Merge pull request #36 from open-atmos/parse_wet_deposition

Parse wet deposition
open-atmos · Jan 23, 2024 · ef7f3a0 · ef7f3a0
2 parents fe81f91 + 5ad59ba
commit ef7f3a0
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Showing 11 changed files with 191 additions and 13 deletions.
diff --git a/examples/full_configuration.json b/examples/full_configuration.json
@@ -358,7 +358,6 @@
     },
     {
       "type": "WET_DEPOSITION",
-      "gas phase": "gas",
       "aerosol phase": "cloud",
       "name": "rxn cloud",
       "scaling factor": 12.3

diff --git a/include/open_atmos/mechanism_configuration/validation.hpp b/include/open_atmos/mechanism_configuration/validation.hpp
@@ -116,6 +116,12 @@ namespace open_atmos
       const std::string FirstOrderLoss_key = "FIRST_ORDER_LOSS";
       // also scaling factor
 
+      // Wet Deposition
+      const std::string WetDeposition_key = "WET_DEPOSITION";
+      // also
+      // scaling factor
+      // aerosol phase
+
       // Henry's Law Phase Transfer
       const std::string HenrysLaw_key = "HL_PHASE_TRANSFER";
       const std::string gas_phase_species = "gas-phase species";
@@ -219,6 +225,12 @@ namespace open_atmos
       const std::vector<std::string> optional_keys{ keys.name, keys.scaling_factor };
     } first_order_loss;
 
+    struct WetDeposition
+    {
+      const std::vector<std::string> required_keys{ keys.aerosol_phase, keys.type };
+      const std::vector<std::string> optional_keys{ keys.name, keys.scaling_factor };
+    } wet_deposition;
+
     struct HenrysLaw
     {
       const std::vector<std::string> required_keys{ keys.type, keys.gas_phase, keys.gas_phase_species, keys.aerosol_phase, keys.aerosol_phase_species, keys.aerosol_phase_water };

diff --git a/include/open_atmos/types.hpp b/include/open_atmos/types.hpp
@@ -182,7 +182,7 @@ namespace open_atmos
     struct Photolysis
     {
       /// @brief Scaling factor to apply to user-provided rate constants
-      double scaling_factor_{ 1.0 };
+      double scaling_factor{ 1.0 };
       /// @brief A list of reactants
       std::vector<ReactionComponent> reactants;
       /// @brief A list of products
@@ -216,7 +216,7 @@ namespace open_atmos
     struct Emission
     {
       /// @brief Scaling factor to apply to user-provided rate constants
-      double scaling_factor_{ 1.0 };
+      double scaling_factor{ 1.0 };
       /// @brief A list of products
       std::vector<ReactionComponent> products;
       /// @brief An identifier, optional, uniqueness not enforced
@@ -230,7 +230,7 @@ namespace open_atmos
     struct FirstOrderLoss
     {
       /// @brief Scaling factor to apply to user-provided rate constants
-      double scaling_factor_{ 1.0 };
+      double scaling_factor{ 1.0 };
       /// @brief A list of reactants
       std::vector<ReactionComponent> reactants;
       /// @brief An identifier, optional, uniqueness not enforced
@@ -241,6 +241,18 @@ namespace open_atmos
       std::unordered_map<std::string, std::string> unknown_properties;
     };
 
+    struct WetDeposition
+    {
+      /// @brief Scaling factor to apply to user-provided rate constants
+      double scaling_factor{ 1.0 };
+      /// @brief An identifier, optional, uniqueness not enforced
+      std::string name;
+      /// @brief An identifier indicating which aerosol phase this reaction takes place in
+      std::string aerosol_phase;
+      /// @brief Unknown properties, prefixed with two underscores (__)
+      std::unordered_map<std::string, std::string> unknown_properties;
+    };
+
     struct HenrysLaw
     {
       /// @brief An identifier, optional, uniqueness not enforced
@@ -267,6 +279,7 @@ namespace open_atmos
       std::vector<types::CondensedPhasePhotolysis> condensed_phase_photolysis;
       std::vector<types::Emission> emission;
       std::vector<types::FirstOrderLoss> first_order_loss;
+      std::vector<types::WetDeposition> wet_deposition;
       std::vector<types::HenrysLaw> henrys_law;
       std::vector<types::Photolysis> photolysis;
       std::vector<types::Surface> surface;

diff --git a/src/parser.cpp b/src/parser.cpp
@@ -1024,7 +1024,7 @@ namespace open_atmos
 
