third draft

include/micm/configure/solver_config.hpp

@@ -102,6 +102,7 @@ namespace micm
     System system_;
     std::vector<Process> processes_;
     RosenbrockSolverParameters parameters_;
+    double relative_tolerance_;    
 
     SolverParameters(const System& system, std::vector<Process>&& processes, const RosenbrockSolverParameters&& parameters)
         : system_(system),
@@ -116,6 +117,13 @@ namespace micm
           parameters_(parameters)
     {
     }
+    SolverParameters(System&& system, std::vector<Process>&& processes, RosenbrockSolverParameters&& parameters, double relative_tolerance)
+        : system_(system),
+          processes_(processes),
+          parameters_(parameters), 
+          relative_tolerance_(relative_tolerance)
+    {
+    }
   };
 
   class ConfigReaderPolicy
@@ -138,6 +146,7 @@ namespace micm
     std::unordered_map<std::string, Phase> phases_;
     std::vector<Process> processes_;
     RosenbrockSolverParameters parameters_;
+    double relative_tolerance_;
 
     // Common YAML
     inline static const std::string DEFAULT_CONFIG_FILE_JSON = "config.json";
@@ -273,7 +282,7 @@ namespace micm
       processes_.clear();
 
       // Parse species object array
-      ParseSpeciesArray(species_objects);
+      ParseSpeciesArray(species_objects);     
 
       // Assign the parsed 'Species' to 'Phase'
       std::vector<Species> species_arr;
@@ -426,7 +435,7 @@ namespace micm
     void ParseRelativeTolerance(const objectType& object)
     {
       ValidateSchema(object, { "value", "type" }, {});
-      //this->parameters_.relative_tolerance_ = object["value"].as<double>();
+      this->relative_tolerance_ = object["value"].as<double>();
     }
 
     void ParseMechanism(const objectType& object)
@@ -959,7 +968,7 @@ namespace micm
     SolverParameters GetSolverParams()
     {
       return SolverParameters(
-          std::move(System(this->gas_phase_, this->phases_)), std::move(this->processes_), std::move(this->parameters_));
+          std::move(System(this->gas_phase_, this->phases_)), std::move(this->processes_), std::move(this->parameters_), std::move(this->relative_tolerance_));
     }
   };
 }  // namespace micm

include/micm/solver/rosenbrock_solver_parameters.hpp

@@ -9,8 +9,6 @@
 #include <limits>
 #include <vector>
 
-//#include "../include/micm/solver/solver.hpp"
-
 namespace micm
 {
 

include/micm/solver/solver_builder.hpp

@@ -50,6 +50,7 @@ namespace micm
     bool reorder_state_ = true;
     bool valid_system_ = false;
     bool valid_reactions_ = false;
+    double relative_tolerance_ = 1e-06;
 
    public:
     SolverBuilder() = delete;

include/micm/solver/solver_builder.inl

@@ -316,7 +316,7 @@ namespace micm
         }
       }
     }
-  }
+  }  
 
   template<
       class SolverParametersPolicy,
@@ -399,7 +399,7 @@ namespace micm
                                          .nonzero_jacobian_elements_ = nonzero_elements };
 
 
-    this->SetAbsoluteTolerances(state_parameters.absolute_tolerance_, species_map); //WHERE TO ADD THIS??????
+    this->SetAbsoluteTolerances(state_parameters.absolute_tolerance_, species_map);
 
     return Solver<SolverPolicy, StatePolicy>(
         SolverPolicy(options, std::move(linear_solver), std::move(rates), jacobian),

include/micm/solver/state.hpp

@@ -31,7 +31,7 @@ namespace micm
     std::vector<std::string> variable_names_{};
     std::vector<std::string> custom_rate_parameter_labels_{};
     std::set<std::pair<std::size_t, std::size_t>> nonzero_jacobian_elements_{};
-    double relative_tolerance_;
+    double relative_tolerance_{ 1e-06 };
     std::vector<double> absolute_tolerance_ {};
   };
 
@@ -140,6 +140,7 @@ namespace micm
     /// @param value new parameter value
     void SetCustomRateParameter(const std::string& label, double value);
     void SetCustomRateParameter(const std::string& label, const std::vector<double>& values);
+    void SetRelativeTolerances(double relativeTolerance);
 
     /// @brief Print a header of species to display concentrations with respect to time
     void PrintHeader();

include/micm/solver/state.inl

@@ -187,6 +187,12 @@ namespace micm
     for (std::size_t i = 0; i < custom_rate_parameters_.NumRows(); ++i)
       custom_rate_parameters_[i][param->second] = values[i];
   }
+
+  template<class DenseMatrixPolicy, class SparseMatrixPolicy>
+  inline void State<DenseMatrixPolicy, SparseMatrixPolicy>::SetRelativeTolerances(double relativeTolerance)
+  {
+    this->relative_tolerance_ = relativeTolerance;
+  }
 
   template<class DenseMatrixPolicy, class SparseMatrixPolicy>
   inline void State<DenseMatrixPolicy, SparseMatrixPolicy>::PrintHeader()

test/integration/test_chapman_integration.cpp

@@ -32,17 +32,17 @@ TEST(ChapmanIntegration, CanBuildChapmanSystemUsingConfig)
   // Get solver parameters ('System', the collection of 'Process')
   micm::SolverParameters solver_params = solverConfig.GetSolverParams();
 
-  auto options = solver_params.parameters_;  
+  auto options = solver_params.parameters_;   
 
   auto solver = micm::CpuSolverBuilder<micm::RosenbrockSolverParameters>(options)
                     .SetSystem(solver_params.system_)
                     .SetReactions(solver_params.processes_)
-                    .SetIgnoreUnusedSpecies(true)
-                    .Build();
+                    .SetIgnoreUnusedSpecies(true)                    
+                    .Build(); 
 
   micm::State state = solver.GetState();
-
-  EXPECT_EQ(state.relative_tolerance_, 1.0e-6);
+  state.SetRelativeTolerances(solver_params.relative_tolerance_); 
+  EXPECT_EQ(state.relative_tolerance_, 1.0e-4);
 
   for (size_t n_grid_cell = 0; n_grid_cell < state.number_of_grid_cells_; ++n_grid_cell)
   {

test/unit/solver/test_solver_builder.cpp

@@ -105,7 +105,6 @@ TEST(SolverBuilder, CanBuildRosenbrock)
                                .SetNumberOfGridCells(1)
                                .Build();
 }
-
 /*
 TEST(SolverBuilder, MismatchedToleranceSizeIsCaught)
 {
@@ -128,5 +127,4 @@ TEST(SolverBuilder, MismatchedToleranceSizeIsCaught)
       micm::SparseMatrix<double, micm::SparseMatrixVectorOrdering<L>>>(params);
 
   EXPECT_ANY_THROW(builder.SetSystem(the_system).SetReactions(reactions).SetNumberOfGridCells(1).Build(););
-}
-*/
+}*/