From 0b84d0eaff2e7f19aaf21ccd922cbd3780ce2f7d Mon Sep 17 00:00:00 2001 From: ghuhs Date: Sun, 23 Sep 2018 20:27:55 +0200 Subject: [PATCH] added bkr file --- encyclopedia/encyclopedia.bkr | 12192 ++++++++++++++++++++++++++++++++ 1 file changed, 12192 insertions(+) create mode 100644 encyclopedia/encyclopedia.bkr diff --git a/encyclopedia/encyclopedia.bkr b/encyclopedia/encyclopedia.bkr new file mode 100644 index 0000000..7abbb26 --- /dev/null +++ b/encyclopedia/encyclopedia.bkr @@ -0,0 +1,12192 @@ +{ + "beaker": "2", + "evaluators": [ + { + "name": "HTML", + "plugin": "HTML", + "view": { + "cm": { + "mode": "htmlmixed" + } + } + }, + { + "name": "JavaScript", + "plugin": "JavaScript", + "view": { + "cm": { + "mode": "javascript", + "background": "#FFE0F0" + } + }, + "languageVersion": "ES2015" + }, + { + "name": "Python3", + "plugin": "Python3", + "setup": "%matplotlib inline\nimport numpy\nimport matplotlib\nfrom matplotlib import pylab, mlab, pyplot\nnp = numpy\nplt = pyplot\nfrom IPython.display import display\nfrom IPython.core.pylabtools import figsize, getfigs\nfrom pylab import *\nfrom numpy import *\n", + "view": { + "cm": { + "mode": "python" + } + } + } + ], + "cells": [ + { + "id": "markdownxEENSq", + "type": "markdown", + "body": [ + "", + "", + "
", + "", + "
", + "
", + "

\"NOMAD NOMAD Encyclopedia

", + "
", + "

Encyclopedia API and code usage ", + "

", + "

", + " created by:", + " Lauri Himanen,", + " Georg Huhs, ", + " Iker Hurtado,", + " Martin Kuban,", + " Ioan Vancea,", + " and Claudia Draxl", + " [Last updated: Sep. 20, 2018]", + "

", + "
", + "
", + "", + "
", + "Encyclopedia GUI ", + "Encyclopedia API Documentation ", + "Back to Analytics Home ", + "Back to NOMAD CoE Home ", + "
", + "", + "
", + "", + "
The NOMAD Encyclopedia presents a materials-oriented view on the data of the NOMAD Archive and allows to effectively browse, explore, and visualize the data of NOMAD. ", + "This can be done using the GUI (Graphical User Interface), or using an API (Application Programming Interface). ", + "Both are web-based, which means that the GUI is a web-page accessible with any modern browser, while the API is implemented as RESTful webservice. ", + "This interface can be accessed by any software which supports HTTP requests - even a simple web-browser - and thus allows building client-applications in many languages and environments.
", + "", + "
", + " In this tutorial we focus on Python and JavaScript with the two main parts: ", + "
    ", + "
  1. A demonstration of how a client application can use the NOMAD Encyclopedia REST API for searching and retrieving data.
    Language: Python
    ", + "
  2. How parts of the Encyclopedia code can be integrated into client applications for easily adding complex functionality.
    Language: JavaScript
    ", + "
", + "", + " For both parts also further exercises are provided. ", + "
", + "" + ], + "evaluatorReader": false + }, + { + "id": "sectionBKwlYy", + "type": "section", + "title": "Authentication", + "level": 1, + "evaluatorReader": false, + "collapsed": false + }, + { + "id": "markdown2f786g", + "type": "markdown", + "body": [ + "
The Encyclopedia uses the central NOMAD Authentication system as the Archive and Analytics Tools. As you use this Beaker Notebook, you are alredy logged in.
", + "For using the API you need the access token belonging to your current login. You can get it by calling https://encyclopedia.nomad-coe.eu/api/v1.0/saml/user/
", + "", + "
The response will be something like:", + "", + "
{",
+                "  \"status\": \"Authenticated\", ",
+                "  \"token\": {",
+                "    \"data\": \"eyJleHAiOjE1MzczNDU4MDksImFsZyI6IkhTMjU2IiwiaWF0IjoxNTM3MjU5NDA5fQ.eyJpZCI6ImdodWhzIn0.StCt6vzrBL2RMBpGYSkxu5rRBdcPdvf3oxOF9gpaqHE\", ",
+                "    \"expires_in\": 86400",
+                "  }, ",
+                "  \"user\": {",
+                "    \"email\": \"user@nomad-coe.eu\", ",
+                "    \"username\": \"user\"",
+                "  }",
+                "}
", + "", + "", + "
You find the access token you need in the field token.data.
