CoreFlows/Models/src/StationaryDiffusionEquation.cxx

   1 #include "StationaryDiffusionEquation.hxx"
   2 #include "DiffusionEquation.hxx"
   3 #include "Node.hxx"
   4 #include "SparseMatrixPetsc.hxx"
   5 #include "math.h"
   6 #include <algorithm>
   7 #include <fstream>
   8 #include <sstream>
   9
  10 using namespace std;
  11
  12 StationaryDiffusionEquation::StationaryDiffusionEquation(int dim, bool FECalculation, double lambda,MPI_Comm comm){
  13         /* Initialisation of PETSC */
  14         //check if PETSC is already initialised
  15         PetscBool petscInitialized;
  16         PetscInitialized(&petscInitialized);
  17         if(!petscInitialized)
  18         {//check if MPI is already initialised
  19                 int mpiInitialized;
  20                 MPI_Initialized(&mpiInitialized);
  21                 if(mpiInitialized)
  22                         PETSC_COMM_WORLD = comm;
  23                 PetscInitialize(NULL,NULL,0,0);//Note this is ok if MPI has been been initialised independently from PETSC
  24         }
  25         MPI_Comm_rank(PETSC_COMM_WORLD,&_mpi_rank);
  26         MPI_Comm_size(PETSC_COMM_WORLD,&_mpi_size);
  27         PetscPrintf(PETSC_COMM_WORLD,"Simulation on %d processors\n",_mpi_size);//Prints to standard out, only from the first processor in the communicator. Calls from other processes are ignored.
  28         PetscSynchronizedPrintf(PETSC_COMM_WORLD,"Processor [%d] ready for action\n",_mpi_rank);//Prints synchronized output from several processors. Output of the first processor is followed by that of the second, etc.
  29         PetscSynchronizedFlush(PETSC_COMM_WORLD,PETSC_STDOUT);
  30
  31     if(lambda < 0.)
  32     {
  33         std::cout<<"Conductivity="<<lambda<<endl;
  34         throw CdmathException("Error : conductivity parameter lambda cannot  be negative");
  35     }
  36     if(dim<=0)
  37     {
  38         std::cout<<"Space dimension="<<dim<<endl;
  39         throw CdmathException("Error : parameter dim cannot  be negative");
  40     }
  41
  42     _FECalculation=FECalculation;
  43     _onlyNeumannBC=false;
  44
  45         _Ndim=dim;
  46         _nVar=1;//scalar prolem
  47         _dt_src=0;
  48         _diffusionMatrixSet=false;
  49         _initializedMemory=false;
  50
  51     //Mesh data
  52     _neibMaxNbCells=0;
  53     _meshSet=false;
  54     _neibMaxNbNodes=0;
  55
  56     //Boundary conditions
  57     _boundaryNodeIds=std::vector< int >(0);
  58     _dirichletNodeIds=std::vector< int >(0);
  59     _NboundaryNodes=0;
  60     _NdirichletNodes=0;
  61     _NunknownNodes=0;
  62     _dirichletValuesSet=false;
  63     _neumannValuesSet=false;
  64
  65     //Linear solver data
  66         _precision=1.e-6;
  67         _precision_Newton=_precision;
  68         _MaxIterLinearSolver=0;//During several newton iterations, stores the max petssc interations
  69         _maxPetscIts=50;
  70         _maxNewtonIts=50;
  71         _NEWTON_its=0;
  72         int _PetscIts=0;//the number of iterations of the linear solver
  73         _ksptype = (char*)&KSPGMRES;
  74         if( _mpi_size>1)
  75                 _pctype = (char*)&PCNONE;
  76         else
  77                 _pctype = (char*)&PCLU;
  78
  79         _conditionNumber=false;
  80         _erreur_rel= 0;
  81
  82     //parameters for monitoring simulation
  83         _verbose = false;
  84         _system = false;
  85         _runLogFile=new ofstream;
  86
  87         //result save parameters
  88         _fileName = "StationaryDiffusionProblem";
  89         char result[ PATH_MAX ];//extracting current directory
  90         getcwd(result, PATH_MAX );
  91         _path=string( result );
  92         _saveFormat=VTK;
  93     _computationCompletedSuccessfully=false;
  94
  95     //heat transfer parameters
  96         _conductivity=lambda;
  97         _fluidTemperatureFieldSet=false;
  98         _fluidTemperature=0;
  99         _heatPowerFieldSet=false;
 100         _heatTransfertCoeff=0;
 101         _heatSource=0;
 102
 103     /* Default diffusion tensor is diagonal */
 104         _DiffusionTensor=Matrix(_Ndim);
 105         for(int idim=0;idim<_Ndim;idim++)
 106                 _DiffusionTensor(idim,idim)=_conductivity;
 107 }
 108
 109 void StationaryDiffusionEquation::initialize()
 110 {
 111         if(_mpi_rank==0)
 112         {
 113                 _runLogFile->open((_fileName+".log").c_str(), ios::out | ios::trunc);;//for creation of a log file to save the history of the simulation
 114
 115                 if(!_meshSet)
 116                         throw CdmathException("StationaryDiffusionEquation::initialize() set mesh first");
 117                 else
 118             {
 119                         cout<<"!!!! Initialisation of the computation of the temperature diffusion in a solid using ";
 120                 *_runLogFile<<"!!!!! Initialisation of the computation of the temperature diffusion in a solid using ";
 121                 if(!_FECalculation)
 122                 {
 123                     cout<< "Finite volumes method"<<endl<<endl;
 124                     *_runLogFile<< "Finite volumes method"<<endl<<endl;
 125                 }
 126                 else
 127                 {
 128                     cout<< "Finite elements method"<<endl<<endl;
 129                     *_runLogFile<< "Finite elements method"<<endl<<endl;
 130                 }
 131             }
 132
 133                 /**************** Field creation *********************/
 134
 135                 if(!_heatPowerFieldSet){
 136                         _heatPowerField=Field("Heat power",_VV.getTypeOfField(),_mesh,1);
 137                         for(int i =0; i<_VV.getNumberOfElements(); i++)
 138                                 _heatPowerField(i) = _heatSource;
 139                 _heatPowerFieldSet=true;
 140             }
 141                 if(!_fluidTemperatureFieldSet){
 142                         _fluidTemperatureField=Field("Fluid temperature",_VV.getTypeOfField(),_mesh,1);
 143                         for(int i =0; i<_VV.getNumberOfElements(); i++)
 144                                 _fluidTemperatureField(i) = _fluidTemperature;
 145                 _fluidTemperatureFieldSet=true;
 146                 }
