A Quick Tutorial - A Single Reactor Scheme

In this tutorial, you will learn to:

  • Create a single reactor reaction scheme
  • Edit the reaction scheme
  • Enter the reaction conditions
  • Set the simulator parameters
  • Run the simulation
  • Display the simulation results
  • Export the simulation results for further analysis

This section leads you through the procedure for simulating a chemical reaction in a homogeneous volume. If you've never used Kinetiscope before, this tutorial will help you become familiar with Kinetiscope's different menus and functions.

Thermal Decomposition of Ozone

The thermal decomposition of ozone is a classic gas phase system whose mechanism has been thoroughly investigated. One of its interesting features is that sufficient energy can be released during its decomposition to trigger an explosion, characterized by formation of large quantities of atomic oxygen, and a rapid increase in system temperature and pressure.

The reaction proceeds as follows:

O3 → O2 + O
O + O3 → 2 O2
2 O + O2 → 2 O2
O + 2 O2 → O3 + O2

If there is a large excess of O2 initially present, and the decomposition of O3 proceeds monotonically, the steady-state approximation can be used to obtain an analytic rate law for the kinetics.

Creating a New Reaction Scheme

You will next create a new reaction scheme based on a single reactor model and save it as a file named tutorial1.rxn.

When you first create a single reactor reaction scheme, you specify the type of model and select the concentration, time, pressure, and energy units to be used throughout. When you later save your input, you specify its file name and the directory where it will be stored.

To create the reaction scheme:

  1. Select File | New Scheme | Single Reactor Model... from the menu bar of Kinetiscope's main window,
    click the push button on the main window's tool bar.

    A Select Units Dialog appears.

  2. Select the following units for time, energy, concentration and pressure using the drop-down list boxes on the first page: sec, kcal, mole/liter, atm.

    Make the selections by clicking the left mouse button on the drop-down list boxes and then clicking on the appropriate entry.

    The dialog should look like this:

  3. Click OK.

    A new, empty single reactor scheme window appears.

This is the only time that the units for a particular file can be specified. The units that are selected here must be used consistently for all input data, and are used for plotting the simulation results.

Entering the Reaction Mechanism

You have now returned to Kinetiscope's main window, where a new scheme window named untitled1 - single reactor model has been created. You are ready to enter the reaction mechanism.

To enter the reaction steps:

  1. Select the Scheme tab on the scheme window.
  2. Click the (Add a reaction step) push button.

    The Reaction Step Editor Dialog that appears is used to enter your reaction mechanism. Later, you may also edit previously entered mechanisms from this dialog. The individual reaction equations are entered much as you would write them on a piece of paper. The generalized format for a non-reversible reaction is:

    x A + y B + z C => w D + v E

    where x, y, z, w, and v are stoichiometric coefficients, and A, B, C, D and E are mnemonics that you choose for the various reactants and products. You must separate coefficients from their species mnemonic by a blank space. Also note that the right arrow is typed in as => using the characters "equals" "greater than" (with no spaces between them). For more on entering the reaction equation, see the detailed discussion in the section entitled Entering the Equation.

  3. Type the first reaction equation in the Equation data entry field:

    O3 => O2 + O

  4. Beneath the Equation data entry field are two drop-down list boxes for specifying additional data options. Using the upper list box you specify whether the rate constant of the current reaction step will be entered in either temperature dependent or independent form. Kinetiscope's default setting is the temperature independent form, where the rate constant is specified as a single value in the scheme's pre-selected units. Temperature dependent rate constants are entered in Arrhenius form. The general Arrhenius form is:

    k  = A Tm e-Ea/RT (1)

    where A is the pre-exponential A factor, m is the temperature exponent, Ea is the activation energy, R is the gas constant and T is the absolute temperature.

    You will enter the rate constant for this reaction in Arrhenius form.

  5. Use the mouse to select Temperature-dependent in the drop-down list box in the Rate Constants area.

    A set of data entry fields for specifying the three Arrhenius parameters are shown. Here you will enter the A, m and Ea values for this reaction step. Only the Forward data entry fields are active because the reaction step is not reversible.

