Modification of parameter values for micro and some minor enhancements

COMOKIT/Core/Models/Entities/Policy.gaml

@@ -235,14 +235,17 @@ species DynamicSpatialPolicy parent: SpatialPolicy {
 
 	action apply {
 		if(every(1#day)) {
-			list<AbstractIndividual> infecteds <- all_individuals where(each.report_status = tested_positive);
+			list<AbstractIndividual> infecteds <- all_individuals where((each.report_status = tested_positive) and each.is_infectious );
+			write sample(length(infecteds));
 			//ask targets {do die;}
 			//target <- target;
 			application_area <- nil;
 			//loop i over: infecteds {
 				if (not empty(infecteds)) {
 				//	write "la: " + length(infecteds);
 					application_area<-union(infecteds collect (circle(radius) at_location each.location));
+					write sample(application_area.perimeter);
+
 					// SpatialPolicy with: [target::target, application_area::union(infecteds collect (circle(radius) at_location each.location))] returns: result;
 					//targets << first(result);
 

COMOKIT/Meso/Models/Entities/Activity.gaml

@@ -216,6 +216,7 @@ global {
 species Activity parent: AbstractActivity frequency: 0 {
 	list<string> types_of_building <- [];
 	map<string,list<Building>> buildings;
+	bool always_allowed <- false;
 
 	map<Building,list<Individual>> find_target (Individual i) {
 		float start <- BENCHMARK ? machine_time : 0.0; 
@@ -318,6 +319,7 @@ species studying parent: Activity {
 
 species staying_home parent: Activity {
 	string name <- act_home;
+	bool always_allowed <- true;
 	map<Building,list<Individual>> find_target (Individual i) {
 		return [i.home::list<Individual>(i.relatives)];
 	}

COMOKIT/Meso/Models/Entities/Individual.gaml

@@ -303,9 +303,9 @@ species Individual parent: AbstractIndividual schedules: use_activity_precomputa
 				is_activity_allowed<- Authority[0].allows(self, act.key);
 				nb_max_fellow <- Authority[0].limitGroupActivity(self, act.key) - 1;
 			}
-			else if (Authority[0].allows(self, act.key)) {
+			else if (act.key.always_allowed or  Authority[0].allows(self, act.key)) {
 				int nb_fellows <- Authority[0].limitGroupActivity(self, act.key) - 1;
-					if (nb_fellows > 0) {
+					if (nb_fellows > 0) { 
 					activity_fellows <-nb_fellows among act.value;
 				} else {
 					activity_fellows <- [];

COMOKIT/Meso/Models/Experiments/Abstract Batch Experiment.gaml

@@ -32,6 +32,7 @@ global{
 	bool sim_stop { return (all_individuals all_match ([susceptible, removed] contains each.state)); }
 
 	init{
+		mode_batch <- true;
 		if (idSimulation = -1){
 			idSimulation <- int(self);
 		}

COMOKIT/Meso/Models/Global.gaml

@@ -39,6 +39,7 @@ global {
 	list agents_history; 
 	list<int> all_individuals_id;
 
+	bool mode_batch <- false;
 	list<Building> all_buildings;
 	geometry shape <- envelope(file_exists(shp_boundary_path) ?shape_file(shp_boundary_path) : shape_file(shp_buildings_path) );
 	Outside the_outside;
@@ -191,7 +192,7 @@ global {
 		firsts <- false;
 	}
 
-	reflex end when:  cycle > 24 and (use_activity_precomputation ? empty(all_individuals): ((all_individuals count (each.is_susceptible or (each.state = removed))) = length(all_individuals))) {
+	reflex end when: not mode_batch and cycle > 24 and (use_activity_precomputation ? empty(all_individuals): ((all_individuals count (each.is_susceptible or (each.state = removed))) = length(all_individuals))) {
 		write "nb cycle: " + cycle;
 		write "time tot: " + (machine_time - t_ref);
 		write "time cycle: " + (machine_time - t_ref2) / cycle;

COMOKIT/Micro/Models/Entities/BuildingIndividual.gaml

@@ -27,6 +27,8 @@ global {
 	int infection_direct;
 	int infection_object;
 	int infection_air;
+	int infection_restaurant;
+	int infection_office;
 }
 
 species IndividualScheduler schedules: shuffle(agents of_generic_species BuildingIndividual) where (each.clinical_status != dead);
@@ -111,7 +113,13 @@ species BuildingIndividual parent: AbstractIndividual  skills: [moving] schedule
 
 					if flip(proba) {
 						do infect_someone(succesful_contact);
-
+						if (succesful_contact.current_room.type = "restaurant") {
+							infection_restaurant <- infection_restaurant + 1;
+						} 
+						if (succesful_contact.current_room.type = "office") {
+							infection_office <- infection_office + 1;
+						} 
+
 						infection_direct <- infection_direct + 1;
 					}
 				}

COMOKIT/Micro/Models/Global.gaml

@@ -162,7 +162,8 @@ global {
 		//map<string, list<Room>> rooms_type <- Room group_by each.type;
 
 		do create_individuals;
-
+		ventilation_viral_decrease <- ventilated_viral_air_decrease_per_day;
+
 		do init_epidemiological_parameters;
 		do init_sars_cov_2;
 		viral_agent <- viruses first_with (each.name = variant);

COMOKIT/Micro/Models/Parameters.gaml

@@ -23,14 +23,14 @@ global {
 	//EPIDEMIOLOGIC PARAMETERS
 	string variant <- DELTA; 
 
-	float infectionDistance <- 1.5#m;
+	float infectionDistance <- 1.4#m;
 	float unit_cell_size <- 1#m;
-
-	float basic_viral_air_increase_per_day <- 2.0;
-	float basic_viral_local_increase_per_day <- 1.0;
-	float basic_viral_air_decrease_per_day <- 0.3;
-	float basic_viral_local_decrease_per_day <- 0.3;
-	float ventilated_viral_air_decrease_per_day <- 1.8;
+	
+	float basic_viral_air_increase_per_day <- 1.0;
+	float basic_viral_local_increase_per_day <- 0.8;
+	float basic_viral_air_decrease_per_day <- 0.2;
+	float basic_viral_local_decrease_per_day <- 0.5;
+	float ventilated_viral_air_decrease_per_day <- 100.0;
 
 	bool allow_air_transmission <- true;
 	bool allow_direct_transmission <- true;