| 1 |
% $Header$ |
% $Header$ |
| 2 |
% $Name$ |
% $Name$ |
| 3 |
|
|
| 4 |
\documentclass[12pt]{book} |
\documentclass[10pt]{book} |
| 5 |
|
|
| 6 |
%To help cross-reference |
%To help cross-reference |
| 7 |
%\usepackage{showlabels} |
%\usepackage{showlabels} |
| 9 |
%aja%\usepackage{amsfonts} |
%aja%\usepackage{amsfonts} |
| 10 |
\usepackage{amsmath} |
\usepackage{amsmath} |
| 11 |
\usepackage{html} |
\usepackage{html} |
| 12 |
|
\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} |
| 21 |
|
|
| 22 |
% Command to reference entries in either "code" or "names" |
%eh3 Commands to reference either files or symbols within the "HTML-ized" |
| 23 |
% directories of browseable code tree. |
%eh3 ("vdb") code. |
| 24 |
\newcommand{\proclink}[2]{ |
%eh3 |
| 25 |
\htmladdnormallink{\em #1()}{../../code_reference/vdb/names/#2_docref.html} |
%afe seems like these need to be long, sorry |
| 26 |
} |
\newcommand{\varlink}[2]{\htmladdnormallink{\tt #1}{../code_reference/vdb/byname/#2.html}} |
| 27 |
\newcommand{\varlink}[2]{ |
\newcommand{\filelink}[2]{\htmladdnormallink{\bf \tt #1}{../code_reference/vdb/byname/#2.html}} |
| 28 |
\htmladdnormallink{\bf \tt #1}{../../code_reference/vdb/names/#2_docref.html} |
\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} |
%ph%\usepackage{epsfig} |
| 95 |
%aja%\gdef\harvardleft{[} |
%aja%\gdef\harvardleft{[} |
| 96 |
%aja%\gdef\harvardright{]} |
%aja%\gdef\harvardright{]} |
| 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) |
| 100 |
|
%% \usepackage[square] |
| 101 |
|
\usepackage[square]{natbib} |
| 102 |
|
\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})} |
| 123 |
% This allows hyperlinks in PDF |
% This allows hyperlinks in PDF |
| 124 |
% hyperref package and colors for hyperref package |
% hyperref package and colors for hyperref package |
| 125 |
\usepackage{color} |
\usepackage{color} |
| 126 |
\usepackage[dvips]{hyperref} |
\usepackage{hyperref} |
| 127 |
|
%\usepackage[dvips] |
| 128 |
\definecolor{darkgreen}{rgb}{0,0.4,0} |
\definecolor{darkgreen}{rgb}{0,0.4,0} |
| 129 |
\definecolor{darkblue}{rgb}{0,0,0.4} |
\definecolor{darkblue}{rgb}{0,0,0.4} |
| 130 |
\definecolor{darkred}{rgb}{0.5,0,0} |
\definecolor{darkred}{rgb}{0.5,0,0} |
| 139 |
non-hydrostatic, finite volume, inverse methods, adjoint method} |
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} |
\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 |
| 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 |
%\pagebreak |
| 217 |
|
|
| 218 |
% Section: Getting started |
% Section: Getting started |
| 219 |
\input{part3/part3} |
\input{s_getstarted/text/top_section} |
| 220 |
%\pagebreak |
%\pagebreak |
| 221 |
|
|
| 222 |
% Section: Software Architecture |
% Section: Software Architecture |
| 223 |
\input{part4/part4} |
\input{s_software/text/top_section} |
| 224 |
%\pagebreak |
%\pagebreak |
| 225 |
|
|
| 226 |
|
|
| 227 |
%\part{Adjoint of the MIT GCM} |
%\part{Adjoint of the MIT GCM} |
| 228 |
|
|
| 229 |
% Section: Automatic Differentiation |
% Section: Automatic Differentiation |
| 230 |
\input{part5/part5} |
\input{s_autodiff/text/top_section} |
| 231 |
%\pagebreak |
%\pagebreak |
| 232 |
|
|
| 233 |
|
|
| 234 |
%\part{Additional features} |
%\part{Additional features} |
| 235 |
|
|
| 236 |
% Section: Physical Packages |
% Section: Physical Packages |
| 237 |
\input{part6/part6} |
\input{s_phys_pkgs/text/top_section} |
| 238 |
%\pagebreak |
%\pagebreak |
| 239 |
|
|
| 240 |
% Section: Diagnostics |
% Section: Pre-processing and Post-processing Tools |
| 241 |
\input{part7/part7} |
\input{s_outp_pkgs/text/top_section} |
| 242 |
%\pagebreak |
%\pagebreak |
| 243 |
|
|
| 244 |
% Section: ECCO |
% Section: ECCO |
| 245 |
\input{part8/part8} |
\input{s_ecco/text/top_section} |
| 246 |
|
%\pagebreak |
| 247 |
|
|
| 248 |
|
% Section: Under Development |
| 249 |
|
\input{s_under_dvlp/text/top_section} |
| 250 |
|
|
| 251 |
|
% Section: Model Uses |
| 252 |
|
\input{model_uses} |
| 253 |
%\pagebreak |
%\pagebreak |
| 254 |
|
|
| 255 |
% Section: References: |
% Section: References: |
| 256 |
%\markboth{BIBLIOGRAPHY}{BIBLIOGRAPHY} |
%\markboth{BIBLIOGRAPHY}{BIBLIOGRAPHY} |
| 257 |
\addcontentsline{toc}{chapter}{BIBLIOGRAPHY} |
\addcontentsline{toc}{chapter}{BIBLIOGRAPHY} |
| 258 |
%aja%\bibliography{\BIBPATH/manual_references} |
%aja%\bibliography{\BIBPATH/manual_references} |
| 259 |
\bibliography{manual_references} |
\bibliography{manual_references,baylor_biblio} |
| 260 |
|
|
| 261 |
\end{document} |
\end{document} |
Parent Directory
| 
Revision Log
| 
Revision Graph
| 
Patch