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.DS_Store*
*.aux
*.log
*.lof
*.lot
*.out
*.gz
*.toc
*.bbl
*.blg
*~
*.nlo

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% Thesis Abstract -----------------------------------------------------
%\begin{abstractslong} %uncommenting this line, gives a different abstract heading
\begin{abstracts} %this creates the heading for the abstract page
This is where you write your abstract ...
\end{abstracts}
%\end{abstractlongs}
% ----------------------------------------------------------------------
%%% Local Variables:
%%% mode: latex
%%% TeX-master: "../thesis"
%%% End:

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% Thesis Acknowledgements ------------------------------------------------
%\begin{acknowledgementslong} %uncommenting this line, gives a different acknowledgements heading
\begin{acknowledgements} %this creates the heading for the acknowlegments
And I would like to acknowledge ...
\end{acknowledgements}
%\end{acknowledgmentslong}
% ------------------------------------------------------------------------
%%% Local Variables:
%%% mode: latex
%%% TeX-master: "../thesis"
%%% End:

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\chapter{Appendix A}
and here I put a bit of postamble ...

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\chapter{Appendix B}
and here I put some more postamble ...

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%*****************************************************************************************
%*********************************** First Chapter ***************************************
%*****************************************************************************************
\chapter{Background} %Title of the First Chapter
%********************************** %First Section **************************************
\section{What is Loren Ipsum?} %Section - 1.1
Lorem Ipsum is simply dummy text of the printing and typesetting industry~\cref{section1.3}. Lorem Ipsum\citet{Agn2007} has been the industry's standard dummy text ever since the 1500s, when an unknown printer took a galley of type and scrambled it to make a type specimen book. It has survived not only five centuries, but also the leap into electronic typesetting, remaining essentially unchanged. It was popularised in the 1960s with the release of Letraset sheets containing Lorem Ipsum passages, and more recently with desktop publishing software like Aldus PageMaker including versions of Lorem Ipsum~\cite{AAB95,Con90,LM65}.
The most famous equation in the world: $E^2 = (m_0c^2)^2 + (pc)^2$ - The \textbf{energy-mass-momentum} relation as an in-line equation.
\begin{equation}
f(x)= \sin^2x+\frac{\tan \mathit{x}}{\log \mathit{x}} + \mathbf{X}^T\times\mathbf{X}
\end{equation}
%********************************** %Second Section *************************************
\section{Why do we use Loren Ipsum?} %Section - 1.2
It is a long established fact that a reader will be distracted by the readable content of a page when looking at its layout. The point of using Lorem Ipsum is that it has a more-or-less normal distribution of letters, as opposed to using `Content here, content here', making it look like readable English. Many desktop publishing packages and web page editors now use Lorem Ipsum as their default model text, and a search for 'lorem ipsum' will uncover many web sites still in their infancy. Various versions have evolved over the years, sometimes by accident, sometimes on purpose (injected humour and the like).
%********************************** % Third Section *************************************
\section{Where does it come from?} %Section - 1.3
\label{section1.3}
Contrary to popular belief, Lorem Ipsum is not simply random text. It has roots in a piece of classical Latin literature from 45 BC, making it over 2000 years old. Richard McClintock, a Latin professor at Hampden-Sydney College in Virginia, looked up one of the more obscure Latin words, consectetur, from a Lorem Ipsum passage, and going through the cites of the word in classical literature, discovered the undoubtable source. Lorem Ipsum comes from sections 1.10.32 and 1.10.33 of "de Finibus Bonorum et Malorum" (The Extremes of Good and Evil) by Cicero, written in 45 BC. This book is a treatise on the theory of ethics, very popular during the Renaissance. The first line of Lorem Ipsum, "Lorem ipsum dolor sit amet..", comes from a line in section 1.10.32.
The standard chunk of Lorem Ipsum used since the 1500s is reproduced below for those interested. Sections 1.10.32 and 1.10.33 from ``de Finibus Bonorum et Malorum" by Cicero are also reproduced in their exact original form, accompanied by English versions from the 1914 translation by H. Rackham
``Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum."
Section 1.10.32 of ``de Finibus Bonorum et Malorum", written by Cicero in 45 BC: ``Sed ut perspiciatis unde omnis iste natus error sit voluptatem accusantium doloremque laudantium, totam rem aperiam, eaque ipsa quae ab illo inventore veritatis et quasi architecto beatae vitae dicta sunt explicabo. Nemo enim ipsam voluptatem quia voluptas sit aspernatur aut odit aut fugit, sed quia consequuntur magni dolores eos qui ratione voluptatem sequi nesciunt. Neque porro quisquam est, qui dolorem ipsum quia dolor sit amet, consectetur, adipisci velit, sed quia non numquam eius modi tempora incidunt ut labore et dolore magnam aliquam quaerat voluptatem. Ut enim ad minima veniam, quis nostrum exercitationem ullam corporis suscipit laboriosam, nisi ut aliquid ex ea commodi consequatur? Quis autem vel eum iure reprehenderit qui in ea voluptate velit esse quam nihil molestiae consequatur, vel illum qui dolorem eum fugiat quo voluptas nulla pariatur?"
