Introduction to Computing

Lecture notes and computer exercises

Karin Carling

Göteborg 2001
Contents

1 Basic Unix 1
1.1 First meeting with the computer . . . . . . . . . . . . . . . . . . . . 1
1.1.1 Commands . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.1.2 Simple file-system exercise . . . . . . . . . . . . . . . . . . . 2
1.2 Basic Emacs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
1.2.1 Make a file . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
1.3 More exercises . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
1.4 How to use the manual . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.5 Redirect and pipelining . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.6 File quota . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
1.7 Security . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
1.7.1 Lock your account! . . . . . . . . . . . . . . . . . . . . . . . 4
1.7.2 Change password! . . . . . . . . . . . . . . . . . . . . . . . 4
1.8 Finally . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
1.9 Log off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
1.10 How to learn more . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

2 Introduction to LATEX 7
2.1 Getting started with LATEX . . . . . . . . . . . . . . . . . . . . . . . 7
2.1.1 Typing text . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
2.1.2 Typing math . . . . . . . . . . . . . . . . . . . . . . . . . . 10
2.1.3 Graphics and tables . . . . . . . . . . . . . . . . . . . . . . . 11
2.1.4 References and bibliography . . . . . . . . . . . . . . . . . . 12
2.2 How to learn more about LATEX . . . . . . . . . . . . . . . . . . . . . 12

3 Computing and programming with MATLAB 15

3.1 How to get started . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
3.1.1 Start and stop . . . . . . . . . . . . . . . . . . . . . . . . . . 15
3.1.2 Basic calculations . . . . . . . . . . . . . . . . . . . . . . . . 15
3.2 Simple graphics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
3.2.1 Save figure to file . . . . . . . . . . . . . . . . . . . . . . . . 17
3.3 Systems of linear equations and eigenvalues . . . . . . . . . . . . . . 17
3.4 Simple programming . . . . . . . . . . . . . . . . . . . . . . . . . . 17
3.5 How to learn more . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

i
ii CONTENTS

A Short guide to basic commands 19

A.1 UNIX commands . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
A.2 Emacs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
A.3 LATEX . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
A.3.1 Environments . . . . . . . . . . . . . . . . . . . . . . . . . . 22
A.3.2 Typesetting text . . . . . . . . . . . . . . . . . . . . . . . . . 22
A.3.3 Special symbols . . . . . . . . . . . . . . . . . . . . . . . . 23
A.3.4 Some mathematical symbols . . . . . . . . . . . . . . . . . . 23
A.4 MATLAB . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Chapter 1

Basic Unix

First you will learn some basic commands for the Unix-system, the basics about the
file-system, and how to make text-files with the editor Emacs. This knowledge is es-
sential if you are going to use the computers at Djungeldata.

1.1 First meeting with the computer

Sit down at a workstation. It is usually turned on. If the screen is black, move the
mouse and wait for a little while. (The screen goes black to save energy when no-
one have been using the computer for a while.) You will see a login-prompt at which
you have to write your user-name and you will be asked for your password. When
the login process is finished you will have a couple of windows on the screen. Move
the pointer into one of the windows. This window will be activated and you can type
Unix-commands here.

1.1.1 Commands
1. Write some simple commands, e.g. date, cal and who.
2. Misspell on purpose and correct it. You can move back and forth on the com-
mand line with the arrow-keys, and
, and remove characters in front of
the marker with Backspace. It is the key above the return-key with an arrow
pointing to the left. You can also use Control-d (the Control-key is held down
simultaneously with the d-key, short: C-d) if you want to remove the character
which the marker covers.
Tab-expansion is also good to know. The command interpreter may fill-in your
commands and file names. Write xre and press the Tab-key, and you will get
xrefresh. This will work if there is an unique choice to make. If you write
ma and try tabular-expansion, you will get a beep as the answer. Now write C-d
and you will get a list of the commands beginning with ma.

3. Give the command man for some program, e.g. who. (New page = space,
end listing = q).

4. Go through your previously executed commands with the arrow-keys and  .
Try the command history.

1
2 CHAPTER 1. BASIC UNIX

1.1.2 Simple file-system exercise

Write the commands you use, and the resulting output.
1. Find out in which directory you are.
2. Move two steps upwards in the library tree, in one command. List the files in
this directory.
3. Move to your home directory.

