Commit b0b5c752 authored by Poulet Camille's avatar Poulet Camille
Browse files

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

parents 38d7b8a1 6d62efb8
......@@ -297,7 +297,7 @@
<initialLength>2.0</initialLength>
<sigmaRecruitment>0.2</sigmaRecruitment>
<survivalRateAfterReproduction>0.1</survivalRateAfterReproduction>
<maxNumberOfSuperIndividualPerReproduction>500.0
<maxNumberOfSuperIndividualPerReproduction>100.0
</maxNumberOfSuperIndividualPerReproduction>
<withDiagnose>false</withDiagnose>
<displayFluxesOnConsole>false</displayFluxesOnConsole>
......
......@@ -10,7 +10,7 @@
<riverBasinShpFile>data/input/northeastamerica/shape/riverbasins.shp</riverBasinShpFile>
<continentShpFile>data/input/northeastamerica/shape/nea_continent.shp</continentShpFile>
<riverBasinNameLabel>NAME</riverBasinNameLabel>
<seaBasinNameLabel>name</seaBasinNameLabel>
<seaBasinNameLabel>NAME</seaBasinNameLabel>
<continentPathName>PATH</continentPathName>
<distanceGridFileName>data/input/northeastamerica/distanceGridNEA.csv</distanceGridFileName>
<temperatureCatchmentFile>data/input/northeastamerica/basins_temperatures_from_1800.csv</temperatureCatchmentFile>
......
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......@@ -201,10 +201,10 @@
<outputPath>data/output/</outputPath>
<minYearToWrite>1900</minYearToWrite>
<fileNameFluxes>nutrientFluxes</fileNameFluxes>
<lengthAtHatching>2.0</lengthAtHatching>
<linfVonBertForFemale>70.0</linfVonBertForFemale>
<linfVonBertForMale>70.0</linfVonBertForMale>
<lFirstMaturityForFemale>55.0</lFirstMaturityForFemale>
<lengthAtHatching>2.8</lengthAtHatching>
<linfVonBertForFemale>76.0</linfVonBertForFemale>
<linfVonBertForMale>76.0</linfVonBertForMale>
<lFirstMaturityForFemale>45.0</lFirstMaturityForFemale>
<lFirstMaturityForMale>40.0</lFirstMaturityForMale>
<processes>
<processesAtBegin>
......@@ -225,7 +225,7 @@
<species.PopulateBasinNetworkSeveralTimesAccordingToBasinSize>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<nbFishPerSI>100000</nbFishPerSI>
<initialLength>2.0</initialLength>
<initialLength>2.8</initialLength>
<etaPopulate>40.0</etaPopulate>
<timesOfPopulate>5</timesOfPopulate>
<populateSeason>SPRING</populateSeason>
......@@ -254,8 +254,8 @@
<standardDeviationBvSurface>35594</standardDeviationBvSurface>
<meanInterDistance>300.0</meanInterDistance>
<standardDeviationInterDistance>978.0</standardDeviationInterDistance>
<pHomingForReachEquil>0.75</pHomingForReachEquil>
<pHomingAfterEquil>0.75</pHomingAfterEquil>
<pHomingForReachEquil>0.97</pHomingForReachEquil>
<pHomingAfterEquil>0.97</pHomingAfterEquil>
<NbYearForInstallPop>0</NbYearForInstallPop>
<riverMigrationSeason>SPRING</riverMigrationSeason>
<alpha2Rep>0.0</alpha2Rep>
......@@ -266,9 +266,9 @@
<species.Survive>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<tempMinSurvivalSpawnerInRiv>10.7</tempMinSurvivalSpawnerInRiv>
<tempMinSurvivalSpawnerInRiv>8</tempMinSurvivalSpawnerInRiv>
<tempOptSurvivalSpawnerInRiv>17.0</tempOptSurvivalSpawnerInRiv>
<tempMaxSurvivalSpawnerInRiv>25.7</tempMaxSurvivalSpawnerInRiv>
<tempMaxSurvivalSpawnerInRiv>26</tempMaxSurvivalSpawnerInRiv>
<survivalProbOptSpawnerInRiv>1.0</survivalProbOptSpawnerInRiv>
<!--<mortalityRateInRiver>0.4</mortalityRateInRiver> -->
<mortalityRateInSea>0.4</mortalityRateInSea>
......@@ -280,13 +280,13 @@
<exportSeason>SPRING</exportSeason>
<fileNameOutput>effectiveBiomassFluxesBeforeReproduction</fileNameOutput>
</species.WriteEffectiveAndBiomassFluxes>
<species.ReproduceAndSurviveAfterReproductionWithDiagnose>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<reproductionSeason>SPRING</reproductionSeason>
<tempMinRep>9.3</tempMinRep>
<tempOptRep>20.8</tempOptRep>
<tempMaxRep>31.0</tempMaxRep>
<tempMinRep>10</tempMinRep>
<tempOptRep>17</tempOptRep>
<tempMaxRep>30</tempMaxRep>
<eta>2.4</eta>
<ratioS95__S50>1.9</ratioS95__S50>
<a>270000</a>
......@@ -294,10 +294,10 @@
<survOptRep>0.0017</survOptRep>
<lambda>4.1E-4</lambda>
<proportionOfFemaleAtBirth>0.5</proportionOfFemaleAtBirth>
<initialLength>2.0</initialLength>
<initialLength>2.8</initialLength>
<sigmaRecruitment>0.2</sigmaRecruitment>
<survivalRateAfterReproduction>0.1</survivalRateAfterReproduction>
<maxNumberOfSuperIndividualPerReproduction>500.0
<maxNumberOfSuperIndividualPerReproduction>150.0
</maxNumberOfSuperIndividualPerReproduction>
<withDiagnose>false</withDiagnose>
<displayFluxesOnConsole>false</displayFluxesOnConsole>
......
......@@ -396,16 +396,19 @@ public class BasinNetworkSWithContinent extends BasinNetwork {
char[] charac = { '"' };
String doublequote = new String(charac);
scanner.nextLine(); // skip the first line with headers
while (scanner.hasNext()) {
scanner.next(); // skip gid
name = scanner.next();
while (scanner.hasNextLine()) {
String[] fields = scanner.nextLine().split(",");
// skip gid
name = fields[1];
name = name.replaceAll(new String(doublequote), "");
year = (long) scanner.nextInt();
year = Long.valueOf (fields[2]);
Double[] seasonalTemperature = new Double[4];
seasonalTemperature[0] = scanner.nextDouble();
seasonalTemperature[1] = scanner.nextDouble();
seasonalTemperature[2] = scanner.nextDouble();
seasonalTemperature[3] = scanner.nextDouble();
seasonalTemperature[0] = Double.valueOf(fields[3]);
seasonalTemperature[1] = Double.valueOf(fields[4]);
seasonalTemperature[2] = Double.valueOf(fields[5]);
seasonalTemperature[3] = Double.valueOf(fields[6]);
// scanner.nextLine();
// store seasonal temperatures for each basin for the
......
......@@ -57,7 +57,7 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
private double tempOptRep = 20. ;
private double eta = 2.4; // parameter linking surface of a basin and S_etoile
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 survOptRep = 0.0017;
private double lambda = 0.00041;
......
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