--- manual/s_examples/baroclinic_gyre/fourlayer.tex	2002/02/28 19:32:19	1.12
+++ manual/s_examples/baroclinic_gyre/fourlayer.tex	2003/08/07 18:27:52	1.15
@@ -1,7 +1,8 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_examples/baroclinic_gyre/fourlayer.tex,v 1.12 2002/02/28 19:32:19 cnh Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_examples/baroclinic_gyre/fourlayer.tex,v 1.15 2003/08/07 18:27:52 edhill Exp $
 % $Name:  $
 
 \section{Four Layer Baroclinic Ocean Gyre In Spherical Coordinates}
+\label{www:tutorials}
 \label{sect:eg-fourlayer}
 
 \bodytext{bgcolor="#FFFFFFFF"}
@@ -26,6 +27,7 @@
 for four layers and in a spherical polar coordinate system.
 
 \subsection{Overview}
+\label{www:tutorials}
 
 This example experiment demonstrates using the MITgcm to simulate
 a baroclinic, wind-forced, ocean gyre circulation. The experiment 
@@ -118,6 +120,7 @@
 \end{figure}
 
 \subsection{Equations solved}
+\label{www:tutorials}
 For this problem
 the implicit free surface, {\bf HPE} (see section \ref{sect:hydrostatic_and_quasi-hydrostatic_forms}) form of the 
 equations described in Marshall et. al \cite{marshall:97a} are
@@ -202,6 +205,7 @@
 
 
 \subsection{Discrete Numerical Configuration}
+\label{www:tutorials}
 
  The domain is discretised with 
 a uniform grid spacing in latitude and longitude
@@ -261,6 +265,7 @@
 \ref{sect:finding_the_pressure_field}.
 
 \subsubsection{Numerical Stability Criteria}
+\label{www:tutorials}
 
 The Laplacian viscosity coefficient, $A_{h}$, is set to $400 m s^{-1}$.
 This value is chosen to yield a Munk layer width,
@@ -340,6 +345,7 @@
 stability limit of 0.25.
   
 \subsection{Code Configuration}
+\label{www:tutorials}
 \label{SEC:eg_fourl_code_config}
 
 The model configuration for this experiment resides under the 
@@ -354,11 +360,12 @@
 \item {\it code/CPP\_OPTIONS.h},
 \item {\it code/SIZE.h}. 
 \end{itemize}
-contain the code customisations and parameter settings for this 
-experiments. Below we describe the customisations
-to these files associated with this experiment.
+contain the code customisations and parameter settings for this
+experiment. Below we describe the customisations to these files
+associated with this experiment.
 
 \subsubsection{File {\it input/data}}
+\label{www:tutorials}
 
 This file, reproduced completely below, specifies the main parameters 
 for the experiment. The parameters that are significant for this configuration
@@ -375,17 +382,19 @@
 depth level the initial and reference profiles will be uniform in
 $x$ and $y$. The values specified here are read into the
 variable 
-{\bf
-\begin{rawhtml} <A href=../../../code_reference/vdb/names/OK.htm> \end{rawhtml}
-tRef
-\begin{rawhtml} </A>\end{rawhtml}
-} 
+\varlink{tRef}{tRef}
+%{\bf
+%\begin{rawhtml} <A href=../code_reference/vdb/names/OK.htm> \end{rawhtml}
+%tRef
+%\begin{rawhtml} </A>\end{rawhtml}
+%} 
 in the model code, by procedure 
-{\it
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}
-INI\_PARMS
-\begin{rawhtml} </A>\end{rawhtml}
-}.
+\filelink{INI\_PARMS}{model-src-ini_parms.F}
+%{\it
+%\begin{rawhtml} <A href=../code_reference/vdb/code/94.htm> \end{rawhtml}
+%INI\_PARMS
+%\begin{rawhtml} </A>\end{rawhtml}
+%}.
 
 %% \codelink{var:tref} tRef \endlink
 %% \codelink{file:ini_parms} {\it INI\_PARMS } \endlink
@@ -395,7 +404,7 @@
 %% \file{ini_parms}
 \newcommand{\VARtref}{
 {\bf
-\begin{rawhtml} <A href=../../../code_reference/vdb/names/OK.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/names/OK.htm> \end{rawhtml}
 tRef
 \begin{rawhtml} </A>\end{rawhtml}
 } 
@@ -409,11 +418,12 @@
 ({\it ini\_theta.F})
 \end{minipage}
 }
-{\bf
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/98.htm> \end{rawhtml}
-goto code
-\begin{rawhtml} </A>\end{rawhtml}
-}
+\filelink{ini\_theta.F}{model-src-ini_theta.F}
+%{\bf
+%\begin{rawhtml} <A href=../code_reference/vdb/code/98.htm> \end{rawhtml}
+%goto code
+%\begin{rawhtml} </A>\end{rawhtml}
+%}
 
 
 \item Line 6, 
@@ -422,36 +432,41 @@
 $1 \times 10^{-2} {\rm m^{2}s^{-1}}$. Boundary conditions
 for this operator are specified later. 
 The variable 
-{\bf 
-\begin{rawhtml} <A href=../../../code_reference/vdb/names/ZQ.htm> \end{rawhtml}
-viscAz
-\begin{rawhtml} </A>\end{rawhtml}
-}
+\varlink{viscAz}{viscAz}
+%{\bf 
+%\begin{rawhtml} <A href=../code_reference/vdb/names/ZQ.htm> \end{rawhtml}
+%viscAz
+%\begin{rawhtml} </A>\end{rawhtml}
+%}
 is read in the routine
-{\it
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}
-INI\_PARMS
-\begin{rawhtml} </A>\end{rawhtml}
-}
+\filelink{ini\_parms.F}{model-src-ini_parms.F}
+%{\it
+%\begin{rawhtml} <A href=../code_reference/vdb/code/94.htm> \end{rawhtml}
+%INI\_PARMS
+%\begin{rawhtml} </A>\end{rawhtml}
+%}
 and is copied into model general vertical coordinate variable 
-{\bf 
-\begin{rawhtml} <A href=../../../code_reference/vdb/names/PF.htm> \end{rawhtml}
-viscAr
-\begin{rawhtml} </A>\end{rawhtml}
-}. At each time step, the viscous term contribution to the momentum equations
+\varlink{viscAr}{viscAr}
+%{\bf 
+%\begin{rawhtml} <A href=../code_reference/vdb/names/PF.htm> \end{rawhtml}
+%viscAr
+%\begin{rawhtml} </A>\end{rawhtml}
+%}.
+At each time step, the viscous term contribution to the momentum equations
 is calculated in routine
-{\it S/R CALC\_DIFFUSIVITY}.
+%{\it S/R CALC\_DIFFUSIVITY}.
+\varlink{CALC\_DIFFUSIVITY}{CALC_DIFFUSIVITY}
 
 \fbox{
 \begin{minipage}{5.0in}
 {\it S/R CALC\_DIFFUSIVITY}({\it calc\_diffusivity.F})
 \end{minipage}
 }
-{\bf
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/53.htm> \end{rawhtml}
-goto code
-\begin{rawhtml} </A>\end{rawhtml}
-}
+%{\bf
+%\begin{rawhtml} <A href=../code_reference/vdb/code/53.htm> \end{rawhtml}
+%goto code
+%\begin{rawhtml} </A>\end{rawhtml}
+%}
 
