CTrajectoryTask Class Reference

#include <CTrajectoryTask.h>

Inheritance diagram for CTrajectoryTask:

Collaboration diagram for CTrajectoryTask:

Public Member Functions
virtual CCopasiMethod *	createMethod (const int &type) const
	CTrajectoryTask (const CCopasiContainer *pParent=NULL)
	CTrajectoryTask (const CTrajectoryTask &src, const CCopasiContainer *pParent=NULL)
CState *	getState ()
const CTimeSeries &	getTimeSeries () const
virtual bool	initialize (const OutputFlag &of, COutputHandler *pOutputHandler, std::ostream *pOstream)
void	load (CReadConfig &configBuffer)
virtual bool	process (const bool &useInitialValues)
void	processStart (const bool &useInitialValues)
bool	processStep (const C_FLOAT64 &nextTime)
virtual bool	restore ()
virtual bool	setMethodType (const int &type)
	~CTrajectoryTask ()
Public Member Functions inherited from CCopasiTask
	CCopasiTask (const std::string &name="NoName", const CCopasiContainer *pParent=NULL, const std::string &type="Task")
	CCopasiTask (const Type &taskType, const CCopasiContainer *pParent=NULL, const std::string &type="Task")
	CCopasiTask (const CCopasiTask &src, const CCopasiContainer *pParent=NULL)
void	cleanup ()
CProcessReport *	getCallBack () const
const CDescription &	getDescription () const
virtual const std::string &	getKey () const
CCopasiMethod *	getMethod ()
const CCopasiMethod *	getMethod () const
COutputHandler *	getOutputHandler () const
const OutputFlag &	getOutputMode () const
CCopasiProblem *	getProblem ()
const CCopasiProblem *	getProblem () const
CReport &	getReport ()
const CResult &	getResult () const
CCopasiParameterGroup *	getSliders ()
Type	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 (CProcessReport *pCallBack)
void	setScheduled (const bool &scheduled)
void	setType (const Type &type)
void	setUpdateModel (const bool &updateModel)
virtual bool	updateMatrices ()
virtual	~CCopasiTask ()
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 CObjectInterface *	getObject (const CCopasiObjectName &cn) 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 CCopasiObjectName	getCN () const
virtual const DataObjectSet &	getDirectDependencies (const DataObjectSet &context=DataObjectSet()) 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 ()
Public Member Functions inherited from CObjectInterface
	CObjectInterface ()
virtual	~CObjectInterface ()

Static Public Attributes
static const unsigned int	ValidMethods []
Static Public Attributes inherited from CCopasiTask
static const std::string	TypeName []
static const unsigned int	ValidMethods []
static const char *	XMLType []
Static Public Attributes inherited from CCopasiContainer
static const std::vector < CCopasiContainer * >	EmptyList

Private Member Functions
void	cleanup ()

Private Attributes
C_FLOAT64	mOutputStartTime
CState *	mpCurrentState
const C_FLOAT64 *	mpCurrentTime
bool(*	mpLess )(const C_FLOAT64 &, const C_FLOAT64 &)
bool(*	mpLessOrEqual )(const C_FLOAT64 &, const C_FLOAT64 &)
CTrajectoryMethod *	mpTrajectoryMethod
CTrajectoryProblem *	mpTrajectoryProblem
CTimeSeries	mTimeSeries
bool	mTimeSeriesRequested
bool	mUpdateMoieties

Additional Inherited Members
Public Types inherited from CCopasiTask
enum	eOutputFlagBase {   INITIALIZE = 0x01, STREAM = 0x02, FINISH = 0x04, REPORT = 0x10,   PLOT = 0x20, TIME_SERIES = 0x40 }
enum	OutputFlag {   NO_OUTPUT = 0, OUTPUT_BEFORE = INITIALIZE, 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 }
enum	Type {   steadyState = 0, timeCourse, scan, fluxMode,   optimization, parameterFitting, mca, lyap,   tssAnalysis, sens, moieties, crosssection,   lna, unset }
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 CCopasiTask
static bool	isValidMethod (const unsigned int &method, const unsigned int *validMethods)
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)
Public Attributes inherited from CCopasiTask
std::string	Error
std::string	Warning
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 CCopasiContainer
template<class CType >
CCopasiObject *	addMatrixReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)
template<class CType >
CCopasiObject *	addObjectReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)
template<class CType >
CCopasiObject *	addVectorReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)
void	initObjects ()
Protected Member Functions inherited from CCopasiObject
	CCopasiObject ()
	CCopasiObject (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &type="CN", const unsigned C_INT32 &flag=0)
Protected Attributes inherited from CCopasiTask
CDescription	mDescription
OutputFlag	mDoOutput
std::string	mKey
unsigned C_INT32	mOutputCounter
CProcessReport *	mpCallBack
CState *	mpInitialState
CCopasiMethod *	mpMethod
COutputHandler *	mpOutputHandler
CCopasiProblem *	mpProblem
CCopasiParameterGroup *	mpSliders
CReport	mReport
CResult	mResult
bool	mScheduled
Type	mType
bool	mUpdateModel
Protected Attributes inherited from CCopasiContainer
objectMap	mObjects
Static Protected Attributes inherited from CCopasiObject
static CRenameHandler *	smpRenameHandler = NULL

Detailed Description

Definition at line 37 of file CTrajectoryTask.h.

Constructor & Destructor Documentation

CTrajectoryTask::CTrajectoryTask

(

const CCopasiContainer *

pParent = NULL

)

Default constructor

Parameters

const

CCopasiContainer * pParent (default: NULL)

Definition at line 73 of file CTrajectoryTask.cpp.

References CCopasiContainer::add(), createMethod(), CCopasiMethod::deterministic, CCopasiParameterGroup::getParameter(), CCopasiParameter::getValue(), CCopasiTask::mpMethod, CCopasiTask::mpProblem, mUpdateMoieties, and CCopasiParameter::Value::pBOOL.

                                                                :
  CCopasiTask(CCopasiTask::timeCourse, pParent),
  mTimeSeriesRequested(true),
  mTimeSeries(),
  mpTrajectoryProblem(NULL),
  mpTrajectoryMethod(NULL),
  mUpdateMoieties(false),
  mpCurrentState(NULL),
  mpCurrentTime(NULL),
  mOutputStartTime(0.0),
  mpLessOrEqual(&fle),
  mpLess(&fl)
{
  mpProblem = new CTrajectoryProblem(this);
  mpMethod = createMethod(CCopasiMethod::deterministic);
  this->add(mpMethod, true);

  CCopasiParameter * pParameter = mpMethod->getParameter("Integrate Reduced Model");

  if (pParameter != NULL)
    mUpdateMoieties = *pParameter->getValue().pBOOL;
  else
    mUpdateMoieties = false;
}

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

Copy constructor

Parameters

const	CTrajectoryTask & src
const	CCopasiContainer * pParent (default: NULL)

Definition at line 98 of file CTrajectoryTask.cpp.

References CCopasiContainer::add(), createMethod(), CCopasiParameterGroup::elevateChildren(), CCopasiMethod::getSubType(), CCopasiParameter::getValue(), CCopasiTask::mpMethod, CCopasiTask::mpProblem, mUpdateMoieties, and CCopasiParameter::Value::pBOOL.

                                                                  :
  CCopasiTask(src, pParent),
  mTimeSeriesRequested(src.mTimeSeriesRequested),
  mTimeSeries(),
  mpTrajectoryProblem(NULL),
  mpTrajectoryMethod(NULL),
  mUpdateMoieties(false),
  mpCurrentState(NULL),
  mpCurrentTime(NULL),
  mOutputStartTime(0.0),
  mpLessOrEqual(src.mpLessOrEqual),
  mpLess(src.mpLess)
{
  mpProblem =
    new CTrajectoryProblem(*static_cast< CTrajectoryProblem * >(src.mpProblem), this);

  mpMethod = createMethod(src.mpMethod->getSubType());
  * mpMethod = * src.mpMethod;

  mpMethod->elevateChildren();

  this->add(mpMethod, true);

  CCopasiParameter * pParameter = mpMethod->getParameter("Integrate Reduced Model");

  if (pParameter != NULL)
    mUpdateMoieties = *pParameter->getValue().pBOOL;
  else
    mUpdateMoieties = false;
}

CTrajectoryTask::~CTrajectoryTask

(

)

Destructor

Definition at line 130 of file CTrajectoryTask.cpp.

References cleanup().

{
  cleanup();
}

Member Function Documentation

void CTrajectoryTask::cleanup ( )

private

cleanup()

Definition at line 135 of file CTrajectoryTask.cpp.

References mpCurrentState, and pdelete.

Referenced by ~CTrajectoryTask().

{
  pdelete(mpCurrentState);
}

CCopasiMethod * CTrajectoryTask::createMethod ( const int &  type ) const

virtual

Create a method of the specified type to solve the task. It is the duty of the caller to release the CCopasiMethod.

Parameters

const

CCopasiMethod::SubType & type

Returns

CCopasiMethod *

Reimplemented from CCopasiTask.

Definition at line 537 of file CTrajectoryTask.cpp.

References CTrajectoryMethod::createMethod().

Referenced by CTrajectoryTask(), and setMethodType().

{
  CCopasiMethod::SubType Type = (CCopasiMethod::SubType) type;

  return CTrajectoryMethod::createMethod(Type);
}

CState * CTrajectoryTask::getState

(

)

Retrieves a pointer to current state of the integration.

Returns

CState * pState

Definition at line 544 of file CTrajectoryTask.cpp.

References mpCurrentState.

Referenced by CNewtonMethod::doIntegration().

{return mpCurrentState;}

const CTimeSeries & CTrajectoryTask::getTimeSeries

(

)

const

gets a reference to the time series

Returns

time series

Definition at line 547 of file CTrajectoryTask.cpp.

References mTimeSeries.

Referenced by CQGLNetworkPainter::createDataSets(), QTimeCourseAnimation::getScales(), getTimeSeriesFromTask(), and QTimeCourseAnimation::initialize().

{return mTimeSeries;}

bool CTrajectoryTask::initialize ( const OutputFlag &  of, COutputHandler *  pOutputHandler, std::ostream *  pOstream  )

virtual

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.

Parameters

const	OutputFlag & of
COutputHandler	* pOutputHandler
std::ostream	* pOstream (default: NULL)

Returns

bool success

Reimplemented from CCopasiTask.

Definition at line 161 of file CTrajectoryTask.cpp.

References COutputHandler::addInterface(), CTimeSeries::allocate(), CTimeSeries::clear(), CTrajectoryProblem::getContinueSimultaneousEvents(), CModel::getMathModel(), CCopasiProblem::getModel(), CCopasiParameterGroup::getParameter(), CMathModel::getProcessQueue(), CModel::getState(), CTrajectoryProblem::getStepNumber(), CState::getTime(), CCopasiParameter::getValue(), CCopasiTask::initialize(), CCopasiMethod::isValidProblem(), mpCurrentState, mpCurrentTime, CCopasiTask::mpMethod, CCopasiTask::mpProblem, mpTrajectoryMethod, mpTrajectoryProblem, mTimeSeries, mTimeSeriesRequested, mUpdateMoieties, CCopasiParameter::Value::pBOOL, pdelete, CProcessQueue::setContinueSimultaneousEvents(), CTrajectoryMethod::setProblem(), CCopasiTask::TIME_SERIES, and CTrajectoryProblem::timeSeriesRequested().

Referenced by CFitProblem::initialize(), CNewtonMethod::initialize(), and test000087::test_simulate_reaction_flux_reference_1().

{
  assert(mpProblem && mpMethod);

  mpTrajectoryProblem = dynamic_cast<CTrajectoryProblem *>(mpProblem);
  assert(mpTrajectoryProblem);

  mpTrajectoryMethod = dynamic_cast<CTrajectoryMethod *>(mpMethod);
  assert(mpTrajectoryMethod);

  mpTrajectoryMethod->setProblem(mpTrajectoryProblem);

  bool success = mpMethod->isValidProblem(mpProblem);

  CCopasiParameter * pParameter = mpMethod->getParameter("Integrate Reduced Model");

  if (pParameter != NULL)
    mUpdateMoieties = *pParameter->getValue().pBOOL;
  else
    mUpdateMoieties = false;

  pdelete(mpCurrentState);
  mpCurrentState = new CState(mpTrajectoryProblem->getModel()->getState());
  mpCurrentTime = &mpCurrentState->getTime();

  //mpOutputStartTime = & mpTrajectoryProblem->getOutputStartTime();

  // Handle the time series as a regular output.
  mTimeSeriesRequested = mpTrajectoryProblem->timeSeriesRequested();

  if ((pOutputHandler != NULL) &&
      mTimeSeriesRequested &&
      (of & CCopasiTask::TIME_SERIES))
    {
      mTimeSeries.allocate(mpTrajectoryProblem->getStepNumber());
      pOutputHandler->addInterface(&mTimeSeries);
    }
  else
    {
      mTimeSeries.clear();
    }

  mpTrajectoryProblem->getModel()->getMathModel()->getProcessQueue().setContinueSimultaneousEvents(mpTrajectoryProblem->getContinueSimultaneousEvents());

  if (!CCopasiTask::initialize(of, pOutputHandler, pOstream)) success = false;

  return success;
}

void CTrajectoryTask::load

(

CReadConfig &

configBuffer

)

Loads parameters for this solver with data coming from a CReadConfig object. (CReadConfig object reads an input stream)

Parameters

configbuffer

reference to a CReadConfig object.

Definition at line 140 of file CTrajectoryTask.cpp.

References CCopasiContainer::add(), CTrajectoryMethod::createMethod(), CCopasiParameterGroup::getParameter(), CCopasiParameter::getValue(), CReadConfig::getVariable(), CReadConfig::LOOP, CCopasiTask::mpMethod, CCopasiTask::mpProblem, CCopasiTask::mScheduled, mUpdateMoieties, CCopasiParameter::Value::pBOOL, and pdelete.

Referenced by CCopasiDataModel::loadModel().

{
  configBuffer.getVariable("Dynamics", "bool", &mScheduled,
                           CReadConfig::LOOP);

  pdelete(mpProblem);
  mpProblem = new CTrajectoryProblem(this);
  ((CTrajectoryProblem *) mpProblem)->load(configBuffer);

  pdelete(mpMethod);
  mpMethod = CTrajectoryMethod::createMethod();
  this->add(mpMethod, true);

  CCopasiParameter * pParameter = mpMethod->getParameter("Integrate Reduced Model");

  if (pParameter != NULL)
    mUpdateMoieties = *pParameter->getValue().pBOOL;

  ((CTrajectoryMethod *)mpMethod)->setProblem((CTrajectoryProblem *) mpProblem);
}

bool CTrajectoryTask::process ( const bool &  useInitialValues )

virtual

Process the task with or without initializing to the initial state.

Parameters

const

bool & useInitialValues

Returns

bool success

Reimplemented from CCopasiTask.

Definition at line 212 of file CTrajectoryTask.cpp.

References CProcessReport::addItem(), COutputInterface::AFTER, COutputInterface::BEFORE, bl(), ble(), C_FLOAT64, C_INT32, COutputInterface::DURING, CCopasiMessage::ERROR, CCopasiMessage::EXCEPTION, CProcessReport::finishItem(), fl(), fle(), CTrajectoryProblem::getDuration(), CCopasiException::getMessage(), CCopasiProblem::getModel(), CTrajectoryProblem::getOutputStartTime(), CTrajectoryProblem::getStepSize(), MCTrajectoryMethod, MCTrajectoryProblem, min, mOutputStartTime, CCopasiTask::mpCallBack, mpCurrentState, mpCurrentTime, mpLess, mpLessOrEqual, mpTrajectoryProblem, mUpdateMoieties, CCopasiTask::output(), processStart(), processStep(), CProcessReport::progressItem(), CProcessReport::setName(), CModel::setState(), and CModel::updateSimulatedValues().

Referenced by CNewtonMethod::doIntegration(), and test000087::test_simulate_reaction_flux_reference_1().

{
  //*****

  processStart(useInitialValues);

  //*****

  //size_t FailCounter = 0;

  C_FLOAT64 Duration = mpTrajectoryProblem->getDuration();
  C_FLOAT64 StepSize = mpTrajectoryProblem->getStepSize();
  C_FLOAT64 StepNumber = fabs(Duration) / StepSize;

  if (isnan(StepNumber) || StepNumber < 1.0)
    StepNumber = 1.0;

  //the output starts only after "outputStartTime" has passed
  if (useInitialValues)
    mOutputStartTime = mpTrajectoryProblem->getOutputStartTime();
  else
    mOutputStartTime = *mpCurrentTime + mpTrajectoryProblem->getOutputStartTime();

  C_FLOAT64 NextTimeToReport;

  const C_FLOAT64 EndTime = *mpCurrentTime + Duration;
  const C_FLOAT64 StartTime = *mpCurrentTime;
  C_FLOAT64 CompareEndTime;

  if (StepSize < 0.0)
    {
      mpLessOrEqual = &ble;
      mpLess = &bl;

      // It suffices to reach the end time within machine precision
      CompareEndTime = EndTime + 100.0 * (fabs(EndTime) * std::numeric_limits< C_FLOAT64 >::epsilon() + std::numeric_limits< C_FLOAT64 >::min());
    }
  else
    {
      mpLessOrEqual = &fle;
      mpLess = &fl;

      // It suffices to reach the end time within machine precision
      CompareEndTime = EndTime - 100.0 * (fabs(EndTime) * std::numeric_limits< C_FLOAT64 >::epsilon() + std::numeric_limits< C_FLOAT64 >::min());
    }

  unsigned C_INT32 StepCounter = 1;

  if (StepSize == 0.0 && Duration != 0.0)
    {
      CCopasiMessage(CCopasiMessage::ERROR, MCTrajectoryProblem + 1, StepSize);
      return false;
    }

  output(COutputInterface::BEFORE);

  bool flagProceed = true;
  C_FLOAT64 handlerFactor = 100.0 / Duration;

  C_FLOAT64 Percentage = 0;
  size_t hProcess;

  if (mpCallBack != NULL && StepNumber > 1.0)
    {
      mpCallBack->setName("performing simulation...");
      C_FLOAT64 hundred = 100;
      hProcess = mpCallBack->addItem("Completion",
                                     Percentage,
                                     &hundred);
    }

  if ((*mpLessOrEqual)(mOutputStartTime, *mpCurrentTime)) output(COutputInterface::DURING);

  try
    {
      do
        {
          // This is numerically more stable then adding
          // mpTrajectoryProblem->getStepSize().
          NextTimeToReport =
            StartTime + (EndTime - StartTime) * StepCounter++ / StepNumber;

          flagProceed &= processStep(NextTimeToReport);

          if (mpCallBack != NULL && StepNumber > 1.0)
            {
              Percentage = (*mpCurrentTime - StartTime) * handlerFactor;
              flagProceed &= mpCallBack->progressItem(hProcess);
            }

          if ((*mpLessOrEqual)(mOutputStartTime, *mpCurrentTime))
            {
              output(COutputInterface::DURING);
            }
        }
      while ((*mpLess)(*mpCurrentTime, CompareEndTime) && flagProceed);
    }

  catch (int)
    {
      mpTrajectoryProblem->getModel()->setState(*mpCurrentState);
      mpTrajectoryProblem->getModel()->updateSimulatedValues(mUpdateMoieties);

      if ((*mpLessOrEqual)(mOutputStartTime, *mpCurrentTime))
        {
          output(COutputInterface::DURING);
        }

      if (mpCallBack != NULL && StepNumber > 1.0) mpCallBack->finishItem(hProcess);

      output(COutputInterface::AFTER);

      CCopasiMessage(CCopasiMessage::EXCEPTION, MCTrajectoryMethod + 16);
    }

  catch (CCopasiException & Exception)
    {
      mpTrajectoryProblem->getModel()->setState(*mpCurrentState);
      mpTrajectoryProblem->getModel()->updateSimulatedValues(mUpdateMoieties);

      if ((*mpLessOrEqual)(mOutputStartTime, *mpCurrentTime))
        {
          output(COutputInterface::DURING);
        }

      if (mpCallBack != NULL && StepNumber > 1.0) mpCallBack->finishItem(hProcess);

      output(COutputInterface::AFTER);

      throw CCopasiException(Exception.getMessage());
    }

  if (mpCallBack != NULL && StepNumber > 1.0) mpCallBack->finishItem(hProcess);

  output(COutputInterface::AFTER);

  return true;
}

void CTrajectoryTask::processStart

(

const bool &

useInitialValues

)

Starts the process of integration by calling CTrajectoryMethod::start

Parameters

const

bool & useInitialValues

Definition at line 351 of file CTrajectoryTask.cpp.

References CModel::applyInitialValues(), CCopasiProblem::getModel(), CModel::getState(), mpCurrentState, mpTrajectoryMethod, mpTrajectoryProblem, CTrajectoryMethod::setCurrentState(), and CTrajectoryMethod::start().

Referenced by CFitProblem::calculate(), CFitProblem::calculateCrossValidation(), and process().

{
  if (useInitialValues)
    mpTrajectoryProblem->getModel()->applyInitialValues();

  *mpCurrentState = mpTrajectoryProblem->getModel()->getState();

  mpTrajectoryMethod->setCurrentState(mpCurrentState);
  mpTrajectoryMethod->start(mpCurrentState);

  return;
}

bool CTrajectoryTask::processStep

(

const C_FLOAT64 &

nextTime

)

Integrates one step

Parameters

const

C_FLOAT64 & nextTime

Returns

bool success;

Definition at line 364 of file CTrajectoryTask.cpp.

References C_FLOAT64, COutputInterface::DURING, CCopasiMessage::EXCEPTION, CTrajectoryMethod::FAILURE, CCopasiProblem::getModel(), CTrajectoryProblem::getOutputEvent(), CModel::getProcessQueueExecutionTime(), CTrajectoryMethod::getRoots(), CModel::getState(), MCTrajectoryMethod, min, mOutputStartTime, CCopasiTask::mpCallBack, mpCurrentState, mpCurrentTime, mpLessOrEqual, mpTrajectoryMethod, mpTrajectoryProblem, mUpdateMoieties, CTrajectoryMethod::NORMAL, CCopasiTask::output(), CProcessReport::proceed(), CModel::processQueue(), CModel::processRoots(), CTrajectoryMethod::ROOT, CModel::setState(), CTrajectoryMethod::stateChanged(), CTrajectoryMethod::step(), and CModel::updateSimulatedValues().

Referenced by CFitProblem::calculate(), CFitProblem::calculateCrossValidation(), and process().

{
  CModel * pModel = mpTrajectoryProblem->getModel();
  bool StateChanged = false;
  bool proceed = true;

  C_FLOAT64 Tolerance = 100.0 * (fabs(endTime) * std::numeric_limits< C_FLOAT64 >::epsilon() + std::numeric_limits< C_FLOAT64 >::min());
  C_FLOAT64 NextTime = endTime;

  while (proceed)
    {
      // TODO Provide a call back method for resolving simultaneous assignments.
      StateChanged = pModel->processQueue(*mpCurrentTime, false, NULL);

      if (StateChanged)
        {
          if ((*mpLessOrEqual)(mOutputStartTime, *mpCurrentTime) &&
              mpTrajectoryProblem->getOutputEvent())
            {
              output(COutputInterface::DURING);
            }

          *mpCurrentState = pModel->getState();
          mpTrajectoryMethod->stateChanged();
          StateChanged = false;
        }

      // std::min suffices since events are only supported in forward integration.
      NextTime = std::min(endTime, pModel->getProcessQueueExecutionTime());

      switch (mpTrajectoryMethod->step(NextTime - *mpCurrentTime))
        {
          case CTrajectoryMethod::NORMAL:
            pModel->setState(*mpCurrentState);
            pModel->updateSimulatedValues(mUpdateMoieties);

            if ((*mpLessOrEqual)(mOutputStartTime, *mpCurrentTime) &&
                *mpCurrentTime == pModel->getProcessQueueExecutionTime() &&
                mpTrajectoryProblem->getOutputEvent())
              {
                output(COutputInterface::DURING);
              }

            // TODO Provide a call back method for resolving simultaneous assignments.
            StateChanged = pModel->processQueue(*mpCurrentTime, true, NULL);

            if (fabs(*mpCurrentTime - endTime) < Tolerance)
              {
                if (StateChanged)
                  {
                    *mpCurrentState = pModel->getState();
                    mpTrajectoryMethod->stateChanged();
                    StateChanged = false;
                  }

                return true;
              }

            if (StateChanged)
              {
                if ((*mpLessOrEqual)(mOutputStartTime, *mpCurrentTime) &&
                    mpTrajectoryProblem->getOutputEvent())
                  {
                    output(COutputInterface::DURING);
                  }

                *mpCurrentState = pModel->getState();
                mpTrajectoryMethod->stateChanged();
                StateChanged = false;
              }

            break;

          case CTrajectoryMethod::ROOT:
            pModel->setState(*mpCurrentState);
            pModel->updateSimulatedValues(mUpdateMoieties);

            pModel->processRoots(*mpCurrentTime, true, true, mpTrajectoryMethod->getRoots());

            if ((*mpLessOrEqual)(mOutputStartTime, *mpCurrentTime) &&
                *mpCurrentTime == pModel->getProcessQueueExecutionTime() &&
                mpTrajectoryProblem->getOutputEvent())
              {
                output(COutputInterface::DURING);
              }

            // TODO Provide a call back method for resolving simultaneous assignments.
            StateChanged = pModel->processQueue(*mpCurrentTime, true, NULL);

            pModel->processRoots(*mpCurrentTime, false, true, mpTrajectoryMethod->getRoots());

            // If the root happens to coincide with end of the step we have to return
            if (fabs(*mpCurrentTime - endTime) < Tolerance)
              {
                if (StateChanged)
                  {
                    *mpCurrentState = pModel->getState();
                    mpTrajectoryMethod->stateChanged();
                    StateChanged = false;
                  }

                return true;
              }

            if ((*mpLessOrEqual)(mOutputStartTime, *mpCurrentTime) &&
                (StateChanged || *mpCurrentTime == pModel->getProcessQueueExecutionTime()) &&
                mpTrajectoryProblem->getOutputEvent())
              {
                output(COutputInterface::DURING);
              }

            if (StateChanged)
              {
                *mpCurrentState = pModel->getState();
                mpTrajectoryMethod->stateChanged();
                StateChanged = false;
              }

            break;

          case CTrajectoryMethod::FAILURE:
            CCopasiMessage(CCopasiMessage::EXCEPTION, MCTrajectoryMethod + 12);

            return false;
            break;
        }

      proceed = mpCallBack == NULL || mpCallBack->proceed();
    }

  return proceed;
}

bool CTrajectoryTask::restore ( )

virtual

Perform necessary cleanup procedures

Reimplemented from CCopasiTask.

Definition at line 497 of file CTrajectoryTask.cpp.

References CCopasiProblem::getModel(), CModel::getState(), mpCurrentState, CCopasiTask::mpProblem, CCopasiTask::mUpdateModel, mUpdateMoieties, CCopasiTask::restore(), CModel::setInitialState(), CModel::setState(), CModel::updateInitialValues(), and CModel::updateSimulatedValues().

Referenced by CFitProblem::restore(), and test000087::test_simulate_reaction_flux_reference_1().

{
  bool success = CCopasiTask::restore();

  if (mUpdateModel)
    {
      CModel * pModel = mpProblem->getModel();

      pModel->setState(*mpCurrentState);
      pModel->updateSimulatedValues(mUpdateMoieties);
      pModel->setInitialState(pModel->getState());
      pModel->updateInitialValues();
    }

  return success;
}

bool CTrajectoryTask::setMethodType ( const int &  type )

virtual

Set the method type applied to solve the task

Parameters

const

CCopasiMethod::SubType & type

Returns

bool success

Reimplemented from CCopasiTask.

