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+                    "<style type=\"text/css\">",
+                    "/*!",
+                    " * Nomad Beaker Notebook Template",
+                    " *",
+                    " * @copyright  Copyright 2017 Fritz Haber Institute of the Max Planck Society,",
+                    " *             Benjamin Regler - Apache 2.0 License",
+                    " * @license    http://www.apache.org/licenses/LICENSE-2.0",
+                    " * @author     Benjamin Regler",
+                    " * @version    1.0.0",
+                    " *",
+                    " * Licensed under the Apache License, Version 2.0 (the \"License\");",
+                    " * you may not use this file except in compliance with the License.",
+                    " * You may obtain a copy of the License at",
+                    " * ",
+                    " *     http://www.apache.org/licenses/LICENSE-2.0",
+                    " *",
+                    " * Unless required by applicable law or agreed to in writing, software",
+                    " * distributed under the License is distributed on an \"AS IS\" BASIS,",
+                    " * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.",
+                    " * See the License for the specific language governing permissions and",
+                    " * limitations under the License.",
+                    " */",
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+                    "object": "<script>\nvar beaker = bkHelper.getBeakerObject().beakerObj;\n</script>\n<style type=\"text/css\">\n/*!\n * Nomad Beaker Notebook Template\n *\n * @copyright  Copyright 2017 Fritz Haber Institute of the Max Planck Society,\n *             Benjamin Regler - Apache 2.0 License\n * @license    http://www.apache.org/licenses/LICENSE-2.0\n * @author     Benjamin Regler\n * @version    1.0.0\n *\n * Licensed under the Apache License, Version 2.0 (the \"License\");\n * you may not use this file except in compliance with the License.\n * You may obtain a copy of the License at\n * \n *     http://www.apache.org/licenses/LICENSE-2.0\n *\n * Unless required by applicable law or agreed to in writing, software\n * distributed under the License is distributed on an \"AS IS\" BASIS,\n * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n * See the License for the specific language governing permissions and\n * limitations under the License.\n */\np{margin-bottom:1.3em}h1,h2,h3,h4{margin:1.414em 0 .5em;font-weight:inherit;line-height:1.2}h1{margin-top:0;font-size:3.998em}h2{font-size:2.827em}h3{font-size:1.999em}h4{font-size:1.414em}.font_small,small{font-size:.707em}.notebook-container{font-size:16px}.notebook-container .bkr{font-size:100%;font-weight:400;line-height:1.45;color:#333}.nomad--header h2{color:#20335d;font-weight:700;margin:0 0 .2em}.nomad--header h3{color:#20335d;font-weight:700;margin-top:0;text-indent:-1em;padding-left:1em}.nomad--header h3:before{content:\"\\2014\";padding-right:.25em}.nomad--header .nomad--description{margin:-1em 0 0 2em}.atomic-data--block,.nomad--last-updated{display:inline-block;margin-top:1em}.nomad--last-updated{color:grey;float:right;position:relative;z-index:1}.nomad--last-updated::before{bottom:-75%;content:attr(data-version);font-size:4em;font-weight:700;opacity:.2;position:absolute;right:0}.atomic-data label{display:block;font-size:medium;font-weight:700}.atomic-data--select,.chosen-container{width:100%!important}.atomic-data--select:disabled{color:#d3d3d3}.atomic-data--reset-buton{display:inline-block;margin-top:1.6em;width:100%}.modal-dialog{max-width:1000px;width:80%}.modal-header h1{font-size:2em;line-height:1.2}.modal-dialog h2{font-size:1.414em}.modal-dialog h2:first-child{margin-top:0}.modal-dialog h3{font-size:1.2em}.modal-dialog dt{font-size:larger;margin-top:1.414em}.modal-dialog img{width:100%}.modal-dialog .authors{text-transform:uppercase}\n</style>"
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+                    "<div class=\"nomad--header\">",
+                    "    <h2>NOMAD Analytics Toolkit</h2>",
+                    "    <h3>On-the-fly search and data analysis for the NOMAD Archive</h3>",
+                    "    <p class=\"nomad--description\">",
+                    "      created by:",
+                    "  <a href=\"mailto:ziletti@fhi-berlin.mpg.de\">Angelo Ziletti</a><sup> 1</sup>,",
+                    "  Carl Poelking<sup>2</sup>, ",
+                    "  Fawzi Mohamed<sup>1</sup>, ",
+                    "  Gábor Csányi<sup>2</sup>,  ",
+                    "  and Luca Ghiringhelli<sup>1</sup> <br><br>",
+                    "   ",
+                    "      <sup>1</sup> Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, D-14195 Berlin, Germany <br>",
+                    "      <sup>2</sup> Engineering Laboratory, University of Cambridge, Trumpington Street, Cambridge CB2 1PZ, UK",
+                    "      <span class=\"nomad--last-updated\" data-version=\"v1.0.0\">[Last updated: November 28, 2017]</span>",
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+                    "object": "<script>\nvar beaker = bkHelper.getBeakerObject().beakerObj;\n</script>\n<div class=\"nomad--header\">\n    <h2>NOMAD Analytics Toolkit</h2>\n    <h3>On-the-fly search and data analysis for the NOMAD Archive</h3>\n    <p class=\"nomad--description\">\n      created by:\n  <a href=\"mailto:ziletti@fhi-berlin.mpg.de\">Angelo Ziletti</a><sup> 1</sup>,\n  Carl Poelking<sup>2</sup>, \n  Fawzi Mohamed<sup>1</sup>, \n  Gábor Csányi<sup>2</sup>,  \n  and Luca Ghiringhelli<sup>1</sup> <br><br>\n   \n      <sup>1</sup> Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, D-14195 Berlin, Germany <br>\n      <sup>2</sup> Engineering Laboratory, University of Cambridge, Trumpington Street, Cambridge CB2 1PZ, UK\n      <span class=\"nomad--last-updated\" data-version=\"v1.0.0\">[Last updated: November 28, 2017]</span>\n    </p>\n</div>"
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+            "body": [
+                "### Introduction",
+                "",
+                "This Notebook allows you to perform searches on the NOMAD Archive, and subsequently perform state-of-the-art machine learning analysis on the set of data retrieved from the NOMAD Archive. <br>",
+                "Given a user-specified chemical composition, the structures of the top-5 spacegroups present in the NOMAD Archive are returned, and then on-the-fly structural similarity model for the navigation and exploration of materials within the NOMAD Archive. <br>",
+                "Please see \"Read Usage Instructions\" and the \"Reference\" below for more details.",
+                "",
+                "<p style=\"font-size: 15px;\"> <b> Machine learning method: </b> Nonlinear dimensionality reduction based on SOAP similarity kernel<br>",
+                " ",
+                " <p style=\"font-size: 15px;\"> <b> Reference: </b>  <a href=\"https://arxiv.org/abs/1601.04077\" target=\"_blank\"> S. De, A. Bartók, G. Csányi, and M. Ceriotti: \"Comparing molecules and solids across structural and chemical space\", Phys. Chem. Chem. Phys. (2016)</a> </p>"
+            ],
+            "evaluatorReader": false
+        },
+        {
+            "id": "codeULbtdi",
+            "type": "code",
+            "evaluator": "HTML",
+            "input": {
+                "body": [
+                    "<button type=\"button\" class=\"btn btn-default\" data-toggle=\"modal\" data-target=\"#modal-credits\" style=\"font-size:larger;\">Motivation</button>",
+                    "<div class=\"modal fade\" id=\"modal-credits\" tabindex=\"-1\" role=\"dialog\" aria-labelledby=\"modal-credits\">",
+                    "  <div class=\"modal-dialog\" role=\"document\">",
+                    "    <div class=\"modal-content\">",
+                    "      <div class=\"modal-header\">",
+                    "        <button type=\"button\" class=\"close\" data-dismiss=\"modal\" aria-label=\"Close\"><span aria-hidden=\"true\">×</span></button>",
+                    "       <h1 class=\"modal-title\" id=\"glosim-intro-modal-label\">Motivation</h1>",
+                    "        <hr>",
+                    "      </div>",
+                    "      <div class=\"modal-body glosim_instructions\">",
+                    "        <!--p> In this tutorial we present a tool for ...</p-->",
+                    "        <p>",
+                    "          The initial compilation and early-stage analysis of materials datasets relies on generic tools that enable",
+                    "          <ul>",
+                    "            <li>insight into how materials within the dataset relate to each other in terms of chemical composition and structure, </li>",
+                    "            <li>feedback on whether or not the selection covers the intended configurational space (or whether it perhaps has \"holes\" that need to be filled),</li>",
+                    "            <li>identification of potential subsets/-classes within the chosen data for further subselection and analysis.</li>",
+                    "          </ul>         ",
+                    "        </p>",
+                    "        ",
+                    "        <p>",
+                    "          Tailored to this purpose, the toolchain presented in this tutorial helps to map and visualize materials databases using generic",
+                    "          kernel- and graph-based similarity measures together with the powerful SOAP descriptor for atomic environments.",
+                    "          As such it also serves as a basis for a range of automated, quantitative data-mining techniques:",
+                    "        </p>",
+                    "        ",
+                    "        <p> \"Evaluating the <a href=\"http://pubs.rsc.org/is/content/articlelanding/2016/cp/c6cp00415f#!divAbstract\" target=\"_blank\">(dis)similarity of crystalline, disordered and molecular compounds</a> is a critical ",
+                    "          step in the development of algorithms to navigate automatically the configuration space of complex materials. ",
+                    "          For instance, a structural similarity metric is crucial for classifying structures, searching chemical space for ",
+                    "          better compounds and materials, and to drive the next generation of machine-learning techniques for predicting the",
+                    "          stability and properties of molecules and materials. In the last few years several strategies have been designed to ",
+                    "          compare atomic coordination environments. In particular, the <a href=\"http://journals.aps.org/prb/abstract/10.1103/PhysRevB.87.184115\" target=\"_blank\">Smooth Overlap of Atomic Positions (SOAP)</a> has emerged as ",
+                    "          a natural framework to obtain translation, rotation and permutation-invariant descriptors of groups of atoms, driven by ",
+                    "          the design of various classes of machine-learned inter-atomic potentials.\"",
+                    "        </p>",
+                    "         ",
+                    "               <br/>",
+                    "        <br/>",
+                    "",
+                    "        <p>",
+                    "          References:</p>",
+                    "        <ol>",
+                    "          <li>",
+                    "            Sandip De, Albert P. Bartók, Gábor Csányi, Michele Ceriotti: \"Comparing molecules and ",
+                    "            solids across structural and alchemical space\". Phys. Chem. Chem. Phys. 18, 13754-13769 (2016)</li>",
+                    "          <li>Albert Bartók, Risi Kondor, Gábor Csányi: \"On Representing Chemical Environments\". Physical Review B 87, 184115 (2013)</li>",
+                    "        </ol>",
+                    "      </div>",
+                    "      <div class=\"modal-footer\">",
+                    "        <button type=\"button\" class=\"btn btn-default\" data-dismiss=\"modal\">Close</button>",
+                    "<!--         <button type=\"button\" class=\"btn btn-primary\">Save changes</button> -->",
+                    "      </div>",
+                    "    </div>",
+                    "  </div>",
+                    "</div>",
+                    "",
+                    "",
+                    "",
+                    "<button type=\"button\" class=\"btn btn-info\" data-toggle=\"modal\" data-target=\"#modal-instructions\" style=\"font-size:larger;\">Read usage instructions</button>",
+                    "<div class=\"modal fade\" id=\"modal-instructions\" tabindex=\"-1\" role=\"dialog\" aria-labelledby=\"modal-instructions\">",
+                    "  <div class=\"modal-dialog\" role=\"document\">",
