From: Martin Kronbichler Date: Thu, 13 Aug 2009 09:34:58 +0000 (+0000) Subject: Finished writing in-code comments. X-Git-Tag: v8.0.0~7318 X-Git-Url: https://gitweb.dealii.org/cgi-bin/gitweb.cgi?a=commitdiff_plain;h=313d330868baa4e85404a44a25d34925258a7ad5;p=dealii.git Finished writing in-code comments. git-svn-id: https://svn.dealii.org/trunk@19250 0785d39b-7218-0410-832d-ea1e28bc413d --- diff --git a/deal.II/examples/step-32/step-32.cc b/deal.II/examples/step-32/step-32.cc index b550aacca1..1db374ec31 100644 --- a/deal.II/examples/step-32/step-32.cc +++ b/deal.II/examples/step-32/step-32.cc @@ -198,18 +198,20 @@ namespace EquationData // previously held the approximation of the // Schur complement by a preconditioner // only (we will choose ILU in the - // application code below). This is the - // same trick we already did for the - // velocity block - the idea of this is - // that the outer iterations will - // eventually also make the inner - // approximation for the Schur complement - // good. If the preconditioner we're using - // is good enough, there will be no - // increase in the (outer) iteration - // count. All we need to do for - // implementing this change here is to give - // the respective variable in the + // application code below), as discussed in + // the introduction. This trick we already + // did for the velocity block - the idea of + // this is that the solver iterations on + // the block system will eventually also + // make the approximation for the Schur + // complement good. If the preconditioner + // we're using is good enough, there will + // be no increase in the outer iteration + // count compared to using converged solves + // for the inverse matrices of velocity and + // Schur complement. All we need to do for + // implementing that change is to give the + // respective variable in the // BlockSchurPreconditioner class another // name. namespace LinearSolvers @@ -1001,7 +1003,7 @@ BoussinesqFlowProblem::BoussinesqFlowProblem () - // @sect4{BoussinesqFlowProblem::get_maximal_velocity} + // @sect4{The BoussinesqFlowProblem helper functions} // // Except two small details, this // function is the very same as in @@ -1087,8 +1089,6 @@ double BoussinesqFlowProblem::get_maximal_velocity () const - - // @sect4{BoussinesqFlowProblem::get_extrapolated_temperature_range} // Again, this is only a slightly // modified version of the respective // function in step-31. What is new is @@ -1191,8 +1191,6 @@ BoussinesqFlowProblem::get_extrapolated_temperature_range () const - // @sect4{BoussinesqFlowProblem::compute_viscosity} - // The function that calculates the // viscosity is purely local, so this is // the same code as in step-31. @@ -1257,6 +1255,110 @@ compute_viscosity (const std::vector &old_temperature, } + + // This function is new compared to + // step-31. What is does is to re-implement + // the library function + // VectorTools::project() for + // an MPI-based parallelization, a function + // we used for generating an initial vector + // for temperature based on some initial + // function. The library function only + // works with shared memory. If run with + // more than one MPI process, this would + // mean that each processor projects the + // whole field, which is clearly not very + // efficient. The details of a + // project() function are not + // very difficult. All we do is to use a + // mass matrix and put the evaluation of + // the initial value function on the right + // hand side. The mass matrix for + // temperature we can simply generate using + // the respective assembly function, so all + // we need to do here is to create the + // right hand side and do a CG solve. The + // assembly function does a loop over all + // cells and evaluates the function in the + // EquationData namespace, and + // does this only on cells pertaining to + // the respective processor. The + // implementation of this assembly differs + // from the assembly we do for the + // principal assembly functions further + // down (which include