--- manual/s_examples/baroclinic_gyre/fourlayer.tex	2001/09/27 00:58:17	1.2
+++ manual/s_examples/baroclinic_gyre/fourlayer.tex	2004/01/29 17:36:26	1.17
@@ -1,7 +1,9 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_examples/baroclinic_gyre/fourlayer.tex,v 1.2 2001/09/27 00:58:17 cnh Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_examples/baroclinic_gyre/fourlayer.tex,v 1.17 2004/01/29 17:36:26 edhill Exp $
 % $Name:  $
 
-\section{Example: Four layer Baroclinic Ocean Gyre In Spherical Coordinates}
+\section{Four Layer Baroclinic Ocean Gyre In Spherical Coordinates}
+\label{www:tutorials}
+\label{sect:eg-fourlayer}
 
 \bodytext{bgcolor="#FFFFFFFF"}
 
@@ -15,19 +17,21 @@
 %{\large May 2001}
 %\end{center}
 
-\subsection{Introduction}
-
-This document describes the second example MITgcm experiment. The first
-example experiment ilustrated how to configure the code for a single layer 
-simulation in a cartesian grid. In this example a similar physical problem
+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.
 
 \subsection{Overview}
+\label{www:tutorials}
 
 This example experiment demonstrates using the MITgcm to simulate
 a baroclinic, wind-forced, ocean gyre circulation. The experiment 
-is a numerical rendition of the gyre circulation problem simliar
+is a numerical rendition of the gyre circulation problem similar
 to the problems described analytically by Stommel in 1966 
 \cite{Stommel66} and numerically in Holland et. al \cite{Holland75}.
 \\
@@ -35,14 +39,14 @@
 In this experiment the model is configured to represent a mid-latitude 
 enclosed sector of fluid on a sphere, $60^{\circ} \times 60^{\circ}$ in 
 lateral extent. The fluid is $2$~km deep and is forced
-by a constant in time zonal wind stress, $\tau_x$, that varies sinusoidally
-in the north-south direction. Topologically the simulated 
+by a constant in time zonal wind stress, $\tau_{\lambda}$, that varies 
+sinusoidally in the north-south direction. Topologically the simulated 
 domain is a sector on a sphere and the coriolis parameter, $f$, is defined 
-according to latitude, $\phi$
+according to latitude, $\varphi$
 
 \begin{equation}
-\label{EQ:fcori}
-f(\phi) = 2 \Omega \sin( \phi )
+\label{EQ:eg-fourlayer-fcori}
+f(\varphi) = 2 \Omega \sin( \varphi )
 \end{equation}
  
 \noindent with the rotation rate, $\Omega$ set to $\frac{2 \pi}{86400s}$.
@@ -52,20 +56,22 @@
 
 \begin{equation}
 \label{EQ:taux}
-\tau_x(\phi) = \tau_{0}\sin(\pi \frac{\phi}{L_{\phi}})
+\tau_{\lambda}(\varphi) = \tau_{0}\sin(\pi \frac{\varphi}{L_{\varphi}})
 \end{equation}
  
-\noindent where $L_{\phi}$ is the lateral domain extent ($60^{\circ}$) and 
+\noindent where $L_{\varphi}$ is the lateral domain extent ($60^{\circ}$) and 
 $\tau_0$ is set to $0.1N m^{-2}$. 
 \\
 
-Figure \ref{FIG:simulation_config}
-summarises the configuration simulated.
-In contrast to example (1) \cite{baro_gyre_case_study}, the current 
-experiment simulates a spherical polar domain. However, as indicated
+Figure \ref{FIG:eg-fourlayer-simulation_config}
+summarizes the configuration simulated.
+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 orthoganal coordinate $(x,y,z)$. In the remainder of this
-document the local coordinate $(x,y,z)$ will be adopted.
+in a locally orthogonal coordinate $(x,y,z)$. For this experiment description 
+the local orthogonal model coordinate $(x,y,z)$ is synonymous 
+with the coordinates $(\lambda,\varphi,r)$ shown in figure
+\ref{fig:spherical-polar-coord}
 \\
 
 The experiment has four levels in the vertical, each of equal thickness,
@@ -78,131 +84,226 @@
 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}
 
 \noindent with $\rho_{0}=999.8\,{\rm kg\,m}^{-3}$ and 
 $\alpha_{\theta}=2\times10^{-4}\,{\rm degrees}^{-1} $. Integrated forward in
-this configuration the model state variable {\bf theta} is synonomous with
+this configuration the model state variable {\bf theta} is equivalent to
 either in-situ temperature, $T$, or potential temperature, $\theta$. For 
 consistency with later examples, in which the equation of state is
 non-linear, we use $\theta$ to represent temperature here. This is
 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]
+%%    {part3/case_studies/fourlayer_gyre/simulation_config.eps} }
+%% \end{center}
+\centerline{
+  \scalefig{.95}
+  \epsfbox{part3/case_studies/fourlayer_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.
-In the four-layer case an initial temperature stratification is 
+An initial stratification is 
 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{Discrete Numerical Configuration}
-
- The model is configured in hydrostatic form.  The domain is discretised with 
-a uniform grid spacing in latitude and longitude
- $\Delta x=\Delta y=1^{\circ}$, so 
-that there are sixty grid cells in the $x$ and $y$ directions. Vertically the 
-model is configured with a four layers with constant depth, 
-$\Delta z$, of $500$~m. 
-The implicit free surface form of the 
-pressure equation described in Marshall et. al \cite{Marshall97a} is 
-employed. 
-A horizontal laplacian operator $\nabla_{h}^2$ provides viscous
-dissipation. The wind-stress momentum input is added to the momentum equation
-for the ``zonal flow'', $u$. Other terms in the model
-are explicitly switched off for this experiement configuration (see section
-\ref{SEC:code_config} ), yielding an active set of equations solved in this 
-configuration as follows
+\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
+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
+dissipation and provides a diffusive sub-grid scale closure for the 
+temperature equation. A wind-stress momentum forcing is added to the momentum 
+equation for the zonal flow, $u$. Other terms in the model
+are explicitly switched off for this experiment configuration (see section
+\ref{SEC:eg_fourl_code_config} ). This yields an active set of equations
+solved in this configuration, written in spherical polar coordinates as 
+follows
 
 \begin{eqnarray}
-\label{EQ:model_equations}
+\label{EQ:eg-fourlayer-model_equations}
 \frac{Du}{Dt} - fv + 
-  \frac{1}{\rho}\frac{\partial p^{'}}{\partial x} - 
+  \frac{1}{\rho}\frac{\partial p^{\prime}}{\partial \lambda} - 
   A_{h}\nabla_{h}^2u - A_{z}\frac{\partial^{2}u}{\partial z^{2}} 
 & = &
-\cal{F}
+\cal{F}_{\lambda}
 \\
 \frac{Dv}{Dt} + fu + 
-  \frac{1}{\rho}\frac{\partial p^{'}}{\partial y} - 
+  \frac{1}{\rho}\frac{\partial p^{\prime}}{\partial \varphi} - 
   A_{h}\nabla_{h}^2v - A_{z}\frac{\partial^{2}v}{\partial z^{2}} 
 & = &
 0
 \\
-\frac{\partial \eta}{\partial t} + \nabla_{h}\cdot \vec{u}
+\frac{\partial \eta}{\partial t} + \frac{\partial H \widehat{u}}{\partial \lambda} +
+\frac{\partial H \widehat{v}}{\partial \varphi}
 &=&
 0
+\label{eq:fourl_example_continuity}
 \\
 \frac{D\theta}{Dt} -
  K_{h}\nabla_{h}^2\theta  - K_{z}\frac{\partial^{2}\theta}{\partial z^{2}} 
 & = &
 0
+\label{eq:eg_fourl_theta}
 \\
-g\rho_{0} \eta + \int^{0}_{-z}\rho^{'} dz & = & p^{'}
+p^{\prime} & = &
+g\rho_{0} \eta + \int^{0}_{-z}\rho^{\prime} dz
 \\
-{\cal F} |_{s} & = & \frac{\tau_{x}}{\rho_{0}\Delta z_{s}}
+\rho^{\prime} & = &- \alpha_{\theta}\rho_{0}\theta^{\prime}
 \\
-{\cal F} |_{i} & = & 0
+{\cal F}_{\lambda} |_{s} & = & \frac{\tau_{\lambda}}{\rho_{0}\Delta z_{s}}
+\\
+{\cal F}_{\lambda} |_{i} & = & 0
 \end{eqnarray}
 
