14.3. Parameters

14.3.1. Overview

  • The parameter system is used to create cellblender variables. They’re just like normal programming variables such that one variable is used for multiple objects and is user defined. This tutorial will run through a basic molecule simulation using the Sweeping Parameter feature.

    • The inital Parameter setup, the expression can be set to either a value or a math expression. You can also enable sweeping expressions that go through a series of values (1:10 goes through the values 1 to 10). The Units and Description are user defined for better variable organizing.

      _images/parameter_init.png
  • Select the Parameter button.

    _images/parameters_panel_h.png
  • Create a new parameter, and press the Enable Sweep button.

    _images/parameters_create.png
  • Different options

    • Name the parameter var.

    • Set the sweep expression to 1e-6,1e-7,1e-8.

    _images/parameters_set.png
  • Create a molecule.

    • Name the molecule mol_1 and set the Diffusion Const to the parameter var.

    _images/parameters_molecule.png
  • Create a release site for the molecule you just created.

    • Keep the name Release_site_1.

    • Use mol_1.

    • Set the Quanity to release to 1000.

    _images/parameter_molecule_place.png
  • Set up the simulation.

    • Click on the Output/Control Options and click on the Mcell via Queue Runne drop down.

      _images/parameter_sim.png
    • Set the simulation to MCell via Sweep runner.

      _images/parameter_sweep_runner.png
    • The final product should look something like the following, with the simulation going through the different Diffusion Constants in the same run.

    _images/parameter_molecule_clump.png