COPASI API
4.16.103
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#include <CMathContainer.h>
Classes | |
struct | sDiscontinuous |
Public Member Functions | |
void | applyInitialValues () |
void | applyUpdateSequence (const CObjectInterface::UpdateSequence &updateSequence) |
CMathContainer (CModel &model) | |
CMathContainer (const CMathContainer &src) | |
CEvaluationNode * | copyBranch (const CEvaluationNode *pSrc, const bool &replaceDiscontinuousNodes) |
CEvaluationNode * | copyBranch (const CEvaluationNode *pSrc, const CMath::Variables< CEvaluationNode * > &variables, const bool &replaceDiscontinuousNodes) |
void | fetchInitialState () |
void | fetchState () |
virtual CCopasiObjectName | getCN () const |
const CVectorCore< C_FLOAT64 > & | getInitialState () const |
CVectorCore< C_FLOAT64 > & | getInitialState () |
C_FLOAT64 * | getInitialValuePointer (const C_FLOAT64 *pValue) const |
CMathObject * | getMathObject (const CObjectInterface *pObject) const |
CMathObject * | getMathObject (const C_FLOAT64 *pDataValue) const |
CMathObject * | getMathObject (const CCopasiObjectName &cn) const |
const CModel & | getModel () const |
virtual const CObjectInterface * | getObject (const CCopasiObjectName &cn) const |
const CVectorCore< C_FLOAT64 > & | getState () const |
CVectorCore< C_FLOAT64 > & | getState () |
const CVectorCore< C_FLOAT64 > & | getStateReduced () const |
CVectorCore< C_FLOAT64 > & | getStateReduced () |
const CVectorCore< C_FLOAT64 > & | getValues () const |
CVectorCore< C_FLOAT64 > & | getValues () |
void | pushInitialState () |
void | pushState () |
CEvaluationNode * | replaceDiscontinuousNode (const CEvaluationNode *pSrc, const std::vector< CEvaluationNode * > &children) |
void | setInitialState (const CVectorCore< C_FLOAT64 > &initialState) |
void | setState (const CVectorCore< C_FLOAT64 > &state) |
void | setStateReduced (const CVectorCore< C_FLOAT64 > &stateReduced) |
void | setValues (const CVectorCore< C_FLOAT64 > &values) |
void | updateInitialValues (const CModelParameter::Framework &framework) |
void | updateSimulatedValues (const bool &useMoieties) |
virtual | ~CMathContainer () |
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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 () |
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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 |
virtual const std::string & | getKey () const |
CCopasiContainer * | getObjectAncestor (const std::string &type) const |
CCopasiDataModel * | getObjectDataModel () |
const CCopasiDataModel * | getObjectDataModel () const |
virtual std::string | getObjectDisplayName (bool regular=true, bool richtext=false) 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 |
virtual void * | getValuePointer () 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 |
virtual void | print (std::ostream *ostream) 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 () |
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CObjectInterface () | |
virtual | ~CObjectInterface () |
Static Private Member Functions | |
static CMath::EntityType | getEntityType (const CModelEntity *pEntity) |
static bool | hasDependencies (const CCopasiObject *pObject) |
Additional Inherited Members | |
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typedef std::multimap < std::string, CCopasiObject * > | objectMap |
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typedef std::set< const CCopasiObject * > | DataObjectSet |
typedef std::vector< Refresh * > | DataUpdateSequence |
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typedef std::set< const CObjectInterface * > | ObjectSet |
typedef std::vector < CObjectInterface * > | UpdateSequence |
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static std::vector< Refresh * > | buildUpdateSequence (const DataObjectSet &objects, const DataObjectSet &uptoDateObjects, const DataObjectSet &context=DataObjectSet()) |
static void | setRenameHandler (CRenameHandler *rh) |
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static const std::vector < CCopasiContainer * > | EmptyList |
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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 } |
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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 () |
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CCopasiObject () | |
CCopasiObject (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &type="CN", const unsigned C_INT32 &flag=0) | |
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objectMap | mObjects |
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static CRenameHandler * | smpRenameHandler = NULL |
Definition at line 28 of file CMathContainer.h.
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Default Constructor
Definition at line 17 of file CMathContainer.cpp.
CMathContainer::CMathContainer | ( | CModel & | model | ) |
Specific Constructor
CModel | & model |
Definition at line 79 of file CMathContainer.cpp.
References CCopasiContainer::getObject(), init(), mpAvogadro, mpModel, mpQuantity2NumberFactor, and CCopasiObject::setObjectParent().
CMathContainer::CMathContainer | ( | const CMathContainer & | src | ) |
Copy constructor
const | CMathContainer & src |
Definition at line 149 of file CMathContainer.cpp.
References CVectorCore< CType >::array(), C_FLOAT64, CMathObject::copy(), CMathReaction::copy(), CMathEventN::copy(), createDependencyGraphs(), mDataObject2MathObject, mDataValue2MathObject, mDependentMasses, mDiscontinuous, mEventAssignments, mEventDelays, mEventPriorities, mEventRoots, mEventRootStates, mEvents, mEventTriggers, mExtensiveRates, mExtensiveValues, mFluxes, mInitialEventTriggers, mInitialExtensiveRates, mInitialExtensiveValues, mInitialFluxes, mInitialIntensiveRates, mInitialIntensiveValues, mInitialParticleFluxes, mInitialState, mInitialTotalMasses, mIntensiveRates, mIntensiveValues, mObjects, mParticleFluxes, mpModel, mPropensities, mReactions, mState, mStateReduced, mTotalMasses, mValues, CCopasiObject::setObjectParent(), and CVectorCore< CType >::size().
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Allocate the memory for objects and values
Definition at line 850 of file CMathContainer.cpp.
