MITgcm/manual/manual.tex

% $Header: /u/gcmpack/manual/manual.tex,v 1.32 2005/08/01 22:14:19 jmc Exp $
% $Name:  $

\documentclass[10pt]{book}

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

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

% 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}


\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	cnh	1.33	% $Header: /u/gcmpack/manual/manual.tex,v 1.32 2005/08/01 22:14:19 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	adcroft	1.8
15	cnh	1.33	% CNH playing around with page widths
16			\usepackage{anysize}
17
18	adcroft	1.8	%cnh%\usepackage{array}
19			%cnh%\usepackage{multirow}
20	cnh	1.12
21	edhill	1.16	%eh3 Commands to reference either files or symbols within the "HTML-ized"
22			%eh3 ("vdb") code.
23			%eh3
24	afe	1.23	%afe seems like these need to be long, sorry
25			\newcommand{\varlink}[2]{\htmladdnormallink{\tt #1}{../code_reference/vdb/byname/#2.html}}
26			\newcommand{\filelink}[2]{\htmladdnormallink{\bf \tt #1}{../code_reference/vdb/byname/#2.html}}
27	afe	1.22
28			% afe Commands to standardize typesetting
29	afe	1.23	\newcommand{\file}[1]{\texttt{#1}}
30			\newcommand{\sectiontitle}[1]{\textsl{#1}}
31			\newcommand{\code}[1]{\texttt{#1}}
32	afe	1.22
33	edhill	1.25	%% EH3 : try out the epsfig package
34	edhill	1.18	\usepackage[dvips]{epsfig}
35			\def\scalefig#1{\epsfxsize #1\textwidth}
36	edhill	1.25
37			%EH3% ==========================================================
38			%EH3% * PRIVATE SECTIONS ** PRIVATE SECTIONS *
39			%EH3%
40			%EH3% Directions: To build the ``private'' or ``local-only''
41			%EH3% version of this manual, then edit the following so
42			%EH3% they appear as:
43			%EH3%
44			%EH3% % \includecomment{versionprivate}
45			%EH3% \excludecoment{versionprivate}
46			%EH3%
47			%EH3% The default is to include everything which is:
48			%EH3%
49			%EH3% \includecomment{versionprivate}
50			%EH3% % \excludecoment{versionprivate}
51
52	afe	1.28	%\includecomment{versionprivate}
53			\excludecomment{versionprivate}
54	edhill	1.25
55			%EH3%
56			%EH3% To use this comment, simply bracket any part of the
57			%EH3% manual with two lines that contain ONLY the following
58			%EH3% pair:
59			%EH3%
60			%EH3% \begin{versionprivate}
61			%EH3% \end{versionprivate}
62			%EH3%
63			%EH3% with NO additional comments or other commands on the
64			%EH3% lines containing the \begin{...}\end{...} statements.
65			%EH3%
66			%EH3% * PRIVATE SECTIONS ** PRIVATE SECTIONS *
67			%EH3% ==========================================================
68	cnh	1.12
69	adcroft	1.8
70			%ph%\usepackage{epsfig}
71			%ph%\usepackage{psfrag}
72			%ph%\usepackage{oldgerm}
73
74	adcroft	1.2	% I commented the following because it introduced excessive white space
75	adcroft	1.8	%aja%\usepackage{palatcm} % better PDF
76	adcroft	1.1
77			% page headers and footers
78	adcroft	1.8	%cnh%\usepackage{fancyhdr}
79	adcroft	1.2	%\pagestyle{fancy}
80	adcroft	1.8	%cnh%\fancyhead{}
81			%cnh%\fancyhead[LO]{\slshape \rightmark}
82			%cnh%\fancyhead[RE]{\slshape \leftmark}
83			%cnh%\fancyhead[RO,LE]{\thepage}
84			%cnh%\fancyfoot[CO,CE]{\today}
85			%cnh%\fancyfoot[RO,LE]{ }
86			%cnh%\renewcommand{\headrulewidth}{0.4pt}
87			%cnh%\renewcommand{\footrulewidth}{0.4pt}
88	adcroft	1.1
89	heimbach	1.5	% bibtex stuff
90	adcroft	1.10	%aja%\newcommand{\BIBPATH}{.}
91			%aja%\usepackage{natbib}
92			%aja%\bibliographystyle{\BIBPATH/jmr_my}
93			%aja%\gdef\harvardleft{[}
94			%aja%\gdef\harvardright{]}
95			%aja%\bibpunct{[}{]}{,}{a}{}{,}
96	jmc	1.32	%\bibliographystyle{plain}
97			%-jmc: try agu bib-style (give author names & year instead of just a number)
98			\usepackage[square]{natbib}
99			\bibliographystyle{agu}
100	heimbach	1.5
101	adcroft	1.1	% referencing
102	adcroft	1.8	%ph%\newcommand{\refequ}[1]{equation (\ref{equ:#1})}
103			%ph%\newcommand{\refequbig}[1]{Equation (\ref{equ:#1})}
104			%ph%\newcommand{\reftab}[1]{Tab.~\ref{tab:#1}}
105			%ph%\newcommand{\reftabno}[1]{\ref{tab:#1}}
106			%ph%\newcommand{\reffig}[1]{Fig.~\ref{fig:#1}}
107			%ph%\newcommand{\reffigno}[1]{\ref{fig:#1}}
108	adcroft	1.1
109			% stuff for psfrag
110	adcroft	1.8	%ph%\newcommand{\textinfigure}[1]{{\footnotesize\textbf{\textsf{#1}}}}
111			%ph%\newcommand{\mathinfigure}[1]{\small\ensuremath{{#1}}}
112	adcroft	1.1
113	adcroft	1.3	% This allows numbering of subsubsections
114			\setcounter{secnumdepth}{3}
115			% This changes the the chapter title
116			%\renewcommand{\chaptername}{Section}
117
118	adcroft	1.11
119			% This allows hyperlinks in PDF
120			% hyperref package and colors for hyperref package
121			\usepackage{color}
122	cnh	1.31	\usepackage{hyperref}
123	cnh	1.29	%\usepackage[dvips]
124	adcroft	1.11	\definecolor{darkgreen}{rgb}{0,0.4,0}
125			\definecolor{darkblue}{rgb}{0,0,0.4}
126			\definecolor{darkred}{rgb}{0.5,0,0}
127			\hypersetup{breaklinks=true,
128			colorlinks=true,
129			linkcolor=darkgreen,
130			citecolor=darkblue,
131			pagecolor=darkred,
132			pdftitle={MITgcm Release 1 Documentation},
133	edhill	1.15	pdfauthor={MITgcm-support@mitgcm.org},
134	adcroft	1.11	pdfkeywords={oceanography, ocean model, general circulation model,
135			non-hydrostatic, finite volume, inverse methods, adjoint method}
136			}
137	molod	1.17
138			% Some definitions (AMM)
139			\def\p#1{{\partial \over {\partial #1}}}
140			\def\pp#1#2{{\partial #1 \over {\partial #2}}}
141			\def\dd#1#2{{d #1 \over {d #2}}}
142			\def\bq{\begin{equation}}
143			\def\bqa{\begin{eqnarray}}
144			\def\eq{\end{equation}}
145			\def\eqa{\end{eqnarray}}
146
147			\def\h{ {1\over2} }
148			\def\txt{\mbox{$2^\circ$ x $2.5^\circ \,$}}
149			\def\fxf{\mbox{$4^\circ$ x $5^\circ \,$}}
150
151			\def\blankpage{ \vspace*{\fill} \vspace{5in} \vfill \newpage}
152
153	adcroft	1.1
154			\begin{document}
155	cnh	1.9
156			\bodytext{bgcolor="#FFFFFFFF"}
157	adcroft	1.1
158			\tableofcontents
159	adcroft	1.10	%\pagebreak
160	adcroft	1.1
161	adcroft	1.10	%\part{MIT GCM basics}
162	adcroft	1.3
163			% Section: Overview
164	adcroft	1.1	\input{part1/part1}
165	adcroft	1.8	%\pagebreak
166	adcroft	1.1
167	adcroft	1.3	% Section: Discretization and Algorithm
168	adcroft	1.1	\input{part2/part2}
169	adcroft	1.8	%\pagebreak
170	adcroft	1.1
171	adcroft	1.3	% Section: Getting started
172	adcroft	1.1	\input{part3/part3}
173	adcroft	1.8	%\pagebreak
174	adcroft	1.1
175	adcroft	1.3	% Section: Software Architecture
176	adcroft	1.1	\input{part4/part4}
177	adcroft	1.8	%\pagebreak
178	adcroft	1.1
179	adcroft	1.3
180	adcroft	1.10	%\part{Adjoint of the MIT GCM}
181	adcroft	1.3
182			% Section: Automatic Differentiation
183	adcroft	1.1	\input{part5/part5}
184	adcroft	1.8	%\pagebreak
185	adcroft	1.1
186	adcroft	1.3
187	adcroft	1.10	%\part{Additional features}
188	adcroft	1.3
189			% Section: Physical Packages
190	adcroft	1.1	\input{part6/part6}
191	adcroft	1.8	%\pagebreak
192	adcroft	1.1
193	molod	1.30	% Section: Pre-processing and Post-processing Tools
194	adcroft	1.1	\input{part7/part7}
195	adcroft	1.14	%\pagebreak
196
197			% Section: ECCO
198			\input{part8/part8}
199	edhill	1.24	%\pagebreak
200
201			% Section: Model Uses
202			\input{model_uses}
203	adcroft	1.8	%\pagebreak
204	adcroft	1.1
205	heimbach	1.5	% Section: References:
206	adcroft	1.10	%\markboth{BIBLIOGRAPHY}{BIBLIOGRAPHY}
207	heimbach	1.6	\addcontentsline{toc}{chapter}{BIBLIOGRAPHY}
208	adcroft	1.10	%aja%\bibliography{\BIBPATH/manual_references}
209			\bibliography{manual_references}
210	heimbach	1.6
211	adcroft	1.1	\end{document}