Cleanup 2

Author: TobiKattmann

SU2_CFD/src/iteration/CDiscAdjFluidIteration.cpp

@@ -540,7 +540,7 @@ void CDiscAdjFluidIteration::SetDependencies(CSolver***** solver, CGeometry****
 
   SU2_OMP_PARALLEL_(if(solver[iZone][iInst][MESH_0][ADJFLOW_SOL]->GetHasHybridParallel())) {
 
-  /*--- Compute coupling between flow and turbulent equations ---*/
+  /*--- Compute coupling between flow, turbulent and species equations ---*/
   solver[iZone][iInst][MESH_0][FLOW_SOL]->Preprocessing(geometry[iZone][iInst][MESH_0], solver[iZone][iInst][MESH_0],
                                                         config[iZone], MESH_0, NO_RK_ITER, RUNTIME_FLOW_SYS, true);
   solver[iZone][iInst][MESH_0][FLOW_SOL]->InitiateComms(geometry[iZone][iInst][MESH_0], config[iZone], SOLUTION);

SU2_CFD/src/numerics/species/species_sources.cpp

@@ -1,7 +1,7 @@
 /*!
- * \file turb_sources.cpp
+ * \file species_sources.cpp
  * \brief Implementation of numerics classes for integration of
- *        turbulence source-terms.
+ *        species transport source-terms.
  * \author T. Kattmann
  * \version 7.2.1 "Blackbird"
  *

SU2_CFD/src/output/CFlowIncOutput.cpp

@@ -393,7 +393,6 @@ void CFlowIncOutput::LoadVolumeData(CConfig *config, CGeometry *geometry, CSolve
     Node_Heat = solver[HEAT_SOL]->GetNodes();
   }
 
-
   LoadCoordinates(Node_Geo->GetCoord(iPoint), iPoint);
 
   SetVolumeOutputValue("PRESSURE",   iPoint, Node_Flow->GetSolution(iPoint, 0));
@@ -448,7 +447,7 @@ void CFlowIncOutput::LoadVolumeData(CConfig *config, CGeometry *geometry, CSolve
       SetVolumeOutputValue("LIMITER_TEMPERATURE", iPoint, Node_Flow->GetLimiter_Primitive(iPoint, nDim+1));
   }
 
-  // All turbulence outputs.
+  // All turbulence and species outputs.
   LoadVolumeData_Scalar(config, solver, geometry, iPoint);
 
   // Streamwise Periodicity

SU2_CFD/src/output/CFlowOutput.cpp

@@ -74,7 +74,7 @@ void CFlowOutput::AddAnalyzeSurfaceOutput(const CConfig *config){
   for (unsigned short iVar = 0; iVar < config->GetnSpecies(); iVar++) {
     AddHistoryOutput("SURFACE_SPECIES_" + std::to_string(iVar), "Avg_Species_" + std::to_string(iVar), ScreenOutputFormat::FIXED, "SPECIES_COEFF", "Total average species " + std::to_string(iVar) + " on all markers set in MARKER_ANALYZE", HistoryFieldType::COEFFICIENT);
   }
-  /// DESCRIPTION: Average Species
+  /// DESCRIPTION: Species Variance
   AddHistoryOutput("SURFACE_SPECIES_VARIANCE", "Species_Variance", ScreenOutputFormat::SCIENTIFIC, "SPECIES_COEFF", "Total species variance, measure for mixing quality. On all markers set in MARKER_ANALYZE", HistoryFieldType::COEFFICIENT);
   /// END_GROUP
 
@@ -114,7 +114,7 @@ void CFlowOutput::AddAnalyzeSurfaceOutput(const CConfig *config){
   for (unsigned short iVar = 0; iVar < config->GetnSpecies(); iVar++) {
     AddHistoryOutputPerSurface("SURFACE_SPECIES_" + std::to_string(iVar), "Avg_Species_" + std::to_string(iVar), ScreenOutputFormat::FIXED, "SPECIES_COEFF_SURF", Marker_Analyze, HistoryFieldType::COEFFICIENT);
   }
-  /// DESCRIPTION: Average Species
+  /// DESCRIPTION: Species Variance
   AddHistoryOutputPerSurface("SURFACE_SPECIES_VARIANCE", "Species_Variance", ScreenOutputFormat::SCIENTIFIC, "SPECIES_COEFF_SURF", Marker_Analyze, HistoryFieldType::COEFFICIENT);
   /// END_GROUP
 }
@@ -632,7 +632,10 @@ void CFlowOutput::SetAnalyzeSurface(const CSolver* const*solver, const CGeometry
   std::cout << std::resetiosflags(std::cout.flags());
 }
 
