Delete intermediate comments. Smaller fixes.

Author: TobiKattmann

Common/include/option_structure.hpp

@@ -76,7 +76,7 @@ const unsigned int MAX_PARAMETERS = 10;       /*!< \brief Maximum number of para
 const unsigned int MAX_NUMBER_PERIODIC = 10;  /*!< \brief Maximum number of periodic boundary conditions. */
 const unsigned int MAX_STRING_SIZE = 200;     /*!< \brief Maximum number of domains. */
 const unsigned int MAX_NUMBER_FFD = 15;       /*!< \brief Maximum number of FFDBoxes for the FFD. */
-enum: unsigned int{MAX_SOLS = 12};            /*!< \brief Maximum number of solutions at the same time (dimension of solution container array). */
+enum: unsigned int{MAX_SOLS = 13};            /*!< \brief Maximum number of solutions at the same time (dimension of solution container array). */
 const unsigned int MAX_TERMS = 6;             /*!< \brief Maximum number of terms in the numerical equations (dimension of solver container array). */
 const unsigned int MAX_ZONES = 3;             /*!< \brief Maximum number of zones. */
 const unsigned int MAX_FE_KINDS = 4;          /*!< \brief Maximum number of Finite Elements. */
@@ -943,21 +943,16 @@ static const MapType<std::string, ENUM_TRANS_MODEL> Trans_Model_Map = {
   MakePair("BC", BC)
 };
 
-/// NOTE TK:: consolidate these options. Just copied for now.
 /*!
  * \brief types of species transport models
  */
 enum class SPECIES_MODEL {
   NONE,              /*!< \brief No scalar transport model. */
   PASSIVE_SCALAR,    /*!< \brief Passive scalar transport model. */
-  PROGRESS_VARIABLE, /*!< \brief Progress variable combustion model. */
-  CUSTOM_SCALAR,     /*!< \brief Custom scalar transport model. */
 };
 static const MapType<std::string, SPECIES_MODEL> Species_Model_Map = {
   MakePair("NONE", SPECIES_MODEL::NONE)
   MakePair("PASSIVE_SCALAR", SPECIES_MODEL::PASSIVE_SCALAR)
-  MakePair("PROGRESS_VARIABLE", SPECIES_MODEL::PROGRESS_VARIABLE)
-  MakePair("CUSTOM_SCALAR", SPECIES_MODEL::CUSTOM_SCALAR)
 };
 
 /*!

Common/src/CConfig.cpp

@@ -1719,7 +1719,7 @@ void CConfig::SetConfig_Options() {
   addEnumOption("TIME_DISCRE_TURB", Kind_TimeIntScheme_Turb, Time_Int_Map, EULER_IMPLICIT);
   /* DESCRIPTION: Time discretization */
   addEnumOption("TIME_DISCRE_ADJTURB", Kind_TimeIntScheme_AdjTurb, Time_Int_Map, EULER_IMPLICIT);
-  /* DESCRIPTION: Time discretization */
+  /* DESCRIPTION: Time discretization for species equations */
   addEnumOption("TIME_DISCRE_SPECIES", Kind_TimeIntScheme_Species, Time_Int_Map, EULER_IMPLICIT);
   /* DESCRIPTION: Time discretization */
   addEnumOption("TIME_DISCRE_FEA", Kind_TimeIntScheme_FEA, Time_Int_Map_FEA, STRUCT_TIME_INT::NEWMARK_IMPLICIT);
@@ -1911,7 +1911,7 @@ void CConfig::SetConfig_Options() {
   addBoolOption("MUSCL_SPECIES", MUSCL_Species, false);
   /*!\brief SLOPE_LIMITER_SPECIES \n DESCRIPTION: Slope limiter \n OPTIONS: See \link Limiter_Map \endlink \n DEFAULT NO_LIMITER \ingroup Config*/
   addEnumOption("SLOPE_LIMITER_SPECIES", Kind_SlopeLimit_Species, Limiter_Map, NO_LIMITER);
-  /*!\brief CONV_NUM_METHOD_SPECIES \n DESCRIPTION: Convective numerical method \ingroup Config*/
+  /*!\brief CONV_NUM_METHOD_SPECIES \n DESCRIPTION: Convective numerical method for species transport \ingroup Config*/
   addConvectOption("CONV_NUM_METHOD_SPECIES", Kind_ConvNumScheme_Species, Kind_Centered_Species, Kind_Upwind_Species);
 
   /*!\brief MUSCL_FLOW \n DESCRIPTION: Check if the MUSCL scheme should be used \ingroup Config*/
@@ -8300,7 +8300,6 @@ void CConfig::SetGlobalParam(unsigned short val_solver,
         SetKind_TimeIntScheme(Kind_TimeIntScheme_Flow);
       }
       if (val_system == RUNTIME_SPECIES_SYS) {
-        /// NOTE TK:: Why do we need this. The old impl also has this for Euler ... does that even make sense to have species transport in invicous flow?
         SetKind_ConvNumScheme(Kind_ConvNumScheme_Species, Kind_Centered_Species,
                               Kind_Upwind_Species, Kind_SlopeLimit_Species,
                               MUSCL_Species, NONE);

