doc/examples/kinetic_energy_distribution.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "ac3fd8d7",
   "metadata": {},
   "source": [
    "# Kinetic energy distribution\n",
    "\n",
    "*Note: This notebook can be run locally by cloning the*\n",
    "[Github repository](https://github.com/shirtsgroup/physical_validation).\n",
    "*The notebook is located in* `doc/examples/kinetic_energy_distribution.ipynb`. *Be aware\n",
    "that probabilistic quantities such as error estimates based on bootstrapping\n",
    "will differ when repeating the analysis.*"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "dc810051",
   "metadata": {},
   "outputs": [],
   "source": [
    "# enable plotting in notebook\n",
    "%matplotlib notebook"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "8f51f45d",
   "metadata": {},
   "source": [
    "The results imported here are the time series of kinetic and potential energy from example simulations, which are\n",
    "stored in another Python file. In real-world usage, the results would\n",
    "either come from the Python interface of the simulation package, from\n",
    "flat files containing the results, or from package-specific parsers. See\n",
    "[SimulationData](../simulation_data.rst)\n",
    "for more details."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "3b8aa316",
   "metadata": {},
   "outputs": [],
   "source": [
    "from simulation_results import example_simulations\n",
    "\n",
    "import physical_validation"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "2b797a5e",
   "metadata": {},
   "source": [
    "In this example, we will check the distributions of two simulations of 900 water molecules simulated under NVT conditions at 298.15K.\n",
    "One simulation used velocity-rescale temperature coupling, the other used Berendsen temperature coupling."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "8143ce85",
   "metadata": {},
   "outputs": [],
   "source": [
    "simulation_vrescale = example_simulations.get(\n",
    "    \"900 water molecules, NVT at 298K with v-rescale thermostat\"\n",
    ")\n",
    "simulation_berendsen = example_simulations.get(\n",
    "    \"900 water molecules, NVT at 298K with Berendsen thermostat\"\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "344bbf24",
   "metadata": {},
   "source": [
    "First, we will create the object containing system information.\n",
    "The example system used in both simulations consists of 900 water molecules which are fully constrained.\n",
    "For the kinetic energy distribution check, we only need information about the\n",
    "complete system (i.e. no per-molecule or per-atom information) so we will only\n",
    "fill these."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "cf44cbd2",
   "metadata": {},
   "outputs": [],
   "source": [
    "num_molecules = 900\n",
    "# Each water molecule has three atoms\n",
    "num_atoms_per_molecule = 3\n",
    "# Each fully constrained water molecule has three constraints\n",
    "num_constraints_per_molecule = 3\n",
    "# In this simulation, translational center of mass motion was removed\n",
    "num_constrained_translational_dof = 3\n",
    "# Rotational center of mass motion was not removed\n",
    "num_constrained_rotational_dof = 0\n",
    "\n",
    "system_data = physical_validation.data.SystemData(\n",
    "    natoms=num_molecules * num_atoms_per_molecule,\n",
    "    nconstraints=num_molecules * num_constraints_per_molecule,\n",
    "    ndof_reduction_tra=num_constrained_translational_dof,\n",
    "    ndof_reduction_rot=num_constrained_rotational_dof,\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "a7cfac80",
   "metadata": {},
   "source": [
    "Next, we will create the ensemble information:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "49758f09",
   "metadata": {},
   "outputs": [],
   "source": [
    "ensemble_data = physical_validation.data.EnsembleData(\n",
    "    ensemble=\"NVT\",\n",
    "    natoms=num_molecules * 3,\n",
    "    volume=3.01125 ** 3,\n",
    "    temperature=298.15,\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "394f0255",
   "metadata": {},
   "source": [
    "Now we will create the simulation data objects which we will feed to the physical validation tests."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "34d81cd8",
   "metadata": {},
   "outputs": [],
   "source": [
    "simulation_data_vrescale = physical_validation.data.SimulationData(\n",
    "    # Example simulations were performed using GROMACS\n",
    "    units=physical_validation.data.UnitData.units(\"GROMACS\"),\n",
    "    system=system_data,\n",
    "    ensemble=ensemble_data,\n",
    "    observables=physical_validation.data.ObservableData(\n",
    "        # This test requires only the kinetic energy\n",
    "        kinetic_energy=simulation_vrescale[\"kinetic energy\"]\n",
    "    ),\n",
    ")\n",
    "simulation_data_berendsen = physical_validation.data.SimulationData(\n",
    "    # Example simulations were performed using GROMACS\n",
    "    units=physical_validation.data.UnitData.units(\"GROMACS\"),\n",
    "    system=system_data,\n",
    "    ensemble=ensemble_data,\n",
    "    observables=physical_validation.data.ObservableData(\n",
    "        # This test requires only the kinetic energy\n",
    "        kinetic_energy=simulation_berendsen[\"kinetic energy\"]\n",
    "    ),\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "c84eda1e",
   "metadata": {},
   "source": [
    "We can now check the velocity-rescale temperature coupling, using first\n",
    "the strict, then the non-strict kinetic energy distribution check.\n",
    "We are using `screen=True` to display a result plot on screen (see argument `filename` to print that same plot to file)."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "732097b2",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "After equilibration, decorrelation and tail pruning, 96.02% (4802 frames) of original Kinetic energy remain.\n"
     ]
    },
    {
     "data": {
      "application/javascript": [
       "/* Put everything inside the global mpl namespace */\n",
       "/* global mpl */\n",
       "window.mpl = {};\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(\n",
       "            '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",
       "\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 = document.createElement('div');\n",
       "    this.root.setAttribute('style', 'display: inline-block');\n",
       "    this._root_extra_style(this.root);\n",
       "\n",
       "    parent_element.appendChild(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 (fig.ratio !== 1) {\n",
       "            fig.send_message('set_dpi_ratio', { dpi_ratio: fig.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 = document.createElement('div');\n",
       "    titlebar.classList =\n",
       "        'ui-dialog-titlebar ui-widget-header ui-corner-all ui-helper-clearfix';\n",
       "    var titletext = document.createElement('div');\n",
       "    titletext.classList = 'ui-dialog-title';\n",
       "    titletext.setAttribute(\n",
       "        'style',\n",
       "        'width: 100%; text-align: center; padding: 3px;'\n",
       "    );\n",
       "    titlebar.appendChild(titletext);\n",
       "    this.root.appendChild(titlebar);\n",
       "    this.header = titletext;\n",
       "};\n",
       "\n",
       "mpl.figure.prototype._canvas_extra_style = function (_canvas_div) {};\n",
       "\n",
       "mpl.figure.prototype._root_extra_style = function (_canvas_div) {};\n",
       "\n",
       "mpl.figure.prototype._init_canvas = function () {\n",
       "    var fig = this;\n",
       "\n",
       "    var canvas_div = (this.canvas_div = document.createElement('div'));\n",
       "    canvas_div.setAttribute(\n",
       "        'style',\n",
       "        'border: 1px solid #ddd;' +\n",
       "            'box-sizing: content-box;' +\n",
       "            'clear: both;' +\n",
       "            'min-height: 1px;' +\n",
       "            'min-width: 1px;' +\n",
       "            'outline: 0;' +\n",
       "            'overflow: hidden;' +\n",
       "            'position: relative;' +\n",
       "            'resize: both;'\n",
       "    );\n",
       "\n",
       "    function on_keyboard_event_closure(name) {\n",
       "        return function (event) {\n",
       "            return fig.key_event(event, name);\n",
       "        };\n",
       "    }\n",
       "\n",
       "    canvas_div.addEventListener(\n",
       "        'keydown',\n",
       "        on_keyboard_event_closure('key_press')\n",
       "    );\n",
       "    canvas_div.addEventListener(\n",
       "        'keyup',\n",
       "        on_keyboard_event_closure('key_release')\n",
       "    );\n",
       "\n",
       "    this._canvas_extra_style(canvas_div);\n",
       "    this.root.appendChild(canvas_div);\n",
       "\n",
       "    var canvas = (this.canvas = document.createElement('canvas'));\n",
       "    canvas.classList.add('mpl-canvas');\n",
       "    canvas.setAttribute('style', 'box-sizing: content-box;');\n",
       "\n",
       "    this.context = canvas.getContext('2d');\n",
       "\n",
       "    var backingStore =\n",
       "        this.context.backingStorePixelRatio ||\n",
       "        this.context.webkitBackingStorePixelRatio ||\n",
       "        this.context.mozBackingStorePixelRatio ||\n",
       "        this.context.msBackingStorePixelRatio ||\n",
       "        this.context.oBackingStorePixelRatio ||\n",
       "        this.context.backingStorePixelRatio ||\n",
       "        1;\n",
       "\n",
       "    this.ratio = (window.devicePixelRatio || 1) / backingStore;\n",
       "\n",
       "    var rubberband_canvas = (this.rubberband_canvas = document.createElement(\n",
       "        'canvas'\n",
       "    ));\n",
       "    rubberband_canvas.setAttribute(\n",
       "        'style',\n",
       "        'box-sizing: content-box; position: absolute; left: 0; top: 0; z-index: 1;'\n",
       "    );\n",
       "\n",
       "    // Apply a ponyfill if ResizeObserver is not implemented by browser.\n",
       "    if (this.ResizeObserver === undefined) {\n",
       "        if (window.ResizeObserver !== undefined) {\n",
       "            this.ResizeObserver = window.ResizeObserver;\n",
       "        } else {\n",
       "            var obs = _JSXTOOLS_RESIZE_OBSERVER({});\n",
       "            this.ResizeObserver = obs.ResizeObserver;\n",
       "        }\n",
       "    }\n",
       "\n",
       "    this.resizeObserverInstance = new this.ResizeObserver(function (entries) {\n",
       "        var nentries = entries.length;\n",
       "        for (var i = 0; i < nentries; i++) {\n",
       "            var entry = entries[i];\n",
       "            var width, height;\n",
       "            if (entry.contentBoxSize) {\n",
       "                if (entry.contentBoxSize instanceof Array) {\n",
       "                    // Chrome 84 implements new version of spec.\n",
       "                    width = entry.contentBoxSize[0].inlineSize;\n",
       "                    height = entry.contentBoxSize[0].blockSize;\n",
       "                } else {\n",
       "                    // Firefox implements old version of spec.\n",
       "                    width = entry.contentBoxSize.inlineSize;\n",
       "                    height = entry.contentBoxSize.blockSize;\n",
       "                }\n",
       "            } else {\n",
       "                // Chrome <84 implements even older version of spec.\n",
       "                width = entry.contentRect.width;\n",