-void CFlowOutput::SetAnalyzeSurface_SpeciesVariance(const CSolver* const*solver, const CGeometry *geometry, CConfig *config, su2activematrix Surface_Species_Total, vector<su2double> Surface_MassFlow_Abs_Total, vector<su2double> Surface_Area_Total) {
+void CFlowOutput::SetAnalyzeSurface_SpeciesVariance(const CSolver* const*solver, const CGeometry *geometry,
+                                                    CConfig *config, su2activematrix Surface_Species_Total,
+                                                    vector<su2double> Surface_MassFlow_Abs_Total,
+                                                    vector<su2double> Surface_Area_Total) {
 
   const unsigned short nMarker      = config->GetnMarker_All();
   const unsigned short nDim         = geometry->GetnDim();
@@ -668,9 +671,6 @@ void CFlowOutput::SetAnalyzeSurface_SpeciesVariance(const CSolver* const*solver,
 
         if (geometry->nodes->GetDomain(iPoint)) {
 
-          su2double Vector[3];
-          geometry->vertex[iMarker][iVertex]->GetNormal(Vector);
-
           su2double AxiFactor = 0.0;
           if (axisymmetric) {
             if (geometry->nodes->GetCoord(iPoint, 1) != 0.0)
@@ -691,15 +691,15 @@ void CFlowOutput::SetAnalyzeSurface_SpeciesVariance(const CSolver* const*solver,
             AxiFactor = 1.0;
           }
 
+          su2double Vector[3];
+          geometry->vertex[iMarker][iVertex]->GetNormal(Vector);
           const su2double Density = flow_nodes->GetDensity(iPoint);
           su2double Area = 0.0;
           su2double MassFlow = 0.0;
-          su2double Velocity[3];
 
           for (unsigned short iDim = 0; iDim < nDim; iDim++) {
             Area += (Vector[iDim] * AxiFactor) * (Vector[iDim] * AxiFactor);
-            Velocity[iDim] = flow_nodes->GetVelocity(iPoint,iDim);
-            MassFlow += Vector[iDim] * AxiFactor * Density * Velocity[iDim];
+            MassFlow += Vector[iDim] * AxiFactor * Density * flow_nodes->GetVelocity(iPoint,iDim);
           }
           Area= sqrt(Area);
 

SU2_CFD/src/solvers/CSpeciesSolver.cpp

@@ -59,42 +59,41 @@ CSpeciesSolver::CSpeciesSolver(CGeometry* geometry, CConfig* config, unsigned sh
   nDim = geometry->GetnDim();
 
   /*--- Single grid simulation ---*/
-  /*--- do not see a reason to use only single grid ---*/
-  // if (iMesh == MESH_0) {
-
-  /*--- Define some auxiliary vector related with the residual ---*/
-
-  Residual_RMS.resize(nVar, 0.0);
-  Residual_Max.resize(nVar, 0.0);
-  Point_Max.resize(nVar, 0);
-  Point_Max_Coord.resize(nVar, nDim) = su2double(0.0);
-
-  /*--- Initialize the BGS residuals in multizone problems. ---*/
-  if (config->GetMultizone_Problem()) {
-    Residual_BGS.resize(nVar, 0.0);
-    Residual_Max_BGS.resize(nVar, 0.0);
-    Point_Max_BGS.resize(nVar, 0);
-    Point_Max_Coord_BGS.resize(nVar, nDim) = su2double(0.0);
-  }
 
-  /*--- Initialization of the structure of the whole Jacobian ---*/
+  if (iMesh == MESH_0 || config->GetMGCycle() == FULLMG_CYCLE) {
 
-  if (rank == MASTER_NODE) cout << "Initialize Jacobian structure (passive scalar model)." << endl;
-  Jacobian.Initialize(nPoint, nPointDomain, nVar, nVar, true, geometry, config, ReducerStrategy);
+    /*--- Define some auxiliary vector related with the residual ---*/
 
