thesis.tex

% ----------------------------------------------------------------------
%                   LATEX TEMPLATE FOR PhD THESIS
% ----------------------------------------------------------------------

% based on Harish Bhanderi's PhD/MPhil template, then Uni Cambridge
% http://www-h.eng.cam.ac.uk/help/tpl/textprocessing/ThesisStyle/
% corrected and extended in 2007 by Jakob Suckale, then MPI-CBG PhD programme
% and made available through OpenWetWare.org - the free biology wiki
% and finally modified in 2015-2017 by Holger Nahrstaedt
% https://github.com/holgern/TUB_PhDThesisTemplate

%: Style file for Latex
% Most style definitions are in the external file PhDthesisTUB.
% In this template package, it can be found in ./Classes/

\documentclass[twoside,11pt,online,a4paper,pdfa1,custommargin,numbered,biblatex]{Classes/PhDthesisTUB}
% *********************** Choosing pdfx standard ******************************
% `pdfa1'
% `pdfa2'
% `pdfx3'
% *********************** Change Thesis-Language to German ******************************
% default is english
% `german' : language is set to german
%
% % *********************** Choosing oneside / twoside ******************************
% `oneside' : layout is optimized for one-side print
% `twoside' : layout is optimized for two-side print
% *********************** Choosing print / online ******************************
% `print' : pdf-file is optimized for print
% `online' : pdf-file is optimized for online submission. The links are colorfull.
% *********************** Choosing biblatex or bibtex ******************
% `biblatex' : biblatex is used. Biblatex is automatically set when using xetex
%
% *********************** Choosing bibliographystyle ******************
% `numbered' : (default option) e.g. [1], [2]
% `authoryear' :  e.g. Name (2008)
% `custombib' : Use your own style, which is defined in preamble.tex
% *********************** Choosing the Fonts size ******************
% `9pt'
% `10pt'
% `11pt'
% `12pt'
% *********************** Choosing the paper size ******************
% `letterpaper'
% `a4paper'
% `a5paper'
% *********************** Choosing the Fonts in Class Options when using pdflatex ******************
% 
%  On Windows, the packge cm-super has to be installed!
%
% `' :  computer modern
% `fontA' :  newtxmath
% `fontB' :  cmbright
% `fontC' :  libertine,newtxmath
% `fontD' :  concmath
% `fontE' :  iwona
% `fontF' :  kurier	
% `fontG' :  anttor
% `fontH' :  kmath,kerkis
% `fontI' :   mathdesign (Utopia)
% `fontJ' :  fouriernc
% `fontK' :  pxfonts
% `fontL' :  mathpazo
% `fontM' :  mathpple
% `fontN' :  txfonts
% `fontO' :  mathtime (Belleek)
% `fontP' :  mathptmx	times	
% `fontQ' :  mbtimes	omega
% `fontR' :  arev
% `fontS' :  mathdesign (Charter)	
% `fontT' :  comicsans
% `fontU' :  mathdesign (Garamond)
% `fontV' :  fourier	utopia
% `fontW' :  ccfonts,eulervm
%
% `customfont': Use `customfont' option in the document class and load the
% package in the preamble.tex
%
% default or leave empty: `Latin Modern' font will be loaded.
%
% *********************** Choosing the Fonts in Class Options when using xelatex/lualatex ***********
%
% `' :  computer modern
% `fontA' :  XITS - XITS Math
% `fontB': Cambria - Cambria Math
% 'fontC': Libertinus - Libertinus Math
% 'fontD': TeX Gyre Pagella - Asana Math
% 'fontE': TeX Gyre Pagella - TeX Gyre Pagella Math
% 'fontF': TeX Gyre Schola - TeX Gyre Schola Math
% 'fontG': TeX Gyre Termes - TeX Gyre Termes Math
% 'fontH': TeX Gyre Bonum - TeX Gyre Bonum Math
% 'fontI': DejaVu Sans - TeX Gyre DejaVu Math
%
% `customfont': Use `customfont' option in the document class and load the
% package in the preamble.tex
%
% default or leave empty: `Latin Modern' font will be loaded.
%
% ************************* Custom Page Margins ********************************
%
% `custommargin`: Use `custommargin' in options to activate custom page margins,
% which can be defined in the preamble.tex. Custom margin will override
% print/online margin setup.
%
% ************************* other options ********************************
% `abstract`: Only the title-page and the abstracts are generated
%

\include{Preamble/preamble}
\include{thesis-info}

%: ----------------------- set languange ------------------------
\ifCLASSINFOlangDE
\selectlanguage{german}
\else
\selectlanguage{english}
\fi
% ***************************** Abstract Separate ******************************
% To printout only the titlepage and the abstract with the PhD title and the
% author name for submission to the Student Registry, use the `abstract' option in
% the document class.

