COPASI API
4.16.103
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#include <CTrajectoryMethodDsaLsodar.h>
Classes | |
class | CPartition |
class | CReactionDependencies |
Public Member Functions | |
void | calculateAmu (const size_t &index) |
void | calculatePropensities () |
void | cleanup () |
CTrajectoryMethodDsaLsodar (const CTrajectoryMethodDsaLsodar &src, const CCopasiContainer *pParent=NULL) | |
virtual C_FLOAT64 | doSingleStep (C_FLOAT64 currentTime, C_FLOAT64 endTime) |
virtual bool | elevateChildren () |
virtual void | evalF (const C_FLOAT64 *t, const C_FLOAT64 *y, C_FLOAT64 *ydot) |
virtual void | evalR (const C_FLOAT64 *t, const C_FLOAT64 *y, const C_INT *nr, C_FLOAT64 *r) |
void | fireReaction (const size_t &index) |
void | integrateDeterministicPart (const C_FLOAT64 &deltaT) |
virtual bool | isValidProblem (const CCopasiProblem *pProblem) |
virtual void | start (const CState *initialState) |
virtual void | stateChanged () |
virtual Status | step (const double &deltaT) |
~CTrajectoryMethodDsaLsodar () | |
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CLsodaMethod (const CLsodaMethod &src, const CCopasiContainer *pParent=NULL) | |
virtual void | evalJ (const C_FLOAT64 *t, const C_FLOAT64 *y, const C_INT *ml, const C_INT *mu, C_FLOAT64 *pd, const C_INT *nRowPD) |
~CLsodaMethod () | |
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CTrajectoryMethod (const CTrajectoryMethod &src, const CCopasiContainer *pParent=NULL) | |
const CVector< C_INT > & | getRoots () const |
void | setCurrentState (CState *currentState) |
void | setProblem (CTrajectoryProblem *problem) |
~CTrajectoryMethod () | |
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CCopasiMethod (const CCopasiMethod &src, const CCopasiContainer *pParent=NULL) | |
const CCopasiMethod::SubType & | getSubType () const |
const CCopasiTask::Type & | getType () const |
virtual void | load (CReadConfig &configBuffer, CReadConfig::Mode mode=CReadConfig::SEARCH) |
virtual void | print (std::ostream *ostream) const |
virtual void | printResult (std::ostream *ostream) const |
virtual bool | setCallBack (CProcessReport *pCallBack) |
virtual | ~CCopasiMethod () |
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bool | addGroup (const std::string &name) |
bool | addParameter (const CCopasiParameter ¶meter) |
bool | addParameter (const std::string &name, const CCopasiParameter::Type type) |
template<class CType > | |
bool | addParameter (const std::string &name, const CCopasiParameter::Type type, const CType &value) |
void | addParameter (CCopasiParameter *pParameter) |
CCopasiParameterGroup * | assertGroup (const std::string &name) |
template<class CType > | |
CCopasiParameter * | assertParameter (const std::string &name, const CCopasiParameter::Type type, const CType &defaultValue) |
index_iterator | beginIndex () const |
name_iterator | beginName () const |
CCopasiParameterGroup (const CCopasiParameterGroup &src, const CCopasiContainer *pParent=NULL) | |
CCopasiParameterGroup (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &objectType="ParameterGroup") | |
void | clear () |
index_iterator | endIndex () const |
name_iterator | endName () const |
CCopasiParameterGroup * | getGroup (const std::string &name) |
const CCopasiParameterGroup * | getGroup (const std::string &name) const |
CCopasiParameterGroup * | getGroup (const size_t &index) |
const CCopasiParameterGroup * | getGroup (const size_t &index) const |
size_t | getIndex (const std::string &name) const |
std::string | getKey (const std::string &name) const |
std::string | getKey (const size_t &index) const |
virtual const std::string & | getName (const size_t &index) const |
virtual const CObjectInterface * | getObject (const CCopasiObjectName &cn) const |
CCopasiParameter * | getParameter (const std::string &name) |
const CCopasiParameter * | getParameter (const std::string &name) const |
CCopasiParameter * | getParameter (const size_t &index) |
const CCopasiParameter * | getParameter (const size_t &index) const |
CCopasiParameter::Type | getType (const std::string &name) const |
CCopasiParameter::Type | getType (const size_t &index) const |
std::string | getUniqueParameterName (const CCopasiParameter *pParameter) const |
const CCopasiParameter::Value & | getValue (const std::string &name) const |
const CCopasiParameter::Value & | getValue (const size_t &index) const |
CCopasiParameter::Value & | getValue (const std::string &name) |
CCopasiParameter::Value & | getValue (const size_t &index) |
CCopasiParameterGroup & | operator= (const CCopasiParameterGroup &rhs) |
bool | removeParameter (const std::string &name) |
bool | removeParameter (const size_t &index) |
template<class CType > | |
bool | setValue (const std::string &name, const CType &value) |
template<class CType > | |
bool | setValue (const size_t &index, const CType &value) |
size_t | size () const |
bool | swap (const size_t &iFrom, const size_t &iTo) |
bool | swap (index_iterator &from, index_iterator &to) |
virtual | ~CCopasiParameterGroup () |
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CCopasiParameter (const CCopasiParameter &src, const CCopasiContainer *pParent=NULL) | |
CCopasiParameter (const std::string &name, const Type &type, const void *pValue=NULL, const CCopasiContainer *pParent=NULL, const std::string &objectType="Parameter") | |
virtual CCopasiObjectName | getCN () const |
virtual const std::string & | getKey () const |
virtual std::string | getObjectDisplayName (bool regular=true, bool richtext=false) const |
const CCopasiParameter::Type & | getType () const |
const Value & | getValue () const |
Value & | getValue () |
virtual void * | getValuePointer () const |
CCopasiObject * | getValueReference () const |
bool | isValidValue (const C_FLOAT64 &value) const |
bool | isValidValue (const C_INT32 &value) const |
bool | isValidValue (const unsigned C_INT32 &value) const |
bool | isValidValue (const bool &value) const |
bool | isValidValue (const std::string &value) const |
bool | isValidValue (const CCopasiObjectName &value) const |
bool | isValidValue (const std::vector< CCopasiParameter * > &value) const |
CCopasiParameter & | operator= (const CCopasiParameter &rhs) |
template<class CType > | |
bool | setValue (const CType &value) |
bool | setValue (const std::vector< CCopasiParameter * > &value) |
virtual | ~CCopasiParameter () |
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virtual bool | add (CCopasiObject *pObject, const bool &adopt=true) |
CCopasiContainer (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &type="CN", const unsigned C_INT32 &flag=CCopasiObject::Container) | |
CCopasiContainer (const CCopasiContainer &src, const CCopasiContainer *pParent=NULL) | |
virtual std::string | getChildObjectUnits (const CCopasiObject *pObject) const |
virtual const objectMap & | getObjects () const |
virtual std::string | getUnits () const |
virtual const CCopasiObject * | getValueObject () const |
virtual bool | remove (CCopasiObject *pObject) |
virtual | ~CCopasiContainer () |
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void | addDirectDependency (const CCopasiObject *pObject) |
CCopasiObject (const CCopasiObject &src, const CCopasiContainer *pParent=NULL) | |
void | clearDirectDependencies () |
void | clearRefresh () |
bool | dependsOn (DataObjectSet candidates, const DataObjectSet &context=DataObjectSet()) const |
void | getAllDependencies (DataObjectSet &dependencies, const DataObjectSet &context) const |
virtual const DataObjectSet & | getDirectDependencies (const DataObjectSet &context=DataObjectSet()) const |
CCopasiContainer * | getObjectAncestor (const std::string &type) const |
CCopasiDataModel * | getObjectDataModel () |
const CCopasiDataModel * | getObjectDataModel () const |
const std::string & | getObjectName () const |
CCopasiContainer * | getObjectParent () const |
const std::string & | getObjectType () const |
virtual const CObjectInterface::ObjectSet & | getPrerequisites () const |
virtual Refresh * | getRefresh () const |
UpdateMethod * | getUpdateMethod () const |
bool | hasCircularDependencies (DataObjectSet &candidates, DataObjectSet &verified, const DataObjectSet &context) const |
bool | hasUpdateMethod () const |
bool | isArray () const |
bool | isContainer () const |
bool | isDataModel () const |
bool | isMatrix () const |
