int main(int argc,char **argv) { PetscErrorCode ierr; PetscBool view = PETSC_FALSE, viewsoln = PETSC_FALSE, noprealloc = PETSC_FALSE; char root[256] = "", nodesname[256], issname[256], solnname[256]; UM mesh; unfemCtx user; SNES snes; KSP ksp; PC pc; Mat A; Vec r, u, uexact; double err, h_max; PetscInitialize(&argc,&argv,NULL,help); ierr = PetscLogStageRegister("Read mesh ", &user.readstage); CHKERRQ(ierr); //STRIP ierr = PetscLogStageRegister("Set-up ", &user.setupstage); CHKERRQ(ierr); //STRIP ierr = PetscLogStageRegister("Solver ", &user.solverstage); CHKERRQ(ierr); //STRIP ierr = PetscLogStageRegister("Residual eval ", &user.resstage); CHKERRQ(ierr); //STRIP ierr = PetscLogStageRegister("Jacobian eval ", &user.jacstage); CHKERRQ(ierr); //STRIP user.quaddeg = 1; user.solncase = 0; ierr = PetscOptionsBegin(PETSC_COMM_WORLD, "un_", "options for unfem", ""); CHKERRQ(ierr); ierr = PetscOptionsInt("-case", "exact solution cases: 0=linear, 1=nonlinear, 2=nonhomoNeumann, 3=chapter3, 4=koch", "unfem.c",user.solncase,&(user.solncase),NULL); CHKERRQ(ierr); ierr = PetscOptionsString("-mesh", "file name root of mesh stored in PETSc binary with .vec,.is extensions", "unfem.c",root,root,sizeof(root),NULL); CHKERRQ(ierr); ierr = PetscOptionsInt("-quaddeg", "quadrature degree (1,2,3)", "unfem.c",user.quaddeg,&(user.quaddeg),NULL); CHKERRQ(ierr); ierr = PetscOptionsBool("-view", "view loaded nodes and elements at stdout", "unfem.c",view,&view,NULL); CHKERRQ(ierr); ierr = PetscOptionsBool("-view_solution", "view solution u(x,y) to binary file; uses root name of mesh plus .soln\nsee petsc2tricontour.py to view graphically", "unfem.c",viewsoln,&viewsoln,NULL); CHKERRQ(ierr); ierr = PetscOptionsBool("-noprealloc", "do not perform preallocation before matrix assembly", "unfem.c",noprealloc,&noprealloc,NULL); CHKERRQ(ierr); ierr = PetscOptionsEnd(); CHKERRQ(ierr); // set parameters and exact solution user.a_fcn = &a_lin; user.f_fcn = &f_lin; user.uexact_fcn = &uexact_lin; user.gD_fcn = &gD_lin; user.gN_fcn = &gN_lin; switch (user.solncase) { case 0 : break; case 1 : user.a_fcn = &a_nonlin; user.f_fcn = &f_nonlin; break; case 2 : user.gN_fcn = &gN_linneu; break; case 3 : user.a_fcn = &a_square; user.f_fcn = &f_square; user.uexact_fcn = &uexact_square; user.gD_fcn = &gD_square; user.gN_fcn = NULL; // seg fault if ever called break; case 4 : user.a_fcn = &a_koch; user.f_fcn = &f_koch; user.uexact_fcn = NULL; user.gD_fcn = &gD_koch; user.gN_fcn = NULL; // seg fault if ever called break; default : SETERRQ(PETSC_COMM_WORLD,1,"other solution cases not implemented"); } // determine filenames strcpy(nodesname, root); strncat(nodesname, ".vec", 4); strcpy(issname, root); strncat(issname, ".is", 3); //STARTMAININITIAL PetscLogStagePush(user.readstage); //STRIP // read mesh object of type UM ierr = UMInitialize(&mesh); CHKERRQ(ierr); ierr = UMReadNodes(&mesh,nodesname); CHKERRQ(ierr); ierr = UMReadISs(&mesh,issname); CHKERRQ(ierr); ierr = UMStats(&mesh, &h_max, NULL, NULL, NULL); CHKERRQ(ierr); if (view) { //STRIP PetscViewer stdoutviewer; //STRIP ierr = PetscViewerASCIIGetStdout(PETSC_COMM_WORLD,&stdoutviewer); CHKERRQ(ierr); //STRIP ierr = UMViewASCII(&mesh,stdoutviewer); CHKERRQ(ierr); //STRIP } //STRIP user.mesh = &mesh; PetscLogStagePop(); //STRIP // configure Vecs and SNES PetscLogStagePush(user.setupstage); //STRIP ierr = VecCreate(PETSC_COMM_WORLD,&r); CHKERRQ(ierr); ierr = VecSetSizes(r,PETSC_DECIDE,mesh.N); CHKERRQ(ierr); ierr = VecSetFromOptions(r); CHKERRQ(ierr); ierr = VecDuplicate(r,&u); CHKERRQ(ierr); ierr = VecSet(u,0.0); CHKERRQ(ierr); ierr = SNESCreate(PETSC_COMM_WORLD,&snes); CHKERRQ(ierr); ierr = SNESSetFunction(snes,r,FormFunction,&user); CHKERRQ(ierr); // reset default KSP and PC ierr = SNESGetKSP(snes,&ksp); CHKERRQ(ierr); ierr = KSPSetType(ksp,KSPCG); CHKERRQ(ierr); ierr = KSPGetPC(ksp,&pc); CHKERRQ(ierr); ierr = PCSetType(pc,PCICC); CHKERRQ(ierr); // setup matrix for Picard iteration, including preallocation ierr = MatCreate(PETSC_COMM_WORLD,&A); CHKERRQ(ierr); ierr = MatSetSizes(A,PETSC_DECIDE,PETSC_DECIDE,mesh.N,mesh.N); CHKERRQ(ierr); ierr = MatSetFromOptions(A); CHKERRQ(ierr); ierr = MatSetOption(A,MAT_SYMMETRIC,PETSC_TRUE); CHKERRQ(ierr); if (noprealloc) { ierr = MatSetUp(A); CHKERRQ(ierr); } else { ierr = Preallocation(A,&user); CHKERRQ(ierr); } ierr = SNESSetJacobian(snes,A,A,FormPicard,&user); CHKERRQ(ierr); ierr = SNESSetFromOptions(snes); CHKERRQ(ierr); PetscLogStagePop(); //STRIP // solve PetscLogStagePush(user.solverstage); //STRIP ierr = SNESSolve(snes,NULL,u);CHKERRQ(ierr); PetscLogStagePop(); //STRIP //ENDMAININITIAL if (viewsoln) { strcpy(solnname, root); strncat(solnname, ".soln", 5); ierr = UMViewSolutionBinary(&mesh,solnname,u); CHKERRQ(ierr); } if (user.uexact_fcn) { // measure error relative to exact solution ierr = VecDuplicate(r,&uexact); CHKERRQ(ierr); ierr = FillExact(uexact,&user); CHKERRQ(ierr); ierr = VecAXPY(u,-1.0,uexact); CHKERRQ(ierr); // u <- u + (-1.0) uexact ierr = VecNorm(u,NORM_INFINITY,&err); CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "case %d result for N=%d nodes with h = %.3e : |u-u_ex|_inf = %g\n", user.solncase,mesh.N,h_max,err); CHKERRQ(ierr); VecDestroy(&uexact); } else { ierr = PetscPrintf(PETSC_COMM_WORLD, "case %d completed for N=%d nodes with h = %.3e (no exact solution)\n", user.solncase,mesh.N,h_max); CHKERRQ(ierr); } // clean-up SNESDestroy(&snes); MatDestroy(&A); VecDestroy(&u); VecDestroy(&r); UMDestroy(&mesh); PetscFinalize(); return 0; }
/******************************************************************************* * For each run, the input filename and restart information (if needed) must * * be given on the command line. For non-restarted case, command line is: * * * * executable <input file name> * * * * For restarted run, command line is: * * * * executable <input file name> <restart directory> <restart number> * * * *******************************************************************************/ bool run_example(int argc, char* argv[]) { // Initialize PETSc, MPI, and SAMRAI. PetscInitialize(&argc, &argv, NULL, NULL); SAMRAI_MPI::setCommunicator(PETSC_COMM_WORLD); SAMRAI_MPI::setCallAbortInSerialInsteadOfExit(); SAMRAIManager::startup(); { // cleanup dynamically allocated objects prior to shutdown // Parse command line options, set some standard options from the input // file, initialize the restart database (if this is a restarted run), // and enable file logging. Pointer<AppInitializer> app_initializer = new AppInitializer(argc, argv, "IB.log"); Pointer<Database> input_db = app_initializer->getInputDatabase(); // Get various standard options set in the input file. const bool dump_viz_data = app_initializer->dumpVizData(); const int viz_dump_interval = app_initializer->getVizDumpInterval(); const bool uses_visit = dump_viz_data && !app_initializer->getVisItDataWriter().isNull(); const bool dump_restart_data = app_initializer->dumpRestartData(); const int restart_dump_interval = app_initializer->getRestartDumpInterval(); const string restart_dump_dirname = app_initializer->getRestartDumpDirectory(); const bool dump_postproc_data = app_initializer->dumpPostProcessingData(); const int postproc_data_dump_interval = app_initializer->getPostProcessingDataDumpInterval(); const string postproc_data_dump_dirname = app_initializer->getPostProcessingDataDumpDirectory(); if (dump_postproc_data && (postproc_data_dump_interval > 0) && !postproc_data_dump_dirname.empty()) { Utilities::recursiveMkdir(postproc_data_dump_dirname); } const bool dump_timer_data = app_initializer->dumpTimerData(); const int timer_dump_interval = app_initializer->getTimerDumpInterval(); // Create major algorithm and data objects that comprise the // application. These objects are configured from the input database // and, if this is a restarted run, from the restart database. Pointer<INSHierarchyIntegrator> navier_stokes_integrator = new INSStaggeredHierarchyIntegrator( "INSStaggeredHierarchyIntegrator", app_initializer->getComponentDatabase("INSStaggeredHierarchyIntegrator")); const int num_structures = input_db->getIntegerWithDefault("num_structures", 1); Pointer<ConstraintIBMethod> ib_method_ops = new ConstraintIBMethod( "ConstraintIBMethod", app_initializer->getComponentDatabase("ConstraintIBMethod"), num_structures); Pointer<IBHierarchyIntegrator> time_integrator = new IBExplicitHierarchyIntegrator("IBHierarchyIntegrator", app_initializer->getComponentDatabase("IBHierarchyIntegrator"), ib_method_ops, navier_stokes_integrator); Pointer<CartesianGridGeometry<NDIM> > grid_geometry = new CartesianGridGeometry<NDIM>( "CartesianGeometry", app_initializer->getComponentDatabase("CartesianGeometry")); Pointer<PatchHierarchy<NDIM> > patch_hierarchy = new PatchHierarchy<NDIM>("PatchHierarchy", grid_geometry); Pointer<StandardTagAndInitialize<NDIM> > error_detector = new StandardTagAndInitialize<NDIM>("StandardTagAndInitialize", time_integrator, app_initializer->getComponentDatabase("StandardTagAndInitialize")); Pointer<BergerRigoutsos<NDIM> > box_generator = new BergerRigoutsos<NDIM>(); Pointer<LoadBalancer<NDIM> > load_balancer = new LoadBalancer<NDIM>("LoadBalancer", app_initializer->getComponentDatabase("LoadBalancer")); Pointer<GriddingAlgorithm<NDIM> > gridding_algorithm = new GriddingAlgorithm<NDIM>("GriddingAlgorithm", app_initializer->getComponentDatabase("GriddingAlgorithm"), error_detector, box_generator, load_balancer); // Configure the IB solver. Pointer<IBStandardInitializer> ib_initializer = new IBStandardInitializer( "IBStandardInitializer", app_initializer->getComponentDatabase("IBStandardInitializer")); ib_method_ops->registerLInitStrategy(ib_initializer); Pointer<IBStandardForceGen> ib_force_fcn = new IBStandardForceGen(); ib_method_ops->registerIBLagrangianForceFunction(ib_force_fcn); // Create Eulerian initial condition specification objects. if (input_db->keyExists("VelocityInitialConditions")) { Pointer<CartGridFunction> u_init = new muParserCartGridFunction( "u_init", app_initializer->getComponentDatabase("VelocityInitialConditions"), grid_geometry); navier_stokes_integrator->registerVelocityInitialConditions(u_init); } if (input_db->keyExists("PressureInitialConditions")) { Pointer<CartGridFunction> p_init = new muParserCartGridFunction( "p_init", app_initializer->getComponentDatabase("PressureInitialConditions"), grid_geometry); navier_stokes_integrator->registerPressureInitialConditions(p_init); } // Create Eulerian boundary condition specification objects (when necessary). const IntVector<NDIM>& periodic_shift = grid_geometry->getPeriodicShift(); vector<RobinBcCoefStrategy<NDIM>*> u_bc_coefs(NDIM); if (periodic_shift.min() > 0) { for (unsigned int d = 0; d < NDIM; ++d) { u_bc_coefs[d] = NULL; } } else { for (unsigned int d = 0; d < NDIM; ++d) { const std::string bc_coefs_name = "u_bc_coefs_" + std::to_string(d); const std::string bc_coefs_db_name = "VelocityBcCoefs_" + std::to_string(d); u_bc_coefs[d] = new muParserRobinBcCoefs( bc_coefs_name, app_initializer->getComponentDatabase(bc_coefs_db_name), grid_geometry); } navier_stokes_integrator->registerPhysicalBoundaryConditions(u_bc_coefs); } // Create Eulerian body force function specification objects. if (input_db->keyExists("ForcingFunction")) { Pointer<CartGridFunction> f_fcn = new muParserCartGridFunction( "f_fcn", app_initializer->getComponentDatabase("ForcingFunction"), grid_geometry); time_integrator->registerBodyForceFunction(f_fcn); } // Set up visualization plot file writers. Pointer<VisItDataWriter<NDIM> > visit_data_writer = app_initializer->getVisItDataWriter(); Pointer<LSiloDataWriter> silo_data_writer = app_initializer->getLSiloDataWriter(); if (uses_visit) { ib_initializer->registerLSiloDataWriter(silo_data_writer); ib_method_ops->registerLSiloDataWriter(silo_data_writer); time_integrator->registerVisItDataWriter(visit_data_writer); } // Initialize hierarchy configuration and data on all patches. time_integrator->initializePatchHierarchy(patch_hierarchy, gridding_algorithm); // Create ConstraintIBKinematics objects vector<Pointer<ConstraintIBKinematics> > ibkinematics_ops_vec; Pointer<ConstraintIBKinematics> ib_kinematics_op; // struct_0 ib_kinematics_op = new IBEELKinematics3d("eel3d", app_initializer->getComponentDatabase("ConstraintIBKinematics")->getDatabase("eel3d"), ib_method_ops->getLDataManager(), patch_hierarchy); ibkinematics_ops_vec.push_back(ib_kinematics_op); // register ConstraintIBKinematics objects with ConstraintIBMethod. ib_method_ops->registerConstraintIBKinematics(ibkinematics_ops_vec); ib_method_ops->initializeHierarchyOperatorsandData(); // Deallocate initialization objects. ib_method_ops->freeLInitStrategy(); ib_initializer.setNull(); app_initializer.setNull(); // Print the input database contents to the log file. plog << "Input database:\n"; input_db->printClassData(plog); // Write out initial visualization data. int iteration_num = time_integrator->getIntegratorStep(); double loop_time = time_integrator->getIntegratorTime(); if (dump_viz_data && uses_visit) { pout << "\n\nWriting visualization files...\n\n"; time_integrator->setupPlotData(); visit_data_writer->writePlotData(patch_hierarchy, iteration_num, loop_time); silo_data_writer->writePlotData(iteration_num, loop_time); } // Main time step loop. double loop_time_end = time_integrator->getEndTime(); double dt = 0.0; while (!MathUtilities<double>::equalEps(loop_time, loop_time_end) && time_integrator->stepsRemaining()) { iteration_num = time_integrator->getIntegratorStep(); loop_time = time_integrator->getIntegratorTime(); pout << "\n"; pout << "+++++++++++++++++++++++++++++++++++++++++++++++++++\n"; pout << "At beginning of timestep # " << iteration_num << "\n"; pout << "Simulation time is " << loop_time << "\n"; dt = time_integrator->getMaximumTimeStepSize(); time_integrator->advanceHierarchy(dt); loop_time += dt; pout << "\n"; pout << "At end of timestep # " << iteration_num << "\n"; pout << "Simulation time is " << loop_time << "\n"; pout << "+++++++++++++++++++++++++++++++++++++++++++++++++++\n"; pout << "\n"; // At specified intervals, write visualization and restart files, // print out timer data, and store hierarchy data for post // processing. iteration_num += 1; const bool last_step = !time_integrator->stepsRemaining(); if (dump_viz_data && uses_visit && (iteration_num % viz_dump_interval == 0 || last_step)) { pout << "\nWriting visualization files...\n\n"; time_integrator->setupPlotData(); visit_data_writer->writePlotData(patch_hierarchy, iteration_num, loop_time); silo_data_writer->writePlotData(iteration_num, loop_time); } if (dump_restart_data && (iteration_num % restart_dump_interval == 0 || last_step)) { pout << "\nWriting restart files...\n\n"; RestartManager::getManager()->writeRestartFile(restart_dump_dirname, iteration_num); } if (dump_timer_data && (iteration_num % timer_dump_interval == 0 || last_step)) { pout << "\nWriting timer data...\n\n"; TimerManager::getManager()->print(plog); } if (dump_postproc_data && (iteration_num % postproc_data_dump_interval == 0 || last_step)) { output_data(patch_hierarchy, navier_stokes_integrator, ib_method_ops->getLDataManager(), iteration_num, loop_time, postproc_data_dump_dirname); } } // Cleanup Eulerian boundary condition specification objects (when // necessary). for (unsigned int d = 0; d < NDIM; ++d) delete u_bc_coefs[d]; } // cleanup dynamically allocated objects prior to shutdown SAMRAIManager::shutdown(); PetscFinalize(); return true; } // run_example
