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Merge pull request 'personalisation' (#1) from personalisation into develop

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4
Chapter1/chapter1.tex
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@ -3,7 +3,7 @@
%*********************************** First Chapter *****************************
%*******************************************************************************
\chapter{Getting started} %Title of the First Chapter
\chapter{Introduction} %Title of the First Chapter
\ifpdf
\graphicspath{{Chapter1/Figs/Raster/}{Chapter1/Figs/PDF/}{Chapter1/Figs/}}
@ -97,4 +97,4 @@ Time}
\nomenclature[z-USL]{USL}{Update Stress Last}
\nomenclature[s-crit]{crit}{Critical state}
\nomenclature[z-DKT]{DKT}{Draft Kiss Tumble}
\nomenclature[z-PPC]{PPC}{Particles per cell}
\nomenclature[z-PPC]{PPC}{Particles per cell}

2
Chapter2/chapter2.tex
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@ -3,7 +3,7 @@
%****************************** Second Chapter *********************************
%*******************************************************************************
\chapter{My second chapter}
\chapter{Preparation}
\ifpdf
\graphicspath{{Chapter2/Figs/Raster/}{Chapter2/Figs/PDF/}{Chapter2/Figs/}}

2
Chapter3/chapter3.tex
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@ -2,7 +2,7 @@
%*******************************************************************************
%****************************** Third Chapter **********************************
%*******************************************************************************
\chapter{My third chapter}
\chapter{Implementation}
% **************************** Define Graphics Path **************************
\ifpdf

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Chapter4/chapter4.tex Normal file
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@ -0,0 +1,156 @@
%!TEX root = ../thesis.tex
%*******************************************************************************
%****************************** Fourth Chapter *********************************
%*******************************************************************************
\chapter{Evaluation}
% **************************** Define Graphics Path **************************
\ifpdf
\graphicspath{{Chapter4/Figs/Raster/}{Chapter4/Figs/PDF/}{Chapter4/Figs/}}
\else
\graphicspath{{Chapter4/Figs/Vector/}{Chapter4/Figs/}}
\fi
\section{First section of the third chapter}
And now I begin my third chapter here \dots
And now to cite some more people~\citet{Rea85,Ancey1996}
\subsection{First subsection in the first section}
\dots and some more
\subsection{Second subsection in the first section}
\dots and some more \dots
\subsubsection{First subsub section in the second subsection}
\dots and some more in the first subsub section otherwise it all looks the same
doesn't it? well we can add some text to it \dots
\subsection{Third subsection in the first section}
\dots and some more \dots
\subsubsection{First subsub section in the third subsection}
\dots and some more in the first subsub section otherwise it all looks the same
doesn't it? well we can add some text to it and some more and some more and
some more and some more and some more and some more and some more \dots
\subsubsection{Second subsub section in the third subsection}
\dots and some more in the first subsub section otherwise it all looks the same
doesn't it? well we can add some text to it \dots
\section{Second section of the third chapter}
and here I write more \dots
\section{The layout of formal tables}
This section has been modified from ``Publication quality tables in \LaTeX*''
by Simon Fear.
The layout of a table has been established over centuries of experience and
should only be altered in extraordinary circumstances.
When formatting a table, remember two simple guidelines at all times:
\begin{enumerate}
\item Never, ever use vertical rules (lines).
\item Never use double rules.
\end{enumerate}
These guidelines may seem extreme but I have
never found a good argument in favour of breaking them. For
example, if you feel that the information in the left half of
a table is so different from that on the right that it needs
to be separated by a vertical line, then you should use two
tables instead. Not everyone follows the second guideline:
There are three further guidelines worth mentioning here as they
are generally not known outside the circle of professional
typesetters and subeditors:
\begin{enumerate}\setcounter{enumi}{2}
\item Put the units in the column heading (not in the body of
the table).
\item Always precede a decimal point by a digit; thus 0.1
{\em not} just .1.
\item Do not use `ditto' signs or any other such convention to
repeat a previous value. In many circumstances a blank
will serve just as well. If it won't, then repeat the value.
\end{enumerate}
A frequently seen mistake is to use `\textbackslash begin\{center\}' \dots `\textbackslash end\{center\}' inside a figure or table environment. This center environment can cause additional vertical space. If you want to avoid that just use `\textbackslash centering'
\begin{table}
\caption{A badly formatted table}
\centering
\label{table:bad_table}
\begin{tabular}{|l|c|c|c|c|}
\hline
& \multicolumn{2}{c}{Species I} & \multicolumn{2}{c|}{Species II} \\
\hline
Dental measurement & mean & SD & mean & SD \\ \hline
\hline
I1MD & 6.23 & 0.91 & 5.2 & 0.7 \\
\hline
I1LL & 7.48 & 0.56 & 8.7 & 0.71 \\
\hline
I2MD & 3.99 & 0.63 & 4.22 & 0.54 \\
\hline
I2LL & 6.81 & 0.02 & 6.66 & 0.01 \\
\hline
CMD & 13.47 & 0.09 & 10.55 & 0.05 \\
\hline
CBL & 11.88 & 0.05 & 13.11 & 0.04\\
\hline
\end{tabular}
\end{table}
\begin{table}
\caption{A nice looking table}
\centering
\label{table:nice_table}
\begin{tabular}{l c c c c}
\hline
\multirow{2}{*}{Dental measurement} & \multicolumn{2}{c}{Species I} & \multicolumn{2}{c}{Species II} \\
\cline{2-5}
& mean & SD & mean & SD \\
\hline
I1MD & 6.23 & 0.91 & 5.2 & 0.7 \\
I1LL & 7.48 & 0.56 & 8.7 & 0.71 \\
I2MD & 3.99 & 0.63 & 4.22 & 0.54 \\
I2LL & 6.81 & 0.02 & 6.66 & 0.01 \\
CMD & 13.47 & 0.09 & 10.55 & 0.05 \\
CBL & 11.88 & 0.05 & 13.11 & 0.04\\
\hline
\end{tabular}
\end{table}
\begin{table}
\caption{Even better looking table using booktabs}
\centering
\label{table:good_table}
\begin{tabular}{l c c c c}
\toprule
\multirow{2}{*}{Dental measurement} & \multicolumn{2}{c}{Species I} & \multicolumn{2}{c}{Species II} \\
\cmidrule{2-5}
& mean & SD & mean & SD \\
\midrule
I1MD & 6.23 & 0.91 & 5.2 & 0.7 \\
I1LL & 7.48 & 0.56 & 8.7 & 0.71 \\
I2MD & 3.99 & 0.63 & 4.22 & 0.54 \\
I2LL & 6.81 & 0.02 & 6.66 & 0.01 \\
CMD & 13.47 & 0.09 & 10.55 & 0.05 \\
CBL & 11.88 & 0.05 & 13.11 & 0.04\\
\bottomrule
\end{tabular}
\end{table}

156
Chapter5/chapter5.tex Normal file
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@ -0,0 +1,156 @@
%!TEX root = ../thesis.tex
%*******************************************************************************
%****************************** Fifth Chapter **********************************
%*******************************************************************************
\chapter{Conclusions}
% **************************** Define Graphics Path **************************
\ifpdf
\graphicspath{{Chapter5/Figs/Raster/}{Chapter5/Figs/PDF/}{Chapter5/Figs/}}
\else
\graphicspath{{Chapter5/Figs/Vector/}{Chapter5/Figs/}}
\fi
\section{First section of the third chapter}
And now I begin my third chapter here \dots
And now to cite some more people~\citet{Rea85,Ancey1996}
\subsection{First subsection in the first section}
\dots and some more
\subsection{Second subsection in the first section}
\dots and some more \dots
\subsubsection{First subsub section in the second subsection}
\dots and some more in the first subsub section otherwise it all looks the same
doesn't it? well we can add some text to it \dots
\subsection{Third subsection in the first section}
\dots and some more \dots
\subsubsection{First subsub section in the third subsection}
\dots and some more in the first subsub section otherwise it all looks the same
doesn't it? well we can add some text to it and some more and some more and
some more and some more and some more and some more and some more \dots
\subsubsection{Second subsub section in the third subsection}
\dots and some more in the first subsub section otherwise it all looks the same
doesn't it? well we can add some text to it \dots
\section{Second section of the third chapter}
and here I write more \dots
\section{The layout of formal tables}
This section has been modified from ``Publication quality tables in \LaTeX*''
by Simon Fear.
The layout of a table has been established over centuries of experience and
should only be altered in extraordinary circumstances.
When formatting a table, remember two simple guidelines at all times:
\begin{enumerate}
\item Never, ever use vertical rules (lines).
\item Never use double rules.
\end{enumerate}
These guidelines may seem extreme but I have
never found a good argument in favour of breaking them. For
example, if you feel that the information in the left half of
a table is so different from that on the right that it needs
to be separated by a vertical line, then you should use two
tables instead. Not everyone follows the second guideline:
There are three further guidelines worth mentioning here as they
are generally not known outside the circle of professional
typesetters and subeditors:
\begin{enumerate}\setcounter{enumi}{2}
\item Put the units in the column heading (not in the body of
the table).
\item Always precede a decimal point by a digit; thus 0.1
{\em not} just .1.
\item Do not use `ditto' signs or any other such convention to
repeat a previous value. In many circumstances a blank
will serve just as well. If it won't, then repeat the value.
\end{enumerate}
A frequently seen mistake is to use `\textbackslash begin\{center\}' \dots `\textbackslash end\{center\}' inside a figure or table environment. This center environment can cause additional vertical space. If you want to avoid that just use `\textbackslash centering'
\begin{table}
\caption{A badly formatted table}
\centering
\label{table:bad_table}
\begin{tabular}{|l|c|c|c|c|}
\hline
& \multicolumn{2}{c}{Species I} & \multicolumn{2}{c|}{Species II} \\
\hline
Dental measurement & mean & SD & mean & SD \\ \hline
\hline
I1MD & 6.23 & 0.91 & 5.2 & 0.7 \\
\hline
I1LL & 7.48 & 0.56 & 8.7 & 0.71 \\
\hline
I2MD & 3.99 & 0.63 & 4.22 & 0.54 \\
\hline
I2LL & 6.81 & 0.02 & 6.66 & 0.01 \\
\hline
CMD & 13.47 & 0.09 & 10.55 & 0.05 \\
\hline
CBL & 11.88 & 0.05 & 13.11 & 0.04\\
\hline
\end{tabular}
\end{table}
\begin{table}
\caption{A nice looking table}
\centering
\label{table:nice_table}
\begin{tabular}{l c c c c}
\hline
\multirow{2}{*}{Dental measurement} & \multicolumn{2}{c}{Species I} & \multicolumn{2}{c}{Species II} \\
\cline{2-5}
& mean & SD & mean & SD \\
\hline
I1MD & 6.23 & 0.91 & 5.2 & 0.7 \\
I1LL & 7.48 & 0.56 & 8.7 & 0.71 \\
I2MD & 3.99 & 0.63 & 4.22 & 0.54 \\
I2LL & 6.81 & 0.02 & 6.66 & 0.01 \\
CMD & 13.47 & 0.09 & 10.55 & 0.05 \\
CBL & 11.88 & 0.05 & 13.11 & 0.04\\
\hline
\end{tabular}
\end{table}
\begin{table}
\caption{Even better looking table using booktabs}
\centering
\label{table:good_table}
\begin{tabular}{l c c c c}
\toprule
\multirow{2}{*}{Dental measurement} & \multicolumn{2}{c}{Species I} & \multicolumn{2}{c}{Species II} \\
\cmidrule{2-5}
& mean & SD & mean & SD \\
\midrule
I1MD & 6.23 & 0.91 & 5.2 & 0.7 \\
I1LL & 7.48 & 0.56 & 8.7 & 0.71 \\
I2MD & 3.99 & 0.63 & 4.22 & 0.54 \\
I2LL & 6.81 & 0.02 & 6.66 & 0.01 \\
CMD & 13.47 & 0.09 & 10.55 & 0.05 \\
CBL & 11.88 & 0.05 & 13.11 & 0.04\\
\bottomrule
\end{tabular}
\end{table}

