void CHybridMethod::start()
{
mFirstMetabIndex = mpContainer->getCountFixedEventTargets() + 1 + mpContainer->getCountODEs();
mpFirstMetabValue = mpContainer->getState(false).array() + mFirstMetabIndex;
// call init of the simulation method, can be overloaded in derived classes
mReactions.initialize(mpContainer->getReactions());
mAmu.clear();
mAmu.resize(mReactions.size());
mAmuOld.clear();
mAmuOld.resize(mReactions.size());
mNumVariableMetabs = mpContainer->getCountIndependentSpecies() + mpContainer->getCountDependentSpecies();
mUpdateSequences.resize(mReactions.size());
mSpeciesRates.initialize(mNumVariableMetabs, const_cast< C_FLOAT64 * >(mpContainer->getRate(false).array()) + mFirstMetabIndex);
mRateOffset = mpContainer->getRate(false).array() - mpContainer->getState(false).array();
mCurrentState.initialize(mNumVariableMetabs, const_cast< C_FLOAT64 * >(mpContainer->getState(false).array()) + mFirstMetabIndex);
mMetab2React.resize(mNumVariableMetabs);
/* get configuration data */
mMaxSteps = getValue< C_INT32 >("Max Internal Steps");
mLowerStochLimit = getValue< C_FLOAT64 >("Lower Limit");
mUpperStochLimit = getValue< C_FLOAT64 >("Upper Limit");
mPartitioningInterval = getValue< unsigned C_INT32 >("Partitioning Interval");
mUseRandomSeed = getValue< bool >("Use Random Seed");
mRandomSeed = getValue< unsigned C_INT32 >("Random Seed");
mpRandomGenerator = &mpContainer->getRandomGenerator();
if (mUseRandomSeed)
{
mpRandomGenerator->initialize(mRandomSeed);
}
mStepsAfterPartitionSystem = 0;
setupDependencyGraph(); // initialize mDG
setupMetab2React(); // initialize mMetab2React
setupPartition(); // initialize mReactionFlags
setupPriorityQueue(); // initialize mPQ
mMaxStepsReached = false;
return;
}
void CStochNextReactionMethod::initMethod(C_FLOAT64 start_time)
{
setupPriorityQueue(start_time);
}
