[Input] Implement 'skip-undeclared-third-bodies' option in YAML format

doc/sphinx/yaml/phases.rst

@@ -45,6 +45,11 @@ The fields of a ``phase`` entry are:
     explicitly included in the phase. The default is ``false``, where the
     presence of such species is considered an error.
 
+``skip-undeclared-third-bodies``
+   If set to ``true``, ignore third body efficiencies for species that are not
+   defined in the phase. The default is ``false``, where the presence of
+   such third body specifications is considered an error.
+
 ``state``
     A mapping specifying the thermodynamic state. See
     :ref:`sec-yaml-setting-state`.

src/kinetics/KineticsFactory.cpp

@@ -96,6 +96,9 @@ unique_ptr<Kinetics> newKinetics(std::vector<ThermoPhase*>& phases,
 
 void addReactions(Kinetics& kin, const AnyMap& phaseNode, const AnyMap& rootNode)
 {
+    kin.skipUndeclaredThirdBodies(
+        phaseNode.getBool("skip-undeclared-third-bodies", false));
+
     // Find sections containing reactions to add
     vector<string> sections, rules;
 
@@ -130,10 +133,8 @@ void addReactions(Kinetics& kin, const AnyMap& phaseNode, const AnyMap& rootNode
     for (size_t i = 0; i < sections.size(); i++) {
         if (rules[i] == "all") {
             kin.skipUndeclaredSpecies(false);
-            kin.skipUndeclaredThirdBodies(false);
         } else if (rules[i] == "declared-species") {
             kin.skipUndeclaredSpecies(true);
-            kin.skipUndeclaredThirdBodies(true);
         } else if (rules[i] != "none") {
             throw InputFileError("setupKinetics", phaseNode.at("reactions"),
                 "Unknown rule '{}' for adding species from the '{}' section.",

test/data/ideal-gas.yaml

@@ -54,6 +54,24 @@ phases:
   reactions: [reactions, test_subdir/species-elements.yaml/nox-reactions]
   state: {T: 300.0, P: 1 atm, X: {AR: 0.2, O2: 0.7, N2: 0.1}}
 
+- name: efficiency-error
+  thermo: ideal-gas
+  kinetics: gas
+  species:
+  - species: [N2, O]
+  - test_subdir/species-elements.yaml/species: [N2O]
+  reactions: [test_subdir/species-elements.yaml/nox-reactions]
+  state: {T: 300.0, P: 1 atm, X: {N2: 1.0}}
+
+- name: efficiency-skip
+  thermo: ideal-gas
+  kinetics: gas
+  skip-undeclared-third-bodies: true
+  species:
+  - species: [N2, O]
+  - test_subdir/species-elements.yaml/species: [N2O]
+  reactions: [test_subdir/species-elements.yaml/nox-reactions]
+  state: {T: 300.0, P: 1 atm, X: {N2: 1.0}}
 
 elements:
 - symbol: Ar

test/kinetics/kineticsFromYaml.cpp

@@ -197,6 +197,22 @@ TEST(Kinetics, GasKineticsFromYaml2)
     EXPECT_EQ(kin->nReactions(), (size_t) 3);
 }
 
+TEST(Kinetics, EfficienciesFromYaml)
+{
+    AnyMap infile = AnyMap::fromYamlFile("ideal-gas.yaml");
+    auto& phaseNode1 = infile["phases"].getMapWhere("name", "efficiency-error");
+    shared_ptr<ThermoPhase> thermo1 = newPhase(phaseNode1, infile);
+    std::vector<ThermoPhase*> phases1{thermo1.get()};
+    // Reaction with efficiency defined for undeclared species "AR"
+    EXPECT_THROW(newKinetics(phases1, phaseNode1, infile), CanteraError);
+
+    auto& phaseNode2 = infile["phases"].getMapWhere("name", "efficiency-skip");
+    shared_ptr<ThermoPhase> thermo2 = newPhase(phaseNode2, infile);
+    std::vector<ThermoPhase*> phases2{thermo2.get()};
+    auto kin = newKinetics(phases2, phaseNode2, infile);
+    EXPECT_EQ(kin->nReactions(), (size_t) 1);
+}
+
 TEST(Kinetics, InterfaceKineticsFromYaml)
 {
     shared_ptr<ThermoPhase> gas(newPhase("surface-phases.yaml", "gas"));