#include <CILDMModifiedMethod.h>

Inheritance diagram for CILDMModifiedMethod:

Collaboration diagram for CILDMModifiedMethod:

Public Member Functions
	CILDMModifiedMethod (const CILDMModifiedMethod &src, const CCopasiContainer *pParent=NULL)

void	createAnnotationsM ()

void	deuflhard_metab (C_INT &slow, C_INT &info)

void	emptyVectors ()

void	evalsort (C_FLOAT64 reval, C_INT index, const C_INT &dim_x)

const CArrayAnnotation *	getVfastSpacePrintAnn () const

const CArrayAnnotation *	getVslowMetabPrintAnn () const

const CArrayAnnotation *	getVslowPrintAnn () const

const CArrayAnnotation *	getVslowSpacePrintAnn () const

virtual void	initializeParameter ()

void	newton_for_timestep (C_INT metabolite_number, C_FLOAT64 &y_consistent, C_INT &info)

void	newton_new (C_INT *index_metab, C_INT &slow, C_INT &info)

void	printResult (std::ostream *ostream) const

virtual bool	setAnnotationM (size_t step)

void	setVectors (int slowMode)

virtual void	start (const CState *initialState)

virtual void	step (const double &deltaT)

	~CILDMModifiedMethod ()

Public Member Functions inherited from CTSSAMethod
void	createAnnotationsM ()

	CTSSAMethod (const CTSSAMethod &src, const CCopasiContainer *pParent=NULL)

void	emptyVectors ()

const int &	getCurrentStep () const

const CArrayAnnotation *	getTable (std::string name)

const std::vector< std::string >	getTableName () const

CVector< C_FLOAT64 >	getVec_TimeScale (int step)

virtual bool	isValidProblem (const CCopasiProblem *pProblem)

virtual void	predifineAnnotation ()

C_FLOAT64	returnCurrentTime (int step)

void	setCurrentState (CState *currentState)

void	setModel (CModel *model)

void	setProblem (CTSSAProblem *problem)

void	setVectors (int slowMode)

	~CTSSAMethod ()

Public Member Functions inherited from CCopasiMethod
	CCopasiMethod (const CCopasiMethod &src, const CCopasiContainer *pParent=NULL)

const CCopasiMethod::SubType &	getSubType () const

const CCopasiTask::Type &	getType () const

virtual void	load (CReadConfig &configBuffer, CReadConfig::Mode mode=CReadConfig::SEARCH)

virtual void	print (std::ostream *ostream) const

virtual bool	setCallBack (CProcessReport *pCallBack)

virtual	~CCopasiMethod ()

Public Member Functions inherited from CCopasiParameterGroup
bool	addGroup (const std::string &name)

bool	addParameter (const CCopasiParameter &parameter)

bool	addParameter (const std::string &name, const CCopasiParameter::Type type)

template<class CType >
bool	addParameter (const std::string &name, const CCopasiParameter::Type type, const CType &value)

void	addParameter (CCopasiParameter *pParameter)

CCopasiParameterGroup *	assertGroup (const std::string &name)

template<class CType >
CCopasiParameter *	assertParameter (const std::string &name, const CCopasiParameter::Type type, const CType &defaultValue)

index_iterator	beginIndex () const

name_iterator	beginName () const

	CCopasiParameterGroup (const CCopasiParameterGroup &src, const CCopasiContainer *pParent=NULL)

	CCopasiParameterGroup (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &objectType="ParameterGroup")

void	clear ()

index_iterator	endIndex () const

name_iterator	endName () const

CCopasiParameterGroup *	getGroup (const std::string &name)

const CCopasiParameterGroup *	getGroup (const std::string &name) const

CCopasiParameterGroup *	getGroup (const size_t &index)

const CCopasiParameterGroup *	getGroup (const size_t &index) const

size_t	getIndex (const std::string &name) const

std::string	getKey (const std::string &name) const

std::string	getKey (const size_t &index) const

virtual const std::string &	getName (const size_t &index) const

virtual const CObjectInterface *	getObject (const CCopasiObjectName &cn) const

CCopasiParameter *	getParameter (const std::string &name)

const CCopasiParameter *	getParameter (const std::string &name) const

CCopasiParameter *	getParameter (const size_t &index)

const CCopasiParameter *	getParameter (const size_t &index) const

CCopasiParameter::Type	getType (const std::string &name) const

CCopasiParameter::Type	getType (const size_t &index) const

std::string	getUniqueParameterName (const CCopasiParameter *pParameter) const

const CCopasiParameter::Value &	getValue (const std::string &name) const

const CCopasiParameter::Value &	getValue (const size_t &index) const

CCopasiParameter::Value &	getValue (const std::string &name)

CCopasiParameter::Value &	getValue (const size_t &index)

CCopasiParameterGroup &	operator= (const CCopasiParameterGroup &rhs)

bool	removeParameter (const std::string &name)

bool	removeParameter (const size_t &index)

template<class CType >
bool	setValue (const std::string &name, const CType &value)

template<class CType >
bool	setValue (const size_t &index, const CType &value)

size_t	size () const

bool	swap (const size_t &iFrom, const size_t &iTo)

bool	swap (index_iterator &from, index_iterator &to)

virtual	~CCopasiParameterGroup ()

Public Member Functions inherited from CCopasiParameter
	CCopasiParameter (const CCopasiParameter &src, const CCopasiContainer *pParent=NULL)

	CCopasiParameter (const std::string &name, const Type &type, const void pValue=NULL, const CCopasiContainer pParent=NULL, const std::string &objectType="Parameter")

virtual CCopasiObjectName	getCN () const

virtual const std::string &	getKey () const

virtual std::string	getObjectDisplayName (bool regular=true, bool richtext=false) const

const CCopasiParameter::Type &	getType () const

const Value &	getValue () const

Value &	getValue ()

virtual void *	getValuePointer () const

CCopasiObject *	getValueReference () const

bool	isValidValue (const C_FLOAT64 &value) const

bool	isValidValue (const C_INT32 &value) const

bool	isValidValue (const unsigned C_INT32 &value) const

bool	isValidValue (const bool &value) const

bool	isValidValue (const std::string &value) const

bool	isValidValue (const CCopasiObjectName &value) const

bool	isValidValue (const std::vector< CCopasiParameter * > &value) const

CCopasiParameter &	operator= (const CCopasiParameter &rhs)

template<class CType >
bool	setValue (const CType &value)

bool	setValue (const std::vector< CCopasiParameter * > &value)

virtual	~CCopasiParameter ()

Public Member Functions inherited from CCopasiContainer
virtual bool	add (CCopasiObject *pObject, const bool &adopt=true)

	CCopasiContainer (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &type="CN", const unsigned C_INT32 &flag=CCopasiObject::Container)

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

virtual std::string	getChildObjectUnits (const CCopasiObject *pObject) const

virtual const objectMap &	getObjects () const

virtual std::string	getUnits () const

virtual const CCopasiObject *	getValueObject () const

virtual bool	remove (CCopasiObject *pObject)

virtual	~CCopasiContainer ()

Public Member Functions inherited from CCopasiObject
void	addDirectDependency (const CCopasiObject *pObject)

	CCopasiObject (const CCopasiObject &src, const CCopasiContainer *pParent=NULL)

void	clearDirectDependencies ()

void	clearRefresh ()

bool	dependsOn (DataObjectSet candidates, const DataObjectSet &context=DataObjectSet()) const

void	getAllDependencies (DataObjectSet &dependencies, const DataObjectSet &context) const

virtual const DataObjectSet &	getDirectDependencies (const DataObjectSet &context=DataObjectSet()) const

