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

Last change on this file since 6956 was 6289, checked in by gm, 5 years ago

#1673 DOC of the trunk - Update, see associated wiki page for description

File size: 12.7 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{longtable}                         % allows multipage tables
26%\usepackage{colortbl}                           % gives coloured panels behind table columns
27
28%hyperref
29\usepackage[               %
30  pdftitle={NEMO ocean engine}%
31  pdfauthor={Gurvan Madec},      % pdfsubject={The preprint document class
32                                       % elsart},% pdfkeywords={diapycnal diffusion,numerical mixing,z-level models},%
33  pdfstartview=FitH,          %
34  bookmarks=true,          %
35  bookmarksopen=true,         %
36  breaklinks=true,            %
37  colorlinks=true,            %
38  linkcolor=blue,anchorcolor=blue,  %
39  citecolor=blue,filecolor=blue,    %
40 menucolor=blue,                    %
41  urlcolor=blue]{hyperref}
42%  usage of exteranl hyperlink :  \href{mailto:my_address@wikibooks.org}{my\_address@wikibooks.org}
43%                                                 \url{http://www.wikibooks.org}
44%                                     or         \href{http://www.wikibooks.org}{wikibooks home}
45
46
47
48%%%% page styles etc................
49\usepackage{fancyhdr}
50\pagestyle{fancy}
51% with this we ensure that the chapter and section
52% headings are in lowercase.
53\renewcommand{\chaptermark}[1]{\markboth{#1}{}}
54\renewcommand{\sectionmark}[1]{\markright{\thesection.\ #1}}
55\fancyhf{}             % delete current setting for header and footer
56\fancyhead[LE,RO]{\bfseries\thepage}
57\fancyhead[LO]{\bfseries\hspace{-0em}\rightmark}
58\fancyhead[RE]{\bfseries\leftmark}
59\renewcommand{\headrulewidth}{0.5pt}
60\renewcommand{\footrulewidth}{0pt}
61\addtolength{\headheight}{2.6pt}   % make space for the rule
62%\addtolength{\headheight}{1.6pt}   % make space for the rule
63\fancypagestyle{plain}{
64  \fancyhead{}         % get rid of headers on plain pages
65  \renewcommand{\headrulewidth}{0pt}  % and the line
66}
67
68
69%%%%  Section number in Margin.......
70% typeset the number of each section in the left margin, with the start of each instance of
71% sectional heading text aligned with the left hand edge of  the body text.
72\makeatletter
73\def\@seccntformat#1{\protect\makebox[0pt][r]{\csname the#1\endcsname\quad}}
74\makeatother
75
76% Leave blank pages completely empty, w/o header
77\makeatletter
78\def\cleardoublepage{\clearpage\if@twoside \ifodd\c@page\else
79  \hbox{}
80  \vspace*{\fill}
81  \vspace{\fill}
82  \thispagestyle{empty}
83  \newpage
84  \if@twocolumn\hbox{}\newpage\fi\fi\fi}
85\makeatother
86
87%%%% define the chapter  style ................
88\usepackage{minitoc}          %In French : \usepackage[french]{minitoc}
89%\usepackage{mtcoff}          % invalidate the use of minitocs
90\usepackage{fancybox}
91
92\makeatletter
93\def\LigneVerticale{\vrule height 5cm depth 2cm\hspace{0.1cm}\relax}
94\def\LignesVerticales{%
95  \let\LV\LigneVerticale\LV\LV\LV\LV\LV\LV\LV\LV\LV\LV}
96\def\GrosCarreAvecUnChiffre#1{%
97  \rlap{\vrule height 0.8cm width 1cm depth 0.2cm}%
98 \rlap{\hbox to 1cm{\hss\mbox{\color{white} #1}\hss}}%
99  \vrule height 0pt width 1cm depth 0pt}
100\def\GrosCarreAvecTroisChiffre#1{%
101  \rlap{\vrule height 0.8cm width 1.6cm depth 0.2cm}%
102 \rlap{\hbox to 1.5cm{\hss\mbox{\color{white} #1}\hss}}%
103  \vrule height 0pt width 1cm depth 0pt}
104
105\def\@makechapterhead#1{\hbox{%
106   \huge
107    \LignesVerticales
108    \hspace{-0.5cm}%
109    \GrosCarreAvecUnChiffre{\thechapter}
110    \hspace{0.2cm}\hbox{#1}%
111%    \GrosCarreAvecTroisChiffre{\thechapter}
112%    \hspace{1cm}\hbox{#1}%
113%}\par\vskip 2cm}
114}\par\vskip 1cm}
115\def\@makeschapterhead#1{\hbox{%
116   \huge
117    \LignesVerticales
118    %\hspace{0.5cm}%
119    \hbox{#1}%
120}\par\vskip 2cm}
121\makeatother
122
123%\def\thechapter{\Roman{chapter}}      % chapter number to be Roman
124
125
126%%%%           Mathematics...............
