick=\"reset_lasso()\">RESET</button> </div>\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>"
},
"selectedType": "BeakerDisplay",
"elapsedTime": 0,
@@ -383,6 +383,33 @@
"evaluatorReader": true,
"lineCount": 10
},
+ {
+ "id": "codefWycat",
+ "type": "code",
+ "evaluator": "HTML",
+ "input": {
+ "body": [
+ "<p style=\"text-align: left; color: #aa3311; font-weight: 900; font-size: 18pt;\"> Note:</p>",
+ "<p style=\"text-align: left; color: #aa3311; font-weight: 400; font-size: 12pt;\"> you will automatically generate atomic descriptors</i>, select an <i>optimal combination</i> among <i>thousands</i> of candidates, and produce a <i>fully-interactive plot</i> of your results. <br>",
+ "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",
+ "object": "<script>\nvar beaker = bkHelper.getBeakerObject().beakerObj;\n</script>\n<p style=\"text-align: left; color: #aa3311; font-weight: 900; font-size: 18pt;\"> Note:</p>\n<p style=\"text-align: left; color: #aa3311; font-weight: 400; font-size: 12pt;\"> you will automatically generate atomic descriptors, select an <i>optimal combination</i> among <i>thousands</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>"
+ },
+ "selectedType": "BeakerDisplay",
+ "elapsedTime": 0,
+ "height": 154
+ },
+ "evaluatorReader": true,
+ "lineCount": 4
+ },
{
"id": "codeGcV7G3",
"type": "code",
@@ -436,10 +463,10 @@
},
"output": {
"state": {},
- "selectedType": "BeakerDisplay",
+ "selectedType": "Hidden",
"pluginName": "IPython",
- "shellId": "FC7AB4B3E63044AB93210497D20C6A4D",
- "elapsedTime": 947
+ "shellId": "CB5FABDBDE4B421A823DE22347D446CC",
+ "elapsedTime": 1136
},
"evaluatorReader": true,
"tags": "calc_cell",
@@ -545,8 +572,8 @@
"state": {},
"selectedType": "Hidden",
"pluginName": "IPython",
- "shellId": "FC7AB4B3E63044AB93210497D20C6A4D",
- "elapsedTime": 409,
+ "shellId": "CB5FABDBDE4B421A823DE22347D446CC",
+ "elapsedTime": 500,
"height": 986
},
"evaluatorReader": true,
@@ -605,8 +632,8 @@
"state": {},
"selectedType": "Results",
"pluginName": "IPython",
- "shellId": "FC7AB4B3E63044AB93210497D20C6A4D",
- "elapsedTime": 15397,
+ "shellId": "CB5FABDBDE4B421A823DE22347D446CC",
+ "elapsedTime": 23222,
"height": 100
},
"evaluatorReader": true,
@@ -635,8 +662,8 @@
"state": {},
"selectedType": "Results",
"pluginName": "IPython",
- "shellId": "FC7AB4B3E63044AB93210497D20C6A4D",
- "elapsedTime": 8112,
+ "shellId": "CB5FABDBDE4B421A823DE22347D446CC",
+ "elapsedTime": 13410,
"height": 78
},
"evaluatorReader": true,
@@ -675,8 +702,8 @@
"selectedType": "Results",
"height": 78,
"pluginName": "IPython",
- "shellId": "FC7AB4B3E63044AB93210497D20C6A4D",
- "elapsedTime": 7813
+ "shellId": "CB5FABDBDE4B421A823DE22347D446CC",
+ "elapsedTime": 11717
},
"evaluatorReader": true,
"lineCount": 18,
@@ -698,7 +725,7 @@
"selectedType": "BeakerDisplay",
"height": 78,
"pluginName": "JavaScript",
- "elapsedTime": 54
+ "elapsedTime": 79
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"evaluatorReader": true,
"lineCount": 2,
@@ -727,7 +754,7 @@
"n_sis": "50",
"n_comb": "1",
"viewer_result": "d934cec27120a732",
- "units": "J_m"
+ "units": "eV_angstrom"
},
"locked": true
}
diff --git a/beaker-notebooks/sis_cscl.bkr b/beaker-notebooks/sis_cscl.bkr
index 7ca9a0539cf7cc2a07567978af7fabed1a76b35c..c7cb1e76c6f2a507220c736960c37c4b8c3aac94 100644
--- a/beaker-notebooks/sis_cscl.bkr
+++ b/beaker-notebooks/sis_cscl.bkr
@@ -70,7 +70,7 @@
},
"selectedType": "BeakerDisplay",
"elapsedTime": 0,
- "height": 436
+ "height": 431
},
"evaluatorReader": true,
"lineCount": 19
@@ -262,7 +262,7 @@
},
"selectedType": "BeakerDisplay",
"elapsedTime": 0,
- "height": 72
+ "height": 73
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"evaluatorReader": true,
"lineCount": 169
@@ -383,7 +383,7 @@
},
"selectedType": "BeakerDisplay",
"elapsedTime": 0,
- "height": 50
+ "height": 51
},
"evaluatorReader": true,
"lineCount": 98,
@@ -417,11 +417,38 @@
},
"selectedType": "BeakerDisplay",
"elapsedTime": 0,
- "height": 86
+ "height": 87
},
"evaluatorReader": true,
"lineCount": 10
},
+ {
+ "id": "code0sZSEt",
+ "type": "code",
+ "evaluator": "HTML",
+ "input": {
+ "body": [
+ "<p style=\"text-align: left; color: #aa3311; font-weight: 900; font-size: 18pt;\"> Note:</p>",
+ "<p style=\"text-align: left; color: #aa3311; font-weight: 400; font-size: 12pt;\"> 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>",
+ "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",
+ "object": "<script>\nvar beaker = bkHelper.getBeakerObject().beakerObj;\n</script>\n<p style=\"text-align: left; color: #aa3311; font-weight: 900; font-size: 18pt;\"> Note:</p>\n<p style=\"text-align: left; color: #aa3311; font-weight: 400; font-size: 12pt;\"> 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>"
+ },
+ "selectedType": "BeakerDisplay",
+ "elapsedTime": 0,
+ "height": 155
+ },
+ "evaluatorReader": true,
+ "lineCount": 4
+ },
{
"id": "codemBpYu9",
"type": "code",
@@ -1192,6 +1219,5 @@
"viewer_result": "6edb65b9776deeb2",
"structures_diff": "0",
"units": "eV_angstrom"
- },
- "locked": true
+ }
}