Thesis Template
I (Josh) wrote, formatted, and edited my thesis using TeXworks, a free, open-source TeX editing software. (You can download it and all necessary associated files using that link.) The formatting used in these documents was accepted by the Graduate School in August, 2014, but you should probably check if there are any changes in the requirements.
Directions for Downloading Files and Compiling Josh's Thesis
I've uploaded .zip files with all of the files you need to compile my thesis. Unfortunately, because of the size limit on uploading files, I had to split it up, so it's a bit more complicated than I would have liked.
First, download the .tex documents:
Unzip the folder, and save them all in a folder, let's call it "Thesis" (but it doesn't really matter). All of the files must eventually be put in this same folder.
Next, download the reference files:
Unzip this files, and put them all in one folder called "References" (this name DOES matter). Put "References" inside "Thesis" with the .tex files.
Finally, download the figure files:
Unzip these files, and save them in a new folder called "Josh" (this name DOES matter). Then, put "Josh" inside another folder called "figures"(this name DOES matter). (I know. I'm sorry that it's complicated. I would have had to change my code to make this easier.) Put "figures" in "Thesis".
Overview of Files
The main file is the file called "thesis.tex". This is the main file that calls all of the other files; it's the only one you ever have to "run". It calls all of the other .tex files, and it automatically generates a PDF every time you run it. (To "run" or typeset the document in TeXworks, use CTRL+T or click on the green circle with the arrow in the top left of the screen.) For all the other .tex files, you just make changes in them, and then save. Then you run thesis.tex, and the changes will be reflected in the new PDF.
thesis.tex
The first big chunk of thesis.tex is all formatting stuff. You really don't have to change any of it, unless you want to add fancy new packages to get more features in the document. (I don't know how to do this.) One thing you can do is use the "Margin Check". If you comment out line 15 (\documentclass[12pt]{withesis}) using a %, and then uncomment line 18 (\documentclass[12pt,margincheck]{withesis}), then it will generate a PDF that has black boxes in the right margin anywhere where your document goes outside of the accepted margins.
The real important part starts at line 112 (\begin{document}).
I don't know what the \bibliographystyle thing is. I just left it how it was from Tyler's thesis.
The next parts are where the other chapters are called. The command
\include{CHAPTERNAME}
calls the file called CHAPTERNAME.tex. (You may have to save the chapter .tex files in the same folder as thesis.tex.) You'll have to change these \include commands to call your chapters.
For the references, \bibliography{REFERENCES} calls the file REFERENCES.bib that should contain your references. (Here it is References/library because my .bib file is called "library", and it is in the folder "References".)
For keeping track of references, both for the thesis and in general, I recommend Mendeley, a free reference manager. It stores PDFs, is searchable (it searches within PDFs), and it creates (and automatically updates!) a .bib file that creates handles the references in the thesis.
For appendices, it is the same as chapters, except you use the \include command between the commands \begin{appendices} and \end{appendices}.
myprelude.tex
The first chapter you'll want is call myprelude.tex. (You can change this file name or any other file name, as long as you change both the file name and the code that calls it.) The prelude is where you enter the title page info, the dedication, the acknowledgements, and the abstracts. It also generates the table of contents and the lists of tables and figures.
There are lots of things you can change in this file. I'll only mention the ones that I changed.
In the "TITLE PAGE" section, you enter the title, your name, and the date. You may want to play around with the spacing by adding vertical spaces if your title is multiple lines. (See below for vertical space command.)
You can edit the department (\department) if you're not in Physics, and you can enter your dedication and acknowledgements in those sections.
The CONTENTS, TABLES, FIGURES section doesn't have to be edited. It automatically generates a table of contents and a list of figures.
Enter your advisor name and title (\advisorname and \advisortitle), and then enter your abstract. For the abstract, you can either have a separate .tex file called abstract, which is called by \include abstract. (If you'd rather, you can comment out that line, and then uncomment the section below. You then type in your entire abstract in between the lines \begin{abstract} and \end{abstract}.)
Chapter .tex Files
For all of the other chapters and appendices, you create a .tex file called CHAPTERNAME.tex, and then you call that chapter in the thesis.tex file using \include{CHAPTERNAME} as described above. (Remember that you can't run/typeset the individual chapters. You just create or change CHAPTERNAME.tex, and save it. The next time your run thesis.tex, the changes will appear in the PDF.)
You don't have to give the .tex file the same name as the chapter itself. (You probably don't want to if it's long.) You name the chapter using the first line in the .tex file.
Each chapter starts out with the following line:
\chapter{This Is The Full Chapter Title, and Spaces are OK Here}\label{ch:chapname}.
This allows you to name the chapter, and the code does the formatting for you. The \label part allows you to refer to the chapter later. (See below for more on \label.)
Style (.sty) and Class (.cls) Files
I don't really understand the Style and Class files (withesis.sty, withe10.sty, withe12.sty, and withesis.cls). Mostly I didn't do anything with them at all.
The only changes I can really remember doing is modifying withesis.cls to include the final oral exam date (which you'll want to change - Line 710) my committee members (a relatively recent requirement - Line 714) and changing the title "List of References" to "References" (Line 437).
