diff --git a/beaker-notebooks/Embedding.bkr b/beaker-notebooks/Embedding.bkr
index fb114cc4d6c06db90897e90687994dd0863c62b5..5ea47558b6a234e43b2eb029d0ed43308553b062 100644
--- a/beaker-notebooks/Embedding.bkr
+++ b/beaker-notebooks/Embedding.bkr
@@ -55,7 +55,7 @@
"<label style=\"text-align: left; color: #20335d; font-weight: 900; font-size: 18pt; padding-top: 2em;\">",
" Visualizing material-similarity:</label><br/><label style=\"color: #20335d;font-weight: 900; font-size: 15pt;\"> Octet-binary zincblende vs. rocksalt semiconductors</label>",
" </p>",
- " <p style=\"font-size: 15px;\">Angelo Ziletti, Ankit Kariryaa, Emre Ahmetcik, Fawzi Mohamed, Luca Ghiringhelli, and Matthias Scheffler <span style=\"font-size: smaller;\">[version 2017-01-30]</span></p>",
+ " <p style=\"font-size: 15px;\">Angelo Ziletti, Ankit Kariryaa, Emre Ahmetcik, Fawzi Mohamed, Luca Ghiringhelli, and Matthias Scheffler <span style=\"font-size: smaller;\">[version 2017-02-03]</span></p>",
" ",
"<div style=\"padding-top: 1em;\">"
],
@@ -66,7 +66,7 @@
"result": {
"type": "BeakerDisplay",
"innertype": "Html",
- "object": "<script>\nvar beaker = bkHelper.getBeakerObject().beakerObj;\n</script>\n<label style=\"text-align: left; color: #20335d; font-weight: 900; font-size: 18pt; padding-top: 2em;\">\n Visualizing material-similarity:</label><br><label style=\"color: #20335d;font-weight: 900; font-size: 15pt;\"> Octet-binary zincblende vs. rocksalt semiconductors</label>\n <p></p>\n <p style=\"font-size: 15px;\">Angelo Ziletti, Ankit Kariryaa, Emre Ahmetcik, Fawzi Mohamed, Luca Ghiringhelli, and Matthias Scheffler <span style=\"font-size: smaller;\">[version 2017-01-30]</span></p>\n \n<div style=\"padding-top: 1em;\"></div>"
+ "object": "<script>\nvar beaker = bkHelper.getBeakerObject().beakerObj;\n</script>\n<label style=\"text-align: left; color: #20335d; font-weight: 900; font-size: 18pt; padding-top: 2em;\">\n Visualizing material-similarity:</label><br><label style=\"color: #20335d;font-weight: 900; font-size: 15pt;\"> Octet-binary zincblende vs. rocksalt semiconductors</label>\n <p></p>\n <p style=\"font-size: 15px;\">Angelo Ziletti, Ankit Kariryaa, Emre Ahmetcik, Fawzi Mohamed, Luca Ghiringhelli, and Matthias Scheffler <span style=\"font-size: smaller;\">[version 2017-02-03]</span></p>\n \n<div style=\"padding-top: 1em;\"></div>"
},
"selectedType": "BeakerDisplay",
"elapsedTime": 0,
@@ -380,7 +380,7 @@
"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": 530
},
"evaluatorReader": true,
"lineCount": 137
@@ -418,7 +418,7 @@
"# 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-022/FhiAimsParser2.0.0-2-gf9335c4/RWApItBGtGUDsfMVlHKqrjUQ4rShT/'",
"lookup_file = '/home/beaker/.beaker/v1/web/tmp/lookup.dat'",
"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'",
@@ -437,12 +437,12 @@
"hidden": true
},
"output": {
- "selectedType": "Results",
+ "selectedType": "BeakerDisplay",
"state": {},
"pluginName": "IPython",
- "shellId": "3A80290908F64F10A4B82404FBACE0BA",
+ "shellId": "9E8C500268B34636A6638516475F2CC6",
"height": 103,
- "elapsedTime": 3244
+ "elapsedTime": 1091
},
"evaluatorReader": true,
"lineCount": 42,
@@ -460,88 +460,88 @@
"",
"# pass only lowest energy structures to save time for demonstation purposes",
"json_list = [",
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+ "'/parsed/prod-022/FhiAimsParser2.0.0-2-gf9335c4/RWApItBGtGUDsfMVlHKqrjUQ4rShT/Pzl8jOEFAC45VXxnxMJ7_nf2xS6v2.json']",
""
],
"hidden": true
@@ -550,8 +550,8 @@
"state": {},
"selectedType": "Hidden",
"pluginName": "IPython",
- "shellId": "3A80290908F64F10A4B82404FBACE0BA",
- "elapsedTime": 392
+ "shellId": "9E8C500268B34636A6638516475F2CC6",
+ "elapsedTime": 457
},
"evaluatorReader": true,
"lineCount": 89,
@@ -603,8 +603,8 @@
"state": {},
"selectedType": "Results",
"pluginName": "IPython",
- "shellId": "3A80290908F64F10A4B82404FBACE0BA",
- "elapsedTime": 13620,
+ "shellId": "9E8C500268B34636A6638516475F2CC6",
+ "elapsedTime": 14684,
"height": 166
},
"evaluatorReader": true,
@@ -709,8 +709,8 @@
"state": {},
"selectedType": "Hidden",
"pluginName": "IPython",
- "shellId": "3A80290908F64F10A4B82404FBACE0BA",
- "elapsedTime": 398,
+ "shellId": "9E8C500268B34636A6638516475F2CC6",
+ "elapsedTime": 471,
"height": 78
},
"evaluatorReader": true,
@@ -739,9 +739,9 @@
"state": {},
"selectedType": "Results",
"pluginName": "IPython",
- "shellId": "3A80290908F64F10A4B82404FBACE0BA",
+ "shellId": "9E8C500268B34636A6638516475F2CC6",
"height": 78,
- "elapsedTime": 385
+ "elapsedTime": 458
},
"evaluatorReader": true,
"lineCount": 9,
@@ -776,9 +776,9 @@
"state": {},
"selectedType": "Results",
"pluginName": "IPython",
- "shellId": "3A80290908F64F10A4B82404FBACE0BA",
+ "shellId": "9E8C500268B34636A6638516475F2CC6",
"height": 78,
- "elapsedTime": 7568
+ "elapsedTime": 7636
},
"evaluatorReader": true,
"lineCount": 16,
@@ -812,7 +812,7 @@
"pluginName": "JavaScript",
"state": {},
"hidden": true,
- "elapsedTime": 48,
+ "elapsedTime": 113,
"height": 51
},
"evaluatorReader": true,
diff --git a/beaker-notebooks/LASSO_L0.bkr b/beaker-notebooks/LASSO_L0.bkr
index 8541b5de458fb080825788c3503e8dfdd5b3fd9d..c628d6b85607c226d179ddec7f6c2cf313ba200b 100644
--- a/beaker-notebooks/LASSO_L0.bkr
+++ b/beaker-notebooks/LASSO_L0.bkr
@@ -42,7 +42,7 @@
"<label style=\"text-align: left; color: #20335d; font-weight: 900; font-size: 18pt; padding-top: 2em;\">",
" Predicting energy differences between crystal structures I (large feature space):</label><br/><label style=\"color: #20335d;font-weight: 900; font-size: 15pt;\"> Octet-binary zincblende vs. rocksalt semiconductors</label>",
" </p>",
- " <p style=\"font-size: 15px;\">Angelo Ziletti, Ankit Kariryaa, Emre Ahmetcik, Fawzi Mohamed, Luca Ghiringhelli, and Matthias Scheffler <span style=\"font-size: smaller;\">[version 2017-01-30]</span></p>",
+ " <p style=\"font-size: 15px;\">Angelo Ziletti, Ankit Kariryaa, Emre Ahmetcik, Fawzi Mohamed, Luca Ghiringhelli, and Matthias Scheffler <span style=\"font-size: smaller;\">[version 2017-02-03]</span></p>",
" ",
"<div style=\"padding-top: 1em;\">",
"This tutorial shows how to find descriptive parameters (short formulas) that predict crystal structure, using the example of octet binary compounds that have either rocksalt (RS) or zincblende (ZB) structure. It is based on</div>",
@@ -63,7 +63,7 @@
"result": {
"type": "BeakerDisplay",
"innertype": "Html",
