Group all methods expected by the interface but common to most of the boundary classes. More...

Inheritance diagram for simulator.geometry.boundaryConditions.AllBC:

Public Member Functions
abstract void	init (Simulator aSim, Domain aDomain, XMLParser root)
	Initialises the boundary condition. Should be overriden by each boundary condition class file. More...

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...

abstract 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)
	Method used if a boundary modifies the local diffusivity constant. Most of boundaries do not modify it. More...

abstract 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...

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

abstract void	applyBoundary (LocatedAgent anAgent, ContinuousVector newLoc)

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...

Static Public Member Functions
static AllBC	staticBuilder (XMLParser root, Simulator aSim, Domain aDomain)
	Generic constructor called to dynamically instantiate a child class object. More...

Protected Attributes
String	_mySide

IsShape	_myShape

boolean	isCyclic = false

boolean	_isSupport = false

boolean	hasBulk = false

boolean	activeForSolute = true

boolean	hasAgar = false

Static Protected Attributes
static DiscreteVector	dcIn = new DiscreteVector()

static DiscreteVector	dcOut = new DiscreteVector()

Detailed Description

Group all methods expected by the interface but common to most of the boundary classes.

Group all methods expected by the interface but common to most of the boundary classes

Author: Laurent Lardon (lardo.nosp@m.nl@s.nosp@m.upagr.nosp@m.o.in.nosp@m.ra.fr), INRA, France

Member Function Documentation

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

pure virtual

Modify the movement vector : the new position is the orthognal projection on the boundary surface

See Also: LocatedAgent.move();

Implemented in simulator.geometry.boundaryConditions.BoundaryGasMembrane, simulator.geometry.boundaryConditions.BoundaryBulk, simulator.geometry.boundaryConditions.BoundaryCyclic, simulator.geometry.boundaryConditions.BoundaryConstant, and simulator.geometry.boundaryConditions.BoundaryZeroFlux.

Bulk simulator.geometry.boundaryConditions.AllBC.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.AllBC.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.AllBC.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.AllBC.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.AllBC.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

IsShape simulator.geometry.boundaryConditions.AllBC.getShape ( )

Returns the Shape object that represents this boundary.

Returns the Shape object that represents this boundary

Returns: Shape object that has been constructed to represent this boundary

String simulator.geometry.boundaryConditions.AllBC.getSide ( )

Return the name of the side of the domain which this boundary is on.

Return the name of the side of the domain which this boundary is on

Returns: String containing the name of the side of the domain (e.g. x0z, xNz, etc)

String simulator.geometry.boundaryConditions.AllBC.getSideName ( )

Return the name of the side of the domain which this boundary is on.

Return the name of the side of the domain which this boundary is on

Returns: String containing the name of the side of the domain (e.g. x0z, xNz, etc)

boolean simulator.geometry.boundaryConditions.AllBC.hasAgar ( )

Determine if the boundary condition is modelling agar.

Determine if the boundary condition is modelling agar

Returns: Boolean noting whether this condition is modelling agar (true) or not (false)

boolean simulator.geometry.boundaryConditions.AllBC.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)

abstract void simulator.geometry.boundaryConditions.AllBC.init	(	Simulator	aSim,
		Domain	aDomain,
		XMLParser	root
	)

pure virtual

Initialises the boundary condition. Should be overriden by each boundary condition class file.

Initialises the boundary condition. This method should be overriden by each boundary condition class file

Parameters

aSim	The current simulation object used to simulate the conditions specified in this protocol file
aDomain	The computation domain to which this boundary condition is assigned
root	Set of XML tags relating to one boundary condition

Implemented in simulator.geometry.boundaryConditions.BoundaryGasMembrane, simulator.geometry.boundaryConditions.BoundaryCyclic, simulator.geometry.boundaryConditions.BoundaryBulk, simulator.geometry.boundaryConditions.BoundaryConstant, and simulator.geometry.boundaryConditions.BoundaryZeroFlux.

boolean simulator.geometry.boundaryConditions.AllBC.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.AllBC.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.AllBC.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.AllBC.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	The grid to check whether a point is outside

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

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

Determine whether this boundary is the supporting structure (substratum)

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

abstract ContinuousVector simulator.geometry.boundaryConditions.AllBC.lookAt ( ContinuousVector cc )

pure 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

Implemented in simulator.geometry.boundaryConditions.BoundaryGasMembrane, simulator.geometry.boundaryConditions.BoundaryBulk, simulator.geometry.boundaryConditions.BoundaryCyclic, simulator.geometry.boundaryConditions.BoundaryConstant, and simulator.geometry.boundaryConditions.BoundaryZeroFlux.

