Merge pull request #35 from open-atmos/parse_henrys_law

parsing henrys law

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
 
+      // 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;
 
     struct Configuration
@@ -210,6 +219,12 @@ namespace open_atmos
       const std::vector<std::string> optional_keys{ keys.name, keys.scaling_factor };
     } first_order_loss;
 
+    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 Mechanism
     {
       const std::vector<std::string> required_keys{};

include/open_atmos/types.hpp

@@ -241,6 +241,24 @@ namespace open_atmos
       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;
@@ -249,6 +267,7 @@ 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::HenrysLaw> henrys_law;
       std::vector<types::Photolysis> photolysis;
       std::vector<types::Surface> surface;
       std::vector<types::Troe> troe;

src/parser.cpp

@@ -1332,6 +1332,88 @@ namespace open_atmos
       return { status, first_order_loss };
     }
 
+    /// @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
+    /// @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::HenrysLaw>
+    ParseHenrysLaw(const json& object, const std::vector<types::Species> existing_species, const std::vector<types::Phase> existing_phases)
+    {
+      ConfigParseStatus status = ConfigParseStatus::Success;
+      types::HenrysLaw henrys_law;
+
+      status = ValidateSchema(object, validation::henrys_law.required_keys, validation::henrys_law.optional_keys);
+      if (status == ConfigParseStatus::Success)
+      {
+        std::string gas_phase = object[validation::keys.gas_phase].get<std::string>();
+        std::string gas_phase_species = object[validation::keys.gas_phase_species].get<std::string>();
+        std::string aerosol_phase = object[validation::keys.aerosol_phase].get<std::string>();
+        std::string aerosol_phase_species = object[validation::keys.aerosol_phase_species].get<std::string>();
+        std::string aerosol_phase_water = object[validation::keys.aerosol_phase_water].get<std::string>();
+
+        if (object.contains(validation::keys.name))
+        {
+          henrys_law.name = object[validation::keys.name].get<std::string>();
+        }
+
+        auto comments = GetComments(object, validation::henrys_law.required_keys, validation::henrys_law.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::vector<std::string> requested_species;
+        requested_species.push_back(gas_phase_species);
+        requested_species.push_back(aerosol_phase_species);
+        requested_species.push_back(aerosol_phase_water);
+
+        std::vector<std::string> requested_aerosol_species;
+        requested_aerosol_species.push_back(aerosol_phase_species);
+        requested_aerosol_species.push_back(aerosol_phase_water);
+
+        if (status == ConfigParseStatus::Success && RequiresUnknownSpecies(requested_species, existing_species))
+        {
+          status = ConfigParseStatus::ReactionRequiresUnknownSpecies;
+        }
+
+        auto it = std::find_if(existing_phases.begin(), existing_phases.end(), [&gas_phase](const auto& phase) { return phase.name == gas_phase; });
+        if (status == ConfigParseStatus::Success && it == existing_phases.end())
+        {
+          status = ConfigParseStatus::UnknownPhase;
+        }
+
+        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_aerosol_species, aerosol_phase_species))
+          {
+            status = ConfigParseStatus::RequestedAerosolSpeciesNotIncludedInAerosolPhase;
+          }
+        }
+        else
+        {
+          status = ConfigParseStatus::UnknownPhase;
+        }
+
+        henrys_law.gas_phase = gas_phase;
+        henrys_law.gas_phase_species = gas_phase_species;
+        henrys_law.aerosol_phase = aerosol_phase;
+        henrys_law.aerosol_phase_species = aerosol_phase_species;
+        henrys_law.aerosol_phase_water = aerosol_phase_water;
+        henrys_law.unknown_properties = unknown_properties;
+      }
+
+      return { status, henrys_law };
+    }
+
     /// @brief Parses all reactions
     /// @param objects A json object that should contain only valid reactions
     /// @param existing_species A list of spcecies configured for a mechanism
@@ -1446,6 +1528,16 @@ namespace open_atmos
           }
           reactions.first_order_loss.push_back(first_order_loss_parse.second);
         }
+        else if (type == validation::keys.HenrysLaw_key)
+        {
+          auto henrys_law_parse = ParseHenrysLaw(object, existing_species, existing_phases);
+          status = henrys_law_parse.first;
+          if (status != ConfigParseStatus::Success)
+          {
+            break;
+          }
+          reactions.henrys_law.push_back(henrys_law_parse.second);
+        }
       }
 
