Merge branch 'develop' of gitlab-ssh.irstea.fr:SimAquaLife/GR3D into exploration_GR3D_process

data/input/northeastamerica/fishRIOBasin_Sapidissima_Rjava.xml

@@ -320,8 +320,14 @@
 
 				<species.SurviveAfterReproduction>
 					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
-					<afterReproductionSeason>SPRING</afterReproductionSeason>
-					<survivalRateAfterReproduction>0.1</survivalRateAfterReproduction>
+					<afterReproductionSeason>SUMMER</afterReproductionSeason>
+					<maximalSurvivalRate>0.1</maximalSurvivalRate>
+<!-- 					<temperatureEffectSurvivalAfterReproduction class="temperatureEffect.LogitEffect"> -->
+<!-- 						<Tref>22</Tref> -->
+<!-- 						<alpha>-.1</alpha> -->
+<!-- 					</temperatureEffectSurvivalAfterReproduction> -->
+					<temperatureEffectSurvivalAfterReproduction class="temperatureEffect.NoEffect">
+					</temperatureEffectSurvivalAfterReproduction>
 				</species.SurviveAfterReproduction>
 
 				<species.MigrateFromRiverToInshore>

src/main/java/species/SurviveAfterReproduction.java

@@ -18,8 +18,8 @@ import fr.cemagref.simaqualife.kernel.util.TransientParameters.InitTransientPara
 import fr.cemagref.simaqualife.pilot.Pilot;
 import miscellaneous.BinomialForSuperIndividualGen;
 import species.DiadromousFish.SpawnerOrigin;
-import umontreal.iro.lecuyer.probdist.NormalDist;
-import umontreal.iro.lecuyer.randvar.NormalGen;
+import temperatureEffect.LogitEffect;
+import temperatureEffect.TemperatureEffect;
 
 @ServiceProvider(service = AquaNismsGroupProcess.class)
 
@@ -27,9 +27,14 @@ public class SurviveAfterReproduction extends AquaNismsGroupProcess<DiadromousFi
 
 	private Season afterReproductionSeason = Season.SUMMER;
 
-	private double survivalRateAfterReproduction = 0.1;
+	/**
+	 * maximum suvival od spawnser after reproduction
+	 * 
+	 * @unit -
+	 */
+	private double maximalSurvivalRate = 0.1;
 
-	private transient NormalGen genNormal;
+	private TemperatureEffect temperatureEffectSurvivalAfterReproduction;
 
 	/**
 	 * the random numbers generator for binomial draws
@@ -39,7 +44,9 @@ public class SurviveAfterReproduction extends AquaNismsGroupProcess<DiadromousFi
 	private transient BinomialForSuperIndividualGen aleaGen;
 
 	public static void main(String[] args) {
-		System.out.println((new XStream(new DomDriver())).toXML(new SurviveAfterReproduction()));
+		SurviveAfterReproduction surviveAfterReproduction = new SurviveAfterReproduction();
+		surviveAfterReproduction.temperatureEffectSurvivalAfterReproduction = new LogitEffect(22, -0.1);
+		System.out.println((new XStream(new DomDriver())).toXML(surviveAfterReproduction));
 	}
 
 
@@ -47,7 +54,6 @@ public class SurviveAfterReproduction extends AquaNismsGroupProcess<DiadromousFi
 	@InitTransientParameters
 	public void initTransientParameters(Pilot pilot) {
 		super.initTransientParameters(pilot);
-		genNormal = new NormalGen(pilot.getRandomStream(), new NormalDist(0., 1.));
 
 		aleaGen = new BinomialForSuperIndividualGen(pilot.getRandomStream());
 
@@ -77,20 +83,25 @@ public class SurviveAfterReproduction extends AquaNismsGroupProcess<DiadromousFi
 						totalInputFluxes.get(origin).put("biomass", 0.);
 					}
 
+					// temperature effect in the riverBasin
+					double currentTemperature = riverBasin.getCurrentTemperature(group.getPilot());
+					double tempEffect = temperatureEffectSurvivalAfterReproduction.getTemperatureEffect(currentTemperature);
+					double survivalProbability = maximalSurvivalRate * tempEffect;
+
 					// iterate on the fish
 					ListIterator<DiadromousFish> fishIterator = fishInBasin.listIterator();
 					while (fishIterator.hasNext()) {
 						DiadromousFish fish = fishIterator.next();
 
+						// only on spawners
 						if (fish.isMature()) {
-
 							// origin of the spwaner
 							SpawnerOrigin spawnerOrigin = (fish.getBirthBasin() == riverBasin ? SpawnerOrigin.AUTOCHTONOUS
 									: SpawnerOrigin.ALLOCHTONOUS);
 
 							// survival amount of fish
 							double biomass = 0.;
-							survivalAmount = aleaGen.getSuccessNumber(fish.getAmount(), survivalRateAfterReproduction);
+							survivalAmount = aleaGen.getSuccessNumber(fish.getAmount(), survivalProbability);
 
 							// at least one fish in the SI survive, the other die
 							if (survivalAmount > 0) {

src/main/java/temperatureEffect/LogitEffect.java

+/**
+ * patrick
+ * @author Patrick Lambert
+ * @copyright Copyright (c) 2020, INRAE
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+ */
+package temperatureEffect;
+
+/**
+ *
+ */
+public class LogitEffect implements TemperatureEffect {
+
+	/**
+	 * 
+	 * @unit
+	 */
+	private static final long serialVersionUID = 3756752294442116413L;
+
+	/**
+	 * temperature reference used to calculate the effect
+	 * 
+	 * @unit °C
+	 */
+	private double Tref = 20.;
+
+	/**
+	 * parameter used to calculate the effect
+	 * 
+	 * @unit °C
+	 */
+	private double alpha = 0.1;
+
+	@Override
+	public double getTemperatureEffect(double temperature) {
+
+		return 1. / (1. + Math.exp(-alpha * (temperature - Tref)));
+	}
+
+
+	public LogitEffect(double Tref, double alpha) {
+		super();
+		this.Tref = Tref;
+		this.alpha = alpha;
+	}
+
+}

src/main/java/temperatureEffect/NoEffect.java

+/**
+ * patrick
+ * @author Patrick Lambert
+ * @copyright Copyright (c) 2020, INRAE
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+ */
+package temperatureEffect;
+
+/**
+ *
+ */
+public class NoEffect implements TemperatureEffect {
+
+	/**
+	 * 
+	 * @unit
+	 */
+	private static final long serialVersionUID = -7686765011254676763L;
+
+	@Override
+	public double getTemperatureEffect(double temperature) {
+
+		return 1.;
+	}
+
+
+	public NoEffect(double Tref, double alpha) {
+		super();
+	}
+
+}

src/main/java/temperatureEffect/RectangularTemperatureEffect.java

+/**
+ * patrick
+ * @author Patrick Lambert
+ * @copyright Copyright (c) 2020, INRAE
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+ */
+package temperatureEffect;
+
+/**
+ *
+ */
+public class RectangularTemperatureEffect implements TemperatureEffect {
+	/**
+	 * 
+	 * @unit
+	 */
+	private static final long serialVersionUID = -611999636717694259L;
+
+	/**
+	 * minimal temperature . Below this value, the temperature effect is 0
+	 * 
+	 * @unit °C
+	 */
+	private double Tmin;
+
+	/**
+	 * maximal temperature. Above this value, the temperature effect is 0
+	 * 
+	 * @unit °C
+	 */
+	private double Tmax;
+
+	@Override
+	public double getTemperatureEffect(double temperature) {
+		if (temperature <= Tmin || temperature >= Tmax) {
+			return 0;
+		} else {
+			return 1;
+		}
+	}
+
+
+	public RectangularTemperatureEffect(double tmin, double tmax) {
+		super();
+		this.Tmin = tmin;
+		this.Tmax = tmax;
+	}
+
+}

src/main/java/temperatureEffect/Rosso.java

+/**
+ * patrick
+ * @author Patrick Lambert
+ * @copyright Copyright (c) 2020, INRAE
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+ */
+package temperatureEffect;
+
+/**
+ *
+ */
+public class Rosso implements TemperatureEffect {
+	/**
+	 * 
+	 * @unit
+	 */
+	private static final long serialVersionUID = -2646246167644233819L;
+
+	/**
+	 * minimal temperature . Below this value, the temperature effect is 0
+	 * 
+	 * @unit °C
+	 */
+	private double Tmin;
+
+	/**
+	 * optimal temperature. At this value, the temperature effect is 1
+	 * 
+	 * @unit °C
+	 */
+	private double Topt;
+
+	/**
+	 * maximal temperature. Above this value, the temperature effect is 0
+	 * 
+	 * @unit °C
+	 */
+	private double Tmax;
+
+	@Override
+	public double getTemperatureEffect(double temperature) {
+		if (temperature <= Tmin || temperature >= Tmax) {
+			return 0;
+		} else {
+			return (temperature - Tmin) * (temperature - Tmax)
+					/ ((temperature - Tmin) * (temperature - Tmax) - ((temperature - Topt) * (temperature - Topt)));
+		}
+	}
+
+
+	public Rosso(double tmin, double topt, double tmax) {
+		super();
+		this.Tmin = tmin;
+		this.Topt = topt;
+		this.Tmax = tmax;
+	}
+
+}

src/main/java/temperatureEffect/TemperatureEffect.java

+/**
+ * patrick
+ * @author Patrick Lambert
+ * @copyright Copyright (c) 2020, INRAE
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+ */
+package temperatureEffect;
+
+import java.io.Serializable;
+
+/**
+ *
+ */
+public interface TemperatureEffect extends Serializable {
+
+	public double getTemperatureEffect(double temperature);
+
+}

src/main/java/temperatureEffect/package-info.java

+/**
+ * patrick
+ * @author Patrick Lambert
+ * @copyright Copyright (c) 2020, INRAE
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+ */
+/**
+ *
+ */
+package temperatureEffect;
\ No newline at end of file