thesis.tex

\documentclass[11pt, a4paper]{book} %A4 is overruled by the geometry package later
\usepackage{geometry} \setlength{\paperwidth}{17cm}\setlength{\paperheight}{24cm} % change a4 sizes to thesis-size
% Color
\usepackage[usenames, dvipsnames]{xcolor} % color package
% Graphics
\usepackage{graphicx,amsmath,amssymb}
\usepackage{epstopdf, epsfig} % To convert eps image files to pdf
\usepackage[font=small]{caption} 
% References and links
% author-year citation
%\usepackage{natbib}
%\bibliographystyle{abbrvnat}
%\setcitestyle{authoryear,open={(},close={)}} %Citation-related commands
% natbib with compression -- does not support backref
\usepackage[square, numbers, sort&compress, comma]{natbib}
\bibliographystyle{unsrtnat}

%\usepackage[square, numbers, sort, comma]{natbib}
%\bibliographystyle{unsrtnat}


\definecolor{MyBlue}{rgb}{0,0,0.45} %color used for clickable links and so on
\definecolor{Myfig}{rgb}{0.45,0,0} %color used for clickable links and so on
\usepackage[colorlinks=true, urlcolor=MyBlue, linkcolor=MyBlue, plainpages=false, citecolor=MyBlue,bookmarks=true,bookmarksopen=true,bookmarksnumbered=true, pagebackref=true]{hyperref}
\renewcommand*{\backref}[1]{}  
    \renewcommand*{\backrefalt}[4]{
      \ifcase #1 
          {}%Cited on page #2. %No cited.
      \or
          Cited on page #2.
      \else
          Cited on pages #2.
      \fi} 
\usepackage{bookmark}    

\newcommand*\red{\textcolor{Myfig}}
%\usepackage[amssymb]{SIunits} % SI-units
\usepackage[nottoc]{tocbibind} % include or not include elements in TOC
\usepackage{lscape} % landscape page
\usepackage[figuresright]{rotating}
\usepackage{afterpage}
\usepackage[pagecolor=none]{pagecolor}
\usepackage{placeins} % floatbarrier
\usepackage{framed} %for quotes and stuff
\usepackage{siunitx}

\newcommand{\makered}[1]{\textcolor{Myfig}{#1}}  %used to insert red text

\newcommand{\publink}[1]{\href{#1}{\texttt{[Link]}}}  %used for adding links in mono-spaced font

\newcommand{\revV}[1]{\textcolor{black}{#1}}
\newcommand{\revP}[1]{\textcolor{black}{#1}}
\newcommand{\revVP}[1]{\textcolor{black}{#1}}

%\setlength{\parindent}{0mm}   %new environment that is a packed version of an itemize, useful for lists in the bio...
\newenvironment{packeditemize}{
\begin{itemize}
  \setlength{\itemsep}{1pt}
  \setlength{\parskip}{0pt}
  \setlength{\parsep}{0pt}
}{\end{itemize}}


\renewcommand{\thefootnote}{\ifcase\value{footnote}\or{$\circ$}\or{$\odot$}\or{$\circledcirc$}\or{$\circledast$}\or($\infty$)\fi} %change footnotes from daggers/stars or numbers to circular shapes

\usepackage[md]{titlesec}

\usepackage[thumblink=none,linefill=dots,height=auto,minheight={33pt},%
width={30pt},distance={10mm},topthumbmargin=auto,bottomthumbmargin=auto,%
nophantomsection=true,ignorehoffset=true,ignorevoffset=true,final=true,%
hidethumbs=false,verbose=true]{thumbs}

% Wanted appendices after every chapter
\usepackage{appendix}
\AtBeginEnvironment{subappendices}{%
	\chapter*{Appendix}
	\addcontentsline{toc}{chapter}{Appendices}
	\counterwithin{figure}{section}
	\counterwithin{table}{section}
}

%\definecolor{ColorDropImpact}{rgb}{0.99,0.88,0.57}
%\makeatletter
%\usepackage{xpatch}
%\xpatchcmd{\part}{\thispagestyle{plain}}
%{\pagecolor{ColorDropImpact}\thispagestyle{plain}}{}{}
%\xpatchcmd{\@endpart}{\vfil\newpage}{\vfil\newpage
%	\pagecolor{white}}{}{}
%\makeatother

\newcommand{\thesistitle}{Viscous Free-Surface Flows}
\newcommand{\thesistitledutch}{Viskeuze Stromingen bij Vrije-Oppervlakken}
\renewcommand{\bibname}{References}

% For 130 mm textwidth
% Whitespace on each side (non-text/non-figure) is approximately 2 cm each.
\setlength{\hoffset}{-0.55cm}  %thesis margins and offsets %don't touch these
\setlength{\textwidth}{13.0cm}
\setlength{\textheight}{18.5cm}
\setlength{\voffset}{-0.8cm}
\setlength{\headheight}{0.5cm}
\setlength{\headsep}{0.8cm}
\setlength{\footskip}{1cm}
\setlength{\oddsidemargin}{0cm}
\setlength{\evensidemargin}{0cm}

