updated ODE library models

gama-platform · May 8, 2022 · 0a9c772 · 0a9c772
1 parent 2954818
commit 0a9c772
Show file tree

Hide file tree

Showing 8 changed files with 103 additions and 108 deletions.
diff --git a/...dinary Differential Equations/models/Examples/Generalized Lotka-Volterra (Toy model).gaml b/...dinary Differential Equations/models/Examples/Generalized Lotka-Volterra (Toy model).gaml
@@ -241,11 +241,11 @@ experiment simulation type: gui autorun: true  {
 
 	output { 
 		layout value: horizontal([0::50,vertical([1::50,2::50])::50]) tabs:true;
-		display action_button name:"Interaction matrix" {
+		display action_button name:"Interaction matrix" toolbar: false{
 			species button aspect:modern ;
 			event mouse_down action:activate_act;    
 		}
-		display LV name: "Time series" refresh: every(1#cycle) type: java2D {
+		display LV name: "Time series" refresh: every(1#cycle) type: java2D toolbar: false{
 			chart "Population size" type: series background: rgb('white') x_range: 200 x_tick_line_visible: false{
 				loop i from: 0 to: max_species-1{
 					data "Species "+i value: first(solver_and_scheduler).pop[i] color: (species_list[i] != nil)?color_list[i]:rgb(0,0,0,0) marker: false;

diff --git a/...extensions.maths/models/Ordinary Differential Equations/models/Examples/SIR (Simple).gaml b/...extensions.maths/models/Ordinary Differential Equations/models/Examples/SIR (Simple).gaml
@@ -43,16 +43,16 @@ species agent_with_SIR_dynamic {
 experiment Simulation type: gui {
 	float minimum_cycle_duration <- 0.1#s;
 	output { 
-		layout #vertical;
-		display display_charts {
-			chart "Time series" type: series background: #white {
+		layout #vertical tabs: false;
+		display display_charts toolbar: false {
+			chart "Time series" type: series background: rgb(47,47,47) color: #white {
 				data 'S' value: first(agent_with_SIR_dynamic).S color: rgb(46,204,113) ;				
 				data 'I' value: first(agent_with_SIR_dynamic).I color: rgb(231,76,60) ;
 				data 'R' value: first(agent_with_SIR_dynamic).R color: rgb(52,152,219) ;
 			}
 		}
-		display display_phase_portrait {
-			chart "Phase portrait" type: xy background: #white x_label:"S" y_label:"Y" x_range: {0,1600} y_range: {0,700}{
+		display display_phase_portrait toolbar: false {
+			chart "Phase portrait" type: xy background: rgb(47,47,47) color: #white x_label:"S" y_label:"Y" x_range: {0,1600} y_range: {0,700}{
 				data 'I vs S' value: [first(agent_with_SIR_dynamic).S,first(agent_with_SIR_dynamic).I] color: rgb(243,156,18)  ;				
 			}
 		}

diff --git a/...fferential Equations/models/For Advanced Users/Displays (Continuous, Phase Portrait).gaml b/...fferential Equations/models/For Advanced Users/Displays (Continuous, Phase Portrait).gaml
@@ -43,28 +43,28 @@ species LV_model {
 experiment Displays type: gui {
 	float minimum_cycle_duration <- 0.1#s;
 	output {
-		layout #split;
-		display D1 synchronized:false {
-			chart 'Time series' type: series background: #white y_label:"pop" x_tick_line_visible: false{
+		layout #split tabs: false;
+		display D1 synchronized:false toolbar: false{
+			chart 'Time series' type: series background: rgb(47,47,47) color: #white y_label:"pop" x_tick_line_visible: false{
 				data "x" value: first(LV_model).x color: rgb(52,152,219);
 				data "y" value: first(LV_model).y color: rgb(41,128,185);
 			}
 		}
-		display D2 synchronized:false {
-			chart 'Time series - continuous display' type: series background: #white y_label:"pop" x_tick_line_visible: false{
+		display D2 synchronized:false toolbar: false{
+			chart 'Time series - continuous display' type: series background:  rgb(47,47,47) color: #white y_label:"pop" x_tick_line_visible: false{
 		//	chart 'Time series - continuous display' type: series x_serie: first(LV_model).t[] background: #white y_label:"pop"{
 				data "x" value: first(LV_model).x[] color: rgb(52,152,219) marker: false;
 				data "y" value: first(LV_model).y[] color: rgb(41,128,185) marker: false;
 			}
 		}
-		display D3 name: "Phase Portrait " synchronized:false {
-			chart 'Phase Portrait' type: xy background: #white x_label: "x" y_label:"y"{
+		display D3 name: "Phase Portrait " synchronized:false toolbar: false{
+			chart 'Phase Portrait' type: xy background:  rgb(47,47,47) color: #white x_label: "x" y_label:"y"{
 				// Continuous display requires to pass a list of two values x and y
 				data "y(x(t))" value: [first(LV_model).x,first(LV_model).y] color: rgb(243,156,18);
 			}
 		}
-		display D4 name: "Phase Portrait - continuous display" synchronized:false {
-			chart 'Phase Portrait - continuous display' type: xy background: #white x_label: "x" y_label:"y"{
+		display D4 name: "Phase Portrait - continuous display" synchronized:false toolbar: false{
+			chart 'Phase Portrait - continuous display' type: xy background:  rgb(47,47,47) color: #white x_label: "x" y_label:"y"{
 				// Continuous display requires to pass a list of two values x and y
 				data "y(x(t))" value: rows_list(matrix(first(LV_model).x[],first(LV_model).y[])) color: rgb(243,156,18) marker: false;
 			}

diff --git a/...erential Equations/models/For Advanced Users/SIR (Split in Agents, Multiple Strains).gaml b/...erential Equations/models/For Advanced Users/SIR (Split in Agents, Multiple Strains).gaml
@@ -112,9 +112,9 @@ experiment Simulation type: gui {
 	parameter 'Delta (I->R)' type: float var: _delta <- 0.2 category: "Parameters";	
 
 	output {
-		layout #split;
-		display chart_3system_eq {
-			chart 'Split system' type: series background: #white x_tick_line_visible: false{
+		layout #split tabs: false;
+		display chart_3system_eq name: "Split system" toolbar: false{
+			chart 'Split system' type: series background: rgb(47,47,47) color: #white x_tick_line_visible: false{
 				data 'susceptible' value: first(S_agt).Ssize color: rgb(46,204,113) marker_shape: marker_circle;
 				data 'infected 1' value: first(I_agt).beta * first(I_agt).Isize color: rgb(231,76,60)+120 marker_shape: marker_diamond;
 				data 'infected 2' value: last(I_agt).beta * last(I_agt).Isize color: rgb(231,76,60)+100 marker_shape: marker_diamond;
@@ -124,8 +124,8 @@ experiment Simulation type: gui {
 
 		}
 
-		display chart_1system_eq  {
-			chart 'unified system' type: series background: #white x_tick_line_visible: false{
+		display chart_1system_eq name: "Unified system" toolbar: false  {
+			chart 'Unified system' type: series background: rgb(47,47,47) color: #white x_tick_line_visible: false{
 				data 'susceptible (maths)' value: first(my_SIR_maths).Sm color: rgb(46,204,113) marker_shape: marker_circle;
 				data 'infected (maths)' value: first(my_SIR_maths).Im color: rgb(231,76,60) marker_shape: marker_circle;
 				data 'recovered (maths)' value: first(my_SIR_maths).Rm color: rgb(52,152,219) marker_shape: marker_circle;

diff --git a/...erential Equations/models/Technical Details/Influence of the integration method (LV).gaml b/...erential Equations/models/Technical Details/Influence of the integration method (LV).gaml
@@ -2,9 +2,17 @@
 * Name: Influence of the integration step
 * Author: Tri, Nghi, Benoit
 * Description: The aim is to show the influence of the integration method on the result precision.
-* 				Note: an integration step of 0.1 is considered as not accurate enough. It is used here to highlight clearly the impact of the integration method.
+* 				Note: an integration step of 0.1 is considered as not accurate enough. It is used here 
+* 				to highlight the impact of the integration method.
+* 
+* 				About the expected dynamics: Lotka-Volterra model solutions are known to be periodic. With
+* 				a step of 0.1, the numerical solution provided by the Runge-Kutta 4 method for Lotka-Volterra 
+* 				model looks periodic (see the phase portrait), while for the Euler the solution is unbounded (which
+* 				is wrong). See as time increases how errors accumulate, leading to negative and unbounded values.
+* 
 * Tags: equation, math
 ***/
+
 model LVInfluenceoftheIntegrationMethod
 
 global {
@@ -24,7 +32,7 @@ species LVRK4 {
 	float beta <- 0.3;
 	float gamma <- 0.2;
 	float delta <- 0.85;
-
+	
 	equation eqLV {
 		diff(x, t) = x * (alpha - beta * y);
 		diff(y, t) = -y * (delta - gamma * x);
@@ -33,7 +41,6 @@ species LVRK4 {
 	reflex solving {
 		solve eqLV method: #rk4 step_size: h;
 	}
-
 }
 