References CObjectLists::ALL_LOCAL_PARAMETER_VALUES, CMathEventN::allocate(), CVectorCore< CType >::array(), CCopasiVector< T >::begin(), C_FLOAT64, createDiscontinuityEvents(), CCopasiVector< T >::end(), CMathEventN::getAssignments(), CModel::getEvents(), CObjectLists::getListOfConstObjects(), CModel::getMoieties(), CModel::getNumMetabs(), CModel::getReactions(), CMathEventN::CTrigger::getRoots(), CModel::getStateTemplate(), CMathEventN::getTrigger(), mDependentCount, mDependentMasses, mDiscontinuityEvents, mDiscontinuous, mEventAssignments, mEventDelays, mEventPriorities, mEventRoots, mEventRootStates, mEvents, mEventTargetCount, mEventTriggers, mExtensiveRates, mExtensiveValues, mFixedCount, mFluxes, mIndependentCount, mInitialEventTriggers, mInitialExtensiveRates, mInitialExtensiveValues, mInitialFluxes, mInitialIntensiveRates, mInitialIntensiveValues, mInitialParticleFluxes, mInitialState, mInitialTotalMasses, mIntensiveRates, mIntensiveValues, mObjects, mODECount, mParticleFluxes, mpModel, mPropensities, mState, mStateReduced, mTotalMasses, mValues, CVector< CType >::resize(), CVectorCore< CType >::size(), CStateTemplate::size(), and CCopasiVector< T >::size().
Referenced by init().
void CMathContainer::applyInitialValues | ( | ) |
Set the transient values to the initial values and calculate all dependent values. Please call updateInitialValues before calling this method to assure that all values are up to date.
Definition at line 409 of file CMathContainer.cpp.
References applyUpdateSequence(), CVectorCore< CType >::array(), C_FLOAT64, mApplyInitialValuesSequence, mExtensiveValues, and mInitialExtensiveValues.
void CMathContainer::applyUpdateSequence | ( | const CObjectInterface::UpdateSequence & | updateSequence | ) |
Apply the given update sequence to the mathematical objects in the container
const | CObjectInterface::UpdateSequence & updateSequence |
Definition at line 431 of file CMathContainer.cpp.
References CMathObject::calculate().
Referenced by applyInitialValues(), updateInitialValues(), and updateSimulatedValues().
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Convert nodes which generate discrete changes into events and compiles them.
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Compile the events
Definition at line 1144 of file CMathContainer.cpp.
References CVectorCore< CType >::array(), CCopasiVector< T >::begin(), CMathEventN::compile(), CCopasiVector< T >::end(), CModel::getEvents(), mEvents, and mpModel.
Referenced by init().
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Compile the objects
Definition at line 1129 of file CMathContainer.cpp.
References CVectorCore< CType >::array(), CMathObject::compile(), mObjects, and CVectorCore< CType >::size().
Referenced by init().
CEvaluationNode * CMathContainer::copyBranch | ( | const CEvaluationNode * | pSrc, |
const bool & | replaceDiscontinuousNodes | ||
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Copy a node and all its children. Nodes are converted to suite the math container, i.e., objects nodes point to math object or numbers, function calls are expanded and discrete nodes are replaced by object node pointing to newly created math objects, which are and targets of automatically generated events.
const | CEvaluationNode * pSrc |
const | bool & replaceDiscontinuousNodes |
Definition at line 657 of file CMathContainer.cpp.
Referenced by CMathExpression::CMathExpression(), CMathEventN::CTrigger::compile(), and copyBranch().
CEvaluationNode * CMathContainer::copyBranch | ( | const CEvaluationNode * | pSrc, |
const CMath::Variables< CEvaluationNode * > & | variables, | ||
const bool & | replaceDiscontinuousNodes | ||
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Copy a node and all its children. Nodes are converted to suite the math container, i.e., objects nodes point to math object or numbers, function calls are expanded and discrete nodes are replaced by object node pointing to newly created math objects, which are and targets of automatically generated events.
const | CEvaluationNode * pSrc |
const | CMath::Variables & variables |
const | bool & replaceDiscontinuousNodes |
Definition at line 665 of file CMathContainer.cpp.
References CEvaluationNodeConstant::_NaN, CEvaluationNodeVariable::ANY, C_INVALID_INDEX, CEvaluationNode::CALL, CEvaluationNodeFunction::CEIL, CEvaluationNode::CHOICE, CEvaluationNodeObject::CN, CNodeContextIterator< Node, Context >::context(), copyBranch(), CEvaluationNode::copyNode(), createNodeFromObject(), CNodeContextIterator< Node, Context >::end(), CEvaluationNodeCall::EXPRESSION, CEvaluationNodeFunction::FLOOR, CEvaluationNodeCall::FUNCTION, CEvaluationNode::FUNCTION, CEvaluationNodeCall::getCalledTree(), CCopasiNode< _Data >::getData(), CEvaluationNodeVariable::getIndex(), getMathObject(), getObject(), CEvaluationTree::getRoot(), CEvaluationNode::getType(), CEvaluationNodeChoice::IF, CEvaluationNodeOperator::MODULUS, CNodeContextIterator< Node, Context >::next(), CEvaluationNode::OBJECT, CEvaluationNode::OPERATOR, CNodeContextIterator< Node, Context >::parentContextPtr(), CEvaluationNodeObject::POINTER, replaceDiscontinuousNode(), and CEvaluationNode::VARIABLE.
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Create the update sequence used when applying the initial state
Definition at line 1312 of file CMathContainer.cpp.
References CVectorCore< CType >::array(), CMath::Default, CMathDependencyGraph::getUpdateSequence(), mApplyInitialValuesSequence, mEventDelays, mExtensiveValues, mObjects, mTransientDependencies, mValues, and CVectorCore< CType >::size().
Referenced by createDependencyGraphs().
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Create Dependency Graphs
Definition at line 1212 of file CMathContainer.cpp.
