MITgcm/manual/manual.tex

% $Header: /u/u3/gcmpack/manual/manual.tex,v 1.21 2004/02/17 21:58:56 edhill 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  
\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	1.22	% $Header: /u/u3/gcmpack/manual/manual.tex,v 1.21 2004/02/17 21:58:56 edhill 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	edhill	1.20	\newcommand{\varlink}[2]{
22	edhill	1.21	\htmladdnormallink{\tt #1}{../code_reference/vdb/byname/#2.html}
23	cnh	1.12	}
24	edhill	1.20	\newcommand{\filelink}[2]{
25	edhill	1.16	\htmladdnormallink{\bf \tt #1}{../code_reference/vdb/byname/#2.html}
26	cnh	1.12	}
27	afe	1.22
28			% afe Commands to standardize typesetting
29			\newcommand{\file}[1]{
30			\texttt{#1}
31			}
32
33			\newcommand{\sectiontitle}[1]{
34			\textsl{#1}
35			}
36
37			\newcommand{\code}[1]{
38			\texttt{#1}
39			}
40
41
42	cnh	1.12
43	edhill	1.18	%eh3 try out the epsfig package
44			\usepackage[dvips]{epsfig}
45			\def\scalefig#1{\epsfxsize #1\textwidth}
46	cnh	1.12
47	adcroft	1.8
48			%ph%\usepackage{epsfig}
49			%ph%\usepackage{psfrag}
50			%ph%\usepackage{oldgerm}
51
52	adcroft	1.2	% I commented the following because it introduced excessive white space
53	adcroft	1.8	%aja%\usepackage{palatcm} % better PDF
54	adcroft	1.1
55			% page headers and footers
56	adcroft	1.8	%cnh%\usepackage{fancyhdr}
57	adcroft	1.2	%\pagestyle{fancy}
58	adcroft	1.8	%cnh%\fancyhead{}
59			%cnh%\fancyhead[LO]{\slshape \rightmark}
60			%cnh%\fancyhead[RE]{\slshape \leftmark}
61			%cnh%\fancyhead[RO,LE]{\thepage}
62			%cnh%\fancyfoot[CO,CE]{\today}
63			%cnh%\fancyfoot[RO,LE]{ }
64			%cnh%\renewcommand{\headrulewidth}{0.4pt}
65			%cnh%\renewcommand{\footrulewidth}{0.4pt}
66	adcroft	1.1
67	heimbach	1.5	% bibtex stuff
68	adcroft	1.10	%aja%\newcommand{\BIBPATH}{.}
69			%aja%\usepackage{natbib}
70			%aja%\bibliographystyle{\BIBPATH/jmr_my}
71			%aja%\gdef\harvardleft{[}
72			%aja%\gdef\harvardright{]}
73			%aja%\bibpunct{[}{]}{,}{a}{}{,}
74			\bibliographystyle{plain}
75	heimbach	1.5
76	adcroft	1.1	% referencing
77	adcroft	1.8	%ph%\newcommand{\refequ}[1]{equation (\ref{equ:#1})}
78			%ph%\newcommand{\refequbig}[1]{Equation (\ref{equ:#1})}
79			%ph%\newcommand{\reftab}[1]{Tab.~\ref{tab:#1}}
80			%ph%\newcommand{\reftabno}[1]{\ref{tab:#1}}
81			%ph%\newcommand{\reffig}[1]{Fig.~\ref{fig:#1}}
82			%ph%\newcommand{\reffigno}[1]{\ref{fig:#1}}
83	adcroft	1.1
84			% stuff for psfrag
85	adcroft	1.8	%ph%\newcommand{\textinfigure}[1]{{\footnotesize\textbf{\textsf{#1}}}}
86			%ph%\newcommand{\mathinfigure}[1]{\small\ensuremath{{#1}}}
87	adcroft	1.1
88	adcroft	1.3	% This allows numbering of subsubsections
89			\setcounter{secnumdepth}{3}
90			% This changes the the chapter title
91			%\renewcommand{\chaptername}{Section}
92
93	adcroft	1.11
94			% This allows hyperlinks in PDF
95			% hyperref package and colors for hyperref package
96			\usepackage{color}
97			\usepackage[dvips]{hyperref}
98			\definecolor{darkgreen}{rgb}{0,0.4,0}
99			\definecolor{darkblue}{rgb}{0,0,0.4}
100			\definecolor{darkred}{rgb}{0.5,0,0}
101			\hypersetup{breaklinks=true,
102			colorlinks=true,
103			linkcolor=darkgreen,
104			citecolor=darkblue,
105			pagecolor=darkred,
106			pdftitle={MITgcm Release 1 Documentation},
107	edhill	1.15	pdfauthor={MITgcm-support@mitgcm.org},
108	adcroft	1.11	pdfkeywords={oceanography, ocean model, general circulation model,
109			non-hydrostatic, finite volume, inverse methods, adjoint method}
110			}
111	molod	1.17
112			% Some definitions (AMM)
113			\def\p#1{{\partial \over {\partial #1}}}
114			\def\pp#1#2{{\partial #1 \over {\partial #2}}}
115			\def\dd#1#2{{d #1 \over {d #2}}}
116			\def\bq{\begin{equation}}
117			\def\bqa{\begin{eqnarray}}
118			\def\eq{\end{equation}}
119			\def\eqa{\end{eqnarray}}
120
121			\def\h{ {1\over2} }
122			\def\txt{\mbox{$2^\circ$ x $2.5^\circ \,$}}
123			\def\fxf{\mbox{$4^\circ$ x $5^\circ \,$}}
124
125			\def\blankpage{ \vspace*{\fill} \vspace{5in} \vfill \newpage}
126
127	adcroft	1.1
128			\begin{document}
129	cnh	1.9
130			\bodytext{bgcolor="#FFFFFFFF"}
131	adcroft	1.1
132			\tableofcontents
133	adcroft	1.10	%\pagebreak
134	adcroft	1.1
135	adcroft	1.10	%\part{MIT GCM basics}
136	adcroft	1.3
137			% Section: Overview
138	adcroft	1.1	\input{part1/part1}
139	adcroft	1.8	%\pagebreak
140	adcroft	1.1
141	adcroft	1.3	% Section: Discretization and Algorithm
142	adcroft	1.1	\input{part2/part2}
143	adcroft	1.8	%\pagebreak
144	adcroft	1.1
145	adcroft	1.3	% Section: Getting started
146	adcroft	1.1	\input{part3/part3}
147	adcroft	1.8	%\pagebreak
148	adcroft	1.1
149	adcroft	1.3	% Section: Software Architecture
150	adcroft	1.1	\input{part4/part4}
151	adcroft	1.8	%\pagebreak
152	adcroft	1.1
153	adcroft	1.3
154	adcroft	1.10	%\part{Adjoint of the MIT GCM}
155	adcroft	1.3
156			% Section: Automatic Differentiation
157	adcroft	1.1	\input{part5/part5}
158	adcroft	1.8	%\pagebreak
159	adcroft	1.1
160	adcroft	1.3
161	adcroft	1.10	%\part{Additional features}
162	adcroft	1.3
163			% Section: Physical Packages
164	adcroft	1.1	\input{part6/part6}
165	adcroft	1.8	%\pagebreak
166	adcroft	1.1
167	adcroft	1.3	% Section: Diagnostics
168	adcroft	1.1	\input{part7/part7}
169	adcroft	1.14	%\pagebreak
170
171			% Section: ECCO
172			\input{part8/part8}
173	adcroft	1.8	%\pagebreak
174	adcroft	1.1
175	heimbach	1.5	% Section: References:
176	adcroft	1.10	%\markboth{BIBLIOGRAPHY}{BIBLIOGRAPHY}
177	heimbach	1.6	\addcontentsline{toc}{chapter}{BIBLIOGRAPHY}
178	adcroft	1.10	%aja%\bibliography{\BIBPATH/manual_references}
179			\bibliography{manual_references}
180	heimbach	1.6
181	adcroft	1.1	\end{document}