Merge branch 'develop' into Dependabot-GitHub-Actions

Author: pcarruscag

.github/ISSUE_TEMPLATE/bug_report.md

@@ -7,14 +7,18 @@ assignees: ''
 
 ---
 
-**Describe the bug**
-*A clear and concise description of what the bug is and what you expect the behavior to be instead. If applicable, add screenshots to help explain your problem.*
+*If this is a general question or difficulty building/using the code, please open a "Discussion" instead.*
 
+**Describe the bug**
+*Give a clear and concise description of what the bug is and what you expect the behavior to be instead. Please provide enough instructions and data for a developer to reproduce the problem (config, mesh, commands, etc.). Please provide the smallest working example that reproduces the problem.*
 
 
-**To Reproduce**
-*Please provide a config file and mesh for a minimal example that recreates the problem.*
+**Bug report checklist**
+*Please make sure that you have followed the checklist below, many common problems can be solved by:*
 
+- [ ] Consulting the build instructions (https://su2code.github.io/docs_v7/Build-SU2-Linux-MacOS/).
+- [ ] Looking for similar problems on GitHub or CFD-Online (https://www.cfd-online.com/Forums/su2/).
+- [ ] Updating to the newest version of SU2 (either develop, master, or the pre-built executables https://su2code.github.io/download.html).
 
 
 **Desktop (please complete the following information):**

.github/pull_request_template.md

@@ -12,7 +12,7 @@
 *Put an X by all that apply. You can fill this out after submitting the PR. If you have any questions, don't hesitate to ask! We want to help. These are a guide for you to know what the reviewers will be looking for in your contribution.*
 
 - [ ] I am submitting my contribution to the develop branch.
-- [ ] My contribution generates no new compiler warnings (try with the '-Wall -Wextra -Wno-unused-parameter -Wno-empty-body' compiler flags, or simply --warnlevel=2 when using meson).
-- [ ] My contribution is commented and consistent with SU2 style.
+- [ ] My contribution generates no new compiler warnings (try with --warnlevel=3 when using meson).
+- [ ] My contribution is commented and consistent with SU2 style (https://su2code.github.io/docs_v7/Style-Guide/).
 - [ ] I have added a test case that demonstrates my contribution, if necessary.
-- [ ] I have updated appropriate documentation (Tutorials, Docs Page, config_template.cpp) , if necessary.
+- [ ] I have updated appropriate documentation (Tutorials, Docs Page, config_template.cpp), if necessary.

.github/workflows/regression.yml

@@ -31,7 +31,7 @@ jobs:
           - config_set: ForwardNoMPI
             flags: '-Denable-directdiff=true -Denable-normal=false -Dwith-mpi=disabled -Denable-tests=true --warnlevel=3 --werror'
           - config_set: BaseOMP
-            flags: '-Dwith-omp=true -Denable-mixedprec=true -Denable-tecio=false --warnlevel=3 --werror'
+            flags: '-Dwith-omp=true -Denable-mixedprec=true -Denable-pywrapper=true -Denable-tecio=false --warnlevel=3 --werror'
           - config_set: ReverseOMP
             flags: '-Denable-autodiff=true -Denable-normal=false -Dwith-omp=true -Denable-mixedprec=true -Denable-tecio=false --warnlevel=3 --werror'
           - config_set: ForwardOMP

.github/workflows/release-management.yml

@@ -23,7 +23,7 @@ jobs:
           - os_bin: macos64-mpi
             flags: '-Dcustom-mpi=true --cross-file=/hostfiles/hostfile_darwin_mpi'
           - os_bin: linux64
-            flags: '-Dwith-mpi=disabled --cross-file=/hostfiles/hostfile_linux'
+            flags: '-Dwith-mpi=disabled -Dstatic-cgns-deps=true --cross-file=/hostfiles/hostfile_linux'
           - os_bin: linux64-mpi
             flags: '-Dcustom-mpi=true --cross-file=/hostfiles/hostfile_linux_mpi'
     runs-on: ubuntu-latest

AUTHORS.md

@@ -77,6 +77,7 @@ Giulio Gori
 Guillaume Bâty
 Harichand M V
 HL Kline
+HL Zhi
 IndianaStokes
 J. Sinsay
 JSmith36

Common/include/CConfig.hpp

@@ -699,8 +699,12 @@ class CConfig {
   *Marker_WallFunctions,              /*!< \brief Markers for which wall functions must be applied. */
   *Marker_SobolevBC;                  /*!< \brief Markers in the gradient solver */
 
