COPASI API
4.40.278
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#include <CSteadyStateTask.h>
Public Member Functions | |
CSteadyStateTask (const CDataContainer *pParent, const CTaskEnum::Task &type=CTaskEnum::Task::steadyState) | |
CSteadyStateTask (const CSteadyStateTask &src, const CDataContainer *pParent) | |
const CEigen & | getEigenValues () const |
const CEigen & | getEigenValuesReduced () const |
const CMatrix< C_FLOAT64 > & | getJacobian () const |
const CDataArray * | getJacobianAnnotated () const |
const CMatrix< C_FLOAT64 > & | getJacobianReduced () const |
const CDataArray * | getJacobianXAnnotated () const |
const CSteadyStateMethod::ReturnCode & | getResult () const |
const CVectorCore< C_FLOAT64 > & | getState () const |
virtual const CTaskEnum::Method * | getValidMethods () const override |
virtual bool | initialize (const OutputFlag &of, COutputHandler *pOutputHandler, std::ostream *pOstream) override |
void | load (CReadConfig &configBuffer) |
virtual void | print (std::ostream *ostream) const override |
virtual bool | process (const bool &useInitialValues) override |
virtual bool | restore (const bool &updateModel=true) override |
virtual bool | updateMatrices () override |
virtual | ~CSteadyStateTask () |
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virtual bool | applyData (const CData &data, CUndoData::CChangeSet &changes) |
CCopasiTask (const CCopasiTask &src, const CDataContainer *pParent) | |
CCopasiTask (const CDataContainer *pParent, const CTaskEnum::Task &taskType, const std::string &type="Task") | |
void | cleanup () |
virtual void | clearCallBack () |
virtual void | createUndoData (CUndoData &undoData, const CUndoData::Type &type, const CData &oldData=CData(), const CCore::Framework &framework=CCore::Framework::ParticleNumbers) const |
const CProcessReportLevel & | getCallBack () const |
const CDescription & | getDescription () const |
virtual const std::string & | getKey () const |
CMathContainer * | getMathContainer () const |
CCopasiMethod * | getMethod () |
const CCopasiMethod * | getMethod () const |
COutputHandler * | getOutputHandler () const |
const OutputFlag & | getOutputMode () const |
CCopasiProblem * | getProblem () |
const CCopasiProblem * | getProblem () const |
CReport & | getReport () |
const CReport & | getReport () const |
const CResult & | getResult () const |
CCopasiParameterGroup * | getSliders () |
CTaskEnum::Task | getType () const |
const bool & | isScheduled () const |
const bool & | isUpdateModel () const |
virtual void | output (const COutputInterface::Activity &activity) |
virtual void | separate (const COutputInterface::Activity &activity) |
virtual bool | setCallBack (CProcessReportLevel callBack) |
void | setIgnoreProblemData (const bool &ignoreProblemData) |
void | setMathContainer (CMathContainer *pContainer) |
bool | setMethodType (const CTaskEnum::Method &type) |
void | setScheduled (const bool &scheduled) |
void | setType (const CTaskEnum::Task &type) |
virtual void | setUpdateModel (const bool &updateModel) |
virtual CData | toData () const |
virtual | ~CCopasiTask () |
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virtual bool | add (CDataObject *pObject, const bool &adopt=true) |
virtual bool | appendDeletedDependentData (CUndoData &undoData) const |
CDataContainer (const CDataContainer &src, const CDataContainer *pParent) | |
CDataContainer (const std::string &name, const CDataContainer *pParent=NO_PARENT, const std::string &type="CN", const CFlags< Flag > &flag=CFlags< Flag >::None) | |
virtual std::string | getChildObjectUnits (const CDataObject *pObject) const |
void | getDescendants (CDataObject::DataObjectSet &descendants, const bool &recursive=false) const |
virtual size_t | getIndex (const CDataObject *pObject) const |
virtual const CObjectInterface * | getObject (const CCommonName &cn) const override |
virtual objectMap & | getObjects () |
virtual const objectMap & | getObjects () const |
virtual const std::string | getUnits () const override |
virtual const CDataObject * | getValueObject () const override |
virtual CUndoObjectInterface * | insert (const CData &data) override |
void | objectRenamed (CDataObject *pObject, const std::string &oldName) |
virtual bool | remove (CDataObject *pObject) |
virtual | ~CDataContainer () |
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void | addIssue (const CIssue &issue) |
void | addReference (const CDataContainer *pReference) |
virtual void | calculateValue () override |
CDataObject (const CDataObject &src, const CDataContainer *pParent=NULL) | |
virtual void | destruct () override |
virtual CCommonName | getCN () const override |
virtual const CDataObject * | getDataObject () const override |
