Inheritance diagram for simulator.diffusionSolver.Solver_chemostat:

Public Member Functions
void	init (Simulator aSimulator, XMLParser xmlRoot)
	Initialise the chemostat: the solute and reaction list, and all variables used by the ODE solvers. More...

void	setDilutionAndY0 ()
	Set the dilution rate and the initial substrate concentration to those specified in the bulk compartment. More...

void	initializeConcentrationFields ()
	Initialise the concentration fields within the chemostat, getting concentration of any catalysts and storing this on a grid. More...

void	solveDiffusionReaction ()
	Use the ODE solver to solve the diffusion reaction and update the bulk. More...

void	odeSolver (double t0, double rtol, double hmax)
	ODE solver for calculating the diffusion reactions. More...

Matrix	calcdYdT (Matrix S, Matrix sInflow, Matrix dYdT)
	Calculates the derivative of substrate concentration (a function parameter) with respect to time. More...

Matrix	calcdFdT (Matrix S, Matrix dFdT, Matrix sInflow, double tdel)
	Provides an estimate of how F (the derivative of S w.r.t. time) is changing (i.e. the second derivative). More...

Matrix	calcJacobian (Matrix S, Matrix dFdY)
	Calculate the Jacobian matrix - the partial derivatives of the rate of change of each substrate. More...

void	updateBulk ()
	Find the connected bulks and update their concentrations. More...

Matrix	updateSInflow (Matrix sInflow)
	Check if the Sinflow has changed (solutes may be pulsed) 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
int	nSolute

int	nReaction

SoluteGrid[]	allSolute

SoluteGrid[]	allReac

Domain	_domain

MultigridSolute[]	_reactiveBiomass

Boolean[]	isConstSol

double	d = 1.0 / (2.0 + Math.sqrt(2.0))

double	e32 = 6.0 + Math.sqrt(2.0)

double	power = 1.0/3.0

double	sqrtE = Math.sqrt(2.22e-16)

double	EPS = 2.22e-16

double	Dilution

double	hmax

double	rtol

ArrayList< Integer >	solReacInd = new ArrayList<Integer>()

double[][]	soluteYield

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...

Member Function Documentation

Matrix simulator.diffusionSolver.Solver_chemostat.calcdFdT	(	Matrix	S,
		Matrix	dFdT,
		Matrix	sInflow,
		double	tdel
	)

Provides an estimate of how F (the derivative of S w.r.t. time) is changing (i.e. the second derivative).

Provides an estimate of how F (the derivative of S w.r.t. time) is changing (i.e. the second derivative). Note that calcdYdT is called with the hypothetical S-value of y + dYdT * tdel, so we'll need to recall calcReacRateAndDiffRate(S) with S as just y.

Parameters

S	Temporary container for solute concentration
dFdT	Estimation of how the derivative of solutes with regard to time is changing
sInflow	Matrix of solute flow information (if solutes are pulsed)
tdel	Mini time-step used for calculating the value of dFdT

Matrix simulator.diffusionSolver.Solver_chemostat.calcdYdT	(	Matrix	S,
		Matrix	sInflow,
		Matrix	dYdT
	)

Calculates the derivative of substrate concentration (a function parameter) with respect to time.

Calculates the derivative of substrate concentration (a function parameter) with respect to time. As part of this process the allReac and allDiffReac values are set according to the (possibly hypothetical) values at substrate concentration S - you'll probably want to rerun calcReacRateAndDiffRate(y); afterwards to get allReac and allDiffReac to the correct values.

Parameters

S	Temporary container for solute concentration
sInflow	Matrix of solute flow information (if solutes are pulsed)
dYdT	Matrix to store the derivatives of substrate concentration

Returns: Matrix of the derivatives of substrate concentration

Matrix simulator.diffusionSolver.Solver_chemostat.calcJacobian	(	Matrix	S,
		Matrix	dFdY
	)

Calculate the Jacobian matrix - the partial derivatives of the rate of change of each substrate.

The Jacobian matrix dFdY gives the partial derivatives of the rate of change of each substrate (F = dYdT, or equivalently, dSdT) with respect to each substrate. Rows correspond to substrates being differentiated (first by time to give F, then by other substrate concentrations to give the elements of this matrix) and columns to the substrate with respect to which we are differentiating.

Parameters

S	Temporary container for solute concentration
dFdY	Jacobian matrix being calculated

Returns: Matrix containing partial derivatives of rate of change of each substrate

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

Initialise the chemostat: the solute and reaction list, and all variables used by the ODE solvers.

