adaptivity_ex2.C File Reference

Go to the source code of this file.

Functions
void	assemble_cd (EquationSystems &es, const std::string &system_name)
void	init_cd (EquationSystems &es, const std::string &system_name)
Real	exact_solution (const Real x, const Real y, const Real t)
	This is the exact solution that we are trying to obtain. More...
Number	exact_value (const Point &p, const Parameters &parameters, const std::string &, const std::string &)
int	main (int argc, char **argv)
void	init_cd (EquationSystems &es, const std::string &libmesh_dbg_var(system_name))
void	assemble_cd (EquationSystems &es, const std::string &libmesh_dbg_var(system_name))

Function Documentation

assemble_cd() [1/2]

void assemble_cd	(	EquationSystems &	es,
		const std::string &	system_name
	)

Definition at line 296 of file transient_ex1.C.

Referenced by main().

{
  // Ignore unused parameter warnings when !LIBMESH_ENABLE_AMR.
  libmesh_ignore(es, system_name);

#ifdef LIBMESH_ENABLE_AMR
  // It is a good idea to make sure we are assembling
  // the proper system.
  libmesh_assert_equal_to (system_name, "Convection-Diffusion");

  // Get a constant reference to the mesh object.
  const MeshBase & mesh = es.get_mesh();

  // The dimension that we are running
  const unsigned int dim = mesh.mesh_dimension();

  // Get a reference to the Convection-Diffusion system object.
  TransientLinearImplicitSystem & system =
    es.get_system<TransientLinearImplicitSystem> ("Convection-Diffusion");

  // Get a constant reference to the Finite Element type
  // for the first (and only) variable in the system.
  FEType fe_type = system.variable_type(0);

  // Build a Finite Element object of the specified type.  Since the
  // FEBase::build() member dynamically creates memory we will
  // store the object as a std::unique_ptr<FEBase>.  This can be thought
  // of as a pointer that will clean up after itself.
  std::unique_ptr<FEBase> fe      (FEBase::build(dim, fe_type));
  std::unique_ptr<FEBase> fe_face (FEBase::build(dim, fe_type));

  // A Gauss quadrature rule for numerical integration.
  // Let the FEType object decide what order rule is appropriate.
  QGauss qrule (dim,   fe_type.default_quadrature_order());
  QGauss qface (dim-1, fe_type.default_quadrature_order());

  // Tell the finite element object to use our quadrature rule.
  fe->attach_quadrature_rule      (&qrule);
  fe_face->attach_quadrature_rule (&qface);

  // Here we define some references to cell-specific data that
  // will be used to assemble the linear system.  We will start
  // with the element Jacobian * quadrature weight at each integration point.
  const std::vector<Real> & JxW      = fe->get_JxW();
  const std::vector<Real> & JxW_face = fe_face->get_JxW();

  // The element shape functions evaluated at the quadrature points.
  const std::vector<std::vector<Real>> & phi = fe->get_phi();
  const std::vector<std::vector<Real>> & psi = fe_face->get_phi();

  // The element shape function gradients evaluated at the quadrature
  // points.
  const std::vector<std::vector<RealGradient>> & dphi = fe->get_dphi();

  // The XY locations of the quadrature points used for face integration
  const std::vector<Point> & qface_points = fe_face->get_xyz();

  // A reference to the DofMap object for this system.  The DofMap
  // object handles the index translation from node and element numbers
  // to degree of freedom numbers.  We will talk more about the DofMap
  // in future examples.
  const DofMap & dof_map = system.get_dof_map();

  // Define data structures to contain the element matrix
  // and right-hand-side vector contribution.  Following
  // basic finite element terminology we will denote these
  // "Ke" and "Fe".
  DenseMatrix<Number> Ke;
  DenseVector<Number> Fe;

  // This vector will hold the degree of freedom indices for
  // the element.  These define where in the global system
  // the element degrees of freedom get mapped.
  std::vector<dof_id_type> dof_indices;

  // Here we extract the velocity & parameters that we put in the
  // EquationSystems object.
  const RealVectorValue velocity =
    es.parameters.get<RealVectorValue> ("velocity");

  const Real dt = es.parameters.get<Real>   ("dt");

  SparseMatrix<Number> & matrix = system.get_system_matrix();

