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1. Creation of a first basic disease spreading model

This first step illustrates how to create simple agents and make them move in their environment.

images/luneray1.tiff

Formulation

Model Definition

Project and model

The first step of this tutorial consists in launching GAMA and choosing a workspace, then to define a new project or to import the existing one. For people that do not want to re-write all the models but just to follow the model construction, they can just download the model project here and the follow this procedure to import it into GAMA. For the other, the project and model creation procedures are detailed here.

Note that the concepts of workspace and projects are explained here.

model structure

A GAMA model is composed of three type of sections:

More details about the different sections of a GAMA model can be found here.

species

A species represents a «prototype» of agents: it defines their common properties.

Three different elements can be defined in a species:

In our model, we define a people species:

species people {
		 
}

In addition, we want add a new capability to our agent: the possibility to move randomly. for that, we add a specific skill to our people agents. A skill is a built-in module that provide the modeler a self-contain and relevant set of actions and variables. The moving provides the agents with several attributes and actions related to movement.

   species people skills: [moving]{
       ...
   }

Internal state

An attribute is defined as follows: type of the attribute and name. Numerous types of attributes are available: int (integer), float (floating point number), string, bool (boolean, true or false), point (coordinates), list, pair, map, file, matrix, espèce d’agents, rgb (color), graph, path…

In addition to the attributes the modeler explicitly defines, species “inherits” other attributes called “built-in” variables:

In our model, we define 2 new attribute to our people agents:

species people skills:[moving]{		
	float speed <- (2 + rnd(3)) #km/#h;
	bool is_infected <- false;
}

Note we use the rnd operator to define a random value between 2 and 5 for the speed. In addition, we precise a unit for the speed value by using the # symbol. For more details about units, see here.

Behavior

GAMA proposes several ways to define the behavior of a species: dynamic variables (update facet), reflexes….

A reflex is a block of statements (that can be defined in global or any species) that will be automatically executed at each simulation step if its condition is true, it is defined as follows:

   reflex reflex_name when: condition {...}

The when facet is optional: when it is omitted, the reflex is activated at each time step. Note that if several reflexes are defined for a species, the reflexes will be activated following their definition order.

We define a first reflex called move that is activated at each simulation step (no condition) and that makes the people move randomly using the wander action from the moving skill.

species people skills:[moving]{		
	//variable definition
	reflex move{
		do wander;
	}
}

We define a second reflex called infect that is activated only when the agent is infected (is_infected = true) and that ask all the people at a distance of 10m to test a probability to be infected.

species people skills:[moving]{		
	//variable definition and move reflex
	
	reflex infect when: is_infected{
		ask people at_distance 10 #m {
			if flip(0.05) {
				is_infected <- true;
			}
		}
	}
}

The ask allows an agent to ask another agents to do something (i.e. to execute a sequence of statements). The at_distance operator allows to get the list of agents (here of people agents) that are located at a distance lower or equal to the given distance (here 10m). The flip operator allows to test a probability.

Display

An agent aspects have to be defined. An aspect is a way to display the agents of a species : aspect aspect_name {…} In the block of an aspect, it is possible to draw :

In our model, we define an aspect for the people agent called circle that draw the agents as a circle of 10m radius with a color that depends on their is_infected attribute. If the people agent is infected, it will be draw in red, in green otherwise.

species people {
	...//variable and reflex definition

	aspect circle {
			draw circle(10) color:is_infected ? #red : #green;
		}
	} 
}

The ? structure allows to return a different value (here red or green) according to a condition (here is_infected = true).

global section

The global section represents a specific agent, called world. Defining this agent follows the same principle as any agent and is, thus, defined after a species. The world agent represents everything that is global to the model : dynamics, variables… It allows to initialize simulations (init block): the world is always created and initialized first when a simulation is launched (before any other agents). The geometry (shape) of the world agent is by default a square with 100m for side size, but can be redefined if necessary. The step attribute of the world agent allows to specify the duration of one simulation step (by default, 1 step = 1 seconde).

global variable

In the current model, we define 4 global attributes:

Model initialization

The init section of the global block allows to initialize the define what will happen at the initialization of a simulation, for instance to create agents. We use the statement create to create agents of a specific species: create species_name + :

For our model, we define the init block in order to create nb_people people agents and ask nb_infected_init of them to be infected:

global {
	// world variable definition
	init{
		create people number:nb_people;
		ask nb_infected_init among people {
			is_infected <- true;
		}
	}
}

experiment

An experiment block defines how a model can be simulated (executed). Several experiments can be defined for a given model. They are defined using : experiment exp_name type: gui/batch {[input] [output]}

In our model, we define a gui experiment called main_experiment :

experiment main_experiment type: gui {
}

input

Experiments can define (input) parameters. A parameter definition allows to make the value of a global variable definable by the user through the graphic interface.

A parameter is defined as follows: parameter title var: global_var category: cat;

Note that the init, min and max values can be defined in the global variable definition.

In our model, we define one parameter:

experiment main_experiment type:gui{
	parameter "Nb people infected at init" var: nb_infected_init min: 1 max: 2147;
	
	output {
	}
}

output

Output blocks are defined in an experiment and define how to visualize a simulation (with one or more display blocks that define separate windows). Each display can be refreshed independently by defining the facet refresh_every: nb (int) (the display will be refreshed every nb steps of the simulation).

Each display can include different layers (like in a GIS) :

Note that it is possible to define a opengl display (for 3D display or just to optimize the display) by using the facet type: opengl.

In our model, we define an OpenGL display to draw the people agents.

output {
	display map type: opengl{
		species people aspect:circle;	
	}
}

Complete Model

model SI_city1

global{ 
	int nb_people <- 2147;
	int nb_infected_init <- 5;
	float step <- 1 #mn;
	geometry shape<-square(1500 #m);
	
	init{
		create people number:nb_people;
		ask nb_infected_init among people {
			is_infected <- true;
		}
	}
	
}

species people skills:[moving]{		
	float speed <- (2 + rnd(3)) #km/#h;
	bool is_infected <- false;
	reflex move{
		do wander;
	}
	reflex infect when: is_infected{
		ask people at_distance 10 #m {
			if flip(0.05) {
				is_infected <- true;
			}
		}
	}
	aspect circle{
		draw circle(10) color:is_infected ? #red : #green;
	}
}

experiment main_experiment type:gui{
	parameter "Nb people infected at init" var: nb_infected_init min: 1 max: 2147;
	output {
		display map type: opengl{
			species people aspect:circle;			
		}
	}
}

Next step: Definition of monitors and chart outputs