source: branches/2012/dev_r3385_NOCS04_HAMF/DOC/NEMO_book.tex @ 3488

Last change on this file since 3488 was 3294, checked in by rblod, 10 years ago

Merge of 3.4beta into the trunk

File size: 12.3 KB
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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%\documentclass[a4paper,11pt,makeidx]{book} <== may need this to generate index
8
9%  makeindex NEMO_book     <== to regenerate the index
10%  bibtex         NEMO_book   <== to generate  the bibliography
11
12% ================================================================
13% HEADERS DEFINITION
14% ================================================================
15
16\usepackage[french]{babel}
17%\usepackage{color}
18\usepackage{xcolor}
19%\usepackage{graphics}           % allows insertion of pictures
20\usepackage{graphicx}            % allows insertion of pictures
21\usepackage[capbesideposition={top,center}]{floatrow} % allows captions
22\floatsetup[table]{style=plaintop}                                   % beside pictures
23\usepackage[margin=10pt,font={small},labelsep=colon,labelfont={bf}]{caption} % Gives small font for captions
24\usepackage{enumitem}                          % allows non-bold description items
25%\usepackage{colortbl}                           % gives coloured panels behind table columns
26
27%hyperref
28\usepackage[               %
29  pdftitle={NEMO ocean engine}%
30  pdfauthor={Gurvan Madec},      % pdfsubject={The preprint document class
31                                       % elsart},% pdfkeywords={diapycnal diffusion,numerical mixing,z-level models},%
32  pdfstartview=FitH,          %
33  bookmarks=true,          %
34  bookmarksopen=true,         %
35  breaklinks=true,            %
36  colorlinks=true,            %
37  linkcolor=blue,anchorcolor=blue,  %
38  citecolor=blue,filecolor=blue,    %
39 menucolor=blue,                    %
40  urlcolor=blue]{hyperref}
41%  usage of exteranl hyperlink :  \href{mailto:my_address@wikibooks.org}{my\_address@wikibooks.org}
42%                                                 \url{http://www.wikibooks.org}
43%                                     or         \href{http://www.wikibooks.org}{wikibooks home}
44
45
46
47%%%% page styles etc................
48\usepackage{fancyhdr}
49\pagestyle{fancy}
50% with this we ensure that the chapter and section
51% headings are in lowercase.
52\renewcommand{\chaptermark}[1]{\markboth{#1}{}}
53\renewcommand{\sectionmark}[1]{\markright{\thesection.\ #1}}
54\fancyhf{}             % delete current setting for header and footer
55\fancyhead[LE,RO]{\bfseries\thepage}
56\fancyhead[LO]{\bfseries\hspace{-0em}\rightmark}
57\fancyhead[RE]{\bfseries\leftmark}
58\renewcommand{\headrulewidth}{0.5pt}
59\renewcommand{\footrulewidth}{0pt}
60\addtolength{\headheight}{2.6pt}   % make space for the rule
61%\addtolength{\headheight}{1.6pt}   % make space for the rule
62\fancypagestyle{plain}{
63  \fancyhead{}         % get rid of headers on plain pages
64  \renewcommand{\headrulewidth}{0pt}  % and the line
65}
66
67
68%%%%  Section number in Margin.......
69% typeset the number of each section in the left margin, with the start of each instance of
70% sectional heading text aligned with the left hand edge of  the body text.
71\makeatletter
72\def\@seccntformat#1{\protect\makebox[0pt][r]{\csname the#1\endcsname\quad}}
73\makeatother
74
75% Leave blank pages completely empty, w/o header
76\makeatletter
77\def\cleardoublepage{\clearpage\if@twoside \ifodd\c@page\else
78  \hbox{}
79  \vspace*{\fill}
80  \vspace{\fill}
81  \thispagestyle{empty}
82  \newpage
83  \if@twocolumn\hbox{}\newpage\fi\fi\fi}
84\makeatother
85
86%%%% define the chapter  style ................
87\usepackage{minitoc}          %In French : \usepackage[french]{minitoc}
88%\usepackage{mtcoff}          % invalidate the use of minitocs
89\usepackage{fancybox}
90
91\makeatletter
92\def\LigneVerticale{\vrule height 5cm depth 2cm\hspace{0.1cm}\relax}
93\def\LignesVerticales{%
94  \let\LV\LigneVerticale\LV\LV\LV\LV\LV\LV\LV\LV\LV\LV}
95\def\GrosCarreAvecUnChiffre#1{%
96  \rlap{\vrule height 0.8cm width 1cm depth 0.2cm}%
97 \rlap{\hbox to 1cm{\hss\mbox{\color{white} #1}\hss}}%
98  \vrule height 0pt width 1cm depth 0pt}
99\def\GrosCarreAvecTroisChiffre#1{%
100  \rlap{\vrule height 0.8cm width 1.6cm depth 0.2cm}%
101 \rlap{\hbox to 1.5cm{\hss\mbox{\color{white} #1}\hss}}%
102  \vrule height 0pt width 1cm depth 0pt}
103
104\def\@makechapterhead#1{\hbox{%
105   \huge
106    \LignesVerticales
107    \hspace{-0.5cm}%
108    \GrosCarreAvecUnChiffre{\thechapter}
109    \hspace{0.2cm}\hbox{#1}%
110%    \GrosCarreAvecTroisChiffre{\thechapter}
111%    \hspace{1cm}\hbox{#1}%
112%}\par\vskip 2cm}
113}\par\vskip 1cm}
114\def\@makeschapterhead#1{\hbox{%
115   \huge
116    \LignesVerticales
117    %\hspace{0.5cm}%
118    \hbox{#1}%
119}\par\vskip 2cm}
120\makeatother
121
122%\def\thechapter{\Roman{chapter}}      % chapter number to be Roman
123
124
125%%%%           Mathematics...............
126%\documentclass{amsart}
127\usepackage{xspace}                              % helpd ensure correct spacing after macros
128\usepackage{latexsym}
129\usepackage{amssymb}
130\usepackage{amsmath}
131\allowdisplaybreaks[1]           % allow page breaks in the middle of equations
132\usepackage{./TexFiles/math_abbrev}    % use maths shortcuts
133
134
135\usepackage{times}                % use times font for text
136%\usepackage{mathtime}                          % font for illustrator to work (belleek fonts )
137%\usepackage[latin1]{inputenc}                % allows some unicode removed (agn)
138
139
140%%% essai commande
141\newcommand{\nl} [1] {\texttt{\small {\textcolor{blue}{#1}} } }
142\newcommand{\nlv} [1] {\texttt{\footnotesize#1}\xspace}
143\newcommand{\smnlv} [1] {\texttt{\scriptsize#1}\xspace}
144
145%%%% namelist & code display................................
146\usepackage{alltt}      %%  alltt for namelist
147\usepackage{verbatim}   %%  alltt for namelist
148% namelists
149\newcommand{\namdisplay} [1] {
150\begin{alltt}
151{\tiny \verbatiminput{./TexFiles/Namelist/#1}}
152\end{alltt}
153  \vspace{-10pt}
154}
155% code display
156%\newcommand{\codedisplay} [1] { \begin{alltt} {\tiny  {\begin{verbatim} {#1}} \end{verbatim} }  \end{alltt}   }
157
158
159
160%%%% commands for working with text................................
161% command to "comment out" portions of text ({} argument) or not ({#1} argument)
162\newcommand{\amtcomment}[1]{}    % command to "commented out" portions of text or not (#1 in argument)
163\newcommand{\sgacomment}[1]{}    % command to "commented out" portions of
164\newcommand{\gmcomment}[1]{}     % command to "commented out" portions of
165%                                               % text that span line breaks
166%Red (NR) or Yellow(WARN)
167%\newcommand{\NR} {\colorbox{red}{#1}}
168%\newcommand{\WARN} {{ \colorbox{yellow}{#1}} }
169
170
171
172%%% index commands......................
