\documentclass[a4paper,11pt]{book} %\documentclass[a4paper,11pt,makeidx]{book} <== may need this to generate index % makeindex NEMO_book <== to regenerate the index % bibtex NEMO_book <== to generate the bibliography %% Silence package: filter output messages and warnings \usepackage{silence} %%% LaTeX warnings: package and label \WarningFilter*{latex}{Package} \WarningFilter*{latex}{Label} %%% minitoc hints \WarningFilter{minitoc(hints)}{W0023} \WarningFilter{minitoc(hints)}{W0024} \WarningFilter{minitoc(hints)}{W0028} \WarningFilter{minitoc(hints)}{W0030} %%% natbib citation warning "Citation ... multiply defined" \WarningFilter*{natbib}{Citation} %%% Filter all warnings %\WarningsOff* %\usepackage[french]{babel} %\usepackage{color} \usepackage{graphicx} % allows insertion of pictures %\usepackage{graphics} % allows insertion of pictures \graphicspath{{Figures/}} % Set global directory for pictures %\DeclareGraphicsExtensions{.pdf,.eps} % Use .eps for LaTeX2HTML %\usepackage{xcolor} % Incompatibility with color -> graphicx \usepackage[capbesideposition={top,center}]{floatrow} % allows captions \floatsetup[table]{style=plaintop} % beside pictures \usepackage[margin=10pt,font={small}, % Gives small font for captions labelsep=colon,labelfont={bf}]{caption} % \usepackage{enumitem} % allows non-bold description items \usepackage{longtable} % allows multipage tables %\usepackage{colortbl} % gives coloured panels behind table columns %hyperref \usepackage[pdftitle={NEMO ocean engine},pdfauthor={Gurvan Madec},pdfstartview=FitH, bookmarks=true,bookmarksopen=true,breaklinks=true,colorlinks=true, linkcolor=blue,anchorcolor=blue,citecolor=blue,filecolor=blue,menucolor=blue,urlcolor=blue]{hyperref} % pdfsubject={The preprint document class % elsart},% pdfkeywords={diapycnal diffusion,numerical mixing,z-level models},%% usage of exteranl hyperlink : \href{mailto:my_address@wikibooks.org}{my\_address@wikibooks.org} % \url{http://www.wikibooks.org} % or \href{http://www.wikibooks.org}{wikibooks home} %%%% page styles etc................ \usepackage{fancyhdr} \pagestyle{fancy} % with this we ensure that the chapter and section % headings are in lowercase. \renewcommand{\chaptermark}[1]{\markboth{#1}{}} \renewcommand{\sectionmark}[1]{\markright{\thesection.\ #1}} \fancyhf{} % delete current setting for header and footer \fancyhead[LE,RO]{\bfseries\thepage} \fancyhead[LO]{\bfseries\hspace{-0em}\rightmark} \fancyhead[RE]{\bfseries\leftmark} \renewcommand{\headrulewidth}{0.5pt} \renewcommand{\footrulewidth}{0pt } \addtolength{\headheight}{2.6pt} % make space for the rule %\addtolength{\headheight}{1.6pt} % make space for the rule % get rid of headers on plain pages \fancypagestyle{plain}{\fancyhead{}\renewcommand{\headrulewidth}{0pt}} %%%% 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 \def\cleardoublepage{\clearpage\if@twoside \ifodd\c@page\else \hbox{} \vspace*{\fill} \vspace{\fill} \thispagestyle{empty} \newpage \if@twocolumn\hbox{}\newpage\fi\fi\fi} \makeatother %%%% define the chapter style ................ \usepackage{minitoc} %In French : \usepackage[french]{minitoc} %\usepackage{mtcoff} % invalidate the use of minitocs \usepackage{fancybox} \makeatletter \def\LigneVerticale{\vrule height 5cm depth 2cm\hspace{0.1cm}\relax} \def\LignesVerticales{% \let\LV\LigneVerticale\LV\LV\LV\LV\LV\LV\LV\LV\LV\LV} \def\GrosCarreAvecUnChiffre#1{% \rlap{\vrule height 0.8cm width 1cm depth 0.2cm}% \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{\color{white} #1}\hss}}% \vrule height 0pt width 1cm depth 0pt} \def\@makechapterhead#1{\hbox{% \huge \LignesVerticales \hspace{-0.5cm}% \GrosCarreAvecUnChiffre{\thechapter} \hspace{0.2cm}\hbox{#1}% % \GrosCarreAvecTroisChiffre{\thechapter} % \hspace{1cm}\hbox{#1}% %}\par\vskip 2cm} }\par\vskip 1cm} \def\@makeschapterhead#1{\hbox{% \huge \LignesVerticales %\hspace{0.5cm}% \hbox{#1}% }\par\vskip 2cm} \makeatother %\def\thechapter{\Roman{chapter}} % chapter number to be Roman %%%% Mathematics............... %\documentclass{amsart} \usepackage{xspace} % helpd ensure correct spacing after macros \usepackage{latexsym,amssymb,amsmath} \allowdisplaybreaks[1] % allow page breaks in the middle of equations \usepackage{TexFiles/Styles/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}}}} \newcommand{\nlv}[1]{\texttt{\footnotesize#1}\xspace} \newcommand{\smnlv}[1]{\texttt{\scriptsize#1}\xspace} %%%% namelist & code display................................ \usepackage{alltt,verbatim} %% alltt & verbatim for namelist % namelists \newcommand{\namdisplay}[1]{\begin{alltt}{\tiny\verbatiminput{Namelists/#1}}\end{alltt}\vspace{-10pt}} \newcommand{\namtools}[1]{\begin{alltt}{\tiny\verbatiminput{Namelists/#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 \newcommand{\sfcomment}[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) \newcommand{\hf}[1]{\textit{#1.h90}\index{h90 file!#1}} %module (h90 files) \newcommand{\ngn}[1]{\textit{#1}\index{Namelist Group Name!#1}} %namelist name (nampar) \newcommand{\np}[1]{\textit{#1}\index{Namelist variables!#1}} %namelist variable \newcommand{\jp}[1]{\textit{#1}\index{Model parameters!#1}} %model parameter (jp) \newcommand{\pp}[1]{\textit{#1}\index{Model parameters!#1}} %namelist parameter (pp) \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}\xspace} %NEMO (nemo) %%%% Bibliography ............. \usepackage[nottoc,notlof,notlot]{tocbibind} \usepackage[square,comma]{natbib} \bibpunct{[}{]}{,}{a}{}{;} %suppress "," after "et al." \providecommand{\bibfont}{\small} \usepackage{subfiles} % Separate compilation of chapters from whole manual %\newcommand{\onlyinsubfile}[1]{#1} % New commands for printing parts according to %\newcommand{\notinsubfile}[1]{} % the file being compiled % Commands to use in the documentfile %\renewcommand{\onlyinsubfile}[1]{} % Appears only if chapter .tex file is compiled %\renewcommand{\notinsubfile}[1]{#1} % " "" "" NEMO_book .tex file is compiled \DeclareMathAlphabet{\mathpzc}{OT1}{pzc}{m}{it}