References CMathDependencyGraph::addObject(), CVectorCore< CType >::array(), createApplyInitialValuesSequence(), createSynchronizeInitialValuesSequence(), createUpdateSimulationValuesSequence(), CMathDependencyGraph::exportDOTFormat(), mExtensiveValues, mInitialDependencies, mInitialExtensiveValues, mObjects, mTransientDependencies, and CVectorCore< CType >::size().
Referenced by CMathContainer(), and init().
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Create an event of type CEvent::Discontinuity for the given node
const | CEvaluationNode * pNode |
Definition at line 1863 of file CMathContainer.cpp.
References CCopasiVector< T >::add(), createDiscontinuityTriggerInfix(), CEvent::Discontinuity, mDiscontinuityEvents, CEvent::setTriggerExpression(), and CEvent::setType().
Referenced by createDiscontinuityEvents().
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Create an event of type CEvent::Discontinuity for each discontinuity in the model
Definition at line 1808 of file CMathContainer.cpp.
References CEvaluationNodeConstant::_NaN, CModel::getTreesWithDiscontinuities(), and mpModel.
Referenced by allocate(), and createDiscontinuityEvents().
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Create an event of type CEvent::Discontinuity for each discontinuity the tree with root pNode
const | CEvaluationTree * pTree |
Definition at line 1827 of file CMathContainer.cpp.
References CEvaluationNodeConstant::_NaN, CEvaluationNode::CALL, CEvaluationNodeFunction::CEIL, CEvaluationNode::CHOICE, createDiscontinuityDataEvent(), createDiscontinuityEvents(), CEvaluationNodeCall::EXPRESSION, CEvaluationNodeFunction::FLOOR, CEvaluationNodeCall::FUNCTION, CEvaluationNode::FUNCTION, CEvaluationTree::getRoot(), CEvaluationNodeChoice::IF, CEvaluationNodeOperator::MODULUS, and CEvaluationNode::OPERATOR.
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Create the infix for trigger of the event which tracks changes in a discontinuity represented by the node.
const | CEvaluationNode * pNode |
Definition at line 1874 of file CMathContainer.cpp.
References CEvaluationNodeFunction::CEIL, CEvaluationNode::CHOICE, fatalError, CEvaluationNodeFunction::FLOOR, CEvaluationNode::FUNCTION, CCopasiNode< _Data >::getChild(), CEvaluationNode::getType(), CEvaluationNodeChoice::IF, CEvaluationNodeOperator::MODULUS, and CEvaluationNode::OPERATOR.
Referenced by createDiscontinuityDataEvent(), and replaceDiscontinuousNode().
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Create a node based on the given pointer to the math object
const | CObjectInterface * pMathObject |
Definition at line 1162 of file CMathContainer.cpp.
References CEvaluationNodeConstant::_NaN, C_FLOAT64, CObjectInterface::getValuePointer(), mpAvogadro, and mpQuantity2NumberFactor.
Referenced by copyBranch().
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Create a node based on the given pointer to a data value
const | C_FLOAT64 * pDataValue |
Definition at line 1184 of file CMathContainer.cpp.
References CEvaluationNodeConstant::_NaN, C_FLOAT64, getMathObject(), and CMathObject::getValuePointer().
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Create the update sequences needed to synchronize the initial values
Definition at line 1244 of file CMathContainer.cpp.
References CVectorCore< CType >::array(), CMathObject::getEntityType(), CMathDependencyGraph::getUpdateSequence(), CMathObject::isIntensiveProperty(), mExtensiveValues, mInitialDependencies, mInitialExtensiveRates, mInitialStateValueExtensive, mInitialStateValueIntensive, mObjects, mSynchronizeInitialValuesSequenceExtensive, mSynchronizeInitialValuesSequenceIntensive, mValues, CMath::Species, and CMath::UpdateMoieties.
Referenced by createDependencyGraphs().
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Create the update sequences used to calculate all values required for simulation
Definition at line 1337 of file CMathContainer.cpp.
References CVectorCore< CType >::array(), CMath::Default, CMath::Dependent, CMathObject::getSimulationType(), CMathDependencyGraph::getUpdateSequence(), CMath::Independent, mEventRoots, mEventRootStates, mEventTargetCount, mExtensiveRates, mExtensiveValues, mFixedCount, mIntensiveRates, mObjects, mReducedStateValues, mSimulationRequiredValues, mSimulationValuesSequence, mSimulationValuesSequenceReduced, mStateValues, mTransientDependencies, mValues, CMath::ODE, CMath::Time, and CMath::UseMoieties.
Referenced by createDependencyGraphs().
void CMathContainer::fetchInitialState | ( | ) |
Fetch the initial state from the associated model
Definition at line 442 of file CMathContainer.cpp.
References CVectorCore< CType >::array(), C_FLOAT64, CMathObject::getDataObject(), CCopasiObject::getValuePointer(), mInitialState, mObjects, and CVectorCore< CType >::size().
void CMathContainer::fetchState | ( | ) |
Fetch the state from the associated model
Definition at line 480 of file CMathContainer.cpp.
References CVectorCore< CType >::array(), C_FLOAT64, CMathObject::getDataObject(), CCopasiObject::getValuePointer(), mObjects, mState, and CVectorCore< CType >::size().
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Retrieve the CN of the math container The math container provides values for the numerical values of model objects. For the CN mechanism to work properly it has to pretend to be the model.
Reimplemented from CCopasiObject.
Definition at line 519 of file CMathContainer.cpp.
References CCopasiObject::getCN(), and mpModel.
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Determine the entity type of an entity
const | CModelEntity * pEntity |
Definition at line 1533 of file CMathContainer.cpp.
References CMath::Compartment, CMath::EntityTypeUndefined, CMath::GlobalQuantity, and CMath::Species.
Referenced by initializeMathObjects().
const CVectorCore< C_FLOAT64 > & CMathContainer::getInitialState | ( | ) | const |
Retrieves the initial state values, i.e., all initial values of objects of simulation type Fixed, Time, ODE, Dependent, and Independent. It includes only extensive values for species.
