Changeset 3218 for branches/2011/dev_NEMO_MERGE_2011/DOC/NEMO_book.tex

Timestamp:

2011-12-13T11:31:24+01:00 (13 years ago)

Author:

agn

Message:

agn: changes to documentation in dev_NEMO_MERGE_2011

--Reordered NEMO_book.tex, changed from 11pt->12pt,

only needs pstricks for logos

--more abbreviations in mathabbrev.sty
--Corrected bug in Abstracts_Foreword.tex that put whole

text into small

--Clarified discussion of LDF operator rotation in
Chap_Model_Basics.tex, Chap_LDF.tex, Annex_B.tex
--Discuss surface tapering of Griffies triads, how they

work in s-coordinates, eddy-induced velocities in
Annex_ISO.tex. Extra ref in Biblio.bib
Extra figures Fig_bdry_triads.pdf, Fig_triad_MLB.pdf
Modified namelist section namtra_ldf

--Minor corrections to Chap_DIA.tex, Chap_CFG.tex,

Chap_SBC.tex, Annex_A.tex, Chap_DOM.tex, Chap_ASM.tex

File:

• branches/2011/dev_NEMO_MERGE_2011/DOC/NEMO_book.tex (modified) (15 diffs)

branches/2011/dev_NEMO_MERGE_2011/DOC/NEMO_book.tex

@@ -4 +4 @@
 % (C) Xavier Perseguers 2002 - xavier.perseguers@epfl.ch
 
-\documentclass[a4paper,12pt]{book}
+\documentclass[a4paper,11pt]{book}
 
 %  makeindex NEMO_book     <== to regenerate the index
@@ -14 +14 @@
 
 \usepackage[french]{babel}
-\usepackage{fancyhdr}
-
-\usepackage{alltt}      %%  alltt for namelist
-\usepackage{verbatim}   %%  alltt for namelist
-
-%hyperref 
+%\usepackage{color}
+\usepackage{xcolor}
+%\usepackage{graphics}           % allows insertion of pictures
+\usepackage{graphicx}            % allows insertion of
+                                        % pictures
+\usepackage[capbesideposition={top,center}]{floatrow}
+\floatsetup[table]{style=plaintop}
+\usepackage[margin=10pt,font={small},labelsep=colon,labelfont={bf}]{caption}
+%\usepackage{colortbl}                           % gives coloured panels behind table columns
+
+%hyperref
 \usepackage[               %
   pdftitle={NEMO ocean engine},  %
@@ -31 +36 @@
   linkcolor=blue,anchorcolor=blue,  %
   citecolor=blue,filecolor=blue,    %
-  menucolor=blue,pagecolor=blue, %
+ menucolor=blue,                    %
   urlcolor=blue]{hyperref}
 %  usage of exteranl hyperlink :  \href{mailto:my_address@wikibooks.org}{my\_address@wikibooks.org}
@@ -39 +44 @@
 
 
-
-%\usepackage{amssymb}
+%%%% page styles etc................
+\usepackage{fancyhdr}
 \pagestyle{fancy}
 % with this we ensure that the chapter and section
@@ -59 +64 @@
 }
 
+
+%%%%  Section number in Margin.......
+% typeset the number of each section in the left margin, with the start of each instance of
+% sectional heading text aligned with the left hand edge of  the body text.
+\makeatletter
+\def\@seccntformat#1{\protect\makebox[0pt][r]{\csname the#1\endcsname\quad}}
+\makeatother
+
 % Leave blank pages completely empty, w/o header
 \makeatletter
@@ -70 +83 @@
 \makeatother
 
-\usepackage{makeidx}
-
-\usepackage{minitoc}          %in french : \usepackage[french]{minitoc}
-
+%%%% define the chapter  style ................
+\usepackage{minitoc}          %In French : \usepackage[french]{minitoc}
 %\usepackage{mtcoff}          % invalidate the use of minitocs
-\usepackage[latin1]{inputenc}
-\usepackage{graphics}            % allows insertion of pictures
-\usepackage{times}               % use vector fonts instead of bitmap
 \usepackage{fancybox}
-\usepackage{graphicx}
-%\usepackage{color}
-%\usepackage{colortbl}
-
-%%%% add by Word2Tex
-%\documentclass{amsart}
-\usepackage{latexsym}
-\usepackage{amssymb}
-\usepackage{amsmath}
-\usepackage{graphicx}
-\allowdisplaybreaks[1]           % allow page breaks in the middle of equations
-%%%%
-
-%%%%
-%\usepackage{mathtime}      % font for illustrator to work (belleek fonts )
-%%%%
-
-%\usepackage{showidx}            % show the index entry
-
-
-
-%%%% define the style of title for chapter  %%%
-\usepackage{pstricks}
+
 \makeatletter
 \def\LigneVerticale{\vrule height 5cm depth 2cm\hspace{0.1cm}\relax}
@@ -108 +94 @@
 \def\GrosCarreAvecUnChiffre#1{%
   \rlap{\vrule height 0.8cm width 1cm depth 0.2cm}%
-  \rlap{\hbox to 1cm{\hss\mbox{\white #1}\hss}}%
+ \rlap{\hbox to 1cm{\hss\mbox{\color{white} #1}\hss}}%
   \vrule height 0pt width 1cm depth 0pt}
 \def\GrosCarreAvecTroisChiffre#1{%
   \rlap{\vrule height 0.8cm width 1.6cm depth 0.2cm}%
-  \rlap{\hbox to 1.5cm{\hss\mbox{\white #1}\hss}}%
+ \rlap{\hbox to 1.5cm{\hss\mbox{\color{white} #1}\hss}}%
   \vrule height 0pt width 1cm depth 0pt}
 
