{ "cells": [ { "cell_type": "code", "execution_count": 18, "metadata": { "collapsed": true }, "outputs": [], "source": [ "# Import the packages we'll need\n", "\n", "%matplotlib notebook\n", "from matplotlib.pyplot import *\n", "import string\n", "from collections import OrderedDict\n", "import numpy as np\n", "from pyobjcryst import loadCrystal\n", "from diffpy.srfit.pdf import PDFGenerator, PDFParser\n", "from diffpy.srfit.fitbase import Profile\n", "from diffpy.srfit.fitbase import FitContribution, FitRecipe\n", "from diffpy.srfit.fitbase import FitResults, initializeRecipe\n", "from diffpy.Structure import loadStructure" ] }, { "cell_type": "code", "execution_count": 19, "metadata": { "collapsed": true }, "outputs": [], "source": [ "# Define functions for optimization and plotting that we will use later\n", "\n", "def scipyOptimize(recipe):\n", " from scipy.optimize.minpack import leastsq\n", " print \"Fit using scipy's LM optimizer\"\n", " leastsq(recipe.residual, recipe.getValues())\n", " return\n", "\n", "def plotRecipe(recipe):\n", " r = recipe.pdf.profile.x\n", " g = recipe.pdf.profile.y\n", " gcalc = recipe.pdf.evaluate()\n", " diffzero = -0.8 * max(g) * np.ones_like(g)\n", " diff = g - gcalc + diffzero\n", " plot(r,g,'bo',label=\"G(r) Data\")\n", " plot(r, gcalc,'r-',label=\"G(r) Fit\")\n", " plot(r,diff,'g-',label=\"G(r) diff\")\n", " plot(r, diffzero,'k-')\n", " xlabel(\"$r (\\AA)$\")\n", " ylabel(\"$G (\\AA^{-2})$\")\n", " legend(loc=1)" ] }, { "cell_type": "code", "execution_count": 20, "metadata": { "collapsed": true }, "outputs": [], "source": [ "# Import the data and make it a PDFprofile. Define the range of the data that will be \n", "# used in the fit.\n", "\n", "grdata = \"E05.gr\"\n", "pdfprofile = Profile()\n", "pdfparser = PDFParser()\n", "pdfparser.parseFile(grdata)\n", "pdfprofile.loadParsedData(pdfparser)\n", "pdfprofile.setCalculationRange(xmin = 1.5, xmax = 30)\n", "\n", "# Setup the PDFgenerator that calculates the PDF from the model\n", "\n", "pdfgenerator = PDFGenerator(\"G\")\n", "pdfgenerator.setQmax(22.0)\n", "pdfgenerator.setQmin(0.5)\n", "pdfgenerator._calc.evaluatortype = 'OPTIMIZED'\n", "\n", "# Load structure from the CIF file.\n", "\n", "ciffile = \"newocc.cif\"\n", "structure = loadCrystal(ciffile)\n", "pdfgenerator.setStructure(structure)\n", "\n", "# Add the profile and generator the the PDFcontribution\n", "\n", "pdfcontribution = FitContribution(\"pdf\")\n", "# IMPORTANT - setup profile with xname=\"r\", because\n", "# `sphericalCF` and `npwave` functions expect it later on.\n", "pdfcontribution.setProfile(pdfprofile, xname=\"r\")\n", "pdfcontribution.addProfileGenerator(pdfgenerator)" ] }, { "cell_type": "code", "execution_count": 21, "metadata": { "collapsed": true }, "outputs": [], "source": [ "# Setup correction scaling due to finite spherical shape. This adds\n", "# the psize parameter from the spherical characteristic function.\n", "\n", "from diffpy.srfit.pdf.characteristicfunctions import sphericalCF\n", "pdfcontribution.registerFunction(sphericalCF, name = \"f\")\n", "\n", "pdfcontribution.psize = 90;\n", "\n", "pdfcontribution.setEquation('f * G')" ] }, { "cell_type": "code", "execution_count": 22, "metadata": { "collapsed": true }, "outputs": [], "source": [ "# Define the recipe to do the fit and add it to the PDFcontribution\n", "\n", "recipe = FitRecipe()\n", "recipe.addContribution(pdfcontribution)\n", "\n", "# Avoid too much output during fitting \n", "recipe.clearFitHooks()\n", "\n", "# Add the scale factor.\n", "recipe.addVar(pdfgenerator.scale, 0.1)\n", "\n", "# Instrumental parameters from standard refinement:\n", "recipe.addVar(pdfgenerator.qbroad, 0.0399, fixed=True)\n", "recipe.addVar(pdfgenerator.qdamp, 0.035, fixed=True)\n", "\n", "# Add the delta2 parameter, and make sure it cannot take unphysical values\n", "recipe.addVar(pdfgenerator.delta2, 2)\n", "\n", "# Add the psize variable for diameter of the spherical nanoparticle.\n", "recipe.addVar(pdfcontribution.psize,30);" ] }, { "cell_type": "code", "execution_count": 23, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "['xyz', 'xyz_mo1', 'xyz_mo']\n", "['xyz', 'xyz_mo1', 'xyz_mo']\n", "['xyz', 'xyz_mo1', 'xyz_mo']\n", "['xyz', 'xyz_o1', 'xyz_o']\n", "['xyz', 'xyz_o1', 'xyz_o']\n", "['xyz', 'xyz_o1', 'xyz_o']\n", "['xyz', 'xyz_o2', 'xyz_o']\n", "['xyz', 'xyz_o2', 'xyz_o']\n", "['xyz', 'xyz_o2', 'xyz_o']\n", "['xyz', 'xyz_mo2', 'xyz_mo']\n", "['xyz', 'xyz_mo2', 'xyz_mo']\n", "['xyz', 'xyz_mo2', 'xyz_mo']\n" ] } ], "source": [ "# Add the structural paramters using space group constaints.\n", "# Ignore the ADP-s which will be set later.\n", "\n", "phase = pdfgenerator.phase\n", "sgpars = phase.sgpars\n", "for par in sgpars.latpars:\n", " recipe.addVar(par, tag='cell')\n", "for par in sgpars.xyzpars:\n", " lclabel = par.par.obj.GetName().lower()\n", " lcsymbol = lclabel.rstrip(string.digits)\n", " # name this variable as x_fe1, y_fe1, etc.\n", " name=\"{}_{}\".format(par.par.name, lclabel)\n", " # tag this variable with (\"xyz\", \"xyz_fe\", \"xyz_fe1\")\n", " tags = ['xyz', 'xyz_' + lclabel, 'xyz_' + lcsymbol]\n", " recipe.addVar(par, name=name, tags=tags)\n", " print tags" ] }, { "cell_type": "code", "execution_count": 24, "metadata": {}, "outputs": [ { "data": { "application/javascript": [ "/* Put everything inside the global mpl namespace */\n", "window.mpl = {};\n", "\n", "\n", "mpl.get_websocket_type = function() {\n", " if (typeof(WebSocket) !== 'undefined') {\n", " return WebSocket;\n", " } else if (typeof(MozWebSocket) !== 'undefined') {\n", " return MozWebSocket;\n", " } else {\n", " alert('Your browser does not have WebSocket support.' +\n", " 'Please try Chrome, Safari or Firefox ≥ 6. ' +\n", " 'Firefox 4 and 5 are also supported but you ' +\n", " 'have to enable WebSockets in about:config.');\n", " };\n", "}\n", "\n", "mpl.figure = function(figure_id, websocket, ondownload, parent_element) {\n", " this.id = figure_id;\n", "\n", " this.ws = websocket;\n", "\n", " this.supports_binary = (this.ws.binaryType != undefined);\n", "\n", " if (!this.supports_binary) {\n", " var warnings = document.getElementById(\"mpl-warnings\");\n", " if (warnings) {\n", " warnings.style.display = 'block';\n", " warnings.textContent = (\n", " \"This browser does not support binary websocket messages. \" +\n", " \"Performance may be slow.\");\n", " }\n", " }\n", "\n", " this.imageObj = new Image();\n", "\n", " this.context = undefined;\n", " this.message = undefined;\n", " this.canvas = undefined;\n", " this.rubberband_canvas = undefined;\n", " this.rubberband_context = undefined;\n", " this.format_dropdown = undefined;\n", "\n", " this.image_mode = 'full';\n", "\n", " this.root = $('
');\n", " this._root_extra_style(this.root)\n", " this.root.attr('style', 'display: inline-block');\n", "\n", " $(parent_element).append(this.root);\n", "\n", " this._init_header(this);\n", " this._init_canvas(this);\n", " this._init_toolbar(this);\n", "\n", " var fig = this;\n", "\n", " this.waiting = false;\n", "\n", " this.ws.onopen = function () {\n", " fig.send_message(\"supports_binary\", {value: fig.supports_binary});\n", " fig.send_message(\"send_image_mode\", {});\n", " if (mpl.ratio != 1) {\n", " fig.send_message(\"set_dpi_ratio\", {'dpi_ratio': mpl.ratio});\n", " }\n", " fig.send_message(\"refresh\", {});\n", " }\n", "\n", " this.imageObj.onload = function() {\n", " if (fig.image_mode == 'full') {\n", " // Full images could contain transparency (where diff images\n", " // almost always do), so we need to clear the canvas so that\n", " // there is no ghosting.\n", " fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n", " }\n", " fig.context.drawImage(fig.imageObj, 0, 0);\n", " };\n", "\n", " this.imageObj.onunload = function() {\n", " fig.ws.close();\n", " }\n", "\n", " this.ws.onmessage = this._make_on_message_function(this);\n", "\n", " this.ondownload = ondownload;\n", "}\n", "\n", "mpl.figure.prototype._init_header = function() {\n", " var titlebar = $(\n", " '
');\n", " var titletext = $(\n", " '
