#include <CStochDirectMethod.h>

Inheritance diagram for CStochDirectMethod:

Collaboration diagram for CStochDirectMethod:

Classes
class	CReactionDependencies

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

virtual bool	elevateChildren ()

virtual bool	isValidProblem (const CCopasiProblem *pProblem)

virtual void	start (const CState *initialState)

virtual Status	step (const double &deltaT)

	~CStochDirectMethod ()

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

const CVector< C_INT > &	getRoots () const

void	setCurrentState (CState *currentState)

void	setProblem (CTrajectoryProblem *problem)

virtual void	stateChanged ()

	~CTrajectoryMethod ()

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 ()

Protected Member Functions
void	calculateAmu (const size_t &index)

	CStochDirectMethod (const CCopasiContainer *pParent=NULL)

C_FLOAT64	doSingleStep (const C_FLOAT64 &curTime, const C_FLOAT64 &endTime)

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

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
C_FLOAT64	mA0

CVector< C_FLOAT64 >	mAmu

bool	mDoCorrection

unsigned C_INT32	mMaxSteps

bool	mMaxStepsReached

CState	mMethodState

size_t	mNextReactionIndex

C_FLOAT64	mNextReactionTime

size_t	mNumReactions

CModel *	mpModel

CRandom *	mpRandomGenerator

std::vector < CReactionDependencies >	mReactionDependencies

Protected Attributes inherited from CTrajectoryMethod
CState *	mpCurrentState

CTrajectoryProblem *	mpProblem

CVector< C_INT >	mRoots

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
void	initializeParameter ()

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

Additional Inherited Members
Public Types inherited from CTrajectoryMethod
enum	Status { FAILURE = -1, NORMAL = 0, ROOT = 1 }

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 CTrajectoryMethod
static CTrajectoryMethod *	createMethod (CCopasiMethod::SubType subType=CCopasiMethod::deterministic)

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 }

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

Detailed Description

Definition at line 39 of file CStochDirectMethod.h.

Constructor & Destructor Documentation

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

protected

Default constructor.

Parameters

const CCopasiContainer * pParent (default: NULL)

Definition at line 86 of file CStochDirectMethod.cpp.

References initializeParameter().

                                                                       :
   CTrajectoryMethod(CCopasiMethod::directMethod, pParent),
   mpRandomGenerator(CRandom::createGenerator(CRandom::mt19937)),
   mpModel(NULL),
   mNumReactions(0),
   mMaxSteps(1000000),
   mNextReactionTime(0.0),
   mNextReactionIndex(C_INVALID_INDEX),
   mDoCorrection(true),
   mAmu(0),
   mA0(0.0),
   mMethodState(),
   mReactionDependencies(0),
   mMaxStepsReached(false)
 {
   initializeParameter();
 }

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

Copy constructor.

Parameters

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

Definition at line 104 of file CStochDirectMethod.cpp.

References initializeParameter().

                                                                         :
   CTrajectoryMethod(src, pParent),
   mpRandomGenerator(CRandom::createGenerator(CRandom::mt19937)),
   mpModel(src.mpModel),
   mNumReactions(src.mNumReactions),
   mMaxSteps(src.mMaxSteps),
   mNextReactionTime(src.mNextReactionTime),
   mNextReactionIndex(src.mNextReactionIndex),
   mDoCorrection(src.mDoCorrection),
   mAmu(src.mAmu),
   mA0(src.mA0),
   mMethodState(src.mMethodState),
   mReactionDependencies(src.mReactionDependencies),
   mMaxStepsReached(src.mMaxStepsReached)
 {
   initializeParameter();
 }

CStochDirectMethod::~CStochDirectMethod ( )

Destructor.

Definition at line 123 of file CStochDirectMethod.cpp.

References mpRandomGenerator, and pdelete.

 {
   pdelete(mpRandomGenerator);
 }

Member Function Documentation

void CStochDirectMethod::calculateAmu ( const size_t & index )

protected

Calculate the propensity of the indexed reaction

Parameters

const size_t & index

Definition at line 522 of file CStochDirectMethod.cpp.