         if (object.contains(validation::keys.scaling_factor))
         {
-          photolysis.scaling_factor_ = object[validation::keys.scaling_factor].get<double>();
+          photolysis.scaling_factor = object[validation::keys.scaling_factor].get<double>();
         }
 
         if (object.contains(validation::keys.name))
@@ -1213,7 +1213,7 @@ namespace open_atmos
 
         if (object.contains(validation::keys.scaling_factor))
         {
-          emission.scaling_factor_ = object[validation::keys.scaling_factor].get<double>();
+          emission.scaling_factor = object[validation::keys.scaling_factor].get<double>();
         }
 
         if (object.contains(validation::keys.name))
@@ -1284,7 +1284,7 @@ namespace open_atmos
 
         if (object.contains(validation::keys.scaling_factor))
         {
-          first_order_loss.scaling_factor_ = object[validation::keys.scaling_factor].get<double>();
+          first_order_loss.scaling_factor = object[validation::keys.scaling_factor].get<double>();
         }
 
         if (object.contains(validation::keys.name))
@@ -1332,6 +1332,55 @@ namespace open_atmos
       return { status, first_order_loss };
     }
 
+    /// @brief Parses a wet deposition reaction
+    /// @param object A json object that should have information containing arrhenius parameters
+    /// @param existing_species A list of species configured in a mechanism
+    /// @param existing_phases A list of phases configured in a mechanism
+    /// @return A pair indicating parsing success and a struct of First Order Loss parameters
+    std::pair<ConfigParseStatus, types::WetDeposition>
+    ParseWetDeposition(const json& object, const std::vector<types::Species> existing_species, const std::vector<types::Phase> existing_phases)
+    {
+      ConfigParseStatus status = ConfigParseStatus::Success;
+      types::WetDeposition wet_deposition;
+
+      status = ValidateSchema(object, validation::wet_deposition.required_keys, validation::wet_deposition.optional_keys);
+      if (status == ConfigParseStatus::Success)
+      {
+        if (object.contains(validation::keys.scaling_factor))
+        {
+          wet_deposition.scaling_factor = object[validation::keys.scaling_factor].get<double>();
+        }
+
+        if (object.contains(validation::keys.name))
+        {
+          wet_deposition.name = object[validation::keys.name].get<std::string>();
+        }
+
+        auto comments = GetComments(object, validation::wet_deposition.required_keys, validation::wet_deposition.optional_keys);
+
+        std::unordered_map<std::string, std::string> unknown_properties;
+        for (const auto& key : comments)
+        {
+          std::string val = object[key].dump();
+          unknown_properties[key] = val;
+        }
+
+        std::string aerosol_phase = object[validation::keys.aerosol_phase].get<std::string>();
+
+        // check if aerosol phase exists
+        auto it = std::find_if(existing_phases.begin(), existing_phases.end(), [&aerosol_phase](const auto& phase) { return phase.name == aerosol_phase; });
+        if (status == ConfigParseStatus::Success && it == existing_phases.end())
+        {
+          status = ConfigParseStatus::UnknownPhase;
+        }
+
+        wet_deposition.aerosol_phase = aerosol_phase;
+        wet_deposition.unknown_properties = unknown_properties;
+      }
+
+      return { status, wet_deposition };
+    }
+
     /// @brief Parses a first order loss reaction
     /// @param object A json object that should have information containing arrhenius parameters
     /// @param existing_species A list of species configured in a mechanism
@@ -1528,6 +1577,16 @@ namespace open_atmos
           }
           reactions.first_order_loss.push_back(first_order_loss_parse.second);
         }
+        else if (type == validation::keys.WetDeposition_key)
+        {
+          auto wet_deposition_parse = ParseWetDeposition(object, existing_species, existing_phases);
+          status = wet_deposition_parse.first;
+          if (status != ConfigParseStatus::Success)
+          {
+            break;
+          }
+          reactions.wet_deposition.push_back(wet_deposition_parse.second);
+        }
         else if (type == validation::keys.HenrysLaw_key)
         {
           auto henrys_law_parse = ParseHenrysLaw(object, existing_species, existing_phases);

diff --git a/test/unit/CMakeLists.txt b/test/unit/CMakeLists.txt
@@ -19,6 +19,7 @@ create_standard_test(NAME parse_species SOURCES test_parse_species.cpp)
 create_standard_test(NAME parse_surface SOURCES test_parse_surface.cpp)
 create_standard_test(NAME parse_troe SOURCES test_parse_troe.cpp)
 create_standard_test(NAME parse_tunneling SOURCES test_parse_tunneling.cpp)
+create_standard_test(NAME parse_wet_deposition SOURCES test_parse_wet_deposition.cpp)
 
