source: branches/DEV_r2191_3partymerge2010/DOC/NEMO_book.tex @ 2205

%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}
\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}

%\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{times}               % use vector fonts instead of bitmap
\usepackage{fancybox}
\usepackage[table]{xcolor}

%%%% add by Word2Tex
%\documentclass{amsart}
\usepackage{latexsym}
\usepackage{amssymb}
\usepackage{amsmath}
\usepackage{graphicx}
%%%%

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

%\usepackage{showidx}            % show the index entry



%%%% define the style of title for chapter  %%%
\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{\textcolor{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{\textcolor{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 %%%

%%% eqution shortcut:
\newcommand{\vect} [1] { \rm{\textbf{#1}} }    % vector style:
                                % non-italic bold
%% agn use maths shortcuts
\usepackage{math_abbrev}

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

%essai commande  
\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{\key} [1] {\textbf{key\_#1}\index{CPP keys!key\_#1}}  %key_cpp (key)
\newcommand{\NEMO} {\textit{NEMO }}                %NEMO (nemo)
\newcommand{\amtcomment}[1]{#1}     % command to allow "commented out" portions of 
\newcommand{\gmcomment}[1]{}     % command to allow "commented out" portions of 
%                                               % text that span line breaks

%--------------------------------------------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{ 
\includegraphics[width=0.2\textwidth]{./TexFiles/Figures/logo_CNRS} 
\quad
\includegraphics[width=0.2\textwidth]{./TexFiles/Figures/logo_MERCATOR} 
\quad
\includegraphics[width=0.1\textwidth]{./TexFiles/Figures/logo_UKMO} 
\quad
\includegraphics[width=0.2\textwidth]{./TexFiles/Figures/logo_NERC} \\
\vspace{3.0cm}
\includegraphics[width=0.3\textwidth]{./TexFiles/Figures/NEMO_logo_Black} \\
\vspace{1.0cm}
\rule{345pt}{1.5pt} \\
\vspace{0.45cm}
 {\Huge NEMO ocean engine} 
\rule{345pt}{1.5pt} \\ 
%{\small NEMO v2.3} \\
{\small  -- version 3.1 --}   }
%{ -- Draft --}   }
%\date{\today}
\date{
May 2008  \\
\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} \\

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

\author{ \Large Gurvan Madec \\
 \texttt{\small gurvan.madec@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{}
%\includeonly{./TexFiles/Chapters/Chap_MISC}
%\includeonly{./TexFiles/Chapters/Annex_ISO}
%\includeonly{./TexFiles/Chapters/Annex_E}
%\includeonly{./TexFiles/Chapters/Chap_LBC,./TexFiles/Chapters/Chap_MISC}
%\includeonly{./TexFiles/Chapters/Chap_Model_Basics_zstar}
%\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_Model_Basics_zstar}   % attent to describe z*-s*

\include{./TexFiles/Chapters/Chap_DOM}

\include{./TexFiles/Chapters/Chap_TRA}

\include{./TexFiles/Chapters/Chap_DYN}

\include{./TexFiles/Chapters/Chap_SBC}

\include{./TexFiles/Chapters/Chap_LBC}

\include{./TexFiles/Chapters/Chap_LDF}

\include{./TexFiles/Chapters/Chap_ZDF}

\include{./TexFiles/Chapters/Chap_MISC}

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

\appendix

%\include{./TexFiles/Chapters/Chap_Conservation}
\include{./TexFiles/Chapters/Annex_A}
\include{./TexFiles/Chapters/Annex_B}
\include{./TexFiles/Chapters/Annex_C}
%\include{./TexFiles/Chapters/Annex_D}
%\include{./TexFiles/Chapters/Annex_E}
\include{./TexFiles/Chapters/Annex_ISO}

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

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

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

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

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

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