int main(int argc, char **argv) { SNES snes; /* nonlinear solver */ Mat A,J; /* Jacobian,preconditioner matrix */ Vec u,r; /* solution, residual vectors */ AppCtx user; /* user-defined work context */ PetscReal error = 0.0; /* L_2 error in the solution */ PetscErrorCode ierr; ierr = PetscInitialize(&argc, &argv, NULL, help);CHKERRQ(ierr); ierr = ProcessOptions(PETSC_COMM_WORLD, &user);CHKERRQ(ierr); ierr = SNESCreate(PETSC_COMM_WORLD, &snes);CHKERRQ(ierr); ierr = CreateMesh(PETSC_COMM_WORLD, &user, &user.dm);CHKERRQ(ierr); ierr = SNESSetDM(snes, user.dm);CHKERRQ(ierr); ierr = SetupExactSolution(&user);CHKERRQ(ierr); ierr = SetupQuadrature(&user);CHKERRQ(ierr); ierr = SetupSection(user.dm, &user);CHKERRQ(ierr); ierr = DMCreateGlobalVector(user.dm, &u);CHKERRQ(ierr); ierr = VecDuplicate(u, &r);CHKERRQ(ierr); ierr = DMSetMatType(user.dm,MATAIJ);CHKERRQ(ierr); ierr = DMCreateMatrix(user.dm, &J);CHKERRQ(ierr); A = J; ierr = DMSNESSetFunctionLocal(user.dm, (PetscErrorCode (*)(DM,Vec,Vec,void*))FormFunctionLocal,&user);CHKERRQ(ierr); ierr = DMSNESSetJacobianLocal(user.dm, (PetscErrorCode (*)(DM,Vec,Mat,Mat,void*))FormJacobianLocal,&user);CHKERRQ(ierr); ierr = SNESSetFromOptions(snes);CHKERRQ(ierr); { PetscReal res; /* Check discretization error */ ierr = PetscPrintf(PETSC_COMM_WORLD, "Initial guess\n");CHKERRQ(ierr); ierr = VecView(u, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); /* ierr = ComputeError(u, &error, &user);CHKERRQ(ierr); */ ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: %g\n", error);CHKERRQ(ierr); /* Check residual */ ierr = SNESComputeFunction(snes,u,r);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "Initial Residual\n");CHKERRQ(ierr); ierr = VecChop(r, 1.0e-10);CHKERRQ(ierr); ierr = VecView(r, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = VecNorm(r, NORM_2, &res);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Residual: %g\n", res);CHKERRQ(ierr); } ierr = VecDestroy(&u);CHKERRQ(ierr); ierr = VecDestroy(&r);CHKERRQ(ierr); ierr = SNESDestroy(&snes);CHKERRQ(ierr); ierr = DMDestroy(&user.dm);CHKERRQ(ierr); ierr = PetscFinalize(); return 0; }
int main(int argc, char **argv) { PetscErrorCode ierr; Vec x; /* Solution vector */ TS ts; /* Time-stepping context */ AppCtx user; /* Application context */ Mat J; PetscViewer viewer; PetscInitialize(&argc,&argv,"petscopt_ex6", help); /* Get physics and time parameters */ ierr = Parameter_settings(&user);CHKERRQ(ierr); /* Create a 2D DA with dof = 1 */ ierr = DMDACreate2d(PETSC_COMM_WORLD,DMDA_BOUNDARY_NONE,DMDA_BOUNDARY_NONE,DMDA_STENCIL_STAR,-4,-4,PETSC_DECIDE,PETSC_DECIDE,1,1,NULL,NULL,&user.da);CHKERRQ(ierr); /* Set x and y coordinates */ ierr = DMDASetUniformCoordinates(user.da,user.xmin,user.xmax,user.ymin,user.ymax,NULL,NULL);CHKERRQ(ierr); /* Get global vector x from DM */ ierr = DMCreateGlobalVector(user.da,&x);CHKERRQ(ierr); ierr = ini_bou(x,&user);CHKERRQ(ierr); ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"ini_x",FILE_MODE_WRITE,&viewer);CHKERRQ(ierr); ierr = VecView(x,viewer);CHKERRQ(ierr); ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); /* Get Jacobian matrix structure from the da */ ierr = DMSetMatType(user.da,MATAIJ);CHKERRQ(ierr); ierr = DMCreateMatrix(user.da,&J);CHKERRQ(ierr); ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr); ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr); ierr = TSSetIFunction(ts,NULL,IFunction,&user);CHKERRQ(ierr); ierr = TSSetIJacobian(ts,J,J,IJacobian,&user);CHKERRQ(ierr); ierr = TSSetApplicationContext(ts,&user);CHKERRQ(ierr); ierr = TSSetDuration(ts,PETSC_DEFAULT,user.tmax);CHKERRQ(ierr); ierr = TSSetInitialTimeStep(ts,user.t0,.005);CHKERRQ(ierr); ierr = TSSetFromOptions(ts);CHKERRQ(ierr); ierr = TSSetPostStep(ts,PostStep);CHKERRQ(ierr); ierr = TSSolve(ts,x);CHKERRQ(ierr); ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"fin_x",FILE_MODE_WRITE,&viewer);CHKERRQ(ierr); ierr = VecView(x,viewer);CHKERRQ(ierr); ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); ierr = VecDestroy(&x);CHKERRQ(ierr); ierr = MatDestroy(&J);CHKERRQ(ierr); ierr = DMDestroy(&user.da);CHKERRQ(ierr); ierr = TSDestroy(&ts);CHKERRQ(ierr); PetscFinalize(); return 0; }
int main(int argc,char **argv) { PetscInt M = 3,N = 4,P = 2,s = 1,w = 2,i, m = PETSC_DECIDE,n = PETSC_DECIDE,p = PETSC_DECIDE; PetscErrorCode ierr; DM da; Mat mat; DMDAStencilType stencil_type = DMDA_STENCIL_BOX; PetscBool flg = PETSC_FALSE; MatStencil idx[2],idy[2]; PetscScalar *values; ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr); /* Read options */ ierr = PetscOptionsGetInt(NULL,"-M",&M,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetInt(NULL,"-N",&N,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetInt(NULL,"-P",&P,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetInt(NULL,"-m",&m,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetInt(NULL,"-n",&n,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetInt(NULL,"-p",&p,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetInt(NULL,"-s",&s,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetInt(NULL,"-w",&w,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetBool(NULL,"-star",&flg,NULL);CHKERRQ(ierr); if (flg) stencil_type = DMDA_STENCIL_STAR; /* Create distributed array and get vectors */ ierr = DMDACreate3d(PETSC_COMM_WORLD,DMDA_BOUNDARY_NONE,DMDA_BOUNDARY_NONE,DMDA_BOUNDARY_NONE,stencil_type,M,N,P,m,n,p,w,s, 0,0,0,&da);CHKERRQ(ierr); ierr = DMSetMatType(da,MATMPIBAIJ);CHKERRQ(ierr); ierr = DMCreateMatrix(da,&mat);CHKERRQ(ierr); idx[0].i = 1; idx[0].j = 1; idx[0].k = 0; idx[1].i = 2; idx[1].j = 1; idx[1].k = 0; idy[0].i = 1; idy[0].j = 2; idy[0].k = 0; idy[1].i = 2; idy[1].j = 2; idy[1].k = 0; ierr = PetscMalloc1(2*2*w*w,&values);CHKERRQ(ierr); for (i=0; i<2*2*w*w; i++) values[i] = i; ierr = MatSetValuesBlockedStencil(mat,2,idx,2,idy,values,INSERT_VALUES);CHKERRQ(ierr); ierr = MatAssemblyBegin(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); /* Free memory */ ierr = PetscFree(values);CHKERRQ(ierr); ierr = MatDestroy(&mat);CHKERRQ(ierr); ierr = DMDestroy(&da);CHKERRQ(ierr); ierr = PetscFinalize(); return 0; }
example is used for testing the subroutine MatLoad_MPI_DA\n\n"; #include <petscdm.h> #include <petscdmda.h> int main(int argc,char **argv) { PetscInt X = 10,Y = 8,Z=8; PetscErrorCode ierr; DM da; PetscViewer viewer; Mat A; ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr; ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"temp.dat",FILE_MODE_WRITE,&viewer);CHKERRQ(ierr); /* Read options */ ierr = PetscOptionsGetInt(NULL,NULL,"-X",&X,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetInt(NULL,NULL,"-Y",&Y,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetInt(NULL,NULL,"-Z",&Z,NULL);CHKERRQ(ierr); /* Create distributed array and get vectors */ ierr = DMDACreate3d(PETSC_COMM_WORLD,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DMDA_STENCIL_STAR,X,Y,Z,PETSC_DECIDE,PETSC_DECIDE,PETSC_DECIDE,1,1,NULL,NULL,NULL,&da);CHKERRQ(ierr); ierr = DMSetFromOptions(da);CHKERRQ(ierr); ierr = DMSetUp(da);CHKERRQ(ierr); ierr = DMSetMatType(da,MATMPIAIJ);CHKERRQ(ierr); ierr = DMCreateMatrix(da,&A);CHKERRQ(ierr); ierr = MatShift(A,X);CHKERRQ(ierr); ierr = MatView(A,viewer);CHKERRQ(ierr); ierr = MatDestroy(&A);CHKERRQ(ierr); ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"temp.dat",FILE_MODE_READ,&viewer);CHKERRQ(ierr); ierr = DMCreateMatrix(da,&A);CHKERRQ(ierr); ierr = MatLoad(A,viewer);CHKERRQ(ierr); /* Free memory */ ierr = MatDestroy(&A);CHKERRQ(ierr); ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); ierr = DMDestroy(&da);CHKERRQ(ierr); ierr = PetscFinalize(); return ierr; }
PetscErrorCode MyComputeFunction(SNES snes,Vec x,Vec F,void *ctx) { PetscErrorCode ierr; Mat J; DM dm; PetscFunctionBeginUser; ierr = SNESGetDM(snes,&dm);CHKERRQ(ierr); ierr = DMGetApplicationContext(dm,&J);CHKERRQ(ierr); if (!J) { ierr = DMSetMatType(dm,MATAIJ);CHKERRQ(ierr); ierr = DMCreateMatrix(dm,&J);CHKERRQ(ierr); ierr = MatSetDM(J, NULL);CHKERRQ(ierr); ierr = FormMatrix(dm,J);CHKERRQ(ierr); ierr = DMSetApplicationContext(dm,J);CHKERRQ(ierr); ierr = DMSetApplicationContextDestroy(dm,(PetscErrorCode (*)(void**))MatDestroy);CHKERRQ(ierr); } ierr = MatMult(J,x,F);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); }
/* Mm_ratio - ration of grid lines between fine and coarse grids. */ int main(int argc,char **argv) { PetscErrorCode ierr; AppCtx user; PetscMPIInt size,rank; PetscInt m,n,M,N,i,nrows; PetscScalar one = 1.0; PetscReal fill=2.0; Mat A,P,R,C,PtAP; PetscScalar *array; PetscRandom rdm; PetscBool Test_3D=PETSC_FALSE,flg; const PetscInt *ia,*ja; ierr = PetscInitialize(&argc,&argv,NULL,help);if (ierr) return ierr; ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr); ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr); /* Get size of fine grids and coarse grids */ user.ratio = 2; user.coarse.mx = 4; user.coarse.my = 4; user.coarse.mz = 4; ierr = PetscOptionsGetInt(NULL,NULL,"-Mx",&user.coarse.mx,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetInt(NULL,NULL,"-My",&user.coarse.my,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetInt(NULL,NULL,"-Mz",&user.coarse.mz,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetInt(NULL,NULL,"-ratio",&user.ratio,NULL);CHKERRQ(ierr); if (user.coarse.mz) Test_3D = PETSC_TRUE; user.fine.mx = user.ratio*(user.coarse.mx-1)+1; user.fine.my = user.ratio*(user.coarse.my-1)+1; user.fine.mz = user.ratio*(user.coarse.mz-1)+1; if (!rank) { if (!Test_3D) { ierr = PetscPrintf(PETSC_COMM_SELF,"coarse grids: %D %D; fine grids: %D %D\n",user.coarse.mx,user.coarse.my,user.fine.mx,user.fine.my);CHKERRQ(ierr); } else { ierr = PetscPrintf(PETSC_COMM_SELF,"coarse grids: %D %D %D; fine grids: %D %D %D\n",user.coarse.mx,user.coarse.my,user.coarse.mz,user.fine.mx,user.fine.my,user.fine.mz);CHKERRQ(ierr); } } /* Set up distributed array for fine grid */ if (!Test_3D) { ierr = DMDACreate2d(PETSC_COMM_WORLD, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE,DMDA_STENCIL_STAR,user.fine.mx,user.fine.my,PETSC_DECIDE,PETSC_DECIDE,1,1,NULL,NULL,&user.fine.da);CHKERRQ(ierr); } else { ierr = DMDACreate3d(PETSC_COMM_WORLD,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DMDA_STENCIL_STAR,user.fine.mx,user.fine.my,user.fine.mz,PETSC_DECIDE,PETSC_DECIDE,PETSC_DECIDE, 1,1,NULL,NULL,NULL,&user.fine.da);CHKERRQ(ierr); } ierr = DMSetFromOptions(user.fine.da);CHKERRQ(ierr); ierr = DMSetUp(user.fine.da);CHKERRQ(ierr); /* Create and set A at fine grids */ ierr = DMSetMatType(user.fine.da,MATAIJ);CHKERRQ(ierr); ierr = DMCreateMatrix(user.fine.da,&A);CHKERRQ(ierr); ierr = MatGetLocalSize(A,&m,&n);CHKERRQ(ierr); ierr = MatGetSize(A,&M,&N);CHKERRQ(ierr); /* set val=one to A (replace with random values!) */ ierr = PetscRandomCreate(PETSC_COMM_WORLD,&rdm);CHKERRQ(ierr); ierr = PetscRandomSetFromOptions(rdm);CHKERRQ(ierr); if (size == 1) { ierr = MatGetRowIJ(A,0,PETSC_FALSE,PETSC_FALSE,&nrows,&ia,&ja,&flg);CHKERRQ(ierr); if (flg) { ierr = MatSeqAIJGetArray(A,&array);CHKERRQ(ierr); for (i=0; i<ia[nrows]; i++) array[i] = one; ierr = MatSeqAIJRestoreArray(A,&array);CHKERRQ(ierr); } ierr = MatRestoreRowIJ(A,0,PETSC_FALSE,PETSC_FALSE,&nrows,&ia,&ja,&flg);CHKERRQ(ierr); } else { Mat AA,AB; ierr = MatMPIAIJGetSeqAIJ(A,&AA,&AB,NULL);CHKERRQ(ierr); ierr = MatGetRowIJ(AA,0,PETSC_FALSE,PETSC_FALSE,&nrows,&ia,&ja,&flg);CHKERRQ(ierr); if (flg) { ierr = MatSeqAIJGetArray(AA,&array);CHKERRQ(ierr); for (i=0; i<ia[nrows]; i++) array[i] = one; ierr = MatSeqAIJRestoreArray(AA,&array);CHKERRQ(ierr); } ierr = MatRestoreRowIJ(AA,0,PETSC_FALSE,PETSC_FALSE,&nrows,&ia,&ja,&flg);CHKERRQ(ierr); ierr = MatGetRowIJ(AB,0,PETSC_FALSE,PETSC_FALSE,&nrows,&ia,&ja,&flg);CHKERRQ(ierr); if (flg) { ierr = MatSeqAIJGetArray(AB,&array);CHKERRQ(ierr); for (i=0; i<ia[nrows]; i++) array[i] = one; ierr = MatSeqAIJRestoreArray(AB,&array);CHKERRQ(ierr); } ierr = MatRestoreRowIJ(AB,0,PETSC_FALSE,PETSC_FALSE,&nrows,&ia,&ja,&flg);CHKERRQ(ierr); } /* Set up distributed array for coarse grid */ if (!Test_3D) { ierr = DMDACreate2d(PETSC_COMM_WORLD, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE,DMDA_STENCIL_STAR,user.coarse.mx,user.coarse.my,PETSC_DECIDE,PETSC_DECIDE,1,1,NULL,NULL,&user.coarse.da);CHKERRQ(ierr); } else { ierr = DMDACreate3d(PETSC_COMM_WORLD,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DMDA_STENCIL_STAR,user.coarse.mx,user.coarse.my,user.coarse.mz,PETSC_DECIDE,PETSC_DECIDE,PETSC_DECIDE,1,1,NULL,NULL,NULL,&user.coarse.da);CHKERRQ(ierr); } ierr = DMSetFromOptions(user.coarse.da);CHKERRQ(ierr); ierr = DMSetUp(user.coarse.da);CHKERRQ(ierr); /* Create interpolation between the fine and coarse grids */ ierr = DMCreateInterpolation(user.coarse.da,user.fine.da,&P,NULL);CHKERRQ(ierr); /* Get R = P^T */ ierr = MatTranspose(P,MAT_INITIAL_MATRIX,&R);CHKERRQ(ierr); /* C = R*A*P */ ierr = MatMatMatMult(R,A,P,MAT_INITIAL_MATRIX,fill,&C);CHKERRQ(ierr); ierr = MatMatMatMult(R,A,P,MAT_REUSE_MATRIX,fill,&C);CHKERRQ(ierr); /* Test C == PtAP */ ierr = MatPtAP(A,P,MAT_INITIAL_MATRIX,fill,&PtAP);CHKERRQ(ierr); ierr = MatPtAP(A,P,MAT_REUSE_MATRIX,fill,&PtAP);CHKERRQ(ierr); ierr = MatEqual(C,PtAP,&flg);CHKERRQ(ierr); if (!flg) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_PLIB,"Matrices are not equal"); ierr = MatDestroy(&PtAP);CHKERRQ(ierr); /* Clean up */ ierr = MatDestroy(&A);CHKERRQ(ierr); ierr = PetscRandomDestroy(&rdm);CHKERRQ(ierr); ierr = DMDestroy(&user.fine.da);CHKERRQ(ierr); ierr = DMDestroy(&user.coarse.da);CHKERRQ(ierr); ierr = MatDestroy(&P);CHKERRQ(ierr); ierr = MatDestroy(&R);CHKERRQ(ierr); ierr = MatDestroy(&C);CHKERRQ(ierr); ierr = PetscFinalize(); return ierr; }
PetscErrorCode efs_setup(efs *slv, int offset[], int stride[]) { PetscErrorCode ierr; PetscInt xs, ys, zs, xm, ym, zm; PCType pc_type; if (efs_log(slv, EFS_LOG_STATUS)) { ierr = ef_io_print(slv->comm, "Setting up electric field solver");CHKERRQ(ierr); } slv->ts = 0; if (efs_log(slv, EFS_LOG_RESIDUAL)) { ierr = PetscOptionsSetValue("-ksp_monitor_short", NULL);CHKERRQ(ierr); } ierr = DMDASetFieldName(slv->dm, 0,"potential");CHKERRQ(ierr); if (slv->grid.nd == 2) { ierr = DMDAGetCorners(slv->dm, &xs, &ys, 0, &xm, &ym, 0);CHKERRQ(ierr); slv->dmap = ef_dmap_create_2d(xs - offset[0], ys - offset[1], xm, ym, stride); } else if (slv->grid.nd == 3) { ierr = DMDAGetCorners(slv->dm, &xs, &ys, &zs, &xm, &ym, &zm);CHKERRQ(ierr); slv->dmap = ef_dmap_create_3d(xs - offset[0], ys - offset[1], zs - offset[2], xm, ym, zm, stride); } else { SETERRQ1(PETSC_COMM_WORLD, PETSC_ERR_SUP, "Unsupported dimmension: %d", slv->grid.nd); } ierr = ef_callback_create(&slv->callback);CHKERRQ(ierr); ierr = KSPCreate(slv->comm, &slv->ksp);CHKERRQ(ierr); if (efs_log(slv, EFS_LOG_EIGS)) { ierr = KSPSetComputeEigenvalues(slv->ksp, PETSC_TRUE);CHKERRQ(ierr); } ierr = KSPSetDM(slv->ksp, slv->dm);CHKERRQ(ierr); ierr = KSPGetPC(slv->ksp, &slv->pc);CHKERRQ(ierr); ierr = PCSetType(slv->pc, PCMG);CHKERRQ(ierr); if (slv->options.galerkin) { ierr = PCMGSetGalerkin(slv->pc, PETSC_TRUE);CHKERRQ(ierr); } else { ierr = PCMGSetGalerkin(slv->pc, PETSC_FALSE);CHKERRQ(ierr); } ierr = KSPSetComputeOperators(slv->ksp, slv->callback->matrix, slv);CHKERRQ(ierr); ierr = KSPSetComputeRHS(slv->ksp, slv->callback->rhs, slv);CHKERRQ(ierr); ierr = KSPSetComputeInitialGuess(slv->ksp, slv->callback->guess, slv);CHKERRQ(ierr); ierr = KSPSetFromOptions(slv->ksp);CHKERRQ(ierr); ierr = PCGetType(slv->pc, &pc_type);CHKERRQ(ierr); ierr = PCMGGetLevels(slv->pc, &slv->options.levels);CHKERRQ(ierr); if (slv->options.levels < 1) slv->options.levels++; ierr = PCMGGetGalerkin(slv->pc, &slv->options.galerkin);CHKERRQ(ierr); if (strcmp(pc_type, PCGAMG) == 0 || strcmp(pc_type, PCHYPRE) == 0) slv->options.galerkin = 1; if (!slv->options.galerkin) { slv->levels = (ef_level*) malloc(slv->options.levels*sizeof(ef_level)); // setup callback for transforming rhs on coarse levels } else { slv->levels = (ef_level*) malloc(sizeof(ef_level)); } ierr = ef_fd_create(&slv->fd, EF_FD_STANDARD_O2);CHKERRQ(ierr); ierr = ef_operator_create(&slv->op, slv->levels, slv->fd, slv->grid.nd);CHKERRQ(ierr); ierr = ef_boundary_create(&slv->boundary, slv->levels, slv->options.levels, slv->dmap, &slv->state, slv->fd);CHKERRQ(ierr); slv->op->axisymmetric = slv->options.axisymmetric; slv->boundary->axisymmetric = slv->options.axisymmetric; ierr = DMSetMatType(slv->dm, MATAIJ);CHKERRQ(ierr); ierr = DMCreateGlobalVector(slv->dm, &slv->levels[0].eps);CHKERRQ(ierr); ierr = DMCreateGlobalVector(slv->dm, &slv->levels[0].g);CHKERRQ(ierr); ierr = DMCreateGlobalVector(slv->dm, &slv->levels[0].ag);CHKERRQ(ierr); ierr = DMCreateGlobalVector(slv->dm, &slv->levels[0].gcomp);CHKERRQ(ierr); ierr = DMCreateGlobalVector(slv->dm, &slv->levels[0].scale);CHKERRQ(ierr); ierr = DMCreateGlobalVector(slv->dm, &slv->levels[0].nscale);CHKERRQ(ierr); ierr = VecSet(slv->levels[0].g, 0);CHKERRQ(ierr); ierr = VecSet(slv->levels[0].gcomp, 1);CHKERRQ(ierr); ierr = VecSet(slv->levels[0].scale, 1);CHKERRQ(ierr); ierr = VecSet(slv->levels[0].nscale, 1);CHKERRQ(ierr); ierr = DMCoarsenHookAdd(slv->dm, slv->callback->coarsen, slv->callback->restrct, slv);CHKERRQ(ierr); return 0; }
