CSteadyStateMethod Class Reference

#include <CSteadyStateMethod.h>

Inheritance diagram for CSteadyStateMethod:

Collaboration diagram for CSteadyStateMethod:

Public Types
enum	ReturnCode { notFound = 0, found, foundEquilibrium, foundNegative }
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

Public Member Functions
	CSteadyStateMethod (const CSteadyStateMethod &src, const CCopasiContainer *pParent=NULL)
void	doJacobian (CMatrix< C_FLOAT64 > &jacobian, CMatrix< C_FLOAT64 > &jacobianX)
bool	elevateChildren ()
std::string	getMethodLog () const
C_FLOAT64	getStabilityResolution ()
virtual bool	initialize (const CSteadyStateProblem *pProblem)
virtual bool	isValidProblem (const CCopasiProblem *pProblem)
CSteadyStateMethod::ReturnCode	process (CState *pState, CMatrix< C_FLOAT64 > &jacobianX, CProcessReport *handler)
	~CSteadyStateMethod ()
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 void	printResult (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 ()

Static Public Member Functions
static CSteadyStateMethod *	createMethod (CCopasiMethod::SubType subType=CCopasiMethod::Newton)
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)

Protected Member Functions
bool	allPositive ()
void	calculateJacobianX (const C_FLOAT64 &oldMaxRate)
	CSteadyStateMethod (CCopasiMethod::SubType subType, const CCopasiContainer *pParent=NULL)
void	initializeParameter ()
bool	isEquilibrium (const C_FLOAT64 &resolution) const
virtual CSteadyStateMethod::ReturnCode	processInternal ()
virtual CSteadyStateMethod::ReturnCode	returnProcess (bool steadyStateFound)
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)

Protected Attributes
std::ostringstream	mMethodLog
C_FLOAT64 *	mpDerivationFactor
C_FLOAT64 *	mpDerivationResolution
CMatrix< C_FLOAT64 > *	mpJacobianX
CModel *	mpModel
CSteadyStateTask *	mpParentTask
const CSteadyStateProblem *	mpProblem
C_FLOAT64 *	mpSSResolution
CState *	mpSteadyState
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

Private Member Functions
	CSteadyStateMethod ()

Additional Inherited Members
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 }
Static Protected Attributes inherited from CCopasiObject
static CRenameHandler *	smpRenameHandler = NULL

Detailed Description

Definition at line 43 of file CSteadyStateMethod.h.

Member Enumeration Documentation

enum CSteadyStateMethod::ReturnCode

Enumerator
notFound
found
foundEquilibrium
foundNegative

Definition at line 46 of file CSteadyStateMethod.h.

  {
    notFound = 0,
    found,
    foundEquilibrium,
    foundNegative
  };

Constructor & Destructor Documentation

CSteadyStateMethod::CSteadyStateMethod ( )

private

Default constructor.

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

protected

Specific constructor.

Parameters

CCopasiMethod::SubType	subType
const	CCopasiContainer * pParent (default: NULL)

Default constructor.

Definition at line 58 of file CSteadyStateMethod.cpp.

References CONSTRUCTOR_TRACE, and initializeParameter().

                                                                        :
  CCopasiMethod(CCopasiTask::steadyState, subType, pParent),
  mpProblem(NULL)
{
  initializeParameter();
  CONSTRUCTOR_TRACE;
}

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

Copy constructor.

Parameters

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

Copy constructor.

Parameters

const CSteadyStateMethod &

src

Definition at line 71 of file CSteadyStateMethod.cpp.

References CONSTRUCTOR_TRACE, and initializeParameter().

                                                                        :
  CCopasiMethod(src, pParent),
  mpProblem(src.mpProblem)
{
  initializeParameter();
  CONSTRUCTOR_TRACE;
}

CSteadyStateMethod::~CSteadyStateMethod

(

)

Destructor.

Definition at line 83 of file CSteadyStateMethod.cpp.

References DESTRUCTOR_TRACE.

{DESTRUCTOR_TRACE;}

Member Function Documentation

bool CSteadyStateMethod::allPositive ( )

protected

Check whether all values make physically sence, i.e., volumes and particle number are positive

Returns

bool allPositive

Definition at line 190 of file CSteadyStateMethod.cpp.

References CStateTemplate::beginIndependent(), CState::beginIndependent(), C_FLOAT64, CState::endDependent(), CModel::getQuantity2NumberFactor(), CModel::getState(), CModel::getStateTemplate(), mpDerivationResolution, mpModel, and CModel::updateSimulatedValues().

Referenced by CNewtonMethod::doIntegration(), CNewtonMethod::doNewtonStep(), and returnProcess().

{
  // Assure that all values are updated.
  mpModel->updateSimulatedValues(true);

  CModelEntity *const* ppEntity = mpModel->getStateTemplate().beginIndependent();
  const C_FLOAT64 * pIt = mpModel->getState().beginIndependent();
  const C_FLOAT64 * pEnd = mpModel->getState().endDependent();

  // Skip Model quantities of type ODE
  for (; pIt != pEnd; ++pIt, ++ppEntity)
    if (dynamic_cast< const CCompartment *>(*ppEntity) != NULL ||
        dynamic_cast< const CMetab *>(*ppEntity) != NULL)
      break;

  // For all compartments of type ODE we check that the volume is positive
  for (; pIt != pEnd; ++pIt, ++ppEntity)
    {
      if (dynamic_cast< const CCompartment *>(*ppEntity) == NULL)
        break;

      if (*pIt < - *mpDerivationResolution)
        return false;
    }

  // We need to check that all metabolites have positive particle numbers
  // with respect to the given resolution.
  C_FLOAT64 ParticleResolution =
    - *mpDerivationResolution * mpModel->getQuantity2NumberFactor();

  for (; pIt != pEnd; ++pIt, ++ppEntity)
    {
      if (dynamic_cast< const CMetab *>(*ppEntity) == NULL)
        break;

      if (*pIt < ParticleResolution)
        return false;
    }

  // For all compartments of type ASSIGNMENT we check that the volume is positive
  for (; pIt != pEnd; ++pIt, ++ppEntity)
    {
      if (dynamic_cast< CCompartment *>(*ppEntity) == NULL)
        break;

      if (*pIt < - *mpDerivationResolution)
        return false;
    }

  return true;
}

void CSteadyStateMethod::calculateJacobianX ( const C_FLOAT64 &  oldMaxRate )

protected

Definition at line 285 of file CSteadyStateMethod.cpp.

References CModel::calculateJacobianX(), min, mpDerivationFactor, mpDerivationResolution, mpJacobianX, mpModel, mpSteadyState, CModel::setState(), and CModel::updateSimulatedValues().

Referenced by CNewtonMethod::doNewtonStep(), and CNewtonMethod::targetFunction().

{
  mpModel->setState(*mpSteadyState);
  mpModel->updateSimulatedValues(true);
  mpModel->calculateJacobianX(*mpJacobianX,
                              std::min(*mpDerivationFactor, oldMaxRate),
                              *mpDerivationResolution);
}

CSteadyStateMethod * CSteadyStateMethod::createMethod ( CCopasiMethod::SubType  subType = CCopasiMethod::Newton )

static

Create a trajectory method. Note: the returned object has to be released after use with delete

CSteadyStateMethod class. This class describes the interface to all steady state methods. The various method like Newton have to be derived from this class.

Created for COPASI by Stefan Hoops 2002

Definition at line 37 of file CSteadyStateMethod.cpp.

References fatalError, CCopasiMethod::Newton, and CCopasiMethod::unset.

Referenced by CSteadyStateTask::createMethod().

{
  CSteadyStateMethod * pMethod = NULL;

  switch (subType)
    {
      case unset:
      case Newton:
        pMethod = new CNewtonMethod();
        break;

      default:
        fatalError();
    }

  return pMethod;
}

void CSteadyStateMethod::doJacobian	(	CMatrix< C_FLOAT64 > &	jacobian,
		CMatrix< C_FLOAT64 > &	jacobianX
	)

calls the CModel methods to calculate the jacobians (at the steady state). This trivial method is implemented in the method because it may need to know about some method parameters

Definition at line 267 of file CSteadyStateMethod.cpp.