  6. Type in the following values in the three Forward data entry fields:
    Prefactor A 1.0e13
    Temperature exponent m 0.0
    Activation energy Ea 25.0

    The lower drop-down list box is used to specify how the rate of the reaction step is to be calculated. When the rate law corresponds directly to the reaction step as written, the simulator can derive it from the stoichiometry of the reaction step. Under circumstances when it differs from the stoichiometry, you may modify the rate law by setting the list box to User-defined rate law. Selecting this option displays and activates the (Edit the rate law expression) pushbutton. Kinetiscope's default behavior is to derive the rate from the stoichiometry of the reaction step. For more on this, see the section entitled Entering the Rate Law.

  7. Select the Derived from stoichiometry option from the drop-down list box in the Rate Laws area..

    You have now completed entering the data for the first reaction step. The window should look like this:

  8. Click OK.

    This will return you to the untitled1 - single reactor model scheme window.

  9. Repeat steps 2-7 twice more, adding the following reaction steps:

    Equation O + O3 => 2 O2
    Prefactor A 1.0e10
    Temperature exponent m 0.0
    Activation energy Ea 5.0
    Rate Laws derived from stoichiometry
    Equation O + O2 => 2 O2
    Prefactor A 1.0e9
    Temperature exponent m -1.5
    Activation energy Ea 0.0
    Rate Laws derived from stoichiometry

Saving your Reaction Scheme

As you modify your reaction scheme, remember to periodically save your changes. This will help prevent accidental loss of data.

To save the reaction scheme as a file:

  1. Select File | Save As... from the menu bar of Kinetiscope's main window
    Click the push button on the main window's tool bar.

    A File Save Dialog appears.

  2. Use the dialog to navigate to the directory you have selected for your files, and enter the name tutorial1.
  3. Click the Save push button on the File Save Dialog.

If you make an undesired change (for example, accidentally delete a step), you now can recover by selecting File | Revert to Saved... from the menu bar of Kinetiscope's main window, or clicking the push button on the main window's tool bar.

Editing your Reaction Scheme

As you look at your reaction list, you realize that you have to make two changes!

  • The stoichiometric coefficient for species O in Reaction Step 3 should be 2, not 1, and
  • You have left out Reaction Step 4. (see the Example Simulation Thermal Decomposition of Ozone (I) ).
You must edit your reaction scheme.

To make changes to Reaction Step 3:
  1. Double-click the left mouse button on Reaction Step 3 in the scheme window's reaction list.

    You may also edit this step by clicking on it once to highlight it, and then clicking the (Edit reaction step) button on the scheme window's tool bar.

    Either action opens the Reaction Step Editor Dialog.

  2. Add the coefficient of 2 in front of O.

    Your Reaction Step 3 should now read:

    2 O + O2 => 2 O2 .

    The rest of the data in this window are correct.

  3. Click OK.

Cutting and Pasting Reaction Steps

You now wish to add Step 4 to this reaction scheme. You will load the example reaction scheme file Ozone.rxn into Kinetiscope's active memory, copy Step 4 onto Kinetiscope's internal clipboard, and paste it into the reaction scheme you are currently building.

To copy and paste Reaction Step 4:
  1. Select File|Open Examples... .
  2. Use the File Open Dialog that appears to select Ozone.rxn from the examples directory.
  3. Click the Open push button on the File Open Dialog.

    You return to the the main window, where the Ozone.rxn reaction scheme has been loaded and is now displayed as a separate scheme window.

  4. Click the Scheme tab on the Ozone.rxn scheme window and highlight Step 4 by clicking once with the left mouse button.
  5. Click the (Copy the selected step) button on the tool bar of the Ozone.rxn scheme window.

    The reaction step is copied onto Kinetiscope's clipboard, and is ready to be pasted.

  6. Click on the tutorial1.rxn scheme window to make your scheme active.
  7. Click the left mouse button once on Step 3 to select it.
  8. Click the (Paste a step) button on the tool bar of the tutorial1.rxn scheme window.

    The reaction step on the clipboard and its accompanying rate constant and rate law data are added to your reaction scheme afterr Reaction Step 3.

    Any initial concentration or species data for reaction species involved in this step must be entered manually.

The complete reaction mechanism is now displayed in the scheme window:

Note: You may save your changes by clicking the (Save) push button on the main window's tool bar.

Entering the Reaction Conditions

You may now set the simulation conditions, including the temperature, pressure and volume of the reacting system and the species concentrations.

Combinations of pressure, volume and temperature conditions can be chosen using the drop-down list boxes on the Reaction Conditions Page. Not all combinations of them are allowed (or physically meaningful). Kinetiscope will display an error message if an unsupported combination is selected. By default, volume, pressure and temperature are all set to be constant. The temperature options allow you to simulate reactions under constant or variable temperature, or temperature which follows either a linear program or an external profile. The current parameters for each option are displayed with it.

