//--------------------------------------------------------- void Maxwell2D::Report(bool bForce) //--------------------------------------------------------- { if (1 == tstep) { // print header umLOG(1, "\n step time Ezmin Ezmax\n" "----------------------------------\n"); } if (1 == tstep || !umMOD(tstep,Nreport) || bForce) { umLOG(1, "%5d %7.3lf %8.5lf %8.5lf\n", tstep, time, Ez.min_val(), Ez.max_val()); } //##################################### // skip field output for timing tests //##################################### //return; if (!umMOD(tstep,Nrender) || bForce) { Q_plot.set_col(1, Hx); // load plot data Q_plot.set_col(2, Hy); Q_plot.set_col(3, Ez); OutputVTK(Q_plot, NvtkInterp); } }
//--------------------------------------------------------- void CurvedINS2D::Report(bool bForce) //--------------------------------------------------------- { static DMat vort; bool normal_report=true; if (eVolkerCylinder == sim_type) {normal_report=false;} #if (1) normal_report=true; #endif // print report header on first step if (1 == tstep) { if (normal_report) { umLOG(1, "\n step time min(Ux) max(Ux) min(Vort) max(Vort)\n" "--------------------------------------------------------------------\n"); } else { umLOG(1, "\n step time Cd/ra Cl/ra dP \n" "---------------------------------------------------\n"); } } if (normal_report) { if (!umMOD(tstep,Nreport)||(1==tstep)||(tstep==Nsteps)||bForce) { Curl2D(Ux, Uy, vort); umLOG(1, "%7d %6.3lf %10.5lf %10.5lf %10.2lf %10.2lf\n", tstep, time, Ux.min_val(), Ux.max_val(), vort.min_val(), vort.max_val()); } } else { // VolkerCylinder: compute coefficients of drag and lift, // as well as the pressure drop at the two sample points. INSLiftDrag2D(0.05); } if (!umMOD(tstep,Nrender)||(1==tstep)||(tstep==Nsteps)||bForce) { // (this->*ExactSolution)(x, y, time, nu, exUx, exUy, exPR); Curl2D(Ux, Uy, vort); // load render data Q_plot.set_col(1, Ux); // -exUx); Q_plot.set_col(2, Uy); // -exUy); Q_plot.set_col(3, PR); // -exPR); Q_plot.set_col(4, vort); OutputVTK(Q_plot, NvtkInterp); } }
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); }
/** Creates \f$ f_n \f$ part of time-stepping scheme. For ODE solvers (aka time-stepping schemes), you think of your problem as \f$ y' = f(y) \f$ and Note that this actually returns something more like \f$ -f_n \f$. */ PetscErrorCode FormTimeStepFunction(User user, Algebra algebra, Vec in, Vec out) { PetscErrorCode ierr; PetscMPIInt rank; Vec inLocal; DM dmFace, dmCell; PetscFunctionBegin; ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr); ierr = VecSet(out, 0.0);CHKERRQ(ierr); // ierr = VecView(in, PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr); /*Since the DMPlexVecSetClosure only works on the local vectors, we need to create a local vector and scatter the global vector to the local vector and insert the values, and then scatter the local updated vectors back to the global vector.*/ ierr = DMGetLocalVector(user->dm, &inLocal);CHKERRQ(ierr); ierr = VecSet(inLocal, 0);CHKERRQ(ierr); ierr = DMGlobalToLocalBegin(user->dm, in, INSERT_VALUES, inLocal);CHKERRQ(ierr); ierr = DMGlobalToLocalEnd(user->dm, in, INSERT_VALUES, inLocal);CHKERRQ(ierr); ierr = ApplyBC(user->dm, user->current_time, inLocal, user);CHKERRQ(ierr); ierr = VecGetDM(user->facegeom,&dmFace);CHKERRQ(ierr); ierr = VecGetDM(user->cellgeom,&dmCell);CHKERRQ(ierr); ierr = ConstructCellCentriodGradient(user->dm, dmFace, dmCell, user->current_time, inLocal, out, user);CHKERRQ(ierr); /*Construct the cell gradient at the current time and save it into the user->dmGrad. If you want to use the cell gradient, following these: ierr = DMGetGlobalVector(user->dmGrad,&Grad);CHKERRQ(ierr); or ierr = DMGetLocalVector(user->dmGrad,&Grad);CHKERRQ(ierr); */ if (user->second_order){ ierr = CaculateLocalFunction_LS(user->dm, dmFace, dmCell, user->current_time, inLocal, out, user);CHKERRQ(ierr); }else{ ierr = CaculateLocalFunction_Upwind(user->dm, dmFace, dmCell, user->current_time, inLocal, out, user);CHKERRQ(ierr); } ierr = CaculateLocalSourceTerm(user->dm, inLocal, out, user);CHKERRQ(ierr); ierr = DMLocalToGlobalBegin(user->dm, inLocal, INSERT_VALUES, in);CHKERRQ(ierr); ierr = DMLocalToGlobalEnd(user->dm, inLocal, INSERT_VALUES, in);CHKERRQ(ierr); ierr = DMRestoreLocalVector(user->dm, &inLocal);CHKERRQ(ierr); //VecView(in,PETSC_VIEWER_STDOUT_WORLD); //VecView(out,PETSC_VIEWER_STDOUT_WORLD); if (0){ PetscViewer viewer; PetscReal fnnorm; ierr = VecNorm(out,NORM_INFINITY,&fnnorm);CHKERRQ(ierr); ierr = OutputVTK(user->dm, "function.vtk", &viewer);CHKERRQ(ierr); ierr = VecView(out, 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); } PetscFunctionReturn(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); }