Add structure outline

%************************************************

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\chapter{Introduction}\label{ch:introduction}

\chapter{Introduction}\label{ch:introduction}

% ************************************************

% ************************************************

This bundle for \LaTeX\ has two goals:

\begin{enumerate}

    \item Provide students with an easy-to-use template for their

    Master's

    or PhD thesis. (Though it might also be used by other types of

    authors

    for reports, books, etc.)

    \item Provide a classic, high-quality typographic style that is

    inspired by \citeauthor{bringhurst:2002}'s ``\emph{The Elements of

    Typographic Style}'' \citep{bringhurst:2002}.

    \marginpar{\myTitle \myVersion}

\end{enumerate}

The bundle is configured to run with a \emph{full} 

MiK\TeX\ or \TeX Live\footnote{See the file \texttt{LISTOFFILES} for

needed packages. Furthermore, \texttt{classicthesis} 

works with most other distributions and, thus, with most systems 

\LaTeX\ is available for.} 

installation right away and, therefore, it uses only freely available 

fonts. (Minion fans can easily adjust the style to their needs.)

People interested only in the nice style and not the whole bundle can

now use the style stand-alone via the file \texttt{classicthesis.sty}.

This works now also with ``plain'' \LaTeX.

As of version 3.0, \texttt{classicthesis} can also be easily used with 

\mLyX\footnote{\url{http://www.lyx.org}} thanks to Nicholas Mariette 

and Ivo Pletikosić. The \mLyX\ version of this manual will contain

more information on the details.

This should enable anyone with a basic knowledge of \LaTeXe\ or \mLyX\ to

produce beautiful documents without too much effort. In the end, this

is my overall goal: more beautiful documents, especially theses, as I

am tired of seeing so many ugly ones.

The whole template and the used style is released under the

\acsfont{GNU} General Public License. 

If you like the style then I would appreciate a postcard:

\begin{center}

 André Miede \\

 Detmolder Straße 32 \\

 31737 Rinteln \\

 Germany

\end{center}

The postcards I received so far are available at:

\begin{center}

 \url{http://postcards.miede.de}

\end{center}

\marginpar{A well-balanced line width improves the legibility of

the text. That's what typography is all about, right?}

So far, many theses, some books, and several other publications have 

been typeset successfully with it. If you are interested in some

typographic details behind it, enjoy Robert Bringhurst's wonderful book.

% \citep{bringhurst:2002}.

\paragraph{Important Note:} Some things of this style might look

unusual at first glance, many people feel so in the beginning.

However, all things are intentionally designed to be as they are,

especially these:

\begin{itemize}

    \item No bold fonts are used. Italics or spaced small caps do the

    job quite well.

    \item The size of the text body is intentionally shaped like it

    is. It supports both legibility and allows a reasonable amount of

    information to be on a page. And, no: the lines are not too short.

    \item The tables intentionally do not use vertical or double

    rules. See the documentation for the \texttt{booktabs} package for

    a nice discussion of this topic.\footnote{To be found online at 

    \url{http://mirror.ctan.org/macros/latex/contrib/booktabs/}.}

    \item And last but not least, to provide the reader with a way

    easier access to page numbers in the table of contents, the page

    numbers are right behind the titles. Yes, they are \emph{not}

    neatly aligned at the right side and they are \emph{not} connected

    with dots that help the eye to bridge a distance that is not

    necessary. If you are still not convinced: is your reader

    interested in the page number or does she want to sum the numbers

    up?

\end{itemize}

Therefore, please do not break the beauty of the style by changing

these things unless you really know what you are doing! Please.

\paragraph{Yet Another Important Note:} Since \texttt{classicthesis}'

first release in 2006, many things have changed in the \LaTeX\ world. 

Trying to keep up-to-date, \texttt{classicthesis} grew and evolved 

into many directions, trying to stay (some kind of) stable and be 

compatible with its port to \mLyX. However, there are still many 

remains from older times in the code, many dirty workarounds here and 

there, and several other things I am absolutely not proud of (for 

example my unwise combination of \acsfont{KOMA} and 

\texttt{titlesec} etc.).

\graffito{An outlook into the future of \texttt{classicthesis}.}

Currently, I am looking into how to completely re-design and 

re-implement \texttt{classicthesis} making it easier to maintain and 

to use. As a general idea, \texttt{classicthesis.sty} should be 

developed and distributed separately from the template bundle itself. 

Excellent spin-offs such as \texttt{arsclassica} could also be 

integrated (with permission by their authors) as format configurations. 

Also, current trends of \texttt{microtype}, \texttt{fontspec}, etc. 

should be included as well. As I am not really into deep 

\LaTeX\ programming, 

I will reach out to the \LaTeX\ community for their expertise and help.

\section{Organization}

A very important factor for successful thesis writing is the

organization of the material. This template suggests a structure as

the following:

\begin{itemize}

    \marginpar{You can use these margins for summaries of the text

    body\dots}

    \item\texttt{Chapters/} is where all the ``real'' content goes in

    separate files such as \texttt{Chapter01.tex} etc.

 %  \item\texttt{Examples/} is where you store all listings and other

 %  examples you want to use for your text.

    \item\texttt{FrontBackMatter/} is where all the stuff goes that

    surrounds the ``real'' content, such as the acknowledgments,

    dedication, etc.

    \item\texttt{gfx/} is where you put all the graphics you use in

    the thesis. Maybe they should be organized into subfolders

    depending on the chapter they are used in, if you have a lot of

    graphics.

    \item\texttt{Bibliography.bib}: the Bib\TeX\ database to organize

    all the references you might want to cite.

    \item\texttt{classicthesis.sty}: the style definition to get this

    awesome look and feel. Does not only work with this thesis template

    but also on its own (see folder \texttt{Examples}). Bonus: works

    with both \LaTeX\ and \textsc{pdf}\LaTeX\dots and \mLyX.

    \item\texttt{ClassicThesis.tcp} a \TeX nicCenter project file.

    Great tool and it's free!

    \item\texttt{ClassicThesis.tex}: the main file of your thesis

    where all gets bundled together.

    \item\texttt{classicthesis-config.tex}: a central place to load all 

    nifty packages that are used. %In there, you can also activate 

    %backrefs in order to have information in the bibliography about 

    %where a source was cited in the text (\ie, the page number).

    \emph{Make your changes and adjustments here.} This means that you  

    specify here the options you want to load \texttt{classicthesis.sty} 

    with. You also adjust the title of your thesis, your name, and all 

    similar information here. Refer to \autoref{sec:custom} for more 

    information.

        This had to change as of version 3.0 in order to enable an easy 

        transition from the ``basic'' style to \mLyX.

\end{itemize}

In total, this should get you started in no time.

\clearpage

\section{Style Options}\label{sec:options}

There are a couple of options for \texttt{classicthesis.sty} that

allow for a bit of freedom concerning the layout:

\marginpar{\dots or your supervisor might use the margins for some

    comments of her own while reading.}

\begin{itemize}

    \item General:

        \begin{itemize}

            \item\texttt{drafting}: prints the date and time at the bottom of

    each page, so you always know which version you are dealing with.

    Might come in handy not to give your Prof. that old draft.

        \end{itemize}

    \item Parts and Chapters:

        \begin{itemize}

            \item\texttt{parts}: if you use Part divisions for your document,

    you should choose this option. (Cannot be used together with 

    \texttt{nochapters}.)

            \item\texttt{nochapters}: allows to use the look-and-feel with 

    classes that do not use chapters, \eg, for articles. Automatically

    turns off a couple of other options: \texttt{eulerchapternumbers}, 

    \texttt{linedheaders}, \texttt{listsseparated}, and \texttt{parts}. 

        \item\texttt{linedheaders}: changes the look of the chapter

        headings a bit by adding a horizontal line above the chapter

        title. The chapter number will also be moved to the top of the

        page, above the chapter title.

        \end{itemize}

  \item Typography:

        \begin{itemize}

            \item\texttt{eulerchapternumbers}: use figures from Hermann Zapf's

            Euler math font for the chapter numbers. By default, old style

            figures from the Palatino font are used.

            \item\texttt{beramono}: loads Bera Mono as typewriter font. 

            (Default setting is using the standard CM typewriter font.)

            \item\texttt{eulermath}: loads the awesome Euler fonts for math. 

            Pala\-tino is used as default font.

            \item\texttt{pdfspacing}: makes use of pdftex' letter spacing

            capabilities via the \texttt{microtype} package.\footnote{Use 

            \texttt{microtype}'s \texttt{DVIoutput} option to generate

            DVI with pdftex.} This fixes some serious issues regarding 

            math formul\ae\ etc. (\eg, ``\ss'') in headers. 

            \item\texttt{minionprospacing}: uses the internal \texttt{textssc}

            command of the \texttt{MinionPro} package for letter spacing. This 

            automatically enables the \texttt{minionpro} option, overriding

            \texttt{pdfspacing}.

        \end{itemize}  

    \item Table of Contents:

        \begin{itemize}

             \item\texttt{tocaligned}: aligns the whole table of contents on

            the left side. Some people like that, some don't.

            \item\texttt{dottedtoc}: sets pagenumbers flushed right in the 

            table of contents.

            \item\texttt{manychapters}: if you need more than nine chapters for 

        your document, you might not be happy with the spacing between the 

        chapter number and the chapter title in the Table of Contents. 

        This option allows for additional space in this context. 

        However, it does not look as ``perfect'' if you use

        \verb|\parts| for structuring your document.

        \end{itemize}

    \item Floats:

        \begin{itemize}

    \item\texttt{listings}: loads the \texttt{listings} package (if not 

    already done) and configures the List of Listings accordingly.

    \item\texttt{floatperchapter}: activates numbering per chapter for

    all floats such as figures, tables, and listings (if used). 

        \item\texttt{subfig}(\texttt{ure}): is passed to the \texttt{tocloft} 

        package to enable compatibility with the \texttt{subfig}(\texttt{ure}) 

        package. Use this option if you want use \texttt{classicthesis} with the

        \texttt{subfig} package.

%    \item\texttt{listsseparated}: will add extra space between table

%    and figure entries of different chapters in the list of tables or

%    figures, respectively. % Deprecated as of version 2.9.

        \end{itemize}    

%   \item\texttt{a5paper}: adjusts the page layout according to the

%    global \texttt{a5paper} option (\emph{experimental} feature).

%    \item\texttt{minionpro}: sets Robert Slimbach's Minion as the 

%    main font of the document. The textblock size is adjusted 

%    accordingly.    

   \end{itemize}

The best way to figure these options out is to try the different

possibilities and see what you and your supervisor like best.

In order to make things easier, \texttt{classicthesis-config.tex} 

contains some useful commands that might help you.

\section{Customization}\label{sec:custom}

%(As of v3.0, the Classic Thesis Style for \LaTeX{} and \mLyX{} share

%the same two \texttt{.sty} files.)

This section will show you some hints how to adapt 

\texttt{classicthesis} to your needs.

The file \texttt{classicthesis.sty}

contains the core functionality of the style and in most cases will

be left intact, whereas the file \texttt{classic\-thesis-config.tex}

is used for some common user customizations. 