bool | isNameVector () const |
bool | isNonUniqueName () const |
virtual bool | isPrerequisiteForContext (const CObjectInterface *pObject, const CMath::SimulationContextFlag &context, const CObjectInterface::ObjectSet &changedObjects) const |
bool | isReference () const |
bool | isRoot () const |
bool | isSeparator () const |
bool | isStaticString () const |
bool | isValueBool () const |
bool | isValueDbl () const |
bool | isValueInt () const |
bool | isValueInt64 () const |
bool | isValueString () const |
bool | isVector () const |
virtual bool | mustBeDeleted (const DataObjectSet &deletedObjects) const |
void | removeDirectDependency (const CCopasiObject *pObject) |
void | setDirectDependencies (const DataObjectSet &directDependencies) |
bool | setObjectName (const std::string &name) |
virtual bool | setObjectParent (const CCopasiContainer *pParent) |
void | setObjectValue (const C_FLOAT64 &value) |
void | setObjectValue (const C_INT32 &value) |
void | setObjectValue (const bool &value) |
template<class CType > | |
void | setRefresh (CType *pType, void(CType::*method)(void)) |
template<class CType > | |
void | setUpdateMethod (CType *pType, void(CType::*method)(const C_FLOAT64 &)) |
template<class CType > | |
void | setUpdateMethod (CType *pType, void(CType::*method)(const C_INT32 &)) |
template<class CType > | |
void | setUpdateMethod (CType *pType, void(CType::*method)(const bool &)) |
virtual | ~CCopasiObject () |
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CObjectInterface () | |
virtual | ~CObjectInterface () |
Protected Member Functions | |
CTrajectoryMethodDsaLsodar (const CCopasiMethod::SubType &subType=DsaLsodar, const CCopasiContainer *pParent=NULL) | |
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CLsodaMethod (const CCopasiMethod::SubType &subType=deterministic, const CCopasiContainer *pParent=NULL) | |
void | destroyRootMask () |
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CTrajectoryMethod (const CCopasiMethod::SubType &subType, const CCopasiContainer *pParent=NULL) | |
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CCopasiMethod (const CCopasiTask::Type &taskType, const SubType &subType, const CCopasiContainer *pParent=NULL) | |
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CCopasiParameterGroup () | |
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template<class CType > | |
CCopasiObject * | addMatrixReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0) |
template<class CType > | |
CCopasiObject * | addObjectReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0) |
template<class CType > | |
CCopasiObject * | addVectorReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0) |
void | initObjects () |
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CCopasiObject () | |
CCopasiObject (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &type="CN", const unsigned C_INT32 &flag=0) | |
Private Member Functions | |
void | initializeParameter () |
Friends | |
CTrajectoryMethod * | CTrajectoryMethod::createMethod (CCopasiMethod::SubType subType) |
Additional Inherited Members | |
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enum | Status { FAILURE = -1, NORMAL = 0, ROOT = 1 } |
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enum | SubType { unset = 0, RandomSearch, RandomSearchMaster, SimulatedAnnealing, CoranaWalk, DifferentialEvolution, ScatterSearch, GeneticAlgorithm, EvolutionaryProgram, SteepestDescent, HybridGASA, GeneticAlgorithmSR, HookeJeeves, LevenbergMarquardt, NelderMead, SRES, Statistics, ParticleSwarm, Praxis, TruncatedNewton, Newton, deterministic, LSODAR, directMethod, stochastic, tauLeap, adaptiveSA, hybrid, hybridLSODA, hybridODE45, DsaLsodar, tssILDM, tssILDMModified, tssCSP, mcaMethodReder, scanMethod, lyapWolf, sensMethod, EFMAlgorithm, EFMBitPatternTreeAlgorithm, EFMBitPatternAlgorithm, Householder, crossSectionMethod, linearNoiseApproximation } |
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typedef parameterGroup::iterator | index_iterator |
typedef CCopasiContainer::objectMap::iterator | name_iterator |
typedef std::vector < CCopasiParameter * > | parameterGroup |
