% $Header: /home/ubuntu/mnt/e9_copy/manual/manual.tex,v 1.37 2006/04/07 15:40:07 edhill Exp $ % $Name: $ \documentclass[10pt]{book} %To help cross-reference %\usepackage{showlabels} %aja%\usepackage{amsfonts} \usepackage{amsmath} \usepackage{html} \usepackage{hthtml} \usepackage{graphicx} \usepackage{rotating} % CNH playing around with page widths \usepackage{anysize} %cnh%\usepackage{array} %cnh%\usepackage{multirow} %eh3 Commands to reference either files or symbols within the "HTML-ized" %eh3 ("vdb") code. %eh3 %afe seems like these need to be long, sorry \newcommand{\varlink}[2]{\htmladdnormallink{\tt #1}{../code_reference/vdb/byname/#2.html}} \newcommand{\filelink}[2]{\htmladdnormallink{\bf \tt #1}{../code_reference/vdb/byname/#2.html}} % afe Commands to standardize typesetting \newcommand{\file}[1]{\texttt{#1}} \newcommand{\sectiontitle}[1]{\textsl{#1}} \newcommand{\code}[1]{\texttt{#1}} %% EH3 : try out the epsfig package \usepackage[dvips]{epsfig} \def\scalefig#1{\epsfxsize #1\textwidth} %EH3% ========================================================== %EH3% *** PRIVATE SECTIONS ****** PRIVATE SECTIONS *** %EH3% %EH3% Directions: To build the ``private'' or ``local-only'' %EH3% version of this manual, then edit the following so %EH3% they appear as: %EH3% %EH3% % \includecomment{versionprivate} %EH3% \excludecoment{versionprivate} %EH3% %EH3% The default is to include everything which is: %EH3% %EH3% \includecomment{versionprivate} %EH3% % \excludecoment{versionprivate} %\includecomment{versionprivate} \excludecomment{versionprivate} %EH3% %EH3% To use this comment, simply bracket any part of the %EH3% manual with two lines that contain ONLY the following %EH3% pair: %EH3% %EH3% \begin{versionprivate} %EH3% \end{versionprivate} %EH3% %EH3% with NO additional comments or other commands on the %EH3% lines containing the \begin{...}\end{...} statements. %EH3% %EH3% *** PRIVATE SECTIONS ****** PRIVATE SECTIONS *** %EH3% ========================================================== %ph%\usepackage{epsfig} %ph%\usepackage{psfrag} %ph%\usepackage{oldgerm} % I commented the following because it introduced excessive white space %aja%\usepackage{palatcm} % better PDF % page headers and footers %cnh%\usepackage{fancyhdr} %\pagestyle{fancy} %cnh%\fancyhead{} %cnh%\fancyhead[LO]{\slshape \rightmark} %cnh%\fancyhead[RE]{\slshape \leftmark} %cnh%\fancyhead[RO,LE]{\thepage} %cnh%\fancyfoot[CO,CE]{\today} %cnh%\fancyfoot[RO,LE]{ } %cnh%\renewcommand{\headrulewidth}{0.4pt} %cnh%\renewcommand{\footrulewidth}{0.4pt} % bibtex stuff %aja%\newcommand{\BIBPATH}{.} %aja%\usepackage{natbib} %aja%\bibliographystyle{\BIBPATH/jmr_my} %aja%\gdef\harvardleft{[} %aja%\gdef\harvardright{]} %aja%\bibpunct{[}{]}{,}{a}{}{,} %\bibliographystyle{plain} %-jmc: try agu bib-style (give author names & year instead of just a number) \usepackage[square]{natbib} \bibliographystyle{agu} % referencing %ph%\newcommand{\refequ}[1]{equation (\ref{equ:#1})} %ph%\newcommand{\refequbig}[1]{Equation (\ref{equ:#1})} %ph%\newcommand{\reftab}[1]{Tab.~\ref{tab:#1}} %ph%\newcommand{\reftabno}[1]{\ref{tab:#1}} %ph%\newcommand{\reffig}[1]{Fig.