source: branches/nemo_v3_3_beta/DOC/NEMO_book.tex @ 2349

%description: Book template

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

\documentclass[a4paper,12pt]{book}

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

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

\usepackage[french]{babel}
\usepackage{fancyhdr}

\usepackage{alltt}      %%  alltt for namelist
\usepackage{verbatim}   %%  alltt for namelist

%hyperref  ===>>>  don't work.....
%\usepackage[a4paper=true,ps2pdf=true,pagebackref=true,breaklinks=true]{hyperref}
%gn
\usepackage[%
  pdftitle={NEMO ocean engine},%
  pdfauthor={Gurvan Madec},% pdfsubject={The preprint document class
                           % elsart},% pdfkeywords={diapycnal diffusion,numerical mixing,z-level models},%
  pdfstartview=FitH,%
  bookmarks=true,%
  bookmarksopen=true,%
  breaklinks=true,%
  colorlinks=true,%
  linkcolor=blue,anchorcolor=blue,%
  citecolor=blue,filecolor=blue,%
  menucolor=blue,pagecolor=blue,%
  urlcolor=blue]{hyperref}
%gn end

%\usepackage{amssymb}
\pagestyle{fancy}
% with this we ensure that the chapter and section
% headings are in lowercase.
\renewcommand{\chaptermark}[1]{\markboth{#1}{}}
\renewcommand{\sectionmark}[1]{\markright{\thesection.\ #1}}
\fancyhf{}             % delete current setting for header and footer
\fancyhead[LE,RO]{\bfseries\thepage}
\fancyhead[LO]{\bfseries\hspace{-0em}\rightmark}
\fancyhead[RE]{\bfseries\leftmark}
\renewcommand{\headrulewidth}{0.5pt}
\renewcommand{\footrulewidth}{0pt}
\addtolength{\headheight}{2.6pt}   % make space for the rule
%\addtolength{\headheight}{1.6pt}   % make space for the rule
\fancypagestyle{plain}{
  \fancyhead{}         % get rid of headers on plain pages
  \renewcommand{\headrulewidth}{0pt}  % and the line
}

% Leave blank pages completely empty, w/o header
\makeatletter
\def\cleardoublepage{\clearpage\if@twoside \ifodd\c@page\else
  \hbox{}
  \vspace*{\fill}
  \vspace{\fill}
  \thispagestyle{empty}
  \newpage
  \if@twocolumn\hbox{}\newpage\fi\fi\fi}
\makeatother

\usepackage{makeidx}

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

%\usepackage{mtcoff}          % invalidate the use of minitocs
\usepackage[latin1]{inputenc}
\usepackage{graphics}            % allows insertion of pictures
\usepackage{times}               % use vector fonts instead of bitmap
\usepackage{fancybox}
\usepackage{graphicx}
%\usepackage{color}
%\usepackage{colortbl}

%%%% add by Word2Tex
%\documentclass{amsart}
\usepackage{latexsym}
\usepackage{amssymb}
\usepackage{amsmath}
\usepackage{graphicx}
\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{%
  \let\LV\LigneVerticale\LV\LV\LV\LV\LV\LV\LV\LV\LV\LV}
\def\GrosCarreAvecUnChiffre#1{%
  \rlap{\vrule height 0.8cm width 1cm depth 0.2cm}%
  \rlap{\hbox to 1cm{\hss\mbox{\white #1}\hss}}%
  \vrule height 0pt width 1cm depth 0pt}
\def\GrosCarreAvecTroisChiffre#1{%
  \rlap{\vrule height 0.8cm width 1.6cm depth 0.2cm}%
  \rlap{\hbox to 1.5cm{\hss\mbox{\white #1}\hss}}%
  \vrule height 0pt width 1cm depth 0pt}

\def\@makechapterhead#1{\hbox{%
    \huge 
    \LignesVerticales
    \hspace{-0.5cm}%
    \GrosCarreAvecUnChiffre{\thechapter}
    \hspace{0.2cm}\hbox{#1}%
%    \GrosCarreAvecTroisChiffre{\thechapter}
%    \hspace{1cm}\hbox{#1}%
%}\par\vskip 2cm}
}\par\vskip 1cm}
\def\@makeschapterhead#1{\hbox{%
    \huge 
    \LignesVerticales
    %\hspace{0.5cm}%
    \hbox{#1}%
}\par\vskip 2cm}

%\def\thechapter{\Roman{chapter}}      % chapter number to be Roman

%%%% end style chapter %%%

%%% use maths shortcuts :
%\newcommand{\vect} [1] { \rm{\textbf{#1}} }    % vector style: non-italic bold
\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)
\newcommand{\amtcomment}[1]{}    % command to "commented out" portions of text or not (#1 in argument)
\newcommand{\sgacomment}[1]{}    % command to "commented out" portions of 
\newcommand{\gmcomment}[1]{}     % command to "commented out" portions of 
%                                               % text that span line breaks
\newcommand{\alpbet} {\left(\alpha / \beta \right)}   % alpha/beta  for slp computation

%--------------------------------------------namlist---------------------------------------------------------
\newcommand{\namdisplay} [1] { 
   \begin{alltt}  {{\tiny \verbatiminput{./TexFiles/Namelist/#1}}}  \end{alltt} 
                               \vspace{-10pt}   }
%--------------------------------------------------------------------------------------------------------------

%Red (NR) or Yellow(WARN)
%\newcommand{\NR} {\colorbox{red}{#1}}
%\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.
\makeatletter 
\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}
%\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

% ================================================================
% 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}