MITgcm/manual/manual.tex

% $Header: /u/u3/gcmpack/manual/manual.tex,v 1.15 2003/07/30 13:42:52 edhill Exp $
% $Name:  $

\documentclass[12pt]{book}

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

%aja%\usepackage{amsfonts}
\usepackage{amsmath}
\usepackage{html}
\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{\filelink}[2]{
\htmladdnormallink{\em #1()}{../code_reference/vdb/byname/#2.html}
}
\newcommand{\varlink}[2]{
\htmladdnormallink{\bf \tt #1}{../code_reference/vdb/byname/#2.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
%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} 
  } 

\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	edhill	1.16	% $Header: /u/u3/gcmpack/manual/manual.tex,v 1.15 2003/07/30 13:42:52 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	adcroft	1.10	\usepackage{graphicx}
13	adcroft	1.8
14			%cnh%\usepackage{array}
15			%cnh%\usepackage{multirow}
16	cnh	1.12
17	edhill	1.16	%eh3 Commands to reference either files or symbols within the "HTML-ized"
18			%eh3 ("vdb") code.
19			%eh3
20			\newcommand{\filelink}[2]{
21			\htmladdnormallink{\em #1()}{../code_reference/vdb/byname/#2.html}
22	cnh	1.12	}
23			\newcommand{\varlink}[2]{
24	edhill	1.16	\htmladdnormallink{\bf \tt #1}{../code_reference/vdb/byname/#2.html}
25	cnh	1.12	}
26
27
28	adcroft	1.8
29			%ph%\usepackage{epsfig}
30			%ph%\usepackage{psfrag}
31			%ph%\usepackage{oldgerm}
32
33	adcroft	1.2	% I commented the following because it introduced excessive white space
34	adcroft	1.8	%aja%\usepackage{palatcm} % better PDF
35	adcroft	1.1
36			% page headers and footers
37	adcroft	1.8	%cnh%\usepackage{fancyhdr}
38	adcroft	1.2	%\pagestyle{fancy}
39	adcroft	1.8	%cnh%\fancyhead{}
40			%cnh%\fancyhead[LO]{\slshape \rightmark}
41			%cnh%\fancyhead[RE]{\slshape \leftmark}
42			%cnh%\fancyhead[RO,LE]{\thepage}
43			%cnh%\fancyfoot[CO,CE]{\today}
44			%cnh%\fancyfoot[RO,LE]{ }
45			%cnh%\renewcommand{\headrulewidth}{0.4pt}
46			%cnh%\renewcommand{\footrulewidth}{0.4pt}
47	adcroft	1.1
48	heimbach	1.5	% bibtex stuff
49	adcroft	1.10	%aja%\newcommand{\BIBPATH}{.}
50			%aja%\usepackage{natbib}
51			%aja%\bibliographystyle{\BIBPATH/jmr_my}
52			%aja%\gdef\harvardleft{[}
53			%aja%\gdef\harvardright{]}
54			%aja%\bibpunct{[}{]}{,}{a}{}{,}
55			\bibliographystyle{plain}
56	heimbach	1.5
57	adcroft	1.1	% referencing
58	adcroft	1.8	%ph%\newcommand{\refequ}[1]{equation (\ref{equ:#1})}
59			%ph%\newcommand{\refequbig}[1]{Equation (\ref{equ:#1})}
60			%ph%\newcommand{\reftab}[1]{Tab.~\ref{tab:#1}}
61			%ph%\newcommand{\reftabno}[1]{\ref{tab:#1}}
62			%ph%\newcommand{\reffig}[1]{Fig.~\ref{fig:#1}}
63			%ph%\newcommand{\reffigno}[1]{\ref{fig:#1}}
64	adcroft	1.1
65			% stuff for psfrag
66	adcroft	1.8	%ph%\newcommand{\textinfigure}[1]{{\footnotesize\textbf{\textsf{#1}}}}
67			%ph%\newcommand{\mathinfigure}[1]{\small\ensuremath{{#1}}}
68	adcroft	1.1
69	adcroft	1.3	% This allows numbering of subsubsections
70			\setcounter{secnumdepth}{3}
71			% This changes the the chapter title
72			%\renewcommand{\chaptername}{Section}
73
74	adcroft	1.11
75			% This allows hyperlinks in PDF
76			% hyperref package and colors for hyperref package
77			\usepackage{color}
78			\usepackage[dvips]{hyperref}
79			\definecolor{darkgreen}{rgb}{0,0.4,0}
80			\definecolor{darkblue}{rgb}{0,0,0.4}
81			\definecolor{darkred}{rgb}{0.5,0,0}
82			\hypersetup{breaklinks=true,
83			colorlinks=true,
84			linkcolor=darkgreen,
85			citecolor=darkblue,
86			pagecolor=darkred,
87			pdftitle={MITgcm Release 1 Documentation},
88	edhill	1.15	pdfauthor={MITgcm-support@mitgcm.org},
89	adcroft	1.11	pdfkeywords={oceanography, ocean model, general circulation model,
90			non-hydrostatic, finite volume, inverse methods, adjoint method}
91			}
92	adcroft	1.1
93			\begin{document}
94	cnh	1.9
95			\bodytext{bgcolor="#FFFFFFFF"}
96	adcroft	1.1
97			\tableofcontents
98	adcroft	1.10	%\pagebreak
99	adcroft	1.1
100	adcroft	1.10	%\part{MIT GCM basics}
101	adcroft	1.3
102			% Section: Overview
103	adcroft	1.1	\input{part1/part1}
104	adcroft	1.8	%\pagebreak
105	adcroft	1.1
106	adcroft	1.3	% Section: Discretization and Algorithm
107	adcroft	1.1	\input{part2/part2}
108	adcroft	1.8	%\pagebreak
109	adcroft	1.1
110	adcroft	1.3	% Section: Getting started
111	adcroft	1.1	\input{part3/part3}
112	adcroft	1.8	%\pagebreak
113	adcroft	1.1
114	adcroft	1.3	% Section: Software Architecture
115	adcroft	1.1	\input{part4/part4}
116	adcroft	1.8	%\pagebreak
117	adcroft	1.1
118	adcroft	1.3
119	adcroft	1.10	%\part{Adjoint of the MIT GCM}
120	adcroft	1.3
121			% Section: Automatic Differentiation
122	adcroft	1.1	\input{part5/part5}
123	adcroft	1.8	%\pagebreak
124	adcroft	1.1
125	adcroft	1.3
126	adcroft	1.10	%\part{Additional features}
127	adcroft	1.3
128			% Section: Physical Packages
129	adcroft	1.1	\input{part6/part6}
130	adcroft	1.8	%\pagebreak
131	adcroft	1.1
132	adcroft	1.3	% Section: Diagnostics
133	adcroft	1.1	\input{part7/part7}
134	adcroft	1.14	%\pagebreak
135
136			% Section: ECCO
137			\input{part8/part8}
138	adcroft	1.8	%\pagebreak
139	adcroft	1.1
140	heimbach	1.5	% Section: References:
141	adcroft	1.10	%\markboth{BIBLIOGRAPHY}{BIBLIOGRAPHY}
142	heimbach	1.6	\addcontentsline{toc}{chapter}{BIBLIOGRAPHY}
143	adcroft	1.10	%aja%\bibliography{\BIBPATH/manual_references}
144			\bibliography{manual_references}
145	heimbach	1.6
146	adcroft	1.1	\end{document}