757 dont store pointers in the abm

cpp/benchmarks/abm.cpp

@@ -1,5 +1,5 @@
 #include "abm/simulation.h"
-#include "memilio/utils/stl_util.h"
+
 #include "benchmark/benchmark.h"
 
 mio::abm::Simulation make_simulation(size_t num_persons, std::initializer_list<uint32_t> seeds)
@@ -23,10 +23,10 @@ mio::abm::Simulation make_simulation(size_t num_persons, std::initializer_list<u
             home_size         = 0;
         }
 
-        auto age     = mio::AgeGroup(mio::UniformIntDistribution<size_t>::get_instance()(
+        auto age    = mio::AgeGroup(mio::UniformIntDistribution<size_t>::get_instance()(
             world.get_rng(), size_t(0), world.parameters.get_num_groups() - 1));
-        auto& person = world.add_person(home, age);
-        person.set_assigned_location(home);
+        auto person = world.add_person(home, age);
+        world.get_person(person).set_assigned_location(home);
         home_size++;
     }
 
@@ -49,7 +49,7 @@ mio::abm::Simulation make_simulation(size_t num_persons, std::initializer_list<u
 
     //infections and masks
     for (auto& person : world.get_persons()) {
-        auto prng = mio::abm::Person::RandomNumberGenerator(world.get_rng(), person);
+        auto prng = mio::abm::PersonalRandomNumberGenerator(world.get_rng(), person);
         //some % of people are infected, large enough to have some infection activity without everyone dying
         auto pct_infected = 0.05;
         if (mio::UniformDistribution<double>::get_instance()(prng, 0.0, 1.0) < pct_infected) {
@@ -114,7 +114,7 @@ mio::abm::Simulation make_simulation(size_t num_persons, std::initializer_list<u
 /**
  * Benchmark for the ABM simulation.
  * @param num_persons Number of persons in the simulation.
- * @param seeds Seeds for the random number generator. 
+ * @param seeds Seeds for the random number generator.
  */
 void abm_benchmark(benchmark::State& state, size_t num_persons, std::initializer_list<uint32_t> seeds)
 {

cpp/examples/abm_history_object.cpp

@@ -17,16 +17,15 @@
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */
-#include "abm/abm.h"
 #include "abm/household.h"
-#include <cstdio>
+#include "abm/lockdown_rules.h"
+#include "abm/simulation.h"
 #include "abm/world.h"
-#include "memilio/io/io.h"
 #include "abm/location_type.h"
+#include "memilio/io/history.h"
+
 #include <fstream>
 #include <string>
-#include <iostream>
-#include "memilio/io/history.h"
 
 std::string convert_loc_id_to_string(std::tuple<mio::abm::LocationType, uint32_t> tuple_id)
 {
@@ -78,7 +77,6 @@ int main()
     // 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);
 
-
     // There are 3 households for each household group.
     int n_households = 3;
 
@@ -110,21 +108,21 @@ int main()
     // Add one social event with 5 maximum contacts.
     // Maximum contacs limit the number of people that a person can infect while being at this location.
     auto event = world.add_location(mio::abm::LocationType::SocialEvent);
-    world.get_individualized_location(event).get_infection_parameters().set<mio::abm::MaximumContacts>(5);
+    world.get_location(event).get_infection_parameters().set<mio::abm::MaximumContacts>(5);
     // Add hospital and ICU with 5 maximum contacs.
     auto hospital = world.add_location(mio::abm::LocationType::Hospital);
-    world.get_individualized_location(hospital).get_infection_parameters().set<mio::abm::MaximumContacts>(5);
+    world.get_location(hospital).get_infection_parameters().set<mio::abm::MaximumContacts>(5);
     auto icu = world.add_location(mio::abm::LocationType::ICU);
-    world.get_individualized_location(icu).get_infection_parameters().set<mio::abm::MaximumContacts>(5);
+    world.get_location(icu).get_infection_parameters().set<mio::abm::MaximumContacts>(5);
     // Add one supermarket, maximum constacts are assumed to be 20.
     auto shop = world.add_location(mio::abm::LocationType::BasicsShop);
-    world.get_individualized_location(shop).get_infection_parameters().set<mio::abm::MaximumContacts>(20);
+    world.get_location(shop).get_infection_parameters().set<mio::abm::MaximumContacts>(20);
     // At every school, the maximum contacts are 20.
     auto school = world.add_location(mio::abm::LocationType::School);
-    world.get_individualized_location(school).get_infection_parameters().set<mio::abm::MaximumContacts>(20);
+    world.get_location(school).get_infection_parameters().set<mio::abm::MaximumContacts>(20);
     // At every workplace, maximum contacts are 10.
     auto work = world.add_location(mio::abm::LocationType::Work);
-    world.get_individualized_location(work).get_infection_parameters().set<mio::abm::MaximumContacts>(10);
+    world.get_location(work).get_infection_parameters().set<mio::abm::MaximumContacts>(10);
 
