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Revision 1.45 - (hide annotations) (download) (as text)
Fri Aug 27 18:22:27 2010 UTC (13 years, 7 months ago) by jmc
Branch: MAIN
Changes since 1.44: +11 -7 lines
File MIME type: application/x-tex
separate "examples" from "getting started" section.

1 jmc 1.45 % $Header: /u/gcmpack/manual/manual.tex,v 1.44 2010/08/27 13:31:32 jmc Exp $
2 adcroft 1.2 % $Name: $
3 adcroft 1.1
4 edhill 1.26 \documentclass[10pt]{book}
5 adcroft 1.1
6 adcroft 1.8 %To help cross-reference
7     %\usepackage{showlabels}
8    
9     %aja%\usepackage{amsfonts}
10 adcroft 1.1 \usepackage{amsmath}
11 cnh 1.7 \usepackage{html}
12 cnh 1.19 \usepackage{hthtml}
13 adcroft 1.10 \usepackage{graphicx}
14 molod 1.34 \usepackage{rotating}
15 adcroft 1.8
16 cnh 1.33 % CNH playing around with page widths
17     \usepackage{anysize}
18    
19 adcroft 1.8 %cnh%\usepackage{array}
20     %cnh%\usepackage{multirow}
21 cnh 1.12
22 edhill 1.16 %eh3 Commands to reference either files or symbols within the "HTML-ized"
23     %eh3 ("vdb") code.
24     %eh3
25 afe 1.23 %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 cnh 1.38 \newcommand{\myhref}[2]{\htmladdnormallink{#2}{#1}}
29 afe 1.22
30     % afe Commands to standardize typesetting
31 afe 1.23 \newcommand{\file}[1]{\texttt{#1}}
32     \newcommand{\sectiontitle}[1]{\textsl{#1}}
33     \newcommand{\code}[1]{\texttt{#1}}
34 afe 1.22
35 edhill 1.25 %% EH3 : try out the epsfig package
36 edhill 1.18 \usepackage[dvips]{epsfig}
37     \def\scalefig#1{\epsfxsize #1\textwidth}
38 edhill 1.25
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 afe 1.28 %\includecomment{versionprivate}
55     \excludecomment{versionprivate}
56 edhill 1.25
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 cnh 1.12
71 adcroft 1.8
72     %ph%\usepackage{epsfig}
73     %ph%\usepackage{psfrag}
74     %ph%\usepackage{oldgerm}
75    
76 adcroft 1.2 % I commented the following because it introduced excessive white space
77 adcroft 1.8 %aja%\usepackage{palatcm} % better PDF
78 adcroft 1.1
79     % page headers and footers
80 adcroft 1.8 %cnh%\usepackage{fancyhdr}
81 adcroft 1.2 %\pagestyle{fancy}
82 adcroft 1.8 %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 adcroft 1.1
91 heimbach 1.5 % bibtex stuff
92 adcroft 1.10 %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 jmc 1.32 %\bibliographystyle{plain}
99     %-jmc: try agu bib-style (give author names & year instead of just a number)
100 cnh 1.38 %% \usepackage[square]
101 jmc 1.32 \usepackage[square]{natbib}
102     \bibliographystyle{agu}
103 cnh 1.38 %% \bibliographystyle{aguurl}
104 heimbach 1.5
105 adcroft 1.1 % referencing
106 adcroft 1.8 %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 adcroft 1.1
113     % stuff for psfrag
114 adcroft 1.8 %ph%\newcommand{\textinfigure}[1]{{\footnotesize\textbf{\textsf{#1}}}}
115     %ph%\newcommand{\mathinfigure}[1]{\small\ensuremath{{#1}}}
116 adcroft 1.1
117 adcroft 1.3 % This allows numbering of subsubsections
118     \setcounter{secnumdepth}{3}
119     % This changes the the chapter title
120     %\renewcommand{\chaptername}{Section}
121    
122 adcroft 1.11
123     % This allows hyperlinks in PDF
124     % hyperref package and colors for hyperref package
125     \usepackage{color}
126 cnh 1.31 \usepackage{hyperref}
127 cnh 1.29 %\usepackage[dvips]
128 adcroft 1.11 \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 edhill 1.15 pdfauthor={MITgcm-support@mitgcm.org},
138 adcroft 1.11 pdfkeywords={oceanography, ocean model, general circulation model,
139     non-hydrostatic, finite volume, inverse methods, adjoint method}
140     }
141 molod 1.17
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 edhill 1.36 % 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 adcroft 1.1
175 edhill 1.40 % Definitions from EH3:
176     \def\CC{C\raise.3ex\hbox{{\footnotesize
177     +}}\raise.3ex\hbox{\footnotesize +}\ }
178    
179 adcroft 1.1 \begin{document}
180 cnh 1.9
181     \bodytext{bgcolor="#FFFFFFFF"}
182 adcroft 1.1
183 edhill 1.37 \title{ \textsc{MITgcm User Manual} }
184    
185     \author{
186 jmc 1.42 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 edhill 1.37 \\
193     \\
194     \\
195     MIT Department of EAPS \\
196     77 Massachusetts Ave. \\
197     Cambridge, MA \ 02139-4307
198     }
199    
200 jmc 1.41 %\date{August 19, 2004}
201     \date{\today}
202 edhill 1.37
203     \maketitle
204    
205 adcroft 1.1 \tableofcontents
206 adcroft 1.10 %\pagebreak
207 adcroft 1.1
208 adcroft 1.10 %\part{MIT GCM basics}
209 adcroft 1.3
210 jmc 1.45 % Section: Overview of MITgcm
211 jmc 1.44 \input{s_overview/text/top_section}
212 adcroft 1.8 %\pagebreak
213 adcroft 1.1
214 adcroft 1.3 % Section: Discretization and Algorithm
215 jmc 1.44 \input{s_algorithm/text/top_section}
216 adcroft 1.8 %\pagebreak
217 adcroft 1.1
218 jmc 1.45 % Section: Getting started with MITgcm
219 jmc 1.44 \input{s_getstarted/text/top_section}
220 adcroft 1.8 %\pagebreak
221 adcroft 1.1
222 jmc 1.45 % Section: Model Example <- not yet a section
223     \input{s_examples/text/top_section}
224     %\pagebreak
225    
226 adcroft 1.3 % Section: Software Architecture
227 jmc 1.44 \input{s_software/text/top_section}
228 adcroft 1.8 %\pagebreak
229 adcroft 1.1
230 adcroft 1.3
231 adcroft 1.10 %\part{Adjoint of the MIT GCM}
232 adcroft 1.3
233     % Section: Automatic Differentiation
234 jmc 1.44 \input{s_autodiff/text/top_section}
235 adcroft 1.8 %\pagebreak
236 adcroft 1.1
237 adcroft 1.3
238 adcroft 1.10 %\part{Additional features}
239 adcroft 1.3
240 jmc 1.45 % Section: Physical Parameterization - Packages I
241 jmc 1.44 \input{s_phys_pkgs/text/top_section}
242 adcroft 1.8 %\pagebreak
243 adcroft 1.1
244 jmc 1.45 % Section: Diagnostics and I/O - Packages II, and Post-Processing Utilities
245 jmc 1.44 \input{s_outp_pkgs/text/top_section}
246 adcroft 1.14 %\pagebreak
247    
248 jmc 1.45 % Section: Interface with ECCO
249 jmc 1.44 \input{s_ecco/text/top_section}
250 edhill 1.24 %\pagebreak
251    
252 jmc 1.43 % Section: Under Development
253 jmc 1.44 \input{s_under_dvlp/text/top_section}
254 jmc 1.43
255 jmc 1.45 % Section: Previous applications of MITgcm
256 cnh 1.39 \input{model_uses}
257 adcroft 1.8 %\pagebreak
258 adcroft 1.1
259 heimbach 1.5 % Section: References:
260 adcroft 1.10 %\markboth{BIBLIOGRAPHY}{BIBLIOGRAPHY}
261 heimbach 1.6 \addcontentsline{toc}{chapter}{BIBLIOGRAPHY}
262 adcroft 1.10 %aja%\bibliography{\BIBPATH/manual_references}
263 edhill 1.35 \bibliography{manual_references,baylor_biblio}
264 heimbach 1.6
265 adcroft 1.1 \end{document}

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