checking that species in condensed reaction are in the requested aero…

…sol phase
open-atmos · Jan 19, 2024 · 2a35273 · 2a35273
1 parent a31f4bd
commit 2a35273
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Showing 10 changed files with 217 additions and 11 deletions.
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,
+      RequestedAerosolSpeciesNotIncludedInAerosolPhase
     };
     std::string configParseStatusToString(const ConfigParseStatus &status);
 

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::RequestedAerosolSpeciesNotIncludedInAerosolPhase: return "RequestedAerosolSpeciesNotIncludedInAerosolPhase";
         default: return "Unknown";
       }
     }
@@ -176,6 +177,21 @@ namespace open_atmos
       return false;
     }
 
+    bool RequiresUnknownSpecies(const std::vector<std::string> requested_species, const std::vector<std::string>& existing_species)
+    {
+      for (const auto& spec : requested_species)
+      {
+        auto it =
+            std::find_if(existing_species.begin(), existing_species.end(), [&spec](const std::string& existing) { return existing == spec; });
+
+        if (it == existing_species.end())
+        {
+          return true;
+        }
+      }
+      return false;
+    }
+
     std::pair<ConfigParseStatus, std::vector<types::Species>> ParseSpecies(const json& objects)
     {
       ConfigParseStatus status = ConfigParseStatus::Success;
@@ -407,7 +423,7 @@ namespace open_atmos
       return { status, arrhenius };
     }
 
-    std::pair<ConfigParseStatus, types::CondensedPhaseArrhenius> ParseCondensedPhaseArrhenius(const json& object, const std::vector<types::Species> existing_species)
+    std::pair<ConfigParseStatus, types::CondensedPhaseArrhenius> ParseCondensedPhaseArrhenius(const json& object, const std::vector<types::Species>& existing_species, const std::vector<types::Phase>& existing_phases)
     {
       ConfigParseStatus status = ConfigParseStatus::Success;
       types::CondensedPhaseArrhenius condensed_phase_arrhenius;
@@ -503,6 +519,21 @@ namespace open_atmos
           status = ConfigParseStatus::ReactionRequiresUnknownSpecies;
         }
 
+        auto phase_it = std::find_if(existing_phases.begin(), existing_phases.end(), [&aerosol_phase](const types::Phase& phase) {
+          return phase.name == aerosol_phase;
+        });
+
+        if (phase_it != existing_phases.end()) {
+          // check if all of the species for this reaction are actually in the aerosol phase
+          std::vector<std::string> aerosol_phase_species = {(*phase_it).species.begin(), (*phase_it).species.end()};
+          if (status == ConfigParseStatus::Success && RequiresUnknownSpecies(requested_species, aerosol_phase_species))
+          {
+            status = ConfigParseStatus::RequestedAerosolSpeciesNotIncludedInAerosolPhase;
+          }
+        }
+        else {
+          // TODO phase check
+        }
 
         condensed_phase_arrhenius.aerosol_phase = aerosol_phase;
         condensed_phase_arrhenius.aerosol_phase_water = aerosol_phase_water;
@@ -890,7 +921,7 @@ namespace open_atmos
         }
         else if (type == validation::keys.CondensedPhaseArrhenius_key)
         {
-          auto condensed_phase_arrhenius_parse = ParseCondensedPhaseArrhenius(object, existing_species);
+          auto condensed_phase_arrhenius_parse = ParseCondensedPhaseArrhenius(object, existing_species, existing_phases);
           status = condensed_phase_arrhenius_parse.first;
           if (status != ConfigParseStatus::Success)
           {

diff --git a/test/integration/test_json_parser.cpp b/test/integration/test_json_parser.cpp
@@ -12,6 +12,7 @@ TEST(JsonParser, ParsesFullConfiguration)
   EXPECT_EQ(mechanism.name, "Full Configuration");
   EXPECT_EQ(mechanism.species.size(), 11);
   EXPECT_EQ(mechanism.reactions.arrhenius.size(), 1);
+  EXPECT_EQ(mechanism.reactions.condensed_phase_arrhenius.size(), 1);
   EXPECT_EQ(mechanism.reactions.troe.size(), 1);
   EXPECT_EQ(mechanism.reactions.branched.size(), 1);
   EXPECT_EQ(mechanism.reactions.tunneling.size(), 1);

