MITgcm/manual/manual.tex

% $Header: /u/gcmpack/manual/manual.tex,v 1.41 2008/03/05 19:11:34 jmc Exp $
% $Name:  $

\documentclass[10pt]{book}

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

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

% CNH playing around with page widths
\usepackage{anysize}

%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}}
\newcommand{\myhref}[2]{\htmladdnormallink{#2}{#1}}

% 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]
\usepackage[square]{natbib}
\bibliographystyle{agu}
%% \bibliographystyle{aguurl}

% 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}

% Some definitions modified from the ones provided by Baylor
\def\BFKav#1{\overline{#1}}
\def\BFKpd#1#2{{\frac{\partial{#2}}{\partial{#1}}}}
\def\BFKpds#1#2{{\frac{\partial^2{#2}}{{\partial{#1}}^2}}}
\def\BFKDt#1{\frac{D{#1}}{Dt}}
\def\BFKaDt#1{\frac{\BFKav D{#1}}{\BFKav{Dt}}}
\def\BFKd#1{{\,\rm d#1}}
\def\BFKRo{{\rm Ro}}
\def\BFKRe{{\rm Re}}
\def\BFKFr{{\rm Fr}}
\def\BFKPr{{\rm Pr}}
\def\BFKMr{{M_{Ro}}}
\def\BFKtu{{\tilde u}}
\def\BFKtv{{\tilde v}}
\def\BFKatu{{\tilde {\BFKav u}}}
\def\BFKatv{{\tilde {\BFKav v}}}
\def\BFKlesssim{{<\atop\sim}}

%  Definitions from EH3:
\def\CC{C\raise.3ex\hbox{{\footnotesize
      +}}\raise.3ex\hbox{\footnotesize +}\ }

\begin{document}

\bodytext{bgcolor="#FFFFFFFF"} 

\title{ \textsc{MITgcm User Manual} }

\author{
  Alistair Adcroft \and Jean-Michel Campin \and Stephanie Dutkiewicz
  \and Constantinos Evangelinos \and David Ferreira %\and Mick Follows 
  \and Gael Forget \and Baylor Fox-Kemper \and Patrick Heimbach 
  \and Chris Hill \and Ed Hill \and Helen Hill 
  \and Oliver Jahn \and Martin Losch \and John Marshall
  \and Guillaume Maze \and Dimitris Menemenlis \and Andrea Molod
  \\
  \\
  \\
  MIT Department of EAPS  \\
  77 Massachusetts Ave. \\
  Cambridge, MA \ 02139-4307
}

