Fix Doxygen warnings

include/cantera/base/AnyMap.h

@@ -593,8 +593,8 @@ class AnyMap : public AnyBase
     class OrderedIterator {
     public:
         OrderedIterator() {}
-        OrderedIterator(const OrderedProxy::OrderVector::const_iterator& start,
-                        const OrderedProxy::OrderVector::const_iterator& stop);
+        OrderedIterator(const AnyMap::OrderedProxy::OrderVector::const_iterator& start,
+                        const AnyMap::OrderedProxy::OrderVector::const_iterator& stop);
 
         const std::pair<const std::string, AnyValue>& operator*() const {
             return *m_iter->second;

include/cantera/equil/ChemEquil.h

@@ -238,7 +238,10 @@ class ChemEquil
      * Given a vector of dimensionless element abundances, this routine
      * calculates the moles of the elements and the moles of the species.
      *
-     * @param[in] x = current dimensionless element potentials..
+     * @param s ThermoPhase object
+     * @param[in] x current dimensionless element potentials
+     * @param[in] Xmol_i_calc Mole fractions of the species
+     * @param[in] pressureConst Pressure
      */
     double calcEmoles(ThermoPhase& s, vector_fp& x,
                       const double& n_t, const vector_fp& Xmol_i_calc,

include/cantera/equil/MultiPhase.h

@@ -476,7 +476,7 @@ class MultiPhase
 
     //! Get the mole numbers of all species in the multiphase object
     /*!
-     * @param[out] molNum Vector of doubles of length nSpecies containing the
+     * @param[out] molNum Vector of doubles of length nSpecies() containing the
      *               global mole numbers (kmol).
      */
     void getMoles(doublereal* molNum) const;
@@ -486,7 +486,7 @@ class MultiPhase
      * The state of each phase object is also updated to have the specified
      * composition and the mixture temperature and pressure.
      *
-     * @param n    Vector of doubles of length nSpecies containing the global
+     * @param n    Vector of doubles of length nSpecies() containing the global
      *             mole numbers (kmol).
      */
     void setMoles(const doublereal* n);

include/cantera/kinetics/Kinetics.h

@@ -422,7 +422,7 @@ class Kinetics
      * array \c deltaProperty would be the standard-state Gibbs free energies of
      * reaction for each reaction.
      *
-     * @param property Input vector of property value. Length: m_kk.
+     * @param property Input vector of property value. Length: #m_kk.
      * @param deltaProperty Output vector of deltaRxn. Length: nReactions().
      */
     virtual void getReactionDelta(const double* property, double* deltaProperty) const;
@@ -569,7 +569,7 @@ class Kinetics
      * creation rates in array cdot, which must be dimensioned at least as
      * large as the total number of species in all phases. @see nTotalSpecies.
      *
-     * @param cdot   Output vector of creation rates. Length: m_kk.
+     * @param cdot   Output vector of creation rates. Length: #m_kk.
      */
     virtual void getCreationRates(doublereal* cdot);
 
@@ -578,7 +578,7 @@ class Kinetics
      * destruction rates in array ddot, which must be dimensioned at least as
      * large as the total number of species. @see nTotalSpecies.
      *
-     * @param ddot   Output vector of destruction rates. Length: m_kk.
+     * @param ddot   Output vector of destruction rates. Length: #m_kk.
      */
     virtual void getDestructionRates(doublereal* ddot);
 
@@ -588,7 +588,7 @@ class Kinetics
      * which must be dimensioned at least as large as the total number of
      * species. @see nTotalSpecies.
      *
-     * @param wdot   Output vector of net production rates. Length: m_kk.
+     * @param wdot   Output vector of net production rates. Length: #m_kk.
      */
     virtual void getNetProductionRates(doublereal* wdot);
 
