1522 Improve DynamicNPI structure through harmonization across models and more options

cpp/benchmarks/CMakeLists.txt

@@ -34,5 +34,8 @@ target_link_libraries(simulation_benchmark PRIVATE memilio ode_secir benchmark::
 add_executable(graph_simulation_benchmark graph_simulation.cpp)
 target_link_libraries(graph_simulation_benchmark PRIVATE memilio ode_secirvvs benchmark::benchmark)
 
+add_executable(secirvvs_advance_benchmark secirvvs_advance.cpp)
+target_link_libraries(secirvvs_advance_benchmark PRIVATE memilio ode_secirvvs benchmark::benchmark)
+
 add_executable(abm_benchmark abm.cpp)
 target_link_libraries(abm_benchmark PRIVATE abm benchmark::benchmark)

cpp/benchmarks/flow_simulation_ode_secirvvs.h

@@ -42,8 +42,8 @@ class FlowlessModel : public CompartmentalModel<ScalarType, osecirvvs::Infection
 {
     using InfectionState = osecirvvs::InfectionState;
     using Base           = CompartmentalModel<ScalarType, osecirvvs::InfectionState,
-                                              mio::Populations<ScalarType, AgeGroup, osecirvvs::InfectionState>,
-                                              osecirvvs::Parameters<ScalarType>>;
+                                    mio::Populations<ScalarType, AgeGroup, osecirvvs::InfectionState>,
+                                    osecirvvs::Parameters<ScalarType>>;
 
 public:
     FlowlessModel(const Populations& pop, const ParameterSet& params)
@@ -539,7 +539,6 @@ class Simulation : public Base
     */
     Eigen::Ref<Eigen::VectorX<ScalarType>> advance(ScalarType tmax)
     {
-        auto& t_end_dyn_npis = this->get_model().parameters.get_end_dynamic_npis();
         auto& dyn_npis =
             this->get_model().parameters.template get<osecirvvs::DynamicNPIsInfectedSymptoms<ScalarType>>();
         auto& contact_patterns  = this->get_model().parameters.template get<osecirvvs::ContactPatterns<ScalarType>>();
@@ -549,45 +548,36 @@ class Simulation : public Base
             this->get_model().parameters.template get<osecirvvs::TransmissionProbabilityOnContact<ScalarType>>();
 
         ScalarType delay_npi_implementation;
-        auto t        = Base::get_result().get_last_time();
-        const auto dt = dyn_npis.get_interval().get();
+        auto t = Base::get_result().get_last_time();
         while (t < tmax) {
 
-            auto dt_eff = std::min({dt, tmax - t, m_t_last_npi_check + dt - t});
-            if (dt_eff >= 1.0) {
-                dt_eff = 1.0;
+            if (t > 0) {
+                delay_npi_implementation = ScalarType(dyn_npis.get_implementation_delay());
+            }
+            else { // DynamicNPIs for t=0 are 'misused' to be from-start NPIs. I.e., do not enforce delay.
+                delay_npi_implementation = 0;
             }
-
             if (t == 0) {
                 //this->apply_vaccination(t); // done in init now?
                 this->apply_variant(t, base_infectiousness);
             }
-            Base::advance(t + dt_eff);
-            if (t + 0.5 + dt_eff - std::floor(t + 0.5) >= 1) {
-                this->apply_vaccination(t + 0.5 + dt_eff);
-                this->apply_variant(t, base_infectiousness);
-            }
-
-            if (t > 0) {
-                delay_npi_implementation = 7;
-            }
-            else {
-                delay_npi_implementation = 0;
-            }
-            t = t + dt_eff;
 
