Merge branch 'patrick' of gitlab-ssh.irstea.fr:SimAquaLife/GR3D into patrick

data/input/fishTryRealBV_CC.xml

@@ -297,7 +297,7 @@
 					<initialLength>2.0</initialLength>
 					<sigmaRecruitment>0.2</sigmaRecruitment>
 					<survivalRateAfterReproduction>0.1</survivalRateAfterReproduction>
-					<maxNumberOfSuperIndividualPerReproduction>500.0
+					<maxNumberOfSuperIndividualPerReproduction>100.0
 					</maxNumberOfSuperIndividualPerReproduction>
 					<withDiagnose>false</withDiagnose>
 					<displayFluxesOnConsole>false</displayFluxesOnConsole>

data/input/northeastamerica/BNneaBasins.xml

@@ -10,7 +10,7 @@
 	<riverBasinShpFile>data/input/northeastamerica/shape/riverbasins.shp</riverBasinShpFile>
 	<continentShpFile>data/input/northeastamerica/shape/nea_continent.shp</continentShpFile>
 	<riverBasinNameLabel>NAME</riverBasinNameLabel>
-	<seaBasinNameLabel>name</seaBasinNameLabel>
+	<seaBasinNameLabel>NAME</seaBasinNameLabel>
 	<continentPathName>PATH</continentPathName>
 	<distanceGridFileName>data/input/northeastamerica/distanceGridNEA.csv</distanceGridFileName>
 	<temperatureCatchmentFile>data/input/northeastamerica/basins_temperatures_from_1800.csv</temperatureCatchmentFile>

data/input/northeastamerica/fishTryRealBV_CC.xml → data/input/northeastamerica/fishTryRealBV_CC_Sapidissima.xml

@@ -201,10 +201,10 @@
 		<outputPath>data/output/</outputPath>
 		<minYearToWrite>1900</minYearToWrite>
 		<fileNameFluxes>nutrientFluxes</fileNameFluxes>
-		<lengthAtHatching>2.0</lengthAtHatching>
-		<linfVonBertForFemale>70.0</linfVonBertForFemale>
-		<linfVonBertForMale>70.0</linfVonBertForMale>
-		<lFirstMaturityForFemale>55.0</lFirstMaturityForFemale>
+		<lengthAtHatching>2.8</lengthAtHatching>
+		<linfVonBertForFemale>76.0</linfVonBertForFemale>
+		<linfVonBertForMale>76.0</linfVonBertForMale>
+		<lFirstMaturityForFemale>45.0</lFirstMaturityForFemale>
 		<lFirstMaturityForMale>40.0</lFirstMaturityForMale>
 		<processes>
 			<processesAtBegin>
@@ -225,7 +225,7 @@
 				<species.PopulateBasinNetworkSeveralTimesAccordingToBasinSize>
 					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
 					<nbFishPerSI>100000</nbFishPerSI>
-					<initialLength>2.0</initialLength>
+					<initialLength>2.8</initialLength>
 					<etaPopulate>40.0</etaPopulate>
 					<timesOfPopulate>5</timesOfPopulate>
 					<populateSeason>SPRING</populateSeason>
@@ -254,8 +254,8 @@
 					<standardDeviationBvSurface>35594</standardDeviationBvSurface>
 					<meanInterDistance>300.0</meanInterDistance>
 					<standardDeviationInterDistance>978.0</standardDeviationInterDistance>
-					<pHomingForReachEquil>0.75</pHomingForReachEquil>
-					<pHomingAfterEquil>0.75</pHomingAfterEquil>
+					<pHomingForReachEquil>0.97</pHomingForReachEquil>
+					<pHomingAfterEquil>0.97</pHomingAfterEquil>
 					<NbYearForInstallPop>0</NbYearForInstallPop>
 					<riverMigrationSeason>SPRING</riverMigrationSeason>
 					<alpha2Rep>0.0</alpha2Rep>
@@ -266,9 +266,9 @@
 
