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

.gitignore

-output
 .settings
 .classpath
 .project
 
+# gitignore for Java (https://github.com/github/gitignore/blob/master/Java.gitignore)
+# Compiled class file
+*.class
+
+# Log file
+*.log
+
+# BlueJ files
+*.ctxt
+
+# Mobile Tools for Java (J2ME)
+.mtj.tmp/
+
+# Package Files #
+*.jar
+*.war
+*.ear
+*.zip
+*.tar.gz
+*.rar
+
+# virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
+hs_err_pid*
+
+# gitignore for eclispe (https://github.com/github/gitignore/blob/master/Global/Eclipse.gitignore)
+.metadata
+bin/
+tmp/
+*.tmp
+*.bak
+*.swp
+*~.nib
+local.properties
+.settings/
+.loadpath
+.recommenders
+
+# External tool builders
+.externalToolBuilders/
+
+# Locally stored "Eclipse launch configurations"
+*.launch
+
+# PyDev specific (Python IDE for Eclipse)
+*.pydevproject
+
+# CDT-specific (C/C++ Development Tooling)
+.cproject
+
+# CDT- autotools 
+.autotools
+
+# Java annotation processor (APT)
+.factorypath
+
+# PDT-specific (PHP Development Tools)
+.buildpath
+
+# sbteclipse plugin
+.target
+
+# Tern plugin
+.tern-project
+
+# TeXlipse plugin
+.texlipse
+
+# STS (Spring Tool Suite)
+.springBeans
+
+# Code Recommenders
+.recommenders/
+
+# Scala IDE specific (Scala & Java development for Eclipse)
+.cache-main
+.scala_dependencies
+.worksheet
+
+# personal
+data/divers/
+data/input/.~*
+data/output/
+bin
+build
+dist
+target
+.classpath
+.project
+org.*
+/src/main/java/miscellaneous/Essai.java

data/input/fishTryRealBV.xml

@@ -15,11 +15,11 @@
 			<processesAtBegin>
 				<species.PopulateBasinNetwork>
 					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
-					<nbSIPerBasin>2500</nbSIPerBasin>
-					<nbFishPerBasin>200</nbFishPerBasin>
+					<nbSIPerBasin>200</nbSIPerBasin>
+					<nbFishPerSI>2500</nbFishPerSI>
 					<initialLength>2.0</initialLength>
 				</species.PopulateBasinNetwork>
-				
+
 				<environment.fixTemperatureInRealBasin>
 					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
 					<selectedYear>1950</selectedYear>

data/input/fishTryRealBV_CC.xml

@@ -10,8 +10,7 @@
               <linfVonBert>60.0</linfVonBert>
               <dMaxDisp>0.0</dMaxDisp>
               <lFirstMaturity>40.0</lFirstMaturity>
-              <fileNameInputForInitialObservation>data/input/reality/Obs1900.csv
-              </fileNameInputForInitialObservation>
+              <fileNameInputForInitialObservation>data/input/reality/Obs1900.csv</fileNameInputForInitialObservation>
 
               <processes>
                      <processesAtBegin>

src/main/java/species/DiadromousFishGroup.java

@@ -97,7 +97,7 @@ public class DiadromousFishGroup extends AquaNismsGroup< DiadromousFish, BasinNe
 			InvocationTargetException {
 		super.initTransientParameters(pilot);
 
-		if (basinsToUpdateFile != null){
+		if ( basinsToUpdate != null){
 			String subDir=basinsToUpdateFile;
 			if (basinsToUpdateFile.lastIndexOf("/")!=-1)
 				subDir=basinsToUpdateFile.substring(basinsToUpdateFile.lastIndexOf("/")+1,