[Kinetics] rename Reaction2::setup to Reaction2::setParameters

Cantera · Mar 19, 2021 · b770450 · b770450
1 parent 5369f51
commit b770450
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Showing 7 changed files with 50 additions and 55 deletions.
diff --git a/include/cantera/kinetics/Reaction.h b/include/cantera/kinetics/Reaction.h
@@ -122,7 +122,7 @@ class Reaction2 : public Reaction
     }
 
     //! Set up reaction based on AnyMap node
-    virtual void setup(const AnyMap& node, const Kinetics& kin);
+    virtual void setParameters(const AnyMap& node, const Kinetics& kin);
 
 protected:
     //! Reaction rate used by generic reactions
@@ -281,7 +281,7 @@ class CustomFunc1Reaction : public Reaction2
 public:
     CustomFunc1Reaction();
 
-    virtual void setup(const AnyMap& node, const Kinetics& kin);
+    virtual void setParameters(const AnyMap& node, const Kinetics& kin);
 
     virtual std::string type() const {
         return "custom-rate-function";
@@ -306,7 +306,7 @@ class TestReaction : public Reaction2
         return "elementary-new";
     }
 
-    virtual void setup(const AnyMap& node, const Kinetics& kin);
+    virtual void setParameters(const AnyMap& node, const Kinetics& kin);
 
     bool allow_negative_pre_exponential_factor;
 };

diff --git a/include/cantera/kinetics/ReactionRate.h b/include/cantera/kinetics/ReactionRate.h
@@ -86,11 +86,6 @@ class ReactionRate : public ReactionRateBase
 public:
     ReactionRate() = default;
 
-    ReactionRate(const AnyMap& node, const Units& rc_units) {
-        throw CanteraError("ReactionRate::ReactionRate",
-            "Constructor needs to be implemented by derived classes.");
-    }
-
     //! Update information specific to reaction
     //! @param shared_data  data shared by all reactions of a given type
     virtual void update(const DataType& shared_data, const ThermoPhase& bulk) {}
@@ -148,8 +143,8 @@ class ArrheniusRate final : public ReactionRate<ArrheniusData>, public Arrhenius
 
     //! Constructor
     //! @param node  AnyMap object containing reaction rate specification
-    //! @param rc_units  Description of units used for rate parameters
-    ArrheniusRate(const AnyMap& node, const Units& rc_units);
+    //! @param rate_units  Description of units used for rate parameters
+    ArrheniusRate(const AnyMap& node, const Units& rate_units);
 
     virtual std::string type() const override { return "ArrheniusRate"; }
 
@@ -182,8 +177,8 @@ class CustomFunc1Rate final : public ReactionRate<CustomFunc1Data>
 
     //! Constructor does nothing, as there is no formalized parameterization
     //! @param node  AnyMap object containing reaction rate specification
-    //! @param rc_units  Description of units used for rate parameters
-    CustomFunc1Rate(const AnyMap& rate, const Units& rc_units) {}
+    //! @param rate_units  Description of units used for rate parameters
+    CustomFunc1Rate(const AnyMap& rate, const Units& rate_units) {}
 
     virtual std::string type() const override { return "custom-function"; }
 

diff --git a/include/cantera/kinetics/RxnRates.h b/include/cantera/kinetics/RxnRates.h
@@ -42,8 +42,8 @@ class Arrhenius
     Arrhenius(doublereal A, doublereal b, doublereal E);
 
     //! Run object setup based on AnyMap node information
-    void setup(const AnyValue& rate,
-               const UnitSystem& units, const Units& rc_units);
+    void setParameters(const AnyValue& rate,
+                       const UnitSystem& units, const Units& rate_units);
 
     //! Update concentration-dependent parts of the rate coefficient.
     /*!

diff --git a/src/kinetics/Reaction.cpp b/src/kinetics/Reaction.cpp
@@ -98,29 +98,6 @@ void Reaction::validate()
     }
 }
 
-void Reaction2::setup(const AnyMap& node, const Kinetics& kin)
-{
-    parseReactionEquation(*this, node["equation"], kin);
-    // Non-stoichiometric reaction orders
-    std::map<std::string, double> orders;
-    if (node.hasKey("orders")) {
-        for (const auto& order : node["orders"].asMap<double>()) {
-            orders[order.first] = order.second;
-            if (kin.kineticsSpeciesIndex(order.first) == npos) {
-                setValid(false);
-            }
-        }
-    }
-
-    // Flags
-    id = node.getString("id", "");
-    duplicate = node.getBool("duplicate", false);
-    allow_negative_orders = node.getBool("negative-orders", false);
-    allow_nonreactant_orders = node.getBool("nonreactant-orders", false);
-
-    input = node;
-}
-
 std::string Reaction::reactantString() const
 {
     std::ostringstream result;
@@ -320,18 +297,41 @@ ChebyshevReaction::ChebyshevReaction(const Composition& reactants_,
     reaction_type = CHEBYSHEV_RXN;
 }
 
