%++++++++ OU DISSERTATION TEX FILE ++++++++++
%
% This accompanies OUthesis.cls and is formatted for a thesis according to
% the rules of the OU grad college in 2013. If you are not in this year, it is your
% responsibility to make sure the rules have not changed.
% A certain basic understanding of the LaTeX mechanisms is assumed when using this document.
% In particular, if your compiler complains that you do not have a package, it is your responsibility to find how to get and install said package.
% For starters, you can try www.ctan.org on the World Wide Web.
%----------------------------------------------------------++
% If you change or update this, please comment so the next person
% can benefit from the upgrade -- Thanks!
% List of known contributors
% - Larry Maddox (original author)
% - Allison McCoy-Fleshman
% - Bobby Fleshman
% - Stephane Valladier

\documentclass[oneside, letterpaper, 12pt]{OUthesis}
%---------------------------------------------------------------
%       Author, Title, and Year
%---------------------------------------------------------------
% Place Author Name, Dissertation Title, and Year of defense here
% The grad college only wants year, not month or day
% I know, ALL CAPS are ugly, but the Grad College does not want small caps, we have to deal with this.
% For title, if it is long, put \\ where you want to break it into two lines the way YOU want it to look (LaTeX breaks stuff where it wants)
\newcommand{\nam}{PHILLIP BRENTON MCCOY}
\newcommand{\disstitle}{
    %Flavor Changing Neutral Currents in a general
    % Two Higgs Doublet Model:
    % using an extended Higgs sector to search for new physics.
    FLAVOR CHANGING NEUTRAL CURRENTS IN A \\
    GENERAL TWO HIGGS DOUBLET MODEL: \\
    USING AN EXTENDED HIGGS SECTOR TO SEARCH FOR NEW PHYSICS
    %A PHENOMENOLOGICAL APPROACH TO PHYSICS BEYOND THE STANDARD MODEL
}
\newcommand{\yr}{2017}
\newcommand{\department}{HOMER L. DODGE DEPARTMENT OF PHYSICS AND ASTRONOMY}

\newcommand{\kts}{\ensuremath{k_T} }
\newcommand{\kt}{\ensuremath{k_T}\index{}}
\newcommand{\unit}[2]{\ensuremath{\,\mathrm{#2}^{#1}}}% easy command for units with exponents
\newcommand{\tto}[1]{\ensuremath{\times10^{#1}}}% makes the typing of powers of ten much easier
%---------------------------------------------------------------
%       Document Specific Packages:
%---------------------------------------------------------------

\usepackage{Brent}
%\usepackage{amsmath}
%\usepackage{atlasphysics}
%\usepackage{url}
\usepackage[utf8]{luainputenc}
\usepackage[]{geometry}
\usepackage{subfigure}
%\usepackage[caption=false]{subfig}
\usepackage{caption}
\usepackage{epstopdf}
\usepackage{multirow}
\usepackage{multicol}
\usepackage{graphicx}
%\usepackage{xspace}
\usepackage{rotating} 
\usepackage{longtable}
%\usepackage{setspace}
\usepackage[mathscr]{euscript}
\usepackage{layout}
\usepackage{xfrac}
\usepackage{cleveref}
\usepackage{enumitem,lipsum}
\usepackage{lscape}
%\usepackage{fancyhdr}
\usepackage[compat=1.1.0]{tikz-feynman}
\usetikzlibrary{positioning,arrows}
\usetikzlibrary{decorations.pathmorphing}
\usetikzlibrary{decorations.markings}
\usetikzlibrary{intersections}
\usepackage{tikz}
\usepackage{xr}
%\usepackage{subfloat}
\usepackage{epigraph}
\usepackage{tablefootnote}[2014/01/26]
%
%\epigraphfontzise{\small\itshape}
\setlength\epigraphwidth{8cm}
\setlength\epigraphrule{0pt}


%===============================================================
%                MARGINS!!!
%===============================================================
%
% THE GRAD COLLEGE IS EXTREMELY PICKY ABOUT THIS
% Here, the settings give:
% Left margin: 1.625"=1"+5/8" (required min=1.6", max=2.0", 1"+5/8" is easy to measure with a standard office ruler, the kind of tool the graduate college people have.)
% Right margin: 1.125"=1"+1/8" (required min=1.0", max=1.5", 1"+1/8" is easy to measure with a standard office ruler, the kind of tool the graduate college people have.)
% Top Margin: 1.125"=1"+1/8" (required min=1.0", max=1.5", 1"+1/8" is easy to measure with a standard office ruler, the kind of tool the graduate college people have.)
% Bottom margin: 1.125"=1"+1/8" (this goes to either the text or footnote if used)(required min=1.0", max=1.5", 1"+1/8" is easy to measure with a standard office ruler, 
% the kind of tool the graduate college people have.)
% These margins are just inside of the minimum margins allowed by the Grad college
% This was done so there will be no debate or issue when the final version is printed
% It is better to be safe than sorry in this case, even if it adds more white space throughout the document
%---------------------------------------------------------------
% LEFT and RIGHT margins
% LaTeX imposes a default left margin of 1in anyway, so we only need to add a tad to that
\setlength{\oddsidemargin}{0.625in} % checked
% LaTeX imposes a default right margin of 1in anyway, so we only need to add a tad to that
\setlength{\evensidemargin}{0.125in} %checked
% If we do not specify the text width, LaTeX algorithms will figure out the optimal text width to typeset your content into, given the required margins. The following 
% \textwidth forces laTeX to use the maximum text width possible, given the required margins.
\setlength{\textwidth}{5.75in}
% The following 2 quantities are set to zero, because you should not be using margin notes in your dissertation. Footnotes are the way to go.
\setlength{\marginparwidth}{0pt}
\setlength{\marginparsep}{0pt}
% TOP and BOTTOM margins
% LaTeX imposes a default top margin of 1in anyway, so we only need to add a tad to that
%%\setlength{\topmargin}{0.125in}
%    \usepackage[
%    top    = 2.75cm,
%    bottom = 2.50cm,
%    left   = 3.00cm,
%    right  = 2.50cm]{geometry}
%    \usepackage[top = 0.125 in, bottom = 0 in, left = 0 in, right = 0 in]{geometry}
% To optimize the total textheight (minimize paper use), set the following 3 lengths to 0
\setlength{\headheight}{0pt}
\setlength{\headsep}{0pt}
\setlength{\topskip}{0pt}
% Setting \textheight to 8.75in ensures that the margin from the bottom of the page to the baseline of the last line of body text or footnote text will equal 1"+1/8"
\setlength{\textheight}{8.75in}
% Setting \footskip to 0.5in ensures that the margin from the bottom of the page to the baseline of the page number equals 0.5"+1/8"
\setlength{\footskip}{0.25in}
\pagestyle{plain}
%--------------------------------------------------------------------------------------------------
%	Layout options for 'fullpage'
%--------------------------------------------------------------------------------------------------
%\setlength{\oddsidemargin}{0pt}
%\setlength{\marginparwidth}{0pt}
%\setlength{\marginparsep}{0pt}
%\setlength{\footskip}{25pt}
%\setlength{\textheight}{676pt}
%\setlength{\textwidth}{550pt}
\setlength{\headsep}{25pt}
\setlength{\voffset}{.125in}
%
%
%===============================================================
%---------------------------------------------------------------
%       Loading packages
%---------------------------------------------------------------
% IMPORTANT: despite what it looks like in the package, setspace DOES produce a spacing between successive baselines of 24pt when using
% \doublespacing and a 12pt size font, which is INDEED a double spacing.
\usepackage{setspace} % Allows to simply switch from \singlespacing to \onehalfspacing or \doublespacing
% UNcomment the line below to add line numbers for reading copies
%\usepackage{lineno} % adds line numbers, OMIT THIS FOR FINAL VERSION!!!!!
\usepackage{graphicx} % Unless your document has absolutely no figures in it, this package is mandatory
\usepackage{multirow} % Allows to combine rows in tables
\usepackage{indentfirst} %indents first line of paragraph after  a new section begins

