roadrunner
2.6.0
Fast simulator for SBML models
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A Runge-Kutta Fehlberg method for roadrunner. More...
#include <RK45Integrator.h>
Public Member Functions | |
RK45Integrator (ExecutableModel *m) | |
Constructor: takes an executable model, does not own the pointer. More... | |
virtual | ~RK45Integrator () |
Destructor. More... | |
virtual void | syncWithModel (ExecutableModel *m) |
Called whenever a new model is loaded to allow integrator to reset internal state. More... | |
virtual double | integrate (double t, double h) |
implement Integrator interface More... | |
virtual void | restart (double t0) |
Restarts the integrator. | |
std::string | getName () const |
Get the name for this integrator. More... | |
std::string | getDescription () const |
Get the description for this integrator. More... | |
std::string | getHint () const |
Get the hint for this integrator. More... | |
Solver * | construct (ExecutableModel *executableModel) const |
Constructs a new Solver of a given type. More... | |
virtual Setting | getValue (std::string key) |
IntegrationMethod | getIntegrationMethod () const |
Always deterministic for RK45. More... | |
void | resetSettings () |
Reset all integrator settings to their respective default values. More... | |
virtual void | setListener (IntegratorListenerPtr) |
the integrator can hold a single listener. More... | |
virtual IntegratorListenerPtr | getListener () |
get the integrator listener | |
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 void | setValue (const std::string &key, Setting value) |
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... | |
Static Public Member Functions | |
static std::string | getRK45Name () |
Get the name for this integrator. More... | |
static std::string | getRK45Description () |
Get the description for this integrator. More... | |
static std::string | getRK45Hint () |
Get the hint for this integrator. 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 | |
A Runge-Kutta Fehlberg method for roadrunner.
Uses the Fehlberg method, an adaptive step method, to integrate models.
rr::RK45Integrator::RK45Integrator | ( | ExecutableModel * | m | ) |
Constructor: takes an executable model, does not own the pointer.
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Destructor.
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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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Get the description for this integrator.
Implements rr::Registrable.
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Always deterministic for RK45.
Implements rr::Integrator.
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Get the description for this integrator.
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Get the hint for this integrator.
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Get the name for this integrator.
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implement Integrator interface
Integrates the model from t to t + h.
Attempts to find the state std::vector at t + h, and returns time t + h if successful. If the integrator does not find a convergent solution, the state std::vector is not updated and t is returned. Also calculates a new timestep and saves it to a member variable for future use.
Implements rr::Integrator.
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Reset all integrator settings to their respective default values.
Reimplemented from rr::Solver.
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the integrator can hold a single listener.
If clients require multicast, they can create a multi-cast listener.
Implements rr::Integrator.
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Called whenever a new model is loaded to allow integrator to reset internal state.
Reimplemented from rr::Integrator.