~\ref{fig:#1}} %ph%\newcommand{\reffigno}[1]{\ref{fig:#1}} % stuff for psfrag %ph%\newcommand{\textinfigure}[1]{{\footnotesize\textbf{\textsf{#1}}}} %ph%\newcommand{\mathinfigure}[1]{\small\ensuremath{{#1}}} % This allows numbering of subsubsections \setcounter{secnumdepth}{3} % This changes the the chapter title %\renewcommand{\chaptername}{Section} % This allows hyperlinks in PDF % hyperref package and colors for hyperref package \usepackage{color} \usepackage{hyperref} %\usepackage[dvips] \definecolor{darkgreen}{rgb}{0,0.4,0} \definecolor{darkblue}{rgb}{0,0,0.4} \definecolor{darkred}{rgb}{0.5,0,0} \hypersetup{breaklinks=true, colorlinks=true, linkcolor=darkgreen, citecolor=darkblue, pagecolor=darkred, pdftitle={MITgcm Release 1 Documentation}, pdfauthor={MITgcm-support@mitgcm.org}, pdfkeywords={oceanography, ocean model, general circulation model, non-hydrostatic, finite volume, inverse methods, adjoint method} } % Some definitions (AMM) \def\p#1{{\partial \over {\partial #1}}} \def\pp#1#2{{\partial #1 \over {\partial #2}}} \def\dd#1#2{{d #1 \over {d #2}}} \def\bq{\begin{equation}} \def\bqa{\begin{eqnarray}} \def\eq{\end{equation}} \def\eqa{\end{eqnarray}} \def\h{ {1\over2} } \def\txt{\mbox{$2^\circ$ x $2.5^\circ \,$}} \def\fxf{\mbox{$4^\circ$ x $5^\circ \,$}} \def\blankpage{ \vspace*{\fill} \vspace{5in} \vfill \newpage} % Some definitions modified from the ones provided by Baylor \def\BFKav#1{\overline{#1}} \def\BFKpd#1#2{{\frac{\partial{#2}}{\partial{#1}}}} \def\BFKpds#1#2{{\frac{\partial^2{#2}}{{\partial{#1}}^2}}} \def\BFKDt#1{\frac{D{#1}}{Dt}} \def\BFKaDt#1{\frac{\BFKav D{#1}}{\BFKav{Dt}}} \def\BFKd#1{{\,\rm d#1}} \def\BFKRo{{\rm Ro}} \def\BFKRe{{\rm Re}} \def\BFKFr{{\rm Fr}} \def\BFKPr{{\rm Pr}} \def\BFKMr{{M_{Ro}}} \def\BFKtu{{\tilde u}} \def\BFKtv{{\tilde v}} \def\BFKatu{{\tilde {\BFKav u}}} \def\BFKatv{{\tilde {\BFKav v}}} \def\BFKlesssim{{<\atop\sim}} \begin{document} \bodytext{bgcolor="#FFFFFFFF"} \title{ \textsc{MITgcm User Manual} } \author{ John Marshall \and Alistair Adcroft \and Jean-Michel Campin \and Patrick Heimbach \and Andrea Molod \and Stephanie Dutkiewicz \and Helen Hill \and Martin Losch \and Baylor Fox-Kemper \and Dimitris Menemenlis \and David Ferreira \and Ed Hill \and Mick Follows \and Chris Hill \and Constantinos Evangelinos \and Gael Forget \\ \\ \\ MIT Department of EAPS \\ 77 Massachusetts Ave. \\ Cambridge, MA \ 02139-4307 } \date{August 19, 2004} \maketitle \tableofcontents %\pagebreak %\part{MIT GCM basics} % Section: Overview \input{part1/part1} %\pagebreak % Section: Discretization and Algorithm \input{part2/part2} %\pagebreak % Section: Getting started \input{part3/part3} %\pagebreak % Section: Software Architecture \input{part4/part4} %\pagebreak %\part{Adjoint of the MIT GCM} % Section: Automatic Differentiation \input{part5/part5} %\pagebreak %\part{Additional features} % Section: Physical Packages \input{part6/part6} %\pagebreak % Section: Pre-processing and Post-processing Tools \input{part7/part7} %\pagebreak % Section: ECCO \input{part8/part8} %\pagebreak % Section: Model Uses \input{model_uses} %\pagebreak % Section: References: %\markboth{BIBLIOGRAPHY}{BIBLIOGRAPHY} \addcontentsline{toc}{chapter}{BIBLIOGRAPHY} %aja%\bibliography{\BIBPATH/manual_references} \bibliography{manual_references,baylor_biblio} \end{document}