https://wiki.physics.wisc.edu/yavuz/api.php?action=feedcontributions&feedformat=atom&user=Jjweber3Yavuz Group - User contributions [en]2026-06-17T19:19:26ZUser contributionsMediaWiki 1.39.17https://wiki.physics.wisc.edu/yavuz/index.php?title=Main_Page&diff=814Main Page2014-08-29T17:59:00Z<p>Jjweber3: /* News/Discussion */</p>
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== News/Discussion ==<br />
<br />
'''8/29/14'''<br />
Josh added a "Thesis Template" page. It has info on formatting your thesis.<br />
<br />
'''8/25/14'''<br />
Josh and Jared and Nick added a page with instructions on how to edit the website. Josh added a section with the copyright policies of many of the journals that we've published in. This has the rules for posting articles on the website. These are both on the [[Website]] page.<br />
<br />
Josh also added a link to the site that you use to sign up for the UW AMO e-mail distribution list. It's on the [[Useful External Links]] page.<br />
<br />
'''5/22/14'''<br />
Kara showed Zach and me [http://noc.hep.wisc.edu/nrg/ this website] that has temperature and humidity for Saffman's labs. The three bottom links are for Saffman's labs. I think all of their labs but the rubidium lab have air conditioning separate from the building.<br />
<br />
<br />
'''5/20/14''' <br />
Chad made it possible to use latex syntax in order to write equations, so that's pretty <math>\sigma\omega\epsilon\epsilon\tau^2</math>.<br />
<br />
'''5/15/14'''<br />
Log-in now required to view pages. Feel free to post your secret crushes and inner most thoughts. <br />
<br />
<br />
'''5/13/14'''<br />
Josh did stuff, including adding the new sections (Vendors and External Links) below. Feel free to add, change, or delete them if you have other ideas.<br />
<br />
<br />
'''5/12/14''' File uploads now accept most file types and up to 20 MB (thanks, Chad!)<br />
<br />
To embed PDFs, the easiest way seems to be to use the "upload file" link in the sidebar, then copy the web address of the uploaded file and just insert it as a hyperlink into the page you're editing. Since the file is hosted on the physics server, this should be safer than just linking to off-site pages, which may not indefinitely keep manuals up. <br />
<br />
'''5/8/14''' "All Pages" moved to sidebar as "Index"<br />
<br />
<br />
<br />
This is our main page:P<br />
<br />
apparently, to add an item to the sidebar, you need to go here:<br />
https://wiki.physics.wisc.edu/yavuz/index.php?title=MediaWiki:Sidebar&action=edit<br />
<br />
<br />
What all pages do you guys want to have? <br />
* Should we each have some kind of log page?<br />
* Equipment List?<br />
* manuals<br /><br />
* Internal/informal documents?<br />
* useful matlab programs/programs we don't want to lose?<br />
<br /><br />
thoughts?<br />
<br />
==Research Projects==<br />
[[Localization of Atomic Excitation]]<br />
<br />
==People==<br />
[[Josh Weber]]<br />
<br><br />
[[Jared]]<br />
<br />
==Lab Notebooks / Logs==<br />
[[David Notebook]]<br />
<br><br />
[[Jared lab notebook]]<br />
<br><br />
[[Josh Notebook]]<br />
<br><br />
[[Nick Brewer]]<br />
<br><br />
[[Zjs log]]</div>Jjweber3https://wiki.physics.wisc.edu/yavuz/index.php?title=Thesis_Template&diff=805Thesis Template2014-08-29T15:16:17Z<p>Jjweber3: /* Basic Commands */</p>
<hr />
<div>I (Josh) wrote, formatted, and edited my thesis using [http://www.tug.org/texworks/ 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 [http://grad.wisc.edu/currentstudents/degree/ Graduate School] in August, 2014, but you should probably check if there are any changes in the requirements.<br />
<br />
== Directions for Downloading Files and Compiling Josh's Thesis ==<br />
<br />
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.<br />
<br />
<br />
First, download the .tex documents:<br />
<br />
[[File:TeX_files.zip]]<br />
<br />
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.<br />
<br />
<br />
Next, download the reference files:<br />
<br />
[[File:Ref1.zip]]<br />
<br />
[[File:Ref2.zip]]<br />
<br />
[[File:Ref3.zip]]<br />
<br />
[[File:Ref4.zip]]<br />
<br />
Unzip this files, and put them all in one folder called "References" (this name DOES matter). Put "References" inside "Thesis" with the .tex files.<br />
<br />
<br />
Finally, download the figure files:<br />
<br />
[[File:Figs1.zip]]<br />
<br />
[[File:Figs2.zip]]<br />
<br />
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".<br />
<br />
== Overview of Files ==<br />
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.<br />
<br />
===thesis.tex===<br />
<br />
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.<br />
<br />
The real important part starts at line 112 (\begin{document}).<br />
<br />
I don't know what the \bibliographystyle thing is. I just left it how it was from Tyler's thesis.<br />
<br />
The next parts are where the other chapters are called. The command <br />
<br />
\include{CHAPTERNAME}<br />
<br />
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.<br />
<br />
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".)<br />
<br />
For keeping track of references, both for the thesis and in general, I recommend [http://www.mendeley.com 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.<br />
<br />
For appendices, it is the same as chapters, except you use the \include command between the commands \begin{appendices} and \end{appendices}.<br />
<br />
===myprelude.tex===<br />
<br />
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.<br />
<br />
There are lots of things you can change in this file. I'll only mention the ones that I changed.<br />
<br />
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.)<br />
<br />
You can edit the department (\department) if you're not in Physics, and you can enter your dedication and acknowledgements in those sections.<br />
<br />
The CONTENTS, TABLES, FIGURES section doesn't have to be edited. It automatically generates a table of contents and a list of figures.<br />
<br />
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}.)<br />
<br />
===Chapter .tex Files===<br />
<br />
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.)<br />
<br />
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.<br />
<br />
Each chapter starts out with the following line:<br />
<br />
\chapter{This Is The Full Chapter Title, and Spaces are OK Here}\label{ch:chapname}.<br />
<br />
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.)<br />
<br />
===Style (.sty) and Class (.cls) Files===<br />
<br />
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.<br />
<br />
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).<br />
<br />
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<br />
<br />
==General .tex Notes==<br />
<br />
===Basic Commands===<br />
<br />
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 [http://tex.stackexchange.com/ Stack Exchange]. Stack Exchange also has the answer to many other [http://scifi.stackexchange.com/questions/66661/exactly-how-secret-was-the-reveal-in-the-empire-strikes-back pressing] [http://scifi.stackexchange.com/questions/47085/who-made-the-decision-for-gandalfs-promotion-from-grey-to-white questions].<br />
<br />
That said, here are a few basic commands and other small tips that I found useful.<br />
<br />
<br />
* To cite a reference, use the command:<br />
<br />
\cite{Citation Key}<br />
<br />
where "Citation Key" is entered in Mendeley Reference manager. Mendeley's default citation key is "[AuthorLastName][YearofPublication]".<br />
<br />
<br />
* If you want text in italics, use:<br />
<br />
\textit{your text here}<br />
<br />
or for bold, use:<br />
<br />
\textbf{your text here}.<br />
<br />
<br />
* If you want to label something, use the command:<br />
<br />
\label{prefix:your_label}<br />
<br />
where "your_label" is whatever you want to use as your label. "prefix" indicates what you are labeling. Some common prefixes I used are:<br />
<br />
ch: for chapters<br />
sec: for sections<br />
subsec: for subsections<br />
fig: for figures<br />
table: for tables<br />
eq: for equations<br />
<br />
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.<br />
<br />
<br />
* For chapters, sections, and subsections, use the commands<br />
<br />
\chapter{Your Chapter Name}<br />
\section{Your Section Name}<br />
\subsection{Your Subsection Name}<br />
<br />
This will do the formatting for you.<br />
<br />
<br />
* 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.<br />
<br />
<br />
* To enter standalone equations, start them with \begin{equation}, enter the equation, and end it with \end{equation}. <br />
<br />
If you want it to be more than one line, do the same thing, but use "eqnarray" instead of "equation".<br />
<br />
The command \\ brings you to the next line of the equation in an equation array.<br />
<br />
The lines in equations and equation arrays are numbered automatically. Use \nonumber if you don't want a line numbered.<br />
<br />
<br />
* 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 [http://www.lyx.org/ 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.<br />
<br />
<br />
* 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<br />
<br />
\begin{eqnarray}<br />
x&=&y^2 \nonumber \\<br />
23x&=&z-903<br />
\label{eq:example}<br />
\end{eqnarray}<br />
<br />
(The first equation wouldn't be numbered here.)<br />
<br />
* 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}. <br />
<br />
<br />
*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.<br />
<br />
<br />
* For figures and tables, I would suggest just modifying existing code.<br />
<br />
Here's an example figure code (I put the bullets in so that the wiki wouldn't format this stuff.):<br />
<br />
<br />
* \begin{figure}[h!]<br />
* \centering<br />
* \includegraphics[angle=0,width=3in]{figures/Josh/AOM.jpg}<br />
* \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.}<br />
* \label{fig:AOM}<br />
* \end{figure}<br />
<br />
<br />
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.<br />
<br />
<br />
Here's an example of a table (I put the bullets in so that the wiki wouldn't format this stuff.):<br />
<br />
<br />
* \begin{table}[h!]<br />
* \begin{center}<br />
* \begin{tabular}{ |c || c | c | c | c |}<br />
* \hline<br />
* Molecule & $\omega_e$ & $\omega_ex_e$ & $B_e$ & $\alpha_e$ \\ \hline \hline<br />
* \textbf{D$_2$} & 3118.4 & 64.09 & 30.429 & 1.0492 \\ \hline <br />
* \textbf{H$_2$} & 4395.2 & 117.99 & 60.800 & 2.993 \\ \hline<br />
* \end{tabular}<br />
* \end{center}<br />
* \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}.}<br />
* \label{table:appendix}<br />
* \end{table}<br />
<br />
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.<br />
<br />
You can also change the number of lines between columns (by adding or subtracting | around the r, l, and cs).<br />
<br />
In the actual data, & separate columns.<br />
<br />
The \hline command puts horizontal lines in the table.<br />
<br />
===Other Thoughts===<br />
* To get (red underline) spell-checking in TeXworks, go to Edit -> Spelling -> en_US.<br />
<br />
<br />
* 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.<br />
<br />
<br />
* I think it screws it up if you use spaces in your file names, so use underscores (_) instead.<br />
<br />
<br />
* Make sure all of your files are in one folder. (Sub-folders are ok.)<br />
<br />
<br />
* 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.</div>Jjweber3https://wiki.physics.wisc.edu/yavuz/index.php?title=Thesis_Template&diff=804Thesis Template2014-08-29T15:15:41Z<p>Jjweber3: /* Basic Commands */</p>
<hr />
<div>I (Josh) wrote, formatted, and edited my thesis using [http://www.tug.org/texworks/ 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 [http://grad.wisc.edu/currentstudents/degree/ Graduate School] in August, 2014, but you should probably check if there are any changes in the requirements.<br />
<br />
== Directions for Downloading Files and Compiling Josh's Thesis ==<br />
<br />
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.<br />
<br />
<br />
First, download the .tex documents:<br />
<br />
[[File:TeX_files.zip]]<br />
<br />
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.<br />
<br />
<br />
Next, download the reference files:<br />
<br />
[[File:Ref1.zip]]<br />
<br />
[[File:Ref2.zip]]<br />
<br />
[[File:Ref3.zip]]<br />
<br />
[[File:Ref4.zip]]<br />
<br />
Unzip this files, and put them all in one folder called "References" (this name DOES matter). Put "References" inside "Thesis" with the .tex files.<br />
<br />
<br />
Finally, download the figure files:<br />
<br />
[[File:Figs1.zip]]<br />
<br />
[[File:Figs2.zip]]<br />
<br />
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".<br />
<br />
== Overview of Files ==<br />
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.<br />
<br />
===thesis.tex===<br />
<br />
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.<br />
<br />
The real important part starts at line 112 (\begin{document}).<br />
<br />
I don't know what the \bibliographystyle thing is. I just left it how it was from Tyler's thesis.<br />
<br />
The next parts are where the other chapters are called. The command <br />
<br />
\include{CHAPTERNAME}<br />
<br />
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.<br />
<br />
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".)<br />
<br />
For keeping track of references, both for the thesis and in general, I recommend [http://www.mendeley.com 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.<br />
<br />
For appendices, it is the same as chapters, except you use the \include command between the commands \begin{appendices} and \end{appendices}.<br />
<br />
===myprelude.tex===<br />
<br />
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.<br />
<br />
There are lots of things you can change in this file. I'll only mention the ones that I changed.<br />
<br />
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.)<br />
<br />
You can edit the department (\department) if you're not in Physics, and you can enter your dedication and acknowledgements in those sections.<br />
<br />
The CONTENTS, TABLES, FIGURES section doesn't have to be edited. It automatically generates a table of contents and a list of figures.<br />
<br />
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}.)<br />
<br />
===Chapter .tex Files===<br />
<br />
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.)<br />
<br />
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.<br />
<br />
Each chapter starts out with the following line:<br />
<br />
\chapter{This Is The Full Chapter Title, and Spaces are OK Here}\label{ch:chapname}.<br />
<br />
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.)<br />
<br />
===Style (.sty) and Class (.cls) Files===<br />
<br />
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.<br />
<br />
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).<br />
<br />
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<br />
<br />
==General .tex Notes==<br />
<br />
===Basic Commands===<br />
<br />
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 [http://tex.stackexchange.com/ Stack Exchange]. Stack Exchange also has the answer to many other [http://scifi.stackexchange.com/questions/66661/exactly-how-secret-was-the-reveal-in-the-empire-strikes-back pressing] [http://scifi.stackexchange.com/questions/47085/who-made-the-decision-for-gandalfs-promotion-from-grey-to-white questions].<br />
<br />
That said, here are a few basic commands and other small tips that I found useful.<br />
<br />
<br />
* To cite a reference, use the command:<br />
<br />
\cite{Citation Key}<br />
<br />
where "Citation Key" is entered in Mendeley Reference manager. Mendeley's default citation key is "[AuthorLastName][YearofPublication]".<br />
<br />
<br />
* If you want text in italics, use:<br />
<br />
\textit{your text here}<br />
<br />
or for bold, use:<br />
<br />
\textbf{your text here}.<br />
<br />
<br />
* If you want to label something, use the command:<br />
<br />
\label{prefix:your_label}<br />
<br />
where "your_label" is whatever you want to use as your label. "prefix" indicates what you are labeling. Some common prefixes I used are:<br />
<br />
ch: for chapters<br />
sec: for sections<br />
subsec: for subsections<br />
fig: for figures<br />
table: for tables<br />
eq: for equations<br />
<br />
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.<br />
<br />
<br />
* For chapters, sections, and subsections, use the commands<br />
<br />
\chapter{Your Chapter Name}<br />
\section{Your Section Name}<br />
\subsection{Your Subsection Name}<br />
<br />
This will do the formatting for you.<br />
<br />
<br />
* 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.<br />
<br />
<br />
* To enter standalone equations, start them with \begin{equation}, enter the equation, and end it with \end{equation}. <br />
<br />
If you want it to be more than one line, do the same thing, but use "eqnarray" instead of "equation".<br />
<br />
The command \\ brings you to the next line of the equation in an equation array.<br />
<br />
The lines in equations and equation arrays are numbered automatically. Use \nonumber if you don't want a line numbered.<br />
<br />
<br />
* 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 [http://www.lyx.org/ 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.<br />
<br />
<br />
* 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<br />
<br />
\begin{eqnarray}<br />
x&=&y^2 \nonumber \\<br />
23x&=&z-903<br />
\label{eq:example}<br />
\end{eqnarray}<br />
<br />
(The first equation wouldn't be numbered here.)<br />
<br />
* 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}. <br />
<br />
<br />
*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.<br />
<br />
<br />
* For figures and tables, I would suggest just modifying existing code.<br />
<br />
Here's an example figure code:<br />
<br />
<br />
* \begin{figure}[h!]<br />
* \centering<br />
* \includegraphics[angle=0,width=3in]{figures/Josh/AOM.jpg}<br />
* \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.}<br />
* \label{fig:AOM}<br />
* \end{figure}<br />
<br />
<br />
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.<br />
<br />
<br />
Here's an example of a table (I put the bullets in so that the wiki wouldn't format this stuff.):<br />
<br />
<br />
* \begin{table}[h!]<br />
* \begin{center}<br />
* \begin{tabular}{ |c || c | c | c | c |}<br />
* \hline<br />
* Molecule & $\omega_e$ & $\omega_ex_e$ & $B_e$ & $\alpha_e$ \\ \hline \hline<br />
* \textbf{D$_2$} & 3118.4 & 64.09 & 30.429 & 1.0492 \\ \hline <br />
* \textbf{H$_2$} & 4395.2 & 117.99 & 60.800 & 2.993 \\ \hline<br />
* \end{tabular}<br />
* \end{center}<br />
* \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}.}<br />
* \label{table:appendix}<br />
* \end{table}<br />
<br />
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.<br />
<br />
You can also change the number of lines between columns (by adding or subtracting | around the r, l, and cs).<br />
<br />
In the actual data, & separate columns.<br />
<br />
The \hline command puts horizontal lines in the table.<br />
<br />
===Other Thoughts===<br />
* To get (red underline) spell-checking in TeXworks, go to Edit -> Spelling -> en_US.<br />
<br />
<br />
* 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.<br />
<br />
<br />
* I think it screws it up if you use spaces in your file names, so use underscores (_) instead.<br />
<br />
<br />
* Make sure all of your files are in one folder. (Sub-folders are ok.)<br />
<br />
<br />
* 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.</div>Jjweber3https://wiki.physics.wisc.edu/yavuz/index.php?title=Thesis_Template&diff=803Thesis Template2014-08-29T15:14:33Z<p>Jjweber3: </p>
<hr />
<div>I (Josh) wrote, formatted, and edited my thesis using [http://www.tug.org/texworks/ 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 [http://grad.wisc.edu/currentstudents/degree/ Graduate School] in August, 2014, but you should probably check if there are any changes in the requirements.<br />
<br />
== Directions for Downloading Files and Compiling Josh's Thesis ==<br />
<br />
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.<br />
<br />
<br />
First, download the .tex documents:<br />
<br />
[[File:TeX_files.zip]]<br />
<br />
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.<br />
<br />
<br />
Next, download the reference files:<br />
<br />
[[File:Ref1.zip]]<br />
<br />
[[File:Ref2.zip]]<br />
<br />
[[File:Ref3.zip]]<br />
<br />
[[File:Ref4.zip]]<br />
<br />
Unzip this files, and put them all in one folder called "References" (this name DOES matter). Put "References" inside "Thesis" with the .tex files.<br />
<br />
<br />
Finally, download the figure files:<br />
<br />
[[File:Figs1.zip]]<br />
<br />
[[File:Figs2.zip]]<br />
<br />
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".<br />
<br />
== Overview of Files ==<br />
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.<br />
<br />
===thesis.tex===<br />
<br />
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.<br />
<br />
The real important part starts at line 112 (\begin{document}).<br />
<br />
I don't know what the \bibliographystyle thing is. I just left it how it was from Tyler's thesis.<br />
<br />
The next parts are where the other chapters are called. The command <br />
<br />
\include{CHAPTERNAME}<br />
<br />
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.<br />
<br />
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".)<br />
<br />
For keeping track of references, both for the thesis and in general, I recommend [http://www.mendeley.com 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.<br />
<br />
For appendices, it is the same as chapters, except you use the \include command between the commands \begin{appendices} and \end{appendices}.<br />
<br />
===myprelude.tex===<br />
<br />
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.<br />
<br />
There are lots of things you can change in this file. I'll only mention the ones that I changed.<br />
<br />
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.)<br />
<br />
You can edit the department (\department) if you're not in Physics, and you can enter your dedication and acknowledgements in those sections.<br />
<br />
The CONTENTS, TABLES, FIGURES section doesn't have to be edited. It automatically generates a table of contents and a list of figures.<br />
<br />
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}.)<br />
<br />
===Chapter .tex Files===<br />
<br />
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.)<br />
<br />
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.<br />
<br />
Each chapter starts out with the following line:<br />
<br />
\chapter{This Is The Full Chapter Title, and Spaces are OK Here}\label{ch:chapname}.<br />
<br />
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.)<br />
<br />
===Style (.sty) and Class (.cls) Files===<br />
<br />
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.<br />
<br />
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).<br />
<br />
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<br />
<br />
==General .tex Notes==<br />
<br />
===Basic Commands===<br />
<br />
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 [http://tex.stackexchange.com/ Stack Exchange]. Stack Exchange also has the answer to many other [http://scifi.stackexchange.com/questions/66661/exactly-how-secret-was-the-reveal-in-the-empire-strikes-back pressing] [http://scifi.stackexchange.com/questions/47085/who-made-the-decision-for-gandalfs-promotion-from-grey-to-white questions].<br />
<br />
That said, here are a few basic commands and other small tips that I found useful.<br />
<br />
<br />
* To cite a reference, use the command:<br />
<br />
\cite{Citation Key}<br />
<br />
where "Citation Key" is entered in Mendeley Reference manager. Mendeley's default citation key is "[AuthorLastName][YearofPublication]".<br />
<br />
<br />
* If you want text in italics, use:<br />
<br />
\textit{your text here}<br />
<br />
or for bold, use:<br />
<br />
\textbf{your text here}.<br />
<br />
<br />
* If you want to label something, use the command:<br />
<br />
\label{prefix:your_label}<br />
<br />
where "your_label" is whatever you want to use as your label. "prefix" indicates what you are labeling. Some common prefixes I used are:<br />
<br />
ch: for chapters<br />
sec: for sections<br />
subsec: for subsections<br />
fig: for figures<br />
table: for tables<br />
eq: for equations<br />
<br />
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.<br />
<br />
<br />
* For chapters, sections, and subsections, use the commands<br />
<br />
\chapter{Your Chapter Name}<br />
\section{Your Section Name}<br />
\subsection{Your Subsection Name}<br />
<br />
This will do the formatting for you.<br />
<br />
<br />
* 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.<br />
<br />
<br />
* To enter standalone equations, start them with \begin{equation}, enter the equation, and end it with \end{equation}. <br />
<br />
If you want it to be more than one line, do the same thing, but use "eqnarray" instead of "equation".<br />
<br />
The command \\ brings you to the next line of the equation in an equation array.<br />
<br />
The lines in equations and equation arrays are numbered automatically. Use \nonumber if you don't want a line numbered.<br />
<br />
<br />
* 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 [http://www.lyx.org/ 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.<br />
<br />
<br />
* 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<br />
<br />
\begin{eqnarray}<br />
x&=&y^2 \nonumber \\<br />
23x&=&z-903<br />
\label{eq:example}<br />
\end{eqnarray}<br />
<br />
(The first equation wouldn't be numbered here.)<br />
<br />
* 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}. <br />
<br />
<br />
*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.<br />
<br />
<br />
* For figures and tables, I would suggest just modifying existing code.<br />
<br />
Here's an example figure code:<br />
<br />
<br />
\begin{figure}[h!]<br />
\centering<br />
\includegraphics[angle=0,width=3in]{figures/Josh/AOM.jpg}<br />
\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.}<br />
\label{fig:AOM}<br />
\end{figure}<br />
<br />
<br />
The only things I really ever changed was the width, the file name, the caption, and the label name.<br />
<br />
<br />
Here's an example of a table (I put the bullets in so that the wiki wouldn't format this stuff.):<br />
<br />
<br />
* \begin{table}[h!]<br />
* \begin{center}<br />
* \begin{tabular}{ |c || c | c | c | c |}<br />
* \hline<br />
* Molecule & $\omega_e$ & $\omega_ex_e$ & $B_e$ & $\alpha_e$ \\ \hline \hline<br />
* \textbf{D$_2$} & 3118.4 & 64.09 & 30.429 & 1.0492 \\ \hline <br />
* \textbf{H$_2$} & 4395.2 & 117.99 & 60.800 & 2.993 \\ \hline<br />
* \end{tabular}<br />
* \end{center}<br />
* \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}.}<br />
* \label{table:appendix}<br />
* \end{table}<br />
<br />
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.<br />
<br />
You can also change the number of lines between columns (by adding or subtracting | around the r, l, and cs).<br />
<br />
In the actual data, & separate columns.<br />
<br />
The \hline command puts horizontal lines in the table.<br />
<br />
<br />
===Other Thoughts===<br />
* To get (red underline) spell-checking in TeXworks, go to Edit -> Spelling -> en_US.<br />
<br />
<br />
* 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.<br />
<br />
<br />
* I think it screws it up if you use spaces in your file names, so use underscores (_) instead.<br />
<br />
<br />
* Make sure all of your files are in one folder. (Sub-folders are ok.)<br />
<br />
<br />
* 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.</div>Jjweber3https://wiki.physics.wisc.edu/yavuz/index.php?title=Thesis_Template&diff=802Thesis Template2014-08-29T15:14:03Z<p>Jjweber3: </p>
<hr />
<div>I (Josh) wrote, formatted, and edited my thesis using [http://www.tug.org/texworks/ 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 [http://grad.wisc.edu/currentstudents/degree/ Graduate School] in August, 2014, but you should probably check if there are any changes in the requirements.<br />
<br />
== Directions for Downloading Files and Compiling Josh's Thesis ==<br />
<br />
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.<br />
<br />
<br />
First, download the .tex documents:<br />
<br />
[[File:TeX_files.zip]]<br />
<br />
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.<br />
<br />
<br />
Next, download the reference files:<br />
<br />
[[File:Ref1.zip]]<br />
<br />
[[File:Ref2.zip]]<br />
<br />
[[File:Ref3.zip]]<br />
<br />
[[File:Ref4.zip]]<br />
<br />
Unzip this files, and put them all in one folder called "References" (this name DOES matter). Put "References" inside "Thesis" with the .tex files.<br />
<br />
<br />
Finally, download the figure files:<br />
<br />
[[File:Figs1.zip]]<br />
<br />
[[File:Figs2.zip]]<br />
<br />
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".<br />
<br />
== Overview of Files ==<br />
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.<br />
<br />
===thesis.tex===<br />
<br />
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.<br />
<br />
The real important part starts at line 112 (\begin{document}).<br />
<br />
I don't know what the \bibliographystyle thing is. I just left it how it was from Tyler's thesis.<br />
<br />
The next parts are where the other chapters are called. The command <br />
<br />
\include{CHAPTERNAME}<br />
<br />
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.<br />
<br />
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".)<br />
<br />
For keeping track of references, both for the thesis and in general, I recommend [http://www.mendeley.com 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.<br />
<br />
For appendices, it is the same as chapters, except you use the \include command between the commands \begin{appendices} and \end{appendices}.<br />
<br />
===myprelude.tex===<br />
<br />
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.<br />
<br />
There are lots of things you can change in this file. I'll only mention the ones that I changed.<br />
<br />
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.)<br />
<br />
You can edit the department (\department) if you're not in Physics, and you can enter your dedication and acknowledgements in those sections.<br />
<br />
The CONTENTS, TABLES, FIGURES section doesn't have to be edited. It automatically generates a table of contents and a list of figures.<br />
<br />
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}.)<br />
<br />
===Chapter .tex Files===<br />
<br />
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.)<br />
<br />
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.<br />
<br />
Each chapter starts out with the following line:<br />
<br />
\chapter{This Is The Full Chapter Title, and Spaces are OK Here}\label{ch:chapname}.<br />
<br />
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.)<br />
<br />
===Style (.sty) and Class (.cls) Files===<br />
<br />
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.<br />
<br />
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).<br />
<br />
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<br />
<br />
==General .tex Notes==<br />
<br />
===Basic Commands===<br />
<br />
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 [http://tex.stackexchange.com/ Stack Exchange]. Stack Exchange also has the answer to many other [http://scifi.stackexchange.com/questions/66661/exactly-how-secret-was-the-reveal-in-the-empire-strikes-back pressing] [http://scifi.stackexchange.com/questions/47085/who-made-the-decision-for-gandalfs-promotion-from-grey-to-white questions].<br />
<br />
That said, here are a few basic commands and other small tips that I found useful.<br />
<br />
<br />
* To cite a reference, use the command:<br />
<br />
\cite{Citation Key}<br />
<br />
where "Citation Key" is entered in Mendeley Reference manager. Mendeley's default citation key is "[AuthorLastName][YearofPublication]".<br />
<br />
<br />
* If you want text in italics, use:<br />
<br />
\textit{your text here}<br />
<br />
or for bold, use:<br />
<br />
\textbf{your text here}.<br />
<br />
<br />
* If you want to label something, use the command:<br />
<br />
\label{prefix:your_label}<br />
<br />
where "your_label" is whatever you want to use as your label. "prefix" indicates what you are labeling. Some common prefixes I used are:<br />
<br />
ch: for chapters<br />
sec: for sections<br />
subsec: for subsections<br />
fig: for figures<br />
table: for tables<br />
eq: for equations<br />
<br />
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.<br />
<br />
<br />
* For chapters, sections, and subsections, use the commands<br />
<br />
\chapter{Your Chapter Name}<br />
\section{Your Section Name}<br />
\subsection{Your Subsection Name}<br />
<br />
This will do the formatting for you.<br />
<br />
<br />
* 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.<br />
<br />
<br />
* To enter standalone equations, start them with \begin{equation}, enter the equation, and end it with \end{equation}. <br />
<br />
If you want it to be more than one line, do the same thing, but use "eqnarray" instead of "equation".<br />
<br />
The command \\ brings you to the next line of the equation in an equation array.<br />
<br />
The lines in equations and equation arrays are numbered automatically. Use \nonumber if you don't want a line numbered.<br />
<br />
<br />
* 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 [http://www.lyx.org/ 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.<br />
<br />
<br />
* 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<br />
<br />
\begin{eqnarray}<br />
x&=&y^2 \nonumber \\<br />
23x&=&z-903<br />
\label{eq:example}<br />
\end{eqnarray}<br />
<br />
(The first equation wouldn't be numbered here.)<br />
<br />
* 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}. <br />
<br />
<br />
*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.<br />
<br />
<br />
* For figures and tables, I would suggest just modifying existing code.<br />
<br />
Here's an example figure code:<br />
<br />
<br />
\begin{figure}[h!]<br />
\centering<br />
\includegraphics[angle=0,width=3in]{figures/Josh/AOM.jpg}<br />
\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.}<br />
\label{fig:AOM}<br />
\end{figure}<br />
<br />
<br />
The only things I really ever changed was the width, the file name, the caption, and the label name.<br />
<br />
<br />
Here's an example of a table (I put % in so that the wiki wouldn't format this stuff.):<br />
<br />
<br />
* \begin{table}[h!]<br />
* \begin{center}<br />
* \begin{tabular}{ |c || c | c | c | c |}<br />
* \hline<br />
* Molecule & $\omega_e$ & $\omega_ex_e$ & $B_e$ & $\alpha_e$ \\ \hline \hline<br />
* \textbf{D$_2$} & 3118.4 & 64.09 & 30.429 & 1.0492 \\ \hline <br />
* \textbf{H$_2$} & 4395.2 & 117.99 & 60.800 & 2.993 \\ \hline<br />
* \end{tabular}<br />
* \end{center}<br />
* \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}.}<br />
* \label{table:appendix}<br />
* \end{table}<br />
<br />
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.<br />
<br />
You can also change the number of lines between columns (by adding or subtracting | around the r, l, and cs).<br />
<br />
In the actual data, & separate columns.<br />
<br />
The \hline command puts horizontal lines in the table.<br />
<br />
<br />
===Other Thoughts===<br />
* To get (red underline) spell-checking in TeXworks, go to Edit -> Spelling -> en_US.<br />
<br />
<br />
* 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.<br />
<br />
<br />
* I think it screws it up if you use spaces in your file names, so use underscores (_) instead.<br />
<br />
<br />
* Make sure all of your files are in one folder. (Sub-folders are ok.)<br />
<br />
<br />
* 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.</div>Jjweber3https://wiki.physics.wisc.edu/yavuz/index.php?title=Thesis_Template&diff=801Thesis Template2014-08-29T15:13:01Z<p>Jjweber3: </p>
<hr />
<div>I (Josh) wrote, formatted, and edited my thesis using [http://www.tug.org/texworks/ 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 [http://grad.wisc.edu/currentstudents/degree/ Graduate School] in August, 2014, but you should probably check if there are any changes in the requirements.<br />
<br />
== Directions for Downloading Files and Compiling Josh's Thesis ==<br />
<br />
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.<br />
<br />
<br />
First, download the .tex documents:<br />
<br />
[[File:TeX_files.zip]]<br />
<br />
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.<br />
<br />
<br />
Next, download the reference files:<br />
<br />
[[File:Ref1.zip]]<br />
<br />
[[File:Ref2.zip]]<br />
<br />
[[File:Ref3.zip]]<br />
<br />
[[File:Ref4.zip]]<br />
<br />
Unzip this files, and put them all in one folder called "References" (this name DOES matter). Put "References" inside "Thesis" with the .tex files.<br />
<br />
<br />
Finally, download the figure files:<br />
<br />
[[File:Figs1.zip]]<br />
<br />
[[File:Figs2.zip]]<br />
<br />