');\n", " titlebar.append(titletext)\n", " this.root.append(titlebar);\n", " this.header = titletext[0];\n", "}\n", "\n", "\n", "\n", "mpl.figure.prototype._canvas_extra_style = function(canvas_div) {\n", "\n", "}\n", "\n", "\n", "mpl.figure.prototype._root_extra_style = function(canvas_div) {\n", "\n", "}\n", "\n", "mpl.figure.prototype._init_canvas = function() {\n", " var fig = this;\n", "\n", " var canvas_div = $('
');\n", "\n", " canvas_div.attr('style', 'position: relative; clear: both; outline: 0');\n", "\n", " function canvas_keyboard_event(event) {\n", " return fig.key_event(event, event['data']);\n", " }\n", "\n", " canvas_div.keydown('key_press', canvas_keyboard_event);\n", " canvas_div.keyup('key_release', canvas_keyboard_event);\n", " this.canvas_div = canvas_div\n", " this._canvas_extra_style(canvas_div)\n", " this.root.append(canvas_div);\n", "\n", " var canvas = $('');\n", " canvas.addClass('mpl-canvas');\n", " canvas.attr('style', \"left: 0; top: 0; z-index: 0; outline: 0\")\n", "\n", " this.canvas = canvas[0];\n", " this.context = canvas[0].getContext(\"2d\");\n", "\n", " var backingStore = this.context.backingStorePixelRatio ||\n", "\tthis.context.webkitBackingStorePixelRatio ||\n", "\tthis.context.mozBackingStorePixelRatio ||\n", "\tthis.context.msBackingStorePixelRatio ||\n", "\tthis.context.oBackingStorePixelRatio ||\n", "\tthis.context.backingStorePixelRatio || 1;\n", "\n", " mpl.ratio = (window.devicePixelRatio || 1) / backingStore;\n", "\n", " var rubberband = $('');\n", " rubberband.attr('style', \"position: absolute; left: 0; top: 0; z-index: 1;\")\n", "\n", " var pass_mouse_events = true;\n", "\n", " canvas_div.resizable({\n", " start: function(event, ui) {\n", " pass_mouse_events = false;\n", " },\n", " resize: function(event, ui) {\n", " fig.request_resize(ui.size.width, ui.size.height);\n", " },\n", " stop: function(event, ui) {\n", " pass_mouse_events = true;\n", " fig.request_resize(ui.size.width, ui.size.height);\n", " },\n", " });\n", "\n", " function mouse_event_fn(event) {\n", " if (pass_mouse_events)\n", " return fig.mouse_event(event, event['data']);\n", " }\n", "\n", " rubberband.mousedown('button_press', mouse_event_fn);\n", " rubberband.mouseup('button_release', mouse_event_fn);\n", " // Throttle sequential mouse events to 1 every 20ms.\n", " rubberband.mousemove('motion_notify', mouse_event_fn);\n", "\n", " rubberband.mouseenter('figure_enter', mouse_event_fn);\n", " rubberband.mouseleave('figure_leave', mouse_event_fn);\n", "\n", " canvas_div.on(\"wheel\", function (event) {\n", " event = event.originalEvent;\n", " event['data'] = 'scroll'\n", " if (event.deltaY < 0) {\n", " event.step = 1;\n", " } else {\n", " event.step = -1;\n", " }\n", " mouse_event_fn(event);\n", " });\n", "\n", " canvas_div.append(canvas);\n", " canvas_div.append(rubberband);\n", "\n", " this.rubberband = rubberband;\n", " this.rubberband_canvas = rubberband[0];\n", " this.rubberband_context = rubberband[0].getContext(\"2d\");\n", " this.rubberband_context.strokeStyle = \"#000000\";\n", "\n", " this._resize_canvas = function(width, height) {\n", " // Keep the size of the canvas, canvas container, and rubber band\n", " // canvas in synch.\n", " canvas_div.css('width', width)\n", " canvas_div.css('height', height)\n", "\n", " canvas.attr('width', width * mpl.ratio);\n", " canvas.attr('height', height * mpl.ratio);\n", " canvas.attr('style', 'width: ' + width + 'px; height: ' + height + 'px;');\n", "\n", " rubberband.attr('width', width);\n", " rubberband.attr('height', height);\n", " }\n", "\n", " // Set the figure to an initial 600x600px, this will subsequently be updated\n", " // upon first draw.\n", " this._resize_canvas(600, 600);\n", "\n", " // Disable right mouse context menu.\n", " $(this.rubberband_canvas).bind(\"contextmenu\",function(e){\n", " return false;\n", " });\n", "\n", " function set_focus () {\n", " canvas.focus();\n", " canvas_div.focus();\n", " }\n", "\n", " window.setTimeout(set_focus, 100);\n", "}\n", "\n", "mpl.figure.prototype._init_toolbar = function() {\n", " var fig = this;\n", "\n", " var nav_element = $('
