Types of boundary conditions
“Which types of boundary conditions does Morpheus provide?”
Morpheus provides three types of boundary conditions.
|Periodic||Wrap-around||Lattice is wrapped around to opposite site, such that there is no border.|
|Constant||Dirichlet||Border states have specified constant values.|
|Noflux||Neumann||Derivative at border is zero.|
These can be specified in
BoundaryConditions. These define the structure of the boundaries.
Note that there are six boundaries (x,-x, y, -y, z, -z,). All need to be specified, expect when periodic boundaries are used (in which case +x=-x, +y=-y, +z=-z).
Define boundary condition
To define boundaries, add entries in
Define boundary values
To specify the values the boundaries should take, we distinguish between Fields (i.e. Reaction-Diffusion models) and cell-based models.
Periodic boundaries do not use boundary values, since these are topologically connected.
Fields (Reaction-Diffusion models, PDE)
constant boundary conditions, values used at the boundary of a reaction-diffusion model can be specified as expressions in
BoundaryValue. Assuming non-zero diffusion, this causes a flux across the boundary depending on the actual concentration gradient at that boundary.
The default value is 0.0.
noflux boundary conditions, the value plays no role in reactions-diffusion systems, since the flux is set to zero. However, the
NeighborhoodReporter accesses these boundary values when computing mappings of the local neighborhood.
Any medium cell type can be specified as
constant boundary. First, define a cell type of type
CellTypes. To specify this at the boundary of a cell-based model with
constant boundary conditions, use
Note that cells interact with the choosen boundary type, but only in the case of
constant boundary the boundary cell type may extend / flow into the simulation space.