% I added 'perpage' to have letters represent footnotes, and refresh the footnote counter on each page
% It is valuable to have letters to call footnotes rather than numbers for scientific documents, as footnote numbers might be mistaken for exponents/powers
\usepackage{perpage}
\MakePerPage{footnote} %the perpage package command
\renewcommand{\thefootnote}{\alph{footnote}}	%Alphabetic (lowercase), e.g., a, b, c...
%
%---------------------------------------------------------------
%       Bibliography information
%---------------------------------------------------------------
\usepackage[numbers, comma, sort&compress]{natbib} % sorts and compresses bib ref numbers into 3-6, instead of 6,3,5,4. Saves you the trouble of thinking about the right order, you have other things to do.
%       See natbib manual for more info.
%       For a bibliography style, you must have the appropriate .bst file
%       Journals you should have been publishing into, or that you have been reading from, have their own bibliography style file available on their website
%       Use whichever you want, Grad College does not care.
%       I wrote my own bst file. The natbib package ships with soem other bst files. One of LaTeX default bst file is unsrt:
\bibliographystyle{unsrt}
%
%---------------------------------------------------------------
%       Define New commands here
%---------------------------------------------------------------
%   I accumulated so many commands over my years in Grad School that I have my own style file (package) of macros.
%   If you have a small set of personal macrocommands, you should define here, like \fig
\newcommand{\rhotc}{ \ensuremath{\widetilde{\rho}_{tc}} } 
\newcommand{\rhotamu}{ \ensuremath{\widetilde{\rho}_{\tau \mu}} } 
\newcommand{\fig}{\textbf{Fig.}~}
\newcommand{\vev}{\ensuremath{VEV\xspace}}
\newcommand{\doublet}[2]
{
   \begin{pmatrix} #1 \\ #2 \end{pmatrix}
}
%
\newcommand{\Tdoublet}[2]{ \ensuremath{ \genfrac{(}{)}{0pt}{1}{#1}{#2} } }
%
\newcommand{\Ctriplet}[3]
{
   \begin{pmatrix} #1 \\ #2 \\ #3 \end{pmatrix}
 }
%
\newcommand{\Rtriplet}[3]
{
   \begin{pmatrix} #1 & #2 & #3 \end{pmatrix}
 }
%
\newcommand{\cosba}{ \ensuremath{\cos(\beta - \alpha)} }
\newcommand{\sinba}{ \ensuremath{\sin(\beta - \alpha)} }
%
\newcommand{\rotmatrix}[1]
{
    \begin{pmatrix}  $\ensuremath{\cos#1}$  &  $\ensuremath{-\sin#1}$  \\  $\ensuremath{\sin#1}$  &  $\ensuremath{\cos#1}$  \end{pmatrix}
}
\newcommand{\INVrotmatrix}[1]
{
    \begin{pmatrix}  $\ensuremath{\cos#1}$  &  $\ensuremath{\sin#1}$  \\  $\ensuremath{-\sin#1}$  &  $\ensuremath{\cos#1}$  \end{pmatrix}
}
\newcommand{\GENrotMat}[4]
{
    \begin{pmatrix}  $\ensuremath{#1}$  &  $\ensuremath{#2}$  \\  $\ensuremath{#3}$  &  $\ensuremath{#4}$  \end{pmatrix}
}
\newcommand{\Gfive}{ \ensuremath{\gamma_{5}} }
\newcommand{\Gdn}[1]{ \ensuremath{\gamma_{#1}} }
\newcommand{\Gup}[1]{ \ensuremath{\gamma^{#1}} }
\newcommand{\Bindentenum}[1][\arabic*)]{\begin{enumerate}[leftmargin=1.5cm, rightmargin=1.5cm, label= #1]}
\newcommand{\Eindentenum}{\end{enumerate}}
\newcommand{\refFlag}[1]{{\color{red} ref: #1}}
\newcommand{\PhiPhidagger}[2]{ \ensuremath{\Phi^{\dagger}_{#1} \Phi_{#2}} }
\newcommand{\hc}{ \ensuremath{ \text{H.c.} } }
\newcommand{\tamu}{ \ensuremath{\tau \mu} }
\newcommand{\MET}{ \ensuremath{\slashed{E}_{T}} }
%
%===============================================================
%===============================================================
%===============================================================
\begin{document}
\doublespacing % The whole thesis is supposed to be double spaced. The spacing will be switched locally when needed
\frontmatter
%---------------------------------------------------------------
%       TITLE Page				
%---------------------------------------------------------------