     // People can get tested at work (and do this with 0.5 probability) from time point 0 to day 30.
     auto testing_min_time      = mio::abm::days(1);
@@ -141,7 +139,7 @@ int main()
     // The infection states are chosen randomly.
     auto persons = world.get_persons();
     for (auto& person : persons) {
-        auto rng = mio::abm::Person::RandomNumberGenerator(world.get_rng(), person);
+        auto rng = mio::abm::PersonalRandomNumberGenerator(world.get_rng(), person);
         mio::abm::InfectionState infection_state =
             (mio::abm::InfectionState)(rand() % ((uint32_t)mio::abm::InfectionState::Count - 1));
         if (infection_state != mio::abm::InfectionState::Susceptible)
@@ -150,19 +148,20 @@ int main()
     }
 
     // Assign locations to the people
-    for (auto& person : persons) {
+    for (auto& person : world.get_persons()) {
+        const auto pid = person.get_id();
         //assign shop and event
-        person.set_assigned_location(event);
-        person.set_assigned_location(shop);
+        world.assign_location(pid, event);
+        world.assign_location(pid, shop);
         //assign hospital and ICU
-        person.set_assigned_location(hospital);
-        person.set_assigned_location(icu);
+        world.assign_location(pid, hospital);
+        world.assign_location(pid, icu);
         //assign work/school to people depending on their age
         if (person.get_age() == age_group_5_to_14) {
-            person.set_assigned_location(school);
+            world.assign_location(pid, school);
         }
         if (person.get_age() == age_group_15_to_34 || person.get_age() == age_group_35_to_59) {
-            person.set_assigned_location(work);
+            world.assign_location(pid, work);
         }
     }
 
@@ -187,7 +186,7 @@ int main()
         {
             Type location_ids{};
             for (auto& location : sim.get_world().get_locations()) {
-                location_ids.push_back(std::make_tuple(location.get_type(), location.get_index()));
+                location_ids.push_back(std::make_tuple(location.get_type(), location.get_id().get()));
             }
             return location_ids;
         }

cpp/examples/abm_minimal.cpp

@@ -17,13 +17,13 @@
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */
-#include "abm/abm.h"
 #include "abm/household.h"
-#include <fstream>
-#include <string>
-#include <iostream>
+#include "abm/lockdown_rules.h"
+#include "abm/world.h"
 #include "abm/common_abm_loggers.h"
 
