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You are on page 1of 165

Mathieu Desroches

mathieu.desroches@inria.fr

Session A3: Mathematics for oscillations

24-25 July

Introduction to XPPAUT

XPP- -AUT

...

Part I

(short) Introduction to

! (parametrised families of) ODEs

! their Bifurcations

! direct simulation of ODEs

! numerical continuation study

Part I

(short) Introduction to

! (parametrised families of) ODEs

! their Bifurcations

! direct simulation of ODEs

! numerical continuation study

Part I

(short) Introduction to

! (parametrised families of) ODEs

! their Bifurcations

! direct simulation of ODEs

! numerical continuation study

Part I

(short) Introduction to

! (parametrised families of) ODEs

! their Bifurcations

! direct simulation of ODEs

! numerical continuation study

Part I

(short) Introduction to

! (parametrised families of) ODEs

! their Bifurcations

! direct simulation of ODEs

! numerical continuation study

topological type: (un)stable focus, (un)stable node, saddle ...

changes (from eq. to periodic, from periodic to quasi-

per., ...) ... structural stability is lost at bifurcation point.

Theory

topological type: (un)stable focus, (un)stable node, saddle ...

changes (from eq. to periodic, from periodic to quasi-

per., ...) ... structural stability is lost at bifurcation point.

Theory

topological type: (un)stable focus, (un)stable node, saddle ...

changes (from eq. to periodic, from periodic to quasi-

per., ...) ... structural stability is lost at bifurcation point.

Theory

topological type: (un)stable focus, (un)stable node, saddle ...

changes (from eq. to periodic, from periodic to quasi-

per., ...) ... structural stability is lost at bifurcation point.

Theory

topological type: (un)stable focus, (un)stable node, saddle ...

changes (from eq. to periodic, from periodic to quasi-

per., ...) ... structural stability is lost at bifurcation point.

Theory

Starting with 1D systems

x (state) variables

parameters

x = f(x, )

x (state) variables

parameters

x = f(x, )

Equilibria: nd all such that f( , )=0 x x

( is xed!)

x (state) variables

parameters

Stability: sign of f ( ) x

x = f(x, )

Equilibria: nd all such that f( , )=0 x x

( is xed!)

x (state) variables

parameters

Stability: sign of f ( ) x

f ( )<0: is stable

f ( )>0: is unstable

x x

x x

x = f(x, )

Equilibria: nd all such that f( , )=0 x x

( is xed!)

1D systems ... lets vary !

! structural stability

1D systems ... lets vary !

! structural stability

! bifurcation

Example 1: transcritical bifurcation

x = x( x)

ODE :

Example 1: transcritical bifurcation

" Equilibria :

x = 0, x =

x = x( x)

ODE :

Example 1: transcritical bifurcation

" Equilibria :

x = 0, x =

" Stability :

f

0

(x) = 2x

x = x( x)

ODE :

Example 1: transcritical bifurcation

" Equilibria :

x = 0, x =

" Stability :

f

0

(x) = 2x

f

0

(0) = , f

0

() =

x = x( x)

ODE :

Example 1: transcritical bifurcation

" Equilibria :

x = 0, x =

" Stability :

f

0

(x) = 2x

f

0

(0) = , f

0

() =

SO 1) it depends on !

x = x( x)

ODE :

Example 1: transcritical bifurcation

" Equilibria :

x = 0, x =

" Stability :

f

0

(x) = 2x

f

0

(0) = , f

0

() =

SO 1) it depends on !

2) always opposite stability BUT at 0!

x = x( x)

ODE :

Bifurcation diagram

Bifurcation diagram

Bifurcation diagram

Bifurcation diagram

Bifurcation diagram

! Transcritical bifurcation point

Example 2: fold bifurcation

ODE : x = x

2

Example 2: fold bifurcation

ODE :

" Equilibria :

x = x

2

Example 2: fold bifurcation

ODE :

" Equilibria :

x =

when > 0

x = x

2

Example 2: fold bifurcation

ODE :

" Equilibria :

x =

when > 0

x = 0 when = 0

x = x

2

Example 2: fold bifurcation

ODE :

" Equilibria :

x =

when > 0

x = 0 when = 0

when < 0 no equilibrium

x = x

2

Example 2: fold bifurcation

ODE :

