--- manual/s_examples/baroclinic_gyre/fourlayer.tex	2004/10/13 05:06:26	1.18
+++ manual/s_examples/baroclinic_gyre/fourlayer.tex	2008/01/15 17:20:54	1.23
@@ -1,9 +1,15 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_examples/baroclinic_gyre/fourlayer.tex,v 1.18 2004/10/13 05:06:26 cnh Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_examples/baroclinic_gyre/fourlayer.tex,v 1.23 2008/01/15 17:20:54 jmc Exp $
 % $Name:  $
 
 \section[Baroclinic Gyre MITgcm Example]{Four Layer Baroclinic Ocean Gyre In Spherical Coordinates}
 \label{www:tutorials}
 \label{sect:eg-fourlayer}
+\begin{rawhtml}
+<!-- CMIREDIR:eg-fourlayer: -->
+\end{rawhtml}
+\begin{center}
+(in directory: {\it verification/tutorial\_baroclinic\_gyre/})
+\end{center}
 
 \bodytext{bgcolor="#FFFFFFFF"}
 
@@ -18,13 +24,9 @@
 %\end{center}
 
 This document describes an example experiment using MITgcm
-to simulate a baroclinic ocean gyre in spherical
-polar coordinates. The barotropic
-example experiment in section \ref{sect:eg-baro}
-illustrated how to configure the code for a single layer 
-simulation in a Cartesian grid. In this example a similar physical problem
-is simulated, but the code is now configured
-for four layers and in a spherical polar coordinate system.
+to simulate a baroclinic ocean gyre for four layers in spherical
+polar coordinates.  The files for this experiment can be found
+in the verification directory under tutorial\_baroclinic\_gyre.
 
 \subsection{Overview}
 \label{www:tutorials}
@@ -353,7 +355,8 @@
 \label{SEC:eg_fourl_code_config}
 
 The model configuration for this experiment resides under the 
-directory {\it verification/exp2/}.  The experiment files 
+directory {\it verification/tutorial\_barotropic\_gyre/}.
+The experiment files 
 \begin{itemize}
 \item {\it input/data}
 \item {\it input/data.pkg}
@@ -380,7 +383,7 @@
 \item Line 4, 
 \begin{verbatim} tRef=20.,10.,8.,6., \end{verbatim} 
 this line sets the initial and reference values of potential
-temperature at each model level in units of $^{\circ}$C.  The entries
+temperature at each model level in units of $^{\circ}\mathrm{C}$.  The entries
 are ordered from surface to depth. For each depth level the initial
 and reference profiles will be uniform in $x$ and $y$. The values
 specified here are read into the variable \varlink{tRef}{tRef} in the
@@ -418,18 +421,12 @@
   coefficient to $1 \times 10^{-2} {\rm m^{2}s^{-1}}$. Boundary
   conditions for this operator are specified later.  The variable
   \varlink{viscAh}{viscAh} is read in the routine
-  \varlink{INI\_PARMS}{INI_PARMS} and applied in routines
-  \varlink{CALC\_MOM\_RHS}{CALC_MOM_RHS} and
-  \varlink{CALC\_GW}{CALC_GW}.
+  \varlink{INI\_PARMS}{INI_PARMS} and applied in routine
+  \varlink{MOM\_FLUXFORM}{MOM_FLUXFORM}.
 
 \fbox{
   \begin{minipage}{5.0in}
-    {\it S/R CALC\_MOM\_RHS}({\it calc\_mom\_rhs.F})
-  \end{minipage}
-}
-\fbox{
-  \begin{minipage}{5.0in}
-    {\it S/R CALC\_GW}({\it calc\_gw.F})
+    {\it S/R MOM\_FLUXFORM}({\it mom\_fluxform.F})
   \end{minipage}
 }
 
@@ -447,10 +444,10 @@
 
   \fbox{
     \begin{minipage}{5.0in}
-      {\it S/R CALC\_MOM\_RHS}({\it calc\_mom\_rhs.F})
+      {\it S/R MOM\_FLUXFORM}({\it mom\_fluxform.F})
     \end{minipage}
   }
-  \filelink{calc\_mom\_rhs.F}{calc_mom_rhs.F}
+  \filelink{mom\_fluxform.F}{pkg-mom_fluxform-mom_fluxform.F}
   
 \item Lines 9,
 \begin{verbatim}
@@ -461,14 +458,14 @@
   at $z=-H$, where $H$ is the local depth of the domain.  The variable
   \varlink{no\_slip\_bottom}{no\_slip\_bottom} is read in the routine
   \filelink{INI\_PARMS}{model-src-ini_parms.F} and is applied in the
-  routine \varlink{CALC\_MOM\_RHS}{CALC_MOM_RHS}.
+  routine \varlink{MOM\_FLUXFORM}{MOM_FLUXFORM}.
 
   \fbox{
     \begin{minipage}{5.0in}
-      {\it S/R CALC\_MOM\_RHS}({\it calc\_mom\_rhs.F})
+      {\it S/R MOM\_FLUXFORM}({\it mom\_fluxform.F})
     \end{minipage}
   }
-  \filelink{calc\_mom\_rhs.F}{calc_mom_rhs.F}
+  \filelink{mom\_fluxform.F}{pkg-mom_fluxform-mom_fluxform.F}
 
 \item Line 10,
 \begin{verbatim}