Modified from the code contributed by Yaning Liu @lbl.gov \n\n"; /* Example: mpiexec -n <np> ./ex103 mpiexec -n <np> ./ex103 -mat_type elemental -mat_view mpiexec -n <np> ./ex103 -mat_type aij */ #include <petscmat.h> int main(int argc, char** argv) { Mat A,A_elemental; PetscInt i,j,M=10,N=5,nrows,ncols; PetscErrorCode ierr; PetscMPIInt rank,size; IS isrows,iscols; const PetscInt *rows,*cols; PetscScalar *v; MatType type; PetscBool isDense,isAIJ,flg; ierr = PetscInitialize(&argc, &argv, (char*)0, help);if (ierr) return ierr; #if !defined(PETSC_HAVE_ELEMENTAL) SETERRQ(PETSC_COMM_WORLD,1,"This example requires ELEMENTAL"); #endif ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr); ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr); /* Creat a matrix */ ierr = PetscOptionsGetInt(NULL,NULL,"-M",&M,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetInt(NULL,NULL,"-N",&N,NULL);CHKERRQ(ierr); ierr = MatCreate(PETSC_COMM_WORLD, &A);CHKERRQ(ierr); ierr = MatSetSizes(A,PETSC_DECIDE,PETSC_DECIDE,M,N);CHKERRQ(ierr); ierr = MatSetType(A,MATDENSE);CHKERRQ(ierr); ierr = MatSetFromOptions(A);CHKERRQ(ierr); ierr = MatSetUp(A);CHKERRQ(ierr); /* Set local matrix entries */ ierr = MatGetOwnershipIS(A,&isrows,&iscols);CHKERRQ(ierr); ierr = ISGetLocalSize(isrows,&nrows);CHKERRQ(ierr); ierr = ISGetIndices(isrows,&rows);CHKERRQ(ierr); ierr = ISGetLocalSize(iscols,&ncols);CHKERRQ(ierr); ierr = ISGetIndices(iscols,&cols);CHKERRQ(ierr); ierr = PetscMalloc1(nrows*ncols,&v);CHKERRQ(ierr); for (i=0; i<nrows; i++) { for (j=0; j<ncols; j++) { if (size == 1) { v[i*ncols+j] = (PetscScalar)(i+j); } else { v[i*ncols+j] = (PetscScalar)rank+j*0.1; } } } ierr = MatSetValues(A,nrows,rows,ncols,cols,v,INSERT_VALUES);CHKERRQ(ierr); ierr = MatAssemblyBegin(A, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(A, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); //ierr = PetscSynchronizedPrintf(PETSC_COMM_WORLD,"[%D] local nrows %D, ncols %D\n",rank,nrows,ncols);CHKERRQ(ierr); //ierr = PetscSynchronizedFlush(PETSC_COMM_WORLD,PETSC_STDOUT);CHKERRQ(ierr); /* Test MatSetValues() by converting A to A_elemental */ ierr = MatGetType(A,&type);CHKERRQ(ierr); if (size == 1) { ierr = PetscObjectTypeCompare((PetscObject)A,MATSEQDENSE,&isDense);CHKERRQ(ierr); ierr = PetscObjectTypeCompare((PetscObject)A,MATSEQAIJ,&isAIJ);CHKERRQ(ierr); } else { ierr = PetscObjectTypeCompare((PetscObject)A,MATMPIDENSE,&isDense);CHKERRQ(ierr); ierr = PetscObjectTypeCompare((PetscObject)A,MATMPIAIJ,&isAIJ);CHKERRQ(ierr); } if (isDense || isAIJ) { Mat Aexplicit; ierr = MatConvert(A, MATELEMENTAL, MAT_INITIAL_MATRIX, &A_elemental);CHKERRQ(ierr); ierr = MatComputeExplicitOperator(A_elemental,&Aexplicit);CHKERRQ(ierr); ierr = MatMultEqual(Aexplicit,A_elemental,5,&flg);CHKERRQ(ierr); if (!flg) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Aexplicit != A_elemental."); ierr = MatDestroy(&Aexplicit);CHKERRQ(ierr); /* Test MAT_REUSE_MATRIX which is only supported for inplace conversion */ ierr = MatConvert(A, MATELEMENTAL, MAT_INPLACE_MATRIX, &A);CHKERRQ(ierr); ierr = MatMultEqual(A_elemental,A,5,&flg);CHKERRQ(ierr); if (!flg) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"A_elemental != A."); ierr = MatDestroy(&A_elemental);CHKERRQ(ierr); } ierr = ISRestoreIndices(isrows,&rows);CHKERRQ(ierr); ierr = ISRestoreIndices(iscols,&cols);CHKERRQ(ierr); ierr = ISDestroy(&isrows);CHKERRQ(ierr); ierr = ISDestroy(&iscols);CHKERRQ(ierr); ierr = PetscFree(v);CHKERRQ(ierr); ierr = MatDestroy(&A);CHKERRQ(ierr); ierr = PetscFinalize(); return ierr; }
/******************************************************************************* * For each run, the input filename and restart information (if needed) must * * be given on the command line. For non-restarted case, command line is: * * * * executable <input file name> * * * * For restarted run, command line is: * * * * executable <input file name> <restart directory> <restart number> * * * *******************************************************************************/ int main(int argc, char* argv[]) { // Initialize PETSc, MPI, and SAMRAI. PetscInitialize(&argc, &argv, NULL, NULL); SAMRAI_MPI::setCommunicator(PETSC_COMM_WORLD); SAMRAI_MPI::setCallAbortInSerialInsteadOfExit(); SAMRAIManager::startup(); { // cleanup dynamically allocated objects prior to shutdown // Parse command line options, set some standard options from the input // file, initialize the restart database (if this is a restarted run), // and enable file logging. Pointer<AppInitializer> app_initializer = new AppInitializer(argc, argv, "INS.log"); Pointer<Database> input_db = app_initializer->getInputDatabase(); // Get various standard options set in the input file. const bool dump_viz_data = app_initializer->dumpVizData(); const int viz_dump_interval = app_initializer->getVizDumpInterval(); const bool uses_visit = dump_viz_data && app_initializer->getVisItDataWriter(); const bool dump_restart_data = app_initializer->dumpRestartData(); const int restart_dump_interval = app_initializer->getRestartDumpInterval(); const string restart_dump_dirname = app_initializer->getRestartDumpDirectory(); const bool dump_postproc_data = app_initializer->dumpPostProcessingData(); const int postproc_data_dump_interval = app_initializer->getPostProcessingDataDumpInterval(); const string postproc_data_dump_dirname = app_initializer->getPostProcessingDataDumpDirectory(); const bool dump_timer_data = app_initializer->dumpTimerData(); const int timer_dump_interval = app_initializer->getTimerDumpInterval(); // Create major algorithm and data objects that comprise the // application. These objects are configured from the input database // and, if this is a restarted run, from the restart database. Pointer<INSHierarchyIntegrator> time_integrator; const string solver_type = app_initializer->getComponentDatabase("Main")->getStringWithDefault("solver_type", "STAGGERED"); if (solver_type == "STAGGERED") { time_integrator = new INSStaggeredHierarchyIntegrator( "INSStaggeredHierarchyIntegrator", app_initializer->getComponentDatabase("INSStaggeredHierarchyIntegrator")); } else if (solver_type == "COLLOCATED") { time_integrator = new INSCollocatedHierarchyIntegrator( "INSCollocatedHierarchyIntegrator", app_initializer->getComponentDatabase("INSCollocatedHierarchyIntegrator")); } else { TBOX_ERROR("Unsupported solver type: " << solver_type << "\n" << "Valid options are: COLLOCATED, STAGGERED"); } Pointer<CartesianGridGeometry<NDIM> > grid_geometry = new CartesianGridGeometry<NDIM>( "CartesianGeometry", app_initializer->getComponentDatabase("CartesianGeometry")); Pointer<PatchHierarchy<NDIM> > patch_hierarchy = new PatchHierarchy<NDIM>("PatchHierarchy", grid_geometry); Pointer<StandardTagAndInitialize<NDIM> > error_detector = new StandardTagAndInitialize<NDIM>("StandardTagAndInitialize", time_integrator, app_initializer->getComponentDatabase("StandardTagAndInitialize")); Pointer<BergerRigoutsos<NDIM> > box_generator = new BergerRigoutsos<NDIM>(); Pointer<LoadBalancer<NDIM> > load_balancer = new LoadBalancer<NDIM>("LoadBalancer", app_initializer->getComponentDatabase("LoadBalancer")); Pointer<GriddingAlgorithm<NDIM> > gridding_algorithm = new GriddingAlgorithm<NDIM>("GriddingAlgorithm", app_initializer->getComponentDatabase("GriddingAlgorithm"), error_detector, box_generator, load_balancer); // Create initial condition specification objects. if (input_db->keyExists("VelocityInitialConditions")) { Pointer<CartGridFunction> u_init = new muParserCartGridFunction( "u_init", app_initializer->getComponentDatabase("VelocityInitialConditions"), grid_geometry); time_integrator->registerVelocityInitialConditions(u_init); } // Create boundary condition specification objects (when necessary). const IntVector<NDIM>& periodic_shift = grid_geometry->getPeriodicShift(); vector<RobinBcCoefStrategy<NDIM>*> u_bc_coefs(NDIM); if (periodic_shift.min() > 0) { for (unsigned int d = 0; d < NDIM; ++d) { u_bc_coefs[d] = NULL; } } else { for (unsigned int d = 0; d < NDIM; ++d) { ostringstream bc_coefs_name_stream; bc_coefs_name_stream << "u_bc_coefs_" << d; const string bc_coefs_name = bc_coefs_name_stream.str(); ostringstream bc_coefs_db_name_stream; bc_coefs_db_name_stream << "VelocityBcCoefs_" << d; const string bc_coefs_db_name = bc_coefs_db_name_stream.str(); u_bc_coefs[d] = new muParserRobinBcCoefs( bc_coefs_name, app_initializer->getComponentDatabase(bc_coefs_db_name), grid_geometry); } time_integrator->registerPhysicalBoundaryConditions(u_bc_coefs); } // Create body force function specification objects (when necessary). if (input_db->keyExists("ForcingFunction")) { Pointer<CartGridFunction> f_fcn = new muParserCartGridFunction( "f_fcn", app_initializer->getComponentDatabase("ForcingFunction"), grid_geometry); time_integrator->registerBodyForceFunction(f_fcn); } // Set up visualization plot file writers. Pointer<VisItDataWriter<NDIM> > visit_data_writer = app_initializer->getVisItDataWriter(); if (uses_visit) { time_integrator->registerVisItDataWriter(visit_data_writer); } // Initialize hierarchy configuration and data on all patches. time_integrator->initializePatchHierarchy(patch_hierarchy, gridding_algorithm); // Deallocate initialization objects. app_initializer.setNull(); // Print the input database contents to the log file. plog << "Input database:\n"; input_db->printClassData(plog); // Write out initial visualization data. int iteration_num = time_integrator->getIntegratorStep(); double loop_time = time_integrator->getIntegratorTime(); if (dump_viz_data && uses_visit) { pout << "\n\nWriting visualization files...\n\n"; time_integrator->setupPlotData(); visit_data_writer->writePlotData(patch_hierarchy, iteration_num, loop_time); } // Main time step loop. double loop_time_end = time_integrator->getEndTime(); double dt = 0.0; while (!MathUtilities<double>::equalEps(loop_time, loop_time_end) && time_integrator->stepsRemaining()) { iteration_num = time_integrator->getIntegratorStep(); loop_time = time_integrator->getIntegratorTime(); pout << "\n"; pout << "+++++++++++++++++++++++++++++++++++++++++++++++++++\n"; pout << "At beginning of timestep # " << iteration_num << "\n"; pout << "Simulation time is " << loop_time << "\n"; dt = time_integrator->getMaximumTimeStepSize(); time_integrator->advanceHierarchy(dt); loop_time += dt; pout << "\n"; pout << "At end of timestep # " << iteration_num << "\n"; pout << "Simulation time is " << loop_time << "\n"; pout << "+++++++++++++++++++++++++++++++++++++++++++++++++++\n"; pout << "\n"; // At specified intervals, write visualization and restart files, // print out timer data, and store hierarchy data for post // processing. iteration_num += 1; const bool last_step = !time_integrator->stepsRemaining(); if (dump_viz_data && uses_visit && (iteration_num % viz_dump_interval == 0 || last_step)) { pout << "\nWriting visualization files...\n\n"; time_integrator->setupPlotData(); visit_data_writer->writePlotData(patch_hierarchy, iteration_num, loop_time); } if (dump_restart_data && (iteration_num % restart_dump_interval == 0 || last_step)) { pout << "\nWriting restart files...\n\n"; RestartManager::getManager()->writeRestartFile(restart_dump_dirname, iteration_num); } if (dump_timer_data && (iteration_num % timer_dump_interval == 0 || last_step)) { pout << "\nWriting timer data...\n\n"; TimerManager::getManager()->print(plog); } if (dump_postproc_data && (iteration_num % postproc_data_dump_interval == 0 || last_step)) { output_data(patch_hierarchy, time_integrator, iteration_num, loop_time, postproc_data_dump_dirname); } } // Cleanup boundary condition specification objects (when necessary). for (unsigned int d = 0; d < NDIM; ++d) delete u_bc_coefs[d]; } // cleanup dynamically allocated objects prior to shutdown SAMRAIManager::shutdown(); PetscFinalize(); return 0; } // main
int main(int argc,char **args) { Vec x,y,b,s1,s2; Mat A; /* linear system matrix */ Mat sA; /* symmetric part of the matrices */ PetscInt n,mbs=16,bs=1,nz=3,prob=2,i,j,col[3],row,Ii,J,n1; const PetscInt *ip_ptr; PetscScalar neg_one = -1.0,value[3],alpha=0.1; PetscMPIInt size; PetscErrorCode ierr; IS ip, isrow, iscol; PetscRandom rdm; PetscBool reorder=PETSC_FALSE; MatInfo minfo1,minfo2; PetscReal norm1,norm2,tol=1.e-10; ierr = PetscInitialize(&argc,&args,(char*)0,help);if (ierr) return ierr; ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr); if (size != 1) SETERRQ(PETSC_COMM_WORLD,1,"This is a uniprocessor example only!"); ierr = PetscOptionsGetInt(NULL,NULL,"-bs",&bs,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetInt(NULL,NULL,"-mbs",&mbs,NULL);CHKERRQ(ierr); n = mbs*bs; ierr=MatCreateSeqBAIJ(PETSC_COMM_WORLD,bs,n,n,nz,NULL, &A);CHKERRQ(ierr); ierr=MatCreateSeqSBAIJ(PETSC_COMM_WORLD,bs,n,n,nz,NULL, &sA);CHKERRQ(ierr); /* Test MatGetOwnershipRange() */ ierr = MatGetOwnershipRange(A,&Ii,&J);CHKERRQ(ierr); ierr = MatGetOwnershipRange(sA,&i,&j);CHKERRQ(ierr); if (i-Ii || j-J) { ierr = PetscPrintf(PETSC_COMM_SELF,"Error: MatGetOwnershipRange() in MatSBAIJ format\n");CHKERRQ(ierr); } /* Assemble matrix */ if (bs == 1) { ierr = PetscOptionsGetInt(NULL,NULL,"-test_problem",&prob,NULL);CHKERRQ(ierr); if (prob == 1) { /* tridiagonal matrix */ value[0] = -1.0; value[1] = 2.0; value[2] = -1.0; for (i=1; i<n-1; i++) { col[0] = i-1; col[1] = i; col[2] = i+1; ierr = MatSetValues(A,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr); ierr = MatSetValues(sA,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr); } i = n - 1; col[0]=0; col[1] = n - 2; col[2] = n - 1; value[0]= 0.1; value[1]=-1; value[2]=2; ierr = MatSetValues(A,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr); ierr = MatSetValues(sA,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr); i = 0; col[0] = 0; col[1] = 1; col[2]=n-1; value[0] = 2.0; value[1] = -1.0; value[2]=0.1; ierr = MatSetValues(A,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr); ierr = MatSetValues(sA,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr); } else if (prob ==2) { /* matrix for the five point stencil */ n1 = (PetscInt) (PetscSqrtReal((PetscReal)n) + 0.001); if (n1*n1 - n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"sqrt(n) must be a positive interger!"); for (i=0; i<n1; i++) { for (j=0; j<n1; j++) { Ii = j + n1*i; if (i>0) { J = Ii - n1; ierr = MatSetValues(A,1,&Ii,1,&J,&neg_one,INSERT_VALUES);CHKERRQ(ierr); ierr = MatSetValues(sA,1,&Ii,1,&J,&neg_one,INSERT_VALUES);CHKERRQ(ierr); } if (i<n1-1) { J = Ii + n1; ierr = MatSetValues(A,1,&Ii,1,&J,&neg_one,INSERT_VALUES);CHKERRQ(ierr); ierr = MatSetValues(sA,1,&Ii,1,&J,&neg_one,INSERT_VALUES);CHKERRQ(ierr); } if (j>0) { J = Ii - 1; ierr = MatSetValues(A,1,&Ii,1,&J,&neg_one,INSERT_VALUES);CHKERRQ(ierr); ierr = MatSetValues(sA,1,&Ii,1,&J,&neg_one,INSERT_VALUES);CHKERRQ(ierr); } if (j<n1-1) { J = Ii + 1; ierr = MatSetValues(A,1,&Ii,1,&J,&neg_one,INSERT_VALUES);CHKERRQ(ierr); ierr = MatSetValues(sA,1,&Ii,1,&J,&neg_one,INSERT_VALUES);CHKERRQ(ierr); } /* ierr = MatSetValues(A,1,&I,1,&I,&four,INSERT_VALUES);CHKERRQ(ierr); ierr = MatSetValues(sA,1,&I,1,&I,&four,INSERT_VALUES);CHKERRQ(ierr); */ } } } } else { /* bs > 1 */ #if defined(DIAGB) for (block=0; block<n/bs; block++) { /* diagonal blocks */ value[0] = -1.0; value[1] = 4.0; value[2] = -1.0; for (i=1+block*bs; i<bs-1+block*bs; i++) { col[0] = i-1; col[1] = i; col[2] = i+1; ierr = MatSetValues(A,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr); ierr = MatSetValues(sA,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr); } i = bs - 1+block*bs; col[0] = bs - 2+block*bs; col[1] = bs - 1+block*bs; value[0]=-1.0; value[1]=4.0; ierr = MatSetValues(A,1,&i,2,col,value,INSERT_VALUES);CHKERRQ(ierr); ierr = MatSetValues(sA,1,&i,2,col,value,INSERT_VALUES);CHKERRQ(ierr); i = 0+block*bs; col[0] = 0+block*bs; col[1] = 1+block*bs; value[0]=4.0; value[1] = -1.0; ierr = MatSetValues(A,1,&i,2,col,value,INSERT_VALUES);CHKERRQ(ierr); ierr = MatSetValues(sA,1,&i,2,col,value,INSERT_VALUES);CHKERRQ(ierr); } #endif /* off-diagonal blocks */ value[0]=-1.0; for (i=0; i<(n/bs-1)*bs; i++) { col[0]=i+bs; ierr = MatSetValues(A,1,&i,1,col,value,INSERT_VALUES);CHKERRQ(ierr); ierr = MatSetValues(sA,1,&i,1,col,value,INSERT_VALUES);CHKERRQ(ierr); col[0]=i; row=i+bs; ierr = MatSetValues(A,1,&row,1,col,value,INSERT_VALUES);CHKERRQ(ierr); ierr = MatSetValues(sA,1,&row,1,col,value,INSERT_VALUES);CHKERRQ(ierr); } } ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); /* PetscPrintf(PETSC_COMM_SELF,"\n The Matrix: \n"); MatView(A, VIEWER_DRAW_WORLD); MatView(A, VIEWER_STDOUT_WORLD); */ ierr = MatAssemblyBegin(sA,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(sA,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); /* PetscPrintf(PETSC_COMM_SELF,"\n Symmetric Part of Matrix: \n"); MatView(sA, VIEWER_DRAW_WORLD); MatView(sA, VIEWER_STDOUT_WORLD); */ /* Test MatNorm() */ ierr = MatNorm(A,NORM_FROBENIUS,&norm1);CHKERRQ(ierr); ierr = MatNorm(sA,NORM_FROBENIUS,&norm2);CHKERRQ(ierr); norm1 -= norm2; if (norm1<-tol || norm1>tol) { ierr = PetscPrintf(PETSC_COMM_SELF,"Error: MatNorm(), fnorm1-fnorm2=%16.14e\n",norm1);CHKERRQ(ierr); } ierr = MatNorm(A,NORM_INFINITY,&norm1);CHKERRQ(ierr); ierr = MatNorm(sA,NORM_INFINITY,&norm2);CHKERRQ(ierr); norm1 -= norm2; if (norm1<-tol || norm1>tol) { ierr = PetscPrintf(PETSC_COMM_SELF,"Error: MatNorm(), inf_norm1-inf_norm2=%16.14e\n",norm1);CHKERRQ(ierr); } /* Test MatGetInfo(), MatGetSize(), MatGetBlockSize() */ ierr = MatGetInfo(A,MAT_LOCAL,&minfo1);CHKERRQ(ierr); ierr = MatGetInfo(sA,MAT_LOCAL,&minfo2);CHKERRQ(ierr); /* printf("matrix nonzeros (BAIJ format) = %d, allocated nonzeros= %d\n", (int)minfo1.nz_used,(int)minfo1.nz_allocated); printf("matrix nonzeros(SBAIJ format) = %d, allocated nonzeros= %d\n", (int)minfo2.nz_used,(int)minfo2.nz_allocated); */ i = (int) (minfo1.nz_used - minfo2.nz_used); j = (int) (minfo1.nz_allocated - minfo2.nz_allocated); if (i<0 || j<0) { ierr = PetscPrintf(PETSC_COMM_SELF,"Error: MatGetInfo()\n");CHKERRQ(ierr); } ierr = MatGetSize(A,&Ii,&J);CHKERRQ(ierr); ierr = MatGetSize(sA,&i,&j);CHKERRQ(ierr); if (i-Ii || j-J) { PetscPrintf(PETSC_COMM_SELF,"Error: MatGetSize()\n");CHKERRQ(ierr); } ierr = MatGetBlockSize(A, &Ii);CHKERRQ(ierr); ierr = MatGetBlockSize(sA, &i);CHKERRQ(ierr); if (i-Ii) { ierr = PetscPrintf(PETSC_COMM_SELF,"Error: MatGetBlockSize()\n");CHKERRQ(ierr); } /* Test MatDiagonalScale(), MatGetDiagonal(), MatScale() */ ierr = PetscRandomCreate(PETSC_COMM_SELF,&rdm);CHKERRQ(ierr); ierr = PetscRandomSetFromOptions(rdm);CHKERRQ(ierr); ierr = VecCreateSeq(PETSC_COMM_SELF,n,&x);CHKERRQ(ierr); ierr = VecDuplicate(x,&s1);CHKERRQ(ierr); ierr = VecDuplicate(x,&s2);CHKERRQ(ierr); ierr = VecDuplicate(x,&y);CHKERRQ(ierr); ierr = VecDuplicate(x,&b);CHKERRQ(ierr); ierr = VecSetRandom(x,rdm);CHKERRQ(ierr); ierr = MatDiagonalScale(A,x,x);CHKERRQ(ierr); ierr = MatDiagonalScale(sA,x,x);CHKERRQ(ierr); ierr = MatGetDiagonal(A,s1);CHKERRQ(ierr); ierr = MatGetDiagonal(sA,s2);CHKERRQ(ierr); ierr = VecNorm(s1,NORM_1,&norm1);CHKERRQ(ierr); ierr = VecNorm(s2,NORM_1,&norm2);CHKERRQ(ierr); norm1 -= norm2; if (norm1<-tol || norm1>tol) { ierr = PetscPrintf(PETSC_COMM_SELF,"Error:MatGetDiagonal() \n");CHKERRQ(ierr); } ierr = MatScale(A,alpha);CHKERRQ(ierr); ierr = MatScale(sA,alpha);CHKERRQ(ierr); /* Test MatMult(), MatMultAdd() */ for (i=0; i<40; i++) { ierr = VecSetRandom(x,rdm);CHKERRQ(ierr); ierr = MatMult(A,x,s1);CHKERRQ(ierr); ierr = MatMult(sA,x,s2);CHKERRQ(ierr); ierr = VecNorm(s1,NORM_1,&norm1);CHKERRQ(ierr); ierr = VecNorm(s2,NORM_1,&norm2);CHKERRQ(ierr); norm1 -= norm2; if (norm1<-tol || norm1>tol) { ierr = PetscPrintf(PETSC_COMM_SELF,"Error: MatMult(), MatDiagonalScale() or MatScale()\n");CHKERRQ(ierr); } } for (i=0; i<40; i++) { ierr = VecSetRandom(x,rdm);CHKERRQ(ierr); ierr = VecSetRandom(y,rdm);CHKERRQ(ierr); ierr = MatMultAdd(A,x,y,s1);CHKERRQ(ierr); ierr = MatMultAdd(sA,x,y,s2);CHKERRQ(ierr); ierr = VecNorm(s1,NORM_1,&norm1);CHKERRQ(ierr); ierr = VecNorm(s2,NORM_1,&norm2);CHKERRQ(ierr); norm1 -= norm2; if (norm1<-tol || norm1>tol) { ierr = PetscPrintf(PETSC_COMM_SELF,"Error:MatMultAdd(), MatDiagonalScale() or MatScale() \n");CHKERRQ(ierr); } } /* Test MatReordering() */ ierr = MatGetOrdering(A,MATORDERINGNATURAL,&isrow,&iscol);CHKERRQ(ierr); ip = isrow; if (reorder) { IS nip; PetscInt *nip_ptr; ierr = PetscMalloc1(mbs,&nip_ptr);CHKERRQ(ierr); ierr = ISGetIndices(ip,&ip_ptr);CHKERRQ(ierr); ierr = PetscMemcpy(nip_ptr,ip_ptr,mbs*sizeof(PetscInt));CHKERRQ(ierr); i = nip_ptr[1]; nip_ptr[1] = nip_ptr[mbs-2]; nip_ptr[mbs-2] = i; i = nip_ptr[0]; nip_ptr[0] = nip_ptr[mbs-1]; nip_ptr[mbs-1] = i; ierr = ISRestoreIndices(ip,&ip_ptr);CHKERRQ(ierr); ierr = ISCreateGeneral(PETSC_COMM_SELF,mbs,nip_ptr,PETSC_COPY_VALUES,&nip);CHKERRQ(ierr); ierr = PetscFree(nip_ptr);CHKERRQ(ierr); ierr = MatReorderingSeqSBAIJ(sA, ip);CHKERRQ(ierr); ierr = ISDestroy(&nip);CHKERRQ(ierr); /* ierr = ISView(ip, VIEWER_STDOUT_SELF);CHKERRQ(ierr); ierr = MatView(sA,VIEWER_DRAW_SELF);CHKERRQ(ierr); */ } ierr = ISDestroy(&iscol);CHKERRQ(ierr); /* ierr = ISDestroy(&isrow);CHKERRQ(ierr);*/ ierr = ISDestroy(&isrow);CHKERRQ(ierr); ierr = MatDestroy(&A);CHKERRQ(ierr); ierr = MatDestroy(&sA);CHKERRQ(ierr); ierr = VecDestroy(&x);CHKERRQ(ierr); ierr = VecDestroy(&y);CHKERRQ(ierr); ierr = VecDestroy(&s1);CHKERRQ(ierr); ierr = VecDestroy(&s2);CHKERRQ(ierr); ierr = VecDestroy(&b);CHKERRQ(ierr); ierr = PetscRandomDestroy(&rdm);CHKERRQ(ierr); ierr = PetscFinalize(); return ierr; }
