simulator.detachment.DS_SolGrad Class Reference

SolGrad detachment method. Loop through solutes to find the maximum gradient and use this as a multiplier to calculate detachment rate. More...

Inheritance diagram for simulator.detachment.DS_SolGrad:

Public Member Functions
void	init (AgentContainer anAgentGrid, XMLParser root)
	Initialise the object by reading attributes from associated agent grid and XML protocol file. More...
Public Member Functions inherited from simulator.detachment.LevelSet
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...

Protected Member Functions
double	getLocalDetachmentSpeed (LocatedGroup aGroup, Simulator aSim)
	Calculate and return the local detachment speed using this detachment method. More...

Additional Inherited Members
Static Public Member Functions inherited from simulator.detachment.LevelSet
static LevelSet	staticBuilder (XMLParser root, AgentContainer anAgentGrid)
	Generic constructor called to dynamically instantiate a child class object. More...
Public Attributes inherited from simulator.detachment.LevelSet
LocatedGroup[]	_shovingGrid

Detailed Description

SolGrad detachment method. Loop through solutes to find the maximum gradient and use this as a multiplier to calculate detachment rate.

The mark-up defines the erosion forces that act on the biofilm surface. Detachment works by removing a layer of biomass based on the detachment speed and the timestep, with the detachment speed calculated via one of the given forms. This class captures the Proportional detachment method.

Author

Robert Clegg (rjc09.nosp@m.6@bh.nosp@m.am.ac.nosp@m..uk), Centre for Systems Biology, University of Birmingham, UK

Member Function Documentation

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

protectedvirtual

Calculate and return the local detachment speed using this detachment method.

Calculate and return the local detachment speed using this detachment method

Parameters

aSim	The simulation object used to simulate the conditions specified in the protocol file
aGroup	Located group for which the local detachment speed is being determined

Returns

Double stating local detachment speed for this group

Implements simulator.detachment.LevelSet.

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

Initialise the object by reading attributes from associated agent grid and XML protocol file.

Initialise the object by reading attributes from associated agent grid and XML protocol file

Parameters

anAgentGrid	Associated grid of agents
root	XML tag containing information related to this detachment mechanism

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

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