thesis.tex

%
% UCSD Doctoral Dissertation Template
% -----------------------------------
% Fernando Serrano Paolo <fpaolo@ucsd.edu>
% Version 0 - Jun 1, 2015
%
%
% ----------------------------------------------------------------------
% WARNING: 
%
%   This template has not endorced by OGS or any other official entity.
%   The official formatting guide can be obtained from OGS.
%   It can be found on the web here:
%   http://ogs.ucsd.edu/AcademicAffairs/Documents/Dissertations_Theses_Formatting_Manual.pdf
%
%   No guaranty is made that this LaTeX class conforms to the official UCSD guidelines.
%   Make sure that you check the final document against the Formatting Manual.
%  
%   That being said, this class has been routinely used for successful 
%   publication of doctoral theses.  
%
%   The ucsd.cls class files are only valid for doctoral dissertations.
%
%
% ----------------------------------------------------------------------
% GETTING STARTED:
%
%   Lots of information can be found on the project wiki:
%   http://code.google.com/p/ucsd-thesis/wiki/GettingStarted
%
%
%   To make a pdf from this template use the command:
%     pdflatex template
%
%
%   To get started please read the comments in this template file 
%   and make changes as appropriate.
%
%   If you successfully submit a thesis with this package please let us
%   know.
%
%
% ----------------------------------------------------------------------
% KNOWN ISSUES:
%
%   Currently only the 12pt size conforms to the UCSD requirements.
%   The 10pt and 11pt options make the footnote fonts too small.
%
%
% ----------------------------------------------------------------------
% HELP/CONTACT:
%
%   If you need help try the ucsd-thesis google group:
%   http://groups.google.com/group/ucsd-thesis
%
%
% ----------------------------------------------------------------------
% BUGS:
%
%   Please report all bugs at:
%   http://code.google.com/p/ucsd-thesis/issues/list
%
%
% ----------------------------------------------------------------------
% More control of the formatting of your thesis can be achieved through
% modifications of the included LaTeX class files:
%
%   * ucsd.cls    -- Class file
%   * uct10.clo   -- Configuration files for font sizes 10pt, 11pt, 12pt
%     uct11.clo                            
%     uct12.clo
%
% ----------------------------------------------------------------------



% Setup the documentclass 
% default options: 12pt, oneside, final
%
% fonts: 10pt, 11pt, 12pt -- are valid for UCSD dissertations.
% sides: oneside, twoside -- note that two-sided theses are not accepted 
%                            by OGS.
% mode: draft, final      -- draft mode switches to single spacing, 
%                            removes hyperlinks, and places a black box
%                            at every overfull hbox (check these before
%                            submission).
% chapterheads            -- Include this if you want your chapters to read:
%                              Chapter 1
%                              Title of Chapter
%
%                            instead of
%                              1 Title of Chapter
\documentclass[12pt,chapterheads]{ucsd}



% Include all packages you need here.  
% Some standard options are suggested below.
%
% See the project wiki for information on how to use 
% these packages. Other useful packages are also listed there.
%
%   http://code.google.com/p/ucsd-thesis/wiki/GettingStarted

%% MARGINS
\usepackage[
left=1.5in,
right=1in,
top=1in,
bottom=1.25in,
]{geometry}


%% LANGUAGE AND QUOTATION MARKS
% it fixes quotation marks: " " => `` ''
\usepackage [english]{babel}
\usepackage [autostyle, english=american]{csquotes}
\MakeOuterQuote{"}


%% MICROTYPE
\usepackage[
activate={true,nocompatibility},
final,
tracking=true,
kerning=true,
spacing=true,
factor=1100,
stretch=10,
shrink=10
]{microtype}
% activate={true,nocompatibility} - activate protrusion and expansion
% final - enable microtype; use "draft" to disable
% tracking=true, kerning=true, spacing=true - activate these techniques
% factor=1100 - add 10% to the protrusion amount (default is 1000)
% stretch=10, shrink=10 - reduce stretchability/shrinkability (default is 20/20)

% CHAPTERS AND SECTIONS
%\usepackage[]{titlesec}
%\titleformat{\chapter}{\normalfont\huge}{\thechapter.}{20pt}{\huge\it}


% FOOTNOTES - formatting the defaul footnotes (reverse indent and marging)
\makeatletter
\renewcommand\@makefntext[1]{\leftskip=2em\hskip-2em\@makefnmark#1} % 2em and -2em
\makeatother

%% AMS PACKAGES - Chances are you will want some or all 
%    of these if writing a dissertation that includes equations.
\usepackage{amsmath, amscd, amssymb, amsthm}

% Define a command \overbar, which reduces the width of \overline by 1.5mu on each side
\newcommand{\overbar}[1]{\mkern1.5mu\overline{\mkern-1.5mu#1\mkern-1.5mu}\mkern 1.5mu}

% Define a command \del, which reduces the spacing of \partial by 1.5mu on the right 
\newcommand{\del}[1][]{\partial\mkern-1.5mu}


% Define a command \vect, for bold non-italic vector notation
\newcommand{\vect}[1]{\mathbf{#1}} % undergrad algebra version
%\newcommand{\vect}[1]{#1}          % pure math version
%\newcommand{\vect}[1]{\bm{#1}}     % ISO complying version

%% BOLD MATH
\usepackage{bm}

%% SYMBOLS
\usepackage{gensymb}

%% GRAPHICX - This is the standard package for 
%    including graphics for latex/pdflatex.
%    use 'draft' to replace the figures with a black frame
\usepackage[final]{graphicx}  % final | draft

%% SUBFIG - Use this to place multiple images in a
%    single figure.  Subfig will handle placement and
%    proper captioning (e.g. Figure 1.2(a))
%\usepackage{subfig}

%% CAPTIONS - Use this to customized captions 
\usepackage[font=footnotesize,labelfont=bf]{caption}
\usepackage[leftcaption,raggedright]{sidecap}
% the following format will be used to emulate the captions produced by fltpage
\DeclareCaptionLabelFormat{adja-page}{\hrulefill\\#1 #2 (\emph{previous page})}

%% TABLES
\usepackage{longtable}

%% FONTS - replacements for Computer Modern
% Times
% \usepackage[T1]{fontenc}
% \usepackage{mathptmx}

% Palatino
%\usepackage{mathpazo}

% Bitstream Charter
\usepackage[T1]{fontenc}
\usepackage[charter]{mathdesign} % w/math

% URLs with hyphenation
\usepackage[hyphens]{url}
\urlstyle{rm}

% DROP CAPS
\usepackage{lettrine}

%% INDEX
%   Uncomment the following two lines to create an index: 
% \usepackage{makeidx}
% \makeindex
%   You will need to uncomment the \printindex line near the
%   bibliography to display the index.  Use the command
% \index{keyword} 
%   within the text to create an entry in the index for keyword.
%   To compile a LaTeX document with an index the 'makeindex'
%   command will need to be run.  See the wiki for more details.

% BIBLIOGRAPHY - Set to be handled with LaTeX + BibLaTeX
\usepackage[
backend=bibtex,
style=authoryear,
%citestyle=authoryear,
%bibstyle=alpha,
maxnames=2,
firstinits=true,
uniquename=false,
isbn=false,
url=false,
doi=false,
eprint=false,
refsegment=chapter,    % if using a global .bib file
%refsection=chapter,   % if using multiple .bib files
]{biblatex}

% suppress 'field' from refs
\AtEveryBibitem{%
  \clearfield{day}%
  \clearfield{month}%
  \clearfield{note}%
  \clearfield{issue}%
  \clearfield{number}%
  \clearfield{series}%
} 

% suppress 'pp.' before page number
\DeclareFieldFormat{pages}{#1}

% thin spaces between initials
\renewcommand*{\mkbibnamefirst}[1]{{\iffirstinits{\let~\,}{}#1}}

% suppres 'in:' for journal names
\renewbibmacro{in:}{%
  \ifentrytype{article}{}{\printtext{\bibstring{in}\intitlepunct}}}

% to use square brackets instead of parenthesis
\newrobustcmd*{\parentexttrack}[1]{%
  \begingroup
  \blx@blxinit
  \blx@setsfcodes
  \blx@bibopenparen#1\blx@bibcloseparen
  \endgroup}
\AtEveryCite{%
  \let\parentext=\parentexttrack%
  \let\bibopenparen=\bibopenbracket%
  \let\bibcloseparen=\bibclosebracket}

