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% $Header: /u/gcmpack/manual/manual.tex,v 1.44 2010/08/27 13:31:32 jmc Exp $ |
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% $Name: $ |
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\documentclass[10pt]{book} |
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%To help cross-reference |
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%\usepackage{showlabels} |
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%aja%\usepackage{amsfonts} |
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\usepackage{amsmath} |
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%eh3 Commands to reference either files or symbols within the "HTML-ized" |
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%eh3 ("vdb") code. |
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%eh3 |
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%afe seems like these need to be long, sorry |
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\newcommand{\varlink}[2]{\htmladdnormallink{\tt #1}{../code_reference/vdb/byname/#2.html}} |
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\newcommand{\filelink}[2]{\htmladdnormallink{\bf \tt #1}{../code_reference/vdb/byname/#2.html}} |
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%% EH3 : try out the epsfig package |
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\usepackage[dvips]{epsfig} |
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\def\scalefig#1{\epsfxsize #1\textwidth} |
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%EH3% ========================================================== |
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%EH3% *** PRIVATE SECTIONS ****** PRIVATE SECTIONS *** |
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%EH3% |
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%EH3% Directions: To build the ``private'' or ``local-only'' |
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%EH3% version of this manual, then edit the following so |
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%EH3% they appear as: |
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%EH3% |
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%EH3% % \includecomment{versionprivate} |
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%EH3% \excludecoment{versionprivate} |
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%EH3% |
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%EH3% To use this comment, simply bracket any part of the |
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%EH3% manual with two lines that contain ONLY the following |
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%EH3% |
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%EH3% \begin{versionprivate} |
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%EH3% *** PRIVATE SECTIONS ****** PRIVATE SECTIONS *** |
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%ph%\usepackage{epsfig} |
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%ph%\usepackage{oldgerm} |
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% I commented the following because it introduced excessive white space |
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%-jmc: try agu bib-style (give author names & year instead of just a number) |
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%% \usepackage[square] |
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\usepackage[square]{natbib} |
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\bibliographystyle{agu} |
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%% \bibliographystyle{aguurl} |
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% referencing |
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%ph%\newcommand{\refequ}[1]{equation (\ref{equ:#1})} |
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%ph%\newcommand{\refequbig}[1]{Equation (\ref{equ:#1})} |
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%ph%\newcommand{\reftab}[1]{Tab.~\ref{tab:#1}} |
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%ph%\newcommand{\reftabno}[1]{\ref{tab:#1}} |
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%ph%\newcommand{\reffig}[1]{Fig.~\ref{fig:#1}} |
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%ph%\newcommand{\mathinfigure}[1]{\small\ensuremath{{#1}}} |
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% This allows numbering of subsubsections |
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\setcounter{secnumdepth}{3} |
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% This changes the the chapter title |
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%\renewcommand{\chaptername}{Section} |
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% This allows hyperlinks in PDF |
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% hyperref package and colors for hyperref package |
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\usepackage{color} |
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%\usepackage[dvips] |
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\hypersetup{breaklinks=true, |
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colorlinks=true, |
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linkcolor=darkgreen, |
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citecolor=darkblue, |
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pagecolor=darkred, |
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pdftitle={MITgcm Release 1 Documentation}, |
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pdfauthor={MITgcm-support@mitgcm.org}, |
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pdfkeywords={oceanography, ocean model, general circulation model, |
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non-hydrostatic, finite volume, inverse methods, adjoint method} |
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} |
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% Some definitions (AMM) |
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\def\p#1{{\partial \over {\partial #1}}} |
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\def\pp#1#2{{\partial #1 \over {\partial #2}}} |
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\def\dd#1#2{{d #1 \over {d #2}}} |
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\def\bq{\begin{equation}} |
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\def\bqa{\begin{eqnarray}} |
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\def\eq{\end{equation}} |
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\def\eqa{\end{eqnarray}} |
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\def\h{ {1\over2} } |
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\def\txt{\mbox{$2^\circ$ x $2.5^\circ \,$}} |
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\def\fxf{\mbox{$4^\circ$ x $5^\circ \,$}} |
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\def\blankpage{ \vspace*{\fill} \vspace{5in} \vfill \newpage} |
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% Some definitions modified from the ones provided by Baylor |
