step-31.h

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,
 *                              const unsigned int /*component*/ = 0) const override
 *         {
 *           return 0;
 *         }
 *   
 *         virtual void vector_value(const Point<dim> &p,
 *                                   Vector<double> &  value) const override
 *         {
 *           for (unsigned int c = 0; c < this->n_components; ++c)
 *             value(c) = TemperatureInitialValues<dim>::value(p, c);
 *         }
 *       };
 *   
 *   
 *   
 *       template <int dim>
 *       class TemperatureRightHandSide : public Function<dim>
 *       {
 *       public:
 *         TemperatureRightHandSide()
 *           : Function<dim>(1)
 *         {}
 *   
 *         virtual double value(const Point<dim> & p,
 *                              const unsigned int component = 0) const override
 *         {
 *           (void)component;
 *           Assert(component == 0,
 *                  ExcMessage("Invalid operation for a scalar function."));
 *   
 *           Assert((dim == 2) || (dim == 3), ExcNotImplemented());
 *   
 *           static const Point<dim> source_centers[3] = {
 *             (dim == 2 ? Point<dim>(.3, .1) : Point<dim>(.3, .5, .1)),
 *             (dim == 2 ? Point<dim>(.45, .1) : Point<dim>(.45, .5, .1)),
 *             (dim == 2 ? Point<dim>(.75, .1) : Point<dim>(.75, .5, .1))};
 *           static const double source_radius = (dim == 2 ? 1. / 32 : 1. / 8);
 *   
 *           return ((source_centers[0].distance(p) < source_radius) ||
 *                       (source_centers[1].distance(p) < source_radius) ||
 *                       (source_centers[2].distance(p) < source_radius) ?
 *                     1 :
 *                     0);
 *         }
 *   
 *         virtual void vector_value(const Point<dim> &p,
 *                                   Vector<double> &  value) const override
 *         {
 *           for (unsigned int c = 0; c < this->n_components; ++c)
 *             value(c) = TemperatureRightHandSide<dim>::value(p, c);
 *         }
 *       };
 *     } // namespace EquationData
 *   
 *   
 *   
 * @endcode
 * 
 * 
 * <a name="Linearsolversandpreconditioners"></a> 
 * <h3>Linear solvers and preconditioners</h3>
 * 
 
 * 
 * This section introduces some objects that are used for the solution of
 * the linear equations of the Stokes system that we need to solve in each
 * time step. Many of the ideas used here are the same as in @ref step_20 "step-20", where
 * Schur complement based preconditioners and solvers have been introduced,
 * with the actual interface taken from @ref step_22 "step-22" (in particular the
 * discussion in the "Results" section of @ref step_22 "step-22", in which we introduce
 * alternatives to the direct Schur complement approach). Note, however,
 * that here we don't use the Schur complement to solve the Stokes
 * equations, though an approximate Schur complement (the mass matrix on the
 * pressure space) appears in the preconditioner.
 * 
 * @code
 *     namespace LinearSolvers
 *     {
 * @endcode
 * 
 * 
 * <a name="ThecodeInverseMatrixcodeclasstemplate"></a> 
 * <h4>The <code>InverseMatrix</code> class template</h4>
 * 
 
 * 
 * This class is an interface to calculate the action of an "inverted"
 * matrix on a vector (using the <code>vmult</code> operation) in the same
 * way as the corresponding class in @ref step_22 "step-22": when the product of an
 * object of this class is requested, we solve a linear equation system
 * with that matrix using the CG method, accelerated by a preconditioner
 * of (templated) class <code>PreconditionerType</code>.
 *     
 
 * 
 * In a minor deviation from the implementation of the same class in
 * @ref step_22 "step-22", we make the <code>vmult</code> function take any
 * kind of vector type (it will yield compiler errors, however, if the
 * matrix does not allow a matrix-vector product with this kind of
 * vector).
 *     
 
 * 
 * Secondly, we catch any exceptions that the solver may have thrown. The
 * reason is as follows: When debugging a program like this one
 * occasionally makes a mistake of passing an indefinite or nonsymmetric
 * matrix or preconditioner to the current class. The solver will, in that
 * case, not converge and throw a run-time exception. If not caught here
 * it will propagate up the call stack and may end up in
 * <code>main()</code> where we output an error message that will say that
 * the CG solver failed. The question then becomes: Which CG solver? The
 * one that inverted the mass matrix? The one that inverted the top left
 * block with the Laplace operator? Or a CG solver in one of the several
 * other nested places where we use linear solvers in the current code? No
 * indication about this is present in a run-time exception because it
 * doesn't store the stack of calls through which we got to the place
 * where the exception was generated.
 *     
 
 * 
 * So rather than letting the exception propagate freely up to
 * <code>main()</code> we realize that there is little that an outer
 * function can do if the inner solver fails and rather convert the
 * run-time exception into an assertion that fails and triggers a call to
 * <code>abort()</code>, allowing us to trace back in a debugger how we
 * got to the current place.
 * 
 * @code
 *       template <class MatrixType, class PreconditionerType>
 *       class InverseMatrix : public Subscriptor
 *       {
 *       public:
 *         InverseMatrix(const MatrixType &        m,
 *                       const PreconditionerType &preconditioner);
 *   
 *   
 *         template <typename VectorType>
 *         void vmult(VectorType &dst, const VectorType &src) const;
 *   
 *       private:
 *         const SmartPointer<const MatrixType> matrix;
 *         const PreconditionerType &           preconditioner;
 *       };
 *   
 *   
 *       template <class MatrixType, class PreconditionerType>
 *       InverseMatrix<MatrixType, PreconditionerType>::InverseMatrix(
 *         const MatrixType &        m,
 *         const PreconditionerType &preconditioner)
 *         : matrix(&m)
 *         , preconditioner(preconditioner)
 *       {}
 *   
 *   
 *   
 *       template <class MatrixType, class PreconditionerType>
 *       template <typename VectorType>
 *       void InverseMatrix<MatrixType, PreconditionerType>::vmult(
 *         VectorType &      dst,
 *         const VectorType &src) const
 *       {
 *         SolverControl        solver_control(src.size(), 1e-7 * src.l2_norm());
 *         SolverCG<VectorType> cg(solver_control);
 *   
 *         dst = 0;
 *   
 *         try
 *           {
 *             cg.solve(*matrix, dst, src, preconditioner);
 *           }
 *         catch (std::exception &e)
 *           {
 *             Assert(false, ExcMessage(e.what()));
 *           }
 *       }
 *   
 * @endcode
 * 
 * 
 * <a name="Schurcomplementpreconditioner"></a> 
 * <h4>Schur complement preconditioner</h4>
 * 
 
 * 
 * This is the implementation of the Schur complement preconditioner as
 * described in detail in the introduction. As opposed to @ref step_20 "step-20" and
 * @ref step_22 "step-22", we solve the block system all-at-once using GMRES, and use the
 * Schur complement of the block structured matrix to build a good
 * preconditioner instead.
 *     
 
 * 
 * Let's have a look at the ideal preconditioner matrix
 * @f$P=\left(\begin{array}{cc} A & 0 \\ B & -S \end{array}\right)@f$
 * described in the introduction. If we apply this matrix in the solution
 * of a linear system, convergence of an iterative GMRES solver will be
 * governed by the matrix @f{eqnarray*} P^{-1}\left(\begin{array}{cc} A &
 * B^T \\ B & 0 \end{array}\right) = \left(\begin{array}{cc} I & A^{-1}
 * B^T \\ 0 & I \end{array}\right), @f} which indeed is very simple. A
 * GMRES solver based on exact matrices would converge in one iteration,
 * since all eigenvalues are equal (any Krylov method takes at most as
 * many iterations as there are distinct eigenvalues). Such a
 * preconditioner for the blocked Stokes system has been proposed by
 * Silvester and Wathen ("Fast iterative solution of stabilised Stokes
 * systems part II.  Using general block preconditioners", SIAM
 * J. Numer. Anal., 31 (1994), pp. 1352-1367).
 *     
 
 * 
 * Replacing @f$P@f$ by @f$\tilde{P}@f$ keeps that spirit alive: the product
 * @f$P^{-1} A@f$ will still be close to a matrix with eigenvalues 1 with a
 * distribution that does not depend on the problem size. This lets us
 * hope to be able to get a number of GMRES iterations that is
 * problem-size independent.
 *     
 
 * 
 * The deal.II users who have already gone through the @ref step_20 "step-20" and @ref step_22 "step-22"
 * tutorials can certainly imagine how we're going to implement this.  We
 * replace the exact inverse matrices in @f$P^{-1}@f$ by some approximate
 * inverses built from the InverseMatrix class, and the inverse Schur
 * complement will be approximated by the pressure mass matrix @f$M_p@f$
 * (weighted by @f$\eta^{-1}@f$ as mentioned in the introduction). As pointed
 * out in the results section of @ref step_22 "step-22", we can replace the exact inverse
 * of @f$A@f$ by just the application of a preconditioner, in this case
 * on a vector Laplace matrix as was explained in the introduction. This
 * does increase the number of (outer) GMRES iterations, but is still
 * significantly cheaper than an exact inverse, which would require
 * between 20 and 35 CG iterations for <em>each</em> outer solver step
 * (using the AMG preconditioner).
 *     
 
 * 
 * Having the above explanations in mind, we define a preconditioner class
 * with a <code>vmult</code> functionality, which is all we need for the
 * interaction with the usual solver functions further below in the
 * program code.
 *     
 
 * 
 * First the declarations. These are similar to the definition of the
 * Schur complement in @ref step_20 "step-20", with the difference that we need some more
 * preconditioners in the constructor and that the matrices we use here
 * are built upon Trilinos:
 * 
 * @code
 *       template <class PreconditionerTypeA, class PreconditionerTypeMp>
 *       class BlockSchurPreconditioner : public Subscriptor
 *       {
 *       public:
 *         BlockSchurPreconditioner(
 *           const TrilinosWrappers::BlockSparseMatrix &S,
 *           const InverseMatrix<TrilinosWrappers::SparseMatrix,
 *                               PreconditionerTypeMp> &Mpinv,
 *           const PreconditionerTypeA &                Apreconditioner);
 *   
 *         void vmult(TrilinosWrappers::MPI::BlockVector &      dst,
 *                    const TrilinosWrappers::MPI::BlockVector &src) const;
 *   
 *       private:
 *         const SmartPointer<const TrilinosWrappers::BlockSparseMatrix>
 *           stokes_matrix;
 *         const SmartPointer<const InverseMatrix<TrilinosWrappers::SparseMatrix,
 *                                                PreconditionerTypeMp>>
 *                                    m_inverse;
 *         const PreconditionerTypeA &a_preconditioner;
 *   
 *         mutable TrilinosWrappers::MPI::Vector tmp;
 *       };
 *   
 *   
 *   
 * @endcode
 * 
 * When using a TrilinosWrappers::MPI::Vector or a
 * TrilinosWrappers::MPI::BlockVector, the Vector is initialized using an
 * IndexSet. IndexSet is used not only to resize the
 * TrilinosWrappers::MPI::Vector but it also associates an index in the
 * TrilinosWrappers::MPI::Vector with a degree of freedom (see @ref step_40 "step-40" for
 * a more detailed explanation). The function complete_index_set() creates
 * an IndexSet where every valid index is part of the set. Note that this
 * program can only be run sequentially and will throw an exception if used
 * in parallel.
 * 
 * @code
 *       template <class PreconditionerTypeA, class PreconditionerTypeMp>
 *       BlockSchurPreconditioner<PreconditionerTypeA, PreconditionerTypeMp>::
 *         BlockSchurPreconditioner(
 *           const TrilinosWrappers::BlockSparseMatrix &S,
 *           const InverseMatrix<TrilinosWrappers::SparseMatrix,
 *                               PreconditionerTypeMp> &Mpinv,
 *           const PreconditionerTypeA &                Apreconditioner)
 *         : stokes_matrix(&S)
 *         , m_inverse(&Mpinv)
 *         , a_preconditioner(Apreconditioner)
 *         , tmp(complete_index_set(stokes_matrix->block(1, 1).m()))
 *       {}
 *   
 *   
 * @endcode
 * 
 * Next is the <code>vmult</code> function. We implement the action of
 * @f$P^{-1}@f$ as described above in three successive steps.  In formulas, we
 * want to compute @f$Y=P^{-1}X@f$ where @f$X,Y@f$ are both vectors with two block
 * components.
 *     
 
 * 
 * The first step multiplies the velocity part of the vector by a
 * preconditioner of the matrix @f$A@f$, i.e., we compute @f$Y_0={\tilde
 * A}^{-1}X_0@f$.  The resulting velocity vector is then multiplied by @f$B@f$
 * and subtracted from the pressure, i.e., we want to compute @f$X_1-BY_0@f$.
 * This second step only acts on the pressure vector and is accomplished
 * by the residual function of our matrix classes, except that the sign is
 * wrong. Consequently, we change the sign in the temporary pressure
 * vector and finally multiply by the inverse pressure mass matrix to get
 * the final pressure vector, completing our work on the Stokes
 * preconditioner:
 * 
 * @code
 *       template <class PreconditionerTypeA, class PreconditionerTypeMp>
 *       void
 *       BlockSchurPreconditioner<PreconditionerTypeA, PreconditionerTypeMp>::vmult(
 *         TrilinosWrappers::MPI::BlockVector &      dst,
 *         const TrilinosWrappers::MPI::BlockVector &src) const
 *       {
 *         a_preconditioner.vmult(dst.block(0), src.block(0));
 *         stokes_matrix->block(1, 0).residual(tmp, dst.block(0), src.block(1));
 *         tmp *= -1;
 *         m_inverse->vmult(dst.block(1), tmp);
 *       }
 *     } // namespace LinearSolvers
 *   
 *   
 *   
 * @endcode
 * 
 * 
 * <a name="ThecodeBoussinesqFlowProblemcodeclasstemplate"></a> 
 * <h3>The <code>BoussinesqFlowProblem</code> class template</h3>
 * 
 
 * 
 * The definition of the class that defines the top-level logic of solving
 * the time-dependent Boussinesq problem is mainly based on the @ref step_22 "step-22"
 * tutorial program. The main differences are that now we also have to solve
 * for the temperature equation, which forces us to have a second DoFHandler
 * object for the temperature variable as well as matrices, right hand
 * sides, and solution vectors for the current and previous time steps. As
 * mentioned in the introduction, all linear algebra objects are going to
 * use wrappers of the corresponding Trilinos functionality.
 *   
 
 * 
 * The member functions of this class are reminiscent of @ref step_21 "step-21", where we
 * also used a staggered scheme that first solve the flow equations (here
 * the Stokes equations, in @ref step_21 "step-21" Darcy flow) and then update the advected
 * quantity (here the temperature, there the saturation). The functions that
 * are new are mainly concerned with determining the time step, as well as
 * the proper size of the artificial viscosity stabilization.
 *   
 
