BoundaryCyclic : close the system along a dimension. More...

Inheritance diagram for simulator.geometry.boundaryConditions.BoundaryCyclic:

Public Member Functions
	BoundaryCyclic ()
	Declare a cyclic boundary and set isCyclic to true to note this is the case. More...

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

void	readGeometry (XMLParser geometryRoot, Domain aDomain)
	Read the geometry of this boundary from the protocol file and construct both this boundary and the opposite side (as this is cyclic) 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...

void	refreshBoundary (SoluteGrid aSoluteGrid)
	Solver for the cyclic boundary condition. Initialises the course along the shape of the boundary, setting the values of solute near the boundary as required. More...

void	applyBoundary (SoluteGrid aSpGrid, DiscreteVector dC)
	Applies boundary conditions for all other BC types - but not used for cyclic boundaries. More...

double	getValueFromBoundary (SoluteGrid aSpGrid, int i, int j, int k)
	Returns the value within a boundary. Not used for cyclic boundaries. More...

BoundaryCyclic	createOtherSide ()
	Creates the opposite side of the cyclic boundary such that agents can 'roll around' to the other side. More...

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

boolean	isOnBoundary (ContinuousVector cC, SpatialGrid aSpatialGrid)
	Determines if a point is on the boundary. More...

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

ContinuousVector	getSymmetric (ContinuousVector cc)
	Return the intersection between the opposite shape and a provided point. 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

BoundaryCyclic : close the system along a dimension.

BoundaryCyclic : close the system along a dimension. It is computationally unfeasible to simulate a micro-scale world on a macro-scale level, so oftentimes a small spatial sub-region is assumed to represent the system as a whole; in this case, periodic boundaries are used to remove artificial edge effects by assuming the simulated region adjoins other, similar, regions. As a consequence, boundaries in some chosen directions (generally for movements parallel to the substratum) are periodic, which means that the solute concentrations and solute gradients are constant across the boundary, and that agents travelling through one boundary will be translated to the other side of the domain

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

Constructor & Destructor Documentation

simulator.geometry.boundaryConditions.BoundaryCyclic.BoundaryCyclic ( )

Declare a cyclic boundary and set isCyclic to true to note this is the case.

Declare a cyclic boundary and set isCyclic to true to note this is the case

Member Function Documentation

void simulator.geometry.boundaryConditions.BoundaryCyclic.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.BoundaryCyclic.applyBoundary	(	SoluteGrid	aSpGrid,
		DiscreteVector	dC
	)

Applies boundary conditions for all other BC types - but not used for cyclic boundaries.

Parameters

aSpGrid	SoluteGrid
dC	DiscreteVector

BoundaryCyclic simulator.geometry.boundaryConditions.BoundaryCyclic.createOtherSide ( )

Creates the opposite side of the cyclic boundary such that agents can 'roll around' to the other side.

Creates the opposite side of the cyclic boundary such that agents can 'roll around' to the other side

Returns: BoundaryCyclic object that captures the opposite side of this boundary

double simulator.geometry.boundaryConditions.BoundaryCyclic.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.BoundaryCyclic.getSymmetric ( ContinuousVector cc )

Return the intersection between the opposite shape and a provided point.

Return the intersection between the opposite shape and a provided point

Parameters

cc	A position on a boundary

Returns: ContinuousVector containing the intersection between the opposite shape and provided point

double simulator.geometry.boundaryConditions.BoundaryCyclic.getValueFromBoundary	(	SoluteGrid	aSpGrid,
		int	i,
		int	j,
		int	k
	)

Returns the value within a boundary. Not used for cyclic boundaries.

Returns the value within a boundary. Not used for cyclic boundaries

Parameters

aSpGrid	Solute grid which the boundary is being applied
i	I Coordinate of grid space to query
j	J Coordinate of grid space to query
k	K Coordinate of grid space to query

Returns: Double balue of the solute level stored in that boundary cell

void simulator.geometry.boundaryConditions.BoundaryCyclic.init	(	Simulator	aSim,
		Domain	aDomain,
		XMLParser	aBCParser
	)

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
aBCParser	The XML tags that have declared this boundary in the protocol file

Implements simulator.geometry.boundaryConditions.AllBC.

boolean simulator.geometry.boundaryConditions.BoundaryCyclic.isOnBoundary	(	ContinuousVector	cC,
		SpatialGrid	aSpatialGrid
	)

Determines if a point is on the boundary.

Determines if a point is on the boundary

Parameters

cC	ContinuousVector to check
aSpatialGrid	Spatial grid to check

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

boolean simulator.geometry.boundaryConditions.BoundaryCyclic.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)

ContinuousVector simulator.geometry.boundaryConditions.BoundaryCyclic.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.BoundaryCyclic.readGeometry	(	XMLParser	geometryRoot,
		Domain	aDomain
	)

Read the geometry of this boundary from the protocol file and construct both this boundary and the opposite side (as this is cyclic)

See Also: Domain constructor

Parameters

geometryRoot	XML tags in the protocol file that describe this boundary
aDomain	The domain which this boundary is associated with

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

virtual

Solver for the cyclic boundary condition. Initialises the course along the shape of the boundary, setting the values of solute near the boundary as required.

Solver for the cyclic boundary condition. Initialises the course along the shape of the boundary, , setting the values of solute near the boundary as required

Parameters

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

Implements simulator.geometry.boundaryConditions.AllBC.

void simulator.geometry.boundaryConditions.BoundaryCyclic.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.BoundaryCyclic.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/BoundaryCyclic.java

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation