source: branches/2011/dev_NEMO_MERGE_2011/DOC/NEMO_book.tex @ 3236

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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,11pt]{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{color}
17\usepackage{xcolor}
18%\usepackage{graphics}           % allows insertion of pictures
19\usepackage{graphicx}            % allows insertion of
20                                        % pictures
21\usepackage[capbesideposition={top,center}]{floatrow}
22\floatsetup[table]{style=plaintop}
23\usepackage[margin=10pt,font={small},labelsep=colon,labelfont={bf}]{caption}
24%\usepackage{colortbl}                           % gives coloured panels behind table columns
25
26%hyperref
27\usepackage[               %
28  pdftitle={NEMO ocean engine}%
29  pdfauthor={Gurvan Madec},      % pdfsubject={The preprint document class
30                                       % elsart},% pdfkeywords={diapycnal diffusion,numerical mixing,z-level models},%
31  pdfstartview=FitH,          %
32  bookmarks=true,          %
33  bookmarksopen=true,         %
34  breaklinks=true,            %
35  colorlinks=true,            %
36  linkcolor=blue,anchorcolor=blue,  %
37  citecolor=blue,filecolor=blue,    %
38 menucolor=blue,                    %
39  urlcolor=blue]{hyperref}
40%  usage of exteranl hyperlink :  \href{mailto:my_address@wikibooks.org}{my\_address@wikibooks.org}
41%                                                 \url{http://www.wikibooks.org}
42%                                     or         \href{http://www.wikibooks.org}{wikibooks home}
43
44
45
46%%%% page styles etc................
47\usepackage{fancyhdr}
48\pagestyle{fancy}
49% with this we ensure that the chapter and section
50% headings are in lowercase.
51\renewcommand{\chaptermark}[1]{\markboth{#1}{}}
52\renewcommand{\sectionmark}[1]{\markright{\thesection.\ #1}}
53\fancyhf{}             % delete current setting for header and footer
54\fancyhead[LE,RO]{\bfseries\thepage}
55\fancyhead[LO]{\bfseries\hspace{-0em}\rightmark}
56\fancyhead[RE]{\bfseries\leftmark}
57\renewcommand{\headrulewidth}{0.5pt}
58\renewcommand{\footrulewidth}{0pt}
59\addtolength{\headheight}{2.6pt}   % make space for the rule
60%\addtolength{\headheight}{1.6pt}   % make space for the rule
61\fancypagestyle{plain}{
62  \fancyhead{}         % get rid of headers on plain pages
63  \renewcommand{\headrulewidth}{0pt}  % and the line
64}
65
66
67%%%%  Section number in Margin.......
68% typeset the number of each section in the left margin, with the start of each instance of
69% sectional heading text aligned with the left hand edge of  the body text.
70\makeatletter
71\def\@seccntformat#1{\protect\makebox[0pt][r]{\csname the#1\endcsname\quad}}
72\makeatother
73
74% Leave blank pages completely empty, w/o header
75\makeatletter
76\def\cleardoublepage{\clearpage\if@twoside \ifodd\c@page\else
77  \hbox{}
78  \vspace*{\fill}
79  \vspace{\fill}
80  \thispagestyle{empty}
81  \newpage
82  \if@twocolumn\hbox{}\newpage\fi\fi\fi}
83\makeatother
84
85%%%% define the chapter  style ................
86\usepackage{minitoc}          %In French : \usepackage[french]{minitoc}
87%\usepackage{mtcoff}          % invalidate the use of minitocs
88\usepackage{fancybox}
89
90\makeatletter
91\def\LigneVerticale{\vrule height 5cm depth 2cm\hspace{0.1cm}\relax}
92\def\LignesVerticales{%
93  \let\LV\LigneVerticale\LV\LV\LV\LV\LV\LV\LV\LV\LV\LV}
94\def\GrosCarreAvecUnChiffre#1{%
95  \rlap{\vrule height 0.8cm width 1cm depth 0.2cm}%
96 \rlap{\hbox to 1cm{\hss\mbox{\color{white} #1}\hss}}%
97  \vrule height 0pt width 1cm depth 0pt}
98\def\GrosCarreAvecTroisChiffre#1{%
99  \rlap{\vrule height 0.8cm width 1.6cm depth 0.2cm}%
100 \rlap{\hbox to 1.5cm{\hss\mbox{\color{white} #1}\hss}}%
101  \vrule height 0pt width 1cm depth 0pt}
102
103\def\@makechapterhead#1{\hbox{%
104   \huge
105    \LignesVerticales
106    \hspace{-0.5cm}%
107    \GrosCarreAvecUnChiffre{\thechapter}
108    \hspace{0.2cm}\hbox{#1}%
109%    \GrosCarreAvecTroisChiffre{\thechapter}
110%    \hspace{1cm}\hbox{#1}%
111%}\par\vskip 2cm}
112}\par\vskip 1cm}
113\def\@makeschapterhead#1{\hbox{%
114   \huge
115    \LignesVerticales
116    %\hspace{0.5cm}%
117    \hbox{#1}%
118}\par\vskip 2cm}
119\makeatother
120
121%\def\thechapter{\Roman{chapter}}      % chapter number to be Roman
122
123
124%%%%           Mathematics...............