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".<br />
<br />
== Overview of Files ==<br />
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.<br />
<br />
===thesis.tex===<br />
<br />
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.<br />
<br />
The real important part starts at line 112 (\begin{document}).<br />
<br />
I don't know what the \bibliographystyle thing is. I just left it how it was from Tyler's thesis.<br />
<br />
The next parts are where the other chapters are called. The command <br />
<br />
\include{CHAPTERNAME}<br />
<br />
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.<br />
<br />
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".)<br />
<br />
For keeping track of references, both for the thesis and in general, I recommend [http://www.mendeley.com 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.<br />
<br />
For appendices, it is the same as chapters, except you use the \include command between the commands \begin{appendices} and \end{appendices}.<br />
<br />
===myprelude.tex===<br />
<br />
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.<br />
<br />
There are lots of things you can change in this file. I'll only mention the ones that I changed.<br />
<br />
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.)<br />
<br />
You can edit the department (\department) if you're not in Physics, and you can enter your dedication and acknowledgements in those sections.<br />
<br />
The CONTENTS, TABLES, FIGURES section doesn't have to be edited. It automatically generates a table of contents and a list of figures.<br />
<br />
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}.)<br />
<br />
===Chapter .tex Files===<br />
<br />
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.)<br />
<br />
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.<br />
<br />
Each chapter starts out with the following line:<br />
<br />
\chapter{This Is The Full Chapter Title, and Spaces are OK Here}\label{ch:chapname}.<br />
<br />
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.)<br />
<br />
===Style (.sty) and Class (.cls) Files===<br />
<br />
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.<br />
<br />
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).<br />
<br />
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<br />
<br />
==General .tex Notes==<br />
<br />
===Basic Commands===<br />
<br />
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 [http://tex.stackexchange.com/ Stack Exchange]. Stack Exchange also has the answer to many other [http://scifi.stackexchange.com/questions/66661/exactly-how-secret-was-the-reveal-in-the-empire-strikes-back pressing] [http://scifi.stackexchange.com/questions/47085/who-made-the-decision-for-gandalfs-promotion-from-grey-to-white questions].<br />
<br />
That said, here are a few basic commands and other small tips that I found useful.<br />
<br />
<br />
* To cite a reference, use the command:<br />
<br />
\cite{Citation Key}<br />
<br />
where "Citation Key" is entered in Mendeley Reference manager. Mendeley's default citation key is "[AuthorLastName][YearofPublication]".<br />
<br />
<br />
* If you want text in italics, use:<br />
<br />
\textit{your text here}<br />
<br />
or for bold, use:<br />
<br />
\textbf{your text here}.<br />
<br />
<br />
* If you want to label something, use the command:<br />
<br />
\label{prefix:your_label}<br />
<br />
where "your_label" is whatever you want to use as your label. "prefix" indicates what you are labeling. Some common prefixes I used are:<br />
<br />
ch: for chapters<br />
sec: for sections<br />
subsec: for subsections<br />
fig: for figures<br />
table: for tables<br />
eq: for equations<br />
<br />
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.<br />
<br />
<br />
* For chapters, sections, and subsections, use the commands<br />
<br />
\chapter{Your Chapter Name}<br />
\section{Your Section Name}<br />
\subsection{Your Subsection Name}<br />
<br />
This will do the formatting for you.<br />
<br />
<br />
* 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.<br />
<br />
<br />
* To enter standalone equations, start them with \begin{equation}, enter the equation, and end it with \end{equation}. <br />
<br />
If you want it to be more than one line, do the same thing, but use "eqnarray" instead of "equation".<br />
<br />
The command \\ brings you to the next line of the equation in an equation array.<br />
<br />
The lines in equations and equation arrays are numbered automatically. Use \nonumber if you don't want a line numbered.<br />
<br />
<br />
* 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 [http://www.lyx.org/ 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.<br />
<br />
<br />
* 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<br />
<br />
\begin{eqnarray}<br />
x&=&y^2 \nonumber \\<br />
23x&=&z-903<br />
\label{eq:example}<br />
\end{eqnarray}<br />
<br />
(The first equation wouldn't be numbered here.)<br />
<br />
* 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}. <br />
<br />
<br />
*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.<br />
<br />
<br />
* For figures and tables, I would suggest just modifying existing code.<br />
<br />
Here's an example figure code:<br />
<br />
<br />
\begin{figure}[h!]<br />
\centering<br />
\includegraphics[angle=0,width=3in]{figures/Josh/AOM.jpg}<br />
\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.}<br />
\label{fig:AOM}<br />
\end{figure}<br />
<br />
<br />
The only things I really ever changed was the width, the file name, the caption, and the label name.<br />
<br />
<br />
Here's an example of a table (I put % in so that the wiki wouldn't format this stuff.):<br />
<br />
<br />
%\begin{table}[h!]<br />
%\begin{center}<br />
%\begin{tabular}{ |c || c | c | c | c |}<br />
%\hline<br />
%Molecule & $\omega_e$ & $\omega_ex_e$ & $B_e$ & $\alpha_e$ \\ \hline %\hline<br />
%\textbf{D$_2$} & 3118.4 & 64.09 & 30.429 & 1.0492 \\ \hline <br />
%\textbf{H$_2$} & 4395.2 & 117.99 & 60.800 & 2.993 \\ \hline<br />
%\end{tabular}<br />
%\end{center}<br />
%\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}.}<br />
%\label{table:appendix}<br />
%\end{table}<br />
<br />
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.<br />
<br />
You can also change the number of lines between columns (by adding or subtracting | around the r, l, and cs).<br />
<br />
In the actual data, & separate columns.<br />
<br />
The \hline command puts horizontal lines in the table.<br />
<br />
<br />
===Other Thoughts===<br />
* To get (red underline) spell-checking in TeXworks, go to Edit -> Spelling -> en_US.<br />
<br />
<br />
* 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.<br />
<br />
<br />
* I think it screws it up if you use spaces in your file names, so use underscores (_) instead.<br />
<br />
<br />
* Make sure all of your files are in one folder. (Sub-folders are ok.)<br />
<br />
<br />
* 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.</div>Jjweber3https://wiki.physics.wisc.edu/yavuz/index.php?title=Thesis_Template&diff=800Thesis Template2014-08-29T15:08:09Z<p>Jjweber3: /* General .tex Notes */</p>
<hr />
<div>I (Josh) wrote, formatted, and edited my thesis using [http://www.tug.org/texworks/ 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 [http://grad.wisc.edu/currentstudents/degree/ Graduate School] in August, 2014, but you should probably check if there are any changes in the requirements.<br />
<br />
== Directions for Downloading Files and Compiling Josh's Thesis ==<br />
<br />
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.<br />
<br />
<br />
First, download the .tex documents:<br />
<br />
[[File:TeX_files.zip]]<br />
<br />
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.<br />
<br />
<br />
Next, download the reference files:<br />
<br />
[[File:Ref1.zip]]<br />
<br />
[[File:Ref2.zip]]<br />
<br />
[[File:Ref3.zip]]<br />
<br />
[[File:Ref4.zip]]<br />
<br />
Unzip this files, and put them all in one folder called "References" (this name DOES matter). Put "References" inside "Thesis" with the .tex files.<br />
<br />
<br />
Finally, download the figure files:<br />
<br />
[[File:Figs1.zip]]<br />
<br />
[[File:Figs2.zip]]<br />
<br />
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".<br />
<br />
== Overview of Files ==<br />
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.<br />
<br />
===thesis.tex===<br />
<br />
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.<br />
<br />
The real important part starts at line 112 (\begin{document}).<br />
<br />
I don't know what the \bibliographystyle thing is. I just left it how it was from Tyler's thesis.<br />
<br />
The next parts are where the other chapters are called. The command <br />
<br />
\include{CHAPTERNAME}<br />
<br />
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.<br />
<br />
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".)<br />
<br />
For keeping track of references, both for the thesis and in general, I recommend [http://www.mendeley.com 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.<br />
<br />
For appendices, it is the same as chapters, except you use the \include command between the commands \begin{appendices} and \end{appendices}.<br />
<br />
===myprelude.tex===<br />
<br />
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.<br />
<br />
There are lots of things you can change in this file. I'll only mention the ones that I changed.<br />
<br />
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.)<br />
<br />
You can edit the department (\department) if you're not in Physics, and you can enter your dedication and acknowledgements in those sections.<br />
<br />
The CONTENTS, TABLES, FIGURES section doesn't have to be edited. It automatically generates a table of contents and a list of figures.<br />
<br />
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}.)<br />
<br />
===Chapter .tex Files===<br />
<br />
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.)<br />
<br />
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.<br />
<br />
Each chapter starts out with the following line:<br />
<br />
\chapter{This Is The Full Chapter Title, and Spaces are OK Here}\label{ch:chapname}.<br />
<br />
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.)<br />
<br />
===Style (.sty) and Class (.cls) Files===<br />
<br />
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.<br />
<br />
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).<br />
<br />
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<br />
<br />
==General .tex Notes==<br />
<br />
===Basic Commands===<br />
<br />
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 [http://tex.stackexchange.com/ Stack Exchange]. Stack Exchange also has the answer to many other [http://scifi.stackexchange.com/questions/66661/exactly-how-secret-was-the-reveal-in-the-empire-strikes-back pressing] [http://scifi.stackexchange.com/questions/47085/who-made-the-decision-for-gandalfs-promotion-from-grey-to-white questions].<br />
<br />
That said, here are a few basic commands and other small tips that I found useful.<br />
<br />
<br />
* To cite a reference, use the command:<br />
<br />
\cite{Citation Key}<br />
<br />
where "Citation Key" is entered in Mendeley Reference manager. Mendeley's default citation key is "[AuthorLastName][YearofPublication]".<br />
<br />
<br />
* If you want text in italics, use:<br />
<br />
\textit{your text here}<br />
<br />
or for bold, use:<br />
<br />
\textbf{your text here}.<br />
<br />
<br />
* If you want to label something, use the command:<br />
<br />
\label{prefix:your_label}<br />
<br />
where "your_label" is whatever you want to use as your label. "prefix" indicates what you are labeling. Some common prefixes I used are:<br />
<br />
ch: for chapters<br />
sec: for sections<br />
subsec: for subsections<br />
fig: for figures<br />
table: for tables<br />
eq: for equations<br />
<br />
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.<br />
<br />
<br />
* For chapters, sections, and subsections, use the commands<br />
<br />
\chapter{Your Chapter Name}<br />
\section{Your Section Name}<br />
\subsection{Your Subsection Name}<br />
<br />
This will do the formatting for you.<br />
<br />
<br />
* 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.<br />
<br />
<br />
* To enter standalone equations, start them with \begin{equation}, enter the equation, and end it with \end{equation}. <br />
<br />
If you want it to be more than one line, do the same thing, but use "eqnarray" instead of "equation".<br />
<br />
The command \\ brings you to the next line of the equation in an equation array.<br />
<br />
The lines in equations and equation arrays are numbered automatically. Use \nonumber if you don't want a line numbered.<br />
<br />
<br />
* 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 [http://www.lyx.org/ 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.<br />
<br />
<br />
* 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<br />
<br />
\begin{eqnarray}<br />
x&=&y^2 \nonumber \\<br />
23x&=&z-903<br />
\label{eq:example}<br />
\end{eqnarray}<br />
<br />
(The first equation wouldn't be numbered here.)<br />
<br />
* 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}. <br />
<br />
<br />
*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.<br />
<br />
<br />
* For figures and tables, I would suggest just modifying existing code.<br />
<br />
Here's an example figure code:<br />
<br />
<br />
\begin{figure}[h!]<br />
\centering<br />
\includegraphics[angle=0,width=3in]{figures/Josh/AOM.jpg}<br />
\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.}<br />
\label{fig:AOM}<br />
\end{figure}<br />
<br />
<br />
The only things I really ever changed was the width, the file name, the caption, and the label name.<br />
<br />
<br />
Here's an example of a table:<br />
<br />
<br />
\begin{table}[h!]<br />
\begin{center}<br />
\begin{tabular}{ |c || c | c | c | c |}<br />
\hline<br />
Molecule & $\omega_e$ & $\omega_ex_e$ & $B_e$ & $\alpha_e$ \\ \hline \hline<br />
\textbf{D$_2$} & 3118.4 & 64.09 & 30.429 & 1.0492 \\ \hline <br />
\textbf{H$_2$} & 4395.2 & 117.99 & 60.800 & 2.993 \\ \hline<br />
\end{tabular}<br />
\end{center}<br />
\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}.}<br />
\label{table:appendix}<br />
\end{table}<br />
<br />
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.<br />
<br />
You can also change the number of lines between columns (by adding or subtracting | around the r, l, and cs).<br />
<br />
In the actual data, & separate columns.<br />
<br />
The \hline command puts horizontal lines in the table.<br />
<br />
<br />
===Other Thoughts===<br />
* To get (red underline) spell-checking in TeXworks, go to Edit -> Spelling -> en_US.<br />
<br />
<br />
* 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.<br />
<br />
<br />
* I think it screws it up if you use spaces in your file names, so use underscores (_) instead.<br />
<br />
<br />
* Make sure all of your files are in one folder. (Sub-folders are ok.)<br />
<br />
<br />
* 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.</div>Jjweber3https://wiki.physics.wisc.edu/yavuz/index.php?title=Thesis_Template&diff=799Thesis Template2014-08-29T14:30:49Z<p>Jjweber3: </p>
<hr />
<div>I (Josh) wrote, formatted, and edited my thesis using [http://www.tug.org/texworks/ 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 [http://grad.wisc.edu/currentstudents/degree/ Graduate School] in August, 2014, but you should probably check if there are any changes in the requirements.<br />
<br />
== Directions for Downloading Files and Compiling Josh's Thesis ==<br />
<br />
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.<br />
<br />
<br />
First, download the .tex documents:<br />
<br />
[[File:TeX_files.zip]]<br />
<br />
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.<br />
<br />
<br />
Next, download the reference files:<br />
<br />
[[File:Ref1.zip]]<br />
<br />
[[File:Ref2.zip]]<br />
<br />
[[File:Ref3.zip]]<br />
<br />
[[File:Ref4.zip]]<br />
<br />
Unzip this files, and put them all in one folder called "References" (this name DOES matter). Put "References" inside "Thesis" with the .tex files.<br />
<br />
<br />
Finally, download the figure files:<br />
<br />
[[File:Figs1.zip]]<br />
<br />
[[File:Figs2.zip]]<br />
<br />
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".<br />
<br />
== Overview of Files ==<br />
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.<br />
<br />
===thesis.tex===<br />
<br />
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.<br />
<br />
The real important part starts at line 112 (\begin{document}).<br />
<br />
I don't know what the \bibliographystyle thing is. I just left it how it was from Tyler's thesis.<br />
<br />
The next parts are where the other chapters are called. The command <br />
<br />
\include{CHAPTERNAME}<br />
<br />
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.<br />
<br />
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".)<br />
<br />
For keeping track of references, both for the thesis and in general, I recommend [http://www.mendeley.com 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.<br />
<br />
For appendices, it is the same as chapters, except you use the \include command between the commands \begin{appendices} and \end{appendices}.<br />
<br />
===myprelude.tex===<br />
<br />
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.<br />
<br />
There are lots of things you can change in this file. I'll only mention the ones that I changed.<br />
<br />
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.)<br />
<br />
You can edit the department (\department) if you're not in Physics, and you can enter your dedication and acknowledgements in those sections.<br />
<br />
The CONTENTS, TABLES, FIGURES section doesn't have to be edited. It automatically generates a table of contents and a list of figures.<br />
<br />
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}.)<br />
<br />
===Chapter .tex Files===<br />
<br />
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.)<br />
<br />
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.<br />
<br />
Each chapter starts out with the following line:<br />
<br />
\chapter{This Is The Full Chapter Title, and Spaces are OK Here}\label{ch:chapname}.<br />
<br />
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.)<br />
<br />
===Style (.sty) and Class (.cls) Files===<br />
<br />
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.<br />
<br />
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).<br />
<br />
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<br />
