source: trunk/DOC/NEMO_book.tex @ 2570

Last change on this file since 2570 was 2541, checked in by gm, 11 years ago

v3.3beta: #658 hopefully the final update, including MPP sum, SIGN, IOM, fldread documentation

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1%description: Book template
2
3% template of document for LaTeX
4% (C) Xavier Perseguers 2002 - xavier.perseguers@epfl.ch
5
6\documentclass[a4paper,12pt]{book}
7
8%  makeindex NEMO_book     <== to regenerate the index
9%  bibtex         NEMO_book   <== to generate  the bibliography
10
11% ================================================================
12% HEADERS DEFINITION
13% ================================================================
14
15\usepackage[french]{babel}
16\usepackage{fancyhdr}
17
18\usepackage{alltt}      %%  alltt for namelist
19\usepackage{verbatim}   %%  alltt for namelist
20
21%hyperref
22\usepackage[               %
23  pdftitle={NEMO ocean engine}%
24  pdfauthor={Gurvan Madec},      % pdfsubject={The preprint document class
25                                       % elsart},% pdfkeywords={diapycnal diffusion,numerical mixing,z-level models},%
26  pdfstartview=FitH,          %
27  bookmarks=true,          %
28  bookmarksopen=true,         %
29  breaklinks=true,            %
30  colorlinks=true,            %
31  linkcolor=blue,anchorcolor=blue,  %
32  citecolor=blue,filecolor=blue,    %
33  menucolor=blue,pagecolor=blue, %
34  urlcolor=blue]{hyperref}
35%  usage of exteranl hyperlink :  \href{mailto:my_address@wikibooks.org}{my\_address@wikibooks.org}
36%                                                 \url{http://www.wikibooks.org}
37%                                     or         \href{http://www.wikibooks.org}{wikibooks home}
38
39
40
41
42%\usepackage{amssymb}
43\pagestyle{fancy}
44% with this we ensure that the chapter and section
45% headings are in lowercase.
46\renewcommand{\chaptermark}[1]{\markboth{#1}{}}
47\renewcommand{\sectionmark}[1]{\markright{\thesection.\ #1}}
48\fancyhf{}             % delete current setting for header and footer
49\fancyhead[LE,RO]{\bfseries\thepage}
50\fancyhead[LO]{\bfseries\hspace{-0em}\rightmark}
51\fancyhead[RE]{\bfseries\leftmark}
52\renewcommand{\headrulewidth}{0.5pt}
53\renewcommand{\footrulewidth}{0pt}
54\addtolength{\headheight}{2.6pt}   % make space for the rule
55%\addtolength{\headheight}{1.6pt}   % make space for the rule
56\fancypagestyle{plain}{
57  \fancyhead{}         % get rid of headers on plain pages
58  \renewcommand{\headrulewidth}{0pt}  % and the line
59}
60
61% Leave blank pages completely empty, w/o header
62\makeatletter
63\def\cleardoublepage{\clearpage\if@twoside \ifodd\c@page\else
64  \hbox{}
65  \vspace*{\fill}
66  \vspace{\fill}
67  \thispagestyle{empty}
68  \newpage
69  \if@twocolumn\hbox{}\newpage\fi\fi\fi}
70\makeatother
71
72\usepackage{makeidx}
73
74\usepackage{minitoc}          %in french : \usepackage[french]{minitoc}
75
76%\usepackage{mtcoff}          % invalidate the use of minitocs
77\usepackage[latin1]{inputenc}
78\usepackage{graphics}            % allows insertion of pictures
79\usepackage{times}               % use vector fonts instead of bitmap
80\usepackage{fancybox}
81\usepackage{graphicx}
82%\usepackage{color}
83%\usepackage{colortbl}
84
85%%%% add by Word2Tex
86%\documentclass{amsart}
87\usepackage{latexsym}
88\usepackage{amssymb}
89\usepackage{amsmath}
90\usepackage{graphicx}
91\allowdisplaybreaks[1]           % allow page breaks in the middle of equations
92%%%%
93
94%%%%
95%\usepackage{mathtime}      % font for illustrator to work (belleek fonts )
96%%%%
97
98%\usepackage{showidx}            % show the index entry
99
100
101
102%%%% define the style of title for chapter  %%%
103\usepackage{pstricks}
104\makeatletter
105\def\LigneVerticale{\vrule height 5cm depth 2cm\hspace{0.1cm}\relax}
106\def\LignesVerticales{%
107  \let\LV\LigneVerticale\LV\LV\LV\LV\LV\LV\LV\LV\LV\LV}
108\def\GrosCarreAvecUnChiffre#1{%
109  \rlap{\vrule height 0.8cm width 1cm depth 0.2cm}%
110  \rlap{\hbox to 1cm{\hss\mbox{\white #1}\hss}}%
111  \vrule height 0pt width 1cm depth 0pt}
112\def\GrosCarreAvecTroisChiffre#1{%
113  \rlap{\vrule height 0.8cm width 1.6cm depth 0.2cm}%
114  \rlap{\hbox to 1.5cm{\hss\mbox{\white #1}\hss}}%
115  \vrule height 0pt width 1cm depth 0pt}
116
117\def\@makechapterhead#1{\hbox{%
118    \huge 
119    \LignesVerticales
120    \hspace{-0.5cm}%
121    \GrosCarreAvecUnChiffre{\thechapter}
122    \hspace{0.2cm}\hbox{#1}%
123%    \GrosCarreAvecTroisChiffre{\thechapter}
124%    \hspace{1cm}\hbox{#1}%
125%}\par\vskip 2cm}
126}\par\vskip 1cm}
127\def\@makeschapterhead#1{\hbox{%
128    \huge 
129    \LignesVerticales
130    %\hspace{0.5cm}%
131    \hbox{#1}%
132}\par\vskip 2cm}
133
134%\def\thechapter{\Roman{chapter}}      % chapter number to be Roman
135
136%%%% end style chapter %%%
137
138%%% use maths shortcuts :
139%\newcommand{\vect} [1] { \rm{\textbf{#1}} }    % vector style: non-italic bold
140\usepackage{./TexFiles/math_abbrev}
141
142
143%%% essai commande
144\newcommand{\nl} [1] {\texttt{\small {\textcolor{blue}{#1}} } } 
145
146%%% index commands :   
147\newcommand{\mdl} [1] {\textit{#1.F90}\index{Modules!#1}}         %module (mdl)
148\newcommand{\rou} [1] {\textit{#1}\index{Routines!#1}}            %module (routine)
149\newcommand{\hf} [1] {\textit{#1.h90}\index{h90 file!#1}}            %module (h90 files)
150\newcommand{\np} [1] {\textit{#1}\index{Namelist parameters!#1}}     %namelist parameter (nampar)
151\newcommand{\jp} [1] {\textit{#1}\index{Model parameters!#1}}        %model parameter (jp)
152\newcommand{\pp} [1] {\textit{#1}\index{Model parameters!#1}}        %namelist parameter (pp)
153\newcommand{\ifile} [1] {\textit{#1.nc}\index{Input NetCDF files!#1.nc}}   %input NetCDF files (.nc)
154\newcommand{\key} [1] {\textbf{key\_#1}\index{CPP keys!key\_#1}}  %key_cpp (key)
155\newcommand{\NEMO} {\textit{NEMO }}                %NEMO (nemo)
156% command to "commented out" portions of text ({} argument) or not ({#1} argument)
157\newcommand{\amtcomment}[1]{}    % command to "commented out" portions of text or not (#1 in argument)
158\newcommand{\sgacomment}[1]{}    % command to "commented out" portions of
159\newcommand{\gmcomment}[1]{}     % command to "commented out" portions of
160%                                               % text that span line breaks
161\newcommand{\alpbet} {\left(\alpha / \beta \right)}   % alpha/beta  for slp computation
162
163%--------------------------------------------namlist---------------------------------------------------------
164\newcommand{\namdisplay} [1] { 
165   \begin{alltt}  {{\tiny \verbatiminput{./TexFiles/Namelist/#1}}}  \end{alltt} 
166                               \vspace{-10pt}   }
167%--------------------------------------------code display---------------------------------------------------------
168%\newcommand{\codedisplay} [1] { \begin{alltt} {\tiny  {\begin{verbatim} {#1}} \end{verbatim} }  \end{alltt}   }
169%--------------------------------------------------------------------------------------------------------------
170%Red (NR) or Yellow(WARN)
171%\newcommand{\NR} {\colorbox{red}{#1}}
172%\newcommand{\WARN} {{ \colorbox{yellow}{#1}} }
173
174%---------------------%%%%%  Section number in Margin  %%%%%-----------------------------
175% typeset the number of each section in the left margin, with the start of each instance of
176% sectional heading text aligned with the left hand edge of  the body text.