- "object": "<script>\nvar beaker = bkHelper.getBeakerObject().beakerObj;\n</script>\n<label style=\"text-align: left; color: #20335d; font-weight: 900; font-size: 18pt; padding-top: 2em;\">\n Predicting energy differences between crystal structures I (large feature space):</label><br><label style=\"color: #20335d;font-weight: 900; font-size: 15pt;\"> Octet-binary zincblende vs. rocksalt semiconductors</label>\n <p></p>\n <p style=\"font-size: 15px;\">Angelo Ziletti, Ankit Kariryaa, Emre Ahmetcik, Fawzi Mohamed, Luca Ghiringhelli, and Matthias Scheffler <span style=\"font-size: smaller;\">[version 2017-01-30]</span></p>\n \n<div style=\"padding-top: 1em;\">\nThis tutorial shows how to find descriptive parameters (short formulas) that predict crystal structure, using the example of octet binary compounds that have either rocksalt (RS) or zincblende (ZB) structure. It is based on</div>\n<div style=\"padding: 1ex; margin-top: 1ex; margin-bottom: 1ex; border-style: dotted; border-width: 1pt; border-color: blue; border-radius: 3px;\">\nL. 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>\n</div>\n<div>\nClick on \"Run\" below to reproduce results from this publication; click \"Background\" for an explanation of the approach; or, modify \"Settings\" to produce your own results.\n</div>\n<div style=\"padding-top: 2ex;\">\n<span style=\"font-weight: bold;\">Idea: </span> Starting from simple physical quantities (\"building blocks\", here properties of the constituent free atoms such as orbital radii), thousands 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 sparse regression method is used to select only a few of these formulas that explain the data.\n</div>"
+ "object": "<script>\nvar beaker = bkHelper.getBeakerObject().beakerObj;\n</script>\n<label style=\"text-align: left; color: #20335d; font-weight: 900; font-size: 18pt; padding-top: 2em;\">\n Predicting energy differences between crystal structures I (large feature space):</label><br><label style=\"color: #20335d;font-weight: 900; font-size: 15pt;\"> Octet-binary zincblende vs. rocksalt semiconductors</label>\n <p></p>\n <p style=\"font-size: 15px;\">Angelo Ziletti, Ankit Kariryaa, Emre Ahmetcik, Fawzi Mohamed, Luca Ghiringhelli, and Matthias Scheffler <span style=\"font-size: smaller;\">[version 2017-02-03]</span></p>\n \n<div style=\"padding-top: 1em;\">\nThis tutorial shows how to find descriptive parameters (short formulas) that predict crystal structure, using the example of octet binary compounds that have either rocksalt (RS) or zincblende (ZB) structure. It is based on</div>\n<div style=\"padding: 1ex; margin-top: 1ex; margin-bottom: 1ex; border-style: dotted; border-width: 1pt; border-color: blue; border-radius: 3px;\">\nL. 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>\n</div>\n<div>\nClick on \"Run\" below to reproduce results from this publication; click \"Background\" for an explanation of the approach; or, modify \"Settings\" to produce your own results.\n</div>\n<div style=\"padding-top: 2ex;\">\n<span style=\"font-weight: bold;\">Idea: </span> Starting from simple physical quantities (\"building blocks\", here properties of the constituent free atoms such as orbital radii), thousands 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 sparse regression method is used to select only a few of these formulas that explain the data.\n</div>"
},
"selectedType": "BeakerDisplay",
"elapsedTime": 0,
@@ -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,
@@ -415,7 +415,7 @@
"# 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-022/FhiAimsParser2.0.0-2-gf9335c4/RWApItBGtGUDsfMVlHKqrjUQ4rShT/'",
"lookup_file = '/home/beaker/.beaker/v1/web/tmp/lookup.dat'",
"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'",
@@ -438,8 +438,8 @@
"state": {},
"selectedType": "Results",
"pluginName": "IPython",
- "shellId": "D5EE44586871408C813A90FDC3539856",
- "elapsedTime": 1721