<br />
==General .tex Notes==<br />
<br />
===Basic Commands===<br />
<br />
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 [http://tex.stackexchange.com/ Stack Exchange]. Stack Exchange also has the answer to many other [http://scifi.stackexchange.com/questions/66661/exactly-how-secret-was-the-reveal-in-the-empire-strikes-back pressing] [http://scifi.stackexchange.com/questions/47085/who-made-the-decision-for-gandalfs-promotion-from-grey-to-white questions].<br />
<br />
That said, here are a few basic commands and other small tips that I found useful.<br />
<br />
* To cite a reference, use the command:<br />
<br />
\cite{Citation Key}<br />
<br />
where "Citation Key" is entered in Mendeley Reference manager. Mendeley's default citation key is "[AuthorLastName][YearofPublication]".<br />
<br />
* If you want text in italics, use:<br />
<br />
\textit{your text here}<br />
<br />
or for bold, use:<br />
<br />
\textbf{your text here}.<br />
<br />
* If you want to label something, use the command:<br />
<br />
\label{prefix:your_label}<br />
<br />
where "your_label" is whatever you want to use as your label. "prefix" indicates what you are labeling. Some common prefixes I used are:<br />
<br />
ch: for chapters<br />
sec: for sections<br />
subsec: for subsections<br />
fig: for figures<br />
table: for tables<br />
eq: for equations<br />
<br />
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.<br />
<br />
For chapters, sections, and subsections, use the commands<br />
<br />
\chapter{Your Chapter Name}<br />
\section{Your Section Name}<br />
\subsection{Your Subsection Name}<br />
<br />
This will do the formatting for you.<br />
<br />
\begin{equation, eqnarray}<br />
\vspace<br />
\! between letters<br />
\text{<br />
<br />
===Other Thoughts===<br />
* To get (red underline) spell-checking in TeXworks, go to Edit -> Spelling -> en_US.<br />
<br />
* 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.<br />
<br />
* I think it screws it up if you use spaces in your file names, so use underscores (_) instead.<br />
<br />
* Make sure all of your files are in one folder. (Sub-folders are ok.)<br />
<br />
* 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.</div>Jjweber3https://wiki.physics.wisc.edu/yavuz/index.php?title=Thesis_Template&diff=798Thesis Template2014-08-29T14:18:34Z<p>Jjweber3: </p>
<hr />
<div>I (Josh) wrote, formatted, and edited my thesis using [http://www.tug.org/texworks/ 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 [http://grad.wisc.edu/currentstudents/degree/ Graduate School] in August, 2014, but you should probably check if there are any changes in the requirements.<br />
<br />
== Directions for Downloading Files and Compiling Josh's Thesis ==<br />
<br />
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.<br />
<br />
<br />
First, download the .tex documents:<br />
<br />
[[File:TeX_files.zip]]<br />
<br />
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.<br />
<br />
<br />
Next, download the reference files:<br />
<br />
[[File:Ref1.zip]]<br />
<br />
[[File:Ref2.zip]]<br />
<br />
[[File:Ref3.zip]]<br />
<br />
[[File:Ref4.zip]]<br />
<br />
Unzip this files, and put them all in one folder called "References" (this name DOES matter). Put "References" inside "Thesis" with the .tex files.<br />
<br />
<br />
Finally, download the figure files:<br />
<br />
[[File:Figs1.zip]]<br />
<br />
[[File:Figs2.zip]]<br />
<br />
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".<br />
<br />
== Overview of Files ==<br />
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.<br />
<br />
===thesis.tex===<br />
<br />
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.<br />
<br />
The real important part starts at line 112 (\begin{document}).<br />
<br />
I don't know what the \bibliographystyle thing is. I just left it how it was from Tyler's thesis.<br />
<br />
The next parts are where the other chapters are called. The command <br />
<br />
\include{CHAPTERNAME}<br />
<br />
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.<br />
<br />
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".)<br />
<br />
For keeping track of references, both for the thesis and in general, I recommend [http://www.mendeley.com 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.<br />
<br />
For appendices, it is the same as chapters, except you use the \include command between the commands \begin{appendices} and \end{appendices}.<br />
<br />
===myprelude.tex===<br />
<br />
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.<br />
<br />
There are lots of things you can change in this file. I'll only mention the ones that I changed.<br />
<br />
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.)<br />
<br />
You can edit the department (\department) if you're not in Physics, and you can enter your dedication and acknowledgements in those sections.<br />
<br />
The CONTENTS, TABLES, FIGURES section doesn't have to be edited. It automatically generates a table of contents and a list of figures.<br />
<br />
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}.)<br />
<br />
===Chapter .tex Files===<br />
<br />
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.)<br />
<br />
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.<br />
<br />
Each chapter starts out with the following line:<br />
<br />
\chapter{This Is The Full Chapter Title, and Spaces are OK Here}\label{ch:chapname}.<br />
<br />
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.)<br />
<br />
===Style (.sty) and Class (.cls) Files===<br />
<br />
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.<br />
<br />
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).<br />
<br />
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<br />
<br />
==General .tex Notes==<br />
<br />
===Basic Commands===<br />
<br />
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 [http://tex.stackexchange.com/ Stack Exchange]. Stack Exchange also has the answer to many other [http://scifi.stackexchange.com/questions/66661/exactly-how-secret-was-the-reveal-in-the-empire-strikes-back pressing] [http://scifi.stackexchange.com/questions/47085/who-made-the-decision-for-gandalfs-promotion-from-grey-to-white questions].<br />
<br />
That said, here are a few basic commands and other small tips that I found useful.<br />
<br />
* To cite a reference, use the command:<br />
<br />
\cite{Citation Key}<br />
<br />
where "Citation Key" is entered in Mendeley Reference manager. Mendeley's default citation key is "[AuthorLastName][YearofPublication]".<br />
<br />
\label{}<br />
\ref{}<br />
\begin{equation, eqnarray}<br />
\vspace<br />
\! between letters<br />
\textit{<br />
\text{<br />
<br />
===Other Thoughts===<br />
* To get (red underline) spell-checking in TeXworks, go to Edit -> Spelling -> en_US.<br />
<br />
* 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.<br />
<br />
* I think it screws it up if you use spaces in your file names, so use underscores (_) instead.<br />
<br />
* Make sure all of your files are in one folder. (Sub-folders are ok.)<br />
<br />
* 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.</div>Jjweber3https://wiki.physics.wisc.edu/yavuz/index.php?title=Thesis_Template&diff=797Thesis Template2014-08-29T14:12:59Z<p>Jjweber3: </p>
<hr />
<div>I (Josh) wrote, formatted, and edited my thesis using [http://www.tug.org/texworks/ 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 [http://grad.wisc.edu/currentstudents/degree/ Graduate School] in August, 2014, but you should probably check if there are any changes in the requirements.<br />
<br />
== Directions for Downloading Files and Compiling Josh's Thesis ==<br />
<br />
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.<br />
<br />
<br />
First, download the .tex documents:<br />
<br />
[[File:TeX_files.zip]]<br />
<br />
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.<br />
<br />
<br />
Next, download the reference files:<br />
<br />
[[File:Ref1.zip]]<br />
<br />
[[File:Ref2.zip]]<br />
<br />
[[File:Ref3.zip]]<br />
<br />
[[File:Ref4.zip]]<br />
<br />
Unzip this files, and put them all in one folder called "References" (this name DOES matter). Put "References" inside "Thesis" with the .tex files.<br />
<br />
<br />
Finally, download the figure files:<br />
<br />
[[File:Figs1.zip]]<br />
<br />
[[File:Figs2.zip]]<br />
<br />
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".<br />
<br />
== Overview of Files ==<br />
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.<br />
<br />
===thesis.tex===<br />
<br />
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.<br />
<br />
The real important part starts at line 112 (\begin{document}).<br />
<br />
I don't know what the \bibliographystyle thing is. I just left it how it was from Tyler's thesis.<br />
<br />
The next parts are where the other chapters are called. The command <br />
<br />
\include{CHAPTERNAME}<br />
<br />
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.<br />
<br />
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".)<br />
<br />
For keeping track of references, both for the thesis and in general, I recommend [http://www.mendeley.com 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.<br />
<br />
For appendices, it is the same as chapters, except you use the \include command between the commands \begin{appendices} and \end{appendices}.<br />
<br />
===myprelude.tex===<br />
<br />
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.<br />
<br />
There are lots of things you can change in this file. I'll only mention the ones that I changed.<br />
<br />
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.)<br />
<br />
You can edit the department (\department) if you're not in Physics, and you can enter your dedication and acknowledgements in those sections.<br />
<br />
The CONTENTS, TABLES, FIGURES section doesn't have to be edited. It automatically generates a table of contents and a list of figures.<br />
<br />
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}.)<br />
<br />
===Chapter .tex Files===<br />
<br />
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.)<br />
<br />
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.<br />
<br />
Each chapter starts out with the following line:<br />
<br />
\chapter{This Is The Full Chapter Title, and Spaces are OK Here}\label{ch:chapname}.<br />
<br />
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.)<br />
<br />
===Style (.sty) and Class (.cls) Files===<br />
<br />
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.<br />
<br />
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).<br />
<br />
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<br />
<br />
==General .tex Notes==<br />
<br />
===Basic Commands===<br />
<br />
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 [http://tex.stackexchange.com/ Stack Exchange]. Stack Exchange also has the answer to many other [http://scifi.stackexchange.com/questions/66661/exactly-how-secret-was-the-reveal-in-the-empire-strikes-back pressing] [http://scifi.stackexchange.com/questions/47085/who-made-the-decision-for-gandalfs-promotion-from-grey-to-white questions].<br />
<br />
That said, here are a few basic commands and other small tips that I found useful.<br />
<br />
\cite{}<br />
\label{}<br />
\ref{}<br />
\begin{equation, eqnarray}<br />
\vspace<br />
! between letters<br />
\textit{<br />
\text{<br />
<br />
===Other Thoughts===<br />
To get (red underline) spell-checking in TeXworks, go to Edit -> Spelling -> en_US.<br />
<br />
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.<br />
<br />
I think it screws it up if you use spaces in your file names, so use underscores (_) instead.<br />
<br />
Make sure all of your files are in one folder. (Sub-folders are ok.)<br />
<br />
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.</div>Jjweber3https://wiki.physics.wisc.edu/yavuz/index.php?title=Thesis_Template&diff=796Thesis Template2014-08-29T01:18:41Z<p>Jjweber3: /* Directions for Downloading Files and Compiling Josh's Thesis */</p>
<hr />
<div>I (Josh) wrote, formatted, and edited my thesis using [http://www.tug.org/texworks/ 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 [http://grad.wisc.edu/currentstudents/degree/ Graduate School] in August, 2014, but you should probably check if there are any changes in the requirements.<br />
<br />
== Directions for Downloading Files and Compiling Josh's Thesis ==<br />
<br />
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.<br />
<br />
<br />
First, download the .tex documents:<br />
<br />
[[File:TeX_files.zip]]<br />
<br />
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.<br />
<br />
<br />
Next, download the reference files:<br />
<br />
[[File:Ref1.zip]]<br />
<br />
[[File:Ref2.zip]]<br />
<br />
[[File:Ref3.zip]]<br />
<br />
[[File:Ref4.zip]]<br />
<br />
Unzip this files, and put them all in one folder called "References" (this name DOES matter). Put "References" inside "Thesis" with the .tex files.<br />
<br />
<br />
Finally, download the figure files:<br />
<br />
[[File:Figs1.zip]]<br />
<br />
[[File:Figs2.zip]]<br />
<br />
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".<br />
<br />
== Overview of Files ==<br />
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.<br />
<br />
===thesis.tex===<br />
<br />
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.<br />
<br />
The real important part starts at line 112 (\begin{document}).<br />
<br />
I don't know what the \bibliographystyle thing is. I just left it how it was from Tyler's thesis.<br />
<br />
The next parts are where the other chapters are called. The command <br />
<br />
\include{CHAPTERNAME}<br />
<br />
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.<br />
<br />
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".)<br />
<br />
For keeping track of references, both for the thesis and in general, I recommend [http://www.mendeley.com 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.<br />
<br />
For appendices, it is the same as chapters, except you use the \include command between the commands \begin{appendices} and \end{appendices}.<br />
<br />
===myprelude.tex===<br />
<br />
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.<br />
<br />
There are lots of things you can change in this file. I'll only mention the ones that I changed.<br />
<br />
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.)<br />
<br />
You can edit the department (\department) if you're not in Physics, and you can enter your dedication and acknowledgements in those sections.<br />
<br />
The CONTENTS, TABLES, FIGURES section doesn't have to be edited. It automatically generates a table of contents and a list of figures.<br />
<br />
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}.)<br />
<br />
===Chapter .tex Files===<br />
<br />
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.)<br />
<br />
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.<br />
<br />
Each chapter starts out with the following line:<br />
<br />
\chapter{This Is The Full Chapter Title, and Spaces are OK Here}\label{ch:chapname}.<br />
<br />
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.)<br />
<br />
===Style (.sty) and Class (.cls) Files===<br />
<br />
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.<br />
<br />
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).<br />
<br />
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<br />
<br />
==General .tex Notes==<br />
<br />
===Basic Commands===<br />
<br />
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 [http://tex.stackexchange.com/ Stack Exchange]. Stack Exchange also has the answer to many other [http://scifi.stackexchange.com/questions/66661/exactly-how-secret-was-the-reveal-in-the-empire-strikes-back pressing] [http://scifi.stackexchange.com/questions/47085/who-made-the-decision-for-gandalfs-promotion-from-grey-to-white questions].<br />
<br />
That said, here are a few basic commands and other small tips that I found useful.<br />
<br />
\cite{}<br />
\label{}<br />
\ref{}<br />
\begin{equation, eqnarray}<br />
\vspace<br />
! between letters<br />
\textit{<br />
\text{<br />
<br />
===Other Thoughts===<br />
spelling<br />
<br />
talk about figures, tables<br />
<br />
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.<br />
<br />
I think it screws it up if you use spaces in your file names, so use underscores (_) instead.<br />
<br />
<br />
other zip files - for alternative formats</div>Jjweber3https://wiki.physics.wisc.edu/yavuz/index.php?title=Thesis_Template&diff=795Thesis Template2014-08-29T01:16:55Z<p>Jjweber3: /* Directions for Downloading Files and Compiling Josh's Thesis */</p>
<hr />
<div>I (Josh) wrote, formatted, and edited my thesis using [http://www.tug.org/texworks/ 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 [http://grad.wisc.edu/currentstudents/degree/ Graduate School] in August, 2014, but you should probably check if there are any changes in the requirements.<br />
<br />
== Directions for Downloading Files and Compiling Josh's Thesis ==<br />
<br />
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.<br />
<br />
<br />
First, download the .tex documents:<br />
<br />
[[File:TeX_files.zip]]<br />
<br />
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.<br />
<br />
<br />
Next, download the reference files:<br />
<br />
[[File:Ref1.zip]]<br />
<br />
[[File:Ref2.zip]]<br />
<br />
[[File:Ref3.zip]]<br />
<br />
[[File:Ref4.zip]]<br />
<br />
Unzip this files, and put them all in one folder called "References" (this name DOES matter). Put "References" inside "Thesis" with the .tex files.<br />
<br />
<br />
Finally, download the figure files:<br />
<br />
[[File:Figs1.zip]]<br />
<br />
[[File:Figs2.zip]]<br />
<br />
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".<br />
<br />
== Overview of Files ==<br />
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.<br />
<br />
===thesis.tex===<br />
<br />
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.<br />
<br />
The real important part starts at line 112 (\begin{document}).<br />
<br />
I don't know what the \bibliographystyle thing is. I just left it how it was from Tyler's thesis.<br />
<br />
The next parts are where the other chapters are called. The command <br />
<br />
\include{CHAPTERNAME}<br />
<br />
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.<br />
<br />
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".)<br />
<br />
For keeping track of references, both for the thesis and in general, I recommend [http://www.mendeley.com 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.<br />
<br />
