CTrajAdaptiveSA Class Reference

#include <CTrajAdaptiveSA.h>

Inheritance diagram for CTrajAdaptiveSA:

List of all members.

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

---

Constructor & Destructor Documentation

CTrajAdaptiveSA::CTrajAdaptiveSA

(

const CCopasiContainer *

pParent = NULL

)

[protected]

Default constructor.

Parameters:

const

CCopasiContainer * pParent (default: NULL)

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

Copy constructor.

Parameters:

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

CTrajAdaptiveSA::~CTrajAdaptiveSA

(

)

Destructor.

---

Member Function Documentation

const C_FLOAT64 & CTrajAdaptiveSA::calculateAmu

(

const size_t &

index

)

[protected]

Calculate the propensity of the indexed reaction

Parameters:

const

size_t & index

CTrajAdaptiveSA * CTrajAdaptiveSA::createTauLeapMethod

(

)

[static]

Chooses a stochastic method adequate for the problem

C_FLOAT64 CTrajAdaptiveSA::doSingleSSAStep	(	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

C_FLOAT64 CTrajAdaptiveSA::doSingleTauLeapStep	(	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 CTrajAdaptiveSA::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 CTrajAdaptiveSA::isValidProblem

(

const CCopasiProblem *

pProblem

)

[virtual]

Check if the method is suitable for this problem

Returns:

bool suitability of the method

Reimplemented from CTrajectoryMethod.

void CTrajAdaptiveSA::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 CTrajAdaptiveSA::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 CTrajAdaptiveSA::mA0 [protected]

Total propensity (sum over mAmu[i])

CVector< C_FLOAT64 > CTrajAdaptiveSA::mAmu [protected]

A vector of reaction propensities

bool CTrajAdaptiveSA::mDoCorrection [protected]

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

unsigned C_INT32 CTrajAdaptiveSA::mMaxSteps [protected]

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

bool CTrajAdaptiveSA::mMaxStepsReached [protected]

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

CState CTrajAdaptiveSA::mMethodState [protected]

The method internal state which contains particle rounded particle numbers.

unsigned C_INT32 CTrajAdaptiveSA::mNextReactionIndex [protected]

The index of the next reaction which fires

C_FLOAT64 CTrajAdaptiveSA::mNextReactionTime [protected]

The time the next reaction fires

size_t CTrajAdaptiveSA::mNumReactions [protected]

The particle and reaction numbers

size_t CTrajAdaptiveSA::mNumReactionSpecies [protected]

Number of variable metabolites.

size_t CTrajAdaptiveSA::mNumSpecies [protected]

CVector< const C_FLOAT64 * > CTrajAdaptiveSA::mPartitionedAmu [protected]

The ordered propensity function

CVector< const CReactionDependencies * > CTrajAdaptiveSA::mPartitionedDependencies [protected]

The Ordered reaction

CModel* CTrajAdaptiveSA::mpModel [protected]

A pointer to the instance of CModel being used.

CRandom* CTrajAdaptiveSA::mpRandomGenerator [protected]

The random number generator

std::vector< CReactionDependencies > CTrajAdaptiveSA::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/CTrajAdaptiveSA.h
• copasi/trajectory/CTrajAdaptiveSA.cpp