dune-copasi simulator

dune-copasi is the default PDE solver, which solves the PDE on a triangular mesh using finite element discretization methods. The mesh is automatically constructed from the geometry image, as described in Mesh generation.

Simulation options

The default settings should work well in most cases, but if desired they can be adjusted by going to Advanced->Simulation options

dune-copasi simulation options

The simulation options that can be used to fine tune-the dune-copasi solver.

  • Discretization
    • currently only 1st order FEM is supported

    • other discretizations (such as 2nd order FEM) may be added in the future

  • Integrator
    • the Runge-Kutta integration scheme used for time integration

    • a variety of implicit and explicit schemes of different orders are available

    • the default is the 2nd order Alexander scheme, which is a Diagonally Implicit Runge Kutta method

  • Initial timestep
    • the timestep used at the start of a simulation

  • Min timestep
    • the minimum allowed timestep

    • for a very stiff model it may be necessary to reduce this value

  • Max timestep
    • the maximum allowed timestep

    • reducing this value may increase the accuracy of the solution but simulations will take longer to run

  • Increase factor
    • after a successful integration step, the timestep is multiplied by this factor

    • this must be greater than or equal to 1

    • if equal to 1, the timestep is never increased between integration steps

    • the larger the value, the more the timestep is increased after successful integration steps

  • Decrease factor
    • if an integration step is unsuccessful, the timestep is multiplied by this factor and the step is repeated

    • this must be less than 1

    • the smaller the value, the more the timestep is decreased in the case of an unsuccessful integration step

  • Output files
    • VTK files of the species concentrations throughout the simulation can be generated

    • these files can be viewed using ParaView

For more information on the solver see the dune-copasi documentation.