diff --git a/beaker-notebooks/LASSO_L0.bkr b/beaker-notebooks/LASSO_L0.bkr index 83c5a201099d8b51bf3320f12959549a08762b61..16704e4979640e0cbdb4ad7a05d44645cf763e6c 100644 --- a/beaker-notebooks/LASSO_L0.bkr +++ b/beaker-notebooks/LASSO_L0.bkr @@ -67,7 +67,7 @@ }, "selectedType": "BeakerDisplay", "elapsedTime": 0, - "height": 330 + "height": 316 }, "evaluatorReader": true, "lineCount": 16 @@ -225,29 +225,23 @@ " </div>", "</div>", "", - "<!-- Button trigger modal -->", - "<button type=\"button\" class=\"btn btn-default\" onclick='toggle_settings()'>", - " Settings", - "</button> ", - "", "", "<a target=\"_blank\" href=\"http://forum.analytics-toolkit.nomad-coe.eu/\" class=\"btn btn-primary\"> Tell us what you think</a>" - ], - "hidden": true + ] }, "output": { "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 getOperators();\n getMaxDim();\n getUnits();\n beaker.evaluate(\"calc_cell\"); // evaluate cells with tag \"calc_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}; \nvar getMaxDim = function() {\n beaker.max_dim = $(\"#lasso_max_dim_selector\").val();\n};\n \nvar getUnits = function() {\n beaker.units = $(\"#units_select\").val();\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</script>\n<style type=\"text/css\">\n .lasso_instructions{\n font-size: 15px;\n } \n</style>\n<!-- Button trigger modal -->\n<button type=\"button\" class=\"btn btn-default\" data-toggle=\"modal\" data-target=\"#lasso-motivation-modal\">\n Background\n</button> \n\n<!-- Modal -->\n<div style=\"display: none;\" class=\"modal fade\" id=\"lasso-motivation-modal\" tabindex=\"-1\" role=\"dialog\" aria-labelledby=\"lasso-motivation-modal-label\">\n <div class=\"modal-dialog modal-lg\" role=\"document\">\n <div class=\"modal-content\">\n <div class=\"modal-header\">\n <button type=\"button\" class=\"close\" data-dismiss=\"modal\" aria-label=\"Close\"><span aria-hidden=\"true\">×</span></button>\n <h4 class=\"modal-title\" id=\"lasso-motivation-modal-label\">Background</h4>\n </div>\n <div class=\"modal-body lasso_instructions\">\n <p> In this tutorial we present a tool for predicting the crystal structure of octet binary compounds, by using a set of descriptive parameters (a descriptor) based on free-atom data of the atomic species constituting the binary material.</p>\n\n <p>In this example, we address only Rocksalt (RS) and Zincblende (ZB) crystal structures, that are the most common for the material class of octet binaries. Specifically, the tool predicts the difference in total energy between RS and ZB equilibrated structures (i.e., each structure is relaxed to its local minimum).</p>\n\n <p>The prediction of RS vs ZB structure from a simple descriptor has a notable history in materials science [1-7], where descriptors were designed by chemically/physically-inspired intuition. The tool presented here allows for the machine-learning-aided automatic discovery of a descriptor and a model for the prediction of the difference in energy between RS and ZB for 82 octet binary materials.</p>\n\n <p>The tool is based on Compressed-sensing (LASSO performed on a tailor-made feature space, followed by L0-regularized minimization, click <a href=\"https://gitlab.rzg.mpg.de/nomad-lab/public-wiki/wikis/analytics/LASSO_L0\" target=\"_blank\">here</a> for more info on the LASSO+L0 method), as introduced in: </p>\n\n <p> \"Big Data of Materials Science: Critical Role of the Descriptor\". L. M. Ghiringhelli, J. Vybiral, S. V. Levchenko, C. Draxl, and M. Scheffler Phys. Rev. Lett. 114, 105503 (2015) <a href=\"http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.114.105503\" target=\"_blank\"> (Click here for the free access pdf) </a></p>\n\n <p> By running the tutorial with the default setting, the results of the <a href=\"http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.114.105503\" target=\"_blank\">PRL 2015</a> can be recovered. In particular, by clicking on “View interactive 2D plot”, an interactive structure-map (a chart where different structures are located in different regions of a low-dimensional representation, here two dimensional) will be opened in a new tab, similar to the following (an extended version of Fig. 2 in <a href=\"http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.114.105503\" target=\"_blank\">PRL 2015</a>): </p>\n \n <img style=\"width:67%;height:67%\" src=\"https://gitlab.mpcdf.mpg.de/nomad-lab/public-wiki/uploads/eb33f1415db1b6d489cbbc3e6a899942/2016-08-02_ZB_RS3-2.png\">\n <br>\n <br>\n <p> In this map the octet binaries are located via the descriptor found by our LASSO+L0 approach. The descriptor is based purely on free-atom data, namely radii of the <i>s</i> and <i>p</i> valence orbitals (rs and rp) of the atomic species and their Ionizaiton Potential and Electron Affinity (IP and EA). Materials in the red (blue) region crystallize preferably in the zincblende (rocksalt) structure. The distance to the green line is proportional to the difference in energy between the two structures. In the interactive plot accessible at the end of the learning performed by the present tool, one can obtain information on the materials by hovering and clicking on the data points. </p>\n <p>References:</p>\n <ol>\n <li>J. A. van Vechten, Phys. Rev. 182, 891 (1969).</li>\n <li>J. C. Phillips, Rev. Mod. Phys. 42, 317 (1970).</li>\n <li>J. St. John and A.N. Bloch, Phys. Rev. Lett. 33, 1095 (1974).</li>\n <li>J. R. Chelikowsky and J. C. Phillips, Phys. Rev. B 17, 2453 (1978).</li>\n <li>A. Zunger, Phys. Rev. B 22, 5839 (1980).</li>\n <li>D. G. Pettifor, Solid State Commun. 51, 31 (1984).</li>\n <li>Y. Saad, D. Gao, T. Ngo, S. Bobbitt, J. R. Chelikowsky, and W. Andreoni, Phys. Rev. B 85, 104104 (2012).</li>\n </ol>\n </div>\n <div class=\"modal-footer\">\n <button type=\"button\" class=\"btn btn-default\" data-dismiss=\"modal\">Close</button>\n<!-- <button type=\"button\" class=\"btn btn-primary\">Save changes</button> -->\n </div>\n </div>\n </div>\n</div>\n\n<!-- Button trigger modal -->\n<button type=\"button\" class=\"btn btn-default\" data-toggle=\"modal\" data-target=\"#lasso-instructions-modal\">\n Instructions\n</button> \n\n<!-- Modal -->\n<div class=\"modal fade\" id=\"lasso-instructions-modal\" tabindex=\"-1\" role=\"dialog\" aria-labelledby=\"lasso-instructions-modal-label\">\n <div class=\"modal-dialog\" role=\"document\">\n <div class=\"modal-content\">\n <div class=\"modal-header\">\n <button type=\"button\" class=\"close\" data-dismiss=\"modal\" aria-label=\"Close\"><span aria-hidden=\"true\">×</span></button>\n <h4 class=\"modal-title\" id=\"lasso-instructions-modal-label\">Instructions</h4>\n </div>\n <div class=\"modal-body lasso_instructions\">\n<p>In this example, you can run a compressed-sensing based algorithm for finding the optimal descriptor (and model) that predicts the difference in energy between crystal structures (here, rocksalt vs. zincblende). </p>\n\n<p>The descriptor is selected out of a large number of candidates constructed as functions of basic input features, the primary features. </p>\n\n<p>You can select the primary features as well as which kind of unary and binary operations are allowed from the checklist below. You can also select the maximum dimensionality of the descriptor. </p>\n<p> After the wished features have been selected, click <b>RUN</b> to perform the calculations (loading the values of the primary features, creation of the feature space, and optimization via LASSO+L0). </p>\n\nDuring the run, a brief summary is printed out below the <b>RUN</b> button. At the end of the run: \n <ul>\n <li> the solution (machine-learned descriptor, model, and its performance in terms of training error) is printed out underneath starting from the one-dimensional solution to the selected maximum dimensionality and</li>\n<li> the “View interactive 2D scatter plot” button unlocks; by clicking, the scatter plot with the two-dimensional descriptor appears in a separate tab. In case a dimensionality higher than 2 was selected for the descriptor, the plot displays the first two dimensions.</li>\n</ul>\n<p>Note: the plot stays active also after another run is performed, so that the output of several sets of input parameters can be compared in the viewer tabs.</p>\n </div>\n <div class=\"modal-footer\">\n <button type=\"button\" class=\"btn btn-default\" data-dismiss=\"modal\">Close</button>\n<!-- <button type=\"button\" class=\"btn btn-primary\">Save changes</button> -->\n </div>\n </div>\n </div>\n</div>\n\n<!-- Button trigger modal -->\n<button type=\"button\" class=\"btn btn-default\" onclick=\"toggle_settings()\">\n Settings\n</button> \n\n\n<a target=\"_blank\" href=\"http://forum.analytics-toolkit.nomad-coe.eu/\" class=\"btn btn-primary\"> Tell us what you think</a>" + "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 getMaxDim();\n getUnits();\n beaker.evaluate(\"calc_cell\"); // evaluate cells with tag \"calc_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}; \nvar getMaxDim = function() {\n beaker.max_dim = $(\"#lasso_max_dim_selector\").val();\n};\n \nvar getUnits = function() {\n beaker.units = $(\"#units_select\").val();\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</script>\n<style type=\"text/css\">\n .lasso_instructions{\n font-size: 15px;\n } \n</style>\n<!-- Button trigger modal -->\n<button type=\"button\" class=\"btn btn-default\" data-toggle=\"modal\" data-target=\"#lasso-motivation-modal\">\n Background\n</button> \n\n<!-- Modal -->\n<div class=\"modal fade\" id=\"lasso-motivation-modal\" tabindex=\"-1\" role=\"dialog\" aria-labelledby=\"lasso-motivation-modal-label\">\n <div class=\"modal-dialog modal-lg\" role=\"document\">\n <div class=\"modal-content\">\n <div class=\"modal-header\">\n <button type=\"button\" class=\"close\" data-dismiss=\"modal\" aria-label=\"Close\"><span aria-hidden=\"true\">×</span></button>\n <h4 class=\"modal-title\" id=\"lasso-motivation-modal-label\">Background</h4>\n </div>\n <div class=\"modal-body lasso_instructions\">\n <p> In this tutorial we present a tool for predicting the crystal structure of octet binary compounds, by using a set of descriptive parameters (a descriptor) based on free-atom data of the atomic species constituting the binary material.</p>\n\n <p>In this example, we address only Rocksalt (RS) and Zincblende (ZB) crystal structures, that are the most common for the material class of octet binaries. Specifically, the tool predicts the difference in total energy between RS and ZB equilibrated structures (i.e., each structure is relaxed to its local minimum).</p>\n\n <p>The prediction of RS vs ZB structure from a simple descriptor has a notable history in materials science [1-7], where descriptors were designed by chemically/physically-inspired intuition. The tool presented here allows for the machine-learning-aided automatic discovery of a descriptor and a model for the prediction of the difference in energy between RS and ZB for 82 octet binary materials.</p>\n\n <p>The tool is based on Compressed-sensing (LASSO performed on a tailor-made feature space, followed by L0-regularized minimization, click <a href=\"https://gitlab.rzg.mpg.de/nomad-lab/public-wiki/wikis/analytics/LASSO_L0\" target=\"_blank\">here</a> for more info on the LASSO+L0 method), as introduced in: </p>\n\n <p> \"Big Data of Materials Science: Critical Role of the Descriptor\". L. M. Ghiringhelli, J. Vybiral, S. V. Levchenko, C. Draxl, and M. Scheffler Phys. Rev. Lett. 114, 105503 (2015) <a href=\"http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.114.105503\" target=\"_blank\"> (Click here for the free access pdf) </a></p>\n\n <p> By running the tutorial with the default setting, the results of the <a href=\"http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.114.105503\" target=\"_blank\">PRL 2015</a> can be recovered. In particular, by clicking on “View interactive 2D plot”, an interactive structure-map (a chart where different structures are located in different regions of a low-dimensional representation, here two dimensional) will be opened in a new tab, similar to the following (an extended version of Fig. 2 in <a href=\"http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.114.105503\" target=\"_blank\">PRL 2015</a>): </p>\n \n <img style=\"width:67%;height:67%\" src=\"https://gitlab.mpcdf.mpg.de/nomad-lab/public-wiki/uploads/eb33f1415db1b6d489cbbc3e6a899942/2016-08-02_ZB_RS3-2.png\">\n <br>\n <br>\n <p> In this map the octet binaries are located via the descriptor found by our LASSO+L0 approach. The descriptor is based purely on free-atom data, namely radii of the <i>s</i> and <i>p</i> valence orbitals (rs and rp) of the atomic species and their Ionizaiton Potential and Electron Affinity (IP and EA). Materials in the red (blue) region crystallize preferably in the zincblende (rocksalt) structure. The distance to the green line is proportional to the difference in energy between the two structures. In the interactive plot accessible at the end of the learning performed by the present tool, one can obtain information on the materials by hovering and clicking on the data points. </p>\n <p>References:</p>\n <ol>\n <li>J. A. van Vechten, Phys. Rev. 182, 891 (1969).</li>\n <li>J. C. Phillips, Rev. Mod. Phys. 42, 317 (1970).</li>\n <li>J. St. John and A.N. Bloch, Phys. Rev. Lett. 33, 1095 (1974).</li>\n <li>J. R. Chelikowsky and J. C. Phillips, Phys. Rev. B 17, 2453 (1978).</li>\n <li>A. Zunger, Phys. Rev. B 22, 5839 (1980).</li>\n <li>D. G. Pettifor, Solid State Commun. 51, 31 (1984).</li>\n <li>Y. Saad, D. Gao, T. Ngo, S. Bobbitt, J. R. Chelikowsky, and W. Andreoni, Phys. Rev. B 85, 104104 (2012).</li>\n </ol>\n </div>\n <div class=\"modal-footer\">\n <button type=\"button\" class=\"btn btn-default\" data-dismiss=\"modal\">Close</button>\n<!-- <button type=\"button\" class=\"btn btn-primary\">Save changes</button> -->\n </div>\n </div>\n </div>\n</div>\n\n<!-- Button trigger modal -->\n<button type=\"button\" class=\"btn btn-default\" data-toggle=\"modal\" data-target=\"#lasso-instructions-modal\">\n Instructions\n</button> \n\n<!