References CVectorCore< CType >::array(), C_FLOAT64, mAmu, mDoCorrection, CStochDirectMethod::CReactionDependencies::mMethodSubstrates, CStochDirectMethod::CReactionDependencies::mModelSubstrates, CStochDirectMethod::CReactionDependencies::mpParticleFlux, mReactionDependencies, CStochDirectMethod::CReactionDependencies::mSubstrateMultiplier, and CVectorCore< CType >::size().

Referenced by doSingleStep(), and start().

 {
   CReactionDependencies & Dependencies = mReactionDependencies[index];
   C_FLOAT64 & Amu = mAmu[index];
 
   Amu = *Dependencies.mpParticleFlux;
 
   if (Amu < 0.0)
     {
       // TODO CRITICAL Create a warning message
       Amu = 0.0;
     }
 
   if (!mDoCorrection)
     {
       return;
     }
 
   C_FLOAT64 SubstrateMultiplier = 1.0;
   C_FLOAT64 SubstrateDevisor = 1.0;
   C_FLOAT64 Multiplicity;
   C_FLOAT64 LowerBound;
   C_FLOAT64 Number;
 
   bool ApplyCorrection = false;
 
   C_FLOAT64 * pMultiplier = Dependencies.mSubstrateMultiplier.array();
   C_FLOAT64 * endMultiplier = pMultiplier + Dependencies.mSubstrateMultiplier.size();
   C_FLOAT64 ** ppLocalSubstrate = Dependencies.mMethodSubstrates.array();
   C_FLOAT64 ** ppModelSubstrate = Dependencies.mModelSubstrates.array();
 
   for (; pMultiplier != endMultiplier; ++pMultiplier, ++ppLocalSubstrate, ++ppModelSubstrate)
     {
       Multiplicity = *pMultiplier;
 
       // TODO We should check the error introduced through rounding.
       **ppLocalSubstrate = floor(**ppModelSubstrate + 0.5);
 
       if (Multiplicity > 1.01)
         {
           ApplyCorrection = true;
 
           Number = **ppLocalSubstrate;
 
           LowerBound = Number - Multiplicity;
           SubstrateDevisor *= pow(Number, Multiplicity - 1.0);  //optimization
           Number -= 1.0;
 
           while (Number > LowerBound)
             {
               SubstrateMultiplier *= Number;
               Number -= 1.0;
             }
         }
     }
 
   // at least one substrate particle number is zero
   if (SubstrateMultiplier < 0.5 || SubstrateDevisor < 0.5)
     {
       Amu = 0.0;
       return;
     }
 
   // rate_factor is the rate function divided by substrate_factor.
   // It would be more efficient if this was generated directly, since in effect we
   // are multiplying and then dividing by the same thing (substrate_factor)!
   //C_FLOAT64 rate_factor = mpModel->getReactions()[index]->calculateParticleFlux();
   if (ApplyCorrection)
     {
       Amu *= SubstrateMultiplier / SubstrateDevisor;
     }
 
   return;
 }

C_FLOAT64 CStochDirectMethod::doSingleStep	(	const C_FLOAT64 &	curTime,
		const C_FLOAT64 &	endTime
	)

protected

Fire the next reaction if it fire before the endTime

Parameters

const	C_FLOAT64 & curTime
const	C_FLOAT64 & endTime

Returns: C_FLOAT64 timeAfterStep

Definition at line 429 of file CStochDirectMethod.cpp.

References CVectorCore< CType >::array(), C_FLOAT64, C_INVALID_INDEX, calculateAmu(), CCopasiMessage::EXCEPTION, CRandom::getRandomOO(), mA0, mAmu, CStochDirectMethod::CReactionDependencies::mCalculations, MCTrajectoryMethod, CStochDirectMethod::CReactionDependencies::mDependentReactions, CStochDirectMethod::CReactionDependencies::mMethodSpecies, CStochDirectMethod::CReactionDependencies::mModelSpecies, mNextReactionIndex, mNextReactionTime, mNumReactions, mpModel, mpRandomGenerator, mReactionDependencies, CStochDirectMethod::CReactionDependencies::mSpeciesMultiplier, CModel::setTime(), and CVectorCore< CType >::size().

