SEIRD model on a grid. More...

#include <SEIRD.hh>

Inheritance diagram for Utopia::Models::SEIRD::SEIRD:

Collaboration diagram for Utopia::Models::SEIRD::SEIRD:

[legend]

Public Types
using	Base = Model< SEIRD, CDTypes >
	The base model type. More...

using	DataGroup = typename Base::DataGroup
	Data type for a data group. More...

using	DataSet = typename Base::DataSet
	Data type for a dataset. More...

using	CellManager = Utopia::CellManager< CDCellTraits, SEIRD >
	Type of the CellManager to use. More...

using	Cell = typename CellManager::Cell
	Type of a cell. More...

using	CellContainer = Utopia::CellContainer< Cell >
	Type of a container of shared pointers to cells. More...

using	RuleFunc = typename CellManager::RuleFunc
	Rule function type. More...

Public Types inherited from Utopia::Model< SEIRD, CDTypes >
using	Config = typename ModelTypes::Config
	Data type that holds the configuration. More...

using	DataManager = DataIO::Default::DefaultDataManager< SEIRD >
	The data manager to use, specialized with the derived model. More...

using	DataGroup = typename ModelTypes::DataGroup
	Data type that is used for storing datasets. More...

using	DataSet = typename ModelTypes::DataSet
	Data type that is used for storing data. More...

using	RNG = typename ModelTypes::RNG
	Data type of the shared RNG. More...

using	Space = typename ModelTypes::Space
	Data type of the space this model resides in. More...

using	Time = typename ModelTypes::Time
	Data type for the model time. More...

using	Monitor = typename ModelTypes::Monitor
	Data type for the monitor. More...

using	MonitorManager = typename ModelTypes::MonitorManager
	Data type for the monitor manager. More...

using	Level = typename ModelTypes::Level
	Data type for the hierarchical level. More...

Public Member Functions
template<class ParentModel >
	SEIRD (const std::string &name, ParentModel &parent_model, const DataIO::Config &custom_cfg={})
	Construct the SEIRD model. More...

void	perform_step ()
	Iterate a single time step. More...

void	monitor ()
	Monitor model information. More...

void	write_data ()
	Write data. More...

Public Member Functions inherited from Utopia::Model< SEIRD, CDTypes >
	Model (const std::string &name, const ParentModel &parent_model, const Config &custom_cfg={}, std::tuple< WriterArgs... > w_args={}, const DataIO::Default::DefaultDecidermap< SEIRD > &w_deciders=DataIO::Default::default_deciders< SEIRD >, const DataIO::Default::DefaultTriggermap< SEIRD > &w_triggers=DataIO::Default::default_triggers< SEIRD >)
	Constructs a Model instance. More...

const std::shared_ptr< Space > &	get_space () const
	Return the space this model resides in. More...

Time	get_time () const
	Return the current time of this model. More...

Time	get_time_max () const
	Return the maximum time possible for this model. More...

Config	get_cfg () const
	Return the config node of this model. More...

std::string	get_name () const
	Return the name of this model instance. More...

std::string	get_full_name () const
	Return the full name of this model within the model hierarchy. More...

std::shared_ptr< DataGroup >	get_hdfgrp () const
	Return a pointer to the HDF group this model stores data in. More...

Time	get_write_start () const
	Return the parameter that controls when write_data is called first. More...

Time	get_write_every () const
	Return the parameter that controls how often write_data is called. More...

DataManager	get_datamanager () const
	return the datamanager More...

hsize_t	get_remaining_num_writes () const
	Return the number of remaining `write_data` calls this model will make. More...

std::shared_ptr< RNG >	get_rng () const
	Return a pointer to the shared RNG. More...

std::shared_ptr< spdlog::logger >	get_logger () const
	Return a pointer to the logger of this model. More...

Monitor	get_monitor () const
	Return the monitor of this model. More...

std::shared_ptr< MonitorManager >	get_monitor_manager () const
	Get the monitor manager of the root model. More...

