Interface describing mandatory methods for a computation domain object. The default class is "ComputationDomain" but other can be defined. More...

Inheritance diagram for simulator.geometry.IsComputationDomain:

Public Member Functions
AllBC	testCrossedBoundary (ContinuousVector newLoc)
	Test if a given location is outside a boundary. Used to detect the crossed boundary when moving an agent. More...

SpatialGrid	getGrid ()
	Returns the domain grid. More...

String	getName ()
	Return the name of this domain. More...

LinkedList< AllBC >	getAllBoundaries ()
	Return all boundaries associated with this domain. More...

SoluteGrid	getBoundaryLayer ()
	Return the boundary layer grid associated with this domain. More...

LinkedList< DiscreteVector >	getBorder ()
	Returns a list of discrete vectors that specify the limit of the boundary layer. More...

SoluteGrid	getDiffusivity ()
	Return the diffusivity grid associated with this domain. More...

SoluteGrid	getBiomass ()
	Return the biomass grid associated with this domain. More...

void	refreshBioFilmGrids ()
	Refresh relative diffusivity and boundary layer grids to ensure biomass updated this step is included. More...

Detailed Description

Interface describing mandatory methods for a computation domain object. The default class is "ComputationDomain" but other can be defined.

Interface describing mandatory methods for a computation domain object. The default class is "ComputationDomain" but other can be defined

Author: Andreas D�tsch (andre.nosp@m.as.d.nosp@m.oetsc.nosp@m.h@he.nosp@m.lmhol.nosp@m.tz-h.nosp@m.zi.de), Helmholtz Centre for Infection Research (Germany); Laurent Lardon (lardo.nosp@m.nl@s.nosp@m.upagr.nosp@m.o.in.nosp@m.ra.fr), INRA, France

Member Function Documentation

LinkedList<AllBC> simulator.geometry.IsComputationDomain.getAllBoundaries ( )

Return all boundaries associated with this domain.

Return all boundaries associated with this domain

Returns: LinkedLIst of all boundaries in the container boundaryList

Implemented in simulator.geometry.Domain.

SoluteGrid simulator.geometry.IsComputationDomain.getBiomass ( )

Return the biomass grid associated with this domain.

Return the biomass grid associated with this domain

Returns: SoluteGrid containing biomass throughout this domain

Implemented in simulator.geometry.Domain.

LinkedList<DiscreteVector> simulator.geometry.IsComputationDomain.getBorder ( )

Returns a list of discrete vectors that specify the limit of the boundary layer.

Returns a list of discrete vectors that specify the limit of the boundary layer

Returns: LinkedList of DiscreteVectors with the limit of the boundary layer

Implemented in simulator.geometry.Domain.

SoluteGrid simulator.geometry.IsComputationDomain.getBoundaryLayer ( )

Return the boundary layer grid associated with this domain.

Return the boundary layer associated with this domain

Returns: SoluteGrid containing boundary between bulk and biofilm

Implemented in simulator.geometry.Domain.

SoluteGrid simulator.geometry.IsComputationDomain.getDiffusivity ( )

Return the diffusivity grid associated with this domain.

Return the diffusivity grid associated with this domain

Returns: SoluteGrid containing diffusivity grid statistics

Implemented in simulator.geometry.Domain.

SpatialGrid simulator.geometry.IsComputationDomain.getGrid ( )

Returns the domain grid.

Returns the domain grid

Returns: SpatialGrid within this domain

Implemented in simulator.geometry.Domain.

String simulator.geometry.IsComputationDomain.getName ( )

Return the name of this domain.

Return the name of this domain

Returns: Name of this domain

Implemented in simulator.geometry.Domain.

void simulator.geometry.IsComputationDomain.refreshBioFilmGrids ( )

Refresh relative diffusivity and boundary layer grids to ensure biomass updated this step is included.

Method to refresh relative diffusivity and boundary layer grids to ensure biomass updated this step is included. Used in the creation of output files

Implemented in simulator.geometry.Domain.

AllBC simulator.geometry.IsComputationDomain.testCrossedBoundary ( ContinuousVector newLoc )

Test if a given location is outside a boundary. Used to detect the crossed boundary when moving an agent.

Test if a given location is outside a boundary. Used to detect the crossed boundary when moving an agent

Parameters

newLoc The location to test

Returns: Boundary that the point has crossed (if applicable - null if no boundary crossed)

Implemented in simulator.geometry.Domain.

The documentation for this interface was generated from the following file:

/home/kieran/Dropbox/workspace/iDynoMiCS/src/simulator/geometry/IsComputationDomain.java

Public Member Functions

Detailed Description

Member Function Documentation