dropping to c++17, using optional for ion pair

open-atmos · Jan 23, 2024 · b7be482 · b7be482
1 parent 4845bfb
commit b7be482
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Showing 12 changed files with 172 additions and 101 deletions.
diff --git a/examples/full_configuration.json b/examples/full_configuration.json
@@ -76,7 +76,10 @@
       "species": [
         "H2O2_aq",
         "H2O_aq",
-        "ethanol_aq"
+        "ethanol_aq",
+        "A",
+        "B",
+        "C"
       ]
     },
     {
@@ -120,7 +123,6 @@
     },
     {
       "type": "AQUEOUS_EQUILIBRIUM",
-      "gas phase": "gas",
       "aerosol phase": "aqueous aerosol",
       "aerosol-phase water": "H2O_aq",
       "A": 1.14e-2,

diff --git a/include/open_atmos/mechanism_configuration/parser.hpp b/include/open_atmos/mechanism_configuration/parser.hpp
@@ -35,7 +35,8 @@ namespace open_atmos
       ReactionRequiresUnknownSpecies,
       UnknownPhase,
       RequestedAerosolSpeciesNotIncludedInAerosolPhase,
-      TooManyReactionComponents
+      TooManyReactionComponents,
+      InvalidIonPair
     };
     std::string configParseStatusToString(const ConfigParseStatus &status);
 

diff --git a/include/open_atmos/types.hpp b/include/open_atmos/types.hpp
@@ -8,6 +8,8 @@
 #include <unordered_map>
 #include <array>
 #include <vector>
+#include <optional>
+
 
 namespace open_atmos
 {
@@ -240,7 +242,7 @@ namespace open_atmos
       /// @brief A list of products
       std::vector<ReactionComponent> products;
       /// @brief Optional ion pairs
-      std::array<ReactionComponent, 2> ion_pair;
+      std::optional<std::array<ReactionComponent, 2>> ion_pair;
       /// @brief Pre-exponential factor (s-1)
       double A{ 1 };
       /// @brief A constant

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
@@ -5,7 +5,7 @@ configure_file(version.hpp.in ${PROJECT_SOURCE_DIR}/include/open_atmos/mechanism
 add_library(mechanism_configuration)
 add_library(open_atmos::mechanism_configuration ALIAS mechanism_configuration)
 
-target_compile_features(mechanism_configuration PUBLIC cxx_std_20)
+target_compile_features(mechanism_configuration PUBLIC cxx_std_17)
 
 target_sources(mechanism_configuration
   PRIVATE

diff --git a/src/parser.cpp b/src/parser.cpp
@@ -32,6 +32,7 @@ namespace open_atmos
         case ConfigParseStatus::UnknownPhase: return "UnknownPhase";
         case ConfigParseStatus::RequestedAerosolSpeciesNotIncludedInAerosolPhase: return "RequestedAerosolSpeciesNotIncludedInAerosolPhase";
         case ConfigParseStatus::TooManyReactionComponents: return "TooManyReactionComponents";
+        case ConfigParseStatus::InvalidIonPair: return "InvalidIonPair";
         default: return "Unknown";
       }
     }
@@ -137,7 +138,7 @@ namespace open_atmos
       // now, anything left must be standard comment starting with __
       for (auto& key : remaining)
       {
-        if (!key.starts_with("__"))
+        if (key.find("__") == std::string::npos)
         {
           std::cerr << "Non-standard key '" << key << "' found in object" << object << std::endl;
 
@@ -1325,22 +1326,21 @@ namespace open_atmos
           status = ConfigParseStatus::UnknownPhase;
         }
 
-        const auto& ion_pair_object = object[validation::keys.ion_pair];
-        status = ValidateSchema(ion_pair_object, validation::ion_pair.required_keys, validation::ion_pair.optional_keys);
-        if (status == ConfigParseStatus::Success) {
+        if (status == ConfigParseStatus::Success && object.contains(validation::keys.ion_pair)) {
+          const auto& ion_pair_object = object[validation::keys.ion_pair];
+          status = ValidateSchema(ion_pair_object, validation::ion_pair.required_keys, validation::ion_pair.optional_keys);
           auto first_parse = ParseReactionComponent(ion_pair_object[validation::keys.first]);
           if (first_parse.first != ConfigParseStatus::Success) {
             status = first_parse.first;
           }
           else {
-            aqueous_equilibrium.ion_pair[0] = first_parse.second;
-          }
-          auto second_parse = ParseReactionComponent(ion_pair_object[validation::keys.second]);
-          if (second_parse.first != ConfigParseStatus::Success) {
-            status = second_parse.first;
-          }
-          else {
-            aqueous_equilibrium.ion_pair[1] = second_parse.second;
+            auto second_parse = ParseReactionComponent(ion_pair_object[validation::keys.second]);
+            if (second_parse.first != ConfigParseStatus::Success) {
+              status = second_parse.first;
+            }
+            else {
+              aqueous_equilibrium.ion_pair = std::array<types::ReactionComponent, 2>{first_parse.second, second_parse.second};
+            }
           }
         }
 

diff --git a/test/unit/test_parse_aqueous_equilibrium.cpp b/test/unit/test_parse_aqueous_equilibrium.cpp
@@ -26,15 +26,16 @@ TEST(JsonParser, CanParseValidAqueousEquilibriumReaction)
   EXPECT_EQ(mechanism.reactions.aqueous_equilibrium[0].products[0].coefficient, 1);
   EXPECT_EQ(mechanism.reactions.aqueous_equilibrium[0].products[1].species_name, "C");
   EXPECT_EQ(mechanism.reactions.aqueous_equilibrium[0].products[1].coefficient, 1);
-  EXPECT_EQ(mechanism.reactions.aqueous_equilibrium[0].ion_pair[0].species_name, "A");
-  EXPECT_EQ(mechanism.reactions.aqueous_equilibrium[0].ion_pair[1].species_name, "B");
+  EXPECT_EQ(mechanism.reactions.aqueous_equilibrium[0].ion_pair.value()[0].species_name, "A");
+  EXPECT_EQ(mechanism.reactions.aqueous_equilibrium[0].ion_pair.value()[1].species_name, "B");
   EXPECT_EQ(mechanism.reactions.aqueous_equilibrium[0].unknown_properties.size(), 1);
   EXPECT_EQ(mechanism.reactions.aqueous_equilibrium[0].unknown_properties["__comment"], "\"GIF is pronounced with a hard g\"");
 
   EXPECT_EQ(mechanism.reactions.aqueous_equilibrium[1].aerosol_phase, "aerosol");
   EXPECT_EQ(mechanism.reactions.aqueous_equilibrium[1].aerosol_phase_water, "H2O_aq");
   EXPECT_EQ(mechanism.reactions.aqueous_equilibrium[1].A, 1);
   EXPECT_EQ(mechanism.reactions.aqueous_equilibrium[1].C, 0);
+  EXPECT_EQ(mechanism.reactions.aqueous_equilibrium[1].ion_pair.has_value(), false);
   EXPECT_EQ(mechanism.reactions.aqueous_equilibrium[1].k_reverse, 0.32);
   EXPECT_EQ(mechanism.reactions.aqueous_equilibrium[1].reactants.size(), 1);
   EXPECT_EQ(mechanism.reactions.aqueous_equilibrium[1].reactants[0].species_name, "A");
@@ -46,30 +47,30 @@ TEST(JsonParser, CanParseValidAqueousEquilibriumReaction)
   EXPECT_EQ(mechanism.reactions.aqueous_equilibrium[1].products[1].coefficient, 1);
 }
 
-// TEST(JsonParser, AqueousEquilibriumDetectsUnknownSpecies)
-// {
-//   JsonParser parser;
-//   auto [status, mechanism] = parser.Parse(std::string("unit_configs/reactions/aqueous_equilibrium/unknown_species.json"));
-//   EXPECT_EQ(status, ConfigParseStatus::ReactionRequiresUnknownSpecies);
-// }
+TEST(JsonParser, AqueousEquilibriumDetectsUnknownSpecies)
+{
+  JsonParser parser;
+  auto [status, mechanism] = parser.Parse(std::string("unit_configs/reactions/aqueous_equilibrium/unknown_species.json"));
+  EXPECT_EQ(status, ConfigParseStatus::ReactionRequiresUnknownSpecies);
+}
 
-// TEST(JsonParser, AqueousEquilibriumDetectsMutuallyExclusiveOptions)
-// {
-//   JsonParser parser;
-//   auto [status, mechanism] = parser.Parse(std::string("unit_configs/reactions/aqueous_equilibrium/mutually_exclusive.json"));
-//   EXPECT_EQ(status, ConfigParseStatus::MutuallyExclusiveOption);
-// }
+TEST(JsonParser, AqueousEquilibriumDetectsBadReactionComponent)
+{
+  JsonParser parser;
+  auto [status, mechanism] = parser.Parse(std::string("unit_configs/reactions/aqueous_equilibrium/bad_reaction_component.json"));
+  EXPECT_EQ(status, ConfigParseStatus::RequiredKeyNotFound);
+}
 
-// TEST(JsonParser, AqueousEquilibriumDetectsBadReactionComponent)
-// {
-//   JsonParser parser;
-//   auto [status, mechanism] = parser.Parse(std::string("unit_configs/reactions/aqueous_equilibrium/bad_reaction_component.json"));
-//   EXPECT_EQ(status, ConfigParseStatus::RequiredKeyNotFound);
-// }
+TEST(JsonParser, AqueousEquilibriumDetectsUnknownPhase)
+{
+  JsonParser parser;
+  auto [status, mechanism] = parser.Parse(std::string("unit_configs/reactions/aqueous_equilibrium/missing_phase.json"));
+  EXPECT_EQ(status, ConfigParseStatus::UnknownPhase);
+}
 
