/[MITgcm]/manual/manual.tex
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revision 1.10 by adcroft, Tue Nov 13 15:00:00 2001 UTC revision 1.36 by edhill, Fri Dec 16 06:26:09 2005 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"}
# Line 99  Line 208 
208  \input{part6/part6}  \input{part6/part6}
209  %\pagebreak  %\pagebreak
210    
211  % Section: Diagnostics  % Section: Pre-processing and Post-processing Tools
212  \input{part7/part7}  \input{part7/part7}
213  %\pagebreak  %\pagebreak
214    
215  % Section: ECCO Interface  % Section: ECCO
216  \input{part8/part8}  \input{part8/part8}
217  %\pagebreak  %\pagebreak
218    
219    % Section: Model Uses
220    \input{model_uses}
221    %\pagebreak
222    
223  % Section: References:  % Section: References:
224  %\markboth{BIBLIOGRAPHY}{BIBLIOGRAPHY}  %\markboth{BIBLIOGRAPHY}{BIBLIOGRAPHY}
225  \addcontentsline{toc}{chapter}{BIBLIOGRAPHY}  \addcontentsline{toc}{chapter}{BIBLIOGRAPHY}
226  %aja%\bibliography{\BIBPATH/manual_references}  %aja%\bibliography{\BIBPATH/manual_references}
227  \bibliography{manual_references}  \bibliography{manual_references,baylor_biblio}
228    
229  \end{document}  \end{document}
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