Merge pull request #37 from open-atmos/parse_aqueous_equilibrium

Parse aqueous equilibrium

.github/workflows/mac.yml

@@ -7,38 +7,13 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
-  xcode_macos_12:
-    if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name
-    runs-on: macos-12
-    strategy:
-      matrix:
-        # all available versions of xcode: https://github.com/actions/runner-images/blob/main/images/macos/macos-12-Readme.md#xcode
-        xcode: ['13.1', '14.1']
-        build_type: [Debug, Release]
-    env:
-      DEVELOPER_DIR: /Applications/Xcode_${{ matrix.xcode }}.app/Contents/Developer
-
-    steps:
-      - uses: actions/checkout@v3
-
-      - name: Run Cmake 
-        run: cmake -S . -B build -D CMAKE_BUILD_TYPE=${{ matrix.build_type }}
-
-      - name: Build
-        run: cmake --build build --parallel 10
-
-      - name: Run tests
-        run: |
-          cd build
-          ctest -C ${{ matrix.build_type }} --rerun-failed --output-on-failure . --verbose -j 10
-
   xcode_macos_13:
     if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name
     runs-on: macos-13
     strategy:
       matrix:
         # all available versions of xcode: https://github.com/actions/runner-images/blob/main/images/macos/macos-13-Readme.md#xcode
-        xcode: ['14.1', '15.0']
+        xcode: ['15.0']
         build_type: [Debug, Release]
     env:
       DEVELOPER_DIR: /Applications/Xcode_${{ matrix.xcode }}.app/Contents/Developer
@@ -63,7 +38,6 @@ jobs:
     strategy:
       matrix:
         compiler:
-          - { cpp: g++-11, c: gcc-11}
           - { cpp: g++-12, c: gcc-12}
           - { cpp: clang++, c: clang}
         build_type: [Debug, Release]

examples/full_configuration.json

@@ -76,7 +76,10 @@
       "species": [
         "H2O2_aq",
         "H2O_aq",
-        "ethanol_aq"
+        "ethanol_aq",
+        "A",
+        "B",
+        "C"
       ]
     },
     {
@@ -120,13 +123,11 @@
     },
     {
       "type": "AQUEOUS_EQUILIBRIUM",
-      "gas phase": "gas",
       "aerosol phase": "aqueous aerosol",
       "aerosol-phase water": "H2O_aq",
       "A": 1.14e-2,
       "C": 2300.0,
       "k_reverse": 0.32,
-      "ion pair": "B-C",
       "reactants": [
         {
           "species name": "A",

include/open_atmos/mechanism_configuration/parser.hpp

@@ -35,7 +35,8 @@ namespace open_atmos
       ReactionRequiresUnknownSpecies,
       UnknownPhase,
       RequestedAerosolSpeciesNotIncludedInAerosolPhase,
-      TooManyReactionComponents
+      TooManyReactionComponents,
+      InvalidIonPair
     };
     std::string configParseStatusToString(const ConfigParseStatus &status);
 

include/open_atmos/mechanism_configuration/validation.hpp

@@ -116,6 +116,15 @@ namespace open_atmos
       const std::string FirstOrderLoss_key = "FIRST_ORDER_LOSS";
       // also scaling factor
 
+      // Aqueous Equilibrium
+      const std::string AqueousPhaseEquilibrium_key = "AQUEOUS_EQUILIBRIUM";
+      // also 
+      // aerosol phase
+      // aerosol-phase water
+      // A
+      // C
+      const std::string k_reverse = "k_reverse";
+
       // Wet Deposition
       const std::string WetDeposition_key = "WET_DEPOSITION";
       // also
@@ -133,11 +142,11 @@ namespace open_atmos
 
     } keys;
 
-    struct Configuration
+    struct Mechanism
     {
       const std::vector<std::string> required_keys{ keys.version, keys.species, keys.phases, keys.reactions };
       const std::vector<std::string> optional_keys{ keys.name };
-    } configuration;
+    } mechanism;
 
     struct Species
     {
@@ -237,11 +246,10 @@ namespace open_atmos
       const std::vector<std::string> optional_keys{ keys.name };
     } henrys_law;
 
