CState Class Reference

#include <CState.h>

Public Member Functions
C_FLOAT64 *	beginDependent ()
const C_FLOAT64 *	beginDependent () const
C_FLOAT64 *	beginFixed ()
const C_FLOAT64 *	beginFixed () const
C_FLOAT64 *	beginIndependent ()
const C_FLOAT64 *	beginIndependent () const
	CState ()
	CState (const CState &src)
C_FLOAT64 *	endDependent ()
const C_FLOAT64 *	endDependent () const
C_FLOAT64 *	endFixed ()
const C_FLOAT64 *	endFixed () const
C_FLOAT64 *	endIndependent ()
const C_FLOAT64 *	endIndependent () const
size_t	getNumDependent () const
size_t	getNumFixed () const
size_t	getNumIndependent () const
size_t	getNumVariable () const
const C_FLOAT64 &	getTime () const
bool	isValid () const
CState &	operator= (const CState &rhs)
void	setTime (const C_FLOAT64 &time)
	~CState ()

Protected Member Functions
C_FLOAT64 *	resize (const size_t &size)
void	updateIterator (const size_t &numIndependent, const size_t &numDependent, const size_t &numFixed)

Private Attributes
C_FLOAT64 *	mpBeginDependent
C_FLOAT64 *	mpBeginFixed
C_FLOAT64 *	mpBeginIndependent
C_FLOAT64 *	mpEnd
C_FLOAT64 *	mpValues
size_t	mSize
bool	mUpdateDependentRequired

Friends
class	CStateTemplate
std::ostream &	operator<< (std::ostream &os, const CState &s)

Detailed Description

Definition at line 305 of file CState.h.

Constructor & Destructor Documentation

CState::CState

(

)

Constructor

Definition at line 279 of file CState.cpp.

              :
    mpValues(NULL),
    mSize(0),
    mpBeginIndependent(NULL),
    mpBeginDependent(NULL),
    mpBeginFixed(NULL),
    mpEnd(NULL),
    mUpdateDependentRequired(false)
{}

CState::CState

(

const CState &

src

)

Copy constructor

Parameters

const

CState & src

Definition at line 289 of file CState.cpp.

References C_FLOAT64, mpValues, and mSize.

                                :
    mpValues(new C_FLOAT64[src.mSize]),
    mSize(src.mSize),
    mpBeginIndependent(mpValues + (src.mpBeginIndependent - src.mpValues)),
    mpBeginDependent(mpValues + (src.mpBeginDependent - src.mpValues)),
    mpBeginFixed(mpValues + (src.mpBeginFixed - src.mpValues)),
    mpEnd(mpValues + (src.mpEnd - src.mpValues)),
    mUpdateDependentRequired(src.mUpdateDependentRequired)
{
  memcpy(mpValues, src.mpValues, sizeof(C_FLOAT64) * mSize);
}

CState::~CState

(

)

Destructor

Definition at line 301 of file CState.cpp.

References mpValues, and pdeletev.

{pdeletev(mpValues);}

Member Function Documentation

C_FLOAT64 * CState::beginDependent

(

)

Retrieve the array of pointers of values of all dependent entities, which are only dependent species for a reduced model.

Returns

C_FLOAT64 * dependentValues

Definition at line 330 of file CState.cpp.

References mpBeginDependent.

Referenced by CHybridMethodODE45::outputState(), and CModel::updateSimulatedValues().

{return mpBeginDependent;}

const C_FLOAT64 * CState::beginDependent

(

)

const

Retrieve the array of pointers of values of all dependent entities, which are only dependent species for a reduced model.

Returns

const C_FLOAT64 * dependentValues

Definition at line 337 of file CState.cpp.

References mpBeginDependent.

{return mpBeginDependent;}

C_FLOAT64 * CState::beginFixed

(

)

Retrieve the array of pointers of values of all fixed entities.

Returns

C_FLOAT64 * fixedValues

Definition at line 332 of file CState.cpp.

References mpBeginFixed.

Referenced by CHybridMethodODE45::outputState(), and CLsodaMethod::stateChanged().

{return mpBeginFixed;}

const C_FLOAT64 * CState::beginFixed

(

)

const

Retrieve the array of pointers of values of all fixed entities.

Returns

const C_FLOAT64 * fixedValues

Definition at line 339 of file CState.cpp.

References mpBeginFixed.

{return mpBeginFixed;}

C_FLOAT64 * CState::beginIndependent

(

)

Retrieve the array of pointers of values of all independent entities.

Returns

C_FLOAT64 * independentValues

Definition at line 328 of file CState.cpp.

References mpBeginIndependent.

