SciCompMod · kilianvolmer · Jan 7, 2026 · Jan 7, 2026 · Jan 7, 2026 · Jan 7, 2026
diff --git a/cpp/benchmarks/abm.cpp b/cpp/benchmarks/abm.cpp
@@ -1,5 +1,5 @@
 /* 
-* Copyright (C) 2020-2025 MEmilio
+* Copyright (C) 2020-2026 MEmilio
 *
 * Authors: Daniel Abele
 *

diff --git a/cpp/benchmarks/flow_simulation_ode_secirvvs.cpp b/cpp/benchmarks/flow_simulation_ode_secirvvs.cpp
@@ -1,5 +1,5 @@
 /* 
-* Copyright (C) 2020-2025 MEmilio
+* Copyright (C) 2020-2026 MEmilio
 *
 * Authors: Rene Schmieding, Daniel Abele, Martin J. Kuehn
 *
@@ -42,9 +42,9 @@ void flowless_sim(::benchmark::State& state)
         // create simulation
         // exclude integrator creation from benchmark
         state.PauseTiming();
-        std::unique_ptr<mio::OdeIntegratorCore<ScalarType>> I =
-            std::make_unique<mio::ControlledStepperWrapper<ScalarType, boost::numeric::odeint::runge_kutta_cash_karp54>>(
-                cfg.abs_tol, cfg.rel_tol, cfg.dt_min, cfg.dt_max);
+        std::unique_ptr<mio::OdeIntegratorCore<ScalarType>> I = std::make_unique<
+            mio::ControlledStepperWrapper<ScalarType, boost::numeric::odeint::runge_kutta_cash_karp54>>(
+            cfg.abs_tol, cfg.rel_tol, cfg.dt_min, cfg.dt_max);
         state.ResumeTiming();
         // This code gets timed
         mio::benchmark::Simulation<mio::Simulation<ScalarType, Model>> sim(model, cfg.t0, cfg.dt);
@@ -69,9 +69,9 @@ void flow_sim_comp_only(::benchmark::State& state)
     for (auto _ : state) {
         // create simulation
         state.PauseTiming();
-        std::unique_ptr<mio::OdeIntegratorCore<ScalarType>> I =
-            std::make_unique<mio::ControlledStepperWrapper<ScalarType, boost::numeric::odeint::runge_kutta_cash_karp54>>(
-                cfg.abs_tol, cfg.rel_tol, cfg.dt_min, cfg.dt_max);
+        std::unique_ptr<mio::OdeIntegratorCore<ScalarType>> I = std::make_unique<
+            mio::ControlledStepperWrapper<ScalarType, boost::numeric::odeint::runge_kutta_cash_karp54>>(
+            cfg.abs_tol, cfg.rel_tol, cfg.dt_min, cfg.dt_max);
         state.ResumeTiming();
         // This code gets timed
         mio::osecirvvs::Simulation<ScalarType, mio::Simulation<ScalarType, Model>> sim(model, cfg.t0, cfg.dt);
@@ -96,9 +96,9 @@ void flow_sim(::benchmark::State& state)
     for (auto _ : state) {
         // create simulation
         state.PauseTiming();
-        std::unique_ptr<mio::OdeIntegratorCore<ScalarType>> I =
-            std::make_unique<mio::ControlledStepperWrapper<ScalarType, boost::numeric::odeint::runge_kutta_cash_karp54>>(
-                cfg.abs_tol, cfg.rel_tol, cfg.dt_min, cfg.dt_max);
+        std::unique_ptr<mio::OdeIntegratorCore<ScalarType>> I = std::make_unique<
+            mio::ControlledStepperWrapper<ScalarType, boost::numeric::odeint::runge_kutta_cash_karp54>>(
+            cfg.abs_tol, cfg.rel_tol, cfg.dt_min, cfg.dt_max);
         state.ResumeTiming();
         // This code gets timed
         mio::osecirvvs::Simulation<ScalarType, mio::FlowSimulation<ScalarType, Model>> sim(model, cfg.t0, cfg.dt);

diff --git a/cpp/benchmarks/flow_simulation_ode_secirvvs.h b/cpp/benchmarks/flow_simulation_ode_secirvvs.h
@@ -1,5 +1,5 @@
 /*
-* Copyright (C) 2020-2025 MEmilio
+* Copyright (C) 2020-2026 MEmilio
 *
 * Authors: Rene Schmieding, Daniel Abele, Martin J. Kuehn
 *

diff --git a/cpp/benchmarks/flow_simulation_ode_seir.cpp b/cpp/benchmarks/flow_simulation_ode_seir.cpp
@@ -1,5 +1,5 @@
 /*
-* Copyright (C) 2020-2025 MEmilio
+* Copyright (C) 2020-2026 MEmilio
 *
 * Authors: Rene Schmieding, Daniel Abele, Martin J. Kuehn
 *
@@ -132,9 +132,9 @@ void flowless_sim(::benchmark::State& state)
         // create simulation
         // exclude integrator creation from benchmark
         state.PauseTiming();
-        std::unique_ptr<mio::OdeIntegratorCore<ScalarType>> I =
-            std::make_unique<mio::ControlledStepperWrapper<ScalarType, boost::numeric::odeint::runge_kutta_cash_karp54>>(
-                cfg.abs_tol, cfg.rel_tol, cfg.dt_min, cfg.dt_max);
+        std::unique_ptr<mio::OdeIntegratorCore<ScalarType>> I = std::make_unique<
+            mio::ControlledStepperWrapper<ScalarType, boost::numeric::odeint::runge_kutta_cash_karp54>>(
+            cfg.abs_tol, cfg.rel_tol, cfg.dt_min, cfg.dt_max);
         state.ResumeTiming();
         // This code gets timed
         results = mio::simulate(cfg.t0, cfg.t_max, cfg.dt, model, std::move(I));
@@ -157,9 +157,9 @@ void flow_sim_comp_only(::benchmark::State& state)
     for (auto _ : state) {
         // create simulation
         state.PauseTiming();
-        std::unique_ptr<mio::OdeIntegratorCore<ScalarType>> I =
-            std::make_unique<mio::ControlledStepperWrapper<ScalarType, boost::numeric::odeint::runge_kutta_cash_karp54>>(
-                cfg.abs_tol, cfg.rel_tol, cfg.dt_min, cfg.dt_max);
+        std::unique_ptr<mio::OdeIntegratorCore<ScalarType>> I = std::make_unique<
+            mio::ControlledStepperWrapper<ScalarType, boost::numeric::odeint::runge_kutta_cash_karp54>>(
+            cfg.abs_tol, cfg.rel_tol, cfg.dt_min, cfg.dt_max);
         state.ResumeTiming();
         // This code gets timed
         results = mio::simulate(cfg.t0, cfg.t_max, cfg.dt, model, std::move(I));
@@ -182,9 +182,9 @@ void flow_sim(::benchmark::State& state)
     for (auto _ : state) {
         // create simulation
         state.PauseTiming();
-        std::unique_ptr<mio::OdeIntegratorCore<ScalarType>> I =
-            std::make_unique<mio::ControlledStepperWrapper<ScalarType, boost::numeric::odeint::runge_kutta_cash_karp54>>(
-                cfg.abs_tol, cfg.rel_tol, cfg.dt_min, cfg.dt_max);
+        std::unique_ptr<mio::OdeIntegratorCore<ScalarType>> I = std::make_unique<
+            mio::ControlledStepperWrapper<ScalarType, boost::numeric::odeint::runge_kutta_cash_karp54>>(
+            cfg.abs_tol, cfg.rel_tol, cfg.dt_min, cfg.dt_max);
         state.ResumeTiming();
         // This code gets timed
         results = mio::simulate_flows(cfg.t0, cfg.t_max, cfg.dt, model, std::move(I))[0];

diff --git a/cpp/benchmarks/graph_simulation.cpp b/cpp/benchmarks/graph_simulation.cpp
@@ -1,5 +1,5 @@
 /*
-* Copyright (C) 2020-2025 MEmilio
+* Copyright (C) 2020-2026 MEmilio
 *
 * Authors: Henrik Zunker
 *

diff --git a/cpp/benchmarks/graph_simulation.h b/cpp/benchmarks/graph_simulation.h
@@ -1,5 +1,5 @@
 /*
-* Copyright (C) 2020-2025 MEmilio
+* Copyright (C) 2020-2026 MEmilio
 *
 * Authors: Henrik Zunker
 *

diff --git a/cpp/benchmarks/integrator_step.cpp b/cpp/benchmarks/integrator_step.cpp
@@ -1,5 +1,5 @@
 /*
-* Copyright (C) 2020-2025 MEmilio
+* Copyright (C) 2020-2026 MEmilio
 *
 * Authors: Rene Schmieding
 *

diff --git a/cpp/benchmarks/integrator_step.h b/cpp/benchmarks/integrator_step.h
@@ -1,5 +1,5 @@
 /*
-* Copyright (C) 2020-2025 MEmilio
+* Copyright (C) 2020-2026 MEmilio
 *
 * Authors: Rene Schmieding
 *

diff --git a/cpp/benchmarks/secir_ageres_setups.h b/cpp/benchmarks/secir_ageres_setups.h
@@ -1,5 +1,5 @@
 /*
-* Copyright (C) 2020-2025 MEmilio
+* Copyright (C) 2020-2026 MEmilio
 *
 * Authors: Rene Schmieding
 *

diff --git a/cpp/benchmarks/simulation.cpp b/cpp/benchmarks/simulation.cpp
@@ -1,5 +1,5 @@
 /*
-* Copyright (C) 2020-2025 MEmilio
+* Copyright (C) 2020-2026 MEmilio
 *
 * Authors: Rene Schmieding
 *

diff --git a/cpp/benchmarks/simulation.h b/cpp/benchmarks/simulation.h
@@ -1,5 +1,5 @@
 /*
-* Copyright (C) 2020-2025 MEmilio
+* Copyright (C) 2020-2026 MEmilio
 *
 * Authors: Rene Schmieding
 *

diff --git a/cpp/examples/abm_history_object.cpp b/cpp/examples/abm_history_object.cpp
@@ -1,5 +1,5 @@
 /*
-* Copyright (C) 2020-2025 MEmilio
+* Copyright (C) 2020-2026 MEmilio
 *
 * Authors: Khoa Nguyen
 *

diff --git a/cpp/examples/abm_minimal.cpp b/cpp/examples/abm_minimal.cpp
@@ -1,5 +1,5 @@
 /*
-* Copyright (C) 2020-2025 MEmilio
+* Copyright (C) 2020-2026 MEmilio
 *
 * Authors: Khoa Nguyen
 *

diff --git a/cpp/examples/abm_parameter_study.cpp b/cpp/examples/abm_parameter_study.cpp
@@ -1,5 +1,5 @@
 /*
-* Copyright (C) 2020-2025 MEmilio
+* Copyright (C) 2020-2026 MEmilio
 *
 * Authors: Rene Schmieding, Sascha Korf
 *

diff --git a/cpp/examples/ad_odeint_example.cpp b/cpp/examples/ad_odeint_example.cpp
@@ -1,5 +1,5 @@
 /*
-* Copyright (C) 2020-2025 MEmilio
+* Copyright (C) 2020-2026 MEmilio
 *
 * Authors: Ralf Hannemann-Tamas
 *

diff --git a/cpp/examples/ad_square_example.cpp b/cpp/examples/ad_square_example.cpp
@@ -1,5 +1,5 @@
 /*
-* Copyright (C) 2020-2025 MEmilio
+* Copyright (C) 2020-2026 MEmilio
 *
 * Authors: Ralf Hannemann-Tamas
 *

diff --git a/cpp/examples/adapt_rk_test.cpp b/cpp/examples/adapt_rk_test.cpp
@@ -1,5 +1,5 @@
 /*
-* Copyright (C) 2020-2025 MEmilio
+* Copyright (C) 2020-2026 MEmilio
 *
 * Authors: Daniel Abele, Martin J. Kuehn
 *

diff --git a/cpp/examples/cli.cpp b/cpp/examples/cli.cpp
@@ -1,5 +1,5 @@
 /*
-* Copyright (C) 2020-2025 MEmilio
+* Copyright (C) 2020-2026 MEmilio
 *
 * Authors: Rene Schmieding
 *

diff --git a/cpp/examples/d_abm.cpp b/cpp/examples/d_abm.cpp
@@ -1,5 +1,5 @@
 /*
-* Copyright (C) 2020-2025 MEmilio
+* Copyright (C) 2020-2026 MEmilio
 *
 * Authors: Julia Bicker, René Schmieding
 *

diff --git a/cpp/examples/data_dir.h.in b/cpp/examples/data_dir.h.in
@@ -1,5 +1,5 @@
 /* 
-* Copyright (C) 2020-2025 MEmilio
+* Copyright (C) 2020-2026 MEmilio
 *
 * Authors: Daniel Abele
 *

diff --git a/cpp/examples/euler_test.cpp b/cpp/examples/euler_test.cpp
@@ -1,5 +1,5 @@
 /*
-* Copyright (C) 2020-2025 MEmilio
+* Copyright (C) 2020-2026 MEmilio
 *
 * Authors: Daniel Abele, Martin J. Kuehn
 *

diff --git a/cpp/examples/glct_secir.cpp b/cpp/examples/glct_secir.cpp
@@ -1,5 +1,5 @@
 /*
-* Copyright (C) 2020-2025 MEmilio
+* Copyright (C) 2020-2026 MEmilio
 *
 * Authors: Lena Ploetzke
 *
@@ -43,7 +43,7 @@ int main()
     constexpr size_t NumExposed = 2, NumInfectedNoSymptoms = 6, NumInfectedSymptoms = 2, NumInfectedSevere = 2,
                      NumInfectedCritical = 10;
     using Model          = mio::glsecir::Model<ScalarType, NumExposed, NumInfectedNoSymptoms, NumInfectedSymptoms,
-                                      NumInfectedSevere, NumInfectedCritical>;
+                                               NumInfectedSevere, NumInfectedCritical>;
     using LctState       = Model::LctState;
     using InfectionState = LctState::InfectionState;
 