 ################################################################################
 # Copy test data

diff --git a/test/unit/test_parse_emission.cpp b/test/unit/test_parse_emission.cpp
@@ -14,15 +14,15 @@ TEST(JsonParser, CanParseValidEmissionReaction)
 
   EXPECT_EQ(mechanism.reactions.emission[0].gas_phase, "gas");
   EXPECT_EQ(mechanism.reactions.emission[0].name, "my emission");
-  EXPECT_EQ(mechanism.reactions.emission[0].scaling_factor_, 12.3);
+  EXPECT_EQ(mechanism.reactions.emission[0].scaling_factor, 12.3);
   EXPECT_EQ(mechanism.reactions.emission[0].products.size(), 1);
   EXPECT_EQ(mechanism.reactions.emission[0].products[0].species_name, "B");
   EXPECT_EQ(mechanism.reactions.emission[0].products[0].coefficient, 1);
   EXPECT_EQ(mechanism.reactions.emission[0].unknown_properties.size(), 1);
   EXPECT_EQ(mechanism.reactions.emission[0].unknown_properties["__comment"], "\"Dr. Pepper outranks any other soda\"");
 
   EXPECT_EQ(mechanism.reactions.emission[1].gas_phase, "gas");
-  EXPECT_EQ(mechanism.reactions.emission[1].scaling_factor_, 1);
+  EXPECT_EQ(mechanism.reactions.emission[1].scaling_factor, 1);
   EXPECT_EQ(mechanism.reactions.emission[1].products.size(), 1);
   EXPECT_EQ(mechanism.reactions.emission[1].products[0].species_name, "B");
   EXPECT_EQ(mechanism.reactions.emission[1].products[0].coefficient, 1);

diff --git a/test/unit/test_parse_first_order_loss.cpp b/test/unit/test_parse_first_order_loss.cpp
@@ -14,15 +14,15 @@ TEST(JsonParser, CanParseValidFirstOrderLossReaction)
 
   EXPECT_EQ(mechanism.reactions.first_order_loss[0].gas_phase, "gas");
   EXPECT_EQ(mechanism.reactions.first_order_loss[0].name, "my first order loss");
-  EXPECT_EQ(mechanism.reactions.first_order_loss[0].scaling_factor_, 12.3);
+  EXPECT_EQ(mechanism.reactions.first_order_loss[0].scaling_factor, 12.3);
   EXPECT_EQ(mechanism.reactions.first_order_loss[0].reactants.size(), 1);
   EXPECT_EQ(mechanism.reactions.first_order_loss[0].reactants[0].species_name, "C");
   EXPECT_EQ(mechanism.reactions.first_order_loss[0].reactants[0].coefficient, 1);
   EXPECT_EQ(mechanism.reactions.first_order_loss[0].unknown_properties.size(), 1);
   EXPECT_EQ(mechanism.reactions.first_order_loss[0].unknown_properties["__comment"], "\"Strawberries are the superior fruit\"");
 
   EXPECT_EQ(mechanism.reactions.first_order_loss[1].gas_phase, "gas");
-  EXPECT_EQ(mechanism.reactions.first_order_loss[1].scaling_factor_, 1);
+  EXPECT_EQ(mechanism.reactions.first_order_loss[1].scaling_factor, 1);
   EXPECT_EQ(mechanism.reactions.first_order_loss[1].reactants.size(), 1);
   EXPECT_EQ(mechanism.reactions.first_order_loss[1].reactants[0].species_name, "C");
   EXPECT_EQ(mechanism.reactions.first_order_loss[1].reactants[0].coefficient, 1);

diff --git a/test/unit/test_parse_photolysis.cpp b/test/unit/test_parse_photolysis.cpp
@@ -14,7 +14,7 @@ TEST(JsonParser, CanParseValidPhotolysisReaction)
 
   EXPECT_EQ(mechanism.reactions.photolysis[0].gas_phase, "gas");
   EXPECT_EQ(mechanism.reactions.photolysis[0].name, "my photolysis");
-  EXPECT_EQ(mechanism.reactions.photolysis[0].scaling_factor_, 12.3);
+  EXPECT_EQ(mechanism.reactions.photolysis[0].scaling_factor, 12.3);
   EXPECT_EQ(mechanism.reactions.photolysis[0].reactants.size(), 1);
   EXPECT_EQ(mechanism.reactions.photolysis[0].reactants[0].species_name, "B");
   EXPECT_EQ(mechanism.reactions.photolysis[0].reactants[0].coefficient, 1);
@@ -25,7 +25,7 @@ TEST(JsonParser, CanParseValidPhotolysisReaction)
   EXPECT_EQ(mechanism.reactions.photolysis[0].unknown_properties["__comment"], "\"hi\"");
 
