Reference documentation for deal.II version Git a0ed999 2017-04-23 20:28:47 -0600
The 'Convection Diffusion Reaction' code gallery program

This program was contributed by David R. Wells wellsd2@rpi.edu.
It comes without any warranty or support by its authors or the authors of deal.II.

This program is part of the deal.II code gallery and consists of the following files (click to inspect):

Annotated version of readme.md

Overview

I started this project with the intent of better understanding adaptive mesh refinement, parallel computing, and CMake. In particular, I started by writing a uniform mesh, single process solver and then ultimately expanded it into solver/cdr.cc. This example program might be useful to look at if you want to see:

The other solvers are available here.

Unlike the other tutorial programs, I have split this solver into a number of files in nested directories. In particular, I used the following strategy (more-or-less copied ASPECT):

Requirements

Compiling and running

Like the example programs, run

1 cmake -DDEAL_II_DIR=/path/to/deal.II .
2 make

in this directory. The solver may be run as

1 make run

or, for parallelism across 16 processes,

1 mpirun -np 16 ./cdr

Why use convection-diffusion-reaction?

This equation exhibits very fine boundary layers (usually, from the literature, these layers have width equal to the square root of the diffusion coefficient on internal layers and the diffusion coefficient on boundary layers). A good way to solve it is to use adaptive mesh refinement to refine the mesh only at interior boundary layers. At the same time, this problem is linear (and does not have a pressure term) so it is much simpler to solve than the Navier-Stokes equations with comparable diffusion (Reynolds number).

I use relatively large diffusion values so I can get away without any additional scheme like SUPG.

Recommended Literature

There are many good books and papers on numerical methods for this equation. A good starting point is "Robust Numerical Methods for Singularly Perturbed Problems" by Roos, Stynes, and Tobiska.

Annotated version of common/include/deal.II-cdr/parameters.h

#ifndef dealii__cdr_parameters_h
#define dealii__cdr_parameters_h
#include <deal.II/base/parameter_handler.h>
#include <string>

I prefer to use the ParameterHandler class in a slightly different way than usual: The class Parameters creates, uses, and then destroys a ParameterHandler inside the read_parameter_file method instead of keeping it around. This is nice because now all of the run time parameters are contained in a simple class and it can be copied or passed around very easily.

namespace CDR
{
using namespace dealii;
class Parameters
{
public:
double inner_radius;
double outer_radius;
double diffusion_coefficient;
double reaction_coefficient;
bool time_dependent_forcing;
unsigned int initial_refinement_level;
unsigned int max_refinement_level;
unsigned int fe_order;
double start_time;
double stop_time;
unsigned int n_time_steps;
unsigned int save_interval;
unsigned int patch_level;
void read_parameter_file(const std::string &file_name);
private:
void configure_parameter_handler(ParameterHandler &parameter_handler);
};
}
#endif

Annotated version of common/include/deal.II-cdr/system_matrix.h

#ifndef dealii__cdr_system_matrix_h
#define dealii__cdr_system_matrix_h
#include <deal.II/base/quadrature_lib.h>
#include <deal.II/dofs/dof_handler.h>
#include <deal.II/lac/constraint_matrix.h>
#include <deal.II-cdr/parameters.h>
#include <functional>

One of the goals I had in writing this entry was to split up functions into different compilation units instead of using one large file. This is the header file for a pair of functions (only one of which I ultimately use) which build the system matrix.

namespace CDR
{
using namespace dealii;
template<int dim, typename MatrixType>
void create_system_matrix
(const DoFHandler<dim> &dof_handler,
const QGauss<dim> &quad,
const std::function<Tensor<1, dim>(const Point<dim>)> &convection_function,
const CDR::Parameters &parameters,
const double time_step,
MatrixType &system_matrix);
template<int dim, typename MatrixType>
void create_system_matrix
(const DoFHandler<dim> &dof_handler,
const QGauss<dim> &quad,
const std::function<Tensor<1, dim>(const Point<dim>)> &convection_function,
const CDR::Parameters &parameters,
const double time_step,
const ConstraintMatrix &constraints,
MatrixType &system_matrix);
}
#endif

Annotated version of common/include/deal.II-cdr/system_matrix.templates.h

#ifndef dealii__cdr_system_matrix_templates_h
#define dealii__cdr_system_matrix_templates_h
#include <deal.II/base/quadrature_lib.h>
#include <deal.II/dofs/dof_handler.h>
#include <deal.II/lac/constraint_matrix.h>
#include <deal.II/fe/fe_q.h>
#include <deal.II/fe/fe_values.h>
#include <deal.II-cdr/parameters.h>
#include <deal.II-cdr/system_matrix.h>
#include <functional>
#include <vector>
namespace CDR
{
using namespace dealii;

This is the actual implementation of the create_system_matrix function described in the header file. It is similar to the system matrix assembly routine in step-40.

template<int dim, typename UpdateFunction>
void internal_create_system_matrix
(const DoFHandler<dim> &dof_handler,
const QGauss<dim> &quad,
const std::function<Tensor<1, dim>(const Point<dim>)> &convection_function,
const CDR::Parameters &parameters,
const double time_step,
UpdateFunction update_system_matrix)
{
auto &fe = dof_handler.get_fe();
const auto dofs_per_cell = fe.dofs_per_cell;
FullMatrix<double> cell_matrix(dofs_per_cell, dofs_per_cell);
std::vector<types::global_dof_index> local_indices(dofs_per_cell);
for (const auto &cell : dof_handler.active_cell_iterators())
{
if (cell->is_locally_owned())
{
fe_values.reinit(cell);
cell_matrix = 0.0;
cell->get_dof_indices(local_indices);
for (unsigned int q = 0; q < quad.size(); ++q)
{
const auto current_convection =
convection_function(fe_values.quadrature_point(q));
for (unsigned int i = 0; i < dofs_per_cell; ++i)
{
for (unsigned int j = 0; j < dofs_per_cell; ++j)
{
const auto convection_contribution = current_convection
*fe_values.shape_grad(j, q);
cell_matrix(i, j) += fe_values.JxW(q)*

Here are the time step, mass, and reaction parts:

((1.0 + time_step/2.0*parameters.reaction_coefficient)
*fe_values.shape_value(i, q)*fe_values.shape_value(j, q)
+ time_step/2.0*

and the convection part:

(fe_values.shape_value(i, q)*convection_contribution

and, finally, the diffusion part:

+ parameters.diffusion_coefficient
*(fe_values.shape_grad(i, q)*fe_values.shape_grad(j, q)))
);
}
}
}
update_system_matrix(local_indices, cell_matrix);
}
}
}
template<int dim, typename MatrixType>
void create_system_matrix
(const DoFHandler<dim> &dof_handler,
const QGauss<dim> &quad,
const std::function<Tensor<1, dim>(const Point<dim>)> &convection_function,
const CDR::Parameters &parameters,
const double time_step,
const ConstraintMatrix &constraints,
MatrixType &system_matrix)
{
internal_create_system_matrix<dim>
(dof_handler, quad, convection_function, parameters, time_step,
[&constraints, &system_matrix](const std::vector<types::global_dof_index> &local_indices,
const FullMatrix<double> &cell_matrix)
{
constraints.distribute_local_to_global
(cell_matrix, local_indices, system_matrix);
});
}
template<int dim, typename MatrixType>
void create_system_matrix
(const DoFHandler<dim> &dof_handler,
const QGauss<dim> &quad,
const std::function<Tensor<1, dim>(const Point<dim>)> &convection_function,
const CDR::Parameters &parameters,
const double time_step,
MatrixType &system_matrix)
{
internal_create_system_matrix<dim>
(dof_handler, quad, convection_function, parameters, time_step,
[&system_matrix](const std::vector<types::global_dof_index> &local_indices,
const FullMatrix<double> &cell_matrix)
{
system_matrix.add(local_indices, cell_matrix);
});
}
}
#endif

Annotated version of common/include/deal.II-cdr/system_rhs.h

#ifndef dealii__cdr_system_rhs_h
#define dealii__cdr_system_rhs_h
#include <deal.II/base/point.h>
#include <deal.II/base/quadrature_lib.h>
#include <deal.II/base/tensor.h>
#include <deal.II/dofs/dof_handler.h>
#include <deal.II/lac/constraint_matrix.h>
#include <deal.II-cdr/parameters.h>
#include <functional>

Similarly to create_system_matrix, I wrote a separate function to compute the right hand side.

namespace CDR
{
using namespace dealii;
template<int dim, typename VectorType>
void create_system_rhs
(const DoFHandler<dim> &dof_handler,
const QGauss<dim> &quad,
const std::function<Tensor<1, dim>(const Point<dim>)> &convection_function,
const std::function<double(double, const Point<dim>)> &forcing_function,
const CDR::Parameters &parameters,
const VectorType &previous_solution,
const ConstraintMatrix &constraints,
const double current_time,
VectorType &system_rhs);
}
#endif

Annotated version of common/include/deal.II-cdr/system_rhs.templates.h

#ifndef dealii__cdr_system_rhs_templates_h
#define dealii__cdr_system_rhs_templates_h
#include <deal.II/base/point.h>
#include <deal.II/base/quadrature_lib.h>
#include <deal.II/base/tensor.h>
#include <deal.II/dofs/dof_handler.h>
#include <deal.II/fe/fe_q.h>
#include <deal.II/fe/fe_values.h>
#include <deal.II/lac/constraint_matrix.h>
#include <deal.II/lac/vector.h>
#include <deal.II-cdr/parameters.h>
#include <deal.II-cdr/system_rhs.h>
#include <functional>
#include <vector>
namespace CDR
{
using namespace dealii;
template<int dim, typename VectorType>
void create_system_rhs
(const DoFHandler<dim> &dof_handler,
const QGauss<dim> &quad,
const std::function<Tensor<1, dim>(const Point<dim>)> &convection_function,
const std::function<double(double, const Point<dim>)> &forcing_function,
const CDR::Parameters &parameters,
const VectorType &previous_solution,
const ConstraintMatrix &constraints,
const double current_time,
VectorType &system_rhs)
{
auto &fe = dof_handler.get_fe();
const auto dofs_per_cell = fe.dofs_per_cell;
const double time_step = (parameters.stop_time - parameters.start_time)
/parameters.n_time_steps;
Vector<double> cell_rhs(dofs_per_cell);
FullMatrix<double> cell_matrix(dofs_per_cell, dofs_per_cell);
Vector<double> current_fe_coefficients(dofs_per_cell);
std::vector<types::global_dof_index> local_indices(dofs_per_cell);
const double previous_time {current_time - time_step};
for (const auto &cell : dof_handler.active_cell_iterators())
{
if (cell->is_locally_owned())
{
fe_values.reinit(cell);
cell_rhs = 0.0;
cell->get_dof_indices(local_indices);
for (unsigned int i = 0; i < dofs_per_cell; ++i)
{
current_fe_coefficients[i] = previous_solution[local_indices[i]];
}
for (unsigned int q = 0; q < quad.size(); ++q)
{
const auto current_convection =
convection_function(fe_values.quadrature_point(q));
const double current_forcing = forcing_function
(current_time, fe_values.quadrature_point(q));
const double previous_forcing = forcing_function
(previous_time, fe_values.quadrature_point(q));
for (unsigned int i = 0; i < dofs_per_cell; ++i)
{
for (unsigned int j = 0; j < dofs_per_cell; ++j)
{
const auto convection_contribution = current_convection
*fe_values.shape_grad(j, q);
cell_rhs(i) += fe_values.JxW(q)*

Here are the mass and reaction part:

(((1.0 - time_step/2.0*parameters.reaction_coefficient)
*fe_values.shape_value(i, q)*fe_values.shape_value(j, q)
- time_step/2.0*

the convection part:

(fe_values.shape_value(i, q)*convection_contribution

the diffusion part:

+ parameters.diffusion_coefficient
*(fe_values.shape_grad(i, q)*fe_values.shape_grad(j, q))))
*current_fe_coefficients[j]

and, finally, the forcing function part:

+ time_step/2.0*
(current_forcing + previous_forcing)
*fe_values.shape_value(i, q));
}
}
}
constraints.distribute_local_to_global(cell_rhs, local_indices, system_rhs);
}
}
}
}
#endif

Annotated version of common/include/deal.II-cdr/write_pvtu_output.h

#ifndef dealii__cdr_write_pvtu_output_h
#define dealii__cdr_write_pvtu_output_h
#include <deal.II/dofs/dof_handler.h>

This is a small class which handles PVTU output.

namespace CDR
{
using namespace dealii;
class WritePVTUOutput
{
public:
WritePVTUOutput(const unsigned int patch_level);
template<int dim, typename VectorType>
void write_output(const DoFHandler<dim> &dof_handler,
const VectorType &solution,
const unsigned int time_step_n,
const double current_time);
private:
const unsigned int patch_level;
const unsigned int this_mpi_process;
};
}
#endif

Annotated version of common/include/deal.II-cdr/write_pvtu_output.templates.h

#ifndef dealii__cdr_write_pvtu_output_templates_h
#define dealii__cdr_write_pvtu_output_templates_h
#include <deal.II/base/data_out_base.h>
#include <deal.II/base/utilities.h>
#include <deal.II/dofs/dof_handler.h>
#include <deal.II/lac/vector.h>
#include <deal.II/numerics/data_out.h>
#include <deal.II-cdr/write_pvtu_output.h>
#include <string>
#include <fstream>
#include <vector>

Here is the implementation of the important function. This is similar to what is presented in step-40.

namespace CDR
{
using namespace dealii;
template<int dim, typename VectorType>
void WritePVTUOutput::write_output(const DoFHandler<dim> &dof_handler,
const VectorType &solution,
const unsigned int time_step_n,
const double current_time)
{
DataOut<dim> data_out;
data_out.attach_dof_handler(dof_handler);
data_out.add_data_vector(solution, "u");
const auto &triangulation = dof_handler.get_triangulation();
Vector<float> subdomain (triangulation.n_active_cells());
for (auto &domain : subdomain)
{
domain = triangulation.locally_owned_subdomain();
}
data_out.add_data_vector(subdomain, "subdomain");
data_out.build_patches(patch_level);
flags.time = current_time;

While the default flag is for the best compression level, using best_speed makes this function much faster.

flags.compression_level = DataOutBase::VtkFlags::ZlibCompressionLevel::best_speed;
data_out.set_flags(flags);
unsigned int subdomain_n;
if (Utilities::MPI::n_mpi_processes(MPI_COMM_WORLD) == 1)
{
subdomain_n = 0;
}
else
{
subdomain_n = triangulation.locally_owned_subdomain();
}
std::ofstream output
("solution-" + Utilities::int_to_string(time_step_n) + "."
+ Utilities::int_to_string(subdomain_n, 4)
+ ".vtu");
data_out.write_vtu(output);
if (this_mpi_process == 0)
{
std::vector<std::string> filenames;
for (unsigned int i = 0; i < Utilities::MPI::n_mpi_processes(MPI_COMM_WORLD);
++i)
filenames.push_back
("solution-" + Utilities::int_to_string (time_step_n) + "."
+ Utilities::int_to_string (i, 4) + ".vtu");
std::ofstream master_output
("solution-" + Utilities::int_to_string(time_step_n) + ".pvtu");
data_out.write_pvtu_record(master_output, filenames);
}
}
}
#endif

Annotated version of common/source/parameters.cc

#include <deal.II-cdr/parameters.h>
#include <fstream>
#include <string>
namespace CDR
{
void Parameters::configure_parameter_handler(ParameterHandler &parameter_handler)
{
parameter_handler.enter_subsection("Geometry");
{
parameter_handler.declare_entry
("inner_radius", "1.0", Patterns::Double(0.0), "Inner radius.");
parameter_handler.declare_entry
("outer_radius", "2.0", Patterns::Double(0.0), "Outer radius.");
}
parameter_handler.leave_subsection();
parameter_handler.enter_subsection("Physical Parameters");
{
parameter_handler.declare_entry
("diffusion_coefficient", "1.0", Patterns::Double(0.0), "Diffusion coefficient.");
parameter_handler.declare_entry
("reaction_coefficient", "1.0", Patterns::Double(0.0), "Reaction coefficient.");
parameter_handler.declare_entry
("time_dependent_forcing", "true", Patterns::Bool(), "Whether or not "
"the forcing function depends on time.");
}
parameter_handler.leave_subsection();
parameter_handler.enter_subsection("Finite Element");
{
parameter_handler.declare_entry
("initial_refinement_level", "1", Patterns::Integer(1),
"Initial number of levels in the mesh.");
parameter_handler.declare_entry
("max_refinement_level", "1", Patterns::Integer(1),
"Maximum number of levels in the mesh.");
parameter_handler.declare_entry
("fe_order", "1", Patterns::Integer(1), "Finite element order.");
}
parameter_handler.leave_subsection();
parameter_handler.enter_subsection("Time Step");
{
parameter_handler.declare_entry
("start_time", "0.0", Patterns::Double(0.0), "Start time.");
parameter_handler.declare_entry
("stop_time", "1.0", Patterns::Double(1.0), "Stop time.");
parameter_handler.declare_entry
("n_time_steps", "1", Patterns::Integer(1), "Number of time steps.");
}
parameter_handler.leave_subsection();
parameter_handler.enter_subsection("Output");
{
parameter_handler.declare_entry
("save_interval", "10", Patterns::Integer(1), "Save interval.");
parameter_handler.declare_entry
("patch_level", "2", Patterns::Integer(0), "Patch level.");
}
parameter_handler.leave_subsection();
}
void Parameters::read_parameter_file(const std::string &file_name)
{
ParameterHandler parameter_handler;
{
std::ifstream file(file_name);
configure_parameter_handler(parameter_handler);
parameter_handler.read_input(file);
}
parameter_handler.enter_subsection("Geometry");
{
inner_radius = parameter_handler.get_double("inner_radius");
outer_radius = parameter_handler.get_double("outer_radius");
}
parameter_handler.leave_subsection();
parameter_handler.enter_subsection("Physical Parameters");
{
diffusion_coefficient = parameter_handler.get_double("diffusion_coefficient");
reaction_coefficient = parameter_handler.get_double("reaction_coefficient");
time_dependent_forcing = parameter_handler.get_bool("time_dependent_forcing");
}
parameter_handler.leave_subsection();
parameter_handler.enter_subsection("Finite Element");
{
initial_refinement_level = parameter_handler.get_integer("initial_refinement_level");
max_refinement_level = parameter_handler.get_integer("max_refinement_level");
fe_order = parameter_handler.get_integer("fe_order");
}
parameter_handler.leave_subsection();
parameter_handler.enter_subsection("Time Step");
{
start_time = parameter_handler.get_double("start_time");
stop_time = parameter_handler.get_double("stop_time");
n_time_steps = parameter_handler.get_integer("n_time_steps");
}
parameter_handler.leave_subsection();
parameter_handler.enter_subsection("Output");
{
save_interval = parameter_handler.get_integer("save_interval");
patch_level = parameter_handler.get_integer("patch_level");
}
parameter_handler.leave_subsection();
}
}