-\noindent where $u$ and $v$ are the $x$ and $y$ components of the
-flow vector $\vec{u}$. The suffices ${s},{i}$ indicate surface and
-interior model levels respectively. As described in
-MITgcm Numerical Solution Procedure \cite{MITgcm_Numerical_Scheme}, the time 
-evolution of potential temperature, $\theta$, equation is solved prognostically.
-The total pressure, $p$, is diagnosed by summing pressure due to surface 
-elevation $\eta$ and the hydrostatic pressure.
-\\
+\noindent where $u$ and $v$ are the components of the horizontal
+flow vector $\vec{u}$ on the sphere ($u=\dot{\lambda},v=\dot{\varphi}$).
+The terms $H\widehat{u}$ and $H\widehat{v}$ are the components of the vertical
+integral term given in equation \ref{eq:free-surface} and
+explained in more detail in section \ref{sect:pressure-method-linear-backward}.
+However, for the problem presented here, the continuity relation (equation
+\ref{eq:fourl_example_continuity}) differs from the general form given
+in section \ref{sect:pressure-method-linear-backward},
+equation \ref{eq:linear-free-surface=P-E+R}, because the source terms
+${\cal P}-{\cal E}+{\cal R}$ 
+are all $0$.
+
+The pressure field, $p^{\prime}$, is separated into a barotropic part
+due to variations in sea-surface height, $\eta$, and a hydrostatic
+part due to variations in density, $\rho^{\prime}$, integrated
+through the water column.
+
+The suffices ${s},{i}$ indicate surface layer and the interior of the domain.
+The windstress forcing, ${\cal F}_{\lambda}$, is applied in the surface layer 
+by a source term in the zonal momentum equation. In the ocean interior
+this term is zero.
+
+In the momentum equations
+lateral and vertical boundary conditions for the $\nabla_{h}^{2}$
+and $\frac{\partial^{2}}{\partial z^{2}}$ operators are specified
+when the numerical simulation is run - see section 
+\ref{SEC:eg_fourl_code_config}. For temperature
+the boundary condition is ``zero-flux'' 
+e.g. $\frac{\partial \theta}{\partial \varphi}=
+\frac{\partial \theta}{\partial \lambda}=\frac{\partial \theta}{\partial z}=0$.
+
+
+
+\subsection{Discrete Numerical Configuration}
+\label{www:tutorials}
+
+ The domain is discretised with 
+a uniform grid spacing in latitude and longitude
+ $\Delta \lambda=\Delta \varphi=1^{\circ}$, so 
+that there are sixty grid cells in the zonal and meridional directions. 
+Vertically the 
+model is configured with four layers with constant depth, 
+$\Delta z$, of $500$~m. The internal, locally orthogonal, model coordinate 
+variables $x$ and $y$ are initialized from the values of
+$\lambda$, $\varphi$, $\Delta \lambda$ and $\Delta \varphi$ in
+radians according to
+
+\begin{eqnarray}
+x=r\cos(\varphi)\lambda,~\Delta x & = &r\cos(\varphi)\Delta \lambda \\
+y=r\varphi,~\Delta y &= &r\Delta \varphi
+\end{eqnarray}
+
+The procedure for generating a set of internal grid variables from a
+spherical polar grid specification is discussed in section 
+\ref{sect:spatial_discrete_horizontal_grid}.
+
+\noindent\fbox{ \begin{minipage}{5.5in}
+{\em S/R INI\_SPHERICAL\_POLAR\_GRID} ({\em
+model/src/ini\_spherical\_polar\_grid.F})
+
+$A_c$, $A_\zeta$, $A_w$, $A_s$: {\bf rAc}, {\bf rAz}, {\bf rAw}, {\bf rAs}
+({\em GRID.h})
+
+$\Delta x_g$, $\Delta y_g$: {\bf DXg}, {\bf DYg} ({\em GRID.h})
+
+$\Delta x_c$, $\Delta y_c$: {\bf DXc}, {\bf DYc} ({\em GRID.h})
+
+$\Delta x_f$, $\Delta y_f$: {\bf DXf}, {\bf DYf} ({\em GRID.h})
+
+$\Delta x_v$, $\Delta y_u$: {\bf DXv}, {\bf DYu} ({\em GRID.h})
+
+\end{minipage} }\\
+
+
+
+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{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{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 
+pressure is diagnosed explicitly by integrating density. The sea-surface
+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{sect:finding_the_pressure_field}.
 
 \subsubsection{Numerical Stability Criteria}
+\label{www:tutorials}
 
-The laplacian dissipation coefficient, $A_{h}$, is set to $400 m s^{-1}$.
-This value is chosen to yield a Munk layer width \cite{Adcroft_thesis},
+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}
 
 \noindent  of $\approx 100$km. This is greater than the model
-resolution in mid-latitudes $\Delta x$, ensuring that the frictional 
+resolution in mid-latitudes 
+$\Delta x=r \cos(\varphi) \Delta \lambda \approx 80~{\rm km}$ at
+$\varphi=45^{\circ}$, ensuring that the frictional 
 boundary layer is well resolved.
 \\
 
 \noindent The model is stepped forward with a 
 time step $\delta t=1200$secs. With this time step the stability 
-parameter to the horizontal laplacian friction \cite{Adcroft_thesis}
+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}
 
 \noindent evaluates to 0.012, which is well below the 0.3 upper limit
-for stability. 
+for stability for this term under ABII time-stepping.
 \\
 
 \noindent The vertical dissipation coefficient, $A_{z}$, is set to 
 $1\times10^{-2} {\rm m}^2{\rm s}^{-1}$. 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}
 
@@ -213,10 +314,9 @@
 \\
 
 \noindent The numerical stability for inertial oscillations
-\cite{Adcroft_thesis} 
 
 \begin{eqnarray}
-\label{EQ:inertial_stability}
+\label{EQ:eg-fourlayer-inertial_stability}
 S_{i} = f^{2} {\delta t}^2
 \end{eqnarray}
 
