MITgcm/manual/manual.tex

% $Header: /u/gcmpack/manual/manual.tex,v 1.31 2005/07/14 20:39:23 cnh Exp $
% $Name:  $

\documentclass[10pt]{book}

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

%aja%\usepackage{amsfonts}
\usepackage{amsmath}
\usepackage{html}
\usepackage{hthtml}
\usepackage{graphicx}

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

%eh3  Commands to reference either files or symbols within the "HTML-ized"
%eh3  ("vdb") code.
%eh3  
%afe seems like these need to be long, sorry
\newcommand{\varlink}[2]{\htmladdnormallink{\tt #1}{../code_reference/vdb/byname/#2.html}}
\newcommand{\filelink}[2]{\htmladdnormallink{\bf \tt #1}{../code_reference/vdb/byname/#2.html}}

% afe  Commands to standardize typesetting 
\newcommand{\file}[1]{\texttt{#1}}
\newcommand{\sectiontitle}[1]{\textsl{#1}}
\newcommand{\code}[1]{\texttt{#1}}

%%  EH3 : try out the epsfig package
\usepackage[dvips]{epsfig}
\def\scalefig#1{\epsfxsize #1\textwidth}

%EH3% ==========================================================
%EH3%  ***   PRIVATE SECTIONS   ******   PRIVATE SECTIONS   ***
%EH3%
%EH3%  Directions: To build the ``private'' or ``local-only'' 
%EH3%    version of this manual, then edit the following so 
%EH3%    they appear as:
%EH3%
%EH3%    % \includecomment{versionprivate}
%EH3%    \excludecoment{versionprivate}
%EH3%
%EH3%    The default is to include everything which is:
%EH3%
%EH3%    \includecomment{versionprivate}
%EH3%    % \excludecoment{versionprivate}

%\includecomment{versionprivate}
\excludecomment{versionprivate}

%EH3%
%EH3%    To use this comment, simply bracket any part of the 
%EH3%    manual with two lines that contain ONLY the following
%EH3%    pair:
%EH3%
%EH3%      \begin{versionprivate}
%EH3%      \end{versionprivate}
%EH3%
%EH3%    with NO additional comments or other commands on the
%EH3%    lines containing the \begin{...}\end{...} statements.
%EH3%
%EH3%  ***   PRIVATE SECTIONS   ******   PRIVATE SECTIONS   ***
%EH3% ==========================================================


%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}
%-jmc: try agu bib-style (give author names & year instead of just a number)
\usepackage[square]{natbib}
\bibliographystyle{agu}

% 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{hyperref} 
%\usepackage[dvips]
\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} 
  } 

% Some definitions (AMM)
\def\p#1{{\partial \over {\partial #1}}}
\def\pp#1#2{{\partial #1 \over {\partial #2}}}
\def\dd#1#2{{d #1 \over {d #2}}}
\def\bq{\begin{equation}}
\def\bqa{\begin{eqnarray}}
\def\eq{\end{equation}}
\def\eqa{\end{eqnarray}}

\def\h{ {1\over2} }
\def\txt{\mbox{$2^\circ$ x $2.5^\circ \,$}}
\def\fxf{\mbox{$4^\circ$ x $5^\circ \,$}}

\def\blankpage{ \vspace*{\fill} \vspace{5in} \vfill \newpage}


\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: Pre-processing and Post-processing Tools
\input{part7/part7}
%\pagebreak

