Thesis master document

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%  Run LaTeX or pdfLaTeX on this file to produce your thesis.
%  To produce the abstract title page followed by the abstract,
%  see the file abstitle-phd.tex or abstitle-mas.tex.
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\documentclass[oneside]{book}
\usepackage[left=1.5in,right=1in,top=1in,bottom=1in]{geometry}
\usepackage{color}
\usepackage{xcolor}
\usepackage{nicefrac}
\usepackage{bm}
\usepackage{mathtools}
\usepackage{amssymb}
\usepackage{cancel}
\usepackage{amsfonts}
\usepackage{amsthm}
\usepackage{graphicx}
\usepackage{color}
\usepackage{tocloft}
\usepackage{setspace}
\usepackage[perpage]{footmisc}
\usepackage{xcolor}
\usepackage{fontspec}
\usepackage{adjustbox}
\usepackage[mmddyyyy]{datetime}
\usepackage[hidelinks]{hyperref}
\usepackage{unicode-math}
\usepackage{titlesec}
\interfootnotelinepenalty=9999
\pretolerance=1500
\relpenalty=9500
\binoppenalty=9500
\emergencystretch=0pt
\righthyphenmin=4
\lefthyphenmin=4
\titleformat{\chapter}
{\filcenter\normalfont\Large\bfseries}
{\MakeUppercase{\chaptertitlename}~\thechapter:} {0.5em} {}
\titlespacing{\chapter}{0pt}{0pt}{10pt}
\defaultfontfeatures{Ligatures=TeX}
\setmathfont[Path=\string~/texmf/,Extension=.otf]{xits-math}
\setmainfont{Latin Modern Roman}
\graphicspath{ {plots/} }
\usepackage{fancyhdr}% http://ctan.org/pkg/fancyhdr
\definecolor{mytext}{HTML}{BBBBBB}
\definecolor{mytext}{HTML}{BBBBBB}
\usepackage[hang]{caption}      % to indent subsequent lines of captions
\renewcommand{\captionfont}{\bfseries} % bold caption (needed with caption
                                       % package to restore boldface.)
%\includeonly{chap1}  % use \includeonly to process only
                         % the file(s) listed inside the braces
\pagestyle{fancy}
\fancyhead{}
\fancyfoot{}
\fancyhead[L]{\S\thesubsection}
\fancyhead[R]{\today}
\fancyfoot[C]{\thepage}
\graphicspath{ {millerpurseyplots/} }
%\renewcommand{\headrulewidth}{0pt}
\renewcommand{\footrulewidth}{0.4pt}
\renewcommand{\contentsname}{TABLE OF CONTENTS \today} %this is so every page has the date on it for drafts
\setlength\parindent{0pt}
\mathtoolsset{showonlyrefs,showmanualtags}
\renewcommand{\thefootnote}{\fnsymbol{footnote}}
\usepackage[toc,xindy,indexonlyfirst]{glossaries}
\newglossarystyle{mylong3col}{%
  \setglossarystyle{long3colheader}%
  \renewcommand\entryname{Symbol}
  \renewcommand{\pagelistname}{Page \mbox{Introduced}}
  \renewenvironment{theglossary}%
    {\setlength\LTleft{0pt}
     \setlength\LTright{0pt}
     \begin{longtable}[l]{@{}lp{0.675\textwidth}p{0.15\textwidth}}}%
    {\end{longtable}}%
}
\setglossarystyle{mylong3col}
\setlength{\glsdescwidth}{0.675\textwidth}
\newcommand{\myj}{\mathscr{j}}
\newcommand{\xs}{\gls*{boldx0}}
\newcommand{\x}{\gls*{boldx}}
\newcommand{\dfn}{\gls*{deltafn}}
\newcommand{\kron}{\gls*{kronecker}}
\newcommand{\dens}{\gls*{dens}}
\newcommand{\gi}{\gls*{gi}_i}
\input{glossary}
\makeatletter
\newcommand \Dotfill {\leavevmode \cleaders \hb@xt@ 0.8em{\hss .\hss }\hfill \kern \z@}
\makeatother
\renewcommand*\glspostdescription{\Dotfill}
\makeglossaries
\newcommand\numberthis{\addtocounter{equation}{1}\tag{\theequation}}
\numberwithin{equation}{section}
\setlength\cftsubsecnumwidth{4em}
\setlength\parskip{\baselineskip}
\newcommand{\negphantom}[1]{\settowidth{\dimen0}{#1}\hspace*{-\dimen0}}
\begin{document}
\newtheorem{prop}{Proposition}
\newtheorem{theorem}{Theorem}
\newtheorem{lemma}{Lemma}
\tableofcontents
\begin{spacing}{1.5}
\include{chap1} % chapter 1
\include{chap2} % chapter 2
\end{spacing}
\include{bib} % bibliography
\begin{spacing}{1.5}
\include{app}
\end{spacing}
\printglossary[title={LIST OF SYMBOLS}]
\end{document}