       return { status, reactions };

test/integration/test_json_parser.cpp

@@ -13,15 +13,19 @@ TEST(JsonParser, ParsesFullConfiguration)
   EXPECT_EQ(mechanism.species.size(), 11);
   EXPECT_EQ(mechanism.phases.size(), 4);
   EXPECT_EQ(mechanism.reactions.arrhenius.size(), 2);
-  EXPECT_EQ(mechanism.reactions.condensed_phase_arrhenius.size(), 2);
-  EXPECT_EQ(mechanism.reactions.troe.size(), 1);
   EXPECT_EQ(mechanism.reactions.branched.size(), 1);
+  EXPECT_EQ(mechanism.reactions.condensed_phase_arrhenius.size(), 2);
   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);
+  EXPECT_EQ(mechanism.reactions.henrys_law.size(), 1);
+  EXPECT_EQ(mechanism.reactions.photolysis.size(), 1);
+  EXPECT_EQ(mechanism.reactions.surface.size(), 1);
+  EXPECT_EQ(mechanism.reactions.troe.size(), 1);
+  EXPECT_EQ(mechanism.reactions.tunneling.size(), 1);
 }
 
 TEST(JsonParser, ParserReportsBadFiles)

test/unit/CMakeLists.txt

@@ -12,6 +12,7 @@ create_standard_test(NAME parse_condensed_phase_arrhenius SOURCES test_parse_con
 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_henrys_law SOURCES test_parse_henrys_law.cpp)
 create_standard_test(NAME parse_phases SOURCES test_parse_phases.cpp)
 create_standard_test(NAME parse_photolysis SOURCES test_parse_photolysis.cpp)
 create_standard_test(NAME parse_species SOURCES test_parse_species.cpp)

