reactors/interactive_path_diagram.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Interactive Path Diagrams\n",
    "\n",
    "This example uses `ipywidgets` to create interactive displays of path diagrams from Cantera simulations."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Using Cantera version: 2.6.0\n"
     ]
    }
   ],
   "source": [
    "from IPython.display import Image, display\n",
    "from ipywidgets import widgets, interact\n",
    "import cantera as ct\n",
    "import numpy as np\n",
    "import graphviz\n",
    "\n",
    "%matplotlib inline\n",
    "%config InlineBackend.figure_formats = [\"svg\"]\n",
    "from matplotlib import pyplot as plt\n",
    "from collections import defaultdict\n",
    "import subprocess\n",
    "\n",
    "plt.rcParams[\"figure.dpi\"] = 120\n",
    "\n",
    "print(f\"Using Cantera version: {ct.__version__}\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "When using Cantera, the first thing you usually need is an object representing some phase of matter. Here, we'll create a gas mixture using GRI-Mech:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "gas = ct.Solution(\"gri30.yaml\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Shock tube ignition delay measurement conditions (Spadaccini, L.J., and Colket, M.B., (1994) Prog. Energy Combust. Sci. 20, 431. ) \n",
    "* $CH_4-C_2H_6-O_2-Ar$ (3.29%-0.21%-7%-89.5%)  \n",
    "* phi = 1.045\n",
    "* P = 6.1 - 7.6 atm\n",
    "* T = 1356 - 1688 K \n",
    "* Set temperature,pressure and composition"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "gas.TPX = 1550.0, 6.5 * ct.one_atm, \"CH4:3.29, C2H6:0.21, O2:7 , Ar:89.5\""
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "* Residence time is close to ignition delay reported by (Spadaccini, L.J., and Colket, M.B., (1994) Prog. Energy Combust. Sci. 20, 431. ) "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "residence_time = 1e-3"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "* Create a batch reactor object and set solver tolerances"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "reactor = ct.IdealGasConstPressureReactor(gas, energy=\"on\")\n",
    "reactor_network = ct.ReactorNet([reactor])\n",
    "reactor_network.atol = 1e-12\n",
    "reactor_network.rtol = 1e-12"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "* Store time, pressure, temperature and mole fractions"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "profiles = defaultdict(list)\n",
    "time = 0\n",
    "steps = 0\n",
    "while time < residence_time:\n",
    "    profiles[\"time\"].append(time)\n",
    "    profiles[\"pressure\"].append(gas.P)\n",
    "    profiles[\"temperature\"].append(gas.T)\n",
    "    profiles[\"mole_fractions\"].append(gas.X)\n",
    "    time = reactor_network.step()\n",
    "    steps += 1"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Interactive reaction path diagram\n",
    "  * Plot steps, threshold and element can be changed using the slider provided by IPyWidgets"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
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      "text/plain": [
       "interactive(children=(IntSlider(value=100, description='plot_step', max=1730, step=10), FloatSlider(value=0.1,…"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "@interact(\n",
    "    plot_step=widgets.IntSlider(value=100, min=0, max=steps, step=10),\n",
    "    threshold=widgets.FloatSlider(value=0.1, min=0, max=1, step=0.01),\n",
    "    details=widgets.ToggleButton(),\n",
    "    species=widgets.Dropdown(\n",
    "        options=gas.element_names,\n",
    "        value=\"C\",\n",
    "        description=\"Element\",\n",
    "        disabled=False,\n",
    "    ),\n",
    ")\n",
    "def plot_reaction_path_diagrams(plot_step, threshold, details, species):\n",
    "    P = profiles[\"pressure\"][plot_step]\n",
    "    T = profiles[\"temperature\"][plot_step]\n",
    "    X = profiles[\"mole_fractions\"][plot_step]\n",
    "    time = profiles[\"time\"][plot_step]\n",
    "    gas.TPX = T, P, X\n",
    "    print(\"time = {:.2g} s\".format(time))\n",
    "\n",
    "    diagram = ct.ReactionPathDiagram(gas, species)\n",
    "    diagram.threshold = threshold\n",
    "\n",
    "    diagram.show_details = details\n",
    "    graph = graphviz.Source(diagram.get_dot())\n",
    "    display(graph)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "* Find reactions containing the specie of interest \n",
    "   * `C2H6` in this case"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "C2H6_stoichiometry = np.zeros_like(gas.reactions())\n",
    "for i, r in enumerate(gas.reactions()):\n",
    "    C2H6_moles = r.products.get(\"C2H6\", 0) - r.reactants.get(\"C2H6\", 0)\n",
    "    C2H6_stoichiometry[i] = C2H6_moles\n",
    "C2H6_reaction_indices = C2H6_stoichiometry.nonzero()[0]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### The following cell calculates net rates of progress of reactions containing the species of interest and stores it"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "profiles[\"C2H6_production_rates\"] = []\n",
    "for i in range(len(profiles[\"time\"])):\n",
    "    X = profiles[\"mole_fractions\"][i]\n",
    "    t = profiles[\"time\"][i]\n",
    "    T = profiles[\"temperature\"][i]\n",
    "    P = profiles[\"pressure\"][i]\n",
    "    gas.TPX = (T, P, X)\n",
    "    C2H6_production_rates = (\n",
    "        gas.net_rates_of_progress\n",
    "        * C2H6_stoichiometry  #  [kmol/m^3/s]\n",
    "        * gas.volume_mass  # Specific volume [m^3/kg].\n",
    "    )  # overall, mol/s/g  (g total in reactor, same basis as N_atoms_in_fuel)\n",
    "\n",
    "    profiles[\"C2H6_production_rates\"].append(\n",
    "        C2H6_production_rates[C2H6_reaction_indices]\n",
    "    )"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Interactive plot of instantaneous fluxes\n",
    "   * Threshold for annotating of reaction strings can be changed using the slider provided by IPyWidgets"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "@interact(\n",
    "    annotation_cutoff=widgets.FloatSlider(value=1e-2, min=1e-2, max=4, steps=10),\n",
    "    profiles=widgets.fixed(profiles),\n",
    ")\n",
    "def plot_instantaneous_fluxes(profiles, annotation_cutoff):\n",
    "    profiles = profiles\n",
    "    fig = plt.figure(figsize=(6, 6))\n",
    "    plt.plot(profiles[\"time\"], np.array(profiles[\"C2H6_production_rates\"]))\n",
    "\n",
    "    for i, C2H6_production_rate in enumerate(\n",
    "        np.array(profiles[\"C2H6_production_rates\"]).T\n",
    "    ):\n",
    "        peak_index = abs(C2H6_production_rate).argmax()\n",
    "        peak_time = profiles[\"time\"][peak_index]\n",
    "        peak_C2H6_production = C2H6_production_rate[peak_index]\n",
    "        reaction_string = gas.reaction_equations(C2H6_reaction_indices)[i]\n",
    "\n",
    "        if abs(peak_C2H6_production) > annotation_cutoff:\n",
    "            plt.annotate(\n",
    "                (reaction_string).replace(\"2\", \"$_2$\").replace(\"<=>\", \"=\"),\n",
    "                xy=(peak_time, peak_C2H6_production),\n",
    "                xytext=(\n",
    "                    peak_time * 2,\n",
    "                    (\n",
    "                        peak_C2H6_production\n",
    "                        + 0.003\n",
    "                        * (peak_C2H6_production / abs(peak_C2H6_production))\n",
    "                        * (abs(peak_C2H6_production) > 0.005)\n",
    "                        * (peak_C2H6_production < 0.06)\n",
    "                    ),\n",
    "                ),\n",
    "                arrowprops=dict(\n",
    "                    arrowstyle=\"->\",\n",
    "                    color=\"black\",\n",
    "                    relpos=(0, 0.6),\n",
    "                    linewidth=2,\n",
    "                ),\n",
    "                horizontalalignment=\"left\",\n",
    "            )\n",
    "\n",
    "    plt.xlabel(\"Time (s)\", fontsize=16)\n",
    "    plt.ylabel(\"Net rates of C2H6 production\", fontsize=16)\n",
    "    plt.tight_layout()\n",
    "    plt.show()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Integrating over time using `scipy.integrate.cumptraz` "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "from scipy import integrate\n",
    "\n",
    "integrated_fluxes = integrate.cumtrapz(\n",
    "    np.array(profiles[\"C2H6_production_rates\"]),\n",
    "    np.array(profiles[\"time\"]),\n",
    "    axis=0,\n",
    "    initial=0,\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Interactive plot of  integrated fluxes\n",
    " * Threshold for annotating of reaction strings can be changed using the slider provided by iPyWidgets"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "@interact(\n",
    "    annotation_cutoff=widgets.FloatLogSlider(\n",
    "        value=1e-5, min=-5, max=-4, base=10, step=0.1\n",
    "    ),\n",
    "    profiles=widgets.fixed(profiles),\n",
    "    integrated_fluxes=widgets.fixed(integrated_fluxes),\n",
    ")\n",
    "def plot_integrated_fluxes(profiles, integrated_fluxes, annotation_cutoff):\n",
    "    profiles = profiles\n",
    "    integrated_fluxes = integrated_fluxes\n",
    "    fig = plt.figure(figsize=(6, 6))\n",
    "    plt.plot(profiles[\"time\"], integrated_fluxes)\n",
    "    final_time = profiles[\"time\"][-1]\n",
    "    for i, C2H6_production in enumerate(integrated_fluxes.T):\n",
    "        total_C2H6_production = C2H6_production[-1]\n",
    "        reaction_string = gas.reaction_equations(C2H6_reaction_indices)[i]\n",
    "\n",
    "        if abs(total_C2H6_production) > annotation_cutoff:\n",
    "            plt.text(final_time * 1.06, total_C2H6_production, reaction_string)\n",
    "\n",
    "    plt.xlabel(\"Time (s)\", fontsize=16)\n",
    "    plt.ylabel(\"Integrated net rate of progress\", fontsize=16)\n",
    "    plt.title(\"Cumulative C2H6 formation\", fontsize=16)\n",
    "    plt.tight_layout()\n",
    "    plt.show()"
   ]
  }
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