-- Modal -->\n<div class=\"modal fade\" id=\"lasso-instructions-modal\" tabindex=\"-1\" role=\"dialog\" aria-labelledby=\"lasso-instructions-modal-label\">\n <div class=\"modal-dialog\" role=\"document\">\n <div class=\"modal-content\">\n <div class=\"modal-header\">\n <button type=\"button\" class=\"close\" data-dismiss=\"modal\" aria-label=\"Close\"><span aria-hidden=\"true\">×</span></button>\n <h4 class=\"modal-title\" id=\"lasso-instructions-modal-label\">Instructions</h4>\n </div>\n <div class=\"modal-body lasso_instructions\">\n<p>In this example, you can run a compressed-sensing based algorithm for finding the optimal descriptor (and model) that predicts the difference in energy between crystal structures (here, rocksalt vs. zincblende). </p>\n\n<p>The descriptor is selected out of a large number of candidates constructed as functions of basic input features, the primary features. </p>\n\n<p>You can select the primary features as well as which kind of unary and binary operations are allowed from the checklist below. You can also select the maximum dimensionality of the descriptor. </p>\n<p> After the wished features have been selected, click <b>RUN</b> to perform the calculations (loading the values of the primary features, creation of the feature space, and optimization via LASSO+L0). </p>\n\nDuring the run, a brief summary is printed out below the <b>RUN</b> button. At the end of the run: \n <ul>\n <li> the solution (machine-learned descriptor, model, and its performance in terms of training error) is printed out underneath starting from the one-dimensional solution to the selected maximum dimensionality and</li>\n<li> the “View interactive 2D scatter plot” button unlocks; by clicking, the scatter plot with the two-dimensional descriptor appears in a separate tab. In case a dimensionality higher than 2 was selected for the descriptor, the plot displays the first two dimensions.</li>\n</ul>\n<p>Note: the plot stays active also after another run is performed, so that the output of several sets of input parameters can be compared in the viewer tabs.</p>\n </div>\n <div class=\"modal-footer\">\n <button type=\"button\" class=\"btn btn-default\" data-dismiss=\"modal\">Close</button>\n<!-- <button type=\"button\" class=\"btn btn-primary\">Save changes</button> -->\n </div>\n </div>\n </div>\n</div>\n\n\n<a target=\"_blank\" href=\"http://forum.analytics-toolkit.nomad-coe.eu/\" class=\"btn btn-primary\"> Tell us what you think</a>" }, "selectedType": "BeakerDisplay", "elapsedTime": 0, "height": 72 }, "evaluatorReader": true, - "lineCount": 154 + "lineCount": 149 }, { "id": "lasso-settings-cell", @@ -256,12 +250,9 @@ "input": { "body": [ "<style type=\"text/css\">", - " #lasso-hidden-settings-div{", - " display:none;", - " } ", - " #lasso-hidden-settings-button{", - " display:none;", - " } ", + " .lasso_control{", + " margin-left: 10px;", + " }", "</style>", "<div class=\"lasso_control\" id=\"lasso-hidden-settings-div\">", " <div class=\"row\">", @@ -324,13 +315,15 @@ " <option value=\"kcal/mol_angstrom\" > [energy]=kcal/mol; [length]=angstrom</option>", " </select> </p>", " </div><!-- End of row-->", - "<!-- <span title=''> <img src=\"http://images.clipartpanda.com/question-purzen_Icon_with_question_mark_Vector_Clipart.png\" style=\"height: 30px; width: 30px;\"> </span> -->", - "<!-- <button class=\"btn btn-default\" onclick='run_lasso()'>RUN LASSO+L0</button> -->", - "<!-- <button class=\"btn btn-default\" onclick='reset_lasso()'>RESET</button> -->", - "<!-- <label title=\"This button becomes active when the", - "run is finished. By clicking it, an interactive plot of the first 2", - "dimensions of the optimized descriptor will be opened\"> ", - " <a href=\"#\" target=\"_blank\" class=\"btn btn-primary disabled\" id=\"lasso_result_button\" >View interactive 2D scatter plot</a> </label> -->", + " <div class=\"lasso_control\">", + " <p style=\"margin-top: 1ex;\"></p>", + " <button class=\"btn btn-default\" onclick='run_lasso()' style=\"font-weight: bold;\">RUN</button> ", + " <button class=\"btn btn-default\" onclick='reset_lasso()'>RESET</button> ", + " <label title=\"This button becomes active when the", + " run is finished. By clicking it, an interactive plot of the first 2", + " dimensions of the optimized descriptor will be opened\"> ", + " <a href=\"#\" target=\"_blank\" class=\"btn btn-primary disabled\" id=\"lasso_result_button\" >View interactive 2D scatter plot</a> </label>", + " </div>", "</div>" ], "hidden": true @@ -340,49 +333,16 @@ "result": { "type": "BeakerDisplay", "innertype": "Html", - "object": "<script>\nvar beaker = bkHelper.getBeakerObject().beakerObj;\n</script>\n<style type=\"text/css\">\n #lasso-hidden-settings-div{\n display:none;\n } \n #lasso-hidden-settings-button{\n display:none;\n } \n</style>\n<div style=\"display: none;\" 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=\"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\" checked=\"\" 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-3\"> <input value=\"atomic_lumo\" checked=\"\" 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 <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"r_sigma\" type=\"checkbox\"> <span title=\"John-Bloch's indicator1: |rp(A) + rs(A) - rp(B) -rs(B)| \n [Phys. Rev. Lett. 33. 1095 (1974)]\"> r<sub>σ</sub> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"r_pi\" type=\"checkbox\"> <span title=\"John-Bloch's indicator2: |rp(A) - rs(A)| +| rp(B) -rs(B)| \n [Phys. Rev. Lett. 33. 1095 (1974)]\"> r<sub>π</sub> </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:</p>\n <form id=\"lasso_operators_select\">\n <div class=\"lasso_form_group\">\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"+\" checked=\"\" type=\"checkbox\"> x+y </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"-\" type=\"checkbox\"> x-y </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"|-|\" checked=\"\" type=\"checkbox\"> |x-y| </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"*\" type=\"checkbox\"> x · y </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"/\" checked=\"\" type=\"checkbox\"> x/y </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"^2\" checked=\"\" type=\"checkbox\"> x^2 </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"^3\" type=\"checkbox\"> x^3 </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"exp\" checked=\"\" type=\"checkbox\"> exp(x) </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>Optimal descriptor maximum dimension: </b> \n <select id=\"lasso_max_dim_selector\">\n <option value=\"2\"> 2D</option>\n <option value=\"3\"> 3D</option>\n <option value=\"4\"> 4D</option>\n <option value=\"5\"> 5D</option>\n </select> </p>\n </div><!-- End of row-->\n <div class=\"row\"> <!-- Start of forth row-->\n <p class=\"lasso_selection_description\"><b>Units of measurement: </b> \n <select id=\"units_select\">\n <option value=\"eV_angstrom\"> [energy]=eV; [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<!-- <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=\"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\" checked=\"\" 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-3\"> <input value=\"atomic_lumo\" checked=\"\" 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 <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"r_sigma\" type=\"checkbox\"> <span title=\"John-Bloch's indicator1: |rp(A) + rs(A) - rp(B) -rs(B)| \n [Phys. Rev. Lett. 33. 1095 (1974)]\"> r<sub>σ</sub> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"r_pi\" type=\"checkbox\"> <span title=\"John-Bloch's indicator2: |rp(A) - rs(A)| +| rp(B) -rs(B)| \n [Phys. Rev. Lett. 33. 1095 (1974)]\"> r<sub>π</sub> </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:</p>\n <form id=\"lasso_operators_select\">\n <div class=\"lasso_form_group\">\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"+\" checked=\"\" type=\"checkbox\"> x+y </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"-\" type=\"checkbox\"> x-y </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"|-|\" checked=\"\" type=\"checkbox\"> |x-y| </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"*\" type=\"checkbox\"> x · y </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"/\" checked=\"\" type=\"checkbox\"> x/y </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"^2\" checked=\"\" type=\"checkbox\"> x^2 </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"^3\" type=\"checkbox\"> x^3 </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"exp\" checked=\"\" type=\"checkbox\"> exp(x) </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>Optimal descriptor maximum dimension: </b> \n <select id=\"lasso_max_dim_selector\">\n <option value=\"2\"> 2D</option>\n <option value=\"3\"> 3D</option>\n <option value=\"4\"> 4D</option>\n <option value=\"5\"> 5D</option>\n </select> </p>\n </div><!