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revision 1.10 by adcroft, Tue Nov 13 19:01:42 2001 UTC revision 1.21 by molod, Tue Jun 27 19:08:22 2006 UTC
# Line 1  Line 1 
1  % $Header$  % $Header$
2  % $Name$  % $Name$
3    
4  \section{Example: Four layer Baroclinic Ocean Gyre In Spherical Coordinates}  \section[Baroclinic Gyre MITgcm Example]{Four Layer Baroclinic Ocean Gyre In Spherical Coordinates}
5  \label{sec:eg-fourlayer}  \label{www:tutorials}
6    \label{sect:eg-fourlayer}
7    \begin{rawhtml}
8    <!-- CMIREDIR:eg-fourlayer: -->
9    \end{rawhtml}
10    
11  \bodytext{bgcolor="#FFFFFFFF"}  \bodytext{bgcolor="#FFFFFFFF"}
12    
# Line 17  Line 21 
21  %\end{center}  %\end{center}
22    
23  This document describes an example experiment using MITgcm  This document describes an example experiment using MITgcm
24  to simulate a baroclinic ocean gyre in spherical  to simulate a baroclinic ocean gyre for four layers in spherical
25  polar coordinates. The barotropic  polar coordinates.  The files for this experiment can be found
26  example experiment in section \ref{sec:eg-baro}  in the verification directory under tutorial\_baroclinic\_gyre.
 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.  
27    
28  \subsection{Overview}  \subsection{Overview}
29    \label{www:tutorials}
30    
31  This example experiment demonstrates using the MITgcm to simulate  This example experiment demonstrates using the MITgcm to simulate
32  a baroclinic, wind-forced, ocean gyre circulation. The experiment  a baroclinic, wind-forced, ocean gyre circulation. The experiment
# Line 43  domain is a sector on a sphere and the c Line 44  domain is a sector on a sphere and the c
44  according to latitude, $\varphi$  according to latitude, $\varphi$
45    
46  \begin{equation}  \begin{equation}
47  \label{EQ:fcori}  \label{EQ:eg-fourlayer-fcori}
48  f(\varphi) = 2 \Omega \sin( \varphi )  f(\varphi) = 2 \Omega \sin( \varphi )
49  \end{equation}  \end{equation}
50    
# Line 61  f(\varphi) = 2 \Omega \sin( \varphi ) Line 62  f(\varphi) = 2 \Omega \sin( \varphi )
62  $\tau_0$ is set to $0.1N m^{-2}$.  $\tau_0$ is set to $0.1N m^{-2}$.
63  \\  \\
64    
65  Figure \ref{FIG:simulation_config}  Figure \ref{FIG:eg-fourlayer-simulation_config}
66  summarizes the configuration simulated.  summarizes the configuration simulated.
67  In contrast to the example in section \ref{sec:eg-baro}, the  In contrast to the example in section \ref{sect:eg-baro}, the
68  current experiment simulates a spherical polar domain. As indicated  current experiment simulates a spherical polar domain. As indicated
69  by the axes in the lower left of the figure the model code works internally  by the axes in the lower left of the figure the model code works internally
70  in a locally orthogonal coordinate $(x,y,z)$. For this experiment description  in a locally orthogonal coordinate $(x,y,z)$. For this experiment description
# Line 82  $\theta_{1750}=6^{\circ}$~C. The equatio Line 83  $\theta_{1750}=6^{\circ}$~C. The equatio
83  linear  linear
84    
85  \begin{equation}  \begin{equation}
86  \label{EQ:linear1_eos}  \label{EQ:eg-fourlayer-linear1_eos}
87  \rho = \rho_{0} ( 1 - \alpha_{\theta}\theta^{'} )  \rho = \rho_{0} ( 1 - \alpha_{\theta}\theta^{'} )
88  \end{equation}  \end{equation}
89    
90  \noindent which is implemented in the model as a density anomaly equation  \noindent which is implemented in the model as a density anomaly equation
91    
92  \begin{equation}  \begin{equation}
93  \label{EQ:linear1_eos_pert}  \label{EQ:eg-fourlayer-linear1_eos_pert}
94  \rho^{'} = -\rho_{0}\alpha_{\theta}\theta^{'}  \rho^{'} = -\rho_{0}\alpha_{\theta}\theta^{'}
95  \end{equation}  \end{equation}
96    
# Line 102  non-linear, we use $\theta$ to represent Line 103  non-linear, we use $\theta$ to represent
103  the quantity that is carried in the model core equations.  the quantity that is carried in the model core equations.
104    
105  \begin{figure}  \begin{figure}
106  \begin{center}  %% \begin{center}
107   \resizebox{7.5in}{5.5in}{  %%  \resizebox{7.5in}{5.5in}{
108     \includegraphics*[0.2in,0.7in][10.5in,10.5in]  %%    \includegraphics*[0.2in,0.7in][10.5in,10.5in]
109     {part3/case_studies/fourlayer_gyre/simulation_config.eps} }  %%    {part3/case_studies/fourlayer_gyre/simulation_config.eps} }
110  \end{center}  %% \end{center}
111    \centerline{
112      \scalefig{.95}
113      \epsfbox{part3/case_studies/fourlayer_gyre/simulation_config.eps}
114    }
115  \caption{Schematic of simulation domain and wind-stress forcing function  \caption{Schematic of simulation domain and wind-stress forcing function
116  for the four-layer gyre numerical experiment. The domain is enclosed by solid  for the four-layer gyre numerical experiment. The domain is enclosed by solid
117  walls at $0^{\circ}$~E, $60^{\circ}$~E, $0^{\circ}$~N and $60^{\circ}$~N.  walls at $0^{\circ}$~E, $60^{\circ}$~E, $0^{\circ}$~N and $60^{\circ}$~N.
# Line 114  An initial stratification is Line 119  An initial stratification is
119  imposed by setting the potential temperature, $\theta$, in each layer.  imposed by setting the potential temperature, $\theta$, in each layer.