  // Now we will loop over all the elements in the mesh that
  // live on the local processor. We will compute the element
  // matrix and right-hand-side contribution.  Since the mesh
  // will be refined we want to only consider the ACTIVE elements,
  // hence we use a variant of the active_elem_iterator.
  for (const auto & elem : mesh.active_local_element_ptr_range())
    {
      // Get the degree of freedom indices for the
      // current element.  These define where in the global
      // matrix and right-hand-side this element will
      // contribute to.
      dof_map.dof_indices (elem, dof_indices);

      // Compute the element-specific data for the current
      // element.  This involves computing the location of the
      // quadrature points (q_point) and the shape functions
      // (phi, dphi) for the current element.
      fe->reinit (elem);

      // Zero the element matrix and right-hand side before
      // summing them.  We use the resize member here because
      // the number of degrees of freedom might have changed from
      // the last element.  Note that this will be the case if the
      // element type is different (i.e. the last element was a
      // triangle, now we are on a quadrilateral).
      Ke.resize (dof_indices.size(),
                 dof_indices.size());

      Fe.resize (dof_indices.size());

      // Now we will build the element matrix and right-hand-side.
      // Constructing the RHS requires the solution and its
      // gradient from the previous timestep.  This myst be
      // calculated at each quadrature point by summing the
      // solution degree-of-freedom values by the appropriate
      // weight functions.
      for (unsigned int qp=0; qp<qrule.n_points(); qp++)
        {
          // Values to hold the old solution & its gradient.
          Number u_old = 0.;
          Gradient grad_u_old;

          // Compute the old solution & its gradient.
          for (std::size_t l=0; l<phi.size(); l++)
            {
              u_old += phi[l][qp]*system.old_solution  (dof_indices[l]);

              // This will work,
              // grad_u_old += dphi[l][qp]*system.old_solution (dof_indices[l]);
              // but we can do it without creating a temporary like this:
              grad_u_old.add_scaled (dphi[l][qp], system.old_solution (dof_indices[l]));
            }

          // Now compute the element matrix and RHS contributions.
          for (std::size_t i=0; i<phi.size(); i++)
            {
              // The RHS contribution
              Fe(i) += JxW[qp]*(
                                // Mass matrix term
                                u_old*phi[i][qp] +
                                -.5*dt*(
                                        // Convection term
                                        // (grad_u_old may be complex, so the
                                        // order here is important!)
                                        (grad_u_old*velocity)*phi[i][qp] +

                                        // Diffusion term
                                        0.01*(grad_u_old*dphi[i][qp]))
                                );

              for (std::size_t j=0; j<phi.size(); j++)
                {
                  // The matrix contribution
                  Ke(i,j) += JxW[qp]*(
                                      // Mass-matrix
                                      phi[i][qp]*phi[j][qp] +

                                      .5*dt*(
                                             // Convection term
                                             (velocity*dphi[j][qp])*phi[i][qp] +

                                             // Diffusion term
                                             0.01*(dphi[i][qp]*dphi[j][qp]))
                                      );
                }
            }
        }

      // At this point the interior element integration has
      // been completed.  However, we have not yet addressed
      // boundary conditions.  For this example we will only
      // consider simple Dirichlet boundary conditions imposed
      // via the penalty method.
      //
      // The following loops over the sides of the element.
      // If the element has no neighbor on a side then that
      // side MUST live on a boundary of the domain.
      {
        // The penalty value.
        const Real penalty = 1.e10;

        // The following loops over the sides of the element.
        // If the element has no neighbor on a side then that
        // side MUST live on a boundary of the domain.
        for (auto s : elem->side_index_range())
          if (elem->neighbor_ptr(s) == nullptr)
            {
              fe_face->reinit(elem, s);

              for (unsigned int qp=0; qp<qface.n_points(); qp++)
                {
                  const Number value = exact_solution (qface_points[qp](0),
                                                       qface_points[qp](1),
                                                       system.time);

                  // RHS contribution
                  for (std::size_t i=0; i<psi.size(); i++)
                    Fe(i) += penalty*JxW_face[qp]*value*psi[i][qp];

                  // Matrix contribution
                  for (std::size_t i=0; i<psi.size(); i++)
                    for (std::size_t j=0; j<psi.size(); j++)
                      Ke(i,j) += penalty*JxW_face[qp]*psi[i][qp]*psi[j][qp];
                }
            }
      }

      // If this assembly program were to be used on an adaptive mesh,
      // we would have to apply any hanging node constraint equations
      dof_map.constrain_element_matrix_and_vector (Ke, Fe, dof_indices);

