Hans Petter Langtangen, Anders Logg

Solving PDEs in Minutes

The FEniCS Tutorial Volume I
Apr 5, 2017

Springer

Center for Biomedical Computing, Simula Research Laboratory and Department of

Informatics, University of Oslo.

Email: logg@chalmers.se. Department of Mathematical Sciences, Chalmers University

of Technology; Center for Biomedical Computing, Simula Research Laboratory; and
Computational Engineering and Design, Fraunhofer-Chalmers Centre.
Contents

Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

1 Preliminaries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.1 The FEniCS Project . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.2 What you will learn . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
1.3 Working with this tutorial . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
1.4 Obtaining the software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
1.4.1 Installation using Docker containers . . . . . . . . . . . . . . . . 6
1.4.2 Installation using Ubuntu packages . . . . . . . . . . . . . . . . . 7
1.4.3 Testing your installation . . . . . . . . . . . . . . . . . . . . . . . . . . 8
1.5 Obtaining the tutorial examples . . . . . . . . . . . . . . . . . . . . . . . . . . 8
1.6 Background knowledge . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
1.6.1 Programming in Python . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
1.6.2 The finite element method . . . . . . . . . . . . . . . . . . . . . . . . . 9

2 Fundamentals: Solving the Poisson equation . . . . . . . . . . . . . . 11

2.1 Mathematical problem formulation . . . . . . . . . . . . . . . . . . . . . . . 11
2.1.1 Finite element variational formulation . . . . . . . . . . . . . . . 12
2.1.2 Abstract finite element variational formulation . . . . . . . 15
2.1.3 Choosing a test problem . . . . . . . . . . . . . . . . . . . . . . . . . . 16
2.2 FEniCS implementation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
2.2.1 The complete program . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
2.2.2 Running the program . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
2.3 Dissection of the program . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
2.3.1 The important first line . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
2.3.2 Generating simple meshes . . . . . . . . . . . . . . . . . . . . . . . . . 20
2.3.3 Defining the finite element function space . . . . . . . . . . . 20
2.3.4 Defining the trial and test functions . . . . . . . . . . . . . . . . 20
2.3.5 Defining the boundary conditions . . . . . . . . . . . . . . . . . . . 21
2.3.6 Defining the source term . . . . . . . . . . . . . . . . . . . . . . . . . . 24
2.3.7 Defining the variational problem . . . . . . . . . . . . . . . . . . . 24

c 2017, Hans Petter Langtangen, Anders Logg.
Released under CC Attribution 4.0 license
vi Contents

2.3.8 Forming and solving the linear system . . . . . . . . . . . . . . 25

2.3.9 Plotting the solution using the plot command . . . . . . . 25
2.3.10 Plotting the solution using ParaView . . . . . . . . . . . . . . . 27
2.3.11 Computing the error . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
2.3.12 Examining degrees of freedom and vertex values . . . . . . 29
2.4 Deflection of a membrane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
2.4.1 Scaling the equation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
2.4.2 Defining the mesh . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
2.4.3 Defining the load . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
2.4.4 Defining the variational problem . . . . . . . . . . . . . . . . . . . 33
2.4.5 Plotting the solution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
2.4.6 Making curve plots through the domain . . . . . . . . . . . . . 34

3 A Gallery of finite element solvers . . . . . . . . . . . . . . . . . . . . . . . . 37

3.1 The heat equation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
3.1.1 PDE problem . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
3.1.2 Variational formulation . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
3.1.3 FEniCS implementation . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
3.2 A nonlinear Poisson equation . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
3.2.1 PDE problem . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
3.2.2 Variational formulation . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
3.2.3 FEniCS implementation . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
3.3 The equations of linear elasticity . . . . . . . . . . . . . . . . . . . . . . . . . 50
3.3.1 PDE problem . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
3.3.2 Variational formulation . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
3.3.3 FEniCS implementation . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
3.4 The NavierStokes equations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
3.4.1 PDE problem . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
3.4.2 Variational formulation . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
3.4.3 FEniCS implementation . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
3.5 A system of advectiondiffusionreaction equations . . . . . . . . . 73
3.5.1 PDE problem . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
3.5.2 Variational formulation . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
3.5.3 FEniCS implementation . . . . . . . . . . . . . . . . . . . . . . . . . . . 76

4 Subdomains and boundary conditions . . . . . . . . . . . . . . . . . . . . . 83

4.1 Combining Dirichlet and Neumann conditions . . . . . . . . . . . . . . 83
4.1.1 PDE problem . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
4.1.2 Variational formulation . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
4.1.3 FEniCS implementation . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
4.2 Setting multiple Dirichlet conditions . . . . . . . . . . . . . . . . . . . . . . 86
4.3 Defining subdomains for different materials . . . . . . . . . . . . . . . . 87
4.3.1 Using expressions to define subdomains . . . . . . . . . . . . . 88
4.3.2 Using mesh functions to define subdomains . . . . . . . . . . 88
4.3.3 Using C++ code snippets to define subdomains . . . . . . 91
Contents vii

4.4 Setting multiple Dirichlet, Neumann, and Robin conditions . . 92

4.4.1 Three types of boundary conditions . . . . . . . . . . . . . . . . . 93
4.4.2 PDE problem . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
4.4.3 Variational formulation . . . . . . . . . . . . . . . . . . . . . . . . . . . 94
4.4.4 FEniCS implementation . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
4.4.5 Test problem . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97
4.4.6 Debugging boundary conditions . . . . . . . . . . . . . . . . . . . . 98
4.5 Generating meshes with subdomains . . . . . . . . . . . . . . . . . . . . . . 99
4.5.1 PDE problem . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100
4.5.2 Variational formulation . . . . . . . . . . . . . . . . . . . . . . . . . . . 102
4.5.3 FEniCS implementation . . . . . . . . . . . . . . . . . . . . . . . . . . . 102

5 Extensions: Improving the Poisson solver . . . . . . . . . . . . . . . . . 109

5.1 Refactoring the Poisson solver . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109
5.1.1 A more general solver function . . . . . . . . . . . . . . . . . . . . . 110
5.1.2 Writing the solver as a Python module . . . . . . . . . . . . . . 111
5.1.3 Verification and unit tests . . . . . . . . . . . . . . . . . . . . . . . . . 111
5.1.4 Parameterizing the number of space dimensions . . . . . . 114
5.2 Working with linear solvers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
5.2.1 Choosing a linear solver and preconditioner . . . . . . . . . . 115
5.2.2 Choosing a linear algebra backend . . . . . . . . . . . . . . . . . . 115
5.2.3 Setting solver parameters . . . . . . . . . . . . . . . . . . . . . . . . . . 116
5.2.4 An extended solver function . . . . . . . . . . . . . . . . . . . . . . . 117
5.2.5 A remark regarding unit tests . . . . . . . . . . . . . . . . . . . . . . 117
5.2.6 List of linear solver methods and preconditioners . . . . . 117
5.3 High-level and low-level solver interfaces . . . . . . . . . . . . . . . . . . . 118
5.3.1 Linear variational problem and solver objects . . . . . . . . 118
5.3.2 Explicit assembly and solve . . . . . . . . . . . . . . . . . . . . . . . . 119
5.3.3 Examining matrix and vector values . . . . . . . . . . . . . . . . 122
5.4 Degrees of freedom and function evaluation . . . . . . . . . . . . . . . . 123
5.4.1 Examining the degrees of freedom . . . . . . . . . . . . . . . . . . 123
5.4.2 Setting the degrees of freedom . . . . . . . . . . . . . . . . . . . . . 125
5.4.3 Function evaluation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126
5.5 Postprocessing computations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127
5.5.1 Test problem . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127
5.5.2 Flux computations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 128
5.5.3 Computing functionals . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130
5.5.4 Computing convergence rates . . . . . . . . . . . . . . . . . . . . . . 132
5.5.5 Taking advantage of structured mesh data . . . . . . . . . . . 136
5.6 Taking the next step . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141

References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143
viii Contents

Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145
Preface

This book gives a concise and gentle introduction to finite element program-
ming in Python based on the popular FEniCS software library. FEniCS can
be programmed in both C++ and Python, but this tutorial focuses exclu-
sively on Python programming, since this is the simplest and most effective
approach for beginners. After having digested the examples in this tutorial,
the reader should be able to learn more from the FEniCS documentation, the
numerous demo programs that come with the software, and the comprehen-
sive FEniCS book Automated Solution of Differential Equations by the Finite
Element Method [26]. This tutorial is a further development of the opening
chapter in [26].
We thank Johan Hake, Kent-Andre Mardal, and Kristian Valen-Sendstad
for many helpful discussions during the preparation of the first version of this
tutorial for the FEniCS book [26]. We are particularly thankful to Professor
Douglas Arnold for very valuable feedback on early versions of the text. ys-
tein Srensen pointed out numerous typos and contributed with many helpful
comments. Many errors and typos were also reported by Mauricio Ange-
les, Ida Drsdal, Miroslav Kuchta, Hans Ekkehard Plesser, Marie Rognes,
Hans Joachim Scroll, Glenn Terje Lines, Simon Funke, Matthew Moelter,
and Magne Nordaas. Ekkehard Ellmann as well as two anonymous reviewers
provided a series of suggestions and improvements. Special thanks go to Ben-
jamin Kehlet for all his work with the mshr tool and for quickly implementing
our requests for this tutorial.
Comments and corrections can be reported as issues for the Git repository
of this book1 , or via email to logg@chalmers.se.

Oslo and Smgen, November 2016 Hans Petter Langtangen, Anders Logg

1
https://github.com/hplgit/fenics-tutorial/

c 2017, Hans Petter Langtangen, Anders Logg.
Released under CC Attribution 4.0 license
Chapter 1
Preliminaries

1.1 The FEniCS Project

The FEniCS Project is a research and software project aimed at creating
mathematical methods and software for automated computational mathe-
matical modeling. This means creating easy, intuitive, efficient, and flexible
software for solving partial differential equations (PDEs) using finite element
methods. FEniCS was initially created in 2003 and is developed in collabo-
ration between researchers from a number of universities and research insti-
tutes around the world. For more information about FEniCS and the latest
updates of the FEniCS software and this tutorial, visit the FEniCS web page
at https://fenicsproject.org.
FEniCS consists of a number of building blocks (software components)
that together form the FEniCS software: DOLFIN [27], FFC [17], FIAT [16],
UFL [1], mshr, and a few others. For an overview, see [26]. FEniCS users
rarely need to think about this internal organization of FEniCS, but since
even casual users may sometimes encounter the names of various FEniCS
components, we briefly list the components and their main roles in FEniCS.
DOLFIN is the computational high-performance C++ backend of FEniCS.
DOLFIN implements data structures such as meshes, function spaces and
functions, compute-intensive algorithms such as finite element assembly and
mesh refinement, and interfaces to linear algebra solvers and data structures
such as PETSc. DOLFIN also implements the FEniCS problem-solving en-
vironment in both C++ and Python. FFC is the code generation engine of
FEniCS (the form compiler), responsible for generating efficient C++ code
from high-level mathematical abstractions. FIAT is the finite element back-
end of FEniCS, responsible for generating finite element basis functions, UFL
implements the abstract mathematical language by which users may express
variational problems, and mshr provides FEniCS with mesh generation ca-
pabilities.

c 2017, Hans Petter Langtangen, Anders Logg.
Released under CC Attribution 4.0 license
4 1 Preliminaries

1.2 What you will learn

The goal of this tutorial is to demonstrate how to apply the finite element to
solve PDEs in FEniCS. Through a series of examples, we demonstrate how
to:
solve linear PDEs (such as the Poisson equation),
solve time-dependent PDEs (such as the heat equation),
solve nonlinear PDEs,
solve systems of time-dependent nonlinear PDEs.
Important topics involve how to set boundary conditions of various types
(Dirichlet, Neumann, Robin), how to create meshes, how to define variable
coefficients, how to interact with linear and nonlinear solvers, and how to
postprocess and visualize solutions.
We will also discuss how to best structure the Python code for a PDE
solver, how to debug programs, and how to take advantage of testing frame-
works.

1.3 Working with this tutorial

The mathematics of the illustrations is kept simple to better focus on FEniCS
functionality and syntax. This means that we mostly use the Poisson equation
and the time-dependent diffusion equation as model problems, often with
input data adjusted such that we get a very simple solution that can be
exactly reproduced by any standard finite element method over a uniform,
structured mesh. This latter property greatly simplifies the verification of the
implementations. Occasionally we insert a physically more relevant example
to remind the reader that the step from solving a simple model problem to a
challenging real-world problem is often quite short and easy with FEniCS.
Using FEniCS to solve PDEs may seem to require a thorough understand-
ing of the abstract mathematical framework of the finite element method
as well as expertise in Python programming. Nevertheless, it turns out that
many users are able to pick up the fundamentals of finite elements and Python
programming as they go along with this tutorial. Simply keep on reading and
try out the examples. You will be amazed at how easy it is to solve PDEs
with FEniCS!
1.4 Obtaining the software 5

1.4 Obtaining the software

Working with this tutorial obviously requires access to the FEniCS software.
FEniCS is a complex software library, both in itself and due to its many de-
pendencies to state-of-the-art open-source scientific software libraries. Man-
ually building FEniCS and all its dependencies from source can thus be a
daunting task. Even for an expert who knows exactly how to configure and
build each component, a full build can literally take hours! In addition to the
complexity of the software itself, there is an additional layer of complexity in
how many different kinds of operating systems (Linux, Mac, Windows) may
be running on a users laptop or compute server, with different requirements
for how to configure and build software.
For this reason, the FEniCS Project provides prebuilt packages to make
the installation easy, fast, and foolproof.

FEniCS download and installation

In this tutorial, we highlight two main options for installing the FEniCS
software: Docker containers and Ubuntu packages. While the Docker
containers work on all operating systems, the Ubuntu packages only
work on Ubuntu-based systems. Note that the built-in FEniCS plotting
does currently not work from Docker, although rudimentary plotting is
supported via the Docker Jupyter notebook option.
FEniCS may also be installed using other methods, including Conda
packages and building from source. For more installation options and
the latest information on the simplest and best options for installing
FEniCS, check out the official FEniCS installation instructions. These
can be found at https://fenicsproject.org/download.

FEniCS version: 2016.2

FEniCS versions are labeled 2016.1, 2016.2, 2017.1 and so on, where the
major number indicates the year of release and the minor number is a
counter starting at 1. The number of releases per year varies but typi-
cally one can expect 23 releases per year. This tutorial was prepared
for and tested with FEniCS version 2016.2.
6 1 Preliminaries

1.4.1 Installation using Docker containers

A modern solution to the challenge of software installation on diverse soft-

ware platforms is to use so-called containers. The FEniCS Project pro-
vides custom-made containers that are controlled, consistent, and high-
performance software environments for FEniCS programming. FEniCS con-
tainers work equally well1 on all operating systems, including Linux, Mac,
and Windows.
To use FEniCS containers, you must first install the Docker platform.
Docker installation is simple and instructions are available on the Docker
web page2 . Once you have installed Docker, just copy the following line into
a terminal window:
Terminal

Terminal> curl -s https://get.fenicsproject.org | bash

The command above will install the program fenicsproject on your sys-
tem. This program lets you easily create FEniCS sessions (containers) on
your system:
Terminal

Terminal> fenicsproject run

This command has several useful options, such as easily switching between
the latest release of FEniCS, the latest development version and many more.
To learn more, type fenicsproject help. FEniCS can also be used directly
with Docker, but this typically requires typing a relatively complex Docker
command, for example:
Terminal

docker run --rm -ti -v pwd:/home/fenics/shared -w

/home/fenics/shared quay.io/fenicsproject/stable:current /bin/bash -l
-c "export TERM=xterm; bash -i"

Sharing files with FEniCS containers

When you run a FEniCS session using fenicsproject run, it will au-
tomatically share your current working directory (the directory from

1
Running Docker containers on Mac and Windows involves a small performance over-
head compared to running Docker containers on Linux. However, this performance
penalty is typically small and is often compensated for by using the highly tuned and
optimized version of FEniCS that comes with the official FEniCS containers, compared
to building FEniCS and its dependencies from source on Mac or Windows.
2
https://www.docker.com
1.4 Obtaining the software 7

which you run the fenicsproject command) with the FEniCS ses-
sion. When the FEniCS session starts, it will automatically enter into
a directory named shared which will be identical with your current
working directory on your host system. This means that you can eas-
ily edit files and write data inside the FEniCS session, and the files
will be directly accessible on your host system. It is recommended that
you edit your programs using your favorite editor (such as Emacs or
Vim) on your host system and use the FEniCS session only to run your
program(s).

1.4.2 Installation using Ubuntu packages

For users of Ubuntu GNU/Linux, FEniCS can also be installed easily via the
standard Ubuntu package manager apt-get. Just copy the following lines
into a terminal window:
Terminal

Terminal> sudo add-apt-repository ppa:fenics-packages/fenics

Terminal> sudo apt-get update
Terminal> sudo apt-get install fenics
Terminal> sudo apt-get dist-upgrade

This will add the FEniCS package archive (PPA) to your Ubuntu com-
puters list of software sources and then install FEniCS. It will will also
automatically install packages for dependencies of FEniCS.

Watch out for old packages!

In addition to being available from the FEniCS PPA, the FEniCS soft-
ware is also part of the official Ubuntu repositories. However, depending
on which release of Ubuntu you are running, and when this release was
created in relation to the latest FEniCS release, the official Ubuntu
repositories might contain an outdated version of FEniCS. For this rea-
son, it is better to install from the FEniCS PPA.
8 1 Preliminaries

1.4.3 Testing your installation

Once you have installed FEniCS, you should make a quick test to see that
your installation works properly. To do this, type the following command in
a FEniCS-enabled3 terminal:
Terminal

Terminal> python -c import fenics

If all goes well, you should be able to run this command without any error
message (or any other output).

1.5 Obtaining the tutorial examples

In this tutorial, you will learn finite element and FEniCS programming
through a number of example programs that demonstrate both how to solve
particular PDEs using the finite element method, how to program solvers in
FEniCS, and how to create well-designed Python code that can later be ex-
tended to solve more complex problems. All example programs are available
from the web page of this book at https://fenicsproject.org/tutorial.
The programs as well as the source code for this text can also be accessed
directly from the Git repository4 for this book.

1.6 Background knowledge

1.6.1 Programming in Python

While you can likely pick up basic Python programming by working through
the examples in this tutorial, you may want to study additional material
on the Python language. A natural starting point for beginners is the classic
Python Tutorial [11], or a tutorial geared towards scientific computing [22]. In
the latter, you will also find pointers to other tutorials for scientific computing
in Python. Among ordinary books we recommend the general introduction
Dive into Python [28] as well as texts that focus on scientific computing with
Python [15, 1821].

3
For users of FEniCS containers, this means first running the command fenicsproject
run.
4
https://github.com/hplgit/fenics-tutorial/
1.6 Background knowledge 9

Python versions
Python comes in two versions, 2 and 3, and these are not compatible.
FEniCS works with both versions of Python. All the programs in this
tutorial are also developed such that they can be run under both Python
2 and 3. Python programs that need to print must then start with
from __future__ import print_function

to enable the print function from Python 3 in Python 2. All use of

print in the programs in this tutorial consists of function calls, like
print(a:, a). Almost all other constructions are of a form that
looks the same in Python 2 and 3.

1.6.2 The finite element method

Many good books have been written on the finite element method. The books
typically fall in either of two categories: the abstract mathematical version
of the method or the engineering structural analysis formulation. FEniCS
builds heavily on concepts from the abstract mathematical exposition. The
first author has a book5 [24] in development that explains all details of the
finite element method in an intuitive way, using the abstract mathematical
formulations that FEniCS employs.
The finite element text by Larson and Bengzon [25] is our recommended
introduction to the finite element method, with a mathematical notation
that goes well with FEniCS. An easy-to-read book, which also provides a
good general background for using FEniCS, is Gockenbach [12]. The book
by Donea and Huerta [8] has a similar style, but aims at readers with an
interest in fluid flow problems. Hughes [14] is also recommended, especially
for readers interested in solid mechanics and heat transfer applications.
Readers with a background in the engineering structural analysis version
of the finite element method may find Bickford [3] an attractive bridge over to
the abstract mathematical formulation that FEniCS builds upon. Those who
have a weak background in differential equations in general should consult
a more fundamental book, and Eriksson et al [9] is a very good choice. On
the other hand, FEniCS users with a strong background in mathematics will
appreciate the texts by Brenner and Scott [5], Braess [4], Ern and Guermond
[10], Quarteroni and Valli [29], or Ciarlet [7].

5
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Chapter 2
Fundamentals: Solving the Poisson
equation

The goal of this chapter is to show how the Poisson equation, the most basic of
all PDEs, can be quickly solved with a few lines of FEniCS code. We introduce
the most fundamental FEniCS objects such as Mesh, Function, FunctionSpace,
TrialFunction, and TestFunction, and learn how to write a basic PDE solver,
including how to formulate the mathematical variational problem, apply boundary
conditions, call the FEniCS solver, and plot the solution.

2.1 Mathematical problem formulation

Many books on programming languages start with a Hello, World! program.
Readers are curious to know how fundamental tasks are expressed in the
language, and printing a text to the screen can be such a task. In the world
of finite element methods for PDEs, the most fundamental task must be to
solve the Poisson equation. Our counterpart to the classical Hello, World!
program therefore solves the following boundary-value problem:

2 u(x) = f (x), x in , (2.1)

u(x) = uD (x), x on . (2.2)

Here, u = u(x) is the unknown function, f = f (x) is a prescribed function,

2 is the Laplace operator (often written as ), is the spatial domain,
and is the boundary of . The Poisson problem, including both the
PDE 2 u = f and the boundary condition u = uD on , is an example
of a boundary-value problem, which must be precisely stated before it makes
sense to start solving it with FEniCS.
In two space dimensions with coordinates x and y, we can write out the
Poisson equation as

c 2017, Hans Petter Langtangen, Anders Logg.
Released under CC Attribution 4.0 license
12 2 Fundamentals: Solving the Poisson equation

2u 2u
= f (x, y) . (2.3)
x2 y 2
The unknown u is now a function of two variables, u = u(x, y), defined over
a two-dimensional domain .
The Poisson equation arises in numerous physical contexts, including heat
conduction, electrostatics, diffusion of substances, twisting of elastic rods, in-
viscid fluid flow, and water waves. Moreover, the equation appears in numer-
ical splitting strategies for more complicated systems of PDEs, in particular
the NavierStokes equations.
Solving a boundary-value problem such as the Poisson equation in FEniCS
consists of the following steps:
1. Identify the computational domain (), the PDE, its boundary conditions,
and source terms (f ).
2. Reformulate the PDE as a finite element variational problem.
3. Write a Python program which defines the computational domain, the
variational problem, the boundary conditions, and source terms, using the
corresponding FEniCS abstractions.
4. Call FEniCS to solve the boundary-value problem and, optionally, extend
the program to compute derived quantities such as fluxes and averages,
and visualize the results.
We shall now go through steps 24 in detail. The key feature of FEniCS is
that steps 3 and 4 result in fairly short code, while a similar program in most
other software frameworks for PDEs require much more code and technically
difficult programming.

What makes FEniCS attractive?

Although many software frameworks have a really elegant Hello,
World! example for the Poisson equation, FEniCS is to our knowl-
edge the only framework where the code stays compact and nice, very
close to the mathematical formulation, even when the mathematical
and algorithmic complexity increases and when moving from a laptop
to a high-performance compute server (cluster).

2.1.1 Finite element variational formulation

FEniCS is based on the finite element method, which is a general and efficient
mathematical machinery for the numerical solution of PDEs. The starting
point for the finite element methods is a PDE expressed in variational form.
Readers who are not familiar with variational problems will get a very brief
introduction to the topic in this tutorial, but reading a proper book on the
2.1 Mathematical problem formulation 13

finite element method in addition is encouraged. Section 1.6.2 contains a list

of recommended books. Experience shows that you can work with FEniCS as
a tool to solve PDEs even without thorough knowledge of the finite element
method, as long as you get somebody to help you with formulating the PDE
as a variational problem.
The basic recipe for turning a PDE into a variational problem is to multiply
the PDE by a function v, integrate the resulting equation over the domain ,
and perform integration by parts of terms with second-order derivatives. The
function v which multiplies the PDE is called a test function. The unknown
function u to be approximated is referred to as a trial function. The terms
trial and test functions are used in FEniCS programs too. The trial and
test functions belong to certain so-called function spaces that specify the
properties of the functions.
In the present case, we first multiply the Poisson equation by the test
function v and integrate over :
Z Z
(2 u)v dx = f v dx . (2.4)

We here let dx denote the differential element for integration over the domain
. We will later let ds denote the differential element for integration over
the boundary of .
A common rule when we derive variational formulations is that we try to
keep the order of the derivatives of u and v as small as possible. Here, we
have a second-order spatial derivative of u, which can be transformed to a
first-derivative of u and v by applying the technique of integration by parts1 .
The formula reads
Z Z Z
2 u
( u)v dx = u v dx v ds, (2.5)
n
u
where n = u n is the derivative of u in the outward normal direction n
on the boundary.
Another feature of variational formulations is that the test function v is
required to vanish on the parts of the boundary where the solution u is known
(the book [24] explains in detail why this requirement is necessary). In the
present problem, this means that v = 0 on the whole boundary . The
second term on the right-hand side of (2.5) therefore vanishes. From (2.4)
and (2.5) it follows that
Z Z
u v dx = f v dx . (2.6)

If we require that this equation holds for all test functions v in some suit-
able space V , the so-called test space, we obtain a well-defined mathematical
problem that uniquely determines the solution u which lies in some (possi-
1
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14 2 Fundamentals: Solving the Poisson equation

bly different) function space V , the so-called trial space. We refer to (2.6) as
the weak form or variational form of the original boundary-value problem
(2.1)(2.2).
The proper statement of our variational problem now goes as follows: find
u V such that
Z Z
u v dx = f v dx v V . (2.7)

The trial and test spaces V and V are in the present problem defined as

V = {v H 1 () : v = uD on },
V = {v H 1 () : v = 0 on } .

In short, H 1 () is the mathematically well-known Sobolev space containing

functions v such that v 2 and |v|2 have finite integrals over (essentially
meaning that the functions are continuous). The solution of the underlying
PDE must lie in a function space where the derivatives are also continuous,
but the Sobolev space H 1 () allows functions with discontinuous derivatives.
This weaker continuity requirement of u in the variational statement (2.7), as
a result of the integration by parts, has great practical consequences when it
comes to constructing finite element function spaces. In particular, it allows
the use of piecewise polynomial function spaces; i.e., function spaces con-
structed by stitching together polynomial functions on simple domains such
as intervals, triangles, or tetrahedrons.
The variational problem (2.7) is a continuous problem: it defines the solu-
tion u in the infinite-dimensional function space V . The finite element method
for the Poisson equation finds an approximate solution of the variational prob-
lem (2.7) by replacing the infinite-dimensional function spaces V and V by
discrete (finite-dimensional) trial and test spaces Vh V and Vh V . The
discrete variational problem reads: find uh Vh V such that
Z Z
uh v dx = f v dx v Vh V . (2.8)

This variational problem, together with a suitable definition of the func-
tion spaces Vh and Vh , uniquely define our approximate numerical solution
of Poissons equation (2.1). Note that the boundary conditions are encoded
as part of the trial and test spaces. The mathematical framework may seem
complicated at first glance, but the good news is that the finite element vari-
ational problem (2.8) looks the same as the continuous variational problem
(2.7), and FEniCS can automatically solve variational problems like (2.8)!
2.1 Mathematical problem formulation 15

What we mean by the notation u and V

The mathematics literature on variational problems writes uh for the
solution of the discrete problem and u for the solution of the continu-
ous problem. To obtain (almost) a one-to-one relationship between the
mathematical formulation of a problem and the corresponding FEniCS
program, we shall drop the subscript h and use u for the solution of the
discrete problem. We will use ue for the exact solution of the continuous
problem, if we need to explicitly distinguish between the two. Similarly,
we will let V denote the discrete finite element function space in which
we seek our solution.

2.1.2 Abstract finite element variational formulation

It turns out to be convenient to introduce the following canonical notation

for variational problems: find u V such that

a(u, v) = L(v) v V . (2.9)

For the Poisson equation, we have:

Z
a(u, v) = u v dx, (2.10)
Z
L(v) = f v dx . (2.11)

From the mathematics literature, a(u, v) is known as a bilinear form and

L(v) as a linear form. We shall, in every linear problem we solve, identify the
terms with the unknown u and collect them in a(u, v), and similarly collect
all terms with only known functions in L(v). The formulas for a and L can
then be expressed directly in our FEniCS programs.
To solve a linear PDE in FEniCS, such as the Poisson equation, a user
thus needs to perform only two steps:
Choose the finite element spaces V and V by specifying the domain (the
mesh) and the type of function space (polynomial degree and type).
Express the PDE as a (discrete) variational problem: find u V such that
a(u, v) = L(v) for all v V .
16 2 Fundamentals: Solving the Poisson equation

2.1.3 Choosing a test problem

The Poisson problem (2.1)(2.2) has so far featured a general domain and
general functions uD for the boundary conditions and f for the right-hand
side. For our first implementation we will need to make specific choices for
, uD , and f . It will be wise to construct a problem with a known analytical
solution so that we can easily check that the computed solution is correct.
Solutions that are lower-order polynomials are primary candidates. Standard
finite element function spaces of degree r will exactly reproduce polynomials
of degree r. And piecewise linear elements (r = 1) are able to exactly repro-
duce a quadratic polynomial on a uniformly partitioned mesh. This important
result can be used to verify our implementation. We just manufacture some
quadratic function in 2D as the exact solution, say

ue (x, y) = 1 + x2 + 2y 2 . (2.12)
By inserting (2.12) into the Poisson equation (2.1), we find that ue (x, y) is a
solution if

f (x, y) = 6, uD (x, y) = ue (x, y) = 1 + x2 + 2y 2 ,

regardless of the shape of the domain as long as ue is prescribed along the
boundary. We choose here, for simplicity, the domain to be the unit square,

= [0, 1] [0, 1] .
This simple but very powerful method for constructing test problems is called
the method of manufactured solutions: pick a simple expression for the exact
solution, plug it into the equation to obtain the right-hand side (source term
f ), then solve the equation with this right-hand side and using the exact
solution as a boundary condition, and try to reproduce the exact solution.