120  The vertical spacing, $\Delta z$, is constant and equal to $500$m.  The vertical spacing, $\Delta z$, is constant and equal to $500$m.
121  }  }
122  \label{FIG:simulation_config}  \label{FIG:eg-fourlayer-simulation_config}
123  \end{figure}  \end{figure}
124    
125  \subsection{Equations solved}  \subsection{Equations solved}
126    \label{www:tutorials}
127  For this problem  For this problem
128  the implicit free surface, {\bf HPE} (see section \ref{sec:hydrostatic_and_quasi-hydrostatic_forms}) form of the  the implicit free surface, {\bf HPE} (see section \ref{sect:hydrostatic_and_quasi-hydrostatic_forms}) form of the
129  equations described in Marshall et. al \cite{marshall:97a} are  equations described in Marshall et. al \cite{marshall:97a} are
130  employed. The flow is three-dimensional with just temperature, $\theta$, as  employed. The flow is three-dimensional with just temperature, $\theta$, as
131  an active tracer.  The equation of state is linear.  an active tracer.  The equation of state is linear.
# Line 133  solved in this configuration, written in Line 139  solved in this configuration, written in
139  follows  follows
140    
141  \begin{eqnarray}  \begin{eqnarray}
142  \label{EQ:model_equations}  \label{EQ:eg-fourlayer-model_equations}
143  \frac{Du}{Dt} - fv +  \frac{Du}{Dt} - fv +
144    \frac{1}{\rho}\frac{\partial p^{\prime}}{\partial \lambda} -    \frac{1}{\rho}\frac{\partial p^{\prime}}{\partial \lambda} -
145    A_{h}\nabla_{h}^2u - A_{z}\frac{\partial^{2}u}{\partial z^{2}}    A_{h}\nabla_{h}^2u - A_{z}\frac{\partial^{2}u}{\partial z^{2}}
# Line 202  e.g. $\frac{\partial \theta}{\partial \v Line 208  e.g. $\frac{\partial \theta}{\partial \v
208    
209    
210  \subsection{Discrete Numerical Configuration}  \subsection{Discrete Numerical Configuration}
211    \label{www:tutorials}
212    
213   The domain is discretised with   The domain is discretised with
214  a uniform grid spacing in latitude and longitude  a uniform grid spacing in latitude and longitude
# Line 221  y=r\varphi,~\Delta y &= &r\Delta \varphi Line 228  y=r\varphi,~\Delta y &= &r\Delta \varphi
228    
229  The procedure for generating a set of internal grid variables from a  The procedure for generating a set of internal grid variables from a
230  spherical polar grid specification is discussed in section  spherical polar grid specification is discussed in section
231  \ref{sec:spatial_discrete_horizontal_grid}.  \ref{sect:spatial_discrete_horizontal_grid}.
232    
233  \noindent\fbox{ \begin{minipage}{5.5in}  \noindent\fbox{ \begin{minipage}{5.5in}
234  {\em S/R INI\_SPHERICAL\_POLAR\_GRID} ({\em  {\em S/R INI\_SPHERICAL\_POLAR\_GRID} ({\em
# Line 242  $\Delta x_v$, $\Delta y_u$: {\bf DXv}, { Line 249  $\Delta x_v$, $\Delta y_u$: {\bf DXv}, {
249    
250    
251    
252  As described in \ref{sec:tracer_equations}, the time evolution of potential  As described in \ref{sect:tracer_equations}, the time evolution of potential
253  temperature,  temperature,
254  $\theta$, (equation \ref{eq:eg_fourl_theta})  $\theta$, (equation \ref{eq:eg_fourl_theta})
255  is evaluated prognostically. The centered second-order scheme with  is evaluated prognostically. The centered second-order scheme with
256  Adams-Bashforth time stepping described in section  Adams-Bashforth time stepping described in section
257  \ref{sec:tracer_equations_abII} is used to step forward the temperature  \ref{sect:tracer_equations_abII} is used to step forward the temperature
258  equation. Prognostic terms in  equation. Prognostic terms in
259  the momentum equations are solved using flux form as  the momentum equations are solved using flux form as
260  described in section \ref{sec:flux-form_momentum_eqautions}.  described in section \ref{sect:flux-form_momentum_eqautions}.
261  The pressure forces that drive the fluid motions, (  The pressure forces that drive the fluid motions, (
262  $\frac{\partial p^{'}}{\partial \lambda}$ and $\frac{\partial p^{'}}{\partial \varphi}$), are found by summing pressure due to surface  $\frac{\partial p^{'}}{\partial \lambda}$ and $\frac{\partial p^{'}}{\partial \varphi}$), are found by summing pressure due to surface
263  elevation $\eta$ and the hydrostatic pressure. The hydrostatic part of the  elevation $\eta$ and the hydrostatic pressure. The hydrostatic part of the
# Line 258  pressure is diagnosed explicitly by inte Line 265  pressure is diagnosed explicitly by inte
265  height, $\eta$, is diagnosed using an implicit scheme. The pressure  height, $\eta$, is diagnosed using an implicit scheme. The pressure
266  field solution method is described in sections  field solution method is described in sections
267  \ref{sect:pressure-method-linear-backward} and  \ref{sect:pressure-method-linear-backward} and
268  \ref{sec:finding_the_pressure_field}.  \ref{sect:finding_the_pressure_field}.
269    
270  \subsubsection{Numerical Stability Criteria}  \subsubsection{Numerical Stability Criteria}
271    \label{www:tutorials}
272    
273  The Laplacian viscosity coefficient, $A_{h}$, is set to $400 m s^{-1}$.  The Laplacian viscosity coefficient, $A_{h}$, is set to $400 m s^{-1}$.
274  This value is chosen to yield a Munk layer width,  This value is chosen to yield a Munk layer width,
275    
276  \begin{eqnarray}  \begin{eqnarray}
277  \label{EQ:munk_layer}  \label{EQ:eg-fourlayer-munk_layer}
278  M_{w} = \pi ( \frac { A_{h} }{ \beta } )^{\frac{1}{3}}  M_{w} = \pi ( \frac { A_{h} }{ \beta } )^{\frac{1}{3}}
279  \end{eqnarray}  \end{eqnarray}
280    
# Line 282  time step $\delta t=1200$secs. With this Line 290  time step $\delta t=1200$secs. With this
290  parameter to the horizontal Laplacian friction  parameter to the horizontal Laplacian friction
291    
292  \begin{eqnarray}  \begin{eqnarray}
293  \label{EQ:laplacian_stability}  \label{EQ:eg-fourlayer-laplacian_stability}
294  S_{l} = 4 \frac{A_{h} \delta t}{{\Delta x}^2}  S_{l} = 4 \frac{A_{h} \delta t}{{\Delta x}^2}
295  \end{eqnarray}  \end{eqnarray}
296    
# Line 294  for stability for this term under ABII t Line 302  for stability for this term under ABII t
302  $1\times10^{-2} {\rm m}^2{\rm s}^{-1}$. The associated stability limit  $1\times10^{-2} {\rm m}^2{\rm s}^{-1}$. The associated stability limit
303    
304  \begin{eqnarray}  \begin{eqnarray}
305  \label{EQ:laplacian_stability_z}  \label{EQ:eg-fourlayer-laplacian_stability_z}
306  S_{l} = 4 \frac{A_{z} \delta t}{{\Delta z}^2}  S_{l} = 4 \frac{A_{z} \delta t}{{\Delta z}^2}
307  \end{eqnarray}  \end{eqnarray}
308    
# Line 307  and vertical ($K_{z}$) diffusion coeffic Line 315  and vertical ($K_{z}$) diffusion coeffic
315  \noindent The numerical stability for inertial oscillations  \noindent The numerical stability for inertial oscillations
316    
317  \begin{eqnarray}  \begin{eqnarray}
318  \label{EQ:inertial_stability}  \label{EQ:eg-fourlayer-inertial_stability}
319  S_{i} = f^{2} {\delta t}^2  S_{i} = f^{2} {\delta t}^2
320  \end{eqnarray}  \end{eqnarray}
321    
# Line 320  horizontal flow Line 328  horizontal flow
328  speed of $ | \vec{u} | = 2 ms^{-1}$  speed of $ | \vec{u} | = 2 ms^{-1}$
329    
330  \begin{eqnarray}  \begin{eqnarray}
331  \label{EQ:cfl_stability}  \label{EQ:eg-fourlayer-cfl_stability}
332  C_{a} = \frac{| \vec{u} | \delta t}{ \Delta x}  C_{a} = \frac{| \vec{u} | \delta t}{ \Delta x}
333  \end{eqnarray}  \end{eqnarray}
334    
# Line 332  limit of 0.5. Line 340  limit of 0.5.
340  propagating at $2~{\rm m}~{\rm s}^{-1}$  propagating at $2~{\rm m}~{\rm s}^{-1}$
341    
342  \begin{eqnarray}  \begin{eqnarray}
343  \label{EQ:igw_stability}  \label{EQ:eg-fourlayer-igw_stability}
344  S_{c} = \frac{c_{g} \delta t}{ \Delta x}  S_{c} = \frac{c_{g} \delta t}{ \Delta x}
345  \end{eqnarray}  \end{eqnarray}
346    
# Line 340  S_{c} = \frac{c_{g} \delta t}{ \Delta x} Line 348  S_{c} = \frac{c_{g} \delta t}{ \Delta x}
348  stability limit of 0.25.  stability limit of 0.25.
349        
350  \subsection{Code Configuration}  \subsection{Code Configuration}
351    \label{www:tutorials}
352  \label{SEC:eg_fourl_code_config}  \label{SEC:eg_fourl_code_config}
353    
354  The model configuration for this experiment resides under the  The model configuration for this experiment resides under the
# Line 354  directory {\it verification/exp2/}.  The Line 363  directory {\it verification/exp2/}.  The
363  \item {\it code/CPP\_OPTIONS.h},  \item {\it code/CPP\_OPTIONS.h},
364  \item {\it code/SIZE.h}.  \item {\it code/SIZE.h}.
365  \end{itemize}  \end{itemize}
366  contain the code customisations and parameter settings for this  contain the code customisations and parameter settings for this
367  experiments. Below we describe the customisations  experiment. Below we describe the customisations to these files
368  to these files associated with this experiment.  associated with this experiment.
369    
370  \subsubsection{File {\it input/data}}  \subsubsection{File {\it input/data}}
371    \label{www:tutorials}
372    
373  This file, reproduced completely below, specifies the main parameters  This file, reproduced completely below, specifies the main parameters
374  for the experiment. The parameters that are significant for this configuration  for the experiment. The parameters that are significant for this configuration
# Line 368  are Line 378  are
378    
379  \item Line 4,  \item Line 4,
380  \begin{verbatim} tRef=20.,10.,8.,6., \end{verbatim}  \begin{verbatim} tRef=20.,10.,8.,6., \end{verbatim}
381  this line sets  this line sets the initial and reference values of potential
382  the initial and reference values of potential temperature at each model  temperature at each model level in units of $^{\circ}\mathrm{C}$.  The entries
383  level in units of $^{\circ}$C.  are ordered from surface to depth. For each depth level the initial
384  The entries are ordered from surface to depth. For each  and reference profiles will be uniform in $x$ and $y$. The values
385  depth level the initial and reference profiles will be uniform in  specified here are read into the variable \varlink{tRef}{tRef} in the
386  $x$ and $y$. The values specified here are read into the  model code, by procedure \filelink{INI\_PARMS}{model-src-ini_parms.F}
 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}  
 }  
 }  
   
   
387    
388  \fbox{  \fbox{
389  \begin{minipage}{5.0in}    \begin{minipage}{5.0in}
390  {\it S/R INI\_THETA}      {\it S/R INI\_THETA}({\it ini\_theta.F})
391  ({\it ini\_theta.F})    \end{minipage}
 \end{minipage}  
392  }  }
393  {\bf  \filelink{ini\_theta.F}{model-src-ini_theta.F}
 \begin{rawhtml} <A href=../../../code_reference/vdb/code/98.htm> \end{rawhtml}  
 goto code  
 \begin{rawhtml} </A>\end{rawhtml}  
 }  
   
394    
395  \item Line 6,  \item Line 6,
396  \begin{verbatim} viscAz=1.E-2, \end{verbatim}  \begin{verbatim} viscAz=1.E-2, \end{verbatim}
397  this line sets the vertical Laplacian dissipation coefficient to  this line sets the vertical Laplacian dissipation coefficient to $1
398  $1 \times 10^{-2} {\rm m^{2}s^{-1}}$. Boundary conditions  \times 10^{-2} {\rm m^{2}s^{-1}}$. Boundary conditions for this
399  for this operator are specified later.  operator are specified later.  The variable \varlink{viscAz}{viscAz}
400  The variable  is read in the routine \filelink{ini\_parms.F}{model-src-ini_parms.F}
401  {\bf  and is copied into model general vertical coordinate variable
402  \begin{rawhtml} <A href=../../../code_reference/vdb/names/ZQ.htm> \end{rawhtml}  \varlink{viscAr}{viscAr} At each time step, the viscous term
403  viscAz  contribution to the momentum equations is calculated in routine
404  \begin{rawhtml} </A>\end{rawhtml}  \varlink{CALC\_DIFFUSIVITY}{CALC_DIFFUSIVITY}
 }  
 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}  
 }. At each time step, the viscous term contribution to the momentum equations  
 is calculated in routine  
 {\it S/R CALC\_DIFFUSIVITY}.  
