Merge pull request #2815 from ReactionMechanismGenerator/fix/notebooks

Update Jupyter notebooks and associated codebase [RMG-Py]

Author: JacksonBurns

ipython/cantera_sensitivity_comparison.ipynb

@@ -80,7 +80,8 @@
     "#job.load_chemkin_model('data/ethane_model/chem_annotated.inp',transport_file='data/ethane_model/tran.dat')\n",
     "\n",
     "# Generate the conditions based on the settings we declared earlier\n",
-    "job.generate_conditions(reactor_type_list, reaction_time_list, mol_frac_list, Tlist, Plist)"
+    "job.generate_conditions(reactor_type_list=reactor_type_list, reaction_time_list=reaction_time_list, \n",
+    "                        mol_frac_list=mol_frac_list, Tlist=Tlist, Plist=Plist)"
    ]
   },
   {
@@ -170,20 +171,13 @@
     "    print('Condition {0}'.format(i+1))\n",
     "    display(Image(filename=\"temp/{0}_mole_fractions.png\".format(i+1)))"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python [conda env:rmg_env]",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
-   "name": "conda-env-rmg_env-py"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
@@ -195,9 +189,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.4"
+   "version": "3.9.23"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 1
+ "nbformat_minor": 4
 }

ipython/cantera_simulation.ipynb

@@ -185,7 +185,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "scrolled": true
+   },
    "outputs": [],
    "source": [
     "import time\n",
@@ -245,12 +247,13 @@
     "mol_frac_list=[{species_dict[fuel_species]: fuel_stoich,\n",
     "                species_dict[O2_species]: 1,\n",
     "                species_dict[N2_species]: 3.76}]\n",
-    "T_list = ([temperature],'K')\n",
-    "P_list = ([pressure],'atm')\n",
+    "Tlist = ([temperature],'K')\n",
+    "Plist = ([pressure],'atm')\n",
     "\n",
     "job = Cantera(species_list=species_list, reaction_list=reaction_list, output_directory=directory)\n",
     "job.load_chemkin_model(os.path.join(chem_path, 'chem_annotated.inp'), os.path.join(chem_path, 'tran.dat'))\n",
-    "job.generate_conditions(reactor_type_list, reaction_time_list, mol_frac_list, T_list, P_list)\n",
+    "job.generate_conditions(reactor_type_list=reactor_type_list, reaction_time_list=reaction_time_list, \n",
+    "                        mol_frac_list=mol_frac_list, Tlist=Tlist, Plist=Plist)\n",
     "\n",
     "alldata = job.simulate()\n",
     "print(\"Simulation Completed\")"
@@ -266,9 +269,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "scrolled": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "############### Settings ###############\n",
@@ -280,7 +281,6 @@
     "import pandas as pd\n",
     "from rmgpy.tools import plot as rmg_plot\n",
     "from operator import itemgetter\n",
-    "%matplotlib notebook\n",
     "\n",
     "times = alldata[0][0].data\n",
     "temperatures = alldata[0][1][0].data\n",
@@ -353,9 +353,6 @@
     "plt.rcParams['ytick.labelsize'] = 12\n",
     "plt.rcParams['figure.autolayout'] = True\n",
     "\n",
-    "plt.style.use('ggplot')\n",
-    "plt.style.use('seaborn-pastel')\n",
-    "\n",
     "fig = plt.figure(figsize=fsize)\n",
     "\n",
     "plt.subplot(1,2,1)\n",
@@ -418,16 +415,14 @@
    "outputs": [],
    "source": [
     "import cantera as ct\n",
-    "gas = ct.Solution(os.path.join(directory, 'cantera', 'chem.cti'))\n",
+    "gas = ct.Solution(os.path.join(directory, 'cantera', 'chem.yaml'))\n",
     "comp = str(species_dict[fuel_species])+\":\"+str(fuel_stoich)+\",\"+str(species_dict[O2_species])+\":1,\"+str(species_dict[N2_species])+\":3.76\"\n",
     "gas.TPX = temperature, pressure, comp\n",
     "reactor = ct.IdealGasConstPressureReactor(gas)\n",
     "network = ct.ReactorNet([reactor])\n",
     "network.advance(ign_delay_time)\n",
     "ROP_C = ct.ReactionPathDiagram(gas, 'C')\n",
     "\n",
-    "from PIL import Image as PILimg\n",
-    "ROP1 = plt.subplot(1,1,1)\n",
     "dot_file = os.path.join(directory, 'cantera', 'rxnpathC.dot')\n",
     "img_file = os.path.join(directory, 'cantera', 'rxnpathC.png')\n",
     "ROP_C.title = 'Reaction path diagram following C'\n",
@@ -439,21 +434,14 @@
     "fullpath = os.getcwd() + '/' + img_file\n",
     "display(Image(fullpath))"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {
   "anaconda-cloud": {},
   "kernelspec": {
-   "display_name": "Python [conda env:rmg_env]",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
-   "name": "conda-env-rmg_env-py"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
@@ -465,9 +453,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.4"
+   "version": "3.9.23"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }