--- manual/s_examples/baroclinic_gyre/fourlayer.tex	2001/10/25 18:36:55	1.9
+++ manual/s_examples/baroclinic_gyre/fourlayer.tex	2003/07/30 13:42:53	1.14
@@ -1,8 +1,9 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_examples/baroclinic_gyre/fourlayer.tex,v 1.9 2001/10/25 18:36:55 cnh Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_examples/baroclinic_gyre/fourlayer.tex,v 1.14 2003/07/30 13:42:53 edhill Exp $
 % $Name:  $
 
-\section{Example: Four layer Baroclinic Ocean Gyre In Spherical Coordinates}
-\label{sec:eg-fourlayer}
+\section{Four Layer Baroclinic Ocean Gyre In Spherical Coordinates}
+\label{www:tutorials}
+\label{sect:eg-fourlayer}
 
 \bodytext{bgcolor="#FFFFFFFF"}
 
@@ -19,13 +20,14 @@
 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{sec:eg-baro}
+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.
 
 \subsection{Overview}
+\label{www:tutorials}
 
 This example experiment demonstrates using the MITgcm to simulate
 a baroclinic, wind-forced, ocean gyre circulation. The experiment 
@@ -43,7 +45,7 @@
 according to latitude, $\varphi$
 
 \begin{equation}
-\label{EQ:fcori}
+\label{EQ:eg-fourlayer-fcori}
 f(\varphi) = 2 \Omega \sin( \varphi )
 \end{equation}
  
@@ -61,9 +63,9 @@
 $\tau_0$ is set to $0.1N m^{-2}$. 
 \\
 
-Figure \ref{FIG:simulation_config}
+Figure \ref{FIG:eg-fourlayer-simulation_config}
 summarizes the configuration simulated.
-In contrast to the example in section \ref{sec:eg-baro}, the 
+In contrast to the example in section \ref{sect:eg-baro}, the 
 current experiment simulates a spherical polar domain. As indicated
 by the axes in the lower left of the figure the model code works internally
 in a locally orthogonal coordinate $(x,y,z)$. For this experiment description 
@@ -82,14 +84,14 @@
 linear
 
 \begin{equation}
-\label{EQ:linear1_eos}
+\label{EQ:eg-fourlayer-linear1_eos}
 \rho = \rho_{0} ( 1 - \alpha_{\theta}\theta^{'} )
 \end{equation}
 
 \noindent which is implemented in the model as a density anomaly equation
 
 \begin{equation}
-\label{EQ:linear1_eos_pert}
+\label{EQ:eg-fourlayer-linear1_eos_pert}
 \rho^{'} = -\rho_{0}\alpha_{\theta}\theta^{'}
 \end{equation}
 
@@ -114,13 +116,14 @@
 imposed by setting the potential temperature, $\theta$, in each layer.
 The vertical spacing, $\Delta z$, is constant and equal to $500$m.
 }
-\label{FIG:simulation_config}
+\label{FIG:eg-fourlayer-simulation_config}
 \end{figure}
 
 \subsection{Equations solved}
+\label{www:tutorials}
 For this problem
-the implicit free surface, {\bf HPE} (see section \ref{sec:hydrostatic_and_quasi-hydrostatic_forms}) form of the 
-equations described in Marshall et. al \cite{Marshall97a} are
+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
 employed. The flow is three-dimensional with just temperature, $\theta$, as 
 an active tracer.  The equation of state is linear.
 A horizontal Laplacian operator $\nabla_{h}^2$ provides viscous
@@ -133,7 +136,7 @@
 follows
 
 \begin{eqnarray}
-\label{EQ:model_equations}
+\label{EQ:eg-fourlayer-model_equations}
 \frac{Du}{Dt} - fv + 
   \frac{1}{\rho}\frac{\partial p^{\prime}}{\partial \lambda} - 
   A_{h}\nabla_{h}^2u - A_{z}\frac{\partial^{2}u}{\partial z^{2}} 
@@ -202,6 +205,7 @@
 
 
 \subsection{Discrete Numerical Configuration}
+\label{www:tutorials}
 
  The domain is discretised with 
 a uniform grid spacing in latitude and longitude
@@ -221,7 +225,7 @@
 
 The procedure for generating a set of internal grid variables from a
 spherical polar grid specification is discussed in section 
-\ref{sec:spatial_discrete_horizontal_grid}.
+\ref{sect:spatial_discrete_horizontal_grid}.
 
 \noindent\fbox{ \begin{minipage}{5.5in}
 {\em S/R INI\_SPHERICAL\_POLAR\_GRID} ({\em
@@ -242,15 +246,15 @@
 
 
 
-As described in \ref{sec:tracer_equations}, the time evolution of potential 
+As described in \ref{sect:tracer_equations}, the time evolution of potential 
 temperature, 
 $\theta$, (equation \ref{eq:eg_fourl_theta})
 is evaluated prognostically. The centered second-order scheme with
 Adams-Bashforth time stepping described in section 
-\ref{sec:tracer_equations_abII} is used to step forward the temperature 
+\ref{sect:tracer_equations_abII} is used to step forward the temperature 
 equation. Prognostic terms in
 the momentum equations are solved using flux form as
-described in section \ref{sec:flux-form_momentum_eqautions}.
+described in section \ref{sect:flux-form_momentum_eqautions}.
 The pressure forces that drive the fluid motions, (
 $\frac{\partial p^{'}}{\partial \lambda}$ and $\frac{\partial p^{'}}{\partial \varphi}$), are found by summing pressure due to surface 
 elevation $\eta$ and the hydrostatic pressure. The hydrostatic part of the 
@@ -258,15 +262,16 @@
 height, $\eta$, is diagnosed using an implicit scheme. The pressure
 field solution method is described in sections
 \ref{sect:pressure-method-linear-backward} and 
-\ref{sec:finding_the_pressure_field}.
+\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,
 
 \begin{eqnarray}
-\label{EQ:munk_layer}
+\label{EQ:eg-fourlayer-munk_layer}
 M_{w} = \pi ( \frac { A_{h} }{ \beta } )^{\frac{1}{3}}
 \end{eqnarray}
 
@@ -282,7 +287,7 @@
 parameter to the horizontal Laplacian friction
 
 \begin{eqnarray}
-\label{EQ:laplacian_stability}
+\label{EQ:eg-fourlayer-laplacian_stability}
 S_{l} = 4 \frac{A_{h} \delta t}{{\Delta x}^2}
 \end{eqnarray}
 
@@ -294,7 +299,7 @@
 $1\times10^{-2} {\rm m}^2{\rm s}^{-1}$. The associated stability limit
 
 \begin{eqnarray}
-\label{EQ:laplacian_stability_z}
+\label{EQ:eg-fourlayer-laplacian_stability_z}
 S_{l} = 4 \frac{A_{z} \delta t}{{\Delta z}^2}
 \end{eqnarray}
 
@@ -307,7 +312,7 @@
 \noindent The numerical stability for inertial oscillations
 
 \begin{eqnarray}
-\label{EQ:inertial_stability}
+\label{EQ:eg-fourlayer-inertial_stability}
 S_{i} = f^{2} {\delta t}^2
 \end{eqnarray}
 
@@ -320,7 +325,7 @@
 speed of $ | \vec{u} | = 2 ms^{-1}$
 
 \begin{eqnarray}
-\label{EQ:cfl_stability}
+\label{EQ:eg-fourlayer-cfl_stability}
 C_{a} = \frac{| \vec{u} | \delta t}{ \Delta x}
 \end{eqnarray}
 
@@ -332,7 +337,7 @@
 propagating at $2~{\rm m}~{\rm s}^{-1}$ 
 
 \begin{eqnarray}
-\label{EQ:igw_stability}
+\label{EQ:eg-fourlayer-igw_stability}
 S_{c} = \frac{c_{g} \delta t}{ \Delta x}
 \end{eqnarray}
 
@@ -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 
@@ -359,6 +365,7 @@
 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
@@ -376,13 +383,13 @@
 $x$ and $y$. The values specified here are read into the
 variable 
 {\bf
-\begin{rawhtml} <A href=../../../code_reference/vdb/names/OK.htm> \end{rawhtml}
+\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}
+\begin{rawhtml} <A href=../code_reference/vdb/code/94.htm> \end{rawhtml}
 INI\_PARMS
 \begin{rawhtml} </A>\end{rawhtml}
 }.
@@ -395,7 +402,7 @@
 %% \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}
 } 
@@ -410,7 +417,7 @@
 \end{minipage}
 }
 {\bf
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/98.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/code/98.htm> \end{rawhtml}
 goto code
 \begin{rawhtml} </A>\end{rawhtml}
 }
@@ -423,19 +430,19 @@
 for this operator are specified later. 
 The variable 
 {\bf 
-\begin{rawhtml} <A href=../../../code_reference/vdb/names/ZQ.htm> \end{rawhtml}
+\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}
+\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}
+\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
@@ -448,7 +455,7 @@
 \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}
 }
@@ -462,13 +469,13 @@
 for this operator are specified later.
 The variable 
 {\bf 
-\begin{rawhtml} <A href=../../../code_reference/vdb/names/SI.htm> \end{rawhtml}
+\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}
+\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}.
@@ -479,7 +486,7 @@
 \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}
 }
@@ -490,7 +497,7 @@
 \end{minipage}
 }
 {\bf
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/58.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/code/58.htm> \end{rawhtml}
 goto code
 \begin{rawhtml} </A>\end{rawhtml}
 }
@@ -505,13 +512,13 @@
 $\frac{\partial v}{\partial x}$=0 along boundaries in $x$.
 The variable
 {\bf
-\begin{rawhtml} <A href=../../../code_reference/vdb/names/UT.htm> \end{rawhtml}
+\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}
+\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
@@ -524,7 +531,7 @@
 \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 +545,13 @@
 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 +562,7 @@
 \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 +577,13 @@
 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 +593,7 @@
 \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 +607,19 @@
 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 +629,7 @@
 \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 +644,13 @@
 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 +661,7 @@
 \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 +673,13 @@
 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 +691,7 @@
 \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 +709,13 @@
 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 +728,7 @@
 \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 +746,13 @@
 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 +763,7 @@
 \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 +776,13 @@
 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 +793,7 @@
 \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 +806,13 @@
 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 +823,7 @@
 \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 +837,20 @@
 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 +861,7 @@
 \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 +883,13 @@
 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 +900,7 @@
 \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 +919,13 @@
 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 +937,7 @@
 \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 +953,19 @@
 \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 +979,7 @@
 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 +991,7 @@
 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 +1018,20 @@
 \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 +1044,18 @@
 \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 +1063,7 @@
 {\it verification/exp2/ }
 
 \subsubsection{Running the Experiment}
+\label{www:tutorials}
 
  To run the experiment
 
