#include <CCSPMethod.h>

Inheritance diagram for CCSPMethod:

Public Member Functions
	CCSPMethod (const CCSPMethod &src, const CCopasiContainer *pParent=NULL)
	~CCSPMethod ()
virtual void	step (const double &deltaT)
virtual void	start (const CState *initialState)
void	initializeParameter ()
void	smmult (CMatrix< C_FLOAT64 > &A, CMatrix< C_FLOAT64 > &B, CMatrix< C_FLOAT64 > &C, C_INT &n1, C_INT &n2, C_INT &n3)
void	smsubst (CMatrix< C_FLOAT64 > &A, CMatrix< C_FLOAT64 > &B, CMatrix< C_FLOAT64 > &C, C_INT &n1, C_INT &n2)
void	smadd (CMatrix< C_FLOAT64 > &A, CMatrix< C_FLOAT64 > &B, CMatrix< C_FLOAT64 > &C, C_INT &n1, C_INT &n2)
void	smnorm (C_INT &n, CMatrix< C_FLOAT64 > &A, CMatrix< C_FLOAT64 > &B, C_INT &n1)
void	perturbateA (C_INT &n, CMatrix< C_FLOAT64 > &A, C_FLOAT64 delta)
void	sminverse (C_INT &n, CMatrix< C_FLOAT64 > &A, CMatrix< C_FLOAT64 > &B)
void	modesAmplitude (C_INT &N, C_INT &M, CVector< C_FLOAT64 > &g, CMatrix< C_FLOAT64 > &B, CMatrix< C_FLOAT64 > &F)
void	CSPradicalPointer (C_INT &N, C_INT &M, CMatrix< C_FLOAT64 > &A, CMatrix< C_FLOAT64 > &B)
void	CSPParticipationIndex (C_INT &N, C_FLOAT64 &tauM1, CMatrix< C_FLOAT64 > &B0)
void	CSPImportanceIndex (C_INT &N, C_FLOAT64 &tauM1, CMatrix< C_FLOAT64 > &Q)
void	yCorrection (C_INT &N, C_INT &M, CVector< C_FLOAT64 > &y, CMatrix< C_FLOAT64 > &TAUM, CMatrix< C_FLOAT64 > &F, CMatrix< C_FLOAT64 > &A)
void	basisRefinement (C_INT &N, C_INT &M, CMatrix< C_FLOAT64 > &ALA, CMatrix< C_FLOAT64 > &TAU, CMatrix< C_FLOAT64 > &A, CMatrix< C_FLOAT64 > &B, CMatrix< C_FLOAT64 > &A0, CMatrix< C_FLOAT64 > &B0)
void	calculateJacobianX (C_INT &n, CVector< C_FLOAT64 > &y, CMatrix< C_FLOAT64 > &J)
void	findTimeScaleSeparation (C_INT &n, C_INT &k, CVector< C_FLOAT64 > &tsc, C_INT &info)
void	findCandidatesNumber (C_INT &n, C_INT &k, CVector< C_FLOAT64 > &tsc, C_INT &info)
bool	modesAreExhausted (C_INT &N, C_INT &M, C_FLOAT64 &tauM, C_FLOAT64 &tauM1, CVector< C_FLOAT64 > &g, CMatrix< C_FLOAT64 > &A, CMatrix< C_FLOAT64 > &B, CMatrix< C_FLOAT64 > &F)
C_INT	isBlockDiagonal (C_INT &N, C_INT &M, CMatrix< C_FLOAT64 > &ALA, C_FLOAT64 small)
void	cspstep (const double &deltaT, C_INT &n, C_INT &m, CMatrix< C_FLOAT64 > &A, CMatrix< C_FLOAT64 > &B)
void	emptyOutputData (C_INT &N, C_INT &M, C_INT &R)
void	CSPOutput (C_INT &N, C_INT &M, C_INT &R)
const CArrayAnnotation *	getAmplitudeAnn () const
const CArrayAnnotation *	getRadicalPointerAnn () const
const CArrayAnnotation *	getFastReactionPointerAnn () const
const CArrayAnnotation *	getFastReactionPointerNormedAnn () const
const CArrayAnnotation *	getParticipationIndexAnn () const
const CArrayAnnotation *	getParticipationIndexNormedRowAnn () const