Definition at line 344 of file CMathContainer.cpp.
References mInitialState.
CVectorCore< C_FLOAT64 > & CMathContainer::getInitialState | ( | ) |
Retrieves the initial state values, i.e., all initial values of objects of simulation type Fixed, Time, ODE, Dependent, and Independent. It includes only extensive values for species.
Definition at line 349 of file CMathContainer.cpp.
References mInitialState.
Retrieve the pointer to the corresponding initial value
const | C_FLOAT64 * pValue |
Definition at line 1794 of file CMathContainer.cpp.
References CVectorCore< CType >::array(), C_FLOAT64, mEventDelays, mExtensiveValues, mInitialExtensiveValues, mValues, and CVectorCore< CType >::size().
CMathObject * CMathContainer::getMathObject | ( | const CObjectInterface * | pObject | ) | const |
Retrieve a pointer to corresponding the mathematical object for the given abject if it exists otherwise NULL
const | CObjectInterface * pObject |
Definition at line 554 of file CMathContainer.cpp.
References mDataObject2MathObject.
Referenced by CMathEventN::CAssignment::compile(), CMathObject::compileDependentMass(), CMathObject::compileInitialValue(), CMathObject::compileValue(), copyBranch(), createNodeFromValue(), getMathObject(), getObject(), and CMathReaction::initialize().
CMathObject * CMathContainer::getMathObject | ( | const C_FLOAT64 * | pDataValue | ) | const |
Retrieve a pointer to the mathematical object for data value pointer
const | C_FLOAT64 * pDataValue |
Definition at line 570 of file CMathContainer.cpp.
References CVectorCore< CType >::array(), C_FLOAT64, mDataValue2MathObject, mObjects, mValues, and CVectorCore< CType >::size().
CMathObject * CMathContainer::getMathObject | ( | const CCopasiObjectName & | cn | ) | const |
Retrieve a pointer to the mathematical object for the given CN
const | CCopasiObjectName & cn |
Definition at line 594 of file CMathContainer.cpp.
References getMathObject(), CCopasiContainer::getObject(), and mpModel.
const CModel & CMathContainer::getModel | ( | ) | const |
Retrieve the model for the container
Definition at line 652 of file CMathContainer.cpp.
References mpModel.
Referenced by CMathObject::compileParticleFlux(), CMathObject::compilePropensity(), CMathObject::createExtensiveODERateExpression(), CMathObject::createExtensiveReactionRateExpression(), CMathObject::createExtensiveValueExpression(), CMathObject::createIntensiveRateExpression(), and CMathObject::createIntensiveValueExpression().
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Retrieve a descendant object by its CN.
Reimplemented from CCopasiContainer.
Definition at line 525 of file CMathContainer.cpp.
References CCopasiObject::getCN(), getMathObject(), CCopasiObject::getObjectDataModel(), CCopasiObjectName::getPrimary(), mpModel, and CCopasiDataModel::ObjectFromCN().
Referenced by copyBranch().
const CVectorCore< C_FLOAT64 > & CMathContainer::getState | ( | ) | const |
Retrieves the state values, i.e., all initial values of objects of simulation type Time, ODE, Dependent, and Independent. It includes only extensive values for species.
Definition at line 361 of file CMathContainer.cpp.
References mState.
CVectorCore< C_FLOAT64 > & CMathContainer::getState | ( | ) |
Retrieves the state values, i.e., all initial values of objects of simulation type Time, ODE, Dependent, and Independent. It includes only extensive values for species.
Definition at line 366 of file CMathContainer.cpp.
References mState.
const CVectorCore< C_FLOAT64 > & CMathContainer::getStateReduced | ( | ) | const |
Retrieves the state values, i.e., all initial values of objects of simulation type Time, ODE, and Dependent. It includes only extensive values for species.
Definition at line 378 of file CMathContainer.cpp.
References mStateReduced.
CVectorCore< C_FLOAT64 > & CMathContainer::getStateReduced | ( | ) |
Retrieves the reduced state values, i.e., all initial values of objects of simulation type Time, ODE, and Dependent. It includes only extensive values for species.
Definition at line 383 of file CMathContainer.cpp.
References mStateReduced.
const CVectorCore< C_FLOAT64 > & CMathContainer::getValues | ( | ) | const |
Retrieve the values of all mathematical objects
Definition at line 327 of file CMathContainer.cpp.
References mValues.
CVectorCore< C_FLOAT64 > & CMathContainer::getValues | ( | ) |
Retrieve the values of all mathematical objects
Definition at line 332 of file CMathContainer.cpp.
References mValues.
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Determine whether on object has calculation dependencies.
Definition at line 1773 of file CMathContainer.cpp.
References CCopasiObject::getDirectDependencies(), and CCopasiObject::getObjectParent().
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Initialize the mathematical model
Definition at line 599 of file CMathContainer.cpp.
References allocate(), CVectorCore< CType >::array(), CCopasiVector< T >::begin(), CCopasiVector< T >::clear(), compileEvents(), compileObjects(), createDependencyGraphs(), CModel::getReactions(), CMathReaction::initialize(), initializeDiscontinuousCreationPointer(), initializeEvents(), initializeObjects(), initializePointers(), mDiscontinuityEvents, mDiscontinuityInfix2Object, mObjects, mpModel, mReactions, mTriggerInfix2Event, CModelParameter::ParticleNumbers, CVector< CType >::resize(), CVectorCore< CType >::size(), CCopasiVector< T >::size(), and updateInitialValues().
Referenced by CMathContainer().
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Initialize the pointers used for the conversion of discontinuous nodes.
Definition at line 1512 of file CMathContainer.cpp.
References CVectorCore< CType >::array(), C_FLOAT64, mCreateDiscontinuousPointer, mDiscontinuous, mEvents, mObjects, mValues, CMathContainer::sDiscontinuous::pDiscontinuous, CMathContainer::sDiscontinuous::pEvent, and CVectorCore< CType >::size().
