Commit b2fa60b6 authored by Poulet Camille's avatar Poulet Camille
Browse files

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

parents 436afde3 b7a07c60
......@@ -13,6 +13,6 @@
<seaBasinNameLabel>BASIN_NAME</seaBasinNameLabel>
<continentPathName>ID</continentPathName>
<distanceGridFileName>data/input/atlanticarea/distanceGridAA.csv</distanceGridFileName>
<temperatureCatchmentFile>data/input/atlanticarea/aa_sst_depuis1800.csv</temperatureCatchmentFile>
<temperatureCatchmentFile>data/input/atlanticarea/aa_sst_histo.csv</temperatureCatchmentFile>
<useRealPDam>false</useRealPDam>
</environment.BasinNetworkSWithContinent>
\ No newline at end of file
......@@ -19,11 +19,11 @@
<excretionRate class="hashtable">
<entry>
<string>P</string>
<double>2.17E-6</double>
<double>5.208E-5</double>
</entry>
<entry>
<string>N</string>
<double>2.471E-5</double>
<double>5.9304E-4</double>
</entry>
</excretionRate>
<fishFeaturesPreSpawning class="hashtable">
......@@ -280,7 +280,7 @@
<exportSeason>SPRING</exportSeason>
<fileNameOutput>effectiveBiomassFluxesBeforeReproduction</fileNameOutput>
</species.WriteEffectiveAndBiomassFluxes>
<species.ReproduceAndSurviveAfterReproductionWithDiagnose>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<reproductionSeason>SPRING</reproductionSeason>
......@@ -297,11 +297,17 @@
<initialLength>2.0</initialLength>
<sigmaRecruitment>0.2</sigmaRecruitment>
<survivalRateAfterReproduction>0.1</survivalRateAfterReproduction>
<maxNumberOfSuperIndividualPerReproduction>500.0</maxNumberOfSuperIndividualPerReproduction>
<maxNumberOfSuperIndividualPerReproduction>100.0</maxNumberOfSuperIndividualPerReproduction>
<withDiagnose>false</withDiagnose>
<displayFluxesOnConsole>false</displayFluxesOnConsole>
</species.ReproduceAndSurviveAfterReproductionWithDiagnose>
<species.WriteEffectiveAndBiomassFluxes>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<exportSeason>SPRING</exportSeason>
<fileNameOutput>effectiveBiomassFluxesAfterReproduction</fileNameOutput>
</species.WriteEffectiveAndBiomassFluxes>
<species.MigrateToSea>
<seaMigrationSeason>SUMMER</seaMigrationSeason>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
......
......@@ -198,7 +198,7 @@
<parameterSetLine>0</parameterSetLine>
<yearOfTheUpdate>0</yearOfTheUpdate>
<basinsToUpdateFile>data/input/reality/basinsToUpdate.csv</basinsToUpdateFile>
<outputPath>data/output/</outputPath>
<outputPath>data/output/northeastamerica/</outputPath>
<minYearToWrite>1900</minYearToWrite>
<fileNameFluxes>nutrientFluxes</fileNameFluxes>
<lengthAtHatching>2.8</lengthAtHatching>
......@@ -297,7 +297,7 @@
<initialLength>2.8</initialLength>
<sigmaRecruitment>0.2</sigmaRecruitment>
<survivalRateAfterReproduction>0.1</survivalRateAfterReproduction>
<maxNumberOfSuperIndividualPerReproduction>150.0
<maxNumberOfSuperIndividualPerReproduction>100.0
</maxNumberOfSuperIndividualPerReproduction>
<withDiagnose>false</withDiagnose>
<displayFluxesOnConsole>false</displayFluxesOnConsole>
......@@ -318,7 +318,7 @@
<processesAtEnd>
<species.WriteNutrientImportFluxes>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<fileName>fluxes</fileName>
<fileName>nutrientImportfFluxes</fileName>
</species.WriteNutrientImportFluxes>
<species.WriteNutrientExportFluxes>
......
