Merge branch 'develop' into reduce_disc_adj_mem

Author: pcarruscag

.gitmodules

@@ -12,3 +12,6 @@
 [submodule "externals/meson"]
 	path = externals/meson
 	url = https://github.com/mesonbuild/meson
+[submodule "subprojects/Mutationpp"]
+        path = subprojects/Mutationpp
+        url = https://github.com/mutationpp/Mutationpp.git	

Common/include/CConfig.hpp

@@ -735,7 +735,8 @@ class CConfig {
   unsigned short Tab_FileFormat;      /*!< \brief Format of the output files. */
   unsigned short ActDisk_Jump;        /*!< \brief Format of the output files. */
   unsigned long StartWindowIteration; /*!< \brief Starting Iteration for long time Windowing apporach . */
-  bool CFL_Adapt;        /*!< \brief Adaptive CFL number. */
+  unsigned short nCFL_AdaptParam;     /*!< \brief Number of CFL parameters provided in config. */
+  bool CFL_Adapt;        /*!< \brief Use adaptive CFL number. */
   bool HB_Precondition;  /*!< \brief Flag to turn on harmonic balance source term preconditioning */
   su2double RefArea,     /*!< \brief Reference area for coefficient computation. */
   RefElemLength,         /*!< \brief Reference element length for computing the slope limiting epsilon. */
@@ -762,7 +763,6 @@ class CConfig {
   Solution_FileName,             /*!< \brief 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. */
   Conv_FileName,                 /*!< \brief Convergence history output file. */
   Breakdown_FileName,            /*!< \brief Breakdown output file. */
   Restart_FileName,              /*!< \brief Restart file for flow variables. */
@@ -1056,10 +1056,10 @@ class CConfig {
   bool Radiation;                      /*!< \brief Determines if a radiation model is incorporated. */
   su2double CFL_Rad;                   /*!< \brief CFL Number for the radiation solver. */
 
+  array<su2double,5> default_cfl_adapt;  /*!< \brief Default CFL adapt param array for the COption class. */
   su2double default_vel_inf[3],  /*!< \brief Default freestream velocity array for the COption class. */
   default_eng_cyl[7],            /*!< \brief Default engine box array for the COption class. */
   default_eng_val[5],            /*!< \brief Default engine box array values for the COption class. */
-  default_cfl_adapt[4],          /*!< \brief Default CFL adapt param array for the COption class. */
   default_jst_coeff[2],          /*!< \brief Default artificial dissipation (flow) array for the COption class. */
   default_ffd_coeff[3],          /*!< \brief Default artificial dissipation (flow) array for the COption class. */
   default_mixedout_coeff[3],     /*!< \brief Default default mixedout algorithm coefficients for the COption class. */
@@ -1538,13 +1538,6 @@ class CConfig {
    */
   su2double GetCFL_AdaptParam(unsigned short val_index) const { return CFL_AdaptParam[val_index]; }
 
-  /*!
-   * \brief Set the values of the CFL adaption parameters.
-   * \param[in] val_index     - Index of the particular CFL adaption parameter
-   * \param[in] val_cfl_param - Value of the CFL adaption parameter
-   */
-  void SetCFL_AdaptParam(unsigned short val_index, su2double val_cfl_param) { CFL_AdaptParam[val_index] = val_cfl_param; }
-
   /*!
    * \brief Get the value of the CFL adaption flag.
    * \return <code>TRUE</code> if CFL adaption is active; otherwise <code>FALSE</code>.
@@ -3652,7 +3645,7 @@ class CConfig {
    * \brief Gas model that we are using.
    * \return Gas model that we are using.
    */
-  string GetGasModel (void) const {return GasModel;}
+  string GetGasModel(void) const {return GasModel;}
 
   /*!
    * \brief Get the transport coefficient model.
@@ -5208,12 +5201,6 @@ class CConfig {
    */
   string GetSolution_AdjFileName(void) const { return Solution_AdjFileName; }
 
-  /*!
-   * \brief Get the name of the file with the residual of the problem.
-   * \return Name of the file with the residual of the problem.
-   */
-  string GetResidual_FileName(void);
-
   /*!
    * \brief Get the format of the input/output grid.
    * \return Format of the input/output grid.

Common/include/adt/CADTElemClass.hpp

@@ -400,4 +400,4 @@ class CADTElemClass : public CADTBaseClass {
    */
   CADTElemClass() = delete;
 
-};
+};

Common/include/fem/fem_standard_element.hpp

@@ -1767,4 +1767,4 @@ class CFEMStandardBoundaryFace : public CFEMStandardElementBase {
   * \param[in] other - Object, whose data is copied.
   */
   void Copy(const CFEMStandardBoundaryFace &other);
-};
+};

Common/include/option_structure.hpp

@@ -94,7 +94,7 @@ const unsigned int INST_0 = 0;  /*!< \brief Definition of the first instance per
 
 const su2double STANDARD_GRAVITY = 9.80665;           /*!< \brief Acceleration due to gravity at surface of earth. */
 const su2double UNIVERSAL_GAS_CONSTANT = 8.3144598;   /*!< \brief Universal gas constant in J/(mol*K) */
-const su2double BOLTZMANN_CONSTANT = 1.3806503E-23; /*! \brief Boltzmann's constant [J K^-1] */
+const su2double BOLTZMANN_CONSTANT = 1.3806503E-23;   /*! \brief Boltzmann's constant [J K^-1] */
 const su2double AVOGAD_CONSTANT = 6.0221415E26; /*!< \brief Avogardro's constant, number of particles in one kmole. */
 
 const su2double EPS = 1.0E-16;        /*!< \brief Error scale. */
@@ -541,9 +541,9 @@ enum ENUM_FLUIDMODEL {
   PR_GAS = 3,             /*!< \brief Perfect Real gas model. */
   CONSTANT_DENSITY = 4,   /*!< \brief Constant density gas model. */
   INC_IDEAL_GAS = 5,      /*!< \brief Incompressible ideal gas model. */
-  INC_IDEAL_GAS_POLY = 6,  /*!< \brief Inc. ideal gas, polynomial gas model. */
+  INC_IDEAL_GAS_POLY = 6, /*!< \brief Inc. ideal gas, polynomial gas model. */
   MUTATIONPP = 7,         /*!< \brief Mutation++ gas model for nonequilibrium flow. */
-  USER_DEFINED_NONEQ = 8        /*!< \brief User defined gas model for nonequilibrium flow. */
+  SU2_NONEQ = 8           /*!< \brief User defined gas model for nonequilibrium flow. */
 };
 static const MapType<string, ENUM_FLUIDMODEL> FluidModel_Map = {
   MakePair("STANDARD_AIR", STANDARD_AIR)
@@ -554,7 +554,7 @@ static const MapType<string, ENUM_FLUIDMODEL> FluidModel_Map = {
   MakePair("INC_IDEAL_GAS", INC_IDEAL_GAS)
   MakePair("INC_IDEAL_GAS_POLY", INC_IDEAL_GAS_POLY)
   MakePair("MUTATIONPP", MUTATIONPP)
-  MakePair("USER_DEFINED_NONEQ", USER_DEFINED_NONEQ)
+  MakePair("SU2_NONEQ", SU2_NONEQ)
 };
 
 /*!