177\makeatletter 
178\def\@seccntformat#1{\protect\makebox[0pt][r]{\csname the#1\endcsname\quad}} 
179\makeatother 
180%--------------------------------------------------------------------------------------------------------------
181
182%----------------------------%%%%%   Bilbiography   %%%%%%-------------------------------%
183\usepackage[nottoc, notlof, notlot]{tocbibind}
184\usepackage[square, comma]{natbib}
185\bibpunct{[}{]}{,}{a}{}{;}                           %suppress "," after "et al."
186\providecommand{\bibfont}{\small}
187%--------------------------------------------------------------------------------------------------------------
188
189% ================================================================
190% FRONT PAGE
191% ================================================================
192
193\title{ 
194\psset{unit=1.1in,linewidth=4pt}    %parameters of the units for pstricks
195\rput(-1.4,2){ \includegraphics[width=0.2\textwidth]{./TexFiles/Figures/logo_CNRS.pdf}           }
196\quad
197\rput(-.15,2){ \includegraphics[width=0.2\textwidth]{./TexFiles/Figures/logo_MERCATOR.pdf} }
198\quad
199\rput(.85,2){ \includegraphics[width=0.1\textwidth]{./TexFiles/Figures/logo_UKMO.pdf}            }
200\quad
201\rput(1.85,2){ \includegraphics[width=0.2\textwidth]{./TexFiles/Figures/logo_NERC.pdf}             } \\
202\vspace{0.1cm}
203\includegraphics[width=0.9\textwidth]{./TexFiles/Figures/NEMO_logo_Black.pdf} \\
204\vspace{1.4cm}
205\rule{345pt}{1.5pt} \\
206\vspace{0.45cm}
207 {\Huge NEMO ocean engine} 
208\rule{345pt}{1.5pt} \\ 
209 }
210%{ -- Draft --}   }
211%\date{\today}
212\date{
213January 2011  \\
214{\small  -- version 3.3 --} \\
215\\
216\textit{\small Note du P\^ole de mod\'{e}lisation de l'Institut Pierre-Simon Laplace No 27 }\\
217\vspace{0.45cm}
218{ ISSN No 1288-1619.}
219}
220
221
222%%\includegraphics[width=0.2\textwidth]{./TexFiles/Figures/logo_NERC.pdf} \\
223
224%%    \hbox{\mbox{%
225%%       \hspace{4pt}%
226%%         \fbox{\includegraphics[width=3em]{./TexFiles/Figures/logo_CNRS.pdf}}%
227%%        \hspace{4pt}
228%%        }  }%
229
230\author{ 
231\Large Gurvan Madec, and the NEMO team  \\
232 \texttt{\small gurvan.madec@locean-ipsl.umpc.fr} \\
233 \texttt{\small nemo\_st@hermes.locean-ipsl.umpc.fr} \\
234%{\small Laboratoire d'Oc\'{e}anographie  et du Climat: Exp\'{e}rimentation et Approches Num\'{e}riques }
235}
236
237\dominitoc
238\makeindex        %type this first :     makeindex -s NEMO.ist NEMO_book.idx
239
240% ================================================================
241%      Include ONLY order
242% ================================================================
243
244%\includeonly{./TexFiles/Chapters/Chap_MISC}
245%\includeonly{./TexFiles/Chapters/Chap_ZDF}
246%\includeonly{./TexFiles/Chapters/Chap_STP,./TexFiles/Chapters/Chap_SBC,./TexFiles/Chapters/Chap_TRA}
247%\includeonly{./TexFiles/Chapters/Chap_LBC,./TexFiles/Chapters/Chap_MISC}
248%\includeonly{./TexFiles/Chapters/Chap_Model_Basics}
249%\includeonly{./TexFiles/Chapters/Annex_A,./TexFiles/Chapters/Annex_B,./TexFiles/Chapters/Annex_C,./TexFiles/Chapters/Annex_D}
250
251% ================================================================
252% ================================================================
253\begin{document}
254
255\maketitle                 % generate the title
256
257\frontmatter
258
259\tableofcontents              % generate a table of content