References CModel::calculateJacobian(), CModel::calculateJacobianX(), mpDerivationResolution, mpModel, mpSteadyState, CModel::setState(), and CModel::updateSimulatedValues().

Referenced by CSteadyStateTask::process().

{
  mpModel->setState(*mpSteadyState);
  mpModel->updateSimulatedValues(true);

  mpModel->calculateJacobian(jacobian, *mpDerivationResolution, *mpDerivationResolution);
  mpModel->calculateJacobianX(jacobianX, *mpDerivationResolution, *mpDerivationResolution);
}

bool CSteadyStateMethod::elevateChildren ( )

virtual

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

Returns

bool success

Reimplemented from CCopasiParameterGroup.

Definition at line 111 of file CSteadyStateMethod.cpp.

References initializeParameter().

{
  initializeParameter();
  return true;
}

std::string CSteadyStateMethod::getMethodLog

(

)

const

Definition at line 294 of file CSteadyStateMethod.cpp.

References mMethodLog.

Referenced by StateSubwidget::loadAll().

{
  return mMethodLog.str();
}

C_FLOAT64 CSteadyStateMethod::getStabilityResolution

(

)

returns the resolution for stability analysis

Definition at line 277 of file CSteadyStateMethod.cpp.

References C_FLOAT64, CCopasiParameter::getValue(), and CCopasiParameter::Value::pUDOUBLE.

Referenced by CSteadyStateTask::process().

{
  //C_FLOAT64* pTmp = (C_FLOAT64*)getValue("Stability Resolution").pUDOUBLE;
  C_FLOAT64* pTmp = (C_FLOAT64*)getValue("Resolution").pUDOUBLE;
  assert(pTmp);
  return *pTmp;
}

bool CSteadyStateMethod::initialize ( const CSteadyStateProblem *  pProblem )

virtual

Initialize the method must be called before process

Parameters

const

CSteadyStateProblem * pProblem

Returns

bool success

Reimplemented in CNewtonMethod.

Definition at line 259 of file CSteadyStateMethod.cpp.

References CCopasiProblem::getModel(), mpModel, and mpProblem.

Referenced by CNewtonMethod::initialize(), and CSteadyStateTask::initialize().

{
  mpProblem = pProblem;
  mpModel = mpProblem->getModel();

  return true;
}

void CSteadyStateMethod::initializeParameter ( )

protected

initialize parameters and handle parameters of old copasi files

Definition at line 86 of file CSteadyStateMethod.cpp.

References CCopasiParameterGroup::assertParameter(), C_FLOAT64, CCopasiParameterGroup::getParameter(), CCopasiParameter::getValue(), mpDerivationFactor, mpDerivationResolution, mpSSResolution, CCopasiParameter::Value::pUDOUBLE, CCopasiParameterGroup::removeParameter(), CCopasiParameterGroup::setValue(), and CCopasiParameter::UDOUBLE.

Referenced by CSteadyStateMethod(), CNewtonMethod::elevateChildren(), and elevateChildren().

{
  CCopasiParameter *pParm;

  assertParameter("Resolution", CCopasiParameter::UDOUBLE, (C_FLOAT64) 1.0e-009);
  mpSSResolution = (C_FLOAT64*)getValue("Resolution").pUDOUBLE;
  mpDerivationResolution = (C_FLOAT64*)getValue("Resolution").pUDOUBLE;

  assertParameter("Derivation Factor", CCopasiParameter::UDOUBLE, (C_FLOAT64) 1.0e-003);
  mpDerivationFactor = (C_FLOAT64*)getValue("Derivation Factor").pUDOUBLE;

  // Check whether we have a method with the old parameter names
  if ((pParm = getParameter("Newton.DerivationFactor")) != NULL)
    {
      setValue("Derivation Factor", *pParm->getValue().pUDOUBLE);
      removeParameter("Newton.DerivationFactor");
    }

  if ((pParm = getParameter("Newton.Resolution")) != NULL)
    {
      setValue("Resolution", *pParm->getValue().pUDOUBLE);
      removeParameter("Newton.Resolution");
    }
}

bool CSteadyStateMethod::isEquilibrium ( const C_FLOAT64 &  resolution ) const

protected

Check whether the steady state is chemical equilibrium

Parameters

const

C_FLOAT64 & resolution bool isEquilibrium

Definition at line 173 of file CSteadyStateMethod.cpp.

