Parse branched

examples/full_configuration.json

@@ -12,6 +12,9 @@
     {
       "name": "C"
     },
+    {
+      "name": "M"
+    },
     {
       "name": "H2O2",
       "HLC(298K) [mol m-3 Pa-1]": 1.011596348,

include/open_atmos/mechanism_configuration/validation.hpp

@@ -51,6 +51,26 @@ namespace open_atmos
       const std::string E = "E";
       const std::string Ea = "Ea";
 
+      // Troe
+      const std::string Troe_key = "TROE";
+      const std::string k0_A = "k0_A";
+      const std::string k0_B = "k0_B";
+      const std::string k0_C = "k0_C";
+      const std::string kinf_A = "kinf_A";
+      const std::string kinf_B = "kinf_B";
+      const std::string kinf_C = "kinf_C";
+      const std::string Fc = "Fc";
+      const std::string N = "N";
+
+      // Branched
+      const std::string Branched_key = "BRANCHED_NO_RO2";
+      const std::string X = "X";
+      const std::string Y = "Y";
+      const std::string a0 = "a0";
+      const std::string n = "n";
+      const std::string nitrate_products = "nitrate products";
+      const std::string alkoxy_products = "alkoxy products";
+
     } keys;
 
     struct Configuration
@@ -89,6 +109,18 @@ namespace open_atmos
       const std::vector<std::string> optional_keys{ keys.A, keys.B, keys.C, keys.D, keys.E, keys.Ea, keys.name };
     } arrhenius;
 
+    struct Troe
+    {
+      const std::vector<std::string> required_keys{ keys.products, keys.reactants, keys.type, keys.gas_phase };
+      const std::vector<std::string> optional_keys{ keys.name, keys.k0_A, keys.k0_B, keys.k0_C, keys.kinf_A, keys.kinf_B, keys.kinf_C, keys.Fc, keys.N };
+    } troe;
+
+    struct Branched
+    {
+      const std::vector<std::string> required_keys{ keys.nitrate_products, keys.alkoxy_products, keys.reactants, keys.type, keys.gas_phase };
+      const std::vector<std::string> optional_keys{ keys.name, keys.X, keys.Y, keys.a0, keys.n };
+    } branched;
+
     struct Mechanism
     {
       const std::vector<std::string> required_keys{};

include/open_atmos/types.hpp

@@ -14,23 +14,24 @@ namespace open_atmos
     struct Species
     {
       std::string name;
-
       std::map<std::string, double> optional_numerical_properties;
-
+      /// @brief Unknown properties, prefixed with two underscores (__)
       std::unordered_map<std::string, std::string> unknown_properties;
     };
 
     struct Phase
     {
       std::string name;
       std::vector<std::string> species;
+      /// @brief Unknown properties, prefixed with two underscores (__)
       std::unordered_map<std::string, std::string> unknown_properties;
     };
 
     struct ReactionComponent
     {
       std::string species_name;
       double coefficient;
+      /// @brief Unknown properties, prefixed with two underscores (__)
       std::unordered_map<std::string, std::string> unknown_properties;
     };
 
@@ -47,7 +48,36 @@ namespace open_atmos
       double D{ 300 };
       /// @brief A factor that determines pressure dependence [Pa-1]
       double E{ 0 };
+      /// @brief A list of reactants
+      std::vector<ReactionComponent> reactants;
+      /// @brief A list of products
+      std::vector<ReactionComponent> products;
+      /// @brief An identifier, optional, uniqueness not enforced
+      std::string name;
+      /// @brief An identifier indicating which gas phase this reaction takes place in
+      std::string gas_phase;
+      /// @brief Unknown properties, prefixed with two underscores (__)
+      std::unordered_map<std::string, std::string> unknown_properties;
+    };
 
+    struct Troe
+    {
+      /// @brief low-pressure pre-exponential factor
+      double k0_A = 1.0;
+      /// @brief low-pressure temperature-scaling parameter
+      double k0_B = 0.0;
+      /// @brief low-pressure exponential factor
+      double k0_C = 0.0;
+      /// @brief high-pressure pre-exponential factor
+      double kinf_A = 1.0;
+      /// @brief high-pressure temperature-scaling parameter
+      double kinf_B = 0.0;
+      /// @brief high-pressure exponential factor
+      double kinf_C = 0.0;
+      /// @brief Troe F_c parameter
+      double Fc = 0.6;
+      /// @brief Troe N parameter
+      double N = 1.0;
       /// @brief A list of reactants
       std::vector<ReactionComponent> reactants;
       /// @brief A list of products
@@ -56,13 +86,39 @@ namespace open_atmos
       std::string name;
       /// @brief An identifier indicating which gas phase this reaction takes place in
       std::string gas_phase;
+      /// @brief Unknown properties, prefixed with two underscores (__)
+      std::unordered_map<std::string, std::string> unknown_properties;
+    };
 
+    struct Branched
+    {
+      /// @brief pre-exponential factor
+      double X;
+      /// @brief exponential factor
+      double Y;
+      /// @brief branching factor
+      double a0;
+      /// @brief number of heavy atoms in the RO2 reacting species (excluding the peroxy moiety)
+      int n;
+      /// @brief A list of reactants
+      std::vector<ReactionComponent> reactants;
+      /// @brief A list of nitrate products
+      std::vector<ReactionComponent> nitrate_products;
+      /// @brief A list of alkoxy products
+      std::vector<ReactionComponent> alkoxy_products;
+      /// @brief An identifier, optional, uniqueness not enforced
+      std::string name;
+      /// @brief An identifier indicating which gas phase this reaction takes place in
+      std::string gas_phase;
+      /// @brief Unknown properties, prefixed with two underscores (__)
       std::unordered_map<std::string, std::string> unknown_properties;
     };
 
     struct Reactions
     {
       std::vector<types::Arrhenius> arrhenius;
+      std::vector<types::Troe> troe;
+      std::vector<types::Branched> branched;
     };
 
     struct Mechanism