--- /dev/null
+/* ---------------------------------------------------------------------
+ *
+ * Copyright (C) 2021 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.
+ *
+ * ---------------------------------------------------------------------
+ */
+
+
+// step-77 for the test suite - verifies KINSOL.
+
+#include <deal.II/base/function.h>
+#include <deal.II/base/mpi.h>
+#include <deal.II/base/quadrature_lib.h>
+#include <deal.II/base/utilities.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/fe/fe_values.h>
+
+#include <deal.II/grid/grid_generator.h>
+#include <deal.II/grid/grid_refinement.h>
+#include <deal.II/grid/tria.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/sparse_direct.h>
+#include <deal.II/lac/sparse_matrix.h>
+#include <deal.II/lac/vector.h>
+
+#include <deal.II/numerics/data_out.h>
+#include <deal.II/numerics/error_estimator.h>
+#include <deal.II/numerics/matrix_tools.h>
+#include <deal.II/numerics/solution_transfer.h>
+#include <deal.II/numerics/vector_tools.h>
+
+#include <deal.II/sundials/kinsol.h>
+
+#include "../tests.h"
+
+namespace Step77
+{
+ using namespace dealii;
+
+ template <int dim>
+ class MinimalSurfaceProblem
+ {
+ public:
+ MinimalSurfaceProblem();
+ void
+ run();
+
+ private:
+ void
+ setup_system(const bool initial_step);
+ void
+ solve(const Vector<double> &rhs,
+ Vector<double> & solution,
+ const double tolerance);
+ void
+ refine_mesh();
+ void
+ output_results(const unsigned int refinement_cycle);
+ void
+ set_boundary_values();
+ void
+ compute_and_factorize_jacobian(const Vector<double> &evaluation_point);
+ void
+ compute_residual(const Vector<double> &evaluation_point,
+ Vector<double> & residual);
+
+ Triangulation<dim> triangulation;
+
+ DoFHandler<dim> dof_handler;
+ FE_Q<dim> fe;
+
+ AffineConstraints<double> hanging_node_constraints;
+
+ SparsityPattern sparsity_pattern;
+ SparseMatrix<double> jacobian_matrix;
+ std::unique_ptr<SparseDirectUMFPACK> jacobian_matrix_factorization;
+
+ Vector<double> current_solution;
+
+ // unlike step-77, don't output timer information.
+ };
+
+
+
+ template <int dim>
+ class BoundaryValues : public Function<dim>
+ {
+ public:
+ virtual double
+ value(const Point<dim> &p, const unsigned int component = 0) const override;
+ };
+
+
+ template <int dim>
+ double
+ BoundaryValues<dim>::value(const Point<dim> &p,
+ const unsigned int /*component*/) const
+ {
+ return std::sin(2 * numbers::PI * (p[0] + p[1]));
+ }
+
+
+
+ template <int dim>
+ MinimalSurfaceProblem<dim>::MinimalSurfaceProblem()
+ : dof_handler(triangulation)
+ , fe(1)
+ {}
+
+
+
+ template <int dim>
+ void
+ MinimalSurfaceProblem<dim>::setup_system(const bool initial_step)
+ {
+ if (initial_step)
+ {
+ dof_handler.distribute_dofs(fe);
+ current_solution.reinit(dof_handler.n_dofs());
+
+ hanging_node_constraints.clear();
+ DoFTools::make_hanging_node_constraints(dof_handler,
+ hanging_node_constraints);
+ hanging_node_constraints.close();
+ }
+
+ DynamicSparsityPattern dsp(dof_handler.n_dofs());
+ DoFTools::make_sparsity_pattern(dof_handler, dsp);
+
+ hanging_node_constraints.condense(dsp);
+
+ sparsity_pattern.copy_from(dsp);
+ jacobian_matrix.reinit(sparsity_pattern);
+ jacobian_matrix_factorization.reset();
+ }
+
+
+
+ template <int dim>
+ void
+ MinimalSurfaceProblem<dim>::compute_and_factorize_jacobian(
+ const Vector<double> &evaluation_point)
+ {
+ {
+ const QGauss<dim> quadrature_formula(fe.degree + 1);
+
+ jacobian_matrix = 0;
+
+ FEValues<dim> fe_values(fe,
+ quadrature_formula,
+ update_gradients | update_quadrature_points |
+ update_JxW_values);
+
+ const unsigned int dofs_per_cell = fe.n_dofs_per_cell();
+ const unsigned int n_q_points = quadrature_formula.size();
+
+ FullMatrix<double> cell_matrix(dofs_per_cell, dofs_per_cell);
+
+ std::vector<Tensor<1, dim>> evaluation_point_gradients(n_q_points);
+