CCopasiContainer *	getObjectAncestor (const std::string &type) const

CCopasiDataModel *	getObjectDataModel ()

const CCopasiDataModel *	getObjectDataModel () const

const std::string &	getObjectName () const

CCopasiContainer *	getObjectParent () const

const std::string &	getObjectType () const

virtual const CObjectInterface::ObjectSet &	getPrerequisites () const

virtual Refresh *	getRefresh () const

UpdateMethod *	getUpdateMethod () const

bool	hasCircularDependencies (DataObjectSet &candidates, DataObjectSet &verified, const DataObjectSet &context) const

bool	hasUpdateMethod () const

bool	isArray () const

bool	isContainer () const

bool	isDataModel () const

bool	isMatrix () const

bool	isNameVector () const

bool	isNonUniqueName () const

virtual bool	isPrerequisiteForContext (const CObjectInterface *pObject, const CMath::SimulationContextFlag &context, const CObjectInterface::ObjectSet &changedObjects) const

bool	isReference () const

bool	isRoot () const

bool	isSeparator () const

bool	isStaticString () const

bool	isValueBool () const

bool	isValueDbl () const

bool	isValueInt () const

bool	isValueInt64 () const

bool	isValueString () const

bool	isVector () const

virtual bool	mustBeDeleted (const DataObjectSet &deletedObjects) const

void	removeDirectDependency (const CCopasiObject *pObject)

void	setDirectDependencies (const DataObjectSet &directDependencies)

bool	setObjectName (const std::string &name)

virtual bool	setObjectParent (const CCopasiContainer *pParent)

void	setObjectValue (const C_FLOAT64 &value)

void	setObjectValue (const C_INT32 &value)

void	setObjectValue (const bool &value)

template<class CType >
void	setRefresh (CType pType, void(CType::method)(void))

template<class CType >
void	setUpdateMethod (CType pType, void(CType::method)(const C_FLOAT64 &))

template<class CType >
void	setUpdateMethod (CType pType, void(CType::method)(const C_INT32 &))

template<class CType >
void	setUpdateMethod (CType pType, void(CType::method)(const bool &))

virtual	~CCopasiObject ()

Public Member Functions inherited from CObjectInterface
	CObjectInterface ()

virtual	~CObjectInterface ()

Public Attributes
std::vector< CVector< C_FLOAT64 > >	mVec_mVfastSpace

std::vector< CMatrix< C_FLOAT64 > >	mVec_mVslow

std::vector< CMatrix< C_FLOAT64 > >	mVec_mVslowMetab

std::vector< CVector< C_FLOAT64 > >	mVec_mVslowSpace

CMatrix< C_FLOAT64 >	mVfastSpacePrint

CMatrix< C_FLOAT64 >	mVslowMetabPrint

CMatrix< C_FLOAT64 >	mVslowPrint

CMatrix< C_FLOAT64 >	mVslowSpacePrint

CArrayAnnotation *	pTmp1

CArrayAnnotation *	pTmp2

CArrayAnnotation *	pTmp3

CArrayAnnotation *	pTmp4

CArrayAnnotation *	pVfastSpacePrintAnn

CArrayAnnotation *	pVslowMetabPrintAnn

CArrayAnnotation *	pVslowPrintAnn

CArrayAnnotation *	pVslowSpacePrintAnn

Public Attributes inherited from CTSSAMethod
std::map< std::string, CArrayAnnotation * >	mapTableToName

std::vector< std::string >	tableNames

Private Member Functions
	CILDMModifiedMethod (const CCopasiContainer *pParent=NULL)

Friends
CTSSAMethod *	CTSSAMethod::createMethod (CCopasiMethod::SubType subType)

Additional Inherited Members
Public Types inherited from CCopasiMethod
enum	SubType { unset = 0, RandomSearch, RandomSearchMaster, SimulatedAnnealing, CoranaWalk, DifferentialEvolution, ScatterSearch, GeneticAlgorithm, EvolutionaryProgram, SteepestDescent, HybridGASA, GeneticAlgorithmSR, HookeJeeves, LevenbergMarquardt, NelderMead, SRES, Statistics, ParticleSwarm, Praxis, TruncatedNewton, Newton, deterministic, LSODAR, directMethod, stochastic, tauLeap, adaptiveSA, hybrid, hybridLSODA, hybridODE45, DsaLsodar, tssILDM, tssILDMModified, tssCSP, mcaMethodReder, scanMethod, lyapWolf, sensMethod, EFMAlgorithm, EFMBitPatternTreeAlgorithm, EFMBitPatternAlgorithm, Householder, crossSectionMethod, linearNoiseApproximation }

Public Types inherited from CCopasiParameterGroup
typedef parameterGroup::iterator	index_iterator

typedef CCopasiContainer::objectMap::iterator	name_iterator

typedef std::vector < CCopasiParameter * >	parameterGroup

Public Types inherited from CCopasiParameter
enum	Type { DOUBLE = 0, UDOUBLE, INT, UINT, BOOL, GROUP, STRING, CN, KEY, FILE, EXPRESSION, INVALID }

Public Types inherited from CCopasiContainer
typedef std::multimap < std::string, CCopasiObject * >	objectMap

Public Types inherited from CCopasiObject
typedef std::set< const CCopasiObject * >	DataObjectSet

typedef std::vector< Refresh * >	DataUpdateSequence

Public Types inherited from CObjectInterface
typedef std::set< const CObjectInterface * >	ObjectSet

typedef std::vector < CObjectInterface * >	UpdateSequence

Static Public Member Functions inherited from CTSSAMethod
static CTSSAMethod *	createMethod (CCopasiMethod::SubType subType=CCopasiMethod::unset)

Static Public Member Functions inherited from CCopasiObject
static std::vector< Refresh * >	buildUpdateSequence (const DataObjectSet &objects, const DataObjectSet &uptoDateObjects, const DataObjectSet &context=DataObjectSet())

static void	setRenameHandler (CRenameHandler *rh)

Static Public Attributes inherited from CCopasiMethod
static const std::string	SubTypeName []

static const char *	XMLSubType []

Static Public Attributes inherited from CCopasiParameter
static const std::string	TypeName []

static const char *	XMLType []

Static Public Attributes inherited from CCopasiContainer
static const std::vector < CCopasiContainer * >	EmptyList

Protected Types inherited from CCopasiObject
enum	Flag { Container = 0x1, Vector = 0x2, Matrix = 0x4, NameVector = 0x8, Reference = 0x10, ValueBool = 0x20, ValueInt = 0x40, ValueInt64 = 0x80, ValueDbl = 0x100, NonUniqueName = 0x200, StaticString = 0x400, ValueString = 0x800, Separator = 0x1000, ModelEntity = 0x2000, Array = 0x4000, DataModel = 0x8000, Root = 0x10000, Gui = 0x20000 }

Protected Member Functions inherited from CTSSAMethod
void	calculateDerivatives (C_FLOAT64 X1, C_FLOAT64 Y1)

void	calculateDerivativesX (C_FLOAT64 X1, C_FLOAT64 Y1)

	CTSSAMethod (const CCopasiMethod::SubType &subType, const CCopasiContainer *pParent=NULL)

bool	elevateChildren ()

void	evalF (const C_FLOAT64 t, const C_FLOAT64 y, C_FLOAT64 *ydot)

void	initializeAtol ()

void	initializeIntegrationsParameter ()

void	integrationMethodStart (const CState *initialState)

void	integrationStep (const double &deltaT)

void	map_index (C_FLOAT64 eval_r, C_INT index, const C_INT &dim)

void	map_index_desc (C_FLOAT64 eval_r, C_INT index, const C_INT &dim)

void	mat_anal_fast_space (C_INT &slow)

void	mat_anal_fast_space_thomas (C_INT &slow)

void	mat_anal_metab (C_INT &slow)

void	mat_anal_mod (C_INT &slow)

void	mat_anal_mod_space (C_INT &slow)

double	orthog (C_INT &number1, C_INT &number2)

void	schur (C_INT &info)

void	schur_desc (C_INT &info)

void	sylvester (C_INT slow, C_INT &info)

void	update_nid (C_INT index, C_INT nid, const C_INT &dim)

void	update_pid (C_INT index, C_INT pid, const C_INT &dim)

Protected Member Functions inherited from CCopasiMethod
	CCopasiMethod (const CCopasiTask::Type &taskType, const SubType &subType, const CCopasiContainer *pParent=NULL)

Protected Member Functions inherited from CCopasiParameterGroup
	CCopasiParameterGroup ()

Protected Member Functions inherited from CCopasiContainer
template<class CType >
CCopasiObject *	addMatrixReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)

template<class CType >
CCopasiObject *	addObjectReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)

template<class CType >
CCopasiObject *	addVectorReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)

void	initObjects ()

Protected Member Functions inherited from CCopasiObject
	CCopasiObject ()

	CCopasiObject (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &type="CN", const unsigned C_INT32 &flag=0)

Static Protected Member Functions inherited from CTSSAMethod
static void	EvalF (const C_INT n, const C_FLOAT64 t, const C_FLOAT64 y, C_FLOAT64 ydot)

