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revision 1.14 by adcroft, Wed Apr 24 20:12:36 2002 UTC revision 1.39 by cnh, Wed Jun 28 21:20:41 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  % 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}
# Line 51  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 74  Line 123 
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}
# Line 84  Line 134 
134    citecolor=darkblue,    citecolor=darkblue,
135    pagecolor=darkred,    pagecolor=darkred,
136    pdftitle={MITgcm Release 1 Documentation},    pdftitle={MITgcm Release 1 Documentation},
137    pdfauthor={support@mitgcm.org},    pdfauthor={MITgcm-support@mitgcm.org},
138    pdfkeywords={oceanography, ocean model, general circulation model,    pdfkeywords={oceanography, ocean model, general circulation model,
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  \begin{document}  \begin{document}
176    
177  \bodytext{bgcolor="#FFFFFFFF"}  \bodytext{bgcolor="#FFFFFFFF"}
178    
179    \title{ \textsc{MITgcm User Manual} }
180    
181    \author{
182      John Marshall \and Alistair Adcroft \and Jean-Michel Campin
183      \and Patrick Heimbach \and Andrea Molod \and Stephanie Dutkiewicz
184      \and Helen Hill \and Martin Losch \and Baylor Fox-Kemper
185      \and Dimitris Menemenlis \and David Ferreira \and Ed Hill
186      \and Mick Follows \and Chris Hill \and Constantinos Evangelinos
187      \and Gael Forget
188      \\
189      \\
190      \\
191      MIT Department of EAPS  \\
192      77 Massachusetts Ave. \\
193      Cambridge, MA \ 02139-4307
194    }
195    
196    \date{August 19, 2004}
197    
198    \maketitle
199    
200  \tableofcontents  \tableofcontents
201  %\pagebreak  %\pagebreak
202    
# Line 128  Line 232 
232  \input{part6/part6}  \input{part6/part6}
233  %\pagebreak  %\pagebreak
234    
235  % Section: Diagnostics  % Section: Pre-processing and Post-processing Tools
236  \input{part7/part7}  \input{part7/part7}
237  %\pagebreak  %\pagebreak
238    
# Line 136  Line 240 
240  \input{part8/part8}  \input{part8/part8}
241  %\pagebreak  %\pagebreak
242    
243    % Section: Model Uses
244    \input{model_uses}
245    %\pagebreak
246    
247  % Section: References:  % Section: References:
248  %\markboth{BIBLIOGRAPHY}{BIBLIOGRAPHY}  %\markboth{BIBLIOGRAPHY}{BIBLIOGRAPHY}
249  \addcontentsline{toc}{chapter}{BIBLIOGRAPHY}  \addcontentsline{toc}{chapter}{BIBLIOGRAPHY}
250  %aja%\bibliography{\BIBPATH/manual_references}  %aja%\bibliography{\BIBPATH/manual_references}
251  \bibliography{manual_references}  \bibliography{manual_references,baylor_biblio}
252    
253  \end{document}  \end{document}
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