From: Timo Heister Date: Sun, 22 May 2016 19:38:19 +0000 (+0100) Subject: fix, cleanup, documentation X-Git-Tag: v8.5.0-rc1~990^2~6 X-Git-Url: https://gitweb.dealii.org/cgi-bin/gitweb.cgi?a=commitdiff_plain;h=5ec0315f1ec65938e978b56f87f23afaedcf5f9c;p=dealii.git fix, cleanup, documentation - fix block/component handling - cleanup - write some documentation --- diff --git a/examples/step-56/step-56.cc b/examples/step-56/step-56.cc index 7475c8286f..770e79fbc8 100644 --- a/examples/step-56/step-56.cc +++ b/examples/step-56/step-56.cc @@ -61,7 +61,7 @@ #include #include -// We need to include the followign file for all of the timings between ILU and Multigrid +// We need to include the following file to do timings: #include // This includes the files necessary for us to use geometric Multigrid @@ -79,8 +79,8 @@ namespace Step56 { using namespace dealii; - // In order to make it easy to switch between the different solvers that are being - // used in step-56, we declare an enum that can be passed as an argument to the + // In order to make it easy to switch between the different solvers that are + // being used, we declare an enum that can be passed as an argument to the // constructor of the main class. struct SolverType { @@ -90,13 +90,12 @@ namespace Step56 // @sect3{Functions for Solution and Righthand side} // // The class Solution is used to define the boundary conditions and to - // compute errors of the numerical solution. Note that we need to define - // the values and gradients in order to compute L2 and H1 errors. Here - // we decided to separate the implementations for 2d and 3d using - // template specialization. We do this to make it easier for us to debug - // as well as its aesthetic value. + // compute errors of the numerical solution. Note that we need to define the + // values and gradients in order to compute L2 and H1 errors. Here we + // decided to separate the implementations for 2d and 3d using template + // specialization. // - // Please note that the first dim components are the velocity components + // Note that the first dim components are the velocity components // and the last is the pressure. template class Solution : public Function @@ -114,7 +113,7 @@ namespace Step56 Solution<2>::value (const Point<2> &p, const unsigned int component) const { - Assert (component <= dim, ExcIndexRange(component,0,dim+1)); + Assert (component <= 2+1, ExcIndexRange(component,0,2+1)); using numbers::PI; const double x = p(0); @@ -135,7 +134,7 @@ namespace Step56 Solution<3>::value (const Point<3> &p, const unsigned int component) const { - Assert (component <= dim, ExcIndexRange(component,0,dim+1)); + Assert (component <= 3+1, ExcIndexRange(component,0,3+1)); using numbers::PI; const double x = p(0); @@ -160,11 +159,12 @@ namespace Step56 Solution<2>::gradient (const Point<2> &p, const unsigned int component) const { - Assert (component <= dim, ExcIndexRange(component,0,dim+1)); + Assert (component <= 2, ExcIndexRange(component,0,2+1)); using numbers::PI; const double x = p(0); const double y = p(1); + Tensor<1,2> return_value; if (component == 0) { @@ -190,12 +190,13 @@ namespace Step56 Solution<3>::gradient (const Point<3> &p, const unsigned int component) const { - Assert (component <= dim, ExcIndexRange(component,0,dim+1)); + Assert (component <= 3, ExcIndexRange(component,0,3+1)); using numbers::PI; const double x = p(0); const double y = p(1); const double z = p(2); + Tensor<1,3> return_value; if (component == 0) { @@ -241,7 +242,7 @@ namespace Step56 RightHandSide<2>::value (const Point<2> &p, const unsigned int component) const { - Assert (component <= dim, ExcIndexRange(component,0,dim+1)); + Assert (component <= 2, ExcIndexRange(component,0,2+1)); using numbers::PI; double x = p(0); @@ -254,7 +255,6 @@ namespace Step56 return 0; return 0; - } template <> @@ -262,7 +262,7 @@ namespace Step56 RightHandSide<3>::value (const Point<3> &p, const unsigned int component) const { - Assert (component <= dim, ExcIndexRange(component,0,dim+1)); + Assert (component <= 3, ExcIndexRange(component,0,3+1)); using numbers::PI; double x = p(0); @@ -316,10 +316,15 @@ namespace Step56 // @sect3{ASPECT BlockSchurPreconditioner} - // In the following, we will implement a preconditioner that expands a - // little bit on the ideas discussed in the Results section of step-22. - // Specifically, we will do X, Y, and Z. A further iteration of this - // approach is also used in the ASPECT code + // In the following, we will implement a preconditioner that expands + // on the ideas discussed in the Results section of step-22. + // Specifically, we + // 1. use an upper block-triangular preconditioner because we want to + // use right preconditioning. + // 2. optionally allow using an inner solver for the velocity block instead + // of a single preconditioner application. + // 3. do not use InverseMatrix but explicitly call SolverCG. + // This approach is also used in the ASPECT code // (see http://aspect.dealii.org) that solves the Stokes equations in // the context of simulating convection in the earth mantle, and which // has been used to solve problems on many thousands of processors. @@ -404,7 +409,7 @@ namespace Step56 utmp += src.block(0); } - // Finally, either solve with the top left block (if do_solve_A==true) + // Finally, either solve with the top left block // or just apply one preconditioner sweep if (do_solve_A == true) { @@ -433,7 +438,8 @@ namespace Step56 class StokesProblem { public: - StokesProblem (const unsigned int degree, SolverType::type solver_type); + StokesProblem (const unsigned int pressure_degree, + SolverType::type solver_type); void run (); private: @@ -444,7 +450,7 @@ namespace Step56 void compute_errors (); void output_results (const unsigned int refinement_cycle) const; - const unsigned int degree; + const unsigned int pressure_degree; SolverType::type solver_type; Triangulation triangulation; @@ -455,16 +461,16 @@ namespace Step56 ConstraintMatrix constraints; - BlockSparsityPattern sparsity_pattern; - BlockSparseMatrix system_matrix; + BlockSparsityPattern sparsity_pattern; + BlockSparseMatrix system_matrix; SparseMatrix pressure_mass_matrix; BlockVector solution; BlockVector system_rhs; MGLevelObject mg_sparsity_patterns; - MGLevelObject > mg_matrices; - MGLevelObject > mg_interface_matrices; + MGLevelObject > mg_matrices; + MGLevelObject > mg_interface_matrices; MGConstrainedDoFs mg_constrained_dofs; TimerOutput computing_timer; @@ -473,14 +479,16 @@ namespace Step56 template - StokesProblem::StokesProblem (const unsigned int degree, SolverType::type solver_type) + StokesProblem::StokesProblem (const unsigned int pressure_degree, + SolverType::type solver_type) : - degree (degree), + pressure_degree (pressure_degree), solver_type (solver_type), triangulation (Triangulation::maximum_smoothing), - velocity_fe (FE_Q(degree+1), dim), // Finite element for velocity-only - fe (velocity_fe, 1, // Finite element for whole system - FE_Q (degree), 1), + // Finite element for the velocity only: + velocity_fe (FE_Q(pressure_degree+1), dim), + // Finite element for the whole system: + fe (velocity_fe, 1, FE_Q (pressure_degree), 1), dof_handler (triangulation), velocity_dof_handler (triangulation), computing_timer (std::cout, TimerOutput::summary, @@ -491,7 +499,8 @@ namespace Step56 // @sect4{StokesProblem::setup_dofs} -// This function sets up things based on if you want to use ILU or GMG as a preconditioner. +// This function sets up the DoFHandler, matrices, vectors, and Multigrid +// structures (if needed). template void StokesProblem::setup_dofs () { @@ -500,40 +509,51 @@ namespace Step56 system_matrix.clear (); pressure_mass_matrix.clear (); - // We don't need the multigrid dofs for whole problem finite element + // The main DoFHandler only needs active DoFs, so we are not calling + // distribute_mg_dofs() here dof_handler.distribute_dofs(fe); - // In the following code block, we first create an array of length dim+1 - // that is initialized to all zeros; we then set the pressure vector - // component to 1. This allows us to keep our velocities together - // and separate from the pressure. - std::vector block_component (dim+1,0); - block_component[dim] = 1; + // This block structure separates the dim velocity components from + // the pressure component (used for reordering). Note that we have + // 2 instead of dim+1 blocks like in step-22, because our FESystem + // is nested and the dim velocity components appear as one block. + std::vector block_component (2); + block_component[0] = 0; + block_component[1] = 1; - // This always knows how to use the dim (start at 0 one) - FEValuesExtractors::Vector velocities(0); + // Velocities start at component 0: + const FEValuesExtractors::Vector velocities(0); + // ILU behaves better if we apply a reordering to reduce fillin. There + // is no advantage in doing this for the other solvers. if (solver_type == SolverType::FGMRES_ILU) { TimerOutput::Scope ilu_specific(computing_timer, "(ILU specific)"); DoFRenumbering::Cuthill_McKee (dof_handler); } - DoFRenumbering::component_wise (dof_handler, block_component); + // This ensures that all velocities DoFs are enumerated before the + // pressure unknowns. This allows us to use blocks for vectors and + // matrices and allows us to get the same DoF numbering for + // dof_handler and velocity_dof_handler. + DoFRenumbering::block_wise (dof_handler); if (solver_type == SolverType::FGMRES_GMG) { TimerOutput::Scope multigrid_specific(computing_timer, "(Multigrid specific)"); TimerOutput::Scope setup_multigrid(computing_timer, "Setup - Multigrid"); - // Distribute only the dofs for velocity finite element + // This distributes the active dofs and multigrid dofs for the + // velocity space in a separate DoFHandler as described in the + // introduction. velocity_dof_handler.distribute_dofs(velocity_fe); - - // Multigrid only needs the dofs for velocity. This does not clear the - // mg_interface_matrices object. Instead, it actually clears the level - // objects it stores. velocity_dof_handler.distribute_mg_dofs(velocity_fe); + // The following block of code initializes the MGConstrainedDofs + // (using the boundary conditions for the velocity), and the + // sparsity patterns and matrices for each level. The resize() + // function of MGLevelObject will destroy all existing contained + // objects. typename FunctionMap::type boundary_condition_function_map; BoundaryValuesForVelocity velocity_boundary_condition; boundary_condition_function_map[0] = &velocity_boundary_condition; @@ -543,11 +563,7 @@ namespace Step56 const unsigned int n_levels = triangulation.n_levels(); mg_interface_matrices.resize(0, n_levels-1); - mg_interface_matrices.clear (); // In contrast to all other container classes' clear() functions which - // delete the contents of the container, this clear() function - // calls the clear function of all elements stored by this container. mg_matrices.resize(0, n_levels-1); - mg_matrices.clear (); mg_sparsity_patterns.resize(0, n_levels-1); for (unsigned int level=0; level dofs_per_block (2); + DoFTools::count_dofs_per_block (dof_handler, dofs_per_block, block_component); + const unsigned int n_u = dofs_per_block[0], + n_p = dofs_per_block[1]; + { constraints.clear (); - // The following makes use of a component mask for interpolation of the boundary values which - // is further explained in the vector valued dealii step-20 tutorial + // The following makes use of a component mask for interpolation of the + // boundary values for the velocity only, which is further explained in + // the vector valued dealii step-20 tutorial. DoFTools::make_hanging_node_constraints (dof_handler, constraints); VectorTools::interpolate_boundary_values (dof_handler, 0, Solution(), constraints, fe.component_mask(velocities)); - } - - std::vector dofs_per_block (2); - DoFTools::count_dofs_per_block (dof_handler, dofs_per_block, block_component); - const unsigned int n_u = dofs_per_block[0], - n_p = dofs_per_block[1]; - // As discussed in the introduction, we need to fix one degree of freedom - // of the pressure variable to ensure solvability of the problem. We do this - // here by marking n_u as a constrained degree of freedom. But not making it - // dependent on any other degree of freedom, this implicitly means that the - // value of this degree of freedom will be forced to zero. - if (solver_type == SolverType::UMFPACK) - { - TimerOutput::Scope umfpack_specific(computing_timer, "(UMFPACK specific)"); + // As discussed in the introduction, we need to fix one degree of freedom + // of the pressure variable to ensure solvability of the problem. We do this + // here by marking the first pressure dof, which has index n_u as a + // constrained dof. + if (solver_type == SolverType::UMFPACK) constraints.add_line(n_u); - } - constraints.close (); + + constraints.close (); + } std::cout << "\tNumber of active cells: " << triangulation.n_active_cells() @@ -600,36 +614,22 @@ namespace Step56 << std::endl; { - BlockDynamicSparsityPattern csp (2,2); - - csp.block(0,0).reinit (n_u, n_u); - csp.block(1,0).reinit (n_p, n_u); - csp.block(0,1).reinit (n_u, n_p); - csp.block(1,1).reinit (n_p, n_p); - - csp.collect_sizes(); - + BlockDynamicSparsityPattern csp (dofs_per_block, dofs_per_block); DoFTools::make_sparsity_pattern (dof_handler, csp, constraints, false); sparsity_pattern.copy_from (csp); - } system_matrix.reinit (sparsity_pattern); - solution.reinit (2); - solution.block(0).reinit (n_u); - solution.block(1).reinit (n_p); - solution.collect_sizes (); - - system_rhs.reinit (2); - system_rhs.block(0).reinit (n_u); - system_rhs.block(1).reinit (n_p); - system_rhs.collect_sizes (); + solution.reinit (dofs_per_block); + system_rhs.reinit (dofs_per_block); } // @sect4{StokesProblem::assemble_system} -// In this function, the system matrix is assembled the same regardless of using ILU and GMG +// In this function, the system matrix is assembled. We assemble the pressure +// mass matrix in the (1,1) block (if needed) and move it out of this location +// at the end of this function. template void StokesProblem::assemble_system () { @@ -637,11 +637,10 @@ namespace Step56 system_matrix=0; system_rhs=0; - // The following bollean is used to signify when you want to assemble the mass matrix - // inside the (1,1) block, which is the case when you are not using UMFPACK + // If true, we will assemble the pressure mass matrix in the (1,1) block: const bool assemble_pressure_mass_matrix = (solver_type == SolverType::UMFPACK) ? false : true; - QGauss quadrature_formula(degree+2); + QGauss quadrature_formula(pressure_degree+2); FEValues fe_values (fe, quadrature_formula, update_values | @@ -730,8 +729,8 @@ namespace Step56 // @sect4{StokesProblem::assemble_multigrid} - // Here, like step-40, we have a function that assembles everything necessary for - // the multigrid preconditioner + // Here, like in step-16, we have a function that assembles the level + // and interface matrices necessary for the multigrid preconditioner. template void StokesProblem::assemble_multigrid () { @@ -740,7 +739,7 @@ namespace Step56 mg_matrices = 0.; - QGauss quadrature_formula(degree+2); + QGauss quadrature_formula(pressure_degree+2); FEValues fe_values (velocity_fe, quadrature_formula, update_values | @@ -749,23 +748,15 @@ namespace Step56 update_gradients); const unsigned int dofs_per_cell = velocity_fe.dofs_per_cell; - const unsigned int n_q_points = quadrature_formula.size(); FullMatrix cell_matrix (dofs_per_cell, dofs_per_cell); std::vector local_dof_indices (dofs_per_cell); - const RightHandSide right_hand_side; - std::vector > rhs_values (n_q_points, - Vector(dim+1)); - const FEValuesExtractors::Vector velocities (0); - const FEValuesExtractors::Scalar pressure (dim); std::vector > symgrad_phi_u (dofs_per_cell); - std::vector div_phi_u (dofs_per_cell); - std::vector phi_p (dofs_per_cell); std::vector boundary_constraints (triangulation.n_levels()); std::vector boundary_interface_constraints (triangulation.n_levels()); @@ -779,8 +770,7 @@ namespace Step56 mg_constrained_dofs.get_refinement_edge_indices(level) & mg_constrained_dofs.get_boundary_indices(level); - boundary_interface_constraints[level] - .add_lines (idx); + boundary_interface_constraints[level].add_lines (idx); boundary_interface_constraints[level].close (); } @@ -793,28 +783,20 @@ namespace Step56 fe_values.reinit (cell); cell_matrix = 0; - right_hand_side.vector_value_list(fe_values.get_quadrature_points(), - rhs_values); - for (unsigned int q=0; q void StokesProblem::solve () { @@ -934,8 +916,7 @@ namespace Step56 MGTransferPrebuilt > mg_transfer(constraints, mg_constrained_dofs); mg_transfer.build_matrices(velocity_dof_handler); - // Coarse grid solver - // Timo: TODO: should we use something like LACIteration? + // Setup coarse grid solver FullMatrix coarse_matrix; coarse_matrix.copy_from (mg_matrices[0]); MGCoarseGridHouseholder<> coarse_grid_solver; @@ -946,8 +927,8 @@ namespace Step56 mg_smoother.initialize(mg_matrices); mg_smoother.set_steps(2); - // Multigrid, when used as a preconditioner for CG, expects the - // smoother to be symmetric, and this takes care of that + // Multigrid, when used as a preconditioner for CG, needs to be a + // symmetric operator, so the smoother must be symmetric mg_smoother.set_symmetric(true); mg::Matrix > mg_matrix(mg_matrices); @@ -996,11 +977,11 @@ namespace Step56 constraints.distribute (solution); std::cout << std::endl - << "\tNumber of iterations used for block GMRES iterations: " + << "\tNumber of FGMRES iterations: " << solver_control.last_step() << std::endl - << "\tNumber of iterations used for approximation of A inverse: " + << "\tTotal number of iterations used for approximation of A inverse: " << n_iterations_A << std::endl - << "\tNumber of iterations used for approximation of S inverse: " + << "\tTotal number of iterations used for approximation of S inverse: " << n_iterations_S << std::endl << std::endl; } @@ -1008,6 +989,8 @@ namespace Step56 // @sect4{StokesProblem::process_solution} +// This function computes the L2 and H1 errors of the solution. For this, +// we need to make sure the pressure has mean zero. template void StokesProblem::compute_errors () { @@ -1017,30 +1000,22 @@ namespace Step56 // the pressure is component $dim$ and that the finite element space // is nodal. const double mean_pressure = VectorTools::compute_mean_value (dof_handler, - QGauss(degree+2), + QGauss(pressure_degree+2), solution, dim); solution.block(1).add(-mean_pressure); - std::cout << " Note: The mean value was adjusted by " << -mean_pressure << std::endl; + std::cout << " Note: The mean value was adjusted by " + << -mean_pressure << std::endl; const ComponentSelectFunction pressure_mask (dim, dim+1); - // Timo: TODO: find a better way to do this inside deal.II, maybe with component_mask const ComponentSelectFunction velocity_mask(std::make_pair(0, dim), dim+1); - /* - Timo: TODO: think about this - Extractor::Vector velocities(0); - const ComponentSelectFunction - velocity_selector(velocities, dim+1); - */ - Vector difference_per_cell (triangulation.n_active_cells()); - VectorTools::integrate_difference (dof_handler, solution, Solution(), difference_per_cell, - QGauss(degree+2), + QGauss(pressure_degree+2), VectorTools::L2_norm, &velocity_mask); @@ -1050,7 +1025,7 @@ namespace Step56 solution, Solution(), difference_per_cell, - QGauss(degree+2), + QGauss(pressure_degree+2), VectorTools::L2_norm, &pressure_mask); @@ -1060,7 +1035,7 @@ namespace Step56 solution, Solution(), difference_per_cell, - QGauss(degree+2), + QGauss(pressure_degree+2), VectorTools::H1_norm, &velocity_mask); @@ -1071,14 +1046,14 @@ namespace Step56 << std::endl << " Pressure L2 Error: " << Pressure_L2_error << std::endl - << " Velocity H1 Error: " - << Velocity_H1_error + << " Velocity H1 Error: " << Velocity_H1_error << std::endl; } // @sect4{StokesProblem::output_results} +// This function generates graphical output like it is done in step-16. template void StokesProblem::output_results (const unsigned int refinement_cycle) const @@ -1137,15 +1112,15 @@ namespace Step56 if (refinement_cycle > 0) triangulation.refine_global (1); - std::cout << " Set-up..." << std::endl << std::flush; + std::cout << " Set-up..." << std::endl; setup_dofs(); - std::cout << " Assembling..." << std::endl << std::flush; + std::cout << " Assembling..." << std::endl; assemble_system (); if (solver_type == SolverType::FGMRES_GMG) { - std::cout << " Assembling Multigrid..." << std::endl << std::flush; + std::cout << " Assembling Multigrid..." << std::endl; assemble_multigrid (); }