#include <CStochNextReactionMethod.h>

Inheritance diagram for CStochNextReactionMethod:

Collaboration diagram for CStochNextReactionMethod:

Public Member Functions
	CStochNextReactionMethod ()

C_FLOAT64	doSingleStep (C_FLOAT64 time, C_FLOAT64 endTime)

Public Member Functions inherited from CStochMethod
	CStochMethod (const CStochMethod &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)

	~CStochMethod ()

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 ()

Private Member Functions
void	initMethod (C_FLOAT64 start_time)

void	setupPriorityQueue (C_FLOAT64 start_time=0)

void	updatePriorityQueue (size_t reaction_index, C_FLOAT64 time)

Private Attributes
CIndexedPriorityQueue	mPQ

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 }

Protected Member Functions inherited from CStochMethod
C_INT32	calculateAmu (size_t reaction_index)

	CStochMethod (const CCopasiContainer *pParent=NULL)

size_t	generateReactionIndex ()

C_FLOAT64	generateReactionTime ()

C_FLOAT64	generateReactionTime (size_t reaction_index)

void	setupDependencyGraphAndBalances ()

C_INT32	updatePropensities ()

C_INT32	updateSystemState (size_t reaction_index, const C_FLOAT64 &time)

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)

Static Protected Member Functions inherited from CStochMethod
static bool	modelHasAssignments (const CModel *pModel)

Protected Attributes inherited from CStochMethod
C_FLOAT64	mA0

std::vector< C_FLOAT64 >	mAmu

std::vector< C_FLOAT64 >	mAmuOld

CDependencyGraph	mDG

bool	mDoCorrection

size_t	mFirstMetabIndex

bool	mHasAssignments

std::vector< std::vector < CStochBalance > >	mLocalBalances

std::vector< std::vector < CStochBalance > >	mLocalSubstrates

std::vector< C_INT64 >	mNumbers

size_t	mNumReactions

CModel *	mpModel

CRandom *	mpRandomGenerator

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

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

Detailed Description

Definition at line 29 of file CStochNextReactionMethod.h.

Constructor & Destructor Documentation

CStochNextReactionMethod::CStochNextReactionMethod ( )

Default constructor

Definition at line 23 of file CStochNextReactionMethod.cpp.

24 : CStochMethod()

25 {}

CStochMethod::CStochMethod

CStochMethod(const CCopasiContainer *pParent=NULL)

Definition: CStochMethod.cpp:48

Member Function Documentation

C_FLOAT64 CStochNextReactionMethod::doSingleStep	(	C_FLOAT64	time,
		C_FLOAT64	endTime
	)

virtual

Do one iteration of the simulation

Returns: Current simulation time or -1 if error.

Implements CStochMethod.

Definition at line 32 of file CStochNextReactionMethod.cpp.

References C_FLOAT64, CCopasiMessage::EXCEPTION, MCTrajectoryMethod, mPQ, CIndexedPriorityQueue::topIndex(), CIndexedPriorityQueue::topKey(), updatePriorityQueue(), and CStochMethod::updateSystemState().

 {
   C_FLOAT64 steptime = mPQ.topKey();
 
   // We need to throw an exception if mA0 is NaN
   if (isnan(steptime))
     {
       CCopasiMessage(CCopasiMessage::EXCEPTION, MCTrajectoryMethod + 27);
     }
 
   if (steptime >= endTime)
     {
       return endTime;
     }
   else
     {
       size_t reaction_index = mPQ.topIndex();
       updateSystemState(reaction_index, steptime);
       updatePriorityQueue(reaction_index, steptime);
       //printDebugInfo();
       return steptime;
     }
 }

void CStochNextReactionMethod::initMethod ( C_FLOAT64 start_time )

privatevirtual

Initialization.

Implements CStochMethod.

Definition at line 27 of file CStochNextReactionMethod.cpp.

References setupPriorityQueue().

 {
   setupPriorityQueue(start_time);
 }

void CStochNextReactionMethod::setupPriorityQueue ( C_FLOAT64 start_time = 0 )

private

print internal information (for debugging) Set up the priority queue.

Parameters

start_time The time at which the simulation starts.

Definition at line 61 of file CStochNextReactionMethod.cpp.

References CIndexedPriorityQueue::buildHeap(), C_FLOAT64, CIndexedPriorityQueue::clear(), CStochMethod::generateReactionTime(), CModel::getReactions(), CStochMethod::mpModel, mPQ, CIndexedPriorityQueue::pushPair(), and CCopasiVector< T >::size().

Referenced by initMethod().

 {
   C_FLOAT64 time;
 
   mPQ.clear();
 
   for (size_t i = 0; i < mpModel->getReactions().size(); i++)
     {
       time = start_time + generateReactionTime(i);
       mPQ.pushPair(i, time);
     }
 
   mPQ.buildHeap();
 }

void CStochNextReactionMethod::updatePriorityQueue	(	size_t	reaction_index,
		C_FLOAT64	time
	)

private

Update the priority queue

Definition at line 76 of file CStochNextReactionMethod.cpp.

References C_FLOAT64, CStochMethod::generateReactionTime(), CDependencyGraph::getDependents(), CIndexedPriorityQueue::getKey(), CStochMethod::mAmu, CStochMethod::mAmuOld, CStochMethod::mDG, CStochMethod::mHasAssignments, CStochMethod::mNumReactions, mPQ, and CIndexedPriorityQueue::updateNode().

Referenced by doSingleStep().

 {
   //first the new time for the currently fired reaction
   C_FLOAT64 new_time = time + generateReactionTime(reaction_index);
   mPQ.updateNode(reaction_index, new_time);
 
   //now the updates for the other reactions (whose propensities may have changed)
 
   //if the model contains assignment we use a less efficient loop over all reactions since
   // we do not know the exact dependencies
   if (mHasAssignments)
     {
       size_t i;
 
       for (i = 0; i < mNumReactions; ++i)
         {
           if (i != reaction_index)
             {
               if (mAmu[i] == mAmuOld[i])
                 continue;
 
               C_FLOAT64 new_time;
 
               if (mAmuOld[i] > 0)
                 {
                   new_time = time + (mAmuOld[i] / mAmu[i]) * (mPQ.getKey(i) - time);
                 }
               else
                 {
                   new_time = time + generateReactionTime(i);
                 }
 
               mPQ.updateNode(i, new_time);
             }
         }
     }
   else
     {
       const std::set<size_t> & dep_nodes = mDG.getDependents(reaction_index);
       std::set<size_t>::const_iterator di;
 
       for (di = dep_nodes.begin(); di != dep_nodes.end(); ++di)
         {
           if (*di != reaction_index)
             {
               size_t index = *di;
               C_FLOAT64 new_time;
 
               if (mAmuOld[index] > 0)
                 {
                   new_time = time + (mAmuOld[index] / mAmu[index]) * (mPQ.getKey(index) - time);
                 }
               else
                 {
                   new_time = time + generateReactionTime(index);
                 }
 
               mPQ.updateNode(index, new_time);
             }
         }
     }
 }

Member Data Documentation

CIndexedPriorityQueue CStochNextReactionMethod::mPQ

private

The set of putative reactions and associated times at which each reaction occurs. This is represented as a priority queue, indexed on the reaction time.

Definition at line 38 of file CStochNextReactionMethod.h.

Referenced by doSingleStep(), setupPriorityQueue(), and updatePriorityQueue().

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

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation