COPASI API  4.40.278
Public Types | Public Member Functions | Private Attributes | List of all members
CMathReaction Class Reference

#include <CMathReaction.h>

Public Types

typedef CVector< std::pair< C_FLOAT64 *, C_FLOAT64 > > Balance
 
typedef std::set< std::pair< const CMathObject *, C_FLOAT64 > > ObjectBalance
 
typedef std::pair< C_FLOAT64 *, C_FLOAT64 > SpeciesBalance
 

Public Member Functions

 CMathReaction ()
 
 CMathReaction (const CMathReaction &src)
 
void copy (const CMathReaction &src, CMathContainer &container)
 
void fire ()
 
void fireMultiple (const C_FLOAT64 &count)
 
const CObjectInterface::ObjectSet & getChangedObjects () const
 
const CMathObject * getFluxObject () const
 
const CReaction * getModelReaction () const
 
const Balance & getNumberBalance () const
 
const ObjectBalance & getObjectBalance () const
 
const CMathObject * getParticleFluxObject () const
 
const CMathObject * getPropensityObject () const
 
void initialize (const CReaction *pReaction, CMathContainer &container)
 
bool isFast () const
 
void relocate (const CMathContainer *pContainer, const std::vector< CMath::sRelocate > &relocations)
 
 ~CMathReaction ()
 

Private Attributes

CObjectInterface::ObjectSet mChangedSpecies
 
Balance mNumberBalance
 
ObjectBalance mObjectBalance
 
CMathObject * mpFlux
 
CMathObject * mpParticleFlux
 
CMathObject * mpPropensity
 
const CReaction * mpReaction
 

Member Typedef Documentation

◆ Balance

typedef CVector< std::pair< C_FLOAT64 *, C_FLOAT64 > > CMathReaction::Balance

◆ ObjectBalance

typedef std::set< std::pair < const CMathObject *, C_FLOAT64 > > CMathReaction::ObjectBalance

◆ SpeciesBalance

typedef std::pair< C_FLOAT64 *, C_FLOAT64 > CMathReaction::SpeciesBalance

Constructor & Destructor Documentation

◆ CMathReaction() [1/2]

CMathReaction::CMathReaction ( )

Constructor

◆ CMathReaction() [2/2]

CMathReaction::CMathReaction ( const CMathReaction &  src)

Copy constructor

◆ ~CMathReaction()

CMathReaction::~CMathReaction ( )

Destructor

Member Function Documentation

◆ copy()

void CMathReaction::copy ( const CMathReaction &  src,
CMathContainer &  container 
)

Copy an existing object

Parameters
constCMathReaction & src
CMathContainer& container

◆ fire()

void CMathReaction::fire ( )

Fire the reaction count times. Note count must not necessarily be an integer

References CVectorCore< CType >::array(), mNumberBalance, and CVectorCore< CType >::size().

Referenced by CHybridMethodODE45::fireReaction().

◆ fireMultiple()

void CMathReaction::fireMultiple ( const C_FLOAT64 &  count)

Fire the reaction count times. Note count must not necessarily be an integer

Parameters
constC_FLOAT64 & count

References CVectorCore< CType >::array(), mNumberBalance, and CVectorCore< CType >::size().

Referenced by CTauLeapMethod::updateSystem().

◆ getChangedObjects()

const CObjectInterface::ObjectSet & CMathReaction::getChangedObjects ( ) const

Retrieve the set of particle number objects changed when the reaction fires.

Returns
const CObjectInterface::ObjectSet & changedObjects

References mChangedSpecies.

Referenced by CStochDirectMethod::start(), CStochMethod::start(), and CTrajAdaptiveSA::start().

◆ getFluxObject()

const CMathObject * CMathReaction::getFluxObject ( ) const

Retrieve a pointer to the mathematical object for the flux.

Returns
const CMathObject * pFluxObject

References mpFlux.

◆ getModelReaction()

const CReaction * CMathReaction::getModelReaction ( ) const

Retrieve a pointer to the model reaction

Returns
const CReaction * pModelReaction

References mpReaction.

◆ getNumberBalance()

const CMathReaction::Balance & CMathReaction::getNumberBalance ( ) const

Retrieve the set of modified species

Returns
const CMathReaction::Balance & balance

References mNumberBalance.

