main.tex

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% kaobook
% LaTeX Template
% Version 1.2 (4/1/2020)
%
% This template originates from:
% https://www.LaTeXTemplates.com
%
% For the latest template development version and to make contributions:
% https://github.com/fmarotta/kaobook
%
% Authors:
% Federico Marotta (federicomarotta@mail.com)
% Based on the doctoral thesis of Ken Arroyo Ohori (https://3d.bk.tudelft.nl/ken/en)
% and on the Tufte-LaTeX class.
% Modified for LaTeX Templates by Vel (vel@latextemplates.com)
%
% License:
% CC0 1.0 Universal (see included MANIFEST.md file)
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%----------------------------------------------------------------------------------------
%	PACKAGES AND OTHER DOCUMENT CONFIGURATIONS
%----------------------------------------------------------------------------------------

\documentclass[
    a4paper, % Page size
    fontsize=10pt, % Base font size
    twoside=true, % Use different layouts for even and odd pages (in particular, if twoside=true, the margin column will be always on the outside)
	%open=any, % If twoside=true, uncomment this to force new chapters to start on any page, not only on right (odd) pages
	%chapterentrydots=true, % Uncomment to output dots from the chapter name to the page number in the table of contents
	numbers=noenddot, % Comment to output dots after chapter numbers; the most common values for this option are: enddot, noenddot and auto (see the KOMAScript documentation for an in-depth explanation)
]{kaobook}

% Set the language
\usepackage[english]{babel} % Load characters and hyphenation
\usepackage[english=british]{csquotes} % English quotes

\setcounter{margintocdepth}{\sectiontocdepth}


% Load packages for testing
\usepackage{blindtext}
%\usepackage{showframe} % Uncomment to show boxes around the text area, margin, header and footer
%\usepackage{showlabels} % Uncomment to output the content of \label commands to the document where they are used
\usepackage{graphicx}
\usepackage[percent]{overpic}
\usepackage[utf8]{inputenc}
% \usepackage{natbib}
\usepackage{amsmath}
\usepackage{siunitx}
\sisetup{group-separator = {\,}}
\usepackage{subcaption}
\usepackage{todonotes}
\usepackage[version=4]{mhchem}
\usepackage{wasysym}
\usepackage{overpic}
\usepackage{lipsum}
\usepackage[dvipsnames]{xcolor}
\usepackage{calrsfs}
\usepackage{pdfpages}
% package for code blocks
\usepackage{listings}

\DeclareMathAlphabet{\pazocal}{OMS}{zplm}{m}{n}
\newcommand{\Aa}{\mathcal{A}}
\newcommand{\Ab}{\pazocal{A}}

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    basicstyle=\ttfamily\footnotesize,
    breakatwhitespace=false,         
    breaklines=true,                 
    captionpos=b,                    
    keepspaces=true,                 
    numbers=left,                    
    numbersep=5pt,                  
    showspaces=false,                
    showstringspaces=false,
    showtabs=false,                  
    tabsize=2
}

\lstset{style=mystyle}

% Load the bibliography package
\usepackage{kaobiblio}
\addbibresource{bibfile.bib} % Bibliography file

\AtEveryBibitem{
    \clearfield{urlyear}
    \clearfield{urldate}
    \clearfield{urlmonth}
}

\RenewDocumentCommand{\formatmargincitation}{m}{%
	\parencite{#1} \citeauthor*{#1} (\citeyear{#1})\\
}

% Load mathematical packages for theorems and related environments
\usepackage[framed=true]{kaotheorems}

% Load the package for hyperreferences
\usepackage{kaorefs}

\graphicspath{{examples/documentation/images/}{images/}} % Paths in which to look for images

\makeindex[columns=3, title=Alphabetical Index, intoc] % Make LaTeX produce the files required to compile the index
\usepackage[automake, acronym]{glossaries-extra}

% uncomment to have the first use of acronyms in italic
\setabbreviationstyle[acronym]{long-short}
% \glssetcategoryattribute{acronym}{glossdescfont}{emph}