" Equilibria :

x =

when > 0

x = 0 when = 0

when < 0 no equilibrium

x = x

2

" Stability : f

0

(x) = 2x

Example 2: fold bifurcation

ODE :

" Equilibria :

SO 1) it depends on !>0

x =

when > 0

x = 0 when = 0

when < 0 no equilibrium

x = x

2

" Stability : f

0

(x) = 2x

Example 2: fold bifurcation

ODE :

" Equilibria :

SO 1) it depends on !>0

2) always opposite stability BUT at 0!

x =

when > 0

x = 0 when = 0

when < 0 no equilibrium

x = x

2

" Stability : f

0

(x) = 2x

Bifurcation diagram

x = x

2

Bifurcation diagram

x = x

2

Bifurcation diagram

x = x

2

Bifurcation diagram

x = x

2

Bifurcation diagram

! Fold bifurcation point

x = x

2

Summary: 1D systems ...

Summary: 1D systems ...

Summary: 1D systems ...

Summary: 1D systems ...

Summary: 1D systems ...

However

The system is still nonlinear, so an exact

solution is unlikely to exist!

Same for equilibria!

Summary: 1D systems ...

However

The system is still nonlinear, so an exact

solution is unlikely to exist!

Same for equilibria!

$ Need to be able to simulate the system ...

Numerical simulation of ODEs

x = f(x, )

(1)

Numerical simulation of ODEs

x = f(x, )

(1)

Idea

$ discretise time :

$ march in time :

Compute numerically approximate sol. to (1)?

x(t

0

) = x

0

x(t

1

) = ...?

t

0

t

1

= t

0

+ h, h = dt

Numerical simulation of ODEs

x = f(x, )

(1)

Idea

$ discretise time :

$ march in time :

Compute numerically approximate sol. to (1)?

x(t

0

) = x

0

x(t

1

) = ...?

t

0

t

1

= t

0

+ h, h = dt

Example 1: Euler scheme

$ Error:

uses the slope of f(x(t0)) at x(t0)

to approximate x(t1)

(Taylor)

x(t

1

) x(t

0

) + f(x(t

0

), )h

O(h

2

)

Numerical simulation of ODEs

x = f(x, )

(1)

Example 1: Euler scheme

$ Error:

uses the slope of f(x(t0)) at x(t0)

to approximate x(t1)

(Taylor)

x(t

1

) x(t

0

) + f(x(t

0

), )h

O(h

2

)

Example 2: 2nd order Runge-Kutta scheme

$ Error: (Taylor) O(h

3

)

takes a half Euler step to the point (t0+0.5h, x(t0)+0.5k )

[see gure next]

1

Numerical simulation of ODEs

x = f(x, )

(1)

x

x

x

x

x

x

2D systems ... (nD, n>2)

vector of (state) variables

vector of parameters

x

x = f (x, )

2D systems ... (nD, n>2)

vector of (state) variables

vector of parameters

x

x = f (x, )

Equilibria: nd all such that f( , )=0

x

is xed!)

2D systems ... (nD, n>2)

vector of (state) variables

vector of parameters

x

x = f (x, )

Stability: Jacobian matrix

J =

f

i

x

j

x

is xed!)

2D systems ... (nD, n>2)

vector of (state) variables

vector of parameters

x

x = f (x, )

Stability: Jacobian matrix

J =

f

i

x

j

Equilibria: nd all such that f( , )=0

x

is xed!)

2D systems : nullclines

x = f(x, y, )

y = g(x, y, )

2D systems : nullclines

x = f(x, y, )

y = g(x, y, )

Equilibria:

(x !=! )

0

f(x

, y

,

0

) = 0 & g(x

, y

,

0

) = 0

2D systems : nullclines

x = f(x, y, )

y = g(x, y, )

Equilibria:

(x !=! )

0

f(x

, y

,

0

) = 0 & g(x

, y

,

0

) = 0

! Geometrically:

{f(x, y,

0

) = 0}{g(x, y,

0

) = 0}

2D systems : nullclines

(example) FitzHugh-Nagumo

v = v v

3

/3 w + I

y = (v + a bw)

I = 1.5

= 0.08

a = 0.7

b = 0.8

2D systems : nullclines

(example) FitzHugh-Nagumo

v = v v

3

/3 w + I

y = (v + a bw)

I = 1.5

= 0.08

a = 0.7

b = 0.8

! f is cubic

! g is linear

2D systems : nullclines

(example) FitzHugh-Nagumo

v = v v

3

/3 w + I

y = (v + a bw)

I = 1.5

= 0.08

a = 0.7

b = 0.8

! f is cubic

! g is linear

2D systems : nullclines

(example) FitzHugh-Nagumo

v = v v

3

/3 w + I

y = (v + a bw)

I = 1.5

= 0.08

a = 0.7

b = 0.8

1 eq.

! f is cubic

! g is linear

2D systems : nullclines

(example) FitzHugh-Nagumo

v = v v

3

/3 w + I

y = (v + a bw)

= 0.08

a = 0.7

I = 0.4

b = 1.8

! f is cubic

! g is linear

2D systems : nullclines

(example) FitzHugh-Nagumo

v = v v

3

/3 w + I

y = (v + a bw)

= 0.08

a = 0.7

I = 0.4

b = 1.8

3 eq.

! f is cubic

! g is linear

Linear approximation: 2D case

source

sink

nodal sink nodal source hyperbolic centre

Re

Im

Linear approximation: 2D case

source

sink

nodal sink nodal source hyperbolic centre

- nonlinear dynamics -

Re

Im

Linear approximation: 2D case

source

sink

nodal sink nodal source hyperbolic centre

focus

- nonlinear dynamics -

Re

Im

Linear approximation: 2D case

source

sink

nodal sink nodal source hyperbolic centre

focus node

- nonlinear dynamics -

Re

Im

Linear approximation: 2D case

source

sink

nodal sink nodal source hyperbolic centre

focus node

saddle

- nonlinear dynamics -

Re

Im

Linear approximation: 2D case

source

sink

nodal sink nodal source hyperbolic centre

focus node

saddle

- nonlinear dynamics -

(un)stable eigenspaces

Re

Im

Linear approximation: 2D case

source

sink

nodal sink nodal source hyperbolic centre

focus node

saddle

- nonlinear dynamics -

(un)stable eigenspaces

! nonlinear equivalent: (un)stable manifolds

W

s,u

Re

Im

Linear systems: stability

Ref.: [Jordan & Smith, 4th ed., Oxford Uni. Press, 2007]

Bifurcations

Bifurcations

1D : Bifurcation when f (x) goes through 0

2D : Bifurcation when an eigenvalue goes through 0

Bifurcations

(complex eigenvalues)

1D : Bifurcation when f (x) goes through 0

2D : Bifurcation when an eigenvalue goes through 0

Bifurcations

(complex eigenvalues)

1 - Damped nonlin. oscillations: focus eq.

2 - Sustained nonlin. oscillations: limit cycle

1D : Bifurcation when f (x) goes through 0

2D : Bifurcation when an eigenvalue goes through 0

Bifurcations

(complex eigenvalues)

1 - Damped nonlin. oscillations: focus eq.

2 - Sustained nonlin. oscillations: limit cycle

Transition 1-2 : Hopf bifurcations

1D : Bifurcation when f (x) goes through 0

2D : Bifurcation when an eigenvalue goes through 0

stable focus

Hopf bifurcation

C

Re

Im

stable focus

unstable focus

Hopf bifurcation

C

Re

Im

stable focus

unstable focus

unstable focus

Hopf bifurcation

C

Re

Im

! focus eq. destabilises when eigenvalues cross Im

stable focus

unstable focus

unstable focus

Hopf bifurcation

C

Re

Im

! focus eq. destabilises when eigenvalues cross Im

stable focus

unstable focus

a stable

limit cycle

is created!

Hopf : bifurcation diagram

Measure of

the solution

H

Hopf : bifurcation diagram

Measure of

the solution

H

Before : stable equilibrium

Hopf : bifurcation diagram

Measure of

the solution

H

After : unstable equilibrium

Hopf : bifurcation diagram

Measure of

the solution

H

After : stable limit cycle

Hopf : bifurcation diagram

Measure of

the solution

H

After : stable limit cycle

Represented

in this diagram by

max. and min. values

Hopf : bifurcation diagram

Measure of

the solution

H

After : stable limit cycle

Represented

in this diagram by

max. and min. values

From stationary to periodic when varying !!

