Geilo Winter School 2012

Lecture 4: Introduction to FEniCS

Anders Logg

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Course outline
Sunday
L1 Introduction to FEM
Monday
L2 Fundamentals of continuum mechanics (I)
L3 Fundamentals of continuum mechanics (II)
L4 Introduction to FEniCS
Tuesday
L5 Solid mechanics
L5 Static hyperelasticity in FEniCS
L5 Dynamic hyperelasticity in FEniCS
Wednesday
L5 Fluid mechanics
L5 Navier–Stokes in FEniCS

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What is FEniCS?

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FEniCS is an automated programming
environment for differential equations

• C++/Python library
• Initiated 2003 in Chicago
• 1000–2000 monthly downloads
• Part of Debian and Ubuntu
• Licensed under the GNU LGPL

http://fenicsproject.org/

Collaborators
Simula Research Laboratory, University of Cambridge,
University of Chicago, Texas Tech University, KTH Royal
Institute of Technology, . . .

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FEniCS is automated FEM
• Automated generation of basis functions
• Automated evaluation of variational forms
• Automated finite element assembly
• Automated adaptive error control

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What has FEniCS been used for?

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Computational hemodynamics

• Low wall shear stress may trigger aneurysm growth

• Solve the incompressible Navier–Stokes equations on
patient-specific geometries

u̇ + u · ∇u − ∇ · σ(u, p) = f
∇·u=0

Valen-Sendstad, Mardal, Logg, Computational hemodynamics (2011)

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Computational hemodynamics (contd.)

# Define Cauchy stress tensor

def sigma (v , w ) :
return 2 . 0 * mu * 0 . 5 * ( grad ( v ) + grad ( v ) . T ) -
w * Identity ( v . cell () . d )

# Define symmetric gradient

def epsilon ( v ) :
return 0 . 5 * ( grad ( v ) + grad ( v ) . T )

# Tentative velocity step ( sigma formulation )

U = 0 . 5 * ( u0 + u )
F1 = rho * ( 1 / k ) * inner (v , u - u0 ) * dx +
rho * inner (v , grad ( u0 ) * ( u0 - w ) ) * dx \
+ inner ( epsilon ( v ) , sigma (U , p0 ) ) * dx \
+ inner (v , p0 * n ) * ds - mu * inner ( grad ( U ) . T *n ,
v ) * ds \
- inner (v , f ) * dx
a1 = lhs ( F1 )
L1 = rhs ( F1 )

# Pressure correction
a2 = inner ( grad ( q ) , k * grad ( p ) ) * dx
L2 = inner ( grad ( q ) , k * grad ( p0 ) ) * dx -
q * div ( u1 ) * dx

# Velocity correction
a3 = inner (v , u ) * dx
L3 = inner (v , u1 ) * dx + inner (v , k * grad ( p0 -
p1 ) ) * dx

• The Navier–Stokes solver is implemented in Python/FEniCS

• FEniCS allows solvers to be implemented in a minimal amount of code
Valen-Sendstad, Mardal, Logg, Computational hemodynamics (2011) 8 / 31
Hyperelasticity

class Twist ( Stat icHy perel ast i ci t y ) :

def mesh ( self ) :

n = 8
return UnitCube (n , n , n )

def dirichlet_conditions ( self ) :

clamp = Expression (( " 0 . 0 " , " 0 . 0 " ,
"0.0"))
twist = Expression (( " 0 . 0 " ,
" y0 + ( x [ 1 ] - y0 ) * cos ( theta )
- ( x [ 2 ] - z0 ) * sin ( theta ) - x [ 1 ] " ,
" z0 + ( x [ 1 ] - y0 ) * sin ( theta )
+ ( x [ 2 ] - z0 ) * cos ( theta ) - x [ 2 ] " ) )
twist . y0 = 0 . 5
twist . z0 = 0 . 5
twist . theta = pi / 3
return [ clamp , twist ]

def dirichlet_boundaries ( self ) :

return [ " x [ 0 ] == 0 . 0 " , " x [ 0 ] == 1 . 0 " ]

def material_model ( self ) :

mu = 3 . 8461
lmbda =
Expression ( " x [ 0 ]* 5 . 8 +( 1 - x [ 0 ]) * 5 . 7 " )

material = StVenantKirchhoff ( [ mu ,
lmbda ] )
return material

def __str__ ( self ) :

return " A cube twisted by 60 degrees "

• CBC.Solve is a collection of FEniCS-based solvers developed at CBC

• CBC.Twist, CBC.Flow, CBC.Swing, CBC.Beat, . . .
H. Narayanan, A computational framework for nonlinear elasticity (2011) 9 / 31
How to use FEniCS?