Referenced by step().

 {
   if (mNextReactionIndex == C_INVALID_INDEX)
     {
       if (mA0 == 0)
         {
           return endTime - curTime;
         }
 
       // We need to throw an exception if mA0 is NaN
       if (isnan(mA0))
         {
           CCopasiMessage(CCopasiMessage::EXCEPTION, MCTrajectoryMethod + 27);
         }
 
       mNextReactionTime = curTime - log(mpRandomGenerator->getRandomOO()) / mA0;
 
       // We are sure that we have at least 1 reaction
       mNextReactionIndex = 0;
 
       C_FLOAT64 sum = 0.0;
       C_FLOAT64 rand = mpRandomGenerator->getRandomOO() * mA0;
 
       C_FLOAT64 * pAmu = mAmu.array();
       C_FLOAT64 * endAmu = pAmu + mNumReactions;
 
       for (; (sum < rand) && (pAmu != endAmu); ++pAmu, ++mNextReactionIndex)
         {
           sum += *pAmu;
         }
 
       mNextReactionIndex--;
     }
 
   if (mNextReactionTime >= endTime)
     {
       return endTime - curTime;
     }
 
   // Update the model time (for explicitly time dependent models)
   mpModel->setTime(mNextReactionTime);
 
   CReactionDependencies & Dependencies = mReactionDependencies[mNextReactionIndex];
 
   // Update the method internal and model species numbers
   C_FLOAT64 ** ppModelSpecies = Dependencies.mModelSpecies.array();
   C_FLOAT64 ** ppLocalSpecies = Dependencies.mMethodSpecies.array();
   C_FLOAT64 * pMultiplier = Dependencies.mSpeciesMultiplier.array();
   C_FLOAT64 * endMultiplier = pMultiplier + Dependencies.mSpeciesMultiplier.size();
 
   for (; pMultiplier != endMultiplier; ++pMultiplier, ++ppLocalSpecies, ++ppModelSpecies)
     {
       **ppLocalSpecies += *pMultiplier;
       **ppModelSpecies = **ppLocalSpecies;
     }
 
   // Calculate all values which depend on the firing reaction
   std::vector< Refresh * >::const_iterator itCalcualtion =  Dependencies.mCalculations.begin();
   std::vector< Refresh * >::const_iterator endCalcualtion =  Dependencies.mCalculations.end();
 
   while (itCalcualtion != endCalcualtion)
     {
       (**itCalcualtion++)();
     }
 
   // We do not need to update the the method state since the only independent state
   // values are species of type reaction which are all controlled by the method.
 
   // calculate the propensities which depend on the firing reaction
   size_t * pDependentReaction = Dependencies.mDependentReactions.array();
   size_t * endDependentReactions = pDependentReaction + Dependencies.mDependentReactions.size();
 
   for (; pDependentReaction != endDependentReactions; ++pDependentReaction)
     {
       calculateAmu(*pDependentReaction);
     }
 
   // calculate the total propensity
   C_FLOAT64 * pAmu = mAmu.array();
   C_FLOAT64 * endAmu = pAmu + mNumReactions;
 
   mA0 = 0.0;
 
   for (; pAmu != endAmu; ++pAmu)
     {
       mA0 += *pAmu;
     }
 
   mNextReactionIndex = C_INVALID_INDEX;
 
   return mNextReactionTime - curTime;
 }

bool CStochDirectMethod::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 135 of file CStochDirectMethod.cpp.

References initializeParameter().

 {
   initializeParameter();
   return true;
 }

void CStochDirectMethod::initializeParameter ( )

private

Initialize the method parameter

Definition at line 128 of file CStochDirectMethod.cpp.

References CCopasiParameterGroup::assertParameter(), CCopasiParameter::BOOL, C_INT32, CCopasiParameter::INT, and CCopasiParameter::UINT.

Referenced by CStochDirectMethod(), and elevateChildren().

