%% ==============================================================================
%% NEMO Reference Manual
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%% Preamble
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%% Document layout
\documentclass{book}

%% Custom style (.sty)
\usepackage{../main/NEMO_manual}
\hypersetup{
	pdftitle={NEMO ocean engine}, pdfauthor={Gurvan Madec, and NEMO System Team},
	colorlinks
}

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

\makeindex

%% End of common preamble between main and sub-files
\begin{document}

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


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

\graphicspath{{../../figures/logos/}}

%% Frontpage
\title{
  \includegraphics[height=0.05\textheight]{CMCC}\hfill
  \includegraphics[height=0.05\textheight]{CNRS}\hfill
  \includegraphics[height=0.05\textheight]{MOI} \hfill
  \includegraphics[height=0.05\textheight]{UKMO}\hfill
  \includegraphics[height=0.05\textheight]{NERC}       \\
  \includegraphics[ width=0.8\textwidth  ]{NEMO_grey}  \\
  {\Huge NEMO ocean engine}                                     \\
}
\author{
  \Large Gurvan Madec and NEMO System Team
%  \thanks{
%
%  }                                                        \\
  \textit{Issue 27, Notes du P\^{o}le de mod\'{e}lisation} \\
  \textit{Institut Pierre-Simon Laplace (IPSL)}            \\
  \textit{ISSN 1288-1619}
}
\date{\today}

\maketitle
\frontmatter

%% ToC i.e. Table of Contents
\dominitoc
\tableofcontents


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

\mainmatter

\graphicspath{{../../figures/NEMO/}}

%% 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_model_basics_zstar}
%\subfile{../subfiles/chap_DIU}
%\subfile{../subfiles/chap_conservation}
%\subfile{../subfiles/annex_E}				% Notes on some on going staff

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

\backmatter

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

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

\end{document}