Common/src/CConfig.cpp

@@ -1162,8 +1162,6 @@ void CConfig::SetConfig_Options() {
   addBoolOption("IONIZATION", ionization, false);
   /* DESCRIPTION: Specify if there is VT transfer residual limiting */
   addBoolOption("VT_RESIDUAL_LIMITING", vt_transfer_res_limit, false);
-  /* DESCRIPTION: Specify if the gas is monoatomic */
-  addBoolOption("MONOATOMIC", monoatomic, false);
   /* DESCRIPTION: List of catalytic walls */
   addStringListOption("CATALYTIC_WALL", nWall_Catalytic, Wall_Catalytic);
   /*!\brief MARKER_MONITORING\n DESCRIPTION: Marker(s) of the surface where evaluate the non-dimensional coefficients \ingroup Config*/
@@ -1620,11 +1618,12 @@ void CConfig::SetConfig_Options() {
   /* DESCRIPTION: Activate The adaptive CFL number. */
   addBoolOption("CFL_ADAPT", CFL_Adapt, false);
   /* !\brief CFL_ADAPT_PARAM
-   * DESCRIPTION: Parameters of the adaptive CFL number (factor down, factor up, CFL limit (min and max) )
+   * DESCRIPTION: Parameters of the adaptive CFL number (factor down, factor up, CFL limit (min and max), acceptable linear residual )
    * Factor down generally <1.0, factor up generally > 1.0 to cause the CFL to increase when the under-relaxation parameter is 1.0
    * and to decrease when the under-relaxation parameter is less than 0.1. Factor is multiplicative. \ingroup Config*/
   default_cfl_adapt[0] = 1.0; default_cfl_adapt[1] = 1.0; default_cfl_adapt[2] = 10.0; default_cfl_adapt[3] = 100.0;
-  addDoubleArrayOption("CFL_ADAPT_PARAM", 4, CFL_AdaptParam, default_cfl_adapt);
+  default_cfl_adapt[4] = 0.001;
+  addDoubleListOption("CFL_ADAPT_PARAM", nCFL_AdaptParam, CFL_AdaptParam);
   /* DESCRIPTION: Reduction factor of the CFL coefficient in the adjoint problem */
   addDoubleOption("CFL_REDUCTION_ADJFLOW", CFLRedCoeff_AdjFlow, 0.8);
   /* DESCRIPTION: Reduction factor of the CFL coefficient in the level set problem */
@@ -2785,7 +2784,6 @@ void CConfig::SetConfig_Options() {
 
   /* DESCRIPTION: Size of the edge groups colored for thread parallel edge loops (0 forces the reducer strategy). */
   addUnsignedLongOption("EDGE_COLORING_GROUP_SIZE", edgeColorGroupSize, 512);
-
   /* END_CONFIG_OPTIONS */
 
 }
@@ -3174,7 +3172,7 @@ void CConfig::SetPostprocessing(unsigned short val_software, unsigned short val_
                     (Kind_FluidModel == INC_IDEAL_GAS_POLY) ||
                     (Kind_FluidModel == CONSTANT_DENSITY));
   bool noneq_gas = ((Kind_FluidModel == MUTATIONPP) ||
-                    (Kind_FluidModel == USER_DEFINED_NONEQ));
+                    (Kind_FluidModel == SU2_NONEQ));
   bool standard_air = ((Kind_FluidModel == STANDARD_AIR));
   bool nemo = GetNEMOProblem();
 
@@ -3539,10 +3537,6 @@ void CConfig::SetPostprocessing(unsigned short val_software, unsigned short val_
     SU2_MPI::Error("Only STANDARD_AIR fluid model can be used with US Measurement System", CURRENT_FUNCTION);
   }
 
-  if (nemo && Kind_FluidModel != USER_DEFINED_NONEQ ) {
-    SU2_MPI::Error("Only USER_DEFINED_NONEQ fluid model can be used with the NEMO solver. Mutation++ library will soon be available.", CURRENT_FUNCTION);
-  }
-
   if (nemo && Kind_TransCoeffModel != WILKE ) {
     SU2_MPI::Error("Only WILKE transport model is stable for the NEMO solver.", CURRENT_FUNCTION);
   }
@@ -3558,6 +3552,14 @@ void CConfig::SetPostprocessing(unsigned short val_software, unsigned short val_
       SU2_MPI::Error("AUSMPW+ is extremely unstable. Feel free to fix me!", CURRENT_FUNCTION);
   }
 