@@ -136,8 +136,9 @@ int main()
     Eigen::VectorX<ScalarType> StartingProbabilitiesInfectedNoSymptoms =
         Eigen::VectorX<ScalarType>::Zero(LctState::get_num_subcompartments<InfectionState::InfectedNoSymptoms>());
     StartingProbabilitiesInfectedNoSymptoms[0] = 1 - recoveredPerInfectedNoSymptoms;
-    StartingProbabilitiesInfectedNoSymptoms[(Eigen::Index)(
-        LctState::get_num_subcompartments<InfectionState::InfectedNoSymptoms>() / 2.)] = recoveredPerInfectedNoSymptoms;
+    StartingProbabilitiesInfectedNoSymptoms[(
+        Eigen::Index)(LctState::get_num_subcompartments<InfectionState::InfectedNoSymptoms>() / 2.)] =
+        recoveredPerInfectedNoSymptoms;
     model.parameters.get<mio::glsecir::StartingProbabilitiesInfectedNoSymptoms<ScalarType>>() =
         StartingProbabilitiesInfectedNoSymptoms;
     // Define equal TransitionMatrices for the strains.
@@ -154,9 +155,10 @@ int main()
     // InfectedSymptoms.
     Eigen::VectorX<ScalarType> StartingProbabilitiesInfectedSymptoms =
         Eigen::VectorX<ScalarType>::Zero(LctState::get_num_subcompartments<InfectionState::InfectedSymptoms>());
-    StartingProbabilitiesInfectedSymptoms[0]                                         = severePerInfectedSymptoms;
-    StartingProbabilitiesInfectedSymptoms[(Eigen::Index)(
-        LctState::get_num_subcompartments<InfectionState::InfectedSymptoms>() / 2.)] = 1 - severePerInfectedSymptoms;
+    StartingProbabilitiesInfectedSymptoms[0] = severePerInfectedSymptoms;
+    StartingProbabilitiesInfectedSymptoms[(
+        Eigen::Index)(LctState::get_num_subcompartments<InfectionState::InfectedSymptoms>() / 2.)] =
+        1 - severePerInfectedSymptoms;
     model.parameters.get<mio::glsecir::StartingProbabilitiesInfectedSymptoms<ScalarType>>() =
         StartingProbabilitiesInfectedSymptoms;
     model.parameters.get<mio::glsecir::TransitionMatrixInfectedSymptomsToInfectedSevere<ScalarType>>() =
@@ -168,9 +170,10 @@ int main()
     // InfectedSevere.
     Eigen::VectorX<ScalarType> StartingProbabilitiesInfectedSevere =
         Eigen::VectorX<ScalarType>::Zero(LctState::get_num_subcompartments<InfectionState::InfectedSevere>());
-    StartingProbabilitiesInfectedSevere[0]                                         = criticalPerSevere;
-    StartingProbabilitiesInfectedSevere[(Eigen::Index)(
-        LctState::get_num_subcompartments<InfectionState::InfectedSevere>() / 2.)] = 1 - criticalPerSevere;
+    StartingProbabilitiesInfectedSevere[0] = criticalPerSevere;
+    StartingProbabilitiesInfectedSevere[(
+        Eigen::Index)(LctState::get_num_subcompartments<InfectionState::InfectedSevere>() / 2.)] =
+        1 - criticalPerSevere;
     model.parameters.get<mio::glsecir::StartingProbabilitiesInfectedSevere<ScalarType>>() =
         StartingProbabilitiesInfectedSevere;
     model.parameters.get<mio::glsecir::TransitionMatrixInfectedSevereToInfectedCritical<ScalarType>>() =
@@ -182,9 +185,10 @@ int main()
     // InfectedCritical.
     Eigen::VectorX<ScalarType> StartingProbabilitiesInfectedCritical =
         Eigen::VectorX<ScalarType>::Zero(LctState::get_num_subcompartments<InfectionState::InfectedCritical>());
-    StartingProbabilitiesInfectedCritical[0]                                         = deathsPerCritical;
-    StartingProbabilitiesInfectedCritical[(Eigen::Index)(
-        LctState::get_num_subcompartments<InfectionState::InfectedCritical>() / 2.)] = 1 - deathsPerCritical;
+    StartingProbabilitiesInfectedCritical[0] = deathsPerCritical;
+    StartingProbabilitiesInfectedCritical[(
+        Eigen::Index)(LctState::get_num_subcompartments<InfectionState::InfectedCritical>() / 2.)] =
+        1 - deathsPerCritical;
     model.parameters.get<mio::glsecir::StartingProbabilitiesInfectedCritical<ScalarType>>() =
         StartingProbabilitiesInfectedCritical;
     model.parameters.get<mio::glsecir::TransitionMatrixInfectedCriticalToDead<ScalarType>>() =

diff --git a/cpp/examples/graph_abm.cpp b/cpp/examples/graph_abm.cpp
@@ -1,5 +1,5 @@
 /*
-* Copyright (C) 2020-2025 MEmilio
+* Copyright (C) 2020-2026 MEmilio
 *
 * Authors: Julia Bicker
 *

diff --git a/cpp/examples/graph_stochastic_mobility.cpp b/cpp/examples/graph_stochastic_mobility.cpp
@@ -1,5 +1,5 @@
 /*
-* Copyright (C) 2020-2025 MEmilio
+* Copyright (C) 2020-2026 MEmilio
 *
 * Authors: Daniel Abele
 *

diff --git a/cpp/examples/history.cpp b/cpp/examples/history.cpp
@@ -1,5 +1,5 @@
 /*
-* Copyright (C) 2020-2025 MEmilio
+* Copyright (C) 2020-2026 MEmilio
 *
 * Authors: Carlotta Gerstein
 *

