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build mvp for brandenburg... updated batch script for cluster 2025/01/29
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@jakobrehmann
jakobrehmann committed Jan 29, 2025
1 parent b5eb20d commit ff7cfb6
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Showing 5 changed files with 218 additions and 46 deletions.
27 changes: 21 additions & 6 deletions src/main/java/org/matsim/episim/model/activity/LocationBasedParticipationModel.java
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Original file line number Diff line number Diff line change
Expand Up @@ -6,9 +6,11 @@
import org.matsim.api.core.v01.Scenario;
import org.matsim.episim.EpisimConfigGroup;
import org.matsim.episim.EpisimPerson;
import org.matsim.episim.VaccinationConfigGroup;
import org.matsim.episim.policy.Restriction;
import org.matsim.facilities.ActivityFacility;

import java.time.LocalDate;
import java.util.*;

/**
Expand All @@ -19,17 +21,23 @@ public class LocationBasedParticipationModel implements ActivityParticipationMod

private final SplittableRandom rnd;
private final EpisimConfigGroup episimConfig;
private final VaccinationConfigGroup vaccinationConfig;
private ImmutableMap<String, Restriction> im;
private int iteration;
private LocalDate date;


/**
* Map of each ActivityFacility with the corresponding subdistrict
*/
private final Map<String, String> subdistrictFacilities;


@Inject
public LocationBasedParticipationModel(SplittableRandom rnd, EpisimConfigGroup episimConfig, Scenario scenario) {
public LocationBasedParticipationModel(SplittableRandom rnd, EpisimConfigGroup episimConfig, Scenario scenario,VaccinationConfigGroup vaccinationConfig) {
this.rnd = rnd;
this.episimConfig = episimConfig;
this.vaccinationConfig = vaccinationConfig;

if (episimConfig.getActivityHandling() == EpisimConfigGroup.ActivityHandling.duringContact)
throw new IllegalStateException("Participation model can only be used with activityHandling startOfDay");
Expand All @@ -55,6 +63,8 @@ public LocationBasedParticipationModel(SplittableRandom rnd, EpisimConfigGroup e
@Override
public void setRestrictionsForIteration(int iteration, ImmutableMap<String, Restriction> im) {
this.im = im;
this.iteration = iteration;
this.date = episimConfig.getStartDate().plusDays(iteration - 1);
}

@Override
Expand Down Expand Up @@ -88,11 +98,16 @@ public void updateParticipation(EpisimPerson person, BitSet trajectory, int offs
}
}

// TODO: is this neccessary?
// if (context.getSusceptibleRf() != null && context.getSusceptibleRf() != 1d)
// if (!(person.getDiseaseStatus() == EpisimPerson.DiseaseStatus.recovered || (person.getVaccinationStatus() == EpisimPerson.VaccinationStatus.yes &&
// person.daysSince(EpisimPerson.VaccinationStatus.yes, iteration) > vaccinationConfig.getParams(person.getVaccinationType()).getDaysBeforeFullEffect())))
// r *= context.getSusceptibleRf();
// reduce fraction for persons that are not vaccinated
if (context.getSusceptibleRf() != null && context.getSusceptibleRf() != 1d) {
if (!vaccinationConfig.hasGreenPass(person, iteration, date))
r *= context.getSusceptibleRf();
}

if (context.getVaccinatedRf() != null && context.getVaccinatedRf() != 1d) {
if (vaccinationConfig.hasGreenPass(person, iteration, date))
r *= context.getVaccinatedRf();
}

if (r == 1.0)
trajectory.set(offset + i, true);
Expand Down
229 changes: 193 additions & 36 deletions src/main/java/org/matsim/run/batch/StarterBatchBrandenburgCoupled.java
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Original file line number Diff line number Diff line change
Expand Up @@ -11,18 +11,17 @@
import org.matsim.episim.analysis.OutputAnalysis;
import org.matsim.episim.model.InfectionModelWithAntibodies;
import org.matsim.episim.model.listener.HouseholdSusceptibility;
import org.matsim.episim.policy.AdaptivePolicy;
import org.matsim.episim.policy.FixedPolicy;
import org.matsim.episim.policy.Restriction;
import org.matsim.episim.policy.ShutdownPolicy;
import org.matsim.run.RunParallel;
import org.matsim.run.modules.AbstractSnzScenario;
import org.matsim.run.modules.SnzBrandenburgProductionScenario;
import org.matsim.run.modules.SnzProductionScenario;
import org.matsim.run.modules.*;

import javax.annotation.Nullable;
import javax.inject.Singleton;
import java.time.LocalDate;
import java.util.Collection;
import java.util.List;
import java.util.NavigableMap;
import java.util.Objects;
import java.util.*;


/**
Expand All @@ -45,6 +44,16 @@ public Module getBindings(int id, @Nullable Params params) {
return Modules.override(getBindings(params)).with(new AbstractModule() {
@Override
protected void configure() {

if(params != null){
if (params.adaptivePolicy != SnzBerlinProductionScenario.AdaptiveRestrictions.no) {
bind(ShutdownPolicy.class).to(AdaptivePolicy.class).in(Singleton.class);
} else {
bind(ShutdownPolicy.class).to(FixedPolicy.class).in(Singleton.class);
}
}


bind(HouseholdSusceptibility.Config.class).toInstance(
HouseholdSusceptibility.newConfig()
.withSusceptibleHouseholds(params == null ? 0.0 : params.pHouseholds, 0.01));
Expand All @@ -59,7 +68,7 @@ protected void configure() {
private SnzBrandenburgProductionScenario getBindings(Params params) {
return new SnzBrandenburgProductionScenario.Builder()
.setScaleForActivityLevels(params == null ? 1.0 : params.scale)
// .setLocationBasedRestrictions(SnzProductionScenario.LocationBasedRestrictions.yes)
.setLocationBasedRestrictions(params == null ? SnzProductionScenario.LocationBasedRestrictions.no : params.locationBasedRestrictions)
.setActivityHandling(EpisimConfigGroup.ActivityHandling.startOfDay)
.setInfectionModel(InfectionModelWithAntibodies.class)
.setSample(25)
Expand Down Expand Up @@ -91,7 +100,8 @@ public Collection<OutputAnalysis> postProcessing() {
public Config prepareConfig(int id, Params params) {

if (DEBUG_MODE) {
if (runCount == 0) { //&& params.strAEsc != 0.0 && params.ba5Inf == 0. && params.eduTest.equals("true")) {
if (runCount == 0 && params.locationBasedRestrictions == SnzProductionScenario.LocationBasedRestrictions.yes) { //&& params.strAEsc != 0.0 && params.ba5Inf == 0. && params.eduTest.equals("true")) {

runCount++;
} else {
return null;
Expand Down Expand Up @@ -145,30 +155,13 @@ public Config prepareConfig(int id, Params params) {
// 2b: specific config groups, e.g. virusStrainConfigGroup
// VirusStrainConfigGroup virusStrainConfigGroup = ConfigUtils.addOrGetModule(config, VirusStrainConfigGroup.class);

// turn off all import

episimConfig.setInitialInfections(0);
// episimConfig.setThreads(1);

for (NavigableMap<LocalDate, Integer> map : episimConfig.getInfections_pers_per_day().values()) {
map.clear();
}
// summer import
// {
// Map<LocalDate, Integer> infPerDayWild = episimConfig.getInfections_pers_per_day().get(VirusStrain.SARS_CoV_2);
// LocalDate startDateImport = LocalDate.parse("2020-08-01");
// LocalDate endDateImport = LocalDate.parse("2020-11-02");
//
// infPerDayWild.put(startDateImport, (int) params.summerImport);
//
// for (LocalDate date : infPerDayWild.keySet()) {
// if (date.isAfter(startDateImport) && date.isBefore(endDateImport)) {
// infPerDayWild.put(date, (int) params.summerImport);
// }
// }
//
// infPerDayWild.put(endDateImport, 1);
// }


if(params.ci.equals("red")){
//work
Expand Down Expand Up @@ -199,14 +192,177 @@ public Config prepareConfig(int id, Params params) {
throw new RuntimeException();
}

// LOCATION BASED RESTRICTIONS
if (params.locationBasedRestrictions == SnzProductionScenario.LocationBasedRestrictions.yes) {
List<String> subdistricts = Arrays.asList("Elbe-Elster", "Barnim", "Prignitz", "Uckermark", "Oberspreewald-Lausitz", "Potsdam-Mittelmark", "Märkisch-Oderland", "Oberhavel", "Ostprignitz-Ruppin", "Potsdam", "Brandenburg an der Havel", "Frankfurt (Oder)", "Dahme-Spreewald", "Teltow-Fläming", "Oder-Spree", "Havelland", "Cottbus", "Spree-Neiße");
episimConfig.setDistricts(subdistricts);
episimConfig.setDistrictLevelRestrictionsAttribute("district");
episimConfig.setDistrictLevelRestrictions(EpisimConfigGroup.DistrictLevelRestrictions.yesForActivityLocation);

// Set up initial policy - remove all location based restrictions from snz data
// FixedPolicy.ConfigBuilder builder = FixedPolicy.parse(episimConfig.getPolicy());
builder.apply("2020-01-01", "2022-01-01", (d, e) -> ((HashMap<String, Double>) e.get("locationBasedRf")).clear(), AbstractSnzScenario2020.DEFAULT_ACTIVITIES);


// General setup of adaptive restrictions
LocalDate minDate = LocalDate.MIN;

double workTrigger = params.trigger;
double leisureTrigger = params.trigger;
double eduTrigger = params.trigger;
double shopErrandsTrigger = params.trigger;

double openFraction = 0.9;
double restrictedFraction = params.restrictedFraction;

String startDate = "2020-01-01";
// GLOBAL ADAPTIVE POLICY
if (params.adaptivePolicy.equals(SnzBerlinProductionScenario.AdaptiveRestrictions.yesGlobal)) {
com.typesafe.config.Config policy = AdaptivePolicy.config()
.startDate(startDate)
.restrictionScope(AdaptivePolicy.RestrictionScope.global.toString())
.incidenceTrigger(workTrigger, workTrigger, "work", "business")
.incidenceTrigger(leisureTrigger, leisureTrigger, "leisure", "leisPublic", "leisPrivate", "visit")
.incidenceTrigger(eduTrigger, eduTrigger, "educ_kiga", "educ_primary", "educ_secondary", "educ_tertiary", "educ_other", "educ_higher")
.incidenceTrigger(shopErrandsTrigger, shopErrandsTrigger, "shop_other", "shop_daily", "errands")
.initialPolicy(builder)
.restrictedPolicy(FixedPolicy.config()
.restrict(minDate, Restriction.of(restrictedFraction), "work")
.restrict(minDate, Restriction.of(restrictedFraction), "shop_daily")
.restrict(minDate, Restriction.of(restrictedFraction), "shop_other")
.restrict(minDate, Restriction.of(restrictedFraction), "errands")
.restrict(minDate, Restriction.of(restrictedFraction), "business")
.restrict(minDate, Restriction.of(restrictedFraction), "visit")
.restrict(minDate, Restriction.of(restrictedFraction), "leisure")
.restrict(minDate, Restriction.of(restrictedFraction), "leisPublic")
.restrict(minDate, Restriction.of(restrictedFraction), "leisPrivate")
.restrict(minDate, Restriction.of(restrictedFraction), "educ_higher")
.restrict(minDate, Restriction.of(restrictedFraction), "educ_kiga")
.restrict(minDate, Restriction.of(restrictedFraction), "educ_primary")
.restrict(minDate, Restriction.of(restrictedFraction), "educ_secondary")
.restrict(minDate, Restriction.of(restrictedFraction), "educ_tertiary")
.restrict(minDate, Restriction.of(restrictedFraction), "educ_other")
.restrict(minDate, Restriction.ofLocationBasedRf(new HashMap<>()), "work", "shop_daily", "shop_other", "errands", "business", "visit", "leisure", "educ_higher", "educ_kiga", "educ_primary", "educ_secondary", "educ_tertiary", "educ_other")
)
.openPolicy(FixedPolicy.config()
.restrict(minDate, Restriction.of(openFraction), "work")
.restrict(minDate, Restriction.of(openFraction), "shop_daily")
.restrict(minDate, Restriction.of(openFraction), "shop_other")
.restrict(minDate, Restriction.of(openFraction), "errands")
.restrict(minDate, Restriction.of(openFraction), "business")
.restrict(minDate, Restriction.of(openFraction), "visit")
.restrict(minDate, Restriction.of(openFraction), "leisure")
.restrict(minDate, Restriction.of(openFraction), "leisPublic")
.restrict(minDate, Restriction.of(openFraction), "leisPrivate")
.restrict(minDate, Restriction.of(openFraction), "educ_higher")
.restrict(minDate, Restriction.of(openFraction), "educ_kiga")
.restrict(minDate, Restriction.of(openFraction), "educ_primary")
.restrict(minDate, Restriction.of(openFraction), "educ_secondary")
.restrict(minDate, Restriction.of(openFraction), "educ_tertiary")
.restrict(minDate, Restriction.of(openFraction), "educ_other")
.restrict(minDate, Restriction.ofLocationBasedRf(new HashMap<>()), "work", "shop_daily", "shop_other", "errands", "business", "visit", "leisure", "leisPublic", "leisPrivate", "educ_higher", "educ_kiga", "educ_primary", "educ_secondary", "educ_tertiary", "educ_other")
)
.build();

episimConfig.setPolicy(AdaptivePolicy.class, policy);
}

// LOCAL ADAPTIVE POLICY
else if (params.adaptivePolicy.equals(SnzBerlinProductionScenario.AdaptiveRestrictions.yesLocal)) {
com.typesafe.config.Config policy = AdaptivePolicy.config()
.startDate(startDate)
.restrictionScope(AdaptivePolicy.RestrictionScope.local.toString())
.incidenceTrigger(workTrigger, workTrigger, "work", "business")
.incidenceTrigger(leisureTrigger, leisureTrigger, "leisure", "leisPublic", "leisPrivate", "visit")
.incidenceTrigger(eduTrigger, eduTrigger, "educ_kiga", "educ_primary", "educ_secondary", "educ_tertiary", "educ_other", "educ_higher")
.incidenceTrigger(shopErrandsTrigger, shopErrandsTrigger, "shop_other", "shop_daily", "errands")
.initialPolicy(builder)
.restrictedPolicy(FixedPolicy.config()
.restrict(minDate, constructRestrictionWithLocalAndGlobalRf(subdistricts, restrictedFraction), "work")
.restrict(minDate, constructRestrictionWithLocalAndGlobalRf(subdistricts, restrictedFraction), "shop_daily")
.restrict(minDate, constructRestrictionWithLocalAndGlobalRf(subdistricts, restrictedFraction), "shop_other")
.restrict(minDate, constructRestrictionWithLocalAndGlobalRf(subdistricts, restrictedFraction), "errands")
.restrict(minDate, constructRestrictionWithLocalAndGlobalRf(subdistricts, restrictedFraction), "business")
.restrict(minDate, constructRestrictionWithLocalAndGlobalRf(subdistricts, restrictedFraction), "visit")
.restrict(minDate, constructRestrictionWithLocalAndGlobalRf(subdistricts, restrictedFraction), "leisure")
.restrict(minDate, constructRestrictionWithLocalAndGlobalRf(subdistricts, restrictedFraction), "leisPublic")
.restrict(minDate, constructRestrictionWithLocalAndGlobalRf(subdistricts, restrictedFraction), "leisPrivate")
.restrict(minDate, constructRestrictionWithLocalAndGlobalRf(subdistricts, restrictedFraction), "educ_higher")
.restrict(minDate, constructRestrictionWithLocalAndGlobalRf(subdistricts, restrictedFraction), "educ_kiga")
.restrict(minDate, constructRestrictionWithLocalAndGlobalRf(subdistricts, restrictedFraction), "educ_primary")
.restrict(minDate, constructRestrictionWithLocalAndGlobalRf(subdistricts, restrictedFraction), "educ_secondary")
.restrict(minDate, constructRestrictionWithLocalAndGlobalRf(subdistricts, restrictedFraction), "educ_tertiary")
.restrict(minDate, constructRestrictionWithLocalAndGlobalRf(subdistricts, restrictedFraction), "educ_other")
)
.openPolicy(FixedPolicy.config()
.restrict(minDate, constructRestrictionWithLocalAndGlobalRf(subdistricts, openFraction), "work")
.restrict(minDate, constructRestrictionWithLocalAndGlobalRf(subdistricts, openFraction), "shop_daily")
.restrict(minDate, constructRestrictionWithLocalAndGlobalRf(subdistricts, openFraction), "shop_other")
.restrict(minDate, constructRestrictionWithLocalAndGlobalRf(subdistricts, openFraction), "errands")
.restrict(minDate, constructRestrictionWithLocalAndGlobalRf(subdistricts, openFraction), "business")
.restrict(minDate, constructRestrictionWithLocalAndGlobalRf(subdistricts, openFraction), "visit")
.restrict(minDate, constructRestrictionWithLocalAndGlobalRf(subdistricts, openFraction), "leisure")
.restrict(minDate, constructRestrictionWithLocalAndGlobalRf(subdistricts, openFraction), "leisPublic")
.restrict(minDate, constructRestrictionWithLocalAndGlobalRf(subdistricts, openFraction), "leisPrivate")
.restrict(minDate, constructRestrictionWithLocalAndGlobalRf(subdistricts, openFraction), "educ_higher")
.restrict(minDate, constructRestrictionWithLocalAndGlobalRf(subdistricts, openFraction), "educ_kiga")
.restrict(minDate, constructRestrictionWithLocalAndGlobalRf(subdistricts, openFraction), "educ_primary")
.restrict(minDate, constructRestrictionWithLocalAndGlobalRf(subdistricts, openFraction), "educ_secondary")
.restrict(minDate, constructRestrictionWithLocalAndGlobalRf(subdistricts, openFraction), "educ_tertiary")
.restrict(minDate, constructRestrictionWithLocalAndGlobalRf(subdistricts, openFraction), "educ_other")
)
.build();

episimConfig.setPolicy(AdaptivePolicy.class, policy);
}

}

return config;
}

private Restriction constructRestrictionWithLocalAndGlobalRf(List<String> subdistricts, double rf) {
Restriction r = Restriction.ofLocationBasedRf(makeUniformLocalRf(subdistricts, rf));
r.merge(Restriction.of(rf).asMap());

return r;
}

private Map<String, Double> makeUniformLocalRf(List<String> districts, Double rf) {
Map<String, Double> localRf = new HashMap<>();
for (String district : districts) {
localRf.put(district, rf);
}
return localRf;
}



/*
* Specify parameter combinations that will be run.
*/
public static final class Params {


// new
@EnumParameter(value = SnzProductionScenario.LocationBasedRestrictions.class, ignore = "no")
SnzProductionScenario.LocationBasedRestrictions locationBasedRestrictions;


//3
@EnumParameter(value = SnzBerlinProductionScenario.AdaptiveRestrictions.class)
SnzBerlinProductionScenario.AdaptiveRestrictions adaptivePolicy;

// @Parameter({0.0, 0.2, 0.4, 0.6})
@Parameter({0.0, 0.2})
double restrictedFraction;

// @Parameter({10, 25, 50, 75, 100, 125, 150})
// @Parameter({0.000000001})
@Parameter({0.001, 1, 10})
double trigger;


// general
@GenerateSeeds(2)
public long seed;
Expand All @@ -219,29 +375,30 @@ public static final class Params {

// @Parameter({ 0.6, 0.8, 1.0, 1.2, 1.4, 1.6, 2.0})
// @Parameter({0.8, 1.0, 1.2})
@Parameter({1.0})
@Parameter({1.0,10.0})
public double thetaFactor;

//5
@Parameter({1.0, 2.5, 5.0, 7.5, 10.})
// @Parameter({1.0, 2.5, 5.0, 7.5, 10.})
// @Parameter({0.5, 1.0, 2.0})
// @Parameter({10.0})
@Parameter({1.0,10.0})
public double couplingfactor;


//5
@StringParameter({"Cottbus", "Brandenburg", "Frankfurt", "Potsdam","All"})
// @StringParameter({"All"})
// @StringParameter({"Cottbus", "Brandenburg", "Frankfurt", "Potsdam","All"})
@StringParameter({"All","Cottbus", "Frankfurt",})
public String district;

//3
@Parameter({0.5, 0.75, 1.0})
// @Parameter({1.0})
// @Parameter({0.5, 0.75, 1.0})
@Parameter({1.0})
public double mobilityMult;


//6
@StringParameter({"base", "0.0", "0.2", "0.4", "0.8", "1.0"})
// @StringParameter({"base", "0.0", "0.2", "0.4", "0.8", "1.0"})
@StringParameter({"0.0", "1.0"})
public String outdoorFrac;


Expand All @@ -262,7 +419,7 @@ public static void main(String[] args) {
RunParallel.OPTION_SETUP, StarterBatchBrandenburgCoupled.class.getName(),
RunParallel.OPTION_PARAMS, Params.class.getName(),
RunParallel.OPTION_TASKS, Integer.toString(1),
RunParallel.OPTION_ITERATIONS, Integer.toString(30),
RunParallel.OPTION_ITERATIONS, Integer.toString(90),
RunParallel.OPTION_METADATA
};

Expand Down
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