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SimAquaLife
GR3D
Commits
2da3219b
Commit
2da3219b
authored
Feb 17, 2021
by
patrick.lambert
Browse files
xml for Rjava use
parent
69b9ba2f
Changes
2
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data/input/northeastamerica/RIOBNneaBasins_Rjava.xml
0 → 100644
View file @
2da3219b
<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>
data/input/northeastamerica/fishRIOBasin_Sapidissima_Rjava.xml
0 → 100644
View file @
2da3219b
<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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