      // The element matrix and right-hand-side are now built
      // for this element.  Add them to the global matrix and
      // right-hand-side vector.  The SparseMatrix::add_matrix()
      // and NumericVector::add_vector() members do this for us.
      matrix.add_matrix         (Ke, dof_indices);
      system.rhs->add_vector    (Fe, dof_indices);
    }

  // That concludes the system matrix assembly routine.
#endif // #ifdef LIBMESH_ENABLE_AMR
}

assemble_cd() [2/2]

void assemble_cd	(	EquationSystems &	es,
		const std::string &	libmesh_dbg_varsystem_name
	)

Definition at line 515 of file adaptivity_ex2.C.

References libMesh::TypeVector< T >::add_scaled(), libMesh::FEGenericBase< OutputType >::build(), libMesh::DofMap::constrain_element_matrix_and_vector(), libMesh::FEType::default_quadrature_order(), dim, libMesh::DofMap::dof_indices(), exact_solution(), libMesh::Parameters::get(), libMesh::EquationSystems::get_mesh(), libMesh::EquationSystems::get_system(), mesh, libMesh::MeshBase::mesh_dimension(), libMesh::TransientSystem< Base >::old_solution(), libMesh::EquationSystems::parameters, libMesh::Real, libMesh::DenseVector< T >::resize(), libMesh::DenseMatrix< T >::resize(), and value.

{
  // It is a good idea to make sure we are assembling
  // the proper system.
  libmesh_assert_equal_to (system_name, "Convection-Diffusion");

  // Get a constant reference to the mesh object.
  const MeshBase & mesh = es.get_mesh();

  // The dimension that we are running
  const unsigned int dim = mesh.mesh_dimension();

  // Get a reference to the Convection-Diffusion system object.
  TransientLinearImplicitSystem & system =
    es.get_system<TransientLinearImplicitSystem> ("Convection-Diffusion");

  // Get a pointer to the StaticCondensation class if it exists
  StaticCondensation * sc = nullptr;
  if (system.has_static_condensation())
    sc = &system.get_static_condensation();

  // Get the Finite Element type for the first (and only)
  // variable in the system.
  FEType fe_type = system.variable_type(0);

  // Build a Finite Element object of the specified type.  Since the
  // FEBase::build() member dynamically creates memory we will
  // store the object as a std::unique_ptr<FEBase>.  This can be thought
  // of as a pointer that will clean up after itself.
  std::unique_ptr<FEBase> fe      (FEBase::build(dim, fe_type));
  std::unique_ptr<FEBase> fe_face (FEBase::build(dim, fe_type));

  // A Gauss quadrature rule for numerical integration.
  // Let the FEType object decide what order rule is appropriate.
  QGauss qrule (dim,   fe_type.default_quadrature_order());
  QGauss qface (dim-1, fe_type.default_quadrature_order());

  // Tell the finite element object to use our quadrature rule.
  fe->attach_quadrature_rule      (&qrule);
  fe_face->attach_quadrature_rule (&qface);

  // Here we define some references to cell-specific data that
  // will be used to assemble the linear system.  We will start
  // with the element Jacobian * quadrature weight at each integration point.
  const std::vector<Real> & JxW      = fe->get_JxW();
  const std::vector<Real> & JxW_face = fe_face->get_JxW();

  // The element shape functions evaluated at the quadrature points.
  const std::vector<std::vector<Real>> & phi = fe->get_phi();
  const std::vector<std::vector<Real>> & psi = fe_face->get_phi();

  // The element shape function gradients evaluated at the quadrature
  // points.
  const std::vector<std::vector<RealGradient>> & dphi = fe->get_dphi();

  // The XY locations of the quadrature points used for face integration
  const std::vector<Point> & qface_points = fe_face->get_xyz();

  // A reference to the DofMap object for this system.  The DofMap
  // object handles the index translation from node and element numbers
  // to degree of freedom numbers.  We will talk more about the DofMap
  // in future examples.
  const DofMap & dof_map = system.get_dof_map();

  // Define data structures to contain the element matrix
  // and right-hand-side vector contribution.  Following
  // basic finite element terminology we will denote these
  // "Ke" and "Fe".
  DenseMatrix<Number> Ke;
  DenseVector<Number> Fe;

  // This vector will hold the degree of freedom indices for
  // the element.  These define where in the global system
  // the element degrees of freedom get mapped.
  std::vector<dof_id_type> dof_indices;

