646 Use graph model with abms

cpp/CMakeLists.txt

@@ -150,6 +150,7 @@ if(MEMILIO_BUILD_MODELS)
     add_subdirectory(models/ode_sir)
     add_subdirectory(models/sde_sir)
     add_subdirectory(models/sde_sirs)
+    add_subdirectory(models/graph_abm)
 endif()
 
 if(MEMILIO_BUILD_EXAMPLES)

cpp/benchmarks/abm.cpp

@@ -1,6 +1,7 @@
 #include "abm/simulation.h"
 
 #include "benchmark/benchmark.h"
+#include <cstddef>
 
 mio::abm::Simulation make_simulation(size_t num_persons, std::initializer_list<uint32_t> seeds)
 {
@@ -144,6 +145,38 @@ void abm_benchmark(benchmark::State& state, size_t num_persons, std::initializer
     }
 }
 
+void abm_inactive_persons_benchmark(benchmark::State& state, size_t num_persons, size_t num_inactive_persons,
+                                    std::initializer_list<uint32_t> seeds)
+{
+    mio::set_log_level(mio::LogLevel::warn);
+    for (auto&& _ : state) {
+        state.PauseTiming(); //exclude the setup from the benchmark
+        auto sim = make_simulation(num_persons + num_inactive_persons, seeds);
+        //deactivate num_inactive_persons
+        for (size_t p_id = 0; p_id < num_inactive_persons; ++p_id) {
+            sim.get_world().set_activeness(mio::abm::PersonId(p_id));
+        }
+        state.ResumeTiming();
+
+        //simulated time should be long enough to have full infection runs and migration to every location
+        auto final_time = sim.get_time() + mio::abm::days(10);
+        sim.advance(final_time);
+
+        //debug output can be enabled to check for unexpected results (e.g. infections dieing out)
+        //normally should have no significant effect on runtime
+        const bool monitor_infection_activity = false;
+        if constexpr (monitor_infection_activity) {
+            std::cout << "num_persons = " << num_persons << "\n";
+            for (auto inf_state = 0; inf_state < (int)mio::abm::InfectionState::Count; inf_state++) {
+                std::cout << "inf_state = " << inf_state << ", sum = "
+                          << sim.get_world().get_subpopulation_combined(sim.get_time(),
+                                                                        mio::abm::InfectionState(inf_state))
+                          << "\n";
+            }
+        }
+    }
+}
+
 //Measure ABM simulation run time with different sizes and different seeds.
 //Fixed RNG seeds to make runs comparable. When there are code changes, the simulation will still
 //run differently due to different sequence of random numbers being drawn. But for large enough sizes
@@ -156,4 +189,34 @@ BENCHMARK_CAPTURE(abm_benchmark, abm_benchmark_50k, 50000, {14159265u, 35897932u
 BENCHMARK_CAPTURE(abm_benchmark, abm_benchmark_100k, 100000, {38462643u, 38327950u})->Unit(benchmark::kMillisecond);
 BENCHMARK_CAPTURE(abm_benchmark, abm_benchmark_200k, 200000, {28841971u, 69399375u})->Unit(benchmark::kMillisecond);
 
+BENCHMARK_CAPTURE(abm_inactive_persons_benchmark, abm_inactive_persons_benchmark_50k, 50000, 50000,
+                  {14159265u, 35897932u})
+    ->Unit(benchmark::kMillisecond);
+BENCHMARK_CAPTURE(abm_inactive_persons_benchmark, abm_inactive_persons_benchmark_100k, 100000, 100000,
+                  {38462643u, 38327950u})
+    ->Unit(benchmark::kMillisecond);
+BENCHMARK_CAPTURE(abm_inactive_persons_benchmark, abm_inactive_persons_benchmark_200k, 200000, 200000,
+                  {28841971u, 69399375u})
+    ->Unit(benchmark::kMillisecond);
+
+BENCHMARK_CAPTURE(abm_inactive_persons_benchmark, abm_inactive_persons_benchmark_50k_2, 50000, 100000,
+                  {14159265u, 35897932u})
+    ->Unit(benchmark::kMillisecond);
+BENCHMARK_CAPTURE(abm_inactive_persons_benchmark, abm_inactive_persons_benchmark_100k_2, 100000, 200000,
+                  {38462643u, 38327950u})
+    ->Unit(benchmark::kMillisecond);
+BENCHMARK_CAPTURE(abm_inactive_persons_benchmark, abm_inactive_persons_benchmark_200k_2, 200000, 400000,
+                  {28841971u, 69399375u})
+    ->Unit(benchmark::kMillisecond);
+
+BENCHMARK_CAPTURE(abm_inactive_persons_benchmark, abm_inactive_persons_benchmark_50k_3, 50000, 150000,
+                  {14159265u, 35897932u})
+    ->Unit(benchmark::kMillisecond);
+BENCHMARK_CAPTURE(abm_inactive_persons_benchmark, abm_inactive_persons_benchmark_100k_3, 100000, 300000,
+                  {38462643u, 38327950u})
+    ->Unit(benchmark::kMillisecond);
+BENCHMARK_CAPTURE(abm_inactive_persons_benchmark, abm_inactive_persons_benchmark_200k_3, 200000, 600000,
+                  {28841971u, 69399375u})
+    ->Unit(benchmark::kMillisecond);
+
 BENCHMARK_MAIN();