Tip: Try to verify your code with exact numerical solutions!

A common approach to testing the implementation of a numerical
method is to compare the numerical solution with an exact analyti-
cal solution of the test problem and conclude that the program works if
the error is small enough. Unfortunately, it is impossible to tell if an
error of size 105 on a 20 20 mesh of linear elements is the expected
(in)accuracy of the numerical approximation or if the error also contains
the effect of a bug in the code. All we usually know about the numerical
error is its asymptotic properties, for instance that it is proportional to
h2 if h is the size of a cell in the mesh. Then we compare the error
on meshes with different h-values to see if the asymptotic behavior is
correct. This is a very powerful verification technique and is explained
2.2 FEniCS implementation 17

in detail in Section 5.5.4. However, if we have a test problem for which

we know that there should be no approximation errors, we know that
the analytical solution of the PDE problem should be reproduced to
machine precision by the program. That is why we emphasize this kind
of test problems throughout this tutorial. Typically, elements of degree
r can reproduce polynomials of degree r exactly, so this is the start-
ing point for constructing a solution without numerical approximation
errors.

2.2 FEniCS implementation

2.2.1 The complete program

A FEniCS program for solving our test problem for the Poisson equation in
2D with the given choices of , uD , and f may look as follows:
from fenics import *

# Create mesh and define function space

mesh = UnitSquareMesh(8, 8)
V = FunctionSpace(mesh, P, 1)

# Define boundary condition

u_D = Expression(1 + x[0]*x[0] + 2*x[1]*x[1], degree=2)

def boundary(x, on_boundary):

return on_boundary

bc = DirichletBC(V, u_D, boundary)

# Define variational problem

u = TrialFunction(V)
v = TestFunction(V)
f = Constant(-6.0)
a = dot(grad(u), grad(v))*dx
L = f*v*dx

# Compute solution
u = Function(V)
solve(a == L, u, bc)

# Plot solution and mesh

plot(u)
plot(mesh)

# Save solution to file in VTK format

vtkfile = File(poisson/solution.pvd)
vtkfile << u
18 2 Fundamentals: Solving the Poisson equation

# Compute error in L2 norm

error_L2 = errornorm(u_D, u, L2)

# Compute maximum error at vertices

vertex_values_u_D = u_D.compute_vertex_values(mesh)
vertex_values_u = u.compute_vertex_values(mesh)
import numpy as np
error_max = np.max(np.abs(vertex_values_u_D - vertex_values_u))

# Print errors
print(error_L2 =, error_L2)
print(error_max =, error_max)

# Hold plot
interactive()

This example program can be found in the file ft01_poisson.py.

2.2.2 Running the program

The FEniCS program must be available in a plain text file, written with a
text editor such as Atom, Sublime Text, Emacs, Vim, or similar. There are
several ways to run a Python program like ft01_poisson.py:
Use a terminal window.
Use an integrated development environment (IDE), e.g., Spyder.
Use a Jupyter notebook.

Terminal window. Open a terminal window, move to the directory con-

taining the program and type the following command:
Terminal

Terminal> python ft01_poisson.py

Note that this command must be run in a FEniCS-enabled terminal. For

users of the FEniCS Docker containers, this means that you must type this
command after you have started a FEniCS session using fenicsproject run
or fenicsproject start.
When running the above command, FEniCS will run the program to com-
pute the approximate solution u. The approximate solution u will be com-
pared to the exact solution ue = uD and the error in the L2 and maximum
norms will be printed. Since we know that our approximate solution should
reproduce the exact solution to within machine precision, this error should be
small, something on the order of 1015 . If plotting is enabled in your FEniCS
installation, then a window with a simple plot of the solution will appear as
in Figure 2.1.
2.3 Dissection of the program 19

Spyder. Many prefer to work in an integrated development environment

that provides an editor for programming, a window for executing code, a
window for inspecting objects, etc. Just open the file ft01_poisson.py and
press the play button to run it. We refer to the Spyder tutorial to learn more
about working in the Spyder environment. Spyder is highly recommended if
you are used to working in the graphical MATLAB environment.
Jupyter notebooks. Notebooks make it possible to mix text and executable
code in the same document, but you can also just use it to run programs in a
web browser. Run the command jupyter notebook from a terminal window,
find the New pulldown menu in the upper right corner of the GUI, choose
a new notebook in Python 2 or 3, write %load ft01_poisson.py in the
blank cell of this notebook, then press Shift+Enter to execute the cell. The
file ft01_poisson.py will then be loaded into the notebook. Re-execute the
cell (Shift+Enter) to run the program. You may divide the entire program
into several cells to examine intermediate results: place the cursor where
you want to split the cell and choose Edit - Split Cell. For users of the
FEniCS Docker images, run the fenicsproject notebook command and
follow the instructions. To enable plotting, make sure to run the command
%matplotlib inline inside the notebook.

2.3 Dissection of the program

We shall now dissect our FEniCS program in detail. The listed FEniCS pro-
gram defines a finite element mesh, a finite element function space V on this
mesh, boundary conditions for u (the function uD ), and the bilinear and lin-
ear forms a(u, v) and L(v). Thereafter, the solution u is computed. At the
end of the program, we compare the numerical and the exact solutions. We
also plot the solution using the plot command and save the solution to a file
for external postprocessing.

2.3.1 The important first line

The first line in the program,

from fenics import *

imports the key classes UnitSquareMesh, FunctionSpace, Function, and so

forth, from the FEniCS library. All FEniCS programs for solving PDEs by
the finite element method normally start with this line.
20 2 Fundamentals: Solving the Poisson equation

2.3.2 Generating simple meshes

The statement
mesh = UnitSquareMesh(8, 8)

defines a uniform finite element mesh over the unit square [0, 1] [0, 1]. The
mesh consists of cells, which in 2D are triangles with straight sides. The
parameters 8 and 8 specify that the square should be divided into 8 8
rectangles, each divided into a pair of triangles. The total number of triangles
(cells) thus becomes 128. The total number of vertices in the mesh is 99 = 81.
In later chapters, you will learn how to generate more complex meshes.

2.3.3 Defining the finite element function space

Once the mesh has been created, we can create a finite element function space
V:
V = FunctionSpace(mesh, P, 1)

The second argument P specifies the type of element. The type of ele-
ment here is P, implying the standard Lagrange family of elements. You may
also use Lagrange to specify this type of element. FEniCS supports all
simplex element families and the notation defined in the Periodic Table of
the Finite Elements2 [2].
The third argument 1 specifies the degree of the finite element. In this case,
the standard P1 linear Lagrange element, which is a triangle with nodes at
the three vertices. Some finite element practitioners refer to this element
as the linear triangle. The computed solution u will be continuous across
elements and linearly varying in x and y inside each element. Higher-degree
polynomial approximations over each cell are trivially obtained by increasing
the third parameter to FunctionSpace, which will then generate function
spaces of type P2 , P3 , and so forth. Changing the second parameter to DP
creates a function space for discontinuous Galerkin methods.

2.3.4 Defining the trial and test functions

In mathematics, we distinguish between the trial and test spaces V and V .

The only difference in the present problem is the boundary conditions. In
FEniCS we do not specify the boundary conditions as part of the function

2
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2.3 Dissection of the program 21

space, so it is sufficient to work with one common space V for both the trial
and test functions in the program:
u = TrialFunction(V)
v = TestFunction(V)

2.3.5 Defining the boundary conditions

The next step is to specify the boundary condition: u = uD on . This is

done by
bc = DirichletBC(V, u_D, boundary)

where u_D is an expression defining the solution values on the boundary,

and boundary is a function (or object) defining which points belong to the
boundary.
Boundary conditions of the type u = uD are known as Dirichlet conditions.
For the present finite element method for the Poisson problem, they are also
called essential boundary conditions, as they need to be imposed explicitly as
part of the trial space (in contrast to being defined implicitly as part of the
variational formulation). Naturally, the FEniCS class used to define Dirichlet
boundary conditions is named DirichletBC.
The variable u_D refers to an Expression object, which is used to represent
a mathematical function. The typical construction is
u_D = Expression(formula, degree=1)

where formula is a string containing a mathematical expression. The for-

mula must be written with C++ syntax and is automatically turned into an
efficient, compiled C++ function.

Expressions and accuracy

When defining an Expression, the second argument degree is a pa-
rameter that specifies how the expression should be treated in compu-
tations. On each local element, FEniCS will interpolate the expression
into a finite element space of the specified degree. To obtain optimal
(order of) accuracy in computations, it is usually a good choice to use
the same degree as for the space V that is used for the trial and test
functions. However, if an Expression is used to represent an exact so-
lution which is used to evaluate the accuracy of a computed solution,
a higher degree must be used for the expression (one or two degrees
higher).
22 2 Fundamentals: Solving the Poisson equation

The expression may depend on the variables x[0] and x[1] correspond-
ing to the x and y coordinates. In 3D, the expression may also depend on
the variable x[2] corresponding to the z coordinate. With our choice of
uD (x, y) = 1 + x2 + 2y 2 , the formula string can be written as 1 + x[0]*x[0]
+ 2*x[1]*x[1]:
u_D = Expression(1 + x[0]*x[0] + 2*x[1]*x[1], degree=2)

We set the degree to 2 so that u_D may represent the exact quadratic
solution to our test problem.

String expressions must have valid C++ syntax!

The string argument to an Expression object must obey C++ syntax.
Most Python syntax for mathematical expressions is also valid C++
syntax, but power expressions make an exception: p**a must be writ-
ten as pow(p, a) in C++ (this is also an alternative Python syntax).
The following mathematical functions can be used directly in C++ ex-
pressions when defining Expression objects: cos, sin, tan, acos, asin,
atan, atan2, cosh, sinh, tanh, exp, frexp, ldexp, log, log10, modf,
pow, sqrt, ceil, fabs, floor, and fmod. Moreover, the number is
available as the symbol pi. All the listed functions are taken from the
cmath C++ header file, and one may hence consult the documentation
of cmath for more information on the various functions.
If/else tests are possible using the C syntax for inline branching. The
function
 2
x , x, y 0,
f (x, y) =
2, otherwise,
is implemented as
f = Expression(x[0]>=0 && x[1]>=0 ? pow(x[0], 2) : 2, degree=2)

Parameters in expression strings are allowed, but must be initial-

ized via keyword arguments when creating the Expression object. For
2
example, the function f (x) = e t sin(kx) can be coded as
f = Expression(exp(-kappa*pow(pi, 2)*t)*sin(pi*k*x[0]), degree=2,
kappa=1.0, t=0, k=4)

At any time, parameters can be updated:

f.t += dt
f.k = 10

The function boundary specifies which points that belong to the part of
the boundary where the boundary condition should be applied:
2.3 Dissection of the program 23

def boundary(x, on_boundary):

return on_boundary

A function like boundary for marking the boundary must return a boolean
value: True if the given point x lies on the Dirichlet boundary and False
otherwise. The argument on_boundary is True if x is on the physical bound-
ary of the mesh, so in the present case, where we are supposed to return
True for all points on the boundary, we can just return the supplied value of
on_boundary. The boundary function will be called for every discrete point
in the mesh, which means that we may define boundaries where u is also
known inside the domain, if desired.
One way to think about the specification of boundaries in FEniCS is that
FEniCS will ask you (or rather the function boundary which you have imple-
mented) whether or not a specific point x is part of the boundary. FEniCS
already knows whether the point belongs to the actual boundary (the math-
ematical boundary of the domain) and kindly shares this information with
you in the variable on_boundary. You may choose to use this information (as
we do here), or ignore it completely.
The argument on_boundary may also be omitted, but in that case we need
to test on the value of the coordinates in x:
def boundary(x):
return x[0] == 0 or x[1] == 0 or x[0] == 1 or x[1] == 1

Comparing floating-point values using an exact match test with == is not good
programming practice, because small round-off errors in the computations of
the x values could make a test x[0] == 1 become false even though x lies on
the boundary. A better test is to check for equality with a tolerance, either
explicitly
tol = 1E-14
def boundary(x):
return abs(x[0]) < tol or abs(x[1]) < tol \
or abs(x[0] - 1) < tol or abs(x[1] - 1) < tol

or using the near command in FEniCS:

def boundary(x):
return near(x[0], 0, tol) or near(x[1], 0, tol) \
or near(x[0], 1, tol) or near(x[1], 1, tol)

Never use == for comparing real numbers!

A comparison like x[0] == 1 should never be used if x[0] is a real
number, because rounding errors in x[0] may make the test fail even
when it is mathematically correct. Consider the following calculations
in Python:
24 2 Fundamentals: Solving the Poisson equation

>>> 0.1 + 0.2 == 0.3

False
>>> 0.1 + 0.2
0.30000000000000004

Comparison of real numbers needs to be made with tolerances! The

values of the tolerances depend on the size of the numbers involved in
arithmetic operations:
>>> abs(0.1 + 0.2 - 0.3)
5.551115123125783e-17
>>> abs(1.1 + 1.2 - 2.3)
0.0
>>> abs(10.1 + 10.2 - 20.3)
3.552713678800501e-15
>>> abs(100.1 + 100.2 - 200.3)
0.0
>>> abs(1000.1 + 1000.2 - 2000.3)
2.2737367544323206e-13
>>> abs(10000.1 + 10000.2 - 20000.3)
3.637978807091713e-12

For numbers of unit size, tolerances as low as 3 1016 can be used (in
fact, this tolerance is known as the constant DOLFIN_EPS in FEniCS).
Otherwise, an appropriately scaled tolerance must be used.

2.3.6 Defining the source term

Before defining the bilinear and linear forms a(u, v) and L(v) we have to
specify the source term f :
f = Expression(-6, degree=0)

When f is constant over the domain, f can be more efficiently represented

as a Constant:
f = Constant(-6)

2.3.7 Defining the variational problem

We now have all the ingredients we need to define the variational problem:
a = dot(grad(u), grad(v))*dx
L = f*v*dx
2.3 Dissection of the program 25

In essence, these two lines specify the PDE to be solved. Note the very close
correspondence between the Python syntax and the mathematical formulas
u v dx and f v dx. This is a key strength of FEniCS: the formulas in
the variational formulation translate directly to very similar Python code,
a feature that makes it easy to specify and solve complicated PDE prob-
lems. The language used to express weak forms is called UFL (Unified Form
Language) [1, 26] and is an integral part of FEniCS.

Expressing inner products

R
The inner product u v dx can be expressed in various ways in
FEniCS. Above, we have used the notation dot(grad(u), grad(v))*dx.
The dot product in FEniCS/UFL computes the sum (contraction) over
the last index of the first factor and the first index of the second factor.
In this case, both factors are tensors of rank one (vectors) and so the
sum is just over the one single index of both u and v. To compute
an inner product of matrices (with two indices), one must instead of
dot use the function inner. For vectors, dot and inner are equivalent.

2.3.8 Forming and solving the linear system

Having defined the finite element variational problem and boundary condi-
tion, we can now ask FEniCS to compute the solution:
u = Function(V)
solve(a == L, u, bc)

Note that we first defined the variable u as a TrialFunction and used it

to represent the unknown in the form a. Thereafter, we redefined u to be a
Function object representing the solution; i.e., the computed finite element
function u. This redefinition of the variable u is possible in Python and is often
used in FEniCS applications for linear problems. The two types of objects
that u refers to are equal from a mathematical point of view, and hence it is
natural to use the same variable name for both objects.

2.3.9 Plotting the solution using the plot command

Once the solution has been computed, it can be visualized by the plot com-
mand:
plot(u)
plot(mesh)
26 2 Fundamentals: Solving the Poisson equation

interactive()

Note the call to the function interactive after the plot commands. This
call makes it possible to interact with the plots (rotating and zooming). The
call to interactive is usually placed at the end of a program that creates
plots. Figure 2.1 displays the two plots.

Fig. 2.1 Plot of the mesh and the solution for the Poisson problem created using the
built-in FEniCS visualization tool (plot command).

The plot command is useful for debugging and initial scientific investi-
gations. More advanced visualizations are better created by exporting the
solution to a file and using an advanced visualization tool like ParaView, as
explained in the next section.
By clicking the left mouse button in the plot window, you may rotate the
solution, while the right mouse button is used for zooming. Point the mouse to
the Help text in the lower left corner to display a list of all available shortcut
commands. The help menu may alternatively be activated by typing h in
the plot window. The plot command also accepts a number of additional
arguments, such as for example setting the title of the plot window:
plot(u, title=Finite element solution)
plot(mesh, title=Finite element mesh)

For detailed documentation, either run the command help(plot) in Python

or pydoc fenics.plot from a terminal window.

Built-in plotting on Mac OS X and in Docker

The built-in plotting in FEniCS may not work as expected when either
running on Mac OS X or when running inside a FEniCS Docker con-
tainer. FEniCS supports plotting using the plot command on Mac OS
X. However, the keyboard shortcuts may fail to work. When running
2.3 Dissection of the program 27

inside a Docker container, plotting is not supported since Docker does

not interact with your windowing system. For Docker users who need
plotting, it is recommended to either work within a Jupyter/FEniCS
notebook (command fenicsproject notebook) or rely on ParaView
or other external tools for visualization.

2.3.10 Plotting the solution using ParaView

The simple plot command is useful for quick visualizations, but for more
advanced visualizations an external tool must be used. In this section we
demonstrate how to visualize solutions in ParaView. ParaView3 is a powerful
tool for visualizing scalar and vector fields, including those computed by
FEniCS.
The first step is to export the solution in VTK format:
vtkfile = File(poisson/solution.pvd)
vtkfile << u

The following steps demonstrate how to create a plot of the solution of our
Poisson problem in ParaView. The resulting plot is shown in Figure 2.2.
1. Start the ParaView application.
2. Click FileOpen... in the top menu and navigate to the directory con-
taining the exported solution. This should be inside a subdirectory named
poisson below the directory where the FEniCS Python program was
started. Select the file named solution.pvd and then click OK.
3. Click Apply in the Properties pane on the left. This will bring up a plot
of the solution.
4. To make a 3D plot of the solution, we will make use of one of ParaViews
many filters. Click FiltersAlphabeticalWarp By Scalar in the top
menu and then Apply in the Properties pane on the left. This create an
elevated surface with the height determined by the solution value.
5. To show the original plot below the elevated surface, click the little eye
icon to the left of solution.pvd in the Pipeline Browser pane on the left.
Also click the little 2D button at the top of the plot window to change the
visualization to 3D. This lets you interact with the plot by rotating (left
mouse button) and zooming (Ctrl + left mouse button).
6. To show the finite element mesh, click on solution.pvd in the Pipeline
Browser, navigate to Representation in the Properties pane, and select
Surface With Edges. This should make the finite element mesh visible.
7. To change the aspect ratio of the plot, click on WarpByScalar1 in the
Pipeline Browser and navigate to Scale Factor in the Properties pane.
Change the value to 0.2 and click Apply. This will change the scale of the
3
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28 2 Fundamentals: Solving the Poisson equation

warped plot. We also unclick Orientation Axis Visibility at the bottom

of the Properties pane to remove the little 3D axes in the lower left corner
of the plot window. You should now see something that resembles the plot
in Figure 2.2.
8. Finally, to export the visualization to a file, click FileSave Screen-
shot... and select a suitable file name such as poisson.png.
For more information, we refer to The ParaView Guide [30] (free PDF avail-
able), the ParaView tutorial4 , and the instruction video Introduction to Par-
aView5 .

Fig. 2.2 Plot of the mesh and the solution for the Poisson problem created using
ParaView.

2.3.11 Computing the error

Finally, we compute the error to check the accuracy of the solution. We do

this by comparing the finite element solution u with the exact solution, which
in this example happens to be the same as the expression u_D used to set the
boundary conditions. We compute the error in two different ways. First, we
compute the L2 norm of the error, defined by

4
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5
https://vimeo.com/34037236
2.3 Dissection of the program 29
sZ
E= (uD u)2 dx .

Since the exact solution is quadratic and the finite element solution is piece-
wise linear, this error will be nonzero. To compute this error in FEniCS, we
simply write
error_L2 = errornorm(u_D, u, L2)

The errornorm function can also compute other error norms such as the H 1
norm. Type pydoc fenics.errornorm in a terminal window for details.
We also compute the maximum value of the error at all the vertices of the
finite element mesh. As mentioned above, we expect this error to be zero to
within machine precision for this particular example. To compute the error
at the vertices, we first ask FEniCS to compute the value of both u_D and u
at all vertices, and then subtract the results:
vertex_values_u_D = u_D.compute_vertex_values(mesh)
vertex_values_u = u.compute_vertex_values(mesh)
import numpy as np
error_max = np.max(np.abs(vertex_values_u_D - vertex_values_u))

We have here used the maximum and absolute value functions from numpy,
because these are much more efficient for large arrays (a factor of 30) than
Pythons built-in max and abs functions.

How to check that the error vanishes

With inexact (floating point) arithmetic, the maximum error at the ver-
tices is not zero, but should be a small number. The machine precision is
about 1016 , but in finite element calculations, rounding errors of this
size may accumulate, to produce an error larger than 1016 . Experi-
ments show that increasing the number of elements and increasing the
degree of the finite element polynomials increases the error. For a mesh
with 2 (20 20) cubic Lagrange elements (degree 3) the error is about
2 1012 , while for 128 linear elements the error is about 2 1015 .

2.3.12 Examining degrees of freedom and vertex values

A finite element function like u is expressed as a linear combination of basis

functions j , spanning the space V :
N
X
u= Uj j . (2.13)
j=1
30 2 Fundamentals: Solving the Poisson equation

By writing solve(a == L, u, bc) in the program, a linear system will be

formed from a and L, and this system is solved for the values U1 , . . . , UN .
The values U1 , . . . , UN are known as the degrees of freedom (dofs) or nodal
values of u. For Lagrange elements (and many other element types) Uj is
simply the value of u at the node with global number j. The locations of
the nodes and cell vertices coincide for linear Lagrange elements, while for
higher-order elements there are additional nodes associated with the facets,
edges and sometimes also the interior of cells.
Having u represented as a Function object, we can either evaluate u(x)
at any point x in the mesh (expensive operation!), or we can grab all the
degrees of freedom in the vector U directly by
nodal_values_u = u.vector()

The result is a Vector object, which is basically an encapsulation of the

vector object used in the linear algebra package that is used to solve the linear
system arising from the variational problem. Since we program in Python it
is convenient to convert the Vector object to a standard numpy array for
further processing:
array_u = nodal_values_u.array()

With numpy arrays we can write MATLAB-like code to analyze the data.
Indexing is done with square brackets: array_u[j], where the index j al-
ways starts at 0. If the solution is computed with piecewise linear Lagrange
elements (P1 ), then the size of the array array_u is equal to the number of
vertices, and each array_u[j] is the value at some vertex in the mesh. How-
ever, the degrees of freedom are not necessarily numbered in the same way as
the vertices of the mesh. (This is discussed in some detail in Section 5.4.1).
If we therefore want to know the values at the vertices, we need to call the
function u.compute_vertex_values. This function returns the values at all
the vertices of the mesh as a numpy array with the same numbering as for
the vertices of the mesh, for example:
vertex_values_u = u.compute_vertex_values()

Note that for P1 elements, the arrays array_u and vertex_values_u have
the same lengths and contain the same values, albeit in different order.

2.4 Deflection of a membrane

Our first FEniCS program for the Poisson equation targeted a simple test
problem where we could easily verify the implementation. We now turn our
attention to a physically more relevant problem with solutions of somewhat
more exciting shape.
2.4 Deflection of a membrane 31

We want to compute the deflection D(x, y) of a two-dimensional, circular

membrane of radius R, subject to a load p over the membrane. The appro-
priate PDE model is

T 2 D = p in = {(x, y) | x2 + y 2 R} . (2.14)
Here, T is the tension in the membrane (constant), and p is the external
pressure load. The boundary of the membrane has no deflection, implying
D = 0 as a boundary condition. A localized load can be modeled as a Gaussian
function:
 2  2 !
A 1 x x0 1 y y0
p(x, y) = exp . (2.15)
2 2 2

The parameter A is the amplitude of the pressure, (x0 , y0 ) the localization

of the maximum point of the load, and the width of p. We will take the
center (x0 , y0 ) of the pressure to be (0, R0 ) for some 0 < R0 < R.

2.4.1 Scaling the equation

There are many physical parameters in this problem, and we can benefit
from grouping them by means of scaling. Let us introduce dimensionless
coordinates x
= x/R, y = y/R, and a dimensionless deflection w = D/Dc ,
0 = R0 /R,
where Dc is a characteristic size of the deflection. Introducing R
we obtain

2w 2w 0 )2 ) for x
2 = exp 2 (
x2 + ( 2 + y2 < 1,


yR
2
x y
where

R2 A R
= , = .
2T Dc 2
With an appropriate scaling, w and its derivatives are of size unity, so the
left-hand side of the scaled PDE is about unity in size, while the right-hand
side has as its characteristic size. This suggest choosing to be unity,
or around unity. We shall in this particular case choose = 4. (One can
also find the analytical solution in scaled coordinates and show that the
maximum deflection D(0, 0) is Dc if we choose = 4 to determine Dc .) With
Dc = AR2 /(8T ) and dropping the bars we obtain the scaled problem

2 w = 4 exp 2 (x2 + (y R0 )2 ) ,


(2.16)
to be solved over the unit disc with w = 0 on the boundary. Now there are
only two parameters to vary: the dimensionless extent of the pressure, , and
32 2 Fundamentals: Solving the Poisson equation

the localization of the pressure peak, R0 [0, 1]. As 0, the solution will
approach the special case w = 1 x2 y 2 .
Given a computed scaled solution w, the physical deflection can be com-
puted by

AR2
D= w.
8T
Just a few modifications are necessary to our previous program to solve
this new problem.

2.4.2 Defining the mesh

A mesh over the unit disk can be created by the mshr tool in FEniCS:
from mshr import *
domain = Circle(Point(0, 0), 1)
mesh = generate_mesh(domain, 64)

The Circle shape from mshr takes the center and radius of the circle as
arguments. The second argument to the generate_mesh function specifies
the desired mesh resolution. The cell size will be (approximately) equal to
the diameter of the domain divided by the resolution.

2.4.3 Defining the load

The right-hand side pressure function is represented by an Expression ob-

ject. There are two physical parameters in the formula for f that enter the
expression string and these parameters must have their values set by keyword
arguments:
beta = 8
R0 = 0.6
p = Expression(4*exp(-pow(beta, 2)*(pow(x[0], 2) + pow(x[1] - R0, 2))),
degree=1, beta=beta, R0=R0)

The coordinates in Expression objects are always an array x with compo-

nents x[0], x[1], and x[2], corresponding to x, y, and z. Otherwise we are
free to introduce names of parameters as long as these are given default values
by keyword arguments. All the parameters initialized by keyword arguments
can at any time have their values modified. For example, we may set
p.beta = 12
p.R0 = 0.3
2.4 Deflection of a membrane 33

2.4.4 Defining the variational problem

The variational problem and the boundary conditions are the same as in
our first Poisson problem, but we may introduce w instead of u as primary
unknown and p instead of f as right-hand side function:
w = TrialFunction(V)
v = TestFunction(V)
a = dot(grad(w), grad(v))*dx
L = p*v*dx

w = Function(V)
solve(a == L, w, bc)

2.4.5 Plotting the solution

It is of interest to visualize the pressure p along with the deflection w so that

we may examine the membranes response to the pressure. We must then
transform the formula (Expression) to a finite element function (Function).
The most natural approach is to construct a finite element function whose
degrees of freedom are calculated from p. That is, we interpolate p to the
function space V :
p = interpolate(p, V)

Note that the assignment to p destroys the previous Expression object p,

so if it is of interest to still have access to this object, another name must be
used for the Function object returned by interpolate. The two functions
w and p may be plotted using the built-in plot command:
plot(w, title=Deflection)
plot(p, title=Load)

As before, we also export the solutions in VTK format for visualization in

ParaView:
vtkfile_w = File(poisson_membrane/deflection.pvd)
vtkfile_w << w
vtkfile_p = File(poisson_membrane/load.pvd)
vtkfile_p << p

Figure 2.3 shows a visualization of the deflection w and the load p created
with ParaView.
34 2 Fundamentals: Solving the Poisson equation

Fig. 2.3 Plot of the deflection (left) and load (right) for the membrane problem created
using ParaView. The plot uses 10 equispaced isolines for the solution values and the
optional jet colormap.

2.4.6 Making curve plots through the domain

Another way to compare the deflection and the load is to make a curve plot
along the line x = 0. This is just a matter of defining a set of points along the
y-axis and evaluating the finite element functions w and p at these points:
# Curve plot along x = 0 comparing p and w
import numpy as np
import matplotlib.pyplot as plt
tol = 0.001 # avoid hitting points outside the domain
y = np.linspace(-1 + tol, 1 - tol, 101)
points = [(0, y_) for y_ in y] # 2D points
w_line = np.array([w(point) for point in points])
p_line = np.array([p(point) for point in points])
plt.plot(y, 50*w_line, k, linewidth=2) # magnify w
plt.plot(y, p_line, b--, linewidth=2)
plt.grid(True)
plt.xlabel($y$)
plt.legend([Deflection ($\\times 50$), Load], loc=upper left)
plt.savefig(poisson_membrane/curves.pdf)
plt.savefig(poisson_membrane/curves.png)

This example program can be found in the file ft02_poisson_membrane.py.

The resulting curve plot is shown in Figure 2.4. The localized input (p)
is heavily damped and smoothed in the output (w). This reflects a typical
property of the Poisson equation.
2.4 Deflection of a membrane 35

Fig. 2.4 Plot of the deflection and load for the membrane problem created using
Matplotlib and sampling of the two functions along the y-axsis.
Chapter 3
A Gallery of finite element solvers

The goal of this chapter is to demonstrate how a range of important PDEs from
science and engineering can be quickly solved with a few lines of FEniCS code.
We start with the heat equation and continue with a nonlinear Poisson equation,
the equations for linear elasticity, the NavierStokes equations, and finally look at
how to solve systems of nonlinear advectiondiffusionreaction equations. These
problems illustrate how to solve time-dependent problems, nonlinear problems,
vector-valued problems, and systems of PDEs. For each problem, we derive the
variational formulation and express the problem in Python in a way that closely
resembles the mathematics.

3.1 The heat equation

As a first extension of the Poisson problem from the previous chapter, we
consider the time-dependent heat equation, or the time-dependent diffusion
equation. This is the natural extension of the Poisson equation describing the
stationary distribution of heat in a body to a time-dependent problem.
We will see that by discretizing time into small time intervals and applying
standard time-stepping methods, we can solve the heat equation by solving
a sequence of variational problems, much like the one we encountered for the
Poisson equation.

3.1.1 PDE problem

Our model problem for time-dependent PDEs reads

c 2017, Hans Petter Langtangen, Anders Logg.
Released under CC Attribution 4.0 license
38 3 A Gallery of finite element solvers

u
= 2 u + f in (0, T ], (3.1)
t
u = uD on (0, T ], (3.2)
u = u0 at t = 0 . (3.3)

Here, u varies with space and time, e.g., u = u(x, y, t) if the spatial domain
is two-dimensional. The source function f and the boundary values uD may
also vary with space and time. The initial condition u0 is a function of space
only.

3.1.2 Variational formulation

A straightforward approach to solving time-dependent PDEs by the finite

element method is to first discretize the time derivative by a finite difference
approximation, which yields a sequence of stationary problems, and then turn
each stationary problem into a variational formulation.
Let superscript n denote a quantity at time tn , where n is an integer count-
ing time levels. For example, un means u at time level n. A finite difference
discretization in time first consists of sampling the PDE at some time level,
say tn+1 :
 n+1
u
= 2 un+1 + f n+1 . (3.4)
t
The time-derivative can be approximated by a difference quotient. For sim-
plicity and stability reasons, we choose a simple backward difference:
n+1
un+1 un

u
, (3.5)
t t
where t is the time discretization parameter. Inserting (3.5) in (3.4) yields

un+1 un
= 2 un+1 + f n+1 . (3.6)
t
This is our time-discrete version of the heat equation (3.1), a so-called back-
ward Euler or implicit Euler discretization.
We may reorder (3.6) so that the left-hand side contains the terms with
the unknown un+1 and the right-hand side contains computed terms only.
The result is a sequence of spatial (stationary) problems for un+1 , assuming
un is known from the previous time step:
3.1 The heat equation 39

u0 = u0 , (3.7)
n+1 2 n+1 n n+1
u t u = u + tf , n = 0, 1, 2, . . . (3.8)

Given u0 , we can solve for u0 , u1 , u2 , and so on.

An alternative to (3.8), which can be convenient in implementations, is to
collect all terms on one side of the equality sign:

un+1 t2 un+1 un tf n+1 = 0, n = 0, 1, 2, . . . (3.9)

We use a finite element method to solve (3.7) and either of the equations
(3.8) or (3.9). This requires turning the equations into weak forms. As usual,
we multiply by a test function v V and integrate second-derivatives by
parts. Introducing the symbol u for un+1 (which is natural in the program),
the resulting weak form arising from formulation (3.8) can be conveniently
written in the standard notation:

a(u, v) = Ln+1 (v),

where

Z
a(u, v) = (uv + tu v) dx, (3.10)
Z
un + tf n+1 v dx .


Ln+1 (v) = (3.11)

The alternative form (3.9) has an abstract formulation

Fn+1 (u; v) = 0,
where

Z
uv + tu v (un + tf n+1 )v dx .


Fn+1 (u; v) = (3.12)

In addition to the variational problem to be solved in each time step, we

also need to approximate the initial condition (3.7). This equation can also
be turned into a variational problem:

a0 (u, v) = L0 (v),
with
40 3 A Gallery of finite element solvers
Z
a0 (u, v) = uv dx, (3.13)
Z
L0 (v) = u0 v dx . (3.14)

When solving this variational problem, u0 becomes the L2 projection of the

given initial value u0 into the finite element space. The alternative is to con-
struct u0 by just interpolating the initial value u0 ; that is, if u0 = N 0
P
j=1 Uj j ,
we simply set Uj = u0 (xj , yj ), where (xj , yj ) are the coordinates of node num-
ber j. We refer to these two strategies as computing the initial condition by
either projection or interpolation. Both operations are easy to compute in
FEniCS through a single statement, using either the project or interpolate
function. The most common choice is project, which computes an approxi-
mation to u0 , but in some applications where we want to verify the code by
reproducing exact solutions, one must use interpolate (and we use such a
test problem here!).
In summary, we thus need to solve the following sequence of variational
problems to compute the finite element solution to the heat equation: find
u0 V such that a0 (u0 , v) = L0 (v) holds for all v V , and then find un+1 V
such that a(un+1 , v) = Ln+1 (v) for all v V , or alternatively, Fn+1 (un+1 , v) =
0 for all v V , for n = 0, 1, 2, . . ..

3.1.3 FEniCS implementation

Our program needs to implement the time-stepping manually, but can rely
on FEniCS to easily compute a0 , L0 , a, and L (or Fn+1 ), and solve the linear
systems for the unknowns.
Test problem 1: A known analytical solution. Just as for the Poisson
problem from the previous chapter, we construct a test problem that makes
it easy to determine if the calculations are correct. Since we know that our
first-order time-stepping scheme is exact for linear functions, we create a
test problem which has a linear variation in time. We combine this with a
quadratic variation in space. We thus take

u = 1 + x2 + y 2 + t, (3.15)
which yields a function whose computed values at the nodes will be exact,
regardless of the size of the elements and t, as long as the mesh is uniformly
partitioned. By inserting (3.15) into the heat equation (3.1), we find that the
right-hand side f must be given by f (x, y, t) = 22. The boundary value
is uD (x, y, t) = 1 +x2 + y 2 + t and the initial value is u0 (x, y) = 1 +x2 + y 2 .
FEniCS implementation. A new programming issue is how to deal
with functions that vary in space and time, such as the boundary condi-
3.1 The heat equation 41

tion uD (x, y, t) = 1 + x2 + y 2 + t. A natural solution is to use a FEniCS

Expression with time t as a parameter, in addition to the parameters and
:
alpha = 3; beta = 1.2
u_D = Expression(1 + x[0]*x[0] + alpha*x[1]*x[1] + beta*t,
degree=2, alpha=alpha, beta=beta, t=0)

This Expression uses the components of x as independent variables, while

alpha, beta, and t are parameters. The time t can later be updated by
u_D.t = t

The essential boundary conditions, along the entire boundary in this case,
are implemented in the same way as we have previously implemented the
boundary conditions for the Poisson problem:
def boundary(x, on_boundary):
return on_boundary

bc = DirichletBC(V, u_D, boundary)

We shall use the variable u for the unknown un+1 at the new time step
and the variable u_n for un at the previous time step. The initial value of
u_n can be computed by either projection or interpolation of u0 . Since we
set t = 0 for the boundary value u_D, we can use u_D to specify the initial
condition:
u_n = project(u_D, V)
# or
u_n = interpolate(u_D, V)

Projecting versus interpolating the initial condition

To actually recover the exact solution (3.15) to machine precision, it is
important to compute the discrete initial condition by interpolating u0 .
This ensures that the degrees of freedom are exact (to machine preci-
sion) at t = 0. Projection results in approximate values at the nodes.

We may either define a or L according to the formulas above, or we may

just define F and ask FEniCS to figure out which terms should go into the
bilinear form a and which should go into the linear form L. The latter is
convenient, especially in more complicated problems, so we illustrate that
construction of a and L:
u = TrialFunction(V)
v = TestFunction(V)
f = Constant(beta - 2 - 2*alpha)
42 3 A Gallery of finite element solvers

F = u*v*dx + dt*dot(grad(u), grad(v))*dx - (u_n + dt*f)*v*dx

a, L = lhs(F), rhs(F)

Finally, we perform the time-stepping in a loop:

u = Function(V)
t = 0
for n in range(num_steps):

# Update current time

t += dt
u_D.t = t

# Solve variational problem

solve(a == L, u, bc)

# Update previous solution

u_n.assign(u)

In the last step of the time-stepping loop, we assign the values of the variable
u (the new computed solution) to the variable u_n containing the values at
the previous time step. This must be done using the assign member function.
If we instead try to do u_n = u, we will set the u_n variable to be the same
variable as u which is not what we want. (We need two variables, one for the
values at the previous time step and one for the values at the current time
step.)

Remember to update expression objects with the current

time!
Inside the time loop, observe that u_D.t must be updated before the
solve statement to enforce computation of Dirichlet conditions at
the current time step. A Dirichlet condition defined in terms of an
Exression looks up and applies the value of a parameter such as t
when it gets evaluated and applied to the linear system.

The time-stepping loop above does not contain any comparison of the
numerical and the exact solutions, which we must include in order to verify
the implementation. As for the Poisson equation in Section 2.3, we compute
the difference between the array of nodal values for u and the array of nodal
values for the interpolated exact solution. This may be done as follows:
u_e = interpolate(u_D, V)
error = np.abs(u_e.vector().array() - u.vector().array()).max()
print(t = %.2f: error = %.3g % (t, error))

For the Poisson example, we used the function compute_vertex_values to

extract the function values at the vertices. Here we illustrate an alternative
method to extract the vertex values, by calling the function vector, which
3.1 The heat equation 43

returns the vector of degrees of freedom. For a P1 function space, this vector
of degrees of freedom will be equal to the array of vertex values obtained by
calling compute_vertex_values, albeit possibly in a different order.
The complete program for solving the heat equation goes as follows:
from fenics import *
import numpy as np

T = 2.0 # final time

num_steps = 10 # number of time steps
dt = T / num_steps # time step size
alpha = 3 # parameter alpha
beta = 1.2 # parameter beta

# Create mesh and define function space

nx = ny = 8
mesh = UnitSquareMesh(nx, ny)
V = FunctionSpace(mesh, P, 1)

# Define boundary condition

u_D = Expression(1 + x[0]*x[0] + alpha*x[1]*x[1] + beta*t,
degree=2, alpha=alpha, beta=beta, t=0)

def boundary(x, on_boundary):

return on_boundary

bc = DirichletBC(V, u_D, boundary)

# Define initial value

u_n = interpolate(u_D, V)
#u_n = project(u_D, V)

# Define variational problem

u = TrialFunction(V)
v = TestFunction(V)
f = Constant(beta - 2 - 2*alpha)

F = u*v*dx + dt*dot(grad(u), grad(v))*dx - (u_n + dt*f)*v*dx

a, L = lhs(F), rhs(F)

# Time-stepping
u = Function(V)
t = 0
for n in range(num_steps):

# Update current time

t += dt
u_D.t = t

# Compute solution
solve(a == L, u, bc)

# Plot solution
44 3 A Gallery of finite element solvers

plot(u)

# Compute error at vertices

u_e = interpolate(u_D, V)
error = np.abs(u_e.vector().array() - u.vector().array()).max()
print(t = %.2f: error = %.3g % (t, error))

# Update previous solution

u_n.assign(u)

# Hold plot
interactive()

This example program can be found in the file ft03_heat.py.

Test problem 2: Diffusion of a Gaussian function. Let us now solve
a more interesting test problem, namely the diffusion of a Gaussian hill. We
take the initial value to be
2
ay 2
u0 (x, y) = eax
for a = 5 on the domain [2, 2] [2, 2]. For this problem we will use homoge-
neous Dirichlet boundary conditions (uD = 0).
FEniCS implementation. Which are the required changes to our previous
program? One major change is that the domain is no longer a unit square.
The new domain can be created easily in FEniCS using RectangleMesh:
nx = ny = 30
mesh = RectangleMesh(Point(-2, -2), Point(2, 2), nx, ny)

Note that we have used a much higher resolution than before to better re-
solve the features of the solution. We also need to redefine the initial condi-
tion and the boundary condition. Both are easily changed by defining a new
Expression and by setting u = 0 on the boundary.
To be able to visualize the solution in an external program such as Par-
aView, we will save the solution to a file in VTK format in each time step.
We do this by first creating a File with the suffix .pvd:
vtkfile = File(heat_gaussian/solution.pvd)

Inside the time loop, we may then append the solution values to this file:
vtkfile << (u, t)

This line is called in each time step, resulting in the creation of a new file
with suffix .vtu containing all data for the time step (the mesh and the
vertex values). The file heat_gaussian/solution.pvd will contain the time
values and references to the .vtu file, which means that the .pvd file will
be a single small file that points to a large number of .vtu files containing
the actual data. Note that we choose to store the solution to a subdirectory
named heat_gaussian. This is to avoid cluttering our source directory with
3.1 The heat equation 45

all the generated data files. One does not need to create the directory before
running the program as it will be created automatically by FEniCS.
The complete program appears below.
from fenics import *
import time

T = 2.0 # final time

num_steps = 50 # number of time steps
dt = T / num_steps # time step size

# Create mesh and define function space

nx = ny = 30
mesh = RectangleMesh(Point(-2, -2), Point(2, 2), nx, ny)
V = FunctionSpace(mesh, P, 1)

# Define boundary condition

def boundary(x, on_boundary):
return on_boundary

bc = DirichletBC(V, Constant(0), boundary)

# Define initial value

u_0 = Expression(exp(-a*pow(x[0], 2) - a*pow(x[1], 2)),
degree=2, a=5)
u_n = interpolate(u_0, V)

# Define variational problem

u = TrialFunction(V)
v = TestFunction(V)
f = Constant(0)

F = u*v*dx + dt*dot(grad(u), grad(v))*dx - (u_n + dt*f)*v*dx

a, L = lhs(F), rhs(F)

# Create VTK file for saving solution

vtkfile = File(heat_gaussian/solution.pvd)

# Time-stepping
u = Function(V)
t = 0
for n in range(num_steps):

# Update current time

t += dt

# Compute solution
solve(a == L, u, bc)

# Save to file and plot solution

vtkfile << (u, t)
plot(u)

# Update previous solution

46 3 A Gallery of finite element solvers

u_n.assign(u)

# Hold plot
interactive()

This example program can be found in the file ft04_heat_gaussian.py.

Visualization in ParaView. To visualize the diffusion of the Gaussian hill,
start ParaView, choose FileOpen..., open heat_gaussian/solution.pvd,
and click Apply in the Properties pane. Click on the play button to display
an animation of the solution. To save the animation to a file, click File
Save Animation... and save the file to a desired file format, for example
AVI or Ogg/Theora. Once the animation has been saved to a file, you can
play the animation offline using a player such as mplayer or VLC, or upload
your animation to YouTube. Figure 3.1 shows a sequence of snapshots of the
solution.

Fig. 3.1 A sequence of snapshots of the solution of the Gaussian hill problem created
with ParaView.

3.2 A nonlinear Poisson equation

We shall now address how to solve nonlinear PDEs. We will see that nonlinear
problems can be solved just as easily as linear problems in FEniCS, by sim-
ply defining a nonlinear variational problem and calling the solve function.
When doing so, we will encounter a subtle difference in how the variational
problem is defined.

3.2.1 PDE problem

As a model problem for the solution of nonlinear PDEs, we take the following
nonlinear Poisson equation:
3.2 A nonlinear Poisson equation 47

(q(u)u) = f, (3.16)
in , with u = uD on the boundary . The coefficient q = q(u) makes the
equation nonlinear (unless q(u) is constant in u).

3.2.2 Variational formulation

As usual, we multiply our PDE by a test function v V , integrate over the

domain, and integrate the second-order derivatives by parts. The bound-
ary integral arising from integration by parts vanishes wherever we employ
Dirichlet conditions. The resulting variational formulation of our model prob-
lem becomes: find u V such that

F (u; v) = 0 v V , (3.17)
where
Z
F (u; v) = (q(u)u v f v) dx, (3.18)

and

V = {v H 1 () : v = uD on },
V = {v H 1 () : v = 0 on } .

The discrete problem arises as usual by restricting V and V to a pair

of discrete spaces. As before, we omit any subscript on the discrete spaces
and discrete solution. The discrete nonlinear problem is then written as: find
u V such that

F (u; v) = 0 v V , (3.19)
PN
with u = j=1 Uj j . Since F is nonlinear in u, the variational statement gives
rise to a system of nonlinear algebraic equations in the unknowns U1 , . . . , UN .

3.2.3 FEniCS implementation

Test problem. To solve a test problem, we need to choose the right-hand

side f , the coefficient q(u) and the boundary value uD . Previously, we have
worked with manufactured solutions that can be reproduced without approx-
imation errors. This is more difficult in nonlinear problems, and the algebra
48 3 A Gallery of finite element solvers

is more tedious. However, we may utilize SymPy for symbolic computing and
integrate such computations in the FEniCS solver. This allows us to eas-
ily experiment with different manufactured solutions. The forthcoming code
with SymPy requires some basic familiarity with this package. In particular,
we will use the SymPy functions diff for symbolic differentiation and ccode
for C/C++ code generation.
We take q(u) = 1 + u2 and define a two-dimensional manufactured solution
that is linear in x and y:
# Warning: from fenics import * will import both sym and
# q from FEniCS. We therefore import FEniCS first and then
# overwrite these objects.
from fenics import *

def q(u):
"Return nonlinear coefficient"
return 1 + u**2

# Use SymPy to compute f from the manufactured solution u

import sympy as sym
x, y = sym.symbols(x[0], x[1])
u = 1 + x + 2*y
f = - sym.diff(q(u)*sym.diff(u, x), x) - sym.diff(q(u)*sym.diff(u, y), y)
f = sym.simplify(f)
u_code = sym.printing.ccode(u)
f_code = sym.printing.ccode(f)
print(u =, u_code)
print(f =, f_code)

Define symbolic coordinates as required in Expression objects

Note that we would normally write x, y = sym.symbols(x, y), but
if we want the resulting expressions to have valid syntax for FEniCS
Expression objects, we must use x[0] and x[1]. This is easily accom-
plished with sympy by defining the names of x and y as x[0] and x[1]:
x, y = sym.symbols(x[0], x[1]).

Turning the expressions for u and f into C or C++ syntax for FEniCS
Expression objects needs two steps. First, we ask for the C code of the
expressions:
u_code = sym.printing.ccode(u)
f_code = sym.printing.ccode(f)

In some cases, one will need to edit the result to match the required syntax
of Expression objects, but not in this case. (The primary example is that
M_PI for in C/C++ must be replaced by pi for Expression objects.) In
the present case, the output of u_code and f_code is
3.2 A nonlinear Poisson equation 49

x[0] + 2*x[1] + 1
-10*x[0] - 20*x[1] - 10

After having defined the mesh, the function space, and the boundary, we
define the boundary value u_D as
u_D = Expression(u_code, degree=1)

Similarly, we define the right-hand side function as

f = Expression(f_code, degree=1)

Name clash between FEniCS and program variables

In a program like the one above, strange errors may occur due to name
clashes. If you define sym and q prior to doing from fenics import *,
the latter statement will also import variables with the names sym and
q, overwriting the objects you have previously defined! This may lead
to strange errors. The safest solution is to do import fenics instead
of from fenics import * and then prefix all FEniCS object names by
fenics. The next best solution is to do from fenics import * first
and then define your own variables that overwrite those imported from
fenics. This is acceptable if we do not need sym and q from fenics.

FEniCS implementation. A solver for the nonlinear Poisson equation is

as easy to implement as a solver for the linear Poisson equation. All we need
to do is to state the formula for F and call solve(F == 0, u, bc) instead
of solve(a == L, u, bc) as we did in the linear case. Here is a minimalistic
code:
from fenics import *

def q(u):
return 1 + u**2

mesh = UnitSquareMesh(8, 8)
V = FunctionSpace(mesh, P, 1)
u_D = Expression(u_code, degree=1)

def boundary(x, on_boundary):

return on_boundary

bc = DirichletBC(V, u_D, boundary)

u = Function(V)
v = TestFunction(V)
f = Expression(f_code, degree=1)
F = q(u)*dot(grad(u), grad(v))*dx - f*v*dx
50 3 A Gallery of finite element solvers

solve(F == 0, u, bc)

A complete version of this example program can be found in the file ft05_
poisson_nonlinear.py.
The major difference from a linear problem is that the unknown function u
in the variational form in the nonlinear case must be defined as a Function,
not as a TrialFunction. In some sense this is a simplification from the linear
case where we must define u first as a TrialFunction and then as a Function.
The solve function takes the nonlinear equations, derives symbolically the
Jacobian matrix, and runs a Newton method to compute the solution.
When we run the code, FEniCS reports on the progress of the Newton
iterations. With 2 (8 8) cells, we reach convergence in eight iterations
with a tolerance of 109 , and the error in the numerical solution is about
1016 . These results bring evidence for a correct implementation. Thinking
in terms of finite differences on a uniform mesh, P1 elements mimic stan-
dard second-order differences, which compute the derivative of a linear or
quadratic function exactly. Here, u is a constant vector, but then multi-
plied by (1 + u2 ), which is a second-order polynomial in x and y, which the
divergence difference operator should compute exactly. We can therefore,
even with P1 elements, expect the manufactured u to be reproduced by the
numerical method. With a nonlinearity like 1 + u4 , this will not be the case,
and we would need to verify convergence rates instead.
The current example shows how easy it is to solve a nonlinear problem
in FEniCS. However, experts on the numerical solution of nonlinear PDEs
know very well that automated procedures may fail for nonlinear problems,
and that it is often necessary to have much better manual control of the
solution process than what we have in the current case. We return to this
problem in [23] and show how we can implement taylored solution algorithms
for nonlinear equations and also how we can steer the parameters in the
automated Newton method used above.

3.3 The equations of linear elasticity

Analysis of structures is one of the major activities of modern engineering,
which likely makes the PDE modeling the deformation of elastic bodies the
most popular PDE in the world. It takes just one page of code to solve the
equations of 2D or 3D elasticity in FEniCS, and the details follow below.
3.3 The equations of linear elasticity 51

3.3.1 PDE problem

The equations governing small elastic deformations of a body can be writ-

ten as

= f in , (3.20)
= tr ()I + 2, (3.21)
1 
= u + (u)> , (3.22)
2
where is the stress tensor, f is the body force per unit volume, and are
Lams elasticity parameters for the material in , I is the identity tensor,
tr is the trace operator on a tensor, is the symmetric strain-rate tensor
(symmetric gradient), and u is the displacement vector field. We have here
assumed isotropic elastic conditions.
We combine (3.21) and (3.22) to obtain

= ( u)I + (u + (u)> ) . (3.23)

Note that (3.20)(3.22) can easily be transformed to a single vector PDE for
u, which is the governing PDE for the unknown u (Naviers equation). In the
derivation of the variational formulation, however, it is convenient to keep
the equations split as above.

3.3.2 Variational formulation

The variational formulation of (3.20)(3.22) consists of forming the inner

product of (3.20) and a vector test function v V , where V is a vector-valued
test function space, and integrating over the domain :
Z Z
( ) v dx = f v dx .

Since contains second-order derivatives of the primary unknown u, we
integrate this term by parts:
Z Z Z
( ) v dx = : v dx ( n) v ds,

where the colon operator is the inner product between tensors (summed pair-
wise product of all elements), and n is the outward unit normal at the bound-
ary. The quantity n is known as the traction or stress vector at the bound-
ary, and is often prescribed as a boundary condition. We here assume that it
is prescribed on a part T of the boundary as n = T . On the remaining
52 3 A Gallery of finite element solvers

part of the boundary, we assume that the value of the displacement is given
as a Dirichlet condition. We thus obtain
Z Z Z
: v dx = f v dx + T v ds .
T

Inserting the expression (3.23) for gives the variational form with u as
unknown. Note that the boundary integral on the remaining part \ T
vanishes due to the Dirichlet condition.
We can now summarize the variational formulation as: find u V such
that

a(u, v) = L(v) v V , (3.24)

where

Z
a(u, v) = (u) : v dx, (3.25)

(u) = ( u)I + (u + (u)> ), (3.26)
Z Z
L(v) = f v dx + T v ds . (3.27)
T

One can show that the inner product of a symmetric tensor A and an anti-
symmetric tensor B vanishes. If we express v as a sum of its symmetric and
anti-symmetric parts, only the symmetric part will survive in the product
: v since is a symmetric tensor. Thus replacing u by the symmetric
gradient (u) gives rise to the slightly different variational form
Z
a(u, v) = (u) : (v) dx, (3.28)

where (v) is the symmetric part of v:
1 
(v) = v + (v)> .
2
The formulation (3.28) is what naturally arises from minimization of elastic
potential energy and is a more popular formulation than (3.25).

3.3.3 FEniCS implementation

Test problem. As a test example, we will model a clamped beam deformed

under its own weight in 3D. This can be modeled by setting the right-hand
side body force per unit volume to f = (0, 0, %g) with % the density of the
beam and g the acceleration of gravity. The beam is box-shaped with length
3.3 The equations of linear elasticity 53

L and has a square cross section of width W . We set u = uD = (0, 0, 0) at the

clamped end, x = 0. The rest of the boundary is traction free; that is, we set
T = 0.
FEniCS implementation. We first list the code and then comment upon
the new constructions compared to the previous examples we have seen.
from fenics import *

# Scaled variables
L = 1; W = 0.2
mu = 1
rho = 1
delta = W/L
gamma = 0.4*delta**2
beta = 1.25
lambda_ = beta
g = gamma

# Create mesh and define function space

mesh = BoxMesh(Point(0, 0, 0), Point(L, W, W), 10, 3, 3)
V = VectorFunctionSpace(mesh, P, 1)

# Define boundary condition

tol = 1E-14

def clamped_boundary(x, on_boundary):

return on_boundary and x[0] < tol

bc = DirichletBC(V, Constant((0, 0, 0)), clamped_boundary)

# Define strain and stress

def epsilon(u):
return 0.5*(nabla_grad(u) + nabla_grad(u).T)
#return sym(nabla_grad(u))

def sigma(u):
return lambda_*nabla_div(u)*Identity(d) + 2*mu*epsilon(u)

# Define variational problem

u = TrialFunction(V)
d = u.geometric_dimension() # space dimension
v = TestFunction(V)
f = Constant((0, 0, -rho*g))
T = Constant((0, 0, 0))
a = inner(sigma(u), epsilon(v))*dx
L = dot(f, v)*dx + dot(T, v)*ds

# Compute solution
u = Function(V)
solve(a == L, u, bc)

# Plot solution
54 3 A Gallery of finite element solvers

plot(u, title=Displacement, mode=displacement)

# Plot stress
s = sigma(u) - (1./3)*tr(sigma(u))*Identity(d) # deviatoric stress
von_Mises = sqrt(3./2*inner(s, s))
V = FunctionSpace(mesh, P, 1)
von_Mises = project(von_Mises, V)
plot(von_Mises, title=Stress intensity)

# Compute magnitude of displacement

u_magnitude = sqrt(dot(u, u))
u_magnitude = project(u_magnitude, V)
plot(u_magnitude, Displacement magnitude)
print(min/max u:,
u_magnitude.vector().array().min(),
u_magnitude.vector().array().max())

This example program can be found in the file ft06_elasticity.py.

Vector function spaces. The primary unknown is now a vector field u and
not a scalar field, so we need to work with a vector function space:
V = VectorFunctionSpace(mesh, P, 1)

With u = Function(V) we get u as a vector-valued finite element function

with three components for this 3D problem.
Constant vectors. For the boundary condition u = (0, 0, 0), we must set
a vector value to zero, not just a scalar. Such a vector constant is specified
as Constant((0, 0, 0)) in FEniCS. The corresponding 2D code would use
Constant((0, 0)). Later in the code, we also need f as a vector and specify
it as Constant((0, 0, rho*g)).
nabla_grad. The gradient and divergence operators now have a prefix
nabla_. This is strictly not necessary in the present problem, but recom-
mended in general for vector PDEs arising from continuum mechanics, if you
interpret as a vector in the PDE notation; see the box about nabla_grad
in Section 3.4.2.
Stress computation. As soon as the displacement u is computed, we can
compute various
q stress measures. We will compute the von Mises stress de-
fined as M = 32 s : s where s is the deviatoric stress tensor
1
s = tr () I .
3
There is a one-to-one mapping between these formulas and the FEniCS code:
s = sigma(u) - (1./3)*tr(sigma(u))*Identity(d)
von_Mises = sqrt(3./2*inner(s, s))

The von_Mises variable is now an expression that must be projected to a

finite element space before we can visualize it:
3.3 The equations of linear elasticity 55

V = FunctionSpace(mesh, P, 1)
von_Mises = project(von_Mises, V)
plot(von_Mises, title=Stress intensity)

Scaling. It is often advantageous to scale a problem as it reduces the need

for setting physical parameters, and one obtains dimensionsless numbers that
reflect the competition of parameters and physical effects. We develop the
code for the original model with dimensions, and run the scaled problem
by tweaking parameters appropriately. Scaling reduces the number of active
parameters from 6 to 2 for the present application.
In Naviers equation for u, arising from inserting (3.21) and (3.22) into
(3.20),

( + )( u) 2 u = f,
we insert coordinates made dimensionless by L, and u
= u/U , which results
in the dimensionless governing equation

( u = f,
2u
) f = (0, 0, ),
where = 1 + / is a dimensionless elasticity parameter and where

%gL2
=
U
is a dimensionless variable reflecting the ratio of the load %g and the shear
stress term 2 u U/L2 in the PDE.
One option for the scaling is to chose U such that is of unit size
(U = %gL2 /). However, in elasticity, this leads to displacements of the size
of the geometry, which makes plots look very strange. We therefore want the
characteristic displacement to be a small fraction of the characteristic length
of the geometry. This can be achieved by choosing U equal to the maxi-
mum deflection of a clamped beam, for which there actually exists a formula:
U = 32 %gL2 2 /E, where = L/W is a parameter reflecting how slender the
beam is, and E is the modulus of elasticity. Thus, the dimensionless param-
eter is very important in the problem (as expected, since  1 is what
gives beam theory!). Taking E to be of the same order as , which is the case
for many materials, we realize that 2 is an appropriate choice. Exper-
imenting with the code to find a displacement that looks right in plots of
the deformed geometry, points to = 0.4 2 as our final choice of .
The simulation code implements the problem with dimensions and physical
parameters , , %, g, L, and W . However, we can easily reuse this code for
a scaled problem: just set = % = L = 1, W as W/L ( 1 ), g = , and = .
56 3 A Gallery of finite element solvers

Fig. 3.2 Plot of gravity-induced deflection in a clamped beam for the elasticity prob-
lem.

