add groups for a bunch of stuff

Common/doc/docmain.hpp

@@ -31,10 +31,22 @@
  * to perform PDE analysis and PDE constrained optimization.  The toolset is designed with 
  * computational fluid dynamics and aerodynamic shape optimization in mind, but is extensible to
  * include other families of governing equations such as potential flow, electrodynamics, chemically reacting
- * flows, and many others.  SU2 is released under an
- * open-source license.
- * 
- * The following technical documentation describes the structure and details of the source code for developers. 
+ * flows, and many others.  SU2 is released under an open-source license.
+ *
+ * The following technical documentation describes the structure and details of the source code for developers.
+ * Each module groups classes and functions dedicated to major areas or features of the code base.
+ * This documentation helps awnsering questions such as
+ * - What are the major classes of the code (architecture)?
+ * - How do those classes interact with each other?
+ * - What low-level functionality is already implemented that can be re-used?
+ *
+ * Given the use of polymorphism in SU2, it is usefull to start studying each module from the base class
+ * (which usually has a generic name), this will show the inheritance diagram for that family. Moreover,
+ * many important functions (defining the interactions between families) are implemented at the base level,
+ * the "call graph" of a function will show these interactions (derived classes only specialize certain details).
+ * Alternatively, "caller graphs" can be used to navigate to the larger classes that use smaller ones, and
+ * thus navigate the architecture from the bottom up (note that this will also be more effective if done
+ * for base classes).
  */
 
 /*!
@@ -88,3 +100,89 @@
  * \defgroup Elasticity_Equations Solving the elasticity equations
  * \brief Group of classes to solve solid deformation problems.
  */
+
+/*!
+ * \defgroup Interfaces Multiphysics interfaces
+ * \brief Classes for data transfer and interpolation across interfaces between zones.
+ */
+
+/*!
+ * \defgroup Drivers Iterative solution strategy
+ * \brief Group of classes which define the iterative process used to converge
+ *        the equations (fluid, turbulence, elasticity, FSI, CHT, etc.).
+ *        In general, "Driver" classes use "Iteration" classes to advance one inner
+ *        iteration, in turn "Iteration" classes use "Integration" classes to perform
+ *        space and time integration. The latter use mostly the "Solvers".
+ */
+
+/*!
+ * \defgroup Variable Storing solution variables
+ * \brief Classes used to store and access the solution variables of all types of problems.
+ */
+
+/*!
+ * \defgroup DiscAdj Discrete Adjoint
+ * \brief Classes and functions used to solve discrete adjoint equations.
+ */
+
+/*!
+ * \defgroup SpLinSys Sparse linear systems
+ * \brief Classes and function to represent and solve large distributed sparse linear systems.
+ */
+
+/*!
+ * \defgroup FvmAlgos General FVM algorithms
+ * \brief Common algorithms used in FVM implementations.
+ */
+
+/*!
+ * \defgroup FemAlgos General FEM algorithms
+ * \brief Common algorithms used in FEM implementations.
+ */
+
+/*!
+ * \defgroup Toolboxes Utility classes and functions
+ * \brief Several classes and functions that implement common operations.
+ */
+
+/*!
+ * \defgroup GeometryToolbox Geometry toolbox
+ * \brief Common geometry operations.
+ * \ingroup Toolboxes
+ */
+
+/*!
+ * \defgroup Containers Data containers
+ * \brief Container classes (vectors, matrices, ND-arrays, etc.).
+ * \ingroup Toolboxes
+ */
+
+/*!
+ * \defgroup LookUpInterp Look up and interpolation
+ * \brief Data look up and interpolation.
+ * \ingroup Toolboxes
+ */
+
+/*!
+ * \defgroup ADT Alternating Digital Tree
+ * \brief Tree-based searches (minimum distance, containment, etc.).
+ * \ingroup Toolboxes
+ */
+
+/*!
+ * \defgroup BLAS Dense linear algebra
+ * \brief Linear algebra functions and classes.
+ * \ingroup Toolboxes
+ */
+
+/*!
+ * \defgroup Graph Graph operations
+ * \brief Classes to represent graphs and functions to manipulate them (coloring, etc.).
+ * \ingroup Toolboxes
+ */
+
+/*!
+ * \defgroup SIMD Vectorization (SIMD)
+ * \brief Classes for explicit (done by the programmer) vectorization (SIMD) of computations.
+ * \ingroup Toolboxes
+ */

Common/include/adt/CADTBaseClass.hpp

@@ -38,6 +38,7 @@ using namespace std;
 
 /*!
  * \class CADTBaseClass
+ * \ingroup ADT
  * \brief  Base class for storing an ADT in an arbitrary number of dimensions.
  * \author E. van der Weide
  */

Common/include/adt/CADTComparePointClass.hpp

@@ -30,6 +30,7 @@
 
 /*!
  * \class CADTComparePointClass
+ * \ingroup ADT
  * \brief  Functor, used for the sorting of the points when building an ADT.
  * \author E. van der Weide
  */

Common/include/adt/CADTElemClass.hpp

@@ -33,6 +33,7 @@
 
 /*!
  * \class CADTElemClass
+ * \ingroup ADT
  * \brief  Class for storing an ADT of (linear) elements in an arbitrary number of dimensions.
  * \author E. van der Weide
  * \version 7.4.0 "Blackbird"

Common/include/adt/CADTNodeClass.hpp

@@ -30,6 +30,7 @@
 
 /*!
  * \class CADTNodeClass
+ * \ingroup ADT
  * \brief  Class for storing the information needed in a node of an ADT.
  * \author E. van der Weide
  */

Common/include/adt/CADTPointsOnlyClass.hpp

@@ -30,6 +30,7 @@
 
 /*!
  * \class CADTPointsOnlyClass
+ * \ingroup ADT
  * \brief  Class for storing an ADT of only points in an arbitrary number of dimensions.
  * \author E. van der Weide
  */

Common/include/adt/CBBoxTargetClass.hpp

@@ -31,6 +31,7 @@
 
 /*!
  * \class CBBoxTargetClass
+ * \ingroup ADT
  * \brief  Class for storing the information of a possible bounding box candidate
            during a minimum distance search.
  * \author E. van der Weide

Common/include/containers/C2DContainer.hpp

@@ -34,6 +34,9 @@
 #include <utility>
 #include <type_traits>
 
+/// \addtogroup Containers
+/// @{
+
 /*!
  * \enum StorageType
  * \brief Supported ways to flatten a matrix into an array.
@@ -635,3 +638,5 @@ using su2activematrix = su2matrix<su2double>;
 
 using su2passivevector = su2vector<passivedouble>;
 using su2passivematrix = su2matrix<passivedouble>;
+
+/// @}

Common/include/containers/CFastFindAndEraseQueue.hpp

@@ -35,6 +35,7 @@
 
 /*!
  * \class CFastFindAndEraseQueue
+ * \ingroup Containers
  * \brief A queue-type container (push back, pop front), but with
  *        fast deletion of arbitrary items (possibly in the middle).
  * \param[in] ItemType_ - Type of the stored items.

Common/include/containers/CFileReaderLUT.hpp

@@ -34,6 +34,10 @@
 #include "../../../Common/include/linear_algebra/blas_structure.hpp"
 #include "../../../Common/include/toolboxes/CSquareMatrixCM.hpp"
 
+/*!
+ * \brief File reader for look up tables.
+ * \ingroup LookUpInterp
+ */
 class CFileReaderLUT {
  protected:
   int rank;

Common/include/containers/CLookUpTable.hpp

@@ -36,6 +36,10 @@
 #include "CFileReaderLUT.hpp"
 #include "CTrapezoidalMap.hpp"
 
+/*!
+ * \brief Look up table.
+ * \ingroup LookUpInterp
+ */
 class CLookUpTable {
  protected:
   int rank; /*!< \brief MPI Rank. */

Common/include/containers/CTrapezoidalMap.hpp

@@ -35,6 +35,7 @@
 
 /*!
  * \class CTrapezoidalMap
+ * \ingroup LookUpInterp
  * \brief Construction of trapezoidal map for tabulated lookup 
  * \author: D. Mayer, T. Economon
  * \version 7.4.0 "Blackbird"

Common/include/containers/CVertexMap.hpp

@@ -33,6 +33,7 @@
 
 /*!
  * \class CVertexMap
+ * \ingroup Containers
  * \brief A lookup type map, maps indices in a large range to indices in a smaller one.
  *
  * The usage case is:

Common/include/containers/container_decorators.hpp

@@ -30,6 +30,9 @@
 
 #include "C2DContainer.hpp"
 
+/// \addtogroup Containers
+/// @{
+
 /*!
  * \brief Class to represent a matrix (without owning the data, this just wraps a pointer).
  */
@@ -283,3 +286,5 @@ inline void AllocVectorOfMatrices(const IndexVector& N, size_t P, VectorOfMatrix
   auto M = N.size();
   AllocVectorOfMatrices(M, N, P, X, val);
 }
+
+/// @}

Common/include/geometry/elements/CElement.hpp

@@ -34,6 +34,7 @@
 
 /*!
  * \class CElement
+ * \ingroup FemAlgos
  * \brief Abstract class for defining finite elements.
  * \note Usage: Element instances are used to compute gradients (in reference or current
  *       coordinates), element matrices (stiffness, mass, etc.), and nodal residuals.
@@ -555,6 +556,7 @@ class CElement {
 
 /*!
  * \class CElementWithKnownSizes
+ * \ingroup FemAlgos
  * \brief Templated class to implement the computation of gradients for specific element sizes.
  * \author P. Gomes, R. Sanchez
  */
@@ -793,6 +795,7 @@ class CElementWithKnownSizes : public CElement {
 
