---------------------------------------------------------------- Note: I typed up these instructions and made various changes to the uithesis.cls file during the summer of 2002. I was under the impression that I would be required to use the new thesis guidelines. Apparently, the uithesis.cls file as I have edited is something of a mixture of the styles. The style file will need further revision to meet the new guidelines. In particular, the spacing between the major heading and the first line of text should be smaller. (though they said it might be okay as long as it is consistent, and it is consisitent as it is now...) Also, some of the text on the title pages is a little off (the word "supervisor" is now supposed to be capitalized, for example). Some of these changes I have not yet made. In short, you may need to make a few more changes to the uithesis.cls file before you will meet the new guidelines. ---------------------------------------------------------------- This file describes how one can type his/her Ph.D. thesis using LaTeX on the unix/linux machines in the math department. It was written in the summer of 2002 by Mike McLendon, a Ph.D. student in topology. I have tried to include both the basic instructions and important detail and background. I hope that other graduate students will find this information useful. See the REFERENCES section at the end of this file for suggested books about latex. In this document: STEP ONE - create a directory for your thesis STEP TWO - download the sample thesis files STEP THREE - edit prelude.tex STEP FOUR - type your thesis STEP FIVE - latex your thesis STEP SIX - preview your thesis STEP SEVEN - print your thesis BACKUP YOUR THESIS INCLUDING FIGURES GRADUATE COLLEGE GUIDELINES PROBLEMS STYLE FILES VS CLASS FILES LATEX ERRORS AND WARNINGS LATEX SLIDES REFERENCES CREDITS ---------------------------------------------------------------- Note: It is important for you to know how to edit text files, save files, create directories, etc. Most windowing environments allow you to do all these things using the graphical user interface. For example, double click on a file to edit it and use menus to create new directories. I will describe how to do most things in a terminal. You can adjust these instructions to work for a graphical user interface if necessary. For people new to unix/linux, I would suggest the "pico" editor or the default editor for your windowing environment. Other popular editors are "emacs" and "vi". I don't use emacs, but I have heard that it has a lot of nice features when working with latex. I use vi, but I would not recommend it to new users. If you are going to use unix commands, you can get help by typing "man commandname" at a unix prompt. These man pages are sometimes cryptic, but they are helpful if you forget the exact syntax of a command. You can also type "man -k keyword" to search the man pages for a keyword. ---------------------------------------------------------------- STEP ONE. Create a directory for your thesis. This is not absolutely essential, but I strongly recommend it. It will help you when you want to make a backup of your thesis and it can help you to keep your thesis files seperated from other things that you may have on your unix account. Open a terminal and type "mkdir thesis" (use whatever name you wish). Then type "cd thesis" when you want to change to that directory. STEP TWO. Get the "sample-thesis.tar.gz" file. Download the file from the math department's website, see "http://www.math.uiowa.edu/latex.html". These are files that you can use to organize your thesis. It includes a main "thesis.tex" file along with many other supplemental files, like "prelude.tex", "mycommands.tex", "chapter1.tex", etc. You don't have to break your thesis up into seperate files, you can put everything in one big latex file. It's up to you. To uncompress this file from a command prompt, type "gunzip sample-thesis.tar.gz" and then "tar xvf sample-thesis.tar". This will create a directory called "sample-thesis" and all the files will be in that directory. The sample thesis tar.gz file contains a copy of the uithesis.cls file and a copy of this instruction file, readme.txt. The uithesis.cls file will take care of much of the formatting details. It sets the margins, creates a table of contents, creates the title pages, signature pages, etc. Note that the sample-thesis directory will be created inside your current directory. You might want to skip step one creating the thesis directory and just get the sample thesis, uncompress it, and then change "sample-thesis" to "thesis" to be used as your main thesis directory. Do this with "mv sample-thesis thesis". STEP THREE. Edit the file "prelude.tex" and change the thesis title, author, advisor, committee member names, submitdate, and copyrightyear fields. STEP FOUR. Type your thesis in the files "chapter1.tex", "chapter2.tex", etc. The sample thesis has six chapters. More chapters can be added by simply adding a line in the "thesis.tex" to "include" other chapters. Then create a file called chapter7.tex and type the text of chapter 7 there. Add bibliographical entries to "thesis.bib". I used shortcut phrases like NameDate to identify a reference. You can use whatever phrase you want, but whatever you use, you put that phrase in the text of the thesis in the "\cite" command. Add custom commands to the file "mycommands.tex", your abstract in "thesisAbstract.tex", your acknoledgements in "thesisAck.tex", your dedication in "dedication.tex" and your epigraph in "epigraph.tex" if you want one. You should look at the "documentclass" options in the "thesis.tex" file to include things like a dedication, an epigraph, or a copyright page. You can also exclude the list of table or