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Numerical integration of Ordinary Differential Equations

This notebook serves as a quick refresher on ordinary differential equations. If you are familiar with the topic:
feel free to skim this notebook.

We will first consider the decay of tritium as an example:

3 3 −
H →   He + e +ν

We will not concern ourselves with the products, instead we will only take interest in the number density of
as function of time, let's call it y(t). The rate of change of y(t) is proportional to itself and the decay

constant (λ ):

= −λy(t)

you probably know the solution to this class of differential equations (either from experience or by guessing
an appropriate ansatz). SymPy can of course also solve this equation:

In [1]: import sympy as sym

t, l = sym.symbols('t lambda')
y = sym.Function('y')(t)
dydt = y.diff(t)
expr = sym.Eq(dydt, -l*y)

Out[1]: d
y(t) = −λy(t)

In [2]: sym.dsolve(expr)

Out[2]: y(t) = C1 e

Now, pretend for a while that this function lacked an analytic solution. We could then integrate this equation
numerically from an initial state for a predetermined amount of time by discretizing the time into a seriers of
small steps.
Explicit methods
For each step taken we would update y by multiplying the derivative with the step size (assuming that the
derivate is approximately constant on the scale of the step-size), formally this method is known as "forward

yn+1 = yn + y (tn ) ⋅ Δh

this is known as an explicit method, i.e. the derivative at the current time step is used to calculate the next
step forward.

For demonstration purposes only, we implement this in Python:

In [3]: import numpy as np

def euler_fw(rhs, y0, tout, params):
y0 = np.atleast_1d(np.asarray(y0, dtype=np.float64))
dydt = np.empty_like(y0)
yout = np.zeros((len(tout), len(y0)))
yout[0] = y0
t_old = tout[0]
for i, t in enumerate(tout[1:], 1):
dydt[:] = rhs(yout[i-1], t, *params)
h = t - t_old
yout[i] = yout[i-1] + dydt*h
t_old = t
return yout

applying this function on our model problem:

In [4]: def rhs(y, t, decay_constant):

return -decay_constant*y # the rate does not depend on time

In [5]: tout = np.linspace(0, 2e9, 100)

y0 = 3
params = (1.78e-9,) # 1 parameter, decay constant of tritium
yout = euler_fw(rhs, y0, tout, params)

and plotting the solution & the numerical error using matplotlib:
In [6]: import matplotlib.pyplot as plt
%matplotlib inline

def my_plot(tout, yout, params, xlbl='time / a.u.', ylabel=None, ana

fig, axes = plt.subplots(1, 2 if analytic else 1, figsize=(14, 4
axes = np.atleast_1d(axes)
for i in range(yout.shape[1]):
axes[0].plot(tout, yout[:, i], label='y%d' % i)
if ylabel:
for ax in axes:
if analytic:
axes[0].plot(tout, analytic(tout, yout, params), '--')
axes[1].plot(tout, yout[:, 0] - yout[0]*np.exp(-params[0]*(t
if ylabel:
axes[1].set_ylabel('Error in ' + ylabel)

In [7]: def analytic(tout, yout, params):

return yout[0, 0]*np.exp(-params[0]*tout)
my_plot(tout, yout, params, analytic=analytic, ylabel='number densit
y / a.u.')

We see that 100 points gave us almost plotting accuracy.

Unfortunately, Euler forward is not practical for most real world problems. Usually we want a higher order
formula (the error in Euler forward scales only as n−1 ), and we want to use an adaptive step size (larger
steps when the function is smooth). So we use the well tested LSODA algorithm (provided in scipy as
In [8]: from scipy.integrate import odeint
yout, info = odeint(rhs, y0, tout, params, full_output=True)
my_plot(tout, yout, params, analytic=analytic)
print("Number of function evaluations: %d" % info['nfe'][-1])

Number of function evaluations: 95

We can see that odeint was able to achieve a much higher precision using fewer number of function
Implicit methods
For a large class of problems we need to base the step not on the derivative at the current time point, but
rather at the next one (giving rise to an implicit expression). The simplest implicit stepper is "backward euler":

yn+1 = yn + y (tn+1 ) ⋅ Δh

Problems requiring this type of steppers are known as "stiff". We will not go into the details of this (LSODA
actually uses something more refined and switches between explicit and implicit steppers).

In the upcoming notebooks we will use odeint to solve systems of ODEs (and not only linear equations as in
this notebook). The emphasis is not on the numerical methods, but rather on how we, from symbolic
expressions, can generate fast functions for the solver.

Systems of differential equations

In order to show how we would formulate a system of differential equations we will here briefly look at the
van der Pol osciallator ( It is a second order differential

d y0 dy0
− μ(1 − y ) + y0 = 0
2 0
dx dx

One way to reduce the order of our second order differential equation is to formulate it as a system of first
order ODEs, using:

y1 = ẏ 0

which gives us:

ẏ 0 = y1
{ 2
ẏ 1 = μ(1 − y )y1 − y0

Let's call the function for this system of ordinary differential equations vdp:

In [9]: def vdp(y, t, mu):

return [
mu*(1-y[0]**2)*y[1] - y[0]

using "Euler forward":

In [10]: tout = np.linspace(0, 200, 1024)
y_init, params = [1, 0], (17,)
y_euler = euler_fw(vdp, y_init, tout, params) # never mind the warn
ings emitted here...

/home/travis/miniconda3/envs/codegen17/lib/python3.6/site-packages/i RuntimeWarning: overflow encountered in doub
after removing the cwd from sys.path.
/home/travis/miniconda3/envs/codegen17/lib/python3.6/site-packages/i RuntimeWarning: invalid value encountered i
n add
# This is added back by InteractiveShellApp.init_path()

In [11]: my_plot(tout, y_euler, params)

That does not look like an oscillator. (we see that Euler forward has deviated to values with enormous
magnitude), here the advanced treatment by the odeint solver is far superior:

In [12]: y_odeint, info = odeint(vdp, y_init, tout, params, full_output=True)

print("Number of function evaluations: %d, number of Jacobian evalua
tions: %d" % (info['nfe'][-1], info['nje'][-1]))
my_plot(tout, y_odeint, params)

Number of function evaluations: 9244, number of Jacobian evaluation

s: 211

We see that LSODA has evaluated the Jacobian. But we never gave it an explicit representation of it―so how
could it?

It estimated the Jacobian matrix by using finite differences. Let's see if we can do better if we provide a
function to calculate the (analytic) Jacobian.
Exercise: manually write a function evaluating a Jacobian
First we need to know what signature odeint expects, we look at the documentation by using the help
command: (or using ? in IPython)
In [13]: help(odeint) # just skip to "Dfun"
Help on function odeint in module scipy.integrate.odepack:

odeint(func, y0, t, args=(), Dfun=None, col_deriv=0, full_output=0,

ml=None, mu=None, rtol=None, atol=None, tcrit=None, h0=0.0, hmax=0.
0, hmin=0.0, ixpr=0, mxstep=0, mxhnil=0, mxordn=12, mxords=5, printm
Integrate a system of ordinary differential equations.

Solve a system of ordinary differential equations using lsoda fr

om the
FORTRAN library odepack.

Solves the initial value problem for stiff or non-stiff systems

of first order ode-s::

dy/dt = func(y, t0, ...)

where y can be a vector.

*Note*: The first two arguments of ``func(y, t0, ...)`` are in t

opposite order of the arguments in the system definition functio
n used
by the `scipy.integrate.ode` class.

func : callable(y, t0, ...)
Computes the derivative of y at t0.
y0 : array
Initial condition on y (can be a vector).
t : array
A sequence of time points for which to solve for y. The ini
value point should be the first element of this sequence.
args : tuple, optional
Extra arguments to pass to function.
Dfun : callable(y, t0, ...)
Gradient (Jacobian) of `func`.
col_deriv : bool, optional
True if `Dfun` defines derivatives down columns (faster),
otherwise `Dfun` should define derivatives across rows.
full_output : bool, optional
True if to return a dictionary of optional outputs as the se
cond output
printmessg : bool, optional
Whether to print the convergence message

y : array, shape (len(t), len(y0))
Array containing the value of y for each desired time in t,
with the initial value `y0` in the first row.
infodict : dict, only returned if full_output == True
Dictionary containing additional output information

======= ===================================================
key meaning
======= ===================================================
'hu' vector of step sizes successfully used for each tim
e step.
'tcur' vector with the value of t reached for each time st
(will always be at least as large as the input time
'tolsf' vector of tolerance scale factors, greater than 1.
computed when a request for too much accuracy was d
'tsw' value of t at the time of the last method switch
(given for each time step)
'nst' cumulative number of time steps
'nfe' cumulative number of function evaluations for each
time step
'nje' cumulative number of jacobian evaluations for each
time step
'nqu' a vector of method orders for each successful step.
'imxer' index of the component of largest magnitude in the
weighted local error vector (e / ewt) on an error r
eturn, -1
'lenrw' the length of the double work array required.
'leniw' the length of integer work array required.
'mused' a vector of method indicators for each successful t
ime step:
1: adams (nonstiff), 2: bdf (stiff)
======= ===================================================

