Merge pull request #17 from open-atmos/parse_troe

Parse troe

examples/full_configuration.json

@@ -12,6 +12,9 @@
     {
       "name": "C"
     },
+    {
+      "name": "M"
+    },
     {
       "name": "H2O2",
       "HLC(298K) [mol m-3 Pa-1]": 1.011596348,

include/open_atmos/mechanism_configuration/validation.hpp

@@ -51,6 +51,17 @@ namespace open_atmos
       const std::string E = "E";
       const std::string Ea = "Ea";
 
+      // Troe
+      const std::string Troe_key = "TROE";
+      const std::string k0_A = "k0_A";
+      const std::string k0_B = "k0_B";
+      const std::string k0_C = "k0_C";
+      const std::string kinf_A = "kinf_A";
+      const std::string kinf_B = "kinf_B";
+      const std::string kinf_C = "kinf_C";
+      const std::string Fc = "Fc";
+      const std::string N = "N";
+
     } keys;
 
     struct Configuration
@@ -89,6 +100,12 @@ namespace open_atmos
       const std::vector<std::string> optional_keys{ keys.A, keys.B, keys.C, keys.D, keys.E, keys.Ea, keys.name };
     } arrhenius;
 
+    struct Troe
+    {
+      const std::vector<std::string> required_keys{ keys.products, keys.reactants, keys.type, keys.gas_phase };
+      const std::vector<std::string> optional_keys{ keys.name, keys.k0_A, keys.k0_B, keys.k0_C, keys.kinf_A, keys.kinf_B, keys.kinf_C, keys.Fc, keys.N };
+    } troe;
+
     struct Mechanism
     {
       const std::vector<std::string> required_keys{};

include/open_atmos/types.hpp

@@ -14,23 +14,24 @@ namespace open_atmos
     struct Species
     {
       std::string name;
-
       std::map<std::string, double> optional_numerical_properties;
-
+      /// @brief Unknown properties, prefixed with two underscores (__)
       std::unordered_map<std::string, std::string> unknown_properties;
     };
 
     struct Phase
     {
       std::string name;
       std::vector<std::string> species;
+      /// @brief Unknown properties, prefixed with two underscores (__)
       std::unordered_map<std::string, std::string> unknown_properties;
     };
 
     struct ReactionComponent
     {
       std::string species_name;
       double coefficient;
+      /// @brief Unknown properties, prefixed with two underscores (__)
       std::unordered_map<std::string, std::string> unknown_properties;
     };
 
@@ -47,7 +48,6 @@ namespace open_atmos
       double D{ 300 };
       /// @brief A factor that determines pressure dependence [Pa-1]
       double E{ 0 };
-
       /// @brief A list of reactants
       std::vector<ReactionComponent> reactants;
       /// @brief A list of products
@@ -56,13 +56,44 @@ namespace open_atmos
       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 Troe
+    {
+      /// @brief low-pressure pre-exponential factor
+      double k0_A = 1.0;
+      /// @brief low-pressure temperature-scaling parameter
+      double k0_B = 0.0;
+      /// @brief low-pressure exponential factor
+      double k0_C = 0.0;
+      /// @brief high-pressure pre-exponential factor
+      double kinf_A = 1.0;
+      /// @brief high-pressure temperature-scaling parameter
+      double kinf_B = 0.0;
+      /// @brief high-pressure exponential factor
+      double kinf_C = 0.0;
+      /// @brief Troe F_c parameter
+      double Fc = 0.6;
+      /// @brief Troe N parameter
+      double N = 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 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;
+      std::vector<types::Troe> troe;
     };
 
     struct Mechanism

src/parser.cpp

@@ -406,6 +406,109 @@ namespace open_atmos
       return { status, arrhenius };
     }
 
+    std::pair<ConfigParseStatus, types::Troe> ParseTroe(const json& object, const std::vector<types::Species> existing_species)
+    {
+      ConfigParseStatus status = ConfigParseStatus::Success;
+      types::Troe troe;
+
+      status = ValidateSchema(object, validation::troe.required_keys, validation::troe.optional_keys);
+      if (status == ConfigParseStatus::Success)
+      {
+        std::vector<types::ReactionComponent> products{};
+        for (const auto& product : object[validation::keys.products])
+        {
+          auto product_parse = ParseReactionComponent(product);
+          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.k0_A))
+        {
+          troe.k0_A = object[validation::keys.k0_A].get<double>();
+        }
+        if (object.contains(validation::keys.k0_B))
+        {
+          troe.k0_B = object[validation::keys.k0_B].get<double>();
+        }
+        if (object.contains(validation::keys.k0_C))
+        {
+          troe.k0_C = object[validation::keys.k0_C].get<double>();
+        }
+        if (object.contains(validation::keys.kinf_A))
+        {
+          troe.kinf_A = object[validation::keys.kinf_A].get<double>();
+        }
+        if (object.contains(validation::keys.kinf_B))
+        {
+          troe.kinf_B = object[validation::keys.kinf_B].get<double>();
+        }
+        if (object.contains(validation::keys.kinf_C))
+        {
+          troe.kinf_C = object[validation::keys.kinf_C].get<double>();
+        }
+        if (object.contains(validation::keys.Fc))
+        {
+          troe.Fc = object[validation::keys.Fc].get<double>();
+        }
+        if (object.contains(validation::keys.N))
+        {
+          troe.N = object[validation::keys.N].get<double>();
+        }
+
+        if (object.contains(validation::keys.name))
+        {
+          troe.name = object[validation::keys.name].get<std::string>();
+        }
+
+        auto comments = GetComments(object, validation::troe.required_keys, validation::troe.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 : products)
+        {
+          requested_species.push_back(spec.species_name);
+        }
+        for (const auto& spec : reactants)
+        {
+          requested_species.push_back(spec.species_name);
+        }
+
+        if (status == ConfigParseStatus::Success && RequiresUnknownSpecies(requested_species, existing_species))
+        {
+          status = ConfigParseStatus::ReactionRequiresUnknownSpecies;
+        }
+
+        troe.gas_phase = object[validation::keys.gas_phase].get<std::string>();
+        troe.products = products;
+        troe.reactants = reactants;
+        troe.unknown_properties = unknown_properties;
+      }
+
+      return { status, troe };
+    }
+
     std::pair<ConfigParseStatus, types::Reactions> ParseReactions(const json& objects, const std::vector<types::Species> existing_species)
     {
       ConfigParseStatus status = ConfigParseStatus::Success;
@@ -424,6 +527,16 @@ namespace open_atmos
           }
           reactions.arrhenius.push_back(arrhenius_parse.second);
         }
+        else if (type == validation::keys.Troe_key)
+        {
+          auto troe_parse = ParseTroe(object, existing_species);
+          status = troe_parse.first;
+          if (status != ConfigParseStatus::Success)
+          {
+            break;
+          }
+          reactions.troe.push_back(troe_parse.second);
+        }
       }
 
       return { status, reactions };

test/integration/test_json_parser.cpp

@@ -10,8 +10,9 @@ TEST(JsonParser, ParsesFullConfiguration)
   auto [status, mechanism] = parser.Parse(std::string("examples/full_configuration.json"));
   EXPECT_EQ(status, ConfigParseStatus::Success);
   EXPECT_EQ(mechanism.name, "Full Configuration");
-  EXPECT_EQ(mechanism.species.size(), 10);
+  EXPECT_EQ(mechanism.species.size(), 11);
   EXPECT_EQ(mechanism.reactions.arrhenius.size(), 1);
+  EXPECT_EQ(mechanism.reactions.troe.size(), 1);
 }
 
 TEST(JsonParser, ParserReportsBadFiles)

test/unit/CMakeLists.txt

@@ -9,6 +9,7 @@ include(test_util)
 create_standard_test(NAME parse_species SOURCES test_parse_species.cpp)
 create_standard_test(NAME parse_phases SOURCES test_parse_phases.cpp)
 create_standard_test(NAME parse_arrhenius SOURCES test_parse_arrhenius.cpp)
+create_standard_test(NAME parse_troe SOURCES test_parse_troe.cpp)
 
 ################################################################################
 # Copy test data