Annotated version of common/source/system_matrix.cc

#include <deal.II/lac/sparse_matrix.h>
#include <deal.II/lac/trilinos_sparse_matrix.h>
#include <deal.II-cdr/parameters.h>
#include <deal.II-cdr/system_matrix.h>
#include <deal.II-cdr/system_matrix.templates.h>

This file exists just to build template specializations of create_system_matrix. Even though the solver is run in parallel with Trilinos objects, other serial solvers can use the same function without recompilation by compiling everything here just one time.

namespace CDR
{
using namespace dealii;
template
void create_system_matrix<2, SparseMatrix<double>>
(const DoFHandler<2> &dof_handler,
const QGauss<2> &quad,
const std::function<Tensor<1, 2>(const Point<2>)> &convection_function,
const CDR::Parameters &parameters,
const double time_step,
SparseMatrix<double> &system_matrix);
template
void create_system_matrix<3, SparseMatrix<double>>
(const DoFHandler<3> &dof_handler,
const QGauss<3> &quad,
const std::function<Tensor<1, 3>(const Point<3>)> &convection_function,
const CDR::Parameters &parameters,
const double time_step,
SparseMatrix<double> &system_matrix);
template
void create_system_matrix<2, SparseMatrix<double>>
(const DoFHandler<2> &dof_handler,
const QGauss<2> &quad,
const std::function<Tensor<1, 2>(const Point<2>)> &convection_function,
const CDR::Parameters &parameters,
const double time_step,
const ConstraintMatrix &constraints,
SparseMatrix<double> &system_matrix);
template
void create_system_matrix<3, SparseMatrix<double>>
(const DoFHandler<3> &dof_handler,
const QGauss<3> &quad,
const std::function<Tensor<1, 3>(const Point<3>)> &convection_function,
const CDR::Parameters &parameters,
const double time_step,
const ConstraintMatrix &constraints,
SparseMatrix<double> &system_matrix);
template
void create_system_matrix<2, TrilinosWrappers::SparseMatrix>
(const DoFHandler<2> &dof_handler,
const QGauss<2> &quad,
const std::function<Tensor<1, 2>(const Point<2>)> &convection_function,
const CDR::Parameters &parameters,
const double time_step,
TrilinosWrappers::SparseMatrix &system_matrix);
template
void create_system_matrix<3, TrilinosWrappers::SparseMatrix>
(const DoFHandler<3> &dof_handler,
const QGauss<3> &quad,
const std::function<Tensor<1, 3>(const Point<3>)> &convection_function,
const CDR::Parameters &parameters,
const double time_step,
TrilinosWrappers::SparseMatrix &system_matrix);
template
void create_system_matrix<2, TrilinosWrappers::SparseMatrix>
(const DoFHandler<2> &dof_handler,
const QGauss<2> &quad,
const std::function<Tensor<1, 2>(const Point<2>)> &convection_function,
const CDR::Parameters &parameters,
const double time_step,
const ConstraintMatrix &constraints,
TrilinosWrappers::SparseMatrix &system_matrix);
template
void create_system_matrix<3, TrilinosWrappers::SparseMatrix>
(const DoFHandler<3> &dof_handler,
const QGauss<3> &quad,
const std::function<Tensor<1, 3>(const Point<3>)> &convection_function,
const CDR::Parameters &parameters,
const double time_step,
const ConstraintMatrix &constraints,
TrilinosWrappers::SparseMatrix &system_matrix);
}

Annotated version of common/source/system_rhs.cc

#include <deal.II/lac/sparse_matrix.h>
#include <deal.II/lac/trilinos_sparse_matrix.h>
#include <deal.II/lac/trilinos_vector.h>
#include <deal.II/lac/vector.h>
#include <deal.II-cdr/system_rhs.templates.h>

Like system_matrix.cc, this file just compiles template specializations.

namespace CDR
{
using namespace dealii;
template
void create_system_rhs<2, Vector<double>>
(const DoFHandler<2> &dof_handler,
const QGauss<2> &quad,
const std::function<Tensor<1, 2>(const Point<2>)> &convection_function,
const std::function<double(double, const Point<2>)> &forcing_function,
const CDR::Parameters &parameters,
const Vector<double> &previous_solution,
const ConstraintMatrix &constraints,
const double current_time,
Vector<double> &system_rhs);
template
void create_system_rhs<3, Vector<double>>
(const DoFHandler<3> &dof_handler,
const QGauss<3> &quad,
const std::function<Tensor<1, 3>(const Point<3>)> &convection_function,
const std::function<double(double, const Point<3>)> &forcing_function,
const CDR::Parameters &parameters,
const Vector<double> &previous_solution,
const ConstraintMatrix &constraints,
const double current_time,
Vector<double> &system_rhs);
template
void create_system_rhs<2, TrilinosWrappers::MPI::Vector>
(const DoFHandler<2> &dof_handler,
const QGauss<2> &quad,
const std::function<Tensor<1, 2>(const Point<2>)> &convection_function,
const std::function<double(double, const Point<2>)> &forcing_function,
const CDR::Parameters &parameters,
const TrilinosWrappers::MPI::Vector &previous_solution,
const ConstraintMatrix &constraints,
const double current_time,
template
void create_system_rhs<3, TrilinosWrappers::MPI::Vector>
(const DoFHandler<3> &dof_handler,
const QGauss<3> &quad,
const std::function<Tensor<1, 3>(const Point<3>)> &convection_function,
const std::function<double(double, const Point<3>)> &forcing_function,
const CDR::Parameters &parameters,
const TrilinosWrappers::MPI::Vector &previous_solution,
const ConstraintMatrix &constraints,
const double current_time,
}

Annotated version of common/source/write_pvtu_output.cc

#include <deal.II/lac/trilinos_vector.h>
#include <deal.II/lac/vector.h>
#include <deal.II-cdr/write_pvtu_output.templates.h>

Again, this file just compiles the constructor and also the templated functions.

namespace CDR
{
using namespace dealii;
WritePVTUOutput::WritePVTUOutput(const unsigned int patch_level)
: patch_level {patch_level},
this_mpi_process {Utilities::MPI::this_mpi_process(MPI_COMM_WORLD)}
{}
template
void WritePVTUOutput::write_output(const DoFHandler<2> &dof_handler,
const Vector<double> &solution,
const unsigned int time_step_n,
const double current_time);
template
void WritePVTUOutput::write_output(const DoFHandler<3> &dof_handler,
const Vector<double> &solution,
const unsigned int time_step_n,
const double current_time);
template
void WritePVTUOutput::write_output(const DoFHandler<2> &dof_handler,
const unsigned int time_step_n,
const double current_time);
template
void WritePVTUOutput::write_output(const DoFHandler<3> &dof_handler,
const unsigned int time_step_n,
const double current_time);
}

Annotated version of solver/cdr.cc

#include <deal.II/base/conditional_ostream.h>
#include <deal.II/base/quadrature_lib.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/manifold_lib.h>
#include <deal.II/lac/dynamic_sparsity_pattern.h>
#include <deal.II/lac/constraint_matrix.h>
#include <deal.II/numerics/error_estimator.h>

These headers are for distributed computations:

#include <deal.II/base/utilities.h>
#include <deal.II/base/index_set.h>
#include <deal.II/distributed/tria.h>
#include <deal.II/distributed/grid_refinement.h>
#include <deal.II/distributed/solution_transfer.h>
#include <deal.II/lac/sparsity_tools.h>
#include <deal.II/lac/trilinos_solver.h>
#include <deal.II/lac/trilinos_sparse_matrix.h>
#include <deal.II/lac/trilinos_precondition.h>
#include <deal.II/lac/trilinos_vector.h>
#include <chrono>
#include <functional>
#include <iostream>
#include <deal.II-cdr/system_matrix.h>
#include <deal.II-cdr/system_rhs.h>
#include <deal.II-cdr/parameters.h>
#include <deal.II-cdr/write_pvtu_output.h>
using namespace dealii;
constexpr int manifold_id {0};

This is the actual solver class which performs time iteration and calls the appropriate library functions to do it.

template<int dim>
class CDRProblem
{
public:
CDRProblem(const CDR::Parameters &parameters);
void run();
private:
const CDR::Parameters parameters;
const double time_step;
double current_time;
MPI_Comm mpi_communicator;
const unsigned int n_mpi_processes;
const unsigned int this_mpi_process;
const SphericalManifold<dim> boundary_description;
DoFHandler<dim> dof_handler;
const std::function<Tensor<1, dim>(const Point<dim>)> convection_function;
const std::function<double(double, const Point<dim>)> forcing_function;
IndexSet locally_owned_dofs;
IndexSet locally_relevant_dofs;
ConstraintMatrix constraints;
bool first_run;

As is usual in parallel programs, I keep two copies of parts of the complete solution: locally_relevant_solution contains both the locally calculated solution as well as the layer of cells at its boundary (the ghost cells) while completely_distributed_solution only contains the parts of the solution computed on the current MPI process.

TrilinosWrappers::MPI::Vector locally_relevant_solution;
TrilinosWrappers::MPI::Vector completely_distributed_solution;
TrilinosWrappers::SparseMatrix system_matrix;
TrilinosWrappers::PreconditionAMG preconditioner;
void setup_geometry();
void setup_system();
void setup_dofs();
void refine_mesh();
void time_iterate();
};
template<int dim>
CDRProblem<dim>::CDRProblem(const CDR::Parameters &parameters) :
parameters(parameters),
time_step {(parameters.stop_time - parameters.start_time)
/parameters.n_time_steps},
current_time {parameters.start_time},
mpi_communicator (MPI_COMM_WORLD),
n_mpi_processes {Utilities::MPI::n_mpi_processes(mpi_communicator)},
this_mpi_process {Utilities::MPI::this_mpi_process(mpi_communicator)},
fe(parameters.fe_order),
quad(parameters.fe_order + 2),
boundary_description(Point<dim>()),
triangulation(mpi_communicator, typename Triangulation<dim>::MeshSmoothing
dof_handler(triangulation),
convection_function
{
[](const Point<dim> p) -> Tensor<1, dim>
{Tensor<1, dim> v; v[0] = -p[1]; v[1] = p[0]; return v;}
},
forcing_function
{
[](double t, const Point<dim> p) -> double
{
return std::exp(-8*t)*std::exp(-40*Utilities::fixed_power<6>(p[0] - 1.5))
*std::exp(-40*Utilities::fixed_power<6>(p[1]));
}
},
first_run {true},
pcout (std::cout, this_mpi_process == 0)
{
Assert(dim == 2, ExcNotImplemented());
}
template<int dim>
void CDRProblem<dim>::setup_geometry()
{
const Point<dim> center;
GridGenerator::hyper_shell(triangulation, center, parameters.inner_radius,
parameters.outer_radius);
triangulation.set_manifold(manifold_id, boundary_description);
for (const auto &cell : triangulation.active_cell_iterators())
{
cell->set_all_manifold_ids(manifold_id);
}
triangulation.refine_global(parameters.initial_refinement_level);
}
template<int dim>
void CDRProblem<dim>::setup_dofs()
{
dof_handler.distribute_dofs(fe);
pcout << "Number of degrees of freedom: "
<< dof_handler.n_dofs()
<< std::endl;
locally_owned_dofs = dof_handler.locally_owned_dofs();
DoFTools::extract_locally_relevant_dofs(dof_handler, locally_relevant_dofs);
constraints.clear();
constraints.reinit(locally_relevant_dofs);
DoFTools::make_hanging_node_constraints(dof_handler, constraints);
DoFTools::make_zero_boundary_constraints(dof_handler, manifold_id, constraints);
constraints.close();
completely_distributed_solution.reinit
(locally_owned_dofs, mpi_communicator);
locally_relevant_solution.reinit(locally_owned_dofs, locally_relevant_dofs,
mpi_communicator);
}
template<int dim>
void CDRProblem<dim>::setup_system()
{
DynamicSparsityPattern dynamic_sparsity_pattern(dof_handler.n_dofs());
DoFTools::make_sparsity_pattern(dof_handler, dynamic_sparsity_pattern,
constraints, / *keep_constrained_dofs* /true);
(dynamic_sparsity_pattern, dof_handler.n_locally_owned_dofs_per_processor(),
mpi_communicator, locally_relevant_dofs);
system_rhs.reinit(locally_owned_dofs, mpi_communicator);
system_matrix.reinit(locally_owned_dofs, dynamic_sparsity_pattern,
mpi_communicator);
CDR::create_system_matrix<dim>
(dof_handler, quad, convection_function, parameters, time_step, constraints,
system_matrix);
system_matrix.compress(VectorOperation::add);
preconditioner.initialize(system_matrix);
}
template<int dim>
void CDRProblem<dim>::time_iterate()
{
double current_time = parameters.start_time;
CDR::WritePVTUOutput pvtu_output(parameters.patch_level);
for (unsigned int time_step_n = 0; time_step_n < parameters.n_time_steps;
++time_step_n)
{
current_time += time_step;
system_rhs = 0.0;
CDR::create_system_rhs<dim>
(dof_handler, quad, convection_function, forcing_function, parameters,
locally_relevant_solution, constraints, current_time, system_rhs);
system_rhs.compress(VectorOperation::add);
SolverControl solver_control(dof_handler.n_dofs(),
1e-6*system_rhs.l2_norm(),
/ *log_history = * / false,
/ *log_result = * / false);
TrilinosWrappers::SolverGMRES solver(solver_control);
solver.solve(system_matrix, completely_distributed_solution, system_rhs,
preconditioner);
constraints.distribute(completely_distributed_solution);
locally_relevant_solution = completely_distributed_solution;
if (time_step_n % parameters.save_interval == 0)
{
pvtu_output.write_output(dof_handler, locally_relevant_solution,
time_step_n, current_time);
}
refine_mesh();
}
}
template<int dim>
void CDRProblem<dim>::refine_mesh()
{
Vector<float> estimated_error_per_cell(triangulation.n_active_cells());
(dof_handler, QGauss<dim - 1>(fe.degree + 1), typename FunctionMap<dim>::type(),
locally_relevant_solution, estimated_error_per_cell);