-- End of row-->\n <div class=\"row\"> <!-- Start of forth row-->\n <p class=\"lasso_selection_description\"><b>Units of measurement: </b> \n <select id=\"units_select\">\n <option value=\"eV_angstrom\"> [energy]=eV; [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 <div class=\"lasso_control\">\n <p style=\"margin-top: 1ex;\"></p>\n <button class=\"btn btn-default\" onclick=\"run_lasso()\" style=\"font-weight: bold;\">RUN</button> \n <button class=\"btn btn-default\" onclick=\"reset_lasso()\">RESET</button> \n <label title=\"This button becomes active when the\n run is finished. By clicking it, an interactive plot of the first 2\n dimensions 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>" }, "selectedType": "BeakerDisplay", "elapsedTime": 0, - "height": 50 + "height": 391 }, "evaluatorReader": true, - "lineCount": 77, + "lineCount": 76, "tags": "lasso-settings" }, - { - "id": "codezrTu93", - "type": "code", - "evaluator": "HTML", - "input": { - "body": [ - "<div class=\"lasso_control\">", - "", - " <p style=\"margin-top: 1ex;\"></p>", - " <button class=\"btn btn-default\" onclick='run_lasso()' style=\"font-weight: bold;\">RUN</button> ", - " <div id=\"lasso-hidden-settings-button\"><button class=\"btn btn-default\" onclick='reset_lasso()'>RESET</button> </div>", - " <label title=\"This button becomes active when the", - "run is finished. By clicking it, an interactive plot of the first 2", - "dimensions of the optimized descriptor will be opened\"> ", - " <a href=\"#\" target=\"_blank\" class=\"btn btn-primary disabled\" id=\"lasso_result_button\" >View interactive 2D scatter plot</a> </label>", - "</div>" - ], - "hidden": true - }, - "output": { - "state": {}, - "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 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, - "height": 86 - }, - "evaluatorReader": true, - "lineCount": 10 - }, { "id": "codefWycat", "type": "code", @@ -465,8 +425,8 @@ "state": {}, "selectedType": "Hidden", "pluginName": "IPython", - "shellId": "CB5FABDBDE4B421A823DE22347D446CC", - "elapsedTime": 1136 + "shellId": "C8F9D784CD744CA082130A0718A9711A", + "elapsedTime": 393 }, "evaluatorReader": true, "tags": "calc_cell", @@ -572,8 +532,8 @@ "state": {}, "selectedType": "Hidden", "pluginName": "IPython", - "shellId": "CB5FABDBDE4B421A823DE22347D446CC", - "elapsedTime": 500, + "shellId": "C8F9D784CD744CA082130A0718A9711A", + "elapsedTime": 421, "height": 986 }, "evaluatorReader": true, @@ -632,8 +592,8 @@ "state": {}, "selectedType": "Results", "pluginName": "IPython", - "shellId": "CB5FABDBDE4B421A823DE22347D446CC", - "elapsedTime": 23222, + "shellId": "C8F9D784CD744CA082130A0718A9711A", + "elapsedTime": 7517, "height": 100 }, "evaluatorReader": true, @@ -662,8 +622,8 @@ "state": {}, "selectedType": "Results", "pluginName": "IPython", - "shellId": "CB5FABDBDE4B421A823DE22347D446CC", - "elapsedTime": 13410, + "shellId": "C8F9D784CD744CA082130A0718A9711A", + "elapsedTime": 7828, "height": 78 }, "evaluatorReader": true, @@ -702,8 +662,8 @@ "selectedType": "Results", "height": 78, "pluginName": "IPython", - "shellId": "CB5FABDBDE4B421A823DE22347D446CC", - "elapsedTime": 11717 + "shellId": "C8F9D784CD744CA082130A0718A9711A", + "elapsedTime": 5288 }, "evaluatorReader": true, "lineCount": 18, @@ -725,7 +685,7 @@ "selectedType": "BeakerDisplay", "height": 78, "pluginName": "JavaScript", - "elapsedTime": 79 + "elapsedTime": 30 }, "evaluatorReader": true, "lineCount": 2, diff --git a/beaker-notebooks/sis_cscl.bkr b/beaker-notebooks/sis_cscl.bkr index c7cb1e76c6f2a507220c736960c37c4b8c3aac94..cc4fb3457bf40787db7d89bb233419e37b346e8c 100644 --- a/beaker-notebooks/sis_cscl.bkr +++ b/beaker-notebooks/sis_cscl.bkr @@ -70,7 +70,7 @@ }, "selectedType": "BeakerDisplay", "elapsedTime": 0, - "height": 431 + "height": 400 }, "evaluatorReader": true, "lineCount": 19 @@ -242,10 +242,10 @@ " </div>", "</div>", "", - "<!-- Button trigger modal -->", + "<!-- Button trigger modal ", "<button type=\"button\" class=\"btn btn-default\" onclick='toggle_settings()'>", " Settings", - "</button> ", + "</button> -->", "", "<a target=\"_blank\" href=\"https://nomad-forum.rz-berlin.mpg.de/\" class=\"btn btn-primary\"> Tell us what you think</a>", "", @@ -258,11 +258,11 @@ "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.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\n\n\n\n\n\n</script>\n<style type=\"text/css\">\n .lasso_instructions{\n font-size: 15px;\n } \n</style>\n<!-- Button trigger modal -->\n<button type=\"button\" class=\"btn btn-default\" data-toggle=\"modal\" data-target=\"#lasso-motivation-modal\">\n Background\n</button> \n\n<!-- Modal -->\n<div class=\"modal fade\" id=\"lasso-motivation-modal\" tabindex=\"-1\" role=\"dialog\" aria-labelledby=\"lasso-motivation-modal-label\">\n <div class=\"modal-dialog modal-lg\" role=\"document\">\n <div class=\"modal-content\">\n <div class=\"modal-header\">\n <button type=\"button\" class=\"close\" data-dismiss=\"modal\" aria-label=\"Close\"><span aria-hidden=\"true\">×</span></button>\n <h4 class=\"modal-title\" id=\"lasso-motivation-modal-label\">Background</h4>\n </div>\n <div class=\"modal-body lasso_instructions\">\n <p>We present a tool for predicting the crystal structure of octet binary compounds, by using a set of descriptive parameters (a descriptor) based on free-atom data of the atomic species constituting the binary material. We apply a newly developed method: Sure Independence Screening + L0-regularization (SIS+L0), that allows to find an optimal descriptor in a huge feature space containing billions of features §.\nThe method is described in:\n</p><div style=\"padding: 1ex; margin-top: 1ex; margin-bottom: 1ex; border-style: dotted; border-width: 1pt; border-color: blue; border-radius: 3px;\">\nR. Ouyang, E. Ahmetcik, L. M. Ghiringhelli, and M. Scheffler: <span style=\"font-style: italic;\">Descriptor identification for material properties via compressed sensing</span>, in preparation.\n</div>\n<p></p>\n \n<p>SIS+L0 works iteratively. In the first iteration, a number k of features is collected that have the largest correlation (scalar product) with the property vector. The feature with the largest correlation is simply the 1D descriptor. Next, a residual is constructed as the error made at the first iteration. A new set of k features is now selected as those having the largest correlation with the residual. The 2D descriptor is the pair of features that yield the smallest fitting error upon least square regression, among all possible pairs contained in the union of the sets selected in this and the first iteration. In each next iteration a new residual is constructed as the error made in the previous iteration, then a new set of k features is extracted as those that have largest correlation with each new residual. The nD descriptor is the n-tuple of features that yield the smallest fitting error upon least square regression, among all possible n-tuples contained in the union of the sets obtained in each new iteration and all the previous iterations. If k=1 the method collapses to the so-called orthogonal matching pursuit.\n</p>\n\n <p>The prediction of the ground-state structure for binary compounds from a simple descriptor has a notable history in materials science [1-7], where descriptors were designed by chemically/physically-inspired intuition. The tool presented here allows for the machine-learning-aided automatic discovery of a descriptor and a model for the prediction of the difference in energy between a selected pair of structures for 82 octet binary materials.</p>\n\n\n <p> By running the tutorial with the default setting, the (RS vs. ZB) results of the <a href=\"http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.114.105503\" target=\"_blank\">PRL 2015</a> identified by the LASSO+L0 method can be recovered.</p>\n\n<p>§ The same task is also addressed in the tutorial <a href=\"http://analytics-toolkit.nomad-coe.eu/tutorial-LASSO_L0\">\"[Predicting energy differences between different crystal structures I: large feature space]\"</a>, where an alternative method, LASSO+L0, is used to find an optimal descriptor in a moderately large feature space. LASSO+L0 was introduced in [PRL 2015] and SIS+L0 was introduced more recently in order to cope with much larger and highly correlated feature spaces.</p>\n\n <p>References:</p>\n <ol>\n <li>J. A. van Vechten, Phys. Rev. 182, 891 (1969).</li>\n <li>J. C. Phillips, Rev. Mod. Phys. 42, 317 (1970).</li>\n <li>J. John and A. N. Bloch, Phys. Rev. Lett. 33, 1095 (1974).</li>\n <li>J. R. Chelikowsky and J. C. Phillips, Phys. Rev. B 17, 2453 (1978).</li>\n <li>A. Zunger, Phys. Rev. B 22, 5839 (1980).</li>\n <li>D. G. Pettifor, Solid State Commun. 51, 31 (1984).</li>\n <li>Y. Saad, D. Gao, T. Ngo, S. Bobbitt, J. R. Chelikowsky, and W. Andreoni, Phys. Rev. B 85, 104104 (2012).</li>\n </ol>\n </div>\n <div class=\"modal-footer\">\n <button type=\"button\" class=\"btn btn-default\" data-dismiss=\"modal\">Close</button>\n<!-- <button type=\"button\" class=\"btn btn-primary\">Save changes</button> -->\n </div>\n </div>\n </div>\n</div>\n\n<!-- Button trigger modal -->\n<button type=\"button\" class=\"btn btn-default\" data-toggle=\"modal\" data-target=\"#lasso-instructions-modal\">\n Instructions\n</button> \n\n<!-- Modal -->\n<div class=\"modal fade\" id=\"lasso-instructions-modal\" tabindex=\"-1\" role=\"dialog\" aria-labelledby=\"lasso-instructions-modal-label\">\n <div class=\"modal-dialog\" role=\"document\">\n <div class=\"modal-content\">\n <div class=\"modal-header\">\n <button type=\"button\" class=\"close\" data-dismiss=\"modal\" aria-label=\"Close\"><span aria-hidden=\"true\">×</span></button>\n <h4 class=\"modal-title\" id=\"lasso-instructions-modal-label\">Instructions</h4>\n </div>\n <div class=\"modal-body lasso_instructions\">\n<p>In this example, you can run a compressed-sensing based algorithm for finding the optimal descriptor and model that predicts the difference in energy between crystal structures (here, zincblende vs. rocksalt, CsCl, NiAs or CrB structure). </p>\n\n<p>The descriptor is selected out of a large number of candidates constructed as functions of basic input features, the primary features. </p>\n\n<p>By clicking <b>Settings</b> you can select the structure pair of interest (either RS/ZB, CsCl/ZB, NiAs/ZB or CrB/ZB), the primary features as well as which kind of unary and binary operations are allowed during feature space construction from the checklist below. Moreover the dimension of the output energies (kcal/mol or eV) and the following three parameters of the SIS+L0 algorithm can be specified: \n </p><ul>\n <li>Number of iterations for the construction for the feature space: How often the selected operations are applied to build the feature space. At each step the opreations are applied on all features created until the current step. </li>\n <li>Maximum dimension of optimal descriptor: Number of SIS+SA iterations.</li>\n <li>Number of collected features per SIS iteration.</li>\n </ul> \n \n<p></p>\n \n \n<p> After the preferred settings have been adjusted, click <b>RUN</b> for performing the calculations (loading the values of the primary features, creation of the feature space, and optimization via SIS+L0). </p>\n\nDuring the run, a brief summary is printed out below the <b>RUN</b> button. At the end of the run: \n <ul>\n <li> the solution (machine-learned descriptor, model, and its performance in terms of training error) is printed out underneath starting from the one-dimensional solution to the selected maximum dimensionality and</li>\n<li> the “View interactive 2D scatter plot” button unlocks. By clicking this button, the scatter plot with the two-dimensional descriptor appears in a separate tab. If a descriptor dimensionality greater than two was selected, the scatter plot displays the two-dimensional descriptor.</li>\n</ul>\n<p>Note: the scatter plot remains active even if another run is performed, which enables the output of several sets of input parameters to be compared.</p>\n </div>\n <div class=\"modal-footer\">\n <button type=\"button\" class=\"btn btn-default\" data-dismiss=\"modal\">Close</button>\n<!-- <button type=\"button\" class=\"btn btn-primary\">Save changes</button> -->\n </div>\n </div>\n </div>\n</div>\n\n<!-- Button trigger modal -->\n<button type=\"button\" class=\"btn btn-default\" onclick=\"toggle_settings()\">\n Settings\n</button> \n\n<a target=\"_blank\" href=\"https://nomad-forum.rz-berlin.mpg.de/\" class=\"btn btn-primary\"> Tell us what you think</a>\n\n" + "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\n\n\n\n\n\n</script>\n<style type=\"text/css\">\n .lasso_instructions{\n font-size: 15px;\n } \n</style>\n<!-- Button trigger modal -->\n<button type=\"button\" class=\"btn btn-default\" data-toggle=\"modal\" data-target=\"#lasso-motivation-modal\">\n Background\n</button> \n\n<!-- Modal -->\n<div class=\"modal fade\" id=\"lasso-motivation-modal\" tabindex=\"-1\" role=\"dialog\" aria-labelledby=\"lasso-motivation-modal-label\">\n <div class=\"modal-dialog modal-lg\" role=\"document\">\n <div class=\"modal-content\">\n <div class=\"modal-header\">\n <button type=\"button\" class=\"close\" data-dismiss=\"modal\" aria-label=\"Close\"><span aria-hidden=\"true\">×</span></button>\n <h4 class=\"modal-title\" id=\"lasso-motivation-modal-label\">Background</h4>\n </div>\n <div class=\"modal-body lasso_instructions\">\n <p>We present a tool for predicting the crystal structure of octet binary compounds, by using a set of descriptive parameters (a descriptor) based on free-atom data of the atomic species constituting the binary material. We apply a newly developed method: Sure Independence Screening + L0-regularization (SIS+L0), that allows to find an optimal descriptor in a huge feature space containing billions of features §.\nThe method is described in:\n</p><div style=\"padding: 1ex; margin-top: 1ex; margin-bottom: 1ex; border-style: dotted; border-width: 1pt; border-color: blue; border-radius: 3px;\">\nR. Ouyang, E. Ahmetcik, L. M. Ghiringhelli, and M. Scheffler: <span style=\"font-style: italic;\">Descriptor identification for material properties via compressed sensing</span>, in preparation.