[docs] Update doxygen numerics groupings

include/cantera/base/Array.h

@@ -25,6 +25,8 @@ namespace Cantera
  *     J(i,j) = data_start + index
  *         i = row
  *         j = column
+ *
+ * @ingroup matrices
  */
 class Array2D
 {

include/cantera/base/global.h

@@ -4,8 +4,6 @@
  * inputfiles, logs, textlogs, (see \ref inputfiles, \ref logs, and
  * \ref textlogs).
  *
- * @ingroup utils
- *
  * These functions store some parameters in global storage that are accessible
  * at all times from the calling application. Contains module definitions for
  *     -  inputfiles  (see \ref inputfiles)

include/cantera/base/utilities.h

@@ -1,17 +1,19 @@
 /**
  *  @file utilities.h
- *  Various templated functions that carry out common vector
- *  operations (see \ref utils).
+ *  Various templated functions that carry out common vector and polynomial operations
+ *  (see \ref mathTemplates).
  */
 
 // This file is part of Cantera. See License.txt in the top-level directory or
 // at https://cantera.org/license.txt for license and copyright information.
 
 /**
- * @defgroup utils Templated Utility Functions
+ * @defgroup mathTemplates Templated Array and Polynomial Operations
  *
  * These are templates to perform various simple operations on arrays. Note that
  * the compiler will inline these, so using them carries no performance penalty.
+ *
+ * @ingroup numerics
  */
 
 #ifndef CT_UTILITIES_H
@@ -30,6 +32,7 @@ namespace Cantera
  * @param x   first reference to the templated class V
  * @param y   second reference to the templated class V
  * @return This class returns a hard-coded type, doublereal.
+ * @ingroup mathTemplates
  */
 template<class V>
 inline doublereal dot4(const V& x, const V& y)
@@ -45,6 +48,7 @@ inline doublereal dot4(const V& x, const V& y)
  * @param x   first reference to the templated class V
  * @param y   second reference to the templated class V
  * @return This class returns a hard-coded type, doublereal.
+ * @ingroup mathTemplates
  */
 template<class V>
 inline doublereal dot5(const V& x, const V& y)
@@ -72,6 +76,7 @@ inline doublereal dot5(const V& x, const V& y)
  * @param y_begin Iterator pointing to the beginning of y, belonging to the
  *               iterator class InputIter2.
  * @return The return is hard-coded to return a double.
+ * @ingroup mathTemplates
  */
 template<class InputIter, class InputIter2>
 inline doublereal dot(InputIter x_begin, InputIter x_end,
@@ -95,6 +100,7 @@ inline doublereal dot(InputIter x_begin, InputIter x_end,
  *               iterator class OutputIter. This is the output variable
  *               for this routine.
  * @param scale_factor  input scale factor belonging to the class S.
+ * @ingroup mathTemplates
  */
 template<class InputIter, class OutputIter, class S>
 inline void scale(InputIter begin, InputIter end,
@@ -108,6 +114,7 @@ inline void scale(InputIter begin, InputIter end,
 /*!
  * @param x   Value of the independent variable - First template parameter
  * @param c   Pointer to the polynomial - Second template parameter
+ * @ingroup mathTemplates
  */
 template<class D, class R>
 R poly6(D x, R* c)
@@ -120,6 +127,7 @@ R poly6(D x, R* c)
 /*!
  * @param x   Value of the independent variable - First template parameter
  * @param c   Pointer to the polynomial - Second template parameter
+ * @ingroup mathTemplates
  */
 template<class D, class R>
 R poly8(D x, R* c)
@@ -132,6 +140,7 @@ R poly8(D x, R* c)
 /*!
  * @param x   Value of the independent variable - First template parameter
  * @param c   Pointer to the polynomial - Second template parameter
+ * @ingroup mathTemplates
  */
 template<class D, class R>
 R poly5(D x, R* c)
@@ -144,6 +153,7 @@ R poly5(D x, R* c)
 /*!
  * @param x   Value of the independent variable.
  * @param c   Pointer to the polynomial coefficient array.
+ * @ingroup mathTemplates
  */
 template<class D, class R>
 R poly4(D x, R* c)
@@ -156,6 +166,7 @@ R poly4(D x, R* c)
 /*!
  * @param x   Value of the independent variable - First template parameter
  * @param c   Pointer to the polynomial - Second template parameter
+ * @ingroup mathTemplates
  */
 template<class D, class R>
 R poly3(D x, R* c)
@@ -187,6 +198,7 @@ const U& getValue(const std::map<T, U>& m, const T& key, const U& default_val) {
 }
 
 //! Get the size of a container, cast to a signed integer type
+//! @ingroup mathTemplates
 template <class T, class U=int>
 U len(const T& container) {
     return static_cast<U>(container.size());

include/cantera/numerics/BandMatrix.h

@@ -30,6 +30,8 @@ namespace Cantera
  * This class is a derived class of the base class GeneralMatrix. However,
  * within the oneD directory, the class is used as is, without reference to the
  * GeneralMatrix base type.
+ *
+ * @ingroup matrices
  */
 class BandMatrix : public GeneralMatrix
 {

include/cantera/numerics/DenseMatrix.h

@@ -18,12 +18,16 @@
 namespace Cantera
 {
 /**
- * @defgroup numerics  Numerical Utilities within Cantera
- *
- * Cantera contains some capabilities for solving nonlinear equations and
- * integrating both ODE and DAE equation systems in time. This section describes
- * these capabilities.
+ * @defgroup numerics  Numerical Utilities
  *
+ * @details Cantera contains some capabilities for solving nonlinear equations and
+ * integrating both ODE and DAE equation systems in time.
+ */
+
+/**
+ * @defgroup matrices  Matrix Handling
+ * Classes and methods implementing matrix operations.
+ * @ingroup numerics
  */
 