" + ], + "evaluatorReader": false + }, + { + "id": "sectionz0g9j2", + "type": "section", + "title": "Using the API with Python", + "level": 1, + "evaluatorReader": false, + "collapsed": false + }, + { + "id": "markdownseuh0y", + "type": "markdown", + "body": [ + "
REST (REpresentational State Transfer) is the most used architectural style on the WWW.
", + "It is a stateless client-server architecture, usually using the HTTP protocol, providing resources (in our case the data we are interested in) via so called \"endpoints\".
", + "", + "
The endpoints of the NOMAD Encyclopedia API are described in the API Documentation.
", + "", + "
To access the API using Python, we use the Requests package.
", + "", + "
The following tutorial shows how to use this package for searching materials and accessing some endpoints. It closes with some exercises which need some more processing of the data.
" + ], + "evaluatorReader": false + }, + { + "id": "sectionGwUFtR", + "type": "section", + "title": "Initialization", + "level": 2, + "evaluatorReader": false, + "collapsed": false + }, + { + "id": "markdownqme45G", + "type": "markdown", + "body": [ + "
First we need to load the needed packages and define some basic data.
", + "Please fill in the correct api_access_token for your session and run the cell.
" + ], + "evaluatorReader": false + }, + { + "id": "codePII3SH", + "type": "code", + "evaluator": "Python3", + "input": { + "body": [ + "import requests", + "", + "# ENCYCLOPEDIA API URL", + "nomad_api_url = \"https://encyclopedia.nomad-coe.eu/api/v1.0\"", + "", + "# ENCYCLOPEDIA API Token", + "api_access_token =\"eyJleHAiOjE1Mzc2ODg3ODcsImFsZyI6IkhTMjU2IiwiaWF0IjoxNTM3NjAyMzg3fQ.eyJpZCI6ImdodWhzIn0.XG-ewbOKA5XWqNjOHYYD98mom4W7F6f_8Jazbg9xz_k\"" + ] + }, + "output": { + "state": {}, + "selectedType": "Hidden", + "pluginName": "Python3", + "shellId": "55871189751F468C8A8543299E9A52B4", + "dataresult": "\n\n\n\n\n \n\n NOMAD Encyclopedia\n\n \n\n \n\n \n \n \n \n \n \n \n\n\n\n \n\n\n\n\n\n
\n
\n \n
\n
\n
\n\n
\n Loading\n
\n\n
\n Report error\n
\n\n
\n
\n
\n
\n\n\n
\n\n
\n\n
\n \n \n Introduction to NOMAD Encyclopedia\n \n
\n\n
\n \n\n Guest\n (LOGIN)\n \n\n \n \n \n (logout)\n \n   \n \n \n
\n\n
\n \n The NOMAD Laboratory\n \n \n
\n\n
\n\n
\n \n\n\n
\n\n
\n
\n \n\n
\n\n
\n
\n Additional information  \n \n
\n
\n
\n
\n\n
\n\n
\n
\n\n\n \n\n\n" + }, + "evaluatorReader": true, + "lineCount": 7 + }, + { + "id": "sectionhitis6", + "type": "section", + "title": "Searching for materials", + "level": 2, + "evaluatorReader": false, + "collapsed": false + }, + { + "id": "markdownhHqQEd", + "type": "markdown", + "body": [ + "
Similarly to the GUI-usage we start with searching for a material. This has to be done via a POST request.
", + "Here we do a very simple search for pure silver.
", + "", + "
The post function returns a Response object, which contains all data of the response-part of the query.
", + "Here we check first the status code, which is always a good idea. The API documentation tells us, that a status code of 200 means, that everything went well.
