--- /dev/null
+// ---------------------------------------------------------------------
+//
+// Copyright (C) 2009 - 2020 by the deal.II authors
+//
+// This file is part of the deal.II library.
+//
+// The deal.II library is free software; you can use it, redistribute
+// it, and/or modify it under the terms of the GNU Lesser General
+// Public License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+// The full text of the license can be found in the file LICENSE.md at
+// the top level directory of deal.II.
+//
+// ---------------------------------------------------------------------
+
+
+
+// same as deal.II/assemble_matrix_parallel_01, but for PETSc matrices
+// and vectors
+//
+// This test requires PETSc to be configured with the option
+// "--with-threadsafety" in case of debug builds of PETSc
+// For optimized builds, the above option is needed only in case
+// users want PETSc to produce useful logs with "-log_view" runtime
+// option
+#include <deal.II/base/function.h>
+#include <deal.II/base/graph_coloring.h>
+#include <deal.II/base/quadrature_lib.h>
+#include <deal.II/base/utilities.h>
+#include <deal.II/base/work_stream.h>
+
+#include <deal.II/dofs/dof_accessor.h>
+#include <deal.II/dofs/dof_handler.h>
+#include <deal.II/dofs/dof_tools.h>
+
+#include <deal.II/fe/fe_q.h>
+
+#include <deal.II/grid/grid_generator.h>
+#include <deal.II/grid/grid_refinement.h>
+#include <deal.II/grid/tria.h>
+#include <deal.II/grid/tria_accessor.h>
+#include <deal.II/grid/tria_iterator.h>
+
+#include <deal.II/hp/fe_values.h>
+
+#include <deal.II/lac/affine_constraints.h>
+#include <deal.II/lac/dynamic_sparsity_pattern.h>
+#include <deal.II/lac/full_matrix.h>
+#include <deal.II/lac/petsc_sparse_matrix.h>
+#include <deal.II/lac/vector.h>
+
+#include <deal.II/numerics/error_estimator.h>
+#include <deal.II/numerics/matrix_tools.h>
+#include <deal.II/numerics/vector_tools.h>
+
+#include <complex>
+#include <iostream>
+
+#include "../tests.h"
+
+std::ofstream logfile("output");
+
+
+
+namespace Assembly
+{
+ namespace Scratch
+ {
+ template <int dim>
+ struct Data
+ {
+ Data(const hp::FECollection<dim> &fe,
+ const hp::QCollection<dim> & quadrature)
+ : hp_fe_values(fe,
+ quadrature,
+ update_values | update_gradients |
+ update_quadrature_points | update_JxW_values)
+ {}
+
+ Data(const Data &data)
+ : hp_fe_values(data.hp_fe_values.get_mapping_collection(),
+ data.hp_fe_values.get_fe_collection(),
+ data.hp_fe_values.get_quadrature_collection(),
+ data.hp_fe_values.get_update_flags())
+ {}
+
+ hp::FEValues<dim> hp_fe_values;
+ };
+ } // namespace Scratch
+
+ namespace Copy
+ {
+ struct Data
+ {
+ std::vector<types::global_dof_index> local_dof_indices;
+ FullMatrix<double> local_matrix;
+ Vector<double> local_rhs;
+ };
+ } // namespace Copy
+} // namespace Assembly
+
+template <int dim>
+class LaplaceProblem
+{
+public:
+ LaplaceProblem();
+ ~LaplaceProblem();
+
+ void
+ run();
+
+private:
+ void
+ setup_system();
+ void
+ test_equality();
+ void
+ assemble_reference();
+ void
+ assemble_test();
+ void
+ solve();
+ void
+ create_coarse_grid();
+ void
+ postprocess();
+
+ void
+ local_assemble(const typename DoFHandler<dim>::active_cell_iterator &cell,
+ Assembly::Scratch::Data<dim> & scratch,
+ Assembly::Copy::Data & data);
+ void
+ copy_local_to_global(const Assembly::Copy::Data &data);
+
+ std::vector<types::global_dof_index>
+ get_conflict_indices(
+ typename DoFHandler<dim>::active_cell_iterator const &cell) const;
+
+ Triangulation<dim> triangulation;
+
+ DoFHandler<dim> dof_handler;
+ hp::FECollection<dim> fe_collection;
+ hp::QCollection<dim> quadrature_collection;
+ hp::QCollection<dim - 1> face_quadrature_collection;
+
+ AffineConstraints<double> constraints;
+
+ PETScWrappers::MPI::SparseMatrix reference_matrix;
+ PETScWrappers::MPI::SparseMatrix test_matrix;
+
+ PETScWrappers::MPI::Vector reference_rhs;
+ PETScWrappers::MPI::Vector test_rhs;
+
+ std::vector<std::vector<typename DoFHandler<dim>::active_cell_iterator>>
+ graph;
+
+ const unsigned int max_degree;