Initialise the chemostat: the solute and reaction list, and all variables used by the ODE solvers

Parameters

aSimulator	The current simulation object
xmlRoot	Root element of XML tags containing chemostat related parameters

void simulator.diffusionSolver.Solver_chemostat.initializeConcentrationFields ( )

virtual

Initialise the concentration fields within the chemostat, getting concentration of any catalysts and storing this on a grid.

Initialise the concentration fields within the chemostat, getting concentration of any catalysts and storing this on a grid

Implements simulator.diffusionSolver.DiffusionSolver.

void simulator.diffusionSolver.Solver_chemostat.odeSolver	(	double	t0,
		double	rtol,
		double	hmax
	)

ODE solver for calculating the diffusion reactions.

ODE solver for calculating the diffusion reactions

Parameters

t0	Simulation time
rtol	Relative tolerance of the calculated error
hmax	Maximum internal step of the solver

void simulator.diffusionSolver.Solver_chemostat.setDilutionAndY0 ( )

Set the dilution rate and the initial substrate concentration to those specified in the bulk compartment.

Set the dilution rate and the initial substrate concentration to those specified in the bulk compartment [Rob: one assumption here is that the dilution rate is constant].

void simulator.diffusionSolver.Solver_chemostat.solveDiffusionReaction ( )

virtual

Use the ODE solver to solve the diffusion reaction and update the bulk.

Use the ODE solver to solve the diffusion reaction and update the bulk

Implements simulator.diffusionSolver.DiffusionSolver.

void simulator.diffusionSolver.Solver_chemostat.updateBulk ( )

Find the connected bulks and update their concentrations.

Find the connected bulks and update their concentrations

Matrix simulator.diffusionSolver.Solver_chemostat.updateSInflow ( Matrix sInflow )

Check if the Sinflow has changed (solutes may be pulsed)

Parameters

sInflow Matrix of solutes in flow

Returns: Updated matrix showing solute flow levels

Member Data Documentation

Domain simulator.diffusionSolver.Solver_chemostat._domain

protected

Computational domain that this solver is associated with

MultigridSolute [] simulator.diffusionSolver.Solver_chemostat._reactiveBiomass

protected

Array of reactive biomasses

SoluteGrid [] simulator.diffusionSolver.Solver_chemostat.allReac

protected

The solute grid of reaction rates for each solute.

SoluteGrid [] simulator.diffusionSolver.Solver_chemostat.allSolute

protected

The solute grid of solute concentrations. As we are in a chemostat this has only one grid position (0,0,0). Note that y will be the vector containing the actual concentrations during odeSolver()... here allSolute will be a temporary variable used for calculating potential reaction rates, etc, in calcReacAndDiffReacRates().

double simulator.diffusionSolver.Solver_chemostat.d = 1.0 / (2.0 + Math.sqrt(2.0))

protected

Constant used by the ODE solvers

double simulator.diffusionSolver.Solver_chemostat.Dilution

protected

The chemostat dilution rate. This will be set when init() calls setDilutionAndY0()

double simulator.diffusionSolver.Solver_chemostat.e32 = 6.0 + Math.sqrt(2.0)

protected

Constant used by the ODE solvers

double simulator.diffusionSolver.Solver_chemostat.EPS = 2.22e-16

protected

The smallest positive floating-point number such that 1.0+EPS > 1.0

double simulator.diffusionSolver.Solver_chemostat.hmax

protected

Maximum internal step of the solver. Used in the ODE solver

Boolean [] simulator.diffusionSolver.Solver_chemostat.isConstSol

protected

Boolean stating whether the bulk concentration remains constant

int simulator.diffusionSolver.Solver_chemostat.nReaction

protected

Number of reactions in simulation

int simulator.diffusionSolver.Solver_chemostat.nSolute

protected

Number of solutes in simulation

double simulator.diffusionSolver.Solver_chemostat.power = 1.0/3.0

protected

Constant used by the ODE solvers

double simulator.diffusionSolver.Solver_chemostat.rtol

protected

Relative tolerance of the calculated error. Used in the ODE solver

ArrayList<Integer> simulator.diffusionSolver.Solver_chemostat.solReacInd = new ArrayList<Integer>()

protected

1D array of arraylists containing the list of reactions in which each of the solutes participates.

double [][] simulator.diffusionSolver.Solver_chemostat.soluteYield

protected

For each reaction (first index) this stores the yield of each solute (second index). Used in calculating the Jacobian. The Jacobian matrix: on each row an "F" (the rate of change of a substrate concentration) is differentiated with respect to each of the substrate concentrations (arranged on the columns).

double simulator.diffusionSolver.Solver_chemostat.sqrtE = Math.sqrt(2.22e-16)

protected

Numerical accuracy for EPS (error per step)

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

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

Public Member Functions

Protected Attributes

Additional Inherited Members

Member Function Documentation

Member Data Documentation