......@@ -89,10 +89,10 @@ public class DiadromousFishGroup extends AquaNismsGroup<DiadromousFish, BasinNet
private long yearOfTheUpdate;
/**
* list of the basins to be updated column 1: name of the basin column 2: Pattractive: how the bassin become
* attractive (0 not attractive, 1 ??? normal weight associated to catchment size) column 3: Paccessible: how the
* bassin become acesssible (0 not accessible, 1 ???normal weight to inter catchment distance )
*
* list of the basins to be updated
* column 1: name of the basin
* column 2: Pattractive: how the bassin become attractive (0 not attractive, 1 ??? normal weight associated to catchment size)
* column 3: Paccessible: how the bassin become acesssible (0 not accessible, 1 ???normal weight to inter catchment distance )
* @unit
*/
private String basinsToUpdateFile = "data/input/reality/basinsToUpdate.csv";
......@@ -108,33 +108,38 @@ public class DiadromousFishGroup extends AquaNismsGroup<DiadromousFish, BasinNet
private transient String sep;
/**
* map <key> basin name <value> Duo <first> pAttractive <second> pAccessible
*
* map
* <key> basin name
* <value> Duo
* <first> pAttractive
* <second> pAccessible
* @unit
*/
private transient Map<String, Duo<Double, Double>> basinsToUpdate;
/**
* length when fish hatchs ( when the diadromousFish is created after reproduction) no diffrence between gender
* length when fish hatchs (when the diadromousFish is created after reproduction) no diffrence between gender
*
* @unit cm
*/
private double lengthAtHatching = 2.;
/**
* L infinity of the van Bertalanffy growth curve for female L = Linf *(1-exp(-K*(t-t0))
*
* L infinity of the van Bertalanffy growth curve for female
* L = Linf *(1-exp(-K*(t-t0))
* @unit cm
*/
public double linfVonBertForFemale = 60.;
/**
* L infinity of the van Bertalanffy growth curve for male L = Linf *(1-exp(-K*(t-t0))
*
* L infinity of the van Bertalanffy growth curve for male
* L = Linf *(1-exp(-K*(t-t0))
*
* @unit cm
*/
public double linfVonBertForMale = 60.;
/**
* Brody growth coefficient of the von Bertalanffy growth curve for female (calculated from the parameterset file) *
* L = Linf *(1-exp(-K*(t-t0))
......@@ -199,11 +204,9 @@ public class DiadromousFishGroup extends AquaNismsGroup<DiadromousFish, BasinNet
double aResidenceTime = 30;
Map<String, Double> anExcretionRate = new Hashtable<String, Double>();
anExcretionRate.put("N", 24.71E-6); // values from Barber et al, Alosa sapidissima in ug/g wet mass/hour :
// convertit en g
anExcretionRate.put("P", 2.17E-6); // values from Barber et al, Alosa sapidissima in ug/g wet mass/hour:
// convertit en g
Map <String, Double> anExcretionRate = new Hashtable <String, Double>();
anExcretionRate.put("N", 24.71E-6 * 24); //values from Barber et al, Alosa sapidissima in ug/g wet mass/hour : convertit en g
anExcretionRate.put("P", 2.17E-6 * 24); //values from Barber et al, Alosa sapidissima in ug/g wet mass/hour: convertit en g
/*
* A feature pre spawning
......@@ -508,11 +511,6 @@ public class DiadromousFishGroup extends AquaNismsGroup<DiadromousFish, BasinNet
}
}
/*
* while (scanner.hasNext()) { scanner.next(); // skip basin_id String basin_name = scanner.next(); String
* obs = scanner.next(); scanner.next(); // skip obs_1851_1950, scanner.next(); // skip obs_1951_2010 if
* (obs != null) obs1900.put(basin_name, Integer.valueOf(obs)); }
*/
reader.close();
scanner.close();
......
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