void CStochDirectMethod::start()
{
CTrajectoryMethod::start();
/* get configuration data */
mMaxSteps = getValue< C_INT32 >("Max Internal Steps");
mpRandomGenerator = &mpContainer->getRandomGenerator();
if (getValue< bool >("Use Random Seed"))
{
mpRandomGenerator->initialize(getValue< unsigned C_INT32 >("Random Seed"));
}
//mpCurrentState is initialized. This state is not used internally in the
//stochastic solver, but it is used for returning the result after each step.
//========Initialize Roots Related Arguments========
mNumRoot = mpContainer->getRoots().size();
mRootsFound.resize(mNumRoot);
mRootsA.resize(mNumRoot);
mRootsB.resize(mNumRoot);
mpRootValueNew = &mRootsA;
mpRootValueOld = &mRootsB;
mRootsNonZero.resize(mNumRoot);
mRootsNonZero = 0.0;
CMathObject * pRootObject = mpContainer->getMathObject(mpContainer->getRoots().array());
CMathObject * pRootObjectEnd = pRootObject + mNumRoot;
CObjectInterface::ObjectSet Requested;
for (; pRootObject != pRootObjectEnd; ++pRootObject)
{
Requested.insert(pRootObject);
}
CObjectInterface::ObjectSet Changed;
// Determine whether we have time dependent roots;
CObjectInterface * pTimeObject = mpContainer->getMathObject(mpContainerStateTime);
Changed.insert(pTimeObject);
mpContainer->getTransientDependencies().getUpdateSequence(mUpdateTimeDependentRoots, CMath::Default, Changed, Requested);
mHaveTimeDependentRoots = (mUpdateTimeDependentRoots.size() > 0);
// 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);
CMathReaction * pReaction = mReactions.array();
CMathReaction * pReactionEnd = pReaction + mNumReactions;
CObjectInterface::UpdateSequence * pUpdateSequence = mUpdateSequences.array();
CMathObject * pPropensityObject = mPropensityObjects.array();
CMathObject * pPropensityObjectEnd = pPropensityObject + mPropensityObjects.size();
for (; pPropensityObject != pPropensityObjectEnd; ++pPropensityObject)
{
Requested.insert(pPropensityObject);
}
pPropensityObject = mPropensityObjects.array();
for (; pReaction != pReactionEnd; ++pReaction, ++pUpdateSequence, ++pPropensityObject)
{
Changed = pReaction->getChangedObjects();
// The time is always updated
Changed.insert(pTimeObject);
pUpdateSequence->clear();
mpContainer->getTransientDependencies().getUpdateSequence(*pUpdateSequence, CMath::Default, Changed, Requested);
}
mMaxStepsReached = false;
mTargetTime = *mpContainerStateTime;
mNextReactionTime = *mpContainerStateTime;
mNextReactionIndex = C_INVALID_INDEX;
stateChange(CMath::State);
return;
}
