Temp PR updates

Author: anthony-walker

doc/sphinx/develop/index.md

@@ -1,6 +1,7 @@
 # Develop
 
 (sec-compiling)=
+
 ## Compiling Cantera from Source
 
 If you're interested in contributing new features to Cantera, or you want to try the
@@ -12,9 +13,9 @@ Cantera](compiling/configure-build) on your computer.
 
 The following additional references may also be useful:
 
-- [](compiling/dependencies.md)
-- [](compiling/config-options)
-- [](compiling/special-cases)
+-   [](compiling/dependencies.md)
+-   [](compiling/config-options)
+-   [](compiling/special-cases)
 
 ```{toctree}
 :caption: Compiling Cantera from Source
@@ -35,7 +36,7 @@ compiling/special-cases
 This section is a work in progress.
 ```
 
-- [](reactor-integration)
+-   [](reactor-integration)
 
 ```{toctree}
 :caption: How Cantera Works
@@ -47,13 +48,13 @@ reactor-integration
 
 ## Adding New Features to Cantera
 
-- [](CONTRIBUTING)
-- [](style-guidelines)
-- [](vscode-tips)
-- [](writing-tests)
-- [](running-tests)
-- [](writing-examples)
-- [](doc-formatting)
+-   [](CONTRIBUTING)
+-   [](style-guidelines)
+-   [](vscode-tips)
+-   [](writing-tests)
+-   [](running-tests)
+-   [](writing-examples)
+-   [](doc-formatting)
 
 ```{toctree}
 :caption: Adding New Features to Cantera

include/cantera/zeroD/FlowDevice.h

@@ -123,7 +123,7 @@ class FlowDevice
     //! @warning This function is an experimental part of the %Cantera API and may be
     //! changed
     //! or removed without notice.
-    //! @since New in %Cantera 3.0.
+    //! @since New in %Cantera 3.1.
     //!
     virtual void buildReactorJacobian(ReactorBase* r, vector<Eigen::Triplet<double>>& jacVector) {
         throw NotImplementedError(type() + "::buildReactorJacobian");
@@ -137,7 +137,7 @@ class FlowDevice
     //! @warning This function is an experimental part of the %Cantera API and may be
     //! changed
     //! or removed without notice.
-    //! @since New in %Cantera 3.0.
+    //! @since New in %Cantera 3.1.
     //!
     virtual void buildNetworkJacobian(vector<Eigen::Triplet<double>>& jacVector) {
         if (!m_jac_calculated) {
@@ -149,16 +149,16 @@ class FlowDevice
     //! @warning This function is an experimental part of the %Cantera API and may be
     //! changed
     //! or removed without notice.
-    //! @since New in %Cantera 3.0.
+    //! @since New in %Cantera 3.1.
     //!
-    void jacobianCalculated() { m_jac_calculated = true; };
+    void calculatedJacobian() { m_jac_calculated = true; };
 
     //! Specify that jacobian terms have not been calculated and should be recalculated.
     //! @warning This function is an experimental part of the %Cantera API and may be changed
     //! or removed without notice.
-    //! @since New in %Cantera 3.0.
+    //! @since New in %Cantera 3.1.
     //!
-    void jacobianNotCalculated() { m_jac_calculated = false; };
+    void notCalculatedJacobian() { m_jac_calculated = false; };
 
 protected:
     //! a variable to switch on and off so calculations are not doubled by the calling

include/cantera/zeroD/IdealGasConstPressureMoleReactor.h

@@ -47,9 +47,7 @@ class IdealGasConstPressureMoleReactor : public ConstPressureMoleReactor
 
     bool preconditionerSupported() const override { return true; };
 
-    double moleDerivative(size_t index) override;
-
-    double moleRadiationDerivative(size_t index) override;
+    double temperature_ddni(size_t index) override;
 
     size_t speciesOffset() const override { return m_sidx; };
 

include/cantera/zeroD/IdealGasMoleReactor.h

@@ -43,9 +43,7 @@ class IdealGasMoleReactor : public MoleReactor
 
     bool preconditionerSupported() const override {return true;};
 
-    double moleDerivative(size_t index) override;
-
-    double moleRadiationDerivative(size_t index) override;
+    double temperature_ddni(size_t index) override;
 
     size_t speciesOffset() const override { return m_sidx; };
 

include/cantera/zeroD/Reactor.h

@@ -84,12 +84,6 @@ class Reactor : public ReactorBase
         m_chem = cflag;
     }
 
-    //! Returns `true` if changes in the reactor composition due to chemical reactions
-    //! are enabled.
-    bool chemistryEnabled() const {
-        return m_chem;
-    }
-
     void setEnergy(int eflag=1) override {
         if (eflag > 0) {
             m_energy = true;
@@ -98,11 +92,6 @@ class Reactor : public ReactorBase
         }
     }
 