+void Reaction2::setParameters(const AnyMap& node, const Kinetics& kin)
+{
+    parseReactionEquation(*this, node["equation"], kin);
+    // Non-stoichiometric reaction orders
+    std::map<std::string, double> orders;
+    if (node.hasKey("orders")) {
+        for (const auto& order : node["orders"].asMap<double>()) {
+            orders[order.first] = order.second;
+            if (kin.kineticsSpeciesIndex(order.first) == npos) {
+                setValid(false);
+            }
+        }
+    }
+
+    // Flags
+    id = node.getString("id", "");
+    duplicate = node.getBool("duplicate", false);
+    allow_negative_orders = node.getBool("negative-orders", false);
+    allow_nonreactant_orders = node.getBool("nonreactant-orders", false);
+
+    input = node;
+}
+
 CustomFunc1Reaction::CustomFunc1Reaction()
     : Reaction2()
 {
     reaction_type = CUSTOMPY_RXN;
 }
 
-void CustomFunc1Reaction::setup(const AnyMap& node, const Kinetics& kin)
+void CustomFunc1Reaction::setParameters(const AnyMap& node, const Kinetics& kin)
 {
-    Reaction2::setup(node, kin);
-    Units rc_units; // @todo Not needed once `rate_units` is implemented.
+    Reaction2::setParameters(node, kin);
+    Units rate_units; // @todo Not needed once `rate_units` is implemented.
     setRate(
-        std::shared_ptr<CustomFunc1Rate>(new CustomFunc1Rate(node, rc_units)));
+        std::shared_ptr<CustomFunc1Rate>(new CustomFunc1Rate(node, rate_units)));
 }
 
 TestReaction::TestReaction()
@@ -340,15 +340,15 @@ TestReaction::TestReaction()
 {
 }
 
-void TestReaction::setup(const AnyMap& node, const Kinetics& kin)
+void TestReaction::setParameters(const AnyMap& node, const Kinetics& kin)
 {
-    Reaction2::setup(node, kin);
+    Reaction2::setParameters(node, kin);
 
     // @todo Rate units will become available as `rate_units` after
     // serialization is fully implemented.
-    Units rc_units = rateCoeffUnits(*this, kin);
+    Units rate_units = rateCoeffUnits(*this, kin);
     setRate(
-        std::shared_ptr<ArrheniusRate>(new ArrheniusRate(node, rc_units)));
+        std::shared_ptr<ArrheniusRate>(new ArrheniusRate(node, rate_units)));
     allow_negative_pre_exponential_factor = node.getBool("negative-A", false);
 }
 
@@ -434,9 +434,9 @@ Arrhenius readArrhenius(const Reaction& R, const AnyValue& rate,
                         const Kinetics& kin, const UnitSystem& units,
                         int pressure_dependence=0)
 {
-    Units rc_units = rateCoeffUnits(R, kin, pressure_dependence);
+    Units rate_units = rateCoeffUnits(R, kin, pressure_dependence);
     Arrhenius arr;
-    arr.setup(rate, units, rc_units);
+    arr.setParameters(rate, units, rate_units);
     return arr;
 }
 

diff --git a/src/kinetics/ReactionFactory.cpp b/src/kinetics/ReactionFactory.cpp
@@ -105,7 +105,7 @@ ReactionFactory::ReactionFactory()
             });
     reg_AnyMap("custom-rate-function",
                [](Reaction* R, const AnyMap& node, const Kinetics& kin) {
-                   ((Reaction2*)R)->setup(node, kin);
+                   ((Reaction2*)R)->setParameters(node, kin);
                });
 
     // register custom Python reactions
@@ -117,7 +117,7 @@ ReactionFactory::ReactionFactory()
             });
     reg_AnyMap("elementary-new",
                [](Reaction* R, const AnyMap& node, const Kinetics& kin) {
-                   (dynamic_cast<Reaction2*>(R))->setup(node, kin);
+                   (dynamic_cast<Reaction2*>(R))->setParameters(node, kin);
                });
 
     // register interface reactions

diff --git a/src/kinetics/ReactionRate.cpp b/src/kinetics/ReactionRate.cpp
@@ -14,8 +14,8 @@ ArrheniusRate::ArrheniusRate(double A, double b, double E)
     : Arrhenius(A, b, E) {
 }
 
-ArrheniusRate::ArrheniusRate(const AnyMap& node, const Units& rc_units) {
-    setup(node["rate-constant"], node.units(), rc_units);
+ArrheniusRate::ArrheniusRate(const AnyMap& node, const Units& rate_units) {
+    setParameters(node["rate-constant"], node.units(), rate_units);
 }
 
 CustomFunc1Rate::CustomFunc1Rate() : m_ratefunc(0) {}

diff --git a/src/kinetics/RxnRates.cpp b/src/kinetics/RxnRates.cpp
@@ -29,17 +29,17 @@ Arrhenius::Arrhenius(doublereal A, doublereal b, doublereal E)
     }
 }
 
-void Arrhenius::setup(const AnyValue& rate,
-                      const UnitSystem& units, const Units& rc_units)
+void Arrhenius::setParameters(const AnyValue& rate,
+                              const UnitSystem& units, const Units& rate_units)
 {
     if (rate.is<AnyMap>()) {
         auto& rate_map = rate.as<AnyMap>();
-        m_A = units.convert(rate_map["A"], rc_units);
+        m_A = units.convert(rate_map["A"], rate_units);
         m_b = rate_map["b"].asDouble();
         m_E = units.convertActivationEnergy(rate_map["Ea"], "K");
     } else {
         auto& rate_vec = rate.asVector<AnyValue>(3);
-        m_A = units.convert(rate_vec[0], rc_units);
+        m_A = units.convert(rate_vec[0], rate_units);
         m_b = rate_vec[1].asDouble();
         m_E = units.convertActivationEnergy(rate_vec[2], "K");
     }