For appendices, it is the same as chapters, except you use the \include command between the commands \begin{appendices} and \end{appendices}.<br />
<br />
===myprelude.tex===<br />
<br />
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.<br />
<br />
There are lots of things you can change in this file. I'll only mention the ones that I changed.<br />
<br />
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.)<br />
<br />
You can edit the department (\department) if you're not in Physics, and you can enter your dedication and acknowledgements in those sections.<br />
<br />
The CONTENTS, TABLES, FIGURES section doesn't have to be edited. It automatically generates a table of contents and a list of figures.<br />
<br />
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}.)<br />
<br />
===Chapter .tex Files===<br />
<br />
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.)<br />
<br />
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.<br />
<br />
Each chapter starts out with the following line:<br />
<br />
\chapter{This Is The Full Chapter Title, and Spaces are OK Here}\label{ch:chapname}.<br />
<br />
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.)<br />
<br />
===Style (.sty) and Class (.cls) Files===<br />
<br />
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.<br />
<br />
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).<br />
<br />
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<br />
<br />
==General .tex Notes==<br />
<br />
===Basic Commands===<br />
<br />
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 [http://tex.stackexchange.com/ Stack Exchange]. Stack Exchange also has the answer to many other [http://scifi.stackexchange.com/questions/66661/exactly-how-secret-was-the-reveal-in-the-empire-strikes-back pressing] [http://scifi.stackexchange.com/questions/47085/who-made-the-decision-for-gandalfs-promotion-from-grey-to-white questions].<br />
<br />
That said, here are a few basic commands and other small tips that I found useful.<br />
<br />
\cite{}<br />
\label{}<br />
\ref{}<br />
\begin{equation, eqnarray}<br />
\vspace<br />
! between letters<br />
\textit{<br />
\text{<br />
<br />
===Other Thoughts===<br />
spelling<br />
<br />
talk about figures, tables<br />
<br />
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.<br />
<br />
I think it screws it up if you use spaces in your file names, so use underscores (_) instead.<br />
<br />
<br />
other zip files - for alternative formats</div>Jjweber3https://wiki.physics.wisc.edu/yavuz/index.php?title=Thesis_Template&diff=794Thesis Template2014-08-29T01:16:36Z<p>Jjweber3: /* Directions for Downloading Files and Compiling Josh's Thesis */</p>
<hr />
<div>I (Josh) wrote, formatted, and edited my thesis using [http://www.tug.org/texworks/ 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 [http://grad.wisc.edu/currentstudents/degree/ Graduate School] in August, 2014, but you should probably check if there are any changes in the requirements.<br />
<br />
== Directions for Downloading Files and Compiling Josh's Thesis ==<br />
<br />
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.<br />
<br />
First, download the .tex documents:<br />
<br />
[[File:TeX_files.zip]]<br />
<br />
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.<br />
<br />
Next, download the reference files:<br />
<br />
[[File:Ref1.zip]]<br />
<br />
[[File:Ref2.zip]]<br />
<br />
[[File:Ref3.zip]]<br />
<br />
[[File:Ref4.zip]]<br />
<br />
Unzip this files, and put them all in one folder called "References" (this name DOES matter). Put "References" inside "Thesis" with the .tex files.<br />
<br />
Finally, download the figure files:<br />
<br />
[[File:Figs1.zip]]<br />
<br />
[[File:Figs2.zip]]<br />
<br />
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".<br />
<br />
== Overview of Files ==<br />
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.<br />
<br />
===thesis.tex===<br />
<br />
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.<br />
<br />
The real important part starts at line 112 (\begin{document}).<br />
<br />
I don't know what the \bibliographystyle thing is. I just left it how it was from Tyler's thesis.<br />
<br />
The next parts are where the other chapters are called. The command <br />
<br />
\include{CHAPTERNAME}<br />
<br />
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.<br />
<br />
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".)<br />
<br />
For keeping track of references, both for the thesis and in general, I recommend [http://www.mendeley.com 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.<br />
<br />
For appendices, it is the same as chapters, except you use the \include command between the commands \begin{appendices} and \end{appendices}.<br />
<br />
===myprelude.tex===<br />
<br />
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.<br />
<br />
There are lots of things you can change in this file. I'll only mention the ones that I changed.<br />
<br />
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.)<br />
<br />
You can edit the department (\department) if you're not in Physics, and you can enter your dedication and acknowledgements in those sections.<br />
<br />
The CONTENTS, TABLES, FIGURES section doesn't have to be edited. It automatically generates a table of contents and a list of figures.<br />
<br />
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}.)<br />
<br />
===Chapter .tex Files===<br />
<br />
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.)<br />
<br />
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.<br />
<br />
Each chapter starts out with the following line:<br />
<br />
\chapter{This Is The Full Chapter Title, and Spaces are OK Here}\label{ch:chapname}.<br />
<br />
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.)<br />
<br />
===Style (.sty) and Class (.cls) Files===<br />
<br />
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.<br />
<br />
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).<br />
<br />
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<br />
<br />
==General .tex Notes==<br />
<br />
===Basic Commands===<br />
<br />
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 [http://tex.stackexchange.com/ Stack Exchange]. Stack Exchange also has the answer to many other [http://scifi.stackexchange.com/questions/66661/exactly-how-secret-was-the-reveal-in-the-empire-strikes-back pressing] [http://scifi.stackexchange.com/questions/47085/who-made-the-decision-for-gandalfs-promotion-from-grey-to-white questions].<br />
<br />
That said, here are a few basic commands and other small tips that I found useful.<br />
<br />
\cite{}<br />
\label{}<br />
\ref{}<br />
\begin{equation, eqnarray}<br />
\vspace<br />
! between letters<br />
\textit{<br />
\text{<br />
<br />
===Other Thoughts===<br />
spelling<br />
<br />
talk about figures, tables<br />
<br />
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.<br />
<br />
I think it screws it up if you use spaces in your file names, so use underscores (_) instead.<br />
<br />
<br />
other zip files - for alternative formats</div>Jjweber3https://wiki.physics.wisc.edu/yavuz/index.php?title=Thesis_Template&diff=793Thesis Template2014-08-29T01:15:43Z<p>Jjweber3: </p>
<hr />
<div>I (Josh) wrote, formatted, and edited my thesis using [http://www.tug.org/texworks/ 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 [http://grad.wisc.edu/currentstudents/degree/ Graduate School] in August, 2014, but you should probably check if there are any changes in the requirements.<br />
<br />
== Directions for Downloading Files and Compiling Josh's Thesis ==<br />
<br />
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.<br />
<br />
First, download the .tex documents:<br />
<br />
[[File:TeX_files.zip]]<br />
<br />
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.<br />
<br />
Next, download the reference files:<br />
<br />
[[File:Ref1.zip]]<br />
<br />
[[File:Ref2.zip]]<br />
<br />
[[File:Ref3.zip]]<br />
<br />
[[File:Ref4.zip]]<br />
<br />
Unzip this files, and put them all in one folder called "References" (this name DOES matter). Put "References" inside "Thesis" with the .tex files.<br />
<br />
Finally, download the figure files:<br />
<br />
[[File:Figs1.zip]]<br />
<br />
[[File:Figs2.zip]]<br />
<br />
Unzip these files, and save them in a new folder called "Josh". Then, put "Josh" inside another folder called "figures". (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".<br />
<br />
== Overview of Files ==<br />
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.<br />
<br />
===thesis.tex===<br />
<br />
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.<br />
<br />
The real important part starts at line 112 (\begin{document}).<br />
<br />
I don't know what the \bibliographystyle thing is. I just left it how it was from Tyler's thesis.<br />
<br />
The next parts are where the other chapters are called. The command <br />
<br />
\include{CHAPTERNAME}<br />
<br />
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.<br />
<br />
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".)<br />
<br />
For keeping track of references, both for the thesis and in general, I recommend [http://www.mendeley.com 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.<br />
<br />
For appendices, it is the same as chapters, except you use the \include command between the commands \begin{appendices} and \end{appendices}.<br />
<br />
===myprelude.tex===<br />
<br />
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.<br />
<br />
There are lots of things you can change in this file. I'll only mention the ones that I changed.<br />
<br />
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.)<br />
<br />
You can edit the department (\department) if you're not in Physics, and you can enter your dedication and acknowledgements in those sections.<br />
<br />
The CONTENTS, TABLES, FIGURES section doesn't have to be edited. It automatically generates a table of contents and a list of figures.<br />
<br />
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}.)<br />
<br />
===Chapter .tex Files===<br />
<br />
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.)<br />
<br />
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.<br />
<br />
Each chapter starts out with the following line:<br />
<br />
\chapter{This Is The Full Chapter Title, and Spaces are OK Here}\label{ch:chapname}.<br />
<br />
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.)<br />
<br />
===Style (.sty) and Class (.cls) Files===<br />
<br />
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.<br />
<br />
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).<br />
<br />
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<br />
<br />
==General .tex Notes==<br />
<br />
===Basic Commands===<br />
<br />
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 [http://tex.stackexchange.com/ Stack Exchange]. Stack Exchange also has the answer to many other [http://scifi.stackexchange.com/questions/66661/exactly-how-secret-was-the-reveal-in-the-empire-strikes-back pressing] [http://scifi.stackexchange.com/questions/47085/who-made-the-decision-for-gandalfs-promotion-from-grey-to-white questions].<br />
<br />
That said, here are a few basic commands and other small tips that I found useful.<br />
<br />
\cite{}<br />
\label{}<br />
\ref{}<br />
\begin{equation, eqnarray}<br />
\vspace<br />
! between letters<br />
\textit{<br />
\text{<br />
<br />
===Other Thoughts===<br />
spelling<br />
<br />
talk about figures, tables<br />
<br />
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.<br />
<br />
I think it screws it up if you use spaces in your file names, so use underscores (_) instead.<br />
<br />
<br />
other zip files - for alternative formats</div>Jjweber3https://wiki.physics.wisc.edu/yavuz/index.php?title=Thesis_Template&diff=792Thesis Template2014-08-29T01:14:50Z<p>Jjweber3: </p>
<hr />
<div>I (Josh) wrote, formatted, and edited my thesis using [http://www.tug.org/texworks/ 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 [http://grad.wisc.edu/currentstudents/degree/ Graduate School] in August, 2014, but you should probably check if there are any changes in the requirements.<br />
<br />
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.<br />
<br />
First, download the .tex documents:<br />
<br />
[[File:TeX_files.zip]]<br />
<br />
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.<br />
<br />
Next, download the reference files:<br />
<br />
[[File:Ref1.zip]]<br />
<br />
[[File:Ref2.zip]]<br />
<br />
[[File:Ref3.zip]]<br />
<br />
[[File:Ref4.zip]]<br />
<br />
Unzip this files, and put them all in one folder called "References" (this name DOES matter). Put "References" inside "Thesis" with the .tex files.<br />
<br />
Finally, download the figure files:<br />
<br />
[[File:Figs1.zip]]<br />
<br />
[[File:Figs2.zip]]<br />
<br />
Unzip these files, and save them in a new folder called "Josh". Then, put "Josh" inside another folder called "figures". (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".<br />
<br />
<br />
== Overview of Files ==<br />
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.<br />
<br />
===thesis.tex===<br />
<br />
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.<br />
<br />
The real important part starts at line 112 (\begin{document}).<br />
<br />
I don't know what the \bibliographystyle thing is. I just left it how it was from Tyler's thesis.<br />
<br />
The next parts are where the other chapters are called. The command <br />
<br />
\include{CHAPTERNAME}<br />
<br />
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.<br />
<br />
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".)<br />
<br />
For keeping track of references, both for the thesis and in general, I recommend [http://www.mendeley.com 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.<br />
<br />
For appendices, it is the same as chapters, except you use the \include command between the commands \begin{appendices} and \end{appendices}.<br />
<br />
===myprelude.tex===<br />
<br />
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.<br />
<br />
There are lots of things you can change in this file. I'll only mention the ones that I changed.<br />
<br />
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.)<br />
<br />
You can edit the department (\department) if you're not in Physics, and you can enter your dedication and acknowledgements in those sections.<br />
<br />
The CONTENTS, TABLES, FIGURES section doesn't have to be edited. It automatically generates a table of contents and a list of figures.<br />
<br />
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}.)<br />
<br />
===Chapter .tex Files===<br />
<br />
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.)<br />
<br />
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.<br />
<br />
Each chapter starts out with the following line:<br />
<br />
\chapter{This Is The Full Chapter Title, and Spaces are OK Here}\label{ch:chapname}.<br />
<br />
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.)<br />
<br />
===Style (.sty) and Class (.cls) Files===<br />
<br />
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.<br />
<br />
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).<br />
<br />
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<br />
<br />
==General .tex Notes==<br />
<br />
===Basic Commands===<br />
<br />
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 [http://tex.stackexchange.com/ Stack Exchange]. Stack Exchange also has the answer to many other [http://scifi.stackexchange.com/questions/66661/exactly-how-secret-was-the-reveal-in-the-empire-strikes-back pressing] [http://scifi.stackexchange.com/questions/47085/who-made-the-decision-for-gandalfs-promotion-from-grey-to-white questions].<br />
<br />
That said, here are a few basic commands and other small tips that I found useful.<br />
<br />
\cite{}<br />
\label{}<br />
\ref{}<br />
\begin{equation, eqnarray}<br />
\vspace<br />
! between letters<br />
\textit{<br />
\text{<br />
<br />
===Other Thoughts===<br />
spelling<br />
<br />
talk about figures, tables<br />
<br />
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.<br />
<br />
I think it screws it up if you use spaces in your file names, so use underscores (_) instead.<br />
<br />
<br />
other zip files - for alternative formats</div>Jjweber3https://wiki.physics.wisc.edu/yavuz/index.php?title=File:Figs2.zip&diff=791File:Figs2.zip2014-08-29T00:57:41Z<p>Jjweber3: 2 of 2 Figures for Josh's Thesis</p>
<hr />
<div>2 of 2 Figures for Josh's Thesis</div>Jjweber3https://wiki.physics.wisc.edu/yavuz/index.php?title=File:Figs1.zip&diff=790File:Figs1.zip2014-08-29T00:57:21Z<p>Jjweber3: 1 of 2 Figures for Josh's Thesis</p>
<hr />
<div>1 of 2 Figures for Josh's Thesis</div>Jjweber3https://wiki.physics.wisc.edu/yavuz/index.php?title=File:TeX_files.zip&diff=789File:TeX files.zip2014-08-29T00:54:44Z<p>Jjweber3: TeX files for Josh's Thesis</p>
<hr />
<div>TeX files for Josh's Thesis</div>Jjweber3https://wiki.physics.wisc.edu/yavuz/index.php?title=File:Ref4.zip&diff=788File:Ref4.zip2014-08-29T00:53:14Z<p>Jjweber3: Fourth and Final set of reference files for Josh's Thesis</p>
<hr />
<div>Fourth and Final set of reference files for Josh's Thesis</div>Jjweber3https://wiki.physics.wisc.edu/yavuz/index.php?title=File:Ref3.zip&diff=787File:Ref3.zip2014-08-29T00:52:51Z<p>Jjweber3: Third set of reference files for Josh's Thesis</p>
<hr />
<div>Third set of reference files for Josh's Thesis</div>Jjweber3https://wiki.physics.wisc.edu/yavuz/index.php?title=File:Ref2.zip&diff=786File:Ref2.zip2014-08-29T00:52:33Z<p>Jjweber3: Second set of reference files for Josh's Thesis</p>
<hr />
<div>Second set of reference files for Josh's Thesis</div>Jjweber3https://wiki.physics.wisc.edu/yavuz/index.php?title=File:Ref1.zip&diff=785File:Ref1.zip2014-08-29T00:51:49Z<p>Jjweber3: First set of reference files for Josh's Thesis</p>
<hr />
<div>First set of reference files for Josh's Thesis</div>Jjweber3https://wiki.physics.wisc.edu/yavuz/index.php?title=Thesis_Template&diff=784Thesis Template2014-08-28T23:16:46Z<p>Jjweber3: /* General .tex Notes */</p>
<hr />
<div>I (Josh) wrote, formatted, and edited my thesis using [http://www.tug.org/texworks/ 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 [http://grad.wisc.edu/currentstudents/degree/ Graduate School] in August, 2014, but you should probably check if there are any changes in the requirements.<br />
<br />
I've uploaded a .zip file with all of the .tex files you need to compile my thesis. (There are also separate folders with the references and figures.)<br />
<br />
== Overview of Files ==<br />
