GillespieIntegrator

class GillespieIntegrator : public rr::Integrator

RoadRunner’s implementation of the Gillespie SSA.

Author

WBC, ETS

Public Functions

GillespieIntegrator(ExecutableModel *model)

~GillespieIntegrator() override

virtual void syncWithModel(ExecutableModel *m) override

Called whenever a new model is loaded to allow integrator to reset internal state.

Author

JKM

virtual std::string getName() const override

Get the name for this integrator.

Author

WBC

Note

Delegates to getName

virtual std::string getDescription() const override

Get the description for this integrator.

Author

WBC

Note

Delegates to getDescription

virtual std::string getHint() const override

Get the hint for this integrator.

Author

WBC

Note

Delegates to getHint

virtual Solver *construct(ExecutableModel *executableModel) const override

Constructs a new Solver of a given type.

the caller is responsible for deleting memory associated with the returned Solver*.

Author

JKM, WBC

virtual IntegrationMethod getIntegrationMethod() const override

Always stochastic for Gillespie.

Author

WBC, ETS

virtual void setValue(const std::string &setting, Setting value) override

Sets the value of an integrator setting (e.g. absolute_tolerance)

Author

WBC, ETS

virtual void resetSettings() override

Reset all integrator settings to their respective default values.

Author

JKM

virtual double integrate(double t0, double tf) override

Main integration routine.

Author

WBC, ETS

virtual void restart(double timeStart) override

Reset time to zero and reinitialize model.

Author

WBC, ETS

virtual IntegratorListenerPtr getListener() override

Gets the integrator listener.

Author

WBC, ETS

virtual void setListener(IntegratorListenerPtr) override

Sets the integrator listener.

Author

WBC, ETS

explicit Integrator(ExecutableModel *model)

Integrator()

Private Functions

void testRootsAtInitialTime()

void applyEvents(double timeEnd, std::vector<unsigned char> &prevEventStatus)

double urand()

void setEngineSeed(Setting seedSetting)

inline double getStoich(uint species, uint reaction)

void initializeFromModel()

Initialize model-specific variables.

Called whenever a model is loaded or a Gillespie integrator is constructed

Author

JKM

Private Members

std::mt19937 engine

double timeScale

double stoichScale

int nReactions

int floatingSpeciesStart

double *reactionRates

double *reactionRatesBuffer

int stateVectorSize

double *stateVector

double *stateVectorRate

std::vector<unsigned char> eventStatus

std::vector<unsigned char> previousEventStatus