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	% $Header: /u/gcmpack/mitgcmdoc/manual.tex,v 1.10 2001/11/13 15:00:00 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	%ph%\usepackage{epsfig}
18	%ph%\usepackage{psfrag}
19	%ph%\usepackage{oldgerm}
20
21	% I commented the following because it introduced excessive white space
22	%aja%\usepackage{palatcm} % better PDF
23
24	% page headers and footers
25	%cnh%\usepackage{fancyhdr}
26	%\pagestyle{fancy}
27	%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
36	% bibtex stuff
37	%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
45	% referencing
46	%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
53	% stuff for psfrag
54	%ph%\newcommand{\textinfigure}[1]{{\footnotesize\textbf{\textsf{#1}}}}
55	%ph%\newcommand{\mathinfigure}[1]{\small\ensuremath{{#1}}}
56
57	% This allows numbering of subsubsections
58	\setcounter{secnumdepth}{3}
59	% This changes the the chapter title
60	%\renewcommand{\chaptername}{Section}
61
62
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
81	\begin{document}
82
83	\bodytext{bgcolor="#FFFFFFFF"}
84
85	\tableofcontents
86	%\pagebreak
87
88	%\part{MIT GCM basics}
89
90	% Section: Overview
91	\input{part1/part1}
92	%\pagebreak
93
94	% Section: Discretization and Algorithm
95	\input{part2/part2}
96	%\pagebreak
97
98	% Section: Getting started
99	\input{part3/part3}
100	%\pagebreak
101
102	% Section: Software Architecture
103	\input{part4/part4}
104	%\pagebreak
105
106
107	%\part{Adjoint of the MIT GCM}
108
109	% Section: Automatic Differentiation
110	\input{part5/part5}
111	%\pagebreak
112
113
114	%\part{Additional features}
115
116	% Section: Physical Packages
117	\input{part6/part6}
118	%\pagebreak
119
120	% Section: Diagnostics
121	\input{part7/part7}
122	%\pagebreak
123
124	% Section: ECCO Interface
125	\input{part8/part8}
126	%\pagebreak
127
128	% Section: References:
129	%\markboth{BIBLIOGRAPHY}{BIBLIOGRAPHY}
130	\addcontentsline{toc}{chapter}{BIBLIOGRAPHY}
131	%aja%\bibliography{\BIBPATH/manual_references}
132	\bibliography{manual_references}
133
134	\end{document}