diff --git a/data/input/northeastamerica/fishRIOBasin_Sapidissima.xml b/data/input/northeastamerica/fishRIOBasin_Sapidissima.xml new file mode 100644 index 0000000000000000000000000000000000000000..e51e5c142a32b5e462f953618b402cc31281b72d --- /dev/null +++ b/data/input/northeastamerica/fishRIOBasin_Sapidissima.xml @@ -0,0 +1,350 @@ +<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/northeastamerica/</outputPath> + <minYearToWrite>1900</minYearToWrite> + <fileNameFluxes>nutrientFluxes</fileNameFluxes> + <lengthAtHatching>2.8</lengthAtHatching> + <linfVonBertForFemale>76.0</linfVonBertForFemale> + <linfVonBertForMale>76.0</linfVonBertForMale> + <lFirstMaturityForFemale>45.0</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>2.8</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.MigrateBetweenOffshores> + <synchronisationMode>ASYNCHRONOUS</synchronisationMode> + <migrationSeasonToReachWinteringOffshore>AUTOMN</migrationSeasonToReachWinteringOffshore> + <migrationSeasonToReachSummeringOffshore>SPRING</migrationSeasonToReachSummeringOffshore> + </species.MigrateBetweenOffshores> + + <species.MigrateFromOffshoreToInshore> + <synchronisationMode>ASYNCHRONOUS</synchronisationMode> + <migrationSeasonToReachInshore>SPRING</migrationSeasonToReachInshore> + </species.MigrateFromOffshoreToInshore> + + <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>0.97</pHomingForReachEquil> + <pHomingAfterEquil>0.97</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>8</tempMinSurvivalSpawnerInRiv> + <tempOptSurvivalSpawnerInRiv>17.0</tempOptSurvivalSpawnerInRiv> + <tempMaxSurvivalSpawnerInRiv>26</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>10</tempMinRep> + <tempOptRep>17</tempOptRep> + <tempMaxRep>30</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>2.8</initialLength> + <sigmaRecruitment>0.2</sigmaRecruitment> + <survivalRateAfterReproduction>0.1</survivalRateAfterReproduction> + <maxNumberOfSuperIndividualPerReproduction>100.0 + </maxNumberOfSuperIndividualPerReproduction> + <withDiagnose>false</withDiagnose> + <displayFluxesOnConsole>false</displayFluxesOnConsole> + </species.ReproduceAndSurviveAfterReproductionWithDiagnose> + + <species.MigrateFromRiverToInshore> + <synchronisationMode>ASYNCHRONOUS</synchronisationMode> + <migrationSeasonToReachInshore>SPRING</migrationSeasonToReachInshore> + <displayFluxesOnConsole>true</displayFluxesOnConsole> + + </species.MigrateFromRiverToInshore> + + <species.MigrateToOffshore> + <synchronisationMode>ASYNCHRONOUS</synchronisationMode> + <migrationSeasonToReachSummeringOffshore>SPRING</migrationSeasonToReachSummeringOffshore> + </species.MigrateToOffshore> + + <environment.updateTemperatureInRealBasin> + <synchronisationMode>ASYNCHRONOUS</synchronisationMode> + <offshoreTemperature>12.0</offshoreTemperature> + </environment.updateTemperatureInRealBasin> + </processesEachStep> + + <processesAtEnd> + <species.WriteNutrientImportFluxes> + <synchronisationMode>ASYNCHRONOUS</synchronisationMode> + <fileName>nutrientImportfFluxes</fileName> + </species.WriteNutrientImportFluxes> + + <species.WriteNutrientExportFluxes> + <synchronisationMode>ASYNCHRONOUS</synchronisationMode> + <fileName>nutrientExportFluxes</fileName> + </species.WriteNutrientExportFluxes> + + </processesAtEnd> + </processes> + <useCemetery>false</useCemetery> + </species.DiadromousFishGroup> +</list> diff --git a/data/input/northeastamerica/fishTryRealBV_CC_Sapidissima.xml b/data/input/northeastamerica/old_fishTryRealBV_CC_Sapidissima.xml similarity index 96% rename from data/input/northeastamerica/fishTryRealBV_CC_Sapidissima.xml rename to data/input/northeastamerica/old_fishTryRealBV_CC_Sapidissima.xml index 742a5344dbe9a9f06b43a6109aadd9a04c2fdc45..5957c7baefccebcba2463cd1e40769dfcc1c7869 100644 --- a/data/input/northeastamerica/fishTryRealBV_CC_Sapidissima.xml +++ b/data/input/northeastamerica/old_fishTryRealBV_CC_Sapidissima.xml @@ -1,333 +1,333 @@ -<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/northeastamerica/</outputPath> - <minYearToWrite>1900</minYearToWrite> - <fileNameFluxes>nutrientFluxes</fileNameFluxes> - <lengthAtHatching>2.8</lengthAtHatching> - <linfVonBertForFemale>76.0</linfVonBertForFemale> - <linfVonBertForMale>76.0</linfVonBertForMale> - <lFirstMaturityForFemale>45.0</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>2.8</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>0.97</pHomingForReachEquil> - <pHomingAfterEquil>0.97</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>8</tempMinSurvivalSpawnerInRiv> - <tempOptSurvivalSpawnerInRiv>17.0</tempOptSurvivalSpawnerInRiv> - <tempMaxSurvivalSpawnerInRiv>26</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>10</tempMinRep> - <tempOptRep>17</tempOptRep> - <tempMaxRep>30</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>2.8</initialLength> - <sigmaRecruitment>0.2</sigmaRecruitment> - <survivalRateAfterReproduction>0.1</survivalRateAfterReproduction> - <maxNumberOfSuperIndividualPerReproduction>100.0 - </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>nutrientImportfFluxes</fileName> - </species.WriteNutrientImportFluxes> - - <species.WriteNutrientExportFluxes> - <synchronisationMode>ASYNCHRONOUS</synchronisationMode> - <fileName>nutrientExportFluxes</fileName> - </species.WriteNutrientExportFluxes> - - </processesAtEnd> - </processes> - <useCemetery>false</useCemetery> - </species.DiadromousFishGroup> -</list> +<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/northeastamerica/</outputPath> + <minYearToWrite>1900</minYearToWrite> + <fileNameFluxes>nutrientFluxes</fileNameFluxes> + <lengthAtHatching>2.8</lengthAtHatching> + <linfVonBertForFemale>76.0</linfVonBertForFemale> + <linfVonBertForMale>76.0</linfVonBertForMale> + <lFirstMaturityForFemale>45.0</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>2.8</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>0.97</pHomingForReachEquil> + <pHomingAfterEquil>0.97</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>8</tempMinSurvivalSpawnerInRiv> + <tempOptSurvivalSpawnerInRiv>17.0</tempOptSurvivalSpawnerInRiv> + <tempMaxSurvivalSpawnerInRiv>26</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>10</tempMinRep> + <tempOptRep>17</tempOptRep> + <tempMaxRep>30</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>2.8</initialLength> + <sigmaRecruitment>0.2</sigmaRecruitment> + <survivalRateAfterReproduction>0.1</survivalRateAfterReproduction> + <maxNumberOfSuperIndividualPerReproduction>100.0 + </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>nutrientImportfFluxes</fileName> + </species.WriteNutrientImportFluxes> + + <species.WriteNutrientExportFluxes> + <synchronisationMode>ASYNCHRONOUS</synchronisationMode> + <fileName>nutrientExportFluxes</fileName> + </species.WriteNutrientExportFluxes> + + </processesAtEnd> + </processes> + <useCemetery>false</useCemetery> + </species.DiadromousFishGroup> +</list>