\n</div>\n<p></p>\n \n<p>SIS+L0 works iteratively. In the first iteration, a number k of features is collected that have the largest correlation (scalar product) with the property vector. The feature with the largest correlation is simply the 1D descriptor. Next, a residual is constructed as the error made at the first iteration. A new set of k features is now selected as those having the largest correlation with the residual. The 2D descriptor is the pair of features that yield the smallest fitting error upon least square regression, among all possible pairs contained in the union of the sets selected in this and the first iteration. In each next iteration a new residual is constructed as the error made in the previous iteration, then a new set of k features is extracted as those that have largest correlation with each new residual. The nD descriptor is the n-tuple of features that yield the smallest fitting error upon least square regression, among all possible n-tuples contained in the union of the sets obtained in each new iteration and all the previous iterations. If k=1 the method collapses to the so-called orthogonal matching pursuit.\n</p>\n\n <p>The prediction of the ground-state structure for binary compounds from a simple descriptor has a notable history in materials science [1-7], where descriptors were designed by chemically/physically-inspired intuition. The tool presented here allows for the machine-learning-aided automatic discovery of a descriptor and a model for the prediction of the difference in energy between a selected pair of structures for 82 octet binary materials.</p>\n\n\n <p> By running the tutorial with the default setting, the (RS vs. ZB) results of the <a href=\"http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.114.105503\" target=\"_blank\">PRL 2015</a> identified by the LASSO+L0 method can be recovered.</p>\n\n<p>§ The same task is also addressed in the tutorial <a href=\"http://analytics-toolkit.nomad-coe.eu/tutorial-LASSO_L0\">\"[Predicting energy differences between different crystal structures I: large feature space]\"</a>, where an alternative method, LASSO+L0, is used to find an optimal descriptor in a moderately large feature space. LASSO+L0 was introduced in [PRL 2015] and SIS+L0 was introduced more recently in order to cope with much larger and highly correlated feature spaces.</p>\n\n <p>References:</p>\n <ol>\n <li>J. A. van Vechten, Phys. Rev. 182, 891 (1969).</li>\n <li>J. C. Phillips, Rev. Mod. Phys. 42, 317 (1970).</li>\n <li>J. John and A. N. Bloch, Phys. Rev. Lett. 33, 1095 (1974).</li>\n <li>J. R. Chelikowsky and J. C. Phillips, Phys. Rev. B 17, 2453 (1978).</li>\n <li>A. Zunger, Phys. Rev. B 22, 5839 (1980).</li>\n <li>D. G. Pettifor, Solid State Commun. 51, 31 (1984).</li>\n <li>Y. Saad, D. Gao, T. Ngo, S. Bobbitt, J. R. Chelikowsky, and W. Andreoni, Phys. Rev. B 85, 104104 (2012).</li>\n </ol>\n </div>\n <div class=\"modal-footer\">\n <button type=\"button\" class=\"btn btn-default\" data-dismiss=\"modal\">Close</button>\n<!-- <button type=\"button\" class=\"btn btn-primary\">Save changes</button> -->\n </div>\n </div>\n </div>\n</div>\n\n<!-- Button trigger modal -->\n<button type=\"button\" class=\"btn btn-default\" data-toggle=\"modal\" data-target=\"#lasso-instructions-modal\">\n Instructions\n</button> \n\n<!-- Modal -->\n<div class=\"modal fade\" id=\"lasso-instructions-modal\" tabindex=\"-1\" role=\"dialog\" aria-labelledby=\"lasso-instructions-modal-label\">\n <div class=\"modal-dialog\" role=\"document\">\n <div class=\"modal-content\">\n <div class=\"modal-header\">\n <button type=\"button\" class=\"close\" data-dismiss=\"modal\" aria-label=\"Close\"><span aria-hidden=\"true\">×</span></button>\n <h4 class=\"modal-title\" id=\"lasso-instructions-modal-label\">Instructions</h4>\n </div>\n <div class=\"modal-body lasso_instructions\">\n<p>In this example, you can run a compressed-sensing based algorithm for finding the optimal descriptor and model that predicts the difference in energy between crystal structures (here, zincblende vs. rocksalt, CsCl, NiAs or CrB structure). </p>\n\n<p>The descriptor is selected out of a large number of candidates constructed as functions of basic input features, the primary features. </p>\n\n<p>By clicking <b>Settings</b> you can select the structure pair of interest (either RS/ZB, CsCl/ZB, NiAs/ZB or CrB/ZB), the primary features as well as which kind of unary and binary operations are allowed during feature space construction from the checklist below. Moreover the dimension of the output energies (kcal/mol or eV) and the following three parameters of the SIS+L0 algorithm can be specified: \n </p><ul>\n <li>Number of iterations for the construction for the feature space: How often the selected operations are applied to build the feature space. At each step the opreations are applied on all features created until the current step. </li>\n <li>Maximum dimension of optimal descriptor: Number of SIS+SA iterations.</li>\n <li>Number of collected features per SIS iteration.</li>\n </ul> \n \n<p></p>\n \n \n<p> After the preferred settings have been adjusted, click <b>RUN</b> for performing the calculations (loading the values of the primary features, creation of the feature space, and optimization via SIS+L0). </p>\n\nDuring the run, a brief summary is printed out below the <b>RUN</b> button. At the end of the run: \n <ul>\n <li> the solution (machine-learned descriptor, model, and its performance in terms of training error) is printed out underneath starting from the one-dimensional solution to the selected maximum dimensionality and</li>\n<li> the “View interactive 2D scatter plot” button unlocks. By clicking this button, the scatter plot with the two-dimensional descriptor appears in a separate tab. If a descriptor dimensionality greater than two was selected, the scatter plot displays the two-dimensional descriptor.</li>\n</ul>\n<p>Note: the scatter plot remains active even if another run is performed, which enables the output of several sets of input parameters to be compared.</p>\n </div>\n <div class=\"modal-footer\">\n <button type=\"button\" class=\"btn btn-default\" data-dismiss=\"modal\">Close</button>\n<!-- <button type=\"button\" class=\"btn btn-primary\">Save changes</button> -->\n </div>\n </div>\n </div>\n</div>\n\n<!-- Button trigger modal \n<button type=\"button\" class=\"btn btn-default\" onclick='toggle_settings()'>\n Settings\n</button> -->\n\n<a target=\"_blank\" href=\"https://nomad-forum.rz-berlin.mpg.de/\" class=\"btn btn-primary\"> Tell us what you think</a>\n\n" }, "selectedType": "BeakerDisplay", "elapsedTime": 0, - "height": 73 + "height": 72 }, "evaluatorReader": true, "lineCount": 169 @@ -274,16 +274,11 @@ "input": { "body": [ "<style type=\"text/css\">", - " #lasso-hidden-settings-div{", - " display:none;", - " } ", - " #lasso-hidden-settings-button{", - " display:none;", - " } ", + " .lasso_control{", + " margin-left: 10px;", + " }", "</style>", - "<div class=\"lasso_control\" id=\"lasso-hidden-settings-div\">", - " ", - " ", + "<div class=\"lasso_control\" id=\"lasso-hidden-settings-div\"> ", " <div class=\"row\"> <!-- Start of third row-->", " <p class=\"lasso_selection_description\"><b>Relative stability (energy difference between two structures): </b> ", " <select id='lasso_structures_diff'>", @@ -371,22 +366,21 @@ "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>" - ], - "hidden": true + ] }, "output": { "state": {}, "result": { "type": "BeakerDisplay", "innertype": "Html", - "object": "<script>\nvar beaker = bkHelper.getBeakerObject().beakerObj;\n</script>\n<style type=\"text/css\">\n #lasso-hidden-settings-div{\n display:none;\n } \n #lasso-hidden-settings-button{\n display:none;\n } \n</style>\n<div class=\"lasso_control\" id=\"lasso-hidden-settings-div\" style=\"display: none;\">\n \n \n <div class=\"row\"> <!