Defines an impermeable boundary to solutes and agents. More...

Inheritance diagram for simulator.geometry.boundaryConditions.BoundaryZeroFlux:

Public Member Functions
void	init (Simulator aSim, Domain aDomain, XMLParser aBoundCondMarkUp)
	Initialises the boundary from information contained in the simulation protocol file. More...

void	refreshBoundary (SoluteGrid aSoluteGrid)
	Solver for the zero flux boundary condition. Initialises the course along the shape of the boundary and moves any points outside the domain inside. 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 target)
	Applies the boundary condition by modifying the movement vector. New position is orthogonal projection of the outside point on the boundary surface. More...

String	toString ()
	Returns a string noting the side of the domain that this boundary condition is on. More...

Public Member Functions inherited from simulator.geometry.boundaryConditions.AllBC
void	readGeometry (XMLParser geometryRoot, Domain aDomain)
	Used during the initialisation, load the class describing the shape of the boundary defined in the parent class. More...

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

String	getSideName ()
	Return the name of the side of the domain which this boundary is on. More...

void	refreshDiffBoundary (SoluteGrid relDiff, SoluteGrid aSolutegrid)
	Method used if a boundary modifies the local diffusivity constant. Most of boundaries do not modify it. More...

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

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

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

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

void	updateBulk (SoluteGrid[] soluteGrid, SoluteGrid[] reacGrid, double timeStep)
	Updates the levels in the bulk. Allows reaction or flux-based bulk treatment. More...

boolean	hasAgar ()
	Determine if the boundary condition is modelling agar. More...

void	updateAgar (SoluteGrid[] soluteGrid, SoluteGrid[] reactionGrid, double timeStep)
	If modelling an agar plate boundary, this method updates the boundary. More...

boolean	isOutside (DiscreteVector dc, SpatialGrid aSpatialGrid)
	Determines if a discrete vector location is outside 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...

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

IsShape	getShape ()
	Returns the Shape object that represents this boundary. More...

String	getSide ()
	Return the name of the side of the domain which this boundary is on. More...

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

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

Additional Inherited Members
Static Public Member Functions inherited from simulator.geometry.boundaryConditions.AllBC
static AllBC	staticBuilder (XMLParser root, Simulator aSim, Domain aDomain)
	Generic constructor called to dynamically instantiate a child class object. More...

Protected Attributes inherited from simulator.geometry.boundaryConditions.AllBC
String	_mySide

IsShape	_myShape

boolean	isCyclic = false

boolean	_isSupport = false

boolean	hasBulk = false

boolean	activeForSolute = true

boolean	hasAgar = false

Static Protected Attributes inherited from simulator.geometry.boundaryConditions.AllBC
static DiscreteVector	dcIn = new DiscreteVector()

static DiscreteVector	dcOut = new DiscreteVector()

Detailed Description

Defines an impermeable boundary to solutes and agents.

Defines an impermeable boundary to solutes and agents. As a consequence the normal components of solute concentration gradients will be zero at this boundary. Agents attempting to cross the boundary are prevented from doing so

Author: 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.BoundaryZeroFlux.applyBoundary	(	LocatedAgent	anAgent,
		ContinuousVector	target
	)

virtual

Applies the boundary condition by modifying the movement vector. New position is orthogonal projection of the outside point on the boundary surface.

Applies the boundary condition by modifying the movement vector. New position is orthogonal projection of the outside point on the boundary surface

Parameters

anAgent	The Located Agent which is attempting to cross the boundary
target	The target position that the agent is moving to

Implements simulator.geometry.boundaryConditions.AllBC.

void simulator.geometry.boundaryConditions.BoundaryZeroFlux.init	(	Simulator	aSim,
		Domain	aDomain,
		XMLParser	aBoundCondMarkUp
	)

virtual

Initialises the boundary from information contained in the simulation protocol file.

Initialises the boundary from information contained in the simulation protocol file

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

Implements simulator.geometry.boundaryConditions.AllBC.

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

virtual

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

Implements simulator.geometry.boundaryConditions.AllBC.

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

virtual

Solver for the zero flux boundary condition. Initialises the course along the shape of the boundary and moves any points outside the domain inside.

Solver for the zero flux boundary condition. Initialises the course along the shape of the boundary and moves any points outside the domain inside

Parameters

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

Implements simulator.geometry.boundaryConditions.AllBC.

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

virtual

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

Implements simulator.geometry.boundaryConditions.AllBC.

String simulator.geometry.boundaryConditions.BoundaryZeroFlux.toString ( )

Returns a string noting the side of the domain that this boundary condition is on.

Returns a string noting the side of the domain that this boundary condition is on

Returns: String noting the side of the domain that this condition applies to (i.e. x0z, xNz, etc)

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

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

Public Member Functions

Additional Inherited Members

Detailed Description

Member Function Documentation