COPASI API
4.16.103
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Public Types | |
typedef std::multimap< size_t, size_t > | speciesToReactionsMap |
Public Member Functions | |
CPartition () | |
CPartition (const CPartition &src) | |
void | determineStochasticSpecies () |
void | intialize (std::vector< CReactionDependencies > &reactions, const speciesToReactionsMap &speciesToReactions, const C_FLOAT64 &lowerThreshold, const C_FLOAT64 &upperThreshold, const CState &state) |
bool | rePartition (const CState &state) |
~CPartition () | |
Public Attributes | |
CVector< CReactionDependencies * > | mDeterministicReactions |
bool | mHasDeterministic |
bool | mHasStochastic |
CVector< CReactionDependencies * > | mStochasticReactions |
CVector< bool > | mStochasticSpecies |
Private Attributes | |
size_t | mFirstReactionSpeciesIndex |
C_FLOAT64 | mLowerThreshold |
CVector< bool > | mLowSpecies |
CVector< size_t > | mNumLowSpecies |
size_t | mNumReactionSpecies |
speciesToReactionsMap | mSpeciesToReactions |
C_FLOAT64 | mUpperThreshold |
Definition at line 139 of file CTrajectoryMethodDsaLsodar.h.
typedef std::multimap< size_t, size_t > CTrajectoryMethodDsaLsodar::CPartition::speciesToReactionsMap |
Definition at line 142 of file CTrajectoryMethodDsaLsodar.h.
CTrajectoryMethodDsaLsodar::CPartition::CPartition | ( | ) |
Default constructor
Definition at line 87 of file CTrajectoryMethodDsaLsodar.cpp.
CTrajectoryMethodDsaLsodar::CPartition::CPartition | ( | const CPartition & | src | ) |
Copy constructor
const | CPartition & src |
Definition at line 102 of file CTrajectoryMethodDsaLsodar.cpp.
CTrajectoryMethodDsaLsodar::CPartition::~CPartition | ( | ) |
void CTrajectoryMethodDsaLsodar::CPartition::determineStochasticSpecies | ( | ) |
Definition at line 295 of file CTrajectoryMethodDsaLsodar.cpp.
References CVectorCore< CType >::array(), CTrajectoryMethodDsaLsodar::mFirstReactionSpeciesIndex, and CTrajectoryMethodDsaLsodar::CReactionDependencies::mSpeciesIndex.
void CTrajectoryMethodDsaLsodar::CPartition::intialize | ( | std::vector< CReactionDependencies > & | reactions, |
const speciesToReactionsMap & | speciesToReactions, | ||
const C_FLOAT64 & | lowerThreshold, | ||
const C_FLOAT64 & | upperThreshold, | ||
const CState & | state | ||
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Definition at line 120 of file CTrajectoryMethodDsaLsodar.cpp.
References CState::beginIndependent(), C_FLOAT64, and CTrajectoryMethodDsaLsodar::mFirstReactionSpeciesIndex.
Referenced by CTrajectoryMethodDsaLsodar::start().
bool CTrajectoryMethodDsaLsodar::CPartition::rePartition | ( | const CState & | state | ) |
Definition at line 200 of file CTrajectoryMethodDsaLsodar.cpp.
References CState::beginIndependent(), C_FLOAT64, and CTrajectoryMethodDsaLsodar::mFirstReactionSpeciesIndex.
Referenced by CTrajectoryMethodDsaLsodar::doSingleStep().
CVector< CReactionDependencies * > CTrajectoryMethodDsaLsodar::CPartition::mDeterministicReactions |
A vector containing pointers to stochastic reaction dependencies
Definition at line 207 of file CTrajectoryMethodDsaLsodar.h.
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The index of the first species determined by reactions in the state
Definition at line 191 of file CTrajectoryMethodDsaLsodar.h.
bool CTrajectoryMethodDsaLsodar::CPartition::mHasDeterministic |
A Boolean flag indicating whether the system has deterministic reactions
Definition at line 222 of file CTrajectoryMethodDsaLsodar.h.
Referenced by CTrajectoryMethodDsaLsodar::doSingleStep().
bool CTrajectoryMethodDsaLsodar::CPartition::mHasStochastic |
A Boolean flag indicating whether the system has stochastic reactions
Definition at line 217 of file CTrajectoryMethodDsaLsodar.h.
Referenced by CTrajectoryMethodDsaLsodar::doSingleStep().
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The threshold for switching to stochastic treatment
Definition at line 181 of file CTrajectoryMethodDsaLsodar.h.
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A vector containing the current treatment of the species
Definition at line 233 of file CTrajectoryMethodDsaLsodar.h.
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A vector containing the number of low species for each reaction
Definition at line 228 of file CTrajectoryMethodDsaLsodar.h.
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The number of species determined by reactions
Definition at line 196 of file CTrajectoryMethodDsaLsodar.h.
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A map from a species index to the indexes of the reactions it participates in
Definition at line 176 of file CTrajectoryMethodDsaLsodar.h.
CVector< CReactionDependencies * > CTrajectoryMethodDsaLsodar::CPartition::mStochasticReactions |
A vector containing pointers to stochastic reaction dependencies
Definition at line 202 of file CTrajectoryMethodDsaLsodar.h.
Referenced by CTrajectoryMethodDsaLsodar::calculatePropensities(), CTrajectoryMethodDsaLsodar::doSingleStep(), and CTrajectoryMethodDsaLsodar::fireReaction().
CVector< bool > CTrajectoryMethodDsaLsodar::CPartition::mStochasticSpecies |
A vector indicating whether a species is treated stochastically or not.
Definition at line 212 of file CTrajectoryMethodDsaLsodar.h.
Referenced by CTrajectoryMethodDsaLsodar::evalF().
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The threshold for switching to deterministic treatment
Definition at line 186 of file CTrajectoryMethodDsaLsodar.h.