Add coloumnn abundance in csv file

data/input/fishTryRealBV_CC.xml

@@ -307,13 +307,13 @@
 					<maxNumberOfSuperIndividualPerReproduction>50.0
 					</maxNumberOfSuperIndividualPerReproduction>
 					<withDiagnose>false</withDiagnose>
-					<displayFluxesOnConsole>false</displayFluxesOnConsole>
+					<displayFluxesOnConsole>true</displayFluxesOnConsole>
 				</species.ReproduceAndSurviveAfterReproductionWithDiagnose>
 
 				<species.MigrateToSea>
 					<seaMigrationSeason>SUMMER</seaMigrationSeason>
 					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
-					<displayFluxesOnConsole>false</displayFluxesOnConsole>
+					<displayFluxesOnConsole>true</displayFluxesOnConsole>
 				</species.MigrateToSea>
 
 				<environment.updateTemperatureInRealBasin>
@@ -331,7 +331,7 @@
 						<long>2000</long>
 						<long>2100</long>
 					</years>
-					<fileNameOutput>fluxes</fileNameOutput>
+					<fileNameOutput>JeuParam100_2100RCP85_A_essai</fileNameOutput>
 				</species.IdentifyPopulation>
 				<species.TypeTrajectoryCV>
 					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>

data/input/fishTryRealBV_PL.xml

@@ -127,7 +127,7 @@
 						<long>2100</long>
 					</years>
 					<fluxesSeason>SPRING</fluxesSeason>
-					<fileNameOutput>fluxes</fileNameOutput>
+					<fileNameOutput>JeuParam100_20100RCP85_A_essai</fileNameOutput>
 				</species.IdentifyPopulation>
 				
 				<species.ExportRecruitment>
@@ -144,7 +144,7 @@
 				
 				<species.ExportPopulationStatus>
   					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
-  					<fileNameMortality>mortalty</fileNameMortality>
+  					<fileNameMortality>mortality</fileNameMortality>
   					<fileNameMortalityCrash>mortalityCrash</fileNameMortalityCrash>
   					<fileNameStockTrap>stockTrap</fileNameStockTrap>
   					<fileNamePopulationStatus>populationStatus</fileNamePopulationStatus>

src/main/java/species/DiadromousFishGroup.java

@@ -409,10 +409,10 @@ public class DiadromousFishGroup extends AquaNismsGroup< DiadromousFish, BasinNe
 		    new File(this.outputPath +fileNameFluxes).getParentFile().mkdirs();
 			try {
 				bWForFluxes = new BufferedWriter(new FileWriter(new File(this.outputPath+
-						fileNameFluxes +this.getSimulationId()+ ".csv")));
+						fileNameFluxes +this.getSimulationId() + ".csv")));
 
 				bWForFluxes.write("timestep"+sep+"year"+sep+"season"+sep+"basin"
-						+sep+"fluxType"+sep+"origine"+sep+"biomass");
+						+sep+"abundance" + sep + "fluxType"+sep+"origine"+sep+"biomass");
 				for (String nutrient : nutrientRoutine.getNutrientsOfInterest()) {
 					bWForFluxes.write(sep+nutrient);
 				}

src/main/java/species/MigrateToSea.java

@@ -84,7 +84,7 @@ public class MigrateToSea extends AquaNismsGroupProcess<DiadromousFish, Diadromo
 					try {
 
 						bW.write(group.getPilot().getCurrentTime() + "; " + Time.getYear(group.getPilot()) + ";" + Time.getSeason(group.getPilot()) 
-						+";"+ basin.getName() +  ";IMPORT; NONE");
+						+";"+ basin.getName() + ";" + basin.getJuvenileNumber() + ";EXPORT; NONE");
 						bW.write(";" + totalOutputFluxes.get("biomass"));
 						for (String nutrient : group.getNutrientRoutine().getNutrientsOfInterest()) {
 							bW.write(";" + totalOutputFluxes.get(nutrient));

src/main/java/species/NutrientRoutine.java

@@ -356,8 +356,8 @@ public class NutrientRoutine {
 
 
 		Map <String, Double> anExcretionRate = new Hashtable <String, Double>(); 
-		anExcretionRate.put("N", 24.71E-6); //values from Barber et al, Alosa sapidissima in ug/g wet mass/hour : convertit en g
-		anExcretionRate.put("P", 2.17E-6); //values from Barber et al, Alosa sapidissima in ug/g wet mass/hour: convertit en g
+		anExcretionRate.put("N", 24.71E-6); //values from Barber et al, Alewifes  in ug/g wet mass/hour : convertit en g
+		anExcretionRate.put("P", 2.17E-6); //values from Barber et al, Alewifes in ug/g wet mass/hour: convertit en g
 