the list of figures if you don't have tables or figures. STEP FIVE. Latex the thesis. Latex is much like a programming language in that you must "compile" the text file to create the formatted document. Simply type "make all" on the command line to latex the document, include the bibliography information, and generate a file called "thesis.ps" that can be printed or viewed. If you are making changes to your thesis that do not involve new references from the bibfile or new references to theorems or figures inside the thesis, you can type "make simple" to skip the bibtex command and the last two latex passes. If you run latex only once, you will frequently see a warning message that tells you to rerun latex to "get cross-references right". You will notice that "make all" actually runs latex 3 times to get all these cross references right. The "make all" command runs the following sequence of commands: latex thesis bibtex thesis latex thesis latex thesis dvips -o thesis.ps thesis.dvi whereas "make simple" runs latex thesis dvips -o thesis.ps thesis.dvi You can type any of these commands in on the command line individually as well and never use the "make" commands. STEP SIX. Preview the thesis. Type "gv thesis.ps" on the command line to preview the thesis. This opens the ghostview program and lets you look at the thesis as it will be printed. You can zoom in and out, move around from page to page, etc. More than likely you will find something that you want to change and you can return to STEP FOUR and edit the appropriate chapter, then do make again, and then preview again. STEP SEVEN. Print the thesis. From within "gv" you can choose to print. However, the computers in the labs can only print to the printer in that lab. You must supply your own paper to the lab printers and frequently these printers are broken or being used to print out something for another user. There is another option for advanced graduate students. If you talk with your advisor, you might be able to get a key from Joanne to one of the departmental printer rooms. You can then print to that printer. To print to a printer in one of the departmental rooms, you need to connect to a computer that had the authority to change its printer. Do this by typing "ssh mathhp.math.uiowa.edu". This will start an "ssh" session where you will log in to another computer. You will be prompted for your unix password and you will log in and be in your home directory. Type "cd thesis" to change to your thesis directory, then type "lp -dname thesis.ps", where "name" is the name of the printer. For example, the printer in room B1K is called "pb1" so the command to print to "pb1" is "lp -dpb1 thesis.ps". As your thesis gets longer and longer, you might want to mark some pages (right mouse button) when you are previewing with "gv" and then choose "save marked pages" and then print just that new file with the marked pages. This workaround has worked for me for several years, but as the computer guys on the 3rd floor are sometimes changing the unix/linux system, you might check with them if this process doesn't work for you. BACKUP YOUR THESIS. I cannot overemphasize how important it is to regularly backup your thesis. At a minimum, you should copy the *.tex files to a diskette, your home computer, or email them to a friend so that they can be saved on a computer outside of the math department. Unix provides a convenient tool called "tar" that will collect all the files in a directory and create a single file from that directory. This is nice because you then only have to backup one file. To tar your thesis directory, move to the directory immediately above your "thesis" directory and type "tar cvf thesis-backup-MMDDYYYY.tar thesis". You can choose any filename for the tarfile, but I would suggest you use some kind of version number or supply the current date (MMDDYYYY) as above. Then you can ftp this file to your home computer or put it on a diskette. You will probably also want to compress the tarfile with the "gzip" program. Just type "gzip thesis-backup-MMDDYYYY.tar". This will create the file "thesis-backup-MMDDYYYY.tar.gz". To uncompress and untar, type "gunzip filename.tar.gz", then "tar xvf filename.tar". Note that on the linux machines, you can tar and zip in one step by typing "tar zcvf filename.tar.gz directoryname" and untar and unzip in one step by typing "tar zxvf filename.tar.gz". As of summer 2002, you have to tar and zip in two steps on the HP's. INCLUDING FIGURES. Including a figure in your thesis is pretty easy. Use a figure drawing program (i like "xfig") to draw the figure. Then using the drawing program, export the figure to an encapsulated postscript file (*.eps). You can then pull this figure into your document using the figure environment. The easiest way to see how to do this is to look at the examples in the chapters in the sample thesis. Figures can sometimes be frustrating. Latex seems to put them in strange places. The class file is supposed to give you 3 blank lines before and 3 blank lines after a figure. I found that sometimes this didn't work exactly right. See some of the figures in chapter 3 of the sample thesis for my workaround. You should also be able to find out more about how latex handles figures in some of the references below. GRADUATE COLLEGE GUIDELINES. The thesis class file was written a while back to implement the Graudate College Thesis Guidelines from 1995. The Graduate College changed their guidelines in 2002 and I tried to updted the class file to reflect those changes. PROBLEMS 1. One common problem with the class file is that if you have a section that ends with an equation or the statement of a theorem, you may get too much space between the that section and the next section. You can