646 Use graph model with abms #1065
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| /* | ||
| * Copyright (C) 2020-2024 MEmilio | ||
| * | ||
| * Authors: Julia Bicker | ||
| * | ||
| * Contact: Martin J. Kuehn <Martin.Kuehn@DLR.de> | ||
| * | ||
| * Licensed under the Apache License, Version 2.0 (the "License"); | ||
| * you may not use this file except in compliance with the License. | ||
| * You may obtain a copy of the License at | ||
| * | ||
| * http://www.apache.org/licenses/LICENSE-2.0 | ||
| * | ||
| * Unless required by applicable law or agreed to in writing, software | ||
| * distributed under the License is distributed on an "AS IS" BASIS, | ||
| * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | ||
| * See the License for the specific language governing permissions and | ||
| * limitations under the License. | ||
| */ | ||
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| #include "abm/household.h" | ||
| #include "abm/world.h" | ||
| #include "abm/infection_state.h" | ||
| #include "abm/location_type.h" | ||
| #include "abm/time.h" | ||
| #include "abm/person_id.h" | ||
| #include "graph_abm/graph_abm_mobility.h" | ||
| #include "graph_abm/mobility_rules.h" | ||
| #include "memilio/io/history.h" | ||
| #include "memilio/mobility/graph.h" | ||
| #include <cstddef> | ||
| #include <cstdint> | ||
| #include <map> | ||
| #include <tuple> | ||
| #include <utility> | ||
| #include <vector> | ||
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| //Logger | ||
| struct Logger : mio::LogAlways { | ||
| /** | ||
| * A vector of tuples with the Location information i.e. each tuple contains the following information: | ||
| * - The LocationId (including the world id) | ||
| * - The total number of Persons at the location | ||
| * - A map containing the number of Persons per InfectionState at the location | ||
| */ | ||
| using Type = std::vector<std::tuple<int, mio::abm::LocationType, mio::abm::LocationId, size_t, | ||
| std::map<mio::abm::InfectionState, size_t>>>; | ||
| static Type log(const mio::abm::Simulation& sim) | ||
| { | ||
| Type location_information{}; | ||
| auto t = sim.get_time(); | ||
| for (auto&& loc : sim.get_world().get_locations()) { | ||
| std::map<mio::abm::InfectionState, size_t> persons_per_infection_state; | ||
| for (size_t i = 0; i < static_cast<size_t>(mio::abm::InfectionState::Count); ++i) { | ||
| auto inf_state = mio::abm::InfectionState(i); | ||
| persons_per_infection_state.insert( | ||
| {inf_state, sim.get_world().get_subpopulation(loc.get_id(), t, inf_state)}); | ||
| } | ||
| location_information.push_back(std::make_tuple(loc.get_world_id(), loc.get_type(), loc.get_id(), | ||
| sim.get_world().get_number_persons(loc.get_id()), | ||
| persons_per_infection_state)); | ||
|
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| } | ||
| return location_information; | ||
| } | ||
| }; | ||
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| int main() | ||
| { | ||
| // This is an example with three age groups representing children, adults and seniors. | ||
| size_t num_age_groups = 3; | ||
| const auto age_group_children = mio::AgeGroup(0); | ||
| const auto age_group_adults = mio::AgeGroup(1); | ||
| const auto age_group_seniors = mio::AgeGroup(2); | ||
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| auto world1 = mio::abm::World(num_age_groups, 0); | ||
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| //Set infection parameters | ||
| world1.parameters.get<mio::abm::IncubationPeriod>() = 4.; | ||
| world1.parameters.get<mio::abm::InfectedNoSymptomsToSymptoms>() = 2.; | ||
| world1.parameters.get<mio::abm::InfectedNoSymptomsToRecovered>() = 4.; | ||
| world1.parameters.get<mio::abm::InfectedSymptomsToRecovered>() = 5.; | ||
| world1.parameters.get<mio::abm::InfectedSymptomsToSevere>() = 6.; | ||
| world1.parameters.get<mio::abm::SevereToRecovered>() = 8.; | ||
| world1.parameters.get<mio::abm::SevereToCritical>() = 7.; | ||
| world1.parameters.get<mio::abm::CriticalToRecovered>() = 10.; | ||
| world1.parameters.get<mio::abm::CriticalToDead>() = 11.; | ||
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| //Age group 0 goes to school and age group 1 goes to work | ||
| world1.parameters.get<mio::abm::AgeGroupGotoSchool>()[age_group_children] = true; | ||
| world1.parameters.get<mio::abm::AgeGroupGotoWork>()[age_group_adults] = true; | ||
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| //Household members can be child, parent or senior | ||
| auto child = mio::abm::HouseholdMember(num_age_groups); | ||
| child.set_age_weight(age_group_children, 1); | ||
| auto parent = mio::abm::HouseholdMember(num_age_groups); | ||
| parent.set_age_weight(age_group_adults, 1); | ||
| auto adult = mio::abm::HouseholdMember(num_age_groups); | ||
| adult.set_age_weight(age_group_adults, 1); | ||
| adult.set_age_weight(age_group_seniors, 1); | ||
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| //Single-Person households | ||
| auto single_hh = mio::abm::Household(); | ||
| single_hh.add_members(adult, 1); | ||
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| //Two-Adult household | ||
| auto two_adult_hh = mio::abm::Household(); | ||
| two_adult_hh.add_members(adult, 2); | ||
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| //Single-Parent household | ||
| auto single_parent_hh = mio::abm::Household(); | ||
| single_parent_hh.add_members(child, 1); | ||
| single_parent_hh.add_members(parent, 1); | ||
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| //Family household | ||
| auto family_hh = mio::abm::Household(); | ||
| family_hh.add_members(child, 1); | ||
| family_hh.add_members(parent, 2); | ||
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| // Vector holding all persons for the graph simulation. This vector is copied to all worlds at the end. | ||
| std::vector<mio::abm::Person> persons; | ||
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| //Household groups for world 1 | ||
| auto single_hh_group_w1 = mio::abm::HouseholdGroup(); | ||
| single_hh_group_w1.add_households(single_hh, 5); | ||
| auto two_adult_hh_group_w1 = mio::abm::HouseholdGroup(); | ||
| two_adult_hh_group_w1.add_households(two_adult_hh, 3); | ||
| auto single_parent_hh_group_w1 = mio::abm::HouseholdGroup(); | ||
| single_parent_hh_group_w1.add_households(single_parent_hh, 5); | ||
| auto family_hh_group_w1 = mio::abm::HouseholdGroup(); | ||
| family_hh_group_w1.add_households(family_hh, 10); | ||
| add_household_group_to_world(world1, single_hh_group_w1); | ||
| add_household_group_to_world(world1, two_adult_hh_group_w1); | ||
| add_household_group_to_world(world1, single_hh_group_w1); | ||
| add_household_group_to_world(world1, family_hh_group_w1); | ||
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| //add persons from world 0 to vector | ||
| for (auto& person : world1.get_persons()) { | ||
| mio::abm::PersonId new_id{static_cast<uint32_t>(persons.size())}; | ||
| persons.emplace_back(person, new_id); | ||
| } | ||
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| auto world2 = mio::abm::World(num_age_groups, 1); | ||
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| //Household groups for world 2 | ||
| auto single_hh_group_w2 = mio::abm::HouseholdGroup(); | ||
| single_hh_group_w2.add_households(single_hh, 6); | ||
| auto two_adult_hh_group_w2 = mio::abm::HouseholdGroup(); | ||
| two_adult_hh_group_w2.add_households(two_adult_hh, 2); | ||
| auto single_parent_hh_group_w2 = mio::abm::HouseholdGroup(); | ||
| single_parent_hh_group_w2.add_households(single_parent_hh, 10); | ||
| auto family_hh_group_w2 = mio::abm::HouseholdGroup(); | ||
| family_hh_group_w2.add_households(family_hh, 11); | ||
| add_household_group_to_world(world2, single_hh_group_w2); | ||