SU2_CFD/src/drivers/CDriver.cpp

@@ -1362,16 +1362,15 @@ void CDriver::InstantiateSpeciesNumerics(unsigned short nVar_Species, int offset
   /*--- Definition of the viscous scheme for each equation and mesh level ---*/
 
   for (auto iMGlevel = 0u; iMGlevel <= config->GetnMGLevels(); iMGlevel++) {
-    /// NOTE TK:: understand the "true" input. Correction of the gradient when to apply and when not. True for now as Turb does that as well. Maybe no correction available on boundaries.
     numerics[iMGlevel][SPECIES_SOL][visc_term] = new CAvgGrad_Species<Indices>(nDim, nVar_Species, true, config);
     numerics[iMGlevel][SPECIES_SOL][visc_bound_term] = new CAvgGrad_Species<Indices>(nDim, nVar_Species, false, config);
   }
 
   /*--- Definition of the source term integration scheme for each equation and mesh level ---*/
 
   for (auto iMGlevel = 0u; iMGlevel <= config->GetnMGLevels(); iMGlevel++) {
-    if (config->GetAxisymmetric() == YES) { //TK:: not implemented yet
-      numerics[iMGlevel][SPECIES_SOL][source_first_term] = new CSourceAxisymmetric_Species<Indices>(nDim, nVar_Species, config); //TK::how to get nVarFLow
+    if (config->GetAxisymmetric() == YES) {
+      numerics[iMGlevel][SPECIES_SOL][source_first_term] = new CSourceAxisymmetric_Species<Indices>(nDim, nVar_Species, config);
     }
     else {
       numerics[iMGlevel][SPECIES_SOL][source_first_term] = new CSourceNothing(nDim, nVar_Species, config);

SU2_CFD/src/solvers/CDiscAdjSolver.cpp

@@ -96,6 +96,9 @@ CDiscAdjSolver::CDiscAdjSolver(CGeometry *geometry, CConfig *config, CSolver *di
   case RUNTIME_TURB_SYS:
     SolverName = "ADJ.TURB";
     break;
+  case RUNTIME_SPECIES_SYS:
+    SolverName = "ADJ.SPECIES";
+    break;
   case RUNTIME_RADIATION_SYS:
     SolverName = "ADJ.RAD";
     break;
@@ -602,10 +605,16 @@ void CDiscAdjSolver::LoadRestart(CGeometry **geometry, CSolver ***solver, CConfi
   unsigned short skipVars = geometry[MESH_0]->GetnDim();
 
   /*--- Skip flow adjoint variables ---*/
-  if (KindDirect_Solver== RUNTIME_TURB_SYS) {
+  if (KindDirect_Solver == RUNTIME_TURB_SYS) {
     skipVars += nDim + 2;
   }
 
+  if (KindDirect_Solver == RUNTIME_SPECIES_SYS) {
+    // Skip the number of Flow Vars and Turb Vars to get to the adjoint species vars
+    skipVars += nDim + 2;
+    if (rans) skipVars += solver[MESH_0][TURB_SOL]->GetnVar();
+  }
+
   /*--- Skip flow adjoint and turbulent variables ---*/
   if (KindDirect_Solver == RUNTIME_RADIATION_SYS) {
     skipVars += nDim + 2;

SU2_CFD/src/solvers/CSolver.cpp

@@ -3637,9 +3637,6 @@ void CSolver::LoadInletProfile(CGeometry **geometry,
           columnValue << config->GetInlet_SpeciesVal(Marker_Tag)[iVar] << "\t";
         }
         break;
-      case SPECIES_MODEL::CUSTOM_SCALAR: case SPECIES_MODEL::PROGRESS_VARIABLE:
-        SU2_MPI::Error("Unsupported Species model for inlet files.", CURRENT_FUNCTION);
-        break;
     }
 
     columnNames.push_back(columnName.str());

SU2_CFD/src/solvers/CSpeciesSolver.cpp

@@ -127,7 +127,6 @@ CSpeciesSolver::CSpeciesSolver(CGeometry* geometry, CConfig* config, unsigned sh
   nodes = new CSpeciesVariable(Species_Inf, nPoint, nDim, nVar, config);
   SetBaseClassPointerToNodes();
 
-  /// NOTE TK:: This should use a MassDiff model!
   /*--- Initialize the mass diffusivity ---*/
   SU2_OMP_FOR_STAT(omp_chunk_size)
   for (unsigned long iPoint = 0; iPoint < nPoint; iPoint++) {
@@ -143,8 +142,6 @@ CSpeciesSolver::CSpeciesSolver(CGeometry* geometry, CConfig* config, unsigned sh
   InitiateComms(geometry, config, SOLUTION);
   CompleteComms(geometry, config, SOLUTION);
 
