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--- manual/s_examples/baroclinic_gyre/fourlayer.tex 2001/10/25 01:15:16 1.7
+++ manual/s_examples/baroclinic_gyre/fourlayer.tex 2001/10/25 12:06:56 1.8
@@ -1,4 +1,4 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_examples/baroclinic_gyre/fourlayer.tex,v 1.7 2001/10/25 01:15:16 cnh Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_examples/baroclinic_gyre/fourlayer.tex,v 1.8 2001/10/25 12:06:56 cnh Exp $
% $Name: $
\section{Example: Four layer Baroclinic Ocean Gyre In Spherical Coordinates}
@@ -67,8 +67,8 @@
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 $(x,y,z)$. For this experiment description
-of this document the local orthogonal model coordinate $(x,y,z)$ is synonomous
-with the spherical polar coordinate shown in figure
+the local orthogonal model coordinate $(x,y,z)$ is synonomous
+with the coordinates $(\lambda,\varphi,r)$ shown in figure
\ref{fig:spherical-polar-coord}
\\
@@ -118,9 +118,9 @@
\end{figure}
\subsection{Equations solved}
-
-The implicit free surface {\bf HPE} form of the
-equations described in Marshall et. al \cite{Marshall97a} is
+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
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
@@ -185,7 +185,7 @@
part due to variations in density, $\rho^{\prime}$, integrated
through the water column.
-The suffices ${s},{i}$ indicate surface and interior of the domain.
+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.
@@ -248,17 +248,22 @@
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
-equation. The pressure forces that drive the fluid motions, (
+equation. Prognostic terms in
+the momentum equations are solved using flux form as
+described in section \ref{sec: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 evaluated explicitly by integrating density. The sea-surface
-height, $\eta$, is solved for implicitly as described in section
-\ref{sect:pressure-method-linear-backward}.
+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{sec:finding_the_pressure_field}.
\subsubsection{Numerical Stability Criteria}
-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}
@@ -266,13 +271,15 @@
\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}
@@ -280,7 +287,7 @@
\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
@@ -298,7 +305,6 @@
\\
\noindent The numerical stability for inertial oscillations
-\cite{Adcroft_thesis}
\begin{eqnarray}
\label{EQ:inertial_stability}
@@ -309,35 +315,35 @@
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}
+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
+propogating at $2~{\rm m}~{\rm s}^{-1}$
\begin{eqnarray}
\label{EQ: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: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}
@@ -432,7 +438,9 @@
\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 eqautions
+is calculated in routine
+{\it S/R CALC\_DIFFUSIVITY}.
\fbox{
\begin{minipage}{5.0in}
@@ -463,7 +471,7 @@
\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}.
\fbox{
\begin{minipage}{5.0in}
@@ -506,7 +514,8 @@
\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{
@@ -538,7 +547,7 @@
\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}.
\fbox{
\begin{minipage}{5.0in}
@@ -570,7 +579,7 @@
\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}.
\fbox{ \begin{minipage}{5.0in}
{\it S/R CALC\_GT}({\it calc\_gt.F})
@@ -606,7 +615,7 @@
\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}.
\fbox{ \begin{minipage}{5.0in}
{\it S/R CALC\_DIFFUSIVITY}({\it calc\_diffusivity.F})
@@ -637,7 +646,7 @@
\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}.
\fbox{
\begin{minipage}{5.0in}
@@ -666,7 +675,8 @@
\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
+{\it FIND\_RHO} is used to calculate density.
\fbox{
\begin{minipage}{5.0in}
@@ -701,7 +711,9 @@
\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
+taken to be in degrees. These values are used in the
+routine {\it INI\_SPEHRICAL\_POLAR\_GRID}.
\fbox{
\begin{minipage}{5.0in}
@@ -736,7 +748,7 @@
\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}.
\fbox{
\begin{minipage}{5.0in}
@@ -766,7 +778,7 @@
\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}.
\fbox{
\begin{minipage}{5.0in}
@@ -796,7 +808,7 @@
\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}.
\fbox{
\begin{minipage}{5.0in}
@@ -834,7 +846,7 @@
\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}.
\fbox{
\begin{minipage}{5.0in}
@@ -873,7 +885,7 @@
\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}.
\fbox{
\begin{minipage}{5.0in}
@@ -892,7 +904,7 @@
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
+(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
@@ -909,7 +921,8 @@
\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
+{\it EXTERNAL\_FIELDS\_LOAD}.
\fbox{
\begin{minipage}{5.0in}
@@ -924,9 +937,7 @@
\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}
@@ -947,11 +958,14 @@
\subsubsection{File {\it input/windx.sin\_y}}
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
+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 latituted, $y$,
+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. The included matlab program {\it input/gendata.m} gives a complete
+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}}
@@ -959,7 +973,7 @@
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
@@ -1020,15 +1034,15 @@
\subsubsection{Code Download}
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}
This example experiments is located under the release sub-directory
\vspace{5mm}
-{\it verification/exp1/ }
+{\it verification/exp2/ }
\subsubsection{Running the Experiment}
@@ -1049,7 +1063,7 @@
You shold 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}
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