-- Start of third row-->\n <p class=\"lasso_selection_description\"><b>Relative stability (energy difference between two structures): </b> \n <select id=\"lasso_structures_diff\">\n <option value=\"0\">RS-ZB</option>\n <option value=\"1\">CsCl-ZB</option>\n <option value=\"2\">NiAs-ZB</option>\n <option value=\"3\">CrB-ZB</option>\n </select> </p>\n </div><!-- End of row--> \n \n \n \n <div class=\"row\">\n <p class=\"lasso_selection_description\"><b>Primary features </b>\n (hover the mouse\npointer over the feature names to see a full description):</p>\n <form id=\"lasso_features_select\">\n <div class=\"lasso_form_group\">\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"atomic_ionization_potential\" checked=\"\" type=\"checkbox\"> <span title=\"Atomic ionization potential\"><i>IP</i> </span></label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"atomic_electron_affinity\" checked=\"\" type=\"checkbox\"> <span title=\"Atomic electron affinity\"> <i>EA</i></span></label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"atomic_rs_max\" checked=\"\" type=\"checkbox\"> <span title=\"Radius at which the radial probability density of the valence s orbital is maximum\"> <i>r</i><sub>s</sub> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"atomic_rp_max\" checked=\"\" type=\"checkbox\"> <span title=\"Radius at which the radial probability density of the valence p orbital is maximum\"> <i>r</i><sub>p</sub> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"atomic_rd_max\" checked=\"\" type=\"checkbox\"> <span title=\"Radius at which the radial probability density of the valence d orbital is maximum\"> <i>r</i><sub>d</sub> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"atomic_number\" type=\"checkbox\"> <span title=\"Atomic number\"> <i>Z</i> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"period\" type=\"checkbox\"> <span title=\"Period (in the periodic table)\"> <i>n</i> <sub>period</sub> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"atomic_r_by_2_dimer\" type=\"checkbox\"> <span title=\"Bond length of atomA-atomA dimer\"> <i>d</i> <sup>AA</sup> </span> </label>\n\n \n </div>\n </form>\n </div> <!-- End of row-->\n <div class=\"row\"> <!-- Start of second row-->\n <p class=\"lasso_selection_description\"><b>Allowed operations:</b> <br>\n Given features x and y, apply these operations for feature space construction:</p>\n <form id=\"lasso_operators_select\">\n <div class=\"lasso_form_group\">\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"+\" checked=\"\" type=\"checkbox\"> x+y </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"-\" type=\"checkbox\"> x-y </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"|-|\" checked=\"\" type=\"checkbox\"> |x-y| </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"*\" type=\"checkbox\"> x · y </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"/\" checked=\"\" type=\"checkbox\"> x/y </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"^-1\" type=\"checkbox\"> x^(-1) </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"^2\" checked=\"\" type=\"checkbox\"> x^2 </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"^3\" type=\"checkbox\"> x^3 </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"sqrt\" type=\"checkbox\"> √<span style=\"text-decoration: overline\">x</span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"exp\" checked=\"\" type=\"checkbox\"> exp(x) </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"exp-\" type=\"checkbox\"> exp(-x) </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"log\" type=\"checkbox\"> log(x) </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"SCD\" type=\"checkbox\"> <span title=\"Standard Cauchy distribution\"> SCD </span> </label>\n </div>\n </form>\n </div> <!-- End of row-->\n <div class=\"row\"> <!-- Start of third row-->\n <p class=\"lasso_selection_description\"><b>Number of iterations for the construction for the feature space: </b> \n <select id=\"n_comb\">\n <option value=\"1\"> 1</option>\n <option value=\"2 \" selected=\"selected\"> 2</option>\n <option value=\"3\"> 3</option>\n </select> \n <br> The required computational resources scale exponentially with the <b>Number of iterations for the construction for the feature space</b>.</p>\n \n <p class=\"lasso_selection_description\"><b>Optimal descriptor maximum dimension (number of SIS iterations): </b> \n <select id=\"lasso_max_dim_selector\">\n <option value=\"2\"> 2D</option>\n <option value=\"3\"> 3D</option>\n <option value=\"4\"> 4D</option>\n <option value=\"5\"> 5D</option>\n </select> </p>\n <p class=\"lasso_selection_description\"><b>Number of collected features per SIS iteration: </b> \n <input name=\"quantity\" id=\"n_sis\" min=\"1\" max=\"1658\" value=\"10\" step=\"100\" type=\"number\"> </p>\n\n </div><!-- End of row-->\n <div class=\"row\"> <!-- Start of forth row-->\n <p class=\"lasso_selection_description\"><b>Units of measurement: </b>\n <select id=\"units_select\">\n <option value=\"eV_angstrom\"> [energy]=eV; [length]=angstrom</option>\n <option value=\"kcal/mol_angstrom\"> [energy]=kcal/mol; [length]=angstrom</option>\n </select> </p>\n </div><!-- End of row-->\n<!-- <span title=''> <img src=\"http://images.clipartpanda.com/question-purzen_Icon_with_question_mark_Vector_Clipart.png\" style=\"height: 30px; width: 30px;\"> </span> -->\n<!-- <button class=\"btn btn-default\" onclick='run_lasso()'>RUN LASSO+L0</button> -->\n<!-- <button class=\"btn btn-default\" onclick='reset_lasso()'>RESET</button> -->\n<!-- <label title=\"This button becomes active when the\nrun is finished. By clicking it, an interactive plot of the first 2\ndimensions of the optimized descriptor will be opened\"> \n <a href=\"#\" target=\"_blank\" class=\"btn btn-primary disabled\" id=\"lasso_result_button\" >View interactive 2D scatter plot</a> </label> -->\n</div>" + "object": "<script>\nvar beaker = bkHelper.getBeakerObject().beakerObj;\n</script>\n<style type=\"text/css\">\n .lasso_control{\n margin-left: 10px;\n }\n</style>\n<div class=\"lasso_control\" id=\"lasso-hidden-settings-div\"> \n <div class=\"row\"> <!-- Start of third row-->\n <p class=\"lasso_selection_description\"><b>Relative stability (energy difference between two structures): </b> \n <select id=\"lasso_structures_diff\">\n <option value=\"0\">RS-ZB</option>\n <option value=\"1\">CsCl-ZB</option>\n <option value=\"2\">NiAs-ZB</option>\n <option value=\"3\">CrB-ZB</option>\n </select> </p>\n </div><!