Protected Attributes inherited from CTSSAMethod
CVector< C_FLOAT64 >	mAtol

CVector< C_FLOAT64 >	mCfast

int	mCurrentStep

std::vector< C_FLOAT64 >	mCurrentTime

Data	mData

C_FLOAT64	mDtol

CVector< C_FLOAT64 >	mDWork

C_FLOAT64	mEPS

std::ostringstream	mErrorMsg

CVector< C_INT >	mIWork

CMatrix< C_FLOAT64 >	mJacobian

CMatrix< C_FLOAT64 >	mJacobian_initial

C_INT	mJType

CLSODA	mLSODA

C_INT	mLsodaStatus

CState *	mpCurrentState

CModel *	mpModel

CTSSAProblem *	mpProblem

CState *	mpState

CMatrix< C_FLOAT64 >	mQ

CMatrix< C_FLOAT64 >	mQ_desc

CMatrix< C_FLOAT64 >	mQz

CMatrix< C_FLOAT64 >	mR

CMatrix< C_FLOAT64 >	mR_desc

bool	mReducedModel

C_FLOAT64	mRtol

C_INT	mSlow

C_INT	mState

CMatrix< C_FLOAT64 >	mTd

CMatrix< C_FLOAT64 >	mTd_save

CMatrix< C_FLOAT64 >	mTdInverse

CMatrix< C_FLOAT64 >	mTdInverse_save

C_FLOAT64	mTime

std::vector< C_INT >	mVec_SlowModes

std::vector< CVector< C_FLOAT64 > >	mVec_TimeScale

CVector< C_FLOAT64 >	mVfast_space

CMatrix< C_FLOAT64 >	mVslow

CMatrix< C_FLOAT64 >	mVslow_metab

CVector< C_FLOAT64 >	mVslow_space

C_FLOAT64 *	mY

CVector< C_FLOAT64 >	mY_cons

CVector< C_FLOAT64 >	mY_initial

CVector< C_FLOAT64 >	mYdot

Protected Attributes inherited from CCopasiMethod
CProcessReport *	mpCallBack

Protected Attributes inherited from CCopasiParameter
std::string	mKey

CCopasiObject *	mpValueReference

size_t	mSize

Value	mValue

Protected Attributes inherited from CCopasiContainer
objectMap	mObjects

Static Protected Attributes inherited from CCopasiObject
static CRenameHandler *	smpRenameHandler = NULL

Detailed Description

Definition at line 41 of file CILDMModifiedMethod.h.

Constructor & Destructor Documentation

CILDMModifiedMethod::CILDMModifiedMethod ( const CCopasiContainer * pParent = NULL )

private

Default constructor.

Parameters

const CCopasiContainer * pParent (default: NULL)

Definition at line 29 of file CILDMModifiedMethod.cpp.

References initializeParameter(), CTSSAMethod::mData, and CTSSAMethod::Data::pMethod.

                                                                         :
   CTSSAMethod(CCopasiMethod::tssILDMModified, pParent) //,
   // mpState(NULL),
   // mY(NULL)
 {
   //  assert((void *) &mData == (void *) &mData.dim);
 
   //  addObjectReference("Number of slow variables", mSlow, CCopasiObject::ValueInt);
   //  addMatrixReference("Contribution of Metabolites to Slow Space", mVslow, CCopasiObject::ValueDbl);
 
   mData.pMethod = this;
   initializeParameter();
 }

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

Copy constructor.

Parameters

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

Definition at line 43 of file CILDMModifiedMethod.cpp.

References initializeParameter(), CTSSAMethod::mData, and CTSSAMethod::Data::pMethod.

                                      :
   CTSSAMethod(src, pParent) //,
   //mpState(NULL),
   //mY(NULL)
 {
   //  assert((void *) &mData == (void *) &mData.dim);
 
   mData.pMethod = this;
   initializeParameter();
 }

CILDMModifiedMethod::~CILDMModifiedMethod ( )

Destructor.

Definition at line 55 of file CILDMModifiedMethod.cpp.

References CTSSAMethod::mpState, and pdelete.

 {
   pdelete(mpState);
 }

Member Function Documentation

void CILDMModifiedMethod::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 seperate CMatrix.

Definition at line 966 of file CILDMModifiedMethod.cpp.

References CTSSAMethod::mapTableToName, mVfastSpacePrint, mVslowMetabPrint, mVslowPrint, mVslowSpacePrint, pTmp1, pTmp2, pTmp3, pTmp4, pVfastSpacePrintAnn, pVslowMetabPrintAnn, pVslowPrintAnn, pVslowSpacePrintAnn, CArrayAnnotation::setDescription(), CArrayAnnotation::setDimensionDescription(), CArrayAnnotation::setMode(), CArrayAnnotation::STRINGS, CTSSAMethod::tableNames, and CArrayAnnotation::VECTOR.

Referenced by initializeParameter().

 {
 
   tableNames.erase(tableNames.begin(), tableNames.end());
 
   std::string name;
 
   name = "Contribution of species to modes";
   tableNames.push_back(name);
 
   CArrayAnnotation *
   pTmp1 = new CArrayAnnotation("Contribution of species to modes", this,
                                new CCopasiMatrixInterface<CMatrix<C_FLOAT64> >(&mVslowPrint), true);
   pTmp1->setMode(0, pTmp1->STRINGS);
   pTmp1->setMode(1, pTmp1->VECTOR);
   pTmp1->setDescription(" ");
   pTmp1->setDimensionDescription(0, "Contribution to  mode (TS - corresponding timescale)");
   pTmp1->setDimensionDescription(1, "Species");
   pVslowPrintAnn = pTmp1;
 
   mapTableToName[name] = pVslowPrintAnn;
 
   name = "Modes distribution for species";
   tableNames.push_back(name);
 
   CArrayAnnotation *
   pTmp2 = new CArrayAnnotation("Modes distribution for species", this,
                                new CCopasiMatrixInterface<CMatrix<C_FLOAT64> >(&mVslowMetabPrint), true);
   pTmp2->setMode(1, pTmp2->STRINGS);
   pTmp2->setMode(0, pTmp2->VECTOR);
   pTmp2->setDescription(" ");
   pTmp2->setDimensionDescription(0, "Mode distribution for each metabolite");
   pTmp2->setDimensionDescription(1, "modes (TS - corresponding  timescale)");
   pVslowMetabPrintAnn = pTmp2;
 
   mapTableToName[name] = pVslowMetabPrintAnn;
 
   name = "Slow space";
   tableNames.push_back(name);
 
   CArrayAnnotation *
   pTmp3 = new CArrayAnnotation("Slow space", this,
                                new CCopasiMatrixInterface<CMatrix<C_FLOAT64> >(&mVslowSpacePrint), true);
   pTmp3->setMode(1, pTmp3->STRINGS);
   pTmp3->setMode(0, pTmp3->VECTOR);
   pTmp3->setDescription(" ");
   pTmp3->setDimensionDescription(0, "Species");
   pTmp3->setDimensionDescription(1, "Contribution to slow space");
   pVslowSpacePrintAnn = pTmp3;
 
   mapTableToName[name] = pVslowSpacePrintAnn;
 
   name = "Fast space";
   tableNames.push_back(name);
 
   CArrayAnnotation *
   pTmp4 = new CArrayAnnotation("Fast space", this,
                                new CCopasiMatrixInterface<CMatrix<C_FLOAT64> >(&mVfastSpacePrint), true);
   pTmp4->setMode(1, pTmp4->STRINGS);
   pTmp4->setMode(0, pTmp4->VECTOR);
   pTmp4->setDescription(" ");
   pTmp4->setDimensionDescription(0, "Species");
   pTmp4->setDimensionDescription(1, "Contribution to fast space");
   pVfastSpacePrintAnn = pTmp4;
 
   mapTableToName[name] = pVfastSpacePrintAnn;
 }

void CILDMModifiedMethod::deuflhard_metab	(	C_INT &	slow,
		C_INT &	info
	)

Deuflhard Iteration: Prove Deuflhard criteria, find consistent initial value for DAE output: info - if Deuflhard is satisfied

Definition at line 497 of file CILDMModifiedMethod.cpp.

