Defines the bulk boundary: the concentration on the boundary is fixed by a dynamical bulk, the agents crossing this line die. More...

Inheritance diagram for simulator.geometry.boundaryConditions.BoundaryBulk:

Public Member Functions
	BoundaryBulk ()
	Declare a variable concentration boundary and set hasBulk to true to note this is the case. More...

void	init (Simulator aSim, Domain aDomain, XMLParser 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 the variable concentration boundary condition. Initialises the course along the shape of the boundary. More...

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

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

double	getBulkValue (int soluteIndex)
	For a specified solute, returns the level of that solute in the bulk. 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)
	Kills any agents that are crossing this boundary as they are leaving the simulated system. 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...

Protected Attributes
Bulk	_connectedBulk

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

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...

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

static DiscreteVector	dcOut = new DiscreteVector()

Detailed Description

Defines the bulk boundary: the concentration on the boundary is fixed by a dynamical bulk, the agents crossing this line die.

Defines the bulk boundary: the concentration on the boundary is fixed by a dynamical bulk, the agents crossing this line die. This boundary simulates the connection to a larger bulk liquid subject to a dilution process, as would be typical for a reactor. Behaviour for agents does not differ from the constant concentration boundary case (and so within the computational domain the boundary condition is identical), but solute dynamics in the bulk compartment require an additional computational step. In this step, ordinary differential equations describing the reactions occurring in the biofilm and the hydraulic processes affecting the bulk liquid are solved in order to determine the bulk concentration at the next time-step.

Author: Laurent Lardon (lardo.nosp@m.nl@s.nosp@m.upagr.nosp@m.o.in.nosp@m.ra.fr), INRA, France; Brian Merkey (brim@.nosp@m.env..nosp@m.dtu.d.nosp@m.k, bvm@n.nosp@m.orth.nosp@m.weste.nosp@m.rn.e.nosp@m.du), Department of Engineering Sciences and Applied Mathematics, Northwestern University (USA); Sónia Martins (SCM80.nosp@m.8@bh.nosp@m.am.ac.nosp@m..uk), Centre for Systems Biology, University of Birmingham (UK)

Constructor & Destructor Documentation

simulator.geometry.boundaryConditions.BoundaryBulk.BoundaryBulk ( )

Declare a variable concentration boundary and set hasBulk to true to note this is the case.

Declare a variable concentration boundary and set hasBulk to true to note this is the case

Member Function Documentation

void simulator.geometry.boundaryConditions.BoundaryBulk.applyBoundary	(	LocatedAgent	anAgent,
		ContinuousVector	target
	)

virtual

Kills any agents that are crossing this boundary as they are leaving the simulated system.

Kills any agents that are crossing this boundary as they are leaving the simulated system

Parameters

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

Implements simulator.geometry.boundaryConditions.AllBC.

Bulk simulator.geometry.boundaryConditions.BoundaryBulk.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.BoundaryBulk.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

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

virtual

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

Implements simulator.geometry.boundaryConditions.AllBC.

ContinuousVector simulator.geometry.boundaryConditions.BoundaryBulk.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.BoundaryBulk.refreshBoundary ( SoluteGrid aSoluteGrid )

virtual

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

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

Parameters

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

Implements simulator.geometry.boundaryConditions.AllBC.

void simulator.geometry.boundaryConditions.BoundaryBulk.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.BoundaryBulk.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)

void simulator.geometry.boundaryConditions.BoundaryBulk.updateBulk	(	SoluteGrid[]	allSG,
		SoluteGrid[]	allRG,
		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

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

Member Data Documentation

Bulk simulator.geometry.boundaryConditions.BoundaryBulk._connectedBulk

protected

The defined bulk in the simulation to which the liquid phase is connected

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

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

Public Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation