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DynGeoTest

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Bob Kuczewski edited this page Nov 18, 2015 · 12 revisions

Overview of Dynamic Geometry Test:

The Dynamic Geometry Test uses the "Capsule Test" addon to generate dynamic geometry for an expanding and dividing capsule. The "Capsule Test" addon supports a number of settings to control the geometry and growth of the capsule. The "Capsule Test" addon also contains some controls to support integration with CellBlender.

The Capsule Test addon performs the following tasks:

  • Draws geometry in the 3D view based on the settings provided
  • Exports the dynamic geometry as a series of MDL files
  • Updates the MDL of the current project to use the dynamic geometry files
  • Can read and display dynamic geometry from generated MDL files

Steps to Run the Dynamic Geometry Test:

  • Start Blender with Factory Settings (may need to save startup and restart)
  • Delete everything from the Scene (a,a,x,Delete)
  • Enable CellBlender and Capsule Test Addons
  • Open CellBlender tab, Initialize CellBlender, Expand the panel
  • Open the "Growing Capsule" Tab (beside CellBlender)
  • Disable "Freeze Geometry" (defaulted to frozen to minimize interference)
  • Check the "Use CellBlender Data" box to get iterations from CellBlender
  • Drag the time line to watch the geometry change
  • Zoom in on object and right click to select it (outlined in orange)
  • When selected, set the Maximum Draw Type to "Wire" (easier to see molecules)
  • You can change Geometry Settings here, but leave as is the first time
  • Save the .blend file somewhere to start a new project (File / SaveAs)
  • Begin building your CellBlender project with the Model Objects Panel
  • With the capsule selected, click the "+" button to add it to the model objects
  • Add volume and surface molecules to the model and release them in and on the capsule
    • Add molecules "v" (Volume 1e-5) and "s" (Surface 1e-4)
    • Release 1000 of each on Object/Region "capsule"
  • Open the Preferences panel and "Set Path to MCell Binary" to dynamic geometry mcell
  • Open the "Run" panel and expand the Output/Control Options subpanel
  • Check the "Decouple Export and Run" button so you can export and run separately
  • Set the time on the timeline to zero (0) so your geometry.mdl file will start there
  • Click the Export CellBlender Project button to export all of your static MDL
  • Open the Growing Capsule tab again
  • Click on Generate Dynamic Geometry MDL and wait for the button to return
    • Note that this may take some time while it's generating the MDL for 1000 frames
  • When the button returns, Click on the "Show MDL Geometry" button
  • Drag the cursor in the timeline to see the Dynamic MDL changing (this is reading MDL)
  • Click the "Update MDL Files" button to insert Dynamic Geometry commands in the static MDL
  • Return to the CellBlender tab and the Run Simulation panel
  • Click the "Run" button and wait while MCell runs the simulation for 1000 steps
  • When done, click the "Reload Visualization Data" button
  • Then drag the cursor through the time line and watch the dynamic geometry simulation
  • Try changing the molecule size, shape, and color in the Molecule Display Options panel
  • The procedure for changing the MCell simulation (not geometry) is:
    • Change the model (molecules, reactions, plots, etc)
    • Set the time to zero to export the original geometry file
    • "Export CellBlender Project" in the CellBlender Run Simulation Panel
    • "Update MDL Files" in the Growing Capsule tab
    • Run the simulation and reload the visualization data
  • The procedure for changing the geometry is very similar:
    • Change values in the Growing Capsule panel and check with timeline
    • Set the time to zero to export the original geometry file
    • "Export CellBlender Project" in the CellBlender Run Simulation Panel
    • "Update MDL Files" in the Growing Capsule tab
    • Run the simulation and reload the visualization data
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