thread-based + // parallelization with the WorkStream + // concept). Here we chose to keep things + // simple, and generating that right hand + // side is cheap anyway so we won't even + // notice that this part is not parallized + // by threads. +template +void BoussinesqFlowProblem::project_temperature_field () +{ + assemble_temperature_matrix (); + + QGauss quadrature(temperature_degree+2); + UpdateFlags update_flags = UpdateFlags(update_values | + update_quadrature_points | + update_JxW_values); + FEValues fe_values (temperature_fe, quadrature, update_flags); + + const unsigned int dofs_per_cell = fe_values.dofs_per_cell, + n_q_points = fe_values.n_quadrature_points; + + std::vector dofs (dofs_per_cell); + Vector cell_vector (dofs_per_cell); + + typename DoFHandler::active_cell_iterator + cell = temperature_dof_handler.begin_active(), + endc = temperature_dof_handler.end(); + + std::vector rhs_values(n_q_points); + + TrilinosWrappers::MPI::Vector rhs (temperature_mass_matrix.row_partitioner()), + sol (temperature_mass_matrix.row_partitioner()); + + for (; cell!=endc; ++cell) + if (cell->subdomain_id() == + Utilities::Trilinos::get_this_mpi_process(trilinos_communicator)) + { + fe_values.reinit(cell); + + const std::vector &weights = fe_values.get_JxW_values (); + EquationData::TemperatureInitialValues().value_list + (fe_values.get_quadrature_points(), rhs_values); + + cell_vector = 0; + for (unsigned int point=0; pointget_dof_indices (dofs); + + temperature_constraints.distribute_local_to_global (cell_vector, + dofs, + rhs); + } + + ReductionControl control(5*rhs.size(), 0., 1e-12, false, false); + GrowingVectorMemory memory; + SolverCG cg(control,memory); + + TrilinosWrappers::PreconditionIC preconditioner_mass; + preconditioner_mass.initialize(temperature_mass_matrix); + + cg.solve (temperature_mass_matrix, sol, rhs, preconditioner_mass); + + old_temperature_solution = sol; + temperature_constraints.distribute (old_temperature_solution); +} + + + + // @sect4{The BoussinesqFlowProblem setup functions} // The following three functions set @@ -1761,6 +1863,13 @@ BoussinesqFlowProblem::assemble_stokes_preconditioner () + // This function builds the Stokes + // preconditioner and is the same as in the + // serial case. The only difference to + // step-31 is that we use an ILU + // preconditioner for the pressure mass + // matrix instead of IC, as discussed in + // the introduction. template void BoussinesqFlowProblem::build_stokes_preconditioner () @@ -1803,6 +1912,25 @@ BoussinesqFlowProblem::build_stokes_preconditioner () + // The next three functions implement the + // assembly of the Stokes system, again + // split up into a part performing local + // calculations, one for writing the local + // data into the global matrix and vector, + // and one for actually running the loop + // over all cells with the help of the + // WorkStream class. Note that the assembly + // of the Stokes matrix needs only to be + // done in case we have changed the + // mesh. Otherwise, just the + // (temperature-dependent) right hand side + // needs to be calculated here. Since we + // are working with distributed matrices + // and vectors, we have to call the + // respective compress() + // functions in the end of the assembly in + // order to send non-local data to the + // owner process. template void BoussinesqFlowProblem:: @@ -1888,7 +2016,6 @@ copy_local_to_global_stokes_system (const Assembly::CopyData::StokesSystem -// @sect4{BoussinesqFlowProblem::assemble_stokes_system} template void BoussinesqFlowProblem::assemble_stokes_system () { @@ -1950,10 +2077,14 @@ void BoussinesqFlowProblem::assemble_stokes_system () - - - - // @sect4{BoussinesqFlowProblem::assemble_temperature_system} + // The task to be performed by the next + // three functions is to calculate a mass + // matrix and a Laplace matrix on the + // temperature system. These will be + // combined in order to yield the + // semi-implicit time stepping matrix that + // consists of the mass matrix plus a time + // step weight times the Laplace matrix. template void BoussinesqFlowProblem:: local_assemble_temperature_matrix (const typename DoFHandler::active_cell_iterator &cell, @@ -1969,7 +2100,6 @@ local_assemble_temperature_matrix (const typename DoFHandler::active_cell_i data.local_mass_matrix = 0; data.local_stiffness_matrix = 0; - for (unsigned int q=0; q::assemble_temperature_matrix () + // This is the last assembly function. It + // calculates the right hand side of the + // temperature system, which includes the + // convection and the stabilization + // terms. It includes a lot of evaluations + // of old solutions at the quadrature + // points (which are necessary for + // calculating the artificial viscosity of + // stabilization), but is otherwise similar + // to the other assembly functions. template void BoussinesqFlowProblem:: local_assemble_temperature_rhs (const std::pair global_T_range, @@ -2191,6 +2331,32 @@ copy_local_to_global_temperature_rhs (const Assembly::CopyData::TemperatureRHS void BoussinesqFlowProblem::assemble_temperature_system (const double maximal_velocity) { @@ -2215,7 +2381,6 @@ void BoussinesqFlowProblem::assemble_temperature_system (const double maxim T_preconditioner = std_cxx1x::shared_ptr (new TrilinosWrappers::PreconditionIC()); T_preconditioner->initialize (temperature_matrix); - rebuild_temperature_preconditioner = false; } @@ -2258,81 +2423,48 @@ void BoussinesqFlowProblem::assemble_temperature_system (const double maxim - // @sect4{BoussinesqFlowProblem::project_temperature_field} - // Manually project the initial - // conditions for the temperature in - // %parallel instead of doing that - // completely on each processor. The - // temperature mass matrix is already - // available, and we need just to - // compute a right hand side in - // %parallel, do a CG solve and - // distribute the hanging node - // constraints. -template -void BoussinesqFlowProblem::project_temperature_field () -{ - assemble_temperature_matrix (); - - QGauss quadrature(temperature_degree+2); - UpdateFlags update_flags = UpdateFlags(update_values | - update_quadrature_points | - update_JxW_values); - FEValues fe_values (temperature_fe, quadrature, update_flags); - - const unsigned int dofs_per_cell = fe_values.dofs_per_cell, - n_q_points = fe_values.n_quadrature_points; - - std::vector dofs (dofs_per_cell); - Vector cell_vector (dofs_per_cell); - - typename DoFHandler::active_cell_iterator - cell = temperature_dof_handler.begin_active(), - endc = temperature_dof_handler.end(); - - std::vector rhs_values(n_q_points); - - TrilinosWrappers::MPI::Vector rhs (temperature_mass_matrix.row_partitioner()), - sol (temperature_mass_matrix.row_partitioner()); - - for (; cell!=endc; ++cell) - if (cell->subdomain_id() == - Utilities::Trilinos::get_this_mpi_process(trilinos_communicator)) - { - fe_values.reinit(cell); - - const std::vector &weights = fe_values.get_JxW_values (); - EquationData::TemperatureInitialValues().value_list - (fe_values.get_quadrature_points(), rhs_values); - - cell_vector = 0; - for (unsigned int point=0; pointget_dof_indices (dofs); - - temperature_constraints.distribute_local_to_global (cell_vector, - dofs, - rhs); - } - - ReductionControl control(5*rhs.size(), 0., 1e-12, false, false); - GrowingVectorMemory memory; - SolverCG cg(control,memory); - - TrilinosWrappers::PreconditionIC preconditioner_mass; - preconditioner_mass.initialize(temperature_mass_matrix); - - cg.solve (temperature_mass_matrix, sol, rhs, preconditioner_mass); - - old_temperature_solution = sol; - temperature_constraints.distribute (old_temperature_solution); -} // @sect4{BoussinesqFlowProblem::solve} + + // This function solves the linear systems + // in the Boussinesq problem. First, we + // work on the Stokes system and then on + // the temperature system. In essence, it + // does the same things as the respective + // function in step-31. However, there are + // a few things that we need to pay some + // attention to. The first thing is, as + // mentioned in the introduction, the