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Installation

Official packages for Debian and Ubuntu

Drag and drop installation on Mac OS X

Binary installer for Windows

Automated installation from source

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Basic API

• Mesh Vertex, Edge, Face, Facet, Cell

• FiniteElement, FunctionSpace
• TrialFunction, TestFunction, Function
• grad(), curl(), div(), . . .
• Matrix, Vector, KrylovSolver, LUSolver
• assemble(), solve(), plot()

• Python interface generated semi-automatically by SWIG

• C++ and Python interfaces almost identical

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Hello World!

We will solve Poisson’s equation, the Hello World of scientific

computing:

−∆u = f in Ω
u = u0 on ∂Ω

Poisson’s equation arises in numerous applications:

• heat conduction, electrostatics, diffusion of substances,
twisting of elastic rods, inviscid fluid flow, water waves,
magnetostatics
• as part of numerical splitting strategies for more
complicated systems of PDEs, in particular the
Navier–Stokes equations

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Solving PDEs in FEniCS

Solving a physical problem with FEniCS consists of the

following steps:
1 Identify the PDE and its boundary conditions
2 Reformulate the PDE problem as a variational problem
3 Make a Python program where the formulas in the
variational problem are coded, along with definitions of
input data such as f , u0 , and a mesh for Ω
4 Add statements in the program for solving the variational
problem, computing derived quantities such as ∇u, and
visualizing the results

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Deriving a variational problem for Poisson’s
equation
The simple recipe is: multiply the PDE by a test function v and
integrate over Ω:
Z Z
− (∆u)v dx = f v dx
Ω Ω

Then integrate by parts and set v = 0 on the Dirichlet

boundary:
Z Z Z
∂u
− (∆u)v dx = ∇u · ∇v dx − v ds
Ω Ω ∂n
| ∂Ω {z }
=0

We find that: Z Z
∇u · ∇v dx = f v dx
Ω Ω

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Variational problem for Poisson’s equation

Find u ∈ V such that

Z Z
∇u · ∇v dx = f v dx
Ω Ω

for all v ∈ V̂

The trial space V and the test space V̂ are (here) given by

V = {v ∈ H 1 (Ω) : v = u0 on ∂Ω}
V̂ = {v ∈ H 1 (Ω) : v = 0 on ∂Ω}

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Discrete variational problem for Poisson’s
equation
We approximate the continuous variational problem with a
discrete variational problem posed on finite dimensional
subspaces of V and V̂ :

Vh ⊂ V
V̂h ⊂ V̂

Find uh ∈ Vh ⊂ V such that

Z Z
∇uh · ∇v dx = f v dx
Ω Ω

for all v ∈ V̂h ⊂ V̂

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Canonical variational problem

The following canonical notation is used in FEniCS: find u ∈ V

such that
a(u, v) = L(v)
for all v ∈ V̂

For Poisson’s equation, we have

Z
a(u, v) = ∇u · ∇v dx
ZΩ
L(v) = f v dx
Ω

a(u, v) is a bilinear form and L(v) is a linear form

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A test problem

We construct a test problem for which we can easily check the

answer. We first define the exact solution by

u(x, y) = 1 + x2 + 2y 2

We insert this into Poisson’s equation:

f = −∆u = −∆(1 + x2 + 2y 2 ) = −(2 + 4) = −6

This technique is called the method of manufactured solutions

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Implementation in FEniCS

from dolfin import *

mesh = UnitSquare (6 , 4 )
V = FunctionSpace ( mesh , " Lagrange " , 1 )
u0 = Expression ( " 1 + x [ 0 ]* x [ 0 ] + 2 * x [ 1 ]* x [ 1 ] " )

def u0_boundary (x , on_boundary ) :

return on_boundary

bc = DirichletBC (V , u0 , u0_boundary )

f = Constant ( - 6 . 0 )
u = TrialFunction ( V )
v = TestFunction ( V )
a = inner ( grad ( u ) , grad ( v ) ) * dx
L = f * v * dx

u = Function ( V )
solve ( a = = L , u , bc )
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Step by step: the first line

