--- manual/s_overview/text/manual.tex	2004/03/23 15:29:39	1.18
+++ manual/s_overview/text/manual.tex	2004/03/23 16:47:04	1.19
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 % $Name:  $
 
 %tci%\documentclass[12pt]{book}
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 % Section: Overview
 
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+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.19 2004/03/23 16:47:04 afe Exp $
 % $Name:  $
 
 This document provides the reader with the information necessary to
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 \section{Introduction}
 \begin{rawhtml}
-<!-- CMIREDIR:innovations -->
+<!-- CMIREDIR:innovations: -->
 \end{rawhtml}
 
 
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 We begin by briefly showing some of the results of the model in action to
 give a feel for the wide range of problems that can be addressed using it.
 
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 % $Name:  $
 
 \section{Illustrations of the model in action}
@@ -155,7 +155,7 @@
 
 \subsection{Global atmosphere: `Held-Suarez' benchmark}
 \begin{rawhtml}
-<!-- CMIREDIR:atmospheric_example -->
+<!-- CMIREDIR:atmospheric_example: -->
 \end{rawhtml}
 
 
@@ -196,10 +196,10 @@
 
 \subsection{Ocean gyres}
 \begin{rawhtml}
-<!-- CMIREDIR:oceanic_example -->
+<!-- CMIREDIR:oceanic_example: -->
 \end{rawhtml}
 \begin{rawhtml}
-<!-- CMIREDIR:ocean_gyres -->
+<!-- CMIREDIR:ocean_gyres: -->
 \end{rawhtml}
 
 Baroclinic instability is a ubiquitous process in the ocean, as well as the
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 \subsection{Global ocean circulation}
 \begin{rawhtml}
-<!-- CMIREDIR:global_ocean_circulation -->
+<!-- CMIREDIR:global_ocean_circulation: -->
 \end{rawhtml}
 
 Figure \ref{fig:large-scale-circ} (top) shows the pattern of ocean currents at 
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 \subsection{Convection and mixing over topography}
 \begin{rawhtml}
-<!-- CMIREDIR:mixing_over_topography -->
+<!-- CMIREDIR:mixing_over_topography: -->
 \end{rawhtml}
 
 
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 \subsection{Boundary forced internal waves}
 \begin{rawhtml}
-<!-- CMIREDIR:boundary_forced_internal_waves -->
+<!-- CMIREDIR:boundary_forced_internal_waves: -->
 \end{rawhtml}
 
 The unique ability of MITgcm to treat non-hydrostatic dynamics in the
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 \subsection{Parameter sensitivity using the adjoint of MITgcm}
 \begin{rawhtml}
-<!-- CMIREDIR:parameter_sensitivity -->
+<!-- CMIREDIR:parameter_sensitivity: -->
 \end{rawhtml}
 
 Forward and tangent linear counterparts of MITgcm are supported using an
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 \subsection{Global state estimation of the ocean}
 \begin{rawhtml}
-<!-- CMIREDIR:global_state_estimation -->
+<!-- CMIREDIR:global_state_estimation: -->
 \end{rawhtml}
 
 
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 \subsection{Ocean biogeochemical cycles}
 \begin{rawhtml}
-<!-- CMIREDIR:ocean_biogeo_cycles -->
+<!-- CMIREDIR:ocean_biogeo_cycles: -->
 \end{rawhtml}
 
 MITgcm is being used to study global biogeochemical cycles in the ocean. For
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 \subsection{Simulations of laboratory experiments}
 \begin{rawhtml}
-<!-- CMIREDIR:classroom_exp -->
+<!-- CMIREDIR:classroom_exp: -->
 \end{rawhtml}
 
 Figure \ref{fig:lab-simulation} shows MITgcm being used to simulate a 
@@ -372,12 +372,12 @@
 \input{part1/lab_figure}
 %%CNHend
 
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+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.19 2004/03/23 16:47:04 afe Exp $
 % $Name:  $
 
 \section{Continuous equations in `r' coordinates}
 \begin{rawhtml}
-<!-- CMIREDIR:z-p_isomorphism -->
+<!-- CMIREDIR:z-p_isomorphism: -->
 \end{rawhtml}
 
 To render atmosphere and ocean models from one dynamical core we exploit
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 \subsection{Hydrostatic, Quasi-hydrostatic, Quasi-nonhydrostatic and
 Non-hydrostatic forms}
 \begin{rawhtml}
-<!-- CMIREDIR:non_hydrostatic -->
+<!-- CMIREDIR:non_hydrostatic: -->
 \end{rawhtml}
 
 
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 Tangent linear and adjoint counterparts of the forward model are described
 in Chapter 5.
 
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 % $Name:  $
 
 \section{Appendix ATMOSPHERE}
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 \frac{D\theta }{Dt} &=&\frac{\mathcal{Q}}{\Pi } 
 \end{eqnarray}
 
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 % $Name:  $
 
 \section{Appendix OCEAN}
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 _{nh}=0$ form of these equations that are used throughout the ocean modeling
 community and referred to as the primitive equations (HPE).
 
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+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.19 2004/03/23 16:47:04 afe Exp $
 % $Name:  $
 
 \section{Appendix:OPERATORS}