+#include <fstream>
+
 int main()
 {
     // This is a minimal example with children and adults < 60 year old.
@@ -79,26 +79,26 @@ int main()
     // Add one social event with 5 maximum contacts.
     // Maximum contacs limit the number of people that a person can infect while being at this location.
     auto event = world.add_location(mio::abm::LocationType::SocialEvent);
-    world.get_individualized_location(event).get_infection_parameters().set<mio::abm::MaximumContacts>(5);
+    world.get_location(event).get_infection_parameters().set<mio::abm::MaximumContacts>(5);
     // Add hospital and ICU with 5 maximum contacs.
     auto hospital = world.add_location(mio::abm::LocationType::Hospital);
-    world.get_individualized_location(hospital).get_infection_parameters().set<mio::abm::MaximumContacts>(5);
+    world.get_location(hospital).get_infection_parameters().set<mio::abm::MaximumContacts>(5);
     auto icu = world.add_location(mio::abm::LocationType::ICU);
-    world.get_individualized_location(icu).get_infection_parameters().set<mio::abm::MaximumContacts>(5);
+    world.get_location(icu).get_infection_parameters().set<mio::abm::MaximumContacts>(5);
     // Add one supermarket, maximum constacts are assumed to be 20.
     auto shop = world.add_location(mio::abm::LocationType::BasicsShop);
-    world.get_individualized_location(shop).get_infection_parameters().set<mio::abm::MaximumContacts>(20);
+    world.get_location(shop).get_infection_parameters().set<mio::abm::MaximumContacts>(20);
     // At every school, the maximum contacts are 20.
     auto school = world.add_location(mio::abm::LocationType::School);
-    world.get_individualized_location(school).get_infection_parameters().set<mio::abm::MaximumContacts>(20);
+    world.get_location(school).get_infection_parameters().set<mio::abm::MaximumContacts>(20);
     // At every workplace, maximum contacts are 20.
     auto work = world.add_location(mio::abm::LocationType::Work);
-    world.get_individualized_location(work).get_infection_parameters().set<mio::abm::MaximumContacts>(20);
+    world.get_location(work).get_infection_parameters().set<mio::abm::MaximumContacts>(20);
 
     // Increase aerosol transmission for all locations
     world.parameters.get<mio::abm::AerosolTransmissionRates>() = 10.0;
     // Increase contact rate for all people between 15 and 34 (i.e. people meet more often in the same location)
-    world.get_individualized_location(work)
+    world.get_location(work)
         .get_infection_parameters()
         .get<mio::abm::ContactRates>()[{age_group_15_to_34, age_group_15_to_34}] = 10.0;
 
@@ -119,7 +119,7 @@ int main()
     for (auto& person : world.get_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::Person::RandomNumberGenerator(world.get_rng(), person);
+        auto rng = mio::abm::PersonalRandomNumberGenerator(world.get_rng(), person);
         if (infection_state != mio::abm::InfectionState::Susceptible) {
             person.add_new_infection(mio::abm::Infection(rng, mio::abm::VirusVariant::Wildtype, person.get_age(),
                                                          world.parameters, start_date, infection_state));
@@ -128,18 +128,19 @@ int main()
 
     // Assign locations to the people
     for (auto& person : world.get_persons()) {
+        const auto id = person.get_id();
         //assign shop and event
-        person.set_assigned_location(event);
-        person.set_assigned_location(shop);
+        world.assign_location(id, event);
+        world.assign_location(id, shop);
         //assign hospital and ICU
-        person.set_assigned_location(hospital);
-        person.set_assigned_location(icu);
+        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) {
-            person.set_assigned_location(school);
+            world.assign_location(id, school);
         }
         if (person.get_age() == age_group_15_to_34 || person.get_age() == age_group_35_to_59) {
-            person.set_assigned_location(work);
+            world.assign_location(id, work);
         }
     }
 

cpp/memilio/utils/custom_index_array.h

@@ -20,16 +20,10 @@
 #ifndef CUSTOMINDEXARRAY_H
 #define CUSTOMINDEXARRAY_H
 
-#include "memilio/config.h"
-#include "memilio/math/eigen.h"
 #include "memilio/math/eigen_util.h"
 #include "memilio/utils/index.h"
 #include "memilio/utils/stl_util.h"
 
-#include <vector>
-#include <array>
-#include <numeric>
-
 namespace
 {
 
@@ -165,6 +159,14 @@ class CustomIndexArray
     using Index             = ::mio::Index<Tags...>;
     using InternalArrayType = Eigen::Array<Type, Eigen::Dynamic, 1>;
 
+    /// @brief Create an empty CustomIndexArray with size 0. Use the resize member function to add entries.
+    explicit CustomIndexArray()
+        : m_dimensions(Index::Zero())
+        , m_numel(0)
+        , m_y()
+    {
+    }
+
     /**
      * @brief CustomIndexArray constructor, that initializes the array
      * to constant instances of `CustsomIndexArray::Type`.

