[Kinetics] Tweak docstrings/formatting and move code from header

Cantera · Dec 14, 2021 · 51a92e3 · 51a92e3
1 parent 5b2e184
commit 51a92e3
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Showing 4 changed files with 60 additions and 64 deletions.
diff --git a/include/cantera/kinetics/GasKinetics.h b/include/cantera/kinetics/GasKinetics.h
@@ -70,62 +70,26 @@ class GasKinetics : public BulkKinetics
     //! reactions.
     virtual void update_rates_C();
 
-private:
+protected:
     //! @name Internal service methods
     /*!
      * These methods are for @internal use, and seek to avoid code duplication
      * while evaluating terms used for rate constants, rates of progress, and
-     * their derivatives. Frequently used methods are defined in the header
-     * file and use raw data pointers to allow inlining and avoid overhead.
+     * their derivatives.
      */
     //! @{
 
     //! Calculate rate coefficients
-    void processFwdRateCoefficients(double* ropf)
-    {
-        update_rates_C();
-        update_rates_T();
-
-        // copy rate coefficients into ropf
-        copy(m_rfn.begin(), m_rfn.end(), ropf);
-
-        if (m_falloff_high_rates.nReactions()) {
-            processFalloffReactions(ropf);
-        }
-
-        // Scale the forward rate coefficient by the perturbation factor
-        for (size_t i = 0; i < nReactions(); ++i) {
-            ropf[i] *= m_perturb[i];
-        }
-    }
+    void processFwdRateCoefficients(double* ropf);
 
     //! Multiply rate with third-body collider concentrations
-    void processThirdBodies(double* rop)
-    {
-        // multiply rop by enhanced 3b conc for all 3b rxns
-        if (!concm_3b_values.empty()) {
-            m_3b_concm.multiply(rop, concm_3b_values.data());
-        }
-
-        // reactions involving third body
-        if (!m_concm.empty()) {
-            m_multi_concm.multiply(rop, m_concm.data());
-        }
-    }
+    void processThirdBodies(double* rop);
 
     //! Multiply rate with inverse equilibrium constant
-    void processEquilibriumConstants(double* rop)
-    {
-        // For reverse rates computed from thermochemistry, multiply the forward
-        // rate coefficients by the reciprocals of the equilibrium constants
-        for (size_t i = 0; i < nReactions(); ++i) {
-            rop[i] *= m_rkcn[i];
-        }
-    }
+    void processEquilibriumConstants(double* rop);
 
     //! @}
 
-protected:
     //! Reaction index of each falloff reaction
     std::vector<size_t> m_fallindx; //!< @deprecated (legacy only)
 

diff --git a/include/cantera/kinetics/ReactionData.h b/include/cantera/kinetics/ReactionData.h
@@ -29,7 +29,7 @@ struct ReactionData
     /**
      * Only used in conjunction with MultiRateBase::evalSingle / ReactionRate::eval.
      * This method allows for testing of a reaction rate expression outside of
-     * Kinetics reaction rate evaluators. Mainly used for testing purposes.
+     * Kinetics reaction rate evaluators.
      */
     virtual void update(double T) {
         temperature = T;
@@ -41,7 +41,7 @@ struct ReactionData
     /**
      * Only used in conjunction with MultiRateBase::evalSingle / ReactionRate::eval.
      * This method allows for testing of a reaction rate expression outside of
-     * Kinetics reaction rate evaluators. Mainly used for testing purposes.
+     * Kinetics reaction rate evaluators.
      */
     virtual void update(double T, double extra);
 
@@ -51,8 +51,7 @@ struct ReactionData
      * @returns A boolean element indicating whether the `evalFromStruct` method
      *      needs to be called (assuming previously-calculated values were cached)
      */
-    virtual bool update(const ThermoPhase& bulk,
-                        const Kinetics& kin) = 0;
+    virtual bool update(const ThermoPhase& bulk, const Kinetics& kin) = 0;
 
     //! Update number of species and reactions
     virtual void resize(size_t n_species, size_t n_reactions) {}
@@ -76,10 +75,9 @@ struct ReactionData
  * The data container `ArrheniusData` holds precalculated data common to
  * all `ArrheniusRate` objects.
  */
-struct ArrheniusData final : public ReactionData
+struct ArrheniusData : public ReactionData
 {
-    virtual bool update(const ThermoPhase& bulk,
-                        const Kinetics& kin);
+    virtual bool update(const ThermoPhase& bulk, const Kinetics& kin);
     using ReactionData::update;
 };
 
@@ -89,12 +87,11 @@ struct ArrheniusData final : public ReactionData
  * The data container `BlowersMaselData` holds precalculated data common to
  * all `BlowersMaselRate` objects.
  */
-struct BlowersMaselData final : public ReactionData
+struct BlowersMaselData : public ReactionData
 {
     BlowersMaselData();
 
-    virtual bool update(const ThermoPhase& bulk,
-                        const Kinetics& kin) override;
+    virtual bool update(const ThermoPhase& bulk, const Kinetics& kin) override;
 
     virtual void update(double T) override;
 