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.<br />
<br />
===thesis.tex===<br />
<br />
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.<br />
<br />
The real important part starts at line 112 (\begin{document}).<br />
<br />
I don't know what the \bibliographystyle thing is. I just left it how it was from Tyler's thesis.<br />
<br />
The next parts are where the other chapters are called. The command <br />
<br />
\include{CHAPTERNAME}<br />
<br />
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.<br />
<br />
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".)<br />
<br />
For keeping track of references, both for the thesis and in general, I recommend [http://www.mendeley.com 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.<br />
<br />
For appendices, it is the same as chapters, except you use the \include command between the commands \begin{appendices} and \end{appendices}.<br />
<br />
===myprelude.tex===<br />
<br />
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.<br />
<br />
There are lots of things you can change in this file. I'll only mention the ones that I changed.<br />
<br />
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.)<br />
<br />
You can edit the department (\department) if you're not in Physics, and you can enter your dedication and acknowledgements in those sections.<br />
<br />
The CONTENTS, TABLES, FIGURES section doesn't have to be edited. It automatically generates a table of contents and a list of figures.<br />
<br />
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}.)<br />
<br />
===Chapter .tex Files===<br />
<br />
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.)<br />
<br />
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.<br />
<br />
Each chapter starts out with the following line:<br />
<br />
\chapter{This Is The Full Chapter Title, and Spaces are OK Here}\label{ch:chapname}.<br />
<br />
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.)<br />
<br />
===Style (.sty) and Class (.cls) Files===<br />
<br />
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.<br />
<br />
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).<br />
<br />
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<br />
<br />
==General .tex Notes==<br />
<br />
===Basic Commands===<br />
<br />
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 [http://tex.stackexchange.com/ Stack Exchange]. Stack Exchange also has the answer to many other [http://scifi.stackexchange.com/questions/66661/exactly-how-secret-was-the-reveal-in-the-empire-strikes-back pressing] [http://scifi.stackexchange.com/questions/47085/who-made-the-decision-for-gandalfs-promotion-from-grey-to-white questions].<br />
<br />
That said, here are a few basic commands and other small tips that I found useful.<br />
<br />
\cite{}<br />
\label{}<br />
\ref{}<br />
\begin{equation, eqnarray}<br />
\vspace<br />
! between letters<br />
\textit{<br />
\text{<br />
<br />
===Other Thoughts===<br />
spelling<br />
<br />
talk about figures, tables<br />
<br />
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.<br />
<br />
I think it screws it up if you use spaces in your file names, so use underscores (_) instead.<br />
<br />
<br />
other zip files - for alternative formats</div>Jjweber3https://wiki.physics.wisc.edu/yavuz/index.php?title=Thesis_Template&diff=783Thesis Template2014-08-28T23:14:56Z<p>Jjweber3: /* General .tex Notes */</p>
<hr />
<div>I (Josh) wrote, formatted, and edited my thesis using [http://www.tug.org/texworks/ 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 [http://grad.wisc.edu/currentstudents/degree/ Graduate School] in August, 2014, but you should probably check if there are any changes in the requirements.<br />
<br />
I've uploaded a .zip file with all of the .tex files you need to compile my thesis. (There are also separate folders with the references and figures.)<br />
<br />
== Overview of Files ==<br />
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.<br />
<br />
===thesis.tex===<br />
<br />
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.<br />
<br />
The real important part starts at line 112 (\begin{document}).<br />
<br />
I don't know what the \bibliographystyle thing is. I just left it how it was from Tyler's thesis.<br />
<br />
The next parts are where the other chapters are called. The command <br />
<br />
\include{CHAPTERNAME}<br />
<br />
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.<br />
<br />
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".)<br />
<br />
For keeping track of references, both for the thesis and in general, I recommend [http://www.mendeley.com 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.<br />
<br />
For appendices, it is the same as chapters, except you use the \include command between the commands \begin{appendices} and \end{appendices}.<br />
<br />
===myprelude.tex===<br />
<br />
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.<br />
<br />
There are lots of things you can change in this file. I'll only mention the ones that I changed.<br />
<br />
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.)<br />
<br />
You can edit the department (\department) if you're not in Physics, and you can enter your dedication and acknowledgements in those sections.<br />
<br />
The CONTENTS, TABLES, FIGURES section doesn't have to be edited. It automatically generates a table of contents and a list of figures.<br />
<br />
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}.)<br />
<br />
===Chapter .tex Files===<br />
<br />
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.)<br />
<br />
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.<br />
<br />
Each chapter starts out with the following line:<br />
<br />
\chapter{This Is The Full Chapter Title, and Spaces are OK Here}\label{ch:chapname}.<br />
<br />
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.)<br />
<br />
===Style (.sty) and Class (.cls) Files===<br />
<br />
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.<br />
<br />
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).<br />
<br />
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<br />
<br />
==General .tex Notes==<br />
<br />
===Basic Commands===<br />
<br />
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 [http://tex.stackexchange.com/ Stack Exchange]. Stack Exchange also has the answer to many other [http://scifi.stackexchange.com/questions/66661/exactly-how-secret-was-the-reveal-in-the-empire-strikes-back pressing] [http://scifi.stackexchange.com/questions/47085/who-made-the-decision-for-gandalfs-promotion-from-grey-to-white questions].<br />
<br />
That said, here are a few basic commands and other small tips that I found useful.<br />
talk about basic commands<br />
\cite{}<br />
\label{}<br />
\ref{}<br />
\begin{equation, eqnarray}<br />
\vspace<br />
! between letters<br />
\textit{<br />
\text{<br />
<br />
===Other Thoughts===<br />
spelling<br />
<br />
talk about figures, tables<br />
<br />
With some changes, especially with reference and figure numbering, you may have to run / typeset thesis.tex before you see the changes take place.<br />
<br />
I think it screws it up if you use spaces in your file names, so use underscores (_) instead.<br />
<br />
<br />
other zip files - for alternative formats</div>Jjweber3https://wiki.physics.wisc.edu/yavuz/index.php?title=Thesis_Template&diff=782Thesis Template2014-08-28T23:05:04Z<p>Jjweber3: </p>
<hr />
<div>I (Josh) wrote, formatted, and edited my thesis using [http://www.tug.org/texworks/ 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 [http://grad.wisc.edu/currentstudents/degree/ Graduate School] in August, 2014, but you should probably check if there are any changes in the requirements.<br />
<br />
I've uploaded a .zip file with all of the .tex files you need to compile my thesis. (There are also separate folders with the references and figures.)<br />
<br />
== Overview of Files ==<br />
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.<br />
<br />
===thesis.tex===<br />
<br />
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.<br />
<br />
The real important part starts at line 112 (\begin{document}).<br />
<br />
I don't know what the \bibliographystyle thing is. I just left it how it was from Tyler's thesis.<br />
<br />
The next parts are where the other chapters are called. The command <br />
<br />
\include{CHAPTERNAME}<br />
<br />
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.<br />
<br />
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".)<br />
<br />
For keeping track of references, both for the thesis and in general, I recommend [http://www.mendeley.com 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.<br />
<br />
For appendices, it is the same as chapters, except you use the \include command between the commands \begin{appendices} and \end{appendices}.<br />
<br />
===myprelude.tex===<br />
<br />
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.<br />
<br />
There are lots of things you can change in this file. I'll only mention the ones that I changed.<br />
<br />
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.)<br />
<br />
You can edit the department (\department) if you're not in Physics, and you can enter your dedication and acknowledgements in those sections.<br />
<br />
The CONTENTS, TABLES, FIGURES section doesn't have to be edited. It automatically generates a table of contents and a list of figures.<br />
<br />
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}.)<br />
<br />
===Chapter .tex Files===<br />
<br />
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.)<br />
<br />
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.<br />
<br />
Each chapter starts out with the following line:<br />
<br />
\chapter{This Is The Full Chapter Title, and Spaces are OK Here}\label{ch:chapname}.<br />
<br />
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.)<br />
<br />
===Style (.sty) and Class (.cls) Files===<br />
<br />
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.<br />
<br />
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).<br />
<br />
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<br />
<br />
==General .tex Notes==<br />
<br />
===Basic Commands===<br />
<br />
talk about basic commands<br />
\cite{}<br />
\label{}<br />
\ref{}<br />
\begin{equation, eqnarray}<br />
\vspace<br />
! between letters<br />
\textit{<br />
\text{<br />
<br />
===Other Thoughts===<br />
spelling<br />
<br />
talk about figures, tables<br />
<br />
sometimes you might have to run it twice to see a change take place<br />
<br />
other zip files - for alternative formats<br />
<br />
no spaces in file names, use _</div>Jjweber3https://wiki.physics.wisc.edu/yavuz/index.php?title=Thesis_Template&diff=776Thesis Template2014-08-28T19:54:52Z<p>Jjweber3: </p>
<hr />
<div>I wrote, formatted, and edited my thesis using [http://www.tug.org/texworks/ 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 [http://grad.wisc.edu/currentstudents/degree/ Graduate School] in August, 2014, but you should probably check if there are any changes in the requirements.<br />
<br />
I've uploaded a .zip file with all of the .tex files you need to compile my thesis. (There are also separate folders with the references and figures.)<br />
<br />
== Overview of Files ==<br />
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.<br />
<br />
===thesis.tex===<br />
<br />
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.<br />
<br />
The real important part starts at line 112 (\begin{document}).<br />
<br />
I don't know what the \bibliographystyle thing is. I just left it how it was from Tyler's thesis.<br />
<br />
The next parts are where the other chapters are called. The command <br />
<br />
\include{CHAPTERNAME}<br />
<br />
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.<br />
<br />
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".)<br />
<br />
For keeping track of references, both for the thesis and in general, I recommend [http://www.mendeley.com 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.<br />
<br />
For appendices, it is the same as chapters, except you use the \include command between the commands \begin{appendices} and \end{appendices}.<br />
<br />
===myprelude.tex===<br />
<br />
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.<br />
<br />
There are lots of things you can change in this file. I'll only mention the ones that I changed.<br />
<br />
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.)<br />
<br />
You can edit the department (\department) if you're not in Physics, and you can enter your dedication and acknowledgements in those sections.<br />
<br />
The CONTENTS, TABLES, FIGURES section doesn't have to be edited. It automatically generates a table of contents and a list of figures.<br />
<br />
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}.)<br />
<br />
===Chapter .tex Files===<br />
<br />
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.)<br />
<br />
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.<br />
<br />
Each chapter starts out with the following line:<br />
<br />
\chapter{This Is The Full Chapter Title, and Spaces are OK Here}\label{ch:chapname}.<br />
<br />
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.)<br />
<br />
===Style (.sty) and Class (.cls) Files===<br />
<br />
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.<br />
<br />
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).<br />
<br />
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<br />
<br />
==General .tex Notes==<br />
<br />
===Basic Commands===<br />
<br />
talk about basic commands<br />
\cite{}<br />
\label{}<br />
\ref{}<br />
\begin{equation, eqnarray}<br />
\vspace<br />
! between letters<br />
\textit{<br />
\text{<br />
<br />
===Other Thoughts===<br />
spelling<br />
<br />
talk about figures, tables<br />
<br />
sometimes you might have to run it twice to see a change take place<br />
<br />
other zip files - for alternative formats<br />
<br />
no spaces in file names, use _</div>Jjweber3https://wiki.physics.wisc.edu/yavuz/index.php?title=Thesis_Template&diff=775Thesis Template2014-08-28T19:51:12Z<p>Jjweber3: /* Overview of Files */</p>
<hr />
<div>== General ==<br />
<br />
I wrote, formatted, and edited my thesis using [http://www.tug.org/texworks/ 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 [http://grad.wisc.edu/currentstudents/degree/ Graduate School] in August, 2014, but you should probably check if there are any changes in the requirements.<br />
<br />
== Overview of Files ==<br />
I've uploaded a .zip file with all of the .tex files you need to compile my thesis. (There are also separate folders with the references and figures.)<br />
<br />
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.<br />
<br />
===thesis.tex===<br />
<br />
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.<br />
<br />
The real important part starts at line 112 (\begin{document}).<br />
<br />
I don't know what the \bibliographystyle thing is. I just left it how it was from Tyler's thesis.<br />
<br />
The next parts are where the other chapters are called. The command <br />
<br />
\include{CHAPTERNAME}<br />
<br />
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.<br />
<br />
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".)<br />
<br />
For keeping track of references, both for the thesis and in general, I recommend [http://www.mendeley.com 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.<br />
<br />
For appendices, it is the same as chapters, except you use the \include command between the commands \begin{appendices} and \end{appendices}.<br />
<br />
===myprelude.tex===<br />
<br />
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.<br />
<br />
There are lots of things you can change in this file. I'll only mention the ones that I changed.<br />
<br />
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.)<br />
<br />
You can edit the department (\department) if you're not in Physics, and you can enter your dedication and acknowledgements in those sections.<br />
<br />
The CONTENTS, TABLES, FIGURES section doesn't have to be edited. It automatically generates a table of contents and a list of figures.<br />
<br />
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}.)<br />
<br />
===Chapter .tex Files===<br />
<br />
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.)<br />
<br />
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.<br />
<br />
Each chapter starts out with the following line:<br />
<br />
\chapter{This Is The Full Chapter Title, and Spaces are OK Here}\label{ch:chapname}.<br />
<br />
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.)<br />
<br />
===Style (.sty) and Class (.cls) Files===<br />
<br />
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.<br />
<br />
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).<br />
<br />
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<br />
<br />
<br />
<br />
talk about basic commands<br />
\cite{}<br />
\label{}<br />
\ref{}<br />
\begin{equation, eqnarray}<br />
\vspace<br />
! between letters<br />
\textit{<br />
\text{<br />
<br />
spelling<br />
<br />
talk about figures, tables<br />
<br />
sometimes you might have to run it twice to see a change take place<br />
<br />
other zip files - for alternative formats<br />
<br />
no spaces in file names, use _</div>Jjweber3https://wiki.physics.wisc.edu/yavuz/index.php?title=Thesis_Template&diff=774Thesis Template2014-08-28T19:50:05Z<p>Jjweber3: </p>
<hr />
<div>== General ==<br />
<br />
I wrote, formatted, and edited my thesis using [http://www.tug.org/texworks/ 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 [http://grad.wisc.edu/currentstudents/degree/ Graduate School] in August, 2014, but you should probably check if there are any changes in the requirements.<br />
<br />
== Overview of Files ==<br />
I've uploaded a .zip file with all of the .tex files you need to compile my thesis. (There are also separate folders with the references and figures.)<br />
<br />
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.<br />
<br />
===thesis.tex===<br />
<br />
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.<br />
<br />
The real important part starts at line 112 (\begin{document}).<br />
<br />
I don't know what the \bibliographystyle thing is. I just left it how it was from Tyler's thesis.<br />
<br />
The next parts are where the other chapters are called. The command <br />
<br />
\include{CHAPTERNAME}<br />
<br />
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.<br />
<br />
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".)<br />
<br />
