Modelled First-Order reactions. This class is deprecated. More...

Inheritance diagram for simulator.reaction.FirstOrder:

Public Member Functions
void	init (Simulator aSim, XMLParser aReactionRoot)

void	initFromAgent (ActiveAgent anAgent, Simulator aSim, XMLParser aReactionRoot)

void	computeUptakeRate (double[] s, ActiveAgent anAgent)

void	computeUptakeRate (double[] s, double mass)

void	computeSpecificGrowthRate (ActiveAgent anAgent)
	Return the specific reaction rate. More...

void	computeSpecificGrowthRate (double[] s)

void	computeSpecificGrowthRate (double[] s, ActiveAgent anAgent)

double	computeMassGrowthRate (ActiveAgent anAgent)

double	computeSpecGrowthRate (ActiveAgent anAgent)
	Compute the specific growth rate. More...

void	computeUptakeRate (double[] s, double conc, double h)

Matrix	calcdMUdS (Matrix S, double biomass)
	Calculate the rate of change of each uptake rate with respect to each solute. Returned as a matrix. More...

Matrix	calcdMUdT (Matrix S, double biomass)
	Calculate the rate of change of each uptake rate with respect to time. More...

double[]	computeMarginalDiffMu (double[] s)
	Compute the marginal difference array. More...

double	computeSpecRate (double[] s)
	Compute the specific growth rate. More...

void	updateMarginalMu (double[] s)
	Update the Marginal Mu data matrix. More...

Public Member Functions inherited from simulator.reaction.Reaction
void	init (Simulator aSim, XMLParser aReactionRoot)
	Initialises a reaction object, giving the object the properties stated in the protocol file. More...

void	initFromAgent (ActiveAgent anAgent, Simulator aSim, XMLParser xmlRoot)
	Use the reaction class to fill the parameters fields of the agent. Populate only the yield vector, the kinetic vector will be filled by the subdefined method in the child classes. More...

void	register (String aReactionName, Simulator aSimulator)
	End of the initialization procedure. Store the name and simulation dictionary index for this reaction. More...

LinkedList< String >	declareSolutes ()
	Utilised by a solver instance to know the solutes affected by this reaction. More...

void	fillParameters (Simulator aSim, XMLParser xmlRoot)
	Reads the reaction information (name, solute yield, particle yield etc) from the XML file and initialises this reaction. More...

void	addAgent (ActiveAgent anAgent)
	Register an agent among the guild of this pathway. More...

void	removeAgent (ActiveAgent anAgent)
	Remove an agent among the guild of this pathway. More...

void	applyReaction (SpatialGrid[] concGrid, SpatialGrid[] reacGrid, SpatialGrid[] diffReacGrid, SpatialGrid biomassGrid)
	Compute reaction rate on each concerned solute grids Assumes same parameters for all the agents of a same guild. More...

void	fitAgentMassOnGrid (SpatialGrid aSpG)
	Add the mass of all the agents of the guild on a received grid. The stored value is a CONCENTRATION. More...

double[]	readConcentrationSeen (ActiveAgent anAgent, SoluteGrid[] concGrid)
	Return a double array with all concentration seen by an agent on the default solute grid. More...

void	writeReport (ResultFile bufferState, ResultFile bufferSum) throws Exception
	Write reaction information to the result file stream. More...

void	fitGuildOnGrid ()
	Build a grid with mass and mass-growth-rate of all agents of the guild. More...

double[]	getSoluteYield ()
	Return the solute yield. More...

int[]	getSoluteIndex ()
	Return the solute index. More...

double[]	getParticulateYield ()
	Return the particulate yield. More...

double[]	getKinetic ()
	Return the kinetic parameters used in this reaction. More...

LinkedList< ActiveAgent >	getGuild ()
	Return the guild of this pathway. More...

Additional Inherited Members
Public Attributes inherited from simulator.reaction.Reaction
String	reactionName

int	reactionIndex

int	_catalystIndex

int[]	_mySoluteIndex

boolean	autocatalytic

double[]	totalUptake

double	Dil

Protected Attributes inherited from simulator.reaction.Reaction
LinkedList< ActiveAgent >	_guild = new LinkedList<ActiveAgent>()

SoluteGrid[]	_soluteList

SoluteGrid	_reacGrid

SoluteGrid	_guildGrid

double	_specRate

double[]	_diffUptakeRate

double[]	_uptakeRate

double[]	_soluteYield

double[]	_kineticParam

double[]	_particleYield

String[]	_particleNameYield

Detailed Description

Modelled First-Order reactions. This class is deprecated.

