simulator.diffusionSolver.Solver_pressure Class Reference

Initialises and calculates pressure affect on the simulation domain. More...

Inheritance diagram for simulator.diffusionSolver.Solver_pressure:

Public Member Functions
void	init (Simulator aSimulator, XMLParser xmlRoot)
	Initialise this solver, by storing the relevant solutes, boundary layer, and biomass grids required to calculate pressure. Initialises required pressure grids. More...
void	initializeConcentrationFields ()
	Initialise concentration fields. Refreshes domain and biomass grids and sets pressure across the grid to zero. More...
void	solveDiffusionReaction ()
void	updateBioVolume ()
	Update the biovolume grid after the biomass grid has been refreshed. More...
SoluteGrid	getPressureGrid ()
	Return the pressure grid. More...
SoluteGrid	getVolumeRateGrid ()
	Return the volume rate grid. More...
Public Member Functions inherited from simulator.diffusionSolver.DiffusionSolver
void	init (Simulator aSim, XMLParser xmlRoot)
	Initialisation procedure for each diffusion solver specified in the XML protocol file. More...
void	register ()
	Registers this solver in the simulation solver array for referencing later on. More...
void	addAllReactions ()
	Small routine to use if you have only one solver instead to add one by one all pathways. More...
Boolean	isActive ()
	Determine if this solver is actually being used. Set in the protocol file. More...
void	initAndSolve ()
	Create the solver, initialise the concentration fields, and solve the diffusion reaction equations. More...

Protected Attributes
SoluteGrid	_bLayer
SoluteGrid	_biovolume
SinglegridPressure[]	_solute
Simulator	mySim
IsComputationDomain	_domain
Protected Attributes inherited from simulator.diffusionSolver.DiffusionSolver
ArrayList< Reaction >	_reactions = new ArrayList<Reaction>()
SoluteGrid[]	_soluteList
ArrayList< Integer >	_soluteIndex = new ArrayList<Integer>()
double	internTimeStep
double	minimalTimeStep
double	internalIteration
double	maxIteration = 1
Boolean	_active = false

Additional Inherited Members
Public Attributes inherited from simulator.diffusionSolver.DiffusionSolver
String	solverName
int	solverIndex
Simulator	mySim
Domain	myDomain
Protected Member Functions inherited from simulator.diffusionSolver.DiffusionSolver
void	addReactionWithSolutes (Reaction aReaction)
	Sets reference to a biochemical pathway this solver has to deal with. More...

Detailed Description

Initialises and calculates pressure affect on the simulation domain.

Initialises and calculates pressure affect on the simulation domain

Author

Andreas D�tsch (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

Member Function Documentation

SoluteGrid simulator.diffusionSolver.Solver_pressure.getPressureGrid

(

)

Return the pressure grid.

Return the pressure grid

Returns

Pressure grid

SoluteGrid simulator.diffusionSolver.Solver_pressure.getVolumeRateGrid

(

)

Return the volume rate grid.

Return the volume rate grid

Returns

Volume rate grid

void simulator.diffusionSolver.Solver_pressure.init	(	Simulator	aSimulator,
		XMLParser	xmlRoot
	)

Initialise this solver, by storing the relevant solutes, boundary layer, and biomass grids required to calculate pressure. Initialises required pressure grids.

Initialise this solver, by storing the relevant solutes, boundary layer, and biomass grids required to calculate pressure. Initialises required pressure grids

Parameters

aSimulator	The current simulation object
xmlRoot	XML tags containing relevant parameters for intialising this object

void simulator.diffusionSolver.Solver_pressure.initializeConcentrationFields ( )

virtual

Initialise concentration fields. Refreshes domain and biomass grids and sets pressure across the grid to zero.

Initialise concentration fields. Refreshes domain and biomass grids and sets pressure across the grid to zero

Implements simulator.diffusionSolver.DiffusionSolver.

void simulator.diffusionSolver.Solver_pressure.solveDiffusionReaction ( )

virtual

Performs the solving algorithm on the diffusion reaction system.

Implements simulator.diffusionSolver.DiffusionSolver.

void simulator.diffusionSolver.Solver_pressure.updateBioVolume

(

)

Update the biovolume grid after the biomass grid has been refreshed.

Update the biovolume grid after the biomass grid has been refreshed

Member Data Documentation

SoluteGrid simulator.diffusionSolver.Solver_pressure._biovolume

protected

Solute grid storing the biomass

SoluteGrid simulator.diffusionSolver.Solver_pressure._bLayer

protected

Solute grid storing the boundary layer

IsComputationDomain simulator.diffusionSolver.Solver_pressure._domain

protected

Computation domain this solver is associated with

SinglegridPressure [] simulator.diffusionSolver.Solver_pressure._solute

protected

Pressure grid

Simulator simulator.diffusionSolver.Solver_pressure.mySim

protected

Current simulation object

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

• /home/kieran/Dropbox/workspace/iDynoMiCS/src/simulator/diffusionSolver/Solver_pressure.java