1914 translation by H. Rackham: ``But I must explain to you how all this mistaken idea of denouncing pleasure and praising pain was born and I will give you a complete account of the system, and expound the actual teachings of the great explorer of the truth, the master-builder of human happiness. No one rejects, dislikes, or avoids pleasure itself, because it is pleasure, but because those who do not know how to pursue pleasure rationally encounter consequences that are extremely painful. Nor again is there anyone who loves or pursues or desires to obtain pain of itself, because it is pain, but because occasionally circumstances occur in which toil and pain can procure him some great pleasure. To take a trivial example, which of us ever undertakes laborious physical exercise, except to obtain some advantage from it? But who has any right to find fault with a man who chooses to enjoy a pleasure that has no annoying consequences, or one who avoids a pain that produces no resultant pleasure?"
Section 1.10.33 of ``de Finibus Bonorum et Malorum", written by Cicero in 45 BC: ``At vero eos et accusamus et iusto odio dignissimos ducimus qui blanditiis praesentium voluptatum deleniti atque corrupti quos dolores et quas molestias excepturi sint occaecati cupiditate non provident, similique sunt in culpa qui officia deserunt mollitia animi, id est laborum et dolorum fuga. Et harum quidem rerum facilis est et expedita distinctio. Nam libero tempore, cum soluta nobis est eligendi optio cumque nihil impedit quo minus id quod maxime placeat facere possimus, omnis voluptas assumenda est, omnis dolor repellendus. Temporibus autem quibusdam et aut officiis debitis aut rerum necessitatibus saepe eveniet ut et voluptates repudiandae sint et molestiae non recusandae. Itaque earum rerum hic tenetur a sapiente delectus, ut aut reiciendis voluptatibus maiores alias consequatur aut perferendis doloribus asperiores repellat."
1914 translation by H. Rackham: ``On the other hand, we denounce with righteous indignation and dislike men who are so beguiled and demoralized by the charms of pleasure of the moment, so blinded by desire, that they cannot foresee the pain and trouble that are bound to ensue; and equal blame belongs to those who fail in their duty through weakness of will, which is the same as saying through shrinking from toil and pain. These cases are perfectly simple and easy to distinguish. In a free hour, when our power of choice is untrammelled and when nothing prevents our being able to do what we like best, every pleasure is to be welcomed and every pain avoided. But in certain circumstances and owing to the claims of duty or the obligations of business it will frequently occur that pleasures have to be repudiated and annoyances accepted. The wise man therefore always holds in these matters to this principle of selection: he rejects pleasures to secure other greater pleasures, or else he endures pains to avoid worse pains."

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\chapter{My Second Chapter}
\section[short title]{This is going to be a section with a very long section title that it might not fit TOC}
If you are having trouble viewing the document please send an email to the computing officer: \href{mailto:kks32@cam.ac.uk}{kks32@cam.ac.uk}\\
You can use SI Units like this: Density is 1000 \si{\kilogram\per\metre\cubed} and dynamic viscosity is $1.002 \times 10^{-3}$ \si{\newton\second\per\metre\squared}
I'm going to randomly include a picture~\cref{fig:minion}
\begin{figure}[htbp!]
\centering
\includegraphics[width=0.5\textwidth]{Chapter2/Figs/minion.jpg}
\caption[Minion]{This is just a long figure caption for the minion in Despicable Me from Pixar}
\label{fig:minion}
\end{figure}
\section*{Enumeration}
\begin{enumerate}
\item The first topic is dull
\item The second topic is duller
\begin{enumerate}
\item The first subtopic is silly
\item The second subtopic is stupid
\end{enumerate}
\item The third topic is dullest
\end{enumerate}
\section*{itemize}
\begin{itemize}
\item The first topic is dull
\item The second topic is duller
\begin{itemize}
\item The first subtopic is silly
\item The second subtopic is stupid
\end{itemize}
\item The third topic is dullest
\end{itemize}
\section*{description}
\begin{description}
\item[The first topic] is dull
\item[The second topic] is duller
\begin{description}
\item[The first subtopic] is silly
\item[The second subtopic] is stupid
\end{description}
\item[The third topic] is dullest
\end{description}
\clearpage
\textbf{Lorem ipsum dolor sit amet}, \textit{consectetur adipiscing elit}. In magna nisi, aliquam id blandit id, congue ac est. Fusce porta consequat leo. Proin feugiat at felis vel consectetur. Ut tempus ipsum sit amet congue posuere. Nulla varius rutrum quam. Donec sed purus luctus, faucibus velit id, ultrices sapien. Cras diam purus, tincidunt eget tristique ut, egestas quis nulla. Curabitur vel iaculis lectus. Nunc nulla urna, ultrices et eleifend in, accumsan ut erat. In ut ante leo. Aenean a lacinia nisl, sit amet ullamcorper dolor. Maecenas blandit, tortor ut scelerisque congue, velit diam volutpat metus, sed vestibulum eros justo ut nulla. Etiam nec ipsum non enim luctus porta in in massa. Cras arcu urna, malesuada ut tellus ut, pellentesque mollis risus.Morbi vel tortor imperdiet arcu auctor mattis sit amet eu nisi. Nulla gravida urna vel nisl egestas varius. Aliquam posuere ante quis malesuada dignissim. Mauris ultrices tristique eros, a dignissim nisl iaculis nec. Praesent dapibus tincidunt mauris nec tempor. Curabitur et consequat nisi. Quisque viverra egestas risus, ut sodales enim blandit at. Mauris quis odio nulla. Cras euismod turpis magna, in facilisis diam congue non. Mauris faucibus nisl a orci dictum, et tempus mi cursus.
