Exemplo n.º 1
0
/** Prepare axes for the numerical solver (and if onlyprepare==false) call the
 * solver
 */
void Particles::PrepareAndRunNumericalSolver(
    vector<vector<double> > &particlespectrum, bool onlyprepare,
    bool dontinitialise) {
  if (EnergyAxisUpperBoundary) {
    GetAxis(Emin, EnergyAxisUpperBoundary, ebins, energyAxis, true);
  } else if (EnergyAxisLowerBoundary) {
    GetAxis(EnergyAxisLowerBoundary, eMax, ebins, energyAxis, true);
  } else if (EnergyAxisLowerBoundary && EnergyAxisUpperBoundary) {
    GetAxis(EnergyAxisLowerBoundary, EnergyAxisUpperBoundary, ebins, energyAxis,
            true);
  } else {
    GetAxis(Emin, eMax, ebins, energyAxis, true);
  }
  CreateGrid();
  if (dontinitialise == false) SetInitialCondition(grid, energyAxis, Tmin);

  /* if onlyprepare=true, only the axes are initialised, but the grid is not
   * computed
   * until t=age. This is useful in conjunction with
   * ComputeGridInTimeInterval().
   */
  if (onlyprepare == false) ComputeGrid(grid, energyAxis, Tmin, Age, timeAxis);
  return;
}
Exemplo n.º 2
0
int main(int argc, char **argv)
{
  MPI_Comm          comm;
  PetscMPIInt       rank;
  PetscErrorCode    ierr;
  User              user;
  PetscLogDouble       v1, v2;
  PetscInt          nplot = 0;
  char              filename1[2048], fileName[2048];
  PetscBool         set = PETSC_FALSE;
  PetscInt          steps_output;

  ierr = PetscInitialize(&argc, &argv, (char*) 0, help);CHKERRQ(ierr);
  comm = PETSC_COMM_WORLD;
  ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
  ierr = PetscNew(&user);CHKERRQ(ierr);
  ierr = PetscNew(&user->algebra);CHKERRQ(ierr);
  ierr = PetscNew(&user->model);CHKERRQ(ierr);
  ierr = PetscNew(&user->model->physics);CHKERRQ(ierr);

  Algebra   algebra = user->algebra;

  ierr = LoadOptions(comm, user);CHKERRQ(ierr);
  ierr = PetscTime(&v1);CHKERRQ(ierr);
  ierr = CreateMesh(comm, user);CHKERRQ(ierr);
  ierr = PetscTime(&v2);CHKERRQ(ierr);
  ierr = PetscPrintf(PETSC_COMM_WORLD,
		       "Read and Distribute mesh takes %f sec \n", v2 - v1);CHKERRQ(ierr);
  ierr = SetUpLocalSpace(user);CHKERRQ(ierr); //Set up the dofs of each element
  ierr = ConstructGeometryFVM(&user->facegeom, &user->cellgeom, user);CHKERRQ(ierr);

  ierr = LimiterSetup(user);CHKERRQ(ierr);

  if(user->output_solution){
  // the output file options
    ierr = PetscOptionsBegin(PETSC_COMM_WORLD,0,"Options for output solution",0);CHKERRQ(ierr);
    ierr = PetscOptionsString("-solutionfile", "solution file", "AeroSim.c", filename1,filename1, 2048, &set);CHKERRQ(ierr);
    if(!set){SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_NULL,"please use option -solutionfile to specify solution file name \n");}
    ierr = PetscOptionsInt("-steps_output", "the number of time steps between two outputs", "", steps_output, &steps_output, &set);CHKERRQ(ierr);
    if(!set){ steps_output = 1;}
    ierr = PetscOptionsEnd();CHKERRQ(ierr);
  }

  if (user->TimeIntegralMethod == EXPLICITMETHOD) {
    if(user->myownexplicitmethod){
      ierr = PetscPrintf(PETSC_COMM_WORLD,"Using the fully explicit method based on my own routing\n");CHKERRQ(ierr);
      user->current_time = user->initial_time;
      user->current_step = 1;
      ierr = DMCreateGlobalVector(user->dm, &algebra->solution);CHKERRQ(ierr);
      ierr = PetscObjectSetName((PetscObject) algebra->solution, "solution");CHKERRQ(ierr);
      ierr = SetInitialCondition(user->dm, algebra->solution, user);CHKERRQ(ierr);
      ierr = VecDuplicate(algebra->solution, &algebra->fn);CHKERRQ(ierr);
      ierr = VecDuplicate(algebra->solution, &algebra->oldsolution);CHKERRQ(ierr);
      if(user->Explicit_RK2){
        ierr = PetscPrintf(PETSC_COMM_WORLD,"Use the second order Runge Kutta method \n");CHKERRQ(ierr);
      }else{
        ierr = PetscPrintf(PETSC_COMM_WORLD,"Use the first order forward Euler method \n");CHKERRQ(ierr);
      }
      nplot = 0; //the plot step
      while(user->current_time < (user->final_time - 0.05 * user->dt)){
        user->current_time = user->current_time + user->dt;