References CCopasiVector< T >::begin(), CCopasiVector< T >::end(), CCopasiProblem::getModel(), CModel::getReactions(), CModelEntity::getValue(), and mpProblem.

Referenced by returnProcess().

{
  CCopasiVectorNS < CReaction >::const_iterator it =  mpProblem->getModel()->getReactions().begin();
  CCopasiVectorNS < CReaction >::const_iterator end =  mpProblem->getModel()->getReactions().end();

  for (; it != end; ++it)
    {
      const CCompartment * pCompartment = (*it)->getLargestCompartment();

      if (pCompartment != NULL &&
          (*it)->getFlux() / pCompartment->getValue() > resolution)
        return false; //TODO: smallest or largest ?
    }

  return true;
}

bool CSteadyStateMethod::isValidProblem ( const CCopasiProblem *  pProblem )

virtual

Check if the method is suitable for this problem

Returns

bool suitability of the method

Reimplemented from CCopasiMethod.

Reimplemented in CNewtonMethod.

Definition at line 243 of file CSteadyStateMethod.cpp.

References CCopasiMessage::EXCEPTION, and CCopasiMethod::isValidProblem().

Referenced by CNewtonMethod::isValidProblem().

{
  if (!CCopasiMethod::isValidProblem(pProblem)) return false;

  const CSteadyStateProblem * pP = dynamic_cast<const CSteadyStateProblem *>(pProblem);

  if (!pP)
    {
      //not a TrajectoryProblem
      CCopasiMessage(CCopasiMessage::EXCEPTION, "Problem is not a steady state problem.");
      return false;
    }

  return true;
}

CSteadyStateMethod::ReturnCode CSteadyStateMethod::process	(	CState *	pState,
		CMatrix< C_FLOAT64 > &	jacobianX,
		CProcessReport *	handler
	)

This instructs the method to calculate a the steady state starting with the initialState given. The steady state is returned in the object pointed to by steadyState.

Parameters

CState	* steadyState
CMatrix<	C_FLOAT64 > & jacobianX
CProcessReport	* handler

Returns

CSteadyStateMethod::ReturnCode returnCode

This instructs the method to calculate a the steady state starting with the initialState given. The steady state is returned in the object pointed to by steadyState.

Parameters

CState	* steadyState
const	CState * initialState
C_FLOAT64	* jacobian
CEigen	* eigenValues

Returns

CSteadyStateMethod::ReturnCode returnCode

Definition at line 128 of file CSteadyStateMethod.cpp.

References CCopasiObject::getObjectParent(), CCopasiMethod::mpCallBack, mpJacobianX, mpParentTask, mpSteadyState, and processInternal().

Referenced by CSteadyStateTask::process().

{
  mpParentTask = dynamic_cast<CSteadyStateTask *>(getObjectParent());
  assert(mpParentTask);

  mpSteadyState = pState;
  mpJacobianX = & jacobianX;
  mpCallBack = handler;

  return processInternal();
}

CSteadyStateMethod::ReturnCode CSteadyStateMethod::processInternal ( )

protectedvirtual

This instructs the method to calculate a the steady state starting with the initialState given. The steady state is returned in the object pointed to by steadyState.

Returns

CSteadyStateMethod::ReturnCode returnCode

This instructs the method to calculate a the steady state

Returns

CSteadyStateMethod::ReturnCode returnCode

Reimplemented in CNewtonMethod.

Definition at line 170 of file CSteadyStateMethod.cpp.

