4. Add Simple Mesh Geometry

4.1. Tutorial Overview

In this tutorial, a sphere will be added to the simulation around the diffusing molecules.

4.2. Initial Configuration

This tutorial builds upon what was done in Unimolecular Reactions. Either complete that tutorial yourself or use the unimol_reactions.blend file to get started.

4.2.1. Save the File with a New Name in Your Working Directory

  • Select File > Save As...
  • Change unimol_reactions.blend to add_meshgeom.blend
  • Click Save As Blender File button

4.2.2. Add Sphere

  • Click the Create tab
  • Hit the Ico Sphere button
_images/add_icosphere1.png
  • The Add Ico Sphere options appear in the lower left corner
  • Change Subdivisions to 3
  • Change Size to 0.5
  • Change each Location (X, Y, and Z) to 0.0 if it isn't set already.
_images/add_icosphere2.png

4.2.3. Add Sphere to Model Objects

  • Click the CellBlender tab
  • Click the Model Objects button
_images/model_objects_button.png
  • Click the "plus" sign (+) to the right of the Model Objects box
  • Expand the Icosphere Display Options panel
  • Select Wire from the drop-down menu.
_images/model_objects.png

4.2.4. Release Molecules inside Sphere

  • Click the Molecule Placement button
  • Select Release_Site
  • Change Release Shape to Object/Region
  • Type Icosphere in the Object/Region field
  • Change Quantity to Release to 1000
_images/sphere_release.png

4.2.5. Simulate the Model

  • Click the Run Simulation button
_images/run_sim_button.png
  • Click the Run button
_images/run_sim.png
  • Wait for the simulation to complete
  • Press the "Reload Visualization Data" button to load the results of the simulation.
_images/reload_viz_data.png

4.2.6. View the Results

  • Press the "Play" (play) button below the time line
_images/diffuse_in_sphere.png

4.2.7. Save Your File

  • File > Save