source: branches/nemo_v3_3_beta/DOC/NEMO_book.tex @ 2414

%description: Book template

% template of document for LaTeX
% (C) Xavier Perseguers 2002 - xavier.perseguers@epfl.ch

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%  makeindex NEMO_book     <== to regenerate the index
%  bibtex         NEMO_book   <== to generate  the bibliography

% ================================================================
% HEADERS DEFINITION
% ================================================================

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%  usage of exteranl hyperlink :  \href{mailto:my_address@wikibooks.org}{my\_address@wikibooks.org}
%                                                 \url{http://www.wikibooks.org}
%                                     or         \href{http://www.wikibooks.org}{wikibooks home}




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\usepackage{minitoc}          %in french : \usepackage[french]{minitoc}

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\allowdisplaybreaks[1]           % allow page breaks in the middle of equations
%%%%

%%%%
%\usepackage{mathtime}      % font for illustrator to work (belleek fonts )
%%%%

%\usepackage{showidx}            % show the index entry



%%%% define the style of title for chapter  %%%
\usepackage{pstricks}
\makeatletter
\def\LigneVerticale{\vrule height 5cm depth 2cm\hspace{0.1cm}\relax}
\def\LignesVerticales{%
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%\def\thechapter{\Roman{chapter}}      % chapter number to be Roman

%%%% end style chapter %%%

%%% use maths shortcuts :
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\usepackage{./TexFiles/math_abbrev}


%%% essai commande
\newcommand{\nl} [1] {\texttt{\small {\textcolor{blue}{#1}} } } 

%%% index commands :   
\newcommand{\mdl} [1] {\textit{#1.F90}\index{Modules!#1}}         %module (mdl)
\newcommand{\rou} [1] {\textit{#1}\index{Routines!#1}}            %module (routine)
\newcommand{\hf} [1] {\textit{#1.h90}\index{h90 file!#1}}            %module (h90 files)
\newcommand{\np} [1] {\textit{#1}\index{Namelist parameters!#1}}     %namelist parameter (nampar)
\newcommand{\jp} [1] {\textit{#1}\index{Model parameters!#1}}        %model parameter (jp)
\newcommand{\pp} [1] {\textit{#1}\index{Model parameters!#1}}        %namelist parameter (pp)
\newcommand{\ifile} [1] {\textit{#1.nc}\index{Input NetCDF files!#1.nc}}   %input NetCDF files (.nc)
\newcommand{\key} [1] {\textbf{key\_#1}\index{CPP keys!key\_#1}}  %key_cpp (key)
\newcommand{\NEMO} {\textit{NEMO }}                %NEMO (nemo)
% command to "commented out" portions of text ({} argument) or not ({#1} argument)
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\newcommand{\gmcomment}[1]{}     % command to "commented out" portions of 
%                                               % text that span line breaks
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%--------------------------------------------------------------------------------------------------------------
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%\newcommand{\WARN} {{ \colorbox{yellow}{#1}} }

%---------------------%%%%%  Section number in Margin  %%%%%-----------------------------
% typeset the number of each section in the left margin, with the start of each instance of
% sectional heading text aligned with the left hand edge of  the body text.
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\def\@seccntformat#1{\protect\makebox[0pt][r]{\csname the#1\endcsname\quad}} 
\makeatother 
%--------------------------------------------------------------------------------------------------------------

%----------------------------%%%%%   Bilbiography   %%%%%%-------------------------------%
\usepackage[nottoc, notlof, notlot]{tocbibind}
\usepackage[square, comma]{natbib}
\bibpunct{[}{]}{,}{a}{}{;}                           %suppress "," after "et al."
\providecommand{\bibfont}{\small}
%--------------------------------------------------------------------------------------------------------------

% ================================================================
% FRONT PAGE
% ================================================================

\title{ 
\psset{unit=1.1in,linewidth=4pt}    %parameters of the units for pstricks
\rput(-1.4,2){ \includegraphics[width=0.2\textwidth]{./TexFiles/Figures/logo_CNRS.pdf}           }
\quad
\rput(-.15,2){ \includegraphics[width=0.2\textwidth]{./TexFiles/Figures/logo_MERCATOR.pdf} }
\quad
\rput(.85,2){ \includegraphics[width=0.1\textwidth]{./TexFiles/Figures/logo_UKMO.pdf}            }
\quad
\rput(1.85,2){ \includegraphics[width=0.2\textwidth]{./TexFiles/Figures/logo_NERC.pdf}             } \\
\vspace{0.1cm}
\includegraphics[width=0.9\textwidth]{./TexFiles/Figures/NEMO_logo_Black.pdf} \\
\vspace{1.4cm}
\rule{345pt}{1.5pt} \\
\vspace{0.45cm}
 {\Huge NEMO ocean engine} 
\rule{345pt}{1.5pt} \\ 
{\small  -- version 3.3 --}   }
%{ -- Draft --}   }
%\date{\today}
\date{
October 2010  \\
~  \\
\textit{\small Note du P\^ole de mod\'{e}lisation de l'Institut Pierre-Simon Laplace No 27 }\\
\vspace{0.45cm}
{ ISSN No 1288-1619.}
}


