Create a complete Kinetics object from a YAML input file

include/cantera/kinetics/KineticsFactory.h

@@ -91,6 +91,35 @@ inline Kinetics* newKineticsMgr(const std::string& model)
     return KineticsFactory::factory()->newKinetics(model);
 }
 
+/*!
+ * Create a new kinetics manager, initialize it, and add reactions
+ *
+ * @param phases     Vector of phases containing species which participate in
+ *     reactions, with the phase where the reactions occur (lowest-dimensional
+ *     phase) listed first.
+ * @param phaseNode  Phase entry for the phase where the reactions occur. This
+ *     phase definition is used to determine the source of the reactions added
+ *     to the Kinetics object.
+ * @param rootNode   The root node of the file containing the phase definition,
+ *     which will be treated as the default source for reactions
+ */
+unique_ptr<Kinetics> newKinetics(std::vector<ThermoPhase*>& phases,
+                                 const AnyMap& phaseNode,
+                                 const AnyMap& rootNode=AnyMap());
+
+/*!
+ * Add reactions to a Kinetics object
+ *
+ * @param kin        The Kinetics object to be initialized
+ * @param phaseNode  Phase entry for the phase where the reactions occur. This
+ *     phase definition is used to determine the source of the reactions added
+ *     to the Kinetics object.
+ * @param rootNode   The root node of the file containing the phase definition,
+ *     which will be treated as the default source for reactions
+ */
+void addReactions(Kinetics& kin, const AnyMap& phaseNode,
+                  const AnyMap& rootNode=AnyMap());
+
 }
 
 #endif

src/kinetics/KineticsFactory.cpp

@@ -41,6 +41,7 @@ Kinetics* KineticsFactory::newKinetics(XML_Node& phaseData,
 KineticsFactory::KineticsFactory() {
     reg("none", []() { return new Kinetics(); });
     reg("gaskinetics", []() { return new GasKinetics(); });
+    m_synonyms["gas"] = "gaskinetics";
     reg("interface", []() { return new InterfaceKinetics(); });
     reg("edge", []() { return new EdgeKinetics(); });
 }
@@ -50,4 +51,82 @@ Kinetics* KineticsFactory::newKinetics(const string& model)
     return create(toLowerCopy(model));
 }
 
+unique_ptr<Kinetics> newKinetics(vector<ThermoPhase*>& phases,
+                                 const AnyMap& phaseNode,
+                                 const AnyMap& rootNode)
+{
+    unique_ptr<Kinetics> kin(KineticsFactory::factory()->newKinetics(
+        phaseNode.getString("kinetics", "none")));
+    for (auto& phase : phases) {
+        kin->addPhase(*phase);
+    }
+    kin->init();
+    if (kin->kineticsType() != "Kinetics") {
+        addReactions(*kin, phaseNode, rootNode);
+    }
+    return kin;
+}
+
+void addReactions(Kinetics& kin, const AnyMap& phaseNode, const AnyMap& rootNode)
+{
+    // Find sections containing reactions to add
+    vector<string> sections, rules;
+
+    if (phaseNode.hasKey("reactions")) {
+        const auto& reactionsNode = phaseNode.at("reactions");
+        if (reactionsNode.is<string>()) {
+            // Specification of the rule for adding species from the default
+            // 'reactions' section
+            sections.push_back("reactions");
+            rules.push_back(reactionsNode.asString());
+        } else if (reactionsNode.is<vector<string>>()) {
+            // List of sections from which all species should be added
+            for (const auto& item : reactionsNode.as<vector<string>>()) {
+                sections.push_back(item);
+                rules.push_back("all");
+            }
+        } else if (reactionsNode.is<vector<AnyMap>>()) {
+            // Mapping of rules to apply for each specified section containing
+            // reactions
+            for (const auto& item : reactionsNode.as<vector<AnyMap>>()) {
+                sections.push_back(item.begin()->first);
+                rules.push_back(item.begin()->second.asString());
+            }
+        }
+    } else {
+        // Default behavior is to add all reactions from the 'reactions' section
+        sections.push_back("reactions");
+        rules.push_back("all");
+    }
+
+    // Add reactions from each section
+    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 CanteraError("setupKinetics", "Unknown rule '{}' for adding "
+                "species from the '{}' section.", rules[i], sections[i]);
+        }
+        const auto& slash = boost::ifind_first(sections[i], "/");
+        if (slash) {
+            // specified section is in a different file
+            string fileName (sections[i].begin(), slash.begin());
+            string node(slash.end(), sections[i].end());
+            AnyMap reactions = AnyMap::fromYamlFile(fileName);
+            for (const auto& R : reactions[node].asVector<AnyMap>()) {
+                kin.addReaction(newReaction(R, kin));
+            }
+        } else {
+            // specified section is in the current file
+            for (const auto& R : rootNode.at(sections[i]).asVector<AnyMap>()) {
+                kin.addReaction(newReaction(R, kin));
+            }
+        }
+    }
+}
+
 }

test/data/ideal-gas.yaml

@@ -40,6 +40,20 @@ phases:
   thermo: ideal-gas
   state: {T: 300.0, P: 1 atm, X: {AR: 0.2, O2: 0.7, N2: 0.1}}
 