Some of these things are repeated in the Style files, too, but they don't seem to have any affect on the PDF. I'm not sure why they are repeated
General .tex Notes
Basic Commands
If you're not familiar with LaTeX, as I wasn't, I would suggest just looking (in my .tex files or others) for examples of things similar to what you want to do and then modifying that code. I found many coding answers just using Google or searching Stack Exchange. Stack Exchange also has the answer to many other pressing questions.
That said, here are a few basic commands and other small tips that I found useful.
- To cite a reference, use the command:
\cite{Citation Key}
where "Citation Key" is entered in Mendeley Reference manager. Mendeley's default citation key is "[AuthorLastName][YearofPublication]".
- If you want text in italics, use:
\textit{your text here}
or for bold, use:
\textbf{your text here}.
- If you want to label something, use the command:
\label{prefix:your_label}
where "your_label" is whatever you want to use as your label. "prefix" indicates what you are labeling. Some common prefixes I used are:
ch: for chapters sec: for sections subsec: for subsections fig: for figures table: for tables eq: for equations
When you want to refer to these things later, just use \ref{prefix:your_label}. This will number everything automatically, and it will update if you change the order of things.
- For chapters, sections, and subsections, use the commands
\chapter{Your Chapter Name} \section{Your Section Name} \subsection{Your Subsection Name}
This will do the formatting for you.
- If you want to enter an equation or symbols inline, you must surround them with dollar signs. That allows you to enter math code. As an example, you could enter $\omega$ like this to have the variable appear. If you want to enter standalone equations, see the next bullet.
- To enter standalone equations, start them with \begin{equation}, enter the equation, and end it with \end{equation}.
If you want it to be more than one line, do the same thing, but use "eqnarray" instead of "equation".
The command \\ brings you to the next line of the equation in an equation array.
The lines in equations and equation arrays are numbered automatically. Use \nonumber if you don't want a line numbered.
- You can enter fractions (\frac{numerator}{denominator}) and Greek letters (\alpha,\Alpha,\beta,...) and symbols (\approx, \times,...) directly into TeXworks. (Stack Exchange and a lot of sites have lists of symbols.) However, if you have really gross equations, I'd recommend entering them in the more user-friendly interface of Lyx LaTeX editor. In Lyx, you can then go to View -> View Source to get the LaTeX source code, which you can copy and paste into TeXworks.
- If you want multiple lines to line up in an equation array, you can use the tab command. For example, if I want the equal signs to line up, you could do
\begin{eqnarray} x&=&y^2 \nonumber \\ 23x&=&z-903 \label{eq:example} \end{eqnarray}
(The first equation wouldn't be numbered here.)
- If you want to enter normal text in math mode (either between $ or in an equation or equation array), you can use \text{your text here}.
- If you want to add vertical or horizontal space in your document, you can use \vspace{1in} or \hspace{1in}. This gives you 1 inch of vertical space, but you can enter in any value, in inches, cm, or a lot of other units. You can also just use ~ to insert extra spaces.
- For figures and tables, I would suggest just modifying existing code.
Here's an example figure code (I put the bullets in so that the wiki wouldn't format this stuff.):
- \begin{figure}[h!]
- \centering
- \includegraphics[angle=0,width=3in]{figures/Josh/AOM.jpg}
- \caption{\textit{Acousto-Optic Modulator} An acousto-optic modulator uses pressure waves to create a time-varying index of refraction in a crystalline structure. This time-varying index can be used to modulate the frequency of laser light. The frequency shift is the result of an exchange of momentum between phonons in the crystal and incident photons.}
- \label{fig:AOM}
- \end{figure}
The only things I really ever changed was the width, the file name, the caption, and the label name. The [h!] has something to do with formatting, but I never messed with that.
Here's an example of a table (I put the bullets in so that the wiki wouldn't format this stuff.):
- \begin{table}[h!]
- \begin{center}
- \begin{tabular}{ |c || c | c | c | c |}
- \hline
- Molecule & $\omega_e$ & $\omega_ex_e$ & $B_e$ & $\alpha_e$ \\ \hline \hline
- \textbf{D$_2$} & 3118.4 & 64.09 & 30.429 & 1.0492 \\ \hline
- \textbf{H$_2$} & 4395.2 & 117.99 & 60.800 & 2.993 \\ \hline
- \end{tabular}
- \end{center}
- \caption{\textit{Deuterium and Hydrogen Constants} This table presents the values of the constants needed to calculate the energies of the molecular states as detailed above. All values are for the ground electronic state, and units for all entries are wavenumbers (cm$^{-1}$). All values are from Table 39 of the appendix of Herzberg \cite{herzberg}.}
- \label{table:appendix}
- \end{table}
Here you can change the alignment of the text in each column next to {tablular}. Each column is represented by a letter - r, l, and c for right, left, or centered text.
You can also change the number of lines between columns (by adding or subtracting | around the r, l, and cs).
In the actual data, & separate columns.
The \hline command puts horizontal lines in the table.
Other Thoughts
- To get (red underline) spell-checking in TeXworks, go to Edit -> Spelling -> en_US.
- With some changes, especially with reference and figure numbering, you may have to run / typeset thesis.tex twice before you see the changes take place in the PDF.
- I think it screws it up if you use spaces in your file names, so use underscores (_) instead.
- Make sure all of your files are in one folder. (Sub-folders are ok.)
- I made my thesis by taking Tyler's, and then gradually editing it into mine. That worked pretty well, and I'd recommend trying it.