" + ], + "evaluatorReader": false + }, + { + "id": "codeA2OtbW", + "type": "code", + "evaluator": "Python3", + "input": { + "body": [ + "nomad_search_url = nomad_api_url + \"/materials\"", + "r = requests.post(nomad_search_url, auth=(api_access_token, ''), \\", + " json = {\"search_by\":{\"element\": \"Ag\", \"exclusive\": \"1\"}})", + "r.status_code" + ] + }, + "output": { + "state": {}, + "selectedType": "Html", + "pluginName": "Python3", + "shellId": "55871189751F468C8A8543299E9A52B4", + "dataresult": 200, + "height": 54 + }, + "evaluatorReader": true, + "lineCount": 4 + }, + { + "id": "markdownTUd10S", + "type": "markdown", + "body": [ + "
The Response object also contains the content we are actually interested in:
", + "
Hint: you can collapse the cell to hide this pretty long answer.
" + ], + "evaluatorReader": false + }, + { + "id": "codemjL29D", + "type": "code", + "evaluator": "Python3", + "input": { + "body": [ + "# check the results of our search", + "content = r.json()", + "content" + ] + }, + "output": { + "state": {}, + "selectedType": "Html", + "pluginName": "Python3", + "shellId": "55871189751F468C8A8543299E9A52B4", + "dataresult": { + "results": [ + { + "space_group": 166, + "id": 174606, + "nr_of_calculations_matching_criteria": 3, + "nr_of_calculations": 3, + "structure_type": "prototype: As (alpha)", + "formula_reduced": "Ag", + "material_name": "Silver", + "system_type": "bulk", + "calculations_list_matching_criteria": [ + 332474, + 563999, + 937861 + ], + "formula": "Ag" + }, + { + "space_group": 227, + "id": 39598, + "nr_of_calculations_matching_criteria": 98, + "nr_of_calculations": 98, + "structure_type": "prototype: C (diamond)", + "formula_reduced": "Ag", + "material_name": "Silver", + "system_type": "bulk", + 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"nr_of_calculations": 2, + "structure_type": "prototype: Mn (beta)", + "formula_reduced": "Ag", + "material_name": "Silver", + "system_type": "bulk", + "calculations_list_matching_criteria": [ + 712461, + 712526 + ], + "formula": "Ag20" + }, + { + "space_group": 139, + "id": 148904, + "nr_of_calculations_matching_criteria": 58, + "nr_of_calculations": 58, + "structure_type": "prototype: Si (bct5)", + "formula_reduced": "Ag", + "material_name": "Silver", + "system_type": "bulk", + "calculations_list_matching_criteria": [ + 287467, + 317614, + 366883, + 418893, + 467464, + 467642, + 498491, + 563742, + 564104, + 591378, + 615773, + 615849, + 712899, + 713349, + 803676, + 803940, + 912554, + 912689, + 937395, + 937479, + 945056, + 945344, + 1279464, + 1340531, + 1349686, + 1645071, + 1645122, + 1653480, + 1653696, + 1725160, + 1732532, + 1764996, + 1765196, + 1813083, + 1882880, + 2027834, + 2031088, + 2031221, + 2077904, + 2101415, + 2101515, + 2377561, + 2484755, + 2484799, + 2488757, + 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(bcc)", + "formula_reduced": "Ag", + "material_name": "Silver", + "system_type": "bulk", + "calculations_list_matching_criteria": [ + 76246, + 203287, + 287570, + 287499, + 290675, + 290679, + 339415, + 366920, + 418828, + 467736, + 563665, + 591296, + 713180, + 803399, + 803838, + 912404, + 937834, + 1279751, + 1340744, + 1349807, + 1352131, + 1352212, + 1668352, + 1668334, + 1725368, + 1732339, + 1764951, + 1765050, + 1813000, + 1883121, + 2031348, + 2377481, + 2488672, + 2499170, + 2595046, + 2595120, + 2617065, + 2616862, + 2622722, + 3234356 + ], + "formula": "Ag" + }, + { + "space_group": 223, + "id": 342371, + "nr_of_calculations_matching_criteria": 2, + "nr_of_calculations": 2, + "structure_type": null, + "formula_reduced": "Ag", + "material_name": "Silver", + "system_type": "bulk", + "calculations_list_matching_criteria": [ + 770424, + 770519 + ], + "formula": "Ag8" + }, + { + "space_group": 69, + "id": 39586, + "nr_of_calculations_matching_criteria": 35, + "nr_of_calculations": 35, + "structure_type": null, + "formula_reduced": "Ag", + "material_name": "Silver", + "system_type": "bulk", + "calculations_list_matching_criteria": [ + 76358, + 270775, + 287625, + 339314, + 363107, + 363142, + 363878, + 363963, + 366792, + 498430, + 506578, + 