Object to hold a group of agents in one location on the agent grid. More...

Classes
class	DistanceValueComparator
	Comparator used by the shrinking levelset algorithm.

class	TValueComparator
	Comparator used by the detachment levelset algorithm.

Public Member Functions
	LocatedGroup (int index, AgentContainer anAgentGrid, Simulator aSimulator)
	Set the coordinates of this group and check these are inside the grid. More...

void	init ()
	Builds neighbourhood reference map. More...

void	refreshElement ()
	Refresh status and concentration of the group. More...

double	refreshVolume ()
	Refresh the volume statistics of this group. More...

double	computeMove (SoluteGrid pressure, double deltaT)
	Compute the gradient due to pressure and use it to set the advective affect. More...

void	resetMove ()

void	addMoveToAgents (double alpha)
	Scale the movement vector for the grid element and apply to each agent. More...

void	killAll ()
	Safely remove located agent from agentList & agentGrid. More...

void	remove (LocatedAgent anAgent)
	Remove an agent from this LocatedGroup. More...

void	add (LocatedAgent anAgent)
	Add an agent to this LocatedGroup. More...

void	host (LocatedAgent aLoc)
	Shuffle coordinates of an agent inside the group. More...

LocatedGroup	moveX (int i)
	Move the X parameter by a specified amount. More...

LocatedGroup	moveY (int i)
	Move the Y parameter by a specified amount. More...

LocatedGroup	moveZ (int i)
	Move the Z parameter by a specified amount. More...

double	computeDifferenceVector (ContinuousVector me, ContinuousVector him, ContinuousVector move)
	Compute the difference vector between two continuous vectors. More...

void	distanceFromBorders ()
	Compute distance to closest carrier and closest bulk. More...

int	freeNbh ()
	Calculate the number of neighbours that contains no biomass. More...

Public Attributes
AgentContainer	agentGrid

LinkedList< LocatedAgent >	group = new LinkedList<LocatedAgent>()

double[]	speciesConcentration

double	totalVolume = 0

double	deltaV = 0

double	totalConcentration = 0

double	totalMass = 0

double	erosionTime = Double.NaN

double	distanceFromCarrier

double	distanceFromBulk

double	ratio

int	gridIndex

ContinuousVector	cc

DiscreteVector	dc

int[][][]	nbhIndex = new int[3][3][3]

LocatedGroup[][][]	nbhGroup = new LocatedGroup[3][3][3]

int	status = 2

boolean	isBulk = false

boolean	isCarrier = false

boolean	isOutside

int	nFreeNbh

ContinuousVector	move = new ContinuousVector()

Protected Member Functions
void	testNbh_3D (LocatedGroup[] shovGrid)
	Use the boundary conditions to build 3D neighbourhood reference map. More...

void	testNbh_2D (LocatedGroup[] shovGrid)
	Use the boundary conditions to build 3D neighbourhood reference map. More...

Detailed Description

Object to hold a group of agents in one location on the agent grid.

Object to hold a group of agents in one location on the agent grid

Author: Andreas Dötsch (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; 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.agent.LocatedGroup.LocatedGroup	(	int	index,
		AgentContainer	anAgentGrid,
		Simulator	aSimulator
	)

Set the coordinates of this group and check these are inside the grid.

Set the coordinates of this group and check these are inside the grid

Parameters

index	Index of the grid in which this group is located
anAgentGrid	The agent grid associated with this index
aSimulator	The current simulation object

Member Function Documentation

void simulator.agent.LocatedGroup.add ( LocatedAgent anAgent )

Add an agent to this LocatedGroup.

Add an agent to this LocatedGroup

Parameters

anAgent LocatedAgent to add to this group

void simulator.agent.LocatedGroup.addMoveToAgents ( double alpha )

Scale the movement vector for the grid element and apply to each agent.

Scale the movement vector for the grid element and apply to each agent

Parameters

alpha Scaling factor to be applied to a move

double simulator.agent.LocatedGroup.computeDifferenceVector	(	ContinuousVector	me,
		ContinuousVector	him,
		ContinuousVector	move
	)

Compute the difference vector between two continuous vectors.

Compute the difference vector between two continuous vectors

Parameters

me	Location of one agent expressed as continuous vector
him	Location of second agent expressed as continuous vector
move	ContinuousVector to hold the difference between the two vectors

Returns: Double distance between the two points

Deprecated:

double simulator.agent.LocatedGroup.computeMove	(	SoluteGrid	pressure,
		double	deltaT
	)

Compute the gradient due to pressure and use it to set the advective affect.

Compute the gradient due to pressure and use it to set the advective affect

Parameters

pressure	Pressure grid
deltaT	DeltaT

Returns: Norm of the movement vector under the affect of the pressure gradient

void simulator.agent.LocatedGroup.distanceFromBorders ( )

Compute distance to closest carrier and closest bulk.

Compute distance to closest carrier and closest bulk

int simulator.agent.LocatedGroup.freeNbh ( )

Calculate the number of neighbours that contains no biomass.