void simulator.geometry.boundaryConditions.AllBC.readGeometry	(	XMLParser	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

abstract void simulator.geometry.boundaryConditions.AllBC.refreshBoundary ( SoluteGrid aSoluteGrid )

pure virtual

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 see ComputationDomain.refreshBoundaries()

Implemented in simulator.geometry.boundaryConditions.BoundaryCyclic, simulator.geometry.boundaryConditions.BoundaryGasMembrane, simulator.geometry.boundaryConditions.BoundaryBulk, simulator.geometry.boundaryConditions.BoundaryConstant, and simulator.geometry.boundaryConditions.BoundaryZeroFlux.

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

Method used if a boundary modifies the local diffusivity constant. Most of boundaries do not modify it.

Method used if a boundary modifies the local diffusivity constant. Most of boundaries do not modify it

Parameters

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

abstract void simulator.geometry.boundaryConditions.AllBC.setBoundary ( LocatedGroup aGroup )

pure 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

Implemented in simulator.geometry.boundaryConditions.BoundaryGasMembrane, simulator.geometry.boundaryConditions.BoundaryBulk, simulator.geometry.boundaryConditions.BoundaryCyclic, simulator.geometry.boundaryConditions.BoundaryConstant, and simulator.geometry.boundaryConditions.BoundaryZeroFlux.

static AllBC simulator.geometry.boundaryConditions.AllBC.staticBuilder	(	XMLParser	root,
		Simulator	aSim,
		Domain	aDomain
	)

static

Generic constructor called to dynamically instantiate a child class object.

Generic constructor called to dynamically instantiate a child class object

Parameters

root	Set of XML tags relating to one boundary condition
aSim	The current simulation object used to simulate the conditions specified in this protocol file
aDomain	The computation domain to which this boundary condition is assigned

void simulator.geometry.boundaryConditions.AllBC.updateAgar	(	SoluteGrid[]	soluteGrid,
		SoluteGrid[]	reactionGrid,
		double	timeStep
	)

If modelling an agar plate boundary, this method updates the boundary.

Parameters

soluteGrid	Grid of all solutes
reactionGrid	Grid of all reactions
timeStep	Current internal timestep of the simulation

void simulator.geometry.boundaryConditions.AllBC.updateBulk	(	SoluteGrid[]	soluteGrid,
		SoluteGrid[]	reacGrid,
		double	timeStep
	)

Updates the levels in the bulk. Allows reaction or flux-based bulk treatment.

Updates the levels in the bulk. Allows reaction or flux-based bulk treatment (BVM 151208)

Parameters

soluteGrid	Array of all solute grids
reacGrid	Array of all reaction grids
timeStep	The internal timestep currently being applied in this simulation

Member Data Documentation

boolean simulator.geometry.boundaryConditions.AllBC._isSupport = false

protected

Boolean noting whether this boundary is the supporting structure (substratum)

IsShape simulator.geometry.boundaryConditions.AllBC._myShape

protected

The shape of the boundary

String simulator.geometry.boundaryConditions.AllBC._mySide

protected

The name of the boundary describing its side (xOy,...)

boolean simulator.geometry.boundaryConditions.AllBC.activeForSolute = true

protected

Boolean noting whether this boundary can contain active solute

DiscreteVector simulator.geometry.boundaryConditions.AllBC.dcIn = new DiscreteVector()

staticprotected

Discrete coordinates of a voxel inside the computation domain but along the boundary

DiscreteVector simulator.geometry.boundaryConditions.AllBC.dcOut = new DiscreteVector()

staticprotected

Discrete coordinates of the voxel in front of the one outside the boundary

boolean simulator.geometry.boundaryConditions.AllBC.hasAgar = false

protected

Boolean noting whether this boundary is modelling agar

boolean simulator.geometry.boundaryConditions.AllBC.hasBulk = false

protected

Boolean noting whether this boundary has an attached bulk

boolean simulator.geometry.boundaryConditions.AllBC.isCyclic = false

protected

Quick test to know if the boundary is cyclic

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

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

Public Member Functions

Static Public Member Functions

Protected Attributes

Static Protected Attributes

Detailed Description

Member Function Documentation

Member Data Documentation