[6998] | 1 | \documentclass[a4paper,11pt]{book} |
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| 2 | %\documentclass[a4paper,11pt,makeidx]{book} <== may need this to generate index |
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| 3 | |
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| 4 | % makeindex NEMO_book <== to regenerate the index |
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| 5 | % bibtex NEMO_book <== to generate the bibliography |
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| 6 | |
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[9347] | 7 | %% Silence package: filter output messages and warnings |
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| 8 | \usepackage{silence} |
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[9350] | 9 | %%% LaTeX warnings: package and label |
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[9347] | 10 | \WarningFilter*{latex}{Package} |
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[9350] | 11 | \WarningFilter*{latex}{Label} |
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[9347] | 12 | %%% minitoc hints |
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| 13 | \WarningFilter{minitoc(hints)}{W0023} |
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[9350] | 14 | \WarningFilter{minitoc(hints)}{W0024} |
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[9347] | 15 | \WarningFilter{minitoc(hints)}{W0028} |
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| 16 | \WarningFilter{minitoc(hints)}{W0030} |
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| 17 | %%% natbib citation warning "Citation ... multiply defined" |
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| 18 | \WarningFilter*{natbib}{Citation} |
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| 19 | %%% Filter all warnings |
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| 20 | %\WarningsOff* |
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| 21 | |
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[6998] | 22 | \usepackage{graphicx} % allows insertion of pictures |
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[9373] | 23 | \graphicspath{{figures/}} % Set global directory for pictures |
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[9365] | 24 | %\usepackage[capbesideposition={top,center}]{floatrow} % allows captions |
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| 25 | %\floatsetup[table]{style=plaintop} % beside pictures |
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[6998] | 26 | \usepackage[margin=10pt,font={small}, % Gives small font for captions |
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| 27 | labelsep=colon,labelfont={bf}]{caption} % |
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| 28 | \usepackage{enumitem} % allows non-bold description items |
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| 29 | \usepackage{longtable} % allows multipage tables |
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| 30 | |
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| 31 | %hyperref |
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[9360] | 32 | \usepackage[obeyspaces]{url} |
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[6998] | 33 | \usepackage[pdftitle={NEMO ocean engine},pdfauthor={Gurvan Madec},pdfstartview=FitH, |
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| 34 | bookmarks=true,bookmarksopen=true,breaklinks=true,colorlinks=true, |
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| 35 | linkcolor=blue,anchorcolor=blue,citecolor=blue,filecolor=blue,menucolor=blue,urlcolor=blue]{hyperref} |
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| 36 | % pdfsubject={The preprint document class |
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| 37 | % elsart},% pdfkeywords={diapycnal diffusion,numerical mixing,z-level models},%% usage of exteranl hyperlink : \href{mailto:my_address@wikibooks.org}{my\_address@wikibooks.org} |
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| 38 | % \url{http://www.wikibooks.org} |
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| 39 | % or \href{http://www.wikibooks.org}{wikibooks home} |
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| 40 | |
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| 41 | |
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| 42 | %%%% page styles etc................ |
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| 43 | \usepackage{fancyhdr} |
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| 44 | \pagestyle{fancy} |
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| 45 | % with this we ensure that the chapter and section |
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| 46 | % headings are in lowercase. |
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| 47 | \renewcommand{\chaptermark}[1]{\markboth{#1}{}} |
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| 48 | \renewcommand{\sectionmark}[1]{\markright{\thesection.\ #1}} |
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| 49 | \fancyhf{} % delete current setting for header and footer |
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| 50 | \fancyhead[LE,RO]{\bfseries\thepage} |
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| 51 | \fancyhead[LO]{\bfseries\hspace{-0em}\rightmark} |
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| 52 | \fancyhead[RE]{\bfseries\leftmark} |
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| 53 | \renewcommand{\headrulewidth}{0.5pt} |
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| 54 | \renewcommand{\footrulewidth}{0pt } |
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| 55 | \addtolength{\headheight}{2.6pt} % make space for the rule |
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| 56 | %\addtolength{\headheight}{1.6pt} % make space for the rule |
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| 57 | % get rid of headers on plain pages |
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| 58 | \fancypagestyle{plain}{\fancyhead{}\renewcommand{\headrulewidth}{0pt}} |
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| 59 | |
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| 60 | |
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| 61 | %%%% Section number in Margin....... |
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| 62 | % typeset the number of each section in the left margin, with the start of each instance of |
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| 63 | % sectional heading text aligned with the left hand edge of the body text. |
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| 64 | \makeatletter |
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| 65 | \def\@seccntformat#1{\protect\makebox[0pt][r]{\csname the#1\endcsname\quad}} |
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| 66 | \makeatother |
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| 67 | |
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| 68 | % Leave blank pages completely empty, w/o header |
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| 69 | \makeatletter |
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| 70 | \def\cleardoublepage{\clearpage\if@twoside \ifodd\c@page\else |
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| 71 | \hbox{} |
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| 72 | \vspace*{\fill} |
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| 73 | \vspace{\fill} |
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| 74 | \thispagestyle{empty} |
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| 75 | \newpage |
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| 76 | \if@twocolumn\hbox{}\newpage\fi\fi\fi} |
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| 77 | \makeatother |
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| 78 | |
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| 79 | %%%% define the chapter style ................ |
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| 80 | \usepackage{minitoc} %In French : \usepackage[french]{minitoc} |
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| 81 | %\usepackage{mtcoff} % invalidate the use of minitocs |
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| 82 | \usepackage{fancybox} |
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| 83 | |
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| 84 | \makeatletter |
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| 85 | \def\LigneVerticale{\vrule height 5cm depth 2cm\hspace{0.1cm}\relax} |
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| 86 | \def\LignesVerticales{% |
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| 87 | \let\LV\LigneVerticale\LV\LV\LV\LV\LV\LV\LV\LV\LV\LV} |
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| 88 | \def\GrosCarreAvecUnChiffre#1{% |
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| 89 | \rlap{\vrule height 0.8cm width 1cm depth 0.2cm}% |
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| 90 | \rlap{\hbox to 1cm{\hss\mbox{\color{white} #1}\hss}}% |
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| 91 | \vrule height 0pt width 1cm depth 0pt} |
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| 92 | \def\GrosCarreAvecTroisChiffre#1{% |
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| 93 | \rlap{\vrule height 0.8cm width 1.6cm depth 0.2cm}% |
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| 94 | \rlap{\hbox to 1.5cm{\hss\mbox{\color{white} #1}\hss}}% |
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| 95 | \vrule height 0pt width 1cm depth 0pt} |
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| 96 | |
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| 97 | \def\@makechapterhead#1{\hbox{% |
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| 98 | \huge |
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| 99 | \LignesVerticales |
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| 100 | \hspace{-0.5cm}% |
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| 101 | \GrosCarreAvecUnChiffre{\thechapter} |
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| 102 | \hspace{0.2cm}\hbox{#1}% |
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| 103 | % \GrosCarreAvecTroisChiffre{\thechapter} |
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| 104 | % \hspace{1cm}\hbox{#1}% |
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| 105 | %}\par\vskip 2cm} |
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| 106 | }\par\vskip 1cm} |
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| 107 | \def\@makeschapterhead#1{\hbox{% |
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| 108 | \huge |
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| 109 | \LignesVerticales |
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| 110 | %\hspace{0.5cm}% |
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| 111 | \hbox{#1}% |
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| 112 | }\par\vskip 2cm} |
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| 113 | \makeatother |
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| 114 | |
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| 115 | %\def\thechapter{\Roman{chapter}} % chapter number to be Roman |
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| 116 | |
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| 117 | |
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| 118 | %%%% Mathematics............... |
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| 119 | %\documentclass{amsart} |
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| 120 | \usepackage{xspace} % helpd ensure correct spacing after macros |
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| 121 | \usepackage{latexsym,amssymb,amsmath} |
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| 122 | \allowdisplaybreaks[1] % allow page breaks in the middle of equations |
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[9373] | 123 | \usepackage{texfiles/styles/NEMO_manual} % use maths shortcuts |
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[6998] | 124 | |
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| 125 | \usepackage{times} % use times font for text |
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| 126 | %\usepackage{mathtime} % font for illustrator to work (belleek fonts ) |
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| 127 | %\usepackage[latin1]{inputenc} % allows some unicode removed (agn) |
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| 128 | |
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| 129 | |
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| 130 | %%% essai commande |
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| 131 | \newcommand{\nl}[1]{\texttt{\small{\textcolor{blue}{#1}}}} |
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| 132 | \newcommand{\nlv}[1]{\texttt{\footnotesize#1}\xspace} |
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| 133 | \newcommand{\smnlv}[1]{\texttt{\scriptsize#1}\xspace} |
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| 134 | |
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| 135 | %%%% namelist & code display................................ |
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| 136 | \usepackage{alltt,verbatim} %% alltt & verbatim for namelist |
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| 137 | % namelists |
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[9373] | 138 | \newcommand{\namdisplay}[1]{\begin{alltt}{\tiny\verbatiminput{namelists/#1}}\end{alltt}\vspace{-10pt}} |
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| 139 | \newcommand{\namtools}[1]{\begin{alltt}{\tiny\verbatiminput{namelists/#1}}\end{alltt}\vspace{-10pt}} |
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[6998] | 140 | % code display |
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[9346] | 141 | \newcommand{\codedisplay} [1] {\begin{alltt}{\tiny {\begin{verbatim} {#1}} \end{verbatim}} \end{alltt} } |
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[6998] | 142 | |
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| 143 | |
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| 144 | |
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| 145 | %%%% commands for working with text................................ |
