%%% -*-LaTeX-*-
%%% ====================================================================
%%% This is a sample top-level LaTeX-2e file for typesetting a thesis
%%% or dissertation at the University of Utah.  Most students find it
%%% convenient to start with a COPY of this file as a template, and
%%% then alter that copy to match their needs.
%%%
%%% This version differs from sample-thesis-1, in that it incorporates
%%% a published paper as the contents of a chapter, and for that reason,
%%% the Thesis Office rules require a separate bibliography in each
%%% chapter that has literature citations.
%%%
%%% There is an associated Unix Makefile that can be similarly
%%% customized, and then the only command ever needed to typeset the
%%% complete thesis is the single word "make".  Of course, during
%%% writing and typesetting, not all of the steps are needed, so
%%% often, one can just name a convenience target such as "make
%%% dvi-pass" or "make pdf-pass" to do just a single pass of LaTeX and
%%% BibTeX.
%%%
%%% There should be no, or very few, macro definitions in this file;
%%% any needed belong in a private style file, called mythesis.sty,
%%% and input below after all other packages.  The bulk of this file
%%% should just be command invocations, and any arguments that they
%%% need.
%%%
%%% We exploit the fact that TeX ignores spaces after command names to
%%% line up arguments for better readability.
%%%
%%% Each chapter should be a separate complete file, so that you can
%%% insert a command like \includeonly{chap_intro} before the first
%%% \include{chap_xxx} command to avoid typesetting all but the
%%% chapter that you are currently working on, to save time.
%%%
%%% Remember that occupants of job positions change jobs from time to
%%% time: YOU are responsible for ensuring correct names of all humans
%%% mentioned in this file!
%%%
%%% [16-Mar-2016]
%%% ====================================================================

\documentclass[11pt,Chicago]{uuthesis2e}

%%% Undefine two macros from uuthesis2e.cls that conflict with
%%% definitions in amsthm.sty that fail to check for prior definitions!
%%% NB: The amsthm package refines the LaTeX theorem environment,
%%% and the uuthesis-color-headings wraps that definition, so the
%%% amsthm package must be read first!
\let \proof    = \relax
\let \endproof = \relax
\usepackage {amsthm}

%%% ====================================================================
%%% Choose an alternate font family for the document if the TeX default
%%% of Computer Modern is not wanted:

\usepackage{mathpazo}

%%% ====================================================================
%%% Some miscellaneous Utah- and student-specific settings:
%%%
%%% Chapter is one level, section and subsection are the next two levels.

\fourlevels

%%% ====================================================================
%%% The remaining packages are required by this particular thesis,
%%% but other theses will almost certainly need different packages:
%%%
%%% WARNING: MANY \LaTeX{} packages change dimensions, glue, and/or
%%% formatting styles, and such changes are likely to conflict with
%%% University of Utah Thesis Office requirements.  Therefore, minimize
%%% the number of packages that you include!

\usepackage {amsmath}
\usepackage {amssymb}
\usepackage {bm}
\usepackage {bibnames}
\usepackage {citesort}
\usepackage {graphicx}
\usepackage {graphpap}
\usepackage {longtable}
\usepackage {multirow}
\usepackage {pdfpages}
\usepackage {tikz}
\usetikzlibrary {decorations.markings}
\usepackage {varioref}

%%% ====================================================================
%%% The various uuthesis-*.sty packages must come AFTER all other
%%% system-provided packages, so that they can correctly override
%%% settings from those packages.

%%% Include latest updates for 2016 (WARNING: the name is subject to
%%% change: see http://www.math.utah.edu/pub/uuthesis/ for the most
%%% current version.)

\usepackage {uuthesis-2016-h}  % MANDATORY package

%%% Use one or the other of these:
% \usepackage {color}
\usepackage {uuthesis-color-headings}
\definecolor{utahheadingcolor} {rgb}  {0.7, 0.0, 0.0}
\definecolor{utahtheoremcolor} {rgb}  {0.490,0.149,0.804} % purple4
\definecolor{utahtheoremcolor} {rgb}  {0.545,0.137,0.137} % brown4

%%% Here is another, and more convenient, way to define colors, via
%%% aliases of named colors in the X11-derived rgb.sty file

\usepackage{coloralias}
\definecoloralias{utahheadingcolor}{steelblue4}
\definecoloralias{utahtheoremcolor}{hotpink3}

