diff --git a/.ipynb_checkpoints/band_structure_visualization-checkpoint.ipynb b/.ipynb_checkpoints/band_structure_visualization-checkpoint.ipynb
new file mode 100644
index 0000000000000000000000000000000000000000..b2c4549632725c1ee3c50a465af06e961f44b6c1
--- /dev/null
+++ b/.ipynb_checkpoints/band_structure_visualization-checkpoint.ipynb
@@ -0,0 +1,4968 @@
+{
+ "cells": [
+ {
+ "cell_type": "code",
+ "execution_count": 1,
+ "metadata": {
+ "init_cell": true
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "<style>.container { width:100% !important; }</style>"
+ ],
+ "text/plain": [
+ "<IPython.core.display.HTML object>"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "from IPython.core.display import display, HTML\n",
+ "display(HTML(\"<style>.container { width:100% !important; }</style>\"))\n",
+ "\n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 2,
+ "metadata": {
+ "init_cell": true
+ },
+ "outputs": [],
+ "source": [
+ "from IPython.core.display import Javascript\n",
+ "from IPython.display import display\n",
+ "\n",
+ "def run_cell_by_tag(tags):\n",
+ " display(Javascript(\"window.runCells('\"+tags+\"')\"))"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 3,
+ "metadata": {
+ "init_cell": true,
+ "scrolled": true
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "<script>\n",
+ " code_show=true; \n",
+ " function code_toggle() {\n",
+ " if (code_show)\n",
+ " {\n",
+ " $('div.input').hide();\n",
+ " } \n",
+ " else \n",
+ " {\n",
+ " $('div.input').show();\n",
+ " }\n",
+ " code_show = !code_show\n",
+ " } \n",
+ " $( document ).ready(code_toggle);\n",
+ "</script>\n",
+ "The raw code for this notebook is by default hidden for easier reading.\n",
+ "To toggle on/off the raw code, click <a href=\"javascript:code_toggle()\">here</a>.\n"
+ ],
+ "text/plain": [
+ "<IPython.core.display.HTML object>"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "%%HTML\n",
+ "<script>\n",
+ " code_show=true; \n",
+ " function code_toggle() {\n",
+ " if (code_show)\n",
+ " {\n",
+ " $('div.input').hide();\n",
+ " } \n",
+ " else \n",
+ " {\n",
+ " $('div.input').show();\n",
+ " }\n",
+ " code_show = !code_show\n",
+ " } \n",
+ " $( document ).ready(code_toggle);\n",
+ "</script>\n",
+ "The raw code for this notebook is by default hidden for easier reading.\n",
+ "To toggle on/off the raw code, click <a href=\"javascript:code_toggle()\">here</a>."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 4,
+ "metadata": {
+ "init_cell": true,
+ "scrolled": false
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ "\n",
+ "<div align=\"left\" style=\"background-color: rgba(149,170,79, 1.0); width: 100%; height: 390px; overflow: hidden;\">\n",
+ " <div >\n",
+ " <table>\n",
+ " <tr></tr>\n",
+ " <tr>\n",
+ " <td><img src=\"Nomad_tutorial_head.png\"></td>\n",
+ " </tr>\n",
+ " </table>\n",
+ " </div>\n",
+ "\n",
+ " <br><br>\n",
+ " <div style=\"position:relative; left:3%\"><font size=6em color=\"#20335d\" ><b> - Visualization of the band structure of materials </b></font></div>\n",
+ " <p style=\"position:relative;left:10%; \">\n",
+ " <br>\n",
+ " Created by:\n",
+ "\n",
+ " Xiangyue Liu<sup>1</sup>(<a href=\"mailto:xyliu@fhi-berlin.mpg.de\">email</a>),\n",
+ " \n",
+ " Fawzi Mohamed<sup>1</sup>,\n",
+ " \n",
+ " and Luca M. Ghiringhelli<sup>1</sup>(<a href=\"mailto:ghiringhelli@fhi-berlin.mpg.de\">email</a>), <br>\n",
+ "\n",
+ " <br><br>\n",
+ " <sup>1</sup> Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, D-14195 Berlin, Germany <br>\n",
+ " <br>\n",
+ "\n",
+ "\n",
+ " </p>\n",
+ " <br>\n",
+ " <div style=\"position:relative;bottom:3%\">\n",
+ " <div style=\"position:absolute;right:5%;bottom: 0%;\"><font color=\"#999999\" size=\"10em\">v2.0.0</font></div>\n",
+ " <div style=\"position:absolute;right:5%;bottom: 0%;\"><font color=\"#666666\" size=\"2.7em\">[Last updated: August 5, 2019]</font></div>\n",
+ " </div>\n",
+ "\n",
+ "</div>\n",
+ "\n",
+ "\n",
+ "<div style='text-align: right;'>\n",
+ " <a href=\"https://analytics-toolkit.nomad-coe.eu/home/\" class=\"btn btn-primary\" style=\"font-size:larger;\">Back to Analytics Home</a> \n",
+ " <a href=\"https://www.nomad-coe.eu/\" class=\"btn btn-primary\" style=\"font-size:larger; \">Back to nomad-coe</a> \n",
+ "</div>\n"
+ ],
+ "text/plain": [
+ "<IPython.core.display.HTML object>"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "%%HTML\n",
+ "\n",
+ "\n",
+ "<div align=\"left\" style=\"background-color: rgba(149,170,79, 1.0); width: 100%; height: 390px; overflow: hidden;\">\n",
+ " <div >\n",
+ " <table>\n",
+ " <tr></tr>\n",
+ " <tr>\n",
+ " <td><img src=\"Nomad_tutorial_head.png\"></td>\n",
+ " </tr>\n",
+ " </table>\n",
+ " </div>\n",
+ "\n",
+ " <br><br>\n",
+ " <div style=\"position:relative; left:3%\"><font size=6em color=\"#20335d\" ><b> - Visualization of the band structure of materials </b></font></div>\n",
+ " <p style=\"position:relative;left:10%; \">\n",
+ " <br>\n",
+ " Created by:\n",
+ "\n",
+ " Xiangyue Liu<sup>1</sup>(<a href=\"mailto:xyliu@fhi-berlin.mpg.de\">email</a>),\n",
+ " \n",
+ " Fawzi Mohamed<sup>1</sup>,\n",
+ " \n",
+ " and Luca M. Ghiringhelli<sup>1</sup>(<a href=\"mailto:ghiringhelli@fhi-berlin.mpg.de\">email</a>), <br>\n",
+ "\n",
+ " <br><br>\n",
+ " <sup>1</sup> Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, D-14195 Berlin, Germany <br>\n",
+ " <br>\n",
+ "\n",
+ "\n",
+ " </p>\n",
+ " <br>\n",
+ " <div style=\"position:relative;bottom:3%\">\n",
+ " <div style=\"position:absolute;right:5%;bottom: 0%;\"><font color=\"#999999\" size=\"10em\">v2.0.0</font></div>\n",
+ " <div style=\"position:absolute;right:5%;bottom: 0%;\"><font color=\"#666666\" size=\"2.7em\">[Last updated: August 5, 2019]</font></div>\n",
+ " </div>\n",
+ "\n",
+ "</div>\n",
+ "\n",
+ "\n",
+ "<div style='text-align: right;'>\n",
+ " <a href=\"https://analytics-toolkit.nomad-coe.eu/home/\" class=\"btn btn-primary\" style=\"font-size:larger;\">Back to Analytics Home</a> \n",
+ " <a href=\"https://www.nomad-coe.eu/\" class=\"btn btn-primary\" style=\"font-size:larger; \">Back to nomad-coe</a> \n",
+ "</div>\n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 5,
+ "metadata": {
+ "init_cell": true
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "<script>\n",
+ " window.findCellIndicesByTag = function findCellIndicesByTag(tagName) {\n",
+ " return (Jupyter.notebook.get_cells()\n",
+ " .filter(\n",
+ " ({metadata: {tags}}) => tags && tags.includes(tagName)\n",
+ " )\n",
+ " .map((cell) => Jupyter.notebook.find_cell_index(cell))\n",
+ " );\n",
+ " };\n",
+ "\n",
+ "\n",
+ " window.runCells = function runPlotCells(tags) {\n",
+ " var c = window.findCellIndicesByTag(tags);\n",
+ " Jupyter.notebook.execute_cells(c);\n",
+ " };\n",
+ "</script>\n"
+ ],
+ "text/plain": [
+ "<IPython.core.display.HTML object>"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "%%HTML\n",
+ "<script>\n",
+ " window.findCellIndicesByTag = function findCellIndicesByTag(tagName) {\n",
+ " return (Jupyter.notebook.get_cells()\n",
+ " .filter(\n",
+ " ({metadata: {tags}}) => tags && tags.includes(tagName)\n",
+ " )\n",
+ " .map((cell) => Jupyter.notebook.find_cell_index(cell))\n",
+ " );\n",
+ " };\n",
+ "\n",
+ "\n",
+ " window.runCells = function runPlotCells(tags) {\n",
+ " var c = window.findCellIndicesByTag(tags);\n",
+ " Jupyter.notebook.execute_cells(c);\n",
+ " };\n",
+ "</script>"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 53,
+ "metadata": {
+ "init_cell": true,
+ "tags": [
+ "search_materials"
+ ]
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "<br><br>\n",
+ "\n",
+ "<p style=\"color: #20335d;font-weight: 450; font-size: 14pt;font-family: Arial;\"> This tutorial visulizes the band structures and density of states (DOS) of the NOMAD materials.</p>\n",
+ "<br><br>\n",
+ "\n",
+ "<style>\n",
+ ".button {\n",
+ " background-color: #e7e7e7;\n",
+ " border: 0.5px solid #A4A4A4;\n",
+ " color: black;\n",
+ " padding: 15px 32px;\n",
+ " text-align: center;\n",
+ " text-decoration: none;\n",
+ " display: inline-block;\n",
+ " font-family: Arial;\n",
+ " font-size: 16px;\n",
+ " margin: 4px 2px;\n",
+ " cursor: pointer;\n",
+ "}\n",
+ "\n",
+ " .text-normal-black{\n",
+ " color: #000;font-weight: 200; font-size: 10pt;\n",
+ " font-family: Arial;\n",
+ " }\n",
+ " .div_band_dos{\n",
+ " box-sizing: border-box;\n",
+ " width: 100%;\n",
+ " height: 600px;\n",
+ " font-weight: 100;\n",
+ " font-family: Arial;\n",
+ " padding-left: 20px;\n",
+ " padding-top: 10px;\n",
+ " padding-right: 1em;\n",
+ " margin: 0;\n",
+ " border: 0;\n",
+ " }\n",
+ " .div_band_dos_compare{\n",
+ " box-sizing: border-box;\n",
+ " width: 1600px;\n",
+ " height: 600px;\n",
+ " color: #00AEFF;\n",
+ " font-weight: 100;\n",
+ " font-family: Arial;\n",
+ " padding-left: 20px;\n",
+ " padding-top: 10px;\n",
+ " padding-right: 1em;\n",
+ " margin: 0;\n",
+ " border: 0;\n",
+ " }\n",
+ " .div_band{\n",
+ " font-family: Arial;\n",
+ " font-size: 0.875em;\n",
+ " width: 37%;\n",
+ " height: 80%;\n",
+ " background-color: #fff;\n",
+ " float:left;\n",
+ " }\n",
+ " .div_dos{\n",
+ " font-family: Arial;\n",
+ " font-size: 0.875em;\n",
+ " width: 13%;\n",
+ " height: 80%;\n",
+ " background-color: #fff;\n",
+ " float:left;\n",
+ " }\n",
+ " .div_tools{\n",
+ " color: #20335d;font-weight: 150; font-size: 13pt;\n",
+ " width: 35%;\n",
+ " height: 80%;\n",
+ " background-color: #fff;\n",
+ " margin-left:20pt;\n",
+ " float:left;\n",
+ " font-family: Arial;\n",
+ "\n",
+ " }\n",
+ " .div_checkbox_compare{\n",
+ " color: #888;font-weight: 150; font-size: 12pt;\n",
+ " width: 10%;\n",
+ " height: 80%;\n",
+ " background-color: #fff;\n",
+ " border: solid #fff 1px;\n",
+ " float:right;\n",
+ " font-family: Arial;\n",
+ "\n",
+ " }\n",
+ " .div_overview{\n",
+ " width: 300px;\n",
+ " height: 200px;\n",
+ " background-color: #fff;\n",
+ " margin-left:10px; \n",
+ " margin-top: 20px;\n",
+ " font-family: Arial;\n",
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+ " }\n",
+ " .button_tools {\n",
+ " background-color: #F0F0F0;\n",
+ " border: 0.5px solid #A4A4A4;\n",
+ " color: black;\n",
+ " padding: 10px 15px;\n",
+ " text-align: center;\n",
+ " text-decoration: none;\n",
+ " display: inline-block;\n",
+ " font-size: 16px;\n",
+ " margin: 4px 2px;\n",
+ " cursor: pointer;\n",
+ " font-family: Arial;\n",
+ "\n",
+ " }\n",
+ "\n",
+ " \n",
+ " .g-before-after{position:relative;overflow:hidden;width:500px}.g-before-after img{display:block}.g-before-after .g-img-before{float:left}.g-before-after .g-img-after,.g-before-after.g-vertical .g-img-after{position:absolute;top:0;right:0;left:50%;bottom:0;overflow:hidden}.g-before-after .g-img-after img{position:absolute;right:0;top:0}.g-before-after .g-img-divider{position:absolute;left:50%;top:0;bottom:0;width:0;border-left:1px solid #fff;border-right:1px solid #fff}.g-before-after .g-img-divider>span{position:absolute;top:50%;display:block;background-color:#fff;padding:5px 10px;line-height:1;text-align:center;-webkit-transform:translate(-50%,-50%);-ms-transform:translate(-50%,-50%);transform:translate(-50%,-50%)}.g-before-after.g-vertical .g-img-after{top:50%;left:0}.g-before-after.g-vertical .g-img-after img{position:absolute;right:auto;top:auto;left:0;bottom:0}.g-before-after.g-vertical .g-img-divider{position:absolute;left:0;top:50%;bottom:auto;right:0;height:0;width:100%;border-top:1px solid #fff;border-bottom:1px solid #fff;border-left:0 none;border-right:0 none}.g-before-after.g-vertical .g-img-divider>span{top:50%;left:50%}\n",
+ "</style>\n",
+ "\n",
+ "<script>\n",
+ " //Search for certain keyword: https://labdev-nomad.esc.rzg.mpg.de/fairdi/nomad/migration/api/repo/?quantities=section_k_band_segment\n",
+ " //FjiYy5-ETRCrs5ktzJA55w/bOY0cPkBvvNAY7pZdbginlKXJ2kF\n",
+ " //\"upload_id\"/\"calc_id\"\n",
+ " \n",
+ " //Global variables\n",
+ " var paths_section_k_band_segment = []; \n",
+ " var paths_section_dos = [];\n",
+ " var band_obj_all = [];\n",
+ " var dos_obj_all = [];\n",
+ " var info_obj_all = [];\n",
+ " \n",
+ " var band_paths = [];\n",
+ " var dos_paths = [];\n",
+ " var N_materials = 0; //Number of materials that have both band and DOS in the same calculation \n",
+ " \n",
+ " \n",
+ " function getJSON(url) {\n",
+ " var resp ;\n",
+ " var xmlHttp ;\n",
+ "\n",
+ " resp = '' ;\n",
+ " xmlHttp = new XMLHttpRequest();\n",
+ "\n",
+ " if(xmlHttp != null)\n",
+ " {\n",
+ " xmlHttp.open( \"GET\", url, false );\n",
+ " xmlHttp.send( null );\n",
+ " resp = xmlHttp.responseText;\n",
+ " }\n",
+ "\n",
+ " return resp;\n",
+ " }\n",
+ " function match_band_dos()\n",
+ " {\n",
+ " //TMP for local tests\n",
+ " /*\n",
+ " paths_section_k_band_segment = [\"data/kOJR-AlPSgiNG9AdZoxd4g_9mxjIU0edrPosfsTc4uyDG9H_UXr.json\",\"data/kOJR-AlPSgiNG9AdZoxd4g_lfkGCmWozYENeiGhu5W7dJUqLTkj.json\"];\n",
+ " paths_section_dos = [\"data/kOJR-AlPSgiNG9AdZoxd4g_8tEGnaz0yY91eSyysKZkIUH9qx8J.json\", \"data/kOJR-AlPSgiNG9AdZoxd4g_lxUT3viRZcC_1IsH_KvO5tChAtV1.json\"];\n",
+ " */\n",
+ "\n",
+ " //band_paths = [];\n",
+ " //dos_paths = [];\n",
+ " //N_materials = 0; \n",
+ " \n",
+ " var data_k_band = [];\n",
+ " for(var i_path_k_band = 0; i_path_k_band < paths_section_k_band_segment.length; i_path_k_band ++)\n",
+ " {\n",
+ " var i_data_k_band_json = JSON.parse(getJSON(paths_section_k_band_segment[i_path_k_band]));\n",
+ " var i_data_k_band = {};\n",
+ " i_data_k_band[\"program_name\"] = i_data_k_band_json[\"section_run\"][\"program_name\"];\n",
+ " i_data_k_band[\"k_mesh_points\"] = i_data_k_band_json[\"section_run\"][\"section_method\"][\"k_mesh_points\"];\n",
+ " i_data_k_band[\"simulation_cell\"] = i_data_k_band_json[\"section_run\"][\"section_system\"][0][\"simulation_cell\"];\n",
+ " i_data_k_band[\"atom_positions\"] = i_data_k_band_json[\"section_run\"][\"section_system\"][0][\"atom_positions\"];\n",
+ " i_data_k_band[\"atom_labels\"] = i_data_k_band_json[\"section_run\"][\"section_system\"][0][\"atom_labels\"];\n",
+ " i_data_k_band[\"XC_functional_name\"] = i_data_k_band_json[\"section_run\"][\"section_method\"][\"section_XC_functionals\"][0][\"XC_functional_name\"] + \"-\" + i_data_k_band_json[\"section_run\"][\"section_method\"][\"section_XC_functionals\"][1][\"XC_functional_name\"]\n",
+ " i_data_k_band[\"path\"] = paths_section_k_band_segment[i_path_k_band];\n",
+ " data_k_band.push(i_data_k_band);\n",
+ " }\n",
+ "\n",
+ " var data_dos = [];\n",
+ " for(var i_path_dos = 0; i_path_dos < paths_section_dos.length; i_path_dos ++)\n",
+ " {\n",
+ " var i_data_dos_json = JSON.parse(getJSON(paths_section_dos[i_path_dos]));\n",
+ " var i_data_dos = {};\n",
+ " i_data_dos[\"program_name\"] = i_data_dos_json[\"section_run\"][\"program_name\"];\n",
+ " i_data_dos[\"k_mesh_points\"] = i_data_dos_json[\"section_run\"][\"section_method\"][\"k_mesh_points\"];\n",
+ " i_data_dos[\"simulation_cell\"] = i_data_dos_json[\"section_run\"][\"section_system\"][0][\"simulation_cell\"];\n",
+ " i_data_dos[\"atom_positions\"] = i_data_dos_json[\"section_run\"][\"section_system\"][0][\"atom_positions\"];\n",
+ " i_data_dos[\"atom_labels\"] = i_data_dos_json[\"section_run\"][\"section_system\"][0][\"atom_labels\"];\n",
+ " i_data_dos[\"XC_functional_name\"] = i_data_dos_json[\"section_run\"][\"section_method\"][\"section_XC_functionals\"][0][\"XC_functional_name\"] + \"-\" + i_data_dos_json[\"section_run\"][\"section_method\"][\"section_XC_functionals\"][1][\"XC_functional_name\"]\n",
+ " i_data_dos[\"path\"] = paths_section_dos[i_path_dos];\n",
+ " data_dos.push(i_data_dos); \n",
+ " }\n",
+ "\n",
+ " //Matching: band[i] ~ dos[i] (the same systems are arranged with the same index)\n",
+ " band_paths = [];\n",
+ " dos_paths = [];\n",
+ " N_materials = 0;\n",
+ " for(var i_k_band = 0; i_k_band < data_k_band.length; i_k_band ++)\n",
+ " {\n",
+ " for(var i_dos = 0; i_dos < data_dos.length; i_dos ++)\n",
+ " {\n",
+ " if(data_k_band[i_k_band][\"program_name\"] != data_dos[i_dos][\"program_name\"])\n",
+ " continue; \n",
+ " //if(data_k_band[i_k_band][\"k_mesh_points\"].join() != data_dos[i_dos][\"k_mesh_points\"].join())\n",
+ " // continue;\n",
+ " if(data_k_band[i_k_band][\"simulation_cell\"].join() != data_dos[i_dos][\"simulation_cell\"].join())\n",
+ " continue;\n",
+ " if(data_k_band[i_k_band][\"atom_positions\"].join() != data_dos[i_dos][\"atom_positions\"].join())\n",
+ " continue;\n",
+ " if(data_k_band[i_k_band][\"atom_labels\"].join() != data_dos[i_dos][\"atom_labels\"].join())\n",
+ " continue;\n",
+ " if(data_k_band[i_k_band][\"XC_functional_name\"] != data_dos[i_dos][\"XC_functional_name\"])\n",
+ " continue;\n",
+ " band_paths.push(data_k_band[i_k_band][\"path\"]);\n",
+ " dos_paths.push(data_dos[i_dos][\"path\"]);\n",
+ " N_materials ++;\n",
+ " }\n",
+ " }\n",
+ " //Pass the arrays to python\n",
+ "\n",
+ " var command = \"N_materials = \" + N_materials + \";\"\n",
+ " var kernel = IPython.notebook.kernel;\n",
+ " command += \"band_paths = \" + \"[\\'\" + band_paths.join(\"\\',\\'\") + \"\\'];\";\n",
+ " command += \"dos_paths = \" + \"[\\'\" + dos_paths.join(\"\\',\\'\") + \"\\'];\";\n",
+ " kernel.execute(command);\n",
+ " \n",
+ " \n",
+ " }\n",
+ "\n",
+ " function get_paths_from_search_results(result_json, div_id_search_results,div_head)\n",
+ " {\n",
+ " paths = [];\n",
+ " search_results_content = [div_head, '<table>', '<tr><th>Chemical formula</th><th>Spacegroup</th><th>Code</th><th>XC functional</th><th>Upload ID</th><th>Calculation ID</th><th>URL</th></tr>'];\n",
+ " for(var i_key in result_json)\n",
+ " {\n",
+ " if(i_key == \"results\")\n",
+ " {\n",
+ " for(var system in result_json[i_key])\n",
+ " {\n",
+ " //Get the path to the data files (json)： https://labdev-nomad.esc.rzg.mpg.de/fairdi/nomad/migration/api/archive/upload_id/calc_id \n",
+ " path = \"https://labdev-nomad.esc.rzg.mpg.de/fairdi/nomad/migration/api/archive/\" + result_json[i_key][system][\"upload_id\"] + \"/\" + result_json[i_key][system][\"calc_id\"]\n",
+ " paths.push(path);\n",
+ " \n",
+ " //Show the results in div\n",
+ " // \"formula\" \"spacegroup_symbol\" \"code_name\" \"xc_functional\"\n",
+ " content = '<tr>';\n",
+ " content += '<td>' + result_json[i_key][system][\"formula\"] + '</td>';\n",
+ " content += '<td>' + result_json[i_key][system][\"spacegroup_symbol\"] + '</td>';\n",
+ " content += '<td>' + result_json[i_key][system][\"code_name\"] + '</td>';\n",
+ " content += '<td>' + result_json[i_key][system][\"xc_functional\"] + '</td>';\n",
+ " content += '<td>' + result_json[i_key][system][\"upload_id\"] + '</td>';\n",
+ " content += '<td>' + result_json[i_key][system][\"calc_id\"] + '</td>'; \n",
+ " content += '<td>' + path + '</td>';\n",
+ " content += '</tr>';\n",
+ " search_results_content.push(content);\n",
+ " }\n",
+ " }\n",
+ " }\n",
+ " search_results_content.push('</table>');\n",
+ " document.getElementById(div_id_search_results).innerHTML = search_results_content.join('');\n",
+ " return paths\n",
+ " }\n",
+ " \n",
+ " \n",
+ " \n",
+ "\n",
+ " \n",
+ " \n",
+ " \n",
+ " function submit_search()\n",
+ " {\n",
+ " \n",
+ " var result;\n",
+ " var formula = document.getElementById(\"keyword_chemical_formula\").value;\n",
+ " var query_command_k_band = \"https://labdev-nomad.esc.rzg.mpg.de/fairdi/nomad/migration/api/repo/?formula=\" + formula + \"&quantities=section_k_band_segment\";\n",
+ " var query_command_dos = \"https://labdev-nomad.esc.rzg.mpg.de/fairdi/nomad/migration/api/repo/?formula=\" + formula + \"&quantities=section_dos\";\n",
+ " //result = getJSON(\"https://labdev-nomad.esc.rzg.mpg.de/fairdi/nomad/migration/api/repo/?quantities=section_k_band_segment\");\n",
+ " var result_k_band = getJSON(query_command_k_band);\n",
+ " var result_dos = getJSON(query_command_dos);\n",
+ " var result_json_k_band = JSON.parse(result_k_band);//parse the searching results to json from URL\n",
+ " var result_json_dos = JSON.parse(result_dos);\n",
+ " paths_section_k_band_segment = []; \n",
+ " paths_section_dos = [];\n",
+ " paths_section_k_band_segment = get_paths_from_search_results(result_json_k_band, \"search_results_section_k_band_segment\", \"<br><br><font size=4em>Calculations containing band structures:</font><br>\");\n",
+ " paths_section_dos = get_paths_from_search_results(result_json_dos, \"search_results_section_dos\", \"<br><font size=4em>Calculations containing DOS:</font><br>\");\n",
+ " \n",
+ " var promise = Promise.resolve();\n",
+ " promise\n",
+ " .then(match_band_dos())\n",
+ " .then(Jupyter.notebook.execute_cells(window.findCellIndicesByTag('process_band_dos_data')))\n",
+ " .then(Jupyter.notebook.execute_cells(window.findCellIndicesByTag('show_results_and_plot')));\n",
+ " \n",
+ " //match_band_dos();\n",
+ " \n",
+ " //Jupyter.notebook.execute_cells(window.findCellIndicesByTag('process_band_dos_data')); //Read the json files, and prepare data for plot\n",
+ " //Jupyter.notebook.execute_cells(window.findCellIndicesByTag('show_results_and_plot')); //Prepare for plot\n",
+ " }\n",
+ " function reset_search()\n",
+ " {\n",
+ " Jupyter.notebook.execute_cells(window.findCellIndicesByTag('search_materials'));\n",
+ " Jupyter.notebook.execute_cells(window.findCellIndicesByTag('show_results_and_plot'));\n",
+ " }\n",
+ " \n",
+ " \n",
+ "</script>\n",
+ "<font size=4em>Please input the chemical formula:</font>\n",
+ "<input type=\"text\" id=\"keyword_chemical_formula\" value=\"AlInO3\"> \n",
+ "<button class=\"button\" onclick=\"submit_search()\">Search</button>\n",
+ "<button class=\"button\" onclick=\"reset_search()\">Reset</button>\n",
+ "<br><br><br>\n",
+ "<div id=\"search_results_section_k_band_segment\"></div>\n",
+ "<div id=\"search_results_section_dos\"></div>\n"
+ ],
+ "text/plain": [
+ "<IPython.core.display.HTML object>"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "%%html\n",
+ "<br><br>\n",
+ "\n",
+ "<p style=\"color: #20335d;font-weight: 450; font-size: 14pt;font-family: Arial;\"> This tutorial visulizes the band structures and density of states (DOS) of the NOMAD materials.</p>\n",
+ "<br><br>\n",
+ "\n",
+ "<style>\n",
+ ".button {\n",
+ " background-color: #e7e7e7;\n",
+ " border: 0.5px solid #A4A4A4;\n",
+ " color: black;\n",
+ " padding: 15px 32px;\n",
+ " text-align: center;\n",
+ " text-decoration: none;\n",
+ " display: inline-block;\n",
+ " font-family: Arial;\n",
+ " font-size: 16px;\n",
+ " margin: 4px 2px;\n",
+ " cursor: pointer;\n",
+ "}\n",
+ "\n",
+ " .text-normal-black{\n",
+ " color: #000;font-weight: 200; font-size: 10pt;\n",
+ " font-family: Arial;\n",
+ " }\n",
+ " .div_band_dos{\n",
+ " box-sizing: border-box;\n",
+ " width: 100%;\n",
+ " height: 600px;\n",
+ " font-weight: 100;\n",
+ " font-family: Arial;\n",
+ " padding-left: 20px;\n",
+ " padding-top: 10px;\n",
+ " padding-right: 1em;\n",
+ " margin: 0;\n",
+ " border: 0;\n",
+ " }\n",
+ " .div_band_dos_compare{\n",
+ " box-sizing: border-box;\n",
+ " width: 1600px;\n",
+ " height: 600px;\n",
+ " color: #00AEFF;\n",
+ " font-weight: 100;\n",
+ " font-family: Arial;\n",
+ " padding-left: 20px;\n",
+ " padding-top: 10px;\n",
+ " padding-right: 1em;\n",
+ " margin: 0;\n",
+ " border: 0;\n",
+ " }\n",
+ " .div_band{\n",
+ " font-family: Arial;\n",
+ " font-size: 0.875em;\n",
+ " width: 37%;\n",
+ " height: 80%;\n",
+ " background-color: #fff;\n",
+ " float:left;\n",
+ " }\n",
+ " .div_dos{\n",
+ " font-family: Arial;\n",
+ " font-size: 0.875em;\n",
+ " width: 13%;\n",
+ " height: 80%;\n",
+ " background-color: #fff;\n",
+ " float:left;\n",
+ " }\n",
+ " .div_tools{\n",
+ " color: #20335d;font-weight: 150; font-size: 13pt;\n",
+ " width: 35%;\n",
+ " height: 80%;\n",
+ " background-color: #fff;\n",
+ " margin-left:20pt;\n",
+ " float:left;\n",
+ " font-family: Arial;\n",
+ "\n",
+ " }\n",
+ " .div_checkbox_compare{\n",
+ " color: #888;font-weight: 150; font-size: 12pt;\n",
+ " width: 10%;\n",
+ " height: 80%;\n",
+ " background-color: #fff;\n",
+ " border: solid #fff 1px;\n",
+ " float:right;\n",
+ " font-family: Arial;\n",
+ "\n",
+ " }\n",
+ " .div_overview{\n",
+ " width: 300px;\n",
+ " height: 200px;\n",
+ " background-color: #fff;\n",
+ " margin-left:10px; \n",
+ " margin-top: 20px;\n",
+ " font-family: Arial;\n",
+ "\n",
+ " }\n",
+ " .button_tools {\n",
+ " background-color: #F0F0F0;\n",
+ " border: 0.5px solid #A4A4A4;\n",
+ " color: black;\n",
+ " padding: 10px 15px;\n",
+ " text-align: center;\n",
+ " text-decoration: none;\n",
+ " display: inline-block;\n",
+ " font-size: 16px;\n",
+ " margin: 4px 2px;\n",
+ " cursor: pointer;\n",
+ " font-family: Arial;\n",
+ "\n",
+ " }\n",
+ "\n",
+ " \n",
+ " .g-before-after{position:relative;overflow:hidden;width:500px}.g-before-after img{display:block}.g-before-after .g-img-before{float:left}.g-before-after .g-img-after,.g-before-after.g-vertical .g-img-after{position:absolute;top:0;right:0;left:50%;bottom:0;overflow:hidden}.g-before-after .g-img-after img{position:absolute;right:0;top:0}.g-before-after .g-img-divider{position:absolute;left:50%;top:0;bottom:0;width:0;border-left:1px solid #fff;border-right:1px solid #fff}.g-before-after .g-img-divider>span{position:absolute;top:50%;display:block;background-color:#fff;padding:5px 10px;line-height:1;text-align:center;-webkit-transform:translate(-50%,-50%);-ms-transform:translate(-50%,-50%);transform:translate(-50%,-50%)}.g-before-after.g-vertical .g-img-after{top:50%;left:0}.g-before-after.g-vertical .g-img-after img{position:absolute;right:auto;top:auto;left:0;bottom:0}.g-before-after.g-vertical .g-img-divider{position:absolute;left:0;top:50%;bottom:auto;right:0;height:0;width:100%;border-top:1px solid #fff;border-bottom:1px solid #fff;border-left:0 none;border-right:0 none}.g-before-after.g-vertical .g-img-divider>span{top:50%;left:50%}\n",
+ "</style>\n",
+ "\n",
+ "<script>\n",
+ " //Search for certain keyword: https://labdev-nomad.esc.rzg.mpg.de/fairdi/nomad/migration/api/repo/?quantities=section_k_band_segment\n",
+ " //FjiYy5-ETRCrs5ktzJA55w/bOY0cPkBvvNAY7pZdbginlKXJ2kF\n",
+ " //\"upload_id\"/\"calc_id\"\n",
+ " \n",
+ " //Global variables\n",
+ " var paths_section_k_band_segment = []; \n",
+ " var paths_section_dos = [];\n",
+ " var band_obj_all = [];\n",
+ " var dos_obj_all = [];\n",
+ " var info_obj_all = [];\n",
+ " \n",
+ " var band_paths = [];\n",
+ " var dos_paths = [];\n",
+ " var N_materials = 0; //Number of materials that have both band and DOS in the same calculation \n",
+ " \n",
+ " \n",
+ " function getJSON(url) {\n",
+ " var resp ;\n",
+ " var xmlHttp ;\n",
+ "\n",
+ " resp = '' ;\n",
+ " xmlHttp = new XMLHttpRequest();\n",
+ "\n",
+ " if(xmlHttp != null)\n",
+ " {\n",
+ " xmlHttp.open( \"GET\", url, false );\n",
+ " xmlHttp.send( null );\n",
+ " resp = xmlHttp.responseText;\n",
+ " }\n",
+ "\n",
+ " return resp;\n",
+ " }\n",
+ " function match_band_dos()\n",
+ " {\n",
+ " //TMP for local tests\n",
+ " /*\n",
+ " paths_section_k_band_segment = [\"data/kOJR-AlPSgiNG9AdZoxd4g_9mxjIU0edrPosfsTc4uyDG9H_UXr.json\",\"data/kOJR-AlPSgiNG9AdZoxd4g_lfkGCmWozYENeiGhu5W7dJUqLTkj.json\"];\n",
+ " paths_section_dos = [\"data/kOJR-AlPSgiNG9AdZoxd4g_8tEGnaz0yY91eSyysKZkIUH9qx8J.json\", \"data/kOJR-AlPSgiNG9AdZoxd4g_lxUT3viRZcC_1IsH_KvO5tChAtV1.json\"];\n",
+ " */\n",
+ "\n",
+ " //band_paths = [];\n",
+ " //dos_paths = [];\n",
+ " //N_materials = 0; \n",
+ " \n",
+ " var data_k_band = [];\n",
+ " for(var i_path_k_band = 0; i_path_k_band < paths_section_k_band_segment.length; i_path_k_band ++)\n",
+ " {\n",
+ " var i_data_k_band_json = JSON.parse(getJSON(paths_section_k_band_segment[i_path_k_band]));\n",
+ " var i_data_k_band = {};\n",
+ " i_data_k_band[\"program_name\"] = i_data_k_band_json[\"section_run\"][\"program_name\"];\n",
+ " i_data_k_band[\"k_mesh_points\"] = i_data_k_band_json[\"section_run\"][\"section_method\"][\"k_mesh_points\"];\n",
+ " i_data_k_band[\"simulation_cell\"] = i_data_k_band_json[\"section_run\"][\"section_system\"][0][\"simulation_cell\"];\n",
+ " i_data_k_band[\"atom_positions\"] = i_data_k_band_json[\"section_run\"][\"section_system\"][0][\"atom_positions\"];\n",
+ " i_data_k_band[\"atom_labels\"] = i_data_k_band_json[\"section_run\"][\"section_system\"][0][\"atom_labels\"];\n",
+ " i_data_k_band[\"XC_functional_name\"] = i_data_k_band_json[\"section_run\"][\"section_method\"][\"section_XC_functionals\"][0][\"XC_functional_name\"] + \"-\" + i_data_k_band_json[\"section_run\"][\"section_method\"][\"section_XC_functionals\"][1][\"XC_functional_name\"]\n",
+ " i_data_k_band[\"path\"] = paths_section_k_band_segment[i_path_k_band];\n",
+ " data_k_band.push(i_data_k_band);\n",
+ " }\n",
+ "\n",
+ " var data_dos = [];\n",
+ " for(var i_path_dos = 0; i_path_dos < paths_section_dos.length; i_path_dos ++)\n",
+ " {\n",
+ " var i_data_dos_json = JSON.parse(getJSON(paths_section_dos[i_path_dos]));\n",
+ " var i_data_dos = {};\n",
+ " i_data_dos[\"program_name\"] = i_data_dos_json[\"section_run\"][\"program_name\"];\n",
+ " i_data_dos[\"k_mesh_points\"] = i_data_dos_json[\"section_run\"][\"section_method\"][\"k_mesh_points\"];\n",
+ " i_data_dos[\"simulation_cell\"] = i_data_dos_json[\"section_run\"][\"section_system\"][0][\"simulation_cell\"];\n",
+ " i_data_dos[\"atom_positions\"] = i_data_dos_json[\"section_run\"][\"section_system\"][0][\"atom_positions\"];\n",
+ " i_data_dos[\"atom_labels\"] = i_data_dos_json[\"section_run\"][\"section_system\"][0][\"atom_labels\"];\n",
+ " i_data_dos[\"XC_functional_name\"] = i_data_dos_json[\"section_run\"][\"section_method\"][\"section_XC_functionals\"][0][\"XC_functional_name\"] + \"-\" + i_data_dos_json[\"section_run\"][\"section_method\"][\"section_XC_functionals\"][1][\"XC_functional_name\"]\n",
+ " i_data_dos[\"path\"] = paths_section_dos[i_path_dos];\n",
+ " data_dos.push(i_data_dos); \n",
+ " }\n",
+ "\n",
+ " //Matching: band[i] ~ dos[i] (the same systems are arranged with the same index)\n",
+ " band_paths = [];\n",
+ " dos_paths = [];\n",
+ " N_materials = 0;\n",
+ " for(var i_k_band = 0; i_k_band < data_k_band.length; i_k_band ++)\n",
+ " {\n",
+ " for(var i_dos = 0; i_dos < data_dos.length; i_dos ++)\n",
+ " {\n",
+ " if(data_k_band[i_k_band][\"program_name\"] != data_dos[i_dos][\"program_name\"])\n",
+ " continue; \n",
+ " //if(data_k_band[i_k_band][\"k_mesh_points\"].join() != data_dos[i_dos][\"k_mesh_points\"].join())\n",
+ " // continue;\n",
+ " if(data_k_band[i_k_band][\"simulation_cell\"].join() != data_dos[i_dos][\"simulation_cell\"].join())\n",
+ " continue;\n",
+ " if(data_k_band[i_k_band][\"atom_positions\"].join() != data_dos[i_dos][\"atom_positions\"].join())\n",
+ " continue;\n",
+ " if(data_k_band[i_k_band][\"atom_labels\"].join() != data_dos[i_dos][\"atom_labels\"].join())\n",
+ " continue;\n",
+ " if(data_k_band[i_k_band][\"XC_functional_name\"] != data_dos[i_dos][\"XC_functional_name\"])\n",
+ " continue;\n",
+ " band_paths.push(data_k_band[i_k_band][\"path\"]);\n",
+ " dos_paths.push(data_dos[i_dos][\"path\"]);\n",
+ " N_materials ++;\n",
+ " }\n",
+ " }\n",
+ " //Pass the arrays to python\n",
+ "\n",
+ " var command = \"N_materials = \" + N_materials + \";\"\n",
+ " var kernel = IPython.notebook.kernel;\n",
+ " command += \"band_paths = \" + \"[\\'\" + band_paths.join(\"\\',\\'\") + \"\\'];\";\n",
+ " command += \"dos_paths = \" + \"[\\'\" + dos_paths.join(\"\\',\\'\") + \"\\'];\";\n",
+ " kernel.execute(command);\n",
+ " \n",
+ " \n",
+ " }\n",
+ "\n",
+ " function get_paths_from_search_results(result_json, div_id_search_results,div_head)\n",
+ " {\n",
+ " paths = [];\n",
+ " search_results_content = [div_head, '<table>', '<tr><th>Chemical formula</th><th>Spacegroup</th><th>Code</th><th>XC functional</th><th>Upload ID</th><th>Calculation ID</th><th>URL</th></tr>'];\n",
+ " for(var i_key in result_json)\n",
+ " {\n",
+ " if(i_key == \"results\")\n",
+ " {\n",
+ " for(var system in result_json[i_key])\n",
+ " {\n",
+ " //Get the path to the data files (json)： https://labdev-nomad.esc.rzg.mpg.de/fairdi/nomad/migration/api/archive/upload_id/calc_id \n",
+ " path = \"https://labdev-nomad.esc.rzg.mpg.de/fairdi/nomad/migration/api/archive/\" + result_json[i_key][system][\"upload_id\"] + \"/\" + result_json[i_key][system][\"calc_id\"]\n",
+ " paths.push(path);\n",
+ " \n",
+ " //Show the results in div\n",
+ " // \"formula\" \"spacegroup_symbol\" \"code_name\" \"xc_functional\"\n",
+ " content = '<tr>';\n",
+ " content += '<td>' + result_json[i_key][system][\"formula\"] + '</td>';\n",
+ " content += '<td>' + result_json[i_key][system][\"spacegroup_symbol\"] + '</td>';\n",
+ " content += '<td>' + result_json[i_key][system][\"code_name\"] + '</td>';\n",
+ " content += '<td>' + result_json[i_key][system][\"xc_functional\"] + '</td>';\n",
+ " content += '<td>' + result_json[i_key][system][\"upload_id\"] + '</td>';\n",
+ " content += '<td>' + result_json[i_key][system][\"calc_id\"] + '</td>'; \n",
+ " content += '<td>' + path + '</td>';\n",
+ " content += '</tr>';\n",
+ " search_results_content.push(content);\n",
+ " }\n",
+ " }\n",
+ " }\n",
+ " search_results_content.push('</table>');\n",
+ " document.getElementById(div_id_search_results).innerHTML = search_results_content.join('');\n",
+ " return paths\n",
+ " }\n",
+ " \n",
+ " \n",
+ " \n",
+ "\n",
+ " \n",
+ " \n",
+ " \n",
+ " function submit_search()\n",
+ " {\n",
+ " \n",
+ " var result;\n",
+ " var formula = document.getElementById(\"keyword_chemical_formula\").value;\n",
+ " var query_command_k_band = \"https://labdev-nomad.esc.rzg.mpg.de/fairdi/nomad/migration/api/repo/?formula=\" + formula + \"&quantities=section_k_band_segment\";\n",
+ " var query_command_dos = \"https://labdev-nomad.esc.rzg.mpg.de/fairdi/nomad/migration/api/repo/?formula=\" + formula + \"&quantities=section_dos\";\n",
+ " //result = getJSON(\"https://labdev-nomad.esc.rzg.mpg.de/fairdi/nomad/migration/api/repo/?quantities=section_k_band_segment\");\n",
+ " var result_k_band = getJSON(query_command_k_band);\n",
+ " var result_dos = getJSON(query_command_dos);\n",
+ " var result_json_k_band = JSON.parse(result_k_band);//parse the searching results to json from URL\n",
+ " var result_json_dos = JSON.parse(result_dos);\n",
+ " paths_section_k_band_segment = []; \n",
+ " paths_section_dos = [];\n",
+ " paths_section_k_band_segment = get_paths_from_search_results(result_json_k_band, \"search_results_section_k_band_segment\", \"<br><br><font size=4em>Calculations containing band structures:</font><br>\");\n",
+ " paths_section_dos = get_paths_from_search_results(result_json_dos, \"search_results_section_dos\", \"<br><font size=4em>Calculations containing DOS:</font><br>\");\n",
+ " \n",
+ " var promise = Promise.resolve();\n",
+ " promise\n",
+ " .then(match_band_dos())\n",
+ " .then(Jupyter.notebook.execute_cells(window.findCellIndicesByTag('process_band_dos_data')))\n",
+ " .then(Jupyter.notebook.execute_cells(window.findCellIndicesByTag('show_results_and_plot')));\n",
+ " \n",
+ " //match_band_dos();\n",
+ " \n",
+ " //Jupyter.notebook.execute_cells(window.findCellIndicesByTag('process_band_dos_data')); //Read the json files, and prepare data for plot\n",
+ " //Jupyter.notebook.execute_cells(window.findCellIndicesByTag('show_results_and_plot')); //Prepare for plot\n",
+ " }\n",
+ " function reset_search()\n",
+ " {\n",
+ " Jupyter.notebook.execute_cells(window.findCellIndicesByTag('search_materials'));\n",
+ " Jupyter.notebook.execute_cells(window.findCellIndicesByTag('show_results_and_plot'));\n",
+ " }\n",
+ " \n",
+ " \n",
+ "</script>\n",
+ "<font size=4em>Please input the chemical formula:</font>\n",
+ "<input type=\"text\" id=\"keyword_chemical_formula\" value=\"AlInO3\"> \n",
+ "<button class=\"button\" onclick=\"submit_search()\">Search</button>\n",
+ "<button class=\"button\" onclick=\"reset_search()\">Reset</button>\n",
+ "<br><br><br>\n",
+ "<div id=\"search_results_section_k_band_segment\"></div>\n",
+ "<div id=\"search_results_section_dos\"></div>\n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 29,
+ "metadata": {
+ "tags": [
+ "process_band_dos_data"
+ ]
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "<script>\n",
+ " var band_obj_all = [];\n",
+ " var dos_obj_all = [];\n",
+ " var info_obj_all = [];\n",
+ " //alert(\"process_band_dos_data: \" +band_paths)\n",
+ " //alert(\"process_band_dos_data: \" +info_obj_all)\n",
+ " function get_label_flag(coor_array)\n",
+ " {\n",
+ " var coor = coor_array.sort().join();\n",
+ " if(coor == '0,0.5,0.5')\n",
+ " return \"X\";\n",
+ " if(coor == '0,0,0.5')\n",
+ " return \"M\";\n",
+ " else if(coor == '0.5,0.5,0.5')\n",
+ " return \"L\";\n",
+ " else if(coor == '0.375,0.375,0.75')\n",
+ " return \"K\";\n",
+ " else if(coor == '0.25,0.5,0.75')\n",
+ " return \"W\";\n",
+ " else if(coor == '0,0,0')\n",
+ " return \"\\u0393\";\n",
+ " else if(coor == '0.25,0.625,0.625')\n",
+ " return \"U\";\n",
+ " else\n",
+ " {\n",
+ " //alert(\"k label not found: \" + coor);\n",
+ " return \"?\";\n",
+ " }\n",
+ " }\n",
+ "\n",
+ "\n",
+ " //============Process the band structure data============\n",
+ " function get_band_obj(band_path, dos_fermi_energy)\n",
+ " {\n",
+ " var band_data = JSON.parse(getJSON(band_path));\n",
+ "\n",
+ " //---------Read section_k_band_segment------------\n",
+ " var section_k_band_segment = band_data['section_run']['section_single_configuration_calculation']['section_k_band'][0]['section_k_band_segment']\n",
+ "\n",
+ " //--------Get the number of k band segments-------------\n",
+ " var N_k_band_segments = section_k_band_segment.length;\n",
+ "\n",
+ "\n",
+ " //----------Get the total number of k points in all segments---------\n",
+ " var N_k_points_all = 0;\n",
+ " for(var i = 0; i < N_k_band_segments; i++)\n",
+ " N_k_points_all = N_k_points_all + section_k_band_segment[i]['band_k_points'].length;\n",
+ "\n",
+ "\n",
+ " //--------Get the x axis for the band structure figure: the coordinates of k points in 1D\n",
+ " // store in k_coor_1D[N_k_points_total]-----------------\n",
+ "\n",
+ " var band_distance_segments = [];\n",
+ " for(i = 0; i < N_k_band_segments; i++)\n",
+ " {\n",
+ " var x1, x2, y1, y2, z1, z2;\n",
+ " [[x1, y1, z1],[x2, y2, z2]]= section_k_band_segment[i]['band_segm_start_end']; //\"band_segm_start_end\": [[0.5, 0.0, 0.5],[0.5, 0.25, 0.75]],\n",
+ " band_distance_segments.push(Math.pow((x1-x2), 2) + Math.pow((y1-y2), 2) + Math.pow((z1-z2), 2));\n",
+ " }\n",
+ "\n",
+ "\n",
+ " var band_distance_total = band_distance_segments.reduce((x,y) => x+y); //sum of band_distance_segments\n",
+ "\n",
+ " var average_N_k_points_per_inverse_distance = N_k_points_all / band_distance_total;\n",
+ "\n",
+ " //Prepare the parameters to rescale the k coordinates into [0,1]\n",
+ " var step_k_point = 1.0 / N_k_points_all;\n",
+ " var step_k_point = (1.0 + step_k_point) / N_k_points_all;\n",
+ "\n",
+ " var k_coor_1D = [];\n",
+ " for(var i_k_points = 0; i_k_points < N_k_points_all; i_k_points ++)\n",
+ " {\n",
+ " k_coor_1D.push(step_k_point * i_k_points)\n",
+ " }\n",
+ "\n",
+ "\n",
+ " //--------Get the eigenvalues of each band trajectory--------------\n",
+ " /*\n",
+ " N_k_points_per_segment = len(section_k_band_segment[0]['band_energies'][0]) #suppose the numebr of k points in all the segments are the same\n",
+ " N_bands = len(section_k_band_segment[0]['band_energies'][0][0])\n",
+ " band_energies_all = np.zeros((N_bands, N_k_points_all)) #store the eigenvalues\n",
+ " N_k_points_all = 0\n",
+ " for i_segments in range(N_k_band_segments):\n",
+ " band_energies = section_k_band_segment[i_segments]['band_energies']\n",
+ " N_spin_channel = len(band_energies) #Number of the spin channel --FIXME: no spin polarized\n",
+ " N_k_points_per_segment = len(band_energies[0])\n",
+ " for i_k_points in range(N_k_points_per_segment):\n",
+ " for i_bands in range(N_bands):\n",
+ " band_energies_all[i_bands][N_k_points_all] = band_energies[0][i_k_points][i_bands] / (1.60217656535 * pow(10, -19))\n",
+ " N_k_points_all = N_k_points_all + 1\n",
+ " */\n",
+ " //var N_k_points_per_segment = section_k_band_segment[0]['band_energies'][0].length; //suppose the numebr of k points in all the segments are the same\n",
+ " var N_bands = section_k_band_segment[0]['band_energies'][0][0].length;\n",
+ " var band_energies_all = new Array(N_bands);\n",
+ " for(var i_bands = 0; i_bands < N_bands; i_bands ++)\n",
+ " band_energies_all[i_bands] = new Array(N_k_points_all);// new Array(N_bands, N_k_points_all); //store the eigenvalues\n",
+ "\n",
+ " var i_k_points_all = 0;\n",
+ "\n",
+ " for(var i_segments = 0; i_segments < N_k_band_segments; i_segments ++)\n",
+ " {\n",
+ " var band_energies = section_k_band_segment[i_segments]['band_energies'];\n",
+ " var N_spin_channel = band_energies.length; //Number of the spin channel --FIXME: no spin polarized\n",
+ " var N_k_points_per_segment = band_energies[0].length;\n",
+ " for(var i_k_points = 0; i_k_points < N_k_points_per_segment; i_k_points ++)\n",
+ " {\n",
+ " for(var i_bands = 0; i_bands < N_bands; i_bands ++)\n",
+ " {\n",
+ " band_energies_all[i_bands][i_k_points_all] = band_energies[0][i_k_points][i_bands] / (1.60217656535 * Math.pow(10, -19)) - dos_fermi_energy;\n",
+ " }\n",
+ " i_k_points_all = i_k_points_all + 1 ;\n",
+ "\n",
+ " }\n",
+ " }\n",
+ "\n",
+ "\n",
+ "\n",
+ " var N_labels = 0\n",
+ " for(var i_segments = 0; i_segments < N_k_band_segments; i_segments ++)\n",
+ " {\n",
+ " for(var j = 0; j < 2; j++)\n",
+ " //labels_tmp = section_k_band_segment[i_segments]['band_segm_start_end'][j];\n",
+ " N_labels = N_labels + 1\n",
+ " }\n",
+ " var label_flag = [];//[\"\" for i in range(N_labels)] //stores the flags of the labels (X, W, G, etc)\n",
+ "\n",
+ "\n",
+ " var i_label = 0;\n",
+ " var label_flag_last_final = \"\";\n",
+ " var label_flag_current_initial = \"\";\n",
+ " for(var i_segments = 0; i_segments < N_k_band_segments; i_segments ++)\n",
+ " {\n",
+ " var labels_coor_0 = section_k_band_segment[i_segments]['band_segm_start_end'][0].sort();\n",
+ " var labels_coor_1 = section_k_band_segment[i_segments]['band_segm_start_end'][1].sort();\n",
+ "\n",
+ " var label_flag_0 = get_label_flag(labels_coor_0);\n",
+ " var label_flag_1 = get_label_flag(labels_coor_1);\n",
+ "\n",
+ " var label_flag_current_initial = label_flag_0;\n",
+ " if(label_flag_last_final == \"\")\n",
+ " label_flag_last_final = label_flag_0;\n",
+ "\n",
+ " if(label_flag_last_final == label_flag_current_initial)\n",
+ " label_flag[i_label] = label_flag_current_initial;\n",
+ " else\n",
+ " label_flag[i_label] = label_flag_last_final + '|' + label_flag_current_initial;\n",
+ " label_flag_last_final = label_flag_1\n",
+ "\n",
+ "\n",
+ " i_label = i_label + 1;\n",
+ " if(i_segments == N_k_band_segments - 1)\n",
+ " {\n",
+ " label_flag[i_label] = label_flag_1;\n",
+ " i_label = i_label + 1;\n",
+ " }\n",
+ " }\n",
+ " N_labels = i_label;\n",
+ "\n",
+ " //------------Get the coordinates for the labels------------\n",
+ " //label_coor_abs = np.zeros((N_labels)) #stores the absolute coordinates of the labels\n",
+ " var label_coor_relative = [];//np.zeros((N_labels))\n",
+ " for(i_label = 0; i_label < N_labels; i_label ++)\n",
+ " {\n",
+ " //Here the evenly-distributed relative coordinates is used, because the coordinates of the labels could be too nerrow when using there absolute coordinates\n",
+ " //x = labels_coor_0[0]\n",
+ " //y = labels_coor_0[1]\n",
+ " //z = labels_coor_0[2]\n",
+ " //label_coor_abs[i_label] = np.sqrt(x*x+y*y+z*z)\n",
+ " label_coor_relative.push(step_k_point * N_k_points_per_segment * i_label / (1 + 1.0 / N_k_points_all));\n",
+ " }\n",
+ " //----Store the label-----------\n",
+ " var label_obj = [];//[['' for i in range(2)] for j in range(N_labels)]\n",
+ " for(i_label = 0; i_label < N_labels; i_label ++)\n",
+ " {\n",
+ " label_obj.push([label_coor_relative[i_label], label_flag[i_label]]);\n",
+ " }\n",
+ "\n",
+ "\n",
+ " //-------Get VBM, CBM----------------\n",
+ "\n",
+ " var HOMO = -1000;\n",
+ " var LUMO = 1000;\n",
+ " var coor_k_point_HOMO = []; //the coordinate of k point that stores HOMO\n",
+ " var coor_k_point_LUMO = [];//np.zeros((3)) #the coordinate of k point that stores LUMO\n",
+ " //band_gap_direct = 0.0\n",
+ " var band_gap_indirect = 0.0;\n",
+ "\n",
+ "\n",
+ " //band_energy_max = np.amax(band_energies[0])/ (1.60217656535* pow(10,-19))\n",
+ " //band_energy_min = np.amin(band_energies[0])/ (1.60217656535* pow(10,-19))\n",
+ " var band_energy_max = 10;\n",
+ " var band_energy_min = -10;\n",
+ " //N_band_energy_index = 10000\n",
+ " //band_energy_step = (band_energy_max - band_energy_min) / N_band_energy_index\n",
+ " //N_allowed_states = np.zeros(N_band_energy_index + 1)\n",
+ " //i_index_fermi = math.floor((0 - band_energy_min) / band_energy_step) #the index that stores states at the Fermi level\n",
+ "\n",
+ "\n",
+ " for(var i_bands = 0; i_bands < N_bands; i_bands ++)\n",
+ " {\n",
+ " for(var i_k_points_all = 0; i_k_points_all< N_k_points_all; i_k_points_all ++)\n",
+ " {\n",
+ " //i_band_index = math.floor((band_energies_all[i_bands][i_k_points_all] - band_energy_min) / band_energy_step)\n",
+ " //N_allowed_states[index_band_energy] = N_allowed_states[index_band_energy] + 1\n",
+ " var band_energy = band_energies_all[i_bands][i_k_points_all];\n",
+ " if(band_energy > 0)\n",
+ " {\n",
+ " if(band_energy < LUMO)\n",
+ " LUMO = band_energy;\n",
+ " }\n",
+ " else\n",
+ " {\n",
+ " if(band_energy > HOMO)\n",
+ " HOMO = band_energy;\n",
+ " }\n",
+ "\n",
+ " }\n",
+ " }\n",
+ "\n",
+ "\n",
+ " //#for i_band_index in range(i_index_fermi, N_band_energy_index): #get LUMO\n",
+ " // if(N_allowed_states[i_band_index] > 0):\n",
+ " // LUMO = band_energy_min + band_energy_step * i_band_index\n",
+ " //print('HOMO, LUMO: ',HOMO, LUMO)\n",
+ " band_gap_indirect = Math.abs(LUMO - HOMO);\n",
+ "\n",
+ " if(band_gap_indirect < 0.5) //VBM and CBM has to be found in another way for metals/charged system:\n",
+ " {\n",
+ " HOMO = -1000.0;\n",
+ " LUMO = 1000.0;\n",
+ " band_energy_max = 10.0;\n",
+ " band_energy_min = 0.0;\n",
+ " var N_band_energy_index = 10000;\n",
+ " var band_energy_step = (band_energy_max - band_energy_min) / N_band_energy_index;\n",
+ " var N_allowed_states = [];\n",
+ " for(var i_state = 0; i_state < N_band_energy_index+1; i_state++)\n",
+ " N_allowed_states.push(0);\n",
+ "\n",
+ "\n",
+ " //get the DOS and store in N_allowed_states[]\n",
+ " for(var i_k_points_all = 0; i_k_points_all < N_k_points_all; i_k_points_all ++)\n",
+ " {\n",
+ " for(var i_bands = 0; i_bands < N_bands; i_bands ++)\n",
+ " {\n",
+ " var band_energy = band_energies_all[i_bands][i_k_points_all];\n",
+ " if((band_energy_min < band_energy)&&(band_energy < band_energy_max))\n",
+ " {\n",
+ " var i_band_index = Math.floor((band_energy - band_energy_min) / band_energy_step);\n",
+ " N_allowed_states[i_band_index] = N_allowed_states[i_band_index] + 1;\n",
+ " }\n",
+ " }\n",
+ " }\n",
+ "\n",
+ "\n",
+ " var if_gapped = 0;\n",
+ " for(var i_band_index = 0; i_band_index < N_band_energy_index; i_band_index ++)//go through the energy levels from the bottom\n",
+ " {\n",
+ " var band_energy = band_energy_min + band_energy_step * i_band_index\n",
+ " if(N_allowed_states[i_band_index] == 0)\n",
+ " if_gapped = if_gapped + 1;\n",
+ " if((band_energy > band_energy_max - 0.5) && (if_gapped == 0))\n",
+ " {\n",
+ " //alert(\"No gap found in this system. It seems to be a metal.\");\n",
+ " HOMO = 1000;\n",
+ " LUMO = 1000;\n",
+ " break;\n",
+ " }\n",
+ " //print(\"At \", band_energy,\": # allowed states = \", N_allowed_states[i_band_index],\" if_gapped = \", if_gapped)\n",
+ "\n",
+ " if(N_allowed_states[i_band_index] > 0)\n",
+ " {\n",
+ " if(if_gapped * band_energy_step > 0.3 )//above VBM-CBM gap: LUMO\n",
+ " {\n",
+ " if(band_energy < LUMO)\n",
+ " {\n",
+ " //print(\"LUMO got!\")\n",
+ " LUMO = band_energy;\n",
+ " break; //break before touching another gap that is above the band gap\n",
+ " }\n",
+ " }\n",
+ "\n",
+ " if(if_gapped * band_energy_step < 0.3) //below VBM-CBM gap: HOMO\n",
+ " {\n",
+ " if(band_energy > HOMO)\n",
+ " {\n",
+ " //print(\"HOMO got!\")\n",
+ " HOMO = band_energy;\n",
+ " }\n",
+ " } \n",
+ " if_gapped = 0;\n",
+ " }\n",
+ " }\n",
+ " //alert('HOMO, LUMO for metal/charged system: '+ HOMO +\",\"+LUMO)\n",
+ "\n",
+ " }\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ " //Find the position of HOMO, LUMO\n",
+ " var coor_k_point_HOMO = 0, coor_k_point_LUMO = 0;\n",
+ " for(var i_k_points = 0; i_k_points < N_k_points_all; i_k_points++)\n",
+ " {\n",
+ " for(var i_bands = 0; i_bands < N_bands; i_bands ++)\n",
+ " {\n",
+ " if(Math.abs(band_energies_all[i_bands][i_k_points] - HOMO) < 0.001)\n",
+ " coor_k_point_HOMO = k_coor_1D[i_k_points];\n",
+ " if(Math.abs(band_energies_all[i_bands][i_k_points] - LUMO) < 0.001)\n",
+ " coor_k_point_LUMO = k_coor_1D[i_k_points]; \n",
+ " }\n",
+ " }\n",
+ "\n",
+ " //alert(coor_k_point_HOMO +\",\" + coor_k_point_LUMO);\n",
+ "\n",
+ "\n",
+ " //Store the band data to band_obj\n",
+ "\n",
+ " var band_obj = {};\n",
+ " band_obj[\"band_x_axis\"] = k_coor_1D;\n",
+ " band_obj[\"band_y_axis\"] = band_energies_all\n",
+ " band_obj[\"labels\"] = label_obj;\n",
+ " band_obj[\"HOMO_energy\"] = HOMO;\n",
+ " band_obj[\"HOMO_coor\"] = coor_k_point_HOMO;\n",
+ " band_obj[\"LUMO_energy\"] = LUMO;\n",
+ " band_obj[\"LUMO_coor\"] = coor_k_point_LUMO;\n",
+ " band_obj[\"average_N_k_points_per_inverse_distance\"] = average_N_k_points_per_inverse_distance;\n",
+ "\n",
+ "\n",
+ " return band_obj\n",
+ "\n",
+ " }\n",
+ "\n",
+ "\n",
+ " function get_dos_obj(dos_path)\n",
+ " {\n",
+ "\n",
+ " var dos_data = JSON.parse(getJSON(dos_path));\n",
+ "\n",
+ " var N_dos_values = dos_data['section_run']['section_single_configuration_calculation']['section_dos'][0]['dos_energies'].length;\n",
+ "\n",
+ " //in new parser, it seems that the spin channel of 'dos_energies' disappears: Shape: [ number_of_dos_values ]\n",
+ "\n",
+ " //dos_energies = new Array(N_dos_values).fill(0.0);\n",
+ " //dos_energies_tmp = new Array(N_dos_values).fill(0.0) #tmp array for unit convertion\n",
+ " //dos_values = new Array(N_dos_values).fill(0.0)\n",
+ "\n",
+ " var dos_energies = dos_data['section_run']['section_single_configuration_calculation']['section_dos'][0]['dos_energies'];\n",
+ " var dos_values = dos_data['section_run']['section_single_configuration_calculation']['section_dos'][0]['dos_integrated_values'];//[0]\n",
+ "\n",
+ " //To do: check if every section_dos has 'dos_fermi_energy'\n",
+ " var dos_fermi_energy = dos_data['section_run']['section_single_configuration_calculation']['section_dos'][0]['dos_fermi_energy'];\n",
+ " dos_fermi_energy = dos_fermi_energy / (1.60217656535 * Math.pow(10,-19));\n",
+ " \n",
+ " for(var i = 0; i < N_dos_values; i++)\n",
+ " {\n",
+ " dos_energies[i] = dos_energies[i] / (1.60217656535 * Math.pow(10,-19)) - dos_fermi_energy;\n",
+ " }\n",
+ " \n",
+ " dos_obj = {}\n",
+ " dos_obj[\"dos_x_axis\"] = dos_energies;\n",
+ " dos_obj[\"dos_y_axis\"] = dos_values;\n",
+ " dos_obj[\"dos_fermi_energy\"] = dos_fermi_energy;\n",
+ " return dos_obj\n",
+ " }\n",
+ " function get_info_obj(band_path)\n",
+ " {\n",
+ "\n",
+ " var band_data = JSON.parse(getJSON(band_path));\n",
+ " var info_obj = {};\n",
+ " //---------Read the information of the calculation--------\n",
+ " info_obj[\"program_name\"] = band_data[\"section_run\"][\"program_name\"];\n",
+ " info_obj[\"program_basis_set_type\"] = band_data[\"section_run\"][\"program_basis_set_type\"];\n",
+ " info_obj[\"atom_labels\"] = band_data[\"section_run\"][\"section_system\"][0][\"atom_labels\"];\n",
+ " info_obj[\"XC_functional_name\"] = band_data[\"section_run\"][\"section_method\"][\"section_XC_functionals\"][0][\"XC_functional_name\"] + \" + \"+ band_data[\"section_run\"][\"section_method\"][\"section_XC_functionals\"][1][\"XC_functional_name\"];\n",
+ "\n",
+ " //----------Get the space group information----------\n",
+ " /*\n",
+ " [space_group_symbol, lattice_constant] = get_space_group(band_data);\n",
+ " info_obj[\"space_group_symbol\"] = np.array(space_group_symbol).tolist();\n",
+ " info_obj[\"lattice_constant\"] = np.array(lattice_constant).tolist();\n",
+ " */\n",
+ "\n",
+ " return info_obj\n",
+ " }\n",
+ " function process_band_dos_data()\n",
+ " {\n",
+ " info_all = [];\n",
+ " band_obj_all = [];\n",
+ " dos_obj_all = [];\n",
+ "\n",
+ " for(var i = 0; i < N_materials; i++)\n",
+ " {\n",
+ " var band_path = band_paths[i];\n",
+ " var dos_path = dos_paths[i];\n",
+ "\n",
+ "\n",
+ " var dos_obj = get_dos_obj(dos_path);\n",
+ " var dos_fermi_energy = dos_obj[\"dos_fermi_energy\"];\n",
+ " band_obj = get_band_obj(band_path, dos_fermi_energy);\n",
+ " var info_obj = get_info_obj(band_path);\n",
+ "\n",
+ " band_obj_all.push(band_obj);\n",
+ " dos_obj_all.push(dos_obj);\n",
+ " info_obj_all.push(info_obj);\n",
+ " }\n",
+ " }\n",
+ " process_band_dos_data();\n",
+ " //alert(\"process_band_dos_data: info_obj_all: \"+JSON.stringify(info_obj_all));\n",
+ "</script>\n"
+ ],
+ "text/plain": [
+ "<IPython.core.display.HTML object>"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "%%HTML\n",
+ "<script>\n",
+ " var band_obj_all = [];\n",
+ " var dos_obj_all = [];\n",
+ " var info_obj_all = [];\n",
+ " //alert(\"process_band_dos_data: \" +band_paths)\n",
+ " //alert(\"process_band_dos_data: \" +info_obj_all)\n",
+ " function get_label_flag(coor_array)\n",
+ " {\n",
+ " var coor = coor_array.sort().join();\n",
+ " if(coor == '0,0.5,0.5')\n",
+ " return \"X\";\n",
+ " if(coor == '0,0,0.5')\n",
+ " return \"M\";\n",
+ " else if(coor == '0.5,0.5,0.5')\n",
+ " return \"L\";\n",
+ " else if(coor == '0.375,0.375,0.75')\n",
+ " return \"K\";\n",
+ " else if(coor == '0.25,0.5,0.75')\n",
+ " return \"W\";\n",
+ " else if(coor == '0,0,0')\n",
+ " return \"\\u0393\";\n",
+ " else if(coor == '0.25,0.625,0.625')\n",
+ " return \"U\";\n",
+ " else\n",
+ " {\n",
+ " //alert(\"k label not found: \" + coor);\n",
+ " return \"?\";\n",
+ " }\n",
+ " }\n",
+ "\n",
+ "\n",
+ " //============Process the band structure data============\n",
+ " function get_band_obj(band_path, dos_fermi_energy)\n",
+ " {\n",
+ " var band_data = JSON.parse(getJSON(band_path));\n",
+ "\n",
+ " //---------Read section_k_band_segment------------\n",
+ " var section_k_band_segment = band_data['section_run']['section_single_configuration_calculation']['section_k_band'][0]['section_k_band_segment']\n",
+ "\n",
+ " //--------Get the number of k band segments-------------\n",
+ " var N_k_band_segments = section_k_band_segment.length;\n",
+ "\n",
+ "\n",
+ " //----------Get the total number of k points in all segments---------\n",
+ " var N_k_points_all = 0;\n",
+ " for(var i = 0; i < N_k_band_segments; i++)\n",
+ " N_k_points_all = N_k_points_all + section_k_band_segment[i]['band_k_points'].length;\n",
+ "\n",
+ "\n",
+ " //--------Get the x axis for the band structure figure: the coordinates of k points in 1D\n",
+ " // store in k_coor_1D[N_k_points_total]-----------------\n",
+ "\n",
+ " var band_distance_segments = [];\n",
+ " for(i = 0; i < N_k_band_segments; i++)\n",
+ " {\n",
+ " var x1, x2, y1, y2, z1, z2;\n",
+ " [[x1, y1, z1],[x2, y2, z2]]= section_k_band_segment[i]['band_segm_start_end']; //\"band_segm_start_end\": [[0.5, 0.0, 0.5],[0.5, 0.25, 0.75]],\n",
+ " band_distance_segments.push(Math.pow((x1-x2), 2) + Math.pow((y1-y2), 2) + Math.pow((z1-z2), 2));\n",
+ " }\n",
+ "\n",
+ "\n",
+ " var band_distance_total = band_distance_segments.reduce((x,y) => x+y); //sum of band_distance_segments\n",
+ "\n",
+ " var average_N_k_points_per_inverse_distance = N_k_points_all / band_distance_total;\n",
+ "\n",
+ " //Prepare the parameters to rescale the k coordinates into [0,1]\n",
+ " var step_k_point = 1.0 / N_k_points_all;\n",
+ " var step_k_point = (1.0 + step_k_point) / N_k_points_all;\n",
+ "\n",
+ " var k_coor_1D = [];\n",
+ " for(var i_k_points = 0; i_k_points < N_k_points_all; i_k_points ++)\n",
+ " {\n",
+ " k_coor_1D.push(step_k_point * i_k_points)\n",
+ " }\n",
+ "\n",
+ "\n",
+ " //--------Get the eigenvalues of each band trajectory--------------\n",
+ " /*\n",
+ " N_k_points_per_segment = len(section_k_band_segment[0]['band_energies'][0]) #suppose the numebr of k points in all the segments are the same\n",
+ " N_bands = len(section_k_band_segment[0]['band_energies'][0][0])\n",
+ " band_energies_all = np.zeros((N_bands, N_k_points_all)) #store the eigenvalues\n",
+ " N_k_points_all = 0\n",
+ " for i_segments in range(N_k_band_segments):\n",
+ " band_energies = section_k_band_segment[i_segments]['band_energies']\n",
+ " N_spin_channel = len(band_energies) #Number of the spin channel --FIXME: no spin polarized\n",
+ " N_k_points_per_segment = len(band_energies[0])\n",
+ " for i_k_points in range(N_k_points_per_segment):\n",
+ " for i_bands in range(N_bands):\n",
+ " band_energies_all[i_bands][N_k_points_all] = band_energies[0][i_k_points][i_bands] / (1.60217656535 * pow(10, -19))\n",
+ " N_k_points_all = N_k_points_all + 1\n",
+ " */\n",
+ " //var N_k_points_per_segment = section_k_band_segment[0]['band_energies'][0].length; //suppose the numebr of k points in all the segments are the same\n",
+ " var N_bands = section_k_band_segment[0]['band_energies'][0][0].length;\n",
+ " var band_energies_all = new Array(N_bands);\n",
+ " for(var i_bands = 0; i_bands < N_bands; i_bands ++)\n",
+ " band_energies_all[i_bands] = new Array(N_k_points_all);// new Array(N_bands, N_k_points_all); //store the eigenvalues\n",
+ "\n",
+ " var i_k_points_all = 0;\n",
+ "\n",
+ " for(var i_segments = 0; i_segments < N_k_band_segments; i_segments ++)\n",
+ " {\n",
+ " var band_energies = section_k_band_segment[i_segments]['band_energies'];\n",
+ " var N_spin_channel = band_energies.length; //Number of the spin channel --FIXME: no spin polarized\n",
+ " var N_k_points_per_segment = band_energies[0].length;\n",
+ " for(var i_k_points = 0; i_k_points < N_k_points_per_segment; i_k_points ++)\n",
+ " {\n",
+ " for(var i_bands = 0; i_bands < N_bands; i_bands ++)\n",
+ " {\n",
+ " band_energies_all[i_bands][i_k_points_all] = band_energies[0][i_k_points][i_bands] / (1.60217656535 * Math.pow(10, -19)) - dos_fermi_energy;\n",
+ " }\n",
+ " i_k_points_all = i_k_points_all + 1 ;\n",
+ "\n",
+ " }\n",
+ " }\n",
+ "\n",
+ "\n",
+ "\n",
+ " var N_labels = 0\n",
+ " for(var i_segments = 0; i_segments < N_k_band_segments; i_segments ++)\n",
+ " {\n",
+ " for(var j = 0; j < 2; j++)\n",
+ " //labels_tmp = section_k_band_segment[i_segments]['band_segm_start_end'][j];\n",
+ " N_labels = N_labels + 1\n",
+ " }\n",
+ " var label_flag = [];//[\"\" for i in range(N_labels)] //stores the flags of the labels (X, W, G, etc)\n",
+ "\n",
+ "\n",
+ " var i_label = 0;\n",
+ " var label_flag_last_final = \"\";\n",
+ " var label_flag_current_initial = \"\";\n",
+ " for(var i_segments = 0; i_segments < N_k_band_segments; i_segments ++)\n",
+ " {\n",
+ " var labels_coor_0 = section_k_band_segment[i_segments]['band_segm_start_end'][0].sort();\n",
+ " var labels_coor_1 = section_k_band_segment[i_segments]['band_segm_start_end'][1].sort();\n",
+ "\n",
+ " var label_flag_0 = get_label_flag(labels_coor_0);\n",
+ " var label_flag_1 = get_label_flag(labels_coor_1);\n",
+ "\n",
+ " var label_flag_current_initial = label_flag_0;\n",
+ " if(label_flag_last_final == \"\")\n",
+ " label_flag_last_final = label_flag_0;\n",
+ "\n",
+ " if(label_flag_last_final == label_flag_current_initial)\n",
+ " label_flag[i_label] = label_flag_current_initial;\n",
+ " else\n",
+ " label_flag[i_label] = label_flag_last_final + '|' + label_flag_current_initial;\n",
+ " label_flag_last_final = label_flag_1\n",
+ "\n",
+ "\n",
+ " i_label = i_label + 1;\n",
+ " if(i_segments == N_k_band_segments - 1)\n",
+ " {\n",
+ " label_flag[i_label] = label_flag_1;\n",
+ " i_label = i_label + 1;\n",
+ " }\n",
+ " }\n",
+ " N_labels = i_label;\n",
+ "\n",
+ " //------------Get the coordinates for the labels------------\n",
+ " //label_coor_abs = np.zeros((N_labels)) #stores the absolute coordinates of the labels\n",
+ " var label_coor_relative = [];//np.zeros((N_labels))\n",
+ " for(i_label = 0; i_label < N_labels; i_label ++)\n",
+ " {\n",
+ " //Here the evenly-distributed relative coordinates is used, because the coordinates of the labels could be too nerrow when using there absolute coordinates\n",
+ " //x = labels_coor_0[0]\n",
+ " //y = labels_coor_0[1]\n",
+ " //z = labels_coor_0[2]\n",
+ " //label_coor_abs[i_label] = np.sqrt(x*x+y*y+z*z)\n",
+ " label_coor_relative.push(step_k_point * N_k_points_per_segment * i_label / (1 + 1.0 / N_k_points_all));\n",
+ " }\n",
+ " //----Store the label-----------\n",
+ " var label_obj = [];//[['' for i in range(2)] for j in range(N_labels)]\n",
+ " for(i_label = 0; i_label < N_labels; i_label ++)\n",
+ " {\n",
+ " label_obj.push([label_coor_relative[i_label], label_flag[i_label]]);\n",
+ " }\n",
+ "\n",
+ "\n",
+ " //-------Get VBM, CBM----------------\n",
+ "\n",
+ " var HOMO = -1000;\n",
+ " var LUMO = 1000;\n",
+ " var coor_k_point_HOMO = []; //the coordinate of k point that stores HOMO\n",
+ " var coor_k_point_LUMO = [];//np.zeros((3)) #the coordinate of k point that stores LUMO\n",
+ " //band_gap_direct = 0.0\n",
+ " var band_gap_indirect = 0.0;\n",
+ "\n",
+ "\n",
+ " //band_energy_max = np.amax(band_energies[0])/ (1.60217656535* pow(10,-19))\n",
+ " //band_energy_min = np.amin(band_energies[0])/ (1.60217656535* pow(10,-19))\n",
+ " var band_energy_max = 10;\n",
+ " var band_energy_min = -10;\n",
+ " //N_band_energy_index = 10000\n",
+ " //band_energy_step = (band_energy_max - band_energy_min) / N_band_energy_index\n",
+ " //N_allowed_states = np.zeros(N_band_energy_index + 1)\n",
+ " //i_index_fermi = math.floor((0 - band_energy_min) / band_energy_step) #the index that stores states at the Fermi level\n",
+ "\n",
+ "\n",
+ " for(var i_bands = 0; i_bands < N_bands; i_bands ++)\n",
+ " {\n",
+ " for(var i_k_points_all = 0; i_k_points_all< N_k_points_all; i_k_points_all ++)\n",
+ " {\n",
+ " //i_band_index = math.floor((band_energies_all[i_bands][i_k_points_all] - band_energy_min) / band_energy_step)\n",
+ " //N_allowed_states[index_band_energy] = N_allowed_states[index_band_energy] + 1\n",
+ " var band_energy = band_energies_all[i_bands][i_k_points_all];\n",
+ " if(band_energy > 0)\n",
+ " {\n",
+ " if(band_energy < LUMO)\n",
+ " LUMO = band_energy;\n",
+ " }\n",
+ " else\n",
+ " {\n",
+ " if(band_energy > HOMO)\n",
+ " HOMO = band_energy;\n",
+ " }\n",
+ "\n",
+ " }\n",
+ " }\n",
+ "\n",
+ "\n",
+ " //#for i_band_index in range(i_index_fermi, N_band_energy_index): #get LUMO\n",
+ " // if(N_allowed_states[i_band_index] > 0):\n",
+ " // LUMO = band_energy_min + band_energy_step * i_band_index\n",
+ " //print('HOMO, LUMO: ',HOMO, LUMO)\n",
+ " band_gap_indirect = Math.abs(LUMO - HOMO);\n",
+ "\n",
+ " if(band_gap_indirect < 0.5) //VBM and CBM has to be found in another way for metals/charged system:\n",
+ " {\n",
+ " HOMO = -1000.0;\n",
+ " LUMO = 1000.0;\n",
+ " band_energy_max = 10.0;\n",
+ " band_energy_min = 0.0;\n",
+ " var N_band_energy_index = 10000;\n",
+ " var band_energy_step = (band_energy_max - band_energy_min) / N_band_energy_index;\n",
+ " var N_allowed_states = [];\n",
+ " for(var i_state = 0; i_state < N_band_energy_index+1; i_state++)\n",
+ " N_allowed_states.push(0);\n",
+ "\n",
+ "\n",
+ " //get the DOS and store in N_allowed_states[]\n",
+ " for(var i_k_points_all = 0; i_k_points_all < N_k_points_all; i_k_points_all ++)\n",
+ " {\n",
+ " for(var i_bands = 0; i_bands < N_bands; i_bands ++)\n",
+ " {\n",
+ " var band_energy = band_energies_all[i_bands][i_k_points_all];\n",
+ " if((band_energy_min < band_energy)&&(band_energy < band_energy_max))\n",
+ " {\n",
+ " var i_band_index = Math.floor((band_energy - band_energy_min) / band_energy_step);\n",
+ " N_allowed_states[i_band_index] = N_allowed_states[i_band_index] + 1;\n",
+ " }\n",
+ " }\n",
+ " }\n",
+ "\n",
+ "\n",
+ " var if_gapped = 0;\n",
+ " for(var i_band_index = 0; i_band_index < N_band_energy_index; i_band_index ++)//go through the energy levels from the bottom\n",
+ " {\n",
+ " var band_energy = band_energy_min + band_energy_step * i_band_index\n",
+ " if(N_allowed_states[i_band_index] == 0)\n",
+ " if_gapped = if_gapped + 1;\n",
+ " if((band_energy > band_energy_max - 0.5) && (if_gapped == 0))\n",
+ " {\n",
+ " //alert(\"No gap found in this system. It seems to be a metal.\");\n",
+ " HOMO = 1000;\n",
+ " LUMO = 1000;\n",
+ " break;\n",
+ " }\n",
+ " //print(\"At \", band_energy,\": # allowed states = \", N_allowed_states[i_band_index],\" if_gapped = \", if_gapped)\n",
+ "\n",
+ " if(N_allowed_states[i_band_index] > 0)\n",
+ " {\n",
+ " if(if_gapped * band_energy_step > 0.3 )//above VBM-CBM gap: LUMO\n",
+ " {\n",
+ " if(band_energy < LUMO)\n",
+ " {\n",
+ " //print(\"LUMO got!\")\n",
+ " LUMO = band_energy;\n",
+ " break; //break before touching another gap that is above the band gap\n",
+ " }\n",
+ " }\n",
+ "\n",
+ " if(if_gapped * band_energy_step < 0.3) //below VBM-CBM gap: HOMO\n",
+ " {\n",
+ " if(band_energy > HOMO)\n",
+ " {\n",
+ " //print(\"HOMO got!\")\n",
+ " HOMO = band_energy;\n",
+ " }\n",
+ " } \n",
+ " if_gapped = 0;\n",
+ " }\n",
+ " }\n",
+ " //alert('HOMO, LUMO for metal/charged system: '+ HOMO +\",\"+LUMO)\n",
+ "\n",
+ " }\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ " //Find the position of HOMO, LUMO\n",
+ " var coor_k_point_HOMO = 0, coor_k_point_LUMO = 0;\n",
+ " for(var i_k_points = 0; i_k_points < N_k_points_all; i_k_points++)\n",
+ " {\n",
+ " for(var i_bands = 0; i_bands < N_bands; i_bands ++)\n",
+ " {\n",
+ " if(Math.abs(band_energies_all[i_bands][i_k_points] - HOMO) < 0.001)\n",
+ " coor_k_point_HOMO = k_coor_1D[i_k_points];\n",
+ " if(Math.abs(band_energies_all[i_bands][i_k_points] - LUMO) < 0.001)\n",
+ " coor_k_point_LUMO = k_coor_1D[i_k_points]; \n",
+ " }\n",
+ " }\n",
+ "\n",
+ " //alert(coor_k_point_HOMO +\",\" + coor_k_point_LUMO);\n",
+ "\n",
+ "\n",
+ " //Store the band data to band_obj\n",
+ "\n",
+ " var band_obj = {};\n",
+ " band_obj[\"band_x_axis\"] = k_coor_1D;\n",
+ " band_obj[\"band_y_axis\"] = band_energies_all\n",
+ " band_obj[\"labels\"] = label_obj;\n",
+ " band_obj[\"HOMO_energy\"] = HOMO;\n",
+ " band_obj[\"HOMO_coor\"] = coor_k_point_HOMO;\n",
+ " band_obj[\"LUMO_energy\"] = LUMO;\n",
+ " band_obj[\"LUMO_coor\"] = coor_k_point_LUMO;\n",
+ " band_obj[\"average_N_k_points_per_inverse_distance\"] = average_N_k_points_per_inverse_distance;\n",
+ "\n",
+ "\n",
+ " return band_obj\n",
+ "\n",
+ " }\n",
+ "\n",
+ "\n",
+ " function get_dos_obj(dos_path)\n",
+ " {\n",
+ "\n",
+ " var dos_data = JSON.parse(getJSON(dos_path));\n",
+ "\n",
+ " var N_dos_values = dos_data['section_run']['section_single_configuration_calculation']['section_dos'][0]['dos_energies'].length;\n",
+ "\n",
+ " //in new parser, it seems that the spin channel of 'dos_energies' disappears: Shape: [ number_of_dos_values ]\n",
+ "\n",
+ " //dos_energies = new Array(N_dos_values).fill(0.0);\n",
+ " //dos_energies_tmp = new Array(N_dos_values).fill(0.0) #tmp array for unit convertion\n",
+ " //dos_values = new Array(N_dos_values).fill(0.0)\n",
+ "\n",
+ " var dos_energies = dos_data['section_run']['section_single_configuration_calculation']['section_dos'][0]['dos_energies'];\n",
+ " var dos_values = dos_data['section_run']['section_single_configuration_calculation']['section_dos'][0]['dos_integrated_values'];//[0]\n",
+ "\n",
+ " //To do: check if every section_dos has 'dos_fermi_energy'\n",
+ " var dos_fermi_energy = dos_data['section_run']['section_single_configuration_calculation']['section_dos'][0]['dos_fermi_energy'];\n",
+ " dos_fermi_energy = dos_fermi_energy / (1.60217656535 * Math.pow(10,-19));\n",
+ " \n",
+ " for(var i = 0; i < N_dos_values; i++)\n",
+ " {\n",
+ " dos_energies[i] = dos_energies[i] / (1.60217656535 * Math.pow(10,-19)) - dos_fermi_energy;\n",
+ " }\n",
+ " \n",
+ " dos_obj = {}\n",
+ " dos_obj[\"dos_x_axis\"] = dos_energies;\n",
+ " dos_obj[\"dos_y_axis\"] = dos_values;\n",
+ " dos_obj[\"dos_fermi_energy\"] = dos_fermi_energy;\n",
+ " return dos_obj\n",
+ " }\n",
+ " function get_info_obj(band_path)\n",
+ " {\n",
+ "\n",
+ " var band_data = JSON.parse(getJSON(band_path));\n",
+ " var info_obj = {};\n",
+ " //---------Read the information of the calculation--------\n",
+ " info_obj[\"program_name\"] = band_data[\"section_run\"][\"program_name\"];\n",
+ " info_obj[\"program_basis_set_type\"] = band_data[\"section_run\"][\"program_basis_set_type\"];\n",
+ " info_obj[\"atom_labels\"] = band_data[\"section_run\"][\"section_system\"][0][\"atom_labels\"];\n",
+ " info_obj[\"XC_functional_name\"] = band_data[\"section_run\"][\"section_method\"][\"section_XC_functionals\"][0][\"XC_functional_name\"] + \" + \"+ band_data[\"section_run\"][\"section_method\"][\"section_XC_functionals\"][1][\"XC_functional_name\"];\n",
+ "\n",
+ " //----------Get the space group information----------\n",
+ " /*\n",
+ " [space_group_symbol, lattice_constant] = get_space_group(band_data);\n",
+ " info_obj[\"space_group_symbol\"] = np.array(space_group_symbol).tolist();\n",
+ " info_obj[\"lattice_constant\"] = np.array(lattice_constant).tolist();\n",
+ " */\n",
+ "\n",
+ " return info_obj\n",
+ " }\n",
+ " function process_band_dos_data()\n",
+ " {\n",
+ " info_all = [];\n",
+ " band_obj_all = [];\n",
+ " dos_obj_all = [];\n",
+ "\n",
+ " for(var i = 0; i < N_materials; i++)\n",
+ " {\n",
+ " var band_path = band_paths[i];\n",
+ " var dos_path = dos_paths[i];\n",
+ "\n",
+ "\n",
+ " var dos_obj = get_dos_obj(dos_path);\n",
+ " var dos_fermi_energy = dos_obj[\"dos_fermi_energy\"];\n",
+ " band_obj = get_band_obj(band_path, dos_fermi_energy);\n",
+ " var info_obj = get_info_obj(band_path);\n",
+ "\n",
+ " band_obj_all.push(band_obj);\n",
+ " dos_obj_all.push(dos_obj);\n",
+ " info_obj_all.push(info_obj);\n",
+ " }\n",
+ " }\n",
+ " process_band_dos_data();\n",
+ " //alert(\"process_band_dos_data: info_obj_all: \"+JSON.stringify(info_obj_all));\n",
+ "</script>"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 54,
+ "metadata": {
+ "scrolled": false,
+ "tags": [
+ "show_results_and_plot"
+ ]
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "<script>\n",
+ " var N_max_show = 10; //Number of results to be shown by default\n",
+ "\n",
+ " function show_materials_submitted_info()\n",
+ " {\n",
+ " //alert(\"N_materials=\" + N_materials)\n",
+ " //\"table_materials_submitted_info\"\n",
+ " //alert(\"show_materials_submitted_info: info_obj_all: \"+JSON.stringify(info_obj_all))\n",
+ " var table_content = new Array(); \n",
+ " str = '<tr>';\n",
+ " str += '<th width=\"5%\"></th>'\n",
+ " str += '<th width=\"10%\"><p style=\\\"text-align:center\\\"><font size = \\\"4pt\\\"><b>Atom labels</b></font></p></th>';\n",
+ " //str += '<th width=\"10%\"><p style=\\\"text-align:center\\\"><font size = \\\"4pt\\\"><b>Space group</b></font></p></th>';\n",
+ " //str += '<th width=\"15%\"><p style=\\\"text-align:center\\\"><font size = \\\"4pt\\\"><b>Lattice constants (in Ang)</b></font></p></th>';\n",
+ " str += '<th width=\"10%\"><p style=\\\"text-align:center\\\"><font size = \\\"4pt\\\"><b>Program name</b></font></p></th>';\n",
+ " str += '<th width=\"10%\"><p style=\\\"text-align:center\\\"><font size = \\\"4pt\\\"><b>Basis set type</b></font></p></th>';\n",
+ " str += '<th width=\"15%\"><p style=\\\"text-align:center\\\"><font size = \\\"4pt\\\"><b>Functional</b></font></p></th>';\n",
+ " //str += '<th width=\"20%\"><p style=\\\"text-align:center\\\"><font size = \\\"4pt\\\"><b>Number of <i>k</i> points per inverse distance</b></font></p></th>';\n",
+ " str += '</tr>'; //first row: head\n",
+ " table_content.push(str);\n",
+ "\n",
+ " for(var i = 0; i < N_materials; i++) //add info of each material\n",
+ " {\n",
+ " //alert(\"show_materials_submitted_info: material \"+ i); \n",
+ " table_content.push('<tr>');\n",
+ "\n",
+ " table_content.push('<td>'); \n",
+ " str = '<input type = \\\"checkbox\\\" name = \"checkbox_material\" id = \\\"checkbox_material' + i.toString() + '\\\" unchecked onclick=\\\"checkbox_material(this.id)\\\">';\n",
+ " str += \"<b>  #\" + (i+1).toString() + \"</b>\";\n",
+ " table_content.push(str);\n",
+ " table_content.push('</td>');\n",
+ "\n",
+ " table_content.push('<td>'); \n",
+ " str = '<font size = \\\"3pt\\\">';\n",
+ " str += info_obj_all[i][\"atom_labels\"] + ';   ';\n",
+ " str += \"</font>\"\n",
+ " table_content.push(str); \n",
+ " table_content.push('</td>');\n",
+ " //alert(\"got atom_labels\");\n",
+ "\n",
+ " /*\n",
+ " table_content.push('<td>'); \n",
+ " str = '<font size = \\\"3pt\\\">';\n",
+ " str += info_obj_all[i][\"space_group_symbol\"] + ';   ';\n",
+ " str += \"</font>\"\n",
+ " table_content.push(str); \n",
+ " table_content.push('</td>');\n",
+ " //alert(\"got space_group_symbol\");\n",
+ "\n",
+ " table_content.push('<td>'); \n",
+ " str = '<font size = \\\"3pt\\\">';\n",
+ " str += info_obj_all[i][\"lattice_constant\"] + ';   ';\n",
+ " str += \"</font>\"\n",
+ " table_content.push(str); \n",
+ " table_content.push('</td>');\n",
+ " //alert(\"got lattice_constant\");\n",
+ " */\n",
+ " \n",
+ " table_content.push('<td>'); \n",
+ " str = '<font size = \\\"3pt\\\">';\n",
+ " str += info_obj_all[i][\"program_name\"].toUpperCase() + ';   ';\n",
+ " str += \"</font>\"\n",
+ " table_content.push(str); \n",
+ " table_content.push('</td>');\n",
+ " //alert(\"got program_name\");\n",
+ "\n",
+ " table_content.push('<td>'); \n",
+ " str = '<font size = \\\"3pt\\\">';\n",
+ " str += info_obj_all[i][\"program_basis_set_type\"] + ';   ';\n",
+ " str += \"</font>\"\n",
+ " table_content.push(str); \n",
+ " table_content.push('</td>');\n",
+ " //alert(\"got program_basis_set_type\");\n",
+ "\n",
+ "\n",
+ " table_content.push('<td>'); \n",
+ " str = '<font size = \\\"3pt\\\">';\n",
+ " str += info_obj_all[i][\"XC_functional_name\"] + ';   ';\n",
+ " str += \"</font>\"\n",
+ " table_content.push(str); \n",
+ " table_content.push('</td>');\n",
+ " //alert(\"got XC_functional_name\");\n",
+ "\n",
+ " /*\n",
+ " table_content.push('<td>'); \n",
+ " str = '<font size = \\\"3pt\\\">';\n",
+ " str += band_obj_all[i][\"average_N_k_points_per_inverse_distance\"].toFixed(3);\n",
+ " str += \"</font>\"\n",
+ " table_content.push(str); \n",
+ " table_content.push('</td>');\n",
+ " //alert(\"got average_N_k_points_per_inverse_distance\");\n",
+ " */\n",
+ " table_content.push('</tr>');\n",
+ "\n",
+ " }\n",
+ " \n",
+ " document.getElementById(\"table_materials_submitted_info\").innerHTML = table_content.join('');\n",
+ " }\n",
+ "\n",
+ " function clean_materials_selection()\n",
+ " {\n",
+ " var choices_compare = document.getElementsByName(\"checkbox_material\");\n",
+ " for(var i=0; i<choices_compare.length; i++)\n",
+ " {\n",
+ " //choices_compare[i].removeAttribute('checked');\n",
+ " //choices_compare[i].setAttribute(\"unchecked\", \"unchecked\");\n",
+ " choices_compare[i].checked = \"\";\n",
+ " }\n",
+ " }\n",
+ "\n",
+ " function select_all()\n",
+ " {\n",
+ " var choices_compare = document.getElementsByName(\"checkbox_material\");\n",
+ " for(var i=0; i<choices_compare.length; i++)\n",
+ " {\n",
+ " //choices_compare[i].removeAttribute('checked');\n",
+ " //choices_compare[i].setAttribute(\"unchecked\", \"unchecked\");\n",
+ " choices_compare[i].checked = \"checked\";\n",
+ " }\n",
+ " }\n",
+ "\n",
+ "\n",
+ "\n",
+ " function process()\n",
+ " {\n",
+ " //alert(\"Process:\"+band_paths)\n",
+ " //Jupyter.notebook.execute_cells(window.findCellIndicesByTag('init_js_plot'));\n",
+ " //Jupyter.notebook.execute_cells(window.findCellIndicesByTag('show_materials_submitted_info'));\n",
+ " show_materials_submitted_info();\n",
+ " document.getElementById(\"table_visualize\").innerHTML = \"\";\n",
+ " str = N_materials.toString();\n",
+ " document.getElementById(\"n_materials\").innerHTML = \"Number of materials submitted: \" + str + \"<font size = 1px color = #C0C0C0 >   Please press \\'Visualize\\' to visualize the band structure. </font>\";\n",
+ " document.getElementById(\"div_showall\").style.visibility=\"hidden\";\n",
+ " }\n",
+ " \n",
+ "\n",
+ " var image_band = '';\n",
+ " var image_dos = '';\n",
+ " var image_band_links = new Array(N_materials); //store the URL of each band figure -> used to compare 2 figures\n",
+ " var image_band_links_selected = [];\n",
+ " var image_band_selected_Number = []; //record which i_material has been selected\n",
+ "\n",
+ "\n",
+ "\n",
+ " function prepare(N_materials_show)\n",
+ " {\n",
+ " document.getElementById(\"table_visualize\").innerHTML = \"\";\n",
+ " var table_content = new Array(); \n",
+ " //document.getElementById(\"table_visualize\").innerHTML = table_content.join('');\n",
+ " //-----Generate the html tables for each material--------\n",
+ " for(var i = 0; i < N_materials_show; i++)\n",
+ " {\n",
+ " checkbox_material_id = \"checkbox_material\" + i.toString();\n",
+ " var if_selected = check_show_VBM(checkbox_material_id);\n",
+ " if(if_selected != 1)\n",
+ " {\n",
+ " continue;\n",
+ " }\n",
+ "\n",
+ " table_content.push('<tr>');\n",
+ " div_string = '<div style = \\\"height: 20px\\\"></div>';\n",
+ " table_content.push(div_string);\n",
+ " table_content.push('<th>');\n",
+ "\n",
+ " //add main container div\n",
+ " div_string = '<div id = \\\"div_band_dos' + i.toString() + '\\\" class = \\\"div_band_dos\\\" >';\n",
+ " table_content.push(div_string);\n",
+ "\n",
+ " //show No. of the material\n",
+ " i_material = i + 1;\n",
+ " div_string = '<div style = \\\"height:30px\\; font-size: 15pt;\">' + '#' + i_material.toString() + '</div>';\n",
+ " table_content.push(div_string);\n",
+ "\n",
+ " //show band_path/dos info\n",
+ " div_string = '<div style = \\\"height:30px\\\">' + 'Band:   ' + band_paths[i] + ',    DOS:   ' + dos_paths[i] + '</div>';\n",
+ " table_content.push(div_string);\n",
+ "\n",
+ " //add div_band\n",
+ " div_string = '<div id = \\\"div_band' + i.toString() + '\\\" class = \\\"div_band\\\" ></div>';\n",
+ " table_content.push(div_string);\n",
+ "\n",
+ " //add div_dos\n",
+ " div_string = '<div id = \\\"div_dos' + i.toString() + '\\\" class = \\\"div_dos\\\" ></div>'; \n",
+ " table_content.push(div_string);\n",
+ "\n",
+ " //add div_tools\n",
+ " div_string = '<div id = \\\"div_tools' + i.toString() + '\\\" class = \\\"div_tools\\\" >'; \n",
+ " table_content.push(div_string);\n",
+ "\n",
+ " //add: infomation\n",
+ " div_string = '<div id = \\\"div_info' + i.toString() + '\\\">atom_labels<br>program_name</div>'; \n",
+ " table_content.push(div_string);\n",
+ "\n",
+ " //add: custom scale\n",
+ " div_string = '<br><p style=\\\"color: #000;font-weight: 100; font-size: 10pt; align:left\\\"> Set the lower and upper limit of energy scale (in eV): <br><br><font color=\\\"black\\\" size = 3px> Lower limit:    </font><textarea id=\\\"lowerlimit' + i.toString() + '\\\" rows=\\\"1\\\" style = \\\"width: 70px;\\\">-10</textarea> <font color=\\\"black\\\" size = 3px>   eV</font>    <font color=\\\"black\\\" size = 3px> Upper limit:    </font><textarea id=\\\"upperlimit' + i.toString() + '\\\" rows=\\\"1\\\" style = \\\"width: 70px;\\\">10</textarea> <font color=\\\"black\\\" size = 3px>   eV   </font></p>';\n",
+ " table_content.push(div_string);\n",
+ " div_string = '<br><button class = \\\"button_tools\\\" id = \\\"button_customscale' + i.toString() + '\\\" onclick = \\\"customscale(this.id)\\\"> Rescale </button>'; \n",
+ " table_content.push(div_string);\n",
+ "\n",
+ "\n",
+ " //add button:autoscale\n",
+ " div_string = '<button class = \\\"button_tools\\\" id = \\\"button_autoscale' + i.toString() + '\\\" onclick = \\\"autoscale(this.id)\\\" title = \\\"(-10 eV, 10 eV)\\\"> Autoscale </button>'; \n",
+ " table_content.push(div_string);\n",
+ " //add button:fullscale\n",
+ " div_string = '<button class = \\\"button_tools\\\" id = \\\"button_fullscale' + i.toString() + '\\\" onclick = \\\"fullscale(this.id)\\\" title = \\\"(-100 eV, 100 eV)\\\"> Full scale </button><br><br>'; \n",
+ " table_content.push(div_string);\n",
+ "\n",
+ " //table_content.push(\"Select and zoom:\");\n",
+ "\n",
+ " /*//overview for select and zoom\n",
+ " div_string = '<div id = \\\"div_overview' + i.toString() + '\\\" class = \\\"div_overview\\\" ></div>'; // <div id=\"overview\" style=\"width:300px;height:200px; margin-left:10px; margin-top: 50px; padding-top: 0px\"></div>\n",
+ " table_content.push(div_string);\n",
+ " div_string = '<p id = \\\"overviewLegend' + i.toString() + '\\\" ></p>'; // <p id=\"overviewLegend\" style=\"margin-left:10px\"></p>\n",
+ " table_content.push(div_string);*/\n",
+ "\n",
+ " //download figures as png\n",
+ " div_string = '<a id = \\\"img_band' + i.toString() + '\\\" class = \\\"button_tools\\\" target=\\\"_blank\\\" style = \\\"text-decoration: none;\\\" > Download band </a>';\n",
+ " table_content.push(div_string); \n",
+ " div_string = '<a id = \\\"img_dos' + i.toString() + '\\\" class = \\\"button_tools\\\" target=\\\"_blank\\\" style = \\\"text-decoration: none;\\\" > Download DOS </a>';\n",
+ " table_content.push(div_string);\n",
+ "\n",
+ " //add show VBM & CBM\n",
+ " div_string = '<br><br><p style = \\\"text-normal-black\\\"> <input type = \\\"checkbox\\\" id = \\\"checkbox_VBM' + i.toString() + '\\\" unchecked onclick=\\\"show_VBM(this.id)\\\"> <font color=\\\"black\\\" size = 3px> Show VBM </font> (<font color=\\\"blue\\\">\\•</font>) <font color=\\\"black\\\" size = 3px> and CBM </font>(<font color=\\\"red\\\">\\•</font>) </p>';\n",
+ " table_content.push(div_string);\n",
+ "\n",
+ "\n",
+ " table_content.push('</div>');//div_tools\n",
+ "\n",
+ " //checkbox for comparison\n",
+ " div_string = '<div id = \\\"div_checkbox_compare' + i.toString() + '\\\" class = \\\"div_checkbox_compare\\\" >';\n",
+ " table_content.push(div_string);\n",
+ " //div_string = '<p style = \\\"text-normal-black\\\"> <input type = \\\"checkbox\\\" id = \\\"checkbox_compare' + i.toString() + '\\\" unchecked name = \\\"checkbox_compare\\\" onclick=\\\"check_compare(this.id)\\\"> <font color=\\\"black\\\" size = 3px> Compare </font></p><p><font size = 2px color = \"#666\">(select max. 2 materials) </font> </p>';\n",
+ " div_string = '<p style = \\\"text-normal-black\\\"> <input type = \\\"checkbox\\\" id = \\\"checkbox_compare' + i.toString() + '\\\" checked = \\\"unchecked\\\" unchecked name = \\\"checkbox_compare\\\" onclick=\\\"check_compare(this.id)\\\"> <font color=\\\"black\\\" size = 3px> Compare </font></p><p><font size = 2px color = \"#666\">(select max. 2 materials) </font> </p>';\n",
+ " table_content.push(div_string);\n",
+ " table_content.push('</div>');//div_checkbox_compare\n",
+ "\n",
+ "\n",
+ " table_content.push('</div>');//div_band_dos\n",
+ " table_content.push('</th>');\n",
+ " table_content.push('</tr>'); \n",
+ " }\n",
+ "\n",
+ " document.getElementById(\"table_visualize\").innerHTML = table_content.join('');\n",
+ " }\n",
+ "\n",
+ "\n",
+ " function visualize_band_dos()\n",
+ " {\n",
+ " Jupyter.notebook.execute_cells(window.findCellIndicesByTag('init_jquery'));\n",
+ " Jupyter.notebook.execute_cells(window.findCellIndicesByTag('init_flot'));\n",
+ " Jupyter.notebook.execute_cells(window.findCellIndicesByTag('init_flot_axislabels'));\n",
+ " //Jupyter.notebook.execute_cells(window.findCellIndicesByTag('init_flot_dashes'));\n",
+ " Jupyter.notebook.execute_cells(window.findCellIndicesByTag('init_flot_navigate'));\n",
+ " //Jupyter.notebook.execute_cells(window.findCellIndicesByTag('init_flot_selection'));\n",
+ " Jupyter.notebook.execute_cells(window.findCellIndicesByTag('js_flot_legendoncanvas'));\n",
+ " document.getElementById(\"div_showall\").style.visibility=\"hidden\";\n",
+ " document.getElementById(\"div_compare_buttons\").style.visibility=\"\";\n",
+ "\n",
+ "\n",
+ "\n",
+ " if(N_materials > N_max_show)\n",
+ " {\n",
+ " document.getElementById(\"div_showall\").style.visibility=\"visible\";\n",
+ " document.getElementById(\"checkbox_showall\").checked = \"\";\n",
+ " } \n",
+ "\n",
+ " N_materials_show = Math.min(N_max_show, N_materials);\n",
+ "\n",
+ " prepare(N_materials_show);\n",
+ " clean_compare_list();\n",
+ " plot_band_dos_status = plot_band_dos(-10,10, N_materials_show);\n",
+ "\n",
+ " }\n",
+ "\n",
+ " function show_all(id)//\"plot_placeholder\"\n",
+ " {\n",
+ " var if_showall=0;\n",
+ " if_showall = check_show_VBM(id);\n",
+ " if(if_showall == 1)\n",
+ " {\n",
+ " N_materials_show = N_materials;\n",
+ " prepare(N_materials_show);\n",
+ " clean_compare_list();\n",
+ " plot_band_dos_status = plot_band_dos(-10,10, N_materials_show);\n",
+ " }\n",
+ " else\n",
+ " {\n",
+ " N_materials_show = Math.min(N_max_show, N_materials);\n",
+ " prepare(N_materials_show);\n",
+ " clean_compare_list();\n",
+ " plot_band_dos_status = plot_band_dos(-10,10, N_materials_show);\n",
+ " }\n",
+ "\n",
+ " }\n",
+ "\n",
+ " \n",
+ " //------------------Tool used to get the content from textarea---------------------\n",
+ " function get_text(textarea_id)\n",
+ " {\n",
+ " var text = document.getElementById(textarea_id).value;\n",
+ " return text;\n",
+ " }\n",
+ "\n",
+ "\n",
+ "\n",
+ " //-------------------Compare 2 band figures----------------------------------------\n",
+ "\n",
+ "\n",
+ " function check_compare(id)//checkbox_compare' + i.toString() + '\\\" unchecked onclick=\\\"check_compare(this.id)\n",
+ " {\n",
+ " var x = document.getElementById(id);\n",
+ " var choices_compare = document.getElementsByName(\"checkbox_compare\");\n",
+ " var N_chosen = 0;\n",
+ " for(var i=0; i<choices_compare.length; i++)\n",
+ " {\n",
+ " if(choices_compare[i].checked)\n",
+ " {\n",
+ " N_chosen ++;\n",
+ " }\n",
+ " }\n",
+ " if(N_chosen == 2) // In max. only 2 figures could be selected and compared.\n",
+ " {\n",
+ " for(var i=0; i<choices_compare.length; i++)\n",
+ " {\n",
+ " if(!choices_compare[i].checked)\n",
+ " {\n",
+ " choices_compare[i].disabled = 'disabled';\n",
+ " }\n",
+ " }\n",
+ " }\n",
+ " else\n",
+ " {\n",
+ " for(var i=0; i<choices_compare.length; i++)\n",
+ " {\n",
+ " choices_compare[i].removeAttribute('disabled');\n",
+ " }\n",
+ " }\n",
+ "\n",
+ " }\n",
+ "\n",
+ " function compare()\n",
+ " {\n",
+ " $(\"#div_compare\").fadeIn(600);//show div for comparison\n",
+ " //check_compare(-100);\n",
+ "\n",
+ " var compare_list = [];\n",
+ " compare_list = make_compare_list();\n",
+ " //[i_material_1, i_material_2] = make_compare_list();\n",
+ " i_material_1 = compare_list[0];\n",
+ " i_material_2 = compare_list[1];\n",
+ " //document.getElementById(\"demo\").innerHTML = \"In add info compare:\" + i_material_1.toString() + i_material_2.toString();\n",
+ " compare_figures(i_material_1, i_material_2); \n",
+ " }\n",
+ " function make_compare_list()\n",
+ " {\n",
+ " //get the links to the images\n",
+ " images_selected_links = []; //store the links to the figures for comparison\n",
+ " var choices_compare = document.getElementsByName(\"checkbox_compare\");\n",
+ " var N_chosen = 0;\n",
+ " var str = ''; //tmp str for debug\n",
+ " var figure_selected = new Array(2);\n",
+ " for(var i=0; i<choices_compare.length; i++) //check which figures are selected\n",
+ " {\n",
+ " if(choices_compare[i].checked)\n",
+ " {\n",
+ " id_chosen = choices_compare[i].id;\n",
+ " i_chosen = Math.round(id_chosen.substring(16));\n",
+ " var tmp_str = image_band_links[i_chosen];\n",
+ " images_selected_links.push(tmp_str);\n",
+ " figure_selected[N_chosen] = i_chosen;\n",
+ " N_chosen ++;\n",
+ " //str += beakerx.image_band_links[i];\n",
+ " }\n",
+ " }\n",
+ " var i_material_1 = 0;\n",
+ " var i_material_2 = 0;\n",
+ " //document.getElementById(\"demo\").innerHTML = 'In making comare list';\n",
+ " image_band_links_selected = images_selected_links;\n",
+ " //document.getElementById(\"demo\").innerHTML = 'In making comare list: next';\n",
+ " if(N_chosen == 2)\n",
+ " {\n",
+ " i_material_1 = figure_selected[0];\n",
+ " i_material_2 = figure_selected[1];\n",
+ " }\n",
+ " //document.getElementById(\"demo\").innerHTML = 'Compare_list: ' +i_material_1.toString() + ' ' + i_material_2.toString();\n",
+ "\n",
+ " return [i_material_1, i_material_2];\n",
+ " }\n",
+ "\n",
+ " function check_compare_scale(i_material_1, i_material_2)\n",
+ " {\n",
+ " lowerlimit_id_1 = \"lowerlimit\" + i_material_1.toString();\n",
+ " lowerlimit_id_2 = \"lowerlimit\" + i_material_2.toString();\n",
+ " upperlimit_id_1 = \"upperlimit\" + i_material_1.toString();\n",
+ " upperlimit_id_2 = \"upperlimit\" + i_material_2.toString();\n",
+ "\n",
+ " lowerlimit_1 = parseFloat(document.getElementById(lowerlimit_id_1).innerHTML);\n",
+ " lowerlimit_2 = parseFloat(document.getElementById(lowerlimit_id_2).innerHTML);\n",
+ " upperlimit_1 = parseFloat(document.getElementById(upperlimit_id_2).innerHTML);\n",
+ " upperlimit_2 = parseFloat(document.getElementById(upperlimit_id_2).innerHTML);\n",
+ " if((lowerlimit_1 != lowerlimit_2) || (upperlimit_1 != upperlimit_2))\n",
+ " return -1;\n",
+ " else\n",
+ " return 1;\n",
+ " }\n",
+ "\n",
+ " function compare_figures(i_material_1, i_material_2)\n",
+ " {\n",
+ " Jupyter.notebook.execute_cells(window.findCellIndicesByTag('js_query_beforeafter'));\n",
+ " Jupyter.notebook.execute_cells(window.findCellIndicesByTag('js_compare_slide'));\n",
+ " add_info_compare(i_material_1, i_material_2);\n",
+ " document.getElementById(\"div_compare_container\").scrollIntoView({ behavior: 'smooth' }); \n",
+ " document.getElementById(\"div_compare_container\").scrollTop += 50;\n",
+ "\n",
+ " }\n",
+ "\n",
+ "\n",
+ " function clean_compare_list()\n",
+ " {\n",
+ " var choices_compare = document.getElementsByName(\"checkbox_compare\");\n",
+ " for(var i=0; i<choices_compare.length; i++)\n",
+ " {\n",
+ " //choices_compare[i].removeAttribute('checked');\n",
+ " //choices_compare[i].setAttribute(\"unchecked\", \"unchecked\");\n",
+ " choices_compare[i].checked = \"\";\n",
+ " choices_compare[i].removeAttribute('disabled');\n",
+ " }\n",
+ " }\n",
+ "\n",
+ " //-----------Add information about the calculation to \"div_tools\"---------------\n",
+ " function add_info(i)\n",
+ " {\n",
+ " \n",
+ " //document.getElementById(\"demoa\").innerHTML = i.toString() + div_info_id;\n",
+ " //for(var i = 0; i < beakerx.N_materials; i++)\n",
+ " //{\n",
+ " div_info_id = \"div_info\" + i.toString();\n",
+ "\n",
+ " var str = '';\n",
+ " str += \"<br> <p style=\\\"text-align:left\\\"><font size = 3pt><b>Atom labels:</b>     \" + info_obj_all[i][\"atom_labels\"] + '</font></p>';\n",
+ " //str += \"<font size = 3pt><b>Space group:</b>     \" + info_obj_all[i][\"space_group_symbol\"] + '</font>';\n",
+ " //str += \"<font size = 3pt><b>Lattice constants (in Ang):</b>     \" + info_obj_all[i][\"lattice_constant\"] + '</font>';\n",
+ " str += \"<p style=\\\"text-align:left\\\"><font size = 3pt><b>Program name:</b>    \" + info_obj_all[i][\"program_name\"].toUpperCase() + '</font></p>';\n",
+ " str += \"<p style=\\\"text-align:left\\\"><font size = 3pt><b>Basis set type:</b>    \" + info_obj_all[i][\"program_basis_set_type\"] + '</font></p>';\n",
+ " str += \"<p style=\\\"text-align:left\\\"><font size = 3pt><b>Functional:</b>    \" + info_obj_all[i][\"XC_functional_name\"] + '</font></p>';\n",
+ " str += \"<p style=\\\"text-align:left\\\"><font size = 3pt><b>Number of <i>k</i> points per inverse distance:</b>    \" + band_obj_all[i][\"average_N_k_points_per_inverse_distance\"].toFixed(3) + '</font></p>';\n",
+ " document.getElementById(div_info_id).innerHTML = str;// + origData[\"atom_labels\"];\n",
+ " //document.getElementById('program_name_1').innerHTML = \"<b>Code:</b>    \" + origData[\"program_name\"];\n",
+ " //document.getElementById('program_basis_set_type_1').innerHTML = \"<b>Basis set type:</b>    \" + origData[\"program_basis_set_type\"];\n",
+ " //document.getElementById('XC_functional_name_1').innerHTML = \"<b>Functional:</b>    \" + origData[\"XC_functional_name\"]; \n",
+ " //}\n",
+ " \n",
+ " }\n",
+ " function add_info_compare(i,j)\n",
+ " {\n",
+ "\n",
+ " div_info_id = \"div_compare_info\";\n",
+ " var str = '';\n",
+ "\n",
+ " if_same_scale = check_compare_scale(i_material_1, i_material_2);\n",
+ " if(if_same_scale == -1)\n",
+ " {\n",
+ " str = '<b><font size = \"15pt\" color=\"#940000\">Error: Different lower/upper limits.</font></b><br>';\n",
+ " document.getElementById(\"div_compare_container\").innerHTML = str;\n",
+ " document.getElementById(div_info_id).innerHTML = '';\n",
+ " return;\n",
+ " }\n",
+ "\n",
+ " str += \"<br><b><font-size:15pt>Information of the first calculation (left):</font></b> <br>\";\n",
+ " str += \"<br> <b>Atom labels:</b>     \" + info_obj_all[i][\"atom_labels\"];\n",
+ " //str += \"<br> <b>Space group:</b>     \" + info_obj_all[i][\"space_group_symbol\"];\n",
+ " //str += \"<br> <b>Lattice constants (in Ang):</b>     \" + info_obj_all[i][\"lattice_constant\"];\n",
+ " str += \"<br> <b>Program name:</b>    \" + info_obj_all[i][\"program_name\"].toUpperCase();\n",
+ " str += \"<br> <b>Basis set type:</b>    \" + info_obj_all[i][\"program_basis_set_type\"];\n",
+ " str += \"<br> <b>Functional:</b>    \" + info_obj_all[i][\"XC_functional_name\"];\n",
+ " str += \"<br> <b>Number of <i>k</i> points per inverse distance:</b>    \" + band_obj_all[j][\"average_N_k_points_per_inverse_distance\"].toFixed(3);\n",
+ " str += \"<br><br><br><b><font-size:15pt>Information of the second calculation (right):</font></b><br>\";\n",
+ " str += \"<br> <b>Atom labels:</b>     \" + info_obj_all[j][\"atom_labels\"];\n",
+ " //str += \"<br> <b>Space group:</b>     \" + info_obj_all[j][\"space_group_symbol\"];\n",
+ " //str += \"<br> <b>Lattice constants (in Ang):</b>     \" + info_obj_all[j][\"lattice_constant\"];\n",
+ " str += \"<br> <b>Program name:</b>    \" + info_obj_all[j][\"program_name\"].toUpperCase();\n",
+ " str += \"<br> <b>Basis set type:</b>    \" + info_obj_all[j][\"program_basis_set_type\"]; \n",
+ " str += \"<br> <b>Functional:</b>    \" + info_obj_all[j][\"XC_functional_name\"];\n",
+ " str += \"<br> <b>Number of <i>k</i> points per inverse distance:</b>    \" + band_obj_all[j][\"average_N_k_points_per_inverse_distance\"].toFixed(3);\n",
+ " document.getElementById(div_info_id).innerHTML = str;// + origData[\"atom_labels\"];\n",
+ " }\n",
+ "\n",
+ "\n",
+ "\n",
+ " //-----------------------Show/hide VBM, CBM-------------------------\n",
+ " function check_show_VBM(checkbox_VBM_id)\n",
+ " {\n",
+ " var x = document.getElementById(checkbox_VBM_id);\n",
+ " var if_checked = 0;\n",
+ " if(x.checked)//== \"checked\")\n",
+ " {\n",
+ " //document.getElementById(\"demoa\").innerHTML = \"checked!\";\n",
+ " if_checked = 1;\n",
+ " }\n",
+ " else if (x.unchecked)// == \"unchecked\")\n",
+ " {\n",
+ " //document.getElementById(\"demoa\").innerHTML = \"unchecked!\";\n",
+ " if_checked = -1;\n",
+ " }\n",
+ " else\n",
+ " {\n",
+ " //document.getElementById(\"demoa\").innerHTML = \"nothing detected!\";\n",
+ " }\n",
+ " return if_checked;\n",
+ " }\n",
+ "\n",
+ " function check_if_in_compare_list(i) // check if the current material i is to be compared\n",
+ " {\n",
+ "\n",
+ " var checkbox_compare_id = \"checkbox_compare\" + i.toString();\n",
+ " var if_compare = check_show_VBM(checkbox_compare_id);\n",
+ " //document.getElementById(\"demo\").innerHTML = 'if_compare of ' + i.toString() + ' : ' + if_compare.toString();\n",
+ " var i_compare_material_1, i_compare_material_2;\n",
+ " [i_compare_material_1, i_compare_material_2] = make_compare_list();\n",
+ " var i_in_compare_list = -1;\n",
+ " if(i_compare_material_1 == i)\n",
+ " {\n",
+ " i_in_compare_list = 1;\n",
+ " }\n",
+ " else if (i_compare_material_2 == i)\n",
+ " {\n",
+ " i_in_compare_list = 2;\n",
+ " }\n",
+ " else\n",
+ " {\n",
+ " i_in_compare_list = 0;\n",
+ " }\n",
+ " //document.getElementById(\"demo\").innerHTML = 'Checking ' + i.toString() + ' in Compare_list: ' + i_in_compare_list.toString();\n",
+ " return [if_compare, i_in_compare_list];\n",
+ " }\n",
+ "\n",
+ " function show_VBM(id)\n",
+ " {\n",
+ " //prepare(\"new\");\n",
+ " //var if_show_VBM = -1;\n",
+ " var len_id = id.length;\n",
+ " var i_material = id.substring(12);\n",
+ " var i = Math.round(i_material);\n",
+ "\n",
+ " var checkbox_VBM_id = \"checkbox_VBM\" + i.toString();\n",
+ " var if_show_VBM = check_show_VBM(checkbox_VBM_id);\n",
+ "\n",
+ " var if_compare, i_in_compare_list;\n",
+ " [if_compare, i_in_compare_list] = check_if_in_compare_list(i);\n",
+ " //document.getElementById(\"demo\").innerHTML = i.toString() + ' in Compare_list: ' + i_in_compare_list.toString();\n",
+ "\n",
+ " plot_band_dos_i(i, -10, 10, if_show_VBM, if_compare, i_in_compare_list);\n",
+ "\n",
+ " }\n",
+ "\n",
+ "\n",
+ " //---------------------Functions to rescale-------------------------------------------\n",
+ " function autoscale(id)\n",
+ " {\n",
+ " var len_id = id.length;\n",
+ " var i_material = id.substring(16);\n",
+ " var i = Math.round(i_material);\n",
+ "\n",
+ " upperlim_id = \"upperlimit\" + i_material;\n",
+ " document.getElementById(upperlim_id).innerHTML =\"10.0\";\n",
+ " lowerlim_id = \"lowerlimit\" + i_material;\n",
+ " document.getElementById(lowerlim_id).innerHTML =\"-10.0\";\n",
+ "\n",
+ "\n",
+ " //document.getElementById(\"demoa\").innerHTML =i_material;\n",
+ " var checkbox_VBM_id = \"checkbox_VBM\" + i.toString();\n",
+ " var if_show_VBM = check_show_VBM(checkbox_VBM_id);\n",
+ "\n",
+ " var if_compare, i_in_compare_list;\n",
+ " [if_compare, i_in_compare_list] = check_if_in_compare_list(i);\n",
+ "\n",
+ "\n",
+ " plot_band_dos_i(i, -10, 10, if_show_VBM, if_compare, i_in_compare_list);\n",
+ "\n",
+ " }\n",
+ "\n",
+ " function fullscale(id)\n",
+ " {\n",
+ " var len_id = id.length;\n",
+ " var i_material = id.substring(16);\n",
+ " var i = Math.round(i_material);\n",
+ "\n",
+ " upperlim_id = \"upperlimit\" + i_material;\n",
+ " document.getElementById(upperlim_id).innerHTML =\"100.0\";\n",
+ " lowerlim_id = \"lowerlimit\" + i_material;\n",
+ " document.getElementById(lowerlim_id).innerHTML =\"-100.0\";\n",
+ "\n",
+ " //document.getElementById(\"demoa\").innerHTML =i_material;\n",
+ " var checkbox_VBM_id = \"checkbox_VBM\" + i.toString();\n",
+ " var if_show_VBM = check_show_VBM(checkbox_VBM_id);\n",
+ "\n",
+ " var if_compare, i_in_compare_list;\n",
+ " [if_compare, i_in_compare_list] = check_if_in_compare_list(i);\n",
+ "\n",
+ "\n",
+ "\n",
+ " plot_band_dos_i(i, -100, 100, if_show_VBM, if_compare, i_in_compare_list);\n",
+ "\n",
+ " }\n",
+ "\n",
+ " function customscale(id)\n",
+ " {\n",
+ " var len_id = id.length;\n",
+ " var i_material = id.substring(18);\n",
+ " var i = Math.round(i_material);\n",
+ " //\n",
+ " upperlim_id = \"upperlimit\" + i_material;\n",
+ " upperlim = document.getElementById(upperlim_id).value;\n",
+ " upperlim_float = Math.round(upperlim);\n",
+ " lowerlim_id = \"lowerlimit\" + i_material;\n",
+ " lowerlim = document.getElementById(lowerlim_id).value;\n",
+ " lowerlim_float = Math.round(lowerlim);\n",
+ "\n",
+ " var checkbox_VBM_id = \"checkbox_VBM\" + i.toString();\n",
+ " var if_show_VBM = check_show_VBM(checkbox_VBM_id);\n",
+ "\n",
+ " var if_compare, i_in_compare_list;\n",
+ " [if_compare, i_in_compare_list] = check_if_in_compare_list(i);\n",
+ "\n",
+ "\n",
+ "\n",
+ " plot_band_dos_i(i, lowerlim_float, upperlim_float, if_show_VBM, if_compare, i_in_compare_list); \n",
+ " }\n",
+ "\n",
+ "\n",
+ " function plot_band_dos(lowerLim, upperLim, N_materials_show)\n",
+ " {\n",
+ " placeholder_band = \"#div_band1\";\n",
+ " placeholder_dos = \"#div_dos1\";\n",
+ " // lowerLim = -10.01\n",
+ " //upperLim = 10.01\n",
+ "\n",
+ "\n",
+ "\n",
+ " //alert(\"plot_band_dos\");\n",
+ " //prepare();\n",
+ " for(var i = 0; i < N_materials_show; i++)\n",
+ " {\n",
+ " \n",
+ " var checkbox_material_id = \"checkbox_material\" + i.toString();\n",
+ " var if_selected = check_show_VBM(checkbox_material_id);\n",
+ " if(if_selected != 1)\n",
+ " {\n",
+ " continue;\n",
+ " }\n",
+ " add_info(i);\n",
+ " }\n",
+ "\n",
+ " //------Plot----------------\n",
+ " /*\n",
+ " for(var i_material = 0; i_material < N_materials_show; i_material++)\n",
+ " {\n",
+ "\n",
+ " //alert(\"Material \"+i);\n",
+ " var checkbox_material_id = \"checkbox_material\" + i_material.toString();\n",
+ " var if_selected = check_show_VBM(checkbox_material_id);\n",
+ " if(if_selected != 1)\n",
+ " {\n",
+ " continue;\n",
+ " }\n",
+ "\n",
+ " plot_band_dos_i(i_material, lowerLim, upperLim, 0, 0, -1);\n",
+ " }\n",
+ " */\n",
+ " //alert(\"next:for\")\n",
+ " for (let i_material = 0, p = Promise.resolve(); i_material < N_materials_show; i_material++) {\n",
+ " p = p.then(_ => new Promise(resolve =>\n",
+ " setTimeout(function () {\n",
+ " //alert(i_material)\n",
+ " var checkbox_material_id = \"checkbox_material\" + i_material.toString();\n",
+ " var if_selected = check_show_VBM(checkbox_material_id);\n",
+ " if(if_selected == 1)\n",
+ " {\n",
+ " plot_band_dos_i(i_material, lowerLim, upperLim, 0, 0, -1);\n",
+ " }\n",
+ " resolve();\n",
+ " }, 0)\n",
+ " ));\n",
+ " }\n",
+ "\n",
+ "\n",
+ " return 1;\n",
+ " }\n",
+ "\n",
+ " var i = 0\n",
+ " var lowerLim = -10\n",
+ " var upperLim = 10\n",
+ " var if_show_VBM = 0\n",
+ " var if_compare = 0\n",
+ " var i_in_compare_list = -1\n",
+ "\n",
+ "\n",
+ " \n",
+ " function plot_band_dos_i(i_material, lowerLim_material, upperLim_material, if_show_VBM_material, if_compare_material, i_in_compare_list_material)\n",
+ " {\n",
+ " //alert(\"plot_band_dos_i\")\n",
+ "\n",
+ " i = i_material;\n",
+ " lowerLim = lowerLim_material;\n",
+ " upperLim = upperLim_material;\n",
+ " if_show_VBM = if_show_VBM_material;\n",
+ " if_compare = if_compare_material;\n",
+ " i_in_compare_list = i_in_compare_list_material;\n",
+ " //alert(\"plot_band_dos_i: i_material: \"+i)\n",
+ " Jupyter.notebook.execute_cells(window.findCellIndicesByTag('plot_band'));\n",
+ " //alert('i, lowerLim, upperLim, if_show_VBM, if_compare, i_in_compare_list')\n",
+ " //plot_band(i, lowerLim, upperLim, if_show_VBM, if_compare, i_in_compare_list);\n",
+ " Jupyter.notebook.execute_cells(window.findCellIndicesByTag('plot_dos'));\n",
+ " } \n",
+ "</script>\n",
+ "\n",
+ " \n",
+ " \n",
+ "<br><br>\n",
+ "<button class=\"button\" onclick=\"process()\">Process data</button>\n",
+ "<br><br>\n",
+ "<div id = \"n_materials\" style = \"font-size: 18px; font-weight: 100; height: 60px; width: 100%;\"> Number of materials submitted: 0</div>\n",
+ "<div id = \"show_materials_submitted\" style = \"font-size: 20px; font-color: black;\"> </div>\n",
+ "\n",
+ "<div style = \"width :100%; height: 30px;\"></div> \n",
+ "<p style=\"color: #20335d;font-weight: 100; font-size: 18pt;\"> Select materials to visualize the band structure and DOS:</p>\n",
+ "<div style = \"width :100%; height: 10px;\"></div> \n",
+ "<button class = \"button\" onclick = \"clean_materials_selection()\"> Clean selections </button> \n",
+ "<button class = \"button\" onclick = \"select_all()\"> Select all </button> \n",
+ "<button class = \"button\" onclick = \"visualize_band_dos()\"> Visualize </button> \n",
+ "<div style = \"width :100%; height: 30px;\"></div> \n",
+ "\n",
+ "<div id = \"show_materials_submitted_info\" style = \"width: 100%; font-size: 20px; font-color: black;\"> \n",
+ " <table id = \"table_materials_submitted_info\" style=\"width:100%\"> </table>\n",
+ "</div>\n",
+ "\n",
+ "<div style = \"width :100%; height: 30px;\"></div> \n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "<div id=\"div_compare_buttons\" style=\"visibility:hidden\">\n",
+ " <br><br><br>\n",
+ " <p style=\"color: #20335d;font-weight: 100; font-size: 18pt;\"> Select two materials in the checkbox on the right for comparison:</p>\n",
+ " <p style=\"color: #000;font-weight: 1000; font-size: 8pt;\"></p>\n",
+ " <button class = \"button\" onclick = \"clean_compare_list()\"> Clean selections </button> \n",
+ " <button class = \"button\" onclick = \"compare();compare()\" title = \"Select 2 materials in the checkbox below and compare: please make sure that the upper/lower limits are the same (using Rescale/Autoscale buttons).\" > Compare</button>\n",
+ "</div>\n",
+ "\n",
+ "\n",
+ "\n",
+ "<div id = \"div_showall\" style = \"width: 100%; visibility:hidden\">\n",
+ " <div style = \"width: 100%; height: 30px; \"></div>\n",
+ " <input type = \"checkbox\" id = \"checkbox_showall\" unchecked onclick=\"show_all(this.id)\"/> <font color=\"black\" size = 3px> Show all results </font><font size = 2px color = \"#666\"> (By default only the first 10 results are shown.) </font> \n",
+ " <div style = \"width: 100%; height: 30px; \"></div>\n",
+ "</div>\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "<div id = \"div_compare\" style = \"position: fixed; top: 20%; left: 10%; width: 1200px; height: 600px; z-index: 999999; border: 1px solid #555; background-color: #fff; display: none\" onclick = \"$(this).fadeOut(500)\"> \n",
+ " \n",
+ " <div style = \"float: right; width: 80px; height: 25px; margin-top: 10px; margin-right: 10px; z-index: 1000000; border: 1px solid #555; text-align: center; vertical-align: middle; background-color: #f9f9f9; font-size:12pt; font-color: #000; cursor:pointer;\" > CLOSE </div> <!--button to close the div-->\n",
+ " <div id = \"div_compare_info\" style = \" width: 350px; height: 500px; float: right; margin-top: 50px; margin-right: 10px; z-index: 10000000;\"></div>\n",
+ " <div id = \"div_compare_container\" style = \"margin-top: 50px; margin-left: 100px; width: 600px; height: 300px;\">\n",
+ " <div class=\"g-before-after\" id = \"div_compare_containerx\"></div>\n",
+ " </div>\n",
+ "</div>\n",
+ "\n",
+ "\n",
+ "<div id = \"demo\"></div>\n",
+ "\n",
+ "<div id = \"plot_placeholder\">\n",
+ " <div><br></div>\n",
+ " <table id = \"table_visualize\"> </table>\n",
+ "</div>\n",
+ "<br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br>\n"
+ ],
+ "text/plain": [
+ "<IPython.core.display.HTML object>"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "%%HTML\n",
+ "<script>\n",
+ " var N_max_show = 10; //Number of results to be shown by default\n",
+ "\n",
+ " function show_materials_submitted_info()\n",
+ " {\n",
+ " //alert(\"N_materials=\" + N_materials)\n",
+ " //\"table_materials_submitted_info\"\n",
+ " //alert(\"show_materials_submitted_info: info_obj_all: \"+JSON.stringify(info_obj_all))\n",
+ " var table_content = new Array(); \n",
+ " str = '<tr>';\n",
+ " str += '<th width=\"5%\"></th>'\n",
+ " str += '<th width=\"10%\"><p style=\\\"text-align:center\\\"><font size = \\\"4pt\\\"><b>Atom labels</b></font></p></th>';\n",
+ " //str += '<th width=\"10%\"><p style=\\\"text-align:center\\\"><font size = \\\"4pt\\\"><b>Space group</b></font></p></th>';\n",
+ " //str += '<th width=\"15%\"><p style=\\\"text-align:center\\\"><font size = \\\"4pt\\\"><b>Lattice constants (in Ang)</b></font></p></th>';\n",
+ " str += '<th width=\"10%\"><p style=\\\"text-align:center\\\"><font size = \\\"4pt\\\"><b>Program name</b></font></p></th>';\n",
+ " str += '<th width=\"10%\"><p style=\\\"text-align:center\\\"><font size = \\\"4pt\\\"><b>Basis set type</b></font></p></th>';\n",
+ " str += '<th width=\"15%\"><p style=\\\"text-align:center\\\"><font size = \\\"4pt\\\"><b>Functional</b></font></p></th>';\n",
+ " //str += '<th width=\"20%\"><p style=\\\"text-align:center\\\"><font size = \\\"4pt\\\"><b>Number of <i>k</i> points per inverse distance</b></font></p></th>';\n",
+ " str += '</tr>'; //first row: head\n",
+ " table_content.push(str);\n",
+ "\n",
+ " for(var i = 0; i < N_materials; i++) //add info of each material\n",
+ " {\n",
+ " //alert(\"show_materials_submitted_info: material \"+ i); \n",
+ " table_content.push('<tr>');\n",
+ "\n",
+ " table_content.push('<td>'); \n",
+ " str = '<input type = \\\"checkbox\\\" name = \"checkbox_material\" id = \\\"checkbox_material' + i.toString() + '\\\" unchecked onclick=\\\"checkbox_material(this.id)\\\">';\n",
+ " str += \"<b>  #\" + (i+1).toString() + \"</b>\";\n",
+ " table_content.push(str);\n",
+ " table_content.push('</td>');\n",
+ "\n",
+ " table_content.push('<td>'); \n",
+ " str = '<font size = \\\"3pt\\\">';\n",
+ " str += info_obj_all[i][\"atom_labels\"] + ';   ';\n",
+ " str += \"</font>\"\n",
+ " table_content.push(str); \n",
+ " table_content.push('</td>');\n",
+ " //alert(\"got atom_labels\");\n",
+ "\n",
+ " /*\n",
+ " table_content.push('<td>'); \n",
+ " str = '<font size = \\\"3pt\\\">';\n",
+ " str += info_obj_all[i][\"space_group_symbol\"] + ';   ';\n",
+ " str += \"</font>\"\n",
+ " table_content.push(str); \n",
+ " table_content.push('</td>');\n",
+ " //alert(\"got space_group_symbol\");\n",
+ "\n",
+ " table_content.push('<td>'); \n",
+ " str = '<font size = \\\"3pt\\\">';\n",
+ " str += info_obj_all[i][\"lattice_constant\"] + ';   ';\n",
+ " str += \"</font>\"\n",
+ " table_content.push(str); \n",
+ " table_content.push('</td>');\n",
+ " //alert(\"got lattice_constant\");\n",
+ " */\n",
+ " \n",
+ " table_content.push('<td>'); \n",
+ " str = '<font size = \\\"3pt\\\">';\n",
+ " str += info_obj_all[i][\"program_name\"].toUpperCase() + ';   ';\n",
+ " str += \"</font>\"\n",
+ " table_content.push(str); \n",
+ " table_content.push('</td>');\n",
+ " //alert(\"got program_name\");\n",
+ "\n",
+ " table_content.push('<td>'); \n",
+ " str = '<font size = \\\"3pt\\\">';\n",
+ " str += info_obj_all[i][\"program_basis_set_type\"] + ';   ';\n",
+ " str += \"</font>\"\n",
+ " table_content.push(str); \n",
+ " table_content.push('</td>');\n",
+ " //alert(\"got program_basis_set_type\");\n",
+ "\n",
+ "\n",
+ " table_content.push('<td>'); \n",
+ " str = '<font size = \\\"3pt\\\">';\n",
+ " str += info_obj_all[i][\"XC_functional_name\"] + ';   ';\n",
+ " str += \"</font>\"\n",
+ " table_content.push(str); \n",
+ " table_content.push('</td>');\n",
+ " //alert(\"got XC_functional_name\");\n",
+ "\n",
+ " /*\n",
+ " table_content.push('<td>'); \n",
+ " str = '<font size = \\\"3pt\\\">';\n",
+ " str += band_obj_all[i][\"average_N_k_points_per_inverse_distance\"].toFixed(3);\n",
+ " str += \"</font>\"\n",
+ " table_content.push(str); \n",
+ " table_content.push('</td>');\n",
+ " //alert(\"got average_N_k_points_per_inverse_distance\");\n",
+ " */\n",
+ " table_content.push('</tr>');\n",
+ "\n",
+ " }\n",
+ " \n",
+ " document.getElementById(\"table_materials_submitted_info\").innerHTML = table_content.join('');\n",
+ " }\n",
+ "\n",
+ " function clean_materials_selection()\n",
+ " {\n",
+ " var choices_compare = document.getElementsByName(\"checkbox_material\");\n",
+ " for(var i=0; i<choices_compare.length; i++)\n",
+ " {\n",
+ " //choices_compare[i].removeAttribute('checked');\n",
+ " //choices_compare[i].setAttribute(\"unchecked\", \"unchecked\");\n",
+ " choices_compare[i].checked = \"\";\n",
+ " }\n",
+ " }\n",
+ "\n",
+ " function select_all()\n",
+ " {\n",
+ " var choices_compare = document.getElementsByName(\"checkbox_material\");\n",
+ " for(var i=0; i<choices_compare.length; i++)\n",
+ " {\n",
+ " //choices_compare[i].removeAttribute('checked');\n",
+ " //choices_compare[i].setAttribute(\"unchecked\", \"unchecked\");\n",
+ " choices_compare[i].checked = \"checked\";\n",
+ " }\n",
+ " }\n",
+ "\n",
+ "\n",
+ "\n",
+ " function process()\n",
+ " {\n",
+ " //alert(\"Process:\"+band_paths)\n",
+ " //Jupyter.notebook.execute_cells(window.findCellIndicesByTag('init_js_plot'));\n",
+ " //Jupyter.notebook.execute_cells(window.findCellIndicesByTag('show_materials_submitted_info'));\n",
+ " show_materials_submitted_info();\n",
+ " document.getElementById(\"table_visualize\").innerHTML = \"\";\n",
+ " str = N_materials.toString();\n",
+ " document.getElementById(\"n_materials\").innerHTML = \"Number of materials submitted: \" + str + \"<font size = 1px color = #C0C0C0 >   Please press \\'Visualize\\' to visualize the band structure. </font>\";\n",
+ " document.getElementById(\"div_showall\").style.visibility=\"hidden\";\n",
+ " }\n",
+ " \n",
+ "\n",
+ " var image_band = '';\n",
+ " var image_dos = '';\n",
+ " var image_band_links = new Array(N_materials); //store the URL of each band figure -> used to compare 2 figures\n",
+ " var image_band_links_selected = [];\n",
+ " var image_band_selected_Number = []; //record which i_material has been selected\n",
+ "\n",
+ "\n",
+ "\n",
+ " function prepare(N_materials_show)\n",
+ " {\n",
+ " document.getElementById(\"table_visualize\").innerHTML = \"\";\n",
+ " var table_content = new Array(); \n",
+ " //document.getElementById(\"table_visualize\").innerHTML = table_content.join('');\n",
+ " //-----Generate the html tables for each material--------\n",
+ " for(var i = 0; i < N_materials_show; i++)\n",
+ " {\n",
+ " checkbox_material_id = \"checkbox_material\" + i.toString();\n",
+ " var if_selected = check_show_VBM(checkbox_material_id);\n",
+ " if(if_selected != 1)\n",
+ " {\n",
+ " continue;\n",
+ " }\n",
+ "\n",
+ " table_content.push('<tr>');\n",
+ " div_string = '<div style = \\\"height: 20px\\\"></div>';\n",
+ " table_content.push(div_string);\n",
+ " table_content.push('<th>');\n",
+ "\n",
+ " //add main container div\n",
+ " div_string = '<div id = \\\"div_band_dos' + i.toString() + '\\\" class = \\\"div_band_dos\\\" >';\n",
+ " table_content.push(div_string);\n",
+ "\n",
+ " //show No. of the material\n",
+ " i_material = i + 1;\n",
+ " div_string = '<div style = \\\"height:30px\\; font-size: 15pt;\">' + '#' + i_material.toString() + '</div>';\n",
+ " table_content.push(div_string);\n",
+ "\n",
+ " //show band_path/dos info\n",
+ " div_string = '<div style = \\\"height:30px\\\">' + 'Band:   ' + band_paths[i] + ',    DOS:   ' + dos_paths[i] + '</div>';\n",
+ " table_content.push(div_string);\n",
+ "\n",
+ " //add div_band\n",
+ " div_string = '<div id = \\\"div_band' + i.toString() + '\\\" class = \\\"div_band\\\" ></div>';\n",
+ " table_content.push(div_string);\n",
+ "\n",
+ " //add div_dos\n",
+ " div_string = '<div id = \\\"div_dos' + i.toString() + '\\\" class = \\\"div_dos\\\" ></div>'; \n",
+ " table_content.push(div_string);\n",
+ "\n",
+ " //add div_tools\n",
+ " div_string = '<div id = \\\"div_tools' + i.toString() + '\\\" class = \\\"div_tools\\\" >'; \n",
+ " table_content.push(div_string);\n",
+ "\n",
+ " //add: infomation\n",
+ " div_string = '<div id = \\\"div_info' + i.toString() + '\\\">atom_labels<br>program_name</div>'; \n",
+ " table_content.push(div_string);\n",
+ "\n",
+ " //add: custom scale\n",
+ " div_string = '<br><p style=\\\"color: #000;font-weight: 100; font-size: 10pt; align:left\\\"> Set the lower and upper limit of energy scale (in eV): <br><br><font color=\\\"black\\\" size = 3px> Lower limit:    </font><textarea id=\\\"lowerlimit' + i.toString() + '\\\" rows=\\\"1\\\" style = \\\"width: 70px;\\\">-10</textarea> <font color=\\\"black\\\" size = 3px>   eV</font>    <font color=\\\"black\\\" size = 3px> Upper limit:    </font><textarea id=\\\"upperlimit' + i.toString() + '\\\" rows=\\\"1\\\" style = \\\"width: 70px;\\\">10</textarea> <font color=\\\"black\\\" size = 3px>   eV   </font></p>';\n",
+ " table_content.push(div_string);\n",
+ " div_string = '<br><button class = \\\"button_tools\\\" id = \\\"button_customscale' + i.toString() + '\\\" onclick = \\\"customscale(this.id)\\\"> Rescale </button>'; \n",
+ " table_content.push(div_string);\n",
+ "\n",
+ "\n",
+ " //add button:autoscale\n",
+ " div_string = '<button class = \\\"button_tools\\\" id = \\\"button_autoscale' + i.toString() + '\\\" onclick = \\\"autoscale(this.id)\\\" title = \\\"(-10 eV, 10 eV)\\\"> Autoscale </button>'; \n",
+ " table_content.push(div_string);\n",
+ " //add button:fullscale\n",
+ " div_string = '<button class = \\\"button_tools\\\" id = \\\"button_fullscale' + i.toString() + '\\\" onclick = \\\"fullscale(this.id)\\\" title = \\\"(-100 eV, 100 eV)\\\"> Full scale </button><br><br>'; \n",
+ " table_content.push(div_string);\n",
+ "\n",
+ " //table_content.push(\"Select and zoom:\");\n",
+ "\n",
+ " /*//overview for select and zoom\n",
+ " div_string = '<div id = \\\"div_overview' + i.toString() + '\\\" class = \\\"div_overview\\\" ></div>'; // <div id=\"overview\" style=\"width:300px;height:200px; margin-left:10px; margin-top: 50px; padding-top: 0px\"></div>\n",
+ " table_content.push(div_string);\n",
+ " div_string = '<p id = \\\"overviewLegend' + i.toString() + '\\\" ></p>'; // <p id=\"overviewLegend\" style=\"margin-left:10px\"></p>\n",
+ " table_content.push(div_string);*/\n",
+ "\n",
+ " //download figures as png\n",
+ " div_string = '<a id = \\\"img_band' + i.toString() + '\\\" class = \\\"button_tools\\\" target=\\\"_blank\\\" style = \\\"text-decoration: none;\\\" > Download band </a>';\n",
+ " table_content.push(div_string); \n",
+ " div_string = '<a id = \\\"img_dos' + i.toString() + '\\\" class = \\\"button_tools\\\" target=\\\"_blank\\\" style = \\\"text-decoration: none;\\\" > Download DOS </a>';\n",
+ " table_content.push(div_string);\n",
+ "\n",
+ " //add show VBM & CBM\n",
+ " div_string = '<br><br><p style = \\\"text-normal-black\\\"> <input type = \\\"checkbox\\\" id = \\\"checkbox_VBM' + i.toString() + '\\\" unchecked onclick=\\\"show_VBM(this.id)\\\"> <font color=\\\"black\\\" size = 3px> Show VBM </font> (<font color=\\\"blue\\\">\\•</font>) <font color=\\\"black\\\" size = 3px> and CBM </font>(<font color=\\\"red\\\">\\•</font>) </p>';\n",
+ " table_content.push(div_string);\n",
+ "\n",
+ "\n",
+ " table_content.push('</div>');//div_tools\n",
+ "\n",
+ " //checkbox for comparison\n",
+ " div_string = '<div id = \\\"div_checkbox_compare' + i.toString() + '\\\" class = \\\"div_checkbox_compare\\\" >';\n",
+ " table_content.push(div_string);\n",
+ " //div_string = '<p style = \\\"text-normal-black\\\"> <input type = \\\"checkbox\\\" id = \\\"checkbox_compare' + i.toString() + '\\\" unchecked name = \\\"checkbox_compare\\\" onclick=\\\"check_compare(this.id)\\\"> <font color=\\\"black\\\" size = 3px> Compare </font></p><p><font size = 2px color = \"#666\">(select max. 2 materials) </font> </p>';\n",
+ " div_string = '<p style = \\\"text-normal-black\\\"> <input type = \\\"checkbox\\\" id = \\\"checkbox_compare' + i.toString() + '\\\" checked = \\\"unchecked\\\" unchecked name = \\\"checkbox_compare\\\" onclick=\\\"check_compare(this.id)\\\"> <font color=\\\"black\\\" size = 3px> Compare </font></p><p><font size = 2px color = \"#666\">(select max. 2 materials) </font> </p>';\n",
+ " table_content.push(div_string);\n",
+ " table_content.push('</div>');//div_checkbox_compare\n",
+ "\n",
+ "\n",
+ " table_content.push('</div>');//div_band_dos\n",
+ " table_content.push('</th>');\n",
+ " table_content.push('</tr>'); \n",
+ " }\n",
+ "\n",
+ " document.getElementById(\"table_visualize\").innerHTML = table_content.join('');\n",
+ " }\n",
+ "\n",
+ "\n",
+ " function visualize_band_dos()\n",
+ " {\n",
+ " Jupyter.notebook.execute_cells(window.findCellIndicesByTag('init_jquery'));\n",
+ " Jupyter.notebook.execute_cells(window.findCellIndicesByTag('init_flot'));\n",
+ " Jupyter.notebook.execute_cells(window.findCellIndicesByTag('init_flot_axislabels'));\n",
+ " //Jupyter.notebook.execute_cells(window.findCellIndicesByTag('init_flot_dashes'));\n",
+ " Jupyter.notebook.execute_cells(window.findCellIndicesByTag('init_flot_navigate'));\n",
+ " //Jupyter.notebook.execute_cells(window.findCellIndicesByTag('init_flot_selection'));\n",
+ " Jupyter.notebook.execute_cells(window.findCellIndicesByTag('js_flot_legendoncanvas'));\n",
+ " document.getElementById(\"div_showall\").style.visibility=\"hidden\";\n",
+ " document.getElementById(\"div_compare_buttons\").style.visibility=\"\";\n",
+ "\n",
+ "\n",
+ "\n",
+ " if(N_materials > N_max_show)\n",
+ " {\n",
+ " document.getElementById(\"div_showall\").style.visibility=\"visible\";\n",
+ " document.getElementById(\"checkbox_showall\").checked = \"\";\n",
+ " } \n",
+ "\n",
+ " N_materials_show = Math.min(N_max_show, N_materials);\n",
+ "\n",
+ " prepare(N_materials_show);\n",
+ " clean_compare_list();\n",
+ " plot_band_dos_status = plot_band_dos(-10,10, N_materials_show);\n",
+ "\n",
+ " }\n",
+ "\n",
+ " function show_all(id)//\"plot_placeholder\"\n",
+ " {\n",
+ " var if_showall=0;\n",
+ " if_showall = check_show_VBM(id);\n",
+ " if(if_showall == 1)\n",
+ " {\n",
+ " N_materials_show = N_materials;\n",
+ " prepare(N_materials_show);\n",
+ " clean_compare_list();\n",
+ " plot_band_dos_status = plot_band_dos(-10,10, N_materials_show);\n",
+ " }\n",
+ " else\n",
+ " {\n",
+ " N_materials_show = Math.min(N_max_show, N_materials);\n",
+ " prepare(N_materials_show);\n",
+ " clean_compare_list();\n",
+ " plot_band_dos_status = plot_band_dos(-10,10, N_materials_show);\n",
+ " }\n",
+ "\n",
+ " }\n",
+ "\n",
+ " \n",
+ " //------------------Tool used to get the content from textarea---------------------\n",
+ " function get_text(textarea_id)\n",
+ " {\n",
+ " var text = document.getElementById(textarea_id).value;\n",
+ " return text;\n",
+ " }\n",
+ "\n",
+ "\n",
+ "\n",
+ " //-------------------Compare 2 band figures----------------------------------------\n",
+ "\n",
+ "\n",
+ " function check_compare(id)//checkbox_compare' + i.toString() + '\\\" unchecked onclick=\\\"check_compare(this.id)\n",
+ " {\n",
+ " var x = document.getElementById(id);\n",
+ " var choices_compare = document.getElementsByName(\"checkbox_compare\");\n",
+ " var N_chosen = 0;\n",
+ " for(var i=0; i<choices_compare.length; i++)\n",
+ " {\n",
+ " if(choices_compare[i].checked)\n",
+ " {\n",
+ " N_chosen ++;\n",
+ " }\n",
+ " }\n",
+ " if(N_chosen == 2) // In max. only 2 figures could be selected and compared.\n",
+ " {\n",
+ " for(var i=0; i<choices_compare.length; i++)\n",
+ " {\n",
+ " if(!choices_compare[i].checked)\n",
+ " {\n",
+ " choices_compare[i].disabled = 'disabled';\n",
+ " }\n",
+ " }\n",
+ " }\n",
+ " else\n",
+ " {\n",
+ " for(var i=0; i<choices_compare.length; i++)\n",
+ " {\n",
+ " choices_compare[i].removeAttribute('disabled');\n",
+ " }\n",
+ " }\n",
+ "\n",
+ " }\n",
+ "\n",
+ " function compare()\n",
+ " {\n",
+ " $(\"#div_compare\").fadeIn(600);//show div for comparison\n",
+ " //check_compare(-100);\n",
+ "\n",
+ " var compare_list = [];\n",
+ " compare_list = make_compare_list();\n",
+ " //[i_material_1, i_material_2] = make_compare_list();\n",
+ " i_material_1 = compare_list[0];\n",
+ " i_material_2 = compare_list[1];\n",
+ " //document.getElementById(\"demo\").innerHTML = \"In add info compare:\" + i_material_1.toString() + i_material_2.toString();\n",
+ " compare_figures(i_material_1, i_material_2); \n",
+ " }\n",
+ " function make_compare_list()\n",
+ " {\n",
+ " //get the links to the images\n",
+ " images_selected_links = []; //store the links to the figures for comparison\n",
+ " var choices_compare = document.getElementsByName(\"checkbox_compare\");\n",
+ " var N_chosen = 0;\n",
+ " var str = ''; //tmp str for debug\n",
+ " var figure_selected = new Array(2);\n",
+ " for(var i=0; i<choices_compare.length; i++) //check which figures are selected\n",
+ " {\n",
+ " if(choices_compare[i].checked)\n",
+ " {\n",
+ " id_chosen = choices_compare[i].id;\n",
+ " i_chosen = Math.round(id_chosen.substring(16));\n",
+ " var tmp_str = image_band_links[i_chosen];\n",
+ " images_selected_links.push(tmp_str);\n",
+ " figure_selected[N_chosen] = i_chosen;\n",
+ " N_chosen ++;\n",
+ " //str += beakerx.image_band_links[i];\n",
+ " }\n",
+ " }\n",
+ " var i_material_1 = 0;\n",
+ " var i_material_2 = 0;\n",
+ " //document.getElementById(\"demo\").innerHTML = 'In making comare list';\n",
+ " image_band_links_selected = images_selected_links;\n",
+ " //document.getElementById(\"demo\").innerHTML = 'In making comare list: next';\n",
+ " if(N_chosen == 2)\n",
+ " {\n",
+ " i_material_1 = figure_selected[0];\n",
+ " i_material_2 = figure_selected[1];\n",
+ " }\n",
+ " //document.getElementById(\"demo\").innerHTML = 'Compare_list: ' +i_material_1.toString() + ' ' + i_material_2.toString();\n",
+ "\n",
+ " return [i_material_1, i_material_2];\n",
+ " }\n",
+ "\n",
+ " function check_compare_scale(i_material_1, i_material_2)\n",
+ " {\n",
+ " lowerlimit_id_1 = \"lowerlimit\" + i_material_1.toString();\n",
+ " lowerlimit_id_2 = \"lowerlimit\" + i_material_2.toString();\n",
+ " upperlimit_id_1 = \"upperlimit\" + i_material_1.toString();\n",
+ " upperlimit_id_2 = \"upperlimit\" + i_material_2.toString();\n",
+ "\n",
+ " lowerlimit_1 = parseFloat(document.getElementById(lowerlimit_id_1).innerHTML);\n",
+ " lowerlimit_2 = parseFloat(document.getElementById(lowerlimit_id_2).innerHTML);\n",
+ " upperlimit_1 = parseFloat(document.getElementById(upperlimit_id_2).innerHTML);\n",
+ " upperlimit_2 = parseFloat(document.getElementById(upperlimit_id_2).innerHTML);\n",
+ " if((lowerlimit_1 != lowerlimit_2) || (upperlimit_1 != upperlimit_2))\n",
+ " return -1;\n",
+ " else\n",
+ " return 1;\n",
+ " }\n",
+ "\n",
+ " function compare_figures(i_material_1, i_material_2)\n",
+ " {\n",
+ " Jupyter.notebook.execute_cells(window.findCellIndicesByTag('js_query_beforeafter'));\n",
+ " Jupyter.notebook.execute_cells(window.findCellIndicesByTag('js_compare_slide'));\n",
+ " add_info_compare(i_material_1, i_material_2);\n",
+ " document.getElementById(\"div_compare_container\").scrollIntoView({ behavior: 'smooth' }); \n",
+ " document.getElementById(\"div_compare_container\").scrollTop += 50;\n",
+ "\n",
+ " }\n",
+ "\n",
+ "\n",
+ " function clean_compare_list()\n",
+ " {\n",
+ " var choices_compare = document.getElementsByName(\"checkbox_compare\");\n",
+ " for(var i=0; i<choices_compare.length; i++)\n",
+ " {\n",
+ " //choices_compare[i].removeAttribute('checked');\n",
+ " //choices_compare[i].setAttribute(\"unchecked\", \"unchecked\");\n",
+ " choices_compare[i].checked = \"\";\n",
+ " choices_compare[i].removeAttribute('disabled');\n",
+ " }\n",
+ " }\n",
+ "\n",
+ " //-----------Add information about the calculation to \"div_tools\"---------------\n",
+ " function add_info(i)\n",
+ " {\n",
+ " \n",
+ " //document.getElementById(\"demoa\").innerHTML = i.toString() + div_info_id;\n",
+ " //for(var i = 0; i < beakerx.N_materials; i++)\n",
+ " //{\n",
+ " div_info_id = \"div_info\" + i.toString();\n",
+ "\n",
+ " var str = '';\n",
+ " str += \"<br> <p style=\\\"text-align:left\\\"><font size = 3pt><b>Atom labels:</b>     \" + info_obj_all[i][\"atom_labels\"] + '</font></p>';\n",
+ " //str += \"<font size = 3pt><b>Space group:</b>     \" + info_obj_all[i][\"space_group_symbol\"] + '</font>';\n",
+ " //str += \"<font size = 3pt><b>Lattice constants (in Ang):</b>     \" + info_obj_all[i][\"lattice_constant\"] + '</font>';\n",
+ " str += \"<p style=\\\"text-align:left\\\"><font size = 3pt><b>Program name:</b>    \" + info_obj_all[i][\"program_name\"].toUpperCase() + '</font></p>';\n",
+ " str += \"<p style=\\\"text-align:left\\\"><font size = 3pt><b>Basis set type:</b>    \" + info_obj_all[i][\"program_basis_set_type\"] + '</font></p>';\n",
+ " str += \"<p style=\\\"text-align:left\\\"><font size = 3pt><b>Functional:</b>    \" + info_obj_all[i][\"XC_functional_name\"] + '</font></p>';\n",
+ " str += \"<p style=\\\"text-align:left\\\"><font size = 3pt><b>Number of <i>k</i> points per inverse distance:</b>    \" + band_obj_all[i][\"average_N_k_points_per_inverse_distance\"].toFixed(3) + '</font></p>';\n",
+ " document.getElementById(div_info_id).innerHTML = str;// + origData[\"atom_labels\"];\n",
+ " //document.getElementById('program_name_1').innerHTML = \"<b>Code:</b>    \" + origData[\"program_name\"];\n",
+ " //document.getElementById('program_basis_set_type_1').innerHTML = \"<b>Basis set type:</b>    \" + origData[\"program_basis_set_type\"];\n",
+ " //document.getElementById('XC_functional_name_1').innerHTML = \"<b>Functional:</b>    \" + origData[\"XC_functional_name\"]; \n",
+ " //}\n",
+ " \n",
+ " }\n",
+ " function add_info_compare(i,j)\n",
+ " {\n",
+ "\n",
+ " div_info_id = \"div_compare_info\";\n",
+ " var str = '';\n",
+ "\n",
+ " if_same_scale = check_compare_scale(i_material_1, i_material_2);\n",
+ " if(if_same_scale == -1)\n",
+ " {\n",
+ " str = '<b><font size = \"15pt\" color=\"#940000\">Error: Different lower/upper limits.</font></b><br>';\n",
+ " document.getElementById(\"div_compare_container\").innerHTML = str;\n",
+ " document.getElementById(div_info_id).innerHTML = '';\n",
+ " return;\n",
+ " }\n",
+ "\n",
+ " str += \"<br><b><font-size:15pt>Information of the first calculation (left):</font></b> <br>\";\n",
+ " str += \"<br> <b>Atom labels:</b>     \" + info_obj_all[i][\"atom_labels\"];\n",
+ " //str += \"<br> <b>Space group:</b>     \" + info_obj_all[i][\"space_group_symbol\"];\n",
+ " //str += \"<br> <b>Lattice constants (in Ang):</b>     \" + info_obj_all[i][\"lattice_constant\"];\n",
+ " str += \"<br> <b>Program name:</b>    \" + info_obj_all[i][\"program_name\"].toUpperCase();\n",
+ " str += \"<br> <b>Basis set type:</b>    \" + info_obj_all[i][\"program_basis_set_type\"];\n",
+ " str += \"<br> <b>Functional:</b>    \" + info_obj_all[i][\"XC_functional_name\"];\n",
+ " str += \"<br> <b>Number of <i>k</i> points per inverse distance:</b>    \" + band_obj_all[j][\"average_N_k_points_per_inverse_distance\"].toFixed(3);\n",
+ " str += \"<br><br><br><b><font-size:15pt>Information of the second calculation (right):</font></b><br>\";\n",
+ " str += \"<br> <b>Atom labels:</b>     \" + info_obj_all[j][\"atom_labels\"];\n",
+ " //str += \"<br> <b>Space group:</b>     \" + info_obj_all[j][\"space_group_symbol\"];\n",
+ " //str += \"<br> <b>Lattice constants (in Ang):</b>     \" + info_obj_all[j][\"lattice_constant\"];\n",
+ " str += \"<br> <b>Program name:</b>    \" + info_obj_all[j][\"program_name\"].toUpperCase();\n",
+ " str += \"<br> <b>Basis set type:</b>    \" + info_obj_all[j][\"program_basis_set_type\"]; \n",
+ " str += \"<br> <b>Functional:</b>    \" + info_obj_all[j][\"XC_functional_name\"];\n",
+ " str += \"<br> <b>Number of <i>k</i> points per inverse distance:</b>    \" + band_obj_all[j][\"average_N_k_points_per_inverse_distance\"].toFixed(3);\n",
+ " document.getElementById(div_info_id).innerHTML = str;// + origData[\"atom_labels\"];\n",
+ " }\n",
+ "\n",
+ "\n",
+ "\n",
+ " //-----------------------Show/hide VBM, CBM-------------------------\n",
+ " function check_show_VBM(checkbox_VBM_id)\n",
+ " {\n",
+ " var x = document.getElementById(checkbox_VBM_id);\n",
+ " var if_checked = 0;\n",
+ " if(x.checked)//== \"checked\")\n",
+ " {\n",
+ " //document.getElementById(\"demoa\").innerHTML = \"checked!\";\n",
+ " if_checked = 1;\n",
+ " }\n",
+ " else if (x.unchecked)// == \"unchecked\")\n",
+ " {\n",
+ " //document.getElementById(\"demoa\").innerHTML = \"unchecked!\";\n",
+ " if_checked = -1;\n",
+ " }\n",
+ " else\n",
+ " {\n",
+ " //document.getElementById(\"demoa\").innerHTML = \"nothing detected!\";\n",
+ " }\n",
+ " return if_checked;\n",
+ " }\n",
+ "\n",
+ " function check_if_in_compare_list(i) // check if the current material i is to be compared\n",
+ " {\n",
+ "\n",
+ " var checkbox_compare_id = \"checkbox_compare\" + i.toString();\n",
+ " var if_compare = check_show_VBM(checkbox_compare_id);\n",
+ " //document.getElementById(\"demo\").innerHTML = 'if_compare of ' + i.toString() + ' : ' + if_compare.toString();\n",
+ " var i_compare_material_1, i_compare_material_2;\n",
+ " [i_compare_material_1, i_compare_material_2] = make_compare_list();\n",
+ " var i_in_compare_list = -1;\n",
+ " if(i_compare_material_1 == i)\n",
+ " {\n",
+ " i_in_compare_list = 1;\n",
+ " }\n",
+ " else if (i_compare_material_2 == i)\n",
+ " {\n",
+ " i_in_compare_list = 2;\n",
+ " }\n",
+ " else\n",
+ " {\n",
+ " i_in_compare_list = 0;\n",
+ " }\n",
+ " //document.getElementById(\"demo\").innerHTML = 'Checking ' + i.toString() + ' in Compare_list: ' + i_in_compare_list.toString();\n",
+ " return [if_compare, i_in_compare_list];\n",
+ " }\n",
+ "\n",
+ " function show_VBM(id)\n",
+ " {\n",
+ " //prepare(\"new\");\n",
+ " //var if_show_VBM = -1;\n",
+ " var len_id = id.length;\n",
+ " var i_material = id.substring(12);\n",
+ " var i = Math.round(i_material);\n",
+ "\n",
+ " var checkbox_VBM_id = \"checkbox_VBM\" + i.toString();\n",
+ " var if_show_VBM = check_show_VBM(checkbox_VBM_id);\n",
+ "\n",
+ " var if_compare, i_in_compare_list;\n",
+ " [if_compare, i_in_compare_list] = check_if_in_compare_list(i);\n",
+ " //document.getElementById(\"demo\").innerHTML = i.toString() + ' in Compare_list: ' + i_in_compare_list.toString();\n",
+ "\n",
+ " plot_band_dos_i(i, -10, 10, if_show_VBM, if_compare, i_in_compare_list);\n",
+ "\n",
+ " }\n",
+ "\n",
+ "\n",
+ " //---------------------Functions to rescale-------------------------------------------\n",
+ " function autoscale(id)\n",
+ " {\n",
+ " var len_id = id.length;\n",
+ " var i_material = id.substring(16);\n",
+ " var i = Math.round(i_material);\n",
+ "\n",
+ " upperlim_id = \"upperlimit\" + i_material;\n",
+ " document.getElementById(upperlim_id).innerHTML =\"10.0\";\n",
+ " lowerlim_id = \"lowerlimit\" + i_material;\n",
+ " document.getElementById(lowerlim_id).innerHTML =\"-10.0\";\n",
+ "\n",
+ "\n",
+ " //document.getElementById(\"demoa\").innerHTML =i_material;\n",
+ " var checkbox_VBM_id = \"checkbox_VBM\" + i.toString();\n",
+ " var if_show_VBM = check_show_VBM(checkbox_VBM_id);\n",
+ "\n",
+ " var if_compare, i_in_compare_list;\n",
+ " [if_compare, i_in_compare_list] = check_if_in_compare_list(i);\n",
+ "\n",
+ "\n",
+ " plot_band_dos_i(i, -10, 10, if_show_VBM, if_compare, i_in_compare_list);\n",
+ "\n",
+ " }\n",
+ "\n",
+ " function fullscale(id)\n",
+ " {\n",
+ " var len_id = id.length;\n",
+ " var i_material = id.substring(16);\n",
+ " var i = Math.round(i_material);\n",
+ "\n",
+ " upperlim_id = \"upperlimit\" + i_material;\n",
+ " document.getElementById(upperlim_id).innerHTML =\"100.0\";\n",
+ " lowerlim_id = \"lowerlimit\" + i_material;\n",
+ " document.getElementById(lowerlim_id).innerHTML =\"-100.0\";\n",
+ "\n",
+ " //document.getElementById(\"demoa\").innerHTML =i_material;\n",
+ " var checkbox_VBM_id = \"checkbox_VBM\" + i.toString();\n",
+ " var if_show_VBM = check_show_VBM(checkbox_VBM_id);\n",
+ "\n",
+ " var if_compare, i_in_compare_list;\n",
+ " [if_compare, i_in_compare_list] = check_if_in_compare_list(i);\n",
+ "\n",
+ "\n",
+ "\n",
+ " plot_band_dos_i(i, -100, 100, if_show_VBM, if_compare, i_in_compare_list);\n",
+ "\n",
+ " }\n",
+ "\n",
+ " function customscale(id)\n",
+ " {\n",
+ " var len_id = id.length;\n",
+ " var i_material = id.substring(18);\n",
+ " var i = Math.round(i_material);\n",
+ " //\n",
+ " upperlim_id = \"upperlimit\" + i_material;\n",
+ " upperlim = document.getElementById(upperlim_id).value;\n",
+ " upperlim_float = Math.round(upperlim);\n",
+ " lowerlim_id = \"lowerlimit\" + i_material;\n",
+ " lowerlim = document.getElementById(lowerlim_id).value;\n",
+ " lowerlim_float = Math.round(lowerlim);\n",
+ "\n",
+ " var checkbox_VBM_id = \"checkbox_VBM\" + i.toString();\n",
+ " var if_show_VBM = check_show_VBM(checkbox_VBM_id);\n",
+ "\n",
+ " var if_compare, i_in_compare_list;\n",
+ " [if_compare, i_in_compare_list] = check_if_in_compare_list(i);\n",
+ "\n",
+ "\n",
+ "\n",
+ " plot_band_dos_i(i, lowerlim_float, upperlim_float, if_show_VBM, if_compare, i_in_compare_list); \n",
+ " }\n",
+ "\n",
+ "\n",
+ " function plot_band_dos(lowerLim, upperLim, N_materials_show)\n",
+ " {\n",
+ " placeholder_band = \"#div_band1\";\n",