Etiam elementum tristique lacus, sit amet eleifend nibh eleifend sed \footnote{My footnote goes blah blah blah! \dots}. Maecenas dapibus augue ut urna malesuada, non tempor nibh mollis. Donec sed sem sollicitudin, convallis velit aliquam, tincidunt diam. In eu venenatis lorem. Aliquam non augue porttitor tellus faucibus porta et nec ante. Proin sodales, libero vitae commodo sodales, dolor nisi cursus magna, non tincidunt ipsum nibh eget purus. Nam rutrum tincidunt arcu, tincidunt vulputate mi sagittis id. Proin et nisi nec orci tincidunt auctor et porta elit. Praesent eu dolor ac magna cursus euismod. Integer non dictum nunc.

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\chapter{My Third Chapter}
\section{First Section of the Third Chapter}
\markboth{\MakeUppercase{\thechapter. My Third Chapter }}{\thechapter. My Third Chapter}
And now I begin my third chapter here ...
And now to cite some more people~\cite{Rea85,Spi65}
\subsection{first subsection in the First Section}
... and some more
\subsection{second subsection in the First Section}
... and some more ...
\subsubsection{first subsub section in the second subsection}
... 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 ...
\subsection{third subsection in the First Section}
... and some more ...
\subsubsection{first subsub section in the third subsection}
... 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 ...
\subsubsection{second subsub section in the third subsection}
... 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 ...
\section{Second Section of the Third Chapter}
\markboth{\MakeUppercase{\thechapter. My Third Chapter }}{\thechapter. My Third Chapter}
and here I write more ...

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% These macros are used to declare arguments needed for the
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% The full (unabbreviated) name of the degree
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% The name of your college or department(eg. Trinity, Pembroke, Maths, Physics)
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% The name of your University
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%
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%
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%ABSTRACT
%
%The abstract environment puts a large, bold, centered "Abstract" label at
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%i.e. tabbed in at both sides, and on its own page.
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\begin{center}
\vspace*{1.5cm}
{\Large \bfseries Abstract}
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\vspace{0.5cm}
\begin{quote}}
{\end{quote}\end{alwayssingle}}
%The abstractlong environment puts a large, bold, centered "Abstract" label at
%the top of the page. The abstract itself does not appears in a quote
%environment so you can get more in.
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\begin{center}
\vspace*{1.5cm}
{\Large \bfseries Abstract}
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%on including title and author etc as required to be handed in separately
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\vspace*{-1in}
\begin{center}
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{{\large \vspace*{1ex} \@author} \par}
{\large \vspace*{1ex}
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%ROMANPAGES
%
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% for the contents and figures lists. It also resets
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\renewcommand{\thepage}{\roman{page}}}
{\newpage\renewcommand{\thepage}{\arabic{page}}}
%{\newpage\renewcommand{\thepage}{\arabic{page}}\setcounter{page}{1}}

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% Thesis Declaration ---------------------------------------------------
\begin{declaration} %this creates the heading for the dedication page
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 entirely the result of my own work and includes nothing which is the outcome of work done in collaboration. This dissertation contains less than 65,000 words, excluding table of contents, tables, figures, titles, footnotes, references and appendices.
%Permission has been granted by board of graduate studies to exceed the recommended limits 150 figures and to include a CD-ROM in the dissertation. This dissertation is presented less than 65,000 words and 210 figures.
\flushright
Krishna Kumar Soundararajan\\
2014
\end{declaration}

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% Thesis Dedictation ---------------------------------------------------
\begin{dedication} %this creates the heading for the dedication page
I would like to dedicate this thesis to my loving parents ...
\end{dedication}
% ----------------------------------------------------------------------
%%% Local Variables:
%%% mode: latex
%%% TeX-master: "../thesis"
%%% End:

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GNU GENERAL PUBLIC LICENSE
Version 2, June 1991
Copyright (C) 1989, 1991 Free Software Foundation, Inc., <http://fsf.org/>
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.
Preamble
The licenses for most software are designed to take away your
freedom to share and change it. By contrast, the GNU General Public
License is intended to guarantee your freedom to share and change free
software--to make sure the software is free for all its users. This
General Public License applies to most of the Free Software
Foundation's software and to any other program whose authors commit to
using it. (Some other Free Software Foundation software is covered by
the GNU Lesser General Public License instead.) You can apply it to
your programs, too.
When we speak of free software, we are referring to freedom, not
price. Our General Public Licenses are designed to make sure that you
have the freedom to distribute copies of free software (and charge for
this service if you wish), that you receive source code or can get it
if you want it, that you can change the software or use pieces of it
in new free programs; and that you know you can do these things.
To protect your rights, we need to make restrictions that forbid
anyone to deny you these rights or to ask you to surrender the rights.
These restrictions translate to certain responsibilities for you if you
distribute copies of the software, or if you modify it.
For example, if you distribute copies of such a program, whether
gratis or for a fee, you must give the recipients all the rights that
you have. You must make sure that they, too, receive or can get the
source code. And you must show them these terms so they know their
rights.
We protect your rights with two steps: (1) copyright the software, and
(2) offer you this license which gives you legal permission to copy,
distribute and/or modify the software.
Also, for each author's protection and ours, we want to make certain
that everyone understands that there is no warranty for this free
software. If the software is modified by someone else and passed on, we
want its recipients to know that what they have is not the original, so
that any problems introduced by others will not reflect on the original
authors' reputations.
Finally, any free program is threatened constantly by software
patents. We wish to avoid the danger that redistributors of a free
program will individually obtain patent licenses, in effect making the
program proprietary. To prevent this, we have made it clear that any
patent must be licensed for everyone's free use or not licensed at all.
The precise terms and conditions for copying, distribution and
modification follow.
GNU GENERAL PUBLIC LICENSE
TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
0. This License applies to any program or other work which contains
a notice placed by the copyright holder saying it may be distributed
under the terms of this General Public License. The "Program", below,
refers to any such program or work, and a "work based on the Program"
means either the Program or any derivative work under copyright law:
that is to say, a work containing the Program or a portion of it,
either verbatim or with modifications and/or translated into another
language. (Hereinafter, translation is included without limitation in
the term "modification".) Each licensee is addressed as "you".
Activities other than copying, distribution and modification are not
covered by this License; they are outside its scope. The act of
running the Program is not restricted, and the output from the Program
is covered only if its contents constitute a work based on the
Program (independent of having been made by running the Program).
Whether that is true depends on what the Program does.
1. You may copy and distribute verbatim copies of the Program's
source code as you receive it, in any medium, provided that you
conspicuously and appropriately publish on each copy an appropriate
copyright notice and disclaimer of warranty; keep intact all the
notices that refer to this License and to the absence of any warranty;
and give any other recipients of the Program a copy of this License
along with the Program.
You may charge a fee for the physical act of transferring a copy, and
you may at your option offer warranty protection in exchange for a fee.
2. You may modify your copy or copies of the Program or any portion
of it, thus forming a work based on the Program, and copy and
distribute such modifications or work under the terms of Section 1
above, provided that you also meet all of these conditions:
a) You must cause the modified files to carry prominent notices
stating that you changed the files and the date of any change.
b) You must cause any work that you distribute or publish, that in
whole or in part contains or is derived from the Program or any
part thereof, to be licensed as a whole at no charge to all third
parties under the terms of this License.
c) If the modified program normally reads commands interactively
when run, you must cause it, when started running for such
interactive use in the most ordinary way, to print or display an
announcement including an appropriate copyright notice and a
notice that there is no warranty (or else, saying that you provide
a warranty) and that users may redistribute the program under
these conditions, and telling the user how to view a copy of this
License. (Exception: if the Program itself is interactive but
does not normally print such an announcement, your work based on
the Program is not required to print an announcement.)
These requirements apply to the modified work as a whole. If
identifiable sections of that work are not derived from the Program,
and can be reasonably considered independent and separate works in
themselves, then this License, and its terms, do not apply to those
sections when you distribute them as separate works. But when you
distribute the same sections as part of a whole which is a work based
on the Program, the distribution of the whole must be on the terms of
this License, whose permissions for other licensees extend to the
entire whole, and thus to each and every part regardless of who wrote it.
Thus, it is not the intent of this section to claim rights or contest
your rights to work written entirely by you; rather, the intent is to
exercise the right to control the distribution of derivative or
collective works based on the Program.
In addition, mere aggregation of another work not based on the Program
with the Program (or with a work based on the Program) on a volume of
a storage or distribution medium does not bring the other work under
the scope of this License.
3. You may copy and distribute the Program (or a work based on it,
under Section 2) in object code or executable form under the terms of
Sections 1 and 2 above provided that you also do one of the following:
a) Accompany it with the complete corresponding machine-readable
source code, which must be distributed under the terms of Sections
1 and 2 above on a medium customarily used for software interchange; or,
b) Accompany it with a written offer, valid for at least three
years, to give any third party, for a charge no more than your
cost of physically performing source distribution, a complete
machine-readable copy of the corresponding source code, to be
distributed under the terms of Sections 1 and 2 above on a medium
customarily used for software interchange; or,
c) Accompany it with the information you received as to the offer
to distribute corresponding source code. (This alternative is
allowed only for noncommercial distribution and only if you
received the program in object code or executable form with such
an offer, in accord with Subsection b above.)
The source code for a work means the preferred form of the work for
making modifications to it. For an executable work, complete source
code means all the source code for all modules it contains, plus any
associated interface definition files, plus the scripts used to
control compilation and installation of the executable. However, as a
special exception, the source code distributed need not include
anything that is normally distributed (in either source or binary
form) with the major components (compiler, kernel, and so on) of the
operating system on which the executable runs, unless that component
itself accompanies the executable.
If distribution of executable or object code is made by offering
access to copy from a designated place, then offering equivalent
access to copy the source code from the same place counts as
distribution of the source code, even though third parties are not
compelled to copy the source along with the object code.
4. You may not copy, modify, sublicense, or distribute the Program
except as expressly provided under this License. Any attempt
otherwise to copy, modify, sublicense or distribute the Program is
void, and will automatically terminate your rights under this License.
However, parties who have received copies, or rights, from you under
this License will not have their licenses terminated so long as such
parties remain in full compliance.
5. You are not required to accept this License, since you have not
signed it. However, nothing else grants you permission to modify or
distribute the Program or its derivative works. These actions are
prohibited by law if you do not accept this License. Therefore, by
modifying or distributing the Program (or any work based on the
Program), you indicate your acceptance of this License to do so, and
all its terms and conditions for copying, distributing or modifying
the Program or works based on it.
6. Each time you redistribute the Program (or any work based on the
Program), the recipient automatically receives a license from the
original licensor to copy, distribute or modify the Program subject to
these terms and conditions. You may not impose any further
restrictions on the recipients' exercise of the rights granted herein.
You are not responsible for enforcing compliance by third parties to
this License.
7. If, as a consequence of a court judgment or allegation of patent
infringement or for any other reason (not limited to patent issues),
conditions are imposed on you (whether by court order, agreement or
otherwise) that contradict the conditions of this License, they do not
excuse you from the conditions of this License. If you cannot
distribute so as to satisfy simultaneously your obligations under this
License and any other pertinent obligations, then as a consequence you
may not distribute the Program at all. For example, if a patent
license would not permit royalty-free redistribution of the Program by
all those who receive copies directly or indirectly through you, then
the only way you could satisfy both it and this License would be to
refrain entirely from distribution of the Program.
If any portion of this section is held invalid or unenforceable under
any particular circumstance, the balance of the section is intended to
apply and the section as a whole is intended to apply in other
circumstances.
It is not the purpose of this section to induce you to infringe any
patents or other property right claims or to contest validity of any
such claims; this section has the sole purpose of protecting the
integrity of the free software distribution system, which is
implemented by public license practices. Many people have made
generous contributions to the wide range of software distributed
through that system in reliance on consistent application of that
system; it is up to the author/donor to decide if he or she is willing
to distribute software through any other system and a licensee cannot
impose that choice.
This section is intended to make thoroughly clear what is believed to
be a consequence of the rest of this License.
8. If the distribution and/or use of the Program is restricted in
certain countries either by patents or by copyrighted interfaces, the
original copyright holder who places the Program under this License
may add an explicit geographical distribution limitation excluding
those countries, so that distribution is permitted only in or among
countries not thus excluded. In such case, this License incorporates
the limitation as if written in the body of this License.
9. The Free Software Foundation may publish revised and/or new versions
of the General Public License from time to time. Such new versions will
be similar in spirit to the present version, but may differ in detail to
address new problems or concerns.
Each version is given a distinguishing version number. If the Program
specifies a version number of this License which applies to it and "any
later version", you have the option of following the terms and conditions
either of that version or of any later version published by the Free
Software Foundation. If the Program does not specify a version number of
this License, you may choose any version ever published by the Free Software
Foundation.
10. If you wish to incorporate parts of the Program into other free
programs whose distribution conditions are different, write to the author
to ask for permission. For software which is copyrighted by the Free
Software Foundation, write to the Free Software Foundation; we sometimes
make exceptions for this. Our decision will be guided by the two goals
of preserving the free status of all derivatives of our free software and
of promoting the sharing and reuse of software generally.
NO WARRANTY
11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN
OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED
OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS
TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE
PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING,
REPAIR OR CORRECTION.
12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING
OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED
TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY
YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER
PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
POSSIBILITY OF SUCH DAMAGES.
END OF TERMS AND CONDITIONS
How to Apply These Terms to Your New Programs
If you develop a new program, and you want it to be of the greatest
possible use to the public, the best way to achieve this is to make it
free software which everyone can redistribute and change under these terms.
To do so, attach the following notices to the program. It is safest
to attach them to the start of each source file to most effectively
convey the exclusion of warranty; and each file should have at least
the "copyright" line and a pointer to where the full notice is found.
