MITgcm/manual/manual.tex

% $Header: /u/gcmpack/manual/manual.tex,v 1.37 2006/04/07 15:40:07 edhill 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}}

\begin{document}

\bodytext{bgcolor="#FFFFFFFF"} 

\title{ \textsc{MITgcm User Manual} }

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

\date{August 19, 2004}

\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	cnh	1.38	% $Header: /u/gcmpack/manual/manual.tex,v 1.37 2006/04/07 15:40:07 edhill 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			\begin{document}
176	cnh	1.9
177			\bodytext{bgcolor="#FFFFFFFF"}
178	adcroft	1.1
179	edhill	1.37	\title{ \textsc{MITgcm User Manual} }
180
181			\author{
182			John Marshall \and Alistair Adcroft \and Jean-Michel Campin
183			\and Patrick Heimbach \and Andrea Molod \and Stephanie Dutkiewicz
184			\and Helen Hill \and Martin Losch \and Baylor Fox-Kemper
185			\and Dimitris Menemenlis \and David Ferreira \and Ed Hill
186			\and Mick Follows \and Chris Hill \and Constantinos Evangelinos
187			\and Gael Forget
188			\\
189			\\
190			\\
191			MIT Department of EAPS \\
192			77 Massachusetts Ave. \\
193			Cambridge, MA \ 02139-4307
194			}
195
196			\date{August 19, 2004}
197
198			\maketitle
199
200	adcroft	1.1	\tableofcontents
201	adcroft	1.10	%\pagebreak
202	adcroft	1.1
203	adcroft	1.10	%\part{MIT GCM basics}
204	adcroft	1.3
205			% Section: Overview
206	adcroft	1.1	\input{part1/part1}
207	adcroft	1.8	%\pagebreak
208	adcroft	1.1
209	adcroft	1.3	% Section: Discretization and Algorithm
210	cnh	1.38	%% \input{part2/part2}
211	adcroft	1.8	%\pagebreak
212	adcroft	1.1
213	adcroft	1.3	% Section: Getting started
214	cnh	1.38	%% \input{part3/part3}
215	adcroft	1.8	%\pagebreak
216	adcroft	1.1
217	adcroft	1.3	% Section: Software Architecture
218	cnh	1.38	%% \input{part4/part4}
219	adcroft	1.8	%\pagebreak
220	adcroft	1.1
221	adcroft	1.3
222	adcroft	1.10	%\part{Adjoint of the MIT GCM}
223	adcroft	1.3
224			% Section: Automatic Differentiation
225	cnh	1.38	%% \input{part5/part5}
226	adcroft	1.8	%\pagebreak
227	adcroft	1.1
228	adcroft	1.3
229	adcroft	1.10	%\part{Additional features}
230	adcroft	1.3
231			% Section: Physical Packages
232	cnh	1.38	%% \input{part6/part6}
233	adcroft	1.8	%\pagebreak
234	adcroft	1.1
235	molod	1.30	% Section: Pre-processing and Post-processing Tools
236	cnh	1.38	%% \input{part7/part7}
237	adcroft	1.14	%\pagebreak
238
239			% Section: ECCO
240	cnh	1.38	%% \input{part8/part8}
241	edhill	1.24	%\pagebreak
242
243			% Section: Model Uses
244	cnh	1.38	%% \input{model_uses}
245	adcroft	1.8	%\pagebreak
246	adcroft	1.1
247	heimbach	1.5	% Section: References:
248	adcroft	1.10	%\markboth{BIBLIOGRAPHY}{BIBLIOGRAPHY}
249	heimbach	1.6	\addcontentsline{toc}{chapter}{BIBLIOGRAPHY}
250	adcroft	1.10	%aja%\bibliography{\BIBPATH/manual_references}
251	edhill	1.35	\bibliography{manual_references,baylor_biblio}
252	heimbach	1.6
253	adcroft	1.1	\end{document}