 147
 148             /* Détection des noeuds frontière avec une condition limite de Dirichlet */
 149             if(_FECalculation)
 150             {
 151                 if(_NboundaryNodes==_Nnodes)
 152                     cout<<"!!!!! Warning : all nodes are boundary nodes !!!!!"<<endl<<endl;
 153
 154                 for(int i=0; i<_NboundaryNodes; i++)
 155                 {
 156                     std::map<int,double>::iterator it=_dirichletBoundaryValues.find(_boundaryNodeIds[i]);
 157                     if( it != _dirichletBoundaryValues.end() )
 158                         _dirichletNodeIds.push_back(_boundaryNodeIds[i]);
 159                     else if( _mesh.getNode(_boundaryNodeIds[i]).getGroupNames().size()==0 )
 160                     {
 161                         cout<<"!!! No boundary group set for boundary node" << _boundaryNodeIds[i]<< endl;
 162                         *_runLogFile<< "!!! No boundary group set for boundary node" << _boundaryNodeIds[i]<<endl;
 163                         _runLogFile->close();
 164                         throw CdmathException("Missing boundary group");
 165                     }
 166                     else if(_limitField[_mesh.getNode(_boundaryNodeIds[i]).getGroupName()].bcType==NoneBCStationaryDiffusion)
 167                     {
 168                         cout<<"!!! No boundary condition set for boundary node " << _boundaryNodeIds[i]<< endl;
 169                         cout<<"!!! Accepted boundary conditions are DirichletStationaryDiffusion "<< DirichletStationaryDiffusion <<" and NeumannStationaryDiffusion "<< NeumannStationaryDiffusion << endl;
 170                         *_runLogFile<< "!!! No boundary condition set for boundary node " << _boundaryNodeIds[i]<<endl;
 171                         *_runLogFile<< "!!! Accepted boundary conditions are DirichletStationaryDiffusion "<< DirichletStationaryDiffusion <<" and NeumannStationaryDiffusion "<< NeumannStationaryDiffusion <<endl;
 172                         _runLogFile->close();
 173                         throw CdmathException("Missing boundary condition");
 174                     }
 175                     else if(_limitField[_mesh.getNode(_boundaryNodeIds[i]).getGroupName()].bcType==DirichletStationaryDiffusion)
 176                         _dirichletNodeIds.push_back(_boundaryNodeIds[i]);
 177                     else if(_limitField[_mesh.getNode(_boundaryNodeIds[i]).getGroupName()].bcType!=NeumannStationaryDiffusion)
 178                     {
 179                         cout<<"!!! Wrong boundary condition "<< _limitField[_mesh.getNode(_boundaryNodeIds[i]).getGroupName()].bcType<< " set for boundary node " << _boundaryNodeIds[i]<< endl;
 180                         cout<<"!!! Accepted boundary conditions are DirichletStationaryDiffusion "<< DirichletStationaryDiffusion <<" and NeumannStationaryDiffusion "<< NeumannStationaryDiffusion << endl;
 181                         *_runLogFile<< "!!! Wrong boundary condition "<< _limitField[_mesh.getNode(_boundaryNodeIds[i]).getGroupName()].bcType<< " set for boundary node " << _boundaryNodeIds[i]<<endl;
 182                         *_runLogFile<< "!!! Accepted boundary conditions are DirichletStationaryDiffusion "<< DirichletStationaryDiffusion <<" and NeumannStationaryDiffusion "<< NeumannStationaryDiffusion <<endl;
 183                         _runLogFile->close();
 184                         throw CdmathException("Wrong boundary condition");
 185                     }
 186                 }
 187                 _NdirichletNodes=_dirichletNodeIds.size();
 188                 _NunknownNodes=_Nnodes - _NdirichletNodes;
 189                 cout<<"Number of unknown nodes " << _NunknownNodes <<", Number of boundary nodes " << _NboundaryNodes<< ", Number of Dirichlet boundary nodes " << _NdirichletNodes <<endl<<endl;
 190                         *_runLogFile<<"Number of unknown nodes " << _NunknownNodes <<", Number of boundary nodes " << _NboundaryNodes<< ", Number of Dirichlet boundary nodes " << _NdirichletNodes <<endl<<endl;
 191             }
 192         }
 193
 194     if(!_FECalculation)
 195                 _globalNbUnknowns = _Nmailles*_nVar;
 196     else{
 197         MPI_Bcast(&_NunknownNodes, 1, MPI_INT, 0, PETSC_COMM_WORLD);
 198                 _globalNbUnknowns = _NunknownNodes*_nVar;
 199         }
 200
 201         /* Vectors creations */
 202         VecCreate(PETSC_COMM_WORLD, &_Tk);//main unknown
 203     VecSetSizes(_Tk,PETSC_DECIDE,_globalNbUnknowns);
 204         VecSetFromOptions(_Tk);
 205         VecGetLocalSize(_Tk, &_localNbUnknowns);
 206
 207         VecDuplicate(_Tk, &_Tkm1);
 208         VecDuplicate(_Tk, &_deltaT);
 209         VecDuplicate(_Tk, &_b);//RHS of the linear system: _b=Tn/dt + _b0 + puisance volumique + couplage thermique avec le fluide
 210
 211         /* Matrix creation */
 212         MatCreateAIJ(PETSC_COMM_WORLD, _localNbUnknowns, _localNbUnknowns, _globalNbUnknowns, _globalNbUnknowns, _d_nnz, PETSC_NULL, _o_nnz, PETSC_NULL, &_A);
 213
 214         /* Local sequential vector creation */
 215         if(_mpi_size>1 && _mpi_rank == 0)
 216                 VecCreateSeq(PETSC_COMM_SELF,_globalNbUnknowns,&_Tk_seq);//For saving results on proc 0
 217         if(_mpi_size==0)
 218                 _Tk_seq=_Tk;
 219         VecScatterCreateToZero(_Tk,&_scat,&_Tk_seq);
 220
 221         //Linear solver
 222         KSPCreate(PETSC_COMM_WORLD, &_ksp);
 223         KSPSetType(_ksp, _ksptype);
 224         // if(_ksptype == KSPGMRES) KSPGMRESSetRestart(_ksp,10000);
 225         KSPSetTolerances(_ksp,_precision,_precision,PETSC_DEFAULT,_maxPetscIts);
 226         KSPGetPC(_ksp, &_pc);
 227         PCSetType(_pc, _pctype);
 228
 229     //Checking whether all boundary conditions are Neumann boundary condition
 230     //if(_FECalculation) _onlyNeumannBC = _NdirichletNodes==0;
 231     if(!_neumannValuesSet)//Boundary conditions set via LimitField structure
 232     {
 233         map<string, LimitFieldStationaryDiffusion>::iterator it = _limitField.begin();
 234         while(it != _limitField.end() and (it->second).bcType == NeumannStationaryDiffusion)
 235             it++;
 236         _onlyNeumannBC = (it == _limitField.end() && _limitField.size()>0);//what if _limitField.size()==0 ???
