--- manual/s_overview/text/manual.tex	2002/02/28 19:32:19	1.16
+++ manual/s_overview/text/manual.tex	2004/03/23 15:29:39	1.18
@@ -1,4 +1,4 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.16 2002/02/28 19:32:19 cnh Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.18 2004/03/23 15:29:39 afe Exp $
 % $Name:  $
 
 %tci%\documentclass[12pt]{book}
@@ -34,7 +34,7 @@
 
 % Section: Overview
 
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.16 2002/02/28 19:32:19 cnh Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.18 2004/03/23 15:29:39 afe Exp $
 % $Name:  $
 
 This document provides the reader with the information necessary to
@@ -48,6 +48,10 @@
 also presented.
 
 \section{Introduction}
+\begin{rawhtml}
+<!-- CMIREDIR:innovations -->
+\end{rawhtml}
+
 
 MITgcm has a number of novel aspects:
 
@@ -133,7 +137,7 @@
 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.
 
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.16 2002/02/28 19:32:19 cnh Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.18 2004/03/23 15:29:39 afe Exp $
 % $Name:  $
 
 \section{Illustrations of the model in action}
@@ -150,6 +154,11 @@
 described in detail in the documentation.
 
 \subsection{Global atmosphere: `Held-Suarez' benchmark}
+\begin{rawhtml}
+<!-- CMIREDIR:atmospheric_example -->
+\end{rawhtml}
+
+
 
 A novel feature of MITgcm is its ability to simulate, using one basic algorithm, 
 both atmospheric and oceanographic flows at both small and large scales.
@@ -186,6 +195,12 @@
 %% CNHend
 
 \subsection{Ocean gyres}
+\begin{rawhtml}
+<!-- CMIREDIR:oceanic_example -->
+\end{rawhtml}
+\begin{rawhtml}
+<!-- CMIREDIR:ocean_gyres -->
+\end{rawhtml}
 
 Baroclinic instability is a ubiquitous process in the ocean, as well as the
 atmosphere. Ocean eddies play an important role in modifying the
@@ -212,6 +227,9 @@
 
 
 \subsection{Global ocean circulation}
+\begin{rawhtml}
+<!-- CMIREDIR:global_ocean_circulation -->
+\end{rawhtml}
 
 Figure \ref{fig:large-scale-circ} (top) shows the pattern of ocean currents at 
 the surface of a 4$^{\circ }$
@@ -230,6 +248,10 @@
 %%CNHend
 
 \subsection{Convection and mixing over topography}
+\begin{rawhtml}
+<!-- CMIREDIR:mixing_over_topography -->
+\end{rawhtml}
+
 
 Dense plumes generated by localized cooling on the continental shelf of the
 ocean may be influenced by rotation when the deformation radius is smaller
@@ -249,6 +271,9 @@
 %%CNHend
 
 \subsection{Boundary forced internal waves}
+\begin{rawhtml}
+<!-- CMIREDIR:boundary_forced_internal_waves -->
+\end{rawhtml}
 
 The unique ability of MITgcm to treat non-hydrostatic dynamics in the
 presence of complex geometry makes it an ideal tool to study internal wave
@@ -268,6 +293,9 @@
 %%CNHend
 
 \subsection{Parameter sensitivity using the adjoint of MITgcm}
+\begin{rawhtml}
+<!-- CMIREDIR:parameter_sensitivity -->
+\end{rawhtml}
 
 Forward and tangent linear counterparts of MITgcm are supported using an
 `automatic adjoint compiler'. These can be used in parameter sensitivity and
@@ -288,6 +316,10 @@
 %%CNHend
 
 \subsection{Global state estimation of the ocean}
+\begin{rawhtml}
+<!-- CMIREDIR:global_state_estimation -->
+\end{rawhtml}
+
 
 An important application of MITgcm is in state estimation of the global
 ocean circulation. An appropriately defined `cost function', which measures
@@ -305,6 +337,9 @@
 %% CNHend
 
 \subsection{Ocean biogeochemical cycles}
+\begin{rawhtml}
+<!-- CMIREDIR:ocean_biogeo_cycles -->
+\end{rawhtml}
 
 MITgcm is being used to study global biogeochemical cycles in the ocean. For
 example one can study the effects of interannual changes in meteorological
@@ -320,9 +355,12 @@
 %%CNHend
 
 \subsection{Simulations of laboratory experiments}
+\begin{rawhtml}
+<!-- CMIREDIR:classroom_exp -->
+\end{rawhtml}
 
 Figure \ref{fig:lab-simulation} shows MITgcm being used to simulate a 
-laboratory experiment inquiring in to the dynamics of the Antarctic Circumpolar Current (ACC). An
+laboratory experiment inquiring into the dynamics of the Antarctic Circumpolar Current (ACC). An
 initially homogeneous tank of water ($1m$ in diameter) is driven from its
 free surface by a rotating heated disk. The combined action of mechanical
 and thermal forcing creates a lens of fluid which becomes baroclinically
@@ -334,10 +372,13 @@
 \input{part1/lab_figure}
 %%CNHend
 
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.16 2002/02/28 19:32:19 cnh Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.18 2004/03/23 15:29:39 afe Exp $
 % $Name:  $
 
 \section{Continuous equations in `r' coordinates}
+\begin{rawhtml}
+<!-- CMIREDIR:z-p_isomorphism -->
+\end{rawhtml}
 
 To render atmosphere and ocean models from one dynamical core we exploit
 `isomorphisms' between equation sets that govern the evolution of the
@@ -346,8 +387,8 @@
 and encoded. The model variables have different interpretations depending on
 whether the atmosphere or ocean is being studied. Thus, for example, the
 vertical coordinate `$r$' is interpreted as pressure, $p$, if we are
-modeling the atmosphere (left hand side of figure \ref{fig:isomorphic-equations})
-and height, $z$, if we are modeling the ocean (right hand side of figure
+modeling the atmosphere (right hand side of figure \ref{fig:isomorphic-equations})
+and height, $z$, if we are modeling the ocean (left hand side of figure
 \ref{fig:isomorphic-equations}).
 
 %%CNHbegin
@@ -471,12 +512,12 @@
 at fixed and moving $r$ surfaces we set (see figure \ref{fig:zandp-vert-coord}):
 
 \begin{equation}
-\dot{r}=0atr=R_{fixed}(x,y)\text{ (ocean bottom, top of the atmosphere)}
+\dot{r}=0 \text{\ at\ } r=R_{fixed}(x,y)\text{ (ocean bottom, top of the atmosphere)}
 \label{eq:fixedbc}
 \end{equation}
 
 \begin{equation}
-\dot{r}=\frac{Dr}{Dt}atr=R_{moving}\text{ \
+\dot{r}=\frac{Dr}{Dt} \text{\ at\ } r=R_{moving}\text{ \
 (ocean surface,bottom of the atmosphere)}  \label{eq:movingbc}
 \end{equation}
 
@@ -614,6 +655,10 @@
 
 \subsection{Hydrostatic, Quasi-hydrostatic, Quasi-nonhydrostatic and
 Non-hydrostatic forms}
+\begin{rawhtml}
+<!-- CMIREDIR:non_hydrostatic -->
+\end{rawhtml}
+
 
 Let us separate $\phi $ in to surface, hydrostatic and non-hydrostatic terms:
 
@@ -1073,7 +1118,7 @@
 Tangent linear and adjoint counterparts of the forward model are described
 in Chapter 5.
 
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.16 2002/02/28 19:32:19 cnh Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.18 2004/03/23 15:29:39 afe Exp $
 % $Name:  $
 
 \section{Appendix ATMOSPHERE}
@@ -1200,7 +1245,7 @@
 \frac{D\theta }{Dt} &=&\frac{\mathcal{Q}}{\Pi } 
 \end{eqnarray}
 
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.16 2002/02/28 19:32:19 cnh Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.18 2004/03/23 15:29:39 afe Exp $
 % $Name:  $
 
 \section{Appendix OCEAN}
@@ -1416,7 +1461,7 @@
 _{nh}=0$ form of these equations that are used throughout the ocean modeling
 community and referred to as the primitive equations (HPE).
 
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.16 2002/02/28 19:32:19 cnh Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.18 2004/03/23 15:29:39 afe Exp $
 % $Name:  $
 
 \section{Appendix:OPERATORS}