/* Notice that this requires the previous momentum solution. The element stiffness matrix for the identity in linear elements is 1 /2 1 1\ - |1 2 1| 12 \1 1 2/ no matter what the shape of the triangle. */ PetscErrorCode TaylorGalerkinStepIIMassEnergy(DM da, UserContext *user) { MPI_Comm comm; Mat mat; Vec rhs_m, rhs_e; PetscScalar identity[9] = {0.16666666667, 0.08333333333, 0.08333333333, 0.08333333333, 0.16666666667, 0.08333333333, 0.08333333333, 0.08333333333, 0.16666666667}; PetscScalar *u_n, *v_n, *p_n, *t_n, *mu_n, *kappa_n; PetscScalar *rho_n, *rho_u_n, *rho_v_n, *rho_e_n; PetscScalar *u_phi, *v_phi; PetscScalar *rho_u_np1, *rho_v_np1; PetscInt idx[3]; PetscScalar psi_x[3], psi_y[3]; PetscScalar values_m[3]; PetscScalar values_e[3]; PetscScalar phi = user->phi; PetscScalar mu, kappa, tau_xx, tau_xy, tau_yy, q_x, q_y; PetscReal hx, hy, area; KSP ksp; const PetscInt *necon; PetscInt j, k, e, ne, nc, mx, my; PetscErrorCode ierr; PetscFunctionBeginUser; ierr = PetscObjectGetComm((PetscObject) da, &comm);CHKERRQ(ierr); ierr = DMSetMatType(da,MATAIJ);CHKERRQ(ierr); ierr = DMCreateMatrix(da, &mat);CHKERRQ(ierr); ierr = MatSetOption(mat,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE);CHKERRQ(ierr); ierr = DMGetGlobalVector(da, &rhs_m);CHKERRQ(ierr); ierr = DMGetGlobalVector(da, &rhs_e);CHKERRQ(ierr); ierr = KSPCreate(comm, &ksp);CHKERRQ(ierr); ierr = KSPSetFromOptions(ksp);CHKERRQ(ierr); ierr = DMDAGetInfo(da, 0, &mx, &my, 0,0,0,0,0,0,0,0,0,0);CHKERRQ(ierr); hx = 1.0 / (PetscReal)(mx-1); hy = 1.0 / (PetscReal)(my-1); area = 0.5*hx*hy; ierr = VecGetArray(user->sol_n.u, &u_n);CHKERRQ(ierr); ierr = VecGetArray(user->sol_n.v, &v_n);CHKERRQ(ierr); ierr = VecGetArray(user->sol_n.p, &p_n);CHKERRQ(ierr); ierr = VecGetArray(user->sol_n.t, &t_n);CHKERRQ(ierr); ierr = VecGetArray(user->mu, &mu_n);CHKERRQ(ierr); ierr = VecGetArray(user->kappa, &kappa_n);CHKERRQ(ierr); ierr = VecGetArray(user->sol_n.rho, &rho_n);CHKERRQ(ierr); ierr = VecGetArray(user->sol_n.rho_u, &rho_u_n);CHKERRQ(ierr); ierr = VecGetArray(user->sol_n.rho_v, &rho_v_n);CHKERRQ(ierr); ierr = VecGetArray(user->sol_n.rho_e, &rho_e_n);CHKERRQ(ierr); ierr = VecGetArray(user->sol_phi.u, &u_phi);CHKERRQ(ierr); ierr = VecGetArray(user->sol_phi.v, &v_phi);CHKERRQ(ierr); ierr = VecGetArray(user->sol_np1.rho_u, &rho_u_np1);CHKERRQ(ierr); ierr = VecGetArray(user->sol_np1.rho_v, &rho_v_np1);CHKERRQ(ierr); ierr = DMDAGetElements(da, &ne, &nc, &necon);CHKERRQ(ierr); for (e = 0; e < ne; e++) { for (j = 0; j < 3; j++) { idx[j] = necon[3*e+j]; values_m[j] = 0.0; values_e[j] = 0.0; } /* Get basis function deriatives (we need the orientation of the element here) */ if (idx[1] > idx[0]) { psi_x[0] = -hy; psi_x[1] = hy; psi_x[2] = 0.0; psi_y[0] = -hx; psi_y[1] = 0.0; psi_y[2] = hx; } else { psi_x[0] = hy; psi_x[1] = -hy; psi_x[2] = 0.0; psi_y[0] = hx; psi_y[1] = 0.0; psi_y[2] = -hx; } /* <\nabla\psi, F^*>: Divergence of the predicted convective fluxes */ for (j = 0; j < 3; j++) { values_m[j] += (psi_x[j]*(phi*rho_u_np1[idx[j]] + rho_u_n[idx[j]]) + psi_y[j]*(rho_v_np1[idx[j]] + rho_v_n[idx[j]]))/3.0; values_e[j] += values_m[j]*((rho_e_n[idx[j]] + p_n[idx[j]]) / rho_n[idx[j]]); } /* -<\nabla\psi, F^n_v>: Divergence of the viscous fluxes */ for (j = 0; j < 3; j++) { /* \tau_{xx} = 2/3 \mu(T) (2 {\partial u\over\partial x} - {\partial v\over\partial y}) */ /* \tau_{xy} = \mu(T) ( {\partial u\over\partial y} + {\partial v\over\partial x}) */ /* \tau_{yy} = 2/3 \mu(T) (2 {\partial v\over\partial y} - {\partial u\over\partial x}) */ /* q_x = -\kappa(T) {\partial T\over\partial x} */ /* q_y = -\kappa(T) {\partial T\over\partial y} */ /* above code commeted out - causing ininitialized variables. */ q_x =0; q_y =0; mu = 0.0; kappa = 0.0; tau_xx = 0.0; tau_xy = 0.0; tau_yy = 0.0; for (k = 0; k < 3; k++) { mu += mu_n[idx[k]]; kappa += kappa_n[idx[k]]; tau_xx += 2.0*psi_x[k]*u_n[idx[k]] - psi_y[k]*v_n[idx[k]]; tau_xy += psi_y[k]*u_n[idx[k]] + psi_x[k]*v_n[idx[k]]; tau_yy += 2.0*psi_y[k]*v_n[idx[k]] - psi_x[k]*u_n[idx[k]]; q_x += psi_x[k]*t_n[idx[k]]; q_y += psi_y[k]*t_n[idx[k]]; } mu /= 3.0; kappa /= 3.0; tau_xx *= (2.0/3.0)*mu; tau_xy *= mu; tau_yy *= (2.0/3.0)*mu; values_e[j] -= area*(psi_x[j]*(u_phi[e]*tau_xx + v_phi[e]*tau_xy + q_x) + psi_y[j]*(u_phi[e]*tau_xy + v_phi[e]*tau_yy + q_y)); } /* Accumulate to global structures */ ierr = VecSetValuesLocal(rhs_m, 3, idx, values_m, ADD_VALUES);CHKERRQ(ierr); ierr = VecSetValuesLocal(rhs_e, 3, idx, values_e, ADD_VALUES);CHKERRQ(ierr); ierr = MatSetValuesLocal(mat, 3, idx, 3, idx, identity, ADD_VALUES);CHKERRQ(ierr); } ierr = DMDARestoreElements(da, &ne, &nc, &necon);CHKERRQ(ierr); ierr = VecRestoreArray(user->sol_n.u, &u_n);CHKERRQ(ierr); ierr = VecRestoreArray(user->sol_n.v, &v_n);CHKERRQ(ierr); ierr = VecRestoreArray(user->sol_n.p, &p_n);CHKERRQ(ierr); ierr = VecRestoreArray(user->sol_n.t, &t_n);CHKERRQ(ierr); ierr = VecRestoreArray(user->mu, &mu_n);CHKERRQ(ierr); ierr = VecRestoreArray(user->kappa, &kappa_n);CHKERRQ(ierr); ierr = VecRestoreArray(user->sol_n.rho, &rho_n);CHKERRQ(ierr); ierr = VecRestoreArray(user->sol_n.rho_u, &rho_u_n);CHKERRQ(ierr); ierr = VecRestoreArray(user->sol_n.rho_v, &rho_v_n);CHKERRQ(ierr); ierr = VecRestoreArray(user->sol_n.rho_e, &rho_e_n);CHKERRQ(ierr); ierr = VecRestoreArray(user->sol_phi.u, &u_phi);CHKERRQ(ierr); ierr = VecRestoreArray(user->sol_phi.v, &v_phi);CHKERRQ(ierr); ierr = VecRestoreArray(user->sol_np1.rho_u, &rho_u_np1);CHKERRQ(ierr); ierr = VecRestoreArray(user->sol_np1.rho_v, &rho_v_np1);CHKERRQ(ierr); ierr = VecAssemblyBegin(rhs_m);CHKERRQ(ierr); ierr = VecAssemblyBegin(rhs_e);CHKERRQ(ierr); ierr = MatAssemblyBegin(mat, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = VecAssemblyEnd(rhs_m);CHKERRQ(ierr); ierr = VecAssemblyEnd(rhs_e);CHKERRQ(ierr); ierr = MatAssemblyEnd(mat, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = VecScale(rhs_m, user->dt);CHKERRQ(ierr); ierr = VecScale(rhs_e, user->dt);CHKERRQ(ierr); ierr = KSPSetOperators(ksp, mat, mat, DIFFERENT_NONZERO_PATTERN);CHKERRQ(ierr); ierr = KSPSolve(ksp, rhs_m, user->sol_np1.rho);CHKERRQ(ierr); ierr = KSPSolve(ksp, rhs_e, user->sol_np1.rho_e);CHKERRQ(ierr); ierr = KSPDestroy(&ksp);CHKERRQ(ierr); ierr = MatDestroy(&mat);CHKERRQ(ierr); ierr = DMRestoreGlobalVector(da, &rhs_m);CHKERRQ(ierr); ierr = DMRestoreGlobalVector(da, &rhs_e);CHKERRQ(ierr); PetscFunctionReturn(0); }
int main(int argc, char **argv) { DM dm; TS ts; Vec X; Mat J; PetscInt steps, maxsteps, mx; PetscReal ftime, hx, dt; TSConvergedReason reason; struct _User user; PetscErrorCode ierr; ierr = PetscInitialize(&argc, &argv, NULL,help);if (ierr) return ierr; ierr = DMDACreate1d(PETSC_COMM_WORLD, DM_BOUNDARY_NONE, -11, 3, 1, NULL, &dm);CHKERRQ(ierr); ierr = DMSetFromOptions(dm);CHKERRQ(ierr); ierr = DMSetUp(dm);CHKERRQ(ierr); ierr = DMDASetUniformCoordinates(dm, 0.0, 20.0, 0.0, 0.0, 0.0, 0.0);CHKERRQ(ierr); ierr = DMCreateGlobalVector(dm, &X);CHKERRQ(ierr); ierr = PetscOptionsBegin(PETSC_COMM_WORLD, NULL, "Dynamic Friction Options", ""); { user.epsilon = 0.1; user.gamma = 0.5; user.gammaTilde = 0.5; user.xi = 0.5; user.c = 0.5; ierr = PetscOptionsReal("-epsilon", "Inverse of seismic ratio", "", user.epsilon, &user.epsilon, NULL);CHKERRQ(ierr); ierr = PetscOptionsReal("-gamma", "Wave frequency for interblock coupling", "", user.gamma, &user.gamma, NULL);CHKERRQ(ierr); ierr = PetscOptionsReal("-gamma_tilde", "Wave frequency for plate coupling", "", user.gammaTilde, &user.gammaTilde, NULL);CHKERRQ(ierr); ierr = PetscOptionsReal("-xi", "Interblock spring constant", "", user.xi, &user.xi, NULL);CHKERRQ(ierr); ierr = PetscOptionsReal("-c", "Wavespeed", "", user.c, &user.c, NULL);CHKERRQ(ierr); } ierr = PetscOptionsEnd();CHKERRQ(ierr); ierr = TSCreate(PETSC_COMM_WORLD, &ts);CHKERRQ(ierr); ierr = TSSetDM(ts, dm);CHKERRQ(ierr); ierr = TSSetRHSFunction(ts, NULL, FormRHSFunction, &user);CHKERRQ(ierr); ierr = TSSetIFunction(ts, NULL, FormIFunction, &user);CHKERRQ(ierr); ierr = DMSetMatType(dm, MATAIJ);CHKERRQ(ierr); ierr = DMCreateMatrix(dm, &J);CHKERRQ(ierr); ierr = TSSetIJacobian(ts, J, J, FormIJacobian, &user);CHKERRQ(ierr); ftime = 800.0; maxsteps = 10000; ierr = TSSetDuration(ts, maxsteps, ftime);CHKERRQ(ierr); ierr = TSSetExactFinalTime(ts,TS_EXACTFINALTIME_STEPOVER);CHKERRQ(ierr); ierr = FormInitialSolution(ts, X, &user);CHKERRQ(ierr); ierr = TSSetSolution(ts, X);CHKERRQ(ierr); ierr = VecGetSize(X, &mx);CHKERRQ(ierr); hx = 20.0/(PetscReal)(mx-1); dt = 0.4 * PetscSqr(hx) / PetscSqr(user.c); /* Diffusive stability limit */ ierr = TSSetInitialTimeStep(ts, 0.0, dt);CHKERRQ(ierr); ierr = TSSetFromOptions(ts);CHKERRQ(ierr); ierr = TSSolve(ts, X);CHKERRQ(ierr); ierr = TSGetSolveTime(ts, &ftime);CHKERRQ(ierr); ierr = TSGetTimeStepNumber(ts, &steps);CHKERRQ(ierr); ierr = TSGetConvergedReason(ts, &reason);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "%s at time %g after %D steps\n", TSConvergedReasons[reason], (double)ftime, steps);CHKERRQ(ierr); ierr = MatDestroy(&J);CHKERRQ(ierr); ierr = VecDestroy(&X);CHKERRQ(ierr); ierr = TSDestroy(&ts);CHKERRQ(ierr); ierr = DMDestroy(&dm);CHKERRQ(ierr); ierr = PetscFinalize(); return ierr; }
PetscErrorCode SetUpMatrices(AppCtx *user) { PetscErrorCode ierr; PetscInt nele,nen,i,j; const PetscInt *ele; PetscScalar dt=user->dt; PetscScalar y[3]; PetscInt idx[3]; PetscScalar eM_0[3][3],eM_2_odd[3][3],eM_2_even[3][3]; Mat M =user->M; PetscScalar epsilon=user->epsilon; PetscScalar hx; PetscInt n,Mda,Nda; DM da; PetscFunctionBeginUser; /* Create the mass matrix M_0 */ ierr = MatGetLocalSize(M,&n,NULL);CHKERRQ(ierr); /* ierr = MatCreate(PETSC_COMM_WORLD,&user->M_0);CHKERRQ(ierr);*/ ierr = DMDAGetInfo(user->da,NULL,&Mda,&Nda,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL); hx = 1.0/(Mda-1); ierr = DMDACreate2d(PETSC_COMM_WORLD,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DMDA_STENCIL_BOX,Mda,Nda,PETSC_DECIDE,PETSC_DECIDE,1,1,NULL,NULL,&da);CHKERRQ(ierr); ierr = DMSetMatType(da,MATAIJ);CHKERRQ(ierr); ierr = DMCreateMatrix(da,&user->M_0);CHKERRQ(ierr); ierr = DMDestroy(&da);CHKERRQ(ierr); eM_0[0][0]=eM_0[1][1]=eM_0[2][2]=hx*hx/12.0; eM_0[0][1]=eM_0[0][2]=eM_0[1][0]=eM_0[1][2]=eM_0[2][0]=eM_0[2][1]=hx*hx/24.0; eM_2_odd[0][0] = eM_2_odd[0][1] = eM_2_odd[0][2] = 0.0; eM_2_odd[1][0] = eM_2_odd[1][1] = eM_2_odd[1][2] = 0.0; eM_2_odd[2][0] = eM_2_odd[2][1] = eM_2_odd[2][2] = 0.0; eM_2_odd[0][0]=1.0; eM_2_odd[1][1]=eM_2_odd[2][2]=0.5; eM_2_odd[0][1]=eM_2_odd[0][2]=eM_2_odd[1][0]=eM_2_odd[2][0]=-0.5; eM_2_even[0][0] = eM_2_even[0][1] = eM_2_even[0][2] = 0.0; eM_2_even[0][0] = eM_2_even[0][1] = eM_2_even[0][2] = 0.0; eM_2_even[0][0] = eM_2_even[0][1] = eM_2_even[0][2] = 0.0; eM_2_even[1][1]=1; eM_2_even[0][0]=eM_2_even[2][2]=0.5; eM_2_even[0][1]=eM_2_even[1][0]=eM_2_even[1][2]=eM_2_even[2][1]=-0.5; /* Get local element info */ ierr = DMDAGetElements(user->da,&nele,&nen,&ele);CHKERRQ(ierr); for (i=0; i < nele; i++) { idx[0] = ele[3*i]; idx[1] = ele[3*i+1]; idx[2] = ele[3*i+2]; PetscInt row,cols[3],r,row_M_0; PetscScalar vals[3],vals_M_0[3]; for (r=0; r<3; r++) { row_M_0 = idx[r]; vals_M_0[0]=eM_0[r][0]; vals_M_0[1]=eM_0[r][1]; vals_M_0[2]=eM_0[r][2]; ierr = MatSetValues(user->M_0,1,&row_M_0,3,idx,vals_M_0,ADD_VALUES);CHKERRQ(ierr); if (y[1]==y[0]) { row = 4*idx[r]; cols[0] = 4*idx[0]; vals[0] = eM_0[r][0]+dt*epsilon*epsilon*eM_2_odd[r][0]; cols[1] = 4*idx[1]; vals[1] = eM_0[r][1]+dt*epsilon*epsilon*eM_2_odd[r][1]; cols[2] = 4*idx[2]; vals[2] = eM_0[r][2]+dt*epsilon*epsilon*eM_2_odd[r][2]; /* Insert values in matrix M for 1st dof */ ierr = MatSetValuesLocal(M,1,&row,3,cols,vals,ADD_VALUES);CHKERRQ(ierr); row = 4*idx[r]+1; cols[0] = 4*idx[0]+1; vals[0] = eM_0[r][0]+dt*epsilon*epsilon*eM_2_odd[r][0]; cols[1] = 4*idx[1]+1; vals[1] = eM_0[r][1]+dt*epsilon*epsilon*eM_2_odd[r][1]; cols[2] = 4*idx[2]+1; vals[2] = eM_0[r][2]+dt*epsilon*epsilon*eM_2_odd[r][2]; /* Insert values in matrix M for 2nd dof */ ierr = MatSetValuesLocal(M,1,&row,3,cols,vals,ADD_VALUES);CHKERRQ(ierr); row = 4*idx[r]+2; cols[0] = 4*idx[0]+2; vals[0] = eM_0[r][0]+dt*epsilon*epsilon*eM_2_odd[r][0]; cols[1] = 4*idx[1]+2; vals[1] = eM_0[r][1]+dt*epsilon*epsilon*eM_2_odd[r][1]; cols[2] = 4*idx[2]+2; vals[2] = eM_0[r][2]+dt*epsilon*epsilon*eM_2_odd[r][2]; /* Insert values in matrix M for 3nd dof */ ierr = MatSetValuesLocal(M,1,&row,3,cols,vals,ADD_VALUES);CHKERRQ(ierr); } else { row = 4*idx[r]; cols[0] = 4*idx[0]; vals[0] = eM_0[r][0]+dt*epsilon*epsilon*eM_2_even[r][0]; cols[1] = 4*idx[1]; vals[1] = eM_0[r][1]+dt*epsilon*epsilon*eM_2_even[r][1]; cols[2] = 4*idx[2]; vals[2] = eM_0[r][2]+dt*epsilon*epsilon*eM_2_even[r][2]; /* Insert values in matrix M for 1st dof */ ierr = MatSetValuesLocal(M,1,&row,3,cols,vals,ADD_VALUES);CHKERRQ(ierr); row = 4*idx[r]+1; cols[0] = 4*idx[0]+1; vals[0] = eM_0[r][0]+dt*epsilon*epsilon*eM_2_even[r][0]; cols[1] = 4*idx[1]+1; vals[1] = eM_0[r][1]+dt*epsilon*epsilon*eM_2_even[r][1]; cols[2] = 4*idx[2]+1; vals[2] = eM_0[r][2]+dt*epsilon*epsilon*eM_2_even[r][2]; /* Insert values in matrix M for 2nd dof */ ierr = MatSetValuesLocal(M,1,&row,3,cols,vals,ADD_VALUES);CHKERRQ(ierr); row = 4*idx[r]+2; cols[0] = 4*idx[0]+2; vals[0] = eM_0[r][0]+dt*epsilon*epsilon*eM_2_even[r][0]; cols[1] = 4*idx[1]+2; vals[1] = eM_0[r][1]+dt*epsilon*epsilon*eM_2_even[r][1]; cols[2] = 4*idx[2]+2; vals[2] = eM_0[r][2]+dt*epsilon*epsilon*eM_2_even[r][2]; /* Insert values in matrix M for 3nd dof */ ierr = MatSetValuesLocal(M,1,&row,3,cols,vals,ADD_VALUES);CHKERRQ(ierr); } } } ierr = MatAssemblyBegin(user->M_0,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(user->M_0,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyBegin(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); PetscScalar vals[9]; vals[0] = -1.0; vals[1] = 0.0; vals[2] = 0.0; vals[3] = 0.0; vals[4] = -1.0; vals[5] = 0.0; vals[6] = 0.0; vals[7] = 0.0; vals[8] = -1.0; for (j=0; j < nele; j++) { idx[0] = ele[3*j]; idx[1] = ele[3*j+1]; idx[2] = ele[3*j+2]; PetscInt r,rows[3],cols[3]; for (r=0; r<3; r++) { rows[0] = 4*idx[0]+r; cols[0] = 4*idx[0]+3; rows[1] = 4*idx[1]+r; cols[1] = 4*idx[1]+3; rows[2] = 4*idx[2]+r; cols[2] = 4*idx[2]+3; ierr = MatSetValuesLocal(M,3,rows,3,cols,vals,INSERT_VALUES);CHKERRQ(ierr); ierr = MatSetValuesLocal(M,3,cols,3,rows,vals,INSERT_VALUES);CHKERRQ(ierr); } } ierr = DMDARestoreElements(user->da,&nele,&nen,&ele);CHKERRQ(ierr); ierr = MatAssemblyBegin(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = VecCreate(PETSC_COMM_WORLD,&user->u1);CHKERRQ(ierr); ierr = VecSetSizes(user->u1,n/4,PETSC_DECIDE);CHKERRQ(ierr); ierr = VecSetFromOptions(user->u1);CHKERRQ(ierr); ierr = VecDuplicate(user->u1,&user->u2);CHKERRQ(ierr); ierr = VecDuplicate(user->u1,&user->u3);CHKERRQ(ierr); ierr = VecDuplicate(user->u1,&user->work1);CHKERRQ(ierr); ierr = VecDuplicate(user->u1,&user->work2);CHKERRQ(ierr); ierr = VecDuplicate(user->u1,&user->work3);CHKERRQ(ierr); ierr = VecDuplicate(user->u1,&user->work4);CHKERRQ(ierr); PetscFunctionReturn(0); }
