MITgcm/manual/manual.tex

% $Header: /u/u3/gcmpack/manual/manual.tex,v 1.22 2004/03/15 22:39:28 afe Exp $
% $Name:  $

\documentclass[12pt]{book}

%To help cross-reference
%\usepackage{showlabels}

%aja%\usepackage{amsfonts}
\usepackage{amsmath}
\usepackage{html}
\usepackage{hthtml}
\usepackage{graphicx}

%cnh%\usepackage{array}
%cnh%\usepackage{multirow}

%eh3  Commands to reference either files or symbols within the "HTML-ized"
%eh3  ("vdb") code.
%eh3  
%afe seems like these need to be long, sorry
\newcommand{\varlink}[2]{\htmladdnormallink{\tt #1}{../code_reference/vdb/byname/#2.html}}
\newcommand{\filelink}[2]{\htmladdnormallink{\bf \tt #1}{../code_reference/vdb/byname/#2.html}}

% afe  Commands to standardize typesetting 
\newcommand{\file}[1]{\texttt{#1}}

\newcommand{\sectiontitle}[1]{\textsl{#1}}

\newcommand{\code}[1]{\texttt{#1}}


%eh3 try out the epsfig package
\usepackage[dvips]{epsfig}
\def\scalefig#1{\epsfxsize #1\textwidth}


%ph%\usepackage{epsfig}
%ph%\usepackage{psfrag}
%ph%\usepackage{oldgerm}

% I commented the following because it introduced excessive white space
%aja%\usepackage{palatcm}              % better PDF 

% page headers and footers
%cnh%\usepackage{fancyhdr}
%\pagestyle{fancy}
%cnh%\fancyhead{}
%cnh%\fancyhead[LO]{\slshape \rightmark}
%cnh%\fancyhead[RE]{\slshape \leftmark}
%cnh%\fancyhead[RO,LE]{\thepage}
%cnh%\fancyfoot[CO,CE]{\today}
%cnh%\fancyfoot[RO,LE]{ }
%cnh%\renewcommand{\headrulewidth}{0.4pt}
%cnh%\renewcommand{\footrulewidth}{0.4pt}

% bibtex stuff
%aja%\newcommand{\BIBPATH}{.}
%aja%\usepackage{natbib}
%aja%\bibliographystyle{\BIBPATH/jmr_my}
%aja%\gdef\harvardleft{[}
%aja%\gdef\harvardright{]}
%aja%\bibpunct{[}{]}{,}{a}{}{,}
\bibliographystyle{plain}

% referencing
%ph%\newcommand{\refequ}[1]{equation (\ref{equ:#1})}
%ph%\newcommand{\refequbig}[1]{Equation (\ref{equ:#1})}
%ph%\newcommand{\reftab}[1]{Tab.~\ref{tab:#1}}
%ph%\newcommand{\reftabno}[1]{\ref{tab:#1}}
%ph%\newcommand{\reffig}[1]{Fig.~\ref{fig:#1}}
%ph%\newcommand{\reffigno}[1]{\ref{fig:#1}}

% stuff for psfrag
%ph%\newcommand{\textinfigure}[1]{{\footnotesize\textbf{\textsf{#1}}}}
%ph%\newcommand{\mathinfigure}[1]{\small\ensuremath{{#1}}}

% This allows numbering of subsubsections
\setcounter{secnumdepth}{3}
% This changes the the chapter title
%\renewcommand{\chaptername}{Section}


% This allows hyperlinks in PDF
% hyperref package and colors for hyperref package 
\usepackage{color} 
\usepackage[dvips]{hyperref} 
\definecolor{darkgreen}{rgb}{0,0.4,0} 
\definecolor{darkblue}{rgb}{0,0,0.4} 
\definecolor{darkred}{rgb}{0.5,0,0} 
\hypersetup{breaklinks=true, 
  colorlinks=true, 
  linkcolor=darkgreen,
  citecolor=darkblue,
  pagecolor=darkred,
  pdftitle={MITgcm Release 1 Documentation}, 
  pdfauthor={MITgcm-support@mitgcm.org}, 
  pdfkeywords={oceanography, ocean model, general circulation model,
    non-hydrostatic, finite volume, inverse methods, adjoint method} 
  } 

% Some definitions (AMM)
\def\p#1{{\partial \over {\partial #1}}}
\def\pp#1#2{{\partial #1 \over {\partial #2}}}
\def\dd#1#2{{d #1 \over {d #2}}}
\def\bq{\begin{equation}}
\def\bqa{\begin{eqnarray}}
\def\eq{\end{equation}}
\def\eqa{\end{eqnarray}}

\def\h{ {1\over2} }
\def\txt{\mbox{$2^\circ$ x $2.5^\circ \,$}}
\def\fxf{\mbox{$4^\circ$ x $5^\circ \,$}}

\def\blankpage{ \vspace*{\fill} \vspace{5in} \vfill \newpage}


\begin{document}

\bodytext{bgcolor="#FFFFFFFF"} 

\tableofcontents
%\pagebreak

%\part{MIT GCM basics}

% Section: Overview
\input{part1/part1}
%\pagebreak

% Section: Discretization and Algorithm
\input{part2/part2}
%\pagebreak

% Section: Getting started
\input{part3/part3}
%\pagebreak

% Section: Software Architecture
\input{part4/part4}
%\pagebreak


%\part{Adjoint of the MIT GCM}

% Section: Automatic Differentiation
\input{part5/part5}
%\pagebreak


%\part{Additional features}

% Section: Physical Packages
\input{part6/part6}
%\pagebreak

% Section: Diagnostics
\input{part7/part7}
%\pagebreak

% Section: ECCO
\input{part8/part8}
%\pagebreak

% Section: References:
%\markboth{BIBLIOGRAPHY}{BIBLIOGRAPHY}
\addcontentsline{toc}{chapter}{BIBLIOGRAPHY}
%aja%\bibliography{\BIBPATH/manual_references}
\bibliography{manual_references}

\end{document}
1	afe	1.23	% $Header: /u/u3/gcmpack/manual/manual.tex,v 1.22 2004/03/15 22:39:28 afe Exp $
2	adcroft	1.2	% $Name: $
3	adcroft	1.1
4			\documentclass[12pt]{book}
5
6	adcroft	1.8	%To help cross-reference
7			%\usepackage{showlabels}
8
9			%aja%\usepackage{amsfonts}
10	adcroft	1.1	\usepackage{amsmath}
11	cnh	1.7	\usepackage{html}
12	cnh	1.19	\usepackage{hthtml}
13	adcroft	1.10	\usepackage{graphicx}
14	adcroft	1.8
15			%cnh%\usepackage{array}
16			%cnh%\usepackage{multirow}
17	cnh	1.12
18	edhill	1.16	%eh3 Commands to reference either files or symbols within the "HTML-ized"
19			%eh3 ("vdb") code.
20			%eh3
21	afe	1.23	%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	afe	1.22
25			% afe Commands to standardize typesetting
26	afe	1.23	\newcommand{\file}[1]{\texttt{#1}}
27
28			\newcommand{\sectiontitle}[1]{\textsl{#1}}
29
30			\newcommand{\code}[1]{\texttt{#1}}
31	afe	1.22
32
33	cnh	1.12
34	edhill	1.18	%eh3 try out the epsfig package
35			\usepackage[dvips]{epsfig}
36			\def\scalefig#1{\epsfxsize #1\textwidth}
37	cnh	1.12
38	adcroft	1.8
39			%ph%\usepackage{epsfig}
40			%ph%\usepackage{psfrag}
41			%ph%\usepackage{oldgerm}
42
43	adcroft	1.2	% I commented the following because it introduced excessive white space
44	adcroft	1.8	%aja%\usepackage{palatcm} % better PDF
45	adcroft	1.1
46			% page headers and footers
47	adcroft	1.8	%cnh%\usepackage{fancyhdr}
48	adcroft	1.2	%\pagestyle{fancy}
49	adcroft	1.8	%cnh%\fancyhead{}
50			%cnh%\fancyhead[LO]{\slshape \rightmark}
51			%cnh%\fancyhead[RE]{\slshape \leftmark}
52			%cnh%\fancyhead[RO,LE]{\thepage}
53			%cnh%\fancyfoot[CO,CE]{\today}
54			%cnh%\fancyfoot[RO,LE]{ }
55			%cnh%\renewcommand{\headrulewidth}{0.4pt}
56			%cnh%\renewcommand{\footrulewidth}{0.4pt}
57	adcroft	1.1
58	heimbach	1.5	% bibtex stuff
59	adcroft	1.10	%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	heimbach	1.5
67	adcroft	1.1	% referencing
68	adcroft	1.8	%ph%\newcommand{\refequ}[1]{equation (\ref{equ:#1})}
69			%ph%\newcommand{\refequbig}[1]{Equation (\ref{equ:#1})}
70			%ph%\newcommand{\reftab}[1]{Tab.~\ref{tab:#1}}
71			%ph%\newcommand{\reftabno}[1]{\ref{tab:#1}}
72			%ph%\newcommand{\reffig}[1]{Fig.~\ref{fig:#1}}
73			%ph%\newcommand{\reffigno}[1]{\ref{fig:#1}}
74	adcroft	1.1
75			% stuff for psfrag
76	adcroft	1.8	%ph%\newcommand{\textinfigure}[1]{{\footnotesize\textbf{\textsf{#1}}}}
77			%ph%\newcommand{\mathinfigure}[1]{\small\ensuremath{{#1}}}
78	adcroft	1.1
79	adcroft	1.3	% This allows numbering of subsubsections
80			\setcounter{secnumdepth}{3}
81			% This changes the the chapter title
82			%\renewcommand{\chaptername}{Section}
83
84	adcroft	1.11
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	edhill	1.15	pdfauthor={MITgcm-support@mitgcm.org},
99	adcroft	1.11	pdfkeywords={oceanography, ocean model, general circulation model,
100			non-hydrostatic, finite volume, inverse methods, adjoint method}
101			}
102	molod	1.17
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	adcroft	1.1
119			\begin{document}
120	cnh	1.9
121			\bodytext{bgcolor="#FFFFFFFF"}
122	adcroft	1.1
123			\tableofcontents
124	adcroft	1.10	%\pagebreak
125	adcroft	1.1
126	adcroft	1.10	%\part{MIT GCM basics}
127	adcroft	1.3
128			% Section: Overview
129	adcroft	1.1	\input{part1/part1}
130	adcroft	1.8	%\pagebreak
131	adcroft	1.1
132	adcroft	1.3	% Section: Discretization and Algorithm
133	adcroft	1.1	\input{part2/part2}
134	adcroft	1.8	%\pagebreak
135	adcroft	1.1
136	adcroft	1.3	% Section: Getting started
137	adcroft	1.1	\input{part3/part3}
138	adcroft	1.8	%\pagebreak
139	adcroft	1.1
140	adcroft	1.3	% Section: Software Architecture
141	adcroft	1.1	\input{part4/part4}
142	adcroft	1.8	%\pagebreak
143	adcroft	1.1
144	adcroft	1.3
145	adcroft	1.10	%\part{Adjoint of the MIT GCM}
146	adcroft	1.3
147			% Section: Automatic Differentiation
148	adcroft	1.1	\input{part5/part5}
149	adcroft	1.8	%\pagebreak
150	adcroft	1.1
151	adcroft	1.3
152	adcroft	1.10	%\part{Additional features}
153	adcroft	1.3
154			% Section: Physical Packages
155	adcroft	1.1	\input{part6/part6}
156	adcroft	1.8	%\pagebreak
157	adcroft	1.1
158	adcroft	1.3	% Section: Diagnostics
159	adcroft	1.1	\input{part7/part7}
160	adcroft	1.14	%\pagebreak
161
162			% Section: ECCO
163			\input{part8/part8}
164	adcroft	1.8	%\pagebreak
165	adcroft	1.1
166	heimbach	1.5	% Section: References:
167	adcroft	1.10	%\markboth{BIBLIOGRAPHY}{BIBLIOGRAPHY}
168	heimbach	1.6	\addcontentsline{toc}{chapter}{BIBLIOGRAPHY}
169	adcroft	1.10	%aja%\bibliography{\BIBPATH/manual_references}
170			\bibliography{manual_references}
171	heimbach	1.6
172	adcroft	1.1	\end{document}