Other Parameters
ml, mu : int, optional
If either of these are not None or non-negative, then the
Jacobian is assumed to be banded. These give the number of
lower and upper non-zero diagonals in this banded matrix.
For the banded case, `Dfun` should return a matrix whose
rows contain the non-zero bands (starting with the lowest di
Thus, the return matrix `jac` from `Dfun` should have shape
``(ml + mu + 1, len(y0))`` when ``ml >=0`` or ``mu >=0``.
The data in `jac` must be stored such that ``jac[i - j + mu,
holds the derivative of the `i`th equation with respect to t
he `j`th
state variable. If `col_deriv` is True, the transpose of th
`jac` must be returned.
rtol, atol : float, optional
The input parameters `rtol` and `atol` determine the error
control performed by the solver. The solver will control th
vector, e, of estimated local errors in y, according to an
inequality of the form ``max-norm of (e / ewt) <= 1``,
where ewt is a vector of positive error weights computed as
``ewt = rtol * abs(y) + atol``.
rtol and atol can be either vectors the same length as y or
Defaults to 1.49012e-8.
tcrit : ndarray, optional
Vector of critical points (e.g. singularities) where integra
care should be taken.
h0 : float, (0: solver-determined), optional
The step size to be attempted on the first step.
hmax : float, (0: solver-determined), optional
The maximum absolute step size allowed.
hmin : float, (0: solver-determined), optional
The minimum absolute step size allowed.
ixpr : bool, optional
Whether to generate extra printing at method switches.
mxstep : int, (0: solver-determined), optional
Maximum number of (internally defined) steps allowed for eac
integration point in t.
mxhnil : int, (0: solver-determined), optional
Maximum number of messages printed.
mxordn : int, (0: solver-determined), optional
Maximum order to be allowed for the non-stiff (Adams) metho
mxords : int, (0: solver-determined), optional
Maximum order to be allowed for the stiff (BDF) method.

See Also
ode : a more object-oriented integrator based on VODE.
quad : for finding the area under a curve.

The second order differential equation for the angle `theta` of
pendulum acted on by gravity with friction can be written::

theta''(t) + b*theta'(t) + c*sin(theta(t)) = 0

where `b` and `c` are positive constants, and a prime (') denote
s a
derivative. To solve this equation with `odeint`, we must first
it to a system of first order equations. By defining the angula
velocity ``omega(t) = theta'(t)``, we obtain the system::

theta'(t) = omega(t)
omega'(t) = -b*omega(t) - c*sin(theta(t))

Let `y` be the vector [`theta`, `omega`]. We implement this sys

in python as:

>>> def pend(y, t, b, c):

... theta, omega = y
... dydt = [omega, -b*omega - c*np.sin(theta)]
... return dydt

We assume the constants are `b` = 0.25 and `c` = 5.0:

>>> b = 0.25
>>> c = 5.0
For initial conditions, we assume the pendulum is nearly vertica
with `theta(0)` = `pi` - 0.1, and it initially at rest, so
`omega(0)` = 0. Then the vector of initial conditions is

>>> y0 = [np.pi - 0.1, 0.0]

We generate a solution 101 evenly spaced samples in the interval

0 <= `t` <= 10. So our array of times is:

>>> t = np.linspace(0, 10, 101)

Call `odeint` to generate the solution. To pass the parameters

`b` and `c` to `pend`, we give them to `odeint` using the `args`

>>> from scipy.integrate import odeint

>>> sol = odeint(pend, y0, t, args=(b, c))

The solution is an array with shape (101, 2). The first column
is `theta(t)`, and the second is `omega(t)`. The following code
plots both components.

>>> import matplotlib.pyplot as plt

>>> plt.plot(t, sol[:, 0], 'b', label='theta(t)')
>>> plt.plot(t, sol[:, 1], 'g', label='omega(t)')
>>> plt.legend(loc='best')
>>> plt.xlabel('t')
>>> plt.grid()

so the signature needs to be: (state-vector, time, parameters) -> matrix

In [14]: %load_ext scipy2017codegen.exercise

Use either the %exercise or %load magic to get the exercise / solution respecitvely (i.e. delete the whole
contents of the cell except for the uncommented magic command). Replace ??? with the correct expression.

Remember that our system is defined as:

ẏ 0 = y1
ẏ 1 = μ(1 − y )y1 − y0

In [15]: # %exercise

def J_func(y, t, mu):
return np.array([
[0, 1],
[-1-2*mu*y[0]*y[1], mu*(1-y[0]**2)] # EXERCISE: -1-2*mu*y

In [16]: J_func(y_init, tout[0], params[0])

Out[16]: array([[ 0, 1],

[-1, 0]])
In [17]: y_odeint, info = odeint(vdp, y_init, tout, params, full_output=True,

In [18]: my_plot(tout, y_odeint, params)

print("Number of function evaluations: %d, number of Jacobian evalua
tions: %d" % (info['nfe'][-1], info['nje'][-1]))

Number of function evaluations: 8557, number of Jacobian evaluation

s: 194

So this time the integration needed to evaluate both the ODE system function and its Jacobian fewer times
than when using finite difference approximations. The reason for this is that the more accurate the Jacobian
is, the better is the convergence in the iterative (Newton's) method solving the implicit system of equations.

For larger systems of ODEs the importance of providing a (correct) analytic Jacobian can be much bigger.

SymPy to the rescue

Instead of writing the jacobian function by hand we could have used SymPy's lambdify which we will
introduce next. Here is a sneak peak on how it could be achieved:

In [19]: y = y0, y1 = sym.symbols('y0 y1')

mu = sym.symbols('mu')
J = sym.Matrix(vdp(y, None, mu)).jacobian(y)
J_func = sym.lambdify((y, t, mu), J)

Out[19]: 0 1
[ ]
−2μy0 y1 − 1 μ (−y + 1)