The first line of a FEniCS program usually begins with

from dolfin import *

This imports key classes like UnitSquare, FunctionSpace,

Function and so forth, from the FEniCS user interface
(DOLFIN)

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Step by step: creating a mesh

Next, we create a mesh of our domain Ω:

mesh = UnitSquare (6 , 4 )

This defines a mesh of 6 × 4 × 2 = 48 triangles of the unit square

Other useful classes for creating meshes include UnitInterval,

UnitCube, UnitCircle, UnitSphere, Rectangle and Box

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Step by step: creating a function space

The following line creates a function space on Ω:

V = FunctionSpace ( mesh , " Lagrange " , 1 )

The second argument reflects the type of element, while the

third argument is the degree of the basis functions on the
element

Other types of elements include "Discontinuous Lagrange",

"Brezzi-Douglas-Marini", "Raviart-Thomas",
"Crouzeix-Raviart", "Nedelec 1st kind H(curl)" and
"Nedelec 2nd kind H(curl)"

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Step by step: defining expressions
Next, we define an expression for the boundary value:

u0 = Expression ( " 1 + x [ 0 ]* x [ 0 ] + 2 * x [ 1 ]* x [ 1 ] " )

The formula must be written in C++ syntax

The Expression class is very flexible and can be used to create

complex user-defined expressions. For more information, try

help ( Expression )

in Python or, in the shell:

pydoc dolfin . Expression

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Step by step: defining boundaries
We next define the Dirichlet boundary:

def u0_boundary (x , on_boundary ) :

return on_boundary

You may want to experiment with the definition of the

boundary:

def u0_boundary ( x ) :
return x [ 0 ] < DOLFIN_EPS or \
x [ 1 ] > 1 . 0 - DOLFIN_EPS

def u0_boundary ( x ) :
return near ( x [ 0 ] , 0 . 0 ) or near ( x [ 1 ] , 1 . 0 )

def u0_boundary (x , on_boundary ) :

return on_boundary and x [ 0 ] > DOLFIN_EPS

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Step by step: defining a boundary condition

The following code defines a Dirichlet boundary condition:

bc = DirichletBC (V , u0 , u0_boundary )

This boundary condition states that a function in the function

space defined by V should be equal to u0 on the boundary
defined by u0 boundary

Note that the above line does not yet apply the boundary
condition to all functions in the function space

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Step by step: defining the right-hand side

The right-hand side f = 6 may be defined as follows:

f = Expression ( " -6 " )

or (more efficiently) as

f = Constant ( - 6 . 0 )

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Step by step: defining variational problems

Variational problems are defined in terms of trial and test

functions:

u = TrialFunction ( V )
v = TestFunction ( V )

We now have all the objects we need in order to specify the

bilinear form a(u, v) and the linear form L(v):

a = inner ( grad ( u ) , grad ( v ) ) * dx

L = f * v * dx

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Step by step: solving variational problems

Once a variational problem has been defined, it may be solved

by calling the solve function:

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

Note the reuse of the variable u as both a TrialFunction in

the variational problem and a Function to store the solution

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Step by step: post-processing
The solution and the mesh may be plotted by simply calling:

plot ( u )
plot ( mesh )
interactive ()

The interactive() call is necessary for the plot to remain on

the screen and allows the plots to be rotated, translated and
zoomed

For postprocessing in ParaView or MayaVi, store the solution

in VTK format:

file = File ( " poisson . pvd " )

file < < u

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The FEniCS challenge!

Solve the partial differential equation

−∆u = f

with homogeneous Dirichlet boundary conditions on the unit

square for f (x, y) = 2π 2 sin(πx) sin(πy). Plot the error in the L2
norm as function of the mesh size h for a sequence of refined
meshes. Try to determine the convergence rate.
• Who can obtain the smallest error?
• Who can compute a solution with an error smaller than
 = 10−6 in the fastest time?
The best students(s) will be rewarded with an exclusive FEniCS
coffee mug!

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