 237     }
 238     else
 239         if(_FECalculation)
 240             _onlyNeumannBC = _neumannBoundaryValues.size()==_NboundaryNodes;
 241         else
 242             _onlyNeumannBC = _neumannBoundaryValues.size()==_mesh.getBoundaryFaceIds().size();
 243
 244     //If only Neumann BC, then matrix is singular and solution should be sought in space of mean zero vectors
 245     if(_onlyNeumannBC)
 246     {
 247         std::cout<<"### Warning : all boundary conditions are Neumann. System matrix is not invertible since constant vectors are in the kernel."<<std::endl;
 248         std::cout<<"### Check the compatibility condition between the right hand side and the boundary data. For homogeneous Neumann BCs, the right hand side must have integral equal to zero."<<std::endl;
 249         std::cout<<"### The system matrix being singular, we seek a zero sum solution, and exact (LU and CHOLESKY) and incomplete factorisations (ILU and ICC) may fail."<<std::endl<<endl;
 250         *_runLogFile<<"### Warning : all boundary condition are Neumann. System matrix is not invertible since constant vectors are in the kernel."<<std::endl;
 251         *_runLogFile<<"### The system matrix being singular, we seek a zero sum solution, and exact (LU and CHOLESKY) and incomplete factorisations (ILU and ICC) may fail."<<std::endl<<endl;
 252         *_runLogFile<<"### Check the compatibility condition between the right hand side and the boundary data. For homogeneous Neumann BCs, the right hand side must have integral equal to zero."<<std::endl;
 253
 254                 MatNullSpace nullsp;
 255                 MatNullSpaceCreate(PETSC_COMM_WORLD, PETSC_TRUE, 0, PETSC_NULL, &nullsp);
 256                 MatSetNullSpace(_A, nullsp);
 257                 MatSetTransposeNullSpace(_A, nullsp);
 258                 MatNullSpaceDestroy(&nullsp);
 259                 //PCFactorSetShiftType(_pc,MAT_SHIFT_NONZERO);
 260                 //PCFactorSetShiftAmount(_pc,1e-10);
 261     }
 262         _initializedMemory=true;
 263 }
 264
 265 double StationaryDiffusionEquation::computeTimeStep(bool & stop){
 266         if(!_diffusionMatrixSet)//The diffusion matrix is computed once and for all time steps
 267                 computeDiffusionMatrix(stop);
 268
 269         _dt_src=computeRHS(stop);
 270         stop=false;
 271         return _dt_src;
 272 }
 273
 274 double StationaryDiffusionEquation::computeDiffusionMatrix(bool & stop)
 275 {
 276     double result;
 277
 278         MatZeroEntries(_A);
 279         VecZeroEntries(_b);
 280
 281     if(_FECalculation)
 282         result=computeDiffusionMatrixFE(stop);
 283     else
 284         result=computeDiffusionMatrixFV(stop);
 285
 286     MatAssemblyBegin(_A, MAT_FINAL_ASSEMBLY);
 287         MatAssemblyEnd(  _A, MAT_FINAL_ASSEMBLY);
 288
 289     //Contribution from the solid/fluid heat exchange with assumption of constant heat transfer coefficient
 290     //update value here if variable  heat transfer coefficient
 291     if(_heatTransfertCoeff>_precision)
 292         MatShift(_A,_heatTransfertCoeff);//Contribution from the liquit/solid heat transfer
 293
 294     if(_verbose or _system)
 295         MatView(_A,PETSC_VIEWER_STDOUT_WORLD);
 296
 297     return  result;
 298 }
 299
 300 double StationaryDiffusionEquation::computeDiffusionMatrixFE(bool & stop){
 301         if(_mpi_rank == 0)
 302                 {
 303                 Cell Cj;
 304                 string nameOfGroup;
 305                 double coeff;
 306
 307             Matrix M(_Ndim+1,_Ndim+1);//cell geometry matrix
 308             std::vector< Vector > GradShapeFuncs(_Ndim+1);//shape functions of cell nodes
 309             std::vector< int > nodeIds(_Ndim+1);//cell node Ids
 310             std::vector< Node > nodes(_Ndim+1);//cell nodes
 311             int i_int, j_int; //index of nodes j and k considered as unknown nodes
 312             bool dirichletCell_treated;
 313
 314             std::vector< vector< double > > values(_Ndim+1,vector< double >(_Ndim+1,0));//values of shape functions on cell node
 315             for (int idim=0; idim<_Ndim+1;idim++)
 316                 values[idim][idim]=1;
 317
 318             /* parameters for boundary treatment */
 319             vector< double > valuesBorder(_Ndim+1);
 320             Vector GradShapeFuncBorder(_Ndim+1);
 321
 322                 for (int j=0; j<_Nmailles;j++)
 323             {
 324                         Cj = _mesh.getCell(j);
 325
 326                 for (int idim=0; idim<_Ndim+1;idim++){
 327                     nodeIds[idim]=Cj.getNodeId(idim);
 328                     nodes[idim]=_mesh.getNode(nodeIds[idim]);
 329                     for (int jdim=0; jdim<_Ndim;jdim++)
 330                         M(idim,jdim)=nodes[idim].getPoint()[jdim];
 331                     M(idim,_Ndim)=1;
 332                 }
 333                 for (int idim=0; idim<_Ndim+1;idim++)
 334                     GradShapeFuncs[idim]=DiffusionEquation::gradientNodal(M,values[idim])/DiffusionEquation::fact(_Ndim);
 335
 336                 /* Loop on the edges of the cell */
 337                 for (int idim=0; idim<_Ndim+1;idim++)
 338                 {
 339                     if(find(_dirichletNodeIds.begin(),_dirichletNodeIds.end(),nodeIds[idim])==_dirichletNodeIds.end())//!_mesh.isBorderNode(nodeIds[idim])
 340                     {//First node of the edge is not Dirichlet node
 341                         i_int=DiffusionEquation::unknownNodeIndex(nodeIds[idim], _dirichletNodeIds);//assumes Dirichlet boundary node numbering is strictly increasing
 342                         dirichletCell_treated=false;
 343                         for (int jdim=0; jdim<_Ndim+1;jdim++)
 344                         {
 345                             if(find(_dirichletNodeIds.begin(),_dirichletNodeIds.end(),nodeIds[jdim])==_dirichletNodeIds.end())//!_mesh.isBorderNode(nodeIds[jdim])
 346                             {//Second node of the edge is not Dirichlet node
 347                                 j_int= DiffusionEquation::unknownNodeIndex(nodeIds[jdim], _dirichletNodeIds);//assumes Dirichlet boundary node numbering is strictly increasing
 348                                 MatSetValue(_A,i_int,j_int,(_DiffusionTensor*GradShapeFuncs[idim])*GradShapeFuncs[jdim]/Cj.getMeasure(), ADD_VALUES);
 349                             }
 350                             else if (!dirichletCell_treated)
 351                             {//Second node of the edge is a Dirichlet node
 352                                 dirichletCell_treated=true;
 353                                 for (int kdim=0; kdim<_Ndim+1;kdim++)
 354                                 {
 355                                                                 std::map<int,double>::iterator it=_dirichletBoundaryValues.find(nodeIds[kdim]);
 356                                                                 if( it != _dirichletBoundaryValues.end() )
 357                                     {
 358                                         if( _dirichletValuesSet )
 359                                             valuesBorder[kdim]=_dirichletBoundaryValues[it->second];
 360                                         else
 361                                             valuesBorder[kdim]=_limitField[_mesh.getNode(nodeIds[kdim]).getGroupName()].T;
 362                                     }
 363                                     else
 364                                         valuesBorder[kdim]=0;
