Diffusion

Implementing diffusions

GAMA provides you the possibility to represent and simulate a diffusion through a grid topology.

Index

• Diffusion statement
• Diffusion with matrix
• Diffusion with parameters
• Further specifications for diffusion

Diffusion statement

The statement to use for the diffusion is diffusion. It has to be used in a grid species. The diffusion uses the following facets:

• var : the name of the variable that will be diffused through the grid. This variable has to be declared as an attribute of the grid.
• on : the list of agents (usually the entire grid) where the diffusion will occur.
• cycle_length (int): the number of diffusion operation applied in one simulation step.
• mat_diffu (matrix): the diffusion matrix.
• mask (matrix): a matrix masking the diffusion (matrix created from a image for example). The cells corresponding to the values smaller than "-1" in the mask matrix will not diffuse, and the other will diffuse.
• method takes values in: {convolution, dot_product}: the diffusion method
• proportion (float): a diffusion rate
• radius (int): a diffusion radius
• variation (float): an absolute decrease of intensity that occurs between each place. It should be a positive number.

To write a diffusion, you first have to declare a grid, and declare a special attribute for the diffusion. You will then have to write the diffusion statement in an other scope (such as the global scope for instance), which will permit the values to be diffused at each step. There, you will specify which variable you want to diffuse (through the var facet), on which species or list of agents you want the diffusion (through the on facet), and how you want this value to be diffused (through all the other facets).

Here is the template of code we will use for the next following part of this page:

global {
	int size <- 50;
  	cells selected_cells;

	// Initialize the emiter cell as the cell at the center of the word
	init {
		selected_cells <- location as cells;
	}
	// Affecting "1" to each step
	reflex new_Value {
		ask(selected_cells){
			phero <- 1.0;
		}	
	}

	reflex diff {
		// Declare a diffusion on the grid "cells" and on "quick_cells". The diffusion declared on "quick_cells" will make 10 computations at each step to accelerate the process. 
		// The value of the diffusion will be store in the new variable "phero" of the cell.
		diffusion var: phero on: cells /*HERE WRITE DOWN THE DIFFUSION PROPERTIES*/;			
	}
}


grid cells height: size width: size {
	// "phero" is the variable storing the value of the diffusion
	float phero  <- 0.0;
	// The color of the cell is linked to the value of "phero".
	rgb color <- hsb(phero,1.0,1.0) update: hsb(phero,1.0,1.0);
}


experiment diffusion type: gui {
	output {
		display a type: opengl {
			// Display the grid with elevation
			grid cells elevation: phero * 10 triangulation: true;
		}
	}
}

This model will simulate a diffusion through a grid at each step, affecting 1 to the center cell diffusing variable value. The diffusion will be seen during the simulation through a color code, and through the elevation of the cell.

Diffusion with matrix

A first way of specifying the behavior of your diffusion is using diffusion matrix. A diffusion matrix is a 2 dimension matrix [n][m] with float values, where both n and m have to be pair values. The most often, diffusion matrix are square matrix, but you can also declare rectangular matrix.

Example of matrix:

matrix<float> math_diff <- matrix([
		[1/9,1/9,1/9],
		[1/9,1/9,1/9],
		[1/9,1/9,1/9]]);

Diffusion with parameters

Further specifications for diffusion