 * 
 * The last three variables indicate whether the various matrices or
 * preconditioners need to be rebuilt the next time the corresponding build
 * functions are called. This allows us to move the corresponding
 * <code>if</code> into the respective function and thereby keeping our main
 * <code>run()</code> function clean and easy to read.
 * 
 * @code
 *     template <int dim>
 *     class BoussinesqFlowProblem
 *     {
 *     public:
 *       BoussinesqFlowProblem();
 *       void run();
 *   
 *     private:
 *       void   setup_dofs();
 *       void   assemble_stokes_preconditioner();
 *       void   build_stokes_preconditioner();
 *       void   assemble_stokes_system();
 *       void   assemble_temperature_system(const double maximal_velocity);
 *       void   assemble_temperature_matrix();
 *       double get_maximal_velocity() const;
 *       std::pair<double, double> get_extrapolated_temperature_range() const;
 *       void                      solve();
 *       void                      output_results() const;
 *       void                      refine_mesh(const unsigned int max_grid_level);
 *   
 *       double compute_viscosity(
 *         const std::vector<double> &        old_temperature,
 *         const std::vector<double> &        old_old_temperature,
 *         const std::vector<Tensor<1, dim>> &old_temperature_grads,
 *         const std::vector<Tensor<1, dim>> &old_old_temperature_grads,
 *         const std::vector<double> &        old_temperature_laplacians,
 *         const std::vector<double> &        old_old_temperature_laplacians,
 *         const std::vector<Tensor<1, dim>> &old_velocity_values,
 *         const std::vector<Tensor<1, dim>> &old_old_velocity_values,
 *         const std::vector<double> &        gamma_values,
 *         const double                       global_u_infty,
 *         const double                       global_T_variation,
 *         const double                       cell_diameter) const;
 *   
 *   
 *       Triangulation<dim> triangulation;
 *       double             global_Omega_diameter;
 *   
 *       const unsigned int        stokes_degree;
 *       FESystem<dim>             stokes_fe;
 *       DoFHandler<dim>           stokes_dof_handler;
 *       AffineConstraints<double> stokes_constraints;
 *   
 *       std::vector<IndexSet>               stokes_partitioning;
 *       TrilinosWrappers::BlockSparseMatrix stokes_matrix;
 *       TrilinosWrappers::BlockSparseMatrix stokes_preconditioner_matrix;
 *   
 *       TrilinosWrappers::MPI::BlockVector stokes_solution;
 *       TrilinosWrappers::MPI::BlockVector old_stokes_solution;
 *       TrilinosWrappers::MPI::BlockVector stokes_rhs;
 *   
 *   
 *       const unsigned int        temperature_degree;
 *       FE_Q<dim>                 temperature_fe;
 *       DoFHandler<dim>           temperature_dof_handler;
 *       AffineConstraints<double> temperature_constraints;
 *   
 *       TrilinosWrappers::SparseMatrix temperature_mass_matrix;
 *       TrilinosWrappers::SparseMatrix temperature_stiffness_matrix;
 *       TrilinosWrappers::SparseMatrix temperature_matrix;
 *   
 *       TrilinosWrappers::MPI::Vector temperature_solution;
 *       TrilinosWrappers::MPI::Vector old_temperature_solution;
 *       TrilinosWrappers::MPI::Vector old_old_temperature_solution;
 *       TrilinosWrappers::MPI::Vector temperature_rhs;
 *   
 *   
 *       double       time_step;
 *       double       old_time_step;
 *       unsigned int timestep_number;
 *   
 *       std::shared_ptr<TrilinosWrappers::PreconditionAMG> Amg_preconditioner;
 *       std::shared_ptr<TrilinosWrappers::PreconditionIC>  Mp_preconditioner;
 *   
 *       bool rebuild_stokes_matrix;
 *       bool rebuild_temperature_matrices;
 *       bool rebuild_stokes_preconditioner;
 *     };
 *   
 *   
 * @endcode
 * 
 * 
 * <a name="BoussinesqFlowProblemclassimplementation"></a> 
 * <h3>BoussinesqFlowProblem class implementation</h3>
 * 
 
 * 
 * 
 * <a name="BoussinesqFlowProblemBoussinesqFlowProblem"></a> 
 * <h4>BoussinesqFlowProblem::BoussinesqFlowProblem</h4>
 *   
 
 * 
 * The constructor of this class is an extension of the constructor in
 * @ref step_22 "step-22". We need to add the various variables that concern the
 * temperature. As discussed in the introduction, we are going to use
 * @f$Q_2\times Q_1@f$ (Taylor-Hood) elements again for the Stokes part, and
 * @f$Q_2@f$ elements for the temperature. However, by using variables that
 * store the polynomial degree of the Stokes and temperature finite
 * elements, it is easy to consistently modify the degree of the elements as
 * well as all quadrature formulas used on them downstream. Moreover, we
 * initialize the time stepping as well as the options for matrix assembly
 * and preconditioning:
 * 
 * @code
 *     template <int dim>
 *     BoussinesqFlowProblem<dim>::BoussinesqFlowProblem()
 *       : triangulation(Triangulation<dim>::maximum_smoothing)
 *       , global_Omega_diameter(std::numeric_limits<double>::quiet_NaN())
 *       , stokes_degree(1)
 *       , stokes_fe(FE_Q<dim>(stokes_degree + 1), dim, FE_Q<dim>(stokes_degree), 1)
 *       , stokes_dof_handler(triangulation)
 *       ,
 *   
 *       temperature_degree(2)
 *       , temperature_fe(temperature_degree)
 *       , temperature_dof_handler(triangulation)
 *       ,
 *   
 *       time_step(0)
 *       , old_time_step(0)
 *       , timestep_number(0)
 *       , rebuild_stokes_matrix(true)
 *       , rebuild_temperature_matrices(true)
 *       , rebuild_stokes_preconditioner(true)
 *     {}
 *   
 *   
 *   
 * @endcode
 * 
 * 
 * <a name="BoussinesqFlowProblemget_maximal_velocity"></a> 
 * <h4>BoussinesqFlowProblem::get_maximal_velocity</h4>
 * 
 
 * 
 * Starting the real functionality of this class is a helper function that
 * determines the maximum (@f$L_\infty@f$) velocity in the domain (at the
 * quadrature points, in fact). How it works should be relatively obvious to
 * all who have gotten to this point of the tutorial. Note that since we are
 * only interested in the velocity, rather than using
 * <code>stokes_fe_values.get_function_values</code> to get the values of
 * the entire Stokes solution (velocities and pressures) we use
 * <code>stokes_fe_values[velocities].get_function_values</code> to extract
 * only the velocities part. This has the additional benefit that we get it
 * as a Tensor<1,dim>, rather than some components in a Vector<double>,
 * allowing us to process it right away using the <code>norm()</code>
 * function to get the magnitude of the velocity.
 *   
 
 * 
 * The only point worth thinking about a bit is how to choose the quadrature
 * points we use here. Since the goal of this function is to find the
 * maximal velocity over a domain by looking at quadrature points on each
 * cell. So we should ask how we should best choose these quadrature points
 * on each cell. To this end, recall that if we had a single @f$Q_1@f$ field
 * (rather than the vector-valued field of higher order) then the maximum
 * would be attained at a vertex of the mesh. In other words, we should use
 * the QTrapezoid class that has quadrature points only at the vertices of
 * cells.
 *   
 
 * 
 * For higher order shape functions, the situation is more complicated: the
 * maxima and minima may be attained at points between the support points of
 * shape functions (for the usual @f$Q_p@f$ elements the support points are the
 * equidistant Lagrange interpolation points); furthermore, since we are
 * looking for the maximum magnitude of a vector-valued quantity, we can
 * even less say with certainty where the set of potential maximal points
 * are. Nevertheless, intuitively if not provably, the Lagrange
 * interpolation points appear to be a better choice than the Gauss points.
 *   
 
 * 
 * There are now different methods to produce a quadrature formula with
 * quadrature points equal to the interpolation points of the finite
 * element. One option would be to use the
 * FiniteElement::get_unit_support_points() function, reduce the output to a
 * unique set of points to avoid duplicate function evaluations, and create
 * a Quadrature object using these points. Another option, chosen here, is
 * to use the QTrapezoid class and combine it with the QIterated class that
 * repeats the QTrapezoid formula on a number of sub-cells in each coordinate
 * direction. To cover all support points, we need to iterate it
 * <code>stokes_degree+1</code> times since this is the polynomial degree of
 * the Stokes element in use:
 * 
 * @code
 *     template <int dim>
 *     double BoussinesqFlowProblem<dim>::get_maximal_velocity() const
 *     {
 *       const QIterated<dim> quadrature_formula(QTrapezoid<1>(), stokes_degree + 1);
 *       const unsigned int   n_q_points = quadrature_formula.size();
 *   
 *       FEValues<dim> fe_values(stokes_fe, quadrature_formula, update_values);
 *       std::vector<Tensor<1, dim>> velocity_values(n_q_points);
 *       double                      max_velocity = 0;
 *   
 *       const FEValuesExtractors::Vector velocities(0);
 *   
 *       for (const auto &cell : stokes_dof_handler.active_cell_iterators())
 *         {
 *           fe_values.reinit(cell);
 *           fe_values[velocities].get_function_values(stokes_solution,
 *                                                     velocity_values);
 *   
 *           for (unsigned int q = 0; q < n_q_points; ++q)
 *             max_velocity = std::max(max_velocity, velocity_values[q].norm());
 *         }
 *   
 *       return max_velocity;
 *     }
 *   
 *   
 *   
 * @endcode
 * 
 * 
 * <a name="BoussinesqFlowProblemget_extrapolated_temperature_range"></a> 
 * <h4>BoussinesqFlowProblem::get_extrapolated_temperature_range</h4>
 * 
 
 * 
 * Next a function that determines the minimum and maximum temperature at
 * quadrature points inside @f$\Omega@f$ when extrapolated from the two previous
 * time steps to the current one. We need this information in the
 * computation of the artificial viscosity parameter @f$\nu@f$ as discussed in
 * the introduction.
 *   
 
 * 
 * The formula for the extrapolated temperature is
 * @f$\left(1+\frac{k_n}{k_{n-1}} \right)T^{n-1} + \frac{k_n}{k_{n-1}}
 * T^{n-2}@f$. The way to compute it is to loop over all quadrature points and
 * update the maximum and minimum value if the current value is
 * bigger/smaller than the previous one. We initialize the variables that
 * store the max and min before the loop over all quadrature points by the
 * smallest and the largest number representable as a double. Then we know
 * for a fact that it is larger/smaller than the minimum/maximum and that
 * the loop over all quadrature points is ultimately going to update the
 * initial value with the correct one.
 *   
 
 * 
 * The only other complication worth mentioning here is that in the first
 * time step, @f$T^{k-2}@f$ is not yet available of course. In that case, we can
 * only use @f$T^{k-1}@f$ which we have from the initial temperature. As
 * quadrature points, we use the same choice as in the previous function
 * though with the difference that now the number of repetitions is
 * determined by the polynomial degree of the temperature field.
 * 
 * @code
 *     template <int dim>
 *     std::pair<double, double>
 *     BoussinesqFlowProblem<dim>::get_extrapolated_temperature_range() const
 *     {
 *       const QIterated<dim> quadrature_formula(QTrapezoid<1>(),
 *                                               temperature_degree);
 *       const unsigned int   n_q_points = quadrature_formula.size();
 *   
 *       FEValues<dim> fe_values(temperature_fe, quadrature_formula, update_values);
 *       std::vector<double> old_temperature_values(n_q_points);
 *       std::vector<double> old_old_temperature_values(n_q_points);
 *   
 *       if (timestep_number != 0)
 *         {
 *           double min_temperature = std::numeric_limits<double>::max(),
 *                  max_temperature = -std::numeric_limits<double>::max();
 *   
 *           for (const auto &cell : temperature_dof_handler.active_cell_iterators())
 *             {
 *               fe_values.reinit(cell);
 *               fe_values.get_function_values(old_temperature_solution,
 *                                             old_temperature_values);
 *               fe_values.get_function_values(old_old_temperature_solution,
 *                                             old_old_temperature_values);
 *   
 *               for (unsigned int q = 0; q < n_q_points; ++q)
 *                 {
 *                   const double temperature =
 *                     (1. + time_step / old_time_step) * old_temperature_values[q] -
 *                     time_step / old_time_step * old_old_temperature_values[q];
 *   
 *                   min_temperature = std::min(min_temperature, temperature);
 *                   max_temperature = std::max(max_temperature, temperature);
 *                 }
 *             }
 *   
 *           return std::make_pair(min_temperature, max_temperature);
 *         }
 *       else
 *         {
 *           double min_temperature = std::numeric_limits<double>::max(),
 *                  max_temperature = -std::numeric_limits<double>::max();
 *   
 *           for (const auto &cell : temperature_dof_handler.active_cell_iterators())
 *             {
 *               fe_values.reinit(cell);
 *               fe_values.get_function_values(old_temperature_solution,
 *                                             old_temperature_values);
 *   
 *               for (unsigned int q = 0; q < n_q_points; ++q)
 *                 {
 *                   const double temperature = old_temperature_values[q];
 *   
 *                   min_temperature = std::min(min_temperature, temperature);
 *                   max_temperature = std::max(max_temperature, temperature);
 *                 }
 *             }
 *   
 *           return std::make_pair(min_temperature, max_temperature);
 *         }
 *     }
 *   
 *   
 *   
 * @endcode
 * 
 * 
 * <a name="BoussinesqFlowProblemcompute_viscosity"></a> 
 * <h4>BoussinesqFlowProblem::compute_viscosity</h4>
 * 
 
 * 
 * The last of the tool functions computes the artificial viscosity
 * parameter @f$\nu|_K@f$ on a cell @f$K@f$ as a function of the extrapolated
 * temperature, its gradient and Hessian (second derivatives), the velocity,
 * the right hand side @f$\gamma@f$ all on the quadrature points of the current
 * cell, and various other parameters as described in detail in the
 * introduction.
 *   
 
 * 
 * There are some universal constants worth mentioning here. First, we need
 * to fix @f$\beta@f$; we choose @f$\beta=0.017\cdot dim@f$, a choice discussed in
 * detail in the results section of this tutorial program. The second is the
 * exponent @f$\alpha@f$; @f$\alpha=1@f$ appears to work fine for the current
 * program, even though some additional benefit might be expected from
 * choosing @f$\alpha = 2@f$. Finally, there is one thing that requires special
 * casing: In the first time step, the velocity equals zero, and the formula
 * for @f$\nu|_K@f$ is not defined. In that case, we return @f$\nu|_K=5\cdot 10^3
 * \cdot h_K@f$, a choice admittedly more motivated by heuristics than
 * anything else (it is in the same order of magnitude, however, as the
 * value returned for most cells on the second time step).
 *   
 