Level	get_level () const
	Return the hierarchical level within the model hierarchy. More...

virtual void	prolog ()
	A function that is called before starting model iteration. More...

virtual void	epilog ()
	A function that is called after the last iteration of a model. More...

void	iterate ()
	Iterate one (time) step of this model. More...

void	run ()
	Run the model from the current time to the maximum time. More...

std::shared_ptr< DataSet >	create_dset (const std::string name, const std::shared_ptr< DataGroup > &hdfgrp, std::vector< hsize_t > add_write_shape, const std::size_t compression_level=1, const std::vector< hsize_t > chunksize={})
	Create a new dataset within the given group. More...

std::shared_ptr< DataSet >	create_dset (const std::string name, const std::vector< hsize_t > add_write_shape, const std::size_t compression_level=1, const std::vector< hsize_t > chunksize={})
	Create a new dataset within the model's base data group. More...

std::shared_ptr< DataSet >	create_cm_dset (const std::string name, const CellManager &cm, const std::size_t compression_level=1, const std::vector< hsize_t > chunksize={})
	Create a dataset storing data from a CellManager. More...

std::shared_ptr< DataSet >	create_am_dset (const std::string name, const AgentManager &am, const std::size_t compression_level=1, const std::vector< hsize_t > chunksize={})
	Create a dataset storing data from a AgentManager. More...

Protected Member Functions
void	update_densities ()
	Update the densities array. More...

void	identify_clusters ()
	Identify clusters. More...

void	exposure_control ()
	Apply exposure control. More...

void	immunity_control ()
	Apply immunity control. More...

void	transmission_control ()
	Apply transmission control. More...

Protected Member Functions inherited from Utopia::Model< SEIRD, CDTypes >
void	__perform_step ()
	Perform the computation of a step. More...

void	__monitor ()
	Monitor information in the terminal. More...

void	__write_data ()
	Write data; calls the implementation's write_data method. More...

void	__write_initial_state ()
	Write the initial state. More...

void	increment_time (const Time dt=1)
	Increment time. More...

void	__prolog ()
	The default prolog of a model. More...

void	__epilog ()
	The default epilog of a model. More...

SEIRD &	impl ()
	cast to the derived class More...

const SEIRD &	impl () const
	const cast to the derived interface More...

Protected Attributes
RuleFunc	_update
	Define the update rule. More...

RuleFunc	_identify_cluster
	Identify each cluster of susceptibles. More...

RuleFunc	_move_away_from_infected
	Move the agent on the cell away from an infected neighboring cell. More...

RuleFunc	_move_randomly
	Move randomly to a neighboring cell if that cell is empty. More...

Protected Attributes inherited from Utopia::Model< SEIRD, CDTypes >
const std::string	_name
	Name of the model instance. More...

const std::string	_full_name
	The full name within the model hierarchy. More...

const Level	_level
	The level within the model hierarchy. More...

const Config	_cfg
	Config node belonging to this model instance. More...

const std::shared_ptr< RNG >	_rng
	The RNG shared between models. More...

const std::shared_ptr< spdlog::logger >	_log
	The (model) logger. More...

std::shared_ptr< Space >	_space
	The space this model resides in. More...

Time	_time
	Model-internal current time stamp. More...

const Time	_time_max
	Model-internal maximum time stamp. More...

const std::shared_ptr< DataGroup >	_hdfgrp
	The HDF group this model instance should write its data to. More...

const Time	_write_start
	First time at which write_data is called. More...

const Time	_write_every
	How often to call write_data from iterate. More...

Monitor	_monitor
	The monitor. More...

DataManager	_datamanager
	Manager object for handling data output; see DataManager. More...

Private Attributes
CellManager	_cm
	The cell manager. More...

const Params	_params
	Model parameters. More...

std::uniform_real_distribution< double >	_prob_distr
	The range [0, 1] distribution to use for probability checks. More...

unsigned int	_cluster_id_cnt
	The incremental cluster tag. More...

std::vector< std::shared_ptr< CellManager::Cell > >	_cluster_members
	A temporary container for use in cluster identification. More...

std::array< double, static_cast< char >Kind::COUNT)>	_densities
	Densities for all states. More...

Counters< std::size_t >	_counts
	Cumulative counters for state transitions and other events More...

const int	_compression
	The compression level used for all datasets. More...

bool	_write_ca_data
	If false, writes only the non-spatial `densities` and `counts` data. More...

std::shared_ptr< DataSet >	_dset_densities
	2D dataset (densities array and time) of density values More...

std::shared_ptr< DataSet >	_dset_counts
	2D dataset (counts array and time) of cumulative state counters More...

std::shared_ptr< DataSet >	_dset_kind
	2D dataset (cell ID and time) of cell kinds More...

std::shared_ptr< DataSet >	_dset_immune
	2D dataset (cell ID and time) of cell's immunity More...

std::shared_ptr< DataSet >	_dset_num_recoveries
	2D dataset (cell ID and time) of cell's number of recoveries More...

std::shared_ptr< DataSet >	_dset_age
	2D dataset (cell ID and time) of cell's age More...

std::shared_ptr< DataSet >	_dset_cluster_id
	The dataset for storing the cluster ID associated with each cell. More...

Additional Inherited Members
Static Protected Attributes inherited from Utopia::Model< SEIRD, CDTypes >
static constexpr WriteMode	_write_mode
	Which data-writing mode the base model should use. More...

Detailed Description

SEIRD model on a grid.

In this model, we model the spread of a disease using a SEIRD (susceptible-exposed-infected-recovered-deceased) model on a 2D grid.

Member Typedef Documentation

◆ Base

using Utopia::Models::SEIRD::SEIRD::Base = Model<SEIRD, CDTypes>

The base model type.

◆ Cell

using Utopia::Models::SEIRD::SEIRD::Cell = typename CellManager::Cell

Type of a cell.

◆ CellContainer

using Utopia::Models::SEIRD::SEIRD::CellContainer = Utopia::CellContainer<Cell>

Type of a container of shared pointers to cells.

◆ CellManager

using Utopia::Models::SEIRD::SEIRD::CellManager = Utopia::CellManager<CDCellTraits, SEIRD>

Type of the CellManager to use.

◆ DataGroup

using Utopia::Models::SEIRD::SEIRD::DataGroup = typename Base::DataGroup

Data type for a data group.

◆ DataSet

using Utopia::Models::SEIRD::SEIRD::DataSet = typename Base::DataSet

Data type for a dataset.

◆ RuleFunc

using Utopia::Models::SEIRD::SEIRD::RuleFunc = typename CellManager::RuleFunc

Rule function type.

Constructor & Destructor Documentation

◆ SEIRD()

template<class ParentModel >

Utopia::Models::SEIRD::SEIRD::SEIRD	(	const std::string &	name,
		ParentModel &	parent_model,
		const DataIO::Config &	custom_cfg = `{}`
	)

inline

Construct the SEIRD model.

Parameters

name	Name of this model instance; is used to extract the configuration from the parent model and set up a HDFGroup for this instance
parent_model	The parent model this model instance resides in
custom_cfg	A custom configuration to use instead of the one extracted from the parent model using the instance name

Member Function Documentation

◆ exposure_control()

void Utopia::Models::SEIRD::SEIRD::exposure_control ( )

inlineprotected

Apply exposure control.

Add exposures if the iteration step matches the ones specified in the configuration. There are two available modes of exposure control that are applied, if provided, in this order:

At specified times (parameter: at_times) a number of additional exposures is added (parameter: num_additional_exposures)
The parameter p_exposed is changed to a new value at given times. This can happen multiple times. Parameter: change_p_exposed

◆ identify_clusters()

void Utopia::Models::SEIRD::SEIRD::identify_clusters ( )

inlineprotected

Identify clusters.

This function identifies clusters and updates the cell specific cluster_id as well as the member variable cluster_id_cnt that counts the number of ids

◆ immunity_control()

void Utopia::Models::SEIRD::SEIRD::immunity_control ( )

inlineprotected

Apply immunity control.

Add cell immunities if the iteration step matches the ones specified in the configuration. There are two available modes of immunity control that are applied, if provided, in this order:

At specified times (parameter: at_times) a number of additional immmunities is added (parameter: num_additional_immmunities)
The parameter immune is changed to a new value at given times. This can happen multiple times. Parameter: change_immune

◆ monitor()

void Utopia::Models::SEIRD::SEIRD::monitor ( )

inline

Monitor model information.

Supplies the densities and counts arrays to the monitor.

◆ perform_step()

void Utopia::Models::SEIRD::SEIRD::perform_step ( )

inline

Iterate a single time step.

This updates all cells (synchronously) according to the _update rule. For specifics, see there.

If exposure control is activated, the cells are first modified according to the specific exposure control parameters.

◆ transmission_control()

void Utopia::Models::SEIRD::SEIRD::transmission_control ( )

inlineprotected

Apply transmission control.

Change the transmitting probability p_transmit for a subset of cells of a specified kind if the iteration step matches the ones specified in the configuration. The parameter p_transmit is changed to a new value at given times for a number of randomly chosen cells of specified kins. This can happen multiple times. Parameter: change_p_transmit

◆ update_densities()

void Utopia::Models::SEIRD::SEIRD::update_densities ( )

inlineprotected

Update the densities array.

Each density is calculated by counting the number of state occurrences and afterwards dividing by the total number of cells.

Attention: It is possible that rounding errors occur due to the division, thus, it is not guaranteed that the densities exactly add up to 1. The errors should be negligible.

◆ write_data()

void Utopia::Models::SEIRD::SEIRD::write_data ( )

inline

Write data.

Member Data Documentation

◆ _cluster_id_cnt

unsigned int Utopia::Models::SEIRD::SEIRD::_cluster_id_cnt

private

The incremental cluster tag.

◆ _cluster_members

std::vector<std::shared_ptr<CellManager::Cell> > Utopia::Models::SEIRD::SEIRD::_cluster_members

private

A temporary container for use in cluster identification.

◆ _cm

CellManager Utopia::Models::SEIRD::SEIRD::_cm

private

The cell manager.

◆ _compression

const int Utopia::Models::SEIRD::SEIRD::_compression

private

The compression level used for all datasets.

◆ _counts

Counters<std::size_t> Utopia::Models::SEIRD::SEIRD::_counts

private

Cumulative counters for state transitions and other events

◆ _densities

std::array<double, static_cast<char>Kind::COUNT)> Utopia::Models::SEIRD::SEIRD::_densities

private

Densities for all states.

Array indices are linked to Utopia::Models::SEIRD::Kind

Warning: This array is used for temporary storage; it is not automatically updated but only upon write operations.

◆ _dset_age

std::shared_ptr<DataSet> Utopia::Models::SEIRD::SEIRD::_dset_age

private

2D dataset (cell ID and time) of cell's age

◆ _dset_cluster_id

std::shared_ptr<DataSet> Utopia::Models::SEIRD::SEIRD::_dset_cluster_id

private

The dataset for storing the cluster ID associated with each cell.

◆ _dset_counts

std::shared_ptr<DataSet> Utopia::Models::SEIRD::SEIRD::_dset_counts

private

2D dataset (counts array and time) of cumulative state counters

◆ _dset_densities

std::shared_ptr<DataSet> Utopia::Models::SEIRD::SEIRD::_dset_densities

private

2D dataset (densities array and time) of density values

◆ _dset_immune

std::shared_ptr<DataSet> Utopia::Models::SEIRD::SEIRD::_dset_immune

private

2D dataset (cell ID and time) of cell's immunity

◆ _dset_kind

std::shared_ptr<DataSet> Utopia::Models::SEIRD::SEIRD::_dset_kind

private

2D dataset (cell ID and time) of cell kinds

◆ _dset_num_recoveries

std::shared_ptr<DataSet> Utopia::Models::SEIRD::SEIRD::_dset_num_recoveries

private

2D dataset (cell ID and time) of cell's number of recoveries

◆ _identify_cluster

RuleFunc Utopia::Models::SEIRD::SEIRD::_identify_cluster

protected

Identify each cluster of susceptibles.

◆ _move_away_from_infected

RuleFunc Utopia::Models::SEIRD::SEIRD::_move_away_from_infected

protected

Initial value:

= [this](const auto& cell) {
        
        auto& state = cell->state;
 
        auto neighbors = _cm.neighbors_of(cell);
 
        for (const auto& nb : neighbors) {
            if (nb->state.kind == Kind::infected) {
                
                std::shuffle(neighbors.begin(), neighbors.end(), *this->_rng);
                
                
                for (const auto& _nb : neighbors) {
                    if (_nb->state.kind == Kind::empty) {
                        
                        std::swap(state, _nb->state);
                        _counts.increment_move_away_from_infected();
                        break;
                    }
                }
                
                
                
                
                break;
            }
        }
 
        return state;
    }

Move the agent on the cell away from an infected neighboring cell.

Check whether there is an infected cell in the neighborhood. If there is an empty cell in the neighborhood, move to it. If there is no empty spot in the neighborhood do nothing.

◆ _move_randomly

RuleFunc Utopia::Models::SEIRD::SEIRD::_move_randomly

protected

Move randomly to a neighboring cell if that cell is empty.

If the cell is not empty, an inert cell, or a source: move to neighboring empty location with probability p_move_randomly. If no neighboring cell is empty, do nothing.

◆ _params

const Params Utopia::Models::SEIRD::SEIRD::_params

private

Model parameters.

◆ _prob_distr

std::uniform_real_distribution<double> Utopia::Models::SEIRD::SEIRD::_prob_distr

private

The range [0, 1] distribution to use for probability checks.

◆ _update

RuleFunc Utopia::Models::SEIRD::SEIRD::_update

protected

Define the update rule.

Update the given cell according to the following rules:

Empty cells grow susceptible cells with probability p_susceptible.
Cells in neighborhood of an infected cell do not get exposed with the probability p_random_immunity.
Exposed cells become infected cells after a certain incubation period.
Infected cells die with probability p_deceased and become an empty cell or they become recovered cells with 1-p_deceased.

◆ _write_ca_data

bool Utopia::Models::SEIRD::SEIRD::_write_ca_data

private

If false, writes only the non-spatial densities and counts data.

The documentation for this class was generated from the following file:

src/utopia/models/SEIRD/SEIRD.hh

Public Types

Public Member Functions

Protected Member Functions

Protected Attributes

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ Base

◆ Cell

◆ CellContainer

◆ CellManager

◆ DataGroup

◆ DataSet

◆ RuleFunc

Constructor & Destructor Documentation

◆ SEIRD()

Member Function Documentation

◆ exposure_control()

◆ identify_clusters()

◆ immunity_control()

◆ monitor()

◆ perform_step()

◆ transmission_control()

◆ update_densities()

◆ write_data()

Member Data Documentation

◆ _cluster_id_cnt

◆ _cluster_members

◆ _cm

◆ _compression

◆ _counts

◆ _densities

◆ _dset_age

◆ _dset_cluster_id

◆ _dset_counts

◆ _dset_densities

◆ _dset_immune

◆ _dset_kind

◆ _dset_num_recoveries

◆ _identify_cluster

◆ _move_away_from_infected

◆ _move_randomly

◆ _params

◆ _prob_distr

◆ _update

◆ _write_ca_data