 365                                 }
 366                                 GradShapeFuncBorder=DiffusionEquation::gradientNodal(M,valuesBorder)/DiffusionEquation::fact(_Ndim);
 367                                 coeff =-1.*(_DiffusionTensor*GradShapeFuncBorder)*GradShapeFuncs[idim]/Cj.getMeasure();
 368                                 VecSetValue(_b,i_int,coeff, ADD_VALUES);
 369                             }
 370                         }
 371                     }
 372                 }
 373                 }
 374
 375             //Calcul de la contribution de la condition limite de Neumann au second membre
 376             if( _NdirichletNodes !=_NboundaryNodes)
 377             {
 378                 vector< int > boundaryFaces = _mesh.getBoundaryFaceIds();
 379                 int NboundaryFaces=boundaryFaces.size();
 380                 for(int i = 0; i< NboundaryFaces ; i++)//On parcourt les faces du bord
 381                 {
 382                     Face Fi = _mesh.getFace(boundaryFaces[i]);
 383                     for(int j = 0 ; j<_Ndim ; j++)//On parcourt les noeuds de la face
 384                     {
 385                         if(find(_dirichletNodeIds.begin(),_dirichletNodeIds.end(),Fi.getNodeId(j))==_dirichletNodeIds.end())//node j is a Neumann BC node (not a Dirichlet BC node)
 386                         {
 387                             j_int=DiffusionEquation::unknownNodeIndex(Fi.getNodeId(j), _dirichletNodeIds);//indice du noeud j en tant que noeud inconnu
 388                             if( _neumannValuesSet )
 389                                 coeff =Fi.getMeasure()/_Ndim*_neumannBoundaryValues[Fi.getNodeId(j)];
 390                             else
 391                                 coeff =Fi.getMeasure()/_Ndim*_limitField[_mesh.getNode(Fi.getNodeId(j)).getGroupName()].normalFlux;
 392                             VecSetValue(_b, j_int, coeff, ADD_VALUES);
 393                         }
 394                     }
 395                 }
 396             }
 397         }
 398
 399         if(_onlyNeumannBC)      //Check that the matrix is symmetric
 400         {
 401                 PetscBool isSymetric;
 402                 MatIsSymmetric(_A,_precision,&isSymetric);
 403                 if(!isSymetric)
 404                 {
 405                         cout<<"Singular matrix is not symmetric, tolerance= "<< _precision<<endl;
 406                         throw CdmathException("Singular matrix should be symmetric with kernel composed of constant vectors");
 407                 }
 408         }
 409
 410         _diffusionMatrixSet=true;
 411     stop=false ;
 412
 413         return INFINITY;
 414 }
 415
 416 double StationaryDiffusionEquation::computeDiffusionMatrixFV(bool & stop){
 417         if(_mpi_rank == 0)
 418         {
 419                 long nbFaces = _mesh.getNumberOfFaces();
 420                 Face Fj;
 421                 Cell Cell1,Cell2;
 422                 string nameOfGroup;
 423                 double inv_dxi, inv_dxj;
 424                 double barycenterDistance;
 425                 Vector normale(_Ndim);
 426                 double dn;
 427                 PetscInt idm, idn;
 428                 std::vector< int > idCells;
 429
 430                 for (int j=0; j<nbFaces;j++){
 431                         Fj = _mesh.getFace(j);
 432
 433                         // compute the normal vector corresponding to face j : from idCells[0] to idCells[1]
 434                         idCells = Fj.getCellsId();
 435                         Cell1 = _mesh.getCell(idCells[0]);
 436                         idm = idCells[0];
 437                 for(int l=0; l<Cell1.getNumberOfFaces(); l++){
 438                     if (j == Cell1.getFacesId()[l]){
 439                         for (int idim = 0; idim < _Ndim; ++idim)
 440                             normale[idim] = Cell1.getNormalVector(l,idim);
 441                         break;
 442                     }
 443                 }
 444
 445                         //Compute velocity at the face Fj
 446                         dn=(_DiffusionTensor*normale)*normale;
 447
 448                         // compute 1/dxi = volume of Ci/area of Fj
 449                 inv_dxi = Fj.getMeasure()/Cell1.getMeasure();
 450
 451                         // If Fj is on the boundary
 452                         if (Fj.getNumberOfCells()==1) {
 453                                 if(_verbose )
 454                                 {
 455                                         cout << "face numero " << j << " cellule frontiere " << idCells[0] << " ; vecteur normal=(";
 456                                         for(int p=0; p<_Ndim; p++)
 457                                                 cout << normale[p] << ",";
 458                                         cout << ") "<<endl;
 459                                 }
 460
 461                     std::map<int,double>::iterator it=_dirichletBoundaryValues.find(j);
 462                     if( it != _dirichletBoundaryValues.end() )
 463                     {
 464                         barycenterDistance=Cell1.getBarryCenter().distance(Fj.getBarryCenter());
 465                         MatSetValue(_A,idm,idm,dn*inv_dxi/barycenterDistance                                     , ADD_VALUES);
 466                         VecSetValue(_b,idm,    dn*inv_dxi/barycenterDistance*it->second, ADD_VALUES);
 467                     }
 468                     else
 469                     {
 470                         nameOfGroup = Fj.getGroupName();
 471
 472                         if (_limitField[nameOfGroup].bcType==NeumannStationaryDiffusion){
 473                             VecSetValue(_b,idm,    -dn*inv_dxi*_limitField[nameOfGroup].normalFlux, ADD_VALUES);
 474                         }
 475                         else if(_limitField[nameOfGroup].bcType==DirichletStationaryDiffusion){
 476                             barycenterDistance=Cell1.getBarryCenter().distance(Fj.getBarryCenter());
 477                             MatSetValue(_A,idm,idm,dn*inv_dxi/barycenterDistance                           , ADD_VALUES);
 478                             VecSetValue(_b,idm,    dn*inv_dxi/barycenterDistance*_limitField[nameOfGroup].T, ADD_VALUES);
 479                         }
 480                         else {
 481                             stop=true ;
 482                             cout<<"!!!!!!!!!!!!!!! Error StationaryDiffusionEquation::computeDiffusionMatrixFV !!!!!!!!!!"<<endl;
 483                             cout<<"!!!!!! No boundary condition set for boundary named "<<nameOfGroup<< "!!!!!!!!!! _limitField[nameOfGroup].bcType= "<<_limitField[nameOfGroup].bcType<<endl;
 484                             cout<<"Accepted boundary conditions are NeumannStationaryDiffusion "<<NeumannStationaryDiffusion<< " and DirichletStationaryDiffusion "<<DirichletStationaryDiffusion<<endl;
 485                             *_runLogFile<<"!!!!!! Boundary condition not set for boundary named "<<nameOfGroup<< "!!!!!!!!!! _limitField[nameOfGroup].bcType= "<<_limitField[nameOfGroup].bcType<<endl;
 486                             _runLogFile->close();
 487                             throw CdmathException("Boundary condition not set");
 488                         }
 489                     }
 490                                 // if Fj is inside the domain
 491                         } else  if (Fj.getNumberOfCells()==2 ){
 492                                 if(_verbose )
