roadrunner
2.6.0
Fast simulator for SBML models
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RoadRunner's implementation of the Gillespie SSA. More...
#include <GillespieIntegrator.h>
Public Member Functions | |
GillespieIntegrator (ExecutableModel *model) | |
void | syncWithModel (ExecutableModel *m) override |
Called whenever a new model is loaded to allow integrator to reset internal state. More... | |
std::string | getName () const override |
Get the name for this integrator. More... | |
std::string | getDescription () const override |
Get the description for this integrator. More... | |
std::string | getHint () const override |
Get the hint for this integrator. More... | |
Solver * | construct (ExecutableModel *executableModel) const override |
Constructs a new Solver of a given type. More... | |
IntegrationMethod | getIntegrationMethod () const override |
Always stochastic for Gillespie. More... | |
void | setValue (const std::string &setting, Setting value) override |
Sets the value of an integrator setting (e.g. absolute_tolerance) More... | |
void | resetSettings () override |
Reset all integrator settings to their respective default values. More... | |
double | integrate (double t0, double tf) override |
Main integration routine. More... | |
void | restart (double timeStart) override |
Reset time to zero and reinitialize model. More... | |
IntegratorListenerPtr | getListener () override |
Gets the integrator listener. More... | |
void | setListener (IntegratorListenerPtr) override |
Sets the integrator listener. More... | |
Integrator (ExecutableModel *model) | |
Integrator () | |
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Integrator (ExecutableModel *model) | |
virtual void | loadConfigSettings () |
virtual void | loadSBMLSettings (const std::string &filename) |
virtual void | tweakTolerances () |
Fix tolerances for SBML tests. More... | |
virtual void | setIndividualTolerance (std::string sid, double value) |
Set tolerance for floating species or variables that have a rate rule, will only be used in CVODEIntegrator. More... | |
virtual std::vector< double > | getAbsoluteToleranceVector () |
Get the absolute tolerance vector for the solver. More... | |
std::string | toString () const |
Return a std::string representation of the solver. More... | |
virtual std::string | toRepr () const |
Return std::string representation a la Python repr method. More... | |
void | setIntegrationStartTime (double time) |
Solver ()=default | |
Solver (ExecutableModel *model) | |
virtual void | setValue (const std::string &key, Setting value) |
Pull down the setValue from superclass. More... | |
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Solver (ExecutableModel *model) | |
void | updateSettings (Dictionary *inputSettings) |
Update settings values. More... | |
std::vector< std::string > | getSettings () const |
Get a list of all settings for this solver. More... | |
std::unordered_map< std::string, Setting > & | getSettingsMap () |
get settings for this solver More... | |
virtual Setting | getValue (const std::string &key) const |
Get the value of an integrator setting. More... | |
virtual Setting | hasValue (const std::string &key) const |
Return true if this setting is supported by the integrator. More... | |
virtual size_t | getNumParams () const |
Get the number of parameters. More... | |
virtual std::string | getParamName (size_t n) const |
Get the name of the parameter at index n. More... | |
virtual std::string | getParamDisplayName (int n) const |
Get the display name of the parameter at index n. More... | |
virtual std::string | getParamHint (int n) const |
Get the hint of the parameter at index n. More... | |
virtual std::string | getParamDesc (int n) const |
Get the description of the parameter at index n. More... | |
virtual std::string | getValueAsString (const std::string &key) |
Wrapper for getValue which converts output to a specific type. More... | |
virtual std::string | getSettingsRepr () const |
Get the solver settings as a std::string. More... | |
virtual std::string | settingsPyDictRepr () const |
Python dictionary-style std::string representation of settings. More... | |
const std::string & | getDisplayName (const std::string &key) const |
Gets the hint associated with a given key. More... | |
const std::string & | getHint (const std::string &key) const |
Gets the hint associated with a given key. More... | |
const std::string & | getDescription (const std::string &key) const |
Gets the description associated with a given key. More... | |
Setting::TypeId | getType (const std::string &key) const |
Gets the type associated with a given key. More... | |
virtual ExecutableModel * | getModel () const |
returns the pointer to the ExecutableModel | |
virtual std::string | getName () const=0 |
Gets the name associated with this Solver type. More... | |
virtual std::string | getHint () const=0 |
Gets the hint associated with this Solver type. More... | |
virtual std::string | getDescription () const=0 |
Gets the description associated with this Solver type. More... | |
Additional Inherited Members | |
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enum | IntegrationMethod { Deterministic , Stochastic , Hybrid , Other } |
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using | SettingsList = std::vector< std::string > |
using | SettingsMap = std::unordered_map< std::string, Setting > |
using | DisplayNameMap = std::unordered_map< std::string, std::string > |
using | HintMap = std::unordered_map< std::string, std::string > |
using | DescriptionMap = std::unordered_map< std::string, std::string > |
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SettingsList | sorted_settings |
SettingsMap | settings |
DisplayNameMap | display_names_ |
HintMap | hints |
DescriptionMap | descriptions |
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void | addSetting (const std::string &name, const Setting &val, const std::string &display_name, const std::string &hint, const std::string &description) |
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double | mIntegrationStartTime |
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ExecutableModel * | mModel = nullptr |
non-owning pointer to model | |
RoadRunner's implementation of the Gillespie SSA.
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overridevirtual |
Constructs a new Solver of a given type.
the caller is responsible for deleting memory associated with the returned Solver*.
Implements rr::Registrable.
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overridevirtual |
Get the description for this integrator.
Implements rr::Registrable.
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overridevirtual |
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overridevirtual |
Always stochastic for Gillespie.
Implements rr::Integrator.
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overridevirtual |
Gets the integrator listener.
Implements rr::Integrator.
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overridevirtual |
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overridevirtual |
Main integration routine.
Implements rr::Integrator.
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overridevirtual |
Reset all integrator settings to their respective default values.
Reimplemented from rr::Solver.
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overridevirtual |
Reset time to zero and reinitialize model.
Implements rr::Integrator.
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overridevirtual |
Sets the integrator listener.
Implements rr::Integrator.
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overridevirtual |
Sets the value of an integrator setting (e.g. absolute_tolerance)
Reimplemented from rr::Solver.
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overridevirtual |
Called whenever a new model is loaded to allow integrator to reset internal state.
Reimplemented from rr::Integrator.