CStochDirectMethod Class Reference

#include <CStochDirectMethod.h>

Inheritance diagram for CStochDirectMethod:

List of all members.

Classes
class	CReactionDependencies
Public Member Functions
	CStochDirectMethod (const CStochDirectMethod &src, const CCopasiContainer *pParent=NULL)
	~CStochDirectMethod ()
virtual bool	elevateChildren ()
virtual Status	step (const double &deltaT)
virtual void	start (const CState *initialState)
virtual bool	isValidProblem (const CCopasiProblem *pProblem)
Protected Member Functions
	CStochDirectMethod (const CCopasiContainer *pParent=NULL)
void	calculateAmu (const C_INT32 &index)
C_FLOAT64	doSingleStep (const C_FLOAT64 &curTime, const C_FLOAT64 &endTime)
Protected Attributes
CRandom *	mpRandomGenerator
CModel *	mpModel
size_t	mNumReactions
unsigned C_INT32	mMaxSteps
C_FLOAT64	mNextReactionTime
unsigned C_INT32	mNextReactionIndex
bool	mDoCorrection
CVector< C_FLOAT64 >	mAmu
C_FLOAT64	mA0
CState	mMethodState
std::vector < CReactionDependencies >	mReactionDependencies
bool	mMaxStepsReached
Friends
CTrajectoryMethod *	CTrajectoryMethod::createTrajectoryMethod (CCopasiMethod::SubType subType, CTrajectoryProblem *pProblem)

---

Constructor & Destructor Documentation

CStochDirectMethod::CStochDirectMethod

(

const CCopasiContainer *

pParent = NULL

)

[protected]

Default constructor.

Parameters:

const

CCopasiContainer * pParent (default: NULL)

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

Copy constructor.

Parameters:

const	CStochDirectMethod & src,
const	CCopasiContainer * pParent (Default: NULL)

CStochDirectMethod::~CStochDirectMethod

(

)

Destructor.

---

Member Function Documentation

void CStochDirectMethod::calculateAmu

(

const C_INT32 &

index

)

[protected]

Calculate the propensity of the indexed reaction

Parameters:

const

C_INT32 & index

C_FLOAT64 CStochDirectMethod::doSingleStep	(	const C_FLOAT64 &	curTime,
		const C_FLOAT64 &	endTime
	)		[protected]

Fire the next reaction if it fire before the endTime

Parameters:

const	C_FLOAT64 & curTime
const	C_FLOAT64 & endTime

Returns:

C_FLOAT64 timeAfterStep

bool CStochDirectMethod::elevateChildren

(

)

[virtual]

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

Returns:

bool success

Reimplemented from CCopasiParameterGroup.

bool CStochDirectMethod::isValidProblem

(

const CCopasiProblem *

pProblem

)

[virtual]

Check if the method is suitable for this problem

Returns:

bool suitability of the method

Reimplemented from CTrajectoryMethod.

void CStochDirectMethod::start

(

const CState *

initialState

)

[virtual]

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

Parameters:

const CState *

initialState

Reimplemented from CTrajectoryMethod.

CTrajectoryMethod::Status CStochDirectMethod::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 timestep taken.

Parameters:

const double &

deltaT

Returns:

Status status

Reimplemented from CTrajectoryMethod.

---

Friends And Related Function Documentation

CTrajectoryMethod* CTrajectoryMethod::createTrajectoryMethod	(	CCopasiMethod::SubType	subType,
		CTrajectoryProblem *	pProblem
	)		[friend]

---

Member Data Documentation

C_FLOAT64 CStochDirectMethod::mA0 [protected]

Total propensity (sum over mAmu[i])

CVector< C_FLOAT64 > CStochDirectMethod::mAmu [protected]

A vector of reaction propensities

bool CStochDirectMethod::mDoCorrection [protected]

A boolean flag indicating whether correction for higher order reactions need to be applied

unsigned C_INT32 CStochDirectMethod::mMaxSteps [protected]

max number of single stochastic steps to do in one step()

bool CStochDirectMethod::mMaxStepsReached [protected]

A boolean flag indicating whether the maximum steps have been reached. This is used to avoid multiple messages.

CState CStochDirectMethod::mMethodState [protected]

The method internal state which contains particle rounded particle numbers.

unsigned C_INT32 CStochDirectMethod::mNextReactionIndex [protected]

The index of the next reaction which fires

C_FLOAT64 CStochDirectMethod::mNextReactionTime [protected]

The time the next reaction fires

size_t CStochDirectMethod::mNumReactions [protected]

The particle and reaction numbers

CModel* CStochDirectMethod::mpModel [protected]

A pointer to the instance of CModel being used.

CRandom* CStochDirectMethod::mpRandomGenerator [protected]

The random number generator

std::vector< CReactionDependencies > CStochDirectMethod::mReactionDependencies [protected]

A vector containing dependency information to minimize the required updates.

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

• copasi/trajectory/CStochDirectMethod.h
• copasi/trajectory/CStochDirectMethod.cpp