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| 146 | % command to "comment out" portions of text ({} argument) or not ({#1} argument) |
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| 147 | \newcommand{\amtcomment}[1]{} % command to "commented out" portions of text or not (#1 in argument) |
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| 148 | \newcommand{\sgacomment}[1]{} % command to "commented out" portions of |
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| 149 | \newcommand{\gmcomment}[1]{} % command to "commented out" portions of |
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[7705] | 150 | \newcommand{\sfcomment}[1]{} % command to "commented out" portions of |
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[6998] | 151 | % % text that span line breaks |
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| 152 | %Red (NR) or Yellow(WARN) |
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| 153 | %\newcommand{\NR} {\colorbox{red} {#1}} |
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| 154 | %\newcommand{\WARN} {\colorbox{yellow}{#1}} |
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| 155 | |
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| 156 | |
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| 157 | |
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| 158 | %%% index commands...................... |
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| 159 | \usepackage{makeidx} |
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| 160 | %\usepackage{showidx} % show the index entry |
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| 161 | |
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| 162 | \newcommand{\mdl}[1]{\textit{#1.F90}\index{Modules!#1}} %module (mdl) |
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| 163 | \newcommand{\rou}[1]{\textit{#1}\index{Routines!#1}} %module (routine) |
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| 164 | \newcommand{\hf}[1]{\textit{#1.h90}\index{h90 file!#1}} %module (h90 files) |
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| 165 | \newcommand{\ngn}[1]{\textit{#1}\index{Namelist Group Name!#1}} %namelist name (nampar) |
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| 166 | \newcommand{\np}[1]{\textit{#1}\index{Namelist variables!#1}} %namelist variable |
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| 167 | \newcommand{\jp}[1]{\textit{#1}\index{Model parameters!#1}} %model parameter (jp) |
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| 168 | \newcommand{\pp}[1]{\textit{#1}\index{Model parameters!#1}} %namelist parameter (pp) |
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| 169 | \newcommand{\ifile}[1]{\textit{#1.nc }\index{Input NetCDF files!#1.nc}} %input NetCDF files (.nc) |
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| 170 | \newcommand{\key}[1]{\textbf{key\_#1}\index{CPP keys!key\_#1}} %key_cpp (key) |
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| 171 | \newcommand{\NEMO}{\textit{NEMO}\xspace} %NEMO (nemo) |
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| 172 | |
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| 173 | %%%% Bibliography ............. |
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| 174 | \usepackage[nottoc,notlof,notlot]{tocbibind} |
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| 175 | \usepackage[square,comma]{natbib} |
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| 176 | \bibpunct{[}{]}{,}{a}{}{;} %suppress "," after "et al." |
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| 177 | \providecommand{\bibfont}{\small} |
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| 178 | |
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| 179 | \usepackage{subfiles} % Separate compilation of chapters from whole manual |
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| 180 | %\newcommand{\onlyinsubfile}[1]{#1} % New commands for printing parts according to |
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| 181 | %\newcommand{\notinsubfile}[1]{} % the file being compiled |
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| 182 | % Commands to use in the documentfile |
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| 183 | %\renewcommand{\onlyinsubfile}[1]{} % Appears only if chapter .tex file is compiled |
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| 184 | %\renewcommand{\notinsubfile}[1]{#1} % " "" "" NEMO_book .tex file is compiled |
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| 185 | |
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| 186 | \DeclareMathAlphabet{\mathpzc}{OT1}{pzc}{m}{it} |
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[9360] | 187 | |
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| 188 | \usepackage{hyphenat} |
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| 189 | \hyphenation{AGRIF FORTRAN NEMOVAR bi-laplacian off-line on-line sea-ice well-known} |
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| 190 | |
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| 191 | %% Add source code highlighting |
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| 192 | %% From LaTeX Wikibooks https://en.wikibooks.org/wiki/LaTeX/Source_Code_Listings |
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| 193 | \usepackage{listings} |
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| 194 | \usepackage{xcolor} |
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| 195 | %% Colors from Trac default style |
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| 196 | \definecolor{backgroundcode}{HTML}{f8f8f8} |
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| 197 | \definecolor{graycode}{HTML}{666666} |
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| 198 | \definecolor{greencode}{HTML}{008800} |
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| 199 | \definecolor{purplecode}{HTML}{AA22FF} |
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| 200 | \definecolor{redcode}{HTML}{BB4444} |
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| 201 | \definecolor{yellowcode}{HTML}{B8860B} |
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| 202 | \lstset{language=[90]Fortran, |
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| 203 | backgroundcolor=\color{backgroundcode}, |
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| 204 | basicstyle=\tiny, |
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| 205 | breaklines=true, |
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| 206 | commentstyle=\color{greencode}, |
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| 207 | identifierstyle=\color{yellowcode}, |
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| 208 | keywordstyle=\color{purplecode}, |
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| 209 | numberstyle=\color{graycode}, |
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| 210 | stringstyle=\color{redcode}, |
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| 211 | title=\lstname, |
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| 212 | } |
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