# Implementation¶

This section presents the complete computational algorithm, its implementation in Python code, animation of the solution, and verification of the implementation.

A real implementation of the basic computational algorithm from the sections Formulating a recursive algorithm and Sketch of an implementation can be encapsulated in a function, taking all the input data for the problem as arguments. The physical input data consists of $$c$$, $$I(x)$$, $$V(x)$$, $$f(x,t)$$, $$L$$, and $$T$$. The numerical input is the mesh parameters $$\Delta t$$ and $$\Delta x$$.

Instead of specifying $$\Delta t$$ and $$\Delta x$$, we can specify one of them and the Courant number $$C$$ instead, since having explicit control of the Courant number is convenient when investigating the numerical method. Many find it natural to prescribe the resolution of the spatial grid and set $$N_x$$. The solver function can then compute $$\Delta t = CL/(cN_x)$$. However, for comparing $$u(x,t)$$ curves (as functions of $$x$$) for various Courant numbers it is more convenient to keep $$\Delta t$$ fixed for all $$C$$ and let $$\Delta x$$ vary according to $$\Delta x = c\Delta t/C$$. With $$\Delta t$$ fixed, all frames correspond to the same time $$t$$, and this simplifies animations that compare simulations with different mesh resolutions. Plotting functions of $$x$$ with different spatial resolution is trivial, so it is easier to let $$\Delta x$$ vary in the simulations than $$\Delta t$$.

## Callback function for user-specific actions¶

The solution at all spatial points at a new time level is stored in an array u of length $$N_x+1$$. We need to decide what to do with this solution, e.g., visualize the curve, analyze the values, or write the array to file for later use. The decision about what to do is left to the user in the form of a user-supplied function user_action(u, x, t, n), where u is the solution at the spatial points x at time t[n]. The user_action function is called from the solver at each time level n.

If the user wants to plot the solution or store the solution at a time point, she needs to write such a function and take appropriate actions inside it. We will show examples on many such user_action functions.

Since the solver function makes calls back to the user’s code via such a function, this type of function is called a callback function. When writing general software, like our solver function, which also needs to carry out special problem- or solution-dependent actions (like visualization), it is a common technique to leave those actions to user-supplied callback functions.

The callback function can be used to terminate the solution process if the user returns True. For example,

def my_user_action_function(u, x, t, n):
return np.abs(u).max() > 10


is a callback function that will terminate the solver function (given below) of the amplitude of the waves exceed 10, which is here considered as a numerical instability.

## The solver function¶

A first attempt at a solver function is listed below.

# NBVAL_IGNORE_OUTPUT
import numpy as np
import time as time
from devito import Constant, Grid, TimeFunction, SparseTimeFunction, Function, Eq, solve, Operator, Buffer

# %load -s solver, src-wave/wave1D/wave1D_u0.py
def solver(I, V, f, c, L, dt, C, T, user_action=None):
"""Solve u_tt=c^2*u_xx + f on (0,L)x(0,T]."""
Nt = int(round(T/dt))
t = np.linspace(0, Nt*dt, Nt+1)   # Mesh points in time
dx = dt*c/float(C)
Nx = int(round(L/dx))
x = np.linspace(0, L, Nx+1)       # Mesh points in space
C2 = C**2                         # Help variable in the scheme

# Make sure dx and dt are compatible with x and t
dx = x[1] - x[0]
dt = t[1] - t[0]

# Initialising functions f and V if not provided
if f is None or f == 0 :
f = lambda x, t: 0
if V is None or V == 0:
V = lambda x: 0

t0 = time.perf_counter()  # Measure CPU time

# Set up grid
grid = Grid(shape=(Nx+1), extent=(L))
t_s = grid.stepping_dim

# Create and initialise u
u = TimeFunction(name='u', grid=grid, time_order=2, space_order=2)
u.data[:,:] = I(x[:])

x_dim = grid.dimensions[0]
t_dim = grid.time_dim

# The wave equation we are trying to solve
pde = (1/c**2)*u.dt2-u.dx2

# Source term and injection into equation
dt_symbolic = grid.time_dim.spacing
src = SparseTimeFunction(name='f', grid=grid, npoint=Nx+1, nt=Nt+1)

for i in range(Nt):
src.data[i] = f(x, t[i])

src.coordinates.data[:, 0] = x
src_term = src.inject(field=u.forward, expr=src * (dt_symbolic**2))
stencil = Eq(u.forward, solve(pde, u.forward))

# Set up special stencil for initial timestep with substitution for u.backward
v = Function(name='v', grid=grid, npoint=Nx+1, nt=1)
v.data[:] = V(x[:])
stencil_init = stencil.subs(u.backward, u.forward - dt_symbolic*v)

# Boundary conditions
bc = [Eq(u[t_s+1, 0], 0)]
bc += [Eq(u[t_s+1, Nx], 0)]

# Create and apply operators
op_init = Operator([stencil_init]+src_term+bc)
op = Operator([stencil]+src_term+bc)

op_init.apply(time_M=1, dt=dt)
op.apply(time_m=1, time_M=Nt, dt=dt)

cpu_time = time.perf_counter() - t0

return u.data[-1], x, t, cpu_time


A couple of remarks about the above code is perhaps necessary:

• Although we give dt and compute dx via C and c, the resulting t and x meshes do not necessarily correspond exactly to these values because of rounding errors. To explicitly ensure that dx and dt correspond to the cell sizes in x and t, we recompute the values.

• According to the particular choice made in the section Callback function for user-specific actions, a true value returned from user_action should terminate the simulation.

# NBVAL_IGNORE_OUTPUT
import matplotlib.pyplot as plt

def u_exact(x, t):
return x*(L-x)*(1 + 0.5*t)

def I(x):
return u_exact(x, 0)

def V(x):
return 0.5*u_exact(x, 0)

def f(x, t):
return 2*(1 + 0.5*t)*c**2

c = 1.5
L = 2.5
Nx = 100
C = 0.75
dt = C*(L/Nx)/c
T = 18
u, x, t, cpu_time = solver(I, V, f, c, L, dt, C, T)

plt.plot(x, u)
plt.xlabel('x')
plt.ylabel('u')
plt.legend(loc='best')
plt.show()

Data type float64 of runtime value dt does not match the Constant data type <class 'numpy.float32'>

Operator Kernel run in 0.01 s

Data type float64 of runtime value dt does not match the Constant data type <class 'numpy.float32'>

Operator Kernel run in 0.01 s

No handles with labels found to put in legend.


We use the test problem derived in the section A slightly generalized model problem for verification. Below is a unit test based on this test problem and realized as a proper test function compatible with the unit test frameworks nose or pytest.

# %load -s test_quadratic, src-wave/wave1D/wave1D_u0.py
"""Check that u(x,t)=x(L-x)(1+t/2) is exactly reproduced."""

def u_exact(x, t):
return x*(L-x)*(1 + 0.5*t)

def I(x):
return u_exact(x, 0)

def V(x):
return 0.5*u_exact(x, 0)

def f(x, t):
return 2*(1 + 0.5*t)*c**2

L = 2.5
c = 1.5
C = 0.75
Nx = 6  # Very coarse mesh for this exact test
dt = C*(L/Nx)/c
T = 18

def assert_no_error(u, x, t, n):
u_e = u_exact(x, t[n])
print(np.abs(u- u_e).min())
diff = np.abs(u - u_e).max()
tol = 1E-7
assert diff < tol

solver(I, V, f, c, L, dt, C, T,
user_action=assert_no_error)


When this function resides in the file wave1D_u0.py, one can run pytest to check that all test functions with names test_*() in this file work:

    Terminal> py.test -s -v wave1D_u0.py


## Verification: convergence rates¶

A more general method, but not so reliable as a verification method, is to compute the convergence rates and see if they coincide with theoretical estimates. Here we expect a rate of 2 according to the various results in the section Analysis of the difference equations . A general function for computing convergence rates can be written like this:

# %load -s convergence_rates, src-wave/wave1D/wave1D_u0.py
def convergence_rates(
u_exact,                 # Python function for exact solution
I, V, f, c, L,           # physical parameters
dt0, num_meshes, C, T):  # numerical parameters
"""
Half the time step and estimate convergence rates for
for num_meshes simulations.
"""
# First define an appropriate user action function
global error
error = 0  # error computed in the user action function

def compute_error(u, x, t, n):
global error  # must be global to be altered here
# (otherwise error is a local variable, different
# from error defined in the parent function)
if n == 0:
error = 0
else:
error = max(error, np.abs(u - u_exact(x, t[n])).max())

