--- /dev/null
+# $Id$
+
+
+# For the small projects Makefile, you basically need to fill in only
+# four fields.
+#
+# The first is the name of the application. It is assumed that the
+# application name is the same as the base file name of the single C++
+# file from which the application is generated.
+target = $(basename $(shell echo step-*.cc))
+
+# The second field determines whether you want to run your program in
+# debug or optimized mode. The latter is significantly faster, but no
+# run-time checking of parameters and internal states is performed, so
+# you should set this value to `on' while you develop your program,
+# and to `off' when running production computations.
+debug-mode = on
+
+
+# As third field, we need to give the path to the top-level deal.II
+# directory. You need to adjust this to your needs. Since this path is
+# probably the most often needed one in the Makefile internals, it is
+# designated by a single-character variable, since that can be
+# reference using $D only, i.e. without the parentheses that are
+# required for most other parameters, as e.g. in $(target).
+D = ../../
+
+
+# The last field specifies the names of data and other files that
+# shall be deleted when calling `make clean'. Object and backup files,
+# executables and the like are removed anyway. Here, we give a list of
+# files in the various output formats that deal.II supports.
+clean-up-files = *gmv *gnuplot *gpl *eps *pov
+
+
+
+
+#
+#
+# Usually, you will not need to change something beyond this point.
+#
+#
+# The next statement tell the `make' program where to find the
+# deal.II top level directory and to include the file with the global
+# settings
+include $D/common/Make.global_options
+
+
+# Since the whole project consists of only one file, we need not
+# consider difficult dependencies. We only have to declare the
+# libraries which we want to link to the object file, and there need
+# to be two sets of libraries: one for the debug mode version of the
+# application and one for the optimized mode. Here we have selected
+# the versions for 2d. Note that the order in which the libraries are
+# given here is important and that your applications won't link
+# properly if they are given in another order.
+#
+# You may need to augment the lists of libraries when compiling your
+# program for other dimensions, or when using third party libraries
+libs.g = $(lib-deal2-2d.g) \
+ $(lib-lac.g) \
+ $(lib-base.g)
+libs.o = $(lib-deal2-2d.o) \
+ $(lib-lac.o) \
+ $(lib-base.o)
+
+
+# We now use the variable defined above which switch between debug and
+# optimized mode to select the set of libraries to link with. Included
+# in the list of libraries is the name of the object file which we
+# will produce from the single C++ file. Note that by default we use
+# the extension .g.o for object files compiled in debug mode and .o for
+# object files in optimized mode (or whatever the local default on your
+# system is instead of .o).
+ifeq ($(debug-mode),on)
+ libraries = $(target).g.$(OBJEXT) $(libs.g)
+else
+ libraries = $(target).$(OBJEXT) $(libs.o)
+endif
+
+
+# Now comes the first production rule: how to link the single object
+# file produced from the single C++ file into the executable. Since
+# this is the first rule in the Makefile, it is the one `make' selects
+# if you call it without arguments.
+$(target) : $(libraries)
+ @echo ============================ Linking $@
+ @$(CXX) -o $@$(EXEEXT) $^ $(LIBS) $(LDFLAGS)
+
+
+# To make running the application somewhat independent of the actual
+# program name, we usually declare a rule `run' which simply runs the
+# program. You can then run it by typing `make run'. This is also
+# useful if you want to call the executable with arguments which do
+# not change frequently. You may then want to add them to the
+# following rule:
+run: $(target)
+ @echo ============================ Running $<
+ @./$(target)$(EXEEXT)
+
+
+# As a last rule to the `make' program, we define what to do when
+# cleaning up a directory. This usually involves deleting object files
+# and other automatically created files such as the executable itself,
+# backup files, and data files. Since the latter are not usually quite
+# diverse, you needed to declare them at the top of this file.
+clean:
+ -rm -f *.$(OBJEXT) *~ Makefile.dep $(target)$(EXEEXT) $(clean-up-files)
+
+
+# Since we have not yet stated how to make an object file from a C++
+# file, we should do so now. Since the many flags passed to the
+# compiler are usually not of much interest, we suppress the actual
+# command line using the `at' sign in the first column of the rules
+# and write the string indicating what we do instead.
+./%.g.$(OBJEXT) :
+ @echo ==============debug========= $(<F)
+ @$(CXX) $(CXXFLAGS.g) -c $< -o $@
+./%.$(OBJEXT) :
+ @echo ==============optimized===== $(<F)
+ @$(CXX) $(CXXFLAGS.o) -c $< -o $@
+
+
+# The following statement tells make that the rules `run' and `clean'
+# are not expected to produce files of the same name as Makefile rules
+# usually do.
+.PHONY: run clean
+
+
+# Finally there is a rule which you normally need not care much about:
+# since the executable depends on some include files from the library,
+# besides the C++ application file of course, it is necessary to
+# re-generate the executable when one of the files it depends on has
+# changed. The following rule to created a dependency file
+# `Makefile.dep', which `make' uses to determine when to regenerate
+# the executable. This file is automagically remade whenever needed,
+# i.e. whenever one of the cc-/h-files changed. Make detects whether
+# to remake this file upon inclusion at the bottom of this file.
+Makefile.dep: $(target).cc Makefile \
+ $(shell echo $(include-path-base)/base/*.h \
+ $(include-path-lac)/lac/*.h \
+ $(include-path-deal2)/*/*.h)
+ @echo ============================ Remaking $@
+ @$D/common/scripts/make_dependencies $(INCLUDE) -B. $(target).cc \
+ > Makefile.dep
+
+# To make the dependencies known to `make', we finally have to include
+# them:
+include Makefile.dep
+
+
--- /dev/null
+/* $Id$ */
+/* Author: Wolfgang Bangerth, University of Heidelberg, 2000 */
+
+/* $Id$ */
+/* Version: $Name$ */
+/* */
+/* Copyright (C) 2004 by the deal.II authors */
+/* */
+/* This file is subject to QPL and may not be distributed */
+/* without copyright and license information. Please refer */
+/* to the file deal.II/doc/license.html for the text and */
+/* further information on this license. */
+
+#include <base/quadrature_lib.h>
+#include <base/function.h>
+#include <base/logstream.h>
+#include <lac/vector.h>
+#include <lac/full_matrix.h>
+
+ // xxx
+#include <lac/petsc_vector.h>
+#include <lac/petsc_sparse_matrix.h>
+#include <lac/petsc_solver.h>
+#include <lac/petsc_precondition.h>
+
+#include <grid/tria.h>
+#include <grid/grid_generator.h>
+#include <grid/grid_refinement.h>
+#include <grid/tria_accessor.h>
+#include <grid/tria_iterator.h>
+#include <grid/tria_boundary_lib.h>
+#include <dofs/dof_handler.h>
+#include <dofs/dof_accessor.h>
+#include <dofs/dof_tools.h>
+#include <fe/fe_values.h>
+#include <fe/fe_system.h>
+#include <fe/fe_q.h>
+#include <numerics/vectors.h>
+#include <numerics/matrices.h>
+#include <numerics/data_out.h>
+#include <dofs/dof_constraints.h>
+#include <numerics/error_estimator.h>
+
+ // xxx
+#include <grid/grid_tools.h>
+
+#include <fstream>
+#include <iostream>
+
+
+template <int dim>
+class ElasticProblem
+{
+ public:
+ ElasticProblem ();
+ ~ElasticProblem ();
+ void run ();
+
+ private:
+ void setup_system ();
+ void assemble_system ();
+ void solve ();
+ void refine_grid ();
+ void output_results (const unsigned int cycle) const;
+
+ Triangulation<dim> triangulation;
+ DoFHandler<dim> dof_handler;
+
+ FESystem<dim> fe;
+
+ ConstraintMatrix hanging_node_constraints;
+
+ // xxx no sparsity
+ PETScWrappers::SparseMatrix system_matrix;
+
+ PETScWrappers::Vector solution;
+ PETScWrappers::Vector system_rhs;
+
+ // xxx
+ const unsigned int n_partitions;
+ const unsigned int this_partition;
+};
+
+
+template <int dim>
+class RightHandSide : public Function<dim>
+{
+ public:
+ RightHandSide ();
+
+ virtual void vector_value (const Point<dim> &p,
+ Vector<double> &values) const;
+
+ virtual void vector_value_list (const std::vector<Point<dim> > &points,
+ std::vector<Vector<double> > &value_list) const;
+};
+
+
+template <int dim>
+RightHandSide<dim>::RightHandSide () :
+ Function<dim> (dim)
+{}
+
+
+template <int dim>
+inline
+void RightHandSide<dim>::vector_value (const Point<dim> &p,
+ Vector<double> &values) const
+{
+ Assert (values.size() == dim,
+ ExcDimensionMismatch (values.size(), dim));
+ Assert (dim >= 2, ExcInternalError());
+
+ Point<dim> point_1, point_2;
+ point_1(0) = 0.5;
+ point_2(0) = -0.5;
+
+ if (((p-point_1).square() < 0.2*0.2) ||
+ ((p-point_2).square() < 0.2*0.2))
+ values(0) = 1;
+ else
+ values(0) = 0;
+
+ if (p.square() < 0.2*0.2)
+ values(1) = 1;
+ else
+ values(1) = 0;
+}
+
+
+
+template <int dim>
+void RightHandSide<dim>::vector_value_list (const std::vector<Point<dim> > &points,
+ std::vector<Vector<double> > &value_list) const
+{
+ const unsigned int n_points = points.size();
+
+ Assert (value_list.size() == n_points,
+ ExcDimensionMismatch (value_list.size(), n_points));
+
+ for (unsigned int p=0; p<n_points; ++p)
+ RightHandSide<dim>::vector_value (points[p],
+ value_list[p]);
+}
+
+
+
+
+template <int dim>
+ElasticProblem<dim>::ElasticProblem ()
+ :
+ dof_handler (triangulation),
+ fe (FE_Q<dim>(1), dim),
+ // xxx
+ n_partitions (8),
+ this_partition (0)
+{}
+
+
+
+template <int dim>
+ElasticProblem<dim>::~ElasticProblem ()
+{
+ dof_handler.clear ();
+}
+
+
+template <int dim>
+void ElasticProblem<dim>::setup_system ()
+{
+ dof_handler.distribute_dofs (fe);
+ hanging_node_constraints.clear ();
+ DoFTools::make_hanging_node_constraints (dof_handler,
+ hanging_node_constraints);
+ hanging_node_constraints.close ();
+
+ // no sparsity pattern
+ system_matrix.reinit (dof_handler.n_dofs(),
+ dof_handler.n_dofs(),
+ dof_handler.max_couplings_between_dofs());
+
+ solution.reinit (dof_handler.n_dofs());
+ system_rhs.reinit (dof_handler.n_dofs());
+}
+
+
+template <int dim>
+void ElasticProblem<dim>::assemble_system ()
+{
+ // move to front
+ std::map<unsigned int,double> boundary_values;
+ VectorTools::interpolate_boundary_values (dof_handler,
+ 0,
+ ZeroFunction<dim>(dim),
+ boundary_values);
+
+ QGauss2<dim> quadrature_formula;
+ FEValues<dim> fe_values (fe, quadrature_formula,