int Brusselator(int argc,char **argv,PetscInt cycle) { TS ts; /* nonlinear solver */ Vec X; /* solution, residual vectors */ Mat J; /* Jacobian matrix */ PetscInt steps,maxsteps,mx; PetscErrorCode ierr; DM da; PetscReal ftime,hx,dt,xmax,xmin; struct _User user; /* user-defined work context */ TSConvergedReason reason; PetscInitialize(&argc,&argv,(char*)0,help); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create distributed array (DMDA) to manage parallel grid and vectors - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = DMDACreate1d(PETSC_COMM_WORLD,DM_BOUNDARY_NONE,-11,2,2,NULL,&da);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Extract global vectors from DMDA; - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = DMCreateGlobalVector(da,&X);CHKERRQ(ierr); /* Initialize user application context */ ierr = PetscOptionsBegin(PETSC_COMM_WORLD,NULL,"Advection-reaction options",""); { user.A = 1; user.B = 3; user.alpha = 0.1; user.uleft = 1; user.uright = 1; user.vleft = 3; user.vright = 3; ierr = PetscOptionsReal("-A","Reaction rate","",user.A,&user.A,NULL);CHKERRQ(ierr); ierr = PetscOptionsReal("-B","Reaction rate","",user.B,&user.B,NULL);CHKERRQ(ierr); ierr = PetscOptionsReal("-alpha","Diffusion coefficient","",user.alpha,&user.alpha,NULL);CHKERRQ(ierr); ierr = PetscOptionsReal("-uleft","Dirichlet boundary condition","",user.uleft,&user.uleft,NULL);CHKERRQ(ierr); ierr = PetscOptionsReal("-uright","Dirichlet boundary condition","",user.uright,&user.uright,NULL);CHKERRQ(ierr); ierr = PetscOptionsReal("-vleft","Dirichlet boundary condition","",user.vleft,&user.vleft,NULL);CHKERRQ(ierr); ierr = PetscOptionsReal("-vright","Dirichlet boundary condition","",user.vright,&user.vright,NULL);CHKERRQ(ierr); } ierr = PetscOptionsEnd();CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create timestepping solver context - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr); ierr = TSSetDM(ts,da);CHKERRQ(ierr); ierr = TSSetType(ts,TSARKIMEX);CHKERRQ(ierr); ierr = TSSetRHSFunction(ts,NULL,FormRHSFunction,&user);CHKERRQ(ierr); ierr = TSSetIFunction(ts,NULL,FormIFunction,&user);CHKERRQ(ierr); ierr = DMSetMatType(da,MATAIJ);CHKERRQ(ierr); ierr = DMCreateMatrix(da,&J);CHKERRQ(ierr); ierr = TSSetIJacobian(ts,J,J,FormIJacobian,&user);CHKERRQ(ierr); ftime = 1.0; maxsteps = 10000; ierr = TSSetDuration(ts,maxsteps,ftime);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set initial conditions - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = FormInitialSolution(ts,X,&user);CHKERRQ(ierr); ierr = TSSetSolution(ts,X);CHKERRQ(ierr); ierr = VecGetSize(X,&mx);CHKERRQ(ierr); hx = 1.0/(PetscReal)(mx/2-1); dt = 0.4 * PetscSqr(hx) / user.alpha; /* Diffusive stability limit */ dt *= PetscPowRealInt(0.2,cycle); /* Shrink the time step in convergence study. */ ierr = TSSetInitialTimeStep(ts,0.0,dt);CHKERRQ(ierr); ierr = TSSetTolerances(ts,1e-3*PetscPowRealInt(0.5,cycle),NULL,1e-3*PetscPowRealInt(0.5,cycle),NULL);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set runtime options - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSetFromOptions(ts);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Solve nonlinear system - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSolve(ts,X);CHKERRQ(ierr); ierr = TSGetSolveTime(ts,&ftime);CHKERRQ(ierr); ierr = TSGetTimeStepNumber(ts,&steps);CHKERRQ(ierr); ierr = TSGetConvergedReason(ts,&reason);CHKERRQ(ierr); ierr = VecMin(X,NULL,&xmin);CHKERRQ(ierr); ierr = VecMax(X,NULL,&xmax);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD,"%s at time %g after % 3D steps. Range [%6.4f,%6.4f]\n",TSConvergedReasons[reason],(double)ftime,steps,(double)xmin,(double)xmax);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Free work space. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = MatDestroy(&J);CHKERRQ(ierr); ierr = VecDestroy(&X);CHKERRQ(ierr); ierr = TSDestroy(&ts);CHKERRQ(ierr); ierr = DMDestroy(&da);CHKERRQ(ierr); ierr = PetscFinalize(); return 0; }
int main(int argc,char **argv) { TS ts; /* nonlinear solver */ Vec x,r; /* solution, residual vectors */ Mat J; /* Jacobian matrix */ PetscInt steps,Mx,maxsteps = 10000000; PetscErrorCode ierr; DM da; MatFDColoring matfdcoloring; ISColoring iscoloring; PetscReal dt; PetscReal vbounds[] = {-100000,100000,-1.1,1.1}; PetscBool wait; Vec ul,uh; SNES snes; UserCtx ctx; /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Initialize program - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr; ctx.kappa = 1.0; ierr = PetscOptionsGetReal(NULL,"-kappa",&ctx.kappa,NULL);CHKERRQ(ierr); ctx.cahnhillard = PETSC_FALSE; ierr = PetscOptionsGetBool(NULL,NULL,"-cahn-hillard",&ctx.cahnhillard,NULL);CHKERRQ(ierr); ierr = PetscViewerDrawSetBounds(PETSC_VIEWER_DRAW_(PETSC_COMM_WORLD),2,vbounds);CHKERRQ(ierr); ierr = PetscViewerDrawResize(PETSC_VIEWER_DRAW_(PETSC_COMM_WORLD),600,600);CHKERRQ(ierr); ctx.energy = 1; /* ierr = PetscOptionsGetInt(NULL,NULL,"-energy",&ctx.energy,NULL);CHKERRQ(ierr); */ ierr = PetscOptionsGetInt(NULL,NULL,"-energy",&ctx.energy,NULL);CHKERRQ(ierr); ctx.tol = 1.0e-8; ierr = PetscOptionsGetReal(NULL,"-tol",&ctx.tol,NULL);CHKERRQ(ierr); ctx.theta = .001; ctx.theta_c = 1.0; ierr = PetscOptionsGetReal(NULL,"-theta",&ctx.theta,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetReal(NULL,"-theta_c",&ctx.theta_c,NULL);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create distributed array (DMDA) to manage parallel grid and vectors - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = DMDACreate1d(PETSC_COMM_WORLD, DM_BOUNDARY_PERIODIC, -10,2,2,NULL,&da);CHKERRQ(ierr); ierr = DMSetFromOptions(da);CHKERRQ(ierr); ierr = DMSetUp(da);CHKERRQ(ierr); ierr = DMDASetFieldName(da,0,"Biharmonic heat equation: w = -kappa*u_xx");CHKERRQ(ierr); ierr = DMDASetFieldName(da,1,"Biharmonic heat equation: u");CHKERRQ(ierr); ierr = DMDAGetInfo(da,0,&Mx,0,0,0,0,0,0,0,0,0,0,0);CHKERRQ(ierr); dt = 1.0/(10.*ctx.kappa*Mx*Mx*Mx*Mx); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Extract global vectors from DMDA; then duplicate for remaining vectors that are the same types - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = DMCreateGlobalVector(da,&x);CHKERRQ(ierr); ierr = VecDuplicate(x,&r);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create timestepping solver context - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr); ierr = TSSetDM(ts,da);CHKERRQ(ierr); ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr); ierr = TSSetIFunction(ts,NULL,FormFunction,&ctx);CHKERRQ(ierr); ierr = TSSetDuration(ts,maxsteps,.02);CHKERRQ(ierr); ierr = TSSetExactFinalTime(ts,TS_EXACTFINALTIME_STEPOVER);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create matrix data structure; set Jacobian evaluation routine < Set Jacobian matrix data structure and default Jacobian evaluation routine. User can override with: -snes_mf : matrix-free Newton-Krylov method with no preconditioning (unless user explicitly sets preconditioner) -snes_mf_operator : form preconditioning matrix as set by the user, but use matrix-free approx for Jacobian-vector products within Newton-Krylov method - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSGetSNES(ts,&snes);CHKERRQ(ierr); ierr = DMCreateColoring(da,IS_COLORING_GLOBAL,&iscoloring);CHKERRQ(ierr); ierr = DMSetMatType(da,MATAIJ);CHKERRQ(ierr); ierr = DMCreateMatrix(da,&J);CHKERRQ(ierr); ierr = MatFDColoringCreate(J,iscoloring,&matfdcoloring);CHKERRQ(ierr); ierr = ISColoringDestroy(&iscoloring);CHKERRQ(ierr); ierr = MatFDColoringSetFunction(matfdcoloring,(PetscErrorCode (*)(void))SNESTSFormFunction,ts);CHKERRQ(ierr); ierr = MatFDColoringSetFromOptions(matfdcoloring);CHKERRQ(ierr); ierr = MatFDColoringSetUp(J,iscoloring,matfdcoloring);CHKERRQ(ierr); ierr = SNESSetJacobian(snes,J,J,SNESComputeJacobianDefaultColor,matfdcoloring);CHKERRQ(ierr); { ierr = VecDuplicate(x,&ul);CHKERRQ(ierr); ierr = VecDuplicate(x,&uh);CHKERRQ(ierr); ierr = VecStrideSet(ul,0,PETSC_NINFINITY);CHKERRQ(ierr); ierr = VecStrideSet(ul,1,-1.0);CHKERRQ(ierr); ierr = VecStrideSet(uh,0,PETSC_INFINITY);CHKERRQ(ierr); ierr = VecStrideSet(uh,1,1.0);CHKERRQ(ierr); ierr = TSVISetVariableBounds(ts,ul,uh);CHKERRQ(ierr); } /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Customize nonlinear solver - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSetType(ts,TSBEULER);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set initial conditions - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = FormInitialSolution(da,x,ctx.kappa);CHKERRQ(ierr); ierr = TSSetInitialTimeStep(ts,0.0,dt);CHKERRQ(ierr); ierr = TSSetSolution(ts,x);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set runtime options - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSetFromOptions(ts);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Solve nonlinear system - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSolve(ts,x);CHKERRQ(ierr); wait = PETSC_FALSE; ierr = PetscOptionsGetBool(NULL,NULL,"-wait",&wait,NULL);CHKERRQ(ierr); if (wait) { ierr = PetscSleep(-1);CHKERRQ(ierr); } ierr = TSGetTimeStepNumber(ts,&steps);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Free work space. All PETSc objects should be destroyed when they are no longer needed. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ { ierr = VecDestroy(&ul);CHKERRQ(ierr); ierr = VecDestroy(&uh);CHKERRQ(ierr); } ierr = MatDestroy(&J);CHKERRQ(ierr); ierr = MatFDColoringDestroy(&matfdcoloring);CHKERRQ(ierr); ierr = VecDestroy(&x);CHKERRQ(ierr); ierr = VecDestroy(&r);CHKERRQ(ierr); ierr = TSDestroy(&ts);CHKERRQ(ierr); ierr = DMDestroy(&da);CHKERRQ(ierr); ierr = PetscFinalize(); PetscFunctionReturn(0); }
int main(int argc, char **argv) { DM dm; /* Problem specification */ DM dmAux; /* Material specification */ SNES snes; /* nonlinear solver */ Vec u,r; /* solution, residual vectors */ Mat A,J; /* Jacobian matrix */ MatNullSpace nullSpace; /* May be necessary for Neumann conditions */ AppCtx user; /* user-defined work context */ JacActionCtx userJ; /* context for Jacobian MF action */ PetscInt its; /* iterations for convergence */ PetscReal error = 0.0; /* L_2 error in the solution */ PetscInt numComponents; PetscErrorCode ierr; ierr = PetscInitialize(&argc, &argv, NULL, help);CHKERRQ(ierr); ierr = ProcessOptions(PETSC_COMM_WORLD, &user);CHKERRQ(ierr); ierr = SNESCreate(PETSC_COMM_WORLD, &snes);CHKERRQ(ierr); ierr = CreateMesh(PETSC_COMM_WORLD, &user, &dm);CHKERRQ(ierr); ierr = SNESSetDM(snes, dm);CHKERRQ(ierr); ierr = DMSetApplicationContext(dm, &user);CHKERRQ(ierr); user.fem.fe = user.fe; ierr = PetscFECreateDefault(dm, user.dim, 1, PETSC_TRUE, NULL, -1, &user.fe[0]);CHKERRQ(ierr); if (user.bcType != NEUMANN) { user.fem.feBd = NULL; user.feBd[0] = NULL; } else { user.fem.feBd = user.feBd; ierr = PetscFECreateDefault(dm, user.dim-1, 1, PETSC_TRUE, "bd_", -1, &user.feBd[0]);CHKERRQ(ierr); } ierr = PetscFEGetNumComponents(user.fe[0], &numComponents);CHKERRQ(ierr); ierr = PetscMalloc(NUM_FIELDS * sizeof(void (*)(const PetscReal[], PetscScalar *, void *)), &user.exactFuncs);CHKERRQ(ierr); ierr = SetupProblem(dm, &user);CHKERRQ(ierr); ierr = SetupSection(dm, &user);CHKERRQ(ierr); /* Setup Material */ ierr = DMClone(dm, &dmAux);CHKERRQ(ierr); ierr = DMPlexCopyCoordinates(dm, dmAux);CHKERRQ(ierr); if (user.variableCoefficient != COEFF_FIELD) { user.fem.feAux = NULL; user.feAux[0] = NULL; } else { PetscQuadrature q; user.fem.feAux = user.feAux; ierr = PetscFECreateDefault(dmAux, user.dim, 1, PETSC_TRUE, "mat_", -1, &user.feAux[0]);CHKERRQ(ierr); ierr = PetscFEGetQuadrature(user.fe[0], &q);CHKERRQ(ierr); ierr = PetscFESetQuadrature(user.feAux[0], q);CHKERRQ(ierr); } ierr = SetupMaterialSection(dmAux, &user);CHKERRQ(ierr); ierr = SetupMaterial(dm, dmAux, &user);CHKERRQ(ierr); ierr = DMDestroy(&dmAux);CHKERRQ(ierr); ierr = DMCreateGlobalVector(dm, &u);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) u, "potential");CHKERRQ(ierr); ierr = VecDuplicate(u, &r);CHKERRQ(ierr); ierr = DMSetMatType(dm,MATAIJ);CHKERRQ(ierr); ierr = DMCreateMatrix(dm, &J);CHKERRQ(ierr); if (user.jacobianMF) { PetscInt M, m, N, n; ierr = MatGetSize(J, &M, &N);CHKERRQ(ierr); ierr = MatGetLocalSize(J, &m, &n);CHKERRQ(ierr); ierr = MatCreate(PETSC_COMM_WORLD, &A);CHKERRQ(ierr); ierr = MatSetSizes(A, m, n, M, N);CHKERRQ(ierr); ierr = MatSetType(A, MATSHELL);CHKERRQ(ierr); ierr = MatSetUp(A);CHKERRQ(ierr); #if 0 ierr = MatShellSetOperation(A, MATOP_MULT, (void (*)(void))FormJacobianAction);CHKERRQ(ierr); #endif userJ.dm = dm; userJ.J = J; userJ.user = &user; ierr = DMCreateLocalVector(dm, &userJ.u);CHKERRQ(ierr); ierr = DMPlexProjectFunctionLocal(dm, user.fe, user.exactFuncs, NULL, INSERT_BC_VALUES, userJ.u);CHKERRQ(ierr); ierr = MatShellSetContext(A, &userJ);CHKERRQ(ierr); } else { A = J; } if (user.bcType == NEUMANN) { ierr = MatNullSpaceCreate(PetscObjectComm((PetscObject) dm), PETSC_TRUE, 0, NULL, &nullSpace);CHKERRQ(ierr); ierr = MatSetNullSpace(J, nullSpace);CHKERRQ(ierr); if (A != J) { ierr = MatSetNullSpace(A, nullSpace);CHKERRQ(ierr); } } ierr = DMSNESSetFunctionLocal(dm, (PetscErrorCode (*)(DM,Vec,Vec,void*)) DMPlexComputeResidualFEM, &user);CHKERRQ(ierr); ierr = DMSNESSetJacobianLocal(dm, (PetscErrorCode (*)(DM,Vec,Mat,Mat,void*)) DMPlexComputeJacobianFEM, &user);CHKERRQ(ierr); ierr = SNESSetJacobian(snes, A, J, NULL, NULL);CHKERRQ(ierr); ierr = SNESSetFromOptions(snes);CHKERRQ(ierr); ierr = DMPlexProjectFunction(dm, user.fe, user.exactFuncs, NULL, INSERT_ALL_VALUES, u);CHKERRQ(ierr); if (user.checkpoint) { #if defined(PETSC_HAVE_HDF5) ierr = PetscViewerHDF5PushGroup(user.checkpoint, "/fields");CHKERRQ(ierr); ierr = VecLoad(u, user.checkpoint);CHKERRQ(ierr); ierr = PetscViewerHDF5PopGroup(user.checkpoint);CHKERRQ(ierr); #endif } ierr = PetscViewerDestroy(&user.checkpoint);CHKERRQ(ierr); if (user.showInitial) { Vec lv; ierr = DMGetLocalVector(dm, &lv);CHKERRQ(ierr); ierr = DMGlobalToLocalBegin(dm, u, INSERT_VALUES, lv);CHKERRQ(ierr); ierr = DMGlobalToLocalEnd(dm, u, INSERT_VALUES, lv);CHKERRQ(ierr); ierr = DMPrintLocalVec(dm, "Local function", 1.0e-10, lv);CHKERRQ(ierr); ierr = DMRestoreLocalVector(dm, &lv);CHKERRQ(ierr); } if (user.runType == RUN_FULL) { void (*initialGuess[numComponents])(const PetscReal x[], PetscScalar *, void *ctx); PetscInt c; for (c = 0; c < numComponents; ++c) initialGuess[c] = zero; ierr = DMPlexProjectFunction(dm, user.fe, initialGuess, NULL, INSERT_VALUES, u);CHKERRQ(ierr); if (user.debug) { ierr = PetscPrintf(PETSC_COMM_WORLD, "Initial guess\n");CHKERRQ(ierr); ierr = VecView(u, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); } ierr = SNESSolve(snes, NULL, u);CHKERRQ(ierr); ierr = SNESGetIterationNumber(snes, &its);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "Number of SNES iterations = %D\n", its);CHKERRQ(ierr); ierr = DMPlexComputeL2Diff(dm, user.fe, user.exactFuncs, NULL, u, &error);CHKERRQ(ierr); if (error < 1.0e-11) {ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: < 1.0e-11\n");CHKERRQ(ierr);} else {ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: %g\n", error);CHKERRQ(ierr);} if (user.showSolution) { ierr = PetscPrintf(PETSC_COMM_WORLD, "Solution\n");CHKERRQ(ierr); ierr = VecChop(u, 3.0e-9);CHKERRQ(ierr); ierr = VecView(u, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); } } else if (user.runType == RUN_PERF) { PetscReal res = 0.0; ierr = SNESComputeFunction(snes, u, r);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "Initial Residual\n");CHKERRQ(ierr); ierr = VecChop(r, 1.0e-10);CHKERRQ(ierr); ierr = VecNorm(r, NORM_2, &res);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Residual: %g\n", res);CHKERRQ(ierr); } else { PetscReal res = 0.0; /* Check discretization error */ ierr = PetscPrintf(PETSC_COMM_WORLD, "Initial guess\n");CHKERRQ(ierr); ierr = VecView(u, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = DMPlexComputeL2Diff(dm, user.fe, user.exactFuncs, NULL, u, &error);CHKERRQ(ierr); if (error < 1.0e-11) {ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: < 1.0e-11\n");CHKERRQ(ierr);} else {ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: %g\n", error);CHKERRQ(ierr);} /* Check residual */ ierr = SNESComputeFunction(snes, u, r);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "Initial Residual\n");CHKERRQ(ierr); ierr = VecChop(r, 1.0e-10);CHKERRQ(ierr); ierr = VecView(r, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = VecNorm(r, NORM_2, &res);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Residual: %g\n", res);CHKERRQ(ierr); /* Check Jacobian */ { Vec b; ierr = SNESComputeJacobian(snes, u, A, A);CHKERRQ(ierr); ierr = VecDuplicate(u, &b);CHKERRQ(ierr); ierr = VecSet(r, 0.0);CHKERRQ(ierr); ierr = SNESComputeFunction(snes, r, b);CHKERRQ(ierr); ierr = MatMult(A, u, r);CHKERRQ(ierr); ierr = VecAXPY(r, 1.0, b);CHKERRQ(ierr); ierr = VecDestroy(&b);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "Au - b = Au + F(0)\n");CHKERRQ(ierr); ierr = VecChop(r, 1.0e-10);CHKERRQ(ierr); ierr = VecView(r, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = VecNorm(r, NORM_2, &res);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "Linear L_2 Residual: %g\n", res);CHKERRQ(ierr); } } ierr = VecViewFromOptions(u, NULL, "-vec_view");CHKERRQ(ierr); if (user.bcType == NEUMANN) { ierr = MatNullSpaceDestroy(&nullSpace);CHKERRQ(ierr); } if (user.jacobianMF) { ierr = VecDestroy(&userJ.u);CHKERRQ(ierr); } if (A != J) {ierr = MatDestroy(&A);CHKERRQ(ierr);} ierr = PetscFEDestroy(&user.fe[0]);CHKERRQ(ierr); ierr = PetscFEDestroy(&user.feBd[0]);CHKERRQ(ierr); ierr = PetscFEDestroy(&user.feAux[0]);CHKERRQ(ierr); ierr = MatDestroy(&J);CHKERRQ(ierr); ierr = VecDestroy(&u);CHKERRQ(ierr); ierr = VecDestroy(&r);CHKERRQ(ierr); ierr = SNESDestroy(&snes);CHKERRQ(ierr); ierr = DMDestroy(&dm);CHKERRQ(ierr); ierr = PetscFree(user.exactFuncs);CHKERRQ(ierr); ierr = PetscFinalize(); return 0; }
