An abstract class used as a parent for all diffusion solvers that could be defined. More...

Inheritance diagram for simulator.diffusionSolver.DiffusionSolver:

Public Member Functions
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...

abstract void	initializeConcentrationFields ()
	Initialize the diffusion-reaction-system according to the solver. More...

abstract void	solveDiffusionReaction ()

Public Attributes
String	solverName

int	solverIndex

Simulator	mySim

Domain	myDomain

Protected Member Functions
void	addReactionWithSolutes (Reaction aReaction)
	Sets reference to a biochemical pathway this solver has to deal with. More...

Protected Attributes
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

Detailed Description

An abstract class used as a parent for all diffusion solvers that could be defined.

This class is used as a parent for all diffusion solvers that can be specified in the XML protocol file. This processes the SOLVER mark-up within the protocol file. Solvers are used to compute the steady-state solute profile within the computational domains.

This class is a component class of iDynoMiCS, released under the CECIL license. Please see www.idynomics.bham.ac.uk for more information

Version: 1.2

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

Member Function Documentation

void simulator.diffusionSolver.DiffusionSolver.addAllReactions ( )

Small routine to use if you have only one solver instead to add one by one all pathways.

Small routine to use if you have only one solver instead to add one by one all pathways

void simulator.diffusionSolver.DiffusionSolver.addReactionWithSolutes ( Reaction aReaction )

protected

Sets reference to a biochemical pathway this solver has to deal with.

Sets reference to a biochemical pathway this solver has to deal with. References to the solutes and agents of the diffusion/reaction-system are provided by the pathways.

Parameters

aReaction : the pathway to add to this solver

void simulator.diffusionSolver.DiffusionSolver.init	(	Simulator	aSim,
		XMLParser	xmlRoot
	)

Initialisation procedure for each diffusion solver specified in the XML protocol file.

This method takes a solver specification from the XML file (as a set of XML tags) and initialises a solver object

Parameters

aSim	The simulation object used to simulate the conditions specified in the protocol file
xmlRoot	The XML object containing the definition of one solver in the protocol file

void simulator.diffusionSolver.DiffusionSolver.initAndSolve ( )

Create the solver, initialise the concentration fields, and solve the diffusion reaction equations.

Create the solver, initialise the concentration fields, and solve the diffusion reaction equations

abstract void simulator.diffusionSolver.DiffusionSolver.initializeConcentrationFields ( )

pure 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

Implemented in simulator.diffusionSolver.Solver_chemostat, simulator.diffusionSolver.Solver_multigrid, and simulator.diffusionSolver.Solver_pressure.

Boolean simulator.diffusionSolver.DiffusionSolver.isActive ( )

Determine if this solver is actually being used. Set in the protocol file.

Determine if this solver is actually being used. Set in the protocol file

Returns: Boolean stating whether this solver is active

void simulator.diffusionSolver.DiffusionSolver.register ( )

Registers this solver in the simulation solver array for referencing later on.

This method adds this solver object to the simulation variable solverList, an array of DiffusionSolver objects used in the simulation

abstract void simulator.diffusionSolver.DiffusionSolver.solveDiffusionReaction ( )

pure virtual

Performs the solving algorithm on the diffusion reaction system. If needed, the time step is provided by the SimTimer.

Implemented in simulator.diffusionSolver.Solver_chemostat, simulator.diffusionSolver.Solver_multigrid, and simulator.diffusionSolver.Solver_pressure.

Member Data Documentation

Boolean simulator.diffusionSolver.DiffusionSolver._active = false

protected

Boolean flag that determines whether this solver will actually be used. Specified in XML protocol file

ArrayList<Reaction> simulator.diffusionSolver.DiffusionSolver._reactions = new ArrayList<Reaction>()

protected

List of pathways (reactions) that this solver is associated with

ArrayList<Integer> simulator.diffusionSolver.DiffusionSolver._soluteIndex = new ArrayList<Integer>()

protected

List of solutes that are used by THIS solver

SoluteGrid [] simulator.diffusionSolver.DiffusionSolver._soluteList

protected

Local copy of the array of solute grids - one for each solute specified in the simulation protocol file. Taken from simulator object

double simulator.diffusionSolver.DiffusionSolver.internalIteration

protected

double simulator.diffusionSolver.DiffusionSolver.internTimeStep

protected

double simulator.diffusionSolver.DiffusionSolver.maxIteration = 1

protected

double simulator.diffusionSolver.DiffusionSolver.minimalTimeStep

protected

Domain simulator.diffusionSolver.DiffusionSolver.myDomain

The computational domain that this solver is associated with. Specified in the XML protocol file

Simulator simulator.diffusionSolver.DiffusionSolver.mySim

The simulation object that this solver is associated with

int simulator.diffusionSolver.DiffusionSolver.solverIndex

The position of this solver in the simulation dictionary

String simulator.diffusionSolver.DiffusionSolver.solverName

A name assigned to this solver. Specified in the XML protocol file

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

/home/kieran/Dropbox/workspace/iDynoMiCS/src/simulator/diffusionSolver/DiffusionSolver.java

Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Detailed Description

Member Function Documentation

Member Data Documentation