PDESolvers in CompuCell3D

One of the most important and time-consuming parts of the CC3D simulation is to solve all sorts of Partial Differential Equations which describe behavior of certain simulation objects (usually chemical fields). Most of the CC3D PDE solvers solve PDE with diffusive terms. Because 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 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 similar pattern .

• Accessing concentration fields managed by PDE solvers
• FlexibleDiffusionSolver
• Instabilities of the Forward Euler Method
• Initial Conditions
• Boundary Conditions
• DiffusionSolverFE
• AdvectionDiffusionSolver.
• FastDiffusionSolver2D
• KernelDiffusionSolver
• ReactionDiffusionSolver Plugin
• ReactionDiffusionSolverFVM Plugin
• Steady State diffusion solver
• Fluctuation Compensator Solver Add-On