127%\documentclass{amsart}
128\usepackage{xspace}                              % helpd ensure correct spacing after macros
129\usepackage{latexsym}
130\usepackage{amssymb}
131\usepackage{amsmath}
132\allowdisplaybreaks[1]           % allow page breaks in the middle of equations
133\usepackage{./TexFiles/math_abbrev}    % use maths shortcuts
134
135\DeclareMathAlphabet{\mathpzc}{OT1}{pzc}{m}{it}
136
137\usepackage{times}                % use times font for text
138%\usepackage{mathtime}                          % font for illustrator to work (belleek fonts )
139%\usepackage[latin1]{inputenc}                % allows some unicode removed (agn)
140
141
142%%% essai commande
143\newcommand{\nl} [1] {\texttt{\small {\textcolor{blue}{#1}} } }
144\newcommand{\nlv} [1] {\texttt{\footnotesize#1}\xspace}
145\newcommand{\smnlv} [1] {\texttt{\scriptsize#1}\xspace}
146
147%%%% namelist & code display................................
148\usepackage{alltt}      %%  alltt for namelist
149\usepackage{verbatim}   %%  alltt for namelist
150% namelists
151\newcommand{\namdisplay} [1] {
152\begin{alltt}
153{\tiny \verbatiminput{./TexFiles/Namelist/#1}}
154\end{alltt}
155  \vspace{-10pt}
156}
157% namelist_tools
158\newcommand{\namtools} [1] {
159\begin{alltt}
160{\tiny \verbatiminput{./TexFiles/Namelist_tools/#1}}
161\end{alltt}
162  \vspace{-10pt}
163}
164% code display
165%\newcommand{\codedisplay} [1] { \begin{alltt} {\tiny  {\begin{verbatim} {#1}} \end{verbatim} }  \end{alltt}   }
166
167
168
169%%%% commands for working with text................................
170% command to "comment out" portions of text ({} argument) or not ({#1} argument)
171\newcommand{\amtcomment}[1]{}    % command to "commented out" portions of text or not (#1 in argument)
172\newcommand{\sgacomment}[1]{}    % command to "commented out" portions of
173\newcommand{\gmcomment}[1]{}     % command to "commented out" portions of
174%                                               % text that span line breaks
175%Red (NR) or Yellow(WARN)
176%\newcommand{\NR} {\colorbox{red}{#1}}
177%\newcommand{\WARN} {{ \colorbox{yellow}{#1}} }
178
179
180
181%%% index commands......................
182\usepackage{makeidx}
183%\usepackage{showidx}            % show the index entry
184
185\newcommand{\mdl} [1] {\textit{#1.F90}\index{Modules!#1}}         %module (mdl)
186\newcommand{\rou} [1] {\textit{#1}\index{Routines!#1}}            %module (routine)
187\newcommand{\hf} [1] {\textit{#1.h90}\index{h90 file!#1}}            %module (h90 files)
188\newcommand{\ngn} [1] {\textit{#1}\index{Namelist Group Name!#1}}    %namelist name (nampar)
189\newcommand{\np} [1] {\textit{#1}\index{Namelist variables!#1}}             %namelist variable
190\newcommand{\jp} [1] {\textit{#1}\index{Model parameters!#1}}        %model parameter (jp)
191\newcommand{\pp} [1] {\textit{#1}\index{Model parameters!#1}}        %namelist parameter (pp)
192\newcommand{\ifile} [1] {\textit{#1.nc}\index{Input NetCDF files!#1.nc}}   %input NetCDF files (.nc)
193\newcommand{\key} [1] {\textbf{key\_#1}\index{CPP keys!key\_#1}}  %key_cpp (key)
194\newcommand{\NEMO} {\textit{NEMO}\xspace}                %NEMO (nemo)
195
196%%%%   Bibliography   .............
197\usepackage[nottoc, notlof, notlot]{tocbibind}
198\usepackage[square, comma]{natbib}
199\bibpunct{[}{]}{,}{a}{}{;}                           %suppress "," after "et al."