% Section: ECCO
\input{part8/part8}
%\pagebreak

% Section: Model Uses
\input{model_uses}
%\pagebreak

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

\end{document}
1	jmc	1.32	% $Header: /u/gcmpack/manual/manual.tex,v 1.31 2005/07/14 20:39:23 cnh Exp $
2	adcroft	1.2	% $Name: $
3	adcroft	1.1
4	edhill	1.26	\documentclass[10pt]{book}
5	adcroft	1.1
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	cnh	1.19	\usepackage{hthtml}
13	adcroft	1.10	\usepackage{graphicx}
14	adcroft	1.8
15			%cnh%\usepackage{array}
16			%cnh%\usepackage{multirow}
17	cnh	1.12
18	edhill	1.16	%eh3 Commands to reference either files or symbols within the "HTML-ized"
19			%eh3 ("vdb") code.
20			%eh3
21	afe	1.23	%afe seems like these need to be long, sorry
22			\newcommand{\varlink}[2]{\htmladdnormallink{\tt #1}{../code_reference/vdb/byname/#2.html}}
23			\newcommand{\filelink}[2]{\htmladdnormallink{\bf \tt #1}{../code_reference/vdb/byname/#2.html}}
24	afe	1.22
25			% afe Commands to standardize typesetting
26	afe	1.23	\newcommand{\file}[1]{\texttt{#1}}
27			\newcommand{\sectiontitle}[1]{\textsl{#1}}
28			\newcommand{\code}[1]{\texttt{#1}}
29	afe	1.22
30	edhill	1.25	%% EH3 : try out the epsfig package
31	edhill	1.18	\usepackage[dvips]{epsfig}
32			\def\scalefig#1{\epsfxsize #1\textwidth}
33	edhill	1.25
34			%EH3% ==========================================================
35			%EH3% * PRIVATE SECTIONS ** PRIVATE SECTIONS *
36			%EH3%
37			%EH3% Directions: To build the ``private'' or ``local-only''
38			%EH3% version of this manual, then edit the following so
39			%EH3% they appear as:
40			%EH3%
41			%EH3% % \includecomment{versionprivate}
42			%EH3% \excludecoment{versionprivate}
43			%EH3%
44			%EH3% The default is to include everything which is:
45			%EH3%
46			%EH3% \includecomment{versionprivate}
47			%EH3% % \excludecoment{versionprivate}
48
49	afe	1.28	%\includecomment{versionprivate}
50			\excludecomment{versionprivate}
51	edhill	1.25
52			%EH3%
53			%EH3% To use this comment, simply bracket any part of the
54			%EH3% manual with two lines that contain ONLY the following
55			%EH3% pair:
56			%EH3%
57			%EH3% \begin{versionprivate}
58			%EH3% \end{versionprivate}
59			%EH3%
60			%EH3% with NO additional comments or other commands on the
61			%EH3% lines containing the \begin{...}\end{...} statements.
62			%EH3%
63			%EH3% * PRIVATE SECTIONS ** PRIVATE SECTIONS *
64			%EH3% ==========================================================
65	cnh	1.12
66	adcroft	1.8
67			%ph%\usepackage{epsfig}
68			%ph%\usepackage{psfrag}
69			%ph%\usepackage{oldgerm}
70
71	adcroft	1.2	% I commented the following because it introduced excessive white space
72	adcroft	1.8	%aja%\usepackage{palatcm} % better PDF
73	adcroft	1.1
74			% page headers and footers
75	adcroft	1.8	%cnh%\usepackage{fancyhdr}
76	adcroft	1.2	%\pagestyle{fancy}
77	adcroft	1.8	%cnh%\fancyhead{}
78			%cnh%\fancyhead[LO]{\slshape \rightmark}
79			%cnh%\fancyhead[RE]{\slshape \leftmark}
80			%cnh%\fancyhead[RO,LE]{\thepage}
81			%cnh%\fancyfoot[CO,CE]{\today}
82			%cnh%\fancyfoot[RO,LE]{ }
83			%cnh%\renewcommand{\headrulewidth}{0.4pt}
84			%cnh%\renewcommand{\footrulewidth}{0.4pt}
85	adcroft	1.1
86	heimbach	1.5	% bibtex stuff
87	adcroft	1.10	%aja%\newcommand{\BIBPATH}{.}
88			%aja%\usepackage{natbib}
89			%aja%\bibliographystyle{\BIBPATH/jmr_my}
90			%aja%\gdef\harvardleft{[}
91			%aja%\gdef\harvardright{]}
92			%aja%\bibpunct{[}{]}{,}{a}{}{,}
93	jmc	1.32	%\bibliographystyle{plain}
94			%-jmc: try agu bib-style (give author names & year instead of just a number)
95			\usepackage[square]{natbib}
96			\bibliographystyle{agu}
97	heimbach	1.5
98	adcroft	1.1	% referencing
99	adcroft	1.8	%ph%\newcommand{\refequ}[1]{equation (\ref{equ:#1})}
100			%ph%\newcommand{\refequbig}[1]{Equation (\ref{equ:#1})}
101			%ph%\newcommand{\reftab}[1]{Tab.~\ref{tab:#1}}
102			%ph%\newcommand{\reftabno}[1]{\ref{tab:#1}}
103			%ph%\newcommand{\reffig}[1]{Fig.~\ref{fig:#1}}
104			%ph%\newcommand{\reffigno}[1]{\ref{fig:#1}}
105	adcroft	1.1
106			% stuff for psfrag
107	adcroft	1.8	%ph%\newcommand{\textinfigure}[1]{{\footnotesize\textbf{\textsf{#1}}}}
108			%ph%\newcommand{\mathinfigure}[1]{\small\ensuremath{{#1}}}
109	adcroft	1.1
110	adcroft	1.3	% This allows numbering of subsubsections
111			\setcounter{secnumdepth}{3}
112			% This changes the the chapter title
113			%\renewcommand{\chaptername}{Section}
114
115	adcroft	1.11
116			% This allows hyperlinks in PDF
117			% hyperref package and colors for hyperref package
118			\usepackage{color}
119	cnh	1.31	\usepackage{hyperref}
120	cnh	1.29	%\usepackage[dvips]
121	adcroft	1.11	\definecolor{darkgreen}{rgb}{0,0.4,0}
122			\definecolor{darkblue}{rgb}{0,0,0.4}
123			\definecolor{darkred}{rgb}{0.5,0,0}
124			\hypersetup{breaklinks=true,
125			colorlinks=true,
126			linkcolor=darkgreen,
127			citecolor=darkblue,
128			pagecolor=darkred,
129			pdftitle={MITgcm Release 1 Documentation},
130	edhill	1.15	pdfauthor={MITgcm-support@mitgcm.org},
131	adcroft	1.11	pdfkeywords={oceanography, ocean model, general circulation model,
132			non-hydrostatic, finite volume, inverse methods, adjoint method}
133			}
134	molod	1.17
135			% Some definitions (AMM)
136			\def\p#1{{\partial \over {\partial #1}}}
137			\def\pp#1#2{{\partial #1 \over {\partial #2}}}
138			\def\dd#1#2{{d #1 \over {d #2}}}
139			\def\bq{\begin{equation}}
140			\def\bqa{\begin{eqnarray}}
141			\def\eq{\end{equation}}
142			\def\eqa{\end{eqnarray}}
143
144			\def\h{ {1\over2} }
145			\def\txt{\mbox{$2^\circ$ x $2.5^\circ \,$}}
146			\def\fxf{\mbox{$4^\circ$ x $5^\circ \,$}}
147
148			\def\blankpage{ \vspace*{\fill} \vspace{5in} \vfill \newpage}
149
150	adcroft	1.1
151			\begin{document}
152	cnh	1.9
153			\bodytext{bgcolor="#FFFFFFFF"}
154	adcroft	1.1
155			\tableofcontents
156	adcroft	1.10	%\pagebreak
157	adcroft	1.1
158	adcroft	1.10	%\part{MIT GCM basics}
159	adcroft	1.3
160			% Section: Overview
161	adcroft	1.1	\input{part1/part1}
162	adcroft	1.8	%\pagebreak
163	adcroft	1.1
164	adcroft	1.3	% Section: Discretization and Algorithm
165	adcroft	1.1	\input{part2/part2}
166	adcroft	1.8	%\pagebreak
167	adcroft	1.1
168	adcroft	1.3	% Section: Getting started
169	adcroft	1.1	\input{part3/part3}
170	adcroft	1.8	%\pagebreak
171	adcroft	1.1
172	adcroft	1.3	% Section: Software Architecture
173	adcroft	1.1	\input{part4/part4}
174	adcroft	1.8	%\pagebreak
175	adcroft	1.1
176	adcroft	1.3
177	adcroft	1.10	%\part{Adjoint of the MIT GCM}
178	adcroft	1.3
179			% Section: Automatic Differentiation
180	adcroft	1.1	\input{part5/part5}
181	adcroft	1.8	%\pagebreak
182	adcroft	1.1
183	adcroft	1.3
184	adcroft	1.10	%\part{Additional features}
185	adcroft	1.3
186			% Section: Physical Packages
187	adcroft	1.1	\input{part6/part6}
188	adcroft	1.8	%\pagebreak
189	adcroft	1.1
190	molod	1.30	% Section: Pre-processing and Post-processing Tools
191	adcroft	1.1	\input{part7/part7}
192	adcroft	1.14	%\pagebreak
193
194			% Section: ECCO
195			\input{part8/part8}
196	edhill	1.24	%\pagebreak
197
198			% Section: Model Uses
199			\input{model_uses}
200	adcroft	1.8	%\pagebreak
201	adcroft	1.1
202	heimbach	1.5	% Section: References:
203	adcroft	1.10	%\markboth{BIBLIOGRAPHY}{BIBLIOGRAPHY}
204	heimbach	1.6	\addcontentsline{toc}{chapter}{BIBLIOGRAPHY}
205	adcroft	1.10	%aja%\bibliography{\BIBPATH/manual_references}
206			\bibliography{manual_references}
207	heimbach	1.6
208	adcroft	1.1	\end{document}