CDataContainer * | getObjectAncestor (const std::string &type) const |
CDataModel * | getObjectDataModel () const |
virtual std::string | getObjectDisplayName () const override |
const CObjectInterface * | getObjectFromCN (const CCommonName &cn) const |
const std::string & | getObjectName () const |
CDataContainer * | getObjectParent () const |
const std::string & | getObjectType () const |
virtual const CObjectInterface::ObjectSet & | getPrerequisites () const override |
virtual const CValidity & | getValidity () const override |
virtual void * | getValuePointer () const override |
bool | hasFlag (const Flag &flag) const |
virtual bool | isPrerequisiteForContext (const CObjectInterface *pObject, const CCore::SimulationContextFlag &context, const CObjectInterface::ObjectSet &changedObjects) const override |
bool | prerequisitsContains (const DataObjectSet &objects) const |
void | removeIssue (const CIssue &issue) |
void | removeReference (const CDataContainer *pReference) |
bool | setObjectName (const std::string &name) |
virtual bool | setObjectParent (const CDataContainer *pParent) |
void | validityChanged (const CValidity &changedValidity) override |
void | validityRemoved (const CValidity &changedValidity) |
virtual | ~CDataObject () |
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CObjectInterface () | |
CObjectInterface (const CObjectInterface &src) | |
virtual | ~CObjectInterface () |
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CUndoObjectInterface () | |
CUndoObjectInterface (const CUndoObjectInterface &src) | |
bool | generateUuid () |
const xg::Guid & | getUuid () const |
bool | setUuid (const std::string &uuid) |
bool | setUuid (const xg::Guid &uuid) |
virtual void | updateIndex (const size_t &index, const CUndoObjectInterface *pUndoObject) |
virtual | ~CUndoObjectInterface () |
Private Member Functions | |
void | cleanup () |
CSteadyStateTask () | |
void | initObjects () |
Friends | |
std::ostream & | operator<< (std::ostream &os, const CSteadyStateTask &A) |
Additional Inherited Members | |
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enum | eOutputFlagBase { INITIALIZE = 0x01 , STREAM = 0x02 , FINISH = 0x04 , REPORT = 0x10 , PLOT = 0x20 , TIME_SERIES = 0x40 } |
enum | OutputFlag { NO_OUTPUT = 0 , OUTPUT_BEFORE = INITIALIZE , OUTPUT_DURING = STREAM , OUTPUT_AFTER = FINISH , OUTPUT = REPORT | PLOT | STREAM , OUTPUT_SE = REPORT | PLOT | INITIALIZE | STREAM | FINISH , OUTPUT_UI = REPORT | PLOT | TIME_SERIES | INITIALIZE | STREAM | FINISH , ONLY_TIME_SERIES = TIME_SERIES | INITIALIZE | STREAM | FINISH } |
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typedef CDataObjectMap | objectMap |
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typedef std::set< const CDataObject * > | DataObjectSet |
enum | Flag { Container , Vector , Matrix , NameVector , Reference , ValueBool , ValueInt , ValueInt64 , ValueDbl , NonUniqueName , StaticString , ValueString , Separator , DisplayName , ModelEntity , Array , DataModel , Root , Gui , __SIZE } |
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typedef std::vector< const CDataContainer * > | ContainerList |
typedef std::set< const CObjectInterface * > | ObjectSet |
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static CCopasiTask * | fromData (const CData &data, CUndoObjectInterface *pParent) |
static bool | isValidMethod (const CTaskEnum::Method &method, const CTaskEnum::Method *validMethods) |
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static CDataContainer * | fromData (const CData &data, CUndoObjectInterface *pParent) |
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static CDataObject * | fromData (const CData &data, CUndoObjectInterface *pParent) |
static void | sanitizeObjectName (std::string &name) |
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static const CDataObject * | DataObject (const CObjectInterface *pInterface) |
static CObjectInterface * | GetObjectFromCN (const ContainerList &listOfContainer, const CCommonName &objName) |
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template<class CType > | |
static CType * | fromData (const CData &, CUndoObjectInterface *) |
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std::string | Error |
std::string | Warning |
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static const CObjectInterface::ContainerList | EmptyList |
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bool | isTaskValid () const |
virtual void | signalMathContainerChanged () |
virtual void | signalMethodChanged () |
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template<class CType > | |
CDataMatrixReference< CType > * | addMatrixReference (const std::string &name, CType &reference, const CFlags< Flag > &flag=CFlags< Flag >::None) |
template<class CType > | |