')\n", " nav_element.attr('style', 'width: 100%');\n", " this.root.append(nav_element);\n", "\n", " // Define a callback function for later on.\n", " function toolbar_event(event) {\n", " return fig.toolbar_button_onclick(event['data']);\n", " }\n", " function toolbar_mouse_event(event) {\n", " return fig.toolbar_button_onmouseover(event['data']);\n", " }\n", "\n", " for(var toolbar_ind in mpl.toolbar_items) {\n", " var name = mpl.toolbar_items[toolbar_ind][0];\n", " var tooltip = mpl.toolbar_items[toolbar_ind][1];\n", " var image = mpl.toolbar_items[toolbar_ind][2];\n", " var method_name = mpl.toolbar_items[toolbar_ind][3];\n", "\n", " if (!name) {\n", " // put a spacer in here.\n", " continue;\n", " }\n", " var button = $('');\n", " button.click(method_name, toolbar_event);\n", " button.mouseover(tooltip, toolbar_mouse_event);\n", " nav_element.append(button);\n", " }\n", "\n", " // Add the status bar.\n", " var status_bar = $('');\n", " nav_element.append(status_bar);\n", " this.message = status_bar[0];\n", "\n", " // Add the close button to the window.\n", " var buttongrp = $('
');\n", " var button = $('');\n", " button.click(function (evt) { fig.handle_close(fig, {}); } );\n", " button.mouseover('Stop Interaction', toolbar_mouse_event);\n", " buttongrp.append(button);\n", " var titlebar = this.root.find($('.ui-dialog-titlebar'));\n", " titlebar.prepend(buttongrp);\n", "}\n", "\n", "mpl.figure.prototype._root_extra_style = function(el){\n", " var fig = this\n", " el.on(\"remove\", function(){\n", "\tfig.close_ws(fig, {});\n", " });\n", "}\n", "\n", "mpl.figure.prototype._canvas_extra_style = function(el){\n", " // this is important to make the div 'focusable\n", " el.attr('tabindex', 0)\n", " // reach out to IPython and tell the keyboard manager to turn it's self\n", " // off when our div gets focus\n", "\n", " // location in version 3\n", " if (IPython.notebook.keyboard_manager) {\n", " IPython.notebook.keyboard_manager.register_events(el);\n", " }\n", " else {\n", " // location in version 2\n", " IPython.keyboard_manager.register_events(el);\n", " }\n", "\n", "}\n", "\n", "mpl.figure.prototype._key_event_extra = function(event, name) {\n", " var manager = IPython.notebook.keyboard_manager;\n", " if (!manager)\n", " manager = IPython.keyboard_manager;\n", "\n", " // Check for shift+enter\n", " if (event.shiftKey && event.which == 13) {\n", " this.canvas_div.blur();\n", " event.shiftKey = false;\n", " // Send a \"J\" for go to next cell\n", " event.which = 74;\n", " event.keyCode = 74;\n", " manager.command_mode();\n", " manager.handle_keydown(event);\n", " }\n", "}\n", "\n", "mpl.figure.prototype.handle_save = function(fig, msg) {\n", " fig.ondownload(fig, null);\n", "}\n", "\n", "\n", "mpl.find_output_cell = function(html_output) {\n", " // Return the cell and output element which can be found *uniquely* in the notebook.\n", " // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n", " // IPython event is triggered only after the cells have been serialised, which for\n", " // our purposes (turning an active figure into a static one), is too late.\n", " var cells = IPython.notebook.get_cells();\n", " var ncells = cells.length;\n", " for (var i=0; i= 3 moved mimebundle to data attribute of output\n", " data = data.data;\n", " }\n", " if (data['text/html'] == html_output) {\n", " return [cell, data, j];\n", " }\n", " }\n", " }\n", " }\n", "}\n", "\n", "// Register the function which deals with the matplotlib target/channel.\n", "// The kernel may be null if the page has been refreshed.\n", "if (IPython.notebook.kernel != null) {\n", " IPython.notebook.kernel.comm_manager.register_target('matplotlib', mpl.mpl_figure_comm);\n", "}\n" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "name": "stdout", "output_type": "stream", "text": [ "Some quantities invalid due to missing profile uncertainty\n", "Overall (Chi2 and Reduced Chi2 invalid)\n", "------------------------------------------------------------------------------\n", "Residual 22.86491073\n", "Contributions 22.86491073\n", "Restraints 0.00000000\n", "Chi2 22.86491073\n", "Reduced Chi2 0.00804819\n", "Rw 0.44632090\n", "\n", "Variables (Uncertainties invalid)\n", "------------------------------------------------------------------------------\n", "Biso_Mo 5.14529807e-01 +/- 2.36585926e-01\n", "a 5.69461778e+00 +/- 4.41533183e-02\n", "b 4.87631900e+00 +/- 2.75140011e-02\n", "beta 2.14707262e+00 +/- 8.72699597e-03\n", "c 5.73975364e+00 +/- 4.94560473e-02\n", "delta2 3.27644499e+00 +/- 2.12953045e+00\n", "scale 1.47618882e-01 +/- 2.18340400e-02\n", "x_mo2 2.80804069e-01 +/- 3.31382943e-02\n", "y_mo2 5.01244897e-01 +/- 3.75036608e-02\n", "z_mo2 9.97247228e-01 +/- 3.53689297e-02\n", "\n", "Fixed Variables\n", "------------------------------------------------------------------------------\n", "Biso_oxygen 8.00000000e-02\n", "occ_mo1 1.00000000e+00\n", "occ_mo2 1.99999998e-01\n", "psize 3.00000000e+01\n", "qbroad 3.99000000e-02\n", "qdamp 3.50000000e-02\n", "x_mo1 2.32900000e-01\n", "x_o1 1.12700000e-01\n", "x_o2 3.90300000e-01\n", "y_mo1 9.92000000e-01\n", "y_o1 2.16400000e-01\n", "y_o2 6.96600000e-01\n", "z_mo1 1.69000000e-02\n", "z_o1 2.33900000e-01\n", "z_o2 2.99000000e-01\n", "\n", "Variable Correlations greater than 25% (Correlations invalid)\n", "------------------------------------------------------------------------------\n", "corr(x_mo2, z_mo2) 0.5986\n", "corr(scale, Biso_Mo) 0.4618\n", "corr(c, beta) 0.3495\n", "corr(scale, beta) 0.3311\n", "corr(a, c) -0.3293\n", "corr(x_mo2, Biso_Mo) -0.2828\n", "corr(delta2, Biso_Mo) 0.2773\n", "corr(a, z_mo2) 0.2687\n", "corr(x_mo2, y_mo2) 0.2542\n", "corr(z_mo2, Biso_Mo) -0.2512\n", "\n" ] } ], "source": [ "# Done with setting up, start the actual refinements!\n", "# First refine only the scale, cell and psize\n", "recipe.fix('all')\n", "recipe.free('scale')\n", "scipyOptimize(recipe)\n", "print 1\n", "recipe.free('cell')\n", "recipe.free('adp_Mo')\n", "recipe.free('delta2')\n", "scipyOptimize(recipe)\n", "print 2\n", "recipe.free('xyz_mo2')\n", "scipyOptimize(recipe)\n", "\n", "%matplotlib notebook\n", "plotRecipe(recipe)\n", "print FitResults(recipe)" ] }, { "cell_type": "code", "execution_count": 26, "metadata": { "scrolled": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Fit using scipy's LM optimizer\n", "Fit using scipy's LM optimizer\n", "Fit using scipy's LM optimizer\n", "Fit using scipy's LM optimizer\n" ] }, { "data": { "application/javascript": [ "/* Put everything inside the global mpl namespace */\n", "window.mpl = {};\n", "\n", "\n", "mpl.get_websocket_type = function() {\n", " if (typeof(WebSocket) !== 'undefined') {\n", " return WebSocket;\n", " } else if (typeof(MozWebSocket) !== 'undefined') {\n", " return MozWebSocket;\n", " } else {\n", " alert('Your browser does not have WebSocket support.' +\n", " 'Please try Chrome, Safari or Firefox ≥ 6. ' +\n", " 'Firefox 4 and 5 are also supported but you ' +\n", " 'have to enable WebSockets in about:config.');\n", " };\n", "}\n", "\n", "mpl.figure = function(figure_id, websocket, ondownload, parent_element) {\n", " this.id = figure_id;\n", "\n", " this.ws = websocket;\n", "\n", " this.supports_binary = (this.ws.binaryType != undefined);\n", "\n", " if (!this.supports_binary) {\n", " var warnings = document.getElementById(\"mpl-warnings\");\n", " if (warnings) {\n", " warnings.style.display = 'block';\n", " warnings.textContent = (\n", " \"This browser does not support binary websocket messages. \" +\n", " \"Performance may be slow.\");\n", " }\n", " }\n", "\n", " this.imageObj = new Image();\n", "\n", " this.context = undefined;\n", " this.message = undefined;\n", " this.canvas = undefined;\n", " this.rubberband_canvas = undefined;\n", " this.rubberband_context = undefined;\n", " this.format_dropdown = undefined;\n", "\n", " this.image_mode = 'full';\n", "\n", " this.root = $('