-    //! Returns `true` if solution of the energy equation is enabled.
-    bool energyEnabled() const {
-        return m_energy;
-    }
-
     //! Number of equations (state variables) for this reactor
     size_t neq() {
         if (!m_nv) {
@@ -335,8 +324,6 @@ class Reactor : public ReactorBase
 
     vector<double> m_wdot; //!< Species net molar production rates
     vector<double> m_uk; //!< Species molar internal energies
-    bool m_chem = false;
-    bool m_energy = true;
     size_t m_nv = 0;
     size_t m_nv_surf; //!!< Number of variables associated with reactor surfaces
 

include/cantera/zeroD/ReactorBase.h

@@ -277,26 +277,15 @@ class ReactorBase
     //! Set the ReactorNet that this reactor belongs to.
     void setNetwork(ReactorNet* net);
 
-    //! Calculate the derivative of T with respect to the ith species in the heat
-    //! transfer equation based on the reactor specific equation of state.
+    //! Calculate the derivative of T with respect to the ith species in the energy
+    //! conservation equation based on the reactor specific equation of state.
     //! @param index index of the species the derivative is with respect too
     //! @warning This function is an experimental part of the %Cantera API and may be changed
     //! or removed without notice.
-    //! @since New in %Cantera 3.0.
-    //!
-    virtual double moleDerivative(size_t index) {
-        throw NotImplementedError("Reactor::moleDerivative");
-    }
-
-    //! Calculate the derivative of T with respect to the ith species in the heat
-    //! transfer radiation equation based on the reactor specific equation of state.
-    //! @param index index of the species the derivative is with respect too
-    //! @warning This function is an experimental part of the %Cantera API and may be changed
-    //! or removed without notice.
-    //! @since New in %Cantera 3.0.
+    //! @since New in %Cantera 3.1.
     //!
-    virtual double moleRadiationDerivative(size_t index) {
-        throw NotImplementedError("Reactor::moleRadiationDerivative");
+    virtual double temperature_ddni(size_t index) {
+        throw NotImplementedError("Reactor::temperature_ddni");
     }
 
     //! Return the index associated with energy of the system
@@ -305,6 +294,17 @@ class ReactorBase
     //! Return the offset between species and state variables
     virtual size_t speciesOffset() const { return m_sidx; };
 
+    //! Returns `true` if solution of the energy equation is enabled.
+    virtual bool energyEnabled() const {
+        return m_energy;
+    }
+
+    //! Returns `true` if changes in the reactor composition due to chemical reactions
+    //! are enabled.
+    bool chemistryEnabled() const {
+        return m_chem;
+    }
+
 protected:
     //! Specify the mixture contained in the reactor. Note that a pointer to
     //! this substance is stored, and as the integration proceeds, the state of
@@ -348,6 +348,12 @@ class ReactorBase
 
     //! Composite thermo/kinetics/transport handler
     shared_ptr<Solution> m_solution;
+
+    //! A bool that enables the energy equation
+    bool m_energy = true;
+
+    //! A bool that enables the chemical kinetics equations
+    bool m_chem = false;
 };
 }
 

include/cantera/zeroD/ReactorNet.h

@@ -239,7 +239,7 @@ class ReactorNet : public FuncEval
     //! Return the index corresponding to the start of the reactor specific state
     //! vector in the reactor with index *reactor* in the global state vector for the
     //! reactor network.
-    size_t globalStartIndex(Reactor* curr_reactor) {
+    size_t globalStartIndex(ReactorBase* curr_reactor) {
         for (size_t i = 0; i < m_reactors.size(); i++) {
             if (curr_reactor == m_reactors[i]) {
                 return m_start[i];

include/cantera/zeroD/Wall.h

@@ -95,12 +95,11 @@ class WallBase
     //! Build the Jacobian terms specific to the flow device for the given connected
     //! reactor.
     //! @param r a pointer to the calling reactor
-    //! @param jacVector a vector of triplets to be added to the jacobian for the
+    //! @param jacVector a vector of triplets to be added to the Jacobian for the
     //! reactor
     //! @warning This function is an experimental part of the %Cantera API and may be
-    //! changed
-    //! or removed without notice.
-    //! @since New in %Cantera 3.0.
+    //! changed or removed without notice.
+    //! @since New in %Cantera 3.1.
     //!
     virtual void buildReactorJacobian(ReactorBase* r, vector<Eigen::Triplet<double>>& jacVector) {
         throw NotImplementedError("WallBase::buildReactorJacobian");
@@ -109,32 +108,29 @@ class WallBase
     //! Build the Jacobian terms specific to the flow device for the network. These
     //! terms
     //! will be adjusted to the networks indexing system outside of the reactor.
-    //! @param jacVector a vector of triplets to be added to the jacobian for the
+    //! @param jacVector a vector of triplets to be added to the Jacobian for the
     //! reactor
     //! @warning This function is an experimental part of the %Cantera API and may be
-    //! changed
-    //! or removed without notice.
-    //! @since New in %Cantera 3.0.
+    //! changed or removed without notice.
+    //! @since New in %Cantera 3.1.
     //!
     virtual void buildNetworkJacobian(vector<Eigen::Triplet<double>>& jacVector) {
         throw NotImplementedError("WallBase::buildNetworkJacobian");
     }
 