This solver uses a crude refinement strategy where cells with relatively high errors are refined and cells with relatively low errors are coarsened. The maximum refinement level is capped to prevent run-away refinement.

for (const auto &cell : triangulation.active_cell_iterators())
{
if (std::abs(estimated_error_per_cell[cell->active_cell_index()]) >= 1e-3)
{
cell->set_refine_flag();
}
else if (std::abs(estimated_error_per_cell[cell->active_cell_index()]) <= 1e-5)
{
cell->set_coarsen_flag();
}
}
if (triangulation.n_levels() > parameters.max_refinement_level)
{
for (const auto &cell :
triangulation.cell_iterators_on_level(parameters.max_refinement_level))
{
cell->clear_refine_flag();
}
}

Transferring the solution between different grids is ultimately just a few function calls but they must be made in exactly the right order.

solution_transfer(dof_handler);
solution_transfer.prepare_for_coarsening_and_refinement
(locally_relevant_solution);
setup_dofs();

The solution_transfer object stores a pointer to locally_relevant_solution, so when parallel::distributed::SolutionTransfer::interpolate is called it uses those values to populate temporary.

(locally_owned_dofs, mpi_communicator);
solution_transfer.interpolate(temporary);

After temporary has the correct value, this call correctly populates completely_distributed_solution, which had its index set updated above with the call to setup_dofs.

completely_distributed_solution = temporary;

Constraints cannot be applied to vectors with ghost entries since the ghost entries are write only, so this first goes through the completely distributed vector.

constraints.distribute(completely_distributed_solution);
locally_relevant_solution = completely_distributed_solution;
setup_system();
}
template<int dim>
void CDRProblem<dim>::run()
{
setup_geometry();
setup_dofs();
setup_system();
time_iterate();
}
constexpr int dim {2};
int main(int argc, char *argv[])
{

One of the new features in C++11 is the chrono component of the standard library. This gives us an easy way to time the output.

auto t0 = std::chrono::high_resolution_clock::now();
Utilities::MPI::MPI_InitFinalize mpi_initialization(argc, argv, 1);
CDR::Parameters parameters;
parameters.read_parameter_file("parameters.prm");
CDRProblem<dim> cdr_problem(parameters);
cdr_problem.run();
auto t1 = std::chrono::high_resolution_clock::now();
if (Utilities::MPI::this_mpi_process(MPI_COMM_WORLD) == 0)
{
std::cout << "time elapsed: "
<< std::chrono::duration_cast<std::chrono::milliseconds>(t1 - t0).count()
<< " milliseconds."
<< std::endl;
}
return 0;
}