+ std::vector<types::global_dof_index> local_dof_indices(dofs_per_cell);
+
+ for (const auto &cell : dof_handler.active_cell_iterators())
+ {
+ cell_matrix = 0;
+
+ fe_values.reinit(cell);
+
+ fe_values.get_function_gradients(evaluation_point,
+ evaluation_point_gradients);
+
+ for (unsigned int q = 0; q < n_q_points; ++q)
+ {
+ const double coeff =
+ 1.0 / std::sqrt(1 + evaluation_point_gradients[q] *
+ evaluation_point_gradients[q]);
+
+ for (unsigned int i = 0; i < dofs_per_cell; ++i)
+ {
+ for (unsigned int j = 0; j < dofs_per_cell; ++j)
+ cell_matrix(i, j) +=
+ (((fe_values.shape_grad(i, q) // ((\nabla \phi_i
+ * coeff // * a_n
+ * fe_values.shape_grad(j, q)) // * \nabla \phi_j)
+ - // -
+ (fe_values.shape_grad(i, q) // (\nabla \phi_i
+ * coeff * coeff * coeff // * a_n^3
+ *
+ (fe_values.shape_grad(j, q) // * (\nabla \phi_j
+ * evaluation_point_gradients[q]) // * \nabla u_n)
+ * evaluation_point_gradients[q])) // * \nabla u_n)))
+ * fe_values.JxW(q)); // * dx
+ }
+ }
+
+ cell->get_dof_indices(local_dof_indices);
+ hanging_node_constraints.distribute_local_to_global(cell_matrix,
+ local_dof_indices,
+ jacobian_matrix);
+ }
+
+ std::map<types::global_dof_index, double> boundary_values;
+ VectorTools::interpolate_boundary_values(dof_handler,
+ 0,
+ Functions::ZeroFunction<dim>(),
+ boundary_values);
+ Vector<double> dummy_solution(dof_handler.n_dofs());
+ Vector<double> dummy_rhs(dof_handler.n_dofs());
+ MatrixTools::apply_boundary_values(boundary_values,
+ jacobian_matrix,
+ dummy_solution,
+ dummy_rhs);
+ }
+
+ {
+ jacobian_matrix_factorization = std::make_unique<SparseDirectUMFPACK>();
+ jacobian_matrix_factorization->factorize(jacobian_matrix);
+ }
+ }
+
+
+
+ template <int dim>
+ void
+ MinimalSurfaceProblem<dim>::compute_residual(
+ const Vector<double> &evaluation_point,
+ Vector<double> & residual)
+ {
+ const QGauss<dim> quadrature_formula(fe.degree + 1);
+ FEValues<dim> fe_values(fe,
+ quadrature_formula,
+ update_gradients | update_quadrature_points |
+ update_JxW_values);
+
+ const unsigned int dofs_per_cell = fe.n_dofs_per_cell();
+ const unsigned int n_q_points = quadrature_formula.size();
+
+ Vector<double> cell_residual(dofs_per_cell);
+ std::vector<Tensor<1, dim>> evaluation_point_gradients(n_q_points);
+
+ std::vector<types::global_dof_index> local_dof_indices(dofs_per_cell);
+
+ for (const auto &cell : dof_handler.active_cell_iterators())
+ {
+ cell_residual = 0;
+ fe_values.reinit(cell);
+
+ fe_values.get_function_gradients(evaluation_point,
+ evaluation_point_gradients);
+
+
+ for (unsigned int q = 0; q < n_q_points; ++q)
+ {
+ const double coeff =
+ 1.0 / std::sqrt(1 + evaluation_point_gradients[q] *
+ evaluation_point_gradients[q]);
+
+ for (unsigned int i = 0; i < dofs_per_cell; ++i)
+ cell_residual(i) =
+ (fe_values.shape_grad(i, q) // \nabla \phi_i
+ * coeff // * a_n
+ * evaluation_point_gradients[q] // * \nabla u_n
+ * fe_values.JxW(q)); // * dx
+ }
+
+ cell->get_dof_indices(local_dof_indices);
+ for (unsigned int i = 0; i < dofs_per_cell; ++i)
+ residual(local_dof_indices[i]) += cell_residual(i);
+ }
+
+ hanging_node_constraints.condense(residual);
+
+ for (const types::global_dof_index i :
+ DoFTools::extract_boundary_dofs(dof_handler))
+ residual(i) = 0;
+
+ for (const types::global_dof_index i :
+ DoFTools::extract_hanging_node_dofs(dof_handler))
+ residual(i) = 0;
+ }
+
+
+
+ template <int dim>
+ void
+ MinimalSurfaceProblem<dim>::solve(const Vector<double> &rhs,
+ Vector<double> & solution,
+ const double /*tolerance*/)
+ {
+ jacobian_matrix_factorization->vmult(solution, rhs);
+
+ hanging_node_constraints.distribute(solution);
+ }
+
+
+
+ template <int dim>
+ void
+ MinimalSurfaceProblem<dim>::refine_mesh()
+ {
+ Vector<float> estimated_error_per_cell(triangulation.n_active_cells());
+
+ KellyErrorEstimator<dim>::estimate(
+ dof_handler,