%% For 135 mm textwidth
%\setlength{\hoffset}{-0.75cm}  %thesis margins and offsets %don't touch these
%\setlength{\textwidth}{13.5cm}
%\setlength{\textheight}{18.5cm}
%\setlength{\voffset}{-0.8cm}
%\setlength{\headheight}{0.5cm}
%\setlength{\headsep}{0.8cm}
%\setlength{\footskip}{1cm}
%\setlength{\oddsidemargin}{0cm}
%\setlength{\evensidemargin}{0cm}

\setcounter{tocdepth}{1} %set depth of the table of contents


% Commands
\newcommand{\Wef}{\mathit{We}_\mathit{f}}
\newcommand{\Cas}{\mathit{Ca}_\mathit{s}}
\newcommand{\Can}{\mathit{Ca}}
%% Oh numbers
\newcommand{\Ohn}{\mathit{Oh}}
\newcommand{\Ohd}{\mathit{Oh}_\mathit{d}}
\newcommand{\Ohc}{\mathit{Oh}_\mathit{d,c}}
\newcommand{\Ohs}{\mathit{Oh}_\mathit{s}}
\newcommand{\Ohf}{\mathit{Oh}_\mathit{f}}
\newcommand{\Oha}{\mathit{Oh}_\mathit{a}}

\newcommand{\gammaaf}{\gamma_\mathit{af}}
\newcommand{\gammasf}{\gamma_\mathit{sf}}
\newcommand{\gammasa}{\gamma_\mathit{sa}}
\newcommand{\Ren}{\mathit{Re}}
\newcommand{\Wen}{\mathit{We}}
\newcommand{\Bon}{\mathit{Bo}}
\newcommand{\Boc}{\mathit{Bo}_\mathit{c}}

%% todonotes
\usepackage[obeyFinal,colorinlistoftodos]{todonotes}
\tikzset{notestyleraw/.append style={align=center}}

% todonotes specific macros begin!
\definecolor{Ch1}{HTML}{aacfed}
\newcommand{\todoChOne}[2]{\todo[color=Ch1!60, #1]{#2}}

\definecolor{Ch2}{HTML}{abceec}
\newcommand{\todoChTwo}[2]{\todo[color=Ch2, #1]{#2}}

\definecolor{Ch3}{HTML}{c9eaf6}
\newcommand{\todoChThree}[2]{\todo[color=Ch3, #1]{#2}}

\definecolor{Ch4}{HTML}{d1ecee}
\newcommand{\todoChFour}[2]{\todo[color=Ch4, #1]{#2}}

\definecolor{Ch5}{HTML}{c6e6dc}
\newcommand{\todoChFive}[2]{\todo[color=Ch5, #1]{#2}}

\definecolor{Ch6}{HTML}{e5f2e0}
\newcommand{\todoChSix}[2]{\todo[color=Ch6, #1]{#2}}

\usepackage{lipsum}

\begin{document}

\frontmatter  %start front matter

\input{frontmatter.tex}  %include front matter file (everything before the table of contents
%
\cleardoublepage \pagenumbering{roman}  \pdfbookmark[1]{Contents}{contents}  \tableofcontents \cleardoublepage  
%start at correct side of left/right pages, change numbering to roman numerals (I II III IV), start TOC, clear double page, change page numbers to arabic numbers (1234)
\pagenumbering{arabic} \setcounter{page}{1} %set the counter to 1
%
\mainmatter

%\addthumb{Chapter  0}{\huge{\textbf{\arabic{chapter}}}}{white}{gray}
\input{Chapter0_Introduction}
\stopthumb

\part{Drop Impact}\label{PartA}

\addthumb{Chapter  1}{\huge{\textbf{\arabic{chapter}}}}{black}{Ch1}
\input{Chapter1}  %Done
%%
\addthumb{Chapter  2}{\huge{\textbf{\arabic{chapter}}}}{black}{Ch2}
\input{Chapter2}
%%
\addthumb{Chapter  3}{\huge{\textbf{\arabic{chapter}}}}{black}{Ch3}
\input{Chapter3}
%%
\addthumb{Chapter  4}{\huge{\textbf{\arabic{chapter}}}}{black}{Ch4}
\input{Chapter4}
%%
\stopthumb
%%
\part{Retraction \& Bursting}\label{PartB}
%%
\addthumb{Chapter  5}{\huge{\textbf{\arabic{chapter}}}}{black}{Ch5}
\input{chapter5}
%%
\addthumb{Chapter  6}{\huge{\textbf{\arabic{chapter}}}}{black}{Ch6}
\input{chapter6}
%%
\stopthumb
%% We need to take conclusion and back matter out of Part B. So, these steps are important.
\bookmarksetup{startatroot}
\addtocontents{toc}{\bigskip}
%%
\input{Chapter0_Conclusion}
%%
%%\nocite{*} % to debug if all references are properly done.
\bibliography{biblioClean_v12}
%%

\backmatter
\include{backmatter/summary}  %summary English (obligatory)
\include{backmatter/samenvatting} %summary Dutch (obligatory)
\include{backmatter/acknowledgements}
\include{backmatter/bio}

\cleardoublepage 

\end{document}