+};
+
+
+
+template <int dim>
+class BoundaryValues : public Function<dim>
+{
+public:
+ BoundaryValues()
+ : Function<dim>()
+ {}
+
+ virtual double
+ value(const Point<dim> &p, const unsigned int component) const;
+};
+
+
+template <int dim>
+double
+BoundaryValues<dim>::value(const Point<dim> &p,
+ const unsigned int /*component*/) const
+{
+ double sum = 0;
+ for (unsigned int d = 0; d < dim; ++d)
+ sum += std::sin(numbers::PI * p[d]);
+ return sum;
+}
+
+
+template <int dim>
+class RightHandSide : public Function<dim>
+{
+public:
+ RightHandSide()
+ : Function<dim>()
+ {}
+
+ virtual double
+ value(const Point<dim> &p, const unsigned int component) const;
+};
+
+
+template <int dim>
+double
+RightHandSide<dim>::value(const Point<dim> &p,
+ const unsigned int /*component*/) const
+{
+ double product = 1;
+ for (unsigned int d = 0; d < dim; ++d)
+ product *= (p[d] + 1);
+ return product;
+}
+
+
+template <int dim>
+LaplaceProblem<dim>::LaplaceProblem()
+ : dof_handler(triangulation)
+ , max_degree(5)
+{
+ if (dim == 2)
+ for (unsigned int degree = 2; degree <= max_degree; ++degree)
+ {
+ fe_collection.push_back(FE_Q<dim>(degree));
+ quadrature_collection.push_back(QGauss<dim>(degree + 1));
+ face_quadrature_collection.push_back(QGauss<dim - 1>(degree + 1));
+ }
+ else
+ for (unsigned int degree = 1; degree < max_degree - 1; ++degree)
+ {
+ fe_collection.push_back(FE_Q<dim>(degree));
+ quadrature_collection.push_back(QGauss<dim>(degree + 1));
+ face_quadrature_collection.push_back(QGauss<dim - 1>(degree + 1));
+ }
+}
+
+
+template <int dim>
+LaplaceProblem<dim>::~LaplaceProblem()
+{
+ dof_handler.clear();
+}
+
+
+
+template <int dim>
+std::vector<types::global_dof_index>
+LaplaceProblem<dim>::get_conflict_indices(
+ typename DoFHandler<dim>::active_cell_iterator const &cell) const
+{
+ std::vector<types::global_dof_index> local_dof_indices(
+ cell->get_fe().dofs_per_cell);
+ cell->get_dof_indices(local_dof_indices);
+
+ constraints.resolve_indices(local_dof_indices);
+ return local_dof_indices;
+}
+
+template <int dim>
+void
+LaplaceProblem<dim>::setup_system()
+{
+ reference_matrix.clear();
+ test_matrix.clear();
+ dof_handler.distribute_dofs(fe_collection);
+
+ constraints.clear();
+
+ DoFTools::make_hanging_node_constraints(dof_handler, constraints);
+
+ // add boundary conditions as inhomogeneous constraints here, do it after
+ // having added the hanging node constraints in order to be consistent and
+ // skip dofs that are already constrained (i.e., are hanging nodes on the
+ // boundary in 3D). In contrast to step-27, we choose a sine function.
+ VectorTools::interpolate_boundary_values(dof_handler,
+ 0,
+ BoundaryValues<dim>(),
+ constraints);
+ constraints.close();
+
+ graph = GraphColoring::make_graph_coloring(
+ dof_handler.begin_active(),
+ dof_handler.end(),
+ static_cast<std::function<std::vector<types::global_dof_index>(
+ typename DoFHandler<dim>::active_cell_iterator const &)>>(
+ std::bind(&LaplaceProblem<dim>::get_conflict_indices,
+ this,
+ std::placeholders::_1)));
+
+
+ DynamicSparsityPattern csp(dof_handler.n_dofs(), dof_handler.n_dofs());
+ DoFTools::make_sparsity_pattern(dof_handler, csp, constraints, false);
+ reference_matrix.reinit(dof_handler.locally_owned_dofs(),
+ csp,
+ MPI_COMM_WORLD);
+ test_matrix.reinit(reference_matrix);
+ reference_rhs.reinit(reference_matrix.locally_owned_range_indices(),
+ reference_matrix.get_mpi_communicator());
+ test_rhs.reinit(reference_rhs);
+}
+
+
+
+template <int dim>
+void
+LaplaceProblem<dim>::local_assemble(
+ const typename DoFHandler<dim>::active_cell_iterator &cell,
+ Assembly::Scratch::Data<dim> & scratch,
+ Assembly::Copy::Data & data)
+{
+ const unsigned int dofs_per_cell = cell->get_fe().dofs_per_cell;
+
+ data.local_matrix.reinit(dofs_per_cell, dofs_per_cell);
+ data.local_matrix = 0;
+
+ data.local_rhs.reinit(dofs_per_cell);
+ data.local_rhs = 0;
+
+ scratch.hp_fe_values.reinit(cell);
+
+ const FEValues<dim> &fe_values = scratch.hp_fe_values.get_present_fe_values();
+
