Merge branch 'develop' into develop

Author: pcarruscag

.gitignore

@@ -87,4 +87,6 @@ Mercurial
 # Ignore build folder
 ./build/
 build/
+
+# ninja binary (build system)
 ninja

Common/include/CConfig.hpp

@@ -28,7 +28,7 @@
 
 #pragma once
 
-#include "./mpi_structure.hpp"
+#include "./parallelization/mpi_structure.hpp"
 
 #include <iostream>
 #include <cstdlib>
@@ -108,8 +108,14 @@ class CConfig {
   unsigned short FFD_Blending;    /*!< \brief Kind of FFD Blending function. */
   su2double* FFD_BSpline_Order;   /*!< \brief BSpline order in i,j,k direction. */
   su2double FFD_Tol;              /*!< \brief Tolerance in the point inversion problem. */
-  su2double Opt_RelaxFactor;      /*!< \brief Scale factor for the line search. */
-  su2double Opt_LineSearch_Bound; /*!< \brief Bounds for the line search. */
+  bool FFD_IntPrev;                       /*!< \brief Enables self-intersection prevention procedure within the FFD box. */
+  unsigned short FFD_IntPrev_MaxIter;     /*!< \brief Amount of iterations for FFD box self-intersection prevention procedure. */
+  unsigned short FFD_IntPrev_MaxDepth;    /*!< \brief Maximum recursion depth for FFD box self-intersection procedure. */
+  bool ConvexityCheck;                    /*!< \brief Enables convexity check on all mesh elements. */
+  unsigned short ConvexityCheck_MaxIter;  /*!< \brief Amount of iterations for convexity check in deformations. */
+  unsigned short ConvexityCheck_MaxDepth; /*!< \brief Maximum recursion depth for convexity check in deformations.*/
+  su2double Opt_RelaxFactor;              /*!< \brief Scale factor for the line search. */
+  su2double Opt_LineSearch_Bound;         /*!< \brief Bounds for the line search. */
   su2double StartTime;
   bool ContinuousAdjoint,   /*!< \brief Flag to know if the code is solving an adjoint problem. */
   Viscous,                  /*!< \brief Flag to know if the code is solving a viscous problem. */
@@ -660,11 +666,6 @@ class CConfig {
   unsigned short Res_FEM_CRIT;        /*!< \brief Criteria to apply to the FEM convergence (absolute/relative). */
   unsigned long StartConv_Iter;       /*!< \brief Start convergence criteria at iteration. */
   su2double Cauchy_Eps;               /*!< \brief Epsilon used for the convergence. */
-  unsigned long Wrt_Sol_Freq,   /*!< \brief Writing solution frequency. */
-  Wrt_Sol_Freq_DualTime,        /*!< \brief Writing solution frequency for Dual Time. */
-  Wrt_Con_Freq,                 /*!< \brief Writing convergence history frequency. */
-  Wrt_Con_Freq_DualTime;        /*!< \brief Writing convergence history frequency. */
-  bool Wrt_Dynamic;             /*!< \brief Write dynamic data adding header and prefix. */
   bool Restart,                 /*!< \brief Restart solution (for direct, adjoint, and linearized problems).*/
   Read_Binary_Restart,          /*!< \brief Read binary SU2 native restart files.*/
   Restart_Flow;                 /*!< \brief Restart flow solution for adjoint and linearized problems. */
@@ -759,7 +760,6 @@ class CConfig {
   string Mesh_FileName,          /*!< \brief Mesh input file. */
   Mesh_Out_FileName,             /*!< \brief Mesh output file. */
   Solution_FileName,             /*!< \brief Flow solution input file. */
-  Solution_LinFileName,          /*!< \brief Linearized flow solution input file. */
   Solution_AdjFileName,          /*!< \brief Adjoint solution input file for drag functional. */
   Volume_FileName,               /*!< \brief Flow variables output file. */
   Residual_FileName,             /*!< \brief Residual variables output file. */
@@ -772,24 +772,13 @@ class CConfig {
   ObjFunc_Value_FileName,        /*!< \brief Objective function. */
   SurfCoeff_FileName,            /*!< \brief Output file with the flow variables on the surface. */
   SurfAdjCoeff_FileName,         /*!< \brief Output file with the adjoint variables on the surface. */
-  New_SU2_FileName,              /*!< \brief Output SU2 mesh file converted from CGNS format. */
   SurfSens_FileName,             /*!< \brief Output file for the sensitivity on the surface (discrete adjoint). */
   VolSens_FileName;              /*!< \brief Output file for the sensitivity in the volume (discrete adjoint). */
 
-  bool Wrt_Output,           /*!< \brief Write any output files */
-  Wrt_Vol_Sol,               /*!< \brief Write a volume solution file */
-  Wrt_Srf_Sol,               /*!< \brief Write a surface solution file */
-  Wrt_Csv_Sol,               /*!< \brief Write a surface comma-separated values solution file */
-  Wrt_Crd_Sol,               /*!< \brief Write a binary file with the grid coordinates only. */
-  Wrt_Residuals,             /*!< \brief Write residuals to solution file */
-  Wrt_Surface,               /*!< \brief Write solution at each surface */
-  Wrt_Limiters,              /*!< \brief Write residuals to solution file */
-  Wrt_SharpEdges,            /*!< \brief Write residuals to solution file */
-  Wrt_Halo,                  /*!< \brief Write rind layers in solution files */
+  bool
   Wrt_Performance,           /*!< \brief Write the performance summary at the end of a calculation.  */
   Wrt_AD_Statistics,         /*!< \brief Write the tape statistics (discrete adjoint).  */
   Wrt_MeshQuality,           /*!< \brief Write the mesh quality statistics to the visualization files.  */
-  Wrt_Slice,                 /*!< \brief Write 1D slice of a 2D cartesian solution */
   Wrt_Projected_Sensitivity, /*!< \brief Write projected sensitivities (dJ/dx) on surfaces to ASCII file. */
   Plot_Section_Forces;       /*!< \brief Write sectional forces for specified markers. */
   unsigned short
@@ -1010,7 +999,6 @@ class CConfig {
   long ParMETIS_edgeWgt;            /*!< \brief Load balancing weight given to edges. */
   unsigned short DirectDiff;        /*!< \brief Direct Differentation mode. */
   bool DiscreteAdjoint;                  /*!< \brief AD-based discrete adjoint mode. */
-  unsigned long Wrt_Surf_Freq_DualTime;  /*!< \brief Writing surface solution frequency for Dual Time. */
   su2double Const_DES;                 /*!< \brief Detached Eddy Simulation Constant. */
   unsigned short Kind_WindowFct;       /*!< \brief Type of window (weight) function for objective functional. */
   unsigned short Kind_HybridRANSLES;   /*!< \brief Kind of Hybrid RANS/LES. */
@@ -3073,102 +3061,6 @@ class CConfig {
    */
   su2double GetPhysicalTime(void) const { return PhysicalTime; }
 
-  /*!
-   * \brief Get the frequency for writing the solution file.
-   * \return It writes the solution file with this frequency.
-   */
-  unsigned long GetWrt_Sol_Freq(void) const { return Wrt_Sol_Freq; }
-
-  /*!
-   * \brief Get the frequency for writing the solution file in Dual Time.
-   * \return It writes the solution file with this frequency.
-   */
-  unsigned long GetWrt_Sol_Freq_DualTime(void) const { return Wrt_Sol_Freq_DualTime; }
-
-  /*!
-   * \brief Get the frequency for writing the convergence file.
-   * \return It writes the convergence file with this frequency.
-   */
-  unsigned long GetWrt_Con_Freq(void) const { return Wrt_Con_Freq; }
-
-  /*!
-   * \brief Set the frequency for writing the convergence file.
-   * \return It writes the convergence file with this frequency.
-   */
-  void SetWrt_Con_Freq(unsigned long val_freq) { Wrt_Con_Freq = val_freq; }
-
-  /*!
-   * \brief Get the frequency for writing the convergence file in Dual Time.
-   * \return It writes the convergence file with this frequency.
-   */
-  unsigned long GetWrt_Con_Freq_DualTime(void) const { return Wrt_Con_Freq_DualTime; }
-
-  /*!
-   * \brief Get information about writing unsteady headers and file extensions.
-   * \return    <code>TRUE</code> means that unsteady solution files will be written.
-   */
-  bool GetWrt_Unsteady(void);
-
-  /*!
-   * \brief Get information about writing output files.
-   * \return <code>TRUE</code> means that output files will be written.
-   */
-  bool GetWrt_Output(void) const { return Wrt_Output; }
-
-  /*!
-   * \brief Get information about writing a volume solution file.
-   * \return <code>TRUE</code> means that a volume solution file will be written.
-   */
-  bool GetWrt_Vol_Sol(void) const { return Wrt_Vol_Sol; }
-
-  /*!
-   * \brief Get information about writing a surface solution file.
-   * \return <code>TRUE</code> means that a surface solution file will be written.
-   */
-  bool GetWrt_Srf_Sol(void) const { return Wrt_Srf_Sol; }
-
-  /*!
-   * \brief Get information about writing a surface comma-separated values (CSV) solution file.
-   * \return <code>TRUE</code> means that a surface comma-separated values (CSV) solution file will be written.
-   */
-  bool GetWrt_Csv_Sol(void) const { return Wrt_Csv_Sol; }
-
-  /*!
-   * \brief Get information about writing a binary coordinates file.
-   * \return <code>TRUE</code> means that a binary coordinates file will be written.
-   */
-  bool GetWrt_Crd_Sol(void) const { return Wrt_Crd_Sol; }
-
-  /*!
-   * \brief Get information about writing residuals to volume solution file.
-   * \return <code>TRUE</code> means that residuals will be written to the solution file.
-   */
-  bool GetWrt_Residuals(void) const { return Wrt_Residuals; }
-
-  /*!
-   * \brief Get information about writing residuals to volume solution file.
-   * \return <code>TRUE</code> means that residuals will be written to the solution file.
-   */
-  bool GetWrt_Limiters(void) const { return Wrt_Limiters; }
-
-  /*!
-   * \brief Write solution at each surface.
-   * \return <code>TRUE</code> means that the solution at each surface will be written.
-   */
-  bool GetWrt_Surface(void) const { return Wrt_Surface; }
-
-  /*!
-   * \brief Get information about writing residuals to volume solution file.
-   * \return <code>TRUE</code> means that residuals will be written to the solution file.
-   */
-  bool GetWrt_SharpEdges(void) const { return Wrt_SharpEdges; }
-
-  /*!
-   * \brief Get information about writing rind layers to the solution files.
-   * \return <code>TRUE</code> means that rind layers will be written to the solution file.
-   */
-  bool GetWrt_Halo(void) const { return Wrt_Halo; }
-
   /*!
    * \brief Get information about writing the performance summary at the end of a calculation.
    * \return <code>TRUE</code> means that the performance summary will be written at the end of a calculation.
@@ -3187,12 +3079,6 @@ class CConfig {
    */
   bool GetWrt_MeshQuality(void) const { return Wrt_MeshQuality; }
 
-  /*!
-   * \brief Get information about writing a 1D slice of a 2D cartesian solution.
-   * \return <code>TRUE</code> means that a 1D slice of a 2D cartesian solution will be written.
-   */
-  bool GetWrt_Slice(void) const { return Wrt_Slice; }
-
   /*!
    * \brief Get information about writing projected sensitivities on surfaces to an ASCII file with rows as x, y, z, dJ/dx, dJ/dy, dJ/dz for each vertex.
    * \return <code>TRUE</code> means that projected sensitivities on surfaces in an ASCII file with rows as x, y, z, dJ/dx, dJ/dy, dJ/dz for each vertex will be written.
@@ -8206,6 +8092,27 @@ class CConfig {
    */
   su2double GetFFD_Tol(void) const { return FFD_Tol; }
 
+  /*!
+   * \brief Get information about whether to do a check on self-intersections within
+      the FFD box based on value on the Jacobian determinant.
+   * \param[out] FFD_IntPrev: <code>TRUE</code> if FFD intersection prevention is active; otherwise <code>FALSE</code>.
+   * \param[out] FFD_IntPrev_MaxIter: Maximum number of iterations in the intersection prevention procedure.
+   * \param[out] FFD_IntPrev_MaxDepth: Maximum recursion depth in the intersection prevention procedure.
+   */
+  tuple<bool, unsigned short, unsigned short> GetFFD_IntPrev(void) const {
+    return make_tuple(FFD_IntPrev, FFD_IntPrev_MaxIter, FFD_IntPrev_MaxDepth);
+  }
+
+  /*!
+   * \brief Get information about whether to do a check on convexity of the mesh elements.
+   * \param[out] ConvexityCheck: <code>TRUE</code> if convexity check is active; otherwise <code>FALSE</code>.
+   * \param[out] ConvexityCheck_MaxIter: Maximum number of iterations in the convexity check.
+   * \param[out] ConvexityCheck_MaxDepth: Maximum recursion depth in the convexity check.
+   */
+  tuple<bool, unsigned short, unsigned short> GetConvexityCheck(void) const {
+    return make_tuple(ConvexityCheck, ConvexityCheck_MaxIter, ConvexityCheck_MaxDepth);
+  }
+
   /*!
    * \brief Get the scale factor for the line search.
    * \return Scale factor for the line search.
@@ -8523,12 +8430,6 @@ class CConfig {
    */
   void SetiInst(unsigned short val_iInst) { iInst = val_iInst; }
 
-  /*!
-   * \brief Get information about writing dynamic structural analysis headers and file extensions.
-   * \return    <code>TRUE</code> means that dynamic structural analysis solution files will be written.
-   */
-  bool GetWrt_Dynamic(void) const { return Wrt_Dynamic; }
-
   /*!
    * \brief Get Newmark alpha parameter.
    * \return Value of the Newmark alpha parameter.
@@ -8908,12 +8809,6 @@ class CConfig {
    */
   su2double GetRestart_Bandwidth_Agg(void) const { return Restart_Bandwidth_Agg; }
 
-  /*!
-   * \brief Get the frequency for writing the surface solution file in Dual Time.
-   * \return It writes the surface solution file with this frequency.
-   */
-  unsigned long GetWrt_Surf_Freq_DualTime(void) const { return Wrt_Surf_Freq_DualTime; }
-
   /*!
    * \brief Get the Kind of Hybrid RANS/LES.
    * \return Value of Hybrid RANS/LES method.
@@ -9303,6 +9198,7 @@ class CConfig {
 
   /*!
    * \brief GetScreen_Wrt_Freq_Inner
+   * \param[in] iter: index for Time (0), Outer (1), or Inner (2) iterations
    * \return
    */
   unsigned long GetScreen_Wrt_Freq(unsigned short iter) const { return ScreenWrtFreq[iter]; }

Common/include/adt/CADTBaseClass.hpp

@@ -32,7 +32,7 @@
 
 #include "../basic_types/datatype_structure.hpp"
 #include "./CADTNodeClass.hpp"
-#include "../omp_structure.hpp"
+#include "../parallelization/omp_structure.hpp"
 
 using namespace std;
 

Common/include/adt/CADTElemClass.hpp

@@ -29,7 +29,7 @@
 
 #include "./CADTBaseClass.hpp"
 #include "./CBBoxTargetClass.hpp"
-#include "../omp_structure.hpp"
+#include "../parallelization/omp_structure.hpp"
 
 /*!
  * \class CADTElemClass

Common/include/containers/C2DContainer.hpp

@@ -613,7 +613,8 @@ class C2DContainer :
  * \brief Useful typedefs with default template parameters
  */
 template<class T> using su2vector = C2DContainer<unsigned long, T, StorageType::ColumnMajor, 64, DynamicSize, 1>;
-template<class T> using su2matrix = C2DContainer<unsigned long, T, StorageType::RowMajor, 64, DynamicSize, DynamicSize>;
+template<class T> using su2matrix = C2DContainer<unsigned long, T, StorageType::RowMajor,    64, DynamicSize, DynamicSize>;
+template<class T> using ColMajorMatrix = C2DContainer<unsigned long, T, StorageType::ColumnMajor, 64, DynamicSize, DynamicSize>;
 
 using su2activevector = su2vector<su2double>;
 using su2activematrix = su2matrix<su2double>;

Common/include/fem/fem_cgns_elements.hpp

@@ -29,7 +29,7 @@
 
 #pragma once
 
-#include "../mpi_structure.hpp"
+#include "../parallelization/mpi_structure.hpp"
 
 #ifdef HAVE_CGNS
   #include "cgnslib.h"

Common/include/fem/fem_geometry_structure.hpp

@@ -34,7 +34,7 @@
 #include "fem_cgns_elements.hpp"
 #endif
 #include "../wall_model.hpp"
-#include "../blas_structure.hpp"
+#include "../linear_algebra/blas_structure.hpp"
 
 using namespace std;
 

Common/include/geometry/CGeometry.hpp

@@ -28,7 +28,7 @@
 
 #pragma once
 
-#include "../mpi_structure.hpp"
+#include "../parallelization/mpi_structure.hpp"
 
 #ifdef HAVE_METIS
 #include "metis.h"
@@ -84,7 +84,7 @@ class CGeometry {
   nPointGhost{0},                 /*!< \brief Number of ghost points of the mesh. */
   nPointNode{0},                  /*!< \brief Size of the node array allocated to hold CPoint objects. */
   Global_nPoint{0},               /*!< \brief Total number of nodes in a simulation across all processors (including halos). */
-  Global_nPointDomain{0},	        /*!< \brief Total number of nodes in a simulation across all processors (excluding halos). */
+  Global_nPointDomain{0},         /*!< \brief Total number of nodes in a simulation across all processors (excluding halos). */
   nElem{0},                       /*!< \brief Number of elements of the mesh. */
   Global_nElem{0},                /*!< \brief Total number of elements in a simulation across all processors (all types). */
   Global_nElemDomain{0},          /*!< \brief Total number of elements in a simulation across all processors (excluding halos). */
@@ -109,7 +109,8 @@ class CGeometry {
   nelem_triangle_bound{0},        /*!< \brief Number of triangles on the mesh boundaries. */
   Global_nelem_triangle_bound{0}, /*!< \brief Total number of triangles on the mesh boundaries across all processors. */
   nelem_quad_bound{0},            /*!< \brief Number of quads on the mesh boundaries. */
-  Global_nelem_quad_bound{0};     /*!< \brief Total number of quads on the mesh boundaries across all processors. */
+  Global_nelem_quad_bound{0},     /*!< \brief Total number of quads on the mesh boundaries across all processors. */
+  nNonconvexElements{0};          /*!< \brief Number of nonconvex elements in the mesh. */
 
   unsigned short nDim{0};         /*!< \brief Number of dimension of the problem. */
   unsigned short nZone{0};        /*!< \brief Number of zones in the problem. */
@@ -189,7 +190,7 @@ class CGeometry {
 
   CPrimalGrid** elem{nullptr};           /*!< \brief Element vector (primal grid information). */
   CPrimalGrid** face{nullptr};           /*!< \brief Face vector (primal grid information). */
-  CPrimalGrid*** bound{nullptr};	       /*!< \brief Boundary vector (primal grid information). */
+  CPrimalGrid*** bound{nullptr};         /*!< \brief Boundary vector (primal grid information). */
   CPoint* nodes{nullptr};                /*!< \brief Node vector (dual grid information). */
   CEdge* edges{nullptr};                 /*!< \brief Edge vector (dual grid information). */
   CVertex*** vertex{nullptr};            /*!< \brief Boundary Vertex vector (dual grid information). */
@@ -856,20 +857,6 @@ class CGeometry {
    */
   inline virtual void SetBoundControlVolume(CConfig *config, CGeometry *geometry, unsigned short action) {}
 
-  /*!
-   * \brief A virtual member.
-   * \param[in] config - Definition of the particular problem.
-   * \param[in] val_mesh_out_filename - Name of the output file.
-   */
-  inline virtual void SetMeshFile(CConfig *config, string val_mesh_out_filename) {}
-
-  /*!
-   * \brief A virtual member.
-   * \param[in] config - Definition of the particular problem.
-   * \param[in] val_mesh_out_filename - Name of the output file.
-   */
-  inline virtual void SetMeshFile(CGeometry *geometry, CConfig *config, string val_mesh_out_filename) {}
-
   /*!
    * \brief A virtual member.
    * \param[in] config - Definition of the particular problem.
@@ -1713,5 +1700,16 @@ class CGeometry {
    */
   static void ComputeWallDistance(const CConfig * const *config_container, CGeometry ****geometry_container);
 
+  /*!
+   * \brief Set the amount of nonconvex elements in the mesh.
+   * \param[in] nonconvex_elems - amount of nonconvex elements in the mesh
+   */
+  void SetnNonconvexElements(unsigned long nonconvex_elems) {nNonconvexElements = nonconvex_elems;}
+
+  /*!
+   * \brief Get the amount of nonconvex elements in the mesh.
+   * \param[out] nNonconvexElements- amount of nonconvex elements in the mesh
+   */
+  unsigned long GetnNonconvexElements() const {return nNonconvexElements;}
 };
 

Common/include/geometry/CMultiGridGeometry.hpp

@@ -40,7 +40,6 @@ class CMultiGridGeometry final : public CGeometry {
 public:
   /*--- This is to suppress Woverloaded-virtual, omitting it has no negative impact. ---*/
   using CGeometry::SetVertex;
-  using CGeometry::SetMeshFile;
   using CGeometry::SetControlVolume;
   using CGeometry::SetBoundControlVolume;
   using CGeometry::SetPoint_Connectivity;