Hopf : bifurcation diagram

- 3D visualisation -

x

y

Transient dynamics

Long-term dynamics (attractors)

nonlinear equations of the form:

F(x) = 0, F : R

n+1

R

n

! under-determined system (one more unknowns than equations)

! away from singularities, solution set = 1-dim. manifold

embedded in (n+1)-dim. space

Numerical continuation : idea

F(x) = 0, F : R

n+1

R

n

! stationary problems (search for equilibria)

! Boundary Value Problems (BVP), including periodic orbits

This will rely on the application of the Implicit Function Theorem !

x = F(x, )

Numerical continuation : idea

Parameter continuation

one component to nd a new solution ...

of solutions parameterised by $: (x($), $).

F(x

0

) = 0, x

0

= (x

0

,

0

) R

n

R

solution of the problem but close to one!

x

#

1

= (x

0

,

0

+ s),

F(x

#

1

) 6= 0,

F(x

#

1

) 1

on the augmented problem

method

x

#

1

= (x

0

,

0

+ s)

F(x) = 0,

(

0

+ ) = 0

Parameter continuation

Tangent continuation

such as the tangent to the curve

augmented problem

x

1

F(x) = 0,

(

0

+ ) = 0

Problem at a fold !!

Kellers pseudo-arclength continuation

continuation cannot parameterise the solution curve

!Arclength s along the curve !

F(x) = 0,

(

0

)

0

+ (x x

0

) x

0

s = 0

Arclength measured along the tangent space !

Periodic orbit continuation

! We seek for solutions of period 1 i.e. such that :

x = F(x(t), )

x

0

= TF(x(t), )

x(1) = x(0)

! The true period T is now an additional parameter

... translation invariance !

! Necessity of a Phase condition

Z

1

0

x

k

(t)

x

0

k1

dt = 0

(x

k

(0) x

k1

(0))

x

0

k1

(0)) = 0

such that :

Periodic orbit continuation

! We seek for solutions of period 1 i.e. such that :

x = F(x(t), )

x

0

= TF(x(t), )

x(1) = x(0)

! The true period T is now an additional parameter

... translation invariance !

! Necessity of a Phase condition

Z

1

0

x

k

(t)

x

0

k1

dt = 0

(x

k

(0) x

k1

(0))

x

0

k1

(0)) = 0

such that :

arclength-continuation equation:

collocation (piecewise polynomials on mesh intervals)

! Solve exactly at mesh points (boundaries of mesh intervals)

Z

1

0

(x

k

(t) x

k1

(t))

x

k1

dt + (T

k

T

k1

)

T

k1

+(

k

k1

)

k1

s = 0

! Inside mesh intervals: well-chosen collocation points (good

convergence properties)

for n+1 conditions ( periodicity + phase)

! varying 1 parameter will give a 1-parameter family of per. orbits

Periodic orbit continuation

Part II: XPPAUT

- main features & capabilities -

Equation file: FitzHugh-Nagumo

Equation file: FitzHugh-Nagumo

Differential Equations

Equation file: FitzHugh-Nagumo

Parameters: initialisation

Equation file: FitzHugh-Nagumo

State variables: initial conditions

Equation file: FitzHugh-Nagumo

Numerical accuracy

learn how to use XPP on this example!

accuracy, ...

integration time, the tolerances, ...

approx. of equilibria / alternatively, use the in-built routine to

nd eq. & assess stability & approximation of (un)stable mds

interesting transitions like eq 2 per i.e. one has gone through

a Hopf bifurcation! ... Can do that more systematically!!

XPP-part

learn how to use XPP on this example!

accuracy, ...

integration time, the tolerances, ...

approx. of equilibria / alternatively, use the in-built routine to

nd eq. & assess stability & approximation of (un)stable mds

interesting transitions like eq 2 per i.e. one has gone through

a Hopf bifurcation! ... Can do that more systematically!!

