thesis.cls

%*********************************************************************
%
% thesis.cls
%
% Astronomy thesis DOCUMENT STYLE for LaTeX2e
%    -- See bottom for AASTeX -> thesis style conversion instructions
%
% Created: 1991: Siebers
%
% Modification History - 
%
%    July 1996, Eric Jensen -
%	Totally overhauled the style.  It was based on the Latex
%	``book'' style (and still is).  Before the whole file was
%	basically a copy of the Latex 2.09 book.sty file, with a few
%	things changed here and there.  Now we load the Latex2e book
%	class at the beginning, and then change only those things which
%	need to be changed (which turns out to be not very much).  A
%	modified version of the AASTeX style is loaded which defines
%	all of the commands and environments used there.
%
%	The ``thesis'' style now can be invoked with various options,
%	including type sizes (10pt, 11pt, 12pt), and with various
%	margins: ``draft'' gives smaller margins and line spacing,
%	suitable for handing to your committee but without using a
%	whole ream of paper; ``final'' conforms to the grad school
%	margin requirements and is suitable for the final copy.
%	Default is \documentclass[12pt,final]{thesis}.
%
%    July 1996, Andrea Cox:
%	Added a \fixspacing command you can use if you want to guarantee
%	  single-spaced figure and table captions in your final draft.
%	  Insert this command within the caption environments (see below).
%	Redefined the table spacing within the \draftsize and \finalsize
%	  commands, to ensure single-spacing of the table rows.  (See the
%	  "arraystretch" option.)
%
%    October 1997, Jerry Acord:
%     *     Added the "sflabels" to the pool of options available in the
%       document declaration.  If "sflabels" is invoked (in the same
%       manner one invokes "12pt", "draft", etc.), then the labelling
%       for the Chapters, Sections, Table of Contents, and the page
%       numbers is done in a sans serif font.  If "sflabels" is not 
%       invoked, then these labels are by default in the roman font, 
%       the same as the rest of the text (boring!!).
%     *     Changed the definition of "\addconentsline" so as to incorporate
%       \labelfamily ("sflabels") when generating the TOC.
%     *     Added the environment "chabstract" for abstracts associated
%       with individual chapters (e.g. if the chapters are actually
%       journal articles).  The "chabstract" is treated like a section
%       in the TOC, and in the "chabstract" itself the word "Abstract"
%       is somewhat smaller than in the true "abstract" environment.  
%       The "abstract" environment generates a chapter-like entry in 
%       the TOC.  Of course these things can be easily modified in this 
%       file.
%     *     Added the commands \ttlpage and \cpypage which when invoked
%       with a few commands will produce the title page and copyright
%       page automatically, without having to type in all the info
%       onesself.  See below for more info.
%     *     Added the "umiabstract" environment, which will produce the 
%       UMI abstract required by the graduate school.  Actually, you
%       have to produce it, this environment just formats it properly.
%       It requires \author, \title, \adviser, and \adviserrank, as well 
%       as the file name of your UMI abstract (less than 350 words!).
%       Note that \adviser should be of the form "Bob Dole", and 
%       \adviserrank is of the form "Professor".
%       Remember, the UMI abstract is _not_ part of your thesis!!!
%       USAGE: \begin{umiabstract} Abstract text \end{umiabstract}
%       (Ideally this is in a file separate from your master.tex file
%       for your thesis; it still REQUIRES the thesis document class!)
%
%   (Added "compact" option, so if you choose "compact" in place of
%   "final" or "draft," you'll end up with something that is single-
%   spaced and more suited for printing lots of copies e.g. to
%   distribute to your neighbors as sleeping aides.  It produces
%   something more like a preprint/reprint, rather than the double-
%   spaced crap that Memorial Library wants. 15 Dec. 1997 Jerry Acord)
%
%    December 1999, Peter Erwin:
%     *     Fixed copyright page format (invoked by \cpypage) to
%       better match Graduate School guideline; important change was
%       moving the year to the end of the copyright line.
%     *     Fixed UMI abstract (now called ``Bell & Howell'' abstract,
%       apparently, but the current forms still say UMI) -- killed
%       generation of page numbers by changing \thispagestyle{thesis}
%       to \thispagestyle{empty}.  Added an additional \this...{empty}
%       before the ``Advisor'' text in case abstract runs to two
%       pages, which it usually does; initial \this...{empty} only
%       works for the first page!
%     *     Note that Graduate School format requirements have
%       changed somewhat: 10 point type is now acceptable!
%       (12 pt type is still acceptable, of course, if you have
%       a strong desire to use up lots of paper.)
%     *     Desiderata: A really ambitious person might want to
%       adapt this style to make use of AASTeX version 5.0 macros,
%       so that future ApJ/AJ/etc. papers can be easily incorporated
%       into a thesis.  However, one probably wants to wait until
%       the bugs in v5.0 are fixed....
%
%    August 2000, Chris Dolan:
%       Added AASTeX V5.0-like citation commands
%       Added notes to the bottom of this file on how to convert a
%          AASTeX paper into a thesis chapter
%       Minor fix in \tablecomments
%       Tweaked compact style (Note: compact style still doesn't space
%          footnotes and tablenotes right.  I don't know how to fix
%          this...)
%
%    July 2001, Birgit Otte:
%       Added a command to ignore the \objectname[]{} command used by ApJ
%          for astronomical catalog databases
%
%    August 2008, Amanda Kepley:
%       Redefined float placement commands so that figures and tables
%       float more sensibly in the document.
%
%    December 2008, Kyle Westfall:
%	Replaced commented line to allow "Abstract" contents entries to be
%	    aligned with section heading instead of section number (also done for
%	    "References" in thesis_aasms.sty file)
%	Removed deluxetable package (uncomment line 240 to regain)
%
%    June 2011, Alex Hill:
%      Add labels to \listoffigures and \listoftables in compact mode
%
%   April 2015, Corey Wood:
%       - Tweaks to title page layout; mostly behind-the-scenes.
%       - Completely re-did margins to be just over 1 inch, with
%         page numbers ~0.6 inches from the top of the page.
%
%   April 2016, Chris Bard:
%       In conversion instructions:
%       - added infomation about bibliography complilation
%       - added infomation about short titles in Table of Contents,
%          list of tables, list of figures
%       - go Phillies!
%
%   June 2016, Chris Bard
%       At the end of this document
%       - Added details about epigraphs
%       - Added details about making list of symbols
%*********************************************************************

%\ProvidesClass{thesis}[1996/07/09 v1.0 UW Astronomy thesis document class]
%\ProvidesClass{thesis}[1997/10/05 v1.1 UW Astronomy thesis document class]
\ProvidesClass{thesis}[2000/06/27 v1.2 UW Astronomy thesis document class]

\newcommand\@myptsize{12}	% Default point size is 12.
        % Note that the Graduate School now permits 10 point type
        % as well.

\newcommand\singlespace{\renewcommand\baselinestretch{1.2}}
\newcommand\doublespace{\renewcommand\baselinestretch{1.8}}
\newcommand\fixspacing{\setlength{\baselineskip}{1.2em}}
	% Insert this command in your table and figure captions if you
	% want them to be single-spaced in the final version.
\newcommand\fixtabspacing{\renewcommand\arraystretch{0.2}}
\newcommand{\objectname}[3]{#3}

%\newcommand\draftsize{
%  \setlength\overfullrule{5pt}
%  \setlength{\textwidth}{6.5in}
%  \setlength{\oddsidemargin}{0in}
%  \setlength{\textheight}{8.7in}
%  \setlength{\topmargin}{0.in}
%  \setlength{\parindent}{0.4in}
%  \setlength{\parskip}{0.1in}
%  \renewcommand\baselinestretch{1.2}
%  \renewcommand\arraystretch{0.9}	% Sets the row spacing of the tables
%					%   to 0.9 times the "baselinestretch"
%  }

%%%%% this is bad and you should feel bad
%\newcommand\finalsize{
%  %% probably better to use geometry package in future.
%  \setlength\overfullrule{0pt}
%  \setlength{\textwidth}{5.95in}  %%% tweaked to get even 1" margins
%  %\setlength{\textwidth}{6.425in}
%  \setlength{\oddsidemargin}{0.3in}  %% tweaked to get even 1" margins, NMG 07/14
%  \setlength{\evensidemargin}{0.5in}
%%  \setlength{\oddsidemargin}{0.5in} % default
%  \setlength{\textheight}{8.7in}
%  \setlength{\topmargin}{0.05in}
%  \setlength{\headsep}{0.225in}
%  \setlength{\parindent}{0.4in}
%  \setlength{\footnotesep}{3ex}
%  \renewcommand\baselinestretch{1.8}
%  \renewcommand\arraystretch{0.6}	% Sets the row spacing of the tables
%					%   to 0.6 times the "baselinestretch"
%  }

% *Really* 1-in margins - CMW 05/04/2015
\newcommand\finalsize{
  %% probably better to use geometry package in future.
  \setlength\overfullrule{5pt} % Something about overfull hboxes, but I dunno.