260%\listoffigures               % generate a table of content
261%\listoftables             % generate a table of content
262
263\mainmatter
264
265% ================================================================
266% Abstract - Foreword
267% ================================================================
268
269\include{./TexFiles/Chapters/Abstracts_Foreword}
270
271% ================================================================
272% INTRODUCTION
273% ================================================================
274
275\include{./TexFiles/Chapters/Introduction}
276
277% ================================================================
278% CHAPTERS
279% ================================================================
280
281\include{./TexFiles/Chapters/Chap_Model_Basics}
282
283\include{./TexFiles/Chapters/Chap_STP}       % Time discretisation (time stepping strategy)
284
285\include{./TexFiles/Chapters/Chap_DOM}       % Space discretisation
286
287\include{./TexFiles/Chapters/Chap_TRA}       % Tracer advection/diffusion equation
288
289\include{./TexFiles/Chapters/Chap_DYN}       % Dynamics : momentum equation
290
291\include{./TexFiles/Chapters/Chap_SBC}       % Surface Boundary Conditions
292
293\include{./TexFiles/Chapters/Chap_LBC}       % Lateral Boundary Conditions
294
295\include{./TexFiles/Chapters/Chap_LDF}       % Lateral diffusion
296
297\include{./TexFiles/Chapters/Chap_ZDF}       % Vertical diffusion
298
299\include{./TexFiles/Chapters/Chap_DIA}       % Miscellaneous topics
300
301\include{./TexFiles/Chapters/Chap_OBS}                  % Observation operator
302
303\include{./TexFiles/Chapters/Chap_ASM}                  % Assimilation increments
304
305\include{./TexFiles/Chapters/Chap_MISC}         % Miscellaneous topics
306
307\include{./TexFiles/Chapters/Chap_CFG}       % Predefined configurations
308
309% ================================================================
310% APPENDIX
311% ================================================================
312
313\appendix
314
315%\include{./TexFiles/Chapters/Chap_Conservation}
316\include{./TexFiles/Chapters/Annex_A}        % generalised vertical coordinate
317\include{./TexFiles/Chapters/Annex_B}        % diffusive operator
318\include{./TexFiles/Chapters/Annex_C}        % Discrete invariants of the eqs.
319\include{./TexFiles/Chapters/Annex_D}        % Coding rules
320\include{./TexFiles/Chapters/Annex_ISO}                     % Isoneutral diffusion using triads
321%\include{./TexFiles/Chapters/Annex_E}                   % Notes on some on going staff (no included in the DOC)
322%\include{./TexFiles/Chapters/Annex_Fox-Kemper}   % Notes on Fox-Kemper (no included in the DOC)
323%\include{./TexFiles/Chapters/Annex_EVP}           % Notes on EVP (no included in the DOC)
324
325% ================================================================
326% INDEX
327% ================================================================
328
329\addcontentsline{toc}{chapter}{Index}
330\printindex
331
332% ================================================================
333% BIBLIOGRAPHY
334% ================================================================
335
336%%\bibliographystyle{plainat}
337\bibliographystyle{./TexFiles/ametsoc}    % AMS biblio style (JPO)
338\bibliography{./TexFiles/Biblio/Biblio}
339
340% ================================================================
341\end{document}
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