       "                height = entry.contentRect.height;\n",
       "            }\n",
       "\n",
       "            // Keep the size of the canvas and rubber band canvas in sync with\n",
       "            // the canvas container.\n",
       "            if (entry.devicePixelContentBoxSize) {\n",
       "                // Chrome 84 implements new version of spec.\n",
       "                canvas.setAttribute(\n",
       "                    'width',\n",
       "                    entry.devicePixelContentBoxSize[0].inlineSize\n",
       "                );\n",
       "                canvas.setAttribute(\n",
       "                    'height',\n",
       "                    entry.devicePixelContentBoxSize[0].blockSize\n",
       "                );\n",
       "            } else {\n",
       "                canvas.setAttribute('width', width * fig.ratio);\n",
       "                canvas.setAttribute('height', height * fig.ratio);\n",
       "            }\n",
       "            canvas.setAttribute(\n",
       "                'style',\n",
       "                'width: ' + width + 'px; height: ' + height + 'px;'\n",
       "            );\n",
       "\n",
       "            rubberband_canvas.setAttribute('width', width);\n",
       "            rubberband_canvas.setAttribute('height', height);\n",
       "\n",
       "            // And update the size in Python. We ignore the initial 0/0 size\n",
       "            // that occurs as the element is placed into the DOM, which should\n",
       "            // otherwise not happen due to the minimum size styling.\n",
       "            if (fig.ws.readyState == 1 && width != 0 && height != 0) {\n",
       "                fig.request_resize(width, height);\n",
       "            }\n",
       "        }\n",
       "    });\n",
       "    this.resizeObserverInstance.observe(canvas_div);\n",
       "\n",
       "    function on_mouse_event_closure(name) {\n",
       "        return function (event) {\n",
       "            return fig.mouse_event(event, name);\n",
       "        };\n",
       "    }\n",
       "\n",
       "    rubberband_canvas.addEventListener(\n",
       "        'mousedown',\n",
       "        on_mouse_event_closure('button_press')\n",
       "    );\n",
       "    rubberband_canvas.addEventListener(\n",
       "        'mouseup',\n",
       "        on_mouse_event_closure('button_release')\n",
       "    );\n",
       "    rubberband_canvas.addEventListener(\n",
       "        'dblclick',\n",
       "        on_mouse_event_closure('dblclick')\n",
       "    );\n",
       "    // Throttle sequential mouse events to 1 every 20ms.\n",
       "    rubberband_canvas.addEventListener(\n",
       "        'mousemove',\n",
       "        on_mouse_event_closure('motion_notify')\n",
       "    );\n",
       "\n",
       "    rubberband_canvas.addEventListener(\n",
       "        'mouseenter',\n",
       "        on_mouse_event_closure('figure_enter')\n",
       "    );\n",
       "    rubberband_canvas.addEventListener(\n",
       "        'mouseleave',\n",
       "        on_mouse_event_closure('figure_leave')\n",
       "    );\n",
       "\n",
       "    canvas_div.addEventListener('wheel', function (event) {\n",
       "        if (event.deltaY < 0) {\n",
       "            event.step = 1;\n",
       "        } else {\n",
       "            event.step = -1;\n",
       "        }\n",
       "        on_mouse_event_closure('scroll')(event);\n",
       "    });\n",
       "\n",
       "    canvas_div.appendChild(canvas);\n",
       "    canvas_div.appendChild(rubberband_canvas);\n",
       "\n",
       "    this.rubberband_context = rubberband_canvas.getContext('2d');\n",
       "    this.rubberband_context.strokeStyle = '#000000';\n",
       "\n",
       "    this._resize_canvas = function (width, height, forward) {\n",
       "        if (forward) {\n",
       "            canvas_div.style.width = width + 'px';\n",
       "            canvas_div.style.height = height + 'px';\n",
       "        }\n",
       "    };\n",
       "\n",
       "    // Disable right mouse context menu.\n",
       "    this.rubberband_canvas.addEventListener('contextmenu', function (_e) {\n",
       "        event.preventDefault();\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 toolbar = document.createElement('div');\n",
       "    toolbar.classList = 'mpl-toolbar';\n",
       "    this.root.appendChild(toolbar);\n",
       "\n",
       "    function on_click_closure(name) {\n",
       "        return function (_event) {\n",
       "            return fig.toolbar_button_onclick(name);\n",
       "        };\n",
       "    }\n",
       "\n",
       "    function on_mouseover_closure(tooltip) {\n",
       "        return function (event) {\n",
       "            if (!event.currentTarget.disabled) {\n",
       "                return fig.toolbar_button_onmouseover(tooltip);\n",
       "            }\n",
       "        };\n",
       "    }\n",
       "\n",
       "    fig.buttons = {};\n",
       "    var buttonGroup = document.createElement('div');\n",
       "    buttonGroup.classList = 'mpl-button-group';\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",
       "            /* Instead of a spacer, we start a new button group. */\n",
       "            if (buttonGroup.hasChildNodes()) {\n",
       "                toolbar.appendChild(buttonGroup);\n",
       "            }\n",
       "            buttonGroup = document.createElement('div');\n",
       "            buttonGroup.classList = 'mpl-button-group';\n",
       "            continue;\n",
       "        }\n",
       "\n",
       "        var button = (fig.buttons[name] = document.createElement('button'));\n",
       "        button.classList = 'mpl-widget';\n",
       "        button.setAttribute('role', 'button');\n",
       "        button.setAttribute('aria-disabled', 'false');\n",
       "        button.addEventListener('click', on_click_closure(method_name));\n",
       "        button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n",
       "\n",
       "        var icon_img = document.createElement('img');\n",
       "        icon_img.src = '_images/' + image + '.png';\n",
       "        icon_img.srcset = '_images/' + image + '_large.png 2x';\n",
       "        icon_img.alt = tooltip;\n",
       "        button.appendChild(icon_img);\n",
       "\n",
       "        buttonGroup.appendChild(button);\n",
       "    }\n",
       "\n",
       "    if (buttonGroup.hasChildNodes()) {\n",
       "        toolbar.appendChild(buttonGroup);\n",
       "    }\n",
       "\n",
       "    var fmt_picker = document.createElement('select');\n",
       "    fmt_picker.classList = 'mpl-widget';\n",
       "    toolbar.appendChild(fmt_picker);\n",
       "    this.format_dropdown = fmt_picker;\n",
       "\n",
       "    for (var ind in mpl.extensions) {\n",
       "        var fmt = mpl.extensions[ind];\n",
       "        var option = document.createElement('option');\n",
       "        option.selected = fmt === mpl.default_extension;\n",
       "        option.innerHTML = fmt;\n",
       "        fmt_picker.appendChild(option);\n",
       "    }\n",
       "\n",
       "    var status_bar = document.createElement('span');\n",
       "    status_bar.classList = 'mpl-message';\n",
       "    toolbar.appendChild(status_bar);\n",
       "    this.message = status_bar;\n",
       "};\n",
       "\n",
       "mpl.figure.prototype.request_resize = function (x_pixels, y_pixels) {\n",
       "    // Request matplotlib to resize the figure. Matplotlib will then trigger a resize in the client,\n",
       "    // which will in turn request a refresh of the image.\n",
       "    this.send_message('resize', { width: x_pixels, height: y_pixels });\n",
       "};\n",
       "\n",
       "mpl.figure.prototype.send_message = function (type, properties) {\n",
       "    properties['type'] = type;\n",
       "    properties['figure_id'] = this.id;\n",
       "    this.ws.send(JSON.stringify(properties));\n",
       "};\n",
       "\n",
       "mpl.figure.prototype.send_draw_message = function () {\n",
       "    if (!this.waiting) {\n",
       "        this.waiting = true;\n",
       "        this.ws.send(JSON.stringify({ type: 'draw', figure_id: this.id }));\n",
       "    }\n",
       "};\n",
       "\n",
       "mpl.figure.prototype.handle_save = function (fig, _msg) {\n",
       "    var format_dropdown = fig.format_dropdown;\n",
       "    var format = format_dropdown.options[format_dropdown.selectedIndex].value;\n",
       "    fig.ondownload(fig, format);\n",
       "};\n",
       "\n",
       "mpl.figure.prototype.handle_resize = function (fig, msg) {\n",
       "    var size = msg['size'];\n",
       "    if (size[0] !== fig.canvas.width || size[1] !== fig.canvas.height) {\n",
       "        fig._resize_canvas(size[0], size[1], msg['forward']);\n",
       "        fig.send_message('refresh', {});\n",
       "    }\n",
       "};\n",
       "\n",
       "mpl.figure.prototype.handle_rubberband = function (fig, msg) {\n",
       "    var x0 = msg['x0'] / fig.ratio;\n",
       "    var y0 = (fig.canvas.height - msg['y0']) / fig.ratio;\n",
       "    var x1 = msg['x1'] / fig.ratio;\n",
       "    var y1 = (fig.canvas.height - msg['y1']) / fig.ratio;\n",
       "    x0 = Math.floor(x0) + 0.5;\n",
       "    y0 = Math.floor(y0) + 0.5;\n",
       "    x1 = Math.floor(x1) + 0.5;\n",
       "    y1 = Math.floor(y1) + 0.5;\n",
       "    var min_x = Math.min(x0, x1);\n",
       "    var min_y = Math.min(y0, y1);\n",
       "    var width = Math.abs(x1 - x0);\n",
       "    var height = Math.abs(y1 - y0);\n",
       "\n",
       "    fig.rubberband_context.clearRect(\n",
       "        0,\n",
       "        0,\n",
       "        fig.canvas.width / fig.ratio,\n",
       "        fig.canvas.height / fig.ratio\n",
       "    );\n",
       "\n",
       "    fig.rubberband_context.strokeRect(min_x, min_y, width, height);\n",
       "};\n",
       "\n",
       "mpl.figure.prototype.handle_figure_label = function (fig, msg) {\n",
       "    // Updates the figure title.\n",
       "    fig.header.textContent = msg['label'];\n",
       "};\n",
       "\n",
       "mpl.figure.prototype.handle_cursor = function (fig, msg) {\n",
       "    var cursor = msg['cursor'];\n",
       "    switch (cursor) {\n",
       "        case 0:\n",
       "            cursor = 'pointer';\n",
       "            break;\n",
       "        case 1:\n",
       "            cursor = 'default';\n",
       "            break;\n",
       "        case 2:\n",
       "            cursor = 'crosshair';\n",
       "            break;\n",
       "        case 3:\n",
       "            cursor = 'move';\n",
       "            break;\n",
       "    }\n",
       "    fig.rubberband_canvas.style.cursor = cursor;\n",
       "};\n",
       "\n",
       "mpl.figure.prototype.handle_message = function (fig, msg) {\n",
       "    fig.message.textContent = msg['message'];\n",
       "};\n",
       "\n",
       "mpl.figure.prototype.handle_draw = function (fig, _msg) {\n",
       "    // Request the server to send over a new figure.\n",
       "    fig.send_draw_message();\n",
       "};\n",
       "\n",
       "mpl.figure.prototype.handle_image_mode = function (fig, msg) {\n",
       "    fig.image_mode = msg['mode'];\n",
       "};\n",
       "\n",
       "mpl.figure.prototype.handle_history_buttons = function (fig, msg) {\n",
       "    for (var key in msg) {\n",
       "        if (!(key in fig.buttons)) {\n",
       "            continue;\n",
       "        }\n",
       "        fig.buttons[key].disabled = !msg[key];\n",
