From 2da3219be1be5ecd7084f753a621f589cbd954c0 Mon Sep 17 00:00:00 2001 From: "patrick.lambert" <patrick.mh.lambert@inrae.fr> Date: Wed, 17 Feb 2021 15:39:36 +0100 Subject: [PATCH] xml for Rjava use --- .../northeastamerica/RIOBNneaBasins_Rjava.xml | 29 ++ .../fishRIOBasin_Sapidissima_Rjava.xml | 340 ++++++++++++++++++ 2 files changed, 369 insertions(+) create mode 100644 data/input/northeastamerica/RIOBNneaBasins_Rjava.xml create mode 100644 data/input/northeastamerica/fishRIOBasin_Sapidissima_Rjava.xml diff --git a/data/input/northeastamerica/RIOBNneaBasins_Rjava.xml b/data/input/northeastamerica/RIOBNneaBasins_Rjava.xml new file mode 100644 index 0000000..4db6f79 --- /dev/null +++ b/data/input/northeastamerica/RIOBNneaBasins_Rjava.xml @@ -0,0 +1,29 @@ +<environment.RIOBasinNetworkWithContinent> + <memorySize>10</memorySize> + <memorySizeLongQueue>30</memorySizeLongQueue> + <cVthresholdForFinalStates>5.0</cVthresholdForFinalStates> + <RecruitmentThresholdForFsAndKappa>50.0</RecruitmentThresholdForFsAndKappa> + <yearOfTheBegin>1801</yearOfTheBegin> + + <riverBasinFile>data/input/northeastamerica/nea_riverbasins.csv</riverBasinFile> + <offshoreBasinFile>data/input/northeastamerica/nea_offshorebasins.csv</offshoreBasinFile> + + <continentShpFile></continentShpFile> + <riverBasinShpFile>data/input/northeastamerica/shape/riverbasins.shp</riverBasinShpFile> + <inshoreBasinShpFile>data/input/northeastamerica/shape/inshorebasins.shp</inshoreBasinShpFile> + <offshoreBasinShpFile>data/input/northeastamerica/shape/offshorebasins.shp</offshoreBasinShpFile> + <continentPathName>PATH</continentPathName> + <riverBasinNameLabel>BASIN_NAME</riverBasinNameLabel> + <inshoreBasinNameLabel>BASIN_NAME</inshoreBasinNameLabel> + <offshoreBasinNameLabel>BASIN_NAME</offshoreBasinNameLabel> + + + <distanceGridFileName>data/input/northeastamerica/distanceGridNEA.csv</distanceGridFileName> + <basinConnectionFileName>data/input/northeastamerica/inshore_offshore_connections.csv</basinConnectionFileName> + + <temperatureOffshoreFile>data/input/northeastamerica/observed_offshore_temperatures.csv</temperatureOffshoreFile> + <temperatureInshoreFile>data/input/northeastamerica/observed_inshore_temperatures.csv</temperatureInshoreFile> + <temperatureRiverFile>data/input/northeastamerica/observed_river_temperatures.csv</temperatureRiverFile> + + <useRealPDam>false</useRealPDam> +</environment.RIOBasinNetworkWithContinent> diff --git a/data/input/northeastamerica/fishRIOBasin_Sapidissima_Rjava.xml b/data/input/northeastamerica/fishRIOBasin_Sapidissima_Rjava.xml new file mode 100644 index 0000000..3925a60 --- /dev/null +++ b/data/input/northeastamerica/fishRIOBasin_Sapidissima_Rjava.xml @@ -0,0 +1,340 @@ +<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 class="species.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></fileNameInputForInitialObservation> + <centileForRange>0.95</centileForRange> + <parameterSetfileName></parameterSetfileName> + <parameterSetLine>0</parameterSetLine> + <yearOfTheUpdate>0</yearOfTheUpdate> + <basinsToUpdateFile></basinsToUpdateFile> + <outputPath>data/output/northeastamerica/</outputPath> + <minYearToWrite>1800</minYearToWrite> + <fileNameFluxes></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.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.WriteEffectiveAndBiomassImportFluxes> <synchronisationMode>ASYNCHRONOUS</synchronisationMode> <exportSeason>SPRING</exportSeason> + <fileNameOutput>effectiveBiomassFluxesBeforeReproduction</fileNameOutput> </species.WriteEffectiveAndBiomassImportFluxes> --> + + <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>false</displayFluxesOnConsole> + </species.MigrateFromRiverToInshore> + + <species.MigrateToOffshore> + <synchronisationMode>ASYNCHRONOUS</synchronisationMode> + <migrationSeasonToReachSummeringOffshore>SPRING</migrationSeasonToReachSummeringOffshore> + </species.MigrateToOffshore> + + <species.MigrateBetweenOffshores> + <synchronisationMode>ASYNCHRONOUS</synchronisationMode> + <migrationSeasonToReachWinteringOffshore>AUTOMN</migrationSeasonToReachWinteringOffshore> + <migrationSeasonToReachSummeringOffshore>SPRING</migrationSeasonToReachSummeringOffshore> + </species.MigrateBetweenOffshores> + + <environment.updateTemperatureInRIOBasin> + <synchronisationMode>ASYNCHRONOUS</synchronisationMode> + </environment.updateTemperatureInRIOBasin> + </processesEachStep> + + <processesAtEnd> + <species.WriteBiomassFluxes> + <synchronisationMode>ASYNCHRONOUS</synchronisationMode> + <exportSeason>SPRING</exportSeason> + <fileNameOutput>biomassFluxes</fileNameOutput> + </species.WriteBiomassFluxes> + </processesAtEnd> + </processes> + <useCemetery>false</useCemetery> + </species.DiadromousFishGroup> +</list> -- GitLab