506711, + 591299, + 1279650, + 1340627, + 1349653, + 1725231, + 1732562, + 1813044, + 1813181, + 1813306, + 1882793, + 2027914, + 2077890, + 2377796, + 2488467, + 2499224, + 2594987, + 2622560, + 2658621, + 2938955, + 2938987, + 2980788, + 3001339, + 3234354 + ], + "formula": "Ag2" + }, + { + "space_group": 164, + "id": 39577, + "nr_of_calculations_matching_criteria": 20, + "nr_of_calculations": 20, + "structure_type": null, + "formula_reduced": "Ag", + "material_name": "Silver", + "system_type": "bulk", + "calculations_list_matching_criteria": [ + 76333, + 366887, + 418995, + 467508, + 591324, + 712883, + 912390, + 1279704, + 1340813, + 1349724, + 1725100, + 1732538, + 1812907, + 1882874, + 2031603, + 2377542, + 2488451, + 2499222, + 2622871, + 3234351 + ], + "formula": "Ag6" + } + ], + "pages": null, + "total_results": 16 + }, + "height": 51, + "hidden": true + }, + "evaluatorReader": true, + "lineCount": 3 + }, + { + "id": "markdownz0zXAD", + "type": "markdown", + "body": [ + "
We see that this response contains only very basic data about the material, but at the same time it is already too long to be nicely readable. So now we want to extract more specific information.
", + "At the top level we find a dictionary, containing the pages key, indicating that pagination can be used (not part of this tutorial), and a list of results
", + "
To get the number of results one can either count this list's entries, or look it up with the key total_results. When using pagination, these numbers will differ!
" + ], + "evaluatorReader": false + }, + { + "id": "codescgBgO", + "type": "code", + "evaluator": "Python3", + "input": { + "body": [ + "# check the number of results by counting the entries in \"results\" list", + "len_results = len(content['results'])", + "print(\"Nr of entries in 'results': {}\".format(len_results))", + "", + "# get the total number of results", + "nr_total_results = content['total_results']", + "print(\"Total number of results: {}\".format(nr_total_results))", + "" + ] + }, + "output": { + "state": {}, + "selectedType": "Results", + "pluginName": "Python3", + "shellId": "55871189751F468C8A8543299E9A52B4", + "dataresult": 16, + "height": 81 + }, + "evaluatorReader": true, + "lineCount": 8 + }, + { + "id": "markdownSAg3ti", + "type": "markdown", + "body": [ + "
To get an overview of the result set, we can show some basic information for every material found:
" + ], + "evaluatorReader": false + }, + { + "id": "codelITufj", + "type": "code", + "evaluator": "Python3", + "input": { + "body": [ + "# let's show the formula, reduced formula, space_group, and number of calculations for each material found", + "for material in content['results']:", + " print(\"material ID: \", material['id'], ", + " \"\\tcell-formula: \", material['formula'], ", + " \"\\treduced formula: \", material['formula_reduced'], ", + " \"\\tspace_group: \", material['space_group'], ", + " \"\\tnr of calculations: \", material[\"nr_of_calculations\"])" + ] + }, + "output": { + "state": {}, + "selectedType": "Results", + "pluginName": "Python3", + "shellId": "55871189751F468C8A8543299E9A52B4", + "height": 78 + }, + "evaluatorReader": true, + "lineCount": 7 + }, + { + "id": "markdownSLej37", + "type": "markdown", + "body": [ + "
For machine-processing often lists are more relevant. As an example, we generate a list of all material-IDs:
" + ], + "evaluatorReader": false + }, + { + "id": "coder8V4ns", + "type": "code", + "evaluator": "Python3", + "input": { + "body": [ + "id_list =[material['id'] for material in content['results']]", + "print(id_list)" + ] + }, + "output": { + "state": {}, + "selectedType": "Results", + "pluginName": "Python3", + "shellId": "55871189751F468C8A8543299E9A52B4", + "height": 115 + }, + "evaluatorReader": true, + "lineCount": 2 + }, + { + "id": "sectionOiaR30", + "type": "section", + "title": "Querying for a specific material", + "level": 2, + "evaluatorReader": false, + "collapsed": false + }, + { + "id": "markdowneWHUPG", + "type": "markdown", + "body": [ + "
In the list above we see, that material with ID 39574 features most calculations, so let's see what it is.
