Merge branch 'patrick' into Camille_Bis

.gitignore

@@ -118,3 +118,4 @@ org.*
 /exploration/scriptR/scriptR.Rproj
 /exploration/scriptR/.Rproj.user/
 /exploration/scriptR/.RData
+/src/main/java/environment/*.ucls

data/input/atlanticarea/BNaaBasins.xml

+<environment.BasinNetworkSWithContinent>
+	<nbBasin>0</nbBasin>
+	<memorySize>10</memorySize>
+	<memorySizeLongQueue>30</memorySizeLongQueue>
+	<cVthresholdForFinalStates>5.0</cVthresholdForFinalStates>
+	<RecruitmentThresholdForFsAndKappa>50.0</RecruitmentThresholdForFsAndKappa>
+	<yearOfTheBegin>1800</yearOfTheBegin>
+	<basinFile>data/input/atlanticarea/aa_basins.csv</basinFile>
+	<seaBasinShpFile>data/input/atlanticarea/shape/seabasins.shp</seaBasinShpFile>
+	<riverBasinShpFile>data/input/atlanticarea/shape/riverbasins.shp</riverBasinShpFile>
+	<continentShpFile>data/input/atlanticarea/shape/aa_continent.shp</continentShpFile>
+	<riverBasinNameLabel>BASIN_NAME</riverBasinNameLabel>
+	<seaBasinNameLabel>BASIN_NAME</seaBasinNameLabel>
+	<continentPathName>ID</continentPathName>
+	<distanceGridFileName>data/input/atlanticarea/distanceGridAA.csv</distanceGridFileName>
+	<temperatureCatchmentFile>data/input/atlanticarea/aa_sst_depuis1800.csv</temperatureCatchmentFile>
+	<useRealPDam>false</useRealPDam>
+</environment.BasinNetworkSWithContinent>
\ No newline at end of file

data/input/atlanticarea/aa_basins.csv

+basin_id,basin_name,surface_area_drainage_basin,long_outlet,lat_outlet,ordre,pdam
+118,Oum_er_Rbia,35000,-8.31,33.32,1,1
+296,Bou_Regreg,10000,-6.839,34.039,2,1
+134,Sebou,39000,-6.62,34.35,3,1
+297,Loukkos,3730,-6.155,35.202,4,1
+333,Barbate,1290,-5.91245785700441,36.1857555572138,5,1
+336,Guadalete,3677,-6.20359012387503,36.5568212517913,6,1
+67,Guadalquivir,56966,-6.34719531559064,36.7955111186177,7,1
+68,Guadiana,55422,-7.40377213873015,37.1764977357446,8,1
+340,Piedras,286,-7.17724110669544,37.2766909157961,9,1
+342,Tinto,1039,-6.84203197415675,37.2980304123919,10,1
+339,Odiel,2111,-6.97741561809518,37.3104571508922,11,1
+383,Mira,1600,-8.78559216309201,37.7194690733053,12,1
+128,Sado,7692,-8.67330668529056,38.4152013395294,13,1
+270,Tagus,80775,-8.99330253446028,38.9405327031516,14,1
+387,Alcoa,415.999996733092,-9.07330739961069,39.5821547050997,15,1
+100,Mondego,6644,-8.86271210007289,40.1458727716157,16,1
+384,Vouga,3635,-8.66069923175738,40.6855001599568,17,1
+45,Douro,97595,-8.67285289141363,41.14548496064,18,1
+385,Ave,1395,-8.74462092012648,41.3416377231104,19,1
+386,Cavado,1648,-8.7848797615787,41.5299562226173,20,1
+88,Lima,2470,-8.8348701291115,41.684979079475,21,1
+98,Minho,17067,-8.87075043963189,41.8649027981078,22,1
+315,Lerez,453,-8.65019407159082,42.4354615172115,23,1
+370,Umia,440,-8.80483103001464,42.5024460741603,24,1
+289,Ulla,2817,-8.72651607979951,42.6771056838815,25,1
+369,Tambre,1530,-8.86740524276748,42.8271030347259,26,1
+358,Anllons,516,-8.90967304043815,43.2406734568706,27,1
+248,Oria,873,-2.12697813576095,43.2751300975342,28,1
+314,Mandeo,368,-8.21577602779556,43.2902960803413,29,1
+371,Urola,350,-2.2509792815169,43.3012643296213,30,1
+262,Oiartzun,94,-1.90826905791347,43.3210497298964,31,1
+362,Deba,555,-2.42013081582084,43.3217476843693,32,1
+261,Urumea,273,-1.9798908932821,43.3235660701073,33,1
+287,Nervion,1801,-3.01977111788142,43.3259985055657,34,1
+360,Barbadun,135,-3.11596326884857,43.341912598422,35,1
+286,Bidassoa,750,-1.78306712844155,43.349302559576,36,1
+365,Lea,128,-2.49741214965209,43.3615119550438,37,1
+359,Artibai,110,-2.49741214965209,43.3615119550438,38,1
+366,Oka,220,-2.67794892993681,43.3637725940997,39,1
+290,Ason,640,-3.42932449789305,43.364859671195,40,1
+110,Nivelle,138,-1.66460382853114,43.3866356063251,41,1
+293,Nansa,428,-4.47121014952064,43.3907314077151,42,1
+284,Deva_Cares,1131,-4.51304820425669,43.3920730293528,43,1
+361,Butron,237,-2.94670590907408,43.4074398220102,44,1
+363,Eume,470,-8.13404128002854,43.4249941285877,45,1
+292,Pas,662,-3.95702259761107,43.4362382043022,46,1
+247,Sella,1297,-5.06449966916832,43.4645728407351,47,1
+291,Eo,1050,-7.05236381792102,43.4725075300948,48,1
+364,Grande,283,-7.05650407856935,43.4948138887598,49,1
+3,Adour,16880,-1.52210544538636,43.5294179298336,50,1
+103,Navia,2584,-6.72404665124113,43.530075820007,51,1
+283,Nalon_Narcea,6749,-6.08841876563135,43.5383883598313,52,1
+313,Masma,301,-7.26722459939125,43.5400536986278,53,1
+245,Esva,465,-6.46955116846017,43.5497234763852,54,1
+367,Ouro,189,-7.29637746617633,43.5939964548703,55,1
+316,Landro,258,-7.60330951464756,43.6589836211942,56,1
+368,Sor,202,-7.70534240795237,43.7075429624571,57,1
+87,Leyre,2661,-1.02030771580152,44.6633866972933,58,1
+60,Garonne,55000,-0.585081601489782,45.0139212839604,59,1
+382,Dordogne,24000,-0.603802010803,45.0447223641735,60,1
+138,Seudre,236,-1.13538587887299,45.7946674358631,61,1
+32,Charente,10000,-1.07020208063444,45.9523663709676,62,1
+269,Sevre Niortaise,3580,-1.08560320969698,46.3169187865894,63,1
+84,Lay,2190,-1.31350193039061,46.331996406945,64,1
+16,Auzance,620,-1.8458267320494,46.5887288484879,65,1
+89,Loire,117000,-2.03962153867848,47.2994091540114,66,1
+177,Vilaine,10475,-2.44461163519601,47.4973998883648,67,1