Referenced by init().
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Initialize the events
sPointers | & pointers |
Definition at line 1115 of file CMathContainer.cpp.
References CVectorCore< CType >::array(), CMathEventN::initialize(), mEvents, and CVectorCore< CType >::size().
Referenced by init().
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Initialize several mathematical objects of a common simulation type and advance relevant pointers
const | std::vector<const CModelEntity*> & entities |
const | CMath::SimulationType & simulationType |
sPointers | & pointers |
Definition at line 1553 of file CMathContainer.cpp.
References CMath::Assignment, CMath::Conversion, CMath::EventTarget, CMath::Fixed, CMetab::getConcentrationRateReference(), CMetab::getConcentrationReference(), getEntityType(), CMetab::getInitialConcentrationReference(), CMathObject::initialize(), map(), CMath::sPointers::pExtensiveRates, CMath::sPointers::pExtensiveRatesObject, CMath::sPointers::pExtensiveValues, CMath::sPointers::pExtensiveValuesObject, CMath::sPointers::pInitialExtensiveRates, CMath::sPointers::pInitialExtensiveRatesObject, CMath::sPointers::pInitialExtensiveValues, CMath::sPointers::pInitialExtensiveValuesObject, CMath::sPointers::pInitialIntensiveRates, CMath::sPointers::pInitialIntensiveRatesObject, CMath::sPointers::pInitialIntensiveValues, CMath::sPointers::pInitialIntensiveValuesObject, CMath::sPointers::pIntensiveRates, CMath::sPointers::pIntensiveRatesObject, CMath::sPointers::pIntensiveValues, CMath::sPointers::pIntensiveValuesObject, CMath::Rate, CMath::Species, and CMath::Value.
Referenced by initializeObjects().
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Initialize several mathematical objects for local reaction parameters and advance relevant pointers
const | std::vector<const CCopasiObject *> & parameters |
CMathContainer::sPointers | & p |
Definition at line 1673 of file CMathContainer.cpp.
References CMath::Fixed, CMathObject::initialize(), CMath::LocalReactionParameter, map(), CMath::sPointers::pExtensiveRates, CMath::sPointers::pExtensiveRatesObject, CMath::sPointers::pExtensiveValues, CMath::sPointers::pExtensiveValuesObject, CMath::sPointers::pInitialExtensiveRates, CMath::sPointers::pInitialExtensiveRatesObject, CMath::sPointers::pInitialExtensiveValues, CMath::sPointers::pInitialExtensiveValuesObject, CMath::Rate, and CMath::Value.
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Initialize several mathematical objects for local reaction parameters and advance relevant pointers
const | CCopasiVector< CReaction > & reactions |
CMathContainer::sPointers | & p |
Definition at line 1705 of file CMathContainer.cpp.
References CCopasiVector< T >::begin(), CCopasiVector< T >::end(), CMath::Flux, CMathObject::initialize(), map(), CMath::ParticleFlux, CMath::sPointers::pFluxes, CMath::sPointers::pFluxesObject, CMath::sPointers::pInitialFluxes, CMath::sPointers::pInitialFluxesObject, CMath::sPointers::pInitialParticleFluxes, CMath::sPointers::pInitialParticleFluxesObject, CMath::sPointers::pParticleFluxes, CMath::sPointers::pParticleFluxesObject, CMath::sPointers::pPropensities, CMath::sPointers::pPropensitiesObject, CMath::Propensity, CMath::Reaction, and CMath::SimulationTypeUndefined.
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Initialize several mathematical objects for local reaction parameters and advance relevant pointers
const | CCopasiVector< CMoiety > & moieties |
CMathContainer::sPointers | & p |
Definition at line 1744 of file CMathContainer.cpp.
References CCopasiVector< T >::begin(), CMath::DependentMass, CCopasiVector< T >::end(), CMathObject::initialize(), map(), CMath::Moiety, CMath::sPointers::pDependentMasses, CMath::sPointers::pDependentMassesObject, CMath::sPointers::pInitialTotalMasses, CMath::sPointers::pInitialTotalMassesObject, CMath::sPointers::pTotalMasses, CMath::sPointers::pTotalMassesObject, CMath::SimulationTypeUndefined, and CMath::TotalMass.
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Initialize the objects
sPointers | & pointers |
Definition at line 974 of file CMathContainer.cpp.
References CObjectLists::ALL_LOCAL_PARAMETER_VALUES, CModelEntity::ASSIGNMENT, CMath::Assignment, CStateTemplate::beginDependent(), CStateTemplate::beginFixed(), CStateTemplate::beginIndependent(), CMath::Dependent, CMath::Discontinuous, CStateTemplate::endDependent(), CStateTemplate::endFixed(), CStateTemplate::endIndependent(), CMath::Event, CMath::EventTarget, CMath::Fixed, CObjectLists::getEventTargets(), CModelEntity::getInitialValueReference(), CObjectLists::getListOfConstObjects(), CModel::getMoieties(), CModelEntity::getRateReference(), CModel::getReactions(), CModel::getStateTemplate(), CModelEntity::getStatus(), CModelEntity::getValueReference(), CMath::Independent, CMathObject::initialize(), initializeMathObjects(), map(), mAssignmentCount, mDependentCount, mDiscontinuous, mEventTargetCount, mFixedCount, mIndependentCount, mODECount, CMath::Model, mpModel, CModelEntity::ODE, CMath::ODE, CMath::sPointers::pDiscontinuous, CMath::sPointers::pDiscontinuousObject, CMath::sPointers::pExtensiveRates, CMath::sPointers::pExtensiveRatesObject, CMath::sPointers::pExtensiveValues, CMath::sPointers::pExtensiveValuesObject, CMath::sPointers::pInitialExtensiveRates, CMath::sPointers::pInitialExtensiveRatesObject, CMath::sPointers::pInitialExtensiveValues, CMath::sPointers::pInitialExtensiveValuesObject, CMath::Rate, CModelEntity::REACTIONS, CMath::SimulationTypeUndefined, CVectorCore< CType >::size(), CMath::Time, and CMath::Value.