+ const RightHandSide<dim> rhs_function;
+
+ for (unsigned int q_point = 0; q_point < fe_values.n_quadrature_points;
+ ++q_point)
+ {
+ const double rhs_value =
+ rhs_function.value(fe_values.quadrature_point(q_point), 0);
+ for (unsigned int i = 0; i < dofs_per_cell; ++i)
+ {
+ for (unsigned int j = 0; j < dofs_per_cell; ++j)
+ data.local_matrix(i, j) +=
+ (fe_values.shape_grad(i, q_point) *
+ fe_values.shape_grad(j, q_point) * fe_values.JxW(q_point));
+
+ data.local_rhs(i) += (fe_values.shape_value(i, q_point) * rhs_value *
+ fe_values.JxW(q_point));
+ }
+ }
+
+ data.local_dof_indices.resize(dofs_per_cell);
+ cell->get_dof_indices(data.local_dof_indices);
+}
+
+
+
+template <int dim>
+void
+LaplaceProblem<dim>::copy_local_to_global(const Assembly::Copy::Data &data)
+{
+ constraints.distribute_local_to_global(data.local_matrix,
+ data.local_rhs,
+ data.local_dof_indices,
+ test_matrix,
+ test_rhs);
+}
+
+
+
+template <int dim>
+void
+LaplaceProblem<dim>::assemble_reference()
+{
+ test_matrix = 0;
+ test_rhs = 0;
+
+ Assembly::Copy::Data copy_data;
+ Assembly::Scratch::Data<dim> assembly_data(fe_collection,
+ quadrature_collection);
+
+ for (unsigned int color = 0; color < graph.size(); ++color)
+ for (typename std::vector<
+ typename DoFHandler<dim>::active_cell_iterator>::const_iterator p =
+ graph[color].begin();
+ p != graph[color].end();
+ ++p)
+ {
+ local_assemble(*p, assembly_data, copy_data);
+ copy_local_to_global(copy_data);
+ }
+ test_matrix.compress(VectorOperation::add);
+ test_rhs.compress(VectorOperation::add);
+
+ reference_matrix.add(1., test_matrix);
+ reference_rhs = test_rhs;
+}
+
+
+
+template <int dim>
+void
+LaplaceProblem<dim>::assemble_test()
+{
+ test_matrix = 0;
+ test_rhs = 0;
+
+ WorkStream::run(graph,
+ std::bind(&LaplaceProblem<dim>::local_assemble,
+ this,
+ std::placeholders::_1,
+ std::placeholders::_2,
+ std::placeholders::_3),
+ std::bind(&LaplaceProblem<dim>::copy_local_to_global,
+ this,
+ std::placeholders::_1),
+ Assembly::Scratch::Data<dim>(fe_collection,
+ quadrature_collection),
+ Assembly::Copy::Data(),
+ 2 * MultithreadInfo::n_threads(),
+ 1);
+ test_matrix.compress(VectorOperation::add);
+ test_rhs.compress(VectorOperation::add);
+
+ test_matrix.add(-1, reference_matrix);
+
+ // there should not even be roundoff difference between matrices
+ deallog << "error in matrix: " << test_matrix.frobenius_norm() << std::endl;
+ test_rhs.add(-1., reference_rhs);
+ deallog << "error in vector: " << test_rhs.l2_norm() << std::endl;
+}
+
+
+
+template <int dim>
+void
+LaplaceProblem<dim>::postprocess()
+{
+ Vector<float> estimated_error_per_cell(triangulation.n_active_cells());
+ for (unsigned int i = 0; i < estimated_error_per_cell.size(); ++i)
+ estimated_error_per_cell(i) = i;
+
+ GridRefinement::refine_and_coarsen_fixed_number(triangulation,
+ estimated_error_per_cell,
+ 0.3,
+ 0.03);
+ triangulation.execute_coarsening_and_refinement();
+
+ for (typename DoFHandler<dim>::active_cell_iterator cell =
+ dof_handler.begin_active();
+ cell != dof_handler.end();
+ ++cell)
+ cell->set_active_fe_index(rand() % fe_collection.size());
+}
+
+
+
+template <int dim>
+void
+LaplaceProblem<dim>::run()
+{
+ for (unsigned int cycle = 0; cycle < 3; ++cycle)
+ {
+ if (cycle == 0)
+ {
+ GridGenerator::hyper_cube(triangulation, 0, 1/* ,
+ Point<dim>(),
+ 0.5, 1., (dim==3) ? 96 : 12, false*/);
+ triangulation.refine_global(2);
+ }
+
+ setup_system();
+
+ assemble_reference();
+ assemble_test();
+
+ if (cycle < 2)
+ postprocess();
+ }
+}
+
+
+
+int
+main(int argc, char **argv)
+{
+ deallog << std::setprecision(2);
+ logfile << std::setprecision(2);
+ deallog.attach(logfile);
+
+ Utilities::MPI::MPI_InitFinalize mpi_initialization(
+ argc, argv, testing_max_num_threads());
+
+ {
+ deallog.push("2d");
+ LaplaceProblem<2> laplace_problem;
+ laplace_problem.run();
+ deallog.pop();
+ }
+
+ {
+ deallog.push("3d");
+ LaplaceProblem<3> laplace_problem;
+ laplace_problem.run();
+ deallog.pop();
+ }
+}
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