source: branches/2015/dev_r5836_NOC3_vvl_by_default/DOC/NEMO_book.tex @ 6040

Last change on this file since 6040 was 6040, checked in by gm, 5 years ago

#1613: vvl by default : start to update the DOC for change in vvl, LDF and solvers

File size: 12.5 KB
Line 
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
136\usepackage{times}                % use times font for text
137%\usepackage{mathtime}                          % font for illustrator to work (belleek fonts )
138%\usepackage[latin1]{inputenc}                % allows some unicode removed (agn)
139
140
141%%% essai commande
142\newcommand{\nl} [1] {\texttt{\small {\textcolor{blue}{#1}} } }
143\newcommand{\nlv} [1] {\texttt{\footnotesize#1}\xspace}
144\newcommand{\smnlv} [1] {\texttt{\scriptsize#1}\xspace}
145
146%%%% namelist & code display................................
147\usepackage{alltt}      %%  alltt for namelist
148\usepackage{verbatim}   %%  alltt for namelist
149% namelists
150\newcommand{\namdisplay} [1] {
151\begin{alltt}
152{\tiny \verbatiminput{./TexFiles/Namelist/#1}}
153\end{alltt}
154  \vspace{-10pt}
155}
156% code display
157%\newcommand{\codedisplay} [1] { \begin{alltt} {\tiny  {\begin{verbatim} {#1}} \end{verbatim} }  \end{alltt}   }
158
159
160
161%%%% commands for working with text................................
162% command to "comment out" portions of text ({} argument) or not ({#1} argument)
163\newcommand{\amtcomment}[1]{}    % command to "commented out" portions of text or not (#1 in argument)
164\newcommand{\sgacomment}[1]{}    % command to "commented out" portions of
165\newcommand{\gmcomment}[1]{}     % command to "commented out" portions of
166%                                               % text that span line breaks
167%Red (NR) or Yellow(WARN)
168%\newcommand{\NR} {\colorbox{red}{#1}}
169%\newcommand{\WARN} {{ \colorbox{yellow}{#1}} }
170
171
172
173%%% index commands......................
174\usepackage{makeidx}
175%\usepackage{showidx}            % show the index entry
176
177\newcommand{\mdl} [1] {\textit{#1.F90}\index{Modules!#1}}         %module (mdl)
178\newcommand{\rou} [1] {\textit{#1}\index{Routines!#1}}            %module (routine)
179\newcommand{\hf} [1] {\textit{#1.h90}\index{h90 file!#1}}            %module (h90 files)
180\newcommand{\ngn} [1] {\textit{#1}\index{Namelist Group Name!#1}}    %namelist name (nampar)
181\newcommand{\np} [1] {\textit{#1}\index{Namelist variables!#1}}             %namelist variable
182\newcommand{\jp} [1] {\textit{#1}\index{Model parameters!#1}}        %model parameter (jp)
183\newcommand{\pp} [1] {\textit{#1}\index{Model parameters!#1}}        %namelist parameter (pp)
184\newcommand{\ifile} [1] {\textit{#1.nc}\index{Input NetCDF files!#1.nc}}   %input NetCDF files (.nc)
185\newcommand{\key} [1] {\textbf{key\_#1}\index{CPP keys!key\_#1}}  %key_cpp (key)
186\newcommand{\NEMO} {\textit{NEMO}\xspace}                %NEMO (nemo)
187
188%%%%   Bibliography   .............
189\usepackage[nottoc, notlof, notlot]{tocbibind}
190\usepackage[square, comma]{natbib}
191\bibpunct{[}{]}{,}{a}{}{;}                           %suppress "," after "et al."
192\providecommand{\bibfont}{\small}
193
194
195% ================================================================
196% FRONT PAGE
197% ================================================================
198
199%\usepackage{pstricks}
200\title{
201%\psset{unit=1.1in,linewidth=4pt}   %parameters of the units for pstricks
202% \rput(0,2){ \includegraphics[width=1.1\textwidth]{./TexFiles/Figures/logo_ALL.pdf}             } \\
203% \vspace{0.1cm}
204\vspace{-6.0cm}
205\includegraphics[width=1.1\textwidth]{./TexFiles/Figures/logo_ALL.pdf}\\
206\vspace{5.1cm}
207\includegraphics[width=0.9\textwidth]{./TexFiles/Figures/NEMO_logo_Black.pdf} \\
208\vspace{1.4cm}
209\rule{345pt}{1.5pt} \\
210\vspace{0.45cm}
211{\Huge NEMO ocean engine}
212\rule{345pt}{1.5pt} \\
213 }
214%{ -- Draft --}   }
215%\date{\today}
216\date{
217November 2015  \\
218{\small  -- draft of version 4.0 --} \\
219\\
220\textit{\small Note du P\^ole de mod\'{e}lisation de l'Institut Pierre-Simon Laplace No 27 }\\
221\vspace{0.45cm}
222{ ISSN No 1288-1619.}
223}
224
225
226\author{
227\Large Gurvan Madec, and the NEMO team  \\
228 \texttt{\small gurvan.madec@locean-ipsl.umpc.fr} \\
229 \texttt{\small nemo\_st@locean-ipsl.umpc.fr} \\
230%{\small Laboratoire d'Oc\'{e}anographie  et du Climat: Exp\'{e}rimentation et Approches Num\'{e}riques }
231}
232
233\dominitoc
234\makeindex        %type this first :     makeindex -s NEMO.ist NEMO_book.idx
