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