  // Here we extract the velocity & parameters that we put in the
  // EquationSystems object.
  const RealVectorValue velocity =
    es.parameters.get<RealVectorValue> ("velocity");

  const Real diffusivity =
    es.parameters.get<Real> ("diffusivity");

  const Real dt = es.parameters.get<Real> ("dt");

  // The global system matrix
  SparseMatrix<Number> & matrix = system.get_system_matrix();

  // Now we will loop over all the elements in the mesh that
  // live on the local processor. We will compute the element
  // matrix and right-hand-side contribution.  Since the mesh
  // will be refined we want to only consider the ACTIVE elements,
  // hence we use a variant of the active_elem_iterator.
  for (const auto & elem : mesh.active_local_element_ptr_range())
    {
      // Get the degree of freedom indices for the
      // current element.  These define where in the global
      // matrix and right-hand-side this element will
      // contribute to.
      dof_map.dof_indices (elem, dof_indices);

      // Compute the element-specific data for the current
      // element.  This involves computing the location of the
      // quadrature points (q_point) and the shape functions
      // (phi, dphi) for the current element.
      fe->reinit (elem);

      const unsigned int n_dofs =
        cast_int<unsigned int>(dof_indices.size());
      libmesh_assert_equal_to (n_dofs, phi.size());

      // Zero the element matrix and right-hand side before
      // summing them.  We use the resize member here because
      // the number of degrees of freedom might have changed from
      // the last element.  Note that this will be the case if the
      // element type is different (i.e. the last element was a
      // triangle, now we are on a quadrilateral).
      Ke.resize (n_dofs, n_dofs);

      Fe.resize (n_dofs);

      // Now we will build the element matrix and right-hand-side.
      // Constructing the RHS requires the solution and its
      // gradient from the previous timestep.  This myst be
      // calculated at each quadrature point by summing the
      // solution degree-of-freedom values by the appropriate
      // weight functions.
      for (unsigned int qp=0; qp<qrule.n_points(); qp++)
        {
          // Values to hold the old solution & its gradient.
          Number   u_old = 0.;
          Gradient grad_u_old;

          // Compute the old solution & its gradient.
          for (unsigned int l=0; l != n_dofs; l++)
            {
              u_old += phi[l][qp]*system.old_solution (dof_indices[l]);

              // This will work,
              // grad_u_old += dphi[l][qp]*system.old_solution (dof_indices[l]);
              // but we can do it without creating a temporary like this:
              grad_u_old.add_scaled (dphi[l][qp], system.old_solution (dof_indices[l]));
            }

          // Now compute the element matrix and RHS contributions.
          for (unsigned int i=0; i != n_dofs; i++)
            {
              // The RHS contribution
              Fe(i) += JxW[qp]*(
                                // Mass matrix term
                                u_old*phi[i][qp] +
                                -.5*dt*(
                                        // Convection term
                                        // (grad_u_old may be complex, so the
                                        // order here is important!)
                                        (grad_u_old*velocity)*phi[i][qp] +

                                        // Diffusion term
                                        diffusivity*(grad_u_old*dphi[i][qp]))
                                );

              for (unsigned int j=0; j != n_dofs; j++)
                {
                  // The matrix contribution
                  Ke(i,j) += JxW[qp]*(
                                      // Mass-matrix
                                      phi[i][qp]*phi[j][qp] +
                                      .5*dt*(
                                             // Convection term
                                             (velocity*dphi[j][qp])*phi[i][qp] +
                                             // Diffusion term
                                             diffusivity*(dphi[i][qp]*dphi[j][qp]))
                                      );
                }
            }
        }

      // At this point the interior element integration has
      // been completed.  However, we have not yet addressed
      // boundary conditions.  For this example we will only
      // consider simple Dirichlet boundary conditions imposed
      // via the penalty method.
      //
      // The following loops over the sides of the element.
      // If the element has no neighbor on a side then that
      // side MUST live on a boundary of the domain.
      {
        // The penalty value.
        const Real penalty = 1.e10;

        // The following loops over the sides of the element.
        // If the element has no neighbor on a side then that
        // side MUST live on a boundary of the domain.
        for (auto s : elem->side_index_range())
          if (elem->neighbor_ptr(s) == nullptr)
            {
              fe_face->reinit(elem, s);

              libmesh_assert_equal_to (n_dofs, psi.size());

              for (unsigned int qp=0; qp<qface.n_points(); qp++)
                {
                  const Number value = exact_solution (qface_points[qp](0),
                                                       qface_points[qp](1),
                                                       system.time);

