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Commit d9bbb6fe authored by Angelo Ziletti's avatar Angelo Ziletti
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Add LASSO, SOAP and Embedding tuts.

parent 420439fc
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beaker-notebooks/Embedding.bkr
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beaker-notebooks/LASSO_L0.bkr
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beaker-notebooks/SOAP_similarity.bkr
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......@@ -81,29 +81,6 @@
}
],
"cells": [
{
"id": "code7ULgzJ",
"type": "code",
"evaluator": "HTML",
"input": {
"body": [
"<a target=\"_blank\" href=\"http://forum.analytics-toolkit.nomad-coe.eu/\" class=\"btn btn-primary\"> Send your feedback to the analytics-toolkit forum</a><h2> Your comments are invaluable in helping us provide a user friendly experience for all! </h2>"
]
},
"output": {
"state": {},
"result": {
"type": "BeakerDisplay",
"innertype": "Html",
"object": "<script>\nvar beaker = bkHelper.getBeakerObject().beakerObj;\n</script>\n<a target=\"_blank\" href=\"http://forum.analytics-toolkit.nomad-coe.eu/\" class=\"btn btn-primary\"> Send your feedback to the analytics-toolkit forum</a><h2> Your comments are invaluable in helping us provide a user friendly experience for all! </h2>"
},
"selectedType": "BeakerDisplay",
"elapsedTime": 0,
"height": 119
},
"evaluatorReader": true,
"lineCount": 1
},
{
"id": "markdownRBGLQA",
"type": "markdown",
......@@ -113,7 +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</p>",
" <p style=\"font-size: 15px;\"> developed by Carl Poelking, Angelo Ziletti, Luca Ghiringhelli and Gábor Csányi [version 2017-01-23]</p>",
" ",
" <p style=\"font-size: 15px;\"> <b> Machine learning method: </b> Nonlinear dimensionality reduction based on SOAP similarity kernel<br>",
" ",
......@@ -595,7 +572,7 @@
},
"selectedType": "BeakerDisplay",
"elapsedTime": 0,
"height": 466
"height": 465
},
"evaluatorReader": true,
"lineCount": 306,
......@@ -625,8 +602,8 @@
"from soap.soapy.momo import osio, endl, flush",
"from soap.tools import AseConfig",
"from nomad_sim.nomad_structures import NOMADStructure",
"from nomad_sim.wrappers_desc_class import get_json_list",
"from nomad_sim.wrappers_desc_class import plot, logger",
"from nomad_sim.wrappers import get_json_list",
"from nomad_sim.wrappers import plot, logger",
"",
"verbose = False",
"logger.setLevel(logging.INFO)",
......@@ -779,8 +756,8 @@
"selectedType": "Results",
"state": {},
"pluginName": "IPython",
"shellId": "233A1B36B390425780D216B6AF523EB8",
"height": 321,
"shellId": "D45DBD5D447246C6841321D07DDCA859",
"height": 222,
"dataresult": [
"HARTREE_TO_EV",
"HARTREE_TO_KCALMOL",
......@@ -869,7 +846,7 @@
"update_node",
"util"
],
"elapsedTime": 32072
"elapsedTime": 20822
},
"evaluatorReader": true,
"lineCount": 165,
......@@ -1206,8 +1183,6 @@
" label = label_list",
" name = list(itertools.chain(*name_list))",
"",
"",
"",
" chemical_formula = rename_material(chemical_formula)",
"",
"",
......@@ -1588,7 +1563,7 @@
" for (var i = 0; i < whichJSmol.length; i++){ ",
" whichJSmol[i] = 1;",
" }",
" writeInfoApplet0(chemical_formula, energy, geo_file);",