-  unsigned short  nConfig_Files;          /*!< \brief Number of config files for multiphysics problems. */
-  string *Config_Filenames;               /*!< \brief List of names for configuration files. */
+  unsigned short nConfig_Files;       /*!< \brief Number of config files for multiphysics problems. */
+  string *Config_Filenames;           /*!< \brief List of names for configuration files. */
+  SST_OPTIONS *SST_Options;           /*!< \brief List of modifications/corrections/versions of SST turbulence model.*/
+  SA_OPTIONS *SA_Options;             /*!< \brief List of modifications/corrections/versions of SA turbulence model.*/
+  unsigned short nSST_Options;        /*!< \brief Number of SST options specified. */
+  unsigned short nSA_Options;         /*!< \brief Number of SA options specified. */
   WALL_FUNCTIONS  *Kind_WallFunctions;        /*!< \brief The kind of wall function to use for the corresponding markers. */
   unsigned short  **IntInfo_WallFunctions;    /*!< \brief Additional integer information for the wall function markers. */
   su2double       **DoubleInfo_WallFunctions; /*!< \brief Additional double information for the wall function markers. */
@@ -798,8 +802,9 @@ class CConfig {
   Beta_Factor,          /*!< \brief Value of the epsilon^2 multiplier for Beta for the incompressible preconditioner. */
   Gas_Constant,         /*!< \brief Specific gas constant. */
   Gas_ConstantND,       /*!< \brief Non-dimensional specific gas constant. */
-  Molecular_Weight,     /*!< \brief Molecular weight of an incompressible ideal gas (g/mol). */
-  Specific_Heat_Cp,           /*!< \brief Specific heat at constant pressure. */
+  *Molecular_Weight;    /*!< \brief Molecular weight of an incompressible ideal gas (g/mol). */
+  unsigned short nMolecular_Weight; /*!< \brief Number of species molecular weights. */
+  su2double Specific_Heat_Cp, /*!< \brief Specific heat at constant pressure. */
   Specific_Heat_CpND,         /*!< \brief Non-dimensional specific heat at constant pressure. */
   Specific_Heat_Cv,           /*!< \brief Specific heat at constant volume. */
   Specific_Heat_CvND,         /*!< \brief Non-dimensional specific heat at constant volume. */
@@ -1013,7 +1018,6 @@ class CConfig {
   WINDOW_FUNCTION Kind_WindowFct;      /*!< \brief Type of window (weight) function for objective functional. */
   unsigned short Kind_HybridRANSLES;   /*!< \brief Kind of Hybrid RANS/LES. */
   unsigned short Kind_RoeLowDiss;      /*!< \brief Kind of Roe scheme with low dissipation for unsteady flows. */
-  bool QCR;                    /*!< \brief Spalart-Allmaras with Quadratic Constitutive Relation, 2000 version (SA-QCR2000) . */
 
   unsigned short nSpanWiseSections; /*!< \brief number of span-wise sections */
   unsigned short nSpanMaxAllZones;  /*!< \brief number of maximum span-wise sections for all zones */
@@ -1135,8 +1139,8 @@ class CConfig {
   unsigned short nScreenOutput,   /*!< \brief Number of screen output variables (max: 6). */
   nHistoryOutput, nVolumeOutput;  /*!< \brief Number of variables printed to the history file. */
   bool Multizone_Residual;        /*!< \brief Determines if memory should be allocated for the multizone residual. */
-
-  bool using_uq;                /*!< \brief Using uncertainty quantification with SST model */
+  SST_ParsedOptions sstParsedOptions; /*!< \brief Additional parameters for the SST turbulence model. */
+  SA_ParsedOptions saParsedOptions;   /*!< \brief Additional parameters for the SA turbulence model. */
   su2double uq_delta_b;         /*!< \brief Parameter used to perturb eigenvalues of Reynolds Stress Matrix */
   unsigned short eig_val_comp;  /*!< \brief Parameter used to determine type of eigenvalue perturbation */
   su2double uq_urlx;            /*!< \brief Under-relaxation factor */
@@ -1161,8 +1165,9 @@ class CConfig {
   unsigned short maxBasisDim,               /*!< \brief Maximum number of POD basis dimensions. */
   rom_save_freq;                            /*!< \brief Frequency of unsteady time steps to save. */
 
+  unsigned short nSpecies,                  /*!< \brief Number of transported species equations (for NEMO and species transport)*/
+
   /* other NEMO configure options*/
-  unsigned short nSpecies,                  /*!< \brief No of species present in flow */
   iWall_Catalytic,
   nWall_Catalytic;                          /*!< \brief No of catalytic walls */
   su2double *Gas_Composition,               /*!< \brief Initial mass fractions of flow [dimensionless] */
@@ -1183,7 +1188,6 @@ class CConfig {
   bool Species_StrongBC;           /*!< \brief Boolean whether strong BC's are used for in- outlet of the species solver. */
   su2double* Species_Init;         /*!< \brief Initial uniform value for scalar transport. */
   unsigned short nSpecies_Init;    /*!< \brief Number of entries of SPECIES_INIT */
-  unsigned short n_species;        /*!< \brief Number of species equations! Not species itself which would be 1 more. */
 
   /*!
    * \brief Set the default values of config options not set in the config file using another config object.
@@ -1605,7 +1609,7 @@ class CConfig {
    * \brief Get the value of the molecular weight for an incompressible ideal gas (g/mol).
    * \return Value of the molecular weight for an incompressible ideal gas (g/mol).
    */
-  su2double GetMolecular_Weight(void) const { return Molecular_Weight; }
+  su2double GetMolecular_Weight(unsigned short val_index = 0) const { return Molecular_Weight[val_index]; }
 
   /*!
    * \brief Get the value of specific heat at constant pressure.
@@ -2694,7 +2698,12 @@ class CConfig {
    * \brief Set the number of multigrid levels.
    * \param[in] val_nMGLevels - Index of the mesh were the CFL is applied
    */
-  void SetMGLevels(unsigned short val_nMGLevels) { nMGLevels = val_nMGLevels; }
+  void SetMGLevels(unsigned short val_nMGLevels) {
+    nMGLevels = val_nMGLevels;
+    if (MGCycle == FULLMG_CYCLE) {
+      SetFinestMesh(val_nMGLevels);
+    }
+  }
 
   /*!
    * \brief Get the index of the finest grid.
@@ -8975,12 +8984,6 @@ class CConfig {
    */
   bool GetPrintInlet_InterpolatedData(void) const { return PrintInlet_InterpolatedData; }
 
-  /*!
-   * \brief Get information about using UQ methodology
-   * \return <code>TRUE</code> means that UQ methodology of eigenspace perturbation will be used
-   */
-  bool GetUsing_UQ(void) const { return using_uq; }
-
   /*!
    * \brief Get the amount of eigenvalue perturbation to be done
    * \return Value of the uq_delta_b parameter
@@ -9058,11 +9061,6 @@ class CConfig {
    */
   su2double GetConst_DES(void) const { return Const_DES; }
 
-  /*!
-   * \brief Get QCR (SA-QCR2000).
-   */
-  bool GetQCR(void) const { return QCR;}
-
   /*!
    * \brief Get if AD preaccumulation should be performed.
    */
@@ -9617,10 +9615,22 @@ class CConfig {
    */
   unsigned short GetKind_Grad_Linear_Solver_Prec(void) const { return Kind_Grad_Linear_Solver_Prec; }
 
-    /*!
+  /*!
    * \brief Get max number of iterations of the for the gradient smoothing.
    * \return Max number of iterations of the linear solver for the gradient smoothing.
    */
   unsigned long GetGrad_Linear_Solver_Iter(void) const { return Grad_Linear_Solver_Iter; }
 
+  /*!
+   * \brief Get parsed SST option data structure.
+   * \return SST option data structure.
+   */
+  SST_ParsedOptions GetSSTParsedOptions() const { return sstParsedOptions; }
+
+  /*!
+   * \brief Get parsed SA option data structure.
+   * \return SA option data structure.
+   */
+  SA_ParsedOptions GetSAParsedOptions() const { return saParsedOptions; }
+
 };

Common/include/geometry/dual_grid/CPoint.hpp

@@ -70,6 +70,7 @@ class CPoint {
   su2vector<bool> Boundary;               /*!< \brief To see if a point belong to the boundary (including MPI). */
   su2vector<bool> PhysicalBoundary;       /*!< \brief To see if a point belong to the physical boundary (without includin MPI). */
   su2vector<bool> SolidBoundary;          /*!< \brief To see if a point belong to the physical boundary (without includin MPI). */
+  su2vector<bool> ViscousBoundary;        /*!< \brief To see if a point belong to the physical boundary (without includin MPI). */
   su2vector<bool> PeriodicBoundary;       /*!< \brief To see if a point belongs to a periodic boundary (without including MPI). */
 
   su2activematrix Coord;                  /*!< \brief vector with the coordinates of the node. */
@@ -351,6 +352,20 @@ class CPoint {
    */
   inline bool GetSolidBoundary(unsigned long iPoint) const { return SolidBoundary(iPoint); }
 
+  /*!
+   * \brief Set if a point belong to the boundary.
+   * \param[in] iPoint - Index of the point.
+   * \param[in] boundary - <code>TRUE</code> if the point belong to the physical boundary; otherwise <code>FALSE</code>.
+   */
+  inline void SetViscousBoundary(unsigned long iPoint, bool boundary) { ViscousBoundary(iPoint) = boundary; }
+
+  /*!
+   * \brief Provides information about if a point belong to the physical boundaries (without MPI).
+   * \param[in] iPoint - Index of the point.
+   * \return <code>TRUE</code> if the point belong to the boundary; otherwise <code>FALSE</code>.
+   */
+  inline bool GetViscousBoundary(unsigned long iPoint) const { return ViscousBoundary(iPoint); }
+
   /*!
    * \brief Set if a point belongs to a periodic boundary.
    * \param[in] iPoint - Index of the point.