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>
-- 
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