+133,Scorff,300,-3.34783554834837,47.7406376360974,68,1
+23,Blavet,2060,-3.30249619582593,47.7644408141433,69,1
+112,Odet,715,-4.11289631499572,47.8710695112605,70,1
+14,Aulne,1495,-4.13568137637758,48.2379658924726,71,1
+52,Elorn,379,-4.28846382025786,48.434583613116,72,1
+124,Rance,1195,-1.97200540567912,48.533751235094,73,1
+36,Couesnon,1134,-1.50938201268339,48.6293742632412,74,1
+137,Selune,1000,-1.35650561540603,48.6343075412333,75,1
+86,Leguer,494,-3.52888876068966,48.7324233127369,76,1
+166,Trieux,846,-3.08515231445815,48.8132763776064,77,1
+116,Orne,1268,-0.246006592811472,49.2640802107755,78,1
+41,Dives,638,-0.103859495141771,49.2951490667409,79,1
+179,Vire,1170,-1.11649407501988,49.3432645160485,80,1
+46,Douve,1670,-1.17394936388458,49.3566008804423,81,1
+163,Touques,1350,0.0748591304250034,49.3655175348664,82,1
+136,Seine,78000,0.293465780629967,49.4335882379052,83,1
+25,Bresle,780,1.37307627665623,50.0616227812808,84,1
+146,Somme,5560,1.64424147904093,50.1840517840067,85,1
+15,Authie,1305,1.61986232531134,50.3693790167365,86,1
+329,Tamar,1820,-4.219603377938,50.4756570726991,87,1
+29,Canche,1274,1.62735357879896,50.5181731607102,88,1
+330,Dorset Frome,548,-2.08165634918555,50.6878694284033,89,1
+332,Hampshire Avon,1749,-1.74124506533082,50.7224155509078,90,1
+1,Aa,1215,2.09915638470239,51.0114998156667,91,1
+188,Yser,1300,2.7252192917766,51.1509791847998,92,1
+55,Escaut,21861,4.39691449491217,51.2284074354138,93,1
+271,Thames,13331,0.414461198131061,51.4496199922222,94,1
+331,Taff,529,-3.17466260691362,51.4635864340131,95,1
+17,Avon,2808,-2.70769881826352,51.4966344101406,96,1
+139,Severn,11165,-2.640046397968,51.6105375948103,97,1
+185,Wye,4141,-2.65964213199856,51.6175068868812,98,1
+96,Meuse,36011,5.13105650196698,51.737836072328,99,1
+164,Towy,1388,-4.32010495808608,51.816946115469,100,1
+268,Rhine,185000,5.01744593656898,51.8204198358017,101,1
+22,Blackwater,2184,-7.85610875594891,51.9813322566461,102,1
+20,Barrow,2983,-6.9718284984703,52.2427457363127,103,1
+144,Slaney,1943,-6.5084074572208,52.3505270190985,104,1
+143,Shannon,11700,-8.63539180409262,52.6617425704881,105,1
+66,Great_Ouse,8254,0.357290189008181,52.8094186808715,106,1
+40,Dee,2235,-3.03620089563304,53.2177278891194,107,1
+53,Ems,17934,7.249231385481,53.326216173278,108,1
+94,Mersey,4065,-2.76882743164587,53.3275929412712,109,1
+184,Weser,48800,8.51788926850392,53.5020649754736,110,1
+165,Trent,10249,-0.688323216976883,53.6762644477959,111,1
+51,Elbe,144055,9.09928064500417,53.8753154523629,112,1
+328,Eider,3300,8.95156148975373,54.3126994349248,113,1
+54,Erne,4374,-8.19654172408902,54.5007277432767,114,1
+50,Eden,2769,-3.01516447282937,54.9472224765298,115,1
+174,Vida,1081,8.6632786851788,54.9624149229005,116,1
+169,Tyne,2940,-1.431820130709,55.0083839125931,117,1
+59,Foyle,2927,-7.26608842147487,55.0425976411679,118,1
+19,Bann,5957,-6.76542973747669,55.1650391423259,119,1
+168,Tweed,5079,-2.00526264747825,55.7659164349314,120,1
+34,Clyde,2956,-4.51514664812052,55.9277267022483,121,1
+58,Forth,1683,-3.72793073831557,56.0640450108391,122,1
+155,Tay,5021,-3.28434377510808,56.354035439052,123,1
+69,Gudenaa,3200,10.2067044768575,56.4720387561255,124,1
+81,Lagan,6440,12.9532172143635,56.546448325511,125,1
+147,Spey,3060,-3.09623170633779,57.6749832555664,126,1
+65,Gotaalv,50200,11.8492505614092,57.6828360778371,127,1
+117,Otra,3740,8.01017428212745,58.1458376145187,128,1
+199,Imsa,128,5.96522872944549,58.9043067821022,129,1
+82,Lagen,5554,10.0721873619662,59.0616969475376,130,1
+62,Glomma,42441,10.9472941736072,59.1951980847507,131,1
+47,Drammens,17000,10.1907153170446,59.7444235502165,132,1
+232,Orkla,3092,9.83229918245138,63.3120346309153,133,1
+233,Namsen,6000,11.6479711083682,64.4745955912813,134,1
+242,Vefsna,4122,13.1845419938346,65.8390195826313,135,1

data/input/atlanticarea/fishTryRealBV_CC.xml

+<list>
+	<species.DiadromousFishGroup>
+		<name>species A</name>
+		<color>
+			<red>255</red>
+			<green>0</green>
+			<blue>0</blue>
+			<alpha>255</alpha>
+		</color>
+
+		<dMaxDisp>300.0</dMaxDisp>
+
+		<nutrientRoutine>
+			<nutrientsOfInterest>
+				<string>N</string>
+				<string>P</string>
+			</nutrientsOfInterest>
+			<residenceTime>30.0</residenceTime>
+			<excretionRate class="hashtable">
+				<entry>
+					<string>P</string>
+					<double>2.17E-6</double>
+				</entry>
+				<entry>
+					<string>N</string>
+					<double>2.471E-5</double>
+				</entry>
+			</excretionRate>
+			<fishFeaturesPreSpawning class="hashtable">
+				<entry>
+					<species.DiadromousFish_-Gender>MALE</species.DiadromousFish_-Gender>
+					<hashtable>
+						<entry>
+							<string>bLW_Gonad</string>
+							<double>3.3838</double>
+						</entry>
+						<entry>
+							<string>aLW_Gonad</string>
+							<double>-8.8744</double>
+						</entry>
+						<entry>
+							<string>bLW</string>
+							<double>3.2252</double>
+						</entry>
+						<entry>
+							<string>aLW</string>
+							<double>0.004095817237891344</double>
+						</entry>
+					</hashtable>
+				</entry>
+				<entry>
+					<species.DiadromousFish_-Gender>FEMALE</species.DiadromousFish_-Gender>
+					<hashtable>
+						<entry>
+							<string>bLW_Gonad</string>
+							<double>2.6729</double>
+						</entry>
+						<entry>
+							<string>aLW_Gonad</string>
+							<double>-5.2425</double>
+						</entry>
+						<entry>
+							<string>bLW</string>
+							<double>3.3429</double>
+						</entry>
+						<entry>
+							<string>aLW</string>
+							<double>0.002665367811305362</double>
+						</entry>
+					</hashtable>
+				</entry>
+			</fishFeaturesPreSpawning>
+			<fishFeaturesPostSpawning class="hashtable">
+				<entry>
+					<species.DiadromousFish_-Gender>MALE</species.DiadromousFish_-Gender>
+					<hashtable>
+						<entry>
+							<string>bLW_Gonad</string>
+							<double>3.8331</double>
+						</entry>
+						<entry>
+							<string>aLW_Gonad</string>
+							<double>-11.285</double>
+						</entry>
+						<entry>
+							<string>bLW</string>
+							<double>2.9973</double>
+						</entry>
+						<entry>
+							<string>aLW</string>
+							<double>0.010383887012522573</double>
+						</entry>
+					</hashtable>
+				</entry>
+				<entry>
+					<species.DiadromousFish_-Gender>FEMALE</species.DiadromousFish_-Gender>
+					<hashtable>
+						<entry>
+							<string>bLW_Gonad</string>
+							<double>2.8545</double>
+						</entry>
+						<entry>
+							<string>aLW_Gonad</string>
+							<double>-6.6234</double>
+						</entry>
+						<entry>
+							<string>bLW</string>
+							<double>2.9418</double>
+						</entry>
+						<entry>
+							<string>aLW</string>
+							<double>0.013199187556948952</double>
+						</entry>
+					</hashtable>
+				</entry>
+			</fishFeaturesPostSpawning>
+			<juvenileFeatures class="hashtable">
+				<entry>
+					<string>bLW</string>
+					<double>3.0306</double>
+				</entry>
+				<entry>
+					<string>aLW</string>
+					<double>0.006986429759979109</double>
+				</entry>
+			</juvenileFeatures>
+			<compoCarcassPreSpawning class="hashtable">
+				<entry>
+					<species.DiadromousFish_-Gender>MALE</species.DiadromousFish_-Gender>
+					<hashtable>
+						<entry>