        ierr = FormTimeStepFunction(user, algebra, algebra->solution, algebra->fn);CHKERRQ(ierr);
        PetscReal fnnorm;
        ierr = VecNorm(algebra->fn,NORM_INFINITY,&fnnorm);CHKERRQ(ierr);
        if(0){
          PetscViewer    viewer;
          ierr = OutputVTK(user->dm, "function.vtk", &viewer);CHKERRQ(ierr);
          ierr = VecView(algebra->fn, viewer);CHKERRQ(ierr);
          ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
          ierr = PetscPrintf(PETSC_COMM_WORLD,"Step %D at time %g with founction norm = %g \n",
                                user->current_step, user->current_time, fnnorm);CHKERRQ(ierr);
          //break;
        }
        if(user->Explicit_RK2){
          ierr = VecCopy(algebra->solution, algebra->oldsolution);CHKERRQ(ierr);//U^n
          ierr = VecAXPY(algebra->solution, user->dt, algebra->fn);CHKERRQ(ierr);//U^{(1)}
          ierr = FormTimeStepFunction(user, algebra, algebra->solution, algebra->fn);CHKERRQ(ierr);//f(U^{(1)})
          ierr = VecAXPY(algebra->solution, 1.0, algebra->oldsolution);CHKERRQ(ierr);//U^n + U^{(1)}
          ierr = VecAXPY(algebra->solution, user->dt, algebra->fn);CHKERRQ(ierr);// + dt*f(U^{(1)})
          ierr = VecScale(algebra->solution, 0.5);CHKERRQ(ierr);
        }else{
          ierr = VecCopy(algebra->solution, algebra->oldsolution);CHKERRQ(ierr);
          ierr = VecAXPY(algebra->solution, user->dt, algebra->fn);CHKERRQ(ierr);
        }

        {// Monitor the solution and function norms
          PetscReal         norm;
          PetscLogDouble    space =0;
          PetscInt          size;

          ierr = VecNorm(algebra->solution,NORM_INFINITY,&norm);CHKERRQ(ierr);
          ierr = VecGetSize(algebra->solution, &size);CHKERRQ(ierr);
          norm = norm/size;
          if (norm>1.e5) {
            SETERRQ2(PETSC_COMM_WORLD, PETSC_ERR_LIB,
            "The norm of the solution is: %f (current time: %f). The explicit method is going to DIVERGE!!!", norm, user->current_time);
          }
          if (user->current_step%10==0) {
            ierr = PetscPrintf(PETSC_COMM_WORLD,"Step %D at time %g with solution norm = %g and founction norm = %g \n",
                                user->current_step, user->current_time, norm, fnnorm);CHKERRQ(ierr);
          }
          ierr =  PetscMallocGetCurrentUsage(&space);CHKERRQ(ierr);
//          if (user->current_step%10==0) {
//            ierr =  PetscPrintf(PETSC_COMM_WORLD,"Current space PetscMalloc()ed %g M\n",
//                                 space/(1024*1024));CHKERRQ(ierr);
//          }
        }

        { // Monitor the difference of two steps' solution
          PetscReal         norm;
          ierr = VecAXPY(algebra->oldsolution, -1, algebra->solution);CHKERRQ(ierr);
          ierr = VecNorm(algebra->oldsolution,NORM_INFINITY,&norm);CHKERRQ(ierr);
          if (user->current_step%10==0) {
            ierr = PetscPrintf(PETSC_COMM_WORLD,"Step %D at time %g with ||u_k-u_{k-1}|| = %g \n",
                              user->current_step, user->current_time, norm);CHKERRQ(ierr);
          }
          if((norm<1.e-6)||(user->current_step > user->max_time_its)) break;
        }

        // output the solution
        if (user->output_solution && (user->current_step%steps_output==0)){
          PetscViewer    viewer;

          // update file name for the current time step
          ierr = PetscSNPrintf(fileName, sizeof(fileName),"%s_%d.vtk",filename1, nplot);CHKERRQ(ierr);
          ierr = PetscPrintf(PETSC_COMM_WORLD,"Outputing solution %s (current time %f)\n", fileName, user->current_time);CHKERRQ(ierr);
          ierr = OutputVTK(user->dm, fileName, &viewer);CHKERRQ(ierr);
          ierr = VecView(algebra->solution, viewer);CHKERRQ(ierr);
          ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
          nplot++;
        }

        user->current_step++;

      }
      ierr = VecDestroy(&algebra->fn);CHKERRQ(ierr);
    }else{
      PetscReal         ftime;
      TS                ts;
      TSConvergedReason reason;
      PetscInt          nsteps;