3.4 The NavierStokes equations

For the next example, we will solve the incompressible NavierStokes equa-
tions. This problem combines many of the challenges from our previously
studied problems: time-dependence, nonlinearity, and vector-valued variables.
We shall touch on a number of FEniCS topics, many of them quite advanced.
But you will see that even a relatively complex algorithm such as a second-
order splitting method for the incompressible NavierStokes equations, can
be implemented with relative ease in FEniCS.

3.4.1 PDE problem

The incompressible NavierStokes equations form a system of equations for

the velocity u and pressure p in an incompressible fluid:

 
u
% + u u = (u, p) + f, (3.29)
t
u = 0. (3.30)

The right-hand side f is a given force per unit volume and just as for the
equations of linear elasticity, (u, p) denotes the stress tensor, which for a
Newtonian fluid is given by
3.4 The NavierStokes equations 57

(u, p) = 2(u) pI, (3.31)

where (u) is the strain-rate tensor
1 
(u) = u + (u)T .
2
The parameter is the dynamic viscosity. Note that the momentum equation
(3.29) is very similar to the elasticity equation (3.20). The difference is in the
two additional terms %(u/t + u u) and the different expression for the
stress tensor. The two extra terms express the acceleration balanced by the
force F = + f per unit volume in Newtons second law of motion.

3.4.2 Variational formulation

The NavierStokes equations are different from the time-dependent heat

equation in that we need to solve a system of equations and this system
is of a special type. If we apply the same technique as for the heat equa-
tion; that is, replacing the time derivative with a simple difference quotient,
we obtain a nonlinear system of equations. This in itself is not a problem
for FEniCS as we saw in Section 3.2, but the system has a so-called saddle
point structure and requires special techniques (special preconditioners and
iterative methods) to be solved efficiently.
Instead, we will apply a simpler and often very efficient approach, known
as a splitting method. The idea is to consider the two equations (3.29) and
(3.30) separately. There exist many splitting strategies for the incompress-
ible NavierStokes equations. One of the oldest is the method proposed by
Chorin [6] and Temam [31], often referred to as Chorins method. We will
use a modified version of Chorins method, the so-called incremental pres-
sure correction scheme (IPCS) due to [13] which gives improved accuracy
compared to the original scheme at little extra cost.
The IPCS scheme involves three steps. First, we compute a tentative ve-
locity u? by advancing the momentum equation (3.29) by a midpoint finite
difference scheme in time, but using the pressure pn from the previous time
interval. We will also linearize the nonlinear convective term by using the
known velocity un from the previous time step: un un . The variational
problem for this first step is

1
h%(u? un )/t, vi + h%un un , vi + h(un+ 2 , pn ), (v)i
1
+ hpn n, vi hun+ 2 n, vi = hf n+1 , vi. (3.32)
58 3 A Gallery of finite element solvers

This notation, suitable for problems with many terms in the variational for-
mulations, requires some explanation. First, we use the short-hand notation
Z Z
hv, wi = vw dx, hv, wi = vw ds.

This allows us to express the variational problem in a more compact way.
1
Second, we use the notation un+ 2 . This notation refers to the value of u at
the midpoint of the interval, usually approximated by an arithmetic mean:
1
un+ 2 (un + un+1 )/2.
Third, we notice that the variational problem (3.32) arises from the integra-
tion by parts of the term h , vi. Just as for the elasticity problem in
Section 3.3, we obtain

h , vi = h, (v)i hT, vi ,
where T = n is the boundary traction. If we solve a problem with a free
boundary, we can take T = 0 on the boundary. However, if we compute the
flow through a channel or a pipe and want to model flow that continues into
an imaginary channel at the outflow, we need to treat this term with some
care. The assumption we then make is that the derivative of the velocity in the
direction of the channel is zero at the outflow, corresponding to a flow that is
fully developed or doesnt change significantly downstream of the outflow.
Doing so, the remaining boundary term at the outflow becomes pn u n,
which is the term appearing in the variational problem (3.32). Note that this
argument and the implementation depends on the exact definition of u,
as either the matrix with components ui /xj or uj /xi . We here choose
the latter, uj /xi , which means that we must use the FEniCS operator
nabla_grad for the implementation. If we use the grad operator and the
definition ui /xj , we must instead keep the terms pn (u)> n!

grad(u) vs. nabla_grad(u)

For scalar functions, u has a clear meaning as the vector
 
u u u
u = , , .
x y z
However, if u is vector-valued, the meaning is less clear. Some sources
define u as the matrix with elements uj /xi , while other sources pre-
fer ui /xj . In FEniCS, grad(u) is defined as the matrix with elements
ui /xj , which is the natural definition of u if we think of this as the
gradient or derivative of u. This way, the matrix u can be applied to
a differential dx to give an increment du = u dx. Since the alterna-
3.4 The NavierStokes equations 59

tive interpretation of u as the matrix with elements uj /xi is very

common, in particular in continuum mechanics, FEniCS provides the
operator nabla_grad for this purpose. For the NavierStokes equations,
it is important to consider the term u u whichshould be interpreted
P  P ui
as the vector w with elements wi = j uj x j
ui = j uj x j
. This
term can be implemented P in FEniCS either as grad(u)*u, since this
is expression becomes j u i /x
P j uj , or as dot(u, nabla_grad(u))
since this expression becomes i ui uj /xi . We will use the notation
dot(u, nabla_grad(u)) below since it corresponds more closely to the
standard notation u u.
To be more precise, there are three different notations used for PDEs
involving gradient, divergence, and curl operators. One employs grad u,
div u, and curl u operators. Another employs u as a synonym for
grad u, u means div u, and u is the name for curl u. The third
operates with u, u, and u in which is a vector and, e.g.,
u is a dyadic expression: (u)i,j = uj /xi = (grad u)> . The latter
notation, with as a vector operator, is often handy when deriving
equations in continuum mechanics, and if this interpretation of is the
foundation of your PDE, you must use nabla_grad, nabla_div, and
nabla_curl in FEniCS code as these operators are compatible with
dyadic computations. From the NavierStokes equations we can easily
see what means: if the convective term has the form u u, actually
meaning (u )u, then is a vector and the implementation becomes
dot(u, nabla_grad(u)) in FEniCS, but if we see u u or (gradu) u,
the corresponding FEniCS expression is dot(grad(u), u).
Similarly, the divergence of a tensor field like the stress tensor
can also be expressed in two different ways, as either div(sigma)
or nabla_div(sigma). The first case corresponds to the components
ij /xj and the second to ij /xi . In general, these expressions will
be different but when the stress measure is symmetric, the expressions
have the same value.

We now move on to the second step in our splitting scheme for the in-
compressible NavierStokes equations. In the first step, we computed the
tentative velocity u? based on the pressure from the previous time step. We
may now use the computed tentative velocity to compute the new pressure
pn :

hpn+1 , qi = hpn , qi t1 h u? , qi. (3.33)

Note here that q is a scalar-valued test function from the pressure space,
whereas the test function v in (3.32) is a vector-valued test function from the
velocity space.
One way to think about this step is to subtract the NavierStokes momen-
tum equation (3.29) expressed in terms of the tentative velocity u? and the
60 3 A Gallery of finite element solvers

pressure pn from the momentum equation expressed in terms of the velocity

un+1 and pressure pn+1 . This results in the equation

(un+1 u? )/t + pn+1 pn = 0. (3.34)

Taking the divergence and requiring that un+1 = 0 by the NavierStokes
continuity equation (3.30), we obtain the equation u? /t + 2 pn+1
2 pn = 0, which is a Poisson problem for the pressure pn+1 resulting in the
variational problem (3.33).
Finally, we compute the corrected velocity un+1 from the equation (3.34).
Multiplying this equation by a test function v, we obtain

hun+1 , vi = hu? , vi th(pn+1 pn ), vi. (3.35)

In summary, we may thus solve the incompressible NavierStokes equa-
tions efficiently by solving a sequence of three linear variational problems in
each time step.

3.4.3 FEniCS implementation

Test problem 1: Channel flow. As a first test problem, we compute the

flow between two infinite plates, so-called channel or Poiseuille flow. As we
shall see, this problem has a known analytical solution. Let H be the distance
between the plates and L the length of the channel. There are no body forces.
We may scale the problem first to get rid of seemingly independent physical
parameters. The physics of this problem is governed by viscous effects only,
in the direction perpendicular to the flow, so a time scale should be based on
diffusion accross the channel: tc = H 2 /. We let U , some characteristic inflow
velocity, be the velocity scale and H the spatial scale. The pressure scale is
taken as the characteristic shear stress, U/H, since this is a primary example
of shear flow. Inserting x
= x/H, y = y/H, z = z/H, u = u/U , p = Hp/(U ),
and t = H 2 / in the equations results in the scaled NavierStokes equations
(dropping bars after the scaling):

u
+ Re u u = p + 2 u,
t
u = 0.

Here, Re = %U H/ is the Reynolds number. Because of the time and pressure

scales, which are different from convection-dominated fluid flow, the Reynolds
number is associated with the convective term and not the viscosity term.
The exact solution is derived by assuming u = (ux (x, y, z), 0, 0), with the
x axis pointing along the channel. Since u = 0, u cannot depend on x.
3.4 The NavierStokes equations 61

The physics of channel flow is also two-dimensional so we can omit the z

coordinate (more precisely: /z = 0). Inserting u = (ux , 0, 0) in the (scaled)
governing equations gives u00x (y) = p/x. Differentiating this equation with
respect to x shows that 2 p/ 2 x = 0 so p/x is a constant, here called .
This is the driving force of the flow and can be specified as a known parameter
in the problem. Integrating u00x (y) = over the width of the channel, [0, 1],
and requiring u = (0, 0, 0) at the channel walls, results in ux = 21 y(1 y).
The characteristic inlet velocity U can be taken as the maximum inflow at
y = 1/2, implying = 8. The length of the channel, L/H in the scaled model,
has no impact on the result, so for simplicity we just compute on the unit
square. Mathematically, the pressure must be prescribed at a point, but since
p does not depend on y, we can set p to a known value, e.g. zero, along the
outlet boundary x = 1. The result is p(x) = 8(1 x) and ux = 4y(1 y).
The boundary conditions can be set as p = 8 at x = 0, p = 0 at x = 1
and u = (0, 0, 0) on the walls y = 0, 1. This defines the pressure drop and
should result in unit maximum velocity at the inlet and outlet and a parabolic
velocity profile without further specifications. Note that it is only meaningful
to solve the NavierStokes equations in 2D or 3D geometries, although the
underlying mathematical problem collapses to two 1D problems, one for ux (y)
and one for p(x).
The scaled model is not so easy to simulate using a standard NavierStokes
solver with dimensions. However, one can argue that the convection term is
zero, so the Re coefficient in front of this term in the scaled PDEs is not
important and can be set to unity. In that case, setting % = = 1 in the
original NavierStokes equations resembles the scaled model.
For a specific engineering problem one wants to simulate a specific fluid
and set corresponding parameters. A general solver is therefore most naturally
implemented with dimensions and the original physical parameters. However,
scaling may greatly simplify numerical simulations. First of all, it shows that
all fluids behave in the same way: it does not matter whether we have oil,
gas, or water flowing between two plates, and it does not matter how fast
the flow is (up to some criticial value of the Reynolds number where the
flow becomes unstable and transitions to a complicated turbulent flow of
totally different nature). This means that one simulation is enough to cover
all types of channel flow! In other applications, scaling shows that it might be
necessary to set just the fraction of some parameters (dimensionless numbers)
rather than the parameters themselves. This simplifies exploring the input
parameter space which is often the purpose of simulation. Frequently, the
scaled problem is run by setting some of the input parameters with dimension
to fixed values (often unity).
FEniCS implementation. Our previous examples have all started out with
the creation of a mesh and then the definition of a FunctionSpace on the
mesh. For the NavierStokes splitting scheme we will need to define two
function spaces, one for the velocity and one for the pressure:
62 3 A Gallery of finite element solvers

V = VectorFunctionSpace(mesh, P, 2)
Q = FunctionSpace(mesh, P, 1)

The first space V is a vector-valued function space for the velocity and the
second space Q is a scalar-valued function space for the pressure. We use
piecewise quadratic elements for the velocity and piecewise linear elements
for the pressure. When creating a VectorFunctionSpace in FEniCS, the
value-dimension (the length of the vectors) will be set equal to the geometric
dimension of the finite element mesh. One can easily create vector-valued
function spaces with other dimensions in FEniCS by adding the keyword
parameter dim:
V = VectorFunctionSpace(mesh, P, 2, dim=10)

Stable finite element spaces for the NavierStokes equations

It is well-known that certain finite element spaces are not stable for the
NavierStokes equations, or even for the simpler Stokes equations. The
prime example of an unstable pair of finite element spaces is to use first
degree continuous piecewise polynomials for both the velocity and the
pressure. Using an unstable pair of spaces typically results in a solu-
tion with spurious (unwanted, non-physical) oscillations in the pressure
solution. The simple remedy is to use continuous piecewise quadratic
elements for the velocity and continuous piecewise linear elements for
the pressure. Together, these elements form the so-called Taylor-Hood
element. Spurious oscillations may occur also for splitting methods if
an unstable element pair is used.

Since we have two different function spaces, we need to create two sets of
trial and test functions:
u = TrialFunction(V)
v = TestFunction(V)
p = TrialFunction(Q)
q = TestFunction(Q)

As we have seen in previous examples, boundaries may be defined in FEn-

iCS by defining Python functions that return True or False depending on
whether a point should be considered part of the boundary, for example
def boundary(x, on_boundary):
return near(x[0], 0)

This function defines the boundary to be all points with x-coordinate

equal to (near) zero. The near function comes from FEniCS and per-
forms a test with tolerance: abs(x[0] - 0) < 3E-16 so we do not run into
rounding troubles. Alternatively, we may give the boundary definition as a
3.4 The NavierStokes equations 63

string of C++ code, much like we have previously defined expressions such
as u_D = Expression(1 + x[0]*x[0] + 2*x[1]*x[1], degree=2). The
above definition of the boundary in terms of a Python function may thus be
replaced by a simple C++ string:
boundary = near(x[0], 0)

This has the advantage of moving the computation of which nodes belong
to the boundary from Python to C++, which improves the efficiency of the
program.
For the current example, we will set three different boundary conditions.
First, we will set u = 0 at the walls of the channel; that is, at y = 0 and y = 1.
Second, we will set p = 8 at the inflow (x = 0) and, finally, p = 0 at the outflow
(x = 1). This will result in a pressure gradient that will accelerate the flow
from the initial state with zero velocity. These boundary conditions may be
defined as follows:
# Define boundaries
inflow = near(x[0], 0)
outflow = near(x[0], 1)
walls = near(x[1], 0) || near(x[1], 1)

# Define boundary conditions

bcu_noslip = DirichletBC(V, Constant((0, 0)), walls)
bcp_inflow = DirichletBC(Q, Constant(8), inflow)
bcp_outflow = DirichletBC(Q, Constant(0), outflow)
bcu = [bcu_noslip]
bcp = [bcp_inflow, bcp_outflow]

At the end, we collect the boundary conditions for the velocity and pressure
in Python lists so we can easily access them in the following computation.
We now move on to the definition of the variational forms. There are three
variational problems to be defined, one for each step in the IPCS scheme. Let
us look at the definition of the first variational problem. We start with some
constants:
U = 0.5*(u_n + u)
n = FacetNormal(mesh)
f = Constant((0, 0))
k = Constant(dt)
mu = Constant(mu)
rho = Constant(rho)

The next step is to set up the variational form for the first step (3.32) in
the solution process. Since the variational problem contains a mix of known
and unknown quantities we will use the following naming convention: u is
the unknown (mathematically un+1 ) as a trial function in the variational
form, u_ is the most recently computed approximation (un+1 available as a
Function object), u_n is un , and the same convention goes for p, p_ (pn+1 ),
and p_n (pn ).
64 3 A Gallery of finite element solvers

# Define strain-rate tensor

def epsilon(u):
return sym(nabla_grad(u))

# Define stress tensor

def sigma(u, p):
return 2*mu*epsilon(u) - p*Identity(len(u))

# Define variational problem for step 1

F1 = rho*dot((u - u_n) / k, v)*dx + \
rho*dot(dot(u_n, nabla_grad(u_n)), v)*dx \
+ inner(sigma(U, p_n), epsilon(v))*dx \
+ dot(p_n*n, v)*ds - dot(mu*nabla_grad(U)*n, v)*ds \
- dot(f, v)*dx
a1 = lhs(F1)
L1 = rhs(F1)

Note that we take advantage of the Python programming language to

define our own operators sigma and epsilon. Using Python this way makes
it easy to extend the mathematical language of FEniCS with special operators
and constitutive laws.
Also note that FEniCS can sort out the bilinear form a(u, v) and linear
form L(v) forms by the lhs and rhs functions. This is particularly convenient
in longer and more complicated variational forms.
The splitting scheme requires the solution of a sequence of three variational
problems in each time step. We have previously used the built-in FEniCS
function solve to solve variational problems. Under the hood, when a user
calls solve(a == L, u, bc), FEniCS will perform the following steps:
A = assemble(A)
b = assemble(L)
bc.apply(A, b)
solve(A, u.vector(), b)

In the last step, FEniCS uses the overloaded solve function to solve the
linear system AUP= b where U is the vector of degrees of freedom for the
function u(x) = j=1 Uj j (x).
In our implementation of the splitting scheme, we will make use of these
low-level commands to first assemble and then call solve. This has the ad-
vantage that we may control when we assemble and when we solve the linear
system. In particular, since the matrices for the three variational problems
are all time-independent, it makes sense to assemble them once and for all
outside of the time-stepping loop:
A1 = assemble(a1)
A2 = assemble(a2)
A3 = assemble(a3)

Within the time-stepping loop, we may then assemble only the right-hand
side vectors, apply boundary conditions, and call the solve function as here
for the first of the three steps:
3.4 The NavierStokes equations 65

# Time-stepping
t = 0
for n in range(num_steps):

# Update current time

t += dt

# Step 1: Tentative velocity step

b1 = assemble(L1)
[bc.apply(b1) for bc in bcu]
solve(A1, u_.vector(), b1)

Notice the Python list comprehension [bc.apply(b1) for bc in bcu] which

iterates over all bc in the list bcu. This is a convenient and compact way to
construct a loop that applies all boundary conditions in a single line. Also,
the code works if we add more Dirichlet boundary conditions in the future.
Note that the boundary conditions only need to be applied to the right-hand
side vectors as they have already been applied to the matrices (not shown).
Finally, let us look at an important detail in how we use parameters such
as the time step dt in the definition of our variational problems. Since we
might want to change these later, for example if we want to experiment with
smaller or larger time steps, we wrap these using a FEniCS Constant:
k = Constant(dt)

The assembly of matrices and vectors in FEniCS is based on code genera-

tion. This means that whenever we change a variational problem, FEniCS will
have to generate new code, which may take a little time. New code will also
be generated and compiled when a float value for the time step is changed. By
wrapping this parameter using Constant, FEniCS will treat the parameter
as a generic constant and not as a specific numerical value, which prevents
repeated code generation. In the case of the time step, we choose a new name
k instead of dt for the Constant since we also want to use the variable dt as
a Python float as part of the time-stepping.
The complete code for simulating 2D channel flow with FEniCS can be
found in the file ft07_navier_stokes_channel.py.
Verification. We compute the error at the nodes as we have done before to
verify that our implementation is correct. Our NavierStokes solver computes
the solution to the time-dependent incompressible NavierStokes equations,
starting from the initial condition u = (0, 0). We have not specified the initial
condition explicitly in our solver which means that FEniCS will initialize all
variables, in particular the previous and current velocities u_n and u_, to
zero. Since the exact solution is quadratic, we expect the solution to be exact
to within machine precision at the nodes at infinite time. For our implemen-
tation, the error quickly approaches zero and is approximately 106 at time
T = 10.
Test problem 2: Flow past a cylinder. We now turn our attention to a
more challenging problem: flow past a circular cylinder. The geometry and pa-
66 3 A Gallery of finite element solvers

Fig. 3.3 Plot of the velocity profile at the final time for the NavierStokes channel
flow example.

rameters are taken from problem DFG 2D-2 in the FEATFLOW/1995-DFG

benchmark suite1 and is illustrated in Figure 3.4. The kinematic viscosity is
given by = 0.001 = /% and the inflow velocity profile is specified as
 
4y(0.41 y)
u(x, y, t) = 1.5 , 0 ,
0.412
which has a maximum magnitude of 1.5 at y = 0.41/2. We do not use any
scaling for this problem since all exact parameters are known.

0.20

0.1
0.21
0.41
0.20

2.20
Fig. 3.4 Geometry for the flow past a cylinder test problem. Notice the slightly per-
turbed and unsymmetric geometry.

1
http://www.featflow.de/en/benchmarks/cfdbenchmarking/flow/dfg_benchmark2_re100.html
3.4 The NavierStokes equations 67

FEniCS implementation. So far all our domains have been simple shapes
such as a unit square or a rectangular box. A number of such simple meshes
may be created using the built-in mesh classes in FEniCS (UnitIntervalMesh,
UnitSquareMesh, UnitCubeMesh, IntervalMesh, RectangleMesh, BoxMesh).
FEniCS supports the creation of more complex meshes via a technique called
constructive solid geometry (CSG), which lets us define geometries in terms
of simple shapes (primitives) and set operations: union, intersection, and set
difference. The set operations are encoded in FEniCS using the operators +
(union), * (intersection), and - (set difference). To access the CSG function-
ality in FEniCS, one must import the FEniCS module mshr which provides
the extended meshing functionality of FEniCS.
The geometry for the cylinder flow test problem can be defined easily by
first defining the rectangular channel and then subtracting the circle:
channel = Rectangle(Point(0, 0), Point(2.2, 0.41))
cylinder = Circle(Point(0.2, 0.2), 0.05)
domain = channel - cylinder

We may then create the mesh by calling the function generate_mesh:

mesh = generate_mesh(domain, 64)

Here the argument 64 indicates that we want to resolve the geometry with
64 cells across its diameter (the channel length).
To solve the cylinder test problem, we only need to make a few minor
changes to the code we wrote for the channel flow test case. Besides defining
the new mesh, the only change we need to make is to modify the boundary
conditions and the time step size. The boundaries are specified as follows:
inflow = near(x[0], 0)
outflow = near(x[0], 2.2)
walls = near(x[1], 0) || near(x[1], 0.41)
cylinder = on_boundary && x[0]>0.1 && x[0]<0.3 && x[1]>0.1 && x[1]<0.3

The last line may seem cryptic before you catch the idea: we want to pick
out all boundary points (on_boundary) that also lie within the 2D domain
[0.1, 0.3] [0.1, 0.3], see Figure 3.4. The only possible points are then the
points on the circular boundary!
In addition to these essential changes, we will make a number of small
changes to improve our solver. First, since we need to choose a relatively
small time step to compute the solution (a time step that is too large will
make the solution blow up) we add a progress bar so that we can follow the
progress of our computation. This can be done as follows:
progress = Progress(Time-stepping)
set_log_level(PROGRESS)

# Time-stepping
t = 0.0
for n in range(num_steps):
68 3 A Gallery of finite element solvers

# Update current time

t += dt

# Place computation here

# Update progress bar

progress.update(t / T)

Log levels and printing in FEniCS

Notice the call to set_log_level(PROGRESS) which is essential to make
FEniCS actually display the progress bar. FEniCS is actually quite in-
formative about what is going on during a computation but the amount
of information printed to screen depends on the current log level. Only
messages with a priority higher than or equal to the current log level
will be displayed. The predefined log levels in FEniCS are DBG, TRACE,
PROGRESS, INFO, WARNING, ERROR, and CRITICAL. By default, the log
level is set to INFO which means that messages at level DBG, TRACE, and
PROGRESS will not be printed. Users may print messages using the FEn-
iCS functions info, warning, and error which will print messages at
the obvious log level (and in the case of error also throw an exception
and exit). One may also use the call log(level, message) to print a
message at a specific log level.

Since the system(s) of linear equations are significantly larger than for the
simple channel flow test problem, we choose to use an iterative method in-
stead of the default direct (sparse) solver used by FEniCS when calling solve.
Efficient solution of linear systems arising from the discretization of PDEs
requires the choice of both a good iterative (Krylov subspace) method and
a good preconditioner. For this problem, we will simply use the biconjugate
gradient stabilized method (BiCGSTAB) and the conjugate gradient method.
This can be done by adding the keywords bicgstab or cg in the call to solve.
We also specify suitable preconditioners to speed up the computations:
solve(A1, u1.vector(), b1, bicgstab, hypre_amg)
solve(A2, p1.vector(), b2, bicgstab, hypre_amg)
solve(A3, u1.vector(), b3, cg, sor)

Finally, to be able to postprocess the computed solution in ParaView, we

store the solution to a file in each time step. We have previously created files
with the suffix .pvd for this purpose. In the example program ft04_heat_
gaussian.py, we first created a file named heat_gaussian/solution.pvd
and then saved the solution in each time step using
vtkfile << (u, t)
3.4 The NavierStokes equations 69

For the present example, we will instead choose to save the solution to
XDMF format. This file format works similarly to the .pvd files we have seen
earlier but has several advantages. First, the storage is much more efficient,
both in terms of speed and file sizes. Second, .xdmf files work in parallell,
both for writing and reading (postprocessing). Much like .pvd files, the actual
data will not be stored in the .xdmf file itself, but will instead be stored in
a (single) separate data file with the suffix .hdf5 which is an advanced file
format designed for high-performance computing. We create the XDMF files
as follows:
xdmffile_u = XDMFFile(navier_stokes_cylinder/velocity.xdmf)
xdmffile_p = XDMFFile(navier_stokes_cylinder/pressure.xdmf)

In each time step, we may then store the velocity and pressure by
xdmffile_u.write(u, t)
xdmffile_p.write(p, t)

We also store the solution using a FEniCS TimeSeries. This allows us to

store the solution not for visualization, but for later reuse in a computation
as we will see in the next section. Using a TimeSeries it is easy and efficient
to read in solutions from certain points in time during a simulation. The
TimeSeries class also uses the HDF5 file format for efficient storage and
access to data.
Figures 3.5 and 3.6 show the velocity and pressure at final time visualized
in ParaView. For the visualization of the velocity, we have used the Glyph
filter to visualize the vector velocity field. For the visualization of the pressure,
we have used the Warp By Scalar filter.

Fig. 3.5 Plot of the velocity for the cylinder test problem at final time.

The complete code for the cylinder test problem looks as follows:
from fenics import *
from mshr import *
import numpy as np

T = 5.0 # final time

num_steps = 5000 # number of time steps
dt = T / num_steps # time step size
mu = 0.001 # dynamic viscosity
70 3 A Gallery of finite element solvers

Fig. 3.6 Plot of the pressure for the cylinder test problem at final time.

rho = 1 # density

# Create mesh
channel = Rectangle(Point(0, 0), Point(2.2, 0.41))
cylinder = Circle(Point(0.2, 0.2), 0.05)
domain = channel - cylinder
mesh = generate_mesh(domain, 64)

# Define function spaces

V = VectorFunctionSpace(mesh, P, 2)
Q = FunctionSpace(mesh, P, 1)

# Define boundaries
inflow = near(x[0], 0)
outflow = near(x[0], 2.2)
walls = near(x[1], 0) || near(x[1], 0.41)
cylinder = on_boundary && x[0]>0.1 && x[0]<0.3 && x[1]>0.1 && x[1]<0.3

# Define inflow profile

inflow_profile = (4.0*1.5*x[1]*(0.41 - x[1]) / pow(0.41, 2), 0)

# Define boundary conditions

bcu_inflow = DirichletBC(V, Expression(inflow_profile, degree=2), inflow)
bcu_walls = DirichletBC(V, Constant((0, 0)), walls)
bcu_cylinder = DirichletBC(V, Constant((0, 0)), cylinder)
bcp_outflow = DirichletBC(Q, Constant(0), outflow)
bcu = [bcu_inflow, bcu_walls, bcu_cylinder]
3.4 The NavierStokes equations 71

bcp = [bcp_outflow]

# Define trial and test functions

u = TrialFunction(V)
v = TestFunction(V)
p = TrialFunction(Q)
q = TestFunction(Q)

# Define functions for solutions at previous and current time steps

u_n = Function(V)
u_ = Function(V)
p_n = Function(Q)
p_ = Function(Q)

# Define expressions used in variational forms

U = 0.5*(u_n + u)
n = FacetNormal(mesh)
f = Constant((0, 0))
k = Constant(dt)
mu = Constant(mu)
rho = Constant(rho)

# Define symmetric gradient

def epsilon(u):
return sym(nabla_grad(u))

# Define stress tensor

def sigma(u, p):
return 2*mu*epsilon(u) - p*Identity(len(u))

# Define variational problem for step 1

F1 = rho*dot((u - u_n) / k, v)*dx \
+ rho*dot(dot(u_n, nabla_grad(u_n)), v)*dx \
+ inner(sigma(U, p_n), epsilon(v))*dx \
+ dot(p_n*n, v)*ds - dot(mu*nabla_grad(U)*n, v)*ds \
- dot(f, v)*dx
a1 = lhs(F1)
L1 = rhs(F1)

# Define variational problem for step 2

a2 = dot(nabla_grad(p), nabla_grad(q))*dx
L2 = dot(nabla_grad(p_n), nabla_grad(q))*dx - (1/k)*div(u_)*q*dx

# Define variational problem for step 3

a3 = dot(u, v)*dx
L3 = dot(u_, v)*dx - k*dot(nabla_grad(p_ - p_n), v)*dx

# Assemble matrices
A1 = assemble(a1)
A2 = assemble(a2)
A3 = assemble(a3)

# Apply boundary conditions to matrices

[bc.apply(A1) for bc in bcu]
72 3 A Gallery of finite element solvers

[bc.apply(A2) for bc in bcp]

# Create XDMF files for visualization output

xdmffile_u = XDMFFile(navier_stokes_cylinder/velocity.xdmf)
xdmffile_p = XDMFFile(navier_stokes_cylinder/pressure.xdmf)

# Create time series (for use in reaction_system.py)

timeseries_u = TimeSeries(navier_stokes_cylinder/velocity_series)
timeseries_p = TimeSeries(navier_stokes_cylinder/pressure_series)

# Save mesh to file (for use in reaction_system.py)

File(navier_stokes_cylinder/cylinder.xml.gz) << mesh

# Create progress bar

progress = Progress(Time-stepping)
set_log_level(PROGRESS)

# Time-stepping
t = 0
for n in range(num_steps):

# Update current time

t += dt

# Step 1: Tentative velocity step

b1 = assemble(L1)
[bc.apply(b1) for bc in bcu]
solve(A1, u_.vector(), b1, bicgstab, hypre_amg)

# Step 2: Pressure correction step

b2 = assemble(L2)
[bc.apply(b2) for bc in bcp]
solve(A2, p_.vector(), b2, bicgstab, hypre_amg)

# Step 3: Velocity correction step

b3 = assemble(L3)
solve(A3, u_.vector(), b3, cg, sor)

# Plot solution
plot(u_, title=Velocity)
plot(p_, title=Pressure)

# Save solution to file (XDMF/HDF5)

xdmffile_u.write(u_, t)
xdmffile_p.write(p_, t)

# Save nodal values to file

timeseries_u.store(u_.vector(), t)
timeseries_p.store(p_.vector(), t)

# Update previous solution

u_n.assign(u_)
p_n.assign(p_)
3.5 A system of advectiondiffusionreaction equations 73

# Update progress bar

progress.update(t / T)
print(u max:, u_.vector().array().max())

# Hold plot
interactive()

This program can be found in the file ft08_navier_stokes_cylinder.py.