\DeclareCiteCommand{\citeyearpar}[\mkbibparens]
  {\boolfalse{citetracker}%
   \boolfalse{pagetracker}%
   \usebibmacro{prenote}}
  {\printfield{year}\printfield{extrayear}}
  {\multicitedelim}
  {\usebibmacro{postnote}}

% spacing between entries
\setlength{\bibitemsep}{.3cm}

%\setlength{\bibitemsep}{\baselineskip}
\bibliography{thesis}  % global bibliography file

%% HYPERLINKS
%   To create a PDF with hyperlinks, you need to include the hyperref package.
%   THIS HAS TO BE THE LAST PACKAGE INCLUDED!
%   Note that the options plainpages=false and pdfpagelabels exist
%   to fix indexing associated with having both (ii) and (2) as pages.
%   Also, all links must be black according to OGS.
%   See: http://www.tex.ac.uk/cgi-bin/texfaq2html?label=hyperdupdest
%   Note: This may not work correctly with all DVI viewers (i.e. Yap breaks).
%   NOTE: hyperref will NOT work in draft mode, as noted above.
% \usepackage[colorlinks=true, pdfstartview=FitV, 
%             linkcolor=black, citecolor=black, 
%             urlcolor=black, plainpages=false,
%             pdfpagelabels]{hyperref}
% \hypersetup{ pdfauthor = {Your Name Here}, 
%              pdftitle = {The Title of The Dissertation}, 
%              pdfkeywords = {Keywords for Searching}, 
%              pdfcreator = {pdfLaTeX with hyperref package}, 
%              pdfproducer = {pdfLaTeX} }


\begin{document}



%% FRONT MATTER
%
%  This includes the title, degree, dedication, vita, abstract, etc..
\include{frontmatter}


%% DISSERTATION

% A common strategy here is to include files for each of the chapters. I.e.,
% Place the chapters is separate files: 
%   chapter1.tex, chapter2.tex
% Then use the commands:

\include{chapter1}
\begingroup
\ssp
\printbibliography[segment=1,heading=subbibliography,maxnames=99]
\endgroup
%%
\include{chapter2}
\begingroup
\ssp
\printbibliography[segment=2,heading=subbibliography,maxnames=99]
\endgroup
%%
\include{chapter3}
\begingroup
\ssp
\printbibliography[segment=3,heading=subbibliography,maxnames=99]
\endgroup

\include{chapter4}
\begingroup
\ssp
\printbibliography[segment=4,heading=subbibliography,maxnames=99]
\endgroup


%
% Of course, if you prefer, you can just start with
%   \chapter{My First Chapter Name}
% and start typing away.  
%\chapter{Just a Test}
%This is only a test.
%\section{A section}
%Lorem ipsum dolor sit amet, consectetuer adipiscing elit. Nulla odio
%sem, bibendum ut, aliquam ac, facilisis id, tellus. Nam posuere pede
%sit amet ipsum. Etiam dolor. In sodales eros quis pede.  Quisque sed
%nulla et ligula vulputate lacinia. In venenatis, ligula id semper
%feugiat, ligula odio adipiscing libero, eget mollis nunc erat id orci.
%Nullam ante dolor, rutrum eget, vestibulum euismod, pulvinar at, nibh.
%In sapien. Quisque ut arcu. Suspendisse potenti. Cras consequat cursus
%nulla.
%\subsection{More Stuff}
%Blah
%
%\begin{figure}[h] 
%  \centering
%  *
%  \caption{A figure of Vonnegut.\index{Vonnegut}} 
%\end{figure}
%
%
%
%\appendix
%\chapter{Final notes}
%  Remove me in case of abdominal pain.





%% END MATTER
% \printindex %% Uncomment to display the index
% \nocite{Shepherd2010}  %% Put any references that you want to include in the bib 
%               but haven't cited in the braces.
% \bibliographystyle{alpha}  %% This is just my personal favorite style. 
%                              There are many others.
% \bibliography{myrefs}  %% This looks for the bibliography in myrefs.bib 
%                          which should be formatted as a bibtex file.
\end{document}