Doxygen fixes

Author: anthony-walker

include/cantera/zeroD/FlowDevice.h

@@ -115,40 +115,47 @@ class FlowDevice
         m_time = time;
     }
 
-    /*! 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 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.
-     */
+    //! 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
+    //! 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.
+    //!
     virtual void buildReactorJacobian(ReactorBase* r, vector<Eigen::Triplet<double>>& jacVector) {
         throw NotImplementedError(type() + "::buildReactorJacobian");
     }
 
-    /*! 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 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.
-     */
+    //! 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
+    //! 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.
+    //!
     virtual void buildNetworkJacobian(vector<Eigen::Triplet<double>>& jacVector) {
         throw NotImplementedError(type() + "::buildNetworkJacobian");
     }
 
-    /*! 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.
-     */
+    //! 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.
+    //!
     void jacobianCalculated() { 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.
-     */
+    //! 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.
+    //!
     void jacobianNotCalculated() { m_jac_calculated = false; };
 
 protected:

include/cantera/zeroD/Reactor.h

@@ -219,8 +219,7 @@ class Reactor : public ReactorBase
     }
 
     //! Calculate the Jacobian of a specific Reactor specialization.
-    //! @param jac_vector vector where jacobian triplets are added
-    //! @param offset offset added to the row and col indices of the elements
+    //! @param jacVector vector where jacobian triplets are added
     //! @warning Depending on the particular implementation, this may return an
     //! approximate Jacobian intended only for use in forming a preconditioner for
     //! iterative solvers.
@@ -244,7 +243,7 @@ class Reactor : public ReactorBase
     virtual void buildWallJacobian(vector<Eigen::Triplet<double>>& jacVector);
 
     //! Calculate flow contributions to the Jacobian of a Reactor specialization.
-    //! @param jac_vector vector where jacobian triplets are added
+    //! @param jacVector vector where jacobian triplets are added
     //! @warning Depending on the particular implementation, this may return an
     //! approximate Jacobian intended only for use in forming a preconditioner for
     //! iterative solvers.

include/cantera/zeroD/ReactorBase.h

@@ -248,48 +248,50 @@ class ReactorBase
     //! Set the ReactorNet that this reactor belongs to.
     void setNetwork(ReactorNet* net);
 
-    /*! Calculate the derivative of temperature with respect to the temperature in the
-     * heat transfer equation based on the reactor specific equation of state.
-     * This function should also transform the state of the derivative to that
-     * appropriate for the jacobian's state/
-     * @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.
-     */
+    //! Calculate the derivative of temperature with respect to the temperature in the
+    //! heat transfer equation based on the reactor specific equation of state.
+    //! This function should also transform the state of the derivative to that
+    //! appropriate for the jacobian's state/
+    //! @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 temperatureDerivative() {
         throw NotImplementedError("Reactor::temperatureDerivative");
     }
 
-    /*! Calculate the derivative of temperature with respect to the temperature in the
-     * heat transfer radiation equation based on the reactor specific equation of state.
-     * This function should also transform the state of the derivative to that
-     * appropriate for the jacobian's state/
-     * @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.
-     */
+    //! Calculate the derivative of temperature with respect to the temperature in the
+    //! heat transfer radiation equation based on the reactor specific equation of
+    //! state.
+    //! This function should also transform the state of the derivative to that
+    //! appropriate for the jacobian's state/
+    //! @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 temperatureRadiationDerivative() {
         throw NotImplementedError("Reactor::temperatureRadiationDerivative");
     }
 
-    /*! Calculate the derivative of T with respect to the ith species in the heat
-     * transfer 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.
-     */
+    //! Calculate the derivative of T with respect to the ith species in the heat
+    //! transfer 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.
-     */
+    //! 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.
+    //!
     virtual double moleRadiationDerivative(size_t index) {
         throw NotImplementedError("Reactor::moleRadiationDerivative");
     }

include/cantera/zeroD/ReactorNet.h

@@ -341,8 +341,7 @@ class ReactorNet : public FuncEval
 
 protected:
     //! Calculate the Jacobian of the entire reactor network.
-    //! @param jac_vector vector where jacobian triplets are added
-    //! @param offset offset added to the row and col indices of the elements
+    //! @param jacVector vector where jacobian triplets are added
     //! @warning Depending on the particular implementation, this may return an
     //! approximate Jacobian intended only for use in forming a preconditioner for
     //! iterative solvers.

include/cantera/zeroD/Wall.h

@@ -116,44 +116,48 @@ class WallBase
         m_time = time;
     }
 
-    /*! 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 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.
-     */
+    //! 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
+    //! 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.
+    //!
     virtual void buildReactorJacobian(ReactorBase* r, vector<Eigen::Triplet<double>>& jacVector) {
         throw NotImplementedError("WallBase::buildReactorJacobian");
     }
 
-    /*! 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 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.
-     */
+    //! 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
+    //! 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.
+    //!
     virtual void buildNetworkJacobian(vector<Eigen::Triplet<double>>& jacVector) {
         throw NotImplementedError("WallBase::buildNetworkJacobian");
     }
 
-    /*! 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.
-     */
+    //! 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.
+    //!
     void jacobianCalculated() { 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.
-     */
+    //! 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.
+    //!
     void jacobianNotCalculated() { m_jac_calculated = false; };
 
 protected:

src/zeroD/ReactorNet.cpp

@@ -554,10 +554,10 @@ void ReactorNet::preconditionerSetup(double t, double* y, double gamma)
     // Update network with adjusted state
     updateState(yCopy.data());
     // Create jacobian triplet vector
-    vector<Eigen::Triplet<double>> jac_vector;
-    buildJacobian(jac_vector);
+    vector<Eigen::Triplet<double>> jacVector;
+    buildJacobian(jacVector);
     // Add to preconditioner with offset
-    for (auto it : jac_vector) {
+    for (auto it : jacVector) {
         precon->setValue(it.row(), it.col(), it.value());
     }
     // post reactor setup operations