add_meshgeom.rst

Add Simple Mesh Geometry

Tutorial Overview

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

Initial Configuration

This tutorial builds upon what was done in :ref:`single_molecule_diffusion`. Either complete that tutorial yourself or use the single_molecule.blend file to get started.

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

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.

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").

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

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.

View the Results

• Press the "Play" () button below the time line

Save Your File

• File > Save