const CArrayAnnotation *	getParticipationIndexNormedColumnAnn () const
const CArrayAnnotation *	getImportanceIndexAnn () const
const CArrayAnnotation *	getImportanceIndexNormedRowAnn () const
void	setVectors (int fast)
void	emptyVectors ()
void	createAnnotationsM ()
bool	setAnnotationM (int step)
void	printResult (std::ostream *ostream) const
Public Attributes
CMatrix< C_FLOAT64 >	mI
C_FLOAT64	mEps
C_FLOAT64	mTsc
C_FLOAT64	mRerror
C_FLOAT64	mAerror
C_INT	mIter
CVector< C_FLOAT64 >	mG
CVector< C_FLOAT64 >	mYerror
CMatrix< C_FLOAT64 >	mB
C_INT	mTStep
C_INT	mCSPbasis
C_INT	mSetVectors
CVector< C_FLOAT64 >	mAmplitude
CMatrix< C_FLOAT64 >	mRadicalPointer
CMatrix< C_FLOAT64 >	mFastReactionPointer
CMatrix< C_FLOAT64 >	mFastReactionPointerNormed
CMatrix< C_FLOAT64 >	mParticipationIndex
CMatrix< C_FLOAT64 >	mParticipationIndexNormedRow
CMatrix< C_FLOAT64 >	mParticipationIndexNormedColumn
CMatrix< C_FLOAT64 >	mImportanceIndex
CMatrix< C_FLOAT64 >	mImportanceIndexNormedRow
std::vector< CMatrix< C_FLOAT64 > >	mVec_mAmplitude
std::vector< CMatrix< C_FLOAT64 > >	mVec_mRadicalPointer
std::vector< CMatrix< C_FLOAT64 > >	mVec_mFastReactionPointer
std::vector< CMatrix< C_FLOAT64 > >	mVec_mFastReactionPointerNormed
std::vector< CMatrix< C_FLOAT64 > >	mVec_mParticipationIndex
std::vector< CMatrix< C_FLOAT64 > >	mVec_mParticipationIndexNormedRow
std::vector< CMatrix< C_FLOAT64 > >	mVec_mParticipationIndexNormedColumn
std::vector< CMatrix< C_FLOAT64 > >	mVec_mImportanceIndex
std::vector< CMatrix< C_FLOAT64 > >	mVec_mImportanceIndexNormedRow
CArrayAnnotation *	pAmplitudeAnn
CArrayAnnotation *	pRadicalPointerAnn
CArrayAnnotation *	pFastReactionPointerAnn
CArrayAnnotation *	pFastReactionPointerNormedAnn
CArrayAnnotation *	pParticipationIndexAnn
CArrayAnnotation *	pParticipationIndexNormedRowAnn
CArrayAnnotation *	pParticipationIndexNormedColumnAnn
CArrayAnnotation *	pImportanceIndexAnn
CArrayAnnotation *	pImportanceIndexNormedRowAnn
CArrayAnnotation *	pTmp1
CArrayAnnotation *	pTmp2
CArrayAnnotation *	pTmp3
CArrayAnnotation *	pTmp3Normed
CArrayAnnotation *	pTmp4
CArrayAnnotation *	pTmp4NormedColumn
CArrayAnnotation *	pTmp4NormedRow
CArrayAnnotation *	pTmp5
CArrayAnnotation *	pTmp5NormedRow
CMatrix< C_FLOAT64 >	mAmplitudeTab
CMatrix< C_FLOAT64 >	mRadicalPointerTab
CMatrix< C_FLOAT64 >	mFastReactionPointerTab
CMatrix< C_FLOAT64 >	mFastReactionPointerNormedTab
CMatrix< C_FLOAT64 >	mParticipationIndexTab
CMatrix< C_FLOAT64 >	mParticipationIndexNormedRowTab
CMatrix< C_FLOAT64 >	mParticipationIndexNormedColumnTab
CMatrix< C_FLOAT64 >	mImportanceIndexTab
CMatrix< C_FLOAT64 >	mImportanceIndexNormedRowTab
Friends
CTSSAMethod *	CTSSAMethod::createTSSAMethod (CCopasiMethod::SubType subType, CTSSAProblem *pProblem)

