simulator.diffusionSolver.Solver_multigrid Class Reference

Inheritance diagram for simulator.diffusionSolver.Solver_multigrid:

Public Member Functions
void	init (Simulator aSimulator, XMLParser xmlRoot)
void	initializeConcentrationFields ()
	Initialize the diffusion-reaction-system according to the solver. More...
void	solveDiffusionReaction ()
void	stepSolveDiffusionReaction ()
void	updateBulk ()
	Update concentration in the reactor. More...
void	solveCoarsest ()
void	relax (int nIter)
void	updateReacRateAndDiffRate (int resOrder)
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
MultigridSolute	_bLayer
MultigridSolute	_diffusivity
MultigridSolute[]	_solute
MultigridSolute[]	_biomass
SoluteGrid[]	allSolute
SoluteGrid[]	allReac
SoluteGrid[]	allDiffReac
int	maxOrder
int	nSolute
int	nReaction
int	nCoarseStep
int	vCycles
int	nPreSteps
int	nPosSteps
Domain	_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

Static Protected Attributes
static int	iSolute
static int	order

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

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

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)

Member Function Documentation

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

void simulator.diffusionSolver.Solver_multigrid.initializeConcentrationFields ( )

virtual

Initialize the diffusion-reaction-system according to the solver.

Initialize the diffusion-reaction-system according to the solver. Creates and initializes internal data structure for solving. Called at each simulation step

Implements simulator.diffusionSolver.DiffusionSolver.

void simulator.diffusionSolver.Solver_multigrid.relax

(

int

nIter

)

Apply several relaxations to the grid at the current resolution

Parameters

nIter

void simulator.diffusionSolver.Solver_multigrid.solveCoarsest

(

)

Solve the coarsest grid by relaxation Coarse grid is initialised to bulk concentration

void simulator.diffusionSolver.Solver_multigrid.solveDiffusionReaction ( )

virtual

Solve by iterative relaxation

Implements simulator.diffusionSolver.DiffusionSolver.

void simulator.diffusionSolver.Solver_multigrid.stepSolveDiffusionReaction

(

)

One step of the solver

void simulator.diffusionSolver.Solver_multigrid.updateBulk

(

)

Update concentration in the reactor.

Update concentration in the reactor

void simulator.diffusionSolver.Solver_multigrid.updateReacRateAndDiffRate

(

int

resOrder

)

Call all the agents and read their uptake-rate for the current concentration

Parameters

resOrder

Member Data Documentation

MultigridSolute [] simulator.diffusionSolver.Solver_multigrid._biomass

protected

MultigridSolute simulator.diffusionSolver.Solver_multigrid._bLayer

protected

MultigridSolute simulator.diffusionSolver.Solver_multigrid._diffusivity

protected

Domain simulator.diffusionSolver.Solver_multigrid._domain

protected

MultigridSolute [] simulator.diffusionSolver.Solver_multigrid._solute

protected

SoluteGrid [] simulator.diffusionSolver.Solver_multigrid.allDiffReac

protected

SoluteGrid [] simulator.diffusionSolver.Solver_multigrid.allReac

protected

SoluteGrid [] simulator.diffusionSolver.Solver_multigrid.allSolute

protected

int simulator.diffusionSolver.Solver_multigrid.iSolute

staticprotected

int simulator.diffusionSolver.Solver_multigrid.maxOrder

protected

int simulator.diffusionSolver.Solver_multigrid.nCoarseStep

protected

int simulator.diffusionSolver.Solver_multigrid.nPosSteps

protected

int simulator.diffusionSolver.Solver_multigrid.nPreSteps

protected

int simulator.diffusionSolver.Solver_multigrid.nReaction

protected

int simulator.diffusionSolver.Solver_multigrid.nSolute

protected

Number of solutes SOLVED by THIS solver

int simulator.diffusionSolver.Solver_multigrid.order

staticprotected

int simulator.diffusionSolver.Solver_multigrid.vCycles

protected

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

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