int main(int argc,char **argv) { AppCtx user; /* user-defined work context */ PetscInt mx,my,its; PetscErrorCode ierr; MPI_Comm comm; SNES snes; DM da; Vec x,X,b; PetscBool youngflg,poissonflg,muflg,lambdaflg,view=PETSC_FALSE,viewline=PETSC_FALSE; PetscReal poisson=0.2,young=4e4; char filename[PETSC_MAX_PATH_LEN] = "ex16.vts"; char filename_def[PETSC_MAX_PATH_LEN] = "ex16_def.vts"; ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr; ierr = FormElements();CHKERRQ(ierr); comm = PETSC_COMM_WORLD; ierr = SNESCreate(comm,&snes);CHKERRQ(ierr); ierr = DMDACreate3d(PETSC_COMM_WORLD,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DMDA_STENCIL_BOX,11,2,2,PETSC_DECIDE,PETSC_DECIDE,PETSC_DECIDE,3,1,NULL,NULL,NULL,&da);CHKERRQ(ierr); ierr = DMSetFromOptions(da);CHKERRQ(ierr); ierr = DMSetUp(da);CHKERRQ(ierr); ierr = SNESSetDM(snes,(DM)da);CHKERRQ(ierr); ierr = SNESSetNGS(snes,NonlinearGS,&user);CHKERRQ(ierr); ierr = DMDAGetInfo(da,0,&mx,&my,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE);CHKERRQ(ierr); user.loading = 0.0; user.arc = PETSC_PI/3.; user.mu = 4.0; user.lambda = 1.0; user.rad = 100.0; user.height = 3.; user.width = 1.; user.ploading = -5e3; ierr = PetscOptionsGetReal(NULL,NULL,"-arc",&user.arc,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetReal(NULL,NULL,"-mu",&user.mu,&muflg);CHKERRQ(ierr); ierr = PetscOptionsGetReal(NULL,NULL,"-lambda",&user.lambda,&lambdaflg);CHKERRQ(ierr); ierr = PetscOptionsGetReal(NULL,NULL,"-rad",&user.rad,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetReal(NULL,NULL,"-height",&user.height,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetReal(NULL,NULL,"-width",&user.width,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetReal(NULL,NULL,"-loading",&user.loading,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetReal(NULL,NULL,"-ploading",&user.ploading,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetReal(NULL,NULL,"-poisson",&poisson,&poissonflg);CHKERRQ(ierr); ierr = PetscOptionsGetReal(NULL,NULL,"-young",&young,&youngflg);CHKERRQ(ierr); if ((youngflg || poissonflg) || !(muflg || lambdaflg)) { /* set the lame' parameters based upon the poisson ratio and young's modulus */ user.lambda = poisson*young / ((1. + poisson)*(1. - 2.*poisson)); user.mu = young/(2.*(1. + poisson)); } ierr = PetscOptionsGetBool(NULL,NULL,"-view",&view,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetBool(NULL,NULL,"-view_line",&viewline,NULL);CHKERRQ(ierr); ierr = DMDASetFieldName(da,0,"x_disp");CHKERRQ(ierr); ierr = DMDASetFieldName(da,1,"y_disp");CHKERRQ(ierr); ierr = DMDASetFieldName(da,2,"z_disp");CHKERRQ(ierr); ierr = DMSetApplicationContext(da,&user);CHKERRQ(ierr); ierr = DMDASNESSetFunctionLocal(da,INSERT_VALUES,(PetscErrorCode (*)(DMDALocalInfo*,void*,void*,void*))FormFunctionLocal,&user);CHKERRQ(ierr); ierr = DMDASNESSetJacobianLocal(da,(DMDASNESJacobian)FormJacobianLocal,&user);CHKERRQ(ierr); ierr = SNESSetFromOptions(snes);CHKERRQ(ierr); ierr = FormCoordinates(da,&user);CHKERRQ(ierr); ierr = DMCreateGlobalVector(da,&x);CHKERRQ(ierr); ierr = DMCreateGlobalVector(da,&b);CHKERRQ(ierr); ierr = InitialGuess(da,&user,x);CHKERRQ(ierr); ierr = FormRHS(da,&user,b);CHKERRQ(ierr); ierr = PetscPrintf(comm,"lambda: %f mu: %f\n",(double)user.lambda,(double)user.mu);CHKERRQ(ierr); /* show a cross-section of the initial state */ if (viewline) { ierr = DisplayLine(snes,x);CHKERRQ(ierr); } /* get the loaded configuration */ ierr = SNESSolve(snes,b,x);CHKERRQ(ierr); ierr = SNESGetIterationNumber(snes,&its);CHKERRQ(ierr); ierr = PetscPrintf(comm,"Number of SNES iterations = %D\n", its);CHKERRQ(ierr); ierr = SNESGetSolution(snes,&X);CHKERRQ(ierr); /* show a cross-section of the final state */ if (viewline) { ierr = DisplayLine(snes,X);CHKERRQ(ierr); } if (view) { PetscViewer viewer; Vec coords; ierr = PetscViewerVTKOpen(PETSC_COMM_WORLD,filename,FILE_MODE_WRITE,&viewer);CHKERRQ(ierr); ierr = VecView(x,viewer);CHKERRQ(ierr); ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); ierr = DMGetCoordinates(da,&coords);CHKERRQ(ierr); ierr = VecAXPY(coords,1.0,x);CHKERRQ(ierr); ierr = PetscViewerVTKOpen(PETSC_COMM_WORLD,filename_def,FILE_MODE_WRITE,&viewer);CHKERRQ(ierr); ierr = VecView(x,viewer);CHKERRQ(ierr); ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); } ierr = VecDestroy(&x);CHKERRQ(ierr); ierr = VecDestroy(&b);CHKERRQ(ierr); ierr = DMDestroy(&da);CHKERRQ(ierr); ierr = SNESDestroy(&snes);CHKERRQ(ierr); ierr = PetscFinalize(); return ierr; }
int main(int argc,char **args) { Vec x,y,u,s1,s2; Mat A,sA,sB; PetscRandom rctx; PetscReal r1,r2,rnorm,tol=1.e-10; PetscScalar one=1.0, neg_one=-1.0, value[3], four=4.0,alpha=0.1; PetscInt n,col[3],n1,block,row,i,j,i2,j2,Ii,J,rstart,rend,bs=1,mbs=16,d_nz=3,o_nz=3,prob=2; PetscErrorCode ierr; PetscMPIInt size,rank; PetscBool flg; MatType type; PetscInitialize(&argc,&args,(char*)0,help); ierr = PetscOptionsGetInt(NULL,"-mbs",&mbs,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetInt(NULL,"-bs",&bs,NULL);CHKERRQ(ierr); ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr); ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr); n = mbs*bs; /* Assemble MPISBAIJ matrix sA */ ierr = MatCreate(PETSC_COMM_WORLD,&sA);CHKERRQ(ierr); ierr = MatSetSizes(sA,PETSC_DECIDE,PETSC_DECIDE,n,n);CHKERRQ(ierr); ierr = MatSetType(sA,MATSBAIJ);CHKERRQ(ierr); ierr = MatSetFromOptions(sA);CHKERRQ(ierr); ierr = MatGetType(sA,&type);CHKERRQ(ierr); /* printf(" mattype: %s\n",type); */ ierr = MatMPISBAIJSetPreallocation(sA,bs,d_nz,NULL,o_nz,NULL);CHKERRQ(ierr); ierr = MatSeqSBAIJSetPreallocation(sA,bs,d_nz,NULL);CHKERRQ(ierr); ierr = MatSetOption(sA,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE);CHKERRQ(ierr); if (bs == 1) { if (prob == 1) { /* tridiagonal matrix */ value[0] = -1.0; value[1] = 2.0; value[2] = -1.0; for (i=1; i<n-1; i++) { col[0] = i-1; col[1] = i; col[2] = i+1; ierr = MatSetValues(sA,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr); } i = n - 1; col[0]=0; col[1] = n - 2; col[2] = n - 1; value[0]= 0.1; value[1]=-1; value[2]=2; ierr = MatSetValues(sA,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr); i = 0; col[0] = 0; col[1] = 1; col[2]=n-1; value[0] = 2.0; value[1] = -1.0; value[2]=0.1; ierr = MatSetValues(sA,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr); } else if (prob ==2) { /* matrix for the five point stencil */ n1 = (int) PetscSqrtReal((PetscReal)n); if (n1*n1 != n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"n must be a perfect square of n1"); for (i=0; i<n1; i++) { for (j=0; j<n1; j++) { Ii = j + n1*i; if (i>0) {J = Ii - n1; ierr = MatSetValues(sA,1,&Ii,1,&J,&neg_one,INSERT_VALUES);CHKERRQ(ierr);} if (i<n1-1) {J = Ii + n1; ierr = MatSetValues(sA,1,&Ii,1,&J,&neg_one,INSERT_VALUES);CHKERRQ(ierr);} if (j>0) {J = Ii - 1; ierr = MatSetValues(sA,1,&Ii,1,&J,&neg_one,INSERT_VALUES);CHKERRQ(ierr);} if (j<n1-1) {J = Ii + 1; ierr = MatSetValues(sA,1,&Ii,1,&J,&neg_one,INSERT_VALUES);CHKERRQ(ierr);} ierr = MatSetValues(sA,1,&Ii,1,&Ii,&four,INSERT_VALUES);CHKERRQ(ierr); } } } /* end of if (bs == 1) */ } else { /* bs > 1 */ for (block=0; block<n/bs; block++) { /* diagonal blocks */ value[0] = -1.0; value[1] = 4.0; value[2] = -1.0; for (i=1+block*bs; i<bs-1+block*bs; i++) { col[0] = i-1; col[1] = i; col[2] = i+1; ierr = MatSetValues(sA,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr); } i = bs - 1+block*bs; col[0] = bs - 2+block*bs; col[1] = bs - 1+block*bs; value[0]=-1.0; value[1]=4.0; ierr = MatSetValues(sA,1,&i,2,col,value,INSERT_VALUES);CHKERRQ(ierr); i = 0+block*bs; col[0] = 0+block*bs; col[1] = 1+block*bs; value[0]=4.0; value[1] = -1.0; ierr = MatSetValues(sA,1,&i,2,col,value,INSERT_VALUES);CHKERRQ(ierr); } /* off-diagonal blocks */ value[0]=-1.0; for (i=0; i<(n/bs-1)*bs; i++) { col[0]=i+bs; ierr = MatSetValues(sA,1,&i,1,col,value,INSERT_VALUES);CHKERRQ(ierr); col[0]=i; row=i+bs; ierr = MatSetValues(sA,1,&row,1,col,value,INSERT_VALUES);CHKERRQ(ierr); } } ierr = MatAssemblyBegin(sA,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(sA,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); /* Test MatView() */ /* ierr = MatView(sA, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = MatView(sA, PETSC_VIEWER_DRAW_WORLD);CHKERRQ(ierr); */ /* Assemble MPIBAIJ matrix A */ ierr = MatCreateBAIJ(PETSC_COMM_WORLD,bs,PETSC_DECIDE,PETSC_DECIDE,n,n,d_nz,NULL,o_nz,NULL,&A);CHKERRQ(ierr); ierr = MatSetOption(A,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE);CHKERRQ(ierr); if (bs == 1) { if (prob == 1) { /* tridiagonal matrix */ value[0] = -1.0; value[1] = 2.0; value[2] = -1.0; for (i=1; i<n-1; i++) { col[0] = i-1; col[1] = i; col[2] = i+1; ierr = MatSetValues(A,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr); } i = n - 1; col[0]=0; col[1] = n - 2; col[2] = n - 1; value[0]= 0.1; value[1]=-1; value[2]=2; ierr = MatSetValues(A,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr); i = 0; col[0] = 0; col[1] = 1; col[2]=n-1; value[0] = 2.0; value[1] = -1.0; value[2]=0.1; ierr = MatSetValues(A,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr); } else if (prob ==2) { /* matrix for the five point stencil */ n1 = (int) PetscSqrtReal((PetscReal)n); for (i=0; i<n1; i++) { for (j=0; j<n1; j++) { Ii = j + n1*i; if (i>0) {J = Ii - n1; ierr = MatSetValues(A,1,&Ii,1,&J,&neg_one,INSERT_VALUES);CHKERRQ(ierr);} if (i<n1-1) {J = Ii + n1; ierr = MatSetValues(A,1,&Ii,1,&J,&neg_one,INSERT_VALUES);CHKERRQ(ierr);} if (j>0) {J = Ii - 1; ierr = MatSetValues(A,1,&Ii,1,&J,&neg_one,INSERT_VALUES);CHKERRQ(ierr);} if (j<n1-1) {J = Ii + 1; ierr = MatSetValues(A,1,&Ii,1,&J,&neg_one,INSERT_VALUES);CHKERRQ(ierr);} ierr = MatSetValues(A,1,&Ii,1,&Ii,&four,INSERT_VALUES);CHKERRQ(ierr); } } } /* end of if (bs == 1) */ } else { /* bs > 1 */ for (block=0; block<n/bs; block++) { /* diagonal blocks */ value[0] = -1.0; value[1] = 4.0; value[2] = -1.0; for (i=1+block*bs; i<bs-1+block*bs; i++) { col[0] = i-1; col[1] = i; col[2] = i+1; ierr = MatSetValues(A,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr); } i = bs - 1+block*bs; col[0] = bs - 2+block*bs; col[1] = bs - 1+block*bs; value[0]=-1.0; value[1]=4.0; ierr = MatSetValues(A,1,&i,2,col,value,INSERT_VALUES);CHKERRQ(ierr); i = 0+block*bs; col[0] = 0+block*bs; col[1] = 1+block*bs; value[0]=4.0; value[1] = -1.0; ierr = MatSetValues(A,1,&i,2,col,value,INSERT_VALUES);CHKERRQ(ierr); } /* off-diagonal blocks */ value[0]=-1.0; for (i=0; i<(n/bs-1)*bs; i++) { col[0]=i+bs; ierr = MatSetValues(A,1,&i,1,col,value,INSERT_VALUES);CHKERRQ(ierr); col[0]=i; row=i+bs; ierr = MatSetValues(A,1,&row,1,col,value,INSERT_VALUES);CHKERRQ(ierr); } } ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); /* Test MatGetSize(), MatGetLocalSize() */ ierr = MatGetSize(sA, &i,&j); ierr = MatGetSize(A, &i2,&j2); i -= i2; j -= j2; if (i || j) { ierr = PetscSynchronizedPrintf(PETSC_COMM_WORLD,"[%d], Error: MatGetSize()\n",rank);CHKERRQ(ierr); ierr = PetscSynchronizedFlush(PETSC_COMM_WORLD,PETSC_STDOUT);CHKERRQ(ierr); } ierr = MatGetLocalSize(sA, &i,&j); ierr = MatGetLocalSize(A, &i2,&j2); i2 -= i; j2 -= j; if (i2 || j2) { ierr = PetscSynchronizedPrintf(PETSC_COMM_WORLD,"[%d], Error: MatGetLocalSize()\n",rank);CHKERRQ(ierr); ierr = PetscSynchronizedFlush(PETSC_COMM_WORLD,PETSC_STDOUT);CHKERRQ(ierr); } /* vectors */ /*--------------------*/ /* i is obtained from MatGetLocalSize() */ ierr = VecCreate(PETSC_COMM_WORLD,&x);CHKERRQ(ierr); ierr = VecSetSizes(x,i,PETSC_DECIDE);CHKERRQ(ierr); ierr = VecSetFromOptions(x);CHKERRQ(ierr); ierr = VecDuplicate(x,&y);CHKERRQ(ierr); ierr = VecDuplicate(x,&u);CHKERRQ(ierr); ierr = VecDuplicate(x,&s1);CHKERRQ(ierr); ierr = VecDuplicate(x,&s2);CHKERRQ(ierr); ierr = PetscRandomCreate(PETSC_COMM_WORLD,&rctx);CHKERRQ(ierr); ierr = PetscRandomSetFromOptions(rctx);CHKERRQ(ierr); ierr = VecSetRandom(x,rctx);CHKERRQ(ierr); ierr = VecSet(u,one);CHKERRQ(ierr); /* Test MatNorm() */ ierr = MatNorm(A,NORM_FROBENIUS,&r1);CHKERRQ(ierr); ierr = MatNorm(sA,NORM_FROBENIUS,&r2);CHKERRQ(ierr); rnorm = PetscAbsReal(r1-r2)/r2; if (rnorm > tol && !rank) { PetscPrintf(PETSC_COMM_SELF,"Error: MatNorm_FROBENIUS(), Anorm=%16.14e, sAnorm=%16.14e bs=%D\n",r1,r2,bs); } ierr = MatNorm(A,NORM_INFINITY,&r1);CHKERRQ(ierr); ierr = MatNorm(sA,NORM_INFINITY,&r2);CHKERRQ(ierr); rnorm = PetscAbsReal(r1-r2)/r2; if (rnorm > tol && !rank) { PetscPrintf(PETSC_COMM_WORLD,"Error: MatNorm_INFINITY(), Anorm=%16.14e, sAnorm=%16.14e bs=%D\n",r1,r2,bs); } ierr = MatNorm(A,NORM_1,&r1);CHKERRQ(ierr); ierr = MatNorm(sA,NORM_1,&r2);CHKERRQ(ierr); rnorm = PetscAbsReal(r1-r2)/r2; if (rnorm > tol && !rank) { PetscPrintf(PETSC_COMM_WORLD,"Error: MatNorm_1(), Anorm=%16.14e, sAnorm=%16.14e bs=%D\n",r1,r2,bs); } /* Test MatGetOwnershipRange() */ ierr = MatGetOwnershipRange(sA,&rstart,&rend);CHKERRQ(ierr); ierr = MatGetOwnershipRange(A,&i2,&j2);CHKERRQ(ierr); i2 -= rstart; j2 -= rend; if (i2 || j2) { ierr = PetscSynchronizedPrintf(PETSC_COMM_WORLD,"[%d], Error: MaGetOwnershipRange()\n",rank);CHKERRQ(ierr); ierr = PetscSynchronizedFlush(PETSC_COMM_WORLD,PETSC_STDOUT);CHKERRQ(ierr); } /* Test MatDiagonalScale() */ ierr = MatDiagonalScale(A,x,x);CHKERRQ(ierr); ierr = MatDiagonalScale(sA,x,x);CHKERRQ(ierr); ierr = MatMultEqual(A,sA,10,&flg);CHKERRQ(ierr); if (!flg) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_NOTSAMETYPE,"Error in MatDiagonalScale"); /* Test MatGetDiagonal(), MatScale() */ ierr = MatGetDiagonal(A,s1);CHKERRQ(ierr); ierr = MatGetDiagonal(sA,s2);CHKERRQ(ierr); ierr = VecNorm(s1,NORM_1,&r1);CHKERRQ(ierr); ierr = VecNorm(s2,NORM_1,&r2);CHKERRQ(ierr); r1 -= r2; if (r1<-tol || r1>tol) { ierr = PetscSynchronizedPrintf(PETSC_COMM_WORLD,"[%d], Error: MatDiagonalScale() or MatGetDiagonal(), r1=%g \n",rank,(double)r1);CHKERRQ(ierr); ierr = PetscSynchronizedFlush(PETSC_COMM_WORLD,PETSC_STDOUT);CHKERRQ(ierr); } ierr = MatScale(A,alpha);CHKERRQ(ierr); ierr = MatScale(sA,alpha);CHKERRQ(ierr); /* Test MatGetRowMaxAbs() */ ierr = MatGetRowMaxAbs(A,s1,NULL);CHKERRQ(ierr); ierr = MatGetRowMaxAbs(sA,s2,NULL);CHKERRQ(ierr); ierr = VecNorm(s1,NORM_1,&r1);CHKERRQ(ierr); ierr = VecNorm(s2,NORM_1,&r2);CHKERRQ(ierr); r1 -= r2; if (r1<-tol || r1>tol) { ierr = PetscPrintf(PETSC_COMM_SELF,"Error: MatGetRowMaxAbs() \n");CHKERRQ(ierr); } /* Test MatMult(), MatMultAdd() */ ierr = MatMultEqual(A,sA,10,&flg);CHKERRQ(ierr); if (!flg) { ierr = PetscSynchronizedPrintf(PETSC_COMM_WORLD,"[%d], Error: MatMult() or MatScale()\n",rank);CHKERRQ(ierr); ierr = PetscSynchronizedFlush(PETSC_COMM_WORLD,PETSC_STDOUT);CHKERRQ(ierr); } ierr = MatMultAddEqual(A,sA,10,&flg);CHKERRQ(ierr); if (!flg) { ierr = PetscSynchronizedPrintf(PETSC_COMM_WORLD,"[%d], Error: MatMultAdd()\n",rank);CHKERRQ(ierr); ierr = PetscSynchronizedFlush(PETSC_COMM_WORLD,PETSC_STDOUT);CHKERRQ(ierr); } /* Test MatMultTranspose(), MatMultTransposeAdd() */ for (i=0; i<10; i++) { ierr = VecSetRandom(x,rctx);CHKERRQ(ierr); ierr = MatMultTranspose(A,x,s1);CHKERRQ(ierr); ierr = MatMultTranspose(sA,x,s2);CHKERRQ(ierr); ierr = VecNorm(s1,NORM_1,&r1);CHKERRQ(ierr); ierr = VecNorm(s2,NORM_1,&r2);CHKERRQ(ierr); r1 -= r2; if (r1<-tol || r1>tol) { ierr = PetscSynchronizedPrintf(PETSC_COMM_WORLD,"[%d], Error: MatMult() or MatScale(), err=%g\n",rank,(double)r1);CHKERRQ(ierr); ierr = PetscSynchronizedFlush(PETSC_COMM_WORLD,PETSC_STDOUT);CHKERRQ(ierr); } } for (i=0; i<10; i++) { ierr = VecSetRandom(x,rctx);CHKERRQ(ierr); ierr = VecSetRandom(y,rctx);CHKERRQ(ierr); ierr = MatMultTransposeAdd(A,x,y,s1);CHKERRQ(ierr); ierr = MatMultTransposeAdd(sA,x,y,s2);CHKERRQ(ierr); ierr = VecNorm(s1,NORM_1,&r1);CHKERRQ(ierr); ierr = VecNorm(s2,NORM_1,&r2);CHKERRQ(ierr); r1 -= r2; if (r1<-tol || r1>tol) { ierr = PetscSynchronizedPrintf(PETSC_COMM_WORLD,"[%d], Error: MatMultAdd(), err=%g \n",rank,(double)r1);CHKERRQ(ierr); ierr = PetscSynchronizedFlush(PETSC_COMM_WORLD,PETSC_STDOUT);CHKERRQ(ierr); } } /* ierr = MatView(sA, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); */ /* ierr = MatView(sA, PETSC_VIEWER_DRAW_WORLD);CHKERRQ(ierr); */ /* Test MatDuplicate() */ ierr = MatDuplicate(sA,MAT_COPY_VALUES,&sB);CHKERRQ(ierr); ierr = MatEqual(sA,sB,&flg);CHKERRQ(ierr); if (!flg) { ierr = PetscPrintf(PETSC_COMM_WORLD," Error in MatDuplicate(), sA != sB \n");CHKERRQ(ierr);CHKERRQ(ierr); } ierr = MatMultEqual(sA,sB,5,&flg);CHKERRQ(ierr); if (!flg) { ierr = PetscSynchronizedPrintf(PETSC_COMM_WORLD,"[%d], Error: MatDuplicate() or MatMult()\n",rank);CHKERRQ(ierr); ierr = PetscSynchronizedFlush(PETSC_COMM_WORLD,PETSC_STDOUT);CHKERRQ(ierr); } ierr = MatMultAddEqual(sA,sB,5,&flg);CHKERRQ(ierr); if (!flg) { ierr = PetscSynchronizedPrintf(PETSC_COMM_WORLD,"[%d], Error: MatDuplicate() or MatMultAdd(()\n",rank);CHKERRQ(ierr); ierr = PetscSynchronizedFlush(PETSC_COMM_WORLD,PETSC_STDOUT);CHKERRQ(ierr); } ierr = MatDestroy(&sB);CHKERRQ(ierr); ierr = VecDestroy(&u);CHKERRQ(ierr); ierr = VecDestroy(&x);CHKERRQ(ierr); ierr = VecDestroy(&y);CHKERRQ(ierr); ierr = VecDestroy(&s1);CHKERRQ(ierr); ierr = VecDestroy(&s2);CHKERRQ(ierr); ierr = MatDestroy(&sA);CHKERRQ(ierr); ierr = MatDestroy(&A);CHKERRQ(ierr); ierr = PetscRandomDestroy(&rctx);CHKERRQ(ierr); ierr = PetscFinalize(); return 0; }
int main(int argc,char **argv) { PetscMPIInt rank; PetscErrorCode ierr; PetscInt M = 10,N = 8,m = PETSC_DECIDE; PetscInt s=2,w=2,n = PETSC_DECIDE,nloc,l,i,j,kk; PetscInt Xs,Xm,Ys,Ym,iloc,*iglobal,*ltog; PetscInt *lx = PETSC_NULL,*ly = PETSC_NULL; PetscBool testorder = PETSC_FALSE,flg; DMDABoundaryType bx = DMDA_BOUNDARY_NONE,by= DMDA_BOUNDARY_NONE; DM da; PetscViewer viewer; Vec local,global; PetscScalar value; DMDAStencilType st = DMDA_STENCIL_BOX; AO ao; ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr); ierr = PetscViewerDrawOpen(PETSC_COMM_WORLD,0,"",300,0,400,400,&viewer);CHKERRQ(ierr); /* Readoptions */ ierr = PetscOptionsGetInt(PETSC_NULL,"-NX",&M,PETSC_NULL);CHKERRQ(ierr); ierr = PetscOptionsGetInt(PETSC_NULL,"-NY",&N,PETSC_NULL);CHKERRQ(ierr); ierr = PetscOptionsGetInt(PETSC_NULL,"-m",&m,PETSC_NULL);CHKERRQ(ierr); ierr = PetscOptionsGetInt(PETSC_NULL,"-n",&n,PETSC_NULL);CHKERRQ(ierr); ierr = PetscOptionsGetInt(PETSC_NULL,"-s",&s,PETSC_NULL);CHKERRQ(ierr); ierr = PetscOptionsGetInt(PETSC_NULL,"-w",&w,PETSC_NULL);CHKERRQ(ierr); flg = PETSC_FALSE; ierr = PetscOptionsGetBool(PETSC_NULL,"-xperiodic",&flg,PETSC_NULL);CHKERRQ(ierr); if (flg) bx = DMDA_BOUNDARY_PERIODIC; flg = PETSC_FALSE; ierr = PetscOptionsGetBool(PETSC_NULL,"-yperiodic",&flg,PETSC_NULL);CHKERRQ(ierr); if (flg) by = DMDA_BOUNDARY_PERIODIC; flg = PETSC_FALSE; ierr = PetscOptionsGetBool(PETSC_NULL,"-xghosted",&flg,PETSC_NULL);CHKERRQ(ierr); if (flg) bx = DMDA_BOUNDARY_GHOSTED; flg = PETSC_FALSE; ierr = PetscOptionsGetBool(PETSC_NULL,"-yghosted",&flg,PETSC_NULL);CHKERRQ(ierr); if (flg) by = DMDA_BOUNDARY_GHOSTED; flg = PETSC_FALSE; ierr = PetscOptionsGetBool(PETSC_NULL,"-star",&flg,PETSC_NULL);CHKERRQ(ierr); if (flg) st = DMDA_STENCIL_STAR; flg = PETSC_FALSE; ierr = PetscOptionsGetBool(PETSC_NULL,"-box",&flg,PETSC_NULL);CHKERRQ(ierr); if (flg) st = DMDA_STENCIL_BOX; flg = PETSC_FALSE; ierr = PetscOptionsGetBool(PETSC_NULL,"-testorder",&testorder,PETSC_NULL);CHKERRQ(ierr); /* Test putting two nodes in x and y on each processor, exact last processor in x and y gets the rest. */ flg = PETSC_FALSE; ierr = PetscOptionsGetBool(PETSC_NULL,"-distribute",&flg,PETSC_NULL);CHKERRQ(ierr); if (flg) { if (m == PETSC_DECIDE) SETERRQ(PETSC_COMM_WORLD,1,"Must set -m option with -distribute option"); ierr = PetscMalloc(m*sizeof(PetscInt),&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 = PetscMalloc(n*sizeof(PetscInt),&ly);CHKERRQ(ierr); for (i=0; i<n-1; i++) { ly[i] = 2;} ly[n-1] = N - 2*(n-1); } /* Create distributed array and get vectors */ ierr = DMDACreate2d(PETSC_COMM_WORLD,bx,by,st,M,N,m,n,w,s,lx,ly,&da);CHKERRQ(ierr); ierr = PetscFree(lx);CHKERRQ(ierr); ierr = PetscFree(ly);CHKERRQ(ierr); ierr = DMView(da,viewer);CHKERRQ(ierr); ierr = DMCreateGlobalVector(da,&global);CHKERRQ(ierr); ierr = DMCreateLocalVector(da,&local);CHKERRQ(ierr); /* Set global vector; send ghost points to local vectors */ value = 1; ierr = VecSet(global,value);CHKERRQ(ierr); ierr = DMGlobalToLocalBegin(da,global,INSERT_VALUES,local);CHKERRQ(ierr); ierr = DMGlobalToLocalEnd(da,global,INSERT_VALUES,local);CHKERRQ(ierr); /* Scale local vectors according to processor rank; pass to global vector */ ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr); value = rank; ierr = VecScale(local,value);CHKERRQ(ierr); ierr = DMLocalToGlobalBegin(da,local,INSERT_VALUES,global);CHKERRQ(ierr); ierr = DMLocalToGlobalEnd(da,local,INSERT_VALUES,global);CHKERRQ(ierr); if (!testorder) { /* turn off printing when testing ordering mappings */ ierr = PetscPrintf (PETSC_COMM_WORLD,"\nGlobal Vectors:\n");CHKERRQ(ierr); ierr = VecView(global,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = PetscPrintf (PETSC_COMM_WORLD,"\n\n");CHKERRQ(ierr); } /* Send ghost points to local vectors */ ierr = DMGlobalToLocalBegin(da,global,INSERT_VALUES,local);CHKERRQ(ierr); ierr = DMGlobalToLocalEnd(da,global,INSERT_VALUES,local);CHKERRQ(ierr); flg = PETSC_FALSE; ierr = PetscOptionsGetBool(PETSC_NULL,"-local_print",&flg,PETSC_NULL);CHKERRQ(ierr); if (flg) { PetscViewer sviewer; ierr = PetscSynchronizedPrintf(PETSC_COMM_WORLD,"\nLocal Vector: processor %d\n",rank);CHKERRQ(ierr); ierr = PetscViewerGetSingleton(PETSC_VIEWER_STDOUT_WORLD,&sviewer);CHKERRQ(ierr); ierr = VecView(local,sviewer);CHKERRQ(ierr); ierr = PetscViewerRestoreSingleton(PETSC_VIEWER_STDOUT_WORLD,&sviewer);CHKERRQ(ierr); } /* Tests mappings betweeen application/PETSc orderings */ if (testorder) { ierr = DMDAGetGhostCorners(da,&Xs,&Ys,PETSC_NULL,&Xm,&Ym,PETSC_NULL);CHKERRQ(ierr); ierr = DMDAGetGlobalIndices(da,&nloc,<og);CHKERRQ(ierr); ierr = DMDAGetAO(da,&ao);CHKERRQ(ierr); ierr = PetscMalloc(nloc*sizeof(PetscInt),&iglobal);CHKERRQ(ierr); /* Set iglobal to be global indices for each processor's local and ghost nodes, using the DMDA ordering of grid points */ kk = 0; for (j=Ys; j<Ys+Ym; j++) { for (i=Xs; i<Xs+Xm; i++) { iloc = w*((j-Ys)*Xm + i-Xs); for (l=0; l<w; l++) { iglobal[kk++] = ltog[iloc+l]; } } } /* Map this to the application ordering (which for DMDAs is just the natural ordering that would be used for 1 processor, numbering most rapidly by x, then y) */ ierr = AOPetscToApplication(ao,nloc,iglobal);CHKERRQ(ierr); /* Then map the application ordering back to the PETSc DMDA ordering */ ierr = AOApplicationToPetsc(ao,nloc,iglobal);CHKERRQ(ierr); /* Verify the mappings */ kk=0; for (j=Ys; j<Ys+Ym; j++) { for (i=Xs; i<Xs+Xm; i++) { iloc = w*((j-Ys)*Xm + i-Xs); for (l=0; l<w; l++) { if (iglobal[kk] != ltog[iloc+l]) { ierr = PetscFPrintf(PETSC_COMM_SELF,stdout,"[%d] Problem with mapping: j=%D, i=%D, l=%D, petsc1=%D, petsc2=%D\n", rank,j,i,l,ltog[iloc+l],iglobal[kk]);} kk++; } } } ierr = PetscFree(iglobal);CHKERRQ(ierr); } /* Free memory */ ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); ierr = VecDestroy(&local);CHKERRQ(ierr); ierr = VecDestroy(&global);CHKERRQ(ierr); ierr = DMDestroy(&da);CHKERRQ(ierr); ierr = PetscFinalize(); return 0; }
int main(int argc,char **argv) { TS ts; /* ODE integrator */ Vec U; /* solution will be stored here */ Mat A; /* Jacobian matrix */ PetscErrorCode ierr; PetscMPIInt size; PetscInt n = 2,idx; AppCtx user; PetscScalar *u; SNES snes; PetscScalar *mat; const PetscScalar *x; Mat B; PetscScalar *amat; PetscViewer viewer; /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Initialize program - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr); ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr); if (size > 1) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_SUP,"Only for sequential runs"); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create necessary matrix and vectors - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr); ierr = MatSetSizes(A,n,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); ierr = MatSetFromOptions(A);CHKERRQ(ierr); ierr = MatSetUp(A);CHKERRQ(ierr); ierr = MatCreateVecs(A,&U,NULL);CHKERRQ(ierr); /* Create wind speed data using Weibull distribution */ ierr = WindSpeeds(&user);CHKERRQ(ierr); /* Set parameters for wind turbine and induction generator */ ierr = SetWindTurbineParams(&user);CHKERRQ(ierr); ierr = SetInductionGeneratorParams(&user);CHKERRQ(ierr); ierr = VecGetArray(U,&u);CHKERRQ(ierr); u[0] = vwa; u[1] = s; ierr = VecRestoreArray(U,&u);CHKERRQ(ierr); /* Create matrix to save solutions at each time step */ user.stepnum = 0; ierr = MatCreateSeqDense(PETSC_COMM_SELF,3,2010,NULL,&user.Sol);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create timestepping solver context - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr); ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr); ierr = TSSetType(ts,TSBEULER);CHKERRQ(ierr); ierr = TSSetIFunction(ts,NULL,(TSIFunction) IFunction,&user);CHKERRQ(ierr); ierr = TSGetSNES(ts,&snes);CHKERRQ(ierr); ierr = SNESSetJacobian(snes,A,A,SNESComputeJacobianDefault,NULL);CHKERRQ(ierr); /* ierr = TSSetIJacobian(ts,A,A,(TSIJacobian)IJacobian,&user);CHKERRQ(ierr); */ ierr = TSSetApplicationContext(ts,&user);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set initial conditions - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSetSolution(ts,U);CHKERRQ(ierr); /* Save initial solution */ idx=3*user.stepnum; ierr = MatDenseGetArray(user.Sol,&mat);CHKERRQ(ierr); ierr = VecGetArrayRead(U,&x);CHKERRQ(ierr); mat[idx] = 0.0; ierr = PetscMemcpy(mat+idx+1,x,2*sizeof(PetscScalar));CHKERRQ(ierr); ierr = MatDenseRestoreArray(user.Sol,&mat);CHKERRQ(ierr); ierr = VecRestoreArrayRead(U,&x);CHKERRQ(ierr); user.stepnum++; /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set solver options - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSetDuration(ts,2000,20.0);CHKERRQ(ierr); ierr = TSSetInitialTimeStep(ts,0.0,.01);CHKERRQ(ierr); ierr = TSSetFromOptions(ts);CHKERRQ(ierr); ierr = TSSetPostStep(ts,SaveSolution);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Solve nonlinear system - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSolve(ts,U);CHKERRQ(ierr); ierr = MatCreateSeqDense(PETSC_COMM_SELF,3,user.stepnum,NULL,&B);CHKERRQ(ierr); ierr = MatDenseGetArray(user.Sol,&mat);CHKERRQ(ierr); ierr = MatDenseGetArray(B,&amat);CHKERRQ(ierr); ierr = PetscMemcpy(amat,mat,user.stepnum*3*sizeof(PetscScalar));CHKERRQ(ierr); ierr = MatDenseRestoreArray(B,&amat);CHKERRQ(ierr); ierr = MatDenseRestoreArray(user.Sol,&mat);CHKERRQ(ierr); ierr = PetscViewerBinaryOpen(PETSC_COMM_SELF,"out.bin",FILE_MODE_WRITE,&viewer);CHKERRQ(ierr); ierr = MatView(B,viewer);CHKERRQ(ierr); ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); ierr = MatDestroy(&user.Sol);CHKERRQ(ierr); ierr = MatDestroy(&B);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Free work space. All PETSc objects should be destroyed when they are no longer needed. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = VecDestroy(&user.wind_data);CHKERRQ(ierr); ierr = VecDestroy(&user.t_wind);CHKERRQ(ierr); ierr = MatDestroy(&A);CHKERRQ(ierr); ierr = VecDestroy(&U);CHKERRQ(ierr); ierr = TSDestroy(&ts);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; PetscInitialize(&argc,&argv,(char *)0,help); ierr = PetscOptionsGetInt(PETSC_NULL,"-dof",&dof,PETSC_NULL);CHKERRQ(ierr); ierr = PetscOptionsGetInt(PETSC_NULL,"-M",&M,PETSC_NULL);CHKERRQ(ierr); ierr = PetscOptionsGetBool(PETSC_NULL,"-trans",&trans,PETSC_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,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,PETSC_NULL,PETSC_NULL,PETSC_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 = DMCreateMatrix(da,MATBAIJ,&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(PETSC_NULL, "-test_sbaij1", &flg,PETSC_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 { printf("Warning: A is non-symmetric\n"); } 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); 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(PETSC_NULL, "-check_final_residual", &flg,PETSC_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) { Mat C; int i,m = 5,rank,size,N,start,end,M; int ierr,idx[4]; PetscScalar Ke[16]; PetscReal h; Vec u,b; KSP ksp; MatNullSpace nullsp; ierr = PetscInitialize(&argc,&args,(char*)0,help);if (ierr) return ierr; ierr = PetscOptionsGetInt(NULL,NULL,"-m",&m,NULL);CHKERRQ(ierr); N = (m+1)*(m+1); /* dimension of matrix */ M = m*m; /* number of elements */ h = 1.0/m; /* mesh width */ ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr); ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr); /* Create stiffness matrix */ ierr = MatCreate(PETSC_COMM_WORLD,&C);CHKERRQ(ierr); ierr = MatSetSizes(C,PETSC_DECIDE,PETSC_DECIDE,N,N);CHKERRQ(ierr); ierr = MatSetFromOptions(C);CHKERRQ(ierr); ierr = MatSetUp(C);CHKERRQ(ierr); start = rank*(M/size) + ((M%size) < rank ? (M%size) : rank); end = start + M/size + ((M%size) > rank); /* Assemble matrix */ ierr = FormElementStiffness(h*h,Ke); /* element stiffness for Laplacian */ for (i=start; i<end; i++) { /* location of lower left corner of element */ /* node numbers for the four corners of element */ idx[0] = (m+1)*(i/m) + (i % m); idx[1] = idx[0]+1; idx[2] = idx[1] + m + 1; idx[3] = idx[2] - 1; ierr = MatSetValues(C,4,idx,4,idx,Ke,ADD_VALUES);CHKERRQ(ierr); } ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); /* Create right-hand-side and solution vectors */ ierr = VecCreate(PETSC_COMM_WORLD,&u);CHKERRQ(ierr); ierr = VecSetSizes(u,PETSC_DECIDE,N);CHKERRQ(ierr); ierr = VecSetFromOptions(u);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject)u,"Approx. Solution");CHKERRQ(ierr); ierr = VecDuplicate(u,&b);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject)b,"Right hand side");CHKERRQ(ierr); ierr = VecSet(b,1.0);CHKERRQ(ierr); ierr = VecSetValue(b,0,1.2,ADD_VALUES);CHKERRQ(ierr); ierr = VecSet(u,0.0);CHKERRQ(ierr); /* Solve linear system */ ierr = KSPCreate(PETSC_COMM_WORLD,&ksp);CHKERRQ(ierr); ierr = KSPSetOperators(ksp,C,C);CHKERRQ(ierr); ierr = KSPSetFromOptions(ksp);CHKERRQ(ierr); ierr = KSPSetInitialGuessNonzero(ksp,PETSC_TRUE);CHKERRQ(ierr); ierr = MatNullSpaceCreate(PETSC_COMM_WORLD,PETSC_TRUE,0,NULL,&nullsp);CHKERRQ(ierr); /* The KSP solver will remove this nullspace from the solution at each iteration */ ierr = MatSetNullSpace(C,nullsp);CHKERRQ(ierr); /* The KSP solver will remove from the right hand side any portion in this nullspace, thus making the linear system consistent. */ ierr = MatSetTransposeNullSpace(C,nullsp);CHKERRQ(ierr); ierr = MatNullSpaceDestroy(&nullsp);CHKERRQ(ierr); ierr = KSPSolve(ksp,b,u);CHKERRQ(ierr); /* Free work space */ ierr = KSPDestroy(&ksp);CHKERRQ(ierr); ierr = VecDestroy(&u);CHKERRQ(ierr); ierr = VecDestroy(&b);CHKERRQ(ierr); ierr = MatDestroy(&C);CHKERRQ(ierr); ierr = PetscFinalize(); return ierr; }