1.2 Basic Emacs

There are a lot of different programs for text editing. Here you will learn the ba-
sics of an editor called Emacs. Start Emacs by writing emacs & in some window  .
End Emacs by choosing Exit Emacs under the File-menu(short: File:Exit
Emacs) or with C-x C-c.
Try editing some text. Save it to a file File:Save Buffer As and give it a
name.
To learn more, try the Emacs tutorial (Help:Emacs Tutorial). I recommend
that you take some time to work it through. There are a lot of useful tips and tricks
in the tutorial. Also, there is a short list of key-bindings that you might find useful in
appendix A.2.
Exit Emacs.

1.2.1 Make a file

You will now make a file in Emacs. Open Emacs again and write the following text:
Mike 345
Tom 968
Kim 23
Mary 136
Evelyn 485
Save this text to a file as testfile. Move the pointer to an xterm-window and make
sure that you are in your home directory. Make sure that you have the testfile in
you present working directory and that the contents is correct by printing the file to the
window with cat. Move the mouse to the Emacs-window and change the file contents
by adding the row “Jane 295”. Save the file and exit Emacs.

1.3 More exercises

Write the commands you use to do the following tasks:
1. Copy the contents of testfile to a new file copyfile and control the exist-
ence of the new file with ls.
2. Change the name on copyfile to indata and remove the file testfile.
3. Check, by using grep, if “Tom” is in the file indata.

The & will put the program in the background, and you will not block the command line for new
commands. Very convenient.
1.4. HOW TO USE THE MANUAL 3

1.4 How to use the manual

In this part of the exercise you will learn how find information about a command by
the help of the manuals, which are available through the command man.
Write the commands you use to solve the following tasks:

1. Find out on which day of the week you are born with cal.

2. Which day of the week was September 3, 1752?

3. Count the number of characters, words and lines in the file indata with wc.

4. How do you write to make wc count words only?

5. What is the action of the flag -a to the command ls?

6. What can you use the command apropos for?

7. Sort the file indata alphabetically, with the command sort.

8. Sort the file indata numerically by the second column.

1.5 Redirect and pipelining

Most of the commands write their output to the screen. In Unix it is easy to redirect
the output to a file with > followed by a filename.

boromir  ls
file1 newfile other.file my.file
boromir  ls > listres
boromir 

Commands that normally read their input from the terminal can be made to read this
data from a file with <. If we would like to count the number of words, i.e. the number
of files in the present directory, in the file listres we created above we can do the
following.

boromir  wc -w < listres

4

It is not necessary to make a file every time you would like to count the number of
files in a directory, you can connect the commands with a pipe (  ). This will cause the
output from the first command to be piped to the other command.

boromir  ls  wc -w

The redirects shown above is only the basic ones. If you are curious of more in-
formation about this read the manual pages of the command shell, i.e. man csh.
And finally a little exercise (write the commands you use):

1. Sort the file indata in the inverse alphabetical order and save the result in the
file atadni with a redirect.
4 CHAPTER 1. BASIC UNIX

1.6 File quota

Every file you have will need disk-space for storage. Do the command ls -l. How
much space do the file indata take? Try the command quota to find out how much
disk space you are allowed to use. Assume that you get the following answer:
Disk quotas for f92kaan (uid 7580):
Filesystem usage quota limit timeleft files quota limit timeleft
/users/dd/mp97
5 50000 75000 6 0 0

This output shows that you use 5 kb disk-space of the allowed usage of 50000 kb, that is
50 Mb, and during a short period of time you may use up to 75 Mb of disk-space. You
have 6 files stored and there are no limits to the number of files that you are allowed to
have on the file-system.
How much disk-space are you using? If you get a message that you have used more
disk-space than your quota allows you should clean up immediately on you account,
that is delete files.

1.7 Security
The world is full of wicked people who enjoy to steal or destroy other peoples work,
including yours, and they are at Chalmers too, actually. Therefore, it is of uttermost
importance that you make everything in your power to prevent unauthorized access to
your account.

1.7.1 Lock your account!

If you leave the computer for a short time, only a few minutes, someone might remove
all your files, steal you printer-quota and send offensive e-mails in your name! To avoid
this, lock the workstation every time you leave it unnoticed.
To avoid the misuse of xlock there is a time limit (usually about 20 minutes) on
the command. When the time is up, anyone may log you out.

1.7.2 Change password!

To stop unauthorized use of your account it is important that you keep your password
a secret. You should change the password you where given when you got your account
with the command nispasswd. You are not allowed to have a password that can be
found in dictionaries or otherwise is too “easy”.
If you forget your password you have to ask the system administrators (fop) for
a new one. System administrators usually dislike people who keep forgetting their
passwords. I suggest that you remember your password.