@@ -121,12 +118,11 @@ struct BlowersMaselData final : public ReactionData
  * The data container `FalloffData` holds precalculated data common to
  * all Falloff related reaction rate classes.
  */
-struct FalloffData final : public ReactionData
+struct FalloffData : public ReactionData
 {
     FalloffData();
 
-    virtual bool update(const ThermoPhase& bulk,
-                        const Kinetics& kin) override;
+    virtual bool update(const ThermoPhase& bulk, const Kinetics& kin) override;
 
     virtual void update(double T) override;
 
@@ -156,10 +152,9 @@ struct FalloffData final : public ReactionData
  * The data container `PlogData` holds precalculated data common to
  * all `PlogRate` objects.
  */
-struct PlogData final : public ReactionData
+struct PlogData : public ReactionData
 {
     PlogData() : pressure(NAN), logP(0.) {}
-    using ReactionData::update;
 
     virtual void update(double T) override;
 
@@ -169,8 +164,7 @@ struct PlogData final : public ReactionData
         logP = std::log(P);
     }
 
-    virtual bool update(const ThermoPhase& bulk,
-                        const Kinetics& kin) override;
+    virtual bool update(const ThermoPhase& bulk, const Kinetics& kin) override;
 
     virtual void invalidateCache() override {
         ReactionData::invalidateCache();
@@ -187,10 +181,9 @@ struct PlogData final : public ReactionData
  * The data container `ChebyshevData` holds precalculated data common to
  * all `ChebyshevRate3` objects.
  */
-struct ChebyshevData final : public ReactionData
+struct ChebyshevData : public ReactionData
 {
     ChebyshevData() : pressure(NAN), log10P(0.) {}
-    using ReactionData::update;
 
     virtual void update(double T) override;
 
@@ -200,8 +193,7 @@ struct ChebyshevData final : public ReactionData
         log10P = std::log10(P);
     }
 
-    virtual bool update(const ThermoPhase& bulk,
-                        const Kinetics& kin) override;
+    virtual bool update(const ThermoPhase& bulk, const Kinetics& kin) override;
 
     virtual void invalidateCache() override {
         ReactionData::invalidateCache();

diff --git a/include/cantera/kinetics/ReactionRate.h b/include/cantera/kinetics/ReactionRate.h
@@ -103,7 +103,7 @@ class ReactionRate
     //! @param T  temperature [K]
     //! Used in conjunction with MultiRateBase::evalSingle / ReactionRate::eval.
     //! This method allows for testing of a reaction rate expression outside of
-    //! Kinetics reaction rate evaluators. Mainly used for testing purposes.
+    //! Kinetics reaction rate evaluators.
     double eval(double T) {
         _evaluator().update(T);
         return _evaluator().evalSingle(*this);
@@ -116,7 +116,7 @@ class ReactionRate
     //! @param extra  extra parameter used by parameterization
     //! Used in conjunction with MultiRateBase::evalSingle / ReactionRate::eval.
     //! This method allows for testing of a reaction rate expression outside of
-    //! Kinetics reaction rate evaluators. Mainly used for testing purposes.
+    //! Kinetics reaction rate evaluators.
     double eval(double T, double extra) {
         _evaluator().update(T, extra);
         return _evaluator().evalSingle(*this);

diff --git a/src/kinetics/GasKinetics.cpp b/src/kinetics/GasKinetics.cpp
@@ -132,6 +132,46 @@ void GasKinetics::updateKc()
     }
 }
 
+void GasKinetics::processFwdRateCoefficients(double* ropf)
+{
+    update_rates_C();
+    update_rates_T();
+
+    // copy rate coefficients into ropf
+    copy(m_rfn.begin(), m_rfn.end(), ropf);
+
+    if (m_falloff_high_rates.nReactions()) {
+        processFalloffReactions(ropf);
+    }
+
+    // Scale the forward rate coefficient by the perturbation factor
+    for (size_t i = 0; i < nReactions(); ++i) {
+        ropf[i] *= m_perturb[i];
+    }
+}
+
+void GasKinetics::processThirdBodies(double* rop)
+{
+    // multiply rop by enhanced 3b conc for all 3b rxns
+    if (!concm_3b_values.empty()) {
+        m_3b_concm.multiply(rop, concm_3b_values.data());
+    }
+
+    // reactions involving third body
+    if (!m_concm.empty()) {
+        m_multi_concm.multiply(rop, m_concm.data());
+    }
+}
+
+void GasKinetics::processEquilibriumConstants(double* rop)
+{
+    // For reverse rates computed from thermochemistry, multiply the forward
+    // rate coefficients by the reciprocals of the equilibrium constants
+    for (size_t i = 0; i < nReactions(); ++i) {
+        rop[i] *= m_rkcn[i];
+    }
+}
+
 void GasKinetics::getEquilibriumConstants(doublereal* kc)
 {
     update_rates_T();