Merge branch 'develop' into feature_NEMO_merge_final

Author: CatarinaGarbacz

Common/include/option_structure.hpp

@@ -74,7 +74,6 @@ enum SU2_COMPONENT {
 
 const unsigned int EXIT_DIVERGENCE = 2;   /*!< \brief Exit code (divergence). */
 
-const unsigned int BUFSIZE = 3000000;         /*!< \brief MPI buffer. */
 const unsigned int MAX_PARAMETERS = 10;       /*!< \brief Maximum number of parameters for a design variable definition. */
 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. */

Common/include/parallelization/mpi_structure.hpp

@@ -144,10 +144,6 @@ class CBaseMPIWrapper {
     winMinRankErrorInUse = true;
   }
 
-  static inline void Buffer_attach(void* buffer, int size) { MPI_Buffer_attach(buffer, size); }
-
-  static inline void Buffer_detach(void* buffer, int* size) { MPI_Buffer_detach(buffer, size); }
-
   static inline void Comm_rank(Comm comm, int* rank) { MPI_Comm_rank(comm, rank); }
 
   static inline void Comm_size(Comm comm, int* size) { MPI_Comm_size(comm, size); }
@@ -176,6 +172,8 @@ class CBaseMPIWrapper {
 
   static inline void Wait(Request* request, Status* status) { MPI_Wait(request, status); }
 
+  static inline int Request_free(Request *request) { return MPI_Request_free(request); }
+
   static inline void Testall(int count, Request* array_of_requests, int* flag, Status* array_of_statuses) {
     MPI_Testall(count, array_of_requests, flag, array_of_statuses);
   }
@@ -198,10 +196,6 @@ class CBaseMPIWrapper {
     MPI_Bcast(buf, count, datatype, root, comm);
   }
 
-  static inline void Bsend(const void* buf, int count, Datatype datatype, int dest, int tag, Comm comm) {
-    MPI_Bsend(buf, count, datatype, dest, tag, comm);
-  }
-
   static inline void Reduce(const void* sendbuf, void* recvbuf, int count, Datatype datatype, Op op, int root,
                             Comm comm) {
     MPI_Reduce(sendbuf, recvbuf, count, datatype, op, root, comm);
@@ -351,10 +345,6 @@ class CMediMPIWrapper : public CBaseMPIWrapper {
     }
   }
 
-  static inline void Buffer_attach(void* buffer, int size) { AMPI_Buffer_attach(buffer, size); }
-
-  static inline void Buffer_detach(void* buffer, int* size) { AMPI_Buffer_detach(buffer, size); }
-
   static inline void Comm_rank(Comm comm, int* rank) { AMPI_Comm_rank(convertComm(comm), rank); }
 
   static inline void Comm_size(Comm comm, int* size) { AMPI_Comm_size(convertComm(comm), size); }
@@ -385,6 +375,8 @@ class CMediMPIWrapper : public CBaseMPIWrapper {
 
   static inline void Wait(SU2_MPI::Request* request, Status* status) { AMPI_Wait(request, status); }
 
+  static inline int Request_free(Request *request) { return AMPI_Request_free(request); }
+
   static inline void Testall(int count, Request* array_of_requests, int* flag, Status* array_of_statuses) {
     AMPI_Testall(count, array_of_requests, flag, array_of_statuses);
   }
@@ -409,10 +401,6 @@ class CMediMPIWrapper : public CBaseMPIWrapper {
     AMPI_Bcast(buf, count, convertDatatype(datatype), root, convertComm(comm));
   }
 
-  static inline void Bsend(const void* buf, int count, Datatype datatype, int dest, int tag, Comm comm) {
-    AMPI_Bsend(buf, count, convertDatatype(datatype), dest, tag, convertComm(comm));
-  }
-
   static inline void Reduce(const void* sendbuf, void* recvbuf, int count, Datatype datatype, Op op, int root,
                             Comm comm) {
     AMPI_Reduce(sendbuf, recvbuf, count, convertDatatype(datatype), convertOp(op), root, convertComm(comm));
@@ -574,10 +562,6 @@ class CBaseMPIWrapper {
 
   static inline void Init_thread(int* argc, char*** argv, int required, int* provided) { *provided = required; }
 
