COMPUTER ALGEBRA WITH MATHEMATICA - DOC - DOC by X1OoHG9

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```									  COMPUTER ALGEBRA WITH MATHEMATICA

The sessions with Mathematica are intended to be self-contained, with all the instructions
you need available on the computer screen and in the lecture/demonstration periods. These
notes are just meant to help to get you started, and to remind you of a number of key points.

GETTING STARTED
Log on to WTS, locate and double-click on the Mathematica icon.

The MATHEMATICA examples
The files which you will be using should be copied from the World-Wide Web. Point your
and follow the links to the Mathematica page. Make copies of the Mathematica files in your
own workspace. The first collection of files you should download consists of a set of
familiarisation exercises:

uclintro.nb      An introduction to Mathematica and what it can do
graph.nb         Graphics and the visualization of functions
diffeq.nb        Ordinary differential equations
numer.nb         Numerical analysis

You should run through all of the above, to see what sort of things Mathematica can do and,
more importantly, to get used to the command syntax. There are some simple exercises
embedded in these files, which you should tackle with as much help as you need from the
demonstrators. Your log-book (see below) should contain records of these exercises.

In addition, there are two short tests, two short programming exercises, and a longer
programming problem to be completed as part of the assessment of the course. The relevant
files are:
test1.nb Deadlines: Wednesday 16th October/Wednesday 20th November;
test2.nb Deadlines: Wednesday 23rd October/Wednesday 27th November.
I will tell you when these files are available.

image.nb           A simple image analysis exercise
plotfield.nb More complex plots and pictures.
final.nb           The Schrodinger equation for a finite potential well
Deadlines: Friday 8th November/Friday 13th December.
The deadlines for the image analysis, complex plot, and final exercise are also the deadlines
for handing in laboratory notebooks.

You might also be interested to see a couple of other examples of the use of Mathematica,
but note that these do not form part of the assessed course.

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animation.nb A simple example of an animated graph
datafit.nb    How to fit experimental data using Mathematica
Huygens.nb    Huygens’s principle and beyond: diffraction
ising.nb      A study of statistical problems in magnetism.
Nacl.nb       Drawing a crystal structure
Pendulum.nb   A double pendulum analysed, with animation
Phase.nb      Simple introduction to phase space plots
varia.nb     The variational principle and perturbation theory in quantum mechanics
applied to the helium atom

THE NOTEBOOK CONCEPT
What you see on the screen is controlled by a Windows package called the Mathematica
Front End (MFE). This serves as an interface between you and the program which does the
computation, the Mathematica Kernel (MK). MK runs as a separate task. In principle it is
possible to have several copies of MK running simultaneously, but as MK is quite a large
program, and can require large amounts of memory, it is more usual to work with only one
active copy. It is also possible to have MFE running on one machine connected to MK on
another. In this case, we will run one copy of MFE, one copy of MK, on a single PC for
each user.
Interaction through MFE is divided into blocks, for formatted text (essentially, comments),
expression input, and output.
Each block of work which is done in Mathematica, which will be a mixture of these types
of block, may be kept together in a 'notebook'. When Mathematica is loaded, it starts one
copy of MFE running and opens a new notebook. When it is asked to do a computation
(rather than just handling text) it will start MK - as a result the first computation will always
appear to take rather a long time.

The MFE notebook has some similarities with a hand-written notebook, but also enough
differences to make the analogy a tricky one. For example, once an expression has been
typed into a notebook and the SHIFT+RETURN key combination has been pressed, it is
passed to MK where it is executed, and the result is returned to MFE. If the expression had
been previously executed, then the result of that execution would be deleted as soon as the
return key was pressed. It is vital to remember that MK has no way of knowing where the
input expression was on the notebook: it is the order in which the expressions are passed to
MK that matters. Another point to be wary of is that if you work with more than one
notebook but one copy of MK then if you alter, say, the value of x in one notebook then that
is the current value of x as far as MK is concerned, and it is the value that will be returned
to either notebook - MK does not keep a separate copy of x for each notebook.

Opening a Notebook
The usual Windows File/Open operation will open an existing Notebook.

As with any computer-based activity, you should save your work frequently. Mathematica
does not have an autosave feature, so if the system crashes you will lose all the work since
the last time you forced a save. Be aware of the fact that under WTS Mathematica may not

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close the file cleanly if you run out of disk quota. Also note that the way in which
Mathematica stores graphical images is very expensive on disk space. It is sometimes a
good idea to click Kernel/Delete All Output before saving: this will save all the
commands in your notebook, but not the output, and will therefore need much less disk
space. You can easily get back to where you were by reloading the file and clicking
Kernel/Evaluate Notebook.

IF THINGS GO WRONG
Problems can be divided into two categories - your errors and Mathematica's problems.
The most likely errors you are likely to make are simple typing errors. To correct such
mistakes, simply select the appropriate input section, correct the input, and press
SHIFT+RETURN again. Note that the automatic numbering which Mathematica applies to
input and output means that once your previous attempt has been overwritten with the new
one the sections in your notebook will no longer be in consecutive numerical order.

The Mathematics Kernel itself is fairly robust, both in the code itself and in the reliability of
its mathematics. It does, however, have to indulge in memory management to clear old
expressions from its memory and to request more memory for new calculations. Very large
calculations can get bogged down in this process, and end up by asking for more memory
than the computer has. Collapse under these circumstances may be gentle (the system exits
gracefully with a message saying that it has run out of memory) or disastrous. If you need to
be reassured that Mathematica is still working, look at the bars on the right of the screen. If
the bar next to one or more cells is darkened, then MK is still busy.
You should be able to run through all the notebooks without encountering these problems,
but it is better to be forewarned.
You may also find the guidelines to debugging helpful (see the link on the web page).
If you are unfortunate enough to have a file corrupted when trying to save it, let me know. I
can sometimes recover some or all of your work – though it takes a bit of time.

PRINTING
You should not find it necessary to print out the whole of every notebook on which you
work. On the other hand you may wish to preserve some graphs to supplement the records

LEAVING MATHEMATICA
The usual Windows sequence of File/Exit will take you out.

LABORATORY NOTEBOOKS FOR THE MATHEMATICA SESSIONS
The content of a laboratory notebook for the Mathematica sessions will, of course be
somewhat different from that for more conventional experimental sessions. Nevertheless,
the same guiding principles apply. The record must contain enough detail to allow you to
retrieve all the work done: a good way of thinking about this is to imagine that at some
future point you might want to repeat exactly the same calculation, so that you must note all

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the quantities that you type as input to the program, and any other factors that you think
might influence the result you are recording (for example, if you are finding out how long a
calculation takes you will need to know at the very least what processor, clock speed and
memory are installed on the machine you are using).

The record must be compiled in your laboratory notebook as work proceeds. As well as
numerical input and results, your notebook should contain notes you write down in response
to the problems posed in the Mathematica sessions. Should the Mathematica session
misbehave in any way, you should record as much detail as possible about the problems
encountered. If there are points about the operation of the program about which you have to
ask a demonstrator, record the details - just as you would record any quirks of a piece of
experimental apparatus.

COURSE ASSESSMENT
The final course mark will comprise 15% for each of the two tests, 5% for the image
analysis exercise, 10% for the complex graphics exercise, 40% for the final programming
exercise, and 15% for the laboratory notebook. The tests will be returned to you during the
sessions, so that I can comment individually on your answers. Nevertheless it is essential
that these marked exercises should be handed in together with your laboratory notebooks
and solutions to the programming exercises by the appropriate deadline for your group.
This will ensure that all your work can be second marked.

A.H. Harker
23 September 2002

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