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You are on page 1of 47

Hans Fangohr

Engineering and the Environment

University of Southampton

United Kingdom

fangohr@soton.ac.uk

May 3, 2012

1 / 47

Outline I

1

Diusion equation

Finite elements

Summary

2 / 47

This lecture

has lecture notes and code available for download at

http://www.soton.ac.uk/fangohr/teaching/comp6024

3 / 47

Ordinary Dierential Equations (ODEs)

one independent variable, for example t in

k

d2 x

= x

2

dt

m

often the indepent variable t is the time

solution is function x(t)

important for dynamical systems, population growth,

control, moving particles

multiple independent variables, for example t, x and y in

u

=D

t

2u 2u

+ 2

x2

y

important for uid dynamics, chemistry,

electromagnetism, . . . , generally problems with spatial

resolution

4 / 47

2d Diusion equation

u

=D

t

2u 2u

+

x2 y 2

t is the time [s]

x is the x-coordinate [m]

y is the y-coordinate [m]

D is the diusion coecient [m2 /s]

Also known as Ficks second law. The heat equation has the

same structure (and u represents the temperature).

Example:

http://www.youtube.com/watch?v=WC6Kj5ySWkQ

5 / 47

Examples of PDEs

Cahn Hilliard Equation (phase separation)

plasma physics, gas turbine and aircraft modelling)

Structural mechanics and vibrations, superconductivity,

micromagnetics, . . .

6 / 47

Computing derivatives

using nite dierences

7 / 47

Overview

Motivation:

We need derivatives of functions for example for

optimisation and root nding algorithms

Not always is the function analytically known (but we

are usually able to compute the function numerically)

The material presented here forms the basis of the

nite-dierence technique that is commonly used to

solve ordinary and partial dierential equations.

the forward dierence technique

the backward dierence technique and the

central dierence technique to approximate the

derivative of a function.

We also derive the accuracy of each of these methods.

8 / 47

(Possible) Denition of the derivative (or dierential

d

operator dx )

f (x)

f (x + h) f (x)

df

(x) = lim

h0

dx

h

operator

f (x) =

df

f (x + h) f (x)

f (x + h) f (x)

(x) = lim

h0

dx

h

h

evaluating f (twice).

This is called the forward dierence because we use f (x)

and f (x + h).

Important questions: How accurate is this approximation?

9 / 47

Formal derivation using the Taylor series of f around x

hn

f (x + h) =

n=0

f (n) (x)

n!

= f (x) + hf (x) + h2

f (x)

f (x)

+ h3

+ ...

2!

3!

hf (x) = f (x + h) f (x) h2

f (x) =

=

=

1

h

f (x)

f (x)

h3

...

2!

3!

f (x + h) f (x) h2

f (x)

f (x)

h3

...

2!

3!

f (x)

f (x)

f (x + h) f (x) h2 2! h3 3!

...

h

h

f (x + h) f (x)

f (x)

f (x)

h

h2

...

h

2!

3!

10 / 47

f (x) =

f (x + h) f (x)

f (x)

f (x)

h

h2

...

h

2!

3!

Eforw (h)

f (x) =

f (x + h) f (x)

+ Eforw (h)

h

f (x)

f (x)

h2

...

2!

3!

Can also be expressed as

Eforw (h) = h

f (x) =

f (x + h) f (x)

+ O(h)

h

11 / 47

Another denition of the derivative (or dierential

d

operator dx )

df

f (x) f (x h)

(x) = lim

h0

dx

h

Use dierence operator to approximate dierential

operator

df

f (x) f (x h)

f (x) f (x h)

(x) = lim

h0

dx

h

h

This is called the backward dierence because we use

f (x) and f (x h).

How accurate is the backward dierence?

12 / 47

Formal derivation using the Taylor Series of f around x

f (x h) = f (x) hf (x) + h2

f (x)

f (x)

h3

+ ...

2!

3!

hf (x) = f (x) f (x h) + h2

f (x) =

=

=

1

h

f (x)

f (x)

h3

...

2!

3!

f (x) f (x h) + h2

f (x)

f (x)

h3

...

2!

3!

f (x)

f (x)

f (x) f (x h) h2 2! h3 3!