-    struct Mechanism
+    struct AqueousEquilibrium
     {
-      const std::vector<std::string> required_keys{};
-      const std::vector<std::string> optional_keys{};
-    } mechanism;
-
+      const std::vector<std::string> required_keys{ keys.type, keys.reactants, keys.products, keys.aerosol_phase, keys.aerosol_phase_water, keys.k_reverse };
+      const std::vector<std::string> optional_keys{ keys.name, keys.A, keys.C };
+    } aqueous_equilibrium;
   }  // namespace validation
 }  // namespace open_atmos

include/open_atmos/types.hpp

@@ -6,6 +6,10 @@
 
 #include <string>
 #include <unordered_map>
+#include <array>
+#include <vector>
+#include <optional>
+
 
 namespace open_atmos
 {
@@ -240,6 +244,29 @@ namespace open_atmos
       /// @brief Unknown properties, prefixed with two underscores (__)
       std::unordered_map<std::string, std::string> unknown_properties;
     };
+    struct AqueousEquilibrium
+    {
+      /// @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 An identifier indicating which aerosol phase this reaction takes place in
+      std::string aerosol_phase;
+      /// @brief An identifier indicating the species label of aqueous phase water
+      std::string aerosol_phase_water;
+      /// @brief A list of reactants
+      std::vector<ReactionComponent> reactants;
+      /// @brief A list of products
+      std::vector<ReactionComponent> products;
+      /// @brief Pre-exponential factor (s-1)
+      double A{ 1 };
+      /// @brief A constant
+      double C{ 0 };
+      /// @brief Reverse reation rate constant (s-1)
+      double k_reverse{ 0 };
+      /// @brief Unknown properties, prefixed with two underscores (__)
+      std::unordered_map<std::string, std::string> unknown_properties;
+    };
 
     struct WetDeposition
     {
@@ -279,6 +306,7 @@ 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::AqueousEquilibrium> aqueous_equilibrium;
       std::vector<types::WetDeposition> wet_deposition;
       std::vector<types::HenrysLaw> henrys_law;
       std::vector<types::Photolysis> photolysis;

src/CMakeLists.txt

@@ -5,7 +5,7 @@ configure_file(version.hpp.in ${PROJECT_SOURCE_DIR}/include/open_atmos/mechanism
 add_library(mechanism_configuration)
 add_library(open_atmos::mechanism_configuration ALIAS mechanism_configuration)
 
-target_compile_features(mechanism_configuration PUBLIC cxx_std_20)
+target_compile_features(mechanism_configuration PUBLIC cxx_std_17)
 
 target_sources(mechanism_configuration
   PRIVATE

src/parser.cpp

@@ -32,6 +32,7 @@ namespace open_atmos
         case ConfigParseStatus::UnknownPhase: return "UnknownPhase";
         case ConfigParseStatus::RequestedAerosolSpeciesNotIncludedInAerosolPhase: return "RequestedAerosolSpeciesNotIncludedInAerosolPhase";
         case ConfigParseStatus::TooManyReactionComponents: return "TooManyReactionComponents";
+        case ConfigParseStatus::InvalidIonPair: return "InvalidIonPair";
         default: return "Unknown";
       }
     }
@@ -137,7 +138,7 @@ namespace open_atmos
       // now, anything left must be standard comment starting with __
       for (auto& key : remaining)
       {
-        if (!key.starts_with("__"))
+        if (key.find("__") == std::string::npos)
         {
           std::cerr << "Non-standard key '" << key << "' found in object" << object << std::endl;
 
@@ -1332,6 +1333,117 @@ namespace open_atmos
       return { status, first_order_loss };
     }
 