 * 
 * The rest of the function should be mostly obvious based on the material
 * discussed in the introduction:
 * 
 * @code
 *     template <int dim>
 *     double BoussinesqFlowProblem<dim>::compute_viscosity(
 *       const std::vector<double> &        old_temperature,
 *       const std::vector<double> &        old_old_temperature,
 *       const std::vector<Tensor<1, dim>> &old_temperature_grads,
 *       const std::vector<Tensor<1, dim>> &old_old_temperature_grads,
 *       const std::vector<double> &        old_temperature_laplacians,
 *       const std::vector<double> &        old_old_temperature_laplacians,
 *       const std::vector<Tensor<1, dim>> &old_velocity_values,
 *       const std::vector<Tensor<1, dim>> &old_old_velocity_values,
 *       const std::vector<double> &        gamma_values,
 *       const double                       global_u_infty,
 *       const double                       global_T_variation,
 *       const double                       cell_diameter) const
 *     {
 *       constexpr double beta  = 0.017 * dim;
 *       constexpr double alpha = 1.0;
 *   
 *       if (global_u_infty == 0)
 *         return 5e-3 * cell_diameter;
 *   
 *       const unsigned int n_q_points = old_temperature.size();
 *   
 *       double max_residual = 0;
 *       double max_velocity = 0;
 *   
 *       for (unsigned int q = 0; q < n_q_points; ++q)
 *         {
 *           const Tensor<1, dim> u =
 *             (old_velocity_values[q] + old_old_velocity_values[q]) / 2;
 *   
 *           const double dT_dt =
 *             (old_temperature[q] - old_old_temperature[q]) / old_time_step;
 *           const double u_grad_T =
 *             u * (old_temperature_grads[q] + old_old_temperature_grads[q]) / 2;
 *   
 *           const double kappa_Delta_T =
 *             EquationData::kappa *
 *             (old_temperature_laplacians[q] + old_old_temperature_laplacians[q]) /
 *             2;
 *   
 *           const double residual =
 *             std::abs((dT_dt + u_grad_T - kappa_Delta_T - gamma_values[q]) *
 *                      std::pow((old_temperature[q] + old_old_temperature[q]) / 2,
 *                               alpha - 1.));
 *   
 *           max_residual = std::max(residual, max_residual);
 *           max_velocity = std::max(std::sqrt(u * u), max_velocity);
 *         }
 *   
 *       const double c_R            = std::pow(2., (4. - 2 * alpha) / dim);
 *       const double global_scaling = c_R * global_u_infty * global_T_variation *
 *                                     std::pow(global_Omega_diameter, alpha - 2.);
 *   
 *       return (
 *         beta * max_velocity *
 *         std::min(cell_diameter,
 *                  std::pow(cell_diameter, alpha) * max_residual / global_scaling));
 *     }
 *   
 *   
 *   
 * @endcode
 * 
 * 
 * <a name="BoussinesqFlowProblemsetup_dofs"></a> 
 * <h4>BoussinesqFlowProblem::setup_dofs</h4>
 *   
 
 * 
 * This is the function that sets up the DoFHandler objects we have here
 * (one for the Stokes part and one for the temperature part) as well as set
 * to the right sizes the various objects required for the linear algebra in
 * this program. Its basic operations are similar to what we do in @ref step_22 "step-22".
 *   
 
 * 
 * The body of the function first enumerates all degrees of freedom for the
 * Stokes and temperature systems. For the Stokes part, degrees of freedom
 * are then sorted to ensure that velocities precede pressure DoFs so that
 * we can partition the Stokes matrix into a @f$2\times 2@f$ matrix. As a
 * difference to @ref step_22 "step-22", we do not perform any additional DoF
 * renumbering. In that program, it paid off since our solver was heavily
 * dependent on ILU's, whereas we use AMG here which is not sensitive to the
 * DoF numbering. The IC preconditioner for the inversion of the pressure
 * mass matrix would of course take advantage of a Cuthill-McKee like
 * renumbering, but its costs are low compared to the velocity portion, so
 * the additional work does not pay off.
 *   
 
 * 
 * We then proceed with the generation of the hanging node constraints that
 * arise from adaptive grid refinement for both DoFHandler objects. For the
 * velocity, we impose no-flux boundary conditions @f$\mathbf{u}\cdot
 * \mathbf{n}=0@f$ by adding constraints to the object that already stores the
 * hanging node constraints matrix. The second parameter in the function
 * describes the first of the velocity components in the total dof vector,
 * which is zero here. The variable <code>no_normal_flux_boundaries</code>
 * denotes the boundary indicators for which to set the no flux boundary
 * conditions; here, this is boundary indicator zero.
 *   
 
 * 
 * After having done so, we count the number of degrees of freedom in the
 * various blocks:
 * 
 * @code
 *     template <int dim>
 *     void BoussinesqFlowProblem<dim>::setup_dofs()
 *     {
 *       std::vector<unsigned int> stokes_sub_blocks(dim + 1, 0);
 *       stokes_sub_blocks[dim] = 1;
 *   
 *       {
 *         stokes_dof_handler.distribute_dofs(stokes_fe);
 *         DoFRenumbering::component_wise(stokes_dof_handler, stokes_sub_blocks);
 *   
 *         stokes_constraints.clear();
 *         DoFTools::make_hanging_node_constraints(stokes_dof_handler,
 *                                                 stokes_constraints);
 *         const std::set<types::boundary_id> no_normal_flux_boundaries = {0};
 *         VectorTools::compute_no_normal_flux_constraints(stokes_dof_handler,
 *                                                         0,
 *                                                         no_normal_flux_boundaries,
 *                                                         stokes_constraints);
 *         stokes_constraints.close();
 *       }
 *       {
 *         temperature_dof_handler.distribute_dofs(temperature_fe);
 *   
 *         temperature_constraints.clear();
 *         DoFTools::make_hanging_node_constraints(temperature_dof_handler,
 *                                                 temperature_constraints);
 *         temperature_constraints.close();
 *       }
 *   
 *       const std::vector<types::global_dof_index> stokes_dofs_per_block =
 *         DoFTools::count_dofs_per_fe_block(stokes_dof_handler, stokes_sub_blocks);
 *   
 *       const types::global_dof_index n_u = stokes_dofs_per_block[0],
 *                                     n_p = stokes_dofs_per_block[1],
 *                                     n_T = temperature_dof_handler.n_dofs();
 *   
 *       std::cout << "Number of active cells: " << triangulation.n_active_cells()
 *                 << " (on " << triangulation.n_levels() << " levels)" << std::endl
 *                 << "Number of degrees of freedom: " << n_u + n_p + n_T << " ("
 *                 << n_u << '+' << n_p << '+' << n_T << ')' << std::endl
 *                 << std::endl;
 *   
 * @endcode
 * 
 * The next step is to create the sparsity pattern for the Stokes and
 * temperature system matrices as well as the preconditioner matrix from
 * which we build the Stokes preconditioner. As in @ref step_22 "step-22", we choose to
 * create the pattern by
 * using the blocked version of DynamicSparsityPattern.
 *     
 
 * 
 * So, we first release the memory stored in the matrices, then set up an
 * object of type BlockDynamicSparsityPattern consisting of
 * @f$2\times 2@f$ blocks (for the Stokes system matrix and preconditioner) or
 * DynamicSparsityPattern (for the temperature part). We then
 * fill these objects with the nonzero pattern, taking into account that
 * for the Stokes system matrix, there are no entries in the
 * pressure-pressure block (but all velocity vector components couple with
 * each other and with the pressure). Similarly, in the Stokes
 * preconditioner matrix, only the diagonal blocks are nonzero, since we
 * use the vector Laplacian as discussed in the introduction. This
 * operator only couples each vector component of the Laplacian with
 * itself, but not with the other vector components. (Application of the
 * constraints resulting from the no-flux boundary conditions will couple
 * vector components at the boundary again, however.)
 *     
 
 * 
 * When generating the sparsity pattern, we directly apply the constraints
 * from hanging nodes and no-flux boundary conditions. This approach was
 * already used in @ref step_27 "step-27", but is different from the one in early
 * tutorial programs where we first built the original sparsity pattern
 * and only then added the entries resulting from constraints. The reason
 * for doing so is that later during assembly we are going to distribute
 * the constraints immediately when transferring local to global
 * dofs. Consequently, there will be no data written at positions of
 * constrained degrees of freedom, so we can let the
 * DoFTools::make_sparsity_pattern function omit these entries by setting
 * the last Boolean flag to <code>false</code>. Once the sparsity pattern
 * is ready, we can use it to initialize the Trilinos matrices. Since the
 * Trilinos matrices store the sparsity pattern internally, there is no
 * need to keep the sparsity pattern around after the initialization of
 * the matrix.
 * 
 * @code
 *       stokes_partitioning.resize(2);
 *       stokes_partitioning[0] = complete_index_set(n_u);
 *       stokes_partitioning[1] = complete_index_set(n_p);
 *       {
 *         stokes_matrix.clear();
 *   
 *         BlockDynamicSparsityPattern dsp(stokes_dofs_per_block,
 *                                         stokes_dofs_per_block);
 *   
 *         Table<2, DoFTools::Coupling> coupling(dim + 1, dim + 1);
 *   
 *         for (unsigned int c = 0; c < dim + 1; ++c)
 *           for (unsigned int d = 0; d < dim + 1; ++d)
 *             if (!((c == dim) && (d == dim)))
 *               coupling[c][d] = DoFTools::always;
 *             else
 *               coupling[c][d] = DoFTools::none;
 *   
 *         DoFTools::make_sparsity_pattern(
 *           stokes_dof_handler, coupling, dsp, stokes_constraints, false);
 *   
 *         stokes_matrix.reinit(dsp);
 *       }
 *   
 *       {
 *         Amg_preconditioner.reset();
 *         Mp_preconditioner.reset();
 *         stokes_preconditioner_matrix.clear();
 *   
 *         BlockDynamicSparsityPattern dsp(stokes_dofs_per_block,
 *                                         stokes_dofs_per_block);
 *   
 *         Table<2, DoFTools::Coupling> coupling(dim + 1, dim + 1);
 *         for (unsigned int c = 0; c < dim + 1; ++c)
 *           for (unsigned int d = 0; d < dim + 1; ++d)
 *             if (c == d)
 *               coupling[c][d] = DoFTools::always;
 *             else
 *               coupling[c][d] = DoFTools::none;
 *   
 *         DoFTools::make_sparsity_pattern(
 *           stokes_dof_handler, coupling, dsp, stokes_constraints, false);
 *   
 *         stokes_preconditioner_matrix.reinit(dsp);
 *       }
 *   
 * @endcode
 * 
 * The creation of the temperature matrix (or, rather, matrices, since we
 * provide a temperature mass matrix and a temperature @ref GlossStiffnessMatrix "stiffness matrix",
 * that will be added together for time discretization) follows the
 * generation of the Stokes matrix &ndash; except that it is much easier
 * here since we do not need to take care of any blocks or coupling
 * between components. Note how we initialize the three temperature
 * matrices: We only use the sparsity pattern for reinitialization of the
 * first matrix, whereas we use the previously generated matrix for the
 * two remaining reinits. The reason for doing so is that reinitialization
 * from an already generated matrix allows Trilinos to reuse the sparsity
 * pattern instead of generating a new one for each copy. This saves both
 * some time and memory.
 * 
 * @code
 *       {
 *         temperature_mass_matrix.clear();
 *         temperature_stiffness_matrix.clear();
 *         temperature_matrix.clear();
 *   
 *         DynamicSparsityPattern dsp(n_T, n_T);
 *         DoFTools::make_sparsity_pattern(temperature_dof_handler,
 *                                         dsp,
 *                                         temperature_constraints,
 *                                         false);
 *   
 *         temperature_matrix.reinit(dsp);
 *         temperature_mass_matrix.reinit(temperature_matrix);
 *         temperature_stiffness_matrix.reinit(temperature_matrix);
 *       }
 *   
 * @endcode
 * 
 * Lastly, we set the vectors for the Stokes solutions @f$\mathbf u^{n-1}@f$
 * and @f$\mathbf u^{n-2}@f$, as well as for the temperatures @f$T^{n}@f$,
 * @f$T^{n-1}@f$ and @f$T^{n-2}@f$ (required for time stepping) and all the system
 * right hand sides to their correct sizes and block structure:
 * 
 * @code
 *       IndexSet temperature_partitioning = complete_index_set(n_T);
 *       stokes_solution.reinit(stokes_partitioning, MPI_COMM_WORLD);
 *       old_stokes_solution.reinit(stokes_partitioning, MPI_COMM_WORLD);
 *       stokes_rhs.reinit(stokes_partitioning, MPI_COMM_WORLD);
 *   
 *       temperature_solution.reinit(temperature_partitioning, MPI_COMM_WORLD);
 *       old_temperature_solution.reinit(temperature_partitioning, MPI_COMM_WORLD);
 *       old_old_temperature_solution.reinit(temperature_partitioning,
 *                                           MPI_COMM_WORLD);
 *   
 *       temperature_rhs.reinit(temperature_partitioning, MPI_COMM_WORLD);
 *     }
 *   
 *   
 *   
 * @endcode
 * 
 * 
 * <a name="BoussinesqFlowProblemassemble_stokes_preconditioner"></a> 
 * <h4>BoussinesqFlowProblem::assemble_stokes_preconditioner</h4>
 *   
 
 * 
 * This function assembles the matrix we use for preconditioning the Stokes
 * system. What we need are a vector Laplace matrix on the velocity
 * components and a mass matrix weighted by @f$\eta^{-1}@f$ on the pressure
 * component. We start by generating a quadrature object of appropriate
 * order, the FEValues object that can give values and gradients at the
 * quadrature points (together with quadrature weights). Next we create data
 * structures for the cell matrix and the relation between local and global
 * DoFs. The vectors <code>grad_phi_u</code> and <code>phi_p</code> are
 * going to hold the values of the basis functions in order to faster build
 * up the local matrices, as was already done in @ref step_22 "step-22". Before we start
 * the loop over all active cells, we have to specify which components are
 * pressure and which are velocity.
 * 
 * @code
 *     template <int dim>
 *     void BoussinesqFlowProblem<dim>::assemble_stokes_preconditioner()
 *     {
 *       stokes_preconditioner_matrix = 0;
 *   
 *       const QGauss<dim> quadrature_formula(stokes_degree + 2);
 *       FEValues<dim>     stokes_fe_values(stokes_fe,
 *                                      quadrature_formula,
 *                                      update_JxW_values | update_values |
 *                                        update_gradients);
 *   
 *       const unsigned int dofs_per_cell = stokes_fe.n_dofs_per_cell();
 *       const unsigned int n_q_points    = quadrature_formula.size();
 *   
 *       FullMatrix<double> local_matrix(dofs_per_cell, dofs_per_cell);
 *       std::vector<types::global_dof_index> local_dof_indices(dofs_per_cell);
 *   
 *       std::vector<Tensor<2, dim>> grad_phi_u(dofs_per_cell);
 *       std::vector<double>         phi_p(dofs_per_cell);
 *   
 *       const FEValuesExtractors::Vector velocities(0);
 *       const FEValuesExtractors::Scalar pressure(dim);
 *   
 *       for (const auto &cell : stokes_dof_handler.active_cell_iterators())
 *         {
 *           stokes_fe_values.reinit(cell);
 *           local_matrix = 0;
 *   
 * @endcode
 * 
 * The creation of the local matrix is rather simple. There are only a
 * Laplace term (on the velocity) and a mass matrix weighted by
 * @f$\eta^{-1}@f$ to be generated, so the creation of the local matrix is
 * done in two lines. Once the local matrix is ready (loop over rows
 * and columns in the local matrix on each quadrature point), we get
 * the local DoF indices and write the local information into the
 * global matrix. We do this as in @ref step_27 "step-27", i.e., we directly apply the
 * constraints from hanging nodes locally. By doing so, we don't have
 * to do that afterwards, and we don't also write into entries of the
 * matrix that will actually be set to zero again later when
 * eliminating constraints.
 * 
 * @code
 *           for (unsigned int q = 0; q < n_q_points; ++q)
 *             {
 *               for (unsigned int k = 0; k < dofs_per_cell; ++k)
 *                 {
 *                   grad_phi_u[k] = stokes_fe_values[velocities].gradient(k, q);
 *                   phi_p[k]      = stokes_fe_values[pressure].value(k, q);
 *                 }
 *   
 *               for (unsigned int i = 0; i < dofs_per_cell; ++i)
 *                 for (unsigned int j = 0; j < dofs_per_cell; ++j)
 *                   local_matrix(i, j) +=
 *                     (EquationData::eta *
 *                        scalar_product(grad_phi_u[i], grad_phi_u[j]) +
 *                      (1. / EquationData::eta) * phi_p[i] * phi_p[j]) *
 *                     stokes_fe_values.JxW(q);
 *             }
 *   
 *           cell->get_dof_indices(local_dof_indices);
 *           stokes_constraints.distribute_local_to_global(
 *             local_matrix, local_dof_indices, stokes_preconditioner_matrix);
 *         }
 *     }
 *   
 *   
 *   
 * @endcode
 * 
 * 
 * <a name="BoussinesqFlowProblembuild_stokes_preconditioner"></a> 
 * <h4>BoussinesqFlowProblem::build_stokes_preconditioner</h4>
 *   
 
 * 
 * This function generates the inner preconditioners that are going to be
 * used for the Schur complement block preconditioner. Since the
 * preconditioners need only to be regenerated when the matrices change,
 * this function does not have to do anything in case the matrices have not
 * changed (i.e., the flag <code>rebuild_stokes_preconditioner</code> has
 * the value <code>false</code>). Otherwise its first task is to call
 * <code>assemble_stokes_preconditioner</code> to generate the
 * preconditioner matrices.
 *   
 
 * 
 * Next, we set up the preconditioner for the velocity-velocity matrix
 * @f$A@f$. As explained in the introduction, we are going to use an AMG
 * preconditioner based on a vector Laplace matrix @f$\hat{A}@f$ (which is
 * spectrally close to the Stokes matrix @f$A@f$). Usually, the
 * TrilinosWrappers::PreconditionAMG class can be seen as a good black-box
 * preconditioner which does not need any special knowledge. In this case,
 * however, we have to be careful: since we build an AMG for a vector
 * problem, we have to tell the preconditioner setup which dofs belong to
 * which vector component. We do this using the function
 * DoFTools::extract_constant_modes, a function that generates a set of
 * <code>dim</code> vectors, where each one has ones in the respective
 * component of the vector problem and zeros elsewhere. Hence, these are the
 * constant modes on each component, which explains the name of the
 * variable.
 * 
 * @code
 *     template <int dim>
 *     void BoussinesqFlowProblem<dim>::build_stokes_preconditioner()
 *     {
 *       if (rebuild_stokes_preconditioner == false)
 *         return;
 *   
 *       std::cout << "   Rebuilding Stokes preconditioner..." << std::flush;
 *   
 *       assemble_stokes_preconditioner();
 *   
 *       Amg_preconditioner = std::make_shared<TrilinosWrappers::PreconditionAMG>();
 *   
 *       std::vector<std::vector<bool>>   constant_modes;
 *       const FEValuesExtractors::Vector velocity_components(0);
 *       DoFTools::extract_constant_modes(stokes_dof_handler,
 *                                        stokes_fe.component_mask(
 *                                          velocity_components),
 *                                        constant_modes);
 *       TrilinosWrappers::PreconditionAMG::AdditionalData amg_data;
 *       amg_data.constant_modes = constant_modes;
 *   
 * @endcode
 * 
 * Next, we set some more options of the AMG preconditioner. In
 * particular, we need to tell the AMG setup that we use quadratic basis
 * functions for the velocity matrix (this implies more nonzero elements
 * in the matrix, so that a more robust algorithm needs to be chosen
 * internally). Moreover, we want to be able to control how the coarsening
 * structure is build up. The way the Trilinos smoothed aggregation AMG
 * does this is to look which matrix entries are of similar size as the
 * diagonal entry in order to algebraically build a coarse-grid
 * structure. By setting the parameter <code>aggregation_threshold</code>
 * to 0.02, we specify that all entries that are more than two percent of
 * size of some diagonal pivots in that row should form one coarse grid
 * point. This parameter is rather ad hoc, and some fine-tuning of it can
 * influence the performance of the preconditioner. As a rule of thumb,
 * larger values of <code>aggregation_threshold</code> will decrease the
 * number of iterations, but increase the costs per iteration. A look at
 * the Trilinos documentation will provide more information on these
 * parameters. With this data set, we then initialize the preconditioner
 * with the matrix we want it to apply to.
 *     
 
 * 
 * Finally, we also initialize the preconditioner for the inversion of the
 * pressure mass matrix. This matrix is symmetric and well-behaved, so we
 * can chose a simple preconditioner. We stick with an incomplete Cholesky
 * (IC) factorization preconditioner, which is designed for symmetric
 * matrices. We could have also chosen an SSOR preconditioner with
 * relaxation factor around 1.2, but IC is cheaper for our example. We
 * wrap the preconditioners into a <code>std::shared_ptr</code>
 * pointer, which makes it easier to recreate the preconditioner next time
 * around since we do not have to care about destroying the previously
 * used object.
 * 
 * @code
 *       amg_data.elliptic              = true;
 *       amg_data.higher_order_elements = true;
 *       amg_data.smoother_sweeps       = 2;
 *       amg_data.aggregation_threshold = 0.02;
 *       Amg_preconditioner->initialize(stokes_preconditioner_matrix.block(0, 0),
 *                                      amg_data);
 *   
 *       Mp_preconditioner = std::make_shared<TrilinosWrappers::PreconditionIC>();
 *       Mp_preconditioner->initialize(stokes_preconditioner_matrix.block(1, 1));
 *   
 *       std::cout << std::endl;
 *   
 *       rebuild_stokes_preconditioner = false;
 *     }
 *   
 *   
 *   
 * @endcode
 * 
 * 
 * <a name="BoussinesqFlowProblemassemble_stokes_system"></a> 
 * <h4>BoussinesqFlowProblem::assemble_stokes_system</h4>
 *   
 
 * 
 * The time lag scheme we use for advancing the coupled Stokes-temperature
 * system forces us to split up the assembly (and the solution of linear
 * systems) into two step. The first one is to create the Stokes system
 * matrix and right hand side, and the second is to create matrix and right
 * hand sides for the temperature dofs, which depends on the result of the
 * linear system for the velocity.
 *   
 
 * 
 * This function is called at the beginning of each time step. In the first
 * time step or if the mesh has changed, indicated by the
 * <code>rebuild_stokes_matrix</code>, we need to assemble the Stokes
 * matrix; on the other hand, if the mesh hasn't changed and the matrix is
 * already available, this is not necessary and all we need to do is
 * assemble the right hand side vector which changes in each time step.
 *   
 
 * 
 * Regarding the technical details of implementation, not much has changed
 * from @ref step_22 "step-22". We reset matrix and vector, create a quadrature formula on
 * the cells, and then create the respective FEValues object. For the update
 * flags, we require basis function derivatives only in case of a full
 * assembly, since they are not needed for the right hand side; as always,
 * choosing the minimal set of flags depending on what is currently needed
 * makes the call to FEValues::reinit further down in the program more
 * efficient.
 *   
 
 * 
 * There is one thing that needs to be commented &ndash; since we have a
 * separate finite element and DoFHandler for the temperature, we need to
 * generate a second FEValues object for the proper evaluation of the
 * temperature solution. This isn't too complicated to realize here: just
 * use the temperature structures and set an update flag for the basis
 * function values which we need for evaluation of the temperature
 * solution. The only important part to remember here is that the same
 * quadrature formula is used for both FEValues objects to ensure that we
 * get matching information when we loop over the quadrature points of the
 * two objects.
 *   
 
 * 
 * The declarations proceed with some shortcuts for array sizes, the
 * creation of the local matrix and right hand side as well as the vector
 * for the indices of the local dofs compared to the global system.
 * 
 * @code
 *     template <int dim>
 *     void BoussinesqFlowProblem<dim>::assemble_stokes_system()
 *     {
 *       std::cout << "   Assembling..." << std::flush;
 *   
 *       if (rebuild_stokes_matrix == true)
 *         stokes_matrix = 0;
 *   
 *       stokes_rhs = 0;
 *   
 *       const QGauss<dim> quadrature_formula(stokes_degree + 2);
 *       FEValues<dim>     stokes_fe_values(
 *         stokes_fe,
 *         quadrature_formula,
 *         update_values | update_quadrature_points | update_JxW_values |
 *           (rebuild_stokes_matrix == true ? update_gradients : UpdateFlags(0)));
 *   
 *       FEValues<dim> temperature_fe_values(temperature_fe,
 *                                           quadrature_formula,
 *                                           update_values);
 *   
 *       const unsigned int dofs_per_cell = stokes_fe.n_dofs_per_cell();
 *       const unsigned int n_q_points    = quadrature_formula.size();
 *   
 *       FullMatrix<double> local_matrix(dofs_per_cell, dofs_per_cell);
 *       Vector<double>     local_rhs(dofs_per_cell);
 *   
 *       std::vector<types::global_dof_index> local_dof_indices(dofs_per_cell);
 *   
 * @endcode
 * 
 * Next we need a vector that will contain the values of the temperature
 * solution at the previous time level at the quadrature points to
 * assemble the source term in the right hand side of the momentum
 * equation. Let's call this vector <code>old_solution_values</code>.
 *     
 
 * 
 * The set of vectors we create next hold the evaluations of the basis
 * functions as well as their gradients and symmetrized gradients that
 * will be used for creating the matrices. Putting these into their own
 * arrays rather than asking the FEValues object for this information each
 * time it is needed is an optimization to accelerate the assembly
 * process, see @ref step_22 "step-22" for details.
 *     
 
 * 
 * The last two declarations are used to extract the individual blocks
 * (velocity, pressure, temperature) from the total FE system.
 * 
 * @code
 *       std::vector<double> old_temperature_values(n_q_points);
 *   
 *       std::vector<Tensor<1, dim>>          phi_u(dofs_per_cell);
 *       std::vector<SymmetricTensor<2, dim>> grads_phi_u(dofs_per_cell);
 *       std::vector<double>                  div_phi_u(dofs_per_cell);
 *       std::vector<double>                  phi_p(dofs_per_cell);
 *   
 *       const FEValuesExtractors::Vector velocities(0);
 *       const FEValuesExtractors::Scalar pressure(dim);
 *   
 * @endcode
 * 
 * Now start the loop over all cells in the problem. We are working on two
 * different DoFHandlers for this assembly routine, so we must have two
 * different cell iterators for the two objects in use. This might seem a
 * bit peculiar, since both the Stokes system and the temperature system
 * use the same grid, but that's the only way to keep degrees of freedom
 * in sync. The first statements within the loop are again all very
 * familiar, doing the update of the finite element data as specified by
 * the update flags, zeroing out the local arrays and getting the values
 * of the old solution at the quadrature points. Then we are ready to loop
 * over the quadrature points on the cell.
 * 
 * @code
 *       auto       cell             = stokes_dof_handler.begin_active();
 *       const auto endc             = stokes_dof_handler.end();
 *       auto       temperature_cell = temperature_dof_handler.begin_active();
 *   
 *       for (; cell != endc; ++cell, ++temperature_cell)
 *         {
 *           stokes_fe_values.reinit(cell);
 *           temperature_fe_values.reinit(temperature_cell);
 *   
 *           local_matrix = 0;
 *           local_rhs    = 0;
 *   
 *           temperature_fe_values.get_function_values(old_temperature_solution,
 *                                                     old_temperature_values);
 *   
 *           for (unsigned int q = 0; q < n_q_points; ++q)
 *             {
 *               const double old_temperature = old_temperature_values[q];
 *   
 * @endcode
 * 
 * Next we extract the values and gradients of basis functions
 * relevant to the terms in the inner products. As shown in
 * @ref step_22 "step-22" this helps accelerate assembly.
 *             
 
 * 
 * Once this is done, we start the loop over the rows and columns
 * of the local matrix and feed the matrix with the relevant
 * products. The right hand side is filled with the forcing term
 * driven by temperature in direction of gravity (which is
 * vertical in our example).  Note that the right hand side term
 * is always generated, whereas the matrix contributions are only
 * updated when it is requested by the
 * <code>rebuild_matrices</code> flag.
 * 
 * @code
 *               for (unsigned int k = 0; k < dofs_per_cell; ++k)
 *                 {
 *                   phi_u[k] = stokes_fe_values[velocities].value(k, q);
 *                   if (rebuild_stokes_matrix)
 *                     {
 *                       grads_phi_u[k] =
 *                         stokes_fe_values[velocities].symmetric_gradient(k, q);
 *                       div_phi_u[k] =
 *                         stokes_fe_values[velocities].divergence(k, q);
 *                       phi_p[k] = stokes_fe_values[pressure].value(k, q);
 *                     }
 *                 }
 *   
 *               if (rebuild_stokes_matrix)
 *                 for (unsigned int i = 0; i < dofs_per_cell; ++i)
 *                   for (unsigned int j = 0; j < dofs_per_cell; ++j)
 *                     local_matrix(i, j) +=
 *                       (EquationData::eta * 2 * (grads_phi_u[i] * grads_phi_u[j]) -
 *                        div_phi_u[i] * phi_p[j] - phi_p[i] * div_phi_u[j]) *
 *                       stokes_fe_values.JxW(q);
 *   
 *               const Point<dim> gravity =
 *                 -((dim == 2) ? (Point<dim>(0, 1)) : (Point<dim>(0, 0, 1)));
 *               for (unsigned int i = 0; i < dofs_per_cell; ++i)
 *                 local_rhs(i) += (-EquationData::density * EquationData::beta *
 *                                  gravity * phi_u[i] * old_temperature) *
 *                                 stokes_fe_values.JxW(q);
 *             }
 *   
 * @endcode
 * 
 * The last step in the loop over all cells is to enter the local
 * contributions into the global matrix and vector structures to the
 * positions specified in <code>local_dof_indices</code>.  Again, we
 * let the AffineConstraints class do the insertion of the cell
 * matrix elements to the global matrix, which already condenses the
 * hanging node constraints.
 * 
 * @code
 *           cell->get_dof_indices(local_dof_indices);
 *   
 *           if (rebuild_stokes_matrix == true)
 *             stokes_constraints.distribute_local_to_global(local_matrix,
 *                                                           local_rhs,
 *                                                           local_dof_indices,
 *                                                           stokes_matrix,
 *                                                           stokes_rhs);
 *           else
 *             stokes_constraints.distribute_local_to_global(local_rhs,
 *                                                           local_dof_indices,
 *                                                           stokes_rhs);
 *         }
 *   
 *       rebuild_stokes_matrix = false;
 *   
 *       std::cout << std::endl;
 *     }
 *   
 *   
 *   
 * @endcode
 * 
 * 
 * <a name="BoussinesqFlowProblemassemble_temperature_matrix"></a> 
 * <h4>BoussinesqFlowProblem::assemble_temperature_matrix</h4>
 *   
 
 * 
 * This function assembles the matrix in the temperature equation. The
 * temperature matrix consists of two parts, a mass matrix and the time step
 * size times a stiffness matrix given by a Laplace term times the amount of
 * diffusion. Since the matrix depends on the time step size (which varies
 * from one step to another), the temperature matrix needs to be updated
 * every time step. We could simply regenerate the matrices in every time
 * step, but this is not really efficient since mass and Laplace matrix do
 * only change when we change the mesh. Hence, we do this more efficiently
 * by generating two separate matrices in this function, one for the mass
 * matrix and one for the stiffness (diffusion) matrix. We will then sum up
 * the matrix plus the stiffness matrix times the time step size once we
 * know the actual time step.
 *   
 
 * 
 * So the details for this first step are very simple. In case we need to
 * rebuild the matrix (i.e., the mesh has changed), we zero the data
 * structures, get a quadrature formula and a FEValues object, and create
 * local matrices, local dof indices and evaluation structures for the basis
 * functions.
 * 
 * @code
 *     template <int dim>
 *     void BoussinesqFlowProblem<dim>::assemble_temperature_matrix()
 *     {
 *       if (rebuild_temperature_matrices == false)
 *         return;
 *   
 *       temperature_mass_matrix      = 0;
 *       temperature_stiffness_matrix = 0;
 *   
 *       QGauss<dim>   quadrature_formula(temperature_degree + 2);
 *       FEValues<dim> temperature_fe_values(temperature_fe,
 *                                           quadrature_formula,
 *                                           update_values | update_gradients |
 *                                             update_JxW_values);
 *   
 *       const unsigned int dofs_per_cell = temperature_fe.n_dofs_per_cell();
 *       const unsigned int n_q_points    = quadrature_formula.size();
 *   
 *       FullMatrix<double> local_mass_matrix(dofs_per_cell, dofs_per_cell);
 *       FullMatrix<double> local_stiffness_matrix(dofs_per_cell, dofs_per_cell);
 *   
 *       std::vector<types::global_dof_index> local_dof_indices(dofs_per_cell);
 *   
 *       std::vector<double>         phi_T(dofs_per_cell);
 *       std::vector<Tensor<1, dim>> grad_phi_T(dofs_per_cell);
 *   
 * @endcode
 * 
 * Now, let's start the loop over all cells in the triangulation. We need
 * to zero out the local matrices, update the finite element evaluations,
 * and then loop over the rows and columns of the matrices on each
 * quadrature point, where we then create the mass matrix and the
 * stiffness matrix (Laplace terms times the diffusion
 * <code>EquationData::kappa</code>. Finally, we let the constraints
 * object insert these values into the global matrix, and directly
 * condense the constraints into the matrix.
 * 
 * @code
 *       for (const auto &cell : temperature_dof_handler.active_cell_iterators())
 *         {
 *           local_mass_matrix      = 0;
 *           local_stiffness_matrix = 0;
 *   
 *           temperature_fe_values.reinit(cell);
 *   
 *           for (unsigned int q = 0; q < n_q_points; ++q)
 *             {
 *               for (unsigned int k = 0; k < dofs_per_cell; ++k)
 *                 {
 *                   grad_phi_T[k] = temperature_fe_values.shape_grad(k, q);
 *                   phi_T[k]      = temperature_fe_values.shape_value(k, q);
 *                 }
 *   
 *               for (unsigned int i = 0; i < dofs_per_cell; ++i)
 *                 for (unsigned int j = 0; j < dofs_per_cell; ++j)
 *                   {
 *                     local_mass_matrix(i, j) +=
 *                       (phi_T[i] * phi_T[j] * temperature_fe_values.JxW(q));
 *                     local_stiffness_matrix(i, j) +=
 *                       (EquationData::kappa * grad_phi_T[i] * grad_phi_T[j] *
 *                        temperature_fe_values.JxW(q));
 *                   }
 *             }
 *   
 *           cell->get_dof_indices(local_dof_indices);
 *   
 *           temperature_constraints.distribute_local_to_global(
 *             local_mass_matrix, local_dof_indices, temperature_mass_matrix);
 *           temperature_constraints.distribute_local_to_global(
 *             local_stiffness_matrix,
 *             local_dof_indices,
 *             temperature_stiffness_matrix);
 *         }
 *   
 *       rebuild_temperature_matrices = false;
 *     }
 *   
 *   
 *   
 * @endcode
 * 
 * 
 * <a name="BoussinesqFlowProblemassemble_temperature_system"></a> 
 * <h4>BoussinesqFlowProblem::assemble_temperature_system</h4>
 *   
 
 * 
 * This function does the second part of the assembly work on the
 * temperature matrix, the actual addition of pressure mass and stiffness
 * matrix (where the time step size comes into play), as well as the
 * creation of the velocity-dependent right hand side. The declarations for
 * the right hand side assembly in this function are pretty much the same as
 * the ones used in the other assembly routines, except that we restrict
 * ourselves to vectors this time. We are going to calculate residuals on
 * the temperature system, which means that we have to evaluate second
 * derivatives, specified by the update flag <code>update_hessians</code>.
 *   
 
 * 
 * The temperature equation is coupled to the Stokes system by means of the
 * fluid velocity. These two parts of the solution are associated with
 * different DoFHandlers, so we again need to create a second FEValues
 * object for the evaluation of the velocity at the quadrature points.
 * 
 * @code
 *     template <int dim>
 *     void BoussinesqFlowProblem<dim>::assemble_temperature_system(
 *       const double maximal_velocity)
 *     {
 *       const bool use_bdf2_scheme = (timestep_number != 0);
 *   
 *       if (use_bdf2_scheme == true)
 *         {
 *           temperature_matrix.copy_from(temperature_mass_matrix);
 *           temperature_matrix *=
 *             (2 * time_step + old_time_step) / (time_step + old_time_step);
 *           temperature_matrix.add(time_step, temperature_stiffness_matrix);
 *         }
 *       else
 *         {
 *           temperature_matrix.copy_from(temperature_mass_matrix);
 *           temperature_matrix.add(time_step, temperature_stiffness_matrix);
 *         }
 *   
 *       temperature_rhs = 0;
 *   
 *       const QGauss<dim> quadrature_formula(temperature_degree + 2);
 *       FEValues<dim>     temperature_fe_values(temperature_fe,
 *                                           quadrature_formula,
 *                                           update_values | update_gradients |
 *                                             update_hessians |
 *                                             update_quadrature_points |
 *                                             update_JxW_values);
 *       FEValues<dim>     stokes_fe_values(stokes_fe,
 *                                      quadrature_formula,
 *                                      update_values);
 *   
 *       const unsigned int dofs_per_cell = temperature_fe.n_dofs_per_cell();
 *       const unsigned int n_q_points    = quadrature_formula.size();
 *   
 *       Vector<double> local_rhs(dofs_per_cell);
 *   
 *       std::vector<types::global_dof_index> local_dof_indices(dofs_per_cell);
 *   
 * @endcode
 * 
 * Next comes the declaration of vectors to hold the old and older
 * solution values (as a notation for time levels @f$n-1@f$ and
 * @f$n-2@f$, respectively) and gradients at quadrature points of the
 * current cell. We also declare an object to hold the temperature right
 * hand side values (<code>gamma_values</code>), and we again use
 * shortcuts for the temperature basis functions. Eventually, we need to
 * find the temperature extrema and the diameter of the computational
 * domain which will be used for the definition of the stabilization
 * parameter (we got the maximal velocity as an input to this function).
 * 
 * @code
 *       std::vector<Tensor<1, dim>> old_velocity_values(n_q_points);
 *       std::vector<Tensor<1, dim>> old_old_velocity_values(n_q_points);
 *       std::vector<double>         old_temperature_values(n_q_points);
 *       std::vector<double>         old_old_temperature_values(n_q_points);
 *       std::vector<Tensor<1, dim>> old_temperature_grads(n_q_points);
 *       std::vector<Tensor<1, dim>> old_old_temperature_grads(n_q_points);
 *       std::vector<double>         old_temperature_laplacians(n_q_points);
 *       std::vector<double>         old_old_temperature_laplacians(n_q_points);
 *   
 *       EquationData::TemperatureRightHandSide<dim> temperature_right_hand_side;
 *       std::vector<double>                         gamma_values(n_q_points);
 *   
 *       std::vector<double>         phi_T(dofs_per_cell);
 *       std::vector<Tensor<1, dim>> grad_phi_T(dofs_per_cell);
 *   
 *       const std::pair<double, double> global_T_range =
 *         get_extrapolated_temperature_range();
 *   
 *       const FEValuesExtractors::Vector velocities(0);
 *   
 * @endcode
 * 
 * Now, let's start the loop over all cells in the triangulation. Again,
 * we need two cell iterators that walk in parallel through the cells of
 * the two involved DoFHandler objects for the Stokes and temperature
 * part. Within the loop, we first set the local rhs to zero, and then get
 * the values and derivatives of the old solution functions at the
 * quadrature points, since they are going to be needed for the definition
 * of the stabilization parameters and as coefficients in the equation,
 * respectively. Note that since the temperature has its own DoFHandler
 * and FEValues object we get the entire solution at the quadrature point
 * (which is the scalar temperature field only anyway) whereas for the
 * Stokes part we restrict ourselves to extracting the velocity part (and
 * ignoring the pressure part) by using
 * <code>stokes_fe_values[velocities].get_function_values</code>.
 * 
 * @code
 *       auto       cell        = temperature_dof_handler.begin_active();
 *       const auto endc        = temperature_dof_handler.end();
 *       auto       stokes_cell = stokes_dof_handler.begin_active();
 *   
 *       for (; cell != endc; ++cell, ++stokes_cell)
 *         {
 *           local_rhs = 0;
 *   
 *           temperature_fe_values.reinit(cell);
 *           stokes_fe_values.reinit(stokes_cell);
 *   
 *           temperature_fe_values.get_function_values(old_temperature_solution,
 *                                                     old_temperature_values);
 *           temperature_fe_values.get_function_values(old_old_temperature_solution,
 *                                                     old_old_temperature_values);
 *   
 *           temperature_fe_values.get_function_gradients(old_temperature_solution,
 *                                                        old_temperature_grads);
 *           temperature_fe_values.get_function_gradients(
 *             old_old_temperature_solution, old_old_temperature_grads);
 *   
 *           temperature_fe_values.get_function_laplacians(
 *             old_temperature_solution, old_temperature_laplacians);
 *           temperature_fe_values.get_function_laplacians(
 *             old_old_temperature_solution, old_old_temperature_laplacians);
 *   
 *           temperature_right_hand_side.value_list(
 *             temperature_fe_values.get_quadrature_points(), gamma_values);
 *   
 *           stokes_fe_values[velocities].get_function_values(stokes_solution,
 *                                                            old_velocity_values);
 *           stokes_fe_values[velocities].get_function_values(
 *             old_stokes_solution, old_old_velocity_values);
 *   
 * @endcode
 * 
 * Next, we calculate the artificial viscosity for stabilization
 * according to the discussion in the introduction using the dedicated
 * function. With that at hand, we can get into the loop over
 * quadrature points and local rhs vector components. The terms here
 * are quite lengthy, but their definition follows the time-discrete
 * system developed in the introduction of this program. The BDF-2
 * scheme needs one more term from the old time step (and involves
 * more complicated factors) than the backward Euler scheme that is
 * used for the first time step. When all this is done, we distribute
 * the local vector into the global one (including hanging node
 * constraints).
 * 
 * @code
 *           const double nu =
 *             compute_viscosity(old_temperature_values,
 *                               old_old_temperature_values,
 *                               old_temperature_grads,
 *                               old_old_temperature_grads,
 *                               old_temperature_laplacians,
 *                               old_old_temperature_laplacians,
 *                               old_velocity_values,
 *                               old_old_velocity_values,
 *                               gamma_values,
 *                               maximal_velocity,
 *                               global_T_range.second - global_T_range.first,
 *                               cell->diameter());
 *   
 *           for (unsigned int q = 0; q < n_q_points; ++q)
 *             {
 *               for (unsigned int k = 0; k < dofs_per_cell; ++k)
 *                 {
 *                   grad_phi_T[k] = temperature_fe_values.shape_grad(k, q);
 *                   phi_T[k]      = temperature_fe_values.shape_value(k, q);
 *                 }
 *   
 *               const double T_term_for_rhs =
 *                 (use_bdf2_scheme ?
 *                    (old_temperature_values[q] * (1 + time_step / old_time_step) -
 *                     old_old_temperature_values[q] * (time_step * time_step) /
 *                       (old_time_step * (time_step + old_time_step))) :
 *                    old_temperature_values[q]);
 *   
 *               const Tensor<1, dim> ext_grad_T =
 *                 (use_bdf2_scheme ?
 *                    (old_temperature_grads[q] * (1 + time_step / old_time_step) -
 *                     old_old_temperature_grads[q] * time_step / old_time_step) :
 *                    old_temperature_grads[q]);
 *   
 *               const Tensor<1, dim> extrapolated_u =
 *                 (use_bdf2_scheme ?
 *                    (old_velocity_values[q] * (1 + time_step / old_time_step) -
 *                     old_old_velocity_values[q] * time_step / old_time_step) :
 *                    old_velocity_values[q]);
 *   
 *               for (unsigned int i = 0; i < dofs_per_cell; ++i)
 *                 local_rhs(i) +=
 *                   (T_term_for_rhs * phi_T[i] -
 *                    time_step * extrapolated_u * ext_grad_T * phi_T[i] -
 *                    time_step * nu * ext_grad_T * grad_phi_T[i] +
 *                    time_step * gamma_values[q] * phi_T[i]) *
 *                   temperature_fe_values.JxW(q);
 *             }
 *   
 *           cell->get_dof_indices(local_dof_indices);
 *           temperature_constraints.distribute_local_to_global(local_rhs,
 *                                                              local_dof_indices,
 *                                                              temperature_rhs);
 *         }
 *     }
 *   
 *   
 *   
 * @endcode
 * 
 * 
 * <a name="BoussinesqFlowProblemsolve"></a> 
 * <h4>BoussinesqFlowProblem::solve</h4>
 *   
 
 * 
 * This function solves the linear systems of equations. Following the
 * introduction, we start with the Stokes system, where we need to generate
 * our block Schur preconditioner. Since all the relevant actions are
 * implemented in the class <code>BlockSchurPreconditioner</code>, all we
 * have to do is to initialize the class appropriately. What we need to pass
 * down is an <code>InverseMatrix</code> object for the pressure mass
 * matrix, which we set up using the respective class together with the IC
 * preconditioner we already generated, and the AMG preconditioner for the
 * velocity-velocity matrix. Note that both <code>Mp_preconditioner</code>
 * and <code>Amg_preconditioner</code> are only pointers, so we use
 * <code>*</code> to pass down the actual preconditioner objects.
 *   
 
 * 
 * Once the preconditioner is ready, we create a GMRES solver for the block
 * system. Since we are working with Trilinos data structures, we have to
 * set the respective template argument in the solver. GMRES needs to
 * internally store temporary vectors for each iteration (see the discussion
 * in the results section of @ref step_22 "step-22") &ndash; the more vectors it can use,
 * the better it will generally perform. To keep memory demands in check, we
 * set the number of vectors to 100. This means that up to 100 solver
 * iterations, every temporary vector can be stored. If the solver needs to
 * iterate more often to get the specified tolerance, it will work on a
 * reduced set of vectors by restarting at every 100 iterations.
 *   
 
 * 
 * With this all set up, we solve the system and distribute the constraints
 * in the Stokes system, i.e., hanging nodes and no-flux boundary condition,
 * in order to have the appropriate solution values even at constrained
 * dofs. Finally, we write the number of iterations to the screen.
 * 
 * @code
 *     template <int dim>
 *     void BoussinesqFlowProblem<dim>::solve()
 *     {
 *       std::cout << "   Solving..." << std::endl;
 *   
 *       {
 *         const LinearSolvers::InverseMatrix<TrilinosWrappers::SparseMatrix,
 *                                            TrilinosWrappers::PreconditionIC>
 *           mp_inverse(stokes_preconditioner_matrix.block(1, 1),
 *                      *Mp_preconditioner);
 *   
 *         const LinearSolvers::BlockSchurPreconditioner<
 *           TrilinosWrappers::PreconditionAMG,
 *           TrilinosWrappers::PreconditionIC>
 *           preconditioner(stokes_matrix, mp_inverse, *Amg_preconditioner);
 *   
 *         SolverControl solver_control(stokes_matrix.m(),
 *                                      1e-6 * stokes_rhs.l2_norm());
 *   
 *         SolverGMRES<TrilinosWrappers::MPI::BlockVector> gmres(
 *           solver_control,
 *           SolverGMRES<TrilinosWrappers::MPI::BlockVector>::AdditionalData(100));
 *   
 *         for (unsigned int i = 0; i < stokes_solution.size(); ++i)
 *           if (stokes_constraints.is_constrained(i))
 *             stokes_solution(i) = 0;
 *   
 *         gmres.solve(stokes_matrix, stokes_solution, stokes_rhs, preconditioner);
 *   
 *         stokes_constraints.distribute(stokes_solution);
 *   
 *         std::cout << "   " << solver_control.last_step()
 *                   << " GMRES iterations for Stokes subsystem." << std::endl;
 *       }
 *   
 * @endcode
 * 
 * Once we know the Stokes solution, we can determine the new time step
 * from the maximal velocity. We have to do this to satisfy the CFL
 * condition since convection terms are treated explicitly in the
 * temperature equation, as discussed in the introduction. The exact form
 * of the formula used here for the time step is discussed in the results
 * section of this program.
 *     
 
 * 
 * There is a snatch here. The formula contains a division by the maximum
 * value of the velocity. However, at the start of the computation, we
 * have a constant temperature field (we start with a constant
 * temperature, and it will be nonconstant only after the first time step
 * during which the source acts). Constant temperature means that no
 * buoyancy acts, and so the velocity is zero. Dividing by it will not
 * likely lead to anything good.
 *     
 
 * 
 * To avoid the resulting infinite time step, we ask whether the maximal
 * velocity is very small (in particular smaller than the values we
 * encounter during any of the following time steps) and if so rather than
 * dividing by zero we just divide by a small value, resulting in a large
 * but finite time step.
 * 
 * @code
 *       old_time_step                 = time_step;
 *       const double maximal_velocity = get_maximal_velocity();
 *   
 *       if (maximal_velocity >= 0.01)
 *         time_step = 1. / (1.7 * dim * std::sqrt(1. * dim)) / temperature_degree *
 *                     GridTools::minimal_cell_diameter(triangulation) /
 *                     maximal_velocity;
 *       else
 *         time_step = 1. / (1.7 * dim * std::sqrt(1. * dim)) / temperature_degree *
 *                     GridTools::minimal_cell_diameter(triangulation) / .01;
 *   
 *       std::cout << "   "
 *                 << "Time step: " << time_step << std::endl;
 *   
 *       temperature_solution = old_temperature_solution;
 *   
 * @endcode
 * 
 * Next we set up the temperature system and the right hand side using the
 * function <code>assemble_temperature_system()</code>.  Knowing the
 * matrix and right hand side of the temperature equation, we set up a
 * preconditioner and a solver. The temperature matrix is a mass matrix
 * (with eigenvalues around one) plus a Laplace matrix (with eigenvalues
 * between zero and @f$ch^{-2}@f$) times a small number proportional to the
 * time step @f$k_n@f$. Hence, the resulting symmetric and positive definite
 * matrix has eigenvalues in the range @f$[1,1+k_nh^{-2}]@f$ (up to
 * constants). This matrix is only moderately ill conditioned even for
 * small mesh sizes and we get a reasonably good preconditioner by simple
 * means, for example with an incomplete Cholesky decomposition
 * preconditioner (IC) as we also use for preconditioning the pressure
 * mass matrix solver. As a solver, we choose the conjugate gradient
 * method CG. As before, we tell the solver to use Trilinos vectors via
 * the template argument <code>TrilinosWrappers::MPI::Vector</code>.
 * Finally, we solve, distribute the hanging node constraints and write out
 * the number of iterations.
 * 
 * @code
 *       assemble_temperature_system(maximal_velocity);
 *       {
 *         SolverControl solver_control(temperature_matrix.m(),
 *                                      1e-8 * temperature_rhs.l2_norm());
 *         SolverCG<TrilinosWrappers::MPI::Vector> cg(solver_control);
 *   
 *         TrilinosWrappers::PreconditionIC preconditioner;
 *         preconditioner.initialize(temperature_matrix);
 *   
 *         cg.solve(temperature_matrix,
 *                  temperature_solution,
 *                  temperature_rhs,
 *                  preconditioner);
 *   
 *         temperature_constraints.distribute(temperature_solution);
 *   
 *         std::cout << "   " << solver_control.last_step()
 *                   << " CG iterations for temperature." << std::endl;
 *   
 * @endcode
 * 
 * At the end of this function, we step through the vector and read out
 * the maximum and minimum temperature value, which we also want to
 * output. This will come in handy when determining the correct constant
 * in the choice of time step as discuss in the results section of this
 * program.
 * 
 * @code
 *         double min_temperature = temperature_solution(0),
 *                max_temperature = temperature_solution(0);
 *         for (unsigned int i = 0; i < temperature_solution.size(); ++i)
 *           {
 *             min_temperature =
 *               std::min<double>(min_temperature, temperature_solution(i));
 *             max_temperature =
 *               std::max<double>(max_temperature, temperature_solution(i));
 *           }
 *   
 *         std::cout << "   Temperature range: " << min_temperature << ' '
 *                   << max_temperature << std::endl;
 *       }
 *     }
 *   
 *   
 *   
 * @endcode
 * 
 * 
 * <a name="BoussinesqFlowProblemoutput_results"></a> 
 * <h4>BoussinesqFlowProblem::output_results</h4>
 *   
 
 * 
 * This function writes the solution to a VTK output file for visualization,
 * which is done every tenth time step. This is usually quite a simple task,
 * since the deal.II library provides functions that do almost all the job
 * for us. There is one new function compared to previous examples: We want
 * to visualize both the Stokes solution and the temperature as one data
 * set, but we have done all the calculations based on two different
 * DoFHandler objects. Luckily, the DataOut class is prepared to deal with
 * it. All we have to do is to not attach one single DoFHandler at the
 * beginning and then use that for all added vector, but specify the
 * DoFHandler to each vector separately. The rest is done as in @ref step_22 "step-22". We
 * create solution names (that are going to appear in the visualization
 * program for the individual components). The first <code>dim</code>
 * components are the vector velocity, and then we have pressure for the
 * Stokes part, whereas temperature is scalar. This information is read out
 * using the DataComponentInterpretation helper class. Next, we actually
 * attach the data vectors with their DoFHandler objects, build patches
 * according to the degree of freedom, which are (sub-) elements that
 * describe the data for visualization programs. Finally, we open a file
 * (that includes the time step number) and write the vtk data into it.
 * 
 * @code
 *     template <int dim>
 *     void BoussinesqFlowProblem<dim>::output_results() const
 *     {
 *       if (timestep_number % 10 != 0)
 *         return;
 *   
 *       std::vector<std::string> stokes_names(dim, "velocity");
 *       stokes_names.emplace_back("p");
 *       std::vector<DataComponentInterpretation::DataComponentInterpretation>
 *         stokes_component_interpretation(
 *           dim + 1, DataComponentInterpretation::component_is_scalar);
 *       for (unsigned int i = 0; i < dim; ++i)
 *         stokes_component_interpretation[i] =
 *           DataComponentInterpretation::component_is_part_of_vector;
 *   
 *       DataOut<dim> data_out;
 *       data_out.add_data_vector(stokes_dof_handler,
 *                                stokes_solution,
 *                                stokes_names,
 *                                stokes_component_interpretation);
 *       data_out.add_data_vector(temperature_dof_handler,
 *                                temperature_solution,
 *                                "T");
 *       data_out.build_patches(std::min(stokes_degree, temperature_degree));
 *   
 *       std::ofstream output("solution-" +
 *                            Utilities::int_to_string(timestep_number, 4) + ".vtk");
 *       data_out.write_vtk(output);
 *     }
 *   
 *   
 *   
 * @endcode
 * 
 * 
 * <a name="BoussinesqFlowProblemrefine_mesh"></a> 
 * <h4>BoussinesqFlowProblem::refine_mesh</h4>
 *   
 
 * 
 * This function takes care of the adaptive mesh refinement. The three tasks
 * this function performs is to first find out which cells to
 * refine/coarsen, then to actually do the refinement and eventually
 * transfer the solution vectors between the two different grids. The first
 * task is simply achieved by using the well-established Kelly error
 * estimator on the temperature (it is the temperature we're mainly
 * interested in for this program, and we need to be accurate in regions of
 * high temperature gradients, also to not have too much numerical
 * diffusion). The second task is to actually do the remeshing. That
 * involves only basic functions as well, such as the
 * <code>refine_and_coarsen_fixed_fraction</code> that refines those cells
 * with the largest estimated error that together make up 80 per cent of the
 * error, and coarsens those cells with the smallest error that make up for
 * a combined 10 per cent of the error.
 *   
 
 * 
 * If implemented like this, we would get a program that will not make much
 * progress: Remember that we expect temperature fields that are nearly
 * discontinuous (the diffusivity @f$\kappa@f$ is very small after all) and
 * consequently we can expect that a freely adapted mesh will refine further
 * and further into the areas of large gradients. This decrease in mesh size
 * will then be accompanied by a decrease in time step, requiring an
 * exceedingly large number of time steps to solve to a given final time. It
 * will also lead to meshes that are much better at resolving
 * discontinuities after several mesh refinement cycles than in the
 * beginning.
 *   
 
 * 
 * In particular to prevent the decrease in time step size and the
 * correspondingly large number of time steps, we limit the maximal
 * refinement depth of the mesh. To this end, after the refinement indicator
 * has been applied to the cells, we simply loop over all cells on the
 * finest level and unselect them from refinement if they would result in
 * too high a mesh level.
 * 
 * @code
 *     template <int dim>
 *     void
 *     BoussinesqFlowProblem<dim>::refine_mesh(const unsigned int max_grid_level)
 *     {
 *       Vector<float> estimated_error_per_cell(triangulation.n_active_cells());
 *   
 *       KellyErrorEstimator<dim>::estimate(temperature_dof_handler,
 *                                          QGauss<dim - 1>(temperature_degree + 1),
 *                                          {},
 *                                          temperature_solution,
 *                                          estimated_error_per_cell);
 *   
 *       GridRefinement::refine_and_coarsen_fixed_fraction(triangulation,
 *                                                         estimated_error_per_cell,
 *                                                         0.8,
 *                                                         0.1);
 *       if (triangulation.n_levels() > max_grid_level)
 *         for (auto &cell :
 *              triangulation.active_cell_iterators_on_level(max_grid_level))
 *           cell->clear_refine_flag();
 *   
 * @endcode
 * 
 * As part of mesh refinement we need to transfer the solution vectors
 * from the old mesh to the new one. To this end we use the
 * SolutionTransfer class and we have to prepare the solution vectors that
 * should be transferred to the new grid (we will lose the old grid once
 * we have done the refinement so the transfer has to happen concurrently
 * with refinement). What we definitely need are the current and the old
 * temperature (BDF-2 time stepping requires two old solutions). Since the
 * SolutionTransfer objects only support to transfer one object per dof
 * handler, we need to collect the two temperature solutions in one data
 * structure. Moreover, we choose to transfer the Stokes solution, too,
 * since we need the velocity at two previous time steps, of which only
 * one is calculated on the fly.
 *     
 
 * 
 * Consequently, we initialize two SolutionTransfer objects for the Stokes
 * and temperature DoFHandler objects, by attaching them to the old dof
 * handlers. With this at place, we can prepare the triangulation and the
 * data vectors for refinement (in this order).
 * 
 * @code
 *       std::vector<TrilinosWrappers::MPI::Vector> x_temperature(2);
 *       x_temperature[0]                            = temperature_solution;
 *       x_temperature[1]                            = old_temperature_solution;
 *       TrilinosWrappers::MPI::BlockVector x_stokes = stokes_solution;
 *   
 *       SolutionTransfer<dim, TrilinosWrappers::MPI::Vector> temperature_trans(
 *         temperature_dof_handler);
 *       SolutionTransfer<dim, TrilinosWrappers::MPI::BlockVector> stokes_trans(
 *         stokes_dof_handler);
 *   
 *       triangulation.prepare_coarsening_and_refinement();
 *       temperature_trans.prepare_for_coarsening_and_refinement(x_temperature);
 *       stokes_trans.prepare_for_coarsening_and_refinement(x_stokes);
 *   
 * @endcode
 * 
 * Now everything is ready, so do the refinement and recreate the dof
 * structure on the new grid, and initialize the matrix structures and the
 * new vectors in the <code>setup_dofs</code> function. Next, we actually
 * perform the interpolation of the solutions between the grids. We create
 * another copy of temporary vectors for temperature (now corresponding to
 * the new grid), and let the interpolate function do the job. Then, the
 * resulting array of vectors is written into the respective vector member
 * variables.
 *     
 
 * 
 * Remember that the set of constraints will be updated for the new
 * triangulation in the setup_dofs() call.
 * 
 * @code
 *       triangulation.execute_coarsening_and_refinement();
 *       setup_dofs();
 *   
 *       std::vector<TrilinosWrappers::MPI::Vector> tmp(2);
 *       tmp[0].reinit(temperature_solution);
 *       tmp[1].reinit(temperature_solution);
 *       temperature_trans.interpolate(x_temperature, tmp);
 *   
 *       temperature_solution     = tmp[0];
 *       old_temperature_solution = tmp[1];
 *   
 * @endcode
 * 
 * After the solution has been transferred we then enforce the constraints
 * on the transferred solution.
 * 
 * @code
 *       temperature_constraints.distribute(temperature_solution);
 *       temperature_constraints.distribute(old_temperature_solution);
 *   
 * @endcode
 * 
 * For the Stokes vector, everything is just the same &ndash; except that
 * we do not need another temporary vector since we just interpolate a
 * single vector. In the end, we have to tell the program that the matrices
 * and preconditioners need to be regenerated, since the mesh has changed.
 * 
 * @code
 *       stokes_trans.interpolate(x_stokes, stokes_solution);
 *   
 *       stokes_constraints.distribute(stokes_solution);
 *   
 *       rebuild_stokes_matrix         = true;
 *       rebuild_temperature_matrices  = true;
 *       rebuild_stokes_preconditioner = true;
 *     }
 *   
 *   
 *   
 * @endcode
 * 
 * 
 * <a name="BoussinesqFlowProblemrun"></a> 
 * <h4>BoussinesqFlowProblem::run</h4>
 *   
 
 * 
 * This function performs all the essential steps in the Boussinesq
 * program. It starts by setting up a grid (depending on the spatial
 * dimension, we choose some different level of initial refinement and
 * additional adaptive refinement steps, and then create a cube in
 * <code>dim</code> dimensions and set up the dofs for the first time. Since
 * we want to start the time stepping already with an adaptively refined
 * grid, we perform some pre-refinement steps, consisting of all assembly,
 * solution and refinement, but without actually advancing in time. Rather,
 * we use the vilified <code>goto</code> statement to jump out of the time
 * loop right after mesh refinement to start all over again on the new mesh
 * beginning at the <code>start_time_iteration</code> label. (The use of the
 * <code>goto</code> is discussed in @ref step_26 "step-26".)
 *   
 