test/unit/test_parse_troe.cpp

@@ -0,0 +1,68 @@
+#include <gtest/gtest.h>
+
+#include <open_atmos/mechanism_configuration/parser.hpp>
+
+using namespace open_atmos::mechanism_configuration;
+
+TEST(JsonParser, CanParseValidTroeReaction)
+{
+  JsonParser parser;
+  auto [status, mechanism] = parser.Parse(std::string("unit_configs/reactions/troe/valid.json"));
+  EXPECT_EQ(status, ConfigParseStatus::Success);
+
+  EXPECT_EQ(mechanism.reactions.troe.size(), 2);
+
+  EXPECT_EQ(mechanism.reactions.troe[0].gas_phase, "gas");
+  EXPECT_EQ(mechanism.reactions.troe[0].k0_A, 1.0);
+  EXPECT_EQ(mechanism.reactions.troe[0].k0_B, 0.0);
+  EXPECT_EQ(mechanism.reactions.troe[0].k0_C, 0.0);
+  EXPECT_EQ(mechanism.reactions.troe[0].kinf_A, 1.0);
+  EXPECT_EQ(mechanism.reactions.troe[0].kinf_B, 0.0);
+  EXPECT_EQ(mechanism.reactions.troe[0].kinf_C, 0.0);
+  EXPECT_EQ(mechanism.reactions.troe[0].Fc, 0.6);
+  EXPECT_EQ(mechanism.reactions.troe[0].N, 1.0);
+  EXPECT_EQ(mechanism.reactions.troe[0].reactants.size(), 1);
+  EXPECT_EQ(mechanism.reactions.troe[0].reactants[0].species_name, "A");
+  EXPECT_EQ(mechanism.reactions.troe[0].reactants[0].coefficient, 1);
+  EXPECT_EQ(mechanism.reactions.troe[0].products.size(), 1);
+  EXPECT_EQ(mechanism.reactions.troe[0].products[0].species_name, "C");
+  EXPECT_EQ(mechanism.reactions.troe[0].products[0].coefficient, 1);
+  EXPECT_EQ(mechanism.reactions.troe[0].unknown_properties.size(), 1);
+  EXPECT_EQ(mechanism.reactions.troe[0].unknown_properties["__my object"], "{\"a\":1.0}");
+
+  EXPECT_EQ(mechanism.reactions.troe[1].name, "my troe");
+  EXPECT_EQ(mechanism.reactions.troe[1].gas_phase, "gas");
+  EXPECT_EQ(mechanism.reactions.troe[1].k0_A, 32.1);
+  EXPECT_EQ(mechanism.reactions.troe[1].k0_B, -2.3);
+  EXPECT_EQ(mechanism.reactions.troe[1].k0_C, 102.3);
+  EXPECT_EQ(mechanism.reactions.troe[1].kinf_A, 63.4);
+  EXPECT_EQ(mechanism.reactions.troe[1].kinf_B, -1.3);
+  EXPECT_EQ(mechanism.reactions.troe[1].kinf_C, 908.5);
+  EXPECT_EQ(mechanism.reactions.troe[1].Fc, 1.3);
+  EXPECT_EQ(mechanism.reactions.troe[1].N, 32.1);
+  EXPECT_EQ(mechanism.reactions.troe[1].reactants.size(), 1);
+  EXPECT_EQ(mechanism.reactions.troe[1].reactants[0].species_name, "C");
+  EXPECT_EQ(mechanism.reactions.troe[1].reactants[0].coefficient, 1);
+  EXPECT_EQ(mechanism.reactions.troe[1].products.size(), 2);
+  EXPECT_EQ(mechanism.reactions.troe[1].products[0].species_name, "A");
+  EXPECT_EQ(mechanism.reactions.troe[1].products[0].coefficient, 0.2);
+  EXPECT_EQ(mechanism.reactions.troe[1].products[0].unknown_properties.size(), 1);
+  EXPECT_EQ(mechanism.reactions.troe[1].products[0].unknown_properties["__optional thing"], "\"hello\"");
+  EXPECT_EQ(mechanism.reactions.troe[1].products[1].species_name, "B");
+  EXPECT_EQ(mechanism.reactions.troe[1].products[1].coefficient, 1.2);
+  EXPECT_EQ(mechanism.reactions.troe[1].products[1].unknown_properties.size(), 0);
+}
+
+TEST(JsonParser, TroeDetectsUnknownSpecies)
+{
+  JsonParser parser;
+  auto [status, mechanism] = parser.Parse(std::string("unit_configs/reactions/troe/unknown_species.json"));
+  EXPECT_EQ(status, ConfigParseStatus::ReactionRequiresUnknownSpecies);
+}
+
+TEST(JsonParser, TroeDetectsBadReactionComponent)
+{
+  JsonParser parser;
+  auto [status, mechanism] = parser.Parse(std::string("unit_configs/reactions/troe/bad_reaction_component.json"));
+  EXPECT_EQ(status, ConfigParseStatus::RequiredKeyNotFound);
+}

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

@@ -1,6 +1,6 @@
 {
   "version": "1.0.0",
-  "name": "Mutually Exclusive",
+  "name": "Bad reaction component",
   "species": [
     {
       "name": "A"

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

@@ -0,0 +1,37 @@
+{
+  "version": "1.0.0",
+  "name": "Bad reaction component",
+  "species": [
+    {
+      "name": "A"
+    },
+    {
+      "name": "B"
+    }
+  ],
+  "phases": [
+    {
+      "name": "gas",
+      "species": [
+        "A",
+        "B"
+      ]
+    }
+  ],
+  "reactions": [
+    {
+      "type": "TROE",
+      "gas phase": "gas",
+      "reactants": [
+        {
+          "Species name": "A"
+        }
+      ],
+      "products": [
+        {
+          "species name": "B"
+        }
+      ]
+    }
+  ]
+}