--- manual/s_phys_pkgs/text/gridalt.tex	2006/04/05 02:27:33	1.8
+++ manual/s_phys_pkgs/text/gridalt.tex	2010/08/30 23:09:21	1.14
@@ -6,7 +6,8 @@
 
 \subsubsection {Introduction} 
 
-The gridalt package is designed to allow different components of MITgcm to
+The gridalt package \citep{mol:09} 
+is designed to allow different components of MITgcm to
 be run using horizontal and/or vertical grids which are different from the main 
 model grid. The gridalt routines handle the definition of the all the various
 alternative grid(s) and the mappings between them and the MITgcm grid.
@@ -43,7 +44,7 @@
 \begin{figure}[htbp]
 \vspace*{-0.4in}
 \begin{center}
-\includegraphics[height=2.4in]{part6/vertical.eps}
+\includegraphics[height=2.4in]{s_phys_pkgs/figs/vertical.eps}
 \caption{Vertical discretization for MITgcm (dark grey lines) and for the
 atmospheric physics (light grey lines). In this implementation, all MITgcm level
 interfaces must coincide with atmospheric physics level interfaces.}
@@ -68,16 +69,16 @@
 a second set of evolution equations for the atmospheric state variables on the modified grid. 
 If the equation for the evolution of $U$ on $p^*$ can be expressed as:
 \[
-\left . {\partial U \over {\partial t}} \right |_{p^*}^{total} = 
-\left . {\partial U \over {\partial t}} \right |_{p^*}^{dynamics} + 
-\left . {\partial U \over {\partial t}} \right |_{p^*}^{physics}
+\left . \frac{\partial U}{\partial t} \right |_{p^*}^{total} = 
+\left . \frac{\partial U}{\partial t} \right |_{p^*}^{dynamics} + 
+\left . \frac{\partial U}{\partial t} \right |_{p^*}^{physics}
 \]
 where the physics forcing terms on $p^*$ have been mapped from the modified grid, then an additional 
 equation to govern the evolution of $U$ (for example) on the modified grid is written:
 \[
-\left . {\partial U \over {\partial t}} \right |_{p^{*m}}^{total} = 
-\left . {\partial U \over {\partial t}} \right |_{p^{*m}}^{dynamics} + 
-\left . {\partial U \over {\partial t}} \right |_{p^{*m}}^{physics} +
+\left . \frac{\partial U}{\partial t} \right |_{p^{*m}}^{total} = 
+\left . \frac{\partial U}{\partial t} \right |_{p^{*m}}^{dynamics} + 
+\left . \frac{\partial U}{\partial t} \right |_{p^{*m}}^{physics} +
 \gamma ({\left . U \right |_{p^*}} - {\left . U \right |_{p^{*m}}})
 \]
 where $p^{*m}$ refers to the modified higher resolution grid, and the dynamics forcing terms have 
@@ -238,6 +239,26 @@
 
 \noindent And similarly, gridalt contains subroutine phys2dyn.
 
+\subsubsection {Gridalt Diagnostics}
+\label{sec:pkg:gridalt:diagnostics}
+
+{\footnotesize
+\begin{verbatim}
+
+------------------------------------------------------------------------
+<-Name->|Levs|<-parsing code->|<--  Units   -->|<- Tile (max=80c) 
+------------------------------------------------------------------------
+DPPHYS  | 20 |SM      ML      |Pascal          |Pressure Thickness of Layers on Fizhi Grid
+\end{verbatim}
+}
+
 \subsubsection {Dos and donts}
 
 \subsubsection {Gridalt Reference} 
+
+\subsubsection{Experiments and tutorials that use gridalt}
+\label{sec:pkg:gridalt:experiments}
+
+\begin{itemize}
+\item{Fizhi experiment, in fizhi-cs-32x32x10 verification directory }
+\end{itemize}