 * 
 * Before we start, we project the initial values to the grid and obtain the
 * first data for the <code>old_temperature_solution</code> vector. Then, we
 * initialize time step number and time step and start the time loop.
 * 
 * @code
 *     template <int dim>
 *     void BoussinesqFlowProblem<dim>::run()
 *     {
 *       const unsigned int initial_refinement     = (dim == 2 ? 4 : 2);
 *       const unsigned int n_pre_refinement_steps = (dim == 2 ? 4 : 3);
 *   
 *   
 *       GridGenerator::hyper_cube(triangulation);
 *       global_Omega_diameter = GridTools::diameter(triangulation);
 *   
 *       triangulation.refine_global(initial_refinement);
 *   
 *       setup_dofs();
 *   
 *       unsigned int pre_refinement_step = 0;
 *   
 *     start_time_iteration:
 *   
 *       VectorTools::project(temperature_dof_handler,
 *                            temperature_constraints,
 *                            QGauss<dim>(temperature_degree + 2),
 *                            EquationData::TemperatureInitialValues<dim>(),
 *                            old_temperature_solution);
 *   
 *       timestep_number = 0;
 *       time_step = old_time_step = 0;
 *   
 *       double time = 0;
 *   
 *       do
 *         {
 *           std::cout << "Timestep " << timestep_number << ":  t=" << time
 *                     << std::endl;
 *   
 * @endcode
 * 
 * The first steps in the time loop are all obvious &ndash; we
 * assemble the Stokes system, the preconditioner, the temperature
 * matrix (matrices and preconditioner do actually only change in case
 * we've remeshed before), and then do the solve. Before going on with
 * the next time step, we have to check whether we should first finish
 * the pre-refinement steps or if we should remesh (every fifth time
 * step), refining up to a level that is consistent with initial
 * refinement and pre-refinement steps. Last in the loop is to advance
 * the solutions, i.e., to copy the solutions to the next "older" time
 * level.
 * 
 * @code
 *           assemble_stokes_system();
 *           build_stokes_preconditioner();
 *           assemble_temperature_matrix();
 *   
 *           solve();
 *   
 *           output_results();
 *   
 *           std::cout << std::endl;
 *   
 *           if ((timestep_number == 0) &&
 *               (pre_refinement_step < n_pre_refinement_steps))
 *             {
 *               refine_mesh(initial_refinement + n_pre_refinement_steps);
 *               ++pre_refinement_step;
 *               goto start_time_iteration;
 *             }
 *           else if ((timestep_number > 0) && (timestep_number % 5 == 0))
 *             refine_mesh(initial_refinement + n_pre_refinement_steps);
 *   
 *           time += time_step;
 *           ++timestep_number;
 *   
 *           old_stokes_solution          = stokes_solution;
 *           old_old_temperature_solution = old_temperature_solution;
 *           old_temperature_solution     = temperature_solution;
 *         }
 * @endcode
 * 
 * Do all the above until we arrive at time 100.
 * 
 * @code
 *       while (time <= 100);
 *     }
 *   } // namespace Step31
 *   
 *   
 *   
 * @endcode
 * 
 * 
 * <a name="Thecodemaincodefunction"></a> 
 * <h3>The <code>main</code> function</h3>
 * 
 
 * 
 * The main function looks almost the same as in all other programs.
 * 
 
 * 
 * There is one difference we have to be careful about. This program uses
 * Trilinos and, typically, Trilinos is configured so that it can run in
 * %parallel using MPI. This doesn't mean that it <i>has</i> to run in
 * %parallel, and in fact this program (unlike @ref step_32 "step-32") makes no attempt at
 * all to do anything in %parallel using MPI. Nevertheless, Trilinos wants the
 * MPI system to be initialized. We do that be creating an object of type
 * Utilities::MPI::MPI_InitFinalize that initializes MPI (if available) using
 * the arguments given to main() (i.e., <code>argc</code> and
 * <code>argv</code>) and de-initializes it again when the object goes out of
 * scope.
 * 
 * @code
 *   int main(int argc, char *argv[])
 *   {
 *     try
 *       {
 *         using namespace dealii;
 *         using namespace Step31;
 *   
 *         Utilities::MPI::MPI_InitFinalize mpi_initialization(
 *           argc, argv, numbers::invalid_unsigned_int);
 *   
 * @endcode
 * 
 * This program can only be run in serial. Otherwise, throw an exception.
 * 
 * @code
 *         AssertThrow(Utilities::MPI::n_mpi_processes(MPI_COMM_WORLD) == 1,
 *                     ExcMessage(
 *                       "This program can only be run in serial, use ./step-31"));
 *   
 *         BoussinesqFlowProblem<2> flow_problem;
 *         flow_problem.run();
 *       }
 *     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;
 *   }
 * @endcode
<a name="Results"></a><h1>Results</h1>
 
 
<a name="Resultsin2d"></a><h3> Results in 2d </h3>
 
 
When you run the program in 2d, the output will look something like
this:
<code>
<pre>
Number of active cells: 256 (on 5 levels)
Number of degrees of freedom: 3556 (2178+289+1089)
 
Timestep 0:  t=0
   Assembling...
   Rebuilding Stokes preconditioner...
   Solving...
   0 GMRES iterations for Stokes subsystem.
   Time step: 0.919118
   9 CG iterations for temperature.
   Temperature range: -0.16687 1.30011
 
Number of active cells: 280 (on 6 levels)
Number of degrees of freedom: 4062 (2490+327+1245)
 
Timestep 0:  t=0
   Assembling...
   Rebuilding Stokes preconditioner...
   Solving...
   0 GMRES iterations for Stokes subsystem.
   Time step: 0.459559
   9 CG iterations for temperature.
   Temperature range: -0.0982971 0.598503
 
Number of active cells: 520 (on 7 levels)
Number of degrees of freedom: 7432 (4562+589+2281)
 
Timestep 0:  t=0
   Assembling...
   Rebuilding Stokes preconditioner...
   Solving...
   0 GMRES iterations for Stokes subsystem.
   Time step: 0.229779
   9 CG iterations for temperature.
   Temperature range: -0.0551098 0.294493
 
Number of active cells: 1072 (on 8 levels)
Number of degrees of freedom: 15294 (9398+1197+4699)
 
Timestep 0:  t=0
   Assembling...
   Rebuilding Stokes preconditioner...
   Solving...
   0 GMRES iterations for Stokes subsystem.
   Time step: 0.11489
   9 CG iterations for temperature.
   Temperature range: -0.0273524 0.156861
 
Number of active cells: 2116 (on 9 levels)
Number of degrees of freedom: 30114 (18518+2337+9259)
 
Timestep 0:  t=0
   Assembling...
   Rebuilding Stokes preconditioner...
   Solving...
   0 GMRES iterations for Stokes subsystem.
   Time step: 0.0574449
   9 CG iterations for temperature.
   Temperature range: -0.014993 0.0738328
 
Timestep 1:  t=0.0574449
   Assembling...
   Solving...
   56 GMRES iterations for Stokes subsystem.
   Time step: 0.0574449
   9 CG iterations for temperature.
   Temperature range: -0.0273934 0.14488
 
...
</pre>
</code>
 
In the beginning we refine the mesh several times adaptively and
always return to time step zero to restart on the newly refined
mesh. Only then do we start the actual time iteration.
 
The program runs for a while. The temperature field for time steps 0,
500, 1000, 1500, 2000, 3000, 4000, and 5000 looks like this (note that
the color scale used for the temperature is not always the same):
 
<table align="center" class="doxtable">
  <tr>
    <td>
        <img src="https://www.dealii.org/images/steps/developer/step-31.2d.solution.00.png" alt="">
    </td>
    <td>
        <img src="https://www.dealii.org/images/steps/developer/step-31.2d.solution.01.png" alt="">
    </td>
    <td>
        <img src="https://www.dealii.org/images/steps/developer/step-31.2d.solution.02.png" alt="">
    </td>
    <td>
        <img src="https://www.dealii.org/images/steps/developer/step-31.2d.solution.03.png" alt="">
    </td>
  </tr>
  <tr>
    <td>
        <img src="https://www.dealii.org/images/steps/developer/step-31.2d.solution.04.png" alt="">
    </td>
    <td>
        <img src="https://www.dealii.org/images/steps/developer/step-31.2d.solution.05.png" alt="">
    </td>
    <td>
        <img src="https://www.dealii.org/images/steps/developer/step-31.2d.solution.06.png" alt="">
    </td>
    <td>
        <img src="https://www.dealii.org/images/steps/developer/step-31.2d.solution.07.png" alt="">
    </td>
  </tr>
</table>
 
The visualizations shown here were generated using a version of the example
which did not enforce the constraints after transferring the mesh.
 
As can be seen, we have three heat sources that heat fluid and
therefore produce a buoyancy effect that lets hots pockets of fluid
rise up and swirl around. By a chimney effect, the three streams are
pressed together by fluid that comes from the outside and wants to
join the updraft party. Note that because the fluid is initially at
rest, those parts of the fluid that were initially over the sources
receive a longer heating time than that fluid that is later dragged
over the source by the fully developed flow field. It is therefore
hotter, a fact that can be seen in the red tips of the three
plumes. Note also the relatively fine features of the flow field, a
result of the sophisticated transport stabilization of the temperature
equation we have chosen.
 
In addition to the pictures above, the following ones show the
adaptive mesh and the flow field at the same time steps:
 
<table align="center" class="doxtable">
  <tr>
    <td>
        <img src="https://www.dealii.org/images/steps/developer/step-31.2d.grid.00.png" alt="">
    </td>
    <td>
        <img src="https://www.dealii.org/images/steps/developer/step-31.2d.grid.01.png" alt="">
    </td>
    <td>
        <img src="https://www.dealii.org/images/steps/developer/step-31.2d.grid.02.png" alt="">
    </td>
    <td>
        <img src="https://www.dealii.org/images/steps/developer/step-31.2d.grid.03.png" alt="">
    </td>
  </tr>
  <tr>
    <td>
        <img src="https://www.dealii.org/images/steps/developer/step-31.2d.grid.04.png" alt="">
    </td>
    <td>
        <img src="https://www.dealii.org/images/steps/developer/step-31.2d.grid.05.png" alt="">
    </td>
    <td>
        <img src="https://www.dealii.org/images/steps/developer/step-31.2d.grid.06.png" alt="">
    </td>
    <td>
        <img src="https://www.dealii.org/images/steps/developer/step-31.2d.grid.07.png" alt="">
    </td>
  </tr>
</table>
 
 
<a name="Resultsin3d"></a><h3> Results in 3d </h3>
 
 
The same thing can of course be done in 3d by changing the template
parameter to the BoussinesqFlowProblem object in <code>main()</code>
from 2 to 3, so that the output now looks like follows:
 
<code>
<pre>
Number of active cells: 64 (on 3 levels)
Number of degrees of freedom: 3041 (2187+125+729)
 
Timestep 0:  t=0
   Assembling...
   Rebuilding Stokes preconditioner...
   Solving...
   0 GMRES iterations for Stokes subsystem.
   Time step: 2.45098
   9 CG iterations for temperature.
   Temperature range: -0.675683 4.94725
 
Number of active cells: 288 (on 4 levels)
Number of degrees of freedom: 12379 (8943+455+2981)
 
Timestep 0:  t=0
   Assembling...
   Rebuilding Stokes preconditioner...
   Solving...
   0 GMRES iterations for Stokes subsystem.
   Time step: 1.22549
   9 CG iterations for temperature.
   Temperature range: -0.527701 2.25764
 
Number of active cells: 1296 (on 5 levels)
Number of degrees of freedom: 51497 (37305+1757+12435)
 
Timestep 0:  t=0
   Assembling...
   Rebuilding Stokes preconditioner...
   Solving...
   0 GMRES iterations for Stokes subsystem.
   Time step: 0.612745
   10 CG iterations for temperature.
   Temperature range: -0.496942 0.847395
 
Number of active cells: 5048 (on 6 levels)
Number of degrees of freedom: 192425 (139569+6333+46523)
 
Timestep 0:  t=0
   Assembling...
   Rebuilding Stokes preconditioner...
   Solving...
   0 GMRES iterations for Stokes subsystem.
   Time step: 0.306373
   10 CG iterations for temperature.
   Temperature range: -0.267683 0.497739
 
Timestep 1:  t=0.306373
   Assembling...
   Solving...
   27 GMRES iterations for Stokes subsystem.
   Time step: 0.306373
   10 CG iterations for temperature.
   Temperature range: -0.461787 0.958679
 
...
</pre>
</code>
 
Visualizing the temperature isocontours at time steps 0,
50, 100, 150, 200, 300, 400, 500, 600, 700, and 800 yields the
following plots:
 
<table align="center" class="doxtable">
  <tr>
    <td>
        <img src="https://www.dealii.org/images/steps/developer/step-31.3d.solution.00.png" alt="">
    </td>
    <td>
        <img src="https://www.dealii.org/images/steps/developer/step-31.3d.solution.01.png" alt="">
    </td>
    <td>
        <img src="https://www.dealii.org/images/steps/developer/step-31.3d.solution.02.png" alt="">
    </td>
    <td>
        <img src="https://www.dealii.org/images/steps/developer/step-31.3d.solution.03.png" alt="">
    </td>
  </tr>
  <tr>
    <td>
        <img src="https://www.dealii.org/images/steps/developer/step-31.3d.solution.04.png" alt="">
    </td>
    <td>
        <img src="https://www.dealii.org/images/steps/developer/step-31.3d.solution.05.png" alt="">
    </td>
    <td>
        <img src="https://www.dealii.org/images/steps/developer/step-31.3d.solution.06.png" alt="">
    </td>
    <td>
        <img src="https://www.dealii.org/images/steps/developer/step-31.3d.solution.07.png" alt="">
    </td>
  </tr>
  <tr>
    <td>
        <img src="https://www.dealii.org/images/steps/developer/step-31.3d.solution.08.png" alt="">
    </td>
    <td>
        <img src="https://www.dealii.org/images/steps/developer/step-31.3d.solution.09.png" alt="">
    </td>
    <td>
        <img src="https://www.dealii.org/images/steps/developer/step-31.3d.solution.10.png" alt="">
    </td>
    <td>
    </td>
  </tr>
</table>
 
That the first picture looks like three hedgehogs stems from the fact that our
scheme essentially projects the source times the first time step size onto the
mesh to obtain the temperature field in the first time step. Since the source
function is discontinuous, we need to expect over- and undershoots from this
project. This is in fact what happens (it's easier to check this in 2d) and
leads to the crumpled appearance of the isosurfaces.  The visualizations shown
here were generated using a version of the example which did not enforce the
constraints after transferring the mesh.
 
 
 
<a name="Numericalexperimentstodetermineoptimalparameters"></a><h3> Numerical experiments to determine optimal parameters </h3>
 
 
The program as is has three parameters that we don't have much of a
theoretical handle on how to choose in an optimal way. These are:
<ul>
  <li>The time step must satisfy a CFL condition
      @f$k\le \min_K \frac{c_kh_K}{\|\mathbf{u}\|_{L^\infty(K)}}@f$. Here, @f$c_k@f$ is
      dimensionless, but what is the right value?
  <li>In the computation of the artificial viscosity,
@f{eqnarray*}
  \nu_\alpha(T)|_K
  =
  \beta
  \|\mathbf{u}\|_{L^\infty(K)}
  \min\left\{
    h_K,
    h_K^\alpha
    \frac{\|R_\alpha(T)\|_{L^\infty(K)}}{c(\mathbf{u},T)}
  \right\},
@f}
      with @f$c(\mathbf{u},T) =
      c_R\ \|\mathbf{u}\|_{L^\infty(\Omega)} \ \mathrm{var}(T)
      \ |\mathrm{diam}(\Omega)|^{\alpha-2}@f$.
      Here, the choice of the dimensionless %numbers @f$\beta,c_R@f$ is of
      interest.
</ul>
In all of these cases, we will have to expect that the correct choice of each
value depends on that of the others, and most likely also on the space
dimension and polynomial degree of the finite element used for the
temperature. Below we'll discuss a few numerical experiments to choose
constants @f$c_k@f$ and @f$\beta@f$.
 