      ierr = PetscPrintf(PETSC_COMM_WORLD,"Using the fully explicit method based on the PETSC TS routing\n");CHKERRQ(ierr);
      ierr = DMCreateGlobalVector(user->dm, &algebra->solution);CHKERRQ(ierr);
      ierr = PetscObjectSetName((PetscObject) algebra->solution, "solution");CHKERRQ(ierr);
      ierr = SetInitialCondition(user->dm, algebra->solution, user);CHKERRQ(ierr);
      ierr = TSCreate(comm, &ts);CHKERRQ(ierr);
      ierr = TSSetType(ts, TSEULER);CHKERRQ(ierr);
      ierr = TSSetDM(ts, user->dm);CHKERRQ(ierr);
      ierr = TSMonitorSet(ts,TSMonitorFunctionError,&user,NULL);CHKERRQ(ierr);
      ierr = TSSetRHSFunction(ts, NULL, MyRHSFunction, user);CHKERRQ(ierr);
      ierr = TSSetDuration(ts, 1000, user->final_time);CHKERRQ(ierr);
      ierr = TSSetInitialTimeStep(ts, user->initial_time, user->dt);CHKERRQ(ierr);
      ierr = TSSetFromOptions(ts);CHKERRQ(ierr);
      ierr = TSSolve(ts, algebra->solution);CHKERRQ(ierr);
      ierr = TSGetSolveTime(ts, &ftime);CHKERRQ(ierr);
      ierr = TSGetTimeStepNumber(ts, &nsteps);CHKERRQ(ierr);
      ierr = TSGetConvergedReason(ts, &reason);CHKERRQ(ierr);
      ierr = PetscPrintf(PETSC_COMM_WORLD,"%s at time %g after %D steps\n",TSConvergedReasons[reason],ftime,nsteps);CHKERRQ(ierr);
      ierr = TSDestroy(&ts);CHKERRQ(ierr);
    }

    if(user->benchmark_couette) {
      ierr = DMCreateGlobalVector(user->dm, &algebra->exactsolution);CHKERRQ(ierr);
      ierr = ComputeExactSolution(user->dm, user->final_time, algebra->exactsolution, user);CHKERRQ(ierr);
    }

    if (user->output_solution){
      PetscViewer    viewer;
      ierr = OutputVTK(user->dm, "solution.vtk", &viewer);CHKERRQ(ierr);
      ierr = VecView(algebra->solution, viewer);CHKERRQ(ierr);
      ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
    }

    if(user->benchmark_couette) {
      PetscViewer    viewer;
      PetscReal      norm;

      ierr = OutputVTK(user->dm, "exact_solution.vtk", &viewer);CHKERRQ(ierr);
      ierr = VecView(algebra->exactsolution, viewer);CHKERRQ(ierr);
      ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);

      ierr = VecAXPY(algebra->exactsolution, -1, algebra->solution);CHKERRQ(ierr);
      ierr = VecNorm(algebra->exactsolution,NORM_INFINITY,&norm);CHKERRQ(ierr);
      ierr = PetscPrintf(PETSC_COMM_WORLD,"Final time at %f, Error: ||u_k-u|| = %g \n", user->final_time, norm);CHKERRQ(ierr);

      ierr = OutputVTK(user->dm, "Error.vtk", &viewer);CHKERRQ(ierr);
      ierr = VecView(algebra->exactsolution, viewer);CHKERRQ(ierr);
      ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
    }

    ierr = VecDestroy(&algebra->solution);CHKERRQ(ierr);
    ierr = VecDestroy(&algebra->oldsolution);CHKERRQ(ierr);
    ierr = DMDestroy(&user->dm);CHKERRQ(ierr);
  } else if (user->TimeIntegralMethod == IMPLICITMETHOD) {
    ierr = PetscPrintf(PETSC_COMM_WORLD,"Using the fully implicit method\n");CHKERRQ(ierr);
    ierr =  SNESCreate(comm,&user->snes);CHKERRQ(ierr);
    ierr =  SNESSetDM(user->snes,user->dm);CHKERRQ(ierr);

    ierr = DMCreateGlobalVector(user->dm, &algebra->solution);CHKERRQ(ierr);
    ierr = VecDuplicate(algebra->solution, &algebra->oldsolution);CHKERRQ(ierr);
    ierr = VecDuplicate(algebra->solution, &algebra->f);CHKERRQ(ierr);
    ierr = VecDuplicate(algebra->solution, &algebra->fn);CHKERRQ(ierr);
    ierr = VecDuplicate(algebra->solution, &algebra->oldfn);CHKERRQ(ierr);

    ierr = PetscObjectSetName((PetscObject) algebra->solution, "solution");CHKERRQ(ierr);
    ierr = SetInitialCondition(user->dm, algebra->solution, user);CHKERRQ(ierr);

    ierr = DMSetMatType(user->dm, MATAIJ);CHKERRQ(ierr);
//    ierr = DMCreateMatrix(user->dm, &algebra->A);CHKERRQ(ierr);
    ierr = DMCreateMatrix(user->dm, &algebra->J);CHKERRQ(ierr);
    if (user->JdiffP) {
     /*Set up the preconditioner matrix*/
     ierr = DMCreateMatrix(user->dm, &algebra->P);CHKERRQ(ierr);
    }else{
     algebra->P = algebra->J;
    }

    ierr = MatSetOption(algebra->J, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE);CHKERRQ(ierr);

    /*set nonlinear function */
    ierr =  SNESSetFunction(user->snes, algebra->f, FormFunction, (void*)user);CHKERRQ(ierr);
    /* compute Jacobian */
    ierr =  SNESSetJacobian(user->snes, algebra->J, algebra->P, FormJacobian, (void*)user);CHKERRQ(ierr);

    ierr = SNESSetFromOptions(user->snes);CHKERRQ(ierr);

