/**
* Update model state after one events happened
*/
void CStochDirectMethod::stateChange(const CMath::StateChange & change)
{
if (change & (CMath::ContinuousSimulation | CMath::State))
{
// Create a local copy of the state where the particle number species determined
// by reactions are rounded to integers.
C_FLOAT64 * pValue = mContainerState.array() + mpContainer->getCountFixedEventTargets() + 1 /* Time */ + mpContainer->getCountODEs();
C_FLOAT64 * pValueEnd = pValue + mpContainer->getCountIndependentSpecies() + mpContainer->getCountDependentSpecies();
for (; pValue != pValueEnd; ++pValue)
{
*pValue = floor(*pValue + 0.5);
}
// The container state is now up to date we just need to calculate all values needed for simulation.
mpContainer->updateSimulatedValues(false); //for assignments
CMathObject * pPropensityObject = mPropensityObjects.array();
CMathObject * pPropensityObjectEnd = pPropensityObject + mPropensityObjects.size();
C_FLOAT64 * pAmu = mAmu.array();
mA0 = 0.0;
// Update the propensity
for (; pPropensityObject != pPropensityObjectEnd; ++pPropensityObject, ++pAmu)
{
pPropensityObject->calculateValue();
mA0 += *pAmu;
}
mNextReactionIndex = C_INVALID_INDEX;
*mpRootValueNew = mpContainer->getRoots();
}
mMaxStepsReached = false;
}
void CTauLeapMethod::updatePropensities()
{
mA0 = 0;
CMathObject * pPropensity = mPropensityObjects.array();
CMathObject * pPropensityEnd = pPropensity + mNumReactions;
C_FLOAT64 * pAmu = mAmu.array();
for (; pPropensity != pPropensityEnd; ++pPropensity, ++pAmu)
{
pPropensity->calculateValue();
mA0 += *pAmu;
}
return;
}
void CTrajectoryMethodDsaLsodar::calculatePropensities()
{
// It suffices to recalculate the propensities for stochastic reactions.
CMathObject * pPropensity = mPropensityObjects.array();
CMathObject * pPropensityEnd = pPropensity + mNumReactions;
const CMathReaction **ppStochastic = mPartition.mStochasticReactions.array();
for (; pPropensity != pPropensityEnd; ++pPropensity, ++ppStochastic)
{
if (*ppStochastic != NULL)
{
pPropensity->calculateValue();
}
}
return;
}
// virtual
void CTrajectoryMethodDsaLsodar::start()
{
CLsodaMethod::start();
mReactions.initialize(mpContainer->getReactions());
mNumReactions = mReactions.size();
mAmu.initialize(mpContainer->getPropensities());
mPropensityObjects.initialize(mNumReactions, mpContainer->getMathObject(mAmu.array()));
mUpdateSequences.resize(mNumReactions);
mFirstReactionSpeciesIndex = mpContainer->getCountFixedEventTargets() + 1 /* Time */ + mpContainer->getCountODEs();
// Create a local copy of the state where the particle number species determined
// by reactions are rounded to integers.
C_FLOAT64 * pValue = mContainerState.array() + mFirstReactionSpeciesIndex;
C_FLOAT64 * pValueEnd = pValue + mpContainer->getCountIndependentSpecies() + mpContainer->getCountDependentSpecies();
for (; pValue != pValueEnd; ++pValue)
{
*pValue = floor(*pValue + 0.5);
}
// The container state is now up to date we just need to calculate all values needed for simulation.
mpContainer->updateSimulatedValues(false);
CMathObject * pTimeObject = mpContainer->getMathObject(mpContainer->getModel().getValueReference());
// Build the reaction dependencies
mReactions.initialize(mpContainer->getReactions());
mNumReactions = mReactions.size();
mAmu.initialize(mpContainer->getPropensities());
mPropensityObjects.initialize(mAmu.size(), mpContainer->getMathObject(mAmu.array()));
mUpdateSequences.resize(mNumReactions);
C_FLOAT64 * pAmu = mAmu.array();
mA0 = 0.0;
CMathReaction * pReaction = mReactions.array();
CMathReaction * pReactionEnd = pReaction + mNumReactions;
CCore::CUpdateSequence * pUpdateSequence;
CMathObject * pPropensityObject = mPropensityObjects.array();
CMathObject * pPropensityObjectEnd = pPropensityObject + mPropensityObjects.size();
CObjectInterface::ObjectSet Requested;
for (; pPropensityObject != pPropensityObjectEnd; ++pPropensityObject)
{
Requested.insert(pPropensityObject);
}
pPropensityObject = mPropensityObjects.array();
for (; pReaction != pReactionEnd; ++pReaction, ++pUpdateSequence, ++pPropensityObject, ++pAmu)
{
// Update the propensity
pPropensityObject->calculateValue();
mA0 += *pAmu;
CObjectInterface::ObjectSet Changed;
// The time is always updated
Changed.insert(pTimeObject);
const CMathReaction::SpeciesBalance * itBalance = pReaction->getNumberBalance().array();
const CMathReaction::SpeciesBalance * endBalance = itBalance + pReaction->getNumberBalance().size();
for (; itBalance != endBalance; ++itBalance)
{
Changed.insert(mpContainer->getMathObject(itBalance->first));
}
pUpdateSequence->clear();
mpContainer->getTransientDependencies().getUpdateSequence(*pUpdateSequence, CCore::SimulationContext::Default, Changed, Requested);
}
mPartition.intialize(mpContainer, *mpLowerLimit, *mpUpperLimit);
return;
}
