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Commit 2fe7b31a authored by Emre Ahmetcik's avatar Emre Ahmetcik
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changed structure names for elements

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beaker-notebooks/sisso-metal-nonmetal.bkr
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......@@ -217,7 +217,7 @@
"",
"During the run, a brief summary is printed out below the <b>RUN</b> button. At the end of the run: ",
" <ul>",
" <li> the solution (identified 2D descriptor, and the number of data points in the overlap region) is printed out.</li>",
" <li> the solution (identified 2D descriptor and the number of data points in the overlap region) is printed out.</li>",
"<li> the “View interactive 2D scatter plot” button unlocks. By clicking this button, the scatter plot with the 2D descriptor appears in a separate tab.</li>",
"</ul>",
"<p>Note: the scatter plot remains active even if another run is performed, which enables the output of several sets of input parameters to be compared.</p>",
......@@ -414,7 +414,7 @@
" <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"IE\" CHECKED > <span title=\"Atomic ionization energy\"><i>IE</i> </span></label>",
" <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"Xp\" CHECKED > <span title=\"Pauling electronegativity\"> <i>&#967</i><sub>p</sub></span></label>",
" <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"x\" CHECKED > <span title=\"Atomic composition\"> <i>x</i> </span> </label>",
" <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"Vg\" CHECKED > <span title=\"Inverse packing factor\"> <i>V</i><sub>g</sub> </span> </label>",
" <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"(1/PF)\" CHECKED > <span title=\"Inverse packing factor: Vcell/&#931; Vatom\"> <i>1/PF</i> </span> </label>",
" </div>",
" </form>",
" </div> <!-- End of row-->",
......@@ -446,7 +446,7 @@
" <option value=\"2\" selected=\"selected\"> 2</option>",
" <option value=\"3\" > 3</option>",
" </select> ",
" <br> The required computational resources scale exponentially with the <b>Number of iterations for the construction for the feature space</b>.</p>",
" </p>",
" ",
" <p class=\"lasso_selection_description\"><b>Number of collected features per SIS iteration: </b> ",
" <input type=\"number\" name=\"quantity\" id=\"n_sis\" min=\"1\" max=\"3701\" value=\"10\" step=\"100\"> </p>",
......@@ -467,11 +467,11 @@
"output": {
"state": {},
"selectedType": "BeakerDisplay",
"height": 352,
"height": 329,
"result": {
"type": "BeakerDisplay",
"innertype": "Html",
"object": "<script>\nvar beaker = bkHelper.getBeakerObject().beakerObj;\n</script>\n<style type=\"text/css\">\n .lasso_control{\n margin-left: 10px;\n }\n</style>\n<div class=\"lasso_control\" id=\"lasso-hidden-settings-div\"> \n <div class=\"row\">\n <p class=\"lasso_selection_description\"><b>Primary features </b>\n (hover the mouse\npointer over the feature names to see a full description):</p>\n <form id=\"lasso_features_select\">\n <div class=\"lasso_form_group\">\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"IE\" checked=\"\" type=\"checkbox\"> <span title=\"Atomic ionization energy\"><i>IE</i> </span></label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"Xp\" checked=\"\" type=\"checkbox\"> <span title=\"Pauling electronegativity\"> <i>χ</i><sub>p</sub></span></label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"x\" checked=\"\" type=\"checkbox\"> <span title=\"Atomic composition\"> <i>x</i> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"Vg\" checked=\"\" type=\"checkbox\"> <span