", + "
In order to do so, we address the right endpoint with a get request and show the response:
" + ], + "evaluatorReader": false + }, + { + "id": "codeCqDc0n", + "type": "code", + "evaluator": "Python3", + "input": { + "body": [ + "nomad_material_url = nomad_api_url + \"/materials\"", + "material_39574 = requests.get(nomad_material_url + \"/39574\", auth=(api_access_token, ''))", + "material_39574.json()" + ] + }, + "output": { + "state": {}, + "selectedType": "Html", + "pluginName": "Python3", + "shellId": "55871189751F468C8A8543299E9A52B4", + "dataresult": { + "bravais_lattice": "cF", + "has_free_wyckoff_parameters": false, + "space_group": 225, + "structure_type": "prototype: Cu (fcc)", + "material_name": "Silver", + "cell_angles_string": "90.0/90.0/90.0", + "periodicity": null, + "material_hash": "2e5a712a699dcdf02ec0128a7c8f453c7b1fbc841d8d680c5a0e1d0ef5dd4b1ae70c22f050589a08383a7cdb711fc68aa50d6965478a1ae457c997d4a44ad276", + "crystal_system": "cubic", + "system_type": "bulk", + "formula_reduced": "Ag", + "point_group": "m-3m", + "id": 39574, + "formula": "Ag" + }, + "height": 492 + }, + "evaluatorReader": true, + "lineCount": 3 + }, + { + "id": "sectionJpG1S0", + "type": "section", + "title": "Working with calculations", + "level": 2, + "evaluatorReader": false, + "collapsed": false + }, + { + "id": "markdownb5oyT3", + "type": "markdown", + "body": [ + "
If we are interested in the calculations done for this material, we can go deeper in the hierarchy of endpoints and extract the JSON with this information:
" + ], + "evaluatorReader": false + }, + { + "id": "codeSEXd4m", + "type": "code", + "evaluator": "Python3", + "input": { + "body": [ + "nomad_39574_calcs_url = nomad_api_url + \"/materials/39574/calculations\"", + "material_39574_calcs = requests.get(nomad_39574_calcs_url, auth=(api_access_token, ''))", + "calculations = material_39574_calcs.json()", + "calculations" + ] + }, + "output": { + "state": {}, + "selectedType": "Html", + "pluginName": "Python3", + "shellId": "55871189751F468C8A8543299E9A52B4", + "dataresult": { + "results": [ + { + "core_electron_treatment": "pseudopotential", + "gw_type": "", + "has_dos": false, + "group_eos_hash": "3d447accb8082e23b51c99f7c6af5a16fe8d857b63845a5db04938096d56eddccf5780efb54d2ed0f27a7b18e0bfc82031d128dc6e94fe8f1dccf90c5bb1b770", + "smearing": "(none,0)", + "functional_type": "GGA", + "brillouin_zone_json": { + "basis": [ + [ + -2408554215.379942, + 2408554215.379942, + 2408554215.379942 + ], + [ + 2408554215.379942, + -2408554215.379942, + 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"http://encyclopedia.nomad-coe.eu/v1.0/materials/39574/calculations?per_page=25&page=1", + "next_url": "http://encyclopedia.nomad-coe.eu/v1.0/materials/39574/calculations?per_page=25&page=2", + "prev_url": null, + "page": 1, + "total": 495 + }, + "total_results": 495 + }, + "height": 273, + "hidden": true + }, + "evaluatorReader": true, + "lineCount": 4 + }, + { + "id": "markdown2gYzbJ", + "type": "markdown", + "body": [ + "
We see, that now pagination is used, so we don't get the full result set at once.
