| 11 |
\usepackage{html} |
\usepackage{html} |
| 12 |
\usepackage{hthtml} |
\usepackage{hthtml} |
| 13 |
\usepackage{graphicx} |
\usepackage{graphicx} |
| 14 |
|
\usepackage{rotating} |
| 15 |
|
|
| 16 |
|
% CNH playing around with page widths |
| 17 |
|
\usepackage{anysize} |
| 18 |
|
|
| 19 |
%cnh%\usepackage{array} |
%cnh%\usepackage{array} |
| 20 |
%cnh%\usepackage{multirow} |
%cnh%\usepackage{multirow} |
| 25 |
%afe seems like these need to be long, sorry |
%afe seems like these need to be long, sorry |
| 26 |
\newcommand{\varlink}[2]{\htmladdnormallink{\tt #1}{../code_reference/vdb/byname/#2.html}} |
\newcommand{\varlink}[2]{\htmladdnormallink{\tt #1}{../code_reference/vdb/byname/#2.html}} |
| 27 |
\newcommand{\filelink}[2]{\htmladdnormallink{\bf \tt #1}{../code_reference/vdb/byname/#2.html}} |
\newcommand{\filelink}[2]{\htmladdnormallink{\bf \tt #1}{../code_reference/vdb/byname/#2.html}} |
| 28 |
|
\newcommand{\myhref}[2]{\htmladdnormallink{#2}{#1}} |
| 29 |
|
|
| 30 |
% afe Commands to standardize typesetting |
% afe Commands to standardize typesetting |
| 31 |
\newcommand{\file}[1]{\texttt{#1}} |
\newcommand{\file}[1]{\texttt{#1}} |
| 97 |
%aja%\bibpunct{[}{]}{,}{a}{}{,} |
%aja%\bibpunct{[}{]}{,}{a}{}{,} |
| 98 |
%\bibliographystyle{plain} |
%\bibliographystyle{plain} |
| 99 |
%-jmc: try agu bib-style (give author names & year instead of just a number) |
%-jmc: try agu bib-style (give author names & year instead of just a number) |
| 100 |
|
%% \usepackage[square] |
| 101 |
\usepackage[square]{natbib} |
\usepackage[square]{natbib} |
| 102 |
\bibliographystyle{agu} |
\bibliographystyle{agu} |
| 103 |
|
%% \bibliographystyle{aguurl} |
| 104 |
|
|
| 105 |
% referencing |
% referencing |
| 106 |
%ph%\newcommand{\refequ}[1]{equation (\ref{equ:#1})} |
%ph%\newcommand{\refequ}[1]{equation (\ref{equ:#1})} |
| 133 |
linkcolor=darkgreen, |
linkcolor=darkgreen, |
| 134 |
citecolor=darkblue, |
citecolor=darkblue, |
| 135 |
pagecolor=darkred, |
pagecolor=darkred, |
| 136 |
pdftitle={MITgcm Release 1 Documentation}, |
pdftitle={MITgcm Documentation}, |
| 137 |
pdfauthor={MITgcm-support@mitgcm.org}, |
pdfauthor={MITgcm-support@mitgcm.org}, |
| 138 |
pdfkeywords={oceanography, ocean model, general circulation model, |
pdfkeywords={oceanography, ocean model, general circulation model, |
| 139 |
non-hydrostatic, finite volume, inverse methods, adjoint method} |
non-hydrostatic, finite volume, inverse methods, adjoint method} |
| 140 |
} |
} |
| 141 |
|
|
| 142 |
% Some definitions (AMM) |
% Some definitions (AMM) |
| 143 |
\def\p#1{{\partial \over {\partial #1}}} |
\def\p#1{\frac{\partial }{\partial #1}} |
| 144 |
\def\pp#1#2{{\partial #1 \over {\partial #2}}} |
\def\pp#1#2{\frac{\partial #1}{\partial #2}} |