235
236% ================================================================
237%      Include ONLY order
238% ================================================================
239
240%\includeonly{./TexFiles/Chapters/Chap_MISC}
241%\includeonly{./TexFiles/Chapters/Chap_ZDF}
242%\includeonly{./TexFiles/Chapters/Chap_STP,./TexFiles/Chapters/Chap_SBC,./TexFiles/Chapters/Chap_TRA}
243%\includeonly{./TexFiles/Chapters/Chap_LBC,./TexFiles/Chapters/Chap_MISC}
244%\includeonly{./TexFiles/Chapters/Chap_Model_Basics}
245%\includeonly{./TexFiles/Chapters/Annex_A,./TexFiles/Chapters/Annex_B,./TexFiles/Chapters/Annex_C,./TexFiles/Chapters/Annex_D}
246
247% ================================================================
248% ================================================================
249
250\begin{document}
251
252\maketitle                 % generate the title
253
254\frontmatter
255
256\tableofcontents              % generate a table of contents
257%\listoffigures               % generate a list  of figures
258%\listoftables                     % generate a list of tables
259
260\mainmatter
261
262% ================================================================
263% Abstract - Foreword
264% ================================================================
265
266\include{./TexFiles/Chapters/Abstracts_Foreword}
267
268% ================================================================
269% INTRODUCTION
270% ================================================================
271
272\include{./TexFiles/Chapters/Introduction}
273
274% ================================================================
275% CHAPTERS
276% ================================================================
277
278\include{./TexFiles/Chapters/Chap_Model_Basics}
279
280\include{./TexFiles/Chapters/Chap_STP}       % Time discretisation (time stepping strategy)
281
282\include{./TexFiles/Chapters/Chap_DOM}       % Space discretisation
283
284\include{./TexFiles/Chapters/Chap_TRA}       % Tracer advection/diffusion equation
285
286\include{./TexFiles/Chapters/Chap_DYN}       % Dynamics : momentum equation
287
288\include{./TexFiles/Chapters/Chap_SBC}       % Surface Boundary Conditions
289
290\include{./TexFiles/Chapters/Chap_LBC}       % Lateral Boundary Conditions
291
292\include{./TexFiles/Chapters/Chap_LDF}       % Lateral diffusion
293
294\include{./TexFiles/Chapters/Chap_ZDF}       % Vertical diffusion
295
296\include{./TexFiles/Chapters/Chap_DIA}       % Outputs and Diagnostics
297
298\include{./TexFiles/Chapters/Chap_OBS}          % Observation operator
299
300\include{./TexFiles/Chapters/Chap_ASM}          % Assimilation increments
301
302\include{./TexFiles/Chapters/Chap_STO}          % Stochastic param.
303
304\include{./TexFiles/Chapters/Chap_MISC}         % Miscellaneous topics
305
306\include{./TexFiles/Chapters/Chap_CFG}       % Predefined configurations
307
308% ================================================================
309% APPENDIX
310% ================================================================
311
312\appendix
313
314%\include{./TexFiles/Chapters/Chap_Conservation}
315\include{./TexFiles/Chapters/Annex_A}        % generalised vertical coordinate
316\include{./TexFiles/Chapters/Annex_B}        % diffusive operator
317\include{./TexFiles/Chapters/Annex_C}        % Discrete invariants of the eqs.
318\include{./TexFiles/Chapters/Annex_D}        % Coding rules
319\include{./TexFiles/Chapters/Annex_ISO}                     % Isoneutral diffusion using triads
320%\include{./TexFiles/Chapters/Annex_E}                   % Notes on some on going staff (no included in the DOC)
321%\include{./TexFiles/Chapters/Annex_Fox-Kemper}   % Notes on Fox-Kemper (no included in the DOC)
322%\include{./TexFiles/Chapters/Annex_EVP}           % Notes on EVP (no included in the DOC)
323
324% ================================================================
325% INDEX
326% ================================================================
327
328\addcontentsline{toc}{chapter}{Index}
329\printindex
330
331% ================================================================
332% BIBLIOGRAPHY
333% ================================================================
334
335%%\bibliographystyle{plainat}
336\bibliographystyle{./TexFiles/ametsoc}    % AMS biblio style (JPO)
337\bibliography{./TexFiles/Biblio/Biblio}
338
339% ================================================================
340\end{document}
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