5. Unimolecular Reactions¶
5.1. Tutorial Overview¶
This tutorial will define a single unimolecular reaction.
5.2. Initial Configuration¶
This tutorial builds upon what was done in Add Simple Mesh Geometry. Either complete that tutorial yourself or use the add_meshgeom.blend file to get started.
5.2.1. Save the File with a New Name in Your Working Directory¶
Select File > Save As…
Change single_molecule.blend to unimol_reactions.blend
Click Save As Blender File button
5.2.2. Define a Reaction¶
Click the Reactions button.

Click the “plus” sign (+) to the right of the Defined Reactions box
Type a in the Reactants text field
Type NULL (all upper case) in the Products text field
Type 5e3 in the Forward Rate text field

5.2.3. Release More Molecules¶
Click the Molecule Placement button
Change the Quantity to Release to 1000

5.2.4. Define Reaction Data to be Saved for Plotting¶
Click the Plot Output Settings button

Click the “plus” sign (+) to the right of the Reaction Data Output box
Ignore the error which indicates an incomplete definition at this time
Select a from the Molecule selector (should clear the error)

Note the descriptive item “Count a in World” in the list
5.2.5. Simulate the Model¶
Click the Run Simulation button to return to the Run Simulation panel

Click the Export & Run button

Wait for the simulation to complete
Press the “Reload Visualization Data” button to load the results of the simulation.

5.2.6. Use the Time Line¶
Press the “Play” (
) button below the time line


Stop the simulation by clicking the “Pause” (
) button below the time line
Click (or Click-and-Drag) in the time line to view the simulation at different points in time
5.2.7. Plot the Reaction Data¶
Click the Plot Output Settings button
Select MatPlotLib Plotter from the plotter drop-down list if it’s available.
Click the Plot button.


5.2.8. Save Your File¶
File > Save