% \renewcommand*{\glsfirstlongdefaultfont}[1]{\emph{#1}}

\makeglossaries % Make LaTeX produce the files required to compile the glossary
\input{glossary.tex} % Include the glossary definitions

\makenomenclature % Make LaTeX produce the files required to compile the nomenclature

% Reset sidenote counter at chapters
%\counterwithin*{sidenote}{chapter}

%----------------------------------------------------------------------------------------

% Changing the width between text and margin
\renewcommand{\marginlayout}{%
    \newgeometry{
        top=27.4mm,             % height of the top margin
        bottom=27.4mm,          % height of the bottom margin
        inner=24.8mm,           % width of the inner margin
        textwidth=127mm,        % width of the text
        marginparsep=8.2mm,     % width between text and margin
        marginparwidth=29.4mm,  % width of the margin
    }%
}


\begin{document}

% Define colours
\definecolor{yellow}{RGB}{180, 95, 6}
\definecolor{grey}{RGB}{183, 183, 183}
\definecolor{orange}{RGB}{228, 146, 64}

% Define column types
\newcolumntype{L}[1]{>{\raggedright\arraybackslash}p{#1}}
\newcolumntype{C}[1]{>{\centering\arraybackslash}p{#1}}
\newcolumntype{R}[1]{>{\raggedleft\arraybackslash}p{#1}}
\newcommand\cruleme[3][black]{\textcolor{#1}{\rule{#2}{#3}}}


%----------------------------------------------------------------------------------------
%	BOOK INFORMATION
%----------------------------------------------------------------------------------------
\titlehead{UNIVERSITE SORBONNE PARIS NORD}
% \subject{My awesome subject}

\title[Hydrogen transport in tokamaks]{
    \noindent\rule{8cm}{0.4pt} \\
    Hydrogen transport in tokamaks\\
    }
\subtitle{
    Estimation of the ITER divertor tritium inventory and influence of helium exposure \\
    \noindent\rule{8cm}{0.4pt}
}

\author[Rémi Delaporte-Mathurin]{Rémi Delaporte-Mathurin}

\date{
    Submitted in fulfillment of the requirements for the degree of \\
    Doctor of Philosophy in Materials science \\
    17th October 2022
}
\publishers{\begin{tabular}{p{12cm}l}
    \textbf{Klaus SCHMID}, Max Planck Institute for Plasma Physics & reader \\
    \textbf{Jamaa BOUHATTATE}, Univ. La Rochelle & reader \\
    \textbf{Sophie BLONDEL}, Univ. of Tennessee, Knoxville & committee member \\
    \textbf{Xavier BONNIN}, ITER Organization & committee member \\
    \textbf{Monique GASPERINI}, Univ. Sorbonne Paris Nord & committee member \\
    \textbf{Dennis WHYTE}, Massachusetts Institute of Technology & committee member \\
    \textbf{Etienne HODILLE}, CEA & invited member \\
    \textbf{Christian GRISOLIA}, CEA & cosupervisor \\
    \textbf{Yann CHARLES}, Univ. Sorbonne Paris Nord & cosupervisor \\
    \textbf{Jonathan MOUGENOT}, Univ. Sorbonne Paris Nord & adviser \\
    \end{tabular}
}

%----------------------------------------------------------------------------------------
% \includepdf[pages={1}]{chapters/front_page.pdf}
\frontmatter % Denotes the start of the pre-document content, uses roman numerals

%----------------------------------------------------------------------------------------
%	OPENING PAGE
%----------------------------------------------------------------------------------------

%\makeatletter
%\extratitle{
%	% In the title page, the title is vspaced by 9.5\baselineskip
%	\vspace*{9\baselineskip}
%	\vspace*{\parskip}
%	\begin{center}
%		% In the title page, \huge is set after the komafont for title
%		\usekomafont{title}\huge\@title
%	\end{center}
%}
%\makeatother

%----------------------------------------------------------------------------------------
%	DEDICATION
%----------------------------------------------------------------------------------------

% \dedication{
% 	The harmony of the world is made manifest in Form and Number, and the heart and soul and all the poetry of Natural Philosophy are embodied in the concept of mathematical beauty.\\
% 	\flushright -- D'Arcy Wentworth Thompson
% }