 \item Line 7, 
 \begin{verbatim}
@@ -461,39 +476,47 @@
 $1 \times 10^{-2} {\rm m^{2}s^{-1}}$. Boundary conditions
 for this operator are specified later.
 The variable 
-{\bf 
-\begin{rawhtml} <A href=../../../code_reference/vdb/names/SI.htm> \end{rawhtml}
-viscAh
-\begin{rawhtml} </A>\end{rawhtml}
-}
+\varlink{viscAh}{viscAh}
+%{\bf 
+%\begin{rawhtml} <A href=../code_reference/vdb/names/SI.htm> \end{rawhtml}
+%viscAh
+%\begin{rawhtml} </A>\end{rawhtml}
+%}
 is read in the routine
-{\it
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}
-INI\_PARMS
-\begin{rawhtml} </A>\end{rawhtml}
-} and applied in routines {\it CALC\_MOM\_RHS} and {\it CALC\_GW}.
+\varlink{INI\_PARMS}{INI_PARMS}
+%{\it
+%\begin{rawhtml} <A href=../code_reference/vdb/code/94.htm> \end{rawhtml}
+%INI\_PARMS
+%\begin{rawhtml} </A>\end{rawhtml}
+%}
+and applied in routines
+%{\it CALC\_MOM\_RHS} and {\it CALC\_GW}.
+\varlink{CALC\_MOM\_RHS}{CALC_MOM_RHS}
+and
+\varlink{CALC\_GW}{CALC_GW}.
+
 
 \fbox{
 \begin{minipage}{5.0in}
 {\it S/R CALC\_MOM\_RHS}({\it calc\_mom\_rhs.F})
 \end{minipage}
 }
-{\bf
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/60.htm> \end{rawhtml}
-goto code
-\begin{rawhtml} </A>\end{rawhtml}
-}
+%{\bf
+%\begin{rawhtml} <A href=../code_reference/vdb/code/60.htm> \end{rawhtml}
+%goto code
+%\begin{rawhtml} </A>\end{rawhtml}
+%}
 
 \fbox{
 \begin{minipage}{5.0in}
 {\it S/R CALC\_GW}({\it calc\_gw.F})
 \end{minipage}
 }
-{\bf
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/58.htm> \end{rawhtml}
-goto code
-\begin{rawhtml} </A>\end{rawhtml}
-}
+%{\bf
+%\begin{rawhtml} <A href=../code_reference/vdb/code/58.htm> \end{rawhtml}
+%goto code
+%\begin{rawhtml} </A>\end{rawhtml}
+%}
 
 \item Lines 8,
 \begin{verbatim}
@@ -504,18 +527,21 @@
 e.g. $\frac{\partial u}{\partial y}$=0 along boundaries in $y$ and
 $\frac{\partial v}{\partial x}$=0 along boundaries in $x$.
 The variable
-{\bf
-\begin{rawhtml} <A href=../../../code_reference/vdb/names/UT.htm> \end{rawhtml}
-no\_slip\_sides
-\begin{rawhtml} </A>\end{rawhtml}
-}
+\varlink{no\_slip\_sides}{no_slip_sides}
+%{\bf
+%\begin{rawhtml} <A href=../code_reference/vdb/names/UT.htm> \end{rawhtml}
+%no\_slip\_sides
+%\begin{rawhtml} </A>\end{rawhtml}
+%}
 is read in the routine
-{\it
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}
-INI\_PARMS
-\begin{rawhtml} </A>\end{rawhtml}
-} and the boundary condition is evaluated in routine
-{\it S/R CALC\_MOM\_RHS}.
+\varlink{INI\_PARMS}{INI_PARMS}
+%{\it
+%\begin{rawhtml} <A href=../code_reference/vdb/code/94.htm> \end{rawhtml}
+%INI\_PARMS
+%\begin{rawhtml} </A>\end{rawhtml}
+%}
+and the boundary condition is evaluated in routine
+%{\it S/R CALC\_MOM\_RHS}.
 
 
 \fbox{
@@ -524,7 +550,7 @@
 \end{minipage}
 }
 {\bf
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/60.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/code/60.htm> \end{rawhtml}
 goto code
 \begin{rawhtml} </A>\end{rawhtml}
 }
@@ -538,13 +564,13 @@
 e.g. $u=v=0$ at $z=-H$, where $H$ is the local depth of the domain.
 The variable
 {\bf
-\begin{rawhtml} <A href=../../../code_reference/vdb/names/UK.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/names/UK.htm> \end{rawhtml}
 no\_slip\_bottom
 \begin{rawhtml} </A>\end{rawhtml}
 }
 is read in the routine
 {\it
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/code/94.htm> \end{rawhtml}
 INI\_PARMS
 \begin{rawhtml} </A>\end{rawhtml}
 } and is applied in the routine {\it S/R CALC\_MOM\_RHS}.
@@ -555,7 +581,7 @@
 \end{minipage}
 }
 {\bf
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/60.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/code/60.htm> \end{rawhtml}
 goto code
 \begin{rawhtml} </A>\end{rawhtml}
 }
@@ -570,13 +596,13 @@
 all boundaries.
 The variable
 {\bf
-\begin{rawhtml} <A href=../../../code_reference/vdb/names/RC.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/names/RC.htm> \end{rawhtml}
 diffKhT
 \begin{rawhtml} </A>\end{rawhtml}
 }
 is read in the routine
 {\it
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/code/94.htm> \end{rawhtml}
 INI\_PARMS
 \begin{rawhtml} </A>\end{rawhtml}
 } and used in routine {\it S/R CALC\_GT}.
@@ -586,7 +612,7 @@
 \end{minipage}
 }
 {\bf
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/57.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/code/57.htm> \end{rawhtml}
 goto code
 \begin{rawhtml} </A>\end{rawhtml}
 }
@@ -600,19 +626,19 @@
 operator is $\frac{\partial}{\partial z}$ = 0 on all boundaries.
 The variable
 {\bf
-\begin{rawhtml} <A href=../../../code_reference/vdb/names/ZT.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/names/ZT.htm> \end{rawhtml}
 diffKzT
 \begin{rawhtml} </A>\end{rawhtml}
 }
 is read in the routine
 {\it
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/code/94.htm> \end{rawhtml}
 INI\_PARMS
 \begin{rawhtml} </A>\end{rawhtml}
 }.
 It is copied into model general vertical coordinate variable
 {\bf
-\begin{rawhtml} <A href=../../../code_reference/vdb/names/PD.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/names/PD.htm> \end{rawhtml}
 diffKrT
 \begin{rawhtml} </A>\end{rawhtml}
 } which is used in routine {\it S/R CALC\_DIFFUSIVITY}.
@@ -622,7 +648,7 @@
 \end{minipage}
 }
 {\bf
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/53.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/code/53.htm> \end{rawhtml}
 goto code
 \begin{rawhtml} </A>\end{rawhtml}
 }
@@ -637,13 +663,13 @@
 to $2 \times 10^{-4}\,{\rm degrees}^{-1}$
 The variable
 {\bf
-\begin{rawhtml} <A href=../../../code_reference/vdb/names/ZV.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/names/ZV.htm> \end{rawhtml}
 tAlpha 
 \begin{rawhtml} </A>\end{rawhtml}
 }
 is read in the routine
 {\it
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/code/94.htm> \end{rawhtml}
 INI\_PARMS
 \begin{rawhtml} </A>\end{rawhtml}
 }. The routine {\it S/R FIND\_RHO} makes use of {\bf tAlpha}.
@@ -654,7 +680,7 @@
 \end{minipage}
 }
 {\bf
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/79.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/code/79.htm> \end{rawhtml}
 goto code
 \begin{rawhtml} </A>\end{rawhtml}
 }
@@ -666,13 +692,13 @@
 This line selects the linear form of the equation of state.
 The variable
 {\bf
-\begin{rawhtml} <A href=../../../code_reference/vdb/names/WV.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/names/WV.htm> \end{rawhtml}
 eosType
 \begin{rawhtml} </A>\end{rawhtml}
 }
 is read in the routine
 {\it
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/code/94.htm> \end{rawhtml}
 INI\_PARMS
 \begin{rawhtml} </A>\end{rawhtml}
 }. The values of {\bf eosType} sets which formula in routine
@@ -684,7 +710,7 @@
 \end{minipage}
 }
 {\bf
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/79.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/code/79.htm> \end{rawhtml}
 goto code
 \begin{rawhtml} </A>\end{rawhtml}
 }
@@ -702,13 +728,13 @@
 on spherical polar geometry.
 The variable
 {\bf
-\begin{rawhtml} <A href=../../../code_reference/vdb/names/10T.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/names/10T.htm> \end{rawhtml}
 usingSphericalPolarGrid
 \begin{rawhtml} </A>\end{rawhtml}
 }
 is read in the routine
 {\it
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/code/94.htm> \end{rawhtml}
 INI\_PARMS
 \begin{rawhtml} </A>\end{rawhtml}
 }. When set to {\bf .TRUE.} the settings of {\bf delX} and {\bf delY} are
@@ -721,7 +747,7 @@
 \end{minipage}
 }
 {\bf
