Interface for the boundary conditions on the system's margins. To be used in solvers and agent move. More...

Public Member Functions
void	readGeometry (Element geometryRoot, Domain aDomain)
	Used during the initialisation, load the class describing the shape of the boundary defined in the parent class. More...

double	getDistance (ContinuousVector cc)
	Returns the distance from a point to the boundary. More...

ContinuousVector	getIntersection (ContinuousVector position, ContinuousVector vector)
	Calculate the intersection between the boundary and a line (defined by a position and a vector) More...

ContinuousVector	getOrthoProj (ContinuousVector cc)
	Calculate the orthogonal projection of a location on the boundary. More...

boolean	isOutside (ContinuousVector cc)
	Determines if a point is outside the boundary. More...

boolean	isOutside (DiscreteVector dC, SpatialGrid aSpatialGrid)
	Determines if a discrete vector location is outside the boundary. More...

boolean	isActive ()
	Determine if this boundary is active for solute. More...

boolean	isCyclic ()
	Determine if this boundary is cyclic. More...

boolean	hasBulk ()
	Determine if this boundary is attached to a bulk. More...

double	getBulkValue (int soluteIndex)
	For a specified solute, returns the level of that solute in the bulk. More...

Bulk	getBulk ()
	Return the bulk that is connected to this boundary. More...

boolean	isSupport ()
	Determine whether this boundary is the supporting structure (substratum) More...

void	init (Simulator aSim, Domain aDomain, Element aBoundCondMarkUp)
	Initialises the boundary from information contained in the simulation protocol file. In this case also links the connected bulk to this boundary. More...

void	refreshBoundary (SoluteGrid aSoluteGrid)
	Solver for then boundary condition. Initialises the course along the shape of the boundary during multigrid computation. More...

void	refreshDiffBoundary (SoluteGrid relDiff, SoluteGrid aSolutegrid)
	Computes and applies gas diffusivity across the gas membrane boundary. More...

ContinuousVector	lookAt (ContinuousVector cc)
	Method used by another which gets the indexed grid position of a continuous vector. Some boundary conditions need the input corrected, some don't and just return the input. More...

void	setBoundary (LocatedGroup aGroup)
	Change the status of a specified LocatedGroup to note that it has been identified as being outside this boundary. More...

void	applyBoundary (LocatedAgent anAgent, ContinuousVector newLoc)
	Modify the movement vector dependent on the boundary condition. In some the agent is killed, in others the agent location is adjusted. More...

Detailed Description

Interface for the boundary conditions on the system's margins. To be used in solvers and agent move.

Interface for the boundary conditions on the system's margins. To be used in solvers and agent move

Author: Andreas Dotsch (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

void simulator.geometry.boundaryConditions.IsBC.applyBoundary	(	LocatedAgent	anAgent,
		ContinuousVector	newLoc
	)

Modify the movement vector dependent on the boundary condition. In some the agent is killed, in others the agent location is adjusted.

Modify the movement vector dependent on the boundary condition. In some the agent is killed, in others the agent location is adjusted

Parameters

anAgent	The LocatedAgent that has crossed the boundary
newLoc	Vector of where this agent was going to be placed

Bulk simulator.geometry.boundaryConditions.IsBC.getBulk ( )

Return the bulk that is connected to this boundary.

Return the bulk that is connected to this boundary

Returns: Bulk object that is connected to this boundary

double simulator.geometry.boundaryConditions.IsBC.getBulkValue ( int soluteIndex )

For a specified solute, returns the level of that solute in the bulk.

For a specified solute, returns the level of that solute in the bulk

Parameters

soluteIndex Index of the solute in the simulation dictionary

Returns: Value of solute in the connected bulk

double simulator.geometry.boundaryConditions.IsBC.getDistance ( ContinuousVector cc )

Returns the distance from a point to the boundary.

Returns the distance from a point to the boundary

Parameters

cc	The continuous vector of points to calculate how far the point is from the boundary

Returns: Double value stating the distance fromt the point to the boundary

ContinuousVector simulator.geometry.boundaryConditions.IsBC.getIntersection	(	ContinuousVector	position,
		ContinuousVector	vector
	)

Calculate the intersection between the boundary and a line (defined by a position and a vector)

Parameters

position	A continuous vector stating the point to be used in the calculation
vector	A continuous vector stating the line to be used in the calculation

Returns: ContinuousVector stating the point of intersection between the boundary and a line

ContinuousVector simulator.geometry.boundaryConditions.IsBC.getOrthoProj ( ContinuousVector cc )

Calculate the orthogonal projection of a location on the boundary.

Calculate the orthogonal projection of a location on the boundary

Parameters

cc	A continuous vector stating the point to be used in the calculation

Returns: ContinuousVector stating the point on the boundary after the orthogonal projection

boolean simulator.geometry.boundaryConditions.IsBC.hasBulk ( )

Determine if this boundary is attached to a bulk.

Determine if this boundary is attached to a bulk

Returns: Boolean noting whether this boundary is attached to a bulk (true) or not (false)

void simulator.geometry.boundaryConditions.IsBC.init	(	Simulator	aSim,
		Domain	aDomain,
		Element	aBoundCondMarkUp
	)

Initialises the boundary from information contained in the simulation protocol file. In this case also links the connected bulk to this boundary.

Initialises the boundary from information contained in the simulation protocol file. In this case also links the connected bulk to this boundary

Parameters

aSim	The simulation object used to simulate the conditions specified in the protocol file
aDomain	The domain which this boundary condition is associated with
aBoundCondMarkUp	The XML tags that have declared this boundary in the protocol file

boolean simulator.geometry.boundaryConditions.IsBC.isActive ( )

Determine if this boundary is active for solute.

Determine if this boundary is active for solute

Returns: Boolean noting whether this boundary is active for solute (true) or not (false)

boolean simulator.geometry.boundaryConditions.IsBC.isCyclic ( )

Determine if this boundary is cyclic.

Determine if this boundary is cyclic

Returns: Boolean noting whether this boundary is cyclic (true) or not (false)

boolean simulator.geometry.boundaryConditions.IsBC.isOutside ( ContinuousVector cc )

Determines if a point is outside the boundary.

Determines if a point is outside the boundary

Parameters

cc	ContinuousVector to check

Returns: Boolean value noting whether this coordinate is outside the boundary (true) or not (false)

boolean simulator.geometry.boundaryConditions.IsBC.isOutside	(	DiscreteVector	dC,
		SpatialGrid	aSpatialGrid
	)

Determines if a discrete vector location is outside the boundary.

Determines if a discrete vector location is outside the boundary

Parameters

dC	DiscreteVector to check
aSpatialGrid	Spatial grid to check

Returns: Boolean value noting whether this coordinate is outside the boundary (true) or not (false)

boolean simulator.geometry.boundaryConditions.IsBC.isSupport ( )

Determine whether this boundary is the supporting structure (substratum)

Returns: Boolean noting whether this boundary is the supporting structure (true) or not (false)

ContinuousVector simulator.geometry.boundaryConditions.IsBC.lookAt ( ContinuousVector cc )

Method used by another which gets the indexed grid position of a continuous vector. Some boundary conditions need the input corrected, some don't and just return the input.

Method used by another which gets the indexed grid position of a continuous vector. Some boundary conditions (e.g. BoundaryCyclic_ need the input corrected due to the condition, some don't and just return the input. Maybe we'll change this at some point as to just return the input looks a bit daft - but we'll leave it here for the moment

Parameters

cc	ContinuousVector that gives the current location of an agent to check on the grid

void simulator.geometry.boundaryConditions.IsBC.readGeometry	(	Element	geometryRoot,
		Domain	aDomain
	)

Used during the initialisation, load the class describing the shape of the boundary defined in the parent class.

Used during the initialisation, load the class describing the shape of the boundary defined in the parent class

Parameters

geometryRoot	Usually an XML set of elements that describe the boundary to be created
aDomain	The computational domain which this boundary is associated with

void simulator.geometry.boundaryConditions.IsBC.refreshBoundary ( SoluteGrid aSoluteGrid )

Solver for then boundary condition. Initialises the course along the shape of the boundary during multigrid computation.

Solver for the variable concentration boundary condition. Initialises the course along the shape of the boundary during multigrid computation

Parameters

aSoluteGrid Grid of solute information which is to be refreshed by the solver

void simulator.geometry.boundaryConditions.IsBC.refreshDiffBoundary	(	SoluteGrid	relDiff,
		SoluteGrid	aSolutegrid
	)

Computes and applies gas diffusivity across the gas membrane boundary.

Computes and applies gas diffusivity across the gas membrane boundary

Parameters

relDiff
aSolutegrid	Grid of solute information which is to be refreshed by the solver

void simulator.geometry.boundaryConditions.IsBC.setBoundary ( LocatedGroup aGroup )

Change the status of a specified LocatedGroup to note that it has been identified as being outside this boundary.

Change the status of a specified LocatedGroup to note that it has been identified as being outside this boundary

Parameters

aGroup LocatedGroup object which has been detected to be outside the boundary

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

/home/kieran/Dropbox/workspace/iDynoMiCS/src/simulator/geometry/boundaryConditions/IsBC.java

Public Member Functions

Detailed Description

Member Function Documentation