--- manual/s_phys_pkgs/text/gmredi.tex	2004/01/28 17:13:33	1.6
+++ manual/s_phys_pkgs/text/gmredi.tex	2010/08/30 23:09:21	1.15
@@ -1,4 +1,8 @@
-\section{Gent/McWiliams/Redi SGS Eddy parameterization}
+\subsection{GMREDI: Gent/McWiliams/Redi SGS Eddy Parameterization}
+\label{sec:pkg:gmredi}
+\begin{rawhtml}
+<!-- CMIREDIR:gmredi: -->
+\end{rawhtml}
 
 There are two parts to the Redi/GM parameterization of geostrophic
 eddies. The first aims to mix tracer properties along isentropes
@@ -31,7 +35,7 @@
 that the horizontal fluxes are unmodified from the lateral diffusion
 parameterization.
 
-\subsection{Redi scheme: Isopycnal diffusion}
+\subsubsection{Redi scheme: Isopycnal diffusion}
 
 The Redi scheme diffuses tracers along isopycnals and introduces a
 term in the tendency (rhs) of such a tracer (here $\tau$) of the form:
@@ -71,7 +75,7 @@
 \end{equation}
 
 
-\subsection{GM parameterization}
+\subsubsection{GM parameterization}
 
 The GM parameterization aims to parameterise the ``advective'' or
 ``transport'' effect of geostrophic eddies by means of a ``bolus''
@@ -100,7 +104,7 @@
 This is the form of the GM parameterization as applied by Donabasaglu,
 1997, in MOM versions 1 and 2.
 
-\subsection{Griffies Skew Flux}
+\subsubsection{Griffies Skew Flux}
 
 Griffies notes that the discretisation of bolus velocities involves
 multiple layers of differencing and interpolation that potentially
@@ -187,7 +191,7 @@
 
 
 
-\subsection{Variable $\kappa_{GM}$}
+\subsubsection{Variable $\kappa_{GM}$}
 
 Visbeck et al., 1996, suggest making the eddy coefficient,
 $\kappa_{GM}$, a function of the Eady growth rate,
@@ -213,7 +217,7 @@
 \end{displaymath}
 
 
-\subsection{Tapering and stability}
+\subsubsection{Tapering and stability}
 
 Experience with the GFDL model showed that the GM scheme has to be
 matched to the convective parameterization. This was originally
@@ -238,7 +242,7 @@
 
 \begin{figure}
 \begin{center}
-\resizebox{5.0in}{3.0in}{\includegraphics{part6/tapers.eps}}
+\resizebox{5.0in}{3.0in}{\includegraphics{s_phys_pkgs/figs/tapers.eps}}
 \end{center}
 \caption{Taper functions used in GKW99 and DM95.}
 \label{fig:tapers}
@@ -246,7 +250,7 @@
 
 \begin{figure}
 \begin{center}
-\resizebox{5.0in}{3.0in}{\includegraphics{part6/effective_slopes.eps}}
+\resizebox{5.0in}{3.0in}{\includegraphics{s_phys_pkgs/figs/effective_slopes.eps}}
 \end{center}
 \caption{Effective slope as a function of ``true'' slope using Cox
 slope clipping, GKW91 limiting and DM95 limiting.}
@@ -254,7 +258,7 @@
 \end{figure}
 
 
-\subsubsection{Slope clipping}
+Slope clipping:
 
 Deep convection sites and the mixed layer are indicated by
 homogenized, unstable or nearly unstable stratification. The slopes in
@@ -301,7 +305,7 @@
 of the GM/Redi parameterization, re-introducing diabatic fluxes in
 regions where the limiting is in effect.
 
-\subsubsection{Tapering: Gerdes, Koberle and Willebrand, Clim. Dyn. 1991}
+Tapering: Gerdes, Koberle and Willebrand, Clim. Dyn. 1991:
 
 The tapering scheme used in Gerdes et al., 1999, (\cite{gkw:99})
 addressed two issues with the clipping method: the introduction of
@@ -325,7 +329,7 @@
 The GKW tapering scheme is activated in the model by setting {\bf
 GM\_tap\-er\_scheme = 'gkw91'} in {\em data.gmredi}.
 
-\subsection{Tapering: Danabasoglu and McWilliams, J. Clim. 1995}
+\subsubsection{Tapering: Danabasoglu and McWilliams, J. Clim. 1995}
 
 The tapering scheme used by Danabasoglu and McWilliams, 1995,
 \cite{dm:95}, followed a similar procedure but used a different
@@ -342,7 +346,7 @@
 The DM tapering scheme is activated in the model by setting {\bf
 GM\_tap\-er\_scheme = 'dm95'} in {\em data.gmredi}.
 
-\subsection{Tapering: Large, Danabasoglu and Doney, JPO 1997}
+\subsubsection{Tapering: Large, Danabasoglu and Doney, JPO 1997}
 
 The tapering used in Large et al., 1997, \cite{ldd:97}, is based on the
 DM95 tapering scheme, but also tapers the scheme with an additional
@@ -372,7 +376,39 @@
 \label{fig-mixedlayer}
 \end{figure}
 
-\subsection{Package Reference}
+\subsubsection{Package Reference}
+\label{sec:pkg:gmredi:diagnostics}
+
+{\footnotesize
+\begin{verbatim}
+------------------------------------------------------------------------
+<-Name->|Levs|<-parsing code->|<--  Units   -->|<- Tile (max=80c) 
+------------------------------------------------------------------------
+GM_VisbK|  1 |SM P    M1      |m^2/s           |Mixing coefficient from Visbeck etal parameterization
+GM_Kux  | 15 |UU P 177MR      |m^2/s           |K_11 element (U.point, X.dir) of GM-Redi tensor
+GM_Kvy  | 15 |VV P 176MR      |m^2/s           |K_22 element (V.point, Y.dir) of GM-Redi tensor
+GM_Kuz  | 15 |UU   179MR      |m^2/s           |K_13 element (U.point, Z.dir) of GM-Redi tensor
+GM_Kvz  | 15 |VV   178MR      |m^2/s           |K_23 element (V.point, Z.dir) of GM-Redi tensor
+GM_Kwx  | 15 |UM   181LR      |m^2/s           |K_31 element (W.point, X.dir) of GM-Redi tensor
+GM_Kwy  | 15 |VM   180LR      |m^2/s           |K_32 element (W.point, Y.dir) of GM-Redi tensor
+GM_Kwz  | 15 |WM P    LR      |m^2/s           |K_33 element (W.point, Z.dir) of GM-Redi tensor
+GM_PsiX | 15 |UU   184LR      |m^2/s           |GM Bolus transport stream-function : X component
+GM_PsiY | 15 |VV   183LR      |m^2/s           |GM Bolus transport stream-function : Y component
+GM_KuzTz| 15 |UU   186MR      |degC.m^3/s      |Redi Off-diagonal Tempetature flux: X component
+GM_KvzTz| 15 |VV   185MR      |degC.m^3/s      |Redi Off-diagonal Tempetature flux: Y component
+\end{verbatim}
+}
+
+\subsubsection{Experiments and tutorials that use gmredi}
+\label{sec:pkg:gmredi:experiments}
+
+\begin{itemize}
+\item{Global Ocean tutorial, in tutorial\_global\_oce\_latlon verification directory,
+described in section \ref{sec:eg-global} }
+\item{ Front Relax experiment, in front\_relax verification directory.}
+\item{ Ideal 2D Ocean experiment, in ideal\_2D\_oce verification directory.}
+\end{itemize}
+
 % DO NOT EDIT HERE
 
 