Referenced by init().
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Initialize the pointers
sPointers | & pointers |
Definition at line 1393 of file CMathContainer.cpp.
References CVectorCore< CType >::array(), C_FLOAT64, mDependentMasses, mDiscontinuous, mEventAssignments, mEventDelays, mEventPriorities, mEventRoots, mEventRootStates, mEventTriggers, mExtensiveRates, mExtensiveValues, mFluxes, mInitialEventTriggers, mInitialExtensiveRates, mInitialExtensiveValues, mInitialFluxes, mInitialIntensiveRates, mInitialIntensiveValues, mInitialParticleFluxes, mInitialTotalMasses, mIntensiveRates, mIntensiveValues, mObjects, mParticleFluxes, mPropensities, mTotalMasses, mValues, CMath::sPointers::pDependentMasses, CMath::sPointers::pDependentMassesObject, CMath::sPointers::pDiscontinuous, CMath::sPointers::pDiscontinuousObject, CMath::sPointers::pEventAssignments, CMath::sPointers::pEventAssignmentsObject, CMath::sPointers::pEventDelays, CMath::sPointers::pEventDelaysObject, CMath::sPointers::pEventPriorities, CMath::sPointers::pEventPrioritiesObject, CMath::sPointers::pEventRoots, CMath::sPointers::pEventRootsObject, CMath::sPointers::pEventRootStates, CMath::sPointers::pEventRootStatesObject, CMath::sPointers::pEventTriggers, CMath::sPointers::pEventTriggersObject, CMath::sPointers::pExtensiveRates, CMath::sPointers::pExtensiveRatesObject, CMath::sPointers::pExtensiveValues, CMath::sPointers::pExtensiveValuesObject, CMath::sPointers::pFluxes, CMath::sPointers::pFluxesObject, CMath::sPointers::pInitialEventTriggers, CMath::sPointers::pInitialEventTriggersObject, CMath::sPointers::pInitialExtensiveRates, CMath::sPointers::pInitialExtensiveRatesObject, CMath::sPointers::pInitialExtensiveValues, CMath::sPointers::pInitialExtensiveValuesObject, CMath::sPointers::pInitialFluxes, CMath::sPointers::pInitialFluxesObject, CMath::sPointers::pInitialIntensiveRates, CMath::sPointers::pInitialIntensiveRatesObject, CMath::sPointers::pInitialIntensiveValues, CMath::sPointers::pInitialIntensiveValuesObject, CMath::sPointers::pInitialParticleFluxes, CMath::sPointers::pInitialParticleFluxesObject, CMath::sPointers::pInitialTotalMasses, CMath::sPointers::pInitialTotalMassesObject, CMath::sPointers::pIntensiveRates, CMath::sPointers::pIntensiveRatesObject, CMath::sPointers::pIntensiveValues, CMath::sPointers::pIntensiveValuesObject, CMath::sPointers::pParticleFluxes, CMath::sPointers::pParticleFluxesObject, CMath::sPointers::pPropensities, CMath::sPointers::pPropensitiesObject, CMath::sPointers::pTotalMasses, and CMath::sPointers::pTotalMassesObject.
Referenced by init().
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Map the data object to the math object
CCopasiObject | * pDataObject |
CMathObject | * pMathObject |
Definition at line 1785 of file CMathContainer.cpp.
References C_FLOAT64, CCopasiObject::getValuePointer(), mDataObject2MathObject, and mDataValue2MathObject.
Referenced by initializeMathObjects(), and initializeObjects().
void CMathContainer::pushInitialState | ( | ) |
Push the initial state to the associated model
Definition at line 461 of file CMathContainer.cpp.
References CVectorCore< CType >::array(), C_FLOAT64, CMathObject::getDataObject(), CCopasiObject::getValuePointer(), mInitialState, mObjects, and CVectorCore< CType >::size().
void CMathContainer::pushState | ( | ) |
Push the state to the associated model
Definition at line 499 of file CMathContainer.cpp.
References CVectorCore< CType >::array(), C_FLOAT64, CMathObject::getDataObject(), CCopasiObject::getValuePointer(), mObjects, mState, and CVectorCore< CType >::size().
CEvaluationNode * CMathContainer::replaceDiscontinuousNode | ( | const CEvaluationNode * | pSrc, |
const std::vector< CEvaluationNode * > & | children | ||
) |
Replace a discontinuous node by an object node pointing to newly created math objects, which are targets of automatically generated events.
const | CEvaluationNode * pSrc |
const | std::vector< CEvaluationNode * > & children |
Definition at line 780 of file CMathContainer.cpp.
References CMathEventN::addAssignment(), CEvaluationNode::buildInfix(), C_FLOAT64, CEvaluationNode::copyNode(), createDiscontinuityTriggerInfix(), CMathObject::getValuePointer(), mCreateDiscontinuousPointer, mDiscontinuityInfix2Object, mTriggerInfix2Event, pdelete, CMathContainer::sDiscontinuous::pDiscontinuous, CMathContainer::sDiscontinuous::pEvent, CMathObject::setExpressionPtr(), and CMathEventN::setTriggerExpression().
Referenced by copyBranch().
void CMathContainer::setInitialState | ( | const CVectorCore< C_FLOAT64 > & | initialState | ) |
Set the initial state values, i.e., all initial values of objects of simulation type Fixed, Time, ODE, Dependent, and Independent. It includes only extensive values for species.
const | CVectorCore< C_FLOAT64 > & initialState |
Definition at line 354 of file CMathContainer.cpp.