');\n", " this._root_extra_style(this.root)\n", " this.root.attr('style', 'display: inline-block');\n", "\n", " $(parent_element).append(this.root);\n", "\n", " this._init_header(this);\n", " this._init_canvas(this);\n", " this._init_toolbar(this);\n", "\n", " var fig = this;\n", "\n", " this.waiting = false;\n", "\n", " this.ws.onopen = function () {\n", " fig.send_message(\"supports_binary\", {value: fig.supports_binary});\n", " fig.send_message(\"send_image_mode\", {});\n", " if (mpl.ratio != 1) {\n", " fig.send_message(\"set_dpi_ratio\", {'dpi_ratio': mpl.ratio});\n", " }\n", " fig.send_message(\"refresh\", {});\n", " }\n", "\n", " this.imageObj.onload = function() {\n", " if (fig.image_mode == 'full') {\n", " // Full images could contain transparency (where diff images\n", " // almost always do), so we need to clear the canvas so that\n", " // there is no ghosting.\n", " fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n", " }\n", " fig.context.drawImage(fig.imageObj, 0, 0);\n", " };\n", "\n", " this.imageObj.onunload = function() {\n", " fig.ws.close();\n", " }\n", "\n", " this.ws.onmessage = this._make_on_message_function(this);\n", "\n", " this.ondownload = ondownload;\n", "}\n", "\n", "mpl.figure.prototype._init_header = function() {\n", " var titlebar = $(\n", " '
');\n", " var titletext = $(\n", " '
');\n", " titlebar.append(titletext)\n", " this.root.append(titlebar);\n", " this.header = titletext[0];\n", "}\n", "\n", "\n", "\n", "mpl.figure.prototype._canvas_extra_style = function(canvas_div) {\n", "\n", "}\n", "\n", "\n", "mpl.figure.prototype._root_extra_style = function(canvas_div) {\n", "\n", "}\n", "\n", "mpl.figure.prototype._init_canvas = function() {\n", " var fig = this;\n", "\n", " var canvas_div = $('
');\n", "\n", " canvas_div.attr('style', 'position: relative; clear: both; outline: 0');\n", "\n", " function canvas_keyboard_event(event) {\n", " return fig.key_event(event, event['data']);\n", " }\n", "\n", " canvas_div.keydown('key_press', canvas_keyboard_event);\n", " canvas_div.keyup('key_release', canvas_keyboard_event);\n", " this.canvas_div = canvas_div\n", " this._canvas_extra_style(canvas_div)\n", " this.root.append(canvas_div);\n", "\n", " var canvas = $('');\n", " canvas.addClass('mpl-canvas');\n", " canvas.attr('style', \"left: 0; top: 0; z-index: 0; outline: 0\")\n", "\n", " this.canvas = canvas[0];\n", " this.context = canvas[0].getContext(\"2d\");\n", "\n", " var backingStore = this.context.backingStorePixelRatio ||\n", "\tthis.context.webkitBackingStorePixelRatio ||\n", "\tthis.context.mozBackingStorePixelRatio ||\n", "\tthis.context.msBackingStorePixelRatio ||\n", "\tthis.context.oBackingStorePixelRatio ||\n", "\tthis.context.backingStorePixelRatio || 1;\n", "\n", " mpl.ratio = (window.devicePixelRatio || 1) / backingStore;\n", "\n", " var rubberband = $('');\n", " rubberband.attr('style', \"position: absolute; left: 0; top: 0; z-index: 1;\")\n", "\n", " var pass_mouse_events = true;\n", "\n", " canvas_div.resizable({\n", " start: function(event, ui) {\n", " pass_mouse_events = false;\n", " },\n", " resize: function(event, ui) {\n", " fig.request_resize(ui.size.width, ui.size.height);\n", " },\n", " stop: function(event, ui) {\n", " pass_mouse_events = true;\n", " fig.request_resize(ui.size.width, ui.size.height);\n", " },\n", " });\n", "\n", " function mouse_event_fn(event) {\n", " if (pass_mouse_events)\n", " return fig.mouse_event(event, event['data']);\n", " }\n", "\n", " rubberband.mousedown('button_press', mouse_event_fn);\n", " rubberband.mouseup('button_release', mouse_event_fn);\n", " // Throttle sequential mouse events to 1 every 20ms.\n", " rubberband.mousemove('motion_notify', mouse_event_fn);\n", "\n", " rubberband.mouseenter('figure_enter', mouse_event_fn);\n", " rubberband.mouseleave('figure_leave', mouse_event_fn);\n", "\n", " canvas_div.on(\"wheel\", function (event) {\n", " event = event.originalEvent;\n", " event['data'] = 'scroll'\n", " if (event.deltaY < 0) {\n", " event.step = 1;\n", " } else {\n", " event.step = -1;\n", " }\n", " mouse_event_fn(event);\n", " });\n", "\n", " canvas_div.append(canvas);\n", " canvas_div.append(rubberband);\n", "\n", " this.rubberband = rubberband;\n", " this.rubberband_canvas = rubberband[0];\n", " this.rubberband_context = rubberband[0].getContext(\"2d\");\n", " this.rubberband_context.strokeStyle = \"#000000\";\n", "\n", " this._resize_canvas = function(width, height) {\n", " // Keep the size of the canvas, canvas container, and rubber band\n", " // canvas in synch.