+ " placeholder_dos = \"#div_dos1\";\n",
+ " // lowerLim = -10.01\n",
+ " //upperLim = 10.01\n",
+ "\n",
+ "\n",
+ "\n",
+ " //alert(\"plot_band_dos\");\n",
+ " //prepare();\n",
+ " for(var i = 0; i < N_materials_show; i++)\n",
+ " {\n",
+ " \n",
+ " var checkbox_material_id = \"checkbox_material\" + i.toString();\n",
+ " var if_selected = check_show_VBM(checkbox_material_id);\n",
+ " if(if_selected != 1)\n",
+ " {\n",
+ " continue;\n",
+ " }\n",
+ " add_info(i);\n",
+ " }\n",
+ "\n",
+ " //------Plot----------------\n",
+ " /*\n",
+ " for(var i_material = 0; i_material < N_materials_show; i_material++)\n",
+ " {\n",
+ "\n",
+ " //alert(\"Material \"+i);\n",
+ " var checkbox_material_id = \"checkbox_material\" + i_material.toString();\n",
+ " var if_selected = check_show_VBM(checkbox_material_id);\n",
+ " if(if_selected != 1)\n",
+ " {\n",
+ " continue;\n",
+ " }\n",
+ "\n",
+ " plot_band_dos_i(i_material, lowerLim, upperLim, 0, 0, -1);\n",
+ " }\n",
+ " */\n",
+ " //alert(\"next:for\")\n",
+ " for (let i_material = 0, p = Promise.resolve(); i_material < N_materials_show; i_material++) {\n",
+ " p = p.then(_ => new Promise(resolve =>\n",
+ " setTimeout(function () {\n",
+ " //alert(i_material)\n",
+ " var checkbox_material_id = \"checkbox_material\" + i_material.toString();\n",
+ " var if_selected = check_show_VBM(checkbox_material_id);\n",
+ " if(if_selected == 1)\n",
+ " {\n",
+ " plot_band_dos_i(i_material, lowerLim, upperLim, 0, 0, -1);\n",
+ " }\n",
+ " resolve();\n",
+ " }, 0)\n",
+ " ));\n",
+ " }\n",
+ "\n",
+ "\n",
+ " return 1;\n",
+ " }\n",
+ "\n",
+ " var i = 0\n",
+ " var lowerLim = -10\n",
+ " var upperLim = 10\n",
+ " var if_show_VBM = 0\n",
+ " var if_compare = 0\n",
+ " var i_in_compare_list = -1\n",
+ "\n",
+ "\n",
+ " \n",
+ " function plot_band_dos_i(i_material, lowerLim_material, upperLim_material, if_show_VBM_material, if_compare_material, i_in_compare_list_material)\n",
+ " {\n",
+ " //alert(\"plot_band_dos_i\")\n",
+ "\n",
+ " i = i_material;\n",
+ " lowerLim = lowerLim_material;\n",
+ " upperLim = upperLim_material;\n",
+ " if_show_VBM = if_show_VBM_material;\n",
+ " if_compare = if_compare_material;\n",
+ " i_in_compare_list = i_in_compare_list_material;\n",
+ " //alert(\"plot_band_dos_i: i_material: \"+i)\n",
+ " Jupyter.notebook.execute_cells(window.findCellIndicesByTag('plot_band'));\n",
+ " //alert('i, lowerLim, upperLim, if_show_VBM, if_compare, i_in_compare_list')\n",
+ " //plot_band(i, lowerLim, upperLim, if_show_VBM, if_compare, i_in_compare_list);\n",
+ " Jupyter.notebook.execute_cells(window.findCellIndicesByTag('plot_dos'));\n",
+ " } \n",
+ "</script>\n",
+ "\n",
+ " \n",
+ " \n",
+ "<br><br>\n",
+ "<button class=\"button\" onclick=\"process()\">Process data</button>\n",
+ "<br><br>\n",
+ "<div id = \"n_materials\" style = \"font-size: 18px; font-weight: 100; height: 60px; width: 100%;\"> Number of materials submitted: 0</div>\n",
+ "<div id = \"show_materials_submitted\" style = \"font-size: 20px; font-color: black;\"> </div>\n",
+ "\n",
+ "<div style = \"width :100%; height: 30px;\"></div> \n",
+ "<p style=\"color: #20335d;font-weight: 100; font-size: 18pt;\"> Select materials to visualize the band structure and DOS:</p>\n",
+ "<div style = \"width :100%; height: 10px;\"></div> \n",
+ "<button class = \"button\" onclick = \"clean_materials_selection()\"> Clean selections </button> \n",
+ "<button class = \"button\" onclick = \"select_all()\"> Select all </button> \n",
+ "<button class = \"button\" onclick = \"visualize_band_dos()\"> Visualize </button> \n",
+ "<div style = \"width :100%; height: 30px;\"></div> \n",
+ "\n",
+ "<div id = \"show_materials_submitted_info\" style = \"width: 100%; font-size: 20px; font-color: black;\"> \n",
+ " <table id = \"table_materials_submitted_info\" style=\"width:100%\"> </table>\n",
+ "</div>\n",
+ "\n",
+ "<div style = \"width :100%; height: 30px;\"></div> \n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "<div id=\"div_compare_buttons\" style=\"visibility:hidden\">\n",
+ " <br><br><br>\n",
+ " <p style=\"color: #20335d;font-weight: 100; font-size: 18pt;\"> Select two materials in the checkbox on the right for comparison:</p>\n",
+ " <p style=\"color: #000;font-weight: 1000; font-size: 8pt;\"></p>\n",
+ " <button class = \"button\" onclick = \"clean_compare_list()\"> Clean selections </button> \n",
+ " <button class = \"button\" onclick = \"compare();compare()\" title = \"Select 2 materials in the checkbox below and compare: please make sure that the upper/lower limits are the same (using Rescale/Autoscale buttons).\" > Compare</button>\n",
+ "</div>\n",
+ "\n",
+ "\n",
+ "\n",
+ "<div id = \"div_showall\" style = \"width: 100%; visibility:hidden\">\n",
+ " <div style = \"width: 100%; height: 30px; \"></div>\n",
+ " <input type = \"checkbox\" id = \"checkbox_showall\" unchecked onclick=\"show_all(this.id)\"/> <font color=\"black\" size = 3px> Show all results </font><font size = 2px color = \"#666\"> (By default only the first 10 results are shown.) </font> \n",
+ " <div style = \"width: 100%; height: 30px; \"></div>\n",
+ "</div>\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "<div id = \"div_compare\" style = \"position: fixed; top: 20%; left: 10%; width: 1200px; height: 600px; z-index: 999999; border: 1px solid #555; background-color: #fff; display: none\" onclick = \"$(this).fadeOut(500)\"> \n",
+ " \n",
+ " <div style = \"float: right; width: 80px; height: 25px; margin-top: 10px; margin-right: 10px; z-index: 1000000; border: 1px solid #555; text-align: center; vertical-align: middle; background-color: #f9f9f9; font-size:12pt; font-color: #000; cursor:pointer;\" > CLOSE </div> <!--button to close the div-->\n",
+ " <div id = \"div_compare_info\" style = \" width: 350px; height: 500px; float: right; margin-top: 50px; margin-right: 10px; z-index: 10000000;\"></div>\n",
+ " <div id = \"div_compare_container\" style = \"margin-top: 50px; margin-left: 100px; width: 600px; height: 300px;\">\n",
+ " <div class=\"g-before-after\" id = \"div_compare_containerx\"></div>\n",
+ " </div>\n",
+ "</div>\n",
+ "\n",
+ "\n",
+ "<div id = \"demo\"></div>\n",
+ "\n",
+ "<div id = \"plot_placeholder\">\n",
+ " <div><br></div>\n",
+ " <table id = \"table_visualize\"> </table>\n",
+ "</div>\n",
+ "<br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br>"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 43,
+ "metadata": {
+ "tags": [
+ "plot_band"
+ ]
+ },
+ "outputs": [
+ {
+ "data": {
+ "application/javascript": [
+ " //alert(\"tag: plot_band\")\n",
+ "\n",
+ "plot_band(i, lowerLim, upperLim, if_show_VBM, if_compare, i_in_compare_list);\n",
+ "\n",
+ "function plot_band(i, lowerLim, upperLim, if_show_VBM, if_compare, i_in_compare_list)\n",
+ "{\n",
+ " //i=0;\n",
+ " //alert(\"plot_band \"+ i)\n",
+ " var placeholder_band = \"#div_band\" + i.toString();\n",
+ " var placeholder_dos = \"#div_dos\" + i.toString();\n",
+ " var placeholder_tools = \"#div_tools\" + i.toString();\n",
+ " var placeholder_overview = \"#div_overview\" + i.toString();\n",
+ " var placeholder_overviewlegend = \"#overviewLegend\" + i.toString();\n",
+ " var checkbox_VBM_id = \"checkbox_VBM\" + i.toString();\n",
+ " var img_band_id = \"img_band\" + i.toString();\n",
+ " var img_dos_id = \"img_dos\" + i.toString();\n",
+ "\n",
+ " var placeholder_band_compare = \"\";\n",
+ "\n",
+ "\n",
+ " if(i_in_compare_list == 1)\n",
+ " {\n",
+ " placeholder_band_compare = \"#div_band_compare_1\";\n",
+ " }\n",
+ " else if(i_in_compare_list == 2)\n",
+ " {\n",
+ " placeholder_band_compare = \"#div_band_compare_2\";\n",
+ " }\n",
+ " else\n",
+ " {\n",
+ " placeholder_band_compare = \"#div_band_compare_1\"; // just for safe\n",
+ " }\n",
+ "\n",
+ " Object.size = function(obj) {\n",
+ " var size = 0, key;\n",
+ " for (key in obj) \n",
+ " {\n",
+ " if (obj.hasOwnProperty(key)) size++;\n",
+ " }\n",
+ " return size;\n",
+ " };\n",
+ "\n",
+ " //Get the number of bands\n",
+ " //alert(\"Getting band\")\n",
+ " //alert(band_obj_all)\n",
+ " //alert(\"band_obj_all got!\")\n",
+ " var N_bands = Object.size(band_obj_all[i][\"band_y_axis\"]);\n",
+ " var N_k_coors = Object.size(band_obj_all[i][\"band_x_axis\"]);\n",
+ " //alert(band_obj_all[i][\"band_y_axis\"])\n",
+ " var band_plotdata = [];\n",
+ " \n",
+ " for(var i_band =0; i_band < N_bands; i_band++)\n",
+ " {\n",
+ " var tmp_data = [];\n",
+ " for(var j_k_coor = 0; j_k_coor < N_k_coors; j_k_coor ++)\n",
+ " {\n",
+ " tmp_data.push([band_obj_all[i][\"band_x_axis\"][j_k_coor],band_obj_all[i][\"band_y_axis\"][i_band][j_k_coor]]);\n",
+ " }\n",
+ " var plotData = { shadowSize: 0 , data: tmp_data, color: 'black', series: { lines: { show: true } , points: {show: false} } };\n",
+ " band_plotdata.push(plotData);\n",
+ " }\n",
+ "\n",
+ "\n",
+ " var tmp_data0 = [[0, 0], [1, 0]];\n",
+ " var plotData0 = { shadowSize:0, color: 'black', data: tmp_data0, dashes:{ show:true, lineWidth: 1.5}};\n",
+ " band_plotdata.push(plotData0);\n",
+ "\n",
+ " var band_plotdata_overview = band_plotdata.slice(0);\n",
+ "\n",
+ " var HOMOdata= [[band_obj_all[i][\"HOMO_coor\"],band_obj_all[i][\"HOMO_energy\"]]];\n",
+ " var HOMOlabel = [\"VBM\"];\n",
+ " var plotHOMO={ shadowSize:0, color: 'blue', data: HOMOdata, points:{show:true, radius: 4 , fill: true, fillColor: 'blue'},lines:{show: false}, showLabels: true, labels: HOMOlabel, canvasRender: true, cColor: 'red', cFont:\"2em Arial\"};\n",
+ "\n",
+ " var LUMOdata= [[band_obj_all[i][\"LUMO_coor\"],band_obj_all[i][\"LUMO_energy\"]]];\n",
+ " var LUMOlabel = [\"CBM\"];\n",
+ " var plotLUMO={ shadowSize:0, color: 'red', data: LUMOdata, points:{show:true, radius: 4 , fill: true, fillColor: 'red'},lines:{show: false}, showLabels: true, labels: LUMOlabel, canvasRender: true, cColor: 'red', cFont:\"2em Arial\"};\n",
+ "\n",
+ " //if_show_VBM = check_show_VBM(checkbox_VBM_id);\n",
+ " if (if_show_VBM == 1)\n",
+ " {\n",
+ " band_plotdata.push(plotHOMO);\n",
+ " band_plotdata.push(plotLUMO);\n",
+ " }\n",
+ "\n",
+ " \n",
+ " //alert(img_band_id + band_plotdata)\n",
+ " \n",
+ " //!!!FIXME: if ($(\"#showVBM:checked\").length > 0 && gap > 0.1) \n",
+ " //plotHOMOLUMO={ shadowSize:0, color: 'red', data: d5, points:{show:true, radius: 0.8 , fill: true}, showLabels: true, labels: d5label, labelPlacement: labelPos, canvasRender: true, cColor: 'red', cFont:\"1em Arial\" }\n",
+ "\n",
+ " var canvas_band;\n",
+ " var options_band = {\n",
+ " canvas: true,\n",
+ " //legend:{ type: \"canvas\" },\n",
+ " series: { lines: { show: true, lineWidth: 2 }, \n",
+ " points: { show: false } }, \n",
+ " xaxis: { \n",
+ " ticks: band_obj_all[i][\"labels\"], \n",
+ " color:\"#000\", \n",
+ " font: {size: 20}, \n",
+ " zoomRange: false,\n",
+ " panRange: false \n",
+ " }, \n",
+ " yaxis: { \n",
+ " axisLabel: \"Energy (eV)\", \n",
+ " axisLabelUseCanvas: true,\n",
+ " //axisLabelUseCanvas: false,\n",
+ " axisLabelFontSizePixels: 20,\n",
+ " axisLabelFontFamily: 'Arial', \n",
+ " axisLabelPadding: 10, \n",
+ " color:\"#000\", \n",
+ " font: {size: 20, family:\"Arial\"},\n",
+ " tickLength:-5, \n",
+ " min: lowerLim, \n",
+ " max: upperLim,\n",
+ " tickDecimals: 0, \n",
+ " zoomRange: [0.001, 1000],\n",
+ " panRange: [-100, 100] \n",
+ " },\n",
+ "\n",
+ " zoom: { \n",
+ " interactive: true\n",
+ " },\n",
+ "\n",
+ " pan: {\n",
+ " interactive: true\n",
+ " }, \n",
+ "\n",
+ " //selection: { mode: \"xy\", color: \"#86a6b4\" }, \n",
+ "\n",
+ " grid: { \n",
+ " labelMargin: 15,\n",
+ " hoverable: true, \n",
+ " backgroundColor: { colors: [\"#fff\", \"#fff\"] }, \n",
+ " borderWidth: {\n",
+ " top: 2, \n",
+ " right: 2,\n",
+ " bottom: 2,\n",
+ " left: 2,\n",
+ " color : null } \n",
+ " }\n",
+ " }\n",
+ " //var plot_band = $.plot($(placeholder_band), band_plotdata, options_band);\n",
+ " //var plot_band = $.plot(\"#div_bandx\", band_plotdata, options_band);\n",
+ " var plot_band = $.plot($(placeholder_band), band_plotdata, options_band).getCanvas(); // save the canvas\n",
+ " var image_band = plot_band.toDataURL();\n",
+ " image_band = image_band.replace(\"image/png\",\"image/octet-stream\");\n",
+ " //beakerx.image_band = image_band;\n",
+ " document.getElementById(img_band_id).href= image_band;\n",
+ " image_band_links[i] = image_band;\n",
+ " //alert(\"band done\")\n",
+ "}\n"
+ ],
+ "text/plain": [
+ "<IPython.core.display.Javascript object>"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "%%javascript\n",
+ " //alert(\"tag: plot_band\")\n",
+ "\n",
+ "plot_band(i, lowerLim, upperLim, if_show_VBM, if_compare, i_in_compare_list);\n",
+ "\n",
+ "function plot_band(i, lowerLim, upperLim, if_show_VBM, if_compare, i_in_compare_list)\n",
+ "{\n",
+ " //i=0;\n",
+ " //alert(\"plot_band \"+ i)\n",
+ " var placeholder_band = \"#div_band\" + i.toString();\n",
+ " var placeholder_dos = \"#div_dos\" + i.toString();\n",
+ " var placeholder_tools = \"#div_tools\" + i.toString();\n",
+ " var placeholder_overview = \"#div_overview\" + i.toString();\n",
+ " var placeholder_overviewlegend = \"#overviewLegend\" + i.toString();\n",
+ " var checkbox_VBM_id = \"checkbox_VBM\" + i.toString();\n",
+ " var img_band_id = \"img_band\" + i.toString();\n",
+ " var img_dos_id = \"img_dos\" + i.toString();\n",
+ "\n",
+ " var placeholder_band_compare = \"\";\n",
+ "\n",
+ "\n",
+ " if(i_in_compare_list == 1)\n",
+ " {\n",
+ " placeholder_band_compare = \"#div_band_compare_1\";\n",
+ " }\n",
+ " else if(i_in_compare_list == 2)\n",
+ " {\n",
+ " placeholder_band_compare = \"#div_band_compare_2\";\n",
+ " }\n",
+ " else\n",
+ " {\n",
+ " placeholder_band_compare = \"#div_band_compare_1\"; // just for safe\n",
+ " }\n",
+ "\n",
+ " Object.size = function(obj) {\n",
+ " var size = 0, key;\n",
+ " for (key in obj) \n",
+ " {\n",
+ " if (obj.hasOwnProperty(key)) size++;\n",
+ " }\n",
+ " return size;\n",
+ " };\n",
+ "\n",
+ " //Get the number of bands\n",
+ " //alert(\"Getting band\")\n",
+ " //alert(band_obj_all)\n",
+ " //alert(\"band_obj_all got!\")\n",
+ " var N_bands = Object.size(band_obj_all[i][\"band_y_axis\"]);\n",
+ " var N_k_coors = Object.size(band_obj_all[i][\"band_x_axis\"]);\n",
+ " //alert(band_obj_all[i][\"band_y_axis\"])\n",
+ " var band_plotdata = [];\n",
+ " \n",
+ " for(var i_band =0; i_band < N_bands; i_band++)\n",
+ " {\n",
+ " var tmp_data = [];\n",
+ " for(var j_k_coor = 0; j_k_coor < N_k_coors; j_k_coor ++)\n",
+ " {\n",
+ " tmp_data.push([band_obj_all[i][\"band_x_axis\"][j_k_coor],band_obj_all[i][\"band_y_axis\"][i_band][j_k_coor]]);\n",
+ " }\n",
+ " var plotData = { shadowSize: 0 , data: tmp_data, color: 'black', series: { lines: { show: true } , points: {show: false} } };\n",
+ " band_plotdata.push(plotData);\n",
+ " }\n",
+ "\n",
+ "\n",
+ " var tmp_data0 = [[0, 0], [1, 0]];\n",
+ " var plotData0 = { shadowSize:0, color: 'black', data: tmp_data0, dashes:{ show:true, lineWidth: 1.5}};\n",
+ " band_plotdata.push(plotData0);\n",
+ "\n",
+ " var band_plotdata_overview = band_plotdata.slice(0);\n",
+ "\n",
+ " var HOMOdata= [[band_obj_all[i][\"HOMO_coor\"],band_obj_all[i][\"HOMO_energy\"]]];\n",
+ " var HOMOlabel = [\"VBM\"];\n",
+ " var plotHOMO={ shadowSize:0, color: 'blue', data: HOMOdata, points:{show:true, radius: 4 , fill: true, fillColor: 'blue'},lines:{show: false}, showLabels: true, labels: HOMOlabel, canvasRender: true, cColor: 'red', cFont:\"2em Arial\"};\n",
+ "\n",
+ " var LUMOdata= [[band_obj_all[i][\"LUMO_coor\"],band_obj_all[i][\"LUMO_energy\"]]];\n",
+ " var LUMOlabel = [\"CBM\"];\n",
+ " var plotLUMO={ shadowSize:0, color: 'red', data: LUMOdata, points:{show:true, radius: 4 , fill: true, fillColor: 'red'},lines:{show: false}, showLabels: true, labels: LUMOlabel, canvasRender: true, cColor: 'red', cFont:\"2em Arial\"};\n",
+ "\n",
+ " //if_show_VBM = check_show_VBM(checkbox_VBM_id);\n",
+ " if (if_show_VBM == 1)\n",
+ " {\n",
+ " band_plotdata.push(plotHOMO);\n",
+ " band_plotdata.push(plotLUMO);\n",
+ " }\n",
+ "\n",
+ " \n",
+ " //alert(img_band_id + band_plotdata)\n",
+ " \n",
+ " //!!!FIXME: if ($(\"#showVBM:checked\").length > 0 && gap > 0.1) \n",
+ " //plotHOMOLUMO={ shadowSize:0, color: 'red', data: d5, points:{show:true, radius: 0.8 , fill: true}, showLabels: true, labels: d5label, labelPlacement: labelPos, canvasRender: true, cColor: 'red', cFont:\"1em Arial\" }\n",
+ "\n",
+ " var canvas_band;\n",
+ " var options_band = {\n",
+ " canvas: true,\n",
+ " //legend:{ type: \"canvas\" },\n",
+ " series: { lines: { show: true, lineWidth: 2 }, \n",
+ " points: { show: false } }, \n",
+ " xaxis: { \n",
+ " ticks: band_obj_all[i][\"labels\"], \n",
+ " color:\"#000\", \n",
+ " font: {size: 20}, \n",
+ " zoomRange: false,\n",
+ " panRange: false \n",
+ " }, \n",
+ " yaxis: { \n",
+ " axisLabel: \"Energy (eV)\", \n",
+ " axisLabelUseCanvas: true,\n",
+ " //axisLabelUseCanvas: false,\n",
+ " axisLabelFontSizePixels: 20,\n",
+ " axisLabelFontFamily: 'Arial', \n",
+ " axisLabelPadding: 10, \n",
+ " color:\"#000\", \n",
+ " font: {size: 20, family:\"Arial\"},\n",
+ " tickLength:-5, \n",
+ " min: lowerLim, \n",
+ " max: upperLim,\n",
+ " tickDecimals: 0, \n",
+ " zoomRange: [0.001, 1000],\n",
+ " panRange: [-100, 100] \n",
+ " },\n",
+ "\n",
+ " zoom: { \n",
+ " interactive: true\n",
+ " },\n",
+ "\n",
+ " pan: {\n",
+ " interactive: true\n",
+ " }, \n",
+ "\n",
+ " //selection: { mode: \"xy\", color: \"#86a6b4\" }, \n",
+ "\n",
+ " grid: { \n",
+ " labelMargin: 15,\n",
+ " hoverable: true, \n",
+ " backgroundColor: { colors: [\"#fff\", \"#fff\"] }, \n",
+ " borderWidth: {\n",
+ " top: 2, \n",
+ " right: 2,\n",
+ " bottom: 2,\n",
+ " left: 2,\n",
+ " color : null } \n",
+ " }\n",
+ " }\n",
+ " //var plot_band = $.plot($(placeholder_band), band_plotdata, options_band);\n",
+ " //var plot_band = $.plot(\"#div_bandx\", band_plotdata, options_band);\n",
+ " var plot_band = $.plot($(placeholder_band), band_plotdata, options_band).getCanvas(); // save the canvas\n",
+ " var image_band = plot_band.toDataURL();\n",
+ " image_band = image_band.replace(\"image/png\",\"image/octet-stream\");\n",
+ " //beakerx.image_band = image_band;\n",
+ " document.getElementById(img_band_id).href= image_band;\n",
+ " image_band_links[i] = image_band;\n",
+ " //alert(\"band done\")\n",
+ "}"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 44,
+ "metadata": {
+ "tags": [
+ "plot_dos"
+ ]
+ },
+ "outputs": [
+ {
+ "data": {
+ "application/javascript": [
+ " //alert(\"tag: plot_dos \" + i)\n",
+ " //i=0;\n",
+ "\n",
+ " var placeholder_dos = \"#div_dos\" + i.toString();\n",
+ " var placeholder_tools = \"#div_tools\" + i.toString();\n",
+ " var placeholder_overview = \"#div_overview\" + i.toString();\n",
+ " var placeholder_overviewlegend = \"#overviewLegend\" + i.toString();\n",
+ " var img_dos_id = \"img_dos\" + i.toString();\n",
+ "\n",
+ "//----Plot DOS----------------------\n",
+ " var dos_plotdata = [];\n",
+ " //alert(\"dos:\"+dos_obj_all[i])\n",
+ " var xdos = dos_obj_all[i][\"dos_x_axis\"];\n",
+ " var ydos = dos_obj_all[i][\"dos_y_axis\"][0];\n",
+ " var dosLabelPos = Math.max.apply(Math, ydos)/2;\n",
+ " var d2 = [];\n",
+ " for (var ii = 0; ii < xdos.length; ii+=1) {\n",
+ " d2.push([ydos[ii],xdos[ii]]);\n",
+ " }\n",
+ " var plotData2={ shadowSize: 0, color: 'black' , data: d2};\n",
+ " dos_plotdata.push(plotData2);\n",
+ " //alert(\"dos_plotdata\"+JSON.stringify(dos_plotdata[0]));\n",
+ " \n",
+ " function find_xaxis_max_min(data, lowerbound, upperbound)\n",
+ " {\n",
+ " //data[xaxis,y] find the max and min value of x axis\n",
+ " //alert(\"dos[0]:\" + data[0][\"data\"]);\n",
+ " //alert(\"Bounds: \" + lowerbound + \" , \" + upperbound)\n",
+ " var n_data = data.length;\n",
+ " //alert(\"N dos: \" + n_data);\n",
+ " var data_min = 1000000;\n",
+ " var data_max = -1000000;\n",
+ " var data_current = 0;\n",
+ " for (var i = 0; i < n_data; i++)\n",
+ " {\n",
+ " if((data[i][1] >= lowerbound) && (data[i][1] <= upperbound))\n",
+ " {\n",
+ " data_current = data[i][0];\n",
+ " //alert(\"data[i]: \" + data[i] + \"data[i][0]: \" + data_current);\n",
+ " if(data_current >= data_max)\n",
+ " {\n",
+ " data_max = data_current;\n",
+ " }\n",
+ " if(data_current <= data_min)\n",
+ " {\n",
+ " data_min = data_current;\n",
+ " }\n",
+ " }\n",
+ " }\n",
+ " var data_max_min = [data_max, data_min];\n",
+ " //alert(\"data_max_min: \" + data_max_min);\n",
+ " return data_max_min;\n",
+ " }\n",
+ " var dos_x_max_min = find_xaxis_max_min(dos_plotdata[0][\"data\"], lowerLim, upperLim);\n",
+ " var dosLabelPos = (dos_x_max_min[0] + dos_x_max_min[1])/2;\n",
+ " //alert(\"dos_x_max_min:\"+dos_x_max_min+\", dosLabelPos:\"+dosLabelPos);\n",
+ " var options_dos ={\n",
+ " canvas: true,\n",
+ " series: {\n",
+ " lines: { show: true, lineWidth:2 },\n",
+ " points: { show: false }\n",
+ " },\n",
+ "\n",
+ " yaxis: { \n",
+ " axisLabel: \"\", \n",
+ " axisLabelUseCanvas: true,\n",
+ " axisLabelFontSizePixels: 20,\n",
+ " axisLabelFontFamily: 'Arial', \n",
+ " axisLabelPadding: 10, \n",
+ " color:\"#000\", \n",
+ " font: {size: 20},\n",
+ " tickLength:-5, \n",
+ " min: lowerLim, \n",
+ " max: upperLim,\n",
+ " tickDecimals: 0, \n",
+ " zoomRange: [0.001, 1000],\n",
+ " panRange: [-100, 100] \n",
+ " },\n",
+ "\n",
+ " xaxis: {\n",
+ " axisLabel: \" \",\n",
+ " axisLabelUseCanvas: false,\n",
+ " axisLabelFontSizePixels: 20,\n",
+ " axisLabelFontFamily: 'Arial',\n",
+ " axisLabelPadding: 3,\n",
+ " color:\"rgb(0, 0, 0)\",\n",
+ " font: {size: 20, family:\"Arial\"},\n",
+ " //ticks: 10,\n",
+ " tickLength:0,\n",
+ " min: dos_x_max_min[1],//0,\n",
+ " max: dos_x_max_min[0],//1,\n",
+ " tickDecimals: 0,\n",
+ " ticks: [[ dosLabelPos ,'DOS']],\n",
+ " //tickFormatter: MyFormatter\n",
+ " panRange: false\n",
+ " },\n",
+ " pan: {\n",
+ " interactive: true\n",
+ " }, \n",
+ "\n",
+ " grid: {\n",
+ " labelMargin: 15,\n",
+ " hoverable: true,\n",
+ " //borderWidth : 1000,\n",
+ " //show : false,\n",
+ " // //backgroundColor: { colors: [ \"#fff\", \"#eee\" ] },\n",
+ " backgroundColor: { colors: [\"#fff\", \"#fff\"] },\n",
+ " borderWidth: {\n",
+ " top: 2,\n",
+ " right: 2,\n",
+ " bottom: 2,\n",
+ " left: 2,\n",
+ " color : null\n",
+ " }\n",
+ " }\n",
+ " }\n",
+ " var plot_dos = $.plot(placeholder_dos, dos_plotdata, options_dos).getCanvas();\n",
+ " var image_dos = plot_dos.toDataURL();\n",
+ " image_dos = image_dos.replace(\"image/png\",\"image/octet-stream\");\n",
+ " image_dos = image_dos;\n",
+ " document.getElementById(img_dos_id).href= image_dos;\n",
+ " //alert(\"dos done.\")\n"
+ ],
+ "text/plain": [
+ "<IPython.core.display.Javascript object>"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "%%javascript\n",
+ " //alert(\"tag: plot_dos \" + i)\n",
+ " //i=0;\n",
+ "\n",
+ " var placeholder_dos = \"#div_dos\" + i.toString();\n",
+ " var placeholder_tools = \"#div_tools\" + i.toString();\n",
+ " var placeholder_overview = \"#div_overview\" + i.toString();\n",
+ " var placeholder_overviewlegend = \"#overviewLegend\" + i.toString();\n",
+ " var img_dos_id = \"img_dos\" + i.toString();\n",
+ "\n",
+ "//----Plot DOS----------------------\n",
+ " var dos_plotdata = [];\n",
+ " //alert(\"dos:\"+dos_obj_all[i])\n",
+ " var xdos = dos_obj_all[i][\"dos_x_axis\"];\n",
+ " var ydos = dos_obj_all[i][\"dos_y_axis\"][0];\n",
+ " var dosLabelPos = Math.max.apply(Math, ydos)/2;\n",
+ " var d2 = [];\n",
+ " for (var ii = 0; ii < xdos.length; ii+=1) {\n",
+ " d2.push([ydos[ii],xdos[ii]]);\n",
+ " }\n",
+ " var plotData2={ shadowSize: 0, color: 'black' , data: d2};\n",
+ " dos_plotdata.push(plotData2);\n",
+ " //alert(\"dos_plotdata\"+JSON.stringify(dos_plotdata[0]));\n",
+ " \n",
+ " function find_xaxis_max_min(data, lowerbound, upperbound)\n",
+ " {\n",
+ " //data[xaxis,y] find the max and min value of x axis\n",
+ " //alert(\"dos[0]:\" + data[0][\"data\"]);\n",
+ " //alert(\"Bounds: \" + lowerbound + \" , \" + upperbound)\n",
+ " var n_data = data.length;\n",
+ " //alert(\"N dos: \" + n_data);\n",
+ " var data_min = 1000000;\n",
+ " var data_max = -1000000;\n",
+ " var data_current = 0;\n",
+ " for (var i = 0; i < n_data; i++)\n",
+ " {\n",
+ " if((data[i][1] >= lowerbound) && (data[i][1] <= upperbound))\n",
+ " {\n",
+ " data_current = data[i][0];\n",
+ " //alert(\"data[i]: \" + data[i] + \"data[i][0]: \" + data_current);\n",
+ " if(data_current >= data_max)\n",
+ " {\n",
+ " data_max = data_current;\n",
+ " }\n",
+ " if(data_current <= data_min)\n",
+ " {\n",
+ " data_min = data_current;\n",
+ " }\n",
+ " }\n",
+ " }\n",
+ " var data_max_min = [data_max, data_min];\n",
+ " //alert(\"data_max_min: \" + data_max_min);\n",
+ " return data_max_min;\n",
+ " }\n",
+ " var dos_x_max_min = find_xaxis_max_min(dos_plotdata[0][\"data\"], lowerLim, upperLim);\n",
+ " var dosLabelPos = (dos_x_max_min[0] + dos_x_max_min[1])/2;\n",
+ " //alert(\"dos_x_max_min:\"+dos_x_max_min+\", dosLabelPos:\"+dosLabelPos);\n",
+ " var options_dos ={\n",
+ " canvas: true,\n",
+ " series: {\n",
+ " lines: { show: true, lineWidth:2 },\n",
+ " points: { show: false }\n",
+ " },\n",
+ "\n",
+ " yaxis: { \n",
+ " axisLabel: \"\", \n",
+ " axisLabelUseCanvas: true,\n",
+ " axisLabelFontSizePixels: 20,\n",
+ " axisLabelFontFamily: 'Arial', \n",
+ " axisLabelPadding: 10, \n",
+ " color:\"#000\", \n",
+ " font: {size: 20},\n",
+ " tickLength:-5, \n",
+ " min: lowerLim, \n",
+ " max: upperLim,\n",
+ " tickDecimals: 0, \n",
+ " zoomRange: [0.001, 1000],\n",
+ " panRange: [-100, 100] \n",
+ " },\n",
+ "\n",
+ " xaxis: {\n",
+ " axisLabel: \" \",\n",
+ " axisLabelUseCanvas: false,\n",
+ " axisLabelFontSizePixels: 20,\n",
+ " axisLabelFontFamily: 'Arial',\n",
+ " axisLabelPadding: 3,\n",
+ " color:\"rgb(0, 0, 0)\",\n",
+ " font: {size: 20, family:\"Arial\"},\n",
+ " //ticks: 10,\n",
+ " tickLength:0,\n",
+ " min: dos_x_max_min[1],//0,\n",
+ " max: dos_x_max_min[0],//1,\n",
+ " tickDecimals: 0,\n",
+ " ticks: [[ dosLabelPos ,'DOS']],\n",
+ " //tickFormatter: MyFormatter\n",
+ " panRange: false\n",
+ " },\n",
+ " pan: {\n",
+ " interactive: true\n",
+ " }, \n",
+ "\n",
+ " grid: {\n",
+ " labelMargin: 15,\n",
+ " hoverable: true,\n",
+ " //borderWidth : 1000,\n",
+ " //show : false,\n",
+ " // //backgroundColor: { colors: [ \"#fff\", \"#eee\" ] },\n",
+ " backgroundColor: { colors: [\"#fff\", \"#fff\"] },\n",
+ " borderWidth: {\n",
+ " top: 2,\n",
+ " right: 2,\n",
+ " bottom: 2,\n",
+ " left: 2,\n",
+ " color : null\n",
+ " }\n",
+ " }\n",
+ " }\n",
+ " var plot_dos = $.plot(placeholder_dos, dos_plotdata, options_dos).getCanvas();\n",
+ " var image_dos = plot_dos.toDataURL();\n",
+ " image_dos = image_dos.replace(\"image/png\",\"image/octet-stream\");\n",
+ " image_dos = image_dos;\n",
+ " document.getElementById(img_dos_id).href= image_dos;\n",
+ " //alert(\"dos done.\")"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 31,
+ "metadata": {
+ "tags": [
+ "init_jquery"
+ ]
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "<script src=\"http://code.jquery.com/jquery-1.8.3.min.js\"></script>\n"
+ ],
+ "text/plain": [
+ "<IPython.core.display.HTML object>"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "%%HTML\n",
+ "<script src=\"http://code.jquery.com/jquery-1.8.3.min.js\"></script>"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 32,
+ "metadata": {
+ "tags": [
+ "init_flot"
+ ]
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "<script src=\"js/jquery.flot.js\"></script>\n"
+ ],
+ "text/plain": [
+ "<IPython.core.display.HTML object>"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "%%HTML\n",
+ "<script src=\"js/jquery.flot.js\"></script>\n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 33,
+ "metadata": {
+ "tags": [
+ "init_flot_axislabels"
+ ]
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "<script src=\"js/jquery.flot.axislabels.js\"></script>\n"
+ ],
+ "text/plain": [
+ "<IPython.core.display.HTML object>"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "%%HTML\n",
+ "<script src=\"js/jquery.flot.axislabels.js\"></script>"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 34,
+ "metadata": {
+ "tags": [
+ "init_flot_navigate"
+ ]
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "<script src=\"js/jquery.flot.navigate.js\"></script>\n"
+ ],
+ "text/plain": [
+ "<IPython.core.display.HTML object>"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "%%HTML\n",
+ "<script src=\"js/jquery.flot.navigate.js\"></script>"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 87,
+ "metadata": {
+ "tags": [
+ "init_flot_selection"
+ ]
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "<script src=\"js/jquery.flot.selection.js\"></script>\n"
+ ],
+ "text/plain": [
+ "<IPython.core.display.HTML object>"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "%%HTML\n",
+ "<script src=\"js/jquery.flot.selection.js\"></script>"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 51,
+ "metadata": {
+ "tags": [
+ "js_query_beforeafter"
+ ]
+ },
+ "outputs": [
+ {
+ "data": {
+ "application/javascript": [
+ "//jquery.beforeafter.min.js\n",
+ "!function(e){e.fn.beforeafter=function(i){var t=e.extend({touch:!0,message:\"Slide\",hide_message:!0,reset:!0,reset_delay:3e3,drag_horizontal:!0,split_horizontal:!0\n",
+ "},i);return this.each(function(){var i=e(this),a=i.find(\"img\"),n=a.data(\"aftersrc\"),s=i.width(),d=0;a.after('<div class=\"g-img-after\"><img style=\"width: '+s+'px;\" src=\"'+n+'\"></div>'),\n",
+ "a.addClass(\"g-img-before\").width(s),i.append('<div class=\"g-img-divider\"><span>'+t.message+\"</span></div>\"),d=i.height(),t.split_horizontal||i.addClass(\"g-vertical\"),\n",
+ "i.on(\"mouseenter touchstart\",function(e){var t=i.data(\"reset-timer\");t&&(window.clearTimeout(t),i.data(\"reset-timer\",!1))}).on(\"mousemove touchmove\",function(a){\n",
+ "var n=0,o=0,r=i.find(\".g-img-divider span\");if(t.drag_horizontal)n=a.pageX-i.offset().left,o=n/s*100;else{var f=i.offset().top-e(window).scrollTop();n=a.clientY/f,\n",
+ "o=(a.clientY-f)/d*100}if(t.touch&&\"undefined\"!=typeof a.originalEvent.touches){var g=a.originalEvent.touches[0];o=t.drag_horizontal?(g.pageX-i.offset().left)/s*100:(g.pageY-i.offset().top)/d*100;\n",
+ "}t.split_horizontal?(i.find(\".g-img-after\").css(\"left\",o+\"%\"),i.find(\".g-img-divider\").css(\"left\",o+\"%\")):(i.find(\".g-img-after\").css(\"top\",o+\"%\"),i.find(\".g-img-divider\").css(\"top\",o+\"%\")),\n",
+ "t.hide_message&&r.is(\":visible\")&&r.fadeOut()}).on(\"mouseleave touchend touchcancel\",function(e){var a=i.data(\"reset-timer\"),n=i.find(\".g-img-divider span\");\n",
+ "t.reset&&(a||(a=window.setTimeout(function(){t.split_horizontal?(i.find(\".g-img-after\").animate({left:\"50%\"},500),i.find(\".g-img-divider\").animate({left:\"50%\"\n",
+ "},500,function(){n.fadeIn()})):(i.find(\".g-img-after\").animate({top:\"50%\"},500),i.find(\".g-img-divider\").animate({top:\"50%\"},500,function(){n.fadeIn()})),\n",
+ "i.data(\"reset-timer\",!1)},t.reset_delay),i.data(\"reset-timer\",a)))})}),this}}(jQuery);\n"
+ ],
+ "text/plain": [
+ "<IPython.core.display.Javascript object>"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "%%javascript\n",
+ "//jquery.beforeafter.min.js\n",
+ "!function(e){e.fn.beforeafter=function(i){var t=e.extend({touch:!0,message:\"Slide\",hide_message:!0,reset:!0,reset_delay:3e3,drag_horizontal:!0,split_horizontal:!0\n",
+ "},i);return this.each(function(){var i=e(this),a=i.find(\"img\"),n=a.data(\"aftersrc\"),s=i.width(),d=0;a.after('<div class=\"g-img-after\"><img style=\"width: '+s+'px;\" src=\"'+n+'\"></div>'),\n",
+ "a.addClass(\"g-img-before\").width(s),i.append('<div class=\"g-img-divider\"><span>'+t.message+\"</span></div>\"),d=i.height(),t.split_horizontal||i.addClass(\"g-vertical\"),\n",
+ "i.on(\"mouseenter touchstart\",function(e){var t=i.data(\"reset-timer\");t&&(window.clearTimeout(t),i.data(\"reset-timer\",!1))}).on(\"mousemove touchmove\",function(a){\n",
+ "var n=0,o=0,r=i.find(\".g-img-divider span\");if(t.drag_horizontal)n=a.pageX-i.offset().left,o=n/s*100;else{var f=i.offset().top-e(window).scrollTop();n=a.clientY/f,\n",
+ "o=(a.clientY-f)/d*100}if(t.touch&&\"undefined\"!=typeof a.originalEvent.touches){var g=a.originalEvent.touches[0];o=t.drag_horizontal?(g.pageX-i.offset().left)/s*100:(g.pageY-i.offset().top)/d*100;\n",
+ "}t.split_horizontal?(i.find(\".g-img-after\").css(\"left\",o+\"%\"),i.find(\".g-img-divider\").css(\"left\",o+\"%\")):(i.find(\".g-img-after\").css(\"top\",o+\"%\"),i.find(\".g-img-divider\").css(\"top\",o+\"%\")),\n",
+ "t.hide_message&&r.is(\":visible\")&&r.fadeOut()}).on(\"mouseleave touchend touchcancel\",function(e){var a=i.data(\"reset-timer\"),n=i.find(\".g-img-divider span\");\n",
+ "t.reset&&(a||(a=window.setTimeout(function(){t.split_horizontal?(i.find(\".g-img-after\").animate({left:\"50%\"},500),i.find(\".g-img-divider\").animate({left:\"50%\"\n",
+ "},500,function(){n.fadeIn()})):(i.find(\".g-img-after\").animate({top:\"50%\"},500),i.find(\".g-img-divider\").animate({top:\"50%\"},500,function(){n.fadeIn()})),\n",
+ "i.data(\"reset-timer\",!1)},t.reset_delay),i.data(\"reset-timer\",a)))})}),this}}(jQuery);"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 52,
+ "metadata": {
+ "tags": [
+ "js_compare_slide"
+ ]
+ },
+ "outputs": [
+ {
+ "data": {
+ "application/javascript": [
+ "var div_str = '';\n",
+ "//div_str = '<style> .g-before-after{position:relative;overflow:hidden}.g-before-after img{display:block}.g-before-after .g-img-before{float:left}.g-before-after .g-img-after,.g-before-after.g-vertical .g-img-after{position:absolute;top:0;right:0;left:50%;bottom:0;overflow:hidden}.g-before-after .g-img-after img{position:absolute;right:0;top:0}.g-before-after .g-img-divider{position:absolute;left:50%;top:0;bottom:0;width:0;border-left:1px solid #fff;border-right:1px solid #fff}.g-before-after .g-img-divider>span{position:absolute;top:50%;display:block;background-color:#fff;padding:5px 10px;line-height:1;text-align:center;-webkit-transform:translate(-50%,-50%);-ms-transform:translate(-50%,-50%);transform:translate(-50%,-50%)}.g-before-after.g-vertical .g-img-after{top:50%;left:0}.g-before-after.g-vertical .g-img-after img{position:absolute;right:auto;top:auto;left:0;bottom:0}.g-before-after.g-vertical .g-img-divider{position:absolute;left:0;top:50%;bottom:auto;right:0;height:0;width:100%;border-top:1px solid #fff;border-bottom:1px solid #fff;border-left:0 none;border-right:0 none}.g-before-after.g-vertical .g-img-divider>span{top:50%;left:50%} </style>'\n",
+ "//div_str += '<script>$(\\'#div_compare_containerx\\').beforeafter(); </script>';\n",
+ "//div_str +='<script type=\\\"text/javascript\\\" src=\\\"https://github.com/jquery/jquery/blob/master/src/jquery.js\\\"></script> '\n",
+ "//div_str += '<div class=\\\"g-before-after\\\" id=\\\"div_compare_containerx\\\">';\n",
+ "div_str +='<img src = \\\"'\n",
+ "\n",
+ "var src1 = image_band_links_selected[0];\n",
+ "var src2 = image_band_links_selected[1];\n",
+ "var tmp_src1 = src1;\n",
+ "var tmp_src2 = src2;\n",
+ "//src1 = \"https://images4.alphacoders.com/640/640956.jpg\";\n",
+ "//src2 = \"http://imgmr.com/wp-content/uploads/2016/06/SAO-anime.jpg\";\n",
+ "div_str +=src1;\n",
+ "div_str += '\\\" data-aftersrc=\\\"'\n",
+ "div_str +=src2;\n",
+ "//div_str += '\\\"></div>';\n",
+ "div_str += '\\\"/>';\n",
+ "//#div_compare_containerx\n",
+ "document.getElementById(\"div_compare_containerx\").innerHTML = div_str;\n",
+ "$('#div_compare_containerx').beforeafter({drag_horizontal: false, split_horizontal: false});\n",
+ "$('#div_compare_containerx').beforeafter({drag_horizontal: false, split_horizontal: false});\n",
+ "//beakerx.image_band_links[i]\n"
+ ],
+ "text/plain": [
+ "<IPython.core.display.Javascript object>"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "%%javascript\n",
+ "var div_str = '';\n",
+ "//div_str = '<style> .g-before-after{position:relative;overflow:hidden}.g-before-after img{display:block}.g-before-after .g-img-before{float:left}.g-before-after .g-img-after,.g-before-after.g-vertical .g-img-after{position:absolute;top:0;right:0;left:50%;bottom:0;overflow:hidden}.g-before-after .g-img-after img{position:absolute;right:0;top:0}.g-before-after .g-img-divider{position:absolute;left:50%;top:0;bottom:0;width:0;border-left:1px solid #fff;border-right:1px solid #fff}.g-before-after .g-img-divider>span{position:absolute;top:50%;display:block;background-color:#fff;padding:5px 10px;line-height:1;text-align:center;-webkit-transform:translate(-50%,-50%);-ms-transform:translate(-50%,-50%);transform:translate(-50%,-50%)}.g-before-after.g-vertical .g-img-after{top:50%;left:0}.g-before-after.g-vertical .g-img-after img{position:absolute;right:auto;top:auto;left:0;bottom:0}.g-before-after.g-vertical .g-img-divider{position:absolute;left:0;top:50%;bottom:auto;right:0;height:0;width:100%;border-top:1px solid #fff;border-bottom:1px solid #fff;border-left:0 none;border-right:0 none}.g-before-after.g-vertical .g-img-divider>span{top:50%;left:50%} </style>'\n",
+ "//div_str += '<script>$(\\'#div_compare_containerx\\').beforeafter(); </script>';\n",
+ "//div_str +='<script type=\\\"text/javascript\\\" src=\\\"https://github.com/jquery/jquery/blob/master/src/jquery.js\\\"></script> '\n",
+ "//div_str += '<div class=\\\"g-before-after\\\" id=\\\"div_compare_containerx\\\">';\n",
+ "div_str +='<img src = \\\"'\n",
+ "\n",
+ "var src1 = image_band_links_selected[0];\n",
+ "var src2 = image_band_links_selected[1];\n",
+ "var tmp_src1 = src1;\n",
+ "var tmp_src2 = src2;\n",
+ "//src1 = \"https://images4.alphacoders.com/640/640956.jpg\";\n",
+ "//src2 = \"http://imgmr.com/wp-content/uploads/2016/06/SAO-anime.jpg\";\n",
+ "div_str +=src1;\n",
+ "div_str += '\\\" data-aftersrc=\\\"'\n",
+ "div_str +=src2;\n",
+ "//div_str += '\\\"></div>';\n",
+ "div_str += '\\\"/>';\n",
+ "//#div_compare_containerx\n",
+ "document.getElementById(\"div_compare_containerx\").innerHTML = div_str;\n",
+ "$('#div_compare_containerx').beforeafter({drag_horizontal: false, split_horizontal: false});\n",
+ "$('#div_compare_containerx').beforeafter({drag_horizontal: false, split_horizontal: false});\n",
+ "//beakerx.image_band_links[i]"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {
+ "scrolled": false,
+ "tags": [
+ "process_band_dos_data_python"
+ ]
+ },
+ "outputs": [],
+ "source": [
+ "#tag:python_2\n",
+ "import urllib.request, json\n",
+ "import numpy as np\n",
+ "import math\n",
+ "\n",
+ "#======Define global objs============\n",
+ "info_all = []\n",
+ "band_obj_all = []\n",
+ "dos_obj_all = []\n",
+ "\n",
+ "def load_jsonfile(path):\n",
+ " #with open(path, encoding='utf-8') as band_file: \n",
+ " # return json.load(band_file)\n",
+ "\n",
+ " \n",
+ " with urllib.request.urlopen(path) as url:\n",
+ " data = json.loads(url.read().decode())\n",
+ " return data\n",
+ "\n",
+ "#-----Get the labels for x axis---------------\n",
+ "def get_label_flag(coor_array):\n",
+ " #np.sort(coor_array)\n",
+ " x = coor_array[0]\n",
+ " y = coor_array[1]\n",
+ " z = coor_array[2]\n",
+ " coor =np.sort([x,y,z])\n",
+ " xx = coor[0]\n",
+ " yy = coor[1]\n",
+ " zz = coor[2]\n",
+ " coor = [xx, yy, zz]\n",
+ " #pprint(coor)\n",
+ " if (coor == [0, 0.5, 0.5]):\n",
+ " return \"X\"\n",
+ " if (coor == [0, 0.0, 0.5]):\n",
+ " return \"M\"\n",
+ " elif (coor == [0.5, 0.5, 0.5]):\n",
+ " return \"L\"\n",
+ " elif (coor == [0.375, 0.375, 0.75]):\n",
+ " return \"K\"\n",
+ " elif (coor == [0.25, 0.5, 0.75]):\n",
+ " return \"W\"\n",
+ " elif (coor == [0, 0, 0]):\n",
+ " return \"\\u0393\"\n",
+ " elif (coor == [0.25, 0.625, 0.625]):\n",
+ " return \"U\"\n",
+ " else:\n",
+ " return \"?\"\n",
+ "\n",
+ "#============Process the band structure data============\n",
+ "def get_band_obj(band_path, dos_fermi_energy):\n",
+ "\n",
+ " #band_data: read from json file \n",
+ " #Load the data files for band\n",
+ " band_data = load_jsonfile(band_path)\n",
+ " \n",
+ " #---------Read section_k_band_segment------------\n",
+ " section_k_band_segment = band_data['section_run']['section_single_configuration_calculation']['section_k_band'][0]['section_k_band_segment']\n",
+ " \n",
+ " #--------Get the number of k band segments-------------\n",
+ " N_k_band_segments = len(section_k_band_segment)\n",
+ " \n",
+ " #----------Get the total number of k points in all segments---------\n",
+ " N_k_points_all = 0\n",
+ " for i in range(N_k_band_segments):\n",
+ " band_k_points = section_k_band_segment[i]['band_k_points']\n",
+ " N_k_points_all = N_k_points_all + len(band_k_points)\n",
+ " \n",
+ " #--------Get the x axis for the band structure figure: the coordinates of k points in 1D\n",
+ " # store in k_coor_1D[N_k_points_total]-----------------\n",
+ "\n",
+ " band_distance_segments = np.zeros(N_k_band_segments)\n",
+ " for i in range(N_k_band_segments):\n",
+ " [[x1, y1, z1],[x2, y2, z2]]= section_k_band_segment[i]['band_segm_start_end'] #\"band_segm_start_end\": [[0.5, 0.0, 0.5],[0.5, 0.25, 0.75]],\n",
+ " band_distance_segments[i] = math.pow((x1-x2), 2) + math.pow((y1-y2), 2) + math.pow((z1-z2), 2)\n",
+ "\n",
+ " \n",
+ " band_distance_total = math.fsum(band_distance_segments)\n",
+ " #print(band_distance_segments)\n",
+ " average_N_k_points_per_inverse_distance = N_k_points_all / band_distance_total\n",
+ " \n",
+ " #Prepare the parameters to rescale the k coordinates into [0,1]\n",
+ " step_k_point = 1.0 / N_k_points_all\n",
+ " step_k_point = (1.0 + step_k_point) / N_k_points_all\n",
+ " \n",
+ " # \n",
+ " k_coor_1D = np.zeros((N_k_points_all))\n",
+ " for i_k_points in range(N_k_points_all):\n",
+ " k_coor_1D[i_k_points] = round( step_k_point * i_k_points, 3)\n",
+ " #for i in range(N_k_band_segments):\n",
+ " # ki[i] = \n",
+ " \n",
+ "\n",
+ " #--------Get the eigenvalues of each band trajectory--------------\n",
+ " N_k_points_per_segment = len(section_k_band_segment[0]['band_energies'][0]) #suppose the numebr of k points in all the segments are the same\n",
+ " N_bands = len(section_k_band_segment[0]['band_energies'][0][0])\n",
+ " band_energies_all = np.zeros((N_bands, N_k_points_all)) #store the eigenvalues\n",
+ " N_k_points_all = 0\n",
+ " for i_segments in range(N_k_band_segments):\n",
+ " band_energies = section_k_band_segment[i_segments]['band_energies']\n",
+ " N_spin_channel = len(band_energies) #Number of the spin channel --FIXME: no spin polarized\n",
+ " N_k_points_per_segment = len(band_energies[0])\n",
+ " for i_k_points in range(N_k_points_per_segment):\n",
+ " for i_bands in range(N_bands):\n",
+ " band_energies_all[i_bands][N_k_points_all] = band_energies[0][i_k_points][i_bands] / (1.60217656535 * pow(10, -19))\n",
+ " N_k_points_all = N_k_points_all + 1\n",
+ " \n",
+ " \n",
+ " N_labels = 0\n",
+ " for i_segments in range(N_k_band_segments):\n",
+ " for j in range(2):\n",
+ " labels_tmp = section_k_band_segment[i_segments]['band_segm_start_end'][j];\n",
+ " N_labels = N_labels + 1\n",
+ "\n",
+ " label_flag = [\"\" for i in range(N_labels)] #stores the flags of the labels (X, W, G, etc)\n",
+ "\n",
+ " i_label = 0\n",
+ " label_flag_last_final = \"\"\n",
+ " label_flag_current_initial = \"\"\n",
+ " for i_segments in range(N_k_band_segments):\n",
+ " labels_coor_0 = section_k_band_segment[i_segments]['band_segm_start_end'][0];\n",
+ " labels_coor_1 = section_k_band_segment[i_segments]['band_segm_start_end'][1];\n",
+ " np.sort(labels_coor_0)\n",
+ " np.sort(labels_coor_1)\n",
+ " label_flag_0 = get_label_flag(labels_coor_0)\n",
+ " label_flag_1 = get_label_flag(labels_coor_1)\n",
+ " label_flag_current_initial = label_flag_0\n",
+ " if(label_flag_last_final == \"\"):\n",
+ " label_flag_last_final = label_flag_0\n",
+ "\n",
+ " if(label_flag_last_final == label_flag_current_initial):\n",
+ " label_flag[i_label] = label_flag_current_initial\n",
+ " else:\n",
+ " label_flag[i_label] = \"\".join([label_flag_last_final, '|', label_flag_current_initial])\n",
+ " label_flag_last_final = label_flag_1\n",
+ " \n",
+ "\n",
+ " i_label = i_label + 1\n",
+ " if(i_segments == N_k_band_segments - 1):\n",
+ " label_flag[i_label] = label_flag_1\n",
+ " i_label = i_label + 1\n",
+ "\n",
+ " N_labels = i_label\n",
+ " \n",
+ " #------------Get the coordinates for the labels------------\n",
+ " #label_coor_abs = np.zeros((N_labels)) #stores the absolute coordinates of the labels\n",
+ " label_coor_relative = np.zeros((N_labels))\n",
+ " for i_label in range(N_labels):\n",
+ " #Here the evenly-distributed relative coordinates is used, because the coordinates of the labels could be too nerrow when using there absolute coordinates\n",
+ " #x = labels_coor_0[0]\n",
+ " #y = labels_coor_0[1]\n",
+ " #z = labels_coor_0[2]\n",
+ " #label_coor_abs[i_label] = np.sqrt(x*x+y*y+z*z)\n",
+ " label_coor_relative[i_label] = step_k_point * N_k_points_per_segment * i_label / (1 + 1.0 / N_k_points_all);\n",
+ "\n",
+ " #----Store the label-----------\n",
+ " label_obj =[['' for i in range(2)] for j in range(N_labels)]\n",
+ " for i_label in range(N_labels):\n",
+ " label_obj[i_label][0] = label_coor_relative[i_label]\n",
+ " label_obj[i_label][1] = label_flag[i_label]\n",
+ " \n",
+ " #print(label_obj)\n",
+ " \n",
+ " \n",
+ " #Rescal the energies with respect to dos_fermi_energy\n",
+ " for i_k_points in range(N_k_points_all):\n",
+ " for i_bands in range(N_bands):\n",
+ " band_energies_all[i_bands][i_k_points] = band_energies_all[i_bands][i_k_points] - dos_fermi_energy\n",
+ "\n",
+ " #-------Get VBM, CBM----------------\n",
+ "\n",
+ " HOMO = -1000\n",
+ " LUMO = 1000\n",
+ " coor_k_point_HOMO = np.zeros((3)) #the coordinate of k point that stores HOMO\n",
+ " coor_k_point_LUMO = np.zeros((3)) #the coordinate of k point that stores LUMO\n",
+ " #band_gap_direct = 0.0\n",
+ " band_gap_indirect = 0.0\n",
+ " \n",
+ " \n",
+ " #band_energy_max = np.amax(band_energies[0])/ (1.60217656535* pow(10,-19))\n",
+ " #band_energy_min = np.amin(band_energies[0])/ (1.60217656535* pow(10,-19))\n",
+ " band_energy_max = 10\n",
+ " band_energy_min = -10\n",
+ " #N_band_energy_index = 10000\n",
+ " #band_energy_step = (band_energy_max - band_energy_min) / N_band_energy_index\n",
+ " #N_allowed_states = np.zeros(N_band_energy_index + 1)\n",
+ " #i_index_fermi = math.floor((0 - band_energy_min) / band_energy_step) #the index that stores states at the Fermi level\n",
+ "\n",
+ " for i_k_points_all in range(N_k_points_all):\n",
+ " for i_bands in range(N_bands):\n",
+ " #i_band_index = math.floor((band_energies_all[i_bands][i_k_points_all] - band_energy_min) / band_energy_step)\n",
+ " #N_allowed_states[index_band_energy] = N_allowed_states[index_band_energy] + 1\n",
+ " band_energy = band_energies_all[i_bands][i_k_points_all]\n",
+ " if(band_energy > 0):\n",
+ " if(band_energy < LUMO):\n",
+ " LUMO = band_energy\n",
+ " else:\n",
+ " if(band_energy > HOMO):\n",
+ " HOMO = band_energy\n",
+ " #for i_band_index in range(i_index_fermi, N_band_energy_index): #get LUMO\n",
+ " # if(N_allowed_states[i_band_index] > 0):\n",
+ " # LUMO = band_energy_min + band_energy_step * i_band_index\n",
+ " print('HOMO, LUMO: ',HOMO, LUMO)\n",
+ " band_gap_indirect = abs(LUMO - HOMO)\n",
+ " \n",
+ " if(band_gap_indirect < 0.5): #VBM and CBM has to be found in another way for metals/charged system:\n",
+ " HOMO = -1000\n",
+ " LUMO = 1000\n",
+ " band_energy_max = 10\n",
+ " band_energy_min = 0\n",
+ " N_band_energy_index = 10000\n",
+ " band_energy_step = (band_energy_max - band_energy_min) / N_band_energy_index\n",
+ " N_allowed_states = np.zeros(N_band_energy_index + 1)\n",
+ " \n",
+ " #get the DOS and store in N_allowed_states[]\n",
+ " for i_k_points_all in range(N_k_points_all):\n",
+ " for i_bands in range(N_bands):\n",
+ " band_energy = band_energies_all[i_bands][i_k_points_all]\n",
+ " if(band_energy_min < band_energy < band_energy_max):\n",
+ " i_band_index = math.floor((band_energy - band_energy_min) / band_energy_step)\n",
+ " N_allowed_states[i_band_index] = N_allowed_states[i_band_index] + 1\n",
+ " if_gapped = 0\n",
+ " for i_band_index in range(N_band_energy_index): #go through the energy levels from the bottom\n",
+ " band_energy = band_energy_min + band_energy_step * i_band_index\n",
+ " if(N_allowed_states[i_band_index] == 0):\n",
+ " if_gapped = if_gapped + 1\n",
+ " if(band_energy > band_energy_max - 0.5) and (if_gapped == 0):\n",
+ " print(\"No gap found in this system. It seems to be a metal.\")\n",
+ " HOMO = 1000\n",
+ " LUMO = 1000\n",
+ " break\n",
+ " #print(\"At \", band_energy,\": # allowed states = \", N_allowed_states[i_band_index],\" if_gapped = \", if_gapped)\n",
+ " \n",
+ " if(N_allowed_states[i_band_index] > 0):\n",
+ " if(if_gapped * band_energy_step> 0.3 ): #above VBM-CBM gap: LUMO\n",
+ " if(band_energy < LUMO):\n",
+ " #print(\"LUMO got!\")\n",
+ " LUMO = band_energy\n",
+ " break #break before touching another gap that is above the band gap\n",
+ " if(if_gapped * band_energy_step < 0.3): #below VBM-CBM gap: HOMO\n",
+ " if(band_energy > HOMO):\n",
+ " #print(\"HOMO got!\")\n",
+ " HOMO = band_energy\n",
+ " \n",
+ " if_gapped = 0\n",
+ " \n",
+ " print('HOMO, LUMO for metal/charged system: ',HOMO, LUMO)\n",
+ " \n",
+ " '''\n",
+ "\n",
+ "# print('HOMO: ',tmp_HOMO_max)\n",
+ " HOMO_global = tmp_HOMO_max\n",
+ " LUMO_global = tmp_LUMO_min\n",
+ " band_gap_indirect = LUMO_global - HOMO_global\n",
+ " E_top_valence = HOMO_global\n",
+ " if(band_gap_indirect < 0):\n",
+ " band_gap_indirect = 0\n",
+ "\n",
+ " #Rescal HOMO and LUMO with respect to HOMO\n",
+ " HOMO_global = round((HOMO_global - E_top_valence), 3)\n",
+ " LUMO_global = round((LUMO_global - E_top_valence), 3)\n",
+ " '''\n",
+ " \n",
+ " \n",
+ " \n",
+ " #Find the position of HOMO, LUMO\n",
+ "\n",
+ " for i_k_points in range(N_k_points_all):\n",
+ " for i_bands in range(N_bands):\n",
+ " if(abs(band_energies_all[i_bands][i_k_points] - HOMO) < 0.001):\n",
+ " coor_k_point_HOMO = k_coor_1D[i_k_points]\n",
+ " if(abs(band_energies_all[i_bands][i_k_points] - LUMO) < 0.001):\n",
+ " coor_k_point_LUMO = k_coor_1D[i_k_points] \n",
+ "\n",
+ "\n",
+ " \n",
+ " \n",
+ " #Store the band data to band_obj\n",
+ "\n",
+ " band_obj = {}\n",
+ " band_obj[\"band_x_axis\"] = np.array(k_coor_1D).tolist()\n",
+ " band_obj[\"band_y_axis\"] = np.array(band_energies_all).tolist()\n",
+ " band_obj[\"labels\"] = np.array(label_obj).tolist()\n",
+ " band_obj[\"HOMO_energy\"] = np.array(HOMO).tolist()\n",
+ " band_obj[\"HOMO_coor\"] = np.array(coor_k_point_HOMO).tolist()\n",
+ " band_obj[\"LUMO_energy\"] = np.array(LUMO).tolist()\n",
+ " band_obj[\"LUMO_coor\"] = np.array(coor_k_point_LUMO).tolist()\n",
+ " band_obj[\"average_N_k_points_per_inverse_distance\"] = np.array(average_N_k_points_per_inverse_distance).tolist()\n",
+ " \n",
+ "\n",
+ " \n",
+ " return band_obj\n",
+ "\n",
+ "\n",
+ "#===============Get the space group information===========\n",
+ "def get_space_group(band_data):\n",
+ " import pymatgen as mg\n",
+ " from pymatgen.symmetry.analyzer import SpacegroupAnalyzer\n",
+ "\n",
+ " simulation_cell = np.array(band_data[\"section_run\"][\"section_system\"][0].get('simulation_cell',\"empty\")) * 10000000000\n",
+ " atom_positions = np.array(band_data[\"section_run\"][\"section_system\"][0].get('atom_positions',\"empty\")) * 10000000000\n",
+ " atom_labels = np.array(band_data[\"section_run\"][\"section_system\"][0].get('atom_labels',\"empty\"))\n",
+ " structure = mg.Structure(simulation_cell,atom_labels, atom_positions, coords_are_cartesian = True)\n",
+ " \n",
+ " finder = SpacegroupAnalyzer(structure, symprec=1e-3, angle_tolerance=5)\n",
+ " space_group_symbol = finder.get_space_group_symbol()\n",
+ " lattice_constant = []\n",
+ " for item in structure.lattice.abc:\n",
+ " lattice_constant.append(item)\n",
+ " for i in range(len(lattice_constant)):\n",
+ " item = str(round(lattice_constant[i], 3))\n",
+ " lattice_constant[i] = item\n",
+ " \n",
+ " return [space_group_symbol, lattice_constant]\n",
+ "\n",
+ "#================Get the DOS data==============================\n",
+ "def get_dos_obj(dos_path):\n",
+ " #dos_data: read from json file \n",
+ " #Load the data files for dos\n",
+ " dos_data = load_jsonfile(dos_path)\n",
+ "\n",
+ " print(dos_path)\n",
+ " #N_dos_values = len(dos_data['sections']['section_run-0']['sections']['section_single_configuration_calculation-0']['section_dos'][0]['dos_energies'])\n",
+ " N_dos_values = len(dos_data['section_run']['section_single_configuration_calculation']['section_dos'][0]['dos_energies'])\n",
+ " #in new parser, it seems that the spin channel of 'dos_energies' disappears: Shape: [ number_of_dos_values ]\n",
+ "\n",
+ " dos_energies = np.zeros((N_dos_values))\n",
+ " dos_energies_tmp = np.zeros((N_dos_values)) #tmp array for unit convertion\n",
+ " dos_values = np.zeros((N_dos_values))\n",
+ "\n",
+ " dos_energies_tmp = dos_data['section_run']['section_single_configuration_calculation']['section_dos'][0]['dos_energies']\n",
+ " dos_values = dos_data['section_run']['section_single_configuration_calculation']['section_dos'][0]['dos_values'][0]\n",
+ " \n",
+ "\n",
+ " dos_fermi_energy= dos_data['section_run']['section_single_configuration_calculation']['section_dos'][0].get('dos_fermi_energy',\"empty\")\n",
+ " if(dos_fermi_energy == \"empty\"): #dos_fermi_energy is not available in EXCITING\n",
+ " dos_fermi_energy_exciting = dos_data['section_run']['section_single_configuration_calculation'].get('x_exciting_dos_fermi',\"empty\")\n",
+ " if(dos_fermi_energy_exciting == \"empty\"):\n",
+ " dos_fermi_energy = 0\n",
+ " else:\n",
+ " dos_fermi_energy = dos_fermi_energy_exciting / (1.60217656535 * pow(10,-19))\n",
+ " else:\n",
+ " dos_fermi_energy = dos_fermi_energy / (1.60217656535 * pow(10,-19))\n",
+ " print(\"dos_fermi_energy:\", dos_fermi_energy)\n",
+ " \n",
+ " for i_dos_values in range(N_dos_values):\n",
+ " dos_energies[i_dos_values] = 0.0\n",
+ " dos_energies[i_dos_values] = dos_energies_tmp[i_dos_values] / (1.60217656535 * pow(10,-19))\n",
+ " dos_energies[i_dos_values] = round((dos_energies[i_dos_values] - dos_fermi_energy), 3) #reference with the fermi level\n",
+ "\n",
+ " dos_obj = {}\n",
+ " dos_obj[\"dos_x_axis\"] = np.array(dos_energies).tolist()\n",
+ " dos_obj[\"dos_y_axis\"] = np.array(dos_values).tolist()\n",
+ " dos_obj[\"dos_fermi_energy\"] = np.array(dos_fermi_energy).tolist()\n",
+ "\n",
+ " return dos_obj\n",
+ "\n",
+ "\n",
+ "def get_info_obj(band_path):\n",
+ "\n",
+ " #band_data: read from json file \n",
+ " #Load the data files for band\n",
+ " band_data = load_jsonfile(band_path)\n",
+ " info_obj = {}\n",
+ " #---------Read the information of the calculation--------\n",
+ " info_obj[\"program_name\"] = band_data[\"section_run\"][\"program_name\"];\n",
+ " info_obj[\"program_basis_set_type\"] = band_data[\"section_run\"][\"program_basis_set_type\"];\n",
+ " info_obj[\"atom_labels\"] = band_data[\"section_run\"][\"section_system\"][0][\"atom_labels\"];\n",
+ " info_obj[\"XC_functional_name\"] = band_data[\"section_run\"][\"section_method\"][\"section_XC_functionals\"][0][\"XC_functional_name\"] + \" + \"+ band_data[\"section_run\"][\"section_method\"][\"section_XC_functionals\"][1][\"XC_functional_name\"];\n",
+ " \n",
+ " #----------Get the space group information----------\n",
+ " \n",
+ " [space_group_symbol, lattice_constant] = get_space_group(band_data)\n",
+ " info_obj[\"space_group_symbol\"] = np.array(space_group_symbol).tolist()\n",
+ " info_obj[\"lattice_constant\"] = np.array(lattice_constant).tolist()\n",
+ " print(\"space group:\", info_obj[\"space_group_symbol\"])\n",
+ " print(\"lattice_constant:\", lattice_constant)\n",
+ " \n",
+ " return info_obj\n",
+ "\n",
+ "\n",
+ "#============main===========================================\n",
+ "\n",
+ "#import matplotlib.pyplot as plt\n",
+ "band_obj_all = []\n",
+ "dos_obj_all = []\n",
+ "info_obj_all = []\n",
+ "print(\"Number of materials: \", N_materials)\n",
+ "\n",
+ "for i in range (N_materials):\n",
+ " print(\"Material: \", i)\n",
+ " band_path = band_paths[i]\n",
+ " dos_path = dos_paths[i]\n",
+ " \n",
+ " \n",
+ " dos_obj = get_dos_obj(dos_path)\n",
+ " dos_fermi_energy = dos_obj[\"dos_fermi_energy\"]\n",
+ " band_obj = get_band_obj(band_path, dos_fermi_energy)\n",
+ " info_obj = get_info_obj(band_path)\n",
+ " \n",
+ " band_obj_all.append(band_obj)\n",
+ " dos_obj_all.append(dos_obj)\n",
+ " info_obj_all.append(info_obj)\n",
+ " \n",
+ " \n",
+ " print(\"average_N_k_points_per_inverse_distance: \", band_obj[\"average_N_k_points_per_inverse_distance\"])\n",
+ "\n",
+ "print(\"Finish processing data.\")\n",
+ "\n",
+ "#run_cell_by_tag('save_data_to_js')\n",
+ "\n",
+ "print(\"Initialization of visulization finished.\")"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 331,
+ "metadata": {
+ "tags": [
+ "js_plot"
+ ]
+ },
+ "outputs": [
+ {
+ "data": {
+ "application/javascript": [
+ " \n",
+ "var N_max_show = 10; //Number of results to be shown by default\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n"
+ ],
+ "text/plain": [
+ "<IPython.core.display.Javascript object>"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "%%javascript\n",
+ " \n",
+ "var N_max_show = 10; //Number of results to be shown by default\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": []
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "%%javascript\n",
+ "// BACKUP!\n",
+ "/*\n",
+ "//Main plot function for given material:\n",
+ " function plot_band_dos_i_backup(i, lowerLim, upperLim, if_show_VBM, if_compare, i_in_compare_list)\n",
+ " {\n",
+ " //alert(\"plot_band_dos_i\")\n",
+ " //i=0;\n",
+ " lowerLim = -10\n",
+ " upperLim = 10\n",
+ " if_show_VBM = 0\n",
+ " if_compare = 0\n",
+ " i_in_compare_list = -1\n",
+ " //i=0;\n",
+ " var placeholder_band = \"#div_band\" + i.toString();\n",
+ " var placeholder_dos = \"#div_dos\" + i.toString();\n",
+ " var placeholder_tools = \"#div_tools\" + i.toString();\n",
+ " var placeholder_overview = \"#div_overview\" + i.toString();\n",
+ " var placeholder_overviewlegend = \"#overviewLegend\" + i.toString();\n",
+ " var checkbox_VBM_id = \"checkbox_VBM\" + i.toString();\n",
+ " var img_band_id = \"img_band\" + i.toString();\n",
+ " var img_dos_id = \"img_dos\" + i.toString();\n",
+ " var placeholder_band_compare = \"\";\n",
+ "\n",
+ " if(i_in_compare_list == 1)\n",
+ " {\n",
+ " placeholder_band_compare = \"#div_band_compare_1\";\n",
+ " }\n",
+ " else if(i_in_compare_list == 2)\n",
+ " {\n",
+ " placeholder_band_compare = \"#div_band_compare_2\";\n",
+ " }\n",
+ " else\n",
+ " {\n",
+ " placeholder_band_compare = \"#div_band_compare_1\"; // just for safe\n",
+ " }\n",
+ "\n",
+ " Object.size = function(obj) {\n",
+ " var size = 0, key;\n",
+ " for (key in obj) \n",
+ " {\n",
+ " if (obj.hasOwnProperty(key)) size++;\n",
+ " }\n",
+ " return size;\n",
+ " };\n",
+ "\n",
+ " //Get the number of bands\n",
+ " //alert(\"Getting band\")\n",
+ " //alert(band_obj_all)\n",
+ " //alert(\"band_obj_all got!\")\n",
+ " var N_bands = Object.size(band_obj_all[i][\"band_y_axis\"]);\n",
+ " var N_k_coors = Object.size(band_obj_all[i][\"band_x_axis\"]);\n",
+ " alert(band_obj_all[i][\"band_y_axis\"])\n",
+ " band_plotdata = [];\n",
+ "\n",
+ " for(var i_band =0; i_band < N_bands; i_band++)\n",
+ " {\n",
+ " var tmp_data = [];\n",
+ " for(var j_k_coor = 0; j_k_coor < N_k_coors; j_k_coor ++)\n",
+ " {\n",
+ " tmp_data.push([band_obj_all[i][\"band_x_axis\"][j_k_coor],band_obj_all[i][\"band_y_axis\"][i_band][j_k_coor]]);\n",
+ " }\n",
+ " plotData = { shadowSize: 0 , data: tmp_data, color: 'black', series: { lines: { show: true } , points: {show: false} } };\n",
+ " band_plotdata.push(plotData);\n",
+ " }\n",
+ "\n",
+ "\n",
+ " var tmp_data0 = [[0, 0], [1, 0]];\n",
+ " plotData0 = { shadowSize:0, color: 'black', data: tmp_data0, dashes:{ show:true, lineWidth: 1.5}};\n",
+ " band_plotdata.push(plotData0);\n",
+ "\n",
+ " band_plotdata_overview = band_plotdata.slice(0);\n",
+ "\n",
+ " var HOMOdata= [[band_obj_all[i][\"HOMO_coor\"],band_obj_all[i][\"HOMO_energy\"]]];\n",
+ " HOMOlabel = [\"VBM\"];\n",
+ " plotHOMO={ shadowSize:0, color: 'blue', data: HOMOdata, points:{show:true, radius: 4 , fill: true, fillColor: 'blue'},lines:{show: false}, showLabels: true, labels: HOMOlabel, canvasRender: true, cColor: 'red', cFont:\"2em Arial\"};\n",
+ "\n",
+ " var LUMOdata= [[band_obj_all[i][\"LUMO_coor\"],band_obj_all[i][\"LUMO_energy\"]]];\n",
+ " LUMOlabel = [\"CBM\"];\n",
+ " plotLUMO={ shadowSize:0, color: 'red', data: LUMOdata, points:{show:true, radius: 4 , fill: true, fillColor: 'red'},lines:{show: false}, showLabels: true, labels: LUMOlabel, canvasRender: true, cColor: 'red', cFont:\"2em Arial\"};\n",
+ "\n",
+ " //if_show_VBM = check_show_VBM(checkbox_VBM_id);\n",
+ " if (if_show_VBM == 1)\n",
+ " {\n",
+ " band_plotdata.push(plotHOMO);\n",
+ " band_plotdata.push(plotLUMO);\n",
+ " }\n",
+ "\n",
+ " \n",
+ " alert(img_band_id + band_plotdata)\n",
+ " \n",
+ " //!!!FIXME: if ($(\"#showVBM:checked\").length > 0 && gap > 0.1) \n",
+ " //plotHOMOLUMO={ shadowSize:0, color: 'red', data: d5, points:{show:true, radius: 0.8 , fill: true}, showLabels: true, labels: d5label, labelPlacement: labelPos, canvasRender: true, cColor: 'red', cFont:\"1em Arial\" }\n",
+ "\n",
+ " var canvas_band;\n",
+ " var options_band = {\n",
+ " canvas: true,\n",
+ " //legend:{ type: \"canvas\" },\n",
+ " series: { lines: { show: true, lineWidth: 2 }, \n",
+ " points: { show: false } }, \n",
+ " xaxis: { \n",
+ " ticks: band_obj_all[i][\"labels\"], \n",
+ " color:\"#000\", \n",
+ " font: {size: 20}, \n",
+ " zoomRange: false,\n",
+ " panRange: false \n",
+ " }, \n",
+ " yaxis: { \n",
+ " axisLabel: \"Energy (eV)\", \n",
+ " axisLabelUseCanvas: true,\n",
+ " //axisLabelUseCanvas: false,\n",
+ " axisLabelFontSizePixels: 20,\n",
+ " axisLabelFontFamily: 'Arial', \n",
+ " axisLabelPadding: 10, \n",
+ " color:\"#000\", \n",
+ " font: {size: 20, family:\"Arial\"},\n",
+ " tickLength:-5, \n",
+ " min: lowerLim, \n",
+ " max: upperLim,\n",
+ " tickDecimals: 0, \n",
+ " zoomRange: [0.001, 1000],\n",
+ " panRange: [-100, 100] \n",
+ " },\n",
+ "\n",
+ " zoom: { \n",
+ " interactive: true\n",
+ " },\n",
+ "\n",
+ " pan: {\n",
+ " interactive: true\n",
+ " }, \n",
+ "\n",
+ " //selection: { mode: \"xy\", color: \"#86a6b4\" }, \n",
+ "\n",
+ " grid: { \n",
+ " labelMargin: 15,\n",
+ " hoverable: true, \n",
+ " backgroundColor: { colors: [\"#fff\", \"#fff\"] }, \n",
+ " borderWidth: {\n",
+ " top: 2, \n",
+ " right: 2,\n",
+ " bottom: 2,\n",
+ " left: 2,\n",
+ " color : null } \n",
+ " }\n",
+ " }\n",
+ " //var plot_band = $.plot($(placeholder_band), band_plotdata, options_band);\n",
+ " //var plot_band = $.plot(\"#div_bandx\", band_plotdata, options_band);\n",
+ " var plot_band = $.plot($(placeholder_band), band_plotdata, options_band).getCanvas(); // save the canvas\n",
+ " image_band = plot_band.toDataURL();\n",
+ " image_band = image_band.replace(\"image/png\",\"image/octet-stream\");\n",
+ " //beakerx.image_band = image_band;\n",
+ " document.getElementById(img_band_id).href= image_band;\n",
+ " image_band_links[i] = image_band;\n",
+ " alert(\"band plot done.\")\n",
+ "\n",
+ "\n",
+ " //----Plot DOS----------------------\n",
+ " var dos_plotdata = [];\n",
+ " alert(\"dos:\"+dos_obj_all[i])\n",
+ " var xdos = dos_obj_all[i][\"dos_x_axis\"];\n",
+ " var ydos = dos_obj_all[i][\"dos_y_axis\"];\n",
+ " var dosLabelPos = Math.max.apply(Math, ydos)/2;\n",
+ " var d2 = [];\n",
+ " for (var ii = 0; ii < xdos.length; ii+=1) {\n",
+ " d2.push([ydos[ii],xdos[ii]]);\n",
+ " }\n",
+ " var plotData2={ shadowSize: 0, color: 'black' , data: d2}\n",
+ " dos_plotdata.push(plotData2)\n",
+ "\n",
+ " function find_xaxis_max_min(data, lowerbound, upperbound)\n",
+ " {\n",
+ " //data[xaxis,y] find the max and min value of x axis\n",
+ " //alert(\"dos[0]:\" + data[0][\"data\"]);\n",
+ " //alert(\"Bounds: \" + lowerbound + \" , \" + upperbound)\n",
+ " var n_data = data.length;\n",
+ " //alert(\"N dos: \" + n_data);\n",
+ " var data_min = 1000000;\n",
+ " var data_max = -1000000;\n",
+ " var data_current = 0;\n",
+ " for (var i = 0; i < n_data; i++)\n",
+ " {\n",
+ " if((data[i][1] >= lowerbound) && (data[i][1] <= upperbound))\n",
+ " {\n",
+ " data_current = data[i][0];\n",
+ " //alert(\"data[i]: \" + data[i] + \"data[i][0]: \" + data_current);\n",
+ " if(data_current >= data_max)\n",
+ " {\n",
+ " data_max = data_current;\n",
+ " }\n",
+ " if(data_current <= data_min)\n",
+ " {\n",
+ " data_min = data_current;\n",
+ " }\n",
+ " }\n",
+ " }\n",
+ " var data_max_min = [data_max, data_min];\n",
+ " //alert(\"data_max_min: \" + data_max_min);\n",
+ " return data_max_min;\n",
+ " }\n",
+ " var dos_x_max_min = find_xaxis_max_min(dos_plotdata[0][\"data\"], lowerLim, upperLim);\n",
+ " var dosLabelPos = (dos_x_max_min[0] + dos_x_max_min[1])/2;\n",
+ "\n",
+ " var options_dos ={\n",
+ " canvas: true,\n",
+ " series: {\n",
+ " lines: { show: true, lineWidth:2 },\n",
+ " points: { show: false }\n",
+ " },\n",
+ "\n",
+ " yaxis: { \n",
+ " axisLabel: \"\", \n",
+ " axisLabelUseCanvas: true,\n",
+ " axisLabelFontSizePixels: 20,\n",
+ " axisLabelFontFamily: 'Arial', \n",
+ " axisLabelPadding: 10, \n",
+ " color:\"#000\", \n",
+ " font: {size: 20},\n",
+ " tickLength:-5, \n",
+ " min: lowerLim, \n",
+ " max: upperLim,\n",
+ " tickDecimals: 0, \n",
+ " zoomRange: [0.001, 1000],\n",
+ " panRange: [-100, 100] \n",
+ " },\n",
+ "\n",
+ " xaxis: {\n",
+ " axisLabel: \" \",\n",
+ " axisLabelUseCanvas: false,\n",
+ " axisLabelFontSizePixels: 20,\n",
+ " axisLabelFontFamily: 'Arial',\n",
+ " axisLabelPadding: 3,\n",
+ " color:\"rgb(0, 0, 0)\",\n",
+ " font: {size: 20, family:\"Arial\"},\n",
+ " //ticks: 10,\n",
+ " tickLength:0,\n",
+ " min: dos_x_max_min[1],//0,\n",
+ " max: dos_x_max_min[0],//1,\n",
+ " tickDecimals: 0,\n",
+ " ticks: [[ dosLabelPos ,'DOS']],\n",
+ " //tickFormatter: MyFormatter\n",
+ " panRange: false\n",
+ " },\n",
+ " pan: {\n",
+ " interactive: true\n",
+ " }, \n",
+ "\n",
+ " grid: {\n",
+ " labelMargin: 15,\n",
+ " hoverable: true,\n",
+ " //borderWidth : 1000,\n",
+ " //show : false,\n",
+ " // //backgroundColor: { colors: [ \"#fff\", \"#eee\" ] },\n",
+ " backgroundColor: { colors: [\"#fff\", \"#fff\"] },\n",
+ " borderWidth: {\n",
+ " top: 2,\n",
+ " right: 2,\n",
+ " bottom: 2,\n",
+ " left: 2,\n",
+ " color : null\n",
+ " }\n",
+ " }\n",
+ " }\n",
+ " var plot_dos = $.plot(placeholder_dos, dos_plotdata, options_dos).getCanvas();\n",
+ " var image_dos = plot_dos.toDataURL();\n",
+ " image_dos = image_dos.replace(\"image/png\",\"image/octet-stream\");\n",
+ " image_dos = image_dos;\n",
+ " document.getElementById(img_dos_id).href= image_dos;\n",
+ " \n",
+ " }\n",
+ "*/"
+ ]
+ }
+ ],
+ "metadata": {
+ "celltoolbar": "Tags",
+ "kernelspec": {
+ "display_name": "Python 3",
+ "language": "python",
+ "name": "python3"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 3
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython3",
+ "version": "3.6.7"
+ },
+ "toc": {
+ "base_numbering": 1,
+ "nav_menu": {},
+ "number_sections": false,
+ "sideBar": false,
+ "skip_h1_title": false,
+ "title_cell": "Table of Contents",
+ "title_sidebar": "Contents",
+ "toc_cell": false,
+ "toc_position": {},
+ "toc_section_display": false,
+ "toc_window_display": false
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}
diff --git a/Nomad_tutorial_head.png b/Nomad_tutorial_head.png
new file mode 100644
index 0000000000000000000000000000000000000000..c31c475de3e3e8df2e858a511b924b65d14a32ee
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@@ -0,0 +1,4968 @@
+{
+ "cells": [
+ {
+ "cell_type": "code",
+ "execution_count": 1,
+ "metadata": {
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+ },
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "<style>.container { width:100% !important; }</style>"
+ ],
+ "text/plain": [
+ "<IPython.core.display.HTML object>"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "from IPython.core.display import display, HTML\n",
+ "display(HTML(\"<style>.container { width:100% !important; }</style>\"))\n",
+ "\n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 2,
+ "metadata": {
+ "init_cell": true
+ },
+ "outputs": [],
+ "source": [
+ "from IPython.core.display import Javascript\n",
+ "from IPython.display import display\n",
+ "\n",
+ "def run_cell_by_tag(tags):\n",
+ " display(Javascript(\"window.runCells('\"+tags+\"')\"))"
+ ]
+ },
+ {
+ "cell_type": "code",
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+ "metadata": {
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+ "scrolled": true
+ },
+ "outputs": [
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+ "data": {
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+ "<script>\n",
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+ " if (code_show)\n",
+ " {\n",
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+ " } \n",
+ " else \n",
+ " {\n",
+ " $('div.input').show();\n",
+ " }\n",
+ " code_show = !code_show\n",
+ " } \n",
+ " $( document ).ready(code_toggle);\n",
+ "</script>\n",
+ "The raw code for this notebook is by default hidden for easier reading.\n",
+ "To toggle on/off the raw code, click <a href=\"javascript:code_toggle()\">here</a>.\n"
+ ],
+ "text/plain": [
+ "<IPython.core.display.HTML object>"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
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+ "%%HTML\n",
+ "<script>\n",
+ " code_show=true; \n",
+ " function code_toggle() {\n",
+ " if (code_show)\n",
+ " {\n",
+ " $('div.input').hide();\n",
+ " } \n",
+ " else \n",
+ " {\n",
+ " $('div.input').show();\n",
+ " }\n",
+ " code_show = !code_show\n",
+ " } \n",
+ " $( document ).ready(code_toggle);\n",
+ "</script>\n",
+ "The raw code for this notebook is by default hidden for easier reading.\n",
+ "To toggle on/off the raw code, click <a href=\"javascript:code_toggle()\">here</a>."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 4,
+ "metadata": {
+ "init_cell": true,
+ "scrolled": false
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ "\n",
+ "<div align=\"left\" style=\"background-color: rgba(149,170,79, 1.0); width: 100%; height: 390px; overflow: hidden;\">\n",
+ " <div >\n",
+ " <table>\n",
+ " <tr></tr>\n",
+ " <tr>\n",
+ " <td><img src=\"Nomad_tutorial_head.png\"></td>\n",
+ " </tr>\n",
+ " </table>\n",
+ " </div>\n",
+ "\n",
+ " <br><br>\n",
+ " <div style=\"position:relative; left:3%\"><font size=6em color=\"#20335d\" ><b> - Visualization of the band structure of materials </b></font></div>\n",
+ " <p style=\"position:relative;left:10%; \">\n",
+ " <br>\n",
+ " Created by:\n",
+ "\n",
+ " Xiangyue Liu<sup>1</sup>(<a href=\"mailto:xyliu@fhi-berlin.mpg.de\">email</a>),\n",
+ " \n",
+ " Fawzi Mohamed<sup>1</sup>,\n",
+ " \n",
+ " and Luca M. Ghiringhelli<sup>1</sup>(<a href=\"mailto:ghiringhelli@fhi-berlin.mpg.de\">email</a>), <br>\n",
+ "\n",
+ " <br><br>\n",
+ " <sup>1</sup> Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, D-14195 Berlin, Germany <br>\n",
+ " <br>\n",
+ "\n",
+ "\n",
+ " </p>\n",
+ " <br>\n",
+ " <div style=\"position:relative;bottom:3%\">\n",
+ " <div style=\"position:absolute;right:5%;bottom: 0%;\"><font color=\"#999999\" size=\"10em\">v2.0.0</font></div>\n",
+ " <div style=\"position:absolute;right:5%;bottom: 0%;\"><font color=\"#666666\" size=\"2.7em\">[Last updated: August 5, 2019]</font></div>\n",
+ " </div>\n",
+ "\n",
+ "</div>\n",
+ "\n",
+ "\n",
+ "<div style='text-align: right;'>\n",
+ " <a href=\"https://analytics-toolkit.nomad-coe.eu/home/\" class=\"btn btn-primary\" style=\"font-size:larger;\">Back to Analytics Home</a> \n",
+ " <a href=\"https://www.nomad-coe.eu/\" class=\"btn btn-primary\" style=\"font-size:larger; \">Back to nomad-coe</a> \n",
+ "</div>\n"
+ ],
+ "text/plain": [
+ "<IPython.core.display.HTML object>"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "%%HTML\n",
+ "\n",
+ "\n",
+ "<div align=\"left\" style=\"background-color: rgba(149,170,79, 1.0); width: 100%; height: 390px; overflow: hidden;\">\n",
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+ " <table>\n",
+ " <tr></tr>\n",
+ " <tr>\n",
+ " <td><img src=\"Nomad_tutorial_head.png\"></td>\n",
+ " </tr>\n",
+ " </table>\n",
+ " </div>\n",
+ "\n",
+ " <br><br>\n",
+ " <div style=\"position:relative; left:3%\"><font size=6em color=\"#20335d\" ><b> - Visualization of the band structure of materials </b></font></div>\n",
+ " <p style=\"position:relative;left:10%; \">\n",
+ " <br>\n",
+ " Created by:\n",
+ "\n",
+ " Xiangyue Liu<sup>1</sup>(<a href=\"mailto:xyliu@fhi-berlin.mpg.de\">email</a>),\n",
+ " \n",
+ " Fawzi Mohamed<sup>1</sup>,\n",
+ " \n",
+ " and Luca M. Ghiringhelli<sup>1</sup>(<a href=\"mailto:ghiringhelli@fhi-berlin.mpg.de\">email</a>), <br>\n",
+ "\n",
+ " <br><br>\n",
+ " <sup>1</sup> Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, D-14195 Berlin, Germany <br>\n",
+ " <br>\n",
+ "\n",
+ "\n",
+ " </p>\n",
+ " <br>\n",
+ " <div style=\"position:relative;bottom:3%\">\n",
+ " <div style=\"position:absolute;right:5%;bottom: 0%;\"><font color=\"#999999\" size=\"10em\">v2.0.0</font></div>\n",
+ " <div style=\"position:absolute;right:5%;bottom: 0%;\"><font color=\"#666666\" size=\"2.7em\">[Last updated: August 5, 2019]</font></div>\n",
+ " </div>\n",
+ "\n",
+ "</div>\n",
+ "\n",
+ "\n",
+ "<div style='text-align: right;'>\n",
+ " <a href=\"https://analytics-toolkit.nomad-coe.eu/home/\" class=\"btn btn-primary\" style=\"font-size:larger;\">Back to Analytics Home</a> \n",
+ " <a href=\"https://www.nomad-coe.eu/\" class=\"btn btn-primary\" style=\"font-size:larger; \">Back to nomad-coe</a> \n",
+ "</div>\n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 5,
+ "metadata": {
+ "init_cell": true
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "<script>\n",
+ " window.findCellIndicesByTag = function findCellIndicesByTag(tagName) {\n",
+ " return (Jupyter.notebook.get_cells()\n",
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+ " ({metadata: {tags}}) => tags && tags.includes(tagName)\n",
+ " )\n",
+ " .map((cell) => Jupyter.notebook.find_cell_index(cell))\n",
+ " );\n",
+ " };\n",
+ "\n",
+ "\n",
+ " window.runCells = function runPlotCells(tags) {\n",
+ " var c = window.findCellIndicesByTag(tags);\n",
+ " Jupyter.notebook.execute_cells(c);\n",
+ " };\n",
+ "</script>\n"
+ ],
+ "text/plain": [
+ "<IPython.core.display.HTML object>"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "%%HTML\n",
+ "<script>\n",
+ " window.findCellIndicesByTag = function findCellIndicesByTag(tagName) {\n",
+ " return (Jupyter.notebook.get_cells()\n",
+ " .filter(\n",
+ " ({metadata: {tags}}) => tags && tags.includes(tagName)\n",
+ " )\n",
+ " .map((cell) => Jupyter.notebook.find_cell_index(cell))\n",
+ " );\n",
+ " };\n",
+ "\n",
+ "\n",
+ " window.runCells = function runPlotCells(tags) {\n",
+ " var c = window.findCellIndicesByTag(tags);\n",
+ " Jupyter.notebook.execute_cells(c);\n",
+ " };\n",
+ "</script>"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 53,
+ "metadata": {
+ "init_cell": true,
+ "tags": [
+ "search_materials"
+ ]
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "<br><br>\n",
+ "\n",
+ "<p style=\"color: #20335d;font-weight: 450; font-size: 14pt;font-family: Arial;\"> This tutorial visulizes the band structures and density of states (DOS) of the NOMAD materials.</p>\n",
+ "<br><br>\n",
+ "\n",
+ "<style>\n",
+ ".button {\n",
+ " background-color: #e7e7e7;\n",
+ " border: 0.5px solid #A4A4A4;\n",
+ " color: black;\n",
+ " padding: 15px 32px;\n",
+ " text-align: center;\n",
+ " text-decoration: none;\n",
+ " display: inline-block;\n",
+ " font-family: Arial;\n",
+ " font-size: 16px;\n",
+ " margin: 4px 2px;\n",
+ " cursor: pointer;\n",
+ "}\n",
+ "\n",
+ " .text-normal-black{\n",
+ " color: #000;font-weight: 200; font-size: 10pt;\n",
+ " font-family: Arial;\n",
+ " }\n",
+ " .div_band_dos{\n",
+ " box-sizing: border-box;\n",
+ " width: 100%;\n",
+ " height: 600px;\n",
+ " font-weight: 100;\n",
+ " font-family: Arial;\n",
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+ " padding-top: 10px;\n",
+ " padding-right: 1em;\n",
+ " margin: 0;\n",
+ " border: 0;\n",
+ " }\n",
+ " .div_band_dos_compare{\n",
+ " box-sizing: border-box;\n",
+ " width: 1600px;\n",
+ " height: 600px;\n",
+ " color: #00AEFF;\n",
+ " font-weight: 100;\n",
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+ " padding-left: 20px;\n",
+ " padding-top: 10px;\n",
+ " padding-right: 1em;\n",
+ " margin: 0;\n",
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+ " }\n",
+ " .div_band{\n",
+ " font-family: Arial;\n",
+ " font-size: 0.875em;\n",
+ " width: 37%;\n",
+ " height: 80%;\n",
+ " background-color: #fff;\n",
+ " float:left;\n",
+ " }\n",
+ " .div_dos{\n",
+ " font-family: Arial;\n",
+ " font-size: 0.875em;\n",
+ " width: 13%;\n",
+ " height: 80%;\n",
+ " background-color: #fff;\n",
+ " float:left;\n",
+ " }\n",
+ " .div_tools{\n",
+ " color: #20335d;font-weight: 150; font-size: 13pt;\n",
+ " width: 35%;\n",
+ " height: 80%;\n",
+ " background-color: #fff;\n",
+ " margin-left:20pt;\n",
+ " float:left;\n",
+ " font-family: Arial;\n",
+ "\n",
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+ " color: #888;font-weight: 150; font-size: 12pt;\n",
+ " width: 10%;\n",
+ " height: 80%;\n",
+ " background-color: #fff;\n",
+ " border: solid #fff 1px;\n",
+ " float:right;\n",
+ " font-family: Arial;\n",
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+ " }\n",
+ " .div_overview{\n",
+ " width: 300px;\n",
+ " height: 200px;\n",
+ " background-color: #fff;\n",
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+ " text-decoration: none;\n",
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+ " margin: 4px 2px;\n",
+ " cursor: pointer;\n",
+ " font-family: Arial;\n",
+ "\n",
+ " }\n",
+ "\n",
+ " \n",
+ " .g-before-after{position:relative;overflow:hidden;width:500px}.g-before-after img{display:block}.g-before-after .g-img-before{float:left}.g-before-after .g-img-after,.g-before-after.g-vertical .g-img-after{position:absolute;top:0;right:0;left:50%;bottom:0;overflow:hidden}.g-before-after .g-img-after img{position:absolute;right:0;top:0}.g-before-after .g-img-divider{position:absolute;left:50%;top:0;bottom:0;width:0;border-left:1px solid #fff;border-right:1px solid #fff}.g-before-after .g-img-divider>span{position:absolute;top:50%;display:block;background-color:#fff;padding:5px 10px;line-height:1;text-align:center;-webkit-transform:translate(-50%,-50%);-ms-transform:translate(-50%,-50%);transform:translate(-50%,-50%)}.g-before-after.g-vertical .g-img-after{top:50%;left:0}.g-before-after.g-vertical .g-img-after img{position:absolute;right:auto;top:auto;left:0;bottom:0}.g-before-after.g-vertical .g-img-divider{position:absolute;left:0;top:50%;bottom:auto;right:0;height:0;width:100%;border-top:1px solid #fff;border-bottom:1px solid #fff;border-left:0 none;border-right:0 none}.g-before-after.g-vertical .g-img-divider>span{top:50%;left:50%}\n",
+ "</style>\n",
+ "\n",
+ "<script>\n",
+ " //Search for certain keyword: https://labdev-nomad.esc.rzg.mpg.de/fairdi/nomad/migration/api/repo/?quantities=section_k_band_segment\n",
+ " //FjiYy5-ETRCrs5ktzJA55w/bOY0cPkBvvNAY7pZdbginlKXJ2kF\n",
+ " //\"upload_id\"/\"calc_id\"\n",
+ " \n",
+ " //Global variables\n",
+ " var paths_section_k_band_segment = []; \n",
+ " var paths_section_dos = [];\n",
+ " var band_obj_all = [];\n",
+ " var dos_obj_all = [];\n",
+ " var info_obj_all = [];\n",
+ " \n",
+ " var band_paths = [];\n",
+ " var dos_paths = [];\n",
+ " var N_materials = 0; //Number of materials that have both band and DOS in the same calculation \n",
+ " \n",
+ " \n",
+ " function getJSON(url) {\n",
+ " var resp ;\n",
+ " var xmlHttp ;\n",
+ "\n",
+ " resp = '' ;\n",
+ " xmlHttp = new XMLHttpRequest();\n",
+ "\n",
+ " if(xmlHttp != null)\n",
+ " {\n",
+ " xmlHttp.open( \"GET\", url, false );\n",
+ " xmlHttp.send( null );\n",
+ " resp = xmlHttp.responseText;\n",
+ " }\n",
+ "\n",
+ " return resp;\n",
+ " }\n",
+ " function match_band_dos()\n",
+ " {\n",
+ " //TMP for local tests\n",
+ " /*\n",
+ " paths_section_k_band_segment = [\"data/kOJR-AlPSgiNG9AdZoxd4g_9mxjIU0edrPosfsTc4uyDG9H_UXr.json\",\"data/kOJR-AlPSgiNG9AdZoxd4g_lfkGCmWozYENeiGhu5W7dJUqLTkj.json\"];\n",
+ " paths_section_dos = [\"data/kOJR-AlPSgiNG9AdZoxd4g_8tEGnaz0yY91eSyysKZkIUH9qx8J.json\", \"data/kOJR-AlPSgiNG9AdZoxd4g_lxUT3viRZcC_1IsH_KvO5tChAtV1.json\"];\n",
+ " */\n",
+ "\n",
+ " //band_paths = [];\n",
+ " //dos_paths = [];\n",
+ " //N_materials = 0; \n",
+ " \n",
+ " var data_k_band = [];\n",
+ " for(var i_path_k_band = 0; i_path_k_band < paths_section_k_band_segment.length; i_path_k_band ++)\n",
+ " {\n",
+ " var i_data_k_band_json = JSON.parse(getJSON(paths_section_k_band_segment[i_path_k_band]));\n",
+ " var i_data_k_band = {};\n",
+ " i_data_k_band[\"program_name\"] = i_data_k_band_json[\"section_run\"][\"program_name\"];\n",
+ " i_data_k_band[\"k_mesh_points\"] = i_data_k_band_json[\"section_run\"][\"section_method\"][\"k_mesh_points\"];\n",
+ " i_data_k_band[\"simulation_cell\"] = i_data_k_band_json[\"section_run\"][\"section_system\"][0][\"simulation_cell\"];\n",
+ " i_data_k_band[\"atom_positions\"] = i_data_k_band_json[\"section_run\"][\"section_system\"][0][\"atom_positions\"];\n",
+ " i_data_k_band[\"atom_labels\"] = i_data_k_band_json[\"section_run\"][\"section_system\"][0][\"atom_labels\"];\n",
+ " i_data_k_band[\"XC_functional_name\"] = i_data_k_band_json[\"section_run\"][\"section_method\"][\"section_XC_functionals\"][0][\"XC_functional_name\"] + \"-\" + i_data_k_band_json[\"section_run\"][\"section_method\"][\"section_XC_functionals\"][1][\"XC_functional_name\"]\n",
+ " i_data_k_band[\"path\"] = paths_section_k_band_segment[i_path_k_band];\n",
+ " data_k_band.push(i_data_k_band);\n",
+ " }\n",
+ "\n",
+ " var data_dos = [];\n",
+ " for(var i_path_dos = 0; i_path_dos < paths_section_dos.length; i_path_dos ++)\n",
+ " {\n",
+ " var i_data_dos_json = JSON.parse(getJSON(paths_section_dos[i_path_dos]));\n",
+ " var i_data_dos = {};\n",
+ " i_data_dos[\"program_name\"] = i_data_dos_json[\"section_run\"][\"program_name\"];\n",
+ " i_data_dos[\"k_mesh_points\"] = i_data_dos_json[\"section_run\"][\"section_method\"][\"k_mesh_points\"];\n",
+ " i_data_dos[\"simulation_cell\"] = i_data_dos_json[\"section_run\"][\"section_system\"][0][\"simulation_cell\"];\n",
+ " i_data_dos[\"atom_positions\"] = i_data_dos_json[\"section_run\"][\"section_system\"][0][\"atom_positions\"];\n",
+ " i_data_dos[\"atom_labels\"] = i_data_dos_json[\"section_run\"][\"section_system\"][0][\"atom_labels\"];\n",
+ " i_data_dos[\"XC_functional_name\"] = i_data_dos_json[\"section_run\"][\"section_method\"][\"section_XC_functionals\"][0][\"XC_functional_name\"] + \"-\" + i_data_dos_json[\"section_run\"][\"section_method\"][\"section_XC_functionals\"][1][\"XC_functional_name\"]\n",
+ " i_data_dos[\"path\"] = paths_section_dos[i_path_dos];\n",
+ " data_dos.push(i_data_dos); \n",
+ " }\n",
+ "\n",
+ " //Matching: band[i] ~ dos[i] (the same systems are arranged with the same index)\n",
+ " band_paths = [];\n",
+ " dos_paths = [];\n",
+ " N_materials = 0;\n",
+ " for(var i_k_band = 0; i_k_band < data_k_band.length; i_k_band ++)\n",
+ " {\n",
+ " for(var i_dos = 0; i_dos < data_dos.length; i_dos ++)\n",
+ " {\n",
+ " if(data_k_band[i_k_band][\"program_name\"] != data_dos[i_dos][\"program_name\"])\n",
+ " continue; \n",
+ " //if(data_k_band[i_k_band][\"k_mesh_points\"].join() != data_dos[i_dos][\"k_mesh_points\"].join())\n",
+ " // continue;\n",
+ " if(data_k_band[i_k_band][\"simulation_cell\"].join() != data_dos[i_dos][\"simulation_cell\"].join())\n",
+ " continue;\n",
+ " if(data_k_band[i_k_band][\"atom_positions\"].join() != data_dos[i_dos][\"atom_positions\"].join())\n",
+ " continue;\n",
+ " if(data_k_band[i_k_band][\"atom_labels\"].join() != data_dos[i_dos][\"atom_labels\"].join())\n",
+ " continue;\n",
+ " if(data_k_band[i_k_band][\"XC_functional_name\"] != data_dos[i_dos][\"XC_functional_name\"])\n",
+ " continue;\n",
+ " band_paths.push(data_k_band[i_k_band][\"path\"]);\n",
+ " dos_paths.push(data_dos[i_dos][\"path\"]);\n",
+ " N_materials ++;\n",
+ " }\n",
+ " }\n",
+ " //Pass the arrays to python\n",
+ "\n",
+ " var command = \"N_materials = \" + N_materials + \";\"\n",
+ " var kernel = IPython.notebook.kernel;\n",
+ " command += \"band_paths = \" + \"[\\'\" + band_paths.join(\"\\',\\'\") + \"\\'];\";\n",
+ " command += \"dos_paths = \" + \"[\\'\" + dos_paths.join(\"\\',\\'\") + \"\\'];\";\n",
+ " kernel.execute(command);\n",
+ " \n",
+ " \n",
+ " }\n",
+ "\n",
+ " function get_paths_from_search_results(result_json, div_id_search_results,div_head)\n",
+ " {\n",
+ " paths = [];\n",
+ " search_results_content = [div_head, '<table>', '<tr><th>Chemical formula</th><th>Spacegroup</th><th>Code</th><th>XC functional</th><th>Upload ID</th><th>Calculation ID</th><th>URL</th></tr>'];\n",
+ " for(var i_key in result_json)\n",
+ " {\n",
+ " if(i_key == \"results\")\n",
+ " {\n",
+ " for(var system in result_json[i_key])\n",
+ " {\n",
+ " //Get the path to the data files (json)： https://labdev-nomad.esc.rzg.mpg.de/fairdi/nomad/migration/api/archive/upload_id/calc_id \n",
+ " path = \"https://labdev-nomad.esc.rzg.mpg.de/fairdi/nomad/migration/api/archive/\" + result_json[i_key][system][\"upload_id\"] + \"/\" + result_json[i_key][system][\"calc_id\"]\n",
+ " paths.push(path);\n",
+ " \n",
+ " //Show the results in div\n",
+ " // \"formula\" \"spacegroup_symbol\" \"code_name\" \"xc_functional\"\n",
+ " content = '<tr>';\n",
+ " content += '<td>' + result_json[i_key][system][\"formula\"] + '</td>';\n",
+ " content += '<td>' + result_json[i_key][system][\"spacegroup_symbol\"] + '</td>';\n",
+ " content += '<td>' + result_json[i_key][system][\"code_name\"] + '</td>';\n",
+ " content += '<td>' + result_json[i_key][system][\"xc_functional\"] + '</td>';\n",
+ " content += '<td>' + result_json[i_key][system][\"upload_id\"] + '</td>';\n",
+ " content += '<td>' + result_json[i_key][system][\"calc_id\"] + '</td>'; \n",
+ " content += '<td>' + path + '</td>';\n",
+ " content += '</tr>';\n",
+ " search_results_content.push(content);\n",
+ " }\n",
+ " }\n",
+ " }\n",
+ " search_results_content.push('</table>');\n",
+ " document.getElementById(div_id_search_results).innerHTML = search_results_content.join('');\n",
+ " return paths\n",
+ " }\n",
+ " \n",
+ " \n",
+ " \n",
+ "\n",
+ " \n",
+ " \n",
+ " \n",
+ " function submit_search()\n",
+ " {\n",
+ " \n",
+ " var result;\n",
+ " var formula = document.getElementById(\"keyword_chemical_formula\").value;\n",
+ " var query_command_k_band = \"https://labdev-nomad.esc.rzg.mpg.de/fairdi/nomad/migration/api/repo/?formula=\" + formula + \"&quantities=section_k_band_segment\";\n",
+ " var query_command_dos = \"https://labdev-nomad.esc.rzg.mpg.de/fairdi/nomad/migration/api/repo/?formula=\" + formula + \"&quantities=section_dos\";\n",
+ " //result = getJSON(\"https://labdev-nomad.esc.rzg.mpg.de/fairdi/nomad/migration/api/repo/?quantities=section_k_band_segment\");\n",
+ " var result_k_band = getJSON(query_command_k_band);\n",
+ " var result_dos = getJSON(query_command_dos);\n",
+ " var result_json_k_band = JSON.parse(result_k_band);//parse the searching results to json from URL\n",
+ " var result_json_dos = JSON.parse(result_dos);\n",
+ " paths_section_k_band_segment = []; \n",
+ " paths_section_dos = [];\n",
+ " paths_section_k_band_segment = get_paths_from_search_results(result_json_k_band, \"search_results_section_k_band_segment\", \"<br><br><font size=4em>Calculations containing band structures:</font><br>\");\n",
+ " paths_section_dos = get_paths_from_search_results(result_json_dos, \"search_results_section_dos\", \"<br><font size=4em>Calculations containing DOS:</font><br>\");\n",
+ " \n",
+ " var promise = Promise.resolve();\n",
+ " promise\n",
+ " .then(match_band_dos())\n",
+ " .then(Jupyter.notebook.execute_cells(window.findCellIndicesByTag('process_band_dos_data')))\n",
+ " .then(Jupyter.notebook.execute_cells(window.findCellIndicesByTag('show_results_and_plot')));\n",
+ " \n",
+ " //match_band_dos();\n",
+ " \n",
+ " //Jupyter.notebook.execute_cells(window.findCellIndicesByTag('process_band_dos_data')); //Read the json files, and prepare data for plot\n",
+ " //Jupyter.notebook.execute_cells(window.findCellIndicesByTag('show_results_and_plot')); //Prepare for plot\n",
+ " }\n",
+ " function reset_search()\n",
+ " {\n",
+ " Jupyter.notebook.execute_cells(window.findCellIndicesByTag('search_materials'));\n",
+ " Jupyter.notebook.execute_cells(window.findCellIndicesByTag('show_results_and_plot'));\n",
+ " }\n",
+ " \n",
+ " \n",
+ "</script>\n",
+ "<font size=4em>Please input the chemical formula:</font>\n",
+ "<input type=\"text\" id=\"keyword_chemical_formula\" value=\"AlInO3\"> \n",
+ "<button class=\"button\" onclick=\"submit_search()\">Search</button>\n",
+ "<button class=\"button\" onclick=\"reset_search()\">Reset</button>\n",
+ "<br><br><br>\n",
+ "<div id=\"search_results_section_k_band_segment\"></div>\n",
+ "<div id=\"search_results_section_dos\"></div>\n"
+ ],
+ "text/plain": [
+ "<IPython.core.display.HTML object>"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "%%html\n",
+ "<br><br>\n",
+ "\n",
+ "<p style=\"color: #20335d;font-weight: 450; font-size: 14pt;font-family: Arial;\"> This tutorial visulizes the band structures and density of states (DOS) of the NOMAD materials.</p>\n",
+ "<br><br>\n",
+ "\n",
+ "<style>\n",
+ ".button {\n",
+ " background-color: #e7e7e7;\n",
+ " border: 0.5px solid #A4A4A4;\n",
+ " color: black;\n",
+ " padding: 15px 32px;\n",
+ " text-align: center;\n",
+ " text-decoration: none;\n",
+ " display: inline-block;\n",
+ " font-family: Arial;\n",
+ " font-size: 16px;\n",
+ " margin: 4px 2px;\n",
+ " cursor: pointer;\n",
+ "}\n",
+ "\n",
+ " .text-normal-black{\n",
+ " color: #000;font-weight: 200; font-size: 10pt;\n",
+ " font-family: Arial;\n",
+ " }\n",
+ " .div_band_dos{\n",
+ " box-sizing: border-box;\n",
+ " width: 100%;\n",
+ " height: 600px;\n",
+ " font-weight: 100;\n",
+ " font-family: Arial;\n",
+ " padding-left: 20px;\n",
+ " padding-top: 10px;\n",
+ " padding-right: 1em;\n",
+ " margin: 0;\n",
+ " border: 0;\n",
+ " }\n",
+ " .div_band_dos_compare{\n",
+ " box-sizing: border-box;\n",
+ " width: 1600px;\n",
+ " height: 600px;\n",
+ " color: #00AEFF;\n",
+ " font-weight: 100;\n",
+ " font-family: Arial;\n",
+ " padding-left: 20px;\n",
+ " padding-top: 10px;\n",
+ " padding-right: 1em;\n",
+ " margin: 0;\n",
+ " border: 0;\n",
+ " }\n",
+ " .div_band{\n",
+ " font-family: Arial;\n",
+ " font-size: 0.875em;\n",
+ " width: 37%;\n",
+ " height: 80%;\n",
+ " background-color: #fff;\n",
+ " float:left;\n",
+ " }\n",
+ " .div_dos{\n",
+ " font-family: Arial;\n",
+ " font-size: 0.875em;\n",
+ " width: 13%;\n",
+ " height: 80%;\n",
+ " background-color: #fff;\n",
+ " float:left;\n",
+ " }\n",
+ " .div_tools{\n",
+ " color: #20335d;font-weight: 150; font-size: 13pt;\n",
+ " width: 35%;\n",
+ " height: 80%;\n",
+ " background-color: #fff;\n",
+ " margin-left:20pt;\n",
+ " float:left;\n",
+ " font-family: Arial;\n",
+ "\n",
+ " }\n",
+ " .div_checkbox_compare{\n",
+ " color: #888;font-weight: 150; font-size: 12pt;\n",
+ " width: 10%;\n",
+ " height: 80%;\n",
+ " background-color: #fff;\n",
+ " border: solid #fff 1px;\n",
+ " float:right;\n",
+ " font-family: Arial;\n",
+ "\n",
+ " }\n",
+ " .div_overview{\n",
+ " width: 300px;\n",
+ " height: 200px;\n",
+ " background-color: #fff;\n",
+ " margin-left:10px; \n",
+ " margin-top: 20px;\n",
+ " font-family: Arial;\n",
+ "\n",
+ " }\n",
+ " .button_tools {\n",
+ " background-color: #F0F0F0;\n",
+ " border: 0.5px solid #A4A4A4;\n",
+ " color: black;\n",
+ " padding: 10px 15px;\n",
+ " text-align: center;\n",
+ " text-decoration: none;\n",
+ " display: inline-block;\n",
+ " font-size: 16px;\n",
+ " margin: 4px 2px;\n",
+ " cursor: pointer;\n",
+ " font-family: Arial;\n",
+ "\n",
+ " }\n",
+ "\n",
+ " \n",
+ " .g-before-after{position:relative;overflow:hidden;width:500px}.g-before-after img{display:block}.g-before-after .g-img-before{float:left}.g-before-after .g-img-after,.g-before-after.g-vertical .g-img-after{position:absolute;top:0;right:0;left:50%;bottom:0;overflow:hidden}.g-before-after .g-img-after img{position:absolute;right:0;top:0}.g-before-after .g-img-divider{position:absolute;left:50%;top:0;bottom:0;width:0;border-left:1px solid #fff;border-right:1px solid #fff}.g-before-after .g-img-divider>span{position:absolute;top:50%;display:block;background-color:#fff;padding:5px 10px;line-height:1;text-align:center;-webkit-transform:translate(-50%,-50%);-ms-transform:translate(-50%,-50%);transform:translate(-50%,-50%)}.g-before-after.g-vertical .g-img-after{top:50%;left:0}.g-before-after.g-vertical .g-img-after img{position:absolute;right:auto;top:auto;left:0;bottom:0}.g-before-after.g-vertical .g-img-divider{position:absolute;left:0;top:50%;bottom:auto;right:0;height:0;width:100%;border-top:1px solid #fff;border-bottom:1px solid #fff;border-left:0 none;border-right:0 none}.g-before-after.g-vertical .g-img-divider>span{top:50%;left:50%}\n",
+ "</style>\n",
+ "\n",
+ "<script>\n",
+ " //Search for certain keyword: https://labdev-nomad.esc.rzg.mpg.de/fairdi/nomad/migration/api/repo/?quantities=section_k_band_segment\n",
+ " //FjiYy5-ETRCrs5ktzJA55w/bOY0cPkBvvNAY7pZdbginlKXJ2kF\n",
+ " //\"upload_id\"/\"calc_id\"\n",
+ " \n",
+ " //Global variables\n",
+ " var paths_section_k_band_segment = []; \n",
+ " var paths_section_dos = [];\n",
+ " var band_obj_all = [];\n",
+ " var dos_obj_all = [];\n",
+ " var info_obj_all = [];\n",
+ " \n",
+ " var band_paths = [];\n",
+ " var dos_paths = [];\n",
+ " var N_materials = 0; //Number of materials that have both band and DOS in the same calculation \n",
+ " \n",
+ " \n",
+ " function getJSON(url) {\n",
+ " var resp ;\n",
+ " var xmlHttp ;\n",
+ "\n",
+ " resp = '' ;\n",
+ " xmlHttp = new XMLHttpRequest();\n",
+ "\n",
+ " if(xmlHttp != null)\n",
+ " {\n",
+ " xmlHttp.open( \"GET\", url, false );\n",
+ " xmlHttp.send( null );\n",
+ " resp = xmlHttp.responseText;\n",
+ " }\n",
+ "\n",
+ " return resp;\n",
+ " }\n",
+ " function match_band_dos()\n",
+ " {\n",
+ " //TMP for local tests\n",
+ " /*\n",
+ " paths_section_k_band_segment = [\"data/kOJR-AlPSgiNG9AdZoxd4g_9mxjIU0edrPosfsTc4uyDG9H_UXr.json\",\"data/kOJR-AlPSgiNG9AdZoxd4g_lfkGCmWozYENeiGhu5W7dJUqLTkj.json\"];\n",
+ " paths_section_dos = [\"data/kOJR-AlPSgiNG9AdZoxd4g_8tEGnaz0yY91eSyysKZkIUH9qx8J.json\", \"data/kOJR-AlPSgiNG9AdZoxd4g_lxUT3viRZcC_1IsH_KvO5tChAtV1.json\"];\n",
+ " */\n",
+ "\n",
+ " //band_paths = [];\n",
+ " //dos_paths = [];\n",
+ " //N_materials = 0; \n",
+ " \n",
+ " var data_k_band = [];\n",
+ " for(var i_path_k_band = 0; i_path_k_band < paths_section_k_band_segment.length; i_path_k_band ++)\n",
+ " {\n",
+ " var i_data_k_band_json = JSON.parse(getJSON(paths_section_k_band_segment[i_path_k_band]));\n",
+ " var i_data_k_band = {};\n",
+ " i_data_k_band[\"program_name\"] = i_data_k_band_json[\"section_run\"][\"program_name\"];\n",
+ " i_data_k_band[\"k_mesh_points\"] = i_data_k_band_json[\"section_run\"][\"section_method\"][\"k_mesh_points\"];\n",
+ " i_data_k_band[\"simulation_cell\"] = i_data_k_band_json[\"section_run\"][\"section_system\"][0][\"simulation_cell\"];\n",
+ " i_data_k_band[\"atom_positions\"] = i_data_k_band_json[\"section_run\"][\"section_system\"][0][\"atom_positions\"];\n",
+ " i_data_k_band[\"atom_labels\"] = i_data_k_band_json[\"section_run\"][\"section_system\"][0][\"atom_labels\"];\n",
+ " i_data_k_band[\"XC_functional_name\"] = i_data_k_band_json[\"section_run\"][\"section_method\"][\"section_XC_functionals\"][0][\"XC_functional_name\"] + \"-\" + i_data_k_band_json[\"section_run\"][\"section_method\"][\"section_XC_functionals\"][1][\"XC_functional_name\"]\n",
+ " i_data_k_band[\"path\"] = paths_section_k_band_segment[i_path_k_band];\n",
+ " data_k_band.push(i_data_k_band);\n",
+ " }\n",
+ "\n",
+ " var data_dos = [];\n",
+ " for(var i_path_dos = 0; i_path_dos < paths_section_dos.length; i_path_dos ++)\n",
+ " {\n",
+ " var i_data_dos_json = JSON.parse(getJSON(paths_section_dos[i_path_dos]));\n",
+ " var i_data_dos = {};\n",
+ " i_data_dos[\"program_name\"] = i_data_dos_json[\"section_run\"][\"program_name\"];\n",
+ " i_data_dos[\"k_mesh_points\"] = i_data_dos_json[\"section_run\"][\"section_method\"][\"k_mesh_points\"];\n",
+ " i_data_dos[\"simulation_cell\"] = i_data_dos_json[\"section_run\"][\"section_system\"][0][\"simulation_cell\"];\n",
+ " i_data_dos[\"atom_positions\"] = i_data_dos_json[\"section_run\"][\"section_system\"][0][\"atom_positions\"];\n",
+ " i_data_dos[\"atom_labels\"] = i_data_dos_json[\"section_run\"][\"section_system\"][0][\"atom_labels\"];\n",
+ " i_data_dos[\"XC_functional_name\"] = i_data_dos_json[\"section_run\"][\"section_method\"][\"section_XC_functionals\"][0][\"XC_functional_name\"] + \"-\" + i_data_dos_json[\"section_run\"][\"section_method\"][\"section_XC_functionals\"][1][\"XC_functional_name\"]\n",
+ " i_data_dos[\"path\"] = paths_section_dos[i_path_dos];\n",
+ " data_dos.push(i_data_dos); \n",
+ " }\n",
+ "\n",
+ " //Matching: band[i] ~ dos[i] (the same systems are arranged with the same index)\n",
+ " band_paths = [];\n",
+ " dos_paths = [];\n",
+ " N_materials = 0;\n",
+ " for(var i_k_band = 0; i_k_band < data_k_band.length; i_k_band ++)\n",
+ " {\n",
+ " for(var i_dos = 0; i_dos < data_dos.length; i_dos ++)\n",
+ " {\n",
+ " if(data_k_band[i_k_band][\"program_name\"] != data_dos[i_dos][\"program_name\"])\n",
+ " continue; \n",
+ " //if(data_k_band[i_k_band][\"k_mesh_points\"].join() != data_dos[i_dos][\"k_mesh_points\"].join())\n",
+ " // continue;\n",
+ " if(data_k_band[i_k_band][\"simulation_cell\"].join() != data_dos[i_dos][\"simulation_cell\"].join())\n",
+ " continue;\n",
+ " if(data_k_band[i_k_band][\"atom_positions\"].join() != data_dos[i_dos][\"atom_positions\"].join())\n",
+ " continue;\n",
+ " if(data_k_band[i_k_band][\"atom_labels\"].join() != data_dos[i_dos][\"atom_labels\"].join())\n",
+ " continue;\n",
+ " if(data_k_band[i_k_band][\"XC_functional_name\"] != data_dos[i_dos][\"XC_functional_name\"])\n",
+ " continue;\n",
+ " band_paths.push(data_k_band[i_k_band][\"path\"]);\n",
+ " dos_paths.push(data_dos[i_dos][\"path\"]);\n",
+ " N_materials ++;\n",
+ " }\n",
+ " }\n",
+ " //Pass the arrays to python\n",
+ "\n",
+ " var command = \"N_materials = \" + N_materials + \";\"\n",
+ " var kernel = IPython.notebook.kernel;\n",
+ " command += \"band_paths = \" + \"[\\'\" + band_paths.join(\"\\',\\'\") + \"\\'];\";\n",
+ " command += \"dos_paths = \" + \"[\\'\" + dos_paths.join(\"\\',\\'\") + \"\\'];\";\n",
+ " kernel.execute(command);\n",
+ " \n",
+ " \n",
+ " }\n",
+ "\n",
+ " function get_paths_from_search_results(result_json, div_id_search_results,div_head)\n",
+ " {\n",
+ " paths = [];\n",
+ " search_results_content = [div_head, '<table>', '<tr><th>Chemical formula</th><th>Spacegroup</th><th>Code</th><th>XC functional</th><th>Upload ID</th><th>Calculation ID</th><th>URL</th></tr>'];\n",
+ " for(var i_key in result_json)\n",
+ " {\n",
+ " if(i_key == \"results\")\n",
+ " {\n",
+ " for(var system in result_json[i_key])\n",
+ " {\n",
+ " //Get the path to the data files (json)： https://labdev-nomad.esc.rzg.mpg.de/fairdi/nomad/migration/api/archive/upload_id/calc_id \n",
+ " path = \"https://labdev-nomad.esc.rzg.mpg.de/fairdi/nomad/migration/api/archive/\" + result_json[i_key][system][\"upload_id\"] + \"/\" + result_json[i_key][system][\"calc_id\"]\n",
+ " paths.push(path);\n",
+ " \n",
+ " //Show the results in div\n",
+ " // \"formula\" \"spacegroup_symbol\" \"code_name\" \"xc_functional\"\n",
+ " content = '<tr>';\n",
+ " content += '<td>' + result_json[i_key][system][\"formula\"] + '</td>';\n",
+ " content += '<td>' + result_json[i_key][system][\"spacegroup_symbol\"] + '</td>';\n",
+ " content += '<td>' + result_json[i_key][system][\"code_name\"] + '</td>';\n",
+ " content += '<td>' + result_json[i_key][system][\"xc_functional\"] + '</td>';\n",
+ " content += '<td>' + result_json[i_key][system][\"upload_id\"] + '</td>';\n",
+ " content += '<td>' + result_json[i_key][system][\"calc_id\"] + '</td>'; \n",
+ " content += '<td>' + path + '</td>';\n",
+ " content += '</tr>';\n",
+ " search_results_content.push(content);\n",
+ " }\n",
+ " }\n",
+ " }\n",
+ " search_results_content.push('</table>');\n",
+ " document.getElementById(div_id_search_results).innerHTML = search_results_content.join('');\n",
+ " return paths\n",
+ " }\n",
+ " \n",
+ " \n",
+ " \n",
+ "\n",
+ " \n",
+ " \n",
+ " \n",
+ " function submit_search()\n",
+ " {\n",
+ " \n",
+ " var result;\n",
+ " var formula = document.getElementById(\"keyword_chemical_formula\").value;\n",
+ " var query_command_k_band = \"https://labdev-nomad.esc.rzg.mpg.de/fairdi/nomad/migration/api/repo/?formula=\" + formula + \"&quantities=section_k_band_segment\";\n",
+ " var query_command_dos = \"https://labdev-nomad.esc.rzg.mpg.de/fairdi/nomad/migration/api/repo/?formula=\" + formula + \"&quantities=section_dos\";\n",
+ " //result = getJSON(\"https://labdev-nomad.esc.rzg.mpg.de/fairdi/nomad/migration/api/repo/?quantities=section_k_band_segment\");\n",
+ " var result_k_band = getJSON(query_command_k_band);\n",
+ " var result_dos = getJSON(query_command_dos);\n",
+ " var result_json_k_band = JSON.parse(result_k_band);//parse the searching results to json from URL\n",
+ " var result_json_dos = JSON.parse(result_dos);\n",
+ " paths_section_k_band_segment = []; \n",
+ " paths_section_dos = [];\n",
+ " paths_section_k_band_segment = get_paths_from_search_results(result_json_k_band, \"search_results_section_k_band_segment\", \"<br><br><font size=4em>Calculations containing band structures:</font><br>\");\n",
+ " paths_section_dos = get_paths_from_search_results(result_json_dos, \"search_results_section_dos\", \"<br><font size=4em>Calculations containing DOS:</font><br>\");\n",
+ " \n",
+ " var promise = Promise.resolve();\n",
+ " promise\n",
+ " .then(match_band_dos())\n",
+ " .then(Jupyter.notebook.execute_cells(window.findCellIndicesByTag('process_band_dos_data')))\n",
+ " .then(Jupyter.notebook.execute_cells(window.findCellIndicesByTag('show_results_and_plot')));\n",
+ " \n",
+ " //match_band_dos();\n",
+ " \n",
+ " //Jupyter.notebook.execute_cells(window.findCellIndicesByTag('process_band_dos_data')); //Read the json files, and prepare data for plot\n",
+ " //Jupyter.notebook.execute_cells(window.findCellIndicesByTag('show_results_and_plot')); //Prepare for plot\n",
+ " }\n",
+ " function reset_search()\n",
+ " {\n",
+ " Jupyter.notebook.execute_cells(window.findCellIndicesByTag('search_materials'));\n",
+ " Jupyter.notebook.execute_cells(window.findCellIndicesByTag('show_results_and_plot'));\n",
+ " }\n",
+ " \n",
+ " \n",
+ "</script>\n",
+ "<font size=4em>Please input the chemical formula:</font>\n",
+ "<input type=\"text\" id=\"keyword_chemical_formula\" value=\"AlInO3\"> \n",
+ "<button class=\"button\" onclick=\"submit_search()\">Search</button>\n",
+ "<button class=\"button\" onclick=\"reset_search()\">Reset</button>\n",
+ "<br><br><br>\n",
+ "<div id=\"search_results_section_k_band_segment\"></div>\n",
+ "<div id=\"search_results_section_dos\"></div>\n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 29,
+ "metadata": {
+ "tags": [
+ "process_band_dos_data"
+ ]
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "<script>\n",
+ " var band_obj_all = [];\n",
+ " var dos_obj_all = [];\n",
+ " var info_obj_all = [];\n",
+ " //alert(\"process_band_dos_data: \" +band_paths)\n",
+ " //alert(\"process_band_dos_data: \" +info_obj_all)\n",
+ " function get_label_flag(coor_array)\n",
+ " {\n",
+ " var coor = coor_array.sort().join();\n",
+ " if(coor == '0,0.5,0.5')\n",
+ " return \"X\";\n",
+ " if(coor == '0,0,0.5')\n",
+ " return \"M\";\n",
+ " else if(coor == '0.5,0.5,0.5')\n",
+ " return \"L\";\n",
+ " else if(coor == '0.375,0.375,0.75')\n",
+ " return \"K\";\n",
+ " else if(coor == '0.25,0.5,0.75')\n",
+ " return \"W\";\n",
+ " else if(coor == '0,0,0')\n",
+ " return \"\\u0393\";\n",
+ " else if(coor == '0.25,0.625,0.625')\n",
+ " return \"U\";\n",
+ " else\n",
+ " {\n",
+ " //alert(\"k label not found: \" + coor);\n",
+ " return \"?\";\n",
+ " }\n",
+ " }\n",
+ "\n",
+ "\n",
+ " //============Process the band structure data============\n",
+ " function get_band_obj(band_path, dos_fermi_energy)\n",
+ " {\n",
+ " var band_data = JSON.parse(getJSON(band_path));\n",
+ "\n",
+ " //---------Read section_k_band_segment------------\n",
+ " var section_k_band_segment = band_data['section_run']['section_single_configuration_calculation']['section_k_band'][0]['section_k_band_segment']\n",
+ "\n",
+ " //--------Get the number of k band segments-------------\n",
+ " var N_k_band_segments = section_k_band_segment.length;\n",
+ "\n",
+ "\n",
+ " //----------Get the total number of k points in all segments---------\n",
+ " var N_k_points_all = 0;\n",
+ " for(var i = 0; i < N_k_band_segments; i++)\n",
+ " N_k_points_all = N_k_points_all + section_k_band_segment[i]['band_k_points'].length;\n",
+ "\n",
+ "\n",
+ " //--------Get the x axis for the band structure figure: the coordinates of k points in 1D\n",
+ " // store in k_coor_1D[N_k_points_total]-----------------\n",
+ "\n",
+ " var band_distance_segments = [];\n",
+ " for(i = 0; i < N_k_band_segments; i++)\n",
+ " {\n",
+ " var x1, x2, y1, y2, z1, z2;\n",
+ " [[x1, y1, z1],[x2, y2, z2]]= section_k_band_segment[i]['band_segm_start_end']; //\"band_segm_start_end\": [[0.5, 0.0, 0.5],[0.5, 0.25, 0.75]],\n",
+ " band_distance_segments.push(Math.pow((x1-x2), 2) + Math.pow((y1-y2), 2) + Math.pow((z1-z2), 2));\n",
+ " }\n",
+ "\n",
+ "\n",
+ " var band_distance_total = band_distance_segments.reduce((x,y) => x+y); //sum of band_distance_segments\n",
+ "\n",
+ " var average_N_k_points_per_inverse_distance = N_k_points_all / band_distance_total;\n",
+ "\n",
+ " //Prepare the parameters to rescale the k coordinates into [0,1]\n",
+ " var step_k_point = 1.0 / N_k_points_all;\n",
+ " var step_k_point = (1.0 + step_k_point) / N_k_points_all;\n",
+ "\n",
+ " var k_coor_1D = [];\n",
+ " for(var i_k_points = 0; i_k_points < N_k_points_all; i_k_points ++)\n",
+ " {\n",
+ " k_coor_1D.push(step_k_point * i_k_points)\n",
+ " }\n",
+ "\n",
+ "\n",
+ " //--------Get the eigenvalues of each band trajectory--------------\n",
+ " /*\n",
+ " N_k_points_per_segment = len(section_k_band_segment[0]['band_energies'][0]) #suppose the numebr of k points in all the segments are the same\n",
+ " N_bands = len(section_k_band_segment[0]['band_energies'][0][0])\n",
+ " band_energies_all = np.zeros((N_bands, N_k_points_all)) #store the eigenvalues\n",
+ " N_k_points_all = 0\n",
+ " for i_segments in range(N_k_band_segments):\n",
+ " band_energies = section_k_band_segment[i_segments]['band_energies']\n",
+ " N_spin_channel = len(band_energies) #Number of the spin channel --FIXME: no spin polarized\n",
+ " N_k_points_per_segment = len(band_energies[0])\n",
+ " for i_k_points in range(N_k_points_per_segment):\n",
+ " for i_bands in range(N_bands):\n",
+ " band_energies_all[i_bands][N_k_points_all] = band_energies[0][i_k_points][i_bands] / (1.60217656535 * pow(10, -19))\n",
+ " N_k_points_all = N_k_points_all + 1\n",
+ " */\n",
+ " //var N_k_points_per_segment = section_k_band_segment[0]['band_energies'][0].length; //suppose the numebr of k points in all the segments are the same\n",
+ " var N_bands = section_k_band_segment[0]['band_energies'][0][0].length;\n",
+ " var band_energies_all = new Array(N_bands);\n",
+ " for(var i_bands = 0; i_bands < N_bands; i_bands ++)\n",
+ " band_energies_all[i_bands] = new Array(N_k_points_all);// new Array(N_bands, N_k_points_all); //store the eigenvalues\n",
+ "\n",
+ " var i_k_points_all = 0;\n",
+ "\n",
+ " for(var i_segments = 0; i_segments < N_k_band_segments; i_segments ++)\n",
+ " {\n",
+ " var band_energies = section_k_band_segment[i_segments]['band_energies'];\n",
+ " var N_spin_channel = band_energies.length; //Number of the spin channel --FIXME: no spin polarized\n",
+ " var N_k_points_per_segment = band_energies[0].length;\n",
+ " for(var i_k_points = 0; i_k_points < N_k_points_per_segment; i_k_points ++)\n",
+ " {\n",
+ " for(var i_bands = 0; i_bands < N_bands; i_bands ++)\n",
+ " {\n",
+ " band_energies_all[i_bands][i_k_points_all] = band_energies[0][i_k_points][i_bands] / (1.60217656535 * Math.pow(10, -19)) - dos_fermi_energy;\n",
+ " }\n",
+ " i_k_points_all = i_k_points_all + 1 ;\n",
+ "\n",
+ " }\n",
+ " }\n",
+ "\n",
+ "\n",
+ "\n",
+ " var N_labels = 0\n",
+ " for(var i_segments = 0; i_segments < N_k_band_segments; i_segments ++)\n",
+ " {\n",
+ " for(var j = 0; j < 2; j++)\n",
+ " //labels_tmp = section_k_band_segment[i_segments]['band_segm_start_end'][j];\n",
+ " N_labels = N_labels + 1\n",
+ " }\n",
+ " var label_flag = [];//[\"\" for i in range(N_labels)] //stores the flags of the labels (X, W, G, etc)\n",
+ "\n",
+ "\n",
+ " var i_label = 0;\n",
+ " var label_flag_last_final = \"\";\n",
+ " var label_flag_current_initial = \"\";\n",
+ " for(var i_segments = 0; i_segments < N_k_band_segments; i_segments ++)\n",
+ " {\n",
+ " var labels_coor_0 = section_k_band_segment[i_segments]['band_segm_start_end'][0].sort();\n",
+ " var labels_coor_1 = section_k_band_segment[i_segments]['band_segm_start_end'][1].sort();\n",
+ "\n",
+ " var label_flag_0 = get_label_flag(labels_coor_0);\n",
+ " var label_flag_1 = get_label_flag(labels_coor_1);\n",
+ "\n",
+ " var label_flag_current_initial = label_flag_0;\n",
+ " if(label_flag_last_final == \"\")\n",
+ " label_flag_last_final = label_flag_0;\n",
+ "\n",
+ " if(label_flag_last_final == label_flag_current_initial)\n",
+ " label_flag[i_label] = label_flag_current_initial;\n",
+ " else\n",
+ " label_flag[i_label] = label_flag_last_final + '|' + label_flag_current_initial;\n",
+ " label_flag_last_final = label_flag_1\n",
+ "\n",
+ "\n",
+ " i_label = i_label + 1;\n",
+ " if(i_segments == N_k_band_segments - 1)\n",
+ " {\n",
+ " label_flag[i_label] = label_flag_1;\n",
+ " i_label = i_label + 1;\n",
+ " }\n",
+ " }\n",
+ " N_labels = i_label;\n",
+ "\n",
+ " //------------Get the coordinates for the labels------------\n",
+ " //label_coor_abs = np.zeros((N_labels)) #stores the absolute coordinates of the labels\n",
+ " var label_coor_relative = [];//np.zeros((N_labels))\n",
+ " for(i_label = 0; i_label < N_labels; i_label ++)\n",
+ " {\n",
+ " //Here the evenly-distributed relative coordinates is used, because the coordinates of the labels could be too nerrow when using there absolute coordinates\n",
+ " //x = labels_coor_0[0]\n",
+ " //y = labels_coor_0[1]\n",
+ " //z = labels_coor_0[2]\n",
+ " //label_coor_abs[i_label] = np.sqrt(x*x+y*y+z*z)\n",
+ " label_coor_relative.push(step_k_point * N_k_points_per_segment * i_label / (1 + 1.0 / N_k_points_all));\n",
+ " }\n",
+ " //----Store the label-----------\n",
+ " var label_obj = [];//[['' for i in range(2)] for j in range(N_labels)]\n",
+ " for(i_label = 0; i_label < N_labels; i_label ++)\n",
+ " {\n",
+ " label_obj.push([label_coor_relative[i_label], label_flag[i_label]]);\n",
+ " }\n",
+ "\n",
+ "\n",
+ " //-------Get VBM, CBM----------------\n",
+ "\n",
+ " var HOMO = -1000;\n",
+ " var LUMO = 1000;\n",
+ " var coor_k_point_HOMO = []; //the coordinate of k point that stores HOMO\n",
+ " var coor_k_point_LUMO = [];//np.zeros((3)) #the coordinate of k point that stores LUMO\n",
+ " //band_gap_direct = 0.0\n",
+ " var band_gap_indirect = 0.0;\n",
+ "\n",
+ "\n",
+ " //band_energy_max = np.amax(band_energies[0])/ (1.60217656535* pow(10,-19))\n",
+ " //band_energy_min = np.amin(band_energies[0])/ (1.60217656535* pow(10,-19))\n",
+ " var band_energy_max = 10;\n",
+ " var band_energy_min = -10;\n",
+ " //N_band_energy_index = 10000\n",
+ " //band_energy_step = (band_energy_max - band_energy_min) / N_band_energy_index\n",
+ " //N_allowed_states = np.zeros(N_band_energy_index + 1)\n",
+ " //i_index_fermi = math.floor((0 - band_energy_min) / band_energy_step) #the index that stores states at the Fermi level\n",
+ "\n",
+ "\n",
+ " for(var i_bands = 0; i_bands < N_bands; i_bands ++)\n",
+ " {\n",
+ " for(var i_k_points_all = 0; i_k_points_all< N_k_points_all; i_k_points_all ++)\n",
+ " {\n",
+ " //i_band_index = math.floor((band_energies_all[i_bands][i_k_points_all] - band_energy_min) / band_energy_step)\n",
+ " //N_allowed_states[index_band_energy] = N_allowed_states[index_band_energy] + 1\n",
+ " var band_energy = band_energies_all[i_bands][i_k_points_all];\n",
+ " if(band_energy > 0)\n",
+ " {\n",
+ " if(band_energy < LUMO)\n",
+ " LUMO = band_energy;\n",
+ " }\n",
+ " else\n",
+ " {\n",
+ " if(band_energy > HOMO)\n",
+ " HOMO = band_energy;\n",
+ " }\n",
+ "\n",
+ " }\n",
+ " }\n",
+ "\n",
+ "\n",
+ " //#for i_band_index in range(i_index_fermi, N_band_energy_index): #get LUMO\n",
+ " // if(N_allowed_states[i_band_index] > 0):\n",
+ " // LUMO = band_energy_min + band_energy_step * i_band_index\n",
+ " //print('HOMO, LUMO: ',HOMO, LUMO)\n",
+ " band_gap_indirect = Math.abs(LUMO - HOMO);\n",
+ "\n",
+ " if(band_gap_indirect < 0.5) //VBM and CBM has to be found in another way for metals/charged system:\n",
+ " {\n",
+ " HOMO = -1000.0;\n",
+ " LUMO = 1000.0;\n",
+ " band_energy_max = 10.0;\n",
+ " band_energy_min = 0.0;\n",
+ " var N_band_energy_index = 10000;\n",
+ " var band_energy_step = (band_energy_max - band_energy_min) / N_band_energy_index;\n",
+ " var N_allowed_states = [];\n",
+ " for(var i_state = 0; i_state < N_band_energy_index+1; i_state++)\n",
+ " N_allowed_states.push(0);\n",
+ "\n",
+ "\n",
+ " //get the DOS and store in N_allowed_states[]\n",
+ " for(var i_k_points_all = 0; i_k_points_all < N_k_points_all; i_k_points_all ++)\n",
+ " {\n",
+ " for(var i_bands = 0; i_bands < N_bands; i_bands ++)\n",
+ " {\n",
+ " var band_energy = band_energies_all[i_bands][i_k_points_all];\n",
+ " if((band_energy_min < band_energy)&&(band_energy < band_energy_max))\n",
+ " {\n",
+ " var i_band_index = Math.floor((band_energy - band_energy_min) / band_energy_step);\n",
+ " N_allowed_states[i_band_index] = N_allowed_states[i_band_index] + 1;\n",
+ " }\n",
+ " }\n",
+ " }\n",
+ "\n",
+ "\n",
+ " var if_gapped = 0;\n",
+ " for(var i_band_index = 0; i_band_index < N_band_energy_index; i_band_index ++)//go through the energy levels from the bottom\n",
+ " {\n",
+ " var band_energy = band_energy_min + band_energy_step * i_band_index\n",
+ " if(N_allowed_states[i_band_index] == 0)\n",
+ " if_gapped = if_gapped + 1;\n",
+ " if((band_energy > band_energy_max - 0.5) && (if_gapped == 0))\n",
+ " {\n",
+ " //alert(\"No gap found in this system. It seems to be a metal.\");\n",
+ " HOMO = 1000;\n",
+ " LUMO = 1000;\n",
+ " break;\n",
+ " }\n",
+ " //print(\"At \", band_energy,\": # allowed states = \", N_allowed_states[i_band_index],\" if_gapped = \", if_gapped)\n",
+ "\n",
+ " if(N_allowed_states[i_band_index] > 0)\n",
+ " {\n",
+ " if(if_gapped * band_energy_step > 0.3 )//above VBM-CBM gap: LUMO\n",
+ " {\n",
+ " if(band_energy < LUMO)\n",
+ " {\n",
+ " //print(\"LUMO got!\")\n",
+ " LUMO = band_energy;\n",
+ " break; //break before touching another gap that is above the band gap\n",
+ " }\n",
+ " }\n",
+ "\n",
+ " if(if_gapped * band_energy_step < 0.3) //below VBM-CBM gap: HOMO\n",
+ " {\n",
+ " if(band_energy > HOMO)\n",
+ " {\n",
+ " //print(\"HOMO got!\")\n",
+ " HOMO = band_energy;\n",
+ " }\n",
+ " } \n",
+ " if_gapped = 0;\n",
+ " }\n",
+ " }\n",
+ " //alert('HOMO, LUMO for metal/charged system: '+ HOMO +\",\"+LUMO)\n",
+ "\n",
+ " }\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ " //Find the position of HOMO, LUMO\n",
+ " var coor_k_point_HOMO = 0, coor_k_point_LUMO = 0;\n",
+ " for(var i_k_points = 0; i_k_points < N_k_points_all; i_k_points++)\n",
+ " {\n",
+ " for(var i_bands = 0; i_bands < N_bands; i_bands ++)\n",
+ " {\n",
+ " if(Math.abs(band_energies_all[i_bands][i_k_points] - HOMO) < 0.001)\n",
+ " coor_k_point_HOMO = k_coor_1D[i_k_points];\n",
+ " if(Math.abs(band_energies_all[i_bands][i_k_points] - LUMO) < 0.001)\n",
+ " coor_k_point_LUMO = k_coor_1D[i_k_points]; \n",
+ " }\n",
+ " }\n",
+ "\n",
+ " //alert(coor_k_point_HOMO +\",\" + coor_k_point_LUMO);\n",
+ "\n",
+ "\n",
+ " //Store the band data to band_obj\n",
+ "\n",
+ " var band_obj = {};\n",
+ " band_obj[\"band_x_axis\"] = k_coor_1D;\n",
+ " band_obj[\"band_y_axis\"] = band_energies_all\n",
+ " band_obj[\"labels\"] = label_obj;\n",
+ " band_obj[\"HOMO_energy\"] = HOMO;\n",
+ " band_obj[\"HOMO_coor\"] = coor_k_point_HOMO;\n",
+ " band_obj[\"LUMO_energy\"] = LUMO;\n",
+ " band_obj[\"LUMO_coor\"] = coor_k_point_LUMO;\n",
+ " band_obj[\"average_N_k_points_per_inverse_distance\"] = average_N_k_points_per_inverse_distance;\n",
+ "\n",
+ "\n",
+ " return band_obj\n",
+ "\n",
+ " }\n",
+ "\n",
+ "\n",
+ " function get_dos_obj(dos_path)\n",
+ " {\n",
+ "\n",
+ " var dos_data = JSON.parse(getJSON(dos_path));\n",
+ "\n",
+ " var N_dos_values = dos_data['section_run']['section_single_configuration_calculation']['section_dos'][0]['dos_energies'].length;\n",
+ "\n",
+ " //in new parser, it seems that the spin channel of 'dos_energies' disappears: Shape: [ number_of_dos_values ]\n",
+ "\n",
+ " //dos_energies = new Array(N_dos_values).fill(0.0);\n",
+ " //dos_energies_tmp = new Array(N_dos_values).fill(0.0) #tmp array for unit convertion\n",
+ " //dos_values = new Array(N_dos_values).fill(0.0)\n",
+ "\n",
+ " var dos_energies = dos_data['section_run']['section_single_configuration_calculation']['section_dos'][0]['dos_energies'];\n",
+ " var dos_values = dos_data['section_run']['section_single_configuration_calculation']['section_dos'][0]['dos_integrated_values'];//[0]\n",
+ "\n",
+ " //To do: check if every section_dos has 'dos_fermi_energy'\n",
+ " var dos_fermi_energy = dos_data['section_run']['section_single_configuration_calculation']['section_dos'][0]['dos_fermi_energy'];\n",
+ " dos_fermi_energy = dos_fermi_energy / (1.60217656535 * Math.pow(10,-19));\n",
+ " \n",
+ " for(var i = 0; i < N_dos_values; i++)\n",
+ " {\n",
+ " dos_energies[i] = dos_energies[i] / (1.60217656535 * Math.pow(10,-19)) - dos_fermi_energy;\n",
+ " }\n",
+ " \n",
+ " dos_obj = {}\n",
+ " dos_obj[\"dos_x_axis\"] = dos_energies;\n",
+ " dos_obj[\"dos_y_axis\"] = dos_values;\n",
+ " dos_obj[\"dos_fermi_energy\"] = dos_fermi_energy;\n",
+ " return dos_obj\n",
+ " }\n",
+ " function get_info_obj(band_path)\n",
+ " {\n",
+ "\n",
+ " var band_data = JSON.parse(getJSON(band_path));\n",
+ " var info_obj = {};\n",
+ " //---------Read the information of the calculation--------\n",
+ " info_obj[\"program_name\"] = band_data[\"section_run\"][\"program_name\"];\n",
+ " info_obj[\"program_basis_set_type\"] = band_data[\"section_run\"][\"program_basis_set_type\"];\n",
+ " info_obj[\"atom_labels\"] = band_data[\"section_run\"][\"section_system\"][0][\"atom_labels\"];\n",
+ " info_obj[\"XC_functional_name\"] = band_data[\"section_run\"][\"section_method\"][\"section_XC_functionals\"][0][\"XC_functional_name\"] + \" + \"+ band_data[\"section_run\"][\"section_method\"][\"section_XC_functionals\"][1][\"XC_functional_name\"];\n",
+ "\n",
+ " //----------Get the space group information----------\n",
+ " /*\n",
+ " [space_group_symbol, lattice_constant] = get_space_group(band_data);\n",
+ " info_obj[\"space_group_symbol\"] = np.array(space_group_symbol).tolist();\n",
+ " info_obj[\"lattice_constant\"] = np.array(lattice_constant).tolist();\n",
+ " */\n",
+ "\n",
+ " return info_obj\n",
+ " }\n",
+ " function process_band_dos_data()\n",
+ " {\n",
+ " info_all = [];\n",
+ " band_obj_all = [];\n",
+ " dos_obj_all = [];\n",
+ "\n",
+ " for(var i = 0; i < N_materials; i++)\n",
+ " {\n",
+ " var band_path = band_paths[i];\n",
+ " var dos_path = dos_paths[i];\n",
+ "\n",
+ "\n",
+ " var dos_obj = get_dos_obj(dos_path);\n",
+ " var dos_fermi_energy = dos_obj[\"dos_fermi_energy\"];\n",
+ " band_obj = get_band_obj(band_path, dos_fermi_energy);\n",
+ " var info_obj = get_info_obj(band_path);\n",
+ "\n",
+ " band_obj_all.push(band_obj);\n",
+ " dos_obj_all.push(dos_obj);\n",
+ " info_obj_all.push(info_obj);\n",
+ " }\n",
+ " }\n",
+ " process_band_dos_data();\n",
+ " //alert(\"process_band_dos_data: info_obj_all: \"+JSON.stringify(info_obj_all));\n",
+ "</script>\n"
+ ],
+ "text/plain": [
+ "<IPython.core.display.HTML object>"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "%%HTML\n",
+ "<script>\n",
+ " var band_obj_all = [];\n",
+ " var dos_obj_all = [];\n",
+ " var info_obj_all = [];\n",
+ " //alert(\"process_band_dos_data: \" +band_paths)\n",
+ " //alert(\"process_band_dos_data: \" +info_obj_all)\n",
+ " function get_label_flag(coor_array)\n",
+ " {\n",
+ " var coor = coor_array.sort().join();\n",
+ " if(coor == '0,0.5,0.5')\n",
+ " return \"X\";\n",
+ " if(coor == '0,0,0.5')\n",
+ " return \"M\";\n",
+ " else if(coor == '0.5,0.5,0.5')\n",
+ " return \"L\";\n",
+ " else if(coor == '0.375,0.375,0.75')\n",
+ " return \"K\";\n",
+ " else if(coor == '0.25,0.5,0.75')\n",
+ " return \"W\";\n",
+ " else if(coor == '0,0,0')\n",
+ " return \"\\u0393\";\n",
+ " else if(coor == '0.25,0.625,0.625')\n",
+ " return \"U\";\n",
+ " else\n",
+ " {\n",
+ " //alert(\"k label not found: \" + coor);\n",
+ " return \"?\";\n",
+ " }\n",
+ " }\n",
+ "\n",
+ "\n",
+ " //============Process the band structure data============\n",
+ " function get_band_obj(band_path, dos_fermi_energy)\n",
+ " {\n",
+ " var band_data = JSON.parse(getJSON(band_path));\n",
+ "\n",
+ " //---------Read section_k_band_segment------------\n",
+ " var section_k_band_segment = band_data['section_run']['section_single_configuration_calculation']['section_k_band'][0]['section_k_band_segment']\n",
+ "\n",
+ " //--------Get the number of k band segments-------------\n",
+ " var N_k_band_segments = section_k_band_segment.length;\n",
+ "\n",
+ "\n",
+ " //----------Get the total number of k points in all segments---------\n",
+ " var N_k_points_all = 0;\n",
+ " for(var i = 0; i < N_k_band_segments; i++)\n",
+ " N_k_points_all = N_k_points_all + section_k_band_segment[i]['band_k_points'].length;\n",
+ "\n",
+ "\n",
+ " //--------Get the x axis for the band structure figure: the coordinates of k points in 1D\n",
+ " // store in k_coor_1D[N_k_points_total]-----------------\n",
+ "\n",
+ " var band_distance_segments = [];\n",
+ " for(i = 0; i < N_k_band_segments; i++)\n",
+ " {\n",
+ " var x1, x2, y1, y2, z1, z2;\n",
+ " [[x1, y1, z1],[x2, y2, z2]]= section_k_band_segment[i]['band_segm_start_end']; //\"band_segm_start_end\": [[0.5, 0.0, 0.5],[0.5, 0.25, 0.75]],\n",
+ " band_distance_segments.push(Math.pow((x1-x2), 2) + Math.pow((y1-y2), 2) + Math.pow((z1-z2), 2));\n",
+ " }\n",
+ "\n",
+ "\n",
+ " var band_distance_total = band_distance_segments.reduce((x,y) => x+y); //sum of band_distance_segments\n",
+ "\n",
+ " var average_N_k_points_per_inverse_distance = N_k_points_all / band_distance_total;\n",
+ "\n",
+ " //Prepare the parameters to rescale the k coordinates into [0,1]\n",
+ " var step_k_point = 1.0 / N_k_points_all;\n",
+ " var step_k_point = (1.0 + step_k_point) / N_k_points_all;\n",
+ "\n",
+ " var k_coor_1D = [];\n",
+ " for(var i_k_points = 0; i_k_points < N_k_points_all; i_k_points ++)\n",
+ " {\n",
+ " k_coor_1D.push(step_k_point * i_k_points)\n",
+ " }\n",
+ "\n",
+ "\n",
+ " //--------Get the eigenvalues of each band trajectory--------------\n",
+ " /*\n",
+ " N_k_points_per_segment = len(section_k_band_segment[0]['band_energies'][0]) #suppose the numebr of k points in all the segments are the same\n",
+ " N_bands = len(section_k_band_segment[0]['band_energies'][0][0])\n",
+ " band_energies_all = np.zeros((N_bands, N_k_points_all)) #store the eigenvalues\n",
+ " N_k_points_all = 0\n",
+ " for i_segments in range(N_k_band_segments):\n",
+ " band_energies = section_k_band_segment[i_segments]['band_energies']\n",
+ " N_spin_channel = len(band_energies) #Number of the spin channel --FIXME: no spin polarized\n",
+ " N_k_points_per_segment = len(band_energies[0])\n",
+ " for i_k_points in range(N_k_points_per_segment):\n",
+ " for i_bands in range(N_bands):\n",
+ " band_energies_all[i_bands][N_k_points_all] = band_energies[0][i_k_points][i_bands] / (1.60217656535 * pow(10, -19))\n",
+ " N_k_points_all = N_k_points_all + 1\n",
+ " */\n",
+ " //var N_k_points_per_segment = section_k_band_segment[0]['band_energies'][0].length; //suppose the numebr of k points in all the segments are the same\n",
+ " var N_bands = section_k_band_segment[0]['band_energies'][0][0].length;\n",
+ " var band_energies_all = new Array(N_bands);\n",
+ " for(var i_bands = 0; i_bands < N_bands; i_bands ++)\n",
+ " band_energies_all[i_bands] = new Array(N_k_points_all);// new Array(N_bands, N_k_points_all); //store the eigenvalues\n",
+ "\n",
+ " var i_k_points_all = 0;\n",
+ "\n",
+ " for(var i_segments = 0; i_segments < N_k_band_segments; i_segments ++)\n",
+ " {\n",
+ " var band_energies = section_k_band_segment[i_segments]['band_energies'];\n",
+ " var N_spin_channel = band_energies.length; //Number of the spin channel --FIXME: no spin polarized\n",
+ " var N_k_points_per_segment = band_energies[0].length;\n",
+ " for(var i_k_points = 0; i_k_points < N_k_points_per_segment; i_k_points ++)\n",
+ " {\n",
+ " for(var i_bands = 0; i_bands < N_bands; i_bands ++)\n",
+ " {\n",
+ " band_energies_all[i_bands][i_k_points_all] = band_energies[0][i_k_points][i_bands] / (1.60217656535 * Math.pow(10, -19)) - dos_fermi_energy;\n",
+ " }\n",
+ " i_k_points_all = i_k_points_all + 1 ;\n",
+ "\n",
+ " }\n",
+ " }\n",
+ "\n",
+ "\n",
+ "\n",
+ " var N_labels = 0\n",
+ " for(var i_segments = 0; i_segments < N_k_band_segments; i_segments ++)\n",
+ " {\n",
+ " for(var j = 0; j < 2; j++)\n",
+ " //labels_tmp = section_k_band_segment[i_segments]['band_segm_start_end'][j];\n",
+ " N_labels = N_labels + 1\n",
+ " }\n",
+ " var label_flag = [];//[\"\" for i in range(N_labels)] //stores the flags of the labels (X, W, G, etc)\n",
+ "\n",
+ "\n",
+ " var i_label = 0;\n",
+ " var label_flag_last_final = \"\";\n",
+ " var label_flag_current_initial = \"\";\n",
+ " for(var i_segments = 0; i_segments < N_k_band_segments; i_segments ++)\n",
+ " {\n",
+ " var labels_coor_0 = section_k_band_segment[i_segments]['band_segm_start_end'][0].sort();\n",
+ " var labels_coor_1 = section_k_band_segment[i_segments]['band_segm_start_end'][1].sort();\n",
+ "\n",
+ " var label_flag_0 = get_label_flag(labels_coor_0);\n",
+ " var label_flag_1 = get_label_flag(labels_coor_1);\n",
+ "\n",
+ " var label_flag_current_initial = label_flag_0;\n",
+ " if(label_flag_last_final == \"\")\n",
+ " label_flag_last_final = label_flag_0;\n",
+ "\n",
+ " if(label_flag_last_final == label_flag_current_initial)\n",
+ " label_flag[i_label] = label_flag_current_initial;\n",
+ " else\n",
+ " label_flag[i_label] = label_flag_last_final + '|' + label_flag_current_initial;\n",
+ " label_flag_last_final = label_flag_1\n",
+ "\n",
+ "\n",
+ " i_label = i_label + 1;\n",
+ " if(i_segments == N_k_band_segments - 1)\n",
+ " {\n",
+ " label_flag[i_label] = label_flag_1;\n",
+ " i_label = i_label + 1;\n",
+ " }\n",
+ " }\n",
+ " N_labels = i_label;\n",
+ "\n",
+ " //------------Get the coordinates for the labels------------\n",
+ " //label_coor_abs = np.zeros((N_labels)) #stores the absolute coordinates of the labels\n",
+ " var label_coor_relative = [];//np.zeros((N_labels))\n",
+ " for(i_label = 0; i_label < N_labels; i_label ++)\n",
+ " {\n",
+ " //Here the evenly-distributed relative coordinates is used, because the coordinates of the labels could be too nerrow when using there absolute coordinates\n",
+ " //x = labels_coor_0[0]\n",
+ " //y = labels_coor_0[1]\n",
+ " //z = labels_coor_0[2]\n",
+ " //label_coor_abs[i_label] = np.sqrt(x*x+y*y+z*z)\n",
+ " label_coor_relative.push(step_k_point * N_k_points_per_segment * i_label / (1 + 1.0 / N_k_points_all));\n",
+ " }\n",
+ " //----Store the label-----------\n",
+ " var label_obj = [];//[['' for i in range(2)] for j in range(N_labels)]\n",
+ " for(i_label = 0; i_label < N_labels; i_label ++)\n",
+ " {\n",
+ " label_obj.push([label_coor_relative[i_label], label_flag[i_label]]);\n",
+ " }\n",
+ "\n",
+ "\n",
+ " //-------Get VBM, CBM----------------\n",
+ "\n",
+ " var HOMO = -1000;\n",
+ " var LUMO = 1000;\n",
+ " var coor_k_point_HOMO = []; //the coordinate of k point that stores HOMO\n",
+ " var coor_k_point_LUMO = [];//np.zeros((3)) #the coordinate of k point that stores LUMO\n",
+ " //band_gap_direct = 0.0\n",
+ " var band_gap_indirect = 0.0;\n",
+ "\n",
+ "\n",
+ " //band_energy_max = np.amax(band_energies[0])/ (1.60217656535* pow(10,-19))\n",
+ " //band_energy_min = np.amin(band_energies[0])/ (1.60217656535* pow(10,-19))\n",
+ " var band_energy_max = 10;\n",
+ " var band_energy_min = -10;\n",
+ " //N_band_energy_index = 10000\n",
+ " //band_energy_step = (band_energy_max - band_energy_min) / N_band_energy_index\n",
+ " //N_allowed_states = np.zeros(N_band_energy_index + 1)\n",
+ " //i_index_fermi = math.floor((0 - band_energy_min) / band_energy_step) #the index that stores states at the Fermi level\n",
+ "\n",
+ "\n",
+ " for(var i_bands = 0; i_bands < N_bands; i_bands ++)\n",
+ " {\n",
+ " for(var i_k_points_all = 0; i_k_points_all< N_k_points_all; i_k_points_all ++)\n",
+ " {\n",
+ " //i_band_index = math.floor((band_energies_all[i_bands][i_k_points_all] - band_energy_min) / band_energy_step)\n",
+ " //N_allowed_states[index_band_energy] = N_allowed_states[index_band_energy] + 1\n",
+ " var band_energy = band_energies_all[i_bands][i_k_points_all];\n",
+ " if(band_energy > 0)\n",
+ " {\n",
+ " if(band_energy < LUMO)\n",
+ " LUMO = band_energy;\n",
+ " }\n",
+ " else\n",
+ " {\n",
+ " if(band_energy > HOMO)\n",
+ " HOMO = band_energy;\n",
+ " }\n",
+ "\n",
+ " }\n",
+ " }\n",
+ "\n",
+ "\n",
+ " //#for i_band_index in range(i_index_fermi, N_band_energy_index): #get LUMO\n",
+ " // if(N_allowed_states[i_band_index] > 0):\n",
+ " // LUMO = band_energy_min + band_energy_step * i_band_index\n",
+ " //print('HOMO, LUMO: ',HOMO, LUMO)\n",
+ " band_gap_indirect = Math.abs(LUMO - HOMO);\n",
+ "\n",
+ " if(band_gap_indirect < 0.5) //VBM and CBM has to be found in another way for metals/charged system:\n",
+ " {\n",
+ " HOMO = -1000.0;\n",
+ " LUMO = 1000.0;\n",
+ " band_energy_max = 10.0;\n",
+ " band_energy_min = 0.0;\n",
+ " var N_band_energy_index = 10000;\n",
+ " var band_energy_step = (band_energy_max - band_energy_min) / N_band_energy_index;\n",
+ " var N_allowed_states = [];\n",
+ " for(var i_state = 0; i_state < N_band_energy_index+1; i_state++)\n",
+ " N_allowed_states.push(0);\n",
+ "\n",
+ "\n",
+ " //get the DOS and store in N_allowed_states[]\n",
+ " for(var i_k_points_all = 0; i_k_points_all < N_k_points_all; i_k_points_all ++)\n",
+ " {\n",
+ " for(var i_bands = 0; i_bands < N_bands; i_bands ++)\n",
+ " {\n",
+ " var band_energy = band_energies_all[i_bands][i_k_points_all];\n",
+ " if((band_energy_min < band_energy)&&(band_energy < band_energy_max))\n",
+ " {\n",
+ " var i_band_index = Math.floor((band_energy - band_energy_min) / band_energy_step);\n",
+ " N_allowed_states[i_band_index] = N_allowed_states[i_band_index] + 1;\n",
+ " }\n",
+ " }\n",
+ " }\n",
+ "\n",
+ "\n",
+ " var if_gapped = 0;\n",
+ " for(var i_band_index = 0; i_band_index < N_band_energy_index; i_band_index ++)//go through the energy levels from the bottom\n",
+ " {\n",
+ " var band_energy = band_energy_min + band_energy_step * i_band_index\n",
+ " if(N_allowed_states[i_band_index] == 0)\n",
+ " if_gapped = if_gapped + 1;\n",
+ " if((band_energy > band_energy_max - 0.5) && (if_gapped == 0))\n",
+ " {\n",
+ " //alert(\"No gap found in this system. It seems to be a metal.\");\n",
+ " HOMO = 1000;\n",
+ " LUMO = 1000;\n",
+ " break;\n",
+ " }\n",
+ " //print(\"At \", band_energy,\": # allowed states = \", N_allowed_states[i_band_index],\" if_gapped = \", if_gapped)\n",
+ "\n",
+ " if(N_allowed_states[i_band_index] > 0)\n",
+ " {\n",
+ " if(if_gapped * band_energy_step > 0.3 )//above VBM-CBM gap: LUMO\n",
+ " {\n",
+ " if(band_energy < LUMO)\n",
+ " {\n",
+ " //print(\"LUMO got!\")\n",
+ " LUMO = band_energy;\n",
+ " break; //break before touching another gap that is above the band gap\n",
+ " }\n",
+ " }\n",
+ "\n",
+ " if(if_gapped * band_energy_step < 0.3) //below VBM-CBM gap: HOMO\n",
+ " {\n",
+ " if(band_energy > HOMO)\n",
+ " {\n",
+ " //print(\"HOMO got!\")\n",
+ " HOMO = band_energy;\n",
+ " }\n",
+ " } \n",
+ " if_gapped = 0;\n",
+ " }\n",
+ " }\n",
+ " //alert('HOMO, LUMO for metal/charged system: '+ HOMO +\",\"+LUMO)\n",
+ "\n",
+ " }\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ " //Find the position of HOMO, LUMO\n",
+ " var coor_k_point_HOMO = 0, coor_k_point_LUMO = 0;\n",
+ " for(var i_k_points = 0; i_k_points < N_k_points_all; i_k_points++)\n",
+ " {\n",
+ " for(var i_bands = 0; i_bands < N_bands; i_bands ++)\n",
+ " {\n",
+ " if(Math.abs(band_energies_all[i_bands][i_k_points] - HOMO) < 0.001)\n",
+ " coor_k_point_HOMO = k_coor_1D[i_k_points];\n",
+ " if(Math.abs(band_energies_all[i_bands][i_k_points] - LUMO) < 0.001)\n",
+ " coor_k_point_LUMO = k_coor_1D[i_k_points]; \n",
+ " }\n",
+ " }\n",
+ "\n",
+ " //alert(coor_k_point_HOMO +\",\" + coor_k_point_LUMO);\n",
+ "\n",
+ "\n",
+ " //Store the band data to band_obj\n",
+ "\n",
+ " var band_obj = {};\n",
+ " band_obj[\"band_x_axis\"] = k_coor_1D;\n",
+ " band_obj[\"band_y_axis\"] = band_energies_all\n",
+ " band_obj[\"labels\"] = label_obj;\n",
+ " band_obj[\"HOMO_energy\"] = HOMO;\n",
+ " band_obj[\"HOMO_coor\"] = coor_k_point_HOMO;\n",
+ " band_obj[\"LUMO_energy\"] = LUMO;\n",
+ " band_obj[\"LUMO_coor\"] = coor_k_point_LUMO;\n",
+ " band_obj[\"average_N_k_points_per_inverse_distance\"] = average_N_k_points_per_inverse_distance;\n",
+ "\n",
+ "\n",
+ " return band_obj\n",
+ "\n",
+ " }\n",
+ "\n",
+ "\n",
+ " function get_dos_obj(dos_path)\n",
+ " {\n",
+ "\n",
+ " var dos_data = JSON.parse(getJSON(dos_path));\n",
+ "\n",
+ " var N_dos_values = dos_data['section_run']['section_single_configuration_calculation']['section_dos'][0]['dos_energies'].length;\n",
+ "\n",
+ " //in new parser, it seems that the spin channel of 'dos_energies' disappears: Shape: [ number_of_dos_values ]\n",
+ "\n",
+ " //dos_energies = new Array(N_dos_values).fill(0.0);\n",
+ " //dos_energies_tmp = new Array(N_dos_values).fill(0.0) #tmp array for unit convertion\n",
+ " //dos_values = new Array(N_dos_values).fill(0.0)\n",
+ "\n",
+ " var dos_energies = dos_data['section_run']['section_single_configuration_calculation']['section_dos'][0]['dos_energies'];\n",
+ " var dos_values = dos_data['section_run']['section_single_configuration_calculation']['section_dos'][0]['dos_integrated_values'];//[0]\n",
+ "\n",
+ " //To do: check if every section_dos has 'dos_fermi_energy'\n",
+ " var dos_fermi_energy = dos_data['section_run']['section_single_configuration_calculation']['section_dos'][0]['dos_fermi_energy'];\n",
+ " dos_fermi_energy = dos_fermi_energy / (1.60217656535 * Math.pow(10,-19));\n",
+ " \n",
+ " for(var i = 0; i < N_dos_values; i++)\n",
+ " {\n",
+ " dos_energies[i] = dos_energies[i] / (1.60217656535 * Math.pow(10,-19)) - dos_fermi_energy;\n",
+ " }\n",
+ " \n",
+ " dos_obj = {}\n",
+ " dos_obj[\"dos_x_axis\"] = dos_energies;\n",
+ " dos_obj[\"dos_y_axis\"] = dos_values;\n",
+ " dos_obj[\"dos_fermi_energy\"] = dos_fermi_energy;\n",
+ " return dos_obj\n",
+ " }\n",
+ " function get_info_obj(band_path)\n",
+ " {\n",
+ "\n",
+ " var band_data = JSON.parse(getJSON(band_path));\n",
+ " var info_obj = {};\n",
+ " //---------Read the information of the calculation--------\n",
+ " info_obj[\"program_name\"] = band_data[\"section_run\"][\"program_name\"];\n",
+ " info_obj[\"program_basis_set_type\"] = band_data[\"section_run\"][\"program_basis_set_type\"];\n",
+ " info_obj[\"atom_labels\"] = band_data[\"section_run\"][\"section_system\"][0][\"atom_labels\"];\n",
+ " info_obj[\"XC_functional_name\"] = band_data[\"section_run\"][\"section_method\"][\"section_XC_functionals\"][0][\"XC_functional_name\"] + \" + \"+ band_data[\"section_run\"][\"section_method\"][\"section_XC_functionals\"][1][\"XC_functional_name\"];\n",
+ "\n",
+ " //----------Get the space group information----------\n",
+ " /*\n",
+ " [space_group_symbol, lattice_constant] = get_space_group(band_data);\n",
+ " info_obj[\"space_group_symbol\"] = np.array(space_group_symbol).tolist();\n",
+ " info_obj[\"lattice_constant\"] = np.array(lattice_constant).tolist();\n",
+ " */\n",
+ "\n",
+ " return info_obj\n",
+ " }\n",
+ " function process_band_dos_data()\n",
+ " {\n",
+ " info_all = [];\n",
+ " band_obj_all = [];\n",
+ " dos_obj_all = [];\n",
+ "\n",
+ " for(var i = 0; i < N_materials; i++)\n",
+ " {\n",
+ " var band_path = band_paths[i];\n",
+ " var dos_path = dos_paths[i];\n",
+ "\n",
+ "\n",
+ " var dos_obj = get_dos_obj(dos_path);\n",
+ " var dos_fermi_energy = dos_obj[\"dos_fermi_energy\"];\n",
+ " band_obj = get_band_obj(band_path, dos_fermi_energy);\n",
+ " var info_obj = get_info_obj(band_path);\n",
+ "\n",
+ " band_obj_all.push(band_obj);\n",
+ " dos_obj_all.push(dos_obj);\n",
+ " info_obj_all.push(info_obj);\n",
+ " }\n",
+ " }\n",
+ " process_band_dos_data();\n",
+ " //alert(\"process_band_dos_data: info_obj_all: \"+JSON.stringify(info_obj_all));\n",
+ "</script>"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 54,
+ "metadata": {
+ "scrolled": false,
+ "tags": [
+ "show_results_and_plot"
+ ]
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "<script>\n",
+ " var N_max_show = 10; //Number of results to be shown by default\n",
+ "\n",
+ " function show_materials_submitted_info()\n",
+ " {\n",
+ " //alert(\"N_materials=\" + N_materials)\n",
+ " //\"table_materials_submitted_info\"\n",
+ " //alert(\"show_materials_submitted_info: info_obj_all: \"+JSON.stringify(info_obj_all))\n",
+ " var table_content = new Array(); \n",
+ " str = '<tr>';\n",
+ " str += '<th width=\"5%\"></th>'\n",
+ " str += '<th width=\"10%\"><p style=\\\"text-align:center\\\"><font size = \\\"4pt\\\"><b>Atom labels</b></font></p></th>';\n",
+ " //str += '<th width=\"10%\"><p style=\\\"text-align:center\\\"><font size = \\\"4pt\\\"><b>Space group</b></font></p></th>';\n",
+ " //str += '<th width=\"15%\"><p style=\\\"text-align:center\\\"><font size = \\\"4pt\\\"><b>Lattice constants (in Ang)</b></font></p></th>';\n",
+ " str += '<th width=\"10%\"><p style=\\\"text-align:center\\\"><font size = \\\"4pt\\\"><b>Program name</b></font></p></th>';\n",
+ " str += '<th width=\"10%\"><p style=\\\"text-align:center\\\"><font size = \\\"4pt\\\"><b>Basis set type</b></font></p></th>';\n",
+ " str += '<th width=\"15%\"><p style=\\\"text-align:center\\\"><font size = \\\"4pt\\\"><b>Functional</b></font></p></th>';\n",
+ " //str += '<th width=\"20%\"><p style=\\\"text-align:center\\\"><font size = \\\"4pt\\\"><b>Number of <i>k</i> points per inverse distance</b></font></p></th>';\n",
+ " str += '</tr>'; //first row: head\n",
+ " table_content.push(str);\n",
+ "\n",
+ " for(var i = 0; i < N_materials; i++) //add info of each material\n",
+ " {\n",
+ " //alert(\"show_materials_submitted_info: material \"+ i); \n",
+ " table_content.push('<tr>');\n",
+ "\n",
+ " table_content.push('<td>'); \n",
+ " str = '<input type = \\\"checkbox\\\" name = \"checkbox_material\" id = \\\"checkbox_material' + i.toString() + '\\\" unchecked onclick=\\\"checkbox_material(this.id)\\\">';\n",
+ " str += \"<b>  #\" + (i+1).toString() + \"</b>\";\n",
+ " table_content.push(str);\n",
+ " table_content.push('</td>');\n",
+ "\n",
+ " table_content.push('<td>'); \n",
+ " str = '<font size = \\\"3pt\\\">';\n",
+ " str += info_obj_all[i][\"atom_labels\"] + ';   ';\n",
+ " str += \"</font>\"\n",
+ " table_content.push(str); \n",
+ " table_content.push('</td>');\n",
+ " //alert(\"got atom_labels\");\n",
+ "\n",
+ " /*\n",
+ " table_content.push('<td>'); \n",
+ " str = '<font size = \\\"3pt\\\">';\n",
+ " str += info_obj_all[i][\"space_group_symbol\"] + ';   ';\n",
+ " str += \"</font>\"\n",
+ " table_content.push(str); \n",
+ " table_content.push('</td>');\n",
+ " //alert(\"got space_group_symbol\");\n",
+ "\n",
+ " table_content.push('<td>'); \n",
+ " str = '<font size = \\\"3pt\\\">';\n",
+ " str += info_obj_all[i][\"lattice_constant\"] + ';   ';\n",
+ " str += \"</font>\"\n",
+ " table_content.push(str); \n",
+ " table_content.push('</td>');\n",
+ " //alert(\"got lattice_constant\");\n",
+ " */\n",
+ " \n",
+ " table_content.push('<td>'); \n",
+ " str = '<font size = \\\"3pt\\\">';\n",
+ " str += info_obj_all[i][\"program_name\"].toUpperCase() + ';   ';\n",
+ " str += \"</font>\"\n",
+ " table_content.push(str); \n",
+ " table_content.push('</td>');\n",
+ " //alert(\"got program_name\");\n",
+ "\n",
+ " table_content.push('<td>'); \n",
+ " str = '<font size = \\\"3pt\\\">';\n",
+ " str += info_obj_all[i][\"program_basis_set_type\"] + ';   ';\n",
+ " str += \"</font>\"\n",
+ " table_content.push(str); \n",
+ " table_content.push('</td>');\n",
+ " //alert(\"got program_basis_set_type\");\n",
+ "\n",
+ "\n",
+ " table_content.push('<td>'); \n",
+ " str = '<font size = \\\"3pt\\\">';\n",
+ " str += info_obj_all[i][\"XC_functional_name\"] + ';   ';\n",
+ " str += \"</font>\"\n",
+ " table_content.push(str); \n",
+ " table_content.push('</td>');\n",
+ " //alert(\"got XC_functional_name\");\n",
+ "\n",
+ " /*\n",
+ " table_content.push('<td>'); \n",
+ " str = '<font size = \\\"3pt\\\">';\n",
+ " str += band_obj_all[i][\"average_N_k_points_per_inverse_distance\"].toFixed(3);\n",
+ " str += \"</font>\"\n",
+ " table_content.push(str); \n",
+ " table_content.push('</td>');\n",
+ " //alert(\"got average_N_k_points_per_inverse_distance\");\n",
+ " */\n",
+ " table_content.push('</tr>');\n",
+ "\n",
+ " }\n",
+ " \n",
+ " document.getElementById(\"table_materials_submitted_info\").innerHTML = table_content.join('');\n",
+ " }\n",
+ "\n",
+ " function clean_materials_selection()\n",
+ " {\n",
+ " var choices_compare = document.getElementsByName(\"checkbox_material\");\n",
+ " for(var i=0; i<choices_compare.length; i++)\n",
+ " {\n",
+ " //choices_compare[i].removeAttribute('checked');\n",
+ " //choices_compare[i].setAttribute(\"unchecked\", \"unchecked\");\n",
+ " choices_compare[i].checked = \"\";\n",
+ " }\n",
+ " }\n",
+ "\n",
+ " function select_all()\n",
+ " {\n",
+ " var choices_compare = document.getElementsByName(\"checkbox_material\");\n",
+ " for(var i=0; i<choices_compare.length; i++)\n",
+ " {\n",
+ " //choices_compare[i].removeAttribute('checked');\n",
+ " //choices_compare[i].setAttribute(\"unchecked\", \"unchecked\");\n",
+ " choices_compare[i].checked = \"checked\";\n",
+ " }\n",
+ " }\n",
+ "\n",
+ "\n",
+ "\n",
+ " function process()\n",
+ " {\n",
+ " //alert(\"Process:\"+band_paths)\n",
+ " //Jupyter.notebook.execute_cells(window.findCellIndicesByTag('init_js_plot'));\n",
+ " //Jupyter.notebook.execute_cells(window.findCellIndicesByTag('show_materials_submitted_info'));\n",
+ " show_materials_submitted_info();\n",
+ " document.getElementById(\"table_visualize\").innerHTML = \"\";\n",
+ " str = N_materials.toString();\n",
+ " document.getElementById(\"n_materials\").innerHTML = \"Number of materials submitted: \" + str + \"<font size = 1px color = #C0C0C0 >   Please press \\'Visualize\\' to visualize the band structure. </font>\";\n",
+ " document.getElementById(\"div_showall\").style.visibility=\"hidden\";\n",
+ " }\n",
+ " \n",
+ "\n",
+ " var image_band = '';\n",
+ " var image_dos = '';\n",
+ " var image_band_links = new Array(N_materials); //store the URL of each band figure -> used to compare 2 figures\n",
+ " var image_band_links_selected = [];\n",
+ " var image_band_selected_Number = []; //record which i_material has been selected\n",
+ "\n",
+ "\n",
+ "\n",
+ " function prepare(N_materials_show)\n",
+ " {\n",
+ " document.getElementById(\"table_visualize\").innerHTML = \"\";\n",
+ " var table_content = new Array(); \n",
+ " //document.getElementById(\"table_visualize\").innerHTML = table_content.join('');\n",
+ " //-----Generate the html tables for each material--------\n",
+ " for(var i = 0; i < N_materials_show; i++)\n",
+ " {\n",
+ " checkbox_material_id = \"checkbox_material\" + i.toString();\n",
+ " var if_selected = check_show_VBM(checkbox_material_id);\n",
+ " if(if_selected != 1)\n",
+ " {\n",
+ " continue;\n",
+ " }\n",
+ "\n",
+ " table_content.push('<tr>');\n",
+ " div_string = '<div style = \\\"height: 20px\\\"></div>';\n",
+ " table_content.push(div_string);\n",
+ " table_content.push('<th>');\n",
+ "\n",
+ " //add main container div\n",
+ " div_string = '<div id = \\\"div_band_dos' + i.toString() + '\\\" class = \\\"div_band_dos\\\" >';\n",
+ " table_content.push(div_string);\n",
+ "\n",
+ " //show No. of the material\n",
+ " i_material = i + 1;\n",
+ " div_string = '<div style = \\\"height:30px\\; font-size: 15pt;\">' + '#' + i_material.toString() + '</div>';\n",
+ " table_content.push(div_string);\n",
+ "\n",
+ " //show band_path/dos info\n",
+ " div_string = '<div style = \\\"height:30px\\\">' + 'Band:   ' + band_paths[i] + ',    DOS:   ' + dos_paths[i] + '</div>';\n",
+ " table_content.push(div_string);\n",
+ "\n",
+ " //add div_band\n",
+ " div_string = '<div id = \\\"div_band' + i.toString() + '\\\" class = \\\"div_band\\\" ></div>';\n",
+ " table_content.push(div_string);\n",
+ "\n",
+ " //add div_dos\n",
+ " div_string = '<div id = \\\"div_dos' + i.toString() + '\\\" class = \\\"div_dos\\\" ></div>'; \n",
+ " table_content.push(div_string);\n",
+ "\n",
+ " //add div_tools\n",
+ " div_string = '<div id = \\\"div_tools' + i.toString() + '\\\" class = \\\"div_tools\\\" >'; \n",
+ " table_content.push(div_string);\n",
+ "\n",
+ " //add: infomation\n",
+ " div_string = '<div id = \\\"div_info' + i.toString() + '\\\">atom_labels<br>program_name</div>'; \n",
+ " table_content.push(div_string);\n",
+ "\n",
+ " //add: custom scale\n",
+ " div_string = '<br><p style=\\\"color: #000;font-weight: 100; font-size: 10pt; align:left\\\"> Set the lower and upper limit of energy scale (in eV): <br><br><font color=\\\"black\\\" size = 3px> Lower limit:    </font><textarea id=\\\"lowerlimit' + i.toString() + '\\\" rows=\\\"1\\\" style = \\\"width: 70px;\\\">-10</textarea> <font color=\\\"black\\\" size = 3px>   eV</font>    <font color=\\\"black\\\" size = 3px> Upper limit:    </font><textarea id=\\\"upperlimit' + i.toString() + '\\\" rows=\\\"1\\\" style = \\\"width: 70px;\\\">10</textarea> <font color=\\\"black\\\" size = 3px>   eV   </font></p>';\n",
+ " table_content.push(div_string);\n",
+ " div_string = '<br><button class = \\\"button_tools\\\" id = \\\"button_customscale' + i.toString() + '\\\" onclick = \\\"customscale(this.id)\\\"> Rescale </button>'; \n",
+ " table_content.push(div_string);\n",
+ "\n",
+ "\n",
+ " //add button:autoscale\n",
+ " div_string = '<button class = \\\"button_tools\\\" id = \\\"button_autoscale' + i.toString() + '\\\" onclick = \\\"autoscale(this.id)\\\" title = \\\"(-10 eV, 10 eV)\\\"> Autoscale </button>'; \n",
+ " table_content.push(div_string);\n",
+ " //add button:fullscale\n",
+ " div_string = '<button class = \\\"button_tools\\\" id = \\\"button_fullscale' + i.toString() + '\\\" onclick = \\\"fullscale(this.id)\\\" title = \\\"(-100 eV, 100 eV)\\\"> Full scale </button><br><br>'; \n",
+ " table_content.push(div_string);\n",
+ "\n",
+ " //table_content.push(\"Select and zoom:\");\n",
+ "\n",
+ " /*//overview for select and zoom\n",
+ " div_string = '<div id = \\\"div_overview' + i.toString() + '\\\" class = \\\"div_overview\\\" ></div>'; // <div id=\"overview\" style=\"width:300px;height:200px; margin-left:10px; margin-top: 50px; padding-top: 0px\"></div>\n",
+ " table_content.push(div_string);\n",
+ " div_string = '<p id = \\\"overviewLegend' + i.toString() + '\\\" ></p>'; // <p id=\"overviewLegend\" style=\"margin-left:10px\"></p>\n",
+ " table_content.push(div_string);*/\n",
+ "\n",
+ " //download figures as png\n",
+ " div_string = '<a id = \\\"img_band' + i.toString() + '\\\" class = \\\"button_tools\\\" target=\\\"_blank\\\" style = \\\"text-decoration: none;\\\" > Download band </a>';\n",
+ " table_content.push(div_string); \n",
+ " div_string = '<a id = \\\"img_dos' + i.toString() + '\\\" class = \\\"button_tools\\\" target=\\\"_blank\\\" style = \\\"text-decoration: none;\\\" > Download DOS </a>';\n",
+ " table_content.push(div_string);\n",
+ "\n",
+ " //add show VBM & CBM\n",
+ " div_string = '<br><br><p style = \\\"text-normal-black\\\"> <input type = \\\"checkbox\\\" id = \\\"checkbox_VBM' + i.toString() + '\\\" unchecked onclick=\\\"show_VBM(this.id)\\\"> <font color=\\\"black\\\" size = 3px> Show VBM </font> (<font color=\\\"blue\\\">\\•</font>) <font color=\\\"black\\\" size = 3px> and CBM </font>(<font color=\\\"red\\\">\\•</font>) </p>';\n",
+ " table_content.push(div_string);\n",
+ "\n",
+ "\n",
+ " table_content.push('</div>');//div_tools\n",
+ "\n",
+ " //checkbox for comparison\n",
+ " div_string = '<div id = \\\"div_checkbox_compare' + i.toString() + '\\\" class = \\\"div_checkbox_compare\\\" >';\n",
+ " table_content.push(div_string);\n",
+ " //div_string = '<p style = \\\"text-normal-black\\\"> <input type = \\\"checkbox\\\" id = \\\"checkbox_compare' + i.toString() + '\\\" unchecked name = \\\"checkbox_compare\\\" onclick=\\\"check_compare(this.id)\\\"> <font color=\\\"black\\\" size = 3px> Compare </font></p><p><font size = 2px color = \"#666\">(select max. 2 materials) </font> </p>';\n",
+ " div_string = '<p style = \\\"text-normal-black\\\"> <input type = \\\"checkbox\\\" id = \\\"checkbox_compare' + i.toString() + '\\\" checked = \\\"unchecked\\\" unchecked name = \\\"checkbox_compare\\\" onclick=\\\"check_compare(this.id)\\\"> <font color=\\\"black\\\" size = 3px> Compare </font></p><p><font size = 2px color = \"#666\">(select max. 2 materials) </font> </p>';\n",
+ " table_content.push(div_string);\n",
+ " table_content.push('</div>');//div_checkbox_compare\n",
+ "\n",
+ "\n",
+ " table_content.push('</div>');//div_band_dos\n",
+ " table_content.push('</th>');\n",
+ " table_content.push('</tr>'); \n",
+ " }\n",
+ "\n",
+ " document.getElementById(\"table_visualize\").innerHTML = table_content.join('');\n",
+ " }\n",
+ "\n",
+ "\n",
+ " function visualize_band_dos()\n",
+ " {\n",
+ " Jupyter.notebook.execute_cells(window.findCellIndicesByTag('init_jquery'));\n",
+ " Jupyter.notebook.execute_cells(window.findCellIndicesByTag('init_flot'));\n",
+ " Jupyter.notebook.execute_cells(window.findCellIndicesByTag('init_flot_axislabels'));\n",
+ " //Jupyter.notebook.execute_cells(window.findCellIndicesByTag('init_flot_dashes'));\n",
+ " Jupyter.notebook.execute_cells(window.findCellIndicesByTag('init_flot_navigate'));\n",
+ " //Jupyter.notebook.execute_cells(window.findCellIndicesByTag('init_flot_selection'));\n",
+ " Jupyter.notebook.execute_cells(window.findCellIndicesByTag('js_flot_legendoncanvas'));\n",
+ " document.getElementById(\"div_showall\").style.visibility=\"hidden\";\n",
+ " document.getElementById(\"div_compare_buttons\").style.visibility=\"\";\n",
+ "\n",
+ "\n",
+ "\n",
+ " if(N_materials > N_max_show)\n",
+ " {\n",
+ " document.getElementById(\"div_showall\").style.visibility=\"visible\";\n",
+ " document.getElementById(\"checkbox_showall\").checked = \"\";\n",
+ " } \n",
+ "\n",
+ " N_materials_show = Math.min(N_max_show, N_materials);\n",
+ "\n",
+ " prepare(N_materials_show);\n",
+ " clean_compare_list();\n",
+ " plot_band_dos_status = plot_band_dos(-10,10, N_materials_show);\n",
+ "\n",
+ " }\n",
+ "\n",
+ " function show_all(id)//\"plot_placeholder\"\n",
+ " {\n",
+ " var if_showall=0;\n",
+ " if_showall = check_show_VBM(id);\n",
+ " if(if_showall == 1)\n",
+ " {\n",
+ " N_materials_show = N_materials;\n",
+ " prepare(N_materials_show);\n",
+ " clean_compare_list();\n",
+ " plot_band_dos_status = plot_band_dos(-10,10, N_materials_show);\n",
+ " }\n",
+ " else\n",
+ " {\n",
+ " N_materials_show = Math.min(N_max_show, N_materials);\n",
+ " prepare(N_materials_show);\n",
+ " clean_compare_list();\n",
+ " plot_band_dos_status = plot_band_dos(-10,10, N_materials_show);\n",
+ " }\n",
+ "\n",
+ " }\n",
+ "\n",
+ " \n",
+ " //------------------Tool used to get the content from textarea---------------------\n",
+ " function get_text(textarea_id)\n",
+ " {\n",
+ " var text = document.getElementById(textarea_id).value;\n",
+ " return text;\n",
+ " }\n",
+ "\n",
+ "\n",
+ "\n",
+ " //-------------------Compare 2 band figures----------------------------------------\n",
+ "\n",
+ "\n",
+ " function check_compare(id)//checkbox_compare' + i.toString() + '\\\" unchecked onclick=\\\"check_compare(this.id)\n",
+ " {\n",
+ " var x = document.getElementById(id);\n",
+ " var choices_compare = document.getElementsByName(\"checkbox_compare\");\n",
+ " var N_chosen = 0;\n",
+ " for(var i=0; i<choices_compare.length; i++)\n",
+ " {\n",
+ " if(choices_compare[i].checked)\n",
+ " {\n",
+ " N_chosen ++;\n",
+ " }\n",
+ " }\n",
+ " if(N_chosen == 2) // In max. only 2 figures could be selected and compared.\n",
+ " {\n",
+ " for(var i=0; i<choices_compare.length; i++)\n",
+ " {\n",
+ " if(!choices_compare[i].checked)\n",
+ " {\n",
+ " choices_compare[i].disabled = 'disabled';\n",
+ " }\n",
+ " }\n",
+ " }\n",
+ " else\n",
+ " {\n",
+ " for(var i=0; i<choices_compare.length; i++)\n",
+ " {\n",
+ " choices_compare[i].removeAttribute('disabled');\n",
+ " }\n",
+ " }\n",
+ "\n",
+ " }\n",
+ "\n",
+ " function compare()\n",
+ " {\n",
+ " $(\"#div_compare\").fadeIn(600);//show div for comparison\n",
+ " //check_compare(-100);\n",
+ "\n",
+ " var compare_list = [];\n",
+ " compare_list = make_compare_list();\n",
+ " //[i_material_1, i_material_2] = make_compare_list();\n",
+ " i_material_1 = compare_list[0];\n",
+ " i_material_2 = compare_list[1];\n",
+ " //document.getElementById(\"demo\").innerHTML = \"In add info compare:\" + i_material_1.toString() + i_material_2.toString();\n",
+ " compare_figures(i_material_1, i_material_2); \n",
+ " }\n",
+ " function make_compare_list()\n",
+ " {\n",
+ " //get the links to the images\n",
+ " images_selected_links = []; //store the links to the figures for comparison\n",
+ " var choices_compare = document.getElementsByName(\"checkbox_compare\");\n",
+ " var N_chosen = 0;\n",
+ " var str = ''; //tmp str for debug\n",
+ " var figure_selected = new Array(2);\n",
+ " for(var i=0; i<choices_compare.length; i++) //check which figures are selected\n",
+ " {\n",
+ " if(choices_compare[i].checked)\n",
+ " {\n",
+ " id_chosen = choices_compare[i].id;\n",
+ " i_chosen = Math.round(id_chosen.substring(16));\n",
+ " var tmp_str = image_band_links[i_chosen];\n",
+ " images_selected_links.push(tmp_str);\n",
+ " figure_selected[N_chosen] = i_chosen;\n",
+ " N_chosen ++;\n",
+ " //str += beakerx.image_band_links[i];\n",
+ " }\n",
+ " }\n",
+ " var i_material_1 = 0;\n",
+ " var i_material_2 = 0;\n",
+ " //document.getElementById(\"demo\").innerHTML = 'In making comare list';\n",
+ " image_band_links_selected = images_selected_links;\n",
+ " //document.getElementById(\"demo\").innerHTML = 'In making comare list: next';\n",
+ " if(N_chosen == 2)\n",
+ " {\n",
+ " i_material_1 = figure_selected[0];\n",
+ " i_material_2 = figure_selected[1];\n",
+ " }\n",
+ " //document.getElementById(\"demo\").innerHTML = 'Compare_list: ' +i_material_1.toString() + ' ' + i_material_2.toString();\n",
+ "\n",
+ " return [i_material_1, i_material_2];\n",
+ " }\n",
+ "\n",
+ " function check_compare_scale(i_material_1, i_material_2)\n",
+ " {\n",
+ " lowerlimit_id_1 = \"lowerlimit\" + i_material_1.toString();\n",
+ " lowerlimit_id_2 = \"lowerlimit\" + i_material_2.toString();\n",
+ " upperlimit_id_1 = \"upperlimit\" + i_material_1.toString();\n",
+ " upperlimit_id_2 = \"upperlimit\" + i_material_2.toString();\n",
+ "\n",
+ " lowerlimit_1 = parseFloat(document.getElementById(lowerlimit_id_1).innerHTML);\n",
+ " lowerlimit_2 = parseFloat(document.getElementById(lowerlimit_id_2).innerHTML);\n",
+ " upperlimit_1 = parseFloat(document.getElementById(upperlimit_id_2).innerHTML);\n",
+ " upperlimit_2 = parseFloat(document.getElementById(upperlimit_id_2).innerHTML);\n",
+ " if((lowerlimit_1 != lowerlimit_2) || (upperlimit_1 != upperlimit_2))\n",
+ " return -1;\n",
+ " else\n",
+ " return 1;\n",
+ " }\n",
+ "\n",
+ " function compare_figures(i_material_1, i_material_2)\n",
+ " {\n",
+ " Jupyter.notebook.execute_cells(window.findCellIndicesByTag('js_query_beforeafter'));\n",
+ " Jupyter.notebook.execute_cells(window.findCellIndicesByTag('js_compare_slide'));\n",
+ " add_info_compare(i_material_1, i_material_2);\n",
+ " document.getElementById(\"div_compare_container\").scrollIntoView({ behavior: 'smooth' }); \n",
+ " document.getElementById(\"div_compare_container\").scrollTop += 50;\n",
+ "\n",
+ " }\n",
+ "\n",
+ "\n",
+ " function clean_compare_list()\n",
+ " {\n",
+ " var choices_compare = document.getElementsByName(\"checkbox_compare\");\n",
+ " for(var i=0; i<choices_compare.length; i++)\n",
+ " {\n",
+ " //choices_compare[i].removeAttribute('checked');\n",
+ " //choices_compare[i].setAttribute(\"unchecked\", \"unchecked\");\n",
+ " choices_compare[i].checked = \"\";\n",
+ " choices_compare[i].removeAttribute('disabled');\n",
+ " }\n",
+ " }\n",
+ "\n",
+ " //-----------Add information about the calculation to \"div_tools\"---------------\n",
+ " function add_info(i)\n",
+ " {\n",
+ " \n",
+ " //document.getElementById(\"demoa\").innerHTML = i.toString() + div_info_id;\n",
+ " //for(var i = 0; i < beakerx.N_materials; i++)\n",
+ " //{\n",
+ " div_info_id = \"div_info\" + i.toString();\n",
+ "\n",
+ " var str = '';\n",
+ " str += \"<br> <p style=\\\"text-align:left\\\"><font size = 3pt><b>Atom labels:</b>     \" + info_obj_all[i][\"atom_labels\"] + '</font></p>';\n",
+ " //str += \"<font size = 3pt><b>Space group:</b>     \" + info_obj_all[i][\"space_group_symbol\"] + '</font>';\n",
+ " //str += \"<font size = 3pt><b>Lattice constants (in Ang):</b>     \" + info_obj_all[i][\"lattice_constant\"] + '</font>';\n",
+ " str += \"<p style=\\\"text-align:left\\\"><font size = 3pt><b>Program name:</b>    \" + info_obj_all[i][\"program_name\"].toUpperCase() + '</font></p>';\n",
+ " str += \"<p style=\\\"text-align:left\\\"><font size = 3pt><b>Basis set type:</b>    \" + info_obj_all[i][\"program_basis_set_type\"] + '</font></p>';\n",
+ " str += \"<p style=\\\"text-align:left\\\"><font size = 3pt><b>Functional:</b>    \" + info_obj_all[i][\"XC_functional_name\"] + '</font></p>';\n",
+ " str += \"<p style=\\\"text-align:left\\\"><font size = 3pt><b>Number of <i>k</i> points per inverse distance:</b>    \" + band_obj_all[i][\"average_N_k_points_per_inverse_distance\"].toFixed(3) + '</font></p>';\n",
+ " document.getElementById(div_info_id).innerHTML = str;// + origData[\"atom_labels\"];\n",
+ " //document.getElementById('program_name_1').innerHTML = \"<b>Code:</b>    \" + origData[\"program_name\"];\n",
+ " //document.getElementById('program_basis_set_type_1').innerHTML = \"<b>Basis set type:</b>    \" + origData[\"program_basis_set_type\"];\n",
+ " //document.getElementById('XC_functional_name_1').innerHTML = \"<b>Functional:</b>    \" + origData[\"XC_functional_name\"]; \n",
+ " //}\n",
+ " \n",
+ " }\n",
+ " function add_info_compare(i,j)\n",
+ " {\n",
+ "\n",
+ " div_info_id = \"div_compare_info\";\n",
+ " var str = '';\n",
+ "\n",
+ " if_same_scale = check_compare_scale(i_material_1, i_material_2);\n",
+ " if(if_same_scale == -1)\n",
+ " {\n",
+ " str = '<b><font size = \"15pt\" color=\"#940000\">Error: Different lower/upper limits.</font></b><br>';\n",
+ " document.getElementById(\"div_compare_container\").innerHTML = str;\n",
+ " document.getElementById(div_info_id).innerHTML = '';\n",
+ " return;\n",
+ " }\n",
+ "\n",
+ " str += \"<br><b><font-size:15pt>Information of the first calculation (left):</font></b> <br>\";\n",
+ " str += \"<br> <b>Atom labels:</b>     \" + info_obj_all[i][\"atom_labels\"];\n",
+ " //str += \"<br> <b>Space group:</b>     \" + info_obj_all[i][\"space_group_symbol\"];\n",
+ " //str += \"<br> <b>Lattice constants (in Ang):</b>     \" + info_obj_all[i][\"lattice_constant\"];\n",
+ " str += \"<br> <b>Program name:</b>    \" + info_obj_all[i][\"program_name\"].toUpperCase();\n",
+ " str += \"<br> <b>Basis set type:</b>    \" + info_obj_all[i][\"program_basis_set_type\"];\n",
+ " str += \"<br> <b>Functional:</b>    \" + info_obj_all[i][\"XC_functional_name\"];\n",
+ " str += \"<br> <b>Number of <i>k</i> points per inverse distance:</b>    \" + band_obj_all[j][\"average_N_k_points_per_inverse_distance\"].toFixed(3);\n",
+ " str += \"<br><br><br><b><font-size:15pt>Information of the second calculation (right):</font></b><br>\";\n",
+ " str += \"<br> <b>Atom labels:</b>     \" + info_obj_all[j][\"atom_labels\"];\n",
+ " //str += \"<br> <b>Space group:</b>     \" + info_obj_all[j][\"space_group_symbol\"];\n",
+ " //str += \"<br> <b>Lattice constants (in Ang):</b>     \" + info_obj_all[j][\"lattice_constant\"];\n",
+ " str += \"<br> <b>Program name:</b>    \" + info_obj_all[j][\"program_name\"].toUpperCase();\n",
+ " str += \"<br> <b>Basis set type:</b>    \" + info_obj_all[j][\"program_basis_set_type\"]; \n",
+ " str += \"<br> <b>Functional:</b>    \" + info_obj_all[j][\"XC_functional_name\"];\n",
+ " str += \"<br> <b>Number of <i>k</i> points per inverse distance:</b>    \" + band_obj_all[j][\"average_N_k_points_per_inverse_distance\"].toFixed(3);\n",
+ " document.getElementById(div_info_id).innerHTML = str;// + origData[\"atom_labels\"];\n",
+ " }\n",
+ "\n",
+ "\n",
+ "\n",
+ " //-----------------------Show/hide VBM, CBM-------------------------\n",
+ " function check_show_VBM(checkbox_VBM_id)\n",
+ " {\n",
+ " var x = document.getElementById(checkbox_VBM_id);\n",
+ " var if_checked = 0;\n",
+ " if(x.checked)//== \"checked\")\n",
+ " {\n",
+ " //document.getElementById(\"demoa\").innerHTML = \"checked!\";\n",
+ " if_checked = 1;\n",
+ " }\n",
+ " else if (x.unchecked)// == \"unchecked\")\n",
+ " {\n",
+ " //document.getElementById(\"demoa\").innerHTML = \"unchecked!\";\n",
+ " if_checked = -1;\n",
+ " }\n",
+ " else\n",
+ " {\n",
+ " //document.getElementById(\"demoa\").innerHTML = \"nothing detected!\";\n",
+ " }\n",
+ " return if_checked;\n",
+ " }\n",
+ "\n",
+ " function check_if_in_compare_list(i) // check if the current material i is to be compared\n",
+ " {\n",
+ "\n",
+ " var checkbox_compare_id = \"checkbox_compare\" + i.toString();\n",
+ " var if_compare = check_show_VBM(checkbox_compare_id);\n",
+ " //document.getElementById(\"demo\").innerHTML = 'if_compare of ' + i.toString() + ' : ' + if_compare.toString();\n",
+ " var i_compare_material_1, i_compare_material_2;\n",
+ " [i_compare_material_1, i_compare_material_2] = make_compare_list();\n",
+ " var i_in_compare_list = -1;\n",
+ " if(i_compare_material_1 == i)\n",
+ " {\n",
+ " i_in_compare_list = 1;\n",
+ " }\n",
+ " else if (i_compare_material_2 == i)\n",
+ " {\n",
+ " i_in_compare_list = 2;\n",
+ " }\n",
+ " else\n",
+ " {\n",
+ " i_in_compare_list = 0;\n",
+ " }\n",
+ " //document.getElementById(\"demo\").innerHTML = 'Checking ' + i.toString() + ' in Compare_list: ' + i_in_compare_list.toString();\n",
+ " return [if_compare, i_in_compare_list];\n",
+ " }\n",
+ "\n",
+ " function show_VBM(id)\n",
+ " {\n",
+ " //prepare(\"new\");\n",
+ " //var if_show_VBM = -1;\n",
+ " var len_id = id.length;\n",
+ " var i_material = id.substring(12);\n",
+ " var i = Math.round(i_material);\n",
+ "\n",
+ " var checkbox_VBM_id = \"checkbox_VBM\" + i.toString();\n",
+ " var if_show_VBM = check_show_VBM(checkbox_VBM_id);\n",
+ "\n",
+ " var if_compare, i_in_compare_list;\n",
+ " [if_compare, i_in_compare_list] = check_if_in_compare_list(i);\n",
+ " //document.getElementById(\"demo\").innerHTML = i.toString() + ' in Compare_list: ' + i_in_compare_list.toString();\n",
+ "\n",
+ " plot_band_dos_i(i, -10, 10, if_show_VBM, if_compare, i_in_compare_list);\n",
+ "\n",
+ " }\n",
+ "\n",
+ "\n",
+ " //---------------------Functions to rescale-------------------------------------------\n",
+ " function autoscale(id)\n",
+ " {\n",
+ " var len_id = id.length;\n",
+ " var i_material = id.substring(16);\n",
+ " var i = Math.round(i_material);\n",
+ "\n",
+ " upperlim_id = \"upperlimit\" + i_material;\n",
+ " document.getElementById(upperlim_id).innerHTML =\"10.0\";\n",
+ " lowerlim_id = \"lowerlimit\" + i_material;\n",
+ " document.getElementById(lowerlim_id).innerHTML =\"-10.0\";\n",
+ "\n",
+ "\n",
+ " //document.getElementById(\"demoa\").innerHTML =i_material;\n",
+ " var checkbox_VBM_id = \"checkbox_VBM\" + i.toString();\n",
+ " var if_show_VBM = check_show_VBM(checkbox_VBM_id);\n",
+ "\n",
+ " var if_compare, i_in_compare_list;\n",
+ " [if_compare, i_in_compare_list] = check_if_in_compare_list(i);\n",
+ "\n",
+ "\n",
+ " plot_band_dos_i(i, -10, 10, if_show_VBM, if_compare, i_in_compare_list);\n",
+ "\n",
+ " }\n",
+ "\n",
+ " function fullscale(id)\n",
+ " {\n",
+ " var len_id = id.length;\n",
+ " var i_material = id.substring(16);\n",
+ " var i = Math.round(i_material);\n",
+ "\n",
+ " upperlim_id = \"upperlimit\" + i_material;\n",
+ " document.getElementById(upperlim_id).innerHTML =\"100.0\";\n",
+ " lowerlim_id = \"lowerlimit\" + i_material;\n",
+ " document.getElementById(lowerlim_id).innerHTML =\"-100.0\";\n",
+ "\n",
+ " //document.getElementById(\"demoa\").innerHTML =i_material;\n",
+ " var checkbox_VBM_id = \"checkbox_VBM\" + i.toString();\n",
+ " var if_show_VBM = check_show_VBM(checkbox_VBM_id);\n",
+ "\n",
+ " var if_compare, i_in_compare_list;\n",
+ " [if_compare, i_in_compare_list] = check_if_in_compare_list(i);\n",
+ "\n",
+ "\n",
+ "\n",
+ " plot_band_dos_i(i, -100, 100, if_show_VBM, if_compare, i_in_compare_list);\n",
+ "\n",
+ " }\n",
+ "\n",
+ " function customscale(id)\n",
+ " {\n",
+ " var len_id = id.length;\n",
+ " var i_material = id.substring(18);\n",
+ " var i = Math.round(i_material);\n",
+ " //\n",
+ " upperlim_id = \"upperlimit\" + i_material;\n",
+ " upperlim = document.getElementById(upperlim_id).value;\n",
+ " upperlim_float = Math.round(upperlim);\n",
+ " lowerlim_id = \"lowerlimit\" + i_material;\n",
+ " lowerlim = document.getElementById(lowerlim_id).value;\n",
+ " lowerlim_float = Math.round(lowerlim);\n",
+ "\n",
+ " var checkbox_VBM_id = \"checkbox_VBM\" + i.toString();\n",
+ " var if_show_VBM = check_show_VBM(checkbox_VBM_id);\n",
+ "\n",
+ " var if_compare, i_in_compare_list;\n",
+ " [if_compare, i_in_compare_list] = check_if_in_compare_list(i);\n",
+ "\n",
+ "\n",
+ "\n",
+ " plot_band_dos_i(i, lowerlim_float, upperlim_float, if_show_VBM, if_compare, i_in_compare_list); \n",
+ " }\n",
+ "\n",
+ "\n",
+ " function plot_band_dos(lowerLim, upperLim, N_materials_show)\n",
+ " {\n",
+ " placeholder_band = \"#div_band1\";\n",
+ " placeholder_dos = \"#div_dos1\";\n",
+ " // lowerLim = -10.01\n",
+ " //upperLim = 10.01\n",
+ "\n",
+ "\n",
+ "\n",
+ " //alert(\"plot_band_dos\");\n",
+ " //prepare();\n",
+ " for(var i = 0; i < N_materials_show; i++)\n",
+ " {\n",
+ " \n",
+ " var checkbox_material_id = \"checkbox_material\" + i.toString();\n",
+ " var if_selected = check_show_VBM(checkbox_material_id);\n",
+ " if(if_selected != 1)\n",
+ " {\n",
+ " continue;\n",
+ " }\n",
+ " add_info(i);\n",
+ " }\n",
+ "\n",
+ " //------Plot----------------\n",
+ " /*\n",
+ " for(var i_material = 0; i_material < N_materials_show; i_material++)\n",
+ " {\n",
+ "\n",
+ " //alert(\"Material \"+i);\n",
+ " var checkbox_material_id = \"checkbox_material\" + i_material.toString();\n",
+ " var if_selected = check_show_VBM(checkbox_material_id);\n",
+ " if(if_selected != 1)\n",
+ " {\n",
+ " continue;\n",
+ " }\n",
+ "\n",
+ " plot_band_dos_i(i_material, lowerLim, upperLim, 0, 0, -1);\n",
+ " }\n",
+ " */\n",
+ " //alert(\"next:for\")\n",
+ " for (let i_material = 0, p = Promise.resolve(); i_material < N_materials_show; i_material++) {\n",
+ " p = p.then(_ => new Promise(resolve =>\n",
+ " setTimeout(function () {\n",
+ " //alert(i_material)\n",
+ " var checkbox_material_id = \"checkbox_material\" + i_material.toString();\n",
+ " var if_selected = check_show_VBM(checkbox_material_id);\n",
+ " if(if_selected == 1)\n",
+ " {\n",
+ " plot_band_dos_i(i_material, lowerLim, upperLim, 0, 0, -1);\n",
+ " }\n",
+ " resolve();\n",
+ " }, 0)\n",
+ " ));\n",
+ " }\n",
+ "\n",
+ "\n",
+ " return 1;\n",
+ " }\n",
+ "\n",
+ " var i = 0\n",
+ " var lowerLim = -10\n",
+ " var upperLim = 10\n",
+ " var if_show_VBM = 0\n",
+ " var if_compare = 0\n",
+ " var i_in_compare_list = -1\n",
+ "\n",
+ "\n",
+ " \n",
+ " function plot_band_dos_i(i_material, lowerLim_material, upperLim_material, if_show_VBM_material, if_compare_material, i_in_compare_list_material)\n",
+ " {\n",
+ " //alert(\"plot_band_dos_i\")\n",
+ "\n",
+ " i = i_material;\n",
+ " lowerLim = lowerLim_material;\n",
+ " upperLim = upperLim_material;\n",
+ " if_show_VBM = if_show_VBM_material;\n",
+ " if_compare = if_compare_material;\n",
+ " i_in_compare_list = i_in_compare_list_material;\n",
+ " //alert(\"plot_band_dos_i: i_material: \"+i)\n",
+ " Jupyter.notebook.execute_cells(window.findCellIndicesByTag('plot_band'));\n",
+ " //alert('i, lowerLim, upperLim, if_show_VBM, if_compare, i_in_compare_list')\n",
+ " //plot_band(i, lowerLim, upperLim, if_show_VBM, if_compare, i_in_compare_list);\n",
+ " Jupyter.notebook.execute_cells(window.findCellIndicesByTag('plot_dos'));\n",
+ " } \n",
+ "</script>\n",
+ "\n",
+ " \n",
+ " \n",
+ "<br><br>\n",
+ "<button class=\"button\" onclick=\"process()\">Process data</button>\n",
+ "<br><br>\n",
+ "<div id = \"n_materials\" style = \"font-size: 18px; font-weight: 100; height: 60px; width: 100%;\"> Number of materials submitted: 0</div>\n",
+ "<div id = \"show_materials_submitted\" style = \"font-size: 20px; font-color: black;\"> </div>\n",
+ "\n",
+ "<div style = \"width :100%; height: 30px;\"></div> \n",
+ "<p style=\"color: #20335d;font-weight: 100; font-size: 18pt;\"> Select materials to visualize the band structure and DOS:</p>\n",
+ "<div style = \"width :100%; height: 10px;\"></div> \n",
+ "<button class = \"button\" onclick = \"clean_materials_selection()\"> Clean selections </button> \n",
+ "<button class = \"button\" onclick = \"select_all()\"> Select all </button> \n",
+ "<button class = \"button\" onclick = \"visualize_band_dos()\"> Visualize </button> \n",
+ "<div style = \"width :100%; height: 30px;\"></div> \n",
+ "\n",
+ "<div id = \"show_materials_submitted_info\" style = \"width: 100%; font-size: 20px; font-color: black;\"> \n",
+ " <table id = \"table_materials_submitted_info\" style=\"width:100%\"> </table>\n",
+ "</div>\n",
+ "\n",
+ "<div style = \"width :100%; height: 30px;\"></div> \n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "<div id=\"div_compare_buttons\" style=\"visibility:hidden\">\n",
+ " <br><br><br>\n",
+ " <p style=\"color: #20335d;font-weight: 100; font-size: 18pt;\"> Select two materials in the checkbox on the right for comparison:</p>\n",
+ " <p style=\"color: #000;font-weight: 1000; font-size: 8pt;\"></p>\n",
+ " <button class = \"button\" onclick = \"clean_compare_list()\"> Clean selections </button> \n",
+ " <button class = \"button\" onclick = \"compare();compare()\" title = \"Select 2 materials in the checkbox below and compare: please make sure that the upper/lower limits are the same (using Rescale/Autoscale buttons).\" > Compare</button>\n",
+ "</div>\n",
+ "\n",
+ "\n",
+ "\n",
+ "<div id = \"div_showall\" style = \"width: 100%; visibility:hidden\">\n",
+ " <div style = \"width: 100%; height: 30px; \"></div>\n",
+ " <input type = \"checkbox\" id = \"checkbox_showall\" unchecked onclick=\"show_all(this.id)\"/> <font color=\"black\" size = 3px> Show all results </font><font size = 2px color = \"#666\"> (By default only the first 10 results are shown.) </font> \n",
+ " <div style = \"width: 100%; height: 30px; \"></div>\n",
+ "</div>\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "<div id = \"div_compare\" style = \"position: fixed; top: 20%; left: 10%; width: 1200px; height: 600px; z-index: 999999; border: 1px solid #555; background-color: #fff; display: none\" onclick = \"$(this).fadeOut(500)\"> \n",
+ " \n",
+ " <div style = \"float: right; width: 80px; height: 25px; margin-top: 10px; margin-right: 10px; z-index: 1000000; border: 1px solid #555; text-align: center; vertical-align: middle; background-color: #f9f9f9; font-size:12pt; font-color: #000; cursor:pointer;\" > CLOSE </div> <!--button to close the div-->\n",
+ " <div id = \"div_compare_info\" style = \" width: 350px; height: 500px; float: right; margin-top: 50px; margin-right: 10px; z-index: 10000000;\"></div>\n",
+ " <div id = \"div_compare_container\" style = \"margin-top: 50px; margin-left: 100px; width: 600px; height: 300px;\">\n",
+ " <div class=\"g-before-after\" id = \"div_compare_containerx\"></div>\n",
+ " </div>\n",
+ "</div>\n",
+ "\n",
+ "\n",
+ "<div id = \"demo\"></div>\n",
+ "\n",
+ "<div id = \"plot_placeholder\">\n",
+ " <div><br></div>\n",
+ " <table id = \"table_visualize\"> </table>\n",
+ "</div>\n",
+ "<br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br>\n"
+ ],
+ "text/plain": [
+ "<IPython.core.display.HTML object>"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "%%HTML\n",
+ "<script>\n",
+ " var N_max_show = 10; //Number of results to be shown by default\n",
+ "\n",
+ " function show_materials_submitted_info()\n",
+ " {\n",
+ " //alert(\"N_materials=\" + N_materials)\n",
+ " //\"table_materials_submitted_info\"\n",
+ " //alert(\"show_materials_submitted_info: info_obj_all: \"+JSON.stringify(info_obj_all))\n",
+ " var table_content = new Array(); \n",
+ " str = '<tr>';\n",
+ " str += '<th width=\"5%\"></th>'\n",
+ " str += '<th width=\"10%\"><p style=\\\"text-align:center\\\"><font size = \\\"4pt\\\"><b>Atom labels</b></font></p></th>';\n",
+ " //str += '<th width=\"10%\"><p style=\\\"text-align:center\\\"><font size = \\\"4pt\\\"><b>Space group</b></font></p></th>';\n",
+ " //str += '<th width=\"15%\"><p style=\\\"text-align:center\\\"><font size = \\\"4pt\\\"><b>Lattice constants (in Ang)</b></font></p></th>';\n",
+ " str += '<th width=\"10%\"><p style=\\\"text-align:center\\\"><font size = \\\"4pt\\\"><b>Program name</b></font></p></th>';\n",
+ " str += '<th width=\"10%\"><p style=\\\"text-align:center\\\"><font size = \\\"4pt\\\"><b>Basis set type</b></font></p></th>';\n",
+ " str += '<th width=\"15%\"><p style=\\\"text-align:center\\\"><font size = \\\"4pt\\\"><b>Functional</b></font></p></th>';\n",
+ " //str += '<th width=\"20%\"><p style=\\\"text-align:center\\\"><font size = \\\"4pt\\\"><b>Number of <i>k</i> points per inverse distance</b></font></p></th>';\n",
+ " str += '</tr>'; //first row: head\n",
+ " table_content.push(str);\n",
+ "\n",
+ " for(var i = 0; i < N_materials; i++) //add info of each material\n",
+ " {\n",
+ " //alert(\"show_materials_submitted_info: material \"+ i); \n",
+ " table_content.push('<tr>');\n",
+ "\n",
+ " table_content.push('<td>'); \n",
+ " str = '<input type = \\\"checkbox\\\" name = \"checkbox_material\" id = \\\"checkbox_material' + i.toString() + '\\\" unchecked onclick=\\\"checkbox_material(this.id)\\\">';\n",
+ " str += \"<b>  #\" + (i+1).toString() + \"</b>\";\n",
+ " table_content.push(str);\n",
+ " table_content.push('</td>');\n",
+ "\n",
+ " table_content.push('<td>'); \n",
+ " str = '<font size = \\\"3pt\\\">';\n",
+ " str += info_obj_all[i][\"atom_labels\"] + ';   ';\n",
+ " str += \"</font>\"\n",
+ " table_content.push(str); \n",
+ " table_content.push('</td>');\n",
+ " //alert(\"got atom_labels\");\n",
+ "\n",
+ " /*\n",
+ " table_content.push('<td>'); \n",
+ " str = '<font size = \\\"3pt\\\">';\n",
+ " str += info_obj_all[i][\"space_group_symbol\"] + ';   ';\n",
+ " str += \"</font>\"\n",
+ " table_content.push(str); \n",
+ " table_content.push('</td>');\n",
+ " //alert(\"got space_group_symbol\");\n",
+ "\n",
+ " table_content.push('<td>'); \n",
+ " str = '<font size = \\\"3pt\\\">';\n",
+ " str += info_obj_all[i][\"lattice_constant\"] + ';   ';\n",
+ " str += \"</font>\"\n",
+ " table_content.push(str); \n",
+ " table_content.push('</td>');\n",
+ " //alert(\"got lattice_constant\");\n",
+ " */\n",
+ " \n",
+ " table_content.push('<td>'); \n",
+ " str = '<font size = \\\"3pt\\\">';\n",
+ " str += info_obj_all[i][\"program_name\"].toUpperCase() + ';   ';\n",
+ " str += \"</font>\"\n",
+ " table_content.push(str); \n",
+ " table_content.push('</td>');\n",
+ " //alert(\"got program_name\");\n",
+ "\n",
+ " table_content.push('<td>'); \n",
+ " str = '<font size = \\\"3pt\\\">';\n",
+ " str += info_obj_all[i][\"program_basis_set_type\"] + ';   ';\n",
+ " str += \"</font>\"\n",
+ " table_content.push(str); \n",
+ " table_content.push('</td>');\n",
+ " //alert(\"got program_basis_set_type\");\n",
+ "\n",
+ "\n",
+ " table_content.push('<td>'); \n",
+ " str = '<font size = \\\"3pt\\\">';\n",
+ " str += info_obj_all[i][\"XC_functional_name\"] + ';   ';\n",
+ " str += \"</font>\"\n",
+ " table_content.push(str); \n",
+ " table_content.push('</td>');\n",
+ " //alert(\"got XC_functional_name\");\n",
+ "\n",
+ " /*\n",
+ " table_content.push('<td>'); \n",
+ " str = '<font size = \\\"3pt\\\">';\n",
+ " str += band_obj_all[i][\"average_N_k_points_per_inverse_distance\"].toFixed(3);\n",
+ " str += \"</font>\"\n",
+ " table_content.push(str); \n",
+ " table_content.push('</td>');\n",
+ " //alert(\"got average_N_k_points_per_inverse_distance\");\n",
+ " */\n",
+ " table_content.push('</tr>');\n",
+ "\n",
+ " }\n",
+ " \n",
+ " document.getElementById(\"table_materials_submitted_info\").innerHTML = table_content.join('');\n",
+ " }\n",
+ "\n",
+ " function clean_materials_selection()\n",
+ " {\n",
+ " var choices_compare = document.getElementsByName(\"checkbox_material\");\n",
+ " for(var i=0; i<choices_compare.length; i++)\n",
+ " {\n",
+ " //choices_compare[i].removeAttribute('checked');\n",
+ " //choices_compare[i].setAttribute(\"unchecked\", \"unchecked\");\n",
+ " choices_compare[i].checked = \"\";\n",
+ " }\n",
+ " }\n",
+ "\n",
+ " function select_all()\n",
+ " {\n",
+ " var choices_compare = document.getElementsByName(\"checkbox_material\");\n",
+ " for(var i=0; i<choices_compare.length; i++)\n",
+ " {\n",
+ " //choices_compare[i].removeAttribute('checked');\n",
+ " //choices_compare[i].setAttribute(\"unchecked\", \"unchecked\");\n",
+ " choices_compare[i].checked = \"checked\";\n",
+ " }\n",
+ " }\n",
+ "\n",
+ "\n",
+ "\n",
+ " function process()\n",
+ " {\n",
+ " //alert(\"Process:\"+band_paths)\n",
+ " //Jupyter.notebook.execute_cells(window.findCellIndicesByTag('init_js_plot'));\n",
+ " //Jupyter.notebook.execute_cells(window.findCellIndicesByTag('show_materials_submitted_info'));\n",
+ " show_materials_submitted_info();\n",
+ " document.getElementById(\"table_visualize\").innerHTML = \"\";\n",
+ " str = N_materials.toString();\n",
+ " document.getElementById(\"n_materials\").innerHTML = \"Number of materials submitted: \" + str + \"<font size = 1px color = #C0C0C0 >   Please press \\'Visualize\\' to visualize the band structure. </font>\";\n",
+ " document.getElementById(\"div_showall\").style.visibility=\"hidden\";\n",
+ " }\n",
+ " \n",
+ "\n",
+ " var image_band = '';\n",
+ " var image_dos = '';\n",
+ " var image_band_links = new Array(N_materials); //store the URL of each band figure -> used to compare 2 figures\n",
+ " var image_band_links_selected = [];\n",
+ " var image_band_selected_Number = []; //record which i_material has been selected\n",
+ "\n",
+ "\n",
+ "\n",
+ " function prepare(N_materials_show)\n",
+ " {\n",
+ " document.getElementById(\"table_visualize\").innerHTML = \"\";\n",
+ " var table_content = new Array(); \n",
+ " //document.getElementById(\"table_visualize\").innerHTML = table_content.join('');\n",
+ " //-----Generate the html tables for each material--------\n",
+ " for(var i = 0; i < N_materials_show; i++)\n",
+ " {\n",
+ " checkbox_material_id = \"checkbox_material\" + i.toString();\n",
+ " var if_selected = check_show_VBM(checkbox_material_id);\n",
+ " if(if_selected != 1)\n",
+ " {\n",
+ " continue;\n",
+ " }\n",
+ "\n",
+ " table_content.push('<tr>');\n",
+ " div_string = '<div style = \\\"height: 20px\\\"></div>';\n",
+ " table_content.push(div_string);\n",
+ " table_content.push('<th>');\n",
+ "\n",
+ " //add main container div\n",
+ " div_string = '<div id = \\\"div_band_dos' + i.toString() + '\\\" class = \\\"div_band_dos\\\" >';\n",
+ " table_content.push(div_string);\n",
+ "\n",
+ " //show No. of the material\n",
+ " i_material = i + 1;\n",
+ " div_string = '<div style = \\\"height:30px\\; font-size: 15pt;\">' + '#' + i_material.toString() + '</div>';\n",
+ " table_content.push(div_string);\n",
+ "\n",
+ " //show band_path/dos info\n",
+ " div_string = '<div style = \\\"height:30px\\\">' + 'Band:   ' + band_paths[i] + ',    DOS:   ' + dos_paths[i] + '</div>';\n",
+ " table_content.push(div_string);\n",
+ "\n",
+ " //add div_band\n",
+ " div_string = '<div id = \\\"div_band' + i.toString() + '\\\" class = \\\"div_band\\\" ></div>';\n",
+ " table_content.push(div_string);\n",
+ "\n",
+ " //add div_dos\n",
+ " div_string = '<div id = \\\"div_dos' + i.toString() + '\\\" class = \\\"div_dos\\\" ></div>'; \n",
+ " table_content.push(div_string);\n",
+ "\n",
+ " //add div_tools\n",
+ " div_string = '<div id = \\\"div_tools' + i.toString() + '\\\" class = \\\"div_tools\\\" >'; \n",
+ " table_content.push(div_string);\n",
+ "\n",
+ " //add: infomation\n",
+ " div_string = '<div id = \\\"div_info' + i.toString() + '\\\">atom_labels<br>program_name</div>'; \n",
+ " table_content.push(div_string);\n",
+ "\n",
+ " //add: custom scale\n",
+ " div_string = '<br><p style=\\\"color: #000;font-weight: 100; font-size: 10pt; align:left\\\"> Set the lower and upper limit of energy scale (in eV): <br><br><font color=\\\"black\\\" size = 3px> Lower limit:    </font><textarea id=\\\"lowerlimit' + i.toString() + '\\\" rows=\\\"1\\\" style = \\\"width: 70px;\\\">-10</textarea> <font color=\\\"black\\\" size = 3px>   eV</font>    <font color=\\\"black\\\" size = 3px> Upper limit:    </font><textarea id=\\\"upperlimit' + i.toString() + '\\\" rows=\\\"1\\\" style = \\\"width: 70px;\\\">10</textarea> <font color=\\\"black\\\" size = 3px>   eV   </font></p>';\n",
+ " table_content.push(div_string);\n",
+ " div_string = '<br><button class = \\\"button_tools\\\" id = \\\"button_customscale' + i.toString() + '\\\" onclick = \\\"customscale(this.id)\\\"> Rescale </button>'; \n",
+ " table_content.push(div_string);\n",
+ "\n",
+ "\n",
+ " //add button:autoscale\n",
+ " div_string = '<button class = \\\"button_tools\\\" id = \\\"button_autoscale' + i.toString() + '\\\" onclick = \\\"autoscale(this.id)\\\" title = \\\"(-10 eV, 10 eV)\\\"> Autoscale </button>'; \n",
+ " table_content.push(div_string);\n",
+ " //add button:fullscale\n",
+ " div_string = '<button class = \\\"button_tools\\\" id = \\\"button_fullscale' + i.toString() + '\\\" onclick = \\\"fullscale(this.id)\\\" title = \\\"(-100 eV, 100 eV)\\\"> Full scale </button><br><br>'; \n",
+ " table_content.push(div_string);\n",
+ "\n",
+ " //table_content.push(\"Select and zoom:\");\n",
+ "\n",
+ " /*//overview for select and zoom\n",
+ " div_string = '<div id = \\\"div_overview' + i.toString() + '\\\" class = \\\"div_overview\\\" ></div>'; // <div id=\"overview\" style=\"width:300px;height:200px; margin-left:10px; margin-top: 50px; padding-top: 0px\"></div>\n",
+ " table_content.push(div_string);\n",
+ " div_string = '<p id = \\\"overviewLegend' + i.toString() + '\\\" ></p>'; // <p id=\"overviewLegend\" style=\"margin-left:10px\"></p>\n",
+ " table_content.push(div_string);*/\n",
+ "\n",
+ " //download figures as png\n",
+ " div_string = '<a id = \\\"img_band' + i.toString() + '\\\" class = \\\"button_tools\\\" target=\\\"_blank\\\" style = \\\"text-decoration: none;\\\" > Download band </a>';\n",
+ " table_content.push(div_string); \n",
+ " div_string = '<a id = \\\"img_dos' + i.toString() + '\\\" class = \\\"button_tools\\\" target=\\\"_blank\\\" style = \\\"text-decoration: none;\\\" > Download DOS </a>';\n",
+ " table_content.push(div_string);\n",
+ "\n",
+ " //add show VBM & CBM\n",
+ " div_string = '<br><br><p style = \\\"text-normal-black\\\"> <input type = \\\"checkbox\\\" id = \\\"checkbox_VBM' + i.toString() + '\\\" unchecked onclick=\\\"show_VBM(this.id)\\\"> <font color=\\\"black\\\" size = 3px> Show VBM </font> (<font color=\\\"blue\\\">\\•</font>) <font color=\\\"black\\\" size = 3px> and CBM </font>(<font color=\\\"red\\\">\\•</font>) </p>';\n",
+ " table_content.push(div_string);\n",
+ "\n",
+ "\n",
+ " table_content.push('</div>');//div_tools\n",
+ "\n",
+ " //checkbox for comparison\n",
+ " div_string = '<div id = \\\"div_checkbox_compare' + i.toString() + '\\\" class = \\\"div_checkbox_compare\\\" >';\n",
+ " table_content.push(div_string);\n",
+ " //div_string = '<p style = \\\"text-normal-black\\\"> <input type = \\\"checkbox\\\" id = \\\"checkbox_compare' + i.toString() + '\\\" unchecked name = \\\"checkbox_compare\\\" onclick=\\\"check_compare(this.id)\\\"> <font color=\\\"black\\\" size = 3px> Compare </font></p><p><font size = 2px color = \"#666\">(select max. 2 materials) </font> </p>';\n",
+ " div_string = '<p style = \\\"text-normal-black\\\"> <input type = \\\"checkbox\\\" id = \\\"checkbox_compare' + i.toString() + '\\\" checked = \\\"unchecked\\\" unchecked name = \\\"checkbox_compare\\\" onclick=\\\"check_compare(this.id)\\\"> <font color=\\\"black\\\" size = 3px> Compare </font></p><p><font size = 2px color = \"#666\">(select max. 2 materials) </font> </p>';\n",
+ " table_content.push(div_string);\n",
+ " table_content.push('</div>');//div_checkbox_compare\n",
+ "\n",
+ "\n",
+ " table_content.push('</div>');//div_band_dos\n",
+ " table_content.push('</th>');\n",
+ " table_content.push('</tr>'); \n",
+ " }\n",
+ "\n",
+ " document.getElementById(\"table_visualize\").innerHTML = table_content.join('');\n",
+ " }\n",
+ "\n",
+ "\n",
+ " function visualize_band_dos()\n",
+ " {\n",
+ " Jupyter.notebook.execute_cells(window.findCellIndicesByTag('init_jquery'));\n",
+ " Jupyter.notebook.execute_cells(window.findCellIndicesByTag('init_flot'));\n",
+ " Jupyter.notebook.execute_cells(window.findCellIndicesByTag('init_flot_axislabels'));\n",
+ " //Jupyter.notebook.execute_cells(window.findCellIndicesByTag('init_flot_dashes'));\n",
+ " Jupyter.notebook.execute_cells(window.findCellIndicesByTag('init_flot_navigate'));\n",
+ " //Jupyter.notebook.execute_cells(window.findCellIndicesByTag('init_flot_selection'));\n",
+ " Jupyter.notebook.execute_cells(window.findCellIndicesByTag('js_flot_legendoncanvas'));\n",
+ " document.getElementById(\"div_showall\").style.visibility=\"hidden\";\n",
+ " document.getElementById(\"div_compare_buttons\").style.visibility=\"\";\n",
+ "\n",
+ "\n",
+ "\n",
+ " if(N_materials > N_max_show)\n",
+ " {\n",
+ " document.getElementById(\"div_showall\").style.visibility=\"visible\";\n",
+ " document.getElementById(\"checkbox_showall\").checked = \"\";\n",
+ " } \n",
+ "\n",
+ " N_materials_show = Math.min(N_max_show, N_materials);\n",
+ "\n",
+ " prepare(N_materials_show);\n",
+ " clean_compare_list();\n",
+ " plot_band_dos_status = plot_band_dos(-10,10, N_materials_show);\n",
+ "\n",
+ " }\n",
+ "\n",
+ " function show_all(id)//\"plot_placeholder\"\n",
+ " {\n",
+ " var if_showall=0;\n",
+ " if_showall = check_show_VBM(id);\n",
+ " if(if_showall == 1)\n",
+ " {\n",
+ " N_materials_show = N_materials;\n",
+ " prepare(N_materials_show);\n",
+ " clean_compare_list();\n",
+ " plot_band_dos_status = plot_band_dos(-10,10, N_materials_show);\n",
+ " }\n",
+ " else\n",
+ " {\n",
+ " N_materials_show = Math.min(N_max_show, N_materials);\n",
+ " prepare(N_materials_show);\n",
+ " clean_compare_list();\n",
+ " plot_band_dos_status = plot_band_dos(-10,10, N_materials_show);\n",
+ " }\n",
+ "\n",
+ " }\n",
+ "\n",
+ " \n",
+ " //------------------Tool used to get the content from textarea---------------------\n",
+ " function get_text(textarea_id)\n",
+ " {\n",
+ " var text = document.getElementById(textarea_id).value;\n",
+ " return text;\n",
+ " }\n",
+ "\n",
+ "\n",
+ "\n",
+ " //-------------------Compare 2 band figures----------------------------------------\n",
+ "\n",
+ "\n",
+ " function check_compare(id)//checkbox_compare' + i.toString() + '\\\" unchecked onclick=\\\"check_compare(this.id)\n",
+ " {\n",
+ " var x = document.getElementById(id);\n",
+ " var choices_compare = document.getElementsByName(\"checkbox_compare\");\n",
+ " var N_chosen = 0;\n",
+ " for(var i=0; i<choices_compare.length; i++)\n",
+ " {\n",
+ " if(choices_compare[i].checked)\n",
+ " {\n",
+ " N_chosen ++;\n",
+ " }\n",
+ " }\n",
+ " if(N_chosen == 2) // In max. only 2 figures could be selected and compared.\n",
+ " {\n",
+ " for(var i=0; i<choices_compare.length; i++)\n",
+ " {\n",
+ " if(!choices_compare[i].checked)\n",
+ " {\n",
+ " choices_compare[i].disabled = 'disabled';\n",
+ " }\n",
+ " }\n",
+ " }\n",
+ " else\n",
+ " {\n",
+ " for(var i=0; i<choices_compare.length; i++)\n",
+ " {\n",
+ " choices_compare[i].removeAttribute('disabled');\n",
+ " }\n",
+ " }\n",
+ "\n",
+ " }\n",
+ "\n",
+ " function compare()\n",
+ " {\n",
+ " $(\"#div_compare\").fadeIn(600);//show div for comparison\n",
+ " //check_compare(-100);\n",
+ "\n",
+ " var compare_list = [];\n",
+ " compare_list = make_compare_list();\n",
+ " //[i_material_1, i_material_2] = make_compare_list();\n",
+ " i_material_1 = compare_list[0];\n",
+ " i_material_2 = compare_list[1];\n",
+ " //document.getElementById(\"demo\").innerHTML = \"In add info compare:\" + i_material_1.toString() + i_material_2.toString();\n",
+ " compare_figures(i_material_1, i_material_2); \n",
+ " }\n",
+ " function make_compare_list()\n",
+ " {\n",
+ " //get the links to the images\n",
+ " images_selected_links = []; //store the links to the figures for comparison\n",
+ " var choices_compare = document.getElementsByName(\"checkbox_compare\");\n",
+ " var N_chosen = 0;\n",
+ " var str = ''; //tmp str for debug\n",
+ " var figure_selected = new Array(2);\n",
+ " for(var i=0; i<choices_compare.length; i++) //check which figures are selected\n",
+ " {\n",
+ " if(choices_compare[i].checked)\n",
+ " {\n",
+ " id_chosen = choices_compare[i].id;\n",
+ " i_chosen = Math.round(id_chosen.substring(16));\n",
+ " var tmp_str = image_band_links[i_chosen];\n",
+ " images_selected_links.push(tmp_str);\n",
+ " figure_selected[N_chosen] = i_chosen;\n",
+ " N_chosen ++;\n",
+ " //str += beakerx.image_band_links[i];\n",
+ " }\n",
+ " }\n",
+ " var i_material_1 = 0;\n",
+ " var i_material_2 = 0;\n",
+ " //document.getElementById(\"demo\").innerHTML = 'In making comare list';\n",
+ " image_band_links_selected = images_selected_links;\n",
+ " //document.getElementById(\"demo\").innerHTML = 'In making comare list: next';\n",
+ " if(N_chosen == 2)\n",
+ " {\n",
+ " i_material_1 = figure_selected[0];\n",
+ " i_material_2 = figure_selected[1];\n",
+ " }\n",
+ " //document.getElementById(\"demo\").innerHTML = 'Compare_list: ' +i_material_1.toString() + ' ' + i_material_2.toString();\n",
+ "\n",
+ " return [i_material_1, i_material_2];\n",
+ " }\n",
+ "\n",
+ " function check_compare_scale(i_material_1, i_material_2)\n",
+ " {\n",
+ " lowerlimit_id_1 = \"lowerlimit\" + i_material_1.toString();\n",
+ " lowerlimit_id_2 = \"lowerlimit\" + i_material_2.toString();\n",
+ " upperlimit_id_1 = \"upperlimit\" + i_material_1.toString();\n",
+ " upperlimit_id_2 = \"upperlimit\" + i_material_2.toString();\n",
+ "\n",
+ " lowerlimit_1 = parseFloat(document.getElementById(lowerlimit_id_1).innerHTML);\n",
+ " lowerlimit_2 = parseFloat(document.getElementById(lowerlimit_id_2).innerHTML);\n",
+ " upperlimit_1 = parseFloat(document.getElementById(upperlimit_id_2).innerHTML);\n",
+ " upperlimit_2 = parseFloat(document.getElementById(upperlimit_id_2).innerHTML);\n",
+ " if((lowerlimit_1 != lowerlimit_2) || (upperlimit_1 != upperlimit_2))\n",
+ " return -1;\n",
+ " else\n",
+ " return 1;\n",
+ " }\n",
+ "\n",
+ " function compare_figures(i_material_1, i_material_2)\n",
+ " {\n",
+ " Jupyter.notebook.execute_cells(window.findCellIndicesByTag('js_query_beforeafter'));\n",
+ " Jupyter.notebook.execute_cells(window.findCellIndicesByTag('js_compare_slide'));\n",
+ " add_info_compare(i_material_1, i_material_2);\n",
+ " document.getElementById(\"div_compare_container\").scrollIntoView({ behavior: 'smooth' }); \n",
+ " document.getElementById(\"div_compare_container\").scrollTop += 50;\n",
+ "\n",
+ " }\n",
+ "\n",
+ "\n",
+ " function clean_compare_list()\n",
+ " {\n",
+ " var choices_compare = document.getElementsByName(\"checkbox_compare\");\n",
+ " for(var i=0; i<choices_compare.length; i++)\n",
+ " {\n",
+ " //choices_compare[i].removeAttribute('checked');\n",
+ " //choices_compare[i].setAttribute(\"unchecked\", \"unchecked\");\n",
+ " choices_compare[i].checked = \"\";\n",
+ " choices_compare[i].removeAttribute('disabled');\n",
+ " }\n",
+ " }\n",
+ "\n",
+ " //-----------Add information about the calculation to \"div_tools\"---------------\n",
+ " function add_info(i)\n",
+ " {\n",
+ " \n",
+ " //document.getElementById(\"demoa\").innerHTML = i.toString() + div_info_id;\n",
+ " //for(var i = 0; i < beakerx.N_materials; i++)\n",
+ " //{\n",
+ " div_info_id = \"div_info\" + i.toString();\n",
+ "\n",
+ " var str = '';\n",
+ " str += \"<br> <p style=\\\"text-align:left\\\"><font size = 3pt><b>Atom labels:</b>     \" + info_obj_all[i][\"atom_labels\"] + '</font></p>';\n",
+ " //str += \"<font size = 3pt><b>Space group:</b>     \" + info_obj_all[i][\"space_group_symbol\"] + '</font>';\n",
+ " //str += \"<font size = 3pt><b>Lattice constants (in Ang):</b>     \" + info_obj_all[i][\"lattice_constant\"] + '</font>';\n",
+ " str += \"<p style=\\\"text-align:left\\\"><font size = 3pt><b>Program name:</b>    \" + info_obj_all[i][\"program_name\"].toUpperCase() + '</font></p>';\n",
+ " str += \"<p style=\\\"text-align:left\\\"><font size = 3pt><b>Basis set type:</b>    \" + info_obj_all[i][\"program_basis_set_type\"] + '</font></p>';\n",
+ " str += \"<p style=\\\"text-align:left\\\"><font size = 3pt><b>Functional:</b>    \" + info_obj_all[i][\"XC_functional_name\"] + '</font></p>';\n",
+ " str += \"<p style=\\\"text-align:left\\\"><font size = 3pt><b>Number of <i>k</i> points per inverse distance:</b>    \" + band_obj_all[i][\"average_N_k_points_per_inverse_distance\"].toFixed(3) + '</font></p>';\n",
+ " document.getElementById(div_info_id).innerHTML = str;// + origData[\"atom_labels\"];\n",
+ " //document.getElementById('program_name_1').innerHTML = \"<b>Code:</b>    \" + origData[\"program_name\"];\n",
+ " //document.getElementById('program_basis_set_type_1').innerHTML = \"<b>Basis set type:</b>    \" + origData[\"program_basis_set_type\"];\n",
+ " //document.getElementById('XC_functional_name_1').innerHTML = \"<b>Functional:</b>    \" + origData[\"XC_functional_name\"]; \n",
+ " //}\n",
+ " \n",
+ " }\n",
+ " function add_info_compare(i,j)\n",
+ " {\n",
+ "\n",
+ " div_info_id = \"div_compare_info\";\n",
+ " var str = '';\n",
+ "\n",
+ " if_same_scale = check_compare_scale(i_material_1, i_material_2);\n",
+ " if(if_same_scale == -1)\n",
+ " {\n",
+ " str = '<b><font size = \"15pt\" color=\"#940000\">Error: Different lower/upper limits.</font></b><br>';\n",
+ " document.getElementById(\"div_compare_container\").innerHTML = str;\n",
+ " document.getElementById(div_info_id).innerHTML = '';\n",
+ " return;\n",
+ " }\n",
+ "\n",
+ " str += \"<br><b><font-size:15pt>Information of the first calculation (left):</font></b> <br>\";\n",
+ " str += \"<br> <b>Atom labels:</b>     \" + info_obj_all[i][\"atom_labels\"];\n",
+ " //str += \"<br> <b>Space group:</b>     \" + info_obj_all[i][\"space_group_symbol\"];\n",
+ " //str += \"<br> <b>Lattice constants (in Ang):</b>     \" + info_obj_all[i][\"lattice_constant\"];\n",
+ " str += \"<br> <b>Program name:</b>    \" + info_obj_all[i][\"program_name\"].toUpperCase();\n",
+ " str += \"<br> <b>Basis set type:</b>    \" + info_obj_all[i][\"program_basis_set_type\"];\n",
+ " str += \"<br> <b>Functional:</b>    \" + info_obj_all[i][\"XC_functional_name\"];\n",
+ " str += \"<br> <b>Number of <i>k</i> points per inverse distance:</b>    \" + band_obj_all[j][\"average_N_k_points_per_inverse_distance\"].toFixed(3);\n",
+ " str += \"<br><br><br><b><font-size:15pt>Information of the second calculation (right):</font></b><br>\";\n",
+ " str += \"<br> <b>Atom labels:</b>     \" + info_obj_all[j][\"atom_labels\"];\n",
+ " //str += \"<br> <b>Space group:</b>     \" + info_obj_all[j][\"space_group_symbol\"];\n",
+ " //str += \"<br> <b>Lattice constants (in Ang):</b>     \" + info_obj_all[j][\"lattice_constant\"];\n",
+ " str += \"<br> <b>Program name:</b>    \" + info_obj_all[j][\"program_name\"].toUpperCase();\n",
+ " str += \"<br> <b>Basis set type:</b>    \" + info_obj_all[j][\"program_basis_set_type\"]; \n",
+ " str += \"<br> <b>Functional:</b>    \" + info_obj_all[j][\"XC_functional_name\"];\n",
+ " str += \"<br> <b>Number of <i>k</i> points per inverse distance:</b>    \" + band_obj_all[j][\"average_N_k_points_per_inverse_distance\"].toFixed(3);\n",
+ " document.getElementById(div_info_id).innerHTML = str;// + origData[\"atom_labels\"];\n",
+ " }\n",
+ "\n",
+ "\n",
+ "\n",
+ " //-----------------------Show/hide VBM, CBM-------------------------\n",
+ " function check_show_VBM(checkbox_VBM_id)\n",
+ " {\n",
+ " var x = document.getElementById(checkbox_VBM_id);\n",
+ " var if_checked = 0;\n",
+ " if(x.checked)//== \"checked\")\n",
+ " {\n",
+ " //document.getElementById(\"demoa\").innerHTML = \"checked!\";\n",
+ " if_checked = 1;\n",
+ " }\n",
+ " else if (x.unchecked)// == \"unchecked\")\n",
+ " {\n",
+ " //document.getElementById(\"demoa\").innerHTML = \"unchecked!\";\n",
+ " if_checked = -1;\n",
+ " }\n",
+ " else\n",
+ " {\n",
+ " //document.getElementById(\"demoa\").innerHTML = \"nothing detected!\";\n",
+ " }\n",
+ " return if_checked;\n",
+ " }\n",
+ "\n",
+ " function check_if_in_compare_list(i) // check if the current material i is to be compared\n",
+ " {\n",
+ "\n",
+ " var checkbox_compare_id = \"checkbox_compare\" + i.toString();\n",
+ " var if_compare = check_show_VBM(checkbox_compare_id);\n",
+ " //document.getElementById(\"demo\").innerHTML = 'if_compare of ' + i.toString() + ' : ' + if_compare.toString();\n",
+ " var i_compare_material_1, i_compare_material_2;\n",
+ " [i_compare_material_1, i_compare_material_2] = make_compare_list();\n",
+ " var i_in_compare_list = -1;\n",
+ " if(i_compare_material_1 == i)\n",
+ " {\n",
+ " i_in_compare_list = 1;\n",
+ " }\n",
+ " else if (i_compare_material_2 == i)\n",
+ " {\n",
+ " i_in_compare_list = 2;\n",
+ " }\n",
+ " else\n",
+ " {\n",
+ " i_in_compare_list = 0;\n",
+ " }\n",
+ " //document.getElementById(\"demo\").innerHTML = 'Checking ' + i.toString() + ' in Compare_list: ' + i_in_compare_list.toString();\n",
+ " return [if_compare, i_in_compare_list];\n",
+ " }\n",
+ "\n",
+ " function show_VBM(id)\n",
+ " {\n",
+ " //prepare(\"new\");\n",
+ " //var if_show_VBM = -1;\n",
+ " var len_id = id.length;\n",
+ " var i_material = id.substring(12);\n",
+ " var i = Math.round(i_material);\n",
+ "\n",
+ " var checkbox_VBM_id = \"checkbox_VBM\" + i.toString();\n",
+ " var if_show_VBM = check_show_VBM(checkbox_VBM_id);\n",
+ "\n",
+ " var if_compare, i_in_compare_list;\n",
+ " [if_compare, i_in_compare_list] = check_if_in_compare_list(i);\n",
+ " //document.getElementById(\"demo\").innerHTML = i.toString() + ' in Compare_list: ' + i_in_compare_list.toString();\n",
+ "\n",
+ " plot_band_dos_i(i, -10, 10, if_show_VBM, if_compare, i_in_compare_list);\n",
+ "\n",
+ " }\n",
+ "\n",
+ "\n",
+ " //---------------------Functions to rescale-------------------------------------------\n",
+ " function autoscale(id)\n",
+ " {\n",
+ " var len_id = id.length;\n",
+ " var i_material = id.substring(16);\n",
+ " var i = Math.round(i_material);\n",
+ "\n",
+ " upperlim_id = \"upperlimit\" + i_material;\n",
+ " document.getElementById(upperlim_id).innerHTML =\"10.0\";\n",
+ " lowerlim_id = \"lowerlimit\" + i_material;\n",
+ " document.getElementById(lowerlim_id).innerHTML =\"-10.0\";\n",
+ "\n",
+ "\n",
+ " //document.getElementById(\"demoa\").innerHTML =i_material;\n",
+ " var checkbox_VBM_id = \"checkbox_VBM\" + i.toString();\n",
+ " var if_show_VBM = check_show_VBM(checkbox_VBM_id);\n",
+ "\n",
+ " var if_compare, i_in_compare_list;\n",
+ " [if_compare, i_in_compare_list] = check_if_in_compare_list(i);\n",
+ "\n",
+ "\n",
+ " plot_band_dos_i(i, -10, 10, if_show_VBM, if_compare, i_in_compare_list);\n",
+ "\n",
+ " }\n",
+ "\n",
+ " function fullscale(id)\n",
+ " {\n",
+ " var len_id = id.length;\n",
+ " var i_material = id.substring(16);\n",
+ " var i = Math.round(i_material);\n",
+ "\n",
+ " upperlim_id = \"upperlimit\" + i_material;\n",
+ " document.getElementById(upperlim_id).innerHTML =\"100.0\";\n",
+ " lowerlim_id = \"lowerlimit\" + i_material;\n",
+ " document.getElementById(lowerlim_id).innerHTML =\"-100.0\";\n",
+ "\n",
+ " //document.getElementById(\"demoa\").innerHTML =i_material;\n",
+ " var checkbox_VBM_id = \"checkbox_VBM\" + i.toString();\n",
+ " var if_show_VBM = check_show_VBM(checkbox_VBM_id);\n",
+ "\n",
+ " var if_compare, i_in_compare_list;\n",
+ " [if_compare, i_in_compare_list] = check_if_in_compare_list(i);\n",
+ "\n",
+ "\n",
+ "\n",
+ " plot_band_dos_i(i, -100, 100, if_show_VBM, if_compare, i_in_compare_list);\n",
+ "\n",
+ " }\n",
+ "\n",
+ " function customscale(id)\n",
+ " {\n",
+ " var len_id = id.length;\n",
+ " var i_material = id.substring(18);\n",
+ " var i = Math.round(i_material);\n",
+ " //\n",
+ " upperlim_id = \"upperlimit\" + i_material;\n",
+ " upperlim = document.getElementById(upperlim_id).value;\n",
+ " upperlim_float = Math.round(upperlim);\n",
+ " lowerlim_id = \"lowerlimit\" + i_material;\n",
+ " lowerlim = document.getElementById(lowerlim_id).value;\n",
+ " lowerlim_float = Math.round(lowerlim);\n",
+ "\n",
+ " var checkbox_VBM_id = \"checkbox_VBM\" + i.toString();\n",
+ " var if_show_VBM = check_show_VBM(checkbox_VBM_id);\n",
+ "\n",
+ " var if_compare, i_in_compare_list;\n",
+ " [if_compare, i_in_compare_list] = check_if_in_compare_list(i);\n",
+ "\n",
+ "\n",
+ "\n",
+ " plot_band_dos_i(i, lowerlim_float, upperlim_float, if_show_VBM, if_compare, i_in_compare_list); \n",
+ " }\n",
+ "\n",
+ "\n",
+ " function plot_band_dos(lowerLim, upperLim, N_materials_show)\n",
+ " {\n",
+ " placeholder_band = \"#div_band1\";\n",
+ " placeholder_dos = \"#div_dos1\";\n",
+ " // lowerLim = -10.01\n",
+ " //upperLim = 10.01\n",
+ "\n",
+ "\n",
+ "\n",
+ " //alert(\"plot_band_dos\");\n",
+ " //prepare();\n",
+ " for(var i = 0; i < N_materials_show; i++)\n",
+ " {\n",
+ " \n",
+ " var checkbox_material_id = \"checkbox_material\" + i.toString();\n",
+ " var if_selected = check_show_VBM(checkbox_material_id);\n",
+ " if(if_selected != 1)\n",
+ " {\n",
+ " continue;\n",
+ " }\n",
+ " add_info(i);\n",
+ " }\n",
+ "\n",
+ " //------Plot----------------\n",
+ " /*\n",
+ " for(var i_material = 0; i_material < N_materials_show; i_material++)\n",
+ " {\n",
+ "\n",
+ " //alert(\"Material \"+i);\n",
+ " var checkbox_material_id = \"checkbox_material\" + i_material.toString();\n",
+ " var if_selected = check_show_VBM(checkbox_material_id);\n",
+ " if(if_selected != 1)\n",
+ " {\n",
+ " continue;\n",
+ " }\n",
+ "\n",
+ " plot_band_dos_i(i_material, lowerLim, upperLim, 0, 0, -1);\n",
+ " }\n",
+ " */\n",
+ " //alert(\"next:for\")\n",
+ " for (let i_material = 0, p = Promise.resolve(); i_material < N_materials_show; i_material++) {\n",
+ " p = p.then(_ => new Promise(resolve =>\n",
+ " setTimeout(function () {\n",
+ " //alert(i_material)\n",
+ " var checkbox_material_id = \"checkbox_material\" + i_material.toString();\n",
+ " var if_selected = check_show_VBM(checkbox_material_id);\n",
+ " if(if_selected == 1)\n",
+ " {\n",
+ " plot_band_dos_i(i_material, lowerLim, upperLim, 0, 0, -1);\n",
+ " }\n",
+ " resolve();\n",
+ " }, 0)\n",
+ " ));\n",
+ " }\n",
+ "\n",
+ "\n",
+ " return 1;\n",
+ " }\n",
+ "\n",
+ " var i = 0\n",
+ " var lowerLim = -10\n",
+ " var upperLim = 10\n",
+ " var if_show_VBM = 0\n",
+ " var if_compare = 0\n",
+ " var i_in_compare_list = -1\n",
+ "\n",
+ "\n",
+ " \n",
+ " function plot_band_dos_i(i_material, lowerLim_material, upperLim_material, if_show_VBM_material, if_compare_material, i_in_compare_list_material)\n",
+ " {\n",
+ " //alert(\"plot_band_dos_i\")\n",
+ "\n",
+ " i = i_material;\n",
+ " lowerLim = lowerLim_material;\n",
+ " upperLim = upperLim_material;\n",
+ " if_show_VBM = if_show_VBM_material;\n",
+ " if_compare = if_compare_material;\n",
+ " i_in_compare_list = i_in_compare_list_material;\n",
+ " //alert(\"plot_band_dos_i: i_material: \"+i)\n",
+ " Jupyter.notebook.execute_cells(window.findCellIndicesByTag('plot_band'));\n",
+ " //alert('i, lowerLim, upperLim, if_show_VBM, if_compare, i_in_compare_list')\n",
+ " //plot_band(i, lowerLim, upperLim, if_show_VBM, if_compare, i_in_compare_list);\n",
+ " Jupyter.notebook.execute_cells(window.findCellIndicesByTag('plot_dos'));\n",
+ " } \n",
+ "</script>\n",
+ "\n",
+ " \n",
+ " \n",
+ "<br><br>\n",
+ "<button class=\"button\" onclick=\"process()\">Process data</button>\n",
+ "<br><br>\n",
+ "<div id = \"n_materials\" style = \"font-size: 18px; font-weight: 100; height: 60px; width: 100%;\"> Number of materials submitted: 0</div>\n",
+ "<div id = \"show_materials_submitted\" style = \"font-size: 20px; font-color: black;\"> </div>\n",
+ "\n",
+ "<div style = \"width :100%; height: 30px;\"></div> \n",
+ "<p style=\"color: #20335d;font-weight: 100; font-size: 18pt;\"> Select materials to visualize the band structure and DOS:</p>\n",
+ "<div style = \"width :100%; height: 10px;\"></div> \n",
+ "<button class = \"button\" onclick = \"clean_materials_selection()\"> Clean selections </button> \n",
+ "<button class = \"button\" onclick = \"select_all()\"> Select all </button> \n",
+ "<button class = \"button\" onclick = \"visualize_band_dos()\"> Visualize </button> \n",
+ "<div style = \"width :100%; height: 30px;\"></div> \n",
+ "\n",
+ "<div id = \"show_materials_submitted_info\" style = \"width: 100%; font-size: 20px; font-color: black;\"> \n",
+ " <table id = \"table_materials_submitted_info\" style=\"width:100%\"> </table>\n",
+ "</div>\n",
+ "\n",
+ "<div style = \"width :100%; height: 30px;\"></div> \n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "<div id=\"div_compare_buttons\" style=\"visibility:hidden\">\n",
+ " <br><br><br>\n",
+ " <p style=\"color: #20335d;font-weight: 100; font-size: 18pt;\"> Select two materials in the checkbox on the right for comparison:</p>\n",
+ " <p style=\"color: #000;font-weight: 1000; font-size: 8pt;\"></p>\n",
+ " <button class = \"button\" onclick = \"clean_compare_list()\"> Clean selections </button> \n",
+ " <button class = \"button\" onclick = \"compare();compare()\" title = \"Select 2 materials in the checkbox below and compare: please make sure that the upper/lower limits are the same (using Rescale/Autoscale buttons).\" > Compare</button>\n",
+ "</div>\n",
+ "\n",
+ "\n",
+ "\n",
+ "<div id = \"div_showall\" style = \"width: 100%; visibility:hidden\">\n",
+ " <div style = \"width: 100%; height: 30px; \"></div>\n",
+ " <input type = \"checkbox\" id = \"checkbox_showall\" unchecked onclick=\"show_all(this.id)\"/> <font color=\"black\" size = 3px> Show all results </font><font size = 2px color = \"#666\"> (By default only the first 10 results are shown.) </font> \n",
+ " <div style = \"width: 100%; height: 30px; \"></div>\n",
+ "</div>\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "<div id = \"div_compare\" style = \"position: fixed; top: 20%; left: 10%; width: 1200px; height: 600px; z-index: 999999; border: 1px solid #555; background-color: #fff; display: none\" onclick = \"$(this).fadeOut(500)\"> \n",
+ " \n",
+ " <div style = \"float: right; width: 80px; height: 25px; margin-top: 10px; margin-right: 10px; z-index: 1000000; border: 1px solid #555; text-align: center; vertical-align: middle; background-color: #f9f9f9; font-size:12pt; font-color: #000; cursor:pointer;\" > CLOSE </div> <!--button to close the div-->\n",
+ " <div id = \"div_compare_info\" style = \" width: 350px; height: 500px; float: right; margin-top: 50px; margin-right: 10px; z-index: 10000000;\"></div>\n",
+ " <div id = \"div_compare_container\" style = \"margin-top: 50px; margin-left: 100px; width: 600px; height: 300px;\">\n",
+ " <div class=\"g-before-after\" id = \"div_compare_containerx\"></div>\n",
+ " </div>\n",
+ "</div>\n",
+ "\n",
+ "\n",
+ "<div id = \"demo\"></div>\n",
+ "\n",
+ "<div id = \"plot_placeholder\">\n",
+ " <div><br></div>\n",
+ " <table id = \"table_visualize\"> </table>\n",
+ "</div>\n",
+ "<br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br>"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 43,
+ "metadata": {
+ "tags": [
+ "plot_band"
+ ]
+ },
+ "outputs": [
+ {
+ "data": {
+ "application/javascript": [
+ " //alert(\"tag: plot_band\")\n",
+ "\n",
+ "plot_band(i, lowerLim, upperLim, if_show_VBM, if_compare, i_in_compare_list);\n",
+ "\n",
+ "function plot_band(i, lowerLim, upperLim, if_show_VBM, if_compare, i_in_compare_list)\n",
+ "{\n",
+ " //i=0;\n",
+ " //alert(\"plot_band \"+ i)\n",
+ " var placeholder_band = \"#div_band\" + i.toString();\n",
+ " var placeholder_dos = \"#div_dos\" + i.toString();\n",
+ " var placeholder_tools = \"#div_tools\" + i.toString();\n",
+ " var placeholder_overview = \"#div_overview\" + i.toString();\n",
+ " var placeholder_overviewlegend = \"#overviewLegend\" + i.toString();\n",
+ " var checkbox_VBM_id = \"checkbox_VBM\" + i.toString();\n",
+ " var img_band_id = \"img_band\" + i.toString();\n",
+ " var img_dos_id = \"img_dos\" + i.toString();\n",
+ "\n",
+ " var placeholder_band_compare = \"\";\n",
+ "\n",
+ "\n",
+ " if(i_in_compare_list == 1)\n",
+ " {\n",
+ " placeholder_band_compare = \"#div_band_compare_1\";\n",
+ " }\n",
+ " else if(i_in_compare_list == 2)\n",
+ " {\n",
+ " placeholder_band_compare = \"#div_band_compare_2\";\n",
+ " }\n",
+ " else\n",
+ " {\n",
+ " placeholder_band_compare = \"#div_band_compare_1\"; // just for safe\n",
+ " }\n",
+ "\n",
+ " Object.size = function(obj) {\n",
+ " var size = 0, key;\n",
+ " for (key in obj) \n",
+ " {\n",
+ " if (obj.hasOwnProperty(key)) size++;\n",
+ " }\n",
+ " return size;\n",
+ " };\n",
+ "\n",
+ " //Get the number of bands\n",
+ " //alert(\"Getting band\")\n",
+ " //alert(band_obj_all)\n",
+ " //alert(\"band_obj_all got!\")\n",
+ " var N_bands = Object.size(band_obj_all[i][\"band_y_axis\"]);\n",
+ " var N_k_coors = Object.size(band_obj_all[i][\"band_x_axis\"]);\n",
+ " //alert(band_obj_all[i][\"band_y_axis\"])\n",
+ " var band_plotdata = [];\n",
+ " \n",
+ " for(var i_band =0; i_band < N_bands; i_band++)\n",
+ " {\n",
+ " var tmp_data = [];\n",
+ " for(var j_k_coor = 0; j_k_coor < N_k_coors; j_k_coor ++)\n",
+ " {\n",
+ " tmp_data.push([band_obj_all[i][\"band_x_axis\"][j_k_coor],band_obj_all[i][\"band_y_axis\"][i_band][j_k_coor]]);\n",
+ " }\n",
+ " var plotData = { shadowSize: 0 , data: tmp_data, color: 'black', series: { lines: { show: true } , points: {show: false} } };\n",
+ " band_plotdata.push(plotData);\n",
+ " }\n",
+ "\n",
+ "\n",
+ " var tmp_data0 = [[0, 0], [1, 0]];\n",
+ " var plotData0 = { shadowSize:0, color: 'black', data: tmp_data0, dashes:{ show:true, lineWidth: 1.5}};\n",
+ " band_plotdata.push(plotData0);\n",
+ "\n",
+ " var band_plotdata_overview = band_plotdata.slice(0);\n",
+ "\n",
+ " var HOMOdata= [[band_obj_all[i][\"HOMO_coor\"],band_obj_all[i][\"HOMO_energy\"]]];\n",
+ " var HOMOlabel = [\"VBM\"];\n",
+ " var plotHOMO={ shadowSize:0, color: 'blue', data: HOMOdata, points:{show:true, radius: 4 , fill: true, fillColor: 'blue'},lines:{show: false}, showLabels: true, labels: HOMOlabel, canvasRender: true, cColor: 'red', cFont:\"2em Arial\"};\n",
+ "\n",
+ " var LUMOdata= [[band_obj_all[i][\"LUMO_coor\"],band_obj_all[i][\"LUMO_energy\"]]];\n",
+ " var LUMOlabel = [\"CBM\"];\n",
+ " var plotLUMO={ shadowSize:0, color: 'red', data: LUMOdata, points:{show:true, radius: 4 , fill: true, fillColor: 'red'},lines:{show: false}, showLabels: true, labels: LUMOlabel, canvasRender: true, cColor: 'red', cFont:\"2em Arial\"};\n",
+ "\n",
+ " //if_show_VBM = check_show_VBM(checkbox_VBM_id);\n",
+ " if (if_show_VBM == 1)\n",
+ " {\n",
+ " band_plotdata.push(plotHOMO);\n",
+ " band_plotdata.push(plotLUMO);\n",
+ " }\n",
+ "\n",
+ " \n",
+ " //alert(img_band_id + band_plotdata)\n",
+ " \n",
+ " //!!!FIXME: if ($(\"#showVBM:checked\").length > 0 && gap > 0.1) \n",
+ " //plotHOMOLUMO={ shadowSize:0, color: 'red', data: d5, points:{show:true, radius: 0.8 , fill: true}, showLabels: true, labels: d5label, labelPlacement: labelPos, canvasRender: true, cColor: 'red', cFont:\"1em Arial\" }\n",
+ "\n",
+ " var canvas_band;\n",
+ " var options_band = {\n",
+ " canvas: true,\n",
+ " //legend:{ type: \"canvas\" },\n",
+ " series: { lines: { show: true, lineWidth: 2 }, \n",
+ " points: { show: false } }, \n",
+ " xaxis: { \n",
+ " ticks: band_obj_all[i][\"labels\"], \n",
+ " color:\"#000\", \n",
+ " font: {size: 20}, \n",
+ " zoomRange: false,\n",
+ " panRange: false \n",
+ " }, \n",
+ " yaxis: { \n",
+ " axisLabel: \"Energy (eV)\", \n",
+ " axisLabelUseCanvas: true,\n",
+ " //axisLabelUseCanvas: false,\n",
+ " axisLabelFontSizePixels: 20,\n",
+ " axisLabelFontFamily: 'Arial', \n",
+ " axisLabelPadding: 10, \n",
+ " color:\"#000\", \n",
+ " font: {size: 20, family:\"Arial\"},\n",
+ " tickLength:-5, \n",
+ " min: lowerLim, \n",
+ " max: upperLim,\n",
+ " tickDecimals: 0, \n",
+ " zoomRange: [0.001, 1000],\n",
+ " panRange: [-100, 100] \n",
+ " },\n",
+ "\n",
+ " zoom: { \n",
+ " interactive: true\n",
+ " },\n",
+ "\n",
+ " pan: {\n",
+ " interactive: true\n",
+ " }, \n",
+ "\n",
+ " //selection: { mode: \"xy\", color: \"#86a6b4\" }, \n",
+ "\n",
+ " grid: { \n",
+ " labelMargin: 15,\n",
+ " hoverable: true, \n",
+ " backgroundColor: { colors: [\"#fff\", \"#fff\"] }, \n",
+ " borderWidth: {\n",
+ " top: 2, \n",
+ " right: 2,\n",
+ " bottom: 2,\n",
+ " left: 2,\n",
+ " color : null } \n",
+ " }\n",
+ " }\n",
+ " //var plot_band = $.plot($(placeholder_band), band_plotdata, options_band);\n",
+ " //var plot_band = $.plot(\"#div_bandx\", band_plotdata, options_band);\n",
+ " var plot_band = $.plot($(placeholder_band), band_plotdata, options_band).getCanvas(); // save the canvas\n",
+ " var image_band = plot_band.toDataURL();\n",
+ " image_band = image_band.replace(\"image/png\",\"image/octet-stream\");\n",
+ " //beakerx.image_band = image_band;\n",
+ " document.getElementById(img_band_id).href= image_band;\n",
+ " image_band_links[i] = image_band;\n",
+ " //alert(\"band done\")\n",
+ "}\n"
+ ],
+ "text/plain": [
+ "<IPython.core.display.Javascript object>"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "%%javascript\n",
+ " //alert(\"tag: plot_band\")\n",
+ "\n",
+ "plot_band(i, lowerLim, upperLim, if_show_VBM, if_compare, i_in_compare_list);\n",
+ "\n",
+ "function plot_band(i, lowerLim, upperLim, if_show_VBM, if_compare, i_in_compare_list)\n",
+ "{\n",
+ " //i=0;\n",
+ " //alert(\"plot_band \"+ i)\n",
+ " var placeholder_band = \"#div_band\" + i.toString();\n",
+ " var placeholder_dos = \"#div_dos\" + i.toString();\n",
+ " var placeholder_tools = \"#div_tools\" + i.toString();\n",
+ " var placeholder_overview = \"#div_overview\" + i.toString();\n",
+ " var placeholder_overviewlegend = \"#overviewLegend\" + i.toString();\n",
+ " var checkbox_VBM_id = \"checkbox_VBM\" + i.toString();\n",
+ " var img_band_id = \"img_band\" + i.toString();\n",
+ " var img_dos_id = \"img_dos\" + i.toString();\n",
+ "\n",
+ " var placeholder_band_compare = \"\";\n",
+ "\n",
+ "\n",
+ " if(i_in_compare_list == 1)\n",
+ " {\n",
+ " placeholder_band_compare = \"#div_band_compare_1\";\n",
+ " }\n",
+ " else if(i_in_compare_list == 2)\n",
+ " {\n",
+ " placeholder_band_compare = \"#div_band_compare_2\";\n",
+ " }\n",
+ " else\n",
+ " {\n",
+ " placeholder_band_compare = \"#div_band_compare_1\"; // just for safe\n",
+ " }\n",
+ "\n",
+ " Object.size = function(obj) {\n",
+ " var size = 0, key;\n",
+ " for (key in obj) \n",
+ " {\n",
+ " if (obj.hasOwnProperty(key)) size++;\n",
+ " }\n",
+ " return size;\n",
+ " };\n",
+ "\n",
+ " //Get the number of bands\n",
+ " //alert(\"Getting band\")\n",
+ " //alert(band_obj_all)\n",
+ " //alert(\"band_obj_all got!\")\n",
+ " var N_bands = Object.size(band_obj_all[i][\"band_y_axis\"]);\n",
+ " var N_k_coors = Object.size(band_obj_all[i][\"band_x_axis\"]);\n",
+ " //alert(band_obj_all[i][\"band_y_axis\"])\n",
+ " var band_plotdata = [];\n",
+ " \n",
+ " for(var i_band =0; i_band < N_bands; i_band++)\n",
+ " {\n",
+ " var tmp_data = [];\n",
+ " for(var j_k_coor = 0; j_k_coor < N_k_coors; j_k_coor ++)\n",
+ " {\n",
+ " tmp_data.push([band_obj_all[i][\"band_x_axis\"][j_k_coor],band_obj_all[i][\"band_y_axis\"][i_band][j_k_coor]]);\n",
+ " }\n",
+ " var plotData = { shadowSize: 0 , data: tmp_data, color: 'black', series: { lines: { show: true } , points: {show: false} } };\n",
+ " band_plotdata.push(plotData);\n",
+ " }\n",
+ "\n",
+ "\n",
+ " var tmp_data0 = [[0, 0], [1, 0]];\n",
+ " var plotData0 = { shadowSize:0, color: 'black', data: tmp_data0, dashes:{ show:true, lineWidth: 1.5}};\n",
+ " band_plotdata.push(plotData0);\n",
+ "\n",
+ " var band_plotdata_overview = band_plotdata.slice(0);\n",
+ "\n",
+ " var HOMOdata= [[band_obj_all[i][\"HOMO_coor\"],band_obj_all[i][\"HOMO_energy\"]]];\n",
+ " var HOMOlabel = [\"VBM\"];\n",
+ " var plotHOMO={ shadowSize:0, color: 'blue', data: HOMOdata, points:{show:true, radius: 4 , fill: true, fillColor: 'blue'},lines:{show: false}, showLabels: true, labels: HOMOlabel, canvasRender: true, cColor: 'red', cFont:\"2em Arial\"};\n",
+ "\n",
+ " var LUMOdata= [[band_obj_all[i][\"LUMO_coor\"],band_obj_all[i][\"LUMO_energy\"]]];\n",
+ " var LUMOlabel = [\"CBM\"];\n",
+ " var plotLUMO={ shadowSize:0, color: 'red', data: LUMOdata, points:{show:true, radius: 4 , fill: true, fillColor: 'red'},lines:{show: false}, showLabels: true, labels: LUMOlabel, canvasRender: true, cColor: 'red', cFont:\"2em Arial\"};\n",
+ "\n",
+ " //if_show_VBM = check_show_VBM(checkbox_VBM_id);\n",
+ " if (if_show_VBM == 1)\n",
+ " {\n",
+ " band_plotdata.push(plotHOMO);\n",
+ " band_plotdata.push(plotLUMO);\n",
+ " }\n",
+ "\n",
+ " \n",
+ " //alert(img_band_id + band_plotdata)\n",
+ " \n",
+ " //!!!FIXME: if ($(\"#showVBM:checked\").length > 0 && gap > 0.1) \n",
+ " //plotHOMOLUMO={ shadowSize:0, color: 'red', data: d5, points:{show:true, radius: 0.8 , fill: true}, showLabels: true, labels: d5label, labelPlacement: labelPos, canvasRender: true, cColor: 'red', cFont:\"1em Arial\" }\n",
+ "\n",
+ " var canvas_band;\n",
+ " var options_band = {\n",
+ " canvas: true,\n",
+ " //legend:{ type: \"canvas\" },\n",
+ " series: { lines: { show: true, lineWidth: 2 }, \n",
+ " points: { show: false } }, \n",
+ " xaxis: { \n",
+ " ticks: band_obj_all[i][\"labels\"], \n",
+ " color:\"#000\", \n",
+ " font: {size: 20}, \n",
+ " zoomRange: false,\n",
+ " panRange: false \n",
+ " }, \n",
+ " yaxis: { \n",
+ " axisLabel: \"Energy (eV)\", \n",
+ " axisLabelUseCanvas: true,\n",
+ " //axisLabelUseCanvas: false,\n",
+ " axisLabelFontSizePixels: 20,\n",
+ " axisLabelFontFamily: 'Arial', \n",
+ " axisLabelPadding: 10, \n",
+ " color:\"#000\", \n",
+ " font: {size: 20, family:\"Arial\"},\n",
+ " tickLength:-5, \n",
+ " min: lowerLim, \n",
+ " max: upperLim,\n",
+ " tickDecimals: 0, \n",
+ " zoomRange: [0.001, 1000],\n",
+ " panRange: [-100, 100] \n",
+ " },\n",
+ "\n",
+ " zoom: { \n",
+ " interactive: true\n",
+ " },\n",
+ "\n",
+ " pan: {\n",
+ " interactive: true\n",
+ " }, \n",
+ "\n",
+ " //selection: { mode: \"xy\", color: \"#86a6b4\" }, \n",
+ "\n",
+ " grid: { \n",
+ " labelMargin: 15,\n",
+ " hoverable: true, \n",
+ " backgroundColor: { colors: [\"#fff\", \"#fff\"] }, \n",
+ " borderWidth: {\n",
+ " top: 2, \n",
+ " right: 2,\n",
+ " bottom: 2,\n",
+ " left: 2,\n",
+ " color : null } \n",
+ " }\n",
+ " }\n",
+ " //var plot_band = $.plot($(placeholder_band), band_plotdata, options_band);\n",
+ " //var plot_band = $.plot(\"#div_bandx\", band_plotdata, options_band);\n",
+ " var plot_band = $.plot($(placeholder_band), band_plotdata, options_band).getCanvas(); // save the canvas\n",
+ " var image_band = plot_band.toDataURL();\n",
+ " image_band = image_band.replace(\"image/png\",\"image/octet-stream\");\n",
+ " //beakerx.image_band = image_band;\n",
+ " document.getElementById(img_band_id).href= image_band;\n",
+ " image_band_links[i] = image_band;\n",
+ " //alert(\"band done\")\n",
+ "}"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 44,
+ "metadata": {
+ "tags": [
+ "plot_dos"
+ ]
+ },
+ "outputs": [
+ {
+ "data": {
+ "application/javascript": [
+ " //alert(\"tag: plot_dos \" + i)\n",
+ " //i=0;\n",
+ "\n",
+ " var placeholder_dos = \"#div_dos\" + i.toString();\n",
+ " var placeholder_tools = \"#div_tools\" + i.toString();\n",
+ " var placeholder_overview = \"#div_overview\" + i.toString();\n",
+ " var placeholder_overviewlegend = \"#overviewLegend\" + i.toString();\n",
+ " var img_dos_id = \"img_dos\" + i.toString();\n",
+ "\n",
+ "//----Plot DOS----------------------\n",
+ " var dos_plotdata = [];\n",
+ " //alert(\"dos:\"+dos_obj_all[i])\n",
+ " var xdos = dos_obj_all[i][\"dos_x_axis\"];\n",
+ " var ydos = dos_obj_all[i][\"dos_y_axis\"][0];\n",
+ " var dosLabelPos = Math.max.apply(Math, ydos)/2;\n",
+ " var d2 = [];\n",
+ " for (var ii = 0; ii < xdos.length; ii+=1) {\n",
+ " d2.push([ydos[ii],xdos[ii]]);\n",
+ " }\n",
+ " var plotData2={ shadowSize: 0, color: 'black' , data: d2};\n",
+ " dos_plotdata.push(plotData2);\n",
+ " //alert(\"dos_plotdata\"+JSON.stringify(dos_plotdata[0]));\n",
+ " \n",
+ " function find_xaxis_max_min(data, lowerbound, upperbound)\n",
+ " {\n",
+ " //data[xaxis,y] find the max and min value of x axis\n",
+ " //alert(\"dos[0]:\" + data[0][\"data\"]);\n",
+ " //alert(\"Bounds: \" + lowerbound + \" , \" + upperbound)\n",
+ " var n_data = data.length;\n",
+ " //alert(\"N dos: \" + n_data);\n",
+ " var data_min = 1000000;\n",
+ " var data_max = -1000000;\n",
+ " var data_current = 0;\n",
+ " for (var i = 0; i < n_data; i++)\n",
+ " {\n",
+ " if((data[i][1] >= lowerbound) && (data[i][1] <= upperbound))\n",
+ " {\n",
+ " data_current = data[i][0];\n",
+ " //alert(\"data[i]: \" + data[i] + \"data[i][0]: \" + data_current);\n",
+ " if(data_current >= data_max)\n",
+ " {\n",
+ " data_max = data_current;\n",
+ " }\n",
+ " if(data_current <= data_min)\n",
+ " {\n",
+ " data_min = data_current;\n",
+ " }\n",
+ " }\n",
+ " }\n",
+ " var data_max_min = [data_max, data_min];\n",
+ " //alert(\"data_max_min: \" + data_max_min);\n",
+ " return data_max_min;\n",
+ " }\n",
+ " var dos_x_max_min = find_xaxis_max_min(dos_plotdata[0][\"data\"], lowerLim, upperLim);\n",
+ " var dosLabelPos = (dos_x_max_min[0] + dos_x_max_min[1])/2;\n",
+ " //alert(\"dos_x_max_min:\"+dos_x_max_min+\", dosLabelPos:\"+dosLabelPos);\n",
+ " var options_dos ={\n",
+ " canvas: true,\n",
+ " series: {\n",
+ " lines: { show: true, lineWidth:2 },\n",
+ " points: { show: false }\n",
+ " },\n",
+ "\n",
+ " yaxis: { \n",
+ " axisLabel: \"\", \n",
+ " axisLabelUseCanvas: true,\n",
+ " axisLabelFontSizePixels: 20,\n",
+ " axisLabelFontFamily: 'Arial', \n",
+ " axisLabelPadding: 10, \n",
+ " color:\"#000\", \n",
+ " font: {size: 20},\n",
+ " tickLength:-5, \n",
+ " min: lowerLim, \n",
+ " max: upperLim,\n",
+ " tickDecimals: 0, \n",
+ " zoomRange: [0.001, 1000],\n",
+ " panRange: [-100, 100] \n",
+ " },\n",
+ "\n",
+ " xaxis: {\n",
+ " axisLabel: \" \",\n",
+ " axisLabelUseCanvas: false,\n",
+ " axisLabelFontSizePixels: 20,\n",
+ " axisLabelFontFamily: 'Arial',\n",
+ " axisLabelPadding: 3,\n",
+ " color:\"rgb(0, 0, 0)\",\n",
+ " font: {size: 20, family:\"Arial\"},\n",
+ " //ticks: 10,\n",
+ " tickLength:0,\n",
+ " min: dos_x_max_min[1],//0,\n",
+ " max: dos_x_max_min[0],//1,\n",
+ " tickDecimals: 0,\n",
+ " ticks: [[ dosLabelPos ,'DOS']],\n",
+ " //tickFormatter: MyFormatter\n",
+ " panRange: false\n",
+ " },\n",
+ " pan: {\n",
+ " interactive: true\n",
+ " }, \n",
+ "\n",
+ " grid: {\n",
+ " labelMargin: 15,\n",
+ " hoverable: true,\n",
+ " //borderWidth : 1000,\n",
+ " //show : false,\n",
+ " // //backgroundColor: { colors: [ \"#fff\", \"#eee\" ] },\n",
+ " backgroundColor: { colors: [\"#fff\", \"#fff\"] },\n",
+ " borderWidth: {\n",
+ " top: 2,\n",
+ " right: 2,\n",
+ " bottom: 2,\n",
+ " left: 2,\n",
+ " color : null\n",
+ " }\n",
+ " }\n",
+ " }\n",
+ " var plot_dos = $.plot(placeholder_dos, dos_plotdata, options_dos).getCanvas();\n",
+ " var image_dos = plot_dos.toDataURL();\n",
+ " image_dos = image_dos.replace(\"image/png\",\"image/octet-stream\");\n",
+ " image_dos = image_dos;\n",
+ " document.getElementById(img_dos_id).href= image_dos;\n",
+ " //alert(\"dos done.\")\n"
+ ],
+ "text/plain": [
+ "<IPython.core.display.Javascript object>"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "%%javascript\n",
+ " //alert(\"tag: plot_dos \" + i)\n",
+ " //i=0;\n",
+ "\n",
+ " var placeholder_dos = \"#div_dos\" + i.toString();\n",
+ " var placeholder_tools = \"#div_tools\" + i.toString();\n",
+ " var placeholder_overview = \"#div_overview\" + i.toString();\n",
+ " var placeholder_overviewlegend = \"#overviewLegend\" + i.toString();\n",
+ " var img_dos_id = \"img_dos\" + i.toString();\n",
+ "\n",
+ "//----Plot DOS----------------------\n",
+ " var dos_plotdata = [];\n",
+ " //alert(\"dos:\"+dos_obj_all[i])\n",
+ " var xdos = dos_obj_all[i][\"dos_x_axis\"];\n",
+ " var ydos = dos_obj_all[i][\"dos_y_axis\"][0];\n",
+ " var dosLabelPos = Math.max.apply(Math, ydos)/2;\n",
+ " var d2 = [];\n",
+ " for (var ii = 0; ii < xdos.length; ii+=1) {\n",
+ " d2.push([ydos[ii],xdos[ii]]);\n",
+ " }\n",
+ " var plotData2={ shadowSize: 0, color: 'black' , data: d2};\n",
+ " dos_plotdata.push(plotData2);\n",
+ " //alert(\"dos_plotdata\"+JSON.stringify(dos_plotdata[0]));\n",
+ " \n",
+ " function find_xaxis_max_min(data, lowerbound, upperbound)\n",
+ " {\n",
+ " //data[xaxis,y] find the max and min value of x axis\n",
+ " //alert(\"dos[0]:\" + data[0][\"data\"]);\n",
+ " //alert(\"Bounds: \" + lowerbound + \" , \" + upperbound)\n",
+ " var n_data = data.length;\n",
+ " //alert(\"N dos: \" + n_data);\n",
+ " var data_min = 1000000;\n",
+ " var data_max = -1000000;\n",
+ " var data_current = 0;\n",
+ " for (var i = 0; i < n_data; i++)\n",
+ " {\n",
+ " if((data[i][1] >= lowerbound) && (data[i][1] <= upperbound))\n",
+ " {\n",
+ " data_current = data[i][0];\n",
+ " //alert(\"data[i]: \" + data[i] + \"data[i][0]: \" + data_current);\n",
+ " if(data_current >= data_max)\n",
+ " {\n",
+ " data_max = data_current;\n",
+ " }\n",
+ " if(data_current <= data_min)\n",
+ " {\n",
+ " data_min = data_current;\n",
+ " }\n",
+ " }\n",
+ " }\n",
+ " var data_max_min = [data_max, data_min];\n",
+ " //alert(\"data_max_min: \" + data_max_min);\n",
+ " return data_max_min;\n",
+ " }\n",
+ " var dos_x_max_min = find_xaxis_max_min(dos_plotdata[0][\"data\"], lowerLim, upperLim);\n",
+ " var dosLabelPos = (dos_x_max_min[0] + dos_x_max_min[1])/2;\n",
+ " //alert(\"dos_x_max_min:\"+dos_x_max_min+\", dosLabelPos:\"+dosLabelPos);\n",
+ " var options_dos ={\n",
+ " canvas: true,\n",
+ " series: {\n",
+ " lines: { show: true, lineWidth:2 },\n",
+ " points: { show: false }\n",
+ " },\n",
+ "\n",
+ " yaxis: { \n",
+ " axisLabel: \"\", \n",
+ " axisLabelUseCanvas: true,\n",
+ " axisLabelFontSizePixels: 20,\n",
+ " axisLabelFontFamily: 'Arial', \n",
+ " axisLabelPadding: 10, \n",
+ " color:\"#000\", \n",
+ " font: {size: 20},\n",
+ " tickLength:-5, \n",
+ " min: lowerLim, \n",
+ " max: upperLim,\n",
+ " tickDecimals: 0, \n",
+ " zoomRange: [0.001, 1000],\n",
+ " panRange: [-100, 100] \n",
+ " },\n",
+ "\n",
+ " xaxis: {\n",
+ " axisLabel: \" \",\n",
+ " axisLabelUseCanvas: false,\n",
+ " axisLabelFontSizePixels: 20,\n",
+ " axisLabelFontFamily: 'Arial',\n",
+ " axisLabelPadding: 3,\n",
+ " color:\"rgb(0, 0, 0)\",\n",
+ " font: {size: 20, family:\"Arial\"},\n",
+ " //ticks: 10,\n",
+ " tickLength:0,\n",
+ " min: dos_x_max_min[1],//0,\n",
+ " max: dos_x_max_min[0],//1,\n",
+ " tickDecimals: 0,\n",
+ " ticks: [[ dosLabelPos ,'DOS']],\n",
+ " //tickFormatter: MyFormatter\n",
+ " panRange: false\n",
+ " },\n",
+ " pan: {\n",
+ " interactive: true\n",
+ " }, \n",
+ "\n",
+ " grid: {\n",
+ " labelMargin: 15,\n",
+ " hoverable: true,\n",
+ " //borderWidth : 1000,\n",
+ " //show : false,\n",
+ " // //backgroundColor: { colors: [ \"#fff\", \"#eee\" ] },\n",
+ " backgroundColor: { colors: [\"#fff\", \"#fff\"] },\n",
+ " borderWidth: {\n",
+ " top: 2,\n",
+ " right: 2,\n",
+ " bottom: 2,\n",
+ " left: 2,\n",
+ " color : null\n",
+ " }\n",
+ " }\n",
+ " }\n",
+ " var plot_dos = $.plot(placeholder_dos, dos_plotdata, options_dos).getCanvas();\n",
+ " var image_dos = plot_dos.toDataURL();\n",
+ " image_dos = image_dos.replace(\"image/png\",\"image/octet-stream\");\n",
+ " image_dos = image_dos;\n",
+ " document.getElementById(img_dos_id).href= image_dos;\n",
+ " //alert(\"dos done.\")"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 31,
+ "metadata": {
+ "tags": [
+ "init_jquery"
+ ]
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "<script src=\"http://code.jquery.com/jquery-1.8.3.min.js\"></script>\n"
+ ],
+ "text/plain": [
+ "<IPython.core.display.HTML object>"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "%%HTML\n",
+ "<script src=\"http://code.jquery.com/jquery-1.8.3.min.js\"></script>"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 32,
+ "metadata": {
+ "tags": [
+ "init_flot"
+ ]
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "<script src=\"js/jquery.flot.js\"></script>\n"
+ ],
+ "text/plain": [
+ "<IPython.core.display.HTML object>"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "%%HTML\n",
+ "<script src=\"js/jquery.flot.js\"></script>\n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 33,
+ "metadata": {
+ "tags": [
+ "init_flot_axislabels"
+ ]
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "<script src=\"js/jquery.flot.axislabels.js\"></script>\n"
+ ],
+ "text/plain": [
+ "<IPython.core.display.HTML object>"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "%%HTML\n",
+ "<script src=\"js/jquery.flot.axislabels.js\"></script>"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 34,
+ "metadata": {
+ "tags": [
+ "init_flot_navigate"
+ ]
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "<script src=\"js/jquery.flot.navigate.js\"></script>\n"
+ ],
+ "text/plain": [
+ "<IPython.core.display.HTML object>"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "%%HTML\n",
+ "<script src=\"js/jquery.flot.navigate.js\"></script>"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 87,
+ "metadata": {
+ "tags": [
+ "init_flot_selection"
+ ]
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "<script src=\"js/jquery.flot.selection.js\"></script>\n"
+ ],
+ "text/plain": [
+ "<IPython.core.display.HTML object>"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "%%HTML\n",
+ "<script src=\"js/jquery.flot.selection.js\"></script>"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 51,
+ "metadata": {
+ "tags": [
+ "js_query_beforeafter"
+ ]
+ },
+ "outputs": [
+ {
+ "data": {
+ "application/javascript": [
+ "//jquery.beforeafter.min.js\n",
+ "!function(e){e.fn.beforeafter=function(i){var t=e.extend({touch:!0,message:\"Slide\",hide_message:!0,reset:!0,reset_delay:3e3,drag_horizontal:!0,split_horizontal:!0\n",
+ "},i);return this.each(function(){var i=e(this),a=i.find(\"img\"),n=a.data(\"aftersrc\"),s=i.width(),d=0;a.after('<div class=\"g-img-after\"><img style=\"width: '+s+'px;\" src=\"'+n+'\"></div>'),\n",
+ "a.addClass(\"g-img-before\").width(s),i.append('<div class=\"g-img-divider\"><span>'+t.message+\"</span></div>\"),d=i.height(),t.split_horizontal||i.addClass(\"g-vertical\"),\n",
+ "i.on(\"mouseenter touchstart\",function(e){var t=i.data(\"reset-timer\");t&&(window.clearTimeout(t),i.data(\"reset-timer\",!1))}).on(\"mousemove touchmove\",function(a){\n",
+ "var n=0,o=0,r=i.find(\".g-img-divider span\");if(t.drag_horizontal)n=a.pageX-i.offset().left,o=n/s*100;else{var f=i.offset().top-e(window).scrollTop();n=a.clientY/f,\n",
+ "o=(a.clientY-f)/d*100}if(t.touch&&\"undefined\"!=typeof a.originalEvent.touches){var g=a.originalEvent.touches[0];o=t.drag_horizontal?(g.pageX-i.offset().left)/s*100:(g.pageY-i.offset().top)/d*100;\n",
+ "}t.split_horizontal?(i.find(\".g-img-after\").css(\"left\",o+\"%\"),i.find(\".g-img-divider\").css(\"left\",o+\"%\")):(i.find(\".g-img-after\").css(\"top\",o+\"%\"),i.find(\".g-img-divider\").css(\"top\",o+\"%\")),\n",
+ "t.hide_message&&r.is(\":visible\")&&r.fadeOut()}).on(\"mouseleave touchend touchcancel\",function(e){var a=i.data(\"reset-timer\"),n=i.find(\".g-img-divider span\");\n",
+ "t.reset&&(a||(a=window.setTimeout(function(){t.split_horizontal?(i.find(\".g-img-after\").animate({left:\"50%\"},500),i.find(\".g-img-divider\").animate({left:\"50%\"\n",
+ "},500,function(){n.fadeIn()})):(i.find(\".g-img-after\").animate({top:\"50%\"},500),i.find(\".g-img-divider\").animate({top:\"50%\"},500,function(){n.fadeIn()})),\n",
+ "i.data(\"reset-timer\",!1)},t.reset_delay),i.data(\"reset-timer\",a)))})}),this}}(jQuery);\n"
+ ],
+ "text/plain": [
+ "<IPython.core.display.Javascript object>"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "%%javascript\n",
+ "//jquery.beforeafter.min.js\n",
+ "!function(e){e.fn.beforeafter=function(i){var t=e.extend({touch:!0,message:\"Slide\",hide_message:!0,reset:!0,reset_delay:3e3,drag_horizontal:!0,split_horizontal:!0\n",
+ "},i);return this.each(function(){var i=e(this),a=i.find(\"img\"),n=a.data(\"aftersrc\"),s=i.width(),d=0;a.after('<div class=\"g-img-after\"><img style=\"width: '+s+'px;\" src=\"'+n+'\"></div>'),\n",
+ "a.addClass(\"g-img-before\").width(s),i.append('<div class=\"g-img-divider\"><span>'+t.message+\"</span></div>\"),d=i.height(),t.split_horizontal||i.addClass(\"g-vertical\"),\n",
+ "i.on(\"mouseenter touchstart\",function(e){var t=i.data(\"reset-timer\");t&&(window.clearTimeout(t),i.data(\"reset-timer\",!1))}).on(\"mousemove touchmove\",function(a){\n",
+ "var n=0,o=0,r=i.find(\".g-img-divider span\");if(t.drag_horizontal)n=a.pageX-i.offset().left,o=n/s*100;else{var f=i.offset().top-e(window).scrollTop();n=a.clientY/f,\n",
+ "o=(a.clientY-f)/d*100}if(t.touch&&\"undefined\"!=typeof a.originalEvent.touches){var g=a.originalEvent.touches[0];o=t.drag_horizontal?(g.pageX-i.offset().left)/s*100:(g.pageY-i.offset().top)/d*100;\n",
+ "}t.split_horizontal?(i.find(\".g-img-after\").css(\"left\",o+\"%\"),i.find(\".g-img-divider\").css(\"left\",o+\"%\")):(i.find(\".g-img-after\").css(\"top\",o+\"%\"),i.find(\".g-img-divider\").css(\"top\",o+\"%\")),\n",
+ "t.hide_message&&r.is(\":visible\")&&r.fadeOut()}).on(\"mouseleave touchend touchcancel\",function(e){var a=i.data(\"reset-timer\"),n=i.find(\".g-img-divider span\");\n",
+ "t.reset&&(a||(a=window.setTimeout(function(){t.split_horizontal?(i.find(\".g-img-after\").animate({left:\"50%\"},500),i.find(\".g-img-divider\").animate({left:\"50%\"\n",
+ "},500,function(){n.fadeIn()})):(i.find(\".g-img-after\").animate({top:\"50%\"},500),i.find(\".g-img-divider\").animate({top:\"50%\"},500,function(){n.fadeIn()})),\n",
+ "i.data(\"reset-timer\",!1)},t.reset_delay),i.data(\"reset-timer\",a)))})}),this}}(jQuery);"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 52,
+ "metadata": {
+ "tags": [
+ "js_compare_slide"
+ ]
+ },
+ "outputs": [
+ {
+ "data": {
+ "application/javascript": [
+ "var div_str = '';\n",
+ "//div_str = '<style> .g-before-after{position:relative;overflow:hidden}.g-before-after img{display:block}.g-before-after .g-img-before{float:left}.g-before-after .g-img-after,.g-before-after.g-vertical .g-img-after{position:absolute;top:0;right:0;left:50%;bottom:0;overflow:hidden}.g-before-after .g-img-after img{position:absolute;right:0;top:0}.g-before-after .g-img-divider{position:absolute;left:50%;top:0;bottom:0;width:0;border-left:1px solid #fff;border-right:1px solid #fff}.g-before-after .g-img-divider>span{position:absolute;top:50%;display:block;background-color:#fff;padding:5px 10px;line-height:1;text-align:center;-webkit-transform:translate(-50%,-50%);-ms-transform:translate(-50%,-50%);transform:translate(-50%,-50%)}.g-before-after.g-vertical .g-img-after{top:50%;left:0}.g-before-after.g-vertical .g-img-after img{position:absolute;right:auto;top:auto;left:0;bottom:0}.g-before-after.g-vertical .g-img-divider{position:absolute;left:0;top:50%;bottom:auto;right:0;height:0;width:100%;border-top:1px solid #fff;border-bottom:1px solid #fff;border-left:0 none;border-right:0 none}.g-before-after.g-vertical .g-img-divider>span{top:50%;left:50%} </style>'\n",
+ "//div_str += '<script>$(\\'#div_compare_containerx\\').beforeafter(); </script>';\n",
+ "//div_str +='<script type=\\\"text/javascript\\\" src=\\\"https://github.com/jquery/jquery/blob/master/src/jquery.js\\\"></script> '\n",
+ "//div_str += '<div class=\\\"g-before-after\\\" id=\\\"div_compare_containerx\\\">';\n",
+ "div_str +='<img src = \\\"'\n",
+ "\n",
+ "var src1 = image_band_links_selected[0];\n",
+ "var src2 = image_band_links_selected[1];\n",
+ "var tmp_src1 = src1;\n",
+ "var tmp_src2 = src2;\n",
+ "//src1 = \"https://images4.alphacoders.com/640/640956.jpg\";\n",
+ "//src2 = \"http://imgmr.com/wp-content/uploads/2016/06/SAO-anime.jpg\";\n",
+ "div_str +=src1;\n",
+ "div_str += '\\\" data-aftersrc=\\\"'\n",
+ "div_str +=src2;\n",
+ "//div_str += '\\\"></div>';\n",
+ "div_str += '\\\"/>';\n",
+ "//#div_compare_containerx\n",
+ "document.getElementById(\"div_compare_containerx\").innerHTML = div_str;\n",
+ "$('#div_compare_containerx').beforeafter({drag_horizontal: false, split_horizontal: false});\n",
+ "$('#div_compare_containerx').beforeafter({drag_horizontal: false, split_horizontal: false});\n",
+ "//beakerx.image_band_links[i]\n"
+ ],
+ "text/plain": [
+ "<IPython.core.display.Javascript object>"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "%%javascript\n",
+ "var div_str = '';\n",
+ "//div_str = '<style> .g-before-after{position:relative;overflow:hidden}.g-before-after img{display:block}.g-before-after .g-img-before{float:left}.g-before-after .g-img-after,.g-before-after.g-vertical .g-img-after{position:absolute;top:0;right:0;left:50%;bottom:0;overflow:hidden}.g-before-after .g-img-after img{position:absolute;right:0;top:0}.g-before-after .g-img-divider{position:absolute;left:50%;top:0;bottom:0;width:0;border-left:1px solid #fff;border-right:1px solid #fff}.g-before-after .g-img-divider>span{position:absolute;top:50%;display:block;background-color:#fff;padding:5px 10px;line-height:1;text-align:center;-webkit-transform:translate(-50%,-50%);-ms-transform:translate(-50%,-50%);transform:translate(-50%,-50%)}.g-before-after.g-vertical .g-img-after{top:50%;left:0}.g-before-after.g-vertical .g-img-after img{position:absolute;right:auto;top:auto;left:0;bottom:0}.g-before-after.g-vertical .g-img-divider{position:absolute;left:0;top:50%;bottom:auto;right:0;height:0;width:100%;border-top:1px solid #fff;border-bottom:1px solid #fff;border-left:0 none;border-right:0 none}.g-before-after.g-vertical .g-img-divider>span{top:50%;left:50%} </style>'\n",
+ "//div_str += '<script>$(\\'#div_compare_containerx\\').beforeafter(); </script>';\n",
+ "//div_str +='<script type=\\\"text/javascript\\\" src=\\\"https://github.com/jquery/jquery/blob/master/src/jquery.js\\\"></script> '\n",
+ "//div_str += '<div class=\\\"g-before-after\\\" id=\\\"div_compare_containerx\\\">';\n",
+ "div_str +='<img src = \\\"'\n",
+ "\n",
+ "var src1 = image_band_links_selected[0];\n",
+ "var src2 = image_band_links_selected[1];\n",
+ "var tmp_src1 = src1;\n",
+ "var tmp_src2 = src2;\n",
+ "//src1 = \"https://images4.alphacoders.com/640/640956.jpg\";\n",
+ "//src2 = \"http://imgmr.com/wp-content/uploads/2016/06/SAO-anime.jpg\";\n",
+ "div_str +=src1;\n",
+ "div_str += '\\\" data-aftersrc=\\\"'\n",
+ "div_str +=src2;\n",
+ "//div_str += '\\\"></div>';\n",
+ "div_str += '\\\"/>';\n",
+ "//#div_compare_containerx\n",
+ "document.getElementById(\"div_compare_containerx\").innerHTML = div_str;\n",
+ "$('#div_compare_containerx').beforeafter({drag_horizontal: false, split_horizontal: false});\n",
+ "$('#div_compare_containerx').beforeafter({drag_horizontal: false, split_horizontal: false});\n",
+ "//beakerx.image_band_links[i]"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {
+ "scrolled": false,
+ "tags": [
+ "process_band_dos_data_python"
+ ]
+ },
+ "outputs": [],
+ "source": [
+ "#tag:python_2\n",
+ "import urllib.request, json\n",
+ "import numpy as np\n",
+ "import math\n",
+ "\n",
+ "#======Define global objs============\n",
+ "info_all = []\n",
+ "band_obj_all = []\n",
+ "dos_obj_all = []\n",
+ "\n",
+ "def load_jsonfile(path):\n",
+ " #with open(path, encoding='utf-8') as band_file: \n",
+ " # return json.load(band_file)\n",
+ "\n",
+ " \n",
+ " with urllib.request.urlopen(path) as url:\n",
+ " data = json.loads(url.read().decode())\n",
+ " return data\n",
+ "\n",
+ "#-----Get the labels for x axis---------------\n",
+ "def get_label_flag(coor_array):\n",
+ " #np.sort(coor_array)\n",
+ " x = coor_array[0]\n",
+ " y = coor_array[1]\n",
+ " z = coor_array[2]\n",
+ " coor =np.sort([x,y,z])\n",
+ " xx = coor[0]\n",
+ " yy = coor[1]\n",
+ " zz = coor[2]\n",
+ " coor = [xx, yy, zz]\n",
+ " #pprint(coor)\n",
+ " if (coor == [0, 0.5, 0.5]):\n",
+ " return \"X\"\n",
+ " if (coor == [0, 0.0, 0.5]):\n",
+ " return \"M\"\n",
+ " elif (coor == [0.5, 0.5, 0.5]):\n",
+ " return \"L\"\n",
+ " elif (coor == [0.375, 0.375, 0.75]):\n",
+ " return \"K\"\n",
+ " elif (coor == [0.25, 0.5, 0.75]):\n",
+ " return \"W\"\n",
+ " elif (coor == [0, 0, 0]):\n",
+ " return \"\\u0393\"\n",
+ " elif (coor == [0.25, 0.625, 0.625]):\n",
+ " return \"U\"\n",
+ " else:\n",
+ " return \"?\"\n",
+ "\n",
+ "#============Process the band structure data============\n",
+ "def get_band_obj(band_path, dos_fermi_energy):\n",
+ "\n",
+ " #band_data: read from json file \n",
+ " #Load the data files for band\n",
+ " band_data = load_jsonfile(band_path)\n",
+ " \n",
+ " #---------Read section_k_band_segment------------\n",
+ " section_k_band_segment = band_data['section_run']['section_single_configuration_calculation']['section_k_band'][0]['section_k_band_segment']\n",
+ " \n",
+ " #--------Get the number of k band segments-------------\n",
+ " N_k_band_segments = len(section_k_band_segment)\n",
+ " \n",
+ " #----------Get the total number of k points in all segments---------\n",
+ " N_k_points_all = 0\n",
+ " for i in range(N_k_band_segments):\n",
+ " band_k_points = section_k_band_segment[i]['band_k_points']\n",
+ " N_k_points_all = N_k_points_all + len(band_k_points)\n",
+ " \n",
+ " #--------Get the x axis for the band structure figure: the coordinates of k points in 1D\n",
+ " # store in k_coor_1D[N_k_points_total]-----------------\n",
+ "\n",
+ " band_distance_segments = np.zeros(N_k_band_segments)\n",
+ " for i in range(N_k_band_segments):\n",
+ " [[x1, y1, z1],[x2, y2, z2]]= section_k_band_segment[i]['band_segm_start_end'] #\"band_segm_start_end\": [[0.5, 0.0, 0.5],[0.5, 0.25, 0.75]],\n",
+ " band_distance_segments[i] = math.pow((x1-x2), 2) + math.pow((y1-y2), 2) + math.pow((z1-z2), 2)\n",
+ "\n",
+ " \n",
+ " band_distance_total = math.fsum(band_distance_segments)\n",
+ " #print(band_distance_segments)\n",
+ " average_N_k_points_per_inverse_distance = N_k_points_all / band_distance_total\n",
+ " \n",
+ " #Prepare the parameters to rescale the k coordinates into [0,1]\n",
+ " step_k_point = 1.0 / N_k_points_all\n",
+ " step_k_point = (1.0 + step_k_point) / N_k_points_all\n",
+ " \n",
+ " # \n",
+ " k_coor_1D = np.zeros((N_k_points_all))\n",
+ " for i_k_points in range(N_k_points_all):\n",
+ " k_coor_1D[i_k_points] = round( step_k_point * i_k_points, 3)\n",
+ " #for i in range(N_k_band_segments):\n",
+ " # ki[i] = \n",
+ " \n",
+ "\n",
+ " #--------Get the eigenvalues of each band trajectory--------------\n",
+ " N_k_points_per_segment = len(section_k_band_segment[0]['band_energies'][0]) #suppose the numebr of k points in all the segments are the same\n",
+ " N_bands = len(section_k_band_segment[0]['band_energies'][0][0])\n",
+ " band_energies_all = np.zeros((N_bands, N_k_points_all)) #store the eigenvalues\n",
+ " N_k_points_all = 0\n",
+ " for i_segments in range(N_k_band_segments):\n",
+ " band_energies = section_k_band_segment[i_segments]['band_energies']\n",
+ " N_spin_channel = len(band_energies) #Number of the spin channel --FIXME: no spin polarized\n",
+ " N_k_points_per_segment = len(band_energies[0])\n",
+ " for i_k_points in range(N_k_points_per_segment):\n",
+ " for i_bands in range(N_bands):\n",
+ " band_energies_all[i_bands][N_k_points_all] = band_energies[0][i_k_points][i_bands] / (1.60217656535 * pow(10, -19))\n",
+ " N_k_points_all = N_k_points_all + 1\n",
+ " \n",
+ " \n",
+ " N_labels = 0\n",
+ " for i_segments in range(N_k_band_segments):\n",
+ " for j in range(2):\n",
+ " labels_tmp = section_k_band_segment[i_segments]['band_segm_start_end'][j];\n",
+ " N_labels = N_labels + 1\n",
+ "\n",
+ " label_flag = [\"\" for i in range(N_labels)] #stores the flags of the labels (X, W, G, etc)\n",
+ "\n",
+ " i_label = 0\n",
+ " label_flag_last_final = \"\"\n",
+ " label_flag_current_initial = \"\"\n",
+ " for i_segments in range(N_k_band_segments):\n",
+ " labels_coor_0 = section_k_band_segment[i_segments]['band_segm_start_end'][0];\n",
+ " labels_coor_1 = section_k_band_segment[i_segments]['band_segm_start_end'][1];\n",
+ " np.sort(labels_coor_0)\n",
+ " np.sort(labels_coor_1)\n",
+ " label_flag_0 = get_label_flag(labels_coor_0)\n",
+ " label_flag_1 = get_label_flag(labels_coor_1)\n",
+ " label_flag_current_initial = label_flag_0\n",
+ " if(label_flag_last_final == \"\"):\n",
+ " label_flag_last_final = label_flag_0\n",
+ "\n",
+ " if(label_flag_last_final == label_flag_current_initial):\n",
+ " label_flag[i_label] = label_flag_current_initial\n",
+ " else:\n",
+ " label_flag[i_label] = \"\".join([label_flag_last_final, '|', label_flag_current_initial])\n",
+ " label_flag_last_final = label_flag_1\n",
+ " \n",
+ "\n",
+ " i_label = i_label + 1\n",
+ " if(i_segments == N_k_band_segments - 1):\n",
+ " label_flag[i_label] = label_flag_1\n",
+ " i_label = i_label + 1\n",
+ "\n",
+ " N_labels = i_label\n",
+ " \n",
+ " #------------Get the coordinates for the labels------------\n",
+ " #label_coor_abs = np.zeros((N_labels)) #stores the absolute coordinates of the labels\n",
+ " label_coor_relative = np.zeros((N_labels))\n",
+ " for i_label in range(N_labels):\n",
+ " #Here the evenly-distributed relative coordinates is used, because the coordinates of the labels could be too nerrow when using there absolute coordinates\n",
+ " #x = labels_coor_0[0]\n",
+ " #y = labels_coor_0[1]\n",
+ " #z = labels_coor_0[2]\n",
+ " #label_coor_abs[i_label] = np.sqrt(x*x+y*y+z*z)\n",
+ " label_coor_relative[i_label] = step_k_point * N_k_points_per_segment * i_label / (1 + 1.0 / N_k_points_all);\n",
+ "\n",
+ " #----Store the label-----------\n",
+ " label_obj =[['' for i in range(2)] for j in range(N_labels)]\n",
+ " for i_label in range(N_labels):\n",
+ " label_obj[i_label][0] = label_coor_relative[i_label]\n",
+ " label_obj[i_label][1] = label_flag[i_label]\n",
+ " \n",
+ " #print(label_obj)\n",
+ " \n",
+ " \n",
+ " #Rescal the energies with respect to dos_fermi_energy\n",
+ " for i_k_points in range(N_k_points_all):\n",
+ " for i_bands in range(N_bands):\n",
+ " band_energies_all[i_bands][i_k_points] = band_energies_all[i_bands][i_k_points] - dos_fermi_energy\n",
+ "\n",
+ " #-------Get VBM, CBM----------------\n",
+ "\n",
+ " HOMO = -1000\n",
+ " LUMO = 1000\n",
+ " coor_k_point_HOMO = np.zeros((3)) #the coordinate of k point that stores HOMO\n",
+ " coor_k_point_LUMO = np.zeros((3)) #the coordinate of k point that stores LUMO\n",
+ " #band_gap_direct = 0.0\n",
+ " band_gap_indirect = 0.0\n",
+ " \n",
+ " \n",
+ " #band_energy_max = np.amax(band_energies[0])/ (1.60217656535* pow(10,-19))\n",
+ " #band_energy_min = np.amin(band_energies[0])/ (1.60217656535* pow(10,-19))\n",
+ " band_energy_max = 10\n",
+ " band_energy_min = -10\n",
+ " #N_band_energy_index = 10000\n",
+ " #band_energy_step = (band_energy_max - band_energy_min) / N_band_energy_index\n",
+ " #N_allowed_states = np.zeros(N_band_energy_index + 1)\n",
+ " #i_index_fermi = math.floor((0 - band_energy_min) / band_energy_step) #the index that stores states at the Fermi level\n",
+ "\n",
+ " for i_k_points_all in range(N_k_points_all):\n",
+ " for i_bands in range(N_bands):\n",
+ " #i_band_index = math.floor((band_energies_all[i_bands][i_k_points_all] - band_energy_min) / band_energy_step)\n",
+ " #N_allowed_states[index_band_energy] = N_allowed_states[index_band_energy] + 1\n",
+ " band_energy = band_energies_all[i_bands][i_k_points_all]\n",
+ " if(band_energy > 0):\n",
+ " if(band_energy < LUMO):\n",
+ " LUMO = band_energy\n",
+ " else:\n",
+ " if(band_energy > HOMO):\n",
+ " HOMO = band_energy\n",
+ " #for i_band_index in range(i_index_fermi, N_band_energy_index): #get LUMO\n",
+ " # if(N_allowed_states[i_band_index] > 0):\n",
+ " # LUMO = band_energy_min + band_energy_step * i_band_index\n",
+ " print('HOMO, LUMO: ',HOMO, LUMO)\n",
+ " band_gap_indirect = abs(LUMO - HOMO)\n",
+ " \n",
+ " if(band_gap_indirect < 0.5): #VBM and CBM has to be found in another way for metals/charged system:\n",
+ " HOMO = -1000\n",
+ " LUMO = 1000\n",
+ " band_energy_max = 10\n",
+ " band_energy_min = 0\n",
+ " N_band_energy_index = 10000\n",
+ " band_energy_step = (band_energy_max - band_energy_min) / N_band_energy_index\n",
+ " N_allowed_states = np.zeros(N_band_energy_index + 1)\n",
+ " \n",
+ " #get the DOS and store in N_allowed_states[]\n",
+ " for i_k_points_all in range(N_k_points_all):\n",
+ " for i_bands in range(N_bands):\n",
+ " band_energy = band_energies_all[i_bands][i_k_points_all]\n",
+ " if(band_energy_min < band_energy < band_energy_max):\n",
+ " i_band_index = math.floor((band_energy - band_energy_min) / band_energy_step)\n",
+ " N_allowed_states[i_band_index] = N_allowed_states[i_band_index] + 1\n",
+ " if_gapped = 0\n",
+ " for i_band_index in range(N_band_energy_index): #go through the energy levels from the bottom\n",
+ " band_energy = band_energy_min + band_energy_step * i_band_index\n",
+ " if(N_allowed_states[i_band_index] == 0):\n",
+ " if_gapped = if_gapped + 1\n",
+ " if(band_energy > band_energy_max - 0.5) and (if_gapped == 0):\n",
+ " print(\"No gap found in this system. It seems to be a metal.\")\n",
+ " HOMO = 1000\n",
+ " LUMO = 1000\n",
+ " break\n",
+ " #print(\"At \", band_energy,\": # allowed states = \", N_allowed_states[i_band_index],\" if_gapped = \", if_gapped)\n",
+ " \n",
+ " if(N_allowed_states[i_band_index] > 0):\n",
+ " if(if_gapped * band_energy_step> 0.3 ): #above VBM-CBM gap: LUMO\n",
+ " if(band_energy < LUMO):\n",
+ " #print(\"LUMO got!\")\n",
+ " LUMO = band_energy\n",
+ " break #break before touching another gap that is above the band gap\n",
+ " if(if_gapped * band_energy_step < 0.3): #below VBM-CBM gap: HOMO\n",
+ " if(band_energy > HOMO):\n",
+ " #print(\"HOMO got!\")\n",
+ " HOMO = band_energy\n",
+ " \n",
+ " if_gapped = 0\n",
+ " \n",
+ " print('HOMO, LUMO for metal/charged system: ',HOMO, LUMO)\n",
+ " \n",
+ " '''\n",
+ "\n",
+ "# print('HOMO: ',tmp_HOMO_max)\n",
+ " HOMO_global = tmp_HOMO_max\n",
+ " LUMO_global = tmp_LUMO_min\n",
+ " band_gap_indirect = LUMO_global - HOMO_global\n",
+ " E_top_valence = HOMO_global\n",
+ " if(band_gap_indirect < 0):\n",
+ " band_gap_indirect = 0\n",
+ "\n",
+ " #Rescal HOMO and LUMO with respect to HOMO\n",
+ " HOMO_global = round((HOMO_global - E_top_valence), 3)\n",
+ " LUMO_global = round((LUMO_global - E_top_valence), 3)\n",
+ " '''\n",
+ " \n",
+ " \n",
+ " \n",
+ " #Find the position of HOMO, LUMO\n",
+ "\n",
+ " for i_k_points in range(N_k_points_all):\n",
+ " for i_bands in range(N_bands):\n",
+ " if(abs(band_energies_all[i_bands][i_k_points] - HOMO) < 0.001):\n",
+ " coor_k_point_HOMO = k_coor_1D[i_k_points]\n",
+ " if(abs(band_energies_all[i_bands][i_k_points] - LUMO) < 0.001):\n",
+ " coor_k_point_LUMO = k_coor_1D[i_k_points] \n",
+ "\n",
+ "\n",
+ " \n",
+ " \n",
+ " #Store the band data to band_obj\n",
+ "\n",
+ " band_obj = {}\n",
+ " band_obj[\"band_x_axis\"] = np.array(k_coor_1D).tolist()\n",
+ " band_obj[\"band_y_axis\"] = np.array(band_energies_all).tolist()\n",
+ " band_obj[\"labels\"] = np.array(label_obj).tolist()\n",
+ " band_obj[\"HOMO_energy\"] = np.array(HOMO).tolist()\n",
+ " band_obj[\"HOMO_coor\"] = np.array(coor_k_point_HOMO).tolist()\n",
+ " band_obj[\"LUMO_energy\"] = np.array(LUMO).tolist()\n",
+ " band_obj[\"LUMO_coor\"] = np.array(coor_k_point_LUMO).tolist()\n",
+ " band_obj[\"average_N_k_points_per_inverse_distance\"] = np.array(average_N_k_points_per_inverse_distance).tolist()\n",
+ " \n",
+ "\n",
+ " \n",
+ " return band_obj\n",
+ "\n",
+ "\n",
+ "#===============Get the space group information===========\n",
+ "def get_space_group(band_data):\n",
+ " import pymatgen as mg\n",
+ " from pymatgen.symmetry.analyzer import SpacegroupAnalyzer\n",
+ "\n",
+ " simulation_cell = np.array(band_data[\"section_run\"][\"section_system\"][0].get('simulation_cell',\"empty\")) * 10000000000\n",
+ " atom_positions = np.array(band_data[\"section_run\"][\"section_system\"][0].get('atom_positions',\"empty\")) * 10000000000\n",
+ " atom_labels = np.array(band_data[\"section_run\"][\"section_system\"][0].get('atom_labels',\"empty\"))\n",
+ " structure = mg.Structure(simulation_cell,atom_labels, atom_positions, coords_are_cartesian = True)\n",
+ " \n",
+ " finder = SpacegroupAnalyzer(structure, symprec=1e-3, angle_tolerance=5)\n",
+ " space_group_symbol = finder.get_space_group_symbol()\n",
+ " lattice_constant = []\n",
+ " for item in structure.lattice.abc:\n",
+ " lattice_constant.append(item)\n",
+ " for i in range(len(lattice_constant)):\n",
+ " item = str(round(lattice_constant[i], 3))\n",
+ " lattice_constant[i] = item\n",
+ " \n",
+ " return [space_group_symbol, lattice_constant]\n",
+ "\n",
+ "#================Get the DOS data==============================\n",
+ "def get_dos_obj(dos_path):\n",
+ " #dos_data: read from json file \n",
+ " #Load the data files for dos\n",
+ " dos_data = load_jsonfile(dos_path)\n",
+ "\n",
+ " print(dos_path)\n",
+ " #N_dos_values = len(dos_data['sections']['section_run-0']['sections']['section_single_configuration_calculation-0']['section_dos'][0]['dos_energies'])\n",
+ " N_dos_values = len(dos_data['section_run']['section_single_configuration_calculation']['section_dos'][0]['dos_energies'])\n",
+ " #in new parser, it seems that the spin channel of 'dos_energies' disappears: Shape: [ number_of_dos_values ]\n",
+ "\n",
+ " dos_energies = np.zeros((N_dos_values))\n",
+ " dos_energies_tmp = np.zeros((N_dos_values)) #tmp array for unit convertion\n",
+ " dos_values = np.zeros((N_dos_values))\n",
+ "\n",
+ " dos_energies_tmp = dos_data['section_run']['section_single_configuration_calculation']['section_dos'][0]['dos_energies']\n",
+ " dos_values = dos_data['section_run']['section_single_configuration_calculation']['section_dos'][0]['dos_values'][0]\n",
+ " \n",
+ "\n",
+ " dos_fermi_energy= dos_data['section_run']['section_single_configuration_calculation']['section_dos'][0].get('dos_fermi_energy',\"empty\")\n",
+ " if(dos_fermi_energy == \"empty\"): #dos_fermi_energy is not available in EXCITING\n",
+ " dos_fermi_energy_exciting = dos_data['section_run']['section_single_configuration_calculation'].get('x_exciting_dos_fermi',\"empty\")\n",
+ " if(dos_fermi_energy_exciting == \"empty\"):\n",
+ " dos_fermi_energy = 0\n",
+ " else:\n",
+ " dos_fermi_energy = dos_fermi_energy_exciting / (1.60217656535 * pow(10,-19))\n",
+ " else:\n",
+ " dos_fermi_energy = dos_fermi_energy / (1.60217656535 * pow(10,-19))\n",
+ " print(\"dos_fermi_energy:\", dos_fermi_energy)\n",
+ " \n",
+ " for i_dos_values in range(N_dos_values):\n",
+ " dos_energies[i_dos_values] = 0.0\n",
+ " dos_energies[i_dos_values] = dos_energies_tmp[i_dos_values] / (1.60217656535 * pow(10,-19))\n",
+ " dos_energies[i_dos_values] = round((dos_energies[i_dos_values] - dos_fermi_energy), 3) #reference with the fermi level\n",
+ "\n",
+ " dos_obj = {}\n",
+ " dos_obj[\"dos_x_axis\"] = np.array(dos_energies).tolist()\n",
+ " dos_obj[\"dos_y_axis\"] = np.array(dos_values).tolist()\n",
+ " dos_obj[\"dos_fermi_energy\"] = np.array(dos_fermi_energy).tolist()\n",
+ "\n",
+ " return dos_obj\n",
+ "\n",
+ "\n",
+ "def get_info_obj(band_path):\n",
+ "\n",
+ " #band_data: read from json file \n",
+ " #Load the data files for band\n",
+ " band_data = load_jsonfile(band_path)\n",
+ " info_obj = {}\n",
+ " #---------Read the information of the calculation--------\n",
+ " info_obj[\"program_name\"] = band_data[\"section_run\"][\"program_name\"];\n",
+ " info_obj[\"program_basis_set_type\"] = band_data[\"section_run\"][\"program_basis_set_type\"];\n",
+ " info_obj[\"atom_labels\"] = band_data[\"section_run\"][\"section_system\"][0][\"atom_labels\"];\n",
+ " info_obj[\"XC_functional_name\"] = band_data[\"section_run\"][\"section_method\"][\"section_XC_functionals\"][0][\"XC_functional_name\"] + \" + \"+ band_data[\"section_run\"][\"section_method\"][\"section_XC_functionals\"][1][\"XC_functional_name\"];\n",
+ " \n",
+ " #----------Get the space group information----------\n",
+ " \n",
+ " [space_group_symbol, lattice_constant] = get_space_group(band_data)\n",
+ " info_obj[\"space_group_symbol\"] = np.array(space_group_symbol).tolist()\n",
+ " info_obj[\"lattice_constant\"] = np.array(lattice_constant).tolist()\n",
+ " print(\"space group:\", info_obj[\"space_group_symbol\"])\n",
+ " print(\"lattice_constant:\", lattice_constant)\n",
+ " \n",
+ " return info_obj\n",
+ "\n",
+ "\n",
+ "#============main===========================================\n",
+ "\n",
+ "#import matplotlib.pyplot as plt\n",
+ "band_obj_all = []\n",
+ "dos_obj_all = []\n",
+ "info_obj_all = []\n",
+ "print(\"Number of materials: \", N_materials)\n",
+ "\n",
+ "for i in range (N_materials):\n",
+ " print(\"Material: \", i)\n",
+ " band_path = band_paths[i]\n",
+ " dos_path = dos_paths[i]\n",
+ " \n",
+ " \n",
+ " dos_obj = get_dos_obj(dos_path)\n",
+ " dos_fermi_energy = dos_obj[\"dos_fermi_energy\"]\n",
+ " band_obj = get_band_obj(band_path, dos_fermi_energy)\n",
+ " info_obj = get_info_obj(band_path)\n",
+ " \n",
+ " band_obj_all.append(band_obj)\n",
+ " dos_obj_all.append(dos_obj)\n",
+ " info_obj_all.append(info_obj)\n",
+ " \n",
+ " \n",
+ " print(\"average_N_k_points_per_inverse_distance: \", band_obj[\"average_N_k_points_per_inverse_distance\"])\n",
+ "\n",
+ "print(\"Finish processing data.\")\n",
+ "\n",
+ "#run_cell_by_tag('save_data_to_js')\n",
+ "\n",
+ "print(\"Initialization of visulization finished.\")"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 331,
+ "metadata": {
+ "tags": [
+ "js_plot"
+ ]
+ },
+ "outputs": [
+ {
+ "data": {
+ "application/javascript": [
+ " \n",
+ "var N_max_show = 10; //Number of results to be shown by default\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n"
+ ],
+ "text/plain": [
+ "<IPython.core.display.Javascript object>"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "%%javascript\n",
+ " \n",
+ "var N_max_show = 10; //Number of results to be shown by default\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": []
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "%%javascript\n",
+ "// BACKUP!\n",
+ "/*\n",
+ "//Main plot function for given material:\n",
+ " function plot_band_dos_i_backup(i, lowerLim, upperLim, if_show_VBM, if_compare, i_in_compare_list)\n",
+ " {\n",
+ " //alert(\"plot_band_dos_i\")\n",
+ " //i=0;\n",
+ " lowerLim = -10\n",
+ " upperLim = 10\n",
+ " if_show_VBM = 0\n",
+ " if_compare = 0\n",
+ " i_in_compare_list = -1\n",
+ " //i=0;\n",
+ " var placeholder_band = \"#div_band\" + i.toString();\n",
+ " var placeholder_dos = \"#div_dos\" + i.toString();\n",
+ " var placeholder_tools = \"#div_tools\" + i.toString();\n",
+ " var placeholder_overview = \"#div_overview\" + i.toString();\n",
+ " var placeholder_overviewlegend = \"#overviewLegend\" + i.toString();\n",
+ " var checkbox_VBM_id = \"checkbox_VBM\" + i.toString();\n",
+ " var img_band_id = \"img_band\" + i.toString();\n",
+ " var img_dos_id = \"img_dos\" + i.toString();\n",
+ " var placeholder_band_compare = \"\";\n",
+ "\n",
+ " if(i_in_compare_list == 1)\n",
+ " {\n",
+ " placeholder_band_compare = \"#div_band_compare_1\";\n",
+ " }\n",
+ " else if(i_in_compare_list == 2)\n",
+ " {\n",
+ " placeholder_band_compare = \"#div_band_compare_2\";\n",
+ " }\n",
+ " else\n",
+ " {\n",
+ " placeholder_band_compare = \"#div_band_compare_1\"; // just for safe\n",
+ " }\n",
+ "\n",
+ " Object.size = function(obj) {\n",
+ " var size = 0, key;\n",
+ " for (key in obj) \n",
+ " {\n",
+ " if (obj.hasOwnProperty(key)) size++;\n",
+ " }\n",
+ " return size;\n",
+ " };\n",
+ "\n",
+ " //Get the number of bands\n",
+ " //alert(\"Getting band\")\n",
+ " //alert(band_obj_all)\n",
+ " //alert(\"band_obj_all got!\")\n",
+ " var N_bands = Object.size(band_obj_all[i][\"band_y_axis\"]);\n",
+ " var N_k_coors = Object.size(band_obj_all[i][\"band_x_axis\"]);\n",
+ " alert(band_obj_all[i][\"band_y_axis\"])\n",
+ " band_plotdata = [];\n",
+ "\n",
+ " for(var i_band =0; i_band < N_bands; i_band++)\n",
+ " {\n",
+ " var tmp_data = [];\n",
+ " for(var j_k_coor = 0; j_k_coor < N_k_coors; j_k_coor ++)\n",
+ " {\n",
+ " tmp_data.push([band_obj_all[i][\"band_x_axis\"][j_k_coor],band_obj_all[i][\"band_y_axis\"][i_band][j_k_coor]]);\n",
+ " }\n",
+ " plotData = { shadowSize: 0 , data: tmp_data, color: 'black', series: { lines: { show: true } , points: {show: false} } };\n",
+ " band_plotdata.push(plotData);\n",
+ " }\n",
+ "\n",
+ "\n",
+ " var tmp_data0 = [[0, 0], [1, 0]];\n",
+ " plotData0 = { shadowSize:0, color: 'black', data: tmp_data0, dashes:{ show:true, lineWidth: 1.5}};\n",
+ " band_plotdata.push(plotData0);\n",
+ "\n",
+ " band_plotdata_overview = band_plotdata.slice(0);\n",
+ "\n",
+ " var HOMOdata= [[band_obj_all[i][\"HOMO_coor\"],band_obj_all[i][\"HOMO_energy\"]]];\n",
+ " HOMOlabel = [\"VBM\"];\n",
+ " plotHOMO={ shadowSize:0, color: 'blue', data: HOMOdata, points:{show:true, radius: 4 , fill: true, fillColor: 'blue'},lines:{show: false}, showLabels: true, labels: HOMOlabel, canvasRender: true, cColor: 'red', cFont:\"2em Arial\"};\n",
+ "\n",
+ " var LUMOdata= [[band_obj_all[i][\"LUMO_coor\"],band_obj_all[i][\"LUMO_energy\"]]];\n",
+ " LUMOlabel = [\"CBM\"];\n",
+ " plotLUMO={ shadowSize:0, color: 'red', data: LUMOdata, points:{show:true, radius: 4 , fill: true, fillColor: 'red'},lines:{show: false}, showLabels: true, labels: LUMOlabel, canvasRender: true, cColor: 'red', cFont:\"2em Arial\"};\n",
+ "\n",
+ " //if_show_VBM = check_show_VBM(checkbox_VBM_id);\n",
+ " if (if_show_VBM == 1)\n",
+ " {\n",
+ " band_plotdata.push(plotHOMO);\n",
+ " band_plotdata.push(plotLUMO);\n",
+ " }\n",
+ "\n",
+ " \n",
+ " alert(img_band_id + band_plotdata)\n",
+ " \n",
+ " //!!!FIXME: if ($(\"#showVBM:checked\").length > 0 && gap > 0.1) \n",
+ " //plotHOMOLUMO={ shadowSize:0, color: 'red', data: d5, points:{show:true, radius: 0.8 , fill: true}, showLabels: true, labels: d5label, labelPlacement: labelPos, canvasRender: true, cColor: 'red', cFont:\"1em Arial\" }\n",
+ "\n",
+ " var canvas_band;\n",
+ " var options_band = {\n",
+ " canvas: true,\n",
+ " //legend:{ type: \"canvas\" },\n",
+ " series: { lines: { show: true, lineWidth: 2 }, \n",
+ " points: { show: false } }, \n",
+ " xaxis: { \n",
+ " ticks: band_obj_all[i][\"labels\"], \n",
+ " color:\"#000\", \n",
+ " font: {size: 20}, \n",
+ " zoomRange: false,\n",
+ " panRange: false \n",
+ " }, \n",
+ " yaxis: { \n",
+ " axisLabel: \"Energy (eV)\", \n",
+ " axisLabelUseCanvas: true,\n",
+ " //axisLabelUseCanvas: false,\n",
+ " axisLabelFontSizePixels: 20,\n",
+ " axisLabelFontFamily: 'Arial', \n",
+ " axisLabelPadding: 10, \n",
+ " color:\"#000\", \n",
+ " font: {size: 20, family:\"Arial\"},\n",
+ " tickLength:-5, \n",
+ " min: lowerLim, \n",
+ " max: upperLim,\n",
+ " tickDecimals: 0, \n",
+ " zoomRange: [0.001, 1000],\n",
+ " panRange: [-100, 100] \n",
+ " },\n",
+ "\n",
+ " zoom: { \n",
+ " interactive: true\n",
+ " },\n",
+ "\n",
+ " pan: {\n",
+ " interactive: true\n",
+ " }, \n",
+ "\n",
+ " //selection: { mode: \"xy\", color: \"#86a6b4\" }, \n",
+ "\n",
+ " grid: { \n",
+ " labelMargin: 15,\n",
+ " hoverable: true, \n",
+ " backgroundColor: { colors: [\"#fff\", \"#fff\"] }, \n",
+ " borderWidth: {\n",
+ " top: 2, \n",
+ " right: 2,\n",
+ " bottom: 2,\n",
+ " left: 2,\n",
+ " color : null } \n",
+ " }\n",
+ " }\n",
+ " //var plot_band = $.plot($(placeholder_band), band_plotdata, options_band);\n",
+ " //var plot_band = $.plot(\"#div_bandx\", band_plotdata, options_band);\n",
+ " var plot_band = $.plot($(placeholder_band), band_plotdata, options_band).getCanvas(); // save the canvas\n",
+ " image_band = plot_band.toDataURL();\n",
+ " image_band = image_band.replace(\"image/png\",\"image/octet-stream\");\n",
+ " //beakerx.image_band = image_band;\n",
+ " document.getElementById(img_band_id).href= image_band;\n",
+ " image_band_links[i] = image_band;\n",
+ " alert(\"band plot done.\")\n",
+ "\n",
+ "\n",
+ " //----Plot DOS----------------------\n",
+ " var dos_plotdata = [];\n",
+ " alert(\"dos:\"+dos_obj_all[i])\n",
+ " var xdos = dos_obj_all[i][\"dos_x_axis\"];\n",
+ " var ydos = dos_obj_all[i][\"dos_y_axis\"];\n",
+ " var dosLabelPos = Math.max.apply(Math, ydos)/2;\n",
+ " var d2 = [];\n",
+ " for (var ii = 0; ii < xdos.length; ii+=1) {\n",
+ " d2.push([ydos[ii],xdos[ii]]);\n",
+ " }\n",
+ " var plotData2={ shadowSize: 0, color: 'black' , data: d2}\n",
+ " dos_plotdata.push(plotData2)\n",
+ "\n",
+ " function find_xaxis_max_min(data, lowerbound, upperbound)\n",
+ " {\n",
+ " //data[xaxis,y] find the max and min value of x axis\n",
+ " //alert(\"dos[0]:\" + data[0][\"data\"]);\n",
+ " //alert(\"Bounds: \" + lowerbound + \" , \" + upperbound)\n",
+ " var n_data = data.length;\n",
+ " //alert(\"N dos: \" + n_data);\n",
+ " var data_min = 1000000;\n",
+ " var data_max = -1000000;\n",
+ " var data_current = 0;\n",
+ " for (var i = 0; i < n_data; i++)\n",
+ " {\n",
+ " if((data[i][1] >= lowerbound) && (data[i][1] <= upperbound))\n",
+ " {\n",
+ " data_current = data[i][0];\n",
+ " //alert(\"data[i]: \" + data[i] + \"data[i][0]: \" + data_current);\n",
+ " if(data_current >= data_max)\n",
+ " {\n",
+ " data_max = data_current;\n",
+ " }\n",
+ " if(data_current <= data_min)\n",
+ " {\n",
+ " data_min = data_current;\n",
+ " }\n",
+ " }\n",
+ " }\n",
+ " var data_max_min = [data_max, data_min];\n",
+ " //alert(\"data_max_min: \" + data_max_min);\n",
+ " return data_max_min;\n",
+ " }\n",
+ " var dos_x_max_min = find_xaxis_max_min(dos_plotdata[0][\"data\"], lowerLim, upperLim);\n",
+ " var dosLabelPos = (dos_x_max_min[0] + dos_x_max_min[1])/2;\n",
+ "\n",
+ " var options_dos ={\n",
+ " canvas: true,\n",
+ " series: {\n",
+ " lines: { show: true, lineWidth:2 },\n",
+ " points: { show: false }\n",
+ " },\n",
+ "\n",
+ " yaxis: { \n",
+ " axisLabel: \"\", \n",
+ " axisLabelUseCanvas: true,\n",
+ " axisLabelFontSizePixels: 20,\n",
+ " axisLabelFontFamily: 'Arial', \n",
+ " axisLabelPadding: 10, \n",
+ " color:\"#000\", \n",
+ " font: {size: 20},\n",
+ " tickLength:-5, \n",
+ " min: lowerLim, \n",
+ " max: upperLim,\n",
+ " tickDecimals: 0, \n",
+ " zoomRange: [0.001, 1000],\n",
+ " panRange: [-100, 100] \n",
+ " },\n",
+ "\n",
+ " xaxis: {\n",
+ " axisLabel: \" \",\n",
+ " axisLabelUseCanvas: false,\n",
+ " axisLabelFontSizePixels: 20,\n",
+ " axisLabelFontFamily: 'Arial',\n",
+ " axisLabelPadding: 3,\n",
+ " color:\"rgb(0, 0, 0)\",\n",
+ " font: {size: 20, family:\"Arial\"},\n",
+ " //ticks: 10,\n",
+ " tickLength:0,\n",
+ " min: dos_x_max_min[1],//0,\n",
+ " max: dos_x_max_min[0],//1,\n",
+ " tickDecimals: 0,\n",
+ " ticks: [[ dosLabelPos ,'DOS']],\n",
+ " //tickFormatter: MyFormatter\n",
+ " panRange: false\n",
+ " },\n",
+ " pan: {\n",
+ " interactive: true\n",
+ " }, \n",
+ "\n",
+ " grid: {\n",
+ " labelMargin: 15,\n",
+ " hoverable: true,\n",
+ " //borderWidth : 1000,\n",
+ " //show : false,\n",
+ " // //backgroundColor: { colors: [ \"#fff\", \"#eee\" ] },\n",
+ " backgroundColor: { colors: [\"#fff\", \"#fff\"] },\n",
+ " borderWidth: {\n",
+ " top: 2,\n",
+ " right: 2,\n",
+ " bottom: 2,\n",
+ " left: 2,\n",
+ " color : null\n",
+ " }\n",
+ " }\n",
+ " }\n",
+ " var plot_dos = $.plot(placeholder_dos, dos_plotdata, options_dos).getCanvas();\n",
+ " var image_dos = plot_dos.toDataURL();\n",
+ " image_dos = image_dos.replace(\"image/png\",\"image/octet-stream\");\n",
+ " image_dos = image_dos;\n",
+ " document.getElementById(img_dos_id).href= image_dos;\n",
+ " \n",
+ " }\n",
+ "*/"
+ ]
+ }
+ ],
+ "metadata": {
+ "celltoolbar": "Tags",
+ "kernelspec": {
+ "display_name": "Python 3",
+ "language": "python",
+ "name": "python3"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 3
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython3",
+ "version": "3.6.7"
+ },
+ "toc": {
+ "base_numbering": 1,
+ "nav_menu": {},
+ "number_sections": false,
+ "sideBar": false,
+ "skip_h1_title": false,
+ "title_cell": "Table of Contents",
+ "title_sidebar": "Contents",
+ "toc_cell": false,
+ "toc_position": {},
+ "toc_section_display": false,
+ "toc_window_display": false
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}
diff --git a/js/jquery-3.2.1.min.js b/js/jquery-3.2.1.min.js
new file mode 100644
index 0000000000000000000000000000000000000000..644d35e274fd64ddaf6d12af813e820c424176a9
--- /dev/null
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diff --git a/js/jquery.event.move.js b/js/jquery.event.move.js
new file mode 100644
index 0000000000000000000000000000000000000000..a792b71330e21da38fdb543f6f754cd61dd9103b
--- /dev/null
+++ b/js/jquery.event.move.js
@@ -0,0 +1,599 @@
+// DOM.event.move
+//
+// 2.0.0
+//
+// Stephen Band
+//
+// Triggers 'movestart', 'move' and 'moveend' events after
+// mousemoves following a mousedown cross a distance threshold,
+// similar to the native 'dragstart', 'drag' and 'dragend' events.
+// Move events are throttled to animation frames. Move event objects
+// have the properties:
+//
+// pageX:
+// pageY: Page coordinates of pointer.
+// startX:
+// startY: Page coordinates of pointer at movestart.
+// distX:
+// distY: Distance the pointer has moved since movestart.
+// deltaX:
+// deltaY: Distance the finger has moved since last event.
+// velocityX:
+// velocityY: Average velocity over last few events.
+
+
+(function(fn) {
+ if (typeof define === 'function' && define.amd) {
+ define([], fn);
+ } else if ((typeof module !== "undefined" && module !== null) && module.exports) {
+ module.exports = fn;
+ } else {
+ fn();
+ }
+})(function(){
+ var assign = Object.assign || window.jQuery && jQuery.extend;
+
+ // Number of pixels a pressed pointer travels before movestart
+ // event is fired.
+ var threshold = 8;
+
+ // Shim for requestAnimationFrame, falling back to timer. See:
+ // see http://paulirish.com/2011/requestanimationframe-for-smart-animating/
+ var requestFrame = (function(){
+ return (
+ window.requestAnimationFrame ||
+ window.webkitRequestAnimationFrame ||
+ window.mozRequestAnimationFrame ||
+ window.oRequestAnimationFrame ||
+ window.msRequestAnimationFrame ||
+ function(fn, element){
+ return window.setTimeout(function(){
+ fn();
+ }, 25);
+ }
+ );
+ })();
+
+ // Shim for customEvent
+ // see https://developer.mozilla.org/en-US/docs/Web/API/CustomEvent/CustomEvent#Polyfill
+ (function () {
+ if ( typeof window.CustomEvent === "function" ) return false;
+ function CustomEvent ( event, params ) {
+ params = params || { bubbles: false, cancelable: false, detail: undefined };
+ var evt = document.createEvent( 'CustomEvent' );
+ evt.initCustomEvent( event, params.bubbles, params.cancelable, params.detail );
+ return evt;
+ }
+
+ CustomEvent.prototype = window.Event.prototype;
+ window.CustomEvent = CustomEvent;
+ })();
+
+ var ignoreTags = {
+ textarea: true,
+ input: true,
+ select: true,
+ button: true
+ };
+
+ var mouseevents = {
+ move: 'mousemove',
+ cancel: 'mouseup dragstart',
+ end: 'mouseup'
+ };
+
+ var touchevents = {
+ move: 'touchmove',
+ cancel: 'touchend',
+ end: 'touchend'
+ };
+
+ var rspaces = /\s+/;
+
+
+ // DOM Events
+
+ var eventOptions = { bubbles: true, cancelable: true };
+
+ var eventsSymbol = typeof Symbol === "function" ? Symbol('events') : {};
+
+ function createEvent(type) {
+ return new CustomEvent(type, eventOptions);
+ }
+
+ function getEvents(node) {
+ return node[eventsSymbol] || (node[eventsSymbol] = {});
+ }
+
+ function on(node, types, fn, data, selector) {
+ types = types.split(rspaces);
+
+ var events = getEvents(node);
+ var i = types.length;
+ var handlers, type;
+
+ function handler(e) { fn(e, data); }
+
+ while (i--) {
+ type = types[i];
+ handlers = events[type] || (events[type] = []);
+ handlers.push([fn, handler]);
+ node.addEventListener(type, handler);
+ }
+ }
+
+ function off(node, types, fn, selector) {
+ types = types.split(rspaces);
+
+ var events = getEvents(node);
+ var i = types.length;
+ var type, handlers, k;
+
+ if (!events) { return; }
+
+ while (i--) {
+ type = types[i];
+ handlers = events[type];
+ if (!handlers) { continue; }
+ k = handlers.length;
+ while (k--) {
+ if (handlers[k][0] === fn) {
+ node.removeEventListener(type, handlers[k][1]);
+ handlers.splice(k, 1);
+ }
+ }
+ }
+ }
+
+ function trigger(node, type, properties) {
+ // Don't cache events. It prevents you from triggering an event of a
+ // given type from inside the handler of another event of that type.
+ var event = createEvent(type);
+ if (properties) { assign(event, properties); }
+ node.dispatchEvent(event);
+ }
+
+
+ // Constructors
+
+ function Timer(fn){
+ var callback = fn,
+ active = false,
+ running = false;
+
+ function trigger(time) {
+ if (active){
+ callback();
+ requestFrame(trigger);
+ running = true;
+ active = false;
+ }
+ else {
+ running = false;
+ }
+ }
+
+ this.kick = function(fn) {
+ active = true;
+ if (!running) { trigger(); }
+ };
+
+ this.end = function(fn) {
+ var cb = callback;
+
+ if (!fn) { return; }
+
+ // If the timer is not running, simply call the end callback.
+ if (!running) {
+ fn();
+ }
+ // If the timer is running, and has been kicked lately, then
+ // queue up the current callback and the end callback, otherwise
+ // just the end callback.
+ else {
+ callback = active ?
+ function(){ cb(); fn(); } :
+ fn ;
+
+ active = true;
+ }
+ };
+ }
+
+
+ // Functions
+
+ function noop() {}
+
+ function preventDefault(e) {
+ e.preventDefault();
+ }
+
+ function isIgnoreTag(e) {
+ return !!ignoreTags[e.target.tagName.toLowerCase()];
+ }
+
+ function isPrimaryButton(e) {
+ // Ignore mousedowns on any button other than the left (or primary)
+ // mouse button, or when a modifier key is pressed.
+ return (e.which === 1 && !e.ctrlKey && !e.altKey);
+ }
+
+ function identifiedTouch(touchList, id) {
+ var i, l;
+
+ if (touchList.identifiedTouch) {
+ return touchList.identifiedTouch(id);
+ }
+
+ // touchList.identifiedTouch() does not exist in
+ // webkit yet… we must do the search ourselves...
+
+ i = -1;
+ l = touchList.length;
+
+ while (++i < l) {
+ if (touchList[i].identifier === id) {
+ return touchList[i];
+ }
+ }
+ }
+
+ function changedTouch(e, data) {
+ var touch = identifiedTouch(e.changedTouches, data.identifier);
+
+ // This isn't the touch you're looking for.
+ if (!touch) { return; }
+
+ // Chrome Android (at least) includes touches that have not
+ // changed in e.changedTouches. That's a bit annoying. Check
+ // that this touch has changed.
+ if (touch.pageX === data.pageX && touch.pageY === data.pageY) { return; }
+
+ return touch;
+ }
+
+
+ // Handlers that decide when the first movestart is triggered
+
+ function mousedown(e){
+ // Ignore non-primary buttons
+ if (!isPrimaryButton(e)) { return; }
+
+ // Ignore form and interactive elements
+ if (isIgnoreTag(e)) { return; }
+
+ on(document, mouseevents.move, mousemove, e);
+ on(document, mouseevents.cancel, mouseend, e);
+ }
+
+ function mousemove(e, data){
+ checkThreshold(e, data, e, removeMouse);
+ }
+
+ function mouseend(e, data) {
+ removeMouse();
+ }
+
+ function removeMouse() {
+ off(document, mouseevents.move, mousemove);
+ off(document, mouseevents.cancel, mouseend);
+ }
+
+ function touchstart(e) {
+ // Don't get in the way of interaction with form elements
+ if (ignoreTags[e.target.tagName.toLowerCase()]) { return; }
+
+ var touch = e.changedTouches[0];
+
+ // iOS live updates the touch objects whereas Android gives us copies.
+ // That means we can't trust the touchstart object to stay the same,
+ // so we must copy the data. This object acts as a template for
+ // movestart, move and moveend event objects.
+ var data = {
+ target: touch.target,
+ pageX: touch.pageX,
+ pageY: touch.pageY,
+ identifier: touch.identifier,
+
+ // The only way to make handlers individually unbindable is by
+ // making them unique.
+ touchmove: function(e, data) { touchmove(e, data); },
+ touchend: function(e, data) { touchend(e, data); }
+ };
+
+ on(document, touchevents.move, data.touchmove, data);
+ on(document, touchevents.cancel, data.touchend, data);
+ }
+
+ function touchmove(e, data) {
+ var touch = changedTouch(e, data);
+ if (!touch) { return; }
+ checkThreshold(e, data, touch, removeTouch);
+ }
+
+ function touchend(e, data) {
+ var touch = identifiedTouch(e.changedTouches, data.identifier);
+ if (!touch) { return; }
+ removeTouch(data);
+ }
+
+ function removeTouch(data) {
+ off(document, touchevents.move, data.touchmove);
+ off(document, touchevents.cancel, data.touchend);
+ }
+
+ function checkThreshold(e, data, touch, fn) {
+ var distX = touch.pageX - data.pageX;
+ var distY = touch.pageY - data.pageY;
+
+ // Do nothing if the threshold has not been crossed.
+ if ((distX * distX) + (distY * distY) < (threshold * threshold)) { return; }
+
+ triggerStart(e, data, touch, distX, distY, fn);
+ }
+
+ function triggerStart(e, data, touch, distX, distY, fn) {
+ var touches = e.targetTouches;
+ var time = e.timeStamp - data.timeStamp;
+
+ // Create a movestart object with some special properties that
+ // are passed only to the movestart handlers.
+ var template = {
+ altKey: e.altKey,
+ ctrlKey: e.ctrlKey,
+ shiftKey: e.shiftKey,
+ startX: data.pageX,
+ startY: data.pageY,
+ distX: distX,
+ distY: distY,
+ deltaX: distX,
+ deltaY: distY,
+ pageX: touch.pageX,
+ pageY: touch.pageY,
+ velocityX: distX / time,
+ velocityY: distY / time,
+ identifier: data.identifier,
+ targetTouches: touches,
+ finger: touches ? touches.length : 1,
+ enableMove: function() {
+ this.moveEnabled = true;
+ this.enableMove = noop;
+ e.preventDefault();
+ }
+ };
+
+ // Trigger the movestart event.
+ trigger(data.target, 'movestart', template);
+
+ // Unbind handlers that tracked the touch or mouse up till now.
+ fn(data);
+ }
+
+
+ // Handlers that control what happens following a movestart
+
+ function activeMousemove(e, data) {
+ var timer = data.timer;
+
+ data.touch = e;
+ data.timeStamp = e.timeStamp;
+ timer.kick();
+ }
+
+ function activeMouseend(e, data) {
+ var target = data.target;
+ var event = data.event;
+ var timer = data.timer;
+
+ removeActiveMouse();
+
+ endEvent(target, event, timer, function() {
+ // Unbind the click suppressor, waiting until after mouseup
+ // has been handled.
+ setTimeout(function(){
+ off(target, 'click', preventDefault);
+ }, 0);
+ });
+ }
+
+ function removeActiveMouse() {
+ off(document, mouseevents.move, activeMousemove);
+ off(document, mouseevents.end, activeMouseend);
+ }
+
+ function activeTouchmove(e, data) {
+ var event = data.event;
+ var timer = data.timer;
+ var touch = changedTouch(e, event);
+
+ if (!touch) { return; }
+
+ // Stop the interface from gesturing
+ e.preventDefault();
+
+ event.targetTouches = e.targetTouches;
+ data.touch = touch;
+ data.timeStamp = e.timeStamp;
+
+ timer.kick();
+ }
+
+ function activeTouchend(e, data) {
+ var target = data.target;
+ var event = data.event;
+ var timer = data.timer;
+ var touch = identifiedTouch(e.changedTouches, event.identifier);
+
+ // This isn't the touch you're looking for.
+ if (!touch) { return; }
+
+ removeActiveTouch(data);
+ endEvent(target, event, timer);
+ }
+
+ function removeActiveTouch(data) {
+ off(document, touchevents.move, data.activeTouchmove);
+ off(document, touchevents.end, data.activeTouchend);
+ }
+
+
+ // Logic for triggering move and moveend events
+
+ function updateEvent(event, touch, timeStamp) {
+ var time = timeStamp - event.timeStamp;
+
+ event.distX = touch.pageX - event.startX;
+ event.distY = touch.pageY - event.startY;
+ event.deltaX = touch.pageX - event.pageX;
+ event.deltaY = touch.pageY - event.pageY;
+
+ // Average the velocity of the last few events using a decay
+ // curve to even out spurious jumps in values.
+ event.velocityX = 0.3 * event.velocityX + 0.7 * event.deltaX / time;
+ event.velocityY = 0.3 * event.velocityY + 0.7 * event.deltaY / time;
+ event.pageX = touch.pageX;
+ event.pageY = touch.pageY;
+ }
+
+ function endEvent(target, event, timer, fn) {
+ timer.end(function(){
+ trigger(target, 'moveend', event);
+ return fn && fn();
+ });
+ }
+
+
+ // Set up the DOM
+
+ function movestart(e) {
+ if (e.defaultPrevented) { return; }
+ if (!e.moveEnabled) { return; }
+
+ var event = {
+ startX: e.startX,
+ startY: e.startY,
+ pageX: e.pageX,
+ pageY: e.pageY,
+ distX: e.distX,
+ distY: e.distY,
+ deltaX: e.deltaX,
+ deltaY: e.deltaY,
+ velocityX: e.velocityX,
+ velocityY: e.velocityY,
+ identifier: e.identifier,
+ targetTouches: e.targetTouches,
+ finger: e.finger
+ };
+
+ var data = {
+ target: e.target,
+ event: event,
+ timer: new Timer(update),
+ touch: undefined,
+ timeStamp: e.timeStamp
+ };
+
+ function update(time) {
+ updateEvent(event, data.touch, data.timeStamp);
+ trigger(data.target, 'move', event);
+ }
+
+ if (e.identifier === undefined) {
+ // We're dealing with a mouse event.
+ // Stop clicks from propagating during a move
+ on(e.target, 'click', preventDefault);
+ on(document, mouseevents.move, activeMousemove, data);
+ on(document, mouseevents.end, activeMouseend, data);
+ }
+ else {
+ // In order to unbind correct handlers they have to be unique
+ data.activeTouchmove = function(e, data) { activeTouchmove(e, data); };
+ data.activeTouchend = function(e, data) { activeTouchend(e, data); };
+
+ // We're dealing with a touch.
+ on(document, touchevents.move, data.activeTouchmove, data);
+ on(document, touchevents.end, data.activeTouchend, data);
+ }
+ }
+
+ on(document, 'mousedown', mousedown);
+ on(document, 'touchstart', touchstart);
+ on(document, 'movestart', movestart);
+
+
+ // jQuery special events
+ //
+ // jQuery event objects are copies of DOM event objects. They need
+ // a little help copying the move properties across.
+
+ if (!window.jQuery) { return; }
+
+ var properties = ("startX startY pageX pageY distX distY deltaX deltaY velocityX velocityY").split(' ');
+
+ function enableMove1(e) { e.enableMove(); }
+ function enableMove2(e) { e.enableMove(); }
+ function enableMove3(e) { e.enableMove(); }
+
+ function add(handleObj) {
+ var handler = handleObj.handler;
+
+ handleObj.handler = function(e) {
+ // Copy move properties across from originalEvent
+ var i = properties.length;
+ var property;
+
+ while(i--) {
+ property = properties[i];
+ e[property] = e.originalEvent[property];
+ }
+
+ handler.apply(this, arguments);
+ };
+ }
+
+ jQuery.event.special.movestart = {
+ setup: function() {
+ // Movestart must be enabled to allow other move events
+ on(this, 'movestart', enableMove1);
+
+ // Do listen to DOM events
+ return false;
+ },
+
+ teardown: function() {
+ off(this, 'movestart', enableMove1);
+ return false;
+ },
+
+ add: add
+ };
+
+ jQuery.event.special.move = {
+ setup: function() {
+ on(this, 'movestart', enableMove2);
+ return false;
+ },
+
+ teardown: function() {
+ off(this, 'movestart', enableMove2);
+ return false;
+ },
+
+ add: add
+ };
+
+ jQuery.event.special.moveend = {
+ setup: function() {
+ on(this, 'movestart', enableMove3);
+ return false;
+ },
+
+ teardown: function() {
+ off(this, 'movestart', enableMove3);
+ return false;
+ },
+
+ add: add
+ };
+});
diff --git a/js/jquery.flot.axislabels.js b/js/jquery.flot.axislabels.js
new file mode 100644
index 0000000000000000000000000000000000000000..cda8038953c76b039e3ab0f1c49607dcbcf6c3ce
--- /dev/null
+++ b/js/jquery.flot.axislabels.js
@@ -0,0 +1,462 @@
+/*
+Axis Labels Plugin for flot.
+http://github.com/markrcote/flot-axislabels
+Original code is Copyright (c) 2010 Xuan Luo.
+Original code was released under the GPLv3 license by Xuan Luo, September 2010.
+Original code was rereleased under the MIT license by Xuan Luo, April 2012.
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+(function ($) {
+ var options = {
+ axisLabels: {
+ show: true
+ }
+ };
+
+ function canvasSupported() {
+ return !!document.createElement('canvas').getContext;
+ }
+
+ function canvasTextSupported() {
+ if (!canvasSupported()) {
+ return false;
+ }
+ var dummy_canvas = document.createElement('canvas');
+ var context = dummy_canvas.getContext('2d');
+ return typeof context.fillText == 'function';
+ }
+
+ function css3TransitionSupported() {
+ var div = document.createElement('div');
+ return typeof div.style.MozTransition != 'undefined' // Gecko
+ || typeof div.style.OTransition != 'undefined' // Opera
+ || typeof div.style.webkitTransition != 'undefined' // WebKit
+ || typeof div.style.transition != 'undefined';
+ }
+
+
+ function AxisLabel(axisName, position, padding, plot, opts) {
+ this.axisName = axisName;
+ this.position = position;
+ this.padding = padding;
+ this.plot = plot;
+ this.opts = opts;
+ this.width = 0;
+ this.height = 0;
+ }
+
+ AxisLabel.prototype.cleanup = function() {
+ };
+
+
+ CanvasAxisLabel.prototype = new AxisLabel();
+ CanvasAxisLabel.prototype.constructor = CanvasAxisLabel;
+ function CanvasAxisLabel(axisName, position, padding, plot, opts) {
+ AxisLabel.prototype.constructor.call(this, axisName, position, padding,
+ plot, opts);
+ }
+
+ CanvasAxisLabel.prototype.calculateSize = function() {
+ if (!this.opts.axisLabelFontSizePixels)
+ this.opts.axisLabelFontSizePixels = 14;
+ if (!this.opts.axisLabelFontFamily)
+ this.opts.axisLabelFontFamily = 'sans-serif';
+
+ var textWidth = this.opts.axisLabelFontSizePixels + this.padding;
+ var textHeight = this.opts.axisLabelFontSizePixels + this.padding;
+ if (this.position == 'left' || this.position == 'right') {
+ this.width = this.opts.axisLabelFontSizePixels + this.padding;
+ this.height = 0;
+ } else {
+ this.width = 0;
+ this.height = this.opts.axisLabelFontSizePixels + this.padding;
+ }
+ };
+
+ CanvasAxisLabel.prototype.draw = function(box) {
+ if (!this.opts.axisLabelColour)
+ this.opts.axisLabelColour = 'black';
+ var ctx = this.plot.getCanvas().getContext('2d');
+ ctx.save();
+ ctx.font = this.opts.axisLabelFontSizePixels + 'px ' +
+ this.opts.axisLabelFontFamily;
+ ctx.fillStyle = this.opts.axisLabelColour;
+ var width = ctx.measureText(this.opts.axisLabel).width;
+ var height = this.opts.axisLabelFontSizePixels;
+ var x, y, angle = 0;
+ if (this.position == 'top') {
+ x = box.left + box.width/2 - width/2;
+ y = box.top + height*0.72;
+ } else if (this.position == 'bottom') {
+ x = box.left + box.width/2 - width/2;
+ y = box.top + box.height - height*0.72;
+ } else if (this.position == 'left') {
+ x = box.left + height*0.72;
+ y = box.height/2 + box.top + width/2;
+ angle = -Math.PI/2;
+ } else if (this.position == 'right') {
+ x = box.left + box.width - height*0.72;
+ y = box.height/2 + box.top - width/2;
+ angle = Math.PI/2;
+ }
+ ctx.translate(x, y);
+ ctx.rotate(angle);
+ ctx.fillText(this.opts.axisLabel, 0, 0);
+ ctx.restore();
+ };
+
+
+ HtmlAxisLabel.prototype = new AxisLabel();
+ HtmlAxisLabel.prototype.constructor = HtmlAxisLabel;
+ function HtmlAxisLabel(axisName, position, padding, plot, opts) {
+ AxisLabel.prototype.constructor.call(this, axisName, position,
+ padding, plot, opts);
+ this.elem = null;
+ }
+
+ HtmlAxisLabel.prototype.calculateSize = function() {
+ var elem = $('<div class="axisLabels" style="position:absolute;">' +
+ this.opts.axisLabel + '</div>');
+ this.plot.getPlaceholder().append(elem);
+ // store height and width of label itself, for use in draw()
+ this.labelWidth = elem.outerWidth(true);
+ this.labelHeight = elem.outerHeight(true);
+ elem.remove();
+
+ this.width = this.height = 0;
+ if (this.position == 'left' || this.position == 'right') {
+ this.width = this.labelWidth + this.padding;
+ } else {
+ this.height = this.labelHeight + this.padding;
+ }
+ };
+
+ HtmlAxisLabel.prototype.cleanup = function() {
+ if (this.elem) {
+ this.elem.remove();
+ }
+ };
+
+ HtmlAxisLabel.prototype.draw = function(box) {
+ this.plot.getPlaceholder().find('#' + this.axisName + 'Label').remove();
+ this.elem = $('<div id="' + this.axisName +
+ 'Label" " class="axisLabels" style="position:absolute;">'
+ + this.opts.axisLabel + '</div>');
+ this.plot.getPlaceholder().append(this.elem);
+ if (this.position == 'top') {
+ this.elem.css('left', box.left + box.width/2 - this.labelWidth/2 +
+ 'px');
+ this.elem.css('top', box.top + 'px');
+ } else if (this.position == 'bottom') {
+ this.elem.css('left', box.left + box.width/2 - this.labelWidth/2 +
+ 'px');
+ this.elem.css('top', box.top + box.height - this.labelHeight +
+ 'px');
+ } else if (this.position == 'left') {
+ this.elem.css('top', box.top + box.height/2 - this.labelHeight/2 +
+ 'px');
+ this.elem.css('left', box.left + 'px');
+ } else if (this.position == 'right') {
+ this.elem.css('top', box.top + box.height/2 - this.labelHeight/2 +
+ 'px');
+ this.elem.css('left', box.left + box.width - this.labelWidth +
+ 'px');
+ }
+ };
+
+
+ CssTransformAxisLabel.prototype = new HtmlAxisLabel();
+ CssTransformAxisLabel.prototype.constructor = CssTransformAxisLabel;
+ function CssTransformAxisLabel(axisName, position, padding, plot, opts) {
+ HtmlAxisLabel.prototype.constructor.call(this, axisName, position,
+ padding, plot, opts);
+ }
+
+ CssTransformAxisLabel.prototype.calculateSize = function() {
+ HtmlAxisLabel.prototype.calculateSize.call(this);
+ this.width = this.height = 0;
+ if (this.position == 'left' || this.position == 'right') {
+ this.width = this.labelHeight + this.padding;
+ } else {
+ this.height = this.labelHeight + this.padding;
+ }
+ };
+
+ CssTransformAxisLabel.prototype.transforms = function(degrees, x, y) {
+ var stransforms = {
+ '-moz-transform': '',
+ '-webkit-transform': '',
+ '-o-transform': '',
+ '-ms-transform': ''
+ };
+ if (x != 0 || y != 0) {
+ var stdTranslate = ' translate(' + x + 'px, ' + y + 'px)';
+ stransforms['-moz-transform'] += stdTranslate;
+ stransforms['-webkit-transform'] += stdTranslate;
+ stransforms['-o-transform'] += stdTranslate;
+ stransforms['-ms-transform'] += stdTranslate;
+ }
+ if (degrees != 0) {
+ var rotation = degrees / 90;
+ var stdRotate = ' rotate(' + degrees + 'deg)';
+ stransforms['-moz-transform'] += stdRotate;
+ stransforms['-webkit-transform'] += stdRotate;
+ stransforms['-o-transform'] += stdRotate;
+ stransforms['-ms-transform'] += stdRotate;
+ }
+ var s = 'top: 0; left: 0; ';
+ for (var prop in stransforms) {
+ if (stransforms[prop]) {
+ s += prop + ':' + stransforms[prop] + ';';
+ }
+ }
+ s += ';';
+ return s;
+ };
+
+ CssTransformAxisLabel.prototype.calculateOffsets = function(box) {
+ var offsets = { x: 0, y: 0, degrees: 0 };
+ if (this.position == 'bottom') {
+ offsets.x = box.left + box.width/2 - this.labelWidth/2;
+ offsets.y = box.top + box.height - this.labelHeight;
+ } else if (this.position == 'top') {
+ offsets.x = box.left + box.width/2 - this.labelWidth/2;
+ offsets.y = box.top;
+ } else if (this.position == 'left') {
+ offsets.degrees = -90;
+ offsets.x = box.left - this.labelWidth/2 + this.labelHeight/2;
+ offsets.y = box.height/2 + box.top;
+ } else if (this.position == 'right') {
+ offsets.degrees = 90;
+ offsets.x = box.left + box.width - this.labelWidth/2
+ - this.labelHeight/2;
+ offsets.y = box.height/2 + box.top;
+ }
+ offsets.x = Math.round(offsets.x);
+ offsets.y = Math.round(offsets.y);
+
+ return offsets;
+ };
+
+ CssTransformAxisLabel.prototype.draw = function(box) {
+ this.plot.getPlaceholder().find("." + this.axisName + "Label").remove();
+ var offsets = this.calculateOffsets(box);
+ this.elem = $('<div class="axisLabels ' + this.axisName +
+ 'Label" style="position:absolute; ' +
+ this.transforms(offsets.degrees, offsets.x, offsets.y) +
+ '">' + this.opts.axisLabel + '</div>');
+ this.plot.getPlaceholder().append(this.elem);
+ };
+
+
+ IeTransformAxisLabel.prototype = new CssTransformAxisLabel();
+ IeTransformAxisLabel.prototype.constructor = IeTransformAxisLabel;
+ function IeTransformAxisLabel(axisName, position, padding, plot, opts) {
+ CssTransformAxisLabel.prototype.constructor.call(this, axisName,
+ position, padding,
+ plot, opts);
+ this.requiresResize = false;
+ }
+
+ IeTransformAxisLabel.prototype.transforms = function(degrees, x, y) {
+ // I didn't feel like learning the crazy Matrix stuff, so this uses
+ // a combination of the rotation transform and CSS positioning.
+ var s = '';
+ if (degrees != 0) {
+ var rotation = degrees/90;
+ while (rotation < 0) {
+ rotation += 4;
+ }
+ s += ' filter: progid:DXImageTransform.Microsoft.BasicImage(rotation=' + rotation + '); ';
+ // see below
+ this.requiresResize = (this.position == 'right');
+ }
+ if (x != 0) {
+ s += 'left: ' + x + 'px; ';
+ }
+ if (y != 0) {
+ s += 'top: ' + y + 'px; ';
+ }
+ return s;
+ };
+
+ IeTransformAxisLabel.prototype.calculateOffsets = function(box) {
+ var offsets = CssTransformAxisLabel.prototype.calculateOffsets.call(
+ this, box);
+ // adjust some values to take into account differences between
+ // CSS and IE rotations.
+ if (this.position == 'top') {
+ // FIXME: not sure why, but placing this exactly at the top causes
+ // the top axis label to flip to the bottom...
+ offsets.y = box.top + 1;
+ } else if (this.position == 'left') {
+ offsets.x = box.left;
+ offsets.y = box.height/2 + box.top - this.labelWidth/2;
+ } else if (this.position == 'right') {
+ offsets.x = box.left + box.width - this.labelHeight;
+ offsets.y = box.height/2 + box.top - this.labelWidth/2;
+ }
+ return offsets;
+ };
+
+ IeTransformAxisLabel.prototype.draw = function(box) {
+ CssTransformAxisLabel.prototype.draw.call(this, box);
+ if (this.requiresResize) {
+ this.elem = this.plot.getPlaceholder().find("." + this.axisName +
+ "Label");
+ // Since we used CSS positioning instead of transforms for
+ // translating the element, and since the positioning is done
+ // before any rotations, we have to reset the width and height
+ // in case the browser wrapped the text (specifically for the
+ // y2axis).
+ this.elem.css('width', this.labelWidth);
+ this.elem.css('height', this.labelHeight);
+ }
+ };
+
+
+ function init(plot) {
+ plot.hooks.processOptions.push(function (plot, options) {
+
+ if (!options.axisLabels.show)
+ return;
+
+ // This is kind of a hack. There are no hooks in Flot between
+ // the creation and measuring of the ticks (setTicks, measureTickLabels
+ // in setupGrid() ) and the drawing of the ticks and plot box
+ // (insertAxisLabels in setupGrid() ).
+ //
+ // Therefore, we use a trick where we run the draw routine twice:
+ // the first time to get the tick measurements, so that we can change
+ // them, and then have it draw it again.
+ var secondPass = false;
+
+ var axisLabels = {};
+ var axisOffsetCounts = { left: 0, right: 0, top: 0, bottom: 0 };
+
+ var defaultPadding = 2; // padding between axis and tick labels
+ plot.hooks.draw.push(function (plot, ctx) {
+ var hasAxisLabels = false;
+ if (!secondPass) {
+ // MEASURE AND SET OPTIONS
+ $.each(plot.getAxes(), function(axisName, axis) {
+ var opts = axis.options // Flot 0.7
+ || plot.getOptions()[axisName]; // Flot 0.6
+
+ // Handle redraws initiated outside of this plug-in.
+ if (axisName in axisLabels) {
+ axis.labelHeight = axis.labelHeight -
+ axisLabels[axisName].height;
+ axis.labelWidth = axis.labelWidth -
+ axisLabels[axisName].width;
+ opts.labelHeight = axis.labelHeight;
+ opts.labelWidth = axis.labelWidth;
+ axisLabels[axisName].cleanup();
+ delete axisLabels[axisName];
+ }
+
+ if (!opts || !opts.axisLabel || !axis.show)
+ return;
+
+ hasAxisLabels = true;
+ var renderer = null;
+
+ if (!opts.axisLabelUseHtml &&
+ navigator.appName == 'Microsoft Internet Explorer') {
+ var ua = navigator.userAgent;
+ var re = new RegExp("MSIE ([0-9]{1,}[\.0-9]{0,})");
+ if (re.exec(ua) != null) {
+ rv = parseFloat(RegExp.$1);
+ }
+ if (rv >= 9 && !opts.axisLabelUseCanvas && !opts.axisLabelUseHtml) {
+ renderer = CssTransformAxisLabel;
+ } else if (!opts.axisLabelUseCanvas && !opts.axisLabelUseHtml) {
+ renderer = IeTransformAxisLabel;
+ } else if (opts.axisLabelUseCanvas) {
+ renderer = CanvasAxisLabel;
+ } else {
+ renderer = HtmlAxisLabel;
+ }
+ } else {
+ if (opts.axisLabelUseHtml || (!css3TransitionSupported() && !canvasTextSupported()) && !opts.axisLabelUseCanvas) {
+ renderer = HtmlAxisLabel;
+ } else if (opts.axisLabelUseCanvas || !css3TransitionSupported()) {
+ renderer = CanvasAxisLabel;
+ } else {
+ renderer = CssTransformAxisLabel;
+ }
+ }
+
+ var padding = opts.axisLabelPadding === undefined ?
+ defaultPadding : opts.axisLabelPadding;
+
+ axisLabels[axisName] = new renderer(axisName,
+ axis.position, padding,
+ plot, opts);
+
+ // flot interprets axis.labelHeight and .labelWidth as
+ // the height and width of the tick labels. We increase
+ // these values to make room for the axis label and
+ // padding.
+
+ axisLabels[axisName].calculateSize();
+
+ // AxisLabel.height and .width are the size of the
+ // axis label and padding.
+ // Just set opts here because axis will be sorted out on
+ // the redraw.
+
+ opts.labelHeight = axis.labelHeight +
+ axisLabels[axisName].height;
+ opts.labelWidth = axis.labelWidth +
+ axisLabels[axisName].width;
+ });
+
+ // If there are axis labels, re-draw with new label widths and
+ // heights.
+
+ if (hasAxisLabels) {
+ secondPass = true;
+ plot.setupGrid();
+ plot.draw();
+ }
+ } else {
+ secondPass = false;
+ // DRAW
+ $.each(plot.getAxes(), function(axisName, axis) {
+ var opts = axis.options // Flot 0.7
+ || plot.getOptions()[axisName]; // Flot 0.6
+ if (!opts || !opts.axisLabel || !axis.show)
+ return;
+
+ axisLabels[axisName].draw(axis.box);
+ });
+ }
+ });
+ });
+ }
+
+
+ $.plot.plugins.push({
+ init: init,
+ options: options,
+ name: 'axisLabels',
+ version: '2.0'
+ });
+})(jQuery);
diff --git a/js/jquery.flot.js b/js/jquery.flot.js
new file mode 100644
index 0000000000000000000000000000000000000000..fd33fd20274d8e2b4c5a6134379e0389572f4e09
--- /dev/null
+++ b/js/jquery.flot.js
@@ -0,0 +1,3175 @@
+/* Javascript plotting library for jQuery, version 0.8.3.
+
+Copyright (c) 2007-2014 IOLA and Ole Laursen.
+Licensed under the MIT license.
+
+*/
+
+// first an inline dependency, jquery.colorhelpers.js, we inline it here
+// for convenience
+
+/* Plugin for jQuery for working with colors.
+ *
+ * Version 1.1.
+ *
+ * Inspiration from jQuery color animation plugin by John Resig.
+ *
+ * Released under the MIT license by Ole Laursen, October 2009.
+ *
+ * Examples:
+ *
+ * $.color.parse("#fff").scale('rgb', 0.25).add('a', -0.5).toString()
+ * var c = $.color.extract($("#mydiv"), 'background-color');
+ * console.log(c.r, c.g, c.b, c.a);
+ * $.color.make(100, 50, 25, 0.4).toString() // returns "rgba(100,50,25,0.4)"
+ *
+ * Note that .scale() and .add() return the same modified object
+ * instead of making a new one.
+ *
+ * V. 1.1: Fix error handling so e.g. parsing an empty string does
+ * produce a color rather than just crashing.
+ */
+(function($){$.color={};$.color.make=function(r,g,b,a){var o={};o.r=r||0;o.g=g||0;o.b=b||0;o.a=a!=null?a:1;o.add=function(c,d){for(var i=0;i<c.length;++i)o[c.charAt(i)]+=d;return o.normalize()};o.scale=function(c,f){for(var i=0;i<c.length;++i)o[c.charAt(i)]*=f;return o.normalize()};o.toString=function(){if(o.a>=1){return"rgb("+[o.r,o.g,o.b].join(",")+")"}else{return"rgba("+[o.r,o.g,o.b,o.a].join(",")+")"}};o.normalize=function(){function clamp(min,value,max){return value<min?min:value>max?max:value}o.r=clamp(0,parseInt(o.r),255);o.g=clamp(0,parseInt(o.g),255);o.b=clamp(0,parseInt(o.b),255);o.a=clamp(0,o.a,1);return o};o.clone=function(){return $.color.make(o.r,o.b,o.g,o.a)};return o.normalize()};$.color.extract=function(elem,css){var c;do{c=elem.css(css).toLowerCase();if(c!=""&&c!="transparent")break;elem=elem.parent()}while(elem.length&&!$.nodeName(elem.get(0),"body"));if(c=="rgba(0, 0, 0, 0)")c="transparent";return $.color.parse(c)};$.color.parse=function(str){var res,m=$.color.make;if(res=/rgb\(\s*([0-9]{1,3})\s*,\s*([0-9]{1,3})\s*,\s*([0-9]{1,3})\s*\)/.exec(str))return m(parseInt(res[1],10),parseInt(res[2],10),parseInt(res[3],10));if(res=/rgba\(\s*([0-9]{1,3})\s*,\s*([0-9]{1,3})\s*,\s*([0-9]{1,3})\s*,\s*([0-9]+(?:\.[0-9]+)?)\s*\)/.exec(str))return m(parseInt(res[1],10),parseInt(res[2],10),parseInt(res[3],10),parseFloat(res[4]));if(res=/rgb\(\s*([0-9]+(?:\.[0-9]+)?)\%\s*,\s*([0-9]+(?:\.[0-9]+)?)\%\s*,\s*([0-9]+(?:\.[0-9]+)?)\%\s*\)/.exec(str))return m(parseFloat(res[1])*2.55,parseFloat(res[2])*2.55,parseFloat(res[3])*2.55);if(res=/rgba\(\s*([0-9]+(?:\.[0-9]+)?)\%\s*,\s*([0-9]+(?:\.[0-9]+)?)\%\s*,\s*([0-9]+(?:\.[0-9]+)?)\%\s*,\s*([0-9]+(?:\.[0-9]+)?)\s*\)/.exec(str))return m(parseFloat(res[1])*2.55,parseFloat(res[2])*2.55,parseFloat(res[3])*2.55,parseFloat(res[4]));if(res=/#([a-fA-F0-9]{2})([a-fA-F0-9]{2})([a-fA-F0-9]{2})/.exec(str))return m(parseInt(res[1],16),parseInt(res[2],16),parseInt(res[3],16));if(res=/#([a-fA-F0-9])([a-fA-F0-9])([a-fA-F0-9])/.exec(str))return m(parseInt(res[1]+res[1],16),parseInt(res[2]+res[2],16),parseInt(res[3]+res[3],16));var name=$.trim(str).toLowerCase();if(name=="transparent")return m(255,255,255,0);else{res=lookupColors[name]||[0,0,0];return m(res[0],res[1],res[2])}};var lookupColors={aqua:[0,255,255],azure:[240,255,255],beige:[245,245,220],black:[0,0,0],blue:[0,0,255],brown:[165,42,42],cyan:[0,255,255],darkblue:[0,0,139],darkcyan:[0,139,139],darkgrey:[169,169,169],darkgreen:[0,100,0],darkkhaki:[189,183,107],darkmagenta:[139,0,139],darkolivegreen:[85,107,47],darkorange:[255,140,0],darkorchid:[153,50,204],darkred:[139,0,0],darksalmon:[233,150,122],darkviolet:[148,0,211],fuchsia:[255,0,255],gold:[255,215,0],green:[0,128,0],indigo:[75,0,130],khaki:[240,230,140],lightblue:[173,216,230],lightcyan:[224,255,255],lightgreen:[144,238,144],lightgrey:[211,211,211],lightpink:[255,182,193],lightyellow:[255,255,224],lime:[0,255,0],magenta:[255,0,255],maroon:[128,0,0],navy:[0,0,128],olive:[128,128,0],orange:[255,165,0],pink:[255,192,203],purple:[128,0,128],violet:[128,0,128],red:[255,0,0],silver:[192,192,192],white:[255,255,255],yellow:[255,255,0]}})(jQuery);
+
+// the actual Flot code
+(function($) {
+
+ // Cache the prototype hasOwnProperty for faster access
+
+ var hasOwnProperty = Object.prototype.hasOwnProperty;
+
+ // A shim to provide 'detach' to jQuery versions prior to 1.4. Using a DOM
+ // operation produces the same effect as detach, i.e. removing the element
+ // without touching its jQuery data.
+
+ // Do not merge this into Flot 0.9, since it requires jQuery 1.4.4+.
+
+ if (!$.fn.detach) {
+ $.fn.detach = function() {
+ return this.each(function() {
+ if (this.parentNode) {
+ this.parentNode.removeChild( this );
+ }
+ });
+ };
+ }
+
+ ///////////////////////////////////////////////////////////////////////////
+ // The Canvas object is a wrapper around an HTML5 <canvas> tag.
+ //
+ // @constructor
+ // @param {string} cls List of classes to apply to the canvas.
+ // @param {element} container Element onto which to append the canvas.
+ //
+ // Requiring a container is a little iffy, but unfortunately canvas
+ // operations don't work unless the canvas is attached to the DOM.
+
+ function Canvas(cls, container) {
+
+ var element = container.children("." + cls)[0];
+
+ if (element == null) {
+
+ element = document.createElement("canvas");
+ element.className = cls;
+
+ $(element).css({ direction: "ltr", position: "absolute", left: 0, top: 0 })
+ .appendTo(container);
+
+ // If HTML5 Canvas isn't available, fall back to [Ex|Flash]canvas
+
+ if (!element.getContext) {
+ if (window.G_vmlCanvasManager) {
+ element = window.G_vmlCanvasManager.initElement(element);
+ } else {
+ throw new Error("Canvas is not available. If you're using IE with a fall-back such as Excanvas, then there's either a mistake in your conditional include, or the page has no DOCTYPE and is rendering in Quirks Mode.");
+ }
+ }
+ }
+
+ this.element = element;
+
+ var context = this.context = element.getContext("2d");
+
+ // Determine the screen's ratio of physical to device-independent
+ // pixels. This is the ratio between the canvas width that the browser
+ // advertises and the number of pixels actually present in that space.
+
+ // The iPhone 4, for example, has a device-independent width of 320px,
+ // but its screen is actually 640px wide. It therefore has a pixel
+ // ratio of 2, while most normal devices have a ratio of 1.
+
+ var devicePixelRatio = window.devicePixelRatio || 1,
+ backingStoreRatio =
+ context.webkitBackingStorePixelRatio ||
+ context.mozBackingStorePixelRatio ||
+ context.msBackingStorePixelRatio ||
+ context.oBackingStorePixelRatio ||
+ context.backingStorePixelRatio || 1;
+
+ this.pixelRatio = devicePixelRatio / backingStoreRatio;
+
+ // Size the canvas to match the internal dimensions of its container
+
+ this.resize(container.width(), container.height());
+
+ // Collection of HTML div layers for text overlaid onto the canvas
+
+ this.textContainer = null;
+ this.text = {};
+
+ // Cache of text fragments and metrics, so we can avoid expensively
+ // re-calculating them when the plot is re-rendered in a loop.
+
+ this._textCache = {};
+ }
+
+ // Resizes the canvas to the given dimensions.
+ //
+ // @param {number} width New width of the canvas, in pixels.
+ // @param {number} width New height of the canvas, in pixels.
+
+ Canvas.prototype.resize = function(width, height) {
+
+ if (width <= 0 || height <= 0) {
+ throw new Error("Invalid dimensions for plot, width = " + width + ", height = " + height);
+ }
+
+ var element = this.element,
+ context = this.context,
+ pixelRatio = this.pixelRatio;
+
+ // Resize the canvas, increasing its density based on the display's
+ // pixel ratio; basically giving it more pixels without increasing the
+ // size of its element, to take advantage of the fact that retina
+ // displays have that many more pixels in the same advertised space.
+
+ // Resizing should reset the state (excanvas seems to be buggy though)
+
+ if (this.width != width) {
+ element.width = width * pixelRatio;
+ element.style.width = width + "px";
+ this.width = width;
+ }
+
+ if (this.height != height) {
+ element.height = height * pixelRatio;
+ element.style.height = height + "px";
+ this.height = height;
+ }
+
+ // Save the context, so we can reset in case we get replotted. The
+ // restore ensure that we're really back at the initial state, and
+ // should be safe even if we haven't saved the initial state yet.
+
+ context.restore();
+ context.save();
+
+ // Scale the coordinate space to match the display density; so even though we
+ // may have twice as many pixels, we still want lines and other drawing to
+ // appear at the same size; the extra pixels will just make them crisper.
+
+ context.scale(pixelRatio, pixelRatio);
+ };
+
+ // Clears the entire canvas area, not including any overlaid HTML text
+
+ Canvas.prototype.clear = function() {
+ this.context.clearRect(0, 0, this.width, this.height);
+ };
+
+ // Finishes rendering the canvas, including managing the text overlay.
+
+ Canvas.prototype.render = function() {
+
+ var cache = this._textCache;
+
+ // For each text layer, add elements marked as active that haven't
+ // already been rendered, and remove those that are no longer active.
+
+ for (var layerKey in cache) {
+ if (hasOwnProperty.call(cache, layerKey)) {
+
+ var layer = this.getTextLayer(layerKey),
+ layerCache = cache[layerKey];
+
+ layer.hide();
+
+ for (var styleKey in layerCache) {
+ if (hasOwnProperty.call(layerCache, styleKey)) {
+ var styleCache = layerCache[styleKey];
+ for (var key in styleCache) {
+ if (hasOwnProperty.call(styleCache, key)) {
+
+ var positions = styleCache[key].positions;
+
+ for (var i = 0, position; position = positions[i]; i++) {
+ if (position.active) {
+ if (!position.rendered) {
+ layer.append(position.element);
+ position.rendered = true;
+ }
+ } else {
+ positions.splice(i--, 1);
+ if (position.rendered) {
+ position.element.detach();
+ }
+ }
+ }
+
+ if (positions.length == 0) {
+ delete styleCache[key];
+ }
+ }
+ }
+ }
+ }
+
+ layer.show();
+ }
+ }
+ };
+
+ // Creates (if necessary) and returns the text overlay container.
+ //
+ // @param {string} classes String of space-separated CSS classes used to
+ // uniquely identify the text layer.
+ // @return {object} The jQuery-wrapped text-layer div.
+
+ Canvas.prototype.getTextLayer = function(classes) {
+
+ var layer = this.text[classes];
+
+ // Create the text layer if it doesn't exist
+
+ if (layer == null) {
+
+ // Create the text layer container, if it doesn't exist
+
+ if (this.textContainer == null) {
+ this.textContainer = $("<div class='flot-text'></div>")
+ .css({
+ position: "absolute",
+ top: 0,
+ left: 0,
+ bottom: 0,
+ right: 0,
+ 'font-size': "smaller",
+ color: "#545454"
+ })
+ .insertAfter(this.element);
+ }
+
+ layer = this.text[classes] = $("<div></div>")
+ .addClass(classes)
+ .css({
+ position: "absolute",
+ top: 0,
+ left: 0,
+ bottom: 0,
+ right: 0
+ })
+ .appendTo(this.textContainer);
+ }
+
+ return layer;
+ };
+
+ // Creates (if necessary) and returns a text info object.
+ //
+ // The object looks like this:
+ //
+ // {
+ // width: Width of the text's wrapper div.
+ // height: Height of the text's wrapper div.
+ // element: The jQuery-wrapped HTML div containing the text.
+ // positions: Array of positions at which this text is drawn.
+ // }
+ //
+ // The positions array contains objects that look like this:
+ //
+ // {
+ // active: Flag indicating whether the text should be visible.
+ // rendered: Flag indicating whether the text is currently visible.
+ // element: The jQuery-wrapped HTML div containing the text.
+ // x: X coordinate at which to draw the text.
+ // y: Y coordinate at which to draw the text.
+ // }
+ //
+ // Each position after the first receives a clone of the original element.
+ //
+ // The idea is that that the width, height, and general 'identity' of the
+ // text is constant no matter where it is placed; the placements are a
+ // secondary property.
+ //
+ // Canvas maintains a cache of recently-used text info objects; getTextInfo
+ // either returns the cached element or creates a new entry.
+ //
+ // @param {string} layer A string of space-separated CSS classes uniquely
+ // identifying the layer containing this text.
+ // @param {string} text Text string to retrieve info for.
+ // @param {(string|object)=} font Either a string of space-separated CSS
+ // classes or a font-spec object, defining the text's font and style.
+ // @param {number=} angle Angle at which to rotate the text, in degrees.
+ // Angle is currently unused, it will be implemented in the future.
+ // @param {number=} width Maximum width of the text before it wraps.
+ // @return {object} a text info object.
+
+ Canvas.prototype.getTextInfo = function(layer, text, font, angle, width) {
+
+ var textStyle, layerCache, styleCache, info;
+
+ // Cast the value to a string, in case we were given a number or such
+
+ text = "" + text;
+
+ // If the font is a font-spec object, generate a CSS font definition
+
+ if (typeof font === "object") {
+ textStyle = font.style + " " + font.variant + " " + font.weight + " " + font.size + "px/" + font.lineHeight + "px " + font.family;
+ } else {
+ textStyle = font;
+ }
+
+ // Retrieve (or create) the cache for the text's layer and styles
+
+ layerCache = this._textCache[layer];
+
+ if (layerCache == null) {
+ layerCache = this._textCache[layer] = {};
+ }
+
+ styleCache = layerCache[textStyle];
+
+ if (styleCache == null) {
+ styleCache = layerCache[textStyle] = {};
+ }
+
+ info = styleCache[text];
+
+ // If we can't find a matching element in our cache, create a new one
+
+ if (info == null) {
+
+ var element = $("<div></div>").html(text)
+ .css({
+ position: "absolute",
+ 'max-width': width,
+ top: -9999
+ })
+ .appendTo(this.getTextLayer(layer));
+
+ if (typeof font === "object") {
+ element.css({
+ font: textStyle,
+ color: font.color
+ });
+ } else if (typeof font === "string") {
+ element.addClass(font);
+ }
+
+ info = styleCache[text] = {
+ width: element.outerWidth(true),
+ height: element.outerHeight(true),
+ element: element,
+ positions: []
+ };
+
+ element.detach();
+ }
+
+ return info;
+ };
+
+ // Adds a text string to the canvas text overlay.
+ //
+ // The text isn't drawn immediately; it is marked as rendering, which will
+ // result in its addition to the canvas on the next render pass.
+ //
+ // @param {string} layer A string of space-separated CSS classes uniquely
+ // identifying the layer containing this text.
+ // @param {number} x X coordinate at which to draw the text.
+ // @param {number} y Y coordinate at which to draw the text.
+ // @param {string} text Text string to draw.
+ // @param {(string|object)=} font Either a string of space-separated CSS
+ // classes or a font-spec object, defining the text's font and style.
+ // @param {number=} angle Angle at which to rotate the text, in degrees.
+ // Angle is currently unused, it will be implemented in the future.
+ // @param {number=} width Maximum width of the text before it wraps.
+ // @param {string=} halign Horizontal alignment of the text; either "left",
+ // "center" or "right".
+ // @param {string=} valign Vertical alignment of the text; either "top",
+ // "middle" or "bottom".
+
+ Canvas.prototype.addText = function(layer, x, y, text, font, angle, width, halign, valign) {
+
+ var info = this.getTextInfo(layer, text, font, angle, width),
+ positions = info.positions;
+
+ // Tweak the div's position to match the text's alignment
+
+ if (halign == "center") {
+ x -= info.width / 2;
+ } else if (halign == "right") {
+ x -= info.width;
+ }
+
+ if (valign == "middle") {
+ y -= info.height / 2;
+ } else if (valign == "bottom") {
+ y -= info.height;
+ }
+
+ // Determine whether this text already exists at this position.
+ // If so, mark it for inclusion in the next render pass.
+
+ for (var i = 0, position; position = positions[i]; i++) {
+ if (position.x == x && position.y == y) {
+ position.active = true;
+ return;
+ }
+ }
+
+ // If the text doesn't exist at this position, create a new entry
+
+ // For the very first position we'll re-use the original element,
+ // while for subsequent ones we'll clone it.
+
+ position = {
+ active: true,
+ rendered: false,
+ element: positions.length ? info.element.clone() : info.element,
+ x: x,
+ y: y
+ };
+
+ positions.push(position);
+
+ // Move the element to its final position within the container
+
+ position.element.css({
+ top: Math.round(y),
+ left: Math.round(x),
+ 'text-align': halign // In case the text wraps
+ });
+ };
+
+ // Removes one or more text strings from the canvas text overlay.
+ //
+ // If no parameters are given, all text within the layer is removed.
+ //
+ // Note that the text is not immediately removed; it is simply marked as
+ // inactive, which will result in its removal on the next render pass.
+ // This avoids the performance penalty for 'clear and redraw' behavior,
+ // where we potentially get rid of all text on a layer, but will likely
+ // add back most or all of it later, as when redrawing axes, for example.
+ //
+ // @param {string} layer A string of space-separated CSS classes uniquely
+ // identifying the layer containing this text.
+ // @param {number=} x X coordinate of the text.
+ // @param {number=} y Y coordinate of the text.
+ // @param {string=} text Text string to remove.
+ // @param {(string|object)=} font Either a string of space-separated CSS
+ // classes or a font-spec object, defining the text's font and style.
+ // @param {number=} angle Angle at which the text is rotated, in degrees.
+ // Angle is currently unused, it will be implemented in the future.
+
+ Canvas.prototype.removeText = function(layer, x, y, text, font, angle) {
+ if (text == null) {
+ var layerCache = this._textCache[layer];
+ if (layerCache != null) {
+ for (var styleKey in layerCache) {
+ if (hasOwnProperty.call(layerCache, styleKey)) {
+ var styleCache = layerCache[styleKey];
+ for (var key in styleCache) {
+ if (hasOwnProperty.call(styleCache, key)) {
+ var positions = styleCache[key].positions;
+ for (var i = 0, position; position = positions[i]; i++) {
+ position.active = false;
+ }
+ }
+ }
+ }
+ }
+ }
+ } else {
+ var positions = this.getTextInfo(layer, text, font, angle).positions;
+ for (var i = 0, position; position = positions[i]; i++) {
+ if (position.x == x && position.y == y) {
+ position.active = false;
+ }
+ }
+ }
+ };
+
+ ///////////////////////////////////////////////////////////////////////////
+ // The top-level container for the entire plot.
+
+ function Plot(placeholder, data_, options_, plugins) {
+ // data is on the form:
+ // [ series1, series2 ... ]
+ // where series is either just the data as [ [x1, y1], [x2, y2], ... ]
+ // or { data: [ [x1, y1], [x2, y2], ... ], label: "some label", ... }
+
+ var series = [],
+ options = {
+ // the color theme used for graphs
+ colors: ["#edc240", "#afd8f8", "#cb4b4b", "#4da74d", "#9440ed"],
+ legend: {
+ show: true,
+ noColumns: 1, // number of colums in legend table
+ labelFormatter: null, // fn: string -> string
+ labelBoxBorderColor: "#ccc", // border color for the little label boxes
+ container: null, // container (as jQuery object) to put legend in, null means default on top of graph
+ position: "ne", // position of default legend container within plot
+ margin: 5, // distance from grid edge to default legend container within plot
+ backgroundColor: null, // null means auto-detect
+ backgroundOpacity: 0.85, // set to 0 to avoid background
+ sorted: null // default to no legend sorting
+ },
+ xaxis: {
+ show: null, // null = auto-detect, true = always, false = never
+ position: "bottom", // or "top"
+ mode: null, // null or "time"
+ font: null, // null (derived from CSS in placeholder) or object like { size: 11, lineHeight: 13, style: "italic", weight: "bold", family: "sans-serif", variant: "small-caps" }
+ color: null, // base color, labels, ticks
+ tickColor: null, // possibly different color of ticks, e.g. "rgba(0,0,0,0.15)"
+ transform: null, // null or f: number -> number to transform axis
+ inverseTransform: null, // if transform is set, this should be the inverse function
+ min: null, // min. value to show, null means set automatically
+ max: null, // max. value to show, null means set automatically
+ autoscaleMargin: null, // margin in % to add if auto-setting min/max
+ ticks: null, // either [1, 3] or [[1, "a"], 3] or (fn: axis info -> ticks) or app. number of ticks for auto-ticks
+ tickFormatter: null, // fn: number -> string
+ labelWidth: null, // size of tick labels in pixels
+ labelHeight: null,
+ reserveSpace: null, // whether to reserve space even if axis isn't shown
+ tickLength: null, // size in pixels of ticks, or "full" for whole line
+ alignTicksWithAxis: null, // axis number or null for no sync
+ tickDecimals: null, // no. of decimals, null means auto
+ tickSize: null, // number or [number, "unit"]
+ minTickSize: null // number or [number, "unit"]
+ },
+ yaxis: {
+ autoscaleMargin: 0.02,
+ position: "left" // or "right"
+ },
+ xaxes: [],
+ yaxes: [],
+ series: {
+ points: {
+ show: false,
+ radius: 3,
+ lineWidth: 2, // in pixels
+ fill: true,
+ fillColor: "#ffffff",
+ symbol: "circle" // or callback
+ },
+ lines: {
+ // we don't put in show: false so we can see
+ // whether lines were actively disabled
+ lineWidth: 2, // in pixels
+ fill: false,
+ fillColor: null,
+ steps: false
+ // Omit 'zero', so we can later default its value to
+ // match that of the 'fill' option.
+ },
+ bars: {
+ show: false,
+ lineWidth: 2, // in pixels
+ barWidth: 1, // in units of the x axis
+ fill: true,
+ fillColor: null,
+ align: "left", // "left", "right", or "center"
+ horizontal: false,
+ zero: true
+ },
+ shadowSize: 3,
+ highlightColor: null
+ },
+ grid: {
+ show: true,
+ aboveData: false,
+ color: "#545454", // primary color used for outline and labels
+ backgroundColor: null, // null for transparent, else color
+ borderColor: null, // set if different from the grid color
+ tickColor: null, // color for the ticks, e.g. "rgba(0,0,0,0.15)"
+ margin: 0, // distance from the canvas edge to the grid
+ labelMargin: 5, // in pixels
+ axisMargin: 8, // in pixels
+ borderWidth: 2, // in pixels
+ minBorderMargin: null, // in pixels, null means taken from points radius
+ markings: null, // array of ranges or fn: axes -> array of ranges
+ markingsColor: "#f4f4f4",
+ markingsLineWidth: 2,
+ TickLineStyle: "dashed",
+ // interactive stuff
+ clickable: false,
+ hoverable: false,
+ autoHighlight: true, // highlight in case mouse is near
+ mouseActiveRadius: 10 // how far the mouse can be away to activate an item
+ },
+ interaction: {
+ redrawOverlayInterval: 1000/60 // time between updates, -1 means in same flow
+ },
+ hooks: {}
+ },
+ surface = null, // the canvas for the plot itself
+ overlay = null, // canvas for interactive stuff on top of plot
+ eventHolder = null, // jQuery object that events should be bound to
+ ctx = null, octx = null,
+ xaxes = [], yaxes = [],
+ plotOffset = { left: 0, right: 0, top: 0, bottom: 0},
+ plotWidth = 0, plotHeight = 0,
+ hooks = {
+ processOptions: [],
+ processRawData: [],
+ processDatapoints: [],
+ processOffset: [],
+ drawBackground: [],
+ drawSeries: [],
+ draw: [],
+ bindEvents: [],
+ drawOverlay: [],
+ shutdown: []
+ },
+ plot = this;
+
+ // public functions
+ plot.setData = setData;
+ plot.setupGrid = setupGrid;
+ plot.draw = draw;
+ plot.getPlaceholder = function() { return placeholder; };
+ plot.getCanvas = function() { return surface.element; };
+ plot.getPlotOffset = function() { return plotOffset; };
+ plot.width = function () { return plotWidth; };
+ plot.height = function () { return plotHeight; };
+ plot.offset = function () {
+ var o = eventHolder.offset();
+ o.left += plotOffset.left;
+ o.top += plotOffset.top;
+ return o;
+ };
+ plot.getData = function () { return series; };
+ plot.getAxes = function () {
+ var res = {}, i;
+ $.each(xaxes.concat(yaxes), function (_, axis) {
+ if (axis)
+ res[axis.direction + (axis.n != 1 ? axis.n : "") + "axis"] = axis;
+ });
+ return res;
+ };
+ plot.getXAxes = function () { return xaxes; };
+ plot.getYAxes = function () { return yaxes; };
+ plot.c2p = canvasToAxisCoords;
+ plot.p2c = axisToCanvasCoords;
+ plot.getOptions = function () { return options; };
+ plot.highlight = highlight;
+ plot.unhighlight = unhighlight;
+ plot.triggerRedrawOverlay = triggerRedrawOverlay;
+ plot.pointOffset = function(point) {
+ return {
+ left: parseInt(xaxes[axisNumber(point, "x") - 1].p2c(+point.x) + plotOffset.left, 10),
+ top: parseInt(yaxes[axisNumber(point, "y") - 1].p2c(+point.y) + plotOffset.top, 10)
+ };
+ };
+ plot.shutdown = shutdown;
+ plot.destroy = function () {
+ shutdown();
+ placeholder.removeData("plot").empty();
+
+ series = [];
+ options = null;
+ surface = null;
+ overlay = null;
+ eventHolder = null;
+ ctx = null;
+ octx = null;
+ xaxes = [];
+ yaxes = [];
+ hooks = null;
+ highlights = [];
+ plot = null;
+ };
+ plot.resize = function () {
+ var width = placeholder.width(),
+ height = placeholder.height();
+ surface.resize(width, height);
+ overlay.resize(width, height);
+ };
+
+ // public attributes
+ plot.hooks = hooks;
+
+ // initialize
+ initPlugins(plot);
+ parseOptions(options_);
+ setupCanvases();
+ setData(data_);
+ setupGrid();
+ draw();
+ bindEvents();
+
+
+ function executeHooks(hook, args) {
+ args = [plot].concat(args);
+ for (var i = 0; i < hook.length; ++i)
+ hook[i].apply(this, args);
+ }
+
+ function initPlugins() {
+
+ // References to key classes, allowing plugins to modify them
+
+ var classes = {
+ Canvas: Canvas
+ };
+
+ for (var i = 0; i < plugins.length; ++i) {
+ var p = plugins[i];
+ p.init(plot, classes);
+ if (p.options)
+ $.extend(true, options, p.options);
+ }
+ }
+
+ function parseOptions(opts) {
+
+ $.extend(true, options, opts);
+
+ // $.extend merges arrays, rather than replacing them. When less
+ // colors are provided than the size of the default palette, we
+ // end up with those colors plus the remaining defaults, which is
+ // not expected behavior; avoid it by replacing them here.
+
+ if (opts && opts.colors) {
+ options.colors = opts.colors;
+ }
+
+ if (options.xaxis.color == null)
+ options.xaxis.color = $.color.parse(options.grid.color).scale('a', 0.22).toString();
+ if (options.yaxis.color == null)
+ options.yaxis.color = $.color.parse(options.grid.color).scale('a', 0.22).toString();
+
+ if (options.xaxis.tickColor == null) // grid.tickColor for back-compatibility
+ options.xaxis.tickColor = options.grid.tickColor || options.xaxis.color;
+ if (options.yaxis.tickColor == null) // grid.tickColor for back-compatibility
+ options.yaxis.tickColor = options.grid.tickColor || options.yaxis.color;
+
+ if (options.grid.borderColor == null)
+ options.grid.borderColor = options.grid.color;
+ if (options.grid.tickColor == null)
+ options.grid.tickColor = $.color.parse(options.grid.color).scale('a', 0.22).toString();
+
+ // Fill in defaults for axis options, including any unspecified
+ // font-spec fields, if a font-spec was provided.
+
+ // If no x/y axis options were provided, create one of each anyway,
+ // since the rest of the code assumes that they exist.
+
+ var i, axisOptions, axisCount,
+ fontSize = placeholder.css("font-size"),
+ fontSizeDefault = fontSize ? +fontSize.replace("px", "") : 14,
+ fontDefaults = {
+ style: placeholder.css("font-style"),
+ size: Math.round(0.8 * fontSizeDefault),
+ variant: placeholder.css("font-variant"),
+ weight: placeholder.css("font-weight"),
+ family: placeholder.css("font-family")
+ };
+
+ axisCount = options.xaxes.length || 1;
+ for (i = 0; i < axisCount; ++i) {
+
+ axisOptions = options.xaxes[i];
+ if (axisOptions && !axisOptions.tickColor) {
+ axisOptions.tickColor = axisOptions.color;
+ }
+
+ axisOptions = $.extend(true, {}, options.xaxis, axisOptions);
+ options.xaxes[i] = axisOptions;
+
+ if (axisOptions.font) {
+ axisOptions.font = $.extend({}, fontDefaults, axisOptions.font);
+ if (!axisOptions.font.color) {
+ axisOptions.font.color = axisOptions.color;
+ }
+ if (!axisOptions.font.lineHeight) {
+ axisOptions.font.lineHeight = Math.round(axisOptions.font.size * 1.15);
+ }
+ }
+ }
+
+ axisCount = options.yaxes.length || 1;
+ for (i = 0; i < axisCount; ++i) {
+
+ axisOptions = options.yaxes[i];
+ if (axisOptions && !axisOptions.tickColor) {
+ axisOptions.tickColor = axisOptions.color;
+ }
+
+ axisOptions = $.extend(true, {}, options.yaxis, axisOptions);
+ options.yaxes[i] = axisOptions;
+
+ if (axisOptions.font) {
+ axisOptions.font = $.extend({}, fontDefaults, axisOptions.font);
+ if (!axisOptions.font.color) {
+ axisOptions.font.color = axisOptions.color;
+ }
+ if (!axisOptions.font.lineHeight) {
+ axisOptions.font.lineHeight = Math.round(axisOptions.font.size * 1.15);
+ }
+ }
+ }
+
+ // backwards compatibility, to be removed in future
+ if (options.xaxis.noTicks && options.xaxis.ticks == null)
+ options.xaxis.ticks = options.xaxis.noTicks;
+ if (options.yaxis.noTicks && options.yaxis.ticks == null)
+ options.yaxis.ticks = options.yaxis.noTicks;
+ if (options.x2axis) {
+ options.xaxes[1] = $.extend(true, {}, options.xaxis, options.x2axis);
+ options.xaxes[1].position = "top";
+ // Override the inherit to allow the axis to auto-scale
+ if (options.x2axis.min == null) {
+ options.xaxes[1].min = null;
+ }
+ if (options.x2axis.max == null) {
+ options.xaxes[1].max = null;
+ }
+ }
+ if (options.y2axis) {
+ options.yaxes[1] = $.extend(true, {}, options.yaxis, options.y2axis);
+ options.yaxes[1].position = "right";
+ // Override the inherit to allow the axis to auto-scale
+ if (options.y2axis.min == null) {
+ options.yaxes[1].min = null;
+ }
+ if (options.y2axis.max == null) {
+ options.yaxes[1].max = null;
+ }
+ }
+ if (options.grid.coloredAreas)
+ options.grid.markings = options.grid.coloredAreas;
+ if (options.grid.coloredAreasColor)
+ options.grid.markingsColor = options.grid.coloredAreasColor;
+ if (options.lines)
+ $.extend(true, options.series.lines, options.lines);
+ if (options.points)
+ $.extend(true, options.series.points, options.points);
+ if (options.bars)
+ $.extend(true, options.series.bars, options.bars);
+ if (options.shadowSize != null)
+ options.series.shadowSize = options.shadowSize;
+ if (options.highlightColor != null)
+ options.series.highlightColor = options.highlightColor;
+
+ // save options on axes for future reference
+ for (i = 0; i < options.xaxes.length; ++i)
+ getOrCreateAxis(xaxes, i + 1).options = options.xaxes[i];
+ for (i = 0; i < options.yaxes.length; ++i)
+ getOrCreateAxis(yaxes, i + 1).options = options.yaxes[i];
+
+ // add hooks from options
+ for (var n in hooks)
+ if (options.hooks[n] && options.hooks[n].length)
+ hooks[n] = hooks[n].concat(options.hooks[n]);
+
+ executeHooks(hooks.processOptions, [options]);
+ }
+
+ function setData(d) {
+ series = parseData(d);
+ fillInSeriesOptions();
+ processData();
+ }
+
+ function parseData(d) {
+ var res = [];
+ for (var i = 0; i < d.length; ++i) {
+ var s = $.extend(true, {}, options.series);
+
+ if (d[i].data != null) {
+ s.data = d[i].data; // move the data instead of deep-copy
+ delete d[i].data;
+
+ $.extend(true, s, d[i]);
+
+ d[i].data = s.data;
+ }
+ else
+ s.data = d[i];
+ res.push(s);
+ }
+
+ return res;
+ }
+
+ function axisNumber(obj, coord) {
+ var a = obj[coord + "axis"];
+ if (typeof a == "object") // if we got a real axis, extract number
+ a = a.n;
+ if (typeof a != "number")
+ a = 1; // default to first axis
+ return a;
+ }
+
+ function allAxes() {
+ // return flat array without annoying null entries
+ return $.grep(xaxes.concat(yaxes), function (a) { return a; });
+ }
+
+ function canvasToAxisCoords(pos) {
+ // return an object with x/y corresponding to all used axes
+ var res = {}, i, axis;
+ for (i = 0; i < xaxes.length; ++i) {
+ axis = xaxes[i];
+ if (axis && axis.used)
+ res["x" + axis.n] = axis.c2p(pos.left);
+ }
+
+ for (i = 0; i < yaxes.length; ++i) {
+ axis = yaxes[i];
+ if (axis && axis.used)
+ res["y" + axis.n] = axis.c2p(pos.top);
+ }
+
+ if (res.x1 !== undefined)
+ res.x = res.x1;
+ if (res.y1 !== undefined)
+ res.y = res.y1;
+
+ return res;
+ }
+
+ function axisToCanvasCoords(pos) {
+ // get canvas coords from the first pair of x/y found in pos
+ var res = {}, i, axis, key;
+
+ for (i = 0; i < xaxes.length; ++i) {
+ axis = xaxes[i];
+ if (axis && axis.used) {
+ key = "x" + axis.n;
+ if (pos[key] == null && axis.n == 1)
+ key = "x";
+
+ if (pos[key] != null) {
+ res.left = axis.p2c(pos[key]);
+ break;
+ }
+ }
+ }
+
+ for (i = 0; i < yaxes.length; ++i) {
+ axis = yaxes[i];
+ if (axis && axis.used) {
+ key = "y" + axis.n;
+ if (pos[key] == null && axis.n == 1)
+ key = "y";
+
+ if (pos[key] != null) {
+ res.top = axis.p2c(pos[key]);
+ break;
+ }
+ }
+ }
+
+ return res;
+ }
+
+ function getOrCreateAxis(axes, number) {
+ if (!axes[number - 1])
+ axes[number - 1] = {
+ n: number, // save the number for future reference
+ direction: axes == xaxes ? "x" : "y",
+ options: $.extend(true, {}, axes == xaxes ? options.xaxis : options.yaxis)
+ };
+
+ return axes[number - 1];
+ }
+
+ function fillInSeriesOptions() {
+
+ var neededColors = series.length, maxIndex = -1, i;
+
+ // Subtract the number of series that already have fixed colors or
+ // color indexes from the number that we still need to generate.
+
+ for (i = 0; i < series.length; ++i) {
+ var sc = series[i].color;
+ if (sc != null) {
+ neededColors--;
+ if (typeof sc == "number" && sc > maxIndex) {
+ maxIndex = sc;
+ }
+ }
+ }
+
+ // If any of the series have fixed color indexes, then we need to
+ // generate at least as many colors as the highest index.
+
+ if (neededColors <= maxIndex) {
+ neededColors = maxIndex + 1;
+ }
+
+ // Generate all the colors, using first the option colors and then
+ // variations on those colors once they're exhausted.
+
+ var c, colors = [], colorPool = options.colors,
+ colorPoolSize = colorPool.length, variation = 0;
+
+ for (i = 0; i < neededColors; i++) {
+
+ c = $.color.parse(colorPool[i % colorPoolSize] || "#666");
+
+ // Each time we exhaust the colors in the pool we adjust
+ // a scaling factor used to produce more variations on
+ // those colors. The factor alternates negative/positive
+ // to produce lighter/darker colors.
+
+ // Reset the variation after every few cycles, or else
+ // it will end up producing only white or black colors.
+
+ if (i % colorPoolSize == 0 && i) {
+ if (variation >= 0) {
+ if (variation < 0.5) {
+ variation = -variation - 0.2;
+ } else variation = 0;
+ } else variation = -variation;
+ }
+
+ colors[i] = c.scale('rgb', 1 + variation);
+ }
+
+ // Finalize the series options, filling in their colors
+
+ var colori = 0, s;
+ for (i = 0; i < series.length; ++i) {
+ s = series[i];
+
+ // assign colors
+ if (s.color == null) {
+ s.color = colors[colori].toString();
+ ++colori;
+ }
+ else if (typeof s.color == "number")
+ s.color = colors[s.color].toString();
+
+ // turn on lines automatically in case nothing is set
+ if (s.lines.show == null) {
+ var v, show = true;
+ for (v in s)
+ if (s[v] && s[v].show) {
+ show = false;
+ break;
+ }
+ if (show)
+ s.lines.show = true;
+ }
+
+ // If nothing was provided for lines.zero, default it to match
+ // lines.fill, since areas by default should extend to zero.
+
+ if (s.lines.zero == null) {
+ s.lines.zero = !!s.lines.fill;
+ }
+
+ // setup axes
+ s.xaxis = getOrCreateAxis(xaxes, axisNumber(s, "x"));
+ s.yaxis = getOrCreateAxis(yaxes, axisNumber(s, "y"));
+ }
+ }
+
+ function processData() {
+ var topSentry = Number.POSITIVE_INFINITY,
+ bottomSentry = Number.NEGATIVE_INFINITY,
+ fakeInfinity = Number.MAX_VALUE,
+ i, j, k, m, length,
+ s, points, ps, x, y, axis, val, f, p,
+ data, format;
+
+ function updateAxis(axis, min, max) {
+ if (min < axis.datamin && min != -fakeInfinity)
+ axis.datamin = min;
+ if (max > axis.datamax && max != fakeInfinity)
+ axis.datamax = max;
+ }
+
+ $.each(allAxes(), function (_, axis) {
+ // init axis
+ axis.datamin = topSentry;
+ axis.datamax = bottomSentry;
+ axis.used = false;
+ });
+
+ for (i = 0; i < series.length; ++i) {
+ s = series[i];
+ s.datapoints = { points: [] };
+
+ executeHooks(hooks.processRawData, [ s, s.data, s.datapoints ]);
+ }
+
+ // first pass: clean and copy data
+ for (i = 0; i < series.length; ++i) {
+ s = series[i];
+
+ data = s.data;
+ format = s.datapoints.format;
+
+ if (!format) {
+ format = [];
+ // find out how to copy
+ format.push({ x: true, number: true, required: true });
+ format.push({ y: true, number: true, required: true });
+
+ if (s.bars.show || (s.lines.show && s.lines.fill)) {
+ var autoscale = !!((s.bars.show && s.bars.zero) || (s.lines.show && s.lines.zero));
+ format.push({ y: true, number: true, required: false, defaultValue: 0, autoscale: autoscale });
+ if (s.bars.horizontal) {
+ delete format[format.length - 1].y;
+ format[format.length - 1].x = true;
+ }
+ }
+
+ s.datapoints.format = format;
+ }
+
+ if (s.datapoints.pointsize != null)
+ continue; // already filled in
+
+ s.datapoints.pointsize = format.length;
+
+ ps = s.datapoints.pointsize;
+ points = s.datapoints.points;
+
+ var insertSteps = s.lines.show && s.lines.steps;
+ s.xaxis.used = s.yaxis.used = true;
+
+ for (j = k = 0; j < data.length; ++j, k += ps) {
+ p = data[j];
+
+ var nullify = p == null;
+ if (!nullify) {
+ for (m = 0; m < ps; ++m) {
+ val = p[m];
+ f = format[m];
+
+ if (f) {
+ if (f.number && val != null) {
+ val = +val; // convert to number
+ if (isNaN(val))
+ val = null;
+ else if (val == Infinity)
+ val = fakeInfinity;
+ else if (val == -Infinity)
+ val = -fakeInfinity;
+ }
+
+ if (val == null) {
+ if (f.required)
+ nullify = true;
+
+ if (f.defaultValue != null)
+ val = f.defaultValue;
+ }
+ }
+
+ points[k + m] = val;
+ }
+ }
+
+ if (nullify) {
+ for (m = 0; m < ps; ++m) {
+ val = points[k + m];
+ if (val != null) {
+ f = format[m];
+ // extract min/max info
+ if (f.autoscale !== false) {
+ if (f.x) {
+ updateAxis(s.xaxis, val, val);
+ }
+ if (f.y) {
+ updateAxis(s.yaxis, val, val);
+ }
+ }
+ }
+ points[k + m] = null;
+ }
+ }
+ else {
+ // a little bit of line specific stuff that
+ // perhaps shouldn't be here, but lacking
+ // better means...
+ if (insertSteps && k > 0
+ && points[k - ps] != null
+ && points[k - ps] != points[k]
+ && points[k - ps + 1] != points[k + 1]) {
+ // copy the point to make room for a middle point
+ for (m = 0; m < ps; ++m)
+ points[k + ps + m] = points[k + m];
+
+ // middle point has same y
+ points[k + 1] = points[k - ps + 1];
+
+ // we've added a point, better reflect that
+ k += ps;
+ }
+ }
+ }
+ }
+
+ // give the hooks a chance to run
+ for (i = 0; i < series.length; ++i) {
+ s = series[i];
+
+ executeHooks(hooks.processDatapoints, [ s, s.datapoints]);
+ }
+
+ // second pass: find datamax/datamin for auto-scaling
+ for (i = 0; i < series.length; ++i) {
+ s = series[i];
+ points = s.datapoints.points;
+ ps = s.datapoints.pointsize;
+ format = s.datapoints.format;
+
+ var xmin = topSentry, ymin = topSentry,
+ xmax = bottomSentry, ymax = bottomSentry;
+
+ for (j = 0; j < points.length; j += ps) {
+ if (points[j] == null)
+ continue;
+
+ for (m = 0; m < ps; ++m) {
+ val = points[j + m];
+ f = format[m];
+ if (!f || f.autoscale === false || val == fakeInfinity || val == -fakeInfinity)
+ continue;
+
+ if (f.x) {
+ if (val < xmin)
+ xmin = val;
+ if (val > xmax)
+ xmax = val;
+ }
+ if (f.y) {
+ if (val < ymin)
+ ymin = val;
+ if (val > ymax)
+ ymax = val;
+ }
+ }
+ }
+
+ if (s.bars.show) {
+ // make sure we got room for the bar on the dancing floor
+ var delta;
+
+ switch (s.bars.align) {
+ case "left":
+ delta = 0;
+ break;
+ case "right":
+ delta = -s.bars.barWidth;
+ break;
+ default:
+ delta = -s.bars.barWidth / 2;
+ }
+
+ if (s.bars.horizontal) {
+ ymin += delta;
+ ymax += delta + s.bars.barWidth;
+ }
+ else {
+ xmin += delta;
+ xmax += delta + s.bars.barWidth;
+ }
+ }
+
+ updateAxis(s.xaxis, xmin, xmax);
+ updateAxis(s.yaxis, ymin, ymax);
+ }
+
+ $.each(allAxes(), function (_, axis) {
+ if (axis.datamin == topSentry)
+ axis.datamin = null;
+ if (axis.datamax == bottomSentry)
+ axis.datamax = null;
+ });
+ }
+
+ function setupCanvases() {
+
+ // Make sure the placeholder is clear of everything except canvases
+ // from a previous plot in this container that we'll try to re-use.
+
+ placeholder.css("padding", 0) // padding messes up the positioning
+ .children().filter(function(){
+ return !$(this).hasClass("flot-overlay") && !$(this).hasClass('flot-base');
+ }).remove();
+
+ if (placeholder.css("position") == 'static')
+ placeholder.css("position", "relative"); // for positioning labels and overlay
+
+ surface = new Canvas("flot-base", placeholder);
+ overlay = new Canvas("flot-overlay", placeholder); // overlay canvas for interactive features
+
+ ctx = surface.context;
+ octx = overlay.context;
+
+ // define which element we're listening for events on
+ eventHolder = $(overlay.element).unbind();
+
+ // If we're re-using a plot object, shut down the old one
+
+ var existing = placeholder.data("plot");
+
+ if (existing) {
+ existing.shutdown();
+ overlay.clear();
+ }
+
+ // save in case we get replotted
+ placeholder.data("plot", plot);
+ }
+
+ function bindEvents() {
+ // bind events
+ if (options.grid.hoverable) {
+ eventHolder.mousemove(onMouseMove);
+
+ // Use bind, rather than .mouseleave, because we officially
+ // still support jQuery 1.2.6, which doesn't define a shortcut
+ // for mouseenter or mouseleave. This was a bug/oversight that
+ // was fixed somewhere around 1.3.x. We can return to using
+ // .mouseleave when we drop support for 1.2.6.
+
+ eventHolder.bind("mouseleave", onMouseLeave);
+ }
+
+ if (options.grid.clickable)
+ eventHolder.click(onClick);
+
+ executeHooks(hooks.bindEvents, [eventHolder]);
+ }
+
+ function shutdown() {
+ if (redrawTimeout)
+ clearTimeout(redrawTimeout);
+
+ eventHolder.unbind("mousemove", onMouseMove);
+ eventHolder.unbind("mouseleave", onMouseLeave);
+ eventHolder.unbind("click", onClick);
+
+ executeHooks(hooks.shutdown, [eventHolder]);
+ }
+
+ function setTransformationHelpers(axis) {
+ // set helper functions on the axis, assumes plot area
+ // has been computed already
+
+ function identity(x) { return x; }
+
+ var s, m, t = axis.options.transform || identity,
+ it = axis.options.inverseTransform;
+
+ // precompute how much the axis is scaling a point
+ // in canvas space
+ if (axis.direction == "x") {
+ s = axis.scale = plotWidth / Math.abs(t(axis.max) - t(axis.min));
+ m = Math.min(t(axis.max), t(axis.min));
+ }
+ else {
+ s = axis.scale = plotHeight / Math.abs(t(axis.max) - t(axis.min));
+ s = -s;
+ m = Math.max(t(axis.max), t(axis.min));
+ }
+
+ // data point to canvas coordinate
+ if (t == identity) // slight optimization
+ axis.p2c = function (p) { return (p - m) * s; };
+ else
+ axis.p2c = function (p) { return (t(p) - m) * s; };
+ // canvas coordinate to data point
+ if (!it)
+ axis.c2p = function (c) { return m + c / s; };
+ else
+ axis.c2p = function (c) { return it(m + c / s); };
+ }
+
+ function measureTickLabels(axis) {
+
+ var opts = axis.options,
+ ticks = axis.ticks || [],
+ labelWidth = opts.labelWidth || 0,
+ labelHeight = opts.labelHeight || 0,
+ maxWidth = labelWidth || (axis.direction == "x" ? Math.floor(surface.width / (ticks.length || 1)) : null),
+ legacyStyles = axis.direction + "Axis " + axis.direction + axis.n + "Axis",
+ layer = "flot-" + axis.direction + "-axis flot-" + axis.direction + axis.n + "-axis " + legacyStyles,
+ font = opts.font || "flot-tick-label tickLabel";
+
+ for (var i = 0; i < ticks.length; ++i) {
+
+ var t = ticks[i];
+
+ if (!t.label)
+ continue;
+
+ var info = surface.getTextInfo(layer, t.label, font, null, maxWidth);
+
+ labelWidth = Math.max(labelWidth, info.width);
+ labelHeight = Math.max(labelHeight, info.height);
+ }
+
+ axis.labelWidth = opts.labelWidth || labelWidth;
+ axis.labelHeight = opts.labelHeight || labelHeight;
+ }
+
+ function allocateAxisBoxFirstPhase(axis) {
+ // find the bounding box of the axis by looking at label
+ // widths/heights and ticks, make room by diminishing the
+ // plotOffset; this first phase only looks at one
+ // dimension per axis, the other dimension depends on the
+ // other axes so will have to wait
+
+ var lw = axis.labelWidth,
+ lh = axis.labelHeight,
+ pos = axis.options.position,
+ isXAxis = axis.direction === "x",
+ tickLength = axis.options.tickLength,
+ axisMargin = options.grid.axisMargin,
+ padding = options.grid.labelMargin,
+ innermost = true,
+ outermost = true,
+ first = true,
+ found = false;
+
+ // Determine the axis's position in its direction and on its side
+
+ $.each(isXAxis ? xaxes : yaxes, function(i, a) {
+ if (a && (a.show || a.reserveSpace)) {
+ if (a === axis) {
+ found = true;
+ } else if (a.options.position === pos) {
+ if (found) {
+ outermost = false;
+ } else {
+ innermost = false;
+ }
+ }
+ if (!found) {
+ first = false;
+ }
+ }
+ });
+
+ // The outermost axis on each side has no margin
+
+ if (outermost) {
+ axisMargin = 0;
+ }
+
+ // The ticks for the first axis in each direction stretch across
+
+ if (tickLength == null) {
+ tickLength = first ? "full" : 5;
+ }
+
+ if (!isNaN(+tickLength))
+ padding += +tickLength;
+
+ if (isXAxis) {
+ lh += padding;
+
+ if (pos == "bottom") {
+ plotOffset.bottom += lh + axisMargin;
+ axis.box = { top: surface.height - plotOffset.bottom, height: lh };
+ }
+ else {
+ axis.box = { top: plotOffset.top + axisMargin, height: lh };
+ plotOffset.top += lh + axisMargin;
+ }
+ }
+ else {
+ lw += padding;
+
+ if (pos == "left") {
+ axis.box = { left: plotOffset.left + axisMargin, width: lw };
+ plotOffset.left += lw + axisMargin;
+ }
+ else {
+ plotOffset.right += lw + axisMargin;
+ axis.box = { left: surface.width - plotOffset.right, width: lw };
+ }
+ }
+
+ // save for future reference
+ axis.position = pos;
+ axis.tickLength = tickLength;
+ axis.box.padding = padding;
+ axis.innermost = innermost;
+ }
+
+ function allocateAxisBoxSecondPhase(axis) {
+ // now that all axis boxes have been placed in one
+ // dimension, we can set the remaining dimension coordinates
+ if (axis.direction == "x") {
+ axis.box.left = plotOffset.left - axis.labelWidth / 2;
+ axis.box.width = surface.width - plotOffset.left - plotOffset.right + axis.labelWidth;
+ }
+ else {
+ axis.box.top = plotOffset.top - axis.labelHeight / 2;
+ axis.box.height = surface.height - plotOffset.bottom - plotOffset.top + axis.labelHeight;
+ }
+ }
+
+ function adjustLayoutForThingsStickingOut() {
+ // possibly adjust plot offset to ensure everything stays
+ // inside the canvas and isn't clipped off
+
+ var minMargin = options.grid.minBorderMargin,
+ axis, i;
+
+ // check stuff from the plot (FIXME: this should just read
+ // a value from the series, otherwise it's impossible to
+ // customize)
+ if (minMargin == null) {
+ minMargin = 0;
+ for (i = 0; i < series.length; ++i)
+ minMargin = Math.max(minMargin, 2 * (series[i].points.radius + series[i].points.lineWidth/2));
+ }
+
+ var margins = {
+ left: minMargin,
+ right: minMargin,
+ top: minMargin,
+ bottom: minMargin
+ };
+
+ // check axis labels, note we don't check the actual
+ // labels but instead use the overall width/height to not
+ // jump as much around with replots
+ $.each(allAxes(), function (_, axis) {
+ if (axis.reserveSpace && axis.ticks && axis.ticks.length) {
+ if (axis.direction === "x") {
+ margins.left = Math.max(margins.left, axis.labelWidth / 2);
+ margins.right = Math.max(margins.right, axis.labelWidth / 2);
+ } else {
+ margins.bottom = Math.max(margins.bottom, axis.labelHeight / 2);
+ margins.top = Math.max(margins.top, axis.labelHeight / 2);
+ }
+ }
+ });
+
+ plotOffset.left = Math.ceil(Math.max(margins.left, plotOffset.left));
+ plotOffset.right = Math.ceil(Math.max(margins.right, plotOffset.right));
+ plotOffset.top = Math.ceil(Math.max(margins.top, plotOffset.top));
+ plotOffset.bottom = Math.ceil(Math.max(margins.bottom, plotOffset.bottom));
+ }
+
+ function setupGrid() {
+ var i, axes = allAxes(), showGrid = options.grid.show;
+
+ // Initialize the plot's offset from the edge of the canvas
+
+ for (var a in plotOffset) {
+ var margin = options.grid.margin || 0;
+ plotOffset[a] = typeof margin == "number" ? margin : margin[a] || 0;
+ }
+
+ executeHooks(hooks.processOffset, [plotOffset]);
+
+ // If the grid is visible, add its border width to the offset
+
+ for (var a in plotOffset) {
+ if(typeof(options.grid.borderWidth) == "object") {
+ plotOffset[a] += showGrid ? options.grid.borderWidth[a] : 0;
+ }
+ else {
+ plotOffset[a] += showGrid ? options.grid.borderWidth : 0;
+ }
+ }
+
+ $.each(axes, function (_, axis) {
+ var axisOpts = axis.options;
+ axis.show = axisOpts.show == null ? axis.used : axisOpts.show;
+ axis.reserveSpace = axisOpts.reserveSpace == null ? axis.show : axisOpts.reserveSpace;
+ setRange(axis);
+ });
+
+ if (showGrid) {
+
+ var allocatedAxes = $.grep(axes, function (axis) {
+ return axis.show || axis.reserveSpace;
+ });
+
+ $.each(allocatedAxes, function (_, axis) {
+ // make the ticks
+ setupTickGeneration(axis);
+ setTicks(axis);
+ snapRangeToTicks(axis, axis.ticks);
+ // find labelWidth/Height for axis
+ measureTickLabels(axis);
+ });
+
+ // with all dimensions calculated, we can compute the
+ // axis bounding boxes, start from the outside
+ // (reverse order)
+ for (i = allocatedAxes.length - 1; i >= 0; --i)
+ allocateAxisBoxFirstPhase(allocatedAxes[i]);
+
+ // make sure we've got enough space for things that
+ // might stick out
+ adjustLayoutForThingsStickingOut();
+
+ $.each(allocatedAxes, function (_, axis) {
+ allocateAxisBoxSecondPhase(axis);
+ });
+ }
+
+ plotWidth = surface.width - plotOffset.left - plotOffset.right;
+ plotHeight = surface.height - plotOffset.bottom - plotOffset.top;
+
+ // now we got the proper plot dimensions, we can compute the scaling
+ $.each(axes, function (_, axis) {
+ setTransformationHelpers(axis);
+ });
+
+ if (showGrid) {
+ drawAxisLabels();
+ }
+
+ insertLegend();
+ }
+
+ function setRange(axis) {
+ var opts = axis.options,
+ min = +(opts.min != null ? opts.min : axis.datamin),
+ max = +(opts.max != null ? opts.max : axis.datamax),
+ delta = max - min;
+
+ if (delta == 0.0) {
+ // degenerate case
+ var widen = max == 0 ? 1 : 0.01;
+
+ if (opts.min == null)
+ min -= widen;
+ // always widen max if we couldn't widen min to ensure we
+ // don't fall into min == max which doesn't work
+ if (opts.max == null || opts.min != null)
+ max += widen;
+ }
+ else {
+ // consider autoscaling
+ var margin = opts.autoscaleMargin;
+ if (margin != null) {
+ if (opts.min == null) {
+ min -= delta * margin;
+ // make sure we don't go below zero if all values
+ // are positive
+ if (min < 0 && axis.datamin != null && axis.datamin >= 0)
+ min = 0;
+ }
+ if (opts.max == null) {
+ max += delta * margin;
+ if (max > 0 && axis.datamax != null && axis.datamax <= 0)
+ max = 0;
+ }
+ }
+ }
+ axis.min = min;
+ axis.max = max;
+ }
+
+ function setupTickGeneration(axis) {
+ var opts = axis.options;
+
+ // estimate number of ticks
+ var noTicks;
+ if (typeof opts.ticks == "number" && opts.ticks > 0)
+ noTicks = opts.ticks;
+ else
+ // heuristic based on the model a*sqrt(x) fitted to
+ // some data points that seemed reasonable
+ noTicks = 0.3 * Math.sqrt(axis.direction == "x" ? surface.width : surface.height);
+
+ var delta = (axis.max - axis.min) / noTicks,
+ dec = -Math.floor(Math.log(delta) / Math.LN10),
+ maxDec = opts.tickDecimals;
+
+ if (maxDec != null && dec > maxDec) {
+ dec = maxDec;
+ }
+
+ var magn = Math.pow(10, -dec),
+ norm = delta / magn, // norm is between 1.0 and 10.0
+ size;
+
+ if (norm < 1.5) {
+ size = 1;
+ } else if (norm < 3) {
+ size = 2;
+ // special case for 2.5, requires an extra decimal
+ if (norm > 2.25 && (maxDec == null || dec + 1 <= maxDec)) {
+ size = 2.5;
+ ++dec;
+ }
+ } else if (norm < 7.5) {
+ size = 5;
+ } else {
+ size = 10;
+ }
+
+ size *= magn;
+
+ if (opts.minTickSize != null && size < opts.minTickSize) {
+ size = opts.minTickSize;
+ }
+
+ axis.delta = delta;
+ axis.tickDecimals = Math.max(0, maxDec != null ? maxDec : dec);
+ axis.tickSize = opts.tickSize || size;
+
+ // Time mode was moved to a plug-in in 0.8, and since so many people use it
+ // we'll add an especially friendly reminder to make sure they included it.
+
+ if (opts.mode == "time" && !axis.tickGenerator) {
+ throw new Error("Time mode requires the flot.time plugin.");
+ }
+
+ // Flot supports base-10 axes; any other mode else is handled by a plug-in,
+ // like flot.time.js.
+
+ if (!axis.tickGenerator) {
+
+ axis.tickGenerator = function (axis) {
+
+ var ticks = [],
+ start = floorInBase(axis.min, axis.tickSize),
+ i = 0,
+ v = Number.NaN,
+ prev;
+
+ do {
+ prev = v;
+ v = start + i * axis.tickSize;
+ ticks.push(v);
+ ++i;
+ } while (v < axis.max && v != prev);
+ return ticks;
+ };
+
+ axis.tickFormatter = function (value, axis) {
+
+ var factor = axis.tickDecimals ? Math.pow(10, axis.tickDecimals) : 1;
+ var formatted = "" + Math.round(value * factor) / factor;
+
+ // If tickDecimals was specified, ensure that we have exactly that
+ // much precision; otherwise default to the value's own precision.
+
+ if (axis.tickDecimals != null) {
+ var decimal = formatted.indexOf(".");
+ var precision = decimal == -1 ? 0 : formatted.length - decimal - 1;
+ if (precision < axis.tickDecimals) {
+ return (precision ? formatted : formatted + ".") + ("" + factor).substr(1, axis.tickDecimals - precision);
+ }
+ }
+
+ return formatted;
+ };
+ }
+
+ if ($.isFunction(opts.tickFormatter))
+ axis.tickFormatter = function (v, axis) { return "" + opts.tickFormatter(v, axis); };
+
+ if (opts.alignTicksWithAxis != null) {
+ var otherAxis = (axis.direction == "x" ? xaxes : yaxes)[opts.alignTicksWithAxis - 1];
+ if (otherAxis && otherAxis.used && otherAxis != axis) {
+ // consider snapping min/max to outermost nice ticks
+ var niceTicks = axis.tickGenerator(axis);
+ if (niceTicks.length > 0) {
+ if (opts.min == null)
+ axis.min = Math.min(axis.min, niceTicks[0]);
+ if (opts.max == null && niceTicks.length > 1)
+ axis.max = Math.max(axis.max, niceTicks[niceTicks.length - 1]);
+ }
+
+ axis.tickGenerator = function (axis) {
+ // copy ticks, scaled to this axis
+ var ticks = [], v, i;
+ for (i = 0; i < otherAxis.ticks.length; ++i) {
+ v = (otherAxis.ticks[i].v - otherAxis.min) / (otherAxis.max - otherAxis.min);
+ v = axis.min + v * (axis.max - axis.min);
+ ticks.push(v);
+ }
+ return ticks;
+ };
+
+ // we might need an extra decimal since forced
+ // ticks don't necessarily fit naturally
+ if (!axis.mode && opts.tickDecimals == null) {
+ var extraDec = Math.max(0, -Math.floor(Math.log(axis.delta) / Math.LN10) + 1),
+ ts = axis.tickGenerator(axis);
+
+ // only proceed if the tick interval rounded
+ // with an extra decimal doesn't give us a
+ // zero at end
+ if (!(ts.length > 1 && /\..*0$/.test((ts[1] - ts[0]).toFixed(extraDec))))
+ axis.tickDecimals = extraDec;
+ }
+ }
+ }
+ }
+
+ function setTicks(axis) {
+ var oticks = axis.options.ticks, ticks = [];
+ if (oticks == null || (typeof oticks == "number" && oticks > 0))
+ ticks = axis.tickGenerator(axis);
+ else if (oticks) {
+ if ($.isFunction(oticks))
+ // generate the ticks
+ ticks = oticks(axis);
+ else
+ ticks = oticks;
+ }
+
+ // clean up/labelify the supplied ticks, copy them over
+ var i, v;
+ axis.ticks = [];
+ for (i = 0; i < ticks.length; ++i) {
+ var label = null;
+ var t = ticks[i];
+ if (typeof t == "object") {
+ v = +t[0];
+ if (t.length > 1)
+ label = t[1];
+ }
+ else
+ v = +t;
+ if (label == null)
+ label = axis.tickFormatter(v, axis);
+ if (!isNaN(v))
+ axis.ticks.push({ v: v, label: label });
+ }
+ }
+
+ function snapRangeToTicks(axis, ticks) {
+ if (axis.options.autoscaleMargin && ticks.length > 0) {
+ // snap to ticks
+ if (axis.options.min == null)
+ axis.min = Math.min(axis.min, ticks[0].v);
+ if (axis.options.max == null && ticks.length > 1)
+ axis.max = Math.max(axis.max, ticks[ticks.length - 1].v);
+ }
+ }
+
+ function draw() {
+
+ surface.clear();
+
+ executeHooks(hooks.drawBackground, [ctx]);
+
+ var grid = options.grid;
+
+ // draw background, if any
+ if (grid.show && grid.backgroundColor)
+ drawBackground();
+
+ if (grid.show && !grid.aboveData) {
+ drawGrid();
+ }
+
+ for (var i = 0; i < series.length; ++i) {
+ executeHooks(hooks.drawSeries, [ctx, series[i]]);
+ drawSeries(series[i]);
+ }
+
+ executeHooks(hooks.draw, [ctx]);
+
+ if (grid.show && grid.aboveData) {
+ drawGrid();
+ }
+
+ surface.render();
+
+ // A draw implies that either the axes or data have changed, so we
+ // should probably update the overlay highlights as well.
+
+ triggerRedrawOverlay();
+ }
+
+ function extractRange(ranges, coord) {
+ var axis, from, to, key, axes = allAxes();
+
+ for (var i = 0; i < axes.length; ++i) {
+ axis = axes[i];
+ if (axis.direction == coord) {
+ key = coord + axis.n + "axis";
+ if (!ranges[key] && axis.n == 1)
+ key = coord + "axis"; // support x1axis as xaxis
+ if (ranges[key]) {
+ from = ranges[key].from;
+ to = ranges[key].to;
+ break;
+ }
+ }
+ }
+
+ // backwards-compat stuff - to be removed in future
+ if (!ranges[key]) {
+ axis = coord == "x" ? xaxes[0] : yaxes[0];
+ from = ranges[coord + "1"];
+ to = ranges[coord + "2"];
+ }
+
+ // auto-reverse as an added bonus
+ if (from != null && to != null && from > to) {
+ var tmp = from;
+ from = to;
+ to = tmp;
+ }
+
+ return { from: from, to: to, axis: axis };
+ }
+
+ function drawBackground() {
+ ctx.save();
+ ctx.translate(plotOffset.left, plotOffset.top);
+
+ ctx.fillStyle = getColorOrGradient(options.grid.backgroundColor, plotHeight, 0, "rgba(255, 255, 255, 0)");
+ ctx.fillRect(0, 0, plotWidth, plotHeight);
+ ctx.restore();
+ }
+
+ function drawGrid() {
+ var i, axes, bw, bc;
+
+ ctx.save();
+ ctx.translate(plotOffset.left, plotOffset.top);
+
+ // draw markings
+ var markings = options.grid.markings;
+ if (markings) {
+ if ($.isFunction(markings)) {
+ axes = plot.getAxes();
+ // xmin etc. is backwards compatibility, to be
+ // removed in the future
+ axes.xmin = axes.xaxis.min;
+ axes.xmax = axes.xaxis.max;
+ axes.ymin = axes.yaxis.min;
+ axes.ymax = axes.yaxis.max;
+
+ markings = markings(axes);
+ }
+
+ for (i = 0; i < markings.length; ++i) {
+ var m = markings[i],
+ xrange = extractRange(m, "x"),
+ yrange = extractRange(m, "y");
+
+ // fill in missing
+ if (xrange.from == null)
+ xrange.from = xrange.axis.min;
+ if (xrange.to == null)
+ xrange.to = xrange.axis.max;
+ if (yrange.from == null)
+ yrange.from = yrange.axis.min;
+ if (yrange.to == null)
+ yrange.to = yrange.axis.max;
+
+ // clip
+ if (xrange.to < xrange.axis.min || xrange.from > xrange.axis.max ||
+ yrange.to < yrange.axis.min || yrange.from > yrange.axis.max)
+ continue;
+
+ xrange.from = Math.max(xrange.from, xrange.axis.min);
+ xrange.to = Math.min(xrange.to, xrange.axis.max);
+ yrange.from = Math.max(yrange.from, yrange.axis.min);
+ yrange.to = Math.min(yrange.to, yrange.axis.max);
+
+ var xequal = xrange.from === xrange.to,
+ yequal = yrange.from === yrange.to;
+
+ if (xequal && yequal) {
+ continue;
+ }
+
+ // then draw
+ xrange.from = Math.floor(xrange.axis.p2c(xrange.from));
+ xrange.to = Math.floor(xrange.axis.p2c(xrange.to));
+ yrange.from = Math.floor(yrange.axis.p2c(yrange.from));
+ yrange.to = Math.floor(yrange.axis.p2c(yrange.to));
+
+ if (xequal || yequal) {
+ var lineWidth = m.lineWidth || options.grid.markingsLineWidth,
+ subPixel = lineWidth % 2 ? 0.5 : 0;
+ ctx.beginPath();
+ ctx.strokeStyle = m.color || options.grid.markingsColor;
+ ctx.lineWidth = lineWidth;
+ if (xequal) {
+ ctx.moveTo(xrange.to + subPixel, yrange.from);
+ ctx.lineTo(xrange.to + subPixel, yrange.to);
+ } else {
+ ctx.moveTo(xrange.from, yrange.to + subPixel);
+ ctx.lineTo(xrange.to, yrange.to + subPixel);
+ }
+ ctx.stroke();
+ } else {
+ ctx.fillStyle = m.color || options.grid.markingsColor;
+ ctx.fillRect(xrange.from, yrange.to,
+ xrange.to - xrange.from,
+ yrange.from - yrange.to);
+ }
+ }
+ }
+
+ // draw the ticks
+ axes = allAxes();
+ bw = options.grid.borderWidth;
+
+ for (var j = 0; j < axes.length; ++j) {
+ var axis = axes[j], box = axis.box,
+ t = axis.tickLength, x, y, xoff, yoff;
+ if (!axis.show || axis.ticks.length == 0)
+ continue;
+
+ ctx.lineWidth = 1;
+
+ // find the edges
+ if (axis.direction == "x") {
+ x = 0;
+ if (t == "full")
+ y = (axis.position == "top" ? 0 : plotHeight);
+ else
+ y = box.top - plotOffset.top + (axis.position == "top" ? box.height : 0);
+ }
+ else {
+ y = 0;
+ if (t == "full")
+ x = (axis.position == "left" ? 0 : plotWidth);
+ else
+ x = box.left - plotOffset.left + (axis.position == "left" ? box.width : 0);
+ }
+
+ // draw tick bar
+ if (!axis.innermost) {
+ ctx.strokeStyle = axis.options.color;
+ ctx.beginPath();
+ xoff = yoff = 0;
+ if (axis.direction == "x")
+ xoff = plotWidth + 1;
+ else
+ yoff = plotHeight + 1;
+
+ if (ctx.lineWidth == 1) {
+ if (axis.direction == "x") {
+ y = Math.floor(y) + 0.5;
+ } else {
+ x = Math.floor(x) + 0.5;
+ }
+ }
+
+ ctx.moveTo(x, y);
+ ctx.lineTo(x + xoff, y + yoff);
+ ctx.stroke();
+ }
+
+ // draw ticks
+
+ ctx.strokeStyle = axis.options.tickColor;
+
+ ctx.beginPath();
+ for (i = 0; i < axis.ticks.length; ++i) {
+ var v = axis.ticks[i].v;
+
+ xoff = yoff = 0;
+
+ if (isNaN(v) || v < axis.min || v > axis.max
+ // skip those lying on the axes if we got a border
+ || (t == "full"
+ && ((typeof bw == "object" && bw[axis.position] > 0) || bw > 0)
+ && (v == axis.min || v == axis.max)))
+ continue;
+
+ if (axis.direction == "x") {
+ x = axis.p2c(v);
+ yoff = t == "full" ? -plotHeight : t;
+
+ if (axis.position == "top")
+ yoff = -yoff;
+ }
+ else {
+ y = axis.p2c(v);
+ xoff = t == "full" ? -plotWidth : t;
+
+ if (axis.position == "left")
+ xoff = -xoff;
+ }
+
+ if (ctx.lineWidth == 1) {
+ if (axis.direction == "x")
+ x = Math.floor(x) + 0.5;
+ else
+ y = Math.floor(y) + 0.5;
+ }
+
+
+ if( (options.grid.TickLineStyle == 'dashed') && (yoff < -5 ) )
+ { for (var yadd = y-2.5 ; yadd > y+yoff+5; yadd++ )
+ {ctx.moveTo(x, yadd);
+ ctx.lineTo(x + xoff, yadd - 5);
+ yadd = yadd-10} }
+ else
+ ctx.moveTo(x, y);
+ ctx.lineTo(x + xoff, y + yoff)
+ }
+ ctx.stroke();
+ }
+
+
+ // draw border
+ if (bw) {
+ // If either borderWidth or borderColor is an object, then draw the border
+ // line by line instead of as one rectangle
+ bc = options.grid.borderColor;
+ if(typeof bw == "object" || typeof bc == "object") {
+ if (typeof bw !== "object") {
+ bw = {top: bw, right: bw, bottom: bw, left: bw};
+ }
+ if (typeof bc !== "object") {
+ bc = {top: bc, right: bc, bottom: bc, left: bc};
+ }
+
+ if (bw.top > 0) {
+ ctx.strokeStyle = bc.top;
+ ctx.lineWidth = bw.top;
+ ctx.beginPath();
+ ctx.moveTo(0 - bw.left, 0 - bw.top/2);
+ ctx.lineTo(plotWidth, 0 - bw.top/2);
+ ctx.stroke();
+ }
+
+ if (bw.right > 0) {
+ ctx.strokeStyle = bc.right;
+ ctx.lineWidth = bw.right;
+ ctx.beginPath();
+ ctx.moveTo(plotWidth + bw.right / 2, 0 - bw.top);
+ ctx.lineTo(plotWidth + bw.right / 2, plotHeight);
+ ctx.stroke();
+ }
+
+ if (bw.bottom > 0) {
+ ctx.strokeStyle = bc.bottom;
+ ctx.lineWidth = bw.bottom;
+ ctx.beginPath();
+ ctx.moveTo(plotWidth + bw.right, plotHeight + bw.bottom / 2);
+ ctx.lineTo(0, plotHeight + bw.bottom / 2);
+ ctx.stroke();
+ }
+
+ if (bw.left > 0) {
+ ctx.strokeStyle = bc.left;
+ ctx.lineWidth = bw.left;
+ ctx.beginPath();
+ ctx.moveTo(0 - bw.left/2, plotHeight + bw.bottom);
+ ctx.lineTo(0- bw.left/2, 0);
+ ctx.stroke();
+ }
+ }
+ else {
+ ctx.lineWidth = bw;
+ ctx.strokeStyle = options.grid.borderColor;
+ ctx.strokeRect(-bw/2, -bw/2, plotWidth + bw, plotHeight + bw);
+ }
+ }
+
+ ctx.restore();
+ }
+
+ function drawAxisLabels() {
+
+ $.each(allAxes(), function (_, axis) {
+ var box = axis.box,
+ legacyStyles = axis.direction + "Axis " + axis.direction + axis.n + "Axis",
+ layer = "flot-" + axis.direction + "-axis flot-" + axis.direction + axis.n + "-axis " + legacyStyles,
+ font = axis.options.font || "flot-tick-label tickLabel",
+ tick, x, y, halign, valign;
+
+ // Remove text before checking for axis.show and ticks.length;
+ // otherwise plugins, like flot-tickrotor, that draw their own
+ // tick labels will end up with both theirs and the defaults.
+
+ surface.removeText(layer);
+
+ if (!axis.show || axis.ticks.length == 0)
+ return;
+
+ for (var i = 0; i < axis.ticks.length; ++i) {
+
+ tick = axis.ticks[i];
+ if (!tick.label || tick.v < axis.min || tick.v > axis.max)
+ continue;
+
+ if (axis.direction == "x") {
+ halign = "center";
+ x = plotOffset.left + axis.p2c(tick.v);
+ if (axis.position == "bottom") {
+ y = box.top + box.padding;
+ } else {
+ y = box.top + box.height - box.padding;
+ valign = "bottom";
+ }
+ } else {
+ valign = "middle";
+ y = plotOffset.top + axis.p2c(tick.v);
+ if (axis.position == "left") {
+ x = box.left + box.width - box.padding;
+ halign = "right";
+ } else {
+ x = box.left + box.padding;
+ }
+ }
+
+ surface.addText(layer, x, y, tick.label, font, null, null, halign, valign);
+ }
+ });
+ }
+
+ function drawSeries(series) {
+ if (series.lines.show)
+ drawSeriesLines(series);
+ if (series.bars.show)
+ drawSeriesBars(series);
+ if (series.points.show)
+ drawSeriesPoints(series);
+ }
+
+ function drawSeriesLines(series) {
+ function plotLine(datapoints, xoffset, yoffset, axisx, axisy) {
+ var points = datapoints.points,
+ ps = datapoints.pointsize,
+ prevx = null, prevy = null;
+
+ ctx.beginPath();
+ for (var i = ps; i < points.length; i += ps) {
+ var x1 = points[i - ps], y1 = points[i - ps + 1],
+ x2 = points[i], y2 = points[i + 1];
+
+ if (x1 == null || x2 == null)
+ continue;
+
+ // clip with ymin
+ if (y1 <= y2 && y1 < axisy.min) {
+ if (y2 < axisy.min)
+ continue; // line segment is outside
+ // compute new intersection point
+ x1 = (axisy.min - y1) / (y2 - y1) * (x2 - x1) + x1;
+ y1 = axisy.min;
+ }
+ else if (y2 <= y1 && y2 < axisy.min) {
+ if (y1 < axisy.min)
+ continue;
+ x2 = (axisy.min - y1) / (y2 - y1) * (x2 - x1) + x1;
+ y2 = axisy.min;
+ }
+
+ // clip with ymax
+ if (y1 >= y2 && y1 > axisy.max) {
+ if (y2 > axisy.max)
+ continue;
+ x1 = (axisy.max - y1) / (y2 - y1) * (x2 - x1) + x1;
+ y1 = axisy.max;
+ }
+ else if (y2 >= y1 && y2 > axisy.max) {
+ if (y1 > axisy.max)
+ continue;
+ x2 = (axisy.max - y1) / (y2 - y1) * (x2 - x1) + x1;
+ y2 = axisy.max;
+ }
+
+ // clip with xmin
+ if (x1 <= x2 && x1 < axisx.min) {
+ if (x2 < axisx.min)
+ continue;
+ y1 = (axisx.min - x1) / (x2 - x1) * (y2 - y1) + y1;
+ x1 = axisx.min;
+ }
+ else if (x2 <= x1 && x2 < axisx.min) {
+ if (x1 < axisx.min)
+ continue;
+ y2 = (axisx.min - x1) / (x2 - x1) * (y2 - y1) + y1;
+ x2 = axisx.min;
+ }
+
+ // clip with xmax
+ if (x1 >= x2 && x1 > axisx.max) {
+ if (x2 > axisx.max)
+ continue;
+ y1 = (axisx.max - x1) / (x2 - x1) * (y2 - y1) + y1;
+ x1 = axisx.max;
+ }
+ else if (x2 >= x1 && x2 > axisx.max) {
+ if (x1 > axisx.max)
+ continue;
+ y2 = (axisx.max - x1) / (x2 - x1) * (y2 - y1) + y1;
+ x2 = axisx.max;
+ }
+
+ if (x1 != prevx || y1 != prevy)
+ ctx.moveTo(axisx.p2c(x1) + xoffset, axisy.p2c(y1) + yoffset);
+
+ prevx = x2;
+ prevy = y2;
+ ctx.lineTo(axisx.p2c(x2) + xoffset, axisy.p2c(y2) + yoffset);
+ }
+ ctx.stroke();
+ }
+
+ function plotLineArea(datapoints, axisx, axisy) {
+ var points = datapoints.points,
+ ps = datapoints.pointsize,
+ bottom = Math.min(Math.max(0, axisy.min), axisy.max),
+ i = 0, top, areaOpen = false,
+ ypos = 1, segmentStart = 0, segmentEnd = 0;
+
+ // we process each segment in two turns, first forward
+ // direction to sketch out top, then once we hit the
+ // end we go backwards to sketch the bottom
+ while (true) {
+ if (ps > 0 && i > points.length + ps)
+ break;
+
+ i += ps; // ps is negative if going backwards
+
+ var x1 = points[i - ps],
+ y1 = points[i - ps + ypos],
+ x2 = points[i], y2 = points[i + ypos];
+
+ if (areaOpen) {
+ if (ps > 0 && x1 != null && x2 == null) {
+ // at turning point
+ segmentEnd = i;
+ ps = -ps;
+ ypos = 2;
+ continue;
+ }
+
+ if (ps < 0 && i == segmentStart + ps) {
+ // done with the reverse sweep
+ ctx.fill();
+ areaOpen = false;
+ ps = -ps;
+ ypos = 1;
+ i = segmentStart = segmentEnd + ps;
+ continue;
+ }
+ }
+
+ if (x1 == null || x2 == null)
+ continue;
+
+ // clip x values
+
+ // clip with xmin
+ if (x1 <= x2 && x1 < axisx.min) {
+ if (x2 < axisx.min)
+ continue;
+ y1 = (axisx.min - x1) / (x2 - x1) * (y2 - y1) + y1;
+ x1 = axisx.min;
+ }
+ else if (x2 <= x1 && x2 < axisx.min) {
+ if (x1 < axisx.min)
+ continue;
+ y2 = (axisx.min - x1) / (x2 - x1) * (y2 - y1) + y1;
+ x2 = axisx.min;
+ }
+
+ // clip with xmax
+ if (x1 >= x2 && x1 > axisx.max) {
+ if (x2 > axisx.max)
+ continue;
+ y1 = (axisx.max - x1) / (x2 - x1) * (y2 - y1) + y1;
+ x1 = axisx.max;
+ }
+ else if (x2 >= x1 && x2 > axisx.max) {
+ if (x1 > axisx.max)
+ continue;
+ y2 = (axisx.max - x1) / (x2 - x1) * (y2 - y1) + y1;
+ x2 = axisx.max;
+ }
+
+ if (!areaOpen) {
+ // open area
+ ctx.beginPath();
+ ctx.moveTo(axisx.p2c(x1), axisy.p2c(bottom));
+ areaOpen = true;
+ }
+
+ // now first check the case where both is outside
+ if (y1 >= axisy.max && y2 >= axisy.max) {
+ ctx.lineTo(axisx.p2c(x1), axisy.p2c(axisy.max));
+ ctx.lineTo(axisx.p2c(x2), axisy.p2c(axisy.max));
+ continue;
+ }
+ else if (y1 <= axisy.min && y2 <= axisy.min) {
+ ctx.lineTo(axisx.p2c(x1), axisy.p2c(axisy.min));
+ ctx.lineTo(axisx.p2c(x2), axisy.p2c(axisy.min));
+ continue;
+ }
+
+ // else it's a bit more complicated, there might
+ // be a flat maxed out rectangle first, then a
+ // triangular cutout or reverse; to find these
+ // keep track of the current x values
+ var x1old = x1, x2old = x2;
+
+ // clip the y values, without shortcutting, we
+ // go through all cases in turn
+
+ // clip with ymin
+ if (y1 <= y2 && y1 < axisy.min && y2 >= axisy.min) {
+ x1 = (axisy.min - y1) / (y2 - y1) * (x2 - x1) + x1;
+ y1 = axisy.min;
+ }
+ else if (y2 <= y1 && y2 < axisy.min && y1 >= axisy.min) {
+ x2 = (axisy.min - y1) / (y2 - y1) * (x2 - x1) + x1;
+ y2 = axisy.min;
+ }
+
+ // clip with ymax
+ if (y1 >= y2 && y1 > axisy.max && y2 <= axisy.max) {
+ x1 = (axisy.max - y1) / (y2 - y1) * (x2 - x1) + x1;
+ y1 = axisy.max;
+ }
+ else if (y2 >= y1 && y2 > axisy.max && y1 <= axisy.max) {
+ x2 = (axisy.max - y1) / (y2 - y1) * (x2 - x1) + x1;
+ y2 = axisy.max;
+ }
+
+ // if the x value was changed we got a rectangle
+ // to fill
+ if (x1 != x1old) {
+ ctx.lineTo(axisx.p2c(x1old), axisy.p2c(y1));
+ // it goes to (x1, y1), but we fill that below
+ }
+
+ // fill triangular section, this sometimes result
+ // in redundant points if (x1, y1) hasn't changed
+ // from previous line to, but we just ignore that
+ ctx.lineTo(axisx.p2c(x1), axisy.p2c(y1));
+ ctx.lineTo(axisx.p2c(x2), axisy.p2c(y2));
+
+ // fill the other rectangle if it's there
+ if (x2 != x2old) {
+ ctx.lineTo(axisx.p2c(x2), axisy.p2c(y2));
+ ctx.lineTo(axisx.p2c(x2old), axisy.p2c(y2));
+ }
+ }
+ }
+
+ ctx.save();
+ ctx.translate(plotOffset.left, plotOffset.top);
+ ctx.lineJoin = "round";
+
+ var lw = series.lines.lineWidth,
+ sw = series.shadowSize;
+ // FIXME: consider another form of shadow when filling is turned on
+ if (lw > 0 && sw > 0) {
+ // draw shadow as a thick and thin line with transparency
+ ctx.lineWidth = sw;
+ ctx.strokeStyle = "rgba(0,0,0,0.1)";
+ // position shadow at angle from the mid of line
+ var angle = Math.PI/18;
+ plotLine(series.datapoints, Math.sin(angle) * (lw/2 + sw/2), Math.cos(angle) * (lw/2 + sw/2), series.xaxis, series.yaxis);
+ ctx.lineWidth = sw/2;
+ plotLine(series.datapoints, Math.sin(angle) * (lw/2 + sw/4), Math.cos(angle) * (lw/2 + sw/4), series.xaxis, series.yaxis);
+ }
+
+ ctx.lineWidth = lw;
+ ctx.strokeStyle = series.color;
+ var fillStyle = getFillStyle(series.lines, series.color, 0, plotHeight);
+ if (fillStyle) {
+ ctx.fillStyle = fillStyle;
+ plotLineArea(series.datapoints, series.xaxis, series.yaxis);
+ }
+
+ if (lw > 0)
+ plotLine(series.datapoints, 0, 0, series.xaxis, series.yaxis);
+ ctx.restore();
+ }
+
+ function drawSeriesPoints(series) {
+ function plotPoints(datapoints, radius, fillStyle, offset, shadow, axisx, axisy, symbol) {
+ var points = datapoints.points, ps = datapoints.pointsize;
+
+ for (var i = 0; i < points.length; i += ps) {
+ var x = points[i], y = points[i + 1];
+ if (x == null || x < axisx.min || x > axisx.max || y < axisy.min || y > axisy.max)
+ continue;
+
+ ctx.beginPath();
+ x = axisx.p2c(x);
+ y = axisy.p2c(y) + offset;
+ if (symbol == "circle")
+ ctx.arc(x, y, radius, 0, shadow ? Math.PI : Math.PI * 2, false);
+ else
+ symbol(ctx, x, y, radius, shadow);
+ ctx.closePath();
+
+ if (fillStyle) {
+ ctx.fillStyle = fillStyle;
+ ctx.fill();
+ }
+ ctx.stroke();
+ }
+ }
+
+ ctx.save();
+ ctx.translate(plotOffset.left, plotOffset.top);
+
+ var lw = series.points.lineWidth,
+ sw = series.shadowSize,
+ radius = series.points.radius,
+ symbol = series.points.symbol;
+
+ // If the user sets the line width to 0, we change it to a very
+ // small value. A line width of 0 seems to force the default of 1.
+ // Doing the conditional here allows the shadow setting to still be
+ // optional even with a lineWidth of 0.
+
+ if( lw == 0 )
+ lw = 0.0001;
+
+ if (lw > 0 && sw > 0) {
+ // draw shadow in two steps
+ var w = sw / 2;
+ ctx.lineWidth = w;
+ ctx.strokeStyle = "rgba(0,0,0,0.1)";
+ plotPoints(series.datapoints, radius, null, w + w/2, true,
+ series.xaxis, series.yaxis, symbol);
+
+ ctx.strokeStyle = "rgba(0,0,0,0.2)";
+ plotPoints(series.datapoints, radius, null, w/2, true,
+ series.xaxis, series.yaxis, symbol);
+ }
+
+ ctx.lineWidth = lw;
+ ctx.strokeStyle = series.color;
+ plotPoints(series.datapoints, radius,
+ getFillStyle(series.points, series.color), 0, false,
+ series.xaxis, series.yaxis, symbol);
+ ctx.restore();
+ }
+
+ function drawBar(x, y, b, barLeft, barRight, fillStyleCallback, axisx, axisy, c, horizontal, lineWidth) {
+ var left, right, bottom, top,
+ drawLeft, drawRight, drawTop, drawBottom,
+ tmp;
+
+ // in horizontal mode, we start the bar from the left
+ // instead of from the bottom so it appears to be
+ // horizontal rather than vertical
+ if (horizontal) {
+ drawBottom = drawRight = drawTop = true;
+ drawLeft = false;
+ left = b;
+ right = x;
+ top = y + barLeft;
+ bottom = y + barRight;
+
+ // account for negative bars
+ if (right < left) {
+ tmp = right;
+ right = left;
+ left = tmp;
+ drawLeft = true;
+ drawRight = false;
+ }
+ }
+ else {
+ drawLeft = drawRight = drawTop = true;
+ drawBottom = false;
+ left = x + barLeft;
+ right = x + barRight;
+ bottom = b;
+ top = y;
+
+ // account for negative bars
+ if (top < bottom) {
+ tmp = top;
+ top = bottom;
+ bottom = tmp;
+ drawBottom = true;
+ drawTop = false;
+ }
+ }
+
+ // clip
+ if (right < axisx.min || left > axisx.max ||
+ top < axisy.min || bottom > axisy.max)
+ return;
+
+ if (left < axisx.min) {
+ left = axisx.min;
+ drawLeft = false;
+ }
+
+ if (right > axisx.max) {
+ right = axisx.max;
+ drawRight = false;
+ }
+
+ if (bottom < axisy.min) {
+ bottom = axisy.min;
+ drawBottom = false;
+ }
+
+ if (top > axisy.max) {
+ top = axisy.max;
+ drawTop = false;
+ }
+
+ left = axisx.p2c(left);
+ bottom = axisy.p2c(bottom);
+ right = axisx.p2c(right);
+ top = axisy.p2c(top);
+
+ // fill the bar
+ if (fillStyleCallback) {
+ c.fillStyle = fillStyleCallback(bottom, top);
+ c.fillRect(left, top, right - left, bottom - top)
+ }
+
+ // draw outline
+ if (lineWidth > 0 && (drawLeft || drawRight || drawTop || drawBottom)) {
+ c.beginPath();
+
+ // FIXME: inline moveTo is buggy with excanvas
+ c.moveTo(left, bottom);
+ if (drawLeft)
+ c.lineTo(left, top);
+ else
+ c.moveTo(left, top);
+ if (drawTop)
+ c.lineTo(right, top);
+ else
+ c.moveTo(right, top);
+ if (drawRight)
+ c.lineTo(right, bottom);
+ else
+ c.moveTo(right, bottom);
+ if (drawBottom)
+ c.lineTo(left, bottom);
+ else
+ c.moveTo(left, bottom);
+ c.stroke();
+ }
+ }
+
+ function drawSeriesBars(series) {
+ function plotBars(datapoints, barLeft, barRight, fillStyleCallback, axisx, axisy) {
+ var points = datapoints.points, ps = datapoints.pointsize;
+
+ for (var i = 0; i < points.length; i += ps) {
+ if (points[i] == null)
+ continue;
+ drawBar(points[i], points[i + 1], points[i + 2], barLeft, barRight, fillStyleCallback, axisx, axisy, ctx, series.bars.horizontal, series.bars.lineWidth);
+ }
+ }
+
+ ctx.save();
+ ctx.translate(plotOffset.left, plotOffset.top);
+
+ // FIXME: figure out a way to add shadows (for instance along the right edge)
+ ctx.lineWidth = series.bars.lineWidth;
+ ctx.strokeStyle = series.color;
+
+ var barLeft;
+
+ switch (series.bars.align) {
+ case "left":
+ barLeft = 0;
+ break;
+ case "right":
+ barLeft = -series.bars.barWidth;
+ break;
+ default:
+ barLeft = -series.bars.barWidth / 2;
+ }
+
+ var fillStyleCallback = series.bars.fill ? function (bottom, top) { return getFillStyle(series.bars, series.color, bottom, top); } : null;
+ plotBars(series.datapoints, barLeft, barLeft + series.bars.barWidth, fillStyleCallback, series.xaxis, series.yaxis);
+ ctx.restore();
+ }
+
+ function getFillStyle(filloptions, seriesColor, bottom, top) {
+ var fill = filloptions.fill;
+ if (!fill)
+ return null;
+
+ if (filloptions.fillColor)
+ return getColorOrGradient(filloptions.fillColor, bottom, top, seriesColor);
+
+ var c = $.color.parse(seriesColor);
+ c.a = typeof fill == "number" ? fill : 0.4;
+ c.normalize();
+ return c.toString();
+ }
+
+ function insertLegend() {
+
+ if (options.legend.container != null) {
+ $(options.legend.container).html("");
+ } else {
+ placeholder.find(".legend").remove();
+ }
+
+ if (!options.legend.show) {
+ return;
+ }
+
+ var fragments = [], entries = [], rowStarted = false,
+ lf = options.legend.labelFormatter, s, label;
+
+ // Build a list of legend entries, with each having a label and a color
+
+ for (var i = 0; i < series.length; ++i) {
+ s = series[i];
+ if (s.label) {
+ label = lf ? lf(s.label, s) : s.label;
+ if (label) {
+ entries.push({
+ label: label,
+ color: s.color
+ });
+ }
+ }
+ }
+
+ // Sort the legend using either the default or a custom comparator
+
+ if (options.legend.sorted) {
+ if ($.isFunction(options.legend.sorted)) {
+ entries.sort(options.legend.sorted);
+ } else if (options.legend.sorted == "reverse") {
+ entries.reverse();
+ } else {
+ var ascending = options.legend.sorted != "descending";
+ entries.sort(function(a, b) {
+ return a.label == b.label ? 0 : (
+ (a.label < b.label) != ascending ? 1 : -1 // Logical XOR
+ );
+ });
+ }
+ }
+
+ // Generate markup for the list of entries, in their final order
+
+ for (var i = 0; i < entries.length; ++i) {
+
+ var entry = entries[i];
+
+ if (i % options.legend.noColumns == 0) {
+ if (rowStarted)
+ fragments.push('</tr>');
+ fragments.push('<tr>');
+ rowStarted = true;
+ }
+
+ fragments.push(
+ '<td class="legendColorBox"><div style="border:1px solid ' + options.legend.labelBoxBorderColor + ';padding:1px"><div style="width:4px;height:0;border:5px solid ' + entry.color + ';overflow:hidden"></div></div></td>' +
+ '<td class="legendLabel">' + entry.label + '</td>'
+ );
+ }
+
+ if (rowStarted)
+ fragments.push('</tr>');
+
+ if (fragments.length == 0)
+ return;
+
+ var table = '<table style="font-size:smaller;color:' + options.grid.color + '">' + fragments.join("") + '</table>';
+ if (options.legend.container != null)
+ $(options.legend.container).html(table);
+ else {
+ var pos = "",
+ p = options.legend.position,
+ m = options.legend.margin;
+ if (m[0] == null)
+ m = [m, m];
+ if (p.charAt(0) == "n")
+ pos += 'top:' + (m[1] + plotOffset.top) + 'px;';
+ else if (p.charAt(0) == "s")
+ pos += 'bottom:' + (m[1] + plotOffset.bottom) + 'px;';
+ if (p.charAt(1) == "e")
+ pos += 'right:' + (m[0] + plotOffset.right) + 'px;';
+ else if (p.charAt(1) == "w")
+ pos += 'left:' + (m[0] + plotOffset.left) + 'px;';
+ var legend = $('<div class="legend">' + table.replace('style="', 'style="position:absolute;' + pos +';') + '</div>').appendTo(placeholder);
+ if (options.legend.backgroundOpacity != 0.0) {
+ // put in the transparent background
+ // separately to avoid blended labels and
+ // label boxes
+ var c = options.legend.backgroundColor;
+ if (c == null) {
+ c = options.grid.backgroundColor;
+ if (c && typeof c == "string")
+ c = $.color.parse(c);
+ else
+ c = $.color.extract(legend, 'background-color');
+ c.a = 1;
+ c = c.toString();
+ }
+ var div = legend.children();
+ $('<div style="position:absolute;width:' + div.width() + 'px;height:' + div.height() + 'px;' + pos +'background-color:' + c + ';"> </div>').prependTo(legend).css('opacity', options.legend.backgroundOpacity);
+ }
+ }
+ }
+
+
+ // interactive features
+
+ var highlights = [],
+ redrawTimeout = null;
+
+ // returns the data item the mouse is over, or null if none is found
+ function findNearbyItem(mouseX, mouseY, seriesFilter) {
+ var maxDistance = options.grid.mouseActiveRadius,
+ smallestDistance = maxDistance * maxDistance + 1,
+ item = null, foundPoint = false, i, j, ps;
+
+ for (i = series.length - 1; i >= 0; --i) {
+ if (!seriesFilter(series[i]))
+ continue;
+
+ var s = series[i],
+ axisx = s.xaxis,
+ axisy = s.yaxis,
+ points = s.datapoints.points,
+ mx = axisx.c2p(mouseX), // precompute some stuff to make the loop faster
+ my = axisy.c2p(mouseY),
+ maxx = maxDistance / axisx.scale,
+ maxy = maxDistance / axisy.scale;
+
+ ps = s.datapoints.pointsize;
+ // with inverse transforms, we can't use the maxx/maxy
+ // optimization, sadly
+ if (axisx.options.inverseTransform)
+ maxx = Number.MAX_VALUE;
+ if (axisy.options.inverseTransform)
+ maxy = Number.MAX_VALUE;
+
+ if (s.lines.show || s.points.show) {
+ for (j = 0; j < points.length; j += ps) {
+ var x = points[j], y = points[j + 1];
+ if (x == null)
+ continue;
+
+ // For points and lines, the cursor must be within a
+ // certain distance to the data point
+ if (x - mx > maxx || x - mx < -maxx ||
+ y - my > maxy || y - my < -maxy)
+ continue;
+
+ // We have to calculate distances in pixels, not in
+ // data units, because the scales of the axes may be different
+ var dx = Math.abs(axisx.p2c(x) - mouseX),
+ dy = Math.abs(axisy.p2c(y) - mouseY),
+ dist = dx * dx + dy * dy; // we save the sqrt
+
+ // use <= to ensure last point takes precedence
+ // (last generally means on top of)
+ if (dist < smallestDistance) {
+ smallestDistance = dist;
+ item = [i, j / ps];
+ }
+ }
+ }
+
+ if (s.bars.show && !item) { // no other point can be nearby
+
+ var barLeft, barRight;
+
+ switch (s.bars.align) {
+ case "left":
+ barLeft = 0;
+ break;
+ case "right":
+ barLeft = -s.bars.barWidth;
+ break;
+ default:
+ barLeft = -s.bars.barWidth / 2;
+ }
+
+ barRight = barLeft + s.bars.barWidth;
+
+ for (j = 0; j < points.length; j += ps) {
+ var x = points[j], y = points[j + 1], b = points[j + 2];
+ if (x == null)
+ continue;
+
+ // for a bar graph, the cursor must be inside the bar
+ if (series[i].bars.horizontal ?
+ (mx <= Math.max(b, x) && mx >= Math.min(b, x) &&
+ my >= y + barLeft && my <= y + barRight) :
+ (mx >= x + barLeft && mx <= x + barRight &&
+ my >= Math.min(b, y) && my <= Math.max(b, y)))
+ item = [i, j / ps];
+ }
+ }
+ }
+
+ if (item) {
+ i = item[0];
+ j = item[1];
+ ps = series[i].datapoints.pointsize;
+
+ return { datapoint: series[i].datapoints.points.slice(j * ps, (j + 1) * ps),
+ dataIndex: j,
+ series: series[i],
+ seriesIndex: i };
+ }
+
+ return null;
+ }
+
+ function onMouseMove(e) {
+ if (options.grid.hoverable)
+ triggerClickHoverEvent("plothover", e,
+ function (s) { return s["hoverable"] != false; });
+ }
+
+ function onMouseLeave(e) {
+ if (options.grid.hoverable)
+ triggerClickHoverEvent("plothover", e,
+ function (s) { return false; });
+ }
+
+ function onClick(e) {
+ triggerClickHoverEvent("plotclick", e,
+ function (s) { return s["clickable"] != false; });
+ }
+
+ // trigger click or hover event (they send the same parameters
+ // so we share their code)
+ function triggerClickHoverEvent(eventname, event, seriesFilter) {
+ var offset = eventHolder.offset(),
+ canvasX = event.pageX - offset.left - plotOffset.left,
+ canvasY = event.pageY - offset.top - plotOffset.top,
+ pos = canvasToAxisCoords({ left: canvasX, top: canvasY });
+
+ pos.pageX = event.pageX;
+ pos.pageY = event.pageY;
+
+ var item = findNearbyItem(canvasX, canvasY, seriesFilter);
+
+ if (item) {
+ // fill in mouse pos for any listeners out there
+ item.pageX = parseInt(item.series.xaxis.p2c(item.datapoint[0]) + offset.left + plotOffset.left, 10);
+ item.pageY = parseInt(item.series.yaxis.p2c(item.datapoint[1]) + offset.top + plotOffset.top, 10);
+ }
+
+ if (options.grid.autoHighlight) {
+ // clear auto-highlights
+ for (var i = 0; i < highlights.length; ++i) {
+ var h = highlights[i];
+ if (h.auto == eventname &&
+ !(item && h.series == item.series &&
+ h.point[0] == item.datapoint[0] &&
+ h.point[1] == item.datapoint[1]))
+ unhighlight(h.series, h.point);
+ }
+
+ if (item)
+ highlight(item.series, item.datapoint, eventname);
+ }
+
+ placeholder.trigger(eventname, [ pos, item ]);
+ }
+
+ function triggerRedrawOverlay() {
+ var t = options.interaction.redrawOverlayInterval;
+ if (t == -1) { // skip event queue
+ drawOverlay();
+ return;
+ }
+
+ if (!redrawTimeout)
+ redrawTimeout = setTimeout(drawOverlay, t);
+ }
+
+ function drawOverlay() {
+ redrawTimeout = null;
+
+ // draw highlights
+ octx.save();
+ overlay.clear();
+ octx.translate(plotOffset.left, plotOffset.top);
+
+ var i, hi;
+ for (i = 0; i < highlights.length; ++i) {
+ hi = highlights[i];
+
+ if (hi.series.bars.show)
+ drawBarHighlight(hi.series, hi.point);
+ else
+ drawPointHighlight(hi.series, hi.point);
+ }
+ octx.restore();
+
+ executeHooks(hooks.drawOverlay, [octx]);
+ }
+
+ function highlight(s, point, auto) {
+ if (typeof s == "number")
+ s = series[s];
+
+ if (typeof point == "number") {
+ var ps = s.datapoints.pointsize;
+ point = s.datapoints.points.slice(ps * point, ps * (point + 1));
+ }
+
+ var i = indexOfHighlight(s, point);
+ if (i == -1) {
+ highlights.push({ series: s, point: point, auto: auto });
+
+ triggerRedrawOverlay();
+ }
+ else if (!auto)
+ highlights[i].auto = false;
+ }
+
+ function unhighlight(s, point) {
+ if (s == null && point == null) {
+ highlights = [];
+ triggerRedrawOverlay();
+ return;
+ }
+
+ if (typeof s == "number")
+ s = series[s];
+
+ if (typeof point == "number") {
+ var ps = s.datapoints.pointsize;
+ point = s.datapoints.points.slice(ps * point, ps * (point + 1));
+ }
+
+ var i = indexOfHighlight(s, point);
+ if (i != -1) {
+ highlights.splice(i, 1);
+
+ triggerRedrawOverlay();
+ }
+ }
+
+ function indexOfHighlight(s, p) {
+ for (var i = 0; i < highlights.length; ++i) {
+ var h = highlights[i];
+ if (h.series == s && h.point[0] == p[0]
+ && h.point[1] == p[1])
+ return i;
+ }
+ return -1;
+ }
+
+ function drawPointHighlight(series, point) {
+ var x = point[0], y = point[1],
+ axisx = series.xaxis, axisy = series.yaxis,
+ highlightColor = (typeof series.highlightColor === "string") ? series.highlightColor : $.color.parse(series.color).scale('a', 0.5).toString();
+
+ if (x < axisx.min || x > axisx.max || y < axisy.min || y > axisy.max)
+ return;
+
+ var pointRadius = series.points.radius + series.points.lineWidth / 2;
+ octx.lineWidth = pointRadius;
+ octx.strokeStyle = highlightColor;
+ var radius = 1.5 * pointRadius;
+ x = axisx.p2c(x);
+ y = axisy.p2c(y);
+
+ octx.beginPath();
+ if (series.points.symbol == "circle")
+ octx.arc(x, y, radius, 0, 2 * Math.PI, false);
+ else
+ series.points.symbol(octx, x, y, radius, false);
+ octx.closePath();
+ octx.stroke();
+ }
+
+ function drawBarHighlight(series, point) {
+ var highlightColor = (typeof series.highlightColor === "string") ? series.highlightColor : $.color.parse(series.color).scale('a', 0.5).toString(),
+ fillStyle = highlightColor,
+ barLeft;
+
+ switch (series.bars.align) {
+ case "left":
+ barLeft = 0;
+ break;
+ case "right":
+ barLeft = -series.bars.barWidth;
+ break;
+ default:
+ barLeft = -series.bars.barWidth / 2;
+ }
+
+ octx.lineWidth = series.bars.lineWidth;
+ octx.strokeStyle = highlightColor;
+
+ drawBar(point[0], point[1], point[2] || 0, barLeft, barLeft + series.bars.barWidth,
+ function () { return fillStyle; }, series.xaxis, series.yaxis, octx, series.bars.horizontal, series.bars.lineWidth);
+ }
+
+ function getColorOrGradient(spec, bottom, top, defaultColor) {
+ if (typeof spec == "string")
+ return spec;
+ else {
+ // assume this is a gradient spec; IE currently only
+ // supports a simple vertical gradient properly, so that's
+ // what we support too
+ var gradient = ctx.createLinearGradient(0, top, 0, bottom);
+
+ for (var i = 0, l = spec.colors.length; i < l; ++i) {
+ var c = spec.colors[i];
+ if (typeof c != "string") {
+ var co = $.color.parse(defaultColor);
+ if (c.brightness != null)
+ co = co.scale('rgb', c.brightness);
+ if (c.opacity != null)
+ co.a *= c.opacity;
+ c = co.toString();
+ }
+ gradient.addColorStop(i / (l - 1), c);
+ }
+
+ return gradient;
+ }
+ }
+ }
+
+ // Add the plot function to the top level of the jQuery object
+
+ $.plot = function(placeholder, data, options) {
+ //var t0 = new Date();
+ var plot = new Plot($(placeholder), data, options, $.plot.plugins);
+ //(window.console ? console.log : alert)("time used (msecs): " + ((new Date()).getTime() - t0.getTime()));
+ return plot;
+ };
+
+ $.plot.version = "0.8.3";
+
+ $.plot.plugins = [];
+
+ // Also add the plot function as a chainable property
+
+ $.fn.plot = function(data, options) {
+ return this.each(function() {
+ $.plot(this, data, options);
+ });
+ };
+
+ // round to nearby lower multiple of base
+ function floorInBase(n, base) {
+ return base * Math.floor(n / base);
+ }
+
+})(jQuery);
diff --git a/js/jquery.flot.navigate.js b/js/jquery.flot.navigate.js
new file mode 100644
index 0000000000000000000000000000000000000000..f2b97603c321bcb9dc1ebee45e61a7c19cdd46f3
--- /dev/null
+++ b/js/jquery.flot.navigate.js
@@ -0,0 +1,336 @@
+/*
+Flot plugin for adding panning and zooming capabilities to a plot.
+
+The default behaviour is double click and scrollwheel up/down to zoom
+in, drag to pan. The plugin defines plot.zoom({ center }),
+plot.zoomOut() and plot.pan(offset) so you easily can add custom
+controls. It also fires a "plotpan" and "plotzoom" event when
+something happens, useful for synchronizing plots.
+
+Options:
+
+ zoom: {
+ interactive: false
+ trigger: "dblclick" // or "click" for single click
+ amount: 1.5 // 2 = 200% (zoom in), 0.5 = 50% (zoom out)
+ }
+
+ pan: {
+ interactive: false
+ cursor: "move" // CSS mouse cursor value used when dragging, e.g. "pointer"
+ frameRate: 20
+ }
+
+ xaxis, yaxis, x2axis, y2axis: {
+ zoomRange: null // or [number, number] (min range, max range) or false
+ panRange: null // or [number, number] (min, max) or false
+ }
+
+"interactive" enables the built-in drag/click behaviour. If you enable
+interactive for pan, then you'll have a basic plot that supports
+moving around; the same for zoom.
+
+"amount" specifies the default amount to zoom in (so 1.5 = 150%)
+relative to the current viewport.
+
+"cursor" is a standard CSS mouse cursor string used for visual
+feedback to the user when dragging.
+
+"frameRate" specifies the maximum number of times per second the plot
+will update itself while the user is panning around on it (set to null
+to disable intermediate pans, the plot will then not update until the
+mouse button is released).
+
+"zoomRange" is the interval in which zooming can happen, e.g. with
+zoomRange: [1, 100] the zoom will never scale the axis so that the
+difference between min and max is smaller than 1 or larger than 100.
+You can set either end to null to ignore, e.g. [1, null]. If you set
+zoomRange to false, zooming on that axis will be disabled.
+
+"panRange" confines the panning to stay within a range, e.g. with
+panRange: [-10, 20] panning stops at -10 in one end and at 20 in the
+other. Either can be null, e.g. [-10, null]. If you set
+panRange to false, panning on that axis will be disabled.
+
+Example API usage:
+
+ plot = $.plot(...);
+
+ // zoom default amount in on the pixel (10, 20)
+ plot.zoom({ center: { left: 10, top: 20 } });
+
+ // zoom out again
+ plot.zoomOut({ center: { left: 10, top: 20 } });
+
+ // zoom 200% in on the pixel (10, 20)
+ plot.zoom({ amount: 2, center: { left: 10, top: 20 } });
+
+ // pan 100 pixels to the left and 20 down
+ plot.pan({ left: -100, top: 20 })
+
+Here, "center" specifies where the center of the zooming should
+happen. Note that this is defined in pixel space, not the space of the
+data points (you can use the p2c helpers on the axes in Flot to help
+you convert between these).
+
+"amount" is the amount to zoom the viewport relative to the current
+range, so 1 is 100% (i.e. no change), 1.5 is 150% (zoom in), 0.7 is
+70% (zoom out). You can set the default in the options.
+
+*/
+
+
+// First two dependencies, jquery.event.drag.js and
+// jquery.mousewheel.js, we put them inline here to save people the
+// effort of downloading them.
+
+/*
+jquery.event.drag.js ~ v1.5 ~ Copyright (c) 2008, Three Dub Media (http://threedubmedia.com)
+Licensed under the MIT License ~ http://threedubmedia.googlecode.com/files/MIT-LICENSE.txt
+*/
+(function(E){E.fn.drag=function(L,K,J){if(K){this.bind("dragstart",L)}if(J){this.bind("dragend",J)}return !L?this.trigger("drag"):this.bind("drag",K?K:L)};var A=E.event,B=A.special,F=B.drag={not:":input",distance:0,which:1,dragging:false,setup:function(J){J=E.extend({distance:F.distance,which:F.which,not:F.not},J||{});J.distance=I(J.distance);A.add(this,"mousedown",H,J);if(this.attachEvent){this.attachEvent("ondragstart",D)}},teardown:function(){A.remove(this,"mousedown",H);if(this===F.dragging){F.dragging=F.proxy=false}G(this,true);if(this.detachEvent){this.detachEvent("ondragstart",D)}}};B.dragstart=B.dragend={setup:function(){},teardown:function(){}};function H(L){var K=this,J,M=L.data||{};if(M.elem){K=L.dragTarget=M.elem;L.dragProxy=F.proxy||K;L.cursorOffsetX=M.pageX-M.left;L.cursorOffsetY=M.pageY-M.top;L.offsetX=L.pageX-L.cursorOffsetX;L.offsetY=L.pageY-L.cursorOffsetY}else{if(F.dragging||(M.which>0&&L.which!=M.which)||E(L.target).is(M.not)){return }}switch(L.type){case"mousedown":E.extend(M,E(K).offset(),{elem:K,target:L.target,pageX:L.pageX,pageY:L.pageY});A.add(document,"mousemove mouseup",H,M);G(K,false);F.dragging=null;return false;case !F.dragging&&"mousemove":if(I(L.pageX-M.pageX)+I(L.pageY-M.pageY)<M.distance){break}L.target=M.target;J=C(L,"dragstart",K);if(J!==false){F.dragging=K;F.proxy=L.dragProxy=E(J||K)[0]}case"mousemove":if(F.dragging){J=C(L,"drag",K);if(B.drop){B.drop.allowed=(J!==false);B.drop.handler(L)}if(J!==false){break}L.type="mouseup"}case"mouseup":A.remove(document,"mousemove mouseup",H);if(F.dragging){if(B.drop){B.drop.handler(L)}C(L,"dragend",K)}G(K,true);F.dragging=F.proxy=M.elem=false;break}return true}function C(M,K,L){M.type=K;var J=E.event.handle.call(L,M);return J===false?false:J||M.result}function I(J){return Math.pow(J,2)}function D(){return(F.dragging===false)}function G(K,J){if(!K){return }K.unselectable=J?"off":"on";K.onselectstart=function(){return J};if(K.style){K.style.MozUserSelect=J?"":"none"}}})(jQuery);
+
+
+/* jquery.mousewheel.min.js
+ * Copyright (c) 2009 Brandon Aaron (http://brandonaaron.net)
+ * Dual licensed under the MIT (http://www.opensource.org/licenses/mit-license.php)
+ * and GPL (http://www.opensource.org/licenses/gpl-license.php) licenses.
+ * Thanks to: http://adomas.org/javascript-mouse-wheel/ for some pointers.
+ * Thanks to: Mathias Bank(http://www.mathias-bank.de) for a scope bug fix.
+ *
+ * Version: 3.0.2
+ *
+ * Requires: 1.2.2+
+ */
+(function(c){var a=["DOMMouseScroll","mousewheel"];c.event.special.mousewheel={setup:function(){if(this.addEventListener){for(var d=a.length;d;){this.addEventListener(a[--d],b,false)}}else{this.onmousewheel=b}},teardown:function(){if(this.removeEventListener){for(var d=a.length;d;){this.removeEventListener(a[--d],b,false)}}else{this.onmousewheel=null}}};c.fn.extend({mousewheel:function(d){return d?this.bind("mousewheel",d):this.trigger("mousewheel")},unmousewheel:function(d){return this.unbind("mousewheel",d)}});function b(f){var d=[].slice.call(arguments,1),g=0,e=true;f=c.event.fix(f||window.event);f.type="mousewheel";if(f.wheelDelta){g=f.wheelDelta/120}if(f.detail){g=-f.detail/3}d.unshift(f,g);return c.event.handle.apply(this,d)}})(jQuery);
+
+
+
+
+(function ($) {
+ var options = {
+ xaxis: {
+ zoomRange: null, // or [number, number] (min range, max range)
+ panRange: null // or [number, number] (min, max)
+ },
+ zoom: {
+ interactive: false,
+ trigger: "dblclick", // or "click" for single click
+ amount: 1.5 // how much to zoom relative to current position, 2 = 200% (zoom in), 0.5 = 50% (zoom out)
+ },
+ pan: {
+ interactive: false,
+ cursor: "move",
+ frameRate: 20
+ }
+ };
+
+ function init(plot) {
+ function onZoomClick(e, zoomOut) {
+ var c = plot.offset();
+ c.left = e.pageX - c.left;
+ c.top = e.pageY - c.top;
+ if (zoomOut)
+ plot.zoomOut({ center: c });
+ else
+ plot.zoom({ center: c });
+ }
+
+ function onMouseWheel(e, delta) {
+ onZoomClick(e, delta < 0);
+ return false;
+ }
+
+ var prevCursor = 'default', prevPageX = 0, prevPageY = 0,
+ panTimeout = null;
+
+ function onDragStart(e) {
+ if (e.which != 1) // only accept left-click
+ return false;
+ var c = plot.getPlaceholder().css('cursor');
+ if (c)
+ prevCursor = c;
+ plot.getPlaceholder().css('cursor', plot.getOptions().pan.cursor);
+ prevPageX = e.pageX;
+ prevPageY = e.pageY;
+ }
+
+ function onDrag(e) {
+ var frameRate = plot.getOptions().pan.frameRate;
+ if (panTimeout || !frameRate)
+ return;
+
+ panTimeout = setTimeout(function () {
+ plot.pan({ left: prevPageX - e.pageX,
+ top: prevPageY - e.pageY });
+ prevPageX = e.pageX;
+ prevPageY = e.pageY;
+
+ panTimeout = null;
+ }, 1 / frameRate * 1000);
+ }
+
+ function onDragEnd(e) {
+ if (panTimeout) {
+ clearTimeout(panTimeout);
+ panTimeout = null;
+ }
+
+ plot.getPlaceholder().css('cursor', prevCursor);
+ plot.pan({ left: prevPageX - e.pageX,
+ top: prevPageY - e.pageY });
+ }
+
+ function bindEvents(plot, eventHolder) {
+ var o = plot.getOptions();
+ if (o.zoom.interactive) {
+ eventHolder[o.zoom.trigger](onZoomClick);
+ eventHolder.mousewheel(onMouseWheel);
+ }
+
+ if (o.pan.interactive) {
+ eventHolder.bind("dragstart", { distance: 10 }, onDragStart);
+ eventHolder.bind("drag", onDrag);
+ eventHolder.bind("dragend", onDragEnd);
+ }
+ }
+
+ plot.zoomOut = function (args) {
+ if (!args)
+ args = {};
+
+ if (!args.amount)
+ args.amount = plot.getOptions().zoom.amount
+
+ args.amount = 1 / args.amount;
+ plot.zoom(args);
+ }
+
+ plot.zoom = function (args) {
+ if (!args)
+ args = {};
+
+ var c = args.center,
+ amount = args.amount || plot.getOptions().zoom.amount,
+ w = plot.width(), h = plot.height();
+
+ if (!c)
+ c = { left: w / 2, top: h / 2 };
+
+ var xf = c.left / w,
+ yf = c.top / h,
+ minmax = {
+ x: {
+ min: c.left - xf * w / amount,
+ max: c.left + (1 - xf) * w / amount
+ },
+ y: {
+ min: c.top - yf * h / amount,
+ max: c.top + (1 - yf) * h / amount
+ }
+ };
+
+ $.each(plot.getAxes(), function(_, axis) {
+ var opts = axis.options,
+ min = minmax[axis.direction].min,
+ max = minmax[axis.direction].max,
+ zr = opts.zoomRange;
+
+ if (zr === false) // no zooming on this axis
+ return;
+
+ min = axis.c2p(min);
+ max = axis.c2p(max);
+ if (min > max) {
+ // make sure min < max
+ var tmp = min;
+ min = max;
+ max = tmp;
+ }
+
+ var range = max - min;
+ if (zr &&
+ ((zr[0] != null && range < zr[0]) ||
+ (zr[1] != null && range > zr[1])))
+ return;
+
+ opts.min = min;
+ opts.max = max;
+ });
+
+ plot.setupGrid();
+ plot.draw();
+
+ if (!args.preventEvent)
+ plot.getPlaceholder().trigger("plotzoom", [ plot ]);
+ }
+
+ plot.pan = function (args) {
+ var delta = {
+ x: +args.left,
+ y: +args.top
+ };
+
+ if (isNaN(delta.x))
+ delta.x = 0;
+ if (isNaN(delta.y))
+ delta.y = 0;
+
+ $.each(plot.getAxes(), function (_, axis) {
+ var opts = axis.options,
+ min, max, d = delta[axis.direction];
+
+ min = axis.c2p(axis.p2c(axis.min) + d),
+ max = axis.c2p(axis.p2c(axis.max) + d);
+
+ var pr = opts.panRange;
+ if (pr === false) // no panning on this axis
+ return;
+
+ if (pr) {
+ // check whether we hit the wall
+ if (pr[0] != null && pr[0] > min) {
+ d = pr[0] - min;
+ min += d;
+ max += d;
+ }
+
+ if (pr[1] != null && pr[1] < max) {
+ d = pr[1] - max;
+ min += d;
+ max += d;
+ }
+ }
+
+ opts.min = min;
+ opts.max = max;
+ });
+
+ plot.setupGrid();
+ plot.draw();
+
+ if (!args.preventEvent)
+ plot.getPlaceholder().trigger("plotpan", [ plot ]);
+ }
+
+ function shutdown(plot, eventHolder) {
+ eventHolder.unbind(plot.getOptions().zoom.trigger, onZoomClick);
+ eventHolder.unbind("mousewheel", onMouseWheel);
+ eventHolder.unbind("dragstart", onDragStart);
+ eventHolder.unbind("drag", onDrag);
+ eventHolder.unbind("dragend", onDragEnd);
+ if (panTimeout)
+ clearTimeout(panTimeout);
+ }
+
+ plot.hooks.bindEvents.push(bindEvents);
+ plot.hooks.shutdown.push(shutdown);
+ }
+
+ $.plot.plugins.push({
+ init: init,
+ options: options,
+ name: 'navigate',
+ version: '1.3'
+ });
+})(jQuery);
diff --git a/js/jquery.flot.navigate.min.js b/js/jquery.flot.navigate.min.js
new file mode 100644
index 0000000000000000000000000000000000000000..1aa03fe0ece2c4357cfa5061da66b2928eb82ea6
--- /dev/null
+++ b/js/jquery.flot.navigate.min.js
@@ -0,0 +1 @@
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
\ No newline at end of file
diff --git a/js/jquery.flot.selection.js b/js/jquery.flot.selection.js
new file mode 100644
index 0000000000000000000000000000000000000000..7f7b32694bda98c39b5f4af4ef54835c72d41dbb
--- /dev/null
+++ b/js/jquery.flot.selection.js
@@ -0,0 +1,344 @@
+/*
+Flot plugin for selecting regions.
+
+The plugin defines the following options:
+
+ selection: {
+ mode: null or "x" or "y" or "xy",
+ color: color
+ }
+
+Selection support is enabled by setting the mode to one of "x", "y" or
+"xy". In "x" mode, the user will only be able to specify the x range,
+similarly for "y" mode. For "xy", the selection becomes a rectangle
+where both ranges can be specified. "color" is color of the selection
+(if you need to change the color later on, you can get to it with
+plot.getOptions().selection.color).
+
+When selection support is enabled, a "plotselected" event will be
+emitted on the DOM element you passed into the plot function. The
+event handler gets a parameter with the ranges selected on the axes,
+like this:
+
+ placeholder.bind("plotselected", function(event, ranges) {
+ alert("You selected " + ranges.xaxis.from + " to " + ranges.xaxis.to)
+ // similar for yaxis - with multiple axes, the extra ones are in
+ // x2axis, x3axis, ...
+ });
+
+The "plotselected" event is only fired when the user has finished
+making the selection. A "plotselecting" event is fired during the
+process with the same parameters as the "plotselected" event, in case
+you want to know what's happening while it's happening,
+
+A "plotunselected" event with no arguments is emitted when the user
+clicks the mouse to remove the selection.
+
+The plugin allso adds the following methods to the plot object:
+
+- setSelection(ranges, preventEvent)
+
+ Set the selection rectangle. The passed in ranges is on the same
+ form as returned in the "plotselected" event. If the selection mode
+ is "x", you should put in either an xaxis range, if the mode is "y"
+ you need to put in an yaxis range and both xaxis and yaxis if the
+ selection mode is "xy", like this:
+
+ setSelection({ xaxis: { from: 0, to: 10 }, yaxis: { from: 40, to: 60 } });
+
+ setSelection will trigger the "plotselected" event when called. If
+ you don't want that to happen, e.g. if you're inside a
+ "plotselected" handler, pass true as the second parameter. If you
+ are using multiple axes, you can specify the ranges on any of those,
+ e.g. as x2axis/x3axis/... instead of xaxis, the plugin picks the
+ first one it sees.
+
+- clearSelection(preventEvent)
+
+ Clear the selection rectangle. Pass in true to avoid getting a
+ "plotunselected" event.
+
+- getSelection()
+
+ Returns the current selection in the same format as the
+ "plotselected" event. If there's currently no selection, the
+ function returns null.
+
+*/
+
+(function ($) {
+ function init(plot) {
+ var selection = {
+ first: { x: -1, y: -1}, second: { x: -1, y: -1},
+ show: false,
+ active: false
+ };
+
+ // FIXME: The drag handling implemented here should be
+ // abstracted out, there's some similar code from a library in
+ // the navigation plugin, this should be massaged a bit to fit
+ // the Flot cases here better and reused. Doing this would
+ // make this plugin much slimmer.
+ var savedhandlers = {};
+
+ var mouseUpHandler = null;
+
+ function onMouseMove(e) {
+ if (selection.active) {
+ updateSelection(e);
+
+ plot.getPlaceholder().trigger("plotselecting", [ getSelection() ]);
+ }
+ }
+
+ function onMouseDown(e) {
+ if (e.which != 1) // only accept left-click
+ return;
+
+ // cancel out any text selections
+ document.body.focus();
+
+ // prevent text selection and drag in old-school browsers
+ if (document.onselectstart !== undefined && savedhandlers.onselectstart == null) {
+ savedhandlers.onselectstart = document.onselectstart;
+ document.onselectstart = function () { return false; };
+ }
+ if (document.ondrag !== undefined && savedhandlers.ondrag == null) {
+ savedhandlers.ondrag = document.ondrag;
+ document.ondrag = function () { return false; };
+ }
+
+ setSelectionPos(selection.first, e);
+
+ selection.active = true;
+
+ // this is a bit silly, but we have to use a closure to be
+ // able to whack the same handler again
+ mouseUpHandler = function (e) { onMouseUp(e); };
+
+ $(document).one("mouseup", mouseUpHandler);
+ }
+
+ function onMouseUp(e) {
+ mouseUpHandler = null;
+
+ // revert drag stuff for old-school browsers
+ if (document.onselectstart !== undefined)
+ document.onselectstart = savedhandlers.onselectstart;
+ if (document.ondrag !== undefined)
+ document.ondrag = savedhandlers.ondrag;
+
+ // no more dragging
+ selection.active = false;
+ updateSelection(e);
+
+ if (selectionIsSane())
+ triggerSelectedEvent();
+ else {
+ // this counts as a clear
+ plot.getPlaceholder().trigger("plotunselected", [ ]);
+ plot.getPlaceholder().trigger("plotselecting", [ null ]);
+ }
+
+ return false;
+ }
+
+ function getSelection() {
+ if (!selectionIsSane())
+ return null;
+
+ var r = {}, c1 = selection.first, c2 = selection.second;
+ $.each(plot.getAxes(), function (name, axis) {
+ if (axis.used) {
+ var p1 = axis.c2p(c1[axis.direction]), p2 = axis.c2p(c2[axis.direction]);
+ r[name] = { from: Math.min(p1, p2), to: Math.max(p1, p2) };
+ }
+ });
+ return r;
+ }
+
+ function triggerSelectedEvent() {
+ var r = getSelection();
+
+ plot.getPlaceholder().trigger("plotselected", [ r ]);
+
+ // backwards-compat stuff, to be removed in future
+ if (r.xaxis && r.yaxis)
+ plot.getPlaceholder().trigger("selected", [ { x1: r.xaxis.from, y1: r.yaxis.from, x2: r.xaxis.to, y2: r.yaxis.to } ]);
+ }
+
+ function clamp(min, value, max) {
+ return value < min ? min: (value > max ? max: value);
+ }
+
+ function setSelectionPos(pos, e) {
+ var o = plot.getOptions();
+ var offset = plot.getPlaceholder().offset();
+ var plotOffset = plot.getPlotOffset();
+ pos.x = clamp(0, e.pageX - offset.left - plotOffset.left, plot.width());
+ pos.y = clamp(0, e.pageY - offset.top - plotOffset.top, plot.height());
+
+ if (o.selection.mode == "y")
+ pos.x = pos == selection.first ? 0 : plot.width();
+
+ if (o.selection.mode == "x")
+ pos.y = pos == selection.first ? 0 : plot.height();
+ }
+
+ function updateSelection(pos) {
+ if (pos.pageX == null)
+ return;
+
+ setSelectionPos(selection.second, pos);
+ if (selectionIsSane()) {
+ selection.show = true;
+ plot.triggerRedrawOverlay();
+ }
+ else
+ clearSelection(true);
+ }
+
+ function clearSelection(preventEvent) {
+ if (selection.show) {
+ selection.show = false;
+ plot.triggerRedrawOverlay();
+ if (!preventEvent)
+ plot.getPlaceholder().trigger("plotunselected", [ ]);
+ }
+ }
+
+ // function taken from markings support in Flot
+ function extractRange(ranges, coord) {
+ var axis, from, to, key, axes = plot.getAxes();
+
+ for (var k in axes) {
+ axis = axes[k];
+ if (axis.direction == coord) {
+ key = coord + axis.n + "axis";
+ if (!ranges[key] && axis.n == 1)
+ key = coord + "axis"; // support x1axis as xaxis
+ if (ranges[key]) {
+ from = ranges[key].from;
+ to = ranges[key].to;
+ break;
+ }
+ }
+ }
+
+ // backwards-compat stuff - to be removed in future
+ if (!ranges[key]) {
+ axis = coord == "x" ? plot.getXAxes()[0] : plot.getYAxes()[0];
+ from = ranges[coord + "1"];
+ to = ranges[coord + "2"];
+ }
+
+ // auto-reverse as an added bonus
+ if (from != null && to != null && from > to) {
+ var tmp = from;
+ from = to;
+ to = tmp;
+ }
+
+ return { from: from, to: to, axis: axis };
+ }
+
+ function setSelection(ranges, preventEvent) {
+ var axis, range, o = plot.getOptions();
+
+ if (o.selection.mode == "y") {
+ selection.first.x = 0;
+ selection.second.x = plot.width();
+ }
+ else {
+ range = extractRange(ranges, "x");
+
+ selection.first.x = range.axis.p2c(range.from);
+ selection.second.x = range.axis.p2c(range.to);
+ }
+
+ if (o.selection.mode == "x") {
+ selection.first.y = 0;
+ selection.second.y = plot.height();
+ }
+ else {
+ range = extractRange(ranges, "y");
+
+ selection.first.y = range.axis.p2c(range.from);
+ selection.second.y = range.axis.p2c(range.to);
+ }
+
+ selection.show = true;
+ plot.triggerRedrawOverlay();
+ if (!preventEvent && selectionIsSane())
+ triggerSelectedEvent();
+ }
+
+ function selectionIsSane() {
+ var minSize = 5;
+ return Math.abs(selection.second.x - selection.first.x) >= minSize &&
+ Math.abs(selection.second.y - selection.first.y) >= minSize;
+ }
+
+ plot.clearSelection = clearSelection;
+ plot.setSelection = setSelection;
+ plot.getSelection = getSelection;
+
+ plot.hooks.bindEvents.push(function(plot, eventHolder) {
+ var o = plot.getOptions();
+ if (o.selection.mode != null) {
+ eventHolder.mousemove(onMouseMove);
+ eventHolder.mousedown(onMouseDown);
+ }
+ });
+
+
+ plot.hooks.drawOverlay.push(function (plot, ctx) {
+ // draw selection
+ if (selection.show && selectionIsSane()) {
+ var plotOffset = plot.getPlotOffset();
+ var o = plot.getOptions();
+
+ ctx.save();
+ ctx.translate(plotOffset.left, plotOffset.top);
+
+ var c = $.color.parse(o.selection.color);
+
+ ctx.strokeStyle = c.scale('a', 0.8).toString();
+ ctx.lineWidth = 1;
+ ctx.lineJoin = "round";
+ ctx.fillStyle = c.scale('a', 0.4).toString();
+
+ var x = Math.min(selection.first.x, selection.second.x),
+ y = Math.min(selection.first.y, selection.second.y),
+ w = Math.abs(selection.second.x - selection.first.x),
+ h = Math.abs(selection.second.y - selection.first.y);
+
+ ctx.fillRect(x, y, w, h);
+ ctx.strokeRect(x, y, w, h);
+
+ ctx.restore();
+ }
+ });
+
+ plot.hooks.shutdown.push(function (plot, eventHolder) {
+ eventHolder.unbind("mousemove", onMouseMove);
+ eventHolder.unbind("mousedown", onMouseDown);
+
+ if (mouseUpHandler)
+ $(document).unbind("mouseup", mouseUpHandler);
+ });
+
+ }
+
+ $.plot.plugins.push({
+ init: init,
+ options: {
+ selection: {
+ mode: null, // one of null, "x", "y" or "xy"
+ color: "#e8cfac"
+ }
+ },
+ name: 'selection',
+ version: '1.1'
+ });
+})(jQuery);