References CVectorCore< CType >::array(), C_FLOAT64, mInitialState, and CVectorCore< CType >::size().
void CMathContainer::setState | ( | const CVectorCore< C_FLOAT64 > & | state | ) |
Set the state values, i.e., all initial values of objects of simulation type Time, ODE, Dependent, and Independent. It includes only extensive values for species.
const | CVectorCore< C_FLOAT64 > & state |
Definition at line 371 of file CMathContainer.cpp.
References CVectorCore< CType >::array(), C_FLOAT64, mState, and CVectorCore< CType >::size().
void CMathContainer::setStateReduced | ( | const CVectorCore< C_FLOAT64 > & | stateReduced | ) |
Set the reduced state values, i.e., all initial values of objects of simulation type Time, ODE, Dependent, and Independent. It includes only extensive values for species.
const | CVectorCore< C_FLOAT64 > & stateReduced |
Definition at line 388 of file CMathContainer.cpp.
References CVectorCore< CType >::array(), C_FLOAT64, mStateReduced, and CVectorCore< CType >::size().
void CMathContainer::setValues | ( | const CVectorCore< C_FLOAT64 > & | values | ) |
Set the values of all mathematical objects
const | CVectorCore< C_FLOAT64 > & values |
Definition at line 337 of file CMathContainer.cpp.
References mValues, and CVectorCore< CType >::size().
void CMathContainer::updateInitialValues | ( | const CModelParameter::Framework & | framework | ) |
Calculate all dependent initial values based on initial extensive or intensive values
const | CModelParameter::Framework & framework |
Definition at line 395 of file CMathContainer.cpp.
References applyUpdateSequence(), CModelParameter::Concentration, mSynchronizeInitialValuesSequenceExtensive, mSynchronizeInitialValuesSequenceIntensive, and CModelParameter::ParticleNumbers.
Referenced by init().
void CMathContainer::updateSimulatedValues | ( | const bool & | useMoieties | ) |
Calculate all values required for simulation based on the current state
const | bool & useMoieties |
Definition at line 419 of file CMathContainer.cpp.
References applyUpdateSequence(), mSimulationValuesSequence, and mSimulationValuesSequenceReduced.
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The sequence of updates needed to apply the initial values
Definition at line 542 of file CMathContainer.h.
Referenced by applyInitialValues(), and createApplyInitialValuesSequence().
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Definition at line 500 of file CMathContainer.h.
Referenced by initializeObjects().
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Structure of pointers used for creating discontinuities.
Definition at line 610 of file CMathContainer.h.
Referenced by initializeDiscontinuousCreationPointer(), and replaceDiscontinuousNode().
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A map from data objects to math objects
Definition at line 615 of file CMathContainer.h.
Referenced by CMathContainer(), getMathObject(), and map().
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A map from data objects values to math objects
Definition at line 620 of file CMathContainer.h.
Referenced by CMathContainer(), getMathObject(), and map().
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Definition at line 499 of file CMathContainer.h.
Referenced by allocate(), and initializeObjects().
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Definition at line 492 of file CMathContainer.h.
Referenced by allocate(), CMathContainer(), and initializePointers().
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A vector of data events for discontinuities
Definition at line 625 of file CMathContainer.h.
Referenced by allocate(), createDiscontinuityDataEvent(), and init().
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A map from the infix of the expression of a discontinuity to the object representing it.
Definition at line 631 of file CMathContainer.h.
Referenced by init(), and replaceDiscontinuousNode().
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Definition at line 493 of file CMathContainer.h.
Referenced by allocate(), CMathContainer(), initializeDiscontinuousCreationPointer(), initializeObjects(), and initializePointers().
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Definition at line 488 of file CMathContainer.h.
Referenced by allocate(), CMathContainer(), and initializePointers().
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Definition at line 486 of file CMathContainer.h.
Referenced by allocate(), CMathContainer(), createApplyInitialValuesSequence(), getInitialValuePointer(), and initializePointers().
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Definition at line 487 of file CMathContainer.h.
Referenced by allocate(), CMathContainer(), and initializePointers().
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Definition at line 489 of file CMathContainer.h.
Referenced by allocate(), CMathContainer(), createUpdateSimulationValuesSequence(), and initializePointers().
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Definition at line 490 of file CMathContainer.h.
Referenced by allocate(), CMathContainer(), createUpdateSimulationValuesSequence(), and initializePointers().
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A vector containing all math events.
Definition at line 600 of file CMathContainer.h.
Referenced by allocate(), CMathContainer(), compileEvents(), initializeDiscontinuousCreationPointer(), and initializeEvents().
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Definition at line 496 of file CMathContainer.h.
Referenced by allocate(), createUpdateSimulationValuesSequence(), and initializeObjects().
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Definition at line 484 of file CMathContainer.h.
Referenced by allocate(), CMathContainer(), and initializePointers().
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Definition at line 479 of file CMathContainer.h.
Referenced by allocate(), CMathContainer(), createUpdateSimulationValuesSequence(), and initializePointers().
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Definition at line 477 of file CMathContainer.h.
Referenced by allocate(), applyInitialValues(), CMathContainer(), createApplyInitialValuesSequence(), createDependencyGraphs(), createSynchronizeInitialValuesSequence(), createUpdateSimulationValuesSequence(), getInitialValuePointer(), and initializePointers().
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Definition at line 495 of file CMathContainer.h.
Referenced by allocate(), createUpdateSimulationValuesSequence(), and initializeObjects().
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Definition at line 482 of file CMathContainer.h.
Referenced by allocate(), CMathContainer(), and initializePointers().
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Definition at line 498 of file CMathContainer.h.
Referenced by allocate(), and initializeObjects().
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Dependency graph for initial value calculations
Definition at line 520 of file CMathContainer.h.
Referenced by createDependencyGraphs(), and createSynchronizeInitialValuesSequence().
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Definition at line 475 of file CMathContainer.h.
Referenced by allocate(), CMathContainer(), and initializePointers().
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Definition at line 470 of file CMathContainer.h.