The first customization you are about to make is to alter the document

title, author name, and other thesis details. In order to do this, replace

the data in the following lines of \texttt{classicthesis-config.tex:}%

\marginpar{Modifications in \texttt{classic\-thesis-config.tex}%

}

\begin{lstlisting}

    % **************************************************

    % 2. Personal data and user ad-hoc commands

    % **************************************************

    \newcommand{\myTitle}{A Classic Thesis Style\xspace} 

    \newcommand{\mySubtitle}{An Homage to...\xspace} 

\end{lstlisting}

Further customization can be made in \texttt{classicthesis-config.tex}

by choosing the options to \texttt{classicthesis.sty} 

(see~\autoref{sec:options}) in a line that looks like this:

\begin{lstlisting}

    \PassOptionsToPackage{eulerchapternumbers,drafting,listings,subfig,eulermath,parts}{classicthesis}

\end{lstlisting}

Many other customizations in \texttt{classicthesis-config.tex} are

possible, but you should be careful making changes there, since some

changes could cause errors.

Finally, changes can be made in the file \texttt{classicthesis.sty},%

\marginpar{Modifications in \texttt{classicthesis.sty}%

} although this is mostly not designed for user customization. The

main change that might be made here is the text-block size, for example,

to get longer lines of text.

\section{Issues}\label{sec:issues}

This section will list some information about problems using

\texttt{classic\-thesis} in general or using it with other packages.

Beta versions of \texttt{classicthesis} can be found at Bitbucket:

\begin{center}

    \url{https://bitbucket.org/amiede/classicthesis/}

\end{center}

There, you can also post serious bugs and problems you encounter.

\subsection*{Compatibility with the \texttt{glossaries} Package}

If you want to use the \texttt{glossaries} package, take care of loading it 

with the following options:

\begin{lstlisting}

    \usepackage[style=long,nolist]{glossaries}

\end{lstlisting}

Thanks to Sven Staehs for this information. 

\subsection*{Compatibility with the (Spanish) \texttt{babel} Package}

Spanish languages need an extra option in order to work with this template:

\begin{lstlisting}

    \usepackage[spanish,es-lcroman]{babel}

\end{lstlisting}

Thanks to an unknown person for this information (via the issue reporting). 

\paragraph{Further information for using \texttt{classicthesis} with Spanish (in addition to the above)}

In the file \texttt{ClassicThesis.tex} activate the language: 

\begin{lstlisting}

    \selectlanguage{spanish}

\end{lstlisting}

If there are issues changing \verb|\tablename|, \eg, using this:

\begin{lstlisting}

    \renewcommand{\tablename}{Tabla}

\end{lstlisting}

This can be solved by passing \texttt{es-tabla} parameter to \texttt{babel}:

\begin{lstlisting}

    \PassOptionsToPackage{es-tabla,spanish,es-lcroman,english}{babel}

    \usepackage{babel}

\end{lstlisting}

But it is also necessary to set \texttt{spanish} in the \verb|\documentclass|.

Thanks to Alvaro Jaramillo Duque for this information. 

\subsection*{Compatibility with the \texttt{pdfsync} Package}

Using the \texttt{pdfsync} package leads to linebreaking problems with the \texttt{graffito} command. 

Thanks to Henrik Schumacher for this information. 

\section{Future Work}

So far, this is a quite stable version that served a couple of people

well during their thesis time. However, some things are still not as

they should be. Proper documentation in the standard format is still

missing. In the long run, the style should probably be published

separately, with the template bundle being only an application of the

style. Alas, there is no time for that at the moment\dots it could be

a nice task for a small group of \LaTeX nicians.

Please do not send me email with questions concerning \LaTeX\ or the

template, as I do not have time for an answer. But if you have

comments, suggestions, or improvements for the style or the template

in general, do not hesitate to write them on that postcard of yours.

\section{Beyond a Thesis}

The layout of \texttt{classicthesis.sty} can be easily used without the

framework of this template. A few examples where it was used to typeset 

an article, a book or a curriculum vitae can be found in the folder 

\texttt{Examples}. The examples have been tested with  

\texttt{latex} and \texttt{pdflatex} and are easy to compile. To 

encourage you even more, PDFs built from the sources can be found in the 

same folder. 

%(It might be necessary to adjust the path to 

%\texttt{classicthesis.sty} and \texttt{Bibliography.bib} within the 

%examples.)

%\lstinputlisting[caption=An Article]%

    %{Examples/classicthesis-article.tex}

    %

%\lstinputlisting[caption=A Book]%

    %{Examples/classicthesis-book.tex}

%

%\lstinputlisting[caption=A Curriculum Vit\ae]%

    %{Examples/classicthesis-cv.tex}

\section{License}

\paragraph{GNU General Public License:} This program is free software;

you can redistribute it and/or modify

 it under the terms of the \acsfont{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 \emph{without any warranty}; without even the implied warranty of

 \emph{merchant\-ability} or \emph{fitness for a particular purpose}.

 See the

 \acsfont{GNU} General Public License for more details.

 You should have received a copy of the \acsfont{GNU} General

 Public License

 along with this program; see the file \texttt{COPYING}.  If not,

 write to

 the Free Software Foundation, Inc., 59 Temple Place - Suite 330,

 Boston, MA 02111-1307, USA.

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\chapter{Math Test Chapter}\label{ch:mathtest} % $\mathbb{ZNR}$

\chapter{Aim of the Work}\label{ch:aims} % $\mathbb{ZNR}$

%************************************************

%************************************************

Ei choro aeterno antiopam mea, labitur bonorum pri no. His no decore

nemore graecis. In eos meis nominavi, liber soluta vim cu. Sea commune

suavitate interpretaris eu, vix eu libris efficiantur.

\section{Some Formulas}

\section{Objectives and Expected Results}

Due to the statistical nature of ionisation energy loss, large

fluctuations can occur in the amount of energy deposited by a particle

traversing an absorber element\footnote{Examples taken from Walter

Schmidt's great gallery: \\

\url{http://home.vrweb.de/~was/mathfonts.html}}.  Continuous processes

such as multiple

scattering and energy loss play a relevant role in the longitudinal

and lateral development of electromagnetic and hadronic

showers, and in the case of sampling calorimeters the

measured resolution can be significantly affected by such fluctuations

in their active layers.  The description of ionisation fluctuations is

characterised by the significance parameter $\kappa$, which is

proportional to the ratio of mean energy loss to the maximum allowed

energy transfer in a single collision with an atomic electron:

\graffito{You might get unexpected results using math in chapter or

section heads. Consider the \texttt{pdfspacing} option.}

\begin{equation}

\kappa =\frac{\xi}{E_{\textrm{max}}} %\mathbb{ZNR}

\end{equation}

$E_{\textrm{max}}$ is the maximum transferable energy in a single

collision with an atomic electron.

\[

E_{\textrm{max}} =\frac{2 m_{\textrm{e}} \beta^2\gamma^2 }{1 +

2\gamma m_{\textrm{e}}/m_{\textrm{x}} + \left ( m_{\textrm{e}}

/m_{\textrm{x}}\right)^2}\ ,

\]

where $\gamma = E/m_{\textrm{x}}$, $E$ is energy and

$m_{\textrm{x}}$ the mass of the incident particle,

$\beta^2 = 1 - 1/\gamma^2$ and $m_{\textrm{e}}$ is the electron mass.

$\xi$ comes from the Rutherford scattering cross section

and is defined as:

\begin{eqnarray*} \xi  = \frac{2\pi z^2 e^4 N_{\textrm{Av}} Z \rho

\delta x}{m_{\textrm{e}} \beta^2 c^2 A} =  153.4 \frac{z^2}{\beta^2}

\frac{Z}{A}

  \rho \delta x \quad\textrm{keV},

\end{eqnarray*}

where

\begin{tabular}{ll}

\section{Expected Outputs}

$z$          & charge of the incident particle \\

$N_{\textrm{Av}}$     & Avogadro's number \\

$Z$          & atomic number of the material \\

$A$          & atomic weight of the material \\

$\rho$       & density \\

$ \delta x$  & thickness of the material \\

\end{tabular}

$\kappa$ measures the contribution of the collisions with energy

\section{Progression Schedule}

transfer close to $E_{\textrm{max}}$.  For a given absorber, $\kappa$

tends

towards large values if $\delta x$ is large and/or if $\beta$ is

small.  Likewise, $\kappa$ tends towards zero if $\delta x $ is small

and/or if $\beta$ approaches $1$.

The value of $\kappa$ distinguishes two regimes which occur in the

description of ionisation fluctuations:

\begin{enumerate}

\item A large number of collisions involving the loss of all or most

  of the incident particle energy during the traversal of an absorber.

  As the total energy transfer is composed of a multitude of small

  energy losses, we can apply the central limit theorem and describe

  the fluctuations by a Gaussian distribution.  This case is

  applicable to non-relativistic particles and is described by the

  inequality $\kappa > 10 $ (\ie, when the mean energy loss in the

  absorber is greater than the maximum energy transfer in a single

  collision).

\item Particles traversing thin counters and incident electrons under

  any conditions.

  The relevant inequalities and distributions are $ 0.01 < \kappa < 10

  $,

  Vavilov distribution, and $\kappa < 0.01 $, Landau distribution.

\end{enumerate}

\section{Various Mathematical Examples}

If $n > 2$, the identity

\[

  t[u_1,\dots,u_n] = t\bigl[t[u_1,\dots,u_{n_1}], t[u_2,\dots,u_n]

  \bigr]

\]

defines $t[u_1,\dots,u_n]$ recursively, and it can be shown that the

alternative definition

\[

  t[u_1,\dots,u_n] = t\bigl[t[u_1,u_2],\dots,t[u_{n-1},u_n]\bigr]

\]

gives the same result.  

%*****************************************

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%\include{FrontBackmatter/DirtyTitlepage}

%\include{FrontBackmatter/DirtyTitlepage}

\include{FrontBackmatter/Titlepage}

\include{FrontBackmatter/Titlepage}

\include{FrontBackmatter/Titleback}

\include{FrontBackmatter/Titleback}

\cleardoublepage\include{FrontBackmatter/Dedication}

%\cleardoublepage\include{FrontBackmatter/Dedication}

%\cleardoublepage\include{FrontBackmatter/Foreword}

%\cleardoublepage\include{FrontBackmatter/Foreword}

\cleardoublepage\include{FrontBackmatter/Abstract}

%\cleardoublepage\include{FrontBackmatter/Abstract}

\cleardoublepage\include{FrontBackmatter/Publications}

%\cleardoublepage\include{FrontBackmatter/Publications}

\cleardoublepage\include{FrontBackmatter/Acknowledgments}

\cleardoublepage\include{FrontBackmatter/Acknowledgments}

\pagestyle{scrheadings}

\pagestyle{scrheadings}

\cleardoublepage\include{FrontBackmatter/Contents}

\cleardoublepage\include{FrontBackmatter/Contents}

\appendix

\appendix

%\renewcommand{\thechapter}{\alph{chapter}}

%\renewcommand{\thechapter}{\alph{chapter}}

\cleardoublepage

\cleardoublepage

\part{Appendix}

\chapter{Appendix}

\include{Chapters/Chapter0A}

% \include{Chapters/Chapter0A}

%********************************************************************

%********************************************************************

% Other Stuff in the Back

% Other Stuff in the Back

%*******************************************************

%*******************************************************

\cleardoublepage\include{FrontBackmatter/Bibliography}

% \cleardoublepage\include{FrontBackmatter/Bibliography}

\cleardoublepage\include{FrontBackmatter/Declaration}

% \cleardoublepage\include{FrontBackmatter/Declaration}

\cleardoublepage\include{FrontBackmatter/Colophon}

% \cleardoublepage\include{FrontBackmatter/Colophon}

% ********************************************************************

% ********************************************************************

% Game Over: Restore, Restart, or Quit?

% Game Over: Restore, Restart, or Quit?

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