| 1 |
% $Header: /u/gcmpack/manual/manual.tex,v 1.39 2006/06/28 21:20:41 cnh Exp $ |
| 2 |
% $Name: $ |
| 3 |
|
| 4 |
\documentclass[10pt]{book} |
| 5 |
|
| 6 |
%To help cross-reference |
| 7 |
%\usepackage{showlabels} |
| 8 |
|
| 9 |
%aja%\usepackage{amsfonts} |
| 10 |
\usepackage{amsmath} |
| 11 |
\usepackage{html} |
| 12 |
\usepackage{hthtml} |
| 13 |
\usepackage{graphicx} |
| 14 |
\usepackage{rotating} |
| 15 |
|
| 16 |
% CNH playing around with page widths |
| 17 |
\usepackage{anysize} |
| 18 |
|
| 19 |
%cnh%\usepackage{array} |
| 20 |
%cnh%\usepackage{multirow} |
| 21 |
|
| 22 |
%eh3 Commands to reference either files or symbols within the "HTML-ized" |
| 23 |
%eh3 ("vdb") code. |
| 24 |
%eh3 |
| 25 |
%afe seems like these need to be long, sorry |
| 26 |
\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}} |
| 28 |
\newcommand{\myhref}[2]{\htmladdnormallink{#2}{#1}} |
| 29 |
|
| 30 |
% afe Commands to standardize typesetting |
| 31 |
\newcommand{\file}[1]{\texttt{#1}} |
| 32 |
\newcommand{\sectiontitle}[1]{\textsl{#1}} |
| 33 |
\newcommand{\code}[1]{\texttt{#1}} |
| 34 |
|
| 35 |
%% EH3 : try out the epsfig package |
| 36 |
\usepackage[dvips]{epsfig} |
| 37 |
\def\scalefig#1{\epsfxsize #1\textwidth} |
| 38 |
|
| 39 |
%EH3% ========================================================== |
| 40 |
%EH3% *** PRIVATE SECTIONS ****** PRIVATE SECTIONS *** |
| 41 |
%EH3% |
| 42 |
%EH3% Directions: To build the ``private'' or ``local-only'' |
| 43 |
%EH3% version of this manual, then edit the following so |
| 44 |
%EH3% they appear as: |
| 45 |
%EH3% |
| 46 |
%EH3% % \includecomment{versionprivate} |
| 47 |
%EH3% \excludecoment{versionprivate} |
| 48 |
%EH3% |
| 49 |
%EH3% The default is to include everything which is: |
| 50 |
%EH3% |
| 51 |
%EH3% \includecomment{versionprivate} |
| 52 |
%EH3% % \excludecoment{versionprivate} |
| 53 |
|
| 54 |
%\includecomment{versionprivate} |
| 55 |
\excludecomment{versionprivate} |
| 56 |
|
| 57 |
%EH3% |
| 58 |
%EH3% To use this comment, simply bracket any part of the |
| 59 |
%EH3% manual with two lines that contain ONLY the following |
| 60 |
%EH3% pair: |
| 61 |
%EH3% |
| 62 |
%EH3% \begin{versionprivate} |
| 63 |
%EH3% \end{versionprivate} |
| 64 |
%EH3% |
| 65 |
%EH3% with NO additional comments or other commands on the |
| 66 |
%EH3% lines containing the \begin{...}\end{...} statements. |
| 67 |
%EH3% |
| 68 |
%EH3% *** PRIVATE SECTIONS ****** PRIVATE SECTIONS *** |
| 69 |
%EH3% ========================================================== |
| 70 |
|
| 71 |
|
| 72 |
%ph%\usepackage{epsfig} |
| 73 |
%ph%\usepackage{psfrag} |
| 74 |
%ph%\usepackage{oldgerm} |
| 75 |
|
| 76 |
% I commented the following because it introduced excessive white space |
| 77 |
%aja%\usepackage{palatcm} % better PDF |
| 78 |
|
| 79 |
% page headers and footers |
| 80 |
%cnh%\usepackage{fancyhdr} |
| 81 |
%\pagestyle{fancy} |
| 82 |
%cnh%\fancyhead{} |
| 83 |
%cnh%\fancyhead[LO]{\slshape \rightmark} |
| 84 |
%cnh%\fancyhead[RE]{\slshape \leftmark} |
| 85 |
%cnh%\fancyhead[RO,LE]{\thepage} |
| 86 |
%cnh%\fancyfoot[CO,CE]{\today} |
| 87 |
%cnh%\fancyfoot[RO,LE]{ } |
| 88 |
%cnh%\renewcommand{\headrulewidth}{0.4pt} |
| 89 |
%cnh%\renewcommand{\footrulewidth}{0.4pt} |
| 90 |
|
| 91 |
% bibtex stuff |
| 92 |
%aja%\newcommand{\BIBPATH}{.} |
| 93 |
%aja%\usepackage{natbib} |
| 94 |
%aja%\bibliographystyle{\BIBPATH/jmr_my} |
| 95 |
%aja%\gdef\harvardleft{[} |
| 96 |
%aja%\gdef\harvardright{]} |
| 97 |
%aja%\bibpunct{[}{]}{,}{a}{}{,} |
| 98 |
%\bibliographystyle{plain} |
| 99 |
%-jmc: try agu bib-style (give author names & year instead of just a number) |
| 100 |
%% \usepackage[square] |
| 101 |
\usepackage[square]{natbib} |
| 102 |
\bibliographystyle{agu} |
| 103 |
%% \bibliographystyle{aguurl} |
| 104 |
|
| 105 |
% referencing |
| 106 |
%ph%\newcommand{\refequ}[1]{equation (\ref{equ:#1})} |
| 107 |
%ph%\newcommand{\refequbig}[1]{Equation (\ref{equ:#1})} |
| 108 |
%ph%\newcommand{\reftab}[1]{Tab.~\ref{tab:#1}} |
| 109 |
%ph%\newcommand{\reftabno}[1]{\ref{tab:#1}} |
| 110 |
%ph%\newcommand{\reffig}[1]{Fig.~\ref{fig:#1}} |
| 111 |
%ph%\newcommand{\reffigno}[1]{\ref{fig:#1}} |
| 112 |
|
| 113 |
% stuff for psfrag |
| 114 |
%ph%\newcommand{\textinfigure}[1]{{\footnotesize\textbf{\textsf{#1}}}} |
| 115 |
%ph%\newcommand{\mathinfigure}[1]{\small\ensuremath{{#1}}} |
| 116 |
|
| 117 |
% This allows numbering of subsubsections |
| 118 |
\setcounter{secnumdepth}{3} |
| 119 |
% This changes the the chapter title |
| 120 |
%\renewcommand{\chaptername}{Section} |
| 121 |
|
| 122 |
|
| 123 |
% This allows hyperlinks in PDF |
| 124 |
% hyperref package and colors for hyperref package |
| 125 |
\usepackage{color} |
| 126 |
\usepackage{hyperref} |
| 127 |
%\usepackage[dvips] |
| 128 |
\definecolor{darkgreen}{rgb}{0,0.4,0} |
| 129 |
\definecolor{darkblue}{rgb}{0,0,0.4} |
| 130 |
\definecolor{darkred}{rgb}{0.5,0,0} |
| 131 |
\hypersetup{breaklinks=true, |
| 132 |
colorlinks=true, |
| 133 |
linkcolor=darkgreen, |
| 134 |
citecolor=darkblue, |
| 135 |
pagecolor=darkred, |
| 136 |
pdftitle={MITgcm Release 1 Documentation}, |
| 137 |
pdfauthor={MITgcm-support@mitgcm.org}, |
| 138 |
pdfkeywords={oceanography, ocean model, general circulation model, |
| 139 |
non-hydrostatic, finite volume, inverse methods, adjoint method} |
| 140 |