1.8 Finally
The command-list, see appendix A.1 contains a lot of useful commands and programs.
The following commands are very useful, I suggest that you learn them by heart: cat,
cd, cp, emacs, grep, kill, lpq, lpr, lprm, ls, man, mkdir, more, mv, nispasswd, pine, ps,
printerquota, pwd, quota, rm, rmdir, top, wc, xlock.
1.9. LOG OFF 5

1.9 Log off

When you are finished working at the workstation you have to quit your programs and
log off. Always quit programs by their exit/quit command! (Be extra careful to do this
with Netscape and Matlab!) When you have done this you click on the button marked
“logout”. Do not turn off the power! The screen will go into an energy-saving mode
automatically.
Make sure that you clean up the desk before you leave the computer room!

1.10 How to learn more

There are a lot of good information available on the web, e.g. at the Djungeldata home-
page. Try these links for more information about Unix:
http://www.dd.chalmers.se/UNIXhelp/
The Faq-O-Matic:
http://www.dd.chalmers.se/fom-serv/cache/1.html
If you would like to pick up a book to learn more about Unix there are a lot of books
available at the main library at Chalmers. Here are some examples of books which I
have found useful:
An Introduction to the Unix Operating System C. Duffy. A bit old but short intro-
duction.
The Unix Operating system K. Christian and S. Richter. The first part of the book
covers basic Unix knowledge, and the second part covers more advanced Unix
skills.
Unix Clearly Explained R.L. Petersen. This book is similar to the previous one, but
a bit less advanced.
Chapter 2

Introduction to LATEX

There are a lot of programs for writing reports and other documents. Some of them
are similar to Word, e.g. StarOffice, some are more enhanced, e.g. FrameMaker, and
then there is LATEX. This part will teach you the basics of LATEX since it is a powerful
typesetting program which can be found, or installed for free, on almost any computer
system. To be able to use LATEX, you also need to know how to use a text editor, e.g.
Emacs.

2.1 Getting started with LATEX

LATEX is a mark-up language. The document you are working on will not appear dir-
ectly on the screen until it is typeset and opened in a viewer. You will be working with
the text in a source file which will include mark-up commands that indicates how to
typeset the document. This might seem complicated but it will give you many advant-
ages when writing equations and documents with cross-references, and LATEX is the
document format that many physics journals and conferences prefer when you want to
submit your contributions.
The basic structure of a LATEX source file is shown in Fig. 2.1. The preamble spe-
cifies the document class and then the packages used by the article. Also, you can
include specialized commands that will be used throughout the document and other
global definitions.
The body of the document is enclosed by

\begin{document}
...
\end{document}

which marks the enclosed text as the part of the document that is to be typeset according
to the “rules” of the preamble, and the mark-up commands in the text of the body.
In the body you have the abstract, the main text which is divided into sections, and
in the end a list of literature references, the bibliography.
To get a typset document from the source file (ltest.tex) you will have to run
the following commands:

latex ltest
xdvi ltest.dvi &

7
8 CHAPTER 2. INTRODUCTION TO LATEX

\documentclass[...]{...}
\usepackage{...} preamble

\begin{document}

\title{...}
\author{...} top matter
\date{...}
\maketitle

\begin{abstract}
... abstract
\end{abstract}
body
\section{...}
\section{...}

\begin{thebibliography}{...}
\bibitem{...}... bibliography
\end{thebibliography}

\end{document}
Figure 2.1: The basic structure of a source file

The formatted document will appear in a new window on the screen. If you want to
print the document you have to apply one more command to the file:
dvips ltest.dvi
This will generate a file ltest.ps which can be viewed (ghostview) or printed
(lpr).

2.1.1 Typing text

Text are typed into any LATEX document with the following keys
a-z A-Z 0-9
+ = * / ( ) [ ]
and the following punctuation marks
2.1. GETTING STARTED WITH LATEX 9

, ; . ? ! : ‘ ’ -
and the space-bar, the tab key (which gives the same effect as the space-bar in the
typeset document), and the Return key. There are also thirteen keys that are mostly
used in LATEX instructions:
# $ % & ˜ _ ˆ \ { } @ " |
If you want to typset these caracters there are commands available, see App. A.3.3.
The other (swedish) keys on your keyboard cannot be used, unless you include a
package that can handle this input. At Djungeldata your can include the inputenc
package.
To give you an idea of how the source file might look like, here is a short example
of how to write some text in LATEX:
\documentclass[a4paper, 12pt]{article}
% This is a comment which will be ignored.
\begin{document}
\section{First section}
\label{thefirst}
Here you can write the text you like. The number of
spaces between the words will be ignored when the
text is typset
as well as
any single linebreaks.

A new paragraph is defined by two or more linebreaks,

that is one or more empty lines.

Sometime you might want to \emph{emphasize} a word.

\end{document}
The source file begins with
\documentclass[a4paper, 12pt]{article}
which specifies the class of the document (article) and includes the optional argu-
ments a4paper and 12pt which states that this document should be typset for the
paper size a4 and with the font size 12 points.
The second line is a comment. When LATEX encounters the %-character the rest of
the line in the source file will be ignored. This can be conveinient if you want to add
some notes to your source file.
The text of the document is typed within the document environment. An envir-
onment is the region between any pair of
\begin{...} \end{...}
where the enviroment type is given within the braces.
The text is sectioned with the  section command which can be accompanied by
a  label command that ties a short name to the section heading to make it easy to
refer to this section later in the document, see Section 2.1.4. There are several levels of
sectioning available. The number of levels depend on the class of the document.
10 CHAPTER 2. INTRODUCTION TO LATEX

As can be seen from the typeset document, LATEX notices that there is a space or tab
in the file but it ignores how many, and puts only one space in the typset document. The
same is true for blank lines, which will cause LATEX to make a new paragraph. Usually
the spacings will be typeset correctly, but once in a while you might run in to trouble.
You might want a space between two words but you do not want a linebreak between
the words. Then you can “tie” the words together with the ˜(tilde), which will give a
nonbreakable space.
Another problem you might encouter is that the hyphenation is incorrect. Usually,
english words will be hyphenated correctly, but there might be names of technical terms
that are difficult to handle. To help with the hyphenation, you can insert one or more
optional hyphen commands (  -) to show LATEX where the word might be hyphenated.
If the word occurs many times in the document, you can use a “global solution”, by
putting the word with optional hyphens in the preamble instruction

\hyphenation{in\-struction}

2.1.2 Typing math

Most problems in physics are connected with equations and formulas. LATEX is an
excellent tool for typesetting equations and mathematical notations. Equations in LATEX
can be inline or displayed environments. The following example of a source file and
the result can give you an idea of how the math environments work.

In first year calculus, we define intervals such as

$(u, v)$ and $(u,\infty)$. Such an interval is a
\emph{neighborhood} of $a$ if $a$ is in the interval.
Students should realize that $\infty$ is only a symbol,
not a number. This is important since we soon introduce
concepts such as $\lim_{x \to \infty} f(x)$.

When we introduce the derivative

\begin{equation}
\label{eq:derivative}
\lim_{x \to a} \frac{f(x) - f(a)}{x - a},
\end{equation}
we assume that the function is defined and continuous
in a neighborhood of $a$.

The typeset document will look something like this:

In first year calculus, we define intervals such as 

 and 
 .
Such an interval is a neighborhood of  if  is in the interval. Students
should realize that  is only a symbol, not a number. This is important
since we soon introduce concepts such as !" #$ .
When we introduce the derivative
" #$)(*" +

%'&
 (2.1)
#(*

we assume that the function is defined and continuous in a neighborhood

of  .
2.1. GETTING STARTED WITH LATEX 11

The inline environment open and close with $, and the displayed environment is
contained within

\begin{equation}
...
\end{equation}

The equation environment includes the possibility to label the equation for easy
cross-referencing, see Section 2.1.4, with the  label , name - command, and the
equation will be numbered.
There are many commands within the math environments to give the components
of an equation. LATEX includes almost any mathematical symbol you might like to use,
and there are a number of packages that give you access to even more symbols. A list
of the most common components is found in App. A.3.4.

2.1.3 Graphics and tables

Usually, the results from an experiment or calculation is presented in a graph. To illus-
trate you text by importing graphics into your document is possible in LATEX. The file
formats that can be imported to a LATEX document is Encapsulated or plain PostScript.
Usually, these files have the suffices .eps or .ps.
To be able to import graphics into the document you must include the graphics
package in the preamble. This package includes the commands

\includegraphics
\scalebox
\rotatebox

which might come in handy when you are importing your graphics.
The graphics you like to import are placed within the figure environment. Below
is an example of the command series used to put a centered figure (my-fig.eps) into
a document.

\begin{figure}[htbp]
\begin{center}
\includegraphics{my-fig}
\caption{The caption of the figure is written here.}
\label{fig:myfigure}
\end{center}
\end{figure}