/* Mm_ratio - ration of grid lines between fine and coarse grids. */ int main(int argc,char **argv) { PetscErrorCode ierr; AppCtx user; PetscInt Npx=PETSC_DECIDE,Npy=PETSC_DECIDE,Npz=PETSC_DECIDE; PetscMPIInt size,rank; PetscInt m,n,M,N,i,nrows; PetscScalar one = 1.0; PetscReal fill=2.0; Mat A,A_tmp,P,C,C1,C2; PetscScalar *array,none = -1.0,alpha; Vec x,v1,v2,v3,v4; PetscReal norm,norm_tmp,norm_tmp1,tol=100.*PETSC_MACHINE_EPSILON; PetscRandom rdm; PetscBool Test_MatMatMult=PETSC_TRUE,Test_MatPtAP=PETSC_TRUE,Test_3D=PETSC_TRUE,flg; const PetscInt *ia,*ja; ierr = PetscInitialize(&argc,&argv,NULL,help);if (ierr) return ierr; ierr = PetscOptionsGetReal(NULL,NULL,"-tol",&tol,NULL);CHKERRQ(ierr); user.ratio = 2; user.coarse.mx = 20; user.coarse.my = 20; user.coarse.mz = 20; ierr = PetscOptionsGetInt(NULL,NULL,"-Mx",&user.coarse.mx,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetInt(NULL,NULL,"-My",&user.coarse.my,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetInt(NULL,NULL,"-Mz",&user.coarse.mz,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetInt(NULL,NULL,"-ratio",&user.ratio,NULL);CHKERRQ(ierr); if (user.coarse.mz) Test_3D = PETSC_TRUE; user.fine.mx = user.ratio*(user.coarse.mx-1)+1; user.fine.my = user.ratio*(user.coarse.my-1)+1; user.fine.mz = user.ratio*(user.coarse.mz-1)+1; ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr); ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr); ierr = PetscOptionsGetInt(NULL,NULL,"-Npx",&Npx,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetInt(NULL,NULL,"-Npy",&Npy,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetInt(NULL,NULL,"-Npz",&Npz,NULL);CHKERRQ(ierr); /* Set up distributed array for fine grid */ if (!Test_3D) { ierr = DMDACreate2d(PETSC_COMM_WORLD, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE,DMDA_STENCIL_STAR,user.fine.mx,user.fine.my,Npx,Npy,1,1,NULL,NULL,&user.fine.da);CHKERRQ(ierr); } else { ierr = DMDACreate3d(PETSC_COMM_WORLD,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DMDA_STENCIL_STAR,user.fine.mx,user.fine.my,user.fine.mz,Npx,Npy,Npz,1,1,NULL,NULL,NULL,&user.fine.da);CHKERRQ(ierr); } ierr = DMSetFromOptions(user.fine.da);CHKERRQ(ierr); ierr = DMSetUp(user.fine.da);CHKERRQ(ierr); /* Test DMCreateMatrix() */ /*------------------------------------------------------------*/ ierr = DMSetMatType(user.fine.da,MATAIJ);CHKERRQ(ierr); ierr = DMCreateMatrix(user.fine.da,&A);CHKERRQ(ierr); ierr = DMSetMatType(user.fine.da,MATBAIJ);CHKERRQ(ierr); ierr = DMCreateMatrix(user.fine.da,&C);CHKERRQ(ierr); ierr = MatConvert(C,MATAIJ,MAT_INITIAL_MATRIX,&A_tmp);CHKERRQ(ierr); /* not work for mpisbaij matrix! */ ierr = MatEqual(A,A_tmp,&flg);CHKERRQ(ierr); if (!flg) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_NOTSAMETYPE,"A != C"); ierr = MatDestroy(&C);CHKERRQ(ierr); ierr = MatDestroy(&A_tmp);CHKERRQ(ierr); /*------------------------------------------------------------*/ ierr = MatGetLocalSize(A,&m,&n);CHKERRQ(ierr); ierr = MatGetSize(A,&M,&N);CHKERRQ(ierr); /* if (!rank) printf("A %d, %d\n",M,N); */ /* set val=one to A */ if (size == 1) { ierr = MatGetRowIJ(A,0,PETSC_FALSE,PETSC_FALSE,&nrows,&ia,&ja,&flg);CHKERRQ(ierr); if (flg) { ierr = MatSeqAIJGetArray(A,&array);CHKERRQ(ierr); for (i=0; i<ia[nrows]; i++) array[i] = one; ierr = MatSeqAIJRestoreArray(A,&array);CHKERRQ(ierr); } ierr = MatRestoreRowIJ(A,0,PETSC_FALSE,PETSC_FALSE,&nrows,&ia,&ja,&flg);CHKERRQ(ierr); } else { Mat AA,AB; ierr = MatMPIAIJGetSeqAIJ(A,&AA,&AB,NULL);CHKERRQ(ierr); ierr = MatGetRowIJ(AA,0,PETSC_FALSE,PETSC_FALSE,&nrows,&ia,&ja,&flg);CHKERRQ(ierr); if (flg) { ierr = MatSeqAIJGetArray(AA,&array);CHKERRQ(ierr); for (i=0; i<ia[nrows]; i++) array[i] = one; ierr = MatSeqAIJRestoreArray(AA,&array);CHKERRQ(ierr); } ierr = MatRestoreRowIJ(AA,0,PETSC_FALSE,PETSC_FALSE,&nrows,&ia,&ja,&flg);CHKERRQ(ierr); ierr = MatGetRowIJ(AB,0,PETSC_FALSE,PETSC_FALSE,&nrows,&ia,&ja,&flg);CHKERRQ(ierr); if (flg) { ierr = MatSeqAIJGetArray(AB,&array);CHKERRQ(ierr); for (i=0; i<ia[nrows]; i++) array[i] = one; ierr = MatSeqAIJRestoreArray(AB,&array);CHKERRQ(ierr); } ierr = MatRestoreRowIJ(AB,0,PETSC_FALSE,PETSC_FALSE,&nrows,&ia,&ja,&flg);CHKERRQ(ierr); } /* ierr = MatView(A, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); */ /* Set up distributed array for coarse grid */ if (!Test_3D) { ierr = DMDACreate2d(PETSC_COMM_WORLD, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE,DMDA_STENCIL_STAR,user.coarse.mx,user.coarse.my,Npx,Npy,1,1,NULL,NULL,&user.coarse.da);CHKERRQ(ierr); } else { ierr = DMDACreate3d(PETSC_COMM_WORLD,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DMDA_STENCIL_STAR,user.coarse.mx,user.coarse.my,user.coarse.mz,Npx,Npy,Npz, 1,1,NULL,NULL,NULL,&user.coarse.da);CHKERRQ(ierr); } ierr = DMSetFromOptions(user.coarse.da);CHKERRQ(ierr); ierr = DMSetUp(user.coarse.da);CHKERRQ(ierr); /* Create interpolation between the fine and coarse grids */ ierr = DMCreateInterpolation(user.coarse.da,user.fine.da,&P,NULL);CHKERRQ(ierr); ierr = MatGetLocalSize(P,&m,&n);CHKERRQ(ierr); ierr = MatGetSize(P,&M,&N);CHKERRQ(ierr); /* if (!rank) printf("P %d, %d\n",M,N); */ /* Create vectors v1 and v2 that are compatible with A */ ierr = VecCreate(PETSC_COMM_WORLD,&v1);CHKERRQ(ierr); ierr = MatGetLocalSize(A,&m,NULL);CHKERRQ(ierr); ierr = VecSetSizes(v1,m,PETSC_DECIDE);CHKERRQ(ierr); ierr = VecSetFromOptions(v1);CHKERRQ(ierr); ierr = VecDuplicate(v1,&v2);CHKERRQ(ierr); ierr = PetscRandomCreate(PETSC_COMM_WORLD,&rdm);CHKERRQ(ierr); ierr = PetscRandomSetFromOptions(rdm);CHKERRQ(ierr); /* Test MatMatMult(): C = A*P */ /*----------------------------*/ if (Test_MatMatMult) { ierr = MatDuplicate(A,MAT_COPY_VALUES,&A_tmp);CHKERRQ(ierr); ierr = MatMatMult(A_tmp,P,MAT_INITIAL_MATRIX,fill,&C);CHKERRQ(ierr); /* Test MAT_REUSE_MATRIX - reuse symbolic C */ alpha=1.0; for (i=0; i<2; i++) { alpha -= 0.1; ierr = MatScale(A_tmp,alpha);CHKERRQ(ierr); ierr = MatMatMult(A_tmp,P,MAT_REUSE_MATRIX,fill,&C);CHKERRQ(ierr); } /* Free intermediate data structures created for reuse of C=Pt*A*P */ ierr = MatFreeIntermediateDataStructures(C);CHKERRQ(ierr); /* Test MatDuplicate() */ /*----------------------------*/ ierr = MatDuplicate(C,MAT_COPY_VALUES,&C1);CHKERRQ(ierr); ierr = MatDuplicate(C1,MAT_COPY_VALUES,&C2);CHKERRQ(ierr); ierr = MatDestroy(&C1);CHKERRQ(ierr); ierr = MatDestroy(&C2);CHKERRQ(ierr); /* Create vector x that is compatible with P */ ierr = VecCreate(PETSC_COMM_WORLD,&x);CHKERRQ(ierr); ierr = MatGetLocalSize(P,NULL,&n);CHKERRQ(ierr); ierr = VecSetSizes(x,n,PETSC_DECIDE);CHKERRQ(ierr); ierr = VecSetFromOptions(x);CHKERRQ(ierr); norm = 0.0; for (i=0; i<10; i++) { ierr = VecSetRandom(x,rdm);CHKERRQ(ierr); ierr = MatMult(P,x,v1);CHKERRQ(ierr); ierr = MatMult(A_tmp,v1,v2);CHKERRQ(ierr); /* v2 = A*P*x */ ierr = MatMult(C,x,v1);CHKERRQ(ierr); /* v1 = C*x */ ierr = VecAXPY(v1,none,v2);CHKERRQ(ierr); ierr = VecNorm(v1,NORM_1,&norm_tmp);CHKERRQ(ierr); ierr = VecNorm(v2,NORM_1,&norm_tmp1);CHKERRQ(ierr); norm_tmp /= norm_tmp1; if (norm_tmp > norm) norm = norm_tmp; } if (norm >= tol && !rank) { ierr = PetscPrintf(PETSC_COMM_SELF,"Error: MatMatMult(), |v1 - v2|/|v2|: %g\n",(double)norm);CHKERRQ(ierr); } ierr = VecDestroy(&x);CHKERRQ(ierr); ierr = MatDestroy(&C);CHKERRQ(ierr); ierr = MatDestroy(&A_tmp);CHKERRQ(ierr); } /* Test P^T * A * P - MatPtAP() */ /*------------------------------*/ if (Test_MatPtAP) { ierr = MatPtAP(A,P,MAT_INITIAL_MATRIX,fill,&C);CHKERRQ(ierr); ierr = MatGetLocalSize(C,&m,&n);CHKERRQ(ierr); /* Test MAT_REUSE_MATRIX - reuse symbolic C */ alpha=1.0; for (i=0; i<1; i++) { alpha -= 0.1; ierr = MatScale(A,alpha);CHKERRQ(ierr); ierr = MatPtAP(A,P,MAT_REUSE_MATRIX,fill,&C);CHKERRQ(ierr); } /* Free intermediate data structures created for reuse of C=Pt*A*P */ ierr = MatFreeIntermediateDataStructures(C);CHKERRQ(ierr); /* Test MatDuplicate() */ /*----------------------------*/ ierr = MatDuplicate(C,MAT_COPY_VALUES,&C1);CHKERRQ(ierr); ierr = MatDuplicate(C1,MAT_COPY_VALUES,&C2);CHKERRQ(ierr); ierr = MatDestroy(&C1);CHKERRQ(ierr); ierr = MatDestroy(&C2);CHKERRQ(ierr); /* Create vector x that is compatible with P */ ierr = VecCreate(PETSC_COMM_WORLD,&x);CHKERRQ(ierr); ierr = MatGetLocalSize(P,&m,&n);CHKERRQ(ierr); ierr = VecSetSizes(x,n,PETSC_DECIDE);CHKERRQ(ierr); ierr = VecSetFromOptions(x);CHKERRQ(ierr); ierr = VecCreate(PETSC_COMM_WORLD,&v3);CHKERRQ(ierr); ierr = VecSetSizes(v3,n,PETSC_DECIDE);CHKERRQ(ierr); ierr = VecSetFromOptions(v3);CHKERRQ(ierr); ierr = VecDuplicate(v3,&v4);CHKERRQ(ierr); norm = 0.0; for (i=0; i<10; i++) { ierr = VecSetRandom(x,rdm);CHKERRQ(ierr); ierr = MatMult(P,x,v1);CHKERRQ(ierr); ierr = MatMult(A,v1,v2);CHKERRQ(ierr); /* v2 = A*P*x */ ierr = MatMultTranspose(P,v2,v3);CHKERRQ(ierr); /* v3 = Pt*A*P*x */ ierr = MatMult(C,x,v4);CHKERRQ(ierr); /* v3 = C*x */ ierr = VecAXPY(v4,none,v3);CHKERRQ(ierr); ierr = VecNorm(v4,NORM_1,&norm_tmp);CHKERRQ(ierr); ierr = VecNorm(v3,NORM_1,&norm_tmp1);CHKERRQ(ierr); norm_tmp /= norm_tmp1; if (norm_tmp > norm) norm = norm_tmp; } if (norm >= tol && !rank) { ierr = PetscPrintf(PETSC_COMM_SELF,"Error: MatPtAP(), |v3 - v4|/|v3|: %g\n",(double)norm);CHKERRQ(ierr); } ierr = MatDestroy(&C);CHKERRQ(ierr); ierr = VecDestroy(&v3);CHKERRQ(ierr); ierr = VecDestroy(&v4);CHKERRQ(ierr); ierr = VecDestroy(&x);CHKERRQ(ierr); } /* Clean up */ ierr = MatDestroy(&A);CHKERRQ(ierr); ierr = PetscRandomDestroy(&rdm);CHKERRQ(ierr); ierr = VecDestroy(&v1);CHKERRQ(ierr); ierr = VecDestroy(&v2);CHKERRQ(ierr); ierr = DMDestroy(&user.fine.da);CHKERRQ(ierr); ierr = DMDestroy(&user.coarse.da);CHKERRQ(ierr); ierr = MatDestroy(&P);CHKERRQ(ierr); ierr = PetscFinalize(); return ierr; }
int main(int argc,char **argv) { TS ts; /* time integrator */ SNES snes; /* nonlinear solver */ SNESLineSearch linesearch; /* line search */ Vec X; /* solution, residual vectors */ Mat J; /* Jacobian matrix */ PetscInt steps,maxsteps,mx; PetscErrorCode ierr; DM da; PetscReal ftime,dt; struct _User user; /* user-defined work context */ TSConvergedReason reason; PetscInitialize(&argc,&argv,(char*)0,help); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create distributed array (DMDA) to manage parallel grid and vectors - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = DMDACreate1d(PETSC_COMM_WORLD,DMDA_BOUNDARY_NONE,-11,2,2,NULL,&da);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Extract global vectors from DMDA; - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = DMCreateGlobalVector(da,&X);CHKERRQ(ierr); /* Initialize user application context */ ierr = PetscOptionsBegin(PETSC_COMM_WORLD,NULL,"Advection-reaction options",""); { user.a[0] = 1; ierr = PetscOptionsReal("-a0","Advection rate 0","",user.a[0],&user.a[0],NULL);CHKERRQ(ierr); user.a[1] = 0; ierr = PetscOptionsReal("-a1","Advection rate 1","",user.a[1],&user.a[1],NULL);CHKERRQ(ierr); user.k[0] = 1e6; ierr = PetscOptionsReal("-k0","Reaction rate 0","",user.k[0],&user.k[0],NULL);CHKERRQ(ierr); user.k[1] = 2*user.k[0]; ierr = PetscOptionsReal("-k1","Reaction rate 1","",user.k[1],&user.k[1],NULL);CHKERRQ(ierr); user.s[0] = 0; ierr = PetscOptionsReal("-s0","Source 0","",user.s[0],&user.s[0],NULL);CHKERRQ(ierr); user.s[1] = 1; ierr = PetscOptionsReal("-s1","Source 1","",user.s[1],&user.s[1],NULL);CHKERRQ(ierr); } ierr = PetscOptionsEnd();CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create timestepping solver context - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr); ierr = TSSetDM(ts,da);CHKERRQ(ierr); ierr = TSSetType(ts,TSARKIMEX);CHKERRQ(ierr); ierr = TSSetRHSFunction(ts,NULL,FormRHSFunction,&user);CHKERRQ(ierr); ierr = TSSetIFunction(ts,NULL,FormIFunction,&user);CHKERRQ(ierr); ierr = DMSetMatType(da,MATAIJ);CHKERRQ(ierr); ierr = DMCreateMatrix(da,&J);CHKERRQ(ierr); ierr = TSSetIJacobian(ts,J,J,FormIJacobian,&user);CHKERRQ(ierr); /* A line search in the nonlinear solve can fail due to ill-conditioning unless an absolute tolerance is set. Since * this problem is linear, we deactivate the line search. For a linear problem, it is usually recommended to also use * SNESSetType(snes,SNESKSPONLY). */ ierr = TSGetSNES(ts,&snes);CHKERRQ(ierr); ierr = SNESGetLineSearch(snes,&linesearch);CHKERRQ(ierr); ierr = SNESLineSearchSetType(linesearch,SNESLINESEARCHBASIC);CHKERRQ(ierr); ftime = 1.0; maxsteps = 10000; ierr = TSSetDuration(ts,maxsteps,ftime);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set initial conditions - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = FormInitialSolution(ts,X,&user);CHKERRQ(ierr); ierr = TSSetSolution(ts,X);CHKERRQ(ierr); ierr = VecGetSize(X,&mx);CHKERRQ(ierr); dt = .1 * PetscMax(user.a[0],user.a[1]) / mx; /* Advective CFL, I don't know why it needs so much safety factor. */ ierr = TSSetInitialTimeStep(ts,0.0,dt);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set runtime options - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSetFromOptions(ts);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Solve nonlinear system - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSolve(ts,X);CHKERRQ(ierr); ierr = TSGetSolveTime(ts,&ftime);CHKERRQ(ierr); ierr = TSGetTimeStepNumber(ts,&steps);CHKERRQ(ierr); ierr = TSGetConvergedReason(ts,&reason);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD,"%s at time %G after %D steps\n",TSConvergedReasons[reason],ftime,steps);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Free work space. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = MatDestroy(&J);CHKERRQ(ierr); ierr = VecDestroy(&X);CHKERRQ(ierr); ierr = TSDestroy(&ts);CHKERRQ(ierr); ierr = DMDestroy(&da);CHKERRQ(ierr); ierr = PetscFinalize(); return 0; }