-  static inline void Buffer_attach(void* buffer, int size) {}
-
-  static inline void Buffer_detach(void* buffer, int* size) {}
-
   static inline void Barrier(Comm comm) {}
 
   static inline void Abort(Comm comm, int error) { exit(EXIT_FAILURE); }
@@ -595,6 +579,8 @@ class CBaseMPIWrapper {
 
   static inline void Wait(Request* request, Status* status) {}
 
+  static inline int Request_free(Request *request) { return 0; }
+
   static inline void Waitall(int nrequests, Request* request, Status* status) {}
 
   static inline void Waitany(int nrequests, Request* request, int* index, Status* status) {}
@@ -605,8 +591,6 @@ class CBaseMPIWrapper {
 
   static inline void Bcast(void* buf, int count, Datatype datatype, int root, Comm comm) {}
 
-  static inline void Bsend(const void* buf, int count, Datatype datatype, int dest, int tag, Comm comm) {}
-
   static inline void Reduce(const void* sendbuf, void* recvbuf, int count, Datatype datatype, Op op, int root,
                             Comm comm) {
     CopyData(sendbuf, recvbuf, count, datatype);

SU2_CFD/src/SU2_CFD.cpp

@@ -61,16 +61,13 @@ int main(int argc, char *argv[]) {
   /*--- MPI initialization, and buffer setting ---*/
 
 #ifdef HAVE_MPI
-  int  buffsize;
-  char *buffptr;
 #ifdef HAVE_OMP
   int required = use_thread_mult? MPI_THREAD_MULTIPLE : MPI_THREAD_FUNNELED;
   int provided;
   SU2_MPI::Init_thread(&argc, &argv, required, &provided);
 #else
   SU2_MPI::Init(&argc, &argv);
 #endif
-  SU2_MPI::Buffer_attach( malloc(BUFSIZE), BUFSIZE );
   SU2_Comm MPICommunicator(MPI_COMM_WORLD);
 #else
   SU2_Comm MPICommunicator(0);
@@ -178,11 +175,7 @@ int main(int argc, char *argv[]) {
 #endif
 
   /*--- Finalize MPI parallelization. ---*/
-#ifdef HAVE_MPI
-  SU2_MPI::Buffer_detach(&buffptr, &buffsize);
-  free(buffptr);
   SU2_MPI::Finalize();
-#endif
 
   return EXIT_SUCCESS;
 

SU2_CFD/src/numerics/NEMO/NEMO_sources.cpp

@@ -296,7 +296,25 @@ CNumerics::ResidualType<> CSource_NEMO::ComputeVibRelaxation(const CConfig *conf
 CNumerics::ResidualType<> CSource_NEMO::ComputeAxisymmetric(const CConfig *config) {
 
   unsigned short iDim, iSpecies, iVar;
-  su2double rho, rhov, vel2, H, yinv;
+  su2double rho, rhov, vel2, H, yinv, T, Tve, qy_ve, Ru, RuSI;
+  su2double *Ds, **GV, ktr, kve;
+  
+  /*--- Rename for convenience ---*/
+  Ds = Diffusion_Coeff_i;
+  ktr = Thermal_Conductivity_i;
+  kve = Thermal_Conductivity_ve_i;
+  rho = V_i[RHO_INDEX];
+  T   = V_i[T_INDEX];
+  Tve  = V_i[TVE_INDEX];
+  GV  = PrimVar_Grad_i;
+  RuSI= UNIVERSAL_GAS_CONSTANT;
+  Ru  = 1000.0*RuSI;
+
+  auto& Ms = fluidmodel->GetSpeciesMolarMass();
+  
+  bool viscous = config->GetViscous();
+  bool rans = (config->GetKind_Turb_Model() != NONE);
+  hs = fluidmodel->ComputeSpeciesEnthalpy(T, Tve, eve_i);
 