-- End of row--> \n \n \n \n <div class=\"row\">\n <p class=\"lasso_selection_description\"><b>Primary features </b>\n (hover the mouse\npointer over the feature names to see a full description):</p>\n <form id=\"lasso_features_select\">\n <div class=\"lasso_form_group\">\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"atomic_ionization_potential\" checked=\"\" type=\"checkbox\"> <span title=\"Atomic ionization potential\"><i>IP</i> </span></label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"atomic_electron_affinity\" checked=\"\" type=\"checkbox\"> <span title=\"Atomic electron affinity\"> <i>EA</i></span></label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"atomic_rs_max\" checked=\"\" type=\"checkbox\"> <span title=\"Radius at which the radial probability density of the valence s orbital is maximum\"> <i>r</i><sub>s</sub> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"atomic_rp_max\" checked=\"\" type=\"checkbox\"> <span title=\"Radius at which the radial probability density of the valence p orbital is maximum\"> <i>r</i><sub>p</sub> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"atomic_rd_max\" checked=\"\" type=\"checkbox\"> <span title=\"Radius at which the radial probability density of the valence d orbital is maximum\"> <i>r</i><sub>d</sub> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"atomic_number\" type=\"checkbox\"> <span title=\"Atomic number\"> <i>Z</i> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"period\" type=\"checkbox\"> <span title=\"Period (in the periodic table)\"> <i>n</i> <sub>period</sub> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"atomic_r_by_2_dimer\" type=\"checkbox\"> <span title=\"Bond length of atomA-atomA dimer\"> <i>d</i> <sup>AA</sup> </span> </label>\n\n \n </div>\n </form>\n </div> <!-- End of row-->\n <div class=\"row\"> <!-- Start of second row-->\n <p class=\"lasso_selection_description\"><b>Allowed operations:</b> <br>\n Given features x and y, apply these operations for feature space construction:</p>\n <form id=\"lasso_operators_select\">\n <div class=\"lasso_form_group\">\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"+\" checked=\"\" type=\"checkbox\"> x+y </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"-\" type=\"checkbox\"> x-y </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"|-|\" checked=\"\" type=\"checkbox\"> |x-y| </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"*\" type=\"checkbox\"> x · y </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"/\" checked=\"\" type=\"checkbox\"> x/y </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"^-1\" type=\"checkbox\"> x^(-1) </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"^2\" checked=\"\" type=\"checkbox\"> x^2 </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"^3\" type=\"checkbox\"> x^3 </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"sqrt\" type=\"checkbox\"> √<span style=\"text-decoration: overline\">x</span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"exp\" checked=\"\" type=\"checkbox\"> exp(x) </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"exp-\" type=\"checkbox\"> exp(-x) </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"log\" type=\"checkbox\"> log(x) </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"SCD\" type=\"checkbox\"> <span title=\"Standard Cauchy distribution\"> SCD </span> </label>\n </div>\n </form>\n </div> <!-- End of row-->\n <div class=\"row\"> <!-- Start of third row-->\n <p class=\"lasso_selection_description\"><b>Number of iterations for the construction for the feature space: </b> \n <select id=\"n_comb\">\n <option value=\"1\"> 1</option>\n <option value=\"2 \" selected=\"selected\"> 2</option>\n <option value=\"3\"> 3</option>\n </select> \n <br> The required computational resources scale exponentially with the <b>Number of iterations for the construction for the feature space</b>.</p>\n \n <p class=\"lasso_selection_description\"><b>Optimal descriptor maximum dimension (number of SIS iterations): </b> \n <select id=\"lasso_max_dim_selector\">\n <option value=\"2\"> 2D</option>\n <option value=\"3\"> 3D</option>\n <option value=\"4\"> 4D</option>\n <option value=\"5\"> 5D</option>\n </select> </p>\n <p class=\"lasso_selection_description\"><b>Number of collected features per SIS iteration: </b> \n <input name=\"quantity\" id=\"n_sis\" min=\"1\" max=\"1658\" value=\"10\" step=\"100\" type=\"number\"> </p>\n\n </div><!-- End of row-->\n <div class=\"row\"> <!-- Start of forth row-->\n <p class=\"lasso_selection_description\"><b>Units of measurement: </b>\n <select id=\"units_select\">\n <option value=\"eV_angstrom\"> [energy]=eV; [length]=angstrom</option>\n <option value=\"kcal/mol_angstrom\"> [energy]=kcal/mol; [length]=angstrom</option>\n </select> </p>\n </div><!-- End of row-->\n<!-- <span title=''> <img src=\"http://images.clipartpanda.com/question-purzen_Icon_with_question_mark_Vector_Clipart.png\" style=\"height: 30px; width: 30px;\"> </span> -->\n<!-- <button class=\"btn btn-default\" onclick='run_lasso()'>RUN LASSO+L0</button> -->\n<!-- <button class=\"btn btn-default\" onclick='reset_lasso()'>RESET</button> -->\n<!-- <label title=\"This button becomes active when the\nrun is finished. By clicking it, an interactive plot of the first 2\ndimensions of the optimized descriptor will be opened\"> \n <a href=\"#\" target=\"_blank\" class=\"btn btn-primary disabled\" id=\"lasso_result_button\" >View interactive 2D scatter plot</a> </label> -->\n</div>" }, "selectedType": "BeakerDisplay", "elapsedTime": 0, - "height": 51 + "height": 445 }, "evaluatorReader": true, - "lineCount": 98, + "lineCount": 93, "tags": "lasso-settings" }, { @@ -413,11 +407,11 @@ "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 id=\"lasso-hidden-settings-button\" style=\"display: none;\"><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=\"/user/tmp/6edb65b9776deeb2.html\" 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\" style=\"display: none;\"><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=\"/user/tmp/6edb65b9776deeb2.html\" target=\"_blank\" class=\"btn btn-primary active\" id=\"lasso_result_button\">View interactive 2D scatter plot</a> </label>\n</div>" }, "selectedType": "BeakerDisplay", "elapsedTime": 0, - "height": 87 + "height": 86 }, "evaluatorReader": true, "lineCount": 10 @@ -444,7 +438,7 @@ }, "selectedType": "BeakerDisplay", "elapsedTime": 0, - "height": 155 + "height": 154 }, "evaluatorReader": true, "lineCount": 4 @@ -543,8 +537,8 @@ "state": {}, "selectedType": "BeakerDisplay", "pluginName": "IPython", - "shellId": "8CC77AA81D35473CB26563948258032D", - "elapsedTime": 1032 + "shellId": "4E634DBF7C86476FAF5BA5E2C4ECCCA0", + "elapsedTime": 1172 }, "evaluatorReader": true, "lineCount": 81, @@ -990,8 +984,8 @@ "state": {}, "selectedType": "Hidden", "pluginName": "IPython", - "shellId": "8CC77AA81D35473CB26563948258032D", - "elapsedTime": 479 + "shellId": "4E634DBF7C86476FAF5BA5E2C4ECCCA0", + "elapsedTime": 1001 }, "evaluatorReader": true, "lineCount": 427, @@ -1099,8 +1093,8 @@ "state": {}, "selectedType": "Results", "pluginName": "IPython", - "shellId": "8CC77AA81D35473CB26563948258032D", - "elapsedTime": 21946, + "shellId": "4E634DBF7C86476FAF5BA5E2C4ECCCA0", + "elapsedTime": 16339, "height": 1206 }, "evaluatorReader": true, @@ -1126,10 +1120,10 @@ }, "output": { "state": {}, - "selectedType": "BeakerDisplay", + "selectedType": "Results", "pluginName": "IPython", - "shellId": "8CC77AA81D35473CB26563948258032D", - "elapsedTime": 15814, + "shellId": "4E634DBF7C86476FAF5BA5E2C4ECCCA0", + "elapsedTime": 1620, "height": 56 }, "evaluatorReader": true, @@ -1164,11 +1158,11 @@ }, "output": { "state": {}, - "selectedType": "BeakerDisplay", + "selectedType": "Results", "height": 56, "pluginName": "IPython", - "shellId": "7E7D60DBA35C434E8DB65935AB7BDAD3", - "elapsedTime": 10513 + "shellId": "4E634DBF7C86476FAF5BA5E2C4ECCCA0", + "elapsedTime": 5647 }, "evaluatorReader": true, "lineCount": 17, @@ -1190,7 +1184,7 @@ "selectedType": "BeakerDisplay", "height": 56, "pluginName": "JavaScript", - "elapsedTime": 160 + "elapsedTime": 76 }, "evaluatorReader": true, "lineCount": 2, @@ -1219,5 +1213,6 @@ "viewer_result": "6edb65b9776deeb2", "structures_diff": "0", "units": "eV_angstrom" - } + }, + "locked": true }