int main(int argc,char **argv) { PetscErrorCode ierr; int time; /* amount of loops */ struct in put; PetscScalar rh; /* relative humidity */ PetscScalar x; /* memory varialbe for relative humidity calculation */ PetscScalar deep_grnd_temp; /* temperature of ground under top soil surface layer */ PetscScalar emma; /* absorption-emission constant for air */ PetscScalar pressure1 = 101300; /* surface pressure */ PetscScalar mixratio; /* mixing ratio */ PetscScalar airtemp; /* temperature of air near boundary layer inversion */ PetscScalar dewtemp; /* dew point temperature */ PetscScalar sfctemp; /* temperature at surface */ PetscScalar pwat; /* total column precipitable water */ PetscScalar cloudTemp; /* temperature at base of cloud */ AppCtx user; /* user-defined work context */ MonitorCtx usermonitor; /* user-defined monitor context */ PetscMPIInt rank,size; TS ts; SNES snes; DM da; Vec T,rhs; /* solution vector */ Mat J; /* Jacobian matrix */ PetscReal ftime,dt; PetscInt steps,dof = 5; PetscBool use_coloring = PETSC_TRUE; MatFDColoring matfdcoloring = 0; PetscBool monitor_off = PETSC_FALSE; PetscInitialize(&argc,&argv,(char*)0,help); ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr); ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr); /* Inputs */ readinput(&put); sfctemp = put.Ts; dewtemp = put.Td; cloudTemp = put.Tc; airtemp = put.Ta; pwat = put.pwt; if (!rank) PetscPrintf(PETSC_COMM_SELF,"Initial Temperature = %g\n",sfctemp); /* input surface temperature */ deep_grnd_temp = sfctemp - 10; /* set underlying ground layer temperature */ emma = emission(pwat); /* accounts for radiative effects of water vapor */ /* Converts from Fahrenheit to Celsuis */ sfctemp = fahr_to_cel(sfctemp); airtemp = fahr_to_cel(airtemp); dewtemp = fahr_to_cel(dewtemp); cloudTemp = fahr_to_cel(cloudTemp); deep_grnd_temp = fahr_to_cel(deep_grnd_temp); /* Converts from Celsius to Kelvin */ sfctemp += 273; airtemp += 273; dewtemp += 273; cloudTemp += 273; deep_grnd_temp += 273; /* Calculates initial relative humidity */ x = calcmixingr(dewtemp,pressure1); mixratio = calcmixingr(sfctemp,pressure1); rh = (x/mixratio)*100; if (!rank) printf("Initial RH = %.1f percent\n\n",rh); /* prints initial relative humidity */ time = 3600*put.time; /* sets amount of timesteps to run model */ /* Configure PETSc TS solver */ /*------------------------------------------*/ /* Create grid */ ierr = DMDACreate2d(PETSC_COMM_WORLD,DMDA_BOUNDARY_PERIODIC,DMDA_BOUNDARY_PERIODIC,DMDA_STENCIL_STAR,-20,-20, PETSC_DECIDE,PETSC_DECIDE,dof,1,NULL,NULL,&da);CHKERRQ(ierr); ierr = DMDASetUniformCoordinates(da, 0.0, 1.0, 0.0, 1.0, 0.0, 1.0);CHKERRQ(ierr); /* Define output window for each variable of interest */ ierr = DMDASetFieldName(da,0,"Ts");CHKERRQ(ierr); ierr = DMDASetFieldName(da,1,"Ta");CHKERRQ(ierr); ierr = DMDASetFieldName(da,2,"u");CHKERRQ(ierr); ierr = DMDASetFieldName(da,3,"v");CHKERRQ(ierr); ierr = DMDASetFieldName(da,4,"p");CHKERRQ(ierr); /* set values for appctx */ user.da = da; user.Ts = sfctemp; user.fract = put.fr; /* fraction of sky covered by clouds */ user.dewtemp = dewtemp; /* dew point temperature (mositure in air) */ user.csoil = 2000000; /* heat constant for layer */ user.dzlay = 0.08; /* thickness of top soil layer */ user.emma = emma; /* emission parameter */ user.wind = put.wnd; /* wind spped */ user.pressure1 = pressure1; /* sea level pressure */ user.airtemp = airtemp; /* temperature of air near boundar layer inversion */ user.Tc = cloudTemp; /* temperature at base of lowest cloud layer */ user.init = put.init; /* user chosen initiation scenario */ user.lat = 70*0.0174532; /* converts latitude degrees to latitude in radians */ user.deep_grnd_temp = deep_grnd_temp; /* temp in lowest ground layer */ /* set values for MonitorCtx */ usermonitor.drawcontours = PETSC_FALSE; ierr = PetscOptionsHasName(NULL,"-drawcontours",&usermonitor.drawcontours);CHKERRQ(ierr); if (usermonitor.drawcontours) { PetscReal bounds[] = {1000.0,-1000., -1000.,-1000., 1000.,-1000., 1000.,-1000., 1000,-1000, 100700,100800}; ierr = PetscViewerDrawOpen(PETSC_COMM_WORLD,0,0,0,0,300,300,&usermonitor.drawviewer);CHKERRQ(ierr); ierr = PetscViewerDrawSetBounds(usermonitor.drawviewer,dof,bounds);CHKERRQ(ierr); } usermonitor.interval = 1; ierr = PetscOptionsGetInt(NULL,"-monitor_interval",&usermonitor.interval,NULL);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Extract global vectors from DA; - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = DMCreateGlobalVector(da,&T);CHKERRQ(ierr); ierr = VecDuplicate(T,&rhs);CHKERRQ(ierr); /* r: vector to put the computed right hand side */ ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr); ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr); ierr = TSSetType(ts,TSBEULER);CHKERRQ(ierr); ierr = TSSetRHSFunction(ts,rhs,RhsFunc,&user);CHKERRQ(ierr); /* Set Jacobian evaluation routine - use coloring to compute finite difference Jacobian efficiently */ ierr = DMSetMatType(da,MATAIJ);CHKERRQ(ierr); ierr = DMCreateMatrix(da,&J);CHKERRQ(ierr); ierr = TSGetSNES(ts,&snes);CHKERRQ(ierr); if (use_coloring) { ISColoring iscoloring; ierr = DMCreateColoring(da,IS_COLORING_GLOBAL,&iscoloring);CHKERRQ(ierr); ierr = MatFDColoringCreate(J,iscoloring,&matfdcoloring);CHKERRQ(ierr); ierr = MatFDColoringSetFromOptions(matfdcoloring);CHKERRQ(ierr); ierr = MatFDColoringSetUp(J,iscoloring,matfdcoloring);CHKERRQ(ierr); ierr = ISColoringDestroy(&iscoloring);CHKERRQ(ierr); ierr = MatFDColoringSetFunction(matfdcoloring,(PetscErrorCode (*)(void))SNESTSFormFunction,ts);CHKERRQ(ierr); ierr = SNESSetJacobian(snes,J,J,SNESComputeJacobianDefaultColor,matfdcoloring);CHKERRQ(ierr); } else { ierr = SNESSetJacobian(snes,J,J,SNESComputeJacobianDefault,NULL);CHKERRQ(ierr); } /* Define what to print for ts_monitor option */ ierr = PetscOptionsHasName(NULL,"-monitor_off",&monitor_off);CHKERRQ(ierr); if (!monitor_off) { ierr = TSMonitorSet(ts,Monitor,&usermonitor,NULL);CHKERRQ(ierr); } ierr = FormInitialSolution(da,T,&user);CHKERRQ(ierr); dt = TIMESTEP; /* initial time step */ ftime = TIMESTEP*time; if (!rank) printf("time %d, ftime %g hour, TIMESTEP %g\n",time,ftime/3600,dt); ierr = TSSetInitialTimeStep(ts,0.0,dt);CHKERRQ(ierr); ierr = TSSetDuration(ts,time,ftime);CHKERRQ(ierr); ierr = TSSetSolution(ts,T);CHKERRQ(ierr); ierr = TSSetDM(ts,da);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set runtime options - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSetFromOptions(ts);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Solve nonlinear system - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSolve(ts,T);CHKERRQ(ierr); ierr = TSGetSolveTime(ts,&ftime);CHKERRQ(ierr); ierr = TSGetTimeStepNumber(ts,&steps);CHKERRQ(ierr); if (!rank) PetscPrintf(PETSC_COMM_WORLD,"Solution T after %g hours %d steps\n",ftime/3600,steps); if (matfdcoloring) {ierr = MatFDColoringDestroy(&matfdcoloring);CHKERRQ(ierr);} if (usermonitor.drawcontours) { ierr = PetscViewerDestroy(&usermonitor.drawviewer);CHKERRQ(ierr); } ierr = MatDestroy(&J);CHKERRQ(ierr); ierr = VecDestroy(&T);CHKERRQ(ierr); ierr = VecDestroy(&rhs);CHKERRQ(ierr); ierr = TSDestroy(&ts);CHKERRQ(ierr); ierr = DMDestroy(&da);CHKERRQ(ierr); PetscFinalize(); return 0; }
int main(int argc,char **argv) { PetscErrorCode ierr; KSP ksp; PC pc; Vec x,b; DM da; Mat A; PetscInt dof=1; PetscBool flg; PetscScalar zero=0.0; PetscInitialize(&argc,&argv,(char*)0,help); ierr = PetscOptionsGetInt(NULL,"-dof",&dof,NULL);CHKERRQ(ierr); ierr = DMDACreate(PETSC_COMM_WORLD,&da);CHKERRQ(ierr); ierr = DMDASetDim(da,3);CHKERRQ(ierr); ierr = DMDASetBoundaryType(da,DMDA_BOUNDARY_NONE,DMDA_BOUNDARY_NONE,DMDA_BOUNDARY_NONE);CHKERRQ(ierr); ierr = DMDASetStencilType(da,DMDA_STENCIL_STAR);CHKERRQ(ierr); ierr = DMDASetSizes(da,3,3,3);CHKERRQ(ierr); ierr = DMDASetNumProcs(da,PETSC_DECIDE,PETSC_DECIDE,PETSC_DECIDE);CHKERRQ(ierr); ierr = DMDASetDof(da,dof);CHKERRQ(ierr); ierr = DMDASetStencilWidth(da,1);CHKERRQ(ierr); ierr = DMDASetOwnershipRanges(da,NULL,NULL,NULL);CHKERRQ(ierr); ierr = DMSetFromOptions(da);CHKERRQ(ierr); ierr = DMSetUp(da);CHKERRQ(ierr); ierr = DMCreateGlobalVector(da,&x);CHKERRQ(ierr); ierr = DMCreateGlobalVector(da,&b);CHKERRQ(ierr); ierr = DMSetMatType(da,MATAIJ);CHKERRQ(ierr); ierr = DMCreateMatrix(da,&A);CHKERRQ(ierr); ierr = VecSet(b,zero);CHKERRQ(ierr); /* Test sbaij matrix */ flg = PETSC_FALSE; ierr = PetscOptionsGetBool(NULL,"-test_sbaij",&flg,NULL);CHKERRQ(ierr); if (flg) { Mat sA; ierr = MatSetOption(A,MAT_SYMMETRIC,PETSC_TRUE);CHKERRQ(ierr); ierr = MatConvert(A,MATSBAIJ,MAT_INITIAL_MATRIX,&sA);CHKERRQ(ierr); ierr = MatDestroy(&A);CHKERRQ(ierr); A = sA; } ierr = KSPCreate(PETSC_COMM_WORLD,&ksp);CHKERRQ(ierr); ierr = KSPSetFromOptions(ksp);CHKERRQ(ierr); ierr = KSPSetOperators(ksp,A,A,SAME_NONZERO_PATTERN);CHKERRQ(ierr); ierr = KSPGetPC(ksp,&pc);CHKERRQ(ierr); ierr = PCSetDM(pc,(DM)da);CHKERRQ(ierr); ierr = KSPSolve(ksp,b,x);CHKERRQ(ierr); /* check final residual */ flg = PETSC_FALSE; ierr = PetscOptionsGetBool(NULL, "-check_final_residual", &flg,NULL);CHKERRQ(ierr); if (flg) { Vec b1; PetscReal norm; ierr = KSPGetSolution(ksp,&x);CHKERRQ(ierr); ierr = VecDuplicate(b,&b1);CHKERRQ(ierr); ierr = MatMult(A,x,b1);CHKERRQ(ierr); ierr = VecAXPY(b1,-1.0,b);CHKERRQ(ierr); ierr = VecNorm(b1,NORM_2,&norm);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD,"Final residual %g\n",norm);CHKERRQ(ierr); ierr = VecDestroy(&b1);CHKERRQ(ierr); } ierr = KSPDestroy(&ksp);CHKERRQ(ierr); ierr = VecDestroy(&x);CHKERRQ(ierr); ierr = VecDestroy(&b);CHKERRQ(ierr); ierr = MatDestroy(&A);CHKERRQ(ierr); ierr = DMDestroy(&da);CHKERRQ(ierr); ierr = PetscFinalize(); return 0; }
int main(int Argc,char **Args) { PetscBool flg; PetscInt n = -6; PetscScalar rho = 1.0; PetscReal h; PetscReal beta = 1.0; DM da; PetscRandom rctx; PetscMPIInt comm_size; Mat H,HtH; PetscInt x, y, xs, ys, xm, ym; PetscReal r1, r2; PetscScalar uxy1, uxy2; MatStencil sxy, sxy_m; PetscScalar val, valconj; Vec b, Htb,xvec; KSP kspmg; PC pcmg; PetscErrorCode ierr; PetscInt ix[1] = {0}; PetscScalar vals[1] = {1.0}; PetscInitialize(&Argc,&Args,(char*)0,help); ierr = PetscOptionsGetInt(NULL,"-size",&n,&flg);CHKERRQ(ierr); ierr = PetscOptionsGetReal(NULL,"-beta",&beta,&flg);CHKERRQ(ierr); ierr = PetscOptionsGetScalar(NULL,"-rho",&rho,&flg);CHKERRQ(ierr); /* Set the fudge parameters, we scale the whole thing by 1/(2*h) later */ h = 1.; rho *= 1./(2.*h); /* Geometry info */ ierr = DMDACreate2d(PETSC_COMM_WORLD, DMDA_BOUNDARY_PERIODIC,DMDA_BOUNDARY_PERIODIC, DMDA_STENCIL_STAR, n, n, PETSC_DECIDE, PETSC_DECIDE, 2 /* this is the # of dof's */, 1, NULL, NULL, &da);CHKERRQ(ierr); /* Random numbers */ ierr = PetscRandomCreate(PETSC_COMM_WORLD,&rctx);CHKERRQ(ierr); ierr = PetscRandomSetFromOptions(rctx);CHKERRQ(ierr); /* Single or multi processor ? */ ierr = MPI_Comm_size(PETSC_COMM_WORLD,&comm_size);CHKERRQ(ierr); /* construct matrix */ ierr = DMSetMatType(da,MATAIJ);CHKERRQ(ierr); ierr = DMCreateMatrix(da, &H);CHKERRQ(ierr); /* get local corners for this processor */ ierr = DMDAGetCorners(da,&xs,&ys,0,&xm,&ym,0);CHKERRQ(ierr); /* Assemble the matrix */ for (x=xs; x<xs+xm; x++) { for (y=ys; y<ys+ym; y++) { /* each lattice point sets only the *forward* pointing parameters (right, down), i.e. Nabla_1^+ and Nabla_2^+. In this way we can use only local random number creation. That means we also have to set the corresponding backward pointing entries. */ /* Compute some normally distributed random numbers via Box-Muller */ ierr = PetscRandomGetValueReal(rctx, &r1);CHKERRQ(ierr); r1 = 1.-r1; /* to change from [0,1) to (0,1], which we need for the log */ ierr = PetscRandomGetValueReal(rctx, &r2);CHKERRQ(ierr); PetscReal R = PetscSqrtReal(-2.*PetscLogReal(r1)); PetscReal c = PetscCosReal(2.*PETSC_PI*r2); PetscReal s = PetscSinReal(2.*PETSC_PI*r2); /* use those to set the field */ uxy1 = PetscExpScalar(((PetscScalar) (R*c/beta))*PETSC_i); uxy2 = PetscExpScalar(((PetscScalar) (R*s/beta))*PETSC_i); sxy.i = x; sxy.j = y; /* the point where we are */ /* center action */ sxy.c = 0; /* spin 0, 0 */ ierr = MatSetValuesStencil(H, 1, &sxy, 1, &sxy, &rho, ADD_VALUES);CHKERRQ(ierr); sxy.c = 1; /* spin 1, 1 */ val = -rho; ierr = MatSetValuesStencil(H, 1, &sxy, 1, &sxy, &val, ADD_VALUES);CHKERRQ(ierr); sxy_m.i = x+1; sxy_m.j = y; /* right action */ sxy.c = 0; sxy_m.c = 0; /* spin 0, 0 */ val = -uxy1; valconj = PetscConj(val); ierr = MatSetValuesStencil(H, 1, &sxy_m, 1, &sxy, &val, ADD_VALUES);CHKERRQ(ierr); ierr = MatSetValuesStencil(H, 1, &sxy, 1, &sxy_m, &valconj, ADD_VALUES);CHKERRQ(ierr); sxy.c = 0; sxy_m.c = 1; /* spin 0, 1 */ val = -uxy1; valconj = PetscConj(val); ierr = MatSetValuesStencil(H, 1, &sxy_m, 1, &sxy, &val, ADD_VALUES);CHKERRQ(ierr); ierr = MatSetValuesStencil(H, 1, &sxy, 1, &sxy_m, &valconj, ADD_VALUES);CHKERRQ(ierr); sxy.c = 1; sxy_m.c = 0; /* spin 1, 0 */ val = uxy1; valconj = PetscConj(val); ierr = MatSetValuesStencil(H, 1, &sxy_m, 1, &sxy, &val, ADD_VALUES);CHKERRQ(ierr); ierr = MatSetValuesStencil(H, 1, &sxy, 1, &sxy_m, &valconj, ADD_VALUES);CHKERRQ(ierr); sxy.c = 1; sxy_m.c = 1; /* spin 1, 1 */ val = uxy1; valconj = PetscConj(val); ierr = MatSetValuesStencil(H, 1, &sxy_m, 1, &sxy, &val, ADD_VALUES);CHKERRQ(ierr); ierr = MatSetValuesStencil(H, 1, &sxy, 1, &sxy_m, &valconj, ADD_VALUES);CHKERRQ(ierr); sxy_m.i = x; sxy_m.j = y+1; /* down action */ sxy.c = 0; sxy_m.c = 0; /* spin 0, 0 */ val = -uxy2; valconj = PetscConj(val); ierr = MatSetValuesStencil(H, 1, &sxy_m, 1, &sxy, &val, ADD_VALUES);CHKERRQ(ierr); ierr = MatSetValuesStencil(H, 1, &sxy, 1, &sxy_m, &valconj, ADD_VALUES);CHKERRQ(ierr); sxy.c = 0; sxy_m.c = 1; /* spin 0, 1 */ val = -PETSC_i*uxy2; valconj = PetscConj(val); ierr = MatSetValuesStencil(H, 1, &sxy_m, 1, &sxy, &val, ADD_VALUES);CHKERRQ(ierr); ierr = MatSetValuesStencil(H, 1, &sxy, 1, &sxy_m, &valconj, ADD_VALUES);CHKERRQ(ierr); sxy.c = 1; sxy_m.c = 0; /* spin 1, 0 */ val = -PETSC_i*uxy2; valconj = PetscConj(val); ierr = MatSetValuesStencil(H, 1, &sxy_m, 1, &sxy, &val, ADD_VALUES);CHKERRQ(ierr); ierr = MatSetValuesStencil(H, 1, &sxy, 1, &sxy_m, &valconj, ADD_VALUES);CHKERRQ(ierr); sxy.c = 1; sxy_m.c = 1; /* spin 1, 1 */ val = PetscConj(uxy2); valconj = PetscConj(val); ierr = MatSetValuesStencil(H, 1, &sxy_m, 1, &sxy, &val, ADD_VALUES);CHKERRQ(ierr); ierr = MatSetValuesStencil(H, 1, &sxy, 1, &sxy_m, &valconj, ADD_VALUES);CHKERRQ(ierr); } } ierr = MatAssemblyBegin(H, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(H, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); /* scale H */ ierr = MatScale(H, 1./(2.*h));CHKERRQ(ierr); /* it looks like H is Hermetian */ /* construct normal equations */ ierr = MatMatMult(H, H, MAT_INITIAL_MATRIX, 1., &HtH);CHKERRQ(ierr); /* permutation matrix to check whether H and HtH are identical to the ones in the paper */ /* Mat perm; */ /* ierr = DMCreateMatrix(da, &perm);CHKERRQ(ierr); */ /* PetscInt row, col; */ /* PetscScalar one = 1.0; */ /* for (PetscInt i=0; i<n; i++) { */ /* for (PetscInt j=0; j<n; j++) { */ /* row = (i*n+j)*2; col = i*n+j; */ /* ierr = MatSetValues(perm, 1, &row, 1, &col, &one, INSERT_VALUES);CHKERRQ(ierr); */ /* row = (i*n+j)*2+1; col = i*n+j + n*n; */ /* ierr = MatSetValues(perm, 1, &row, 1, &col, &one, INSERT_VALUES);CHKERRQ(ierr); */ /* } */ /* } */ /* ierr = MatAssemblyBegin(perm, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); */ /* ierr = MatAssemblyEnd(perm, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); */ /* Mat Hperm; */ /* ierr = MatPtAP(H, perm, MAT_INITIAL_MATRIX, 1.0, &Hperm);CHKERRQ(ierr); */ /* ierr = PetscPrintf(PETSC_COMM_WORLD, "Matrix H after construction\n");CHKERRQ(ierr); */ /* ierr = MatView(Hperm, PETSC_VIEWER_STDOUT_(PETSC_COMM_WORLD));CHKERRQ(ierr); */ /* Mat HtHperm; */ /* ierr = MatPtAP(HtH, perm, MAT_INITIAL_MATRIX, 1.0, &HtHperm);CHKERRQ(ierr); */ /* ierr = PetscPrintf(PETSC_COMM_WORLD, "Matrix HtH:\n");CHKERRQ(ierr); */ /* ierr = MatView(HtHperm, PETSC_VIEWER_STDOUT_(PETSC_COMM_WORLD));CHKERRQ(ierr); */ /* right hand side */ ierr = DMCreateGlobalVector(da, &b);CHKERRQ(ierr); ierr = VecSet(b,0.0);CHKERRQ(ierr); ierr = VecSetValues(b, 1, ix, vals, INSERT_VALUES);CHKERRQ(ierr); ierr = VecAssemblyBegin(b);CHKERRQ(ierr); ierr = VecAssemblyEnd(b);CHKERRQ(ierr); /* ierr = VecSetRandom(b, rctx);CHKERRQ(ierr); */ ierr = VecDuplicate(b, &Htb);CHKERRQ(ierr); ierr = MatMultTranspose(H, b, Htb);CHKERRQ(ierr); /* construct solver */ ierr = KSPCreate(PETSC_COMM_WORLD,&kspmg);CHKERRQ(ierr); ierr = KSPSetType(kspmg, KSPCG);CHKERRQ(ierr); ierr = KSPGetPC(kspmg,&pcmg);CHKERRQ(ierr); ierr = PCSetType(pcmg,PCASA);CHKERRQ(ierr); /* maybe user wants to override some of the choices */ ierr = KSPSetFromOptions(kspmg);CHKERRQ(ierr); ierr = KSPSetOperators(kspmg, HtH, HtH, DIFFERENT_NONZERO_PATTERN);CHKERRQ(ierr); ierr = DMDASetRefinementFactor(da, 3, 3, 3);CHKERRQ(ierr); ierr = PCSetDM(pcmg,da);CHKERRQ(ierr); ierr = PCASASetTolerances(pcmg, 1.e-6, 1.e-10,PETSC_DEFAULT,PETSC_DEFAULT);CHKERRQ(ierr); ierr = VecDuplicate(b, &xvec);CHKERRQ(ierr); ierr = VecSet(xvec, 0.0);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Solve the linear system - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = KSPSolve(kspmg, Htb, xvec);CHKERRQ(ierr); /* ierr = VecView(xvec, PETSC_VIEWER_STDOUT_(PETSC_COMM_WORLD));CHKERRQ(ierr); */ ierr = KSPDestroy(&kspmg);CHKERRQ(ierr); ierr = VecDestroy(&xvec);CHKERRQ(ierr); /* seems to be destroyed by KSPDestroy */ ierr = VecDestroy(&b);CHKERRQ(ierr); ierr = VecDestroy(&Htb);CHKERRQ(ierr); ierr = MatDestroy(&HtH);CHKERRQ(ierr); ierr = MatDestroy(&H);CHKERRQ(ierr); ierr = DMDestroy(&da);CHKERRQ(ierr); ierr = PetscRandomDestroy(&rctx);CHKERRQ(ierr); ierr = PetscFinalize(); return 0; }