title=\"Inverse packing factor\"> <i>V</i><sub>g</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 for feature space construction:</p>\n <form id=\"lasso_operators_select\">\n <div class=\"lasso_form_group\">\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"+\" checked=\"\" type=\"checkbox\"> x+y </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"-\" checked=\"\" type=\"checkbox\"> x-y </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"|-|\" checked=\"\" type=\"checkbox\"> |x-y| </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"*\" checked=\"\" type=\"checkbox\"> x · y </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"/\" checked=\"\" type=\"checkbox\"> x/y </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"^-1\" checked=\"\" type=\"checkbox\"> x^(-1) </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"^2\" checked=\"\" type=\"checkbox\"> x^2 </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"^3\" checked=\"\" type=\"checkbox\"> x^3 </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"sqrt\" checked=\"\" type=\"checkbox\"> √<span style=\"text-decoration: overline\">x</span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"exp\" checked=\"\" type=\"checkbox\"> exp(x) </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"exp-\" type=\"checkbox\"> exp(-x) </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"log\" checked=\"\" type=\"checkbox\"> log(x) </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"SCD\" type=\"checkbox\"> <span title=\"Standard Cauchy distribution\"> SCD </span> </label>\n </div> \n </form>\n </div> <!-- End of row-->\n <div class=\"row\"> <!-- Start of third row-->\n <p class=\"lasso_selection_description\"><b>Number of iterations for the construction for the feature space: </b> \n <select id=\"n_comb\">\n <option value=\"1\"> 1</option>\n <option value=\"2\" selected=\"selected\"> 2</option>\n <option value=\"3\"> 3</option>\n </select> \n <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>Number of collected features per SIS iteration: </b> \n <input name=\"quantity\" id=\"n_sis\" min=\"1\" max=\"3701\" value=\"10\" step=\"100\" type=\"number\"> </p>\n\n </div><!-- End of row-->\n\n<!-- <span title=''> <img src=\"http://images.clipartpanda.com/question-purzen_Icon_with_question_mark_Vector_Clipart.png\" style=\"height: 30px; width: 30px;\"> </span> -->\n<!-- <button class=\"btn btn-default\" onclick='run_lasso()'>RUN LASSO+L0</button> -->\n<!-- <button class=\"btn btn-default\" onclick='reset_lasso()'>RESET</button> -->\n<!-- <label title=\"This button becomes active when the\nrun is finished. By clicking it, an interactive plot of the first 2\ndimensions of the optimized descriptor will be opened\"> \n <a href=\"#\" target=\"_blank\" class=\"btn btn-primary disabled\" id=\"lasso_result_button\" >View interactive 2D scatter plot</a> </label> -->\n</div>"
"object": "<script>\nvar beaker = bkHelper.getBeakerObject().beakerObj;\n</script>\n<style type=\"text/css\">\n .lasso_control{\n margin-left: 10px;\n }\n</style>\n<div class=\"lasso_control\" id=\"lasso-hidden-settings-div\"> \n <div class=\"row\">\n <p class=\"lasso_selection_description\"><b>Primary features </b>\n (hover the mouse\npointer over the feature names to see a full description):</p>\n <form id=\"lasso_features_select\">\n <div class=\"lasso_form_group\">\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"IE\" checked=\"\" type=\"checkbox\"> <span title=\"Atomic ionization energy\"><i>IE</i> </span></label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"Xp\" checked=\"\" type=\"checkbox\"> <span title=\"Pauling electronegativity\"> <i>χ</i><sub>p</sub></span></label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"x\" checked=\"\" type=\"checkbox\"> <span title=\"Atomic composition\"> <i>x</i> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"(1/PF)\" checked=\"\" type=\"checkbox\"> <span title=\"Inverse packing factor: Vcell/Σ Vatom\"> <i>1/PF</i> </span> </label>\n </div>\n </form>\n </div> <!