+							<string>P</string>
+							<double>0.00666</double>
+						</entry>
+						<entry>
+							<string>N</string>
+							<double>0.02941</double>
+						</entry>
+					</hashtable>
+				</entry>
+				<entry>
+					<species.DiadromousFish_-Gender>FEMALE</species.DiadromousFish_-Gender>
+					<hashtable>
+						<entry>
+							<string>P</string>
+							<double>0.006730000000000001</double>
+						</entry>
+						<entry>
+							<string>N</string>
+							<double>0.029580000000000002</double>
+						</entry>
+					</hashtable>
+				</entry>
+			</compoCarcassPreSpawning>
+			<compoGametes class="hashtable">
+				<entry>
+					<species.DiadromousFish_-Gender>MALE</species.DiadromousFish_-Gender>
+					<hashtable>
+						<entry>
+							<string>P</string>
+							<double>0.00724</double>
+						</entry>
+						<entry>
+							<string>N</string>
+							<double>0.0325</double>
+						</entry>
+					</hashtable>
+				</entry>
+				<entry>
+					<species.DiadromousFish_-Gender>FEMALE</species.DiadromousFish_-Gender>
+					<hashtable>
+						<entry>
+							<string>P</string>
+							<double>0.0032</double>
+						</entry>
+						<entry>
+							<string>N</string>
+							<double>0.03242</double>
+						</entry>
+					</hashtable>
+				</entry>
+			</compoGametes>
+			<compoJuvenile class="hashtable">
+				<entry>
+					<string>P</string>
+					<double>0.00887</double>
+				</entry>
+				<entry>
+					<string>N</string>
+					<double>0.02803</double>
+				</entry>
+			</compoJuvenile>
+		</nutrientRoutine>
+
+		<fileNameInputForInitialObservation>data/input/reality/Obs1900.csv</fileNameInputForInitialObservation>
+		<centileForRange>0.95</centileForRange>
+		<parameterSetfileName>data/input/reality/parameterSet.csv</parameterSetfileName>
+		<parameterSetLine>0</parameterSetLine>
+		<yearOfTheUpdate>0</yearOfTheUpdate>
+		<basinsToUpdateFile>data/input/reality/basinsToUpdate.csv</basinsToUpdateFile>
+		<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>
+		<lFirstMaturityForMale>40.0</lFirstMaturityForMale>
+		<processes>
+			<processesAtBegin>
+
+			</processesAtBegin>
+
+			<processesEachStep>
+				<environment.InformTime>
+					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
+					<consoleDisplay>true</consoleDisplay>
+				</environment.InformTime>
+
+				<species.PlopProcess>
+					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
+					<temporisation>0</temporisation>
+				</species.PlopProcess>
+
+				<species.PopulateBasinNetworkSeveralTimesAccordingToBasinSize>
+					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
+					<nbFishPerSI>100000</nbFishPerSI>
+					<initialLength>2.0</initialLength>
+					<etaPopulate>40.0</etaPopulate>
+					<timesOfPopulate>5</timesOfPopulate>
+					<populateSeason>SPRING</populateSeason>
+				</species.PopulateBasinNetworkSeveralTimesAccordingToBasinSize>
+
+				<species.Age>
+					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
+				</species.Age>
+
+				<species.Grow>
+					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
+					<tempMinGrow>3.0</tempMinGrow>
+					<tempMaxGrow>26.0</tempMaxGrow>
+					<tempOptGrow>17.0</tempOptGrow>
+					<kOptForFemale>0.3236</kOptForFemale>
+					<kOptForMale>0.2141</kOptForMale>
+					<sigmaDeltaLVonBert>0.2</sigmaDeltaLVonBert>
+				</species.Grow>
+
+				<species.DisperseAndMigrateToRiverWithMultiNomDistriAndDeathBasin>
+					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
+					<alpha0Rep>-2.9</alpha0Rep>
+					<alpha1Rep>19.7</alpha1Rep>
+					<alpha3Rep>0.0</alpha3Rep>
+					<meanBvSurface>17351</meanBvSurface>
+					<standardDeviationBvSurface>35594</standardDeviationBvSurface>
+					<meanInterDistance>300.0</meanInterDistance>
+					<standardDeviationInterDistance>978.0</standardDeviationInterDistance>
+					<pHomingForReachEquil>0.75</pHomingForReachEquil>
+					<pHomingAfterEquil>0.75</pHomingAfterEquil>
+					<NbYearForInstallPop>0</NbYearForInstallPop>
+					<riverMigrationSeason>SPRING</riverMigrationSeason>
+					<alpha2Rep>0.0</alpha2Rep>
+					<meanSpawnersLengthAtRepro>45.0</meanSpawnersLengthAtRepro>
+					<standardDeviationOfSpawnersLengthAtRepro>2.0</standardDeviationOfSpawnersLengthAtRepro>
+					<weightOfDeathBasin>0.4</weightOfDeathBasin>
+				</species.DisperseAndMigrateToRiverWithMultiNomDistriAndDeathBasin>
+
+				<species.Survive>
+					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
+					<tempMinSurvivalSpawnerInRiv>10.7</tempMinSurvivalSpawnerInRiv>
+					<tempOptSurvivalSpawnerInRiv>17.0</tempOptSurvivalSpawnerInRiv>
+					<tempMaxSurvivalSpawnerInRiv>25.7</tempMaxSurvivalSpawnerInRiv>
+					<survivalProbOptSpawnerInRiv>1.0</survivalProbOptSpawnerInRiv>
+					<!--<mortalityRateInRiver>0.4</mortalityRateInRiver> -->
+					<mortalityRateInSea>0.4</mortalityRateInSea>
+					<mortalityRateInOffshore>0.4</mortalityRateInOffshore>
+				</species.Survive>
+
+				<species.WriteEffectiveAndBiomassFluxes>
+					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
+					<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>
+					<eta>2.4</eta>
+					<ratioS95__S50>1.9</ratioS95__S50>
+					<a>270000</a>
+					<delta__t>0.33</delta__t>
+					<survOptRep>0.0017</survOptRep>
+					<lambda>4.1E-4</lambda>
+					<proportionOfFemaleAtBirth>0.5</proportionOfFemaleAtBirth>
+					<initialLength>2.0</initialLength>
+					<sigmaRecruitment>0.2</sigmaRecruitment>
+					<survivalRateAfterReproduction>0.1</survivalRateAfterReproduction>
+					<maxNumberOfSuperIndividualPerReproduction>500.0
+					</maxNumberOfSuperIndividualPerReproduction>
+					<withDiagnose>false</withDiagnose>
+					<displayFluxesOnConsole>false</displayFluxesOnConsole>
+				</species.ReproduceAndSurviveAfterReproductionWithDiagnose>
+
+				<species.MigrateToSea>
+					<seaMigrationSeason>SUMMER</seaMigrationSeason>
+					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
+					<displayFluxesOnConsole>false</displayFluxesOnConsole>
+				</species.MigrateToSea>
+
+				<environment.updateTemperatureInRealBasin>
+					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
+					<offshoreTemperature>12.0</offshoreTemperature>
+				</environment.updateTemperatureInRealBasin>
+			</processesEachStep>
+
+			<processesAtEnd>
+				<species.WriteNutrientImportFluxes>
+					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
+					<fileName>fluxes</fileName>
+				</species.WriteNutrientImportFluxes>
+
+				<species.WriteNutrientExportFluxes>
+					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
+					<fileName>nutrientExportFluxes</fileName>
+				</species.WriteNutrientExportFluxes>
+
+			</processesAtEnd>
+		</processes>
+		<useCemetery>false</useCemetery>
+	</species.DiadromousFishGroup>
+</list>

data/input/atlanticarea/obsRealAA.xml

+<hashtable>
+	<entry>
+		<java-class>fr.cemagref.simaqualife.kernel.AquaticWorld</java-class>
+		<fr.cemagref.observation.kernel.ObservablesHandler>
+			<observers>
+				<environment.BasinNetworkObserverWithContinent>
+					<title>Atlantic Area</title>
+					<threshold>10000</threshold>
+				</environment.BasinNetworkObserverWithContinent>
+
+			</observers>
+		</fr.cemagref.observation.kernel.ObservablesHandler>
+	</entry>
+<!--	<entry>
+		<java-class>species.DiadromousFishGroup</java-class>
+		<fr.cemagref.observation.kernel.ObservablesHandler>
+			<observers>
+				<fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
+					<graphType>LINE</graphType>
+					<title>Number of colonized basins</title>
+					<xAxisLabel>Time (season)</xAxisLabel>
+					<yAxisLabel>number of basins</yAxisLabel>
+					<variableName>getNbColonizedBasins</variableName>
+				</fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
+
+				<fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
+					<graphType>LINE</graphType>
+					<title>Total Abundance</title>
+					<xAxisLabel>Time (season)</xAxisLabel>
+					<yAxisLabel>number of fishes</yAxisLabel>
+					<variableName>getFishEffective</variableName>
+				</fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
+
+				<fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
+					<graphType>LINE</graphType>
+					<title>Abundance of spawners</title>
+					<xAxisLabel>Time (season)</xAxisLabel>
+					<yAxisLabel>number of fishes</yAxisLabel>
+					<variableName>getSpawnerEffective</variableName>
+				</fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
+
+				<fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
+					<graphType>LINE</graphType>
+					<title>Abundance of male spawners</title>
+					<xAxisLabel>Time (season)</xAxisLabel>
+					<yAxisLabel>number of fishes</yAxisLabel>
+					<variableName>getMaleSpawnerEffective</variableName>
+				</fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
+
+				<fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
+					<graphType>LINE</graphType>
+					<title>Abundance of female spawners</title>
+					<xAxisLabel>Time (season)</xAxisLabel>
+					<yAxisLabel>number of fishes</yAxisLabel>
+					<variableName>getFemaleSpawnerEffective</variableName>
+				</fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
+				
+				<miscellaneous.TemporalRangeSerieChart>
+					<title>Range distribution</title>
+					<xAxisLabel>Time (season)</xAxisLabel>
+					<yAxisLabel>latitude</yAxisLabel>
+					<variableName>getRangeDistributionWithLat</variableName>
+				</miscellaneous.TemporalRangeSerieChart>
+
+				<fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
+					<graphType>LINE</graphType>
+					<title>Mean age at first reproduction for female</title>
+					<xAxisLabel>Time (season)</xAxisLabel>
+					<yAxisLabel>age (year)</yAxisLabel>
+					<variableName>getMeanAgeOfFirstReprodutionForFemale</variableName>
+				</fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
+
+				<fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
+					<graphType>LINE</graphType>
+					<title>Mean age at first reproduction for male</title>
+					<xAxisLabel>Time (season)</xAxisLabel>
+					<yAxisLabel>age (year)</yAxisLabel>
+					<variableName>getMeanAgeOfFirstReprodutionForMale</variableName>
+				</fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
+
+
+				<fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
+					<graphType>LINE</graphType>
+					<title>Statistic for male spawners age</title>
+					<xAxisLabel>Time (season)</xAxisLabel>
+					<yAxisLabel></yAxisLabel>
+					<variableName>computeMaleSpawnerForFirstTimeSummaryStatistic</variableName>
+				</fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
+
+				<fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
+					<graphType>LINE</graphType>
+					<title>Statistic for female spawners age</title>
+					<xAxisLabel>Time (season)</xAxisLabel>
+					<yAxisLabel></yAxisLabel>
+					<variableName>computeFemaleSpawnerForFirstTimeSummaryStatistic</variableName>
+				</fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
+
+				<fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
+					<graphType>LINE</graphType>
+					<title>Mean length at first reproduction for female</title>
+					<xAxisLabel>Time (season)</xAxisLabel>
+					<yAxisLabel>length (cm)</yAxisLabel>
+					<variableName>getMeanLengthOfFirstReprodutionForFemale</variableName>
+				</fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
+
+				<fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
+					<graphType>LINE</graphType>
+					<title>Mean length at first reproduction for male</title>
+					<xAxisLabel>Time (season)</xAxisLabel>
+					<yAxisLabel>length (cm)</yAxisLabel>
+					<variableName>getMeanLengthOfFirstReprodutionForMale</variableName>
+				</fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
+
+			</observers>
+		</fr.cemagref.observation.kernel.ObservablesHandler>
+	</entry>
+	<entry>
+		<java-class>environment.RiverBasin</java-class>
+		<fr.cemagref.observation.kernel.ObservablesHandler>
+			<observers>
+				<miscellaneous.TemporalSerieChartForBasin>
+					<graphType>LINE</graphType>
+					<title>Number of juveniles</title>
+					<xAxisLabel>Time (season)</xAxisLabel>
+					<yAxisLabel>number of juveniles</yAxisLabel>
+					<variableName>getJuvenileNumber</variableName>
+				</miscellaneous.TemporalSerieChartForBasin>
+
+				<miscellaneous.TemporalSerieChartForBasin>
+					<graphType>LINE</graphType>
+					<title>% Autochtone</title>
+					<xAxisLabel>Time (season)</xAxisLabel>
+					<yAxisLabel>% Autochtone</yAxisLabel>
+					<variableName>getLastPercentageOfAutochtone</variableName>
+				</miscellaneous.TemporalSerieChartForBasin>
+
+			</observers>
+		</fr.cemagref.observation.kernel.ObservablesHandler>
+	</entry> -->
+</hashtable>
\ No newline at end of file