diff --git a/test/unit/test_parse_condensed_phase_arrhenius.cpp b/test/unit/test_parse_condensed_phase_arrhenius.cpp
@@ -85,4 +85,18 @@ TEST(JsonParser, CondensedPhaseArrheniusDetectsBadReactionComponent)
   JsonParser parser;
   auto [status, mechanism] = parser.Parse(std::string("unit_configs/reactions/condensed_phase_arrhenius/bad_reaction_component.json"));
   EXPECT_EQ(status, ConfigParseStatus::RequiredKeyNotFound);
+}
+
+TEST(JsonParser, CondensedPhaseArrheniusDetectsUnknownAerosolPhaseWater)
+{
+  JsonParser parser;
+  auto [status, mechanism] = parser.Parse(std::string("unit_configs/reactions/condensed_phase_arrhenius/missing_aerosol_phase_water.json"));
+  EXPECT_EQ(status, ConfigParseStatus::ReactionRequiresUnknownSpecies);
+}
+
+TEST(JsonParser, CondensedPhaseArrheniusDetectsWhenRequestedSpeciesAreNotInAerosolPhase)
+{
+  JsonParser parser;
+  auto [status, mechanism] = parser.Parse(std::string("unit_configs/reactions/condensed_phase_arrhenius/species_not_in_aerosol_phase.json"));
+  EXPECT_EQ(status, ConfigParseStatus::RequestedAerosolSpeciesNotIncludedInAerosolPhase);
 }
diff --git a/test/unit/unit_configs/reactions/condensed_phase_arrhenius/bad_reaction_component.json b/test/unit/unit_configs/reactions/condensed_phase_arrhenius/bad_reaction_component.json
@@ -7,21 +7,26 @@
     },
     {
       "name": "B"
+    },
+    {
+      "name": "H2O_aq"
     }
   ],
   "phases": [
     {
       "name": "gas",
       "species": [
         "A",
-        "B"
+        "B",
+        "H2O_aq"
       ]
     }
   ],
   "reactions": [
     {
-      "type": "ARRHENIUS",
-      "gas phase": "gas",
+      "type": "CONDENSED_PHASE_ARRHENIUS",
+      "aerosol phase": "aqueous aerosol",
+      "aerosol-phase water": "H2O_a",
       "reactants": [
         {
           "Species name": "A"

diff --git a/test/unit/unit_configs/reactions/condensed_phase_arrhenius/missing_aerosol_phase_water.json b/test/unit/unit_configs/reactions/condensed_phase_arrhenius/missing_aerosol_phase_water.json
@@ -0,0 +1,46 @@
+{
+  "version": "1.0.0",
+  "name": "Missing condensed phase arrhenius aerosol phase water",
+  "species": [
+    {
+      "name": "A"
+    },
+    {
+      "name": "B"
+    },
+    {
+      "name": "C"
+    },
+    {
+      "name": "H2O_aq"
+    }
+  ],
+  "phases": [
+    {
+      "name": "aqueous aerosol",
+      "species": [
+        "A",
+        "B",
+        "C",
+        "H2O_aq"
+      ]
+    }
+  ],
+  "reactions": [
+    {
+      "type": "CONDENSED_PHASE_ARRHENIUS",
+      "aerosol phase": "aqueous aerosol",
+      "aerosol-phase water": "H2O_a",
+      "reactants": [
+        {
+          "species name": "A"
+        }
+      ],
+      "products": [
+        {
+          "species name": "C"
+        }
+      ]
+    }
+  ]
+}
diff --git a/test/unit/unit_configs/reactions/condensed_phase_arrhenius/mutually_exclusive.json b/test/unit/unit_configs/reactions/condensed_phase_arrhenius/mutually_exclusive.json
@@ -7,21 +7,26 @@
     },
     {
       "name": "B"
+    },
+    {
+      "name": "H2O_aq"
     }
   ],
   "phases": [
     {
       "name": "gas",
       "species": [
         "A",
-        "B"
+        "B",
+        "H2O_aq"
       ]
     }
   ],
   "reactions": [
     {
-      "type": "ARRHENIUS",
-      "gas phase": "gas",
+      "type": "CONDENSED_PHASE_ARRHENIUS",
+      "aerosol phase": "aqueous aerosol",
+      "aerosol-phase water": "H2O_aq",
       "reactants": [
         {
           "species name": "A"