 {
   assertParameter("Max Internal Steps", CCopasiParameter::INT, (C_INT32) 1000000);
   assertParameter("Use Random Seed", CCopasiParameter::BOOL, false);
   assertParameter("Random Seed", CCopasiParameter::UINT, (unsigned C_INT32) 1);
 }

bool CStochDirectMethod::isValidProblem ( const CCopasiProblem * pProblem )

virtual

Check if the method is suitable for this problem

Returns: bool suitability of the method

Reimplemented from CTrajectoryMethod.

Definition at line 351 of file CStochDirectMethod.cpp.

References CStateTemplate::beginIndependent(), CStateTemplate::endIndependent(), CCopasiMessage::ERROR, CTrajectoryProblem::getDuration(), CModel::getEvents(), CCopasiProblem::getModel(), CModel::getStateTemplate(), CModel::getTotSteps(), CCopasiParameter::getValue(), CTrajectoryMethod::isValidProblem(), MCTrajectoryMethod, CModelEntity::ODE, CCopasiParameter::Value::pINT, CCopasiVector< T >::size(), and CModel::suitableForStochasticSimulation().

 {
   if (!CTrajectoryMethod::isValidProblem(pProblem)) return false;
 
   const CTrajectoryProblem * pTP = dynamic_cast<const CTrajectoryProblem *>(pProblem);
 
   if (pTP->getDuration() < 0.0)
     {
       //back integration not possible
       CCopasiMessage(CCopasiMessage::ERROR, MCTrajectoryMethod + 9);
       return false;
     }
 
   if (pTP->getModel()->getTotSteps() < 1)
     {
       //at least one reaction necessary
       CCopasiMessage(CCopasiMessage::ERROR, MCTrajectoryMethod + 17);
       return false;
     }
 
   // check for ODEs
   const CStateTemplate & StateTemplate = pTP->getModel()->getStateTemplate();
   CModelEntity *const* ppEntity = StateTemplate.beginIndependent();
   CModelEntity *const* ppEntityEnd = StateTemplate.endIndependent();
 
   for (; ppEntity != ppEntityEnd; ++ppEntity)
     {
       if ((*ppEntity)->getStatus() == CModelEntity::ODE)
         {
           if (dynamic_cast<const CModelValue *>(*ppEntity) != NULL)
             {
               // global quantity ode rule found
               CCopasiMessage(CCopasiMessage::ERROR, MCTrajectoryMethod + 18);
               return false;
             }
           else if (dynamic_cast<const CCompartment *>(*ppEntity) != NULL)
             {
               // compartment ode rule found
               CCopasiMessage(CCopasiMessage::ERROR, MCTrajectoryMethod + 21);
               return false;
             }
           else
             {
               // species ode rule found
               CCopasiMessage(CCopasiMessage::ERROR, MCTrajectoryMethod + 20);
               return false;
             }
         }
     }
 
   //TODO: rewrite CModel::suitableForStochasticSimulation() to use
   //      CCopasiMessage
   std::string message = pTP->getModel()->suitableForStochasticSimulation();
 
   if (message != "")
     {
       //model not suitable, message describes the problem
       CCopasiMessage(CCopasiMessage::ERROR, message.c_str());
       return false;
     }
 
   if (* getValue("Max Internal Steps").pINT <= 0)
     {
       //max steps should be at least 1
       CCopasiMessage(CCopasiMessage::ERROR, MCTrajectoryMethod + 15);
       return false;
     }
 
   //events are not supported at the moment
   if (pTP->getModel()->getEvents().size() > 0)
     {
       CCopasiMessage(CCopasiMessage::ERROR, MCTrajectoryMethod + 23);
       return false;
     }
 
   return true;
 }

void CStochDirectMethod::start ( const CState * initialState )

virtual

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

Parameters

const CState * initialState

Reimplemented from CTrajectoryMethod.

Definition at line 166 of file CStochDirectMethod.cpp.