                  // RHS contribution
                  for (unsigned int i=0; i != n_dofs; i++)
                    Fe(i) += penalty*JxW_face[qp]*value*psi[i][qp];

                  // Matrix contribution
                  for (unsigned int i=0; i != n_dofs; i++)
                    for (unsigned int j=0; j != n_dofs; j++)
                      Ke(i,j) += penalty*JxW_face[qp]*psi[i][qp]*psi[j][qp];
                }
            }
      }


      // We have now built the element matrix and RHS vector in terms
      // of the element degrees of freedom.  However, it is possible
      // that some of the element DOFs are constrained to enforce
      // solution continuity, i.e. they are not really "free".  We need
      // to constrain those DOFs in terms of non-constrained DOFs to
      // ensure a continuous solution.  The
      // DofMap::constrain_element_matrix_and_vector() method does
      // just that.
      dof_map.constrain_element_matrix_and_vector (Ke, Fe, dof_indices);

      if (sc)
        sc->set_current_elem(*elem);

      // The element matrix and right-hand-side are now built
      // for this element.  Add them to the global matrix and
      // right-hand-side vector.  The SparseMatrix::add_matrix()
      // and NumericVector::add_vector() members do this for us.
      matrix.add_matrix (Ke, dof_indices);
      system.rhs->add_vector    (Fe, dof_indices);

    }
  // Finished computing the system matrix and right-hand side.
}

exact_solution()

Real exact_solution	(	const Real	x,
		const Real	y,
		const Real	z = 0.
	)

This is the exact solution that we are trying to obtain.

We will solve

• (u_xx + u_yy) = f

and take a finite difference approximation using this function to get f. This is the well-known "method of manufactured solutions".

Definition at line 43 of file exact_solution.C.

Referenced by assemble_cd(), and exact_value().

{
  static const Real pi = acos(-1.);

  return cos(.5*pi*x)*sin(.5*pi*y)*cos(.5*pi*z);
}

exact_value()

Number exact_value	(	const Point &	p,
		const Parameters &	parameters,
		const std::string &	,
		const std::string &
	)

Definition at line 105 of file adaptivity_ex2.C.

References exact_solution(), libMesh::Parameters::get(), and libMesh::Real.

Referenced by init_cd(), and libMesh::DofMap::max_constraint_error().

{
  return exact_solution(p(0), p(1), parameters.get<Real> ("time"));
}

init_cd() [1/2]

void init_cd	(	EquationSystems &	es,
		const std::string &	system_name
	)

Referenced by main().

init_cd() [2/2]

void init_cd	(	EquationSystems &	es,
		const std::string &	libmesh_dbg_varsystem_name
	)

Definition at line 491 of file adaptivity_ex2.C.

References exact_value(), libMesh::EquationSystems::get_system(), libMesh::EquationSystems::parameters, libMesh::Real, and libMesh::Parameters::set().

{
  // It is a good idea to make sure we are initializing
  // the proper system.
  libmesh_assert_equal_to (system_name, "Convection-Diffusion");

  // Get a reference to the Convection-Diffusion system object.
  TransientLinearImplicitSystem & system =
    es.get_system<TransientLinearImplicitSystem>("Convection-Diffusion");

  // Project initial conditions at time 0
  es.parameters.set<Real> ("time") = system.time = 0;

  system.project_solution(exact_value, nullptr, es.parameters);
}

main()

int main	(	int	argc,
		char **	argv
	)

Definition at line 120 of file adaptivity_ex2.C.

References libMesh::MeshBase::all_second_order(), assemble_cd(), libMesh::MeshRefinement::coarsen_fraction(), libMesh::command_line_next(), libMesh::default_solver_package(), libMesh::JumpErrorEstimator::estimate_error(), libMesh::MeshRefinement::flag_elements_by_error_fraction(), libMesh::H1, libMesh::HIERARCHIC, libMesh::TriangleWrapper::init(), init_cd(), libMesh::INVALID_SOLVER_PACKAGE, libMesh::invalid_uint, libMesh::LAGRANGE, libMesh::MeshRefinement::max_h_level(), mesh, libMesh::on_command_line(), libMesh::out, libMesh::MeshBase::print_info(), libMesh::READ, libMesh::MeshBase::read(), libMesh::Real, libMesh::MeshRefinement::refine_and_coarsen_elements(), libMesh::MeshRefinement::refine_fraction(), libMesh::TOLERANCE, libMesh::TRILINOS_SOLVERS, libMesh::MeshRefinement::uniformly_refine(), libMesh::JumpErrorEstimator::use_unweighted_quadrature_rules, libMesh::WRITE, libMesh::MeshBase::write(), and libMesh::ExodusII_IO::write_equation_systems().