# Run finer and finer resolutions and compute true errors
E = []
h = []  # dt, devito_solver adjusts dx such that C=dt*c/dx
dt = dt0
for i in range(num_meshes):
solver(I, V, f, c, L, dt, C, T,
user_action=compute_error)
# error is computed in the final call to compute_error
E.append(error)
h.append(dt)
dt /= 2  # halve the time step for next simulation
print('E:')
print(E)
print('h:')
print(h)
# Convergence rates for two consecutive experiments
r = [np.log(E[i]/E[i-1])/np.log(h[i]/h[i-1])
for i in range(1,num_meshes) if h[i-1] != 0 and h[i] != h[i-1] and E[i-1] != 0]
return r


Using the analytical solution from the section Using an analytical solution of physical significance, we can call convergence_rates to see if we get a convergence rate that approaches 2 and use the final estimate of the rate in an assert statement such that this function becomes a proper test function:

# %load -s test_convrate_sincos, src-wave/wave1D/wave1D_u0.py
def test_convrate_sincos():
n = m = 2
L = 1.0
u_exact = lambda x, t: np.cos(m*np.pi/L*t)*np.sin(m*np.pi/L*x)

r = convergence_rates(
u_exact=u_exact,
I=lambda x: u_exact(x, 0),
V=lambda x: 0,
f=0,
c=1,
L=L,
dt0=0.1,
num_meshes=6,
C=0.9,
T=1)
print('rates sin(x)*cos(t) solution:')
print([round(r_,2) for r_ in r])
assert abs(r[-1] - 2) < 0.002


Doing py.test -s -v wave1D_u0.py will run also this test function and show the rates 2.05, 1.98, 2.00, 2.00, and 2.00 (to two decimals).

## Visualization: animating the solution¶

Now that we have verified the implementation it is time to do a real computation where we also display evolution of the waves on the screen. Since the solver function knows nothing about what type of visualizations we may want, it calls the callback function user_action(u, x, t, n). We must therefore write this function and find the proper statements for plotting the solution.

### Function for administering the simulation¶

The following viz function

1. defines a user_action callback function for plotting the solution at each time level,

2. calls the solver function, and

3. combines all the plots (in files) to video in different formats.

# %load -s viz, src-wave/wave1D/wave1D_u0.py
def viz(
I, V, f, c, L, dt, C, T,  # PDE parameters
umin, umax,               # Interval for u in plots
animate=True,             # Simulation with animation?
tool='matplotlib',        # 'matplotlib' or 'scitools'
devito_solver_function=solver,   # Function with numerical algorithm
):
"""Run devito_solver and visualize u at each time level."""

def plot_u_st(u, x, t, n):
"""user_action function for devito_solver."""
plt.plot(x, u, 'r-',
xlabel='x', ylabel='u',
axis=[0, L, umin, umax],
title='t=%f' % t[n], show=True)
# Let the initial condition stay on the screen for 2
# seconds, else insert a pause of 0.2 s between each plot
time.sleep(2) if t[n] == 0 else time.sleep(0.2)
plt.savefig('frame_%04d.png' % n)  # for movie making

class PlotMatplotlib:
def __call__(self, u, x, t, n):
"""user_action function for devito_solver."""
if n == 0:
plt.ion()
self.lines = plt.plot(x, u, 'r-')
plt.xlabel('x');  plt.ylabel('u')
plt.axis([0, L, umin, umax])
plt.legend(['t=%f' % t[n]], loc='lower left')
else:
self.lines[0].set_ydata(u)
plt.legend(['t=%f' % t[n]], loc='lower left')
plt.draw()
time.sleep(2) if t[n] == 0 else time.sleep(0.2)
plt.savefig('tmp_%04d.png' % n)  # for movie making

if tool == 'matplotlib':
import matplotlib.pyplot as plt
plot_u = PlotMatplotlib()
elif tool == 'scitools':
import scitools.std as plt  # scitools.easyviz interface
plot_u = plot_u_st
import time, glob, os

# Clean up old movie frames
for filename in glob.glob('tmp_*.png'):
os.remove(filename)

# Call devito_solver and do the simulaton
user_action = plot_u if animate else None
u, x, t, cpu = devito_solver_function(
I, V, f, c, L, dt, C, T, user_action)

# Make video files
fps = 4  # frames per second
codec2ext = dict(flv='flv', libx264='mp4', libvpx='webm',
libtheora='ogg')  # video formats
filespec = 'tmp_%04d.png'
movie_program = 'ffmpeg'
for codec in codec2ext:
ext = codec2ext[codec]
cmd = '%(movie_program)s -r %(fps)d -i %(filespec)s '\
'-vcodec %(codec)s movie.%(ext)s' % vars()
os.system(cmd)

if tool == 'scitools':
# Make an HTML play for showing the animation in a browser
plt.movie('tmp_*.png', encoder='html', fps=fps,
output_file='movie.html')
return cpu


### Dissection of the code¶

The viz function can either use SciTools or Matplotlib for visualizing the solution. The user_action function based on SciTools is called plot_u_st, while the user_action function based on Matplotlib is a bit more complicated as it is realized as a class and needs statements that differ from those for making static plots. SciTools can utilize both Matplotlib and Gnuplot (and many other plotting programs) for doing the graphics, but Gnuplot is a relevant choice for large $$N_x$$ or in two-dimensional problems as Gnuplot is significantly faster than Matplotlib for screen animations.

A function inside another function, like plot_u_st in the above code segment, has access to and remembers all the local variables in the surrounding code inside the viz function (!). This is known in computer science as a closure and is very convenient to program with. For example, the plt and time modules defined outside plot_u are accessible for plot_u_st when the function is called (as user_action) in the solver function. Some may think, however, that a class instead of a closure is a cleaner and easier-to-understand implementation of the user action function, see the section Building a general 1D wave equation solver.

The plot_u_st function just makes a standard SciTools plot command for plotting u as a function of x at time t[n]. To achieve a smooth animation, the plot command should take keyword arguments instead of being broken into separate calls to xlabel, ylabel, axis, time, and show. Several plot calls will automatically cause an animation on the screen. In addition, we want to save each frame in the animation to file. We then need a filename where the frame number is padded with zeros, here tmp_0000.png, tmp_0001.png, and so on. The proper printf construction is then tmp_%04d.png. The section Making animations contains more basic information on making animations.

The solver is called with an argument plot_u as user_function. If the user chooses to use SciTools, plot_u is the plot_u_st callback function, but for Matplotlib it is an instance of the class PlotMatplotlib. Also this class makes use of variables defined in the viz function: plt and time. With Matplotlib, one has to make the first plot the standard way, and then update the $$y$$ data in the plot at every time level. The update requires active use of the returned value from plt.plot in the first plot. This value would need to be stored in a local variable if we were to use a closure for the user_action function when doing the animation with Matplotlib. mathcal{I}_t is much easier to store the variable as a class attribute self.lines. Since the class is essentially a function, we implement the function as the special method __call__ such that the instance plot_u(u, x, t, n) can be called as a standard callback function from solver.

### Making movie files¶

From the frame_*.png files containing the frames in the animation we can make video files.

the section vib:ode1:anim presents basic information on how to use the ffmpeg program for producing video files in different modern formats: Flash, MP4, Webm, and Ogg.

We use the ffmpeg program to combine individual plot files to movies in modern formats: Flash, MP4, Webm, and Ogg. A typical ffmpeg command for creating a movie file in Ogg format with 4 frames per second built from a collection of plot files with names generated by frame_%04d.png, look like

    Terminal> ffmpeg -r 25 -i frame_%04d.png -c:v libtheora movie.ogg


The different formats require different video encoders (-c:v) to be installed: Flash applies flv, WebM applies libvpx, and MP4 applies libx264:

    Terminal> ffmpeg -r 25 -i frame_%04d.png -c:v flv movie.flv
Terminal> ffmpeg -r 25 -i frame_%04d.png -c:v libvpx movie.webm
Terminal> ffmpeg -r 25 -i frame_%04d.png -c:v libx264 movie.mp4


Players like vlc, mplayer, gxine, and totem can be used to play these movie files.

Note that padding the frame counter with zeros in the frame_*.png files, as specified by the %04d format, is essential so that the wildcard notation frame_*.png expands to the correct set of files.

The viz function creates an ffmpeg command with the proper arguments for each of the formats Flash, MP4, WebM, and Ogg. The task is greatly simplified by having a codec2ext dictionary for mapping video codec names to filename extensions.

As mentioned in the section vib:ode1:anim, only

Only

two formats are actually needed to ensure that all browsers can successfully play the video: MP4 and WebM.

Some animations having a large number of plot files may not be properly combined into a video using ffmpeg. A method that always works is to play the PNG files as an animation in a browser using JavaScript code in an HTML file. The SciTools package has a function movie (or a stand-alone command scitools movie) for creating such an HTML player. The plt.movie call in the viz function shows how the function is used. The file movie.html can be loaded into a browser and features a user interface where the speed of the animation can be controlled. Note that the movie in this case consists of the movie.html file and all the frame files tmp_*.png.

### Skipping frames for animation speed¶

Sometimes the time step is small and $$T$$ is large, leading to an inconveniently large number of plot files and a slow animation on the screen. The solution to such a problem is to decide on a total number of frames in the animation, num_frames, and plot the solution only for every skip_frame frames. For example, setting skip_frame=5 leads to plots of every 5 frames. The default value skip_frame=1 plots every frame. The total number of time levels (i.e., maximum possible number of frames) is the length of t, t.size (or len(t)), so if we want num_frames frames in the animation, we need to plot every t.size/num_frames frames:

def plot_u(t):
skip_frame = int(t.size/float(num_frames))
if n % skip_frame == 0 or n == t.size-1:
st.plot(x, u, 'r-', ...)


The initial condition (n=0) is included by n % skip_frame == 0, as well as every skip_frame-th frame. As n % skip_frame == 0 will very seldom be true for the very final frame, we must also check if n == t.size-1 to get the final frame included.

A simple choice of numbers may illustrate the formulas: say we have 801 frames in total (t.size) and we allow only 60 frames to be plotted. As n then runs from 801 to 0, we need to plot every 801/60 frame, which with integer division yields 13 as skip_frame. Using the mod function, n % skip_frame, this operation is zero every time n can be divided by 13 without a remainder. That is, the if test is true when n equals $$0, 13, 26, 39, ..., 780, 801$$. The associated code is included in the plot_u function, inside the viz function, in the file wave1D_u0.py.

## Running a case¶

The first demo of our 1D wave equation solver concerns vibrations of a string that is initially deformed to a triangular shape, like when picking a guitar string:

$\begin{split} $$I(x) = \left\lbrace \begin{array}{ll} ax/x_0, & x < x_0,\\ a(L-x)/(L-x_0), & \hbox{otherwise} \end{array}\right. \label{wave:pde1:guitar:I} \tag{1}$$ \end{split}$

We choose $$L=75$$ cm, $$x_0=0.8L$$, $$a=5$$ mm, and a time frequency $$\nu = 440$$ Hz. The relation between the wave speed $$c$$ and $$\nu$$ is $$c=\nu\lambda$$, where $$\lambda$$ is the wavelength, taken as $$2L$$ because the longest wave on the string forms frac{1}{2} a wavelength. There is no external force, so $$f=0$$ (meaning we can neglect gravity), and the string is at rest initially, implying $$V=0$$.

Regarding numerical parameters, we need to specify a $$\Delta t$$. Sometimes it is more natural to think of a spatial resolution instead of a time step. A natural semi-coarse spatial resolution in the present problem is $$N_x=50$$. We can then choose the associated $$\Delta t$$ (as required by the viz and solver functions) as the stability limit: $$\Delta t = L/(N_xc)$$. This is the $$\Delta t$$ to be specified, but notice that if $$C<1$$, the actual $$\Delta x$$ computed in solver gets larger than $$L/N_x$$: $$\Delta x = c\Delta t/C = L/(N_xC)$$. (The reason is that we fix $$\Delta t$$ and adjust $$\Delta x$$, so if $$C$$ gets smaller, the code implements this effect in terms of a larger $$\Delta x$$.)

A function for setting the physical and numerical parameters and calling viz in this application goes as follows:

# %load -s guitar, src-wave/wave1D/wave1D_u0.py
def guitar(C):
"""Triangular wave (pulled guitar string)."""
L = 0.75
x0 = 0.8*L
a = 0.005
freq = 440
wavelength = 2*L
c = freq*wavelength
omega = 2*pi*freq
num_periods = 1
T = 2*pi/omega*num_periods
# Choose dt the same as the stability limit for Nx=50
dt = L/50./c

def I(x):
return a*x/x0 if x < x0 else a/(L-x0)*(L-x)

umin = -1.2*a;  umax = -umin
cpu = viz(I, 0, 0, c, L, dt, C, T, umin, umax,
animate=True, tool='scitools')


The associated program has the name wave1D_u0.py. Run the program and watch the movie of the vibrating string. The string should ideally consist of straight segments, but these are somewhat wavy due to numerical approximation. Run the case with the wave1D_u0.py code and $$C=1$$ to see the exact solution.

## Working with a scaled PDE model¶

Depending on the model, it may be a substantial job to establish consistent and relevant physical parameter values for a case. The guitar string example illustrates the point. However, by scaling the mathematical problem we can often reduce the need to estimate physical parameters dramatically. The scaling technique consists of introducing new independent and dependent variables, with the aim that the absolute values of these lie in $$[0,1]$$. We introduce the dimensionless variables (details are found in Section 3.1.1 in [Langtangen_scaling])

$\bar x = \frac{x}{L},\quad \bar t = \frac{c}{L}t,\quad \bar u = \frac{u}{a}$

Here, $$L$$ is a typical length scale, e.g., the length of the domain, and $$a$$ is a typical size of $$u$$, e.g., determined from the initial condition: $$a=\max_x|I(x)|$$.

We get by the chain rule that

$\frac{\partial u}{\partial t} = \frac{\partial}{\partial\bar t}\left(a\bar u\right) \frac{d\bar t}{dt} = \frac{ac}{L}\frac{\partial\bar u}{\partial\bar t}$

Similarly,

$\frac{\partial u}{\partial x} = \frac{a}{L}\frac{\partial\bar u}{\partial\bar x}$

Inserting the dimensionless variables in the PDE gives, in case $$f=0$$,

$\frac{a^2c^2}{L^2}\frac{\partial^2\bar u}{\partial\bar t^2} = \frac{a^2c^2}{L^2}\frac{\partial^2\bar u}{\partial\bar x^2}$

Dropping the bars, we arrive at the scaled PDE

$$$\frac{\partial^2 u}{\partial t^2} = \frac{\partial^2 u}{\partial x^2}, \quad x\in (0,1),\ t\in (0,cT/L), \label{_auto1} \tag{2}$$$

which has no parameter $$c^2$$ anymore. The initial conditions are scaled as

$a\bar u(\bar x, 0) = I(L\bar x)$

and

$\frac{a}{L/c}\frac{\partial\bar u}{\partial\bar t}(\bar x,0) = V(L\bar x),$

resulting in

$\bar u(\bar x, 0) = \frac{I(L\bar x)}{\max_x |I(x)|},\quad \frac{\partial\bar u}{\partial\bar t}(\bar x,0) = \frac{L}{ac}V(L\bar x)$

In the common case $$V=0$$ we see that there are no physical parameters to be estimated in the PDE model!

If we have a program implemented for the physical wave equation with dimensions, we can obtain the dimensionless, scaled version by setting $$c=1$$. The initial condition of a guitar string, given in (1), gets its scaled form by choosing $$a=1$$, $$L=1$$, and $$x_0\in [0,1]$$. This means that we only need to decide on the $$x_0$$ value as a fraction of unity, because the scaled problem corresponds to setting all other parameters to unity. In the code we can just set a=c=L=1, x0=0.8, and there is no need to calculate with wavelengths and frequencies to estimate $$c$$!

The only non-trivial parameter to estimate in the scaled problem is the final end time of the simulation, or more precisely, how it relates to periods in periodic solutions in time, since we often want to express the end time as a certain number of periods. The period in the dimensionless problem is 2, so the end time can be set to the desired number of periods times 2.

Why the dimensionless period is 2 can be explained by the following reasoning. Suppose that $$u$$ behaves as $$\cos (\omega t)$$ in time in the original problem with dimensions. The corresponding period is then $$P=2\pi/\omega$$, but we need to estimate $$\omega$$. A typical solution of the wave equation is $$u(x,t)=A\cos(kx)\cos(\omega t)$$, where $$A$$ is an amplitude and $$k$$ is related to the wave length $$\lambda$$ in space: $$\lambda = 2\pi/k$$. Both $$\lambda$$ and $$A$$ will be given by the initial condition $$I(x)$$. Inserting this $$u(x,t)$$ in the PDE yields $$-\omega^2 = -c^2k^2$$, i.e., $$\omega = kc$$. The period is therefore $$P=2\pi/(kc)$$. If the boundary conditions are $$u(0,t)=u(L,t)$$, we need to have $$kL = n\pi$$ for integer $$n$$. The period becomes $$P=2L/nc$$. The longest period is $$P=2L/c$$. The dimensionless period $$\tilde P$$ is obtained by dividing $$P$$ by the time scale $$L/c$$, which results in $$\tilde P=2$$. Shorter waves in the initial condition will have a dimensionless shorter period $$\tilde P=2/n$$ ($$n>1$$).

# Exercises¶

## Exercise 1: Simulate a standing wave¶

The purpose of this exercise is to simulate standing waves on $$[0,L]$$ and illustrate the error in the simulation. Standing waves arise from an initial condition

$u(x,0)= A \sin\left(\frac{\pi}{L}mx\right),$

where $$m$$ is an integer and $$A$$ is a freely chosen amplitude. The corresponding exact solution can be computed and reads

$u(x,t) = A\sin\left(\frac{\pi}{L}mx\right) \cos\left(\frac{\pi}{L}mct\right)$

a) Explain that for a function $$\sin kx\cos \omega t$$ the wave length in space is $$\lambda = 2\pi /k$$ and the period in time is $$P=2\pi/\omega$$. Use these expressions to find the wave length in space and period in time of $$u$$ above.

Solution. Since the sin and cos functions depend on $$x$$ and $$t$$, respectively, the sin function will run through one period as $$x$$ increases by $$\frac{2\pi}{k}$$, while the cos function starts repeating as $$t$$ increases by $$\frac{2\pi}{\omega}$$.

The wave length in space becomes

$\lambda = \frac{2\pi}{\frac{\pi}{L}m} = \frac{2L}{m}$

The period in time becomes

$P = \frac{2\pi}{\frac{\pi}{L}mc} = \frac{2L}{mc}$

b) Import the solver function from wave1D_u0.py into a new file where the viz function is reimplemented such that it plots either the numerical and the exact solution, or the error.

Solution. See code below.

c) Make animations where you illustrate how the error $$e^n_i =u(x_i, t_n)- u^n_i$$ develops and increases in time. Also make animations of $$u$$ and $$u$$ simultaneously.

Hint 1. Quite long time simulations are needed in order to display significant discrepancies between the numerical and exact solution.

Hint 2. A possible set of parameters is $$L=12$$, $$m=9$$, $$c=2$$, $$A=1$$, $$N_x=80$$, $$C=0.8$$. The error mesh function $$e^n$$ can be simulated for 10 periods, while 20-30 periods are needed to show significant differences between the curves for the numerical and exact solution.

Solution. The code:

import sys
sys.path.insert(1, "src-wave/wave1D")

from wave1D_u0 import devito_solver
#from wave1D_u0v import devito_solver  # allows faster vectorized operations
import numpy as np

def viz(I, V, f, c, L, dt, C, T,
ymax,                      # y axis: [-ymax, ymax]
u_exact,                   # u_exact(x, t)
animate='u and u_exact',   # or 'error'
movie_filename='movie',
):
"""Run devito_solver and visualize u at each time level."""
import matplotlib as plt
import time, glob, os

class Plot:
def __init__(self, ymax, frame_name='frame'):
self.max_error = []   # hold max amplitude errors
self.max_error_t = [] # time points corresp. to max_error
self.frame_name = frame_name
self.ymax = ymax

def __call__(self, u, x, t, n):
"""user_action function for devito_solver."""
if animate == 'u and u_exact':
plt.plot(x, u, 'r-',
x, u_exact(x, t[n]), 'b--',
xlabel='x', ylabel='u',
axis=[0, L, -self.ymax, self.ymax],
title='t=%f' % t[n], show=True)
else:
error = u_exact(x, t[n]) - u
local_max_error = np.abs(error).max()
# self.max_error holds the increasing amplitude error
if self.max_error == [] or \
local_max_error > max(self.max_error):
self.max_error.append(local_max_error)
self.max_error_t.append(t[n])
# Use user's ymax until the error exceeds that value.
# This gives a growing max value of the yaxis (but
# never shrinking)
self.ymax = max(self.ymax, max(self.max_error))
plt.plot(x, error, 'r-',
xlabel='x', ylabel='error',
axis=[0, L, -self.ymax, self.ymax],
title='t=%f' % t[n], show=True)
plt.savefig('%s_%04d.png' % (self.frame_name, n))

# Clean up old movie frames
for filename in glob.glob('frame_*.png'):
os.remove(filename)

plot = Plot(ymax)
u, x, t, cpu = devito_solver(I, V, f, c, L, dt, C, T, plot)

# Make plot of max error versus time
plt.figure()
plt.plot(plot.max_error_t, plot.max_error)
plt.xlabel('time'); plt.ylabel('max abs(error)')
plt.savefig('error.png')
plt.savefig('error.pdf')

# Make .flv movie file
fps = 4  # Frames per second
codec2ext = dict(flv='flv') #, libx64='mp4',
#libvpx='webm', libtheora='ogg')

filespec = 'frame_%04d.png'
movie_program = 'ffmpeg'
for codec in codec2ext:
ext = codec2ext[codec]
cmd = '%(movie_program)s -r %(fps)d -i %(filespec)s '\
'-vcodec %(codec)s %(movie_filename)s.%(ext)s' % vars()
os.system(cmd)

def simulations():
from numpy import sin, cos, pi
L = 12  # length of domain
m = 9   # 2L/m: wave length or period in space (2*pi/k, k=pi*m/L)
c = 2   # wave velocity
A = 1   # amplitude
Nx = 80
C = 0.8
P = 2*pi/(pi*m*c/L)  # 1 period in time
#T = 10*P
# Choose dt the same as the stability limit for Nx=50
dt = L/50./c

def u_exact(x, t):
return A*sin(pi*m*x/L)*cos(pi*m*c*t/L)

def I(x):
return u_exact(x, 0)

V = 0
f = 0

viz(I, V, f, c, L, dt, C, 10.5*P,
0.1, u_exact,
animate='error',
movie_filename='error')

# Very long simulation to demonstrate different curves
viz(I, V, f, c, L, dt, C, 30*P,
1.2*A, u_exact,
animate='u and u_exact',
movie_filename='solution')

if __name__ == '__main__':
simulations()


Filename: wave_standing.

### Remarks¶

The important parameters for numerical quality are $$C$$ and $$k\Delta x$$, where $$C=c\Delta t/\Delta x$$ is the Courant number and $$k$$ is defined above ($$k\Delta x$$ is proportional to how many mesh points we have per wave length in space, see the Numerical dispersion relation section for explanation).

## Exercise 2: Add storage of solution in a user action function¶

Extend the plot_u function in the file wave1D_u0.py to also store the solutions u in a list. To this end, declare all_u as an empty list in the viz function, outside plot_u, and perform an append operation inside the plot_u function. Note that a function, like plot_u, inside another function, like viz, remembers all local variables in viz function, including all_u, even when plot_u is called (as user_action) in the solver function. Test both all_u.append(u) and all_u.append(u.copy()). Why does one of these constructions fail to store the solution correctly? Let the viz function return the all_u list converted to a two-dimensional numpy array.

Solution. We have to explicitly use a copy of u, i.e. as all_u.append(u.copy()), otherwise we just get a reference to u, which goes on changing with the computations.

#!/usr/bin/env python
"""
1D wave equation with u=0 at the boundary.
Simplest possible implementation.