@@ -732,7 +732,7 @@ class Kinetics
      * Calculate derivatives for forward rates-of-progress with respect to species
      * mole fractions at constant temperature, pressure and molar concentration.
      *
-     * The method returns a matrix with nReactions rows and nTotalSpecies columns.
+     * The method returns a matrix with nReactions() rows and nTotalSpecies() columns.
      * For a derivative with respect to @f$ X_i @f$, all other @f$ X_j @f$ are held
      * constant, rather than enforcing @f$ \sum X_j = 1 @f$.
      *
@@ -750,7 +750,7 @@ class Kinetics
      * concentration at constant temperature, pressure and remaining species
      * concentrations.
      *
-     * The method returns a matrix with nReactions rows and nTotalSpecies columns.
+     * The method returns a matrix with nReactions() rows and nTotalSpecies() columns.
      * For a derivative with respect to @f$ c_i @f$, all other @f$ c_j @f$ are held
      * constant.
      *
@@ -805,7 +805,7 @@ class Kinetics
      * Calculate derivatives for reverse rates-of-progress with respect to species
      * mole fractions at constant temperature, pressure and molar concentration.
      *
-     * The method returns a matrix with nReactions rows and nTotalSpecies columns.
+     * The method returns a matrix with nReactions() rows and nTotalSpecies() columns.
      * For a derivative with respect to @f$ X_i @f$, all other @f$ X_j @f$ are held
      * constant, rather than enforcing @f$ \sum X_j = 1 @f$.
      *
@@ -823,7 +823,7 @@ class Kinetics
      * concentration at constant temperature, pressure and remaining species
      * concentrations.
      *
-     * The method returns a matrix with nReactions rows and nTotalSpecies columns.
+     * The method returns a matrix with nReactions() rows and nTotalSpecies() columns.
      * For a derivative with respect to @f$ c_i @f$, all other @f$ c_j @f$ are held
      * constant.
      *
@@ -878,7 +878,7 @@ class Kinetics
      * Calculate derivatives for net rates-of-progress with respect to species
      * mole fractions at constant temperature, pressure and molar concentration.
      *
-     * The method returns a matrix with nReactions rows and nTotalSpecies columns.
+     * The method returns a matrix with nReactions() rows and nTotalSpecies() columns.
      * For a derivative with respect to @f$ X_i @f$, all other @f$ X_j @f$ are held
      * constant, rather than enforcing @f$ \sum X_j = 1 @f$.
      *
@@ -896,7 +896,7 @@ class Kinetics
      * concentration at constant temperature, pressure, and remaining species
      * concentrations.
      *
-     * The method returns a matrix with nReactions rows and nTotalSpecies columns.
+     * The method returns a matrix with nReactions() rows and nTotalSpecies() columns.
      * For a derivative with respect to @f$ c_i @f$, all other @f$ c_j @f$ are held
      * constant.
      *
@@ -914,21 +914,21 @@ class Kinetics
     /**
      * Calculate derivatives for species creation rates with respect to temperature
      * at constant pressure, molar concentration and mole fractions.
-     * @param[out] dwdot  Output vector of derivatives. Length: m_kk.
+     * @param[out] dwdot  Output vector of derivatives. Length: #m_kk.
      */
     void getCreationRates_ddT(double* dwdot);
 
     /**
      * Calculate derivatives for species creation rates with respect to pressure
      * at constant temperature, molar concentration and mole fractions.
-     * @param[out] dwdot  Output vector of derivatives. Length: m_kk.
+     * @param[out] dwdot  Output vector of derivatives. Length: #m_kk.
      */
     void getCreationRates_ddP(double* dwdot);
 
     /**
      * Calculate derivatives for species creation rates with respect to molar
      * concentration at constant temperature, pressure and mole fractions.
-     * @param[out] dwdot  Output vector of derivatives. Length: m_kk.
+     * @param[out] dwdot  Output vector of derivatives. Length: #m_kk.
      *
      * @warning  This method is an experimental part of the %Cantera API and
      *      may be changed or removed without notice.
@@ -939,7 +939,7 @@ class Kinetics
      * Calculate derivatives for species creation rates with respect to species
      * mole fractions at constant temperature, pressure and molar concentration.
      *
-     * The method returns a matrix with nTotalSpecies rows and nTotalSpecies columns.
+     * The method returns a square matrix with nTotalSpecies() rows and columns.
      * For a derivative with respect to @f$ X_i @f$, all other @f$ X_j @f$ are held
      * constant, rather than enforcing @f$ \sum X_j = 1 @f$.
      *
@@ -953,7 +953,7 @@ class Kinetics
      * concentration at constant temperature, pressure, and concentration of all other
      * species.
      *
-     * The method returns a matrix with nTotalSpecies rows and nTotalSpecies columns.
+     * The method returns a square matrix with nTotalSpecies() rows and columns.
      * For a derivative with respect to @f$ c_i @f$, all other @f$ c_j @f$ are held
      * constant.
      *
@@ -967,21 +967,21 @@ class Kinetics
     /**
      * Calculate derivatives for species destruction rates with respect to temperature
      * at constant pressure, molar concentration and mole fractions.
-     * @param[out] dwdot  Output vector of derivatives. Length: m_kk.
+     * @param[out] dwdot  Output vector of derivatives. Length: #m_kk.
      */
     void getDestructionRates_ddT(double* dwdot);
 