 
@@ -56,6 +63,8 @@ species LVEuler {
 		solve eqLV method: #Euler step_size: h;    
 	}
 
+
+
 	reflex end_simulation when: cycle > 126{
 		ask world{do pause;}
 	}
@@ -65,10 +74,22 @@ species LVEuler {
 experiment examples type: gui {
 	float minimum_cycle_duration <- 0.1#s;
 	output {
-		display LV synchronized:false {
-			chart 'Comparison Euler - RK4 (RK4 is more accurate)' type: xy x_serie:first(LVRK4).t[] background: #white {
-				data "RK4" value: [first(LVRK4).x,first(LVRK4).y] color: #blue marker: false;
-				data "Euler" value: [first(LVEuler).x,first(LVEuler).y] color: #red marker: false;
+		layout #split tabs: false;
+		display LV_series name: "Time series" synchronized:false toolbar: false {
+			chart 'Comparison Euler - RK4 (RK4 is more accurate)' type: series 
+			x_serie: first(LVRK4).t[] y_label: "pop" background: rgb(47,47,47) color: #white x_tick_line_visible: false {
+				data "x (rk4)" value: first(LVRK4).x[] color: rgb(52,152,219) marker: false thickness: 2;
+				data "y (rk4)" value: first(LVRK4).y[] color: rgb(41,128,185) marker: false thickness: 2;
+				data "x (Euler)" value: first(LVEuler).x[] color: rgb(243,156,18) marker: false thickness: 2;
+				data "y (Euler)" value: first(LVEuler).y[] color: rgb(230,126,34) marker: false thickness: 2;
+			}
+
+		}
+		display LV_phase_portrait name: "Phase portrait" synchronized:false toolbar: false{
+			chart 'Comparison Euler - RK4 (RK4 is more accurate)' type: xy 
+			background: rgb(47,47,47) color: #white x_label: "x" y_label: "y" x_tick_line_visible: false y_tick_line_visible: false{
+				data "y(x(t)) rk4" value: rows_list(matrix(first(LVRK4).x[],first(LVRK4).y[])) color: rgb(52,152,219) marker: false thickness: 2;
+				data "y(x(t)) Euler" value: rows_list(matrix(first(LVEuler).x[],first(LVEuler).y[])) color: rgb(243,156,18) marker: false thickness: 2;
 			}
 
 		}

diff --git a/...fferential Equations/models/Technical Details/Influence of the integration step (LV).gaml b/...fferential Equations/models/Technical Details/Influence of the integration step (LV).gaml
@@ -1,8 +1,10 @@
 /***
 * Name: Influence of the integration step
 * Author: Tri, Nghi, Benoit
-* Description: The aim is to show the influence of the integration step on the result precision.
-* 			   Notice that a step of value 1.0 is not realistic, but this value is necessary with the RK4 method to show the influence of the integration step.
+* Description:  The aim is to show the influence of the integration step on the result precision.
+* 				The solutions of the Lotka-Volterra are periodic. When the integration step is not
+* 				small enough, this periodicity is lost, as illustrated with h=1.
+* 
 * Tags: equation, math
 ***/
 