For keeping track of references, both for the thesis and in general, I recommend [http://www.mendeley.com 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.<br />
<br />
For appendices, it is the same as chapters, except you use the \include command between the commands \begin{appendices} and \end{appendices}.<br />
<br />
===myprelude.tex===<br />
<br />
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.<br />
<br />
There are lots of things you can change in this file. I'll only mention the ones that I changed.<br />
<br />
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.)<br />
<br />
You can edit the department (\department) if you're not in Physics, and you can enter your dedication and acknowledgements in those sections.<br />
<br />
The CONTENTS, TABLES, FIGURES section doesn't have to be edited. It automatically generates a table of contents and a list of figures.<br />
<br />
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}.)<br />
<br />
===Chapter .tex files===<br />
<br />
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.)<br />
<br />
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.<br />
<br />
Each chapter starts out with the following line:<br />
<br />
\chapter{This Is The Full Chapter Title, and Spaces are OK Here}\label{ch:chapname}.<br />
<br />
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.)<br />
<br />
===Style (.sty) and Class (.cls) Files===<br />
<br />
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.<br />
<br />
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).<br />
<br />
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<br />
<br />
<br />
<br />
talk about basic commands<br />
\cite{}<br />
\label{}<br />
\ref{}<br />
\begin{equation, eqnarray}<br />
\vspace<br />
! between letters<br />
\textit{<br />
\text{<br />
<br />
spelling<br />
<br />
talk about figures, tables<br />
<br />
sometimes you might have to run it twice to see a change take place<br />
<br />
other zip files - for alternative formats<br />
<br />
no spaces in file names, use _</div>Jjweber3https://wiki.physics.wisc.edu/yavuz/index.php?title=Thesis_Template&diff=773Thesis Template2014-08-28T19:47:11Z<p>Jjweber3: </p>
<hr />
<div>== General ==<br />
<br />
I wrote, formatted, and edited my thesis using [http://www.tug.org/texworks/ 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 [http://grad.wisc.edu/currentstudents/degree/ Graduate School] in August, 2014, but you should probably check if there are any changes in the requirements.<br />
<br />
== Overview of Files ==<br />
I've uploaded a .zip file with all of the .tex files you need to compile my thesis. (There are also separate folders with the references and figures.)<br />
<br />
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.<br />
<br />
===thesis.tex===<br />
<br />
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.<br />
<br />
The real important part starts at line 112 (\begin{document}).<br />
<br />
I don't know what the \bibliographystyle thing is. I just left it how it was from Tyler's thesis.<br />
<br />
The next parts are where the other chapters are called. The command <br />
<br />
\include{CHAPTERNAME}<br />
<br />
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.<br />
<br />
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".)<br />
<br />
For keeping track of references, both for the thesis and in general, I recommend [http://www.mendeley.com 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.<br />
<br />
For appendices, it is the same as chapters, except you use the \include command between the commands \begin{appendices} and \end{appendices}.<br />
<br />
===myprelude.tex===<br />
<br />
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.<br />
<br />
There are lots of things you can change in this file. I'll only mention the ones that I changed.<br />
<br />
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.)<br />
<br />
You can edit the department (\department) if you're not in Physics, and you can enter your dedication and acknowledgements in those sections.<br />
<br />
The CONTENTS, TABLES, FIGURES section doesn't have to be edited. It automatically generates a table of contents and a list of figures.<br />
<br />
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}.)<br />
<br />
===Chapter .tex files===<br />
<br />
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.)<br />
<br />
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.<br />
<br />
Each chapter starts out with the following line:<br />
<br />
\chapter{This Is The Full Chapter Title, and Spaces are OK Here}\label{ch:chapname}.<br />
<br />
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.)<br />
<br />
===Style (.sty) and Class (.cls) Files===<br />
<br />
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.<br />
<br />
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).<br />
<br />
<br />
<br />
<br />
<br />
talk about basic commands<br />
\cite{}<br />
\label{}<br />
\ref{}<br />
\begin{equation, eqnarray}<br />
\vspace<br />
! between letters<br />
\textit{<br />
\text{<br />
<br />
spelling<br />
<br />
talk about figures, tables<br />
<br />
sometimes you might have to run it twice to see a change take place<br />
<br />
other zip files - for alternative formats<br />
<br />
no spaces in file names, use _</div>Jjweber3https://wiki.physics.wisc.edu/yavuz/index.php?title=Thesis_Template&diff=772Thesis Template2014-08-28T19:35:38Z<p>Jjweber3: </p>
<hr />
<div>== General ==<br />
<br />
I wrote, formatted, and edited my thesis using [http://www.tug.org/texworks/ 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 [http://grad.wisc.edu/currentstudents/degree/ Graduate School] in August, 2014, but you should probably check if there are any changes in the requirements.<br />
<br />
== Overview of Files ==<br />
I've uploaded a .zip file with all of the .tex files you need to compile my thesis. (There are also separate folders with the references and figures.)<br />
<br />
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.<br />
<br />
===thesis.tex===<br />
<br />
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.<br />
<br />
The real important part starts at line 112 (\begin{document}).<br />
<br />
I don't know what the \bibliographystyle thing is. I just left it how it was from Tyler's thesis.<br />
<br />
The next parts are where the other chapters are called. The command <br />
<br />
\include{CHAPTERNAME}<br />
<br />
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.<br />
<br />
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".)<br />
<br />
For keeping track of references, both for the thesis and in general, I recommend [http://www.mendeley.com 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.<br />
<br />
For appendices, it is the same as chapters, except you use the \include command between the commands \begin{appendices} and \end{appendices}.<br />
<br />
===myprelude.tex===<br />
<br />
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.<br />
<br />
There are lots of things you can change in this file. I'll only mention the ones that I changed.<br />
<br />
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.)<br />
<br />
You can edit the department (\department) if you're not in Physics, and you can enter your dedication and acknowledgements in those sections.<br />
<br />
The CONTENTS, TABLES, FIGURES section doesn't have to be edited. It automatically generates a table of contents and a list of figures.<br />
<br />
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}.)<br />
<br />
===Chapter .tex files===<br />
<br />
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.)<br />
<br />
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.<br />
<br />
Each chapter starts out with the following line:<br />
<br />
\chapter{This Is The Full Chapter Title, and Spaces are OK Here}\label{ch:chapname}.<br />
<br />
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.)<br />
<br />
<br />
talk about style, class files<br />
<br />
<br />
<br />
talk about basic commands<br />
\cite{}<br />
\label{}<br />
\ref{}<br />
\begin{equation, eqnarray}<br />
\vspace<br />
! between letters<br />
\textit{<br />
\text{<br />
<br />
spelling<br />
<br />
talk about figures, tables<br />
<br />
sometimes you might have to run it twice to see a change take place<br />
<br />
other zip files - for alternative formats<br />
<br />
no spaces in file names, use _</div>Jjweber3https://wiki.physics.wisc.edu/yavuz/index.php?title=Thesis_Template&diff=771Thesis Template2014-08-28T19:27:17Z<p>Jjweber3: </p>
<hr />
<div>== General ==<br />
<br />
I wrote, formatted, and edited my thesis using [http://www.tug.org/texworks/ 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 [http://grad.wisc.edu/currentstudents/degree/ Graduate School] in August, 2014, but you should probably check if there are any changes in the requirements.<br />
<br />
== Overview of Files ==<br />
I've uploaded a .zip file with all of the .tex files you need to compile my thesis. (There are also separate folders with the references and figures.)<br />
<br />
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.<br />
<br />
===thesis.tex===<br />
<br />
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.<br />
<br />
The real important part starts at line 112 (\begin{document}).<br />
<br />
I don't know what the \bibliographystyle thing is. I just left it how it was from Tyler's thesis.<br />
<br />
The next parts are where the other chapters are called. The command <br />
<br />
\include{CHAPTERNAME}<br />
<br />
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.<br />
<br />
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".)<br />
<br />
For keeping track of references, both for the thesis and in general, I recommend [http://www.mendeley.com 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.<br />
<br />
For appendices, it is the same as chapters, except you use the \include command between the commands \begin{appendices} and \end{appendices}.<br />
<br />
===myprelude.tex===<br />
<br />
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.<br />
<br />
There are lots of things you can change in this file. I'll only mention the ones that I changed.<br />
<br />
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.)<br />
<br />
You can edit the department (\department) if you're not in Physics, and you can enter your dedication and acknowledgements in those sections.<br />
<br />
The CONTENTS, TABLES, FIGURES section doesn't have to be edited. It automatically generates a table of contents and a list of figures.<br />
<br />
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}.)<br />
<br />
===Chapter .tex files===<br />
<br />
For all of the other chapters, 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.)<br />
<br />
talk about basic commands<br />
\cite{}<br />
\label{}<br />
\ref{}<br />
\begin{equation, eqnarray}<br />
\vspace<br />
! between letters<br />
\textit{<br />
\text{<br />
<br />
spelling<br />
<br />
talk about style, class files<br />
<br />
sometimes you might have to run it twice to see a change take place<br />
<br />
other zip files - for alternative formats</div>Jjweber3https://wiki.physics.wisc.edu/yavuz/index.php?title=Thesis_Template&diff=770Thesis Template2014-08-28T19:20:28Z<p>Jjweber3: </p>
<hr />
<div>== General ==<br />
<br />
I wrote, formatted, and edited my thesis using [http://www.tug.org/texworks/ 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 [http://grad.wisc.edu/currentstudents/degree/ Graduate School] in August, 2014, but you should probably check if there are any changes in the requirements.<br />
<br />
== Overview of Files ==<br />
I've uploaded a .zip file with all of the .tex files you need to compile my thesis. (There are also separate folders with the references and figures.)<br />
<br />
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.<br />
<br />
===thesis.tex===<br />
<br />
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.<br />
<br />
The real important part starts at line 112 (\begin{document}).<br />
<br />
I don't know what the \bibliographystyle thing is. I just left it how it was from Tyler's thesis.<br />
<br />
The next parts are where the other chapters are called. The command <br />
<br />
\include{CHAPTERNAME}<br />
<br />
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.<br />
<br />
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".)<br />
<br />
For keeping track of references, both for the thesis and in general, I recommend [http://www.mendeley.com 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.<br />
<br />
For appendices, it is the same as chapters, except you use the \include command between the commands \begin{appendices} and \end{appendices}.<br />
<br />
===myprelude.tex===<br />
<br />
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.<br />
<br />
There are lots of things you can change in this file. I'll only mention the ones that I changed.<br />
<br />
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.)<br />
<br />
You can edit the department (\department) if you're not in Physics, and you can enter your dedication and acknowledgements in those sections.<br />
<br />
The CONTENTS, TABLES, FIGURES section doesn't have to be edited. It automatically generates a table of contents and a list of figures.<br />
<br />
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}.)<br />
<br />
===Chapter .tex files==<br />
general chapter<br />
<br />
talk about basic commands<br />
\cite{}<br />
\label{}<br />
\ref{}<br />
\begin{equation, eqnarray}<br />
\vspace<br />
! between letters<br />
\textit{<br />
\text{<br />
<br />
spelling<br />
<br />
talk about style, class files<br />
<br />
other zip files - for alternative formats</div>Jjweber3https://wiki.physics.wisc.edu/yavuz/index.php?title=Thesis_Template&diff=769Thesis Template2014-08-28T19:08:14Z<p>Jjweber3: </p>
<hr />
<div>== General ==<br />
<br />
I wrote, formatted, and edited my thesis using [http://www.tug.org/texworks/ 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 [http://grad.wisc.edu/currentstudents/degree/ Graduate School] in August, 2014, but you should probably check if there are any changes in the requirements.<br />
<br />
== Overview of Files ==<br />
I've uploaded a .zip file with all of the .tex files you need to compile my thesis. (There are also separate folders with the references and figures.)<br />
<br />
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.<br />
<br />
==thesis.tex==<br />
<br />
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.<br />
<br />
The real important part starts at line 112 (\begin{document}).<br />
<br />
I don't know what the \bibliographystyle thing is. I just left it how it was from Tyler's thesis.<br />
<br />
The next parts are where the other chapters are called. The command <br />
<br />
\include{CHAPTERNAME}<br />
<br />
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.<br />
<br />
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".)<br />
<br />
For keeping track of references, both for the thesis and in general, I recommend [http://www.mendeley.com 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.<br />
<br />
For appendices, it is the same as chapters, except you use the \include command between the commands \begin{appendices} and \end{appendices}.<br />
<br />
==Chapter .tex files==<br />
<br />
myprelude<br />
<br />
general chapter<br />
<br />
talk about basic commands<br />
\cite{}<br />
\label{}<br />
\ref{}<br />
\begin{equation, eqnarray}<br />
<br />
spelling<br />
<br />
talk about style, class files<br />
<br />
other zip files - for alternative formats</div>Jjweber3https://wiki.physics.wisc.edu/yavuz/index.php?title=Thesis_Template&diff=768Thesis Template2014-08-28T19:06:04Z<p>Jjweber3: </p>
<hr />
<div>== General ==<br />
<br />
I wrote, formatted, and edited my thesis using [http://www.tug.org/texworks/ 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 [http://grad.wisc.edu/currentstudents/degree/ Graduate School] in August, 2014, but you should probably check if there are any changes in the requirements.<br />
<br />
== Overview of Files ==<br />
I've uploaded a .zip file with all of the .tex files you need to compile my thesis. (There are also separate folders with the references and figures.)<br />
<br />
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.<br />
<br />
==thesis.tex==<br />
<br />
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.<br />
<br />
The real important part starts at line 112 (\begin{document}).<br />
<br />
I don't know what the \bibliographystyle thing is. I just left it how it was from Tyler's thesis.<br />
<br />
The next parts are where the other chapters are called. The command <br />
<br />
\include{CHAPTERNAME}<br />
<br />
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.<br />
<br />
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".)<br />
<br />
For keeping track of references, both for the thesis and in general, I recommend [http://www.mendeley.com 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.<br />
<br />
For appendices, it is the same as chapters, except you use the \include command between the commands \begin{appendices} and \end{appendices}.<br />
<br />
==Chapter .tex files==<br />
<br />
<br />
talk about basic commands<br />
\cite{}<br />
\label{}<br />
\ref{}<br />
\begin{equation, eqnarray}<br />
<br />
spelling<br />
<br />
<br />
other zip files - for alternative formats</div>Jjweber3https://wiki.physics.wisc.edu/yavuz/index.php?title=Thesis_Template&diff=767Thesis Template2014-08-28T19:01:18Z<p>Jjweber3: </p>
<hr />
<div>== General ==<br />
<br />
I wrote, formatted, and edited my thesis using [http://www.tug.org/texworks/ 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 [http://grad.wisc.edu/currentstudents/degree/ Graduate School] in August, 2014, but you should probably check if there are any changes in the requirements.<br />
<br />
== Overview of Files ==<br />
I've uploaded a .zip file with all of the .tex files you need to compile my thesis. (There are also separate folders with the references and figures.)<br />
<br />
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.<br />
<br />
==thesis.tex==<br />
<br />
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.<br />
<br />
The real important part starts at line 112 (\begin{document}).<br />
<br />
I don't know what the \bibliographystyle thing is. I just left it how it was from Tyler's thesis.<br />
<br />
The next parts are where the other chapters are called. The command <br />
<br />
\include{CHAPTERNAME}<br />
<br />
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.<br />