XPP-part

learn how to use XPP on this example!

accuracy, ...

integration time, the tolerances, ...

approx. of equilibria / alternatively, use the in-built routine to

nd eq. & assess stability & approximation of (un)stable mds

interesting transitions like eq 2 per i.e. one has gone through

a Hopf bifurcation! ... Can do that more systematically!!

XPP-part

learn how to use XPP on this example!

accuracy, ...

integration time, the tolerances, ...

approx. of equilibria / alternatively, use the in-built routine to

nd eq. & assess stability & approximation of (un)stable mds

interesting transitions like eq 2 per i.e. one has gone through

a Hopf bifurcation! ... Can do that more systematically!!

XPP-part

learn how to use XPP on this example!

accuracy, ...

integration time, the tolerances, ...

approx. of equilibria / alternatively, use the in-built routine to

nd eq. & assess stability & approximation of (un)stable mds

interesting transitions like eq 2 per i.e. one has gone through

a Hopf bifurcation! ... Can do that more systematically!!

XPP-part

learn how to use XPP on this example!

accuracy, ...

integration time, the tolerances, ...

approx. of equilibria / alternatively, use the in-built routine to

nd eq. & assess stability & approximation of (un)stable mds

interesting transitions like eq 2 per i.e. one has gone through

a Hopf bifurcation! ... Can do that more systematically!!

XPP-part

learn how to use XPP on this example!

accuracy, ...

integration time, the tolerances, ...

approx. of equilibria / alternatively, use the in-built routine to

nd eq. & assess stability & approximation of (un)stable mds

interesting transitions like eq 2 per i.e. one has gone through

a Hopf bifurcation! ... Can do that more systematically!!

XPP-part

learn how to use XPP on this example!

accuracy, ...

integration time, the tolerances, ...

approx. of equilibria / alternatively, use the in-built routine to

nd eq. & assess stability & approximation of (un)stable mds

interesting transitions like eq 2 per i.e. one has gone through

a Hopf bifurcation! ... Can do that more systematically!!

XPP-part

Lets launch it and try!

Lets launch it and try!

Were now going to learn XPP

with the FitzHugh-Nagumo

equation ...

emanating family of periodic orbits ...

AUT-part

emanating family of periodic orbits ...

AUT-part

AUTO

Lets launch it and try!

Lets launch it and try!

! !"# $ $"# %

%

$

!

$

%

I

v

HB

HB

stable

unstable

stable

max(v)

min(v)

FHN: 1-par. continuation results

b=0.8

! !"#$ !"$ !"%$ &

#

&

!

&

#

FHN: 1-par. continuation results

b=1.8

I

v

HB

HB

stable

unstable

stable

LP

LP

HO

HO

FHN: 2-par. continuation results

I & b

! ! " #$

$

#%!&

!%&

'%(&

&

I

b

HB

LP

0.8

1.8

1.25

2.5

FHN: 2-par. continuation results

I & b

I

b

LP

HB

0.8

1.8

Part III: XPPAUT

- practice it yourself -

Hindmarsh-Rose equation file

Hindmarsh-Rose equation file

D.E.

Hindmarsh-Rose equation file

D.E.

Par.

Hindmarsh-Rose equation file

D.E.

Par.

I.C.

Hindmarsh-Rose equation file

D.E.

Par.

I.C.

Num.

the Van der Pol system, that is,

Practice XPPAUT on your own!

periodic solutions

Simulating the system for different values of I, you

should obtain time series that look like these ones

Simulating the system for different values of I, you

should obtain time series that look like these ones

Simulating the system for different values of I, you

should obtain time series that look like these ones

b

u

r

s

t

i

n

g

Simulating the system for different values of I, you

should obtain time series that look like these ones

b

u

r

s

t

i

n

g

b

u

r

s

t

i

n

g

Simulating the system for different values of I, you

should obtain time series that look like these ones

b

u

r

s

t

i

n

g

b

u

r

s

t

i

n

g

i

r

r

e

g

u

l

a

r

s

p

i

k

i

n

g

Simulating the system for different values of I, you

should obtain time series that look like these ones

b

u

r

s

t

i

n

g

b

u

r

s

t

i

n

g

i

r

r

e

g

u

l

a

r

s

p

i

k

i

n

g

r

e

g

u

l

a

r s

p

i

k

i

n

g

You should obtain a bifurcation

diagram that looks like this one

0 7 14 21 28

2

0.75

0.5

1.75

3

I

x

HB

HB HB

HB

References

XPPAUT

References

% Bard Ermentrout (University of Pittsburgh, USA):