{description}
Copyright (C) {year} {fullname}
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License along
with this program; if not, write to the Free Software Foundation, Inc.,
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
Also add information on how to contact you by electronic and paper mail.
If the program is interactive, make it output a short notice like this
when it starts in an interactive mode:
Gnomovision version 69, Copyright (C) year name of author
Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
This is free software, and you are welcome to redistribute it
under certain conditions; type `show c' for details.
The hypothetical commands `show w' and `show c' should show the appropriate
parts of the General Public License. Of course, the commands you use may
be called something other than `show w' and `show c'; they could even be
mouse-clicks or menu items--whatever suits your program.
You should also get your employer (if you work as a programmer) or your
school, if any, to sign a "copyright disclaimer" for the program, if
necessary. Here is a sample; alter the names:
Yoyodyne, Inc., hereby disclaims all copyright interest in the program
`Gnomovision' (which makes passes at compilers) written by James Hacker.
{signature of Ty Coon}, 1 April 1989
Ty Coon, President of Vice
This General Public License does not permit incorporating your program into
proprietary programs. If your program is a subroutine library, you may
consider it more useful to permit linking proprietary applications with the
library. If this is what you want to do, use the GNU Lesser General
Public License instead of this License.

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VERSION=
LATEXTARGET=thesis$(VERSION)
