Merge pull request #34 from open-atmos/parse_condensed_phase_photolysis

parsing condensed phase photolysis

examples/full_configuration.json

@@ -207,10 +207,6 @@
         {
           "species name": "H2O2_aq",
           "coefficient": 1
-        },
-        {
-          "species name": "H2O_aq",
-          "coefficient": 1
         }
       ],
       "products": [

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
@@ -185,6 +192,12 @@ 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 };

include/open_atmos/types.hpp

@@ -195,6 +195,24 @@ namespace open_atmos
       std::unordered_map<std::string, std::string> unknown_properties;
     };
 
+    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
@@ -226,14 +244,15 @@ namespace open_atmos
     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::Photolysis> photolysis;
+      std::vector<types::Surface> surface;
+      std::vector<types::Troe> troe;
+      std::vector<types::Tunneling> tunneling;
     };
 
     struct Mechanism

src/parser.cpp

@@ -1077,6 +1077,114 @@ namespace open_atmos
       return { status, photolysis };
     }
 
+    /// @brief Parses a photolysis 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 Photolysis parameters
+    std::pair<ConfigParseStatus, types::CondensedPhasePhotolysis>
+    ParseCondensedPhasePhotolysis(const json& object, const std::vector<types::Species> existing_species, const std::vector<types::Phase> existing_phases)
+    {
+      ConfigParseStatus status = ConfigParseStatus::Success;
+      types::CondensedPhasePhotolysis condensed_phase_photolysis;
+
+      status = ValidateSchema(object, validation::condensed_phase_photolysis.required_keys, validation::photolysis.optional_keys);
+      if (status == ConfigParseStatus::Success)
+      {
+        std::vector<types::ReactionComponent> products{};
+        for (const auto& reactant : object[validation::keys.products])
+        {
+          auto product_parse = ParseReactionComponent(reactant);
+          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.scaling_factor))
+        {
+          condensed_phase_photolysis.scaling_factor_ = object[validation::keys.scaling_factor].get<double>();
+        }
+
+        if (object.contains(validation::keys.name))
+        {
+          condensed_phase_photolysis.name = object[validation::keys.name].get<std::string>();
+        }
+
+        auto comments = GetComments(object, validation::condensed_phase_photolysis.required_keys, validation::photolysis.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;
+        }
+
+        if (status == ConfigParseStatus::Success && reactants.size() > 1)
+        {
+          status = ConfigParseStatus::TooManyReactionComponents;
+        }
+
+        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;
+        }
+
+        condensed_phase_photolysis.aerosol_phase = aerosol_phase;
+        condensed_phase_photolysis.aerosol_phase_water = aerosol_phase_water;
+        condensed_phase_photolysis.products = products;
+        condensed_phase_photolysis.reactants = reactants;
+        condensed_phase_photolysis.unknown_properties = unknown_properties;
+      }
+
+      return { status, condensed_phase_photolysis };
+    }
+
     /// @brief Parses a emission reaction
     /// @param object A json object that should have information containing arrhenius parameters
     /// @param existing_species A list of species configured in a mechanism
@@ -1308,6 +1416,16 @@ namespace open_atmos
           }
           reactions.photolysis.push_back(photolysis_parse.second);
         }
+        else if (type == validation::keys.CondensedPhasePhotolysis_key)
+        {
+          auto condensed_phase_photolysis_parse = ParseCondensedPhasePhotolysis(object, existing_species, existing_phases);
+          status = condensed_phase_photolysis_parse.first;
+          if (status != ConfigParseStatus::Success)
+          {
+            break;
+          }
+          reactions.condensed_phase_photolysis.push_back(condensed_phase_photolysis_parse.second);
+        }
         else if (type == validation::keys.Emission_key)
         {
           auto emission_parse = ParseEmission(object, existing_species, existing_phases);

