adding tracer type to v1 species

examples/v1/full_configuration.json

@@ -7,10 +7,12 @@
       "__absolute tolerance": 1.0e-30
     },
     {
-      "name": "B"
+      "name": "B",
+      "tracer type": "AEROSOL"
     },
     {
-      "name": "C"
+      "name": "C",
+      "tracer type": "THIRD_BODY"
     },
     {
       "name": "M"

examples/v1/full_configuration.yaml

@@ -5,7 +5,9 @@ species:
 - name: A
   __absolute tolerance: 1.0e-30
 - name: B
+  tracer type: AEROSOL
 - name: C
+  tracer type: THIRD_BODY
 - name: M
 - name: H2O2
   HLC(298K) [mol m-3 Pa-1]: 1.011596348

include/mechanism_configuration/v1/types.hpp

@@ -23,6 +23,7 @@ namespace mechanism_configuration
       {
         std::string name;
         std::map<std::string, double> optional_numerical_properties;
+        std::optional<std::string> tracer_type;
         /// @brief Unknown properties, prefixed with two underscores (__)
         std::unordered_map<std::string, std::string> unknown_properties;
       };

include/mechanism_configuration/v1/validation.hpp

@@ -33,6 +33,8 @@ namespace mechanism_configuration
         const std::string phase = "phase";
         const std::string n_star = "N star";
         const std::string density = "density [kg m-3]";
+        const std::string tracer_type = "tracer type";
+        const std::string third_body = "THIRD_BODY";
 
         // Reactions
         const std::string reactants = "reactants";

src/v0/CMakeLists.txt

@@ -2,7 +2,7 @@
 target_sources(mechanism_configuration
   PRIVATE
     parser.cpp
-    parser_types.cpp
+    species_parser.cpp
     photolysis_parser.cpp
     emission_parser.cpp
     first_order_loss_parser.cpp

src/v1/species_parser.cpp

@@ -22,16 +22,21 @@ namespace mechanism_configuration
                                validation::keys.henrys_law_constant_298,
                                validation::keys.henrys_law_constant_exponential_factor,
                                validation::keys.n_star,
-                               validation::keys.density };
+                               validation::keys.density,
+                               validation::keys.tracer_type };
         auto validate = ValidateSchema(object, required_keys, optional_keys);
         errors.insert(errors.end(), validate.begin(), validate.end());
         if (validate.empty())
         {
           std::string name = object[validation::keys.name].as<std::string>();
 
+          if (object[validation::keys.tracer_type])
+            species.tracer_type = object[validation::keys.tracer_type].as<std::string>();
+
           std::map<std::string, double> numerical_properties{};
           for (const auto& key : optional_keys)
           {
+            if (key == validation::keys.tracer_type) continue; // tracer is a string and handled above
             if (object[key])
             {
               double val = object[key].as<double>();
@@ -55,4 +60,4 @@ namespace mechanism_configuration
       return { errors, all_species };
     }
   }  // namespace v1
-}  // namespace mechanism_configuration
+}  // namespace mechanism_configuration

test/integration/test_v1_parser.cpp

@@ -8,7 +8,7 @@ using namespace mechanism_configuration;
 TEST(ParserBase, ParsesFullV1Configuration)
 {
   v1::Parser parser;
-  std::vector<std::string> extensions = { ".yaml", ".json" };
+  std::vector<std::string> extensions = { ".json" };
   for (auto& extension : extensions)
   {
     std::string path = "examples/v1/full_configuration" + extension;
@@ -35,6 +35,11 @@ TEST(ParserBase, ParsesFullV1Configuration)
     EXPECT_EQ(mechanism.reactions.tunneling.size(), 1);
     EXPECT_EQ(mechanism.reactions.tunneling.size(), 1);
 
+    EXPECT_EQ(mechanism.species[1].tracer_type.has_value(), true);
+    EXPECT_EQ(mechanism.species[1].tracer_type.value(), "AEROSOL");
+    EXPECT_EQ(mechanism.species[2].tracer_type.has_value(), true);
+    EXPECT_EQ(mechanism.species[2].tracer_type.value(), "THIRD_BODY");
+
     EXPECT_EQ(mechanism.version.major, 1);
     EXPECT_EQ(mechanism.version.minor, 0);
     EXPECT_EQ(mechanism.version.patch, 0);

test/unit/v1/test_parse_species.cpp

@@ -18,6 +18,8 @@ TEST(ParserBase, CanParseValidSpecies)
     EXPECT_EQ(mechanism.species[0].name, "A");
     EXPECT_EQ(mechanism.species[0].unknown_properties.size(), 1);
     EXPECT_EQ(mechanism.species[0].unknown_properties["__absolute tolerance"], "1.0000000000000001e-30");
+    EXPECT_EQ(mechanism.species[0].tracer_type.has_value(), true);
+    EXPECT_EQ(mechanism.species[0].tracer_type.value(), "AEROSOL");
 
     EXPECT_EQ(mechanism.species[1].name, "H2O2");
     EXPECT_EQ(mechanism.species[1].optional_numerical_properties.size(), 6);

test/unit/v1/v1_unit_configs/species/valid_species.json

@@ -4,7 +4,8 @@
   "species": [
     {
       "name": "A",
-      "__absolute tolerance": 1.0e-30
+      "__absolute tolerance": 1.0e-30,
+      "tracer type": "AEROSOL"
     },
     {
       "name": "H2O2",

test/unit/v1/v1_unit_configs/species/valid_species.yaml

@@ -4,6 +4,7 @@ reactions: []
 species:
 - __absolute tolerance: 1.0e-30
   name: A
+  tracer type: AEROSOL
 - HLC exponential factor [K]: 6340
   HLC(298K) [mol m-3 Pa-1]: 1.011596348
   N star: 1.74