" writeInfoApplet0(chemical_formula, 'NaN', geo_file);",
" } ",
" else if (whichJSmol[inds] == 1) {",
" //var file= \\\"javascript:Jmol.script(jmolApplet1,\" + \"'load \"+ geo_file + \" {3 3 3}; rotate x 10; rotate y 12; rotate z 6; set bondTolerance 0.45; ')\" ; ",
......@@ -1597,16 +1572,16 @@
" for (var i = 0; i < whichJSmol.length; i++){",
" whichJSmol[i] = 0;",
" } ",
" writeInfoApplet1(chemical_formula, energy, geo_file);",
" writeInfoApplet1(chemical_formula, 'NaN', geo_file);",
" }",
" \"\"\"",
" ",
" if target_pred_list:",
" js_loadJmol_4 = \"\"\"writeSummary(chemical_formula, target, target_pred);\"\"\"",
" elif label_name == None:",
" js_loadJmol_4 = \"\"\"writeSummary(chemical_formula, energy, target);\"\"\"",
" js_loadJmol_4 = \"\"\"writeSummary(chemical_formula, 'NaN', target);\"\"\"",
" else:",
" js_loadJmol_4 = \"\"\"writeSummary(chemical_formula, energy, label);\"\"\"",
" js_loadJmol_4 = \"\"\"writeSummary(chemical_formula, 'NaN', label);\"\"\"",
"",
" js_loadJmol_5 = \"\"\"",
" // save the modification in the ColumnDataSource to keep the information for the next user click",
......@@ -2080,12 +2055,11 @@
"state": {},
"selectedType": "Hidden",
"pluginName": "IPython",
"shellId": "233A1B36B390425780D216B6AF523EB8",
"height": 78,
"elapsedTime": 1897
"shellId": "D45DBD5D447246C6841321D07DDCA859",
"elapsedTime": 1812
},
"evaluatorReader": true,
"lineCount": 1192,
"lineCount": 1190,
"tags": "cell_soap_run"
},
{
......@@ -2095,7 +2069,7 @@
"input": {
"body": [
"#from nomad_sim.viewer import Viewer",
"from nomad_sim.wrappers_desc_class import view",
"from nomad_sim.wrappers import view",
"",
"def _get_structures_local(",
" json_list=None, ",
......@@ -2204,9 +2178,9 @@
"state": {},
"selectedType": "Hidden",
"pluginName": "IPython",
"shellId": "233A1B36B390425780D216B6AF523EB8",
"shellId": "D45DBD5D447246C6841321D07DDCA859",
"height": 78,
"elapsedTime": 399
"elapsedTime": 583
},
"evaluatorReader": true,
"lineCount": 103,
......@@ -2269,7 +2243,7 @@
" clustering_y_list=clust_y_list, ",
" target_list=targ_list,",
" target_name=target_name,",
" target_unit=target_unit,",
" target_unit='',",
" target_type=target_type,",
" label_list = label_list,",
" label_name = label_name,",
......@@ -2290,9 +2264,9 @@
"state": {},
"selectedType": "Results",
"pluginName": "IPython",
"shellId": "233A1B36B390425780D216B6AF523EB8",
"height": 78,
"elapsedTime": 2564
"shellId": "D45DBD5D447246C6841321D07DDCA859",
"height": 1462,
"elapsedTime": 7510
},
"evaluatorReader": true,
"lineCount": 65,
......@@ -2314,7 +2288,7 @@
"selectedType": "BeakerDisplay",
"pluginName": "JavaScript",
"height": 78,
"elapsedTime": 79
"elapsedTime": 54
},
"evaluatorReader": true,
"lineCount": 2,
......@@ -2356,7 +2330,7 @@
"viewer_result": "similarity-map",
"options": {
"run": {
"config_folder": "gdb",
"config_folder": "zcrs",
"n_configs": -1,
"n_procs": 2,
"n_blocksize": 200,
......@@ -2366,7 +2340,7 @@
"verbose": false
},
"atomic_density": {
"density_type": "number_density",
"density_type": "number_density_generic",
"atomic_radius": 0.5,
"use_covrad": false
},
......@@ -2418,7 +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": [],
......
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