The reader should be advised that this example program is considerably more
demanding than our previous examples in terms of CPU time and memory,
but it should be possible to run the program on a reasonably modern laptop.

3.5 A system of advectiondiffusionreaction

equations
The problems we have encountered so farwith the notable exception of the
NavierStokes equationsall share a common feature: they all involve mod-
els expressed by a single scalar or vector PDE. In many situations the model
is instead expressed as a system of PDEs, describing different quantities pos-
sibly governed by (very) different physics. As we saw for the NavierStokes
equations, one way to solve a system of PDEs in FEniCS is to use a splitting
method where we solve one equation at a time and feed the solution from
one equation into the next. However, one of the strengths with FEniCS is
the ease by which one can instead define variational problems that couple
several PDEs into one compound system. In this section, we will look at how
to use FEniCS to write solvers for such systems of coupled PDEs. The goal
is to demonstrate how easy it is to implement fully implicit, also known as
monolithic, solvers in FEniCS.

3.5.1 PDE problem

Our model problem is the following system of advectiondiffusionreaction

equations:

u1
+ w u1 (u1 ) = f1 Ku1 u2 , (3.36)
t
u2
+ w u2 (u2 ) = f2 Ku1 u2 , (3.37)
t
u3
+ w u3 (u3 ) = f3 + Ku1 u2 Ku3 . (3.38)
t
74 3 A Gallery of finite element solvers

This system models the chemical reaction between two species A and B
in some domain :

A + B C.
We assume that the reaction is first-order, meaning that the reaction rate
is proportional to the concentrations [A] and [B] of the two species A and B:
d
[C] = K[A][B].
dt
We also assume that the formed species C spontaneously decays with a rate
proportional to the concentration [C]. In the PDE system (3.36)(3.38), we
use the variables u1 , u2 , and u3 to denote the concentrations of the three
species:

u1 = [A], u2 = [B], u3 = [C].

We see that the chemical reactions are accounted for in the right-hand sides
of the PDE system (3.36)(3.38).
The chemical reactions take part at each point in the domain . In addi-
tion, we assume that the species A, B, and C diffuse throughout the domain
with diffusivity  (the terms (ui )) and are advected with velocity w
(the terms w ui ).
To make things visually and physically interesting, we shall let the chemical
reaction take place in the velocity field computed from the solution of the
incompressible NavierStokes equations around a cylinder from the previous
section. In summary, we will thus be solving the following coupled system of
nonlinear PDEs:

 
w
% + w w = (w, p) + f, (3.39)
t
w = 0, (3.40)
u1
+ w u1 (u1 ) = f1 Ku1 u2 , (3.41)
t
u2
+ w u2 (u2 ) = f2 Ku1 u2 , (3.42)
t
u3
+ w u3 (u3 ) = f3 + Ku1 u2 Ku3 . (3.43)
t
We assume that u1 = u2 = u3 = 0 at t = 0 and inject the species A and B into
the system by specifying nonzero source terms f1 and f2 close to the corners
at the inflow, and take f3 = 0. The result will be that A and B are convected
by advection and diffusion throughout the channel, and when they mix the
species C will be formed.
3.5 A system of advectiondiffusionreaction equations 75

Since the system is one-way coupled from the NavierStokes subsystem to

the advectiondiffusionreaction subsystem, we do not need to recompute the
solution to the NavierStokes equations, but can just read back the previously
computed velocity field w and feed it into our equations. But we do need to
learn how to read and write solutions for time-dependent PDE problems.

3.5.2 Variational formulation

We obtain the variational formulation of our system by multiplying each

equation by a test function, integrating the second-order terms (ui )
by parts, and summing up the equations. When working with FEniCS it is
convenient to think of the PDE system as a vector of equations. The test
functions are collected in a vector too, and the variational formulation is the
inner product of the vector PDE and the vector test function.
We also need introduce some discretization in time. We will use the back-
ward Euler method as before when we solved the heat equation and approx-
imate the time derivatives by (un+1
i uni )/t. Let v1 , v2 , and v3 be the test
functions, or the components of the test vector function. The inner product
results in

Z
(t1 (un+1
1 un n+1
1 )v1 + w u1 v1 + un+1
1 v1 ) dx (3.44)

Z
+ (t1 (un+1
2 un n+1
2 )v2 + w u2 v2 + un+1
2 v2 ) dx
Z
+ (t1 (un+1
3 un n+1
3 )v3 + w u3 v3 + un+1
3 v3 ) dx

Z
(f1 v1 + f2 v2 + f3 v3 ) dx
Z
(Kun+1
1 un+1
2 v1 Kun+1
1 un+1
2 v2 + Kun+1
1 un+1
2 v3 Kun+1
3 v3 ) dx = 0.

For this problem it is natural to assume homogeneous Neumann boundary

conditions on the entire boundary for u1 , u2 , and u3 ; that is, ui /n = 0 for
i = 1, 2, 3. This means that the boundary terms vanish when we integrate by
parts.
76 3 A Gallery of finite element solvers

3.5.3 FEniCS implementation

The first step is to read the mesh from file. Luckily, we made sure to save the
mesh to file in the NavierStokes example and can now easily read it back
from file:
mesh = Mesh(navier_stokes_cylinder/cylinder.xml.gz)

The mesh is stored in the native FEniCS XML format (with additional gzip-
ping to decrease the file size).
Next, we need to define the finite element function space. For this problem,
we need to define several spaces. The first space we create is the space for
the velocity field w from the NavierStokes simulation. We call this space W
and define the space by
W = VectorFunctionSpace(mesh, P, 2)

It is important that this space is exactly the same as the space we used for the
velocity field in the NavierStokes solver. To read the values for the velocity
field, we use a TimeSeries:
timeseries_w = TimeSeries(navier_stokes_cylinder/velocity_series)

This will initialize the object timeseries_w which we will call later in the
time-stepping loop to retrieve values from the file velocity_series.h5 (in
binary HDF5 format).
For the three concentrations u1 , u2 , and u3 , we want to create a mixed
space with functions that represent the full system (u1 , u2 , u3 ) as a single
entity. To do this, we need to define a MixedElement as the product space of
three simple finite elements and then used the mixed element to define the
function space:
P1 = FiniteElement(P, triangle, 1)
element = MixedElement([P1, P1, P1])
V = FunctionSpace(mesh, element)

Mixed elements as products of elements

FEniCS also allows finite elements to be defined as products of simple
elements (or mixed elements). For example, the well-known Taylor
Hood element, with quadratic velocity components and linear pressure
functions, may be defined as follows:
P2 = VectorElement(P, triangle, 2)
P1 = FiniteElement(P, triangle, 1)
TH = P2 * P1
3.5 A system of advectiondiffusionreaction equations 77

This syntax works great for two elements, but for three or more ele-
ments we meet a subtle issue in how the Python interpreter handles the
* operator. For the reaction system, we create the mixed element by
element = MixedElement([P1, P1, P1]) and one would be tempted
to write
element = P1 * P1 * P1

However, this is equivalent to writing element = (P1 * P1) * P1 so

the result will be a mixed element consisting of two subsystems, the
first of which in turn consists of two scalar subsystems.
Finally, we remark that for the simple case of a mixed system con-
sisting of three scalar elements as for the reaction system, the definition
is in fact equivalent to using a standard vector-valued element:
element = VectorElement(P, triangle, 1, dim=3)
V = FunctionSpace(mesh, element)

Once the space has been created, we need to define our test functions and
finite element functions. Test functions for a mixed function space can be
created by replacing TestFunction by TestFunctions:
v_1, v_2, v_3 = TestFunctions(V)

Since the problem is nonlinear, we need to work with functions rather than
trial functions for the unknowns. This can be done by using the corresponding
Functions construction in FEniCS. However, as we will need to access the
Function for the entire system itself, we first need to create that function
and then access its components:
u = Function(V)
u_1, u_2, u_3 = split(u)

These functions will be used to represent the unknowns u1 , u2 , and u3 at the

new time level n + 1. The corresponding values at the previous time level n
are denoted by u_n1, u_n2, and u_n3 in our program.
When now all functions and test functions have been defined, we can
express the nonlinear variational problem (3.44):
F = ((u_1 - u_n1) / k)*v_1*dx + dot(w, grad(u_1))*v_1*dx \
+ eps*dot(grad(u_1), grad(v_1))*dx + K*u_1*u_2*v_1*dx \
+ ((u_2 - u_n2) / k)*v_2*dx + dot(w, grad(u_2))*v_2*dx \
+ eps*dot(grad(u_2), grad(v_2))*dx + K*u_1*u_2*v_2*dx \
+ ((u_3 - u_n3) / k)*v_3*dx + dot(w, grad(u_3))*v_3*dx \
+ eps*dot(grad(u_3), grad(v_3))*dx - K*u_1*u_2*v_3*dx + K*u_3*v_3*dx \
- f_1*v_1*dx - f_2*v_2*dx - f_3*v_3*dx

The time-stepping simply consists of solving this variational problem in

each time step by a call to the solve function:
78 3 A Gallery of finite element solvers

t = 0
for n in range(num_steps):
t += dt
timeseries_w.retrieve(w.vector(), t)
solve(F == 0, u)
u_n.assign(u)

In each time step, we first read the current value for the velocity field from the
time series we have previously stored. We then solve the nonlinear system,
and assign the computed values to the left-hand side values for the next
time interval. When retrieving values from a TimeSeries, the values will by
default be interpolated (linearly) to the given time t if the time does not
exactly match a sample in the series.
The solution at the final time is shown in Figure 3.7. We clearly see the
advection of the species A and B and the formation of C along the center of
the channel where A and B meet.

Fig. 3.7 Plot of the concentrations of the three species A, B, and C (from top to
bottom) at final time.

The complete code is presented below.

from fenics import *

T = 5.0 # final time

num_steps = 500 # number of time steps
dt = T / num_steps # time step size
eps = 0.01 # diffusion coefficient
K = 10.0 # reaction rate
3.5 A system of advectiondiffusionreaction equations 79

# Read mesh from file

mesh = Mesh(navier_stokes_cylinder/cylinder.xml.gz)

# Define function space for velocity

W = VectorFunctionSpace(mesh, P, 2)

# Define function space for system of concentrations

P1 = FiniteElement(P, triangle, 1)
element = MixedElement([P1, P1, P1])
V = FunctionSpace(mesh, element)

# Define test functions

v_1, v_2, v_3 = TestFunctions(V)

# Define functions for velocity and concentrations

w = Function(W)
u = Function(V)
u_n = Function(V)

# Split system functions to access components

u_1, u_2, u_3 = split(u)
u_n1, u_n2, u_n3 = split(u_n)

# Define source terms

f_1 = Expression(pow(x[0]-0.1,2)+pow(x[1]-0.1,2)<0.05*0.05 ? 0.1 : 0,
degree=1)
f_2 = Expression(pow(x[0]-0.1,2)+pow(x[1]-0.3,2)<0.05*0.05 ? 0.1 : 0,
degree=1)
f_3 = Constant(0)

# Define expressions used in variational forms

k = Constant(dt)
K = Constant(K)
eps = Constant(eps)

# Define variational problem

F = ((u_1 - u_n1) / k)*v_1*dx + dot(w, grad(u_1))*v_1*dx \
+ eps*dot(grad(u_1), grad(v_1))*dx + K*u_1*u_2*v_1*dx \
+ ((u_2 - u_n2) / k)*v_2*dx + dot(w, grad(u_2))*v_2*dx \
+ eps*dot(grad(u_2), grad(v_2))*dx + K*u_1*u_2*v_2*dx \
+ ((u_3 - u_n3) / k)*v_3*dx + dot(w, grad(u_3))*v_3*dx \
+ eps*dot(grad(u_3), grad(v_3))*dx - K*u_1*u_2*v_3*dx + K*u_3*v_3*dx \
- f_1*v_1*dx - f_2*v_2*dx - f_3*v_3*dx

# Create time series for reading velocity data

timeseries_w = TimeSeries(navier_stokes_cylinder/velocity_series)

# Create VTK files for visualization output

vtkfile_u_1 = File(reaction_system/u_1.pvd)
vtkfile_u_2 = File(reaction_system/u_2.pvd)
vtkfile_u_3 = File(reaction_system/u_3.pvd)

# Create progress bar

80 3 A Gallery of finite element solvers

progress = Progress(Time-stepping)
set_log_level(PROGRESS)

# Time-stepping
t = 0
for n in range(num_steps):

# Update current time

t += dt

# Read velocity from file

timeseries_w.retrieve(w.vector(), t)

# Solve variational problem for time step

solve(F == 0, u)

# Save solution to file (VTK)

_u_1, _u_2, _u_3 = u.split()
vtkfile_u_1 << (_u_1, t)
vtkfile_u_2 << (_u_2, t)
vtkfile_u_3 << (_u_3, t)

# Update previous solution

u_n.assign(u)

# Update progress bar

progress.update(t / T)

# Hold plot
interactive()

This example program can be found in the file ft09_reaction_system.py.

Finally, we comment on three important techniques that are very use-
ful when working with systems of PDEs: setting initial conditions, setting
boundary conditions, and extracting components of the system for plotting
or postprocessing.
Setting initial conditions for mixed systems. In our example, we did
not need to worry about setting an initial condition, since we start with
u1 = u2 = u3 = 0. This happens automatically in the code when we set
u_n = Function(V). This creates a Function for the whole system and all
degrees of freedom are set to zero.
If we want to set initial conditions for the components of the system sepa-
rately, the easiest solution is to define the initial conditions as a vector-valued
Expression and then project (or interpolate) this to the Function represent-
ing the whole system. For example,
u_0 = Expression((sin(x[0]), cos(x[0]*x[1]), exp(x[1])), degree=1)
u_n = project(u_0, V)

This defines u1 , u2 , and u2 to be the projections of sin x, cos(xy), and exp(y),

respectively.
3.5 A system of advectiondiffusionreaction equations 81

Setting boundary conditions for mixed systems. In our example, we

also did not need to worry about setting boundary conditions since we used
a natural Neumann condition. If we want to set Dirichlet conditions for in-
dividual components of the system, this can be done as usual by the class
DirichletBC, but we must specify for which subsystem we set the bound-
ary condition. For example, to specify that u2 should be equal to xy on the
boundary defined by boundary, we do
u_D = Expression(x[0]*x[1], degree=1)
bc = DirichletBC(V.sub(1), u_D, boundary)

The object bc or a list of such objects containing different boundary condi-

tions, can then be passed to the solve function as usual. Note that numbering
starts at 0 in FEniCS so the subspace corresponding to u2 is V.sub(1).
Accessing components of mixed systems. If u is a Function defined on
a mixed function space in FEniCS, there are several ways in which u can be
split into components. Above we already saw an example of the first of these:
u_1, u_2, u_3 = split(u)

This extracts the components of u as symbols that can be used in a variational

problem. The above statement is in fact equivalent to
u_1 = u[0]
u_2 = u[1]
u_3 = u[2]

Note that u[0] is not really a Function object, but merely a symbolic ex-
pression, just like grad(u) in FEniCS is a symbolic expression and not a
Function representing the gradient. This means that u_1, u_2, u_3 can be
used in a variational problem, but cannot be used for plotting or postpro-
cessing.
To access the components of u for plotting and saving the solution to file,
we need to use a different variant of the split function:
u_1_, u_2_, u_3_ = u.split()

This returns three subfunctions as actual objects with access to the common
underlying data stored in u, which makes plotting and saving to file possible.
Alternatively, we can do
u_1_, u_2_, u_3_ = u.split(deepcopy=True)

which will create u_1_, u_2_, and u_3_ as stand-alone Function objects,
each holding a copy of the subfunction data extracted from u. This is useful
in many situations but is not necessary for plotting and saving solutions to
file.
Chapter 4
Subdomains and boundary conditions

So far, we have only looked briefly at how to specify boundary conditions. In this
chapter, we look more closely at how to specify boundary conditions on specific
parts (subdomains) of the boundary and how to combine multiple boundary con-
ditions. We will also look at how to generate meshes with subdomains and how
to define coefficients with different values in different subdomains.

4.1 Combining Dirichlet and Neumann

conditions
Lets return to the Poisson problem from Chapter 2 and see how to extend
the mathematics and the implementation to handle a Dirichlet condition in
combination with a Neumann condition. The domain is still the unit square,
but now we set the Dirichlet condition u = uD at the left and right sides,
x = 0 and x = 1, while the Neumann condition
u
=g
n
is applied to the remaining sides y = 0 and y = 1.

4.1.1 PDE problem

Let D and N denote the parts of the boundary where the Dirichlet
and Neumann conditions apply, respectively. The complete boundary-value
problem can be written as

c 2017, Hans Petter Langtangen, Anders Logg.
Released under CC Attribution 4.0 license
84 4 Subdomains and boundary conditions

2 u = f in , (4.1)
u = uD on D , (4.2)
u
= g on N . (4.3)
n
Again, we choose u = 1 + x2 + 2y 2 as the exact solution and adjust f , g, and
uD accordingly:

f (x, y) = 6,

0, y = 0,
g(x, y) =
4, y = 1,
uD (x, y) = 1 + x2 + 2y 2 .

For ease of programming, we define g as a function over the whole domain

such that g takes on the correct values at y = 0 and y = 1. One possible
extension is

g(x, y) = 4y .

4.1.2 Variational formulation

The first task is to derive the variational formulation. This time we cannot
omit the boundary term arising from the integration by parts, because v is
only zero on D . We have
Z Z Z
u
(2 u)v dx = u v dx v ds,
n
and since v = 0 on D ,
Z Z Z
u u
v ds = v ds = gv ds,
n n
N
N

by applying the boundary condition on N . The resulting weak form reads

Z Z Z
u v dx = f v dx gv ds . (4.4)
N

Expressing this equation in the standard notation a(u, v) = L(v) is straight-

forward with
4.1 Combining Dirichlet and Neumann conditions 85
Z
a(u, v) = u v dx, (4.5)
Z Z
L(v) = f v dx gv ds . (4.6)
N

4.1.3 FEniCS implementation

How does the Neumann condition impact the implementation? Let us revisit
our previous implementation ft01_poisson.py from Section 2.2 and examine
which changes we need to make to incorporate the Neumann condition. It
turns out that only two changes are necessary:
The function boundary defining the Dirichlet boundary must be modified.
The new boundary term must be added to the expression for L.
The first adjustment can be coded as
tol = 1E-14

def boundary_D(x, on_boundary):

if on_boundary:
if near(x[0], 0, tol) or near(x[0], 1, tol):
return True
else:
return False
else:
return False

A more compact implementation reads

def boundary_D(x, on_boundary):
return on_boundary and (near(x[0], 0, tol) or near(x[0], 1, tol))

The second adjustment of our program concerns the definition of L, which

needs to include the Neumann condition:
g = Expression(4*x[1], degree=1)
L = f*v*dx - g*v*ds

The ds variable implies a boundary integral, while dx implies an integral over

the domain . No other modifications are necessary.
Note that the integration *ds is carried out over the entire boundary,
including the Dirichlet boundary. However, since the test function v vanishes
on the Dirichlet boundary (as a result specifying a DirichletBC), the integral
will only include the contribution from the Neumann boundary.
86 4 Subdomains and boundary conditions

4.2 Setting multiple Dirichlet conditions

In the previous section, we used a single function uD (x, y) for setting Dirichlet
conditions on two parts of the boundary. Often it is more practical to use
multiple functions, one for each subdomain of the boundary. Let us return to
the case from Section 4.1 and redefine the problem in terms of two Dirichlet
conditions:

2 u = f in ,
L
u = uL on D ,
R
u = uR on D ,
u
=g on N .
n
L R
Here, D is the left boundary x = 0, while D is the right boundary x = 1.
We note that uL (x, y) = 1 + 2y 2 , uR (x, y) = 2 + 2y 2 , and g(x, y) = 4y.
L
For the boundary condition on D , we define the usual triple of an expres-
sion for the boundary value, a function defining the location of the boundary,
and a DirichletBC object:
u_L = Expression(1 + 2*x[1]*x[1], degree=2)

def boundary_L(x, on_boundary):

tol = 1E-14
return on_boundary and near(x[0], 0, tol)

bc_L = DirichletBC(V, u_L, boundary_L)

R
For the boundary condition on D , we write a similar code snippet:

u_R = Expression(2 + 2*x[1]*x[1], degree=2)

def boundary_R(x, on_boundary):

tol = 1E-14
return on_boundary and near(x[0], 1, tol)

bc_R = DirichletBC(V, u_R, boundary_R)

We collect the two boundary conditions in a list which we can pass to the
solve function to compute the solution:
bcs = [bc_L, bc_R]
...
solve(a == L, u, bcs)

Note that for boundary values that do not depend on x or y, we might

replace the Expression objects by Constant objects.
4.3 Defining subdomains for different materials 87

4.3 Defining subdomains for different materials

Solving PDEs in domains made up of different materials is a frequently en-
countered task. In FEniCS, these kinds of problems are handled by defining
subdomains inside the domain. A simple example with two materials (subdo-
mains) in 2D will demonstrate the idea. We consider the following variable-
coefficient extension of the Poisson equation from Chapter 2:

[(x, y)u(x, y)] = f (x, y), (4.7)

in some domain . Physically, this problem may be viewed as a model of
heat conduction, with variable heat conductivity (x, y) > 0.
For illustration purposes, we consider the domain = [0, 1] [0, 1] and
divide it into two equal subdomains, as depicted in Figure 4.1:

0 = [0, 1] [0, 1/2], 1 = [0, 1] (1/2, 1] .

We define (x, y) = 0 in 0 and (x, y) = 1 in 1 , where 0 , 1 > 0 are
given constants.

Fig. 4.1 Two subdomains with different material parameters.

The variational formulation may be easily expressed in FEniCS as follows:

a = kappa*dot(grad(u), grad(v))*dx
L = f*v*dx

In the remainder of this section, we will discuss different strategies for defining
the coefficient kappa as an Expression that takes on different values in the
two subdomains.
88 4 Subdomains and boundary conditions

4.3.1 Using expressions to define subdomains

The simplest way to implement a variable coefficient = (x, y) is to define an

Expression which depends on the coordinates x and y. We have previously
used the Expression class to define expressions based on simple formulas.
Aternatively, an Expression can be defined as a Python class which allows for
more complex logic. The following code snippet illustrates this construction:
class K(Expression):
def set_k_values(self, k_0, k_1):
self.k_0, self.k_1 = k_0, k_1

def eval(self, value, x):

"Set value[0] to value at point x"
tol = 1E-14
if x[1] <= 0.5 + tol:
value[0] = self.k_0
else:
value[0] = self.k_1

# Initialize kappa
kappa = K(degree=0)
kappa.set_k_values(1, 0.01)

The eval method gives great flexibility in defining functions, but a downside
is that FEniCS will call eval in Python for each node x, which is a slow
process.
An alternative method is to use a C++ string expression as we have seen
before, which is much more efficient in FEniCS. This can be done using an
inline if test:
tol = 1E-14
k_0 = 1.0
k_1 = 0.01
kappa = Expression(x[1] <= 0.5 + tol ? k_0 : k_1, degree=0,
tol=tol, k_0=k_0, k_1=k_1)

This method of defining variable coefficients works if the subdomains are

simple shapes that can be expressed in terms of geometric inequalities. How-
ever, for more complex subdomains, we will need to use a more general tech-
nique, as we will see next.

4.3.2 Using mesh functions to define subdomains

We now address how to specify the subdomains 0 and 1 using a more gen-
eral technique. This technique involves the use of two classes that are essential
in FEniCS when working with subdomains: SubDomain and MeshFunction.
Consider the following definition of the boundary x = 0:
4.3 Defining subdomains for different materials 89

def boundary(x, on_boundary):

tol = 1E-14
return on_boundary and near(x[0], 0, tol)

This boundary definition is actually a shortcut to the more general FEniCS

concept SubDomain. A SubDomain is a class which defines a region in space
(a subdomain) in terms of a member function inside which returns True for
points that belong to the subdomain and False for points that dont belong
to the subdomain. Here is how to specify the boundary x = 0 as a SubDomain:
class Boundary(SubDomain):
def inside(self, x, on_boundary):
tol = 1E-14
return on_boundary and near(x[0], 0, tol)

boundary = Boundary()
bc = DirichletBC(V, Constant(0), boundary)

We notice that the inside function of the class Boundary is (almost) iden-
tical to the previous boundary definition in terms of the boundary function.
Technically, our class Boundary is a subclass of the FEniCS class SubDomain.
We will use two SubDomain subclasses to define the two subdomains 0
and 1 :
tol = 1E-14

class Omega_0(SubDomain):
def inside(self, x, on_boundary):
return x[1] <= 0.5 + tol

class Omega_1(SubDomain):
def inside(self, x, on_boundary):
return x[1] >= 0.5 - tol

Notice the use of <= and >= in both tests. FEniCS will call the inside
function for each vertex in a cell to determine whether or not the cell belongs
to a particular subdomain. For this reason, it is important that the test
holds for all vertices in cells aligned with the boundary. In addition, we use a
tolerance to make sure that vertices on the internal boundary at y = 0.5 will
belong to both subdomains. This is a little counter-intuitive, but is necessary
to make the cells both above and below the internal boundary belong to
either 0 or 1 .
To define the variable coefficient , we will use a powerful tool in FEn-
iCS called a MeshFunction. A MeshFunction is a discrete function that can
be evaluated at a set of so-called mesh entities. A mesh entity in FEn-
iCS is either a vertex, an edge, a face, or a cell (triangle or tetrahedron).
A MeshFunction over cells is suitable to represent subdomains (materials),
while a MeshFunction over facets (edges or faces) is used to represent pieces
of external or internal boundaries. A MeshFunction over cells can also be used
to represent boundary markers for mesh refinement. A FEniCS MeshFunction
90 4 Subdomains and boundary conditions

is parameterized both over its data type (like integers or booleans) and its
dimension (0 = vertex, 1 = edge etc.). Special subclasses VertexFunction,
EdgeFunction etc. are provided for easy definition of a MeshFunction of a
particular dimension.
Since we need to define subdomains of in the present example, we make
use of a CellFunction. The constructor is given two arguments: (1) the type
of value: int for integers, size_t for non-negative (unsigned) integers,
double for real numbers, and bool for logical values; (2) a Mesh ob-
ject. Alternatively, the constructor can take just a filename and initialize the
CellFunction from data in a file.
We first create a CellFunction with non-negative integer values (size_t):
materials = CellFunction(size_t, mesh)

Next, we use the two subdomains to mark the cells belonging to each
subdomain:
subdomain_0 = Omega_0()
subdomain_1 = Omega_1()
subdomain_0.mark(materials, 0)
subdomain_1.mark(materials, 1)

This will set the values of the mesh function materials to 0 on each cell
belonging to 0 and 1 on all cells belonging to 1 . Alternatively, we can use
the following equivalent code to mark the cells:
materials.set_all(0)
subdomain_1.mark(materials, 1)

To examine the values of the mesh function and see that we have indeed
defined our subdomains correctly, we can simply plot the mesh function:
plot(materials, interactive=True)

We may also wish to store the values of the mesh function for later use:
File(materials.xml.gz) << materials

which can later be read back from file as follows:

File(materials.xml.gz) >> materials

Now, to use the values of the mesh function materials to define the
variable coefficient , we create a FEniCS Expression:
class K(Expression):
def __init__(self, materials, k_0, k_1, **kwargs):
self.materials = materials
self.k_0 = k_0
self.k_1 = k_1

def eval_cell(self, values, x, cell):

if self.materials[cell.index] == 0:
4.3 Defining subdomains for different materials 91

values[0] = self.k_0
else:
values[0] = self.k_1

kappa = K(materials, k_0, k_1, degree=0)

This is similar to the Expression subclass we defined above, but we make

use of the member function eval_cell in place of the regular eval function.
This version of the evaluation function has an additional cell argument
which we can use to check on which cell we are currently evaluating the
function. We also defined the special function __init__ (the constructor) so
that we can pass all data to the Expression when it is created.
Since we make use of geometric tests to define the two SubDomains for 0
and 1 , the MeshFunction method may seem like an unnecessary compli-
cation of the simple method using an Expression with an if-test. However,
in general the definition of subdomains may be available as a MeshFunction
(from a data file), perhaps generated as part of the mesh generation process,
and not as a simple geometric test. In such cases the method demonstrated
here is the recommended way to work with subdomains.