-  /// NOTE TK:: Hinder sliding mesh in cfg postprocessing
-
   /*--- Set the column number for species in inlet-files.
    * e.g. Coords(nDim), Temp(1), VelMag(1), Normal(nDim), Turb(1 or 2), Species(arbitrary) ---*/
   Inlet_Position = nDim + 2 + nDim + config->GetnTurbVar();
@@ -224,7 +221,8 @@ void CSpeciesSolver::LoadRestart(CGeometry** geometry, CSolver*** solver, CConfi
          offset in the buffer of data from the restart file and load it. ---*/
 
         const auto index = counter * Restart_Vars[1] + skipVars;
-        for (auto iVar = 0u; iVar < nVar; iVar++) nodes->SetSolution(iPoint_Local, iVar, Restart_Data[index + iVar]);
+        for (auto iVar = 0u; iVar < nVar; iVar++)
+          nodes->SetSolution(iPoint_Local, iVar, Restart_Data[index + iVar]);
 
         /*--- Increment the overall counter for how many points have been loaded. ---*/
         counter++;
@@ -289,9 +287,10 @@ void CSpeciesSolver::LoadRestart(CGeometry** geometry, CSolver*** solver, CConfi
                                            false);
 
     if (config->GetKind_Turb_Model() != TURB_MODEL::NONE)
-      solver[MESH_0][TURB_SOL]->Postprocessing(geometry[MESH_0], solver[MESH_0], config, MESH_0);
+      solver[iMesh][TURB_SOL]->Postprocessing(geometry[MESH_0], solver[MESH_0], config, MESH_0);
 
-    solver[iMesh][SPECIES_SOL]->Postprocessing(geometry[iMesh], solver[iMesh], config, iMesh);
+    solver[iMesh][SPECIES_SOL]->Preprocessing(geometry[MESH_0], solver[MESH_0], config, MESH_0, NO_RK_ITER,
+                                              RUNTIME_FLOW_SYS, false);
   }
 
   /*--- Go back to single threaded execution. ---*/
@@ -313,8 +312,7 @@ void CSpeciesSolver::Preprocessing(CGeometry* geometry, CSolver** solver_contain
 
   SU2_OMP_FOR_STAT(omp_chunk_size)
   for (auto iPoint = 0u; iPoint < nPoint; iPoint++) {
-    /// NOTE TK:: needs to be value by a model
-    const su2double mass_diffusivity = config->GetDiffusivity_Constant();
+    const su2double mass_diffusivity = config->GetDiffusivity_Constant(); //TK:: ND
 
     for (auto iVar = 0u; iVar < nVar; iVar++) {
       nodes->SetDiffusivity(iPoint, mass_diffusivity, iVar);
@@ -370,9 +368,6 @@ void CSpeciesSolver::Viscous_Residual(unsigned long iEdge, CGeometry* geometry,
 
 void CSpeciesSolver::BC_Inlet(CGeometry* geometry, CSolver** solver_container, CNumerics* conv_numerics,
                               CNumerics* visc_numerics, CConfig* config, unsigned short val_marker) {
-
-  /// NOTE TK:: This is a strong impl whereas TurbSA and inceuler implement a weak version. Testing required.
-  // bool grid_movement  = config->GetGrid_Movement();
   string Marker_Tag = config->GetMarker_All_TagBound(val_marker);
 
   /*--- Loop over all the vertices on this boundary marker ---*/
@@ -530,7 +525,6 @@ void CSpeciesSolver::BC_Outlet(CGeometry* geometry, CSolver** solver_container,
     if (!geometry->nodes->GetDomain(iPoint)) continue;
 
     if (config->GetSpecies_StrongBC()) {
-      //TK:: document how this works
       /*--- Allocate the value at the outlet ---*/
       auto Point_Normal = geometry->vertex[val_marker][iVertex]->GetNormal_Neighbor();
 

SU2_CFD/src/variables/CSpeciesVariable.cpp

@@ -31,7 +31,7 @@ CSpeciesVariable::CSpeciesVariable(const su2double* species_inf, unsigned long n
                                    unsigned long nvar, const CConfig* config)
     : CScalarVariable(npoint, ndim, nvar, config) {
   /*--- Allocate space for the mass diffusivity. ---*/
-  Diffusivity.resize(nPoint, nVar) = su2double(0.0);  /// TK:: more appropriate init here possible?
+  Diffusivity.resize(nPoint, nVar) = su2double(0.0);
 
   /// NOTE TK: Consistent with SST and SA.
   for (unsigned long iPoint = 0; iPoint < nPoint; iPoint++)
@@ -40,8 +40,6 @@ CSpeciesVariable::CSpeciesVariable(const su2double* species_inf, unsigned long n
 
   Solution_Old = Solution;
 
-  /// NOTE TK:: check everything below whether that is necessary. SA does it, but SST not. Maybe put into ScalarVar
-
   /*--- Allocate and initialize solution for the dual time strategy ---*/
   bool dual_time = ((config->GetTime_Marching() == TIME_MARCHING::DT_STEPPING_1ST) ||
                     (config->GetTime_Marching() == TIME_MARCHING::DT_STEPPING_2ND));