Hello All !
I was trying the step-3
<https://www.dealii.org/current/doxygen/deal.II/step_3.html> with periodic
boundary conditions and dim = 2 and spacedim = 3. The main reason behind
this is I want to test periodic boundary conditions for dim != spacedim. I
have tested the code for dim = spacedim = 2 and the periodic boundary
conditions and it works (never mind the results for now !). I have also
tested the code for dim = 2 and spacedim = 3 without periodic boundary
conditions and it works too. But only when I add periodic conditions for
that case, the issue arises.
I got the following error,
error: undefined reference to 'void
dealii::DoFTools::make_periodicity_constraints<2, 3,
double>(dealii::DoFHandler<2, 3> const&, unsigned int, unsigned int, unsigned
int, dealii::AffineConstraints<double>&, dealii::ComponentMask const&, double)'
collect2: error: ld returned 1 exit status
make[2]: *** [CMakeFiles/step1.dir/build.make:139: step1] Error 1
make[1]: *** [CMakeFiles/Makefile2:76: CMakeFiles/step1.dir/all] Error 2
make: *** [Makefile:84: all] Error 2
The version that I am using is 9.3.0-pre. Although I am not really great at
C++ but according to the template
<https://github.com/dealii/dealii/blob/a56c8585863b774de9dce5f7dd5c334ef56f3a51/include/deal.II/dofs/dof_tools.h#L1144>
and source
<https://github.com/dealii/dealii/blob/a56c8585863b774de9dce5f7dd5c334ef56f3a51/source/dofs/dof_tools_constraints.cc#L2552>,
it should have worked, but I could not find anything here
<https://github.com/dealii/dealii/blob/a56c8585863b774de9dce5f7dd5c334ef56f3a51/source/dofs/dof_tools_constraints.inst.in#L69>.
I tried running it without template arguments or with only '2' as a
template argument, but couldn't make it work. I have attached the code
which I have tried, and also the code dim = 2 and spacedim = 3 without
periodic boundary conditions. Any help will be greatly appreciated.
Thank You
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/* ---------------------------------------------------------------------
*
* Copyright (C) 1999 - 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.
*
* ---------------------------------------------------------------------
*
* Authors: Wolfgang Bangerth, 1999,
* Guido Kanschat, 2011
*/
#include <deal.II/grid/tria.h>
#include <deal.II/dofs/dof_handler.h>
#include <deal.II/grid/grid_generator.h>
#include <deal.II/grid/tria_accessor.h>
#include <deal.II/grid/tria_iterator.h>
#include <deal.II/dofs/dof_accessor.h>
#include <deal.II/grid/grid_tools.h>
#include <deal.II/fe/fe_q.h>
#include <deal.II/dofs/dof_tools.h>
#include <deal.II/fe/fe_values.h>
#include <deal.II/fe/mapping_q.h>
#include <deal.II/base/quadrature_lib.h>
#include <deal.II/base/function.h>
#include <deal.II/numerics/vector_tools.h>
#include <deal.II/numerics/matrix_tools.h>
#include <deal.II/lac/vector.h>
#include <deal.II/lac/full_matrix.h>
#include <deal.II/lac/sparse_matrix.h>
#include <deal.II/lac/dynamic_sparsity_pattern.h>
#include <deal.II/lac/solver_cg.h>
#include <deal.II/lac/precondition.h>
#include <deal.II/lac/affine_constraints.h>
#include <deal.II/numerics/data_out.h>
#include <fstream>
#include <iostream>
using namespace dealii;
class Step3
{
public:
Step3();
void run();
private:
void make_grid();
void setup_system();
void assemble_system();
void solve();
void output_results() const;
Triangulation<2,3> triangulation;
FE_Q<2,3> fe;
DoFHandler<2,3> dof_handler;
MappingQ<2,3> mapping;
SparsityPattern sparsity_pattern;
SparseMatrix<double> system_matrix;
Vector<double> solution;
Vector<double> system_rhs;
};
Step3::Step3()
: fe(1)
, dof_handler(triangulation)
