Merge pull request #28 from open-atmos/parse_first_order_loss

Parse first order loss

examples/full_configuration.json

@@ -205,7 +205,7 @@
     {
       "type": "FIRST_ORDER_LOSS",
       "gas phase": "gas",
-      "products": [
+      "reactants": [
         {
           "species name": "C",
           "coefficient": 1

include/open_atmos/mechanism_configuration/parser.hpp

@@ -33,7 +33,8 @@ namespace open_atmos
       DuplicatePhasesDetected,
       PhaseRequiresUnknownSpecies,
       ReactionRequiresUnknownSpecies,
-      UnknownPhase
+      UnknownPhase,
+      TooManyReactionComponents
     };
     std::string configParseStatusToString(const ConfigParseStatus &status);
 

include/open_atmos/mechanism_configuration/validation.hpp

@@ -93,6 +93,10 @@ namespace open_atmos
       const std::string Emission_key = "EMISSION";
       // also scaling factor
 
+      // First Order Loss
+      const std::string FirstOrderLoss_key = "FIRST_ORDER_LOSS";
+      // also scaling factor
+
     } keys;
 
     struct Configuration
@@ -169,6 +173,12 @@ namespace open_atmos
       const std::vector<std::string> optional_keys{ keys.name, keys.scaling_factor };
     } emission;
 
+    struct FirstOrderLoss
+    {
+      const std::vector<std::string> required_keys{ keys.reactants, keys.type, keys.gas_phase };
+      const std::vector<std::string> optional_keys{ keys.name, keys.scaling_factor };
+    } first_order_loss;
+
     struct Mechanism
     {
       const std::vector<std::string> required_keys{};

include/open_atmos/types.hpp

@@ -182,6 +182,20 @@ namespace open_atmos
       std::unordered_map<std::string, std::string> unknown_properties;
     };
 
+    struct FirstOrderLoss
+    {
+      /// @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 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 Unknown properties, prefixed with two underscores (__)
+      std::unordered_map<std::string, std::string> unknown_properties;
+    };
+
     struct Reactions
     {
       std::vector<types::Arrhenius> arrhenius;
@@ -191,6 +205,7 @@ namespace open_atmos
       std::vector<types::Surface> surface;
       std::vector<types::Photolysis> photolysis;
       std::vector<types::Emission> emission;
+      std::vector<types::FirstOrderLoss> first_order_loss;
     };
 
     struct Mechanism

src/parser.cpp

@@ -30,6 +30,7 @@ namespace open_atmos
         case ConfigParseStatus::PhaseRequiresUnknownSpecies: return "PhaseRequiresUnknownSpecies";
         case ConfigParseStatus::ReactionRequiresUnknownSpecies: return "ReactionRequiresUnknownSpecies";
         case ConfigParseStatus::UnknownPhase: return "UnknownPhase";
+        case ConfigParseStatus::TooManyReactionComponents: return "TooManyReactionComponents";
         default: return "Unknown";
       }
     }
@@ -944,6 +945,77 @@ namespace open_atmos
       return { status, emission };
     }
 
+    std::pair<ConfigParseStatus, types::FirstOrderLoss> ParseFirstOrderLoss(const json& object, const std::vector<types::Species> existing_species, const std::vector<types::Phase> existing_phases)
+    {
+      ConfigParseStatus status = ConfigParseStatus::Success;
+      types::FirstOrderLoss first_order_loss;
+
+      status = ValidateSchema(object, validation::first_order_loss.required_keys, validation::first_order_loss.optional_keys);
+      if (status == ConfigParseStatus::Success)
+      {
+        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))
+        {
+          first_order_loss.scaling_factor_ = object[validation::keys.scaling_factor].get<double>();
+        }
+
+        if (object.contains(validation::keys.name))
+        {
+          first_order_loss.name = object[validation::keys.name].get<std::string>();
+        }
+
+        auto comments = GetComments(object, validation::first_order_loss.required_keys, validation::first_order_loss.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;
+        for (const auto& spec : reactants)
+        {
+          requested_species.push_back(spec.species_name);
+        }
+
+        if (status == ConfigParseStatus::Success && RequiresUnknownSpecies(requested_species, existing_species))
+        {
+          status = ConfigParseStatus::ReactionRequiresUnknownSpecies;
+        }
+
+        std::string gas_phase = object[validation::keys.gas_phase].get<std::string>();
+        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;
+        }
+
+        if (status == ConfigParseStatus::Success && reactants.size() > 1)
+        {
+          status = ConfigParseStatus::TooManyReactionComponents;
+        }
+
+        first_order_loss.gas_phase = gas_phase;
+        first_order_loss.reactants = reactants;
+        first_order_loss.unknown_properties = unknown_properties;
+      }
+
+      return { status, first_order_loss };
+    }
+
     std::pair<ConfigParseStatus, types::Reactions>
     ParseReactions(const json& objects, const std::vector<types::Species>& existing_species, const std::vector<types::Phase>& existing_phases)
     {
@@ -1023,6 +1095,16 @@ namespace open_atmos
           }
           reactions.emission.push_back(emission_parse.second);
         }
+        else if (type == validation::keys.FirstOrderLoss_key)
+        {
+          auto first_order_loss_parse = ParseFirstOrderLoss(object, existing_species, existing_phases);
+          status = first_order_loss_parse.first;
+          if (status != ConfigParseStatus::Success)
+          {
+            break;
+          }
+          reactions.first_order_loss.push_back(first_order_loss_parse.second);
+        }
       }
 
       return { status, reactions };

test/integration/test_json_parser.cpp

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

test/unit/CMakeLists.txt

@@ -15,6 +15,7 @@ create_standard_test(NAME parse_tunneling SOURCES test_parse_tunneling.cpp)
 create_standard_test(NAME parse_surface SOURCES test_parse_surface.cpp)
 create_standard_test(NAME parse_photolysis SOURCES test_parse_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)
 
