 Reference documentation for deal.II version Git d84be816e2 2019-07-13 22:20:17 -0400
The step-2 tutorial program

This tutorial depends on step-1.

1. Introduction
2. The commented program
1. Results
2. The plain program

# Introduction

Note
The material presented here is also discussed in video lecture 9. (All video lectures are also available here.)

After we have created a grid in the previous example, we now show how to define degrees of freedom on this mesh. For this example, we will use the lowest order ( $$Q_1$$) finite elements, for which the degrees of freedom are associated with the vertices of the mesh. Later examples will demonstrate higher order elements where degrees of freedom are not necessarily associated with vertices any more, but can be associated with edges, faces, or cells.

The term "degree of freedom" is commonly used in the finite element community to indicate two slightly different, but related things. The first is that we'd like to represent the finite element solution as a linear combination of shape functions, in the form $$u_h(\mathbf x) = \sum_{j=0}^{N-1} U_j \varphi_j(\mathbf x)$$. Here, $$U_j$$ is a vector of expansion coefficients. Because we don't know their values yet (we will compute them as the solution of a linear or nonlinear system), they are called "unknowns" or "degrees of freedom". The second meaning of the term can be explained as follows: A mathematical description of finite element problems is often to say that we are looking for a finite dimensional function $$u_h \in V_h$$ that satisfies some set of equations (e.g. $$a(u_h,\varphi_h)=(f,\varphi_h)$$ for all test functions $$\varphi_h\in V_h$$). In other words, all we say here that the solution needs to lie in some space $$V_h$$. However, to actually solve this problem on a computer we need to choose a basis of this space; this is the set of shape functions $$\varphi_j(\mathbf x)$$ we have used above in the expansion of $$u_h(\mathbf x)$$ with coefficients $$U_j$$. There are of course many bases of the space $$V_h$$, but we will specifically choose the one that is described by the finite element functions that are traditionally defined locally on the cells of the mesh. Describing "degrees of freedom" in this context requires us to simply enumerate the basis functions of the space $$V_h$$. For $$Q_1$$ elements this means simply enumerating the vertices of the mesh in some way, but for higher order elements, one also has to enumerate the shape functions that are associated with edges, faces, or cell interiors of the mesh. In other words, the enumeration of degrees of freedom is an entirely separate thing from the indices we use for vertices. The class that provides this enumeration of the basis functions of $$V_h$$ is called DoFHandler.

Defining degrees of freedom ("DoF"s in short) on a mesh is a rather simple task, since the library does all the work for you. Essentially, all you have to do is create a finite element object (from one of the many finite element classes deal.II already has, see for example the Finite element space descriptions documentation) and give it to a DoFHandler object through the DoFHandler::distribute_dofs function ("distributing DoFs" is the term we use to describe the process of enumerating the basis functions as discussed above). The DoFHandler is a class that knows which degrees of freedom live where, i.e., it can answer questions like "how many degrees of freedom are there globally" and "on this cell, give me the global indices of the shape functions that live here". This is the sort of information you need when determining how big your system matrix should be, and when copying the contributions of a single cell into the global matrix.

### Sparsity

The next step would then be to compute a matrix and right hand side corresponding to a particular differential equation using this finite element and mesh. We will keep this step for the step-3 program and rather talk about one practical aspect of a finite element program, namely that finite element matrices are always very sparse: almost all entries in these matrices are zero.

To be more precise, we say that a matrix is sparse if the number of nonzero entries per row in the matrix is bounded by a number that is independent of the overall number of degrees of freedom. For example, the simple 5-point stencil of a finite difference approximation of the Laplace equation leads to a sparse matrix since the number of nonzero entries per row is five, and therefore independent of the total size of the matrix. For more complicated problems – say, the Stokes problem of step-22 – and in particular in 3d, the number of entries per row may be several hundred. But the important point is that this number is independent of the overall size of the problem: If you refine the mesh, the maximal number of unknowns per row remains the same.

Sparsity is one of the distinguishing feature of the finite element method compared to, say, approximating the solution of a partial differential equation using a Taylor expansion and matching coefficients, or using a Fourier basis.

In practical terms, it is the sparsity of matrices that enables us to solve problems with millions or billions of unknowns. To understand this, note that a matrix with $$N$$ rows, each with a fixed upper bound for the number of nonzero entries, requires $${\cal O}(N)$$ memory locations for storage, and a matrix-vector multiplication also requires only $${\cal O}(N)$$ operations. Consequently, if we had a linear solver that requires only a fixed number of matrix-vector multiplications to come up with the solution of a linear system with this matrix, then we would have a solver that can find the values of all $$N$$ unknowns with optimal complexity, i.e., with a total of $${\cal O}(N)$$ operations. It is clear that this wouldn't be possible if the matrix were not sparse (because then the number of entries in the matrix would have to be $${\cal O}(N^s)$$ with some $$s>1$$, and doing a fixed number of matrix-vector products would take $${\cal O}(N^s)$$ operations), but it also requires very specialized solvers such as multigrid methods to satisfy the requirement that the solution requires only a fixed number of matrix-vector multiplications. We will frequently look at the question of what solver to use in the remaining programs of this tutorial.

The sparsity is generated by the fact that finite element shape functions are defined locally on individual cells, rather than globally, and that the local differential operators in the bilinear form only couple shape functions whose support overlaps. (The "support" of a function is the area where it is nonzero. For the finite element method, the support of a shape function is generally the cells adjacent to the vertex, edge, or face it is defined on.) In other words, degrees of freedom $$i$$ and $$j$$ that are not defined on the same cell do not overlap, and consequently the matrix entry $$A_{ij}$$ will be zero. (In some cases such as the Discontinuous Galerkin method, shape functions may also connect to neighboring cells through face integrals. But finite element methods do not generally couple shape functions beyond the immediate neighbors of a cell on which the function is defined.)

### How degrees of freedom are enumerated

By default, the DoFHandler class enumerates degrees of freedom on a mesh in a rather random way; consequently, the sparsity pattern is also not optimized for any particular purpose. To show this, the code below will demonstrate a simple way to output the "sparsity pattern" that corresponds to a DoFHandler, i.e., an object that represents all of the potentially nonzero elements of a matrix one may build when discretizing a partial differential equation on a mesh and its DoFHandler. This lack of structure in the sparsity pattern will be apparent from the pictures we show below.

For most applications and algorithms, the exact way in which degrees of freedom are numbered does not matter. For example, the Conjugate Gradient method we use to solve linear systems does not care. On the other hand, some algorithms do care: in particular, some preconditioners such as SSOR will work better if they can walk through degrees of freedom in a particular order, and it would be nice if we could just sort them in such a way that SSOR can iterate through them from zero to $$N$$ in this order. Other examples include computing incomplete LU or Cholesky factorizations, or if we care about the block structure of matrices (see step-20 for an example). deal.II therefore has algorithms that can re-enumerate degrees of freedom in particular ways in namespace DoFRenumbering. Renumbering can be thought of as choosing a different, permuted basis of the finite element space. The sparsity pattern and matrices that result from this renumbering are therefore also simply a permutation of rows and columns compared to the ones we would get without explicit renumbering.

In the program below, we will use the algorithm of Cuthill and McKee to do so. We will show the sparsity pattern for both the original enumeration of degrees of freedom and of the renumbered version below, in the results section.

# The commented program

The first few includes are just like in the previous program, so do not require additional comments:

#include <deal.II/grid/tria.h>
#include <deal.II/grid/tria_accessor.h>
#include <deal.II/grid/tria_iterator.h>
#include <deal.II/grid/grid_generator.h>
#include <deal.II/grid/manifold_lib.h>

However, the next file is new. We need this include file for the association of degrees of freedom ("DoF"s) to vertices, lines, and cells:

#include <deal.II/dofs/dof_handler.h>

The following include contains the description of the bilinear finite element, including the facts that it has one degree of freedom on each vertex of the triangulation, but none on faces and none in the interior of the cells.

(In fact, the file contains the description of Lagrange elements in general, i.e. also the quadratic, cubic, etc versions, and not only for 2d but also 1d and 3d.)

#include <deal.II/fe/fe_q.h>

In the following file, several tools for manipulating degrees of freedom can be found:

#include <deal.II/dofs/dof_tools.h>

We will use a sparse matrix to visualize the pattern of nonzero entries resulting from the distribution of degrees of freedom on the grid. That class can be found here:

#include <deal.II/lac/sparse_matrix.h>

We will also need to use an intermediate sparsity pattern structure, which is found in this file :

#include <deal.II/lac/dynamic_sparsity_pattern.h>

We will want to use a special algorithm to renumber degrees of freedom. It is declared here:

#include <deal.II/dofs/dof_renumbering.h>

And this is again needed for C++ output:

#include <fstream>

Finally, as in step-1, we import the deal.II namespace into the global scope:

using namespace dealii;

### Mesh generation

This is the function that produced the circular grid in the previous step-1 example program with fewer refinements steps. The sole difference is that it returns the grid it produces via its argument.

