SimulationBase< FP, M, Integrands > Class Template Reference

CPP API: mio::details::SimulationBase< FP, M, Integrands > Class Template Reference

CPP API

Base class to define a Simulation. More...

#include <simulation_base.h>

Collaboration diagram for mio::details::SimulationBase< FP, M, Integrands >:

Public Types
using	Core = IntegratorCore< FP, Integrands... >

using	Model = M

Public Member Functions
SimulationBase &	operator= (const SimulationBase &other)

void	set_integrator_core (std::unique_ptr< Core > &&integrator_core)
	Set the IntegratorCore used in the simulation. More...

	SimulationBase (const SimulationBase &other)

	SimulationBase (Model const &model, std::unique_ptr< Core > &&integrator_core, FP t0, FP dt)
	Create a SimulationBase. More...


Core &	get_integrator_core ()
	Access the IntegratorCore used in the simulation. More...

const Core &	get_integrator_core () const
	Access the IntegratorCore used in the simulation. More...


TimeSeries< FP > &	get_result ()
	Returns the simulation result describing the model population in each time step. More...

const TimeSeries< FP > &	get_result () const
	Returns the simulation result describing the model population in each time step. More...


const Model &	get_model () const
	Get a reference to the model owned and used by the simulation. More...

Model &	get_model ()
	Get a reference to the model owned and used by the simulation. More...


FP &	get_dt ()
	Returns the step size used by the integrator. More...

const FP &	get_dt () const
	Returns the step size used by the integrator. More...

Protected Member Functions
Eigen::Ref< Eigen::VectorX< FP > >	advance (const Integrands &... fs, FP tmax, TimeSeries< FP > &results)
	Run the simulation up to a given time. More...

Private Attributes
FP	m_dt
	The time step used (and possibly set) by m_integrator::m_core::step. More...

SystemIntegrator< FP, Integrands... >	m_integrator
	Integrates the DerivFunction (see advance) and stores resutls in m_result. More...

std::unique_ptr< Model >	m_model
	The model defining the ODE system and initial conditions. More...

TimeSeries< FP >	m_result
	The simulation results. More...

Detailed Description

template<typename FP, IsCompartmentalModel< FP > M, class... Integrands>
class mio::details::SimulationBase< FP, M, Integrands >

Base class to define a Simulation.

Provides a protected advance method that accepts the specified integrands, that must be exposed by the Derived class. Also defines all relevant members and accessors for a Simulation.

Template Parameters

FP	A floating point type, e.g. double.
M	An implementation of CompartmentalModel.
Integrands	One or more function types used for defining the right hand side of a system of equations.

Member Typedef Documentation

◆ Core

template<typename FP , IsCompartmentalModel< FP > M, class... Integrands>

using mio::details::SimulationBase< FP, M, Integrands >::Core = IntegratorCore<FP, Integrands...>

◆ Model

template<typename FP , IsCompartmentalModel< FP > M, class... Integrands>

using mio::details::SimulationBase< FP, M, Integrands >::Model = M

Constructor & Destructor Documentation

◆ SimulationBase() [1/2]

template<typename FP , IsCompartmentalModel< FP > M, class... Integrands>

mio::details::SimulationBase< FP, M, Integrands >::SimulationBase	(	Model const &	model,
		std::unique_ptr< Core > &&	integrator_core,
		FP	t0,
		FP	dt
	)

inline

Create a SimulationBase.

Parameters

[in]	model	An instance of a compartmental model
[in]	integrator_core	A unique pointer to an object derived from IntegratorCore.
[in]	t0	Start time.
[in]	dt	Initial step size of integration

◆ SimulationBase() [2/2]

template<typename FP , IsCompartmentalModel< FP > M, class... Integrands>

mio::details::SimulationBase< FP, M, Integrands >::SimulationBase ( const SimulationBase< FP, M, Integrands > & other )

inline

Member Function Documentation

◆ advance()

template<typename FP , IsCompartmentalModel< FP > M, class... Integrands>

Eigen::Ref<Eigen::VectorX<FP> > mio::details::SimulationBase< FP, M, Integrands >::advance	(	const Integrands &...	fs,
		FP	tmax,
		TimeSeries< FP > &	results
	)

inlineprotected

Run the simulation up to a given time.

Parameters

[in]	fs	Integrands passed to the integrator, e.g. a wrapper for `get_derivatives`.
[in]	tmax	Next stopping point of the simulation.
[in,out]	results	The TimeSeries to use as initial value and for storing integration results.

Returns: The simulation result at tmax.

◆ get_dt() [1/2]

template<typename FP , IsCompartmentalModel< FP > M, class... Integrands>

FP& mio::details::SimulationBase< FP, M, Integrands >::get_dt ( )

inline

Returns the step size used by the integrator.

When using a integration scheme with adaptive time stepping, the integrator will store its estimate for the next step size in this value.

◆ get_dt() [2/2]

template<typename FP , IsCompartmentalModel< FP > M, class... Integrands>

const FP& mio::details::SimulationBase< FP, M, Integrands >::get_dt ( ) const

inline

Returns the step size used by the integrator.

When using a integration scheme with adaptive time stepping, the integrator will store its estimate for the next step size in this value.

◆ get_integrator_core() [1/2]

template<typename FP , IsCompartmentalModel< FP > M, class... Integrands>

Core& mio::details::SimulationBase< FP, M, Integrands >::get_integrator_core ( )

inline

Access the IntegratorCore used in the simulation.

Returns: A reference to the IntegratorCore used in the simulation

◆ get_integrator_core() [2/2]

template<typename FP , IsCompartmentalModel< FP > M, class... Integrands>

const Core& mio::details::SimulationBase< FP, M, Integrands >::get_integrator_core ( ) const

inline

Access the IntegratorCore used in the simulation.

Returns: A reference to the IntegratorCore used in the simulation

◆ get_model() [1/2]

template<typename FP , IsCompartmentalModel< FP > M, class... Integrands>

Model& mio::details::SimulationBase< FP, M, Integrands >::get_model ( )

inline

Get a reference to the model owned and used by the simulation.

Returns: The simulation model.

◆ get_model() [2/2]

template<typename FP , IsCompartmentalModel< FP > M, class... Integrands>

const Model& mio::details::SimulationBase< FP, M, Integrands >::get_model ( ) const

inline

Get a reference to the model owned and used by the simulation.

Returns: The simulation model.

◆ get_result() [1/2]

template<typename FP , IsCompartmentalModel< FP > M, class... Integrands>

TimeSeries<FP>& mio::details::SimulationBase< FP, M, Integrands >::get_result ( )

inline

Returns the simulation result describing the model population in each time step.

Which compartments are used by the model is defined by the Comp template argument for the CompartmentalModel (usually an enum named InfectionState).

Returns: A TimeSeries to represent a numerical solution for the population of the model. For each simulated time step, the TimeSeries contains the population size in each compartment.

◆ get_result() [2/2]

template<typename FP , IsCompartmentalModel< FP > M, class... Integrands>

const TimeSeries<FP>& mio::details::SimulationBase< FP, M, Integrands >::get_result ( ) const

inline

Returns the simulation result describing the model population in each time step.

Which compartments are used by the model is defined by the Comp template argument for the CompartmentalModel (usually an enum named InfectionState).

Returns: A TimeSeries to represent a numerical solution for the population of the model. For each simulated time step, the TimeSeries contains the population size in each compartment.

◆ operator=()

template<typename FP , IsCompartmentalModel< FP > M, class... Integrands>

SimulationBase& mio::details::SimulationBase< FP, M, Integrands >::operator= ( const SimulationBase< FP, M, Integrands > & other )

inline

◆ set_integrator_core()

template<typename FP , IsCompartmentalModel< FP > M, class... Integrands>

void mio::details::SimulationBase< FP, M, Integrands >::set_integrator_core ( std::unique_ptr< Core > && integrator_core )

inline

Set the IntegratorCore used in the simulation.

Parameters

[in] integrator_core A unique pointer to an object derived from IntegratorCore.

Member Data Documentation

◆ m_dt

template<typename FP , IsCompartmentalModel< FP > M, class... Integrands>

FP mio::details::SimulationBase< FP, M, Integrands >::m_dt

private

The time step used (and possibly set) by m_integrator::m_core::step.

◆ m_integrator

template<typename FP , IsCompartmentalModel< FP > M, class... Integrands>

SystemIntegrator<FP, Integrands...> mio::details::SimulationBase< FP, M, Integrands >::m_integrator

private

Integrates the DerivFunction (see advance) and stores resutls in m_result.

◆ m_model

template<typename FP , IsCompartmentalModel< FP > M, class... Integrands>

std::unique_ptr<Model> mio::details::SimulationBase< FP, M, Integrands >::m_model

private

The model defining the ODE system and initial conditions.

◆ m_result

template<typename FP , IsCompartmentalModel< FP > M, class... Integrands>

TimeSeries<FP> mio::details::SimulationBase< FP, M, Integrands >::m_result

private

The simulation results.

SimulationBase&lt; FP, M, Integrands &gt; Class Template Reference

Public Types

Public Member Functions

Protected Member Functions

Private Attributes

Detailed Description

template<typename FP, IsCompartmentalModel< FP > M, class... Integrands> class mio::details::SimulationBase< FP, M, Integrands >

Member Typedef Documentation

◆ Core

◆ Model

Constructor & Destructor Documentation

◆ SimulationBase() [1/2]

◆ SimulationBase() [2/2]

Member Function Documentation

◆ advance()

◆ get_dt() [1/2]

◆ get_dt() [2/2]

◆ get_integrator_core() [1/2]

◆ get_integrator_core() [2/2]

◆ get_model() [1/2]

◆ get_model() [2/2]

◆ get_result() [1/2]

◆ get_result() [2/2]

◆ operator=()

◆ set_integrator_core()

Member Data Documentation

◆ m_dt

◆ m_integrator

◆ m_model

◆ m_result

SimulationBase< FP, M, Integrands > Class Template Reference

template<typename FP, IsCompartmentalModel< FP > M, class... Integrands>
class mio::details::SimulationBase< FP, M, Integrands >