| add_household_group_to_world(world2, two_adult_hh_group_w2); | ||
| add_household_group_to_world(world2, single_hh_group_w2); | ||
| add_household_group_to_world(world2, family_hh_group_w2); | ||
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| //add persons from world 1 to vector | ||
| for (auto& person : world2.get_persons()) { | ||
| mio::abm::PersonId new_id{static_cast<uint32_t>(persons.size())}; | ||
| persons.emplace_back(person, new_id); | ||
| } | ||
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| //Create locations for both worlds | ||
| //world 0 | ||
| auto event_w1 = world1.add_location(mio::abm::LocationType::SocialEvent); | ||
| world1.get_location(event_w1).get_infection_parameters().set<mio::abm::MaximumContacts>(10); | ||
| auto hospital_w1 = world1.add_location(mio::abm::LocationType::Hospital); | ||
| world1.get_location(hospital_w1).get_infection_parameters().set<mio::abm::MaximumContacts>(10); | ||
| auto icu_w1 = world1.add_location(mio::abm::LocationType::ICU); | ||
| world1.get_location(icu_w1).get_infection_parameters().set<mio::abm::MaximumContacts>(5); | ||
| auto shop_w1 = world1.add_location(mio::abm::LocationType::BasicsShop); | ||
| world1.get_location(shop_w1).get_infection_parameters().set<mio::abm::MaximumContacts>(20); | ||
| auto school_w1 = world1.add_location(mio::abm::LocationType::School); | ||
| world1.get_location(school_w1).get_infection_parameters().set<mio::abm::MaximumContacts>(20); | ||
| auto work_w1 = world1.add_location(mio::abm::LocationType::Work); | ||
| world1.get_location(work_w1).get_infection_parameters().set<mio::abm::MaximumContacts>(10); | ||
| //World 1 | ||
| auto event_w2 = world2.add_location(mio::abm::LocationType::SocialEvent); | ||
| world2.get_location(event_w2).get_infection_parameters().set<mio::abm::MaximumContacts>(10); | ||
| auto hospital_w2 = world2.add_location(mio::abm::LocationType::Hospital); | ||
| world2.get_location(hospital_w2).get_infection_parameters().set<mio::abm::MaximumContacts>(10); | ||
| auto icu_w2 = world2.add_location(mio::abm::LocationType::ICU); | ||
| world2.get_location(icu_w2).get_infection_parameters().set<mio::abm::MaximumContacts>(5); | ||
| auto shop_w2 = world2.add_location(mio::abm::LocationType::BasicsShop); | ||
| world2.get_location(shop_w2).get_infection_parameters().set<mio::abm::MaximumContacts>(20); | ||
| auto school_w2 = world2.add_location(mio::abm::LocationType::School); | ||
| world2.get_location(school_w2).get_infection_parameters().set<mio::abm::MaximumContacts>(20); | ||
| auto work_w2 = world2.add_location(mio::abm::LocationType::Work); | ||
| world2.get_location(work_w2).get_infection_parameters().set<mio::abm::MaximumContacts>(10); | ||
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| auto start_date = mio::abm::TimePoint(0); | ||
| auto end_date = mio::abm::TimePoint(0) + mio::abm::days(30); | ||
| std::vector<uint32_t> params_e1; | ||
| std::vector<uint32_t> params_e2; | ||
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| //Assign infection states and locations | ||
| std::vector<double> infection_distribution{0.5, 0.3, 0.05, 0.05, 0.05, 0.05, 0.0, 0.0}; | ||
| for (auto& person : persons) { | ||
| mio::abm::InfectionState infection_state = mio::abm::InfectionState( | ||
| mio::DiscreteDistribution<size_t>::get_instance()(mio::thread_local_rng(), infection_distribution)); | ||
| auto rng = mio::abm::PersonalRandomNumberGenerator(mio::thread_local_rng(), person); | ||
| if (infection_state != mio::abm::InfectionState::Susceptible) { | ||
| person.add_new_infection(mio::abm::Infection(rng, mio::abm::VirusVariant::Wildtype, person.get_age(), | ||
| world1.parameters, start_date, infection_state)); | ||
| } | ||
| // Assign locations to persons from world 1 | ||
| if (person.get_assigned_location_world_id(mio::abm::LocationType::Home) == world1.get_id()) { | ||