, mapping(2)
{}
void Step3::make_grid()
{
GridGenerator::subdivided_hyper_cube(triangulation, 10, -10.0, 10.0, 1);
// triangulation.refine_global(5);
std::cout << "Number of active cells: " << triangulation.n_active_cells()
<< std::endl;
}
void Step3::setup_system()
{
dof_handler.distribute_dofs(fe);
std::cout << "Number of degrees of freedom: " << dof_handler.n_dofs()
<< std::endl;
DynamicSparsityPattern dsp(dof_handler.n_dofs());
DoFTools::make_sparsity_pattern(dof_handler, dsp);
sparsity_pattern.copy_from(dsp);
system_matrix.reinit(sparsity_pattern);
solution.reinit(dof_handler.n_dofs());
system_rhs.reinit(dof_handler.n_dofs());
}
void Step3::assemble_system()
{
QGauss<2> quadrature_formula(fe.degree + 1);
FEValues<2,3> fe_values(mapping, fe,
quadrature_formula,
update_values | update_gradients | update_JxW_values);
const unsigned int dofs_per_cell = fe.dofs_per_cell;
FullMatrix<double> cell_matrix(dofs_per_cell, dofs_per_cell);
Vector<double> cell_rhs(dofs_per_cell);
std::vector<types::global_dof_index> local_dof_indices(dofs_per_cell);
for (const auto &cell : dof_handler.active_cell_iterators())
{
fe_values.reinit(cell);
cell_matrix = 0;
cell_rhs = 0;
for (const unsigned int q_index : fe_values.quadrature_point_indices())
{
for (const unsigned int i : fe_values.dof_indices())
for (const unsigned int j : fe_values.dof_indices())
cell_matrix(i, j) +=
(fe_values.shape_grad(i, q_index) * // grad phi_i(x_q)
fe_values.shape_grad(j, q_index) * // grad phi_j(x_q)
fe_values.JxW(q_index)); // dx
for (const unsigned int i : fe_values.dof_indices())
cell_rhs(i) += (fe_values.shape_value(i, q_index) * // phi_i(x_q)
1 * // f(x_q)
fe_values.JxW(q_index)); // dx
}
cell->get_dof_indices(local_dof_indices);
for (const unsigned int i : fe_values.dof_indices())
for (const unsigned int j : fe_values.dof_indices())
system_matrix.add(local_dof_indices[i],
local_dof_indices[j],
cell_matrix(i, j));
for (const unsigned int i : fe_values.dof_indices())
system_rhs(local_dof_indices[i]) += cell_rhs(i);
}
std::map<types::global_dof_index, double> boundary_values;
VectorTools::interpolate_boundary_values(mapping, dof_handler,
0,
Functions::ZeroFunction<3>(),
boundary_values);
MatrixTools::apply_boundary_values(boundary_values,
system_matrix,
solution,
system_rhs);
}
void Step3::solve()
{
SolverControl solver_control(1000, 1e-12);
SolverCG<Vector<double>> solver(solver_control);
solver.solve(system_matrix, solution, system_rhs, PreconditionIdentity());
}
void Step3::output_results() const
{
DataOut<2, DoFHandler<2,3>> data_out;
data_out.attach_dof_handler(dof_handler);
data_out.add_data_vector(solution, "solution");
data_out.build_patches();
std::ofstream output("solution.vtk");
data_out.write_vtk(output);
}
void Step3::run()
{
make_grid();
setup_system();
{
FEValuesExtractors::Scalar u(0);
std::vector<GridTools::PeriodicFacePair<typename DoFHandler<2,3>::cell_iterator>> periodicity_vector;
const unsigned int direction = 0;
GridTools::collect_periodic_faces(dof_handler, 0, 1, direction, periodicity_vector);
std::cout << "\nSize of periodicity_vector : " << periodicity_vector.size() << std::endl;
AffineConstraints<double> constraints;
constraints.clear();
DoFTools::make_periodicity_constraints<2,3>(dof_handler, 0, 1, direction, constraints, fe.component_mask(u));
constraints.close();
}
assemble_system();
solve();
output_results();
}
int main()
{
deallog.depth_console(2);
Step3 laplace_problem;
laplace_problem.run();
return 0;
}/* ---------------------------------------------------------------------
*
* Copyright (C) 1999 - 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.
*
* ---------------------------------------------------------------------
*
* Authors: Wolfgang Bangerth, 1999,
* Guido Kanschat, 2011
*/
#include <deal.II/grid/tria.h>
#include <deal.II/dofs/dof_handler.h>
#include <deal.II/grid/grid_generator.h>
#include <deal.II/grid/tria_accessor.h>
#include <deal.II/grid/tria_iterator.h>
#include <deal.II/dofs/dof_accessor.h>
#include <deal.II/grid/grid_tools.h>
#include <deal.II/fe/fe_q.h>
#include <deal.II/dofs/dof_tools.h>
#include <deal.II/fe/fe_values.h>
#include <deal.II/fe/mapping_q.h>
#include <deal.II/base/quadrature_lib.h>
#include <deal.II/base/function.h>
#include <deal.II/numerics/vector_tools.h>
#include <deal.II/numerics/matrix_tools.h>
#include <deal.II/lac/vector.h>
#include <deal.II/lac/full_matrix.h>
#include <deal.II/lac/sparse_matrix.h>
#include <deal.II/lac/dynamic_sparsity_pattern.h>
#include <deal.II/lac/solver_cg.h>
#include <deal.II/lac/precondition.h>
#include <deal.II/lac/affine_constraints.h>
#include <deal.II/numerics/data_out.h>
#include <fstream>
#include <iostream>
using namespace dealii;
class Step3
{
public:
Step3();
void run();
private:
void make_grid();
void setup_system();
void assemble_system();
void solve();
void output_results() const;
Triangulation<2,3> triangulation;
FE_Q<2,3> fe;
DoFHandler<2,3> dof_handler;
MappingQ<2,3> mapping;
SparsityPattern sparsity_pattern;
SparseMatrix<double> system_matrix;
Vector<double> solution;
Vector<double> system_rhs;
};
Step3::Step3()
: fe(1)
, dof_handler(triangulation)
, mapping(2)
{}
void Step3::make_grid()
{
GridGenerator::subdivided_hyper_cube(triangulation, 10, -10.0, 10.0, 1);
// triangulation.refine_global(5);
std::cout << "Number of active cells: " << triangulation.n_active_cells()
<< std::endl;
}
void Step3::setup_system()
{
dof_handler.distribute_dofs(fe);
std::cout << "Number of degrees of freedom: " << dof_handler.n_dofs()
<< std::endl;
DynamicSparsityPattern dsp(dof_handler.n_dofs());
DoFTools::make_sparsity_pattern(dof_handler, dsp);
sparsity_pattern.copy_from(dsp);
system_matrix.reinit(sparsity_pattern);
solution.reinit(dof_handler.n_dofs());
system_rhs.reinit(dof_handler.n_dofs());
}
void Step3::assemble_system()
{
QGauss<2> quadrature_formula(fe.degree + 1);
FEValues<2,3> fe_values(mapping, fe,
quadrature_formula,
update_values | update_gradients | update_JxW_values);
const unsigned int dofs_per_cell = fe.dofs_per_cell;
FullMatrix<double> cell_matrix(dofs_per_cell, dofs_per_cell);
Vector<double> cell_rhs(dofs_per_cell);
std::vector<types::global_dof_index> local_dof_indices(dofs_per_cell);
for (const auto &cell : dof_handler.active_cell_iterators())
{
fe_values.reinit(cell);
cell_matrix = 0;
cell_rhs = 0;
for (const unsigned int q_index : fe_values.quadrature_point_indices())
{
for (const unsigned int i : fe_values.dof_indices())
for (const unsigned int j : fe_values.dof_indices())
cell_matrix(i, j) +=
(fe_values.shape_grad(i, q_index) * // grad phi_i(x_q)
fe_values.shape_grad(j, q_index) * // grad phi_j(x_q)
fe_values.JxW(q_index)); // dx
for (const unsigned int i : fe_values.dof_indices())
cell_rhs(i) += (fe_values.shape_value(i, q_index) * // phi_i(x_q)
1 * // f(x_q)
fe_values.JxW(q_index)); // dx
}
cell->get_dof_indices(local_dof_indices);
for (const unsigned int i : fe_values.dof_indices())
for (const unsigned int j : fe_values.dof_indices())
system_matrix.add(local_dof_indices[i],
local_dof_indices[j],
cell_matrix(i, j));
for (const unsigned int i : fe_values.dof_indices())
system_rhs(local_dof_indices[i]) += cell_rhs(i);
}
std::map<types::global_dof_index, double> boundary_values;
VectorTools::interpolate_boundary_values(mapping, dof_handler,
0,
Functions::ZeroFunction<3>(),
boundary_values);
MatrixTools::apply_boundary_values(boundary_values,
system_matrix,
solution,
system_rhs);
}
void Step3::solve()
{
SolverControl solver_control(1000, 1e-12);
SolverCG<Vector<double>> solver(solver_control);
solver.solve(system_matrix, solution, system_rhs, PreconditionIdentity());
}
void Step3::output_results() const
{
DataOut<2, DoFHandler<2,3>> data_out;
data_out.attach_dof_handler(dof_handler);
data_out.add_data_vector(solution, "solution");
data_out.build_patches();
std::ofstream output("solution.vtk");
data_out.write_vtk(output);
}
void Step3::run()
{
make_grid();
setup_system();
{
FEValuesExtractors::Scalar u(0);
std::vector<GridTools::PeriodicFacePair<typename DoFHandler<2,3>::cell_iterator>> periodicity_vector;
const unsigned int direction = 0;
GridTools::collect_periodic_faces(dof_handler, 0, 1, direction, periodicity_vector);
std::cout << "\nSize of periodicity_vector : " << periodicity_vector.size() << std::endl;
// AffineConstraints<double> constraints;
// constraints.clear();
// DoFTools::make_periodicity_constraints<2,3>(dof_handler, 0, 1, direction, constraints, fe.component_mask(u));
// constraints.close();
}
assemble_system();
solve();
output_results();
}
int main()
{
deallog.depth_console(2);
Step3 laplace_problem;
laplace_problem.run();
return 0;
}
