Types of boundary conditions

“Which types of boundary conditions does Morpheus provide?”

Morpheus provides three types of boundary conditions.

Name Synonym Meaning
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 SpaceLatticeBoundaryConditions. These define the structure of the boundaries.

The structure of the borders is defined in ```Space``` → ```Lattice``` → ```BoundaryConditions```.
The structure of the borders is defined in SpaceLatticeBoundaryConditions.

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 SpaceLatticeBoundaryConditions.

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)

When using constant boundary conditions, values used at the boundary of a reaction-diffusion model can be specified as expressions in FieldBoundaryValue. 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.

When using 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.

Specify values at boundaries in ```Field``` → ```BoundaryValue```.
Specify values at boundaries in FieldBoundaryValue.

Cell-based models

Any medium cell type can be specified as noflux or constant boundary. First, define a cell type of type medium under CellTypes. To specify this at the boundary of a cell-based model with constant boundary conditions, use CellPopulatonsBoundaryValue.
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.