-m # : the size of the vectors\n \ -n # : the numer of indices (with n<=m)\n \ -toFirst # : the starting index of the output vector for strided scatters\n \ -toStep # : the step size into the output vector for strided scatters\n \ -fromFirst # : the starting index of the input vector for strided scatters\n\ -fromStep # : the step size into the input vector for strided scatters\n\n"; int main(int argc, char * argv[]) { Vec X,Y; PetscInt m,n,i,n1,n2; PetscInt toFirst,toStep,fromFirst,fromStep; PetscInt *idx,*idy; PetscBool flg; IS toISStrided,fromISStrided,toISGeneral,fromISGeneral; VecScatter vscatSStoSS,vscatSStoSG,vscatSGtoSS,vscatSGtoSG; ScatterMode mode; InsertMode addv; PetscErrorCode ierr; ierr = PetscInitialize(&argc,&argv,0,help);if (ierr) return ierr; ierr = PetscOptionsGetInt(NULL,NULL,"-m",&m,&flg);CHKERRQ(ierr); if (!flg) m = 100; ierr = PetscOptionsGetInt(NULL,NULL,"-n",&n,&flg);CHKERRQ(ierr); if (!flg) n = 30; ierr = PetscOptionsGetInt(NULL,NULL,"-toFirst",&toFirst,&flg);CHKERRQ(ierr); if (!flg) toFirst = 3; ierr = PetscOptionsGetInt(NULL,NULL,"-toStep",&toStep,&flg);CHKERRQ(ierr); if (!flg) toStep = 3; ierr = PetscOptionsGetInt(NULL,NULL,"-fromFirst",&fromFirst,&flg);CHKERRQ(ierr); if (!flg) fromFirst = 2; ierr = PetscOptionsGetInt(NULL,NULL,"-fromStep",&fromStep,&flg);CHKERRQ(ierr); if (!flg) fromStep = 2; if (n>m) { ierr = PetscPrintf(PETSC_COMM_WORLD,"The vector sizes are %D. The number of elements being scattered is %D\n",m,n);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD,"Adjust the parameters such that m>=n\n");CHKERRQ(ierr); } else if (toFirst+(n-1)*toStep >=m) { ierr = PetscPrintf(PETSC_COMM_WORLD,"The vector sizes are %D. The number of elements being scattered is %D\n",m,n);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD,"For the Strided Scatter, toFirst=%D and toStep=%D.\n",toFirst,toStep);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD,"This produces an index (toFirst+(n-1)*toStep)>=m\n");CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD,"Adjust the parameterrs accordingly with -m, -n, -toFirst, or -toStep\n");CHKERRQ(ierr); } else if (fromFirst+(n-1)*fromStep>=m) { ierr = PetscPrintf(PETSC_COMM_WORLD,"The vector sizes are %D. The number of elements being scattered is %D\n",m,n);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD,"For the Strided Scatter, fromFirst=%D and fromStep=%D.\n",fromFirst,toStep);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD,"This produces an index (fromFirst+(n-1)*fromStep)>=m\n");CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD,"Adjust the parameterrs accordingly with -m, -n, -fromFirst, or -fromStep\n");CHKERRQ(ierr); } else { ierr = PetscPrintf(PETSC_COMM_WORLD,"m=%D\tn=%D\tfromFirst=%D\tfromStep=%D\ttoFirst=%D\ttoStep=%D\n",m,n,fromFirst,fromStep,toFirst,toStep);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD,"fromFirst+(n-1)*fromStep=%D\ttoFirst+(n-1)*toStep=%D\n",fromFirst+(n-1)*fromStep,toFirst+(n-1)*toStep);CHKERRQ(ierr); /* Build the vectors */ ierr = VecCreate(PETSC_COMM_WORLD,&Y);CHKERRQ(ierr); ierr = VecSetSizes(Y,m,PETSC_DECIDE);CHKERRQ(ierr); ierr = VecCreate(PETSC_COMM_WORLD,&X);CHKERRQ(ierr); ierr = VecSetSizes(X,m,PETSC_DECIDE);CHKERRQ(ierr); ierr = VecSetFromOptions(Y);CHKERRQ(ierr); ierr = VecSetFromOptions(X);CHKERRQ(ierr); ierr = VecSet(X,2.0);CHKERRQ(ierr); ierr = VecSet(Y,1.0);CHKERRQ(ierr); /* Build the strided index sets */ ierr = ISCreate(PETSC_COMM_WORLD,&toISStrided);CHKERRQ(ierr); ierr = ISCreate(PETSC_COMM_WORLD,&fromISStrided);CHKERRQ(ierr); ierr = ISSetType(toISStrided, ISSTRIDE);CHKERRQ(ierr); ierr = ISSetType(fromISStrided, ISSTRIDE);CHKERRQ(ierr); ierr = ISStrideSetStride(fromISStrided,n,fromFirst,fromStep);CHKERRQ(ierr); ierr = ISStrideSetStride(toISStrided,n,toFirst,toStep);CHKERRQ(ierr); /* Build the general index sets */ ierr = PetscMalloc1(n,&idx);CHKERRQ(ierr); ierr = PetscMalloc1(n,&idy);CHKERRQ(ierr); for (i=0; i<n; i++) { idx[i] = i % m; idy[i] = (i+m) % m; } n1 = n; n2 = n; ierr = PetscSortRemoveDupsInt(&n1,idx);CHKERRQ(ierr); ierr = PetscSortRemoveDupsInt(&n2,idy);CHKERRQ(ierr); ierr = ISCreateGeneral(PETSC_COMM_WORLD,n1,idx,PETSC_COPY_VALUES,&toISGeneral);CHKERRQ(ierr); ierr = ISCreateGeneral(PETSC_COMM_WORLD,n2,idy,PETSC_COPY_VALUES,&fromISGeneral);CHKERRQ(ierr); /* set the mode and the insert/add parameter */ mode = SCATTER_FORWARD; addv = ADD_VALUES; /* VecScatter : Seq Strided to Seq Strided */ ierr = VecScatterCreate(X,fromISStrided,Y,toISStrided,&vscatSStoSS);CHKERRQ(ierr); ierr = VecScatterBegin(vscatSStoSS,X,Y,addv,mode);CHKERRQ(ierr); ierr = VecScatterEnd(vscatSStoSS,X,Y,addv,mode);CHKERRQ(ierr); ierr = VecScatterDestroy(&vscatSStoSS);CHKERRQ(ierr); /* VecScatter : Seq General to Seq Strided */ ierr = VecScatterCreate(Y,fromISGeneral,X,toISStrided,&vscatSGtoSS);CHKERRQ(ierr); ierr = VecScatterBegin(vscatSGtoSS,Y,X,addv,mode);CHKERRQ(ierr); ierr = VecScatterEnd(vscatSGtoSS,Y,X,addv,mode);CHKERRQ(ierr); ierr = VecScatterDestroy(&vscatSGtoSS);CHKERRQ(ierr); /* VecScatter : Seq General to Seq General */ ierr = VecScatterCreate(X,fromISGeneral,Y,toISGeneral,&vscatSGtoSG);CHKERRQ(ierr); ierr = VecScatterBegin(vscatSGtoSG,X,Y,addv,mode);CHKERRQ(ierr); ierr = VecScatterEnd(vscatSGtoSG,X,Y,addv,mode);CHKERRQ(ierr); ierr = VecScatterDestroy(&vscatSGtoSG);CHKERRQ(ierr); /* VecScatter : Seq Strided to Seq General */ ierr = VecScatterCreate(Y,fromISStrided,X,toISGeneral,&vscatSStoSG);CHKERRQ(ierr); ierr = VecScatterBegin(vscatSStoSG,Y,X,addv,mode);CHKERRQ(ierr); ierr = VecScatterEnd(vscatSStoSG,Y,X,addv,mode);CHKERRQ(ierr); ierr = VecScatterDestroy(&vscatSStoSG);CHKERRQ(ierr); /* view the results */ ierr = VecView(Y,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); /* Cleanup */ ierr = VecDestroy(&X);CHKERRQ(ierr); ierr = VecDestroy(&Y);CHKERRQ(ierr); ierr = ISDestroy(&toISStrided);CHKERRQ(ierr); ierr = ISDestroy(&fromISStrided);CHKERRQ(ierr); ierr = ISDestroy(&toISGeneral);CHKERRQ(ierr); ierr = ISDestroy(&fromISGeneral);CHKERRQ(ierr); ierr = PetscFree(idx);CHKERRQ(ierr); ierr = PetscFree(idy);CHKERRQ(ierr); } ierr = PetscFinalize(); return ierr; }
int main(int argc,char **args) { Mat A; PetscErrorCode ierr; PetscMPIInt rank,size; PetscInt *ia,*ja; MatPartitioning part; IS is,isn; PetscInitialize(&argc,&args,(char*)0,help); ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr); if (size != 4) SETERRQ(PETSC_COMM_WORLD,1,"Must run with 4 processors"); ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr); ierr = PetscMalloc(5*sizeof(PetscInt),&ia);CHKERRQ(ierr); ierr = PetscMalloc(16*sizeof(PetscInt),&ja);CHKERRQ(ierr); if (!rank) { ja[0] = 1; ja[1] = 4; ja[2] = 0; ja[3] = 2; ja[4] = 5; ja[5] = 1; ja[6] = 3; ja[7] = 6; ja[8] = 2; ja[9] = 7; ia[0] = 0; ia[1] = 2; ia[2] = 5; ia[3] = 8; ia[4] = 10; } else if (rank == 1) { ja[0] = 0; ja[1] = 5; ja[2] = 8; ja[3] = 1; ja[4] = 4; ja[5] = 6; ja[6] = 9; ja[7] = 2; ja[8] = 5; ja[9] = 7; ja[10] = 10; ja[11] = 3; ja[12] = 6; ja[13] = 11; ia[0] = 0; ia[1] = 3; ia[2] = 7; ia[3] = 11; ia[4] = 14; } else if (rank == 2) { ja[0] = 4; ja[1] = 9; ja[2] = 12; ja[3] = 5; ja[4] = 8; ja[5] = 10; ja[6] = 13; ja[7] = 6; ja[8] = 9; ja[9] = 11; ja[10] = 14; ja[11] = 7; ja[12] = 10; ja[13] = 15; ia[0] = 0; ia[1] = 3; ia[2] = 7; ia[3] = 11; ia[4] = 14; } else { ja[0] = 8; ja[1] = 13; ja[2] = 9; ja[3] = 12; ja[4] = 14; ja[5] = 10; ja[6] = 13; ja[7] = 15; ja[8] = 11; ja[9] = 14; ia[0] = 0; ia[1] = 2; ia[2] = 5; ia[3] = 8; ia[4] = 10; } ierr = MatCreateMPIAdj(PETSC_COMM_WORLD,4,16,ia,ja,NULL,&A);CHKERRQ(ierr); ierr = MatView(A,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); /* Partition the graph of the matrix */ ierr = MatPartitioningCreate(PETSC_COMM_WORLD,&part);CHKERRQ(ierr); ierr = MatPartitioningSetAdjacency(part,A);CHKERRQ(ierr); ierr = MatPartitioningSetFromOptions(part);CHKERRQ(ierr); /* get new processor owner number of each vertex */ ierr = MatPartitioningApply(part,&is);CHKERRQ(ierr); /* get new global number of each old global number */ ierr = ISPartitioningToNumbering(is,&isn);CHKERRQ(ierr); ierr = ISView(isn,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = ISDestroy(&is);CHKERRQ(ierr); ierr = ISDestroy(&isn);CHKERRQ(ierr); ierr = MatPartitioningDestroy(&part);CHKERRQ(ierr); /* Free work space. All PETSc objects should be destroyed when they are no longer needed. */ ierr = MatDestroy(&A);CHKERRQ(ierr); ierr = PetscFinalize(); return 0; }
Example: mpiexec -n <np> ./ex130 -f <matrix binary file> -mat_solver_type 1 -mat_superlu_equil \n\n"; #include <petscmat.h> int main(int argc,char **args) { Mat A,F; Vec u,x,b; PetscErrorCode ierr; PetscMPIInt rank,size; PetscInt m,n,nfact,ipack=0; PetscReal norm,tol=1.e-12,Anorm; IS perm,iperm; MatFactorInfo info; PetscBool flg,testMatSolve=PETSC_TRUE; PetscViewer fd; /* viewer */ char file[PETSC_MAX_PATH_LEN]; /* input file name */ ierr = PetscInitialize(&argc,&args,(char*)0,help);if (ierr) return ierr; ierr = MPI_Comm_rank(PETSC_COMM_WORLD, &rank);CHKERRQ(ierr); ierr = MPI_Comm_size(PETSC_COMM_WORLD, &size);CHKERRQ(ierr); /* Determine file from which we read the matrix A */ ierr = PetscOptionsGetString(NULL,NULL,"-f",file,PETSC_MAX_PATH_LEN,&flg);CHKERRQ(ierr); if (!flg) SETERRQ(PETSC_COMM_WORLD,1,"Must indicate binary file with the -f option"); /* Load matrix A */ ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,file,FILE_MODE_READ,&fd);CHKERRQ(ierr); ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr); ierr = MatLoad(A,fd);CHKERRQ(ierr); ierr = VecCreate(PETSC_COMM_WORLD,&b);CHKERRQ(ierr); ierr = VecLoad(b,fd);CHKERRQ(ierr); ierr = PetscViewerDestroy(&fd);CHKERRQ(ierr); ierr = MatGetLocalSize(A,&m,&n);CHKERRQ(ierr); if (m != n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ, "This example is not intended for rectangular matrices (%d, %d)", m, n); ierr = MatNorm(A,NORM_INFINITY,&Anorm);CHKERRQ(ierr); /* Create vectors */ ierr = VecDuplicate(b,&x);CHKERRQ(ierr); ierr = VecDuplicate(x,&u);CHKERRQ(ierr); /* save the true solution */ /* Test LU Factorization */ ierr = MatGetOrdering(A,MATORDERINGNATURAL,&perm,&iperm);CHKERRQ(ierr); ierr = PetscOptionsGetInt(NULL,NULL,"-mat_solver_type",&ipack,NULL);CHKERRQ(ierr); switch (ipack) { case 1: #if defined(PETSC_HAVE_SUPERLU) if (!rank) printf(" SUPERLU LU:\n"); ierr = MatGetFactor(A,MATSOLVERSUPERLU,MAT_FACTOR_LU,&F);CHKERRQ(ierr); break; #endif case 2: #if defined(PETSC_HAVE_MUMPS) if (!rank) printf(" MUMPS LU:\n"); ierr = MatGetFactor(A,MATSOLVERMUMPS,MAT_FACTOR_LU,&F);CHKERRQ(ierr); { /* test mumps options */ PetscInt icntl_7 = 5; ierr = MatMumpsSetIcntl(F,7,icntl_7);CHKERRQ(ierr); } break; #endif default: if (!rank) printf(" PETSC LU:\n"); ierr = MatGetFactor(A,MATSOLVERPETSC,MAT_FACTOR_LU,&F);CHKERRQ(ierr); } info.fill = 5.0; ierr = MatLUFactorSymbolic(F,A,perm,iperm,&info);CHKERRQ(ierr); for (nfact = 0; nfact < 1; nfact++) { if (!rank) printf(" %d-the LU numfactorization \n",nfact); ierr = MatLUFactorNumeric(F,A,&info);CHKERRQ(ierr); /* Test MatSolve() */ if (testMatSolve) { ierr = MatSolve(F,b,x);CHKERRQ(ierr); /* Check the residual */ ierr = MatMult(A,x,u);CHKERRQ(ierr); ierr = VecAXPY(u,-1.0,b);CHKERRQ(ierr); ierr = VecNorm(u,NORM_INFINITY,&norm);CHKERRQ(ierr); if (norm > tol) { if (!rank) { ierr = PetscPrintf(PETSC_COMM_SELF,"MatSolve: rel residual %g/%g = %g, LU numfact %d\n",norm,Anorm,norm/Anorm,nfact);CHKERRQ(ierr); } } } } /* Free data structures */ ierr = MatDestroy(&A);CHKERRQ(ierr); ierr = MatDestroy(&F);CHKERRQ(ierr); ierr = ISDestroy(&perm);CHKERRQ(ierr); ierr = ISDestroy(&iperm);CHKERRQ(ierr); ierr = VecDestroy(&x);CHKERRQ(ierr); ierr = VecDestroy(&b);CHKERRQ(ierr); ierr = VecDestroy(&u);CHKERRQ(ierr); ierr = PetscFinalize(); return ierr; }
int main(int argc,char **argv) { TS ts; /* nonlinear solver */ PetscBool monitor = PETSC_FALSE; PetscScalar *x_ptr,*y_ptr; PetscMPIInt size; struct _n_User user; PetscErrorCode ierr; /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Initialize program - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = PetscInitialize(&argc,&argv,NULL,help);if (ierr) return ierr; ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr); if (size != 1) SETERRQ(PETSC_COMM_SELF,1,"This is a uniprocessor example only!"); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set runtime options - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ user.next_output = 0.0; user.mu = 1.0e6; user.steps = 0; user.ftime = 0.5; ierr = PetscOptionsGetBool(NULL,NULL,"-monitor",&monitor,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetReal(NULL,NULL,"-mu",&user.mu,NULL);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create necessary matrix and vectors, solve same ODE on every process - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = MatCreate(PETSC_COMM_WORLD,&user.A);CHKERRQ(ierr); ierr = MatSetSizes(user.A,PETSC_DECIDE,PETSC_DECIDE,2,2);CHKERRQ(ierr); ierr = MatSetFromOptions(user.A);CHKERRQ(ierr); ierr = MatSetUp(user.A);CHKERRQ(ierr); ierr = MatCreateVecs(user.A,&user.x,NULL);CHKERRQ(ierr); ierr = MatCreate(PETSC_COMM_WORLD,&user.Jacp);CHKERRQ(ierr); ierr = MatSetSizes(user.Jacp,PETSC_DECIDE,PETSC_DECIDE,2,1);CHKERRQ(ierr); ierr = MatSetFromOptions(user.Jacp);CHKERRQ(ierr); ierr = MatSetUp(user.Jacp);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create timestepping solver context - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr); ierr = TSSetType(ts,TSCN);CHKERRQ(ierr); ierr = TSSetIFunction(ts,NULL,IFunction,&user);CHKERRQ(ierr); ierr = TSSetIJacobian(ts,user.A,user.A,IJacobian,&user);CHKERRQ(ierr); ierr = TSSetMaxTime(ts,user.ftime);CHKERRQ(ierr); ierr = TSSetExactFinalTime(ts,TS_EXACTFINALTIME_MATCHSTEP);CHKERRQ(ierr); if (monitor) { ierr = TSMonitorSet(ts,Monitor,&user,NULL);CHKERRQ(ierr); } /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set initial conditions - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = VecGetArray(user.x,&x_ptr);CHKERRQ(ierr); x_ptr[0] = 2.0; x_ptr[1] = -0.66666654321; ierr = VecRestoreArray(user.x,&x_ptr);CHKERRQ(ierr); ierr = TSSetTimeStep(ts,.0001);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Save trajectory of solution so that TSAdjointSolve() may be used - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSetSaveTrajectory(ts);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set runtime options - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSetFromOptions(ts);CHKERRQ(ierr); ierr = TSSolve(ts,user.x);CHKERRQ(ierr); ierr = TSGetSolveTime(ts,&user.ftime);CHKERRQ(ierr); ierr = TSGetStepNumber(ts,&user.steps);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Adjoint model starts here - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = MatCreateVecs(user.A,&user.lambda[0],NULL);CHKERRQ(ierr); /* Set initial conditions for the adjoint integration */ ierr = VecGetArray(user.lambda[0],&y_ptr);CHKERRQ(ierr); y_ptr[0] = 1.0; y_ptr[1] = 0.0; ierr = VecRestoreArray(user.lambda[0],&y_ptr);CHKERRQ(ierr); ierr = MatCreateVecs(user.A,&user.lambda[1],NULL);CHKERRQ(ierr); ierr = VecGetArray(user.lambda[1],&y_ptr);CHKERRQ(ierr); y_ptr[0] = 0.0; y_ptr[1] = 1.0; ierr = VecRestoreArray(user.lambda[1],&y_ptr);CHKERRQ(ierr); ierr = MatCreateVecs(user.Jacp,&user.mup[0],NULL);CHKERRQ(ierr); ierr = VecGetArray(user.mup[0],&x_ptr);CHKERRQ(ierr); x_ptr[0] = 0.0; ierr = VecRestoreArray(user.mup[0],&x_ptr);CHKERRQ(ierr); ierr = MatCreateVecs(user.Jacp,&user.mup[1],NULL);CHKERRQ(ierr); ierr = VecGetArray(user.mup[1],&x_ptr);CHKERRQ(ierr); x_ptr[0] = 0.0; ierr = VecRestoreArray(user.mup[1],&x_ptr);CHKERRQ(ierr); ierr = TSSetCostGradients(ts,2,user.lambda,user.mup);CHKERRQ(ierr); /* Set RHS JacobianP */ ierr = TSSetRHSJacobianP(ts,user.Jacp,RHSJacobianP,&user);CHKERRQ(ierr); ierr = TSAdjointSolve(ts);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD,"\n sensitivity wrt initial conditions: d[y(tf)]/d[y0] d[y(tf)]/d[z0]\n");CHKERRQ(ierr); ierr = VecView(user.lambda[0],PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD,"\n sensitivity wrt initial conditions: d[z(tf)]/d[y0] d[z(tf)]/d[z0]\n");CHKERRQ(ierr); ierr = VecView(user.lambda[1],PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD,"\n sensitivity wrt parameters: d[y(tf)]/d[mu]\n");CHKERRQ(ierr); ierr = VecView(user.mup[0],PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD,"\n sensivitity wrt parameters: d[z(tf)]/d[mu]\n");CHKERRQ(ierr); ierr = VecView(user.mup[1],PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Free work space. All PETSc objects should be destroyed when they are no longer needed. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = MatDestroy(&user.A);CHKERRQ(ierr); ierr = MatDestroy(&user.Jacp);CHKERRQ(ierr); ierr = VecDestroy(&user.x);CHKERRQ(ierr); ierr = VecDestroy(&user.lambda[0]);CHKERRQ(ierr); ierr = VecDestroy(&user.lambda[1]);CHKERRQ(ierr); ierr = VecDestroy(&user.mup[0]);CHKERRQ(ierr); ierr = VecDestroy(&user.mup[1]);CHKERRQ(ierr); ierr = TSDestroy(&ts);CHKERRQ(ierr); ierr = PetscFinalize(); return(ierr); }