 ################################################################################
 # Copy test data

test/unit/test_parse_first_order_loss.cpp

@@ -0,0 +1,57 @@
+#include <gtest/gtest.h>
+
+#include <open_atmos/mechanism_configuration/parser.hpp>
+
+using namespace open_atmos::mechanism_configuration;
+
+TEST(JsonParser, CanParseValidFirstOrderLossReaction)
+{
+  JsonParser parser;
+  auto [status, mechanism] = parser.Parse(std::string("unit_configs/reactions/first_order_loss/valid.json"));
+  EXPECT_EQ(status, ConfigParseStatus::Success);
+
+  EXPECT_EQ(mechanism.reactions.first_order_loss.size(), 2);
+
+  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].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].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);
+}
+
+TEST(JsonParser, FirstOrderLossDetectsUnknownSpecies)
+{
+  JsonParser parser;
+  auto [status, mechanism] = parser.Parse(std::string("unit_configs/reactions/first_order_loss/unknown_species.json"));
+  EXPECT_EQ(status, ConfigParseStatus::ReactionRequiresUnknownSpecies);
+}
+
+TEST(JsonParser, FirstOrderLossDetectsBadReactionComponent)
+{
+  JsonParser parser;
+  auto [status, mechanism] = parser.Parse(std::string("unit_configs/reactions/first_order_loss/bad_reaction_component.json"));
+  EXPECT_EQ(status, ConfigParseStatus::RequiredKeyNotFound);
+}
+
+TEST(JsonParser, FirstOrderLossDetectsUnknownPhase)
+{
+  JsonParser parser;
+  auto [status, mechanism] = parser.Parse(std::string("unit_configs/reactions/first_order_loss/missing_phase.json"));
+  EXPECT_EQ(status, ConfigParseStatus::UnknownPhase);
+}
+
+TEST(JsonParser, FirstOrderLossDetectsMoreThanOneSpecies)
+{
+  JsonParser parser;
+  auto [status, mechanism] = parser.Parse(std::string("unit_configs/reactions/first_order_loss/too_many_reactants.json"));
+  EXPECT_EQ(status, ConfigParseStatus::TooManyReactionComponents);
+}

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

@@ -0,0 +1,32 @@
+{
+  "version": "1.0.0",
+  "name": "Bad reaction component",
+  "species": [
+    {
+      "name": "A"
+    },
+    {
+      "name": "B"
+    }
+  ],
+  "phases": [
+    {
+      "name": "gas",
+      "species": [
+        "A",
+        "B"
+      ]
+    }
+  ],
+  "reactions": [
+    {
+      "type": "FIRST_ORDER_LOSS",
+      "gas phase": "gas",
+      "reactants": [
+        {
+          "Species name": "C"
+        }
+      ]
+    }
+  ]
+}

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

@@ -0,0 +1,27 @@
+{
+  "version": "1.0.0",
+  "name": "Missing phase",
+  "species": [
+    {
+      "name": "A"
+    },
+    {
+      "name": "B"
+    },
+    {
+      "name": "C"
+    }
+  ],
+  "phases": [ ],
+  "reactions": [
+    {
+      "type": "FIRST_ORDER_LOSS",
+      "gas phase": "gas",
+      "reactants": [
+        {
+          "species name": "C"
+        }
+      ]
+    }
+  ]
+}

test/unit/unit_configs/reactions/first_order_loss/too_many_reactants.json

@@ -0,0 +1,41 @@
+{
+  "version": "1.0.0",
+  "name": "Too many reactants",
+  "species": [
+    {
+      "name": "A"
+    },
+    {
+      "name": "B"
+    },
+    {
+      "name": "C"
+    }
+  ],
+  "phases": [
+    {
+      "name": "gas",
+      "species": [
+        "A",
+        "B",
+        "C"
+      ]
+    }
+  ],
+  "reactions": [
+    {
+      "type": "FIRST_ORDER_LOSS",
+      "gas phase": "gas",
+      "reactants": [
+        {
+          "species name": "C",
+          "coefficient": 1
+        },
+        {
+          "species name": "B",
+          "coefficient": 1
+        }
+      ]
+    }
+  ]
+}

test/unit/unit_configs/reactions/first_order_loss/unknown_species.json

@@ -0,0 +1,32 @@
+{
+  "version": "1.0.0",
+  "name": "Unknown species",
+  "species": [
+    {
+      "name": "A"
+    },
+    {
+      "name": "B"
+    }
+  ],
+  "phases": [
+    {
+      "name": "gas",
+      "species": [
+        "A",
+        "B"
+      ]
+    }
+  ],
+  "reactions": [
+    {
+      "type": "FIRST_ORDER_LOSS",
+      "gas phase": "gas",
+      "reactants": [
+        {
+          "species name": "C"
+        }
+      ]
+    }
+  ]
+}