Merge branch 'develop' into misc_fixes

RichRoos · Sep 28, 2022 · 9cced8e · 9cced8e
2 parents dc6b77d + 3c783fa
commit 9cced8e
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diff --git a/.github/workflows/release-management.yml b/.github/workflows/release-management.yml
@@ -29,7 +29,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Cache Object Files
-        uses: actions/cache@v1
+        uses: actions/cache@v3
         with:
           path: ccache
           key: ${{ matrix.os_bin }}-${{ github.sha }}
@@ -44,7 +44,7 @@ jobs:
           zip -r ../${{matrix.os_bin}}.zip bin/*
         # Uploads binaries as artifacts (just as a backup)
       - name: Upload Binaries
-        uses: actions/upload-artifact@v1
+        uses: actions/upload-artifact@v3
         with:
           name: ${{matrix.os_bin}}
           path: ${{matrix.os_bin}}.zip

diff --git a/AUTHORS.md b/AUTHORS.md
@@ -126,6 +126,7 @@ TobiKattmann
 Trent Lukaczyk
 VivaanKhatri
 Wally Maier
+Zan Xu
 aaronyicongfu
 aeroamit
 anilvar

diff --git a/Common/doc/docmain.hpp b/Common/doc/docmain.hpp
diff --git a/Common/include/adt/CADTBaseClass.hpp b/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
  */

diff --git a/Common/include/adt/CADTComparePointClass.hpp b/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
  */

diff --git a/Common/include/adt/CADTElemClass.hpp b/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"

diff --git a/Common/include/adt/CADTNodeClass.hpp b/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
  */

diff --git a/Common/include/adt/CADTPointsOnlyClass.hpp b/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
  */

diff --git a/Common/include/adt/CBBoxTargetClass.hpp b/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

diff --git a/Common/include/basic_types/datatype_structure.hpp b/Common/include/basic_types/datatype_structure.hpp
@@ -114,6 +114,21 @@ namespace SU2_TYPE {
   FORCEINLINE void SetDerivative(su2double &, const passivedouble &) {}
 #endif
 
+  /*!
+   * \brief Get the passive value of any variable. For most types return directly,
+   * specialize for su2double to call GetValue.
+   * \note This is a struct instead of a function because the return type of the
+   * su2double specialization changes.
+   */
+  template <class T>
+  struct Passive {
+    FORCEINLINE static T Value(const T& val) {return val;}
+  };
+  template <>
+  struct Passive<su2double> {
+    FORCEINLINE static passivedouble Value(const su2double& val) {return GetValue(val);}
+  };
+
   /*!
    * \brief Casts the primitive value to int (uses GetValue, already implemented for each type).
    * \param[in] data - The non-primitive datatype.

diff --git a/Common/include/containers/C2DContainer.hpp b/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>;
+
+/// @}
diff --git a/Common/include/containers/CFastFindAndEraseQueue.hpp b/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.

diff --git a/Common/include/containers/CFileReaderLUT.hpp b/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;

diff --git a/Common/include/containers/CLookUpTable.hpp b/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. */

diff --git a/Common/include/containers/CTrapezoidalMap.hpp b/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"

diff --git a/Common/include/containers/CVertexMap.hpp b/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:

diff --git a/Common/include/containers/container_decorators.hpp b/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);
 }
+
+/// @}
diff --git a/Common/include/geometry/elements/CElement.hpp b/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> {

diff --git a/Common/include/geometry/elements/CElementProperty.hpp b/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"

diff --git a/Common/include/geometry/elements/CGaussVariable.hpp b/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"
  */