{
  // Initialize libMesh.
  LibMeshInit init (argc, argv);

  // This example requires a linear solver package.
  libmesh_example_requires(libMesh::default_solver_package() != INVALID_SOLVER_PACKAGE,
                           "--enable-petsc, --enable-trilinos, or --enable-eigen");

#ifndef LIBMESH_ENABLE_AMR
  libmesh_example_requires(false, "--enable-amr");
#else

  // Our Trilinos interface does not yet support adaptive transient
  // problems
  libmesh_example_requires(libMesh::default_solver_package() != TRILINOS_SOLVERS, "--enable-petsc");

  // Brief message to the user regarding the program name
  // and command line arguments.

  // Use commandline parameter to specify if we are to
  // read in an initial solution or generate it ourself
  libMesh::out << "Usage:\n"
               <<"\t " << argv[0] << " -init_timestep 0 -n_timesteps 25 [-n_refinements 5]\n"
               << "OR\n"
               <<"\t " << argv[0] << " -read_solution -init_timestep 26 -n_timesteps 25\n"
               << std::endl;

  libMesh::out << "Running: " << argv[0];

  for (int i=1; i<argc; i++)
    libMesh::out << " " << argv[i];

  libMesh::out << std::endl << std::endl;

  // This boolean value is obtained from the command line, it is true
  // if the flag "-read_solution" is present, false otherwise.
  // It indicates whether we are going to read in
  // the mesh and solution files "saved_mesh.xda" and "saved_solution.xda"
  // or whether we are going to start from scratch by just reading
  // "mesh.xda"
  const bool read_solution = libMesh::on_command_line("-read_solution");

  // This value is also obtained from the commandline and it specifies the
  // initial value for the t_step looping variable. We must
  // distinguish between the two cases here, whether we read in the
  // solution or we started from scratch, so that we do not overwrite the
  // gmv output files.
  const unsigned int init_timestep =
    libMesh::command_line_next("-init_timestep",
                               libMesh::invalid_uint);

  if (init_timestep == libMesh::invalid_uint)
    {
      // This handy function will print the file name, line number,
      // specified message, and then throw an exception.
      libmesh_error_msg("ERROR: Initial timestep not specified!");
    }

  // This command line value specifies how many time steps to take.
  const unsigned int n_timesteps =
    libMesh::command_line_next("-n_timesteps",
                               libMesh::invalid_uint);

  if (n_timesteps == libMesh::invalid_uint)
    libmesh_error_msg("ERROR: Number of timesteps not specified");

  // This command line value specifies how far to allow refinement
  const unsigned int max_h_level =
    libMesh::command_line_next("-max_h_level", 5);

  // Skip this 2D example if libMesh was compiled as 1D-only.
  libmesh_example_requires(2 <= LIBMESH_DIM, "2D support");

  // Create a new mesh on the default MPI communicator.
  // We still need some work on automatic parallel restarts with
  // DistributedMesh
  ReplicatedMesh mesh(init.comm());

  // Create an equation systems object.
  EquationSystems equation_systems (mesh);
  MeshRefinement mesh_refinement (mesh);

  // First we process the case where we do not read in the solution
  if (!read_solution)
    {
      // Read the mesh from file.
      mesh.read ("mesh.xda");

      // Again do a search on the command line for an argument
      const int order =
        libMesh::command_line_next("-order", 1);

      // If we need a higher-order variable, we'll need second-order
      // geometric elements to store edge DoFs.  In 2D every
      // second-order geometric can support every polynomial degree
      // (even higher-than-second), but we'll leave the 3D-compatible
      // thing in comments here for didactic purposes.
      //if (order > 2)
      //  mesh.all_complete_order();
      //else
      if (order > 1)
        mesh.all_second_order();

      const unsigned int n_refinements =
        libMesh::command_line_next("-n_refinements", 5);

      // Uniformly refine the mesh n times
      if (!read_solution)
        mesh_refinement.uniformly_refine (n_refinements);