test/integration/test_json_parser.cpp

@@ -19,6 +19,7 @@ TEST(JsonParser, ParsesFullConfiguration)
   EXPECT_EQ(mechanism.reactions.tunneling.size(), 1);
   EXPECT_EQ(mechanism.reactions.surface.size(), 1);
   EXPECT_EQ(mechanism.reactions.photolysis.size(), 1);
+  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);
 }

test/unit/CMakeLists.txt

@@ -9,6 +9,7 @@ include(test_util)
 create_standard_test(NAME parse_arrhenius SOURCES test_parse_arrhenius.cpp)
 create_standard_test(NAME parse_branched SOURCES test_parse_branched.cpp)
 create_standard_test(NAME parse_condensed_phase_arrhenius SOURCES test_parse_condensed_phase_arrhenius.cpp)
+create_standard_test(NAME parse_condensed_phase_photolysis SOURCES test_parse_condensed_phase_photolysis.cpp)
 create_standard_test(NAME parse_emission SOURCES test_parse_emission.cpp)
 create_standard_test(NAME parse_first_order_loss SOURCES test_parse_first_order_loss.cpp)
 create_standard_test(NAME parse_phases SOURCES test_parse_phases.cpp)

test/unit/test_parse_condensed_phase_photolysis.cpp

@@ -0,0 +1,79 @@
+#include <gtest/gtest.h>
+
+#include <open_atmos/mechanism_configuration/parser.hpp>
+
+using namespace open_atmos::mechanism_configuration;
+
+TEST(JsonParser, CanParseValidCondensedPhasePhotolysisReaction)
+{
+  JsonParser parser;
+  auto [status, mechanism] = parser.Parse(std::string("unit_configs/reactions/condensed_phase_photolysis/valid.json"));
+  EXPECT_EQ(status, ConfigParseStatus::Success);
+
+  EXPECT_EQ(mechanism.reactions.condensed_phase_photolysis.size(), 2);
+
+  EXPECT_EQ(mechanism.reactions.condensed_phase_photolysis[0].aerosol_phase, "aqueous aerosol");
+  EXPECT_EQ(mechanism.reactions.condensed_phase_photolysis[0].aerosol_phase_water, "H2O_aq");
+  EXPECT_EQ(mechanism.reactions.condensed_phase_photolysis[0].name, "my condensed phase photolysis");
+  EXPECT_EQ(mechanism.reactions.condensed_phase_photolysis[0].scaling_factor_, 12.3);
+  EXPECT_EQ(mechanism.reactions.condensed_phase_photolysis[0].reactants.size(), 1);
+  EXPECT_EQ(mechanism.reactions.condensed_phase_photolysis[0].reactants[0].species_name, "B");
+  EXPECT_EQ(mechanism.reactions.condensed_phase_photolysis[0].reactants[0].coefficient, 1);
+  EXPECT_EQ(mechanism.reactions.condensed_phase_photolysis[0].products.size(), 1);
+  EXPECT_EQ(mechanism.reactions.condensed_phase_photolysis[0].products[0].species_name, "C");
+  EXPECT_EQ(mechanism.reactions.condensed_phase_photolysis[0].products[0].coefficient, 1);
+  EXPECT_EQ(mechanism.reactions.condensed_phase_photolysis[0].unknown_properties.size(), 1);
+  EXPECT_EQ(mechanism.reactions.condensed_phase_photolysis[0].unknown_properties["__comment"], "\"hi\"");
+
+  EXPECT_EQ(mechanism.reactions.condensed_phase_photolysis[1].aerosol_phase, "aqueous aerosol");
+  EXPECT_EQ(mechanism.reactions.condensed_phase_photolysis[1].aerosol_phase_water, "H2O_aq");
+  EXPECT_EQ(mechanism.reactions.condensed_phase_photolysis[1].scaling_factor_, 1);
+  EXPECT_EQ(mechanism.reactions.condensed_phase_photolysis[1].reactants.size(), 1);
+  EXPECT_EQ(mechanism.reactions.condensed_phase_photolysis[1].reactants[0].species_name, "B");
