Diffusion (PDE Solvers) in CompuCell3D

One of the most important and time-consuming parts of the CC3D simulation is the process of solving Partial Differential Equations, which describe behavior of certain simulation objects (usually chemical fields). Most of the CC3D PDE solvers solve PDEs with diffusive terms. Since we are dealing with moving boundary condition problems, it was easiest and probably most practical to use explicit scheme of Finite Difference method. Most of CC3D PDE solvers run on multi core architectures and we also have GPU solvers which run and high performance GPU’s and they also provide biggest speedups in terms of performance. Because CC3D solvers were implemented at different stages of the CC3D life cycle and often in response to particular user requests, CC3DML specification may differ from solver to solver. However, the basic structure of CC3DML PDE solver code follows a pattern.

For most use cases, we recommend Diffusion Solver FE. For the highest level of customization, we recommend Reaction Diffusion Solver with Finite Volume Method (FVM). Please see the below reference to find the right PDE solver for your use case.

General Reference

• Accessing concentration fields managed by PDE solvers
• Boundary Conditions for Diffusion
• Diffusion Solver Settings

Solvers

• AdvectionDiffusionSolver
• DiffusionSolverFE
• FastDiffusionSolver2D
• FlexibleDiffusionSolver
• KernelDiffusionSolver
• ReactionDiffusionSolverFE Plugin
• ReactionDiffusionSolverFVM Plugin
• Steady State diffusion solver
• Fluctuation Compensator Solver Add-On