125%\documentclass{amsart}
126\usepackage{xspace}                              % helpd ensure correct spacing after macros
127\usepackage{latexsym}
128\usepackage{amssymb}
129\usepackage{amsmath}
130\allowdisplaybreaks[1]           % allow page breaks in the middle of equations
131\usepackage{./TexFiles/math_abbrev}    % use maths shortcuts
132
133
134\usepackage{times}                % use times font for text
135%\usepackage{mathtime}                          % font for illustrator to work (belleek fonts )
136%\usepackage[latin1]{inputenc}                % allows some unicode removed (agn)
137
138
139%%% essai commande
140\newcommand{\nl} [1] {\texttt{\small {\textcolor{blue}{#1}} } }
141\newcommand{\nlv} [1] {\texttt{\footnotesize#1}\xspace}
142\newcommand{\smnlv} [1] {\texttt{\scriptsize#1}\xspace}
143
144%%%% namelist & code display................................
145\usepackage{alltt}      %%  alltt for namelist
146\usepackage{verbatim}   %%  alltt for namelist
147% namelists
148\newcommand{\namdisplay} [1] {
149\begin{alltt}
150{\tiny \verbatiminput{./TexFiles/Namelist/#1}}
151\end{alltt}
152  \vspace{-10pt}
153}
154% code display
155%\newcommand{\codedisplay} [1] { \begin{alltt} {\tiny  {\begin{verbatim} {#1}} \end{verbatim} }  \end{alltt}   }
156
157
158
159%%%% commands for working with text................................
160% command to "comment out" portions of text ({} argument) or not ({#1} argument)
161\newcommand{\amtcomment}[1]{}    % command to "commented out" portions of text or not (#1 in argument)
162\newcommand{\sgacomment}[1]{}    % command to "commented out" portions of
163\newcommand{\gmcomment}[1]{}     % command to "commented out" portions of
164%                                               % text that span line breaks
165%Red (NR) or Yellow(WARN)
166%\newcommand{\NR} {\colorbox{red}{#1}}
167%\newcommand{\WARN} {{ \colorbox{yellow}{#1}} }
168
169
170
171%%% index commands......................
172\usepackage{makeidx}
173%\usepackage{showidx}            % show the index entry
174
175\newcommand{\mdl} [1] {\textit{#1.F90}\index{Modules!#1}}         %module (mdl)
176\newcommand{\rou} [1] {\textit{#1}\index{Routines!#1}}            %module (routine)
177\newcommand{\hf} [1] {\textit{#1.h90}\index{h90 file!#1}}            %module (h90 files)
178\newcommand{\np} [1] {\textit{#1}\index{Namelist parameters!#1}}     %namelist parameter (nampar)
179\newcommand{\jp} [1] {\textit{#1}\index{Model parameters!#1}}        %model parameter (jp)
180\newcommand{\pp} [1] {\textit{#1}\index{Model parameters!#1}}        %namelist parameter (pp)
181\newcommand{\ifile} [1] {\textit{#1.nc}\index{Input NetCDF files!#1.nc}}   %input NetCDF files (.nc)
182\newcommand{\key} [1] {\textbf{key\_#1}\index{CPP keys!key\_#1}}  %key_cpp (key)
183\newcommand{\NEMO} {\textit{NEMO}\xspace}                %NEMO (nemo)
184
185%%%%   Bibliography   .............
186\usepackage[nottoc, notlof, notlot]{tocbibind}
187\usepackage[square, comma]{natbib}
188\bibpunct{[}{]}{,}{a}{}{;}                           %suppress "," after "et al."
189\providecommand{\bibfont}{\small}
190
191
192% ================================================================
193% FRONT PAGE
194% ================================================================
195
196\usepackage{pstricks}
197\title{
198\psset{unit=1.1in,linewidth=4pt}    %parameters of the units for pstricks
199%\rput(-1.4,2){ \includegraphics[width=0.2\textwidth]{./TexFiles/Figures/logo_CNRS.pdf}           }
200%\quad
201%\rput(-.15,2){ \includegraphics[width=0.2\textwidth]{./TexFiles/Figures/logo_MERCATOR.pdf} }
202%\quad
203%\rput(.85,2){ \includegraphics[width=0.1\textwidth]{./TexFiles/Figures/logo_UKMO.pdf}            }
204%\quad
205%\rput(1.85,2){ \includegraphics[width=0.2\textwidth]{./TexFiles/Figures/logo_NERC.pdf}             } \\
206%\begin{figure}[t]
207%   \includegraphics[width=0.9\textwidth]{./TexFiles/Figures/logo_ALL.pdf}
208%\end{figure}
209\rput(0,2){ \includegraphics[width=1.1\textwidth]{./TexFiles/Figures/logo_ALL.pdf}             } \\
210\vspace{0.1cm}
211\includegraphics[width=0.9\textwidth]{./TexFiles/Figures/NEMO_logo_Black.pdf} \\
212\vspace{1.4cm}
213\rule{345pt}{1.5pt} \\
214\vspace{0.45cm}
215{\Huge NEMO ocean engine}
216\rule{345pt}{1.5pt} \\
217 }
218%{ -- Draft --}   }
219%\date{\today}
220\date{
221January 2012  \\
222{\small  -- version 3.4 --} \\
223\\
224\textit{\small Note du P\^ole de mod\'{e}lisation de l'Institut Pierre-Simon Laplace No 27 }\\
225\vspace{0.45cm}
226{ ISSN No 1288-1619.}
227}
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 contents
260%\listoffigures               % generate a list  of figures
261%\listoftables                     % generate a list of tables
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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