/[MITgcm]/manual/manual.tex
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revision 1.2 by adcroft, Wed Aug 8 22:14:44 2001 UTC revision 1.15 by edhill, Wed Jul 30 13:42:52 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{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}  % Command to reference entries in either "code" or "names"
18  %\usepackage{oldgerm}  % directories of browseable code tree.
19    \newcommand{\proclink}[2]{
20    \htmladdnormallink{\em #1()}{../../code_reference/vdb/names/#2_docref.html}
21    }
22    \newcommand{\varlink}[2]{
23    \htmladdnormallink{\bf \tt #1}{../../code_reference/vdb/names/#2_docref.html}
24    }
25    
26    
27    
28    %ph%\usepackage{epsfig}
29    %ph%\usepackage{psfrag}
30    %ph%\usepackage{oldgerm}
31    
32  % I commented the following because it introduced excessive white space  % I commented the following because it introduced excessive white space
33  %\usepackage{palatcm}              % better PDF  %aja%\usepackage{palatcm}              % better PDF
34    
35  % page headers and footers  % page headers and footers
36    %cnh%\usepackage{fancyhdr}
37  %\pagestyle{fancy}  %\pagestyle{fancy}
38  \fancyhead{}  %cnh%\fancyhead{}
39  \fancyhead[LO]{\slshape \rightmark}  %cnh%\fancyhead[LO]{\slshape \rightmark}
40  \fancyhead[RE]{\slshape \leftmark}  %cnh%\fancyhead[RE]{\slshape \leftmark}
41  \fancyhead[RO,LE]{\thepage}  %cnh%\fancyhead[RO,LE]{\thepage}
42  \fancyfoot[CO,CE]{\today}  %cnh%\fancyfoot[CO,CE]{\today}
43  \fancyfoot[RO,LE]{ }  %cnh%\fancyfoot[RO,LE]{ }
44  \renewcommand{\headrulewidth}{0.4pt}  %cnh%\renewcommand{\headrulewidth}{0.4pt}
45  \renewcommand{\footrulewidth}{0.4pt}  %cnh%\renewcommand{\footrulewidth}{0.4pt}
46    
47    % bibtex stuff
48    %aja%\newcommand{\BIBPATH}{.}
49    %aja%\usepackage{natbib}
50    %aja%\bibliographystyle{\BIBPATH/jmr_my}
51    %aja%\gdef\harvardleft{[}
52    %aja%\gdef\harvardright{]}
53    %aja%\bibpunct{[}{]}{,}{a}{}{,}
54    \bibliographystyle{plain}
55    
56  % referencing  % referencing
57  \newcommand{\refequ}[1]{equation (\ref{equ:#1})}  %ph%\newcommand{\refequ}[1]{equation (\ref{equ:#1})}
58  \newcommand{\refequbig}[1]{Equation (\ref{equ:#1})}  %ph%\newcommand{\refequbig}[1]{Equation (\ref{equ:#1})}
59  \newcommand{\reftab}[1]{Tab.~\ref{tab:#1}}  %ph%\newcommand{\reftab}[1]{Tab.~\ref{tab:#1}}
60  \newcommand{\reftabno}[1]{\ref{tab:#1}}  %ph%\newcommand{\reftabno}[1]{\ref{tab:#1}}
61  \newcommand{\reffig}[1]{Fig.~\ref{fig:#1}}  %ph%\newcommand{\reffig}[1]{Fig.~\ref{fig:#1}}
62  \newcommand{\reffigno}[1]{\ref{fig:#1}}  %ph%\newcommand{\reffigno}[1]{\ref{fig:#1}}
63    
64  % stuff for psfrag  % stuff for psfrag
65  \newcommand{\textinfigure}[1]{{\footnotesize\textbf{\textsf{#1}}}}  %ph%\newcommand{\textinfigure}[1]{{\footnotesize\textbf{\textsf{#1}}}}
66  \newcommand{\mathinfigure}[1]{\small\ensuremath{{#1}}}  %ph%\newcommand{\mathinfigure}[1]{\small\ensuremath{{#1}}}
   
67    
68    % This allows numbering of subsubsections
69    \setcounter{secnumdepth}{3}
70    % This changes the the chapter title
71    %\renewcommand{\chaptername}{Section}
72    
73    
74    % This allows hyperlinks in PDF
75    % hyperref package and colors for hyperref package
76    \usepackage{color}
77    \usepackage[dvips]{hyperref}
78    \definecolor{darkgreen}{rgb}{0,0.4,0}
79    \definecolor{darkblue}{rgb}{0,0,0.4}
80    \definecolor{darkred}{rgb}{0.5,0,0}
81    \hypersetup{breaklinks=true,
82      colorlinks=true,
83      linkcolor=darkgreen,
84      citecolor=darkblue,
85      pagecolor=darkred,
86      pdftitle={MITgcm Release 1 Documentation},
87      pdfauthor={MITgcm-support@mitgcm.org},
88      pdfkeywords={oceanography, ocean model, general circulation model,
89        non-hydrostatic, finite volume, inverse methods, adjoint method}
90      }
91    
92  \begin{document}  \begin{document}
93    
94    \bodytext{bgcolor="#FFFFFFFF"}
95    
96  \tableofcontents  \tableofcontents
97  \pagebreak  %\pagebreak
98    
99    %\part{MIT GCM basics}
100    
101  % Part: Overview  % Section: Overview
102  \input{part1/part1}  \input{part1/part1}
103  \pagebreak  %\pagebreak
104    
105  % Part: Discretization and Algorithm  % Section: Discretization and Algorithm
106  \input{part2/part2}  \input{part2/part2}
107  \pagebreak  %\pagebreak
108    
109  % Part: Getting started  % Section: Getting started
110  \input{part3/part3}  \input{part3/part3}
111  \pagebreak  %\pagebreak
112    
113  % Part: Software Architecture  % Section: Software Architecture
114  \input{part4/part4}  \input{part4/part4}
115  \pagebreak  %\pagebreak
116    
117    
118    %\part{Adjoint of the MIT GCM}
119    
120  % Part: Automatic Differentiation  % Section: Automatic Differentiation
121  \input{part5/part5}  \input{part5/part5}
122  \pagebreak  %\pagebreak
123    
124  % Part: Physical Packages  
125    %\part{Additional features}
126    
127    % Section: Physical Packages
128  \input{part6/part6}  \input{part6/part6}
129  \pagebreak  %\pagebreak
130    
131  % Part: Diagnostics  % Section: Diagnostics
132  \input{part7/part7}  \input{part7/part7}
133  \pagebreak  %\pagebreak
134    
135  % Part: ECCO Interface  % Section: ECCO
136  \input{part8/part8}  \input{part8/part8}
137    %\pagebreak
138    
139    % Section: References:
140    %\markboth{BIBLIOGRAPHY}{BIBLIOGRAPHY}
141    \addcontentsline{toc}{chapter}{BIBLIOGRAPHY}
142    %aja%\bibliography{\BIBPATH/manual_references}
143    \bibliography{manual_references}
144    
145  \end{document}  \end{document}
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