void make_grid(Triangulation<2> &triangulation)
{
const Point<2> center(1, 0);
for (unsigned int step = 0; step < 3; ++step)
{
for (auto &cell : triangulation.active_cell_iterators())
for (unsigned int v = 0; v < GeometryInfo<2>::vertices_per_cell; ++v)
{
const double distance_from_center =
center.distance(cell->vertex(v));
if (std::fabs(distance_from_center - inner_radius) < 1e-10)
{
cell->set_refine_flag();
break;
}
}
}
}

### Creation of a DoFHandler

Up to now, we only have a grid, i.e. some geometrical (the position of the vertices) and some topological information (how vertices are connected to lines, and lines to cells, as well as which cells neighbor which other cells). To use numerical algorithms, one needs some logic information in addition to that: we would like to associate degree of freedom numbers to each vertex (or line, or cell, in case we were using higher order elements) to later generate matrices and vectors which describe a finite element field on the triangulation.

This function shows how to do this. The object to consider is the DoFHandler class template. Before we do so, however, we first need something that describes how many degrees of freedom are to be associated to each of these objects. Since this is one aspect of the definition of a finite element space, the finite element base class stores this information. In the present context, we therefore create an object of the derived class FE_Q that describes Lagrange elements. Its constructor takes one argument that states the polynomial degree of the element, which here is one (indicating a bi-linear element); this then corresponds to one degree of freedom for each vertex, while there are none on lines and inside the quadrilateral. A value of, say, three given to the constructor would instead give us a bi-cubic element with one degree of freedom per vertex, two per line, and four inside the cell. In general, FE_Q denotes the family of continuous elements with complete polynomials (i.e. tensor-product polynomials) up to the specified order.

We first need to create an object of this class and then pass it on to the DoFHandler object to allocate storage for the degrees of freedom (in deal.II lingo: we distribute degrees of freedom).

void distribute_dofs(DoFHandler<2> &dof_handler)
{
const FE_Q<2> finite_element(1);
dof_handler.distribute_dofs(finite_element);

Now that we have associated a degree of freedom with a global number to each vertex, we wonder how to visualize this? There is no simple way to directly visualize the DoF number associated with each vertex. However, such information would hardly ever be truly important, since the numbering itself is more or less arbitrary. There are more important factors, of which we will demonstrate one in the following.

Associated with each vertex of the triangulation is a shape function. Assume we want to solve something like Laplace's equation, then the different matrix entries will be the integrals over the gradient of each pair of such shape functions. Obviously, since the shape functions are nonzero only on the cells adjacent to the vertex they are associated with, matrix entries will be nonzero only if the supports of the shape functions associated to that column and row numbers intersect. This is only the case for adjacent shape functions, and therefore only for adjacent vertices. Now, since the vertices are numbered more or less randomly by the above function (DoFHandler::distribute_dofs), the pattern of nonzero entries in the matrix will be somewhat ragged, and we will take a look at it now.

First we have to create a structure which we use to store the places of nonzero elements. This can then later be used by one or more sparse matrix objects that store the values of the entries in the locations stored by this sparsity pattern. The class that stores the locations is the SparsityPattern class. As it turns out, however, this class has some drawbacks when we try to fill it right away: its data structures are set up in such a way that we need to have an estimate for the maximal number of entries we may wish to have in each row. In two space dimensions, reasonable values for this estimate are available through the DoFHandler::max_couplings_between_dofs() function, but in three dimensions the function almost always severely overestimates the true number, leading to a lot of wasted memory, sometimes too much for the machine used, even if the unused memory can be released immediately after computing the sparsity pattern. In order to avoid this, we use an intermediate object of type DynamicSparsityPattern that uses a different internal data structure and that we can later copy into the SparsityPattern object without much overhead. (Some more information on these data structures can be found in the Sparsity patterns module.) In order to initialize this intermediate data structure, we have to give it the size of the matrix, which in our case will be square with as many rows and columns as there are degrees of freedom on the grid:

DynamicSparsityPattern dynamic_sparsity_pattern(dof_handler.n_dofs(),
dof_handler.n_dofs());

We then fill this object with the places where nonzero elements will be located given the present numbering of degrees of freedom:

DoFTools::make_sparsity_pattern(dof_handler, dynamic_sparsity_pattern);

Now we are ready to create the actual sparsity pattern that we could later use for our matrix. It will just contain the data already assembled in the DynamicSparsityPattern.

SparsityPattern sparsity_pattern;
sparsity_pattern.copy_from(dynamic_sparsity_pattern);

With this, we can now write the results to a file :

std::ofstream out("sparsity_pattern1.svg");
sparsity_pattern.print_svg(out);

The result is stored in an .svg file, where each nonzero entry in the matrix corresponds with a red square in the image. The output will be shown below.

If you look at it, you will note that the sparsity pattern is symmetric. This should not come as a surprise, since we have not given the DoFTools::make_sparsity_pattern any information that would indicate that our bilinear form may couple shape functions in a non-symmetric way. You will also note that it has several distinct region, which stem from the fact that the numbering starts from the coarsest cells and moves on to the finer ones; since they are all distributed symmetrically around the origin, this shows up again in the sparsity pattern.

}

### Renumbering of DoFs

In the sparsity pattern produced above, the nonzero entries extended quite far off from the diagonal. For some algorithms, for example for incomplete LU decompositions or Gauss-Seidel preconditioners, this is unfavorable, and we will show a simple way how to improve this situation.

Remember that for an entry $$(i,j)$$ in the matrix to be nonzero, the supports of the shape functions i and j needed to intersect (otherwise in the integral, the integrand would be zero everywhere since either the one or the other shape function is zero at some point). However, the supports of shape functions intersected only if they were adjacent to each other, so in order to have the nonzero entries clustered around the diagonal (where $$i$$ equals $$j$$), we would like to have adjacent shape functions to be numbered with indices (DoF numbers) that differ not too much.

This can be accomplished by a simple front marching algorithm, where one starts at a given vertex and gives it the index zero. Then, its neighbors are numbered successively, making their indices close to the original one. Then, their neighbors, if not yet numbered, are numbered, and so on.

One algorithm that adds a little bit of sophistication along these lines is the one by Cuthill and McKee. We will use it in the following function to renumber the degrees of freedom such that the resulting sparsity pattern is more localized around the diagonal. The only interesting part of the function is the first call to DoFRenumbering::Cuthill_McKee, the rest is essentially as before:

void renumber_dofs(DoFHandler<2> &dof_handler)
{
DynamicSparsityPattern dynamic_sparsity_pattern(dof_handler.n_dofs(),
dof_handler.n_dofs());
DoFTools::make_sparsity_pattern(dof_handler, dynamic_sparsity_pattern);
SparsityPattern sparsity_pattern;
sparsity_pattern.copy_from(dynamic_sparsity_pattern);
std::ofstream out("sparsity_pattern2.svg");
sparsity_pattern.print_svg(out);
}

Again, the output is shown below. Note that the nonzero entries are clustered far better around the diagonal than before. This effect is even more distinguished for larger matrices (the present one has 1260 rows and columns, but large matrices often have several 100,000s).

It is worth noting that the DoFRenumbering class offers a number of other algorithms as well to renumber degrees of freedom. For example, it would of course be ideal if all couplings were in the lower or upper triangular part of a matrix, since then solving the linear system would among to only forward or backward substitution. This is of course unachievable for symmetric sparsity patterns, but in some special situations involving transport equations, this is possible by enumerating degrees of freedom from the inflow boundary along streamlines to the outflow boundary. Not surprisingly, DoFRenumbering also has algorithms for this.

### The main function

Finally, this is the main program. The only thing it does is to allocate and create the triangulation, then create a DoFHandler object and associate it to the triangulation, and finally call above two functions on it:

int main()
{
Triangulation<2> triangulation;
make_grid(triangulation);
DoFHandler<2> dof_handler(triangulation);
distribute_dofs(dof_handler);
renumber_dofs(dof_handler);
}

# Results

The program has, after having been run, produced two sparsity patterns. We can visualize them by opening the .svg files in a web browser.

The results then look like this (every point denotes an entry which might be nonzero; of course the fact whether the entry actually is zero or not depends on the equation under consideration, but the indicated positions in the matrix tell us which shape functions can and which can't couple when discretizing a local, i.e. differential, equation):

The different regions in the left picture, indicated by kinks in the lines and single dots on the left and top, represent the degrees of freedom on the different refinement levels of the triangulation. As can be seen in the right picture, the sparsity pattern is much better clustered around the main diagonal of the matrix after renumbering. Although this might not be apparent, the number of nonzero entries is the same in both pictures, of course.

### Possible extensions

Just as with step-1, you may want to play with the program a bit to familiarize yourself with deal.II. For example, in the distribute_dofs function, we use linear finite elements (that's what the argument "1" to the FE_Q object is). Explore how the sparsity pattern changes if you use higher order elements, for example cubic or quintic ones (by using 3 and 5 as the respective arguments).

