Maciej H. Swat, Julio Belmonte, Randy W. Heiland, Benjamin L. Zaitlen, James A. Glazier, Abbas Shirinifard




НазваниеMaciej H. Swat, Julio Belmonte, Randy W. Heiland, Benjamin L. Zaitlen, James A. Glazier, Abbas Shirinifard
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Equation Chapter 1 Section 1CompuCell3D Reference Manual

Version 3.6.2


Maciej H. Swat, Julio Belmonte, Randy W. Heiland, Benjamin L. Zaitlen, James A. Glazier, Abbas Shirinifard


Biocomplexity Institute and Department of Physics, Indiana University, 727 East 3rd Street, Bloomington IN, 47405-7105, USA



1CC3DML Syntax of CompuCell3D modules 3

1.1Potts Section 3

1.1.1Lattice Type 8

1.2Plugins Section 10

1.3CellType Plugin 10

1.4Simple Volume and Surface Constraints 11

1.5VolumeTracker and SurfaceTracker plugins 11

1.6VolumeFlex Plugin 12

1.7SurfaceFlex Plugin 12

1.8VolumeLocalFlex Plugin 13

1.9SurfaceLocalFlex Plugin 13

1.10NeighborTracker Plugin 13

1.11Chemotaxis 14

1.12ExternalPotential plugin 17

1.13CellOrientation Plugin 18

1.14PolarizationVector Plugin 19

1.15CenterOfMass Plugin 20

1.16Contact Energy 20

1.17ContactLocalProduct Plugin 21

1.18AdhesionFlex Plugin 23

1.19ContactMultiCad Plugin 25

1.20Compartmentalized cells. ContactInternal Plugin 26

1.21LengthConstraint Plugin 28

1.22Connectivity Plugins 30

1.23Mitosis Plugin 31

1.24Secretion Plugin 32

1.25 PDESolverCaller Plugin 34

1.26Elasticity Plugin and ElasticityTracker Plugin 34

1.27FocalPointPlasticity Plugin 36

1.28Curvature Plugin 39

1.29PlayerSettings Plugin 40

1.30BoundaryPixelTracker Plugin 42

1.31GlobalBoundaryPixelTracker 42

1.32PixelTracker Plugin 42

1.33MomentOfInertia Plugin 43

1.34SimpleClock plugin 43

1.35ConvergentExtension plugin 43

2Steppable Section 44

2.1UniformInitializer Steppable 44

2.2BlobInitializer Steppable 45

2.3PIF Initializer 46

2.4PIFDumper Steppable 47

2.5Mitosis Steppabe. 48

2.6PDESolvers in CompuCell3D 50

2.7FlexibleDiffusionSolver 50

2.7.1Instabilities of the Forward Euler Method 53

2.7.2Initial Conditions 54

2.7.3Boundary Conditions 55

2.8DiffusionSolverFE 57

2.8.1GPU Solver 58

2.9AdvectionDiffusionSolver. 58

2.10FastDiffusionSolver2D 59

2.11KernelDiffusionSolver 59

2.12ReactionDiffusionSolver 60

2.13Steady State diffusion solver 61

2.14BoxWatcher Steppable 63

2.15Additional Plugins and Modules 63

3References 65

4Appendix 71

4.1Calculating Inertia Tensor in CompuCell3D. 71

4.2Calculating shape constraint of a cell – elongation term 73

4.2.1Diagonalizing inertia tensor 74

4.3Forward Euler method for solving PDE's in CompuCell3D. 75

4.4Calculating center of mass when using periodic boundary conditions. 76

4.5Dividing cluster cells 77

4.6Command line options of CompuCell3D 79

4.6.1CompuCell3D Player Command Line Options 80

4.6.2Runnig CompuCell3D in a GUI-Less Mode - Command Line Options. 80

4.7Managing CompuCell3D simulations (CC3D project files) 82

4.8Keeping Track of Simulation Files (deprecated!) 83



1CC3DML Syntax of CompuCell3D modules


This CompuCell3D reference material provides users with fairly detaild description of CC3DML syntax (CC3DML is XML-based model description format) of CC3D modules. The presented material is indended for users who are already familiar with CompuCell3D basics and know how to build and run simple simulations such as cellsorting, bacterium macrophage or cell-type-oscillator. Since we often show CC3DML syntax and accompanying Python syntax for CC3D scripting we assume that users are familiar with Python. For readers who are using CompuCell3D for the first time we strongly recommend reading “Introduction To CompuCell3D”. Complete description of CC3D Python scripting can be found in “CC3D Python Scripting Manual”. Both manuals are available from www.compucell3d.org or at your nearest bookstore.
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