Below, we will not discuss the choice of @f$c_R@f$. In the program, we set
it to @f$c_R=2^{\frac{4-2\alpha}{d}}@f$. The reason for this value is a
bit complicated and has more to do with the history of the program
than reasoning: while the correct formula for the global scaling
parameter @f$c(\mathbf{u},T)@f$ is shown above, the program (including the
version shipped with deal.II 6.2) initially had a bug in that we
computed
@f$c(\mathbf{u},T) =
      \|\mathbf{u}\|_{L^\infty(\Omega)} \ \mathrm{var}(T)
      \ \frac{1}{|\mathrm{diam}(\Omega)|^{\alpha-2}}@f$ instead, where
we had set the scaling parameter to one. Since we only computed on the
unit square/cube where @f$\mathrm{diam}(\Omega)=2^{1/d}@f$, this was
entirely equivalent to using the correct formula with
@f$c_R=\left(2^{1/d}\right)^{4-2\alpha}=2^{\frac{4-2\alpha}{d}}@f$. Since
this value for @f$c_R@f$ appears to work just fine for the current
program, we corrected the formula in the program and set @f$c_R@f$ to a
value that reproduces exactly the results we had before. We will,
however, revisit this issue again in @ref step_32 "step-32".
 
Now, however, back to the discussion of what values of @f$c_k@f$ and
@f$\beta@f$ to choose:
 
 
<a name="Choosingicsubksubiandbeta"></a><h4> Choosing <i>c<sub>k</sub></i> and beta </h4>
 
 
These two constants are definitely linked in some way. The reason is easy to
see: In the case of a pure advection problem,
@f$\frac{\partial T}{\partial t} + \mathbf{u}\cdot\nabla T = \gamma@f$, any
explicit scheme has to satisfy a CFL condition of the form
@f$k\le \min_K \frac{c_k^a h_K}{\|\mathbf{u}\|_{L^\infty(K)}}@f$. On the other hand,
for a pure diffusion problem,
@f$\frac{\partial T}{\partial t} + \nu \Delta T = \gamma@f$,
explicit schemes need to satisfy a condition
@f$k\le \min_K \frac{c_k^d h_K^2}{\nu}@f$. So given the form of @f$\nu@f$ above, an
advection diffusion problem like the one we have to solve here will result in
a condition of the form
@f$
k\le \min_K \min \left\{
  \frac{c_k^a h_K}{\|\mathbf{u}\|_{L^\infty(K)}},
  \frac{c_k^d h_K^2}{\beta \|\mathbf{u}\|_{L^\infty(K)} h_K}\right\}
  =
  \min_K \left( \min \left\{
  c_k^a,
  \frac{c_k^d}{\beta}\right\}
  \frac{h_K}{\|\mathbf{u}\|_{L^\infty(K)}} \right)
@f$.
It follows that we have to face the fact that we might want to choose @f$\beta@f$
larger to improve the stability of the numerical scheme (by increasing the
amount of artificial diffusion), but we have to pay a price in the form of
smaller, and consequently more time steps. In practice, one would therefore
like to choose @f$\beta@f$ as small as possible to keep the transport problem
sufficiently stabilized while at the same time trying to choose the time step
as large as possible to reduce the overall amount of work.
 
The find the right balance, the only way is to do a few computational
experiments. Here's what we did: We modified the program slightly to allow
less mesh refinement (so we don't always have to wait that long) and to choose
@f$
  \nu(T)|_K
  =
  \beta
  \|\mathbf{u}\|_{L^\infty(K)} h_K
@f$ to eliminate the effect of the constant @f$c_R@f$ (we know that
solutions are stable by using this version of @f$\nu(T)@f$ as an artificial
viscosity, but that we can improve things -- i.e. make the solution
sharper -- by using the more complicated formula for this artificial
viscosity). We then run the program
for different values @f$c_k,\beta@f$ and observe maximal and minimal temperatures
in the domain. What we expect to see is this: If we choose the time step too
big (i.e. choose a @f$c_k@f$ bigger than theoretically allowed) then we will get
exponential growth of the temperature. If we choose @f$\beta@f$ too small, then
the transport stabilization becomes insufficient and the solution will show
significant oscillations but not exponential growth.
 
 
<a name="ResultsforQsub1subelements"></a><h5>Results for Q<sub>1</sub> elements</h5>
 
 
Here is what we get for
@f$\beta=0.01, \beta=0.1@f$, and @f$\beta=0.5@f$, different choices of @f$c_k@f$, and
bilinear elements (<code>temperature_degree=1</code>) in 2d:
 
<table align="center" class="doxtable">
  <tr>
    <td>
        <img src="https://www.dealii.org/images/steps/developer/step-31.timestep.q1.beta=0.01.png" alt="">
    </td>
    <td>
        <img src="https://www.dealii.org/images/steps/developer/step-31.timestep.q1.beta=0.03.png" alt="">
    </td>
  </tr>
  <tr>
    <td>
        <img src="https://www.dealii.org/images/steps/developer/step-31.timestep.q1.beta=0.1.png" alt="">
    </td>
    <td>
        <img src="https://www.dealii.org/images/steps/developer/step-31.timestep.q1.beta=0.5.png" alt="">
    </td>
  </tr>
</table>
 
The way to interpret these graphs goes like this: for @f$\beta=0.01@f$ and
@f$c_k=\frac 12,\frac 14@f$, we see exponential growth or at least large
variations, but if we choose
@f$k=\frac 18\frac{h_K}{\|\mathbf{u}\|_{L^\infty(K)}}@f$
or smaller, then the scheme is
stable though a bit wobbly. For more artificial diffusion, we can choose
@f$k=\frac 14\frac{h_K}{\|\mathbf{u}\|_{L^\infty(K)}}@f$
or smaller for @f$\beta=0.03@f$,
@f$k=\frac 13\frac{h_K}{\|\mathbf{u}\|_{L^\infty(K)}}@f$
or smaller for @f$\beta=0.1@f$, and again need
@f$k=\frac 1{15}\frac{h_K}{\|\mathbf{u}\|_{L^\infty(K)}}@f$
for @f$\beta=0.5@f$ (this time because much diffusion requires a small time
step).
 
So how to choose? If we were simply interested in a large time step, then we
would go with @f$\beta=0.1@f$ and
@f$k=\frac 13\frac{h_K}{\|\mathbf{u}\|_{L^\infty(K)}}@f$.
On the other hand, we're also interested in accuracy and here it may be of
interest to actually investigate what these curves show. To this end note that
we start with a zero temperature and that our sources are positive &mdash; so
we would intuitively expect that the temperature can never drop below
zero. But it does, a consequence of Gibb's phenomenon when using continuous
elements to approximate a discontinuous solution. We can therefore see that
choosing @f$\beta@f$ too small is bad: too little artificial diffusion leads to
over- and undershoots that aren't diffused away. On the other hand, for large
@f$\beta@f$, the minimum temperature drops below zero at the beginning but then
quickly diffuses back to zero.
 
On the other hand, let's also look at the maximum temperature. Watching the
movie of the solution, we see that initially the fluid is at rest. The source
keeps heating the same volume of fluid whose temperature increases linearly at
the beginning until its buoyancy is able to move it upwards. The hottest part
of the fluid is therefore transported away from the solution and fluid taking
its place is heated for only a short time before being moved out of the source
region, therefore remaining cooler than the initial bubble. If @f$\kappa=0@f$
(in the program it is nonzero but very small) then the hottest part of the
fluid should be advected along with the flow with its temperature
constant. That's what we can see in the graphs with the smallest @f$\beta@f$: Once
the maximum temperature is reached, it hardly changes any more. On the other
hand, the larger the artificial diffusion, the more the hot spot is
diffused. Note that for this criterion, the time step size does not play a
significant role.
 
So to sum up, likely the best choice would appear to be @f$\beta=0.03@f$
and @f$k=\frac 14\frac{h_K}{\|\mathbf{u}\|_{L^\infty(K)}}@f$. The curve is
a bit wobbly, but overall pictures looks pretty reasonable with the
exception of some over and undershoots close to the start time due to
Gibb's phenomenon.
 
 
<a name="ResultsforQsub2subelements"></a><h5>Results for Q<sub>2</sub> elements</h5>
 
 
One can repeat the same sequence of experiments for higher order
elements as well. Here are the graphs for bi-quadratic shape functions
(<code>temperature_degree=2</code>) for the temperature, while we
retain the @f$Q_2/Q_1@f$ stable Taylor-Hood element for the Stokes system:
 
<table align="center" class="doxtable">
  <tr>
    <td>
        <img src="https://www.dealii.org/images/steps/developer/step-31.timestep.q2.beta=0.01.png" alt="">
    </td>
    <td>
        <img src="https://www.dealii.org/images/steps/developer/step-31.timestep.q2.beta=0.03.png" alt="">
    </td>
  </tr>
  <tr>
    <td>
        <img src="https://www.dealii.org/images/steps/developer/step-31.timestep.q2.beta=0.1.png" alt="">
    </td>
  </tr>
</table>
 
Again, small values of @f$\beta@f$ lead to less diffusion but we have to
choose the time step very small to keep things under control. Too
large values of @f$\beta@f$ make for more diffusion, but again require
small time steps. The best value would appear to be @f$\beta=0.03@f$, as
for the @f$Q_1@f$ element, and then we have to choose
@f$k=\frac 18\frac{h_K}{\|\mathbf{u}\|_{L^\infty(K)}}@f$ &mdash; exactly
half the size for the @f$Q_1@f$ element, a fact that may not be surprising
if we state the CFL condition as the requirement that the time step be
small enough so that the distance transport advects in each time step
is no longer than one <i>grid point</i> away (which for @f$Q_1@f$ elements
is @f$h_K@f$, but for @f$Q_2@f$ elements is @f$h_K/2@f$). It turns out that @f$\beta@f$
needs to be slightly larger for obtaining stable results also late in
the simulation at times larger than 60, so we actually choose it as
@f$\beta = 0.034@f$ in the code.
 
 
<a name="Resultsfor3d"></a><h5>Results for 3d</h5>
 
 
One can repeat these experiments in 3d and find the optimal time step
for each value of @f$\beta@f$ and find the best value of @f$\beta@f$. What one
finds is that for the same @f$\beta@f$ already used in 2d, the time steps
needs to be a bit smaller, by around a factor of 1.2 or so. This is
easily explained: the time step restriction is
@f$k=\min_K \frac{ch_K}{\|\mathbf{u}\|_{L^\infty(K)}}@f$ where @f$h_K@f$ is
the <i>diameter</i> of the cell. However, what is really needed is the
distance between mesh points, which is @f$\frac{h_K}{\sqrt{d}}@f$. So a
more appropriate form would be
@f$k=\min_K \frac{ch_K}{\|\mathbf{u}\|_{L^\infty(K)}\sqrt{d}}@f$.
 
The second find is that one needs to choose @f$\beta@f$ slightly bigger
(about @f$\beta=0.05@f$ or so). This then again reduces the time step we
can take.
 
 
 
 
<a name="Conclusions"></a><h5>Conclusions</h5>
 
 
Concluding, from the simple computations above, @f$\beta=0.034@f$ appears to be a
good choice for the stabilization parameter in 2d, and @f$\beta=0.05@f$ in 3d. In
a dimension independent way, we can model this as @f$\beta=0.017d@f$. If one does
longer computations (several thousand time steps) on finer meshes, one
realizes that the time step size is not quite small enough and that for
stability one will have to reduce the above values a bit more (by about a
factor of @f$\frac 78@f$).
 
As a consequence, a formula that reconciles 2d, 3d, and variable polynomial
degree and takes all factors in account reads as follows:
@f{eqnarray*}
  k =
  \frac 1{2 \cdot 1.7} \frac 1{\sqrt{d}}
  \frac 2d
  \frac 1{q_T}
  \frac{h_K}{\|\mathbf{u}\|_{L^\infty(K)}}
  =
  \frac 1{1.7 d\sqrt{d}}
  \frac 1{q_T}
  \frac{h_K}{\|\mathbf{u}\|_{L^\infty(K)}}.
@f}
In the first form (in the center of the equation), @f$\frac
1{2 \cdot 1.7}@f$ is a universal constant, @f$\frac 1{\sqrt{d}}@f$
is the factor that accounts for the difference between cell diameter
and grid point separation,
@f$\frac 2d@f$ accounts for the increase in @f$\beta@f$ with space dimension,
@f$\frac 1{q_T}@f$ accounts for the distance between grid points for
higher order elements, and @f$\frac{h_K}{\|\mathbf{u}\|_{L^\infty(K)}}@f$
for the local speed of transport relative to the cell size. This is
the formula that we use in the program.
 
As for the question of whether to use @f$Q_1@f$ or @f$Q_2@f$ elements for the
temperature, the following considerations may be useful: First,
solving the temperature equation is hardly a factor in the overall
scheme since almost the entire compute time goes into solving the
Stokes system in each time step. Higher order elements for the
temperature equation are therefore not a significant drawback. On the
other hand, if one compares the size of the over- and undershoots the
solution produces due to the discontinuous source description, one
notices that for the choice of @f$\beta@f$ and @f$k@f$ as above, the @f$Q_1@f$
solution dips down to around @f$-0.47@f$, whereas the @f$Q_2@f$ solution only
goes to @f$-0.13@f$ (remember that the exact solution should never become
negative at all. This means that the @f$Q_2@f$ solution is significantly
more accurate; the program therefore uses these higher order elements,
despite the penalty we pay in terms of smaller time steps.
 
 
<a name="Possibilitiesforextensions"></a><h3> Possibilities for extensions </h3>
 
 
There are various ways to extend the current program. Of particular interest
is, of course, to make it faster and/or increase the resolution of the
program, in particular in 3d. This is the topic of the @ref step_32 "step-32"
tutorial program which will implement strategies to solve this problem in
%parallel on a cluster. It is also the basis of the much larger open
source code ASPECT (see https://aspect.geodynamics.org/ ) that can solve realistic
problems and that constitutes the further development of @ref step_32 "step-32".
 
Another direction would be to make the fluid flow more realistic. The program
was initially written to simulate various cases simulating the convection of
material in the earth's mantle, i.e. the zone between the outer earth core and
the solid earth crust: there, material is heated from below and cooled from
above, leading to thermal convection. The physics of this fluid are much more
complicated than shown in this program, however: The viscosity of mantle
material is strongly dependent on the temperature, i.e. @f$\eta=\eta(T)@f$, with
the dependency frequently modeled as a viscosity that is reduced exponentially
with rising temperature. Secondly, much of the dynamics of the mantle is
determined by chemical reactions, primarily phase changes of the various
crystals that make up the mantle; the buoyancy term on the right hand side of
the Stokes equations then depends not only on the temperature, but also on the
chemical composition at a given location which is advected by the flow field
but also changes as a function of pressure and temperature. We will
investigate some of these effects in later tutorial programs as well.
 *
 *
<a name="PlainProg"></a>
<h1> The plain program</h1>
@include "step-31.cc"
*/