test/unit/test_parse_henrys_law.cpp

@@ -0,0 +1,59 @@
+#include <gtest/gtest.h>
+
+#include <open_atmos/mechanism_configuration/parser.hpp>
+
+using namespace open_atmos::mechanism_configuration;
+
+TEST(JsonParser, CanParseValidHenrysLawReaction)
+{
+  JsonParser parser;
+  auto [status, mechanism] = parser.Parse(std::string("unit_configs/reactions/henrys_law/valid.json"));
+  EXPECT_EQ(status, ConfigParseStatus::Success);
+
+  EXPECT_EQ(mechanism.reactions.henrys_law.size(), 2);
+
+  EXPECT_EQ(mechanism.reactions.henrys_law[0].name, "my henry's law");
+  EXPECT_EQ(mechanism.reactions.henrys_law[0].gas_phase, "gas");
+  EXPECT_EQ(mechanism.reactions.henrys_law[0].gas_phase_species, "A");
+  EXPECT_EQ(mechanism.reactions.henrys_law[0].aerosol_phase, "aqueous aerosol");
+  EXPECT_EQ(mechanism.reactions.henrys_law[0].aerosol_phase_species, "B");
+  EXPECT_EQ(mechanism.reactions.henrys_law[0].aerosol_phase_water, "H2O_aq");
+  EXPECT_EQ(mechanism.reactions.henrys_law[0].unknown_properties.size(), 1);
+  EXPECT_EQ(mechanism.reactions.henrys_law[0].unknown_properties["__comment"], "\"hi\"");
+
+  EXPECT_EQ(mechanism.reactions.henrys_law[1].name, "");
+  EXPECT_EQ(mechanism.reactions.henrys_law[1].gas_phase, "gas");
+  EXPECT_EQ(mechanism.reactions.henrys_law[1].gas_phase_species, "A");
+  EXPECT_EQ(mechanism.reactions.henrys_law[1].aerosol_phase, "aqueous aerosol");
+  EXPECT_EQ(mechanism.reactions.henrys_law[1].aerosol_phase_species, "B");
+  EXPECT_EQ(mechanism.reactions.henrys_law[1].aerosol_phase_water, "H2O_aq");
+  EXPECT_EQ(mechanism.reactions.henrys_law[1].unknown_properties.size(), 0);
+}
+
+TEST(JsonParser, HenrysLawDetectsUnknownSpecies)
+{
+  JsonParser parser;
+  auto [status, mechanism] = parser.Parse(std::string("unit_configs/reactions/henrys_law/unknown_species.json"));
+  EXPECT_EQ(status, ConfigParseStatus::ReactionRequiresUnknownSpecies);
+}
+
+TEST(JsonParser, HenrysLawDetectsUnknownPhase)
+{
+  JsonParser parser;
+  auto [status, mechanism] = parser.Parse(std::string("unit_configs/reactions/henrys_law/missing_phase.json"));
+  EXPECT_EQ(status, ConfigParseStatus::UnknownPhase);
+}
+
+TEST(JsonParser, HenrysLawDetectsUnknownAerosolPhaseWater)
+{
+  JsonParser parser;
+  auto [status, mechanism] = parser.Parse(std::string("unit_configs/reactions/condensed_phase_arrhenius/missing_aerosol_phase_water.json"));
+  EXPECT_EQ(status, ConfigParseStatus::ReactionRequiresUnknownSpecies);
+}
+
+TEST(JsonParser, HenrysLawDetectsWhenRequestedSpeciesAreNotInAerosolPhase)
+{
+  JsonParser parser;
+  auto [status, mechanism] = parser.Parse(std::string("unit_configs/reactions/condensed_phase_arrhenius/species_not_in_aerosol_phase.json"));
+  EXPECT_EQ(status, ConfigParseStatus::RequestedAerosolSpeciesNotIncludedInAerosolPhase);
+}

test/unit/unit_configs/reactions/henrys_law/missing_aerosol_phase_water.json

@@ -0,0 +1,46 @@
+{
+  "version": "1.0.0",
+  "name": "Missing condensed phase arrhenius aerosol phase water",
+  "species": [
+    {
+      "name": "A"
+    },
+    {
+      "name": "B"
+    },
+    {
+      "name": "C"
+    },
+    {
+      "name": "H2O_aq"
+    }
+  ],
+  "phases": [
+    {
+      "name": "aqueous aerosol",
+      "species": [
+        "A",
+        "B",
+        "C",
+        "H2O_aq"
+      ]
+    }
+  ],
+  "reactions": [
+    {
+      "type": "CONDENSED_PHASE_ARRHENIUS",
+      "aerosol phase": "aqueous aerosol",
+      "aerosol-phase water": "H2O_a",
+      "reactants": [
+        {
+          "species name": "A"
+        }
+      ],
+      "products": [
+        {
+          "species name": "C"
+        }
+      ]
+    }
+  ]
+}

test/unit/unit_configs/reactions/henrys_law/missing_phase.json

@@ -0,0 +1,27 @@
+{
+  "version": "1.0.0",
+  "name": "Missing phase",
+  "species": [
+    {
+      "name": "A"
+    },
+    {
+      "name": "B"
+    },
+    {
+      "name": "C"
+    }
+  ],
+  "phases": [ ],
+  "reactions": [
+    {
+      "type": "HL_PHASE_TRANSFER",
+      "gas phase": "gas",
+      "gas-phase species": "H2O2",
+      "aerosol phase": "aqueous aerosol",
+      "aerosol-phase species": "H2O2_aq",
+      "aerosol-phase water": "H2O_aq",
+      "name": "my henry's law"
+    }
+  ]
+}