    /* do the solve */
    if (user->timestep == TIMESTEP_STEADY_STATE) {
      ierr = SolveSteadyState(user);CHKERRQ(ierr);
    } else {
      ierr = SolveTimeDependent(user);CHKERRQ(ierr);
    }

    if (user->output_solution){
      PetscViewer    viewer;
      ierr = OutputVTK(user->dm, "solution.vtk", &viewer);CHKERRQ(ierr);
      ierr = VecView(algebra->solution, viewer);CHKERRQ(ierr);
      ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
    }

    if(user->benchmark_couette) {
      PetscViewer    viewer;
      PetscReal      norm;

      ierr = OutputVTK(user->dm, "exact_solution.vtk", &viewer);CHKERRQ(ierr);
      ierr = VecView(algebra->exactsolution, viewer);CHKERRQ(ierr);
      ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);

      ierr = VecAXPY(algebra->exactsolution, -1, algebra->solution);CHKERRQ(ierr);
      ierr = VecNorm(algebra->exactsolution,NORM_INFINITY,&norm);CHKERRQ(ierr);
      ierr = PetscPrintf(PETSC_COMM_WORLD,"Error: ||u_k-u|| = %g \n", norm);CHKERRQ(ierr);

      ierr = OutputVTK(user->dm, "Error.vtk", &viewer);CHKERRQ(ierr);
      ierr = VecView(algebra->exactsolution, viewer);CHKERRQ(ierr);
      ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
    }

    ierr = VecDestroy(&algebra->solution);CHKERRQ(ierr);
    ierr = VecDestroy(&algebra->f);CHKERRQ(ierr);
    ierr = VecDestroy(&algebra->oldsolution);CHKERRQ(ierr);
    ierr = VecDestroy(&algebra->fn);CHKERRQ(ierr);
    ierr = VecDestroy(&algebra->oldfn);CHKERRQ(ierr);

    ierr = SNESDestroy(&user->snes);CHKERRQ(ierr);
    ierr = DMDestroy(&user->dm);CHKERRQ(ierr);

  } else {
    SETERRQ(PETSC_COMM_SELF,PETSC_ERR_USER,"WRONG option for the time integral method. Using the option '-time_integral_method 0 or 1'");
  }

  ierr = VecDestroy(&user->cellgeom);CHKERRQ(ierr);
  ierr = VecDestroy(&user->facegeom);CHKERRQ(ierr);
  ierr = DMDestroy(&user->dmGrad);CHKERRQ(ierr);

  ierr = PetscFunctionListDestroy(&LimitList);CHKERRQ(ierr);
  ierr = PetscFree(user->model->physics);CHKERRQ(ierr);
  ierr = PetscFree(user->algebra);CHKERRQ(ierr);
  ierr = PetscFree(user->model);CHKERRQ(ierr);
  ierr = PetscFree(user);CHKERRQ(ierr);

  {
    PetscLogDouble    space =0;
    ierr =  PetscMallocGetCurrentUsage(&space);CHKERRQ(ierr);
    ierr =  PetscPrintf(PETSC_COMM_WORLD,"Unfreed space at the End %g M\n", space/(1024*1024));CHKERRQ(ierr);
  }

  ierr = PetscFinalize();
  return(0);
}
Exemplo n.º 3
0
int main(int argc, char **argv)
{
  MPI_Comm          comm;
  PetscMPIInt       rank;
  PetscErrorCode    ierr;
  User              user;
  PetscLogDouble       v1, v2;
  PetscInt          nplot = 0;
  char              fileName[2048];


  ierr = PetscInitialize(&argc, &argv, (char*) 0, help);CHKERRQ(ierr);
  comm = PETSC_COMM_WORLD;
  ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
  ierr = PetscNew(&user);CHKERRQ(ierr);
  ierr = PetscNew(&user->algebra);CHKERRQ(ierr);
  ierr = PetscNew(&user->model);CHKERRQ(ierr);
  ierr = PetscNew(&user->model->physics);CHKERRQ(ierr);

  Algebra   algebra = user->algebra;

  ierr = LoadOptions(comm, user);CHKERRQ(ierr);
  ierr = PetscTime(&v1);CHKERRQ(ierr);
  ierr = CreateMesh(comm, user);CHKERRQ(ierr);
  ierr = PetscTime(&v2);CHKERRQ(ierr);
  ierr = PetscPrintf(PETSC_COMM_WORLD,
		       "Read and Distribute mesh takes %f sec \n", v2 - v1);CHKERRQ(ierr);
  ierr = SetUpLocalSpace(user);CHKERRQ(ierr); //Set up the dofs of each element
  ierr = ConstructGeometryFVM(&user->facegeom, &user->cellgeom, user);CHKERRQ(ierr);

  ierr = LimiterSetup(user);CHKERRQ(ierr);

