111Equation Chapter 1 Section 1 CompuCell3d reference Manual Version 4
Download 0.81 Mb.
|
| 111Equation Chapter 1 Section 1CompuCell3D Reference Manual
Version 3.7.4 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 5 1.1Potts Section 5 1.1.1Lattice Type 10 1.2Plugins Section 12 1.3CellType Plugin 12 1.4Simple Volume and Surface Constraints 13 1.5VolumeTracker and SurfaceTracker plugins 13 1.6VolumeFlex Plugin 14 1.7SurfaceFlex Plugin 14 1.8VolumeLocalFlex Plugin 15 1.9SurfaceLocalFlex Plugin 15 1.10NeighborTracker Plugin 15 1.11Chemotaxis 16 1.12ExternalPotential plugin 19 1.13CellOrientation Plugin 21 1.14PolarizationVector Plugin 22 1.15CenterOfMass Plugin 22 1.16Contact Energy 22 1.17ContactLocalProduct Plugin 23 1.18AdhesionFlex Plugin 25 1.19ContactMultiCad Plugin 27 1.20Compartmentalized cells. ContactInternal Plugin 28 1.21LengthConstraint Plugin 31 1.22Connectivity Plugins 32 1.23Mitosis Plugin 33 1.24Secretion / SecretionLocalFlex Plugin 34 1.25Secretion Plugin (legacy version) 37 1.26 PDESolverCaller Plugin 39 1.27Elasticity Plugin and ElasticityTracker Plugin 40 1.28FocalPointPlasticity Plugin 41 1.29Curvature Plugin 45 1.30PlayerSettings Plugin 46 1.31BoundaryPixelTracker Plugin 47 1.32GlobalBoundaryPixelTracker 47 1.33PixelTracker Plugin 48 1.34MomentOfInertia Plugin 48 1.35SimpleClock plugin 49 1.36ConvergentExtension plugin 49 2Steppable Section 49 2.1UniformInitializer Steppable 50 2.2BlobInitializer Steppable 51 2.3PIF Initializer 51 2.4PIFDumper Steppable 53 2.5Mitosis Steppabe. 53 2.6PDESolvers in CompuCell3D 55 2.7FlexibleDiffusionSolver 56 2.7.1Instabilities of the Forward Euler Method 59 2.7.2Initial Conditions 60 2.7.3Boundary Conditions 61 2.8DiffusionSolverFE 63 2.8.1GPU Solver 64 2.9AdvectionDiffusionSolver. 64 2.10FastDiffusionSolver2D 65 2.11KernelDiffusionSolver 66 2.12ReactionDiffusionSolver 67 2.13Steady State diffusion solver 69 2.14BoxWatcher Steppable 71 2.15muParser 72 2.16Additional Plugins and Modules 72 3References 74 4Appendix 80 4.1Calculating Inertia Tensor in CompuCell3D. 80 4.2Calculating shape constraint of a cell – elongation term 84 4.2.1Diagonalizing inertia tensor 85 4.3Forward Euler method for solving PDE's in CompuCell3D. 86 4.4Calculating center of mass when using periodic boundary conditions. 87 4.5Dividing cluster cells 88 4.6Command line options of CompuCell3D 91 4.6.1CompuCell3D Player Command Line Options 91 4.6.2Runnig CompuCell3D in a GUI-Less Mode - Command Line Options. 92 4.7Managing CompuCell3D simulations (CC3D project files) 93 4.8Keeping Track of Simulation Files (deprecated!) 94 1 CC3DML Syntax of CompuCell3D modules 4 1.1 Potts Section 4 1.1.1 Lattice Type 9 1.2 Plugins Section 11 1.3 CellType Plugin 11 1.4 Simple Volume and Surface Constraints 12 1.5 VolumeTracker and SurfaceTracker plugins 12 1.6 VolumeFlex Plugin 13 1.7 SurfaceFlex Plugin 13 1.8 VolumeLocalFlex Plugin 14 1.9 SurfaceLocalFlex Plugin 14 1.10 NeighborTracker Plugin 14 1.11 Chemotaxis 15 1.12 ExternalPotential plugin 18 1.13 CellOrientation Plugin 19 1.14 PolarizationVector Plugin 20 1.15 CenterOfMass Plugin 21 1.16 Contact Energy 21 1.17 ContactLocalProduct Plugin 22 1.18 AdhesionFlex Plugin 23 1.19 ContactMultiCad Plugin 26 1.20 Compartmentalized cells. ContactInternal Plugin 27 1.21 LengthConstraint Plugin 29 1.22 Connectivity Plugins 30 1.23 Mitosis Plugin 32 1.24 Secretion / SecretionLocalFlex Plugin 32 1.25 Secretion Plugin (legacy version) 35 1.26 PDESolverCaller Plugin 38 1.27 Elasticity Plugin and ElasticityTracker Plugin 38 1.28 FocalPointPlasticity Plugin 40 1.29 Curvature Plugin 43 1.30 PlayerSettings Plugin 44 1.31 BoundaryPixelTracker Plugin 45 1.32 GlobalBoundaryPixelTracker 46 1.33 PixelTracker Plugin 46 1.34 MomentOfInertia Plugin 46 1.35 SimpleClock plugin 47 1.36 ConvergentExtension plugin 47 2 Steppable Section 48 2.1 UniformInitializer Steppable 48 2.2 BlobInitializer Steppable 49 2.3 PIF Initializer 50 2.4 PIFDumper Steppable 51 2.5 Mitosis Steppabe. 51 2.6 PDESolvers in CompuCell3D 54 2.7 FlexibleDiffusionSolver 54 2.7.1 Instabilities of the Forward Euler Method 57 2.7.2 Initial Conditions 58 2.7.3 Boundary Conditions 59 2.8 DiffusionSolverFE 61 2.8.1 GPU Solver 62 2.9 AdvectionDiffusionSolver. 62 2.10 FastDiffusionSolver2D 63 2.11 KernelDiffusionSolver 64 2.12 ReactionDiffusionSolver 65 2.13 Steady State diffusion solver 67 2.14 BoxWatcher Steppable 69 2.15 muParser 70 2.16 Additional Plugins and Modules 70 3 References 72 4 Appendix 78 4.1 Calculating Inertia Tensor in CompuCell3D. 78 4.2 Calculating shape constraint of a cell – elongation term 81 4.2.1 Diagonalizing inertia tensor 81 4.3 Forward Euler method for solving PDE's in CompuCell3D. 82 4.4 Calculating center of mass when using periodic boundary conditions. 83 4.5 Dividing cluster cells 84 4.6 Command line options of CompuCell3D 86 4.6.1 CompuCell3D Player Command Line Options 87 4.6.2 Runnig CompuCell3D in a GUI-Less Mode - Command Line Options. 87 4.7 Managing CompuCell3D simulations (CC3D project files) 89 4.8 Keeping Track of Simulation Files (deprecated!) 90 Download 0.81 Mb. Share with your friends:
|