405    
406  \fbox{  \fbox{
407  \begin{minipage}{5.0in}  \begin{minipage}{5.0in}
408  {\it S/R CALC\_DIFFUSIVITY}({\it calc\_diffusivity.F})  {\it S/R CALC\_DIFFUSIVITY}({\it calc\_diffusivity.F})
409  \end{minipage}  \end{minipage}
410  }  }
 {\bf  
 \begin{rawhtml} <A href=../../../code_reference/vdb/code/53.htm> \end{rawhtml}  
 goto code  
 \begin{rawhtml} </A>\end{rawhtml}  
 }  
411    
412  \item Line 7,  \item Line 7,
413  \begin{verbatim}  \begin{verbatim}
414  viscAh=4.E2,  viscAh=4.E2,
415  \end{verbatim}  \end{verbatim}
416  this line sets the horizontal laplacian frictional dissipation coefficient to    this line sets the horizontal laplacian frictional dissipation
417  $1 \times 10^{-2} {\rm m^{2}s^{-1}}$. Boundary conditions    coefficient to $1 \times 10^{-2} {\rm m^{2}s^{-1}}$. Boundary
418  for this operator are specified later.    conditions for this operator are specified later.  The variable
419  The variable    \varlink{viscAh}{viscAh} is read in the routine
420  {\bf    \varlink{INI\_PARMS}{INI_PARMS} and applied in routines
421  \begin{rawhtml} <A href=../../../code_reference/vdb/names/SI.htm> \end{rawhtml}    \varlink{CALC\_MOM\_RHS}{CALC_MOM_RHS} and
422  viscAh    \varlink{CALC\_GW}{CALC_GW}.
 \begin{rawhtml} </A>\end{rawhtml}  
 }  
 is read in the routine  
 {\it  
 \begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}  
 INI\_PARMS  
 \begin{rawhtml} </A>\end{rawhtml}  
 } and applied in routines {\it CALC\_MOM\_RHS} and {\it CALC\_GW}.  
423    
424  \fbox{  \fbox{
425  \begin{minipage}{5.0in}    \begin{minipage}{5.0in}
426  {\it S/R CALC\_MOM\_RHS}({\it calc\_mom\_rhs.F})      {\it S/R CALC\_MOM\_RHS}({\it calc\_mom\_rhs.F})
427  \end{minipage}    \end{minipage}
 }  
 {\bf  
 \begin{rawhtml} <A href=../../../code_reference/vdb/code/60.htm> \end{rawhtml}  
 goto code  
 \begin{rawhtml} </A>\end{rawhtml}  
428  }  }
   
429  \fbox{  \fbox{
430  \begin{minipage}{5.0in}    \begin{minipage}{5.0in}
431  {\it S/R CALC\_GW}({\it calc\_gw.F})      {\it S/R CALC\_GW}({\it calc\_gw.F})
432  \end{minipage}    \end{minipage}
 }  
 {\bf  
 \begin{rawhtml} <A href=../../../code_reference/vdb/code/58.htm> \end{rawhtml}  
 goto code  
 \begin{rawhtml} </A>\end{rawhtml}  
433  }  }
434    
435  \item Lines 8,  \item Line 8,
436  \begin{verbatim}  \begin{verbatim}
437  no_slip_sides=.FALSE.  no_slip_sides=.FALSE.
438  \end{verbatim}  \end{verbatim}
439  this line selects a free-slip lateral boundary condition for    this line selects a free-slip lateral boundary condition for the
440  the horizontal laplacian friction operator    horizontal laplacian friction operator e.g. $\frac{\partial
441  e.g. $\frac{\partial u}{\partial y}$=0 along boundaries in $y$ and      u}{\partial y}$=0 along boundaries in $y$ and $\frac{\partial
442  $\frac{\partial v}{\partial x}$=0 along boundaries in $x$.      v}{\partial x}$=0 along boundaries in $x$.  The variable
443  The variable    \varlink{no\_slip\_sides}{no_slip_sides} is read in the routine
444  {\bf    \varlink{INI\_PARMS}{INI_PARMS} and the boundary condition is
445  \begin{rawhtml} <A href=../../../code_reference/vdb/names/UT.htm> \end{rawhtml}    evaluated in routine
446  no\_slip\_sides  
447  \begin{rawhtml} </A>\end{rawhtml}    \fbox{
448  }      \begin{minipage}{5.0in}
449  is read in the routine        {\it S/R CALC\_MOM\_RHS}({\it calc\_mom\_rhs.F})
450  {\it      \end{minipage}
451  \begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}    }
452  INI\_PARMS    \filelink{calc\_mom\_rhs.F}{calc_mom_rhs.F}
453  \begin{rawhtml} </A>\end{rawhtml}    
 } and the boundary condition is evaluated in routine  
 {\it S/R CALC\_MOM\_RHS}.  
