manual.tex

% $Header: /u/gcmpack/manual/manual.tex,v 1.47 2017/06/19 20:07:25 jmc Exp $
% $Name:  $

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\newcommand{\filelink}[2]{\htmladdnormallink{\bf \tt #1}{../code_reference/vdb/byname/#2.html}}
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%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:
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%EH3%    % \includecomment{versionprivate}
%EH3%    \excludecoment{versionprivate}
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%EH3%    \includecomment{versionprivate}
%EH3%    % \excludecoment{versionprivate}

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%EH3%
%EH3%    To use this comment, simply bracket any part of the 
%EH3%    manual with two lines that contain ONLY the following
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%EH3%      \begin{versionprivate}
%EH3%      \end{versionprivate}
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%EH3%    with NO additional comments or other commands on the
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%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}
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%cnh%\fancyhead[LO]{\slshape \rightmark}
%cnh%\fancyhead[RE]{\slshape \leftmark}
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%aja%\newcommand{\BIBPATH}{.}
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%-jmc: try agu bib-style (give author names & year instead of just a number)
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% referencing
%ph%\newcommand{\refequ}[1]{equation (\ref{equ:#1})}
%ph%\newcommand{\refequbig}[1]{Equation (\ref{equ:#1})}
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% 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 
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%\usepackage[dvips]
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  pdftitle={MITgcm Documentation}, 
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  pdfkeywords={oceanography, ocean model, general circulation model,
    non-hydrostatic, finite volume, inverse methods, adjoint method} 
  } 

% Some definitions (AMM)
\def\p#1{\frac{\partial }{\partial #1}}
\def\pp#1#2{\frac{\partial #1}{\partial #2}}
\def\dd#1#2{\frac{d #1}{d #2}}
\def\bq{\begin{equation}}
\def\bqa{\begin{eqnarray}}
\def\eq{\end{equation}}
\def\eqa{\end{eqnarray}}

\def\h{ \frac{1}{2} }
\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}}

%  Definitions from EH3:
\def\CC{C\raise.3ex\hbox{{\footnotesize
      +}}\raise.3ex\hbox{\footnotesize +}\ }

\begin{document}

\bodytext{bgcolor="#FFFFFFFF"} 

\title{ \textsc{MITgcm User Manual} }

\author{
  Alistair Adcroft \and Jean-Michel Campin \and Stephanie Dutkiewicz
  \and Constantinos Evangelinos \and David Ferreira %\and Mick Follows 
  \and Gael Forget \and Baylor Fox-Kemper \and Patrick Heimbach 
  \and Chris Hill \and Ed Hill \and Helen Hill 
  \and Oliver Jahn \and Martin Losch \and John Marshall
  \and Guillaume Maze \and Dimitris Menemenlis \and Andrea Molod
  \\
  \\
  \\
  MIT Department of EAPS  \\
  77 Massachusetts Ave. \\
  Cambridge, MA \ 02139-4307
}

%\date{August 19, 2004}
\date{\today}

\maketitle

\tableofcontents
%\pagebreak

%\part{MIT GCM basics}

% Section: Overview of MITgcm
\input{s_overview/text/top_section}
%\pagebreak

% Section: Discretization and Algorithm
\input{s_algorithm/text/top_section}
%\pagebreak

% Section: Getting started with MITgcm
\input{s_getstarted/text/top_section}
%\pagebreak

% Section: Model Example <- not yet a section
\input{s_examples/text/top_section}
%\pagebreak

% Section: Software Architecture
\input{s_software/text/top_section}
%\pagebreak


%\part{Adjoint of the MIT GCM}

% Section: Automatic Differentiation
\input{s_autodiff/text/top_section}
%\pagebreak


%\part{Additional features}

% Section: Physical Parameterization - Packages I
\input{s_phys_pkgs/text/top_section}
%\pagebreak

% Section: Diagnostics and I/O - Packages II, and Post-Processing Utilities
\input{s_outp_pkgs/text/top_section}
%\pagebreak

% Section: Interface with ECCO
\input{s_ecco/text/top_section}
%\pagebreak

% Section: Under Development
\input{s_under_dvlp/text/top_section}

% Section: Previous applications of MITgcm
\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}