--- manual/s_examples/baroclinic_gyre/fourlayer.tex 2002/05/16 15:54:37 1.13
+++ manual/s_examples/baroclinic_gyre/fourlayer.tex 2003/08/07 18:27:52 1.15
@@ -1,4 +1,4 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_examples/baroclinic_gyre/fourlayer.tex,v 1.13 2002/05/16 15:54:37 adcroft 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}
@@ -360,9 +360,9 @@
\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}
@@ -382,17 +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} \end{rawhtml}
-tRef
-\begin{rawhtml} \end{rawhtml}
-}
+\varlink{tRef}{tRef}
+%{\bf
+%\begin{rawhtml} \end{rawhtml}
+%tRef
+%\begin{rawhtml} \end{rawhtml}
+%}
in the model code, by procedure
-{\it
-\begin{rawhtml} \end{rawhtml}
-INI\_PARMS
-\begin{rawhtml} \end{rawhtml}
-}.
+\filelink{INI\_PARMS}{model-src-ini_parms.F}
+%{\it
+%\begin{rawhtml} \end{rawhtml}
+%INI\_PARMS
+%\begin{rawhtml} \end{rawhtml}
+%}.
%% \codelink{var:tref} tRef \endlink
%% \codelink{file:ini_parms} {\it INI\_PARMS } \endlink
@@ -402,7 +404,7 @@
%% \file{ini_parms}
\newcommand{\VARtref}{
{\bf
-\begin{rawhtml} \end{rawhtml}
+\begin{rawhtml} \end{rawhtml}
tRef
\begin{rawhtml} \end{rawhtml}
}
@@ -416,11 +418,12 @@
({\it ini\_theta.F})
\end{minipage}
}
-{\bf
-\begin{rawhtml} \end{rawhtml}
-goto code
-\begin{rawhtml} \end{rawhtml}
-}
+\filelink{ini\_theta.F}{model-src-ini_theta.F}
+%{\bf
+%\begin{rawhtml} \end{rawhtml}
+%goto code
+%\begin{rawhtml} \end{rawhtml}
+%}
\item Line 6,
@@ -429,36 +432,41 @@
$1 \times 10^{-2} {\rm m^{2}s^{-1}}$. Boundary conditions
for this operator are specified later.
The variable
-{\bf
-\begin{rawhtml} \end{rawhtml}
-viscAz
-\begin{rawhtml} \end{rawhtml}
-}
-is read in the routine
-{\it
-\begin{rawhtml} \end{rawhtml}
-INI\_PARMS
-\begin{rawhtml} \end{rawhtml}
-}
+\varlink{viscAz}{viscAz}
+%{\bf
+%\begin{rawhtml} \end{rawhtml}
+%viscAz
+%\begin{rawhtml} \end{rawhtml}
+%}
+is read in the routine
+\filelink{ini\_parms.F}{model-src-ini_parms.F}
+%{\it
+%\begin{rawhtml} \end{rawhtml}
+%INI\_PARMS
+%\begin{rawhtml} \end{rawhtml}
+%}
and is copied into model general vertical coordinate variable
-{\bf
-\begin{rawhtml} \end{rawhtml}
-viscAr
-\begin{rawhtml} \end{rawhtml}
-}. At each time step, the viscous term contribution to the momentum equations
+\varlink{viscAr}{viscAr}
+%{\bf
+%\begin{rawhtml} \end{rawhtml}
+%viscAr
+%\begin{rawhtml} \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} \end{rawhtml}
-goto code
-\begin{rawhtml} \end{rawhtml}
-}
+%{\bf
+%\begin{rawhtml} \end{rawhtml}
+%goto code
+%\begin{rawhtml} \end{rawhtml}
+%}
\item Line 7,
\begin{verbatim}
@@ -468,39 +476,47 @@
$1 \times 10^{-2} {\rm m^{2}s^{-1}}$. Boundary conditions
for this operator are specified later.
The variable
-{\bf
-\begin{rawhtml} \end{rawhtml}
-viscAh
-\begin{rawhtml} \end{rawhtml}
-}
-is read in the routine
-{\it
-\begin{rawhtml} \end{rawhtml}
-INI\_PARMS
-\begin{rawhtml} \end{rawhtml}
-} and applied in routines {\it CALC\_MOM\_RHS} and {\it CALC\_GW}.
+\varlink{viscAh}{viscAh}
+%{\bf
+%\begin{rawhtml} \end{rawhtml}
+%viscAh
+%\begin{rawhtml} \end{rawhtml}
+%}
+is read in the routine
+\varlink{INI\_PARMS}{INI_PARMS}
+%{\it
+%\begin{rawhtml} \end{rawhtml}
+%INI\_PARMS
+%\begin{rawhtml} \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} \end{rawhtml}
-goto code
-\begin{rawhtml} \end{rawhtml}
-}
+%{\bf
+%\begin{rawhtml} \end{rawhtml}
+%goto code
+%\begin{rawhtml} \end{rawhtml}
+%}
\fbox{
\begin{minipage}{5.0in}
{\it S/R CALC\_GW}({\it calc\_gw.F})
\end{minipage}
}
-{\bf
-\begin{rawhtml} \end{rawhtml}
-goto code
-\begin{rawhtml} \end{rawhtml}
-}
+%{\bf
+%\begin{rawhtml} \end{rawhtml}
+%goto code
+%\begin{rawhtml} \end{rawhtml}
+%}
\item Lines 8,
\begin{verbatim}
@@ -511,18 +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} \end{rawhtml}
-no\_slip\_sides
-\begin{rawhtml} \end{rawhtml}
-}
-is read in the routine
-{\it
-\begin{rawhtml} \end{rawhtml}
-INI\_PARMS
-\begin{rawhtml} \end{rawhtml}
-} and the boundary condition is evaluated in routine
-{\it S/R CALC\_MOM\_RHS}.
+\varlink{no\_slip\_sides}{no_slip_sides}
+%{\bf
+%\begin{rawhtml} \end{rawhtml}
+%no\_slip\_sides
+%\begin{rawhtml} \end{rawhtml}
+%}
+is read in the routine
+\varlink{INI\_PARMS}{INI_PARMS}
+%{\it
+%\begin{rawhtml} \end{rawhtml}
+%INI\_PARMS
+%\begin{rawhtml} \end{rawhtml}
+%}
+and the boundary condition is evaluated in routine
+%{\it S/R CALC\_MOM\_RHS}.
\fbox{
@@ -531,7 +550,7 @@
\end{minipage}
}
{\bf
-\begin{rawhtml} \end{rawhtml}
+\begin{rawhtml} \end{rawhtml}
goto code
\begin{rawhtml} \end{rawhtml}
}
@@ -545,13 +564,13 @@
e.g. $u=v=0$ at $z=-H$, where $H$ is the local depth of the domain.
The variable
{\bf
-\begin{rawhtml} \end{rawhtml}
+\begin{rawhtml} \end{rawhtml}
no\_slip\_bottom
\begin{rawhtml} \end{rawhtml}
}
is read in the routine
{\it
-\begin{rawhtml} \end{rawhtml}
+\begin{rawhtml} \end{rawhtml}
INI\_PARMS
\begin{rawhtml} \end{rawhtml}
} and is applied in the routine {\it S/R CALC\_MOM\_RHS}.
@@ -562,7 +581,7 @@
\end{minipage}
}
{\bf
-\begin{rawhtml} \end{rawhtml}
+\begin{rawhtml} \end{rawhtml}
goto code
\begin{rawhtml} \end{rawhtml}
}
@@ -577,13 +596,13 @@
all boundaries.
The variable
{\bf
-\begin{rawhtml} \end{rawhtml}
+\begin{rawhtml} \end{rawhtml}
diffKhT
\begin{rawhtml} \end{rawhtml}
}
is read in the routine
{\it
-\begin{rawhtml} \end{rawhtml}
+\begin{rawhtml} \end{rawhtml}
INI\_PARMS
\begin{rawhtml} \end{rawhtml}
} and used in routine {\it S/R CALC\_GT}.
@@ -593,7 +612,7 @@
\end{minipage}
}
{\bf
-\begin{rawhtml} \end{rawhtml}
+\begin{rawhtml} \end{rawhtml}
goto code
\begin{rawhtml} \end{rawhtml}
}
@@ -607,19 +626,19 @@
operator is $\frac{\partial}{\partial z}$ = 0 on all boundaries.
The variable
{\bf
-\begin{rawhtml} \end{rawhtml}
+\begin{rawhtml} \end{rawhtml}
diffKzT
\begin{rawhtml} \end{rawhtml}
}
is read in the routine
{\it
-\begin{rawhtml} \end{rawhtml}
+\begin{rawhtml} \end{rawhtml}
INI\_PARMS
\begin{rawhtml} \end{rawhtml}
}.
It is copied into model general vertical coordinate variable
{\bf
-\begin{rawhtml} \end{rawhtml}
+\begin{rawhtml} \end{rawhtml}
diffKrT
\begin{rawhtml} \end{rawhtml}
} which is used in routine {\it S/R CALC\_DIFFUSIVITY}.
@@ -629,7 +648,7 @@
\end{minipage}
}
{\bf
-\begin{rawhtml} \end{rawhtml}
+\begin{rawhtml} \end{rawhtml}
goto code
\begin{rawhtml} \end{rawhtml}
}
@@ -644,13 +663,13 @@
to $2 \times 10^{-4}\,{\rm degrees}^{-1}$
The variable
{\bf
-\begin{rawhtml} \end{rawhtml}
+\begin{rawhtml} \end{rawhtml}
tAlpha
\begin{rawhtml} \end{rawhtml}
}
is read in the routine
{\it
-\begin{rawhtml} \end{rawhtml}
+\begin{rawhtml} \end{rawhtml}
INI\_PARMS
\begin{rawhtml} \end{rawhtml}
}. The routine {\it S/R FIND\_RHO} makes use of {\bf tAlpha}.
@@ -661,7 +680,7 @@
\end{minipage}
}
{\bf
-\begin{rawhtml} \end{rawhtml}
+\begin{rawhtml} \end{rawhtml}
goto code
\begin{rawhtml} \end{rawhtml}
}
@@ -673,13 +692,13 @@
This line selects the linear form of the equation of state.
The variable
{\bf
-\begin{rawhtml} \end{rawhtml}
+\begin{rawhtml} \end{rawhtml}
eosType
\begin{rawhtml} \end{rawhtml}
}
is read in the routine
{\it
-\begin{rawhtml} \end{rawhtml}
+\begin{rawhtml} \end{rawhtml}
INI\_PARMS
\begin{rawhtml} \end{rawhtml}
}. The values of {\bf eosType} sets which formula in routine
@@ -691,7 +710,7 @@
\end{minipage}
}
{\bf
-\begin{rawhtml} \end{rawhtml}
+\begin{rawhtml} \end{rawhtml}
goto code
\begin{rawhtml} \end{rawhtml}
}
@@ -709,13 +728,13 @@
on spherical polar geometry.
The variable
{\bf
-\begin{rawhtml} \end{rawhtml}
+\begin{rawhtml} \end{rawhtml}
usingSphericalPolarGrid
\begin{rawhtml} \end{rawhtml}
}
is read in the routine
{\it
-\begin{rawhtml} \end{rawhtml}
+\begin{rawhtml} \end{rawhtml}
INI\_PARMS
\begin{rawhtml} \end{rawhtml}
}. When set to {\bf .TRUE.} the settings of {\bf delX} and {\bf delY} are
@@ -728,7 +747,7 @@
\end{minipage}
}
{\bf
-\begin{rawhtml} \end{rawhtml}
+\begin{rawhtml} \end{rawhtml}
goto code
\begin{rawhtml} \end{rawhtml}
}
@@ -746,13 +765,13 @@
not alter the kernel equation discretisation.
The variable
{\bf
-\begin{rawhtml} \end{rawhtml}
+\begin{rawhtml} \end{rawhtml}
phiMin
\begin{rawhtml} \end{rawhtml}
}
is read in the routine
{\it
-\begin{rawhtml} \end{rawhtml}
+\begin{rawhtml} \end{rawhtml}
INI\_PARMS
\begin{rawhtml} \end{rawhtml}
} and is used in routine {\it INI\_SPEHRICAL\_POLAR\_GRID}.
@@ -763,7 +782,7 @@
\end{minipage}
}
{\bf
-\begin{rawhtml} \end{rawhtml}
+\begin{rawhtml} \end{rawhtml}
goto code
\begin{rawhtml} \end{rawhtml}
}
@@ -776,13 +795,13 @@
in the discrete grid to $1^{\circ}$ in longitude.
The variable
{\bf
-\begin{rawhtml} \end{rawhtml}
+\begin{rawhtml} \end{rawhtml}
delX
\begin{rawhtml} \end{rawhtml}
}
is read in the routine
{\it
-\begin{rawhtml} \end{rawhtml}
+\begin{rawhtml} \end{rawhtml}
INI\_PARMS
\begin{rawhtml} \end{rawhtml}
} and is used in routine {\it INI\_SPEHRICAL\_POLAR\_GRID}.
@@ -793,7 +812,7 @@
\end{minipage}
}
{\bf
-\begin{rawhtml} \end{rawhtml}
+\begin{rawhtml} \end{rawhtml}
goto code
\begin{rawhtml} \end{rawhtml}
}
@@ -806,13 +825,13 @@
in the discrete grid to $1^{\circ}$ in latitude.
The variable
{\bf
-\begin{rawhtml} \end{rawhtml}
+\begin{rawhtml} \end{rawhtml}
delY
\begin{rawhtml} \end{rawhtml}
}
is read in the routine
{\it
-\begin{rawhtml} \end{rawhtml}
+\begin{rawhtml} \end{rawhtml}
INI\_PARMS
\begin{rawhtml} \end{rawhtml}
} and is used in routine {\it INI\_SPEHRICAL\_POLAR\_GRID}.
@@ -823,7 +842,7 @@
\end{minipage}
}
{\bf
-\begin{rawhtml} \end{rawhtml}
+\begin{rawhtml} \end{rawhtml}
goto code
\begin{rawhtml} \end{rawhtml}
}
@@ -837,20 +856,20 @@
is $2\,{\rm km}$.
The variable
{\bf
-\begin{rawhtml} \end{rawhtml}
+\begin{rawhtml} \end{rawhtml}
delZ
\begin{rawhtml} \end{rawhtml}
}
is read in the routine
{\it
-\begin{rawhtml} \end{rawhtml}
+\begin{rawhtml} \end{rawhtml}
INI\_PARMS
\begin{rawhtml} \end{rawhtml}
}.
It is copied into the internal
model coordinate variable
{\bf
-\begin{rawhtml} \end{rawhtml}
+\begin{rawhtml} \end{rawhtml}
delR
\begin{rawhtml} \end{rawhtml}
} which is used in routine {\it INI\_VERTICAL\_GRID}.
@@ -861,7 +880,7 @@
\end{minipage}
}
{\bf
-\begin{rawhtml} \end{rawhtml}
+\begin{rawhtml} \end{rawhtml}
goto code
\begin{rawhtml} \end{rawhtml}
}
@@ -883,13 +902,13 @@
bathymetry file.
The variable
{\bf
-\begin{rawhtml} \end{rawhtml}
+\begin{rawhtml} \end{rawhtml}
bathyFile
\begin{rawhtml} \end{rawhtml}
}
is read in the routine
{\it
-\begin{rawhtml} \end{rawhtml}
+\begin{rawhtml} \end{rawhtml}
INI\_PARMS
\begin{rawhtml} \end{rawhtml}
}. The bathymetry file is read in the routine {\it INI\_DEPTHS}.
@@ -900,7 +919,7 @@
\end{minipage}
}
{\bf
-\begin{rawhtml} \end{rawhtml}
+\begin{rawhtml} \end{rawhtml}
goto code
\begin{rawhtml} \end{rawhtml}
}
@@ -919,13 +938,13 @@
file.
The variable
{\bf
-\begin{rawhtml} \end{rawhtml}
+\begin{rawhtml} \end{rawhtml}
zonalWindFile
\begin{rawhtml} \end{rawhtml}
}
is read in the routine
{\it
-\begin{rawhtml} \end{rawhtml}
+\begin{rawhtml} \end{rawhtml}
INI\_PARMS
\begin{rawhtml} \end{rawhtml}
}. The wind-stress file is read in the routine
@@ -937,7 +956,7 @@
\end{minipage}
}
{\bf
-\begin{rawhtml} \end{rawhtml}
+\begin{rawhtml} \end{rawhtml}
goto code
\begin{rawhtml} \end{rawhtml}
}