 				<species.Survive>
 					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
-					<tempMinSurvivalSpawnerInRiv>10.7</tempMinSurvivalSpawnerInRiv>
+					<tempMinSurvivalSpawnerInRiv>8</tempMinSurvivalSpawnerInRiv>
 					<tempOptSurvivalSpawnerInRiv>17.0</tempOptSurvivalSpawnerInRiv>
-					<tempMaxSurvivalSpawnerInRiv>25.7</tempMaxSurvivalSpawnerInRiv>
+					<tempMaxSurvivalSpawnerInRiv>26</tempMaxSurvivalSpawnerInRiv>
 					<survivalProbOptSpawnerInRiv>1.0</survivalProbOptSpawnerInRiv>
 					<!--<mortalityRateInRiver>0.4</mortalityRateInRiver> -->
 					<mortalityRateInSea>0.4</mortalityRateInSea>
@@ -280,13 +280,13 @@
 					<exportSeason>SPRING</exportSeason>
 					<fileNameOutput>effectiveBiomassFluxesBeforeReproduction</fileNameOutput>
 				</species.WriteEffectiveAndBiomassFluxes>
-				
+
 				<species.ReproduceAndSurviveAfterReproductionWithDiagnose>
 					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
 					<reproductionSeason>SPRING</reproductionSeason>
-					<tempMinRep>9.3</tempMinRep>
-					<tempOptRep>20.8</tempOptRep>
-					<tempMaxRep>31.0</tempMaxRep>
+					<tempMinRep>10</tempMinRep>
+					<tempOptRep>17</tempOptRep>
+					<tempMaxRep>30</tempMaxRep>
 					<eta>2.4</eta>
 					<ratioS95__S50>1.9</ratioS95__S50>
 					<a>270000</a>
@@ -294,10 +294,10 @@
 					<survOptRep>0.0017</survOptRep>
 					<lambda>4.1E-4</lambda>
 					<proportionOfFemaleAtBirth>0.5</proportionOfFemaleAtBirth>
-					<initialLength>2.0</initialLength>
+					<initialLength>2.8</initialLength>
 					<sigmaRecruitment>0.2</sigmaRecruitment>
 					<survivalRateAfterReproduction>0.1</survivalRateAfterReproduction>
-					<maxNumberOfSuperIndividualPerReproduction>500.0
+					<maxNumberOfSuperIndividualPerReproduction>150.0
 					</maxNumberOfSuperIndividualPerReproduction>
 					<withDiagnose>false</withDiagnose>
 					<displayFluxesOnConsole>false</displayFluxesOnConsole>

src/main/java/environment/BasinNetworkSWithContinent.java

@@ -396,16 +396,19 @@ public class BasinNetworkSWithContinent extends BasinNetwork {
 			char[] charac = { '"' };
 			String doublequote = new String(charac);
 			scanner.nextLine(); // skip the first line with headers
-			while (scanner.hasNext()) {
-				scanner.next(); // skip gid
-				name = scanner.next();
+		
+			while (scanner.hasNextLine()) {
+					String[] fields = scanner.nextLine().split(",");
+			
+				 // skip gid
+				name = fields[1];
 				name = name.replaceAll(new String(doublequote), "");
-				year = (long) scanner.nextInt();
+				year = Long.valueOf (fields[2]);
 				Double[] seasonalTemperature = new Double[4];
-				seasonalTemperature[0] = scanner.nextDouble();
-				seasonalTemperature[1] = scanner.nextDouble();
-				seasonalTemperature[2] = scanner.nextDouble();
-				seasonalTemperature[3] = scanner.nextDouble();
+				seasonalTemperature[0] = Double.valueOf(fields[3]);
+				seasonalTemperature[1] = Double.valueOf(fields[4]);
+				seasonalTemperature[2] = Double.valueOf(fields[5]);
+				seasonalTemperature[3] = Double.valueOf(fields[6]);
 				// scanner.nextLine();
 
 				// store seasonal temperatures for each basin for the

src/main/java/species/ReproduceAndSurviveAfterReproductionWithDiagnose.java

@@ -57,7 +57,7 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
 	private double tempOptRep = 20. ;
 	private double eta = 2.4; // parameter linking surface of a basin and S_etoile
 	private double ratioS95_S50 = 2.;	
-	private double a=135000.; // Parameter of fecndity (number of eggs per individual)
+	private double a=270000.; // Parameter of fecndity (number of eggs per individual) Modifié depuis la valeur initial de tHibault, qui était 135000
 	private double delta_t=0.33; // duration of the mortality considered in the reproduction process (ex.: from eggs to juvenile in estuary for alosa alosa = 0.33)
 	private double survOptRep = 0.0017;
 	private double lambda = 0.00041;