Commit 6d62efb8 authored by Lambert Patrick's avatar Lambert Patrick
Browse files

Merge branch 'Camille_Bis' into patrick

parents 921b5964 0b050b0d
...@@ -297,7 +297,7 @@ ...@@ -297,7 +297,7 @@
<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>100.0
</maxNumberOfSuperIndividualPerReproduction> </maxNumberOfSuperIndividualPerReproduction>
<withDiagnose>false</withDiagnose> <withDiagnose>false</withDiagnose>
<displayFluxesOnConsole>false</displayFluxesOnConsole> <displayFluxesOnConsole>false</displayFluxesOnConsole>
......
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...@@ -201,10 +201,10 @@ ...@@ -201,10 +201,10 @@
<outputPath>data/output/</outputPath> <outputPath>data/output/</outputPath>
<minYearToWrite>1900</minYearToWrite> <minYearToWrite>1900</minYearToWrite>
<fileNameFluxes>nutrientFluxes</fileNameFluxes> <fileNameFluxes>nutrientFluxes</fileNameFluxes>
<lengthAtHatching>2.0</lengthAtHatching> <lengthAtHatching>2.8</lengthAtHatching>
<linfVonBertForFemale>70.0</linfVonBertForFemale> <linfVonBertForFemale>76.0</linfVonBertForFemale>
<linfVonBertForMale>70.0</linfVonBertForMale> <linfVonBertForMale>76.0</linfVonBertForMale>
<lFirstMaturityForFemale>55.0</lFirstMaturityForFemale> <lFirstMaturityForFemale>45.0</lFirstMaturityForFemale>
<lFirstMaturityForMale>40.0</lFirstMaturityForMale> <lFirstMaturityForMale>40.0</lFirstMaturityForMale>
<processes> <processes>
<processesAtBegin> <processesAtBegin>
...@@ -225,7 +225,7 @@ ...@@ -225,7 +225,7 @@
<species.PopulateBasinNetworkSeveralTimesAccordingToBasinSize> <species.PopulateBasinNetworkSeveralTimesAccordingToBasinSize>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode> <synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<nbFishPerSI>100000</nbFishPerSI> <nbFishPerSI>100000</nbFishPerSI>
<initialLength>2.0</initialLength> <initialLength>2.8</initialLength>
<etaPopulate>40.0</etaPopulate> <etaPopulate>40.0</etaPopulate>
<timesOfPopulate>5</timesOfPopulate> <timesOfPopulate>5</timesOfPopulate>
<populateSeason>SPRING</populateSeason> <populateSeason>SPRING</populateSeason>
...@@ -254,8 +254,8 @@ ...@@ -254,8 +254,8 @@
<standardDeviationBvSurface>35594</standardDeviationBvSurface> <standardDeviationBvSurface>35594</standardDeviationBvSurface>
<meanInterDistance>300.0</meanInterDistance> <meanInterDistance>300.0</meanInterDistance>
<standardDeviationInterDistance>978.0</standardDeviationInterDistance> <standardDeviationInterDistance>978.0</standardDeviationInterDistance>
<pHomingForReachEquil>0.75</pHomingForReachEquil> <pHomingForReachEquil>0.97</pHomingForReachEquil>
<pHomingAfterEquil>0.75</pHomingAfterEquil> <pHomingAfterEquil>0.97</pHomingAfterEquil>
<NbYearForInstallPop>0</NbYearForInstallPop> <NbYearForInstallPop>0</NbYearForInstallPop>
<riverMigrationSeason>SPRING</riverMigrationSeason> <riverMigrationSeason>SPRING</riverMigrationSeason>
<alpha2Rep>0.0</alpha2Rep> <alpha2Rep>0.0</alpha2Rep>
...@@ -266,9 +266,9 @@ ...@@ -266,9 +266,9 @@
<species.Survive> <species.Survive>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode> <synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<tempMinSurvivalSpawnerInRiv>10.7</tempMinSurvivalSpawnerInRiv> <tempMinSurvivalSpawnerInRiv>8</tempMinSurvivalSpawnerInRiv>
<tempOptSurvivalSpawnerInRiv>17.0</tempOptSurvivalSpawnerInRiv> <tempOptSurvivalSpawnerInRiv>17.0</tempOptSurvivalSpawnerInRiv>
<tempMaxSurvivalSpawnerInRiv>25.7</tempMaxSurvivalSpawnerInRiv> <tempMaxSurvivalSpawnerInRiv>26</tempMaxSurvivalSpawnerInRiv>
<survivalProbOptSpawnerInRiv>1.0</survivalProbOptSpawnerInRiv> <survivalProbOptSpawnerInRiv>1.0</survivalProbOptSpawnerInRiv>
<!--<mortalityRateInRiver>0.4</mortalityRateInRiver> --> <!--<mortalityRateInRiver>0.4</mortalityRateInRiver> -->
<mortalityRateInSea>0.4</mortalityRateInSea> <mortalityRateInSea>0.4</mortalityRateInSea>
...@@ -280,13 +280,13 @@ ...@@ -280,13 +280,13 @@
<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>
<tempMinRep>9.3</tempMinRep> <tempMinRep>10</tempMinRep>
<tempOptRep>20.8</tempOptRep> <tempOptRep>17</tempOptRep>
<tempMaxRep>31.0</tempMaxRep> <tempMaxRep>30</tempMaxRep>
<eta>2.4</eta> <eta>2.4</eta>
<ratioS95__S50>1.9</ratioS95__S50> <ratioS95__S50>1.9</ratioS95__S50>
<a>270000</a> <a>270000</a>
...@@ -294,10 +294,10 @@ ...@@ -294,10 +294,10 @@
<survOptRep>0.0017</survOptRep> <survOptRep>0.0017</survOptRep>
<lambda>4.1E-4</lambda> <lambda>4.1E-4</lambda>
<proportionOfFemaleAtBirth>0.5</proportionOfFemaleAtBirth> <proportionOfFemaleAtBirth>0.5</proportionOfFemaleAtBirth>
<initialLength>2.0</initialLength> <initialLength>2.8</initialLength>
<sigmaRecruitment>0.2</sigmaRecruitment> <sigmaRecruitment>0.2</sigmaRecruitment>
<survivalRateAfterReproduction>0.1</survivalRateAfterReproduction> <survivalRateAfterReproduction>0.1</survivalRateAfterReproduction>
<maxNumberOfSuperIndividualPerReproduction>500.0 <maxNumberOfSuperIndividualPerReproduction>150.0
</maxNumberOfSuperIndividualPerReproduction> </maxNumberOfSuperIndividualPerReproduction>
<withDiagnose>false</withDiagnose> <withDiagnose>false</withDiagnose>
<displayFluxesOnConsole>false</displayFluxesOnConsole> <displayFluxesOnConsole>false</displayFluxesOnConsole>
......
...@@ -396,16 +396,19 @@ public class BasinNetworkSWithContinent extends BasinNetwork { ...@@ -396,16 +396,19 @@ public class BasinNetworkSWithContinent extends BasinNetwork {
char[] charac = { '"' }; char[] charac = { '"' };
String doublequote = new String(charac); String doublequote = new String(charac);
scanner.nextLine(); // skip the first line with headers scanner.nextLine(); // skip the first line with headers
while (scanner.hasNext()) {
scanner.next(); // skip gid while (scanner.hasNextLine()) {
name = scanner.next(); String[] fields = scanner.nextLine().split(",");
// skip gid
name = fields[1];
name = name.replaceAll(new String(doublequote), ""); name = name.replaceAll(new String(doublequote), "");
year = (long) scanner.nextInt(); year = Long.valueOf (fields[2]);
Double[] seasonalTemperature = new Double[4]; Double[] seasonalTemperature = new Double[4];
seasonalTemperature[0] = scanner.nextDouble(); seasonalTemperature[0] = Double.valueOf(fields[3]);
seasonalTemperature[1] = scanner.nextDouble(); seasonalTemperature[1] = Double.valueOf(fields[4]);
seasonalTemperature[2] = scanner.nextDouble(); seasonalTemperature[2] = Double.valueOf(fields[5]);
seasonalTemperature[3] = scanner.nextDouble(); seasonalTemperature[3] = Double.valueOf(fields[6]);
// scanner.nextLine(); // scanner.nextLine();
// store seasonal temperatures for each basin for the // store seasonal temperatures for each basin for the
......
...@@ -57,7 +57,7 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG ...@@ -57,7 +57,7 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
private double tempOptRep = 20. ; private double tempOptRep = 20. ;
private double eta = 2.4; // parameter linking surface of a basin and S_etoile private double eta = 2.4; // parameter linking surface of a basin and S_etoile
private double ratioS95_S50 = 2.; private double ratioS95_S50 = 2.;
private double a=135000.; // Parameter of fecndity (number of eggs per individual) private double a=270000.; // Parameter of fecndity (number of eggs per individual) Modifié depuis la valeur initial de tHibault, qui était 135000
private double delta_t=0.33; // duration of the mortality considered in the reproduction process (ex.: from eggs to juvenile in estuary for alosa alosa = 0.33) private double delta_t=0.33; // duration of the mortality considered in the reproduction process (ex.: from eggs to juvenile in estuary for alosa alosa = 0.33)
private double survOptRep = 0.0017; private double survOptRep = 0.0017;
private double lambda = 0.00041; private double lambda = 0.00041;
......
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