       "        fig.buttons[key].setAttribute('aria-disabled', !msg[key]);\n",
       "    }\n",
       "};\n",
       "\n",
       "mpl.figure.prototype.handle_navigate_mode = function (fig, msg) {\n",
       "    if (msg['mode'] === 'PAN') {\n",
       "        fig.buttons['Pan'].classList.add('active');\n",
       "        fig.buttons['Zoom'].classList.remove('active');\n",
       "    } else if (msg['mode'] === 'ZOOM') {\n",
       "        fig.buttons['Pan'].classList.remove('active');\n",
       "        fig.buttons['Zoom'].classList.add('active');\n",
       "    } else {\n",
       "        fig.buttons['Pan'].classList.remove('active');\n",
       "        fig.buttons['Zoom'].classList.remove('active');\n",
       "    }\n",
       "};\n",
       "\n",
       "mpl.figure.prototype.updated_canvas_event = function () {\n",
       "    // Called whenever the canvas gets updated.\n",
       "    this.send_message('ack', {});\n",
       "};\n",
       "\n",
       "// A function to construct a web socket function for onmessage handling.\n",
       "// Called in the figure constructor.\n",
       "mpl.figure.prototype._make_on_message_function = function (fig) {\n",
       "    return function socket_on_message(evt) {\n",
       "        if (evt.data instanceof Blob) {\n",
       "            var img = evt.data;\n",
       "            if (img.type !== 'image/png') {\n",
       "                /* FIXME: We get \"Resource interpreted as Image but\n",
       "                 * transferred with MIME type text/plain:\" errors on\n",
       "                 * Chrome.  But how to set the MIME type?  It doesn't seem\n",
       "                 * to be part of the websocket stream */\n",
       "                img.type = 'image/png';\n",
       "            }\n",
       "\n",
       "            /* Free the memory for the previous frames */\n",
       "            if (fig.imageObj.src) {\n",
       "                (window.URL || window.webkitURL).revokeObjectURL(\n",
       "                    fig.imageObj.src\n",
       "                );\n",
       "            }\n",
       "\n",
       "            fig.imageObj.src = (window.URL || window.webkitURL).createObjectURL(\n",
       "                img\n",
       "            );\n",
       "            fig.updated_canvas_event();\n",
       "            fig.waiting = false;\n",
       "            return;\n",
       "        } else if (\n",
       "            typeof evt.data === 'string' &&\n",
       "            evt.data.slice(0, 21) === 'data:image/png;base64'\n",
       "        ) {\n",
       "            fig.imageObj.src = evt.data;\n",
       "            fig.updated_canvas_event();\n",
       "            fig.waiting = false;\n",
       "            return;\n",
       "        }\n",
       "\n",
       "        var msg = JSON.parse(evt.data);\n",
       "        var msg_type = msg['type'];\n",
       "\n",
       "        // Call the  \"handle_{type}\" callback, which takes\n",
       "        // the figure and JSON message as its only arguments.\n",
       "        try {\n",
       "            var callback = fig['handle_' + msg_type];\n",
       "        } catch (e) {\n",
       "            console.log(\n",
       "                \"No handler for the '\" + msg_type + \"' message type: \",\n",
       "                msg\n",
       "            );\n",
       "            return;\n",
       "        }\n",
       "\n",
       "        if (callback) {\n",
       "            try {\n",
       "                // console.log(\"Handling '\" + msg_type + \"' message: \", msg);\n",
       "                callback(fig, msg);\n",
       "            } catch (e) {\n",
       "                console.log(\n",
       "                    \"Exception inside the 'handler_\" + msg_type + \"' callback:\",\n",
       "                    e,\n",
       "                    e.stack,\n",
       "                    msg\n",
       "                );\n",
       "            }\n",
       "        }\n",
       "    };\n",
       "};\n",
       "\n",
       "// from http://stackoverflow.com/questions/1114465/getting-mouse-location-in-canvas\n",
       "mpl.findpos = function (e) {\n",
       "    //this section is from http://www.quirksmode.org/js/events_properties.html\n",
       "    var targ;\n",
       "    if (!e) {\n",
       "        e = window.event;\n",
       "    }\n",
       "    if (e.target) {\n",
       "        targ = e.target;\n",
       "    } else if (e.srcElement) {\n",
       "        targ = e.srcElement;\n",
       "    }\n",
       "    if (targ.nodeType === 3) {\n",
       "        // defeat Safari bug\n",
       "        targ = targ.parentNode;\n",
       "    }\n",
       "\n",
       "    // pageX,Y are the mouse positions relative to the document\n",
       "    var boundingRect = targ.getBoundingClientRect();\n",
       "    var x = e.pageX - (boundingRect.left + document.body.scrollLeft);\n",
       "    var y = e.pageY - (boundingRect.top + document.body.scrollTop);\n",
       "\n",
       "    return { x: x, y: y };\n",
       "};\n",
       "\n",
       "/*\n",
       " * return a copy of an object with only non-object keys\n",
       " * we need this to avoid circular references\n",
       " * http://stackoverflow.com/a/24161582/3208463\n",
       " */\n",
       "function simpleKeys(original) {\n",
       "    return Object.keys(original).reduce(function (obj, key) {\n",
       "        if (typeof original[key] !== 'object') {\n",
       "            obj[key] = original[key];\n",
       "        }\n",
       "        return obj;\n",
       "    }, {});\n",
       "}\n",
       "\n",
       "mpl.figure.prototype.mouse_event = function (event, name) {\n",
       "    var canvas_pos = mpl.findpos(event);\n",
       "\n",
       "    if (name === 'button_press') {\n",
       "        this.canvas.focus();\n",
       "        this.canvas_div.focus();\n",
       "    }\n",
       "\n",
       "    var x = canvas_pos.x * this.ratio;\n",
       "    var y = canvas_pos.y * this.ratio;\n",
       "\n",
       "    this.send_message(name, {\n",
       "        x: x,\n",
       "        y: y,\n",
       "        button: event.button,\n",
       "        step: event.step,\n",
       "        guiEvent: simpleKeys(event),\n",
       "    });\n",
       "\n",
       "    /* This prevents the web browser from automatically changing to\n",
       "     * the text insertion cursor when the button is pressed.  We want\n",
       "     * to control all of the cursor setting manually through the\n",
       "     * 'cursor' event from matplotlib */\n",
       "    event.preventDefault();\n",
       "    return false;\n",
       "};\n",
       "\n",
       "mpl.figure.prototype._key_event_extra = function (_event, _name) {\n",
       "    // Handle any extra behaviour associated with a key event\n",
       "};\n",
       "\n",
       "mpl.figure.prototype.key_event = function (event, name) {\n",
       "    // Prevent repeat events\n",
       "    if (name === 'key_press') {\n",
       "        if (event.key === this._key) {\n",
       "            return;\n",
       "        } else {\n",
       "            this._key = event.key;\n",
       "        }\n",
       "    }\n",
       "    if (name === 'key_release') {\n",
       "        this._key = null;\n",
       "    }\n",
       "\n",
       "    var value = '';\n",
       "    if (event.ctrlKey && event.key !== 'Control') {\n",
       "        value += 'ctrl+';\n",
       "    }\n",
       "    else if (event.altKey && event.key !== 'Alt') {\n",
       "        value += 'alt+';\n",
       "    }\n",
       "    else if (event.shiftKey && event.key !== 'Shift') {\n",
       "        value += 'shift+';\n",
       "    }\n",
       "\n",
       "    value += 'k' + event.key;\n",
       "\n",
       "    this._key_event_extra(event, name);\n",
       "\n",
       "    this.send_message(name, { key: value, guiEvent: simpleKeys(event) });\n",
       "    return false;\n",
       "};\n",
       "\n",
       "mpl.figure.prototype.toolbar_button_onclick = function (name) {\n",
       "    if (name === 'download') {\n",
       "        this.handle_save(this, null);\n",
       "    } else {\n",
       "        this.send_message('toolbar_button', { name: name });\n",
       "    }\n",
       "};\n",
       "\n",
       "mpl.figure.prototype.toolbar_button_onmouseover = function (tooltip) {\n",
       "    this.message.textContent = tooltip;\n",
       "};\n",
       "\n",
       "///////////////// REMAINING CONTENT GENERATED BY embed_js.py /////////////////\n",
       "// prettier-ignore\n",
       "var _JSXTOOLS_RESIZE_OBSERVER=function(A){var t,i=new WeakMap,n=new WeakMap,a=new WeakMap,r=new WeakMap,o=new Set;function s(e){if(!(this instanceof s))throw new TypeError(\"Constructor requires 'new' operator\");i.set(this,e)}function h(){throw new TypeError(\"Function is not a constructor\")}function c(e,t,i,n){e=0 in arguments?Number(arguments[0]):0,t=1 in arguments?Number(arguments[1]):0,i=2 in arguments?Number(arguments[2]):0,n=3 in arguments?Number(arguments[3]):0,this.right=(this.x=this.left=e)+(this.width=i),this.bottom=(this.y=this.top=t)+(this.height=n),Object.freeze(this)}function d(){t=requestAnimationFrame(d);var s=new WeakMap,p=new Set;o.forEach((function(t){r.get(t).forEach((function(i){var r=t instanceof window.SVGElement,o=a.get(t),d=r?0:parseFloat(o.paddingTop),f=r?0:parseFloat(o.paddingRight),l=r?0:parseFloat(o.paddingBottom),u=r?0:parseFloat(o.paddingLeft),g=r?0:parseFloat(o.borderTopWidth),m=r?0:parseFloat(o.borderRightWidth),w=r?0:parseFloat(o.borderBottomWidth),b=u+f,F=d+l,v=(r?0:parseFloat(o.borderLeftWidth))+m,W=g+w,y=r?0:t.offsetHeight-W-t.clientHeight,E=r?0:t.offsetWidth-v-t.clientWidth,R=b+v,z=F+W,M=r?t.width:parseFloat(o.width)-R-E,O=r?t.height:parseFloat(o.height)-z-y;if(n.has(t)){var k=n.get(t);if(k[0]===M&&k[1]===O)return}n.set(t,[M,O]);var S=Object.create(h.prototype);S.target=t,S.contentRect=new c(u,d,M,O),s.has(i)||(s.set(i,[]),p.add(i)),s.get(i).push(S)}))})),p.forEach((function(e){i.get(e).call(e,s.get(e),e)}))}return s.prototype.observe=function(i){if(i instanceof window.Element){r.has(i)||(r.set(i,new Set),o.add(i),a.set(i,window.getComputedStyle(i)));var n=r.get(i);n.has(this)||n.add(this),cancelAnimationFrame(t),t=requestAnimationFrame(d)}},s.prototype.unobserve=function(i){if(i instanceof window.Element&&r.has(i)){var n=r.get(i);n.has(this)&&(n.delete(this),n.size||(r.delete(i),o.delete(i))),n.size||r.delete(i),o.size||cancelAnimationFrame(t)}},A.DOMRectReadOnly=c,A.ResizeObserver=s,A.ResizeObserverEntry=h,A}; // eslint-disable-line\n",
       "mpl.toolbar_items = [[\"Home\", \"Reset original view\", \"fa fa-home icon-home\", \"home\"], [\"Back\", \"Back to previous view\", \"fa fa-arrow-left icon-arrow-left\", \"back\"], [\"Forward\", \"Forward to next view\", \"fa fa-arrow-right icon-arrow-right\", \"forward\"], [\"\", \"\", \"\", \"\"], [\"Pan\", \"Left button pans, Right button zooms\\nx/y fixes axis, CTRL fixes aspect\", \"fa fa-arrows icon-move\", \"pan\"], [\"Zoom\", \"Zoom to rectangle\\nx/y fixes axis, CTRL fixes aspect\", \"fa fa-square-o icon-check-empty\", \"zoom\"], [\"\", \"\", \"\", \"\"], [\"Download\", \"Download plot\", \"fa fa-floppy-o icon-save\", \"download\"]];\n",
       "\n",
       "mpl.extensions = [\"eps\", \"jpeg\", \"pgf\", \"pdf\", \"png\", \"ps\", \"raw\", \"svg\", \"tif\"];\n",
       "\n",
       "mpl.default_extension = \"png\";/* global mpl */\n",
       "\n",
       "var comm_websocket_adapter = function (comm) {\n",
       "    // Create a \"websocket\"-like object which calls the given IPython comm\n",
       "    // object with the appropriate methods. Currently this is a non binary\n",
       "    // socket, so there is still some room for performance tuning.\n",
       "    var ws = {};\n",
       "\n",
       "    ws.binaryType = comm.kernel.ws.binaryType;\n",
       "    ws.readyState = comm.kernel.ws.readyState;\n",
       "    function updateReadyState(_event) {\n",
       "        if (comm.kernel.ws) {\n",
       "            ws.readyState = comm.kernel.ws.readyState;\n",
       "        } else {\n",
       "            ws.readyState = 3; // Closed state.\n",
       "        }\n",
       "    }\n",
       "    comm.kernel.ws.addEventListener('open', updateReadyState);\n",
       "    comm.kernel.ws.addEventListener('close', updateReadyState);\n",
       "    comm.kernel.ws.addEventListener('error', updateReadyState);\n",
       "\n",
       "    ws.close = function () {\n",
       "        comm.close();\n",
       "    };\n",
       "    ws.send = function (m) {\n",
       "        //console.log('sending', m);\n",
       "        comm.send(m);\n",
       "    };\n",
       "    // Register the callback with on_msg.\n",
       "    comm.on_msg(function (msg) {\n",
       "        //console.log('receiving', msg['content']['data'], msg);\n",
       "        var data = msg['content']['data'];\n",
       "        if (data['blob'] !== undefined) {\n",
       "            data = {\n",
       "                data: new Blob(msg['buffers'], { type: data['blob'] }),\n",
       "            };\n",
       "        }\n",
       "        // Pass the mpl event to the overridden (by mpl) onmessage function.\n",
       "        ws.onmessage(data);\n",
       "    });\n",
       "    return ws;\n",
       "};\n",
       "\n",
       "mpl.mpl_figure_comm = function (comm, msg) {\n",
       "    // This is the function which gets called when the mpl process\n",
       "    // starts-up an IPython Comm through the \"matplotlib\" channel.\n",
       "\n",
       "    var id = msg.content.data.id;\n",
       "    // Get hold of the div created by the display call when the Comm\n",
       "    // socket was opened in Python.\n",
       "    var element = document.getElementById(id);\n",
       "    var ws_proxy = comm_websocket_adapter(comm);\n",
       "\n",
       "    function ondownload(figure, _format) {\n",
       "        window.open(figure.canvas.toDataURL());\n",
       "    }\n",
       "\n",
       "    var fig = new mpl.figure(id, ws_proxy, ondownload, element);\n",
       "\n",
       "    // Call onopen now - mpl needs it, as it is assuming we've passed it a real\n",
       "    // web socket which is closed, not our websocket->open comm proxy.\n",
       "    ws_proxy.onopen();\n",
       "\n",
       "    fig.parent_element = element;\n",
       "    fig.cell_info = mpl.find_output_cell(\"<div id='\" + id + \"'></div>\");\n",
       "    if (!fig.cell_info) {\n",
       "        console.error('Failed to find cell for figure', id, fig);\n",
       "        return;\n",
       "    }\n",
       "    fig.cell_info[0].output_area.element.on(\n",
       "        'cleared',\n",
       "        { fig: fig },\n",
       "        fig._remove_fig_handler\n",
       "    );\n",
       "};\n",
       "\n",
       "mpl.figure.prototype.handle_close = function (fig, msg) {\n",
       "    var width = fig.canvas.width / fig.ratio;\n",
       "    fig.cell_info[0].output_area.element.off(\n",
       "        'cleared',\n",
       "        fig._remove_fig_handler\n",
       "    );\n",
       "    fig.resizeObserverInstance.unobserve(fig.canvas_div);\n",
       "\n",
       "    // Update the output cell to use the data from the current canvas.\n",
       "    fig.push_to_output();\n",
       "    var dataURL = fig.canvas.toDataURL();\n",
       "    // Re-enable the keyboard manager in IPython - without this line, in FF,\n",
       "    // the notebook keyboard shortcuts fail.\n",
       "    IPython.keyboard_manager.enable();\n",
       "    fig.parent_element.innerHTML =\n",
       "        '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n",
       "    fig.close_ws(fig, msg);\n",
       "};\n",
       "\n",
       "mpl.figure.prototype.close_ws = function (fig, msg) {\n",
       "    fig.send_message('closing', msg);\n",
       "    // fig.ws.close()\n",
       "};\n",
       "\n",
       "mpl.figure.prototype.push_to_output = function (_remove_interactive) {\n",
       "    // Turn the data on the canvas into data in the output cell.\n",
       "    var width = this.canvas.width / this.ratio;\n",
       "    var dataURL = this.canvas.toDataURL();\n",
       "    this.cell_info[1]['text/html'] =\n",
       "        '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n",
       "};\n",
       "\n",
       "mpl.figure.prototype.updated_canvas_event = function () {\n",
       "    // Tell IPython that the notebook contents must change.\n",
       "    IPython.notebook.set_dirty(true);\n",
       "    this.send_message('ack', {});\n",
       "    var fig = this;\n",
       "    // Wait a second, then push the new image to the DOM so\n",
       "    // that it is saved nicely (might be nice to debounce this).\n",
       "    setTimeout(function () {\n",
       "        fig.push_to_output();\n",
       "    }, 1000);\n",
       "};\n",
       "\n",
       "mpl.figure.prototype._init_toolbar = function () {\n",
       "    var fig = this;\n",
       "\n",
       "    var toolbar = document.createElement('div');\n",
       "    toolbar.classList = 'btn-toolbar';\n",
       "    this.root.appendChild(toolbar);\n",
       "\n",
       "    function on_click_closure(name) {\n",
       "        return function (_event) {\n",
       "            return fig.toolbar_button_onclick(name);\n",
       "        };\n",
       "    }\n",
       "\n",
       "    function on_mouseover_closure(tooltip) {\n",
       "        return function (event) {\n",
       "            if (!event.currentTarget.disabled) {\n",
       "                return fig.toolbar_button_onmouseover(tooltip);\n",
       "            }\n",
       "        };\n",
       "    }\n",
       "\n",
       "    fig.buttons = {};\n",
       "    var buttonGroup = document.createElement('div');\n",
       "    buttonGroup.classList = 'btn-group';\n",
       "    var button;\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",
       "            /* Instead of a spacer, we start a new button group. */\n",
       "            if (buttonGroup.hasChildNodes()) {\n",
       "                toolbar.appendChild(buttonGroup);\n",
       "            }\n",
       "            buttonGroup = document.createElement('div');\n",
       "            buttonGroup.classList = 'btn-group';\n",
       "            continue;\n",
       "        }\n",
       "\n",
       "        button = fig.buttons[name] = document.createElement('button');\n",
       "        button.classList = 'btn btn-default';\n",
       "        button.href = '#';\n",
       "        button.title = name;\n",
       "        button.innerHTML = '<i class=\"fa ' + image + ' fa-lg\"></i>';\n",
       "        button.addEventListener('click', on_click_closure(method_name));\n",
       "        button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n",
       "        buttonGroup.appendChild(button);\n",
       "    }\n",
       "\n",
       "    if (buttonGroup.hasChildNodes()) {\n",
       "        toolbar.appendChild(buttonGroup);\n",
       "    }\n",
       "\n",
       "    // Add the status bar.\n",
       "    var status_bar = document.createElement('span');\n",
       "    status_bar.classList = 'mpl-message pull-right';\n",
       "    toolbar.appendChild(status_bar);\n",
       "    this.message = status_bar;\n",
       "\n",
       "    // Add the close button to the window.\n",
       "    var buttongrp = document.createElement('div');\n",
       "    buttongrp.classList = 'btn-group inline pull-right';\n",
       "    button = document.createElement('button');\n",
       "    button.classList = 'btn btn-mini btn-primary';\n",
       "    button.href = '#';\n",
       "    button.title = 'Stop Interaction';\n",
       "    button.innerHTML = '<i class=\"fa fa-power-off icon-remove icon-large\"></i>';\n",
       "    button.addEventListener('click', function (_evt) {\n",
       "        fig.handle_close(fig, {});\n",
       "    });\n",
       "    button.addEventListener(\n",
       "        'mouseover',\n",
       "        on_mouseover_closure('Stop Interaction')\n",
       "    );\n",
       "    buttongrp.appendChild(button);\n",
       "    var titlebar = this.root.querySelector('.ui-dialog-titlebar');\n",
       "    titlebar.insertBefore(buttongrp, titlebar.firstChild);\n",
       "};\n",
       "\n",
       "mpl.figure.prototype._remove_fig_handler = function (event) {\n",
       "    var fig = event.data.fig;\n",
       "    if (event.target !== this) {\n",
       "        // Ignore bubbled events from children.\n",
       "        return;\n",
       "    }\n",
       "    fig.close_ws(fig, {});\n",
       "};\n",
       "\n",
       "mpl.figure.prototype._root_extra_style = function (el) {\n",
       "    el.style.boxSizing = 'content-box'; // override notebook setting of border-box.\n",
       "};\n",
       "\n",
       "mpl.figure.prototype._canvas_extra_style = function (el) {\n",
       "    // this is important to make the div 'focusable\n",
       "    el.setAttribute('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",
       "    } else {\n",
       "        // location in version 2\n",
       "        IPython.keyboard_manager.register_events(el);\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",
       "\n",
       "    // Check for shift+enter\n",
       "    if (event.shiftKey && event.which === 13) {\n",
       "        this.canvas_div.blur();\n",
       "        // select the cell after this one\n",
       "        var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n",
       "        IPython.notebook.select(index + 1);\n",
       "    }\n",
       "};\n",
       "\n",
       "mpl.figure.prototype.handle_save = function (fig, _msg) {\n",
       "    fig.ondownload(fig, null);\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 < ncells; i++) {\n",
       "        var cell = cells[i];\n",
       "        if (cell.cell_type === 'code') {\n",
       "            for (var j = 0; j < cell.output_area.outputs.length; j++) {\n",
       "                var data = cell.output_area.outputs[j];\n",
       "                if (data.data) {\n",
       "                    // IPython >= 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(\n",
       "        'matplotlib',\n",
       "        mpl.mpl_figure_comm\n",
       "    );\n",
       "}\n"
      ],
      "text/plain": [
       "<IPython.core.display.Javascript object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<div id='ebb6a5fb-d213-4a3f-af4f-9e0b36f8273b'></div>"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Kinetic energy distribution check (strict)\n",
      "Kolmogorov-Smirnov test result: p = 0.898369\n",
      "Null hypothesis: Kinetic energy is Maxwell-Boltzmann distributed\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "0.89836894520092"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "physical_validation.kinetic_energy.distribution(\n",
    "    data=simulation_data_vrescale, strict=True, screen=True\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "5ae87bc8",
   "metadata": {},
   "source": [
    "The `strict` test prints and returns a p-value which indicates that the null hypothesis stands with high confidence. The printed figure confirms that the sampled and the analytical distribution are very similar."
   ]
  },
  {
   "cell_type": "markdown",
   "id": "f4ad4389",
   "metadata": {},
   "source": [
    "The non-strict test confirms this result:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "291acdc0",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "After equilibration, decorrelation and tail pruning, 96.02% (4802 frames) of original Kinetic energy remain.\n",
      "Kinetic energy distribution check (non-strict)\n",
      "Analytical distribution (T=298.15 K):\n",
      " * mu: 6689.47 kJ/mol\n",
      " * sigma: 128.77 kJ/mol\n",
      "Trajectory:\n",
      " * mu: 6688.12 +- 1.88 kJ/mol\n",
      "   T(mu) = 298.09 +- 0.08 K\n",
      " * sigma: 128.70 +- 1.35 kJ/mol\n",
      "   T(sigma) = 297.98 +- 3.14 K\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "(0.714917087637526, 0.053451278986070015)"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# We turn plotting off here (`screen=False`), because the plot is \n",
    "# identical to the one in the strict test\n",
    "physical_validation.kinetic_energy.distribution(\n",
    "    data=simulation_data_vrescale, strict=False, screen=False\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "0c4fddc2",
   "metadata": {},
   "source": [
    "The non-strict test calculates the temperature of the mean and the width of the distribution. Analytically, we are expecting both to be close to 298.15K. The result confirms that the simulation behaves as expected, with both the calculated mean and variance being within one standard deviation of the analytical value. The returned tuple is the number of standard deviations the calculated mean and variance differ from the expected value - less than a standard deviations for the mean, and only about 0.05 standard deviations for the variance. Note that any deviation within about 2-3 standard deviations is usually considered as statistically insignificant.\n",
    "\n",
    "Also note that the error estimates were computed using bootstrapping and are hence a probabilistic quantity which will slightly differ when repeating the analysis."
   ]
  },
  {
   "cell_type": "markdown",
   "id": "a20305f8",
   "metadata": {},
   "source": [
    "We can now compare this to the Berendsen temperature coupling, using first\n",
    "the strict, then the non-strict kinetic energy distribution check."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "56ac1572",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "After equilibration, decorrelation and tail pruning, 95.96% (4799 frames) of original Kinetic energy remain.\n"
     ]
    },
    {
     "data": {
      "application/javascript": [
       "/* Put everything inside the global mpl namespace */\n",
       "/* global mpl */\n",
       "window.mpl = {};\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(\n",
       "            '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",
       "\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 = document.createElement('div');\n",
       "    this.root.setAttribute('style', 'display: inline-block');\n",
       "    this._root_extra_style(this.root);\n",
       "\n",
       "    parent_element.appendChild(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 (fig.ratio !== 1) {\n",
       "            fig.send_message('set_dpi_ratio', { dpi_ratio: fig.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 = document.createElement('div');\n",
       "    titlebar.classList =\n",
       "        'ui-dialog-titlebar ui-widget-header ui-corner-all ui-helper-clearfix';\n",
       "    var titletext = document.createElement('div');\n",
       "    titletext.classList = 'ui-dialog-title';\n",
       "    titletext.setAttribute(\n",
       "        'style',\n",
       "        'width: 100%; text-align: center; padding: 3px;'\n",
       "    );\n",
       "    titlebar.appendChild(titletext);\n",
       "    this.root.appendChild(titlebar);\n",
       "    this.header = titletext;\n",
       "};\n",
       "\n",
       "mpl.figure.prototype._canvas_extra_style = function (_canvas_div) {};\n",
       "\n",
       "mpl.figure.prototype._root_extra_style = function (_canvas_div) {};\n",
       "\n",
       "mpl.figure.prototype._init_canvas = function () {\n",
       "    var fig = this;\n",
       "\n",
       "    var canvas_div = (this.canvas_div = document.createElement('div'));\n",
       "    canvas_div.setAttribute(\n",
       "        'style',\n",
       "        'border: 1px solid #ddd;' +\n",
       "            'box-sizing: content-box;' +\n",
       "            'clear: both;' +\n",
       "            'min-height: 1px;' +\n",
       "            'min-width: 1px;' +\n",
       "            'outline: 0;' +\n",
       "            'overflow: hidden;' +\n",
       "            'position: relative;' +\n",
       "            'resize: both;'\n",
       "    );\n",
       "\n",
       "    function on_keyboard_event_closure(name) {\n",
       "        return function (event) {\n",
       "            return fig.key_event(event, name);\n",
       "        };\n",
       "    }\n",
       "\n",
       "    canvas_div.addEventListener(\n",
       "        'keydown',\n",
       "        on_keyboard_event_closure('key_press')\n",
       "    );\n",
       "    canvas_div.addEventListener(\n",
       "        'keyup',\n",
       "        on_keyboard_event_closure('key_release')\n",
       "    );\n",
       "\n",
       "    this._canvas_extra_style(canvas_div);\n",
       "    this.root.appendChild(canvas_div);\n",
       "\n",
       "    var canvas = (this.canvas = document.createElement('canvas'));\n",
       "    canvas.classList.add('mpl-canvas');\n",
       "    canvas.setAttribute('style', 'box-sizing: content-box;');\n",
       "\n",
       "    this.context = canvas.getContext('2d');\n",
       "\n",
       "    var backingStore =\n",
       "        this.context.backingStorePixelRatio ||\n",
       "        this.context.webkitBackingStorePixelRatio ||\n",
       "        this.context.mozBackingStorePixelRatio ||\n",
       "        this.context.msBackingStorePixelRatio ||\n",
       "        this.context.oBackingStorePixelRatio ||\n",
       "        this.context.backingStorePixelRatio ||\n",
       "        1;\n",
       "\n",
       "    this.ratio = (window.devicePixelRatio || 1) / backingStore;\n",
       "\n",
       "    var rubberband_canvas = (this.rubberband_canvas = document.createElement(\n",
       "        'canvas'\n",
       "    ));\n",
       "    rubberband_canvas.setAttribute(\n",
       "        'style',\n",
       "        'box-sizing: content-box; position: absolute; left: 0; top: 0; z-index: 1;'\n",
       "    );\n",
       "\n",
       "    // Apply a ponyfill if ResizeObserver is not implemented by browser.\n",
       "    if (this.ResizeObserver === undefined) {\n",
       "        if (window.ResizeObserver !== undefined) {\n",
       "            this.ResizeObserver = window.ResizeObserver;\n",
       "        } else {\n",
       "            var obs = _JSXTOOLS_RESIZE_OBSERVER({});\n",
       "            this.ResizeObserver = obs.ResizeObserver;\n",
       "        }\n",
       "    }\n",
       "\n",
       "    this.resizeObserverInstance = new this.ResizeObserver(function (entries) {\n",
       "        var nentries = entries.length;\n",
       "        for (var i = 0; i < nentries; i++) {\n",
       "            var entry = entries[i];\n",
       "            var width, height;\n",
       "            if (entry.contentBoxSize) {\n",
       "                if (entry.contentBoxSize instanceof Array) {\n",
       "                    // Chrome 84 implements new version of spec.\n",
       "                    width = entry.contentBoxSize[0].inlineSize;\n",
       "                    height = entry.contentBoxSize[0].blockSize;\n",
       "                } else {\n",
       "                    // Firefox implements old version of spec.\n",
       "                    width = entry.contentBoxSize.inlineSize;\n",
       "                    height = entry.contentBoxSize.blockSize;\n",
       "                }\n",
       "            } else {\n",
       "                // Chrome <84 implements even older version of spec.\n",
       "                width = entry.contentRect.width;\n",
       "                height = entry.contentRect.height;\n",
       "            }\n",
       "\n",
       "            // Keep the size of the canvas and rubber band canvas in sync with\n",
       "            // the canvas container.\n",
       "            if (entry.devicePixelContentBoxSize) {\n",
       "                // Chrome 84 implements new version of spec.\n",
       "                canvas.setAttribute(\n",
       "                    'width',\n",
       "                    entry.devicePixelContentBoxSize[0].inlineSize\n",
       "                );\n",
       "                canvas.setAttribute(\n",
       "                    'height',\n",
       "                    entry.devicePixelContentBoxSize[0].blockSize\n",
       "                );\n",
       "            } else {\n",
       "                canvas.setAttribute('width', width * fig.ratio);\n",
       "                canvas.setAttribute('height', height * fig.ratio);\n",
       "            }\n",
       "            canvas.setAttribute(\n",
       "                'style',\n",
       "                'width: ' + width + 'px; height: ' + height + 'px;'\n",
       "            );\n",
       "\n",
       "            rubberband_canvas.setAttribute('width', width);\n",
       "            rubberband_canvas.setAttribute('height', height);\n",
       "\n",
       "            // And update the size in Python. We ignore the initial 0/0 size\n",
       "            // that occurs as the element is placed into the DOM, which should\n",
       "            // otherwise not happen due to the minimum size styling.\n",
       "            if (fig.ws.readyState == 1 && width != 0 && height != 0) {\n",
       "                fig.request_resize(width, height);\n",
       "            }\n",
       "        }\n",
       "    });\n",
       "    this.resizeObserverInstance.observe(canvas_div);\n",
       "\n",
       "    function on_mouse_event_closure(name) {\n",
       "        return function (event) {\n",
       "            return fig.mouse_event(event, name);\n",
       "        };\n",
       "    }\n",
       "\n",
       "    rubberband_canvas.addEventListener(\n",
       "        'mousedown',\n",
       "        on_mouse_event_closure('button_press')\n",
       "    );\n",
       "    rubberband_canvas.addEventListener(\n",
       "        'mouseup',\n",
       "        on_mouse_event_closure('button_release')\n",
       "    );\n",
       "    rubberband_canvas.addEventListener(\n",
       "        'dblclick',\n",
       "        on_mouse_event_closure('dblclick')\n",
       "    );\n",
       "    // Throttle sequential mouse events to 1 every 20ms.\n",
       "    rubberband_canvas.addEventListener(\n",
       "        'mousemove',\n",
       "        on_mouse_event_closure('motion_notify')\n",
       "    );\n",
       "\n",
       "    rubberband_canvas.addEventListener(\n",
       "        'mouseenter',\n",
       "        on_mouse_event_closure('figure_enter')\n",
       "    );\n",
       "    rubberband_canvas.addEventListener(\n",
       "        'mouseleave',\n",
       "        on_mouse_event_closure('figure_leave')\n",