 //! A class for full (non-sparse) matrices with Fortran-compatible data storage,
@@ -45,7 +49,7 @@ namespace Cantera
  * m_printLevel. The default is for no reporting. If m_printLevel is nonzero,
  * the error condition is reported to Cantera's log file.
  *
- * @ingroup numerics
+ * @ingroup matrices
  */
 class DenseMatrix : public Array2D
 {

include/cantera/numerics/Func1.h

@@ -43,6 +43,7 @@ class TimesConstant1;
 //! Functors implement functions of a single variable \f$ f(x) \f$.
 //! Functor objects can be combined to form compound expressions, which allows for
 //! the implementation of generic mathematical expressions.
+//! @ingroup numerics
 
 //! @defgroup func1simple Simple Functors
 //! Simple functors implement standard mathematical expressions with a single

include/cantera/numerics/FuncEval.h

@@ -15,6 +15,10 @@
 namespace Cantera
 {
 
+/**
+ * @defgroup odeGroup  ODE and DAE Function Utilities
+*/
+
 /**
  *  Virtual base class for ODE/DAE right-hand-side function evaluators.
  *  Classes derived from FuncEval evaluate the right-hand-side function

include/cantera/numerics/GeneralMatrix.h

@@ -1,7 +1,7 @@
 /**
  *  @file GeneralMatrix.h
  *   Declarations for the class GeneralMatrix which is a virtual base class for matrices handled by solvers
- *    (see class \ref numerics and \link Cantera::GeneralMatrix GeneralMatrix\endlink).
+ *    (see class \ref matrices and \link Cantera::GeneralMatrix GeneralMatrix\endlink).
  */
 
 // This file is part of Cantera. See License.txt in the top-level directory or
@@ -18,6 +18,7 @@ namespace Cantera
 {
 
 //! Generic matrix
+//! @ingroup matrices
 class GeneralMatrix
 {
 public:

include/cantera/numerics/eigen_dense.h

@@ -18,11 +18,22 @@
 namespace Cantera
 {
 
+//! @ingroup matrices
 typedef Eigen::Map<Eigen::MatrixXd> MappedMatrix;
+
+//! @ingroup matrices
 typedef Eigen::Map<const Eigen::MatrixXd> ConstMappedMatrix;
+
+//! @ingroup matrices
 typedef Eigen::Map<Eigen::VectorXd> MappedVector;
+
+//! @ingroup matrices
 typedef Eigen::Map<const Eigen::VectorXd> ConstMappedVector;
+
+//! @ingroup matrices
 typedef Eigen::Map<Eigen::RowVectorXd> MappedRowVector;
+
+//! @ingroup matrices
 typedef Eigen::Map<const Eigen::RowVectorXd> ConstMappedRowVector;
 }
 

include/cantera/numerics/eigen_sparse.h

@@ -17,6 +17,7 @@
 
 namespace Cantera
 {
+//! @ingroup matrices
 typedef std::vector<Eigen::Triplet<double>> SparseTriplets;
 }
 

include/cantera/numerics/funcs.h

@@ -15,6 +15,13 @@
 namespace Cantera
 {
 
+/**
+ * @defgroup mathUtils  Numerical Integration and Interpolation
+ * Collection of numerical utility functions for integration, interpolation and data
+ * fitting.
+ * @ingroup numerics
+*/
+
 //! Linearly interpolate a function defined on a discrete grid.
 /*!
  * Vector xpts contains a monotonic sequence of grid points, and vector fpts
@@ -26,6 +33,7 @@ namespace Cantera
  * @param xpts value of the grid points
  * @param fpts value of the interpolant at the grid points
  * @returns the value of of the interpolated function at x.
+ * @ingroup mathUtils
  */
 doublereal linearInterp(doublereal x, const vector_fp& xpts,
                         const vector_fp& fpts);
@@ -38,6 +46,7 @@ doublereal linearInterp(doublereal x, const vector_fp& xpts,
  *
  * @param  f vector of function value
  * @param  x vector of function coordinate
+ * @ingroup mathUtils
  */
 double trapezoidal(const Eigen::ArrayXd& f, const Eigen::ArrayXd& x);
 
@@ -52,6 +61,7 @@ double trapezoidal(const Eigen::ArrayXd& f, const Eigen::ArrayXd& x);
  *
  * @param  f vector of function value
  * @param  x vector of function coordinate
+ * @ingroup mathUtils
  */
 double simpson(const Eigen::ArrayXd& f, const Eigen::ArrayXd& x);
 
@@ -64,6 +74,7 @@ double simpson(const Eigen::ArrayXd& f, const Eigen::ArrayXd& x);
  * @param  method method name
  * @param  f vector of function value
  * @param  x vector of function coordinate
+ * @ingroup mathUtils
  */
 double numericalQuadrature(const std::string& method,
                            const Eigen::ArrayXd& f,

include/cantera/numerics/polyfit.h

@@ -28,6 +28,7 @@ namespace Cantera
  * @param[out] p  Array of polynomial coefficients, starting with the constant
  *     term. Length *deg+1*.
  * @returns the root mean squared error of the fit at the input points.
+ * @ingroup mathUtils
  */
 double polyfit(size_t n, size_t deg, const double* x, const double* y,
                const double* w, double* p);