% YOU SHOULDN'T HAVE TO CHANGE ANYTHING HERE!!
% If you are getting something other than Doctor of Philosophy
% like fine arts or education, then change "Degree of " whatever you are getting
% GRAD COLLEGE has the appropriate name of your college and degree, so follow that

\thispagestyle{empty}
\begin{center}
UNIVERSITY OF OKLAHOMA \\
GRADUATE COLLEGE

\vspace*{\fill}
{\disstitle}

\vspace{1.5in}
\textsc {A DISSERTATION\\ SUBMITTED TO THE GRADUATE FACULTY} \\
in partial fulfillment of the requirements for the \\
Degree of \\
\textsc{DOCTOR OF PHILOSOPHY}

\vspace*{\fill}

By

\singlespacing
\nam\\
Norman, Oklahoma\\
\yr

\end{center}
\newpage

%---------------------------------------------------------------
%       Committee SIGNATURE Page   			
%---------------------------------------------------------------

\thispagestyle{empty}
\vspace*{\fill}

% Your dissertation/thesis title is retyped here. Thanks to the package setspace, we can easily apply the necessary changes to the line spacing requirements of the Grad College.
% The grad college requires a multi line title to be single spaced here, as opposed to double spaced on the previous page.
\begin{center}
\singlespacing
\disstitle

%\vspace*{\fill}
\vfill
A DISSERTATION APPROVED FOR THE \\
% The Graduate college has a list for the official name of your department/unit
\department

\vfill
BY
\end{center}
%
\vspace*{\fill}
%
\begin{flushright}
 \begin{minipage}[t]{3in}
  \begin{flushleft}
% Grad college requires that you include prefix to name (Dr., Mr., or Mrs/Ms.)
% Do not put anything else other than name and (Chair) or (Co-chair)
\raggedleft{
% ________________________________________
  \hrulefill\\[-8pt]
  \vspace{-5pt}
  Dr. Chung Kao, Chair \\[15pt]
% ________________________________________
  \hrulefill\\[-8pt]
  \vspace{-5pt}
  Dr. Keri Kornelson \\[15pt]
% ________________________________________
  \hrulefill\\[-8pt]
  \vspace{-5pt}
  Dr. Howard Baer \\[15pt] 
% ________________________________________
  \hrulefill\\[-8pt]
  \vspace{-5pt}
  Dr. Ronald Kantowski   \\[15pt]
% ________________________________________
  \hrulefill\\[-8pt]
  \vspace{-5pt}
  Dr. Ian Sellers \\[15pt]
% ________________________________________
}
 % \hrulefill\\[-8pt]
 % Dr.\ Committee M.\ Member4
% Copy and paste the above as many times as necessary to add committee members. Remove the cochair if you don't have one.
\end{flushleft}
 \end{minipage}
\end{flushright}
%\vspace*{\fill}
\newpage