+  EXPECT_EQ(mechanism.reactions.condensed_phase_photolysis[1].reactants[0].coefficient, 1.2);
+  EXPECT_EQ(mechanism.reactions.condensed_phase_photolysis[1].products.size(), 1);
+  EXPECT_EQ(mechanism.reactions.condensed_phase_photolysis[1].products[0].species_name, "C");
+  EXPECT_EQ(mechanism.reactions.condensed_phase_photolysis[1].products[0].coefficient, 0.2);
+}
+
+TEST(JsonParser, CondensedPhasePhotolysisDetectsUnknownSpecies)
+{
+  JsonParser parser;
+  auto [status, mechanism] = parser.Parse(std::string("unit_configs/reactions/condensed_phase_photolysis/unknown_species.json"));
+  EXPECT_EQ(status, ConfigParseStatus::ReactionRequiresUnknownSpecies);
+}
+
+TEST(JsonParser, CondensedPhasePhotolysisDetectsBadReactionComponent)
+{
+  JsonParser parser;
+  auto [status, mechanism] = parser.Parse(std::string("unit_configs/reactions/condensed_phase_photolysis/bad_reaction_component.json"));
+  EXPECT_EQ(status, ConfigParseStatus::InvalidKey);
+}
+
+TEST(JsonParser, CondensedPhasePhotolysisDetectsUnknownPhase)
+{
+  JsonParser parser;
+  auto [status, mechanism] = parser.Parse(std::string("unit_configs/reactions/condensed_phase_photolysis/missing_phase.json"));
+  EXPECT_EQ(status, ConfigParseStatus::UnknownPhase);
+}
+
+TEST(JsonParser, CondensedPhasePhotolysisDoesNotAcceptMoreThanOneReactant)
+{
+  JsonParser parser;
+  auto [status, mechanism] = parser.Parse(std::string("unit_configs/reactions/condensed_phase_photolysis/more_than_one_reactant.json"));
+  EXPECT_EQ(status, ConfigParseStatus::TooManyReactionComponents);
+}
+
+TEST(JsonParser, CondensedPhasePhotolysisDetectsWhenRequestedSpeciesAreNotInAerosolPhase)
+{
+  JsonParser parser;
+  auto [status, mechanism] = parser.Parse(std::string("unit_configs/reactions/condensed_phase_photolysis/species_not_in_aerosol_phase.json"));
+  EXPECT_EQ(status, ConfigParseStatus::RequestedAerosolSpeciesNotIncludedInAerosolPhase);
+}
+
+TEST(JsonParser, CondensedPhaseArrheniusDetectsUnknownAerosolPhaseWater)
+{
+  JsonParser parser;
+  auto [status, mechanism] = parser.Parse(std::string("unit_configs/reactions/condensed_phase_photolysis/missing_aerosol_phase_water.json"));
+  EXPECT_EQ(status, ConfigParseStatus::ReactionRequiresUnknownSpecies);
+}

test/unit/unit_configs/reactions/condensed_phase_photolysis/bad_reaction_component.json

@@ -0,0 +1,48 @@
+{
+  "version": "1.0.0",
+  "name": "Bad reaction component",
+  "species": [
+    {
+      "name": "A"
+    },
+    {
+      "name": "B"
+    },
+    {
+      "name": "C"
+    },
+    {
+      "name": "H2O_aq"
+    }
+  ],
+  "phases": [
+    {
+      "name": "aqueous aerosol",
+      "species": [
+        "A",
+        "B",
+        "C",
+        "H2O_aq"
+      ]
+    }
+  ],
+  "reactions": [
+    {
+      "type": "CONDENSED_PHASE_PHOTOLYSIS",
+      "aerosol phase": "aqueous aerosol",
+      "aerosol-phase water": "H2O_aq",
+      "reactants": [
+        {
+          "species name": "A",
+          "Coefficient": 1.2
+        }
+      ],
+      "products": [
+        {
+          "species name": "B",
+          "coefficient": 0.2
+        }
+      ]
+    }
+  ]
+}