References CCopasiVector< T >::begin(), CStateTemplate::beginIndependent(), CState::beginIndependent(), CCopasiObject::buildUpdateSequence(), C_FLOAT64, C_INT32, C_INVALID_INDEX, calculateAmu(), CModel::deterministic, CCopasiVector< T >::end(), CStateTemplate::endFixed(), CStateTemplate::getIndex(), CCopasiProblem::getModel(), CModel::getModelType(), CModel::getReactions(), CModel::getState(), CModel::getStateTemplate(), CModelEntity::getStatus(), CState::getTime(), CCopasiParameter::getValue(), CCopasiObject::getValuePointer(), CModelEntity::getValueReference(), CRandom::initialize(), mA0, mAmu, mDoCorrection, mMaxSteps, mMaxStepsReached, mMethodState, mNextReactionIndex, mNextReactionTime, mNumReactions, CTrajectoryMethod::mpCurrentState, mpModel, CTrajectoryMethod::mpProblem, mpRandomGenerator, mReactionDependencies, CCopasiParameter::Value::pBOOL, CCopasiParameter::Value::pINT, CCopasiParameter::Value::pUINT, CModelEntity::REACTIONS, CVector< CType >::resize(), CModel::setState(), CCopasiVector< T >::size(), and CModel::updateSimulatedValues().

 {
   /* get configuration data */
   mMaxSteps = * getValue("Max Internal Steps").pINT;
 
   bool useRandomSeed = * getValue("Use Random Seed").pBOOL;
   unsigned C_INT32 randomSeed = * getValue("Random Seed").pUINT;
 
   if (useRandomSeed) mpRandomGenerator->initialize(randomSeed);
 
   //mpCurrentState is initialized. This state is not used internally in the
   //stochastic solver, but it is used for returning the result after each step.
   *mpCurrentState = *initialState;
 
   mpModel = mpProblem->getModel();
   assert(mpModel);
 
   if (mpModel->getModelType() == CModel::deterministic)
     mDoCorrection = true;
   else
     mDoCorrection = false;
 
   //initialize the vector of ints that contains the particle numbers
   //for the discrete simulation. This also floors all particle numbers in the model.
 
   mNumReactions = mpModel->getReactions().size();
 
   mReactionDependencies.resize(mNumReactions);
   mAmu.resize(mNumReactions);
   mAmu = 0.0;
 
   // Create a local copy of the state where the particle number are rounded to integers
   mMethodState = mpModel->getState();
 
   const CStateTemplate & StateTemplate = mpModel->getStateTemplate();
 
   CModelEntity *const* ppEntity = StateTemplate.beginIndependent();
   CModelEntity *const* endEntity = StateTemplate.endFixed();
   C_FLOAT64 * pValue = mMethodState.beginIndependent();
 
   for (; ppEntity != endEntity; ++ppEntity, ++pValue)
     {
       if (dynamic_cast< const CMetab * >(*ppEntity) != NULL)
         {
           *pValue = floor(*pValue + 0.5);
         }
     }
 
   // Update the model state so that the species are all represented by integers.
   mpModel->setState(mMethodState);
   mpModel->updateSimulatedValues(false); //for assignments
 
   // TODO CRITICAL Handle species of type ASSIGNMENT.
   // These need to be checked whether they are sufficiently close to an integer
 
   C_FLOAT64 * pMethodStateValue = mMethodState.beginIndependent() - 1;
 
   // Build the reaction dependencies
   size_t NumReactions = 0;
 
   CCopasiVector< CReaction >::const_iterator it = mpModel->getReactions().begin();
   CCopasiVector< CReaction >::const_iterator end = mpModel->getReactions().end();
   std::vector< CReactionDependencies >::iterator itDependencies = mReactionDependencies.begin();
 
   for (; it  != end; ++it)
     {
       const CCopasiVector<CChemEqElement> & Balances = (*it)->getChemEq().getBalances();
       const CCopasiVector<CChemEqElement> & Substrates = (*it)->getChemEq().getSubstrates();
 
       // This reactions does not change anything we ignore it
       if (Balances.size() == 0 && Substrates.size() == 0)
         {
           continue;
         }
 
       itDependencies->mpParticleFlux = (C_FLOAT64 *)(*it)->getParticleFluxReference()->getValuePointer();
 
       itDependencies->mSpeciesMultiplier.resize(Balances.size());
       itDependencies->mMethodSpecies.resize(Balances.size());
       itDependencies->mModelSpecies.resize(Balances.size());
 
       std::set< const CCopasiObject * > changed;
 
