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 Single Molecule Diffusion. Either complete that tutorial yourself or use the single_molecule.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 a Sphere¶
Click the Model Objects button to open the Model Objects panel
When you create new objects, Blender will place them at the location of the 3D cursor (). 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:
With the cursor centered, click the icosphere button to create a new icosphere at the 3D cursor location
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.
4.2.3. Add the new Sphere to the Model Objects¶
Click the “plus” sign (+) to the right of the Model Objects box
Expand the Icosphere Object Options panel
Select Wire from the drop-down menu (may originally show “Solid”).
4.2.4. 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 100
4.2.5. Simulate the Model¶
Click the Run Simulation button
Click the Export & Run button
Wait for the simulation to complete
Press the “Reload Visualization Data” button to load the results of the simulation.
4.2.6. View the Results¶
Press the “Play” () button below the time line
4.2.7. Save Your File¶
File > Save