-// TEST(JsonParser, AqueousEquilibriumDetectsUnknownPhase)
-// {
-//   JsonParser parser;
-//   auto [status, mechanism] = parser.Parse(std::string("unit_configs/reactions/aqueous_equilibrium/missing_phase.json"));
-//   EXPECT_EQ(status, ConfigParseStatus::UnknownPhase);
-// }
+TEST(JsonParser, AqueousEquilibriumDetectsInvalidIonPair)
+{
+  JsonParser parser;
+  auto [status, mechanism] = parser.Parse(std::string("unit_configs/reactions/aqueous_equilibrium/invalid_ion_pair.json"));
+  EXPECT_EQ(status, ConfigParseStatus::InvalidIonPair);
+}
diff --git a/test/unit/unit_configs/reactions/aqueous_equilibrium/bad_reaction_component.json b/test/unit/unit_configs/reactions/aqueous_equilibrium/bad_reaction_component.json
@@ -7,29 +7,49 @@
     },
     {
       "name": "B"
+    },
+    {
+      "name": "C"
+    },
+    {
+      "name": "H2O_aq"
     }
   ],
   "phases": [
     {
-      "name": "gas",
+      "name": "aerosol",
       "species": [
         "A",
-        "B"
+        "B",
+        "C",
+        "H2O_aq"
       ]
     }
   ],
   "reactions": [
     {
-      "type": "ARRHENIUS",
-      "gas phase": "gas",
+      "type": "AQUEOUS_EQUILIBRIUM",
+      "aerosol phase": "aerosol",
+      "aerosol-phase water": "H2O_aq",
+      "k_reverse": 0.32,
+      "ion pair": {
+        "first": { "species name": "A"},
+        "second": { "species name": "B"}
+      },
       "reactants": [
         {
-          "Species name": "A"
+          "Species name": "A",
+          "coefficient": 2
         }
       ],
       "products": [
         {
-          "species name": "B"
+          "Species name": "B",
+          "coefficient": 1
+        },
+        {
+          "Species name": "C",
+          "coefficient": 1
         }
       ]
     }

diff --git a/test/unit/unit_configs/reactions/aqueous_equilibrium/invalid_ion_pair.json b/test/unit/unit_configs/reactions/aqueous_equilibrium/invalid_ion_pair.json
@@ -0,0 +1,57 @@
+{
+  "version": "1.0.0",
+  "name": "Valid aqueous equilibrium",
+  "species": [
+    {
+      "name": "A"
+    },
+    {
+      "name": "B"
+    },
+    {
+      "name": "C"
+    },
+    {
+      "name": "H2O_aq"
+    }
+  ],
+  "phases": [
+    {
+      "name": "aerosol",
+      "species": [
+        "A",
+        "B",
+        "C",
+        "H2O_aq"
+      ]
+    }
+  ],
+  "reactions": [
+    {
+      "type": "AQUEOUS_EQUILIBRIUM",
+      "aerosol phase": "aerosol",
+      "aerosol-phase water": "H2O_aq",
+      "k_reverse": 0.32,
+      "ion pair": {
+        "first": { "species name": "A"},
+        "second": { "species name": "B"}
+      },
+      "reactants": [
+        {
+          "species name": "A",
+          "coefficient": 2
+        }
+      ],
+      "products": [
+        {
+          "species name": "B",
+          "coefficient": 1
+        },
+        {
+          "species name": "C",
+          "coefficient": 1
+        }
+      ]
+    }
+  ]
+}
diff --git a/test/unit/unit_configs/reactions/aqueous_equilibrium/missing_phase.json b/test/unit/unit_configs/reactions/aqueous_equilibrium/missing_phase.json
@@ -10,21 +10,36 @@
     },
     {
       "name": "C"
+    },
+    {
+      "name": "H2O_aq"
     }
   ],
   "phases": [ ],
   "reactions": [
     {
-      "type": "ARRHENIUS",
-      "gas phase": "gas",
+      "type": "AQUEOUS_EQUILIBRIUM",
+      "aerosol phase": "aerosol",
+      "aerosol-phase water": "H2O_aq",
+      "k_reverse": 0.32,
+      "ion pair": {
+        "first": { "species name": "A"},
+        "second": { "species name": "B"}
+      },
       "reactants": [
         {
-          "species name": "A"
+          "species name": "A",
+          "coefficient": 2
         }
       ],
       "products": [
         {
-          "species name": "C"
+          "species name": "B",
+          "coefficient": 1
+        },
+        {
+          "species name": "C",
+          "coefficient": 1
         }
       ]
     }

diff --git a/test/unit/unit_configs/reactions/aqueous_equilibrium/mutually_exclusive.json b/test/unit/unit_configs/reactions/aqueous_equilibrium/mutually_exclusive.json