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}
\usepackage{html}
\usepackage{graphicx}

%cnh%\usepackage{array}
%cnh%\usepackage{multirow}

% Command to reference entries in either "code" or "names"
% directories of browseable code tree.
\newcommand{\proclink}[2]{
\htmladdnormallink{\em #1()}{../../code_reference/vdb/names/#2_docref.html}
}
\newcommand{\varlink}[2]{
\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
%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	1.15	% $Header: /u/u3/gcmpack/manual/manual.tex,v 1.14 2002/04/24 20:12:36 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	cnh	1.12
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	adcroft	1.8
28			%ph%\usepackage{epsfig}
29			%ph%\usepackage{psfrag}
30			%ph%\usepackage{oldgerm}
31
32	adcroft	1.2	% I commented the following because it introduced excessive white space
33	adcroft	1.8	%aja%\usepackage{palatcm} % better PDF
34	adcroft	1.1
35			% page headers and footers
36	adcroft	1.8	%cnh%\usepackage{fancyhdr}
37	adcroft	1.2	%\pagestyle{fancy}
38	adcroft	1.8	%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	adcroft	1.1
47	heimbach	1.5	% bibtex stuff
48	adcroft	1.10	%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	heimbach	1.5
56	adcroft	1.1	% referencing
57	adcroft	1.8	%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	adcroft	1.1
64			% stuff for psfrag
65	adcroft	1.8	%ph%\newcommand{\textinfigure}[1]{{\footnotesize\textbf{\textsf{#1}}}}
66			%ph%\newcommand{\mathinfigure}[1]{\small\ensuremath{{#1}}}
67	adcroft	1.1
68	adcroft	1.3	% This allows numbering of subsubsections
69			\setcounter{secnumdepth}{3}
70			% This changes the the chapter title
71			%\renewcommand{\chaptername}{Section}
72
73	adcroft	1.11
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	edhill	1.15	pdfauthor={MITgcm-support@mitgcm.org},
88	adcroft	1.11	pdfkeywords={oceanography, ocean model, general circulation model,
89			non-hydrostatic, finite volume, inverse methods, adjoint method}
90			}
91	adcroft	1.1
92			\begin{document}
93	cnh	1.9
94			\bodytext{bgcolor="#FFFFFFFF"}
95	adcroft	1.1
96			\tableofcontents
97	adcroft	1.10	%\pagebreak
98	adcroft	1.1
99	adcroft	1.10	%\part{MIT GCM basics}
100	adcroft	1.3
101			% Section: Overview
102	adcroft	1.1	\input{part1/part1}
103	adcroft	1.8	%\pagebreak
104	adcroft	1.1
105	adcroft	1.3	% Section: Discretization and Algorithm
106	adcroft	1.1	\input{part2/part2}
107	adcroft	1.8	%\pagebreak
108	adcroft	1.1
109	adcroft	1.3	% Section: Getting started
110	adcroft	1.1	\input{part3/part3}
111	adcroft	1.8	%\pagebreak
112	adcroft	1.1
113	adcroft	1.3	% Section: Software Architecture
114	adcroft	1.1	\input{part4/part4}
115	adcroft	1.8	%\pagebreak
116	adcroft	1.1
117	adcroft	1.3
118	adcroft	1.10	%\part{Adjoint of the MIT GCM}
119	adcroft	1.3
120			% Section: Automatic Differentiation
121	adcroft	1.1	\input{part5/part5}
122	adcroft	1.8	%\pagebreak
123	adcroft	1.1
124	adcroft	1.3
125	adcroft	1.10	%\part{Additional features}
126	adcroft	1.3
127			% Section: Physical Packages
128	adcroft	1.1	\input{part6/part6}
129	adcroft	1.8	%\pagebreak
130	adcroft	1.1
131	adcroft	1.3	% Section: Diagnostics
132	adcroft	1.1	\input{part7/part7}
133	adcroft	1.14	%\pagebreak
134
135			% Section: ECCO
136			\input{part8/part8}
137	adcroft	1.8	%\pagebreak
138	adcroft	1.1
139	heimbach	1.5	% Section: References:
140	adcroft	1.10	%\markboth{BIBLIOGRAPHY}{BIBLIOGRAPHY}
141	heimbach	1.6	\addcontentsline{toc}{chapter}{BIBLIOGRAPHY}
142	adcroft	1.10	%aja%\bibliography{\BIBPATH/manual_references}
143			\bibliography{manual_references}
144	heimbach	1.6
145	adcroft	1.1	\end{document}