      // Print information about the mesh to the screen.
      mesh.print_info();

      // Declare the system and its variables.
      // Begin by creating a transient system
      // named "Convection-Diffusion".
      TransientLinearImplicitSystem & system =
        equation_systems.add_system<TransientLinearImplicitSystem>("Convection-Diffusion");

      // Adds the variable "u" to "Convection-Diffusion".  "u"
      // will be approximated using first- or second-order
      // approximation.  For higher than second-order FE we need a
      // non-Lagrange type.
      system.add_variable ("u", Order(order), order > 2 ? HIERARCHIC : LAGRANGE);

      // Give the system a pointer to the matrix assembly
      // and initialization functions.
      system.attach_assemble_function (assemble_cd);
      system.attach_init_function (init_cd);

      // Initialize the data structures for the equation system.
      equation_systems.init ();
    }
  // Otherwise we read in the solution and mesh
  else
    {
      // Read in the mesh stored in "saved_mesh.xda"
      mesh.read("saved_mesh.xda");

      // Print information about the mesh to the screen.
      mesh.print_info();

      // Read in the solution stored in "saved_solution.xda"
      equation_systems.read("saved_solution.xda", READ);

      // Get a reference to the system so that we can call update() on it
      TransientLinearImplicitSystem & system =
        equation_systems.get_system<TransientLinearImplicitSystem>("Convection-Diffusion");

      // We need to call update to put system in a consistent state
      // with the solution that was read in
      system.update();

      // Attach the same matrix assembly function as above. Note, we do not
      // have to attach an init() function since we are initializing the
      // system by reading in "saved_solution.xda"
      system.attach_assemble_function (assemble_cd);

      // Print out the H1 norm of the saved solution, for verification purposes:
      Real H1norm = system.calculate_norm(*system.solution, SystemNorm(H1));

      libMesh::out << "Initial H1 norm = " << H1norm << std::endl << std::endl;
    }

  // Prints information about the system to the screen.
  equation_systems.print_info();

  equation_systems.parameters.set<unsigned int>("linear solver maximum iterations") = 250;
  equation_systems.parameters.set<Real>("linear solver tolerance") = TOLERANCE;

  // Get some output to visualize
#ifdef LIBMESH_HAVE_EXODUS_API
  if (!read_solution)
    // Write out the initial condition
    ExodusII_IO(mesh).write_equation_systems ("out.e.000", equation_systems);
  else
    // Write out the solution that was read in
    ExodusII_IO(mesh).write_equation_systems ("solution_read_in.e", equation_systems);
#endif // LIBMESH_HAVE_EXODUS_API

  // The Convection-Diffusion system requires that we specify
  // the flow velocity.  We will specify it as a RealVectorValue
  // data type and then use the Parameters object to pass it to
  // the assemble function.
  equation_systems.parameters.set<RealVectorValue>("velocity") =
    RealVectorValue (0.8, 0.8);

  // The Convection-Diffusion system also requires a specified
  // diffusivity.  We use an isotropic (hence Real) value.
  equation_systems.parameters.set<Real>("diffusivity") = 0.01;

  // Solve the system "Convection-Diffusion".  This will be done by
  // looping over the specified time interval and calling the
  // solve() member at each time step.  This will assemble the
  // system and call the linear solver.

  // Since only TransientLinearImplicitSystems (and systems
  // derived from them) contain old solutions, to use the
  // old_local_solution later we now need to specify the system
  // type when we ask for it.
  TransientLinearImplicitSystem & system =
    equation_systems.get_system<TransientLinearImplicitSystem>("Convection-Diffusion");

  const Real dt = 0.025;
  system.time = init_timestep*dt;

  // We're going to refine and coarsen based on some heuristics.
  const Real refine_fraction =
    libMesh::command_line_next("-refine_fraction", 0.80);

  const Real coarsen_fraction =
    libMesh::command_line_next("-coarsen_fraction", 0.07);

  // We do 25 timesteps both before and after writing out the
  // intermediate solution
  for (unsigned int t_step=init_timestep; t_step<(init_timestep+n_timesteps); t_step++)
    {
      // Increment the time counter, set the time and the
      // time step size as parameters in the EquationSystem.
      system.time += dt;

      equation_systems.parameters.set<Real> ("time") = system.time;
      equation_systems.parameters.set<Real> ("dt")   = dt;

      // A pretty update message
      libMesh::out << " Solving time step ";

      // Add a set of scope braces to enforce data locality.
      {
        std::ostringstream out;

        out << std::setw(2)
            << std::right
            << t_step
            << ", time="
            << std::fixed
            << std::setw(6)
            << std::setprecision(3)
            << std::setfill('0')
            << std::left
            << system.time
            <<  "...";

        libMesh::out << out.str() << std::endl;
      }

      // At this point we need to update the old
      // solution vector.  The old solution vector
      // will be the current solution vector from the
      // previous time step.