The includegraphics command assumes that the file suffix is .eps. If there is
no such file it looks for a file with suffix .ps. The figure can be labelled for easy
cross-referencing, and you can include a figure caption with explanatory text.
Sometimes your data is better shown as a table. In LATEX you will construct a table
with the tabular and table environments. The following text in the source will
produce the table as shown below.

\begin{table}[h]
\begin{center}
\begin{tabular}{| l | l | r|}
\hline
12 CHAPTER 2. INTRODUCTION TO LATEX

First & Second & Third \\

\hline
34 & 678 & 2020\\
\hline
\end{tabular}
\caption{This is the caption of the table}
\label{tab:name}
\end{center}
\end{table}
This table will be the result

First Second Third

34 678 2020

Table 2.1: This is the caption of the table

2.1.4 References and bibliography

When a document begins to contain more than five to ten pages, figures, equations,
or bibliographic references it becomes difficult to keep the cross-references in order.
LATEX includes commands that makes life much more easy when it comes to cross-
referencing. You have already encountered the  label command that will give you a
name for every figure, table, or equation in your document. These names are used with
the  ref , name - command to make a reference to the figure, table, or equation called
name. Also, you can make references to the different sections of your document.
To cite a book or article you need to create a list of the bibliographic references you
use in your document. This list is created in the thebibliography environment,
and each item in this list is a bibitem. The bibitem has a label which is used for
referencing the book, or article, with the  cite , name - command.

2.2 How to learn more about LATEX

You can get almost anything out of LATEX. The material you get in this course is all
written in LATEX. You can make a reference list, include pictures, write complicated
equations and include footnotes. Everything, which is not simple text, is “marked”
with format marks to tell the typesetting program, i.e. LATEX, how to do format the text.
In App. A.3 there are some examples of environments and commands which are used
a lot for typesetting with LATEX.
Try to write a small report, a couple of pages, with at least an equation, a table,
a book reference, a footnote and a picture. To learn more on how to include all these
items look at the Djungeldata-LATEX home page:
http://www.dd.chalmers.se/latex/index e.html.
There you will find nice examples of reports and other documents you might want to
write.
To get a more or less complete list of commands to LATEX you can go to:
http://mitra.phys.uit.no/edb/latex/index.html.
There are books about LATEX available at the main library at Chalmers and here are
some of the books I have found useful:
2.2. HOW TO LEARN MORE ABOUT LATEX 13

First Steps in LATEX G. Grätzer. If you read and do the exercises of this book you
have achieved the skills you need to make an article. Quite short.

A Guide to LATEX H. Kopka and P.W. Daly. A more comprehensive book.

LATEX – a document preparation system L. Lamport. The book about LATEX. If you
should buy one book, buy this one.
The LATEX companion Goossens, Mittelbach and Samarin. This is the second mostly
bought book about LATEX.
Chapter 3

Computing and programming

with MATLAB

This part will get you started with MATLAB and give you the basic knowledge for
using the program. If you are going to pass the Computational Physics course in the
spring it is important that you continue to practice and improve on your MATLAB
skills.

3.1 How to get started

3.1.1 Start and stop
To start MATLAB you type matlab at a command-prompt in an available window, or
click on the MATLAB-icon. Whenever you want to quit MATLAB you type quit at
the MATLAB prompt. Do not forget to quit MATLAB before you logout!
There are some commands you can try immediately, e.g. tour and demo. The
last one is very useful for getting started with MATLAB. To get help you should learn
how to use the commands help, helpwin and helpdesk.
If your computation is running out of hand, you can force it to stop with ctrl-c,
which will send a stop signal to the process and you will get the MATLAB-prompt
back.

3.1.2 Basic calculations

You can use MATLAB as an ordinary calculator. You can try to compute the sum
.0/2101435176
. If you want to save the result of a computation you need to assign it to
a variable: (In the examples I will only write the MATLAB commands and, on some
occasions, the output.)

x=14
y=3*x
The usual mathematical functions are available within MATLAB, e.g. sin. Par-
entheses are used as usual. If you put a semicolon at the end of a command the com-
putation will be performed as usual but there will be no output on the screen. This is
convenient when you are working with large arrays of data.