16
Declaration/declaration.tex
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@ -2,16 +2,14 @@
\begin{declaration}
I hereby declare that except where specific reference is made to the work of
others, the contents of this dissertation are original and have not been
submitted in whole or in part for consideration for any other degree or
qualification in this, or any other university. This dissertation is my own
work and contains nothing which is the outcome of work done in collaboration
with others, except as specified in the text and Acknowledgements. This
dissertation contains fewer than 65,000 words including appendices,
bibliography, footnotes, tables and equations and has fewer than 150 figures.
I, Jake Hillion of Queens' College, being a candidate for Part II of the Computer Science
Tripos, hereby declare that this dissertation and the work described in it are my own work,
unaided except as may be specified below, and that the dissertation does not
contain material that has already been used to any substantial extent for a
comparable purpose. I am content for my dissertation to be made available to the
students and staff of the University.
% Author and date will be inserted automatically from thesis.tex \author \degreedate
\vspace{25mm}
\end{declaration}

29
PhDThesisPSnPDF.cls
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@ -1016,8 +1016,7 @@ wish to left align your text}
\chapter*{\centering \Large \@declarationtitle}
\thispagestyle{empty}
}{
\flushright
\@author{}\\
\noindent\@author{}\\
\@degreedate{}
\vfill
}
@ -1037,6 +1036,32 @@ wish to left align your text}
% ********************************** Proforma ***********************************
% The acknowledgements environment puts a large, bold, centered
% "Proforma" label at the top of the page.
\newenvironment{proforma}{
\cleardoublepage
\setsinglecolumn
\chapter*{\centering \Large Proforma}
\thispagestyle{empty}
}
% ********************************** Proposal ***********************************
% The acknowledgements environment puts a large, bold, centered
% "Project Proposal" label at the top of the page.
\newenvironment{proposal}{
\cleardoublepage
\setsinglecolumn
\chapter*{\centering \Large Project Proposal}
\addcontentsline{toc}{chapter}{Project Proposal}
\thispagestyle{empty}
}
% ******************************* Nomenclature *********************************
\RequirePackage[intoc]{nomencl}
\makenomenclature

4
Preamble/preamble.tex
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@ -73,6 +73,8 @@
% This is for people stuck with older versions of texlive
%\usepackage{sty/caption/subcaption}
\usepackage{subcaption}
\usepackage{pdfpages}
\usepackage{graphicx}
% ********************************** Tables ************************************
\usepackage{booktabs} % For professional looking tables
@ -123,7 +125,7 @@
\fi
% changes the default name `Bibliography` -> `References'
\renewcommand{\bibname}{References}
%\renewcommand{\bibname}{References}
% ******************************************************************************

9
Proforma/proforma.tex Normal file
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@ -0,0 +1,9 @@
% ************************** Thesis Proforma **************************
\begin{proforma}
Stuff to be filled in later.
\end{proforma}

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Proposal/proposal.tex Normal file
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@ -0,0 +1,6 @@
% ************************** Proposal **************************
\begin{proposal}
\includepdf[pages=-]{Proposal/project-proposal.pdf}
\end{proposal}

