918 add function to change the tolerance in ide model (#919)

added new model parameter m_tol to IDE-SECIR model

Author: lenaploetzke

cpp/models/ide_secir/model.cpp

@@ -126,7 +126,7 @@ void Model::compute_flow(int idx_InfectionTransitions, Eigen::Index idx_Incoming
     This needs to be adjusted if we are changing the finite difference scheme */
 
     Eigen::Index calc_time_index = (Eigen::Index)std::ceil(
-        parameters.get<TransitionDistributions>()[idx_InfectionTransitions].get_support_max(dt) / dt);
+        parameters.get<TransitionDistributions>()[idx_InfectionTransitions].get_support_max(dt, m_tol) / dt);
 
     Eigen::Index num_time_points = m_transitions.get_num_time_points();
 
@@ -196,13 +196,13 @@ void Model::update_forceofinfection(ScalarType dt, bool initialization)
     // determine the relevant calculation area = union of the supports of the relevant transition distributions
     ScalarType calc_time = std::max(
         {parameters.get<TransitionDistributions>()[(int)InfectionTransition::InfectedNoSymptomsToInfectedSymptoms]
-             .get_support_max(dt),
+             .get_support_max(dt, m_tol),
          parameters.get<TransitionDistributions>()[(int)InfectionTransition::InfectedNoSymptomsToRecovered]
-             .get_support_max(dt),
+             .get_support_max(dt, m_tol),
          parameters.get<TransitionDistributions>()[(int)InfectionTransition::InfectedSymptomsToInfectedSevere]
-             .get_support_max(dt),
+             .get_support_max(dt, m_tol),
          parameters.get<TransitionDistributions>()[(int)InfectionTransition::InfectedSymptomsToRecovered]
-             .get_support_max(dt)});
+             .get_support_max(dt, m_tol)});
 
     // corresponding index
     /* need calc_time_index timesteps in sum,
@@ -262,8 +262,8 @@ void Model::compute_compartment(Eigen::Index idx_InfectionState, Eigen::Index id
 
     // determine relevant calculation area and corresponding index
     ScalarType calc_time =
-        std::max(parameters.get<TransitionDistributions>()[idx_TransitionDistribution1].get_support_max(dt),
-                 parameters.get<TransitionDistributions>()[idx_TransitionDistribution2].get_support_max(dt));
+        std::max(parameters.get<TransitionDistributions>()[idx_TransitionDistribution1].get_support_max(dt, m_tol),
+                 parameters.get<TransitionDistributions>()[idx_TransitionDistribution2].get_support_max(dt, m_tol));
 
     Eigen::Index calc_time_index = (Eigen::Index)std::ceil(calc_time / dt) - 1;
 

cpp/models/ide_secir/model.h

@@ -74,23 +74,23 @@ class Model
 
         ScalarType support_max = std::max(
             {parameters.get<TransitionDistributions>()[(int)InfectionTransition::ExposedToInfectedNoSymptoms]
-                 .get_support_max(dt),
+                 .get_support_max(dt, m_tol),
              parameters.get<TransitionDistributions>()[(int)InfectionTransition::InfectedNoSymptomsToInfectedSymptoms]
-                 .get_support_max(dt),
+                 .get_support_max(dt, m_tol),
              parameters.get<TransitionDistributions>()[(int)InfectionTransition::InfectedNoSymptomsToRecovered]
-                 .get_support_max(dt),
+                 .get_support_max(dt, m_tol),
              parameters.get<TransitionDistributions>()[(int)InfectionTransition::InfectedSymptomsToInfectedSevere]
-                 .get_support_max(dt),
+                 .get_support_max(dt, m_tol),
              parameters.get<TransitionDistributions>()[(int)InfectionTransition::InfectedSymptomsToRecovered]
-                 .get_support_max(dt),
+                 .get_support_max(dt, m_tol),
              parameters.get<TransitionDistributions>()[(int)InfectionTransition::InfectedSevereToInfectedCritical]
-                 .get_support_max(dt),
+                 .get_support_max(dt, m_tol),
              parameters.get<TransitionDistributions>()[(int)InfectionTransition::InfectedSevereToRecovered]
-                 .get_support_max(dt),
+                 .get_support_max(dt, m_tol),
              parameters.get<TransitionDistributions>()[(int)InfectionTransition::InfectedCriticalToDead]
-                 .get_support_max(dt),
+                 .get_support_max(dt, m_tol),
              parameters.get<TransitionDistributions>()[(int)InfectionTransition::InfectedCriticalToRecovered]
-                 .get_support_max(dt)});
+                 .get_support_max(dt, m_tol)});
 
         if (m_transitions.get_num_time_points() < (Eigen::Index)std::ceil(support_max / dt)) {
             log_error(
@@ -195,6 +195,16 @@ class Model
      */
     void compute_recovered();
 
+    /**
+     * @brief Setter for the tolerance used to calculate the maximum support of the TransitionDistributions.
+     *
+     * @param[in] new_tol New tolerance.
+     */
+    void set_tol_for_support_max(ScalarType new_tol)
+    {
+        m_tol = new_tol;
+    }
+
     ParameterSet parameters{}; ///< ParameterSet of Model Parameters.
     /* Attention: m_populations and m_transitions do not necessarily have the same number of time points due to the initialization part. */
     TimeSeries<ScalarType>
@@ -206,6 +216,7 @@ class Model
     ScalarType m_forceofinfection{0}; ///< Force of infection term needed for numerical scheme.
     ScalarType m_N{0}; ///< Total population size of the considered region.
     ScalarType m_deaths_before{0}; ///< Deaths before start of simulation (at time -m_dt).
+    ScalarType m_tol{1e-10}; ///< Tolerance used to calculate the maximum support of the TransitionDistributions.
 };
 
 } // namespace isecir

cpp/tests/test_ide_secir.cpp

@@ -86,6 +86,8 @@ class ModelTestIdeSecir : public testing::Test
         model->parameters.set<mio::isecir::TransmissionProbabilityOnContact>(prob);
         model->parameters.set<mio::isecir::RelativeTransmissionNoSymptoms>(prob);
         model->parameters.set<mio::isecir::RiskOfInfectionFromSymptomatic>(prob);
+
+        model->set_tol_for_support_max(1e-10);
     }
 
     virtual void TearDown()