200\providecommand{\bibfont}{\small}
201
202
203% ================================================================
204% FRONT PAGE
205% ================================================================
206
207%\usepackage{pstricks}
208\title{
209%\psset{unit=1.1in,linewidth=4pt}   %parameters of the units for pstricks
210% \rput(0,2){ \includegraphics[width=1.1\textwidth]{./TexFiles/Figures/logo_ALL.pdf}             } \\
211% \vspace{0.1cm}
212\vspace{-6.0cm}
213\includegraphics[width=1.1\textwidth]{./TexFiles/Figures/logo_ALL.pdf}\\
214\vspace{5.1cm}
215\includegraphics[width=0.9\textwidth]{./TexFiles/Figures/NEMO_logo_Black.pdf} \\
216\vspace{1.4cm}
217\rule{345pt}{1.5pt} \\
218\vspace{0.45cm}
219{\Huge NEMO ocean engine}
220\rule{345pt}{1.5pt} \\
221 }
222%{ -- Draft --}   }
223%\date{\today}
224\date{
225January 2016  \\
226{\small  -- draft of version 4.0 --} \\
227\\
228\textit{\small Note du P\^ole de mod\'{e}lisation de l'Institut Pierre-Simon Laplace No 27 }\\
229\vspace{0.45cm}
230{ ISSN No 1288-1619.}
231}
232
233
234\author{
235\Large Gurvan Madec, and the NEMO team  \\
236 \texttt{\small gurvan.madec@locean-ipsl.umpc.fr} \\
237 \texttt{\small nemo\_st@locean-ipsl.umpc.fr} \\
238%{\small Laboratoire d'Oc\'{e}anographie  et du Climat: Exp\'{e}rimentation et Approches Num\'{e}riques }
239}
240
241\dominitoc
242\makeindex        %type this first :     makeindex -s NEMO.ist NEMO_book.idx
243
244% ================================================================
245%      Include ONLY order
246% ================================================================
247
248%\includeonly{./TexFiles/Chapters/Chap_MISC}
249%\includeonly{./TexFiles/Chapters/Chap_ZDF}
250%\includeonly{./TexFiles/Chapters/Chap_STP,./TexFiles/Chapters/Chap_SBC,./TexFiles/Chapters/Chap_TRA}
251%\includeonly{./TexFiles/Chapters/Chap_LBC,./TexFiles/Chapters/Chap_MISC}
252%\includeonly{./TexFiles/Chapters/Chap_Model_Basics}
253%\includeonly{./TexFiles/Chapters/Annex_A,./TexFiles/Chapters/Annex_B,./TexFiles/Chapters/Annex_C,./TexFiles/Chapters/Annex_D}
254
255% ================================================================
256% ================================================================
257
258\begin{document}
259
260\maketitle                 % generate the title
261
262\frontmatter
263
264\tableofcontents              % generate a table of contents
265%\listoffigures               % generate a list  of figures
266%\listoftables                     % generate a list of tables
267
268\mainmatter
269
270% ================================================================
271% Abstract - Foreword
272% ================================================================
273
274\include{./TexFiles/Chapters/Abstracts_Foreword}
275
276% ================================================================
277% INTRODUCTION
278% ================================================================
279
280\include{./TexFiles/Chapters/Introduction}
281
282% ================================================================
283% CHAPTERS
284% ================================================================
285
286\include{./TexFiles/Chapters/Chap_Model_Basics}
287
288\include{./TexFiles/Chapters/Chap_STP}       % Time discretisation (time stepping strategy)
289
290\include{./TexFiles/Chapters/Chap_DOM}       % Space discretisation
291
292\include{./TexFiles/Chapters/Chap_TRA}       % Tracer advection/diffusion equation
293
294\include{./TexFiles/Chapters/Chap_DYN}       % Dynamics : momentum equation
295
296\include{./TexFiles/Chapters/Chap_SBC}       % Surface Boundary Conditions
297
298\include{./TexFiles/Chapters/Chap_LBC}       % Lateral Boundary Conditions
299
300\include{./TexFiles/Chapters/Chap_LDF}       % Lateral diffusion
301
302\include{./TexFiles/Chapters/Chap_ZDF}       % Vertical diffusion
303
304\include{./TexFiles/Chapters/Chap_DIA}       % Outputs and Diagnostics
305
306\include{./TexFiles/Chapters/Chap_OBS}          % Observation operator
307
308\include{./TexFiles/Chapters/Chap_ASM}          % Assimilation increments
309
310\include{./TexFiles/Chapters/Chap_STO}          % Stochastic param.
311
312\include{./TexFiles/Chapters/Chap_DIU}          % Diurnal SST models.
313
314\include{./TexFiles/Chapters/Chap_MISC}         % Miscellaneous topics
315
316\include{./TexFiles/Chapters/Chap_CFG}       % Predefined configurations
317
318% ================================================================
319% APPENDIX
320% ================================================================
321
322\appendix
323
324%\include{./TexFiles/Chapters/Chap_Conservation}
325\include{./TexFiles/Chapters/Annex_A}        % generalised vertical coordinate
326\include{./TexFiles/Chapters/Annex_B}        % diffusive operator
327\include{./TexFiles/Chapters/Annex_C}        % Discrete invariants of the eqs.
328\include{./TexFiles/Chapters/Annex_ISO}                     % Isoneutral diffusion using triads
329\include{./TexFiles/Chapters/Annex_D}        % Coding rules
330%\include{./TexFiles/Chapters/Annex_E}                   % Notes on some on going staff (no included in the DOC)
331%\include{./TexFiles/Chapters/Annex_Fox-Kemper}   % Notes on Fox-Kemper (no included in the DOC)
332%\include{./TexFiles/Chapters/Annex_EVP}           % Notes on EVP (no included in the DOC)
333
334% ================================================================
335% INDEX
336% ================================================================
337
338\addcontentsline{toc}{chapter}{Index}
339\printindex
340
341% ================================================================
342% BIBLIOGRAPHY
343% ================================================================
344
345%%\bibliographystyle{plainat}
346\bibliographystyle{./TexFiles/ametsoc}    % AMS biblio style (JPO)
347\bibliography{./TexFiles/Biblio/Biblio}
348
349% ================================================================
350\end{document}
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