thesis.tex

\documentclass[12pt, a4paper]{report}

% Add paths to search for files. This should be before the imports.
\makeatletter
\def\input@path{%
  {Classes/}%
}
\makeatother

% Define language as Australian when loading babel package
% This is primarily for the hyphenation
\PassOptionsToPackage{australian}{babel}

\usepackage{thesis}
\usepackage{preamble}

\setstretch{1.4}

% Get version number
\input{version}

\title{Liquid Dynamics and Crystal Melting of a Two Dimensional Molecule}
\author{Malcolm Ramsay}
\uni{The University of Sydney}
\dept{School of Chemistry}
% This is to put the version information on the title page, to replace with the
% crest upon submission/acceptance
\crest{\vspace{25mm}}
% \crest{\Huge\bf v\version}
%\crest{\includegraphics[width=25mm]{USYD_Logo}}
\principaladvisor{Professor Peter Harrowell}
\coprincipaladvisor{Dr Asaph Widmer-Cooper}

\tablespagefalse{}
\figurespagefalse{}

\addbibresource{bibliography/bibliography.bib}

\usepackage[style=iso]{datetime2}
\date{\today{}}

\begin{document}

\beforepreface{}
\contributionsignature
\abstract{
  \input{99_Frontmatter/abstract}
}
\afterpreface{}

\chapter{Introduction} \label{sec:Introduction}
\input{00_Introduction/introduction}

\chapter{Methods} \label{sec:Methods}

\input{01_Methods/Molecular_Dynamics}
\input{01_Methods/Dynamics}
\input{01_Methods/Machine_Learning}
\input{01_Methods/Measuring_Melting}
\input{01_Methods/Simulation_Conditions}

\chapter{Dynamics of the Trimer Model} \label{sec:Dynamics}
\input{02_Dynamics/introduction}
\input{02_Dynamics/standard_dynamics}
\input{02_Dynamics/conclusion}

\chapter{Understanding Glassy Dynamics} \label{sec:Glassy_Dynamics}
\input{03_Glassy_Dynamics/introduction}
\input{03_Glassy_Dynamics/molecular_relaxation}
\input{03_Glassy_Dynamics/stokes_einstein_debye}
\input{03_Glassy_Dynamics/conclusion}

\chapter{Local Structure Identification Using Machine Learning} \label{sec:Machine_Learning}
\input{04_Machine_Learning/introduction}
\input{04_Machine_Learning/clustering}
\input{04_Machine_Learning/supervised_learning}
\input{04_Machine_Learning/conclusion}

\chapter{Modelling Crystal Melting Rates} \label{sec:Crystal_Melting}
\input{05_Crystal_Melting/introduction}
\input{05_Crystal_Melting/thermodynamics}
\input{05_Crystal_Melting/rates}
\input{05_Crystal_Melting/conclusion}

\chapter{Understanding Crystal Melting} \label{sec:Melting_Behaviour}
\input{06_Melting_Behaviour/introduction}
\input{06_Melting_Behaviour/static_analysis}
\input{06_Melting_Behaviour/dynamic_analysis}
\input{06_Melting_Behaviour/conclusion}

\chapter{Conclusion}
\input{07_Conclusion/conclusion}

{
  \sloppy
  \printbibliography[title={Literature Cited}, heading=bibintoc]{}
}

\begin{appendices}
  \chapter{Computational Methods}  \label{sec:computational_methods}
  \input{08_Appendix/Computational_Methods}
  \chapter{Software Projects} \label{sec:software_projects}
  \input{08_Appendix/Projects}
  \chapter{Code Snippets} \label{sec:code_snippets}
  \input{08_Appendix/code_snippets}
\end{appendices}

\end{document}