NEMO - link with mutation++

.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

@@ -758,6 +758,7 @@ class CConfig {
   su2double* Mesh_Box_Length;    /*!< \brief Array containing the length in the x-, y-, and z-directions for the analytic RECTANGLE and BOX grid formats. */
   su2double* Mesh_Box_Offset;    /*!< \brief Array containing the offset from 0.0 in the x-, y-, and z-directions for the analytic RECTANGLE and BOX grid formats. */
   string Mesh_FileName,          /*!< \brief Mesh input file. */
+  Target_Mesh_FileName,          /*!< \brief Mesh name to be adapted. */
   Mesh_Out_FileName,             /*!< \brief Mesh output file. */
   Solution_FileName,             /*!< \brief Flow solution input file. */
   Solution_AdjFileName,          /*!< \brief Adjoint solution input file for drag functional. */
@@ -1156,7 +1157,7 @@ class CConfig {
   monoatomic;                               /*!< \brief Flag for monoatomic mixture. */
   string GasModel,                          /*!< \brief Gas Model. */
   *Wall_Catalytic;                          /*!< \brief Pointer to catalytic walls. */
-
+  
   /*!
    * \brief Set the default values of config options not set in the config file using another config object.
    * \param config - Config object to use the default values from.
@@ -3652,7 +3653,7 @@ 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.
@@ -5111,6 +5112,11 @@ class CConfig {
    */
   bool GetRestart(void) const { return Restart; }
 
+  /*!
+   * \brief Sets the restart information.
+   */
+  void SetRestart(bool val_restart) { Restart = val_restart; }
+
   /*!
    * \brief Flag for whether binary SU2 native restart files are read.
    * \return Flag for whether binary SU2 native restart files are read, if <code>TRUE</code> then the code will load binary restart files.

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

@@ -543,7 +543,7 @@ enum ENUM_FLUIDMODEL {
   INC_IDEAL_GAS = 5,      /*!< \brief Incompressible ideal 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*/
@@ -2785,7 +2783,6 @@ 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 +3171,7 @@ 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 +3536,6 @@ 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 +3551,14 @@ 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];
@@ -4978,6 +4979,7 @@ 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 +5561,14 @@ 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);
         }

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;  
-};
+};

SU2_CFD/include/fluid/CUserDefinedTCLib.hpp → SU2_CFD/include/fluid/CSU2TCLib.hpp

@@ -1,5 +1,5 @@
 /*!
- * \file CUserDefinedTCLib.hpp
+ * \file CSU2TCLib.hpp
  * \brief Defines the classes for different user defined ThermoChemistry libraries.
  * \author C. Garbacz, W. Maier, S. R. Copeland
  * \version 7.0.8 "Blackbird"
@@ -30,11 +30,11 @@
 #include "CNEMOGas.hpp"
 
 /*!
- * \derived class CUserDefinedTCLib
+ * \derived class CSU2TCLib
  * \brief Child class for user defined nonequilibrium gas model.
  * \author: C. Garbacz, W. Maier, S. R. Copeland
  */
-class CUserDefinedTCLib : public CNEMOGas {
+class CSU2TCLib : public CNEMOGas {
 
 private:
 
@@ -77,12 +77,12 @@ class CUserDefinedTCLib : public CNEMOGas {
   /*!
    * \brief Constructor of the class.
    */
-  CUserDefinedTCLib(const CConfig* config, unsigned short val_nDim, bool val_viscous);
+  CSU2TCLib(const CConfig* config, unsigned short val_nDim, bool val_viscous);
 
   /*!
    * \brief Destructor of the class.
    */
-  virtual ~CUserDefinedTCLib(void);
+  virtual ~CSU2TCLib(void);
 
   /*!
    * \brief Set mixture thermodynamic state.

SU2_CFD/include/numerics/CNumerics.hpp

@@ -36,7 +36,7 @@
 #include "../../../Common/include/CConfig.hpp"
 #include "../fluid/CNEMOGas.hpp"
 #include "../../include/fluid/CMutationTCLib.hpp"
-#include "../../include/fluid/CUserDefinedTCLib.hpp"
+#include "../../include/fluid/CSU2TCLib.hpp"
 #include "../../../Common/include/linear_algebra/blas_structure.hpp"
 
 using namespace std;

SU2_CFD/include/variables/CNEMOEulerVariable.hpp

@@ -455,16 +455,6 @@ class CNEMOEulerVariable : public CVariable {
      }
   }
 
-  /*!
-   * \brief Set the Energy vector from the old solution.
-   * \param[in] val_energy - Pointer to energy.
-   */
-  inline void SetEnergy_Old(unsigned long iPoint, const vector<su2double>& val_energy)  {
-    for (unsigned long i = 0; i < 2; i++){
-      Solution_Old(iPoint,nSpecies+nDim+i) = val_energy[i]*Primitive(iPoint,RHO_INDEX);
-     }
-  }
-
   /*!
    * \brief A virtual member.
    * \return Value of the vibrational-electronic temperature.

SU2_CFD/obj/Makefile.am

@@ -54,7 +54,7 @@ libSU2Core_sources = ../src/definition_structure.cpp \
   ../src/fluid/CPengRobinson.cpp \
   ../src/fluid/CVanDerWaalsGas.cpp \
   ../src/fluid/CNEMOGas.cpp \
-  ../src/fluid/CUserDefinedTCLib.cpp \
+  ../src/fluid/CSU2TCLib.cpp \
   ../src/fluid/CMutationTCLib.cpp \
   ../src/integration/CIntegration.cpp \
   ../src/integration/CSingleGridIntegration.cpp \