@@ -36,14 +38,36 @@ species userLV {
 }
 
 experiment examples type: gui {
-	output {		
-		display LV  {
-			chart 'examplesUserLV' type: series background: #lightgray {
-				data "x" value: first(userLV).x color: #yellow;
-				data "y" value: first(userLV).y color: #blue;
-				data "x1" value: last(userLV).x color: #red;
-				data "y1" value: last(userLV).y color: #green;				
+	float minimum_cycle_duration <- 0.05#s;
+	output {	
+		layout horizontal([vertical([0::100,1::100])::100,2::100]) tabs: false;	
+		display "h=0.01"  toolbar: false{
+			chart 'Lotka-Voltera dynamics (time series)' type: series 
+				background: rgb(47,47,47) color: #white
+				y_label: "pop" x_tick_line_visible: false{
+				data "x (h=0.01)" value: first(userLV).x[] color: rgb(52,152,219) marker: false thickness: 2;
+				data "y (h=0.01)" value: first(userLV).y[] color: rgb(41,128,185) marker: false thickness: 2;
+//				data "x (h=1)" value: last(userLV).x color: rgb(243,156,18) marker: false thickness: 2;
+//				data "y (h=1)" value: last(userLV).y color: rgb(230,126,34) marker: false thickness: 2;				
 			}			
+		}
+		display "h=1"   toolbar: false{
+			chart 'Lotka-Voltera dynamics (time series)' type: series 
+			background: rgb(47,47,47) color: #white
+			y_label: "pop" x_tick_line_visible: false{
+//				data "x (h=0.01)" value: first(userLV).x color: rgb(52,152,219) marker: false thickness: 2;
+//				data "y (h=0.01)" value: first(userLV).y color: rgb(41,128,185) marker: false thickness: 2;
+				data "x (h=1)" value: last(userLV).x[] color: rgb(243,156,18) marker: false thickness: 2;
+				data "y (h=1)" value: last(userLV).y[] color: rgb(230,126,34) marker: false thickness: 2;				
+			}			
+		}		
+		display "Phase Portrait"  toolbar: false {
+		chart 'Lotka-Voltera dynamics (phase portrait)' type: xy 
+			background: rgb(47,47,47) color: #white y_label: "y" x_label: "x"
+			x_range: {0,8} y_range: {0,5.3}{
+				data "h=0.01" value: [first(userLV).x,first(userLV).y] color: rgb(52,152,219) marker: false;			
+				data "h=1" value: [last(userLV).x,last(userLV).y] color: rgb(243,156,18) marker: false;			
+			}		
 		}						
 	}
 }
diff --git a/...fferential Equations/models/Technical Details/Influence of the simulation step (SIR).gaml b/...fferential Equations/models/Technical Details/Influence of the simulation step (SIR).gaml
@@ -8,9 +8,11 @@
 
 model SIRInfluenceofSimulationStep
 
-global {	
+global {
+	string step_string;
 	init {
 		write name + "" + step;
+		step_string <- string(step)+"s";
 		create userSIR with: [h::0.1,N::500,I::1.0];
 	}
 
@@ -43,19 +45,29 @@ species userSIR {
 
 
 experiment examples type: gui {
+	float minimum_cycle_duration <- 0.1#s;
 
-	init {
+	action _init_ {
 		create simulation with: [step::2#s,name::"s2s"]   ;
 		create simulation with: [step::10#s,name::"s10s"] ;		
 	}
 
-	output {		
-		display SIR  {
-			chart 'examplesUserSIR' type: series background: #lightgray {
-				data "S" value: first(userSIR).S color: #green;
-				data "I" value: first(userSIR).I color: #red;
-				data "R" value: first(userSIR).R color: #blue;
+	output {
+		layout #split tabs: false;	
+		display SIR toolbar: false {
+			chart 'Time Teries ('+step_string+' per cycle)' type: series 
+			background: rgb(47,47,47) color: #white y_label: "pop" x_tick_line_visible: false{
+				data "S" value: first(userSIR).S[] color: rgb(46,204,113) marker: false thickness: 2;
+				data "I" value: first(userSIR).I[] color: rgb(231,76,60) marker: false thickness: 2;
+				data "R" value: first(userSIR).R[] color: rgb(52,152,219) marker: false thickness: 2;
 			}			
-		}				
+		}
+		display "Phase Portrait" toolbar: false {
+		chart 'Phase Portrait ('+step_string+' per cycle)' type: xy 
+		background: rgb(47,47,47) color: #white y_label: "y" x_label: "x"
+			x_range: {0,500} y_range: {0,450}{
+				data "I vs S" value: rows_list(matrix(first(userSIR).S[],first(userSIR).I[])) color: rgb(52,152,219) marker: false;			
+			}		
+		}					
 	}
 }
diff --git a/...els/Ordinary Differential Equations/models/Technical Details/Solve statement options.gaml b/...els/Ordinary Differential Equations/models/Technical Details/Solve statement options.gaml