--- manual/manual.tex 2001/10/21 04:19:40 1.9 +++ manual/manual.tex 2002/03/01 20:03:35 1.12 @@ -1,4 +1,4 @@ -% $Header: /home/ubuntu/mnt/e9_copy/manual/manual.tex,v 1.9 2001/10/21 04:19:40 cnh Exp $ +% $Header: /home/ubuntu/mnt/e9_copy/manual/manual.tex,v 1.12 2002/03/01 20:03:35 cnh Exp $ % $Name: $ \documentclass[12pt]{book} @@ -9,11 +9,22 @@ %aja%\usepackage{amsfonts} \usepackage{amsmath} \usepackage{html} -\usepackage{graphics} +\usepackage{graphicx} %cnh%\usepackage{array} %cnh%\usepackage{multirow} +% Command to reference entries in either "code" or "names" +% directories of browseable code tree. +\newcommand{\proclink}[2]{ +\htmladdnormallink{\em #1()}{../../code_reference/vdb/names/#2_docref.html} +} +\newcommand{\varlink}[2]{ +\htmladdnormallink{\bf \tt #1}{../../code_reference/vdb/names/#2_docref.html} +} + + + %ph%\usepackage{epsfig} %ph%\usepackage{psfrag} %ph%\usepackage{oldgerm} @@ -34,12 +45,13 @@ %cnh%\renewcommand{\footrulewidth}{0.4pt} % bibtex stuff -\newcommand{\BIBPATH}{.} -\usepackage{natbib} -\bibliographystyle{\BIBPATH/jmr_my} -\gdef\harvardleft{[} -\gdef\harvardright{]} -\bibpunct{[}{]}{,}{a}{}{,} +%aja%\newcommand{\BIBPATH}{.} +%aja%\usepackage{natbib} +%aja%\bibliographystyle{\BIBPATH/jmr_my} +%aja%\gdef\harvardleft{[} +%aja%\gdef\harvardright{]} +%aja%\bibpunct{[}{]}{,}{a}{}{,} +\bibliographystyle{plain} % referencing %ph%\newcommand{\refequ}[1]{equation (\ref{equ:#1})} @@ -59,14 +71,32 @@ %\renewcommand{\chaptername}{Section} +% This allows hyperlinks in PDF +% hyperref package and colors for hyperref package +\usepackage{color} +\usepackage[dvips]{hyperref} +\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={support@mitgcm.org}, + pdfkeywords={oceanography, ocean model, general circulation model, + non-hydrostatic, finite volume, inverse methods, adjoint method} + } + \begin{document} \bodytext{bgcolor="#FFFFFFFF"} \tableofcontents -\pagebreak +%\pagebreak -\part{MIT GCM basics} +%\part{MIT GCM basics} % Section: Overview \input{part1/part1} @@ -85,14 +115,14 @@ %\pagebreak -\part{Adjoint of the MIT GCM} +%\part{Adjoint of the MIT GCM} % Section: Automatic Differentiation \input{part5/part5} %\pagebreak -\part{Additional features} +%\part{Additional features} % Section: Physical Packages \input{part6/part6} @@ -107,8 +137,9 @@ %\pagebreak % Section: References: -\markboth{BIBLIOGRAPHY}{BIBLIOGRAPHY} +%\markboth{BIBLIOGRAPHY}{BIBLIOGRAPHY} \addcontentsline{toc}{chapter}{BIBLIOGRAPHY} -\bibliography{\BIBPATH/manual_references} +%aja%\bibliography{\BIBPATH/manual_references} +\bibliography{manual_references} \end{document}