Merge branch 'Camille_Bis' into patrick

data/input/atlanticarea/BNaaBasins.xml

@@ -13,6 +13,6 @@
 	<seaBasinNameLabel>BASIN_NAME</seaBasinNameLabel>
 	<continentPathName>ID</continentPathName>
 	<distanceGridFileName>data/input/atlanticarea/distanceGridAA.csv</distanceGridFileName>
-	<temperatureCatchmentFile>data/input/atlanticarea/aa_sst_depuis1800.csv</temperatureCatchmentFile>
+	<temperatureCatchmentFile>data/input/atlanticarea/aa_sst_histo.csv</temperatureCatchmentFile>
 	<useRealPDam>false</useRealPDam>
 </environment.BasinNetworkSWithContinent>
\ No newline at end of file

data/input/atlanticarea/fishTryRealBV_CC.xml → data/input/atlanticarea/fishTryRealBV_CC_Alosa.xml

@@ -19,11 +19,11 @@
 			<excretionRate class="hashtable">
 				<entry>
 					<string>P</string>
-					<double>2.17E-6</double>
+					<double>5.208E-5</double>
 				</entry>
 				<entry>
 					<string>N</string>
-					<double>2.471E-5</double>
+					<double>5.9304E-4</double>
 				</entry>
 			</excretionRate>
 			<fishFeaturesPreSpawning class="hashtable">
@@ -280,7 +280,7 @@
 					<exportSeason>SPRING</exportSeason>
 					<fileNameOutput>effectiveBiomassFluxesBeforeReproduction</fileNameOutput>
 				</species.WriteEffectiveAndBiomassFluxes>
-				
+
 				<species.ReproduceAndSurviveAfterReproductionWithDiagnose>
 					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
 					<reproductionSeason>SPRING</reproductionSeason>
@@ -297,11 +297,17 @@
 					<initialLength>2.0</initialLength>
 					<sigmaRecruitment>0.2</sigmaRecruitment>
 					<survivalRateAfterReproduction>0.1</survivalRateAfterReproduction>
-					<maxNumberOfSuperIndividualPerReproduction>500.0</maxNumberOfSuperIndividualPerReproduction>
+					<maxNumberOfSuperIndividualPerReproduction>100.0</maxNumberOfSuperIndividualPerReproduction>
 					<withDiagnose>false</withDiagnose>
 					<displayFluxesOnConsole>false</displayFluxesOnConsole>
 				</species.ReproduceAndSurviveAfterReproductionWithDiagnose>
 
+				<species.WriteEffectiveAndBiomassFluxes>
+					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
+					<exportSeason>SPRING</exportSeason>
+					<fileNameOutput>effectiveBiomassFluxesAfterReproduction</fileNameOutput>
+				</species.WriteEffectiveAndBiomassFluxes>
+				
 				<species.MigrateToSea>
 					<seaMigrationSeason>SUMMER</seaMigrationSeason>
 					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>

data/input/northeastamerica/fishTryRealBV_CC_Sapidissima.xml

@@ -198,7 +198,7 @@
 		<parameterSetLine>0</parameterSetLine>
 		<yearOfTheUpdate>0</yearOfTheUpdate>
 		<basinsToUpdateFile>data/input/reality/basinsToUpdate.csv</basinsToUpdateFile>
-		<outputPath>data/output/</outputPath>
+		<outputPath>data/output/northeastamerica/</outputPath>
 		<minYearToWrite>1900</minYearToWrite>
 		<fileNameFluxes>nutrientFluxes</fileNameFluxes>
 		<lengthAtHatching>2.8</lengthAtHatching>
@@ -297,7 +297,7 @@
 					<initialLength>2.8</initialLength>
 					<sigmaRecruitment>0.2</sigmaRecruitment>
 					<survivalRateAfterReproduction>0.1</survivalRateAfterReproduction>
-					<maxNumberOfSuperIndividualPerReproduction>150.0
+					<maxNumberOfSuperIndividualPerReproduction>100.0
 					</maxNumberOfSuperIndividualPerReproduction>
 					<withDiagnose>false</withDiagnose>
 					<displayFluxesOnConsole>false</displayFluxesOnConsole>
@@ -318,7 +318,7 @@
 			<processesAtEnd>
 				<species.WriteNutrientImportFluxes>
 					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
-					<fileName>fluxes</fileName>
+					<fileName>nutrientImportfFluxes</fileName>
 				</species.WriteNutrientImportFluxes>
 