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/97.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/code/97.htm> \end{rawhtml}
 goto code
 \begin{rawhtml} </A>\end{rawhtml}
 }
@@ -739,13 +765,13 @@
 not alter the kernel equation discretisation.
 The variable
 {\bf
-\begin{rawhtml} <A href=../../../code_reference/vdb/names/110.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/names/110.htm> \end{rawhtml}
 phiMin
 \begin{rawhtml} </A>\end{rawhtml}
 }
 is read in the routine
 {\it
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/code/94.htm> \end{rawhtml}
 INI\_PARMS
 \begin{rawhtml} </A>\end{rawhtml}
 } and is used in routine {\it INI\_SPEHRICAL\_POLAR\_GRID}.
@@ -756,7 +782,7 @@
 \end{minipage}
 }
 {\bf
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/97.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/code/97.htm> \end{rawhtml}
 goto code
 \begin{rawhtml} </A>\end{rawhtml}
 }
@@ -769,13 +795,13 @@
 in the discrete grid to $1^{\circ}$ in longitude.
 The variable
 {\bf
-\begin{rawhtml} <A href=../../../code_reference/vdb/names/10Z.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/names/10Z.htm> \end{rawhtml}
 delX
 \begin{rawhtml} </A>\end{rawhtml}
 }
 is read in the routine
 {\it
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/code/94.htm> \end{rawhtml}
 INI\_PARMS
 \begin{rawhtml} </A>\end{rawhtml}
 } and is used in routine {\it INI\_SPEHRICAL\_POLAR\_GRID}. 
@@ -786,7 +812,7 @@
 \end{minipage}
 }
 {\bf
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/97.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/code/97.htm> \end{rawhtml}
 goto code
 \begin{rawhtml} </A>\end{rawhtml}
 }
@@ -799,13 +825,13 @@
 in the discrete grid to $1^{\circ}$ in latitude.
 The variable
 {\bf
-\begin{rawhtml} <A href=../../../code_reference/vdb/names/UB.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/names/UB.htm> \end{rawhtml}
 delY   
 \begin{rawhtml} </A>\end{rawhtml}
 }
 is read in the routine
 {\it
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/code/94.htm> \end{rawhtml}
 INI\_PARMS
 \begin{rawhtml} </A>\end{rawhtml}
 } and is used in routine {\it INI\_SPEHRICAL\_POLAR\_GRID}. 
@@ -816,7 +842,7 @@
 \end{minipage}
 }
 {\bf
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/97.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/code/97.htm> \end{rawhtml}
 goto code
 \begin{rawhtml} </A>\end{rawhtml}
 }
@@ -830,20 +856,20 @@
 is $2\,{\rm km}$.
 The variable
 {\bf
-\begin{rawhtml} <A href=../../../code_reference/vdb/names/10W.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/names/10W.htm> \end{rawhtml}
 delZ
 \begin{rawhtml} </A>\end{rawhtml}
 }
 is read in the routine
 {\it
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/code/94.htm> \end{rawhtml}
 INI\_PARMS
 \begin{rawhtml} </A>\end{rawhtml}
 }.
 It is copied into the internal
 model coordinate variable 
 {\bf 
-\begin{rawhtml} <A href=../../../code_reference/vdb/names/10Y.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/names/10Y.htm> \end{rawhtml}
 delR
 \begin{rawhtml} </A>\end{rawhtml}
 } which is used in routine {\it INI\_VERTICAL\_GRID}.
@@ -854,7 +880,7 @@
 \end{minipage}
 }
 {\bf
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/100.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/code/100.htm> \end{rawhtml}
 goto code
 \begin{rawhtml} </A>\end{rawhtml}
 }
@@ -876,13 +902,13 @@
 bathymetry file.
 The variable
 {\bf
-\begin{rawhtml} <A href=../../../code_reference/vdb/names/179.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/names/179.htm> \end{rawhtml}
 bathyFile
 \begin{rawhtml} </A>\end{rawhtml}
 }
 is read in the routine
 {\it
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/code/94.htm> \end{rawhtml}
 INI\_PARMS
 \begin{rawhtml} </A>\end{rawhtml}
 }. The bathymetry file is read in the routine {\it INI\_DEPTHS}.
@@ -893,7 +919,7 @@
 \end{minipage}
 }
 {\bf
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/88.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/code/88.htm> \end{rawhtml}
 goto code
 \begin{rawhtml} </A>\end{rawhtml}
 }
@@ -912,13 +938,13 @@
 file.  
 The variable
 {\bf
-\begin{rawhtml} <A href=../../../code_reference/vdb/names/13W.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/names/13W.htm> \end{rawhtml}
 zonalWindFile
 \begin{rawhtml} </A>\end{rawhtml}
 }
 is read in the routine
 {\it
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/code/94.htm> \end{rawhtml}
 INI\_PARMS
 \begin{rawhtml} </A>\end{rawhtml}
 }.  The wind-stress file is read in the routine 
@@ -930,7 +956,7 @@
 \end{minipage}
 }
 {\bf
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/75.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/code/75.htm> \end{rawhtml}
 goto code
 \begin{rawhtml} </A>\end{rawhtml}
 }
@@ -946,16 +972,19 @@
 \begin{rawhtml}</PRE>\end{rawhtml}
 