way + // we store our solution: we keep the full + // vector with all degrees of freedom on + // each MPI node. When we enter a solver + // which is supposed to perform + // matrix-vector products with a + // distributed matrix, this is not the + // appropriate form, though. There, we will + // want to have the solution vector to be + // distributed in the same way as the + // matrix. So what we do first (after + // initializing the Schur-complement based + // preconditioner) is to generate a + // distributed vector called + // distributed_stokes_solution + // and put only the locally owned dofs into + // that, which is neatly done by the + // operator= of the Trilinos + // vector. Next, we need to set the + // pressure values at hanging nodes to + // zero. This we also did in step-31 in + // order not to disturb the Schur + // complement by some vector entries that + // actually are irrelevant during the solve + // stage. As a difference to step-31, here + // we do it only for the locally owned + // pressure dofs. + // + // Apart from these two changes, everything + // is the same as in step-31, so we don't + // need to further comment on it. template void BoussinesqFlowProblem::solve () { @@ -2344,17 +2476,10 @@ void BoussinesqFlowProblem::solve () TrilinosWrappers::PreconditionILU> preconditioner (stokes_matrix, *Mp_preconditioner, *Amg_preconditioner); - SolverControl solver_control (stokes_matrix.m(), - 1e-6*stokes_rhs.l2_norm()); - - SolverBicgstab - bicgstab (solver_control, false); - TrilinosWrappers::MPI::BlockVector distributed_stokes_solution (stokes_partitioner); distributed_stokes_solution = stokes_solution; - // now treat the hanging nodes correctly. const unsigned int start = distributed_stokes_solution.block(1).local_range().first + distributed_stokes_solution.block(0).size(); @@ -2365,6 +2490,11 @@ void BoussinesqFlowProblem::solve () if (stokes_constraints.is_constrained (i)) distributed_stokes_solution(i) = 0; + + SolverControl solver_control (stokes_matrix.m(), 1e-6*stokes_rhs.l2_norm()); + SolverBicgstab + bicgstab (solver_control, false); + bicgstab.solve(stokes_matrix, distributed_stokes_solution, stokes_rhs, preconditioner); @@ -2439,6 +2569,10 @@ void BoussinesqFlowProblem::solve () // @sect4{BoussinesqFlowProblem::output_results} + + // This function has remained completely + // unchanged compared to step-31, so + // everything should be clear here. template void BoussinesqFlowProblem::output_results () const { @@ -2529,6 +2663,8 @@ void BoussinesqFlowProblem::output_results () const // @sect4{BoussinesqFlowProblem::refine_mesh} + + // Nothing new here, either... template void BoussinesqFlowProblem::refine_mesh (const unsigned int max_grid_level) { @@ -2594,17 +2730,32 @@ void BoussinesqFlowProblem::refine_mesh (const unsigned int max_grid_level) // @sect4{BoussinesqFlowProblem::run} + + // This is the final function in this + // class. It actually runs the program. It + // is, once more, very similar to + // step-31. The only thing that really + // changed is that we use the + // project_temperature_field() + // function instead of the library function + // VectorTools::project, the + // rest is as before. template void BoussinesqFlowProblem::run () { const unsigned int initial_refinement = (dim == 2 ? 4 : 2); const unsigned int n_pre_refinement_steps = (dim == 2 ? 4 : 3); - //GridGenerator::half_hyper_shell (triangulation, - // Point(), 0.5, 1.0); + /* Data for the shell problem. */ + /* + GridGenerator::half_hyper_shell (triangulation, + Point(), 0.5, 1.0); - //static HyperShellBoundary boundary; - //triangulation.set_boundary (0, boundary); + static HyperShellBoundary boundary; + triangulation.set_boundary (0, boundary); + */ + + /* Data for the cube problem. */ GridGenerator::hyper_cube (triangulation); global_Omega_diameter = GridTools::diameter (triangulation); @@ -2663,6 +2814,8 @@ void BoussinesqFlowProblem::run () // @sect3{The main function} + + // This is copied verbatim from step-31. int main (int argc, char *argv[]) { try