       "    );\n",
       "\n",
       "    canvas_div.addEventListener('wheel', function (event) {\n",
       "        if (event.deltaY < 0) {\n",
       "            event.step = 1;\n",
       "        } else {\n",
       "            event.step = -1;\n",
       "        }\n",
       "        on_mouse_event_closure('scroll')(event);\n",
       "    });\n",
       "\n",
       "    canvas_div.appendChild(canvas);\n",
       "    canvas_div.appendChild(rubberband_canvas);\n",
       "\n",
       "    this.rubberband_context = rubberband_canvas.getContext('2d');\n",
       "    this.rubberband_context.strokeStyle = '#000000';\n",
       "\n",
       "    this._resize_canvas = function (width, height, forward) {\n",
       "        if (forward) {\n",
       "            canvas_div.style.width = width + 'px';\n",
       "            canvas_div.style.height = height + 'px';\n",
       "        }\n",
       "    };\n",
       "\n",
       "    // Disable right mouse context menu.\n",
       "    this.rubberband_canvas.addEventListener('contextmenu', function (_e) {\n",
       "        event.preventDefault();\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 toolbar = document.createElement('div');\n",
       "    toolbar.classList = 'mpl-toolbar';\n",
       "    this.root.appendChild(toolbar);\n",
       "\n",
       "    function on_click_closure(name) {\n",
       "        return function (_event) {\n",
       "            return fig.toolbar_button_onclick(name);\n",
       "        };\n",
       "    }\n",
       "\n",
       "    function on_mouseover_closure(tooltip) {\n",
       "        return function (event) {\n",
       "            if (!event.currentTarget.disabled) {\n",
       "                return fig.toolbar_button_onmouseover(tooltip);\n",
       "            }\n",
       "        };\n",
       "    }\n",
       "\n",
       "    fig.buttons = {};\n",
       "    var buttonGroup = document.createElement('div');\n",
       "    buttonGroup.classList = 'mpl-button-group';\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",
       "            /* Instead of a spacer, we start a new button group. */\n",
       "            if (buttonGroup.hasChildNodes()) {\n",
       "                toolbar.appendChild(buttonGroup);\n",
       "            }\n",
       "            buttonGroup = document.createElement('div');\n",
       "            buttonGroup.classList = 'mpl-button-group';\n",
       "            continue;\n",
       "        }\n",
       "\n",
       "        var button = (fig.buttons[name] = document.createElement('button'));\n",
       "        button.classList = 'mpl-widget';\n",
       "        button.setAttribute('role', 'button');\n",
       "        button.setAttribute('aria-disabled', 'false');\n",
       "        button.addEventListener('click', on_click_closure(method_name));\n",
       "        button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n",
       "\n",
       "        var icon_img = document.createElement('img');\n",
       "        icon_img.src = '_images/' + image + '.png';\n",
       "        icon_img.srcset = '_images/' + image + '_large.png 2x';\n",
       "        icon_img.alt = tooltip;\n",
       "        button.appendChild(icon_img);\n",
       "\n",
       "        buttonGroup.appendChild(button);\n",
       "    }\n",
       "\n",
       "    if (buttonGroup.hasChildNodes()) {\n",
       "        toolbar.appendChild(buttonGroup);\n",
       "    }\n",
       "\n",
       "    var fmt_picker = document.createElement('select');\n",
       "    fmt_picker.classList = 'mpl-widget';\n",
       "    toolbar.appendChild(fmt_picker);\n",
       "    this.format_dropdown = fmt_picker;\n",
       "\n",
       "    for (var ind in mpl.extensions) {\n",
       "        var fmt = mpl.extensions[ind];\n",
       "        var option = document.createElement('option');\n",
       "        option.selected = fmt === mpl.default_extension;\n",
       "        option.innerHTML = fmt;\n",
       "        fmt_picker.appendChild(option);\n",
       "    }\n",
       "\n",
       "    var status_bar = document.createElement('span');\n",
       "    status_bar.classList = 'mpl-message';\n",
       "    toolbar.appendChild(status_bar);\n",
       "    this.message = status_bar;\n",
       "};\n",
       "\n",
       "mpl.figure.prototype.request_resize = function (x_pixels, y_pixels) {\n",
       "    // Request matplotlib to resize the figure. Matplotlib will then trigger a resize in the client,\n",
       "    // which will in turn request a refresh of the image.\n",
       "    this.send_message('resize', { width: x_pixels, height: y_pixels });\n",
       "};\n",
       "\n",
       "mpl.figure.prototype.send_message = function (type, properties) {\n",
       "    properties['type'] = type;\n",
       "    properties['figure_id'] = this.id;\n",
       "    this.ws.send(JSON.stringify(properties));\n",
       "};\n",
       "\n",
       "mpl.figure.prototype.send_draw_message = function () {\n",
       "    if (!this.waiting) {\n",
       "        this.waiting = true;\n",
       "        this.ws.send(JSON.stringify({ type: 'draw', figure_id: this.id }));\n",
       "    }\n",
       "};\n",
       "\n",
       "mpl.figure.prototype.handle_save = function (fig, _msg) {\n",
       "    var format_dropdown = fig.format_dropdown;\n",
       "    var format = format_dropdown.options[format_dropdown.selectedIndex].value;\n",
       "    fig.ondownload(fig, format);\n",
       "};\n",
       "\n",
       "mpl.figure.prototype.handle_resize = function (fig, msg) {\n",
       "    var size = msg['size'];\n",
       "    if (size[0] !== fig.canvas.width || size[1] !== fig.canvas.height) {\n",
       "        fig._resize_canvas(size[0], size[1], msg['forward']);\n",
       "        fig.send_message('refresh', {});\n",
       "    }\n",
       "};\n",
       "\n",
       "mpl.figure.prototype.handle_rubberband = function (fig, msg) {\n",
       "    var x0 = msg['x0'] / fig.ratio;\n",
       "    var y0 = (fig.canvas.height - msg['y0']) / fig.ratio;\n",
       "    var x1 = msg['x1'] / fig.ratio;\n",
       "    var y1 = (fig.canvas.height - msg['y1']) / fig.ratio;\n",
       "    x0 = Math.floor(x0) + 0.5;\n",
       "    y0 = Math.floor(y0) + 0.5;\n",
       "    x1 = Math.floor(x1) + 0.5;\n",
       "    y1 = Math.floor(y1) + 0.5;\n",
       "    var min_x = Math.min(x0, x1);\n",
       "    var min_y = Math.min(y0, y1);\n",
       "    var width = Math.abs(x1 - x0);\n",
       "    var height = Math.abs(y1 - y0);\n",
       "\n",
       "    fig.rubberband_context.clearRect(\n",
       "        0,\n",
       "        0,\n",
       "        fig.canvas.width / fig.ratio,\n",
       "        fig.canvas.height / fig.ratio\n",
       "    );\n",
       "\n",
       "    fig.rubberband_context.strokeRect(min_x, min_y, width, height);\n",
       "};\n",
       "\n",
       "mpl.figure.prototype.handle_figure_label = function (fig, msg) {\n",
       "    // Updates the figure title.\n",
       "    fig.header.textContent = msg['label'];\n",
       "};\n",
       "\n",
       "mpl.figure.prototype.handle_cursor = function (fig, msg) {\n",
       "    var cursor = msg['cursor'];\n",
       "    switch (cursor) {\n",
       "        case 0:\n",
       "            cursor = 'pointer';\n",
       "            break;\n",
       "        case 1:\n",
       "            cursor = 'default';\n",
       "            break;\n",
       "        case 2:\n",
       "            cursor = 'crosshair';\n",
       "            break;\n",
       "        case 3:\n",
       "            cursor = 'move';\n",
       "            break;\n",
       "    }\n",
       "    fig.rubberband_canvas.style.cursor = cursor;\n",
       "};\n",
       "\n",
       "mpl.figure.prototype.handle_message = function (fig, msg) {\n",
       "    fig.message.textContent = msg['message'];\n",
       "};\n",
       "\n",
       "mpl.figure.prototype.handle_draw = function (fig, _msg) {\n",
       "    // Request the server to send over a new figure.\n",
       "    fig.send_draw_message();\n",
       "};\n",
       "\n",
       "mpl.figure.prototype.handle_image_mode = function (fig, msg) {\n",
       "    fig.image_mode = msg['mode'];\n",
       "};\n",
       "\n",
       "mpl.figure.prototype.handle_history_buttons = function (fig, msg) {\n",
       "    for (var key in msg) {\n",
       "        if (!(key in fig.buttons)) {\n",
       "            continue;\n",
       "        }\n",
       "        fig.buttons[key].disabled = !msg[key];\n",
       "        fig.buttons[key].setAttribute('aria-disabled', !msg[key]);\n",
       "    }\n",
       "};\n",
       "\n",
       "mpl.figure.prototype.handle_navigate_mode = function (fig, msg) {\n",
       "    if (msg['mode'] === 'PAN') {\n",
       "        fig.buttons['Pan'].classList.add('active');\n",
       "        fig.buttons['Zoom'].classList.remove('active');\n",
       "    } else if (msg['mode'] === 'ZOOM') {\n",
       "        fig.buttons['Pan'].classList.remove('active');\n",
       "        fig.buttons['Zoom'].classList.add('active');\n",
       "    } else {\n",
       "        fig.buttons['Pan'].classList.remove('active');\n",
       "        fig.buttons['Zoom'].classList.remove('active');\n",
       "    }\n",
       "};\n",
       "\n",
       "mpl.figure.prototype.updated_canvas_event = function () {\n",
       "    // Called whenever the canvas gets updated.\n",
       "    this.send_message('ack', {});\n",
       "};\n",
       "\n",
       "// A function to construct a web socket function for onmessage handling.\n",
       "// Called in the figure constructor.\n",
       "mpl.figure.prototype._make_on_message_function = function (fig) {\n",
       "    return function socket_on_message(evt) {\n",
       "        if (evt.data instanceof Blob) {\n",
       "            var img = evt.data;\n",
       "            if (img.type !== 'image/png') {\n",
       "                /* FIXME: We get \"Resource interpreted as Image but\n",
       "                 * transferred with MIME type text/plain:\" errors on\n",
       "                 * Chrome.  But how to set the MIME type?  It doesn't seem\n",
       "                 * to be part of the websocket stream */\n",
       "                img.type = 'image/png';\n",
       "            }\n",
       "\n",
       "            /* Free the memory for the previous frames */\n",
       "            if (fig.imageObj.src) {\n",
       "                (window.URL || window.webkitURL).revokeObjectURL(\n",
       "                    fig.imageObj.src\n",
       "                );\n",
       "            }\n",
       "\n",
       "            fig.imageObj.src = (window.URL || window.webkitURL).createObjectURL(\n",
       "                img\n",
       "            );\n",
       "            fig.updated_canvas_event();\n",
       "            fig.waiting = false;\n",
       "            return;\n",
       "        } else if (\n",
       "            typeof evt.data === 'string' &&\n",
       "            evt.data.slice(0, 21) === 'data:image/png;base64'\n",
       "        ) {\n",
       "            fig.imageObj.src = evt.data;\n",
       "            fig.updated_canvas_event();\n",
       "            fig.waiting = false;\n",
       "            return;\n",
       "        }\n",
       "\n",
       "        var msg = JSON.parse(evt.data);\n",
       "        var msg_type = msg['type'];\n",
       "\n",
       "        // Call the  \"handle_{type}\" callback, which takes\n",
       "        // the figure and JSON message as its only arguments.\n",
       "        try {\n",
       "            var callback = fig['handle_' + msg_type];\n",
       "        } catch (e) {\n",
       "            console.log(\n",
       "                \"No handler for the '\" + msg_type + \"' message type: \",\n",
       "                msg\n",
       "            );\n",
       "            return;\n",
       "        }\n",
       "\n",
       "        if (callback) {\n",
       "            try {\n",
       "                // console.log(\"Handling '\" + msg_type + \"' message: \", msg);\n",
       "                callback(fig, msg);\n",
       "            } catch (e) {\n",
       "                console.log(\n",
       "                    \"Exception inside the 'handler_\" + msg_type + \"' callback:\",\n",
       "                    e,\n",
       "                    e.stack,\n",
       "                    msg\n",
       "                );\n",
       "            }\n",
       "        }\n",
       "    };\n",
       "};\n",
       "\n",
       "// from http://stackoverflow.com/questions/1114465/getting-mouse-location-in-canvas\n",
       "mpl.findpos = function (e) {\n",
       "    //this section is from http://www.quirksmode.org/js/events_properties.html\n",
       "    var targ;\n",
       "    if (!e) {\n",
       "        e = window.event;\n",
       "    }\n",
       "    if (e.target) {\n",
       "        targ = e.target;\n",
       "    } else if (e.srcElement) {\n",
       "        targ = e.srcElement;\n",
       "    }\n",
       "    if (targ.nodeType === 3) {\n",
       "        // defeat Safari bug\n",
       "        targ = targ.parentNode;\n",
       "    }\n",
       "\n",
       "    // pageX,Y are the mouse positions relative to the document\n",
       "    var boundingRect = targ.getBoundingClientRect();\n",
       "    var x = e.pageX - (boundingRect.left + document.body.scrollLeft);\n",
       "    var y = e.pageY - (boundingRect.top + document.body.scrollTop);\n",
       "\n",
       "    return { x: x, y: y };\n",
       "};\n",
       "\n",
       "/*\n",
       " * return a copy of an object with only non-object keys\n",
       " * we need this to avoid circular references\n",
       " * http://stackoverflow.com/a/24161582/3208463\n",
       " */\n",
       "function simpleKeys(original) {\n",
       "    return Object.keys(original).reduce(function (obj, key) {\n",
       "        if (typeof original[key] !== 'object') {\n",
       "            obj[key] = original[key];\n",
       "        }\n",
       "        return obj;\n",
       "    }, {});\n",
       "}\n",
       "\n",
       "mpl.figure.prototype.mouse_event = function (event, name) {\n",
       "    var canvas_pos = mpl.findpos(event);\n",
       "\n",
       "    if (name === 'button_press') {\n",
       "        this.canvas.focus();\n",
       "        this.canvas_div.focus();\n",
       "    }\n",
       "\n",
       "    var x = canvas_pos.x * this.ratio;\n",
       "    var y = canvas_pos.y * this.ratio;\n",
       "\n",
       "    this.send_message(name, {\n",
       "        x: x,\n",
       "        y: y,\n",
       "        button: event.button,\n",
       "        step: event.step,\n",
       "        guiEvent: simpleKeys(event),\n",
       "    });\n",
       "\n",
       "    /* This prevents the web browser from automatically changing to\n",
       "     * the text insertion cursor when the button is pressed.  We want\n",
       "     * to control all of the cursor setting manually through the\n",
       "     * 'cursor' event from matplotlib */\n",
       "    event.preventDefault();\n",
       "    return false;\n",
       "};\n",
       "\n",
       "mpl.figure.prototype._key_event_extra = function (_event, _name) {\n",
       "    // Handle any extra behaviour associated with a key event\n",
       "};\n",
       "\n",
       "mpl.figure.prototype.key_event = function (event, name) {\n",
       "    // Prevent repeat events\n",
       "    if (name === 'key_press') {\n",
       "        if (event.key === this._key) {\n",
       "            return;\n",
       "        } else {\n",
       "            this._key = event.key;\n",
       "        }\n",
       "    }\n",
       "    if (name === 'key_release') {\n",
       "        this._key = null;\n",
       "    }\n",
       "\n",
       "    var value = '';\n",
       "    if (event.ctrlKey && event.key !== 'Control') {\n",
       "        value += 'ctrl+';\n",
       "    }\n",
       "    else if (event.altKey && event.key !== 'Alt') {\n",
       "        value += 'alt+';\n",
       "    }\n",
       "    else if (event.shiftKey && event.key !== 'Shift') {\n",
       "        value += 'shift+';\n",
       "    }\n",
       "\n",
       "    value += 'k' + event.key;\n",
       "\n",
       "    this._key_event_extra(event, name);\n",
       "\n",
       "    this.send_message(name, { key: value, guiEvent: simpleKeys(event) });\n",
       "    return false;\n",
       "};\n",
       "\n",
       "mpl.figure.prototype.toolbar_button_onclick = function (name) {\n",
       "    if (name === 'download') {\n",
       "        this.handle_save(this, null);\n",
       "    } else {\n",
       "        this.send_message('toolbar_button', { name: name });\n",
       "    }\n",
       "};\n",
       "\n",
       "mpl.figure.prototype.toolbar_button_onmouseover = function (tooltip) {\n",
       "    this.message.textContent = tooltip;\n",
       "};\n",
       "\n",
       "///////////////// REMAINING CONTENT GENERATED BY embed_js.py /////////////////\n",
       "// prettier-ignore\n",
       "var _JSXTOOLS_RESIZE_OBSERVER=function(A){var t,i=new WeakMap,n=new WeakMap,a=new WeakMap,r=new WeakMap,o=new Set;function s(e){if(!(this instanceof s))throw new TypeError(\"Constructor requires 'new' operator\");i.set(this,e)}function h(){throw new TypeError(\"Function is not a constructor\")}function c(e,t,i,n){e=0 in arguments?Number(arguments[0]):0,t=1 in arguments?Number(arguments[1]):0,i=2 in arguments?Number(arguments[2]):0,n=3 in arguments?Number(arguments[3]):0,this.right=(this.x=this.left=e)+(this.width=i),this.bottom=(this.y=this.top=t)+(this.height=n),Object.freeze(this)}function d(){t=requestAnimationFrame(d);var s=new WeakMap,p=new Set;o.forEach((function(t){r.get(t).forEach((function(i){var r=t instanceof window.SVGElement,o=a.get(t),d=r?0:parseFloat(o.paddingTop),f=r?0:parseFloat(o.paddingRight),l=r?0:parseFloat(o.paddingBottom),u=r?0:parseFloat(o.paddingLeft),g=r?0:parseFloat(o.borderTopWidth),m=r?0:parseFloat(o.borderRightWidth),w=r?0:parseFloat(o.borderBottomWidth),b=u+f,F=d+l,v=(r?0:parseFloat(o.borderLeftWidth))+m,W=g+w,y=r?0:t.offsetHeight-W-t.clientHeight,E=r?0:t.offsetWidth-v-t.clientWidth,R=b+v,z=F+W,M=r?t.width:parseFloat(o.width)-R-E,O=r?t.height:parseFloat(o.height)-z-y;if(n.has(t)){var k=n.get(t);if(k[0]===M&&k[1]===O)return}n.set(t,[M,O]);var S=Object.create(h.prototype);S.target=t,S.contentRect=new c(u,d,M,O),s.has(i)||(s.set(i,[]),p.add(i)),s.get(i).push(S)}))})),p.forEach((function(e){i.get(e).call(e,s.get(e),e)}))}return s.prototype.observe=function(i){if(i instanceof window.Element){r.has(i)||(r.set(i,new Set),o.add(i),a.set(i,window.getComputedStyle(i)));var n=r.get(i);n.has(this)||n.add(this),cancelAnimationFrame(t),t=requestAnimationFrame(d)}},s.prototype.unobserve=function(i){if(i instanceof window.Element&&r.has(i)){var n=r.get(i);n.has(this)&&(n.delete(this),n.size||(r.delete(i),o.delete(i))),n.size||r.delete(i),o.size||cancelAnimationFrame(t)}},A.DOMRectReadOnly=c,A.ResizeObserver=s,A.ResizeObserverEntry=h,A}; // eslint-disable-line\n",
       "mpl.toolbar_items = [[\"Home\", \"Reset original view\", \"fa fa-home icon-home\", \"home\"], [\"Back\", \"Back to previous view\", \"fa fa-arrow-left icon-arrow-left\", \"back\"], [\"Forward\", \"Forward to next view\", \"fa fa-arrow-right icon-arrow-right\", \"forward\"], [\"\", \"\", \"\", \"\"], [\"Pan\", \"Left button pans, Right button zooms\\nx/y fixes axis, CTRL fixes aspect\", \"fa fa-arrows icon-move\", \"pan\"], [\"Zoom\", \"Zoom to rectangle\\nx/y fixes axis, CTRL fixes aspect\", \"fa fa-square-o icon-check-empty\", \"zoom\"], [\"\", \"\", \"\", \"\"], [\"Download\", \"Download plot\", \"fa fa-floppy-o icon-save\", \"download\"]];\n",
       "\n",
       "mpl.extensions = [\"eps\", \"jpeg\", \"pgf\", \"pdf\", \"png\", \"ps\", \"raw\", \"svg\", \"tif\"];\n",
       "\n",
       "mpl.default_extension = \"png\";/* global mpl */\n",
       "\n",
       "var comm_websocket_adapter = function (comm) {\n",
       "    // Create a \"websocket\"-like object which calls the given IPython comm\n",
       "    // object with the appropriate methods. Currently this is a non binary\n",
       "    // socket, so there is still some room for performance tuning.\n",
       "    var ws = {};\n",
       "\n",
       "    ws.binaryType = comm.kernel.ws.binaryType;\n",
       "    ws.readyState = comm.kernel.ws.readyState;\n",
       "    function updateReadyState(_event) {\n",
       "        if (comm.kernel.ws) {\n",
       "            ws.readyState = comm.kernel.ws.readyState;\n",
       "        } else {\n",
       "            ws.readyState = 3; // Closed state.\n",
       "        }\n",
       "    }\n",
       "    comm.kernel.ws.addEventListener('open', updateReadyState);\n",
       "    comm.kernel.ws.addEventListener('close', updateReadyState);\n",
       "    comm.kernel.ws.addEventListener('error', updateReadyState);\n",
       "\n",
       "    ws.close = function () {\n",
       "        comm.close();\n",
       "    };\n",
       "    ws.send = function (m) {\n",
       "        //console.log('sending', m);\n",
       "        comm.send(m);\n",
       "    };\n",
       "    // Register the callback with on_msg.\n",
       "    comm.on_msg(function (msg) {\n",
       "        //console.log('receiving', msg['content']['data'], msg);\n",
       "        var data = msg['content']['data'];\n",
       "        if (data['blob'] !== undefined) {\n",
       "            data = {\n",
       "                data: new Blob(msg['buffers'], { type: data['blob'] }),\n",
       "            };\n",
       "        }\n",
       "        // Pass the mpl event to the overridden (by mpl) onmessage function.\n",
       "        ws.onmessage(data);\n",
       "    });\n",
       "    return ws;\n",
       "};\n",
       "\n",
       "mpl.mpl_figure_comm = function (comm, msg) {\n",
       "    // This is the function which gets called when the mpl process\n",
       "    // starts-up an IPython Comm through the \"matplotlib\" channel.\n",
       "\n",
       "    var id = msg.content.data.id;\n",
       "    // Get hold of the div created by the display call when the Comm\n",
       "    // socket was opened in Python.\n",
       "    var element = document.getElementById(id);\n",
       "    var ws_proxy = comm_websocket_adapter(comm);\n",
       "\n",
       "    function ondownload(figure, _format) {\n",
       "        window.open(figure.canvas.toDataURL());\n",
       "    }\n",
       "\n",
       "    var fig = new mpl.figure(id, ws_proxy, ondownload, element);\n",
       "\n",
       "    // Call onopen now - mpl needs it, as it is assuming we've passed it a real\n",
       "    // web socket which is closed, not our websocket->open comm proxy.\n",
       "    ws_proxy.onopen();\n",
       "\n",
       "    fig.parent_element = element;\n",
       "    fig.cell_info = mpl.find_output_cell(\"<div id='\" + id + \"'></div>\");\n",
       "    if (!fig.cell_info) {\n",
       "        console.error('Failed to find cell for figure', id, fig);\n",
       "        return;\n",
       "    }\n",
       "    fig.cell_info[0].output_area.element.on(\n",
       "        'cleared',\n",
       "        { fig: fig },\n",
       "        fig._remove_fig_handler\n",
       "    );\n",
       "};\n",
       "\n",
       "mpl.figure.prototype.handle_close = function (fig, msg) {\n",
       "    var width = fig.canvas.width / fig.ratio;\n",
       "    fig.cell_info[0].output_area.element.off(\n",
       "        'cleared',\n",
       "        fig._remove_fig_handler\n",
       "    );\n",
       "    fig.resizeObserverInstance.unobserve(fig.canvas_div);\n",
       "\n",
       "    // Update the output cell to use the data from the current canvas.\n",
       "    fig.push_to_output();\n",
       "    var dataURL = fig.canvas.toDataURL();\n",
       "    // Re-enable the keyboard manager in IPython - without this line, in FF,\n",
       "    // the notebook keyboard shortcuts fail.\n",
       "    IPython.keyboard_manager.enable();\n",
       "    fig.parent_element.innerHTML =\n",
       "        '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n",
       "    fig.close_ws(fig, msg);\n",
       "};\n",
       "\n",
       "mpl.figure.prototype.close_ws = function (fig, msg) {\n",
       "    fig.send_message('closing', msg);\n",
       "    // fig.ws.close()\n",
       "};\n",
       "\n",
       "mpl.figure.prototype.push_to_output = function (_remove_interactive) {\n",
       "    // Turn the data on the canvas into data in the output cell.\n",
       "    var width = this.canvas.width / this.ratio;\n",
       "    var dataURL = this.canvas.toDataURL();\n",
       "    this.cell_info[1]['text/html'] =\n",
       "        '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n",
       "};\n",
       "\n",
       "mpl.figure.prototype.updated_canvas_event = function () {\n",
       "    // Tell IPython that the notebook contents must change.\n",
       "    IPython.notebook.set_dirty(true);\n",
       "    this.send_message('ack', {});\n",
       "    var fig = this;\n",
       "    // Wait a second, then push the new image to the DOM so\n",
       "    // that it is saved nicely (might be nice to debounce this).\n",
       "    setTimeout(function () {\n",
       "        fig.push_to_output();\n",
       "    }, 1000);\n",
       "};\n",
       "\n",
       "mpl.figure.prototype._init_toolbar = function () {\n",
       "    var fig = this;\n",
       "\n",
       "    var toolbar = document.createElement('div');\n",
       "    toolbar.classList = 'btn-toolbar';\n",
       "    this.root.appendChild(toolbar);\n",
       "\n",
       "    function on_click_closure(name) {\n",
       "        return function (_event) {\n",
       "            return fig.toolbar_button_onclick(name);\n",
       "        };\n",
       "    }\n",
       "\n",
       "    function on_mouseover_closure(tooltip) {\n",
       "        return function (event) {\n",
       "            if (!event.currentTarget.disabled) {\n",
       "                return fig.toolbar_button_onmouseover(tooltip);\n",
       "            }\n",
       "        };\n",
       "    }\n",
       "\n",
       "    fig.buttons = {};\n",
       "    var buttonGroup = document.createElement('div');\n",
       "    buttonGroup.classList = 'btn-group';\n",
       "    var button;\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",
       "            /* Instead of a spacer, we start a new button group. */\n",
       "            if (buttonGroup.hasChildNodes()) {\n",
       "                toolbar.appendChild(buttonGroup);\n",
       "            }\n",
       "            buttonGroup = document.createElement('div');\n",
       "            buttonGroup.classList = 'btn-group';\n",
       "            continue;\n",
       "        }\n",
       "\n",
       "        button = fig.buttons[name] = document.createElement('button');\n",
       "        button.classList = 'btn btn-default';\n",
       "        button.href = '#';\n",
       "        button.title = name;\n",
       "        button.innerHTML = '<i class=\"fa ' + image + ' fa-lg\"></i>';\n",
       "        button.addEventListener('click', on_click_closure(method_name));\n",
       "        button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n",
       "        buttonGroup.appendChild(button);\n",
       "    }\n",
       "\n",
       "    if (buttonGroup.hasChildNodes()) {\n",
       "        toolbar.appendChild(buttonGroup);\n",
       "    }\n",
       "\n",
       "    // Add the status bar.\n",
       "    var status_bar = document.createElement('span');\n",
       "    status_bar.classList = 'mpl-message pull-right';\n",
       "    toolbar.appendChild(status_bar);\n",
       "    this.message = status_bar;\n",
       "\n",
       "    // Add the close button to the window.\n",
       "    var buttongrp = document.createElement('div');\n",
       "    buttongrp.classList = 'btn-group inline pull-right';\n",
       "    button = document.createElement('button');\n",
       "    button.classList = 'btn btn-mini btn-primary';\n",
       "    button.href = '#';\n",
       "    button.title = 'Stop Interaction';\n",
       "    button.innerHTML = '<i class=\"fa fa-power-off icon-remove icon-large\"></i>';\n",
       "    button.addEventListener('click', function (_evt) {\n",
       "        fig.handle_close(fig, {});\n",
       "    });\n",
       "    button.addEventListener(\n",
       "        'mouseover',\n",
       "        on_mouseover_closure('Stop Interaction')\n",
       "    );\n",
       "    buttongrp.appendChild(button);\n",
       "    var titlebar = this.root.querySelector('.ui-dialog-titlebar');\n",
       "    titlebar.insertBefore(buttongrp, titlebar.firstChild);\n",
       "};\n",
       "\n",
       "mpl.figure.prototype._remove_fig_handler = function (event) {\n",
       "    var fig = event.data.fig;\n",
       "    if (event.target !== this) {\n",
       "        // Ignore bubbled events from children.\n",
       "        return;\n",
       "    }\n",
       "    fig.close_ws(fig, {});\n",
       "};\n",
       "\n",
       "mpl.figure.prototype._root_extra_style = function (el) {\n",
       "    el.style.boxSizing = 'content-box'; // override notebook setting of border-box.\n",
       "};\n",
       "\n",
       "mpl.figure.prototype._canvas_extra_style = function (el) {\n",
       "    // this is important to make the div 'focusable\n",
       "    el.setAttribute('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",
       "    } else {\n",
       "        // location in version 2\n",
       "        IPython.keyboard_manager.register_events(el);\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",
       "\n",
       "    // Check for shift+enter\n",
       "    if (event.shiftKey && event.which === 13) {\n",
       "        this.canvas_div.blur();\n",
       "        // select the cell after this one\n",
       "        var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n",
       "        IPython.notebook.select(index + 1);\n",
       "    }\n",
       "};\n",
       "\n",
       "mpl.figure.prototype.handle_save = function (fig, _msg) {\n",
       "    fig.ondownload(fig, null);\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 < ncells; i++) {\n",
       "        var cell = cells[i];\n",
       "        if (cell.cell_type === 'code') {\n",
       "            for (var j = 0; j < cell.output_area.outputs.length; j++) {\n",
       "                var data = cell.output_area.outputs[j];\n",
       "                if (data.data) {\n",
       "                    // IPython >= 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(\n",
       "        'matplotlib',\n",
       "        mpl.mpl_figure_comm\n",
       "    );\n",
       "}\n"
      ],
      "text/plain": [
       "<IPython.core.display.Javascript object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<div id='0dddb269-2eb7-4a9d-a01a-b24ed0ce752b'></div>"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Kinetic energy distribution check (strict)\n",
      "Kolmogorov-Smirnov test result: p = 1.85798e-17\n",
      "Null hypothesis: Kinetic energy is Maxwell-Boltzmann distributed\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "1.8579783151867675e-17"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "physical_validation.kinetic_energy.distribution(\n",
    "    data=simulation_data_berendsen, strict=True, screen=True\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "3ec477bc",
   "metadata": {},
   "source": [
    "The calculated p-value means that the trajectory is _very_ unklikely to come from a Maxwell-Boltzmann distribution at 298.15K. Commonly, one would consider a p-value of less than 0.05 (5% confidence interval) a reasonable cut-off, which means that the test results make it easy to reject the null hypothesis that the kinetic energy samples the correct distribution. This does not come as a suprise, the Berendsen thermostat is known to keep the correct mean temperature, but not to sample the right distribution."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "c5baf34d",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "After equilibration, decorrelation and tail pruning, 95.96% (4799 frames) of original Kinetic energy remain.\n",
      "Kinetic energy distribution check (non-strict)\n",
      "Analytical distribution (T=298.15 K):\n",
      " * mu: 6689.47 kJ/mol\n",
      " * sigma: 128.77 kJ/mol\n",
      "Trajectory:\n",
      " * mu: 6690.21 +- 1.29 kJ/mol\n",
      "   T(mu) = 298.18 +- 0.06 K\n",
      " * sigma: 98.81 +- 1.01 kJ/mol\n",
      "   T(sigma) = 228.78 +- 2.33 K\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "(0.5763182556173292, 29.80276265170178)"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# We turn plotting off here (`screen=False`), because the plot is \n",
    "# identical to the one in the strict test\n",
    "physical_validation.kinetic_energy.distribution(\n",
    "    data=simulation_data_berendsen, strict=False, screen=False\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "01b5371e",
   "metadata": {},
   "source": [
    "The non-strict test confirms the conclusion from the strict test, but adds another explanation of the sampled distribution. The mean is found to be within about half a standard deviation of the expected value. The width of the sampled distribution, however, is what we would expect for a simulation at about 229K. This means that especially for simulations which rely on correct sampling of the tail regions, the Berendsen temperature coupling is likely to introduce artefacts. Again, the tuple returned here could be slightly different in different trials due to its probabilistic nature."
   ]
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 3 (ipykernel)",
   "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": "3.7.12"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 5
}