-    //! Specify the jacobian terms have been calculated and should not be recalculated.
+    //! Specify the Jacobian terms have been calculated and should not be recalculated.
     //! @warning This function is an experimental part of the %Cantera API and may be
-    //! changed
-    //! or removed without notice.
-    //! @since New in %Cantera 3.0.
+    //! changed or removed without notice.
+    //! @since New in %Cantera 3.1.
     //!
-    void jacobianCalculated() { m_jac_calculated = true; };
+    void calculatedJacobian() { m_jac_calculated = true; };
 
-    //! Specify that jacobian terms have not been calculated and should be recalculated.
+    //! Specify that Jacobian terms have not been calculated and should be recalculated.
     //! @warning This function is an experimental part of the %Cantera API and may be
-    //! changed
-    //! or removed without notice.
-    //! @since New in %Cantera 3.0.
+    //! changed or removed without notice.
+    //! @since New in %Cantera 3.1.
     //!
-    void jacobianNotCalculated() { m_jac_calculated = false; };
+    void notCalculatedJacobian() { m_jac_calculated = false; };
 
 protected:
     ReactorBase* m_left = nullptr;

src/zeroD/IdealGasConstPressureMoleReactor.cpp

@@ -273,23 +273,11 @@ string IdealGasConstPressureMoleReactor::componentName(size_t k) {
                        "Index is out of bounds.");
 }
 
-double IdealGasConstPressureMoleReactor::moleDerivative(size_t index)
+double IdealGasConstPressureMoleReactor::temperature_ddni(size_t index)
 {
     // derivative of temperature transformed by ideal gas law
-    vector<double> moles(m_nsp);
-    getMoles(moles.data());
-    double dTdni = pressure() * m_vol / GasConstant / std::accumulate(moles.begin(), moles.end(), 0.0);
-    return dTdni;
-}
-
-double IdealGasConstPressureMoleReactor::moleRadiationDerivative(size_t index)
-{
-    // derivative of temperature transformed by ideal gas law
-    vector<double> moles(m_nsp);
-    getMoles(moles.data());
-    double dT4dni = std::pow(pressure() * m_vol / GasConstant, 4);
-    dT4dni *= std::pow(1 / std::accumulate(moles.begin(), moles.end(), 0.0), 5);
-    return dT4dni;
+    double n_total = m_mass / m_thermo->meanMolecularWeight();
+    return pressure() * m_vol / GasConstant / n_total;
 }
 
 }

src/zeroD/IdealGasMoleReactor.cpp

@@ -244,32 +244,16 @@ void IdealGasMoleReactor::buildJacobian(vector<Eigen::Triplet<double>>& jacVecto
             jacVector.emplace_back(0, static_cast<int>(j + m_sidx),
                 (specificHeat[j] * qdot - NCv * uk_dnkdnj_sums[j]) * denom);
         }
-
-        // build wall jacobian
         buildWallJacobian(jacVector);
     }
-
-    // build flow jacobian
     buildFlowJacobian(jacVector);
 }
 
-double IdealGasMoleReactor::moleDerivative(size_t index)
-{
-    // derivative of temperature transformed by ideal gas law
-    vector<double> moles(m_nsp);
-    getMoles(moles.data());
-    double dTdni = pressure() * m_vol / GasConstant / std::accumulate(moles.begin(), moles.end(), 0.0);
-    return dTdni;
-}
-
-double IdealGasMoleReactor::moleRadiationDerivative(size_t index)
+double IdealGasMoleReactor::temperature_ddni(size_t index)
 {
     // derivative of temperature transformed by ideal gas law
-    vector<double> moles(m_nsp);
-    getMoles(moles.data());
-    double dT4dni = std::pow(pressure() * m_vol / GasConstant, 4);
-    dT4dni *= std::pow(1 / std::accumulate(moles.begin(), moles.end(), 0.0), 5);
-    return dT4dni;
+    double n_total = m_mass / m_thermo->meanMolecularWeight();
+    return pressure() * m_vol / GasConstant / n_total;
 }
 
 }

src/zeroD/Reactor.cpp

@@ -603,7 +603,7 @@ void Reactor::setAdvanceLimit(const string& nm, const double limit)
     }
 }
 
-void Reactor:: buildWallJacobian(vector<Eigen::Triplet<double>>& jacVector)
+void Reactor::buildWallJacobian(vector<Eigen::Triplet<double>>& jacVector)
 {
     if (!m_jac_skip_walls) {
         for (size_t i = 0; i < m_wall.size(); i++) {