     /**
      * Calculate derivatives for species destruction rates with respect to pressure
      * at constant temperature, molar concentration and mole fractions.
-     * @param[out] dwdot  Output vector of derivatives. Length: m_kk.
+     * @param[out] dwdot  Output vector of derivatives. Length: #m_kk.
      */
     void getDestructionRates_ddP(double* dwdot);
 
     /**
      * Calculate derivatives for species destruction rates with respect to molar
      * concentration at constant temperature, pressure and mole fractions.
-     * @param[out] dwdot  Output vector of derivatives. Length: m_kk.
+     * @param[out] dwdot  Output vector of derivatives. Length: #m_kk.
      *
      * @warning  This method is an experimental part of the %Cantera API and
      *      may be changed or removed without notice.
@@ -992,7 +992,7 @@ class Kinetics
      * Calculate derivatives for species destruction rates with respect to species
      * mole fractions at constant temperature, pressure and molar concentration.
      *
-     * The method returns a matrix with nTotalSpecies rows and nTotalSpecies columns.
+     * The method returns a square matrix with nTotalSpecies() rows and columns.
      * For a derivative with respect to @f$ X_i @f$, all other @f$ X_j @f$ are held
      * constant, rather than enforcing @f$ \sum X_j = 1 @f$.
      *
@@ -1006,7 +1006,7 @@ class Kinetics
      * concentration at constant temperature, pressure, and concentration of all other
      * species.
      *
-     * The method returns a matrix with nTotalSpecies rows and nTotalSpecies columns.
+     * The method returns a square matrix with nTotalSpecies() rows and columns.
      * For a derivative with respect to @f$ c_i @f$, all other @f$ c_j @f$ are held
      * constant.
      *
@@ -1020,21 +1020,21 @@ class Kinetics
     /**
      * Calculate derivatives for species net production rates with respect to
      * temperature at constant pressure, molar concentration and mole fractions.
-     * @param[out] dwdot  Output vector of derivatives. Length: m_kk.
+     * @param[out] dwdot  Output vector of derivatives. Length: #m_kk.
      */
     void getNetProductionRates_ddT(double* dwdot);
 
     /**
      * Calculate derivatives for species net production rates with respect to pressure
      * at constant temperature, molar concentration and mole fractions.
-     * @param[out] dwdot  Output vector of derivatives. Length: m_kk.
+     * @param[out] dwdot  Output vector of derivatives. Length: #m_kk.
      */
     void getNetProductionRates_ddP(double* dwdot);
 
     /**
      * Calculate derivatives for species net production rates with respect to molar
      * concentration at constant temperature, pressure and mole fractions.
-     * @param[out] dwdot  Output vector of derivatives. Length: m_kk.
+     * @param[out] dwdot  Output vector of derivatives. Length: #m_kk.
      *
      * @warning  This method is an experimental part of the %Cantera API and
      *      may be changed or removed without notice.
@@ -1045,9 +1045,9 @@ class Kinetics
      * Calculate derivatives for species net production rates with respect to species
      * mole fractions at constant temperature, pressure and molar concentration.
      *
-     * The method returns a matrix with nTotalSpecies rows and nTotalSpecies columns.
-     * For a derivative with respect to @f$ X_i @f$, all other @f$ X_j @f$ are held constant,
-     * rather than enforcing @f$ \sum X_j = 1 @f$.
+     * The method returns a square matrix with nTotalSpecies() rows and columns.
+     * For a derivative with respect to @f$ X_i @f$, all other @f$ X_j @f$ are held
+     * constant, rather than enforcing @f$ \sum X_j = 1 @f$.
      *
      * @warning  This method is an experimental part of the %Cantera API and
      *      may be changed or removed without notice.
@@ -1059,7 +1059,7 @@ class Kinetics
      * concentration at constant temperature, pressure, and concentration of all other
      * species.
      *
-     * The method returns a matrix with nTotalSpecies rows and nTotalSpecies columns.
+     * The method returns a square matrix with nTotalSpecies() rows and columns.
      * For a derivative with respect to @f$ c_i @f$, all other @f$ c_j @f$ are held
      * constant.
      *