The key function is::

u, x, t, cpu = solver(I, V, f, c, L, dt, C, T, user_action)

which solves the wave equation u_tt = c**2*u_xx on (0,L) with u=0
on x=0,L, for t in (0,T].  Initial conditions: u=I(x), u_t=V(x).

T is the stop time for the simulation.
dt is the desired time step.
C is the Courant number (=c*dt/dx), which specifies dx.
f(x,t) is a function for the source term (can be 0 or None).
I and V are functions of x.

user_action is a function of (u, x, t, n) where the calling
code can add visualization, error computations, etc.
"""

import numpy as np

def solver(I, V, f, c, L, dt, C, T, user_action=None):
"""Solve u_tt=c^2*u_xx + f on (0,L)x(0,T]."""
Nt = int(round(T/dt))
t = np.linspace(0, Nt*dt, Nt+1)   # Mesh points in time
dx = dt*c/float(C)
Nx = int(round(L/dx))
x = np.linspace(0, L, Nx+1)       # Mesh points in space
C2 = C**2                         # Help variable in the scheme
# Make sure dx and dt are compatible with x and t
dx = x[1] - x[0]
dt = t[1] - t[0]

if f is None or f == 0 :
f = lambda x, t: 0
if V is None or V == 0:
V = lambda x: 0

u   = np.zeros(Nx+1)   # Solution array at new time level
u_1 = np.zeros(Nx+1)   # Solution at 1 time level back
u_2 = np.zeros(Nx+1)   # Solution at 2 time levels back

import time;  t0 = time.clock()  # for measuring CPU time

# Load initial condition into u_1
for i in range(0,Nx+1):
u_1[i] = I(x[i])

if user_action is not None:
user_action(u_1, x, t, 0)

# Special formula for first time step
n = 0
for i in range(1, Nx):
u[i] = u_1[i] + dt*V(x[i]) + \
0.5*C2*(u_1[i-1] - 2*u_1[i] + u_1[i+1]) + \
0.5*dt**2*f(x[i], t[n])
u[0] = 0;  u[Nx] = 0

if user_action is not None:
user_action(u, x, t, 1)

# Switch variables before next step
u_2[:] = u_1;  u_1[:] = u

for n in range(1, Nt):
# Update all inner points at time t[n+1]
for i in range(1, Nx):
u[i] = - u_2[i] + 2*u_1[i] + \
C2*(u_1[i-1] - 2*u_1[i] + u_1[i+1]) + \
dt**2*f(x[i], t[n])

# Insert boundary conditions
u[0] = 0;  u[Nx] = 0
if user_action is not None:
if user_action(u, x, t, n+1):
break

# Switch variables before next step
u_2[:] = u_1;  u_1[:] = u

cpu_time = t0 - time.clock()
return u, x, t, cpu_time

"""Check that u(x,t)=x(L-x)(1+t/2) is exactly reproduced."""

def u_exact(x, t):
return x*(L-x)*(1 + 0.5*t)

def I(x):
return u_exact(x, 0)

def V(x):
return 0.5*u_exact(x, 0)

def f(x, t):
return 2*(1 + 0.5*t)*c**2

L = 2.5
c = 1.5
C = 0.75
Nx = 6  # Very coarse mesh for this exact test
dt = C*(L/Nx)/c
T = 18

def assert_no_error(u, x, t, n):
u_e = u_exact(x, t[n])
diff = np.abs(u - u_e).max()
tol = 1E-13
assert diff < tol

solver(I, V, f, c, L, dt, C, T,
user_action=assert_no_error)

def test_constant():
"""Check that u(x,t)=Q=0 is exactly reproduced."""
u_const = 0  # Require 0 because of the boundary conditions
C = 0.75
dt = C # Very coarse mesh
u, x, t, cpu = solver(I=lambda x:
0, V=0, f=0, c=1.5, L=2.5,
dt=dt, C=C, T=18)
tol = 1E-14
assert np.abs(u - u_const).max() < tol

def viz(
I, V, f, c, L, dt, C, T,  # PDE parameters
umin, umax,               # Interval for u in plots
animate=True,             # Simulation with animation?
tool='matplotlib',        # 'matplotlib' or 'scitools'
solver_function=solver,   # Function with numerical algorithm
):
"""Run solver, store and visualize u at each time level."""

all_u = []
def plot_u_st(u, x, t, n):
"""user_action function for solver."""
plt.plot(x, u, 'r-',
xlabel='x', ylabel='u',
axis=[0, L, umin, umax],
title='t=%f' % t[n], show=True)
# Let the initial condition stay on the screen for 2
# seconds, else insert a pause of 0.2 s between each plot
time.sleep(2) if t[n] == 0 else time.sleep(0.2)
#plt.savefig('frame_%04d.png' % n)  # for movie making
plt.savefig('tmp_%04d.png' % n)  # for movie making
all_u.append(u.copy())

class PlotMatplotlib:
def __call__(self, u, x, t, n):
"""user_action function for solver."""
if n == 0:
plt.ion()
self.lines = plt.plot(x, u, 'r-')
plt.xlabel('x');  plt.ylabel('u')
plt.axis([0, L, umin, umax])
plt.legend(['t=%f' % t[n]], loc='lower left')
else:
self.lines[0].set_ydata(u)
plt.legend(['t=%f' % t[n]], loc='lower left')
plt.draw()
time.sleep(2) if t[n] == 0 else time.sleep(0.2)
plt.savefig('tmp_%04d.png' % n)  # for movie making

if tool == 'matplotlib':
import matplotlib.pyplot as plt
plot_u = PlotMatplotlib()
elif tool == 'scitools':
import scitools.std as plt  # scitools.easyviz interface
plot_u = plot_u_st
import time, glob, os

# Clean up old movie frames
for filename in glob.glob('tmp_*.png'):
os.remove(filename)

# Call solver and do the simulaton
user_action = plot_u if animate else None
u, x, t, cpu = solver_function(
I, V, f, c, L, dt, C, T, user_action)

# Make video files
fps = 4  # frames per second
codec2ext = dict(flv='flv', libx264='mp4', libvpx='webm',
libtheora='ogg')  # video formats
filespec = 'tmp_%04d.png'
movie_program = 'ffmpeg'
for codec in codec2ext:
ext = codec2ext[codec]
cmd = '%(movie_program)s -r %(fps)d -i %(filespec)s '\
'-vcodec %(codec)s movie.%(ext)s' % vars()
os.system(cmd)

if tool == 'scitools':
# Make an HTML play for showing the animation in a browser
plt.movie('tmp_*.png', encoder='html', fps=fps,
output_file='movie.html')
return cpu, np.array(all_u)

def guitar(C):
"""Triangular wave (pulled guitar string)."""
L = 0.75
x0 = 0.8*L
a = 0.005
freq = 440
wavelength = 2*L
c = freq*wavelength
from math import pi
w = 2*pi*freq
num_periods = 1
T = 2*pi/w*num_periods
# Choose dt the same as the stability limit for Nx=50
dt = L/50./c

def I(x):
return a*x/x0 if x < x0 else a/(L-x0)*(L-x)

umin = -1.2*a;  umax = -umin
cpu, all_u = viz(I, 0, 0, c, L, dt, C, T, umin, umax,
animate=True, tool='scitools')
# checking
#for e in all_u:
#    print e[int(len(all_u[1])/2)]

if __name__ == '__main__':
import sys
try:
C = float(sys.argv[1])
print('C=%g' % C)
except IndexError:
C = 0.85
print('Courant number: %.2f' % C)
guitar(C)


Filename: wave1D_u0_s_store.

## Exercise 3: Use a class for the user action function¶

Redo Exercise 2: Add storage of solution in a user action function using a class for the user action function. Let the all_u list be an attribute in this class and implement the user action function as a method (the special method __call__ is a natural choice). The class versions avoid that the user action function depends on parameters defined outside the function (such as all_u in Exercise 2: Add storage of solution in a user action function).

Solution. Using a class, we get

#!/usr/bin/env python
"""
1D wave equation with u=0 at the boundary.
Simplest possible implementation.

The key function is::

u, x, t, cpu = solver(I, V, f, c, L, dt, C, T, user_action)

which solves the wave equation u_tt = c**2*u_xx on (0,L) with u=0
on x=0,L, for t in (0,T].  Initial conditions: u=I(x), u_t=V(x).