+

...

h

h

f (x) f (x h)

f (x)

f (x)

+h

h2

...

h

2!

3!

13 / 47

f (x) =

f (x)

f (x) f (x h)

f (x)

+h

h2

...

h

2!

3!

Eback (h)

f (x) =

f (x) f (x h)

+ Eback (h)

h

(1)

Eback (h) = h

f (x)

f (x)

h2

...

2!

3!

f (x) =

f (x) f (x h)

+ O(h)

h

14 / 47

The approximations are

forward:

f (x) =

f (x + h) f (x)

+ Eforw (h)

h

(2)

f (x) =

f (x) f (x h)

+ Eback (h)

h

(3)

backward

f (x)

f (x)

f (x)

f (x)

h2

h3

h4

...

2!

3!

4!

5!

f (x)

f (x)

f (x)

f (x)

Eback (h) = h

h2

+ h3

h4

+ ...

2!

3!

4!

5!

Eforw (h) = h

Add equations (2) and (3) together, then the error cancels

partly!

15 / 47

Add these lines together

f (x) =

f (x) =

f (x + h) f (x)

+ Eforw (h)

h

f (x) f (x h)

+ Eback (h)

h

f (x + h) f (x h)

+ Eforw (h) + Eback (h)

h

Adding the error terms:

2f (x) =

f (x)

f (x)

2h4

...

3!

5!

The combined (central) dierence operator is

Eforw (h) + Eback (h) = 2h2

f (x) =

f (x + h) f (x h)

+ Ecent (h)

2h

with

Ecent (h) = h2

f (x)

f (x)

h4

...

3!

5!

16 / 47

Central dierence

Can be derived (as on previous slides) by adding forward

and backward dierence

Can also be interpreted geometrically by dening the

dierential operator as

df

f (x + h) f (x h)

(x) = lim

h0

dx

2h

and taking the nite dierence form

df

f (x + h) f (x h)

(x)

dx

2h

Error of the central dierence is only O(h2 ), i.e. better

than forward or backward dierence

It is generally the case that symmetric dierences

are more accurate than asymmetric expressions.

17 / 47

Example (1)

Using forward dierence to estimate the derivative of

f (x) = exp(x)

f (x) fforw =

f (x + h) f (x)

exp(x + h) exp(x)

=

h

h

Numerical example:

h = 0.1, x = 1

f (1) fforw (1.0) = exp(1.1)exp(1) = 2.8588

0.1

Exact answers is f (1.0) = exp(1) = 2.71828

(Central di: fcent (1.0) =

exp(1+0.1)exp(10.1)

0.2

= 2.72281)

18 / 47

Example (2)

Comparison: forward dierence, central dierence and exact

derivative of f (x) = exp(x)

140

120

df/dx(x)

100

forward h=1

central h=1

forward h=0.0001

exact

80

60

40

20

00

19 / 47

Summary

function evaluations of f

size of step h very important

central dierences has smallest error term

name

formula

forward

f (x) = f (x+h)f (x)

h

backward f (x) = f (x)f (xh)

h

central

f (x) = f (x+h)f (xh)

2h

error

O(h)

O(h)

O(h2 )

20 / 47

EPS =1 # very large EPS to provoke i n a c c u r a c y

def forwarddiff (f ,x , h = EPS ):

# df / dx = ( f ( x + h ) - f ( x ) )/ h + O ( h )

return ( f ( x + h ) - f ( x ) )/ h

def backwarddiff (f ,x , h = EPS ):

# df / dx = ( f ( x ) - f (x - h ) )/ h + O ( h )

return ( f ( x ) - f (x - h ) )/ h

def centraldiff (f ,x , h = EPS ):

# df / dx = ( f ( x + h ) - f (x - h ))/ h + O ( h ^2)

return ( f ( x + h ) - f (x - h ))/(2* h )

if __name__ == " __main__ " :

# create example plot

import pylab

import numpy as np

a =0

# left and

b =5

# right limits for x

N =11

# steps

21 / 47

def f ( x ):

""" Our test funtion with

c o n v e n i e n t p r o p e r t y that

df / dx = f """

return np . exp ( x )

xs = np . linspace (a ,b , N )

forward = []

f or wa rd _ sm al l_ h = []

central = []

for x in xs :

forward . append ( forwarddiff (f , x ) )

central . append ( centraldiff (f , x ) )

f or wa rd _ sm al l_ h . append (

forwarddiff (f ,x , h =1 e -4))

pylab . figure ( figsize =(6 ,4))

pylab . axis ([ a ,b ,0 , np . exp ( b )])

pylab . plot ( xs , forward , ^ , label = forward h =% g % EPS )

pylab . plot ( xs , central , x , label = central h =% g % EPS )

pylab . plot ( xs , forward_small_h , o ,

label = forward h =% g % 1e -4)

xsfine = np . linspace (a ,b , N *100)

22 / 47

pylab . grid ()

pylab . legend ( loc = upper left )

pylab . xlabel ( " x " )

pylab . ylabel ( " df / dx ( x ) " )

pylab . title ( " A pproxim ations of df / dx for f ( x )= exp ( x ) " )

pylab . plot ()

pylab . savefig ( central - and - forward - difference . pdf )

pylab . show ()

23 / 47

using nite dierence operator

Use forward dierence operator to approximate

dierential operator

y(x + h) y(x)

dy

y(x + h) y(x)

(x) = lim

h0

dx

h

h

Change dierential to dierence operator in

dy

dx

= f (x, y)

y(x + h) y(x)

dy

dx

h

hf (x, y) y(x + h) y(x)

= yi+1 = yi + hf (xi , yi )

f (x, y) =

forward dierence operator.

24 / 47

derivation from Taylor series

We are looking for a root, i.e. we are looking for a x so that

f (x) = 0.

We have an initial guess x0 which we rene in subsequent iterations:

xi+1 = xi hi

where

hi =

f (xi )

.

f (xi )

(4)

.

This equation can be derived from the Taylor series of f around x.

Suppose we guess the root to be at x and x + h is the actual

location of the root (so h is unknown and f (x + h) = 0):

f (x + h)

f (x) + hf (x) + . . .

f (x) + hf (x) + . . .

= 0

f (x) + hf (x)

f (x)

.

f (x)

(5)

25 / 47

26 / 47

Diusion equation

2

operator , so that we can also write

u

=D

t

2

2

+ 2

x2 y

= Du

coecient D) reads u = Du where the Laplace

t

operator depends on the number d of spatial dimensions

d = 1: =

d = 2: =

d = 3: =

2

x2

2

x2

2

x2

+

+

2

y 2

2

y 2

2

z 2

27 / 47

u

t

1d Diusion equation

= D u

x2

u

2u

=D 2

t

x

u(x,t_0)

Lets assume an initial concentration

2

1

mean

u(x, t0 ) = 2 exp (xx2 ) with xmean = 0 and

width = 0.5.

0.8

0.7

0.6

0.5

0.4

0.3

0.2

0.1

0.0 6

(x,t0 )

0

x

6

28 / 47

1d Diusion eqn

u

t

= D u , time integration I

x2

2

D u at time t0 and lets call this g(x, t0 ), i.e.

x2

g(x, t0 ) D

2 u(x, t0 )

x2

We like to solve

u(x, t)

= g(x, t0 )

t

to compute u(x, t1 ) at some later time t1 .

Use nite dierence time integration scheme:

Introduce a time step size h so that t1 = t0 + h.

29 / 47

1d Diusion eqn

u

t

= D u , time integration II

x2

g(x, t0 ) =

u(x, t)

u(x, t0 + h) u(x, t0 )

= lim

(6)

h0

t

h

u(x, t0 + h) u(x, t0 )

(7)

h

u(x, t1 ) u(x, t0 ) + hg(x, t0 )

We can generalise this using ti = t0 + ih to read

u(x, ti+1 ) u(x, ti ) + hg(x, ti )

(8)

30 / 47

1d Diusion eqn

u

t

= D u , spatial part I

x2

u

2u

= D 2 = g(x, t)

t

x

2

u(x,t)

Need to compute g(x, t) = D x2 for a given u(x, t).

