%% ==============================================================================
%% NEMO_book.tex: build the NEMO Reference Manual
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%% Run ../build_NEMO_manual.sh to generate the PDF version (with pdflatex)

%% Document layout
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\documentclass[a4paper, 11pt]{book}


%% Preamble
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%% Custom style
\usepackage{../main/NEMO_manual}

\makeindex


%% 
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%% Include references and index for single subfile compilation
\newcommand{\biblio}{\bibliography{../main/NEMO_manual}}
\newcommand{\pindex}{\printindex}

\begin{document}

%% Override custom cmds for full manual compilation
\renewcommand{\biblio}{}
\renewcommand{\pindex}{}


%% Frontmatter
%% ==============================================================================

%% Frontpage

\title{
%\vspace{-6.0cm}\includegraphics[width=1.1\textwidth]{logo_ALL}				\\
%\vspace{ 5.1cm}\includegraphics[width=0.9\textwidth]{NEMO_logo_Black}	\\
\vspace{ 1.4cm}\rule{345pt}{1.5pt}													\\
\vspace{0.45cm}{\Huge NEMO ocean engine}											\\
\rule{345pt}{1.5pt}
}

\author{
  \Large Gurvan Madec and NEMO System Team
  \thanks{
    Yevgeny Aksenov, Mireck Andrejczuk, Mike Bell, Romain Bourdalle-Badie, Cl\'{e}ment Bricaud,
    J\'{e}r\^{o}me Chanut, Stefania Ciliberti, Emanuela Clementi, Andrew Coward, Damiano Delrosso,
    Massimiliano Drudi, Christian Eth\'{e}, Simona Flavoni, Doroteaciro Iovino, Claire L\'{e}vy, Tomas Lovato,
    Nicolas Martin, S\'{e}bastien Masson, Pierre Mathiot, Gelsomina Mattia, Francesca Mele, Silvia Mocavero,
    George Nurser, Enda O'Dea, Julien Paul, Cl\'{e}ment Rousset, Dave Storkey, Martin Vancoppenolle
  }                                                        \\
                                                           \\
  \textit{Issue 27, Notes du P\^{o}le de mod\'{e}lisation} \\
  \textit{Institut Pierre-Simon Laplace (IPSL)}            \\
  \textit{ISSN 1288-1619}
}

\date{Version 4.0 -- January 2019}
%\date{\today}

\maketitle
\frontmatter


%% ToC i.e. Table of Contents

\dominitoc
\tableofcontents


%% Mainmatter
%% ==============================================================================

\mainmatter


%% Foreword

\subfile{../subfiles/foreword}


% Introduction

\subfile{../subfiles/introduction}


% Chapters

\subfile{../subfiles/chap_model_basics}

\subfile{../subfiles/chap_time_domain}   % Time discretisation (time stepping strategy)

\subfile{../subfiles/chap_DOM}           % Space discretisation

\subfile{../subfiles/chap_TRA}           % Tracer advection/diffusion equation

\subfile{../subfiles/chap_DYN}           % Dynamics : momentum equation

\subfile{../subfiles/chap_SBC}           % Surface Boundary Conditions

\subfile{../subfiles/chap_LBC}           % Lateral Boundary Conditions

\subfile{../subfiles/chap_LDF}           % Lateral diffusion

\subfile{../subfiles/chap_ZDF}           % Vertical diffusion

\subfile{../subfiles/chap_DIA}           % Outputs and Diagnostics

\subfile{../subfiles/chap_OBS}           % Observation operator

\subfile{../subfiles/chap_ASM}           % Assimilation increments

\subfile{../subfiles/chap_STO}           % Stochastic param.

\subfile{../subfiles/chap_misc}          % Miscellaneous topics

\subfile{../subfiles/chap_CONFIG}        % Predefined configurations


%% Appendix

\appendix

\subfile{../subfiles/annex_A}					% Generalised vertical coordinate

\subfile{../subfiles/annex_B}					% Diffusive operator

\subfile{../subfiles/annex_C}					% Discrete invariants of the eqs.

\subfile{../subfiles/annex_iso}				% Isoneutral diffusion using triads

\subfile{../subfiles/annex_D}					% Coding rules

%% Not included
%\subfile{../subfiles/chap_conservation}	%
%\subfile{../subfiles/annex_E}				% Notes on some on going staff
%\subfile{../subfiles/annex_Fox-Kemper}	% Notes on Fox-Kemper
%\subfile{../subfiles/annex_EVP}				% Notes on EVP


%% Backmatter
%% ==============================================================================

\backmatter


%% Bibliography

\cleardoublepage
\phantomsection
\addcontentsline{toc}{chapter}{Bibliography}
\bibliography{../main/NEMO_manual}


%% Index

\cleardoublepage
\phantomsection
\addcontentsline{toc}{chapter}{Index}
\printindex


\end{document}