T is the stop time for the simulation.
dt is the desired time step.
C is the Courant number (=c*dt/dx), which specifies dx.
f(x,t) is a function for the source term (can be 0 or None).
I and V are functions of x.

user_action is a function of (u, x, t, n) where the calling
code can add visualization, error computations, etc.
"""

import numpy as np

def solver(I, V, f, c, L, dt, C, T, user_action=None):
"""Solve u_tt=c^2*u_xx + f on (0,L)x(0,T]."""
Nt = int(round(T/dt))
t = np.linspace(0, Nt*dt, Nt+1)   # Mesh points in time
dx = dt*c/float(C)
Nx = int(round(L/dx))
x = np.linspace(0, L, Nx+1)       # Mesh points in space
C2 = C**2                         # Help variable in the scheme
# Make sure dx and dt are compatible with x and t
dx = x[1] - x[0]
dt = t[1] - t[0]

if f is None or f == 0 :
f = lambda x, t: 0
if V is None or V == 0:
V = lambda x: 0

u   = np.zeros(Nx+1)   # Solution array at new time level
u_1 = np.zeros(Nx+1)   # Solution at 1 time level back
u_2 = np.zeros(Nx+1)   # Solution at 2 time levels back

import time;  t0 = time.clock()  # for measuring CPU time

# Load initial condition into u_1
for i in range(0,Nx+1):
u_1[i] = I(x[i])

if user_action is not None:
user_action(u_1, x, t, 0)

# Special formula for first time step
n = 0
for i in range(1, Nx):
u[i] = u_1[i] + dt*V(x[i]) + \
0.5*C2*(u_1[i-1] - 2*u_1[i] + u_1[i+1]) + \
0.5*dt**2*f(x[i], t[n])
u[0] = 0;  u[Nx] = 0

if user_action is not None:
user_action(u, x, t, 1)

# Switch variables before next step
u_2[:] = u_1;  u_1[:] = u

for n in range(1, Nt):
# Update all inner points at time t[n+1]
for i in range(1, Nx):
u[i] = - u_2[i] + 2*u_1[i] + \
C2*(u_1[i-1] - 2*u_1[i] + u_1[i+1]) + \
dt**2*f(x[i], t[n])

# Insert boundary conditions
u[0] = 0;  u[Nx] = 0
if user_action is not None:
if user_action(u, x, t, n+1):
break

# Switch variables before next step
u_2[:] = u_1;  u_1[:] = u

cpu_time = t0 - time.clock()
return u, x, t, cpu_time

"""Check that u(x,t)=x(L-x)(1+t/2) is exactly reproduced."""

def u_exact(x, t):
return x*(L-x)*(1 + 0.5*t)

def I(x):
return u_exact(x, 0)

def V(x):
return 0.5*u_exact(x, 0)

def f(x, t):
return 2*(1 + 0.5*t)*c**2

L = 2.5
c = 1.5
C = 0.75
Nx = 6  # Very coarse mesh for this exact test
dt = C*(L/Nx)/c
T = 18

def assert_no_error(u, x, t, n):
u_e = u_exact(x, t[n])
diff = np.abs(u - u_e).max()
tol = 1E-13
assert diff < tol

solver(I, V, f, c, L, dt, C, T,
user_action=assert_no_error)

def test_constant():
"""Check that u(x,t)=Q=0 is exactly reproduced."""
u_const = 0  # Require 0 because of the boundary conditions
C = 0.75
dt = C # Very coarse mesh
u, x, t, cpu = solver(I=lambda x:
0, V=0, f=0, c=1.5, L=2.5,
dt=dt, C=C, T=18)
tol = 1E-14
assert np.abs(u - u_const).max() < tol

def viz(
I, V, f, c, L, dt, C, T,  # PDE parameters
umin, umax,               # Interval for u in plots
animate=True,             # Simulation with animation?
tool='matplotlib',        # 'matplotlib' or 'scitools'
solver_function=solver,   # Function with numerical algorithm
):
"""Run solver, store and visualize u at each time level."""

class PlotUst:
def __init__(self):
self.all_u = []
def __call__(self, u, x, t, n):
"""user_action function for solver."""
plt.plot(x, u, 'r-',
xlabel='x', ylabel='u',
axis=[0, L, umin, umax],
title='t=%f' % t[n], show=True)
# Let the initial condition stay on the screen for 2
# seconds, else insert a pause of 0.2 s between each plot
time.sleep(2) if t[n] == 0 else time.sleep(0.2)
plt.savefig('tmp_%04d.png' % n)  # for movie making
self.all_u.append(u.copy())

class PlotMatplotlib:
def __call__(self, u, x, t, n):
"""user_action function for solver."""
if n == 0:
plt.ion()
self.lines = plt.plot(x, u, 'r-')
plt.xlabel('x');  plt.ylabel('u')
plt.axis([0, L, umin, umax])
plt.legend(['t=%f' % t[n]], loc='lower left')
else:
self.lines[0].set_ydata(u)
plt.legend(['t=%f' % t[n]], loc='lower left')
plt.draw()
time.sleep(2) if t[n] == 0 else time.sleep(0.2)
plt.savefig('tmp_%04d.png' % n)  # for movie making

if tool == 'matplotlib':
import matplotlib.pyplot as plt
plot_u = PlotMatplotlib()
elif tool == 'scitools':
import scitools.std as plt  # scitools.easyviz interface
plot_u = PlotUst()
import time, glob, os

# Clean up old movie frames
for filename in glob.glob('tmp_*.png'):
os.remove(filename)

# Call solver and do the simulaton
user_action = plot_u if animate else None
u, x, t, cpu = solver_function(
I, V, f, c, L, dt, C, T, user_action)

# Make video files
fps = 4  # frames per second
codec2ext = dict(flv='flv', libx264='mp4', libvpx='webm',
libtheora='ogg')  # video formats
filespec = 'tmp_%04d.png'
movie_program = 'ffmpeg'
for codec in codec2ext:
ext = codec2ext[codec]
cmd = '%(movie_program)s -r %(fps)d -i %(filespec)s '\
'-vcodec %(codec)s movie.%(ext)s' % vars()
os.system(cmd)

if tool == 'scitools':
# Make an HTML play for showing the animation in a browser
plt.movie('tmp_*.png', encoder='html', fps=fps,
output_file='movie.html')
return cpu, np.array(plot_u.all_u)

def guitar(C):
"""Triangular wave (pulled guitar string)."""
L = 0.75
x0 = 0.8*L
a = 0.005
freq = 440
wavelength = 2*L
c = freq*wavelength
from math import pi
w = 2*pi*freq
num_periods = 1
T = 2*pi/w*num_periods
# Choose dt the same as the stability limit for Nx=50
dt = L/50./c

def I(x):
return a*x/x0 if x < x0 else a/(L-x0)*(L-x)

umin = -1.2*a;  umax = -umin
cpu, all_u = viz(I, 0, 0, c, L, dt, C, T, umin, umax,
animate=True, tool='scitools')
# checking
#for e in all_u:
#    print e[int(len(all_u[1])/2)]

if __name__ == '__main__':
import sys
try:
C = float(sys.argv[1])
print('C=%g' % C)
except IndexError:
C = 0.85
print('Courant number: %.2f' % C)
guitar(C)


Filename: wave1D_u0_s2c.

## Exercise 4: Compare several Courant numbers in one movie¶

The goal of this exercise is to make movies where several curves, corresponding to different Courant numbers, are visualized. Write a program that resembles wave1D_u0_s2c.py in Exercise 3: Use a class for the user action function, but with a viz function that can take a list of C values as argument and create a movie with solutions corresponding to the given C values. The plot_u function must be changed to store the solution in an array (see Exercise 2: Add storage of solution in a user action function or Exercise 3: Use a class for the user action function for details), solver must be computed for each value of the Courant number, and finally one must run through each time step and plot all the spatial solution curves in one figure and store it in a file.

The challenge in such a visualization is to ensure that the curves in one plot correspond to the same time point. The easiest remedy is to keep the time resolution constant and change the space resolution to change the Courant number. Note that each spatial grid is needed for the final plotting, so it is an option to store those grids too.

Solution. Modifying the code to store all solutions for each $$C$$ value and also each corresponding spatial grid (needed for final plotting), we get

#!/usr/bin/env python
"""
1D wave equation with u=0 at the boundary.
Simplest possible implementation.

