CTauLeapMethod Class Reference

#include <CTauLeapMethod.h>

Inheritance diagram for CTauLeapMethod:

List of all members.

Classes
class	CReactionDependencies
Public Member Functions
	CTauLeapMethod (const CTauLeapMethod &src, const CCopasiContainer *pParent=NULL)
	~CTauLeapMethod ()
virtual bool	elevateChildren ()
virtual Status	step (const double &deltaT)
virtual void	start (const CState *initialState)
virtual bool	isValidProblem (const CCopasiProblem *pProblem)
Protected Member Functions
	CTauLeapMethod (const CCopasiContainer *pParent=NULL)
void	cleanup ()
C_FLOAT64	doSingleStep (C_FLOAT64 ds)
void	updatePropensities ()
const C_FLOAT64 &	calculateAmu (const size_t &index)
bool	updateSystem ()
Protected Attributes
CModel *	mpModel
CState	mMethodState
unsigned C_INT32	mNumReactions
std::vector < CReactionDependencies >	mReactionDependencies
unsigned C_INT32	mNumReactionSpecies
CVector< C_FLOAT64 >	mAmu
C_FLOAT64	mA0
CVector< C_FLOAT64 >	mK
CVector< C_FLOAT64 >	mAvgDX
CVector< C_FLOAT64 >	mSigDX
C_FLOAT64	mEpsilon
unsigned C_INT32	mMaxSteps
bool	mUseRandomSeed
unsigned C_INT32	mRandomSeed
CRandom *	mpRandomGenerator
bool	mDoCorrection
size_t	mFirstReactionSpeciesIndex
Friends
CTrajectoryMethod *	CTrajectoryMethod::createTrajectoryMethod (CCopasiMethod::SubType subType, CTrajectoryProblem *pProblem)

---

Constructor & Destructor Documentation

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

Copy constructor

Parameters:

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

CTauLeapMethod::~CTauLeapMethod

(

)

Destructor.

CTauLeapMethod::CTauLeapMethod

(

const CCopasiContainer *

pParent = NULL

)

[protected]

Default constructor.

Parameters:

const

CCopasiContainer * pParent (default: NULL)

Default constructor.

---

Member Function Documentation

const C_FLOAT64 & CTauLeapMethod::calculateAmu

(

const size_t &

index

)

[protected]

Calculate one of the propensities

Parameters:

const

size_t & index

Returns:

const C_FLOAT64 & amu

void CTauLeapMethod::cleanup

(

)

[protected]

Cleans up memory, etc.

Initializes the solver and sets the model to be used.

Parameters:

model

A reference to an instance of a CModel Cleans up memory, etc.

C_FLOAT64 CTauLeapMethod::doSingleStep

(

C_FLOAT64

ds

)

[protected]

Simulates the system over the next interval of time. The timestep is given as argument.

Parameters:

ds	A C_FLOAT64 specifying the timestep

bool CTauLeapMethod::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 CTauLeapMethod::isValidProblem

(

const CCopasiProblem *

pProblem

)

[virtual]

Check if the method is suitable for this problem

Returns:

bool suitability of the method

Reimplemented from CTrajectoryMethod.

void CTauLeapMethod::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 CTauLeapMethod::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.

void CTauLeapMethod::updatePropensities

(

)

[protected]

Calculate the propensities for all reactions

bool CTauLeapMethod::updateSystem

(

)

[protected]

Updates the system according to the probabilistic number of firings mK[i] of each reaction i

---

Friends And Related Function Documentation

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

---

Member Data Documentation

C_FLOAT64 CTauLeapMethod::mA0 [protected]

Total propensity (sum over mAmu[i])

CVector< C_FLOAT64 > CTauLeapMethod::mAmu [protected]

A vector of reaction propensities

CVector< C_FLOAT64> CTauLeapMethod::mAvgDX [protected]

For tau-selection method

bool CTauLeapMethod::mDoCorrection [protected]

indicates if the correction N^2 -> N*(N-1) should be performed

C_FLOAT64 CTauLeapMethod::mEpsilon [protected]

The tolerance ratio x(t+t')< eps*x(t)

size_t CTauLeapMethod::mFirstReactionSpeciesIndex [protected]

index of first species in a CState

CVector< C_FLOAT64 > CTauLeapMethod::mK [protected]

The k-values of the reactions, that is the probabilistic number of firings within one leap.

unsigned C_INT32 CTauLeapMethod::mMaxSteps [protected]

The maximum number of tau leap steps allowed for an integrations step

CState CTauLeapMethod::mMethodState [protected]

The method internal state which contains particle rounded particle numbers.

unsigned C_INT32 CTauLeapMethod::mNumReactions [protected]

Number of reactions.

unsigned C_INT32 CTauLeapMethod::mNumReactionSpecies [protected]

Number of variable metabolites.

CModel* CTauLeapMethod::mpModel [protected]

Pointer to the model.

CRandom* CTauLeapMethod::mpRandomGenerator [protected]

The random number generator.

unsigned C_INT32 CTauLeapMethod::mRandomSeed [protected]

The random seed to use.

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

A vector containing dependency information to minimize the required updates.

CVector< C_FLOAT64> CTauLeapMethod::mSigDX [protected]

For tau-selection method

bool CTauLeapMethod::mUseRandomSeed [protected]

Specifies if the mRandomSeed should be used. otherwise a randomly chosen seed is used.

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

• copasi/trajectory/CTauLeapMethod.h
• copasi/trajectory/CTauLeapMethod.cpp