       // The time is always updated
       changed.insert(mpModel->getValueReference());
 
       CCopasiVector< CChemEqElement >::const_iterator itBalance = Balances.begin();
       CCopasiVector< CChemEqElement >::const_iterator endBalance = Balances.end();
 
       size_t Index = 0;
 
       for (; itBalance != endBalance; ++itBalance)
         {
           const CMetab * pMetab = (*itBalance)->getMetabolite();
 
           if (pMetab->getStatus() == CModelEntity::REACTIONS)
             {
               itDependencies->mSpeciesMultiplier[Index] = floor((*itBalance)->getMultiplicity() + 0.5);
               itDependencies->mMethodSpecies[Index] = pMethodStateValue + StateTemplate.getIndex(pMetab);
               itDependencies->mModelSpecies[Index] = (C_FLOAT64 *) pMetab->getValueReference()->getValuePointer();
 
               changed.insert(pMetab->getValueReference());
 
               Index++;
             }
         }
 
       // Correct allocation for metabolites which are not determined by reactions
       itDependencies->mSpeciesMultiplier.resize(Index, true);
       itDependencies->mMethodSpecies.resize(Index, true);
       itDependencies->mModelSpecies.resize(Index, true);
 
       itDependencies->mSubstrateMultiplier.resize(Substrates.size());
       itDependencies->mMethodSubstrates.resize(Substrates.size());
       itDependencies->mModelSubstrates.resize(Substrates.size());
 
       CCopasiVector< CChemEqElement >::const_iterator itSubstrate = Substrates.begin();
       CCopasiVector< CChemEqElement >::const_iterator endSubstrate = Substrates.end();
 
       Index = 0;
 
       for (; itSubstrate != endSubstrate; ++itSubstrate, ++Index)
         {
           const CMetab * pMetab = (*itSubstrate)->getMetabolite();
 
           itDependencies->mSubstrateMultiplier[Index] = floor((*itSubstrate)->getMultiplicity() + 0.5);
           itDependencies->mMethodSubstrates[Index] = pMethodStateValue + StateTemplate.getIndex(pMetab);
           itDependencies->mModelSubstrates[Index] = (C_FLOAT64 *) pMetab->getValueReference()->getValuePointer();
         }
 
       std::set< const CCopasiObject * > dependend;
 
       CCopasiVector< CReaction >::const_iterator itReaction = mpModel->getReactions().begin();
       itDependencies->mDependentReactions.resize(mNumReactions);
 
       Index = 0;
       size_t Count = 0;
 
       for (; itReaction != end; ++itReaction, ++Index)
         {
           if ((*itReaction)->getParticleFluxReference()->dependsOn(changed))
             {
               dependend.insert((*itReaction)->getParticleFluxReference());
               itDependencies->mDependentReactions[Count] = Index;
 
               Count++;
             }
         }
 
       itDependencies->mDependentReactions.resize(Count, true);
 
       itDependencies->mCalculations = CCopasiObject::buildUpdateSequence(dependend, changed);
 
       ++itDependencies;
       ++NumReactions;
     }
 
   mNumReactions = NumReactions;
 
   mReactionDependencies.resize(mNumReactions);
   mAmu.resize(mNumReactions, true);
 
   size_t i;
 
   for (i = 0; i < mNumReactions; i++)
     {
       calculateAmu(i);
     }
 
   mA0 = 0;
 
   for (i = 0; i < mNumReactions; i++)
     {
       mA0 += mAmu[i];
     }
 
   mMaxStepsReached = false;
 
   mNextReactionTime = mpCurrentState->getTime();
   mNextReactionIndex = C_INVALID_INDEX;
 
   return;
 }

CTrajectoryMethod::Status CStochDirectMethod::step ( const double & deltaT )

virtual

This instructs the method to calculate a time step of deltaT starting with the current state, i.e., the result of the previous step. The new state (after deltaT) is expected in the current state. The return value is the actual timestep taken.