Constructor & Destructor Documentation

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

Copy constructor.

Parameters:

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

CCSPMethod::~CCSPMethod ( )

Destructor.

Member Function Documentation

void CCSPMethod::basisRefinement	(	C_INT &	N,
		C_INT &	M,
		CMatrix< C_FLOAT64 > &	ALA,
		CMatrix< C_FLOAT64 > &	TAU,
		CMatrix< C_FLOAT64 > &	A,
		CMatrix< C_FLOAT64 > &	B,
		CMatrix< C_FLOAT64 > &	A0,
		CMatrix< C_FLOAT64 > &	B0
	)

Refinement Procedre : Lamm, Combustion Science and Technoligy, 1993.

void CCSPMethod::calculateJacobianX	(	C_INT &	n,
		CVector< C_FLOAT64 > &	y,
		CMatrix< C_FLOAT64 > &	J
	)

evaluate Jacobian for the current y

void CCSPMethod::createAnnotationsM ( )

create the CArraAnnotations for every ILDM-tab in the CQTSSAResultSubWidget input for each CArraAnnotations is a seperate CMatrix

Create the CArraAnnotations for every ILDM-tab in the CQTSSAResultSubWidget. Input for each CArraAnnotations is a separate CMatrix.

Reimplemented from CTSSAMethod.

void CCSPMethod::CSPImportanceIndex	(	C_INT &	N,
		C_FLOAT64 &	tauM1,
		CMatrix< C_FLOAT64 > &	Q
	)

compute CSP Importance Index

compute CSP Importance Index : a measure of relative importance of the contribution of r-th elementary reaction to the current reaction rate of the i-th species

void CCSPMethod::CSPOutput	(	C_INT &	N,
		C_INT &	M,
		C_INT &	R
	)

CSP output

void CCSPMethod::CSPParticipationIndex	(	C_INT &	N,
		C_FLOAT64 &	tauM1,
		CMatrix< C_FLOAT64 > &	B0
	)

compute CSP Participation Index

compute CSP Participation Index: a measure of participation of the r-th elementary reaction to the balancing act of the i-th mode It is assumed that forward and reverse reactions are counted as distinct

void CCSPMethod::CSPradicalPointer	(	C_INT &	N,
		C_INT &	M,
		CMatrix< C_FLOAT64 > &	A,
		CMatrix< C_FLOAT64 > &	B
	)

compute CSP radical pointer and fast reaction pointers

some comments on the Qm matrix: Qm(i,i) , i = 0,1,...,N, is a measure of projection of i-th unit vector in the m-th mode, whenever Qm(i,i) is not a small number, species m is said to be a CSP radical

Pmr is a measure of projection of r-th stoichiometric vector in the m-th mode, whenever Pmr is not a small number, the r-th reaction is said to be a fast reaction

void CCSPMethod::cspstep	(	const double &	deltaT,
		C_INT &	n,
		C_INT &	m,
		CMatrix< C_FLOAT64 > &	A,
		CMatrix< C_FLOAT64 > &	B
	)

Start procedure of the CSP algorithm. S.H. Lam and D.A. Gaussis, International Journal of Chemical Kinetics, 26, pp. 461-486, 1994

compute CSP Participation Index: a measure of participation of the r-th elementary reaction to the balancing act of the i-th mode It is assumed that forward and reverse reactions are counted as distinct

compute CSP Importance Index : a measure of relative importance of the contribution of r-th elementary reaction to the current reaction rate of the i-th species

void CCSPMethod::emptyOutputData	(	C_INT &	N,
		C_INT &	M,
		C_INT &	R
	)

CSP output : empty

void CCSPMethod::emptyVectors ( )

empty every vector to be able to fill them with new values for a new calculation also nullify the step counter

Empty every vector to be able to fill them with new values for a new calculation. Also nullify the step counter.

Reimplemented from CTSSAMethod.

void CCSPMethod::findCandidatesNumber	(	C_INT &	n,
		C_INT &	k,
		CVector< C_FLOAT64 > &	tsc,
		C_INT &	info
	)

find the number of candidates to fast according to the time-scale separation ratio

void CCSPMethod::findTimeScaleSeparation	(	C_INT &	n,
		C_INT &	k,
		CVector< C_FLOAT64 > &	tsc,
		C_INT &	info
	)

find the new number of fast according to the time-scale separation ratio

const CArrayAnnotation* CCSPMethod::getAmplitudeAnn ( ) const [inline]

return CArrayAnnotation for visualization in ILDM-tab in the CQTSSAResultSubWidget

const CArrayAnnotation* CCSPMethod::getFastReactionPointerAnn ( ) const [inline]