Referenced by allocate(), CMathContainer(), createSynchronizeInitialValuesSequence(), and initializePointers().
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Definition at line 468 of file CMathContainer.h.
Referenced by allocate(), applyInitialValues(), CMathContainer(), createDependencyGraphs(), getInitialValuePointer(), and initializePointers().
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Definition at line 473 of file CMathContainer.h.
Referenced by allocate(), CMathContainer(), and initializePointers().
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Definition at line 471 of file CMathContainer.h.
Referenced by allocate(), CMathContainer(), and initializePointers().
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Definition at line 469 of file CMathContainer.h.
Referenced by allocate(), CMathContainer(), and initializePointers().
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Definition at line 472 of file CMathContainer.h.
Referenced by allocate(), CMathContainer(), and initializePointers().
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The initial state contains also all fixed values
Definition at line 505 of file CMathContainer.h.
Referenced by allocate(), CMathContainer(), fetchInitialState(), getInitialState(), pushInitialState(), and setInitialState().
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The set of objects which determine the initial state of the model based on extensive values
Definition at line 560 of file CMathContainer.h.
Referenced by createSynchronizeInitialValuesSequence().
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The set of objects which determine the initial state of the model based on intensive values
Definition at line 566 of file CMathContainer.h.
Referenced by createSynchronizeInitialValuesSequence().
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Definition at line 474 of file CMathContainer.h.
Referenced by allocate(), CMathContainer(), and initializePointers().
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Definition at line 480 of file CMathContainer.h.
Referenced by allocate(), CMathContainer(), createUpdateSimulationValuesSequence(), and initializePointers().
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Definition at line 478 of file CMathContainer.h.
Referenced by allocate(), CMathContainer(), and initializePointers().
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The objects which are required to be up to date for simulation of the reduced model, i.e., the right hand side of ODEs, rates of independent species determined by reaction, and event roots. A vector containing all math objects.
Definition at line 595 of file CMathContainer.h.
Referenced by allocate(), CMathContainer(), compileObjects(), createApplyInitialValuesSequence(), createDependencyGraphs(), createSynchronizeInitialValuesSequence(), createUpdateSimulationValuesSequence(), fetchInitialState(), fetchState(), getMathObject(), init(), initializeDiscontinuousCreationPointer(), initializePointers(), pushInitialState(), and pushState().
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Definition at line 497 of file CMathContainer.h.
Referenced by allocate(), and initializeObjects().
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Definition at line 481 of file CMathContainer.h.
Referenced by allocate(), CMathContainer(), and initializePointers().
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Definition at line 463 of file CMathContainer.h.
Referenced by CMathContainer(), and createNodeFromObject().
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A pointer to the data model which mathematics are contained
Definition at line 462 of file CMathContainer.h.
Referenced by allocate(), CMathContainer(), compileEvents(), createDiscontinuityEvents(), getCN(), getMathObject(), getModel(), getObject(), init(), and initializeObjects().
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Definition at line 464 of file CMathContainer.h.
Referenced by CMathContainer(), and createNodeFromObject().
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Definition at line 491 of file CMathContainer.h.
Referenced by allocate(), CMathContainer(), and initializePointers().
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A vector containing all math reactions.
Definition at line 605 of file CMathContainer.h.
Referenced by CMathContainer(), and init().
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The set of objects which determine the transient state of the reduced model
Definition at line 576 of file CMathContainer.h.
Referenced by createUpdateSimulationValuesSequence().
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The objects which are required to be up to date for simulation of the full model, i.e., the right hand side of ODEs, rates of species determined by reaction, and event roots.
Definition at line 583 of file CMathContainer.h.
Referenced by createUpdateSimulationValuesSequence().
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The sequence of updates needed to calculate all simulation required values based on the assumption that all state values may have changed
Definition at line 548 of file CMathContainer.h.
Referenced by createUpdateSimulationValuesSequence(), and updateSimulatedValues().
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The sequence of updates needed to calculate all simulation required values based on the assumption that all state values may have changed
Definition at line 554 of file CMathContainer.h.
Referenced by createUpdateSimulationValuesSequence(), and updateSimulatedValues().
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The state contains values of type Time, ODE, Independent, and Dependent
Definition at line 510 of file CMathContainer.h.
Referenced by allocate(), CMathContainer(), fetchState(), getState(), pushState(), and setState().
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The state contains values of type Time, ODE, Independent
Definition at line 515 of file CMathContainer.h.
Referenced by allocate(), CMathContainer(), getStateReduced(), and setStateReduced().
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The set of objects which determine the transient state of the model
Definition at line 571 of file CMathContainer.h.
Referenced by createUpdateSimulationValuesSequence().
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The sequence of updates needed to synchronize the initial values based on extensive values, i.e., species amounts
Definition at line 531 of file CMathContainer.h.
Referenced by createSynchronizeInitialValuesSequence(), and updateInitialValues().
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The sequence of updates needed to synchronize the initial values based on intensive values, i.e., species concentrations.
Definition at line 537 of file CMathContainer.h.
Referenced by createSynchronizeInitialValuesSequence(), and updateInitialValues().
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Definition at line 483 of file CMathContainer.h.
Referenced by allocate(), CMathContainer(), and initializePointers().
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Dependency graph for transient value calculations
Definition at line 525 of file CMathContainer.h.
Referenced by createApplyInitialValuesSequence(), createDependencyGraphs(), and createUpdateSimulationValuesSequence().
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A map from the discontinuity trigger infix of to event representing it.
Definition at line 637 of file CMathContainer.h.
Referenced by init(), and replaceDiscontinuousNode().
Definition at line 466 of file CMathContainer.h.
Referenced by allocate(), CMathContainer(), createApplyInitialValuesSequence(), createSynchronizeInitialValuesSequence(), createUpdateSimulationValuesSequence(), getInitialValuePointer(), getMathObject(), getValues(), initializeDiscontinuousCreationPointer(), initializePointers(), and setValues().