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” (play) button below the time line

_images/150_iters.png _images/750_iters.png
  • Stop the simulation by clicking the “Pause” (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.

_images/plot2.png _images/plot3.png

5.2.8. Save Your File

  • File > Save