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 :doc:`mesh`.
Simulation options
------------------
The default settings should work well in most cases, but if desired they can be adjusted by going to `Advanced->Simulation options`
.. figure:: img/dune_options.png
:alt: 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 `_
* 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 `_.