", + "Again we can check the total number of results:
" + ], + "evaluatorReader": false + }, + { + "id": "codeZPt7fn", + "type": "code", + "evaluator": "Python3", + "input": { + "body": [ + "# check how many calculations we have available for this specific material", + "calculations['total_results']" + ] + }, + "output": { + "state": {}, + "selectedType": "Html", + "pluginName": "Python3", + "shellId": "55871189751F468C8A8543299E9A52B4", + "dataresult": 495, + "height": 276 + }, + "evaluatorReader": true, + "lineCount": 2 + }, + { + "id": "markdownCuomEM", + "type": "markdown", + "body": [ + "
Let's peek into this list and see if we find calculations with DOS data:
" + ], + "evaluatorReader": false + }, + { + "id": "codeGl3ViA", + "type": "code", + "evaluator": "Python3", + "input": { + "body": [ + "# get the \"id\" and the \"functional long name\" property for the first calculation in our list", + "for idx in range(10):", + " calc_id = calculations['results'][idx]['id']", + " functional = calculations['results'][idx]['functional_type']", + " has_dos = calculations['results'][idx]['has_dos']", + " print(\"ID: \", calc_id, \"\\tDOS: \", str(has_dos), \"\\tfunctional: \", functional)" + ] + }, + "output": { + "state": {}, + "selectedType": "Results", + "pluginName": "Python3", + "shellId": "55871189751F468C8A8543299E9A52B4", + "dataresult": "GGA_C_PBE+GGA_X_PBE", + "height": 427 + }, + "evaluatorReader": true, + "lineCount": 6 + }, + { + "id": "markdownZdoDfb", + "type": "markdown", + "body": [ + "
If we are interested in specific properties, we can request it specifically. This avoids sending and processing large responses with data we are mostly not interested in.
", + "We see, that the first GGA calculation with DOS data has the ID 164573. This data is requested by:
" + ], + "evaluatorReader": false + }, + { + "id": "codefaPv6Q", + "type": "code", + "evaluator": "Python3", + "input": { + "body": [ + "nomad_calc_url = nomad_39574_calcs_url + \"/164573?property=dos\"", + "r = requests.get(nomad_calc_url, auth=(api_access_token, ''))", + "dos = r.json()", + "dos" + ] + }, + "output": { + "state": {}, + "selectedType": "Html", + "pluginName": "Python3", + "shellId": "55871189751F468C8A8543299E9A52B4", + "dataresult": { + "dos": { + "dos_energies": [ + -4.3400558932905e-18, + -4.3352493637005e-18, + -4.3304268123452e-18, + -4.3256202827552004e-18, + -4.3208137531651996e-18, + -4.3159912018098994e-18, + -4.3111846722199e-18, + -4.3063781426299e-18, + -4.3015716130399e-18, + -4.2967490616846e-18, + -4.2919425320946005e-18, + -4.2871360025046e-18, + -4.2823134511493e-18, + -4.2775069215593e-18, + -4.2727003919692994e-18, + -4.267877840613999e-18, + -4.263071311024e-18, + -4.258264781434e-18, + -4.253458251844e-18, + -4.2486357004887004e-18, + 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"hidden": true + }, + "evaluatorReader": true, + "lineCount": 4 + }, + { + "id": "markdownnrBQvQ", + "type": "markdown", + "body": [ + "
Again, due to the large amount of values, the response is quite long. To examine it more systematically, we can see which keys the dictionary contains:
" + ], + "evaluatorReader": false + }, + { + "id": "codejmh1zU", + "type": "code", + "evaluator": "Python3", + "input": { + "body": [ + "dos['dos'].keys()" + ] + }, + "output": { + "state": {}, + "selectedType": "Html", + "pluginName": "Python3", + "shellId": "55871189751F468C8A8543299E9A52B4", + "dataresult": "dict_keys(['dos_energies', 'dos_values'])", + "height": 276 + }, + "evaluatorReader": true, + "lineCount": 1 + }, + { + "id": "markdownCCyO7n", + "type": "markdown", + "body": [ + "
We see that these keywords correspond to the keys in the NOMAD Metainfo: dos_energies and dos_values
", + "In the Metainfo definition we also find, that the values are a two-dimensional array, with the first dimension holding the spin-channels. As all data in the Archive is in SI units, we better scale the data to be shown in eV.