+                    "    <div class=\"modal-content\">",
+                    "      <div class=\"modal-header\">",
+                    "        <button type=\"button\" class=\"close\" data-dismiss=\"modal\" aria-label=\"Close\"><span aria-hidden=\"true\">×</span></button>",
+                    "        <h1 class=\"modal-title\" id=\"modal-instructions-label\">Instructions</h1>",
+                    "        <hr>",
+                    "      </div>",
+                    "      <div class=\"modal-body modal-instruction-body\">",
+                    "     <p>The task is to query the NOMAD Archive and build on-the-fly structural-similarity models for the navigation and exploration of materials. The procedure is composed of two steps, reflected in the control panel further below:</p>",
+                    "        <ol>",
+                    "          <li> <b>Query of the NOMAD Archive</b> <br/>",
+                    "            ",
+                    "            <i> System composition </i>: specifies the chemical composition for which structures will be retrieved from the NOMAD Archive and then analyzed. The case of NaCl is presented as default.",
+                    "             The keyword <i> Max number or results for each spacegroup </i> allows to choose the maximum number of results shown for each of the top-5 spacegroups. Small number of results will lead to fast analysis.",
+                    "          </li>",
+                    "",
+                    "          <li> <b>On-the-fly data analysis</b> <br/>",
+                    "       A structural-similarity map of the results retrieved from the NOMAD Archive is calculated on-the-fly using the SOAP framework, as detailed below.",
+                    "            For additional information (and references) about the SOAP method, please refer to the section \"Motivation\" of this notebook.",
+                    "           </li>",
+                    "        <ul>",
+                    "          <li> <i>Definition of the atomic density</i> ",
+                    "            Within the SOAP framework, the atomic density is modelled as a linear superposition of atom-centered spherical Gaussians.",
+                    "            The density coefficient of these Gaussians as well as their width can be chosen atom-type-dependent (based on, e.g., covalent radius, ",
+                    "            core charge, valence charge, etc.) or be set constant. Additionally, the density expansions can be performed separately for each atomic type ",
+                    "            (leading to an element-specific representation and hence cross-terms in the power spectrum) or for the total, summed density (leading to an element-agnostic representation).</li>",
+                    "          <br>",
+                    "          <li> <i>Specification of the basis set</i> ",
+                    "            Prior to rotational averaging, the atomic density is expanded in terms of radial Gaussians and spherical harmonics. The radial basis set can be chosen ",
+                    "            equispaced or adaptive. In the latter case, the centres and widths of the Gaussians are optimized such that radial and angular resolution are matched, while providing",
+                    "            sufficient overlap between neighbouring Gaussians. The effective radial cutoff is then determined by the number of radial basis functions and the width of the innermost Gaussian.",
+                    "            The angular basis set is fully specified by the angular-momentum cutoff <i>L</i>. </li>",
+                    "          <br>",
+                    "          <li> <i>Configuration of the base kernel</i> ",
+                    "            The base kernel defines how the similarity between pairs of atomic environments is to be computed. ",
+                    "            SOAP has a native kernel, which is simply the dot-product between the descriptor vectors, raised to some positive power (3 is usually a good choice).  </li>",
+                    "          <br>",
+                    "          <li> <i>Configuration of the top kernel</i> ",
+                    "            The top kernel specifies how two sets of atomic environments (i.e., structures rather than individual atomic environments) should be compared. ",
+                    "            A straightforward way to accomplish this is to compute an \"average\" descriptor for both structures, and submit these to the base kernel. This \"average\" can either be formed",
+                    "           coherently (in which case the rotational averaging is performed after summation of the atomic density expansions) or incoherently (through direct averaging of the atomic descriptor vectors).",
+                    "           Other options in this tutorial include the regularized-entropy kernel, which interpolates between the incoherent average above and an atomic pairwise best match, ",
+                    "           and a spectral graph kernel computed from the spectral overlap of the Markov random field induced by the graph Laplacian of a structure. ",
+                    "           The top kernel can be applied hierarchically: In this case, \"super-atom\" environments/kernels are recursively built from the original atomic environments ",
+                    "           via a sequence of subgraphs. The subgraphs are obtained sequentially, starting from a base cutoff radius, which is then scaled by a constant factor from ",
+                    "            one level of the hierarchy to the next.</li><br>",
+                    "          <li> <i>Specification of the embedding procedure</i> ",
+                    "            The similarity/distance between structures can be visualized through decomposition of the kernel/distance matrix. Here, this is achieved",
+                    "            via a spectral decomposition of the kernel matrix and subsequent projection onto principal components (Kernel PCA) i.e., ",
+                    "            by an approximate representation of relative distances as induced by the kernel in a low-dimensional space. </li>          ",
+                    "        </ul>",
+                    "        </ol>",
+                    "        ",
+                    "      </div>",
+                    "      <div class=\"modal-footer\">",
+                    "        <button type=\"button\" class=\"btn btn-default\" data-dismiss=\"modal\" style=\"font-size:larger;\">Close</button>",
+                    "      </div>",
+                    "    </div>",
+                    "  </div>",
+                    "</div>",
+                    "",
+                    "",
+                    "",
+                    "",
+                    "",
+                    "",
+                    "",
+                    "<p></p>"
+                ],
+                "hidden": true
+            },
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+                "result": {
+                    "type": "BeakerDisplay",
+                    "innertype": "Html",
+                    "object": "<script>\nvar beaker = bkHelper.getBeakerObject().beakerObj;\n</script>\n<button type=\"button\" class=\"btn btn-default\" data-toggle=\"modal\" data-target=\"#modal-credits\" style=\"font-size:larger;\">Motivation</button>\n<div class=\"modal fade\" id=\"modal-credits\" tabindex=\"-1\" role=\"dialog\" aria-labelledby=\"modal-credits\">\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       <h1 class=\"modal-title\" id=\"glosim-intro-modal-label\">Motivation</h1>\n        <hr>\n      </div>\n      <div class=\"modal-body glosim_instructions\">\n        <!--p> In this tutorial we present a tool for ...</p-->\n        <p>\n          The initial compilation and early-stage analysis of materials datasets relies on generic tools that enable\n          </p><ul>\n            <li>insight into how materials within the dataset relate to each other in terms of chemical composition and structure, </li>\n            <li>feedback on whether or not the selection covers the intended configurational space (or whether it perhaps has \"holes\" that need to be filled),</li>\n            <li>identification of potential subsets/-classes within the chosen data for further subselection and analysis.</li>\n          </ul>         \n        <p></p>\n        \n        <p>\n          Tailored to this purpose, the toolchain presented in this tutorial helps to map and visualize materials databases using generic\n          kernel- and graph-based similarity measures together with the powerful SOAP descriptor for atomic environments.\n          As such it also serves as a basis for a range of automated, quantitative data-mining techniques:\n        </p>\n        \n        <p> \"Evaluating the <a href=\"http://pubs.rsc.org/is/content/articlelanding/2016/cp/c6cp00415f#!divAbstract\" target=\"_blank\">(dis)similarity of crystalline, disordered and molecular compounds</a> is a critical \n          step in the development of algorithms to navigate automatically the configuration space of complex materials. \n          For instance, a structural similarity metric is crucial for classifying structures, searching chemical space for \n          better compounds and materials, and to drive the next generation of machine-learning techniques for predicting the\n          stability and properties of molecules and materials. In the last few years several strategies have been designed to \n          compare atomic coordination environments. In particular, the <a href=\"http://journals.aps.org/prb/abstract/10.1103/PhysRevB.87.184115\" target=\"_blank\">Smooth Overlap of Atomic Positions (SOAP)</a> has emerged as \n          a natural framework to obtain translation, rotation and permutation-invariant descriptors of groups of atoms, driven by \n          the design of various classes of machine-learned inter-atomic potentials.\"\n        </p>\n         \n               <br>\n        <br>\n\n        <p>\n          References:</p>\n        <ol>\n          <li>\n            Sandip De, Albert P. Bartók, Gábor Csányi, Michele Ceriotti: \"Comparing molecules and \n            solids across structural and alchemical space\". Phys. Chem. Chem. Phys. 18, 13754-13769 (2016)</li>\n          <li>Albert Bartók, Risi Kondor, Gábor Csányi: \"On Representing Chemical Environments\". Physical Review B 87, 184115 (2013)</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\n\n<button type=\"button\" class=\"btn btn-info\" data-toggle=\"modal\" data-target=\"#modal-instructions\" style=\"font-size:larger;\">Read usage instructions</button>\n<div class=\"modal fade\" id=\"modal-instructions\" tabindex=\"-1\" role=\"dialog\" aria-labelledby=\"modal-instructions\">\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        <h1 class=\"modal-title\" id=\"modal-instructions-label\">Instructions</h1>\n        <hr>\n      </div>\n      <div class=\"modal-body modal-instruction-body\">\n     <p>The task is to query the NOMAD Archive and build on-the-fly structural-similarity models for the navigation and exploration of materials. The procedure is composed of two steps, reflected in the control panel further below:</p>\n        <ol>\n          <li> <b>Query of the NOMAD Archive</b> <br>\n            \n            <i> System composition </i>: specifies the chemical composition for which structures will be retrieved from the NOMAD Archive and then analyzed. The case of NaCl is presented as default.\n             The keyword <i> Max number or results for each spacegroup </i> allows to choose the maximum number of results shown for each of the top-5 spacegroups. Small number of results will lead to fast analysis.\n          </li>\n\n          <li> <b>On-the-fly data analysis</b> <br>\n       A structural-similarity map of the results retrieved from the NOMAD Archive is calculated on-the-fly using the SOAP framework, as detailed below.\n            For additional information (and references) about the SOAP method, please refer to the section \"Motivation\" of this notebook.\n           </li>\n        <ul>\n          <li> <i>Definition of the atomic density</i> \n            Within the SOAP framework, the atomic density is modelled as a linear superposition of atom-centered spherical Gaussians.\n            The density coefficient of these Gaussians as well as their width can be chosen atom-type-dependent (based on, e.g., covalent radius, \n            core charge, valence charge, etc.) or be set constant. Additionally, the density expansions can be performed separately for each atomic type \n            (leading to an element-specific representation and hence cross-terms in the power spectrum) or for the total, summed density (leading to an element-agnostic representation).