5. Add Simple Mesh Geometry

5.1. Tutorial Overview

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

5.2. 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.

5.2.1. 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

5.2.2. Add a Sphere

  • Click the Model Objects button to open the Model Objects panel
_images/add_icosphere_model_object1.png

When you create new objects, Blender will place them at the location of the 3D cursor (cursor3d). To create a new sphere object at the origin, be sure to center the 3D cursor in all 3 dimensions. The Model Objects panel includes a convenient button for that purpose:

_images/add_icosphere_model_object2.png
  • With the cursor centered, click the icosphere button to create a new icosphere at the 3D cursor location
_images/add_icosphere_model_object3.png
  • The Add Ico Sphere options panel will 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

5.2.3. Add the new Sphere to the Model Objects

  • 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 (may originally show "Solid").
_images/model_objects.png

5.2.4. Release Molecules inside Sphere

  • Click the Molecule Placement button
  • Select Release_Site_1 (should already be selected)
  • Change Release Shape to Object/Region
  • Type "Icosphere" in the Object/Region field
  • Change Quantity to Release to 1000
_images/sphere_release.png

5.2.5. Simulate the Model

  • Click the Run Simulation button
./images/single_molecule/run_sim_button.png
  • Click the Export & 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/single_molecule/reload_viz_data.png

5.2.6. View the Results

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

5.2.7. Save Your File

  • File > Save