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% $Header$ |
% $Header$ |
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% $Name$ |
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\documentclass[12pt]{book} |
\documentclass[10pt]{book} |
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%To help cross-reference |
%To help cross-reference |
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%\usepackage{showlabels} |
%\usepackage{showlabels} |
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%aja%\usepackage{amsfonts} |
%aja%\usepackage{amsfonts} |
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\usepackage{amsmath} |
\usepackage{amsmath} |
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\usepackage{html} |
\usepackage{html} |
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\usepackage{graphics} |
\usepackage{hthtml} |
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\usepackage{graphicx} |
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%cnh%\usepackage{array} |
%cnh%\usepackage{array} |
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%cnh%\usepackage{multirow} |
%cnh%\usepackage{multirow} |
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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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% afe Commands to standardize typesetting |
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\newcommand{\file}[1]{\texttt{#1}} |
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\newcommand{\code}[1]{\texttt{#1}} |
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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% The default is to include everything which is: |
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%EH3% |
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%EH3% \includecomment{versionprivate} |
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%EH3% % \excludecoment{versionprivate} |
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%\includecomment{versionprivate} |
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\excludecomment{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% pair: |
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%EH3% |
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%EH3% \begin{versionprivate} |
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%EH3% \end{versionprivate} |
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%EH3% |
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%EH3% with NO additional comments or other commands on the |
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%EH3% lines containing the \begin{...}\end{...} statements. |
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%EH3% |
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%EH3% *** PRIVATE SECTIONS ****** PRIVATE SECTIONS *** |
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%EH3% ========================================================== |
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%ph%\usepackage{epsfig} |
%ph%\usepackage{epsfig} |
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%ph%\usepackage{psfrag} |
%ph%\usepackage{psfrag} |
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%ph%\usepackage{oldgerm} |
%ph%\usepackage{oldgerm} |
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%cnh%\renewcommand{\footrulewidth}{0.4pt} |
%cnh%\renewcommand{\footrulewidth}{0.4pt} |
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% bibtex stuff |
% bibtex stuff |
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\newcommand{\BIBPATH}{.} |
%aja%\newcommand{\BIBPATH}{.} |
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\usepackage{natbib} |
%aja%\usepackage{natbib} |
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\bibliographystyle{\BIBPATH/jmr_my} |
%aja%\bibliographystyle{\BIBPATH/jmr_my} |
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\gdef\harvardleft{[} |
%aja%\gdef\harvardleft{[} |
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\gdef\harvardright{]} |
%aja%\gdef\harvardright{]} |
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\bibpunct{[}{]}{,}{a}{}{,} |
%aja%\bibpunct{[}{]}{,}{a}{}{,} |
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%\bibliographystyle{plain} |
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%-jmc: try agu bib-style (give author names & year instead of just a number) |
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\usepackage[square]{natbib} |
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\bibliographystyle{agu} |
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% referencing |
% referencing |
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%ph%\newcommand{\refequ}[1]{equation (\ref{equ:#1})} |
%ph%\newcommand{\refequ}[1]{equation (\ref{equ:#1})} |
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%\renewcommand{\chaptername}{Section} |
%\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{hyperref} |
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%\usepackage[dvips] |
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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} |
%\part{MIT GCM basics} |
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% Section: Overview |
% Section: Overview |
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\input{part1/part1} |
\input{part1/part1} |
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%\pagebreak |
%\pagebreak |
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\part{Adjoint of the MIT GCM} |
%\part{Adjoint of the MIT GCM} |
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% Section: Automatic Differentiation |
% Section: Automatic Differentiation |
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\input{part5/part5} |
\input{part5/part5} |
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%\pagebreak |
%\pagebreak |
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\part{Additional features} |
%\part{Additional features} |
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% Section: Physical Packages |
% Section: Physical Packages |
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\input{part6/part6} |
\input{part6/part6} |
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%\pagebreak |
%\pagebreak |
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% Section: Diagnostics |
% Section: Pre-processing and Post-processing Tools |
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\input{part7/part7} |
\input{part7/part7} |
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%\pagebreak |
%\pagebreak |
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% Section: ECCO Interface |
% Section: ECCO |
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\input{part8/part8} |
\input{part8/part8} |
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%\pagebreak |
%\pagebreak |
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% Section: Model Uses |
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\input{model_uses} |
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%\pagebreak |
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% Section: References: |
% Section: References: |
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\markboth{BIBLIOGRAPHY}{BIBLIOGRAPHY} |
%\markboth{BIBLIOGRAPHY}{BIBLIOGRAPHY} |
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\addcontentsline{toc}{chapter}{BIBLIOGRAPHY} |
\addcontentsline{toc}{chapter}{BIBLIOGRAPHY} |
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\bibliography{\BIBPATH/manual_references} |
%aja%\bibliography{\BIBPATH/manual_references} |
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\bibliography{manual_references} |
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\end{document} |
\end{document} |
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