wip

src/main/java/org/matsim/episim/InfectionEventHandler.java

@@ -772,7 +772,15 @@ public void reset(int iteration) {
 		// Sum of antibodies
 		Object2DoubleMap<VirusStrain> antibodies = new Object2DoubleOpenHashMap<>();
 
+		boolean fakeAgentsPossible = contactModel instanceof SymmetricContactModelWithOdeCoupling;
+
 		for (EpisimPerson person : personMap.values()) {
+
+			if (fakeAgentsPossible && person.getPersonId().toString().startsWith("fake_")) {
+				progressionModel.removeAgent(person.getPersonId());
+			}
+
+
 			progressionModel.updateState(person, iteration);
 			antibodyModel.updateAntibodies(person, iteration);
 

src/main/java/org/matsim/episim/model/AbstractProgressionModel.java

@@ -50,10 +50,6 @@ private static long compoundLong(int x, int y) {
 	@Override
 	public void updateState(EpisimPerson person, int day) {
 
-//		// This is useful for fake agents in SymmetricContactModelWithOdeCoupling.
-//		if (person.isExcludeFromDiseaseStateProgression()) {
-//			return;
-//		}
 
 		EpisimPerson.DiseaseStatus status = person.getDiseaseStatus();
 

src/main/java/org/matsim/episim/model/SymmetricContactModelWithOdeCoupling.java

@@ -144,7 +144,7 @@ public void resetOdeDiseaseImportCount() {
 //		unknownCnt = 0L;
 //	}
 
-	private EpisimPerson borrowPerson(Attributes sharedAttributes, EpisimReporting reporting) {
+	private EpisimPerson borrowPerson(Attributes sharedAttributes, EpisimReporting reporting, double now, int dayCounter) {
 		Deque<EpisimPerson> pool = personPool.get();
 		EpisimPerson person = pool.poll();
 		if (person == null) {
@@ -157,6 +157,19 @@ private EpisimPerson borrowPerson(Attributes sharedAttributes, EpisimReporting r
 			person.setDiseaseStatus(0, DiseaseStatus.susceptible);
 //			person.getActivities().clear();  // Clear any leftover activities
 		}
+
+//		if (person.getDiseaseStatus().equals(DiseaseStatus.contagious)) {
+//			return person;
+//		}
+
+		// this do-while loop will add a person, check if they are actually contagious; if not, they'll add another person.
+		do {
+			progressionModel.removeAgent(person.getPersonId());
+			person.setDiseaseStatus(now, DiseaseStatus.infectedButNotContagious);
+			//todo: talk to kai: should we this be a distribution of when they become infectious, because infectivity depends on how long they've been infectious.
+			progressionModel.updateState(person, dayCounter);
+		} while (!person.getDiseaseStatus().equals(DiseaseStatus.contagious));
+
 		return person;
 	}
 
@@ -330,21 +343,11 @@ private void infectionDynamicsGeneralized(EpisimPerson personLeavingContainer, E
 
 
 //						Id<Person> personId = Id.createPersonId("fake_task" + taskId + "_" + i);
-						EpisimPerson person = borrowPerson(sharedAttributes, reporting);
+						EpisimPerson person = borrowPerson(sharedAttributes, reporting, now, dayCounter);
 //
 //						EpisimPerson person = new EpisimPerson(personId, sharedAttributes, reporting);
 
 						containerFake.addPerson(person, 0, new EpisimPerson.PerformedActivity(0, episimConfig.getOrAddContainerParams(actType), null));
-
-						// this do-while loop will add a person, check if they are actually contagious; if not, they'll add another person.
-						do {
-							progressionModel.removeAgent(person.getPersonId());
-							person.setDiseaseStatus(now, DiseaseStatus.infectedButNotContagious);
-							//todo: talk to kai: should we this be a distribution of when they become infectious, because infectivity depends on how long they've been infectious.
-							progressionModel.updateState(person, dayCounter);
-						} while (!person.getDiseaseStatus().equals(DiseaseStatus.contagious));
-
-
 					}
 				}
 			}
@@ -544,7 +547,10 @@ private void infectionDynamicsGeneralized(EpisimPerson personLeavingContainer, E
 				EpisimPerson person = iterator.next();
 				if (person.getPersonId().toString().startsWith("fake")) {
 					returnPerson(person);
+
+					// remove from progression model
 					((AbstractProgressionModel) progressionModel).removeAgent(person.getPersonId());
+
 					iterator.remove();  // Properly remove from the list
 				}
 			}

src/main/java/org/matsim/run/CreateBatteryForCluster.java

@@ -66,7 +66,7 @@
 )
 @SuppressWarnings("unchecked, rawtypes")
 public class CreateBatteryForCluster<T> implements Callable<Integer> {
-	private static final String CLASS_NAME = "newC_berlin_brand";
+	private static final String CLASS_NAME = "newA_berlin";
 
 	private static final Logger log = LogManager.getLogger(CreateBatteryForCluster.class);
 

src/main/java/org/matsim/run/batch/newA_berlin.java

@@ -118,8 +118,8 @@ public static final class Params {
 		@Parameter({1.0})
 		public double thetaFactor;
 
-//		@Parameter({-1.0, 0.5, 0.75, 1.0, 1.25, 1.5})
-		@Parameter({1.})
+		@Parameter({0.5, 0.75, 1.0, 1.25, 1.5})
+//		@Parameter({1.})
 		public double ode;
 
 	}
@@ -133,7 +133,7 @@ public static void main(String[] args) {
 		String[] args2 = {
 				RunParallel.OPTION_SETUP, newA_berlin.class.getName(),
 				RunParallel.OPTION_PARAMS, Params.class.getName(),
-				RunParallel.OPTION_TASKS, Integer.toString(2),
+				RunParallel.OPTION_TASKS, Integer.toString(1),
 				RunParallel.OPTION_ITERATIONS, Integer.toString(50),
 				RunParallel.OPTION_METADATA
 		};