Parameters

const double & deltaT

Returns: Status status

Reimplemented from CTrajectoryMethod.

Definition at line 141 of file CStochDirectMethod.cpp.

References C_FLOAT64, doSingleStep(), CCopasiMessage::EXCEPTION, CCopasiProblem::getModel(), CModel::getState(), CState::getTime(), MCTrajectoryMethod, mMaxSteps, mMethodState, CTrajectoryMethod::mpCurrentState, CTrajectoryMethod::mpProblem, CTrajectoryMethod::NORMAL, and CState::setTime().

 {
   // do several steps
   C_FLOAT64 Time = mpCurrentState->getTime();
   C_FLOAT64 EndTime = Time + deltaT;
 
   size_t Steps = 0;
 
   while (Time < EndTime)
     {
       mMethodState.setTime(Time);
       Time += doSingleStep(Time, EndTime);
 
       if (++Steps > mMaxSteps)
         {
           CCopasiMessage(CCopasiMessage::EXCEPTION, MCTrajectoryMethod + 12);
         }
     }
 
   *mpCurrentState = mpProblem->getModel()->getState();
   mpCurrentState->setTime(Time);
 
   return NORMAL;
 }

Friends And Related Function Documentation

CTrajectoryMethod* CTrajectoryMethod::createMethod ( CCopasiMethod::SubType subType )

friend

Member Data Documentation

C_FLOAT64 CStochDirectMethod::mA0

protected

Total propensity (sum over mAmu[i])

Definition at line 237 of file CStochDirectMethod.h.

Referenced by doSingleStep(), and start().

CVector< C_FLOAT64 > CStochDirectMethod::mAmu

protected

A vector of reaction propensities

Definition at line 232 of file CStochDirectMethod.h.

Referenced by calculateAmu(), doSingleStep(), and start().

bool CStochDirectMethod::mDoCorrection

protected

A boolean flag indicating whether correction for higher order reactions need to be applied

Definition at line 227 of file CStochDirectMethod.h.

Referenced by calculateAmu(), and start().

unsigned C_INT32 CStochDirectMethod::mMaxSteps

protected

max number of single stochastic steps to do in one step()

Definition at line 212 of file CStochDirectMethod.h.

Referenced by start(), and step().

bool CStochDirectMethod::mMaxStepsReached

protected

A boolean flag indicating whether the maximum steps have been reached. This is used to avoid multiple messages.

Definition at line 253 of file CStochDirectMethod.h.

Referenced by start().

CState CStochDirectMethod::mMethodState

protected

The method internal state which contains particle rounded particle numbers.

Definition at line 242 of file CStochDirectMethod.h.

Referenced by start(), and step().

size_t CStochDirectMethod::mNextReactionIndex

protected

The index of the next reaction which fires

Definition at line 222 of file CStochDirectMethod.h.

Referenced by doSingleStep(), and start().

C_FLOAT64 CStochDirectMethod::mNextReactionTime

protected

The time the next reaction fires

Definition at line 217 of file CStochDirectMethod.h.

Referenced by doSingleStep(), and start().

size_t CStochDirectMethod::mNumReactions

protected

The particle and reaction numbers

Definition at line 207 of file CStochDirectMethod.h.

Referenced by doSingleStep(), and start().

CModel* CStochDirectMethod::mpModel

protected

A pointer to the instance of CModel being used.

Definition at line 202 of file CStochDirectMethod.h.

Referenced by doSingleStep(), and start().

CRandom* CStochDirectMethod::mpRandomGenerator

protected

The random number generator

Definition at line 197 of file CStochDirectMethod.h.

Referenced by doSingleStep(), start(), and ~CStochDirectMethod().

std::vector< CReactionDependencies > CStochDirectMethod::mReactionDependencies

protected

A vector containing dependency information to minimize the required updates.

Definition at line 247 of file CStochDirectMethod.h.

Referenced by calculateAmu(), doSingleStep(), and start().

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

Classes

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation