Commit 3f1bc7ea authored by Poulet Camille's avatar Poulet Camille
Browse files

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

parents 7ef602b5 1b615869
<<<<<<< HEAD
output
.settings
.classpath
.project
/bin/
/target/
=======
.settings
.classpath
.project
......@@ -92,3 +101,4 @@ target
.project
org.*
/src/main/java/miscellaneous/Essai.java
>>>>>>> master
<list>
<species.DiadromousFishGroup>
<name>species A</name>
<color>
<red>255</red>
<green>0</green>
<blue>0</blue>
<alpha>255</alpha>
</color>
<linfVonBert>60.0</linfVonBert>
<dMaxDisp>0.0</dMaxDisp>
<lFirstMaturity>40.0</lFirstMaturity>
<fileNameInputForInitialObservation>data/input/reality/Obs1900.csv</fileNameInputForInitialObservation>
<species.DiadromousFishGroup>
<name>species A</name>
<color>
<red>255</red>
<green>0</green>
<blue>0</blue>
<alpha>255</alpha>
</color>
<processes>
<processesAtBegin>
<species.PopulateBasinNetworkWithANorthLimit>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<nbSIPerBasin>200</nbSIPerBasin>
<initialLength>2.0</initialLength>
<nbFishPerSI>2500</nbFishPerSI>
<northLimitLatitude>43.54</northLimitLatitude>
</species.PopulateBasinNetworkWithANorthLimit>
</processesAtBegin>
<dMaxDisp>300.0</dMaxDisp>
<processesEachStep>
<environment.InformTime>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
</environment.InformTime>
<species.PlopProcess>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<temporisation>0</temporisation>
</species.PlopProcess>
<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>
<compoCarcassPostSpawning class="hashtable">
<entry>
<species.DiadromousFish_-Gender>MALE</species.DiadromousFish_-Gender>
<hashtable>
<entry>
<string>P</string>
<double>0.00961</double>
</entry>
<entry>
<string>N</string>
<double>0.0279</double>
</entry>
</hashtable>
</entry>
<entry>
<species.DiadromousFish_-Gender>FEMALE</species.DiadromousFish_-Gender>
<hashtable>
<entry>
<string>P</string>
<double>0.00997</double>
</entry>
<entry>
<string>N</string>
<double>0.03216</double>
</entry>
</hashtable>
</entry>
</compoCarcassPostSpawning>
<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>
<species.Age>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
</species.Age>
<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>
<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>
<species.PopulateBasinNetwork>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<nbSIPerBasin>200</nbSIPerBasin>
<initialLength>20.0</initialLength>
<nbFishPerSI>2500</nbFishPerSI>
</species.PopulateBasinNetwork>
</processesAtBegin>
<species.Grow>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<tempMinGrow>3.0</tempMinGrow>
<tempMaxGrow>26.0</tempMaxGrow>
<tempOptGrow>17.0</tempOptGrow>
<kOpt>0.3900707</kOpt>
<sigmaDeltaLVonBert>0.2</sigmaDeltaLVonBert>
</species.Grow>
<processesEachStep>
<environment.InformTime>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
</environment.InformTime>
<species.PlopProcess>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<temporisation>0</temporisation>
</species.PlopProcess>
<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.Age>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
</species.Age>
<species.Survive>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<tempMinMortGenInRiv>10.0</tempMinMortGenInRiv>
<tempMaxMortGenInRiv>23.0</tempMaxMortGenInRiv>
<tempOptMortGenInRiv>20.0</tempOptMortGenInRiv>
<survivalProbOptGenInRiv>1.0</survivalProbOptGenInRiv>
<mortalityRateInRiver>0.4</mortalityRateInRiver>
<mortalityRateInSea>0.4</mortalityRateInSea>
<mortalityRateInOffshore>0.4</mortalityRateInOffshore>
</species.Survive>
<species.Grow>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<tempMinGrow>3.0</tempMinGrow>
<tempMaxGrow>26.0</tempMaxGrow>
<tempOptGrow>17.0</tempOptGrow>
<kOptForFemale>0.20323011454056628</kOptForFemale>
<kOptForMale>0.3004992503785338</kOptForMale>
<sigmaDeltaLVonBert>0.2</sigmaDeltaLVonBert>
</species.Grow>
<species.ReproduceAndSurviveAfterReproduction>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<reproductionSeason>SPRING</reproductionSeason>
<tempMinRep>9.846984</tempMinRep>
<tempMaxRep>26.0</tempMaxRep>
<tempOptRep>20.0</tempOptRep>
<eta>2.4</eta>
<ratioS95__S50>1.9</ratioS95__S50>
<a>135000.0</a>
<delta__t>0.33</delta__t>
<survOptRep>0.0017</survOptRep>
<lambda>4.1E-4</lambda>
<initialLength>2.0</initialLength>
<sigmaRecruitment>0.2</sigmaRecruitment>
<survivalRateAfterReproduction>0.1</survivalRateAfterReproduction>
<maxNumberOfSuperIndividualPerReproduction>50.0
</maxNumberOfSuperIndividualPerReproduction>
</species.ReproduceAndSurviveAfterReproduction>
<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.MigrateToSea>
<seaMigrationSeason>SUMMER</seaMigrationSeason>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
</species.MigrateToSea>
<species.Survive>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<tempMinMortGenInRiv>10.0</tempMinMortGenInRiv>
<tempMaxMortGenInRiv>23.0</tempMaxMortGenInRiv>
<tempOptMortGenInRiv>20.0</tempOptMortGenInRiv>
<survivalProbOptGenInRiv>1.0</survivalProbOptGenInRiv>
<mortalityRateInRiver>0.4</mortalityRateInRiver>
<mortalityRateInSea>0.4</mortalityRateInSea>
<mortalityRateInOffshore>0.4</mortalityRateInOffshore>
</species.Survive>
<environment.updateTemperatureInRealBasin>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<offshoreTemperature>12.0</offshoreTemperature>
</environment.updateTemperatureInRealBasin>
</processesEachStep>
<species.ExportFluxes>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<exportSeason>SPRING</exportSeason>
<fileNameOutput>EffectiveFluxes</fileNameOutput>
</species.ExportFluxes>
<processesAtEnd>
<species.IdentifyPopulation>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
</species.IdentifyPopulation>
<species.TypeTrajectoryCV>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<fileNameOutput>data/output/JeuParam100_2100RCP85_A
</fileNameOutput>
</species.TypeTrajectoryCV>
<species.ExportBiomass>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<survivalRateAfterReproduction>0.1</survivalRateAfterReproduction>
<exportSeason>SPRING</exportSeason>
<fileNameOutput>BiomassFluxes</fileNameOutput>
</species.ExportBiomass>
</processesAtEnd>
</processes>
<useCemetery>false</useCemetery>
</species.DiadromousFishGroup>
</list>
\ No newline at end of file
<species.ReproduceAndSurviveAfterReproductionWithDiagnose>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<reproductionSeason>SPRING</reproductionSeason>
<tempMinRep>10.443039492695249</tempMinRep>
<tempMaxRep>26.0</tempMaxRep>
<tempOptRep>20.0</tempOptRep>
<eta>2.4</eta>
<ratioS95__S50>1.9</ratioS95__S50>
<a>135000.0</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>50.0
</maxNumberOfSuperIndividualPerReproduction>
<withDiagnose>false</withDiagnose>
<displayFluxesOnConsole>true</displayFluxesOnConsole>
</species.ReproduceAndSurviveAfterReproductionWithDiagnose>
<species.MigrateToSea>
<seaMigrationSeason>SUMMER</seaMigrationSeason>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<displayFluxesOnConsole>true</displayFluxesOnConsole>
</species.MigrateToSea>
<environment.updateTemperatureInRealBasin>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<offshoreTemperature>12.0</offshoreTemperature>
</environment.updateTemperatureInRealBasin>
</processesEachStep>
<processesAtEnd>
<species.IdentifyPopulation>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<consoleDisplay>false</consoleDisplay>
<fluxesSeason>SPRING</fluxesSeason>
<years>
<long>2000</long>
<long>2100</long>
</years>
<fileNameOutput>JeuParam100_2100RCP85_A_essai</fileNameOutput>
</species.IdentifyPopulation>
<species.TypeTrajectoryCV>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<fileNameOutput>JeuParam100_2100RCP85_A_essai</fileNameOutput>
</species.TypeTrajectoryCV>
</processesAtEnd>
</processes>
<useCemetery>false</useCemetery>
</species.DiadromousFishGroup>
</list>
......@@ -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>
......
<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>
<linfVonBertForFemale>70.0</linfVonBertForFemale>
<linfVonBertForMale>70.0</linfVonBertForMale>
<lFirstMaturityForFemale>55.0</lFirstMaturityForFemale>
<lFirstMaturityForMale>40.0</lFirstMaturityForMale>
<lengthAtHatching>2</lengthAtHatching>
<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>2.1774</double>
</entry>
<entry>
<string>aLW</string>
<double>0.27144384321211973</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>3.147</double>
</entry>
<entry>
<string>aLW</string>
<double>0.007388725660209693</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>