data/input/atlanticarea/shape/aa_continent.cpg

+UTF-8
\ No newline at end of file

data/input/atlanticarea/shape/aa_continent.prj

+GEOGCS["WGS 84",DATUM["WGS_1984",SPHEROID["WGS 84",6378137,298.257223563,AUTHORITY["EPSG","7030"]],AUTHORITY["EPSG","6326"]],PRIMEM["Greenwich",0,AUTHORITY["EPSG","8901"]],UNIT["degree",0.0174532925199433,AUTHORITY["EPSG","9122"]],AUTHORITY["EPSG","4326"]]
\ No newline at end of file

data/input/atlanticarea/shape/riverbasins.cpg

+UTF-8
\ No newline at end of file

data/input/atlanticarea/shape/riverbasins.prj

+GEOGCS["WGS 84",DATUM["WGS_1984",SPHEROID["WGS 84",6378137,298.257223563,AUTHORITY["EPSG","7030"]],AUTHORITY["EPSG","6326"]],PRIMEM["Greenwich",0,AUTHORITY["EPSG","8901"]],UNIT["degree",0.0174532925199433,AUTHORITY["EPSG","9122"]],AUTHORITY["EPSG","4326"]]
\ No newline at end of file

data/input/atlanticarea/shape/seabasins.cpg

+UTF-8
\ No newline at end of file

data/input/atlanticarea/shape/seabasins.prj

+GEOGCS["WGS 84",DATUM["WGS_1984",SPHEROID["WGS 84",6378137,298.257223563,AUTHORITY["EPSG","7030"]],AUTHORITY["EPSG","6326"]],PRIMEM["Greenwich",0,AUTHORITY["EPSG","8901"]],UNIT["degree",0.0174532925199433,AUTHORITY["EPSG","9122"]],AUTHORITY["EPSG","4326"]]
\ No newline at end of file