 \def\@makechapterhead#1{\hbox{%
-    \huge 
+   \huge
     \LignesVerticales
     \hspace{-0.5cm}%
@@ -126 +112 @@
 }\par\vskip 1cm}
 \def\@makeschapterhead#1{\hbox{%
-    \huge 
+   \huge
     \LignesVerticales
     %\hspace{0.5cm}%
     \hbox{#1}%
 }\par\vskip 2cm}
+\makeatother
 
 %\def\thechapter{\Roman{chapter}}      % chapter number to be Roman
 
-%%%% end style chapter %%%
-
-%%% use maths shortcuts :
-%\newcommand{\vect} [1] { \rm{\textbf{#1}} }    % vector style: non-italic bold
-\usepackage{./TexFiles/math_abbrev}
+
+%%%%           Mathematics...............
+%\documentclass{amsart}
+\usepackage{xspace}                              % helpd ensure correct spacing after macros
+\usepackage{latexsym}
+\usepackage{amssymb}
+\usepackage{amsmath}
+\allowdisplaybreaks[1]           % allow page breaks in the middle of equations
+\usepackage{./TexFiles/math_abbrev}    % use maths shortcuts
+
+
+\usepackage{times}                % use times font for text
+%\usepackage{mathtime}                          % font for illustrator to work (belleek fonts )
+%\usepackage[latin1]{inputenc}                % allows some unicode removed (agn)
 
 
 %%% essai commande
-\newcommand{\nl} [1] {\texttt{\small {\textcolor{blue}{#1}} } } 
-
-%%% index commands :   
+\newcommand{\nl} [1] {\texttt{\small {\textcolor{blue}{#1}} } }
+\newcommand{\nlv} [1] {\texttt{\footnotesize#1}\xspace}
+\newcommand{\smnlv} [1] {\texttt{\scriptsize#1}\xspace}
+
+%%%% namelist & code display................................
+\usepackage{alltt}      %%  alltt for namelist
+\usepackage{verbatim}   %%  alltt for namelist
+% namelists
+\newcommand{\namdisplay} [1] {
+\begin{alltt}
+{\tiny \verbatiminput{./TexFiles/Namelist/#1}}
+\end{alltt}
+  \vspace{-10pt}
+}
+% code display
+%\newcommand{\codedisplay} [1] { \begin{alltt} {\tiny  {\begin{verbatim} {#1}} \end{verbatim} }  \end{alltt}   }
+
+
+
+%%%% commands for working with text................................
+% command to "comment out" portions of text ({} argument) or not ({#1} argument)
+\newcommand{\amtcomment}[1]{}    % command to "commented out" portions of text or not (#1 in argument)
+\newcommand{\sgacomment}[1]{}    % command to "commented out" portions of
+\newcommand{\gmcomment}[1]{}     % command to "commented out" portions of
+%                                               % text that span line breaks
+%Red (NR) or Yellow(WARN)
+%\newcommand{\NR} {\colorbox{red}{#1}}
+%\newcommand{\WARN} {{ \colorbox{yellow}{#1}} }
+
+
+
+%%% index commands......................
+\usepackage{makeidx}
+%\usepackage{showidx}            % show the index entry
+
 \newcommand{\mdl} [1] {\textit{#1.F90}\index{Modules!#1}}         %module (mdl)
 \newcommand{\rou} [1] {\textit{#1}\index{Routines!#1}}            %module (routine)
@@ -153 +181 @@
 \newcommand{\ifile} [1] {\textit{#1.nc}\index{Input NetCDF files!#1.nc}}   %input NetCDF files (.nc)
 \newcommand{\key} [1] {\textbf{key\_#1}\index{CPP keys!key\_#1}}  %key_cpp (key)
-\newcommand{\NEMO} {\textit{NEMO }}                %NEMO (nemo)
-% command to "commented out" portions of text ({} argument) or not ({#1} argument)
-\newcommand{\amtcomment}[1]{}    % command to "commented out" portions of text or not (#1 in argument)
-\newcommand{\sgacomment}[1]{}    % command to "commented out" portions of 
-\newcommand{\gmcomment}[1]{}     % command to "commented out" portions of 
-%                                               % text that span line breaks
-\newcommand{\alpbet} {\left(\alpha / \beta \right)}   % alpha/beta  for slp computation
-
-%--------------------------------------------namlist---------------------------------------------------------
-\newcommand{\namdisplay} [1] { 
-   \begin{alltt}  {{\tiny \verbatiminput{./TexFiles/Namelist/#1}}}  \end{alltt} 
-                               \vspace{-10pt}   }
-%--------------------------------------------code display---------------------------------------------------------
-%\newcommand{\codedisplay} [1] { \begin{alltt} {\tiny  {\begin{verbatim} {#1}} \end{verbatim} }  \end{alltt}   }
-%--------------------------------------------------------------------------------------------------------------
-%Red (NR) or Yellow(WARN)
-%\newcommand{\NR} {\colorbox{red}{#1}}
-%\newcommand{\WARN} {{ \colorbox{yellow}{#1}} }
-
-%---------------------%%%%%  Section number in Margin  %%%%%-----------------------------
-% typeset the number of each section in the left margin, with the start of each instance of
-% sectional heading text aligned with the left hand edge of  the body text.
-\makeatletter 
-\def\@seccntformat#1{\protect\makebox[0pt][r]{\csname the#1\endcsname\quad}} 
-\makeatother 
-%--------------------------------------------------------------------------------------------------------------
-
-%----------------------------%%%%%   Bilbiography   %%%%%%-------------------------------%
+\newcommand{\NEMO} {\textit{NEMO}\xspace}                %NEMO (nemo)
+
+%%%%   Bibliography   .............
 \usepackage[nottoc, notlof, notlot]{tocbibind}
 \usepackage[square, comma]{natbib}
 \bibpunct{[}{]}{,}{a}{}{;}                           %suppress "," after "et al."
 \providecommand{\bibfont}{\small}
-%--------------------------------------------------------------------------------------------------------------
+
 