References notFound.

Referenced by process().

{return CSteadyStateMethod::notFound;}

CSteadyStateMethod::ReturnCode CSteadyStateMethod::returnProcess ( bool  steadyStateFound )

protectedvirtual

This function has to be called at the return of any implementation of the protected function process()

Returns

CSteadyStateMethod::ReturnCode returnCode

This function has to be called at the return of any implementation of the protected function process

Parameters

bool	success
const	C_FLOAT64 & factor
const	C_FLOAT64 & resolution

Returns

CSteadyStateMethod::ReturnCode returnCode

Definition at line 151 of file CSteadyStateMethod.cpp.

References allPositive(), found, foundEquilibrium, foundNegative, isEquilibrium(), mpSSResolution, and notFound.

Referenced by CNewtonMethod::processInternal().

{
  if (!steadyStateFound)
    return CSteadyStateMethod::notFound;

  if (!allPositive())
    return CSteadyStateMethod::foundNegative;

  if (isEquilibrium(*mpSSResolution))
    return CSteadyStateMethod::foundEquilibrium;

  return CSteadyStateMethod::found;
}

Member Data Documentation

std::ostringstream CSteadyStateMethod::mMethodLog

protected

Definition at line 95 of file CSteadyStateMethod.h.

Referenced by CNewtonMethod::doIntegration(), CNewtonMethod::doNewtonStep(), getMethodLog(), CNewtonMethod::processInternal(), and CNewtonMethod::processNewton().

C_FLOAT64* CSteadyStateMethod::mpDerivationFactor

protected

The factor for numerical derivation

Definition at line 88 of file CSteadyStateMethod.h.

Referenced by calculateJacobianX(), and initializeParameter().

C_FLOAT64* CSteadyStateMethod::mpDerivationResolution

protected

The resolution of the variable of numerical derivation

Definition at line 93 of file CSteadyStateMethod.h.

Referenced by allPositive(), calculateJacobianX(), doJacobian(), and initializeParameter().

CMatrix< C_FLOAT64 >* CSteadyStateMethod::mpJacobianX

protected

The jacobian of the steadystate

Definition at line 78 of file CSteadyStateMethod.h.

Referenced by calculateJacobianX(), process(), and CNewtonMethod::solveJacobianXeqB().

CModel* CSteadyStateMethod::mpModel

protected

A pointer to the model.

Definition at line 63 of file CSteadyStateMethod.h.

Referenced by allPositive(), CNewtonMethod::calculateDerivativesX(), calculateJacobianX(), CNewtonMethod::doIntegration(), doJacobian(), CNewtonMethod::initialize(), initialize(), CNewtonMethod::solveJacobianXeqB(), and CNewtonMethod::targetFunction().

CSteadyStateTask* CSteadyStateMethod::mpParentTask

protected

A pointer to the task.

Definition at line 68 of file CSteadyStateMethod.h.

Referenced by process().

const CSteadyStateProblem* CSteadyStateMethod::mpProblem

protected

A pointer to the problem.

Definition at line 58 of file CSteadyStateMethod.h.

Referenced by CNewtonMethod::initialize(), initialize(), and isEquilibrium().

C_FLOAT64* CSteadyStateMethod::mpSSResolution

protected

The concentration rate that is considered zero

Definition at line 83 of file CSteadyStateMethod.h.

Referenced by CNewtonMethod::initialize(), initializeParameter(), CNewtonMethod::isSteadyState(), returnProcess(), and CNewtonMethod::targetFunction().

CState* CSteadyStateMethod::mpSteadyState

protected

A pointer to the steady state

Definition at line 73 of file CSteadyStateMethod.h.

Referenced by CNewtonMethod::calculateDerivativesX(), calculateJacobianX(), CNewtonMethod::containsNaN(), CNewtonMethod::doIntegration(), doJacobian(), process(), CNewtonMethod::processInternal(), CNewtonMethod::solveJacobianXeqB(), and CNewtonMethod::targetFunction().

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

• CSteadyStateMethod.h
• CSteadyStateMethod.cpp