\n", " canvas_div.css('width', width)\n", " canvas_div.css('height', height)\n", "\n", " canvas.attr('width', width * mpl.ratio);\n", " canvas.attr('height', height * mpl.ratio);\n", " canvas.attr('style', 'width: ' + width + 'px; height: ' + height + 'px;');\n", "\n", " rubberband.attr('width', width);\n", " rubberband.attr('height', height);\n", " }\n", "\n", " // Set the figure to an initial 600x600px, this will subsequently be updated\n", " // upon first draw.\n", " this._resize_canvas(600, 600);\n", "\n", " // Disable right mouse context menu.\n", " $(this.rubberband_canvas).bind(\"contextmenu\",function(e){\n", " return false;\n", " });\n", "\n", " function set_focus () {\n", " canvas.focus();\n", " canvas_div.focus();\n", " }\n", "\n", " window.setTimeout(set_focus, 100);\n", "}\n", "\n", "mpl.figure.prototype._init_toolbar = function() {\n", " var fig = this;\n", "\n", " var nav_element = $('
')\n", " nav_element.attr('style', 'width: 100%');\n", " this.root.append(nav_element);\n", "\n", " // Define a callback function for later on.\n", " function toolbar_event(event) {\n", " return fig.toolbar_button_onclick(event['data']);\n", " }\n", " function toolbar_mouse_event(event) {\n", " return fig.toolbar_button_onmouseover(event['data']);\n", " }\n", "\n", " for(var toolbar_ind in mpl.toolbar_items) {\n", " var name = mpl.toolbar_items[toolbar_ind][0];\n", " var tooltip = mpl.toolbar_items[toolbar_ind][1];\n", " var image = mpl.toolbar_items[toolbar_ind][2];\n", " var method_name = mpl.toolbar_items[toolbar_ind][3];\n", "\n", " if (!name) {\n", " // put a spacer in here.\n", " continue;\n", " }\n", " var button = $('');\n", " button.click(method_name, toolbar_event);\n", " button.mouseover(tooltip, toolbar_mouse_event);\n", " nav_element.append(button);\n", " }\n", "\n", " // Add the status bar.\n", " var status_bar = $('');\n", " nav_element.append(status_bar);\n", " this.message = status_bar[0];\n", "\n", " // Add the close button to the window.\n", " var buttongrp = $('
');\n", " var button = $('');\n", " button.click(function (evt) { fig.handle_close(fig, {}); } );\n", " button.mouseover('Stop Interaction', toolbar_mouse_event);\n", " buttongrp.append(button);\n", " var titlebar = this.root.find($('.ui-dialog-titlebar'));\n", " titlebar.prepend(buttongrp);\n", "}\n", "\n", "mpl.figure.prototype._root_extra_style = function(el){\n", " var fig = this\n", " el.on(\"remove\", function(){\n", "\tfig.close_ws(fig, {});\n", " });\n", "}\n", "\n", "mpl.figure.prototype._canvas_extra_style = function(el){\n", " // this is important to make the div 'focusable\n", " el.attr('tabindex', 0)\n", " // reach out to IPython and tell the keyboard manager to turn it's self\n", " // off when our div gets focus\n", "\n", " // location in version 3\n", " if (IPython.notebook.keyboard_manager) {\n", " IPython.notebook.keyboard_manager.register_events(el);\n", " }\n", " else {\n", " // location in version 2\n", " IPython.keyboard_manager.register_events(el);\n", " }\n", "\n", "}\n", "\n", "mpl.figure.prototype._key_event_extra = function(event, name) {\n", " var manager = IPython.notebook.keyboard_manager;\n", " if (!manager)\n", " manager = IPython.keyboard_manager;\n", "\n", " // Check for shift+enter\n", " if (event.shiftKey && event.which == 13) {\n", " this.canvas_div.blur();\n", " event.shiftKey = false;\n", " // Send a \"J\" for go to next cell\n", " event.which = 74;\n", " event.keyCode = 74;\n", " manager.command_mode();\n", " manager.handle_keydown(event);\n", " }\n", "}\n", "\n", "mpl.figure.prototype.handle_save = function(fig, msg) {\n", " fig.ondownload(fig, null);\n", "}\n", "\n", "\n", "mpl.find_output_cell = function(html_output) {\n", " // Return the cell and output element which can be found *uniquely* in the notebook.\n", " // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n", " // IPython event is triggered only after the cells have been serialised, which for\n", " // our purposes (turning an active figure into a static one), is too late.\n", " var cells = IPython.notebook.get_cells();\n", " var ncells = cells.length;\n", " for (var i=0; i= 3 moved mimebundle to data attribute of output\n", " data = data.data;\n", " }\n", " if (data['text/html'] == html_output) {\n", " return [cell, data, j];\n", " }\n", " }\n", " }\n", " }\n", "}\n", "\n", "// Register the function which deals with the matplotlib target/channel.