%----------------------------------------------------------------------------------------
%	OUTPUT TITLE PAGE AND PREVIOUS
%----------------------------------------------------------------------------------------

% Note that \maketitle outputs the pages before here

% If twoside=false, \uppertitleback and \lowertitleback are not printed
% To overcome this issue, we set twoside=semi just before printing the title pages, and set it back to false just after the title pages
% \KOMAoptions{twoside=semi}
\maketitle
% \KOMAoptions{twoside=false}

%----------------------------------------------------------------------------------------
%	Abstract
%----------------------------------------------------------------------------------------

\input{chapters/abstract.tex}
\input{chapters/introduction.tex}

%----------------------------------------------------------------------------------------
%	TABLE OF CONTENTS & LIST OF FIGURES/TABLES
%----------------------------------------------------------------------------------------

\begingroup % Local scope for the following commands

% Define the style for the TOC, LOF, and LOT
%\setstretch{1} % Uncomment to modify line spacing in the ToC
%\hypersetup{linkcolor=blue} % Uncomment to set the colour of links in the ToC
\setlength{\textheight}{23cm} % Manually adjust the height of the ToC pages

% Turn on compatibility mode for the etoc package
\etocstandarddisplaystyle % "toc display" as if etoc was not loaded
\etocstandardlines % toc lines as if etoc was not loaded

\tableofcontents % Output the table of contents

\listoffigures % Output the list of figures

% Comment both of the following lines to have the LOF and the LOT on different pages
\let\cleardoublepage\bigskip
\let\clearpage\bigskip

\listoftables % Output the list of tables

% %----------------------------------------------------------------------------------------
% %	NOMENCLATURE
% %----------------------------------------------------------------------------------------

% % The nomenclature needs to be compiled on the command line with 'makeindex main.nlo -s nomencl.ist -o main.nls' from the template directory
\newcommand{\nomunit}[1]{%
  \renewcommand{\nomentryend}{\hspace*{\fill}#1}%
}
\nomenclature{$c_\mathrm{m}$}{mobile concentration of hydrogen \nomunit{\si{m^{-3}}}}
\nomenclature{$c_\mathrm{t, \, i}$}{concentration of trapped hydrogen in trap $i$ \nomunit{\si{m^{-3}}}}
\nomenclature{$T$}{Temperature \nomunit{\si{K}}}
\nomenclature{$T_\mathrm{coolant}$}{Coolant temperature \nomunit{\si{K}}}
\nomenclature{$D$}{Diffusion coefficient \nomunit{\si{m^2.s^{-1}}}}
\nomenclature{$S$}{Solubility \nomunit{\si{m^{-3}.Pa^{-0.5}}}}
\nomenclature{$k_i$}{Trapping rate of trap $i$ \nomunit{\si{m^{3}.s^{-1}}}}
\nomenclature{$p_i$}{Detrapping rate of trap $i$ \nomunit{\si{s^{-1}}}}
\nomenclature{$k_{0, \, i}$}{Trapping rate of trap $i$ pre-exponential factor \nomunit{\si{m^{3}.s^{-1}}}}
\nomenclature{$E_{k, \, i}$}{Trapping rate of trap $i$ activation energy \nomunit{\si{eV}}}
\nomenclature{$p_{0, \, i}$}{Detrapping rate of trap $i$ pre-exponential factor \nomunit{\si{s^{-1}}}}
\nomenclature{$E_{p, \, i}$}{Detrapping rate of trap $i$ activation energy \nomunit{\si{eV}}}

\nomenclature{$D_{0}$}{Diffusivity pre-exponential factor \nomunit{\si{m^2.s^{-1}}}}
\nomenclature{$E_{D}$}{Diffusivity activation energy \nomunit{\si{eV}}}
\nomenclature{$S_{0}$}{Solubility pre-exponential factor \nomunit{\si{m^{-3}.Pa^{-0.5}}}}
\nomenclature{$E_{S}$}{Solubility activation energy \nomunit{\si{eV}}}