%---------------------------------------------------------------
%       Copyright Page   			
%---------------------------------------------------------------
%You should not have to alter this page

\thispagestyle{empty}
\vspace*{\fill}

\begin{center}
\singlespacing
\copyright\ Copyright \nam \ \yr \\
 All Rights Reserved.
\end{center}
\doublespacing
%
%---------------------------------------------------------------
%       Acknowledgments  Page   			
%---------------------------------------------------------------
% This is where your acknowledgments file goes, make sure to include directory if not in
% the same folder as this *.tex file
%\begin{acknowledgements}
    \input{Acknowledgements}
%`\end{acknowledgements}
%
%---------------------------------------------------------------
%       Lists of Tables and Lists of Figures			
%---------------------------------------------------------------

\singlespacing\small
\tableofcontents


%Automatically updates list of tables (with captions and page numbers)
\listoftables

%Automatically updates list of Figures (with captions and page numbers)
\listoffigures

\doublespacing
\normalsize

%---------------------------------------------------------------
%       Abstract  Page   			
%---------------------------------------------------------------

% This is where your abstract goes, make sure to include directory if not in
% the same folder as this *.tex file
%\input{definitions}
\include{abstract_v1.1}


\mainmatter

%---------------------------------------------------------------
%       Text of Dissertation begins		
%---------------------------------------------------------------
%   Use \input statements to add text.  This keeps the main
%   tex file smaller.  This will also make revisions easier.
%   Remember that the name of the file is <filename>.tex,
%   but extensions are not entered in the input statement.
%---------------------------------------------------------------
%\linenumbers

\externaldocument[1-]{./Chapter1/chapter1_v2.1}
\input{./Chapter1/chapter1_v2.0}

\externaldocument[2-]{./Chapter2/chapter2_v2.0}
\input{./Chapter2/chapter2_v2.0}

\externaldocument[3-]{./Chapter3/chapter3_v2.0}
\input{./Chapter3/chapter3_v2.0}

\externaldocument[4-]{./Chapter4/chapter4_v2.0}
\input{./Chapter4/chapter4_v2.0}

\externaldocument[5-]{./Chapter5/chapter5_v2.0}
\input{./Chapter5/chapter5_v2.0}

%\input{./Chapter/theory2}
%\input{results}


\backmatter
%---------------------------------------------------------------
%       BIBLIOGRAPHY go here 			
%---------------------------------------------------------------
\addcontentsline{toc}{chapter}{REFERENCES} %  adds "REFERENCES" to the table of content
%======================== IMPORTANT ===========================
% As of 2013, within one reference, the space between baselines must be single.
% The space between items must be double.
% It seems the LaTeX uses list-spacing parameters to typeset the bibliography (other formatting options belonging to the bst file).
%---------------------------------------------------------------
\singlespacing\small
%This is a *.bib file
%\bibliography{H:/Doc_de_Stef/PhD/Literature/JabRefDatabases/Literature}
%\bibliographystyle{utphys}
\bibliographystyle{h-physrev5}
%\bibliography{bmccoyDissertation_bibliography}
\bibliography{bmccoyDissertation_bibliography_v2.0}
%---------------------------------------------------------------
%       In this area, the appendices, and possibly the index
%       will go in.  Refer to your favorite LaTeX book for
%       more details.
%---------------------------------------------------------------
\doublespacing
\normalsize

\appendix

\input{./Appendices/AppendixA_software}

\input{./Appendices/AppendixB_dataTables}
%---------------------------------------------------------------
%       APPENDICES go here 			
%---------------------------------------------------------------
%\doublespacing
%\normalsize
%\appendix
%\input{tune.tex}
%\input{experimental/appendix.tex}

%\pagebreak
%\layout

\end{document}


% CONGRATULATIONS ON YOUR DEFENSE AND GRADUATION! GOOD LUCK WITH YOUR FUTURE! 