173\usepackage{makeidx}
174%\usepackage{showidx}            % show the index entry
175
176\newcommand{\mdl} [1] {\textit{#1.F90}\index{Modules!#1}}         %module (mdl)
177\newcommand{\rou} [1] {\textit{#1}\index{Routines!#1}}            %module (routine)
178\newcommand{\hf} [1] {\textit{#1.h90}\index{h90 file!#1}}            %module (h90 files)
179\newcommand{\np} [1] {\textit{#1}\index{Namelist parameters!#1}}     %namelist parameter (nampar)
180\newcommand{\jp} [1] {\textit{#1}\index{Model parameters!#1}}        %model parameter (jp)
181\newcommand{\pp} [1] {\textit{#1}\index{Model parameters!#1}}        %namelist parameter (pp)
182\newcommand{\ifile} [1] {\textit{#1.nc}\index{Input NetCDF files!#1.nc}}   %input NetCDF files (.nc)
183\newcommand{\key} [1] {\textbf{key\_#1}\index{CPP keys!key\_#1}}  %key_cpp (key)
184\newcommand{\NEMO} {\textit{NEMO}\xspace}                %NEMO (nemo)
185
186%%%%   Bibliography   .............
187\usepackage[nottoc, notlof, notlot]{tocbibind}
188\usepackage[square, comma]{natbib}
189\bibpunct{[}{]}{,}{a}{}{;}                           %suppress "," after "et al."
190\providecommand{\bibfont}{\small}
191
192
193% ================================================================
194% FRONT PAGE
195% ================================================================
196
197%\usepackage{pstricks}
198\title{
199%\psset{unit=1.1in,linewidth=4pt}   %parameters of the units for pstricks
200% \rput(0,2){ \includegraphics[width=1.1\textwidth]{./TexFiles/Figures/logo_ALL.pdf}             } \\
201% \vspace{0.1cm}
202\vspace{-6.0cm}
203\includegraphics[width=1.1\textwidth]{./TexFiles/Figures/logo_ALL.pdf}\\
204\vspace{5.1cm}
205\includegraphics[width=0.9\textwidth]{./TexFiles/Figures/NEMO_logo_Black.pdf} \\
206\vspace{1.4cm}
207\rule{345pt}{1.5pt} \\
208\vspace{0.45cm}
209{\Huge NEMO ocean engine}
210\rule{345pt}{1.5pt} \\
211 }
212%{ -- Draft --}   }
213%\date{\today}
214\date{
215January 2012  \\
216{\small  -- version 3.4 --} \\
217\\
218\textit{\small Note du P\^ole de mod\'{e}lisation de l'Institut Pierre-Simon Laplace No 27 }\\
219\vspace{0.45cm}
220{ ISSN No 1288-1619.}
221}
222
223
224\author{
225\Large Gurvan Madec, and the NEMO team  \\
226 \texttt{\small gurvan.madec@locean-ipsl.umpc.fr} \\
227 \texttt{\small nemo\_st@hermes.locean-ipsl.umpc.fr} \\
228%{\small Laboratoire d'Oc\'{e}anographie  et du Climat: Exp\'{e}rimentation et Approches Num\'{e}riques }
229}
230
231\dominitoc
232\makeindex        %type this first :     makeindex -s NEMO.ist NEMO_book.idx
233
234% ================================================================
235%      Include ONLY order
236% ================================================================
237
238%\includeonly{./TexFiles/Chapters/Chap_MISC}
239%\includeonly{./TexFiles/Chapters/Chap_ZDF}
240%\includeonly{./TexFiles/Chapters/Chap_STP,./TexFiles/Chapters/Chap_SBC,./TexFiles/Chapters/Chap_TRA}
241%\includeonly{./TexFiles/Chapters/Chap_LBC,./TexFiles/Chapters/Chap_MISC}
242%\includeonly{./TexFiles/Chapters/Chap_Model_Basics}
243%\includeonly{./TexFiles/Chapters/Annex_A,./TexFiles/Chapters/Annex_B,./TexFiles/Chapters/Annex_C,./TexFiles/Chapters/Annex_D}
244
245% ================================================================
246% ================================================================
247\begin{document}
248
249\maketitle                 % generate the title
250
251\frontmatter
252
253\tableofcontents              % generate a table of contents