-- End of row-->\n <div class=\"row\"> <!-- Start of second row-->\n <p class=\"lasso_selection_description\"><b>Allowed operations:</b> <br>\n Given features x and y, apply these operations for feature space construction:</p>\n <form id=\"lasso_operators_select\">\n <div class=\"lasso_form_group\">\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"+\" checked=\"\" type=\"checkbox\"> x+y </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"-\" checked=\"\" type=\"checkbox\"> x-y </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"|-|\" checked=\"\" type=\"checkbox\"> |x-y| </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"*\" checked=\"\" type=\"checkbox\"> x · y </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"/\" checked=\"\" type=\"checkbox\"> x/y </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"^-1\" checked=\"\" type=\"checkbox\"> x^(-1) </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"^2\" checked=\"\" type=\"checkbox\"> x^2 </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"^3\" checked=\"\" type=\"checkbox\"> x^3 </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"sqrt\" checked=\"\" type=\"checkbox\"> √<span style=\"text-decoration: overline\">x</span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"exp\" checked=\"\" type=\"checkbox\"> exp(x) </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"exp-\" type=\"checkbox\"> exp(-x) </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"log\" checked=\"\" type=\"checkbox\"> log(x) </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"SCD\" type=\"checkbox\"> <span title=\"Standard Cauchy distribution\"> SCD </span> </label>\n </div> \n </form>\n </div> <!-- End of row-->\n <div class=\"row\"> <!-- Start of third row-->\n <p class=\"lasso_selection_description\"><b>Number of iterations for the construction for the feature space: </b> \n <select id=\"n_comb\">\n <option value=\"1\"> 1</option>\n <option value=\"2\" selected=\"selected\"> 2</option>\n <option value=\"3\"> 3</option>\n </select> \n </p>\n \n <p class=\"lasso_selection_description\"><b>Number of collected features per SIS iteration: </b> \n <input name=\"quantity\" id=\"n_sis\" min=\"1\" max=\"3701\" value=\"10\" step=\"100\" type=\"number\"> </p>\n\n </div><!-- End of row-->\n\n<!-- <span title=''> <img src=\"http://images.clipartpanda.com/question-purzen_Icon_with_question_mark_Vector_Clipart.png\" style=\"height: 30px; width: 30px;\"> </span> -->\n<!-- <button class=\"btn btn-default\" onclick='run_lasso()'>RUN LASSO+L0</button> -->\n<!-- <button class=\"btn btn-default\" onclick='reset_lasso()'>RESET</button> -->\n<!-- <label title=\"This button becomes active when the\nrun is finished. By clicking it, an interactive plot of the first 2\ndimensions of the optimized descriptor will be opened\"> \n <a href=\"#\" target=\"_blank\" class=\"btn btn-primary disabled\" id=\"lasso_result_button\" >View interactive 2D scatter plot</a> </label> -->\n</div>"
},
"elapsedTime": 0
},
......@@ -546,7 +546,7 @@
"evaluator": "IPython",
"input": {
"body": [
"data = [['compound', 'structure', 'target', 'IE(A)', 'IE(B)', 'Xp(A)', 'Xp(B)', 'Vg', 'x(A)', 'x(B)'],",