const CArrayAnnotation* CCSPMethod::getFastReactionPointerNormedAnn ( ) const [inline]

const CArrayAnnotation* CCSPMethod::getImportanceIndexAnn ( ) const [inline]

const CArrayAnnotation* CCSPMethod::getImportanceIndexNormedRowAnn ( ) const [inline]

const CArrayAnnotation* CCSPMethod::getParticipationIndexAnn ( ) const [inline]

const CArrayAnnotation* CCSPMethod::getParticipationIndexNormedColumnAnn ( ) const [inline]

const CArrayAnnotation* CCSPMethod::getParticipationIndexNormedRowAnn ( ) const [inline]

const CArrayAnnotation* CCSPMethod::getRadicalPointerAnn ( ) const [inline]

void CCSPMethod::initializeParameter ( ) [virtual]

Intialize the method parameter

Reimplemented from CTSSAMethod.

C_INT CCSPMethod::isBlockDiagonal	(	C_INT &	N,
		C_INT &	M,
		CMatrix< C_FLOAT64 > &	ALA,
		C_FLOAT64	small
	)

compute the norm C of the off-diagonal blocks

void CCSPMethod::modesAmplitude	(	C_INT &	N,
		C_INT &	M,
		CVector< C_FLOAT64 > &	g,
		CMatrix< C_FLOAT64 > &	B,
		CMatrix< C_FLOAT64 > &	F
	)

compute amplitudes of fast and slow modes

bool CCSPMethod::modesAreExhausted	(	C_INT &	N,
		C_INT &	M,
		C_FLOAT64 &	tauM,
		C_FLOAT64 &	tauM1,
		CVector< C_FLOAT64 > &	g,
		CMatrix< C_FLOAT64 > &	A,
		CMatrix< C_FLOAT64 > &	B,
		CMatrix< C_FLOAT64 > &	F
	)

check : whether each of the analysed M modes is exhausted

void CCSPMethod::perturbateA	(	C_INT &	n,
		CMatrix< C_FLOAT64 > &	A,
		C_FLOAT64	delta
	)

TEST: perturbate basis vectors A

void CCSPMethod::printResult ( std::ostream * ostream ) const [virtual]

print of the standart report sequence for ILDM Method

Parameters:

std::ostream * ostream

Reimplemented from CCopasiMethod.

bool CCSPMethod::setAnnotationM ( int step ) [virtual]

set the every CArrayAnnotation for the requested step set the desription of CArayAnnotation for both dimensions

Set the every CArrayAnnotation for the requested step. Set also the description of CArayAnnotation for both dimensions:

dimension description could consists of some std::strings some strings contain the Time Scale values for requested step
dimension description could consists of arrays of CommonNames

Implements CTSSAMethod.

void CCSPMethod::setVectors ( int fast )

upgrade all vectors with values from actually calculalion for current step

upgrade all vectors with values from actually calculation for current step

Reimplemented from CTSSAMethod.

void CCSPMethod::smadd	(	CMatrix< C_FLOAT64 > &	A,
		CMatrix< C_FLOAT64 > &	B,
		CMatrix< C_FLOAT64 > &	C,
		C_INT &	n1,
		C_INT &	n2
	)

Addition of submatrix

void CCSPMethod::sminverse	(	C_INT &	n,
		CMatrix< C_FLOAT64 > &	A,
		CMatrix< C_FLOAT64 > &	B
	)

Inverse submatrix

void CCSPMethod::smmult	(	CMatrix< C_FLOAT64 > &	A,
		CMatrix< C_FLOAT64 > &	B,
		CMatrix< C_FLOAT64 > &	C,
		C_INT &	n1,
		C_INT &	n2,
		C_INT &	n3
	)

CSP related staff Multiplication of submatrix

void CCSPMethod::smnorm	(	C_INT &	n,
		CMatrix< C_FLOAT64 > &	A,
		CMatrix< C_FLOAT64 > &	B,
		C_INT &	n1
	)

Normalize submatrix

void CCSPMethod::smsubst	(	CMatrix< C_FLOAT64 > &	A,
		CMatrix< C_FLOAT64 > &	B,
		CMatrix< C_FLOAT64 > &	C,
		C_INT &	n1,
		C_INT &	n2
	)

Substruction of submatrix

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

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

Parameters:

const CState * initialState

Reimplemented from CTSSAMethod.

void CCSPMethod::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

Reimplemented from CTSSAMethod.