%description: Book template
% template of document for LaTeX
% (C) Xavier Perseguers 2002 - xavier.perseguers@epfl.ch
\documentclass[a4paper,11pt]{book}
%\documentclass[a4paper,11pt,makeidx]{book} <== may need this to generate index
% makeindex NEMO_BDY_tools <== to regenerate the index
% bibtex NEMO_BDY_tools <== to generate the bibliography
% ================================================================
% HEADERS DEFINITION
% ================================================================
\usepackage[french]{babel}
%\usepackage{color}
\usepackage{xcolor}
%\usepackage{graphics} % allows insertion of pictures
\usepackage{graphicx} % allows insertion of pictures
\usepackage[capbesideposition={top,center}]{floatrow} % allows captions
\floatsetup[table]{style=plaintop} % beside pictures
\usepackage[margin=10pt,font={small},labelsep=colon,labelfont={bf}]{caption} % Gives small font for captions
\usepackage{enumitem} % allows non-bold description items
%\usepackage{colortbl} % gives coloured panels behind table columns
%hyperref
\usepackage[ %
pdftitle={NEMO BDY tools}, %
pdfauthor={James Harle}, % pdfsubject={The preprint document class
% elsart},% pdfkeywords={diapycnal diffusion,numerical mixing,z-level models},%
pdfstartview=FitH, %
bookmarks=true, %
bookmarksopen=true, %
breaklinks=true, %
colorlinks=true, %
linkcolor=blue,anchorcolor=blue, %
citecolor=blue,filecolor=blue, %
menucolor=blue, %
urlcolor=blue]{hyperref}
% 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
\fancypagestyle{plain}{
\fancyhead{} % get rid of headers on plain pages
\renewcommand{\headrulewidth}{0pt} % and the line
}
%%%% 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}
\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}} } }
\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{#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)
\newcommand{\hf} [1] {\textit{#1.h90}\index{h90 file!#1}} %module (h90 files)
\newcommand{\np} [1] {\textit{#1}\index{Namelist parameters!#1}} %namelist parameter (nampar)
\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}
% ================================================================
% FRONT PAGE
% ================================================================
%\usepackage{pstricks}
\title{
%\psset{unit=1.1in,linewidth=4pt} %parameters of the units for pstricks
% \rput(0,2){ \includegraphics[width=1.1\textwidth]{./TexFiles/Figures/logo_ALL.pdf} } \\
% \vspace{0.1cm}
\vspace{-6.0cm}
%\includegraphics[width=1.1\textwidth]{./TexFiles/Figures/logo_ALL.pdf}\\
\vspace{5.1cm}
\includegraphics[width=0.9\textwidth]{./TexFiles/Figures/NEMO_logo_Black.pdf} \\
\vspace{1.4cm}
\rule{345pt}{1.5pt} \\
\vspace{0.45cm}
{\Huge PyNEMO}
\rule{345pt}{1.5pt} \\
}
%{ -- Draft --} }
\date{\today \\
{\small -- version 0.1.0 --} \\
}
%\date{
%January 2012 \\
%{\small -- version 3.4 --} \\
%~ \\
%\textit{\small Note du P\^ole de mod\'{e}lisation de l'Institut Pierre-Simon Laplace No 27 }\\
%\vspace{0.45cm}
%{ ISSN No 1288-1619.}
%}
\author{
\Large James Harle \\
\texttt{\small jdha@noc.ac.uk} \\
{\small National Oceanography Centre, UK}
}
\dominitoc
\makeindex %type this first : makeindex -s NEMO.ist NEMO_book.idx
% ================================================================
% Include ONLY order
% ================================================================
%\includeonly{./TexFiles/Chapters/Chap_MISC}
%\includeonly{./TexFiles/Chapters/Chap_ZDF}
%\includeonly{./TexFiles/Chapters/Chap_STP,./TexFiles/Chapters/Chap_SBC,./TexFiles/Chapters/Chap_TRA}
%\includeonly{./TexFiles/Chapters/Chap_LBC,./TexFiles/Chapters/Chap_MISC}
%\includeonly{./TexFiles/Chapters/Chap_Model_Basics}
%\includeonly{./TexFiles/Chapters/Annex_A,./TexFiles/Chapters/Annex_B,./TexFiles/Chapters/Annex_C,./TexFiles/Chapters/Annex_D}
% ================================================================
% ================================================================
\begin{document}
\maketitle % generate the title
\frontmatter
\tableofcontents % generate a table of contents
%\listoffigures % generate a list of figures
%\listoftables % generate a list of tables
\mainmatter
% ================================================================
% Abstract - Foreword
% ================================================================
\include{./TexFiles/Chapters/Abstracts_Foreword}
% ================================================================
% INTRODUCTION
% ================================================================
\include{./TexFiles/Chapters/Introduction}
% ================================================================
% CHAPTERS
% ================================================================
\include{./TexFiles/Chapters/Chap_qs}
\include{./TexFiles/Chapters/Chap_Setup}
\include{./TexFiles/Chapters/Chap_examples}
% bit on code style , harmonisation, f-c and python coding conventions
% ================================================================
% INDEX
% ================================================================
\addcontentsline{toc}{chapter}{Index}
\printindex
% ================================================================
% BIBLIOGRAPHY
% ================================================================
%%\bibliographystyle{plainat}
\bibliographystyle{./TexFiles/ametsoc} % AMS biblio style (JPO)
\bibliography{./TexFiles/Biblio/Biblio}
% ================================================================
\end{document}