| person.set_assigned_location(mio::abm::LocationType::SocialEvent, event_w1, world1.get_id()); | ||
| person.set_assigned_location(mio::abm::LocationType::BasicsShop, shop_w1, world1.get_id()); | ||
| person.set_assigned_location(mio::abm::LocationType::Hospital, hospital_w1, world1.get_id()); | ||
| person.set_assigned_location(mio::abm::LocationType::ICU, icu_w1, world1.get_id()); | ||
| if (person.get_age() == age_group_children) { | ||
| person.set_assigned_location(mio::abm::LocationType::School, school_w1, world1.get_id()); | ||
| } | ||
| if (person.get_age() == age_group_adults) { | ||
| //10% of adults in world 0 work in world 1 | ||
| size_t work_world = mio::DiscreteDistribution<size_t>::get_instance()(mio::thread_local_rng(), | ||
| std::vector<double>{0.9, 0.1}); | ||
| if (work_world == 1) { //person works in other world | ||
| person.set_assigned_location(mio::abm::LocationType::Work, work_w2, world2.get_id()); | ||
| //add person to edge parameters | ||
| params_e1.push_back(person.get_id().get()); | ||
| } | ||
| else { //person works in same world | ||
| person.set_assigned_location(mio::abm::LocationType::Work, work_w1, world1.get_id()); | ||
| } | ||
| } | ||
| } | ||
| else { | ||
| person.set_assigned_location(mio::abm::LocationType::SocialEvent, event_w2, world2.get_id()); | ||
| person.set_assigned_location(mio::abm::LocationType::BasicsShop, shop_w2, world2.get_id()); | ||
| person.set_assigned_location(mio::abm::LocationType::Hospital, hospital_w2, world2.get_id()); | ||
| person.set_assigned_location(mio::abm::LocationType::ICU, icu_w2, world2.get_id()); | ||
| if (person.get_age() == age_group_children) { | ||
| person.set_assigned_location(mio::abm::LocationType::School, school_w2, world2.get_id()); | ||
| } | ||
| if (person.get_age() == age_group_adults) { | ||
| //20% of adults in world 1 work in world 0 | ||
| size_t work_world = mio::DiscreteDistribution<size_t>::get_instance()(mio::thread_local_rng(), | ||
| std::vector<double>{0.2, 0.8}); | ||
| if (work_world == 0) { //person works in other world | ||
| person.set_assigned_location(mio::abm::LocationType::Work, work_w1, world1.get_id()); | ||
| //add person to edge parameters | ||
| params_e2.push_back(person.get_id().get()); | ||
| } | ||
| else { //person works in same world | ||
| person.set_assigned_location(mio::abm::LocationType::Work, work_w2, world2.get_id()); | ||
| } | ||
| } | ||
| } | ||
| } | ||
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| //copy persons to both worlds | ||
| world1.set_persons(persons); | ||
| world2.set_persons(persons); | ||
|
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| using HistoryType = mio::History<mio::DataWriterToMemory, Logger>; | ||
| mio::Graph<mio::ABMSimulationNode<HistoryType>, mio::ABMMobilityEdge<HistoryType>> graph; | ||
| graph.add_node(world1.get_id(), HistoryType{}, start_date, std::move(world1)); | ||
| graph.add_node(world2.get_id(), HistoryType{}, start_date, std::move(world2)); | ||
| graph.add_edge(0, 1, params_e1, | ||
| std::vector<mio::ABMMobilityEdge<HistoryType>::MobilityRuleType>{&mio::apply_commuting}); | ||
| graph.add_edge(1, 0, params_e2, | ||
| std::vector<mio::ABMMobilityEdge<HistoryType>::MobilityRuleType>{&mio::apply_commuting}); | ||
|
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| auto sim = mio::make_abm_graph_sim<HistoryType>(start_date, mio::abm::hours(12), std::move(graph)); | ||
| sim.advance(end_date); | ||
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| auto& log_n1 = std::get<0>(sim.get_graph().nodes()[0].property.get_history()).get_log(); | ||
| auto& log_n2 = std::get<0>(sim.get_graph().nodes()[1].property.get_history()).get_log(); | ||
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| return 0; | ||
| } | ||
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A slightly more descriptive name would be neat. It is fine as long as this stays in the example.