+ "shellId": "6EF6C49F5D2D40F383601486E08EC433",
+ "elapsedTime": 3516
},
"evaluatorReader": true,
"tags": "calc_cell",
@@ -451,90 +451,92 @@
"evaluator": "IPython",
"input": {
"body": [
+ "# pass only lowest energy structures to save time for demonstation purposes",
"# pass only lowest energy structures to save time for demonstation purposes",
"json_list = [",
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- "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/P0e8gRRxOvcJquPDa7SeYFk2OCiFS.json', ",
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- "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/P36pL30yblwhze_vHZYZ_cybqeH4V.json', ",
- "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/P39GmzBY478BzuXrZM-0i2Z-njyb9.json', ",
- "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/P3hSpXydSB6z3p79OEIOQK6llto1K.json', ",
- "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/P51AKUeSNYXrRBK_-uc8y1-bCfUNg.json', ",
- "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/P5q6OPnbkCI9OZnxRMmigkwjECTEe.json', ",
- "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/P7JW4GQVa_xQ4YKM88F9LFzyVoXke.json', ",
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- "shellId": "D5EE44586871408C813A90FDC3539856",
- "elapsedTime": 6001
+ "shellId": "6EF6C49F5D2D40F383601486E08EC433",
+ "elapsedTime": 10695
},
"evaluatorReader": true,
"lineCount": 18,
@@ -696,7 +698,7 @@
"selectedType": "BeakerDisplay",
"height": 78,
"pluginName": "JavaScript",
- "elapsedTime": 56
+ "elapsedTime": 85
},
"evaluatorReader": true,
"lineCount": 2,
@@ -707,6 +709,8 @@
"selected_feature_list": [
"atomic_ionization_potential",
"atomic_electron_affinity",
+ "atomic_homo",
+ "atomic_lumo",
"atomic_rs_max",
"atomic_rp_max",
"atomic_rd_max"
@@ -722,7 +726,7 @@
"ncomb": "1",
"n_sis": "50",
"n_comb": "1",
- "viewer_result": "6edb65b9776deeb2",
+ "viewer_result": "d934cec27120a732",
"units": "eV_angstrom"
},
"locked": true
diff --git a/beaker-notebooks/SOAP_similarity.bkr b/beaker-notebooks/SOAP_similarity.bkr
index 292b7beec082a20e8e92c0a64852bd286aa1d49c..d4676475fee6d79e528bc4b7925ea63a7330c717 100644
--- a/beaker-notebooks/SOAP_similarity.bkr
+++ b/beaker-notebooks/SOAP_similarity.bkr
@@ -90,7 +90,7 @@
"<!--label style=\"color: #20335d;font-weight: 900; font-size: 15pt;\"> Visualizing global similarity</label-->",
" </p>",
" <hr style=\"border-width:2px\">",
- " <p style=\"font-size: 15px;\"> developed by Carl Poelking, Angelo Ziletti, Luca Ghiringhelli and Gábor Csányi [version 2017-01-27]</p>",
+ " <p style=\"font-size: 15px;\"> developed by Carl Poelking, Angelo Ziletti, Luca Ghiringhelli and Gábor Csányi [version 2017-02-03]</p>",
" ",
" <p style=\"font-size: 15px;\"> <b> Machine learning method: </b> Nonlinear dimensionality reduction based on SOAP similarity kernel<br>",
" ",
@@ -571,8 +571,8 @@
"object": "<script>\nvar beaker = bkHelper.getBeakerObject().beakerObj;\n</script>\n<script>\nvar run_soap = function() {\n $(\"#plot_result_button\").removeClass(\"active\").addClass(\"disabled\");\n get_options();\n beaker.evaluate(\"cell_soap_run\");\n};\n \nvar show_hide = function(tag, bt_tag) {\n $(\"#\"+tag).toggle();\n $(\"#\"+bt_tag).toggleClass(\"active\");\n /*if ($(\"#\"+bt_tag).attr(\"clicked\")) {\n $(\"#\"+bt_tag).css('background-color','lightgray');\n $(\"#\"+bt_tag).attr(\"clicked\", 0)\n }\n else {\n $(\"#\"+bt_tag).css('background-color','red');\n $(\"#\"+bt_tag).attr(\"clicked\", 1)\n }*/\n}\n\nvar allow = function(yesno) {\n if (yesno) {\n $(\"#option_el_spec_dens\").removeAttr('disabled');\n $(\"#atomic_density_type\").val('number_density').change();\n }\n else {\n if ($(\"#atomic_density_type\").val() == \"number_density\") {\n $(\"#atomic_density_type\").val('number_density_generic').change();\n }\n $(\"#option_el_spec_dens\").attr('disabled', 'disabled');\n }\n}\n \nvar reset_soap = function() {\n beaker.evaluate(\"cell_soap_gui\");\n};\n \nvar get_options = function() {\n \n // Determine kernel adaptor function\n // [i.e., choose from specific/generic/global-specific/global-generic] \n var density_type = $(\"#atomic_density_type\").val(); \n var adaptor_type = \"?\";\n if (density_type == \"number_density\") {\n adaptor_type = \"specific\";\n }\n else { // element-agnostic, core charge, valence charge, electronegativity\n adaptor_type = \"generic\";\n }\n var kernel_method = $(\"#kernel_method\").val();\n if (kernel_method == \"global\") {\n adaptor_type = \"global-\" + adaptor_type;\n }\n \n var n_procs = parseInt($(\"#exe_n_procs\").val());\n if ($(\"#threading_mode\").val() == \"single_threaded\") n_procs = 1;\n \n beaker.options = {\n \"run\": {\n \"config_folder\": $(\"#dataset_example\").val(),\n \"n_configs\": -1,\n \"n_procs\": n_procs,\n \"n_blocksize\": parseInt($(\"#exe_batch_size\").val()),\n \"queue\": \"?\",\n \"walltime\": 12,\n \"out_folder\": \"out.kernel\",\n \"verbose\": false\n },\n \"atomic_density\": {\n \"density_type\": $(\"#atomic_density_type\").val(),\n \"atomic_radius\": parseFloat($(\"#atomic_density_atomic_radius\").val()),\n \"use_covrad\": $(\"#atomic_density_use_covrad:checked\").val() == \"true\"\n },\n \"kernel\": {\n \"method\": kernel_method\n },\n \"basekernel\": {\n \"kernel.type\": \"dot\",\n \"kernel.delta\": 1.0,\n \"kernel.xi\": parseFloat($(\"#basekernel_kernel_xi\").val())\n },\n \"laplacian\": {\n \"inverse_dist\": true,\n \"coulomb\": true,\n \"scale\": 0.01,\n \"eta\": 1.0,\n \"gamma\": 0.01,\n \"optimize_eta_gamma\": false\n },\n \"dimred\": {\n \"method\": $(\"#dimred_method\").val()\n },\n \"graph\": {\n \"descriptor\": \"soap\",\n \"pca\": \"none\",\n \"hierarchical\": $(\"#kernel_hierarchical\").val() == \"true\",\n \"r0\": 1.0,\n \"alpha\": 2.0,\n \"n_levels\": 3,\n \"optimize_hierarchy\": false\n },\n \"lamatch\": {\n \"gamma\": 0.3,\n \"optimize_rematch\": false\n },\n \"descriptor\": {\n \"soap\": {\n \"spectrum.gradients\": false,\n \"spectrum.2l1_norm\": false,\n \"radialbasis.type\" : \"gaussian\",\n \"radialbasis.mode\" : $(\"#soap_radialbasis_mode\").val(),\n \"radialbasis.N\" : parseInt($(\"#soap_radialbasis_N\").val()),\n \"radialbasis.sigma\": parseFloat($(\"#soap_radialbasis_sigma\").val()),\n \"radialbasis.integration_steps\": 15,\n \"radialcutoff.Rc\": parseFloat($(\"#soap_radialbasis_Rc\").val()),\n \"radialcutoff.Rc_width\": parseFloat($(\"#soap_radialbasis_sigma\").val()),\n \"radialcutoff.type\": \"heaviside\",\n \"radialcutoff.center_weight\": 1.0,\n \"angularbasis.type\": \"spherical-harmonic\",\n \"angularbasis.L\": parseInt($(\"#soap_angularbasis_L\").val()),\n \"kernel.type\": \"dot\",\n \"kernel.adaptor\": adaptor_type,\n \"kernel.delta\": 1.0,\n \"kernel.xi\": parseFloat($(\"#basekernel_kernel_xi\").val()),\n \"exclude_centers\": [],\n \"exclude_targets\": [],\n \"type_list\": [\"C\"]\n }\n }\n };\n\n}; \n \nbeaker.view_result = function(result_link) {\n $(\"#plot_result_button\").attr(\"href\", result_link);\n $(\"#plot_result_button\").removeClass(\"disabled\"); //.addClass(\"active\");\n}\n</script>\n<style type=\"text/css\">\n .in11f {\n width: 3.5em;\n }\n .in3d {\n width: 5em;\n }\n .select_main {\n width: 20em;\n }\n .btn.active, .btn:active {\n background: #cecece;\n text-decoration: none;\n }\n</style>\n\n <p style=\"color:#20335d; font-weight:900; font-size:18pt;\"> Control options <br> </p><hr style=\"border-width:2px\"> <p></p>\n \n \n <table class=\"glosim_control\">\n \n <!-- DATASETS -->\n <tbody><tr style=\"line-height:40px\">\n <td><b>Dataset examples</b> </td>\n <td>\n <select class=\"select_main\" id=\"dataset_example\">\n <option value=\"zcrs\" onclick=\"allow(0)\" selected=\"\"> Zincblende / Rocksalt </option>\n <option value=\"gdb\" onclick=\"allow(1)\"> GDB7 </option> \n </select>\n <!--button class=\"btn btn-xs active\" onclick='show_hide(\"in_detail_1\")' style=\"border:1;\" >\\></button-->\n <button id=\"toggle_detail_1\" type=\"button\" class=\"btn btn-xs\" onclick=\"show_hide("in_detail_1", "toggle_detail_1")\">Configure</button>\n <!--button id=\"toggle_detail_1\"type=\"button\" onclick='show_hide(\"in_detail_1\", \"toggle_detail_1\")'>Configure</button-->\n <g id=\"in_detail_1\" hidden=\"\"> Subsample structures <input id=\"exe_batch_size\" value=\"200\" min=\"50\" max=\"1000\" step=\"50\" class=\"in3d\" type=\"number\"> </g>\n </td>\n </tr> \n \n <!-- ATOMIC DENSITY --> \n <tr style=\"line-height:40px\">\n <td><b>Atomic density</b> </td>\n <td>\n <select class=\"select_main\" id=\"atomic_density_type\">\n <option id=\"option_el_agno_dens\" value=\"number_density_generic\" selected=\"\"> Density type: element-agnostic density </option>\n <option id=\"option_el_spec_dens\" value=\"number_density\" disabled=\"\"> Density type: element-specific density </option> \n <option value=\"valence_charge_density\"> Density type: valence charge </option>\n <option value=\"z_density\"> Density type: core charge </option>\n <option value=\"elneg_density\"> Density type: electronegativity </option>\n </select>\n <button id=\"toggle_detail_2\" type=\"button\" class=\"btn btn-xs\" onclick=\"show_hide("in_detail_2", "toggle_detail_2")\">Configure</button>\n <g id=\"in_detail_2\" hidden=\"\"> Use covalent radii <input id=\"atomic_density_use_covrad\" value=\"true\" unchecked=\"\" type=\"checkbox\">\n Constant atomic radius (Angstrom) <input id=\"atomic_density_atomic_radius\" value=\"0.5\" min=\"0.0\" max=\"2.0\" step=\"0.1\" class=\"in11f\" type=\"number\"> </g>\n </td>\n </tr>\n \n <!-- BASIS SET --> \n <tr style=\"line-height:40px\">\n <td><b>Basis set</b> </td>\n <td>\n <select class=\"select_main\" id=\"soap_radialbasis_mode\">\n <option value=\"adaptive\"> Radial basis: adaptive </option>\n <option value=\"equispaced\"> Radial basis: equispaced </option>\n </select>\n <button id=\"toggle_detail_3\" type=\"button\" class=\"btn btn-xs\" onclick=\"show_hide("in_detail_3", "toggle_detail_3")\">Configure</button>\n <g id=\"in_detail_3\" hidden=\"\">\n Radial functions N = <input id=\"soap_radialbasis_N\" value=\"9\" min=\"1\" max=\"14\" step=\"1\" class=\"in11f\" type=\"number\">\n Radial cutoff (equispaced only) <input id=\"soap_radialbasis_Rc\" value=\"3.5\" min=\"0.1\" max=\"10.0\" step=\"0.1\" class=\"in11f\" type=\"number\">\n Radial Gaussian width <input id=\"soap_radialbasis_sigma\" value=\"0.5\" min=\"0.1\" max=\"3.0\" step=\"0.1\" class=\"in11f\" type=\"number\">\n Angular functions L = <input id=\"soap_angularbasis_L\" value=\"6\" min=\"1\" max=\"14\" step=\"1\" class=\"in11f\" type=\"number\"> \n </g>\n </td>\n </tr> \n \n <!