-  if (config->GetKind_Linear_Solver_Prec() == LINELET) {
-    const auto nLineLets = Jacobian.BuildLineletPreconditioner(geometry, config);
-    if (rank == MASTER_NODE)
-      cout << "Compute linelet structure. " << nLineLets << " elements in each line (average)." << endl;
-  }
+    Residual_RMS.resize(nVar, 0.0);
+    Residual_Max.resize(nVar, 0.0);
+    Point_Max.resize(nVar, 0);
+    Point_Max_Coord.resize(nVar, nDim) = su2double(0.0);
+
+    /*--- Initialize the BGS residuals in multizone problems. ---*/
+    if (config->GetMultizone_Problem()) {
+      Residual_BGS.resize(nVar, 0.0);
+      Residual_Max_BGS.resize(nVar, 0.0);
+      Point_Max_BGS.resize(nVar, 0);
+      Point_Max_Coord_BGS.resize(nVar, nDim) = su2double(0.0);
+    }
 
-  LinSysSol.Initialize(nPoint, nPointDomain, nVar, 0.0);
-  LinSysRes.Initialize(nPoint, nPointDomain, nVar, 0.0);
-  System.SetxIsZero(true);
+    /*--- Initialization of the structure of the whole Jacobian ---*/
 
-  if (ReducerStrategy) EdgeFluxes.Initialize(geometry->GetnEdge(), geometry->GetnEdge(), nVar, nullptr);
+    if (rank == MASTER_NODE) cout << "Initialize Jacobian structure (passive scalar model)." << endl;
+    Jacobian.Initialize(nPoint, nPointDomain, nVar, nVar, true, geometry, config, ReducerStrategy);
 
-  //} //iMESH_0
+    if (config->GetKind_Linear_Solver_Prec() == LINELET) {
+      const auto nLineLets = Jacobian.BuildLineletPreconditioner(geometry, config);
+      if (rank == MASTER_NODE)
+        cout << "Compute linelet structure. " << nLineLets << " elements in each line (average)." << endl;
+    }
+
+    LinSysSol.Initialize(nPoint, nPointDomain, nVar, 0.0);
+    LinSysRes.Initialize(nPoint, nPointDomain, nVar, 0.0);
+    System.SetxIsZero(true);
+
+    if (ReducerStrategy) EdgeFluxes.Initialize(geometry->GetnEdge(), geometry->GetnEdge(), nVar, nullptr);
+  }
 
   /*--- Initialize lower and upper limits---*/
 
@@ -376,9 +375,7 @@ void CSpeciesSolver::BC_Inlet(CGeometry* geometry, CSolver** solver_container, C
 
       conv_numerics->SetPrimitive(V_domain, V_inlet);
 
-      /*--- Set the turbulent variable states. Use free-stream SST
-      values for the turbulent state at the inflow. ---*/
-      /*--- Load the inlet turbulence variables (uniform by default). ---*/
+      /*--- Set the species variable state at the inlet. ---*/
 
       conv_numerics->SetScalarVar(nodes->GetSolution(iPoint), Inlet_SpeciesVars[val_marker][iVertex]);
 

SU2_CFD/src/variables/CSpeciesVariable.cpp

@@ -33,7 +33,6 @@ CSpeciesVariable::CSpeciesVariable(const su2double* species_inf, unsigned long n
   /*--- Allocate space for the mass diffusivity. ---*/
   Diffusivity.resize(nPoint, nVar) = su2double(0.0);
 
-  /// NOTE TK: Consistent with SST and SA.
   for (unsigned long iPoint = 0; iPoint < nPoint; iPoint++)
     for (unsigned long iVar = 0; iVar < nVar; iVar++)
       Solution(iPoint, iVar) = species_inf[iVar];

TestCases/species_transport/passive_transport_validation/passive_transport.cfg

@@ -40,9 +40,8 @@ SLOPE_LIMITER_SPECIES= NONE
 %
 TIME_DISCRE_SPECIES= EULER_IMPLICIT
 %
-% Scalar clipping
-SPECIES_CLIPPING= YES
 SPECIES_INIT = 0
+SPECIES_CLIPPING= YES
 SPECIES_CLIPPING_MIN= 0.0
 SPECIES_CLIPPING_MAX= 1.0
 %
@@ -90,7 +89,6 @@ CONV_STARTITER= 10
 %
 % ------------------------- INPUT/OUTPUT INFORMATION --------------------------%
 %
-% Mesh input file
 MESH_FILENAME = rectangle_mixing.su2
 %
 SCREEN_OUTPUT = INNER_ITER WALL_TIME RMS_PRESSURE RMS_VELOCITY-X RMS_VELOCITY-Y RMS_SPECIES_0 LINSOL_ITER LINSOL_RESIDUAL LINSOL_ITER_SPECIES LINSOL_RESIDUAL_SPECIES