\nomenclature{$u$}{An arbitrary solution}
\nomenclature{$v$}{A test function}

\nomenclature{$n_i$}{Density of trap $i$ \nomunit{\si{m ^{-3}}}}
\nomenclature{$k_B$}{Boltzmann constant \nomunit{\si{eV.K^{-1}}}}
\nomenclature{$R_p$}{Implantation range \nomunit{\si{m}}}
\nomenclature{$r$}{Particle reflection coefficient}
\nomenclature{$r_A$}{Capture radius of species A \nomunit{\si{m}}}
\nomenclature{$K_r$}{Recombination coefficient \nomunit{\si{m^{4}.s^{-1}}}}
\nomenclature{$\varphi_\mathrm{imp}$}{Implanted particle flux per unit surface \nomunit{\si{m^{-2}.s^{-1}}}}
\nomenclature{$\varphi_\mathrm{incident}$}{Incident particle flux per unit surface \nomunit{\si{m^{-2}.s^{-1}}}}
\nomenclature{$\varphi_\mathrm{heat}$}{Heat flux per unit surface \nomunit{\si{W.m^{-2}}}}
\nomenclature{$t$}{Time \nomunit{\si{s}}}
\nomenclature{$\lambda$}{Thermal conductivity \nomunit{\si{W.m^{-1}.K^{-1}}}}
\nomenclature{$\lambda_\mathrm{decay}$}{Radioactive decay constant \nomunit{\si{s}}}
\nomenclature{$C_p$}{Heat capacity \nomunit{\si{W.K^{-1}}}}
\nomenclature{$\rho$}{Volumetric density \nomunit{\si{kg.m^{-3}}}}
\nomenclature{$h$}{Convective heat transfer coefficient per unit surface \nomunit{\si{W.m^{-2}.K^{-1}}}}
\nomenclature{$\Omega$}{Geometrical domain}
\nomenclature{$\partial \Omega$}{Boundary of a geometrical domain}

\nomenclature{$c_b$}{Total concentration of helium clusters above a given threshold \nomunit{\si{m^{-3}}}}
\nomenclature{$\langle i_b \rangle$}{Average helium content in $c_b$}
\nomenclature{$\langle r_b \rangle$}{Average radius in $c_b$ \nomunit{\si{m}}}
\nomenclature{$\tau_{1/2}$}{Radioactive half-life \nomunit{\si{s}}}
\nomenclature{$Q$}{Plasma amplification factor. The ratio of the fusion power generated by the power absorbed by the plasma.}



\renewcommand{\nomname}{Notation} % Rename the default 'Nomenclature'
\renewcommand{\nompreamble}{The next list describes several symbols that will be later used within the body of the document.} % Prepend this text to the nomenclature

\printnomenclature % Output the nomenclature

%----------------------------------------------------------------------------------------
%	GREEK ALPHABET
% 	Originally from https://gitlab.com/jim.hefferon/linear-algebra
%----------------------------------------------------------------------------------------