You will simulate the decomposition of ozone at variable temperature, with an initial temperature of 500 °K.

To set the reaction conditions:
  1. Click the Reaction Conditions tab.
  2. Select

    Volume is constant

    for the top left list box.

  3. Select

    Pressure is variable

    for the bottom left list box.

  4. Select

    Temperature is variable

    for the top right list box.

    This will display below the list boxes data entry fields for the Initial Temperature and the Temperature Convergence Standard.

  5. Type into these two data entry fields the values of

    500 °K


    0.5 °K,

    respectively. The window should now appear like this:

Setting Initial Concentrations and Species Properties

To enter or review the initial concentration of a particular reaction species, select the Species Data tab to view that page.

The initial concentration value for each species appears in the Initial Concentration data column. The units of concentration are those specified when you created the reaction scheme. The default value for the initial concentrations of all reaction species is 0.0. You will give O3 an initial concentration of 0.1 mole/l.

To set the initial concentration of O3:
  1. Double-click on the value in the Initial Concentration column in the row starting with Species O3.
  2. Type over the value 0.0 with the value 0.1 and press the Enter key.

When variable volume and/or variable temperature conditions are selected, you must supply Kinetiscope with more information for each species: physical state, density information, and/or thermochemical coefficients as needed. When variable temperature conditions are selected, you must supply heat capacities and enthalpies for all species in the reaction. You provide these inputs on the Species Data Page.

If temperature is variable, you must specify the thermochemical coefficients for every species in the system. Temperature changes are calculated iteratively from the change in the temperature-dependent enthalpy and heat capacity of the system as the reaction progresses. The expression for the change in enthalpy with temperature for each species is:

ΔHf (T)  = ΔH0 + a + bT + cT2 + dT3 (2)

where ΔH0 is the enthalpy in energy units, and the coefficients a, b, c and d are the temperature-dependent heat capacity in (energy units)/mol-degn, where energy can be in joules or kcals. In precise calculations, ΔH0 must be the enthalpy of formation at 0 K. If constant heat capacity is used, Cp=b and the coefficients a, c and d are explicitly set equal to zero.

If you are not using variable volume and/or variable temperature reaction conditions, this option is not active.

To enter species thermochemical data:
  1. Select the Species Data tab to show this page.

    All reaction species and their properties are listed in the table that appears. Thermochemical data for the each species are displayed in the data entry fields. The units used are those that you specified when you created this reaction file.

  2. Enter the following data for in the line for the O species:
    Enthalpy 59.0
    A 320.5
    B 5.072
    C -4.636e-5
    D -0.796e-8
    Enter the data for O2 and O3 in the same manner.
  3. Enter the following data for O2:
    Enthalpy 0.00
    A -296.9
    B 7.395
    C 0.4874e-3
    D 0.302e-7
  4. Enter the following data for O3:
    Enthalpy 34.0
    A 0.0
    B 9.0
    C 0.0
    D 0.0

Your screen should appear as follows:

Entering the Simulation Settings

A number of parameters must be specified to configure the simulator. These settings are listed in three groups: General Settings, which include the total number of particles representing molecules and the recording interval; Limits, which allow you to set stopping points for the simulation; and Equilibrium Detect, settings for the Kinetiscope equilibrium detection and emulation system. You access the simulation parameters on the Simulation Settings Page.

To enter the simulation settings:
  1. Select the Simulation Settings tab.
  2. Set the Total Number of Particles to


    This parameter specifies the initial number of particles in the simulation. They are apportioned among all species which have a nonzero initial concentration. The number should be large enough to accommodate the dynamic range of concentrations that will occur in the simulation. A larger number will also reduce stochastic noise. There is a trade-off between these benefits and the larger amount of computer time required to reach a given point in the simulation (see the Example Simulation Simulation Precision: Parallel Reactions ).

  3. Set the Record State at Intervals of to


  4. Set the Random Number Seed to


    The exact time calculated for the onset of an ozone explosion depends on the time required for a critical number of oxygen atoms to be formed in the system. Since this depends in turn on the details of event selection in Kinetiscope, some variation in time to explosion is expected for different random number seeds. For a more accurate estimate of the onset time, several runs using different random number seeds should be averaged. This applies to all reactions which involve chemical instabilities, or which depend on instantaneous fluctuations, including nucleation phenomena and phase changes.

    The next group of parameters control the limits of the simulation.

  5. Set the Maximum Number of Events to a value of

    2000 events.

    When this maximum is reached, the simulation will end, unless other termination conditions occur first.

  6. Set the Maximum time in Simulation to

    0.0 seconds.

    Setting this parameter to zero disables it. If it is set to a particular time, the simulation will stop when that elapsed time in the reaction is reached - unless other termination conditions occur first.

    The third set of simulation settings are the Equilibrium Detect settings. This is used for systems with reversible reactions steps which may come into equilibrium during a simulation. In the decomposition of ozone, however, there are no reversible steps, and this option is not used.

  7. Uncheck the box in the Equilibrium Detect area.

Your screen should now appear like this:

Running the Simulation

Now you are ready to run the simulation.

To start the simulation:

  1. Select the Scheme tab.
  2. Click the (Start a simulation) push button on the scheme window's tool bar.

    A Simulator Window opens that tells you that the simulation is running. You can track the reaction as it progresses, with this window displaying the internal elapsed time in the simulation, the number of events that have occurred, how long the simulation has been running, and the number of times the system state has been recorded for later analysis:

  3. Click the OK push button on the simulator window when the simulation completes.

    If you do not click OK, the window will close automatically after 5 seconds. When you return to the main window, the status display at the bottom of the scheme window now tells you that the simulation has finished, and the reason why the simulation stopped.

    Note: Kinetiscope automatically saves your reaction file with the new simulation results when the simulation is complete.

Viewing the Simulation Results

To view the results of the last simulation:

  1. Select the Scheme tab on the scheme window
  2. Click the (Create a new results window) push button on the scheme window's tool bar.

    The new window displays, as an initial default, a concentration-vs-time graph for all species defined in the scheme:

    This plot clearly shows that ozone suddenly and completely disappears under the selected reaction conditions. The kinetics of the explosion cannot be modelled using the steady-state approximation.

  3. You may zoom in to a specific range of the graph by pressing the left mouse button and drawing a rubber-band box around the region of interest.
  4. You may change the type of information displayed on the graph through the context menu that appears when the right mouse button is clicked.

    For example, select the Modify... action; on the Line Plot Settings Dialog that appears, check the Pressure/time and Temperature/time check boxes and then click OK. Two new graphs are added to the results window that show the rises in pressure and temperature at the moment of explosion.

Exporting Your Simulation Results

Kinetiscope can save the plot displayed in the results window in graphical format, as a Portable Network Graphics (PNG) file.

To export an image file of the results:
  1. Set the results window to appear as you want the image file to appear.

    An exact copy of the screen image will be saved.

  2. Click the right mouse button.

    A context menu appears.

  3. Select Export to Image File... from the context menu.

    A File Save Dialog appears.

  4. Use the File Save Dialog to choose a directory location and enter the file name.
  5. Click the Save push button on the File Save Dialog.

Kinetiscope can also create a text file which contains the plot data in tabular form. The file is saved in ASCII text format, with space-delimited entries, and will contain the simulation data that appears in the plot window.

To export the simulation results as text:
  1. Click the right mouse button.

    A context menu appears.

  2. Select Show in Text Format from the context menu.

    The results window converts to a scrollable text display of the simulation results shown in the graphs.

  3. From the text display view, click the right mouse button.

    A context menu appears.

  4. Select Export to Text File... from the context menu.

    A File Save Dialog appears.

  5. Use the File Save Dialog to choose a directory location and enter the file name.
  6. Click the Save push button on the File Save Dialog.

Next Steps

You have now completed this tutorial. You should now know the basics for simulating a single reactor reaction scheme using Kinetiscope.

Other tutorials lead you through the procedures for setting up other types of reaction systems:

  • In the Compartmental Reaction Scheme Tutorial, a simple compartmental reaction scheme that uses an external stimulus to control its kinetic behavior is constructed.
  • In the Three-dimensional Reaction Scheme Tutorial, a reaction scheme depicting acid catalyzed chemistry in a thin film is constructed. An externally generated concentration profile is used to set the initial composition.
  • In the Electrochemistry Tutorial, the steps you take to perform a simulation of a system containing electrochemical steps are detailed. This system uses an exponentially expanding grid of compartments.