25
thesis-info.tex
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@ -1,30 +1,30 @@
% ************************ Thesis Information & Meta-data **********************
%% The title of the thesis
\title{Writing your PhD thesis in \texorpdfstring{\\ \LaTeX2e}{LaTeX2e}}
\title{A Multi-Path Bidirectional Layer 3 Proxy}
%\texorpdfstring is used for PDF metadata. Usage:
%\texorpdfstring{LaTeX_Version}{PDF Version (non-latex)} eg.,
%\texorpdfstring{$sigma$}{sigma}
%% Subtitle (Optional)
\subtitle{Using the CUED template}
%\subtitle{Using the CUED template}
%% The full name of the author
\author{Krishna Kumar}
\author{Jake Hillion}
%% Department (eg. Department of Engineering, Maths, Physics)
\dept{Department of Engineering}
\dept{Department of Computer Science}
%% University and Crest
\university{University of Cambridge}
% Crest minimum should be 30mm.
\crest{\includegraphics[width=0.2\textwidth]{University_Crest}}
%\crest{\includegraphics[width=0.2\textwidth]{University_Crest}}
%% Use this crest, if you are using the college crest
%% Crest long miminum should be 65mm
%\crest{\includegraphics[width=0.45\textwidth]{University_Crest_Long}}
\crest{\includegraphics[width=0.45\textwidth]{University_Crest_Long}}
%% College shield [optional]
% Crest minimum should be 30mm.
%\collegeshield{\includegraphics[width=0.2\textwidth]{CollegeShields/Kings}}
\collegeshield{\includegraphics[width=0.2\textwidth]{CollegeShields/Queens}}
%% Supervisor (optional)
@ -32,13 +32,15 @@
%\supervisor{Prof. A.B. Supervisor\newline
%Prof. C.D. Supervisor}
%\supervisor{Mike Dodson}
%% Supervisor Role (optional) - Supervisor (default) or advisor
% \supervisorrole{\textbf{Supervisors: }}
%% if no title is desired:
% \supervisorrole{}
%% Supervisor line width: required to align supervisors
%\supervisorlinewidth{0.35\textwidth}
%\supervisorlinewidth{0.20\textwidth}
%% Advisor (optional)
%% for multiple advisors, append each advisor with the \newline command
@ -60,15 +62,14 @@
%\renewcommand{\submissiontext}{change the default text here if needed}
%% Full title of the Degree
\degreetitle{Doctor of Philosophy}
\degreetitle{Bachelor of Arts}
%% College affiliation (optional)
\college{King's College}
\college{Queens' College}
%% Submission date
% Default is set as {\monthname[\the\month]\space\the\year}
%\degreedate{September 2014}
%% Meta information
\subject{LaTeX} \keywords{{LaTeX} {PhD Thesis} {Engineering} {University of
Cambridge}}
\subject{LaTeX} \keywords{{LaTeX} {Part II Dissertation} {Computer Science} {University of Cambridge}}

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thesis.pdf
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14
thesis.tex
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@ -113,10 +113,11 @@
\maketitle
\include{Dedication/dedication}
%\include{Dedication/dedication}
\include{Declaration/declaration}
\include{Acknowledgement/acknowledgement}
\include{Abstract/abstract}
\include{Proforma/proforma}
%\include{Acknowledgement/acknowledgement}
%\include{Abstract/abstract}
% *********************** Adding TOC and List of Figures ***********************
@ -137,8 +138,8 @@
\include{Chapter1/chapter1}
\include{Chapter2/chapter2}
\include{Chapter3/chapter3}
%\include{Chapter4/chapter4}
%\include{Chapter5/chapter5}
\include{Chapter4/chapter4}
\include{Chapter5/chapter5}
%\include{Chapter6/chapter6}
%\include{Chapter7/chapter7}
@ -184,4 +185,7 @@
% *************************************** Index ********************************
\printthesisindex % If index is present
% ************************************** Proposal ******************************
\include{Proposal/proposal}
\end{document}