--- manual/s_overview/text/manual.tex	2001/11/16 21:18:36	1.11
+++ manual/s_overview/text/manual.tex	2006/04/05 02:27:32	1.24
@@ -1,4 +1,4 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.11 2001/11/16 21:18:36 cnh Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.24 2006/04/05 02:27:32 edhill Exp $
 % $Name:  $
 
 %tci%\documentclass[12pt]{book}
@@ -34,12 +34,10 @@
 
 % Section: Overview
 
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.11 2001/11/16 21:18:36 cnh Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.24 2006/04/05 02:27:32 edhill Exp $
 % $Name:  $
 
-\section{Introduction}
-
-This documentation provides the reader with the information necessary to
+This document provides the reader with the information necessary to
 carry out numerical experiments using MITgcm. It gives a comprehensive
 description of the continuous equations on which the model is based, the
 numerical algorithms the model employs and a description of the associated
@@ -49,6 +47,12 @@
 both process and general circulation studies of the atmosphere and ocean are
 also presented.
 
+\section{Introduction}
+\begin{rawhtml}
+<!-- CMIREDIR:innovations: -->
+\end{rawhtml}
+
+
 MITgcm has a number of novel aspects:
 
 \begin{itemize}
@@ -84,17 +88,61 @@
 \end{itemize}
 
 Key publications reporting on and charting the development of the model are
-listed in an Appendix.
+\cite{hill:95,marshall:97a,marshall:97b,adcroft:97,marshall:98,adcroft:99,hill:99,maro-eta:99,adcroft:04a,adcroft:04b,marshall:04}:
+
+\begin{verbatim}
+Hill, C. and J. Marshall, (1995)
+Application of a Parallel Navier-Stokes Model to Ocean Circulation in 
+Parallel Computational Fluid Dynamics
+In Proceedings of Parallel Computational Fluid Dynamics: Implementations 
+and Results Using Parallel Computers, 545-552.
+Elsevier Science B.V.: New York
+
+Marshall, J., C. Hill, L. Perelman, and A. Adcroft, (1997)
+Hydrostatic, quasi-hydrostatic, and nonhydrostatic ocean modeling
+J. Geophysical Res., 102(C3), 5733-5752.
+
+Marshall, J., A. Adcroft, C. Hill, L. Perelman, and C. Heisey, (1997)
+A finite-volume, incompressible Navier Stokes model for studies of the ocean
+on parallel computers,
+J. Geophysical Res., 102(C3), 5753-5766.
+
+Adcroft, A.J., Hill, C.N. and J. Marshall, (1997)
+Representation of topography by shaved cells in a height coordinate ocean
+model
+Mon Wea Rev, vol 125, 2293-2315
+
+Marshall, J., Jones, H. and C. Hill, (1998)
+Efficient ocean modeling using non-hydrostatic algorithms
+Journal of Marine Systems, 18, 115-134
+
+Adcroft, A., Hill C. and J. Marshall: (1999)
+A new treatment of the Coriolis terms in C-grid models at both high and low
+resolutions,
+Mon. Wea. Rev. Vol 127, pages 1928-1936
+
+Hill, C, Adcroft,A., Jamous,D., and J. Marshall, (1999)
+A Strategy for Terascale Climate Modeling.
+In Proceedings of the Eighth ECMWF Workshop on the Use of Parallel Processors
+in Meteorology, pages 406-425
+World Scientific Publishing Co: UK
+
+Marotzke, J, Giering,R., Zhang, K.Q., Stammer,D., Hill,C., and T.Lee, (1999)
+Construction of the adjoint MIT ocean general circulation model and 
+application to Atlantic heat transport variability
+J. Geophysical Res., 104(C12), 29,529-29,547.
+
+\end{verbatim}
 
 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 1.11 2001/11/16 21:18:36 cnh Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.24 2006/04/05 02:27:32 edhill Exp $
 % $Name:  $
 