CDataObjectReference< CType > * | addObjectReference (const std::string &name, CType &reference, const CFlags< Flag > &flag=CFlags< Flag >::None) |
template<class CType > | |
CDataVectorReference< CType > * | addVectorReference (const std::string &name, CType &reference, const CFlags< Flag > &flag=CFlags< Flag >::None) |
CDataContainer (const CDataContainer &src) | |
void | initObjects () |
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CDataObject () | |
CDataObject (const std::string &name, const CDataContainer *pParent=static_cast< CDataContainer * >((void *) 0), const std::string &type="CN", const CFlags< Flag > &flag=CFlags< Flag >::None) | |
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CDescription | mDescription |
OutputFlag | mDoOutput |
bool | mIgnoreProblemData |
CVector< C_FLOAT64 > | mInitialState |
std::string | mKey |
unsigned C_INT32 | mOutputCounter |
CMathContainer * | mpContainer |
CCopasiMethod * | mpMethod |
COutputHandler * | mpOutputHandler |
CCopasiProblem * | mpProblem |
CProcessReportLevel | mProcessReport |
CCopasiParameterGroup * | mpSliders |
CReport | mReport |
CResult | mResult |
bool | mScheduled |
CTaskEnum::Task | mType |
bool | mUpdateModel |
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objectMap | mObjects |
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ObjectSet | mPrerequisits |
std::set< CDataContainer * > | mReferences |
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CValidity | mValidity |
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Default constructor
CSteadyStateTask::CSteadyStateTask | ( | const CDataContainer * | pParent, |
const CTaskEnum::Task & | type = CTaskEnum::Task::steadyState |
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Specific constructor
const | CDataContainer * pParent |
const | CTaskEnum::Task & type (default: steadyState) |
References CMethodFactory::create(), CCopasiTask::getType(), initObjects(), CCopasiTask::mpMethod, and CTaskEnum::Newton.
CSteadyStateTask::CSteadyStateTask | ( | const CSteadyStateTask & | src, |
const CDataContainer * | pParent | ||
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Copy constructor
const | CSteadyStateTask & src |
const | CDataContainer * pParent (default: NULL) |
References initObjects().
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Destructor
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const CEigen & CSteadyStateTask::getEigenValues | ( | ) | const |
Retrieves a the eigenvalues of the steady state.
References mEigenValues.
const CEigen & CSteadyStateTask::getEigenValuesReduced | ( | ) | const |
Retrieves a the eigenvalues of the steady state.
References mEigenValuesX.
Referenced by CLNATask::process().
Retrieves a the jacobian of the steady state.
References mJacobian.
Referenced by CMCAMethod::createLinkMatrix().
const CDataArray * CSteadyStateTask::getJacobianAnnotated | ( | ) | const |
References mpJacobianAnn.
Retrieves a the jacobian of the steady state.
References mJacobianReduced.
const CDataArray * CSteadyStateTask::getJacobianXAnnotated | ( | ) | const |
References mpJacobianXAnn.
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Converts the eigenvalues vector to matrix
CEigen | &eigenvalues |
References mResult.
Referenced by CLNATask::process(), and CMCAMethod::setSteadyStateTask().
const CVectorCore< C_FLOAT64 > & CSteadyStateTask::getState | ( | ) | const |
Retrieves a pointer to steady state.
References mSteadyState.
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Retrieve the list of valid methods
Reimplemented from CCopasiTask.
References CTaskEnum::Newton, and CTaskEnum::UnsetMethod.
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Initialize the task. If an ostream is given this ostream is used instead of the target specified in the report. This allows nested tasks to share the same output device.
const | OutputFlag & of |
COutputHandler | * pOutputHandler |
std::ostream | * pOstream (default: NULL) |
Reimplemented from CCopasiTask.
References CMathContainer::getState(), CSteadyStateProblem::initialize(), CSteadyStateMethod::initialize(), CCopasiTask::initialize(), CSteadyStateMethod::isValidProblem(), CCopasiTask::mpContainer, CCopasiTask::mpMethod, CCopasiTask::mpProblem, mSteadyState, and updateMatrices().
Referenced by CFitProblem::initialize(), CTimeSensTask::initialize(), and CTrajectoryTask::initialize().
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References mEigenvaluesMatrix, mEigenvaluesXMatrix, mJacobian, mJacobianReduced, mpEigenvaluesJacobianAnn, mpEigenvaluesJacobianXAnn, mpJacobianAnn, mpJacobianXAnn, CDataArray::Objects, CDataArray::setDescription(), CDataArray::setDimensionDescription(), CDataArray::setMode(), and CDataArray::Vector.