%%\includegraphics[width=0.2\textwidth]{./TexFiles/Figures/logo_NERC.pdf} \\

%%    \hbox{\mbox{%
%%       \hspace{4pt}%
%%         \fbox{\includegraphics[width=3em]{./TexFiles/Figures/logo_CNRS.pdf}}%
%%        \hspace{4pt}
%%        }  }%

\author{ 
\Large Gurvan Madec, and the NEMO team  \\
 \texttt{\small gurvan.madec@locean-ipsl.umpc.fr} \\
 \texttt{\small nemo\_st@hermes.locean-ipsl.umpc.fr} \\
%{\small Laboratoire d'Oc\'{e}anographie  et du Climat: Exp\'{e}rimentation et Approches Num\'{e}riques }
}

\dominitoc
\makeindex        %type this first :     makeindex -s NEMO.ist NEMO_book.idx

% ================================================================
%      Include ONLY order
% ================================================================

%\includeonly{./TexFiles/Chapters/Chap_MISC, ./TexFiles/Chapters/Chap_CFG}
%\includeonly{./TexFiles/Chapters/Chap_ZDF}
%\includeonly{./TexFiles/Chapters/Chap_STP,./TexFiles/Chapters/Chap_SBC,./TexFiles/Chapters/Chap_TRA}
%\includeonly{./TexFiles/Chapters/Chap_LBC,./TexFiles/Chapters/Chap_MISC}
%\includeonly{./TexFiles/Chapters/Chap_Model_Basics}
%\includeonly{./TexFiles/Chapters/Annex_A,./TexFiles/Chapters/Annex_B,./TexFiles/Chapters/Annex_C,./TexFiles/Chapters/Annex_D}

% ================================================================
% ================================================================
\begin{document}

\maketitle                 % generate the title

\frontmatter

\tableofcontents              % generate a table of content
%\listoffigures               % generate a table of content
%\listoftables             % generate a table of content

\mainmatter

% ================================================================
% Abstract - Foreword
% ================================================================

\include{./TexFiles/Chapters/Abstracts_Foreword}

% ================================================================
% INTRODUCTION
% ================================================================

\include{./TexFiles/Chapters/Introduction}

% ================================================================
% CHAPTERS
% ================================================================

\include{./TexFiles/Chapters/Chap_Model_Basics}

\include{./TexFiles/Chapters/Chap_STP}       % Time discretisation (time stepping strategy)

\include{./TexFiles/Chapters/Chap_DOM}       % Space discretisation 

\include{./TexFiles/Chapters/Chap_TRA}       % Tracer advection/diffusion equation

\include{./TexFiles/Chapters/Chap_DYN}       % Dynamics : momentum equation

\include{./TexFiles/Chapters/Chap_SBC}       % Surface Boundary Conditions

\include{./TexFiles/Chapters/Chap_LBC}       % Lateral Boundary Conditions

\include{./TexFiles/Chapters/Chap_LDF}       % Lateral diffusion

\include{./TexFiles/Chapters/Chap_ZDF}       % Vertical diffusion

\include{./TexFiles/Chapters/Chap_OBS}                  % Observation operator

\include{./TexFiles/Chapters/Chap_ASM}                  % Assimilation increments

\include{./TexFiles/Chapters/Chap_MISC}         % Miscellaneous topics

\include{./TexFiles/Chapters/Chap_CFG}       % Predefined configurations

% ================================================================
% APPENDIX
% ================================================================

\appendix

%\include{./TexFiles/Chapters/Chap_Conservation}
\include{./TexFiles/Chapters/Annex_A}        % generalised vertical coordinate
\include{./TexFiles/Chapters/Annex_B}        % diffusive operator
\include{./TexFiles/Chapters/Annex_C}        % Discrete invariants of the eqs.
\include{./TexFiles/Chapters/Annex_D}        % Coding rules
\include{./TexFiles/Chapters/Annex_ISO}                     % Isoneutral diffusion using triads 
%\include{./TexFiles/Chapters/Annex_E}                   % Notes on some on going staff (no included in the DOC) 

% ================================================================
% INDEX
% ================================================================

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

% ================================================================
% BIBLIOGRAPHY
% ================================================================

%%\bibliographystyle{plainat}
\bibliographystyle{./TexFiles/ametsoc}    % AMS biblio style (JPO)
\bibliography{./TexFiles/Biblio/Biblio}

% ================================================================
\end{document}