 493                                 {
 494                                         cout << "face numero " << j << " cellule gauche " << idCells[0] << " cellule droite " << idCells[1];
 495                                         cout << " ; vecteur normal=(";
 496                                         for(int p=0; p<_Ndim; p++)
 497                                                 cout << normale[p] << ",";
 498                                         cout << ") "<<endl;
 499                                 }
 500                                 Cell2 = _mesh.getCell(idCells[1]);
 501                                 idn = idCells[1];
 502                                 if (_Ndim > 1)
 503                                         inv_dxj = Fj.getMeasure()/Cell2.getMeasure();
 504                                 else
 505                                         inv_dxj = 1/Cell2.getMeasure();
 506
 507                                 barycenterDistance=Cell1.getBarryCenter().distance(Cell2.getBarryCenter());
 508
 509                                 MatSetValue(_A,idm,idm, dn*inv_dxi/barycenterDistance, ADD_VALUES);
 510                                 MatSetValue(_A,idm,idn,-dn*inv_dxi/barycenterDistance, ADD_VALUES);
 511                                 MatSetValue(_A,idn,idn, dn*inv_dxj/barycenterDistance, ADD_VALUES);
 512                                 MatSetValue(_A,idn,idm,-dn*inv_dxj/barycenterDistance, ADD_VALUES);
 513                         }
 514                         else
 515                 {
 516                     *_runLogFile<<"StationaryDiffusionEquation::computeDiffusionMatrixFV(): incompatible number of cells around a face"<<endl;
 517                                 throw CdmathException("StationaryDiffusionEquation::computeDiffusionMatrixFV(): incompatible number of cells around a face");
 518                 }
 519                 }
 520         }
 521
 522         if(_onlyNeumannBC)      //Check that the matrix is symmetric
 523         {
 524                 PetscBool isSymetric;
 525                 MatIsSymmetric(_A,_precision,&isSymetric);
 526                 if(!isSymetric)
 527                 {
 528                         cout<<"Singular matrix is not symmetric, tolerance= "<< _precision<<endl;
 529                         throw CdmathException("Singular matrix should be symmetric with kernel composed of constant vectors");
 530                 }
 531         }
 532
 533         _diffusionMatrixSet=true;
 534     stop=false ;
 535
 536     return INFINITY;
 537 }
 538
 539 double StationaryDiffusionEquation::computeRHS(bool & stop)//Contribution of the PDE RHS to the linear systemm RHS (boundary conditions do contribute to the system RHS via the function computeDiffusionMatrix
 540 {
 541
 542         if(_mpi_rank == 0)
 543         {
 544             if(!_FECalculation)
 545                 for (int i=0; i<_Nmailles;i++)
 546                     VecSetValue(_b,i, _heatTransfertCoeff*_fluidTemperatureField(i) + _heatPowerField(i) ,ADD_VALUES);
 547             else
 548                 {
 549                     Cell Ci;
 550                     std::vector< int > nodesId;
 551                     for (int i=0; i<_Nmailles;i++)
 552                     {
 553                         Ci=_mesh.getCell(i);
 554                         nodesId=Ci.getNodesId();
 555                         for (int j=0; j<nodesId.size();j++)
 556                             if(!_mesh.isBorderNode(nodesId[j]))
 557                             {
 558                                 double coeff = _heatTransfertCoeff*_fluidTemperatureField(nodesId[j]) + _heatPowerField(nodesId[j]);
 559                                 VecSetValue(_b,DiffusionEquation::unknownNodeIndex(nodesId[j], _dirichletNodeIds), coeff*Ci.getMeasure()/(_Ndim+1),ADD_VALUES);
 560                             }
 561                     }
 562                 }
 563         }
 564         VecAssemblyBegin(_b);
 565         VecAssemblyEnd(_b);
 566
 567     if(_verbose or _system)
 568         VecView(_b,PETSC_VIEWER_STDOUT_WORLD);
 569
 570     stop=false ;
 571         return INFINITY;
 572 }
 573
 574 bool StationaryDiffusionEquation::iterateNewtonStep(bool &converged)
 575 {
 576         bool stop;
 577
 578     //Only implicit scheme considered
 579
 580 #if PETSC_VERSION_GREATER_3_5
 581     KSPSetOperators(_ksp, _A, _A);
 582 #else
 583     KSPSetOperators(_ksp, _A, _A,SAME_NONZERO_PATTERN);
 584 #endif
 585
 586     if(_conditionNumber)
 587         KSPSetComputeEigenvalues(_ksp,PETSC_TRUE);
 588     KSPSolve(_ksp, _b, _Tk);
 589
 590         KSPConvergedReason reason;
 591         KSPGetConvergedReason(_ksp,&reason);
 592     KSPGetIterationNumber(_ksp, &_PetscIts);
 593     double residu;
 594     KSPGetResidualNorm(_ksp,&residu);
 595         if (reason!=2 and reason!=3)
 596     {
 597         PetscPrintf(PETSC_COMM_WORLD,"!!!!!!!!!!!!! Erreur système linéaire : pas de convergence de Petsc.");
 598         PetscPrintf(PETSC_COMM_WORLD,"!!!!!!!!!!!!! Itérations maximales %d atteintes, résidu = %1.2f, précision demandée= %1.2f",_maxPetscIts,residu,_precision);
 599         PetscPrintf(PETSC_COMM_WORLD,"Solver used %s, preconditioner %s, Final number of iteration = %d",_ksptype,_pctype,_PetscIts);
 600                 *_runLogFile<<"!!!!!!!!!!!!! Erreur système linéaire : pas de convergence de Petsc."<<endl;
 601         *_runLogFile<<"!!!!!!!!!!!!! Itérations maximales "<<_maxPetscIts<<" atteintes, résidu="<<residu<<", précision demandée= "<<_precision<<endl;
 602         *_runLogFile<<"Solver used "<<  _ksptype<<", preconditioner "<<_pctype<<", Final number of iteration= "<<_PetscIts<<endl;
 603                 _runLogFile->close();
 604         converged = false;
 605         stop = true;
 606     }
 607     else{
 608         if( _MaxIterLinearSolver < _PetscIts)
 609             _MaxIterLinearSolver = _PetscIts;
 610         PetscPrintf(PETSC_COMM_WORLD,"## Système linéaire résolu en %d itérations par le solveur %s et le preconditioneur %s, précision demandée = %1.2f",_PetscIts,_ksptype,_pctype,_precision);
 611                 *_runLogFile<<"## Système linéaire résolu en "<<_PetscIts<<" itérations par le solveur "<<  _ksptype<<" et le preconditioneur "<<_pctype<<", précision demandée= "<<_precision<<endl<<endl;
 612         VecCopy(_Tk, _deltaT);//ici on a deltaT=Tk
 613         VecAXPY(_deltaT,  -1, _Tkm1);//On obtient deltaT=Tk-Tkm1
 614
 615         VecAssemblyBegin(_Tk);
 616         VecAssemblyEnd(  _Tk);
 617         VecAssemblyBegin(_deltaT);
 618         VecAssemblyEnd(  _deltaT);
 619
 620                 if(_verbose)
 621                         PetscPrintf(PETSC_COMM_WORLD,"Début calcul de l'erreur maximale");
 622
 623                 VecNorm(_deltaT,NORM_INFINITY,&_erreur_rel);
 624
 625                 if(_verbose)
 626                         PetscPrintf(PETSC_COMM_WORLD,"Fin calcul de la variation relative, erreur maximale : %1.2f", _erreur_rel );
 627         stop=false;
 628         converged = (_erreur_rel <= _precision) ;//converged=convergence des iterations de Newton
 629     }
 630
 631         VecCopy(_Tk, _Tkm1);
 632
 633         return stop;
 634 }
 635
 636 void StationaryDiffusionEquation::setMesh(const Mesh &M)
 637 {
 638         if(_mpi_rank==0)
 639         {
 640                 if(_Ndim != M.getSpaceDimension() or _Ndim!=M.getMeshDimension())//for the moment we must have space dim=mesh dim
 641                 {