Can ignore the time dependence here, and obtain

g(x) = D

Recall that

2 u(x)

.

x2

2u

u

=

2

x

x x

dierences.

u

x

using central

31 / 47

df

f (x + h) f (x h)

(x)

dx

2h

1

will be more convenient to replace h by 2 h:

f (x + 1 h) f (x 1 h)

df

2

2

(x)

dx

h

32 / 47

Apply the central dierence equation twice to obtain

d2 f

:

dx2

d2 f

d df

(x) =

(x)

2

dx

dx dx

1

d f (x + 1 h) f (x 2 h)

2

dx

h

1 d

1

d

1

=

f x+ h

f x h

h dx

2

dx

2

1 f (x + h) f (x) f (x) f (x h)

h

h

h

f (x + h) 2f (x) + f (x h)

=

(9)

h2

33 / 47

Recipe to solve

1

2

u

t

= D u

x2

ui u(xj , ti ) where

j

xj x0 + jx and

ti t0 + it.

3

4

Need to know conguration u(x, ti ).

2

6

7

x2

(9).

Then compute u(x, ti+1 ) based on g(x, ti ) using (8)

increase i to i + 1, then go back to 5.

34 / 47

A sample solution

u

t

= D u, I

x2

import numpy as np

import matplotlib . pyplot as plt

import matplotlib . animation as animation

a , b = -5 ,5

N = 51

x = np . linspace (a ,b , N )

h = x [1] - x [0]

# size of box

# number of s u b d i v i s i o n s

# p o s i t i o n s of s u b d i v i s i o n s

# d i s c r e t i s a t i o n s t e p s i z e in x - d i r e c t i o n

def total ( u ):

""" C o m p u t e s total number of moles in u . """

return (( b - a )/ float ( N )* np . sum ( u ))

def gaussdistr ( mean , sigma , x ):

""" Return gauss d i s t r i b u t i o n for given numpy array x """

return 1./( sigma * np . sqrt (2* np . pi ))* np . exp (

-0.5*( x - mean )**2/ sigma **2)

# s t a r t i n g c o n f i g u r a t i o n for u (x , t0 )

u = gaussdistr ( mean =0. , sigma =0.5 , x = x )

35 / 47

A sample solution

u

t

= D u , II

x2

def compute_g ( u , D , h ):

""" given a u (x , t ) in array , compute g (x , t )= D * d ^2 u / dx ^2

using central d i f f e r e n c e s with spacing h ,

and return g (x , t ). """

d2u_dx2 = np . zeros ( u . shape , np . float )

for i in range (1 , len ( u ) -1):

d2u_dx2 [ i ] = ( u [ i +1] - 2* u [ i ]+ u [i -1])/ h **2

# special cases at b o u n d a r y : assume Neuman b o u n d a r y

# conditions , i . e . no change of u over b o u n d a r y

# so that u [0] - u [ -1]=0 and thus u [ -1]= u [0]

i =0

d2u_dx2 [ i ] = ( u [ i +1] - 2* u [ i ]+ u [ i ])/ h **2

# same at other end so that u [N -1] - u [ N ]=0

# and thus u [ N ]= u [N -1]

i = len ( u ) -1

d2u_dx2 [ i ] = ( u [ i ] - 2* u [ i ]+ u [i -1])/ h **2

return D * d2u_dx2

def advance_time ( u , g , dt ):

""" Given the array u , the rate of change array g ,

and a t i m e s t e p dt , compute the s o l u t i o n for u

after t , using simple Euler method . """

u = u + dt * g

36 / 47

A sample solution

u

t

= D u , III

x2

return u

# show example , quick and dirtly , lots of global v a r i a b l e s

dt = 0.01

# step size or time

s t e p s b e f o r e u p d a t i n g g r a p h = 20 # p l o t t i n g is slow

D = 1.

# Diffusion coefficient

stepsdone = 0

# keep track of i t e r a t i o n s

def do_steps (j , nsteps = s t e p s b e f o r e u p d a t i n g g r a p h ):

""" F u n c t i o n called by F u n c A n i m a t i o n class . C o m p u t e s

nsteps iterations , i . e . carries forward s o l u t i o n from

u (x , t_i ) to u (x , t_ { i + nsteps }).