             if (dyn_npis.get_thresholds().size() > 0) {
-                if (floating_point_greater_equal(t, m_t_last_npi_check + dt)) {
-                    if (t < t_end_dyn_npis) {
-                        auto inf_rel = get_infections_relative(*this, t, this->get_result().get_last_value()) *
-                                       dyn_npis.get_base_value();
-                        auto exceeded_threshold = dyn_npis.get_max_exceeded_threshold(inf_rel);
-                        if (exceeded_threshold != dyn_npis.get_thresholds().end() &&
-                            (exceeded_threshold->first > m_dynamic_npi.first ||
-                             t > ScalarType(m_dynamic_npi.second))) { //old npi was weaker or is expired
-
+                ScalarType direc_begin = ScalarType(dyn_npis.get_directive_begin());
+                ScalarType direc_end   = ScalarType(dyn_npis.get_directive_end());
+                if (floating_point_greater_equal(t, direc_begin, 1e-10) && t < direc_end) {
+                    auto inf_rel = get_infections_relative(*this, t, this->get_result().get_last_value()) *
+                                   dyn_npis.get_base_value();
+                    auto exceeded_threshold = dyn_npis.get_max_exceeded_threshold(inf_rel);
+                    if (exceeded_threshold != dyn_npis.get_thresholds().end() &&
+                        (exceeded_threshold->first > m_dynamic_npi.first ||
+                         t > ScalarType(m_dynamic_npi.second))) { // old npi was weaker or is expired
+
+                        if (t + delay_npi_implementation < direc_end) {
                             auto t_start = SimulationTime<ScalarType>(t + delay_npi_implementation);
-                            auto t_end   = t_start + SimulationTime<ScalarType>(dyn_npis.get_duration());
+                            // set the end to the minimum of start+delay and the end of the directive
+                            auto t_end = SimulationTime<ScalarType>(
+                                min<ScalarType>(direc_end, ScalarType(t_start + dyn_npis.get_duration())));
                             this->get_model().parameters.get_start_commuter_detection() = t_start.get();
                             this->get_model().parameters.get_end_commuter_detection()   = t_end.get();
                             m_dynamic_npi = std::make_pair(exceeded_threshold->first, t_end);
@@ -597,12 +587,16 @@ class Simulation : public Base
                                                    });
                         }
                     }
-                    m_t_last_npi_check = t;
                 }
             }
-            else {
-                m_t_last_npi_check = t;
+
+            auto dt_eff = min<ScalarType>(1.0, tmax - t);
+            Base::advance(t + dt_eff);
+            if (t + 0.5 + dt_eff - std::floor(t + 0.5) >= 1) {
+                this->apply_vaccination(t + 0.5 + dt_eff);
+                this->apply_variant(t, base_infectiousness);
             }
+            t = t + dt_eff;
         }
 
         this->get_model().parameters.template get<osecirvvs::TransmissionProbabilityOnContact<ScalarType>>() =
@@ -719,6 +713,15 @@ void setup_model(Model& model)
     model.parameters.template get<osecirvvs::ReducTimeInfectedMild<ScalarType>>()[AgeGroup(0)]               = 0.9;
 
     model.parameters.template get<osecirvvs::Seasonality<ScalarType>>() = 0.2;
+
+    auto& npis      = model.parameters.template get<osecirvvs::DynamicNPIsInfectedSymptoms<ScalarType>>();
+    auto npi_groups = Eigen::VectorXd::Ones(contact_matrix[0].get_num_groups());
+    npis.set_threshold(0.01 * 100'000, {DampingSampling<ScalarType>(0.5, DampingLevel(0), DampingType(0),
+                                                                    SimulationTime<ScalarType>(0), {0}, npi_groups)});
+    npis.set_base_value(100'000);
+    npis.set_implementation_delay(SimulationTime<ScalarType>(7.0));
+    npis.set_duration(SimulationTime<ScalarType>(14.0));
+
     // The function apply_constraints() ensures that all parameters are within their defined bounds.
     // Note that negative values are set to zero instead of stopping the simulation.
     model.apply_constraints();