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enum | Type { DOUBLE = 0, UDOUBLE, INT, UINT, BOOL, GROUP, STRING, CN, KEY, FILE, EXPRESSION, INVALID } |
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typedef std::multimap < std::string, CCopasiObject * > | objectMap |
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typedef std::set< const CCopasiObject * > | DataObjectSet |
typedef std::vector< Refresh * > | DataUpdateSequence |
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typedef std::set< const CObjectInterface * > | ObjectSet |
typedef std::vector < CObjectInterface * > | UpdateSequence |
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static void | EvalF (const C_INT *n, const C_FLOAT64 *t, const C_FLOAT64 *y, C_FLOAT64 *ydot) |
static void | EvalJ (const C_INT *n, const C_FLOAT64 *t, const C_FLOAT64 *y, const C_INT *ml, const C_INT *mu, C_FLOAT64 *pd, const C_INT *nRowPD) |
static void | EvalR (const C_INT *n, const C_FLOAT64 *t, const C_FLOAT64 *y, const C_INT *nr, C_FLOAT64 *r) |
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static CTrajectoryMethod * | createMethod (CCopasiMethod::SubType subType=CCopasiMethod::deterministic) |
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static std::vector< Refresh * > | buildUpdateSequence (const DataObjectSet &objects, const DataObjectSet &uptoDateObjects, const DataObjectSet &context=DataObjectSet()) |
static void | setRenameHandler (CRenameHandler *rh) |
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static const std::string | SubTypeName [] |
static const char * | XMLSubType [] |
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static const std::string | TypeName [] |
static const char * | XMLType [] |
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static const std::vector < CCopasiContainer * > | EmptyList |
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enum | RootMasking { NONE = 0, ALL, DISCRETE } |
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enum | Flag { Container = 0x1, Vector = 0x2, Matrix = 0x4, NameVector = 0x8, Reference = 0x10, ValueBool = 0x20, ValueInt = 0x40, ValueInt64 = 0x80, ValueDbl = 0x100, NonUniqueName = 0x200, StaticString = 0x400, ValueString = 0x800, Separator = 0x1000, ModelEntity = 0x2000, Array = 0x4000, DataModel = 0x8000, Root = 0x10000, Gui = 0x20000 } |
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static CRenameHandler * | smpRenameHandler = NULL |
Definition at line 52 of file CTrajectoryMethodDsaLsodar.h.
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Default constructor.
const | CCopasiMethod::SubType & subType (default: DsaLsodar) |
const | CCopasiContainer * pParent (default: NULL) |
Default constructor.
Definition at line 321 of file CTrajectoryMethodDsaLsodar.cpp.
References CRandom::createGenerator(), initializeParameter(), mpRandomGenerator, and CRandom::mt19937.
CTrajectoryMethodDsaLsodar::CTrajectoryMethodDsaLsodar | ( | const CTrajectoryMethodDsaLsodar & | src, |
const CCopasiContainer * | pParent = NULL |
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Copy constructor
const | CTrajectoryMethodDsaLsodar & src |
const | CCopasiContainer * pParent (default: NULL) |
Definition at line 329 of file CTrajectoryMethodDsaLsodar.cpp.
References CRandom::createGenerator(), initializeParameter(), mpRandomGenerator, and CRandom::mt19937.
CTrajectoryMethodDsaLsodar::~CTrajectoryMethodDsaLsodar | ( | ) |
Destructor.
Definition at line 340 of file CTrajectoryMethodDsaLsodar.cpp.
References cleanup(), and DESTRUCTOR_TRACE.
void CTrajectoryMethodDsaLsodar::calculateAmu | ( | const size_t & | index | ) |
Calculates an amu value for a given reaction.
const | size_t & index |
Definition at line 869 of file CTrajectoryMethodDsaLsodar.cpp.
References CVectorCore< CType >::array(), C_FLOAT64, mAmu, mDoCorrection, CTrajectoryMethodDsaLsodar::CReactionDependencies::mMethodSubstrates, CTrajectoryMethodDsaLsodar::CReactionDependencies::mModelSubstrates, CTrajectoryMethodDsaLsodar::CReactionDependencies::mpParticleFlux, mReactionDependencies, CTrajectoryMethodDsaLsodar::CReactionDependencies::mSubstrateMultiplier, and CVectorCore< CType >::size().