%%% The default heading color is utahred (defined by University Printing
%%% Services as 0.8 red, 0.0 green, 0.0 blue), but you could redefine
%%% that to, for example, a dark blue color, like this AFTER including
%%% the package:
%%%
%%%     \definecolor{utahheading}{rgb}{0,0,0.8}
%%%
%%% NB: Be careful with use of colors in typesetting, and in figures,
%%% because about 6 percent of the human male population is red/green
%%% color blind: they see those colors as shades of brown.  Red and
%%% blue, or blue and green, are better choices for choosing
%%% distinguishable colors.  Also, avoid light colors, especially
%%% yellow, because they are hard to see against white paper and
%%% screen backgrounds, and when printed on black-and-white printers,
%%% where they are rendered in gray, they may be too faint to read.

%%% ====================================================================
%%% Support for a subject index:

\usepackage {uuthesis-index}

%%% ====================================================================
%%% Support for running page headers

%%: \usepackage{uuthesis-pageheaders}

%%% ====================================================================
%%% Support for chapter bibliographies (must come AFTER
%%% uuthesis-pageheaders, if that package is loaded)

\usepackage {uuthesis-chapterbib}

%%% ====================================================================
%%% This single user-specific file is where all personal customizations
%%% and macro definitions should be placed, and it should come LAST,
%%% after ALL OTHER packages, in case it needs to override some of their
%%% definitions.

\usepackage {mythesis}

%%% ====================================================================
%%% The student-specific front matter fields are defined here:

\author                 {Jane Doe}
\title                  {INTEGRAL ESTIMATION IN QUANTUM PHYSICS}
\thesistype             {dissertation}

\dedication             {For my parents, Alice and Bob.}

%%% Most students need just a short degree name, like this:
\degree                 {Doctor of Philosophy}
%%% However, multiline degrees are possible, and are done like this:
\degree                 {Doctor of Philosophy \\
                         in \\
                         Mathematical Physics}

%%% College- and Department-level definitions:
\approvaldepartment     {Mathematics}
\department             {Department of Mathematics}
\graduatedean           {Alice B. Toklas}
\departmentchair        {Petrus Marcus Aurelius Featherstone-Hough}

%%% The graduate student's committee members:
\committeechair         {Cornelius L{\'a}nczos}
\firstreader            {Hans Bethe}
\secondreader           {Niels Bohr}
\thirdreader            {Max Born}
\fourthreader           {Paul A. M. Dirac}
\chairtitle             {Professor}

%%% NB: It is rare, but possible, for there to be two chairs, For
%%% example, one student had
%%%
%%% \committeechair{\mbox{\small Andrej Cherkaev and Andrejs Treibergs}}
%%%
%%% The \mbox{} ensures that line breaks cannot happen, and the \small
%%% is necessary to make the names fit on the Dissertation Approval form

%%% Dates that must be adjusted for each academic term, and be permitted
%%% according to the University of Utah Thesis Office:
\submitdate             {May 2016}
\copyrightyear          {2016}

%%% Dates on which committee members approved the thesis
\chairdateapproved      {17 Feb 2016}
\firstdateapproved      {17 Feb 2016}
\seconddateapproved     {17 Feb 2016}
\thirddateapproved      {17 Feb 2016}
\fourthdateapproved     {17 Feb 2016}

%%% ====================================================================
%%% Typesetting begins here:

\begin{document}

%% Comment out items by inserting a percent % character
\frontmatterformat
\titlepage
\copyrightpage
\dissertationapproval
\setcounter {page}     {2}             % UofU Thesis Office demands abstract on p. iii: start one lower
\preface    {abstract} {Abstract}
\dedicationpage
\tableofcontents
\listoffigures
\listoftables
%
%%% Optional front matter page(s), made from source "notation.tex". If
%%% you don't need it, then comment out the \optionalfront command
%%% line!  The first argument is the (unnumbered) section header for
%%% the text supplied by the file input by the second argument; that
%%% file must NOT contain \chapter, \section, \subsection, \ldots{}
%%% sectioning commands.

\optionalfront {Notation and Symbols} {\input{notation}}

%%% Uncomment this is you want the contents of acknowledge.tex typeset here.
%%% Note that both "Acknowledgement" and "Acknowledgment" are accepted
%%% spellings of that word.

% \preface{acknowledge}{Acknowledgements}

%%% Demonstrations of thesis typesetting features for the sample thesis.
%%% Once you have seen the examples, you can comment out this line.
\optionalfront {Typesetting Experiments} {\input{samples.tex}}
\maintext       % Start normal page numbering: parts and chapters follow.