The key function is::

u, x, t, cpu = solver(I, V, f, c, L, dt, C, T, user_action)

which solves the wave equation u_tt = c**2*u_xx on (0,L) with u=0
on x=0,L, for t in (0,T].  Initial conditions: u=I(x), u_t=V(x).

T is the stop time for the simulation.
dt is the desired time step.
C is the Courant number (=c*dt/dx), which specifies dx.
f(x,t) is a function for the source term (can be 0 or None).
I and V are functions of x.

user_action is a function of (u, x, t, n) where the calling
code can add visualization, error computations, etc.
"""

import numpy as np

def solver(I, V, f, c, L, dt, C, T, user_action=None):
"""Solve u_tt=c^2*u_xx + f on (0,L)x(0,T]."""
Nt = int(round(T/dt))
t = np.linspace(0, Nt*dt, Nt+1)   # Mesh points in time
dx = c*dt/C
Nx = int(round(L/dx))
x = np.linspace(0, L, Nx+1)     # Mesh points in space
C2 = C**2                       # Help variable in the scheme
# Recompute to make sure dx and dt are compatible with x and t
dx = x[1] - x[0]
dt = t[1] - t[0]

if f is None or f == 0 :
f = lambda x, t: 0
if V is None or V == 0:
V = lambda x: 0

u   = np.zeros(Nx+1)   # Solution array at new time level
u_1 = np.zeros(Nx+1)   # Solution at 1 time level back
u_2 = np.zeros(Nx+1)   # Solution at 2 time levels back

import time;  t0 = time.clock()  # for measuring CPU time

# Load initial condition into u_1
for i in range(0,Nx+1):
u_1[i] = I(x[i])

if user_action is not None:
user_action(u_1, x, t, 0)

# Special formula for first time step
n = 0
for i in range(1, Nx):
u[i] = u_1[i] + dt*V(x[i]) + \
0.5*C2*(u_1[i-1] - 2*u_1[i] + u_1[i+1]) + \
0.5*dt**2*f(x[i], t[n])
u[0] = 0;  u[Nx] = 0

if user_action is not None:
user_action(u, x, t, 1)

# Switch variables before next step
u_2[:] = u_1;  u_1[:] = u

for n in range(1, Nt):
# Update all inner points at time t[n+1]
for i in range(1, Nx):
u[i] = - u_2[i] + 2*u_1[i] + \
C2*(u_1[i-1] - 2*u_1[i] + u_1[i+1]) + \
dt**2*f(x[i], t[n])

# Insert boundary conditions
u[0] = 0;  u[Nx] = 0
if user_action is not None:
if user_action(u, x, t, n+1):
break

# Switch variables before next step
u_2[:] = u_1;  u_1[:] = u

cpu_time = time.clock() - t0
return u, x, t, cpu_time

def viz(
I, V, f, c, L, dt, C, T,  # PDE parameters
umin, umax,               # Interval for u in plots
animate=True,             # Simulation with animation?
tool='matplotlib',        # 'matplotlib' or 'scitools'
solver_function=solver,   # Function with numerical algorithm
):
"""
Run solver, store and viz. u at each time level with all C values.
"""

class PlotUst:
def __init__(self):
self.all_u = []
self.all_u_for_all_C = []
self.x_mesh = []   # need each mesh for final plots
def __call__(self, u, x, t, n):
"""user_action function for solver."""
self.all_u.append(u.copy())
if t[n] == T: # i.e., whole time interv. done for this C
self.x_mesh.append(x)
self.all_u_for_all_C.append(self.all_u)
self.all_u = []     # reset to empty list

if len(self.all_u_for_all_C) == len(C):  # all C done
print('Finished all C. Proceed with plots...')
# note: n will here be the last index in t[n]
for n_ in range(0, n+1):      # for each tn
plt.plot(self.x_mesh[0],
self.all_u_for_all_C[0][n_],
axis=[0, L, umin, umax],
title='Solutions for all \
C at t=%f' % t[n_])
plt.hold('on')

for j in range(1, len(C)):
# build plot at this tn with each
# sol. from the different C values
plt.plot(self.x_mesh[j],
self.all_u_for_all_C[j][n_],
axis=[0, L, umin, umax])
plt.xlabel('x'); plt.ylabel('u')
plt.hold('off')
plt.show()
# Let the init. cond. stay on the screen for
# 2 sec, else insert a pause of 0.2 s
# between each plot
time.sleep(2) if t[n_] == 0 else \
time.sleep(0.2)
plt.savefig('tmp_%04d.png' % n_)  # for movie

class PlotMatplotlib:
def __init__(self):
self.all_u = []
self.all_u_for_all_C = []
def __call__(self, u, x, t, n):
"""user_action function for solver."""
self.all_u.append(u.copy())
if t[n] == T: # i.e., whole time interv. done for this C
self.all_u_for_all_C.append(self.all_u)
self.all_u = []     # reset to empty list

if len(self.all_u_for_all_C) == len(C):  # all C done
print('Finished all C. Proceed with plots...')
plt.ion()
# note: n will here be the last index in t[n]
for n_ in range(0, n+1):      # for each tn
plt.plot(x, self.all_u_for_all_C[0][n_])
plt.axis([0, L, umin, umax])
plt.hold(True)
for j in range(1, len(C)):
# build plot at this tn with each
# sol. from the different C values
plt.plot(x, self.all_u_for_all_C[j][n_])
plt.axis([0, L, umin, umax])
plt.xlabel('x'); plt.ylabel('u')
plt.title('Solutions for all \
C at t=%f' % t[n_])
plt.hold(False)
plt.draw()
# Let the init. cond. stay on the screen for
# 2 sec, else insert a pause of 0.2 s
# between each plot
time.sleep(2) if t[n_] == 0 else \
time.sleep(0.2)
plt.savefig('tmp_%04d.png' % n_)  # for movie

if tool == 'matplotlib':
import matplotlib.pyplot as plt
plot_u = PlotMatplotlib()
elif tool == 'scitools':
import scitools.std as plt  # scitools.easyviz interface
plot_u = PlotUst()
import time, glob, os

# Clean up old movie frames
for filename in glob.glob('tmp_*.png'):
os.remove(filename)

# Call solver and do the simulaton
user_action = plot_u if animate else None
for C_value in C:
print('C_value --------------------------------- ')
print(C_value)
u, x, t, cpu = solver_function(
I, V, f, c, L, dt, C_value, T, user_action)

# Make video files
fps = 4  # frames per second
codec2ext = dict(flv='flv', libx264='mp4', libvpx='webm',
libtheora='ogg')  # video formats
filespec = 'tmp_%04d.png'
movie_program = 'ffmpeg'
for codec in codec2ext:
ext = codec2ext[codec]
cmd = '%(movie_program)s -r %(fps)d -i %(filespec)s '\
'-vcodec %(codec)s movie.%(ext)s' % vars()
os.system(cmd)

if tool == 'scitools':
# Make an HTML play for showing the animation in a browser
plt.movie('tmp_*.png', encoder='html', fps=fps,
output_file='movie.html')
return cpu

def guitar(C):
"""Triangular wave (pulled guitar string)."""
L = 0.75
x0 = 0.8*L
a = 0.005
freq = 440
wavelength = 2*L
c = freq*wavelength
from math import pi
w = 2*pi*freq
num_periods = 1
T = 2*pi/w*num_periods
# Choose dt the same as the stability limit for Nx=50
dt = L/50./c
dx = dt*c/float(C)
# Now dt is considered fixed and a list of C
# values is made by reducing increasing the dx value
# in steps of 10%.
all_C = [C]
all_C.append(c*dt/(1.1*dx))
all_C.append(c*dt/(1.2*dx))

def I(x):
return a*x/x0 if x < x0 else a/(L-x0)*(L-x)

umin = -1.2*a;  umax = -umin
cpu = viz(I, 0, 0, c, L, dt, all_C, T, umin, umax,
animate=True, tool='scitools')
#cpu = viz(I, 0, 0, c, L, dt, all_C, T, umin, umax,
#             animate=True, tool='matplotlib')
print('cpu = ')
print(cpu)

if __name__ == '__main__':
import sys
try:
C = float(sys.argv[1])
print('C=%g' % C)
except IndexError:
C = 0.85
print('Courant number: %.2f' % C)
# The list of C values will be generated from this C value
guitar(C)


Filename: wave_numerics_comparison.