 642                 cout<< "Problem : dimension defined is "<<_Ndim<< " but mesh dimension= "<<M.getMeshDimension()<<", and space dimension is "<<M.getSpaceDimension()<<endl;
 643                         *_runLogFile<< "Problem : dim = "<<_Ndim<< " but mesh dim= "<<M.getMeshDimension()<<", mesh space dim= "<<M.getSpaceDimension()<<endl;
 644                         *_runLogFile<<"StationaryDiffusionEquation::setMesh: mesh has incorrect dimension"<<endl;
 645                         _runLogFile->close();
 646                         throw CdmathException("StationaryDiffusionEquation::setMesh: mesh has incorrect  dimension");
 647                 }
 648
 649                 _mesh=M;
 650                 _Nmailles = _mesh.getNumberOfCells();
 651                 _Nnodes =   _mesh.getNumberOfNodes();
 652
 653             cout<<"Mesh has "<< _Nmailles << " cells and " << _Nnodes << " nodes"<<endl<<endl;;
 654                 *_runLogFile<<"Mesh has "<< _Nmailles << " cells and " << _Nnodes << " nodes"<<endl<<endl;
 655
 656                 // find  maximum nb of neibourghs
 657             if(!_FECalculation)
 658             {
 659                 _VV=Field ("Temperature", CELLS, _mesh, 1);
 660                 _neibMaxNbCells=_mesh.getMaxNbNeighbours(CELLS);
 661             }
 662             else
 663             {
 664                 if(_Ndim==1 )//The 1D cdmath mesh is necessarily made of segments
 665                                 cout<<"1D Finite element method on segments"<<endl;
 666                 else if(_Ndim==2)
 667                 {
 668                                 if( _mesh.isTriangular() )//Mesh dim=2
 669                                         cout<<"2D Finite element method on triangles"<<endl;
 670                                 else if (_mesh.getMeshDimension()==1)//Mesh dim=1
 671                                         cout<<"1D Finite element method on a 2D network : space dimension is "<<_Ndim<< ", mesh dimension is "<<_mesh.getMeshDimension()<<endl;
 672                                 else
 673                                 {
 674                                         cout<<"Error Finite element with Space dimension "<<_Ndim<< ", and mesh dimension  "<<_mesh.getMeshDimension()<< ", mesh should be either triangular either 1D network"<<endl;
 675                                         *_runLogFile<<"StationaryDiffusionEquation::setMesh: mesh has incorrect dimension"<<endl;
 676                                         _runLogFile->close();
 677                                         throw CdmathException("StationaryDiffusionEquation::setMesh: mesh has incorrect cell types");
 678                                 }
 679                 }
 680                 else if(_Ndim==3)
 681                 {
 682                                 if( _mesh.isTetrahedral() )//Mesh dim=3
 683                                         cout<<"3D Finite element method on tetrahedra"<<endl;
 684                                 else if (_mesh.getMeshDimension()==2 and _mesh.isTriangular())//Mesh dim=2
 685                                         cout<<"2D Finite element method on a 3D surface : space dimension is "<<_Ndim<< ", mesh dimension is "<<_mesh.getMeshDimension()<<endl;
 686                                 else if (_mesh.getMeshDimension()==1)//Mesh dim=1
 687                                         cout<<"1D Finite element method on a 3D network : space dimension is "<<_Ndim<< ", mesh dimension is "<<_mesh.getMeshDimension()<<endl;
 688                                 else
 689                                 {
 690                                         cout<<"Error Finite element with Space dimension "<<_Ndim<< ", and mesh dimension  "<<_mesh.getMeshDimension()<< ", mesh should be either tetrahedral, either a triangularised surface or 1D network"<<endl;
 691                                         *_runLogFile<<"StationaryDiffusionEquation::setMesh: mesh has incorrect dimension"<<endl;
 692                                         _runLogFile->close();
 693                                         throw CdmathException("StationaryDiffusionEquation::setMesh: mesh has incorrect cell types");
 694                                 }
 695                 }
 696
 697                         _VV=Field ("Temperature", NODES, _mesh, 1);
 698
 699                 _neibMaxNbNodes=_mesh.getMaxNbNeighbours(NODES);
 700                 _boundaryNodeIds = _mesh.getBoundaryNodeIds();
 701                 _NboundaryNodes=_boundaryNodeIds.size();
 702             }
 703         }
 704
 705         /* MPI distribution parameters */
 706         int nbVoisinsMax;//Mettre en attribut ?
 707         if(!_FECalculation){
 708                 MPI_Bcast(&_Nmailles      , 1, MPI_INT, 0, PETSC_COMM_WORLD);
 709                 MPI_Bcast(&_neibMaxNbCells, 1, MPI_INT, 0, PETSC_COMM_WORLD);
 710                 nbVoisinsMax = _neibMaxNbCells;
 711         }
 712         else{
 713                 MPI_Bcast(&_Nnodes        , 1, MPI_INT, 0, PETSC_COMM_WORLD);
 714                 MPI_Bcast(&_neibMaxNbNodes, 1, MPI_INT, 0, PETSC_COMM_WORLD);
 715                 nbVoisinsMax = _neibMaxNbNodes;
 716         }
 717     _d_nnz = (nbVoisinsMax+1)*_nVar;
 718     _o_nnz =  nbVoisinsMax   *_nVar;
 719
 720         _meshSet=true;
 721 }
 722
 723 void StationaryDiffusionEquation::setLinearSolver(linearSolver kspType, preconditioner pcType)
 724 {
 725         //_maxPetscIts=maxIterationsPetsc;
 726         // set linear solver algorithm
 727         if (kspType==GMRES)
 728                 _ksptype = (char*)&KSPGMRES;
 729         else if (kspType==CG)
 730                 _ksptype = (char*)&KSPCG;
 731         else if (kspType==BCGS)
 732                 _ksptype = (char*)&KSPBCGS;
 733         else {
 734                 cout << "!!! Error : only 'GMRES', 'CG' or 'BCGS' is acceptable as a linear solver !!!" << endl;
 735                 *_runLogFile << "!!! Error : only 'GMRES', 'CG' or 'BCGS' is acceptable as a linear solver !!!" << endl;
 736                 _runLogFile->close();
 737                 throw CdmathException("!!! Error : only 'GMRES', 'CG' or 'BCGS' algorithm is acceptable !!!");
 738         }
 739         // set preconditioner
 740         if (pcType == NONE)
 741                 _pctype = (char*)&PCNONE;
 742         else if (pcType ==LU)
 743                 _pctype = (char*)&PCLU;
 744         else if (pcType == ILU)
 745                 _pctype = (char*)&PCILU;
 746         else if (pcType ==CHOLESKY)
 747                 _pctype = (char*)&PCCHOLESKY;
 748         else if (pcType == ICC)
 749                 _pctype = (char*)&PCICC;
 750         else {
 751                 cout << "!!! Error : only 'NOPC', 'LU', 'ILU', 'CHOLESKY' or 'ICC' preconditioners are acceptable !!!" << endl;
 752                 *_runLogFile << "!!! Error : only 'NOPC' or 'LU' or 'ILU' preconditioners are acceptable !!!" << endl;
 753                 _runLogFile->close();
 754                 throw CdmathException("!!! Error : only 'NOPC' or 'LU' or 'ILU' preconditioners are acceptable !!!" );
 755         }
 756 }
 757
 758 bool StationaryDiffusionEquation::solveStationaryProblem()
 759 {
 760         if(!_initializedMemory)
 761         {
 762                 *_runLogFile<< "ProblemCoreFlows::run() call initialize() first"<< _fileName<<endl;
 763                 _runLogFile->close();
 764                 throw CdmathException("ProblemCoreFlows::run() call initialize() first");
 765         }
 766         bool stop=false; // Does the Problem want to stop (error) ?