</li>\n          <br>\n          <li> <i>Specification of the basis set</i> \n            Prior to rotational averaging, the atomic density is expanded in terms of radial Gaussians and spherical harmonics. The radial basis set can be chosen \n            equispaced or adaptive. In the latter case, the centres and widths of the Gaussians are optimized such that radial and angular resolution are matched, while providing\n            sufficient overlap between neighbouring Gaussians. The effective radial cutoff is then determined by the number of radial basis functions and the width of the innermost Gaussian.\n            The angular basis set is fully specified by the angular-momentum cutoff <i>L</i>. </li>\n          <br>\n          <li> <i>Configuration of the base kernel</i> \n            The base kernel defines how the similarity between pairs of atomic environments is to be computed. \n            SOAP has a native kernel, which is simply the dot-product between the descriptor vectors, raised to some positive power (3 is usually a good choice).  </li>\n          <br>\n          <li> <i>Configuration of the top kernel</i> \n            The top kernel specifies how two sets of atomic environments (i.e., structures rather than individual atomic environments) should be compared. \n            A straightforward way to accomplish this is to compute an \"average\" descriptor for both structures, and submit these to the base kernel. This \"average\" can either be formed\n           coherently (in which case the rotational averaging is performed after summation of the atomic density expansions) or incoherently (through direct averaging of the atomic descriptor vectors).\n           Other options in this tutorial include the regularized-entropy kernel, which interpolates between the incoherent average above and an atomic pairwise best match, \n           and a spectral graph kernel computed from the spectral overlap of the Markov random field induced by the graph Laplacian of a structure. \n           The top kernel can be applied hierarchically: In this case, \"super-atom\" environments/kernels are recursively built from the original atomic environments \n           via a sequence of subgraphs. The subgraphs are obtained sequentially, starting from a base cutoff radius, which is then scaled by a constant factor from \n            one level of the hierarchy to the next.</li><br>\n          <li> <i>Specification of the embedding procedure</i> \n            The similarity/distance between structures can be visualized through decomposition of the kernel/distance matrix. Here, this is achieved\n            via a spectral decomposition of the kernel matrix and subsequent projection onto principal components (Kernel PCA) i.e., \n            by an approximate representation of relative distances as induced by the kernel in a low-dimensional space. </li>          \n        </ul>\n        </ol>\n        \n      </div>\n      <div class=\"modal-footer\">\n        <button type=\"button\" class=\"btn btn-default\" data-dismiss=\"modal\" style=\"font-size:larger;\">Close</button>\n      </div>\n    </div>\n  </div>\n</div>\n\n\n\n\n\n\n\n<p></p>"
+                },
+                "selectedType": "BeakerDisplay",
+                "elapsedTime": 0,
+                "height": 101
+            },
+            "evaluatorReader": true,
+            "lineCount": 128,
+            "isError": false
+        },
+        {
+            "id": "codeU7KLkT",
+            "type": "code",
+            "evaluator": "HTML",
+            "input": {
+                "body": [
+                    "<script>",
+                    "var run_soap = function() {",
+                    "  $(\"#plot_result_button\").removeClass(\"active\").addClass(\"disabled\");",
+                    "  get_options();",
+                    "  beaker.evaluate(\"cell_soap_run\");",
+                    "};",
+                    "  ",
+                    "var show_hide = function(tag, bt_tag) {",
+                    "  $(\"#\"+tag).toggle();",
+                    "  $(\"#\"+bt_tag).toggleClass(\"active\");",
+                    "}",
+                    "",
+                    "var allow = function(yesno) {",
+                    "  if (yesno) {",
+                    "    $(\"#option_el_spec_dens\").removeAttr('disabled');",
+                    "    $(\"#atomic_density_type\").val('number_density').change();",
+                    "  }",
+                    "  else {",
+                    "    if ($(\"#atomic_density_type\").val() == \"number_density\") {",
+                    "      $(\"#atomic_density_type\").val('number_density_generic').change();",
+                    "    }",
+                    "    $(\"#option_el_spec_dens\").attr('disabled', 'disabled');",
+                    "  }",
+                    "}",
+                    "  ",
+                    "var reset_soap = function() {",
+                    "  beaker.evaluate(\"cell_soap_gui\");",
+                    "};",
+                    "  ",
+                    "var get_options = function() {",
+                    "  ",
+                    "    var system_reweighted_composition = $(\"#system_reweighted_composition\").val();  ",
+                    "    var max_nb_res = $(\"#max_nb_res\").val();  ",
+                    "",
+                    "    // Determine kernel adaptor function",
+                    "    // [i.e., choose from specific/generic/global-specific/global-generic]    ",
+                    "    var density_type = $(\"#atomic_density_type\").val();  ",
+                    "    var adaptor_type = \"?\";",
+                    "    if (density_type == \"number_density\") {",
+                    "        adaptor_type = \"specific\";",
+                    "    }",
+                    "    else { // element-agnostic, core charge, valence charge, electronegativity",
+                    "        adaptor_type = \"generic\";",
+                    "    }",
+                    "    var kernel_method = $(\"#kernel_method\").val();",
+                    "    if (kernel_method == \"global\") {",
+                    "        adaptor_type = \"global-\" + adaptor_type;",
+                    "    }",
+                    "  ",
+                    "    var n_procs = parseInt($(\"#exe_n_procs\").val());",
+                    "    if ($(\"#threading_mode\").val() == \"single_threaded\") n_procs = 1;",
+                    "    ",
+                    "    beaker.options = {",
+                    "      \"query\": {",
+                    "        \"system_reweighted_composition\": $(\"#system_reweighted_composition\").val(),",
+                    "        \"max_nb_res\": $(\"#max_nb_res\").val()",
+                    "      },",
+                    "      \"run\": {",
+                    "        \"config_folder\": $(\"#dataset_example\").val(),",
+                    "        \"n_configs\": -1,",
+                    "        \"n_procs\": n_procs,",
+                    "        \"n_blocksize\": parseInt($(\"#exe_batch_size\").val()),",
+                    "        \"queue\": \"?\",",
+                    "        \"walltime\": 12,",
+                    "        \"out_folder\": \"out.kernel\",",
+                    "        \"verbose\": false",
+                    "      },",
+                    "      \"atomic_density\": {",
+                    "        \"density_type\": $(\"#atomic_density_type\").val(),",
+                    "        \"atomic_radius\": parseFloat($(\"#atomic_density_atomic_radius\").val()),",
+                    "        \"use_covrad\": $(\"#atomic_density_use_covrad:checked\").val() == \"true\"",
+                    "      },",
+                    "      \"kernel\": {",
+                    "        \"method\": kernel_method",
+                    "      },",
+                    "    ",
+                    "      \"basekernel\": {",
+                    "      \"type\": \"dot\",",
+                    "      \"dot\": {",
+                    "        \"xi\": parseFloat($(\"#basekernel_kernel_xi\").val()),",
+                    "        \"delta\": 1.0",
+                    "        }",
+                    "      },",
+                    "      ",
+                    "      \"topkernel\": {",
+                    "      \"type\": \"rematch\",",
+                    "      \"rematch\": {",
+                    "        \"gamma\": 0.01",
+                    "        },",
+                    "      \"rematch-atomic\": {",
+                    "        \"gamma\": 0.01",
+                    "        },",
+                    "      \"average\": {",
+                    "        \"xi\": 1.0,",
+                    "        \"delta\": 1.0",
+                    "        }",
+                    "       },",
+                    "      ",
+                    "      \"laplacian\": {",
+                    "        \"inverse_dist\": true,",
+                    "        \"coulomb\": true,",
+                    "        \"scale\": 0.01,",
+                    "        \"eta\": 1.0,",
+                    "        \"gamma\": 0.01,",
+                    "        \"optimize_eta_gamma\": false",
+                    "      },",
+                    "      \"dimred\": {",
+                    "        \"method\": $(\"#dimred_method\").val()",
+                    "      },",
+                    "      \"graph\": {",
+                    "        \"descriptor\": \"soap\",",
+                    "        \"pca\": \"none\",",
+                    "        \"hierarchical\": $(\"#kernel_hierarchical\").val() == \"true\",",
+                    "        \"r0\": 1.0,",
+                    "        \"alpha\": 2.0,",
+                    "        \"n_levels\": 3,",
+                    "        \"optimize_hierarchy\": false",
+                    "      },",
+                    "      \"lamatch\": {",
+                    "        \"gamma\": 0.3,",
+                    "        \"optimize_rematch\": false",
+                    "      },",
+                    "",
+                    "    \"descriptor\": {",
+                    "    \"type\": \"soap-atomic-dmap\",",
+                    "    \"soap-atomic\": {",
+                    "      \"spectrum.global\": false,",
+                    "      \"spectrum.gradients\": false,",
+                    "      \"spectrum.2l1_norm\": false,",
+                    "      \"_spectrum.2l1_norm\": true,",
+                    "      \"radialbasis.type\" : \"gaussian\",",
+                    "      \"radialbasis.mode\" : $(\"#soap_radialbasis_mode\").val(),",
+                    "      \"radialbasis.N\" : parseInt($(\"#soap_radialbasis_N\").val()),",
+                    "      \"radialbasis.sigma\": parseFloat($(\"#soap_radialbasis_sigma\").val()),",
+                    "      \"radialbasis.integration_steps\": 15,",
+                    "      \"radialcutoff.Rc\": parseFloat($(\"#soap_radialbasis_Rc\").val()),",
+                    "      \"radialcutoff.Rc_width\": parseFloat($(\"#soap_radialbasis_sigma\").val()),",
+                    "      \"radialcutoff.type\": \"heaviside\",",
+                    "      \"radialcutoff.center_weight\": 1.0,",
+                    "      \"angularbasis.type\": \"spherical-harmonic\",",
+                    "      \"angularbasis.L\": parseInt($(\"#soap_angularbasis_L\").val()),",
+                    "      \"kernel.adaptor\": \"specific-unique\",",
+                    "      \"exclude_centers\": [],",
+                    "      \"exclude_targets\": [],",
+                    "      \"type_list\": []",
+                    "    },",
+                    "    \"soap-atomic-dmap\": {",
+                    "      \"spectrum.global\": false,",
+                    "      \"spectrum.gradients\": false,",
+                    "      \"spectrum.2l1_norm\": false,",
+                    "      \"radialbasis.type\" : \"gaussian\",",
+                    "      \"radialbasis.mode\" : \"adaptive\",",
+                    "      \"radialbasis.N\" : 9,",
+                    "      \"radialbasis.sigma\": 0.5,",
+                    "      \"radialbasis.integration_steps\": 15,",
+                    "      \"radialcutoff.Rc\": 3.5,",
+                    "      \"radialcutoff.Rc_width\": 0.5,",
+                    "      \"radialcutoff.type\": \"heaviside\",",
+                    "      \"radialcutoff.center_weight\": 1.0,",
+                    "      \"angularbasis.type\": \"spherical-harmonic\",",
+                    "      \"angularbasis.L\": 6,",
+                    "      \"kernel.adaptor\": \"specific-unique-dmap\",",
+                    "      \"exclude_centers\": [],",
+                    "      \"exclude_targets\": [],",
+                    "      \"type_list\": []",
+                    "    }",
+                    "  }",
+                    "",
+                    "      ",
+                    "    };",
+                    "",
+                    "}; ",
+                    "  ",
+                    "beaker.view_result = function(result_link) {",
+                    "    $(\"#plot_result_button\").attr(\"href\", result_link);",
+                    "    $(\"#plot_result_button\").removeClass(\"disabled\"); //.addClass(\"active\");",
+                    "}",
+                    "</script>",
+                    "<style type=\"text/css\">",
+                    "    .in11f {",
+                    "        width: 3.5em;",
+                    "    }",
+                    "    .in3d {",
+                    "        width: 5em;",
+                    "    }",
+                    "    .select_main {",
+                    "        width: 20em;",
+                    "    }",
+                    "   .btn.active, .btn:active {",
+                    "    background: #cecece;",
+                    "    text-decoration: none;",
+                    "   }",
+                    "</style>",
+                    "",
+                    "  <p style=\"color:#20335d; font-weight:900; font-size:18pt;\"> Control options Query<br> <hr style=\"border-width:2px\"> </p>",
+                    "",
+                    " <table class=\"query_control\">",
+                    "    ",
+                    "    <!-- SYSTEM REWEIHGTED COMPOSITION -->  ",
+                    "  <tr style=\"line-height:40px\">",
+                    "    <td><b>System composition</b> </td>",
+                    "    <td>",
+                    "      <input type=\"text\" id=\"system_reweighted_composition\" value=\"NaCl\" /> ",
+                    "    </td>",
+                    "  </tr>",
+                    "  ",
+                    "    ",
+                    "    <!-- BASE KERNEL -->    ",
+                    "    <tr style=\"line-height:40px\">",
+                    "      <td><b>Max number or results for each spacegroup</b> </td>",
+                    "      <td>",
+                    "          <input type=\"number\" name=\"quantity\" id=\"max_nb_res\" min=\"1\" max=\"10\" value=\"5\" step=\"1\"> ",
+                    "      </td>",
+                    "    </tr>    ",
+                    "    ",
+                    "   ",
+                    "    ",
+                    "</table>",
+                    "  ",
+                    "<br> <br>",
+                    "",
+                    "  <p style=\"color:#20335d; font-weight:900; font-size:18pt;\"> Control options Analysis (similarity) <br> <hr style=\"border-width:2px\"> </p>",
+                    "  ",
+                    "  ",
+                    "  <table class=\"glosim_control\">",
+                    "    ",
+                    "    <!-- ATOMIC DENSITY -->  ",
+                    "  <tr style=\"line-height:40px\">",
+                    "    <td><b>Atomic density</b> </td>",
+                    "    <td>",
+                    "        <select class=\"select_main\" id=\"atomic_density_type\">",
+                    "        <option id=\"option_el_agno_dens\" value=\"number_density_generic\" SELECTED> Density type: element-agnostic density </option>",
+                    "        <option id=\"option_el_spec_dens\" value=\"number_density\" DISABLED> Density type: element-specific density </option>        ",
+                    "        <option value=\"valence_charge_density\"> Density type: valence charge </option>",
+                    "        <option value=\"z_density\"> Density type: core charge </option>",
+                    "        <option value=\"elneg_density\"> Density type: electronegativity </option>",
+                    "      </select>    <!-- DATASETS -->",
+                    " ",
+                    "       <button id=\"toggle_detail_2\"type=\"button\" class=\"btn btn-xs\" onclick='show_hide(\"in_detail_2\", \"toggle_detail_2\")'>Configure</button>",
+                    "      <g id=\"in_detail_2\" hidden>    Use covalent radii   <input id=\"atomic_density_use_covrad\" type=\"checkbox\" value=\"true\" UNCHECKED/>",
+                    "          Constant atomic radius (Angstrom)   <input id=\"atomic_density_atomic_radius\" type=\"number\" value=\"0.5\" min=\"0.0\" max=\"2.0\" step=\"0.1\" class=\"in11f\" /> </g>",
+                    "    </td>",
+                    "  </tr>",
+                    "  ",
+                    "  <!-- BASIS SET -->  ",
+                    "  <tr style=\"line-height:40px\">",
+                    "    <td><b>Basis set</b> </td>",
+                    "    <td>",
+                    "        <select class=\"select_main\" id=\"soap_radialbasis_mode\">",
+                    "        <option value=\"adaptive\"> Radial basis: adaptive </option>",
+                    "        <option value=\"equispaced\"> Radial basis: equispaced </option>",
+                    "      </select>",
+                    "       <button id=\"toggle_detail_3\"type=\"button\" class=\"btn btn-xs\" onclick='show_hide(\"in_detail_3\", \"toggle_detail_3\")'>Configure</button>",
+                    "      <g id=\"in_detail_3\" hidden>",
+                    "          Radial functions N =   <input id=\"soap_radialbasis_N\" type=\"number\" value=\"9\" min=\"1\" max=\"14\" step=\"1\" class=\"in11f\" />",
+                    "              Radial cutoff (equispaced only)   <input id=\"soap_radialbasis_Rc\" type=\"number\" value=\"3.5\" min=\"0.1\" max=\"10.0\" step=\"0.1\" class=\"in11f\" />",
+                    "              Radial Gaussian width   <input id=\"soap_radialbasis_sigma\" type=\"number\" value=\"0.5\" min=\"0.1\" max=\"3.0\" step=\"0.1\" class=\"in11f\" />",
+                    "          Angular functions L =   <input id=\"soap_angularbasis_L\" type=\"number\" value=\"6\" min=\"1\" max=\"14\" step=\"1\" class=\"in11f\" /> ",
+                    "      </g>",
+                    "    </td>",
+                    "  </tr>    ",
+                    "    ",
+                    "    <!-- BASE KERNEL -->    ",
+                    "    <tr style=\"line-height:40px\">",
+                    "      <td><b>Base kernel</b> </td>",
+                    "      <td>",
+                    "          <select class=\"select_main\" id=\"basekernel_method\">",
+                    "          <option value=\"dot\"> Dot-product kernel </option>",
+                    "          <option value=\"laplacian\" DISABLED> Laplacian kernel </option>",
+                    "          <option value=\"gaussian\" DISABLED> Gaussian kernel </option>",
+                    "        </select>",
+                    "         <button id=\"toggle_detail_4\"type=\"button\" class=\"btn btn-xs\" onclick='show_hide(\"in_detail_4\", \"toggle_detail_4\")'>Configure</button>",
+                    "        <g id=\"in_detail_4\" hidden>",
+                    "            Exponent   <input id=\"basekernel_kernel_xi\" type=\"number\" value=\"3.0\" min=\"0.1\" max=\"5.0\" step=\"0.1\" class=\"in11f\" />",
+                    "        </g>",
+                    "      </td>",
+                    "    </tr>    ",
+                    "    ",
+                    "    <!-- TOP KERNEL -->",
+                    "    <tr style=\"line-height:40px\">",
+                    "      <td><b>Top kernel</b> </td>",
+                    "      <td>",
+                    "          <select class=\"select_main\" id=\"kernel_method\">",
+                    "          <option value=\"global\" SELECTED> Global average (coherent)</option>",
+                    "          <option value=\"average\" > Global average (incoherent)</option>",
+                    "          <option value=\"rematch\" > Regularized-entropy match</option>          ",
+                    "          <option value=\"laplacian\" > Laplacian Markov random field</option>",
+                    "        </select>",
+                    "         <button id=\"toggle_detail_5\"type=\"button\" class=\"btn btn-xs\" onclick='show_hide(\"in_detail_5\", \"toggle_detail_5\")'>Configure</button>",
+                    "        <g id=\"in_detail_5\" hidden>",
+                    "            Mode    ",
+                    "        <select id=\"kernel_hierarchical\">",
+                    "          <option value=\"false\" > single-level</option>",
+                    "          <option value=\"true\" > hierarchical</option>",
+                    "        </select>",
+                    "            Graph Laplacian    ",
+                    "        <select id=\"opt_top_kernel_hierarchy\">",
+                    "          <option value=\"invdist\" > inverse distance</option>",
+                    "          <option value=\"coulomb\" > Coulomb matrix</option>",
+                    "        </select>",
+                    "            Levels   <input id=\"graph:n_levels\" type=\"number\" value=\"1\" min=\"1\" max=\"5\" step=\"1\" class=\"in11f\" />",
+                    "            Base radius   <input id=\"graph:r0\" type=\"number\" value=\"1.0\" min=\"0.1\" max=\"5.0\" step=\"0.1\" class=\"in11f\" />",
+                    "            Scale   <input id=\"graph:alpha\" type=\"number\" value=\"2.0\" min=\"0.1\" max=\"5.0\" step=\"0.1\" class=\"in11f\" />",
+                    "        </g>",
+                    "      </td>",
+                    "    </tr> ",
+                    "    ",
+                    "  <!-- EXECUTION -->",
+                    "  <tr style=\"line-height:40px\">",
+                    "    <td><b>Parallel execution</b></td>",
+                    "    <td>",
+                    "      &nbsp&nbsp<select class=\"select_main\" id=\"threading_mode\">",
+                    "        <option value=\"single_threaded\"> Single-threaded </option>",
+                    "        <option value=\"multi_threaded\" SELECTED> Multi-threaded </option>        ",
+                    "      </select>",
+                    "      &nbsp<button id=\"toggle_detail_7\"type=\"button\" class=\"btn btn-xs\" onclick='show_hide(\"in_detail_7\", \"toggle_detail_7\")'>Configure</button>",
+                    "      <g id=\"in_detail_7\" hidden>",
+                    "          Number of cores   <input id=\"exe_n_procs\" type=\"number\" value=\"2\" min=\"1\" max=\"4\" step=\"1\" class=\"in11f\" />",
+                    "          Batch size   <input id=\"exe_batch_size_parallel\" type=\"number\" value=\"200\" min=\"50\" max=\"1000\" step=\"50\" class=\"in3d\" /> </g>",
+                    "    </td>",
+                    "  </tr>",
+                    "    ",
+                    "</table>",
+                    "  ",
+                    "<hr style=\"border-width:2px\">",
+                    "  ",
+                    "  <button class=\"btn btn-default\" onclick='run_soap()' >RUN Search &amp; Analysis</button> ",
+                    "  <button class=\"btn btn-default\" onclick='reset_soap()'>RESET </button> ",
+                    "  <label title=\"Activate once run is complete.\"> ",
+                    "    <a href=\"#\" target=\"_blank\" class=\"btn btn-primary disabled\" id=\"plot_result_button\" >View 2D similarity map</a> ",
+                    "  </label>",
+                    ""
+                ],
+                "hidden": true
+            },
+            "output": {
+                "state": {},
+                "result": {
+                    "type": "BeakerDisplay",
+                    "innertype": "Html",
