dune-copasi simulator
dune-copasi is the default PDE solver, which solves the PDE on a tetrahedral 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
- 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
- Newton relative error
the relative error where Newton iteration is considered to have converged
currently this may need to be altered depending on the units and geometry size (see #315)
- Newton absolute error
the absolute error where Newton iteration is considered to have converged
currently this may need to be altered depending on the units and geometry size (see #315)
- Linear solver
a variety of iterative and direct solvers are available
the default is RestartedGMRes
For more information see the dune-copasi documentation.