int main(int argc,char **argv) { PetscErrorCode ierr; DM da,*subda; PetscInt i,dim=3; PetscMPIInt size,rank; Vec v; Vec slvec,sgvec; IS *ois,*iis; VecScatter oscata; VecScatter *iscat,*oscat,*gscat; DMDALocalInfo info; ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr); ierr = PetscOptionsGetInt(NULL,NULL,"-dim",&dim,NULL);CHKERRQ(ierr); /* Create distributed array and get vectors */ ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr); ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr); if (dim == 2) { ierr = DMDACreate2d(PETSC_COMM_WORLD,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DMDA_STENCIL_STAR,-4,-4,PETSC_DECIDE,PETSC_DECIDE,3,1,NULL,NULL,&da);CHKERRQ(ierr); } else if (dim == 3) { ierr = DMDACreate3d(PETSC_COMM_WORLD, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DMDA_STENCIL_STAR,-4,-4,-4,PETSC_DECIDE,PETSC_DECIDE,PETSC_DECIDE,3,1,NULL,NULL,NULL,&da);CHKERRQ(ierr); } ierr = DMDAGetLocalInfo(da,&info);CHKERRQ(ierr); ierr = DMCreateDomainDecomposition(da,NULL,NULL,&iis,&ois,&subda);CHKERRQ(ierr); ierr = DMCreateDomainDecompositionScatters(da,1,subda,&iscat,&oscat,&gscat);CHKERRQ(ierr); { DMDALocalInfo subinfo; MatStencil lower,upper; IS patchis,subpatchis; Vec smallvec; Vec largevec; VecScatter patchscat; ierr = DMDAGetLocalInfo(subda[0],&subinfo);CHKERRQ(ierr); lower.i = info.xs; lower.j = info.ys; lower.k = info.zs; upper.i = info.xs+info.xm; upper.j = info.ys+info.ym; upper.k = info.zs+info.zm; /* test the patch IS as a thing to scatter to/from */ ierr = DMDACreatePatchIS(da,&lower,&upper,&patchis);CHKERRQ(ierr); ierr = DMGetGlobalVector(da,&largevec);CHKERRQ(ierr); ierr = VecCreate(PETSC_COMM_SELF,&smallvec);CHKERRQ(ierr); ierr = VecSetSizes(smallvec,info.dof*(upper.i - lower.i)*(upper.j - lower.j)*(upper.k - lower.k),PETSC_DECIDE);CHKERRQ(ierr); ierr = VecSetFromOptions(smallvec);CHKERRQ(ierr); ierr = VecScatterCreate(smallvec,NULL,largevec,patchis,&patchscat);CHKERRQ(ierr); ierr = FillLocalSubdomain(subda[0],smallvec);CHKERRQ(ierr); ierr = VecSet(largevec,0);CHKERRQ(ierr); ierr = VecScatterBegin(patchscat,smallvec,largevec,ADD_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); ierr = VecScatterEnd(patchscat,smallvec,largevec,ADD_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); for (i = 0; i < size; i++) { if (i == rank) { ierr = ISView(patchis,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr); ierr = VecScatterView(patchscat,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr); ierr = VecView(smallvec,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr); } ierr = MPI_Barrier(PETSC_COMM_WORLD);CHKERRQ(ierr); } ierr = MPI_Barrier(PETSC_COMM_WORLD);CHKERRQ(ierr); ierr = VecView(largevec,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = VecDestroy(&smallvec);CHKERRQ(ierr); ierr = DMRestoreGlobalVector(da,&largevec);CHKERRQ(ierr); ierr = ISDestroy(&patchis);CHKERRQ(ierr); ierr = VecScatterDestroy(&patchscat);CHKERRQ(ierr); } /* view the various parts */ { for (i = 0; i < size; i++) { if (i == rank) { ierr = PetscPrintf(PETSC_COMM_SELF,"Processor %d: \n",i);CHKERRQ(ierr); ierr = DMView(subda[0],PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr); } ierr = MPI_Barrier(PETSC_COMM_WORLD);CHKERRQ(ierr); } ierr = DMGetLocalVector(subda[0],&slvec);CHKERRQ(ierr); ierr = DMGetGlobalVector(subda[0],&sgvec);CHKERRQ(ierr); ierr = DMGetGlobalVector(da,&v);CHKERRQ(ierr); /* test filling outer between the big DM and the small ones with the IS scatter*/ ierr = VecScatterCreate(v,ois[0],sgvec,NULL,&oscata);CHKERRQ(ierr); ierr = FillLocalSubdomain(subda[0],sgvec);CHKERRQ(ierr); ierr = VecScatterBegin(oscata,sgvec,v,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); ierr = VecScatterEnd(oscata,sgvec,v,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); /* test the local-to-local scatter */ /* fill up the local subdomain and then add them together */ ierr = FillLocalSubdomain(da,v);CHKERRQ(ierr); ierr = VecScatterBegin(gscat[0],v,slvec,ADD_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); ierr = VecScatterEnd(gscat[0],v,slvec,ADD_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); ierr = VecView(v,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); /* test ghost scattering backwards */ ierr = VecSet(v,0);CHKERRQ(ierr); ierr = VecScatterBegin(gscat[0],slvec,v,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); ierr = VecScatterEnd(gscat[0],slvec,v,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); ierr = VecView(v,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); /* test overlap scattering backwards */ ierr = DMLocalToGlobalBegin(subda[0],slvec,ADD_VALUES,sgvec);CHKERRQ(ierr); ierr = DMLocalToGlobalEnd(subda[0],slvec,ADD_VALUES,sgvec);CHKERRQ(ierr); ierr = VecSet(v,0);CHKERRQ(ierr); ierr = VecScatterBegin(oscat[0],sgvec,v,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); ierr = VecScatterEnd(oscat[0],sgvec,v,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); ierr = VecView(v,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); /* test interior scattering backwards */ ierr = VecSet(v,0);CHKERRQ(ierr); ierr = VecScatterBegin(iscat[0],sgvec,v,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); ierr = VecScatterEnd(iscat[0],sgvec,v,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); ierr = VecView(v,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); /* test matrix allocation */ for (i = 0; i < size; i++) { if (i == rank) { Mat m; ierr = PetscPrintf(PETSC_COMM_SELF,"Processor %d: \n",i);CHKERRQ(ierr); ierr = DMSetMatType(subda[0],MATAIJ);CHKERRQ(ierr); ierr = DMCreateMatrix(subda[0],&m);CHKERRQ(ierr); ierr = MatView(m,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr); ierr = MatDestroy(&m);CHKERRQ(ierr); } ierr = MPI_Barrier(PETSC_COMM_WORLD);CHKERRQ(ierr); } ierr = DMRestoreLocalVector(subda[0],&slvec);CHKERRQ(ierr); ierr = DMRestoreGlobalVector(subda[0],&sgvec);CHKERRQ(ierr); ierr = DMRestoreGlobalVector(da,&v);CHKERRQ(ierr); } ierr = DMDestroy(&subda[0]);CHKERRQ(ierr); ierr = ISDestroy(&ois[0]);CHKERRQ(ierr); ierr = ISDestroy(&iis[0]);CHKERRQ(ierr); ierr = VecScatterDestroy(&iscat[0]);CHKERRQ(ierr); ierr = VecScatterDestroy(&oscat[0]);CHKERRQ(ierr); ierr = VecScatterDestroy(&gscat[0]);CHKERRQ(ierr); ierr = VecScatterDestroy(&oscata);CHKERRQ(ierr); ierr = PetscFree(iscat);CHKERRQ(ierr); ierr = PetscFree(oscat);CHKERRQ(ierr); ierr = PetscFree(gscat);CHKERRQ(ierr); ierr = PetscFree(oscata);CHKERRQ(ierr); ierr = PetscFree(subda);CHKERRQ(ierr); ierr = PetscFree(ois);CHKERRQ(ierr); ierr = PetscFree(iis);CHKERRQ(ierr); ierr = DMDestroy(&da);CHKERRQ(ierr); ierr = PetscFinalize(); return 0; }
int main(int argc, char **argv) { SNES snes; /* nonlinear solver */ DM dm; /* problem definition */ Vec u,r; /* solution, residual vectors */ Mat A,J; /* Jacobian matrix */ MatNullSpace nullSpace; /* May be necessary for pressure */ AppCtx user; /* user-defined work context */ JacActionCtx userJ; /* context for Jacobian MF action */ PetscInt its; /* iterations for convergence */ PetscReal error = 0.0; /* L_2 error in the solution */ PetscInt numComponents = 0, f; PetscErrorCode ierr; ierr = PetscInitialize(&argc, &argv, NULL, help);CHKERRQ(ierr); ierr = ProcessOptions(PETSC_COMM_WORLD, &user);CHKERRQ(ierr); ierr = SNESCreate(PETSC_COMM_WORLD, &snes);CHKERRQ(ierr); ierr = CreateMesh(PETSC_COMM_WORLD, &user, &dm);CHKERRQ(ierr); ierr = SNESSetDM(snes, dm);CHKERRQ(ierr); ierr = SetupElement(dm, &user);CHKERRQ(ierr); for (f = 0; f < NUM_FIELDS; ++f) { PetscInt numComp; ierr = PetscFEGetNumComponents(user.fe[f], &numComp);CHKERRQ(ierr); numComponents += numComp; } ierr = PetscMalloc(NUM_FIELDS * sizeof(void (*)(const PetscReal[], PetscScalar *)), &user.exactFuncs);CHKERRQ(ierr); user.fem.bcFuncs = (void (**)(const PetscReal[], PetscScalar *)) user.exactFuncs; ierr = SetupExactSolution(dm, &user);CHKERRQ(ierr); ierr = SetupSection(dm, &user);CHKERRQ(ierr); ierr = DMPlexCreateClosureIndex(dm, NULL);CHKERRQ(ierr); ierr = DMCreateGlobalVector(dm, &u);CHKERRQ(ierr); ierr = VecDuplicate(u, &r);CHKERRQ(ierr); ierr = DMSetMatType(dm,MATAIJ);CHKERRQ(ierr); ierr = DMCreateMatrix(dm, &J);CHKERRQ(ierr); if (user.jacobianMF) { PetscInt M, m, N, n; ierr = MatGetSize(J, &M, &N);CHKERRQ(ierr); ierr = MatGetLocalSize(J, &m, &n);CHKERRQ(ierr); ierr = MatCreate(PETSC_COMM_WORLD, &A);CHKERRQ(ierr); ierr = MatSetSizes(A, m, n, M, N);CHKERRQ(ierr); ierr = MatSetType(A, MATSHELL);CHKERRQ(ierr); ierr = MatSetUp(A);CHKERRQ(ierr); ierr = MatShellSetOperation(A, MATOP_MULT, (void (*)(void))FormJacobianAction);CHKERRQ(ierr); userJ.dm = dm; userJ.J = J; userJ.user = &user; ierr = DMCreateLocalVector(dm, &userJ.u);CHKERRQ(ierr); ierr = DMPlexProjectFunctionLocal(dm, user.fe, user.exactFuncs, INSERT_BC_VALUES, userJ.u);CHKERRQ(ierr); ierr = MatShellSetContext(A, &userJ);CHKERRQ(ierr); } else { A = J; } ierr = CreatePressureNullSpace(dm, &user, &nullSpace);CHKERRQ(ierr); ierr = MatSetNullSpace(J, nullSpace);CHKERRQ(ierr); if (A != J) { ierr = MatSetNullSpace(A, nullSpace);CHKERRQ(ierr); } ierr = DMSNESSetFunctionLocal(dm, (PetscErrorCode (*)(DM,Vec,Vec,void*))DMPlexComputeResidualFEM,&user);CHKERRQ(ierr); ierr = DMSNESSetJacobianLocal(dm, (PetscErrorCode (*)(DM,Vec,Mat,Mat,MatStructure*,void*))DMPlexComputeJacobianFEM,&user);CHKERRQ(ierr); ierr = SNESSetJacobian(snes, A, J, NULL, NULL);CHKERRQ(ierr); ierr = SNESSetFromOptions(snes);CHKERRQ(ierr); ierr = DMPlexProjectFunction(dm, user.fe, user.exactFuncs, INSERT_ALL_VALUES, u);CHKERRQ(ierr); if (user.showInitial) {ierr = DMVecViewLocal(dm, u, PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);} if (user.runType == RUN_FULL) { ierr = DMPlexProjectFunction(dm, user.fe, user.initialGuess, INSERT_VALUES, u);CHKERRQ(ierr); if (user.showInitial) {ierr = DMVecViewLocal(dm, u, PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);} if (user.debug) { ierr = PetscPrintf(PETSC_COMM_WORLD, "Initial guess\n");CHKERRQ(ierr); ierr = VecView(u, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); } ierr = SNESSolve(snes, NULL, u);CHKERRQ(ierr); ierr = SNESGetIterationNumber(snes, &its);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "Number of SNES iterations = %D\n", its);CHKERRQ(ierr); ierr = DMPlexComputeL2Diff(dm, user.fe, user.exactFuncs, u, &error);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: %.3g\n", error);CHKERRQ(ierr); if (user.showSolution) { ierr = PetscPrintf(PETSC_COMM_WORLD, "Solution\n");CHKERRQ(ierr); ierr = VecChop(u, 3.0e-9);CHKERRQ(ierr); ierr = VecView(u, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); } } else { PetscReal res = 0.0; /* Check discretization error */ ierr = PetscPrintf(PETSC_COMM_WORLD, "Initial guess\n");CHKERRQ(ierr); ierr = VecView(u, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = DMPlexComputeL2Diff(dm, user.fe, user.exactFuncs, u, &error);CHKERRQ(ierr); if (error >= 1.0e-11) { ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: %g\n", error);CHKERRQ(ierr); } else { ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: < 1.0e-11\n", error);CHKERRQ(ierr); } /* Check residual */ ierr = SNESComputeFunction(snes, u, r);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "Initial Residual\n");CHKERRQ(ierr); ierr = VecChop(r, 1.0e-10);CHKERRQ(ierr); ierr = VecView(r, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = VecNorm(r, NORM_2, &res);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Residual: %g\n", res);CHKERRQ(ierr); /* Check Jacobian */ { Vec b; MatStructure flag; PetscBool isNull; ierr = SNESComputeJacobian(snes, u, &A, &A, &flag);CHKERRQ(ierr); ierr = MatNullSpaceTest(nullSpace, J, &isNull);CHKERRQ(ierr); if (!isNull) SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_PLIB, "The null space calculated for the system operator is invalid."); ierr = VecDuplicate(u, &b);CHKERRQ(ierr); ierr = VecSet(r, 0.0);CHKERRQ(ierr); ierr = SNESComputeFunction(snes, r, b);CHKERRQ(ierr); ierr = MatMult(A, u, r);CHKERRQ(ierr); ierr = VecAXPY(r, 1.0, b);CHKERRQ(ierr); ierr = VecDestroy(&b);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "Au - b = Au + F(0)\n");CHKERRQ(ierr); ierr = VecChop(r, 1.0e-10);CHKERRQ(ierr); ierr = VecView(r, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = VecNorm(r, NORM_2, &res);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "Linear L_2 Residual: %g\n", res);CHKERRQ(ierr); } } if (user.runType == RUN_FULL) { PetscViewer viewer; Vec uLocal; const char *name; ierr = PetscViewerCreate(PETSC_COMM_WORLD, &viewer);CHKERRQ(ierr); ierr = PetscViewerSetType(viewer, PETSCVIEWERVTK);CHKERRQ(ierr); ierr = PetscViewerSetFormat(viewer, PETSC_VIEWER_ASCII_VTK);CHKERRQ(ierr); ierr = PetscViewerFileSetName(viewer, "ex62_sol.vtk");CHKERRQ(ierr); ierr = DMGetLocalVector(dm, &uLocal);CHKERRQ(ierr); ierr = PetscObjectGetName((PetscObject) u, &name);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) uLocal, name);CHKERRQ(ierr); ierr = DMGlobalToLocalBegin(dm, u, INSERT_VALUES, uLocal);CHKERRQ(ierr); ierr = DMGlobalToLocalEnd(dm, u, INSERT_VALUES, uLocal);CHKERRQ(ierr); ierr = VecView(uLocal, viewer);CHKERRQ(ierr); ierr = DMRestoreLocalVector(dm, &uLocal);CHKERRQ(ierr); ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); } ierr = PetscFree(user.exactFuncs);CHKERRQ(ierr); ierr = DestroyElement(&user);CHKERRQ(ierr); ierr = MatNullSpaceDestroy(&nullSpace);CHKERRQ(ierr); if (user.jacobianMF) { ierr = VecDestroy(&userJ.u);CHKERRQ(ierr); } if (A != J) { ierr = MatDestroy(&A);CHKERRQ(ierr); } ierr = MatDestroy(&J);CHKERRQ(ierr); ierr = VecDestroy(&u);CHKERRQ(ierr); ierr = VecDestroy(&r);CHKERRQ(ierr); ierr = SNESDestroy(&snes);CHKERRQ(ierr); ierr = DMDestroy(&dm);CHKERRQ(ierr); ierr = PetscFinalize(); return 0; }
