/[MITgcm]/manual/manual.tex
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revision 1.1 by adcroft, Wed Aug 8 16:15:12 2001 UTC revision 1.23 by afe, Tue Mar 16 15:43:05 2004 UTC
# Line 3  Line 3 
3    
4  \documentclass[12pt]{book}  \documentclass[12pt]{book}
5    
6  \usepackage{amsfonts}  %To help cross-reference
7    %\usepackage{showlabels}
8    
9    %aja%\usepackage{amsfonts}
10  \usepackage{amsmath}  \usepackage{amsmath}
11  \usepackage{html}  \usepackage{html}
12  \usepackage{epsfig}  \usepackage{hthtml}
13  \usepackage{graphics,subfigure}  \usepackage{graphicx}
14  \usepackage{array}  
15  \usepackage{multirow}  %cnh%\usepackage{array}
16  \usepackage{fancyhdr}  %cnh%\usepackage{multirow}
17  \usepackage{psfrag}  
18  \usepackage{oldgerm}  %eh3  Commands to reference either files or symbols within the "HTML-ized"
19  \usepackage{palatcm}              % better PDF  %eh3  ("vdb") code.
20    %eh3  
21    %afe seems like these need to be long, sorry
22    \newcommand{\varlink}[2]{\htmladdnormallink{\tt #1}{../code_reference/vdb/byname/#2.html}}
23    \newcommand{\filelink}[2]{\htmladdnormallink{\bf \tt #1}{../code_reference/vdb/byname/#2.html}}
24    
25    % afe  Commands to standardize typesetting
26    \newcommand{\file}[1]{\texttt{#1}}
27    
28    \newcommand{\sectiontitle}[1]{\textsl{#1}}
29    
30    \newcommand{\code}[1]{\texttt{#1}}
31    
32    
33    
34    %eh3 try out the epsfig package
35    \usepackage[dvips]{epsfig}
36    \def\scalefig#1{\epsfxsize #1\textwidth}
37    
38    
39    %ph%\usepackage{epsfig}
40    %ph%\usepackage{psfrag}
41    %ph%\usepackage{oldgerm}
42    
43    % I commented the following because it introduced excessive white space
44    %aja%\usepackage{palatcm}              % better PDF
45    
46  % page headers and footers  % page headers and footers
47  \pagestyle{fancy}  %cnh%\usepackage{fancyhdr}
48  \fancyhead{}  %\pagestyle{fancy}
49  \fancyhead[LO]{\slshape \rightmark}  %cnh%\fancyhead{}
50  \fancyhead[RE]{\slshape \leftmark}  %cnh%\fancyhead[LO]{\slshape \rightmark}
51  \fancyhead[RO,LE]{\thepage}  %cnh%\fancyhead[RE]{\slshape \leftmark}
52  \fancyfoot[CO,CE]{\today}  %cnh%\fancyhead[RO,LE]{\thepage}
53  \fancyfoot[RO,LE]{ }  %cnh%\fancyfoot[CO,CE]{\today}
54  \renewcommand{\headrulewidth}{0.4pt}  %cnh%\fancyfoot[RO,LE]{ }
55  \renewcommand{\footrulewidth}{0.4pt}  %cnh%\renewcommand{\headrulewidth}{0.4pt}
56    %cnh%\renewcommand{\footrulewidth}{0.4pt}
57    
58    % bibtex stuff
59    %aja%\newcommand{\BIBPATH}{.}
60    %aja%\usepackage{natbib}
61    %aja%\bibliographystyle{\BIBPATH/jmr_my}
62    %aja%\gdef\harvardleft{[}
63    %aja%\gdef\harvardright{]}
64    %aja%\bibpunct{[}{]}{,}{a}{}{,}
65    \bibliographystyle{plain}
66    
67  % referencing  % referencing
68  \newcommand{\refequ}[1]{equation (\ref{equ:#1})}  %ph%\newcommand{\refequ}[1]{equation (\ref{equ:#1})}
69  \newcommand{\refequbig}[1]{Equation (\ref{equ:#1})}  %ph%\newcommand{\refequbig}[1]{Equation (\ref{equ:#1})}
70  \newcommand{\reftab}[1]{Tab.~\ref{tab:#1}}  %ph%\newcommand{\reftab}[1]{Tab.~\ref{tab:#1}}
71  \newcommand{\reftabno}[1]{\ref{tab:#1}}  %ph%\newcommand{\reftabno}[1]{\ref{tab:#1}}
72  \newcommand{\reffig}[1]{Fig.~\ref{fig:#1}}  %ph%\newcommand{\reffig}[1]{Fig.~\ref{fig:#1}}
73  \newcommand{\reffigno}[1]{\ref{fig:#1}}  %ph%\newcommand{\reffigno}[1]{\ref{fig:#1}}
74    
75  % stuff for psfrag  % stuff for psfrag