"data = [['compound', 'structure', 'target', 'IE(A)', 'IE(B)', 'Xp(A)', 'Xp(B)', '(1/PF)', 'x(A)', 'x(B)'],",
" ['Li', 'bcc', 'metal', 5.391, 5.391, 0.98, 0.98, 2.4611, 0.5, 0.5],",
" ['Na', 'bcc', 'metal', 5.138, 5.138, 0.93, 0.93, 2.0505, 0.5, 0.5],",
" ['K', 'bcc', 'metal', 4.34, 4.34, 0.82, 0.82, 2.1364, 0.5, 0.5],",
......@@ -601,16 +601,16 @@
" ['La', 'dhcp', 'metal', 5.577, 5.577, 1.1, 1.1, 0.921, 0.5, 0.5],",
" ['Am', 'dhcp', 'metal', 5.991, 5.991, 1.3, 1.3, 1.0803, 0.5, 0.5],",
" ['Cm', 'dhcp', 'metal', 6.022, 6.022, 1.3, 1.3, 1.512, 0.5, 0.5],",
" ['Pa', 'tetr', 'metal', 5.887, 5.887, 1.5, 1.5, 0.7442, 0.5, 0.5],",
" ['Hg', 'rho', 'metal', 10.43, 10.43, 2.0, 2.0, 2.3946, 0.5, 0.5],",
" ['Ga', 'orth', 'metal', 5.998, 5.998, 1.81, 1.81, 2.5663, 0.5, 0.5],",
" ['Pa', 'tetragonal', 'metal', 5.887, 5.887, 1.5, 1.5, 0.7442, 0.5, 0.5],",
" ['Hg', 'rhombohedral', 'metal', 10.43, 10.43, 2.0, 2.0, 2.3946, 0.5, 0.5],",
" ['Ga', 'orthorhombic', 'metal', 5.998, 5.998, 1.81, 1.81, 2.5663, 0.5, 0.5],",
" ['Tl', 'hcp', 'metal', 6.108, 6.108, 1.62, 1.62, 2.2404, 0.5, 0.5],",
" ['Sn', 'tetr', 'metal', 7.344, 7.344, 1.96, 1.96, 2.4046, 0.5, 0.5],",
" ['Sn', 'tetragonal', 'metal', 7.344, 7.344, 1.96, 1.96, 2.4046, 0.5, 0.5],",
" ['Pb', 'fcc', 'metal', 7.416, 7.416, 2.33, 2.33, 2.3259, 0.5, 0.5],",
" ['In', 'tet', 'metal', 5.786, 5.786, 1.78, 1.78, 2.172, 0.5, 0.5],",
" ['Pu', 'ele', 'metal', 6.059, 6.059, 1.28, 1.28, 0.7313, 0.5, 0.5],",
" ['Np', 'ele', 'metal', 6.265, 6.265, 1.36, 1.36, 0.6686, 0.5, 0.5],",
" ['U', 'ele', 'metal', 6.193, 6.193, 1.38, 1.38, 0.6579, 0.5, 0.5],",
" ['In', 'tetragonal', 'metal', 5.786, 5.786, 1.78, 1.78, 2.172, 0.5, 0.5],",
" ['Pu', 'monoclinic', 'metal', 6.059, 6.059, 1.28, 1.28, 0.7313, 0.5, 0.5],",
" ['Np', 'orthorhombic', 'metal', 6.265, 6.265, 1.36, 1.36, 0.6686, 0.5, 0.5],",
" ['U', 'orthorhombic', 'metal', 6.193, 6.193, 1.38, 1.38, 0.6579, 0.5, 0.5],",
" ['Cr3Ge', 'Cr3Si', 'metal', 6.766, 7.897, 1.66, 2.01, 1.2069, 0.75, 0.25],",
" ['Cr3Si', 'Cr3Si', 'metal', 6.766, 8.151, 1.66, 1.9, 1.2088, 0.75, 0.25],",
" ['Nb3Ga', 'Cr3Si', 'metal', 6.758, 5.998, 1.6, 1.81, 1.0967, 0.75, 0.25],",
......@@ -912,10 +912,10 @@
},
"output": {
"state": {},
"selectedType": "BeakerDisplay",
"selectedType": "Hidden",
"pluginName": "IPython",
"shellId": "FFAEAF5250B743C6A75B61128AE3B92F",
"elapsedTime": 4316
"shellId": "2BB4DC50E8A74F72A57B5B1FF807D8C8",
"elapsedTime": 4129
},
"evaluatorReader": true,
"lineCount": 361,
......@@ -943,7 +943,7 @@
"# reference units/ dimensions",
"f_lists_by_units = [['IE(A)', 'IE(B)'],",
" ['Xp(A)', 'Xp(B)'],",
" ['Vg']]",
" ['(1/PF)']]",
"f_lists_by_units_flat = [b for a in f_lists_by_units for b in a]",
"",
"# set unit_classes",
......@@ -1009,8 +1009,8 @@
"output": {
"state": {},
"pluginName": "IPython",
"shellId": "0B07ABF9E949416BAA5B389E0B885A73",
"elapsedTime": 1095,
"shellId": "2BB4DC50E8A74F72A57B5B1FF807D8C8",
"elapsedTime": 328,
"selectedType": "Hidden"
},
"evaluatorReader": true,
......@@ -1159,7 +1159,7 @@
"target_name='Metal/non metal class'",
"plot_title = 'SISSO(L0) structure map'",
"tmp_folder='/home/beaker/.beaker/v1/web/tmp/'",
"parameter_list = selected_feature_list+[beaker.allowed_operations]",
"parameter_list = selected_feature_list+[beaker.allowed_operations]+[[beaker.n_comb, beaker.n_sis]]",
"name_html_page = hashlib.sha224(str(parameter_list)).hexdigest()[:16]",
"beaker.viewer_result_5_strucs = name_html_page",
"with open(tmp_folder+'output.log', 'w') as f:",
......
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