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\documentclass[12pt]{book} |
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\usepackage{amsfonts} |
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\usepackage{amsmath} |
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\usepackage{html} |
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\usepackage{epsfig} |
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\usepackage{graphics,subfigure} |
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\usepackage{array} |
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\usepackage{multirow} |
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\usepackage{fancyhdr} |
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\usepackage{psfrag} |
\usepackage{anysize} |
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%\usepackage{oldgerm} |
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%cnh%\usepackage{array} |
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%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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%% 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} |
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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 |
% I commented the following because it introduced excessive white space |
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%\usepackage{palatcm} % better PDF |
%aja%\usepackage{palatcm} % better PDF |
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% page headers and footers |
% page headers and footers |
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%cnh%\usepackage{fancyhdr} |
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%\pagestyle{fancy} |
%\pagestyle{fancy} |
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\fancyhead{} |
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\fancyhead[LO]{\slshape \rightmark} |
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\fancyhead[RE]{\slshape \leftmark} |
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\fancyhead[RO,LE]{\thepage} |
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\fancyfoot[CO,CE]{\today} |
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\fancyfoot[RO,LE]{ } |
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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%\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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\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 |
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\newcommand{\textinfigure}[1]{{\footnotesize\textbf{\textsf{#1}}}} |
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\newcommand{\mathinfigure}[1]{\small\ensuremath{{#1}}} |
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% This allows numbering of subsubsections |
% This allows numbering of subsubsections |
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\setcounter{secnumdepth}{3} |
\setcounter{secnumdepth}{3} |
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% This changes the the chapter title |
% This changes the the chapter title |
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%\renewcommand{\chaptername}{Section} |
%\renewcommand{\chaptername}{Section} |
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\usepackage{showlabels} |
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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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% 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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\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{The 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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% Section: 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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% Section: 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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% Section: 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{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 |
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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: |
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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} |
\end{document} |
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