-- BASE KERNEL --> \n <tr style=\"line-height:40px\">\n <td><b>Base kernel</b> </td>\n <td>\n <select class=\"select_main\" id=\"basekernel_method\">\n <option value=\"dot\"> Dot-product kernel </option>\n <option value=\"laplacian\" disabled=\"\"> Laplacian kernel </option>\n <option value=\"gaussian\" disabled=\"\"> Gaussian kernel </option>\n </select>\n <button id=\"toggle_detail_4\" type=\"button\" class=\"btn btn-xs\" onclick=\"show_hide("in_detail_4", "toggle_detail_4")\">Configure</button>\n <g id=\"in_detail_4\" hidden=\"\">\n Exponent <input id=\"basekernel_kernel_xi\" value=\"3.0\" min=\"0.1\" max=\"5.0\" step=\"0.1\" class=\"in11f\" type=\"number\">\n </g>\n </td>\n </tr> \n \n <!-- TOP KERNEL -->\n <tr style=\"line-height:40px\">\n <td><b>Top kernel</b> </td>\n <td>\n <select class=\"select_main\" id=\"kernel_method\">\n <option value=\"global\" selected=\"\"> Global average (coherent)</option>\n <option value=\"average\"> Global average (incoherent)</option>\n <option value=\"rematch\"> Regularized-entropy match</option> \n <option value=\"laplacian\"> Laplacian Markov random field</option>\n </select>\n <button id=\"toggle_detail_5\" type=\"button\" class=\"btn btn-xs\" onclick=\"show_hide("in_detail_5", "toggle_detail_5")\">Configure</button>\n <g id=\"in_detail_5\" hidden=\"\">\n Mode \n <select id=\"kernel_hierarchical\">\n <option value=\"false\"> single-level</option>\n <option value=\"true\"> hierarchical</option>\n </select>\n Graph Laplacian \n <select id=\"opt_top_kernel_hierarchy\">\n <option value=\"invdist\"> inverse distance</option>\n <option value=\"coulomb\"> Coulomb matrix</option>\n </select>\n Levels <input id=\"graph:n_levels\" value=\"1\" min=\"1\" max=\"5\" step=\"1\" class=\"in11f\" type=\"number\">\n Base radius <input id=\"graph:r0\" value=\"1.0\" min=\"0.1\" max=\"5.0\" step=\"0.1\" class=\"in11f\" type=\"number\">\n Scale <input id=\"graph:alpha\" value=\"2.0\" min=\"0.1\" max=\"5.0\" step=\"0.1\" class=\"in11f\" type=\"number\">\n </g>\n </td>\n </tr> \n \n <!-- KERNEL DECOMPOSITION -->\n <tr style=\"line-height:40px\">\n <td><b>Embedding</b> </td>\n <td>\n <select class=\"select_main\" id=\"dimred_method\">\n <option value=\"kernelpca\" selected=\"\"> Kernel PCA </option>\n <option value=\"mds\"> Multi-dimensional scaling </option> \n </select>\n <button id=\"toggle_detail_6\" type=\"button\" class=\"btn btn-xs\" onclick=\"show_hide("in_detail_6", "toggle_detail_6")\">Configure</button>\n <g id=\"in_detail_6\" hidden=\"\">\n Distance metric (MDS) \n <select id=\"dimred_distance\">\n <option value=\"dot\"> Hypersphere chord </option>\n </select>\n </g>\n </td>\n </tr>\n \n <!-- EXECUTION -->\n <tr style=\"line-height:40px\">\n <td><b>Parallel execution</b></td>\n <td>\n <select class=\"select_main\" id=\"threading_mode\">\n <option value=\"single_threaded\"> Single-threaded </option>\n <option value=\"multi_threaded\" selected=\"\"> Multi-threaded </option> \n </select>\n <button id=\"toggle_detail_7\" type=\"button\" class=\"btn btn-xs\" onclick=\"show_hide("in_detail_7", "toggle_detail_7")\">Configure</button>\n <g id=\"in_detail_7\" hidden=\"\">\n Number of cores <input id=\"exe_n_procs\" value=\"2\" min=\"1\" max=\"4\" step=\"1\" class=\"in11f\" type=\"number\">\n Batch size <input id=\"exe_batch_size_parallel\" value=\"200\" min=\"50\" max=\"1000\" step=\"50\" class=\"in3d\" type=\"number\"> </g>\n </td>\n </tr>\n \n</tbody></table>\n \n<hr style=\"border-width:2px\">\n \n <button class=\"btn btn-default\" onclick=\"run_soap()\">RUN SOAP</button> \n <button class=\"btn btn-default\" onclick=\"reset_soap()\">RESET SOAP</button> \n <label title=\"Activate once run is complete.