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revision 1.10 by adcroft, Tue Nov 13 15:00:00 2001 UTC revision 1.37 by edhill, Fri Apr 7 15:40:07 2006 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    
29    % afe  Commands to standardize typesetting
30    \newcommand{\file}[1]{\texttt{#1}}
31    \newcommand{\sectiontitle}[1]{\textsl{#1}}
32    \newcommand{\code}[1]{\texttt{#1}}
33    
34    %%  EH3 : try out the epsfig package
35    \usepackage[dvips]{epsfig}
36    \def\scalefig#1{\epsfxsize #1\textwidth}
37    
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    %\includecomment{versionprivate}
54    \excludecomment{versionprivate}
55    
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    
70    
71  %ph%\usepackage{epsfig}  %ph%\usepackage{epsfig}
72  %ph%\usepackage{psfrag}  %ph%\usepackage{psfrag}
73  %ph%\usepackage{oldgerm}  %ph%\usepackage{oldgerm}
# Line 40  Line 94 
94  %aja%\gdef\harvardleft{[}  %aja%\gdef\harvardleft{[}
95  %aja%\gdef\harvardright{]}  %aja%\gdef\harvardright{]}
96  %aja%\bibpunct{[}{]}{,}{a}{}{,}  %aja%\bibpunct{[}{]}{,}{a}{}{,}
97  \bibliographystyle{plain}  %\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    
102  % referencing  % referencing
103  %ph%\newcommand{\refequ}[1]{equation (\ref{equ:#1})}  %ph%\newcommand{\refequ}[1]{equation (\ref{equ:#1})}
# Line 60  Line 117 
117  %\renewcommand{\chaptername}{Section}  %\renewcommand{\chaptername}{Section}
118    
119    
120    % This allows hyperlinks in PDF
121    % hyperref package and colors for hyperref package
122    \usepackage{color}
123    \usepackage{hyperref}
124    %\usepackage[dvips]
125    \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      pdfauthor={MITgcm-support@mitgcm.org},
135      pdfkeywords={oceanography, ocean model, general circulation model,
136        non-hydrostatic, finite volume, inverse methods, adjoint method}
137      }
138    
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    % 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    
172  \begin{document}  \begin{document}
173    
174  \bodytext{bgcolor="#FFFFFFFF"}  \bodytext{bgcolor="#FFFFFFFF"}
175    
176    \title{ \textsc{MITgcm User Manual} }
177    
178    \author{
179      John Marshall \and Alistair Adcroft \and Jean-Michel Campin
180      \and Patrick Heimbach \and Andrea Molod \and Stephanie Dutkiewicz
181      \and Helen Hill \and Martin Losch \and Baylor Fox-Kemper
182      \and Dimitris Menemenlis \and David Ferreira \and Ed Hill
183      \and Mick Follows \and Chris Hill \and Constantinos Evangelinos
184      \and Gael Forget
185      \\
186      \\
187      \\
188      MIT Department of EAPS  \\
189      77 Massachusetts Ave. \\
190      Cambridge, MA \ 02139-4307
191    }
192    
193    \date{August 19, 2004}
194    
195    \maketitle
196    
197  \tableofcontents  \tableofcontents
198  %\pagebreak  %\pagebreak
199    
# Line 99  Line 229 
229  \input{part6/part6}  \input{part6/part6}
230  %\pagebreak  %\pagebreak
231    
232  % Section: Diagnostics  % Section: Pre-processing and Post-processing Tools
233  \input{part7/part7}  \input{part7/part7}
234  %\pagebreak  %\pagebreak
235    
236  % Section: ECCO Interface  % Section: ECCO
237  \input{part8/part8}  \input{part8/part8}
238  %\pagebreak  %\pagebreak
239    
240    % Section: Model Uses
241    \input{model_uses}
242    %\pagebreak
243    
244  % Section: References:  % Section: References:
245  %\markboth{BIBLIOGRAPHY}{BIBLIOGRAPHY}  %\markboth{BIBLIOGRAPHY}{BIBLIOGRAPHY}
246  \addcontentsline{toc}{chapter}{BIBLIOGRAPHY}  \addcontentsline{toc}{chapter}{BIBLIOGRAPHY}
247  %aja%\bibliography{\BIBPATH/manual_references}  %aja%\bibliography{\BIBPATH/manual_references}
248  \bibliography{manual_references}  \bibliography{manual_references,baylor_biblio}
249    
250  \end{document}  \end{document}
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