1 |
% $Header$ |
% $Header$ |
2 |
% $Name$ |
% $Name$ |
3 |
|
|
4 |
\documentclass[12pt]{book} |
\documentclass[10pt]{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} |
\usepackage{rotating} |
15 |
\usepackage{multirow} |
|
16 |
\usepackage{fancyhdr} |
% CNH playing around with page widths |
17 |
\usepackage{psfrag} |
\usepackage{anysize} |
18 |
\usepackage{oldgerm} |
|
19 |
\usepackage{palatcm} % better PDF |
%cnh%\usepackage{array} |
20 |
|
%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} |
72 |
|
%ph%\usepackage{psfrag} |
73 |
|
%ph%\usepackage{oldgerm} |
74 |
|
|
75 |
|
% I commented the following because it introduced excessive white space |
76 |
|
%aja%\usepackage{palatcm} % better PDF |
77 |
|
|
78 |
% page headers and footers |
% page headers and footers |
79 |
\pagestyle{fancy} |
%cnh%\usepackage{fancyhdr} |
80 |
\fancyhead{} |
%\pagestyle{fancy} |
81 |
\fancyhead[LO]{\slshape \rightmark} |
%cnh%\fancyhead{} |
82 |
\fancyhead[RE]{\slshape \leftmark} |
%cnh%\fancyhead[LO]{\slshape \rightmark} |
83 |
\fancyhead[RO,LE]{\thepage} |
%cnh%\fancyhead[RE]{\slshape \leftmark} |
84 |
\fancyfoot[CO,CE]{\today} |
%cnh%\fancyhead[RO,LE]{\thepage} |
85 |
\fancyfoot[RO,LE]{ } |
%cnh%\fancyfoot[CO,CE]{\today} |
86 |
\renewcommand{\headrulewidth}{0.4pt} |
%cnh%\fancyfoot[RO,LE]{ } |
87 |
\renewcommand{\footrulewidth}{0.4pt} |
%cnh%\renewcommand{\headrulewidth}{0.4pt} |
88 |
|
%cnh%\renewcommand{\footrulewidth}{0.4pt} |
89 |
|
|
90 |
|
% bibtex stuff |
91 |
|
%aja%\newcommand{\BIBPATH}{.} |
92 |
|
%aja%\usepackage{natbib} |
93 |
|
%aja%\bibliographystyle{\BIBPATH/jmr_my} |
94 |
|
%aja%\gdef\harvardleft{[} |
95 |
|
%aja%\gdef\harvardright{]} |
96 |
|
%aja%\bibpunct{[}{]}{,}{a}{}{,} |
97 |
|
%\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 |
\newcommand{\refequ}[1]{equation (\ref{equ:#1})} |
%ph%\newcommand{\refequ}[1]{equation (\ref{equ:#1})} |
104 |
\newcommand{\refequbig}[1]{Equation (\ref{equ:#1})} |
%ph%\newcommand{\refequbig}[1]{Equation (\ref{equ:#1})} |
105 |
\newcommand{\reftab}[1]{Tab.~\ref{tab:#1}} |
%ph%\newcommand{\reftab}[1]{Tab.~\ref{tab:#1}} |
106 |
\newcommand{\reftabno}[1]{\ref{tab:#1}} |
%ph%\newcommand{\reftabno}[1]{\ref{tab:#1}} |
107 |
\newcommand{\reffig}[1]{Fig.~\ref{fig:#1}} |
%ph%\newcommand{\reffig}[1]{Fig.~\ref{fig:#1}} |
108 |
\newcommand{\reffigno}[1]{\ref{fig:#1}} |
%ph%\newcommand{\reffigno}[1]{\ref{fig:#1}} |
109 |
|
|
110 |
% stuff for psfrag |
% stuff for psfrag |
111 |
\newcommand{\textinfigure}[1]{{\footnotesize\textbf{\textsf{#1}}}} |
%ph%\newcommand{\textinfigure}[1]{{\footnotesize\textbf{\textsf{#1}}}} |
112 |
\newcommand{\mathinfigure}[1]{\small\ensuremath{{#1}}} |
%ph%\newcommand{\mathinfigure}[1]{\small\ensuremath{{#1}}} |
113 |
|
|
114 |
|
% This allows numbering of subsubsections |
115 |
|
\setcounter{secnumdepth}{3} |
116 |
|
% This changes the the chapter title |
117 |
|
%\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 |
|
|
155 |
\begin{document} |
\begin{document} |
156 |
|
|
157 |
|
\bodytext{bgcolor="#FFFFFFFF"} |
158 |
|
|
159 |
\tableofcontents |
\tableofcontents |
160 |
\pagebreak |
%\pagebreak |
161 |
|
|
162 |
|
%\part{MIT GCM basics} |
163 |
|
|
164 |
% Part: Overview |
% Section: Overview |
165 |
\input{part1/part1} |
\input{part1/part1} |
166 |
\pagebreak |
%\pagebreak |
167 |
|
|
168 |
% Part: Discretization and Algorithm |
% Section: Discretization and Algorithm |
169 |
\input{part2/part2} |
\input{part2/part2} |
170 |
\pagebreak |
%\pagebreak |
171 |
|
|
172 |
% Part: Getting started |
% Section: Getting started |
173 |
\input{part3/part3} |
\input{part3/part3} |
174 |
\pagebreak |
%\pagebreak |
175 |
|
|
176 |
% Part: Software Architecture |
% Section: Software Architecture |
177 |
\input{part4/part4} |
\input{part4/part4} |
178 |
\pagebreak |
%\pagebreak |
179 |
|
|
180 |
% Part: Automatic Differentiation |
|
181 |
|
%\part{Adjoint of the MIT GCM} |
182 |
|
|
183 |
|
% Section: Automatic Differentiation |
184 |
\input{part5/part5} |
\input{part5/part5} |
185 |
\pagebreak |
%\pagebreak |
186 |
|
|
187 |
|
|
188 |
% Part: Physical Packages |
%\part{Additional features} |
189 |
|
|
190 |
|
% Section: Physical Packages |
191 |
\input{part6/part6} |
\input{part6/part6} |
192 |
\pagebreak |
%\pagebreak |
193 |
|
|
194 |
% Part: Diagnostics |
% Section: Pre-processing and Post-processing Tools |
195 |
\input{part7/part7} |
\input{part7/part7} |
196 |
\pagebreak |
%\pagebreak |
197 |
|
|
198 |
% Part: ECCO Interface |
% Section: ECCO |
199 |
\input{part8/part8} |
\input{part8/part8} |
200 |
|
%\pagebreak |
201 |
|
|
202 |
|
% Section: Model Uses |
203 |
|
\input{model_uses} |
204 |
|
%\pagebreak |
205 |
|
|
206 |
|
% Section: References: |
207 |
|
%\markboth{BIBLIOGRAPHY}{BIBLIOGRAPHY} |
208 |
|
\addcontentsline{toc}{chapter}{BIBLIOGRAPHY} |
209 |
|
%aja%\bibliography{\BIBPATH/manual_references} |
210 |
|
\bibliography{manual_references} |
211 |
|
|
212 |
\end{document} |
\end{document} |