include/cantera/kinetics/solveSP.h

@@ -12,10 +12,8 @@
 #include "cantera/kinetics/InterfaceKinetics.h"
 #include "cantera/numerics/DenseMatrix.h"
 
-//! @addtogroup surfSolverGroup
-//! @{
-
 //! @defgroup solvesp_methods Surface Problem Solver Methods
+//! @ingroup surfSolverGroup
 //! @{
 
 //! This assumes that the initial guess supplied to the routine is far from
@@ -47,6 +45,7 @@ const int SFLUX_TRANSIENT = 4;
 //! @defgroup solvesp_bulkFunc Surface Problem Bulk Phase Mode
 //! Functionality expected from the bulk phase. This changes the equations
 //! that will be used to solve for the bulk mole fractions.
+//! @ingroup surfSolverGroup
 //! @{
 
 //! Deposition of a bulk phase is to be expected. Bulk mole fractions are
@@ -62,6 +61,9 @@ const int BULK_ETCH = 2;
 namespace Cantera
 {
 
+//! @addtogroup surfSolverGroup
+//! @{
+
 //! Method to solve a pseudo steady state surface problem
 /*!
  *  The following class handles solving the surface problem. The calculation

include/cantera/oneD/Domain1D.h

@@ -576,7 +576,7 @@ class Domain1D
 
     double m_rdt = 0.0;
     size_t m_nv = 0;
-    size_t m_points;
+    size_t m_points; //!< Number of grid points
     vector_fp m_slast;
     vector_fp m_max;
     vector_fp m_min;

include/cantera/oneD/StFlow.h

@@ -482,13 +482,13 @@ class StFlow : public Domain1D
     //! Array of size #m_nsp by #m_points for saving molar enthalpies
     Array2D m_hk;
 
-    //! Array of size #m_nsp by #m_points -1 for saving enthalpy fluxes
+    //! Array of size #m_nsp by #m_points-1 for saving enthalpy fluxes
     Array2D m_dhk_dz;
 
     // production rates
     Array2D m_wdot;
 
-    size_t m_nsp;
+    size_t m_nsp; //!< Number of species in the mechanism
 
     ThermoPhase* m_thermo = nullptr;
     Kinetics* m_kin = nullptr;

include/cantera/zeroD/ConstPressureMoleReactor.h

@@ -11,7 +11,7 @@
 namespace Cantera
 {
 
-/*!
+/**
  * ConstPressureMoleReactor is a class for constant-pressure reactors
  * which use a state of moles.
  * @since New in %Cantera 3.0

include/cantera/zeroD/IdealGasConstPressureMoleReactor.h

@@ -11,9 +11,10 @@
 namespace Cantera
 {
 
-/*!
+/**
  * IdealGasConstPressureMoleReactor is a class for ideal gas constant-pressure reactors
  * which use a state of moles.
+ * @since New in %Cantera 3.0
  * @ingroup reactorGroup
  */
 class IdealGasConstPressureMoleReactor : public ConstPressureMoleReactor

include/cantera/zeroD/IdealGasMoleReactor.h

@@ -11,9 +11,10 @@
 namespace Cantera
 {
 
-/*!
+/**
  * IdealGasMoleReactor is a class for ideal gas constant-volume reactors which use a
  * state of moles.
+ * @since New in %Cantera 3.0
  * @ingroup reactorGroup
  */
 class IdealGasMoleReactor : public MoleReactor

include/cantera/zeroD/MoleReactor.h

@@ -11,9 +11,10 @@
 namespace Cantera
 {
 
-/*!
+/**
  * MoleReactor is meant to serve the same purpose as the reactor class but with a state
  * vector composed of moles. It also serves as the base class for other mole reactors.
+ * @since New in %Cantera 3.0
  * @ingroup reactorGroup
  */
 class MoleReactor : public Reactor