Or, you could see how the sparsity pattern changes with more refinements. You will see that not only the size of the matrix changes, but also its bandwidth (the distance from the diagonal of those nonzero elements of the matrix that are farthest away from the diagonal), though the ratio of bandwidth to size typically shrinks, i.e. the matrix clusters more around the diagonal.

Another idea of experiments would be to try other renumbering strategies than Cuthill-McKee from the DoFRenumbering namespace and see how they affect the sparsity pattern.

You can also visualize the output using GNUPLOT (one of the simpler visualization programs; maybe not the easiest to use since it is command line driven, but also universally available on all Linux and other Unix-like systems) by changing from print_svg() to print_gnuplot() in distribute_dofs() and renumber_dofs():

examples/step-2> gnuplot
G N U P L O T
Version 3.7 patchlevel 3
System: Linux 2.6.11.4-21.10-default
Copyright(C) 1986 - 1993, 1998 - 2002
Thomas Williams, Colin Kelley and many others
Type help to access the on-line reference manual
The gnuplot FAQ is available from
http://www.gnuplot.info/gnuplot-faq.html
Send comments and requests for help to <info-gnuplot@dartmouth.edu>
Send bugs, suggestions and mods to <bug-gnuplot@dartmouth.edu>
Terminal type set to 'x11'
gnuplot> set style data points
gnuplot> plot "sparsity_pattern.1"

# The plain program

/* ---------------------------------------------------------------------
*
* Copyright (C) 1999 - 2019 by the deal.II authors
*
* This file is part of the deal.II library.
*
* The deal.II library is free software; you can use it, redistribute
* it, and/or modify it under the terms of the GNU Lesser General
* version 2.1 of the License, or (at your option) any later version.
* The full text of the license can be found in the file LICENSE.md at
* the top level directory of deal.II.
*
* ---------------------------------------------------------------------
*
* Author: Wolfgang Bangerth, University of Heidelberg, 1999
*/
#include <deal.II/grid/tria.h>
#include <deal.II/grid/tria_accessor.h>
#include <deal.II/grid/tria_iterator.h>
#include <deal.II/grid/grid_generator.h>
#include <deal.II/grid/manifold_lib.h>
#include <deal.II/dofs/dof_handler.h>
#include <deal.II/fe/fe_q.h>
#include <deal.II/dofs/dof_tools.h>
#include <deal.II/lac/sparse_matrix.h>
#include <deal.II/lac/dynamic_sparsity_pattern.h>
#include <deal.II/dofs/dof_renumbering.h>
#include <fstream>
using namespace dealii;
void make_grid(Triangulation<2> &triangulation)
{
const Point<2> center(1, 0);
for (unsigned int step = 0; step < 3; ++step)
{
for (auto &cell : triangulation.active_cell_iterators())
for (unsigned int v = 0; v < GeometryInfo<2>::vertices_per_cell; ++v)
{
const double distance_from_center =
center.distance(cell->vertex(v));
if (std::fabs(distance_from_center - inner_radius) < 1e-10)
{
cell->set_refine_flag();
break;
}
}
}
}
void distribute_dofs(DoFHandler<2> &dof_handler)
{
const FE_Q<2> finite_element(1);
dof_handler.distribute_dofs(finite_element);
DynamicSparsityPattern dynamic_sparsity_pattern(dof_handler.n_dofs(),
dof_handler.n_dofs());
DoFTools::make_sparsity_pattern(dof_handler, dynamic_sparsity_pattern);
SparsityPattern sparsity_pattern;
sparsity_pattern.copy_from(dynamic_sparsity_pattern);
std::ofstream out("sparsity_pattern1.svg");
sparsity_pattern.print_svg(out);
}
void renumber_dofs(DoFHandler<2> &dof_handler)
{
DynamicSparsityPattern dynamic_sparsity_pattern(dof_handler.n_dofs(),
dof_handler.n_dofs());
DoFTools::make_sparsity_pattern(dof_handler, dynamic_sparsity_pattern);
SparsityPattern sparsity_pattern;
sparsity_pattern.copy_from(dynamic_sparsity_pattern);
std::ofstream out("sparsity_pattern2.svg");
sparsity_pattern.print_svg(out);
}
int main()
{
Triangulation<2> triangulation;
make_grid(triangulation);
DoFHandler<2> dof_handler(triangulation);
distribute_dofs(dof_handler);
renumber_dofs(dof_handler);
}