Calculate the number of neighbours that contains no biomass

Returns: the number of empty neighbours

void simulator.agent.LocatedGroup.host ( LocatedAgent aLoc )

Shuffle coordinates of an agent inside the group.

Parameters

aLoc	LocatedAgent which is to be shuffled

void simulator.agent.LocatedGroup.init ( )

Builds neighbourhood reference map.

Builds neighbourhood reference map

void simulator.agent.LocatedGroup.killAll ( )

Safely remove located agent from agentList & agentGrid.

Safely remove located agent from agentList & agentGrid

LocatedGroup simulator.agent.LocatedGroup.moveX ( int i )

Move the X parameter by a specified amount.

Move the X parameter by a specified amount

Parameters

i	The current I grid element

Returns: Located group reached by that move

LocatedGroup simulator.agent.LocatedGroup.moveY ( int i )

Move the Y parameter by a specified amount.

Move the Y parameter by a specified amount

Parameters

i	The current grid element

Returns: Located group reached by that move

LocatedGroup simulator.agent.LocatedGroup.moveZ ( int i )

Move the Z parameter by a specified amount.

Move the Z parameter by a specified amount

Parameters

i	The current grid element

Returns: Located group reached by that move

void simulator.agent.LocatedGroup.refreshElement ( )

Refresh status and concentration of the group.

Refresh status and concentration of the group

double simulator.agent.LocatedGroup.refreshVolume ( )

Refresh the volume statistics of this group.

Refresh the volume statistics of this group

Returns: Double noting the total volume of agents in this group

void simulator.agent.LocatedGroup.remove ( LocatedAgent anAgent )

Remove an agent from this LocatedGroup.

Remove an agent from this LocatedGroup

Parameters

anAgent LocatedAgent to remove from this group

void simulator.agent.LocatedGroup.resetMove ( )

void simulator.agent.LocatedGroup.testNbh_2D ( LocatedGroup[] shovGrid )

protected

Use the boundary conditions to build 3D neighbourhood reference map.

Use the boundary conditions to build 3D neighbourhood reference map

Parameters

shovGrid The shoving grid used to build reference map

void simulator.agent.LocatedGroup.testNbh_3D ( LocatedGroup[] shovGrid )

protected

Use the boundary conditions to build 3D neighbourhood reference map.

Use the boundary conditions to build 3D neighbourhood reference map

Parameters

shovGrid The shoving grid used to build reference map

Member Data Documentation

AgentContainer simulator.agent.LocatedGroup.agentGrid

Agent container this located group is within

ContinuousVector simulator.agent.LocatedGroup.cc

Coordinates of this location as a continuous vector

DiscreteVector simulator.agent.LocatedGroup.dc

Coordinates of this location as a discrete

double simulator.agent.LocatedGroup.deltaV = 0

double simulator.agent.LocatedGroup.distanceFromBulk

Distance of the group at this location from the bulk

double simulator.agent.LocatedGroup.distanceFromCarrier

Distance of the group at this location from the carrier

double simulator.agent.LocatedGroup.erosionTime = Double.NaN

int simulator.agent.LocatedGroup.gridIndex

The index of the grid at which this located group represents

LinkedList<LocatedAgent> simulator.agent.LocatedGroup.group = new LinkedList<LocatedAgent>()

Linked list to hold members of this group

boolean simulator.agent.LocatedGroup.isBulk = false

Boolean stating whether this location is in the bulk

boolean simulator.agent.LocatedGroup.isCarrier = false

Boolean stating whether this location is in the carrier

boolean simulator.agent.LocatedGroup.isOutside

Boolean stating whether this location is outside the grid

ContinuousVector simulator.agent.LocatedGroup.move = new ContinuousVector()

Vector to hold an amount of distance an agent is to move

LocatedGroup [][][] simulator.agent.LocatedGroup.nbhGroup = new LocatedGroup[3][3][3]

Neighbouring groups around this group

int [][][] simulator.agent.LocatedGroup.nbhIndex = new int[3][3][3]

Index of the neighbours of this group

int simulator.agent.LocatedGroup.nFreeNbh

Number of free neighbours around this location

double simulator.agent.LocatedGroup.ratio

double [] simulator.agent.LocatedGroup.speciesConcentration

Concentration of species in this group, thus area represented

int simulator.agent.LocatedGroup.status = 2

Space occupation (-1->outside, 0->carrier, 1->biofilm, 2->liquid, 3->bulk)

double simulator.agent.LocatedGroup.totalConcentration = 0

Total concentration of agents in this group

double simulator.agent.LocatedGroup.totalMass = 0

Total mass of agents in this group

double simulator.agent.LocatedGroup.totalVolume = 0

Total volume of agents in this group

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

/home/kieran/Dropbox/workspace/iDynoMiCS/src/simulator/agent/LocatedGroup.java

Classes

Public Member Functions

Public Attributes

Protected Member Functions

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation