MITgcm/manual/manual.tex

% $Header: /u/gcmpack/manual/manual.tex,v 1.36 2005/12/16 06:26:09 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}}

% 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}

% 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	edhill	1.37	% $Header: /u/gcmpack/manual/manual.tex,v 1.36 2005/12/16 06:26:09 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	afe	1.22
29			% afe Commands to standardize typesetting
30	afe	1.23	\newcommand{\file}[1]{\texttt{#1}}
31			\newcommand{\sectiontitle}[1]{\textsl{#1}}
32			\newcommand{\code}[1]{\texttt{#1}}
33	afe	1.22
34	edhill	1.25	%% EH3 : try out the epsfig package
35	edhill	1.18	\usepackage[dvips]{epsfig}
36			\def\scalefig#1{\epsfxsize #1\textwidth}
37	edhill	1.25
38			%EH3% ==========================================================
39			%EH3% * PRIVATE SECTIONS ** PRIVATE SECTIONS *
40			%EH3%
41			%EH3% Directions: To build the ``private'' or ``local-only''
42			%EH3% version of this manual, then edit the following so
43			%EH3% they appear as:
44			%EH3%
45			%EH3% % \includecomment{versionprivate}
46			%EH3% \excludecoment{versionprivate}
47			%EH3%
48			%EH3% The default is to include everything which is:
49			%EH3%
50			%EH3% \includecomment{versionprivate}
51			%EH3% % \excludecoment{versionprivate}
52
53	afe	1.28	%\includecomment{versionprivate}
54			\excludecomment{versionprivate}
55	edhill	1.25
56			%EH3%
57			%EH3% To use this comment, simply bracket any part of the
58			%EH3% manual with two lines that contain ONLY the following
59			%EH3% pair:
60			%EH3%
61			%EH3% \begin{versionprivate}
62			%EH3% \end{versionprivate}
63			%EH3%
64			%EH3% with NO additional comments or other commands on the
65			%EH3% lines containing the \begin{...}\end{...} statements.
66			%EH3%
67			%EH3% * PRIVATE SECTIONS ** PRIVATE SECTIONS *
68			%EH3% ==========================================================
69	cnh	1.12
70	adcroft	1.8
71			%ph%\usepackage{epsfig}
72			%ph%\usepackage{psfrag}
73			%ph%\usepackage{oldgerm}
74
75	adcroft	1.2	% I commented the following because it introduced excessive white space
76	adcroft	1.8	%aja%\usepackage{palatcm} % better PDF
77	adcroft	1.1
78			% page headers and footers
79	adcroft	1.8	%cnh%\usepackage{fancyhdr}
80	adcroft	1.2	%\pagestyle{fancy}
81	adcroft	1.8	%cnh%\fancyhead{}
82			%cnh%\fancyhead[LO]{\slshape \rightmark}
83			%cnh%\fancyhead[RE]{\slshape \leftmark}
84			%cnh%\fancyhead[RO,LE]{\thepage}
85			%cnh%\fancyfoot[CO,CE]{\today}
86			%cnh%\fancyfoot[RO,LE]{ }
87			%cnh%\renewcommand{\headrulewidth}{0.4pt}
88			%cnh%\renewcommand{\footrulewidth}{0.4pt}
89	adcroft	1.1
90	heimbach	1.5	% bibtex stuff
91	adcroft	1.10	%aja%\newcommand{\BIBPATH}{.}
92			%aja%\usepackage{natbib}
93			%aja%\bibliographystyle{\BIBPATH/jmr_my}
94			%aja%\gdef\harvardleft{[}
95			%aja%\gdef\harvardright{]}
96			%aja%\bibpunct{[}{]}{,}{a}{}{,}
97	jmc	1.32	%\bibliographystyle{plain}
98			%-jmc: try agu bib-style (give author names & year instead of just a number)
99			\usepackage[square]{natbib}
100			\bibliographystyle{agu}
101	heimbach	1.5
102	adcroft	1.1	% referencing
103	adcroft	1.8	%ph%\newcommand{\refequ}[1]{equation (\ref{equ:#1})}
104			%ph%\newcommand{\refequbig}[1]{Equation (\ref{equ:#1})}
105			%ph%\newcommand{\reftab}[1]{Tab.~\ref{tab:#1}}
106			%ph%\newcommand{\reftabno}[1]{\ref{tab:#1}}
107			%ph%\newcommand{\reffig}[1]{Fig.~\ref{fig:#1}}
108			%ph%\newcommand{\reffigno}[1]{\ref{fig:#1}}
109	adcroft	1.1
110			% stuff for psfrag
111	adcroft	1.8	%ph%\newcommand{\textinfigure}[1]{{\footnotesize\textbf{\textsf{#1}}}}
112			%ph%\newcommand{\mathinfigure}[1]{\small\ensuremath{{#1}}}
113	adcroft	1.1
114	adcroft	1.3	% This allows numbering of subsubsections
115			\setcounter{secnumdepth}{3}
116			% This changes the the chapter title
117			%\renewcommand{\chaptername}{Section}
118
119	adcroft	1.11
120			% This allows hyperlinks in PDF
121			% hyperref package and colors for hyperref package
122			\usepackage{color}
123	cnh	1.31	\usepackage{hyperref}
124	cnh	1.29	%\usepackage[dvips]
125	adcroft	1.11	\definecolor{darkgreen}{rgb}{0,0.4,0}
