diff --git a/Ipython/pyrms example.ipynb b/Ipython/pyrms example.ipynb
index c47e5f1..2bdd438 100644
--- a/Ipython/pyrms example.ipynb	
+++ b/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\", 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
-}
+}
\ No newline at end of file
diff --git a/pyrms/testing/superminimal.rms b/pyrms/testing/superminimal.rms
index 290ee61..d3b47c1 100644
--- a/pyrms/testing/superminimal.rms
+++ b/pyrms/testing/superminimal.rms
@@ -1,260 +1,288 @@
 Phases:
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-      Species:
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-        type: Species
-        smiles: '[Ar]'
-        thermo:
-          polys:
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-            Tmin: 200.0
-            coefs: [0.0, 0.0, 2.5, 0.0, 0.0, 0.0, 0.0, -745.375, 4.37967]
-            type: NASApolynomial
-          - Tmax: 6000.0
-            Tmin: 1000.0
-            coefs: [0.0, 0.0, 2.5, 0.0, 0.0, 0.0, 0.0, -745.375, 4.37967]
-            type: NASApolynomial
-          type: NASA
-      - name: He
-        type: Species
-        smiles: '[He]'
-        thermo:
-          polys:
-          - Tmax: 1000.0
-            Tmin: 200.0
-            coefs: [0.0, 0.0, 2.5, 0.0, 0.0, 0.0, 0.0, -745.375, 0.928724]
-            type: NASApolynomial
-          - Tmax: 6000.0
-            Tmin: 1000.0
-            coefs: [0.0, 0.0, 2.5, 0.0, 0.0, 0.0, 0.0, -745.375, 0.928724]
-            type: NASApolynomial
-          type: NASA
-      - name: Ne
-        type: Species
-        smiles: '[Ne]'
-        thermo:
-          polys:
-          - Tmax: 1000.0
-            Tmin: 200.0
-            coefs: [0.0, 0.0, 2.5, 0.0, 0.0, 0.0, 0.0, -745.375, 3.35532]
-            type: NASApolynomial
-          - Tmax: 6000.0
-            Tmin: 1000.0
-            coefs: [0.0, 0.0, 2.5, 0.0, 0.0, 0.0, 0.0, -745.375, 3.35532]
-            type: NASApolynomial
-          type: NASA
-      - name: N2
-        type: Species
-        smiles: N#N
-        thermo:
-          polys:
-          - Tmax: 1000.0
-            Tmin: 200.0
-            coefs: [0.0, 0.0, 3.53101, -0.000123661, -5.02999e-07, 2.43531e-09, -1.40881e-12,
-              -1046.98, 2.96747]
-            type: NASApolynomial
-          - Tmax: 6000.0
-            Tmin: 1000.0
-            coefs: [0.0, 0.0, 2.95258, 0.0013969, -4.92632e-07, 7.8601e-11, -4.60755e-15,
-              -923.949, 5.87189]
-            type: NASApolynomial
-          type: NASA
-      - name: H2
-        type: Species
-        smiles: '[H][H]'
-        thermo:
-          polys:
-          - Tmax: 1959.07
-            Tmin: 100.0
-            coefs: [0.0, 0.0, 3.43536401, 0.000212711277, -2.78627139e-07, 3.40268811e-10,
-              -7.76036069e-14, -1031.35983, -3.90841691]
-            type: NASApolynomial
-          - Tmax: 5000.0
-            Tmin: 1959.07
-            coefs: [0.0, 0.0, 2.78817696, 0.000587626487, 1.59017184e-07, -5.52752608e-11,
-              4.34320884e-15, -596.150834, 0.112666705]
-            type: NASApolynomial
-          type: NASA
-      - name: O2
-        type: Species
-        smiles: '[O][O]'
-        thermo:
-          polys:
-          - Tmax: 1074.56
-            Tmin: 100.0
-            coefs: [0.0, 0.0, 3.53732181, -0.00121570933, 5.31617835e-06, -4.89443434e-09,
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-            type: NASApolynomial
-          - Tmax: 5000.0
-            Tmin: 1074.56
-            coefs: [0.0, 0.0, 3.15382424, 0.00167803804, -7.69971033e-07, 1.51274717e-10,
-              -1.08781803e-14, -1040.81878, 6.16753891]
-            type: NASApolynomial
-          type: NASA
-      - name: H
-        type: Species
-        smiles: '[H]'
-        thermo:
-          polys:
-          - Tmax: 4484.82
-            Tmin: 100.0
-            coefs: [0.0, 0.0, 2.5, -1.08860897e-13, 1.40734568e-16, -5.92258814e-20, 7.66587112e-24,
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-            type: NASApolynomial
-          - Tmax: 5000.0
-            Tmin: 4484.82
-            coefs: [0.0, 0.0, 2.50003916, -3.40586045e-08, 1.10996924e-11, -1.60664106e-15,
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-            type: NASApolynomial
-          type: NASA
-      - name: '[O]O'
-        type: Species
-        smiles: '[O]O'
-        thermo:
-          polys:
-          - Tmax: 932.15
-            Tmin: 100.0
-            coefs: [0.0, 0.0, 4.04594466, -0.00173464517, 1.03766421e-05, -1.02202388e-08,
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-            type: NASApolynomial
-          - Tmax: 5000.0
-            Tmin: 932.15
-            coefs: [0.0, 0.0, 3.21023922, 0.00367941878, -1.27701506e-06, 2.18045101e-10,
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-            type: NASApolynomial
-          type: NASA
-      - name: OH(D)
-        type: Species
-        smiles: '[OH]'
-        thermo:
-          polys:
-          - Tmax: 1145.74
-            Tmin: 100.0
-            coefs: [0.0, 0.0, 3.51456708, 2.9288145e-05, -5.32198348e-07, 1.01953157e-09,
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-          - Tmax: 5000.0
-            Tmin: 1145.74
-            coefs: [0.0, 0.0, 3.07194683, 0.000604004352, -1.39719923e-08, -2.13460568e-11,
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-            type: NASApolynomial
-          type: NASA
-      - name: O(T)
-        type: Species
-        smiles: '[O]'
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-          type: NASA
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+    radicalelectrons: 0
+    smiles: '[Ar]'
+    thermo:
+      polys:
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+        Tmin: 200.0
+        coefs: [2.5, 0.0, 0.0, 0.0, 0.0, -745.375, 4.37967]
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+      type: NASA
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+    smiles: '[O]'
+    thermo:
+      polys:
+      - Tmax: 4879.8
+        Tmin: 100.0
+        coefs: [2.5, -3.01680531e-12, 3.74582141e-15, -1.50856878e-18, 1.86626471e-22,
+          29230.2441, 4.09104286]
+        type: NASApolynomial
+      - Tmax: 5000.0
+        Tmin: 4879.8
+        coefs: [4.28461071, -0.00145494649, 4.44804306e-07, -6.04359642e-11, 3.07921551e-15,
+          27479.1187, -7.35711496]
+        type: NASApolynomial
+      type: NASA
+    type: Species
+  name: phase
 Reactions:
-- products: [H2]
+- kinetics: {A: 54500.00000000001, Ea: 6276.0, n: 0.0, type: Arrhenius}
+  products: [H2]
+  radicalchange: -2
   reactants: [H, H]
-  kinetics: {A: 54500.00000000001, Ea: 6276.0, n: 0.0, type: Arrhenius}
   type: ElementaryReaction
-- products: ['[O]O', H]
-  reactants: [O2, H2]
-  kinetics: {A: 290000000.00000006, Ea: 236981.76, n: 0.0, type: Arrhenius}
+- kinetics: {A: 290000000.00000006, Ea: 236981.76, n: 0.0, type: Arrhenius}
+  products: [HO2, H]
+  radicalchange: 2
+  reactants: [H2, O2]
   type: ElementaryReaction
-- products: ['[O]O']
+- kinetics: {A: 87900.00000000001, Ea: 1882.8, n: 1.0, type: Arrhenius}
+  products: [HO2]
+  radicalchange: 0
   reactants: [O2, H]
-  kinetics: {A: 87900.00000000001, Ea: 1882.8, n: 1.0, type: Arrhenius}
   type: ElementaryReaction
-- products: [H2, '[O]O']
-  reactants: [H, OO]
-  kinetics: {A: 1.2350200000000002, Ea: 25463.824, n: 1.634, type: Arrhenius}
+- kinetics: {A: 1.2350200000000002, Ea: 25463.824, n: 1.634, type: Arrhenius}
+  products: [H2, HO2]
+  radicalchange: 0
+  reactants: [H, H2O2]
   type: ElementaryReaction
-- products: [OO]
-  reactants: ['[O]O', H]
-  kinetics: {A: 5005182.000000001, Ea: 7096.063999999999, n: 0.282, type: Arrhenius}
+- kinetics: {A: 5005182.000000001, Ea: 7096.063999999999, n: 0.282, type: Arrhenius}
+  products: [H2O2]
+  radicalchange: -2
+  reactants: [HO2, H]
   type: ElementaryReaction
-- products: [O2, OO]
-  reactants: ['[O]O', '[O]O']
-  kinetics: {A: 17500.000000000004, Ea: -13702.6, n: 0.0, type: Arrhenius}
+- kinetics: {A: 17500.000000000004, Ea: -13702.6, n: 0.0, type: Arrhenius}
+  products: [O2, H2O2]
+  radicalchange: -2
+  reactants: [HO2, HO2]
   type: ElementaryReaction
-- products: [OO]
-  reactants: [OH(D), OH(D)]
-  kinetics: {A: 7850000.000000001, Ea: 0.0, n: 0.0, type: Arrhenius}
+- kinetics: {A: 7850000.000000001, Ea: 0.0, n: 0.0, type: Arrhenius}
+  products: [H2O2]
+  radicalchange: -2
+  reactants: [OH, OH]
   type: ElementaryReaction
-- products: [H, H2O]
-  reactants: [H2, OH(D)]
-  kinetics: {A: 1820.0000000000002, Ea: 83972.88, n: 1.21, type: Arrhenius}
+- kinetics: {A: 1820.0000000000002, Ea: 83972.88, n: 1.21, type: Arrhenius}
+  products: [H, H2O]
+  radicalchange: 0
+  reactants: [H2, OH]
   type: ElementaryReaction
-- products: [H2O]
-  reactants: [H, OH(D)]
-  kinetics: {A: 162000000.00000003, Ea: 627.6, n: 0.0, type: Arrhenius}
+- kinetics: {A: 162000000.00000003, Ea: 627.6, n: 0.0, type: Arrhenius}
+  products: [H2O]
+  radicalchange: -2
+  reactants: [OH, H]
   type: ElementaryReaction
-- products: ['[O]O', OH(D)]
+- kinetics: {A: 9300000.000000002, Ea: 310118.08, n: 0.0, type: Arrhenius}
+  products: [HO2, OH]
+  radicalchange: 2
   reactants: [O2, H2O]
-  kinetics: {A: 9300000.000000002, Ea: 310118.08, n: 0.0, type: Arrhenius}
   type: ElementaryReaction
-- products: ['[O]O', H2O]
-  reactants: [OH(D), OO]
-  kinetics: {A: 0.4994995000000001, Ea: 26463.8, n: 1.927, type: Arrhenius}
+- kinetics: {A: 0.4994995000000001, Ea: 26463.8, n: 1.927, type: Arrhenius}
+  products: [HO2, H2O]
+  radicalchange: 0
+  reactants: [OH, H2O2]
   type: ElementaryReaction
-- products: ['[O]O']
-  reactants: [OH(D), O(T)]
-  kinetics: {A: 43.58386000000001, Ea: 5167.240000000001, n: 1.88, type: Arrhenius}
+- kinetics: {A: 43.58386000000001, Ea: 5167.240000000001, n: 1.88, type: Arrhenius}
+  products: [HO2]
+  radicalchange: -2
+  reactants: [OH, O(T)]
   type: ElementaryReaction
-- products: [OH(D)]
+- kinetics: {A: 10000000.000000002, Ea: 0.0, n: 0.0, type: Arrhenius}
+  products: [OH]
+  radicalchange: -2
   reactants: [H, O(T)]
-  kinetics: {A: 10000000.000000002, Ea: 0.0, n: 0.0, type: Arrhenius}
   type: ElementaryReaction
-- products: [O2, OH(D)]
-  reactants: ['[O]O', O(T)]
-  kinetics: {A: 3680.3920000000007, Ea: 24681.416, n: 0.678, type: Arrhenius}
+- kinetics: {A: 3680.3920000000007, Ea: 24681.416, n: 0.678, type: Arrhenius}
+  products: [O2, OH]
+  radicalchange: -2
+  reactants: [HO2, O(T)]
   type: ElementaryReaction
-- products: [H, OH(D)]
+- kinetics: {A: 340.00000000000006, Ea: 96022.8, n: 1.5, type: Arrhenius}
+  products: [OH, H]
+  radicalchange: 0
   reactants: [H2, O(T)]
-  kinetics: {A: 340.00000000000006, Ea: 96022.8, n: 1.5, type: Arrhenius}
   type: ElementaryReaction
-- products: ['[O]O', OH(D)]
-  reactants: [O(T), OO]
-  kinetics: {A: 17400000.000000004, Ea: 19874.0, n: 0.0, type: Arrhenius}
+- kinetics: {A: 17400000.000000004, Ea: 19874.0, n: 0.0, type: Arrhenius}
+  products: [HO2, OH]
+  radicalchange: 0
+  reactants: [H2O2, O(T)]
   type: ElementaryReaction
-- products: [OH(D), OH(D)]
-  reactants: [O(T), H2O]
-  kinetics: {A: 5260.000000000001, Ea: 74600.71999999999, n: 1.2, type: Arrhenius}
+- kinetics: {A: 5260.000000000001, Ea: 74600.71999999999, n: 1.2, type: Arrhenius}
+  products: [OH, OH]
+  radicalchange: 0
+  reactants: [H2O, O(T)]
   type: ElementaryReaction
 Units: {}