+                    "object": "<script>\nvar beaker = bkHelper.getBeakerObject().beakerObj;\n</script>\n<script>\nvar run_soap = function() {\n  $(\"#plot_result_button\").removeClass(\"active\").addClass(\"disabled\");\n  get_options();\n  beaker.evaluate(\"cell_soap_run\");\n};\n  \nvar show_hide = function(tag, bt_tag) {\n  $(\"#\"+tag).toggle();\n  $(\"#\"+bt_tag).toggleClass(\"active\");\n}\n\nvar allow = function(yesno) {\n  if (yesno) {\n    $(\"#option_el_spec_dens\").removeAttr('disabled');\n    $(\"#atomic_density_type\").val('number_density').change();\n  }\n  else {\n    if ($(\"#atomic_density_type\").val() == \"number_density\") {\n      $(\"#atomic_density_type\").val('number_density_generic').change();\n    }\n    $(\"#option_el_spec_dens\").attr('disabled', 'disabled');\n  }\n}\n  \nvar reset_soap = function() {\n  beaker.evaluate(\"cell_soap_gui\");\n};\n  \nvar get_options = function() {\n  \n    var system_reweighted_composition = $(\"#system_reweighted_composition\").val();  \n    var max_nb_res = $(\"#max_nb_res\").val();  \n\n    // Determine kernel adaptor function\n    // [i.e., choose from specific/generic/global-specific/global-generic]    \n    var density_type = $(\"#atomic_density_type\").val();  \n    var adaptor_type = \"?\";\n    if (density_type == \"number_density\") {\n        adaptor_type = \"specific\";\n    }\n    else { // element-agnostic, core charge, valence charge, electronegativity\n        adaptor_type = \"generic\";\n    }\n    var kernel_method = $(\"#kernel_method\").val();\n    if (kernel_method == \"global\") {\n        adaptor_type = \"global-\" + adaptor_type;\n    }\n  \n    var n_procs = parseInt($(\"#exe_n_procs\").val());\n    if ($(\"#threading_mode\").val() == \"single_threaded\") n_procs = 1;\n    \n    beaker.options = {\n      \"query\": {\n        \"system_reweighted_composition\": $(\"#system_reweighted_composition\").val(),\n        \"max_nb_res\": $(\"#max_nb_res\").val()\n      },\n      \"run\": {\n        \"config_folder\": $(\"#dataset_example\").val(),\n        \"n_configs\": -1,\n        \"n_procs\": n_procs,\n        \"n_blocksize\": parseInt($(\"#exe_batch_size\").val()),\n        \"queue\": \"?\",\n        \"walltime\": 12,\n        \"out_folder\": \"out.kernel\",\n        \"verbose\": false\n      },\n      \"atomic_density\": {\n        \"density_type\": $(\"#atomic_density_type\").val(),\n        \"atomic_radius\": parseFloat($(\"#atomic_density_atomic_radius\").val()),\n        \"use_covrad\": $(\"#atomic_density_use_covrad:checked\").val() == \"true\"\n      },\n      \"kernel\": {\n        \"method\": kernel_method\n      },\n    \n      \"basekernel\": {\n      \"type\": \"dot\",\n      \"dot\": {\n        \"xi\": parseFloat($(\"#basekernel_kernel_xi\").val()),\n        \"delta\": 1.0\n        }\n      },\n      \n      \"topkernel\": {\n      \"type\": \"rematch\",\n      \"rematch\": {\n        \"gamma\": 0.01\n        },\n      \"rematch-atomic\": {\n        \"gamma\": 0.01\n        },\n      \"average\": {\n        \"xi\": 1.0,\n        \"delta\": 1.0\n        }\n       },\n      \n      \"laplacian\": {\n        \"inverse_dist\": true,\n        \"coulomb\": true,\n        \"scale\": 0.01,\n        \"eta\": 1.0,\n        \"gamma\": 0.01,\n        \"optimize_eta_gamma\": false\n      },\n      \"dimred\": {\n        \"method\": $(\"#dimred_method\").val()\n      },\n      \"graph\": {\n        \"descriptor\": \"soap\",\n        \"pca\": \"none\",\n        \"hierarchical\": $(\"#kernel_hierarchical\").val() == \"true\",\n        \"r0\": 1.0,\n        \"alpha\": 2.0,\n        \"n_levels\": 3,\n        \"optimize_hierarchy\": false\n      },\n      \"lamatch\": {\n        \"gamma\": 0.3,\n        \"optimize_rematch\": false\n      },\n\n    \"descriptor\": {\n    \"type\": \"soap-atomic-dmap\",\n    \"soap-atomic\": {\n      \"spectrum.global\": false,\n      \"spectrum.gradients\": false,\n      \"spectrum.2l1_norm\": false,\n      \"_spectrum.2l1_norm\": true,\n      \"radialbasis.type\" : \"gaussian\",\n      \"radialbasis.mode\" : $(\"#soap_radialbasis_mode\").val(),\n      \"radialbasis.N\" : parseInt($(\"#soap_radialbasis_N\").val()),\n      \"radialbasis.sigma\": parseFloat($(\"#soap_radialbasis_sigma\").val()),\n      \"radialbasis.integration_steps\": 15,\n      \"radialcutoff.Rc\": parseFloat($(\"#soap_radialbasis_Rc\").val()),\n      \"radialcutoff.Rc_width\": parseFloat($(\"#soap_radialbasis_sigma\").val()),\n      \"radialcutoff.type\": \"heaviside\",\n      \"radialcutoff.center_weight\": 1.0,\n      \"angularbasis.type\": \"spherical-harmonic\",\n      \"angularbasis.L\": parseInt($(\"#soap_angularbasis_L\").val()),\n      \"kernel.adaptor\": \"specific-unique\",\n      \"exclude_centers\": [],\n      \"exclude_targets\": [],\n      \"type_list\": []\n    },\n    \"soap-atomic-dmap\": {\n      \"spectrum.global\": false,\n      \"spectrum.gradients\": false,\n      \"spectrum.2l1_norm\": false,\n      \"radialbasis.type\" : \"gaussian\",\n      \"radialbasis.mode\" : \"adaptive\",\n      \"radialbasis.N\" : 9,\n      \"radialbasis.sigma\": 0.5,\n      \"radialbasis.integration_steps\": 15,\n      \"radialcutoff.Rc\": 3.5,\n      \"radialcutoff.Rc_width\": 0.5,\n      \"radialcutoff.type\": \"heaviside\",\n      \"radialcutoff.center_weight\": 1.0,\n      \"angularbasis.type\": \"spherical-harmonic\",\n      \"angularbasis.L\": 6,\n      \"kernel.adaptor\": \"specific-unique-dmap\",\n      \"exclude_centers\": [],\n      \"exclude_targets\": [],\n      \"type_list\": []\n    }\n  }\n\n      \n    };\n\n}; \n  \nbeaker.view_result = function(result_link) {\n    $(\"#plot_result_button\").attr(\"href\", result_link);\n    $(\"#plot_result_button\").removeClass(\"disabled\"); //.addClass(\"active\");\n}\n</script>\n<style type=\"text/css\">\n    .in11f {\n        width: 3.5em;\n    }\n    .in3d {\n        width: 5em;\n    }\n    .select_main {\n        width: 20em;\n    }\n   .btn.active, .btn:active {\n    background: #cecece;\n    text-decoration: none;\n   }\n</style>\n\n  <p style=\"color:#20335d; font-weight:900; font-size:18pt;\"> Control options Query<br> </p><hr style=\"border-width:2px\"> <p></p>\n\n <table class=\"query_control\">\n    \n    <!-- SYSTEM REWEIHGTED COMPOSITION -->  \n  <tbody><tr style=\"line-height:40px\">\n    <td><b>System composition</b> </td>\n    <td>\n      <input type=\"text\" id=\"system_reweighted_composition\" value=\"NaCl\"> \n    </td>\n  </tr>\n  \n    \n    <!-- BASE KERNEL -->    \n    <tr style=\"line-height:40px\">\n      <td><b>Max number or results for each spacegroup</b> </td>\n      <td>\n          <input type=\"number\" name=\"quantity\" id=\"max_nb_res\" min=\"1\" max=\"10\" value=\"5\" step=\"1\"> \n      </td>\n    </tr>    \n    \n   \n    \n</tbody></table>\n  \n<br> <br>\n\n  <p style=\"color:#20335d; font-weight:900; font-size:18pt;\"> Control options Analysis (similarity) <br> </p><hr style=\"border-width:2px\"> <p></p>\n  \n  \n  <table class=\"glosim_control\">\n    \n    <!-- ATOMIC DENSITY -->  \n  <tbody><tr style=\"line-height:40px\">\n    <td><b>Atomic density</b> </td>\n    <td>\n        <select class=\"select_main\" id=\"atomic_density_type\">\n        <option id=\"option_el_agno_dens\" value=\"number_density_generic\" selected=\"\"> Density type: element-agnostic density </option>\n        <option id=\"option_el_spec_dens\" value=\"number_density\" disabled=\"\"> Density type: element-specific density </option>        \n        <option value=\"valence_charge_density\"> Density type: valence charge </option>\n        <option value=\"z_density\"> Density type: core charge </option>\n        <option value=\"elneg_density\"> Density type: electronegativity </option>\n      </select>    <!-- DATASETS -->\n \n       <button id=\"toggle_detail_2\" type=\"button\" class=\"btn btn-xs\" onclick=\"show_hide(&quot;in_detail_2&quot;, &quot;toggle_detail_2&quot;)\">Configure</button>\n      <g id=\"in_detail_2\" hidden=\"\">    Use covalent radii   <input id=\"atomic_density_use_covrad\" type=\"checkbox\" value=\"true\" unchecked=\"\">\n          Constant atomic radius (Angstrom)   <input id=\"atomic_density_atomic_radius\" type=\"number\" value=\"0.5\" min=\"0.0\" max=\"2.0\" step=\"0.1\" class=\"in11f\"> </g>\n    </td>\n  </tr>\n  \n  <!-- BASIS SET -->  \n  <tr style=\"line-height:40px\">\n    <td><b>Basis set</b> </td>\n    <td>\n        <select class=\"select_main\" id=\"soap_radialbasis_mode\">\n        <option value=\"adaptive\"> Radial basis: adaptive </option>\n        <option value=\"equispaced\"> Radial basis: equispaced </option>\n      </select>\n       <button id=\"toggle_detail_3\" type=\"button\" class=\"btn btn-xs\" onclick=\"show_hide(&quot;in_detail_3&quot;, &quot;toggle_detail_3&quot;)\">Configure</button>\n      <g id=\"in_detail_3\" hidden=\"\">\n          Radial functions N =   <input id=\"soap_radialbasis_N\" type=\"number\" value=\"9\" min=\"1\" max=\"14\" step=\"1\" class=\"in11f\">\n              Radial cutoff (equispaced only)   <input id=\"soap_radialbasis_Rc\" type=\"number\" value=\"3.5\" min=\"0.1\" max=\"10.0\" step=\"0.1\" class=\"in11f\">\n              Radial Gaussian width   <input id=\"soap_radialbasis_sigma\" type=\"number\" value=\"0.5\" min=\"0.1\" max=\"3.0\" step=\"0.1\" class=\"in11f\">\n          Angular functions L =   <input id=\"soap_angularbasis_L\" type=\"number\" value=\"6\" min=\"1\" max=\"14\" step=\"1\" class=\"in11f\"> \n      </g>\n    </td>\n  </tr>    \n    \n    <!-- BASE KERNEL -->    \n    <tr style=\"line-height:40px\">\n      <td><b>Base kernel</b> </td>\n      <td>\n          <select class=\"select_main\" id=\"basekernel_method\">\n          <option value=\"dot\"> Dot-product kernel </option>\n          <option value=\"laplacian\" disabled=\"\"> Laplacian kernel </option>\n          <option value=\"gaussian\" disabled=\"\"> Gaussian kernel </option>\n        </select>\n         <button id=\"toggle_detail_4\" type=\"button\" class=\"btn btn-xs\" onclick=\"show_hide(&quot;in_detail_4&quot;, &quot;toggle_detail_4&quot;)\">Configure</button>\n        <g id=\"in_detail_4\" hidden=\"\">\n            Exponent   <input id=\"basekernel_kernel_xi\" type=\"number\" value=\"3.0\" min=\"0.1\" max=\"5.0\" step=\"0.1\" class=\"in11f\">\n        </g>\n      </td>\n    </tr>    \n    \n    <!-- TOP KERNEL -->\n    <tr style=\"line-height:40px\">\n      <td><b>Top kernel</b> </td>\n      <td>\n          <select class=\"select_main\" id=\"kernel_method\">\n          <option value=\"global\" selected=\"\"> Global average (coherent)</option>\n          <option value=\"average\"> Global average (incoherent)</option>\n          <option value=\"rematch\"> Regularized-entropy match</option>          \n          <option value=\"laplacian\"> Laplacian Markov random field</option>\n        </select>\n         <button id=\"toggle_detail_5\" type=\"button\" class=\"btn btn-xs\" onclick=\"show_hide(&quot;in_detail_5&quot;, &quot;toggle_detail_5&quot;)\">Configure</button>\n        <g id=\"in_detail_5\" hidden=\"\">\n            Mode    \n        <select id=\"kernel_hierarchical\">\n          <option value=\"false\"> single-level</option>\n          <option value=\"true\"> hierarchical</option>\n        </select>\n            Graph Laplacian    \n        <select id=\"opt_top_kernel_hierarchy\">\n          <option value=\"invdist\"> inverse distance</option>\n          <option value=\"coulomb\"> Coulomb matrix</option>\n        </select>\n            Levels   <input id=\"graph:n_levels\" type=\"number\" value=\"1\" min=\"1\" max=\"5\" step=\"1\" class=\"in11f\">\n            Base radius   <input id=\"graph:r0\" type=\"number\" value=\"1.0\" min=\"0.1\" max=\"5.0\" step=\"0.1\" class=\"in11f\">\n            Scale   <input id=\"graph:alpha\" type=\"number\" value=\"2.0\" min=\"0.1\" max=\"5.0\" step=\"0.1\" class=\"in11f\">\n        </g>\n      </td>\n    </tr> \n    \n  <!-- EXECUTION -->\n  <tr style=\"line-height:40px\">\n    <td><b>Parallel execution</b></td>\n    <td>\n      &nbsp;&nbsp;<select class=\"select_main\" id=\"threading_mode\">\n        <option value=\"single_threaded\"> Single-threaded </option>\n        <option value=\"multi_threaded\" selected=\"\"> Multi-threaded </option>        \n      </select>\n      &nbsp;<button id=\"toggle_detail_7\" type=\"button\" class=\"btn btn-xs\" onclick=\"show_hide(&quot;in_detail_7&quot;, &quot;toggle_detail_7&quot;)\">Configure</button>\n      <g id=\"in_detail_7\" hidden=\"\">\n          Number of cores   <input id=\"exe_n_procs\" type=\"number\" value=\"2\" min=\"1\" max=\"4\" step=\"1\" class=\"in11f\">\n          Batch size   <input id=\"exe_batch_size_parallel\" type=\"number\" value=\"200\" min=\"50\" max=\"1000\" step=\"50\" class=\"in3d\"> </g>\n    </td>\n  </tr>\n    \n</tbody></table>\n  \n<hr style=\"border-width:2px\">\n  \n  <button class=\"btn btn-default\" onclick=\"run_soap()\">RUN Search &amp; Analysis</button> \n  <button class=\"btn btn-default\" onclick=\"reset_soap()\">RESET </button> \n  <label title=\"Activate once run is complete.\"> \n    <a href=\"/user/tmp/69476a2fdd65f922.html\" target=\"_blank\" class=\"btn btn-primary\" id=\"plot_result_button\">View 2D similarity map</a> \n  </label>\n"
+                },
+                "selectedType": "BeakerDisplay",
+                "elapsedTime": 0,
+                "height": 618
+            },
+            "evaluatorReader": true,
+            "lineCount": 332,
+            "tags": "cell_soap_gui",
+            "isError": false
+        },
+        {
+            "id": "codeqmgejH",
+            "type": "code",
+            "evaluator": "IPython",
+            "input": {
+                "body": [
+                    "import os",
+                    "import sys",
+                    "import datetime",
+                    "import hashlib",
+                    "import ase.io",
+                    "import logging",
+                    "import json",
+                    "import time",
+                    "import multiprocessing as mp",
+                    "import numpy as np",
+                    "import pickle",
+                    "import h5py",
+                    "",
+                    "import soap",
+                    "import soap.soapy.util",
+                    "import soap.soapy.lagraph",
+                    "import soap.soapy.lamatch",
+                    "from soap.soapy.momo import osio, endl, flush",
+                    "from soap.tools import AseConfig",
+                    "",
+                    "from nomad_sim.nomad_structures import NOMADStructure",
+                    "from nomad_sim.wrappers import get_json_list",
+                    "from nomad_sim.wrappers import plot, logger",
+                    "from nomad_sim.utils_crystals import get_spacegroup",
+                    "from nomad_sim.utils_crystals import create_supercell",
+                    "from nomad_sim.utils_crystals import filter_json_list",
+                    "from nomad_sim.soap_kernel import calc_soap_similarity",
+                    "",
+                    "verbose = False",
+                    "logger.setLevel(logging.INFO)",
+                    "soap.silence()",
+                    "np.set_printoptions(precision=2)",
+                    "",
+                    "logger.info(\"Started @ %s\" % str(datetime.datetime.now()))",
+                    "",
+                    "# LOAD OPTIONS",
+                    "logger.debug(\"Loading options ...\")",
+                    "options = beaker.options # soap.soapy.util.json_load_utf8(open(options_file))",
+                    "logger.info(\"Query parameters: {}.\".format(options['query']))",
+                    "kernel_method = options['kernel']['method']",
+                    "dimred_method = options['dimred']['method']",
+                    "adaptor_type = options['descriptor']['soap-atomic']['kernel.adaptor']",
+                    "density_type = options['atomic_density']['density_type']",
+                    "",
+                    "options_file = '/home/beaker/mnt/options.json'",
+                    "tmp_folder = '/home/beaker/.beaker/v1/web/tmp/'",
+                    "control_file = '/home/beaker/.beaker/v1/web/tmp/control.json'",
+                    "lookup_file = '/home/beaker/.beaker/v1/web/tmp/lookup.dat'",
+                    "",
+                    "data_folder = '/parsed/production/VaspRunParser1.2.0-3-g4facbeb/Rnh_4DFTJQgTSOib4e4d-5GByiTVB'",
+                    "h5_filename = 'configs2.hdf5'",
+                    "",
+                    "",
+                    "# visualize structrues with 3x3 supercells in the Viewer",
+                    "operations_on_structure = [(create_supercell, {'replicas': [3, 3, 3]})]",
+                    "",
+                    "#logger.info(options)",
+                    "dimred_method = 'kernelpca'",
+                    "logger.debug(\"Kernel method:    %s\" % kernel_method)",
+                    "logger.debug(\"Kernel adaptor:   %s\" % adaptor_type)",
+                    "logger.debug(\"Density type:     %s\" % density_type)",
+                    "logger.debug(\"Dim.-red. method: %s\" % dimred_method)",
+                    "",
+                    "# HANDLE SPECIAL CASES",
+                    "if options['graph']['hierarchical'] and kernel_method == 'laplacian':",
+                    "    logger.warn(\"Hierarchical laplacian kernel requested, evaluation may take several minutes. You have 10s to abort ...\")",
+                    "    for i in range(10):",
+                    "        osio << i << osio.flush",
+                    "        time.sleep(1)"
+                ],
+                "hidden": true
+            },
+            "output": {
+                "state": {},
+                "selectedType": "Results",
+                "pluginName": "IPython",
+                "shellId": "C1C6FE2667BD47A5889798855EAC2A94",
+                "elapsedTime": 695,
+                "height": 85
+            },
+            "evaluatorReader": true,
+            "lineCount": 69,
+            "tags": "cell_soap_run",
+            "isError": false
+        },
+        {
+            "id": "codeSVEB46",
+            "type": "code",
+            "evaluator": "IPython",
+            "input": {
+                "body": [
+                    "def read_data (json_list):          ",
+                    "    frame_list = None",
+                    "    frame_list_idcs = [ (0,0) ]",
+                    "    ",
+                    "    data_file_format='NOMAD'      ",
+                    "  ",
+                    "    def get_set_target(ase_struct, nmd_struct, frame_idx, json_idx, json_file):",
+                    "        chemical_formula, energy, label = get_spacegroup(nmd_struct)",
+                    "        #chemical_formula, energy, label = get_lattice_type(nmd_struct)",
+                    "        return label",
+                    "    def get_set_label(ase_struct, nmd_struct, frame_idx, json_idx, json_file):",
+                    "        chemical_formula, energy, label = get_spacegroup(nmd_struct)",
+                    "        return label",
+                    "",
+                    "    op_list = np.zeros(len(json_list))",
+                    "",
+                    "    logger.debug(\"Converting data (%d archives)...\" % len(json_list))",
+                    "    ase_atoms_list = []",
+                    "    nmd_struct_list = []",
+                    "    frame_list_idx_list = []",
+                    "    target_list = []",
+                    "    label_list = []",
+                    "    z_count_global = {}",
+                    "    ",
+                    "    json_list_correct_read = []",
+                    "    for json_idx, json_file in enumerate(json_list):",
+                    "        try:",
+                    "            nmd_struct = NOMADStructure(in_file=json_file, frame_list=frame_list, file_format=data_file_format)",
+                    "            frame_list_idx_list.append([])",
+                    "            for idx in frame_list_idcs:",
+                    "                ase_atoms = nmd_struct.atoms[idx]",
+                    "                ase_atoms_list.append(ase_atoms)",
+                    "                frame_list_idx_list[-1].append(idx[1])",
+                    "                target_list.append(get_set_target(ase_atoms, nmd_struct, idx, json_idx, json_file))",
+                    "                label_list.append(get_set_label(ase_atoms, nmd_struct, idx, json_idx, json_file))",
+                    "            nmd_struct_list.append(nmd_struct)",
+                    "            json_list_correct_read.append(json_file)",
+                    "        except:",
+                    "            logger.debug(\"Problems reading {0}\".format(json_file))        ",
+                    "",
+                    "    # TODO Embed idx/hash. This idx wil be used as an hdf5 tag - ",
+                    "    # probably better to use a unique hash instead.",
+                    "    for idx, c in enumerate(ase_atoms_list):",
+                    "        c.info['idx'] = idx ",
+                    "        c.info['label'] = json_list[idx] ",
+                    "",
+                    "    return ase_atoms_list, target_list, json_list_correct_read"
+                ],
+                "hidden": true
+            },
+            "output": {
+                "state": {},
+                "selectedType": "Hidden",
+                "pluginName": "IPython",
+                "shellId": "C1C6FE2667BD47A5889798855EAC2A94",
+                "elapsedTime": 334,
+                "height": 51
+            },
+            "evaluatorReader": true,
+            "lineCount": 47,
+            "tags": "cell_soap_run",
+            "isError": false
+        },
+        {
+            "id": "code3ZwJgJ",
+            "type": "code",
+            "evaluator": "IPython",
+            "input": {
+                "body": [
+                    "soap_options = soap.soapy.util.json_loads_utf8(\"\"\"",
+                    "    {",
+                    "  \"basekernel\": {",
+                    "    \"type\": \"dot\",",
+                    "    \"dot\": {",
+                    "      \"xi\": 3.0,",
+                    "      \"delta\": 1.0",
+                    "    }",
+                    "  },",
+                    "  \"topkernel\": {",
+                    "    \"type\": \"rematch\",",
+                    "    \"rematch\": {",
+                    "      \"gamma\": 0.01",
+                    "    },",
+                    "    \"rematch-atomic\": {",
+                    "      \"gamma\": 0.01",
+                    "    },",
+                    "    \"average\": {",
+                    "      \"xi\": 1.0,",
+                    "      \"delta\": 1.0",
+                    "    }",
+                    "  },",
+                    "  \"descriptor\": {",
+                    "    \"type\": \"soap-atomic-dmap\",",
+                    "    \"soap-atomic\": {",
+                    "      \"spectrum.global\": false,",
+                    "      \"spectrum.gradients\": false,",
+                    "      \"spectrum.2l1_norm\": false,",
+                    "      \"_spectrum.2l1_norm\": true,",
+                    "      \"radialbasis.type\" : \"gaussian\",",
+                    "      \"radialbasis.mode\" : \"adaptive\",",
+                    "      \"radialbasis.N\" : 9,",
+                    "      \"radialbasis.sigma\": 0.5,",
+                    "      \"radialbasis.integration_steps\": 15,",
+                    "      \"radialcutoff.Rc\": 3.5,",
+                    "      \"radialcutoff.Rc_width\": 0.5,",
+                    "      \"radialcutoff.type\": \"heaviside\",",
+                    "      \"radialcutoff.center_weight\": 1.0,",
+                    "      \"angularbasis.type\": \"spherical-harmonic\",",
+                    "      \"angularbasis.L\": 6,",
+                    "      \"kernel.adaptor\": \"specific-unique\",",
+                    "      \"exclude_centers\": [],",
+                    "      \"exclude_targets\": [],",
+                    "      \"type_list\": []",
+                    "    },",
+                    "    \"soap-atomic-dmap\": {",
+                    "      \"spectrum.global\": false,",
+                    "      \"spectrum.gradients\": false,",
+                    "      \"spectrum.2l1_norm\": false,",
+                    "      \"radialbasis.type\" : \"gaussian\",",
+                    "      \"radialbasis.mode\" : \"adaptive\",",
+                    "      \"radialbasis.N\" : 9,",
+                    "      \"radialbasis.sigma\": 0.5,",
+                    "      \"radialbasis.integration_steps\": 15,",
+                    "      \"radialcutoff.Rc\": 3.5,",
+                    "      \"radialcutoff.Rc_width\": 0.5,",
+                    "      \"radialcutoff.type\": \"heaviside\",",
+                    "      \"radialcutoff.center_weight\": 1.0,",
+                    "      \"angularbasis.type\": \"spherical-harmonic\",",
+                    "      \"angularbasis.L\": 6,",
+                    "      \"kernel.adaptor\": \"specific-unique-dmap\",",
+                    "      \"exclude_centers\": [],",
+                    "      \"exclude_targets\": [],",
+                    "      \"type_list\": []",
+                    "    }",
+                    "  }",
+                    "}",
+                    "    \"\"\")"
+                ],
+                "hidden": true
+            },
+            "output": {
+                "state": {},
+                "selectedType": "Hidden",
+                "pluginName": "IPython",
+                "shellId": "C1C6FE2667BD47A5889798855EAC2A94",
+                "elapsedTime": 353,
+                "height": 58
+            },
+            "evaluatorReader": true,
+            "lineCount": 68,
+            "tags": "cell_soap_run",
+            "isError": false
+        },
+        {
+            "id": "codeyx5LNs",
+            "type": "code",
+            "evaluator": "IPython",
+            "input": {
+                "body": [
+                    "def nomad_id_to_json_path(nomad_id, prefix=\"/parsed/productionJson/\"):",
+                    "    archive = list(nomad_id.split(\"/\")[-2])",
+                    "    archive[0] = 'S'",
+                    "    filename = list(nomad_id.split(\"/\")[-1])",
+                    "    filename[0] = 'P'",
+                    "    json_path = prefix + str(\"\".join(archive)[:3]) + \"/\" + str(\"\".join(archive)) + \"/\" + str(\"\".join(filename)) + \".json\"",
+                    "    return json_path",
+                    "",
+                    "def getJsonPathsFromNomadQuery(query,group):",
+                    "    from urllib2 import urlopen",
+                    "    from urllib import quote_plus",
+                    "    import json",
+                    "    import re",
+                    "    url = 'http://analytics-toolkit.nomad-coe.eu/api/queryGroup/section_run'",
+                    "    params = '?filter=' + quote_plus(query + \" GROUPBY \" + group)",
+                    "    logger.debug(\"Query: {}\".format(url + params))",
+                    "    response = urlopen(url + params).read().decode('utf-8')",
+                    "    buckets=json.loads(response).get(\"result\").get(\"aggregations\").get(\"top_uploader\").get(\"buckets\")",
+                    "    res=[]",
+                    "    for bucket in buckets:",
+                    "      key=bucket.get(\"key\")",
+                    "      for hit in bucket.get(\"top_uploader_hits\").get(\"hits\").get(\"hits\"):",
+                    "         res.append((key,hit.get(\"_id\")))",
+                    "    return res "
+                ]
+            },
+            "output": {
+                "state": {},
+                "selectedType": "Hidden",
+                "pluginName": "IPython",
+                "shellId": "C1C6FE2667BD47A5889798855EAC2A94",
+                "elapsedTime": 332
+            },
+            "evaluatorReader": true,
+            "lineCount": 24,
+            "tags": "cell_soap_run",
+            "isError": false
+        },
+        {
+            "id": "code79GUgq",
+            "type": "code",
+            "evaluator": "IPython",
+            "input": {
+                "body": [
+                    "query = 'system_reweighted_composition:' + options['query']['system_reweighted_composition']   ",
+                    "groupby=\"section_repository_info.repository_spacegroup_nr\"",
+                    "",
+                    "paths = getJsonPathsFromNomadQuery(query,groupby)"
+                ]
+            },
+            "output": {
+                "state": {},
+                "selectedType": "Hidden",
+                "pluginName": "IPython",
+                "shellId": "C1C6FE2667BD47A5889798855EAC2A94",
+                "elapsedTime": 445
+            },
+            "evaluatorReader": true,
+            "lineCount": 4,
+            "tags": "cell_soap_run"
+        },
+        {
+            "id": "codeG5h9tB",
+            "type": "code",
+            "evaluator": "IPython",
+            "input": {
+                "body": [
+                    "# Collect the nomad_ids and obtain json paths grouped by spgroup",
+                    "spgroup_jsons = dict() ",
+                    "for item in paths:",
+                    "    spgroup, nomad_id = item",
+                    "    json_path = nomad_id_to_json_path(nomad_id)",
+                    "    if spgroup in spgroup_jsons:",
+                    "        # append the new filename to existing array at this slot",
+                    "        spgroup_jsons[spgroup].append(json_path)",
+                    "    else:",
+                    "        # create a new array in this slot",
+                    "        spgroup_jsons[spgroup] = [json_path]",
+                    "",
+                    "# encode is ascii for printing",
+                    "spgroups_ascii = [item.encode(\"ascii\") for item in spgroup_jsons.keys()]",
+                    "logger.debug(\"Spacegroups found: {0}\".format(spgroups_ascii))",
+                    "",
+                    "MAX_NB_RES = int(options['query']['max_nb_res'])     #for faster computation",
+                    "MAX_CATEGORIES = 5 #for compatibility with the Viewer",
+                    "",
+                    "# case of NaCl",
+                    "#99 -> strange absorbed structure (optional, but it shows that we can also deal/identify crazy/wrong structures)",
+                    "#191 -> hexagonal structure",
+                    "#194 -> NiAs structure",
+                    "#216 -> Zincblende",
+                    "#225 -> Rocksalt",
+                    "",
+                    "# sort spacegroups according to number of structures, and get top MAX_CATEGORIES",
+                    "sorted_spgroups = sorted([(k, len(v)) for k, v in spgroup_jsons.iteritems()], key=lambda x: x[1], reverse=True)",
+                    "top_k_spgroups = [item[0] for item in sorted_spgroups][:MAX_CATEGORIES]",
+                    "top_k_spgroups = [item.encode(\"ascii\") for item in top_k_spgroups]",
+                    "logger.info(\"Top-{0} spacegroups: {1}\".format(MAX_CATEGORIES, top_k_spgroups))"
+                ],
+                "hidden": true
+            },
+            "output": {
+                "state": {},
+                "selectedType": "Results",
+                "pluginName": "IPython",
+                "shellId": "C1C6FE2667BD47A5889798855EAC2A94",
+                "elapsedTime": 232,
+                "height": 62
+            },
+            "evaluatorReader": true,
+            "lineCount": 31,
+            "tags": "cell_soap_run",
+            "isError": false
+        },
+        {
+            "id": "codebN4dYR",
+            "type": "code",
+            "evaluator": "IPython",
+            "input": {
+                "body": [
+                    "json_list = []",
+                    "target_list = []",
+                    "sp_count=0",
+                    "for key in spgroup_jsons:",
+                    "    if key in top_k_spgroups:",
+                    "        if sp_count < MAX_CATEGORIES:",
+                    "            json_list_spgroup = spgroup_jsons[key][:MAX_NB_RES]",
+                    "            json_list.extend(json_list_spgroup)",
+                    "            for i in range(len(json_list_spgroup)):",
+                    "                target_list.append(key)",
+                    "            sp_count += 1",
+                    "    ",
+                    "logger.debug(\"Processing {} files from the NOMAD Archive\".format(len(json_list)))",
+                    "",
+                    "# use target_list from the NOMAD archive and not nomad_sim",
+                    "# (discrepancy rpobably due to difference thresholds in spglib)",
+                    "ase_atoms_list, _, json_list_correct_read = read_data(json_list)",
+                    "",
+                    "soap_options = beaker.options",
+                    "kmat, dmat = calc_soap_similarity(ase_atoms_list, tmp_folder, h5_filename, soap_options)"
+                ],
+                "hidden": true
+            },
+            "output": {
+                "state": {},
+                "result": {
+                    "type": "Results",
+                    "outputdata": [
+                        {
+                            "type": "out",
+                            "value": "\u001b[92mComputing graphs ... \u001b[0;1m\n"
+                        },
+                        {
+                            "type": "out",
+                            "value": "Descriptor soap-atomic-dmap {\n  \"angularbasis.L\": 6, \n  \"angularbasis.type\": \"spherical-harmonic\", \n  \"exclude_centers\": [], \n  \"exclude_targets\": [], \n  \"kernel.adaptor\": \"specific-unique-dmap\", \n  \"radialbasis.N\": 9, \n  \"radialbasis.integration_steps\": 15, \n  \"radialbasis.mode\": \"adaptive\", \n  \"radialbasis.sigma\": 0.5, \n  \"radialbasis.type\": \"gaussian\", \n  \"radialcutoff.Rc\": 3.5, \n  \"radialcutoff.Rc_width\": 0.5, \n  \"radialcutoff.center_weight\": 1, \n  \"radialcutoff.type\": \"heaviside\", \n  \"spectrum.2l1_norm\": false, \n  \"spectrum.global\": false, \n  \"spectrum.gradients\": false, \n  \"type_list\": []\n} \n"
+                        },
+                        {
+                            "type": "out",
+                            "value": "\r"
+                        },
+                        {
+                            "type": "out",
+                            "value": "[Graph] /parsed/productionJson/SJY/SJYwKZ8zrRB52nhBgpdhktPLdch9O/P2BHv0Y7V5J80cK-jwn5Vp88HiTpE.json \n"
+                        },
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+                        },
+                        {
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+                        },
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+                        },
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+                        },
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+                        },
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+                        },
+                        {
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+                            "value": "\u001b[92mComputing kernel ... \u001b[0;1m\n"
+                        },
+                        {
+                            "type": "out",
+                            "value": "Base-kernel dot {\n  \"delta\": 1, \n  \"xi\": 3\n} \n"
+                        },
+                        {
+                            "type": "out",
+                            "value": "Top-kernel rematch {\n  \"gamma\": 0.01\n} \n"
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+                        {
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+                            "value": "[Kernel] /parsed/productionJson/StW/StWXnFiiVtrVb-3TOz9-k-ogZr2-t/PnYGe2cstDFcd3_Qymm3Wa2k5_jBf.json /parsed/productionJson/Sms/SmspZJAsh6w4QWU6ROe1DfcXJzVtt/PEeyA8ja7CDtGDkxouPx3XpqvuCNp.json \n"
+                        },
+                        {
+                            "type": "out",
+                            "value": "[Kernel] /parsed/productionJson/StW/StWXnFiiVtrVb-3TOz9-k-ogZr2-t/PnYGe2cstDFcd3_Qymm3Wa2k5_jBf.json /parsed/productionJson/SXJ/SXJhcZlYNpglfFL-8H8ypsQSiGKBk/PwnK_ZJzAtliMd_VsZ-nOJhGsDU0k.json \n"
+                        },
+                        {
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+                        },
+                        {
+                            "type": "out",
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+                        },
+                        {
+                            "type": "out",
+                            "value": "[Kernel] /parsed/productionJson/StW/StWXnFiiVtrVb-3TOz9-k-ogZr2-t/PbgiwgunOxXk2mAe8E0WXQsbzRDzx.json /parsed/productionJson/StW/StWXnFiiVtrVb-3TOz9-k-ogZr2-t/PIvqEqW0Nd_BnexG3NN4rDU6WXK0Z.json \n"
+                        },
+                        {
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+                        },
+                        {
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+                        },
+                        {
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+                        },
+                        {
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+                        },
+                        {
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+                        {
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+                        },
+                        {
+                            "type": "out",
+                            "value": "[Kernel] /parsed/productionJson/StW/StWXnFiiVtrVb-3TOz9-k-ogZr2-t/PCPTmlBXoysiELCF1tqwtSrR_BE2R.json /parsed/productionJson/StW/StWXnFiiVtrVb-3TOz9-k-ogZr2-t/PIvqEqW0Nd_BnexG3NN4rDU6WXK0Z.json \n"
+                        },
+                        {
+                            "type": "out",
+                            "value": "[Kernel] /parsed/productionJson/StW/StWXnFiiVtrVb-3TOz9-k-ogZr2-t/PCPTmlBXoysiELCF1tqwtSrR_BE2R.json /parsed/productionJson/SbK/SbKhzgDoURagWFiWCqpn5vl4wR83_/PueP_NZTOk-PgG8zryGPN1Ytm2FZq.json \n"
+                        },
+                        {
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+                            "value": "[Kernel] /parsed/productionJson/StW/StWXnFiiVtrVb-3TOz9-k-ogZr2-t/PCPTmlBXoysiELCF1tqwtSrR_BE2R.json /parsed/productionJson/SjG/SjGkqzG3oJ9eTsxNr_mLFVa8QTmyi/PrdNKJj9t8sMOVomw91_0GK8dH9bQ.json \n"
+                        },
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+                        },
+                        {
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+                            "value": "[Kernel] /parsed/productionJson/StW/StWXnFiiVtrVb-3TOz9-k-ogZr2-t/PCPTmlBXoysiELCF1tqwtSrR_BE2R.json /parsed/productionJson/Sms/SmspZJAsh6w4QWU6ROe1DfcXJzVtt/PEeyA8ja7CDtGDkxouPx3XpqvuCNp.json \n"
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+                        },
+                        {
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+                            "value": "[Kernel] /parsed/productionJson/StW/StWXnFiiVtrVb-3TOz9-k-ogZr2-t/PIvqEqW0Nd_BnexG3NN4rDU6WXK0Z.json /parsed/productionJson/StW/StWXnFiiVtrVb-3TOz9-k-ogZr2-t/PIvqEqW0Nd_BnexG3NN4rDU6WXK0Z.json \n"
+                        },
+                        {
+                            "type": "out",
+                            "value": "[Kernel] /parsed/productionJson/StW/StWXnFiiVtrVb-3TOz9-k-ogZr2-t/PIvqEqW0Nd_BnexG3NN4rDU6WXK0Z.json /parsed/productionJson/SbK/SbKhzgDoURagWFiWCqpn5vl4wR83_/PueP_NZTOk-PgG8zryGPN1Ytm2FZq.json \n"
+                        },
+                        {
+                            "type": "out",
+                            "value": "[Kernel] /parsed/productionJson/StW/StWXnFiiVtrVb-3TOz9-k-ogZr2-t/PIvqEqW0Nd_BnexG3NN4rDU6WXK0Z.json /parsed/productionJson/SjG/SjGkqzG3oJ9eTsxNr_mLFVa8QTmyi/PrdNKJj9t8sMOVomw91_0GK8dH9bQ.json \n"
+                        },
+                        {
+                            "type": "out",
+                            "value": "[Kernel] /parsed/productionJson/StW/StWXnFiiVtrVb-3TOz9-k-ogZr2-t/PIvqEqW0Nd_BnexG3NN4rDU6WXK0Z.json /parsed/productionJson/SjG/SjGkqzG3oJ9eTsxNr_mLFVa8QTmyi/Pg8szKak4RXJBtkrxv7XB3fSRIgjk.json \n"
+                        },
+                        {
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+                            "value": "[Kernel] /parsed/productionJson/StW/StWXnFiiVtrVb-3TOz9-k-ogZr2-t/PIvqEqW0Nd_BnexG3NN4rDU6WXK0Z.json /parsed/productionJson/Sms/SmspZJAsh6w4QWU6ROe1DfcXJzVtt/PEeyA8ja7CDtGDkxouPx3XpqvuCNp.json \n"
+                        },
+                        {
+                            "type": "out",
+                            "value": "[Kernel] /parsed/productionJson/StW/StWXnFiiVtrVb-3TOz9-k-ogZr2-t/PIvqEqW0Nd_BnexG3NN4rDU6WXK0Z.json /parsed/productionJson/SXJ/SXJhcZlYNpglfFL-8H8ypsQSiGKBk/PwnK_ZJzAtliMd_VsZ-nOJhGsDU0k.json \n"
+                        },
+                        {
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+                        },
+                        {
+                            "type": "out",
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+                        },
+                        {
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+                        },
+                        {
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+                        },
+                        {
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+                        },
+                        {
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+                        },
+                        {
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+                        },
+                        {
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+                        },
+                        {
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+                        },
+                        {
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+                        },
+                        {
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+                        },
+                        {
+                            "type": "out",
+                            "value": "[Kernel] /parsed/productionJson/SXJ/SXJhcZlYNpglfFL-8H8ypsQSiGKBk/PwnK_ZJzAtliMd_VsZ-nOJhGsDU0k.json /parsed/productionJson/SXJ/SXJhcZlYNpglfFL-8H8ypsQSiGKBk/PwnK_ZJzAtliMd_VsZ-nOJhGsDU0k.json \n"
+                        }
+                    ]
+                },
+                "selectedType": "Results",
+                "pluginName": "IPython",
+                "shellId": "C1C6FE2667BD47A5889798855EAC2A94",
+                "elapsedTime": 23028,
+                "height": 50,
+                "hidden": true
+            },
+            "evaluatorReader": true,
+            "lineCount": 20,
+            "tags": "cell_soap_run",
+            "isError": false
+        },
+        {
+            "id": "codenaInta",
+            "type": "code",
+            "evaluator": "IPython",
+            "input": {
+                "body": [
+                    "# DECOMPOSE KERNEL MATRIX",
+                    "dimred_positions = soap.soapy.dimred_matrix(dimred_method, kmat=kmat, distmat=dmat)",
+                    "#print dimred_positions[:,0:4]",
+                    "x_list = list(dimred_positions[:,0])",
+                    "y_list = list(dimred_positions[:,1])",
+                    "",
+                    "# write a lookup file for the viewer",
+                    "lookup_out = []",
+                    "for i in range(len(ase_atoms_list)):",
+                    "    lookup_out.append((",
+                    "            json_list_correct_read[i],",
+                    "            '0',",
+                    "            # x_coord",
+                    "            str(x_list[i]),",
+                    "            # y_coord",
+                    "            str(y_list[i]),",
+                    "            # target value",
+                    "            str(target_list[i]),",
+                    "            # chemical_formula",
+                    "            'NaN',",
+                    "            'NaN',",
+                    "            # predicted value (2D descriptor)",
+                    "            'NaN'",
+                    "        ))",
+                    "",
+                    "# write log file with general info about the model",
+                    "with open(lookup_file, \"w\") as f:",
+                    "    f.write(\"\\n\".join([\" \".join(x) for x in lookup_out]))",
+                    "",
+                    "with open(control_file, \"w\") as f:",
+                    "    f.write(\"\"\"",
+                    "    {",
+                    "          \"model_info\":[\"\"\")",
+                    "    writeColon = False",
+                    "",
+                    "    model_info = {",
+                    "            \"x_axis_label\": 'x (kernel pca)',",
+                    "            \"y_axis_label\": 'y (kernel pca)',",
+                    "        }",
+                    "    if (writeColon):",
+                    "        f.write(\", \")",
+                    "            ",
+                    "    writeColon = True",
+                    "    json.dump(model_info, f, indent=2)",
+                    "            ",
+                    "    f.write(\"\"\"",
+                    "    ] }\"\"\")",
+                    "    f.flush()"
+                ],
+                "hidden": true
+            },
+            "output": {
+                "state": {},
+                "selectedType": "Hidden",
+                "pluginName": "IPython",
+                "shellId": "C1C6FE2667BD47A5889798855EAC2A94",
+                "elapsedTime": 698,
+                "height": 88
+            },
+            "evaluatorReader": true,
+            "lineCount": 48,
+            "tags": "cell_soap_run",
+            "isError": true
+        },
+        {
+            "id": "codeyp572I",
+            "type": "code",
+            "evaluator": "IPython",
+            "input": {
+                "body": [
+                    "operations_on_structure = [(create_supercell, {'replicas': [3, 3, 3]})]",
+                    "",
+                    "json_list, frame_list, x_list, y_list, target_list, target_pred_list = get_json_list(method='file', data_folder=data_folder,",
+                    "        path_to_file=lookup_file, drop_duplicates=False, displace_duplicates=True, predicted_value=True)",
+                    "op_list = np.zeros(len(json_list))",
+                    "",
+                    "# get classes from spacegroup value",
+                    "# the classes for the Viewer needs to start from 0 onwards (integers)",
+                    "from sklearn import preprocessing",
+                    "le = preprocessing.LabelEncoder()",
+                    "le.fit(target_list)",
+                    "target_class = le.transform(target_list)",
+                    "classes = list(le.classes_)",
+                    "",
+                    "target_class = [int(item) for item in target_class]",
+                    "",
+                    "# make target_list a list of lists for compatibility with Viewer",
+                    "new_target_list=[]",
+                    "for idx, item in enumerate(target_class):",
+                    "    new_target_list.append([target_class[idx]])",
+                    "",
+                    "name_html_page = hashlib.sha224(str(json_list)).hexdigest()[:16]",
+                    "",
+                    "beaker.viewer_result = name_html_page",
+                    "",
+                    "energy_unit='eV'",
+                    "",
+                    "plot_result = plot(",
+                    "    name=name_html_page, ",
+                    "    json_list=json_list, ",
+                    "    frames='list', ",
+                    "    frame_list=frame_list, ",
+                    "    file_format='NOMAD', ",
+                    "    clustering_x_list=x_list, ",
+                    "    clustering_y_list=y_list, ",
+                    "    # changed to have labels with spacegroup numer",
+                    "    target_list=new_target_list,",
+                    "    target_unit='', ",
+                    "    legend_title='Space group number(classes)', ",
+                    "    #legend_title='Similarity measure', ",
+                    "    target_name='class number',",
+                    "    energy_unit=energy_unit,",
+                    "    plot_title='SOAP structure map',",
+                    "    op_list=op_list, ",
+                    "    operations_on_structure=operations_on_structure,",
+                    "    clustering_point_size=12, ",
+                    "    tmp_folder=tmp_folder, ",
+                    "    control_file=control_file,",
+                    "    descriptor=None,",
+                    "    is_classification=True,",
+                    "    #is_classification=False)",
+                    "    target_class_names=classes)",
+                    "",
+                    "    #log_string=('\\n Options for this run:\\n'+json.dumps(options, indent=2)).replace('\\n','<br>').replace('  ', '&nbsp '))",
+                    "",
+                    "        ",
+                    "# ACTIVATE VIEWER",
+                    "beaker.viewer_result = name_html_page",
+                    "logger.info(\"Finished @ %s\" % datetime.datetime.now())"
+                ],
+                "hidden": true
+            },
+            "output": {
+                "state": {},
+                "selectedType": "Results",
+                "pluginName": "IPython",
+                "shellId": "C1C6FE2667BD47A5889798855EAC2A94",
+                "elapsedTime": 4503,
+                "height": 315
+            },
+            "evaluatorReader": true,
+            "lineCount": 59,
+            "tags": "cell_soap_run",
+            "isError": true
+        },
+        {
+            "id": "codevwRk7a",
+            "type": "code",
+            "evaluator": "JavaScript",
+            "input": {
+                "body": [
+                    "var result_link = '/user/tmp/' + beaker.viewer_result + '.html';",
+                    "beaker.view_result(result_link);"
+                ],
+                "hidden": true
+            },
+            "output": {
+                "state": {},
+                "selectedType": "BeakerDisplay",
+                "pluginName": "JavaScript",
+                "elapsedTime": 20,
+                "height": 125
+            },
+            "evaluatorReader": true,
+            "lineCount": 2,
+            "tags": "cell_soap_run",
+            "isError": true
+        },
+        {
+            "id": "code17MDPY",
+            "type": "code",
+            "evaluator": "HTML",
+            "input": {
+                "body": [
+                    "<h3 style=\"margin-top: 0;\">Feedback</h3>",
+                    "<p>Want to give feedback?<br /><br />",
+                    " <a target=\"_blank\" href=\"https://nomad-forum.rz-berlin.mpg.de\" class=\"btn btn-primary\" style=\"font-size: larger\">Send your feedback to the analytics-toolkit forum</a>",
+                    "</p>",
+                    "<p>Your comments are invaluable in helping us to provide a user-friendly experience for all!<p>"
+                ],
+                "hidden": true
+            },
+            "output": {
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+                "selectedType": "BeakerDisplay",
+                "elapsedTime": 0,
+                "height": 245,
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+                    "innertype": "Html",
+                    "object": "<script>\nvar beaker = bkHelper.getBeakerObject().beakerObj;\n</script>\n<h3 style=\"margin-top: 0;\">Feedback</h3>\n<p>Want to give feedback?<br><br>\n <a target=\"_blank\" href=\"https://nomad-forum.rz-berlin.mpg.de\" class=\"btn btn-primary\" style=\"font-size: larger\">Send your feedback to the analytics-toolkit forum</a>\n</p>\n<p>Your comments are invaluable in helping us to provide a user-friendly experience for all!</p><p></p>"
+                }
+            },
+            "evaluatorReader": true,
+            "lineCount": 5,
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+}