126			\definecolor{darkblue}{rgb}{0,0,0.4}
127			\definecolor{darkred}{rgb}{0.5,0,0}
128			\hypersetup{breaklinks=true,
129			colorlinks=true,
130			linkcolor=darkgreen,
131			citecolor=darkblue,
132			pagecolor=darkred,
133			pdftitle={MITgcm Release 1 Documentation},
134	edhill	1.15	pdfauthor={MITgcm-support@mitgcm.org},
135	adcroft	1.11	pdfkeywords={oceanography, ocean model, general circulation model,
136			non-hydrostatic, finite volume, inverse methods, adjoint method}
137			}
138	molod	1.17
139			% Some definitions (AMM)
140			\def\p#1{{\partial \over {\partial #1}}}
141			\def\pp#1#2{{\partial #1 \over {\partial #2}}}
142			\def\dd#1#2{{d #1 \over {d #2}}}
143			\def\bq{\begin{equation}}
144			\def\bqa{\begin{eqnarray}}
145			\def\eq{\end{equation}}
146			\def\eqa{\end{eqnarray}}
147
148			\def\h{ {1\over2} }
149			\def\txt{\mbox{$2^\circ$ x $2.5^\circ \,$}}
150			\def\fxf{\mbox{$4^\circ$ x $5^\circ \,$}}
151
152			\def\blankpage{ \vspace*{\fill} \vspace{5in} \vfill \newpage}
153
154	edhill	1.36	% Some definitions modified from the ones provided by Baylor
155			\def\BFKav#1{\overline{#1}}
156			\def\BFKpd#1#2{{\frac{\partial{#2}}{\partial{#1}}}}
157			\def\BFKpds#1#2{{\frac{\partial^2{#2}}{{\partial{#1}}^2}}}
158			\def\BFKDt#1{\frac{D{#1}}{Dt}}
159			\def\BFKaDt#1{\frac{\BFKav D{#1}}{\BFKav{Dt}}}
160			\def\BFKd#1{{\,\rm d#1}}
161			\def\BFKRo{{\rm Ro}}
162			\def\BFKRe{{\rm Re}}
163			\def\BFKFr{{\rm Fr}}
164			\def\BFKPr{{\rm Pr}}
165			\def\BFKMr{{M_{Ro}}}
166			\def\BFKtu{{\tilde u}}
167			\def\BFKtv{{\tilde v}}
168			\def\BFKatu{{\tilde {\BFKav u}}}
169			\def\BFKatv{{\tilde {\BFKav v}}}
170			\def\BFKlesssim{{<\atop\sim}}
171	adcroft	1.1
172			\begin{document}
173	cnh	1.9
174			\bodytext{bgcolor="#FFFFFFFF"}
175	adcroft	1.1
176	edhill	1.37	\title{ \textsc{MITgcm User Manual} }
177
178			\author{
179			John Marshall \and Alistair Adcroft \and Jean-Michel Campin
180			\and Patrick Heimbach \and Andrea Molod \and Stephanie Dutkiewicz
181			\and Helen Hill \and Martin Losch \and Baylor Fox-Kemper
182			\and Dimitris Menemenlis \and David Ferreira \and Ed Hill
183			\and Mick Follows \and Chris Hill \and Constantinos Evangelinos
184			\and Gael Forget
185			\\
186			\\
187			\\
188			MIT Department of EAPS \\
189			77 Massachusetts Ave. \\
190			Cambridge, MA \ 02139-4307
191			}
192
193			\date{August 19, 2004}
194
195			\maketitle
196
197	adcroft	1.1	\tableofcontents
198	adcroft	1.10	%\pagebreak
199	adcroft	1.1
200	adcroft	1.10	%\part{MIT GCM basics}
201	adcroft	1.3
202			% Section: Overview
203	adcroft	1.1	\input{part1/part1}
204	adcroft	1.8	%\pagebreak
205	adcroft	1.1
206	adcroft	1.3	% Section: Discretization and Algorithm
207	adcroft	1.1	\input{part2/part2}
208	adcroft	1.8	%\pagebreak
209	adcroft	1.1
210	adcroft	1.3	% Section: Getting started
211	adcroft	1.1	\input{part3/part3}
212	adcroft	1.8	%\pagebreak
213	adcroft	1.1
214	adcroft	1.3	% Section: Software Architecture
215	adcroft	1.1	\input{part4/part4}
216	adcroft	1.8	%\pagebreak
217	adcroft	1.1
218	adcroft	1.3
219	adcroft	1.10	%\part{Adjoint of the MIT GCM}
220	adcroft	1.3
221			% Section: Automatic Differentiation
222	adcroft	1.1	\input{part5/part5}
223	adcroft	1.8	%\pagebreak
224	adcroft	1.1
225	adcroft	1.3
226	adcroft	1.10	%\part{Additional features}
227	adcroft	1.3
228			% Section: Physical Packages
229	adcroft	1.1	\input{part6/part6}
230	adcroft	1.8	%\pagebreak
231	adcroft	1.1
232	molod	1.30	% Section: Pre-processing and Post-processing Tools
233	adcroft	1.1	\input{part7/part7}
234	adcroft	1.14	%\pagebreak
235
236			% Section: ECCO
237			\input{part8/part8}
238	edhill	1.24	%\pagebreak
239
240			% Section: Model Uses
241			\input{model_uses}
242	adcroft	1.8	%\pagebreak
243	adcroft	1.1
244	heimbach	1.5	% Section: References:
245	adcroft	1.10	%\markboth{BIBLIOGRAPHY}{BIBLIOGRAPHY}
246	heimbach	1.6	\addcontentsline{toc}{chapter}{BIBLIOGRAPHY}
247	adcroft	1.10	%aja%\bibliography{\BIBPATH/manual_references}
248	edhill	1.35	\bibliography{manual_references,baylor_biblio}
249	heimbach	1.6
250	adcroft	1.1	\end{document}