 /*!
  * \class CTRIA1
+ * \ingroup FemAlgos
  * \brief Tria element with 1 Gauss Points
  * \author R. Sanchez
  */
@@ -819,6 +822,7 @@ class CTRIA1 final : public CElementWithKnownSizes<1,3,2> {
 
 /*!
  * \class CQUAD4
+ * \ingroup FemAlgos
  * \brief Quadrilateral element with 4 Gauss Points
  * \author R. Sanchez
  */
@@ -865,6 +869,7 @@ class CQUAD4 final : public CElementWithKnownSizes<4,4,2> {
 
 /*!
  * \class CTETRA1
+ * \ingroup FemAlgos
  * \brief Tetrahedral element with 1 Gauss Point
  * \author R. Sanchez
  */
@@ -890,6 +895,7 @@ class CTETRA1 final : public CElementWithKnownSizes<1,4,3> {
 
 /*!
  * \class CHEXA8
+ * \ingroup FemAlgos
  * \brief Hexahedral element with 8 Gauss Points
  * \author R. Sanchez
  */
@@ -916,6 +922,7 @@ class CHEXA8 final : public CElementWithKnownSizes<8,8,3> {
 
 /*!
  * \class CPYRAM5
+ * \ingroup FemAlgos
  * \brief Pyramid element with 5 Gauss Points
  * \author R. Sanchez, F. Palacios, A. Bueno, T. Economon, S. Padron.
  */
@@ -942,6 +949,7 @@ class CPYRAM5 final : public CElementWithKnownSizes<5,5,3> {
 
 /*!
  * \class CPRISM6
+ * \ingroup FemAlgos
  * \brief Prism element with 6 Gauss Points
  * \author R. Sanchez, F. Palacios, A. Bueno, T. Economon, S. Padron.
  * \version 7.4.0 "Blackbird"
@@ -969,6 +977,7 @@ class CPRISM6 final : public CElementWithKnownSizes<6,6,3> {
 
 /*!
  * \class CTRIA3
+ * \ingroup FemAlgos
  * \brief Tria element with 3 Gauss Points
  * \author T.Dick
  */
@@ -995,6 +1004,7 @@ class CTRIA3 final : public CElementWithKnownSizes<3,3,2> {
 
 /*!
  * \class CTETRA4
+ * \ingroup FemAlgos
  * \brief Tetrahedral element with 4 Gauss Points
  * \author T.Dick
  */
@@ -1021,6 +1031,7 @@ class CTETRA4 final : public CElementWithKnownSizes<4,4,3> {
 
 /*!
  * \class CPYRAM6
+ * \ingroup FemAlgos
  * \brief Pyramid element with 6 Gauss Points
  * \author T.Dick
  */
@@ -1047,7 +1058,8 @@ class CPYRAM6 final : public CElementWithKnownSizes<6,5,3> {
 
 /*!
  * \class CLINE
- * \brief line element with 2 Gauss Points
+ * \ingroup FemAlgos
+ * \brief Line element with 2 Gauss Points
  * \author T.Dick
  */
 class CLINE final : public CElementWithKnownSizes<2,2,1> {

Common/include/geometry/elements/CElementProperty.hpp

@@ -29,6 +29,7 @@
 
 /*!
  * \class CProperty
+ * \ingroup Elasticity_Equations
  * \brief Base class for defining element properties.
  * \author R. Sanchez
  * \version 7.4.0 "Blackbird"
@@ -104,6 +105,7 @@ class CProperty {
 
 /*!
  * \class CElementProperty
+ * \ingroup Elasticity_Equations
  * \brief Class for defining element properties for the structural solver.
  * \author R. Sanchez
  * \version 7.4.0 "Blackbird"

Common/include/geometry/elements/CGaussVariable.hpp

@@ -31,6 +31,7 @@
 
 /*!
  * \class CGaussVariable
+ * \ingroup FemAlgos
  * \brief Main class for defining the gaussian points.
  * \version 7.4.0 "Blackbird"
  */

Common/include/graph_coloring_structure.hpp

@@ -38,22 +38,13 @@ using namespace std;
 
 /*!
  * \class CGraphColoringStructure
- * \brief Class, which provides graph coloring algorithms.
+ * \ingroup Graph
+ * \brief Class, which provides distributed graph coloring algorithms.
  * \author: E. van der Weide
  * \version 7.4.0 "Blackbird"
  */
 class CGraphColoringStructure {
 public:
-  /*!
-   * \brief Constructor of the class. Nothing to be done.
-   */
-  CGraphColoringStructure(void);
-
-  /*!
-   * \brief Constructor of the class. Nothing to be done.
-   */
-  ~CGraphColoringStructure(void);
-
   /*!
    * \brief Function, which determines the colors for the vertices of the given graph.
    * \param[in]  config             - Definition of the particular problem.