511 Compute inflow and outflow of models (#574)

Co-authored-by: reneSchm <49305466+reneSchm@users.noreply.github.com>
Co-authored-by: Martin J. Kühn <62713180+mknaranja@users.noreply.github.com>
Co-authored-by: dabele <daniel.abele@dlr.de>

- Compute and Integrate Flows between the Compartments of the ODE model
  - Backwards compatibility with old design (see FlowModel::get_derivatives)
- New FlowModel extending the existing Compartmentalmodel
  - New FlowSimulation extending current Simulation which also calculates flows
  - Converted all ODE models (except ode_sir) to use the FlowModel/FlowSimulation
- Adding Plot table feature for the time series
- Some Performance/Design gains for the Integrator/Simulation
- Removed TotalInfections compartment. This can now easily be computed using the flows
- Added a TypeList with metaprogramming utilities:
  - type_at_index
  - index_of_type
  - is_type_in_list
- Added function extend_index and reduce_index
- And some benchmarks ... :)

cpp/benchmarks/CMakeLists.txt

@@ -37,11 +37,16 @@ endif()
 
 set_target_properties(benchmark PROPERTIES FOLDER "Extern")
 
-add_executable(simulation_benchmark simulation.cpp)
-target_link_libraries(simulation_benchmark PRIVATE memilio ode_secir benchmark::benchmark)
-
 add_executable(integrator_step_benchmark integrator_step.cpp)
 target_link_libraries(integrator_step_benchmark PRIVATE memilio ode_secir benchmark::benchmark)
 
+add_executable(flow_simulation_ode_secirvvs_benchmark flow_simulation_ode_secirvvs.cpp)
+target_link_libraries(flow_simulation_ode_secirvvs_benchmark PRIVATE memilio ode_secirvvs benchmark::benchmark)
+
+add_executable(flow_simulation_ode_seir_benchmark flow_simulation_ode_seir.cpp)
+target_link_libraries(flow_simulation_ode_seir_benchmark PRIVATE memilio ode_seir benchmark::benchmark)
+
+add_executable(simulation_benchmark simulation.cpp)
+target_link_libraries(simulation_benchmark PRIVATE memilio ode_secir benchmark::benchmark)
 add_executable(graph_simulation_benchmark graph_simulation.cpp)
-target_link_libraries(graph_simulation_benchmark PRIVATE memilio ode_secirvvs benchmark::benchmark)
+target_link_libraries(graph_simulation_benchmark PRIVATE memilio ode_secirvvs benchmark::benchmark)

cpp/benchmarks/flow_simulation_ode_secirvvs.cpp

@@ -0,0 +1,116 @@
+/* 
+* Copyright (C) 2020-2023 German Aerospace Center (DLR-SC)
+*
+* Authors: Rene Schmieding, Daniel Abele, Martin J. Kuehn
+*
+* 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.
+*/
+#include "benchmarks/simulation.h"
+#include "benchmarks/flow_simulation_ode_secirvvs.h"
+#include "memilio/compartments/flow_simulation.h"
+#include "memilio/compartments/simulation.h"
+#include "ode_secirvvs/model.h"
+#include <string>
+
+const std::string config_path = "../../benchmarks/simulation.config";
+
+// simulation without flows (not in Model definition and not calculated by Simulation)
+void flowless_sim(::benchmark::State& state)
+{
+    using Model = mio::benchmark::FlowlessModel;
+    // suppress non-critical messages
+    mio::set_log_level(mio::LogLevel::critical);
+    // load config
+    auto cfg = mio::benchmark::SimulationConfig::initialize(config_path);
+    // create model
+    Model model(cfg.num_agegroups);
+    mio::benchmark::setup_model(model);
+    // create simulation
+    std::shared_ptr<mio::IntegratorCore> I =
+        std::make_shared<mio::ControlledStepperWrapper<boost::numeric::odeint::runge_kutta_cash_karp54>>(
+            cfg.abs_tol, cfg.rel_tol, cfg.dt_min, cfg.dt_max);
+    // run benchmark
+    for (auto _ : state) {
+        // This code gets timed
+        mio::benchmark::Simulation<mio::Simulation<Model>> sim(model, cfg.t0, cfg.dt);
+        sim.set_integrator(I);
+        // run sim
+        sim.advance(cfg.t_max);
+    }
+}
+
+// simulation with flows (in Model definition, but NOT calculated by Simulation)
+void flow_sim_comp_only(::benchmark::State& state)
+{
+    using Model = mio::benchmark::FlowModel;
+    // suppress non-critical messages
+    mio::set_log_level(mio::LogLevel::critical);
+    // load config
+    auto cfg = mio::benchmark::SimulationConfig::initialize(config_path);
+    // create model
+    Model model(cfg.num_agegroups);
+    mio::benchmark::setup_model(model);
+    // create simulation
+    std::shared_ptr<mio::IntegratorCore> I =
+        std::make_shared<mio::ControlledStepperWrapper<boost::numeric::odeint::runge_kutta_cash_karp54>>(
+            cfg.abs_tol, cfg.rel_tol, cfg.dt_min, cfg.dt_max);
+    // run benchmark
+    for (auto _ : state) {
+        // This code gets timed
+        mio::osecirvvs::Simulation<mio::Simulation<Model>> sim(model, cfg.t0, cfg.dt);
+        sim.set_integrator(I);
+        // run sim
+        sim.advance(cfg.t_max);
+    }
+}
+
+// simulation with flows (in Model definition and calculated by Simulation)
+void flow_sim(::benchmark::State& state)
+{
+    using Model = mio::benchmark::FlowModel;
+    // suppress non-critical messages
+    mio::set_log_level(mio::LogLevel::critical);
+    // load config
+    auto cfg = mio::benchmark::SimulationConfig::initialize(config_path);
+    // create model
+    Model model(cfg.num_agegroups);
+    mio::benchmark::setup_model(model);
+    // create simulation
+    std::shared_ptr<mio::IntegratorCore> I =
+        std::make_shared<mio::ControlledStepperWrapper<boost::numeric::odeint::runge_kutta_cash_karp54>>(
+            cfg.abs_tol, cfg.rel_tol, cfg.dt_min, cfg.dt_max);
+    // run benchmark
+    for (auto _ : state) {
+        // This code gets timed
+        mio::osecirvvs::Simulation<mio::FlowSimulation<Model>> sim(model, cfg.t0, cfg.dt);
+        sim.set_integrator(I);
+        // run sim
+        sim.advance(cfg.t_max);
+    }
+}
+
+// register functions as a benchmarks and set a name
+// mitigate influence of cpu scaling
+BENCHMARK(flowless_sim)->Name("Dummy 1/3");
+BENCHMARK(flowless_sim)->Name("Dummy 2/3");
+BENCHMARK(flowless_sim)->Name("Dummy 3/3");
+// actual benchmarks
+BENCHMARK(flowless_sim)
+    ->Name(
+        "osecirvvs::Simulation<mio::Simulation> on osecirvvs::Model (osecirvvs::* from pre 511 branch) without flows");
+BENCHMARK(flow_sim_comp_only)->Name("osecirvvs::Simulation<mio::Simulation> on osecirvvs::Model with flows");
+BENCHMARK(flow_sim)->Name("osecirvvs::Simulation<mio::FlowSimulation> on osecirvvs::Model with flows");
+// run all benchmarks
+BENCHMARK_MAIN();