 767         bool converged=false; // has the newton scheme converged (end) ?
 768
 769         PetscPrintf(PETSC_COMM_WORLD,"!!! Running test case %s using ",_fileName);
 770         *_runLogFile<< "!!! Running test case "<< _fileName<< " using ";
 771
 772     if(!_FECalculation)
 773     {
 774         PetscPrintf(PETSC_COMM_WORLD,"Finite volumes method\n\n");
 775                 *_runLogFile<< "Finite volumes method"<<endl<<endl;
 776         }
 777     else
 778         {
 779         PetscPrintf(PETSC_COMM_WORLD,"Finite elements method\n\n");
 780                 *_runLogFile<< "Finite elements method"<< endl<<endl;
 781         }
 782
 783     computeDiffusionMatrix( stop);//For the moment the conductivity does not depend on the temperature (linear LHS)
 784     if (stop){
 785         PetscPrintf(PETSC_COMM_WORLD,"Error : failed computing diffusion matrix, stopping calculation\n");
 786         *_runLogFile << "Error : failed computing diffusion matrix, stopping calculation"<< endl;
 787                 _runLogFile->close();
 788        throw CdmathException("Failed computing diffusion matrix");
 789     }
 790     computeRHS(stop);//For the moment the heat power does not depend on the unknown temperature (linear RHS)
 791     if (stop){
 792         PetscPrintf(PETSC_COMM_WORLD,"Error : failed computing right hand side, stopping calculation\n");
 793         *_runLogFile << "Error : failed computing right hand side, stopping calculation"<< endl;
 794         throw CdmathException("Failed computing right hand side");
 795     }
 796     stop = iterateNewtonStep(converged);
 797     if (stop){
 798         PetscPrintf(PETSC_COMM_WORLD,"Error : failed solving linear system, stopping calculation\n");
 799         *_runLogFile << "Error : failed linear system, stopping calculation"<< endl;
 800                 _runLogFile->close();
 801         throw CdmathException("Failed solving linear system");
 802     }
 803
 804     _computationCompletedSuccessfully=true;
 805     save();
 806
 807         // Newton iteration loop for non linear problems
 808     /*
 809         while(!stop and !converged and _NEWTON_its<_maxNewtonIts)
 810         {
 811         computeDiffusionMatrix( stop);//case when the conductivity depends on the temperature (nonlinear LHS)
 812         computeRHS(stop);//case the heat power depends on the unknown temperature (nonlinear RHS)
 813         stop = iterateNewtonStep(converged);
 814         _NEWTON_its++;
 815         }
 816     if (stop){
 817         cout << "Error : failed solving Newton iteration "<<_NEWTON_its<<", stopping calculation"<< endl;
 818         *_runLogFile << "Error : failed solving Newton iteration "<<_NEWTON_its<<", stopping calculation"<< endl;
 819         throw CdmathException("Failed solving a Newton iteration");
 820     }
 821     else if(_NEWTON_its==_maxNewtonIts){
 822         cout << "Error : no convergence of Newton scheme. Maximum Newton iterations "<<_maxNewtonIts<<" reached, stopping calculation"<< endl;
 823         *_runLogFile << "Error : no convergence of Newton scheme. Maximum Newton iterations "<<_maxNewtonIts<<" reached, stopping calculation"<< endl;
 824         throw CdmathException("No convergence of Newton scheme");
 825     }
 826     else{
 827         cout << "Convergence of Newton scheme at iteration "<<_NEWTON_its<<", end of calculation"<< endl;
 828         *_runLogFile << "Convergence of Newton scheme at iteration "<<_NEWTON_its<<", end of calculation"<< endl;
 829         save();
 830     }
 831     */
 832
 833     *_runLogFile<< "!!!!!! Computation successful !!!!!!"<< endl;
 834         _runLogFile->close();
 835
 836         return !stop;
 837 }
 838
 839 void StationaryDiffusionEquation::save(){
 840     PetscPrintf(PETSC_COMM_WORLD,"Saving numerical results\n\n");
 841     *_runLogFile<< "Saving numerical results"<< endl<<endl;
 842
 843         string resultFile(_path+"/StationaryDiffusionEquation");//Results
 844
 845         resultFile+="_";
 846         resultFile+=_fileName;
 847
 848         // create mesh and component info
 849     string suppress ="rm -rf "+resultFile+"_*";
 850     system(suppress.c_str());//Nettoyage des précédents calculs identiques
 851
 852         if(_mpi_size>1){
 853                 VecScatterBegin(_scat,_Tk,_Tk_seq,INSERT_VALUES,SCATTER_FORWARD);
 854                 VecScatterEnd(  _scat,_Tk,_Tk_seq,INSERT_VALUES,SCATTER_FORWARD);
 855         }
 856
 857     if(_verbose or _system)
 858         VecView(_Tk,PETSC_VIEWER_STDOUT_WORLD);
 859
 860         if(_mpi_rank==0){
 861             double Ti;
 862             if(!_FECalculation)
 863                 for(int i=0; i<_Nmailles; i++)
 864                     {
 865                                         if(_mpi_size>1)
 866                                                 VecGetValues(_Tk_seq, 1, &i, &Ti);
 867                                         else
 868                                                 VecGetValues(_Tk    , 1, &i, &Ti);
 869                         _VV(i)=Ti;
 870                     }
 871             else
 872             {
 873                 int globalIndex;
 874                 for(int i=0; i<_NunknownNodes; i++)
 875                 {
 876                                 if(_mpi_size>1)
 877                                         VecGetValues(_Tk_seq, 1, &i, &Ti);
 878                                 else
 879                                         VecGetValues(_Tk    , 1, &i, &Ti);
 880                     globalIndex = DiffusionEquation::globalNodeIndex(i, _dirichletNodeIds);
 881                     _VV(globalIndex)=Ti;
 882                 }
 883
 884                 Node Ni;
 885                 string nameOfGroup;
 886                 for(int i=0; i<_NdirichletNodes; i++)
 887                 {
 888                     Ni=_mesh.getNode(_dirichletNodeIds[i]);
 889                     nameOfGroup = Ni.getGroupName();
 890                     _VV(_dirichletNodeIds[i])=_limitField[nameOfGroup].T;