References CVectorCore< CType >::array(), C_FLOAT64, C_INT, CTSSAMethod::calculateDerivativesX(), CTSSAMethod::Data::dim, evalsort(), CModel::getCompartments(), CModel::getNumber2QuantityFactor(), CTSSAMethod::mat_anal_fast_space(), max, CTSSAMethod::mData, CTSSAMethod::mDtol, CTSSAMethod::mpModel, CTSSAMethod::mR, CTSSAMethod::mVfast_space, CTSSAMethod::mY_cons, CTSSAMethod::mY_initial, newton_new(), and CVector< CType >::resize().

Referenced by step().

 {
   C_INT i, j, info_newton;
   C_INT dim = mData.dim;
   C_INT fast = dim - slow;
 
   C_INT flag_deufl;
 
   flag_deufl = 1;  // set flag_deufl=0  to print temporaly steps for this function
 
   C_FLOAT64 max = 0;
   CVector<C_FLOAT64> re;
   CVector<C_FLOAT64> dxdt_relax;
   CVector<C_FLOAT64> x_relax;
   CVector<C_FLOAT64> x_help;
   CVector<C_FLOAT64> dxdt;
 
   CVector<C_FLOAT64> help;
   help.resize(dim);
   CVector<C_INT> index;
   index.resize(dim);
   CVector<C_INT> index_temp;
   index_temp.resize(dim);
 
   C_FLOAT64 eps;
   eps = 1 / fabs(mR(dim - fast , dim - fast));
   //eps = fabs(mR(dim - fast - 1, dim - fast - 1)) / fabs(mR(dim - fast , dim - fast));
 
   mat_anal_fast_space(slow);
 
   for (i = 0; i < dim; i++)
     {
       index[i] = i;
       index_temp[i] = i;
     }
 
   for (i = 0; i < dim; i++)
     {
       help[i] = mVfast_space[i];
     }
 
   evalsort(help.array(), index.array(), dim);
 
   for (i = 0; i < dim; i++)
     index_temp[i] = index[i];
 
   for (i = 0; i < dim; i++)
     {
       index[i] = index_temp[dim - i - 1];
     }
 
   C_FLOAT64 number2conc = mpModel->getNumber2QuantityFactor() / mpModel->getCompartments()[0]->getInitialValue();
   //C_FLOAT64 number2conc = 1.;
 
   dxdt.resize(dim);
 
   for (j = 0; j < dim; j++)
     dxdt[j] = 0.;
 
   //CVector<C_FLOAT64> x_help;
   x_help.resize(dim);
 
   for (j = 0; j < dim; j++)
     {
       x_help[j] = mY_initial[j] * number2conc;
     }
 
   // mpModel->calculateDerivativesX(dxdt.array());
   calculateDerivativesX(x_help.array(), dxdt.array());
 
   info_newton = 0;
 
   newton_new(index.array(), slow, info_newton);
 
   if (info_newton)
     {
       // TODO
       info = 1;
       return;
     }
 
   x_relax.resize(dim);
 
   for (i = 0; i < dim; i++)
     x_relax[i] = mY_cons[i];
 
   //CVector<C_FLOAT64> dxdt_relax;
   dxdt_relax.resize(dim);
 
   calculateDerivativesX(x_relax.array(), dxdt_relax.array());
 
   //CVector<C_FLOAT64> re;
   re.resize(dim);
 
   // stop criterion for slow reaction modes
 
   for (i = 0; i < dim; i++)
     {
       re[i] = fabs(dxdt_relax[i] - dxdt[i]);
       re[i] = re[i] * eps;
 
       for (j = 0; j < fast; j ++)
         if (i == index[j])
           re[i] = 0;
     }
 
   for (i = 0; i < dim; i++)
     if (max < re[i])
       max = re[i];
 
   if (max >= mDtol)
     info = 1;
   else
     info = 0;
 
   return;
 }

void CILDMModifiedMethod::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.

Definition at line 917 of file CILDMModifiedMethod.cpp.

References CTSSAMethod::mCurrentStep, mVec_mVslow, mVec_mVslowMetab, mVec_mVslowSpace, CTSSAMethod::mVec_SlowModes, and CTSSAMethod::mVec_TimeScale.

Referenced by initializeParameter(), and start().

 {
   mCurrentStep = 0;
   mVec_mVslow.erase(mVec_mVslow.begin(), mVec_mVslow.end());
   mVec_TimeScale.erase(mVec_TimeScale.begin(), mVec_TimeScale.end());
   mVec_mVslowMetab.erase(mVec_mVslowMetab.begin(), mVec_mVslowMetab.end());
   mVec_mVslowSpace.erase(mVec_mVslowSpace.begin(), mVec_mVslowSpace.end());
   mVec_SlowModes.erase(mVec_SlowModes.begin(), mVec_SlowModes.end());
 }

void CILDMModifiedMethod::evalsort	(	C_FLOAT64 *	reval,
		C_INT *	index,
		const C_INT &	dim
	)

EVALSORT for vector sorting

Definition at line 467 of file CILDMModifiedMethod.cpp.

References C_FLOAT64, C_INT, and min.

Referenced by deuflhard_metab().

 {
   C_INT i, j, min, tmp_ind;
   C_FLOAT64 tmp1r;
 
   for (i = 0; i < dim - 1; i++)
     {
       min = i;
 
       for (j = i + 1; j < dim; j++)
         {
           if (reval[j] <= reval[min])
             min = j;
         }
 
       tmp1r = reval[min];
       tmp_ind = index[min];
       reval[min] = reval[i];
       index[min] = index[i];
       reval[i] = tmp1r;
       index[i] = tmp_ind;
     }
 
   return;
 }

const CArrayAnnotation* CILDMModifiedMethod::getVfastSpacePrintAnn ( ) const

inline

Definition at line 155 of file CILDMModifiedMethod.h.

References pVfastSpacePrintAnn.

156 {return pVfastSpacePrintAnn;}

CILDMModifiedMethod::pVfastSpacePrintAnn

CArrayAnnotation * pVfastSpacePrintAnn

Definition: CILDMModifiedMethod.h:118

const CArrayAnnotation* CILDMModifiedMethod::getVslowMetabPrintAnn ( ) const

inline

Definition at line 157 of file CILDMModifiedMethod.h.

References pVslowMetabPrintAnn.

158 {return pVslowMetabPrintAnn;}

CILDMModifiedMethod::pVslowMetabPrintAnn

CArrayAnnotation * pVslowMetabPrintAnn

Definition: CILDMModifiedMethod.h:116

const CArrayAnnotation* CILDMModifiedMethod::getVslowPrintAnn ( ) const

inline

return CArrayAnnotation for visualization in ILDM-tab in the CQTSSAResultSubWidget

Definition at line 151 of file CILDMModifiedMethod.h.

References pVslowPrintAnn.

152 {return pVslowPrintAnn;}

CILDMModifiedMethod::pVslowPrintAnn

CArrayAnnotation * pVslowPrintAnn

Definition: CILDMModifiedMethod.h:115

const CArrayAnnotation* CILDMModifiedMethod::getVslowSpacePrintAnn ( ) const

inline

Definition at line 153 of file CILDMModifiedMethod.h.

References pVslowSpacePrintAnn.

154 {return pVslowSpacePrintAnn;}

CILDMModifiedMethod::pVslowSpacePrintAnn

CArrayAnnotation * pVslowSpacePrintAnn

Definition: CILDMModifiedMethod.h:117

void CILDMModifiedMethod::initializeParameter ( )

virtual

Initialize the method parameter

Reimplemented from CTSSAMethod.

Definition at line 60 of file CILDMModifiedMethod.cpp.

References CCopasiContainer::addMatrixReference(), CCopasiContainer::addObjectReference(), CCopasiParameterGroup::assertParameter(), C_FLOAT64, createAnnotationsM(), emptyVectors(), CTSSAMethod::initializeIntegrationsParameter(), CTSSAMethod::mReducedModel, CTSSAMethod::mSlow, CTSSAMethod::mVslow, CCopasiParameter::UDOUBLE, CCopasiObject::ValueDbl, and CCopasiObject::ValueInt.

Referenced by CILDMModifiedMethod().

 {
   addObjectReference("Number of slow variables", mSlow, CCopasiObject::ValueInt);
   addMatrixReference("Contribution of Species to Slow Space", mVslow, CCopasiObject::ValueDbl);
 
   initializeIntegrationsParameter();
 
   assertParameter("Deuflhard Tolerance", CCopasiParameter::UDOUBLE, (C_FLOAT64) 1.0e-6);
   mReducedModel = true;
 
   //mData.dim = mpState->getNumIndependent();
 
   createAnnotationsM();
   emptyVectors();
 }

void CILDMModifiedMethod::newton_for_timestep	(	C_INT	metabolite_number,
		C_FLOAT64 &	y_consistent,
		C_INT &	info
	)

NEWTON for "postprove": Prove of "fast" varibles Output: y_consistent, info

Definition at line 848 of file CILDMModifiedMethod.cpp.

References CVectorCore< CType >::array(), C_FLOAT64, C_INT, CTSSAMethod::calculateDerivativesX(), CTSSAMethod::Data::dim, CModel::getCompartments(), CModel::getNumber2QuantityFactor(), CTSSAMethod::mData, CTSSAMethod::mJacobian_initial, CTSSAMethod::mpModel, CTSSAMethod::mY_initial, and CVector< CType >::resize().

Referenced by step().

 {
   C_INT i, iter, itermax, flag_newton;
   iter = 0;
   itermax = 150;
 
   flag_newton = 1;  // set flag_newton=0 to print the iteration steps
 
   C_FLOAT64 tol, err;
   tol = 1e-6;
   err = 10.0;
 
   C_INT dim = mData.dim;
 
   C_FLOAT64 d_y, deriv;
   d_y = 0;
   deriv = mJacobian_initial(metabolite_number, metabolite_number);
 
   if (deriv == 0)
     {
       return;
     }
 
   info = 0;
 
   C_FLOAT64 number2conc = mpModel->getNumber2QuantityFactor() / mpModel->getCompartments()[0]->getInitialValue();
   //C_FLOAT62number2conc = 1.;
 
   //this is an ugly hack that only makes sense if all metabs are in the same compartment
   //at the moment is is the only case the algorithm deals with
 
   CVector<C_FLOAT64> y_newton; //current state converted to concentrations
   y_newton.resize(dim);
 
   for (i = 0; i < dim; ++i)
     y_newton[i] = mY_initial[i] * number2conc;
 
   CVector<C_FLOAT64> dydt;
   dydt.resize(dim);
 
   while (err > tol)
     {
       iter ++;
 
       if (iter > itermax)
         {
           info = 1;
           break;
         }
 
       y_newton[metabolite_number] = y_newton[metabolite_number] + d_y;
 
       calculateDerivativesX(y_newton.array(), dydt.array());
 
       d_y = - 1 / deriv * dydt[metabolite_number];
 
       if (err > fabs(d_y))
         err = fabs(d_y);
     }
 
   y_consistent = y_newton[metabolite_number];
 
   return;
 }

void CILDMModifiedMethod::newton_new	(	C_INT *	index_metab,
		C_INT &	slow,
		C_INT &	info
	)

Definition at line 615 of file CILDMModifiedMethod.cpp.

References CVectorCore< CType >::array(), C_FLOAT64, C_INT, CTSSAMethod::calculateDerivativesX(), dgesv_(), CTSSAMethod::Data::dim, CModel::getCompartments(), CModel::getNumber2QuantityFactor(), CTSSAMethod::mData, CTSSAMethod::mJacobian_initial, CTSSAMethod::mpModel, CTSSAMethod::mY_cons, CTSSAMethod::mY_initial, CMatrix< CType >::resize(), and CVector< CType >::resize().

Referenced by deuflhard_metab().

 {
   C_INT i, j, k, m, iter, iterations, itermax;
   C_INT nrhs, ok, fast, flag_newton;
 
   flag_newton = 1;  // set flag_newton=1  to print temporaly steps of newton iterations
 
   C_FLOAT64 tol, err;
   C_INT dim = mData.dim;
 
   fast = dim - slow;
 
   CVector<C_INT> ipiv;
   ipiv.resize(fast);
 
   CVector<C_FLOAT64> s_22_array;
   s_22_array.resize(fast * fast);
 
   CVector<C_FLOAT64> gf_newton;
   gf_newton.resize(fast);
 
   CVector<C_FLOAT64> d_yf;
   d_yf.resize(dim);
 
   CVector<C_FLOAT64> y_newton;
   y_newton.resize(dim);
 
   CVector<C_FLOAT64> yf_newton;
   yf_newton.resize(fast);
 
   CVector<C_FLOAT64> dydt_newton;
   dydt_newton.resize(dim);
 
   CVector<C_FLOAT64> g_newton;
   g_newton.resize(dim);
 
   CMatrix<C_FLOAT64> Jac_fast;
   Jac_fast.resize(fast, fast);
 
   C_FLOAT64 g1, g2 = 0.0;
   mY_cons.resize(dim);
 
   nrhs = 1;
   tol = 1e-6;
   err = 10.0;
   iter = 0;
 
   itermax = 150;
   iterations = 0;
 
   info = 0;
 
   C_FLOAT64 number2conc = mpModel->getNumber2QuantityFactor() / mpModel->getCompartments()[0]->getInitialValue();
   //C_FLOAT64 number2conc = 1.;
 
   for (i = 0; i < fast; i++)
     {
       m = index_metab[i];
 
       for (j = 0; j < fast; j++)
         {
           k = index_metab[ j];
 
           if ((m > -1) & (k > -1))
             Jac_fast(i, j) = mJacobian_initial(m, k);
           else
             {
               info = 3;
               return;
             }
         }
     }
 
   for (i = 0; i < dim; i++)
     y_newton[i] = mY_initial[i] * number2conc;
 
   for (i = 0; i < fast; i++)
     for (j = 0; j < fast; j++)
       s_22_array[j + fast * i] = Jac_fast(j, i);
 
   for (i = 0; i < dim; i++)
     d_yf[i] = 0.;
 
   while (err > tol)
     {
       iter ++;
 
       if (iter > itermax)
         {
           info = 1;
           return;
         }
 
       for (i = 0; i < dim; i++)
         y_newton[i] = y_newton[i] + d_yf[i];
 
       calculateDerivativesX(y_newton.array(), dydt_newton.array());
 
       for (i = 0; i < fast; i++)
         {
           j = index_metab[i];
           gf_newton[i] = -1. * dydt_newton[j];
         }
 
       /*       int dgesv_(integer *n, integer *nrhs, doublereal *a, integer
        * *lda, integer *ipiv, doublereal *b, integer *ldb, integer *info)
        *
        *  -- LAPACK driver routine (version 3.0) --
        *     Univ. of Tennessee, Univ. of California Berkeley, NAG Ltd.,
        *     Courant Institute, Argonne National Lab, and Rice University
        *     March 31, 1993
        *
        *
        *  Purpose
        *  =======
        *
        *  DGESV computes the solution to a real system of linear equations
        *     A * X = B,
        *  where A is an N-by-N matrix and X and B are N-by-NRHS matrices.
        *
        *  The LU decomposition with partial pivoting and row interchanges is
        *  used to factor A as
        *     A = P * L * U,
        *  where P is a permutation matrix, L is unit lower triangular, and U is
        *  upper triangular.  The factored form of A is then used to solve the
        *  system of equations A * X = B.
        *
        *  Arguments
        *  =========
        *
        *  N       (input) INTEGER
        *          The number of linear equations, i.e., the order of the
        *          matrix A.  N >= 0.
        *
        *  NRHS    (input) INTEGER
        *          The number of right hand sides, i.e., the number of columns
        *          of the matrix B.  NRHS >= 0.
        *
        *  A       (input/output) DOUBLE PRECISION array, dimension (LDA,N)
        *          On entry, the N-by-N coefficient matrix A.
        *          On exit, the factors L and U from the factorization
        *          A = P*L*U; the unit diagonal elements of L are not stored.
        *
        *  LDA     (input) INTEGER
        *          The leading dimension of the array A.  LDA >= max(1,N).
        *
        *  IPIV    (output) INTEGER array, dimension (N)
        *          The pivot indices that define the permutation matrix P;
        *          row i of the matrix was interchanged with row IPIV(i).
        *
        *  B       (input/output) DOUBLE PRECISION array, dimension (LDB,NRHS)
        *          On entry, the N-by-NRHS matrix of right hand side matrix B.
        *          On exit, if INFO = 0, the N-by-NRHS solution matrix X.
        *
        *  LDB     (input) INTEGER
        *          The leading dimension of the array B.  LDB >= max(1,N).
        *
        *
        * INFO    (output) INTEGER
        *          = 0:  successful exit
        *          < 0:  if INFO = -i, the i-th argument had an illegal value
        *          > 0:  if INFO = i, U(i,i) is exactly zero.  The factorization
        *                has been completed, but the factor U is exactly
        *                singular, so the solution could not be computed.
        */
 
       dgesv_(&fast, &nrhs, s_22_array.array(), &fast, ipiv.array(), gf_newton.array(), &fast, &ok);
 
       if (ok != 0)
         {
           info = 2;
           return;
         }
 
       for (i = 0; i < fast; i++)
         d_yf[i] = 0;
 
       for (j = 0; j < fast; j++)
         {
           k = index_metab[j];
 
           for (i = 0; i < dim; i ++)
             {
               if (i == k)
                 d_yf[k] = gf_newton[j];
             }
         }
 
       err = -10.;
 
       for (i = 0; i < fast; i++)
         {
           gf_newton[i] = fabs(gf_newton[i]);
 
           if (err < gf_newton[i])
             err = gf_newton[i];
         }
 
       iterations = iterations + 1;
 
       // stop criterion of newton method
 
       //   C_FLOAT64 g1, g2 = 0.0;
 
       //   g2 = err;
 
       if (iter == 1)
         g1 = 3.0 * err;
       else
         g1 = g2;
 
       g2 = err;
 
       if (g2 / g1 > 1.0)
         {
           info = 1;
           return;
         }
     } /* end while */
 
   for (i = 0; i < dim; i++)
     mY_cons[i] = y_newton[i];
 
   info = 0;
 
   return;
 }

void CILDMModifiedMethod::printResult ( std::ostream * ostream ) const

virtual

print of the standart report sequence for ILDM Method

Parameters

std::ostream * ostream

Reimplemented from CCopasiMethod.

Definition at line 1134 of file CILDMModifiedMethod.cpp.

References C_INT, C_INT32, CTSSAMethod::Data::dim, CModel::getMetabolitesX(), CCopasiObject::getObjectDataModel(), CCopasiObject::getObjectName(), CTSSAMethod::mData, CTSSAMethod::mpModel, mVec_mVfastSpace, mVec_mVslow, mVec_mVslowMetab, mVec_mVslowSpace, CTSSAMethod::mVec_SlowModes, CTSSAMethod::mVec_TimeScale, and CCopasiMethod::print().

 {
   std::ostream & os = *ostream;
   double timeScale;
   C_INT i, j, istep = 0;
 
   this->print(&os);
 
   C_INT32 stepNumber;
 
   assert(getObjectDataModel() != NULL);
 
   //stepNumber = pProblem->getStepNumber();
   stepNumber = mVec_SlowModes.size();
 
   for (istep = 0; istep < stepNumber; istep++)
     {
 
       os << std::endl;
       os << "**************** Time step " << istep + 1 << " **************************  " << std::endl;
 
       os << std::endl;
 
       os << "Contribution of species to modes" << std::endl;
 
       os << "Rows : contribution to  mode (TS - corresponding timescale)" << std::endl;
       os << "Columns: species  ";
 
       for (j = 0; j < mData.dim; j++)
         {
           os << mpModel->getMetabolitesX()[j]->getObjectName() << "   ";
         }
 
       os << std::endl;
 
       for (i = 0; i < mData.dim; i++)
         {
           timeScale = mVec_TimeScale[istep][i];
 
           if (i < mVec_SlowModes[istep])
             os << "Slow (";
           else
             os << "Fast (";
 
           os << timeScale << "): ";
 
           for (j = 0; j < mData.dim; j++)
             os << mVec_mVslow[istep][i][j] << " ";
 
           os << std::endl;
         }
 
       os << std::endl;
 
       os << "Modes distribution for species" << std::endl;
 
       os << "Rows : Mode distribution for each species" << std::endl;
       os << "Columns: Modes (TS - corresponding  timescale) ";
       os << std::endl;
 
       for (i = 0; i < mData.dim; i++)
         {
           timeScale = mVec_TimeScale[istep][i];
 
           if (i < mVec_SlowModes[istep])
             os << "Slow (";
           else
             os << "Fast (";
 
           os << timeScale << ")  ";
         }
 
       os << std::endl;
 
       for (j = 0; j < mData.dim; j++)
         {
           os << mpModel->getMetabolitesX()[j]->getObjectName() << "  ";
 
           for (i = 0; i < mData.dim; i++)
             os << mVec_mVslowMetab[istep][j][i] << "  ";
 
           os << std::endl;
         }
 
       os << std::endl;
 
       os << "Slow space" << std::endl;
 
       os << "Rows : Species" << std::endl;
       os << "Column: Contribution to slow space ";
       os << std::endl;
 
       os << mVec_SlowModes[istep];
       os << " slow; ";
 
       os << mData.dim - mVec_SlowModes[istep];
       os << " fast";
       os << std::endl;
 
       for (j = 0; j < mData.dim; j++)
         {
           os << mpModel->getMetabolitesX()[j]->getObjectName() << "  ";
           os << mVec_mVslowSpace[istep][j] << "  ";
 
           os << std::endl;
         }
 
       os << std::endl;
       os << "Fast space" << std::endl;
 
       os << "Rows : Species" << std::endl;
       os << "Column: Contribution to fast space ";
       os << std::endl;
 
       os << mVec_SlowModes[istep];
       os << " slow; ";
 
       os << mData.dim - mVec_SlowModes[istep];
       os << " fast";
       os << std::endl;
 
       for (j = 0; j < mData.dim; j++)
         {
           os << mpModel->getMetabolitesX()[j]->getObjectName() << "  ";
           os << mVec_mVfastSpace[istep][j] << "  ";
 
           os << std::endl;
         }
 
       os << std::endl;
     }
 
   return;
 }

bool CILDMModifiedMethod::setAnnotationM ( size_t 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 desription of CArayAnnotation for both dimensions:

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

Implements CTSSAMethod.

Definition at line 1041 of file CILDMModifiedMethod.cpp.

References C_INT, CTSSAMethod::Data::dim, CModel::getMetabolitesX(), CTSSAMethod::mData, CTSSAMethod::mpModel, mVec_mVfastSpace, mVec_mVslow, mVec_mVslowMetab, mVec_mVslowSpace, CTSSAMethod::mVec_SlowModes, CTSSAMethod::mVec_TimeScale, mVfastSpacePrint, mVslowMetabPrint, mVslowPrint, mVslowSpacePrint, pVfastSpacePrintAnn, pVslowMetabPrintAnn, pVslowPrintAnn, pVslowSpacePrintAnn, CMatrix< CType >::resize(), CArrayAnnotation::resize(), CArrayAnnotation::setAnnotationString(), CArrayAnnotation::setCopasiVector(), and step().

 {
   if (step == 0) return false;
 
   if (mVec_mVslow.size() == 0) return false;
 
   //if (step > mVec_mVslow.size()) return false;
 
   if (step > mVec_SlowModes.size()) return false;
 
   step -= 1;
   double timeScale;
   std::string str;
   std::stringstream sstr;
   sstr.str("");
   sstr.clear();
   int i;
 
   mVslowPrint.resize(mData.dim, mData.dim);
   mVslowPrint = mVec_mVslow[step];
   pVslowPrintAnn->resize();
   pVslowPrintAnn->setCopasiVector(1, &mpModel->getMetabolitesX());
 
   for (i = 0; i < mData.dim; i++)
     {
       timeScale = mVec_TimeScale[step][i];
 
       if (i < mVec_SlowModes[step])
         sstr << "Slow: ";
       else
         sstr << "Fast: ";
 
       sstr << timeScale;
       str = sstr.str();
       pVslowPrintAnn->setAnnotationString(0, i, str);
       sstr.str("");
       sstr.clear();
     }
 
   mVslowMetabPrint.resize(mData.dim, mData.dim);
   mVslowMetabPrint = mVec_mVslowMetab[step];
   pVslowMetabPrintAnn->resize();
   pVslowMetabPrintAnn->setCopasiVector(0, &mpModel->getMetabolitesX());
 
   for (i = 0; i < mData.dim; i++)
     {
       timeScale = mVec_TimeScale[step][i];
 
       if (i < mVec_SlowModes[step])
         sstr << "Slow: ";
       else
         sstr << "Fast: ";
 
       sstr << timeScale;
       str = sstr.str();
       pVslowMetabPrintAnn->setAnnotationString(1, i, str);
       sstr.str("");
       sstr.clear();
     }
 
   sstr << mVec_SlowModes[step];
   // if (mVec_SlowModes[step] > 1)
   // sstr << " slow modes";
   //else
   // sstr << " slow mode";
   sstr << " slow; ";
 