+    /// @brief Parses an aqueous equilibrium 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 Condensed Phase Arrhenius parameters
+    std::pair<ConfigParseStatus, types::AqueousEquilibrium> ParseAqueousEquilibrium(
+        const json& object,
+        const std::vector<types::Species>& existing_species,
+        const std::vector<types::Phase>& existing_phases)
+    {
+      ConfigParseStatus status = ConfigParseStatus::Success;
+      types::AqueousEquilibrium aqueous_equilibrium;
+
+      status = ValidateSchema(object, validation::aqueous_equilibrium.required_keys, validation::aqueous_equilibrium.optional_keys);
+      if (status == ConfigParseStatus::Success)
+      {
+        std::vector<types::ReactionComponent> products{};
+        for (const auto& product : object[validation::keys.products])
+        {
+          auto product_parse = ParseReactionComponent(product);
+          status = product_parse.first;
+          if (status != ConfigParseStatus::Success)
+          {
+            break;
+          }
+          products.push_back(product_parse.second);
+        }
+
+        std::vector<types::ReactionComponent> reactants{};
+        for (const auto& reactant : object[validation::keys.reactants])
+        {
+          auto reactant_parse = ParseReactionComponent(reactant);
+          status = reactant_parse.first;
+          if (status != ConfigParseStatus::Success)
+          {
+            break;
+          }
+          reactants.push_back(reactant_parse.second);
+        }
+
+        if (object.contains(validation::keys.A))
+        {
+          aqueous_equilibrium.A = object[validation::keys.A].get<double>();
+        }
+        if (object.contains(validation::keys.C))
+        {
+          aqueous_equilibrium.C = object[validation::keys.C].get<double>();
+        }
+
+        aqueous_equilibrium.k_reverse = object[validation::keys.k_reverse].get<double>();
+
+        if (object.contains(validation::keys.name))
+        {
+          aqueous_equilibrium.name = object[validation::keys.name].get<std::string>();
+        }
+
+        auto comments = GetComments(object, validation::aqueous_equilibrium.required_keys, validation::aqueous_equilibrium.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>();
+        std::string aerosol_phase_water = object[validation::keys.aerosol_phase_water].get<std::string>();
+
+        std::vector<std::string> requested_species;
+        for (const auto& spec : products)
+        {
+          requested_species.push_back(spec.species_name);
+        }
+        for (const auto& spec : reactants)
+        {
+          requested_species.push_back(spec.species_name);
+        }
+        requested_species.push_back(aerosol_phase_water);
+
+        if (status == ConfigParseStatus::Success && RequiresUnknownSpecies(requested_species, existing_species))
+        {
+          status = ConfigParseStatus::ReactionRequiresUnknownSpecies;
+        }
+
+        auto phase_it = std::find_if(
+            existing_phases.begin(), existing_phases.end(), [&aerosol_phase](const types::Phase& phase) { return phase.name == aerosol_phase; });
+
+        if (phase_it != existing_phases.end())
+        {
+          // check if all of the species for this reaction are actually in the aerosol phase
+          std::vector<std::string> aerosol_phase_species = { (*phase_it).species.begin(), (*phase_it).species.end() };
+          if (status == ConfigParseStatus::Success && RequiresUnknownSpecies(requested_species, aerosol_phase_species))
+          {
+            status = ConfigParseStatus::RequestedAerosolSpeciesNotIncludedInAerosolPhase;
+          }
+        }
+        else
+        {
+          status = ConfigParseStatus::UnknownPhase;
+        }
+
+        aqueous_equilibrium.aerosol_phase = aerosol_phase;
+        aqueous_equilibrium.aerosol_phase_water = aerosol_phase_water;
+        aqueous_equilibrium.products = products;
+        aqueous_equilibrium.reactants = reactants;
+        aqueous_equilibrium.unknown_properties = unknown_properties;
+      }
+
+      return { status, aqueous_equilibrium };
+    }
+
     /// @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
@@ -1577,6 +1689,16 @@ namespace open_atmos
           }
           reactions.first_order_loss.push_back(first_order_loss_parse.second);
         }
+        else if (type == validation::keys.AqueousPhaseEquilibrium_key)
+        {
+          auto aqueous_equilibrium_parse = ParseAqueousEquilibrium(object, existing_species, existing_phases);
+          status = aqueous_equilibrium_parse.first;
+          if (status != ConfigParseStatus::Success)
+          {
+            break;
+          }
+          reactions.aqueous_equilibrium.push_back(aqueous_equilibrium_parse.second);
+        }
         else if (type == validation::keys.WetDeposition_key)
         {
           auto wet_deposition_parse = ParseWetDeposition(object, existing_species, existing_phases);
@@ -1638,7 +1760,7 @@ namespace open_atmos
       ConfigParseStatus status;
       types::Mechanism mechanism;
 
-      status = ValidateSchema(object, validation::configuration.required_keys, validation::configuration.optional_keys);
+      status = ValidateSchema(object, validation::mechanism.required_keys, validation::mechanism.optional_keys);
 
       if (status != ConfigParseStatus::Success)
       {

test/integration/test_json_parser.cpp

@@ -21,6 +21,7 @@ TEST(JsonParser, ParsesFullConfiguration)
   EXPECT_EQ(mechanism.reactions.condensed_phase_photolysis.size(), 1);
   EXPECT_EQ(mechanism.reactions.emission.size(), 1);
   EXPECT_EQ(mechanism.reactions.first_order_loss.size(), 1);
+  EXPECT_EQ(mechanism.reactions.aqueous_equilibrium.size(), 1);
   EXPECT_EQ(mechanism.reactions.henrys_law.size(), 1);
   EXPECT_EQ(mechanism.reactions.photolysis.size(), 1);
   EXPECT_EQ(mechanism.reactions.surface.size(), 1);

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_aqueous_equilibrium SOURCES test_parse_aqueous_equilibrium.cpp)
 create_standard_test(NAME parse_wet_deposition SOURCES test_parse_wet_deposition.cpp)
 
 ################################################################################