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Revision 1.36 - (hide annotations) (download) (as text)
Fri Dec 16 06:26:09 2005 UTC (14 years ago) by edhill
Branch: MAIN
Changes since 1.35: +18 -1 lines
File MIME type: application/x-tex
 o after 4+hrs of fighting, Baylor's discussion of the nonlinear
   viscosity syntax now works with the latex2html translator
   - people should pay very close attention to LaTeX macros that *they*
     create, particularly the {}-protection of the macro arguments and
     possible name collisions
   - putting too much junk in one equation or eqnarray may look sexy
     in a PDF format but it can be murder for latex2html

1 edhill 1.36 % $Header: /u/gcmpack/manual/manual.tex,v 1.35 2005/10/05 19:52:47 edhill 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 afe 1.22
29     % afe Commands to standardize typesetting
30 afe 1.23 \newcommand{\file}[1]{\texttt{#1}}
31     \newcommand{\sectiontitle}[1]{\textsl{#1}}
32     \newcommand{\code}[1]{\texttt{#1}}
33 afe 1.22
34 edhill 1.25 %% EH3 : try out the epsfig package
35 edhill 1.18 \usepackage[dvips]{epsfig}
36     \def\scalefig#1{\epsfxsize #1\textwidth}
37 edhill 1.25
38     %EH3% ==========================================================
39     %EH3% *** PRIVATE SECTIONS ****** PRIVATE SECTIONS ***
40     %EH3%
41     %EH3% Directions: To build the ``private'' or ``local-only''
42     %EH3% version of this manual, then edit the following so
43     %EH3% they appear as:
44     %EH3%
45     %EH3% % \includecomment{versionprivate}
46     %EH3% \excludecoment{versionprivate}
47     %EH3%
48     %EH3% The default is to include everything which is:
49     %EH3%
50     %EH3% \includecomment{versionprivate}
51     %EH3% % \excludecoment{versionprivate}
52    
53 afe 1.28 %\includecomment{versionprivate}
54     \excludecomment{versionprivate}
55 edhill 1.25
56     %EH3%
57     %EH3% To use this comment, simply bracket any part of the
58     %EH3% manual with two lines that contain ONLY the following
59     %EH3% pair:
60     %EH3%
61     %EH3% \begin{versionprivate}
62     %EH3% \end{versionprivate}
63     %EH3%
64     %EH3% with NO additional comments or other commands on the
65     %EH3% lines containing the \begin{...}\end{...} statements.
66     %EH3%
67     %EH3% *** PRIVATE SECTIONS ****** PRIVATE SECTIONS ***
68     %EH3% ==========================================================
69 cnh 1.12
70 adcroft 1.8
71     %ph%\usepackage{epsfig}
72     %ph%\usepackage{psfrag}
73     %ph%\usepackage{oldgerm}
74    
75 adcroft 1.2 % I commented the following because it introduced excessive white space
76 adcroft 1.8 %aja%\usepackage{palatcm} % better PDF
77 adcroft 1.1
78     % page headers and footers
79 adcroft 1.8 %cnh%\usepackage{fancyhdr}
80 adcroft 1.2 %\pagestyle{fancy}
81 adcroft 1.8 %cnh%\fancyhead{}
82     %cnh%\fancyhead[LO]{\slshape \rightmark}
83     %cnh%\fancyhead[RE]{\slshape \leftmark}
84     %cnh%\fancyhead[RO,LE]{\thepage}
85     %cnh%\fancyfoot[CO,CE]{\today}
86     %cnh%\fancyfoot[RO,LE]{ }
87     %cnh%\renewcommand{\headrulewidth}{0.4pt}
88     %cnh%\renewcommand{\footrulewidth}{0.4pt}
89 adcroft 1.1
90 heimbach 1.5 % bibtex stuff
91 adcroft 1.10 %aja%\newcommand{\BIBPATH}{.}
92     %aja%\usepackage{natbib}
93     %aja%\bibliographystyle{\BIBPATH/jmr_my}
94     %aja%\gdef\harvardleft{[}
95     %aja%\gdef\harvardright{]}
96     %aja%\bibpunct{[}{]}{,}{a}{}{,}
97 jmc 1.32 %\bibliographystyle{plain}
98     %-jmc: try agu bib-style (give author names & year instead of just a number)
99     \usepackage[square]{natbib}
100     \bibliographystyle{agu}
101 heimbach 1.5
102 adcroft 1.1 % referencing
103 adcroft 1.8 %ph%\newcommand{\refequ}[1]{equation (\ref{equ:#1})}
104     %ph%\newcommand{\refequbig}[1]{Equation (\ref{equ:#1})}
105     %ph%\newcommand{\reftab}[1]{Tab.~\ref{tab:#1}}
106     %ph%\newcommand{\reftabno}[1]{\ref{tab:#1}}
107     %ph%\newcommand{\reffig}[1]{Fig.~\ref{fig:#1}}
108     %ph%\newcommand{\reffigno}[1]{\ref{fig:#1}}
109 adcroft 1.1
110     % stuff for psfrag
111 adcroft 1.8 %ph%\newcommand{\textinfigure}[1]{{\footnotesize\textbf{\textsf{#1}}}}
