QuadWell< InfectionState > Class Template Reference

CPP API: QuadWell< InfectionState > Class Template Reference

CPP API

Implementation of diffusive ABM, see dabm::Model. More...

#include <quad_well.h>

Classes
struct	Agent
	Struct defining an agent for the diffusive ABM. More...

Public Types
using	Status = InfectionState

Public Member Functions
ScalarType	adoption_rate (const Agent &agent, const Status &new_status) const
	Calculate adoption rate for an Agent. More...

std::map< std::tuple< mio::regions::Region, Status, Status >, mio::AdoptionRate< ScalarType, Status > > &	get_adoption_rates ()
	Get AdoptionRate mapping. More...

mio::RandomNumberGenerator &	get_rng ()
	Get the RandomNumberGenerator used by this Model for random events. More...

void	move (const ScalarType, const ScalarType dt, Agent &agent)
	Perform one integration step of the diffusion process for a given Agent using the Euler-Maruyama method. More...

std::vector< Eigen::MatrixX< ScalarType > > &	number_transitions ()

const std::vector< Eigen::MatrixX< ScalarType > > &	number_transitions () const
	Get the number of spatial transitions that happened until the current system state. More...

	QuadWell (const std::vector< Agent > &agents, const std::vector< mio::AdoptionRate< ScalarType, Status >> &rates, ScalarType contact_radius=0.4, ScalarType sigma=0.4, std::vector< Status > non_moving_states={})
	Set up a diffusive ABM using the quadwell potential F(x,y) = (x^2 -1)^2+(y^2-1)^2. More...

void	set_non_moving_regions (std::vector< size_t > non_moving_regions)
	Set regions where no movement happens. More...

Eigen::VectorX< ScalarType >	time_point () const
	Calculate the current system state i.e. More...

Static Public Member Functions
static constexpr void	adopt (Agent &agent, const Status &new_status)
	Perform infection state adoption for an Agent. More...

Public Attributes
std::vector< Agent >	populations
	Vector containing all Agents in the model. More...

Private Member Functions
bool	is_contact (const Agent &agent, const Agent &contact) const
	Evaluate whether two agents are within their contact radius. More...

bool	is_in_domain (const Position &p) const
	Restrict domain to [-2, 2]^2 where "escaping" is impossible. More...

Static Private Member Functions
static Position	grad_U (const Position x)
	Claculate the gradient of the potential at a given position. More...

Private Attributes
std::map< std::tuple< mio::regions::Region, Status, Status >, mio::AdoptionRate< ScalarType, Status > >	m_adoption_rates
	Map of AdoptionRates according to their region index and their from -> to infection states. More...

ScalarType	m_contact_radius
	Agents' interaction radius. Within this radius agents are considered as contacts. More...

std::vector< size_t >	m_non_moving_regions {}
	Regions without movement. More...

std::vector< Status >	m_non_moving_states
	Infection states within which agents do not change their location. More...

std::vector< Eigen::MatrixX< ScalarType > >	m_number_transitions
	Vector that contains for every infection state a matrix with entry (k,l) the number of spatial transitions from Region k to Regionl. More...

mio::RandomNumberGenerator	m_rng
	Model's random number generator. More...

ScalarType	m_sigma
	Noise term of the diffusion process. More...

Detailed Description

template<class InfectionState>
class QuadWell< InfectionState >

Implementation of diffusive ABM, see dabm::Model.

This implementation defines a diffusion process for the potential F(x,y) = (x^2 -1)^2+(y^2-1)^2.

Template Parameters

InfectionState An infection state enum.

Member Typedef Documentation

◆ Status

template<class InfectionState >

using QuadWell< InfectionState >::Status = InfectionState

Constructor & Destructor Documentation

◆ QuadWell()

template<class InfectionState >

QuadWell< InfectionState >::QuadWell	(	const std::vector< Agent > &	agents,
		const std::vector< mio::AdoptionRate< ScalarType, Status >> &	rates,
		ScalarType	contact_radius = `0.4`,
		ScalarType	sigma = `0.4`,
		std::vector< Status >	non_moving_states = `{}`
	)

inline

Set up a diffusive ABM using the quadwell potential F(x,y) = (x^2 -1)^2+(y^2-1)^2.

Parameters

[in]	agents	A vector of Agents representing the population.
[in]	rates	AdoptionRates defining InfectionState adoptions, see mio::AdoptionRate.
[in]	contact_radius	Contact radius for second-order adoptions.
[in]	sigma	Noise term for the diffusion process.
[in]	non_moving_state	InfectionStates that are excluded from movement e.g. Dead.

Member Function Documentation

◆ adopt()

template<class InfectionState >

static constexpr void QuadWell< InfectionState >::adopt	(	Agent &	agent,
		const Status &	new_status
	)

inlinestaticconstexpr

Perform infection state adoption for an Agent.

Parameters

[in,out]	agent	Agent whose infection state is changed.
[in]	new_status	Agent's new infection state.

◆ adoption_rate()

template<class InfectionState >

ScalarType QuadWell< InfectionState >::adoption_rate	(	const Agent &	agent,
		const Status &	new_status
	)		const

inline

Calculate adoption rate for an Agent.

Parameters

[in]	agent	Agent for whom the adoption rate is calculated.
[in]	new_status	Target infection state of the adoption rate, see mio::AdoptionRate.to.

Returns: Value of agent-dependent AdoptionRate.

◆ get_adoption_rates()

template<class InfectionState >

std::map<std::tuple<mio::regions::Region, Status, Status>, mio::AdoptionRate<ScalarType, Status> >& QuadWell< InfectionState >::get_adoption_rates ( )

inline

Get AdoptionRate mapping.

Returns: Map of AdoptionRates based on their region index and source and target infection state.

◆ get_rng()

template<class InfectionState >

mio::RandomNumberGenerator& QuadWell< InfectionState >::get_rng ( )

inline

Get the RandomNumberGenerator used by this Model for random events.

Returns: The random number generator.

◆ grad_U()

template<class InfectionState >

static Position QuadWell< InfectionState >::grad_U ( const Position x )

inlinestaticprivate

Claculate the gradient of the potential at a given position.

Parameters

[in] x Position at which the gradient is evaluated.

Returns: Value of potential gradient.

◆ is_contact()

template<class InfectionState >

bool QuadWell< InfectionState >::is_contact	(	const Agent &	agent,
		const Agent &	contact
	)		const

inlineprivate

Evaluate whether two agents are within their contact radius.

Parameters

[in]	agent	Agent whose position specifies the contact area.
[in]	contact	Potential contact of agent.

Returns: Boolean specifying whether are within each others contact radius.

◆ is_in_domain()

template<class InfectionState >

bool QuadWell< InfectionState >::is_in_domain ( const Position & p ) const

inlineprivate

Restrict domain to [-2, 2]^2 where "escaping" is impossible.

Parameters

[in] p Position to check.

Returns: Boolean specifying whether p is in [-2, 2]^2.

◆ move()

template<class InfectionState >

void QuadWell< InfectionState >::move	(	const	ScalarType,
		const ScalarType	dt,
		Agent &	agent
	)

inline

Perform one integration step of the diffusion process for a given Agent using the Euler-Maruyama method.

Parameters

[in]	dt	Step size.
[in]	agent	Agent to be moved.

◆ number_transitions() [1/2]

template<class InfectionState >

std::vector<Eigen::MatrixX<ScalarType> >& QuadWell< InfectionState >::number_transitions ( )

inline

◆ number_transitions() [2/2]

template<class InfectionState >

const std::vector<Eigen::MatrixX<ScalarType> >& QuadWell< InfectionState >::number_transitions ( ) const

inline

Get the number of spatial transitions that happened until the current system state.

Returns: Matrix with entries (from_well, to_well) for every infection state.

◆ set_non_moving_regions()

template<class InfectionState >

void QuadWell< InfectionState >::set_non_moving_regions ( std::vector< size_t > non_moving_regions )

inline

Set regions where no movement happens.

◆ time_point()

template<class InfectionState >

Eigen::VectorX<ScalarType> QuadWell< InfectionState >::time_point ( ) const

inline

Calculate the current system state i.e.

the populations for each region and infection state.

Returns: Vector containing the number of agents per infection state for each region.

Member Data Documentation

◆ m_adoption_rates

template<class InfectionState >

std::map<std::tuple<mio::regions::Region, Status, Status>, mio::AdoptionRate<ScalarType, Status> > QuadWell< InfectionState >::m_adoption_rates

private

Map of AdoptionRates according to their region index and their from -> to infection states.

◆ m_contact_radius

template<class InfectionState >

ScalarType QuadWell< InfectionState >::m_contact_radius

private

Agents' interaction radius. Within this radius agents are considered as contacts.

◆ m_non_moving_regions

template<class InfectionState >

std::vector<size_t> QuadWell< InfectionState >::m_non_moving_regions {}

private

Regions without movement.

◆ m_non_moving_states

template<class InfectionState >

std::vector<Status> QuadWell< InfectionState >::m_non_moving_states

private

Infection states within which agents do not change their location.

◆ m_number_transitions

template<class InfectionState >

std::vector<Eigen::MatrixX<ScalarType> > QuadWell< InfectionState >::m_number_transitions

private

Vector that contains for every infection state a matrix with entry (k,l) the number of spatial transitions from Region k to Regionl.

◆ m_rng

template<class InfectionState >

mio::RandomNumberGenerator QuadWell< InfectionState >::m_rng

private

Model's random number generator.

◆ m_sigma

template<class InfectionState >

ScalarType QuadWell< InfectionState >::m_sigma

private

Noise term of the diffusion process.

◆ populations

template<class InfectionState >

std::vector<Agent> QuadWell< InfectionState >::populations

Vector containing all Agents in the model.

QuadWell&lt; InfectionState &gt; Class Template Reference

Classes

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Private Member Functions

Static Private Member Functions

Private Attributes

Detailed Description

template<class InfectionState> class QuadWell< InfectionState >

Member Typedef Documentation

◆ Status

Constructor & Destructor Documentation

◆ QuadWell()

Member Function Documentation

◆ adopt()

◆ adoption_rate()

◆ get_adoption_rates()

◆ get_rng()

◆ grad_U()

◆ is_contact()

◆ is_in_domain()

◆ move()

◆ number_transitions() [1/2]

◆ number_transitions() [2/2]

◆ set_non_moving_regions()

◆ time_point()

Member Data Documentation

◆ m_adoption_rates

◆ m_contact_radius

◆ m_non_moving_regions

◆ m_non_moving_states

◆ m_number_transitions

◆ m_rng

◆ m_sigma

◆ populations

QuadWell< InfectionState > Class Template Reference

template<class InfectionState>
class QuadWell< InfectionState >