  if (user->TimeIntegralMethod == EXPLICITMETHOD) { // explicit method
    if(user->myownexplicitmethod){// Using the fully explicit method based on my own routing
      ierr = PetscPrintf(PETSC_COMM_WORLD,"Using the fully explicit method based on my own routing\n");CHKERRQ(ierr);
      user->current_time = user->initial_time;
      user->current_step = 1;
      ierr = DMCreateGlobalVector(user->dm, &algebra->solution);CHKERRQ(ierr);
      ierr = PetscObjectSetName((PetscObject) algebra->solution, "solution");CHKERRQ(ierr);
      ierr = VecSet(algebra->solution, 0);CHKERRQ(ierr);
      ierr = SetInitialCondition(user->dm, algebra->solution, user);CHKERRQ(ierr);
      if(1){
        PetscViewer    viewer;
        ierr = OutputVTK(user->dm, "intialcondition.vtk", &viewer);CHKERRQ(ierr);
        ierr = VecView(algebra->solution, viewer);CHKERRQ(ierr);
        ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
        ierr = PetscPrintf(PETSC_COMM_WORLD,"Outputing the initial condition intialcondition.vtk!!! \n");CHKERRQ(ierr);
      }
      ierr = VecDuplicate(algebra->solution, &algebra->fn);CHKERRQ(ierr);
      ierr = VecDuplicate(algebra->solution, &algebra->oldsolution);CHKERRQ(ierr);
      if(user->Explicit_RK2||user->Explicit_RK4){
        ierr = PetscPrintf(PETSC_COMM_WORLD,"Use the second order Runge Kutta method \n");CHKERRQ(ierr);
      }else{
        ierr = PetscPrintf(PETSC_COMM_WORLD,"Use the first order forward Euler method \n");CHKERRQ(ierr);
      }
      nplot = 0; //the plot step
      while(user->current_time < (user->final_time - 0.05 * user->dt)){

        user->current_time = user->current_time + user->dt;
        ierr = FormTimeStepFunction(user, algebra, algebra->solution, algebra->fn);CHKERRQ(ierr);
        if(0){
            PetscViewer    viewer;
            ierr = OutputVTK(user->dm, "function.vtk", &viewer);CHKERRQ(ierr);
            ierr = VecView(algebra->fn, viewer);CHKERRQ(ierr);
            ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
          }

        if(user->Explicit_RK2){
        /*
          U^n_1   = U^n + 0.5*dt*f(U^n)
          U^{n+1} = U^n + dt*f(U^n_1)
        */
          ierr = VecCopy(algebra->solution, algebra->oldsolution);CHKERRQ(ierr);
          //note that algebra->oldsolution and algebra->solution are both U^n
          ierr = VecAXPY(algebra->solution, 0.5*user->dt, algebra->fn);CHKERRQ(ierr);
          //U^n_1 = U^n + 0.5*dt*f(U^n), now algebra->solution is U^n_1, and algebra->fn is f(U^n)

          ierr = FormTimeStepFunction(user, algebra, algebra->solution, algebra->fn);CHKERRQ(ierr);
          //algebra->fn is f(U^n_1)

          // reset the algebra->solution to U^n
          ierr = VecCopy(algebra->oldsolution, algebra->solution);CHKERRQ(ierr);
          ierr = VecAXPY(algebra->solution, user->dt, algebra->fn);CHKERRQ(ierr);
          // now algebra->solution is U^{n+1} = U^n + dt*f(U^n_1)
        }else if(user->Explicit_RK4){
        /* refer to https://en.wikipedia.org/wiki/Runge%E2%80%93Kutta_methods
          k_1     = f(U^n)
          U^n_1   = U^n + 0.5*dt*k_1
          k_2     = f(U^n_1)
          U^n_2   = U^n + 0.5*dt*k_2
          k_3     = f(U^n_2)
          U^n_3   = U^n + 0.5*dt*k_3
          k_4     = f(U^n_3)

          U^{n+1} = U^n + dt/6*(k_1 + 2*k_2 + 2*k_3 + k_4)
        */
          Vec  VecTemp; // store the U^n_1
          Vec  k1, k2, k3, k4;

          ierr = VecDuplicate(algebra->solution, &k1);CHKERRQ(ierr);
          ierr = VecDuplicate(algebra->solution, &k2);CHKERRQ(ierr);
          ierr = VecDuplicate(algebra->solution, &k3);CHKERRQ(ierr);
          ierr = VecDuplicate(algebra->solution, &k4);CHKERRQ(ierr);
          ierr = VecCopy(algebra->solution, algebra->oldsolution);CHKERRQ(ierr);

          ierr = VecCopy(algebra->fn, k1);CHKERRQ(ierr);
          //note that algebra->oldsolution and algebra->solution are both U^n
          ierr = VecAXPY(algebra->solution, 0.5*user->dt, k1);CHKERRQ(ierr);
          //U^n_1 = U^n + 0.5*dt*k1, now algebra->solution is U^n_1, and algebra->fn is f(U^n)

          ierr = FormTimeStepFunction(user, algebra, algebra->solution, algebra->fn);CHKERRQ(ierr);
          //algebra->fn is f(U^n_1)
          ierr = VecCopy(algebra->fn, k2);CHKERRQ(ierr);
          // reset the algebra->solution to U^n
          ierr = VecCopy(algebra->oldsolution, algebra->solution);CHKERRQ(ierr);
          ierr = VecAXPY(algebra->solution, 0.5*user->dt, k2);CHKERRQ(ierr);
          //U^n_2 = U^n + 0.5*dt*k2, now algebra->solution is U^n_2, and algebra->fn is f(U^n_1)

          ierr = FormTimeStepFunction(user, algebra, algebra->solution, algebra->fn);CHKERRQ(ierr);
          //algebra->fn is f(U^n_2)
          ierr = VecCopy(algebra->fn, k3);CHKERRQ(ierr);
          // reset the algebra->solution to U^n
          ierr = VecCopy(algebra->oldsolution, algebra->solution);CHKERRQ(ierr);
          ierr = VecAXPY(algebra->solution, 0.5*user->dt, k3);CHKERRQ(ierr);
          //U^n_3 = U^n + 0.5*dt*k3, now algebra->solution is U^n_3, and algebra->fn is f(U^n_2)

          ierr = FormTimeStepFunction(user, algebra, algebra->solution, algebra->fn);CHKERRQ(ierr);
          //algebra->fn is f(U^n_3)
          ierr = VecCopy(algebra->fn, k4);CHKERRQ(ierr);