usually fix this by adding negative space with the command \vspace{-\li} The "\li" command is defined in the class file and it is the height of one single spaced line. If you need to add two lines of negative space, use "\vspace{-2\li}" or if you need to add positive space you can use "\vspace{\li}" or "\vspace{2\li}", etc. 2. Another problem can occur if you have some chapters that have subsections and other chapters (like the introduction) that don't have subsections. Sometimes the table to contents will have too much space after the chapter that doesn't have subsections. You can correct this by editing the "thesis.toc" file (table of contents file) directly. Then you need to do a "make simple" to incorporate the new table of contents into the document. Be careful with this. If you do a "make all", you will recreate the old *.toc file and you will not see changes to your table of contents. It is probably a good idea to do this right before you submit the thesis to the graduate college. 3. If you have problems that you can't seem to resolve and if the graudate college is giving you a hard time about formatting issues, you might try talking with Prof. Atkinson. He has worked with the graudate college on many occasions and he has explained to them some of the things that latex does and how it can be very difficult to change these things. 4. My table of contents wasn't giving the correct page number for the "list of figures". I was able to correct this by editing the thesis.toc file and then doing a "make simple" as described above in problem 2. Any small changes to the table of contents can be done in this way. STYLE FILES VS CLASS FILES. Latex version 2.09 used "style" files, the current version of latex is Latex 2e. Latex 2e uses "class" files instead of style files. I mention this because you might also find the uithesis.sty style file on the ftp site or you might get it from former graduate students. The uithesis.sty file and the uithesis.cls file do about the same things. I have updated the uithesis.cls file to reflect the new (summer 2002) graduate college guidelines, so if you choose to use the uithesis.sty file, you will have to update it yourself. You might also get a warning message from latex if you try to use any *.sty file. I recommend that you use class files as that is now the preferred method for the newest version of latex. LATEX ERRORS AND WARNINGS. Don't ignore latex warnings. As a rule, if you get an error when you try to latex your document, you won't be able to proceed until you have corrected the mistake. If you just get a warning, though, latex will generally continue and generate a document. The most common mistakes are missing brackets, and missing dollar signs. (Dollar signs indicate math mode.) Latex will sometimes try to interpret what you want and still produce a document. It is in your best interest to address warnings as the occur. If you ignore them, then you might be faced with lots of little hard-to-find changes when you get ready to fix the warnings. Also, latex may not interpret your wishes correctly and you may get unexpected results. The warning "overful hbox" means that a line extends past the right margin. This is an important issue to address since the graduate college insists that text not extend into the margins. LATEX SLIDES. Latex includes the "slides" document class. You can use this class (if you want) to prepare slides for your presentation. The slides class is a little more limited in that you cannot use the "figure" or "table" environment. You can include figures and tables, using the "epsfig", "picture", and "tabular" environments, but latex will not number your figures/tables and it will not put captions on the figures/tables. I did a Google search on "latex, slides, figures" and found the following helpful website that explains how to use the slides document class: http://www.colorado.edu/ITS/docs/latex/Unix/examples/sampleC.html REFERENCES. There are lots of good latex books out there and there is also a lot of information available on the web. Also, if you find a book that you think you like, you might check the engineering library and take a look at the book before you buy it. Here are a few references that I have used. [1] Google. That's right, Google. A carefully worded search on Google will usually lead you to a webpage that answers your question. In case you don't know, Google is a search engine, http://www.google.com/ [2] Gratzer, George. First Steps into Latex. This is a very nice first book. It is short (100 pages), inexpensive ($15), and gives a nice explaination of how to create a simple latex document. [3] Gratzer, George. Math into Latex. This is a very thorough latex book. It would make sense to get [2] above first and then "graduate" to this book once you need to understand more complicated topics. This book is about 600 pages and costs around $45. [4] Fellow and Former graduate students. Don't be afraid to ask a fellow gradaute student for hints and advice. CREDITS. The sample thesis that you see here follows Sean Forman's thesis files very closely. He is definitely the person to thank. All I did was take his thesis, delete his chapter data, and type my chapters. I also made a few changes to the uithesis.cls file to reflect the new graduate college requirements. If you look at the uithesis.cls file, you will see that much of it was written and modified by Paul Henning, Pete Willemsen, and Kenny Hunt. I don't know these guys personally, but I appreciate their efforts on all of our behalf. I should also mention Larry Peterson, who wrote much of the uithesis.sty style file. Though the newer class file has superseeded the style file, many, many students have used Larry's style file since he created it in 1996.