4.3.3 Using C++ code snippets to define subdomains

The SubDomain and Expression Python classes are very convenient, but
their use leads to function calls from C++ to Python for each node in the
mesh. Since this involves a significant cost, we need to make use of C++ code
if performance is an issue.
Instead of writing the SubDomain subclass in Python, we may instead use
the CompiledSubDomain tool in FEniCS to specify the subdomain in C++
code and thereby speed up our code. Consider the definition of the classes
Omega_0 and Omega_1 above in Python. The key strings that define these
subdomains can be expressed in C++ syntax and given as arguments to
CompiledSubDomain as follows:
tol = 1E-14
subdomain_0 = CompiledSubDomain(x[1] <= 0.5 + tol, tol=tol)
subdomain_1 = CompiledSubDomain(x[1] >= 0.5 - tol, tol=tol)

As seen, parameters can be specified using keyword arguments. The resulting

objects, subdomain_0 and subdomain_1, can be used as ordinary SubDomain
objects.
Compiled subdomain strings can be applied for specifying boundaries as
well:
boundary_R = CompiledSubDomain(on_boundary && near(x[0], 1, tol),
tol=1E-14)
92 4 Subdomains and boundary conditions

It is also possible to feed the C++ string (without parameters) directly

as the third argument to DirichletBC without explicitly constructing a
CompiledSubDomain object:
bc1 = DirichletBC(V, value, on_boundary && near(x[0], 1, tol))

Python Expression classes may also be redefined using C++ for more ef-
ficient code. Consider again the definition of the class K above for the variable
coefficient = (x). This may be redefined using a C++ code snippet and
the keyword cppcode to the regular FEniCS Expression class:
cppcode = """
class K : public Expression
{
public:

void eval(Array<double>& values,

const Array<double>& x,
const ufc::cell& cell) const
{
if ((*materials)[cell.index] == 0)
values[0] = k_0;
else
values[0] = k_1;
}

std::shared_ptr<MeshFunction<std::size_t>> materials;
double k_0;
double k_1;

};
"""

kappa = Expression(cppcode=cppcode, degree=0)

kappa.materials = materials
kappa.k_0 = k_0
kappa.k_1 = k_1

4.4 Setting multiple Dirichlet, Neumann, and

Robin conditions

Consider again the variable-coefficient Poisson problem from Section 4.3. We

will now discuss how to implement general combinations of boundary condi-
tions of Dirichlet, Neumann, and Robin type for this model problem.
4.4 Setting multiple Dirichlet, Neumann, and Robin conditions 93

4.4.1 Three types of boundary conditions

We extend our repertoire of boundary conditions to three types: Dirichlet,

Neumann, and Robin. Dirichlet conditions apply to some parts D0 , D1 , . . ., of
the boundary:

u = u0D on D0 , u = u1D on D1 , ...,

where uiD are prescribed functions, i = 0, 1, . . .. On other parts, N0 , N1 , . . ., we
have Neumann conditions:
u u
= g0 on N0 , = g1 on N1 , ...,
n n
Finally, we have Robin conditions:
u
= r(u s),
n
where r and s are specified functions. The Robin condition is most often
used to model heat transfer to the surroundings and arise naturally from
Newtons cooling law. In that case, r is a heat transfer coefficient, and s is
the temperature of the surroundings. Both can be space and time-dependent.
The Robin conditions apply at some parts R0 , R1 , . . ., of the boundary:
u u
= r0 (u s0 ) on R0 , = r1 (u s1 ) on R1 , ...
n n

4.4.2 PDE problem

With the notation above, the model problem to be solved with multiple
Dirichlet, Neumann, and Robin conditions can be formulated as follows:

(u) = f in , (4.8)
i i
u = uD on D , i = 0, 1, . . . (4.9)
u
= gi on Ni , i = 0, 1, . . . (4.10)
n
u
= ri (u si ) on Ri , i = 0, 1, . . . (4.11)
n
94 4 Subdomains and boundary conditions

4.4.3 Variational formulation

As usual, we multiply by a test function v and integrate by parts:

Z Z Z
u
(u)v dx = u v dx v ds .
n
On the Dirichlet part of the boundary (Di ), the boundary integral vanishes
since v = 0. On the remaining part of the boundary, we split the boundary
integral into contributions from the Neumann parts (Ni ) and Robin parts
(Ri ). Inserting the boundary conditions, we obtain

Z Z XZ
u X u u
v ds = ds
ds
n i n i n
i N i R
XZ XZ
= gi ds + ri (u si ) ds .
i i i i
N R

We thus obtain the following variational problem:

Z XZ XZ Z
F= u v dx + gi v ds + ri (u si )v ds f v dx = 0 .
i i i i
N R
(4.12)
We have been used to writing this variational formulation in the standard
notation a(u, v) = L(v), which requires that we identify all integral depend-
ing on the trial function u, and collect these in a(u, v), while the remaining
integrals go into L(v). The integrals from the Robin condition must for this
reason be split into two parts:
Z Z Z
ri (u si )v ds = ri uv ds ri si v ds .
i i i
R R R

We then have

Z XZ
a(u, v) = u v dx + ri uv ds, (4.13)
i i
R
Z XZ XZ
L(v) = f v dx gi v ds + ri si v ds . (4.14)
i i i i
N R

Alternatively, we may keep the formulation (4.12) and either solve the varia-
tional problem as a nonlinear problem (F == 0) in FEniCS or use the FEniCS
functions lhs and rhs to extract the bilinear and linear parts of F:
a = lhs(F)
4.4 Setting multiple Dirichlet, Neumann, and Robin conditions 95

L = rhs(F)
Note that if we choose to solve this linear problem as a nonlinear problem,
the Newton iteration will converge in a single iteration.

4.4.4 FEniCS implementation

Let us examine how to extend our Poisson solver to handle general combina-
tions of Dirichlet, Neumann, and Robin boundary conditions. Compared to
our previous code, we must consider the following extensions:
Defining markers for the different parts of the boundary.
Splitting the boundary integral into parts using the markers.
A general approach to the first task is to mark each of the desired boundary
parts with markers 0, 1, 2, and so forth. Here we aim at the four sides of the
unit square, marked with 0 (x = 0), 1 (x = 1), 2 (y = 0), and 3 (y = 1). The
markers will be defined using a MeshFunction, but contrary to Section 4.3,
this is not a function over cells, but a function over the facets of the mesh.
We use a FacetFunction for this purpose:
boundary_markers = FacetFunction(size_t, mesh)
As in Section 4.3 we use a subclass of SubDomain to identify the various
parts of the mesh function. Problems with domains of more complicated
geometries may set the mesh function for marking boundaries as part of the
mesh generation. In our case, the boundary x = 0 can be marked as follows:
class BoundaryX0(SubDomain):
tol = 1E-14
def inside(self, x, on_boundary):
return on_boundary and near(x[0], 0, tol)

bx0 = BoundaryX0()
bx0.mark(boundary_markers, 0)
Similarly, we create the classes BoundaryX1 (x = 1), BoundaryY0 (y = 0), and
BoundaryY1 (y = 1) boundary, and mark these as subdomains 1, 2, and 3,
respectively.
For generality of the implementation, we let the user specify what kind
of boundary condition that applies to each of the four boundaries. We set
up a Python dictionary for this purpose, with the key as subdomain number
and the value as a dictionary specifying the kind of condition as key and a
function as its value. For example,
boundary_conditions = {0: {Dirichlet: u_D},
1: {Robin: (r, s)},
2: {Neumann: g},
3: {Neumann, 0}}
96 4 Subdomains and boundary conditions

specifies
a Dirichlet condition u = uD for x = 0;
a Robin condition n u = r(u s) for x = 1;
a Neumann condition n u = g for y = 0;
a Neumann condition n u = 0 for y = 1.
As explained in Section 4.2, multiple Dirichlet conditions must be collected
in a list of DirichletBC objects. Based on the boundary_conditions data
structure above, we can construct this list by the following code snippet:
bcs = []
for i in boundary_conditions:
if Dirichlet in boundary_conditions[i]:
bc = DirichletBC(V, boundary_conditions[i][Dirichlet],
boundary_markers, i)
bcs.append(bc)

A new aspect of the variational problem is the two distinct boundary

integrals over Ni and Ri . Having a mesh function over exterior cell facets
(our boundary_markers object), where subdomains (boundary parts) are
numbered as 0, 1, 2, . . ., the special symbol ds(0) implies integration over
subdomain (part) 0, ds(1) denotes integration over subdomain (part) 1, and
so on. The idea of multiple ds-type objects generalizes to volume integrals
too: dx(0), dx(1), etc., are used to integrate over subdomain 0, 1, etc., inside
.
To express integrals over the boundary parts using ds(i), we must first
redefine the measure ds in terms of our boundary markers:
ds = Measure(ds, domain=mesh, subdomain_data=boundary_markers)

Similarly, if we want integration over different parts of the domain, we redefine

dx as
dx = Measure(dx, domain=mesh, subdomain_data=domain_markers)

where domain_markers is a CellFunction defining subdomains in .

Suppose we have a Robin condition with values r and s on subdomain
R, and a Neumann condition with value g on subdomain N. The variational
form can then be written
a = kappa*dot(grad(u), grad(v))*dx + r*u*v*ds(R)
L = f*v*dx - g*v*ds(N) + r*s*v*ds(R)

In our case, things get a bit more complicated since the information about
integrals in Neumann and Robin conditions are in the boundary_conditions
data structure. We can collect all Neumann conditions by the following code
snippet:
integrals_N = []
for i in boundary_conditions:
4.4 Setting multiple Dirichlet, Neumann, and Robin conditions 97

if Neumann in boundary_conditions[i]:
if boundary_conditions[i][Neumann] != 0:
g = boundary_conditions[i][Neumann]
integrals_N.append(g*v*ds(i))

Applying sum(integrals_N) will apply the + operator to the variational

forms in the integrals_N list and result in the integrals we need for the
right-hand side L of the variational form.
The integrals in the Robin condition can similarly be collected in lists:
integrals_R_a = []
integrals_R_L = []
for i in boundary_conditions:
if Robin in boundary_conditions[i]:
r, s = boundary_conditions[i][Robin]
integrals_R_a.append(r*u*v*ds(i))
integrals_R_L.append(r*s*v*ds(i))

We are now in a position to define the a and L expressions in the variational

formulation:
a = kappa*dot(grad(u), grad(v))*dx + sum(integrals_R_a)
L = f*v*dx - sum(integrals_N) + sum(integrals_R_L)

Alternatively, we may use the FEniCS functions lhs and rhs as mentioned
above to simplify the extraction of terms for the Robin integrals:
integrals_R = []
for i in boundary_conditions:
if Robin in boundary_conditions[i]:
r, s = boundary_conditions[i][Robin]
integrals_R.append(r*(u - s)*v*ds(i))

F = kappa*dot(grad(u), grad(v))*dx + \
sum(integrals_R) - f*v*dx + sum(integrals_N)
a, L = lhs(F), rhs(F)

This time we can more naturally define the integrals from the Robin condition
as r*(u - s)*v*ds(i).
The complete code can be found in the function solver_bcs in the pro-
gram ft10_poisson_extended.py.

4.4.5 Test problem

We will use the same exact solution ue = 1+x2 +2y 2 as in Chapter 2, and thus
take = 1 and f = 6. Our domain is the unit square, and we assign Dirichlet
conditions at x = 0 and x = 1, a Robin condition at y = 0, and a Neumann
condition at y = 1. With the given exact solution ue , we realize that the
Neumann condition at y = 1 is u/n = u/y = 4y = 4, while the Robin
condition at y = 0 can be selected in many ways. Since u/n = u/y = 0
98 4 Subdomains and boundary conditions

at y = 0, we can select s = ue and specify r 6= 0 arbitrarily in the Robin

condition. We will set r = 1000 and s = ue .
The boundary parts are thus D0 : x = 0, D1 : x = 1, R0 : y = 0, and N0 :
y = 1.
When implementing this test problem, and especially other test problems
with more complicated expressions, it is advantageous to use symbolic com-
puting. Below we define the exact solution as a sympy expression and derive
other functions from their mathematical definitions. Then we turn these ex-
pressions into C/C++ code, which can then be used to define Expression
objects.
# Define manufactured solution in sympy and derive f, g, etc.
import sympy as sym
x, y = sym.symbols(x[0], x[1]) # needed by UFL
u = 1 + x**2 + 2*y**2 # exact solution
u_e = u # exact solution
u_00 = u.subs(x, 0) # restrict to x = 0
u_01 = u.subs(x, 1) # restrict to x = 1
f = -sym.diff(u, x, 2) - sym.diff(u, y, 2) # -Laplace(u)
f = sym.simplify(f) # simplify f
g = -sym.diff(u, y).subs(y, 1) # compute g = -du/dn
r = 1000 # Robin data, arbitrary
s = u # Robin data, u = s

# Collect variables
variables = [u_e, u_00, u_01, f, g, r, s]

# Turn into C/C++ code strings

variables = [sym.printing.ccode(var) for var in variables]

# Turn into FEniCS Expressions

variables = [Expression(var, degree=2) for var in variables]

# Extract variables
u_e, u_00, u_01, f, g, r, s = variables

# Define boundary conditions

boundary_conditions = {0: {Dirichlet: u_00}, # x = 0
1: {Dirichlet: u_01}, # x = 1
2: {Robin: (r, s)}, # y = 0
3: {Neumann: g}} # y = 1

The complete code can be found in the function demo_bcs in the program
ft10_poisson_extended.py.

4.4.6 Debugging boundary conditions

It is easy to make mistakes when implementing a problem with many different

types of boundary conditions, as in the present case. One method to debug
4.5 Generating meshes with subdomains 99

boundary conditions is to run through all vertex coordinates and check if the
SubDomain.inside method marks the vertex as on the boundary. Another
useful method is to list which degrees of freedom that are subject to Dirichlet
conditions, and for first-order Lagrange (P1 ) elements, print the correspond-
ing vertex coordinates as illustrated by the following code snippet:
if debug1:

# Print all vertices that belong to the boundary parts

for x in mesh.coordinates():
if bx0.inside(x, True): print(%s is on x = 0 % x)
if bx1.inside(x, True): print(%s is on x = 1 % x)
if by0.inside(x, True): print(%s is on y = 0 % x)
if by1.inside(x, True): print(%s is on y = 1 % x)

# Print the Dirichlet conditions

print(Number of Dirichlet conditions:, len(bcs))
if V.ufl_element().degree() == 1: # P1 elements
d2v = dof_to_vertex_map(V)
coor = mesh.coordinates()
for i, bc in enumerate(bcs):
print(Dirichlet condition %d % i)
boundary_values = bc.get_boundary_values()
for dof in boundary_values:
print( dof %2d: u = %g % (dof, boundary_values[dof]))
if V.ufl_element().degree() == 1:
print( at point %s %
(str(tuple(coor[d2v[dof]].tolist()))))

Calls to the inside method

In the code snippet above, we call the inside method for each coordinate
of the mesh. We could also place a printout inside the inside method.
Then it will be surprising to see that this method is called not only
for the points assoicated with degrees of freedom. For P1 elements the
method is also called for each midpoint on each facet of the cells. This
is because a Dirichlet condition is by default set only if the entire facet
can be said to be subject to the condition defining the boundary.

4.5 Generating meshes with subdomains

So far, we have worked mostly with simple meshes (the unit square) and
defined boundaries and subdomains in terms of simple geometric tests like
x = 0 or y 0.5. For more complex geometries, it is not realistic to specify
boundaries and subdomains in this way. Instead, the boundaries and subdo-
mains must be defined as part of the mesh generation process. We will now
100 4 Subdomains and boundary conditions

look at how to use the FEniCS mesh generation tool mshr to generate meshes
and define subdomains.

4.5.1 PDE problem

We will again solve the Poisson equation, but this time for a different applica-
tion. Consider an iron cylinder with copper wires wound around the cylinder
as in Figure 4.2. Through the copper wires a static current J = 1 A is flowing
and we want to compute the magnetic field B in the iron cylinder, the copper
wires, and the surrounding vacuum.

Fig. 4.2 Cross-section of an iron cylinder with copper wires wound around the cylinder,
here with n = 8 windings. The inner circles are cross-sections of the copper wire coming
up (north) and the outer circles are cross-sections of the copper wire going down into
the plane (south).

First, we simplify the problem to a 2D problem. We can do this by assum-

ing that the cylinder extends far along the z-axis and as a consequence the
field is virtually independent of the z-coordinate. Next, we consider Maxwells
equation to derive a Poisson equation for the magnetic field (or rather its po-
tential):
4.5 Generating meshes with subdomains 101

D = %, (4.15)
B = 0, (4.16)
B
E = , (4.17)
t
D
H = + J. (4.18)
t
Here, D is the displacement field, B is the magnetic field, E is the electric
field, and H is the magnetizing field. In addition to Maxwells equations, we
also need a constitutive relation between B and H,

B = H, (4.19)
which holds for an isotropic linear magnetic medium. Here, is the magnetic
permeability of the material. Now, since B is solenoidal (divergence free)
according to Maxwells equations, we know that B must be the curl of some
vector field A. This field is called the magnetic vector potential. Since the
problem is static and thus D/t = 0, it follows that

J = H = (1 B) = (1 A) = (1 A). (4.20)

In the last step, we have expanded the second derivatives and used the gauge
freedom of A to simplify the equations to a simple vector-valued Poisson
problem for the magnetic vector potential; if B = A, then B = (A +
) for any scalar field (the gauge function). For the current problem, we
thus need to solve the following 2D Poisson problem for the z-component Az
of the magnetic vector potential:

(1 Az ) = Jz in R2 , (4.21)
lim Az = 0. (4.22)
|(x,y)|

Since we cannot solve this problem on an infinite domain, we will truncate

the domain using a large disk and set Az = 0 on the boundary. The current
Jz is set to +1 A in the interior set of circles (copper wire cross-sections) and
to 1 A in the exterior set of circles in Figure 4.2.
Once the magnetic vector potential has been computed, we can compute
the magnetic field B = B(x, y) by

 
Az Az
B(x, y) = , . (4.23)
y x
102 4 Subdomains and boundary conditions

4.5.2 Variational formulation

The variational problem is derived as before by multiplying the PDE with a

test function v and integrating by parts. Since the boundary integral vanishes
due to the Dirichlet condition, we obtain
Z Z
1
Az v dx = Jz v dx, (4.24)

or, in other words, a(Az , v) = L(v) with

Z
a(Az , v) = 1 Az v dx, (4.25)

Z
L(v) = Jz v dx. (4.26)

4.5.3 FEniCS implementation

The first step is to generate a mesh for the geometry described in Figure 4.2.
We let a and b be the inner and outer radii of the iron cylinder and let c1
and c2 be the radii of the two concentric distributions of copper wire cross-
sections. Furthermore, we let r be the radius of a copper wire, R be the
radius of our domain, and n be the number of windings (giving a total of
2n copper-wire cross-sections). This geometry can be described easily using
mshr and a little bit of Python programming:
# Define geometry for background
domain = Circle(Point(0, 0), R)

# Define geometry for iron cylinder

cylinder = Circle(Point(0, 0), b) - Circle(Point(0, 0), a)

# Define geometry for wires (N = North (up), S = South (down))

angles_N = [i*2*pi/n for i in range(n)]
angles_S = [(i + 0.5)*2*pi/n for i in range(n)]
wires_N = [Circle(Point(c_1*cos(v), c_1*sin(v)), r) for v in angles_N]
wires_S = [Circle(Point(c_2*cos(v), c_2*sin(v)), r) for v in angles_S]

The mesh that we generate will be a mesh of the entire disk with radius
R but we need the mesh generation to respect the internal boundaries de-
fined by the iron cylinder and the copper wires. We also want mshr to label
the subdomains so that we can easily specify material parameters () and
currents. To do this, we use the mshr function set_subdomain as follows:
# Set subdomain for iron cylinder
domain.set_subdomain(1, cylinder)
4.5 Generating meshes with subdomains 103

# Set subdomains for wires

for (i, wire) in enumerate(wires_N):
domain.set_subdomain(2 + i, wire)
for (i, wire) in enumerate(wires_S):
domain.set_subdomain(2 + n + i, wire)

Once the subdomains have been created, we can generate the mesh:
mesh = generate_mesh(domain, 32)

A detail of the mesh is shown in Figure 4.3.

Fig. 4.3 Plot of (part of) the mesh generated for the magnetostatics test problem. The
subdomains for the iron cylinder and copper wires are clearly visible

The mesh generated with mshr will contain information about the sub-
domains we have defined. To use this information in the definition of our
variational problem and subdomain-dependent parameters, we will need to
create a MeshFunction that marks the subdomains. This can be easily created
by a call to the member function mesh.domains, which holds the subdomain
data generated by mshr:
markers = MeshFunction(size_t, mesh, 2, mesh.domains())

This line creates a MeshFunction with unsigned integer values (the subdo-
main numbers) with dimension 2, which is the cell dimension for this 2D
problem.
104 4 Subdomains and boundary conditions

We can now use the markers as we have done before to redefine the inte-
gration measure dx:
dx = Measure(dx, domain=mesh, subdomain_data=markers)

Integrals over subdomains can then be expressed by dx(0), dx(1), and so

on. We use this to define the current Jz = 1 A in the coppper wires:
J_N = Constant(1.0)
J_S = Constant(-1.0)
A_z = TrialFunction(V)
v = TestFunction(V)
a = (1 / mu)*dot(grad(A_z), grad(v))*dx
L_N = sum(J_N*v*dx(i) for i in range(2, 2 + n))
L_S = sum(J_S*v*dx(i) for i in range(2 + n, 2 + 2*n))
L = L_N + L_S

The permeability is defined as an Expression that depends on the sub-

domain number:
class Permeability(Expression):
def __init__(self, mesh, **kwargs):
self.markers = markers
def eval_cell(self, values, x, ufc_cell):
if markers[ufc_cell.index] == 0:
values[0] = 4*pi*1e-7 # vacuum
elif markers[ufc_cell.index] == 1:
values[0] = 1e-5 # iron (should really be 2.5e-1)
else:
values[0] = -6.4e-6 # copper (yes, its negative!)

mu = Permeability(mesh, degree=1)

As seen in this code snippet, we have used a somewhat less extreme value for
the magnetic permeability of iron. This is to make the solution a little more
interesting. It would otherwise be completely dominated by the field in the
iron cylinder.
Finally, when Az has been computed, we can compute the magnetic field:
W = VectorFunctionSpace(mesh, P, 1)
B = project(as_vector((A_z.dx(1), -A_z.dx(0))), W)

We use as_vector to interpret (A_z.dx(1), -A_z.dx(0)) as a vector in

the sense of the UFL form language, and not as a Python tuple. The result-
ing plots of the magnetic vector potential and magnetic field are shown in
Figures 4.4 and 4.5.
The complete code for computing the magnetic field follows below.
from fenics import *
from mshr import *
from math import sin, cos, pi

a = 1.0 # inner radius of iron cylinder

b = 1.2 # outer radius of iron cylinder
4.5 Generating meshes with subdomains 105

Fig. 4.4 Plot of the z-component Az of the magnetic vector potential.

Fig. 4.5 Plot of the magnetic field B in the xy-plane.

c_1 = 0.8 # radius for inner circle of copper wires

c_2 = 1.4 # radius for outer circle of copper wires
r = 0.1 # radius of copper wires
R = 5.0 # radius of domain
n = 10 # number of windings

# Define geometry for background

106 4 Subdomains and boundary conditions

domain = Circle(Point(0, 0), R)

# Define geometry for iron cylinder

cylinder = Circle(Point(0, 0), b) - Circle(Point(0, 0), a)

# Define geometry for wires (N = North (up), S = South (down))

angles_N = [i*2*pi/n for i in range(n)]
angles_S = [(i + 0.5)*2*pi/n for i in range(n)]
wires_N = [Circle(Point(c_1*cos(v), c_1*sin(v)), r) for v in angles_N]
wires_S = [Circle(Point(c_2*cos(v), c_2*sin(v)), r) for v in angles_S]

# Set subdomain for iron cylinder

domain.set_subdomain(1, cylinder)

# Set subdomains for wires

for (i, wire) in enumerate(wires_N):
domain.set_subdomain(2 + i, wire)
for (i, wire) in enumerate(wires_S):
domain.set_subdomain(2 + n + i, wire)

# Create mesh
mesh = generate_mesh(domain, 32)

# Define function space

V = FunctionSpace(mesh, P, 1)

# Define boundary condition

bc = DirichletBC(V, Constant(0), on_boundary)

# Define subdomain markers and integration measure

markers = MeshFunction(size_t, mesh, 2, mesh.domains())
dx = Measure(dx, domain=mesh, subdomain_data=markers)

# Define current densities

J_N = Constant(1.0)
J_S = Constant(-1.0)

# Define magnetic permeability

class Permeability(Expression):
def __init__(self, mesh, **kwargs):
self.markers = markers
def eval_cell(self, values, x, cell):
if markers[cell.index] == 0:
values[0] = 4*pi*1e-7 # vacuum
elif markers[cell.index] == 1:
values[0] = 1e-5 # iron (should really be 2.5e-1)
else:
values[0] = -6.4e-6 # copper (yes, its negative!)

mu = Permeability(mesh, degree=1)

# Define variational problem

A_z = TrialFunction(V)
v = TestFunction(V)
4.5 Generating meshes with subdomains 107

a = (1 / mu)*dot(grad(A_z), grad(v))*dx
L_N = sum(J_N*v*dx(i) for i in range(2, 2 + n))
L_S = sum(J_S*v*dx(i) for i in range(2 + n, 2 + 2*n))
L = L_N + L_S

# Solve variational problem

A_z = Function(V)
solve(a == L, A_z, bc)

# Compute magnetic field (B = curl A)

W = VectorFunctionSpace(mesh, P, 1)
B = project(as_vector((A_z.dx(1), -A_z.dx(0))), W)

# Plot solution
plot(A_z)
plot(B)

# Save solution to file

vtkfile_A_z = File(magnetostatics/potential.pvd)
vtkfile_B = File(magnetostatics/field.pvd)
vtkfile_A_z << A_z
vtkfile_B << B

# Hold plot
interactive()

This example program can be found in the file ft11_magnetostatics.py.

Chapter 5
Extensions: Improving the Poisson
solver

The FEniCS programs we have written so far have been designed as flat Python
scripts. This works well for solving simple demo problems. However, when you
build a solver for an advanced application, you will quickly find the need for more
structured programming. In particular, you may want to reuse your solver to solve
a large number of problems where you vary the boundary conditions, the domain,
and coefficients such as material parameters. In this chapter, we will see how to
write general solver functions to improve the usability of FEniCS programs. We
will also discuss how to utilize iterative solvers with preconditioners for solving
linear systems, how to compute derived quantities, such as, e.g., the flux on a part
of the boundary, and how to compute errors and convergence rates.

5.1 Refactoring the Poisson solver

Most programs discussed in this book are flat; that is, they are not orga-
nized into logical, reusable units in terms of Python functions. Such flat pro-
grams are useful for quickly testing ideas and sketching solution algorithms,
but are not well suited for serious problem solving. We shall therefore look
at how to refactor the Poisson solver from Chapter 2. For a start, this means
splitting the code into functions. But refactoring is not just a reordering of
existing statements. During refactoring, we also try to make the functions
we create as reusable as possible in other contexts. We will also encapsu-
late statements specific to a certain problem into (non-reusable) functions.
Being able to distinguish reusable code from specialized code is a key issue
when refactoring code, and this ability depends on a good mathematical un-
derstanding of the problem at hand (what is general, what is special?). In
a flat program, general and specialized code (and mathematics) are often
mixed together, which tends to give a blurred understanding of the problem
at hand.

c 2017, Hans Petter Langtangen, Anders Logg.
Released under CC Attribution 4.0 license
110 5 Extensions: Improving the Poisson solver

5.1.1 A more general solver function

We consider the flat program ft01_poisson.py for solving the Poisson prob-
lem developed in Chapter 2. Some of the code in this program is needed to
solve any Poisson problem 2 u = f on [0, 1] [0, 1] with u = uD on the
boundary, while other statements arise from our simple test problem. Let
us collect the general, reusable code in a function called solver. Our spe-
cial test problem will then just be an application of our solver with some
additional statements. We limit the solver function to just compute the nu-
merical solution. Plotting and comparing the solution with the exact solution
are considered to be problem-specific activities to be performed elsewhere.
We parameterize solver by f , uD , and the resolution of the mesh. Since
it is so trivial to use higher-order finite element functions by changing the
third argument to FunctionSpace, we also add the polynomial degree of the
finite element function space as an argument to solver.
from fenics import *
import numpy as np

def solver(f, u_D, Nx, Ny, degree=1):

"""
Solve -Laplace(u) = f on [0,1] x [0,1] with 2*Nx*Ny Lagrange
elements of specified degree and u = u_D (Expresssion) on
the boundary.
"""

# Create mesh and define function space

mesh = UnitSquareMesh(Nx, Ny)
V = FunctionSpace(mesh, P, degree)

# Define boundary condition

def boundary(x, on_boundary):
return on_boundary

bc = DirichletBC(V, u_D, boundary)

# Define variational problem

u = TrialFunction(V)
v = TestFunction(V)
a = dot(grad(u), grad(v))*dx
L = f*v*dx

# Compute solution
u = Function(V)
solve(a == L, u, bc)

return u

The remaining tasks of our initial program, such as calling the solver
function with problem-specific parameters and plotting, can be placed in
5.1 Refactoring the Poisson solver 111

a separate function. Here we choose to put this code in a function named

run_solver:
def run_solver():
"Run solver to compute and post-process solution"

# Set up problem parameters and call solver

u_D = Expression(1 + x[0]*x[0] + 2*x[1]*x[1], degree=2)
f = Constant(-6.0)
u = solver(f, u_D, 8, 8, 1)

# Plot solution and mesh

plot(u)
plot(u.function_space().mesh())

# Save solution to file in VTK format

vtkfile = File(poisson_solver/solution.pvd)
vtkfile << u

The solution can now be computed, plotted, and saved to file by simply
calling the run_solver function.

5.1.2 Writing the solver as a Python module

The refactored code is placed in a file ft12_poisson_solver.py. We should

make sure that such a file can be imported (and hence reused) in other pro-
grams. This means that all statements in the main program that are not
inside functions should appear within a test if __name__ == __main__:.
This test is true if the file is executed as a program, but false if the file
is imported. If we want to run this file in the same way as we can run
ft01_poisson.py, the main program is simply a call to run_solver followed
by a call to interactive to hold the plot:
if __name__ == __main__:
run_solver()
interactive()

This complete program can be found in the file ft12_poisson_solver.py.

