# 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.