XPPAUT

References

% Bard Ermentrout (University of Pittsburgh, USA):

XPPAUT

References

% Bard Ermentrout (University of Pittsburgh, USA):

XPPAUT

References

XPPAUT

References

% Other tutorials :

XPPAUT

http://www.math.ualberta.ca/~devries/math570-winter2008/XPPtutorial.pdf

http://people.uleth.ca/~roussel/nld/bifurc_analysis.pdf

http://www.math.osu.edu/~kao/Math865Lsourcecode/Handout/xppaut_tutorial.pdf

http://www.iiserpune.ac.in/~pgoel/XPP_Tutorial.pdf

References

% Other tutorials :

XPPAUT

http://www.math.ualberta.ca/~devries/math570-winter2008/XPPtutorial.pdf

http://people.uleth.ca/~roussel/nld/bifurc_analysis.pdf

http://www.math.osu.edu/~kao/Math865Lsourcecode/Handout/xppaut_tutorial.pdf

http://www.iiserpune.ac.in/~pgoel/XPP_Tutorial.pdf

% Examples of ode les :

http://mrb.niddk.nih.gov/sherman/gallery/index.html

http://www.math.fsu.edu/~bertram/software/

References ...

ODEs & Bifurcations

References ...

ODEs & Bifurcations

(Tutorials & Software sections)

(MathDoctorMitchells Channel)

References ...

ODEs & Bifurcations

(Tutorials & Software sections)

http://www.bio.vu.nl/thb/research/project/globif/

(MathDoctorMitchells Channel)

References ...

ODEs & Bifurcations

(Tutorials & Software sections)

http://www.bio.vu.nl/thb/research/project/globif/

(MathDoctorMitchells Channel)

Beyond XPPAUT!

Beyond XPPAUT!

Command-line AUTO: the proper way to do continuation!

Beyond XPPAUT!

Command-line AUTO: the proper way to do continuation!

! Allows to continue: equilibria, limit cycles

AND boundary-value problems

Beyond XPPAUT!

Command-line AUTO: the proper way to do continuation!

! Allows to continue: equilibria, limit cycles

AND boundary-value problems

Other continuation packages:

MatCont Matlab based !

CoCo

Beyond XPPAUT!

Command-line AUTO: the proper way to do continuation!

! Allows to continue: equilibria, limit cycles

AND boundary-value problems

Other continuation packages:

MatCont Matlab based !

!! mostly for ODEs !!

CoCo

Beyond XPPAUT!

Command-line AUTO: the proper way to do continuation!

! Allows to continue: equilibria, limit cycles

AND boundary-value problems

Other continuation packages:

MatCont Matlab based !

Beyond ODEs:

!! mostly for ODEs !!

CoCo

Beyond XPPAUT!

Command-line AUTO: the proper way to do continuation!

! Allows to continue: equilibria, limit cycles

AND boundary-value problems

Other continuation packages:

MatCont Matlab based !

Beyond ODEs:

%codes exist for PDEs ( ) and DDEs ( )

!! mostly for ODEs !!

CoCo

LOCA Knut

Beyond XPPAUT!

Command-line AUTO: the proper way to do continuation!

! Allows to continue: equilibria, limit cycles

AND boundary-value problems

Other continuation packages:

MatCont Matlab based !

Beyond ODEs:

%codes exist for PDEs ( ) and DDEs ( )

& on-going work for SDEs and equation-free problems ...

!! mostly for ODEs !!

CoCo

LOCA Knut

References

AUTO - 07p

References

% Eusebius Doedel (Concordia University, Montreal):

AUTO - 07p

References

% Eusebius Doedel (Concordia University, Montreal):

AUTO - 07p

References

% Eusebius Doedel (Concordia University, Montreal):

AUTO - 07p

References

% Eusebius Doedel (Concordia University, Montreal):

AUTO - 07p

http://www2.imperial.ac.uk/~jswlamb/LDSG/grad0506/auto_course.htm

Thanks for your attention!

... questions?

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