%\date{August 19, 2004}
\date{\today}

\maketitle

\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,baylor_biblio}

\end{document}
1	jmc	1.42	% $Header: /u/gcmpack/manual/manual.tex,v 1.41 2008/03/05 19:11:34 jmc 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	molod	1.34	\usepackage{rotating}
15	adcroft	1.8
16	cnh	1.33	% CNH playing around with page widths
17			\usepackage{anysize}
18
19	adcroft	1.8	%cnh%\usepackage{array}
20			%cnh%\usepackage{multirow}
21	cnh	1.12
22	edhill	1.16	%eh3 Commands to reference either files or symbols within the "HTML-ized"
23			%eh3 ("vdb") code.
24			%eh3
25	afe	1.23	%afe seems like these need to be long, sorry
26			\newcommand{\varlink}[2]{\htmladdnormallink{\tt #1}{../code_reference/vdb/byname/#2.html}}
27			\newcommand{\filelink}[2]{\htmladdnormallink{\bf \tt #1}{../code_reference/vdb/byname/#2.html}}
28	cnh	1.38	\newcommand{\myhref}[2]{\htmladdnormallink{#2}{#1}}
29	afe	1.22
30			% afe Commands to standardize typesetting
31	afe	1.23	\newcommand{\file}[1]{\texttt{#1}}
32			\newcommand{\sectiontitle}[1]{\textsl{#1}}
33			\newcommand{\code}[1]{\texttt{#1}}
34	afe	1.22
35	edhill	1.25	%% EH3 : try out the epsfig package
36	edhill	1.18	\usepackage[dvips]{epsfig}
37			\def\scalefig#1{\epsfxsize #1\textwidth}
38	edhill	1.25
39			%EH3% ==========================================================
40			%EH3% * PRIVATE SECTIONS ** PRIVATE SECTIONS *
41			%EH3%
42			%EH3% Directions: To build the ``private'' or ``local-only''
43			%EH3% version of this manual, then edit the following so
44			%EH3% they appear as:
45			%EH3%
46			%EH3% % \includecomment{versionprivate}
47			%EH3% \excludecoment{versionprivate}
48			%EH3%
49			%EH3% The default is to include everything which is:
50			%EH3%
51			%EH3% \includecomment{versionprivate}
52			%EH3% % \excludecoment{versionprivate}
53
54	afe	1.28	%\includecomment{versionprivate}
55			\excludecomment{versionprivate}
56	edhill	1.25
57			%EH3%
58			%EH3% To use this comment, simply bracket any part of the
59			%EH3% manual with two lines that contain ONLY the following
60			%EH3% pair:
61			%EH3%
62			%EH3% \begin{versionprivate}
63			%EH3% \end{versionprivate}
64			%EH3%
65			%EH3% with NO additional comments or other commands on the
66			%EH3% lines containing the \begin{...}\end{...} statements.
67			%EH3%
68			%EH3% * PRIVATE SECTIONS ** PRIVATE SECTIONS *
69			%EH3% ==========================================================
70	cnh	1.12
71	adcroft	1.8
72			%ph%\usepackage{epsfig}
73			%ph%\usepackage{psfrag}
74			%ph%\usepackage{oldgerm}
75
76	adcroft	1.2	% I commented the following because it introduced excessive white space
77	adcroft	1.8	%aja%\usepackage{palatcm} % better PDF
78	adcroft	1.1
79			% page headers and footers
80	adcroft	1.8	%cnh%\usepackage{fancyhdr}
81	adcroft	1.2	%\pagestyle{fancy}
82	adcroft	1.8	%cnh%\fancyhead{}
83			%cnh%\fancyhead[LO]{\slshape \rightmark}
84			%cnh%\fancyhead[RE]{\slshape \leftmark}
85			%cnh%\fancyhead[RO,LE]{\thepage}
86			%cnh%\fancyfoot[CO,CE]{\today}
87			%cnh%\fancyfoot[RO,LE]{ }
88			%cnh%\renewcommand{\headrulewidth}{0.4pt}
89			%cnh%\renewcommand{\footrulewidth}{0.4pt}
90	adcroft	1.1
91	heimbach	1.5	% bibtex stuff
92	adcroft	1.10	%aja%\newcommand{\BIBPATH}{.}
93			%aja%\usepackage{natbib}
94			%aja%\bibliographystyle{\BIBPATH/jmr_my}
95			%aja%\gdef\harvardleft{[}
96			%aja%\gdef\harvardright{]}
97			%aja%\bibpunct{[}{]}{,}{a}{}{,}
98	jmc	1.32	%\bibliographystyle{plain}
99			%-jmc: try agu bib-style (give author names & year instead of just a number)
100	cnh	1.38	%% \usepackage[square]
101	jmc	1.32	\usepackage[square]{natbib}
102			\bibliographystyle{agu}
103	cnh	1.38	%% \bibliographystyle{aguurl}
104	heimbach	1.5
105	adcroft	1.1	% referencing
106	adcroft	1.8	%ph%\newcommand{\refequ}[1]{equation (\ref{equ:#1})}
107			%ph%\newcommand{\refequbig}[1]{Equation (\ref{equ:#1})}
108			%ph%\newcommand{\reftab}[1]{Tab.~\ref{tab:#1}}
109			%ph%\newcommand{\reftabno}[1]{\ref{tab:#1}}
110			%ph%\newcommand{\reffig}[1]{Fig.~\ref{fig:#1}}
111			%ph%\newcommand{\reffigno}[1]{\ref{fig:#1}}
112	adcroft	1.1
113			% stuff for psfrag
114	adcroft	1.8	%ph%\newcommand{\textinfigure}[1]{{\footnotesize\textbf{\textsf{#1}}}}
115			%ph%\newcommand{\mathinfigure}[1]{\small\ensuremath{{#1}}}
116	adcroft	1.1
117	adcroft	1.3	% This allows numbering of subsubsections
118			\setcounter{secnumdepth}{3}
119			% This changes the the chapter title
120			%\renewcommand{\chaptername}{Section}
121
122	adcroft	1.11
123			% This allows hyperlinks in PDF
124			% hyperref package and colors for hyperref package
125			\usepackage{color}
126	cnh	1.31	\usepackage{hyperref}
127	cnh	1.29	%\usepackage[dvips]
128	adcroft	1.11	\definecolor{darkgreen}{rgb}{0,0.4,0}
129			\definecolor{darkblue}{rgb}{0,0,0.4}
130			\definecolor{darkred}{rgb}{0.5,0,0}
131			\hypersetup{breaklinks=true,
132			colorlinks=true,
133			linkcolor=darkgreen,
134			citecolor=darkblue,
135			pagecolor=darkred,
136			pdftitle={MITgcm Release 1 Documentation},
137	edhill	1.15	pdfauthor={MITgcm-support@mitgcm.org},
138	adcroft	1.11	pdfkeywords={oceanography, ocean model, general circulation model,
139			non-hydrostatic, finite volume, inverse methods, adjoint method}
140			}
141	molod	1.17
142			% Some definitions (AMM)
143			\def\p#1{{\partial \over {\partial #1}}}
144			\def\pp#1#2{{\partial #1 \over {\partial #2}}}
145			\def\dd#1#2{{d #1 \over {d #2}}}
146			\def\bq{\begin{equation}}
147			\def\bqa{\begin{eqnarray}}
148			\def\eq{\end{equation}}
149			\def\eqa{\end{eqnarray}}
150
151			\def\h{ {1\over2} }
152			\def\txt{\mbox{$2^\circ$ x $2.5^\circ \,$}}
153			\def\fxf{\mbox{$4^\circ$ x $5^\circ \,$}}
154
155			\def\blankpage{ \vspace*{\fill} \vspace{5in} \vfill \newpage}
156
157	edhill	1.36	% Some definitions modified from the ones provided by Baylor
158			\def\BFKav#1{\overline{#1}}
159			\def\BFKpd#1#2{{\frac{\partial{#2}}{\partial{#1}}}}
160			\def\BFKpds#1#2{{\frac{\partial^2{#2}}{{\partial{#1}}^2}}}
161			\def\BFKDt#1{\frac{D{#1}}{Dt}}
162			\def\BFKaDt#1{\frac{\BFKav D{#1}}{\BFKav{Dt}}}
163			\def\BFKd#1{{\,\rm d#1}}
164			\def\BFKRo{{\rm Ro}}
165			\def\BFKRe{{\rm Re}}
166			\def\BFKFr{{\rm Fr}}
167			\def\BFKPr{{\rm Pr}}
168			\def\BFKMr{{M_{Ro}}}
169			\def\BFKtu{{\tilde u}}
170			\def\BFKtv{{\tilde v}}
171			\def\BFKatu{{\tilde {\BFKav u}}}
172			\def\BFKatv{{\tilde {\BFKav v}}}
173			\def\BFKlesssim{{<\atop\sim}}
174	adcroft	1.1
175	edhill	1.40	% Definitions from EH3:
176			\def\CC{C\raise.3ex\hbox{{\footnotesize
177			+}}\raise.3ex\hbox{\footnotesize +}\ }
178
179	adcroft	1.1	\begin{document}
180	cnh	1.9
181			\bodytext{bgcolor="#FFFFFFFF"}
182	adcroft	1.1
183	edhill	1.37	\title{ \textsc{MITgcm User Manual} }
184
185			\author{
186	jmc	1.42	Alistair Adcroft \and Jean-Michel Campin \and Stephanie Dutkiewicz
187			\and Constantinos Evangelinos \and David Ferreira %\and Mick Follows
188			\and Gael Forget \and Baylor Fox-Kemper \and Patrick Heimbach
189			\and Chris Hill \and Ed Hill \and Helen Hill
190			\and Oliver Jahn \and Martin Losch \and John Marshall
191			\and Guillaume Maze \and Dimitris Menemenlis \and Andrea Molod
192	edhill	1.37	\\
193			\\
194			\\
195			MIT Department of EAPS \\
196			77 Massachusetts Ave. \\
197			Cambridge, MA \ 02139-4307
198			}
199
200	jmc	1.41	%\date{August 19, 2004}
201			\date{\today}
202	edhill	1.37
203			\maketitle
204
205	adcroft	1.1	\tableofcontents
206	adcroft	1.10	%\pagebreak
207	adcroft	1.1
208	adcroft	1.10	%\part{MIT GCM basics}
209	adcroft	1.3
210			% Section: Overview
211	adcroft	1.1	\input{part1/part1}
212	adcroft	1.8	%\pagebreak
213	adcroft	1.1
214	adcroft	1.3	% Section: Discretization and Algorithm
215	cnh	1.39	\input{part2/part2}
216	adcroft	1.8	%\pagebreak
217	adcroft	1.1
218	adcroft	1.3	% Section: Getting started
219	cnh	1.39	\input{part3/part3}
220	adcroft	1.8	%\pagebreak
221	adcroft	1.1
222	adcroft	1.3	% Section: Software Architecture
223	cnh	1.39	\input{part4/part4}
224	adcroft	1.8	%\pagebreak
225	adcroft	1.1
226	adcroft	1.3
227	adcroft	1.10	%\part{Adjoint of the MIT GCM}
228	adcroft	1.3
229			% Section: Automatic Differentiation
230	cnh	1.39	\input{part5/part5}
231	adcroft	1.8	%\pagebreak
232	adcroft	1.1
233	adcroft	1.3
234	adcroft	1.10	%\part{Additional features}
235	adcroft	1.3
236			% Section: Physical Packages
237	cnh	1.39	\input{part6/part6}
238	adcroft	1.8	%\pagebreak
239	adcroft	1.1
240	molod	1.30	% Section: Pre-processing and Post-processing Tools
241	cnh	1.39	\input{part7/part7}
242	adcroft	1.14	%\pagebreak
243
244			% Section: ECCO
245	cnh	1.39	\input{part8/part8}
246	edhill	1.24	%\pagebreak
247
248			% Section: Model Uses
249	cnh	1.39	\input{model_uses}
250	adcroft	1.8	%\pagebreak
251	adcroft	1.1
252	heimbach	1.5	% Section: References:
253	adcroft	1.10	%\markboth{BIBLIOGRAPHY}{BIBLIOGRAPHY}
254	heimbach	1.6	\addcontentsline{toc}{chapter}{BIBLIOGRAPHY}
255	adcroft	1.10	%aja%\bibliography{\BIBPATH/manual_references}
256	edhill	1.35	\bibliography{manual_references,baylor_biblio}
257	heimbach	1.6
258	adcroft	1.1	\end{document}