merging

.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

@@ -128,10 +128,6 @@
       "A": 1.14e-2,
       "C": 2300.0,
       "k_reverse": 0.32,
-      "ion pair": {
-        "first": { "species name": "A"},
-        "second": { "species name": "B"}
-      },
       "reactants": [
         {
           "species name": "A",
@@ -212,10 +208,6 @@
         {
           "species name": "H2O2_aq",
           "coefficient": 1
-        },
-        {
-          "species name": "H2O_aq",
-          "coefficient": 1
         }
       ],
       "products": [
@@ -367,7 +359,6 @@
     },
     {
       "type": "WET_DEPOSITION",
-      "gas phase": "gas",
       "aerosol phase": "cloud",
       "name": "rxn cloud",
       "scaling factor": 12.3

include/open_atmos/mechanism_configuration/validation.hpp

@@ -101,6 +101,13 @@ namespace open_atmos
       const std::string Photolysis_key = "PHOTOLYSIS";
       const std::string scaling_factor = "scaling factor";
 
+      // Condensed Phae Photolysis
+      const std::string CondensedPhasePhotolysis_key = "CONDENSED_PHASE_PHOTOLYSIS";
+      // also 
+      // scaling factor
+      // aerosol phase
+      // aerosol-phase water
+
       // Emissions
       const std::string Emission_key = "EMISSION";
       // also scaling factor
@@ -117,10 +124,21 @@ namespace open_atmos
       // A
       // C
       const std::string k_reverse = "k_reverse";
-      const std::string ion_pair = "ion pair";
-      // ion pair
-      const std::string first = "first";
-      const std::string second = "second";
+
+      // 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";
+      const std::string aerosol_phase_species = "aerosol-phase species";
+      // also
+      // gas phase
+      // aerosol phase
+      // aerosol-phase water
 
     } keys;
 
@@ -198,6 +216,12 @@ namespace open_atmos
       const std::vector<std::string> optional_keys{ keys.name, keys.scaling_factor };
     } photolysis;
 
+    struct CondensedPhasePhotolysis
+    {
+      const std::vector<std::string> required_keys{ keys.reactants, keys.products, keys.type, keys.aerosol_phase, keys.aerosol_phase_water };
+      const std::vector<std::string> optional_keys{ keys.name, keys.scaling_factor };
+    } condensed_phase_photolysis;
+
     struct Emission
     {
       const std::vector<std::string> required_keys{ keys.products, keys.type, keys.gas_phase };
@@ -210,16 +234,22 @@ 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 };
+      const std::vector<std::string> optional_keys{ keys.name };
+    } henrys_law;
+
     struct AqueousEquilibrium
     {
       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, keys.ion_pair };
+      const std::vector<std::string> optional_keys{ keys.name, keys.A, keys.C };
     } aqueous_equilibrium;
-
-    struct IonPair
-    {
-      const std::vector<std::string> required_keys{ keys.first, keys.second };
-      const std::vector<std::string> optional_keys{};
-    } ion_pair;
   }  // namespace validation
 }  // namespace open_atmos

include/open_atmos/types.hpp

@@ -186,7 +186,7 @@ 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
@@ -199,10 +199,28 @@ namespace open_atmos
       std::unordered_map<std::string, std::string> unknown_properties;
     };
 
-    struct Emission
+    struct CondensedPhasePhotolysis
     {
       /// @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 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 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
@@ -216,7 +234,7 @@ 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
@@ -226,7 +244,6 @@ 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
@@ -241,8 +258,6 @@ namespace open_atmos
       std::vector<ReactionComponent> reactants;
       /// @brief A list of products
       std::vector<ReactionComponent> products;
-      /// @brief Optional ion pairs
-      std::optional<std::array<ReactionComponent, 2>> ion_pair;
       /// @brief Pre-exponential factor (s-1)
       double A{ 1 };
       /// @brief A constant
@@ -253,18 +268,51 @@ 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
+      std::string name;
+      /// @brief An identifier indicating which gas phase this reaction takes place in
+      std::string gas_phase;
+      /// @brief An identifier indicating which gas phase species this reaction involves
+      std::string gas_phase_species;
+      /// @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 An identifier indicating which aerosol phase species this reaction involves
+      std::string aerosol_phase_species;
+      /// @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::CondensedPhaseArrhenius> condensed_phase_arrhenius;
-      std::vector<types::Troe> troe;
       std::vector<types::Branched> branched;
-      std::vector<types::Tunneling> tunneling;
-      std::vector<types::Surface> surface;
-      std::vector<types::Photolysis> photolysis;
+      std::vector<types::CondensedPhaseArrhenius> condensed_phase_arrhenius;
+      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;
+      std::vector<types::Surface> surface;
+      std::vector<types::Troe> troe;
+      std::vector<types::Tunneling> tunneling;
     };
 
     struct Mechanism