15
16 CHAPTER 3. COMPUTING AND PROGRAMMING WITH MATLAB

If you are curious of the variables saved by MATLAB, check them with the com-
mands who and whos. The last command will give more details about the variables
stored. To clear all variables you type clear, which can be used to clear one variable
at the time too. (How do you do that?)
Variables in MATLAB are vectors and matrices. Enter this and comment on the
output.

vcol=[1;2;3;4], vrow=[1 2 3 4]
A=[1 2 3 4;5 6 7 8;9 10 11 12]
sqrt(vcol),sqrt(A)

If you need a long vector you do not want to enter every number by hand. The
colon-operator is a tool for the construction of vectors:

vector=0:8
vector2=0:0.5:2

You should also learn how to use linspace and logspace.

You can do operations element-wise on vectors and matrices.

values=2.ˆvector

If you have defined some variables you can use those to create new variables.

table=[vector;vector.ˆ2;vector.ˆ3]

3.2 Simple graphics

To get a graph you choose which type of graph you would like to have, and learn what
type of data you need to give the command. One of the simplest graphs you get with
plot. Try to plot the powers of two you have made previously.

plot(vector,values)

To get a smoother curve you use more values. Try to make a smooth plot of the
powers of 2. Read the help-file and learn how to get different colors and line-types in
your graph.
It is also possible to do 3D-graphics.

vector2=0:0.5:8;
[X,Y]=meshgrid(vector2);
mesh(X,Y,2.ˆX+2.ˆY);

What happens if you change mesh to surf?

When you make statistics the command hist is handy. You can create random
numbers with rand and check how random they are.

random=rand(1,7)
hist(random);
3.3. SYSTEMS OF LINEAR EQUATIONS AND EIGENVALUES 17

3.2.1 Save figure to file

When you have plotted an illustrative figure you might want to put it into your report.
To do this you have to save the picture to a file and import the file into the document.
There are many formats for pictures but the one recommended in this course is Encap-
sulated PostScript (eps), which is easy to import into a LATEX-document.
To save a MATLAB figure to a eps-file you can write the following command:

print -depsc -epsi filename

or use the menus of the figure window. This will give you a file filename.eps in
the working directory. This file can be imported into your document. (If you want to
learn more about the flags given to the print-command try the MATLAB-helpdesk.)

3.3 Systems of linear equations and eigenvalues

When you are doing computational physics you need to know your linear algebra.
MATLAB is based on matrices as data format, and there are many built-in tools for
extracting information from a matrix and solve a wide range of problems.
Begin with these matrices:
9: 6<;=. BC
1F>?6
.?>@>
A 8 B 8ED 1@1?1HG (3.1)
1A>@6

Enter them into MATLAB. You can multiply the matrices with B*A. What happens if
you type A*B? Why? Try some other matrix commands on these matrices, e.g. det,
trace, null, orth and inv. Try to understand what these commands do.
To solve a system of linear equations e.g.
I 6 3 ; 3 . >.
JK #ML #ON #QPR8
. 3 > 3 > 17S
#ML #ON #QPR8 (3.2)
3 > 3 6 176
#ML #ON #QPR8

This system of equations can be written as A T x 8 b which is solved with

b=[25;18;13];
x=A\b

Check the solution by solving the system of equations by hand.

In MATLAB the A*B will give you the matrix multiplication. If you would like
to do element-wise multiplication you have to use the operator .*. There are other
operators and functions that are available as matrix or element operations.

3.4 Simple programming

A program is a list of commands that are to be executed, often controlled by condition
and repetition clauses, to solve a certain problem. In MATLAB you write you programs
to files with the suffix .m.
A MATLAB program can be a routine or a function. If you want to write a function
the first line of the file have to begin with function, e.g.
18 CHAPTER 3. COMPUTING AND PROGRAMMING WITH MATLAB

function y = div(n,d)
To avoid problems, do not give your functions the same name as a built-in MATLAB
function, and give the source file the same name as the function, e.g. div.m for the
function div.
On the home page of the course there is a program available for you to read and
run. Try to understand every command in this program and what they do before you
run to see the result.
Try to make some MATLAB programs on you own. You might have some prob-
lems from one of the other courses you are taking that you might try and solve with
MATLAB.

3.5 How to learn more

To learn more about MATLAB try the MATLAB-helpdesk, available on the web, which
includes a tutorial and other resources.
There are quite a large number of books available on MATLAB, for example:
The MATLAB 5 Handbook Pärt-Enander, E et al. (Addison Wesley Longman, 1999
(ISBN 0-201-398451). This is a nice book which you probably will find useful
no matter of your previous knowledge of MATLAB. If you are going to buy a
book, I recommend this one.
Introduction to MATLAB for engineers and scientists D.M. Etter. A short book for
the beginner that includes several exercises. If you need ideas and practice, bor-
row this book from the library and use it.
Appendix A

Short guide to basic commands

This document contains some lists with the most common commands used on the Djun-
geldata computer system, and in some of the programs that you will use during your
education at the Physics Department. It is a good idea to check that you are famil-
iar with these commands. If not, learn more about them through the manual and help
pages.