+ UpdateFlags(update_values |
+ update_gradients |
+ update_q_points |
+ update_JxW_values));
+
+ const unsigned int dofs_per_cell = fe.dofs_per_cell;
+ const unsigned int n_q_points = quadrature_formula.n_quadrature_points;
+
+ FullMatrix<double> cell_matrix (dofs_per_cell, dofs_per_cell);
+ Vector<double> cell_rhs (dofs_per_cell);
+
+ std::vector<unsigned int> local_dof_indices (dofs_per_cell);
+
+ std::vector<double> lambda_values (n_q_points);
+ std::vector<double> mu_values (n_q_points);
+
+ ConstantFunction<dim> lambda(1.), mu(1.);
+
+ RightHandSide<dim> right_hand_side;
+ std::vector<Vector<double> > rhs_values (n_q_points,
+ Vector<double>(dim));
+
+
+ typename DoFHandler<dim>::active_cell_iterator cell = dof_handler.begin_active(),
+ endc = dof_handler.end();
+ for (; cell!=endc; ++cell)
+ {
+ cell_matrix.clear ();
+ cell_rhs.clear ();
+
+ fe_values.reinit (cell);
+
+ lambda.value_list (fe_values.get_quadrature_points(), lambda_values);
+ mu.value_list (fe_values.get_quadrature_points(), mu_values);
+
+ for (unsigned int i=0; i<dofs_per_cell; ++i)
+ {
+ const unsigned int
+ component_i = fe.system_to_component_index(i).first;
+
+ for (unsigned int j=0; j<dofs_per_cell; ++j)
+ {
+ const unsigned int
+ component_j = fe.system_to_component_index(j).first;
+
+ for (unsigned int q_point=0; q_point<n_q_points;
+ ++q_point)
+ {
+ cell_matrix(i,j)
+ +=
+ (
+ (fe_values.shape_grad(i,q_point)[component_i] *
+ fe_values.shape_grad(j,q_point)[component_j] *
+ lambda_values[q_point])
+ +
+ (fe_values.shape_grad(i,q_point)[component_j] *
+ fe_values.shape_grad(j,q_point)[component_i] *
+ mu_values[q_point])
+ +
+ ((component_i == component_j) ?
+ (fe_values.shape_grad(i,q_point) *
+ fe_values.shape_grad(j,q_point) *
+ mu_values[q_point]) :
+ 0)
+ )
+ *
+ fe_values.JxW(q_point);
+ };
+ };
+ };
+
+ right_hand_side.vector_value_list (fe_values.get_quadrature_points(),
+ rhs_values);
+ for (unsigned int i=0; i<dofs_per_cell; ++i)
+ {
+ const unsigned int
+ component_i = fe.system_to_component_index(i).first;
+
+ for (unsigned int q_point=0; q_point<n_q_points; ++q_point)
+ cell_rhs(i) += fe_values.shape_value(i,q_point) *
+ rhs_values[q_point](component_i) *
+ fe_values.JxW(q_point);
+ };
+
+ cell->get_dof_indices (local_dof_indices);
+
+ //xxx
+ MatrixTools::local_apply_boundary_values (boundary_values,
+ local_dof_indices,
+ cell_matrix,
+ cell_rhs,
+ false);
+
+ // xxx
+ hanging_node_constraints
+ .distribute_local_to_global (cell_matrix,
+ local_dof_indices,
+ system_matrix);
+
+ hanging_node_constraints
+ .distribute_local_to_global (cell_rhs,
+ local_dof_indices,
+ system_rhs);
+ }
+
+ //xxx no condense necessary, no apply_b_v
+ //either
+
+
+ // xxx
+ system_matrix.compress ();
+ system_rhs.compress ();
+}
+
+
+
+template <int dim>
+void ElasticProblem<dim>::solve ()
+{
+ // xxx
+ SolverControl solver_control (1000, 1e-10);
+ PETScWrappers::SolverCG cg (solver_control);
+
+ PETScWrappers::PreconditionSSOR preconditioner(system_matrix, 1.2);
+
+ cg.solve (system_matrix, solution, system_rhs,
+ preconditioner);
+
+ hanging_node_constraints.distribute (solution);
+}
+
+
+
+template <int dim>
+void ElasticProblem<dim>::refine_grid ()
+{
+ Vector<float> estimated_error_per_cell (triangulation.n_active_cells());
+
+ typename FunctionMap<dim>::type neumann_boundary;
+ KellyErrorEstimator<dim>::estimate (dof_handler,
+ QGauss2<dim-1>(),
+ neumann_boundary,
+ solution,
+ estimated_error_per_cell);
+
+ GridRefinement::refine_and_coarsen_fixed_number (triangulation,
+ estimated_error_per_cell,
+ 0.3, 0.03);
+
+ triangulation.execute_coarsening_and_refinement ();
+
+ // xxx
+ GridTools::partition_triangulation (n_partitions, triangulation);
+}
+
+
+template <int dim>
+void ElasticProblem<dim>::output_results (const unsigned int cycle) const
+{
+ std::string filename = "solution-";
+ filename += ('0' + cycle);
+ Assert (cycle < 10, ExcInternalError());
+
+ filename += ".gmv";
+ std::ofstream output (filename.c_str());
+
+ DataOut<dim> data_out;
+ data_out.attach_dof_handler (dof_handler);
+
+
+
+ std::vector<std::string> solution_names;
+ switch (dim)
+ {
+ case 1:
+ solution_names.push_back ("displacement");
+ break;
+ case 2:
+ solution_names.push_back ("x_displacement");
+ solution_names.push_back ("y_displacement");
+ break;
+ case 3:
+ solution_names.push_back ("x_displacement");
+ solution_names.push_back ("y_displacement");
+ solution_names.push_back ("z_displacement");
+ break;
+ default:
+ Assert (false, ExcInternalError());
+ };
+
+ data_out.add_data_vector (solution, solution_names);
+ data_out.build_patches ();
+ data_out.write_gmv (output);
+}
+
+
+
+template <int dim>
+void ElasticProblem<dim>::run ()
+{
+ for (unsigned int cycle=0; cycle<12; ++cycle)
+ {
+ std::cout << "Cycle " << cycle << ':' << std::endl;
+
+ if (cycle == 0)
+ {
+ GridGenerator::hyper_cube (triangulation, -1, 1);
+ triangulation.refine_global (2);
+
+ // xxx
+ GridTools::partition_triangulation (n_partitions, triangulation);
+ }
+ else
+ refine_grid ();
+
+ std::cout << " Number of active cells: "
+ << triangulation.n_active_cells()
+ << std::endl;
+
+ setup_system ();
+
+ std::cout << " Number of degrees of freedom: "
+ << dof_handler.n_dofs()
+ << std::endl;
+
+ assemble_system ();
+ solve ();
+ output_results (cycle);
+ };
+}
+
+
+int main (int argc, char **argv)
+{
+ try
+ {
+ // xxx
+ PetscInitialize(&argc,&argv,0,0);
+ deallog.depth_console (0);
+
+ // xxx localize scope
+ {
+ ElasticProblem<2> elastic_problem_2d;
+ elastic_problem_2d.run ();
+ }
+
+ // xxx
+ PetscFinalize();
+ }
+ catch (std::exception &exc)
+ {
+ std::cerr << std::endl << std::endl
+ << "----------------------------------------------------"
+ << std::endl;
+ std::cerr << "Exception on processing: " << std::endl
+ << exc.what() << std::endl
+ << "Aborting!" << std::endl
+ << "----------------------------------------------------"
+ << std::endl;
+
+ return 1;
+ }
+ catch (...)
+ {
+ std::cerr << std::endl << std::endl
+ << "----------------------------------------------------"
+ << std::endl;
+ std::cerr << "Unknown exception!" << std::endl
+ << "Aborting!" << std::endl
+ << "----------------------------------------------------"
+ << std::endl;
+ return 1;
+ };
+
+ return 0;
+}