 		System.out.println("anExcretionRate: " + anExcretionRate.toString()); //
 
@@ -431,13 +431,13 @@ public class NutrientRoutine {
 		// carcass composition for fish before spawning
 		Map<Gender, Map<String, Double>> aCompoCarcassPreSpawning = new Hashtable<DiadromousFish.Gender,Map<String,Double>>();
 		Map<String,Double> aCompo = new Hashtable<String,Double>();
-		aCompo.put("N", 2.958 / 100.); //On remplit une collection avec un put. 
-		aCompo.put("P", 0.673 / 100.);
+		aCompo.put("N", 2.958 / 100.); //On remplit une collection avec un put. Values from Haskell (2018) Alosa sapidissima (%)
+		aCompo.put("P", 0.673 / 100.); //Values from Haskell (2018) Alosa sapidissima (%)
 		aCompoCarcassPreSpawning.put(Gender.FEMALE,aCompo);
 
 		aCompo = new Hashtable<String,Double>();
-		aCompo.put("N", 2.941 / 100.);
-		aCompo.put("P", 0.666 / 100.);
+		aCompo.put("N", 2.941 / 100.); //Values from Haskell (2018) Alosa sapidissima (%)
+		aCompo.put("P", 0.666 / 100.);// Values from Haskell (2018) Alosa sapidissima (%)
 		aCompoCarcassPreSpawning.put(Gender.MALE,aCompo);
 
 		System.out.println("aCompoCarcassPreSpawning: " + aCompoCarcassPreSpawning.toString()); //

src/main/java/species/ReproduceAndSurviveAfterReproductionWithDiagnose.java

@@ -169,6 +169,7 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
 					// age of autochnonous spawnser
 					Map<Integer, Long> ageOfNativeSpawners = new TreeMap<Integer, Long>(); 
 
+					
 					// compute the number of spawners and keep the origines of the spawners
 					for (DiadromousFish fish : fishInBasin){
 
@@ -310,7 +311,7 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
 								}
 							}
 						}
-						System.out.println("\t"+message);
+						//System.out.println("\t"+message);
 					}
 
 					// --------------------------------------------------------------------------------------------------
@@ -401,18 +402,17 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
 					}
 					deadFish.clear();
 
-
 					if 	(displayFluxesOnConsole)
 						System.out.println(group.getPilot().getCurrentTime() + "; " + Time.getYear(group.getPilot()) + ";" + Time.getSeason(group.getPilot()) + ";IMPORT;"
-								+ riverBasin.getName() + "; " + totalInputFluxes);
-
+								+ riverBasin.getName() + ";" + riverBasin.getSpawnerNumber() +  "; " + totalInputFluxes); 
 					BufferedWriter bW = group.getbWForFluxes();
 					if ( bW != null) {
 						try {
 							for (fluxOrigin origin : totalInputFluxes.keySet()) {
 								bW.write(group.getPilot().getCurrentTime() + "; " + Time.getYear(group.getPilot()) + ";" + Time.getSeason(group.getPilot()) 
-								+";"+ riverBasin.getName() +  ";IMPORT;"+origin);
+								+";"+ riverBasin.getName() +  ";" + riverBasin.getSpawnerNumber() + ";" + ";IMPORT;"+origin);
 								bW.write(";" + totalInputFluxes.get(origin).get("biomass"));
+						
 								for (String nutrient : group.getNutrientRoutine().getNutrientsOfInterest()) {
 									bW.write(";" + totalInputFluxes.get(origin).get(nutrient));
 								}
@@ -429,11 +429,13 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
 				}
 
 
-				// System.out.println("("+numberOfGenitors+")");
+				//System.out.println("("+numberOfGenitors+")");
 				//System.out.println("  BEFORE " +riverBasin.getSpawnerOrigins().keySet());
 				riverBasin.getSpawnerOrigins().push(spawnerOriginsDuringReproduction);
 				//System.out.println("  AFTER " +riverBasin.getSpawnerOrigins().keySet());
 			}
+			
+			
 			// --------------------------------------------------------------------------------------------------
 			// update the observers
 			// --------------------------------------------------------------------------------------------------