  % 6.5" is exactly 1" margins, so let's buffer it for safety.
  % This gets mucked with below if it's two-sided.
  \setlength{\textwidth}{6.4in}
  % 9" is exactly 1" margins, so let's buffer it for descenders.
  % This looks just over 8.8 on my printed sheet.
  \setlength{\textheight}{8.9in}

  % Header goes *above* the page margins.
  \setlength{\topmargin}{-0.4in}

  % Space between page #s and text box; this is iffy since it is after the text
  % (and thus *not* just the opposite of a negative \topmargin).
  \setlength{\headsep}{0.35in}

  \iftwosided
      \setlength{\textwidth}{6.4in}
      \setlength{\oddsidemargin}{0.05in} % Only needed to center text after 1" margins.
      \setlength{\evensidemargin}{0.05in} % Yep, it was fake 2-sided before.
  \else
      \setlength{\textwidth}{6.4in}
      \setlength{\oddsidemargin}{0.05in} % Only needed to center text after 1" margins.
      \setlength{\evensidemargin}{0.05in} % Yep, it was fake 2-sided before.
  \fi

  % Separation between footnotes on one page.
  \setlength{\footnotesep}{\baselineskip}
  % Footer separation from the text.
  % (But there's no footer, so this likely never matters.)
  \setlength{\footskip}{2\baselineskip}

  \setlength{\parindent}{0.4in}

  \renewcommand\baselinestretch{1.8}
  \renewcommand\arraystretch{0.6} % Sets the row spacing of the tables
                                  % to 0.6 times the "baselinestretch"
}

% As far as I care, draft should just be the same layout as the final.
\newcommand\draftsize{\finalsize}

\newcommand\compactopts{
  \setlength\overfullrule{0pt}
  \setlength{\textwidth}{6in}
  \setlength{\oddsidemargin}{0.5in}
  \setlength{\evensidemargin}{0in}
  \setlength{\textheight}{8.5in}
  \setlength{\topmargin}{0in}
  \renewcommand\baselinestretch{1.0}    % Standard value=1.0.
  \renewcommand\arraystretch{1.0}	% Sets the row spacing of the tables
					%   as a multiple of "baselinestretch"
  }

% If the option "sflabels" is used in the document declaration, then 
% the sans serif font family will be used for chapters, sections, the
% table of contents, and page numbers.  In practice, this is implemented 
% by defining the command "\labelfamily" to be either "\rmfamily" 
% (default) or "\sfamily" (if "sflabels" is invoked).
%
\newcommand{\labelfamily}{\rmfamily}
\DeclareOption{sflabels}{\renewcommand{\labelfamily}{\sffamily}}

\DeclareOption{10pt}{\renewcommand\@myptsize{10}}
\DeclareOption{11pt}{\renewcommand\@myptsize{11}}
\DeclareOption{12pt}{\renewcommand\@myptsize{12}}

\newcommand\@sides{oneside}	% Default is one-sided.
\newif\iftwosided\twosidedfalse
\DeclareOption{oneside}{\renewcommand\@sides{oneside}
                        \twosidedfalse}
\DeclareOption{twoside}{\renewcommand\@sides{twoside}
                        \twosidedtrue}

% The next two options, ``draft'' and ``final'' determine how big the
% margins are.  ``Final'' is the default.  Their processing is deferred
% to the end of the class so that the ``book'' class below doesn't step
% on the definitions.

% Use the draft option for printing to save paper when you don't have
% to generate a copy that meets grad school requirements.
\DeclareOption{draft}{\AtEndOfClass{\draftsize}
                        \newif\ifkompakt
                        \kompaktfalse}

% The ``final'' option will pass the Margin Lady.
\DeclareOption{final}{\AtEndOfClass{\finalsize}
                        \newif\ifkompakt
                        \kompaktfalse}

% The ``compact'' option actually looks halfway decent
\DeclareOption{compact}{\AtEndOfClass{\compactopts}
                        \newif\ifkompakt
                        \kompakttrue}

% If they don't specify "draft" or "final", use final for the default:
\ExecuteOptions{final}

\ProcessOptions

% Construct a point-size option name (e.g. ``12pt'') based on the
% options specified above:

\def\ptoption{\@myptsize pt}

% Load the Latex2e ``book'' class to get the basic definitions:
%\ifkompakt\LoadClass[twoside,\ptoption]{book}\else\LoadClass[oneside,\ptoption]{book}\fi
\LoadClass[\@sides,\ptoption]{book}
%\if@twoside\else\raggedbottom\fi % Ragged bottom unless twoside option.


% This style file defines AASTeX V5.0-like citation commands
\RequirePackage{natbib}% 

% Also input a modified version of the AAS MS style to add various
% symbol definitions (note this was written for AASTeX 4.0 and has
% been partially updated for AASTeX 5.0.  Some minor differences may
% remain...)
\input{thesis_aasms.sty}
%\RequirePackage{deluxetable}

%%%%%%%%%%%%%%%%%%%%%%%%%%%
%                         %
%  \ttlpage and \cpypage  %
%                         %
%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% I envision the commands \ttlpage and \cpypage invoked thusly:
% (in your master.tex file:)
%
%    \title{My Wonderful Graduate Student Life}
%    \author{Bob Dole}
%    \year{1697}
%    \ttlpage
%    \cpypage
%
% (that's it.)
%
% The command \ttlpage will produce the standard thesis title page.
% It requires 3 variables be set: 1) \mytitle, 2) \myname, and 3) 
% \myyear.  These should be set in your master.tex file prior to 
% invoking \ttlpage.  Nota Bene: you may have to provide your own 
% line breaks if your thesis title is too long.  
% The command \cpypage will produce the standard thesis copyright page.
% It also requires \myname and \myyear be set.
%                                         -- Jerry Acord, October 1997
%
% Redefine the \title, \author, \year commands to simply repeat 
% their arguments, and define \adviser similarly:
\renewcommand{\title}[1]{\renewcommand{\title}{#1}}
\renewcommand{\author}[1]{\renewcommand{\author}{#1}}
\renewcommand{\year}[1]{\renewcommand{\year}{#1}}
\newcommand{\adviser}[1]{\renewcommand{\adviser}{#1}}
\newcommand{\adviserrank}[1]{\renewcommand{\adviserrank}{#1}}
\newcommand{\oralexamdate}[1]{\gdef\@oralexamdate{#1}} 
\newcommand{\committeeone}[1]{\gdef\@committeeone{#1}}
\newcommand{\committeetwo}[1]{\gdef\@committeetwo{#1}}
\newcommand{\committeethree}[1]{\gdef\@committeethree{#1}}
\newcommand{\committeefour}[1]{\gdef\@committeefour{#1}}
\newcommand{\committeefive}[1]{\gdef\@committeefive{#1}}
\newcommand{\committeesix}[1]{\gdef\@committeesix{#1}}
\newcommand{\committeeseven}[1]{\gdef\@committeeseven{#1}}

\newcommand{\ttlpage}{
     \thispagestyle{empty}
     \begin{center}
         \title
         \vspace{\baselineskip}

         By

         \author
         \vspace{\baselineskip}

         A dissertation submitted in partial fulfillment of

         the requirements for the degree of
         \vspace{\baselineskip}

         Doctor of Philosophy

         (Astronomy)
         \vspace{\baselineskip}

         at the

         UNIVERSITY OF WISCONSIN--MADISON

         {\year}
     \end{center}
     \vfill

     \noindent
     Date of final oral examination: \@oralexamdate

     \noindent
     The dissertation is approved by the following members of the Final Oral Committee:

     \vspace{-0.5\baselineskip} % Kill the double-spacing before committee names.
     \begin{minipage}[t]{0.925\textwidth}
         \fixspacing
         \@committeeone\\
         \@committeetwo\\
         \@committeethree\\
         \@committeefour\\
        % \@committeefive
     \end{minipage}
%     \indent \@committeesix 

     \clearpage
     % Make page inside front cover be really blank (get rid of page number)
     \iftwosided\thispagestyle{empty}\newpage\else\fi
     }

% Copyright page amended to fit with Graduate School format:
% ``(c) Copyright by Bob Dole 1697\\All Rights Reserved''
%                                         -- Peter Erwin, December 1999
\newcommand{\cpypage}{%
     \thispagestyle{empty} {\ }
     \vfill
     \begin{center}
         \copyright\ 
         Copyright by \author\ \year 
         
         All Rights Reserved
     \end{center}
     %\clearpage
}%
     

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%                                                %
% Define the UMI abstract-generating environment %
%                                                %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% December 1999, Peter Erwin: I added two \thispagestyle{empty}
%   commands to ensure that the UMI abstract has no page numbers;
%   the second command seems to be necessary to ensure that the
%   second page (anything but a really short abstract will run
%   two pages, at least in 12 pt type) has no page numbers, either.
%

\newenvironment{umiabstract}{%
  \thispagestyle{empty} \begin{center} \textsc{\large \title} \\ \vspace{0.5cm}
  \textsc{\large \author}\\ \vspace{0.25cm} 
  {\large Under the supervision of \adviserrank\ \adviser \\
  At the University of Wisconsin -- Madison} \end{center}
%  \vspace{1.0cm} \begin{center} \textbf{\large ABSTRACT} \end{center}
%  \vspace{1.0cm}
}%
%{\thispagestyle{empty} \vfill {\hfill \adviser\ (Advisor)}}



% Fix the "chapter" command so it doesn't change the page style for
% the first page of each chapter (took out "\thispagestyle{plain}"

\renewcommand\chapter{
	\if@openright\cleardoublepage\else\clearpage\fi
	\global\@topnum\z@
	\@afterindentfalse
	\secdef\@chapter\@schapter
	}

% Slight redefinition of two commands which change the size of the chapter
% headings.  If you want different sizes, change the two commands below.

% This controls the size of chapter titles.
\newcommand\chaptertitlesize{\LARGE}

% This controls the size of the heading for table of contents, list
% of figures, and list of tables.
\newcommand\toctitlesize{\LARGE}

% Here's where those sizes get implemented:
\def\@makechapterhead#1{%
  \vspace*{50\p@}%
  {\parindent \z@ \raggedright \normalfont
    \ifnum \c@secnumdepth >\m@ne
      \if@mainmatter
        \chaptertitlesize\bfseries\labelfamily \@chapapp{} \thechapter
        \par\nobreak
        \vskip 20\p@
      \fi
    \fi
    \interlinepenalty\@M
    \chaptertitlesize\bfseries\labelfamily #1\par\nobreak
    \vskip 40\p@
  }}

\def\@makeschapterhead#1{%
  \vspace*{50\p@}%
  {\parindent \z@ \raggedright
    \normalfont
    \interlinepenalty\@M
    \toctitlesize\bfseries\labelfamily  #1\par\nobreak
    \vskip 40\p@
  }}

% Changed the definitions of section, subsection, and subsubsection 
% here to allow more control of the spacing around them.
% --- And to incorporate \labelfamily ...

\newlength{\beforesecskip}
\newlength{\aftersecskip}
\beforesecskip = 2.ex		% Originally -1.ex
\aftersecskip = 1.ex		% Originally -2.ex
\def\section#1{
\vspace*{\beforesecskip}
\@startsection {section}{1}{\z@}
 {0ex}{0.001ex}{\labelfamily\large\bfseries}{#1}
\vspace*{\aftersecskip}}
\def\subsection#1{\vspace*{\beforesecskip}
\@startsection{subsection}{2}{\z@}
 {0ex}{0.001ex}{\labelfamily\normalsize\bfseries}{#1}\vspace*{\aftersecskip}}
\def\subsubsection#1{\vspace*{\beforesecskip}
\@startsection{subsubsection}{3}{\z@}
 {0ex}{0.001ex}{\labelfamily\normalsize\bfseries}{#1}\vspace*{\aftersecskip}}


% Change \addcontentsline to incorporate \labelfamily -- this is
% modified from the file "latex.ltx"  -- October 1997, Jerry Acord

\def\addcontentsline#1#2#3{%
  \addtocontents{#1}{\protect\contentsline{#2}%
     {\labelfamily #3}{\labelfamily \thepage}}}


% Also give the user the opportunity to set the page footer and header
% from within the document.  By default, the header does the page
% numbering, but you might want to put extra info in the footers.  One
% example: \setfoot{\tiny \hss DRAFT \today\hss} will create a footer
% with the word "DRAFT" and today's date in small print centered at the
% bottom of each page - handy when dealing with multiple drafts and
% trying to remember what you printed when.

\def\setfoot#1{\def\@evenfoot{#1}\let\@oddfoot=\@evenfoot}
\def\sethead#1{\let\savehead=\@evenhead\def\@evenhead{#1}
           \let\@oddhead=\@evenhead\let\oldhead=\savehead}

% Appendix for an individual chapter; reset the section and equation
% counters, saving the old values to be restored with the
% \endchapappendix command.

\def\chapappendix{\par
\setcounter{section}{0}
\setcounter{subsection}{0}
\setcounter{equation}{0}
\let\savesection=\thesection
\let\saveequation=\theequation
\def\thesection{\Alph{section}}
\def\theequation{\hbox{\normalsize\Alph{section}\arabic{equation}}}
}

% End of chapappendix def.
\def\endchapappendix{\let\thesection=\savesection
  \let\theequation=\saveequation
}

% If you want a footnote with no marker, just the footnote text at the
% bottom of the page, use \blanknote{text}

\long\def\@makeblankfntext#1{\parindent 1em\noindent
            \hbox to 1.8em{\hss$^{}$}#1}

\def\blanknote#1{\let\savefn=\@makefntext
\let\@makefntext=\@makeblankfntext
\footnotetext{#1}\let\@makefntext=\savefn}

% Allow hyphenation, but only if absolutely necessary:
   \pretolerance=500
   \tolerance=600

% Change tocdepth and secnumdepth; these control which level of
% sectioning will be numbered in the text and will be included in the
% table of contents; default is 2, which is subsection for this style;
% change to 3 to include subsubsections:

\setcounter{tocdepth}{2}
\setcounter{secnumdepth}{4}



%    ****************************************
%    *             FOOTNOTES                *
%    ****************************************
%
% \footnoterule is a macro to draw the rule separating the footnotes from
% the text.  It should take zero vertical space, so it needs a negative
% skip to compensate for any positive space taken by the rule.  (See
% PLAIN.TEX.)

