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\documentclass[10pt,twoside]{report}
% Files to include
\includeonly{
preamble/title,
preamble/authorship,
preamble/abstract,
preamble/acknowledgements,
chapters/introduction,
chapters/chap1,
chapters/chap2,
chapters/chap3,
chapters/conclusion,
}
% Boolean variables
\newif \ifcontents \contentsfalse
\newif \ifbib \bibtrue
\newif \iflong \longtrue
% Packages
\usepackage[utf8]{inputenx}
\usepackage[english]{babel}
\usepackage{microtype}
\usepackage{fancyhdr}
\usepackage{listings}
\usepackage{appendix}
\usepackage{vmargin}
\usepackage{setspace}
\usepackage{mathenv}
\usepackage{amsmath}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amscd}
\usepackage{amsthm}
\usepackage{hyperref}
\usepackage{cleveref}
\usepackage{graphicx}
\usepackage{epstopdf}
\usepackage{subfigure}
\usepackage{color}
% Packages with options
\usepackage[labelfont=sc]{caption}
\usepackage[square, numbers, comma, sort&compress]{natbib}
% Layout options
\setlength{\parskip}{6pt}
% Compilation options
\synctex=1
% Setting for the table of contents
\setcounter{secnumdepth}{3}
\setcounter{tocdepth}{3}
% Macros
\definecolor{darkred}{rgb}{.7,0,0}
\newcommand{\real}[0]{\mathbf R}
\newcommand{\nat}[0]{\mathbf N}
\newcommand{\op}[0]{\mathcal}
\newcommand{\grad}[0]{\,\nabla\,}
\newcommand{\dive}[0] {\,\nabla\,\cdot\,}
\newcommand{\ip}[2]{\left \langle #1,#2 \right\rangle}
\newcommand{\norm}[1]{\,\| #1 \|\,}
\newcommand{\pard}[2]{\partial_{#2} #1}
\newcommand{\pardl}[2]{\frac{\partial #1}{\partial #2}}
\newcommand{\pardd}[2]{\partial_{#2}^2 #1}
\newcommand{\parddl}[2]{\frac{\partial^2 #1}{\partial #2^2}}
\newcommand{\dx}[0]{\mathrm d}
\newcommand{\hermite}[0]{\mathcal}
\newcommand{\gaussian}[1]{g_{#1}}
\newcommand{\stdgaussian}[0]{g}
\newcommand{\test}[1]{C^\infty_c(#1)}
\newcommand{\flp}[2]{L^{#1}(#2)}
\newcommand{\wlp}[3]{L^{#1}(#2, #3)}
\newcommand{\sobolev}[2]{H^{#1}(#2)}
\newcommand{\wsobolev}[3]{H^{#1}(#2, #3)}
\newcommand{\red}[1]{\textcolor{darkred}{#1}}
\newcommand{\HRule}{\rule{\linewidth}{0.5mm}}
% Theorems
\theoremstyle{plain}
\newtheorem{assumption}{Assumption}[section]
\newtheorem{example}{Example}[section]
\newtheorem{theorem}{Theorem}[section]
\newtheorem{corollary}[theorem]{Corollary}
\newtheorem{lemma}[theorem]{Lemma}
\newtheorem{proposition}[theorem]{Proposition}
\newtheorem{axiom}[theorem]{Axiom}
\theoremstyle{definition}
\newtheorem{definition}[theorem]{Definition}
\theoremstyle{remark}
\newtheorem{remark}[theorem]{Remark}
\begin{document}
\pagestyle{empty}
\setstretch{1.3}
\include{preamble/title} \cleardoublepage
\include{preamble/authorship} \cleardoublepage
\include{preamble/abstract} \cleardoublepage
\include{preamble/acknowledgements} \cleardoublepage
\ifcontents \tableofcontents \fi
\pagestyle{plain}
\include{chapters/introduction} \cleardoublepage
\include{chapters/chap1} \cleardoublepage
\include{chapters/chap2} \cleardoublepage
\include{chapters/chap3} \cleardoublepage
\include{chapters/conclusion} \cleardoublepage
\nocite*
\bibliographystyle{unsrtnat}
\bibliography{Bibliography}
\end{document}
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