void CLsodaMethod::maskRoots(CVectorCore< C_FLOAT64 > & rootValues)
{
const bool *pMask = mRootMask.array();
const bool *pMaskEnd = pMask + mRootMask.size();
C_FLOAT64 * pRoot = rootValues.array();
for (; pMask != pMaskEnd; ++pMask, ++pRoot)
{
if (*pMask)
{
*pRoot = 1.0;
}
}
}
bool CTrajectoryMethodDsaLsodar::CPartition::rePartition(const CVectorCore< C_FLOAT64 > & state)
{
// Modify the partition if species values move beyond the threshold
const C_FLOAT64 * pValue = state.array() + mFirstReactionSpeciesIndex;
const C_FLOAT64 * pValueEnd = pValue + mNumReactionSpecies;
bool * pStochasticSpecies = mStochasticSpecies.array();
bool PartitionChanged = false;
size_t Index = 0;
for (; pValue != pValueEnd; ++pValue, ++Index, ++pStochasticSpecies)
{
if (!*pStochasticSpecies && *pValue < mLowerThreshold)
{
*pStochasticSpecies = true;
PartitionChanged = true;
std::pair< speciesToReactionsMap::const_iterator, speciesToReactionsMap::const_iterator > Range
= mSpeciesToReactions.equal_range(Index);
for (; Range.first != Range.second; ++Range.first)
{
(*Range.first->second)++;
}
}
else if (*pStochasticSpecies && *pValue > mUpperThreshold)
{
*pStochasticSpecies = false;
PartitionChanged = true;
std::pair< speciesToReactionsMap::const_iterator, speciesToReactionsMap::const_iterator > Range
= mSpeciesToReactions.equal_range(Index);
for (; Range.first != Range.second; ++Range.first)
{
(*Range.first->second)--;
}
}
}
if (!PartitionChanged)
{
return false;
}
PartitionChanged = false;
// Reactions for which the count of species with low numbers is non zero
// are treated stochastically.
const size_t * pLow = mNumLowSpecies.array();
const size_t * pLowEnd = pLow + mNumLowSpecies.size();
const CMathReaction ** ppStochastic = mStochasticReactions.array();
const CMathReaction ** ppDeterministic = mDeterministicReactions.array();
mHasStochastic = false;
mHasDeterministic = false;
for (; pLow != pLowEnd; ++pLow, ++ppStochastic, ++ppDeterministic)
{
if (*pLow != 0)
{
mHasStochastic = true;
if (*ppDeterministic != NULL)
{
PartitionChanged = true;
*ppStochastic = *ppDeterministic;
*ppDeterministic = NULL;
}
}
else
{
mHasDeterministic = true;
if (*ppStochastic != NULL)
{
PartitionChanged = true;
*ppDeterministic = *ppStochastic;
*ppStochastic = NULL;
}
}
}
if (PartitionChanged)
{
// determineStochasticSpecies();
}
return PartitionChanged;
}