Referenced by CSteadyStateTask().
void CSteadyStateTask::load | ( | CReadConfig & | configBuffer | ) |
Loads parameters for this solver with data coming from a CReadConfig object. (CReadConfig object reads an input stream)
configbuffer | reference to a CReadConfig object. |
References CReadConfig::getVariable(), CReadConfig::LOOP, CCopasiTask::mpMethod, CCopasiTask::mpProblem, and CCopasiTask::mScheduled.
Referenced by CDataModel::loadModel().
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This is the output method for any object. The default implementation provided with CDataObject uses the ostream operator<< of the object to print the object.To override this default behavior one needs to reimplement the virtual print function.
std::ostream | * ostream |
Reimplemented from CDataObject.
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Process the task with or without initializing to the initial state.
const | bool & useInitialValues |
Reimplemented from CCopasiTask.
References COutputInterface::AFTER, CMathContainer::applyInitialValues(), CMatrix< CType >::array(), COutputInterface::BEFORE, C_FLOAT64, C_INT32, CEigen::calcEigenValues(), CSteadyStateMethod::doJacobian(), CMathContainer::getCountFixedEventTargets(), CEigen::getI(), CEigen::getR(), CSteadyStateMethod::getStabilityResolution(), CMathContainer::getState(), CMathContainer::isAutonomous(), CSteadyStateProblem::isJacobianRequested(), CSteadyStateProblem::isStabilityAnalysisRequested(), CMathContainer::isStateValid(), mEigenValues, mEigenvaluesMatrix, mEigenValuesX, mEigenvaluesXMatrix, mJacobian, mJacobianReduced, CCopasiTask::mpContainer, CCopasiTask::mpMethod, CCopasiTask::mpProblem, CCopasiTask::mProcessReport, mResult, mSteadyState, CSteadyStateMethod::notFound, CCopasiTask::output(), CSteadyStateMethod::process(), CMathContainer::pushAllTransientValues(), CMathContainer::setState(), CMatrix< CType >::size(), CVectorCore< CType >::size(), CEigen::stabilityAnalysis(), CMathContainer::updateSimulatedValues(), and CMathContainer::updateTransientDataValues().
Referenced by CFitProblem::calculate(), CFitProblem::calculateCrossValidation(), CLNATask::process(), CMCATask::process(), CTimeSensTask::processStart(), and CTrajectoryTask::processStart().
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Perform necessary cleanup procedures
Reimplemented from CCopasiTask.
References CMathContainer::getState(), CMathContainer::isStateValid(), CCopasiTask::mInitialState, CCopasiTask::mpContainer, mResult, mSteadyState, CCopasiTask::mUpdateModel, CSteadyStateMethod::notFound, CCore::ParticleNumbers, CMathContainer::pushInitialState(), CCopasiTask::setCallBack(), CMathContainer::setInitialState(), CMathContainer::setState(), CMathContainer::updateInitialValues(), and CMathContainer::updateSimulatedValues().
Referenced by CFitProblem::restore().
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Resizes result matrices and updates array annotations for a specific task. This is used when we need to know about the data structures of a task result without actually performing the task, e.g. when selecting objects for output. For now we assume that this functionality is also performed when initialize() is called.
Reimplemented from CCopasiTask.
References CVectorCore< CType >::array(), CMathContainer::getCountFixedEventTargets(), CMathObject::getDataObject(), CMathContainer::getMathObject(), CDataObject::getObjectParent(), CMathContainer::getState(), mEigenvaluesMatrix, mEigenvaluesXMatrix, mJacobian, mJacobianReduced, CCopasiTask::mpContainer, mpJacobianAnn, mpJacobianXAnn, CDataArray::resize(), CMatrix< CType >::resize(), CDataArray::setAnnotation(), and CVectorCore< CType >::size().
Referenced by initialize().
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The Eigenvalues of the Jacobian of the system
Referenced by getEigenValues(), and process().
The Eigenvalues matrix of the Jacobian of the system
Referenced by initObjects(), process(), and updateMatrices().
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The Eigenvalues of the Jacobian of the reduced system
Referenced by getEigenValuesReduced(), and process().
The Eigenvalues matrix of the Jacobian of the reduced system
Referenced by initObjects(), process(), and updateMatrices().
The jacobian of the steady state.
Referenced by getJacobian(), initObjects(), process(), and updateMatrices().
The jacobian of the steady state.
Referenced by getJacobianReduced(), initObjects(), process(), and updateMatrices().
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Referenced by initObjects().
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Referenced by initObjects().
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Referenced by getJacobianAnnotated(), initObjects(), and updateMatrices().
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Referenced by getJacobianXAnnotated(), initObjects(), and updateMatrices().
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The result of the steady state analysis.
Referenced by getResult(), process(), and restore().
A pointer to the found steady state.
Referenced by getState(), initialize(), process(), and restore().