   /*--- Initialize residual and Jacobian arrays ---*/
   for (iVar = 0; iVar < nVar; iVar++) {
@@ -312,6 +330,7 @@ CNumerics::ResidualType<> CSource_NEMO::ComputeAxisymmetric(const CConfig *confi
   rhov   = U_i[nSpecies+1];
   H      = V_i[H_INDEX];
   vel2   = 0.0;
+
   for (iDim = 0; iDim < nDim; iDim++)
     vel2 += V_i[VEL_INDEX+iDim]*V_i[VEL_INDEX+iDim];
   for (iSpecies = 0; iSpecies < nSpecies; iSpecies++)
@@ -324,6 +343,43 @@ CNumerics::ResidualType<> CSource_NEMO::ComputeAxisymmetric(const CConfig *confi
   residual[nSpecies+2] = yinv*rhov*H*Volume;
   residual[nSpecies+3] = yinv*rhov*U_i[nSpecies+nDim+1]/rho*Volume;
 
+  if (viscous) {
+    if (!rans){ turb_ke_i = 0.0; }
+
+    su2double sumJhs_y  = 0.0;
+    su2double sumJeve_y = 0.0;
+    su2double Mass      = 0.0;
+
+    for (iSpecies=0; iSpecies<nSpecies; iSpecies++)
+      Mass += V_i[iSpecies]*Ms[iSpecies];
+        
+    su2double heat_capacity_cp_i   = V_i[RHOCVTR_INDEX]+Ru/Mass;
+    su2double total_viscosity_i    = Laminar_Viscosity_i + Eddy_Viscosity_i;
+    su2double total_conductivity_i = ktr + kve + heat_capacity_cp_i*Eddy_Viscosity_i/Prandtl_Turb;      
+    su2double u                    = V_i[VEL_INDEX];
+    su2double v                    = V_i[VEL_INDEX+1];
+    su2double qy_ve                = kve*GV[TVE_INDEX][1];
+
+    /*--- Enthalpy and vib-el energy transport due to y-direction diffusion---*/
+    for (iSpecies = 0; iSpecies < nHeavy; iSpecies++) { 
+      sumJhs_y  += (rho*Ds[iSpecies]*GV[RHOS_INDEX+iSpecies][1] - V_i[RHOS_INDEX+iSpecies]*Vector[1]) * hs[iSpecies];
+      sumJeve_y += (rho*Ds[iSpecies]*GV[RHOS_INDEX+iSpecies][1] - V_i[RHOS_INDEX+iSpecies]*Vector[1]) * eve_i[iSpecies];
+    }
+
+    for (iSpecies = 0; iSpecies < nSpecies; iSpecies++)
+      residual[iSpecies] -= 0.0;
+    residual[nSpecies] -= Volume*(yinv*total_viscosity_i*(PrimVar_Grad_i[nSpecies+2][1]+PrimVar_Grad_i[nSpecies+3][0]) 
+                                                                    -TWO3*AuxVar_Grad_i[0][0]);
+    residual[nSpecies+1] -= Volume*(yinv*total_viscosity_i*2*(PrimVar_Grad_i[nSpecies+3][1]-v*yinv)
+                                                                    -TWO3*AuxVar_Grad_i[0][1]);
+    residual[nSpecies+2] -= Volume*(yinv*(- sumJhs_y + total_viscosity_i*(u*(PrimVar_Grad_i[nSpecies+3][0]+PrimVar_Grad_i[nSpecies+2][1])
+                                                     +v*TWO3*(2*PrimVar_Grad_i[nSpecies+2][1]-PrimVar_Grad_i[nSpecies+2][0]
+                                                     -v*yinv+rho*turb_ke_i))
+                                                     -total_conductivity_i*PrimVar_Grad_i[nSpecies][1])
+                                                     -TWO3*(AuxVar_Grad_i[1][1]+AuxVar_Grad_i[2][1]));
+    residual[nSpecies+3] -= Volume*(yinv*(-sumJeve_y -qy_ve));
+  }
+
 //  if (implicit) {
 //
 //    /*--- Initialize ---*/