% Changed 7/1/96 allow a little more space around footnotes; the
% default vertical spacing is too crowded for my tastes; ELNJ
%\renewcommand\footnoterule{%
%  \hrule\@width.4\columnwidth
%  \kern8.6\p@}

%%%%%%%%%%%%%%%%%%%%%%%%%
%                       %
%    ABSTRACT STYLES    %
%                       %
%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Not sure if these abstract definitions are actually useful, but
% it doesn't hurt to leave them here...
%
% October 1997, Jerry Acord: I've found it necessary to change 
%   \thispagestyle to "thesis" from "plain" to ensure the page
%   numbers go in the upper right as required (and that they 
%   conform to \labelfamily just like all the other page numbers).
%
%   I commented out the entry for the (blank) section number of
%   the abstract; removing it justifies the "Abstract" title with
%   the chapter numbers on the left-hand margin.
%

\def\abstractpage{\@restonecolfalse\if@twocolumn\@restonecoltrue\onecolumn
     \else \newpage \fi \thispagestyle{thesis}}
\def\endabstractpage{\if@restonecol\twocolumn \else \newpage \fi}

\def\abstract{\abstractpage
     %\addcontentsline{toc}{chapter}{Abstract}				%Align with Chapter #
     \addcontentsline{toc}{chapter}{\protect\numberline{\ }Abstract}	%Align with Chapter heading
     %\null\vfil
     \begin{center}
     {\labelfamily \bfseries \Large Abstract}
\end{center}}

\def\endabstract{\par\vfil\null\endabstractpage}

%
% The \chabstract environment is used for an abstract for an 
% individual chapter, rather than the global \abstract at the
% beginning of the manuscript.  This is particularly useful 
% if your chapters are actually journal articles with individual
% abstracts of their own.  Note that the \chabstract entry in 
% the table of contents appears as an unnumbered section, 
% whereas the \abstract appears as an unnumbered chapter.
%                                    - October 1997, Jerry Acord
%

\def\chabstractpage{\@restonecolfalse\if@twocolumn\@restonecoltrue\onecolumn
     \else \newpage \fi \thispagestyle{thesis}}
\def\endchabstractpage{\if@restonecol\twocolumn \else \newpage \fi}

\def\chabstract{\chabstractpage
     %\addcontentsline{toc}{section}{Abstract}				%Align with Section #
     \addcontentsline{toc}{section}{\protect\numberline{\ }Abstract}	%Align with Section heading
     \null\vfil
     \begin{center}
     {\labelfamily \bfseries \large Abstract}
     \end{center}}
\def\endchabstract{\par\vfil\null\endchabstractpage}


%    ****************************************
%    *            PAGE STYLES               *
%    ****************************************
%
% The page style 'foo' is defined by defining the command \ps@foo.  This
% command should make only local definitions.  There should be no stray
% spaces in the definition, since they could lead to mysterious extra
% spaces in the output.
%
% The \ps@... command defines the macros \@oddhead, \@oddfoot,
% \@evenhead, and \@evenfoot to define the running heads and
% feet---e.g., \@oddhead is the macro to produce the contents of the
% heading box for odd-numbered pages.  It is called inside an \hbox of
% width \textwidth.
%
% To make headings determined by the sectioning commands, the page style
% defines the commands \chaptermark, \sectionmark, ... , where
% \chaptermark{TEXT} is called by \chapter to set a mark, and so on.
% The \...mark commands and the \...head macros are defined with the
% help of the following macros.  (All the \...mark commands should be
% initialized to no-ops.)
%
% MARKING CONVENTIONS:
% LaTeX extends TeX's \mark facility by producing two kinds of marks
% a 'left' and a 'right' mark, using the following commands:
%     \markboth{LEFT}{RIGHT} : Adds both marks.
%     \markright{RIGHT}      : Adds a 'right' mark.
%     \leftmark  : Used in the \@oddhead, \@oddfoot, \@evenhead or \@evenfoot
%                  macro, gets the current 'left'  mark.  Works like TeX's
%                  \botmark command.
%     \rightmark : Used in the \@oddhead, \@oddfoot, \@evenhead or \@evenfoot
%                  macro, gets the current 'right'  mark.  Works like TeX's
%                  \firstmark command.
% The marking commands work reasonably well for right marks 'numbered
% within' left marks--e.g., the left mark is changed by a \chapter command and
% the right mark is changed by a \section command.  However, it does
% produce somewhat anomalous results if two \bothmark's occur on the same page.
%
% Commands like \tableofcontents that should set the marks in some page styles
% use a \@mkboth command, which is \let by the pagestyle command (\ps@...)
% to \markboth for setting the heading or \@gobbletwo to do nothing.