Referenced by calculatePropensities(), and fireReaction().
void CTrajectoryMethodDsaLsodar::calculatePropensities | ( | ) |
Calculate the propensities of all stochastic reactions
Definition at line 944 of file CTrajectoryMethodDsaLsodar.cpp.
References CVectorCore< CType >::array(), C_FLOAT64, calculateAmu(), mA0, mAmu, CLsodaMethod::mMethodState, mNumReactions, mPartition, CLsodaMethod::mpModel, CTrajectoryMethodDsaLsodar::CPartition::mStochasticReactions, CModel::setState(), and CModel::updateSimulatedValues().
Referenced by doSingleStep(), and start().
void CTrajectoryMethodDsaLsodar::cleanup | ( | ) |
Cleans up memory, etc.
Definition at line 774 of file CTrajectoryMethodDsaLsodar.cpp.
References CLsodaMethod::mpModel, and mpRandomGenerator.
Referenced by ~CTrajectoryMethodDsaLsodar().
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Simulates the system over the next interval of time. The current time and the end time of the current step() are given as arguments.
currentTime | A C_FLOAT64 specifying the current time |
endTime | A C_FLOAT64 specifying the end time of the step() |
Definition at line 441 of file CTrajectoryMethodDsaLsodar.cpp.
References CVectorCore< CType >::array(), C_FLOAT64, C_INVALID_INDEX, calculatePropensities(), fireReaction(), CRandom::getRandomOO(), integrateDeterministicPart(), mA0, mAmu, CTrajectoryMethodDsaLsodar::CPartition::mHasDeterministic, CTrajectoryMethodDsaLsodar::CPartition::mHasStochastic, min, CLsodaMethod::mMethodState, mNextReactionIndex, mNextReactionTime, mNumReactions, mPartition, CTrajectoryMethod::mpCurrentState, CLsodaMethod::mpModel, mpPartitioningInterval, mpPartitioningSteps, mpRandomGenerator, mStepsAfterPartitionSystem, CTrajectoryMethodDsaLsodar::CPartition::mStochasticReactions, CTrajectoryMethodDsaLsodar::CPartition::rePartition(), CState::setTime(), and CModel::setTime().
Referenced by step().
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This methods must be called to elevate subgroups to derived objects. The default implementation does nothing.
Reimplemented from CLsodaMethod.
Definition at line 398 of file CTrajectoryMethodDsaLsodar.cpp.
References CLsodaMethod::elevateChildren(), and initializeParameter().
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This evaluates the derivatives
Reimplemented from CLsodaMethod.
Definition at line 729 of file CTrajectoryMethodDsaLsodar.cpp.
References CVectorCore< CType >::array(), C_FLOAT64, CModel::calculateDerivatives(), CModel::calculateDerivativesX(), mFirstReactionSpeciesIndex, CLsodaMethod::mMethodState, CLsodaMethod::mNoODE, mPartition, CLsodaMethod::mpModel, CLsodaMethod::mpReducedModel, CTrajectoryMethodDsaLsodar::CPartition::mStochasticSpecies, CModel::setState(), CState::setTime(), CVectorCore< CType >::size(), and CModel::updateSimulatedValues().
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This evaluates the roots
Reimplemented from CLsodaMethod.
Definition at line 765 of file CTrajectoryMethodDsaLsodar.cpp.
void CTrajectoryMethodDsaLsodar::fireReaction | ( | const size_t & | index | ) |
Executes the specified reaction in the system once.
const | size_t & index |
Executes the specified reaction in the system once.
index | A size_t specifying the index of the reaction, which will be fired. |
time | The current time |
Definition at line 803 of file CTrajectoryMethodDsaLsodar.cpp.
References CVectorCore< CType >::array(), C_FLOAT64, calculateAmu(), CLsodaMethod::destroyRootMask(), CState::getTime(), mA0, mAmu, CTrajectoryMethodDsaLsodar::CReactionDependencies::mCalculations, CTrajectoryMethodDsaLsodar::CReactionDependencies::mDependentReactions, CLsodaMethod::mLsodaStatus, CTrajectoryMethodDsaLsodar::CReactionDependencies::mMethodSpecies, CLsodaMethod::mMethodState, CTrajectoryMethodDsaLsodar::CReactionDependencies::mModelSpecies, mNumReactions, mPartition, mReactionDependencies, CTrajectoryMethodDsaLsodar::CReactionDependencies::mSpeciesMultiplier, CTrajectoryMethodDsaLsodar::CPartition::mStochasticReactions, CLsodaMethod::mTime, and CVectorCore< CType >::size().
Referenced by doSingleStep().
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Initialize the method parameter
Definition at line 346 of file CTrajectoryMethodDsaLsodar.cpp.
References CCopasiParameterGroup::assertParameter(), C_FLOAT64, C_INT32, CCopasiParameterGroup::getParameter(), CCopasiParameter::getValue(), mpLowerLimit, mpMaxSteps, mpPartitioningInterval, mpPartitioningSteps, mpUpperLimit, CCopasiParameter::Value::pDOUBLE, CCopasiParameter::Value::pUDOUBLE, CCopasiParameter::Value::pUINT, CCopasiParameterGroup::removeParameter(), CCopasiParameterGroup::setValue(), CCopasiParameter::UDOUBLE, and CCopasiParameter::UINT.
Referenced by CTrajectoryMethodDsaLsodar(), and elevateChildren().
Integrates the deterministic reactions of the system over the specified time interval.
const | C_FLOAT64 & deltaT. |
Definition at line 784 of file CTrajectoryMethodDsaLsodar.cpp.
References CLsodaMethod::mMethodState, CLsodaMethod::mpModel, CLsodaMethod::mpReducedModel, CModel::setState(), CLsodaMethod::step(), and CModel::updateSimulatedValues().
Referenced by doSingleStep().
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Check if the method is suitable for this problem
Reimplemented from CTrajectoryMethod.
Definition at line 984 of file CTrajectoryMethodDsaLsodar.cpp.
References CCopasiMessage::ERROR, CModel::getCompartments(), CTrajectoryProblem::getDuration(), CModel::getEvents(), CModel::getMetabolites(), CCopasiProblem::getModel(), CModel::getModelValues(), CModel::getNumMetabs(), CModel::getNumModelValues(), CCopasiParameter::getValue(), CTrajectoryMethod::isValidProblem(), MCTrajectoryMethod, mpLowerLimit, mpUpperLimit, CModelEntity::ODE, CCopasiParameter::Value::pDOUBLE, CCopasiParameter::Value::pINT, CCopasiVector< T >::size(), and CModel::suitableForStochasticSimulation().
This instructs the method to prepare for integration starting with the initialState given.
const CState * | initialState |
Reimplemented from CLsodaMethod.
Definition at line 538 of file CTrajectoryMethodDsaLsodar.cpp.
References CCopasiVector< T >::begin(), CStateTemplate::beginIndependent(), CState::beginIndependent(), CCopasiObject::buildUpdateSequence(), C_FLOAT64, C_INVALID_INDEX, calculatePropensities(), CModel::deterministic, CCopasiVector< T >::end(), CStateTemplate::endFixed(), CStateTemplate::getIndex(), CModel::getModelType(), CModel::getReactions(), CModel::getStateTemplate(), CModelEntity::getStatus(), CCopasiObject::getValuePointer(), CModelEntity::getValueReference(), CTrajectoryMethodDsaLsodar::CPartition::intialize(), mAmu, mDoCorrection, mFirstReactionSpeciesIndex, CLsodaMethod::mMethodState, mNextReactionIndex, mNextReactionTime, mNumReactions, mPartition, mpLowerLimit, CLsodaMethod::mpModel, mpUpperLimit, mReactionDependencies, CModelEntity::REACTIONS, CVector< CType >::resize(), CModel::setState(), CCopasiVector< T >::size(), CLsodaMethod::start(), and CModel::updateSimulatedValues().