cpp/examples/CMakeLists.txt

@@ -112,6 +112,10 @@ add_executable(history_example history.cpp)
 target_link_libraries(history_example PRIVATE memilio)
 target_compile_options(history_example PRIVATE ${MEMILIO_CXX_FLAGS_ENABLE_WARNING_ERRORS})
 
+add_executable(graph_abm_example graph_abm.cpp)
+target_link_libraries(graph_abm_example PRIVATE memilio graph_abm abm)
+target_compile_options(abm_minimal_example PRIVATE ${MEMILIO_CXX_FLAGS_ENABLE_WARNING_ERRORS})
+
 if(MEMILIO_HAS_JSONCPP)
     add_executable(ode_secir_read_graph_example ode_secir_read_graph.cpp)
     target_link_libraries(ode_secir_read_graph_example PRIVATE memilio ode_secir)
@@ -144,7 +148,7 @@ if(MEMILIO_HAS_HDF5)
 endif()
 
 if(MEMILIO_HAS_JSONCPP)
-  add_executable(ide_initialization_example ide_initialization.cpp)
-  target_link_libraries(ide_initialization_example PRIVATE memilio ide_secir)
-  target_compile_options(ide_initialization_example PRIVATE ${MEMILIO_CXX_FLAGS_ENABLE_WARNING_ERRORS})
+    add_executable(ide_initialization_example ide_initialization.cpp)
+    target_link_libraries(ide_initialization_example PRIVATE memilio ide_secir)
+    target_compile_options(ide_initialization_example PRIVATE ${MEMILIO_CXX_FLAGS_ENABLE_WARNING_ERRORS})
 endif()

cpp/examples/abm_minimal.cpp

@@ -41,7 +41,7 @@ int main()
     world.parameters.get<mio::abm::IncubationPeriod>() = 4.;
 
     // Set the age group the can go to school is AgeGroup(1) (i.e. 5-14)
-    world.parameters.get<mio::abm::AgeGroupGotoSchool>() = false;
+    world.parameters.get<mio::abm::AgeGroupGotoSchool>()                    = false;
     world.parameters.get<mio::abm::AgeGroupGotoSchool>()[age_group_5_to_14] = true;
     // Set the age group the can go to work is AgeGroup(2) and AgeGroup(3) (i.e. 15-34 and 35-59)
     world.parameters.get<mio::abm::AgeGroupGotoWork>().set_multiple({age_group_15_to_34, age_group_35_to_59}, true);
@@ -55,7 +55,7 @@ int main()
     // For more than 1 family households we need families. These are parents and children and randoms (which are distributed like the data we have for these households).
     auto child = mio::abm::HouseholdMember(num_age_groups); // A child is 50/50% 0-4 or 5-14.
     child.set_age_weight(age_group_0_to_4, 1);
-    child.set_age_weight(age_group_0_to_4, 1);
+    child.set_age_weight(age_group_5_to_14, 1);
 
     auto parent = mio::abm::HouseholdMember(num_age_groups); // A parent is 50/50% 15-34 or 35-59.
     parent.set_age_weight(age_group_15_to_34, 1);
@@ -138,7 +138,7 @@ int main()
         world.assign_location(id, hospital);
         world.assign_location(id, icu);
         //assign work/school to people depending on their age
-        if (person.get_age() == age_group_0_to_4) {
+        if (person.get_age() == age_group_5_to_14) {
             world.assign_location(id, school);
         }
         if (person.get_age() == age_group_15_to_34 || person.get_age() == age_group_35_to_59) {