simulator.detachment.LevelSet Class Reference

Solver used for modelling detachment. More...

Inheritance diagram for simulator.detachment.LevelSet:

Public Member Functions
void	init (AgentContainer anAgentGrid, XMLParser root)
	Initialise this LevelSet object by taking information from the associated grid and protocol file. More...
void	refreshBorder (boolean evalErosion, Simulator aSim)
	Identify the biofilm border. More...
LocatedGroup	getLandingPoint ()
	Return a random LocatedGroup grid element of the shoving grid where a attaching agent could land. More...
void	refreshCarrier ()
	Build list of groups belonging to the carrier. More...
void	computeLevelSet (Simulator aSim)
	Compute erosion time for the whole biofilm. More...
LinkedList< LocatedGroup >	getBorder ()
	Return list of agent groups on the biofilm/liquid border. More...

Static Public Member Functions
static LevelSet	staticBuilder (XMLParser root, AgentContainer anAgentGrid)
	Generic constructor called to dynamically instantiate a child class object. More...

Public Attributes
LocatedGroup[]	_shovingGrid

Protected Member Functions
abstract double	getLocalDetachmentSpeed (LocatedGroup aGroup, Simulator aSim)
	Return the local detachment speed. More...

Detailed Description

Solver used for modelling detachment.

Solver used for modelling detachment

Author

*

João Xavier (xavie.nosp@m.rj@m.nosp@m.skcc..nosp@m.org), Memorial Sloan-Kettering Cancer Center (NY, USA)

Member Function Documentation

void simulator.detachment.LevelSet.computeLevelSet

(

Simulator

aSim

)

Compute erosion time for the whole biofilm.

Compute erosion time for the whole biofilm

Parameters

aSim	The simulation object used to simulate the conditions specified in the protocol file

LinkedList<LocatedGroup> simulator.detachment.LevelSet.getBorder

(

)

Return list of agent groups on the biofilm/liquid border.

Return list of agent groups on the biofilm/liquid border

Returns

LinkedList of agent groups on the biofilm/liquid border

LocatedGroup simulator.detachment.LevelSet.getLandingPoint

(

)

Return a random LocatedGroup grid element of the shoving grid where a attaching agent could land.

Return a random LocatedGroup grid element of the shoving grid where a attaching agent could land

Returns

LocatedGroup from a random element of the shoving grid

abstract double simulator.detachment.LevelSet.getLocalDetachmentSpeed ( LocatedGroup  aGroup, Simulator  aSim  )

protectedpure virtual

Return the local detachment speed.

Return the local detachment speed

Parameters

aGroup	Group of located agents on the grid
aSim	The simulation object used to simulate the conditions specified in the protocol file

Returns

An erosion speed (micrometer by hour)

Implemented in simulator.detachment.DS_SolGrad, simulator.detachment.DS_Biomass, simulator.detachment.DS_Proportional, and simulator.detachment.DS_Quadratic.

void simulator.detachment.LevelSet.init	(	AgentContainer	anAgentGrid,
		XMLParser	root
	)

Initialise this LevelSet object by taking information from the associated grid and protocol file.

Initialise this LevelSet object by taking information from the associated grid and protocol file

Parameters

anAgentGrid	Agent grid which this solver is associated to
root	XML tags that contain parameters relating to detachment

void simulator.detachment.LevelSet.refreshBorder	(	boolean	evalErosion,
		Simulator	aSim
	)

Identify the biofilm border.

Identify the biofilm border

Parameters

evalErosion	Boolean noting whether biofilm erosion should be considered
aSim	The simulation object used to simulate the conditions specified in the protocol file

void simulator.detachment.LevelSet.refreshCarrier

(

)

Build list of groups belonging to the carrier.

Build list of groups belonging to the carrier

static LevelSet simulator.detachment.LevelSet.staticBuilder ( XMLParser  root, AgentContainer  anAgentGrid  )

static

Generic constructor called to dynamically instantiate a child class object.

Generic constructor called to dynamically instantiate a child class object

Parameters

root	XML tags that contain parameters relating to detachment
anAgentGrid	Agent grid associated with this solver

Member Data Documentation

LocatedGroup [] simulator.detachment.LevelSet._shovingGrid

Shoving grid associated with the agent grid associated with this object

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

• /home/kieran/Dropbox/workspace/iDynoMiCS/src/simulator/detachment/LevelSet.java