\mark{{}{}}   % Initializes TeX's marks

%    ****************************************
%    *     THESIS PAGE STYLE                *
%    ****************************************
%
%
% Dec 1997 -- Acord -- added the if/else clause to change the
%   page style definition if the "compact" option is being used.
%   The "compact" page style has chapters & sections in the 
%   page headers in addition to the page numbers.
%
\ifkompakt%
\def\ps@thesis{%
      \let\@oddfoot\@empty\let\@evenfoot\@empty
      %% The following used to put the chapter title by the bold-faced
      %% page number, but it looked terrible, IMHO   --- Dolan
      %\def\@evenhead{\labelfamily\bfseries\thepage\hfil\leftmark}%
      %\def\@oddhead{\labelfamily\bfseries\rightmark\hfil\thepage}%
      \def\@evenhead{\labelfamily\thepage\hfil}%
      \def\@oddhead{\labelfamily\hfil\thepage}%
      \let\@mkboth\markboth
    \def\chaptermark##1{%
      \markboth {{%
        \ifnum \c@secnumdepth >\m@ne
          \if@mainmatter
            \@chapapp\ \thechapter. \ %
          \fi
        \fi
        ##1}}{}}%
    \def\sectionmark##1{%
      \markright {{%
        \ifnum \c@secnumdepth >\z@
          \thesection. \ %
        \fi
        ##1}}}}%
\else%
\def\ps@thesis{\let\@mkboth\@gobbletwo%
    \def\@oddfoot{}\def\@evenfoot{}%
    \def\@oddhead{\labelfamily\hfil\thepage}%
    \def\@evenhead{\labelfamily\thepage\hfil}}%
\fi

%    ****************************************
%    *   MORE CRAP FOR THE COMPACT STYLE    *
%    ****************************************
%
% Changed the \chapter* commands to \section* commands,
% so that the list of figures and list of tables are
% treated as sections in the TOC, rather than separate
% chapters (duh!).  Otherwise this is more or less
% straight from book.cls (except I removed the \MakeUppercase
% command and added \labelfamily, of course).
% -- Acord 12/97
% Fix bug in which chapter headings for \listoffigures and \listoftables
% were not included in compact mode
% -- Alex Hill 6/2011

\ifkompakt%
\renewcommand\tableofcontents{%
    \if@twocolumn
      \@restonecoltrue\onecolumn
    \else
      \@restonecolfalse
    \fi
    \chapter*{\contentsname
        \@mkboth{%
           \labelfamily\contentsname}{\labelfamily\contentsname}}%
    \addcontentsline{toc}{section}{Contents}		% add contents line for List of Figures
    \@starttoc{toc}%
    \if@restonecol\twocolumn\fi
}
\renewcommand\listoffigures{%
    \if@twocolumn
      \@restonecoltrue\onecolumn
    \else
      \@restonecolfalse
    \fi
    \chapter*{\listfigurename
        \@mkboth{%
           \labelfamily\listfigurename}{\labelfamily\listfigurename}}%
    \addcontentsline{toc}{section}{List of Figures}		% add contents line for List of Figures
    \@starttoc{lof}%
    \if@restonecol\twocolumn\fi
}
\renewcommand\listoftables{%
    \if@twocolumn
      \@restonecoltrue\onecolumn
    \else
      \@restonecolfalse
    \fi
    \chapter*{\listtablename
        \@mkboth{%
           \labelfamily\listtablename}{\labelfamily\listtablename}}%
    \addcontentsline{toc}{section}{List of Tables}		% add contents line for List of Tables
    \@starttoc{lot}%
    \if@restonecol\twocolumn\fi
}
\else
% for non-compact styles:
% Putting the addcontentsline commands here instead of Thesis.tex
% to make sure page #s are right in the ToC/PDF index.
% Added 5/26/15 by CMW
\renewcommand\tableofcontents{%
    \chapter*{\contentsname
        \@mkboth{%
           \labelfamily\contentsname}{\labelfamily\contentsname}}%
    \addcontentsline{toc}{section}{Contents}		% add contents line for List of Figures
    \@starttoc{toc}%
}
\renewcommand\listoffigures{%
    \chapter*{\listfigurename
        \@mkboth{%
           \labelfamily\listfigurename}{\labelfamily\listfigurename}}%
    \addcontentsline{toc}{section}{List of Figures}		% add contents line for List of Figures
    \@starttoc{lof}%
}
\renewcommand\listoftables{%
    \chapter*{\listtablename
        \@mkboth{%
           \labelfamily\listtablename}{\labelfamily\listtablename}}%
    \addcontentsline{toc}{section}{List of Tables}		% add contents line for List of Tables
    \@starttoc{lot}%
}
\fi

%    ****************************************
%    *           INITIALIZATION             *
%    ****************************************
%
% Default initializations

\ps@thesis                  % 'thesis' page style
\pagenumbering{arabic}      % Arabic page numbers
\onecolumn                  % Single-column.
\if@twoside\else\raggedbottom\fi % Ragged bottom unless twoside option.