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\def\BFKav#1{\overline{#1}} |
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\def\BFKpd#1#2{{\frac{\partial{#2}}{\partial{#1}}}} |
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\def\BFKpds#1#2{{\frac{\partial^2{#2}}{{\partial{#1}}^2}}} |
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\def\BFKDt#1{\frac{D{#1}}{Dt}} |
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\def\BFKaDt#1{\frac{\BFKav D{#1}}{\BFKav{Dt}}} |
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\def\BFKd#1{{\,\rm d#1}} |
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\def\BFKRo{{\rm Ro}} |
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\def\BFKRe{{\rm Re}} |
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\def\BFKFr{{\rm Fr}} |
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\def\BFKPr{{\rm Pr}} |
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\def\BFKMr{{M_{Ro}}} |
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\def\BFKtu{{\tilde u}} |
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\def\BFKtv{{\tilde v}} |
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\def\BFKatu{{\tilde {\BFKav u}}} |
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\def\BFKatv{{\tilde {\BFKav v}}} |
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\def\BFKlesssim{{<\atop\sim}} |
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% Definitions from EH3: |
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\def\CC{C\raise.3ex\hbox{{\footnotesize |
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+}}\raise.3ex\hbox{\footnotesize +}\ } |
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\begin{document} |
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\bodytext{bgcolor="#FFFFFFFF"} |
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\title{ \textsc{MITgcm User Manual} } |
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\author{ |
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Alistair Adcroft \and Jean-Michel Campin \and Stephanie Dutkiewicz |
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\and Constantinos Evangelinos \and David Ferreira %\and Mick Follows |
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\and Gael Forget \and Baylor Fox-Kemper \and Patrick Heimbach |
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\and Chris Hill \and Ed Hill \and Helen Hill |
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\and Oliver Jahn \and Martin Losch \and John Marshall |
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\and Guillaume Maze \and Dimitris Menemenlis \and Andrea Molod |
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\\ |
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\\ |
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\\ |
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MIT Department of EAPS \\ |
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77 Massachusetts Ave. \\ |
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Cambridge, MA \ 02139-4307 |
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} |
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%\date{August 19, 2004} |
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\date{\today} |
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\maketitle |
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\tableofcontents |
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%\pagebreak |
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%\part{MIT GCM basics} |
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% Section: Overview of MITgcm |
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\input{s_overview/text/top_section} |
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%\pagebreak |
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% Section: Discretization and Algorithm |
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\input{s_algorithm/text/top_section} |
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%\pagebreak |
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% Section: Getting started with MITgcm |
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\input{s_getstarted/text/top_section} |
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%\pagebreak |
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% Section: Model Example <- not yet a section |
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\input{s_examples/text/top_section} |
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%\pagebreak |
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% Section: Software Architecture |
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\input{s_software/text/top_section} |
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%\pagebreak |
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%\part{Adjoint of the MIT GCM} |
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% Section: Automatic Differentiation |
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\input{s_autodiff/text/top_section} |
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%\pagebreak |
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%\part{Additional features} |
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% Section: Physical Parameterization - Packages I |
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\input{s_phys_pkgs/text/top_section} |
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%\pagebreak |
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% Section: Diagnostics and I/O - Packages II, and Post-Processing Utilities |
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\input{s_outp_pkgs/text/top_section} |
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%\pagebreak |
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% Section: Interface with ECCO |
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\input{s_ecco/text/top_section} |
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%\pagebreak |
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% Section: Under Development |
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\input{s_under_dvlp/text/top_section} |
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% Section: Previous applications of MITgcm |
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\input{model_uses} |
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%\pagebreak |
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% Section: References: |
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%\markboth{BIBLIOGRAPHY}{BIBLIOGRAPHY} |
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\addcontentsline{toc}{chapter}{BIBLIOGRAPHY} |
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%aja%\bibliography{\BIBPATH/manual_references} |
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\bibliography{manual_references,baylor_biblio} |
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\end{document} |
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