source: branches/2016/dev_r6409_SIMPLIF_2_usrdef/DOC/NEMO_book.tex @ 6956

%description: Book template

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

\documentclass[a4paper,11pt]{book}
%\documentclass[a4paper,11pt,makeidx]{book} <== may need this to generate index

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

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

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% with this we ensure that the chapter and section
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%%%%           Mathematics...............
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%%%% commands for working with text................................
% command to "comment out" portions of text ({} argument) or not ({#1} argument)
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%%% index commands......................
\usepackage{makeidx}
%\usepackage{showidx}            % show the index entry

\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)
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\newcommand{\np} [1] {\textit{#1}\index{Namelist variables!#1}}             %namelist variable
\newcommand{\jp} [1] {\textit{#1}\index{Model parameters!#1}}        %model parameter (jp)
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\newcommand{\key} [1] {\textbf{key\_#1}\index{CPP keys!key\_#1}}  %key_cpp (key)
\newcommand{\NEMO} {\textit{NEMO}\xspace}                %NEMO (nemo)

%%%%   Bibliography   .............
\usepackage[nottoc, notlof, notlot]{tocbibind}
\usepackage[square, comma]{natbib}
\bibpunct{[}{]}{,}{a}{}{;}                           %suppress "," after "et al."
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% ================================================================
% FRONT PAGE
% ================================================================

%\usepackage{pstricks}
\title{
%\psset{unit=1.1in,linewidth=4pt}   %parameters of the units for pstricks
% \rput(0,2){ \includegraphics[width=1.1\textwidth]{./TexFiles/Figures/logo_ALL.pdf}             } \\
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\vspace{5.1cm}
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\vspace{1.4cm}
\rule{345pt}{1.5pt} \\
\vspace{0.45cm}
{\Huge NEMO ocean engine}
\rule{345pt}{1.5pt} \\
 }
%{ -- Draft --}   }
%\date{\today}
\date{
January 2016  \\
{\small  -- draft of version 4.0 --} \\
~  \\
\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.}
}


\author{
\Large Gurvan Madec, and the NEMO team  \\
 \texttt{\small gurvan.madec@locean-ipsl.umpc.fr} \\
 \texttt{\small nemo\_st@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 contents
%\listoffigures               % generate a list  of figures
%\listoftables                     % generate a list of tables

\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_DIA}       % Outputs and Diagnostics

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

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

\include{./TexFiles/Chapters/Chap_STO}          % Stochastic param.

\include{./TexFiles/Chapters/Chap_DIU}          % Diurnal SST models.

\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_ISO}                     % Isoneutral diffusion using triads
\include{./TexFiles/Chapters/Annex_D}        % Coding rules
%\include{./TexFiles/Chapters/Annex_E}                   % Notes on some on going staff (no included in the DOC)
%\include{./TexFiles/Chapters/Annex_Fox-Kemper}   % Notes on Fox-Kemper (no included in the DOC)
%\include{./TexFiles/Chapters/Annex_EVP}           % Notes on EVP (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}