 % ================================================================
@@ -191 +194 @@
 % ================================================================
 
-\title{ 
+\usepackage{pstricks}
+\title{
 \psset{unit=1.1in,linewidth=4pt}    %parameters of the units for pstricks
 \rput(-1.4,2){ \includegraphics[width=0.2\textwidth]{./TexFiles/Figures/logo_CNRS.pdf}           }
@@ -205 +209 @@
 \rule{345pt}{1.5pt} \\
 \vspace{0.45cm}
- {\Huge NEMO ocean engine} 
-\rule{345pt}{1.5pt} \\ 
+{\Huge NEMO ocean engine}
+\rule{345pt}{1.5pt} \\
  }
 %{ -- Draft --}   }
@@ -220 +224 @@
 
 
-%%\includegraphics[width=0.2\textwidth]{./TexFiles/Figures/logo_NERC.pdf} \\
-
-%%    \hbox{\mbox{%
-%%       \hspace{4pt}%
-%%         \fbox{\includegraphics[width=3em]{./TexFiles/Figures/logo_CNRS.pdf}}%
-%%        \hspace{4pt}
-%%        }  }%
-
-\author{ 
+\author{
 \Large Gurvan Madec, and the NEMO team  \\
  \texttt{\small gurvan.madec@locean-ipsl.umpc.fr} \\
@@ -257 +253 @@
 \frontmatter
 
-\tableofcontents              % generate a table of content
-%\listoffigures               % generate a table of content
-%\listoftables             % generate a table of content
+\tableofcontents              % generate a table of contents
+%\listoffigures               % generate a list  of figures
+%\listoftables                     % generate a list of tables
 
 \mainmatter
@@ -283 +279 @@
 \include{./TexFiles/Chapters/Chap_STP}       % Time discretisation (time stepping strategy)
 
-\include{./TexFiles/Chapters/Chap_DOM}       % Space discretisation 
+\include{./TexFiles/Chapters/Chap_DOM}       % Space discretisation
 
 \include{./TexFiles/Chapters/Chap_TRA}       % Tracer advection/diffusion equation
@@ -318 +314 @@
 \include{./TexFiles/Chapters/Annex_C}        % Discrete invariants of the eqs.
 \include{./TexFiles/Chapters/Annex_D}        % Coding rules
-\include{./TexFiles/Chapters/Annex_ISO}                     % Isoneutral diffusion using triads 
-%\include{./TexFiles/Chapters/Annex_E}                   % Notes on some on going staff (no included in the DOC) 
-%\include{./TexFiles/Chapters/Annex_Fox-Kemper}   % Notes on Fox-Kemper (no included in the DOC) 
-%\include{./TexFiles/Chapters/Annex_EVP}           % Notes on EVP (no included in the DOC) 
+\include{./TexFiles/Chapters/Annex_ISO}                     % Isoneutral diffusion using triads
+%\include{./TexFiles/Chapters/Annex_E}                   % Notes on some on going staff (no included in the DOC)
+%\include{./TexFiles/Chapters/Annex_Fox-Kemper}   % Notes on Fox-Kemper (no included in the DOC)
+%\include{./TexFiles/Chapters/Annex_EVP}           % Notes on EVP (no included in the DOC)
 
 % ================================================================