#
# LaTeX Makefile
# --------------
#
# Author : s.m.vandenoord@student.utwente.nl (Stefan van den Oord)
# Date : March 18, 1999, second version of today.
#
# This Makefile is a generic makefile for LaTeX documents. Distribute it
# as you wish, but please don't edit or remove this initial comment.
#
# The Makefile can be used by setting the environment variable "MAKEFILES",
# e.g. export MAKEFILES=~/data/TeX/Makefile.
# It requires GNU Make and bash or better, like zsh. Simply sh is not
# sufficient, I believe. The first few lines of the Makefile contains
# the executables that are used, edit them to point to the executables
# on your system.
#
# DISCLAIMER: Using this Makefile is fully at your own risk. I am not
# responsible for anything! So if crucial files are removed
# by the Makefile, it is your own problem. But you should
# have backups anyway. :-)
#
# Usage
# -----
# The Makefile can do the following things for you:
# - generate PostScript equivalents of XFig figures;
# - run makeindex and BibTeX, but only if necessary;
# - compile the .dvi file, running LaTeX as many times as needed;
# - run XDvi with the compiled .dvi file;
# - create a PostScript equivalent of the .dvi file;
# - generate a HTML equivalent of the .dvi file (if Latex2HTML is
# installed);
# - remove all generated output.
# The Makefile is in some points even RCS aware.
#
# In many cases, you don't even have to tell the Makefile which LaTeX
# file it has to compile. The Makefile uses the following strategy:
# 1. Check if the environment variable LATEXTARGET is set; if it is,
# generate $LATEXTARGET.dvi.
# 2. If there is only one .tex file, use that one.
# 3. Check if there is a LaTeX file that has the same basename as the
# directory. For example, if the directory is named "Thesis" and
# there is a file "Thesis.tex", "Thesis.dvi" is generated.
#
# Invocation
# ----------
# When the MAKEFILES environment variable is set, you can use the
# following commands:
# - make latexhelp
# Prints an overview of the available commands.
# - make latexfigures
# Only generate the PostScript equivalents of XFig figures.
# - make file.dvi
# Generates the specified DVI file.
# - make file.ps
# Generates the DVI file and then runs dvips.
# - make latex
# Use the above explained strategy to find out what has to be
# generated, and generate it.
# - make view
# Do a make latex and then run XDvi.
# - make latexps
# Do a make latex and then run dvips.
# - make html
# Do a make latex and then use LaTeX2HTML to create the HTML equivalent.
# To do this, the following environment variables are used:
# * HTMLDIR : the base dir in which the output is written. For example,
# if HTMLDIR=~/public_html/LaTeX, and the file that is
# generated is "Thesis", the output will be written in the
# directory ~/public_html/LaTeX/Thesis.
# * LATEX2HTML_OPTS : if you want to pass options to LaTeX2HTML, put
# them in this variable.
# - make latexclean
# This command removes all generated output. CAUTION: the files that are
# removed are thought out pretty well, but it is possible that files are
# removed that you wanted to keep! Check below what files are removed if
# you want to be certain!
# Note that a file figure.eps is only removed if a file figure.fig exists.
# (Even if the file figure.fig exists, but is checked in using RCS, the
# file figure.eps will be removed.)
#
# Tip
# ---
# For some projects it is useful to have a separate Makefile in the project's
# directory. For example, when you use RCS, you could add functionality for
# automatic checkouts of the right files (adding dependencies is sufficient;
# GNU Make rocks :-).
# The command "latexclean" is declared so that you can add your own
# functionality in the project's Makefile; instead of one colon, declare it
# with two colons if you want to do that.
# For example:
# latexclean::
# rm -f foo.bar
# This way both the origional definition in this Makefile and your own are
# used.
#.SILENT:
# SHELL=/usr/local/bin/bash
LATEX=latex
PDFLATEX=pdflatex
BIBTEX=bibtex
DVIPS=dvips
MAKEINDEX=makeindex
DVIVIEWER=xdvi -geometry 710x950-0+10
LATEX2HTML=latex2html
FIGURES=$(wildcard *.fig)
FIGUREOBJS=$(FIGURES:.fig=.eps)
TEXFILES=$(wildcard *.tex)
# Disable standard pattern rule:
%.dvi: %.tex
# Do not delete the following targets:
.PRECIOUS: %.aux %.bbl %.eps %.ind
%.aux: %.tex $(FIGUREOBJS) $(TEXFILES)
@$(LATEX) $*
# Look for citations. Make sure grep never returns an error code.
@grep "^\\\\citation" *.aux > .btmp.new || true
# If the citations are not changed, don't do anything. Otherwise replace
# the .btmp file to make sure Bibtex will be run.
@if ( diff .btmp.new .btmp >& /dev/null ); then \
rm .btmp.new; \
else \
mv .btmp.new .btmp; \
fi
@if [ -f $*.idx ]; then cp $*.idx .itmp.new; else touch .itmp.new; fi
@if ( diff .itmp.new .itmp >& /dev/null ); then \
rm .itmp.new; \
else \
mv .itmp.new .itmp; \
fi
.btmp:
%.bbl: $(BIBFILES) .btmp
# Only use BibTeX if \bibliography occurs in the document. In that case,
# run BibTeX and recompile. .btmp is touched to prevent useless making
# next time.
@if ( grep "^\\\\bibliography{" $*.tex > /dev/null ); then \
$(BIBTEX) $*; \
touch .rerun; \
fi
@touch .btmp
.itmp:
%.ind: .itmp
@if [ -f $*.idx ]; then \
$(MAKEINDEX) $*; \
touch .rerun; \
touch .itmp; \
fi
%.eps:%.fig
@echo Generating figure $@...
@fig2dev -L ps $< $@
%.dvi: %.aux %.ind %.bbl
# Make sure the dvi-file exists; if not: recompile.
@if [ ! -f $*.dvi ]; then \
touch .rerun; \
fi
@if [ -f .rerun ]; then \
rm .rerun; \
$(LATEX) $*; \
else \
$(MAKE) $*.aux; \
fi
# While references et al. are changed: recompile.
@while ( grep Rerun $*.log > /dev/null ); do \
$(LATEX) $*; \
done
# Touch the figureobjects to prevent making next time
@if [ -n "$(FIGUREOBJS)" ]; then \
touch $(FIGUREOBJS); \
touch $*.aux; \
fi
@if [ -f $*.ind ]; then \
touch $*.ind; \
fi
@$(MAKEINDEX) -s nomencl.ist -o $*.nls $*.nlo
latex:
# Below the 'true' is included to prevent unnecessarily many errors.
@if [ -n "${LATEXTARGET}" ]; then \
$(MAKE) ${LATEXTARGET}.dvi; \
true; \
else \
if [ `ls *.tex | wc -l` = "1" ]; then \
$(MAKE) `basename \`ls *.tex\` .tex`.dvi; \
true; \
else \
$(MAKE) `echo $$PWD|tr '/' '\n'|tail -1`.dvi; \
true; \
fi; \
fi
latexfigures:
@for i in $(FIGUREOBJS); do \
$(MAKE) $$i; \
done
view:
# Below the 'true' is included to prevent unnecessarily many errors.
@if [ -n "${LATEXTARGET}" ]; then \
$(MAKE) ${LATEXTARGET}.dvi && \
$(DVIVIEWER) ${LATEXTARGET}.dvi ; \
true; \
else \
if [ `ls *.tex | wc -l` = "1" ]; then \
$(MAKE) `basename \`ls *.tex\` .tex`.dvi && \
$(DVIVIEWER) `basename \`ls *.tex\` .tex`.dvi; \
true; \
else \
$(MAKE) `echo $$PWD|tr '/' '\n'|tail -1`.dvi && \
$(DVIVIEWER) `echo $$PWD|tr '/' '\n'|tail -1`.dvi; \
true; \
fi; \
fi
%.ps: %.dvi
$(DVIPS) -o $*.ps $<
@$(MAKEINDEX) -s nomencl.ist -o $*.nls $*.nlo
$(DVIPS) -o $*.ps $<
%.pdf: %.tex
$(PDFLATEX) $<
@$(MAKEINDEX) -s nomencl.ist -o $*.nls $*.nlo
$(BIBTEX) $*
$(PDFLATEX) $<
$(PDFLATEX) $<
latexps:
@if [ -n "${LATEXTARGET}" ]; then \
$(MAKE) ${LATEXTARGET}.ps && \
true; \
else \
if [ `ls *.tex | wc -l` = "1" ]; then \
$(MAKE) `basename \`ls *.tex\` .tex`.ps && \
true; \
else \
$(MAKE) `echo $$PWD|tr '/' '\n'|tail -1`.ps && \
true; \
fi; \
fi
html: .html
.html:
@if [ -n "${LATEXTARGET}" ]; then \
if [ -n "${HTMLDIR}" ]; then \
$(MAKE) ${LATEXTARGET}.dvi; \
$(LATEX2HTML) $(LATEX2HTML_OPTS) -dir $(HTMLDIR)/$(LATEXTARGET) $(LATEXTARGET) && \
chmod a+rx $(HTMLDIR)/$(LATEXTARGET) && \
chmod a+r $(HTMLDIR)/$(LATEXTARGET)/* && \
touch .html; \
else \
echo Set variable HTMLDIR\!; \
fi; \
else \
echo Set variable LATEXTARGET\!; \
fi
latexhelp:
@echo "LaTeX Makefile Options"
@echo "----------------------"
@echo ""
@echo "Environment variables:"
@echo " LATEXTARGET Filename to make (without extension)"
@echo " HTMLDIR Directory for HTML-output"
@echo " FIGURES Figures that have to be compiled"
@echo ""
@echo "Targets:"
@echo " all Make the LATEXTARGET or <dirname>.dvi"
@echo " <name>.dvi Make the given dvi file"
@echo " latex Make the LATEXTARGET or <dirname>.dvi"
@echo " view Make and view the LATEXTARGET or <dirname>.dvi"
@echo " html Make the LATEXTARGET or <dirname>.dvi and generate HTML output"
@echo " latexhelp This overview"
@echo " latexclean Remove all generated files"
clean latexclean::
@rm -f *.log *.aux *.dvi *.bbl *.blg *.ilg *.toc *.lof *.lot *.idx *.ind *.out *.brf *.html *.btmp *.itmp *.rerun *.glo *.gls *.nlo *.nls
@epsfiles=`find * -maxdepth 0 -name "*.eps" `; \
if [ -n "$$epsfiles" ]; then \
for i in *.eps; do \
if [ -f `basename $$i .eps`.fig ]; then \
rm -f $$i; \
elif ( rcs `basename $$i .eps`.fig >& /dev/null ); then \
rm -f $$i; \
fi \
done \
fi
cleanpspdf : clean
@rm -f *.ps *.pdf
clobber : cleanpspdf
@rm -f *~

4
README.md Normal file
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phd-thesis-template
===================
A PhD thesis LaTeX template for Cambridge University, based on Krishna Kumar's King's latex course and CUED V1.1 Template

369
References/references.bib Normal file
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% ------------------------------------------------------------------------
% SAMPLE BIBLIOGRAPHY FILE
% ------------------------------------------------------------------------
@MISC{prime-number-theorem,
author = "Charles Louis Xavier Joseph de la Vall{\'e}e Poussin",
note = "A strong form of the prime number theorem, 19th century" }
% ------------------------------------------------------------------------
@BOOK{texbook,
author = "Donald E. Knuth",
title= "The {{\TeX}book}",
publisher = "Addison-Wesley",
year = 1984 }
@BOOK{latex,
author = "Leslie Lamport",
title = "{\LaTeX:} {A} Document Preparation System",
publisher = "Addison-Wesley",
year = 1986 }
% ------------------------------------------------------------------------
@BOOK{RR73,
author={H. Radjavi and P. Rosenthal},
title={Invariant {Subspaces}},
publisher={Springer-Verlag},
address={New York},
year={1973},
}
@BOOK{Aup91,
author={B. Aupetit},
title={A {Primer} on {Spectral} {Theory}},
publisher={Springer-Verlag},
address={New York},
year={1991},
}
@BOOK{Dou72,
author={R. G. Douglas},
title={Banach {Algebra} {Techniques} in {Operator} {Theory}},
publisher={Academic Press},
address={New York},
year={1972},
}
@BOOK{Hal82,
author={P. R. Halmos},
title={A {Hilbert} {Space} {Problem} {Book}},
edition={Second},
publisher={Springer-Verlag},
address={New York},
year={1982},
}
@BOOK{Rud73,
author={W. Rudin},
title={Functional {Analysis}},
publisher={McGraw-Hill},
address={New York},
year={1973},
}
@BOOK{Con90,
author={J. B. Conway},
title={A {Course} in {Functional} {Analysis}},
edition={Second},
publisher={Springer-Verlag},
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% ------------------------------------------------------------------------
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% --------------------------------------------------------------------------
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% ------------------------------------------------------------------------
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}
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\pdfinfo { /Title (Multiscale Modelling of Granular Flows)
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/Author (Krishna Kumar, kks32@cam.ac.uk)
/CreationDate (D:20131113000000)
/ModDate (D:20131113121606)
/Subject (GeoMechanics)
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% ***************************** Title ******************************************** %
% PhD Thesis Title, Author, Degree, etc
\title{Multiscale Modelling of Granular Flows}
\author{Krishna Kumar}
\collegeordept{Department of Engineering}
\university{University of Cambridge}
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