%% ==============================================================================
%% NEMO Reference Manual
%% ==============================================================================


%% Run ./PDF_creation.sh to generate the manual with latexmk


%% Preamble
%% ==============================================================================

%% Document layout
\documentclass{book}

%% Custom style (.sty)
\usepackage{../main/NEMO_manual}

%% 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_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}