MITgcm/manual/manual.tex

% $Header: /u/u3/gcmpack/manual/manual.tex,v 1.14 2002/04/24 20:12:36 adcroft Exp $
% $Name:  $

\documentclass[12pt]{book}

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

%aja%\usepackage{amsfonts}
\usepackage{amsmath}
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%cnh%\usepackage{array}
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% Command to reference entries in either "code" or "names"
% directories of browseable code tree.
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}
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\htmladdnormallink{\bf \tt #1}{../../code_reference/vdb/names/#2_docref.html}
}


%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
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% bibtex stuff
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% 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} 
  } 

\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	% $Header: /u/u3/gcmpack/manual/manual.tex,v 1.14 2002/04/24 20:12:36 adcroft Exp $
2	% $Name: $
3
4	\documentclass[12pt]{book}
5
6	%To help cross-reference
7	%\usepackage{showlabels}
8
9	%aja%\usepackage{amsfonts}
10	\usepackage{amsmath}
11	\usepackage{html}
12	\usepackage{graphicx}
13
14	%cnh%\usepackage{array}
15	%cnh%\usepackage{multirow}
16
17	% Command to reference entries in either "code" or "names"
18	% 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
33	%aja%\usepackage{palatcm} % better PDF
34
35	% page headers and footers
36	%cnh%\usepackage{fancyhdr}
37	%\pagestyle{fancy}
38	%cnh%\fancyhead{}
39	%cnh%\fancyhead[LO]{\slshape \rightmark}
40	%cnh%\fancyhead[RE]{\slshape \leftmark}
41	%cnh%\fancyhead[RO,LE]{\thepage}
42	%cnh%\fancyfoot[CO,CE]{\today}
43	%cnh%\fancyfoot[RO,LE]{ }
44	%cnh%\renewcommand{\headrulewidth}{0.4pt}
45	%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
57	%ph%\newcommand{\refequ}[1]{equation (\ref{equ:#1})}
58	%ph%\newcommand{\refequbig}[1]{Equation (\ref{equ:#1})}
59	%ph%\newcommand{\reftab}[1]{Tab.~\ref{tab:#1}}
60	%ph%\newcommand{\reftabno}[1]{\ref{tab:#1}}
61	%ph%\newcommand{\reffig}[1]{Fig.~\ref{fig:#1}}
62	%ph%\newcommand{\reffigno}[1]{\ref{fig:#1}}
63
64	% stuff for psfrag
65	%ph%\newcommand{\textinfigure}[1]{{\footnotesize\textbf{\textsf{#1}}}}
66	%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}
93
94	\bodytext{bgcolor="#FFFFFFFF"}
95
96	\tableofcontents
97	%\pagebreak
98
99	%\part{MIT GCM basics}
100
101	% Section: Overview
102	\input{part1/part1}
103	%\pagebreak
104
105	% Section: Discretization and Algorithm
106	\input{part2/part2}
107	%\pagebreak
108
109	% Section: Getting started
110	\input{part3/part3}
111	%\pagebreak
112
113	% Section: Software Architecture
114	\input{part4/part4}
115	%\pagebreak
116
117
118	%\part{Adjoint of the MIT GCM}
119
120	% Section: Automatic Differentiation
121	\input{part5/part5}
122	%\pagebreak
123
124
125	%\part{Additional features}
126
127	% Section: Physical Packages
128	\input{part6/part6}
129	%\pagebreak
130
131	% Section: Diagnostics
132	\input{part7/part7}
133	%\pagebreak
134
135	% Section: ECCO
136	\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}