 \subsubsection{File {\it input/data.pkg}}
+\label{www:tutorials}
 
 This file uses standard default values and does not contain
 customisations for this experiment.
 
 \subsubsection{File {\it input/eedata}}
+\label{www:tutorials}
 
 This file uses standard default values and does not contain
 customisations for this experiment.
 
 \subsubsection{File {\it input/windx.sin\_y}}
+\label{www:tutorials}
 
 The {\it input/windx.sin\_y} file specifies a two-dimensional ($x,y$) 
 map of wind stress ,$\tau_{x}$, values. The units used are $Nm^{-2}$ (the
@@ -969,6 +998,7 @@
 code for creating the {\it input/windx.sin\_y} file.
 
 \subsubsection{File {\it input/topog.box}}
+\label{www:tutorials}
 
 
 The {\it input/topog.box} file specifies a two-dimensional ($x,y$) 
@@ -980,6 +1010,7 @@
 code for creating the {\it input/topog.box} file.
 
 \subsubsection{File {\it code/SIZE.h}}
+\label{www:tutorials}
 
 Two lines are customized in this file for the current experiment
 
@@ -1006,17 +1037,20 @@
 \end{small}
 
 \subsubsection{File {\it code/CPP\_OPTIONS.h}}
+\label{www:tutorials}
 
 This file uses standard default values and does not contain
 customisations for this experiment.
 
 
 \subsubsection{File {\it code/CPP\_EEOPTIONS.h}}
+\label{www:tutorials}
 
 This file uses standard default values and does not contain
 customisations for this experiment.
 
 \subsubsection{Other Files }
+\label{www:tutorials}
 
 Other files relevant to this experiment are
 \begin{itemize}
@@ -1029,15 +1063,18 @@
 \end{itemize}
 
 \subsection{Running The Example}
+\label{www:tutorials}
 \label{SEC:running_the_example}
 
 \subsubsection{Code Download}
+\label{www:tutorials}
 
  In order to run the examples you must first download the code distribution.
 Instructions for downloading the code can be found in section
 \ref{sect:obtainingCode}.
 
 \subsubsection{Experiment Location}
+\label{www:tutorials}
 
  This example experiments is located under the release sub-directory
 
@@ -1045,6 +1082,7 @@
 {\it verification/exp2/ }
 
 \subsubsection{Running the Experiment}
+\label{www:tutorials}
 
  To run the experiment
 
