MITgcm/manual/manual.tex

% $Header: /u/gcmpack/mitgcmdoc/manual.tex,v 1.10 2001/11/13 15:00:00 adcroft 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}

%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={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 Interface
\input{part8/part8}
%\pagebreak

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

\end{document}
1	adcroft	1.11	% $Header: /u/gcmpack/mitgcmdoc/manual.tex,v 1.10 2001/11/13 15:00:00 adcroft 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
17			%ph%\usepackage{epsfig}
18			%ph%\usepackage{psfrag}
19			%ph%\usepackage{oldgerm}
20
21	adcroft	1.2	% I commented the following because it introduced excessive white space
22	adcroft	1.8	%aja%\usepackage{palatcm} % better PDF
23	adcroft	1.1
24			% page headers and footers
25	adcroft	1.8	%cnh%\usepackage{fancyhdr}
26	adcroft	1.2	%\pagestyle{fancy}
27	adcroft	1.8	%cnh%\fancyhead{}
28			%cnh%\fancyhead[LO]{\slshape \rightmark}
29			%cnh%\fancyhead[RE]{\slshape \leftmark}
30			%cnh%\fancyhead[RO,LE]{\thepage}
31			%cnh%\fancyfoot[CO,CE]{\today}
32			%cnh%\fancyfoot[RO,LE]{ }
33			%cnh%\renewcommand{\headrulewidth}{0.4pt}
34			%cnh%\renewcommand{\footrulewidth}{0.4pt}
35	adcroft	1.1
36	heimbach	1.5	% bibtex stuff
37	adcroft	1.10	%aja%\newcommand{\BIBPATH}{.}
38			%aja%\usepackage{natbib}
39			%aja%\bibliographystyle{\BIBPATH/jmr_my}
40			%aja%\gdef\harvardleft{[}
41			%aja%\gdef\harvardright{]}
42			%aja%\bibpunct{[}{]}{,}{a}{}{,}
43			\bibliographystyle{plain}
44	heimbach	1.5
45	adcroft	1.1	% referencing
46	adcroft	1.8	%ph%\newcommand{\refequ}[1]{equation (\ref{equ:#1})}
47			%ph%\newcommand{\refequbig}[1]{Equation (\ref{equ:#1})}
48			%ph%\newcommand{\reftab}[1]{Tab.~\ref{tab:#1}}
49			%ph%\newcommand{\reftabno}[1]{\ref{tab:#1}}
50			%ph%\newcommand{\reffig}[1]{Fig.~\ref{fig:#1}}
51			%ph%\newcommand{\reffigno}[1]{\ref{fig:#1}}
52	adcroft	1.1
53			% stuff for psfrag
54	adcroft	1.8	%ph%\newcommand{\textinfigure}[1]{{\footnotesize\textbf{\textsf{#1}}}}
55			%ph%\newcommand{\mathinfigure}[1]{\small\ensuremath{{#1}}}
56	adcroft	1.1
57	adcroft	1.3	% This allows numbering of subsubsections
58			\setcounter{secnumdepth}{3}
59			% This changes the the chapter title
60			%\renewcommand{\chaptername}{Section}
61
62	adcroft	1.11
63			% This allows hyperlinks in PDF
64			% hyperref package and colors for hyperref package
65			\usepackage{color}
66			\usepackage[dvips]{hyperref}
67			\definecolor{darkgreen}{rgb}{0,0.4,0}
68			\definecolor{darkblue}{rgb}{0,0,0.4}
69			\definecolor{darkred}{rgb}{0.5,0,0}
70			\hypersetup{breaklinks=true,
71			colorlinks=true,
72			linkcolor=darkgreen,
73			citecolor=darkblue,
74			pagecolor=darkred,
75			pdftitle={MITgcm Release 1 Documentation},
76			pdfauthor={support@mitgcm.org},
77			pdfkeywords={oceanography, ocean model, general circulation model,
78			non-hydrostatic, finite volume, inverse methods, adjoint method}
79			}
80	adcroft	1.1
81			\begin{document}
82	cnh	1.9
83			\bodytext{bgcolor="#FFFFFFFF"}
84	adcroft	1.1
85			\tableofcontents
86	adcroft	1.10	%\pagebreak
87	adcroft	1.1
88	adcroft	1.10	%\part{MIT GCM basics}
89	adcroft	1.3
90			% Section: Overview
91	adcroft	1.1	\input{part1/part1}
92	adcroft	1.8	%\pagebreak
93	adcroft	1.1
94	adcroft	1.3	% Section: Discretization and Algorithm
95	adcroft	1.1	\input{part2/part2}
96	adcroft	1.8	%\pagebreak
97	adcroft	1.1
98	adcroft	1.3	% Section: Getting started
99	adcroft	1.1	\input{part3/part3}
100	adcroft	1.8	%\pagebreak
101	adcroft	1.1
102	adcroft	1.3	% Section: Software Architecture
103	adcroft	1.1	\input{part4/part4}
104	adcroft	1.8	%\pagebreak
105	adcroft	1.1
106	adcroft	1.3
107	adcroft	1.10	%\part{Adjoint of the MIT GCM}
108	adcroft	1.3
109			% Section: Automatic Differentiation
110	adcroft	1.1	\input{part5/part5}
111	adcroft	1.8	%\pagebreak
112	adcroft	1.1
113	adcroft	1.3
114	adcroft	1.10	%\part{Additional features}
115	adcroft	1.3
116			% Section: Physical Packages
117	adcroft	1.1	\input{part6/part6}
118	adcroft	1.8	%\pagebreak
119	adcroft	1.1
120	adcroft	1.3	% Section: Diagnostics
121	adcroft	1.1	\input{part7/part7}
122	adcroft	1.8	%\pagebreak
123	adcroft	1.1
124	adcroft	1.3	% Section: ECCO Interface
125	adcroft	1.1	\input{part8/part8}
126	adcroft	1.8	%\pagebreak
127	adcroft	1.1
128	heimbach	1.5	% Section: References:
129	adcroft	1.10	%\markboth{BIBLIOGRAPHY}{BIBLIOGRAPHY}
130	heimbach	1.6	\addcontentsline{toc}{chapter}{BIBLIOGRAPHY}
131	adcroft	1.10	%aja%\bibliography{\BIBPATH/manual_references}
132			\bibliography{manual_references}
133	heimbach	1.6
134	adcroft	1.1	\end{document}