          //U^{n+1} = U^n + dt/6*(k_1 + 2*k_2 + 2*k_3 + k_4)
          PetscReal temp;
          temp = user->dt/6;
          // reset the algebra->solution to U^n
          ierr = VecCopy(algebra->oldsolution, algebra->solution);CHKERRQ(ierr);
          ierr = VecAXPY(algebra->solution, temp, k1);CHKERRQ(ierr);
          // now algebra->solution is U^n + dt/6*k_1
          ierr = VecAXPY(algebra->solution, 2*temp, k2);CHKERRQ(ierr);
          // now algebra->solution is U^n + dt/6*k_1 + 2*dt/6*k_2
          ierr = VecAXPY(algebra->solution, 2*temp, k3);CHKERRQ(ierr);
          // now algebra->solution is U^n + dt/6*k_1 + 2*dt/6*k_2 + 2*dt/6*k_3
          ierr = VecAXPY(algebra->solution, temp, k4);CHKERRQ(ierr);
          // now algebra->solution is U^n + dt/6*k_1 + 2*dt/6*k_2 + 2*dt/6*k_3 + dt/6*k_4

          ierr = VecDestroy(&k1);CHKERRQ(ierr);
          ierr = VecDestroy(&k2);CHKERRQ(ierr);
          ierr = VecDestroy(&k3);CHKERRQ(ierr);
          ierr = VecDestroy(&k4);CHKERRQ(ierr);
        }else{
          ierr = VecCopy(algebra->solution, algebra->oldsolution);CHKERRQ(ierr);
          ierr = VecAXPY(algebra->solution, user->dt, algebra->fn);CHKERRQ(ierr);
        }

        {// Monitor the solution and function norms
          PetscReal         norm;
          PetscLogDouble    space =0;
          PetscInt          size;

          PetscReal fnnorm;
          ierr = VecNorm(algebra->fn,NORM_2,&fnnorm);CHKERRQ(ierr);
          //ierr = VecView(algebra->fn, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);

          ierr = VecNorm(algebra->solution,NORM_2,&norm);CHKERRQ(ierr);
          ierr = VecGetSize(algebra->solution, &size);CHKERRQ(ierr);
          norm   = norm/size;
          fnnorm = fnnorm/size;
          if (norm>1.e5) {
            SETERRQ2(PETSC_COMM_WORLD, PETSC_ERR_LIB,
            "The norm of the solution is: %f (current time: %f). The explicit method is going to DIVERGE!!!", norm, user->current_time);
          }
          if (user->current_step%10==0) {
            ierr = PetscPrintf(PETSC_COMM_WORLD,"Step %D at time %g with solution norm = %g and founction norm = %g \n",
                                user->current_step, user->current_time, norm, fnnorm);CHKERRQ(ierr);
          }
//          ierr =  PetscMallocGetCurrentUsage(&space);CHKERRQ(ierr);
//          if (user->current_step%10==0) {
//            ierr =  PetscPrintf(PETSC_COMM_WORLD,"Current space PetscMalloc()ed %g M\n",
//                                 space/(1024*1024));CHKERRQ(ierr);
//          }
        }

        { // Monitor the difference of two steps' solution
          PetscReal         norm;
          ierr = VecAXPY(algebra->oldsolution, -1, algebra->solution);CHKERRQ(ierr);
          ierr = VecNorm(algebra->oldsolution,NORM_2,&norm);CHKERRQ(ierr);
          if (user->current_step%10==0) {
            ierr = PetscPrintf(PETSC_COMM_WORLD,"Step %D at time %g with ||u_k-u_{k-1}|| = %g \n",
                              user->current_step, user->current_time, norm);CHKERRQ(ierr);
          }
          if((norm<1.e-6)||(user->current_step > user->max_time_its)){
            if(norm<1.e-6) ierr = PetscPrintf(PETSC_COMM_WORLD,"\n Convergence with ||u_k-u_{k-1}|| = %g < 1.e-6\n\n", norm);CHKERRQ(ierr);
            if(user->current_step > user->max_time_its) ierr = PetscPrintf(PETSC_COMM_WORLD,"\n Convergence with reaching the max time its\n\n");CHKERRQ(ierr);
            break;
          }
        }