   EXPECT_EQ(mechanism.reactions.photolysis[1].gas_phase, "gas");
-  EXPECT_EQ(mechanism.reactions.photolysis[1].scaling_factor_, 1);
+  EXPECT_EQ(mechanism.reactions.photolysis[1].scaling_factor, 1);
   EXPECT_EQ(mechanism.reactions.photolysis[1].reactants.size(), 1);
   EXPECT_EQ(mechanism.reactions.photolysis[1].reactants[0].species_name, "B");
   EXPECT_EQ(mechanism.reactions.photolysis[1].reactants[0].coefficient, 1.2);

diff --git a/test/unit/test_parse_wet_deposition.cpp b/test/unit/test_parse_wet_deposition.cpp
@@ -0,0 +1,31 @@
+#include <gtest/gtest.h>
+
+#include <open_atmos/mechanism_configuration/parser.hpp>
+
+using namespace open_atmos::mechanism_configuration;
+
+TEST(JsonParser, CanParseValidWetDepositionReaction)
+{
+  JsonParser parser;
+  auto [status, mechanism] = parser.Parse(std::string("unit_configs/reactions/wet_deposition/valid.json"));
+  EXPECT_EQ(status, ConfigParseStatus::Success);
+
+  EXPECT_EQ(mechanism.reactions.wet_deposition.size(), 2);
+
+  EXPECT_EQ(mechanism.reactions.wet_deposition[0].name, "rxn cloud");
+  EXPECT_EQ(mechanism.reactions.wet_deposition[0].aerosol_phase, "cloud");
+  EXPECT_EQ(mechanism.reactions.wet_deposition[0].scaling_factor, 12.3);
+  EXPECT_EQ(mechanism.reactions.wet_deposition[0].unknown_properties.size(), 1);
+  EXPECT_EQ(mechanism.reactions.wet_deposition[0].unknown_properties["__comment"], "\"Tuxedo cats are the best\"");
+
+  EXPECT_EQ(mechanism.reactions.wet_deposition[1].name, "rxn cloud2");
+  EXPECT_EQ(mechanism.reactions.wet_deposition[1].aerosol_phase, "cloud");
+  EXPECT_EQ(mechanism.reactions.wet_deposition[1].scaling_factor, 1);
+}
+
+TEST(JsonParser, WetDepositionDetectsUnknownPhase)
+{
+  JsonParser parser;
+  auto [status, mechanism] = parser.Parse(std::string("unit_configs/reactions/wet_deposition/missing_phase.json"));
+  EXPECT_EQ(status, ConfigParseStatus::UnknownPhase);
+}
diff --git a/test/unit/unit_configs/reactions/wet_deposition/missing_phase.json b/test/unit/unit_configs/reactions/wet_deposition/missing_phase.json
@@ -0,0 +1,24 @@
+{
+  "version": "1.0.0",
+  "name": "Missing phase",
+  "species": [
+    {
+      "name": "A"
+    },
+    {
+      "name": "B"
+    },
+    {
+      "name": "C"
+    }
+  ],
+  "phases": [
+  ],
+  "reactions": [
+    {
+      "type": "WET_DEPOSITION",
+      "aerosol phase": "cloud",
+      "name": "rxn cloud"
+    }
+  ]
+}
diff --git a/test/unit/unit_configs/reactions/wet_deposition/valid.json b/test/unit/unit_configs/reactions/wet_deposition/valid.json
@@ -0,0 +1,39 @@
+{
+  "version": "1.0.0",
+  "name": "Valid wet deposition",
+  "species": [
+    {
+      "name": "A"
+    },
+    {
+      "name": "B"
+    },
+    {
+      "name": "C"
+    }
+  ],
+  "phases": [
+    {
+      "name": "cloud",
+      "species": [
+        "A",
+        "B",
+        "C"
+      ]
+    }
+  ],
+  "reactions": [
+    {
+      "type": "WET_DEPOSITION",
+      "aerosol phase": "cloud",
+      "name": "rxn cloud",
+      "scaling factor": 12.3,
+      "__comment": "Tuxedo cats are the best"
+    },
+    {
+      "type": "WET_DEPOSITION",
+      "aerosol phase": "cloud",
+      "name": "rxn cloud2"
+    }
+  ]
+}