A.1 UNIX commands

To learn more about a UNIX command, what arguments it takes and which flags that
can be used, check the manual page with man command. For more information about
UNIX check this web page: http://www.dd.chalmers.se/UNIXhelp/.
There is also a lot of other useful information on the Djungeldata web pages.

man command Show the manual page for the command. I strongly suggest that you
learn how to use this command and how to read the manual pages.
apropos keyword Locate commands by keyword lookup.
nispasswd Use this to change your password.
xlock Lock the workstation for a short period of time.
pwd Print the path to the present working directory, i.e. the directory in which you
currently are positioned.
ls List the files and directories in the current directory. Some optional flags:
-l Long listing, gives information about size, owner, date, and status of files and
directories.
-a Show all files and directories, including the hidden ones (.name).
-F Shows markers at the file and directory names, e.g. a directory is marked
with a trailing slash(/).
mkdir name Create a new directory called name in the current directory
rmdir name Remove the directory called name. (This requires that the directory is
empty.)

19
20 APPENDIX A. SHORT GUIDE TO BASIC COMMANDS

cd name Change directory. If no directory name is give you will end up in your home
directory.

mv file1 file2 Move, actually rename, file1 to file2.

mv file(s) dir Move the file(s) to directory dir.

cp file1 file2 Copy file1 to file2.

chmod flags file Change the status (mode) of the file or directory. Use this to protect
you files. Some flags:

u+x Gives the user (you) the right to execute the file.
og-rwx Removes all rights for other users to read, write or execute your file
(directory).

ps List the process numbers of the processes that are running on the computer.
top Allows you to check the load of the computer. Can be used to identify and kill a
looping process.

kill pid This command kills the process which you tell it to kill. Be careful when using
this.

quota -v Show how much of your quota of disk-space that you are using.
printerquota Show how many pages you can print from your account. If you need
more pages you can by extra printer quota from F-styret.

lpr file(s) Print the file(s) to the default printer.

lpq Show the default printer queue.

lprm jobid Remove your printer job from the printer queue.
more file Show file contents on the screen one page at the time.

grep pattern file Find the pattern in the file.

wc file Count the number of lines, words and characters in the file.

sort flags file Sort the contents of the file (the flags are optional). You can sort in a lot
of ways if you learn how to use the flags.

A.2 Emacs
This is a short list of key bindings that is useful when you are working with emacs. If
there is a dash (-) you should hold these keys down at the same time, and key bindings
should be done in sequence. The C-x is short for holding down the Control-key and x-
key at the same time, and M-x is the Meta-key and the x-key at the same time. Usually,
the Meta-key is a rhombi-marked key.

C-g Interrupt previous command. Use this if emacs is behaving strangely.

C-x C-c Quit emacs.

A.2. EMACS 21

C-x C-f Find file, i.e. read a file into emacs for editing.
C-x i Insert file into the active buffer.
C-x C-s Save buffer to file.
C-x C-w Save buffer to a new file-name and make that file the active buffer.
C-x b Change to another buffer.
C-x u or C- Undo the previous change, can be repeated.
C-f One character forward.
C-b One character backward.
C-p Go upward one line.
C-n Go down one line.
M-f Move one word forward.
M-b Move one word backward.
C-a Move to the beginning of the line.
C-e Move to the end of the line.
M- U Move to the beginning of the document.
M-  Move to the end of the document.
M-x goto-line Go to line n in the buffer. You will get a prompt asking for the line
number.
C-v Page down.
M-v Page up.
C-Space Put the mark here, the current position.
C-k Cut from the marker to the end of line. Repeat for several rows.
C-w Cut the area from the mark to the current position of the marker.
M-w Copy the area from the mark to the current position of the marker.
C-y Paste the latest cut/copy. Can be used repeatedly.
C-s Search forward.
C-r Search backward.
M-x doctor If you find Emacs frustrating.
M-x hanoi If you are bored...
22 APPENDIX A. SHORT GUIDE TO BASIC COMMANDS

A.3 LATEX
Here are some of the most common tags that are used when you write a document
in LATEX. Every tag begins with a  and the environments have a  begin , env - at the
beginning and a  end , env - at the end.