Referenced by CLNAMethod::calculateCovarianceMatrixReduced(), CHybridMethod::calculateDerivative(), CTauLeapMethod::doSingleStep(), CTrajAdaptiveSA::doSingleTauLeapStep(), CTrajectoryMethodDsaLsodar::CPartition::intialize(), CSteadyStateMethod::isEquilibrium(), and CTrajectoryMethodDsaLsodar::start().

◆ getObjectBalance()

const CMathReaction::ObjectBalance & CMathReaction::getObjectBalance ( ) const

Retrieve the set of modified species objects

Returns
CMathReaction::ObjectBalance & objectBalance

References mObjectBalance.

Referenced by CMathContainer::getLargestReactionCompartment(), and CHybridMethod::setupDependencyGraph().

◆ getParticleFluxObject()

const CMathObject * CMathReaction::getParticleFluxObject ( ) const

Retrieve a pointer to the mathematical object for the particle flux.

Returns
const CMathObject * pParticleFluxObject

References mpParticleFlux.

Referenced by CHybridMethod::calculateDerivative(), and CSteadyStateMethod::isEquilibrium().

◆ getPropensityObject()

const CMathObject * CMathReaction::getPropensityObject ( ) const

Retrieve a pointer to the mathematical object for the propensity.

Returns
const CMathObject * pPropensityObject

References mpPropensity.

Referenced by CHybridMethodODE45::partitionSystem(), and CHybridMethod::updatePriorityQueue().

◆ initialize()

void CMathReaction::initialize ( const CReaction *  pReaction,
CMathContainer &  container 
)

Initialize the reaction from the model reaction in the given container context

Parameters
constCReaction * pReaction
CMathContainer& container

References CVectorCore< CType >::array(), CDataVector< CType >::begin(), C_FLOAT64, CMath::Dependent, CDataVector< CType >::end(), CChemEq::getBalances(), CReaction::getChemEq(), CReaction::getFluxReference(), CMathContainer::getMathObject(), CReaction::getParticleFluxReference(), CReaction::getPropensityReference(), CMathObject::getSimulationType(), CMathObject::getValuePointer(), CModelEntity::getValueReference(), CMath::Independent, mChangedSpecies, mNumberBalance, mObjectBalance, mpFlux, mpParticleFlux, mpPropensity, mpReaction, CVector< CType >::resize(), and CDataVector< CType >::size().

Referenced by CMathContainer::compile().

◆ isFast()

bool CMathReaction::isFast ( ) const

Check whether the reaction is fast

Returns
bool isFast

References CReaction::isFast(), and mpReaction.

◆ relocate()

void CMathReaction::relocate ( const CMathContainer *  pContainer,
const std::vector< CMath::sRelocate > &  relocations 
)

The objects and values are relocated

Parameters
constCMathContainer * pContainer
conststd::vector< CMath::sRelocate > & relocations

References CVectorCore< CType >::array(), mChangedSpecies, mNumberBalance, mObjectBalance, mpFlux, mpParticleFlux, mpPropensity, CMathContainer::relocateObject(), CMathContainer::relocateObjectSet(), CMathContainer::relocateValue(), and CVectorCore< CType >::size().

Member Data Documentation

◆ mChangedSpecies

CObjectInterface::ObjectSet CMathReaction::mChangedSpecies
private

The set of changed species

Referenced by getChangedObjects(), initialize(), and relocate().

◆ mNumberBalance

Balance CMathReaction::mNumberBalance
private

Information for updating the species particle numbers when the reaction fires.

Referenced by fire(), fireMultiple(), getNumberBalance(), initialize(), and relocate().

◆ mObjectBalance

ObjectBalance CMathReaction::mObjectBalance
private

The set of modified species and their change per reaction event

Referenced by getObjectBalance(), initialize(), and relocate().

◆ mpFlux

CMathObject* CMathReaction::mpFlux
private

A pointer to the mathematical flux.

Referenced by getFluxObject(), initialize(), and relocate().

◆ mpParticleFlux

CMathObject* CMathReaction::mpParticleFlux
private

A pointer to the mathematical particle flux.

Referenced by getParticleFluxObject(), initialize(), and relocate().

◆ mpPropensity

CMathObject* CMathReaction::mpPropensity
private

A pointer to the mathematical propensity.

Referenced by getPropensityObject(), initialize(), and relocate().

◆ mpReaction

const CReaction* CMathReaction::mpReaction
private

A pointer to model reaction.

Referenced by getModelReaction(), initialize(), and isFast().

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