\n", "// The kernel may be null if the page has been refreshed.\n", "if (IPython.notebook.kernel != null) {\n", " IPython.notebook.kernel.comm_manager.register_target('matplotlib', mpl.mpl_figure_comm);\n", "}\n" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "name": "stdout", "output_type": "stream", "text": [ "Some quantities invalid due to missing profile uncertainty\n", "Overall (Chi2 and Reduced Chi2 invalid)\n", "------------------------------------------------------------------------------\n", "Residual 20.67795561\n", "Contributions 20.67795561\n", "Restraints 0.00000000\n", "Chi2 20.67795561\n", "Reduced Chi2 0.00729639\n", "Rw 0.42443996\n", "\n", "Variables (Uncertainties invalid)\n", "------------------------------------------------------------------------------\n", "Biso_Mo 5.35898282e-01 +/- 2.52215175e-01\n", "Biso_oxygen 3.89732441e-01 +/- 1.44464553e+00\n", "a 5.73865252e+00 +/- 6.49326734e-02\n", "b 4.84300268e+00 +/- 3.76759439e-02\n", "beta 2.13888783e+00 +/- 1.27480480e-02\n", "c 5.72077264e+00 +/- 7.03980646e-02\n", "delta2 3.91463068e+00 +/- 1.56835967e-01\n", "occ_mo1 1.01834598e+00 +/- 4.52450351e-01\n", "occ_mo2 3.09238910e-01 +/- 1.70964995e-01\n", "psize 2.44822838e+01 +/- 4.48502706e+00\n", "scale 1.63493958e-01 +/- 6.17533530e-02\n", "x_mo1 2.32980201e-01 +/- 1.03747901e-02\n", "x_mo2 2.90548376e-01 +/- 2.28748293e-02\n", "y_mo1 9.96139217e-01 +/- 3.05557431e-02\n", "y_mo2 5.12796174e-01 +/- 2.97672026e-02\n", "z_mo1 2.19062048e-02 +/- 1.07169920e-02\n", "z_mo2 7.88907114e-03 +/- 2.60129633e-02\n", "\n", "Fixed Variables\n", "------------------------------------------------------------------------------\n", "qbroad 3.99000000e-02\n", "qdamp 3.50000000e-02\n", "x_o1 1.12700000e-01\n", "x_o2 3.90300000e-01\n", "y_o1 2.16400000e-01\n", "y_o2 6.96600000e-01\n", "z_o1 2.33900000e-01\n", "z_o2 2.99000000e-01\n", "\n", "Variable Correlations greater than 25% (Correlations invalid)\n", "------------------------------------------------------------------------------\n", "corr(delta2, y_mo1) 0.9425\n", "corr(scale, occ_mo1) -0.8660\n", "corr(delta2, y_mo2) 0.8241\n", "corr(y_mo1, y_mo2) 0.8054\n", "corr(x_mo1, z_mo1) 0.7900\n", "corr(occ_mo1, Biso_oxygen) -0.5142\n", "corr(scale, Biso_oxygen) 0.5049\n", "corr(a, c) -0.4984\n", "corr(x_mo2, z_mo2) 0.4921\n", "corr(z_mo1, x_mo2) -0.4146\n", "corr(scale, occ_mo2) -0.3862\n", "corr(occ_mo2, Biso_oxygen) -0.3598\n", "corr(occ_mo1, occ_mo2) 0.3436\n", "corr(b, beta) 0.3344\n", "corr(x_mo1, x_mo2) -0.3306\n", "corr(x_mo1, z_mo2) -0.3194\n", "corr(beta, z_mo2) 0.3038\n", "corr(b, c) -0.2928\n", "corr(psize, beta) 0.2843\n", "corr(z_mo1, z_mo2) -0.2772\n", "corr(scale, psize) -0.2518\n", "corr(scale, x_mo1) -0.2502\n", "\n" ] } ], "source": [ "recipe.free('Biso_oxygen')\n", "recipe.free('psize')\n", "scipyOptimize(recipe)\n", "\n", "\n", "%matplotlib notebook\n", "plotRecipe(recipe)\n", "\n", "print FitResults(recipe)" ] }, { "cell_type": "code", "execution_count": 23, "metadata": { "collapsed": true }, "outputs": [], "source": [ "r = recipe.pdf.profile.x\n", "gobs = recipe.pdf.profile.y\n", "\n", "gcalc = recipe.pdf.evaluate()\n", "gdiff = gobs - gcalc\n", "\n", "plot_export = np.column_stack((r,gobs,gcalc,gdiff))\n", "np.savetxt('E05_onephase_newoccFit.txt', plot_export)" ] }, { "cell_type": "code", "execution_count": 10, "metadata": { "collapsed": true }, "outputs": [], "source": [ "def export_cifs():\n", " name = 'refined_'+ciffile+'.cif'\n", " with open(name, 'wb') as fp:\n", " structure.CIFOutput(fp)\n", " return\n", "\n", "# uncomment to really export\n", "export_cifs()" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "collapsed": true }, "outputs": [], "source": [] } ], "metadata": { "anaconda-cloud": {}, "kernelspec": { "display_name": "Python 2", "language": "python", "name": "python2" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 2 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython2", "version": "2.7.14" } }, "nbformat": 4, "nbformat_minor": 1 }