+  if (GetGasModel() == "ARGON" && GetKind_FluidModel() == SU2_NONEQ){
+      SU2_MPI::Error("ARGON is not working with SU2_NONEQ fluid model!", CURRENT_FUNCTION);
+  }
+
+  if (GetKind_FluidModel() == MUTATIONPP && GetFrozen() == true){
+      SU2_MPI::Error("The option of FROZEN_MIXTURE is not yet working with Mutation++ support.", CURRENT_FUNCTION);
+  }
+
   if(GetBoolTurbomachinery()){
     nBlades = new su2double[nZone];
     FreeStreamTurboNormal= new su2double[3];
@@ -4142,6 +4144,19 @@ void CConfig::SetPostprocessing(unsigned short val_software, unsigned short val_
   CFL = new su2double[nCFL];
   CFL[0] = CFLFineGrid;
 
+  /*--- Handle optional CFL adapt parameter values ---*/
+
+  if (nCFL_AdaptParam < default_cfl_adapt.size()) {
+    auto newParam = new su2double [default_cfl_adapt.size()];
+    for (iCFL = 0; iCFL < default_cfl_adapt.size(); ++iCFL) {
+      if (iCFL < nCFL_AdaptParam) newParam[iCFL] = CFL_AdaptParam[iCFL];
+      else newParam[iCFL] = default_cfl_adapt[iCFL];
+    }
+    swap(newParam, CFL_AdaptParam);
+    delete [] newParam;
+    nCFL_AdaptParam = default_cfl_adapt.size();
+  }
+
   /*--- Evaluate when the Cl should be evaluated ---*/
 
   Iter_Fixed_CM        = SU2_TYPE::Int(nInnerIter / (su2double(Update_iH)+1));
@@ -4978,6 +4993,7 @@ void CConfig::SetPostprocessing(unsigned short val_software, unsigned short val_
   /*--- Specifying a deforming surface requires a mesh deformation solver. ---*/
   if (GetSurface_Movement(DEFORMING)) Deform_Mesh = true;
 
+  if (GetGasModel() == "ARGON") monoatomic = true;
 }
 
 void CConfig::SetMarkers(unsigned short val_software) {
@@ -5559,14 +5575,14 @@ void CConfig::SetOutput(unsigned short val_software, unsigned short val_izone) {
         break;
       case NEMO_EULER:
         if (Kind_Regime == COMPRESSIBLE) cout << "Compressible two-temperature thermochemical non-equilibrium Euler equations." << endl;
-        if(Kind_FluidModel == USER_DEFINED_NONEQ){
+        if(Kind_FluidModel == SU2_NONEQ){
           if ((GasModel != "N2") && (GasModel != "AIR-5") && (GasModel != "ARGON"))
           SU2_MPI::Error("The GAS_MODEL given as input is not valid. Choose one of the options: N2, AIR-5, ARGON.", CURRENT_FUNCTION);
         }
         break;
       case NEMO_NAVIER_STOKES:
         if (Kind_Regime == COMPRESSIBLE) cout << "Compressible two-temperature thermochemical non-equilibrium Navier-Stokes equations." << endl;
-        if(Kind_FluidModel == USER_DEFINED_NONEQ){
+        if(Kind_FluidModel == SU2_NONEQ){
           if ((GasModel != "N2") && (GasModel != "AIR-5") && (GasModel != "ARGON"))
           SU2_MPI::Error("The GAS_MODEL given as input is not valid. Choose one of the options: N2, AIR-5, ARGON.", CURRENT_FUNCTION);
         }
@@ -6538,7 +6554,8 @@ void CConfig::SetOutput(unsigned short val_software, unsigned short val_izone) {
 
       if (!CFL_Adapt) cout << "No CFL adaptation." << endl;
       else cout << "CFL adaptation. Factor down: "<< CFL_AdaptParam[0] <<", factor up: "<< CFL_AdaptParam[1]
-        <<",\n                lower limit: "<< CFL_AdaptParam[2] <<", upper limit: " << CFL_AdaptParam[3] <<"."<< endl;
+        <<",\n                lower limit: "<< CFL_AdaptParam[2] <<", upper limit: " << CFL_AdaptParam[3]
+        <<",\n                acceptable linear residual: "<< CFL_AdaptParam[4] << "." << endl;
 
       if (nMGLevels !=0) {
         PrintingToolbox::CTablePrinter MGTable(&std::cout);

