--- manual/manual.tex 2001/08/08 16:15:12 1.1.1.1 +++ manual/manual.tex 2017/06/19 20:07:25 1.47 @@ -1,79 +1,265 @@ -% $Header: /home/ubuntu/mnt/e9_copy/manual/manual.tex,v 1.1.1.1 2001/08/08 16:15:12 adcroft Exp $ +% $Header: /home/ubuntu/mnt/e9_copy/manual/manual.tex,v 1.47 2017/06/19 20:07:25 jmc Exp $ % $Name: $ -\documentclass[12pt]{book} +\documentclass[10pt]{book} -\usepackage{amsfonts} +%To help cross-reference +%\usepackage{showlabels} + +%aja%\usepackage{amsfonts} \usepackage{amsmath} \usepackage{html} -\usepackage{epsfig} -\usepackage{graphics,subfigure} -\usepackage{array} -\usepackage{multirow} -\usepackage{fancyhdr} -\usepackage{psfrag} -\usepackage{oldgerm} -\usepackage{palatcm} % better PDF +\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 -\pagestyle{fancy} -\fancyhead{} -\fancyhead[LO]{\slshape \rightmark} -\fancyhead[RE]{\slshape \leftmark} -\fancyhead[RO,LE]{\thepage} -\fancyfoot[CO,CE]{\today} -\fancyfoot[RO,LE]{ } -\renewcommand{\headrulewidth}{0.4pt} -\renewcommand{\footrulewidth}{0.4pt} +%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 -\newcommand{\refequ}[1]{equation (\ref{equ:#1})} -\newcommand{\refequbig}[1]{Equation (\ref{equ:#1})} -\newcommand{\reftab}[1]{Tab.~\ref{tab:#1}} -\newcommand{\reftabno}[1]{\ref{tab:#1}} -\newcommand{\reffig}[1]{Fig.~\ref{fig:#1}} -\newcommand{\reffigno}[1]{\ref{fig:#1}} +%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 -\newcommand{\textinfigure}[1]{{\footnotesize\textbf{\textsf{#1}}}} -\newcommand{\mathinfigure}[1]{\small\ensuremath{{#1}}} - +%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 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{\frac{\partial }{\partial #1}} +\def\pp#1#2{\frac{\partial #1}{\partial #2}} +\def\dd#1#2{\frac{d #1}{d #2}} +\def\bq{\begin{equation}} +\def\bqa{\begin{eqnarray}} +\def\eq{\end{equation}} +\def\eqa{\end{eqnarray}} + +\def\h{ \frac{1}{2} } +\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 +%\pagebreak + +%\part{MIT GCM basics} + +% Section: Overview of MITgcm +\input{s_overview/text/top_section} +%\pagebreak + +% Section: Discretization and Algorithm +\input{s_algorithm/text/top_section} +%\pagebreak + +% Section: Getting started with MITgcm +\input{s_getstarted/text/top_section} +%\pagebreak + +% Section: Model Example <- not yet a section +\input{s_examples/text/top_section} +%\pagebreak + +% Section: Software Architecture +\input{s_software/text/top_section} +%\pagebreak + + +%\part{Adjoint of the MIT GCM} + +% Section: Automatic Differentiation +\input{s_autodiff/text/top_section} +%\pagebreak + + +%\part{Additional features} + +% Section: Physical Parameterization - Packages I +\input{s_phys_pkgs/text/top_section} +%\pagebreak + +% Section: Diagnostics and I/O - Packages II, and Post-Processing Utilities +\input{s_outp_pkgs/text/top_section} +%\pagebreak + +% Section: Interface with ECCO +\input{s_ecco/text/top_section} +%\pagebreak + +% Section: Under Development +\input{s_under_dvlp/text/top_section} -% Part: Overview -\input{part1/part1} -\pagebreak - -% Part: Discretization and Algorithm -\input{part2/part2} -\pagebreak - -% Part: Getting started -\input{part3/part3} -\pagebreak - -% Part: Software Architecture -\input{part4/part4} -\pagebreak - -% Part: Automatic Differentiation -\input{part5/part5} -\pagebreak - -% Part: Physical Packages -\input{part6/part6} -\pagebreak - -% Part: Diagnostics -\input{part7/part7} -\pagebreak +% Section: Previous applications of MITgcm +\input{model_uses} +%\pagebreak -% Part: ECCO Interface -\input{part8/part8} +% Section: References: +%\markboth{BIBLIOGRAPHY}{BIBLIOGRAPHY} +\addcontentsline{toc}{chapter}{BIBLIOGRAPHY} +%aja%\bibliography{\BIBPATH/manual_references} +\bibliography{manual_references,baylor_biblio} \end{document}