@@ -224,35 +324,36 @@
 limit for stability.
 \\
 
-\noindent The advective CFL \cite{Adcroft_thesis} for a extreme maximum 
+\noindent The advective CFL for a extreme maximum 
 horizontal flow
 speed of $ | \vec{u} | = 2 ms^{-1}$
 
 \begin{eqnarray}
-\label{EQ:cfl_stability}
-S_{a} = \frac{| \vec{u} | \delta t}{ \Delta x}
+\label{EQ:eg-fourlayer-cfl_stability}
+C_{a} = \frac{| \vec{u} | \delta t}{ \Delta x}
 \end{eqnarray}
 
 \noindent evaluates to $5 \times 10^{-2}$. This is well below the stability 
 limit of 0.5.
 \\
 
-\noindent The stability parameter for internal gravity waves 
-\cite{Adcroft_thesis}
+\noindent The stability parameter for internal gravity waves
+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}
 
-\noindent evaluates to $5 \times 10^{-2}$. This is well below the linear
+\noindent evaluates to $\approx 5 \times 10^{-2}$. This is well below the linear
 stability limit of 0.25.
   
 \subsection{Code Configuration}
-\label{SEC:code_config}
+\label{www:tutorials}
+\label{SEC:eg_fourl_code_config}
 
 The model configuration for this experiment resides under the 
-directory {\it verification/exp1/}.  The experiment files 
+directory {\it verification/exp2/}.  The experiment files 
 \begin{itemize}
 \item {\it input/data}
 \item {\it input/data.pkg}
@@ -263,11 +364,12 @@
 \item {\it code/CPP\_OPTIONS.h},
 \item {\it code/SIZE.h}. 
 \end{itemize}
-contain the code customisations and parameter settings for this 
-experiements. 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
@@ -277,571 +379,306 @@
 
 \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 are ordered from surface to depth. For each
-depth level the inital 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}
-} 
-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}
-}.
-
-%% \codelink{var:tref} tRef \endlink
-%% \codelink{file:ini_parms} {\it INI\_PARMS } \endlink
-%% \codelink{proc:ini_parms} {\it INI\_PARMS } \endlink
-%% \var{tref}
-%% \proc{ini_parms}
-%% \file{ini_parms}
-\newcommand{\VARtref}{
-{\bf
-\begin{rawhtml} <A href=../../../code_reference/vdb/names/OK.htm> \end{rawhtml}
-tRef
-\begin{rawhtml} </A>\end{rawhtml}
-} 
-}
-
-
+this line sets the initial and reference values of potential
+temperature at each model level in units of $^{\circ}$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
+model code, by procedure \filelink{INI\_PARMS}{model-src-ini_parms.F}
 
 \fbox{
-\begin{minipage}{5.0in}
-{\it S/R INI\_THETA}
-({\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}
+  \begin{minipage}{5.0in}
+    {\it S/R INI\_THETA}({\it ini\_theta.F})
+  \end{minipage}
 }
-
+\filelink{ini\_theta.F}{model-src-ini_theta.F}
 
 \item Line 6, 
 \begin{verbatim} viscAz=1.E-2, \end{verbatim} 
-this line sets the vertical laplacian dissipation coefficient to
-$1 \times 10^{-2} {\rm m^{2}s^{-1}}$. 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}
-}
-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 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}
-}.
+this line sets the vertical Laplacian dissipation coefficient to $1
+\times 10^{-2} {\rm m^{2}s^{-1}}$. Boundary conditions for this
+operator are specified later.  The variable \varlink{viscAz}{viscAz}
+is read in the routine \filelink{ini\_parms.F}{model-src-ini_parms.F}
+and is copied into model general vertical coordinate variable
+\varlink{viscAr}{viscAr} At each time step, the viscous term
+contribution to the momentum equations is calculated in routine
+\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}
-}
 
 \item Line 7, 
 \begin{verbatim}
 viscAh=4.E2,
 \end{verbatim} 
-this line sets the horizontal laplacian frictional dissipation coefficient to
-$1 \times 10^{-2} {\rm m^{2}s^{-1}}$. 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}
-}
-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}
-}.
+  this line sets the horizontal laplacian frictional dissipation
+  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}.
 
 \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}
+  \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})
-\end{minipage}
-}
-{\bf
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/58.htm> \end{rawhtml}
-goto code
-\begin{rawhtml} </A>\end{rawhtml}
+  \begin{minipage}{5.0in}
+    {\it S/R CALC\_GW}({\it calc\_gw.F})
+  \end{minipage}
 }
 
-\item Lines 8,
+\item Line 8,
 \begin{verbatim}
 no_slip_sides=.FALSE.
 \end{verbatim}
-this line selects a free-slip lateral boundary condition for
-the horizontal laplacian friction operator 
-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}
-}
-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}
-}.
-
-
-\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}
-}
-
+  this line selects a free-slip lateral boundary condition for the
+  horizontal laplacian friction operator 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
+  \varlink{no\_slip\_sides}{no_slip_sides} is read in the routine
+  \varlink{INI\_PARMS}{INI_PARMS} and the boundary condition is
+  evaluated in routine
+
+  \fbox{
+    \begin{minipage}{5.0in}
+      {\it S/R CALC\_MOM\_RHS}({\it calc\_mom\_rhs.F})
+    \end{minipage}
+  }
+  \filelink{calc\_mom\_rhs.F}{calc_mom_rhs.F}
+  
 \item Lines 9,
 \begin{verbatim}
 no_slip_bottom=.TRUE.
 \end{verbatim}
-this line selects a no-slip boundary condition for bottom
-boundary condition in the vertical laplacian friction operator 
-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}
-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}
-INI\_PARMS
-\begin{rawhtml} </A>\end{rawhtml}
-}.
-
-\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}
-}
+  this line selects a no-slip boundary condition for bottom boundary
+  condition in the vertical laplacian friction operator e.g. $u=v=0$
+  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}.
+
+  \fbox{
+    \begin{minipage}{5.0in}
+      {\it S/R CALC\_MOM\_RHS}({\it calc\_mom\_rhs.F})
+    \end{minipage}
+  }
+  \filelink{calc\_mom\_rhs.F}{calc_mom_rhs.F}
 
 \item Line 10,
 \begin{verbatim}
 diffKhT=4.E2,
 \end{verbatim}
-this line sets the horizontal diffusion coefficient for temperature
-to $400\,{\rm m^{2}s^{-1}}$. The boundary condition on this
-operator is $\frac{\partial}{\partial x}=\frac{\partial}{\partial y}=0$ at
-all boundaries.
-The variable
-{\bf
-\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}
-INI\_PARMS
-\begin{rawhtml} </A>\end{rawhtml}
-}.
-
-\fbox{ \begin{minipage}{5.0in}
-{\it S/R CALC\_GT}({\it calc\_gt.F})
-\end{minipage}
-}
-{\bf
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/57.htm> \end{rawhtml}
-goto code
-\begin{rawhtml} </A>\end{rawhtml}
-}
+  this line sets the horizontal diffusion coefficient for temperature
+  to $400\,{\rm m^{2}s^{-1}}$. The boundary condition on this operator
+  is $\frac{\partial}{\partial x}=\frac{\partial}{\partial y}=0$ at
+  all boundaries.  The variable \varlink{diffKhT}{diffKhT} is read in
+  the routine \varlink{INI\_PARMS}{INI_PARMS} and used in routine
+  \varlink{CALC\_GT}{CALC_GT}.
+
+  \fbox{ \begin{minipage}{5.0in}
+      {\it S/R CALC\_GT}({\it calc\_gt.F})
+    \end{minipage}
+  }
+  \filelink{calc\_gt.F}{model-src-calc_gt.F}
 
 \item Line 11,
 \begin{verbatim}
 diffKzT=1.E-2,
 \end{verbatim}
-this line sets the vertical diffusion coefficient for temperature
-to $10^{-2}\,{\rm m^{2}s^{-1}}$. The boundary condition on this
-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}
-diffKzT
-\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}
-}.
-It is copied into model general vertical coordinate variable
-{\bf
-\begin{rawhtml} <A href=../../../code_reference/vdb/names/PD.htm> \end{rawhtml}
-diffKrT
-\begin{rawhtml} </A>\end{rawhtml}
-}.
-
-\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}
-}
-
-
+  this line sets the vertical diffusion coefficient for temperature to
+  $10^{-2}\,{\rm m^{2}s^{-1}}$. The boundary condition on this
+  operator is $\frac{\partial}{\partial z}$ = 0 on all boundaries.
+  The variable \varlink{diffKzT}{diffKzT} is read in the routine
+  \varlink{INI\_PARMS}{INI_PARMS}. It is copied into model general
+  vertical coordinate variable \varlink{diffKrT}{diffKrT} which is
+  used in routine \varlink{CALC\_DIFFUSIVITY}{CALC_DIFFUSIVITY}.
+
+  \fbox{ \begin{minipage}{5.0in}
+      {\it S/R CALC\_DIFFUSIVITY}({\it calc\_diffusivity.F})
+    \end{minipage}
+  }
+  \filelink{calc\_diffusivity.F}{model-src-calc_diffusivity.F}
 
 \item Line 13,
 \begin{verbatim}
 tAlpha=2.E-4,
 \end{verbatim}
-This line sets the thermal expansion coefficient for the fluid
-to $2 \times 10^{-4}\,{\rm degrees}^{-1}$
-The variable
-{\bf
-\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}
-INI\_PARMS
-\begin{rawhtml} </A>\end{rawhtml}
-}.
-
-\fbox{
-\begin{minipage}{5.0in}
-{\it S/R FIND\_RHO}({\it find\_rho.F})
-\end{minipage}
-}
-{\bf
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/79.htm> \end{rawhtml}
-goto code
-\begin{rawhtml} </A>\end{rawhtml}
-}
+  This line sets the thermal expansion coefficient for the fluid to $2
+  \times 10^{-4}\,{\rm degrees}^{-1}$ The variable
+  \varlink{tAlpha}{tAlpha} is read in the routine
+  \varlink{INI\_PARMS}{INI_PARMS}. The routine
+  \varlink{FIND\_RHO}{FIND\_RHO} makes use of {\bf tAlpha}.
+
+  \fbox{
+    \begin{minipage}{5.0in}
+      {\it S/R FIND\_RHO}({\it find\_rho.F})
+    \end{minipage}
+  }
+  \filelink{find\_rho.F}{model-src-find_rho.F}
 
 \item Line 18,
 \begin{verbatim}
 eosType='LINEAR'
 \end{verbatim}
-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}
-eosType
-\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}
-}.
-
-\fbox{
-\begin{minipage}{5.0in}
-{\it S/R FIND\_RHO}({\it find\_rho.F})
-\end{minipage}
-}
-{\bf
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/79.htm> \end{rawhtml}
-goto code
-\begin{rawhtml} </A>\end{rawhtml}
-}
-
-
+  This line selects the linear form of the equation of state.  The
+  variable \varlink{eosType}{eosType} is read in the routine
+  \varlink{INI\_PARMS}{INI_PARMS}. The values of {\bf eosType} sets
+  which formula in routine {\it FIND\_RHO} is used to calculate
+  density.
+
+  \fbox{
+    \begin{minipage}{5.0in}
+      {\it S/R FIND\_RHO}({\it find\_rho.F})
+    \end{minipage}
+  }
+  \filelink{find\_rho.F}{model-src-find_rho.F}
 
 \item Line 40,
 \begin{verbatim}
 usingSphericalPolarGrid=.TRUE.,
 \end{verbatim}
-This line requests that the simulation be performed in a 
-spherical polar coordinate system. It affects the interpretation of
-grid inoput parameters, for exampl {\bf delX} and {\bf delY} and
-causes the grid generation routines to initialise an internal grid based
-on spherical polar geometry.
-The variable
-{\bf
-\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}
-INI\_PARMS
-\begin{rawhtml} </A>\end{rawhtml}
-}.
-
-\fbox{
-\begin{minipage}{5.0in}
-{\it S/R INI\_SPEHRICAL\_POLAR\_GRID}({\it ini\_spherical\_polar\_grid.F})
-\end{minipage}
-}
-{\bf
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/97.htm> \end{rawhtml}
-goto code
-\begin{rawhtml} </A>\end{rawhtml}
-}
+  This line requests that the simulation be performed in a spherical
+  polar coordinate system. It affects the interpretation of grid input
+  parameters, for example {\bf delX} and {\bf delY} and causes the
+  grid generation routines to initialize an internal grid based on
+  spherical polar geometry.  The variable
+  \varlink{usingSphericalPolarGrid}{usingSphericalPolarGrid} is read
+  in the routine \varlink{INI\_PARMS}{INI_PARMS}. When set to {\bf
+    .TRUE.} the settings of {\bf delX} and {\bf delY} are taken to be
+  in degrees. These values are used in the routine
+
+  \fbox{
+    \begin{minipage}{5.0in}
+      {\it S/R INI\_SPEHRICAL\_POLAR\_GRID}({\it ini\_spherical\_polar\_grid.F})
+    \end{minipage}
+  }
+  \filelink{ini\_spherical\_polar\_grid.F}{model-src-ini_spherical_polar_grid.F}
 
 \item Line 41,
 \begin{verbatim}
 phiMin=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 locally orthogonal grid that the model
-uses internally and affects the initialisation 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
-{\bf
-\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}
-INI\_PARMS
-\begin{rawhtml} </A>\end{rawhtml}
-}.
-
-\fbox{
-\begin{minipage}{5.0in}
-{\it S/R INI\_SPEHRICAL\_POLAR\_GRID}({\it ini\_spherical\_polar\_grid.F})
-\end{minipage}
-}
-{\bf
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/97.htm> \end{rawhtml}
-goto code
-\begin{rawhtml} </A>\end{rawhtml}
-}
+  This line sets the southern boundary of the modeled domain to
+  $0^{\circ}$ latitude. This value affects both the generation of the
+  locally orthogonal grid that the model uses internally and affects
+  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
+  routine \varlink{INI\_PARMS}{INI_PARMS} and is used in routine
+
+  \fbox{
+    \begin{minipage}{5.0in}
+      {\it S/R INI\_SPEHRICAL\_POLAR\_GRID}({\it ini\_spherical\_polar\_grid.F})
+    \end{minipage}
+  }
+  \filelink{ini\_spherical\_polar\_grid.F}{model-src-ini_spherical_polar_grid.F}
 
 \item Line 42,
 \begin{verbatim}
 delX=60*1.,
 \end{verbatim}
-This line sets the horizontal grid spacing between each y-coordinate line
-in the discrete grid to $1^{\circ}$ in longitude.
-The variable
-{\bf
-\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}
-INI\_PARMS
-\begin{rawhtml} </A>\end{rawhtml}
-}.
-
-\fbox{
-\begin{minipage}{5.0in}
-{\it S/R INI\_SPEHRICAL\_POLAR\_GRID}({\it ini\_spherical\_polar\_grid.F})
-\end{minipage}
-}
-{\bf
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/97.htm> \end{rawhtml}
-goto code
-\begin{rawhtml} </A>\end{rawhtml}
-}
+  This line sets the horizontal grid spacing between each y-coordinate
+  line in the discrete grid to $1^{\circ}$ in longitude.  The variable
+  \varlink{delX}{delX} is read in the routine
+  \varlink{INI\_PARMS}{INI_PARMS} and is used in routine
+ 
+  \fbox{
+    \begin{minipage}{5.0in}
+      {\it S/R INI\_SPEHRICAL\_POLAR\_GRID}({\it ini\_spherical\_polar\_grid.F})
+    \end{minipage}
+  }
+  \filelink{ini\_spherical\_polar\_grid.F}{model-src-ini_spherical_polar_grid.F}
 
 \item Line 43,
 \begin{verbatim}
 delY=60*1.,
 \end{verbatim}
-This line sets the horizontal grid spacing between each y-coordinate line
-in the discrete grid to $1^{\circ}$ in latitude.
-The variable
-{\bf
-\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}
-INI\_PARMS
-\begin{rawhtml} </A>\end{rawhtml}
-}.
-
-\fbox{
-\begin{minipage}{5.0in}
-{\it S/R INI\_SPEHRICAL\_POLAR\_GRID}({\it ini\_spherical\_polar\_grid.F})
-\end{minipage}
-}
-{\bf
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/97.htm> \end{rawhtml}
-goto code
-\begin{rawhtml} </A>\end{rawhtml}
-}
+  This line sets the horizontal grid spacing between each y-coordinate
+  line in the discrete grid to $1^{\circ}$ in latitude.  The variable
+  \varlink{delY}{delY} is read in the routine
+  \varlink{INI\_PARMS}{INI_PARMS} and is used in routine
+
+  \fbox{
+    \begin{minipage}{5.0in}
+      {\it S/R INI\_SPEHRICAL\_POLAR\_GRID}({\it ini\_spherical\_polar\_grid.F})
+    \end{minipage}
+  }
+  \filelink{ini\_spherical\_polar\_grid.F}{model-src-ini_spherical_polar_grid.F}
 
 \item Line 44,
 \begin{verbatim}
 delZ=500.,500.,500.,500.,
 \end{verbatim}
-This line sets the vertical grid spacing between each z-coordinate line
-in the discrete grid to $500\,{\rm m}$, so that the total model depth 
-is $2\,{\rm km}$.
-The variable
-{\bf
-\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}
-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}
-delR
-\begin{rawhtml} </A>\end{rawhtml}
-}. 
-
-\fbox{
-\begin{minipage}{5.0in}
-{\it S/R INI\_VERTICAL\_GRID}({\it ini\_vertical\_grid.F})
-\end{minipage}
-}
-{\bf
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/100.htm> \end{rawhtml}
-goto code
-\begin{rawhtml} </A>\end{rawhtml}
-}
+  This line sets the vertical grid spacing between each z-coordinate
+  line in the discrete grid to $500\,{\rm m}$, so that the total model
+  depth is $2\,{\rm km}$.  The variable \varlink{delZ}{delZ} is read
+  in the routine \varlink{INI\_PARMS}{INI_PARMS}.  It is copied into
+  the internal model coordinate variable \varlink{delR}{delR} which is
+  used in routine
+
+  \fbox{
+    \begin{minipage}{5.0in}
+      {\it S/R INI\_VERTICAL\_GRID}({\it ini\_vertical\_grid.F})
+    \end{minipage}
+  }
+  \filelink{ini\_vertical\_grid.F}{model-src-ini_vertical_grid.F}
 
 \item Line 47,
 \begin{verbatim}
 bathyFile='topog.box'
 \end{verbatim}
-This line specifies the name of the file from which the domain
-bathymetry is read. This file is a two-dimensional ($x,y$) map of
-depths. This file is assumed to contain 64-bit binary numbers 
-giving the depth of the model at each grid cell, ordered with the x 
-coordinate varying fastest. The points are ordered from low coordinate
-to high coordinate for both axes. The units and orientation of the
-depths in this file are the same as used in the MITgcm code. In this
-experiment, a depth of $0m$ indicates a solid wall and a depth
-of $-2000m$ indicates open ocean. The matlab program
-{\it input/gendata.m} shows an example of how to generate a
-bathymetry file.
-The variable
-{\bf
-\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}
-INI\_PARMS
-\begin{rawhtml} </A>\end{rawhtml}
-}.
-
-\fbox{
-\begin{minipage}{5.0in}
-{\it S/R INI\_DEPTHS}({\it ini\_depths.F})
-\end{minipage}
-}
-{\bf
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/88.htm> \end{rawhtml}
-goto code
-\begin{rawhtml} </A>\end{rawhtml}
-}
-
+  This line specifies the name of the file from which the domain
+  bathymetry is read. This file is a two-dimensional ($x,y$) map of
+  depths. This file is assumed to contain 64-bit binary numbers giving
+  the depth of the model at each grid cell, ordered with the x
+  coordinate varying fastest. The points are ordered from low
+  coordinate to high coordinate for both axes. The units and
+  orientation of the depths in this file are the same as used in the
+  MITgcm code. In this experiment, a depth of $0m$ indicates a solid
+  wall and a depth of $-2000m$ indicates open ocean. The matlab
+  program {\it input/gendata.m} shows an example of how to generate a
+  bathymetry file.  The variable \varlink{bathyFile}{bathyFile} is
+  read in the routine \varlink{INI\_PARMS}{INI_PARMS}.  The bathymetry
+  file is read in the routine
+
+  \fbox{
+    \begin{minipage}{5.0in}
+      {\it S/R INI\_DEPTHS}({\it ini\_depths.F})
+    \end{minipage}
+  }
+  \filelink{ini\_depths.F}{model-src-ini_depths.F}
 
 \item Line 50,
 \begin{verbatim}
 zonalWindFile='windx.sin_y'
 \end{verbatim}
-This line specifies the name of the file from which the x-direction
-surface wind stress is read. This file is also a two-dimensional
-($x,y$) map and is enumerated and formatted in the same manner as the 
-bathymetry file. The matlab program {\it input/gendata.m} includes example 
-code to generate a valid 
-{\bf zonalWindFile} 
-file.  
-The variable
-{\bf
-\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}
-INI\_PARMS
-\begin{rawhtml} </A>\end{rawhtml}
-}.
-
-\fbox{
-\begin{minipage}{5.0in}
-{\it S/R EXTERNAL\_FIELDS\_LOAD}({\it external\_fields\_load.F})
-\end{minipage}
-}
-{\bf
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/75.htm> \end{rawhtml}
-goto code
-\begin{rawhtml} </A>\end{rawhtml}
-}
+  This line specifies the name of the file from which the x-direction
+  (zonal) surface wind stress is read. This file is also a
+  two-dimensional ($x,y$) map and is enumerated and formatted in the
+  same manner as the bathymetry file. The matlab program {\it
+    input/gendata.m} includes example code to generate a valid {\bf
+    zonalWindFile} file.  The variable
+  \varlink{zonalWindFile}{zonalWindFile} is read in the routine
+  \varlink{INI\_PARMS}{INI_PARMS}.  The wind-stress file is read in
+  the routine
+
+  \fbox{
+    \begin{minipage}{5.0in}
+      {\it S/R EXTERNAL\_FIELDS\_LOAD}({\it external\_fields\_load.F})
+    \end{minipage}
+  }
+  \filelink{external\_fields\_load.F}{model-src-external_fields_load.F}
 
 \end{itemize}
 
-\noindent other lines in the file {\it input/data} are standard values
-that are described in the MITgcm Getting Started and MITgcm Parameters
-notes.
+\noindent other lines in the file {\it input/data} are standard values.
 
 \begin{rawhtml}<PRE>\end{rawhtml}
 \begin{small}
@@ -850,37 +687,44 @@
 \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 $Nm^{-2}$.
-Although $\tau_{x}$ is only a function of $y$n in this experiment
-this file must still define a complete two-dimensional map in order
-to be compatible with the standard code for loading forcing fields 
-in MITgcm. The included matlab program {\it input/gendata.m} gives a complete
-code for creating the {\it input/windx.sin\_y} file.
+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 default for MITgcm).  Although $\tau_{x}$ is only a function of
+latitude, $y$, in this experiment this file must still define a
+complete two-dimensional map in order to be compatible with the
+standard code for loading forcing fields in MITgcm (routine {\it
+  EXTERNAL\_FIELDS\_LOAD}.  The included matlab program {\it
+  input/gendata.m} gives a complete 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 ($x,y$) 
 map of depth values. For this experiment values are either
-$0m$ or $-2000\,{\rm m}$, corresponding respectively to a wall or to deep
+$0~{\rm m}$ or $-2000\,{\rm m}$, corresponding respectively to a wall or to deep
 ocean. The file contains a raw binary stream of data that is enumerated
 in the same way as standard MITgcm two-dimensional, horizontal arrays.
 The included matlab program {\it input/gendata.m} gives a complete
 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
 
@@ -907,17 +751,20 @@
 \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}
@@ -930,22 +777,26 @@
 \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 the Getting Started
-Guide \cite{MITgcm_Getting_Started}.
+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
 
 \vspace{5mm}
-{\it verification/exp1/ }
+{\it verification/exp2/ }
 
 \subsubsection{Running the Experiment}
+\label{www:tutorials}
 
  To run the experiment
 
@@ -962,9 +813,9 @@
 % pwd
 \end{verbatim}
 
- You shold see a response on the screen ending in
+ You should see a response on the screen ending in
 
-{\it verification/exp1/input }
+{\it verification/exp2/input }
 
 
 \item Run the genmake script to create the experiment {\it Makefile}