5.1.3 Verification and unit tests

The remaining part of our first program is to compare the numerical and
the exact solutions. Every time we edit the code we must rerun the test
and examine that error_max is sufficiently small so we know that the code
still works. To this end, we shall adopt unit testing, meaning that we create
a mathematical test and corresponding software that can run all our tests
112 5 Extensions: Improving the Poisson solver

automatically and check that all tests pass. Python has several tools for unit
testing. Two very popular ones are pytest and nose. These are almost identical
and very easy to use. More classical unit testing with test classes is offered by
the built-in module unittest, but here we are going to use pytest (or nose)
since that will result in shorter and clearer code.
Mathematically, our unit test is that the finite element solution of our
problem when f = 6 equals the exact solution u = uD = 1 + x2 + 2y 2 at the
vertices of the mesh. We have already created a code that finds the error
at the vertices for our numerical solution. Because of rounding errors, we
cannot demand this error to be zero, but we have to use a tolerance, which
depends on the number of elements and the degrees of the polynomials in
the finite element basis. If we want to test that the solver function works
for meshes up to 2 (20 20) elements and cubic Lagrange elements, 1010
is an appropriate tolerance for testing that the maximum error vanishes.
To make our test case work together with pytest and nose, we have to
make a couple of small adjustments to our program. The simple rule is that
each test must be placed in a function that
has a name starting with test_,
has no arguments, and
implements a test expressed as assert success, msg.

Regarding the last point, success is a boolean expression that is False if

the test fails, and in that case the string msg is written to the screen. When
the test fails, assert raises an AssertionError exception in Python, and
otherwise runs silently. The msg string is optional, so assert success is the
minimal test. In our case, we will write assert error_max < tol, where tol
is the tolerance mentioned above.
A proper test function for implementing this unit test in the pytest or nose
testing frameworks has the following form. Note that we perform the test for
different mesh resolutions and degrees of finite elements.
def test_solver():
"Test solver by reproducing u = 1 + x^2 + 2y^2"

# Set up parameters for testing

tol = 1E-10
u_D = Expression(1 + x[0]*x[0] + 2*x[1]*x[1], degree=2)
f = Constant(-6.0)

# Iterate over mesh sizes and degrees

for Nx, Ny in [(3, 3), (3, 5), (5, 3), (20, 20)]:
for degree in 1, 2, 3:
print(Solving on a 2 x (%d x %d) mesh with P%d elements.
% (Nx, Ny, degree))

# Compute solution
u = solver(f, u_D, Nx, Ny, degree)
5.1 Refactoring the Poisson solver 113

# Extract the mesh

mesh = u.function_space().mesh()

# Compute maximum error at vertices

vertex_values_u_D = u_D.compute_vertex_values(mesh)
vertex_values_u = u.compute_vertex_values(mesh)
error_max = np.max(np.abs(vertex_values_u_D - \
vertex_values_u))

# Check maximum error

msg = error_max = %g % error_max
assert error_max < tol, msg

To run the test, we type the following command:

Terminal

Terminal> py.test ft12_poisson_solver.py

This will run all functions named test_* (currently only the test_solver
function) found in the file and report the results. For more verbose output,
add the flags -s -v.
We shall make it a habit to encapsulate numerical test problems in unit
tests as above, and we strongly encourage the reader to create similar unit
tests whenever a FEniCS solver is implemented.

Tip: Print messages in test functions

The assert statement runs silently when the test passes so users may
become uncertain if all the statements in a test function are really
executed. A psychological help is to print out something before assert
(as we do in the example above) such that it is clear that the test really
takes place. Note that py.test needs the -s option to show printout
from the test functions.

Tip: Debugging with iPython

One can easily enter iPython from a Python script by adding the fol-
lowing line anywhere in the code:
from IPython import embed; embed()

This line starts an interactive Python session which lets you print and
plot variables, which can be very helpful for debugging.
114 5 Extensions: Improving the Poisson solver

5.1.4 Parameterizing the number of space dimensions

FEniCS makes it is easy to write a unified simulation code that can op-
erate in 1D, 2D, and 3D. As an appetizer, go back to the previous pro-
grams ft01_poisson.py or ft12_poisson_solver.py and change the mesh
construction from UnitSquareMesh(8, 8) to UnitCubeMesh(8, 8, 8). Now
the domain is the unit cube partitioned into 8 8 8 boxes, and each box
is divided into six tetrahedron-shaped finite elements for computations. Run
the program and observe that we can solve a 3D problem without any other
modifications! (In 1D, expressions must be modified to not depend on x[1].)
The visualization allows you to rotate the cube and observe the function
values as colors on the boundary.
If we want to parameterize the creation of unit interval, unit square, or unit
cube over dimension, we can do so by encapsulating this part of the code in a
function. Given a list or tuple specifying the division into cells in the spatial
coordinates, the following function returns the mesh for a d-dimensional cube:
def UnitHyperCube(divisions):
mesh_classes = [UnitIntervalMesh, UnitSquareMesh, UnitCubeMesh]
d = len(divisions)
mesh = mesh_classes[d - 1](*divisions)
return mesh

The construction mesh_class[d - 1] will pick the right name of the object
used to define the domain and generate the mesh. Moreover, the argument
*divisions sends all the components of the list divisions as separate ar-
guments to the constructor of the mesh construction class picked out by
mesh_class[d - 1]. For example, in a 2D problem where divisions has
two elements, the statement
mesh = mesh_classes[d - 1](*divisions)

is equivalent to
mesh = UnitSquareMesh(divisions[0], divisions[1])

The solver function from ft12_poisson_solver.py may be modified

to solve d-dimensional problems by replacing the Nx and Ny parameters by
divisions, and calling the function UnitHyperCube to create the mesh. Note
that UnitHyperCube is a function and not a class, but we have named it using
so-called CamelCase notation to make it look like a class:
mesh = UnitHyperCube(divisions)
5.2 Working with linear solvers 115

5.2 Working with linear solvers

Sparse LU decomposition (Gaussian elimination) is used by default to solve
linear systems of equations in FEniCS programs. This is a very robust and
simple method. It is the recommended method for systems with up to a few
thousand unknowns and may hence be the method of choice for many 2D
and smaller 3D problems. However, sparse LU decomposition becomes slow
and one quickly runs out of memory for larger problems. For large problems,
we instead need to use iterative methods which are faster and require much
less memory. We will now look at how to take advantage of state-of-the-art
iterative solution methods in FEniCS.

5.2.1 Choosing a linear solver and preconditioner

Preconditioned Krylov solvers is a type of popular iterative methods that

are easily accessible in FEniCS programs. The Poisson equation results in
a symmetric, positive definite system matrix, for which the optimal Krylov
solver is the Conjugate Gradient (CG) method. For non-symmetric problems,
a Krylov solver for non-symmetric systems, such as GMRES, is a better
choice. Incomplete LU factorization (ILU) is a popular and robust all-round
preconditioner, so let us try the GMRES-ILU pair:
solve(a == L, u, bc,
solver_parameters={linear_solver: gmres,
preconditioner: ilu})
# Alternative syntax
solve(a == L, u, bc,
solver_parameters=dict(linear_solver=gmres,
preconditioner=ilu))

Section 5.2.6 lists the most popular choices of Krylov solvers and precondi-
tioners available in FEniCS.

5.2.2 Choosing a linear algebra backend

The actual GMRES and ILU implementations that are brought into action
depend on the choice of linear algebra package. FEniCS interfaces several
linear algebra packages, called linear algebra backends in FEniCS terminology.
PETSc is the default choice if FEniCS is compiled with PETSc. If PETSc is
not available, then FEniCS falls back to using the Eigen backend. The linear
algebra backend in FEniCS can be set using the following command:
parameters.linear_algebra_backend = backendname
116 5 Extensions: Improving the Poisson solver

where backendname is a string. To see which linear algebra backends are avail-
able, you can call the FEniCS function list_linear_algebra_backends.
Similarly, one may check which linear algebra backend is currently being
used by the following command:
print(parameters.linear_algebra_backend)

5.2.3 Setting solver parameters

We will normally want to control the tolerance in the stopping criterion and
the maximum number of iterations when running an iterative method. Such
parameters can be controlled at both a global and a local level. We will start
by looking at how to set global parameters. For more advanced programs,
one may want to use a number of different linear solvers and set different
tolerances and other parameters. Then it becomes important to control the
parameters at a local level. We will return to this issue in Section 5.3.1.
Changing a parameter in the global FEniCS parameter database affects all
linear solvers (created after the parameter has been set). The global FEniCS
parameter database is simply called parameters and it behaves as a nested
dictionary. Write
info(parameters, verbose=True)

to list all parameters and their default values in the database. The nesting of
parameter sets is indicated through indentation in the output from info. Ac-
cording to this output, the relevant parameter set is named krylov_solver,
and the parameters are set like this:
prm = parameters.krylov_solver # short form
prm.absolute_tolerance = 1E-10
prm.relative_tolerance = 1E-6
prm.maximum_iterations = 1000

Stopping criteria for Krylov solvers usually involve some norm of the residual,
which must be smaller than the absolute tolerance parameter or smaller than
the relative tolerance parameter times the initial residual.
We remark that default values for the global parameter database can be
defined in an XML file. To generate such a file from the current set of pa-
rameters in a program, run
File(parameters.xml) << parameters

If a dolfin_parameters.xml file is found in the directory where a FEniCS

program is run, this file is read and used to initialize the parameters object.
Otherwise, the file .config/fenics/dolfin_parameters.xml in the users
home directory is read, if it exists. Another alternative is to load the XML
file (with any name) manually in the program:
5.2 Working with linear solvers 117

File(parameters.xml) >> parameters

The XML file can also be in gziped form with the extension .xml.gz.

5.2.4 An extended solver function

We may extend the previous solver function from ft12_poisson_solver.py

in Section 5.1.1 such that it also offers the GMRES+ILU preconditioned
Krylov solver:
This new solver function, found in the file ft10_poisson_extended.py,
replaces the one in ft12_poisson_solver.py. It has all the functionality
of the previous solver function, but can also solve the linear system with
iterative methods.

5.2.5 A remark regarding unit tests

Regarding verification of the new solver function in terms of unit tests,

it turns out that unit testing for a problem where the approximation error
vanishes gets more complicated when we use iterative methods. The problem
is to keep the error due to iterative solution smaller than the tolerance used
in the verification tests. First of all, this means that the tolerances used in the
Krylov solvers must be smaller than the tolerance used in the assert test,
but this is no guarantee to keep the linear solver error this small. For linear
elements and small meshes, a tolerance of 1011 works well in the case of
Krylov solvers too (using a tolerance 1012 in those solvers). The interested
reader is referred to the demo_solvers function in ft10_poisson_extended.
py for details: this function tests the numerical solution for direct and iterative
linear solvers, for different meshes, and different degrees of the polynomials
in the finite element basis functions.

5.2.6 List of linear solver methods and preconditioners

Which linear solvers and preconditioners that are available in FEniCS de-
pends on how FEniCS has been configured and which linear algebra backend
is currently active. The following table shows an example of which linear
solvers that can be available through FEniCS when the PETSc backend is
active:
118 5 Extensions: Improving the Poisson solver

Name Method

bicgstab Biconjugate gradient stabilized method

cg Conjugate gradient method
gmres Generalized minimal residual method
minres Minimal residual method
petsc PETSc built in LU solver
richardson Richardson method
superlu_dist Parallel SuperLU
tfqmr Transpose-free quasi-minimal residual method
umfpack UMFPACK

The set of available preconditioners also depends on configuration and linear

algebra backend. The following table shows an example of which precondi-
tioners may be available:

Name Method

icc Incomplete Cholesky factorization

ilu Incomplete LU factorization
petsc_amg PETSc algebraic multigrid
sor Successive over-relaxation

An up-to-date list of the available solvers and preconditioners for your FEn-
iCS installation can be produced by
list_linear_solver_methods()
list_krylov_solver_preconditioners()

5.3 High-level and low-level solver interfaces

The FEniCS interface allows different ways to access the core functionality,
ranging from very high-level to low-level access. So far, we have mostly used
the high-level call solve(a == L, u, bc) to solve a variational problem a
== L with a certain boundary condition bc. However, sometimes you may
need more fine-grained control of the solution process. In particular, the call
to solve will create certain objects that are thrown away after the solution
has been computed, and it may be practical or efficient to reuse those objects.

5.3.1 Linear variational problem and solver objects

In this section, we will look at an alternative interface to solving linear varia-

tional problems in FEniCS, which may be preferable in many situations com-
5.3 High-level and low-level solver interfaces 119

pared to the high-level solve function interface. This interface uses the two
classes LinearVariationalProblem and LinearVariationalSolver. Using
this interface, the equivalent of solve(a == L, u, bc) looks as follows:
u = Function(V)
problem = LinearVariationalProblem(a, L, u, bc)
solver = LinearVariationalSolver(problem)
solver.solve()

Many FEniCS objects have an attribute parameters, similar to the global

parameters database, but local to the object. Here, solver.parameters play
that role. Setting the CG method with ILU preconditioning as the solution
method and specifying solver-specific parameters can be done like this:
solver.parameters.linear_solver = gmres
solver.parameters.preconditioner = ilu
prm = solver.parameters.krylov_solver # short form
prm.absolute_tolerance = 1E-7
prm.relative_tolerance = 1E-4
prm.maximum_iterations = 1000

Settings in the global parameters database are propagated to parameter sets

in individual objects, with the possibility of being overwritten as above. Note
that global parameter values can only affect local parameter values if set
before the time of creation of the local object. Thus, changing the value of
the tolerance in the global parameter database will not affect the parameters
for already created solvers.

5.3.2 Explicit assembly and solve

As we saw already in Section 3.4, linear variational problems can be as-

sembled explicitly in FEniCS into matrices and vectors using the assemble
function. This allows even more fine-grained control of the solution pro-
cess compared to using the high-level solve function or using the classes
LinearVariationalProblem and LinearVariationalSolver. We will now
look more closely into how to use the assemble function and how to combine
this with low-level calls for solving the assembled linear systems.
Given a variational problem a(u, v) = L(v), the discrete solution u is com-
puted by inserting u = N
P
j=1 Uj j into a(u, v) and demanding a(u, v) = L(v)
to be fulfilled for N test functions 1 , . . . , N . This implies
N
X
a(j , i )Uj = L(i ), i = 1, . . . , N,
j=1

which is nothing but a linear system,

120 5 Extensions: Improving the Poisson solver

AU = b,
where the entries of A and b are given by

Aij = a(j , i ),
bi = L(i ) .

The examples so far have specified the left- and right-hand sides of the
variational formulation and then asked FEniCS to assemble the linear system
and solve it. An alternative is to explicitly call functions for assembling the
coefficient matrix A and the right-hand side vector b, and then solve the
linear system AU = b for the vector U . Instead of solve(a == L, U, b) we
now write
A = assemble(a)
b = assemble(L)
bc.apply(A, b)
u = Function(V)
U = u.vector()
solve(A, U, b)

The variables a and L are the same as before; that is, a refers to the bilinear
form involving a TrialFunction object u and a TestFunction object v, and
L involves the same TestFunction object v. From a and L, the assemble
function can compute A and b.
Creating the linear system explicitly in a program can have some advan-
tages in more advanced problem settings. For example, A may be constant
throughout a time-dependent simulation, so we can avoid recalculating A at
every time level and save a significant amount of simulation time.
The matrix A and vector b are first assembled without incorporating es-
sential (Dirichlet) boundary conditions. Thereafter, the call bc.apply(A,
b) performs the necessary modifications of the linear system such that u is
guaranteed to equal the prescribed boundary values. When we have multiple
Dirichlet conditions stored in a list bcs, we must apply each condition in bcs
to the system:
for bc in bcs:
bc.apply(A, b)

# Alternative syntax using list comprehension

[bc.apply(A, b) for bc in bcs]

Alternatively, we can use the function assemble_system, which takes the

boundary conditions into account when assembling the linear system. This
method preserves the symmetry of the linear system for a symmetric bilinear
form. Even if the matrix A that comes out of the call to assemble is sym-
metric (for a symmetric bilinear form a), the call to bc.apply will break the
symmetry. Preserving the symmetry of a variational problem is important
5.3 High-level and low-level solver interfaces 121

when using particular linear solvers designed for symmetric systems, such as
the conjugate gradient method.
Once the linear system has been assembled, we need to compute the so-
lution U = A1 b and store the solution U in the vector U = u.vector().
In the same way as linear variational problems can be programmed us-
ing different interfaces in FEniCSthe high-level solve function, the class
LinearVariationalSolver, and the low-level assemble functionlinear
systems can also be programmed using different interfaces in FEniCS. The
high-level interface to solving a linear system in FEniCS is also named solve:
solve(A, U, b)

By default, solve(A, U, b) uses sparse LU decomposition to compute

the solution. Specification of an iterative solver and preconditioner can be
made through two optional arguments:
solve(A, U, b, cg, ilu)

Appropriate names of solvers and preconditioners are found in Section 5.2.6.

This high-level interface is useful for many applications, but sometimes
more fine-grained control is needed. One can then create one or more
KrylovSolver objects that are then used to solve linear systems. Each differ-
ent solver object can have its own set of parameters and selection of iterative
method and preconditioner. Here is an example:
solver = KrylovSolver(cg, ilu)
prm = solver.parameters
prm.absolute_tolerance = 1E-7
prm.relative_tolerance = 1E-4
prm.maximum_iterations = 1000
u = Function(V)
U = u.vector()
solver.solve(A, U, b)

The function solver_linalg in the program file ft10_poisson_extended.

py implements such a solver.
The choice of start vector for the iterations in a linear solver is often
important. By default, the values of u and thus the vector U = u.vector()
will be initialized to zero. If we instead wanted to initialize U with random
numbers in the interval [100, 100] this can be done as follows:
n = u.vector().array().size
U = u.vector()
U[:] = numpy.random.uniform(-100, 100, n)
solver.parameters.nonzero_initial_guess = True
solver.solve(A, U, b)

Note that we must both turn off the default behavior of setting the start
vector (initial guess) to zero, and also set the values of the vector U to
nonzero values. This is useful if we happen to know a good initial guess for
the solution.
122 5 Extensions: Improving the Poisson solver

Using a nonzero initial guess can be particularly important for time-

dependent problems or when solving a linear system as part of a nonlinear
iteration, since then the previous solution vector U will often be a good ini-
tial guess for the solution in the next time step or iteration. In this case, the
values in the vector U will naturally be initialized with the previous solution
vector (if we just used it to solve a linear system), so the only extra step
necessary is to set the parameter nonzero_initial_guess to True.

5.3.3 Examining matrix and vector values

When calling A = assemble(a) and b = assemble(L), the object A will be

of type Matrix, while b and u.vector() are of type Vector. To examine the
values, we may convert the matrix and vector data to numpy arrays by calling
the array method as shown before. For example, if you wonder how essential
boundary conditions are incorporated into linear systems, you can print out
A and b before and after the bc.apply(A, b) call:
A = assemble(a)
b = assemble(L)
if mesh.num_cells() < 16: # print for small meshes only
print(A.array())
print(b.array())
bc.apply(A, b)
if mesh.num_cells() < 16:
print(A.array())
print(b.array())

With access to the elements in A through a numpy array, we can easily per-
form computations on this matrix, such as computing the eigenvalues (using
the eig function in numpy.linalg). We can alternatively dump A.array()
and b.array() to file in MATLAB format and invoke MATLAB or Octave to
analyze the linear system. Dumping the arrays to MATLAB format is done
by
import scipy.io
scipy.io.savemat(Ab.mat, {A: A.array(), b: b.array()})

Writing load Ab.mat in MATLAB or Octave will then make the array vari-
ables A and b available for computations.
Matrix processing in Python or MATLAB/Octave is only feasible for
small PDE problems since the numpy arrays or matrices in MATLAB file
format are dense matrices. FEniCS also has an interface to the eigen-
solver package SLEPc, which is the preferred tool for computing the eigen-
values of large, sparse matrices of the type encountered in PDE prob-
lems (see demo/documented/eigenvalue/python/ in the FEniCS/DOLFIN
source code tree for a demo).
5.4 Degrees of freedom and function evaluation 123

5.4 Degrees of freedom and function evaluation

5.4.1 Examining the degrees of freedom

We have seen before how to grab the degrees of freedom array from a finite
element function u:
nodal_values = u.vector().array()

For a finite element function from a standard continuous piecewise linear

function space (P1 Lagrange elements), these values will be the same as the
values we get by the following statement:
vertex_values = u.compute_vertex_values(mesh)

Both nodal_values and vertex_values will be numpy arrays and they will
be of the same length and contain the same values (for P1 elements), but
with possibly different ordering. The array vertex_values will have the same
ordering as the vertices of the mesh, while nodal_values will be ordered in
a way that (nearly) minimizes the bandwidth of the system matrix and thus
improves the efficiency of linear solvers.
A fundamental question is: what are the coordinates of the vertex whose
value is nodal_values[i]? To answer this question, we need to understand
how to get our hands on the coordinates, and in particular, the numbering
of degrees of freedom and the numbering of vertices in the mesh.
The function mesh.coordinates returns the coordinates of the vertices
as a numpy array with shape (M, d), M being the number of vertices in the
mesh and d being the number of space dimensions:
>>> from fenics import *
>>> mesh = UnitSquareMesh(2, 2)
>>> coordinates = mesh.coordinates()
>>> coordinates
array([[ 0. , 0. ],
[ 0.5, 0. ],
[ 1. , 0. ],
[ 0. , 0.5],
[ 0.5, 0.5],
[ 1. , 0.5],
[ 0. , 1. ],
[ 0.5, 1. ],
[ 1. , 1. ]])

We see from this output that for this particular mesh, the vertices are first
numbered along y = 0 with increasing x coordinate, then along y = 0.5, and
so on.
Next we compute a function u on this mesh. Lets take u = x + y:
>>> V = FunctionSpace(mesh, P, 1)
>>> u = interpolate(Expression(x[0] + x[1], degree=1), V)
124 5 Extensions: Improving the Poisson solver

>>> plot(u, interactive=True)

>>> nodal_values = u.vector().array()
>>> nodal_values
array([ 1. , 0.5, 1.5, 0. , 1. , 2. , 0.5, 1.5, 1. ])

We observe that nodal_values[0] is not the value of x + y at vertex num-

ber 0, since this vertex has coordinates x = y = 0. The numbering of the
nodal values (degrees of freedom) U1 , . . . , UN is obviously not the same as the
numbering of the vertices.
The vertex numbering may be examined by using the FEniCS plot com-
mand. To do this, plot the function u, press w to turn on wireframe instead of
a fully colored surface, m to show the mesh, and then v to show the numbering
of the vertices.

Lets instead examine the values by calling u.compute_vertex_values:

>>> vertex_values = u.compute_vertex_values()
>>> for i, x in enumerate(coordinates):
... print(vertex %d: vertex_values[%d] = %g\tu(%s) = %g %
... (i, i, vertex_values[i], x, u(x)))
vertex 0: vertex_values[0] = 0 u([ 0. 0.]) = 8.46545e-16
vertex 1: vertex_values[1] = 0.5 u([ 0.5 0. ]) = 0.5
vertex 2: vertex_values[2] = 1 u([ 1. 0.]) = 1
vertex 3: vertex_values[3] = 0.5 u([ 0. 0.5]) = 0.5
vertex 4: vertex_values[4] = 1 u([ 0.5 0.5]) = 1
vertex 5: vertex_values[5] = 1.5 u([ 1. 0.5]) = 1.5
vertex 6: vertex_values[6] = 1 u([ 0. 1.]) = 1
vertex 7: vertex_values[7] = 1.5 u([ 0.5 1. ]) = 1.5
vertex 8: vertex_values[8] = 2 u([ 1. 1.]) = 2
5.4 Degrees of freedom and function evaluation 125

We can ask FEniCS to give us the mapping from vertices to degrees of

freedom for a certain function space V :
v2d = vertex_to_dof_map(V)

Now, nodal_values[v2d[i]] will give us the value of the degree of free-

dom corresponding to vertex i (v2d[i]). In particular, nodal_values[v2d]
is an array with all the elements in the same (vertex numbered) order as
coordinates. The inverse map, from degrees of freedom number to vertex
number is given by dof_to_vertex_map(V). This means that we may call
coordinates[dof_to_vertex_map(V)] to get an array of all the coordinates
in the same order as the degrees of freedom. Note that these mappings are
only available in FEniCS for P1 elements.
For Lagrange elements of degree larger than 1, there are degrees of free-
dom (nodes) that do not correspond to vertices. For these elements, we may
get the vertex values by calling u.compute_vertex_values(mesh), and we
can get the degrees of freedom by the call u.vector().array(). To get the
coordinates associated with all degrees of freedom, we need to iterate over
the elements of the mesh and ask FEniCS to return the coordinates and
dofs associated with each element (cell). This information is stored in the
FiniteElement and DofMap object of a FunctionSpace. The following code
illustrates how to iterate over all elements of a mesh and print the coordinates
and degrees of freedom associated with the element.
element = V.element()
dofmap = V.dofmap()
for cell in cells(mesh):
print(element.tabulate_dof_coordinates(cell))
print(dofmap.cell_dofs(cell.index()))

5.4.2 Setting the degrees of freedom

We have seen how to extract the nodal values in a numpy array. If desired,
we can adjust the nodal values too. Say we want to normalize the solution
such that maxj |Uj | = 1. Then we must divide all Uj values by maxj |Uj |. The
following function performs the task:
def normalize_solution(u):
"Normalize u: return u divided by max(u)"
u_array = u.vector().array()
u_max = np.max(np.abs(u_array))
u_array /= u_max
u.vector()[:] = u_array
#u.vector().set_local(u_array) # alternative
return u
126 5 Extensions: Improving the Poisson solver

When using Lagrange elements, this (approximately) ensures that the maxi-
mum value of the function u is 1.
The /= operator implies an in-place modification of the object on the left-
hand side: all elements of the array nodal_values are divided by the value
u_max. Alternatively, we could do nodal_values = nodal_values / u_max,
which implies creating a new array on the right-hand side and assigning this
array to the name nodal_values.

Be careful when manipulating degrees of freedom

A call like u.vector().array() returns a copy of the data in u.vector().
One must therefore never perform assignments like u.vector.array()[:]
= ..., but instead extract the numpy array (i.e., a copy), manipulate it,
and insert it back with u.vector()[:] = or use u.set_local(...).

5.4.3 Function evaluation

A FEniCS Function object is uniquely defined in the interior of each cell

of the finite element mesh. For continuous (Lagrange) function spaces, the
function values are also uniquely defined on cell boundaries. A Function
object u can be evaluated by simply calling
u(x)

where x is either a Point or a Python tuple of the correct space dimension.

When a Function is evaluated, FEniCS must first find which cell of the mesh
that contains the given point (if any), and then evaluate a linear combination
of basis functions at the given point inside the cell in question. FEniCS uses
efficient data structures (bounding box trees) to quickly find the point, but
building the tree is a relatively expensive operation so the cost of evaluating
a Function at a single point is costly. Repeated evaluation will reuse the
computed data structures and thus be relatively less expensive.

Cheap vs expensive function evaluation

A Function object u can be evaluated in various ways:

1. u(x) for an arbitrary point x

2. u.vector().array()[i] for degree of freedom number i
3. u.compute_vertex_values()[i] at vertex number i
The first method, though very flexible, is in general expensive while the
other two are very efficient (but limited to certain points).
5.5 Postprocessing computations 127

To demonstrate the use of point evaluation of Function objects, we print

the value of the computed finite element solution u for the Poisson problem
at the center point of the domain and compare it with the exact solution:
center = (0.5, 0.5)
error = u_D(center) - u(center)
print(Error at %s: %g % (center, error))
For a 2 (3 3) mesh, the output from the previous snippet becomes
Error at (0.5, 0.5): -0.0833333
The discrepancy is due to the fact that the center point is not a node in this
particular mesh, but a point in the interior of a cell, and u varies linearly over
the cell while u_D is a quadratic function. When the center point is a node,
as in a 2 (2 2) or 2 (4 4) mesh, the error is of the order 1015 .

5.5 Postprocessing computations

As the final theme in this chapter, we will look at how to postprocess computa-
tions; that is, how to compute various derived quantities from the computed
solution of a PDE. The solution u itself may be of interest for visualizing gen-
eral features of the solution, but sometimes one is interested in computing
the solution of a PDE to compute a specific quantity that derives from the
solution, such as, e.g., the flux, a point-value, or some average of the solution.