Referenced by CSteadyStateMethod::allPositive(), CLyapWolfMethod::calculate(), CModel::calculateJacobian(), CModel::calculateJacobianX(), CMathModel::calculateRootJacobian(), CNewtonMethod::containsNaN(), CHybridMethodODE45::doInverseInterpolation(), CTauLeapMethod::doSingleStep(), CCopasiXMLParser::InitialStateElement::end(), CLyapWolfMethod::evalF(), CHybridMethodODE45::evalF(), CHybridMethodLSODA::integrateDeterministicPart(), CHybridMethodODE45::integrateDeterministicPart(), CTSSAMethod::integrationMethodStart(), CTrajectoryMethodDsaLsodar::CPartition::intialize(), CHybridMethodODE45::outputState(), CLsodaMethod::peekAhead(), CNewtonMethod::processInternal(), CCrossSectionTask::relativeDifferenceOfStates(), CTrajectoryMethodDsaLsodar::CPartition::rePartition(), CNewtonMethod::solveJacobianXeqB(), CTauLeapMethod::start(), CStochDirectMethod::start(), CLyapWolfMethod::start(), CTrajAdaptiveSA::start(), CLsodaMethod::start(), CTrajectoryMethodDsaLsodar::start(), CLsodaMethod::stateChanged(), CHybridMethod::step(), CHybridMethodLSODA::step(), CStochMethod::step(), CNewtonMethod::targetFunction(), and CTauLeapMethod::updateSystem().

{return mpBeginIndependent;}

const C_FLOAT64 * CState::beginIndependent

(

)

const

Retrieve the array of pointers of values of all independent entities.

Returns

const C_FLOAT64 * independentValues

Definition at line 335 of file CState.cpp.

References mpBeginIndependent.

{return mpBeginIndependent;}

C_FLOAT64 * CState::endDependent

(

)

Retrieve pointer just beyond the values of all dependent entities.

Returns

C_FLOAT64 * endDependentValues

Definition at line 331 of file CState.cpp.

References mpBeginFixed.

Referenced by CSteadyStateMethod::allPositive(), and CHybridMethodODE45::outputState().

{return mpBeginFixed;}

const C_FLOAT64 * CState::endDependent

(

)

const

Retrieve pointer just beyond the values of all dependent entities.

Returns

const C_FLOAT64 * endDependentValues

Definition at line 338 of file CState.cpp.

References mpBeginFixed.

{return mpBeginFixed;}

C_FLOAT64 * CState::endFixed

(

)

Retrieve pointer just beyond the values of all fixed entities.

Returns

C_FLOAT64 * endFixedValues

Definition at line 333 of file CState.cpp.

References mpEnd.

Referenced by CHybridMethodODE45::outputState(), and CLsodaMethod::stateChanged().

{return mpEnd;}

const C_FLOAT64 * CState::endFixed

(

)

const

Retrieve pointer just beyond the values of all fixed entities.

Returns

const C_FLOAT64 * endFixedValues

Definition at line 340 of file CState.cpp.

References mpEnd.

{return mpEnd;}

C_FLOAT64 * CState::endIndependent

(

)

Retrieve pointer just beyond the values of all independent entities.

Returns

C_FLOAT64 * endIndependentValues

Definition at line 329 of file CState.cpp.

References mpBeginDependent.

Referenced by CNewtonMethod::containsNaN(), CHybridMethodODE45::outputState(), and CCrossSectionTask::relativeDifferenceOfStates().

{return mpBeginDependent;}

const C_FLOAT64 * CState::endIndependent

(

)

const

Retrieve pointer just beyond the values of all independent entities.

Returns

const C_FLOAT64 * endIndependentValues

Definition at line 336 of file CState.cpp.

References mpBeginDependent.

{return mpBeginDependent;}

size_t CState::getNumDependent

(

)

const

Retrieve the number of dependent entities.

Returns

size_t numDependent

Definition at line 344 of file CState.cpp.

References mpBeginDependent, and mpBeginFixed.

Referenced by CSteadyStateTask::initialize(), CHybridMethodODE45::outputState(), and resize().

{return mpBeginFixed - mpBeginDependent;}

size_t CState::getNumFixed

(

)

const

Retrieve the number of fixed entities.

Returns

size_t numFixed

Definition at line 348 of file CState.cpp.

References mpBeginFixed, and mpEnd.

Referenced by resize().

{return mpEnd - mpBeginFixed;}

size_t CState::getNumIndependent

(

)

const

Retrieve the number of independent entities.

Returns

size_t numIndependent

Definition at line 342 of file CState.cpp.

