--- manual/s_overview/text/manual.tex	2004/03/23 15:29:39	1.18
+++ manual/s_overview/text/manual.tex	2004/10/17 04:15:13	1.22
@@ -1,4 +1,4 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.18 2004/03/23 15:29:39 afe Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.22 2004/10/17 04:15:13 jmc 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 1.18 2004/03/23 15:29:39 afe Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.22 2004/10/17 04:15:13 jmc Exp $
 % $Name:  $
 
 This document provides the reader with the information necessary to
@@ -49,7 +49,7 @@
 
 \section{Introduction}
 \begin{rawhtml}
-<!-- CMIREDIR:innovations -->
+<!-- CMIREDIR:innovations: -->
 \end{rawhtml}
 
 
@@ -137,7 +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 1.18 2004/03/23 15:29:39 afe Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.22 2004/10/17 04:15:13 jmc Exp $
 % $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
@@ -228,7 +228,7 @@
 
 \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 
@@ -249,7 +249,7 @@
 
 \subsection{Convection and mixing over topography}
 \begin{rawhtml}
-<!-- CMIREDIR:mixing_over_topography -->
+<!-- CMIREDIR:mixing_over_topography: -->
 \end{rawhtml}
 
 
@@ -272,7 +272,7 @@
 
 \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
@@ -294,7 +294,7 @@
 
 \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
@@ -317,7 +317,7 @@
 
 \subsection{Global state estimation of the ocean}
 \begin{rawhtml}
-<!-- CMIREDIR:global_state_estimation -->
+<!-- CMIREDIR:global_state_estimation: -->
 \end{rawhtml}
 
 
@@ -338,7 +338,7 @@
 
 \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
@@ -356,7 +356,7 @@
 
 \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
 
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.18 2004/03/23 15:29:39 afe Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.22 2004/10/17 04:15:13 jmc 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
@@ -409,11 +409,11 @@
 \input{part1/vertcoord_figure.tex}
 %%CNHend
 
-\begin{equation*}
+\begin{equation}
 \frac{D\vec{\mathbf{v}_{h}}}{Dt}+\left( 2\vec{\Omega}\times \vec{\mathbf{v}}
 \right) _{h}+\mathbf{\nabla }_{h}\phi =\mathcal{F}_{\vec{\mathbf{v}_{h}}}
 \text{ horizontal mtm} \label{eq:horizontal_mtm}
-\end{equation*}
+\end{equation}
 
 \begin{equation}
 \frac{D\dot{r}}{Dt}+\widehat{k}\cdot \left( 2\vec{\Omega}\times \vec{\mathbf{
@@ -611,9 +611,11 @@
 atmosphere)}  \label{eq:moving-bc-atmos}
 \end{eqnarray}
 
-Then the (hydrostatic form of) equations (\ref{eq:horizontal_mtm}-\ref{eq:humidity_salt}) 
-yields a consistent set of atmospheric equations which, for convenience, are written out in $p$
-coordinates in Appendix Atmosphere - see eqs(\ref{eq:atmos-prime}).
+Then the (hydrostatic form of) equations
+(\ref{eq:horizontal_mtm}-\ref{eq:humidity_salt}) yields a consistent
+set of atmospheric equations which, for convenience, are written out
+in $p$ coordinates in Appendix Atmosphere - see
+eqs(\ref{eq:atmos-prime}).
 
 \subsection{Ocean}
 
@@ -656,7 +658,7 @@
 \subsection{Hydrostatic, Quasi-hydrostatic, Quasi-nonhydrostatic and
 Non-hydrostatic forms}
 \begin{rawhtml}
-<!-- CMIREDIR:non_hydrostatic -->
+<!-- CMIREDIR:non_hydrostatic: -->
 \end{rawhtml}
 
 
@@ -666,7 +668,9 @@
 \phi (x,y,r)=\phi _{s}(x,y)+\phi _{hyd}(x,y,r)+\phi _{nh}(x,y,r)
 \label{eq:phi-split}
 \end{equation}
-and write eq(\ref{eq:incompressible}) in the form:
+%and write eq(\ref{eq:incompressible}) in the form: 
+%                  ^- this eq is missing (jmc) ; replaced with:
+and write eq( \ref{eq:horizontal_mtm}) in the form:
 
 \begin{equation}
 \frac{\partial \vec{\mathbf{v}_{h}}}{\partial t}+\mathbf{\nabla }_{h}\phi
@@ -1096,8 +1100,9 @@
 
 \subsection{Vector invariant form}
 
-For some purposes it is advantageous to write momentum advection in eq(\ref
-{eq:horizontal_mtm}) and (\ref{eq:vertical_mtm}) in the (so-called) `vector invariant' form:
+For some purposes it is advantageous to write momentum advection in
+eq(\ref {eq:horizontal_mtm}) and (\ref{eq:vertical_mtm}) in the
+(so-called) `vector invariant' form:
 
 \begin{equation}
 \frac{D\vec{\mathbf{v}}}{Dt}=\frac{\partial \vec{\mathbf{v}}}{\partial t}
@@ -1118,7 +1123,7 @@
 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 1.18 2004/03/23 15:29:39 afe Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.22 2004/10/17 04:15:13 jmc Exp $
 % $Name:  $
 
 \section{Appendix ATMOSPHERE}
@@ -1208,6 +1213,7 @@
 surface ($\phi $ is imposed and $\omega \neq 0$).
 
 \subsubsection{Splitting the geo-potential}
+\label{sec:hpe-p-geo-potential-split}
 
 For the purposes of initialization and reducing round-off errors, the model
 deals with perturbations from reference (or ``standard'') profiles. For
@@ -1237,7 +1243,8 @@
 The final form of the HPE's in p coordinates is then: 
 \begin{eqnarray}
 \frac{D\vec{\mathbf{v}}_{h}}{Dt}+f\hat{\mathbf{k}}\times \vec{\mathbf{v}}
-_{h}+\mathbf{\nabla }_{p}\phi ^{\prime } &=&\vec{\mathbf{\mathcal{F}}} \label{eq:atmos-prime} \\
+_{h}+\mathbf{\nabla }_{p}\phi ^{\prime } &=&\vec{\mathbf{\mathcal{F}}} 
+\label{eq:atmos-prime} \\
 \frac{\partial \phi ^{\prime }}{\partial p}+\alpha ^{\prime } &=&0 \\
 \mathbf{\nabla }_{p}\cdot \vec{\mathbf{v}}_{h}+\frac{\partial \omega }{
 \partial p} &=&0 \\
@@ -1245,7 +1252,7 @@
 \frac{D\theta }{Dt} &=&\frac{\mathcal{Q}}{\Pi } 
 \end{eqnarray}
 
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.18 2004/03/23 15:29:39 afe Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.22 2004/10/17 04:15:13 jmc Exp $
 % $Name:  $
 
 \section{Appendix OCEAN}
@@ -1283,8 +1290,9 @@
 _{\theta ,S}\frac{Dp}{Dt}  \label{EOSexpansion}
 \end{equation}
 
-Note that $\frac{\partial \rho }{\partial p}=\frac{1}{c_{s}^{2}}$ is the
-reciprocal of the sound speed ($c_{s}$) squared. Substituting into \ref{eq-zns-cont} gives: 
+Note that $\frac{\partial \rho }{\partial p}=\frac{1}{c_{s}^{2}}$ is
+the reciprocal of the sound speed ($c_{s}$) squared. Substituting into
+\ref{eq-zns-cont} gives:
 \begin{equation}
 \frac{1}{\rho c_{s}^{2}}\frac{Dp}{Dt}+\mathbf{\nabla }_{z}\cdot \vec{\mathbf{
 v}}+\partial _{z}w\approx 0  \label{eq-zns-pressure}
@@ -1461,7 +1469,7 @@
 _{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 1.18 2004/03/23 15:29:39 afe Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.22 2004/10/17 04:15:13 jmc Exp $
 % $Name:  $
 
 \section{Appendix:OPERATORS}