Common/src/adt/CADTElemClass.cpp

@@ -2158,4 +2158,4 @@ bool CADTElemClass::Dist2ToQuadrilateral(const unsigned long i0,
   }
 
   return true;
-}
+}

Common/src/fem/fem_standard_element.cpp

@@ -4015,4 +4015,4 @@ void CFEMStandardBoundaryFace::Copy(const CFEMStandardBoundaryFace &other) {
   matDerBasisElemIntegrationTranspose = other.matDerBasisElemIntegrationTranspose;
 
   subConnForPlotting = other.subConnForPlotting;
-}
+}

SU2_CFD/include/fluid/CMutationTCLib.hpp

@@ -29,6 +29,9 @@
 
 #include "CNEMOGas.hpp"
 
+#if defined(HAVE_MPP) && !defined(CODI_REVERSE_TYPE) && !defined(CODI_FORWARD_TYPE)
+#include "mutation++.h"
+
 /*!
  * \derived class CMutationTCLib
  * \brief Child class for Mutation++ nonequilibrium gas model.
@@ -38,6 +41,8 @@ class CMutationTCLib : public CNEMOGas {
 
 private:
 
+  std::unique_ptr<Mutation::Mixture> mix; /*!< \brief Pointer to object Mixture from Mutation++ library. */
+
   vector<su2double> Cv_ks,                /*!< \brief Species specific heats at constant volume. */
   es,                                     /*!< \brief Species energies. */
   omega_vec,                              /*!< \brief Dummy vector for vibrational energy source term. */
@@ -110,6 +115,7 @@ class CMutationTCLib : public CNEMOGas {
    */
   su2double GetViscosity() final;
 
+  
   /*!
    * \brief Get T-R and V-E thermal conductivities vector.
    */
@@ -136,3 +142,4 @@ class CMutationTCLib : public CNEMOGas {
   vector<su2double>& GetSpeciesFormationEnthalpy() final;
 
 };
+#endif

SU2_CFD/include/fluid/CNEMOGas.hpp

@@ -42,7 +42,7 @@ class CNEMOGas : public CFluidModel {
   bool frozen,                           /*!< \brief Indicates if mixture is frozen. */
   ionization;                            /*!< \brief Presence of charged species in gas mixture. */
 
-  string Kind_GasModel;                  /*!< \brief String gas model. */
+  string gas_model;                      /*!< \brief String gas model. */
 
   unsigned short nSpecies,               /*!< \brief Number of species in the gas mixture. */
   nHeavy,                                /*!< \brief Number of heavy particles in gas */
@@ -101,7 +101,6 @@ class CNEMOGas : public CFluidModel {
   /*!
    * \brief Set mixture thermodynamic state.
    * \param[in] P    - Pressure.
-   * \param[in] Ms   - Mass fraction of the gas.
    * \param[in] T    - Translational/Rotational temperature.
    * \param[in] Tve  - Vibrational/Electronic temperature.
    */
@@ -183,17 +182,17 @@ class CNEMOGas : public CFluidModel {
   su2double ComputeGamma();
 
   /*!
-   * \brief Get derivative of pressure w.r.t. conservative variables.
+   * \brief Compute derivative of pressure w.r.t. conservative variables.
    */
   void ComputedPdU(su2double *V, vector<su2double>& val_eves, su2double *val_dPdU);
 
   /*!
-   * \brief Get derivative of temperature w.r.t. conservative variables.
+   * \brief Compute derivative of temperature w.r.t. conservative variables.
    */
   void ComputedTdU(su2double *V, su2double *val_dTdU);
 
   /*!
-   * \brief Get derivative of vibrational temperature w.r.t. conservative variables.
+   * \brief Compute derivative of vibrational temperature w.r.t. conservative variables.
    */
   void ComputedTvedU(su2double *V, vector<su2double>& val_eves, su2double *val_dTvedU);
 
@@ -241,4 +240,4 @@ class CNEMOGas : public CFluidModel {
    * \brief Get species formation enthalpy.
    */
   virtual const vector<su2double>& GetSpeciesFormationEnthalpy() = 0;  
-};
+};