diff --git a/test/unit/unit_configs/reactions/condensed_phase_arrhenius/species_not_in_aerosol_phase.json b/test/unit/unit_configs/reactions/condensed_phase_arrhenius/species_not_in_aerosol_phase.json
@@ -0,0 +1,101 @@
+{
+  "version": "1.0.0",
+  "name": "Condensed phase arrhenius using species not in its requested aerosol phase",
+  "species": [
+    {
+      "name": "A"
+    },
+    {
+      "name": "B"
+    },
+    {
+      "name": "C"
+    },
+    {
+      "name": "H2O_aq"
+    }
+  ],
+  "phases": [
+    {
+      "name": "aqueous aerosol",
+      "species": [
+        "A",
+        "C",
+        "H2O_aq"
+      ]
+    }
+  ],
+  "reactions": [
+    {
+      "type": "CONDENSED_PHASE_ARRHENIUS",
+      "aerosol phase": "aqueous aerosol",
+      "aerosol-phase water": "H2O_aq",
+      "reactants": [
+        {
+          "species name": "A",
+          "coefficient": 1
+        }
+      ],
+      "products": [
+        {
+          "species name": "B",
+          "coefficient": 1.2
+        },
+        {
+          "species name": "C",
+          "coefficient": 0.3
+        }
+      ],
+      "A": 32.1,
+      "B": -2.3,
+      "C": 102.3,
+      "D": 63.4,
+      "E": -1.3,
+      "name": "my arrhenius",
+      "__solver_param": 0.1
+    },
+    {
+      "type": "CONDENSED_PHASE_ARRHENIUS",
+      "aerosol phase": "aqueous aerosol",
+      "aerosol-phase water": "H2O_aq",
+      "reactants": [
+        {
+          "species name": "A",
+          "coefficient": 2
+        },
+        {
+          "species name": "B",
+          "coefficient": 0.1
+        }
+      ],
+      "products": [
+        {
+          "species name": "C",
+          "coefficient": 0.5,
+          "__optional thing": "hello"
+        }
+      ],
+      "A": 3.1,
+      "B": -0.3,
+      "C": 12.3,
+      "D": 6.4,
+      "E": -0.3,
+      "name": "my arrhenius2"
+    },
+    {
+      "type": "CONDENSED_PHASE_ARRHENIUS",
+      "aerosol phase": "aqueous aerosol",
+      "aerosol-phase water": "H2O_aq",
+      "reactants": [
+        {
+          "species name": "A"
+        }
+      ],
+      "products": [
+        {
+          "species name": "C"
+        }
+      ]
+    }
+  ]
+}
diff --git a/test/unit/unit_configs/reactions/condensed_phase_arrhenius/unknown_species.json b/test/unit/unit_configs/reactions/condensed_phase_arrhenius/unknown_species.json
@@ -18,7 +18,8 @@
       "species": [
         "A",
         "B",
-        "C"
+        "C",
+        "H2O_aq"
       ]
     }
   ],

diff --git a/test/unit/unit_configs/reactions/condensed_phase_arrhenius/valid.json b/test/unit/unit_configs/reactions/condensed_phase_arrhenius/valid.json
@@ -21,7 +21,8 @@
       "species": [
         "A",
         "B",
-        "C"
+        "C",
+        "H2O_aq"
       ]
     }
   ],