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\documentclass[12pt]{book} |
\documentclass[12pt]{book} |
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\usepackage{amsfonts} |
%To help cross-reference |
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%\usepackage{showlabels} |
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%aja%\usepackage{amsfonts} |
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\usepackage{amsmath} |
\usepackage{amsmath} |
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\usepackage{html} |
\usepackage{html} |
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\usepackage{epsfig} |
\usepackage{hthtml} |
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\usepackage{graphics,subfigure} |
\usepackage{graphicx} |
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\usepackage{array} |
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\usepackage{multirow} |
%cnh%\usepackage{array} |
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\usepackage{fancyhdr} |
%cnh%\usepackage{multirow} |
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\usepackage{psfrag} |
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\usepackage{oldgerm} |
%eh3 Commands to reference either files or symbols within the "HTML-ized" |
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\usepackage{palatcm} % better PDF |
%eh3 ("vdb") code. |
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%eh3 |
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\newcommand{\varlink}[2]{ |
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\htmladdnormallink{\tt #1}{../code_reference/vdb/byname/#2.html} |
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} |
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\newcommand{\filelink}[2]{ |
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\htmladdnormallink{\bf \tt #1}{../code_reference/vdb/byname/#2.html} |
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} |
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% afe Commands to standardize typesetting |
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\newcommand{\file}[1]{ |
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\texttt{#1} |
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} |
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\newcommand{\sectiontitle}[1]{ |
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\textsl{#1} |
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} |
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\newcommand{\code}[1]{ |
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\texttt{#1} |
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} |
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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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%ph%\usepackage{epsfig} |
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%ph%\usepackage{psfrag} |
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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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%aja%\usepackage{palatcm} % better PDF |
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% page headers and footers |
% page headers and footers |
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\pagestyle{fancy} |
%cnh%\usepackage{fancyhdr} |
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\fancyhead{} |
%\pagestyle{fancy} |
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\fancyhead[LO]{\slshape \rightmark} |
%cnh%\fancyhead{} |
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\fancyhead[RE]{\slshape \leftmark} |
%cnh%\fancyhead[LO]{\slshape \rightmark} |
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\fancyhead[RO,LE]{\thepage} |
%cnh%\fancyhead[RE]{\slshape \leftmark} |
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\fancyfoot[CO,CE]{\today} |
%cnh%\fancyhead[RO,LE]{\thepage} |
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\fancyfoot[RO,LE]{ } |
%cnh%\fancyfoot[CO,CE]{\today} |
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\renewcommand{\headrulewidth}{0.4pt} |
%cnh%\fancyfoot[RO,LE]{ } |
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\renewcommand{\footrulewidth}{0.4pt} |
%cnh%\renewcommand{\headrulewidth}{0.4pt} |
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%cnh%\renewcommand{\footrulewidth}{0.4pt} |
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% bibtex stuff |
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%aja%\newcommand{\BIBPATH}{.} |
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%aja%\usepackage{natbib} |
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%aja%\bibliographystyle{\BIBPATH/jmr_my} |
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%aja%\gdef\harvardleft{[} |
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%aja%\gdef\harvardright{]} |
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%aja%\bibpunct{[}{]}{,}{a}{}{,} |
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\bibliographystyle{plain} |
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% referencing |
% referencing |
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\newcommand{\refequ}[1]{equation (\ref{equ:#1})} |
%ph%\newcommand{\refequ}[1]{equation (\ref{equ:#1})} |
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\newcommand{\refequbig}[1]{Equation (\ref{equ:#1})} |
%ph%\newcommand{\refequbig}[1]{Equation (\ref{equ:#1})} |
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\newcommand{\reftab}[1]{Tab.~\ref{tab:#1}} |
%ph%\newcommand{\reftab}[1]{Tab.~\ref{tab:#1}} |
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\newcommand{\reftabno}[1]{\ref{tab:#1}} |
%ph%\newcommand{\reftabno}[1]{\ref{tab:#1}} |
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\newcommand{\reffig}[1]{Fig.~\ref{fig:#1}} |
%ph%\newcommand{\reffig}[1]{Fig.~\ref{fig:#1}} |
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\newcommand{\reffigno}[1]{\ref{fig:#1}} |
%ph%\newcommand{\reffigno}[1]{\ref{fig:#1}} |
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% stuff for psfrag |
% stuff for psfrag |
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\newcommand{\textinfigure}[1]{{\footnotesize\textbf{\textsf{#1}}}} |
%ph%\newcommand{\textinfigure}[1]{{\footnotesize\textbf{\textsf{#1}}}} |
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\newcommand{\mathinfigure}[1]{\small\ensuremath{{#1}}} |
%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]{hyperref} |
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\definecolor{darkgreen}{rgb}{0,0.4,0} |
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\definecolor{darkblue}{rgb}{0,0,0.4} |
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\definecolor{darkred}{rgb}{0.5,0,0} |
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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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\begin{document} |
\begin{document} |
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\bodytext{bgcolor="#FFFFFFFF"} |
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\tableofcontents |
\tableofcontents |
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\pagebreak |
%\pagebreak |
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%\part{MIT GCM basics} |
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% Part: Overview |
% Section: Overview |
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\input{part1/part1} |
\input{part1/part1} |
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\pagebreak |
%\pagebreak |
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% Part: Discretization and Algorithm |
% Section: Discretization and Algorithm |
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\input{part2/part2} |
\input{part2/part2} |
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\pagebreak |
%\pagebreak |
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% Part: Getting started |
% Section: Getting started |
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\input{part3/part3} |
\input{part3/part3} |
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\pagebreak |
%\pagebreak |
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% Part: Software Architecture |
% Section: Software Architecture |
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\input{part4/part4} |
\input{part4/part4} |
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\pagebreak |
%\pagebreak |
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% Part: Automatic Differentiation |
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%\part{Adjoint of the MIT GCM} |
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% Section: Automatic Differentiation |
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\input{part5/part5} |
\input{part5/part5} |
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\pagebreak |
%\pagebreak |
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% Part: Physical Packages |
%\part{Additional features} |
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% Section: Physical Packages |
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\input{part6/part6} |
\input{part6/part6} |
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\pagebreak |
%\pagebreak |
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% Part: Diagnostics |
% Section: Diagnostics |
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\input{part7/part7} |
\input{part7/part7} |
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\pagebreak |
%\pagebreak |
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% Part: ECCO Interface |
% Section: ECCO |
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\input{part8/part8} |
\input{part8/part8} |
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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} |
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\end{document} |
\end{document} |
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