int main(int argc,char **argv) { TS ts; /* nonlinear solver */ Vec C; /* solution */ PetscErrorCode ierr; DM da; /* manages the grid data */ AppCtx ctx; /* holds problem specific paramters */ PetscInt He,dof = 3*N+N*N,*ofill; /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Initialize program - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ PetscInitialize(&argc,&argv,(char *)0,help); PetscFunctionBeginUser; ctx.noreactions = PETSC_FALSE; ctx.nodissociations = PETSC_FALSE; ierr = PetscOptionsHasName(PETSC_NULL,"-noreactions",&ctx.noreactions);CHKERRQ(ierr); ierr = PetscOptionsHasName(PETSC_NULL,"-nodissociations",&ctx.nodissociations);CHKERRQ(ierr); ctx.HeDiffusion[1] = 1000*2.95e-4; /* From Tibo's notes times 1,000 */ ctx.HeDiffusion[2] = 1000*3.24e-4; ctx.HeDiffusion[3] = 1000*2.26e-4; ctx.HeDiffusion[4] = 1000*1.68e-4; ctx.HeDiffusion[5] = 1000*5.20e-5; ctx.VDiffusion[1] = 1000*2.71e-3; ctx.IDiffusion[1] = 1000*2.13e-4; ctx.forcingScale = 100.; /* made up numbers */ ctx.reactionScale = .001; ctx.dissociationScale = .0001; /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create distributed array (DMDA) to manage parallel grid and vectors - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = DMDACreate1d(PETSC_COMM_WORLD, DMDA_BOUNDARY_MIRROR,-8,dof,1,PETSC_NULL,&da);CHKERRQ(ierr); /* The only spatial coupling in the Jacobian (diffusion) is for the first 5 He, the first V, and the first I. The ofill (thought of as a dof by dof 2d (row-oriented) array represents the nonzero coupling between degrees of freedom at one point with degrees of freedom on the adjacent point to the left or right. A 1 at i,j in the ofill array indicates that the degree of freedom i at a point is coupled to degree of freedom j at the adjacent point. In this case ofill has only a few diagonal entries since the only spatial coupling is regular diffusion. */ ierr = PetscMalloc(dof*dof*sizeof(PetscInt),&ofill);CHKERRQ(ierr); ierr = PetscMemzero(ofill,dof*dof*sizeof(PetscInt));CHKERRQ(ierr); for (He=0; He<PetscMin(N,5); He++) ofill[He*dof + He] = 1; ofill[N*dof + N] = ofill[2*N*dof + 2*N] = 1; ierr = DMDASetBlockFills(da,PETSC_NULL,ofill);CHKERRQ(ierr); ierr = PetscFree(ofill);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Extract global vector from DMDA to hold solution - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = DMCreateGlobalVector(da,&C);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,PETSC_NULL,IFunction,&ctx);CHKERRQ(ierr); ierr = TSSetSolution(ts,C);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set solver options - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSetInitialTimeStep(ts,0.0,.001);CHKERRQ(ierr); ierr = TSSetDuration(ts,100,50.0);CHKERRQ(ierr); ierr = TSSetFromOptions(ts);CHKERRQ(ierr); ierr = MyMonitorSetUp(ts);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set initial conditions - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = InitialConditions(da,C);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Solve the ODE system - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSolve(ts,C);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Free work space. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = VecDestroy(&C);CHKERRQ(ierr); ierr = TSDestroy(&ts);CHKERRQ(ierr); ierr = DMDestroy(&da);CHKERRQ(ierr); ierr = PetscFinalize(); PetscFunctionReturn(0); }
int main(int argc,char **argv) { PetscMPIInt rank,size; PetscInt M = 14,time_steps = 20,w=1,s=1,localsize,j,i,mybase,myend; PetscErrorCode ierr; DM da; Vec local,global,copy; PetscScalar *localptr,*copyptr; PetscReal h,k; ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr); ierr = PetscOptionsGetInt(PETSC_NULL,"-M",&M,PETSC_NULL);CHKERRQ(ierr); ierr = PetscOptionsGetInt(PETSC_NULL,"-time",&time_steps,PETSC_NULL);CHKERRQ(ierr); /* Set up the array */ ierr = DMDACreate1d(PETSC_COMM_WORLD,DMDA_BOUNDARY_NONE,M,w,s,PETSC_NULL,&da);CHKERRQ(ierr); ierr = DMCreateGlobalVector(da,&global);CHKERRQ(ierr); ierr = DMCreateLocalVector(da,&local);CHKERRQ(ierr); ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr); ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr); /* Make copy of local array for doing updates */ ierr = VecDuplicate(local,©);CHKERRQ(ierr); ierr = VecGetArray (copy,©ptr);CHKERRQ(ierr); /* determine starting point of each processor */ ierr = VecGetOwnershipRange(global,&mybase,&myend);CHKERRQ(ierr); /* Initialize the Array */ ierr = VecGetLocalSize (local,&localsize);CHKERRQ(ierr); ierr = VecGetArray (local,&localptr);CHKERRQ(ierr); localptr[0] = copyptr[0] = 0.0; localptr[localsize-1] = copyptr[localsize-1] = 1.0; for (i=1; i<localsize-1; i++) { j=(i-1)+mybase; localptr[i] = sin((PETSC_PI*j*6)/((PetscReal)M) + 1.2 * sin((PETSC_PI*j*2)/((PetscReal)M))) * 4+4; } ierr = VecRestoreArray (copy,©ptr);CHKERRQ(ierr); ierr = VecRestoreArray(local,&localptr);CHKERRQ(ierr); ierr = DMLocalToGlobalBegin(da,local,INSERT_VALUES,global);CHKERRQ(ierr); ierr = DMLocalToGlobalEnd(da,local,INSERT_VALUES,global);CHKERRQ(ierr); /* Assign Parameters */ h= 1.0/M; k= h*h/2.2; for (j=0; j<time_steps; j++) { /* Global to Local */ ierr = DMGlobalToLocalBegin(da,global,INSERT_VALUES,local);CHKERRQ(ierr); ierr = DMGlobalToLocalEnd(da,global,INSERT_VALUES,local);CHKERRQ(ierr); /*Extract local array */ ierr = VecGetArray(local,&localptr);CHKERRQ(ierr); ierr = VecGetArray (copy,©ptr);CHKERRQ(ierr); /* Update Locally - Make array of new values */ /* Note: I don't do anything for the first and last entry */ for (i=1; i< localsize-1; i++) { copyptr[i] = localptr[i] + (k/(h*h)) * (localptr[i+1]-2.0*localptr[i]+localptr[i-1]); } ierr = VecRestoreArray (copy,©ptr);CHKERRQ(ierr); ierr = VecRestoreArray(local,&localptr);CHKERRQ(ierr); /* Local to Global */ ierr = DMLocalToGlobalBegin(da,copy,INSERT_VALUES,global);CHKERRQ(ierr); ierr = DMLocalToGlobalEnd(da,copy,INSERT_VALUES,global);CHKERRQ(ierr); /* View Wave */ /* Set Up Display to Show Heat Graph */ #if defined(PETSC_USE_SOCKET_VIEWER) ierr = VecView(global,PETSC_VIEWER_SOCKET_WORLD);CHKERRQ(ierr); #endif } ierr = VecDestroy(©);CHKERRQ(ierr); ierr = VecDestroy(&local);CHKERRQ(ierr); ierr = VecDestroy(&global);CHKERRQ(ierr); ierr = DMDestroy(&da);CHKERRQ(ierr); ierr = PetscFinalize(); return 0; }
int main(int argc,char **argv) { PetscErrorCode ierr; PetscMPIInt rank,nproc; PetscInt rstart,rend,i,k,N,numPoints=1000000; PetscScalar dummy,result=0,h=1.0/numPoints,*xarray; Vec x,xend; PetscInitialize(&argc,&argv,(char *)0,help); ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr); ierr = MPI_Comm_size(PETSC_COMM_WORLD,&nproc);CHKERRQ(ierr); /* Create a parallel vector. Here we set up our x vector which will be given values below. The xend vector is a dummy vector to find the value of the elements at the endpoints for use in the trapezoid rule. */ ierr = VecCreate(PETSC_COMM_WORLD,&x);CHKERRQ(ierr); ierr = VecSetSizes(x,PETSC_DECIDE,numPoints);CHKERRQ(ierr); ierr = VecSetFromOptions(x);CHKERRQ(ierr); ierr = VecGetSize(x,&N);CHKERRQ(ierr); ierr = VecSet(x,result);CHKERRQ(ierr); ierr = VecDuplicate(x,&xend);CHKERRQ(ierr); result=0.5; if (rank == 0){ i=0; ierr = VecSetValues(xend,1,&i,&result,INSERT_VALUES);CHKERRQ(ierr); } else if (rank == nproc){ i=N-1; ierr = VecSetValues(xend,1,&i,&result,INSERT_VALUES);CHKERRQ(ierr); } /* Assemble vector, using the 2-step process: VecAssemblyBegin(), VecAssemblyEnd() Computations can be done while messages are in transition by placing code between these two statements. */ ierr = VecAssemblyBegin(xend);CHKERRQ(ierr); ierr = VecAssemblyEnd(xend);CHKERRQ(ierr); /* Set the x vector elements. i*h will return 0 for i=0 and 1 for i=N-1. The function evaluated (2x/(1+x^2)) is defined above. Each evaluation is put into the local array of the vector without message passing. */ ierr = VecGetOwnershipRange(x,&rstart,&rend);CHKERRQ(ierr); ierr = VecGetArray(x,&xarray);CHKERRQ(ierr); k = 0; for (i=rstart; i<rend; i++){ xarray[k] = i*h; xarray[k] = func(xarray[k]); k++; } ierr = VecRestoreArray(x,&xarray);CHKERRQ(ierr); /* Evaluates the integral. First the sum of all the points is taken. That result is multiplied by the step size for the trapezoid rule. Then half the value at each endpoint is subtracted, this is part of the composite trapezoid rule. */ ierr = VecSum(x,&result);CHKERRQ(ierr); result = result*h; ierr = VecDot(x,xend,&dummy);CHKERRQ(ierr); result = result-h*dummy; /* Return the value of the integral. */ ierr = PetscPrintf(PETSC_COMM_WORLD,"ln(2) is %G\n",result);CHKERRQ(ierr); ierr = VecDestroy(&x);CHKERRQ(ierr); ierr = VecDestroy(&xend);CHKERRQ(ierr); ierr = PetscFinalize(); return 0; }
int main(int argc,char **args) { const ptrdiff_t N0=2056,N1=2056; fftw_plan bplan,fplan; fftw_complex *out; double *in1,*in2; ptrdiff_t alloc_local,local_n0,local_0_start; ptrdiff_t local_n1,local_1_start; PetscInt i,j; PetscMPIInt size,rank; int n,N,N_factor,NM; PetscScalar one=2.0,zero=0.5; PetscScalar two=4.0,three=8.0,four=16.0; PetscScalar a,*x_arr,*y_arr,*z_arr,enorm; Vec fin,fout,fout1; Vec ini,final; PetscRandom rnd; PetscErrorCode ierr; PetscInt *indx3,tempindx,low,*indx4,tempindx1; ierr = PetscInitialize(&argc,&args,(char*)0,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); ierr = PetscRandomCreate(PETSC_COMM_WORLD,&rnd);CHKERRQ(ierr); alloc_local = fftw_mpi_local_size_2d_transposed(N0,N1/2+1,PETSC_COMM_WORLD,&local_n0,&local_0_start,&local_n1,&local_1_start); #if defined(DEBUGGING) printf("The value alloc_local is %ld from process %d\n",alloc_local,rank); printf("The value local_n0 is %ld from process %d\n",local_n0,rank); printf("The value local_0_start is %ld from process %d\n",local_0_start,rank); /* printf("The value local_n1 is %ld from process %d\n",local_n1,rank); */ /* printf("The value local_1_start is %ld from process %d\n",local_1_start,rank); */ /* printf("The value local_n0 is %ld from process %d\n",local_n0,rank); */ #endif /* Allocate space for input and output arrays */ in1=(double*)fftw_malloc(sizeof(double)*alloc_local*2); in2=(double*)fftw_malloc(sizeof(double)*alloc_local*2); out=(fftw_complex*)fftw_malloc(sizeof(fftw_complex)*alloc_local); N = 2*N0*(N1/2+1); N_factor = N0*N1; n = 2*local_n0*(N1/2+1); /* printf("The value N is %d from process %d\n",N,rank); */ /* printf("The value n is %d from process %d\n",n,rank); */ /* printf("The value n1 is %d from process %d\n",n1,rank);*/ /* Creating data vector and accompanying array with VeccreateMPIWithArray */ ierr = VecCreateMPIWithArray(PETSC_COMM_WORLD,1,n,N,(PetscScalar*)in1,&fin);CHKERRQ(ierr); ierr = VecCreateMPIWithArray(PETSC_COMM_WORLD,1,n,N,(PetscScalar*)out,&fout);CHKERRQ(ierr); ierr = VecCreateMPIWithArray(PETSC_COMM_WORLD,1,n,N,(PetscScalar*)in2,&fout1);CHKERRQ(ierr); /* Set the vector with random data */ ierr = VecSet(fin,zero);CHKERRQ(ierr); /* for (i=0;i<N0*N1;i++) */ /* { */ /* VecSetValues(fin,1,&i,&one,INSERT_VALUES); */ /* } */ /* VecSet(fin,one); */ i =0; ierr = VecSetValues(fin,1,&i,&one,INSERT_VALUES);CHKERRQ(ierr); i =1; ierr = VecSetValues(fin,1,&i,&two,INSERT_VALUES);CHKERRQ(ierr); i =4; ierr = VecSetValues(fin,1,&i,&three,INSERT_VALUES);CHKERRQ(ierr); i =5; ierr = VecSetValues(fin,1,&i,&four,INSERT_VALUES);CHKERRQ(ierr); ierr = VecAssemblyBegin(fin);CHKERRQ(ierr); ierr = VecAssemblyEnd(fin);CHKERRQ(ierr); ierr = VecSet(fout,zero);CHKERRQ(ierr); ierr = VecSet(fout1,zero);CHKERRQ(ierr); /* Get the meaningful portion of array */ ierr = VecGetArray(fin,&x_arr);CHKERRQ(ierr); ierr = VecGetArray(fout1,&z_arr);CHKERRQ(ierr); ierr = VecGetArray(fout,&y_arr);CHKERRQ(ierr); fplan=fftw_mpi_plan_dft_r2c_2d(N0,N1,(double*)x_arr,(fftw_complex*)y_arr,PETSC_COMM_WORLD,FFTW_ESTIMATE); bplan=fftw_mpi_plan_dft_c2r_2d(N0,N1,(fftw_complex*)y_arr,(double*)z_arr,PETSC_COMM_WORLD,FFTW_ESTIMATE); fftw_execute(fplan); fftw_execute(bplan); ierr = VecRestoreArray(fin,&x_arr); ierr = VecRestoreArray(fout1,&z_arr); ierr = VecRestoreArray(fout,&y_arr); /* VecView(fin,PETSC_VIEWER_STDOUT_WORLD); */ ierr = VecCreate(PETSC_COMM_WORLD,&ini);CHKERRQ(ierr); ierr = VecCreate(PETSC_COMM_WORLD,&final);CHKERRQ(ierr); ierr = VecSetSizes(ini,local_n0*N1,N0*N1);CHKERRQ(ierr); ierr = VecSetSizes(final,local_n0*N1,N0*N1);CHKERRQ(ierr); ierr = VecSetFromOptions(ini);CHKERRQ(ierr); ierr = VecSetFromOptions(final);CHKERRQ(ierr); if (N1%2==0) { NM = N1+2; } else { NM = N1+1; } /*printf("The Value of NM is %d",NM); */ ierr = VecGetOwnershipRange(fin,&low,NULL); /*printf("The local index is %d from %d\n",low,rank); */ ierr = PetscMalloc1(local_n0*N1,&indx3); ierr = PetscMalloc1(local_n0*N1,&indx4); for (i=0;i<local_n0;i++) { for (j=0;j<N1;j++) { tempindx = i*N1 + j; tempindx1 = i*NM + j; indx3[tempindx]=local_0_start*N1+tempindx; indx4[tempindx]=low+tempindx1; /* printf("index3 %d from proc %d is \n",indx3[tempindx],rank); */ /* printf("index4 %d from proc %d is \n",indx4[tempindx],rank); */ } } ierr = PetscMalloc2(local_n0*N1,&x_arr,local_n0*N1,&y_arr);CHKERRQ(ierr); /* arr must be allocated for VecGetValues() */ ierr = VecGetValues(fin,local_n0*N1,indx4,(PetscScalar*)x_arr);CHKERRQ(ierr); ierr = VecSetValues(ini,local_n0*N1,indx3,x_arr,INSERT_VALUES);CHKERRQ(ierr); ierr = VecAssemblyBegin(ini);CHKERRQ(ierr); ierr = VecAssemblyEnd(ini);CHKERRQ(ierr); ierr = VecGetValues(fout1,local_n0*N1,indx4,y_arr); ierr = VecSetValues(final,local_n0*N1,indx3,y_arr,INSERT_VALUES); ierr = VecAssemblyBegin(final); ierr = VecAssemblyEnd(final); ierr = PetscFree2(x_arr,y_arr);CHKERRQ(ierr); /* VecScatter vecscat; IS indx1,indx2; for (i=0;i<N0;i++) { indx = i*NM; ISCreateStride(PETSC_COMM_WORLD,N1,indx,1,&indx1); indx = i*N1; ISCreateStride(PETSC_COMM_WORLD,N1,indx,1,&indx2); VecScatterCreate(fin,indx1,ini,indx2,&vecscat); VecScatterBegin(vecscat,fin,ini,INSERT_VALUES,SCATTER_FORWARD); VecScatterEnd(vecscat,fin,ini,INSERT_VALUES,SCATTER_FORWARD); VecScatterBegin(vecscat,fout1,final,INSERT_VALUES,SCATTER_FORWARD); VecScatterEnd(vecscat,fout1,final,INSERT_VALUES,SCATTER_FORWARD); } */ a = 1.0/(PetscReal)N_factor; ierr = VecScale(fout1,a);CHKERRQ(ierr); ierr = VecScale(final,a);CHKERRQ(ierr); /* VecView(ini,PETSC_VIEWER_STDOUT_WORLD); */ /* VecView(final,PETSC_VIEWER_STDOUT_WORLD); */ ierr = VecAXPY(final,-1.0,ini);CHKERRQ(ierr); ierr = VecNorm(final,NORM_1,&enorm);CHKERRQ(ierr); if (enorm > 1.e-10) { ierr = PetscPrintf(PETSC_COMM_WORLD," Error norm of |x - z| = %e\n",enorm);CHKERRQ(ierr); } /* Execute fftw with function fftw_execute and destory it after execution */ fftw_destroy_plan(fplan); fftw_destroy_plan(bplan); fftw_free(in1); ierr = VecDestroy(&fin);CHKERRQ(ierr); fftw_free(out); ierr = VecDestroy(&fout);CHKERRQ(ierr); fftw_free(in2); ierr = VecDestroy(&fout1);CHKERRQ(ierr); ierr = VecDestroy(&ini);CHKERRQ(ierr); ierr = VecDestroy(&final);CHKERRQ(ierr); ierr = PetscRandomDestroy(&rnd);CHKERRQ(ierr); ierr = PetscFree(indx3);CHKERRQ(ierr); ierr = PetscFree(indx4);CHKERRQ(ierr); ierr = PetscFinalize(); return ierr; }
int main(int argc, char **argv) { PetscErrorCode ierr; Vec x,yp1,yp2,yp3,yp4,ym1,ym2,ym3,ym4; PetscReal *values; PetscViewer viewer_in,viewer_outp1,viewer_outp2,viewer_outp3,viewer_outp4; PetscViewer viewer_outm1,viewer_outm2,viewer_outm3,viewer_outm4; DM daf,dac1,dac2,dac3,dac4,daf1,daf2,daf3,daf4; Vec scaling_p1,scaling_p2,scaling_p3,scaling_p4; Mat interp_p1,interp_p2,interp_p3,interp_p4,interp_m1,interp_m2,interp_m3,interp_m4; ierr = PetscInitialize(&argc,&argv, (char*)0, help);if (ierr) return ierr; ierr = DMDACreate2d(PETSC_COMM_WORLD,DM_BOUNDARY_PERIODIC,DM_BOUNDARY_PERIODIC,DMDA_STENCIL_BOX,1024,1024,PETSC_DECIDE,PETSC_DECIDE,1,1,NULL,NULL,&daf);CHKERRQ(ierr); ierr = DMSetFromOptions(daf);CHKERRQ(ierr); ierr = DMSetUp(daf);CHKERRQ(ierr); ierr = DMCreateGlobalVector(daf,&x);CHKERRQ(ierr); ierr = VecGetArray(x,&values);CHKERRQ(ierr); ierr = DMCoarsen(daf,PETSC_COMM_WORLD,&dac1);CHKERRQ(ierr); ierr = DMCoarsen(dac1,PETSC_COMM_WORLD,&dac2);CHKERRQ(ierr); ierr = DMCoarsen(dac2,PETSC_COMM_WORLD,&dac3);CHKERRQ(ierr); ierr = DMCoarsen(dac3,PETSC_COMM_WORLD,&dac4);CHKERRQ(ierr); ierr = DMRefine(daf,PETSC_COMM_WORLD,&daf1);CHKERRQ(ierr); ierr = DMRefine(daf1,PETSC_COMM_WORLD,&daf2);CHKERRQ(ierr); ierr = DMRefine(daf2,PETSC_COMM_WORLD,&daf3);CHKERRQ(ierr); ierr = DMRefine(daf3,PETSC_COMM_WORLD,&daf4);CHKERRQ(ierr); ierr = DMCreateGlobalVector(dac1,&yp1);CHKERRQ(ierr); ierr = DMCreateGlobalVector(dac2,&yp2);CHKERRQ(ierr); ierr = DMCreateGlobalVector(dac3,&yp3);CHKERRQ(ierr); ierr = DMCreateGlobalVector(dac4,&yp4);CHKERRQ(ierr); ierr = DMCreateGlobalVector(daf1,&ym1);CHKERRQ(ierr); ierr = DMCreateGlobalVector(daf2,&ym2);CHKERRQ(ierr); ierr = DMCreateGlobalVector(daf3,&ym3);CHKERRQ(ierr); ierr = DMCreateGlobalVector(daf4,&ym4);CHKERRQ(ierr); ierr = DMCreateInterpolation(dac1,daf,&interp_p1,&scaling_p1);CHKERRQ(ierr); ierr = DMCreateInterpolation(dac2,dac1,&interp_p2,&scaling_p2);CHKERRQ(ierr); ierr = DMCreateInterpolation(dac3,dac2,&interp_p3,&scaling_p3);CHKERRQ(ierr); ierr = DMCreateInterpolation(dac4,dac3,&interp_p4,&scaling_p4);CHKERRQ(ierr); ierr = DMCreateInterpolation(daf,daf1,&interp_m1,NULL);CHKERRQ(ierr); ierr = DMCreateInterpolation(daf1,daf2,&interp_m2,NULL);CHKERRQ(ierr); ierr = DMCreateInterpolation(daf2,daf3,&interp_m3,NULL);CHKERRQ(ierr); ierr = DMCreateInterpolation(daf3,daf4,&interp_m4,NULL);CHKERRQ(ierr); ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"phi",FILE_MODE_READ,&viewer_in);CHKERRQ(ierr); ierr = PetscViewerBinaryRead(viewer_in,values,1048576,NULL,PETSC_DOUBLE);CHKERRQ(ierr); ierr = MatRestrict(interp_p1,x,yp1);CHKERRQ(ierr); ierr = VecPointwiseMult(yp1,yp1,scaling_p1);CHKERRQ(ierr); ierr = MatRestrict(interp_p2,yp1,yp2);CHKERRQ(ierr); ierr = VecPointwiseMult(yp2,yp2,scaling_p2);CHKERRQ(ierr); ierr = MatRestrict(interp_p3,yp2,yp3);CHKERRQ(ierr); ierr = VecPointwiseMult(yp3,yp3,scaling_p3);CHKERRQ(ierr); ierr = MatRestrict(interp_p4,yp3,yp4);CHKERRQ(ierr); ierr = VecPointwiseMult(yp4,yp4,scaling_p4);CHKERRQ(ierr); ierr = MatRestrict(interp_m1,x,ym1);CHKERRQ(ierr); ierr = MatRestrict(interp_m2,ym1,ym2);CHKERRQ(ierr); ierr = MatRestrict(interp_m3,ym2,ym3);CHKERRQ(ierr); ierr = MatRestrict(interp_m4,ym3,ym4);CHKERRQ(ierr); ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"phi1",FILE_MODE_WRITE,&viewer_outp1);CHKERRQ(ierr); ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"phi2",FILE_MODE_WRITE,&viewer_outp2);CHKERRQ(ierr); ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"phi3",FILE_MODE_WRITE,&viewer_outp3);CHKERRQ(ierr); ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"phi4",FILE_MODE_WRITE,&viewer_outp4);CHKERRQ(ierr); ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"phim1",FILE_MODE_WRITE,&viewer_outm1);CHKERRQ(ierr); ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"phim2",FILE_MODE_WRITE,&viewer_outm2);CHKERRQ(ierr); ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"phim3",FILE_MODE_WRITE,&viewer_outm3);CHKERRQ(ierr); ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"phim4",FILE_MODE_WRITE,&viewer_outm4);CHKERRQ(ierr); ierr = VecView(yp1,viewer_outp1);CHKERRQ(ierr); ierr = VecView(x,viewer_outp1);CHKERRQ(ierr); ierr = VecView(yp2,viewer_outp2);CHKERRQ(ierr); ierr = VecView(yp3,viewer_outp3);CHKERRQ(ierr); ierr = VecView(yp4,viewer_outp4);CHKERRQ(ierr); ierr = VecView(ym1,viewer_outm1);CHKERRQ(ierr); ierr = VecView(ym2,viewer_outm2);CHKERRQ(ierr); ierr = VecView(ym3,viewer_outm3);CHKERRQ(ierr); ierr = VecView(ym4,viewer_outm4);CHKERRQ(ierr); ierr = PetscViewerDestroy(&viewer_in);CHKERRQ(ierr); ierr = PetscViewerDestroy(&viewer_outp1);CHKERRQ(ierr); ierr = PetscViewerDestroy(&viewer_outp2);CHKERRQ(ierr); ierr = PetscViewerDestroy(&viewer_outp3);CHKERRQ(ierr); ierr = PetscViewerDestroy(&viewer_outp4);CHKERRQ(ierr); ierr = PetscViewerDestroy(&viewer_outm1);CHKERRQ(ierr); ierr = PetscViewerDestroy(&viewer_outm2);CHKERRQ(ierr); ierr = PetscViewerDestroy(&viewer_outm3);CHKERRQ(ierr); ierr = PetscViewerDestroy(&viewer_outm4);CHKERRQ(ierr); ierr = VecDestroy(&x);CHKERRQ(ierr); ierr = VecDestroy(&yp1);CHKERRQ(ierr); ierr = VecDestroy(&yp2);CHKERRQ(ierr); ierr = VecDestroy(&yp3);CHKERRQ(ierr); ierr = VecDestroy(&yp4);CHKERRQ(ierr); ierr = VecDestroy(&ym1);CHKERRQ(ierr); ierr = VecDestroy(&ym2);CHKERRQ(ierr); ierr = VecDestroy(&ym3);CHKERRQ(ierr); ierr = VecDestroy(&ym4);CHKERRQ(ierr); ierr = PetscFinalize(); return ierr; }
int main(int argc, char *argv[]) { PetscInitialize(&argc, &argv, NULL, help); // Get command line options. Options options; options.setOptions(); // Get mesh. Mesh *mesh = Mesh::factory(options); mesh->read(options); // Get model. ExodusModel model(options); model.initializeParallel(); // Get source. std::vector<Source*> sources = Source::factory(options); // Setup reference element. Square *reference_element = new Acoustic(options); mesh->setupGlobalDof(reference_element->NumberDofVertex(), reference_element->NumberDofEdge(), reference_element->NumberDofFace(), reference_element->NumberDofVolume(), reference_element->NumberDimensions()); mesh->registerFields(); // Clone a list of all local elements. std::vector<Square *> elements; for (auto i = 0; i < mesh->NumberElementsLocal(); i++) { elements.push_back(reference_element->clone()); } // Now things that only local elements are allowed to do. int element_number = 0; for (auto &element: elements) { element->SetLocalElementNumber(element_number++); element->attachVertexCoordinates(mesh->DistributedMesh()); element->attachSource(sources); element->interpolateMaterialProperties(model); element->readOperators(); element->assembleMassMatrix(); element->scatterMassMatrix(mesh); } mesh->checkInMassMatrix(); mesh->setUpMovie(); double time = 0; double timestep = 1e-3; while (time < 2.0) { // Pull down fields from global dof. mesh->checkOutFields(); mesh->zeroFields(); // Compute element-wise terms. for (auto &element: elements) { element->SetTime(time); element->checkOutFields(mesh); element->computeStiffnessTerm(); element->computeSourceTerm(); element->computeSurfaceTerm(); element->checkInField(mesh); } // Sum fields back into global dof. mesh->checkInFieldsBegin(); mesh->checkInFieldsEnd(); // Invert mass matrix and take time step. mesh->applyInverseMassMatrix(); mesh->advanceField(); mesh->saveFrame(); time += timestep; if (!MPI::COMM_WORLD.Get_rank()) std::cout << time << std::endl; // break; } mesh->finalizeMovie(); PetscFinalize(); }
PetscInt main(PetscInt argc,char **args) { typedef enum {RANDOM, CONSTANT, TANH, NUM_FUNCS} FuncType; const char *funcNames[NUM_FUNCS] = {"random", "constant", "tanh"}; Mat A, AA; PetscMPIInt size; PetscInt N,i, stencil=1,dof=3; PetscInt dim[3] = {10,10,10}, ndim = 3; Vec coords,x,y,z,xx, yy, zz; Vec xxsplit[DOF], yysplit[DOF], zzsplit[DOF]; PetscReal h[3]; PetscScalar s; PetscRandom rdm; PetscReal norm, enorm; PetscInt func; FuncType function = TANH; DM da, da1, coordsda; PetscBool view_x = PETSC_FALSE, view_y = PETSC_FALSE, view_z = PETSC_FALSE; PetscErrorCode ierr; ierr = PetscInitialize(&argc,&args,(char *)0,help);CHKERRQ(ierr); #if !defined(PETSC_USE_COMPLEX) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_SUP, "This example requires complex numbers"); #endif ierr = MPI_Comm_size(PETSC_COMM_WORLD, &size);CHKERRQ(ierr); if (size != 1) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_SUP, "This is a uniprocessor example only!"); ierr = PetscOptionsBegin(PETSC_COMM_WORLD, PETSC_NULL, "USFFT Options", "ex27");CHKERRQ(ierr); ierr = PetscOptionsEList("-function", "Function type", "ex27", funcNames, NUM_FUNCS, funcNames[function], &func, PETSC_NULL);CHKERRQ(ierr); function = (FuncType) func; ierr = PetscOptionsEnd();CHKERRQ(ierr); ierr = PetscOptionsGetBool(PETSC_NULL,"-view_x",&view_x,PETSC_NULL);CHKERRQ(ierr); ierr = PetscOptionsGetBool(PETSC_NULL,"-view_y",&view_y,PETSC_NULL);CHKERRQ(ierr); ierr = PetscOptionsGetBool(PETSC_NULL,"-view_z",&view_z,PETSC_NULL);CHKERRQ(ierr); ierr = PetscOptionsGetIntArray(PETSC_NULL,"-dim",dim,&ndim,PETSC_NULL);CHKERRQ(ierr); // DMDA with the correct fiber dimension ierr = DMDACreate3d(PETSC_COMM_SELF,DMDA_BOUNDARY_NONE,DMDA_BOUNDARY_NONE,DMDA_BOUNDARY_NONE,DMDA_STENCIL_STAR, dim[0], dim[1], dim[2], PETSC_DECIDE, PETSC_DECIDE, PETSC_DECIDE, dof, stencil, PETSC_NULL, PETSC_NULL, PETSC_NULL, &da); CHKERRQ(ierr); // DMDA with fiber dimension 1 for split fields ierr = DMDACreate3d(PETSC_COMM_SELF,DMDA_BOUNDARY_NONE,DMDA_BOUNDARY_NONE,DMDA_BOUNDARY_NONE,DMDA_STENCIL_STAR, dim[0], dim[1], dim[2], PETSC_DECIDE, PETSC_DECIDE, PETSC_DECIDE, 1, stencil, PETSC_NULL, PETSC_NULL, PETSC_NULL, &da1); CHKERRQ(ierr); // Coordinates ierr = DMDAGetCoordinateDA(da, &coordsda); ierr = DMGetGlobalVector(coordsda, &coords);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) coords, "Grid coordinates");CHKERRQ(ierr); for(i = 0, N = 1; i < 3; i++) { h[i] = 1.0/dim[i]; PetscScalar *a; ierr = VecGetArray(coords, &a);CHKERRQ(ierr); PetscInt j,k,n = 0; for(i = 0; i < 3; ++i) { for(j = 0; j < dim[i]; ++j){ for(k = 0; k < 3; ++k) { a[n] = j*h[i]; // coordinate along the j-th point in the i-th dimension ++n; } } } ierr = VecRestoreArray(coords, &a);CHKERRQ(ierr); } ierr = DMDASetCoordinates(da, coords);CHKERRQ(ierr); ierr = VecDestroy(&coords);CHKERRQ(ierr); // Work vectors ierr = DMGetGlobalVector(da, &x);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) x, "Real space vector");CHKERRQ(ierr); ierr = DMGetGlobalVector(da, &xx);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) xx, "Real space vector");CHKERRQ(ierr); ierr = DMGetGlobalVector(da, &y);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) y, "USFFT frequency space vector");CHKERRQ(ierr); ierr = DMGetGlobalVector(da, &yy);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) yy, "FFTW frequency space vector");CHKERRQ(ierr); ierr = DMGetGlobalVector(da, &z);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) z, "USFFT reconstructed vector");CHKERRQ(ierr); ierr = DMGetGlobalVector(da, &zz);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) zz, "FFTW reconstructed vector");CHKERRQ(ierr); // Split vectors for FFTW for(int ii = 0; ii < 3; ++ii) { ierr = DMGetGlobalVector(da1, &xxsplit[ii]);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) xxsplit[ii], "Real space split vector");CHKERRQ(ierr); ierr = DMGetGlobalVector(da1, &yysplit[ii]);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) yysplit[ii], "FFTW frequency space split vector");CHKERRQ(ierr); ierr = DMGetGlobalVector(da1, &zzsplit[ii]);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) zzsplit[ii], "FFTW reconstructed split vector");CHKERRQ(ierr); } ierr = PetscPrintf(PETSC_COMM_SELF, "%3-D: USFFT on vector of ");CHKERRQ(ierr); for(i = 0, N = 1; i < 3; i++) { ierr = PetscPrintf(PETSC_COMM_SELF, "dim[%d] = %d ",i,dim[i]);CHKERRQ(ierr); N *= dim[i]; } ierr = PetscPrintf(PETSC_COMM_SELF, "; total size %d \n",N);CHKERRQ(ierr); if (function == RANDOM) { ierr = PetscRandomCreate(PETSC_COMM_SELF, &rdm);CHKERRQ(ierr); ierr = PetscRandomSetFromOptions(rdm);CHKERRQ(ierr); ierr = VecSetRandom(x, rdm);CHKERRQ(ierr); ierr = PetscRandomDestroy(&rdm);CHKERRQ(ierr); } else if (function == CONSTANT) { ierr = VecSet(x, 1.0);CHKERRQ(ierr); } else if (function == TANH) { PetscScalar *a; ierr = VecGetArray(x, &a);CHKERRQ(ierr); PetscInt j,k = 0; for(i = 0; i < 3; ++i) { for(j = 0; j < dim[i]; ++j) { a[k] = tanh((j - dim[i]/2.0)*(10.0/dim[i])); ++k; } } ierr = VecRestoreArray(x, &a);CHKERRQ(ierr); } if(view_x) { ierr = VecView(x, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); } ierr = VecCopy(x,xx);CHKERRQ(ierr); // Split xx ierr = VecStrideGatherAll(xx,xxsplit, INSERT_VALUES);CHKERRQ(ierr); //YES! 'Gather' means 'split' (or maybe 'scatter'?)! ierr = VecNorm(x,NORM_2,&norm);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_SELF, "|x|_2 = %g\n",norm);CHKERRQ(ierr); /* create USFFT object */ ierr = MatCreateSeqUSFFT(da,da,&A);CHKERRQ(ierr); /* create FFTW object */ ierr = MatCreateSeqFFTW(PETSC_COMM_SELF,3,dim,&AA);CHKERRQ(ierr); /* apply USFFT and FFTW FORWARD "preemptively", so the fftw_plans can be reused on different vectors */ ierr = MatMult(A,x,z);CHKERRQ(ierr); for(int ii = 0; ii < 3; ++ii) { ierr = MatMult(AA,xxsplit[ii],zzsplit[ii]);CHKERRQ(ierr); } // Now apply USFFT and FFTW forward several (3) times for (i=0; i<3; ++i){ ierr = MatMult(A,x,y);CHKERRQ(ierr); for(int ii = 0; ii < 3; ++ii) { ierr = MatMult(AA,xxsplit[ii],yysplit[ii]);CHKERRQ(ierr); } ierr = MatMultTranspose(A,y,z);CHKERRQ(ierr); for(int ii = 0; ii < 3; ++ii) { ierr = MatMult(AA,yysplit[ii],zzsplit[ii]);CHKERRQ(ierr); } } // Unsplit yy ierr = VecStrideScatterAll(yysplit, yy, INSERT_VALUES);CHKERRQ(ierr); //YES! 'Scatter' means 'collect' (or maybe 'gather'?)! // Unsplit zz ierr = VecStrideScatterAll(zzsplit, zz, INSERT_VALUES);CHKERRQ(ierr); //YES! 'Scatter' means 'collect' (or maybe 'gather'?)! if(view_y) { ierr = PetscPrintf(PETSC_COMM_WORLD, "y = \n");CHKERRQ(ierr); ierr = VecView(y, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "yy = \n");CHKERRQ(ierr); ierr = VecView(yy, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); } if(view_z) { ierr = PetscPrintf(PETSC_COMM_WORLD, "z = \n");CHKERRQ(ierr); ierr = VecView(z, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "zz = \n");CHKERRQ(ierr); ierr = VecView(zz, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); } /* compare x and z. USFFT computes an unnormalized DFT, thus z = N*x */ s = 1.0/(PetscReal)N; ierr = VecScale(z,s);CHKERRQ(ierr); ierr = VecAXPY(x,-1.0,z);CHKERRQ(ierr); ierr = VecNorm(x,NORM_1,&enorm);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_SELF, "|x-z| = %g\n",enorm);CHKERRQ(ierr); /* compare xx and zz. FFTW computes an unnormalized DFT, thus zz = N*x */ s = 1.0/(PetscReal)N; ierr = VecScale(zz,s);CHKERRQ(ierr); ierr = VecAXPY(xx,-1.0,zz);CHKERRQ(ierr); ierr = VecNorm(xx,NORM_1,&enorm);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_SELF, "|xx-zz| = %g\n",enorm);CHKERRQ(ierr); /* compare y and yy: USFFT and FFTW results*/ ierr = VecNorm(y,NORM_2,&norm);CHKERRQ(ierr); ierr = VecAXPY(y,-1.0,yy);CHKERRQ(ierr); ierr = VecNorm(y,NORM_1,&enorm);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_SELF, "|y|_2 = %g\n",norm);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_SELF, "|y-yy| = %g\n",enorm);CHKERRQ(ierr); /* compare z and zz: USFFT and FFTW results*/ ierr = VecNorm(z,NORM_2,&norm);CHKERRQ(ierr); ierr = VecAXPY(z,-1.0,zz);CHKERRQ(ierr); ierr = VecNorm(z,NORM_1,&enorm);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_SELF, "|z|_2 = %g\n",norm);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_SELF, "|z-zz| = %g\n",enorm);CHKERRQ(ierr); /* free spaces */ ierr = DMRestoreGlobalVector(da,&x);CHKERRQ(ierr); ierr = DMRestoreGlobalVector(da,&xx);CHKERRQ(ierr); ierr = DMRestoreGlobalVector(da,&y);CHKERRQ(ierr); ierr = DMRestoreGlobalVector(da,&yy);CHKERRQ(ierr); ierr = DMRestoreGlobalVector(da,&z);CHKERRQ(ierr); ierr = DMRestoreGlobalVector(da,&zz);CHKERRQ(ierr); ierr = PetscFinalize(); return 0; }
int main(int argc, char* argv[]){ PetscErrorCode ierr; ierr = PetscInitialize(&argc,&argv,NULL,NULL); CHKERRQ(ierr); std::map<std::string,bool> commandline; observeCommand(commandline,"-readLocally"); observeCommand(commandline,"-mshBinary"); observeCommand(commandline,"-outBinary"); observeCommand(commandline,"-cgns"); if(!parseCommand(commandline)){ ierr = PetscFinalize(); CHKERRQ(ierr); return 0; } /****************************************** * START UP ******************************************/ NavierStokesSolver* nsSolver = new NavierStokesSolver; nsSolver->initSolverParam(); //root only : read param.in and check nsSolver->readCommand(commandline); nsSolver->broadcastSolverParam(); //collective fetch param from root int* elementBuffer = NULL; double* vertexBuffer = NULL; int* interfaceBuffer = NULL; if(!commandline["-readLocally"]){ //transfer geometry through MPI nsSolver->readAndPartition(getCommand(commandline,"-mshBinary"), getCommand(commandline,"-cgns")); //root only : read msh and partition nsSolver->broadcastPartitionInfo(); nsSolver->scatterGridFile(&elementBuffer,&vertexBuffer,&interfaceBuffer);//collective }else{ //read geometry locally } //parse the gridfile as original, buffer freeed, boundInfo got; nsSolver->ReadGridFile(elementBuffer,vertexBuffer,interfaceBuffer); nsSolver->dataPartition->initPetsc(); //build faces. same sequence as Original; nsSolver->CreateFaces(); nsSolver->CellFaceInfo(); nsSolver->CheckAndAllocate(); nsSolver->InitFlowField(); /****************************************** * NS_solve * MAIN CFD ******************************************/ nsSolver->NSSolve(); /****************************************** * Post Process * VTK, Tecplot, etc. ******************************************/ MPI_Barrier(MPI_COMM_WORLD); nsSolver->dataPartition->deinit(); delete nsSolver; //PetscPrintf(MPI_COMM_WORLD,"done\n"); PetscPrintf(MPI_COMM_WORLD,"done\n"); MPI_Barrier(MPI_COMM_WORLD); ierr = PetscFinalize(); CHKERRQ(ierr); return 0; }
int main(int argc, char **args) { int res = ERR_SUCCESS; #ifdef WITH_PETSC PetscInitialize(&argc, &args, (char *) PETSC_NULL, PETSC_NULL); #endif if (argc < 2) error("Not enough parameters."); printf("* Loading mesh '%s'\n", args[1]); Mesh mesh1; H3DReader mesh_loader; if (!mesh_loader.load(args[1], &mesh1)) error("Loading mesh file '%s'\n", args[1]); #if defined RHS2 Ord3 order(P_INIT_X, P_INIT_Y, P_INIT_Z); printf(" - Setting uniform order to (%d, %d, %d)\n", order.x, order.y, order.z); // Create an H1 space with default shapeset. printf("* Setting the space up\n"); H1Space space(&mesh1, bc_types, essential_bc_values, order); int ndofs = space.assign_dofs(); printf(" - Number of DOFs: %d\n", ndofs); printf("* Calculating a solution\n"); // duplicate the mesh Mesh mesh2; mesh2.copy(mesh1); // do some changes mesh2.refine_all_elements(H3D_H3D_H3D_REFT_HEX_XYZ); mesh2.refine_all_elements(H3D_H3D_H3D_REFT_HEX_XYZ); Solution fsln(&mesh2); fsln.set_const(-6.0); #else // duplicate the mesh Mesh mesh2; mesh2.copy(mesh1); Mesh mesh3; mesh3.copy(mesh1); // change meshes mesh1.refine_all_elements(H3D_REFT_HEX_X); mesh2.refine_all_elements(H3D_REFT_HEX_Y); mesh3.refine_all_elements(H3D_REFT_HEX_Z); printf("* Setup spaces\n"); Ord3 o1(2, 2, 2); printf(" - Setting uniform order to (%d, %d, %d)\n", o1.x, o1.y, o1.z); H1Space space1(&mesh1, bc_types_1, essential_bc_values_1, o1); Ord3 o2(2, 2, 2); printf(" - Setting uniform order to (%d, %d, %d)\n", o2.x, o2.y, o2.z); H1Space space2(&mesh2, bc_types_2, essential_bc_values_2, o2); Ord3 o3(1, 1, 1); printf(" - Setting uniform order to (%d, %d, %d)\n", o3.x, o3.y, o3.z); H1Space space3(&mesh3, bc_types_3, essential_bc_values_3, o3); int ndofs = 0; ndofs += space1.assign_dofs(); ndofs += space2.assign_dofs(ndofs); ndofs += space3.assign_dofs(ndofs); printf(" - Number of DOFs: %d\n", ndofs); #endif #if defined WITH_UMFPACK MatrixSolverType matrix_solver = SOLVER_UMFPACK; #elif defined WITH_PETSC MatrixSolverType matrix_solver = SOLVER_PETSC; #elif defined WITH_MUMPS MatrixSolverType matrix_solver = SOLVER_MUMPS; #endif #ifdef RHS2 WeakForm wf; wf.add_matrix_form(bilinear_form<double, scalar>, bilinear_form<Ord, Ord>, HERMES_SYM); wf.add_vector_form(linear_form<double, scalar>, linear_form<Ord, Ord>, HERMES_ANY_INT, &fsln); // Initialize discrete problem. bool is_linear = true; DiscreteProblem dp(&wf, &space, is_linear); #elif defined SYS3 WeakForm wf(3); wf.add_matrix_form(0, 0, biform_1_1<double, scalar>, biform_1_1<Ord, Ord>, HERMES_SYM); wf.add_matrix_form(0, 1, biform_1_2<double, scalar>, biform_1_2<Ord, Ord>, HERMES_NONSYM); wf.add_vector_form(0, liform_1<double, scalar>, liform_1<Ord, Ord>); wf.add_matrix_form(1, 1, biform_2_2<double, scalar>, biform_2_2<Ord, Ord>, HERMES_SYM); wf.add_matrix_form(1, 2, biform_2_3<double, scalar>, biform_2_3<Ord, Ord>, HERMES_NONSYM); wf.add_vector_form(1, liform_2<double, scalar>, liform_2<Ord, Ord>); wf.add_matrix_form(2, 2, biform_3_3<double, scalar>, biform_3_3<Ord, Ord>, HERMES_SYM); // Initialize discrete problem. bool is_linear = true; DiscreteProblem dp(&wf, Hermes::vector<Space *>(&space1, &space2, &space3), is_linear); #endif // Time measurement. TimePeriod cpu_time; cpu_time.tick(); // Set up the solver, matrix, and rhs according to the solver