76  \newcommand{\textinfigure}[1]{{\footnotesize\textbf{\textsf{#1}}}}  %ph%\newcommand{\textinfigure}[1]{{\footnotesize\textbf{\textsf{#1}}}}
77  \newcommand{\mathinfigure}[1]{\small\ensuremath{{#1}}}  %ph%\newcommand{\mathinfigure}[1]{\small\ensuremath{{#1}}}
78    
79    % This allows numbering of subsubsections
80    \setcounter{secnumdepth}{3}
81    % This changes the the chapter title
82    %\renewcommand{\chaptername}{Section}
83    
84    
85    % This allows hyperlinks in PDF
86    % hyperref package and colors for hyperref package
87    \usepackage{color}
88    \usepackage[dvips]{hyperref}
89    \definecolor{darkgreen}{rgb}{0,0.4,0}
90    \definecolor{darkblue}{rgb}{0,0,0.4}
91    \definecolor{darkred}{rgb}{0.5,0,0}
92    \hypersetup{breaklinks=true,
93      colorlinks=true,
94      linkcolor=darkgreen,
95      citecolor=darkblue,
96      pagecolor=darkred,
97      pdftitle={MITgcm Release 1 Documentation},
98      pdfauthor={MITgcm-support@mitgcm.org},
99      pdfkeywords={oceanography, ocean model, general circulation model,
100        non-hydrostatic, finite volume, inverse methods, adjoint method}
101      }
102    
103    % Some definitions (AMM)
104    \def\p#1{{\partial \over {\partial #1}}}
105    \def\pp#1#2{{\partial #1 \over {\partial #2}}}
106    \def\dd#1#2{{d #1 \over {d #2}}}
107    \def\bq{\begin{equation}}
108    \def\bqa{\begin{eqnarray}}
109    \def\eq{\end{equation}}
110    \def\eqa{\end{eqnarray}}
111    
112    \def\h{ {1\over2} }
113    \def\txt{\mbox{$2^\circ$ x $2.5^\circ \,$}}
114    \def\fxf{\mbox{$4^\circ$ x $5^\circ \,$}}
115    
116    \def\blankpage{ \vspace*{\fill} \vspace{5in} \vfill \newpage}
117    
118    
119  \begin{document}  \begin{document}
120    
121    \bodytext{bgcolor="#FFFFFFFF"}
122    
123  \tableofcontents  \tableofcontents
124  \pagebreak  %\pagebreak
125    
126    %\part{MIT GCM basics}
127    
128  % Part: Overview  % Section: Overview
129  \input{part1/part1}  \input{part1/part1}
130  \pagebreak  %\pagebreak
131    
132  % Part: Discretization and Algorithm  % Section: Discretization and Algorithm
133  \input{part2/part2}  \input{part2/part2}
134  \pagebreak  %\pagebreak
135    
136  % Part: Getting started  % Section: Getting started
137  \input{part3/part3}  \input{part3/part3}
138  \pagebreak  %\pagebreak
139    
140  % Part: Software Architecture  % Section: Software Architecture
141  \input{part4/part4}  \input{part4/part4}
142  \pagebreak  %\pagebreak
143    
144  % Part: Automatic Differentiation  
145    %\part{Adjoint of the MIT GCM}
146    
147    % Section: Automatic Differentiation
148  \input{part5/part5}  \input{part5/part5}
149  \pagebreak  %\pagebreak
150    
151    
152  % Part: Physical Packages  %\part{Additional features}
153    
154    % Section: Physical Packages
155  \input{part6/part6}  \input{part6/part6}
156  \pagebreak  %\pagebreak
157    
158  % Part: Diagnostics  % Section: Diagnostics
159  \input{part7/part7}  \input{part7/part7}
160  \pagebreak  %\pagebreak
161    
162  % Part: ECCO Interface  % Section: ECCO
163  \input{part8/part8}  \input{part8/part8}
164    %\pagebreak
165    
166    % Section: References:
167    %\markboth{BIBLIOGRAPHY}{BIBLIOGRAPHY}
168    \addcontentsline{toc}{chapter}{BIBLIOGRAPHY}
169    %aja%\bibliography{\BIBPATH/manual_references}
170    \bibliography{manual_references}
171    
172  \end{document}  \end{document}
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