        // output the solution
        if (user->output_solution && (user->current_step%user->steps_output==0)){
          PetscViewer    viewer;
          Vec            solution_unscaled; // Note the the algebra->solution is scaled by the density, so this is for the unscaled solution

          nplot = user->current_step/user->steps_output;
          // update file name for the current time step
          ierr = VecDuplicate(algebra->solution, &solution_unscaled);CHKERRQ(ierr);

          ierr = ReformatSolution(algebra->solution, solution_unscaled, user);CHKERRQ(ierr);

          ierr = PetscSNPrintf(fileName, sizeof(fileName),"%s_%d.vtk",user->solutionfile, nplot);CHKERRQ(ierr);
          ierr = PetscPrintf(PETSC_COMM_WORLD,"Outputing solution %s (current time %f)\n", fileName, user->current_time);CHKERRQ(ierr);
          ierr = OutputVTK(user->dm, fileName, &viewer);CHKERRQ(ierr);
          ierr = VecView(solution_unscaled, viewer);CHKERRQ(ierr);
          ierr = VecDestroy(&solution_unscaled);CHKERRQ(ierr);
          ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
        }

        user->current_step++;

      }

      ierr = VecDestroy(&algebra->fn);CHKERRQ(ierr);
    }else{ // Using the fully explicit method based on the PETSC TS routing
      PetscReal         ftime;
      TS                ts;
      TSConvergedReason reason;
      PetscInt          nsteps;
      //PetscReal         minRadius;

      //ierr = DMPlexTSGetGeometry(user->dm, NULL, NULL, &minRadius);CHKERRQ(ierr);
      //user->dt  = 0.9*4 * minRadius / 1.0;

      ierr = PetscPrintf(PETSC_COMM_WORLD,"Using the fully explicit method based on the PETSC TS routing\n");CHKERRQ(ierr);
      ierr = DMCreateGlobalVector(user->dm, &algebra->solution);CHKERRQ(ierr);
      ierr = PetscObjectSetName((PetscObject) algebra->solution, "solution");CHKERRQ(ierr);
      ierr = VecSet(algebra->solution, 0.0);CHKERRQ(ierr);
      ierr = SetInitialCondition(user->dm, algebra->solution, user);CHKERRQ(ierr);
      ierr = TSCreate(comm, &ts);CHKERRQ(ierr);
      ierr = TSSetType(ts, TSEULER);CHKERRQ(ierr);
      ierr = TSSetDM(ts, user->dm);CHKERRQ(ierr);
      ierr = TSMonitorSet(ts,TSMonitorFunctionError,(void*)user,NULL);CHKERRQ(ierr);
      ierr = TSSetRHSFunction(ts, NULL, MyRHSFunction, user);CHKERRQ(ierr);
      ierr = TSSetDuration(ts, 1000, user->final_time);CHKERRQ(ierr);
      ierr = TSSetInitialTimeStep(ts, user->initial_time, user->dt);CHKERRQ(ierr);
      ierr = TSSetFromOptions(ts);CHKERRQ(ierr);
      ierr = TSSolve(ts, algebra->solution);CHKERRQ(ierr);
      ierr = TSGetSolveTime(ts, &ftime);CHKERRQ(ierr);
      ierr = TSGetTimeStepNumber(ts, &nsteps);CHKERRQ(ierr);
      ierr = TSGetConvergedReason(ts, &reason);CHKERRQ(ierr);
      ierr = PetscPrintf(PETSC_COMM_WORLD,"%s at time %g after %D steps\n",TSConvergedReasons[reason],ftime,nsteps);CHKERRQ(ierr);
      ierr = TSDestroy(&ts);CHKERRQ(ierr);

    }

    if(user->benchmark_couette) {
      ierr = DMCreateGlobalVector(user->dm, &algebra->exactsolution);CHKERRQ(ierr);
      ierr = ComputeExactSolution(user->dm, user->current_time, algebra->exactsolution, user);CHKERRQ(ierr);
    }

    if(user->benchmark_couette) {
      PetscViewer    viewer;
      PetscReal      norm;

      ierr = OutputVTK(user->dm, "exact_solution.vtk", &viewer);CHKERRQ(ierr);
      ierr = VecView(algebra->exactsolution, viewer);CHKERRQ(ierr);
      ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);

      ierr = VecAXPY(algebra->exactsolution, -1, algebra->solution);CHKERRQ(ierr);
      ierr = VecNorm(algebra->exactsolution,NORM_INFINITY,&norm);CHKERRQ(ierr);
      ierr = PetscPrintf(PETSC_COMM_WORLD,"Final time at %f, Error: ||u_k-u|| = %g \n", user->current_time, norm);CHKERRQ(ierr);

      ierr = OutputVTK(user->dm, "Error.vtk", &viewer);CHKERRQ(ierr);
      ierr = VecView(algebra->exactsolution, viewer);CHKERRQ(ierr);
      ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
    }

    ierr = VecDestroy(&algebra->solution);CHKERRQ(ierr);
    if(user->myownexplicitmethod){ierr = VecDestroy(&algebra->oldsolution);CHKERRQ(ierr);}
    ierr = VecDestroy(&algebra->exactsolution);CHKERRQ(ierr);
    ierr = DMDestroy(&user->dm);CHKERRQ(ierr);
  } else if (user->TimeIntegralMethod == IMPLICITMETHOD) { // Using the fully implicit method
    ierr = PetscPrintf(PETSC_COMM_WORLD,"Using the fully implicit method\n");CHKERRQ(ierr);
    ierr =  SNESCreate(comm,&user->snes);CHKERRQ(ierr);
    ierr =  SNESSetDM(user->snes,user->dm);CHKERRQ(ierr);