      *system.old_local_solution = *system.current_local_solution;

      // The number of refinement steps per time step.
      const unsigned int max_r_steps = 2;

      // A refinement loop.
      for (unsigned int r_step=0; r_step<max_r_steps; r_step++)
        {
          // Assemble & solve the linear system
          system.solve();

          // Print out the H1 norm, for verification purposes:
          Real H1norm = system.calculate_norm(*system.solution, SystemNorm(H1));

          libMesh::out << "H1 norm = " << H1norm << std::endl;

          // Possibly refine the mesh
          if (r_step+1 != max_r_steps)
            {
              libMesh::out << "  Refining the mesh..." << std::endl;

              // The ErrorVector is a particular StatisticsVector
              // for computing error information on a finite element mesh.
              ErrorVector error;

              // The ErrorEstimator class interrogates a finite element
              // solution and assigns to each element a positive error value.
              // This value is used for deciding which elements to refine
              // and which to coarsen.
              KellyErrorEstimator error_estimator;

              // This is a subclass of JumpErrorEstimator, based on
              // measuring discontinuities across sides between
              // elements, and we can tell it to use a cheaper
              // "unweighted" quadrature rule when numerically
              // integrating those discontinuities.
              error_estimator.use_unweighted_quadrature_rules = true;

              // Compute the error for each active element using the provided
              // flux_jump indicator.  Note in general you will need to
              // provide an error estimator specifically designed for your
              // application.
              error_estimator.estimate_error (system,
                                              error);

              // This takes the error in error and decides which elements
              // will be coarsened or refined.  Any element within 20% of the
              // maximum error on any element will be refined, and any
              // element within 7% of the minimum error on any element might
              // be coarsened. Note that the elements flagged for refinement
              // will be refined, but those flagged for coarsening _might_ be
              // coarsened.
              mesh_refinement.refine_fraction() = refine_fraction;
              mesh_refinement.coarsen_fraction() = coarsen_fraction;
              mesh_refinement.max_h_level() = max_h_level;
              mesh_refinement.flag_elements_by_error_fraction (error);

              // This call actually refines and coarsens the flagged
              // elements.
              mesh_refinement.refine_and_coarsen_elements();

              // This call reinitializes the EquationSystems object for
              // the newly refined mesh.  One of the steps in the
              // reinitialization is projecting the solution,
              // old_solution, etc... vectors from the old mesh to
              // the current one.
              equation_systems.reinit ();
            }
        }

      // Again do a search on the command line for an argument
      const unsigned int output_freq =
        libMesh::command_line_next("-output_freq", 10);

      // Every N timesteps, output solutions to file and summaries to
      // the console.
      if ((t_step+1)%output_freq == 0)
        {
          equation_systems.print_info();

          std::ostringstream file_name;

          file_name << "out.e."
                    << std::setw(3)
                    << std::setfill('0')
                    << std::right
                    << t_step+1;

          // Get some output to visualize
#ifdef LIBMESH_HAVE_EXODUS_API
          ExodusII_IO(mesh).write_equation_systems (file_name.str(),
                                              equation_systems);
#endif // LIBMESH_HAVE_EXODUS_API
        }
    }

  if (!read_solution)
    {
      // Print out the H1 norm of the saved solution, for verification purposes:
      Real H1norm = system.calculate_norm(*system.solution, SystemNorm(H1));

      libMesh::out << "Final H1 norm = " << H1norm << std::endl << std::endl;

      mesh.write("saved_mesh.xda");
      equation_systems.write("saved_solution.xda", WRITE);
#ifdef LIBMESH_HAVE_EXODUS_API
      ExodusII_IO(mesh).write_equation_systems ("saved_solution.e",
                                                equation_systems);
#endif // LIBMESH_HAVE_EXODUS_API
    }
#endif // #ifndef LIBMESH_ENABLE_AMR

  return 0;
}