<br />
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".)<br />
<br />
For keeping track of references, both for the thesis and in general, I recommend [http://www.mendeley.com Mendeley], a free reference manager. It stores PDFs, is searchable, and it creates (and automatically updates!) a .bib file that creates handles the references in the thesis.<br />
<br />
talk about basic commands<br />
\cite{}<br />
\label{}<br />
\ref{}<br />
\begin{equation, eqnarray}<br />
<br />
spelling<br />
<br />
<br />
other zip files - for alternative formats</div>Jjweber3https://wiki.physics.wisc.edu/yavuz/index.php?title=Thesis_Template&diff=766Thesis Template2014-08-28T18:55:37Z<p>Jjweber3: </p>
<hr />
<div>== General ==<br />
<br />
I wrote, formatted, and edited my thesis using [http://www.tug.org/texworks/ 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 [http://grad.wisc.edu/currentstudents/degree/ Graduate School] in August, 2014, but you should probably check if there are any changes in the requirements.<br />
<br />
== Overview of Files ==<br />
I've uploaded a .zip file with all of the .tex files you need to compile my thesis. (There are also separate folders with the references and figures.)<br />
<br />
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.<br />
<br />
==thesis.tex==<br />
<br />
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.<br />
<br />
The real important part starts at line 112 (<br />
<br />
spelling<br />
<br />
For keeping track of references, both for the thesis and in general, I recommend [http://www.mendeley.com Mendeley], a free reference manager. It stores PDFs, is searchable, and it creates (and automatically updates!) a bibTeX file that creates handles the references in the thesis.<br />
<br />
talk about basic commands<br />
\cite{}<br />
\label{}<br />
\ref{}<br />
\begin{equation, eqnarray}<br />
<br />
<br />
<br />
other zip files - for alternative formats</div>Jjweber3https://wiki.physics.wisc.edu/yavuz/index.php?title=Thesis_Template&diff=765Thesis Template2014-08-28T18:48:31Z<p>Jjweber3: </p>
<hr />
<div>== General ==<br />
<br />
I wrote, formatted, and edited my thesis using [http://www.tug.org/texworks/ 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 [http://grad.wisc.edu/currentstudents/degree/ Graduate School] in August, 2014, but you should probably check if there are any changes in the requirements.<br />
<br />
== Files ==<br />
I've uploaded a .zip file with all of the .tex files you need to compile my thesis. (There are also separate folders with the references and figures.)<br />
<br />
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.<br />
<br />
spelling<br />
<br />
For keeping track of references, both for the thesis and in general, I recommend [http://www.mendeley.com Mendeley], a free reference manager. It stores PDFs, is searchable, and it creates (and automatically updates!) a bibTeX file that creates handles the references in the thesis.<br />
<br />
talk about basic commands<br />
\cite{}<br />
\label{}<br />
\ref{}<br />
\begin{equation, eqnarray}<br />
<br />
<br />
<br />
other zip files - for alternative formats</div>Jjweber3https://wiki.physics.wisc.edu/yavuz/index.php?title=Thesis_Template&diff=764Thesis Template2014-08-28T18:48:08Z<p>Jjweber3: </p>
<hr />
<div>== General==<br />
<br />
I wrote, formatted, and edited my thesis using [http://www.tug.org/texworks/ 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 [http://grad.wisc.edu/currentstudents/degree/ Graduate School] in August, 2014, but you should probably check if there are any changes in the requirements.<br />
<br />
I've uploaded a .zip file with all of the .tex files you need to compile my thesis. (There are also separate folders with the references and figures.)<br />
<br />
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.<br />
<br />
spelling<br />
<br />
For keeping track of references, both for the thesis and in general, I recommend [http://www.mendeley.com Mendeley], a free reference manager. It stores PDFs, is searchable, and it creates (and automatically updates!) a bibTeX file that creates handles the references in the thesis.<br />
<br />
talk about basic commands<br />
\cite{}<br />
\label{}<br />
\ref{}<br />
\begin{equation, eqnarray}<br />
<br />
<br />
<br />
other zip files - for alternative formats</div>Jjweber3https://wiki.physics.wisc.edu/yavuz/index.php?title=Thesis_Template&diff=763Thesis Template2014-08-28T18:47:04Z<p>Jjweber3: </p>
<hr />
<div>I wrote, formatted, and edited my thesis using [http://www.tug.org/texworks/ 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 [http://grad.wisc.edu/currentstudents/degree/ Graduate School] in August, 2014, but you should probably check if there are any changes in the requirements.<br />
<br />
I've uploaded a .zip file with all of the .tex files you need to compile my thesis. (There are also separate folders with the references and figures.)<br />
<br />
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.<br />
<br />
spelling<br />
<br />
For keeping track of references, both for the thesis and in general, I recommend [http://www.mendeley.com Mendeley], a free reference manager. It stores PDFs, is searchable, and it creates (and automatically updates!) a bibTeX file that creates handles the references in the thesis.<br />
<br />
talk about basic commands<br />
\cite{}<br />
\label{}<br />
\ref{}<br />
\begin{equation, eqnarray}<br />
<br />
<br />
<br />
other zip files - for alternative formats</div>Jjweber3https://wiki.physics.wisc.edu/yavuz/index.php?title=Thesis_Template&diff=733Thesis Template2014-08-26T19:57:29Z<p>Jjweber3: </p>
<hr />
<div>I wrote, formatted, and edited my thesis using [http://www.tug.org/texworks/ 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 [http://grad.wisc.edu/currentstudents/degree/ Graduate School] in August, 2014, but you should probably check if there are any changes in the requirements.<br />
<br />
what do the different files do?<br />
<br />
spelling<br />
<br />
For keeping track of references, both for the thesis and in general, I recommend [http://www.mendeley.com Mendeley], a free reference manager. It stores PDFs, is searchable, and it creates (and automatically updates!) a bibTeX file that creates handles the references in the thesis.<br />
<br />
talk about basic commands<br />
\cite{}<br />
\label{}<br />
\ref{}<br />
\begin{equation, eqnarray}<br />
<br />
<br />
<br />
other zip files - for alternative formats</div>Jjweber3https://wiki.physics.wisc.edu/yavuz/index.php?title=Thesis_Template&diff=732Thesis Template2014-08-26T19:52:59Z<p>Jjweber3: </p>
<hr />
<div>I wrote, formatted, and edited my thesis using [http://www.tug.org/texworks/ TeXworks], a free, open-source TeX editing software. (You can download it and all necessary associated files using that link.)<br />
<br />
<br />
<br />
spelling<br />
<br />
For keeping track of references, both for the thesis and in general, I recommend [http://www.mendeley.com Mendeley], a free reference manager. It stores PDFs, is searchable, and it creates (and automatically updates!) a bibTeX file that creates handles the references in the thesis.<br />
<br />
talk about basic commands<br />
\cite{}<br />
\label{}<br />
\ref{}<br />
<br />
<br />
<br />
other zip files - for alternative formats</div>Jjweber3https://wiki.physics.wisc.edu/yavuz/index.php?title=Thesis_Template&diff=731Thesis Template2014-08-26T19:52:11Z<p>Jjweber3: </p>
<hr />
<div>I wrote, formatted, and edited my thesis using [http://www.tug.org/texworks/ TeXworks], a free, open-source TeX editing software. (You can download it and all necessary associated files using that link.)<br />
<br />
<br />
<br />
spelling<br />
<br />
For keeping track of references, both for the thesis and in general, I recommend [http://www.mendeley.com Mendeley], a free reference manager. It stores PDFs, is searchable, and it creates (and automatically updates!) a bibTeX file that creates handles the references in the thesis.<br />
<br />
<br />
<br />
<br />
other zip files</div>Jjweber3https://wiki.physics.wisc.edu/yavuz/index.php?title=Thesis_Template&diff=730Thesis Template2014-08-26T19:49:21Z<p>Jjweber3: </p>
<hr />
<div>I wrote, formatted, and edited my thesis using [http://www.tug.org/texworks/ TeXworks], a free, open-source TeX editing software. (You can download it and all necessary associated files using that link.)<br />
<br />
<br />
<br />
spelling<br />
<br />
For keeping track of references, both for the thesis and in general, I recommend [http://www.mendeley.com Mendeley], a free reference manager. It stores PDFs, is searchable, and it creates<br />
<br />
<br />
other zip files</div>Jjweber3https://wiki.physics.wisc.edu/yavuz/index.php?title=Thesis_Template&diff=729Thesis Template2014-08-26T19:48:45Z<p>Jjweber3: </p>
<hr />
<div>I wrote, formatted, and edited my thesis using [http://www.tug.org/texworks/ TeXworks], a free, open-source TeX editing software. (You can download it and all necessary associated files using that link.)<br />
<br />
<br />
<br />
spelling<br />
<br />
For keeping track of references, both for the thesis and in general, I recommend [www.mendeley.com Mendeley], a free reference manager. It stores PDFs, is searchable, and it creates<br />
<br />
<br />
other zip files</div>Jjweber3https://wiki.physics.wisc.edu/yavuz/index.php?title=Thesis_Template&diff=726Thesis Template2014-08-26T19:43:37Z<p>Jjweber3: </p>
<hr />
<div>I wrote, formatted, and edited my thesis using [http://www.tug.org/texworks/ TeXworks], a free, open-source TeX editing software. (You can download it and all necessary associated files using that link.)<br />
<br />
<br />
<br />
spelling<br />
<br />
Mendeley</div>Jjweber3https://wiki.physics.wisc.edu/yavuz/index.php?title=Thesis_Template&diff=723Thesis Template2014-08-26T19:42:35Z<p>Jjweber3: Created page with "I wrote, formatted, and edited my thesis using [http://www.tug.org/texworks/ TeXworks], a free, open-source TeX editing software. (You can download it and all necessary assoc..."</p>
<hr />
<div>I wrote, formatted, and edited my thesis using [http://www.tug.org/texworks/ TeXworks], a free, open-source TeX editing software. (You can download it and all necessary associated files using that link.)</div>Jjweber3https://wiki.physics.wisc.edu/yavuz/index.php?title=Useful_External_Links&diff=721Useful External Links2014-08-25T23:17:38Z<p>Jjweber3: </p>
<hr />
<div>[http:////www.doit.wisc.edu/software/ Software Downloads from UW DoIT]<br />
<br />
''Download security software, MatLab, Mathematica, and several other programs for free''<br /> <br /><br />
<br />
[http://mail.physics.wisc.edu/mailman/listinfo/amo Subscribe to the UW AMO E-mail Distribution List]</div>Jjweber3https://wiki.physics.wisc.edu/yavuz/index.php?title=Main_Page&diff=720Main Page2014-08-25T23:16:45Z<p>Jjweber3: /* News/Discussion */</p>
<hr />
<div>'''MediaWiki has been successfully installed.'''<br />
<br />
Consult the [//meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.<br />
<br />
== Getting started ==<br />
* [//www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]<br />
* [//www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]<br />
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]<br />
<br />
<br />
== News/Discussion ==<br />
<br />
'''8/25/14'''<br />
Josh and Jared and Nick added a page with instructions on how to edit the website. Josh added a section with the copyright policies of many of the journals that we've published in. This has the rules for posting articles on the website. These are both on the [[Website]] page.<br />
<br />
Josh also added a link to the site that you use to sign up for the UW AMO e-mail distribution list. It's on the [[Useful External Links]] page.<br />
<br />
'''5/22/14'''<br />
Kara showed Zach and me [http://noc.hep.wisc.edu/nrg/ this website] that has temperature and humidity for Saffman's labs. The three bottom links are for Saffman's labs. I think all of their labs but the rubidium lab have air conditioning separate from the building.<br />
<br />
<br />
'''5/20/14''' <br />
Chad made it possible to use latex syntax in order to write equations, so that's pretty <math>\sigma\omega\epsilon\epsilon\tau^2</math>.<br />
<br />
'''5/15/14'''<br />
Log-in now required to view pages. Feel free to post your secret crushes and inner most thoughts. <br />
<br />
<br />
'''5/13/14'''<br />
Josh did stuff, including adding the new sections (Vendors and External Links) below. Feel free to add, change, or delete them if you have other ideas.<br />
<br />
<br />
'''5/12/14''' File uploads now accept most file types and up to 20 MB (thanks, Chad!)<br />
<br />
To embed PDFs, the easiest way seems to be to use the "upload file" link in the sidebar, then copy the web address of the uploaded file and just insert it as a hyperlink into the page you're editing. Since the file is hosted on the physics server, this should be safer than just linking to off-site pages, which may not indefinitely keep manuals up. <br />
<br />
'''5/8/14''' "All Pages" moved to sidebar as "Index"<br />
<br />
<br />
<br />
This is our main page:P<br />
<br />
apparently, to add an item to the sidebar, you need to go here:<br />
https://wiki.physics.wisc.edu/yavuz/index.php?title=MediaWiki:Sidebar&action=edit<br />
<br />
<br />
What all pages do you guys want to have? <br />
* Should we each have some kind of log page?<br />
* Equipment List?<br />
* manuals<br /><br />
* Internal/informal documents?<br />
* useful matlab programs/programs we don't want to lose?<br />
<br /><br />
thoughts?<br />
<br />
==Research Projects==<br />
[[Localization of Atomic Excitation]]<br />
<br />
==People==<br />
[[Josh Weber]]<br />
<br><br />
[[Jared]]<br />
<br />
==Lab Notebooks / Logs==<br />
[[David Notebook]]<br />
<br><br />
[[Jared lab notebook]]<br />
<br><br />
[[Josh Notebook]]<br />
<br><br />
[[Nick Brewer]]<br />
<br><br />
[[Zjs log]]</div>Jjweber3https://wiki.physics.wisc.edu/yavuz/index.php?title=Useful_External_Links&diff=719Useful External Links2014-08-25T23:02:49Z<p>Jjweber3: </p>
<hr />
<div>[http:////www.doit.wisc.edu/software/ Software Downloads from UW DoIT]<br />
<br />
''Download security software, MatLab, Mathematica, and several other programs for free''<br /> <br /><br />
<br />
[http://mail.physics.wisc.edu/mailman/listinfo/amo Subscribe to AMO Physics Distribution List]</div>Jjweber3https://wiki.physics.wisc.edu/yavuz/index.php?title=Website&diff=711Website2014-08-25T16:33:52Z<p>Jjweber3: /* Copyright Policies for Posting Articles */</p>
<hr />
<div>== Editing the Website ==<br />
<br />
How to change the Yavuz Lab website. <br />
<br />
1. Go to SSH Secure Shell.<br /><br />
<br />
2. Click on Secure File Transfer Client<br /><br />
<br />
3. Click Quick Connect<br /><br />
<br />
<br />
In the Connect to Remote Host Box.<br />
<br />
Host Name: login01.physics.wisc.edu<br /><br />
<br />
User Name: naproite<br /><br />
<br />
Password: EIT6.8GHz<br /><br />
<br />
Authentication: <profile setting><br /><br />
<br />
Open Yavuz folder on right half of screen. The main HTML file is index.html.<br />
<br />
<br />
== Copyright Policies for Posting Articles ==<br />
<br />
<br />
[http://publishing.aip.org/authors/web-posting-guidelines ''AIP Journals'']<br /><br />
<br />
(''Rev. Sci. Instrum.'', ...)<br /><br />
<br />
Can post AIP-prepared version with the following information: <br /><br />
<br />
Copyright (year) American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics.<br /><br />
<br />
along with the following message:<br /><br />
<br />
The following article appeared in (citation of published article) and may be found at (URL/link for published article abstract).<br /><br /><br />
<br />
<br />
[http://journals.aps.org/copyrightFAQ.html#post ''APS Journals'']<br /><br />
<br />
(''Physical Review Letters'', ''Reviews of Modern Physics'', all ''Physical Review...'' Journals)<br /><br />
<br />
Official APS-prepared PDF can be posted <br /><br /><br />
<br />
<br />
[http://www.elsevier.com/journal-authors/author-rights-and-responsibilities?a=105167 ''Elsevier Publications'']<br /><br />
<br />
(''Optics Communications'', ...)<br /><br />
<br />
Can only post OUR version, not the final published version<br /><br />
<br />
Authors posting an accepted author manuscript online should later add a citation for the published journal article indicating that the article was subsequently published, and may mention the journal title provided that they add the following text at the beginning of the document:<br />
<br />
“NOTICE: this is the author’s version of a work that was accepted for publication in <Journal title>. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in PUBLICATION, [VOL#, ISSUE#, (DATE)] DOI#"<br /><br /><br />
<br />
<br />
[http://www.nature.com/authors/policies/license.html ''Nature'']<br /><br />
<br />
(''Nature Physics'', ...)<br /><br />
<br />
Can post our version of the article SIX MONTHS after the publication date<br /><br />
<br />
Must include a link to the published article using article DOI#<br /><br /><br />
<br />
<br />
[http://www.opticsinfobase.org/submit/review/copyright_permissions.cfm#posting ''Optics InfoBase Publications'']<br /><br />
<br />
(''Optics Letters'', ''Optics Express'', ''Optics and Photonics News'', ...)<br /><br />
<br />
Can be posted to site, but must include a working link the [http://www.opticsinfobase.org/ OSA's journals website] AND the following disclaimer:<br /><br />
<br />
This paper was published in [Journal Name] and is made available as an electronic reprint with the permission of OSA. The paper can be found at the following URL on the OSA website: [article URL]. Systematic or multiple reproduction or distribution to multiple locations via electronic or other means is prohibited and is subject to penalties under law. <br /><br /><br />
<br />
<br />
[http://www.sciencemag.org/site/feature/contribinfo/prep/gen_info.xhtml ''Science'']<br /><br />
<br />
Accepted version of the article can be posted <br /><br /><br />
<br />
<br />
[http://journalauthors.tandf.co.uk/copyright/assignmentAndYourRights.asp ''Taylor & Francis Publications'']<br /><br />
<br />
(''Journal of Modern Optics'', ...)<br /><br />
<br />
Can only post OUR version, not the final published version<br /><br />
<br />
You must insert a link from your posted Accepted Manuscript to the published article on the publisher site with the following text:<br />
<br />
"This is an Accepted Manuscript of an article published by Taylor & Francis Group in [JOURNAL TITLE] on [date of publication], available online: http://www.tandfonline.com/[Article DOI]."<br /><br /></div>Jjweber3