    ierr = DMCreateGlobalVector(user->dm, &algebra->solution);CHKERRQ(ierr);
    ierr = VecDuplicate(algebra->solution, &algebra->oldsolution);CHKERRQ(ierr);
    ierr = VecDuplicate(algebra->solution, &algebra->f);CHKERRQ(ierr);
    ierr = VecDuplicate(algebra->solution, &algebra->fn);CHKERRQ(ierr);
    ierr = VecDuplicate(algebra->solution, &algebra->oldfn);CHKERRQ(ierr);

    ierr = PetscObjectSetName((PetscObject) algebra->solution, "solution");CHKERRQ(ierr);
    ierr = SetInitialCondition(user->dm, algebra->solution, user);CHKERRQ(ierr);

    ierr = DMSetMatType(user->dm, MATAIJ);CHKERRQ(ierr);
//    ierr = DMCreateMatrix(user->dm, &algebra->A);CHKERRQ(ierr);
    ierr = DMCreateMatrix(user->dm, &algebra->J);CHKERRQ(ierr);
    if (user->JdiffP) {
     /*Set up the preconditioner matrix*/
     ierr = DMCreateMatrix(user->dm, &algebra->P);CHKERRQ(ierr);
    }else{
     algebra->P = algebra->J;
    }

    ierr = MatSetOption(algebra->J, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE);CHKERRQ(ierr);

    /*set nonlinear function */
    ierr =  SNESSetFunction(user->snes, algebra->f, FormFunction, (void*)user);CHKERRQ(ierr);
    /* compute Jacobian */
    ierr =  SNESSetJacobian(user->snes, algebra->J, algebra->P, FormJacobian, (void*)user);CHKERRQ(ierr);

    ierr = SNESSetFromOptions(user->snes);CHKERRQ(ierr);

    /* do the solve */
    if (user->timestep == TIMESTEP_STEADY_STATE) {
      ierr = SolveSteadyState(user);CHKERRQ(ierr);
    } else {
      ierr = SolveTimeDependent(user);CHKERRQ(ierr);
    }

    if (user->output_solution){
      PetscViewer    viewer;
      Vec            solution_unscaled; // Note the the algebra->solution is scaled by the density, so this is for the unscaled solution

      ierr = VecDuplicate(algebra->solution, &solution_unscaled);CHKERRQ(ierr);
      ierr = ReformatSolution(algebra->solution, solution_unscaled, user);CHKERRQ(ierr);
      ierr = OutputVTK(user->dm, "solution.vtk", &viewer);CHKERRQ(ierr);
      ierr = VecView(solution_unscaled, viewer);CHKERRQ(ierr);
      ierr = VecDestroy(&solution_unscaled);CHKERRQ(ierr);
      ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
    }

    if(user->benchmark_couette) {
      PetscViewer    viewer;
      PetscReal      norm;

      ierr = OutputVTK(user->dm, "exact_solution.vtk", &viewer);CHKERRQ(ierr);
      ierr = VecView(algebra->exactsolution, viewer);CHKERRQ(ierr);
      ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);

      ierr = VecAXPY(algebra->exactsolution, -1, algebra->solution);CHKERRQ(ierr);
      ierr = VecNorm(algebra->exactsolution,NORM_INFINITY,&norm);CHKERRQ(ierr);
      ierr = PetscPrintf(PETSC_COMM_WORLD,"Error: ||u_k-u|| = %g \n", norm);CHKERRQ(ierr);

      ierr = OutputVTK(user->dm, "Error.vtk", &viewer);CHKERRQ(ierr);
      ierr = VecView(algebra->exactsolution, viewer);CHKERRQ(ierr);
      ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
    }

    ierr = VecDestroy(&algebra->solution);CHKERRQ(ierr);
    ierr = VecDestroy(&algebra->f);CHKERRQ(ierr);
    ierr = VecDestroy(&algebra->oldsolution);CHKERRQ(ierr);
    ierr = VecDestroy(&algebra->fn);CHKERRQ(ierr);
    ierr = VecDestroy(&algebra->oldfn);CHKERRQ(ierr);

    ierr = SNESDestroy(&user->snes);CHKERRQ(ierr);
    ierr = DMDestroy(&user->dm);CHKERRQ(ierr);

  } else {
    SETERRQ(PETSC_COMM_SELF,PETSC_ERR_USER,"WRONG option for the time integral method. Using the option '-time_integral_method 0 or 1'");
  }

  ierr = VecDestroy(&user->cellgeom);CHKERRQ(ierr);
  ierr = VecDestroy(&user->facegeom);CHKERRQ(ierr);
  ierr = DMDestroy(&user->dmGrad);CHKERRQ(ierr);

  ierr = PetscFunctionListDestroy(&LimitList);CHKERRQ(ierr);
  ierr = PetscFree(user->model->physics);CHKERRQ(ierr);
  ierr = PetscFree(user->algebra);CHKERRQ(ierr);
  ierr = PetscFree(user->model);CHKERRQ(ierr);
  ierr = PetscFree(user);CHKERRQ(ierr);

  {
    PetscLogDouble    space =0;
    ierr =  PetscMallocGetCurrentUsage(&space);CHKERRQ(ierr);
    ierr =  PetscPrintf(PETSC_COMM_WORLD,"Unfreed space at the End %g M\n", space/(1024*1024));CHKERRQ(ierr);
  }

  ierr = PetscFinalize();
  return(0);
}