   C_INT dim = mData.dim;
   sstr << dim - mVec_SlowModes[step];
   sstr << " fast";
 
   str = sstr.str();
   mVslowSpacePrint.resize(mData.dim, 1);
 
   for (i = 0; i < mData.dim; i++)
     mVslowSpacePrint(i, 0) = mVec_mVslowSpace[step][i];
 
   pVslowSpacePrintAnn->resize();
   pVslowSpacePrintAnn->setCopasiVector(0, &mpModel->getMetabolitesX());
   pVslowSpacePrintAnn->setAnnotationString(1, 0, str);
 
   mVfastSpacePrint.resize(mData.dim, 1);
 
   for (i = 0; i < mData.dim; i++)
     mVfastSpacePrint(i, 0) = mVec_mVfastSpace[step][i];
 
   pVfastSpacePrintAnn->resize();
   pVfastSpacePrintAnn->setCopasiVector(0, &mpModel->getMetabolitesX());
   pVfastSpacePrintAnn->setAnnotationString(1, 0, str);
 
   return true;
 }

void CILDMModifiedMethod::setVectors ( int slowMode )

upgrade all vectors with values from actually calculalion for current step

Definition at line 930 of file CILDMModifiedMethod.cpp.

References CTSSAMethod::Data::dim, CTSSAMethod::mCurrentStep, CTSSAMethod::mCurrentTime, CTSSAMethod::mData, CTSSAMethod::mR, CTSSAMethod::mTime, mVec_mVfastSpace, mVec_mVslow, mVec_mVslowMetab, mVec_mVslowSpace, CTSSAMethod::mVec_SlowModes, CTSSAMethod::mVec_TimeScale, CTSSAMethod::mVfast_space, CTSSAMethod::mVslow, CTSSAMethod::mVslow_metab, and CTSSAMethod::mVslow_space.

Referenced by step().

 {
   mVec_mVslow.push_back(mCurrentStep);
   mVec_mVslow[mCurrentStep].resize(mData.dim, mData.dim);
   mVec_mVslow[mCurrentStep] = mVslow;
 
   mVec_TimeScale.push_back(mCurrentStep);
   mVec_TimeScale[mCurrentStep].resize(mData.dim);
   int i;
 
   for (i = 0; i < mData.dim; i++)
     mVec_TimeScale[mCurrentStep][i] = -1 / mR(i, i);
 
   mVec_mVslowMetab.push_back(mCurrentStep);
   mVec_mVslowMetab[mCurrentStep].resize(mData.dim, mData.dim);
   mVec_mVslowMetab[mCurrentStep] = mVslow_metab;
 
   mVec_mVslowSpace.push_back(mCurrentStep);
   mVec_mVslowSpace[mCurrentStep].resize(mData.dim);
   mVec_mVslowSpace[mCurrentStep] = mVslow_space;
 
   mVec_mVfastSpace.push_back(mCurrentStep);
   mVec_mVfastSpace[mCurrentStep].resize(mData.dim);
   mVec_mVfastSpace[mCurrentStep] = mVfast_space;
 
   mVec_SlowModes.push_back(mCurrentStep);
   mVec_SlowModes[mCurrentStep] = slowMode;
 
   mCurrentTime.push_back(mCurrentStep);
   mCurrentTime[mCurrentStep] = mTime;
 }

void CILDMModifiedMethod::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.

Definition at line 76 of file CILDMModifiedMethod.cpp.

References CTSSAMethod::Data::dim, emptyVectors(), CCopasiParameter::getValue(), CTSSAMethod::integrationMethodStart(), CTSSAMethod::mData, CTSSAMethod::mDtol, CTSSAMethod::mReducedModel, CTSSAMethod::mVfast_space, CTSSAMethod::mVslow, CTSSAMethod::mVslow_metab, CTSSAMethod::mVslow_space, CCopasiParameter::Value::pUDOUBLE, CMatrix< CType >::resize(), and CVector< CType >::resize().

 {
   mReducedModel = true;
 
   integrationMethodStart(initialState);
 
   /* ILDM related staff  */
 
   mDtol = * getValue("Deuflhard Tolerance").pUDOUBLE;
 
   mVslow.resize(mData.dim, mData.dim);
   mVslow_metab.resize(mData.dim, mData.dim);
   mVslow_space.resize(mData.dim);
   mVfast_space.resize(mData.dim);
 
   emptyVectors();
 
   return;
 }

void CILDMModifiedMethod::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

Schur Decomposition of Jacobian (reordered). Output: mQ - transformation matrix mR - block upper triangular matrix (with ordered eigenvalues)

Schur transformation of Jacobian

end of the block %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

Begin of the block %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

end of the of block %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

Reimplemented from CTSSAMethod.

Definition at line 96 of file CILDMModifiedMethod.cpp.

References CVectorCore< CType >::array(), C_FLOAT64, C_INT, CTSSAMethod::calculateDerivativesX(), CModel::calculateJacobianX(), deuflhard_metab(), CTSSAMethod::Data::dim, CModel::getCompartments(), CModel::getNumber2QuantityFactor(), CTSSAMethod::integrationStep(), CTSSAMethod::mat_anal_fast_space(), CTSSAMethod::mat_anal_metab(), CTSSAMethod::mat_anal_mod(), CTSSAMethod::mat_anal_mod_space(), max, MCTSSAMethod, CTSSAMethod::mCurrentStep, CTSSAMethod::mData, CTSSAMethod::mDtol, CTSSAMethod::mJacobian, CTSSAMethod::mJacobian_initial, CTSSAMethod::mpModel, CTSSAMethod::mQ, CTSSAMethod::mQz, CTSSAMethod::mR, CTSSAMethod::mReducedModel, CTSSAMethod::mSlow, CTSSAMethod::mTd, CTSSAMethod::mTd_save, CTSSAMethod::mTdInverse, CTSSAMethod::mTdInverse_save, CTSSAMethod::mTime, CTSSAMethod::mVslow, CTSSAMethod::mY, CTSSAMethod::mY_cons, CTSSAMethod::mY_initial, newton_for_timestep(), CMatrix< CType >::resize(), CVector< CType >::resize(), CTSSAMethod::schur(), setVectors(), CModel::updateSimulatedValues(), and CCopasiMessage::WARNING.

Referenced by setAnnotationM().

 {
 
   C_INT dim = mData.dim;
   C_INT fast = 0;
   C_INT slow = dim - fast;
 
   C_INT slow2, fast2;
 
   slow2 = dim;
   fast2 = dim - slow2;
 
   C_INT i, j;
 
   mY_initial.resize(dim);
   mJacobian_initial.resize(dim, dim);
   mQ.resize(dim, dim);
   mR.resize(dim, dim);
   mTd.resize(dim, dim);
   mTdInverse.resize(dim, dim);
   mQz.resize(dim, dim);
 
   mTd_save.resize(dim, dim);
 
   mTdInverse_save.resize(dim, dim);
 
   mpModel->updateSimulatedValues(mReducedModel);
   // TO REMOVE : mpModel->applyAssignments();
   mpModel->calculateJacobianX(mJacobian, 1e-6, 1e-12);
 
   C_INT flag_jacob;
   flag_jacob = 1;  // Set flag_jacob=0 to print Jacobian
 
   C_FLOAT64 number2conc = mpModel->getNumber2QuantityFactor() / mpModel->getCompartments()[0]->getInitialValue();
   //C_FLOAT64 number2conc = 1.;
 
   //this is an ugly hack that only makes sense if all metabs are in the same compartment
   //at the moment is is the only case the algorithm deals with
 
   CVector<C_FLOAT64> Xconc; //current state converted to concentrations
   Xconc.resize(dim);
 
   for (i = 0; i < dim; ++i)
     Xconc[i] = mY[i] * number2conc;
 
   for (i = 0; i < dim; i++)
     mY_initial[i] = mY[i];
 
   CVector<C_FLOAT64> Xconc_initial; //current state converted to concentrations
   Xconc_initial.resize(dim);
 
   for (i = 0; i < dim; ++i)
     Xconc_initial[i] = mY_initial[i] * number2conc;
 