\"> \n <a href=\"#\" target=\"_blank\" class=\"btn btn-primary disabled\" id=\"plot_result_button\">View 2D similarity map</a> \n </label>\n\n<!-- \nGDB7:\nel-spec + cov-radii + re-match + pca\nel-agno - cov-radii + re-match + pca\n\nRS/ZB\ncore-chrg + cov-radii + re-match + pca\nel-agno - cov-radii + re-match + pca\n-->"
},
"selectedType": "BeakerDisplay",
- "elapsedTime": 0,
- "height": 465
+ "elapsedTime": 1,
+ "height": 466
},
"evaluatorReader": true,
"lineCount": 306,
@@ -640,7 +640,7 @@
"# LOAD DATA, CONVERT TO ASE",
"logger.info(\"Loading data (%s) ...\" % options['run']['config_folder'])",
"if options['run']['config_folder'] == 'zcrs':",
- " data_folder='/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/' ",
+ " data_folder='/parsed/prod-022/FhiAimsParser2.0.0-2-gf9335c4/RWApItBGtGUDsfMVlHKqrjUQ4rShT/' ",
" json_list = get_json_list(",
" method='folder', ",
" drop_duplicates=True, ",
@@ -756,7 +756,7 @@
"selectedType": "Results",
"state": {},
"pluginName": "IPython",
- "shellId": "685C15C25B544E2D849B1938008390FD",
+ "shellId": "A1E72F9FF9EF4FA68AC9A7FD1424AD63",
"height": 222,
"dataresult": [
"HARTREE_TO_EV",
@@ -846,7 +846,7 @@
"update_node",
"util"
],
- "elapsedTime": 42257
+ "elapsedTime": 34386
},
"evaluatorReader": true,
"lineCount": 165,
@@ -2055,8 +2055,8 @@
"state": {},
"selectedType": "Hidden",
"pluginName": "IPython",
- "shellId": "685C15C25B544E2D849B1938008390FD",
- "elapsedTime": 2057
+ "shellId": "A1E72F9FF9EF4FA68AC9A7FD1424AD63",
+ "elapsedTime": 2322
},
"evaluatorReader": true,
"lineCount": 1190,
@@ -2178,9 +2178,9 @@
"state": {},
"selectedType": "Hidden",
"pluginName": "IPython",
- "shellId": "685C15C25B544E2D849B1938008390FD",
+ "shellId": "A1E72F9FF9EF4FA68AC9A7FD1424AD63",
"height": 78,
- "elapsedTime": 405
+ "elapsedTime": 428
},
"evaluatorReader": true,
"lineCount": 103,
@@ -2264,9 +2264,9 @@
"state": {},
"selectedType": "Results",
"pluginName": "IPython",
- "shellId": "685C15C25B544E2D849B1938008390FD",
+ "shellId": "A1E72F9FF9EF4FA68AC9A7FD1424AD63",
"height": 1462,
- "elapsedTime": 3335
+ "elapsedTime": 9310
},
"evaluatorReader": true,
"lineCount": 65,
@@ -2288,7 +2288,7 @@
"selectedType": "BeakerDisplay",
"pluginName": "JavaScript",
"height": 78,
- "elapsedTime": 39
+ "elapsedTime": 65
},
"evaluatorReader": true,
"lineCount": 2,
@@ -2330,7 +2330,7 @@
"viewer_result": "similarity-map",
"options": {
"run": {
- "config_folder": "gdb",
+ "config_folder": "zcrs",
"n_configs": -1,
"n_procs": 2,
"n_blocksize": 200,
@@ -2340,7 +2340,7 @@
"verbose": false
},
"atomic_density": {
- "density_type": "number_density",
+ "density_type": "number_density_generic",
"atomic_radius": 0.5,
"use_covrad": false
},
@@ -2392,7 +2392,7 @@
"angularbasis.type": "spherical-harmonic",
"angularbasis.L": 6,
"kernel.type": "dot",
- "kernel.adaptor": "global-specific",
+ "kernel.adaptor": "global-generic",
"kernel.delta": 1,
"kernel.xi": 3,
"exclude_centers": [],