\pagestyle{plain} % TEMPORARY EXPERIMENT: override default page headers
\pagestyle{headings} % TEMPORARY EXPERIMENT: override default page headers

\include {chap1}
\include {chap2}
\include {chap3}
\include {chap4}
\include {chap5}     % NEW for sample-thesis-2

% \numberofappendices = 1   % Set 0 for none, else number of appendices.
\numberofappendices = 3
\appendix       % Chapters, sections are now appendix style A, A.1, A.2, B, C, D, ...

\include {appa}
\include {appb}
\include {appc}

%%% The choice of bibliography style is a major decision, jointly made
%%% by you, your thesis advisor and the thesis editor. Common choices are
%%% one of the four standard BibTeX styles (abbrv, alpha, plain, and unsrt),
%%% or enhanced styles like acm, amsplain, siam, and hundreds of others
%%% available in TeX Live, and other Unix and Windows TeX distributions.
%%%
%%% Do NOT handcode your reference list, because you are unlikely to
%%% achieve consistency or conformance to the University of Utah Thesis Office
%%% requirements: let BibTeX do that tedious job for you!
%%%
%%% Remember that reference-list metadata in BibTeX files remains
%%% constant across journals and publishers, and is are often reused
%%% in other documents and shared with others, whereas formatted
%%% reference-list styles change: with BibTeX, you only need to record
%%% the metadata once.
%%%
%%% If you prefer named, rather than numeric or tagged citations, you
%%% may use styles such as authordate{1,2,3,4}, chicago, harvard, or
%%% natbib.  Be aware, however, that most of those require an
%%% additional \usepackage{} command to supply \LaTeX{} with
%%% definitions of commands that the style needs, and that there are
%%% usually several flavors of LaTeX citation commands beyond the
%%% standard \cite{} command that you need to understand before you
%%% can use them properly in your prose.

%%% This tells BibTeX to read siam.bst from the first directory where
%%% it is found in the BSTINPUTS search path.  However, for chapterbib
%%% use, the style is defined in each chapter/appendix file that needs
%%% a bibliography.  Thus, we suppress it here:

%%% \bibliographystyle{siam}

%%% This can also specify a comma-separated list (without embedded
%%% spaces) of *.bib files found by BibTeX in its BIBINPUTS search
%%% path.  The argument \jobname means the base name of the top-level
%%% LaTeX file, avoiding an unnecessary filename dependence here.
%%%
%%% BibTeX writes only one .bbl file, no matter how many *.bib files
%%% are listed here, using the name \jobname.bbl.
%%%
%%% LaTeX reads BibTeX's formatted reference list from the file
%%% \jobname.bbl.  For chapterbib use, there is no end-of-volume
%%% bibliography, so we suppress it here:

%%% \bibliography{\jobname}

%%% The last part of this sample thesis is two specialized indexes,
%%% and a general topic index.  If the companion Makefile is used to
%%% create the DVI or PDF file for this work, the topic index excludes
%%% the lengthy list of free software packages.  However, the biology
%%% names of the first index are included in the topic index.

%%% Switch from thesis double spacing to single spacing for the three
%%% indexes, as a matter of style (to match the reference list), and
%%% for compactness.

\singlespace

%%% Define several index cross references (there are many more such
%%% in chap1.tex, but the examples here give a useful summary of how
%%% they are made):

\index{DCT|see{discrete cosine transform}}
\index{DWT|see{discrete wavelet transform}}
\index{Borel measure ($\mu$)}
\index{mu@$\mu$ (mu)|see{Borel measure}}
\index{Escherichia coli@\bioname{Escherichia coli}|see{E. coli}}
\index{transform|seealso{Discrete DCT Transform}}
\index{transform|seealso{Fast Fourier Transform}}

\renewcommand {\bioname} [1] {\emph{#1}}   % redefine to suppress color and indexing in index
\renewcommand {\fsfname} [1] {\texttt{#1}} % redefine to suppress color and indexing in index

\renewcommand {\indexname} {Binomial Nomenclature Index}

\input{\jobname-bioname.ind}

\renewcommand {\indexname} {Free Software Index}

\input{\jobname-fsfname.ind}

\renewcommand {\indexname} {Topic Index}

\overfullrule = 0pt % suppress visible warnings about overfull hboxes
\printindex

\end {document}
