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revision 1.10 by adcroft, Tue Nov 13 15:00:00 2001 UTC revision 1.42 by jmc, Fri Mar 7 18:02:53 2008 UTC
# Line 1  Line 1 
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}
# Line 9  Line 9 
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    %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}  %ph%\usepackage{epsfig}
73  %ph%\usepackage{psfrag}  %ph%\usepackage{psfrag}
74  %ph%\usepackage{oldgerm}  %ph%\usepackage{oldgerm}
# Line 40  Line 95 
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})}
# Line 60  Line 120 
120  %\renewcommand{\chaptername}{Section}  %\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}  \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    
# Line 99  Line 237 
237  \input{part6/part6}  \input{part6/part6}
238  %\pagebreak  %\pagebreak
239    
240  % Section: Diagnostics  % Section: Pre-processing and Post-processing Tools
241  \input{part7/part7}  \input{part7/part7}
242  %\pagebreak  %\pagebreak
243    
244  % Section: ECCO Interface  % Section: ECCO
245  \input{part8/part8}  \input{part8/part8}
246  %\pagebreak  %\pagebreak
247    
248    % Section: Model Uses
249    \input{model_uses}
250    %\pagebreak
251    
252  % Section: References:  % Section: References:
253  %\markboth{BIBLIOGRAPHY}{BIBLIOGRAPHY}  %\markboth{BIBLIOGRAPHY}{BIBLIOGRAPHY}
254  \addcontentsline{toc}{chapter}{BIBLIOGRAPHY}  \addcontentsline{toc}{chapter}{BIBLIOGRAPHY}
255  %aja%\bibliography{\BIBPATH/manual_references}  %aja%\bibliography{\BIBPATH/manual_references}
256  \bibliography{manual_references}  \bibliography{manual_references,baylor_biblio}
257    
258  \end{document}  \end{document}
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