Various fixes

.travis.yml

@@ -76,7 +76,7 @@ before_script:
     - cp -R ./TestData/* ./TestCases/
 
     # Get the tutorial cases
-    - git clone --depth=1 -b develop https://github.com/su2code/su2code.github.io ./Tutorials
+    - git clone --depth=1 -b cleanup_linsol_options https://github.com/su2code/su2code.github.io ./Tutorials
 
     # Enter the SU2/TestCases/ directory, which is now ready to run
     - cd TestCases/

Common/include/ad_structure.hpp

@@ -72,14 +72,9 @@ namespace AD{
   /*!
    * \brief Registers the variable as an input and saves internal data (indices). I.e. as a leaf of the computational graph.
    * \param[in] data - The variable to be registered as input.
+   * \param[in] push_index - boolean whether we also want to push the index.
    */
-  void RegisterInput(su2double &data);
-
-  /*!
-   * \brief Registers the variable as an input. I.e. as a leaf of the computational graph.
-   * \param[in] data - The variable to be registered as input.
-   */
-  void RegisterInput_intIndexBased(su2double &data);
+  void RegisterInput(su2double &data, bool push_index = true);
 
   /*!
    * \brief Registers the variable as an output. I.e. as the root of the computational graph.
@@ -246,7 +241,7 @@ namespace AD{
    * \param[in] data - variable whose gradient information will be extracted.
    * \param[in] index - where obtained gradient information will be stored.
    */
-  void SetAdjIndex(int &index, const su2double &data);
+  void SetIndex(int &index, const su2double &data);
 
   /*!
    * \brief Pushes back the current tape position to the tape position's vector.

Common/include/ad_structure.inl

@@ -76,10 +76,12 @@ namespace AD{
 
   extern codi::PreaccumulationHelper<su2double> PreaccHelper;  
 
-  inline void RegisterInput(su2double &data) {AD::globalTape.registerInput(data);
-                                             inputValues.push_back(data.getGradientData());}
-
-  inline void RegisterInput_intIndexBased(su2double &data) {AD::globalTape.registerInput(data);}
+  inline void RegisterInput(su2double &data, bool push_index) {
+    AD::globalTape.registerInput(data);
+    if (push_index) {
+      inputValues.push_back(data.getGradientData());
+    }
+  }
 
   inline void RegisterOutput(su2double& data) {AD::globalTape.registerOutput(data);}
 
@@ -116,7 +118,7 @@ namespace AD{
     }    
   }
 
-  inline void SetAdjIndex(int &index, const su2double &data) {
+  inline void SetIndex(int &index, const su2double &data) {
     index = data.getGradientData();
   }
 
@@ -269,9 +271,7 @@ namespace AD{
 
   /*--- Default implementation if reverse mode is disabled ---*/
 
-  inline void RegisterInput(su2double &data) {}
-
-  inline void RegisterInput_intIndexBased(su2double &data) {}
+  inline void RegisterInput(su2double &data, bool push_index) {}
 
   inline void RegisterOutput(su2double& data) {}
 
@@ -289,7 +289,7 @@ namespace AD{
 
   inline void ComputeAdjoint(unsigned short enter, unsigned short leave) {}
 
-  inline void SetAdjIndex(int &index, const su2double &data) {}
+  inline void SetIndex(int &index, const su2double &data) {}
 
   inline void SetDerivative(int index, const double val) {}
 

Common/include/config_structure.hpp

@@ -585,8 +585,7 @@ class CConfig {
 
   su2double Min_Beta_RoeTurkel,		/*!< \brief Minimum value of Beta for the Roe-Turkel low Mach preconditioner. */
   Max_Beta_RoeTurkel;		/*!< \brief Maximum value of Beta for the Roe-Turkel low Mach preconditioner. */
-  unsigned long GridDef_Nonlinear_Iter, /*!< \brief Number of nonlinear increments for grid deformation. */
-  GridDef_Linear_Iter; /*!< \brief Number of linear smoothing iterations for grid deformation. */
+  unsigned long GridDef_Nonlinear_Iter; /*!< \brief Number of nonlinear increments for grid deformation. */
   unsigned short Deform_Stiffness_Type; /*!< \brief Type of element stiffness imposed for FEA mesh deformation. */
   bool Deform_Mesh;    /*!< \brief Determines whether the mesh will be deformed. */
   bool Deform_Output;  /*!< \brief Print the residuals during mesh deformation to the console. */
@@ -4166,12 +4165,6 @@ class CConfig {
    */
   su2double GetCFLRedCoeff_AdjTurb(void);
 
-  /*!
-   * \brief Get the number of linear smoothing iterations for mesh deformation.
-   * \return Number of linear smoothing iterations for mesh deformation.
-   */
-  unsigned long GetGridDef_Linear_Iter(void);
-
   /*!
    * \brief Get the number of nonlinear increments for mesh deformation.
    * \return Number of nonlinear increments for mesh deformation.

Common/include/config_structure.inl

@@ -1046,8 +1046,6 @@ inline unsigned short CConfig::GetAdjTurb_Linear_Iter(void) { return AdjTurb_Lin
 
 inline su2double CConfig::GetCFLRedCoeff_AdjTurb(void) { return CFLRedCoeff_AdjTurb; }
 
-inline unsigned long CConfig::GetGridDef_Linear_Iter(void) { return GridDef_Linear_Iter; }
-
 inline unsigned long CConfig::GetGridDef_Nonlinear_Iter(void) { return GridDef_Nonlinear_Iter; }
 
 inline bool CConfig::GetDeform_Mesh(void) { return Deform_Mesh; }

Common/include/dual_grid_structure.hpp

@@ -176,8 +176,8 @@ class CPoint : public CDualGrid {
   unsigned short nNeighbor;           /*!< \brief Number of neighbors. */
   bool Flip_Orientation;              /*!< \brief Flip the orientation of the normal. */
   su2double MaxLength;                /*!< \brief The maximum cell-center to cell-center length. */
-  int *Input_AdjIndices,              /*!< \brief Indices of Coord variables in the adjoint vector. */
-  *Output_AdjIndices;                 /*!< \brief Indices of Coord variables in the adjoint vector after having been updated. */
+  int *AD_InputIndex,                 /*!< \brief Indices of Coord variables in the adjoint vector. */
+  *AD_OutputIndex;                    /*!< \brief Indices of Coord variables in the adjoint vector after having been updated. */
 
 public:
 
@@ -297,7 +297,7 @@ class CPoint : public CDualGrid {
    * \brief Set the adjoint vector indices of Coord vector.
    * \param[in] input - Save them to the input or output indices vector.
    */
-  void SetAdjIndices(bool input);
+  void SetIndex(bool input);
 
   /*!
    * \brief Set the adjoint values of the (geometric) coordinates.
@@ -814,7 +814,7 @@ class CPoint : public CDualGrid {
    * \brief Set the adjoint values of the coordinates.
    * \param[in] adj_sol - The adjoint values of the coordinates.
    */
-  void SetAdjointCoord_intIndexBased(su2double *adj_coor);
+  void SetAdjointCoord_LocalIndex(su2double *adj_coor);
 
   /*!
    * \brief Get the adjoint values of the coordinates.
@@ -826,7 +826,7 @@ class CPoint : public CDualGrid {
    * \brief Get the adjoint values of the coordinates.
    * \param[in] adj_sol - The adjoint values of the coordinates.
    */
-  void GetAdjointCoord_intIndexBased(su2double *adj_coor);
+  void GetAdjointCoord_LocalIndex(su2double *adj_coor);
 
 };
 

Common/include/dual_grid_structure.inl

@@ -267,19 +267,19 @@ inline void CPoint::SetAdjointCoord(su2double *adj_coor){
     SU2_TYPE::SetDerivative(Coord[iDim], SU2_TYPE::GetValue(adj_coor[iDim]));
 }
 
-inline void CPoint::SetAdjointCoord_intIndexBased(su2double *adj_coor){
+inline void CPoint::SetAdjointCoord_LocalIndex(su2double *adj_coor){
   for (unsigned short iDim = 0; iDim < nDim; iDim++)
-    AD::SetDerivative(Output_AdjIndices[iDim], SU2_TYPE::GetValue(adj_coor[iDim]));
+    AD::SetDerivative(AD_OutputIndex[iDim], SU2_TYPE::GetValue(adj_coor[iDim]));
 }
 
 inline void CPoint::GetAdjointCoord(su2double *adj_coor){
   for (unsigned short iDim = 0; iDim < nDim; iDim++)
     adj_coor[iDim] = SU2_TYPE::GetDerivative(Coord[iDim]);
 }
 
-inline void CPoint::GetAdjointCoord_intIndexBased(su2double *adj_coor){
+inline void CPoint::GetAdjointCoord_LocalIndex(su2double *adj_coor){
   for (unsigned short iDim = 0; iDim < nDim; iDim++)
-    adj_coor[iDim] = AD::GetDerivative(Input_AdjIndices[iDim]);
+    adj_coor[iDim] = AD::GetDerivative(AD_InputIndex[iDim]);
 }
 
 inline unsigned short CEdge::GetnNodes() { return 2; }

Common/include/interpolation_structure.hpp

@@ -76,15 +76,16 @@ class CInterpolator {
   *Buffer_Send_nVertex_Donor,/*!\brief Buffer to send number of vertices on the local processor*/
   *Buffer_Send_nFace_Donor,/*!\brief Buffer to send number of faces on the local processor*/
   *Buffer_Send_nFaceNodes_Donor,/*!\brief Buffer to send the number of nodes assocated with faces per processor*/
-  *Buffer_Receive_GlobalPoint, /*!\brief Buffer to receive global point indices*/
-  *Buffer_Send_GlobalPoint,/*!\brief Buffer to send global point indices*/
   *Buffer_Send_FaceIndex,/*!\brief Buffer to send indices pointing to the node indices that define the faces*/
   *Buffer_Receive_FaceIndex,/*!\brief Buffer to receive indices pointing to the node indices that define the faces*/
   *Buffer_Send_FaceNodes,/*!\brief Buffer to send indices pointing to the location of node information in other buffers, defining faces*/
   *Buffer_Receive_FaceNodes,/*!\brief Buffer to receive indices pointing to the location of node information in other buffers, defining faces*/
   *Buffer_Send_FaceProc,/*!\brief Buffer to send processor which stores the node indicated in Buffer_Receive_FaceNodes*/
   *Buffer_Receive_FaceProc;/*!\brief Buffer to receive processor which stores the node indicated in Buffer_Receive_FaceNodes*/
 
+  long   *Buffer_Send_GlobalPoint,/*!\brief Buffer to send global point indices*/
+  *Buffer_Receive_GlobalPoint; /*!\brief Buffer to receive global point indices*/
+
   su2double *Buffer_Send_Coord,/*!\brief Buffer to send coordinate values*/
   *Buffer_Send_Normal,/*!\brief Buffer to send normal vector values */
   *Buffer_Receive_Coord,/*!\brief Buffer to receive coordinate values*/

Common/include/toolboxes/C2DContainer.hpp

@@ -81,7 +81,7 @@ class AccessorImpl
   alignas(AlignSize) Scalar_t m_data[StaticRows*StaticCols];
 
   /*!
-   * Static size specializations use this do-nothing macro.
+   * Static size specializations use this do-nothing allocation macro.
    */
 #define DUMMY_ALLOCATOR \
   void m_allocate(size_t sz, Index_t rows, Index_t cols) noexcept {}
@@ -90,18 +90,27 @@ class AccessorImpl
    * runtime internal value that depend on the number of rows/columns.
    * What values need setting depends on the specialization as not all have
    * members for e.g. number of rows and cols (static size optimization).
+   * \note Aligned dynamic allocation is disabled for compilation on MAC.
    */
-#define REAL_ALLOCATOR(EXTRA)                                           \
+#ifndef __APPLE__
+#define REAL_ALLOCATOR(EXTRA)                                             \
   static_assert(AlignSize % alignof(Scalar_t)==0,                         \
-      "AlignSize is not a multiple of the type's alignment spec.");       \
+    "AlignSize is not a multiple of the type's alignment spec.");         \
                                                                           \
   void m_allocate(size_t sz, Index_t rows, Index_t cols) noexcept {       \
-      EXTRA;                                                              \
-      if(AlignSize==0)                                                    \
-          m_data = static_cast<Scalar_t*>(malloc(sz));                    \
-      else                                                                \
-          m_data = static_cast<Scalar_t*>(aligned_alloc(AlignSize,sz));   \
+    EXTRA;                                                                \
+    if(AlignSize==0)                                                      \
+      m_data = static_cast<Scalar_t*>(malloc(sz));                        \
+    else                                                                  \
+      m_data = static_cast<Scalar_t*>(aligned_alloc(AlignSize,sz));       \
   }
+#else
+#define REAL_ALLOCATOR(EXTRA)                                             \
+  void m_allocate(size_t sz, Index_t rows, Index_t cols) noexcept {       \
+    EXTRA;                                                                \
+    m_data = static_cast<Scalar_t*>(malloc(sz));                          \
+  }
+#endif
 
   DUMMY_ALLOCATOR
 

Common/src/config_structure.cpp

@@ -1996,8 +1996,6 @@ void CConfig::SetConfig_Options() {
   addBoolOption("DEFORM_CONSOLE_OUTPUT", Deform_Output, false);
   /* DESCRIPTION: Number of nonlinear deformation iterations (surface deformation increments) */
   addUnsignedLongOption("DEFORM_NONLINEAR_ITER", GridDef_Nonlinear_Iter, 1);
-  /* DESCRIPTION: Number of smoothing iterations for FEA mesh deformation */
-  addUnsignedLongOption("DEFORM_LINEAR_ITER", GridDef_Linear_Iter, 1000);
   /* DESCRIPTION: Deform coefficient (-1.0 to 0.5) */
   addDoubleOption("DEFORM_COEFF", Deform_Coeff, 1E6);
   /* DESCRIPTION: Deform limit in m or inches */
@@ -2895,7 +2893,7 @@ void CConfig::SetPostprocessing(unsigned short val_software, unsigned short val_
   }
 
   /*--- Set the default output files ---*/
-  if (nVolumeOutputFiles == 0){
+  if (!OptionIsSet("OUTPUT_FILES")){
     nVolumeOutputFiles = 3;
     VolumeOutputFiles = new unsigned short[nVolumeOutputFiles];
     VolumeOutputFiles[0] = RESTART_BINARY;
@@ -2916,12 +2914,14 @@ void CConfig::SetPostprocessing(unsigned short val_software, unsigned short val_
     SU2_MPI::Error("A turbulence model must be specified with KIND_TURB_MODEL if SOLVER= INC_RANS", CURRENT_FUNCTION);
   }
 
-//#ifndef HAVE_TECIO
-//  if (Output_FileFormat == TECPLOT_BINARY) {
-//    cout << "Tecplot binary file requested but SU2 was built without TecIO support." << "\n";
-//    Output_FileFormat = TECPLOT;
-//  }
-//#endif
+#ifndef HAVE_TECIO
+  for (unsigned short iVolumeFile = 0; iVolumeFile < nVolumeOutputFiles; iVolumeFile++){
+    if (VolumeOutputFiles[iVolumeFile] == TECPLOT_BINARY ||
+        VolumeOutputFiles[iVolumeFile] == SURFACE_TECPLOT_BINARY) {
+      SU2_MPI::Error(string("Tecplot binary file requested in option OUTPUT_FILES but SU2 was built without TecIO support.\n"), CURRENT_FUNCTION);
+    }
+  }
+#endif
 
   /*--- Set the boolean Wall_Functions equal to true if there is a
    definition for the wall founctions ---*/
@@ -6243,8 +6243,15 @@ void CConfig::SetOutput(unsigned short val_software, unsigned short val_izone) {
     cout << endl <<"------------------ Convergence Criteria  ( Zone "  << iZone << " ) ---------------------" << endl;
 
     cout << "Maximum number of solver subiterations: " << nInnerIter <<"."<< endl;
-    cout << "Maximum number of physical time-steps: " << nTimeIter <<"."<< endl;
+    if (Multizone_Problem)
+      cout << "Maximum number of solver outer iterations: " << nOuterIter <<"."<< endl;
+    if (Time_Domain)
+      cout << "Maximum number of physical time-steps: " << nTimeIter <<"."<< endl;
 
+    cout << "Begin convergence monitoring at iteration " << StartConv_Iter << "." << endl;    
+    cout << "Residual minimum value: 1e" << MinLogResidual << "." << endl;
+    cout << "Cauchy series min. value: " << Cauchy_Eps << "." << endl;
+    cout << "Number of Cauchy elements: " << Cauchy_Elems << "." << endl;
   }
 
   if (val_software == SU2_MSH) {
@@ -6282,18 +6289,25 @@ void CConfig::SetOutput(unsigned short val_software, unsigned short val_izone) {
 
   if (val_software == SU2_CFD) {
 
-    cout << "Writing a solution file every " << Wrt_Sol_Freq <<" iterations."<< endl;
-    cout << "Writing the convergence history every " << Wrt_Con_Freq <<" iterations."<< endl;
-    if ((TimeMarching == DT_STEPPING_1ST) || (TimeMarching == DT_STEPPING_2ND)) {
-      cout << "Writing the dual time flow solution every " << Wrt_Sol_Freq_DualTime <<" iterations."<< endl;
-      cout << "Writing the dual time convergence history every " << Wrt_Con_Freq_DualTime <<" iterations."<< endl;
+    cout << "Writing solution files every " << VolumeWrtFreq <<" iterations."<< endl;
+    cout << "Writing the convergence history file every " << HistoryWrtFreq[2] <<" inner iterations."<< endl;
+    if (Multizone_Problem){
+      cout << "Writing the convergence history file every " << HistoryWrtFreq[1] <<" outer iterations."<< endl;      
+    }
+    if (Time_Domain) {
+      cout << "Writing the convergence history file every " << HistoryWrtFreq[0] <<" time iterations."<< endl;      
+    }
+    cout << "Writing the screen convergence history every " << ScreenWrtFreq[2] <<" inner iterations."<< endl;
+    if (Multizone_Problem){
+      cout << "Writing the screen convergence history every " << ScreenWrtFreq[1] <<" outer iterations."<< endl;      
+    }
+    if (Time_Domain) {
+      cout << "Writing the screen convergence history every " << ScreenWrtFreq[0] <<" time iterations."<< endl;      
     }
 
     switch (Tab_FileFormat) {
-      case PARAVIEW: cout << "The output file format is Paraview ASCII legacy (.vtk)." << endl; break;
-      case PARAVIEW_BINARY: cout << "The output file format is Paraview binary legacy (.vtk)." << endl; break;
-      case TECPLOT: cout << "The output file format is Tecplot ASCII (.dat)." << endl; break;
-      case TECPLOT_BINARY: cout << "The output file format is Tecplot binary (.plt)." << endl; break;
+      case TAB_CSV: cout << "The tabular file format is CSV (.csv)." << endl; break;
+      case TAB_TECPLOT: cout << "The tabular file format is Tecplot (.dat)." << endl; break;
     }
 
     cout << "Convergence history file name: " << Conv_FileName << "." << endl;
@@ -6302,7 +6316,7 @@ void CConfig::SetOutput(unsigned short val_software, unsigned short val_izone) {
 
 
     if (!ContinuousAdjoint && !DiscreteAdjoint) {
-      cout << "Surface coefficients file name: " << SurfCoeff_FileName << "." << endl;
+      cout << "Surface file name: " << SurfCoeff_FileName << "." << endl;
       cout << "Volume file name: " << Volume_FileName << "." << endl;
       cout << "Restart file name: " << Restart_FileName << "." << endl;
     }
@@ -6311,17 +6325,15 @@ void CConfig::SetOutput(unsigned short val_software, unsigned short val_izone) {
       cout << "Adjoint solution file name: " << Solution_AdjFileName << "." << endl;
       cout << "Restart adjoint file name: " << Restart_AdjFileName << "." << endl;
       cout << "Adjoint variables file name: " << Adj_FileName << "." << endl;
-      cout << "Surface adjoint coefficients file name: " << SurfAdjCoeff_FileName << "." << endl;
+      cout << "Surface adjoint file name: " << SurfAdjCoeff_FileName << "." << endl;
     }
 
   }
 
   if (val_software == SU2_SOL) {
     switch (Tab_FileFormat) {
-      case PARAVIEW: cout << "The output file format is Paraview ASCII legacy (.vtk)." << endl; break;
-      case PARAVIEW_BINARY: cout << "The output file format is Paraview binary legacy (.vtk)." << endl; break;
-      case TECPLOT: cout << "The output file format is Tecplot ASCII (.dat)." << endl; break;
-      case TECPLOT_BINARY: cout << "The output file format is Tecplot binary (.plt)." << endl; break;
+      case TAB_CSV: cout << "The tabular file format is CSV (.csv)." << endl; break;
+      case TAB_TECPLOT: cout << "The tabular file format is Tecplot (.dat)." << endl; break;
     }
     cout << "Flow variables file name: " << Volume_FileName << "." << endl;
   }