/[MITgcm]/manual/manual.tex
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revision 1.7 by cnh, Tue Oct 9 10:48:01 2001 UTC revision 1.20 by edhill, Thu Feb 12 03:35:05 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    %eh3  ("vdb") code.
20    %eh3  
21    \newcommand{\varlink}[2]{
22    \htmladdnormallink{\em #1()}{../code_reference/vdb/byname/#2.html}
23    }
24    \newcommand{\filelink}[2]{
25    \htmladdnormallink{\bf \tt #1}{../code_reference/vdb/byname/#2.html}
26    }
27    
28    %eh3 try out the epsfig package
29    \usepackage[dvips]{epsfig}
30    \def\scalefig#1{\epsfxsize #1\textwidth}
31    
32    
33    %ph%\usepackage{epsfig}
34    %ph%\usepackage{psfrag}
35    %ph%\usepackage{oldgerm}
36    
37  % I commented the following because it introduced excessive white space  % I commented the following because it introduced excessive white space
38  %\usepackage{palatcm}              % better PDF  %aja%\usepackage{palatcm}              % better PDF
39    
40  % page headers and footers  % page headers and footers
41    %cnh%\usepackage{fancyhdr}
42  %\pagestyle{fancy}  %\pagestyle{fancy}
43  \fancyhead{}  %cnh%\fancyhead{}
44  \fancyhead[LO]{\slshape \rightmark}  %cnh%\fancyhead[LO]{\slshape \rightmark}
45  \fancyhead[RE]{\slshape \leftmark}  %cnh%\fancyhead[RE]{\slshape \leftmark}
46  \fancyhead[RO,LE]{\thepage}  %cnh%\fancyhead[RO,LE]{\thepage}
47  \fancyfoot[CO,CE]{\today}  %cnh%\fancyfoot[CO,CE]{\today}
48  \fancyfoot[RO,LE]{ }  %cnh%\fancyfoot[RO,LE]{ }
49  \renewcommand{\headrulewidth}{0.4pt}  %cnh%\renewcommand{\headrulewidth}{0.4pt}
50  \renewcommand{\footrulewidth}{0.4pt}  %cnh%\renewcommand{\footrulewidth}{0.4pt}
51    
52  % bibtex stuff  % bibtex stuff
53  \newcommand{\BIBPATH}{.}  %aja%\newcommand{\BIBPATH}{.}
54  \usepackage{natbib}  %aja%\usepackage{natbib}
55  \bibliographystyle{\BIBPATH/jmr_my}  %aja%\bibliographystyle{\BIBPATH/jmr_my}
56  \gdef\harvardleft{[}  %aja%\gdef\harvardleft{[}
57  \gdef\harvardright{]}  %aja%\gdef\harvardright{]}
58  \bibpunct{[}{]}{,}{a}{}{,}  %aja%\bibpunct{[}{]}{,}{a}{}{,}
59    \bibliographystyle{plain}
60    
61  % referencing  % referencing
62  \newcommand{\refequ}[1]{equation (\ref{equ:#1})}  %ph%\newcommand{\refequ}[1]{equation (\ref{equ:#1})}
63  \newcommand{\refequbig}[1]{Equation (\ref{equ:#1})}  %ph%\newcommand{\refequbig}[1]{Equation (\ref{equ:#1})}
64  \newcommand{\reftab}[1]{Tab.~\ref{tab:#1}}  %ph%\newcommand{\reftab}[1]{Tab.~\ref{tab:#1}}
65  \newcommand{\reftabno}[1]{\ref{tab:#1}}  %ph%\newcommand{\reftabno}[1]{\ref{tab:#1}}
66  \newcommand{\reffig}[1]{Fig.~\ref{fig:#1}}  %ph%\newcommand{\reffig}[1]{Fig.~\ref{fig:#1}}
67  \newcommand{\reffigno}[1]{\ref{fig:#1}}  %ph%\newcommand{\reffigno}[1]{\ref{fig:#1}}
68    
69  % stuff for psfrag  % stuff for psfrag
70  \newcommand{\textinfigure}[1]{{\footnotesize\textbf{\textsf{#1}}}}  %ph%\newcommand{\textinfigure}[1]{{\footnotesize\textbf{\textsf{#1}}}}
71  \newcommand{\mathinfigure}[1]{\small\ensuremath{{#1}}}  %ph%\newcommand{\mathinfigure}[1]{\small\ensuremath{{#1}}}
72    
73  % This allows numbering of subsubsections  % This allows numbering of subsubsections
74  \setcounter{secnumdepth}{3}  \setcounter{secnumdepth}{3}
75  % This changes the the chapter title  % This changes the the chapter title
76  %\renewcommand{\chaptername}{Section}  %\renewcommand{\chaptername}{Section}
77    
78  \usepackage{showlabels}  
79    % This allows hyperlinks in PDF
80    % hyperref package and colors for hyperref package
81    \usepackage{color}
82    \usepackage[dvips]{hyperref}
83    \definecolor{darkgreen}{rgb}{0,0.4,0}
84    \definecolor{darkblue}{rgb}{0,0,0.4}
85    \definecolor{darkred}{rgb}{0.5,0,0}
86    \hypersetup{breaklinks=true,
87      colorlinks=true,
88      linkcolor=darkgreen,
89      citecolor=darkblue,
90      pagecolor=darkred,
91      pdftitle={MITgcm Release 1 Documentation},
92      pdfauthor={MITgcm-support@mitgcm.org},
93      pdfkeywords={oceanography, ocean model, general circulation model,
94        non-hydrostatic, finite volume, inverse methods, adjoint method}
95      }
96    
97    % Some definitions (AMM)
98    \def\p#1{{\partial \over {\partial #1}}}
99    \def\pp#1#2{{\partial #1 \over {\partial #2}}}
100    \def\dd#1#2{{d #1 \over {d #2}}}
101    \def\bq{\begin{equation}}
102    \def\bqa{\begin{eqnarray}}
103    \def\eq{\end{equation}}
104    \def\eqa{\end{eqnarray}}
105    
106    \def\h{ {1\over2} }
107    \def\txt{\mbox{$2^\circ$ x $2.5^\circ \,$}}
108    \def\fxf{\mbox{$4^\circ$ x $5^\circ \,$}}
109    
110    \def\blankpage{ \vspace*{\fill} \vspace{5in} \vfill \newpage}
111    
112    
113  \begin{document}  \begin{document}
114    
115    \bodytext{bgcolor="#FFFFFFFF"}
116    
117  \tableofcontents  \tableofcontents
118  \pagebreak  %\pagebreak
119    
120  \part{MIT GCM basics}  %\part{MIT GCM basics}
121    
122  % Section: Overview  % Section: Overview
123  \input{part1/part1}  \input{part1/part1}
124  \pagebreak  %\pagebreak
125    
126  % Section: Discretization and Algorithm  % Section: Discretization and Algorithm
127  \input{part2/part2}  \input{part2/part2}
128  \pagebreak  %\pagebreak
129    
130  % Section: Getting started  % Section: Getting started
131  \input{part3/part3}  \input{part3/part3}
132  \pagebreak  %\pagebreak
133    
134  % Section: Software Architecture  % Section: Software Architecture
135  \input{part4/part4}  \input{part4/part4}
136  \pagebreak  %\pagebreak
137    
138    
139  \part{Adjoint of the MIT GCM}  %\part{Adjoint of the MIT GCM}
140    
141  % Section: Automatic Differentiation  % Section: Automatic Differentiation
142  \input{part5/part5}  \input{part5/part5}
143  \pagebreak  %\pagebreak
144    
145    
146  \part{Additional features}  %\part{Additional features}
147    
148  % Section: Physical Packages  % Section: Physical Packages
149  \input{part6/part6}  \input{part6/part6}
150  \pagebreak  %\pagebreak
151    
152  % Section: Diagnostics  % Section: Diagnostics
153  \input{part7/part7}  \input{part7/part7}
154  \pagebreak  %\pagebreak
155    
156  % Section: ECCO Interface  % Section: ECCO
157  \input{part8/part8}  \input{part8/part8}
158  \pagebreak  %\pagebreak
159    
160  % Section: References:  % Section: References:
161  \markboth{BIBLIOGRAPHY}{BIBLIOGRAPHY}  %\markboth{BIBLIOGRAPHY}{BIBLIOGRAPHY}
162  \addcontentsline{toc}{chapter}{BIBLIOGRAPHY}  \addcontentsline{toc}{chapter}{BIBLIOGRAPHY}
163  \bibliography{\BIBPATH/manual_references}  %aja%\bibliography{\BIBPATH/manual_references}
164    \bibliography{manual_references}
165    
166  \end{document}  \end{document}
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