PredatorPreyPlant Model on grid cells. More...

#include <PredatorPreyPlant.hh>

Inheritance diagram for Utopia::Models::PredatorPreyPlant::PredatorPreyPlant:

Collaboration diagram for Utopia::Models::PredatorPreyPlant::PredatorPreyPlant:

[legend]

Public Types
using	Base = Model< PredatorPreyPlant, ModelTypes >
	The base model. More...

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

using	CellManager = Utopia::CellManager< CellTraits, PredatorPreyPlant >
	The type of the cell manager. More...

using	Cell = typename CellManager::Cell
	The type of a cell. More...

using	Rule = typename CellManager::RuleFunc
	Type of the update rules. More...

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

using	DataManager = DataIO::Default::DefaultDataManager< PredatorPreyPlant >
	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 >
	PredatorPreyPlant (const std::string &name, ParentModel &parent_model, const DataIO::Config &custom_cfg={})
	Construct the PredatorPreyPlant model. More...

void	perform_step ()
	Perform an iteration step. More...

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

void	write_data ()
	Write data. More...

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

Private Member Functions
std::shared_ptr< Cell >	get_random_neighbor (const CellContainer< Cell > &nbs) const
	Returns a random neighbor. More...

void	move_predator_to_nb_cell (const std::shared_ptr< Cell > &cell, const std::shared_ptr< Cell > &nb_cell)
	Move a predator to a neighboring cell. More...

void	move_prey_to_nb_cell (const std::shared_ptr< Cell > &cell, const std::shared_ptr< Cell > &nb_cell)
	Move a prey to a neighboring cell. More...

auto	move_prey (std::shared_ptr< Cell > cell)
	Move the prey looking for resources. More...

auto	move_predator (std::shared_ptr< Cell > cell)
	Move the predator looking for preys. More...

void	move_entities (std::shared_ptr< Cell > cell)
	Define the movement rule of an individual. More...

void	setup_cell_states_from_file (const Config &cs_cfg)
	Sets predator, prey, and plant positions from loaded HDF5 data. More...

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

SpeciesParams	_params
	All species-specific parameters. More...

std::size_t	_num_moves
	How many cells the movement rule should be applied to each time step. More...

CellContainer< Cell >	_prey_cell
	A container to temporarily accumulate the prey neighbour cells. More...

CellContainer< Cell >	_empty_cell
	A container to temporarily accumulate empty neighbour cells. More...

CellContainer< Cell >	_repro_cell
	A container to temporarily accumulate neighbour cells for reproduction. More...

CellContainer< Cell >	_resource_cell
	A container to temporarily accumulate neighbour cells with mature plants. More...

std::uniform_real_distribution< double >	_prob_distr
	Uniform real distribution [0, 1) for evaluating probabilities. More...

std::uniform_int_distribution	_cm_dist
	Distribution for randomly selecting a cell in your cellmanager. More...

const std::shared_ptr< DataSet >	_dset_prey
	Dataset of Prey locations on the grid. More...

const std::shared_ptr< DataSet >	_dset_predator
	Dataset of Predator locations on the grid. More...

const std::shared_ptr< DataSet >	_dset_resource_prey
	Dataset of Prey resources on the grid. More...

const std::shared_ptr< DataSet >	_dset_resource_predator
	Dataset of Predator resources on the grid. More...

const std::shared_ptr< DataSet >	_dset_plant
	Dataset of Plant resources. More...

Rule	_cost_of_living
	Cost of Living. More...

Rule	_flee_prey
	If a prey is on the cell, determine whether it may flee and where to. More...

Rule	_eat
	Define the eating rule. More...

Rule	_reproduce
	Define the reproduction rule. More...

Additional Inherited Members
Protected Member Functions inherited from Utopia::Model< PredatorPreyPlant, ModelTypes >
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...

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

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

Protected Attributes inherited from Utopia::Model< PredatorPreyPlant, ModelTypes >
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...

Static Protected Attributes inherited from Utopia::Model< PredatorPreyPlant, ModelTypes >
static constexpr WriteMode	_write_mode
	Which data-writing mode the base model should use. More...

Detailed Description

PredatorPreyPlant Model on grid cells.

Predators and prey correspond to the Population state of each cell, either empty, prey, predator or both. Cells are updated based on the following interactions: 1) resource levels are reduced by a cost_of_living for both species and individuals are removed if resource <= 0 2) predators move to neighbouring cells if there is a no prey on their own cell. Prey flees with a certain probability, if there is a predator on the same cell. Prey looks for resources if there are none on its cell. 3) predators eat prey if on the same cell, else if there is only a prey it takes up resources, when this are present 4) both predators and prey reproduce if resources are sufficient and if there is a cell in their neighbourhood not already occupied by the same species. The plant grows if it is set in mode other than 0.

Member Typedef Documentation

◆ Base

using Utopia::Models::PredatorPreyPlant::PredatorPreyPlant::Base = Model<PredatorPreyPlant, ModelTypes>

The base model.

◆ Cell

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

The type of a cell.

◆ CellManager

using Utopia::Models::PredatorPreyPlant::PredatorPreyPlant::CellManager = Utopia::CellManager<CellTraits, PredatorPreyPlant>

The type of the cell manager.

◆ DataSet

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

Data type for a dataset.

◆ Rule

using Utopia::Models::PredatorPreyPlant::PredatorPreyPlant::Rule = typename CellManager::RuleFunc

Type of the update rules.

Constructor & Destructor Documentation

◆ PredatorPreyPlant()

template<class ParentModel >

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

inline

Construct the PredatorPreyPlant 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

◆ get_random_neighbor()

std::shared_ptr<Cell> Utopia::Models::PredatorPreyPlant::PredatorPreyPlant::get_random_neighbor ( const CellContainer< Cell > & nbs ) const

inlineprivate

Returns a random neighbor.

This method chooses uniform randomly a cell from the neighborhood of the given cell.

◆ monitor()

void Utopia::Models::PredatorPreyPlant::PredatorPreyPlant::monitor ( )

inline

Monitor model information.

◆ move_entities()

void Utopia::Models::PredatorPreyPlant::PredatorPreyPlant::move_entities ( std::shared_ptr< Cell > cell )

inlineprivate

Define the movement rule of an individual.

◆ move_predator()

auto Utopia::Models::PredatorPreyPlant::PredatorPreyPlant::move_predator ( std::shared_ptr< Cell > cell )

inlineprivate

Move the predator looking for preys.

Predators looks for prey in the neighborhood. If there are multiple cells with prey on them randomly choose one cell to move to. If there is no cell with prey just do a movement towards a randomly selected neighboring cell. A predator can never move to a cell with another predator on it.

◆ move_predator_to_nb_cell()

void Utopia::Models::PredatorPreyPlant::PredatorPreyPlant::move_predator_to_nb_cell	(	const std::shared_ptr< Cell > &	cell,
		const std::shared_ptr< Cell > &	nb_cell
	)

inlineprivate

Move a predator to a neighboring cell.

This function resets the states predator state and updates the neighboring predator state.

◆ move_prey()

auto Utopia::Models::PredatorPreyPlant::PredatorPreyPlant::move_prey ( std::shared_ptr< Cell > cell )

inlineprivate

Move the prey looking for resources.

If plants are enabled, prey might need to look for available resources in the form of plants in the neighboring cells. If there is a plant on a neighboring cell and no predator, the prey will move there. If there are multiple cells with plants on them, one is selected at random. If there are no free cells just take your chance and randomly select a cell, if there is a predator on it nevertheless move to it.

◆ move_prey_to_nb_cell()

void Utopia::Models::PredatorPreyPlant::PredatorPreyPlant::move_prey_to_nb_cell	(	const std::shared_ptr< Cell > &	cell,
		const std::shared_ptr< Cell > &	nb_cell
	)

inlineprivate

Move a prey to a neighboring cell.

This function resets the states prey state and updates the neighboring prey state.

◆ perform_step()

void Utopia::Models::PredatorPreyPlant::PredatorPreyPlant::perform_step ( )

inline

Perform an iteration step.

An iteration step consists of:

Subtracting costs of living
Let predator and prey move
Lunch time: Prey eats grass and predator eats prey if on the same cell
Reproduction: Create offspring and grow plant

◆ setup_cell_states_from_file()

void Utopia::Models::PredatorPreyPlant::PredatorPreyPlant::setup_cell_states_from_file ( const Config & cs_cfg )

inlineprivate

Sets predator, prey, and plant positions from loaded HDF5 data.

◆ write_data()

void Utopia::Models::PredatorPreyPlant::PredatorPreyPlant::write_data ( )

inline

Write data.

When invoked, stores cell positions and resources of both prey and predators.

Note: Positions are cast to char and therefore stored as such. This is because C has no native boolean type, and the HDF5 library thus cannot store it directly. With 8 bit width, char is the smallest data type available; short int is already 16 bit.

Member Data Documentation

◆ _cm

CellManager Utopia::Models::PredatorPreyPlant::PredatorPreyPlant::_cm

private

The cell manager.

◆ _cm_dist

std::uniform_int_distribution Utopia::Models::PredatorPreyPlant::PredatorPreyPlant::_cm_dist

private

Distribution for randomly selecting a cell in your cellmanager.

◆ _cost_of_living

Rule Utopia::Models::PredatorPreyPlant::PredatorPreyPlant::_cost_of_living

private

Initial value:

= [this](const auto& cell) {
        
        auto& state = cell->state;
 
        
        
        
        state.predator.resources =
            std::clamp(  state.predator.resources
                       - _params.predator.cost_of_living,
                       0., _params.predator.resource_max);
        state.prey.resources =
            std::clamp(  state.prey.resources 
                       - _params.prey.cost_of_living, 
                       0., _params.prey.resource_max);
 
        
        if (state.predator.on_cell and state.predator.resources <= 0.)
            state.predator.on_cell = false;
 
        
        if (state.prey.on_cell and state.prey.resources <= 0.) 
            state.prey.on_cell = false;
 
        return state;
    }

Cost of Living.

subtract the cost of living from the resources of an individual and map the values below zero back to zero, then remove all individuals that do not have sufficient resources. This function applies only to predator and prey, but not to plants.

◆ _dset_plant

const std::shared_ptr<DataSet> Utopia::Models::PredatorPreyPlant::PredatorPreyPlant::_dset_plant

private

Dataset of Plant resources.

◆ _dset_predator

const std::shared_ptr<DataSet> Utopia::Models::PredatorPreyPlant::PredatorPreyPlant::_dset_predator

private

Dataset of Predator locations on the grid.

◆ _dset_prey

const std::shared_ptr<DataSet> Utopia::Models::PredatorPreyPlant::PredatorPreyPlant::_dset_prey

private

Dataset of Prey locations on the grid.

◆ _dset_resource_predator

const std::shared_ptr<DataSet> Utopia::Models::PredatorPreyPlant::PredatorPreyPlant::_dset_resource_predator

private

Dataset of Predator resources on the grid.

◆ _dset_resource_prey

const std::shared_ptr<DataSet> Utopia::Models::PredatorPreyPlant::PredatorPreyPlant::_dset_resource_prey

private

Dataset of Prey resources on the grid.

◆ _eat

Rule Utopia::Models::PredatorPreyPlant::PredatorPreyPlant::_eat

private

Define the eating rule.

Update procedure is as follows:

prey is consumed by a predator if they are on the same cell. The predator increases its resources.
prey eats plants which increases its resources; if the plant growth model is not none the plant is removed from the cell.

◆ _empty_cell

CellContainer<Cell> Utopia::Models::PredatorPreyPlant::PredatorPreyPlant::_empty_cell

private

A container to temporarily accumulate empty neighbour cells.

◆ _flee_prey

Rule Utopia::Models::PredatorPreyPlant::PredatorPreyPlant::_flee_prey

private

Initial value:

= [this](const auto& cell) {
        auto& state = cell->state;
        
        if (state.prey.on_cell and state.predator.on_cell and 
            (_prob_distr(*this->_rng) < _params.prey.p_flee)) {
            
            _empty_cell.clear();
            for (const auto& nb : this->_cm.neighbors_of(cell)) {
                if (    not nb->state.prey.on_cell
                    and not nb->state.predator.on_cell)
                    _empty_cell.push_back(nb);
            }
 
            
            if (_empty_cell.size() > 0) {
                
                std::uniform_int_distribution<> 
                    dist(0, _empty_cell.size() - 1);
                auto nb_cell = _empty_cell[dist(*this->_rng)];
                move_prey_to_nb_cell(cell, nb_cell);
            }
        }
        return state;
    }

If a prey is on the cell, determine whether it may flee and where to.

A prey should only flee if there is a predator on the cell, too. First empty neighboring cells are collected to which a prey can potentially flee. Choose a random cell out of the selection to flee to. If there is no empty cell nothing happens.

◆ _num_moves

std::size_t Utopia::Models::PredatorPreyPlant::PredatorPreyPlant::_num_moves

private

How many cells the movement rule should be applied to each time step.

◆ _params

SpeciesParams Utopia::Models::PredatorPreyPlant::PredatorPreyPlant::_params

private

All species-specific parameters.

◆ _prey_cell

CellContainer<Cell> Utopia::Models::PredatorPreyPlant::PredatorPreyPlant::_prey_cell

private

A container to temporarily accumulate the prey neighbour cells.

◆ _prob_distr

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

private

Uniform real distribution [0, 1) for evaluating probabilities.

◆ _repro_cell

CellContainer<Cell> Utopia::Models::PredatorPreyPlant::PredatorPreyPlant::_repro_cell

private

A container to temporarily accumulate neighbour cells for reproduction.

◆ _reproduce

Rule Utopia::Models::PredatorPreyPlant::PredatorPreyPlant::_reproduce

private

Define the reproduction rule.

If a neighboring cell if not already occupied by an individual of the same species, individuals reproduce with reproduction probabilities of predator and prey respectively. Plants reproduce according to their GrowthMode.

◆ _resource_cell

CellContainer<Cell> Utopia::Models::PredatorPreyPlant::PredatorPreyPlant::_resource_cell

private

A container to temporarily accumulate neighbour cells with mature plants.

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

src/utopia/models/PredatorPreyPlant/PredatorPreyPlant.hh

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ Base

◆ Cell

◆ CellManager

◆ DataSet

◆ Rule

Constructor & Destructor Documentation

◆ PredatorPreyPlant()

Member Function Documentation

◆ get_random_neighbor()

◆ monitor()

◆ move_entities()

◆ move_predator()

◆ move_predator_to_nb_cell()

◆ move_prey()

◆ move_prey_to_nb_cell()

◆ perform_step()

◆ setup_cell_states_from_file()

◆ write_data()

Member Data Documentation

◆ _cm

◆ _cm_dist

◆ _cost_of_living

◆ _dset_plant

◆ _dset_predator

◆ _dset_prey

◆ _dset_resource_predator

◆ _dset_resource_prey

◆ _eat

◆ _empty_cell

◆ _flee_prey

◆ _num_moves

◆ _params

◆ _prey_cell

◆ _prob_distr

◆ _repro_cell

◆ _reproduce

◆ _resource_cell