References mpBeginDependent, and mpBeginIndependent.

Referenced by CModel::calculateJacobian(), CModel::calculateJacobianX(), CMathModel::calculateRootJacobian(), CSteadyStateTask::initialize(), CTSSAMethod::integrationMethodStart(), CLyapMethod::isValidProblem(), CHybridMethodODE45::outputState(), CLyapTask::process(), resize(), CLyapWolfMethod::start(), and CLsodaMethod::start().

{return mpBeginDependent - mpBeginIndependent;}

size_t CState::getNumVariable

(

)

const

Retrieve the number of variable entities, i.e., the sum of independent and dependent variables.

Returns

size_t numVariable

Definition at line 346 of file CState.cpp.

References mpBeginFixed, and mpBeginIndependent.

{return mpBeginFixed - mpBeginIndependent;}

const C_FLOAT64 & CState::getTime

(

)

const

Retrieve the time of the state

Returns

const C_FLOAT64 & time

Definition at line 325 of file CState.cpp.

References mpValues.

Referenced by CHybridMethodODE45::doSingleStep(), CTrajectoryMethodDsaLsodar::fireReaction(), CTSSATask::initialize(), CTrajectoryTask::initialize(), CCrossSectionTask::initialize(), CHybridMethodLSODA::integrateDeterministicPart(), CHybridMethodODE45::integrateDeterministicPart(), CTSSAMethod::integrationMethodStart(), CTimeSeries::output(), CHybridMethod::outputData(), CHybridMethodLSODA::outputData(), CHybridMethod::outputDebug(), CHybridMethodODE45::outputDebug(), CHybridMethodLSODA::outputDebug(), CHybridMethodODE45::outputState(), CHybridMethod::partitionSystem(), CLsodaMethod::peekAhead(), CSteadyStateTask::process(), CHybridMethod::start(), CStochDirectMethod::start(), CLyapWolfMethod::start(), CTrajAdaptiveSA::start(), CStochMethod::start(), CLsodaMethod::start(), CLsodaMethod::stateChanged(), CTauLeapMethod::step(), CHybridMethod::step(), CStochDirectMethod::step(), CTrajAdaptiveSA::step(), CStochMethod::step(), CLsodaMethod::step(), and CTrajectoryMethodDsaLsodar::step().

{return *mpValues;}

bool CState::isValid

(

)

const

Check whether the current state is valid (contains no NaN)

Returns

bool isValid

Definition at line 351 of file CState.cpp.

References C_FLOAT64, mpBeginDependent, and mpBeginIndependent.

Referenced by CSteadyStateTask::process(), and CLsodaMethod::step().

{
  const C_FLOAT64 * pIt = mpBeginIndependent;
  const C_FLOAT64 * pEnd = mpBeginDependent;

  for (; pIt != pEnd; ++pIt)
    {
      if (isnan(*pIt))
        return false;
    }

  return true;
}

CState & CState::operator=

(

const CState &

rhs

)

Assignment operator

Parameters

const

CState & rhs

Returns

CState & lhs

Definition at line 303 of file CState.cpp.

References C_FLOAT64, mpBeginDependent, mpBeginFixed, mpBeginIndependent, mpEnd, mpValues, mSize, mUpdateDependentRequired, and pdeletev.

{
  if (this != &rhs)
    {
      if (mSize != rhs.mSize)
        {
          pdeletev(mpValues);
          mpValues = new C_FLOAT64[rhs.mSize];
          mSize = rhs.mSize;
        }

      memcpy(mpValues, rhs.mpValues, sizeof(C_FLOAT64) * mSize);
      mpBeginIndependent = mpValues + (rhs.mpBeginIndependent - rhs.mpValues);
      mpBeginDependent = mpValues + (rhs.mpBeginDependent - rhs.mpValues);
      mpBeginFixed = mpValues + (rhs.mpBeginFixed - rhs.mpValues);
      mpEnd = mpValues + (rhs.mpEnd - rhs.mpValues);
      mUpdateDependentRequired = rhs.mUpdateDependentRequired;
    }

  return *this;
}

C_FLOAT64 * CState::resize ( const size_t &  size )

protected

Definition at line 365 of file CState.cpp.

References C_FLOAT64, getNumDependent(), getNumFixed(), getNumIndependent(), min, mpValues, mSize, pdeletev, and updateIterator().

Referenced by CStateTemplate::resize().

