diff --git a/src/main/java/species/ReproduceAndSurviveAfterReproduction.java b/src/main/java/species/ReproduceAndSurviveAfterReproduction.java
index 8e8f773cbb3aa64198476c7b0995999594a281c2..21007cc5c241d066babeeea8d86a749b06d95a81 100644
--- a/src/main/java/species/ReproduceAndSurviveAfterReproduction.java
+++ b/src/main/java/species/ReproduceAndSurviveAfterReproduction.java
@@ -163,6 +163,7 @@ public class ReproduceAndSurviveAfterReproduction extends AquaNismsGroupProcess<
survivalAmount = Miscellaneous.binomialForSuperIndividual(group.getPilot(), fish.getAmount(), survivalRateAfterReproduction);
if (survivalAmount > 0)
fish.setAmount(survivalAmount);
+
else
deadFish.add(fish);
}
diff --git a/src/main/java/species/ReproduceAndSurviveAfterReproductionWithDiagnose.java b/src/main/java/species/ReproduceAndSurviveAfterReproductionWithDiagnose.java
index 9ce8025f331561c8aeeb69174221c86f9a144b72..67113f6caf1763a15923a4eb7f1cc4e2aeb9caef 100644
--- a/src/main/java/species/ReproduceAndSurviveAfterReproductionWithDiagnose.java
+++ b/src/main/java/species/ReproduceAndSurviveAfterReproductionWithDiagnose.java
@@ -80,8 +80,8 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
super.initTransientParameters(pilot);
genNormal = new NormalGen( pilot.getRandomStream(),
new NormalDist(0., 1.));
- mortalityFunction=new MortalityFunction();
- stockRecruitmentRelationship= new StockRecruitmentRelationship();
+ mortalityFunction = new MortalityFunction();
+ stockRecruitmentRelationship = new StockRecruitmentRelationship();
}
@Override
@@ -108,20 +108,17 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
List<DiadromousFish> fishInBasin = riverBasin.getFishs(group);
if (fishInBasin != null){
-
+
+ //Initiate the total fluxes for this basin
Map<String, Double> totalFluxes = new Hashtable<String, Double>(); //On créer la Map pour stocker les flux
-
for (String nutrient : group.getFishNutrient().getNutrientsOfInterest()) {
-
totalFluxes.put(nutrient, 0.); // ON MET A JOUR NOTRE map
-
}
-
// --------------------------------------------------------------------------------------------------
// definition of the stock recruiment relationship
// --------------------------------------------------------------------------------------------------
-
+
// effective temperature for reproduction (priority to the ANG value)
double tempEffectRep;
if (Double.isNaN(group.getTempMinRep())){
@@ -152,7 +149,7 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
// initilisation of the stock recruitment relationship
stockRecruitmentRelationship.init(alpha, beta, S50, S95);
-
+
// --------------------------------------------------------------------------------------------------
// calulation of the spawner number
// --------------------------------------------------------------------------------------------------
@@ -162,9 +159,9 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
// compute the number of spawners and keep the origines of the spawners
for (DiadromousFish fish : fishInBasin){
-
+
if (fish.getGender() == Gender.FEMALE & fish.isMature()){
-
+
//System.out.println(fish.getAge() + " -> "+ fish.getLength() + " ("+fish.getStage()+")");
if (fish.getNumberOfReproduction() < 1) {
numberOfFemaleSpawnerForFirstTime++;
@@ -190,12 +187,31 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
fish.incNumberOfReproduction();
// survival after reproduction (semelparity or iteroparity) of SI (change the amount of the SI)
- survivalAmount = Miscellaneous.binomialForSuperIndividual(group.getPilot(), fish.getAmount(), survivalRateAfterReproduction);
- if (survivalAmount > 0)
- fish.setAmount(survivalAmount);
- else
+ survivalAmount = Miscellaneous.binomialForSuperIndividual(group.getPilot(), fish.getAmount(), survivalRateAfterReproduction);
+ if (survivalAmount > 0) {
+
+ //Export for fishes survived after spawning (survivalAmount) : excretion + gametes
+ Map <String, Double> aFluxAfterSurvival = group.getFishNutrient().computeNutrientsInputForSurvivalAfterSpawning(fish);
+ for (String nutrient: aFluxAfterSurvival.keySet()) {
+ totalFluxes.put(nutrient,totalFluxes.get(nutrient) + aFluxAfterSurvival.get(nutrient) * survivalAmount);
+ }
+ fish.setAmount(survivalAmount); }
+ else {
+
deadFish.add(fish);
+
+ //Export for fished died before spawning (fish.getAmount): carcasses + excretion + gametes
+ Map<String, Double> aFlux = group.getFishNutrient().computeNutrientsInputForDeathAfterSpawning(fish); //
+ for (String nutrient: aFlux.keySet()) {
+ totalFluxes.put(nutrient,totalFluxes.get(nutrient) + aFlux.get(nutrient) * (fish.getAmount()) - survivalAmount); //Fish.getAmount - survivalAmount = total fishes died.
+
+ }
+
+
+ }
+
}
+
}
// keep the spawner number
@@ -269,9 +285,9 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
// --------------------------------------------------------------------------------------------------
// Reproduction process (number of recruits)
// --------------------------------------------------------------------------------------------------
-
+
if (numberOfFemaleGenitors > 0.) {
-
+
//BH Stock-Recruitment relationship with logistic depensation
double meanNumberOfRecruit = stockRecruitmentRelationship.getRecruitment(numberOfFemaleGenitors);
@@ -280,7 +296,7 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
long numberOfRecruit = Math.round(Math.exp(genNormal.nextDouble()*sigmaRecruitment + muRecruitment));
//System.out.println(group.getPilot().getCurrentTime()+" "+Time.getSeason(group.getPilot())+" "+ riverBasin.getName()+": " + numberOfGenitors + " spwaners \tgive "+ numberOfRecruit + " recruits");
-
+
// keep last % of autochtone
riverBasin.getLastPercentagesOfAutochtones().push(numberOfAutochtones * 100 / numberOfFemaleGenitors);
@@ -350,28 +366,21 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
// Remove deadfish and compute the related nutrient fluxes
// --------------------------------------------------------------------------------------------------
for (DiadromousFish fish : deadFish){
-
- Map<String, Double> aFlux = group.getFishNutrient().computeNutrientsInputForDeathAfterSpawning(fish); //
-
- for (String nutrient: aFlux.keySet()) {
-
- totalFluxes.put(nutrient,totalFluxes.get(nutrient) + aFlux.get(nutrient) * fish.getAmount());
- }
-
-
-
+
+
+
group.removeAquaNism(fish);
}
deadFish.clear();
-
+
System.out.println(group.getPilot().getCurrentTime() + "; " + Time.getYear(group.getPilot()) + ";" + Time.getSeason(group.getPilot()) + ";"
- + riverBasin.getName() + "; " + totalFluxes);
-
+ + riverBasin.getName() + "; " + totalFluxes);
+
}
else {
riverBasin.setYearOfLastNulRep(Time.getYear(group.getPilot()));
}
-
+
// System.out.println("("+numberOfGenitors+")");
//System.out.println(" BEFORE " +riverBasin.getSpawnerOrigins().keySet());