cpp/memilio/utils/random_number_generator.cpp

@@ -21,7 +21,7 @@
 
 namespace mio
 {
-    
+
 RandomNumberGenerator& thread_local_rng()
 {
     static thread_local auto rng = RandomNumberGenerator();

cpp/memilio/utils/random_number_generator.h

@@ -18,8 +18,8 @@
 * limitations under the License.
 */
 
-#ifndef EPI_ABM_RANDOM_NUMBER_GENERATOR_H
-#define EPI_ABM_RANDOM_NUMBER_GENERATOR_H
+#ifndef MIO_RANDOM_NUMBER_GENERATOR_H
+#define MIO_RANDOM_NUMBER_GENERATOR_H
 
 #include "memilio/utils/compiler_diagnostics.h"
 #include "memilio/utils/logging.h"
@@ -182,7 +182,9 @@ static_assert(sizeof(Key<uint32_t>) == sizeof(uint32_t), "Empty Base Optimizatio
 * @tparam an unsigned integer type that determines the size of the counter, i.e., the length of the random sequence.
 */
 template <class T>
-struct MEMILIO_ENABLE_EBO Counter : TypeSafe<T, Counter<T>>, OperatorComparison<Counter<T>>, OperatorAdditionSubtraction<Counter<T>> {
+struct MEMILIO_ENABLE_EBO Counter : TypeSafe<T, Counter<T>>,
+                                    OperatorComparison<Counter<T>>,
+                                    OperatorAdditionSubtraction<Counter<T>> {
     static_assert(std::is_unsigned<T>::value, "Underlying Integer type must be unsigned.");
     using TypeSafe<T, Counter<T>>::TypeSafe;
 };
@@ -243,12 +245,13 @@ Counter<UIntC> rng_totalsequence_counter(UIntN subsequence_idx, CounterS counter
     static_assert(N_BITS <= C_BITS, "Subsequence index must not be bigger than total sequence counter.");
     static_assert(N_BITS <= sizeof(UIntN) * BITS_PER_BYTE, "Subsequence index must be at least N bits");
 
-    assert(UIntC(subsequence_idx) <= (UIntC(1) << N_BITS) && "Subsequence index is too large."); //(1 << N) is the same as (2^N)
+    assert(UIntC(subsequence_idx) <= (UIntC(1) << N_BITS) &&
+           "Subsequence index is too large."); //(1 << N) is the same as (2^N)
 
     //N high bits: subsequence idx
     //S low bits: subsequence counter
     //=> C = N + S bits: total sequence counter
-    //example: 
+    //example:
     //subsequence index uint32_t(181) = 0x000000B5
     //subsequence counter uint32_t(41309) = 0x0000A15D
     //total sequence counter = 0x000000B50000A15D
@@ -271,7 +274,7 @@ Counter<UIntC> rng_totalsequence_counter(UIntN subsequence_idx, CounterS counter
 template <class UIntS, class CounterC>
 Counter<UIntS> rng_subsequence_counter(CounterC counter)
 {
-    using UIntC = typename CounterC::ValueType;
+    using UIntC                = typename CounterC::ValueType;
     static const UIntC C_BYTES = sizeof(UIntC);
     static const UIntC S_BYTES = sizeof(UIntS);
 

cpp/models/abm/CMakeLists.txt

@@ -1,12 +1,16 @@
 add_library(abm
     location.cpp
     location.h
+    location_id.h
     household.cpp
     household.h
     simulation.cpp
     simulation.h
     person.cpp
     person.h
+    person_id.h
+    personal_rng.cpp
+    personal_rng.h
     testing_strategy.cpp
     testing_strategy.h
     world.cpp
@@ -16,6 +20,8 @@ add_library(abm
     parameters.cpp
     migration_rules.cpp
     migration_rules.h
+    model_functions.cpp
+    model_functions.h
     trip_list.cpp
     trip_list.h
     lockdown_rules.cpp

cpp/models/abm/analyze_result.h

@@ -20,11 +20,8 @@
 #ifndef ABM_ANALYZE_RESULT_H
 #define ABM_ANALYZE_RESULT_H
 
-#include "abm/simulation.h"
 #include "abm/parameters.h"
-#include "memilio/data/analyze_result.h"
 
-#include <functional>
 #include <vector>
 
 namespace mio