+- name: simple-kinetics
+  thermo: ideal-gas
+  kinetics: gas
+  state: {T: 300.0, P: 1 atm, X: {AR: 0.2, O2: 0.7, N2: 0.1}}
+
+- name: remote-kinetics
+  thermo: ideal-gas
+  kinetics: gas
+  species:
+  - species: all
+  - species-elements.yaml/species: all
+  reactions: [reactions, species-elements.yaml/nox-reactions]
+  state: {T: 300.0, P: 1 atm, X: {AR: 0.2, O2: 0.7, N2: 0.1}}
+
 
 elements:
 - symbol: Ar
@@ -94,3 +108,36 @@ species:
     - [2.500000000E+00, 0.000000000E+00, 0.000000000E+00, 0.000000000E+00,
        0.000000000E+00, -7.453750000E+02, 4.366000000E+00]
     note: "120186"
+
+- name: O
+  composition: {O: 1}
+  thermo:
+    model: NASA7
+    temperature-ranges: [200, 1000, 3500]
+    data:
+    - [3.168267100E+00, -3.279318840E-03, 6.643063960E-06, -6.128066240E-09,
+        2.112659710E-12, 2.912225920E+04, 2.051933460E+00]
+    - [2.569420780E+00, -8.597411370E-05, 4.194845890E-08, -1.001777990E-11,
+       1.228336910E-15, 2.921757910E+04, 4.784338640E+00]
+    note: "L 1/90"
+
+- name: N
+  composition: {N: 1}
+  thermo:
+    model: NASA7
+    temperature-ranges: [200.00, 1000.00, 6000.00]
+    data:
+    - [2.500000000E+00, 0.000000000E+00, 0.000000000E+00, 0.000000000E+00,
+       0.000000000E+00, 5.610463700E+04, 4.193908700E+00]
+    - [2.415942900E+00, 1.748906500E-04, -1.190236900E-07, 3.022624500E-11,
+       -2.036098200E-15, 5.613377300E+04, 4.649609600E+00]
+    note: "L 6/88"
+
+
+reactions:
+- equation: N + NO <=> N2 + O
+  rate-constant: [2.70000E+13, 0, 355]
+  id: NOx-R1
+
+- equation: N + O2 <=> NO + O
+  rate-constant: [9.00000E+09, 1, 6500]

test/data/species-elements.yaml

@@ -30,3 +30,10 @@ species:
     - [4.823072900E+00, 2.627025100E-03, -9.585087400E-07, 1.600071200E-10,
        -9.775230300E-15, 8.073404800E+03, -2.201720700E+00]
     note: "L 7/88"
+
+nox-reactions:
+- equation: N2O (+ M) <=> N2 + O (+ M)
+  type: falloff
+  high-P-rate-constant: [7.91000E+10, 0, 56020]
+  low-P-rate-constant: [6.37000E+14, 0, 56640]
+  efficiencies: {AR: 0.625}

test/kinetics/kineticsFromYaml.cpp

@@ -1,6 +1,8 @@
 #include "gtest/gtest.h"
 #include "cantera/base/Units.h"
 #include "cantera/IdealGasMix.h"
+#include "cantera/kinetics/KineticsFactory.h"
+#include "cantera/thermo/ThermoFactory.h"
 
 using namespace Cantera;
 
@@ -163,3 +165,31 @@ TEST(Reaction, ChebyshevFromYaml)
     EXPECT_DOUBLE_EQ(CR.rate.Pmin(), 1000);
     EXPECT_NEAR(CR.rate.updateRC(std::log(T), 1.0/T), 130512.2773948636, 1e-9);
 }
+
+TEST(Kinetics, GasKineticsFromYaml1)
+{
+    AnyMap infile = AnyMap::fromYamlFile("ideal-gas.yaml");
+    auto phaseNodes = infile["phases"].asMap("name");
+    auto phaseNode = phaseNodes.at("simple-kinetics");
+    shared_ptr<ThermoPhase> thermo = newPhase(*phaseNode, infile);
+    std::vector<ThermoPhase*> phases{thermo.get()};
+    auto kin = newKinetics(phases, *phaseNode, infile);
+    EXPECT_EQ(kin->nReactions(), (size_t) 2);
+    const auto& R = kin->reaction(0);
+    EXPECT_EQ(R->reactants.at("NO"), 1);
+    EXPECT_EQ(R->products.at("N2"), 1);
+    EXPECT_EQ(R->id, "NOx-R1");
+    const auto& ER = std::dynamic_pointer_cast<ElementaryReaction>(R);
+    EXPECT_DOUBLE_EQ(ER->rate.preExponentialFactor(), 2.7e10);
+}
+
+TEST(Kinetics, GasKineticsFromYaml2)
+{
+    AnyMap infile = AnyMap::fromYamlFile("ideal-gas.yaml");
+    auto phaseNodes = infile["phases"].asMap("name");
+    auto phaseNode = phaseNodes.at("remote-kinetics");
+    shared_ptr<ThermoPhase> thermo = newPhase(*phaseNode, infile);
+    std::vector<ThermoPhase*> phases{thermo.get()};
+    auto kin = newKinetics(phases, *phaseNode, infile);
+    EXPECT_EQ(kin->nReactions(), (size_t) 3);
+}

test/thermo/thermoFromYaml.cpp

@@ -63,7 +63,7 @@ TEST(ThermoFromYaml, speciesAll)
     auto phaseNodes = infile["phases"].asMap("name");
     auto thermo = newPhase(*phaseNodes.at("species-all"), infile);
     EXPECT_EQ(thermo->nElements(), (size_t) 3);
-    EXPECT_EQ(thermo->nSpecies(), (size_t) 4);
+    EXPECT_EQ(thermo->nSpecies(), (size_t) 6);
     EXPECT_EQ(thermo->species(1)->name, "NO");
     EXPECT_EQ(thermo->species(2)->name, "N2");
 }