"""

global u , stepsdone

for i in range ( nsteps ):

g = compute_g ( u , D , h )

u = advance_time ( u , g , dt )

stepsdone += 1

time_passed = stepsdone * dt

print ( " stepsdone =%5 d , time =%8 gs , total ( u )=%8 g " %

( stepsdone , time_passed , total ( u )))

l . set_ydata ( u )

# update data in plot

fig1 . canvas . draw () # redraw the canvas

37 / 47

A sample solution

u

t

= D u , IV

x2

return l ,

fig1 = plt . figure ()

l ,= plt . plot (x ,u , b - o )

# setup a n i m a t i o n

# plot initial u (x , t )

# then compute s o l u t i o n and animate

line_ani = animation . FuncAnimation ( fig1 ,

do_steps , range (10000))

plt . show ()

38 / 47

Boundary conditions I

know the initial value(s) to be able to compute a solution.

For partial dierential equations (PDEs), we need to

know the initial values and extra information about the

behaviour of the solution u(x, t) at the boundary of the

spatial domain (i.e. at x = a and x = b in this example).

Commonly used boundary conditions are

Dirichlet boundary conditions: x u(a) = c to some

constant.

Would correspond here to some mechanism that keeps

the concentration u at position x = a constant.

39 / 47

Boundary conditions II

the boundary, i.e.

u

(a) = c.

x

For positive/negative c this corresponds to an imposed

concentration gradient.

For c = 0, this corresponds to conservation of the atoms

in the solution: as the gradient across the boundary

cannot change, no atoms can move out of the box.

(Used in our program on slide 35)

40 / 47

Numerical issues

The time integration scheme we use is explicit because we

have an explicit equation that tells us how to compute

u(x, ti+1 ) based on u(x, ti ) (equation (8) on slide 30)

An implicit scheme would compute u(x, ti+1 ) based on

u(x, ti ) and on u(x, ti+1 ).

The implicit scheme is more complicated as it requires

solving an additional equation system just to nd

u(x, ti+1 ) but allows larger step sizes t for the time.

The explicit integration scheme becomes quickly unstable

if t is too large. t depends on the chose spatial

discretisation x.

41 / 47

Performance issues

interpreted language

explicit for loops

enforced small step size from explicit scheme

Solutions:

Refactor for-loops into matrix operations and use

(compiled) matrix library (numpy for small systems, use

scipy.sparse for larger systems)

Use library function to carry out time integration (will

use implicit method if required), for example

scipy.integrate.odeint.

42 / 47

Finite Elements

Another widely spread way of solving PDEs is using so-called

nite elements.

Mathematically, the solution u(x) for a problem like

2u

= f (x) is written as

x2

N

u(x) =

ui i (x)

(10)

i=1

a known function of space.

The i are called basis or shape functions.

Each i is normally chosen to be zero for nearly all x, and

to be non-zero close to a particular node in the nite

element mesh.

By substitution (10) into the PDE, a matrix system can

be obtained, which if solved provides the coecients

ui , and thus the solution.

43 / 47

Finite dierences

are mathematically much simpler and

for simple geometries (such as cuboids) easier to

program

Finite elements

have greater exibility in the shape of the domain,

the specication and implementation of boundary

conditions is easier

but the basic mathematics and code is more

complicated.

44 / 47

discretisation scheme such as nite dierences and nite

elements).

This results in a set of coupled ordinary dierential

equations (where time is the independent variable).

Can think of this as one ODE for every cube from our

discretisation.

This temporal part is then solved using time integration

schemes for (systems of) ordinary dierential equations.

45 / 47

Summary

Partial dierential equations important in many contexts

If no analytical solution known, use numerics.

Discretise the problem through

nite dierences (replace dierential with dierence

operator, corresponds to chopping space and time in

little cuboids)

nite elements (project solution on localised basis

functions, often used with tetrahedral meshes)

related methods (nite volumes, meshless methods).

standard tools in many areas of engineering, physics,

chemistry, but increasingly in other elds.

46 / 47

changeset:

tag:

user:

date:

53:a22b7f13329e

tip

Hans Fangohr [MBP13] <fangohr@soton.ac.uk>

Fri Dec 16 10:57:15 2011 +0000

47 / 47

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