 				<species.WriteNutrientExportFluxes>

src/main/java/species/DiadromousFishGroup.java

@@ -89,10 +89,10 @@ public class DiadromousFishGroup extends AquaNismsGroup<DiadromousFish, BasinNet
 	private long yearOfTheUpdate;
 
 	/**
-	 * list of the basins to be updated column 1: name of the basin column 2: Pattractive: how the bassin become
-	 * attractive (0 not attractive, 1 ??? normal weight associated to catchment size) column 3: Paccessible: how the
-	 * bassin become acesssible (0 not accessible, 1 ???normal weight to inter catchment distance )
-	 * 
+	 * list of the basins to be updated
+	 * column 1: name of the basin
+	 * column 2: Pattractive: how the bassin become attractive (0 not attractive, 1 ??? normal weight associated to catchment size)
+	 * column 3: Paccessible: how the bassin become acesssible (0 not accessible, 1 ???normal weight to inter catchment distance )
 	 * @unit
 	 */
 	private String basinsToUpdateFile = "data/input/reality/basinsToUpdate.csv";
@@ -108,33 +108,38 @@ public class DiadromousFishGroup extends AquaNismsGroup<DiadromousFish, BasinNet
 	private transient String sep;
 
 	/**
-	 * map <key> basin name <value> Duo <first> pAttractive <second> pAccessible
-	 * 
+	 *  map
+	 *  <key> basin name
+	 *  <value> Duo
+	 *  	<first>       pAttractive
+	 *  	<second>  pAccessible
 	 * @unit
 	 */
 	private transient Map<String, Duo<Double, Double>> basinsToUpdate;
 
 	/**
-	 * length when fish hatchs ( when the diadromousFish is created after reproduction) no diffrence between gender
+	 * length when fish hatchs (when the diadromousFish is created after reproduction) no diffrence between gender
 	 * 
 	 * @unit cm
 	 */
 	private double lengthAtHatching = 2.;
 
 	/**
-	 * L infinity of the van Bertalanffy growth curve for female L = Linf *(1-exp(-K*(t-t0))
-	 * 
+	 * L infinity of the van Bertalanffy growth curve for  female
+	 * L = Linf *(1-exp(-K*(t-t0))
 	 * @unit cm
 	 */
 	public double linfVonBertForFemale = 60.;
 
 	/**
-	 * L infinity of the van Bertalanffy growth curve for male L = Linf *(1-exp(-K*(t-t0))
-	 * 
+	 * L infinity of the van Bertalanffy growth curve for  male
+	 * L = Linf *(1-exp(-K*(t-t0))
+         *
 	 * @unit cm
 	 */
 	public double linfVonBertForMale = 60.;
 
+
 	/**
 	 * Brody growth coefficient of the von Bertalanffy growth curve for female (calculated from the parameterset file) *
 	 * L = Linf *(1-exp(-K*(t-t0))
@@ -199,11 +204,9 @@ public class DiadromousFishGroup extends AquaNismsGroup<DiadromousFish, BasinNet
 
 		double aResidenceTime = 30;
 
-		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
+		Map <String, Double> anExcretionRate = new Hashtable <String, Double>(); 
+		anExcretionRate.put("N", 24.71E-6 * 24); //values from Barber et al, Alosa sapidissima in ug/g wet mass/hour : convertit en g
+		anExcretionRate.put("P", 2.17E-6 * 24); //values from Barber et al, Alosa sapidissima in ug/g wet mass/hour: convertit en g
 
 		/*
 		 * A feature pre spawning
@@ -508,11 +511,6 @@ public class DiadromousFishGroup extends AquaNismsGroup<DiadromousFish, BasinNet
 				}
 			}
 
-			/*
-			 * while (scanner.hasNext()) { scanner.next(); // skip basin_id String basin_name = scanner.next(); String
-			 * obs = scanner.next(); scanner.next(); // skip obs_1851_1950, scanner.next(); // skip obs_1951_2010 if
-			 * (obs != null) obs1900.put(basin_name, Integer.valueOf(obs)); }
-			 */
 			reader.close();
 			scanner.close();