 891                 }
 892             }
 893
 894             _VV.setInfoOnComponent(0,"Temperature_(K)");
 895             switch(_saveFormat)
 896             {
 897                 case VTK :
 898                     _VV.writeVTK(resultFile);
 899                     break;
 900                 case MED :
 901                     _VV.writeMED(resultFile);
 902                     break;
 903                 case CSV :
 904                     _VV.writeCSV(resultFile);
 905                     break;
 906             }
 907         }
 908 }
 909
 910 void StationaryDiffusionEquation::terminate()
 911 {
 912         VecDestroy(&_Tk);
 913         VecDestroy(&_Tkm1);
 914         VecDestroy(&_deltaT);
 915         VecDestroy(&_b);
 916         MatDestroy(&_A);
 917         if(_mpi_size>1 && _mpi_rank == 0)
 918                 VecDestroy(&_Tk_seq);
 919
 920         PetscBool petscInitialized;
 921         PetscInitialized(&petscInitialized);
 922         if(petscInitialized)
 923                 PetscFinalize();
 924
 925         delete _runLogFile;
 926 }
 927 void
 928 StationaryDiffusionEquation::setDirichletValues(map< int, double> dirichletBoundaryValues)
 929 {
 930     _dirichletValuesSet=true;
 931     _dirichletBoundaryValues=dirichletBoundaryValues;
 932 }
 933
 934 void
 935 StationaryDiffusionEquation::setNeumannValues(map< int, double> neumannBoundaryValues)
 936 {
 937     _neumannValuesSet=true;
 938     _neumannBoundaryValues=neumannBoundaryValues;
 939 }
 940
 941 double
 942 StationaryDiffusionEquation::getConditionNumber(bool isSingular, double tol) const
 943 {
 944   SparseMatrixPetsc A = SparseMatrixPetsc(_A);
 945   return A.getConditionNumber( isSingular, tol);
 946 }
 947 std::vector< double >
 948 StationaryDiffusionEquation::getEigenvalues(int nev, EPSWhich which, double tol) const
 949 {
 950   SparseMatrixPetsc A = SparseMatrixPetsc(_A);
 951
 952   if(_FECalculation)//We need to scale the FE matrix, otherwise the eigenvalues go to zero as the mesh is refined
 953   {
 954       Vector nodal_volumes(_NunknownNodes);
 955       int j_int;
 956       for(int i = 0; i< _Nmailles ; i++)//On parcourt les cellules du maillage
 957       {
 958         Cell Ci = _mesh.getCell(i);
 959         for(int j = 0 ; j<_Ndim+1 ; j++)//On parcourt les noeuds de la cellule
 960         {
 961             if(find(_dirichletNodeIds.begin(),_dirichletNodeIds.end(),Ci.getNodeId(j))==_dirichletNodeIds.end())//node j is an unknown node (not a Dirichlet node)
 962                         {
 963                 j_int=DiffusionEquation::unknownNodeIndex(Ci.getNodeId(j), _dirichletNodeIds);//indice du noeud j en tant que noeud inconnu
 964                 nodal_volumes[j_int]+=Ci.getMeasure()/(_Ndim+1);
 965             }
 966         }
 967        }
 968       for( j_int = 0; j_int< _NunknownNodes ; j_int++)
 969         nodal_volumes[j_int]=1/nodal_volumes[j_int];
 970       A.leftDiagonalScale(nodal_volumes);
 971   }
 972
 973   return A.getEigenvalues( nev, which, tol);
 974 }
 975 std::vector< Vector >
 976 StationaryDiffusionEquation::getEigenvectors(int nev, EPSWhich which, double tol) const
 977 {
 978   SparseMatrixPetsc A = SparseMatrixPetsc(_A);
 979   return A.getEigenvectors( nev, which, tol);
 980 }
 981 Field
 982 StationaryDiffusionEquation::getEigenvectorsField(int nev, EPSWhich which, double tol) const
 983 {
 984   SparseMatrixPetsc A = SparseMatrixPetsc(_A);
 985   MEDCoupling::DataArrayDouble * d = A.getEigenvectorsDataArrayDouble( nev, which, tol);
 986   Field my_eigenfield;
 987
 988     my_eigenfield = Field("Eigenvectors field", _VV.getTypeOfField(), _mesh, nev);
 989
 990   my_eigenfield.setFieldByDataArrayDouble(d);
 991
 992   return my_eigenfield;
 993 }
 994
 995 Field&
 996 StationaryDiffusionEquation::getOutputTemperatureField()
 997 {
 998     if(!_computationCompletedSuccessfully)
 999         throw("Computation not performed yet or failed. No temperature field available");
1000     else
1001         return _VV;
1002 }
1003
1004 Field&
1005 StationaryDiffusionEquation::getRodTemperatureField()
1006 {
1007    return getOutputTemperatureField();
1008 }
1009
1010 vector<string>
1011 StationaryDiffusionEquation::getInputFieldsNames()
1012 {
1013         vector<string> result(2);
1014
1015         result[0]="FluidTemperature";
1016         result[1]="HeatPower";
1017
1018         return result;
1019 }
1020 vector<string>
1021 StationaryDiffusionEquation::getOutputFieldsNames()
1022 {
1023         vector<string> result(1);
1024
1025         result[0]="RodTemperature";
1026
1027         return result;
1028 }
1029
1030 Field&
1031 StationaryDiffusionEquation::getOutputField(const string& nameField )
1032 {
1033         if(nameField=="RodTemperature" || nameField=="RODTEMPERATURE" || nameField=="TEMPERATURECOMBUSTIBLE" || nameField=="TemperatureCombustible" )
1034                 return getRodTemperatureField();
1035     else
1036     {
1037         cout<<"Error : Field name "<< nameField << " does not exist, call getOutputFieldsNames first" << endl;
1038         throw CdmathException("DiffusionEquation::getOutputField error : Unknown Field name");
1039     }
1040 }
1041
1042 void
1043 StationaryDiffusionEquation::setInputField(const string& nameField, Field& inputField )
1044 {
1045         if(nameField=="FluidTemperature" || nameField=="FLUIDTEMPERATURE" || nameField=="TemperatureFluide" || nameField=="TEMPERATUREFLUIDE")
1046                 return setFluidTemperatureField( inputField) ;
1047         else if(nameField=="HeatPower" || nameField=="HEATPOWER" || nameField=="PuissanceThermique" || nameField=="PUISSANCETHERMIQUE" )
1048                 return setHeatPowerField( inputField );
1049         else
1050     {
1051         cout<<"Error : Field name "<< nameField << " is not an input field name, call getInputFieldsNames first" << endl;
1052         throw CdmathException("StationaryDiffusionEquation::setInputField error : Unknown Field name");
1053     }
1054 }