%%%% Changed this commands to avoid floats all ending up at end of
%%%% chapter.

\renewcommand{\textfraction}{0.10}
\renewcommand{\topfraction}{0.80}
\renewcommand{\bottomfraction}{0.80}
\renewcommand{\floatpagefraction}{0.80}
\setcounter{totalnumber}{10}

%% END %%


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%        How to convert a AASTeX 5.0 paper into a thesis chapter        %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
%  (Note changing a AASTeX 4.0 paper to thesis style requires nearly
%  identical steps)
%
%  * Change paper title -> chapter title:
%        \title{text} -> \chapter[text]{text}
%           (the two versions in \chapter are for what shows up in the
%           table of contents vs. what shows up at the start of the
%           chapter)
%
%  * Optional: Label the chapter   e.g. \label{ch2}
%
%  * Optional: Define a \FigDir (only if you are using the \figcaption
%        macro that CJD created
%
%  * Remove header stuff:
%        \documentclass (or \documentstyle for old papers)
%        \begin{document}
%        \slugcomment
%        \author, \affil, \email, \shortauthors, \shorttitle, etc
%        \keywords
%
%  * Optional: Move the \newcommand{}s to define.tex
%
%  * Optional: Move \usepackage{}s to Thesis.tex and delete in chapter
%
%  * Change \begin{abstract} -> \begin{chabstract}  (ditto for \end{})
%
%  * Optional: change all citations and references to have, for
%        example, ``ch1'' in them.  That is, \citet{dol00} ->
%        \citet{ch1:dol00}.  This is to prevent instances of
%        ``Citation multiply defined'' or (even worse) a section
%        number multiply defined (i.e., what happens if you have
%        \label{sec:discussion} in both Chapters 1 & 2 and then you
%        have a \ref{sec:discussion} in Chapter 3?  Better to have
%        \ref{ch2:discussion}, I say)
%
%  * Move figures to their appropriate places in the text (usually
%        where you put the \placefigure{}s eariler)
%
%  * Put \fixspacing in every figure caption, and add short captions for the figures to go in the list of figures
%
%  * Define short titles for each figure/table
%    (they will show up in List of Tables/Figures)
%   ex: \caption[short title goes here]{\fixspacing Longer caption...}
%
%  * Input subdirectories in path for each chapter (AAK, 8/2/08)
%
%  * Put \fixspacing in every footnote
%
%  * Change \appendix to \chapappendix and add \endchapappendix
%
%  * Fix tables:
%        - Put \fixspacing in every \tablenotetext
%        - Remove the \rotate commands and put \begin{landscape} and
%          \end{landscape around the \begin,\end{deluxetable} commands
%          where needed
%        - Take out \tabletypesize{\scriptsize} (AAK, 8/2/08)
%
%  * Remove footer stuff:
%        \end{document}
%           (Note if you forget to do this you will get a very
%           mysterious error message like:
%           \end occurred when \iftrue on line 85 was incomplete)
%
%  * If references/citations do not work for you when compiling Thesis.tex
%     with whatever LaTeX editor you use, you may have to manually create
%     each chapter's .bbl file with BibTex.
%    Process:
%      1. latex/pdftex/etc. Thesis.tex 
%          -> will produce .aux files for each chapter
%      2. in Chap# directory, ln -s ../thesis.bst
%         -> creates symbolic link to bibliography style file
%      3. in Chap# directory, bibtex chap#.aux
%         -> creates chap#.bbl file
%      4. latex/pdftex/etc. Thesis.tex (repeat as needed)
%
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Other miscellanea
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
%    If you have so many equations and symbols floating around that
%     you actually run out of Greek letters to use, a table of symbols
%     would be greatly appreciated by your committee.
%
%    To do this, use the nomenclature package (nomencl) and in Thesis.tex,
%      - uncomment the \makenomenclature 
%      - uncomment \renewcommand{\nomlabel}[1]{\hfil #1\hfil}
%      - uncomment \renewcommand{\nomname}{List of Abbreviations and Symbols}
%      - uncomment \addcontentsline{toc}{section}{List of Selected Abbreviations and Symbols}
%      - uncomment {\fixspacing \small
%                  \printnomenclature[1in]
%                  }
%
%       or else just put these lines in! 
%       usepackage and makenomenclature go before begin{document}
%       the rest go after \listoffigures and before \mainmatter
%
%       In order to properly compile, you need to:
%        - pdflatex (or whatever)
%        - makeindex Thesis.nlo -s nomencl.ist -o Thesis.nls
%        - pdflatex
%
%%%%%%%%
%
%      If you want to have epigraphs, use the epigraph package!
%       \epigraph{bon mot, \textit{format it too!}}{clever person}
%
%      These go after \chapter and before \cleardoublepage