correcting first order loss format

open-atmos · Jan 19, 2024 · dc129fe · dc129fe
1 parent c238872
commit dc129fe
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Showing 12 changed files with 79 additions and 31 deletions.
diff --git a/examples/full_configuration.json b/examples/full_configuration.json
@@ -205,7 +205,7 @@
     {
       "type": "FIRST_ORDER_LOSS",
       "gas phase": "gas",
-      "products": [
+      "reactants": [
         {
           "species name": "C",
           "coefficient": 1

diff --git a/include/open_atmos/mechanism_configuration/parser.hpp b/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);
 

diff --git a/include/open_atmos/mechanism_configuration/validation.hpp b/include/open_atmos/mechanism_configuration/validation.hpp
@@ -175,7 +175,7 @@ namespace open_atmos
 
     struct FirstOrderLoss
     {
-      const std::vector<std::string> required_keys{ keys.products, keys.type, keys.gas_phase };
+      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;
 

diff --git a/include/open_atmos/types.hpp b/include/open_atmos/types.hpp
@@ -186,8 +186,8 @@ namespace open_atmos
     {
       /// @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 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

diff --git a/src/parser.cpp b/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";
       }
     }
@@ -952,16 +953,16 @@ namespace open_atmos
       status = ValidateSchema(object, validation::first_order_loss.required_keys, validation::first_order_loss.optional_keys);
       if (status == ConfigParseStatus::Success)
       {
-        std::vector<types::ReactionComponent> products{};
-        for (const auto& reactant : object[validation::keys.products])
+        std::vector<types::ReactionComponent> reactants{};
+        for (const auto& reactant : object[validation::keys.reactants])
         {
-          auto product_parse = ParseReactionComponent(reactant);
-          status = product_parse.first;
+          auto reactant_parse = ParseReactionComponent(reactant);
+          status = reactant_parse.first;
           if (status != ConfigParseStatus::Success)
           {
             break;
           }
-          products.push_back(product_parse.second);
+          reactants.push_back(reactant_parse.second);
         }
 
         if (object.contains(validation::keys.scaling_factor))
@@ -984,7 +985,7 @@ namespace open_atmos
         }
 
         std::vector<std::string> requested_species;
-        for (const auto& spec : products)
+        for (const auto& spec : reactants)
         {
           requested_species.push_back(spec.species_name);
         }
@@ -1002,8 +1003,13 @@ namespace open_atmos
           status = ConfigParseStatus::UnknownPhase;
         }
 
+        if (status == ConfigParseStatus::Success && reactants.size() > 1)
+        {
+          status = ConfigParseStatus::TooManyReactionComponents;
+        }
+
         first_order_loss.gas_phase = gas_phase;
-        first_order_loss.products = products;
+        first_order_loss.reactants = reactants;
         first_order_loss.unknown_properties = unknown_properties;
       }
 

diff --git a/test/integration/test_json_parser.cpp b/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)

diff --git a/test/unit/test_parse_first_order_loss.cpp b/test/unit/test_parse_first_order_loss.cpp
@@ -15,17 +15,17 @@ TEST(JsonParser, CanParseValidFirstOrderLossReaction)
   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].products.size(), 1);
-  EXPECT_EQ(mechanism.reactions.first_order_loss[0].products[0].species_name, "C");
-  EXPECT_EQ(mechanism.reactions.first_order_loss[0].products[0].coefficient, 1);
+  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].products.size(), 1);
-  EXPECT_EQ(mechanism.reactions.first_order_loss[1].products[0].species_name, "C");
-  EXPECT_EQ(mechanism.reactions.first_order_loss[1].products[0].coefficient, 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)
@@ -47,4 +47,11 @@ 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);
 }
diff --git a/test/unit/unit_configs/reactions/first_order_loss/bad_reaction_component.json b/test/unit/unit_configs/reactions/first_order_loss/bad_reaction_component.json
@@ -22,7 +22,7 @@
     {
       "type": "FIRST_ORDER_LOSS",
       "gas phase": "gas",
-      "products": [
+      "reactants": [
         {
           "Species name": "C"
         }

diff --git a/test/unit/unit_configs/reactions/first_order_loss/missing_phase.json b/test/unit/unit_configs/reactions/first_order_loss/missing_phase.json
@@ -17,7 +17,7 @@
     {
       "type": "FIRST_ORDER_LOSS",
       "gas phase": "gas",
-      "products": [
+      "reactants": [
         {
           "species name": "C"
         }

diff --git a/test/unit/unit_configs/reactions/first_order_loss/too_many_reactants.json b/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
+        }
+      ]
+    }
+  ]
+}
diff --git a/test/unit/unit_configs/reactions/first_order_loss/unknown_species.json b/test/unit/unit_configs/reactions/first_order_loss/unknown_species.json
@@ -22,7 +22,7 @@
     {
       "type": "FIRST_ORDER_LOSS",
       "gas phase": "gas",
-      "products": [
+      "reactants": [
         {
           "species name": "C"
         }

diff --git a/test/unit/unit_configs/reactions/first_order_loss/valid.json b/test/unit/unit_configs/reactions/first_order_loss/valid.json
@@ -20,21 +20,13 @@
         "B",
         "C"
       ]
-    },
-    {
-      "name": "surface reacting phase",
-      "species": [
-        "A",
-        "B",
-        "C"
-      ]
     }
   ],
   "reactions": [
     {
       "type": "FIRST_ORDER_LOSS",
       "gas phase": "gas",
-      "products": [
+      "reactants": [
         {
           "species name": "C",
           "coefficient": 1
@@ -47,7 +39,7 @@
     {
       "type": "FIRST_ORDER_LOSS",
       "gas phase": "gas",
-      "products": [
+      "reactants": [
         {
           "species name": "C",
           "coefficient": 1