MITgcm/manual/manual.tex

% $Header: /u/gcmpack/manual/manual.tex,v 1.35 2005/10/05 19:52:47 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"} 

\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	1.36	% $Header: /u/gcmpack/manual/manual.tex,v 1.35 2005/10/05 19:52:47 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			\tableofcontents
177	adcroft	1.10	%\pagebreak
178	adcroft	1.1
179	adcroft	1.10	%\part{MIT GCM basics}
180	adcroft	1.3
181			% Section: Overview
182	adcroft	1.1	\input{part1/part1}
183	adcroft	1.8	%\pagebreak
184	adcroft	1.1
185	adcroft	1.3	% Section: Discretization and Algorithm
186	adcroft	1.1	\input{part2/part2}
187	adcroft	1.8	%\pagebreak
188	adcroft	1.1
189	adcroft	1.3	% Section: Getting started
190	adcroft	1.1	\input{part3/part3}
191	adcroft	1.8	%\pagebreak
192	adcroft	1.1
193	adcroft	1.3	% Section: Software Architecture
194	adcroft	1.1	\input{part4/part4}
195	adcroft	1.8	%\pagebreak
196	adcroft	1.1
197	adcroft	1.3
198	adcroft	1.10	%\part{Adjoint of the MIT GCM}
199	adcroft	1.3
200			% Section: Automatic Differentiation
201	adcroft	1.1	\input{part5/part5}
202	adcroft	1.8	%\pagebreak
203	adcroft	1.1
204	adcroft	1.3
205	adcroft	1.10	%\part{Additional features}
206	adcroft	1.3
207			% Section: Physical Packages
208	adcroft	1.1	\input{part6/part6}
209	adcroft	1.8	%\pagebreak
210	adcroft	1.1
211	molod	1.30	% Section: Pre-processing and Post-processing Tools
212	adcroft	1.1	\input{part7/part7}
213	adcroft	1.14	%\pagebreak
214
215			% Section: ECCO
216			\input{part8/part8}
217	edhill	1.24	%\pagebreak
218
219			% Section: Model Uses
220			\input{model_uses}
221	adcroft	1.8	%\pagebreak
222	adcroft	1.1
223	heimbach	1.5	% Section: References:
224	adcroft	1.10	%\markboth{BIBLIOGRAPHY}{BIBLIOGRAPHY}
225	heimbach	1.6	\addcontentsline{toc}{chapter}{BIBLIOGRAPHY}
226	adcroft	1.10	%aja%\bibliography{\BIBPATH/manual_references}
227	edhill	1.35	\bibliography{manual_references,baylor_biblio}
228	heimbach	1.6
229	adcroft	1.1	\end{document}