", + "We can extract and plot the DOS for the first spin channel as follows:
" + ], + "evaluatorReader": false + }, + { + "id": "codeMK8XPq", + "type": "code", + "evaluator": "Python3", + "input": { + "body": [ + "import numpy as np", + "import matplotlib.pyplot as plt", + "", + "energies = np.array(dos['dos']['dos_energies'])", + "values = np.array(dos['dos']['dos_values'][0])", + "", + "# rescale the energy values by atomic unit of charge: 1.602176565e-19 (C)", + "energies_ev = energies/1.602176565e-19", + "", + "# plotting it", + "plot = plt.plot(values, energies_ev, color=\"darkorange\", linewidth=1.5)" + ] + }, + "output": { + "state": {}, + "selectedType": "Html", + "pluginName": "Python3", + "shellId": "55871189751F468C8A8543299E9A52B4", + "height": 597 + }, + "evaluatorReader": true, + "lineCount": 11 + }, + { + "id": "sectionwRMqPk", + "type": "section", + "title": "Exercises", + "level": 2, + "evaluatorReader": false, + "collapsed": false + }, + { + "id": "sectionDSvU8Q", + "type": "section", + "title": "A) Advanced material search and DOS processing", + "level": 3, + "evaluatorReader": false, + "collapsed": false + }, + { + "id": "markdownN0P1C2", + "type": "markdown", + "body": [ + "
For the material Al2O3 with space group 167 are various calculations with DOS data available.
", + "", + "" + ], + "evaluatorReader": false + }, + { + "id": "sectionOOpMqx", + "type": "section", + "title": "B) Band structure", + "level": 3, + "evaluatorReader": false, + "collapsed": false + }, + { + "id": "markdown6sO041", + "type": "markdown", + "body": [ + "
Another type of data of high interest is the electronic band structure of a material. ", + "This data is way more complex, as it consists of various bands in several sections of the k-point path, and some additional information like the labels of the section borders (high symmetry points).
", + "", + "", + "" + ], + "evaluatorReader": false + }, + { + "id": "sectionmbwzC8", + "type": "section", + "title": "Structure viewer", + "level": 1, + "evaluatorReader": false, + "collapsed": false + }, + { + "id": "markdowngHPxNx", + "type": "markdown", + "body": [ + "
This tutorial will demonstrate the use of the browser-based structure visualization that we have developed for the Encyclopedia.
", + "We will first setup the visualization so that it can be accessed on a local machine through any browser.
", + "Then we will go through the basics of how to interact with the visualization and how to customize it. Finally we will visualize different structures by modifying the Javascript code.
", + "Through these tasks we show that the visualization tool is suitable for various atomic structure visualization tasks and can be easily integrated also into third-party websites.
" + ], + "evaluatorReader": false + }, + { + "id": "sectionrLU5Te", + "type": "section", + "title": "Setup", + "level": 2, + "evaluatorReader": false, + "collapsed": false + }, + { + "id": "markdown9ajmE2", + "type": "markdown", + "body": [ + "
    ", + "
  1. Download the file enc_viewer_tutorial.zip
    2. ", + "
  2. Unzip its contents to you local computer.
    3. ", + "
  3. Open the index.html file on a web browser of your choice.
    4. ", + "
", + "", + "
The browser should display a default structure.
" + ], + "evaluatorReader": false + }, + { + "id": "sectionkBlhrL", + "type": "section", + "title": "Interaction with the structure", + "level": 2, + "evaluatorReader": false, + "collapsed": false + }, + { + "id": "markdown0TYVXO", + "type": "markdown", + "body": [ + "
You can use your mouse to control the structure visualization.
", + "", + "" + ], + "evaluatorReader": false + }, + { + "id": "sectionRLEwiV", + "type": "section", + "title": "Changing the default visualization settings", + "level": 2, + "evaluatorReader": false, + "collapsed": false + }, + { + "id": "markdownzYVzxy", + "type": "markdown", + "body": [ + "
In the browser you can see an orange settings panel at the top left corner. Through it you can control the visualization settings:
", + "", + "" + ], + "evaluatorReader": false + }, + { + "id": "sectionJwLfZd", + "type": "section", + "title": "Changing the Structure", + "level": 2, + "evaluatorReader": false, + "collapsed": false + }, + { + "id": "markdownzDGtvr", + "type": "markdown", + "body": [ + "
Open the index.html in a text editor of your choice. Inside it you will see a", + "<script> element at the bottom. This is where the visualization is set up.
", + "There are predefined examples that you can activate by changing the the", + "variable name in the viewer.load()-function.
", + "", + "
The examples include:
", + "", + "", + "
After making changes, you will have to refresh the browser in order to see the new visualization.
" + ], + "evaluatorReader": false + }, + { + "id": "sectionNixWVD", + "type": "section", + "title": "Technical details", + "level": 2, + "evaluatorReader": false, + "collapsed": false + }, + { + "id": "markdownmL628A", + "type": "markdown", + "body": [ + "
The viewer is created with a Javascript library called three.js, which is used to wrap the WebGL-calls into easily", + "accessible Javascript objects and functions.
", + "The WebGL-acceleration enables smooth real-time 3D rendering on the browser.", + "Most modern browsers support this feature, but also as a fallback we provide a", + "canvas-based rendering if WebGL is not available.
", + "Using the visualizer on a third-party website is as easy as importing the", + "needed dependencies and creating a StructureViewer-object with a DOM-element", + "and the visualization data, as seen in these examples.
", + "For a more easily accessible and centralized distribution of this viewer, an npm-based", + "(https://www.npmjs.com/) package can be made.
" + ], + "evaluatorReader": false + }, + { + "id": "sectionRpoQ6b", + "type": "section", + "title": "Exercise", + "level": 2, + "evaluatorReader": false, + "collapsed": false + }, + { + "id": "markdown0xRXjz", + "type": "markdown", + "body": [ + "
The following code ", + "(also downloadble here) ", + "provides some routines for accessing the API and preparing the crystal structure data for the 3D viewer.
", + "", + "" + ], + "evaluatorReader": false + }, + { + "id": "markdownxsXzgn", + "type": "markdown", + "body": [ + "
function apiReq(materialId, dataType, authToken, callback){",
+                "  let oReq = new XMLHttpRequest();",
+                "  oReq.addEventListener(\"load\", callback);",
+                "  oReq.open(\"GET\", \"https://encyclopedia-api.nomad-coe.eu/v1.0/materials/\"+materialId+\"/\"+dataType);",
+                "  oReq.setRequestHeader('Authorization', 'Basic '+btoa(authToken));",
+                "  oReq.send();",
+                "  return oReq;",
+                "}",
+                "",
+                "",
+                "function getMaterialStructureDataFromAPI(materialId, authToken, callback){",
+                "",
+                "  apiReq(materialId, 'elements', authToken, e => {",
+                "          let elements = JSON.parse(e.target.response).results;",
+                "",
+                "          apiReq(materialId, 'cells', authToken, e1 => {",
+                "                  let cells = JSON.parse(e1.target.response).results;",
+                "                  let cell;",
+                "                  if (!cells[0].is_primitive) cell= cells[0];",
+                "                  else cell= cells[1];",
+                "",
+                "                  callback(getCellDataForViewer(elements, cell));",
+                "          });",
+                "  });",
+                "}",
+                "",
+                "",
+                "function getNumberArray(string){",
+                "  let sArray= string.substring(1,string.length-1).split(',');",
+                "  let fArray= [];",
+                "  for (let i = 0; i < sArray.length; i++) {",
+                "    fArray.push(parseFloat(sArray[i]));",
+                "  }",
+                "  return fArray;",
+                "}",
+                "",
+                "",
+                "function getCellDataForViewer(elements, cell){",
+                "  let cellData= {};",
+                "  cellData.normalizedCell= [",
+                "    getNumberArray(cell.a),",
+                "    getNumberArray(cell.b),",
+                "    getNumberArray(cell.c)",
+                "  ];",
+                "",
+                "  cellData.labels= [];",
+                "  cellData.positions= [];",
+                "",
+                "  for (let i = 0; i < elements.length; i++) {",
+                "    cellData.labels.push(elements[i].label);",
+                "    cellData.positions.push(getNumberArray(elements[i].position));",
+                "  }",
+                "",
+                "  //cellData.periodicity = JSON.parse(matData.periodicity);",
+                "",
+                "  return cellData;",
+                "}
" + ], + "evaluatorReader": false + } + ], + "namespace": {} +} -- GitLab