| 145 |
\def\dd#1#2{{d #1 \over {d #2}}} |
\def\dd#1#2{\frac{d #1}{d #2}} |
| 146 |
\def\bq{\begin{equation}} |
\def\bq{\begin{equation}} |
| 147 |
\def\bqa{\begin{eqnarray}} |
\def\bqa{\begin{eqnarray}} |
| 148 |
\def\eq{\end{equation}} |
\def\eq{\end{equation}} |
| 149 |
\def\eqa{\end{eqnarray}} |
\def\eqa{\end{eqnarray}} |
| 150 |
|
|
| 151 |
\def\h{ {1\over2} } |
\def\h{ \frac{1}{2} } |
| 152 |
\def\txt{\mbox{$2^\circ$ x $2.5^\circ \,$}} |
\def\txt{\mbox{$2^\circ$ x $2.5^\circ \,$}} |
| 153 |
\def\fxf{\mbox{$4^\circ$ x $5^\circ \,$}} |
\def\fxf{\mbox{$4^\circ$ x $5^\circ \,$}} |
| 154 |
|
|
| 155 |
\def\blankpage{ \vspace*{\fill} \vspace{5in} \vfill \newpage} |
\def\blankpage{ \vspace*{\fill} \vspace{5in} \vfill \newpage} |
| 156 |
|
|
| 157 |
|
% Some definitions modified from the ones provided by Baylor |
| 158 |
|
\def\BFKav#1{\overline{#1}} |
| 159 |
|
\def\BFKpd#1#2{{\frac{\partial{#2}}{\partial{#1}}}} |
| 160 |
|
\def\BFKpds#1#2{{\frac{\partial^2{#2}}{{\partial{#1}}^2}}} |
| 161 |
|
\def\BFKDt#1{\frac{D{#1}}{Dt}} |
| 162 |
|
\def\BFKaDt#1{\frac{\BFKav D{#1}}{\BFKav{Dt}}} |
| 163 |
|
\def\BFKd#1{{\,\rm d#1}} |
| 164 |
|
\def\BFKRo{{\rm Ro}} |
| 165 |
|
\def\BFKRe{{\rm Re}} |
| 166 |
|
\def\BFKFr{{\rm Fr}} |
| 167 |
|
\def\BFKPr{{\rm Pr}} |
| 168 |
|
\def\BFKMr{{M_{Ro}}} |
| 169 |
|
\def\BFKtu{{\tilde u}} |
| 170 |
|
\def\BFKtv{{\tilde v}} |
| 171 |
|
\def\BFKatu{{\tilde {\BFKav u}}} |
| 172 |
|
\def\BFKatv{{\tilde {\BFKav v}}} |
| 173 |
|
\def\BFKlesssim{{<\atop\sim}} |
| 174 |
|
|
| 175 |
|
% Definitions from EH3: |
| 176 |
|
\def\CC{C\raise.3ex\hbox{{\footnotesize |
| 177 |
|
+}}\raise.3ex\hbox{\footnotesize +}\ } |
| 178 |
|
|
| 179 |
\begin{document} |
\begin{document} |
| 180 |
|
|
| 181 |
\bodytext{bgcolor="#FFFFFFFF"} |
\bodytext{bgcolor="#FFFFFFFF"} |
| 182 |
|
|
| 183 |
|
\title{ \textsc{MITgcm User Manual} } |
| 184 |
|
|
| 185 |
|
\author{ |
| 186 |
|
Alistair Adcroft \and Jean-Michel Campin \and Stephanie Dutkiewicz |
| 187 |
|
\and Constantinos Evangelinos \and David Ferreira %\and Mick Follows |
| 188 |
|
\and Gael Forget \and Baylor Fox-Kemper \and Patrick Heimbach |
| 189 |
|
\and Chris Hill \and Ed Hill \and Helen Hill |
| 190 |
|
\and Oliver Jahn \and Martin Losch \and John Marshall |
| 191 |
|
\and Guillaume Maze \and Dimitris Menemenlis \and Andrea Molod |
| 192 |
|
\\ |
| 193 |
|
\\ |
| 194 |
|
\\ |
| 195 |
|
MIT Department of EAPS \\ |
| 196 |
|
77 Massachusetts Ave. \\ |
| 197 |
|
Cambridge, MA \ 02139-4307 |
| 198 |
|
} |
| 199 |
|
|
| 200 |
|
%\date{August 19, 2004} |
| 201 |
|
\date{\today} |
| 202 |
|
|
| 203 |
|
\maketitle |
| 204 |
|
|
| 205 |
\tableofcontents |
\tableofcontents |
| 206 |
%\pagebreak |
%\pagebreak |
| 207 |
|
|
| 208 |
%\part{MIT GCM basics} |