{
  if (mSize != size)
    {
      C_FLOAT64 * pTmp = mpValues;

      if (size > 0)
        {
          mpValues = new C_FLOAT64[size];
          memcpy(mpValues, pTmp, sizeof(C_FLOAT64) * std::min(mSize, size));
        }
      else
        mpValues = NULL;

      pdeletev(pTmp);
      mSize = size;
    }

  updateIterator(getNumIndependent(), getNumDependent(), getNumFixed());

  return mpValues;
}

void CState::setTime

(

const C_FLOAT64 &

time

)

Set the time of the state

Parameters

const

C_FLOAT64 & time

Definition at line 326 of file CState.cpp.

References mpValues.

Referenced by CLyapWolfMethod::calculate(), CHybridMethodODE45::doInverseInterpolation(), CHybridNextReactionLSODAMethod::doSingleStep(), CHybridNextReactionRKMethod::doSingleStep(), CHybridMethodODE45::doSingleStep(), CTrajectoryMethodDsaLsodar::doSingleStep(), CTrajAdaptiveSA::doSingleTauLeapStep(), CLyapWolfMethod::evalF(), CLsodaMethod::evalF(), CHybridMethodLSODA::evalF(), CHybridMethodODE45::evalF(), CTrajectoryMethodDsaLsodar::evalF(), CTSSAMethod::evalF(), CLsodaMethod::evalR(), CHybridMethodLSODA::integrateDeterministicPart(), CHybridMethodODE45::integrateDeterministicPart(), CTSSAMethod::integrationStep(), CLsodaMethod::peekAhead(), CSteadyStateTask::process(), CModel::setInitialState(), CTauLeapMethod::step(), CHybridMethod::step(), CHybridMethodLSODA::step(), CStochDirectMethod::step(), CLyapWolfMethod::step(), CTrajAdaptiveSA::step(), CStochMethod::step(), CLsodaMethod::step(), and CTrajectoryMethodDsaLsodar::step().

{*mpValues = time;}

void CState::updateIterator ( const size_t &  numIndependent, const size_t &  numDependent, const size_t &  numFixed  )

protected

Update the pointers to the different types of entities

Parameters

const	size_t & numIndependent
const	size_t & numDependent
const	size_t & numFixed

Definition at line 388 of file CState.cpp.

References mpBeginDependent, mpBeginFixed, mpBeginIndependent, mpEnd, and mpValues.

Referenced by CStateTemplate::reorder(), and resize().

{
  mpBeginIndependent = mpValues + 1; // One for Time
  mpBeginDependent = mpBeginIndependent + numIndependent;
  mpBeginFixed = mpBeginDependent + numDependent;
  mpEnd = mpBeginFixed + numFixed;
}

Friends And Related Function Documentation

friend class CStateTemplate

friend

Definition at line 453 of file CState.h.

std::ostream& operator<< ( std::ostream &  os, const CState &  s  )

friend

Definition at line 398 of file CState.cpp.

{
  os << "(";

  const C_FLOAT64 * pValue = s.mpValues;

  for (; pValue != s.mpEnd; ++pValue)
    {
      os << "\t" << *pValue;
    }

  os << "\t)";

  return os;
}

Member Data Documentation

C_FLOAT64* CState::mpBeginDependent

private

Pointer to the beginning of values of dependent entities.

Definition at line 485 of file CState.h.

Referenced by beginDependent(), endIndependent(), getNumDependent(), getNumIndependent(), isValid(), operator=(), and updateIterator().

C_FLOAT64* CState::mpBeginFixed

private

Pointer to the beginning of values of fixed entities.

Definition at line 490 of file CState.h.

Referenced by beginFixed(), endDependent(), getNumDependent(), getNumFixed(), getNumVariable(), operator=(), and updateIterator().

C_FLOAT64* CState::mpBeginIndependent

private

Pointer to the beginning of values of independent entities.

Definition at line 480 of file CState.h.

Referenced by beginIndependent(), getNumIndependent(), getNumVariable(), isValid(), operator=(), and updateIterator().

C_FLOAT64* CState::mpEnd

private

Pointer just beyond the values of fixed entities.

Definition at line 495 of file CState.h.

Referenced by endFixed(), getNumFixed(), operator<<(), operator=(), and updateIterator().

C_FLOAT64* CState::mpValues

private

Array of entity values

Definition at line 470 of file CState.h.

Referenced by CState(), getTime(), operator<<(), operator=(), resize(), setTime(), updateIterator(), and ~CState().

size_t CState::mSize

private

Size of the state

Definition at line 475 of file CState.h.

Referenced by CState(), operator=(), and resize().

bool CState::mUpdateDependentRequired

private

Indicates whether the state is of a reduced or complete model

Definition at line 500 of file CState.h.

Referenced by operator=().

---

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

• CState.h
• CState.cpp