/[MITgcm]/manual/manual.tex
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revision 1.6 by heimbach, Fri Oct 5 22:22:20 2001 UTC revision 1.16 by edhill, Thu Aug 7 18:27:51 2003 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{/usr/local/pkg/latex2html/current/texinputs/html}  \usepackage{html}
12  \usepackage{epsfig}  \usepackage{graphicx}
13  \usepackage{graphics,subfigure}  
14  \usepackage{array}  %cnh%\usepackage{array}
15  \usepackage{multirow}  %cnh%\usepackage{multirow}
16  \usepackage{fancyhdr}  
17  \usepackage{psfrag}  %eh3  Commands to reference either files or symbols within the "HTML-ized"
18  %\usepackage{oldgerm}  %eh3  ("vdb") code.
19    %eh3  
20    \newcommand{\filelink}[2]{
21    \htmladdnormallink{\em #1()}{../code_reference/vdb/byname/#2.html}
22    }
23    \newcommand{\varlink}[2]{
24    \htmladdnormallink{\bf \tt #1}{../code_reference/vdb/byname/#2.html}
25    }
26    
27    
28    
29    %ph%\usepackage{epsfig}
30    %ph%\usepackage{psfrag}
31    %ph%\usepackage{oldgerm}
32    
33  % I commented the following because it introduced excessive white space  % I commented the following because it introduced excessive white space
34  %\usepackage{palatcm}              % better PDF  %aja%\usepackage{palatcm}              % better PDF
35    
36  % page headers and footers  % page headers and footers
37    %cnh%\usepackage{fancyhdr}
38  %\pagestyle{fancy}  %\pagestyle{fancy}
39  \fancyhead{}  %cnh%\fancyhead{}
40  \fancyhead[LO]{\slshape \rightmark}  %cnh%\fancyhead[LO]{\slshape \rightmark}
41  \fancyhead[RE]{\slshape \leftmark}  %cnh%\fancyhead[RE]{\slshape \leftmark}
42  \fancyhead[RO,LE]{\thepage}  %cnh%\fancyhead[RO,LE]{\thepage}
43  \fancyfoot[CO,CE]{\today}  %cnh%\fancyfoot[CO,CE]{\today}
44  \fancyfoot[RO,LE]{ }  %cnh%\fancyfoot[RO,LE]{ }
45  \renewcommand{\headrulewidth}{0.4pt}  %cnh%\renewcommand{\headrulewidth}{0.4pt}
46  \renewcommand{\footrulewidth}{0.4pt}  %cnh%\renewcommand{\footrulewidth}{0.4pt}
47    
48  % bibtex stuff  % bibtex stuff
49  \newcommand{\BIBPATH}{.}  %aja%\newcommand{\BIBPATH}{.}
50  \usepackage{natbib}  %aja%\usepackage{natbib}
51  \bibliographystyle{\BIBPATH/jmr_my}  %aja%\bibliographystyle{\BIBPATH/jmr_my}
52  \gdef\harvardleft{[}  %aja%\gdef\harvardleft{[}
53  \gdef\harvardright{]}  %aja%\gdef\harvardright{]}
54  \bibpunct{[}{]}{,}{a}{}{,}  %aja%\bibpunct{[}{]}{,}{a}{}{,}
55    \bibliographystyle{plain}
56    
57  % referencing  % referencing
58  \newcommand{\refequ}[1]{equation (\ref{equ:#1})}  %ph%\newcommand{\refequ}[1]{equation (\ref{equ:#1})}
59  \newcommand{\refequbig}[1]{Equation (\ref{equ:#1})}  %ph%\newcommand{\refequbig}[1]{Equation (\ref{equ:#1})}
60  \newcommand{\reftab}[1]{Tab.~\ref{tab:#1}}  %ph%\newcommand{\reftab}[1]{Tab.~\ref{tab:#1}}
61  \newcommand{\reftabno}[1]{\ref{tab:#1}}  %ph%\newcommand{\reftabno}[1]{\ref{tab:#1}}
62  \newcommand{\reffig}[1]{Fig.~\ref{fig:#1}}  %ph%\newcommand{\reffig}[1]{Fig.~\ref{fig:#1}}
63  \newcommand{\reffigno}[1]{\ref{fig:#1}}  %ph%\newcommand{\reffigno}[1]{\ref{fig:#1}}
64    
65  % stuff for psfrag  % stuff for psfrag
66  \newcommand{\textinfigure}[1]{{\footnotesize\textbf{\textsf{#1}}}}  %ph%\newcommand{\textinfigure}[1]{{\footnotesize\textbf{\textsf{#1}}}}
67  \newcommand{\mathinfigure}[1]{\small\ensuremath{{#1}}}  %ph%\newcommand{\mathinfigure}[1]{\small\ensuremath{{#1}}}
68    
69  % This allows numbering of subsubsections  % This allows numbering of subsubsections
70  \setcounter{secnumdepth}{3}  \setcounter{secnumdepth}{3}
71  % This changes the the chapter title  % This changes the the chapter title
72  %\renewcommand{\chaptername}{Section}  %\renewcommand{\chaptername}{Section}
73    
 \usepackage{showlabels}  
74    
75    % This allows hyperlinks in PDF
76    % hyperref package and colors for hyperref package
77    \usepackage{color}
78    \usepackage[dvips]{hyperref}
79    \definecolor{darkgreen}{rgb}{0,0.4,0}
80    \definecolor{darkblue}{rgb}{0,0,0.4}
81    \definecolor{darkred}{rgb}{0.5,0,0}
82    \hypersetup{breaklinks=true,
83      colorlinks=true,
84      linkcolor=darkgreen,
85      citecolor=darkblue,
86      pagecolor=darkred,
87      pdftitle={MITgcm Release 1 Documentation},
88      pdfauthor={MITgcm-support@mitgcm.org},
89      pdfkeywords={oceanography, ocean model, general circulation model,
90        non-hydrostatic, finite volume, inverse methods, adjoint method}
91      }
92    
93  \begin{document}  \begin{document}
94    
95    \bodytext{bgcolor="#FFFFFFFF"}
96    
97  \tableofcontents  \tableofcontents
98  \pagebreak  %\pagebreak
99    
100  \part{The MIT GCM basics}  %\part{MIT GCM basics}
101    
102  % Section: Overview  % Section: Overview
103  \input{part1/part1}  \input{part1/part1}
104  \pagebreak  %\pagebreak
105    
106  % Section: Discretization and Algorithm  % Section: Discretization and Algorithm
107  \input{part2/part2}  \input{part2/part2}
108  \pagebreak  %\pagebreak
109    
110  % Section: Getting started  % Section: Getting started
111  \input{part3/part3}  \input{part3/part3}
112  \pagebreak  %\pagebreak
113    
114  % Section: Software Architecture  % Section: Software Architecture
115  \input{part4/part4}  \input{part4/part4}
116  \pagebreak  %\pagebreak
117    
118    
119  \part{Adjoint of the MIT GCM}  %\part{Adjoint of the MIT GCM}
120    
121  % Section: Automatic Differentiation  % Section: Automatic Differentiation
122  \input{part5/part5}  \input{part5/part5}
123  \pagebreak  %\pagebreak
124    
125    
126  \part{Additional features}  %\part{Additional features}
127    
128  % Section: Physical Packages  % Section: Physical Packages
129  \input{part6/part6}  \input{part6/part6}
130  \pagebreak  %\pagebreak
131    
132  % Section: Diagnostics  % Section: Diagnostics
133  \input{part7/part7}  \input{part7/part7}
134  \pagebreak  %\pagebreak
135    
136  % Section: ECCO Interface  % Section: ECCO
137  \input{part8/part8}  \input{part8/part8}
138  \pagebreak  %\pagebreak
139    
140  % Section: References:  % Section: References:
141  \markboth{BIBLIOGRAPHY}{BIBLIOGRAPHY}  %\markboth{BIBLIOGRAPHY}{BIBLIOGRAPHY}
142  \addcontentsline{toc}{chapter}{BIBLIOGRAPHY}  \addcontentsline{toc}{chapter}{BIBLIOGRAPHY}
143  \bibliography{\BIBPATH/manual_references}  %aja%\bibliography{\BIBPATH/manual_references}
144    \bibliography{manual_references}
145    
146  \end{document}  \end{document}
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