+ QGauss<dim - 1>(fe.degree + 1),
+ std::map<types::boundary_id, const Function<dim> *>(),
+ current_solution,
+ estimated_error_per_cell);
+
+ GridRefinement::refine_and_coarsen_fixed_number(triangulation,
+ estimated_error_per_cell,
+ 0.3,
+ 0.03);
+
+ triangulation.prepare_coarsening_and_refinement();
+
+ SolutionTransfer<dim> solution_transfer(dof_handler);
+ solution_transfer.prepare_for_coarsening_and_refinement(current_solution);
+
+ triangulation.execute_coarsening_and_refinement();
+
+ dof_handler.distribute_dofs(fe);
+
+ Vector<double> tmp(dof_handler.n_dofs());
+ solution_transfer.interpolate(current_solution, tmp);
+ current_solution = std::move(tmp);
+
+ hanging_node_constraints.clear();
+
+ DoFTools::make_hanging_node_constraints(dof_handler,
+ hanging_node_constraints);
+ hanging_node_constraints.close();
+
+ hanging_node_constraints.distribute(current_solution);
+
+ set_boundary_values();
+
+ setup_system(/*initial_step=*/false);
+ }
+
+
+
+ template <int dim>
+ void
+ MinimalSurfaceProblem<dim>::set_boundary_values()
+ {
+ std::map<types::global_dof_index, double> boundary_values;
+ VectorTools::interpolate_boundary_values(dof_handler,
+ 0,
+ BoundaryValues<dim>(),
+ boundary_values);
+ for (const auto &boundary_value : boundary_values)
+ current_solution(boundary_value.first) = boundary_value.second;
+
+ hanging_node_constraints.distribute(current_solution);
+ }
+
+
+
+ template <int dim>
+ void
+ MinimalSurfaceProblem<dim>::output_results(
+ const unsigned int refinement_cycle)
+ {
+ DataOut<dim> data_out;
+
+ data_out.attach_dof_handler(dof_handler);
+ data_out.add_data_vector(current_solution, "solution");
+ data_out.build_patches();
+
+ deallog << "Current refinement cycle = " << refinement_cycle << std::endl;
+ data_out.write_vtk(deallog.get_file_stream());
+ }
+
+
+
+ template <int dim>
+ void
+ MinimalSurfaceProblem<dim>::run()
+ {
+ GridGenerator::hyper_ball(triangulation);
+ triangulation.refine_global(2);
+
+ setup_system(/*initial_step=*/true);
+ set_boundary_values();
+
+ for (unsigned int refinement_cycle = 0; refinement_cycle < 3;
+ ++refinement_cycle)
+ {
+ if (refinement_cycle != 0)
+ refine_mesh();
+
+ const double target_tolerance = 1e-10 * std::pow(0.1, refinement_cycle);
+
+ {
+ typename SUNDIALS::KINSOL<Vector<double>>::AdditionalData
+ additional_data;
+ additional_data.function_tolerance = target_tolerance;
+
+ SUNDIALS::KINSOL<Vector<double>> nonlinear_solver(additional_data);
+
+ nonlinear_solver.reinit_vector = [&](Vector<double> &x) {
+ x.reinit(dof_handler.n_dofs());
+ };
+
+ nonlinear_solver.residual =
+ [&](const Vector<double> &evaluation_point,
+ Vector<double> & residual) {
+ compute_residual(evaluation_point, residual);
+
+ return 0;
+ };
+
+ nonlinear_solver.setup_jacobian =
+ [&](const Vector<double> ¤t_u,
+ const Vector<double> & /*current_f*/) {
+ compute_and_factorize_jacobian(current_u);
+
+ return 0;
+ };
+
+ nonlinear_solver.solve_with_jacobian = [&](const Vector<double> &rhs,
+ Vector<double> & dst,
+ const double tolerance) {
+ this->solve(rhs, dst, tolerance);
+
+ return 0;
+ };
+
+ nonlinear_solver.solve(current_solution);
+ }
+
+ output_results(refinement_cycle);
+ }
+ }
+} // namespace Step77
+
+
+int
+main(int argc, char **argv)
+{
+ initlog();
+ using namespace Step77;
+ // SUNDIALS will duplicate communicators even if we are running in serial
+#ifdef DEAL_II_WITH_MPI
+ dealii::Utilities::MPI::MPI_InitFinalize mpi_initialization(argc, argv, 1);
+#else
+ (void)argc;
+ (void)argv;
+#endif
+
+ MinimalSurfaceProblem<2> laplace_problem_2d;
+ laplace_problem_2d.run();
+ return 0;
+}
--- /dev/null
+
+DEAL::Current refinement cycle = 0
+# vtk DataFile Version 3.0
+#This file was generated
+ASCII
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+
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projects / dealii.git / commitdiff