\ifdefineAbstract
 \pagestyle{empty}
 \includeonly{0_frontmatter/zusammenfassung, 0_frontmatter/abstract}
\fi

%: ----------------------- generate glossary ------------------------
\loadglsentries{0_frontmatter/glossary}
\makeglossaries
\begin{document}



%: ----------------------- generate cover page ------------------------
\frontmatter
% \maketitle generates a title page for the final submission
% \makepretitle generates a title page for evaluation process
% title and author... can be set in thesis-info.tex
\phantomsection
\addcontentsline{toc}{chapter}{Title Page}
\maketitle  
%\makepretitle

%: ----------------------- Choose spacing ------------------------
%\singlespacing
\onehalfspacing
%\doublespacing

%: ----------------------- abstract ------------------------

% Your institution may have specific regulations if you need an abstract and where it is to be placed in the document. The default here is just after title.

\include{0_frontmatter/zusammenfassung}
\include{0_frontmatter/abstract}


%: ----------------------- tie in front matter ------------------------

%\frontmatter
\include{0_frontmatter/dedication}
\include{0_frontmatter/acknowledgement}


%: ----------------------- contents ------------------------
\tableofcontents            % print the table of contents

%: ----------------------- list of figures/tables ------------------------
\cleardoublepage
\listoffigures	% print list of figures
\cleardoublepage
\listoftables  % print list of tables


%: ----------------------- glossary ------------------------

% Tie in external source file for definitions: /0_frontmatter/glossary.tex
% Glossary entries can also be defined in the main text. See glossary.tex
\cleardoublepage
%\chapter{Glossary}
\begin{multicols}{2} % \begin{multicols}{#columns}[header text][space]
\begin{footnotesize} % scriptsize(7) < footnotesize(8) < small (9) < normal (10)
\ifCLASSINFOlangDE
\printglossary[type=\acronymtype,title=Abkürzungsverzeichnis]
\else
\printglossary[type=\acronymtype,title=Abbreviations]
\fi
%\printglossary
%\printnomenclature[1.5cm] % [] = distance between entry and description
%\printglossery
\label{nom} % target name for links to glossary
\end{footnotesize}
\end{multicols}

\begin{multicols}{2} % \begin{multicols}{#columns}[header text][space]
\begin{footnotesize} 
\printglossary[type=symbolslist,title=Symbols]
\end{footnotesize}
\end{multicols}
%: --------------------------------------------------------------
%:                  MAIN DOCUMENT SECTION
% --------------------------------------------------------------

\mainmatter

%: ----------------------- subdocuments ------------------------

% Parts of the thesis are included below. Rename the files as required.
% But take care that the paths match. You can also change the order of appearance by moving the include commands.
% \cfchapter[short name] {full name} {folder name} {file name}.
\tikzsetexternalprefix{./1_introduction/TikzPictures/}
\cfchapter{Introduction}{1_introduction}{introduction}
\tikzsetexternalprefix{./2/TikzPictures/}
\cfchapter{State of the Art}{2}{chapter2}
\tikzsetexternalprefix{./3/TikzPictures/}
\cfchapter{Including tikz\label{ch:chapter3}}{3}{chapter3}
\tikzsetexternalprefix{./4/TikzPictures/}
\cfchapter{Sum - Algorithm\label{ch:chapter4}}{4}{chapter4}
\tikzsetexternalprefix{./5/TikzPictures/}
\cfchapter{PGF-plots from python\label{ch:chapter5}}{5}{chapter5}
\tikzsetexternalprefix{./6/TikzPictures/}
\cfchapter{Asymptote\label{ch:chapter6}}{6}{chapter6}
\tikzsetexternalprefix{./7/TikzPictures/}
\cfchapter{Discussion\label{ch:chapter7}}{7}{discussion}
\tikzsetexternalprefix{./8/TikzPictures/}
\cfchapter{Materials and Methods}{8}{materials_methods}
\cleardoublepage
       % description of lab methods



% --------------------------------------------------------------
%:                  BACK MATTER: appendices, refs,..
% --------------------------------------------------------------

% the back matter: appendix and references close the thesis


%: ----------------------- bibliography ------------------------

% The section below defines how references are listed and formatted
% The default below is one column, small font, complete author names.
% Entries are also linked back to the page number in the text and to external URL if provided in the BibTex file.

\begin{footnotesize} % tiny(5) < scriptsize(7) < footnotesize(8) < small (9)

\ifCLASSINFOlangDE
%\renewcommand{\bibname}{References}
\else
\renewcommand{\bibname}{References} % changes the header; default: Bibliography
\fi
% add bib to toc
\cleardoublepage
\phantomsection
\addcontentsline{toc}{chapter}{\bibname}

\ifCLASSINFObiblatex
\printbibliography
\else
% PhDbiblio-url2 = names small caps, title bold & hyperlinked, link to page 
\bibliographystyle{Classes/PhDbiblio-url2} % Title is link if provided
%\bibliographystyle{apalike}
\bibliography{9_backmatter/references} % adjust this to fit your BibTex file
\fi
\end{footnotesize}


% ********************************** Appendices ********************************

\begin{appendices} % Using appendices environment for more functionality
\tikzsetexternalprefix{./Appendix1/TikzPictures/}
\include{Appendix1/appendix1}
\end{appendices}

\end{document}