diff --git a/cpp/examples/ide_initialization.cpp b/cpp/examples/ide_initialization.cpp
@@ -1,5 +1,5 @@
 /*
-* Copyright (C) 2020-2025 MEmilio
+* Copyright (C) 2020-2026 MEmilio
 *
 * Authors:  Lena Ploetzke, Anna Wendler
 *

diff --git a/cpp/examples/ide_secir.cpp b/cpp/examples/ide_secir.cpp
@@ -1,5 +1,5 @@
 /*
-* Copyright (C) 2020-2025 MEmilio
+* Copyright (C) 2020-2026 MEmilio
 *
 * Authors: Anna Wendler, Lena Ploetzke, Hannah Tritzschak
 *

diff --git a/cpp/examples/ide_secir_graph.cpp b/cpp/examples/ide_secir_graph.cpp
@@ -1,5 +1,5 @@
 /*
-* Copyright (C) 2020-2025 MEmilio
+* Copyright (C) 2020-2026 MEmilio
 *
 * Authors: Anna Wendler
 *

diff --git a/cpp/examples/ide_seir.cpp b/cpp/examples/ide_seir.cpp
@@ -1,5 +1,5 @@
 /*
-* Copyright (C) 2020-2025 MEmilio
+* Copyright (C) 2020-2026 MEmilio
 *
 * Authors: Lena Ploetzke
 *

diff --git a/cpp/examples/lct_secir.cpp b/cpp/examples/lct_secir.cpp
@@ -1,5 +1,5 @@
 /*
-* Copyright (C) 2020-2025 MEmilio
+* Copyright (C) 2020-2026 MEmilio
 *
 * Authors: Lena Ploetzke
 *

diff --git a/cpp/examples/ode_mseirs4.cpp b/cpp/examples/ode_mseirs4.cpp
@@ -1,5 +1,5 @@
 /* 
-* Copyright (C) 2020-2025 MEmilio
+* Copyright (C) 2020-2026 MEmilio
 *
 * Authors: Henrik Zunker
 *

diff --git a/cpp/examples/ode_seair.cpp b/cpp/examples/ode_seair.cpp
@@ -1,5 +1,5 @@
 /*
-* Copyright (C) 2020-2025 MEmilio
+* Copyright (C) 2020-2026 MEmilio
 *
 * Authors: Ralf Hannemann-Tamas
 *

diff --git a/cpp/examples/ode_seair_optimization.cpp b/cpp/examples/ode_seair_optimization.cpp
@@ -1,5 +1,5 @@
 /*
-* Copyright (C) 2020-2025 MEmilio
+* Copyright (C) 2020-2026 MEmilio
 *
 * Authors: Ralf Hannemann-Tamas
 *

diff --git a/cpp/examples/ode_secir.cpp b/cpp/examples/ode_secir.cpp
@@ -1,5 +1,5 @@
 /*
-* Copyright (C) 2020-2025 MEmilio
+* Copyright (C) 2020-2026 MEmilio
 *
 * Authors: Daniel Abele, Martin J. Kuehn
 *

diff --git a/cpp/examples/ode_secir_ageres.cpp b/cpp/examples/ode_secir_ageres.cpp
@@ -1,5 +1,5 @@
 /*
-* Copyright (C) 2020-2025 MEmilio
+* Copyright (C) 2020-2026 MEmilio
 *
 * Authors: Daniel Abele, Martin J. Kuehn
 *

diff --git a/cpp/examples/ode_secir_contact_changes.cpp b/cpp/examples/ode_secir_contact_changes.cpp
@@ -1,5 +1,5 @@
 /*
-* Copyright (C) 2020-2025 MEmilio
+* Copyright (C) 2020-2026 MEmilio
 *
 * Authors: Daniel Abele, Martin J. Kuehn
 *

diff --git a/cpp/examples/ode_secir_feedback.cpp b/cpp/examples/ode_secir_feedback.cpp
@@ -1,5 +1,5 @@
 /*
-* Copyright (C) 2020-2025 MEmilio
+* Copyright (C) 2020-2026 MEmilio
 *
 * Authors: Henrik Zunker
 *