5.5.1 Test problem

As a test problem, we consider again the variable-coefficient Poisson problem

with a single Dirichlet boundary condition:

(u) = f in , (5.1)
u = uD on . (5.2)

Let us continue to use our favorite solution u(x, y) = 1 + x2 + 2y 2 and then

prescribe (x, y) = x + y. It follows that uD (x, y) = 1 + x2 + 2y 2 and f (x, y) =
8x 10y.
As before, the variational formulation for this model problem can be spec-
ified in FEniCS as
a = kappa*dot(grad(u), grad(v))*dx
L = f*v*dx
with the coefficient and right-hand side f given by
128 5 Extensions: Improving the Poisson solver

kappa = Expression(x[0] + x[1], degree=1)

f = Expression(-8*x[0] - 10*x[1], degree=1)

5.5.2 Flux computations

PN
It is often of interest to compute the flux Q = u. Since u = j=1 Uj j ,
it follows that
N
X
Q = Uj j .
j=1

We note that the gradient of a piecewise continuous finite element scalar field
is a discontinuous vector field since the basis functions {j } have discontin-
uous derivatives at the boundaries of the cells. For example, using Lagrange
elements of degree 1, u is linear over each cell, and the gradient becomes a
piecewise constant vector field. On the contrary, the exact gradient is con-
tinuous. For visualization and data analysis purposes, we often want the
computed gradient to be a continuous vector field. Typically, we want each
component of u to be represented in the same way as u itself. To this end,
we can project the components of u onto the same function space as we
used for u. This means that we solve w = u approximately by a finite ele-
ment method, using the same elements for the components of w as we used
for u. This process is known as projection.
Projection is a common operation in finite element analysis and, as we have
already seen, FEniCS has a function for easily performing the projection:
project(expression, W), which returns the projection of some expression
into the space W.
In our case, the flux Q = u is vector-valued and we need to pick W as
the vector-valued function space of the same degree as the space V where u
resides:
V = u.function_space()
mesh = V.mesh()
degree = V.ufl_element().degree()
W = VectorFunctionSpace(mesh, P, degree)

grad_u = project(grad(u), W)
flux_u = project(-k*grad(u), W)

The applications of projection are many, including turning discontinuous

gradient fields into continuous ones, comparing higher- and lower-order func-
tion approximations, and transforming a higher-order finite element solution
down to a piecewise linear field, which is required by many visualization
packages.
Plotting the flux vector field is naturally as easy as plotting anything else:
5.5 Postprocessing computations 129

plot(flux_u, title=flux field)

flux_x, flux_y = flux_u.split(deepcopy=True) # extract components

plot(flux_x, title=x-component of flux (-kappa*grad(u)))
plot(flux_y, title=y-component of flux (-kappa*grad(u)))

The deepcopy=True argument signifies a deep copy, which is a general term in

computer science implying that a copy of the data is returned. (The opposite,
deepcopy=False, means a shallow copy, where the returned objects are just
pointers to the original data.)
For data analysis of the nodal values of the flux field, we can grab the
underlying numpy arrays (which demands a deepcopy=True in the split of
flux):
flux_x_nodal_values = flux_x.vector().dofs()
flux_y_nodal_values = flux_y.vector().dofs()

The degrees of freedom of the flux_u vector field can also be reached by
flux_u_nodal_values = flux_u.vector().array()

However, this is a flat numpy array containing the degrees of freedom for both
the x and y components of the flux and the ordering of the components may
be mixed up by FEniCS in order to improve computational efficiency.
The function demo_flux in the program ft10_poisson_extended.py
demonstrates the computations described above.

Manual projection.
Although you will always use project to project a finite element func-
tion, it can be instructive to look at how to formulate the projection
mathematically and implement its steps manually in FEniCS.
Lets say we have an expression g = g(u) that we want to project into
some space W . The mathematical formulation of the (L2 ) projection
w = PW g into W is the variational problem
Z Z
wv dx = gv dx (5.3)

for all test functions v W . In other words, we have a standard varia-
tional problem a(w, v) = L(v) where now
Z
a(w, v) = wv dx, (5.4)

Z
L(v) = gv dx . (5.5)

130 5 Extensions: Improving the Poisson solver

Note that when the functions in W are vector-valued, as is the case

when we project the gradient g(u) = u, we must replace the products
above by w v and g v.
The variational problem is easy to define in FEniCS.
w = TrialFunction(W)
v = TestFunction(W)

a = w*v*dx # or dot(w, v)*dx when w is vector-valued

L = g*v*dx # or dot(g, v)*dx when g is vector-valued
w = Function(W)
solve(a == L, w)

The boundary condition argument to solve is dropped since there are

no essential boundary conditions in this problem.

5.5.3 Computing functionals

After the solution u of a PDE is computed, we occasionally want to compute

functionals of u, for example,
Z
1 1
||u||2 = u u dx, (5.6)
2 2
which often reflects some energy quantity. Another frequently occurring func-
tional is the error
Z 1/2
2
||ue u|| = (ue u) dx , (5.7)

where ue is the exact solution. The error is of particular interest when study-
ing convergence properties of finite element methods. Other times, we may
instead be interested in computing the flux out through a part of the
boundary ,
Z
F = u n ds, (5.8)

where n is the outward-pointing unit normal on .
All these functionals are easy to compute with FEniCS, as we shall see in
the examples below.
Energy functional. The integrand of the energy functional (5.6) is de-
scribed in the UFL language in the same manner as we describe weak forms:
energy = 0.5*dot(grad(u), grad(u))*dx
E = assemble(energy)
5.5 Postprocessing computations 131

The functional energy is evaluated by calling the assemble function that we

have previously used to assemble matrices and vectors. FEniCS will recognize
that the form has rank 0 (since it contains no trial and test functions) and
return the result as a scalar value.
Error functional. The functional (5.7) can be computed as follows:
error = (u_e - u)**2*dx
E = sqrt(abs(assemble(error)))

The exact solution ue is here represented by a Function or Expression

object u_e, while u is the finite element approximation (and thus a Function).
Sometimes, for very small error values, the result of assemble(error) can
be a (very small) negative number, so we have used abs in the expression for
E above to ensure a positive value for the sqrt function.
As will be explained and demonstrated in Section 5.5.4, the integration of
(u_e - u)**2*dx can result in too optimistic convergence rates unless one is
careful how the difference u_e - u is evaluated. The general recommendation
for reliable error computation is to use the errornorm function:
E = errornorm(u_e, u)
R
Flux Functional. To compute flux integrals like F = u n ds, we
need to define the n vector, referred to as a facet normal in FEniCS. If
the surface domain in the flux integral is the complete boundary, we can
perform the flux computation by
n = FacetNormal(mesh)
flux = -k*dot(grad(u), n)*ds
total_flux = assemble(flux)

Although grad(u) and nabla_grad(u) are interchangeable in the above

expression when u is a scalar function, we have chosen to write grad(u)
because this is the right expression if we generalize the underlying equa-
tion to a vector PDE. With nabla_grad(u) we must in that case write
dot(n, nabla_grad(u)).
It is possible to restrict the integration to a part of the boundary by using a
mesh function to mark the relevant part, as explained in Section 4.4. Assum-
ing that the part corresponds to subdomain number i, the relevant syntax
for the variational formulation of the flux is -k*dot(grad(u), n)*ds(i).

A note on the accuracy of integration

As we have seen before, FEniCS Expressions must be defined using
a particular degree. The degree tells FEniCS into which local finite
element space the expression should be interpolated when performing
local computations (integration). As an illustration, consider the com-
132 5 Extensions: Improving the Poisson solver
R1
putation of the integral 0 cos x dx = sin 1. This may be computed in
FEniCS by
mesh = UnitIntervalMesh(1)
I = assemble(Expression(cos(x[0]), degree=degree)*dx(domain=mesh))

Note that we must here specify the argument domain=mesh to the mea-
sure dx. This is normally not necessary when defining forms in FEniCS
but is necessary here since cos(x[0]) is not associated with any domain
(as is the case when we integrate a Function from some FunctionSpace
defined on some Mesh).
Varying the degree between 0 and 5, the value of | sin(1)I| is 0.036,
0.071, 0.00030, 0.00013, 4.5E-07, and 2.5E-07.
FEniCS also allows expressions to be expressed directly as part of a
form. This requires the creation of a SpatialCoordinate. In this case,
the accuracy is dictated by the accuracy of the integration, which may
be controlled by a degree argument to the integration measure dx.
The degree argument specifies that the integration should be exact for
polynomials of that degree.
The following code snippet shows how to compute the integral
R1
0 cos x dx using this approach:

mesh = UnitIntervalMesh(1)
x = SpatialCoordinate(mesh)
I = assemble(cos(x[0])*dx(degree=degree))

Varying the degree between 0 and 5, the value of | sin(1) I| is 0.036,

0.036, 0.00020, 0.00020, 4.3E-07, 4.3E-07. Note that the quadrature
degrees are only available for odd degrees so that degree 0 will use the
same quadrature rule as degree 1, degree 2 will give the same quadrature
rule as degree 3 and so on.

5.5.4 Computing convergence rates

A central question for any numerical method is its convergence rate: how
fast does the error approach zero when the resolution is increased? For finite
element methods, this typically corresponds to proving, theoretically or em-
pirically, that the error e = ue u is bounded by the mesh size h to some
power r; that is, kek Chr for some constant C. The number r is called the
convergence rate of the method. Note that different norms, like the L2 -norm
kek or H01 -norm kek typically have different convergence rates.
To illustrate how to compute errors and convergence rates in FEniCS,
we have included the function compute_convergence_rates in the tutorial
program ft10_poisson_extended.py. This is a tool that is very handy when
verifying finite element codes and will therefore be explained in detail here.
5.5 Postprocessing computations 133

Computing error norms. As we have already seen, the L2 -norm of the

error ue u can be implemented in FEniCS by
error = (u_e - u)**2*dx
E = sqrt(abs(assemble(error)))

As above, we have used abs in the expression for E above to ensure a positive
value for the sqrt function.
It is important to understand how FEniCS computes the error from the
above code, since we may otherwise run into subtle issues when using the
value for computing convergence rates. The first subtle issue is that if u_e is
not already a finite element function (an object created using Function(V)),
which is the case if u_e is defined as an Expression, FEniCS must interpolate
u_e into some local finite element space on each element of the mesh. The
degree used for the interpolation is determined by the mandatory keyword
argument to the Expression class, for example:
u_e = Expression(sin(x[0]), degree=1)

This means that the error computed will not be equal to the actual error
kue uk but rather the difference between the finite element solution u and
the piecewise linear interpolant of ue . This may yield a too optimistic (too
small) value for the error. A better value may be achieved by interpolating
the exact solution into a higher-order function space, which can be done by
simply increasing the degree:
u_e = Expression(sin(x[0]), degree=3)

The second subtle issue is that when FEniCS evaluates the expression
(u_e - u)**2, this will be expanded into u_e**2 + u**2 - 2*u_e*u. If the
error is small (and the solution itself is of moderate size), this calculation
will correspond to the subtraction of two positive numbers (u_e**2 + u**2
1 and 2*u_e*u 1) yielding a small number. Such a computation is very
prone to round-off errors, which may again lead to an unreliable value for the
error. To make this situation worse, FEniCS may expand this computation
into a large number of terms, in particular for higher order elements, making
the computation very unstable.
To help with these issues, FEniCS provides the built-in function errornorm
which computes the error norm in a more intelligent way. First, both u_e and
u are interpolated into a higher-order function space. Then, the degrees of
freedom of u_e and u are subtracted to produce a new function in the higher-
order function space. Finally, FEniCS integrates the square of the difference
function and then takes the square root to get the value of the error norm.
Using the errornorm function is simple:
E = errornorm(u_e, u, normtype=L2)

It is illustrative to look at a short implementation of errornorm:

def errornorm(u_e, u):
134 5 Extensions: Improving the Poisson solver

V = u.function_space()
mesh = V.mesh()
degree = V.ufl_element().degree()
W = FunctionSpace(mesh, P, degree + 3)
u_e_W = interpolate(u_e, W)
u_W = interpolate(u, W)
e_W = Function(W)
e_W.vector()[:] = u_e_W.vector().array() - u_W.vector().array()
error = e_W**2*dx
return sqrt(abs(assemble(error)))

Sometimes it is of interest to compute the error of the gradient field:

||(ue u)||, often referred to as the H01 or H 1 seminorm of the error.
This can either be expressed as above, replacing the expression for error
by error = dot(grad(e_W), grad(e_W))*dx, or by calling errornorm in
FEniCS:
E = errornorm(u_e, u, norm_type=H10)

Type help(errornorm) in Python for more information about available norm

types.
The function compute_errors in ft10_poisson_extended.py illustrates
the computation of various error norms in FEniCS.
Computing convergence rates. Lets examine how to compute conver-
gence rates in FEniCS. The solver function in ft10_poisson_extended.py
allows us to easily compute solutions for finer and finer meshes and enables
us to study the convergence rate. Define the element size h = 1/n, where n
is the number of cell divisions in the x and y directions (n = Nx = Ny in
the code). We perform experiments with h0 > h1 > h2 > and compute
the corresponding errors E0 , E1 , E2 and so forth. Assuming Ei = Chri for
unknown constants C and r, we can compare two consecutive experiments,
Ei1 = Chri1 and Ei = Chri , and solve for r:

ln(Ei /Ei1 )
r= .
ln(hi /hi1 )
The r values should approach the expected convergence rate (typically the
polynomial degree + 1 for the L2 -error) as i increases.
The procedure above can easily be turned into Python code. Here we run
through a list of element degrees (P1 , P2 , and P3 ), perform experiments over
a series of refined meshes, and for each experiment report the six error types
as returned by compute_errors.
Test problem. To demonstrate the computation of convergence rates, we
pick an exact solution ue , this time a little more interesting than for the test
problem in Chapter 2:

ue (x, y) = sin(x) sin(y).

5.5 Postprocessing computations 135

This choice implies f (x, y) = 2 2 2 u(x, y). With restricted to an integer,

it follows that the boundary value is given by uD = 0.
We need to define the appropriate boundary conditions, the exact solution,
and the f function in the code:
def boundary(x, on_boundary):
return on_boundary

bc = DirichletBC(V, Constant(0), boundary)

omega = 1.0
u_e = Expression(sin(omega*pi*x[0])*sin(omega*pi*x[1]),
degree=6, omega=omega)

f = 2*pi**2*omega**2*u_e

Experiments. An implementation of the computation of the convergence

rate can be found in the function demo_convergence_rates in the demo
program ft10_poisson_extended.py. We achieve some interesting results.
Using the infinity norm of the difference of the degrees of freedom, we obtain
the following table:

element n = 8 n = 16 n = 32 n = 64

P1 1.99 2.00 2.00 2.00

P2 3.99 4.00 4.00 4.01
P3 3.95 3.99 3.99 3.92

An entry like 3.99 for n = 32 and P3 means that we estimate the rate 3.99
by comparing two meshes, with resolutions n = 32 and n = 16, using P3
elements. Note the superconvergence for P2 at the nodes. The best estimates
of the rates appear in the right-most column, since these rates are based
on the finest resolutions and are hence deepest into the asymptotic regime
(until we reach a level where round-off errors and inexact solution of the
linear system starts to play a role).
The L2 -norm errors computed using the FEniCS errornorm function show
the expected hd+1 rate for u:

element n = 8 n = 16 n = 32 n = 64

P1 1.97 1.99 2.00 2.00

P2 3.00 3.00 3.00 3.00
P3 4.04 4.02 4.01 4.00

However, using (u_e - u)**2 for the error computation, with the same de-
gree for the interpolation of u_e as for u, gives strange results:
136 5 Extensions: Improving the Poisson solver

element n = 8 n = 16 n = 32 n = 64

P1 1.97 1.99 2.00 2.00

P2 3.00 3.00 3.00 3.01
P3 4.04 4.07 1.91 0.00

This is an example where it is important to interpolate u_e to a higher-

order space (polynomials of degree 3 are sufficient here). This is handled
automatically by using the errornorm function.
Checking convergence rates is an excellent method for verifying PDE
codes.

5.5.5 Taking advantage of structured mesh data

Many readers have extensive experience with visualization and data analysis
of 1D, 2D, and 3D scalar and vector fields on uniform, structured meshes,
while FEniCS solvers exclusively work with unstructured meshes. Since it
can many times be practical to work with structured data, we discuss in this
section how to extract structured data for finite element solutions computed
with FEniCS.
A necessary first step is to transform our Mesh object to an object repre-
senting a rectangle (or a 3D box) with equally-shaped rectangular cells. The
second step is to transform the one-dimensional array of nodal values to a
two-dimensional array holding the values at the corners of the cells in the
structured mesh. We want to access a value by its i and j indices, i counting
cells in the x direction, and j counting cells in the y direction. This trans-
formation is in principle straightforward, yet it frequently leads to obscure
indexing errors, so using software tools to ease the work is advantageous.
In the directory of example programs included with this book, we have
included the Python module boxfield which provides utilities for working
with structured mesh data in FEniCS. Given a finite element function u, the
following function returns a BoxField object that represents u on a structured
mesh:
from boxfield import *
u_box = FEniCSBoxField(u, (nx, ny))

The u_box object contains several useful data structures:

u_box.grid: object for the structured mesh
u_box.grid.coor[X]: grid coordinates in X=0 direction
u_box.grid.coor[Y]: grid coordinates in Y=1 direction
u_box.grid.coor[Z]: grid coordinates in Z=2 direction
u_box.grid.coorv[X]: vectorized version of u_box.grid.coor[X]
u_box.grid.coorv[Y]: vectorized version of u_box.grid.coor[Y]
5.5 Postprocessing computations 137

u_box.grid.coorv[Z]: vectorized version of u_box.grid.coor[Z]

u_box.values: numpy array holding the u values; u_box.values[i,j]
holds u at the mesh point with coordinates
(u_box.grid.coor[X][i], u_box.grid.coor[Y][j])

Iterating over points and values. Let us now use the solver function
from the ft10_poisson_extended.py code to compute u, map it onto a
BoxField object for a structured mesh representation, and print the coordi-
nates and function values at all mesh points:
u = solver(p, f, u_b, nx, ny, 1, linear_solver=direct)
u_box = structured_mesh(u, (nx, ny))
u_ = u_box.values

# Iterate over 2D mesh points (i, j)

for j in range(u_.shape[1]):
for i in range(u_.shape[0]):
print(u[%d, %d] = u(%g, %g) = %g %
(i, j,
u_box.grid.coor[X][i], u_box.grid.coor[Y][j],
u_[i, j]))

Computing finite difference approximations. Using the multidimen-

sional array u_ = u_box.values, we can easily express finite difference ap-
proximations of derivatives:
x = u_box.grid.coor[X]
dx = x[1] - x[0]
u_xx = (u_[i - 1, j] - 2*u_[i, j] + u_[i + 1, j]) / dx**2

Making surface plots. The ability to access a finite element field as struc-
tured data is handy in many occasions, e.g., for visualization and data anal-
ysis. Using Matplotlib, we can create a surface plot, as shown in Figure 5.1
(upper left):
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D # necessary for 3D plotting
from matplotlib import cm
fig = plt.figure()
ax = fig.gca(projection=3d)
cv = u_box.grid.coorv # vectorized mesh coordinates
ax.plot_surface(cv[X], cv[Y], u_, cmap=cm.coolwarm,
rstride=1, cstride=1)
plt.title(Surface plot of solution)

The key issue is to know that the coordinates needed for the surface plot is
in u_box.grid.coorv and that the values are in u_.
Making contour plots. A contour plot can also be made by Matplotlib:
138 5 Extensions: Improving the Poisson solver

1.0 Contour plot of solution

Surface plot of solution

1.0 0.8
0.8
0.6 0.000 0.000
0.4 0.6
0.2

0.600
0.400
00
0
0.80
0.0

0.2
0.2 0.4
0.4
1.0
0.8 0.2

0.000
0.0 0.6
0.2 0.4
0.4
0.6 0.2
0.8
1.0 0.0 0.0
0.0 0.2 0.4 0.6 0.8 1.0

0.6 Solution along line y=0.409091 6 Flux along line y=0.409091

P1 elements P1 elements
0.5 exact exact
4
0.4
2
0.3

0.2 0
u

u
0.1
2
0.0
4
0.1

0.2 6
0.0 0.2 0.4 0.6 0.8 1.0 0.0 0.2 0.4 0.6 0.8 1.0
x x

Fig. 5.1 Various plots of the solution on a structured mesh.

fig = plt.figure()
ax = fig.gca()
levels = [1.5, 2.0, 2.5, 3.5]
cs = ax.contour(cv[X], cv[Y], u_, levels=levels)
plt.clabel(cs) # add labels to contour lines
plt.axis(equal)
plt.title(Contour plot of solution)

The result appears in Figure 5.1 (upper right).

Making curve plots through the domain. A handy feature of BoxField
objects is the ability to give a starting point in the domain and a direction,
and then extract the field and corresponding coordinates along the nearest
line of mesh points. We have already seen how to interpolate the solution along
a line in the mesh, but with BoxField you can pick out the computational
points (vertices) for examination of these points. Numerical methods often
show improved behavior at such points so this is of interest. For 3D fields one
can also extract data in a plane.
Say we want to plot u along the line y = 0.4. The mesh points, x, and the
u values along this line, u_val, can be extracted by
start = (0, 0.4)
x, u_val, y_fixed, snapped = u_box.gridline(start, direction=X)
5.5 Postprocessing computations 139

The variable snapped is true if the line is snapped onto to nearest gridline
and in that case y_fixed holds the snapped (altered) y value. The keyword
argument snap is by default True to avoid interpolation and force snapping.
A comparison of the numerical and exact solution along the line y 0.41
(snapped from y = 0.4) is made by the following code:
# Plot u along a line y = const and compare with exact solution
start = (0, 0.4)
x, u_val, y_fixed, snapped = u_box.gridline(start, direction=X)
u_e_val = [u_D((x_, y_fixed)) for x_ in x]
plt.figure()
plt.plot(x, u_val, r-)
plt.plot(x, u_e_val, bo)
plt.legend([P1 elements, exact], loc=best)
plt.title(Solution along line y=%g % y_fixed)
plt.xlabel(x); plt.ylabel(u)

See Figure 5.1 (lower left) for the resulting curve plot.
Making curve plots of the flux. Let us also compare the numerical and
exact fluxes u/x along the same line as above:
# Plot the numerical and exact flux along the same line
flux_u = flux(u, kappa)
flux_u_x, flux_u_y = flux_u.split(deepcopy=True)
flux2_x = flux_u_x if flux_u_x.ufl_element().degree() == 1 \
else interpolate(flux_x,
FunctionSpace(u.function_space().mesh(), P, 1))
flux_u_x_box = FEniCSBoxField(flux_u_x, (nx,ny))
x, flux_u_val, y_fixed, snapped = \
flux_u_x_box.gridline(start, direction=X)
y = y_fixed
plt.figure()
plt.plot(x, flux_u_val, r-)
plt.plot(x, flux_u_x_exact(x, y_fixed), bo)
plt.legend([P1 elements, exact], loc=best)
plt.title(Flux along line y=%g % y_fixed)
plt.xlabel(x); plt.ylabel(u)

The function flux called at the beginning of the code snippet is defined in
the example program ft10_poisson_extended.py and interpolates the flux
back into the function space.
Note that Matplotlib is one choice of plotting package. With the unified
interface in the SciTools package1 one can access Matplotlib, Gnuplot, MAT-
LAB, OpenDX, VisIt, and other plotting engines through the same API.
Test problem. The graphics referred to in Figure 5.1 correspond to a test
problem with prescribed solution ue = H(x)H(y), where
1 2
H(x) = e16(x 2 ) sin(3x) .

1
https://github.com/hplgit/scitools
140 5 Extensions: Improving the Poisson solver

The corresponding right-hand side f is obtained by inserting the exact solu-

tion into the PDE and differentiating as before. Although it is easy to carry
out the differentiation of f by hand and hardcode the resulting expressions
in an Expression object, a more reliable habit is to use Pythons symbolic
computing engine, SymPy, to perform mathematics and automatically turn
formulas into C++ syntax for Expression objects. A short introduction was
given in Section 3.2.3.
We start out with defining the exact solution in sympy:
from sympy import exp, sin, pi # for use in math formulas
import sympy as sym

H = lambda x: exp(-16*(x-0.5)**2)*sin(3*pi*x)
x, y = sym.symbols(x[0], x[1])
u = H(x)*H(y)

Turning the expression for u into C or C++ syntax for Expression objects
needs two steps. First we ask for the C code of the expression:
u_code = sym.printing.ccode(u)

Printing u_code gives (the output is here manually broken into two lines):
-exp(-16*pow(x[0] - 0.5, 2) - 16*pow(x[1] - 0.5, 2))*
sin(3*M_PI*x[0])*sin(3*M_PI*x[1])

The necessary syntax adjustment is replacing the symbol M_PI for in

C/C++ by pi (or DOLFIN_PI):
u_code = u_code.replace(M_PI, pi)
u_b = Expression(u_code, degree=1)

Thereafter, we can progress with the computation of f = (u):

kappa = 1
f = sym.diff(-kappa*sym.diff(u, x), x) + \
sym.diff(-kappa*sym.diff(u, y), y)
f = sym.simplify(f)
f_code = sym.printing.ccode(f)
f_code = f_code.replace(M_PI, pi)
f = Expression(f_code, degree=1)

We also need a Python function for the exact flux u/x:

flux_u_x_exact = sym.lambdify([x, y], -kappa*sym.diff(u, x),
modules=numpy)

It remains to define kappa = Constant(1) and set nx and ny before calling

solver to compute the finite element solution of this problem.
5.6 Taking the next step 141

5.6 Taking the next step

If you have come this far, you have learned how to both write simple script-
like solvers for a range of PDEs, and how to structure Python solvers using
functions and unit tests. Solving a more complex PDE and writing a more
full-featured PDE solver is not much harder and the first step is typically to
write a solver for a stripped-down test case as a simple Python script. As the
script matures and becomes more complex, it is time to think about design,
in particular how to modularize the code and organize it into reusable pieces
that can be used to build a flexible and extensible solver.
On the FEniCS web site you will find more extensive documentation, more
example programs, and links to advanced solvers and applications written on
top of FEniCS. Get inspired and develop your own solver for your favorite
application, publish your code and share your knowledge with the FEniCS
community and the world!
PS: Stay tuned for the FEniCS Tutorial Volume 2!
References

[1] M. S. Alns, A. Logg, K. B. lgaard, M. E. Rognes, and G. N. Wells.

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[2] Douglas N. Arnold and Anders Logg. Periodic table of the finite ele-
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[3] W. B. Bickford. A First Course in the Finite Element Method. Irwin,
2nd edition, 1994.
[4] D. Braess. Finite Elements. Cambridge University Press, Cambridge,
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[5] S. C. Brenner and L. R. Scott. The Mathematical Theory of Finite
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Index

.hdf5 file, 69 constructive solid geometry, 67

.pvd file, 45 contour plot, 137
.vtu file, 45 convergence rate, 132
.xdmf file, 69 coordinates, 123
coupled systems, 73
abstract variational formulation, 15 CSG, 67
advectiondiffusionreaction, 73 curve plots, 34
assemble, 64, 119, 120 cylinder flow, 65
assemble_system, 120
assembly, 119 Debian, 7
DEBUG log level, 67
backward difference, 38 deep copy, 81
boundary conditions, 92 degrees of freedom, 25, 29, 30, 129
boundary markers, 88 degrees of freedrom, 123
boundary specification (class), 88 dimension-independent code, 114
boundary specification (function), 21, Dirichlet boundary condition, 92
22 Dirichlet boundary conditions, 20
BoxField, 136 DirichletBC, 20
Docker, 6
C++ expression syntax, 22 dof to vertex map, 124
CellFunction, 88 dofs, 29
CFD, 56 DOLFIN, 3
channel flow, 60
chemical reactions, 73 editor, 7
Chorins method, 57 Eigen, 115
Circle, 102 elasticity, 50
code, 8 Emacs, 7
CompiledSubDomain, 91 energy functional, 130
components, 81 error, 28, 133

145
146 INDEX

error functional, 131 initial condition, 80

errornorm, 131 installation, 5
exact solution, 16 integration by parts, 13
exporting solutions, 27 interpolate, 40
Expression, 21, 32 interpolation, 41
expression syntax (C++), 22
Jacobian, 50
FacetFunction, 88 Jupyter, 19
fenicsproject, 6
FFC, 3 Krylov solver, 68, 115, 117
FIAT, 3 KrylovSolver, 121
finite element method, 9
finite element space, 20 Lagrange finite element, 20
flat program, 109 lhs, 41, 97
flux functional, 131 linear algebra backend, 115
ft01_poisson.py, 18 linear solver, 115, 117
ft02_poisson_membrane.py, 34 linear system, 64, 120
ft03_heat.py, 44 LinearVariationalProblem, 118
ft04_heat_gaussian.py, 46 LinearVariationalSolver, 118
ft05_poisson_nonlinear.py, 50 Linux, 5
ft06_elasticity.py, 54
Mac OS X, 5
ft07_navier_stokes_channel.py, 65
magnetostatics, 100
ft08_navier_stokes_cylinder.py, 73
MATLAB, 122
ft09_reaction_system.py, 80
Maxwells equations, 100
ft10_poisson_extended.py, 97, 117,
Measure, 104
127
Mesh, 19
ft11_magnetostatics.py, 107
mesh, 19
ft12_poisson_solver.py, 111
mesh generation, 102
function evaluation, 126
MeshFunction, 88
function space, 20
method of manufactured solutions, 16,
functionals, 130
48
FunctionSpace, 20
mixed finite element, 76
generate_mesh, 67, 102 mixed function space, 76
GNU/Linux, 5 MixedElement, 76
grad, 58 mshr, 3, 67, 102
multi-material domain, 87
HDF5 format, 69
heat equation, 37 nabla_grad, 54, 58
heterogeneous media, 87 Navier-Stokes equations, 56
near, 62, 85
implicit Euler, 38 Neumann boundary condition, 83, 92
incremental pressure correction scheme, Newtons method, 50
57 nodal values, 29, 30, 129
infinite domain, 101 nonlinear problem, 46
info, 116 norm, 133
INDEX 147

numbering system of PDEs, 50

cell vertices, 30
degrees of freedom, 30 tensor, 51
terminal window, 18
P1 element, 20 test function, 13
packages, 7 test problem, 16
parameters, 116 TestFunction, 20
ParaView, 27 time step, 38
performance, 6 time-dependent expression, 41
Periodic Table of the Finite Elements, time-dependent problem, 37
20 TimeSeries, 69, 76
PETSc, 3, 115 tolerance, 23
plot, 25 trial function, 13
plotting, 25 TrialFunction, 20
Poissons equation, 11
postprocessing, 27, 127 Ubuntu, 7
preconditioner, 68, 115, 117 UFL, 3, 24
PROGRESS log level, 67 unit testing, 111
Progress, 67
project, 40, 128 variational formulation, 12
projection, 41 vector-valued functions, 54
Python, 8 VectorElement, 77
Python module, 111 VectorFunctionSpace, 54, 62
verification, 16, 65, 111
reaction system, 73 vertex to dof map, 124
Reynolds number, 60 vertex values, 29, 123, 124
rhs, 41, 97 Vim, 7
Robin boundary condition, 92 visualization, structured mesh, 136
rounding errors, 23 VTK format, 45

scaling, 55, 60 Windows, 5

scitools, 136
set_log_level, 67 XDMF format, 69
SLEPc, 122
source, 5
space dimensions, 114
split, 81
splitting method, 57
Spyder, 19
strain-rate tensor, 57
stress tensor, 51, 56
structured mesh, 136
subdomains, 83
surface plot (structured mesh), 137
SymPy, 48
sympy, 139