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Inform the trajectory method that the state has changed outside its control
Reimplemented from CLsodaMethod.
Definition at line 407 of file CTrajectoryMethodDsaLsodar.cpp.
References CLsodaMethod::mMethodState, CTrajectoryMethod::mpCurrentState, and CLsodaMethod::stateChanged().
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This instructs the method to calculate a time step of deltaT starting with the current state, i.e., the result of the previous step. The new state (after deltaT) is expected in the current state. The return value is the actual time step taken.
const double & | deltaT |
Reimplemented from CLsodaMethod.
Definition at line 414 of file CTrajectoryMethodDsaLsodar.cpp.
References C_FLOAT64, doSingleStep(), CCopasiMessage::EXCEPTION, CState::getTime(), MCTrajectoryMethod, min, CLsodaMethod::mMethodState, CTrajectoryMethod::mpCurrentState, mpMaxSteps, CTrajectoryMethod::NORMAL, and CState::setTime().
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Total propensity (sum over mAmu[i])
Definition at line 434 of file CTrajectoryMethodDsaLsodar.h.
Referenced by calculatePropensities(), doSingleStep(), and fireReaction().
A vector of reaction propensities
Definition at line 429 of file CTrajectoryMethodDsaLsodar.h.
Referenced by calculateAmu(), calculatePropensities(), doSingleStep(), fireReaction(), and start().
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A boolean flag indicating whether correction for higher order reactions need to be applied
Definition at line 424 of file CTrajectoryMethodDsaLsodar.h.
Referenced by calculateAmu(), and start().
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Index of the first species determined by reactions in CState
Definition at line 396 of file CTrajectoryMethodDsaLsodar.h.
Referenced by CTrajectoryMethodDsaLsodar::CPartition::determineStochasticSpecies(), evalF(), CTrajectoryMethodDsaLsodar::CPartition::intialize(), CTrajectoryMethodDsaLsodar::CPartition::rePartition(), and start().
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Definition at line 399 of file CTrajectoryMethodDsaLsodar.h.
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The index of the next reaction which fires
Definition at line 419 of file CTrajectoryMethodDsaLsodar.h.
Referenced by doSingleStep(), and start().
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The time the next reaction fires
Definition at line 414 of file CTrajectoryMethodDsaLsodar.h.
Referenced by doSingleStep(), and start().
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The particle and reaction numbers
Definition at line 409 of file CTrajectoryMethodDsaLsodar.h.
Referenced by calculatePropensities(), doSingleStep(), fireReaction(), and start().
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The partition of the system
Definition at line 444 of file CTrajectoryMethodDsaLsodar.h.
Referenced by calculatePropensities(), doSingleStep(), evalF(), fireReaction(), and start().
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Pointer to the method parameter "Lower Limit"
Definition at line 371 of file CTrajectoryMethodDsaLsodar.h.
Referenced by initializeParameter(), isValidProblem(), and start().
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Pointer to the method parameter "Max Internal Steps"
Definition at line 366 of file CTrajectoryMethodDsaLsodar.h.
Referenced by initializeParameter(), and step().
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Pointer to the method parameter "Partitioning Interval"
Definition at line 381 of file CTrajectoryMethodDsaLsodar.h.
Referenced by doSingleStep(), and initializeParameter().
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Pointer to the method parameter "Partitioning Stepsize"
Definition at line 386 of file CTrajectoryMethodDsaLsodar.h.
Referenced by doSingleStep(), and initializeParameter().
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The random number generator.
Definition at line 391 of file CTrajectoryMethodDsaLsodar.h.
Referenced by cleanup(), CTrajectoryMethodDsaLsodar(), and doSingleStep().
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Pointer to the method parameter "Upper Limit"
Definition at line 376 of file CTrajectoryMethodDsaLsodar.h.
Referenced by initializeParameter(), isValidProblem(), and start().
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A vector containing dependency information to minimize the required updates.
Definition at line 439 of file CTrajectoryMethodDsaLsodar.h.
Referenced by calculateAmu(), fireReaction(), and start().
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Number of elementary steps after the last partitioning.
Definition at line 404 of file CTrajectoryMethodDsaLsodar.h.
Referenced by doSingleStep().