Merge pull request #116 from matsim-org/workshop_boiler_plate

added boiler plate batch classes for episim workshop
matsim-org · Apr 29, 2024 · 1390a01 · 1390a01
2 parents e7e0322 + d2d4d9e
commit 1390a01
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Showing 3 changed files with 258 additions and 2 deletions.
diff --git a/src/main/java/org/matsim/run/CreateBatteryForCluster.java b/src/main/java/org/matsim/run/CreateBatteryForCluster.java
@@ -84,10 +84,10 @@ public class CreateBatteryForCluster<T> implements Callable<Integer> {
 	@CommandLine.Option(names = "--jvm-opts", description = "Additional options for JVM", defaultValue = "-Xms82G -Xmx82G -XX:+UseParallelGC")
 	private String jvmOpts;
 
-	@CommandLine.Option(names = "--setup", defaultValue = "org.matsim.run.batch.CologneBMBF202310XX_soup")
+	@CommandLine.Option(names = "--setup", defaultValue = "org.matsim.run.batch.StarterBatchCologne")
 	private Class<? extends BatchRun<T>> setup;
 
-	@CommandLine.Option(names = "--params", defaultValue = "org.matsim.run.batch.CologneBMBF202310XX_soup$Params")
+	@CommandLine.Option(names = "--params", defaultValue = "org.matsim.run.batch.StarterBatchCologne$Params")
 	private Class<T> params;
 
 	@SuppressWarnings("rawtypes")

diff --git a/src/main/java/org/matsim/run/batch/StarterBatchBerlin.java b/src/main/java/org/matsim/run/batch/StarterBatchBerlin.java
@@ -0,0 +1,120 @@
+package org.matsim.run.batch;
+
+import com.google.inject.Module;
+import org.matsim.core.config.Config;
+import org.matsim.core.config.ConfigUtils;
+import org.matsim.episim.BatchRun;
+import org.matsim.episim.EpisimConfigGroup;
+import org.matsim.episim.VirusStrainConfigGroup;
+import org.matsim.episim.analysis.OutputAnalysis;
+import org.matsim.episim.model.InfectionModelWithAntibodies;
+import org.matsim.run.RunParallel;
+import org.matsim.run.modules.SnzBerlinProductionScenario;
+import org.matsim.run.modules.SnzCologneProductionScenario;
+
+import javax.annotation.Nullable;
+import java.util.Collection;
+import java.util.List;
+
+
+/**
+ * boilerplate batch for berlin
+ */
+public class StarterBatchBerlin implements BatchRun<StarterBatchBerlin.Params> {
+
+	/*
+	 * here you can swap out vaccination model, antibody model, etc.
+	 * See CologneBMBF202310XX_soup.java for an example
+	 */
+	@Nullable
+	@Override
+	public Module getBindings(int id, @Nullable Params params) {
+		return getBindings(params);
+	}
+
+
+	/*
+	 * here you select & modify models specified in the SnzCologneProductionScenario & SnzProductionScenario.
+	 */
+	private SnzBerlinProductionScenario getBindings(Params params) {
+		return new SnzBerlinProductionScenario.Builder()
+			.setActivityHandling(EpisimConfigGroup.ActivityHandling.startOfDay)
+			.setInfectionModel(InfectionModelWithAntibodies.class)
+			.setEasterModel(SnzBerlinProductionScenario.EasterModel.no)
+			.setChristmasModel(SnzBerlinProductionScenario.ChristmasModel.no)
+			.setSample(1)
+			.build();
+	}
+
+	/*
+	 * Metadata is needed for covid-sim.
+	 */
+	@Override
+	public Metadata getMetadata() {
+		return Metadata.of("berlin", "calibration");
+	}
+
+
+	/*
+	 * Here you can add post-processing classes, that will be executed after the simulation.
+	 */
+	@Override
+	public Collection<OutputAnalysis> postProcessing() {
+		return List.of();
+	}
+
+	/*
+	 * Here you can specify configuration options
+	 */
+	@Override
+	public Config prepareConfig(int id, Params params) {
+
+		// Level 1: General (matsim) config. Here you can specify number of iterations and the seed.
+		Config config = getBindings(params).config();
+
+		config.global().setRandomSeed(params.seed);
+
+		// Level 2: Episim specific configs:
+		// 		 2a: general episim config
+		EpisimConfigGroup episimConfig = ConfigUtils.addOrGetModule(config, EpisimConfigGroup.class);
+
+		episimConfig.setCalibrationParameter(episimConfig.getCalibrationParameter() * 1.2 * 1.7 * params.thetaFactor);
+
+		//		 2b: specific config groups, e.g. virusStrainConfigGroup
+		VirusStrainConfigGroup virusStrainConfigGroup = ConfigUtils.addOrGetModule(config, VirusStrainConfigGroup.class);
+
+		return config;
+	}
+
+
+	/*
+	 * Specify parameter combinations that will be run.
+	 */
+	public static final class Params {
+		// general
+		@GenerateSeeds(1)
+		public long seed;
+
+		@Parameter({1.0, 2.0})
+		public double thetaFactor;
+	}
+
+
+
+	/*
+	 * top-level parameters for a run on your local machine.
+	 */
+	public static void main(String[] args) {
+		String[] args2 = {
+				RunParallel.OPTION_SETUP, StarterBatchBerlin.class.getName(),
+				RunParallel.OPTION_PARAMS, Params.class.getName(),
+				RunParallel.OPTION_TASKS, Integer.toString(8),
+				RunParallel.OPTION_ITERATIONS, Integer.toString(50),
+				RunParallel.OPTION_METADATA
+		};
+
+		RunParallel.main(args2);
+	}
+
+}
+
diff --git a/src/main/java/org/matsim/run/batch/StarterBatchCologne.java b/src/main/java/org/matsim/run/batch/StarterBatchCologne.java
@@ -0,0 +1,136 @@
+package org.matsim.run.batch;
+
+import com.google.inject.AbstractModule;
+import com.google.inject.Module;
+import com.google.inject.Singleton;
+import com.google.inject.multibindings.Multibinder;
+import com.google.inject.util.Modules;
+import it.unimi.dsi.fastutil.ints.Int2DoubleAVLTreeMap;
+import it.unimi.dsi.fastutil.ints.Int2DoubleMap;
+import org.matsim.core.config.Config;
+import org.matsim.core.config.ConfigUtils;
+import org.matsim.episim.*;
+import org.matsim.episim.analysis.HospitalNumbersFromEvents;
+import org.matsim.episim.analysis.OutputAnalysis;
+import org.matsim.episim.model.*;
+import org.matsim.episim.model.listener.HouseholdSusceptibility;
+import org.matsim.episim.model.vaccination.VaccinationModel;
+import org.matsim.episim.model.vaccination.VaccinationStrategyBMBF202310XX;
+import org.matsim.episim.policy.FixedPolicy;
+import org.matsim.episim.policy.Restriction;
+import org.matsim.run.RunParallel;
+import org.matsim.run.modules.SnzCologneProductionScenario;
+
+import javax.annotation.Nullable;
+import java.io.IOException;
+import java.io.UncheckedIOException;
+import java.time.LocalDate;
+import java.time.temporal.ChronoUnit;
+import java.util.*;
+import java.util.Map.Entry;
+
+
+/**
+ * boilerplate batch for cologne
+ */
+public class StarterBatchCologne implements BatchRun<StarterBatchCologne.Params> {
+
+	/*
+	 * here you can swap out vaccination model, antibody model, etc.
+	 * See CologneBMBF202310XX_soup.java for an example
+	 */
+	@Nullable
+	@Override
+	public Module getBindings(int id, @Nullable Params params) {
+		return getBindings(params);
+	}
+
+
+	/*
+	 * here you select & modify models specified in the SnzCologneProductionScenario & SnzProductionScenario.
+	 */
+	private SnzCologneProductionScenario getBindings(Params params) {
+		return new SnzCologneProductionScenario.Builder()
+			.setCarnivalModel(SnzCologneProductionScenario.CarnivalModel.yes)
+			.setFutureVacations(SnzCologneProductionScenario.FutureVacations.yes)
+			.setSebastianUpdate(true)
+			.setLeisureCorrection(1.3) //params == null ? 0.0 : params.actCorrection)
+			.setScaleForActivityLevels(1.3)
+			.setSuscHouseholds_pct(0.35)
+			.setActivityHandling(EpisimConfigGroup.ActivityHandling.startOfDay)
+			.setInfectionModel(InfectionModelWithAntibodies.class)
+			.build();
+	}
+
+	/*
+	 * Metadata is needed for covid-sim.
+	 */
+	@Override
+	public Metadata getMetadata() {
+		return Metadata.of("cologne", "calibration");
+	}
+
+
+	/*
+	 * Here you can add post-processing classes, that will be executed after the simulation.
+	 */
+	@Override
+	public Collection<OutputAnalysis> postProcessing() {
+		return List.of();
+	}
+
+	/*
+	 * Here you can specify configuration options
+	 */
+	@Override
+	public Config prepareConfig(int id, Params params) {
+
+		// Level 1: General (matsim) config. Here you can specify number of iterations and the seed.
+		Config config = getBindings(params).config();
+
+		config.global().setRandomSeed(params.seed);
+
+		// Level 2: Episim specific configs:
+		// 		 2a: general episim config
+		EpisimConfigGroup episimConfig = ConfigUtils.addOrGetModule(config, EpisimConfigGroup.class);
+
+		episimConfig.setCalibrationParameter(episimConfig.getCalibrationParameter() * 1.2 * 1.7 * params.thetaFactor);
+
+		//		 2b: specific config groups, e.g. virusStrainConfigGroup
+		VirusStrainConfigGroup virusStrainConfigGroup = ConfigUtils.addOrGetModule(config, VirusStrainConfigGroup.class);
+
+		return config;
+	}
+
+
+	/*
+	 * Specify parameter combinations that will be run.
+	 */
+	public static final class Params {
+		// general
+		@GenerateSeeds(1)
+		public long seed;
+
+		@Parameter({1.0, 2.0})
+		public double thetaFactor;
+	}
+
+
+
+	/*
+	 * top-level parameters for a run on your local machine.
+	 */
+	public static void main(String[] args) {
+		String[] args2 = {
+				RunParallel.OPTION_SETUP, StarterBatchCologne.class.getName(),
+				RunParallel.OPTION_PARAMS, Params.class.getName(),
+				RunParallel.OPTION_TASKS, Integer.toString(8),
+				RunParallel.OPTION_ITERATIONS, Integer.toString(10),
+				RunParallel.OPTION_METADATA
+		};
+
+		RunParallel.main(args2);
+	}
+
+}
+