%\part{MIT GCM basics} |
| 209 |
|
|
| 210 |
% Section: Overview |
% Section: Overview of MITgcm |
| 211 |
\input{part1/part1} |
\input{s_overview/text/top_section} |
| 212 |
%\pagebreak |
%\pagebreak |
| 213 |
|
|
| 214 |
% Section: Discretization and Algorithm |
% Section: Discretization and Algorithm |
| 215 |
\input{part2/part2} |
\input{s_algorithm/text/top_section} |
| 216 |
|
%\pagebreak |
| 217 |
|
|
| 218 |
|
% Section: Getting started with MITgcm |
| 219 |
|
\input{s_getstarted/text/top_section} |
| 220 |
%\pagebreak |
%\pagebreak |
| 221 |
|
|
| 222 |
% Section: Getting started |
% Section: Model Example <- not yet a section |
| 223 |
\input{part3/part3} |
\input{s_examples/text/top_section} |
| 224 |
%\pagebreak |
%\pagebreak |
| 225 |
|
|
| 226 |
% Section: Software Architecture |
% Section: Software Architecture |
| 227 |
\input{part4/part4} |
\input{s_software/text/top_section} |
| 228 |
%\pagebreak |
%\pagebreak |
| 229 |
|
|
| 230 |
|
|
| 231 |
%\part{Adjoint of the MIT GCM} |
%\part{Adjoint of the MIT GCM} |
| 232 |
|
|
| 233 |
% Section: Automatic Differentiation |
% Section: Automatic Differentiation |
| 234 |
\input{part5/part5} |
\input{s_autodiff/text/top_section} |
| 235 |
%\pagebreak |
%\pagebreak |
| 236 |
|
|
| 237 |
|
|
| 238 |
%\part{Additional features} |
%\part{Additional features} |
| 239 |
|
|
| 240 |
% Section: Physical Packages |
% Section: Physical Parameterization - Packages I |
| 241 |
\input{part6/part6} |
\input{s_phys_pkgs/text/top_section} |
| 242 |
%\pagebreak |
%\pagebreak |
| 243 |
|
|
| 244 |
% Section: Pre-processing and Post-processing Tools |
% Section: Diagnostics and I/O - Packages II, and Post-Processing Utilities |
| 245 |
\input{part7/part7} |
\input{s_outp_pkgs/text/top_section} |
| 246 |
%\pagebreak |
%\pagebreak |
| 247 |
|
|
| 248 |
% Section: ECCO |
% Section: Interface with ECCO |
| 249 |
\input{part8/part8} |
\input{s_ecco/text/top_section} |
| 250 |
%\pagebreak |
%\pagebreak |
| 251 |
|
|
| 252 |
% Section: Model Uses |
% Section: Under Development |
| 253 |
|
\input{s_under_dvlp/text/top_section} |
| 254 |
|
|
| 255 |
|
% Section: Previous applications of MITgcm |
| 256 |
\input{model_uses} |
\input{model_uses} |
| 257 |
%\pagebreak |
%\pagebreak |
| 258 |
|
|
| 260 |
%\markboth{BIBLIOGRAPHY}{BIBLIOGRAPHY} |
%\markboth{BIBLIOGRAPHY}{BIBLIOGRAPHY} |
| 261 |
\addcontentsline{toc}{chapter}{BIBLIOGRAPHY} |
\addcontentsline{toc}{chapter}{BIBLIOGRAPHY} |
| 262 |
%aja%\bibliography{\BIBPATH/manual_references} |
%aja%\bibliography{\BIBPATH/manual_references} |
| 263 |
\bibliography{manual_references} |
\bibliography{manual_references,baylor_biblio} |
| 264 |
|
|
| 265 |
\end{document} |
\end{document} |
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