int main(int argc, char **argv) { PetscErrorCode ierr; /* used to check for functions returning nonzeros */ Vec x; /* variables vector */ Vec xl,xu; /* lower and upper bound on variables */ PetscBool flg; /* A return variable when checking for user options */ SNESConvergedReason reason; AppCtx user; /* user-defined work context */ SNES snes; Vec r; PetscReal zero=0.0,thnd=1000; /* Initialize PETSC */ PetscInitialize(&argc, &argv,(char*)0,help); #if defined(PETSC_USE_COMPLEX) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_SUP,"This example does not work for scalar type complex\n"); #endif /* Set the default values for the problem parameters */ user.nx = 50; user.ny = 50; user.ecc = 0.1; user.b = 10.0; /* Check for any command line arguments that override defaults */ ierr = PetscOptionsGetReal(NULL,"-ecc",&user.ecc,&flg);CHKERRQ(ierr); ierr = PetscOptionsGetReal(NULL,"-b",&user.b,&flg);CHKERRQ(ierr); /* A two dimensional distributed array will help define this problem, which derives from an elliptic PDE on two dimensional domain. From the distributed array, Create the vectors. */ ierr = DMDACreate2d(PETSC_COMM_WORLD, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE,DMDA_STENCIL_STAR,-50,-50,PETSC_DECIDE,PETSC_DECIDE,1,1,NULL,NULL,&user.da);CHKERRQ(ierr); ierr = DMDAGetIerr(user.da,PETSC_IGNORE,&user.nx,&user.ny,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE);CHKERRQ(ierr); PetscPrintf(PETSC_COMM_WORLD,"\n---- Journal Bearing Problem -----\n"); PetscPrintf(PETSC_COMM_WORLD,"mx: %d, my: %d, ecc: %4.3f, b:%3.1f \n", user.nx,user.ny,user.ecc,user.b); /* Extract global and local vectors from DA; the vector user.B is used solely as work space for the evaluation of the function, gradient, and Hessian. Duplicate for remaining vectors that are the same types. */ ierr = DMCreateGlobalVector(user.da,&x);CHKERRQ(ierr); /* Solution */ ierr = VecDuplicate(x,&user.B);CHKERRQ(ierr); /* Linear objective */ ierr = VecDuplicate(x,&r);CHKERRQ(ierr); /* Create matrix user.A to store quadratic, Create a local ordering scheme. */ ierr = DMSetMatType(user.da,MATAIJ);CHKERRQ(ierr); ierr = DMCreateMatrix(user.da,&user.A);CHKERRQ(ierr); /* User defined function -- compute linear term of quadratic */ ierr = ComputeB(&user);CHKERRQ(ierr); /* Create nonlinear solver context */ ierr = SNESCreate(PETSC_COMM_WORLD,&snes);CHKERRQ(ierr); /* Set function evaluation and Jacobian evaluation routines */ ierr = SNESSetFunction(snes,r,FormGradient,&user);CHKERRQ(ierr); ierr = SNESSetJacobian(snes,user.A,user.A,FormHessian,&user);CHKERRQ(ierr); /* Set the initial solution guess */ ierr = VecSet(x, zero);CHKERRQ(ierr); ierr = SNESSetFromOptions(snes);CHKERRQ(ierr); /* Set variable bounds */ ierr = VecDuplicate(x,&xl);CHKERRQ(ierr); ierr = VecDuplicate(x,&xu);CHKERRQ(ierr); ierr = VecSet(xl,zero);CHKERRQ(ierr); ierr = VecSet(xu,thnd);CHKERRQ(ierr); ierr = SNESVISetVariableBounds(snes,xl,xu);CHKERRQ(ierr); /* Solve the application */ ierr = SNESSolve(snes,NULL,x);CHKERRQ(ierr); ierr = SNESGetConvergedReason(snes,&reason);CHKERRQ(ierr); if (reason <= 0) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_SUP,"The SNESVI solver did not converge, adjust some parameters, or check the function evaluation routines\n"); /* Free memory */ ierr = VecDestroy(&x);CHKERRQ(ierr); ierr = VecDestroy(&xl);CHKERRQ(ierr); ierr = VecDestroy(&xu);CHKERRQ(ierr); ierr = VecDestroy(&r);CHKERRQ(ierr); ierr = MatDestroy(&user.A);CHKERRQ(ierr); ierr = VecDestroy(&user.B);CHKERRQ(ierr); ierr = DMDestroy(&user.da);CHKERRQ(ierr); ierr = SNESDestroy(&snes);CHKERRQ(ierr); ierr = PetscFinalize(); return 0; }
int main(int argc,char **argv) { PetscErrorCode ierr; KSP ksp; PC pc; Vec x,b; DM da; Mat A,Atrans; PetscInt dof=1,M=8; PetscBool flg,trans=PETSC_FALSE; ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr; ierr = PetscOptionsGetInt(NULL,NULL,"-dof",&dof,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetInt(NULL,NULL,"-M",&M,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetBool(NULL,NULL,"-trans",&trans,NULL);CHKERRQ(ierr); ierr = DMDACreate(PETSC_COMM_WORLD,&da);CHKERRQ(ierr); ierr = DMSetDimension(da,3);CHKERRQ(ierr); ierr = DMDASetBoundaryType(da,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE);CHKERRQ(ierr); ierr = DMDASetStencilType(da,DMDA_STENCIL_STAR);CHKERRQ(ierr); ierr = DMDASetSizes(da,M,M,M);CHKERRQ(ierr); ierr = DMDASetNumProcs(da,PETSC_DECIDE,PETSC_DECIDE,PETSC_DECIDE);CHKERRQ(ierr); ierr = DMDASetDof(da,dof);CHKERRQ(ierr); ierr = DMDASetStencilWidth(da,1);CHKERRQ(ierr); ierr = DMDASetOwnershipRanges(da,NULL,NULL,NULL);CHKERRQ(ierr); ierr = DMSetFromOptions(da);CHKERRQ(ierr); ierr = DMSetUp(da);CHKERRQ(ierr); ierr = DMCreateGlobalVector(da,&x);CHKERRQ(ierr); ierr = DMCreateGlobalVector(da,&b);CHKERRQ(ierr); ierr = ComputeRHS(da,b);CHKERRQ(ierr); ierr = DMSetMatType(da,MATBAIJ);CHKERRQ(ierr); ierr = DMSetFromOptions(da);CHKERRQ(ierr); ierr = DMCreateMatrix(da,&A);CHKERRQ(ierr); ierr = ComputeMatrix(da,A);CHKERRQ(ierr); /* A is non-symmetric. Make A = 0.5*(A + Atrans) symmetric for testing icc and cholesky */ ierr = MatTranspose(A,MAT_INITIAL_MATRIX,&Atrans);CHKERRQ(ierr); ierr = MatAXPY(A,1.0,Atrans,DIFFERENT_NONZERO_PATTERN);CHKERRQ(ierr); ierr = MatScale(A,0.5);CHKERRQ(ierr); ierr = MatDestroy(&Atrans);CHKERRQ(ierr); /* Test sbaij matrix */ flg = PETSC_FALSE; ierr = PetscOptionsGetBool(NULL,NULL, "-test_sbaij1", &flg,NULL);CHKERRQ(ierr); if (flg) { Mat sA; PetscBool issymm; ierr = MatIsTranspose(A,A,0.0,&issymm);CHKERRQ(ierr); if (issymm) { ierr = MatSetOption(A,MAT_SYMMETRIC,PETSC_TRUE);CHKERRQ(ierr); } else {ierr = PetscPrintf(PETSC_COMM_WORLD,"Warning: A is non-symmetric\n");CHKERRQ(ierr);} ierr = MatConvert(A,MATSBAIJ,MAT_INITIAL_MATRIX,&sA);CHKERRQ(ierr); ierr = MatDestroy(&A);CHKERRQ(ierr); A = sA; } ierr = KSPCreate(PETSC_COMM_WORLD,&ksp);CHKERRQ(ierr); ierr = KSPSetFromOptions(ksp);CHKERRQ(ierr); ierr = KSPSetOperators(ksp,A,A);CHKERRQ(ierr); ierr = KSPGetPC(ksp,&pc);CHKERRQ(ierr); ierr = PCSetDM(pc,(DM)da);CHKERRQ(ierr); if (trans) { ierr = KSPSolveTranspose(ksp,b,x);CHKERRQ(ierr); } else { ierr = KSPSolve(ksp,b,x);CHKERRQ(ierr); } /* check final residual */ flg = PETSC_FALSE; ierr = PetscOptionsGetBool(NULL,NULL, "-check_final_residual", &flg,NULL);CHKERRQ(ierr); if (flg) { Vec b1; PetscReal norm; ierr = KSPGetSolution(ksp,&x);CHKERRQ(ierr); ierr = VecDuplicate(b,&b1);CHKERRQ(ierr); ierr = MatMult(A,x,b1);CHKERRQ(ierr); ierr = VecAXPY(b1,-1.0,b);CHKERRQ(ierr); ierr = VecNorm(b1,NORM_2,&norm);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD,"Final residual %g\n",norm);CHKERRQ(ierr); ierr = VecDestroy(&b1);CHKERRQ(ierr); } ierr = KSPDestroy(&ksp);CHKERRQ(ierr); ierr = VecDestroy(&x);CHKERRQ(ierr); ierr = VecDestroy(&b);CHKERRQ(ierr); ierr = MatDestroy(&A);CHKERRQ(ierr); ierr = DMDestroy(&da);CHKERRQ(ierr); ierr = PetscFinalize(); return ierr; }
int main(int argc,char **argv) { TS ts; /* nonlinear solver */ Vec U; /* solution, residual vectors */ Mat J; /* Jacobian matrix */ PetscInt maxsteps = 1000; PetscErrorCode ierr; DM da; AppCtx user; PetscInt i; char Name[16]; /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Initialize program - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ PetscInitialize(&argc,&argv,(char*)0,help); user.N = 1; ierr = PetscOptionsGetInt(NULL,"-N",&user.N,NULL);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create distributed array (DMDA) to manage parallel grid and vectors - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = DMDACreate1d(PETSC_COMM_WORLD, DMDA_BOUNDARY_MIRROR,-8,user.N,1,NULL,&da);CHKERRQ(ierr); for (i=0; i<user.N; i++) { ierr = PetscSNPrintf(Name,16,"Void size %d",(int)(i+1)); ierr = DMDASetFieldName(da,i,Name);CHKERRQ(ierr); } /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Extract global vectors from DMDA; then duplicate for remaining vectors that are the same types - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = DMCreateGlobalVector(da,&U);CHKERRQ(ierr); ierr = DMSetMatType(da,MATAIJ);CHKERRQ(ierr); ierr = DMCreateMatrix(da,&J);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create timestepping solver context - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr); ierr = TSSetType(ts,TSARKIMEX);CHKERRQ(ierr); ierr = TSSetDM(ts,da);CHKERRQ(ierr); ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr); ierr = TSSetIFunction(ts,NULL,IFunction,&user);CHKERRQ(ierr); ierr = TSSetIJacobian(ts,J,J,IJacobian,&user);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set initial conditions - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = InitialConditions(da,U);CHKERRQ(ierr); ierr = TSSetSolution(ts,U);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set solver options - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSetInitialTimeStep(ts,0.0,.001);CHKERRQ(ierr); ierr = TSSetDuration(ts,maxsteps,1.0);CHKERRQ(ierr); ierr = TSSetFromOptions(ts);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Solve nonlinear system - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSolve(ts,U);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Free work space. All PETSc objects should be destroyed when they are no longer needed. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = VecDestroy(&U);CHKERRQ(ierr); ierr = MatDestroy(&J);CHKERRQ(ierr); ierr = TSDestroy(&ts);CHKERRQ(ierr); ierr = DMDestroy(&da);CHKERRQ(ierr); ierr = PetscFinalize(); PetscFunctionReturn(0); }
/* The element stiffness matrix for the identity in linear elements is 1 /2 1 1\ - |1 2 1| 12 \1 1 2/ no matter what the shape of the triangle. */ PetscErrorCode TaylorGalerkinStepIIMomentum(DM da, UserContext *user) { MPI_Comm comm; KSP ksp; Mat mat; Vec rhs_u, rhs_v; PetscScalar identity[9] = {0.16666666667, 0.08333333333, 0.08333333333, 0.08333333333, 0.16666666667, 0.08333333333, 0.08333333333, 0.08333333333, 0.16666666667}; PetscScalar *u_n, *v_n, *mu_n; PetscScalar *u_phi, *v_phi; PetscScalar *rho_u_phi, *rho_v_phi; PetscInt idx[3]; PetscScalar values_u[3]; PetscScalar values_v[3]; PetscScalar psi_x[3], psi_y[3]; PetscScalar mu, tau_xx, tau_xy, tau_yy; PetscReal hx, hy, area; const PetscInt *necon; PetscInt j, k, e, ne, nc, mx, my; PetscErrorCode ierr; PetscFunctionBeginUser; ierr = PetscObjectGetComm((PetscObject) da, &comm);CHKERRQ(ierr); ierr = DMSetMatType(da,MATAIJ);CHKERRQ(ierr); ierr = DMCreateMatrix(da, &mat);CHKERRQ(ierr); ierr = MatSetOption(mat,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE);CHKERRQ(ierr); ierr = DMGetGlobalVector(da, &rhs_u);CHKERRQ(ierr); ierr = DMGetGlobalVector(da, &rhs_v);CHKERRQ(ierr); ierr = KSPCreate(comm, &ksp);CHKERRQ(ierr); ierr = KSPSetFromOptions(ksp);CHKERRQ(ierr); ierr = DMDAGetInfo(da, 0, &mx, &my, 0,0,0,0,0,0,0,0,0,0);CHKERRQ(ierr); hx = 1.0 / (PetscReal)(mx-1); hy = 1.0 / (PetscReal)(my-1); area = 0.5*hx*hy; ierr = VecGetArray(user->sol_n.u, &u_n);CHKERRQ(ierr); ierr = VecGetArray(user->sol_n.v, &v_n);CHKERRQ(ierr); ierr = VecGetArray(user->mu, &mu_n);CHKERRQ(ierr); ierr = VecGetArray(user->sol_phi.u, &u_phi);CHKERRQ(ierr); ierr = VecGetArray(user->sol_phi.v, &v_phi);CHKERRQ(ierr); ierr = VecGetArray(user->sol_phi.rho_u, &rho_u_phi);CHKERRQ(ierr); ierr = VecGetArray(user->sol_phi.rho_v, &rho_v_phi);CHKERRQ(ierr); ierr = DMDAGetElements(da, &ne, &nc, &necon);CHKERRQ(ierr); for (e = 0; e < ne; e++) { for (j = 0; j < 3; j++) { idx[j] = necon[3*e+j]; values_u[j] = 0.0; values_v[j] = 0.0; } /* Get basis function deriatives (we need the orientation of the element here) */ if (idx[1] > idx[0]) { psi_x[0] = -hy; psi_x[1] = hy; psi_x[2] = 0.0; psi_y[0] = -hx; psi_y[1] = 0.0; psi_y[2] = hx; } else { psi_x[0] = hy; psi_x[1] = -hy; psi_x[2] = 0.0; psi_y[0] = hx; psi_y[1] = 0.0; psi_y[2] = -hx; } /* <\nabla\psi, F^{n+\phi}_e>: Divergence of the element-averaged convective fluxes */ for (j = 0; j < 3; j++) { values_u[j] += psi_x[j]*rho_u_phi[e]*u_phi[e] + psi_y[j]*rho_u_phi[e]*v_phi[e]; values_v[j] += psi_x[j]*rho_v_phi[e]*u_phi[e] + psi_y[j]*rho_v_phi[e]*v_phi[e]; } /* -<\nabla\psi, F^n_v>: Divergence of the viscous fluxes */ for (j = 0; j < 3; j++) { /* \tau_{xx} = 2/3 \mu(T) (2 {\partial u\over\partial x} - {\partial v\over\partial y}) */ /* \tau_{xy} = \mu(T) ( {\partial u\over\partial y} + {\partial v\over\partial x}) */ /* \tau_{yy} = 2/3 \mu(T) (2 {\partial v\over\partial y} - {\partial u\over\partial x}) */ mu = 0.0; tau_xx = 0.0; tau_xy = 0.0; tau_yy = 0.0; for (k = 0; k < 3; k++) { mu += mu_n[idx[k]]; tau_xx += 2.0*psi_x[k]*u_n[idx[k]] - psi_y[k]*v_n[idx[k]]; tau_xy += psi_y[k]*u_n[idx[k]] + psi_x[k]*v_n[idx[k]]; tau_yy += 2.0*psi_y[k]*v_n[idx[k]] - psi_x[k]*u_n[idx[k]]; } mu /= 3.0; tau_xx *= (2.0/3.0)*mu; tau_xy *= mu; tau_yy *= (2.0/3.0)*mu; values_u[j] -= area*(psi_x[j]*tau_xx + psi_y[j]*tau_xy); values_v[j] -= area*(psi_x[j]*tau_xy + psi_y[j]*tau_yy); } /* Accumulate to global structures */ ierr = VecSetValuesLocal(rhs_u, 3, idx, values_u, ADD_VALUES);CHKERRQ(ierr); ierr = VecSetValuesLocal(rhs_v, 3, idx, values_v, ADD_VALUES);CHKERRQ(ierr); ierr = MatSetValuesLocal(mat, 3, idx, 3, idx, identity, ADD_VALUES);CHKERRQ(ierr); } ierr = DMDARestoreElements(da, &ne, &nc, &necon);CHKERRQ(ierr); ierr = VecRestoreArray(user->sol_n.u, &u_n);CHKERRQ(ierr); ierr = VecRestoreArray(user->sol_n.v, &v_n);CHKERRQ(ierr); ierr = VecRestoreArray(user->mu, &mu_n);CHKERRQ(ierr); ierr = VecRestoreArray(user->sol_phi.u, &u_phi);CHKERRQ(ierr); ierr = VecRestoreArray(user->sol_phi.v, &v_phi);CHKERRQ(ierr); ierr = VecRestoreArray(user->sol_phi.rho_u, &rho_u_phi);CHKERRQ(ierr); ierr = VecRestoreArray(user->sol_phi.rho_v, &rho_v_phi);CHKERRQ(ierr); ierr = VecAssemblyBegin(rhs_u);CHKERRQ(ierr); ierr = VecAssemblyBegin(rhs_v);CHKERRQ(ierr); ierr = MatAssemblyBegin(mat, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = VecAssemblyEnd(rhs_u);CHKERRQ(ierr); ierr = VecAssemblyEnd(rhs_v);CHKERRQ(ierr); ierr = MatAssemblyEnd(mat, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = VecScale(rhs_u,user->dt);CHKERRQ(ierr); ierr = VecScale(rhs_v,user->dt);CHKERRQ(ierr); ierr = KSPSetOperators(ksp, mat, mat, DIFFERENT_NONZERO_PATTERN);CHKERRQ(ierr); ierr = KSPSolve(ksp, rhs_u, user->sol_np1.rho_u);CHKERRQ(ierr); ierr = KSPSolve(ksp, rhs_v, user->sol_np1.rho_v);CHKERRQ(ierr); ierr = KSPDestroy(&ksp);CHKERRQ(ierr); ierr = MatDestroy(&mat);CHKERRQ(ierr); ierr = DMRestoreGlobalVector(da, &rhs_u);CHKERRQ(ierr); ierr = DMRestoreGlobalVector(da, &rhs_v);CHKERRQ(ierr); PetscFunctionReturn(0); }
int main(int argc,char *argv[]) { char mat_type[256] = "aij"; /* default matrix type */ PetscErrorCode ierr; MPI_Comm comm; PetscMPIInt rank,size; DM slice; PetscInt i,bs=1,N=5,n,m,rstart,ghosts[2],*d_nnz,*o_nnz,dfill[4]={1,0,0,1},ofill[4]={1,1,1,1}; PetscReal alpha =1,K=1,rho0=1,u0=0,sigma=0.2; PetscBool useblock=PETSC_TRUE; PetscScalar *xx; Mat A; Vec x,b,lf; ierr = PetscInitialize(&argc,&argv,0,help);CHKERRQ(ierr); comm = PETSC_COMM_WORLD; ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); ierr = PetscOptionsBegin(comm,0,"Options for DMSliced test",0);CHKERRQ(ierr); { ierr = PetscOptionsInt("-n","Global number of nodes","",N,&N,NULL);CHKERRQ(ierr); ierr = PetscOptionsInt("-bs","Block size (1 or 2)","",bs,&bs,NULL);CHKERRQ(ierr); if (bs != 1) { if (bs != 2) SETERRQ(PETSC_COMM_WORLD,1,"Block size must be 1 or 2"); ierr = PetscOptionsReal("-alpha","Inverse time step for wave operator","",alpha,&alpha,NULL);CHKERRQ(ierr); ierr = PetscOptionsReal("-K","Bulk modulus of compressibility","",K,&K,NULL);CHKERRQ(ierr); ierr = PetscOptionsReal("-rho0","Reference density","",rho0,&rho0,NULL);CHKERRQ(ierr); ierr = PetscOptionsReal("-u0","Reference velocity","",u0,&u0,NULL);CHKERRQ(ierr); ierr = PetscOptionsReal("-sigma","Width of Gaussian density perturbation","",sigma,&sigma,NULL);CHKERRQ(ierr); ierr = PetscOptionsBool("-block","Use block matrix assembly","",useblock,&useblock,NULL);CHKERRQ(ierr); } ierr = PetscOptionsString("-sliced_mat_type","Matrix type to use (aij or baij)","",mat_type,mat_type,sizeof(mat_type),NULL);CHKERRQ(ierr); } ierr = PetscOptionsEnd();CHKERRQ(ierr); /* Split ownership, set up periodic grid in 1D */ n = PETSC_DECIDE; ierr = PetscSplitOwnership(comm,&n,&N);CHKERRQ(ierr); rstart = 0; ierr = MPI_Scan(&n,&rstart,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); rstart -= n; ghosts[0] = (N+rstart-1)%N; ghosts[1] = (rstart+n)%N; ierr = PetscMalloc2(n,PetscInt,&d_nnz,n,PetscInt,&o_nnz);CHKERRQ(ierr); for (i=0; i<n; i++) { if (size > 1 && (i==0 || i==n-1)) { d_nnz[i] = 2; o_nnz[i] = 1; } else { d_nnz[i] = 3; o_nnz[i] = 0; } } ierr = DMSlicedCreate(comm,bs,n,2,ghosts,d_nnz,o_nnz,&slice);CHKERRQ(ierr); /* Currently does not copy X_nnz so we can't free them until after DMSlicedGetMatrix */ if (!useblock) {ierr = DMSlicedSetBlockFills(slice,dfill,ofill);CHKERRQ(ierr);} /* Irrelevant for baij formats */ ierr = DMSetMatType(slice,mat_type);CHKERRQ(ierr); ierr = DMCreateMatrix(slice,&A);CHKERRQ(ierr); ierr = PetscFree2(d_nnz,o_nnz);CHKERRQ(ierr); ierr = MatSetOption(A,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); ierr = DMCreateGlobalVector(slice,&x);CHKERRQ(ierr); ierr = VecDuplicate(x,&b);CHKERRQ(ierr); ierr = VecGhostGetLocalForm(x,&lf);CHKERRQ(ierr); ierr = VecGetSize(lf,&m);CHKERRQ(ierr); if (m != (n+2)*bs) SETERRQ2(PETSC_COMM_SELF,1,"size of local form %D, expected %D",m,(n+2)*bs); ierr = VecGetArray(lf,&xx);CHKERRQ(ierr); for (i=0; i<n; i++) { PetscInt row[2],col[9],im,ip; PetscScalar v[12]; const PetscReal xref = 2.0*(rstart+i)/N - 1; /* [-1,1] */ const PetscReal h = 1.0/N; /* grid spacing */ im = (i==0) ? n : i-1; ip = (i==n-1) ? n+1 : i+1; switch (bs) { case 1: /* Laplacian with periodic boundaries */ col[0] = im; col[1] = i; col[2] = ip; v[0] = -h; v[1] = 2*h; v[2] = -h; ierr = MatSetValuesLocal(A,1,&i,3,col,v,INSERT_VALUES);CHKERRQ(ierr); xx[i] = sin(xref*PETSC_PI); break; case 2: /* Linear acoustic wave operator in variables [rho, u], central differences, periodic, timestep 1/alpha */ v[0] = -0.5*u0; v[1] = -0.5*K; v[2] = alpha; v[3] = 0; v[4] = 0.5*u0; v[5] = 0.5*K; v[6] = -0.5/rho0; v[7] = -0.5*u0; v[8] = 0; v[9] = alpha; v[10] = 0.5/rho0; v[11] = 0.5*u0; if (useblock) { row[0] = i; col[0] = im; col[1] = i; col[2] = ip; ierr = MatSetValuesBlockedLocal(A,1,row,3,col,v,INSERT_VALUES);CHKERRQ(ierr); } else { row[0] = 2*i; row[1] = 2*i+1; col[0] = 2*im; col[1] = 2*im+1; col[2] = 2*i; col[3] = 2*ip; col[4] = 2*ip+1; v[3] = v[4]; v[4] = v[5]; /* pack values in first row */ ierr = MatSetValuesLocal(A,1,row,5,col,v,INSERT_VALUES);CHKERRQ(ierr); col[2] = 2*i+1; v[8] = v[9]; v[9] = v[10]; v[10] = v[11]; /* pack values in second row */ ierr = MatSetValuesLocal(A,1,row+1,5,col,v+6,INSERT_VALUES);CHKERRQ(ierr); } /* Set current state (gaussian density perturbation) */ xx[2*i] = 0.2*exp(-PetscSqr(xref)/(2*PetscSqr(sigma))); xx[2*i+1] = 0; break; default: SETERRQ1(PETSC_COMM_SELF,1,"not implemented for block size %D",bs); } } ierr = VecRestoreArray(lf,&xx);CHKERRQ(ierr); ierr = VecGhostRestoreLocalForm(x,&lf);CHKERRQ(ierr); ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatMult(A,x,b);CHKERRQ(ierr); ierr = MatView(A,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = VecView(x,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = VecView(b,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); /* Update the ghosted values, view the result on rank 0. */ ierr = VecGhostUpdateBegin(b,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); ierr = VecGhostUpdateEnd(b,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); if (!rank) { ierr = VecGhostGetLocalForm(b,&lf);CHKERRQ(ierr); ierr = PetscViewerASCIIPrintf(PETSC_VIEWER_STDOUT_SELF,"Local form of b on rank 0, last two nodes are ghost nodes\n");CHKERRQ(ierr); ierr = VecView(lf,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr); ierr = VecGhostRestoreLocalForm(b,&lf);CHKERRQ(ierr); } ierr = DMDestroy(&slice);CHKERRQ(ierr); ierr = VecDestroy(&x);CHKERRQ(ierr); ierr = VecDestroy(&b);CHKERRQ(ierr); ierr = MatDestroy(&A);CHKERRQ(ierr); ierr = PetscFinalize(); return 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); }
int main(int argc,char **argv) { PetscInt i,M = 3,N = 5,P=3,s=1,w=2,m = PETSC_DECIDE,n = PETSC_DECIDE,p = PETSC_DECIDE; PetscErrorCode ierr; PetscInt *lx = NULL,*ly = NULL,*lz = NULL; DM da; PetscBool flg = PETSC_FALSE,test_order = PETSC_FALSE; ISColoring coloring; Mat mat; DMDAStencilType stencil_type = DMDA_STENCIL_BOX; Vec lvec,dvec; MatFDColoring fdcoloring; ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr); /* Read options */ ierr = PetscOptionsGetInt(NULL,"-M",&M,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetInt(NULL,"-N",&N,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetInt(NULL,"-P",&P,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetInt(NULL,"-m",&m,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetInt(NULL,"-n",&n,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetInt(NULL,"-p",&p,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetInt(NULL,"-s",&s,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetInt(NULL,"-w",&w,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetBool(NULL,"-star",&flg,NULL);CHKERRQ(ierr); if (flg) stencil_type = DMDA_STENCIL_STAR; ierr = PetscOptionsGetBool(NULL,"-test_order",&test_order,NULL);CHKERRQ(ierr); flg = PETSC_FALSE; ierr = PetscOptionsGetBool(NULL,"-distribute",&flg,NULL);CHKERRQ(ierr); if (flg) { if (m == PETSC_DECIDE) SETERRQ(PETSC_COMM_WORLD,1,"Must set -m option with -distribute option"); ierr = PetscMalloc1(m,&lx);CHKERRQ(ierr); for (i=0; i<m-1; i++) lx[i] = 4; lx[m-1] = M - 4*(m-1); if (n == PETSC_DECIDE) SETERRQ(PETSC_COMM_WORLD,1,"Must set -n option with -distribute option"); ierr = PetscMalloc1(n,&ly);CHKERRQ(ierr); for (i=0; i<n-1; i++) ly[i] = 2; ly[n-1] = N - 2*(n-1); if (p == PETSC_DECIDE) SETERRQ(PETSC_COMM_WORLD,1,"Must set -p option with -distribute option"); ierr = PetscMalloc1(p,&lz);CHKERRQ(ierr); for (i=0; i<p-1; i++) lz[i] = 2; lz[p-1] = P - 2*(p-1); } /* Create distributed array and get vectors */ ierr = DMDACreate3d(PETSC_COMM_WORLD,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,stencil_type,M,N,P,m,n,p,w,s,lx,ly,lz,&da);CHKERRQ(ierr); ierr = PetscFree(lx);CHKERRQ(ierr); ierr = PetscFree(ly);CHKERRQ(ierr); ierr = PetscFree(lz);CHKERRQ(ierr); ierr = DMSetMatType(da,MATMPIAIJ);CHKERRQ(ierr); ierr = DMCreateColoring(da,IS_COLORING_GLOBAL,&coloring);CHKERRQ(ierr); ierr = DMSetMatType(da,MATMPIAIJ);CHKERRQ(ierr); ierr = DMCreateMatrix(da,&mat);CHKERRQ(ierr); ierr = MatFDColoringCreate(mat,coloring,&fdcoloring);CHKERRQ(ierr); ierr = MatFDColoringSetUp(mat,coloring,fdcoloring);CHKERRQ(ierr); ierr = DMCreateGlobalVector(da,&dvec);CHKERRQ(ierr); ierr = DMCreateLocalVector(da,&lvec);CHKERRQ(ierr); /* Free memory */ ierr = MatFDColoringDestroy(&fdcoloring);CHKERRQ(ierr); ierr = VecDestroy(&dvec);CHKERRQ(ierr); ierr = VecDestroy(&lvec);CHKERRQ(ierr); ierr = MatDestroy(&mat);CHKERRQ(ierr); ierr = ISColoringDestroy(&coloring);CHKERRQ(ierr); ierr = DMDestroy(&da);CHKERRQ(ierr); ierr = PetscFinalize(); return 0; }
int main(int argc,char **argv) { DM da; /* distributed array */ Vec x,b,u; /* approx solution, RHS, exact solution */ Mat A; /* linear system matrix */ KSP ksp; /* linear solver context */ PetscRandom rctx; /* random number generator context */ PetscReal norm; /* norm of solution error */ PetscInt i,j,its; PetscErrorCode ierr; PetscBool flg = PETSC_FALSE; PetscLogStage stage; DMDALocalInfo info; ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr); /* Create distributed array to handle parallel distribution. The problem size will default to 8 by 7, but this can be changed using -da_grid_x M -da_grid_y N */ ierr = DMDACreate2d(PETSC_COMM_WORLD, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE,DMDA_STENCIL_STAR,-8,-7,PETSC_DECIDE,PETSC_DECIDE,1,1,NULL,NULL,&da);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Compute the matrix and right-hand-side vector that define the linear system, Ax = b. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ /* Create parallel matrix preallocated according to the DMDA, format AIJ by default. To use symmetric storage, run with -dm_mat_type sbaij -mat_ignore_lower_triangular */ ierr = DMSetMatType(da,MATAIJ);CHKERRQ(ierr); ierr = DMCreateMatrix(da,&A);CHKERRQ(ierr); /* Set matrix elements for the 2-D, five-point stencil in parallel. - Each processor needs to insert only elements that it owns locally (but any non-local elements will be sent to the appropriate processor during matrix assembly). - Rows and columns are specified by the stencil - Entries are normalized for a domain [0,1]x[0,1] */ ierr = PetscLogStageRegister("Assembly", &stage);CHKERRQ(ierr); ierr = PetscLogStagePush(stage);CHKERRQ(ierr); ierr = DMDAGetLocalInfo(da,&info);CHKERRQ(ierr); for (j=info.ys; j<info.ys+info.ym; j++) { for (i=info.xs; i<info.xs+info.xm; i++) { PetscReal hx = 1./info.mx,hy = 1./info.my; MatStencil row = {0},col[5] = {{0}}; PetscScalar v[5]; PetscInt ncols = 0; row.j = j; row.i = i; col[ncols].j = j; col[ncols].i = i; v[ncols++] = 2*(hx/hy + hy/hx); /* boundaries */ if (i>0) {col[ncols].j = j; col[ncols].i = i-1; v[ncols++] = -hy/hx;} if (i<info.mx-1) {col[ncols].j = j; col[ncols].i = i+1; v[ncols++] = -hy/hx;} if (j>0) {col[ncols].j = j-1; col[ncols].i = i; v[ncols++] = -hx/hy;} if (j<info.my-1) {col[ncols].j = j+1; col[ncols].i = i; v[ncols++] = -hx/hy;} ierr = MatSetValuesStencil(A,1,&row,ncols,col,v,INSERT_VALUES);CHKERRQ(ierr); } } /* Assemble matrix, using the 2-step process: MatAssemblyBegin(), MatAssemblyEnd() Computations can be done while messages are in transition by placing code between these two statements. */ ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = PetscLogStagePop();CHKERRQ(ierr); /* Create parallel vectors compatible with the DMDA. */ ierr = DMCreateGlobalVector(da,&u);CHKERRQ(ierr); ierr = VecDuplicate(u,&b);CHKERRQ(ierr); ierr = VecDuplicate(u,&x);CHKERRQ(ierr); /* Set exact solution; then compute right-hand-side vector. By default we use an exact solution of a vector with all elements of 1.0; Alternatively, using the runtime option -random_sol forms a solution vector with random components. */ ierr = PetscOptionsGetBool(NULL,"-random_exact_sol",&flg,NULL);CHKERRQ(ierr); if (flg) { ierr = PetscRandomCreate(PETSC_COMM_WORLD,&rctx);CHKERRQ(ierr); ierr = PetscRandomSetFromOptions(rctx);CHKERRQ(ierr); ierr = VecSetRandom(u,rctx);CHKERRQ(ierr); ierr = PetscRandomDestroy(&rctx);CHKERRQ(ierr); } else { ierr = VecSet(u,1.);CHKERRQ(ierr); } ierr = MatMult(A,u,b);CHKERRQ(ierr); /* View the exact solution vector if desired */ flg = PETSC_FALSE; ierr = PetscOptionsGetBool(NULL,"-view_exact_sol",&flg,NULL);CHKERRQ(ierr); if (flg) {ierr = VecView(u,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);} /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create the linear solver and set various options - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ /* Create linear solver context */ ierr = KSPCreate(PETSC_COMM_WORLD,&ksp);CHKERRQ(ierr); /* Set operators. Here the matrix that defines the linear system also serves as the preconditioning matrix. */ ierr = KSPSetOperators(ksp,A,A);CHKERRQ(ierr); /* Set runtime options, e.g., -ksp_type <type> -pc_type <type> -ksp_monitor -ksp_rtol <rtol> These options will override those specified above as long as KSPSetFromOptions() is called _after_ any other customization routines. */ ierr = KSPSetFromOptions(ksp);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Solve the linear system - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = KSPSolve(ksp,b,x);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Check solution and clean up - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ /* Check the error */ ierr = VecAXPY(x,-1.,u);CHKERRQ(ierr); ierr = VecNorm(x,NORM_2,&norm);CHKERRQ(ierr); ierr = KSPGetIterationNumber(ksp,&its);CHKERRQ(ierr); /* Print convergence information. PetscPrintf() produces a single print statement from all processes that share a communicator. An alternative is PetscFPrintf(), which prints to a file. */ ierr = PetscPrintf(PETSC_COMM_WORLD,"Norm of error %g iterations %D\n",(double)norm,its);CHKERRQ(ierr); /* Free work space. All PETSc objects should be destroyed when they are no longer needed. */ ierr = KSPDestroy(&ksp);CHKERRQ(ierr); ierr = VecDestroy(&u);CHKERRQ(ierr); ierr = VecDestroy(&x);CHKERRQ(ierr); ierr = VecDestroy(&b);CHKERRQ(ierr); ierr = MatDestroy(&A);CHKERRQ(ierr); ierr = DMDestroy(&da);CHKERRQ(ierr); /* Always call PetscFinalize() before exiting a program. This routine - finalizes the PETSc libraries as well as MPI - provides summary and diagnostic information if certain runtime options are chosen (e.g., -log_summary). */ ierr = PetscFinalize(); return 0; }
int main(int argc,char **argv) { TS ts; /* nonlinear solver */ Vec u; /* solution, residual vectors */ Mat J; /* Jacobian matrix */ PetscInt maxsteps = 1000; /* iterations for convergence */ PetscInt nsteps; PetscReal vmin,vmax,norm; PetscErrorCode ierr; DM da; PetscReal ftime,dt; AppCtx user; /* user-defined work context */ JacobianType jacType; PetscInitialize(&argc,&argv,(char*)0,help); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create distributed array (DMDA) to manage parallel grid and vectors - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = DMDACreate1d(PETSC_COMM_WORLD,DMDA_BOUNDARY_NONE,-11,1,1,NULL,&da); CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Extract global vectors from DMDA; - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = DMCreateGlobalVector(da,&u); CHKERRQ(ierr); /* Initialize user application context */ user.c = -30.0; user.boundary = 0; /* 0: Dirichlet BC; 1: Neumann BC */ user.viewJacobian = PETSC_FALSE; ierr = PetscOptionsGetInt(NULL,"-boundary",&user.boundary,NULL); CHKERRQ(ierr); ierr = PetscOptionsHasName(NULL,"-viewJacobian",&user.viewJacobian); CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create timestepping solver context - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSCreate(PETSC_COMM_WORLD,&ts); CHKERRQ(ierr); ierr = TSSetProblemType(ts,TS_NONLINEAR); CHKERRQ(ierr); ierr = TSSetType(ts,TSTHETA); CHKERRQ(ierr); ierr = TSThetaSetTheta(ts,1.0); CHKERRQ(ierr); /* Make the Theta method behave like backward Euler */ ierr = TSSetIFunction(ts,NULL,FormIFunction,&user); CHKERRQ(ierr); ierr = DMSetMatType(da,MATAIJ); CHKERRQ(ierr); ierr = DMCreateMatrix(da,&J); CHKERRQ(ierr); jacType = JACOBIAN_ANALYTIC; /* use user-provide Jacobian */ ierr = TSSetDM(ts,da); CHKERRQ(ierr); /* Use TSGetDM() to access. Setting here allows easy use of geometric multigrid. */ ftime = 1.0; ierr = TSSetDuration(ts,maxsteps,ftime); CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set initial conditions - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = FormInitialSolution(ts,u,&user); CHKERRQ(ierr); ierr = TSSetSolution(ts,u); CHKERRQ(ierr); dt = .01; ierr = TSSetInitialTimeStep(ts,0.0,dt); CHKERRQ(ierr); /* Use slow fd Jacobian or fast fd Jacobian with colorings. Note: this requirs snes which is not created until TSSetUp()/TSSetFromOptions() is called */ ierr = PetscOptionsBegin(PETSC_COMM_WORLD,NULL,"Options for Jacobian evaluation",NULL); CHKERRQ(ierr); ierr = PetscOptionsEnum("-jac_type","Type of Jacobian","",JacobianTypes,(PetscEnum)jacType,(PetscEnum*)&jacType,0); CHKERRQ(ierr); ierr = PetscOptionsEnd(); CHKERRQ(ierr); if (jacType == JACOBIAN_ANALYTIC) { ierr = TSSetIJacobian(ts,J,J,FormIJacobian,&user); CHKERRQ(ierr); } else if (jacType == JACOBIAN_FD_COLORING) { SNES snes; ierr = TSGetSNES(ts,&snes); CHKERRQ(ierr); ierr = SNESSetJacobian(snes,J,J,SNESComputeJacobianDefaultColor,0); CHKERRQ(ierr); } else if (jacType == JACOBIAN_FD_FULL) { SNES snes; ierr = TSGetSNES(ts,&snes); CHKERRQ(ierr); ierr = SNESSetJacobian(snes,J,J,SNESComputeJacobianDefault,&user); CHKERRQ(ierr); } /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set runtime options - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSetFromOptions(ts); CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Integrate ODE system - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSolve(ts,u); CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Compute diagnostics of the solution - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = VecNorm(u,NORM_1,&norm); CHKERRQ(ierr); ierr = VecMax(u,NULL,&vmax); CHKERRQ(ierr); ierr = VecMin(u,NULL,&vmin); CHKERRQ(ierr); ierr = TSGetTimeStepNumber(ts,&nsteps); CHKERRQ(ierr); ierr = TSGetTime(ts,&ftime); CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD,"timestep %D: time %G, solution norm %G, max %G, min %G\n",nsteps,ftime,norm,vmax,vmin); CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Free work space. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = MatDestroy(&J); CHKERRQ(ierr); ierr = VecDestroy(&u); CHKERRQ(ierr); ierr = TSDestroy(&ts); CHKERRQ(ierr); ierr = DMDestroy(&da); CHKERRQ(ierr); ierr = PetscFinalize(); PetscFunctionReturn(0); }