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open-atmos · Jan 19, 2024 · 12734bd · 12734bd
2 parents 2a35273 + 80da0d7
commit 12734bd
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Showing 38 changed files with 1,336 additions and 27 deletions.
diff --git a/examples/full_configuration.json b/examples/full_configuration.json
@@ -198,7 +198,7 @@
     {
       "type": "EMISSION",
       "gas phase": "gas",
-      "reactants": [
+      "products": [
         {
           "species name": "B",
           "coefficient": 1
@@ -210,7 +210,7 @@
     {
       "type": "FIRST_ORDER_LOSS",
       "gas phase": "gas",
-      "products": [
+      "reactants": [
         {
           "species name": "C",
           "coefficient": 1

diff --git a/include/open_atmos/mechanism_configuration/parser.hpp b/include/open_atmos/mechanism_configuration/parser.hpp
@@ -34,7 +34,8 @@ namespace open_atmos
       PhaseRequiresUnknownSpecies,
       ReactionRequiresUnknownSpecies,
       UnknownPhase,
-      RequestedAerosolSpeciesNotIncludedInAerosolPhase
+      RequestedAerosolSpeciesNotIncludedInAerosolPhase,
+      TooManyReactionComponents
     };
     std::string configParseStatusToString(const ConfigParseStatus &status);
 

diff --git a/include/open_atmos/mechanism_configuration/validation.hpp b/include/open_atmos/mechanism_configuration/validation.hpp
@@ -97,6 +97,18 @@ namespace open_atmos
       const std::string gas_phase_products = "gas-phase products";
       const std::string aerosol_phase = "aerosol phase";
 
+      // Photolysis
+      const std::string Photolysis_key = "PHOTOLYSIS";
+      const std::string scaling_factor = "scaling factor";
+
+      // Emissions
+      const std::string Emission_key = "EMISSION";
+      // also scaling factor
+
+      // First Order Loss
+      const std::string FirstOrderLoss_key = "FIRST_ORDER_LOSS";
+      // also scaling factor
+
     } keys;
 
     struct Configuration
@@ -167,6 +179,24 @@ namespace open_atmos
       const std::vector<std::string> optional_keys{ keys.name, keys.reaction_probability };
     } surface;
 
+    struct Photolysis
+    {
+      const std::vector<std::string> required_keys{ keys.reactants, keys.products, keys.type, keys.gas_phase };
+      const std::vector<std::string> optional_keys{ keys.name, keys.scaling_factor };
+    } photolysis;
+
+    struct Emission
+    {
+      const std::vector<std::string> required_keys{ keys.products, keys.type, keys.gas_phase };
+      const std::vector<std::string> optional_keys{ keys.name, keys.scaling_factor };
+    } emission;
+
+    struct FirstOrderLoss
+    {
+      const std::vector<std::string> required_keys{ keys.reactants, keys.type, keys.gas_phase };
+      const std::vector<std::string> optional_keys{ keys.name, keys.scaling_factor };
+    } first_order_loss;
+
     struct Mechanism
     {
       const std::vector<std::string> required_keys{};

diff --git a/include/open_atmos/types.hpp b/include/open_atmos/types.hpp
@@ -179,6 +179,50 @@ namespace open_atmos
       std::unordered_map<std::string, std::string> unknown_properties;
     };
 
+    struct Photolysis
+    {
+      /// @brief Scaling factor to apply to user-provided rate constants
+      double scaling_factor_{ 1.0 };
+      /// @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 Emission
+    {
+      /// @brief Scaling factor to apply to user-provided rate constants
+      double scaling_factor_{ 1.0 };
+      /// @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 FirstOrderLoss
+    {
+      /// @brief Scaling factor to apply to user-provided rate constants
+      double scaling_factor_{ 1.0 };
+      /// @brief A list of reactants
+      std::vector<ReactionComponent> reactants;
+      /// @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;
@@ -187,6 +231,9 @@ namespace open_atmos
       std::vector<types::Branched> branched;
       std::vector<types::Tunneling> tunneling;
       std::vector<types::Surface> surface;
+      std::vector<types::Photolysis> photolysis;
+      std::vector<types::Emission> emission;
+      std::vector<types::FirstOrderLoss> first_order_loss;
     };
 
     struct Mechanism