--- manual/s_examples/baroclinic_gyre/fourlayer.tex	2006/04/08 01:50:50	1.20
+++ manual/s_examples/baroclinic_gyre/fourlayer.tex	2010/08/27 13:25:31	1.27
@@ -1,4 +1,4 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_examples/baroclinic_gyre/fourlayer.tex,v 1.20 2006/04/08 01:50:50 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[Baroclinic Gyre MITgcm Example]{Four Layer Baroclinic Ocean Gyre In Spherical Coordinates}
@@ -7,6 +7,9 @@
 \begin{rawhtml}
 <!-- CMIREDIR:eg-fourlayer: -->
 \end{rawhtml}
+\begin{center}
+(in directory: {\it verification/tutorial\_baroclinic\_gyre/})
+\end{center}
 
 \bodytext{bgcolor="#FFFFFFFF"}
 
@@ -21,13 +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}
@@ -110,11 +109,11 @@
 %% \begin{center}
 %%  \resizebox{7.5in}{5.5in}{
 %%    \includegraphics*[0.2in,0.7in][10.5in,10.5in]
-%%    {part3/case_studies/fourlayer_gyre/simulation_config.eps} }
+%%    {s_examples/baroclinic_gyre/simulation_config.eps} }
 %% \end{center}
 \centerline{
   \scalefig{.95}
-  \epsfbox{part3/case_studies/fourlayer_gyre/simulation_config.eps}
+  \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
@@ -356,7 +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}
@@ -421,18 +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}
 }
 
@@ -450,10 +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}
@@ -464,14 +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}
@@ -565,7 +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
@@ -573,7 +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{
@@ -685,7 +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}
 
@@ -750,7 +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}}