#include <CTrajectoryMethodDsaLsodar.h>

Inheritance diagram for CTrajectoryMethodDsaLsodar:

Classes
class	CPartition
class	CReactionDependencies
Public Member Functions
	CTrajectoryMethodDsaLsodar (const CTrajectoryMethodDsaLsodar &src, const CCopasiContainer *pParent=NULL)
	~CTrajectoryMethodDsaLsodar ()
virtual bool	elevateChildren ()
virtual void	stateChanged ()
virtual Status	step (const double &deltaT)
virtual void	start (const CState *initialState)
virtual void	evalF (const C_FLOAT64 t, const C_FLOAT64 y, C_FLOAT64 *ydot)
virtual void	evalR (const C_FLOAT64 t, const C_FLOAT64 y, const C_INT nr, C_FLOAT64 r)
virtual bool	isValidProblem (const CCopasiProblem *pProblem)
void	cleanup ()
virtual C_FLOAT64	doSingleStep (C_FLOAT64 currentTime, C_FLOAT64 endTime)
void	integrateDeterministicPart (const C_FLOAT64 &deltaT)
void	fireReaction (const size_t &index)
void	calculateAmu (const size_t &index)
void	calculatePropensities ()
Protected Member Functions
	CTrajectoryMethodDsaLsodar (const CCopasiMethod::SubType &subType=DsaLsodar, const CCopasiContainer *pParent=NULL)
Protected Attributes
unsigned C_INT32 *	mpMaxSteps
C_FLOAT64 *	mpLowerLimit
C_FLOAT64 *	mpUpperLimit
unsigned C_INT32 *	mpPartitioningInterval
C_FLOAT64 *	mpPartitioningSteps
CRandom *	mpRandomGenerator
unsigned C_INT32	mFirstReactionSpeciesIndex
bool	mMaxStepsReached
unsigned C_INT32	mStepsAfterPartitionSystem
size_t	mNumReactions
C_FLOAT64	mNextReactionTime
unsigned C_INT32	mNextReactionIndex
bool	mDoCorrection
CVector< C_FLOAT64 >	mAmu
C_FLOAT64	mA0
std::vector < CReactionDependencies >	mReactionDependencies
CPartition	mPartition
Friends
CTrajectoryMethod *	CTrajectoryMethod::createTrajectoryMethod (CCopasiMethod::SubType subType, CTrajectoryProblem *pProblem)

Constructor & Destructor Documentation

CTrajectoryMethodDsaLsodar::CTrajectoryMethodDsaLsodar	(	const CCopasiMethod::SubType &	subType = `DsaLsodar`,
		const CCopasiContainer *	pParent = `NULL`
	)		`[protected]`

Default constructor.

Parameters:

const	CCopasiMethod::SubType & subType (default: DsaLsodar)
const	CCopasiContainer * pParent (default: NULL)

Default constructor.

CTrajectoryMethodDsaLsodar::CTrajectoryMethodDsaLsodar	(	const CTrajectoryMethodDsaLsodar &	src,
		const CCopasiContainer *	pParent = `NULL`
	)

Copy constructor

Parameters:

const	CTrajectoryMethodDsaLsodar & src
const	CCopasiContainer * pParent (default: NULL)

CTrajectoryMethodDsaLsodar::~CTrajectoryMethodDsaLsodar ( )

Destructor.

Member Function Documentation

void CTrajectoryMethodDsaLsodar::calculateAmu ( const size_t & index )

Calculates an amu value for a given reaction.

Parameters:

const size_t & index

void CTrajectoryMethodDsaLsodar::calculatePropensities ( )

Calculate the propensities of all stochastic reactions

void CTrajectoryMethodDsaLsodar::cleanup ( )

Cleans up memory, etc.

C_FLOAT64 CTrajectoryMethodDsaLsodar::doSingleStep	(	C_FLOAT64	currentTime,
		C_FLOAT64	endTime
	)		`[virtual]`

Simulates the system over the next interval of time. The current time and the end time of the current step() are given as arguments.

Parameters:

currentTime	A C_FLOAT64 specifying the current time
endTime	A C_FLOAT64 specifying the end time of the step()

Returns:: A C_FLOAT giving the new time

bool CTrajectoryMethodDsaLsodar::elevateChildren ( ) [virtual]

This methods must be called to elevate subgroups to derived objects. The default implementation does nothing.

Returns:: bool success

Reimplemented from CLsodaMethod.

void CTrajectoryMethodDsaLsodar::evalF	(	const C_FLOAT64 *	t,
		const C_FLOAT64 *	y,
		C_FLOAT64 *	ydot
	)		`[virtual]`

This evaluates the derivatives

Reimplemented from CLsodaMethod.

void CTrajectoryMethodDsaLsodar::evalR	(	const C_FLOAT64 *	t,
		const C_FLOAT64 *	y,
		const C_INT *	nr,
		C_FLOAT64 *	r
	)		`[virtual]`

This evaluates the roots

Reimplemented from CLsodaMethod.

void CTrajectoryMethodDsaLsodar::fireReaction ( const size_t & index )

Executes the specified reaction in the system once.

Parameters:

const size_t & index

Executes the specified reaction in the system once.

Parameters:

index	A C_INT32 specifying the index of the reaction, which will be fired.
time	The current time

void CTrajectoryMethodDsaLsodar::integrateDeterministicPart ( const C_FLOAT64 & deltaT )

Integrates the deterministic reactions of the system over the specified time interval.

Parameters:

const C_FLOAT64 & deltaT.

bool CTrajectoryMethodDsaLsodar::isValidProblem ( const CCopasiProblem * pProblem ) [virtual]

Check if the method is suitable for this problem

Returns:: bool suitability of the method

Reimplemented from CTrajectoryMethod.

void CTrajectoryMethodDsaLsodar::start ( const CState * initialState ) [virtual]

This instructs the method to prepare for integration starting with the initialState given.

Parameters:

const CState * initialState

Reimplemented from CLsodaMethod.

void CTrajectoryMethodDsaLsodar::stateChanged ( ) [virtual]

Inform the trajectory method that the state has changed outside its control

Reimplemented from CLsodaMethod.

CTrajectoryMethod::Status CTrajectoryMethodDsaLsodar::step ( const double & deltaT ) [virtual]

This instructs the method to calculate a time step of deltaT starting with the current state, i.e., the result of the previous step. The new state (after deltaT) is expected in the current state. The return value is the actual time step taken.

Parameters:

const double & deltaT