selection. SparseMatrix* matrix = create_matrix(matrix_solver); Vector* rhs = create_vector(matrix_solver); Solver* solver = create_linear_solver(matrix_solver, matrix, rhs); // Initialize the preconditioner in the case of SOLVER_AZTECOO. if (matrix_solver == SOLVER_AZTECOO) { ((AztecOOSolver*) solver)->set_solver(iterative_method); ((AztecOOSolver*) solver)->set_precond(preconditioner); // Using default iteration parameters (see solver/aztecoo.h). } // Assemble stiffness matrix and load vector. dp.assemble(matrix, rhs); // Solve the linear system. If successful, obtain the solution. info("Solving the linear problem."); bool solved = solver->solve(); // Time measurement. cpu_time.tick(); // Print timing information. info("Solution and mesh with polynomial orders saved. Total running time: %g s", cpu_time.accumulated()); // Time measurement. TimePeriod sln_time; sln_time.tick(); if (solved) { #ifdef RHS2 // Solve the linear system. If successful, obtain the solution. info("Solving the linear problem."); Solution sln(&mesh1); Solution::vector_to_solution(solver->get_solution(), &space, &sln); // Set exact solution. ExactSolution ex_sln(&mesh1, exact_solution); // Norm. double h1_sln_norm = h1_norm(&sln); double h1_err_norm = h1_error(&sln, &ex_sln); printf(" - H1 solution norm: % le\n", h1_sln_norm); printf(" - H1 error norm: % le\n", h1_err_norm); double l2_sln_norm = l2_norm(&sln); double l2_err_norm = l2_error(&sln, &ex_sln); printf(" - L2 solution norm: % le\n", l2_sln_norm); printf(" - L2 error norm: % le\n", l2_err_norm); if (h1_err_norm > EPS || l2_err_norm > EPS) { // Calculated solution is not enough precise. res = ERR_FAILURE; } #elif defined SYS3 // Solution 1. Solution sln1(&mesh1); Solution sln2(&mesh2); Solution sln3(&mesh3); Solution::vector_to_solution(solver->get_solution(), &space1, &sln1); Solution::vector_to_solution(solver->get_solution(), &space2, &sln2); Solution::vector_to_solution(solver->get_solution(), &space3, &sln3); ExactSolution esln1(&mesh1, exact_sln_fn_1); ExactSolution esln2(&mesh2, exact_sln_fn_2); ExactSolution esln3(&mesh3, exact_sln_fn_3); // Norm. double h1_err_norm1 = h1_error(&sln1, &esln1); double h1_err_norm2 = h1_error(&sln2, &esln2); double h1_err_norm3 = h1_error(&sln3, &esln3); double l2_err_norm1 = l2_error(&sln1, &esln1); double l2_err_norm2 = l2_error(&sln2, &esln2); double l2_err_norm3 = l2_error(&sln3, &esln3); printf(" - H1 error norm: % le\n", h1_err_norm1); printf(" - L2 error norm: % le\n", l2_err_norm1); if (h1_err_norm1 > EPS || l2_err_norm1 > EPS) { // Calculated solution is not enough precise. res = ERR_FAILURE; } printf(" - H1 error norm: % le\n", h1_err_norm2); printf(" - L2 error norm: % le\n", l2_err_norm2); if (h1_err_norm2 > EPS || l2_err_norm2 > EPS) { // Calculated solution is not enough precise. res = ERR_FAILURE; } printf(" - H1 error norm: % le\n", h1_err_norm3); printf(" - L2 error norm: % le\n", l2_err_norm3); if (h1_err_norm3 > EPS || l2_err_norm3 > EPS) { // Calculated solution is not enough precise. res = ERR_FAILURE; } #endif #ifdef RHS2 out_fn_vtk(&sln, "solution"); #elif defined SYS3 out_fn_vtk(&sln1, "sln1"); out_fn_vtk(&sln2, "sln2"); out_fn_vtk(&sln3, "sln3"); #endif } else res = ERR_FAILURE; // Print timing information. info("Solution and mesh with polynomial orders saved. Total running time: %g s", sln_time.accumulated()); // Clean up. delete matrix; delete rhs; delete solver; return res; }
int main(int argc,char **args) { Mat C,C1,F; Vec u,x,b; PetscErrorCode ierr; PetscMPIInt rank,nproc; PetscInt i,M = 10,m,n,nfact,nsolve; PetscScalar *array,rval; PetscReal norm,tol=1.e-12; IS perm,iperm; MatFactorInfo info; PetscRandom rand; PetscTruth flg; PetscInitialize(&argc,&args,(char *)0,help); ierr = MPI_Comm_rank(PETSC_COMM_WORLD, &rank);CHKERRQ(ierr); ierr = MPI_Comm_size(PETSC_COMM_WORLD, &nproc);CHKERRQ(ierr); /* Create matrix and vectors */ ierr = PetscOptionsGetInt(PETSC_NULL,"-M",&M,PETSC_NULL);CHKERRQ(ierr); ierr = MatCreate(PETSC_COMM_WORLD,&C);CHKERRQ(ierr); ierr = MatSetSizes(C,PETSC_DECIDE,PETSC_DECIDE,M,M);CHKERRQ(ierr); ierr = MatSetType(C,MATDENSE);CHKERRQ(ierr); ierr = MatSetFromOptions(C);CHKERRQ(ierr); ierr = MatGetLocalSize(C,&m,&n);CHKERRQ(ierr); if (m != n) SETERRQ2(PETSC_ERR_ARG_WRONG,"Matrix local size m %d must equal n %d",m,n); ierr = VecCreate(PETSC_COMM_WORLD,&x);CHKERRQ(ierr); ierr = VecSetSizes(x,n,PETSC_DECIDE);CHKERRQ(ierr); ierr = VecSetFromOptions(x);CHKERRQ(ierr); ierr = VecDuplicate(x,&b);CHKERRQ(ierr); ierr = VecDuplicate(x,&u);CHKERRQ(ierr); /* save the true solution */ /* Assembly */ ierr = PetscRandomCreate(PETSC_COMM_WORLD,&rand);CHKERRQ(ierr); ierr = PetscRandomSetFromOptions(rand);CHKERRQ(ierr); ierr = MatGetArray(C,&array);CHKERRQ(ierr); for (i=0; i<m*M; i++){ ierr = PetscRandomGetValue(rand,&rval);CHKERRQ(ierr); array[i] = rval; } ierr = MatRestoreArray(C,&array);CHKERRQ(ierr); ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); /*if (!rank) {printf("main, C: \n");} ierr = MatView(C,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); */ /* Test MatDuplicate() */ ierr = MatDuplicate(C,MAT_COPY_VALUES,&C1);CHKERRQ(ierr); ierr = MatEqual(C,C1,&flg);CHKERRQ(ierr); if (!flg){ SETERRQ(PETSC_ERR_ARG_WRONG,"Duplicate C1 != C"); } /* Test LU Factorization */ ierr = MatGetOrdering(C1,MATORDERING_NATURAL,&perm,&iperm);CHKERRQ(ierr); if (nproc == 1){ ierr = MatGetFactor(C1,MAT_SOLVER_PETSC,MAT_FACTOR_LU,&F);CHKERRQ(ierr); } else { ierr = MatGetFactor(C1,MAT_SOLVER_PLAPACK,MAT_FACTOR_LU,&F);CHKERRQ(ierr); } ierr = MatLUFactorSymbolic(F,C1,perm,iperm,&info);CHKERRQ(ierr); for (nfact = 0; nfact < 2; nfact++){ if (!rank) printf(" LU nfact %d\n",nfact); ierr = MatLUFactorNumeric(F,C1,&info);CHKERRQ(ierr); /* Test MatSolve() */ for (nsolve = 0; nsolve < 5; nsolve++){ ierr = VecGetArray(x,&array);CHKERRQ(ierr); for (i=0; i<m; i++){ ierr = PetscRandomGetValue(rand,&rval);CHKERRQ(ierr); array[i] = rval; } ierr = VecRestoreArray(x,&array);CHKERRQ(ierr); ierr = VecCopy(x,u);CHKERRQ(ierr); ierr = MatMult(C,x,b);CHKERRQ(ierr); ierr = MatSolve(F,b,x);CHKERRQ(ierr); /* Check the error */ ierr = VecAXPY(u,-1.0,x);CHKERRQ(ierr); /* u <- (-1.0)x + u */ ierr = VecNorm(u,NORM_2,&norm);CHKERRQ(ierr); if (norm > tol){ if (!rank){ ierr = PetscPrintf(PETSC_COMM_SELF,"Error: Norm of error %g, LU nfact %d\n",norm,nfact);CHKERRQ(ierr); } } } } ierr = MatDestroy(C1);CHKERRQ(ierr); ierr = MatDestroy(F);CHKERRQ(ierr); /* Test Cholesky Factorization */ ierr = MatTranspose(C,MAT_INITIAL_MATRIX,&C1);CHKERRQ(ierr); /* C1 = C^T */ ierr = MatAXPY(C,1.0,C1,SAME_NONZERO_PATTERN);CHKERRQ(ierr); /* make C symmetric: C <- C + C^T */ ierr = MatShift(C,M);CHKERRQ(ierr); /* make C positive definite */ ierr = MatDestroy(C1);CHKERRQ(ierr); ierr = MatSetOption(C,MAT_SYMMETRIC,PETSC_TRUE);CHKERRQ(ierr); ierr = MatSetOption(C,MAT_SYMMETRY_ETERNAL,PETSC_TRUE);CHKERRQ(ierr); if (nproc == 1){ ierr = MatGetFactor(C,MAT_SOLVER_PETSC,MAT_FACTOR_CHOLESKY,&F);CHKERRQ(ierr); } else { ierr = MatGetFactor(C,MAT_SOLVER_PLAPACK,MAT_FACTOR_CHOLESKY,&F);CHKERRQ(ierr); } ierr = MatCholeskyFactorSymbolic(F,C,perm,&info);CHKERRQ(ierr); for (nfact = 0; nfact < 2; nfact++){ if (!rank) printf(" Cholesky nfact %d\n",nfact); ierr = MatCholeskyFactorNumeric(F,C,&info);CHKERRQ(ierr); /* Test MatSolve() */ for (nsolve = 0; nsolve < 5; nsolve++){ ierr = VecGetArray(x,&array);CHKERRQ(ierr); for (i=0; i<m; i++){ ierr = PetscRandomGetValue(rand,&rval);CHKERRQ(ierr); array[i] = rval; } ierr = VecRestoreArray(x,&array);CHKERRQ(ierr); ierr = VecCopy(x,u);CHKERRQ(ierr); ierr = MatMult(C,x,b);CHKERRQ(ierr); ierr = MatSolve(F,b,x);CHKERRQ(ierr); /* Check the error */ ierr = VecAXPY(u,-1.0,x);CHKERRQ(ierr); /* u <- (-1.0)x + u */ ierr = VecNorm(u,NORM_2,&norm);CHKERRQ(ierr); if (norm > tol){ if (!rank){ ierr = PetscPrintf(PETSC_COMM_SELF,"Error: Norm of error %g, Cholesky nfact %d\n",norm,nfact);CHKERRQ(ierr); } } } } ierr = MatDestroy(F);CHKERRQ(ierr); /* Free data structures */ ierr = PetscRandomDestroy(rand);CHKERRQ(ierr); ierr = ISDestroy(perm);CHKERRQ(ierr); ierr = ISDestroy(iperm);CHKERRQ(ierr); ierr = VecDestroy(x);CHKERRQ(ierr); ierr = VecDestroy(b);CHKERRQ(ierr); ierr = VecDestroy(u);CHKERRQ(ierr); ierr = MatDestroy(C);CHKERRQ(ierr); ierr = PetscFinalize();CHKERRQ(ierr); return 0; }
int main(int argc, char **argv) { PetscErrorCode info; /* 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 */ info = PetscOptionsGetReal(NULL,"-ecc",&user.ecc,&flg);CHKERRQ(info); info = PetscOptionsGetReal(NULL,"-b",&user.b,&flg);CHKERRQ(info); /* 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. */ info = DMDACreate2d(PETSC_COMM_WORLD, DMDA_BOUNDARY_NONE, DMDA_BOUNDARY_NONE,DMDA_STENCIL_STAR,-50,-50,PETSC_DECIDE,PETSC_DECIDE,1,1,NULL,NULL,&user.da);CHKERRQ(info); info = DMDAGetInfo(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(info); 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. */ info = DMCreateGlobalVector(user.da,&x);CHKERRQ(info); /* Solution */ info = VecDuplicate(x,&user.B);CHKERRQ(info); /* Linear objective */ info = VecDuplicate(x,&r);CHKERRQ(info); /* Create matrix user.A to store quadratic, Create a local ordering scheme. */ info = DMCreateMatrix(user.da,MATAIJ,&user.A);CHKERRQ(info); /* User defined function -- compute linear term of quadratic */ info = ComputeB(&user);CHKERRQ(info); /* Create nonlinear solver context */ info = SNESCreate(PETSC_COMM_WORLD,&snes);CHKERRQ(info); /* Set function evaluation and Jacobian evaluation routines */ info = SNESSetFunction(snes,r,FormGradient,&user);CHKERRQ(info); info = SNESSetJacobian(snes,user.A,user.A,FormHessian,&user);CHKERRQ(info); /* Set the initial solution guess */ info = VecSet(x, zero);CHKERRQ(info); info = SNESSetFromOptions(snes);CHKERRQ(info); /* Set variable bounds */ info = VecDuplicate(x,&xl);CHKERRQ(info); info = VecDuplicate(x,&xu);CHKERRQ(info); info = VecSet(xl,zero);CHKERRQ(info); info = VecSet(xu,thnd);CHKERRQ(info); info = SNESVISetVariableBounds(snes,xl,xu);CHKERRQ(info); /* Solve the application */ info = SNESSolve(snes,NULL,x);CHKERRQ(info); info = SNESGetConvergedReason(snes,&reason);CHKERRQ(info); 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 */ info = VecDestroy(&x);CHKERRQ(info); info = VecDestroy(&xl);CHKERRQ(info); info = VecDestroy(&xu);CHKERRQ(info); info = VecDestroy(&r);CHKERRQ(info); info = MatDestroy(&user.A);CHKERRQ(info); info = VecDestroy(&user.B);CHKERRQ(info); info = DMDestroy(&user.da);CHKERRQ(info); info = SNESDestroy(&snes);CHKERRQ(info); info = 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); }
PetscInt main(PetscInt argc,char **args) { PetscErrorCode ierr; PetscMPIInt rank,size; PetscInt N0=2048,N1=2048,N2=3,N3=5,N4=5,N=N0*N1; PetscRandom rdm; PetscReal enorm; Vec x,y,z,input,output; Mat A; PetscInt DIM, dim[5],vsize; PetscReal fac; PetscScalar one=1,two=2,three=3; ierr = PetscInitialize(&argc,&args,(char*)0,help);CHKERRQ(ierr); #if defined(PETSC_USE_COMPLEX) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_SUP, "This example requires real numbers"); #endif ierr = MPI_Comm_size(PETSC_COMM_WORLD, &size);CHKERRQ(ierr); ierr = MPI_Comm_rank(PETSC_COMM_WORLD, &rank);CHKERRQ(ierr); ierr = PetscRandomCreate(PETSC_COMM_WORLD, &rdm);CHKERRQ(ierr); ierr = PetscRandomSetFromOptions(rdm);CHKERRQ(ierr); ierr = VecCreate(PETSC_COMM_WORLD,&input);CHKERRQ(ierr); ierr = VecSetSizes(input,PETSC_DECIDE,N);CHKERRQ(ierr); ierr = VecSetFromOptions(input);CHKERRQ(ierr); /* ierr = VecSet(input,one);CHKERRQ(ierr); */ /* ierr = VecSetValue(input,1,two,INSERT_VALUES);CHKERRQ(ierr); */ /* ierr = VecSetValue(input,2,three,INSERT_VALUES);CHKERRQ(ierr); */ /* ierr = VecSetValue(input,3,three,INSERT_VALUES);CHKERRQ(ierr); */ ierr = VecSetRandom(input,rdm);CHKERRQ(ierr); /* ierr = VecSetRandom(input,rdm);CHKERRQ(ierr); */ /* ierr = VecSetRandom(input,rdm);CHKERRQ(ierr); */ ierr = VecDuplicate(input,&output); DIM = 2; dim[0] = N0; dim[1] = N1; dim[2] = N2; dim[3] = N3; dim[4] = N4; ierr = MatCreateFFT(PETSC_COMM_WORLD,DIM,dim,MATFFTW,&A);CHKERRQ(ierr); ierr = MatGetVecsFFTW(A,&x,&y,&z);CHKERRQ(ierr); /* ierr = MatGetVecs(A,&x,&y);CHKERRQ(ierr); */ /* ierr = MatGetVecs(A,&z,NULL);CHKERRQ(ierr); */ ierr = VecGetSize(x,&vsize);CHKERRQ(ierr); printf("The vector size of input from the main routine is %d\n",vsize); ierr = VecGetSize(z,&vsize);CHKERRQ(ierr); printf("The vector size of output from the main routine is %d\n",vsize); ierr = InputTransformFFT(A,input,x);CHKERRQ(ierr); ierr = MatMult(A,x,y);CHKERRQ(ierr); ierr = VecAssemblyBegin(y);CHKERRQ(ierr); ierr = VecAssemblyEnd(y);CHKERRQ(ierr); ierr = VecView(y,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = MatMultTranspose(A,y,z);CHKERRQ(ierr); ierr = OutputTransformFFT(A,z,output);CHKERRQ(ierr); fac = 1.0/(PetscReal)N; ierr = VecScale(output,fac);CHKERRQ(ierr); ierr = VecAssemblyBegin(input);CHKERRQ(ierr); ierr = VecAssemblyEnd(input);CHKERRQ(ierr); ierr = VecAssemblyBegin(output);CHKERRQ(ierr); ierr = VecAssemblyEnd(output);CHKERRQ(ierr); /* ierr = VecView(input,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); */ /* ierr = VecView(output,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); */ ierr = VecAXPY(output,-1.0,input);CHKERRQ(ierr); ierr = VecNorm(output,NORM_1,&enorm);CHKERRQ(ierr); /* if (enorm > 1.e-14) { */ ierr = PetscPrintf(PETSC_COMM_SELF," Error norm of |x - z| %e\n",enorm);CHKERRQ(ierr); /* } */ ierr = VecDestroy(&output);CHKERRQ(ierr); ierr = VecDestroy(&input);CHKERRQ(ierr); ierr = VecDestroy(&x);CHKERRQ(ierr); ierr = VecDestroy(&y);CHKERRQ(ierr); ierr = VecDestroy(&z);CHKERRQ(ierr); ierr = MatDestroy(&A);CHKERRQ(ierr); ierr = PetscRandomDestroy(&rdm);CHKERRQ(ierr); PetscFinalize(); return 0; }
int main(int argc,char **argv) { PetscErrorCode ierr; DM dmstag; PetscInt dim; PetscBool setSizes; /* Initialize PETSc and process command line arguments */ ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr; dim = 2; ierr = PetscOptionsGetInt(NULL,NULL,"-dim",&dim,NULL);CHKERRQ(ierr); setSizes = PETSC_FALSE; ierr = PetscOptionsGetBool(NULL,NULL,"-setsizes",&setSizes,NULL);CHKERRQ(ierr); /* Creation (normal) */ if (!setSizes) { switch (dim) { case 1: ierr = DMStagCreate1d(PETSC_COMM_WORLD,DM_BOUNDARY_NONE,3,1,1,DMSTAG_STENCIL_BOX,1,NULL,&dmstag);CHKERRQ(ierr); break; case 2: ierr = DMStagCreate2d(PETSC_COMM_WORLD,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,3,2,PETSC_DECIDE,PETSC_DECIDE,1,1,1,DMSTAG_STENCIL_BOX,1,NULL,NULL,&dmstag);CHKERRQ(ierr); break; case 3: ierr = DMStagCreate3d(PETSC_COMM_WORLD,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,3,2,4,PETSC_DECIDE,PETSC_DECIDE,PETSC_DECIDE,1,1,1,1,DMSTAG_STENCIL_BOX,1,NULL,NULL,NULL,&dmstag);CHKERRQ(ierr); break; default: SETERRQ1(PETSC_COMM_WORLD,PETSC_ERR_SUP,"No support for dimension %D",dim); } } else { /* Creation (test providing decomp exactly)*/ PetscMPIInt size; PetscInt lx[4] = {1,2,3}, ranksx = 3, mx = 6; PetscInt ly[3] = {4,5}, ranksy = 2, my = 9; PetscInt lz[2] = {6,7}, ranksz = 2, mz = 13; ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr); switch (dim) { case 1: if (size != ranksx) SETERRQ1(PETSC_COMM_WORLD,PETSC_ERR_ARG_WRONG,"Must run on %D ranks with -dim 1 -setSizes",ranksx); ierr = DMStagCreate1d(PETSC_COMM_WORLD,DM_BOUNDARY_NONE,mx,1,1,DMSTAG_STENCIL_BOX,1,lx,&dmstag);CHKERRQ(ierr); break; case 2: if (size != ranksx * ranksy) SETERRQ1(PETSC_COMM_WORLD,PETSC_ERR_ARG_WRONG,"Must run on %D ranks with -dim 2 -setSizes",ranksx * ranksy); ierr = DMStagCreate2d(PETSC_COMM_WORLD,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,mx,my,ranksx,ranksy,1,1,1,DMSTAG_STENCIL_BOX,1,lx,ly,&dmstag);CHKERRQ(ierr); break; case 3: if (size != ranksx * ranksy * ranksz) SETERRQ1(PETSC_COMM_WORLD,PETSC_ERR_ARG_WRONG,"Must run on %D ranks with -dim 3 -setSizes", ranksx * ranksy * ranksz); ierr = DMStagCreate3d(PETSC_COMM_WORLD,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,mx,my,mz,ranksx,ranksy,ranksz,1,1,1,1,DMSTAG_STENCIL_BOX,1,lx,ly,lz,&dmstag);CHKERRQ(ierr); break; default: SETERRQ1(PETSC_COMM_WORLD,PETSC_ERR_SUP,"No support for dimension %D",dim); } } /* Setup */ ierr = DMSetFromOptions(dmstag);CHKERRQ(ierr); ierr = DMSetUp(dmstag);CHKERRQ(ierr); /* Field Creation */ ierr = TestFields(dmstag);CHKERRQ(ierr); /* Clean up and finalize PETSc */ ierr = DMDestroy(&dmstag);CHKERRQ(ierr); ierr = PetscFinalize(); return ierr; }
int main(int argc, char** args) { int ntdim = 31; double* t = (double*)malloc(ntdim*sizeof(double)); for (int i = 0; i<ntdim; i++) { t[i] = 0.1*i; } int nsdim = 2244; double* u0 = (double*)malloc(ntdim*nsdim*sizeof(double)); std::string line; std::ifstream myfile ("vortex_51.txt"); double a; int linenum = -1; if(myfile.is_open()) { while(! myfile.eof()) { getline(myfile,line); linenum ++; if (linenum >= nsdim) { break; } std::istringstream iss(line); for (int i = 0; i<ntdim; i++) { iss >> a; u0[i*nsdim+linenum] = a; } } } double* s; double alpha = 10; lssSolver A(t,u0,s,ntdim,nsdim,alpha); MPI_Init(&argc,&args); PetscInitialize(&argc,&args,(char*)0,NULL); double* uf = A.lss(); std::ofstream outfile ("uf_31.txt"); if(outfile.is_open()) { for(int i = 0 ; i < ntdim; i++) { for (int j = 0; j < nsdim; j++) { outfile << uf[i*nsdim+j] << ", "; } outfile << std::endl; } } PetscFinalize(); MPI_Finalize(); return 0; }