% \vspace{1cm}

% {\usekomafont{chapter}Greek Letters with Pronounciation} \\[2ex]
% \begin{center}
% 	\newcommand{\pronounced}[1]{\hspace*{.2em}\small\textit{#1}}
% 	\begin{tabular}{l l @{\hspace*{3em}} l l}
% 		\toprule
% 		Character & Name & Character & Name \\ 
% 		\midrule
% 		$\alpha$ & alpha \pronounced{AL-fuh} & $\nu$ & nu \pronounced{NEW} \\
% 		$\beta$ & beta \pronounced{BAY-tuh} & $\xi$, $\Xi$ & xi \pronounced{KSIGH} \\ 
% 		$\gamma$, $\Gamma$ & gamma \pronounced{GAM-muh} & o & omicron \pronounced{OM-uh-CRON} \\
% 		$\delta$, $\Delta$ & delta \pronounced{DEL-tuh} & $\pi$, $\Pi$ & pi \pronounced{PIE} \\
% 		$\epsilon$ & epsilon \pronounced{EP-suh-lon} & $\rho$ & rho \pronounced{ROW} \\
% 		$\zeta$ & zeta \pronounced{ZAY-tuh} & $\sigma$, $\Sigma$ & sigma \pronounced{SIG-muh} \\
% 		$\eta$ & eta \pronounced{AY-tuh} & $\tau$ & tau \pronounced{TOW (as in cow)} \\
% 		$\theta$, $\Theta$ & theta \pronounced{THAY-tuh} & $\upsilon$, $\Upsilon$ & upsilon \pronounced{OOP-suh-LON} \\
% 		$\iota$ & iota \pronounced{eye-OH-tuh} & $\phi$, $\Phi$ & phi \pronounced{FEE, or FI (as in hi)} \\
% 		$\kappa$ & kappa \pronounced{KAP-uh} & $\chi$ & chi \pronounced{KI (as in hi)} \\
% 		$\lambda$, $\Lambda$ & lambda \pronounced{LAM-duh} & $\psi$, $\Psi$ & psi \pronounced{SIGH, or PSIGH} \\
% 		$\mu$ & mu \pronounced{MEW} & $\omega$, $\Omega$ & omega \pronounced{oh-MAY-guh} \\
% 		\bottomrule
% 	\end{tabular} \\[1.5ex]
% 	Capitals shown are the ones that differ from Roman capitals.
% \end{center}

%----------------------------------------------------------------------------------------
%	GLOSSARY
%----------------------------------------------------------------------------------------

% The glossary needs to be compiled on the command line with 'makeglossaries main' from the template directory

\setglossarystyle{listgroup} % Set the style of the glossary (see https://en.wikibooks.org/wiki/LaTeX/Glossary for a reference)
\printglossary[title=List of Terms, toctitle=List of Terms] % Output the glossary, 'title' is the chapter heading for the glossary, toctitle is the table of contents heading

\endgroup

%----------------------------------------------------------------------------------------
%	MAIN BODY
%----------------------------------------------------------------------------------------

\mainmatter % Denotes the start of the main document content, resets page numbering and uses arabic numbers
\setchapterstyle{kao} % Choose the default chapter heading style

\glsresetall % resets first use of glossary entries

\input{chapters/chapter1/intro}
\input{chapters/chapter2/model_description}
\input{chapters/chapter3/monoblocks}
\input{chapters/chapter4/divertor}
\input{chapters/chapter5/he_transport_in_pfcs}
\input{chapters/conclusion}

\appendix % From here onwards, chapters are numbered with letters, as is the appendix convention

\pagelayout{wide} % No margins
\addpart{Appendix}
\pagelayout{margin} % Restore margins

\input{chapters/v_and_v}
\input{chapters/interface_transient.tex}
\input{chapters/demo_monoblock.tex}
% \input{chapters/appendix.tex}
% \input{chapters/breeding_blankets}
% \input{chapters/codeposition_model}

%----------------------------------------------------------------------------------------

\backmatter % Denotes the end of the main document content
\setchapterstyle{plain} % Output plain chapters from this point onwards

%----------------------------------------------------------------------------------------
%	BIBLIOGRAPHY
%----------------------------------------------------------------------------------------

% The bibliography needs to be compiled with biber using your LaTeX editor, or on the command line with 'biber main' from the template directory

% Redefine the citation style to Author (year) and using bracket like [i-ii]

\defbibnote{bibnote}{Here are the references in citation order.\par\bigskip} % Prepend this text to the bibliography
\printbibliography[heading=bibintoc, title=Bibliography, prenote=bibnote] % Add the bibliography heading to the ToC, set the title of the bibliography and output the bibliography note

%----------------------------------------------------------------------------------------
%	INDEX
%----------------------------------------------------------------------------------------

% The index needs to be compiled on the command line with 'makeindex main' from the template directory

\printindex % Output the index

%----------------------------------------------------------------------------------------
%	BACK COVER
%----------------------------------------------------------------------------------------

% If you have a PDF/image file that you want to use as a back cover, uncomment the following lines

%\clearpage
%\thispagestyle{empty}
%\null%
%\clearpage
%\includepdf{cover-back.pdf}

%----------------------------------------------------------------------------------------

\end{document}