A.3.1 Environments
document This is the environment in which the document is set. Everything that is
written before this environment begins is called the pre-amble.

abstract Write the abstract within this environment.

equation Will put you in math-mode and allow you to type an equation that you can
for reference. The equation will be numbered.

figure Put pictures in this environment.

table You can typeset tables within this environment. Mostly used together with the
tabular.

tabular Here you order the contents of a table.

thebibliography The environment for the items in your reference list.

A.3.2 Typesetting text

section This is one of the available levels of sectioning. Which of the sectioning com-
mands that are available depends on the specification attached to the document-
class.

maketitle Typeset the title, author and date of the document.

tableofcontents Make a table of contents.

emph Typeset the text in an emphasized style, usually italics.

textbf Typeset text in bold font.

caption The text to a table or figure caption.

ref Used to cross-reference a figure, table, or section.

cite Reference a book, article or other bibliographic item from the reference list.

bibitem Marks the items in the reference list.

includegraphics Used when you want to import a picture, ps or eps formatted, into the
document. (You will need to include the graphics-package in the pre-amble.)

footnote Create a footnote at the bottom of the page containing the text included in
the command.
A.3. LATEX 23

A.3.3 Special symbols

Type Print
 # #
 $ $
 % %
 & &
 textasciitilde ˜

 textasciicirsum ˆ
 textbackslash 
V, ,
V- -
@ @
 textquotedblright ”
 textbar 

A.3.4 Some mathematical symbols

frac Makes a fraction of the two entries.
sum The sign for a sum.
int The integral
alpha Produces the Greek letter W . You can get the other letters from the Greek alpha-
bet by calling them by their name.
pm Plus-minus, X .
leq Less or equal to, Y .
parallel Parallel to, Z .
perp Perpendicular to, [ .
>\ ^
hbar The h-bar, Planck’s constant divided by , ] 8`N_ a .

There are a lot of other tags and environments available. Read the dd-LATEX home
pages and take a look at the commands at
http://mitra.phys.uit.no/edb/latex/index.html,
or buy the book “LATEX – user’s guide and reference manual” by L. Lamport.
24 APPENDIX A. SHORT GUIDE TO BASIC COMMANDS

A.4 MATLAB
This is a short list of useful command in MATLAB. Consult the MATLAB-help to
learn more about how to use them.
quit Quit the MATLAB session. Remember to always quit MATLAB before you log
out!
help On-line help, display text at command line.
helpwin On-line help, separate window for navigation.
helpdesk Comprehensive hypertext documentation and troubleshooting. Helpdesk
loads the main MATLAB Help Desk page into the Web browser.
lookfor Search MATLAB for functions that matches some keyword.
format Set the output format.
more Control paged output in command window.
ones Gives you an array of only ones.
zeros Gives you an array of only zeros.
eye Gives you the identity matrix.
rand Gives you an array of uniformly distributed random numbers.
size Gives the dimensions of an array.
length Gives the size of the largest dimension of the array.
eps Floating point relative accuracy. This is the highest accuracy you can get out of
MATLAB.
abs Get the absolute values of the elements in an array.
/ Right matrix divide.
./ Right array divide, elementwise.
* Matrix multiply.
.* Elementwise array multiply.
eig Get the eigenvalues and eigenvectors of a matrix.
diag If you give a vector as the argument you will get a diagonal matrix with that
vector as the diagonal, if you give a matrix as the argument you will get the
diagonal of that matrix as a vector.
sum Returns the sum of the elements in an array.
fft One-dimensional discrete Fourier transform.
ifft One-dimensional inverse discrete Fourier transform.
fftshift Shift DC component to center of spectrum.
A.4. MATLAB 25

ode45 Solve non-stiff differential equations, medium order method. MATLAB also
provides some other methods of solving differential equations.

who List current variables.

whos List current variables with more information.
clear Clear variables and functions from memory. Warning! There is no undo avail-
able!
plot Linear plot.
xlabel Set the text to be put on the x-axis. To set the text of the other axis there is
ylabel.
title Set the title of the figure.
mesh 3-D mesh surface plot.
surf 3-D colored surface plot.
subplot Split the figure into several plots.
hist Analyze data to produce a histogram.
bar Draws a bar graph.
print Print a figure to a file, or the printer.
print -dps filename Print the figure to a PostScript-file.
print -deps -epsi filename Print the figure in Encapsulated PostScript to file-
name.
(You can also use the scroll-bar of the figure window to save a figure to a file.)