CStochMethod Class Reference

#include <CStochMethod.h>

Inheritance diagram for CStochMethod:

List of all members.

Public Member Functions
	CStochMethod (const CStochMethod &src, const CCopasiContainer *pParent=NULL)
	~CStochMethod ()
virtual bool	elevateChildren ()
virtual Status	step (const double &deltaT)
virtual void	start (const CState *initialState)
virtual bool	isValidProblem (const CCopasiProblem *pProblem)
Protected Member Functions
virtual void	initMethod (C_FLOAT64 start_time)=0
virtual C_FLOAT64	doSingleStep (C_FLOAT64 time, C_FLOAT64 endtime)=0
C_INT32	updatePropensities ()
C_INT32	calculateAmu (C_INT32 reaction_index)
C_INT32	generateReactionIndex ()
C_FLOAT64	generateReactionTime ()
C_FLOAT64	generateReactionTime (C_INT32 reaction_index)
C_INT32	updateSystemState (C_INT32 reaction_index)
void	setupDependencyGraphAndBalances ()
	CStochMethod (const CCopasiContainer *pParent=NULL)
Static Protected Member Functions
static bool	modelHasAssignments (const CModel *pModel)
Protected Attributes
std::vector< C_FLOAT64 >	mAmu
C_FLOAT64	mA0
std::vector< C_FLOAT64 >	mAmuOld
bool	mDoCorrection
bool	mHasAssignments
CRandom *	mpRandomGenerator
CModel *	mpModel
CDependencyGraph	mDG
std::vector< std::vector < CStochBalance > >	mLocalBalances
std::vector< std::vector < CStochBalance > >	mLocalSubstrates
std::vector< C_INT64 >	mNumbers
unsigned C_INT32	mNumReactions
unsigned C_INT32	mFirstMetabIndex
Friends
CTrajectoryMethod *	CTrajectoryMethod::createTrajectoryMethod (CCopasiMethod::SubType subType, CTrajectoryProblem *pProblem)

---

Constructor & Destructor Documentation

CStochMethod::CStochMethod

(

const CCopasiContainer *

pParent = NULL

)

[protected]

Default constructor.

Parameters:

const

CCopasiContainer * pParent (default: NULL)

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

Copy constructor.

Parameters:

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

CStochMethod::~CStochMethod

(

)

Destructor.

---

Member Function Documentation

C_INT32 CStochMethod::calculateAmu

(

C_INT32

reaction_index

)

[protected]

Calculate one of the propensities

Returns:

mFail

See also:

mFail

virtual C_FLOAT64 CStochMethod::doSingleStep	(	C_FLOAT64	time,
		C_FLOAT64	endtime
	)		[protected, pure virtual]

Do one iteration of the simulation

Returns:

Current simulation time or -1 if error.

Implemented in CStochNextReactionMethod.

bool CStochMethod::elevateChildren

(

)

[virtual]

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

Returns:

bool success

Reimplemented from CCopasiParameterGroup.

C_INT32 CStochMethod::generateReactionIndex

(

)

[protected]

Generate the index of a putative reaction.

Returns:

The reaction index

C_FLOAT64 CStochMethod::generateReactionTime

(

)

[protected]

Generate the putative time taken before any reaction takes place

Returns:

The time before the reaction

C_FLOAT64 CStochMethod::generateReactionTime

(

C_INT32

reaction_index

)

[protected]

Generate the putative time taken before a special reaction takes place

Returns:

The time before the reaction

virtual void CStochMethod::initMethod

(

C_FLOAT64

start_time

)

[protected, pure virtual]

Initialization.

bool CStochMethod::isValidProblem

(

const CCopasiProblem *

pProblem

)

[virtual]

Check if the method is suitable for this problem

Returns:

bool suitability of the method

Reimplemented from CTrajectoryMethod.

bool CStochMethod::modelHasAssignments

(

const CModel *

pModel

)

[static, protected]

tests if the model contains a global value with an assignment rule that is used in calculations

void CStochMethod::setupDependencyGraphAndBalances

(

)

[protected]

Set up the dependency graph and the balances

void CStochMethod::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 CStochMethod::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.

C_INT32 CStochMethod::updatePropensities

(

)

[protected]

Calculate the propensities for all reactions

Returns:

mFail

See also:

mFail

C_INT32 CStochMethod::updateSystemState

(

C_INT32

reaction_index

)

[protected]

Update the particle numbers according to which reaction ocurred

Returns:

mFail

See also:

mFail

---

Friends And Related Function Documentation

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

---

Member Data Documentation

C_FLOAT64 CStochMethod::mA0 [protected]

The sum of the propensities

std::vector<C_FLOAT64> CStochMethod::mAmu [protected]

The propensities for the reactions

std::vector<C_FLOAT64> CStochMethod::mAmuOld [protected]

The stored propensities for the reactions before the last update

CDependencyGraph CStochMethod::mDG [protected]

The graph of reactions and their dependent reactions. When a reaction is executed, the propensities for each of its dependents must be updated.

bool CStochMethod::mDoCorrection [protected]

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

unsigned C_INT32 CStochMethod::mFirstMetabIndex [protected]

index of first metab in a CState

bool CStochMethod::mHasAssignments [protected]

Indicates whether the model has global quantities with assignment rules. If it has, we will use a less efficient way to update the model state to handle this.

std::vector< std::vector <CStochBalance> > CStochMethod::mLocalBalances [protected]

The balances of the reactions as integers

std::vector< std::vector <CStochBalance> > CStochMethod::mLocalSubstrates [protected]

the substrates of each reaction with their multiplicities

std::vector<C_INT64> CStochMethod::mNumbers [protected]

The particle numbers

unsigned C_INT32 CStochMethod::mNumReactions [protected]

CModel* CStochMethod::mpModel [protected]

A pointer to the instance of CModel being used.

CRandom* CStochMethod::mpRandomGenerator [protected]

The random number generator

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

• copasi/trajectory/CStochMethod.h
• copasi/trajectory/CStochMethod.cpp