} |
| 141 |
|
| 142 |
% Some definitions (AMM) |
| 143 |
\def\p#1{{\partial \over {\partial #1}}} |
| 144 |
\def\pp#1#2{{\partial #1 \over {\partial #2}}} |
| 145 |
\def\dd#1#2{{d #1 \over {d #2}}} |
| 146 |
\def\bq{\begin{equation}} |
| 147 |
\def\bqa{\begin{eqnarray}} |
| 148 |
\def\eq{\end{equation}} |
| 149 |
\def\eqa{\end{eqnarray}} |
| 150 |
|
| 151 |
\def\h{ {1\over2} } |
| 152 |
\def\txt{\mbox{$2^\circ$ x $2.5^\circ \,$}} |
| 153 |
\def\fxf{\mbox{$4^\circ$ x $5^\circ \,$}} |
| 154 |
|
| 155 |
\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} |
| 180 |
|
| 181 |
\bodytext{bgcolor="#FFFFFFFF"} |
| 182 |
|
| 183 |
\title{ \textsc{MITgcm User Manual} } |
| 184 |
|
| 185 |
\author{ |
| 186 |
John Marshall \and Alistair Adcroft \and Jean-Michel Campin |
| 187 |
\and Patrick Heimbach \and Andrea Molod \and Stephanie Dutkiewicz |
| 188 |
\and Helen Hill \and Martin Losch \and Baylor Fox-Kemper |
| 189 |
\and Dimitris Menemenlis \and David Ferreira \and Ed Hill |
| 190 |
\and Mick Follows \and Chris Hill \and Constantinos Evangelinos |
| 191 |
\and Gael Forget |
| 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 |
|
| 202 |
\maketitle |
| 203 |
|
| 204 |
\tableofcontents |
| 205 |
%\pagebreak |
| 206 |
|
| 207 |
%\part{MIT GCM basics} |
| 208 |
|
| 209 |
% Section: Overview |
| 210 |
\input{part1/part1} |
| 211 |
%\pagebreak |
| 212 |
|
| 213 |
% Section: Discretization and Algorithm |
| 214 |
\input{part2/part2} |
| 215 |
%\pagebreak |
| 216 |
|
| 217 |
% Section: Getting started |
| 218 |
\input{part3/part3} |
| 219 |
%\pagebreak |
| 220 |
|
| 221 |
% Section: Software Architecture |
| 222 |
\input{part4/part4} |
| 223 |
%\pagebreak |
| 224 |
|
| 225 |
|
| 226 |
%\part{Adjoint of the MIT GCM} |
| 227 |
|
| 228 |
% Section: Automatic Differentiation |
| 229 |
\input{part5/part5} |
| 230 |
%\pagebreak |
| 231 |
|
| 232 |
|
| 233 |
%\part{Additional features} |
| 234 |
|
| 235 |
% Section: Physical Packages |
| 236 |
\input{part6/part6} |
| 237 |
%\pagebreak |
| 238 |
|
| 239 |
% Section: Pre-processing and Post-processing Tools |
| 240 |
\input{part7/part7} |
| 241 |
%\pagebreak |
| 242 |
|
| 243 |
% Section: ECCO |
| 244 |
\input{part8/part8} |
| 245 |
%\pagebreak |
| 246 |
|
| 247 |
% Section: Model Uses |
| 248 |
\input{model_uses} |
| 249 |
%\pagebreak |
| 250 |
|
| 251 |
% Section: References: |
| 252 |
%\markboth{BIBLIOGRAPHY}{BIBLIOGRAPHY} |
| 253 |
\addcontentsline{toc}{chapter}{BIBLIOGRAPHY} |
| 254 |
%aja%\bibliography{\BIBPATH/manual_references} |
| 255 |
\bibliography{manual_references,baylor_biblio} |
| 256 |
|
| 257 |
\end{document} |
Parent Directory
| 
Revision Log
| 
Revision Graph