254%\listoffigures               % generate a list  of figures
255%\listoftables                     % generate a list of tables
256
257\mainmatter
258
259% ================================================================
260% Abstract - Foreword
261% ================================================================
262
263\include{./TexFiles/Chapters/Abstracts_Foreword}
264
265% ================================================================
266% INTRODUCTION
267% ================================================================
268
269\include{./TexFiles/Chapters/Introduction}
270
271% ================================================================
272% CHAPTERS
273% ================================================================
274
275\include{./TexFiles/Chapters/Chap_Model_Basics}
276
277\include{./TexFiles/Chapters/Chap_STP}       % Time discretisation (time stepping strategy)
278
279\include{./TexFiles/Chapters/Chap_DOM}       % Space discretisation
280
281\include{./TexFiles/Chapters/Chap_TRA}       % Tracer advection/diffusion equation
282
283\include{./TexFiles/Chapters/Chap_DYN}       % Dynamics : momentum equation
284
285\include{./TexFiles/Chapters/Chap_SBC}       % Surface Boundary Conditions
286
287\include{./TexFiles/Chapters/Chap_LBC}       % Lateral Boundary Conditions
288
289\include{./TexFiles/Chapters/Chap_LDF}       % Lateral diffusion
290
291\include{./TexFiles/Chapters/Chap_ZDF}       % Vertical diffusion
292
293\include{./TexFiles/Chapters/Chap_DIA}       % Miscellaneous topics
294
295\include{./TexFiles/Chapters/Chap_OBS}                  % Observation operator
296
297\include{./TexFiles/Chapters/Chap_ASM}                  % Assimilation increments
298
299\include{./TexFiles/Chapters/Chap_MISC}         % Miscellaneous topics
300
301\include{./TexFiles/Chapters/Chap_CFG}       % Predefined configurations
302
303% ================================================================
304% APPENDIX
305% ================================================================
306
307\appendix
308
309%\include{./TexFiles/Chapters/Chap_Conservation}
310\include{./TexFiles/Chapters/Annex_A}        % generalised vertical coordinate
311\include{./TexFiles/Chapters/Annex_B}        % diffusive operator
312\include{./TexFiles/Chapters/Annex_C}        % Discrete invariants of the eqs.
313\include{./TexFiles/Chapters/Annex_D}        % Coding rules
314\include{./TexFiles/Chapters/Annex_ISO}                     % Isoneutral diffusion using triads
315%\include{./TexFiles/Chapters/Annex_E}                   % Notes on some on going staff (no included in the DOC)
316%\include{./TexFiles/Chapters/Annex_Fox-Kemper}   % Notes on Fox-Kemper (no included in the DOC)
317%\include{./TexFiles/Chapters/Annex_EVP}           % Notes on EVP (no included in the DOC)
318
319% ================================================================
320% INDEX
321% ================================================================
322
323\addcontentsline{toc}{chapter}{Index}
324\printindex
325
326% ================================================================
327% BIBLIOGRAPHY
328% ================================================================
329
330%%\bibliographystyle{plainat}
331\bibliographystyle{./TexFiles/ametsoc}    % AMS biblio style (JPO)
332\bibliography{./TexFiles/Biblio/Biblio}
333
334% ================================================================
335\end{document}
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