Definition at line 514 of file CTrajectoryTask.cpp.

References CCopasiContainer::add(), createMethod(), CCopasiParameterGroup::getParameter(), CCopasiMethod::getSubType(), CCopasiParameter::getValue(), CCopasiTask::isValidMethod(), CCopasiTask::mpMethod, mUpdateMoieties, CCopasiParameter::Value::pBOOL, pdelete, and ValidMethods.

Referenced by CNewtonMethod::initialize(), test000087::test_simulate_reaction_flux_reference_1(), and SEDMLImporter::updateCopasiTaskForSimulation().

{
  CCopasiMethod::SubType Type = (CCopasiMethod::SubType) type;

  if (!isValidMethod(Type, ValidMethods)) return false;

  if (mpMethod->getSubType() == Type) return true;

  pdelete(mpMethod);
  mpMethod = createMethod(Type);
  this->add(mpMethod, true);

  CCopasiParameter * pParameter = mpMethod->getParameter("Integrate Reduced Model");

  if (pParameter != NULL)
    mUpdateMoieties = *pParameter->getValue().pBOOL;
  else
    mUpdateMoieties = false;

  return true;
}

Member Data Documentation

C_FLOAT64 CTrajectoryTask::mOutputStartTime

private

A pointer to the time at which the output starts.

Definition at line 86 of file CTrajectoryTask.h.

Referenced by process(), and processStep().

CState* CTrajectoryTask::mpCurrentState

private

A pointer to the current state of the integration.

Definition at line 76 of file CTrajectoryTask.h.

Referenced by cleanup(), getState(), initialize(), process(), processStart(), processStep(), and restore().

const C_FLOAT64* CTrajectoryTask::mpCurrentTime

private

A pointer to the current time of the integration.

Definition at line 81 of file CTrajectoryTask.h.

Referenced by initialize(), process(), and processStep().

bool(* CTrajectoryTask::mpLess)(const C_FLOAT64 &, const C_FLOAT64 &)

private

A pointer to less comparison

Definition at line 96 of file CTrajectoryTask.h.

Referenced by process().

bool(* CTrajectoryTask::mpLessOrEqual)(const C_FLOAT64 &, const C_FLOAT64 &)

private

A pointer to lessOrEqual comparison

Definition at line 91 of file CTrajectoryTask.h.

Referenced by process(), and processStep().

CTrajectoryMethod* CTrajectoryTask::mpTrajectoryMethod

private

A pointer to the trajectory method

Definition at line 66 of file CTrajectoryTask.h.

Referenced by initialize(), processStart(), and processStep().

CTrajectoryProblem* CTrajectoryTask::mpTrajectoryProblem

private

A pointer to the trajectory Problem

Definition at line 61 of file CTrajectoryTask.h.

Referenced by initialize(), process(), processStart(), and processStep().

CTimeSeries CTrajectoryTask::mTimeSeries

private

the time series (if requested)

Definition at line 56 of file CTrajectoryTask.h.

Referenced by getTimeSeries(), and initialize().

bool CTrajectoryTask::mTimeSeriesRequested

private

whether the time series should be stored in mTimeSeries

Definition at line 51 of file CTrajectoryTask.h.

Referenced by initialize().

bool CTrajectoryTask::mUpdateMoieties

private

Indicates whether we need to update moieties.

Definition at line 71 of file CTrajectoryTask.h.

Referenced by CTrajectoryTask(), initialize(), load(), process(), processStep(), restore(), and setMethodType().

const unsigned int CTrajectoryTask::ValidMethods

static

Initial value:

=
{
  CCopasiMethod::deterministic,
  CCopasiMethod::stochastic,
  CCopasiMethod::directMethod,
  CCopasiMethod::tauLeap,
  CCopasiMethod::adaptiveSA,
  CCopasiMethod::hybrid,
  CCopasiMethod::hybridLSODA,



 
  CCopasiMethod::unset
}

The methods which can be selected for performing this task.

Definition at line 44 of file CTrajectoryTask.h.

Referenced by CQTrajectoryWidget::init(), and setMethodType().

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

• CTrajectoryTask.h
• CTrajectoryTask.cpp