   // save initial  Jacobian before next time step
   for (i = 0; i < dim; i++)
     for (j = 0; j < dim; j++)
       mJacobian_initial(i, j) = mJacobian(i, j);
 
   // Next time step
   integrationStep(deltaT);
 
   mpModel->updateSimulatedValues(mReducedModel);
   // TO REMOVE : mpModel->applyAssignments();
 
   // Calculate Jacobian for time step control
   mpModel->calculateJacobianX(mJacobian, 1e-6, 1e-12);
 
   //CMatrix<C_FLOAT64> mTd_save;
   for (i = 0; i < dim; i++)
     for (j = 0; j < dim; j++)
       {
         mTd_save(i, j) = 0;
         mTdInverse_save(i, j) = 0;
       }
 
   for (i = 0; i < dim; i++)
     for (j = 0; j < dim; j++)
       {
         mTd(i, j) = 0;
         mTdInverse(i, j) = 0;
       }
 
   /** Schur  Decomposition of Jacobian (reordered).
   Output:  mQ - transformation matrix mR - block upper triangular matrix (with ordered eigenvalues) */
 
   C_INT failed = 0;
   C_INT info_schur = 0;
 
   C_INT number, k;
   C_INT failed_while = 0;
 
   C_INT flag_deufl;
   flag_deufl = 1;
 
   C_FLOAT64 max = 0.;
 
   //C_FLOAT64 max = 0;
   CVector<C_FLOAT64> re;
   CVector<C_FLOAT64> dxdt_relax;
   CVector<C_FLOAT64> x_relax;
   CVector<C_FLOAT64> x_help;
   CVector<C_FLOAT64> dxdt;
 
   CVector<C_FLOAT64> x_zero;
 
   CVector<C_FLOAT64> dxdt_zero;
 
   CVector<C_FLOAT64> dxdt_real;
 
   CVector<C_FLOAT64> help;
 
   CVector<C_INT> index;
   CVector<C_INT> index_temp;
   CMatrix<C_FLOAT64> orthog_prove;
   orthog_prove.resize(dim, dim);
 
   C_INT info;
 
   CVector<C_INT> index_metab;
   index_metab.resize(dim);
 
   /** Schur transformation of Jacobian */
   schur(info_schur);
 
   if (info_schur)
     {
       CCopasiMessage(CCopasiMessage::WARNING,
                      MCTSSAMethod + 9, mTime - deltaT);
 
       goto integration;
     }
 
   for (i = 0; i < dim; i++)
     for (j = 0; j < dim; j++)
       mTdInverse(i, j) = mQ(j, i);
 
   C_INT flag_schur;
 
   flag_schur = 1;  // set flag_schur = 0 to print Schur decomposition of jacobian (matrices mR and transformation mQ)
 
   mY_cons.resize(dim);  // consistent initial vector for DAE
 
   /* If complex eigenvalues */
   //BUG 873
   if (mR(dim - 1, dim - 1) == mR(dim - 2 , dim - 2))
     if (dim == 2)
       {
         slow = dim;
         goto integration;
       }
 
   // If positive eigenvalues
 
   if (mR(dim - 1, dim - 1) >= 0)
     {
       slow = dim;
       fast = 0;
       CCopasiMessage(CCopasiMessage::WARNING,
                      MCTSSAMethod + 10, mTime - deltaT);
 
       failed = 1;
       goto integration;
     }
 
   // Iterations to determine the number of slow metabolites
 
   while ((slow2 > 1))
     {
       slow2 = slow2 - 1;
       fast2 = dim - slow2;
 
       if (mR(dim - fast2, dim - fast2) >= 0)
         {
           failed = 1;
           goto integration;
         }
 
       deuflhard_metab(slow2, info);
 
       if (info)
         {
           failed_while = 1;
           goto integration;
         }
     }
 
   //end of iterations to determine the number of slow metabolites
 
   /** end of the block %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%  */
   /** %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%  */
 
 integration:
 
   slow = slow2;
   fast = fast2;
 
   if ((failed == 1) || (failed_while == 1))
     {
       if (slow < dim)
         {
           fast = fast - 1;
           slow = dim - fast;
 
           if ((fast >= 1) && (mR(slow - 1, slow - 1) == mR(slow , slow)))
             fast = fast - 1;
 
           slow = dim - fast;
         }
     }
 
   mSlow = slow;
 
   if (slow == dim)
     CCopasiMessage(CCopasiMessage::WARNING,
                    MCTSSAMethod + 11, mTime);
 
   for (i = 0; i < dim; i++)
     for (j = 0; j < dim; j++)
       // mTdInverse(i,j) = mQ(i,j);
       mTd(i, j) = mQ(i, j);
 
   // Flag for print Tabs
 
   mat_anal_mod(slow);
   mat_anal_metab(slow);
   mat_anal_mod_space(slow);
   mat_anal_fast_space(slow);
 
   // This block proves which metabolite could be considered as QSS. In development
   /** Begin of the block %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%  */
 
   C_INT flag_dev;
   flag_dev = 1;
 
   if (flag_dev == 0)
     {
       C_INT temp;
       temp = dim - 1;
 
       // Mode Analysis to find the dominant metabolites in the modes
       mat_anal_mod(temp);
 
       //index_metab = -1, if there is no dominant metabolites in corresponding mode,
       //and is equal
       // to the number of dominant metabolite in opposite case
       // Dominant metabolite - its contribution to the mode is larger as 70%
 
       for (j = 0; j < dim; j++)
         index_metab[j] = -1;
 
       for (i = 0; i < dim ; i ++)
         for (j = 0; j < dim; j++)
           if (mVslow(dim - i - 1, j) > 70)
             index_metab[i] = j;
 
       C_FLOAT64 y_cons;
 
       info = 0;
       k = 0;
       number = index_metab[k];
 
       if (number > - 1)
         newton_for_timestep(number, y_cons, info);
 
       while (k < dim - 1)
         {
           if (number > -1)
             {
               dxdt.resize(dim);
 
               for (j = 0; j < dim; j++)
                 dxdt[j] = 0.;
 
               //CVector<C_FLOAT64> x_help;
               x_help.resize(dim);
 
               for (j = 0; j < dim; j++)
                 {
                   x_help[j] = mY_initial[j] * number2conc;
                 }
 
               calculateDerivativesX(x_help.array(), dxdt.array());
               info = 0;
 
               //NEWTON: Looking for consistent initial value for DAE system
               //Output:  y_cons, info
 
               newton_for_timestep(number, y_cons, info);
 
               if (info)
                 {
                   // TODO info: newton iteration stop
                 }
 
               if (info == 0)
                 {
                   // CVector<C_FLOAT64> x_relax;
                   x_relax.resize(dim);
 
                   for (i = 0; i < dim; i ++)
                     if (i == number)
                       x_relax[i] = y_cons;
                     else
                       x_relax[i] = x_help[i];
 
                   //CVector<C_FLOAT64> dxdt_relax;
                   dxdt_relax.resize(dim);
 
                   calculateDerivativesX(x_relax.array(), dxdt_relax.array());
 
                   //CVector<C_FLOAT64> re;
                   re.resize(dim);
 
                   C_FLOAT64 eps;
                   eps = 1 / fabs(mR(dim - k - 1 , dim - k - 1));
 
                   // stop criterion for slow reaction modes
 
                   for (i = 0; i < dim; i++)
                     {
                       if (i == number)
                         re[i] = 0;
                       else
                         {
                           re[i] = fabs(dxdt_relax[i] - dxdt[i]);
                           re[i] = re[i] * eps;
                         }
                     }
 
                   //C_FLOAT64 max = 0.;
                   for (i = 0; i < dim; i++)
                     if (max < re[i])
                       max = re[i];
 
                   if (max >= mDtol)
                     info = 1;
                   else
                     info = 0;
                 }
             }
 
           k = k + 1;
           number = index_metab[k];
           max = 0;
         }
     }
 
   /** end of the of block %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%  */
   /** %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%  */
 
   mpModel->updateSimulatedValues(mReducedModel);
   // TO REMOVE : mpModel->applyAssignments();
 
   // Calculate Jacobian for time step control
 
   mpModel->calculateJacobianX(mJacobian, 1e-6, 1e-12);
 
   // new entry for every entry contains the current data of currently step
   setVectors(slow);
 
   // set the stepcounter
   mCurrentStep += 1;
 
   return;
 }