Modelled First-Order reactions. This class is deprecated

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

Matrix simulator.reaction.FirstOrder.calcdMUdS	(	Matrix	S,
		double	biomass
	)

virtual

Calculate the rate of change of each uptake rate with respect to each solute. Returned as a matrix.

Calculate the rate of change of each uptake rate with respect to each solute. Returned as a matrix

Parameters

S	Temporary container for solute concentration
biomass	Total particle mass in the system which catalyses this reaction

Returns: Matrix containing rate of change of each uptake rate with respect to each solute

Implements simulator.reaction.Reaction.

Matrix simulator.reaction.FirstOrder.calcdMUdT	(	Matrix	S,
		double	biomass
	)

virtual

Calculate the rate of change of each uptake rate with respect to time.

Calculate the rate of change of each uptake rate with respect to time. dMUdT = catalyticBiomass*specificGrowthRate*soluteYield. Returned as a matrix

Parameters

S	Temporary container for solute concentration
biomass	Total particle mass in the system which catalyses this reaction

Returns: Matrix containing rate of change of each uptake rate with respect to time

Implements simulator.reaction.Reaction.

double [] simulator.reaction.FirstOrder.computeMarginalDiffMu ( double[] s )

virtual

Compute the marginal difference array.

Compute the marginal difference array. Don't forget to update marginalMu before calling this!

Parameters

s	Temporary container for solute concentration

Returns: Marginal diff array

Implements simulator.reaction.Reaction.

double simulator.reaction.FirstOrder.computeMassGrowthRate ( ActiveAgent anAgent )

virtual

return the marginal growth rate (i.e the specific growth rate times the mass of the particle who is mediating this reaction)

Parameters

anAgent

Returns

Implements simulator.reaction.Reaction.

double simulator.reaction.FirstOrder.computeSpecGrowthRate ( ActiveAgent anAgent )

virtual

Compute the specific growth rate.

Compute the specific growth rate

Parameters

anAgent Specific growth rate for this ActiveAgent

Returns: The specific growth rate

Implements simulator.reaction.Reaction.

void simulator.reaction.FirstOrder.computeSpecificGrowthRate ( ActiveAgent anAgent )

virtual

Return the specific reaction rate.

Return the specific reaction rate

Parameters

anAgent The agent

Deprecated:

Implements simulator.reaction.Reaction.

void simulator.reaction.FirstOrder.computeSpecificGrowthRate ( double[] s )

virtual

Parameters

s	Double array

Deprecated:

Implements simulator.reaction.Reaction.

void simulator.reaction.FirstOrder.computeSpecificGrowthRate	(	double[]	s,
		ActiveAgent	anAgent
	)

virtual

Compute specific growth rate in fonction to concentrations sent

Parameters

s	array of solute concentration
anAgent	Parameters used are those defined for THIS agent

Deprecated:

Implements simulator.reaction.Reaction.

double simulator.reaction.FirstOrder.computeSpecRate ( double[] s )

virtual

Compute the specific growth rate.

Compute the specific growth rate. Don't forget to update marginalMu before calling this!

Parameters

s	Temporary container for solute concentration

Returns: The specific growth rate

Implements simulator.reaction.Reaction.

void simulator.reaction.FirstOrder.computeUptakeRate	(	double[]	s,
		ActiveAgent	anAgent
	)

void simulator.reaction.FirstOrder.computeUptakeRate	(	double[]	s,
		double	mass
	)

Parameters

s	Array of concentration
mass	Concentration of reactant

void simulator.reaction.FirstOrder.computeUptakeRate	(	double[]	s,
		double	conc,
		double	h
	)

virtual

Parameters

s	Double array
conc	Concentration factor
h	Double

Deprecated:

Implements simulator.reaction.Reaction.

void simulator.reaction.FirstOrder.init	(	Simulator	aSim,
		XMLParser	aReactionRoot
	)

void simulator.reaction.FirstOrder.initFromAgent	(	ActiveAgent	anAgent,
		Simulator	aSim,
		XMLParser	aReactionRoot
	)

void simulator.reaction.FirstOrder.updateMarginalMu ( double[] s )

virtual

Update the Marginal Mu data matrix.

Update the Marginal Mu data matrix

Parameters

s	Temporary container for solute concentration

Implements simulator.reaction.Reaction.

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

/home/kieran/Dropbox/workspace/iDynoMiCS/src/simulator/reaction/FirstOrder.java

Public Member Functions

Additional Inherited Members

Detailed Description

Member Function Documentation