112     %ph%\newcommand{\mathinfigure}[1]{\small\ensuremath{{#1}}}
113 adcroft 1.1
114 adcroft 1.3 % This allows numbering of subsubsections
115     \setcounter{secnumdepth}{3}
116     % This changes the the chapter title
117     %\renewcommand{\chaptername}{Section}
118    
119 adcroft 1.11
120     % This allows hyperlinks in PDF
121     % hyperref package and colors for hyperref package
122     \usepackage{color}
123 cnh 1.31 \usepackage{hyperref}
124 cnh 1.29 %\usepackage[dvips]
125 adcroft 1.11 \definecolor{darkgreen}{rgb}{0,0.4,0}
126     \definecolor{darkblue}{rgb}{0,0,0.4}
127     \definecolor{darkred}{rgb}{0.5,0,0}
128     \hypersetup{breaklinks=true,
129     colorlinks=true,
130     linkcolor=darkgreen,
131     citecolor=darkblue,
132     pagecolor=darkred,
133     pdftitle={MITgcm Release 1 Documentation},
134 edhill 1.15 pdfauthor={MITgcm-support@mitgcm.org},
135 adcroft 1.11 pdfkeywords={oceanography, ocean model, general circulation model,
136     non-hydrostatic, finite volume, inverse methods, adjoint method}
137     }
138 molod 1.17
139     % Some definitions (AMM)
140     \def\p#1{{\partial \over {\partial #1}}}
141     \def\pp#1#2{{\partial #1 \over {\partial #2}}}
142     \def\dd#1#2{{d #1 \over {d #2}}}
143     \def\bq{\begin{equation}}
144     \def\bqa{\begin{eqnarray}}
145     \def\eq{\end{equation}}
146     \def\eqa{\end{eqnarray}}
147    
148     \def\h{ {1\over2} }
149     \def\txt{\mbox{$2^\circ$ x $2.5^\circ \,$}}
150     \def\fxf{\mbox{$4^\circ$ x $5^\circ \,$}}
151    
152     \def\blankpage{ \vspace*{\fill} \vspace{5in} \vfill \newpage}
153    
154 edhill 1.36 % Some definitions modified from the ones provided by Baylor
155     \def\BFKav#1{\overline{#1}}
156     \def\BFKpd#1#2{{\frac{\partial{#2}}{\partial{#1}}}}
157     \def\BFKpds#1#2{{\frac{\partial^2{#2}}{{\partial{#1}}^2}}}
158     \def\BFKDt#1{\frac{D{#1}}{Dt}}
159     \def\BFKaDt#1{\frac{\BFKav D{#1}}{\BFKav{Dt}}}
160     \def\BFKd#1{{\,\rm d#1}}
161     \def\BFKRo{{\rm Ro}}
162     \def\BFKRe{{\rm Re}}
163     \def\BFKFr{{\rm Fr}}
164     \def\BFKPr{{\rm Pr}}
165     \def\BFKMr{{M_{Ro}}}
166     \def\BFKtu{{\tilde u}}
167     \def\BFKtv{{\tilde v}}
168     \def\BFKatu{{\tilde {\BFKav u}}}
169     \def\BFKatv{{\tilde {\BFKav v}}}
170     \def\BFKlesssim{{<\atop\sim}}
171 adcroft 1.1
172     \begin{document}
173 cnh 1.9
174     \bodytext{bgcolor="#FFFFFFFF"}
175 adcroft 1.1
176     \tableofcontents
177 adcroft 1.10 %\pagebreak
178 adcroft 1.1
179 adcroft 1.10 %\part{MIT GCM basics}
180 adcroft 1.3
181     % Section: Overview
182 adcroft 1.1 \input{part1/part1}
183 adcroft 1.8 %\pagebreak
184 adcroft 1.1
185 adcroft 1.3 % Section: Discretization and Algorithm
186 adcroft 1.1 \input{part2/part2}
187 adcroft 1.8 %\pagebreak
188 adcroft 1.1
189 adcroft 1.3 % Section: Getting started
190 adcroft 1.1 \input{part3/part3}
191 adcroft 1.8 %\pagebreak
192 adcroft 1.1
193 adcroft 1.3 % Section: Software Architecture
194 adcroft 1.1 \input{part4/part4}
195 adcroft 1.8 %\pagebreak
196 adcroft 1.1
197 adcroft 1.3
198 adcroft 1.10 %\part{Adjoint of the MIT GCM}
199 adcroft 1.3
200     % Section: Automatic Differentiation
201 adcroft 1.1 \input{part5/part5}
202 adcroft 1.8 %\pagebreak
203 adcroft 1.1
204 adcroft 1.3
205 adcroft 1.10 %\part{Additional features}
206 adcroft 1.3
207     % Section: Physical Packages
208 adcroft 1.1 \input{part6/part6}
209 adcroft 1.8 %\pagebreak
210 adcroft 1.1
211 molod 1.30 % Section: Pre-processing and Post-processing Tools
212 adcroft 1.1 \input{part7/part7}
213 adcroft 1.14 %\pagebreak
214    
215     % Section: ECCO
216     \input{part8/part8}
217 edhill 1.24 %\pagebreak
218    
219     % Section: Model Uses
220     \input{model_uses}
221 adcroft 1.8 %\pagebreak
222 adcroft 1.1
223 heimbach 1.5 % Section: References:
224 adcroft 1.10 %\markboth{BIBLIOGRAPHY}{BIBLIOGRAPHY}
225 heimbach 1.6 \addcontentsline{toc}{chapter}{BIBLIOGRAPHY}
226 adcroft 1.10 %aja%\bibliography{\BIBPATH/manual_references}
227 edhill 1.35 \bibliography{manual_references,baylor_biblio}
228 heimbach 1.6
229 adcroft 1.1 \end{document}

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