cpp/benchmarks/secirvvs_advance.cpp

@@ -0,0 +1,93 @@
+/*
+* Copyright (C) 2020-2026 MEmilio
+*
+* Authors: Henrik Zunker
+*
+* 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.
+*/
+
+/**
+ * Benchmark comparing the overhead of the model-specific osecirvvs::Simulation::advance()
+ * (which uses substeps and calls apply_vaccination / apply_variant / dynamic NPI checks)
+ * versus the generic mio::Simulation::advance() (a single integrator call for the entire range).
+ */
+
+#include "ode_secirvvs/model.h"
+#include "memilio/compartments/simulation.h"
+#include "memilio/utils/logging.h"
+#include "benchmark/benchmark.h"
+
+using FP    = double;
+using Model = mio::osecirvvs::Model<FP>;
+
+static Model make_model(bool with_npis = false)
+{
+    constexpr int tmax = 10;
+    Model model(1);
+    model.populations[{mio::AgeGroup(0), mio::osecirvvs::InfectionState::InfectedSymptomsNaive}] = 100.0;
+    model.populations.set_difference_from_total({mio::AgeGroup(0), mio::osecirvvs::InfectionState::SusceptibleNaive},
+                                                10000.0);
+    model.parameters.get<mio::osecirvvs::DailyPartialVaccinations<FP>>().resize(mio::SimulationDay(size_t(tmax + 1)));
+    model.parameters.get<mio::osecirvvs::DailyFullVaccinations<FP>>().resize(mio::SimulationDay(size_t(tmax + 1)));
+    if (with_npis) {
+        auto& npis = model.parameters.get<mio::osecirvvs::DynamicNPIsInfectedSymptoms<FP>>();
+        npis.set_threshold(0.01 * 100'000, {mio::DampingSampling<FP>{1.0,
+                                                                     mio::DampingLevel(0),
+                                                                     mio::DampingType(0),
+                                                                     mio::SimulationTime<FP>(0),
+                                                                     {0},
+                                                                     Eigen::VectorXd::Ones(1)}});
+        npis.set_duration(mio::SimulationTime<FP>(14.0));
+        npis.set_base_value(100'000);
+    }
+    return model;
+}
+
+// Generic advance: single integrator call for the full [t0, tmax] range.
+static void BM_generic(benchmark::State& state)
+{
+    mio::set_log_level(mio::LogLevel::off);
+    auto model = make_model();
+    for (auto _ : state) {
+        mio::simulate<FP, Model>(0., 10., 0.1, model);
+    }
+}
+
+// Model-specific advance without dynamic NPIs: 1-day loop with apply_vaccination + apply_variant,
+// dynamic NPI threshold check is skipped (thresholds empty).
+static void BM_secirvvs_no_npis(benchmark::State& state)
+{
+    mio::set_log_level(mio::LogLevel::off);
+    auto model = make_model(/*with_npis=*/false);
+    for (auto _ : state) {
+        mio::osecirvvs::simulate<FP>(0., 10., 0.1, model);
+    }
+}
+
+// Model-specific advance with dynamic NPIs: same as above plus get_infections_relative +
+// threshold comparison on every day step.
+static void BM_secirvvs_with_npis(benchmark::State& state)
+{
+    mio::set_log_level(mio::LogLevel::off);
+    auto model = make_model(/*with_npis=*/true);
+    for (auto _ : state) {
+        mio::osecirvvs::simulate<FP>(0., 10., 0.1, model);
+    }
+}
+
+BENCHMARK(BM_generic)->Name("SECIRVVS generic advance");
+BENCHMARK(BM_secirvvs_no_npis)->Name("SECIRVVS model-specific advance (no dynamic NPIs)");
+BENCHMARK(BM_secirvvs_with_npis)->Name("SECIRVVS model-specific advance (with dynamic NPIs)");
+BENCHMARK_MAIN();

cpp/examples/ode_secirvvs.cpp

@@ -79,7 +79,6 @@ int main()
             .get<mio::osecirvvs::DailyFullVaccinations<double>>()[{(mio::AgeGroup)0, mio::SimulationDay(i)}] =
             num_vaccinations;
     }
-    model.parameters.get<mio::osecirvvs::DynamicNPIsImplementationDelay<double>>() = 7;
 
     auto& contacts       = model.parameters.get<mio::osecirvvs::ContactPatterns<double>>();
     auto& contact_matrix = contacts.get_cont_freq_mat();