## Exercise 5: Implementing the solver function as a generator¶

The callback function user_action(u, x, t, n) is called from the solver function (in, e.g., wave1D_u0.py) at every time level and lets the user work perform desired actions with the solution, like plotting it on the screen. We have implemented the callback function in the typical way it would have been done in C and Fortran. Specifically, the code looks like

if user_action is not None:
if user_action(u, x, t, n):
break


Many Python programmers, however, may claim that solver is an iterative process, and that iterative processes with callbacks to the user code is more elegantly implemented as generators. The rest of the text has little meaning unless you are familiar with Python generators and the yield statement.

Instead of calling user_action, the solver function issues a yield statement, which is a kind of return statement:

yield u, x, t, n


The program control is directed back to the calling code:

for u, x, t, n in solver(...):
# Do something with u at t[n]


When the block is done, solver continues with the statement after yield. Note that the functionality of terminating the solution process if user_action returns a True value is not possible to implement in the generator case.

Implement the solver function as a generator, and plot the solution at each time step. Filename: wave1D_u0_generator.

## Project 6: Calculus with 1D mesh functions¶

This project explores integration and differentiation of mesh functions, both with scalar and vectorized implementations. We are given a mesh function $$f_i$$ on a spatial one-dimensional mesh $$x_i=i\Delta x$$, $$i=0,\ldots,N_x$$, over the interval $$[a,b]$$.

a) Define the discrete derivative of $$f_i$$ by using centered differences at internal mesh points and one-sided differences at the end points. Implement a scalar version of the computation in a Python function and write an associated unit test for the linear case $$f(x)=4x-2.5$$ where the discrete derivative should be exact.

Solution. See code below.

b) Vectorize the implementation of the discrete derivative. Extend the unit test to check the validity of the implementation.

Solution. See code below.

c) To compute the discrete integral $$F_i$$ of $$f_i$$, we assume that the mesh function $$f_i$$ varies linearly between the mesh points. Let $$f(x)$$ be such a linear interpolant of $$f_i$$. We then have

$F_i = \int_{x_0}^{x_i} f(x) dx$

The exact integral of a piecewise linear function $$f(x)$$ is given by the Trapezoidal rule. Show that if $$F_{i}$$ is already computed, we can find $$F_{i+1}$$ from

$F_{i+1} = F_i + \frac{1}{2}(f_i + f_{i+1})\Delta x$

Make a function for the scalar implementation of the discrete integral as a mesh function. That is, the function should return $$F_i$$ for $$i=0,\ldots,N_x$$. For a unit test one can use the fact that the above defined discrete integral of a linear function (say $$f(x)=4x-2.5$$) is exact.

Solution. We know that the difference $$F_{i+1} - F_i$$ must amount to the area of a trapezoid, which is exactly what $$\frac{1}{2}(f_i + f_{i+1})\Delta x$$ is. To show the relation above, we may start with the Trapezoidal rule:

$F_{i+1} = \Delta x \left[\frac{1}{2}f(x_0) + \sum_{j=1}^{n-1}f(x_j) + \frac{1}{2}f(x_n) \right] \thinspace . \nonumber$

Since $$n = i+1$$, and since the final term in the sum may be separated out from the sum and split in two, this may be written as

$F_{i+1} = \Delta x \left[\frac{1}{2}f(x_0) + \sum_{j=1}^{i-1}f(x_j) + \frac{1}{2}f(x_i) + \frac{1}{2}f(x_i) + \frac{1}{2}f(x_{i+1}) \right] \thinspace . \nonumber$

This may further be written as

$F_{i+1} = \Delta x \left[\frac{1}{2}f(x_0) + \sum_{j=1}^{i-1}f(x_j) + \frac{1}{2}f(x_i)\right] + \Delta x \left[\frac{1}{2}f(x_i) + \frac{1}{2}f(x_{i+1}) \right] \thinspace . \nonumber$

Finally, this gives

$F_{i+1} = F_i + \frac{1}{2}(f_i + f_{i+1})\Delta x$

See code below for implementation.

d) Vectorize the implementation of the discrete integral. Extend the unit test to check the validity of the implementation.

Hint. Interpret the recursive formula for $$F_{i+1}$$ as a sum. Make an array with each element of the sum and use the “cumsum” (numpy.cumsum) operation to compute the accumulative sum: numpy.cumsum([1,3,5]) is [1,4,9].

Solution. See code below.

e) Create a class MeshCalculus that can integrate and differentiate mesh functions. The class can just define some methods that call the previously implemented Python functions. Here is an example on the usage:

import numpy as np
calc = MeshCalculus(vectorized=True)
x = np.linspace(0, 1, 11)        # mesh
f = np.exp(x)                    # mesh function
df = calc.differentiate(f, x)    # discrete derivative
F = calc.integrate(f, x)         # discrete anti-derivative


Solution. See code below.

Solution. The final version of the code reads

# -*- coding: utf-8 -*-
"""
Calculus with a 1D mesh function.
"""
import numpy as np

class MeshCalculus:
def __init__(self, vectorized=True):
self.vectorized = vectorized

def differentiate(self, f, x):
'''
Computes the derivative of f by centered differences, but
forw and back difference at the start and end, respectively.
'''
dx = x[1] - x[0]
Nx = len(x) - 1     # number of spatial steps
num_dfdx = np.zeros(Nx+1)
# Compute approximate derivatives at end-points first
num_dfdx[0] = (f(x[1]) - f(x[0]))/dx          # FD approx.
num_dfdx[Nx] = (f(x[Nx]) - f(x[Nx-1]))/dx     # BD approx.
# proceed with approximate derivatives for inner mesh points
if self.vectorized:
num_dfdx[1:-1] = (f(x[2:]) - f(x[:-2]))/(2*dx)
else:   # scalar version
for i in range(1, Nx):
num_dfdx[i] = (f(x[i+1]) - f(x[i-1]))/(2*dx)
return num_dfdx

def integrate(self, f, x):
'''
Computes the integral of f(x) over the interval
covered by x.
'''
dx = x[1] - x[0]
F = np.zeros(len(x))
F[0] = 0    # starting value for iterative scheme
if self.vectorized:
all_trapezoids = np.zeros(len(x)-1)
all_trapezoids[:] = 0.5*(f(x[:-1]) + f(x[1:]))*dx
F[1:] = np.cumsum(all_trapezoids)
else:   # scalar version
for i in range(0, len(x)-1):
F[i+1] = F[i] + 0.5*(f(x[i]) + f(x[i+1]))*dx
return F

def test_differentiate():
def f(x):
return 4*x - 2.5
def dfdx(x):
derivatives = np.zeros(len(x))
derivatives[:] = 4
return derivatives

a = 0; b = 1; Nx = 10
x = np.linspace(a, b, Nx+1)
exact_dfdx = dfdx(x)        # compute exact derivatives
# test vectorized version
calc_v = MeshCalculus(vectorized=True)
num_dfdx  = calc_v.differentiate(f, x)
print np.abs(num_dfdx - exact_dfdx)
diff = np.abs(num_dfdx - exact_dfdx).max()
tol = 1E-14
assert diff < tol
# test scalar version
calc = MeshCalculus(vectorized=False)
num_dfdx  = calc.differentiate(f, x)
print np.abs(num_dfdx - exact_dfdx)
diff = np.abs(num_dfdx - exact_dfdx).max()
assert diff < tol

def test_integrate():
def f(x):
return 4*x - 2.5
a = 0; b = 1; Nx = 10
#    a = 2.5/4; b = 10; Nx = 2
x = np.linspace(a, b, Nx+1)
# The exact integral amounts to the total area of two triangles
I_exact = 0.5*abs(2.5/4 - a)*f(a) + 0.5*abs(b - 2.5/4)*f(b)
# test vectorized version
calc_v = MeshCalculus(vectorized=True)
F = calc_v.integrate(f, x)
print F, I_exact
diff = np.abs(F[-1] - I_exact)
print diff
tol = 1E-14
assert diff < tol
# test scalar version
calc = MeshCalculus(vectorized=False)
F = calc.integrate(f, x)
print F, I_exact
diff = np.abs(F[-1] - I_exact)
print diff
assert diff < tol

if __name__ == '__main__':
test_differentiate()
test_integrate()


Filename: mesh_calculus_1D.