 \section{Illustrations of the model in action}
 
-The MITgcm has been designed and used to model a wide range of phenomena,
+MITgcm has been designed and used to model a wide range of phenomena,
 from convection on the scale of meters in the ocean to the global pattern of
 atmospheric winds - see figure \ref{fig:all-scales}. To give a flavor of the
 kinds of problems the model has been used to study, we briefly describe some
@@ -106,6 +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.
@@ -142,6 +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
@@ -168,6 +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$^{\circ }$
@@ -186,6 +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
@@ -205,6 +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
@@ -224,6 +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
@@ -244,22 +316,30 @@
 %%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
 the departure of the model from observations (both remotely sensed and
 in-situ) over an interval of time, is minimized by adjusting `control
 parameters' such as air-sea fluxes, the wind field, the initial conditions
-etc. Figure \ref{fig:assimilated-globes} shows an estimate of the time-mean
-surface elevation of the ocean obtained by bringing the model in to
+etc. Figure \ref{fig:assimilated-globes} shows the large scale planetary
+circulation and a Hopf-Muller plot of Equatorial sea-surface height.
+Both are obtained from assimilation bringing the model in to
 consistency with altimetric and in-situ observations over the period
-1992-1997. {\bf CHANGE THIS TEXT - FIG FROM PATRICK/CARL/DETLEF}
+1992-1997.
 
 %% CNHbegin
-\input{part1/globes_figure}
+\input{part1/assim_figure}
 %% 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
@@ -275,9 +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
@@ -289,10 +372,13 @@
 \input{part1/lab_figure}
 %%CNHend
 
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.11 2001/11/16 21:18:36 cnh Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.24 2006/04/05 02:27:32 edhill 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
@@ -301,8 +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
@@ -323,11 +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{
@@ -426,12 +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}
 
@@ -525,9 +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}
 
@@ -569,6 +657,10 @@
 
 \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:
 
@@ -576,7 +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
@@ -676,15 +770,16 @@
 
 \subsubsection{Shallow atmosphere approximation}
 
-Most models are based on the `hydrostatic primitive equations' (HPE's) in
-which the vertical momentum equation is reduced to a statement of
-hydrostatic balance and the `traditional approximation' is made in which the
-Coriolis force is treated approximately and the shallow atmosphere
-approximation is made.\ The MITgcm need not make the `traditional
-approximation'. To be able to support consistent non-hydrostatic forms the
-shallow atmosphere approximation can be relaxed - when dividing through by $
-r $ in, for example, (\ref{eq:gu-speherical}), we do not replace $r$ by $a$,
-the radius of the earth.
+Most models are based on the `hydrostatic primitive equations' (HPE's)
+in which the vertical momentum equation is reduced to a statement of
+hydrostatic balance and the `traditional approximation' is made in
+which the Coriolis force is treated approximately and the shallow
+atmosphere approximation is made.  MITgcm need not make the
+`traditional approximation'. To be able to support consistent
+non-hydrostatic forms the shallow atmosphere approximation can be
+relaxed - when dividing through by $ r $ in, for example,
+(\ref{eq:gu-speherical}), we do not replace $r$ by $a$, the radius of
+the earth.
 
 \subsubsection{Hydrostatic and quasi-hydrostatic forms}
 \label{sec:hydrostatic_and_quasi-hydrostatic_forms}
@@ -721,7 +816,7 @@
 
 \subsubsection{Non-hydrostatic and quasi-nonhydrostatic forms}
 
-The MIT model presently supports a full non-hydrostatic ocean isomorph, but
+MITgcm presently supports a full non-hydrostatic ocean isomorph, but
 only a quasi-non-hydrostatic atmospheric isomorph.
 
 \paragraph{Non-hydrostatic Ocean}
@@ -1006,8 +1101,9 @@
 
 \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}
@@ -1028,7 +1124,7 @@
 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 1.11 2001/11/16 21:18:36 cnh Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.24 2006/04/05 02:27:32 edhill Exp $
 % $Name:  $
 
 \section{Appendix ATMOSPHERE}
@@ -1118,6 +1214,7 @@
 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
@@ -1147,7 +1244,8 @@
 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 \\
@@ -1155,7 +1253,7 @@
 \frac{D\theta }{Dt} &=&\frac{\mathcal{Q}}{\Pi } 
 \end{eqnarray}
 
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.11 2001/11/16 21:18:36 cnh Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.24 2006/04/05 02:27:32 edhill Exp $
 % $Name:  $
 
 \section{Appendix OCEAN}
@@ -1193,8 +1291,9 @@
 _{\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}
@@ -1371,7 +1470,7 @@
 _{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 1.11 2001/11/16 21:18:36 cnh Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.24 2006/04/05 02:27:32 edhill Exp $
 % $Name:  $
 
 \section{Appendix:OPERATORS}
