Update ipython show case

Major fixes: 1. domain function now returns 3 objects. Add 'p' to the LHS of the equation; 2. the original superminimal model raises error when generating the ideal gas object. Replace with the superminimal model in RMS.jl; 3. Add few more instructions to the notebook.

Author: xiaoruiDong

Ipython/pyrms example.ipynb

@@ -1,123 +1,195 @@
 {
  "cells": [
+  {
+   "cell_type": "markdown",
+   "source": [
+    "## 0. Package Loading"
+   ],
+   "metadata": {}
+  },
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
-   "outputs": [],
    "source": [
     "from diffeqpy import de\n",
     "from pyrms import rms\n",
     "from matplotlib import pyplot as plt\n",
     "%matplotlib inline"
-   ]
+   ],
+   "outputs": [],
+   "metadata": {}
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "## 1. Read input file\n",
+    "\n",
+    "An example of H2 combustion is included."
+   ],
+   "metadata": {}
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
-   "outputs": [],
    "source": [
     "phaseDict = rms.readinput(\"../pyrms/testing/superminimal.rms\")"
-   ]
+   ],
+   "outputs": [],
+   "metadata": {}
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
-   "outputs": [],
    "source": [
-    "spcs = phaseDict[\"gas\"][\"Species\"]\n",
-    "rxns = phaseDict[\"gas\"][\"Reactions\"]"
-   ]
+    "spcs = phaseDict[\"phase\"][\"Species\"]\n",
+    "rxns = phaseDict[\"phase\"][\"Reactions\"]"
+   ],
+   "outputs": [],
+   "metadata": {}
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "source": [
+    "ig = rms.IdealGas(spcs, rxns, name=\"phase\")"
+   ],
    "outputs": [],
+   "metadata": {}
+  },
+  {
+   "cell_type": "markdown",
    "source": [
-    "ig = rms.IdealGas(spcs,rxns,name=\"gas\")"
-   ]
+    "## 2. Define initial condition and domain\n",
+    "An example of constant TP domain is shown, where initial T, p, and composition is required."
+   ],
+   "metadata": {}
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
-   "outputs": [],
    "source": [
-    "initialconds = {\"T\":1000.0,\"P\":10.0e5,\"H2\":2.0,\"O2\":1.0}"
-   ]
+    "initialconds = {\"T\": 1000.0, \"P\": 10.0e5, \"H2\": 2.0, \"O2\": 1.0}"
+   ],
+   "outputs": [],
+   "metadata": {}
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "source": [
+    "domain, y0, p = rms.ConstantTPDomain(phase=ig, initialconds=initialconds)"
+   ],
    "outputs": [],
+   "metadata": {}
+  },
+  {
+   "cell_type": "markdown",
    "source": [
-    "domain,y0 = rms.ConstantTPDomain(phase=ig,initialconds=initialconds)"
-   ]
+    "## 3. Construct the reactor instance and simulate the system\n",
+    "input"
+   ],
+   "metadata": {}
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
-   "outputs": [],
    "source": [
-    "react = rms.Reactor(domain,y0,(0.0,10.001))"
-   ]
+    "tf = 10.001\n",
+    "solver = de.CVODE_BDF()\n",
+    "abstol=1e-20\n",
+    "reltol=1e-8"
+   ],
+   "outputs": [],
+   "metadata": {}
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "source": [
+    "react = rms.Reactor(domain, y0, (0.0, tf))"
+   ],
    "outputs": [],
+   "metadata": {}
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
    "source": [
-    "sol = de.solve(react.ode,de.CVODE_BDF(),abstol=1e-20,reltol=1e-8)"
-   ]
+    "sol = de.solve(react.ode, solver, abstol=abstol, reltol=reltol)"
+   ],
+   "outputs": [],
+   "metadata": {}
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "source": [
+    "sim = rms.Simulation(sol, domain)"
+   ],
    "outputs": [],
+   "metadata": {}
+  },
+  {
+   "cell_type": "markdown",
    "source": [
-    "sim = rms.Simulation(sol,domain)"
-   ]
+    "## 4. Results"
+   ],
+   "metadata": {}
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "Mole fraction"
+   ],
+   "metadata": {}
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "source": [
+    "rms.plotmolefractions(sim, 10.0)"
+   ],
    "outputs": [],
+   "metadata": {}
+  },
+  {
+   "cell_type": "markdown",
    "source": [
-    "rms.plotmolefractions(sim,10.0)"
-   ]
+    "ROP"
+   ],
+   "metadata": {}
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "source": [
+    "rms.plotrops(sim, \"OH(D)\", 1.0, N=10)"
+   ],
    "outputs": [],
+   "metadata": {}
+  },
+  {
+   "cell_type": "markdown",
    "source": [
-    "rms.plotrops(sim,\"OH(D)\",1.0,N=10)"
-   ]
+    "Flux Diagram"
+   ],
+   "metadata": {}
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
-   "outputs": [],
    "source": [
-    "rms.getfluxdiagram(sim,1.0)"
-   ]
+    "rms.getfluxdiagram(sim, 1.0)"
+   ],
+   "outputs": [],
+   "metadata": {}
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "source": [],
    "outputs": [],
-   "source": []
+   "metadata": {}
   }
  ],
  "metadata": {
@@ -141,4 +213,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 2
-}
+}