--- manual/s_examples/baroclinic_gyre/fourlayer.tex	2003/09/15 19:39:04	1.16
+++ manual/s_examples/baroclinic_gyre/fourlayer.tex	2010/08/27 13:25:31	1.27
@@ -1,9 +1,15 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_examples/baroclinic_gyre/fourlayer.tex,v 1.16 2003/09/15 19:39:04 edhill Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_examples/baroclinic_gyre/fourlayer.tex,v 1.27 2010/08/27 13:25:31 jmc Exp $
 % $Name:  $
 
-\section{Four Layer Baroclinic Ocean Gyre In Spherical Coordinates}
+\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}
@@ -104,11 +106,15 @@
 the quantity that is carried in the model core equations.
 
 \begin{figure}
-\begin{center}
- \resizebox{7.5in}{5.5in}{
-   \includegraphics*[0.2in,0.7in][10.5in,10.5in]
-   {part3/case_studies/fourlayer_gyre/simulation_config.eps} }
-\end{center}
+%% \begin{center}
+%%  \resizebox{7.5in}{5.5in}{
+%%    \includegraphics*[0.2in,0.7in][10.5in,10.5in]
+%%    {s_examples/baroclinic_gyre/simulation_config.eps} }
+%% \end{center}
+\centerline{
+  \scalefig{.95}
+  \epsfbox{s_examples/baroclinic_gyre/simulation_config.eps}
+}
 \caption{Schematic of simulation domain and wind-stress forcing function 
 for the four-layer gyre numerical experiment. The domain is enclosed by solid
 walls at $0^{\circ}$~E, $60^{\circ}$~E, $0^{\circ}$~N and $60^{\circ}$~N.
@@ -349,7 +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}
@@ -376,7 +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
@@ -414,18 +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}
 }
 
@@ -443,10 +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}
@@ -457,14 +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}
@@ -558,7 +559,7 @@
 
 \item Line 41,
 \begin{verbatim}
-phiMin=0.,
+ygOrigin=0.,
 \end{verbatim}
   This line sets the southern boundary of the modeled domain to
   $0^{\circ}$ latitude. This value affects both the generation of the
@@ -566,7 +567,7 @@
   the initialization of the coriolis force.  Note - it is not required
   to set a longitude boundary, since the absolute longitude does not
   alter the kernel equation discretisation.  The variable
-  \varlink{phiMin}{phiMin} is read in the
+  \varlink{ygOrigin}{ygOrigin} is read in the
   routine \varlink{INI\_PARMS}{INI_PARMS} and is used in routine
 
   \fbox{
@@ -678,7 +679,7 @@
 
 \begin{rawhtml}<PRE>\end{rawhtml}
 \begin{small}
-\input{part3/case_studies/fourlayer_gyre/input/data}
+\input{s_examples/baroclinic_gyre/input/data}
 \end{small}
 \begin{rawhtml}</PRE>\end{rawhtml}
 
@@ -743,7 +744,7 @@
 \end{itemize}
 
 \begin{small}
-\include{part3/case_studies/fourlayer_gyre/code/SIZE.h}
+\include{s_examples/baroclinic_gyre/code/SIZE.h}
 \end{small}
 
 \subsubsection{File {\it code/CPP\_OPTIONS.h}}