   
   
 \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}  
 }  
   
454  \item Lines 9,  \item Lines 9,
455  \begin{verbatim}  \begin{verbatim}
456  no_slip_bottom=.TRUE.  no_slip_bottom=.TRUE.
457  \end{verbatim}  \end{verbatim}
458  this line selects a no-slip boundary condition for bottom    this line selects a no-slip boundary condition for bottom boundary
459  boundary condition in the vertical laplacian friction operator    condition in the vertical laplacian friction operator e.g. $u=v=0$
460  e.g. $u=v=0$ at $z=-H$, where $H$ is the local depth of the domain.    at $z=-H$, where $H$ is the local depth of the domain.  The variable
461  The variable    \varlink{no\_slip\_bottom}{no\_slip\_bottom} is read in the routine
462  {\bf    \filelink{INI\_PARMS}{model-src-ini_parms.F} and is applied in the
463  \begin{rawhtml} <A href=../../../code_reference/vdb/names/UK.htm> \end{rawhtml}    routine \varlink{CALC\_MOM\_RHS}{CALC_MOM_RHS}.
464  no\_slip\_bottom  
465  \begin{rawhtml} </A>\end{rawhtml}    \fbox{
466  }      \begin{minipage}{5.0in}
467  is read in the routine        {\it S/R CALC\_MOM\_RHS}({\it calc\_mom\_rhs.F})
468  {\it      \end{minipage}
469  \begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}    }
470  INI\_PARMS    \filelink{calc\_mom\_rhs.F}{calc_mom_rhs.F}
 \begin{rawhtml} </A>\end{rawhtml}  
 } and is applied in the routine {\it S/R CALC\_MOM\_RHS}.  
   
 \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}  
 }  
471    
472  \item Line 10,  \item Line 10,
473  \begin{verbatim}  \begin{verbatim}
474  diffKhT=4.E2,  diffKhT=4.E2,
475  \end{verbatim}  \end{verbatim}
476  this line sets the horizontal diffusion coefficient for temperature    this line sets the horizontal diffusion coefficient for temperature
477  to $400\,{\rm m^{2}s^{-1}}$. The boundary condition on this    to $400\,{\rm m^{2}s^{-1}}$. The boundary condition on this operator
478  operator is $\frac{\partial}{\partial x}=\frac{\partial}{\partial y}=0$ at    is $\frac{\partial}{\partial x}=\frac{\partial}{\partial y}=0$ at
479  all boundaries.    all boundaries.  The variable \varlink{diffKhT}{diffKhT} is read in
480  The variable    the routine \varlink{INI\_PARMS}{INI_PARMS} and used in routine
481  {\bf    \varlink{CALC\_GT}{CALC_GT}.
482  \begin{rawhtml} <A href=../../../code_reference/vdb/names/RC.htm> \end{rawhtml}  
483  diffKhT    \fbox{ \begin{minipage}{5.0in}
484  \begin{rawhtml} </A>\end{rawhtml}        {\it S/R CALC\_GT}({\it calc\_gt.F})
485  }      \end{minipage}
486  is read in the routine    }
487  {\it    \filelink{calc\_gt.F}{model-src-calc_gt.F}
 \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})  
 \end{minipage}  
 }  
 {\bf  
 \begin{rawhtml} <A href=../../../code_reference/vdb/code/57.htm> \end{rawhtml}  
 goto code  
 \begin{rawhtml} </A>\end{rawhtml}  
 }  
488    
489  \item Line 11,  \item Line 11,
490  \begin{verbatim}  \begin{verbatim}
491  diffKzT=1.E-2,  diffKzT=1.E-2,
492  \end{verbatim}  \end{verbatim}
493  this line sets the vertical diffusion coefficient for temperature    this line sets the vertical diffusion coefficient for temperature to
494  to $10^{-2}\,{\rm m^{2}s^{-1}}$. The boundary condition on this    $10^{-2}\,{\rm m^{2}s^{-1}}$. The boundary condition on this
495  operator is $\frac{\partial}{\partial z}$ = 0 on all boundaries.    operator is $\frac{\partial}{\partial z}$ = 0 on all boundaries.
496  The variable    The variable \varlink{diffKzT}{diffKzT} is read in the routine
497  {\bf    \varlink{INI\_PARMS}{INI_PARMS}. It is copied into model general
498  \begin{rawhtml} <A href=../../../code_reference/vdb/names/ZT.htm> \end{rawhtml}    vertical coordinate variable \varlink{diffKrT}{diffKrT} which is
499  diffKzT    used in routine \varlink{CALC\_DIFFUSIVITY}{CALC_DIFFUSIVITY}.
500  \begin{rawhtml} </A>\end{rawhtml}  
501  }    \fbox{ \begin{minipage}{5.0in}
502  is read in the routine        {\it S/R CALC\_DIFFUSIVITY}({\it calc\_diffusivity.F})
503  {\it      \end{minipage}
504  \begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}    }
505  INI\_PARMS    \filelink{calc\_diffusivity.F}{model-src-calc_diffusivity.F}
 \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}  
 } which is used in routine {\it S/R 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}  
 }  
   
   
506    
507  \item Line 13,  \item Line 13,
508  \begin{verbatim}  \begin{verbatim}
509  tAlpha=2.E-4,  tAlpha=2.E-4,
510  \end{verbatim}  \end{verbatim}
511  This line sets the thermal expansion coefficient for the fluid    This line sets the thermal expansion coefficient for the fluid to $2
512  to $2 \times 10^{-4}\,{\rm degrees}^{-1}$    \times 10^{-4}\,{\rm degrees}^{-1}$ The variable
513  The variable    \varlink{tAlpha}{tAlpha} is read in the routine
514  {\bf    \varlink{INI\_PARMS}{INI_PARMS}. The routine
515  \begin{rawhtml} <A href=../../../code_reference/vdb/names/ZV.htm> \end{rawhtml}    \varlink{FIND\_RHO}{FIND\_RHO} makes use of {\bf tAlpha}.
516  tAlpha  
517  \begin{rawhtml} </A>\end{rawhtml}    \fbox{
518  }      \begin{minipage}{5.0in}
519  is read in the routine        {\it S/R FIND\_RHO}({\it find\_rho.F})
520  {\it      \end{minipage}
521  \begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}    }
522  INI\_PARMS    \filelink{find\_rho.F}{model-src-find_rho.F}
 \begin{rawhtml} </A>\end{rawhtml}  
 }. The routine {\it S/R FIND\_RHO} makes use of {\bf tAlpha}.  
   
 \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}  
 }  
523    
524  \item Line 18,  \item Line 18,
525  \begin{verbatim}  \begin{verbatim}
526  eosType='LINEAR'  eosType='LINEAR'
527  \end{verbatim}  \end{verbatim}
528  This line selects the linear form of the equation of state.    This line selects the linear form of the equation of state.  The
529  The variable    variable \varlink{eosType}{eosType} is read in the routine
530  {\bf    \varlink{INI\_PARMS}{INI_PARMS}. The values of {\bf eosType} sets
531  \begin{rawhtml} <A href=../../../code_reference/vdb/names/WV.htm> \end{rawhtml}    which formula in routine {\it FIND\_RHO} is used to calculate
532  eosType    density.
533  \begin{rawhtml} </A>\end{rawhtml}  
534  }    \fbox{
535  is read in the routine      \begin{minipage}{5.0in}
536  {\it        {\it S/R FIND\_RHO}({\it find\_rho.F})
537  \begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}      \end{minipage}
538  INI\_PARMS    }
539  \begin{rawhtml} </A>\end{rawhtml}    \filelink{find\_rho.F}{model-src-find_rho.F}
 }. 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}  
 }  
 {\bf  
 \begin{rawhtml} <A href=../../../code_reference/vdb/code/79.htm> \end{rawhtml}  
 goto code  
 \begin{rawhtml} </A>\end{rawhtml}  
 }  
   
   
540    
541  \item Line 40,  \item Line 40,
542  \begin{verbatim}  \begin{verbatim}
543  usingSphericalPolarGrid=.TRUE.,  usingSphericalPolarGrid=.TRUE.,
544  \end{verbatim}  \end{verbatim}
545  This line requests that the simulation be performed in a    This line requests that the simulation be performed in a spherical
546  spherical polar coordinate system. It affects the interpretation of    polar coordinate system. It affects the interpretation of grid input
547  grid input parameters, for example {\bf delX} and {\bf delY} and    parameters, for example {\bf delX} and {\bf delY} and causes the
548  causes the grid generation routines to initialize an internal grid based    grid generation routines to initialize an internal grid based on
549  on spherical polar geometry.    spherical polar geometry.  The variable
550  The variable    \varlink{usingSphericalPolarGrid}{usingSphericalPolarGrid} is read
551  {\bf    in the routine \varlink{INI\_PARMS}{INI_PARMS}. When set to {\bf
552  \begin{rawhtml} <A href=../../../code_reference/vdb/names/10T.htm> \end{rawhtml}      .TRUE.} the settings of {\bf delX} and {\bf delY} are taken to be
553  usingSphericalPolarGrid    in degrees. These values are used in the routine
554  \begin{rawhtml} </A>\end{rawhtml}  
555  }    \fbox{
556  is read in the routine      \begin{minipage}{5.0in}
557  {\it        {\it S/R INI\_SPEHRICAL\_POLAR\_GRID}({\it ini\_spherical\_polar\_grid.F})
558  \begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}      \end{minipage}
559  INI\_PARMS    }
560  \begin{rawhtml} </A>\end{rawhtml}    \filelink{ini\_spherical\_polar\_grid.F}{model-src-ini_spherical_polar_grid.F}
 }. 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}  
 {\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}  
 }  
561    
562  \item Line 41,  \item Line 41,
563  \begin{verbatim}  \begin{verbatim}
564  phiMin=0.,  phiMin=0.,
565  \end{verbatim}  \end{verbatim}
566  This line sets the southern boundary of the modeled    This line sets the southern boundary of the modeled domain to
567  domain to $0^{\circ}$ latitude. This value affects both the    $0^{\circ}$ latitude. This value affects both the generation of the
568  generation of the locally orthogonal grid that the model    locally orthogonal grid that the model uses internally and affects
569  uses internally and affects the initialization of the coriolis force.    the initialization of the coriolis force.  Note - it is not required
570  Note - it is not required to set    to set a longitude boundary, since the absolute longitude does not
571  a longitude boundary, since the absolute longitude does    alter the kernel equation discretisation.  The variable
572  not alter the kernel equation discretisation.    \varlink{phiMin}{phiMin} is read in the
573  The variable    routine \varlink{INI\_PARMS}{INI_PARMS} and is used in routine
574  {\bf  
575  \begin{rawhtml} <A href=../../../code_reference/vdb/names/110.htm> \end{rawhtml}    \fbox{
576  phiMin      \begin{minipage}{5.0in}
577  \begin{rawhtml} </A>\end{rawhtml}        {\it S/R INI\_SPEHRICAL\_POLAR\_GRID}({\it ini\_spherical\_polar\_grid.F})
578  }      \end{minipage}
579  is read in the routine    }
580  {\it    \filelink{ini\_spherical\_polar\_grid.F}{model-src-ini_spherical_polar_grid.F}
 \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}  
 {\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}  
 }  
581    
582  \item Line 42,  \item Line 42,
583  \begin{verbatim}  \begin{verbatim}
584  delX=60*1.,  delX=60*1.,
585  \end{verbatim}  \end{verbatim}
586  This line sets the horizontal grid spacing between each y-coordinate line    This line sets the horizontal grid spacing between each y-coordinate
587  in the discrete grid to $1^{\circ}$ in longitude.    line in the discrete grid to $1^{\circ}$ in longitude.  The variable
588  The variable    \varlink{delX}{delX} is read in the routine
589  {\bf    \varlink{INI\_PARMS}{INI_PARMS} and is used in routine
590  \begin{rawhtml} <A href=../../../code_reference/vdb/names/10Z.htm> \end{rawhtml}  
591  delX    \fbox{
592  \begin{rawhtml} </A>\end{rawhtml}      \begin{minipage}{5.0in}
593  }        {\it S/R INI\_SPEHRICAL\_POLAR\_GRID}({\it ini\_spherical\_polar\_grid.F})
594  is read in the routine      \end{minipage}
595  {\it    }
596  \begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}    \filelink{ini\_spherical\_polar\_grid.F}{model-src-ini_spherical_polar_grid.F}
 INI\_PARMS  
 \begin{rawhtml} </A>\end{rawhtml}  
 } and is used in routine {\it INI\_SPEHRICAL\_POLAR\_GRID}.  
   
 \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}  
 }  
597    
598  \item Line 43,  \item Line 43,
599  \begin{verbatim}  \begin{verbatim}
600  delY=60*1.,  delY=60*1.,
601  \end{verbatim}  \end{verbatim}
602  This line sets the horizontal grid spacing between each y-coordinate line    This line sets the horizontal grid spacing between each y-coordinate
603  in the discrete grid to $1^{\circ}$ in latitude.    line in the discrete grid to $1^{\circ}$ in latitude.  The variable
604  The variable    \varlink{delY}{delY} is read in the routine
605  {\bf    \varlink{INI\_PARMS}{INI_PARMS} and is used in routine
606  \begin{rawhtml} <A href=../../../code_reference/vdb/names/UB.htm> \end{rawhtml}  
607  delY      \fbox{
608  \begin{rawhtml} </A>\end{rawhtml}      \begin{minipage}{5.0in}
609  }        {\it S/R INI\_SPEHRICAL\_POLAR\_GRID}({\it ini\_spherical\_polar\_grid.F})
610  is read in the routine      \end{minipage}
611  {\it    }
612  \begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}    \filelink{ini\_spherical\_polar\_grid.F}{model-src-ini_spherical_polar_grid.F}
 INI\_PARMS  
 \begin{rawhtml} </A>\end{rawhtml}  
 } and is used in routine {\it INI\_SPEHRICAL\_POLAR\_GRID}.  
   
 \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}  
 }  
613    
614  \item Line 44,  \item Line 44,
615  \begin{verbatim}  \begin{verbatim}
616  delZ=500.,500.,500.,500.,  delZ=500.,500.,500.,500.,
617  \end{verbatim}  \end{verbatim}
618  This line sets the vertical grid spacing between each z-coordinate line    This line sets the vertical grid spacing between each z-coordinate
619  in the discrete grid to $500\,{\rm m}$, so that the total model depth    line in the discrete grid to $500\,{\rm m}$, so that the total model
620  is $2\,{\rm km}$.    depth is $2\,{\rm km}$.  The variable \varlink{delZ}{delZ} is read
621  The variable    in the routine \varlink{INI\_PARMS}{INI_PARMS}.  It is copied into
622  {\bf    the internal model coordinate variable \varlink{delR}{delR} which is
623  \begin{rawhtml} <A href=../../../code_reference/vdb/names/10W.htm> \end{rawhtml}    used in routine
624  delZ  
625  \begin{rawhtml} </A>\end{rawhtml}    \fbox{
626  }      \begin{minipage}{5.0in}
627  is read in the routine        {\it S/R INI\_VERTICAL\_GRID}({\it ini\_vertical\_grid.F})
628  {\it      \end{minipage}
629  \begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}    }
630  INI\_PARMS    \filelink{ini\_vertical\_grid.F}{model-src-ini_vertical_grid.F}
 \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}  
 } which is used in routine {\it INI\_VERTICAL\_GRID}.  
   
 \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}  
 }  
631    
632  \item Line 47,  \item Line 47,
633  \begin{verbatim}  \begin{verbatim}
634  bathyFile='topog.box'  bathyFile='topog.box'
635  \end{verbatim}  \end{verbatim}
636  This line specifies the name of the file from which the domain    This line specifies the name of the file from which the domain
637  bathymetry is read. This file is a two-dimensional ($x,y$) map of    bathymetry is read. This file is a two-dimensional ($x,y$) map of
638  depths. This file is assumed to contain 64-bit binary numbers    depths. This file is assumed to contain 64-bit binary numbers giving
639  giving the depth of the model at each grid cell, ordered with the x    the depth of the model at each grid cell, ordered with the x
640  coordinate varying fastest. The points are ordered from low coordinate    coordinate varying fastest. The points are ordered from low
641  to high coordinate for both axes. The units and orientation of the    coordinate to high coordinate for both axes. The units and
642  depths in this file are the same as used in the MITgcm code. In this    orientation of the depths in this file are the same as used in the
643  experiment, a depth of $0m$ indicates a solid wall and a depth    MITgcm code. In this experiment, a depth of $0m$ indicates a solid
644  of $-2000m$ indicates open ocean. The matlab program    wall and a depth of $-2000m$ indicates open ocean. The matlab
645  {\it input/gendata.m} shows an example of how to generate a    program {\it input/gendata.m} shows an example of how to generate a
646  bathymetry file.    bathymetry file.  The variable \varlink{bathyFile}{bathyFile} is
647  The variable    read in the routine \varlink{INI\_PARMS}{INI_PARMS}.  The bathymetry
648  {\bf    file is read in the routine
649  \begin{rawhtml} <A href=../../../code_reference/vdb/names/179.htm> \end{rawhtml}  
650  bathyFile    \fbox{
651  \begin{rawhtml} </A>\end{rawhtml}      \begin{minipage}{5.0in}
652  }        {\it S/R INI\_DEPTHS}({\it ini\_depths.F})
653  is read in the routine      \end{minipage}
654  {\it    }
655  \begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}    \filelink{ini\_depths.F}{model-src-ini_depths.F}
 INI\_PARMS  
 \begin{rawhtml} </A>\end{rawhtml}  
 }. The bathymetry file is read in the routine {\it INI\_DEPTHS}.  
   
 \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}  
 }  
   
656    
657  \item Line 50,  \item Line 50,
658  \begin{verbatim}  \begin{verbatim}
659  zonalWindFile='windx.sin_y'  zonalWindFile='windx.sin_y'
660  \end{verbatim}  \end{verbatim}
661  This line specifies the name of the file from which the x-direction    This line specifies the name of the file from which the x-direction
662  (zonal) surface wind stress is read. This file is also a two-dimensional    (zonal) surface wind stress is read. This file is also a
663  ($x,y$) map and is enumerated and formatted in the same manner as the    two-dimensional ($x,y$) map and is enumerated and formatted in the
664  bathymetry file. The matlab program {\it input/gendata.m} includes example    same manner as the bathymetry file. The matlab program {\it
665  code to generate a valid      input/gendata.m} includes example code to generate a valid {\bf
666  {\bf zonalWindFile}      zonalWindFile} file.  The variable
667  file.      \varlink{zonalWindFile}{zonalWindFile} is read in the routine
668  The variable    \varlink{INI\_PARMS}{INI_PARMS}.  The wind-stress file is read in
669  {\bf    the routine
670  \begin{rawhtml} <A href=../../../code_reference/vdb/names/13W.htm> \end{rawhtml}  
671  zonalWindFile    \fbox{
672  \begin{rawhtml} </A>\end{rawhtml}      \begin{minipage}{5.0in}
673  }        {\it S/R EXTERNAL\_FIELDS\_LOAD}({\it external\_fields\_load.F})
674  is read in the routine      \end{minipage}
675  {\it    }
676  \begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}    \filelink{external\_fields\_load.F}{model-src-external_fields_load.F}
 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}  
 {\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}  
 }  
677    
678  \end{itemize}  \end{itemize}
679    
# Line 946  goto code Line 686  goto code
686  \begin{rawhtml}</PRE>\end{rawhtml}  \begin{rawhtml}</PRE>\end{rawhtml}
687    
688  \subsubsection{File {\it input/data.pkg}}  \subsubsection{File {\it input/data.pkg}}
689    \label{www:tutorials}
690    
691  This file uses standard default values and does not contain  This file uses standard default values and does not contain
692  customisations for this experiment.  customisations for this experiment.
693    
694  \subsubsection{File {\it input/eedata}}  \subsubsection{File {\it input/eedata}}
695    \label{www:tutorials}
696    
697  This file uses standard default values and does not contain  This file uses standard default values and does not contain
698  customisations for this experiment.  customisations for this experiment.
699    
700  \subsubsection{File {\it input/windx.sin\_y}}  \subsubsection{File {\it input/windx.sin\_y}}
701    \label{www:tutorials}
702    
703  The {\it input/windx.sin\_y} file specifies a two-dimensional ($x,y$)  The {\it input/windx.sin\_y} file specifies a two-dimensional ($x,y$)
704  map of wind stress ,$\tau_{x}$, values. The units used are $Nm^{-2}$ (the  map of wind stress ,$\tau_{x}$, values. The units used are $Nm^{-2}$
705  default for MITgcm).  (the default for MITgcm).  Although $\tau_{x}$ is only a function of
706  Although $\tau_{x}$ is only a function of latitude, $y$,  latitude, $y$, in this experiment this file must still define a
707  in this experiment  complete two-dimensional map in order to be compatible with the
708  this file must still define a complete two-dimensional map in order  standard code for loading forcing fields in MITgcm (routine {\it
709  to be compatible with the standard code for loading forcing fields    EXTERNAL\_FIELDS\_LOAD}.  The included matlab program {\it
710  in MITgcm (routine {\it EXTERNAL\_FIELDS\_LOAD}.    input/gendata.m} gives a complete code for creating the {\it
711  The included matlab program {\it input/gendata.m} gives a complete    input/windx.sin\_y} file.
 code for creating the {\it input/windx.sin\_y} file.  
712    
713  \subsubsection{File {\it input/topog.box}}  \subsubsection{File {\it input/topog.box}}
714    \label{www:tutorials}
715    
716    
717  The {\it input/topog.box} file specifies a two-dimensional ($x,y$)  The {\it input/topog.box} file specifies a two-dimensional ($x,y$)
# Line 980  The included matlab program {\it input/g Line 723  The included matlab program {\it input/g
723  code for creating the {\it input/topog.box} file.  code for creating the {\it input/topog.box} file.
724    
725  \subsubsection{File {\it code/SIZE.h}}  \subsubsection{File {\it code/SIZE.h}}
726    \label{www:tutorials}
727    
728  Two lines are customized in this file for the current experiment  Two lines are customized in this file for the current experiment
729    
# Line 1006  the vertical domain extent in grid point Line 750  the vertical domain extent in grid point
750  \end{small}  \end{small}
751    
752  \subsubsection{File {\it code/CPP\_OPTIONS.h}}  \subsubsection{File {\it code/CPP\_OPTIONS.h}}
753    \label{www:tutorials}
754    
755  This file uses standard default values and does not contain  This file uses standard default values and does not contain
756  customisations for this experiment.  customisations for this experiment.
757    
758    
759  \subsubsection{File {\it code/CPP\_EEOPTIONS.h}}  \subsubsection{File {\it code/CPP\_EEOPTIONS.h}}
760    \label{www:tutorials}
761    
762  This file uses standard default values and does not contain  This file uses standard default values and does not contain
763  customisations for this experiment.  customisations for this experiment.
764    
765  \subsubsection{Other Files }  \subsubsection{Other Files }
766    \label{www:tutorials}
767    
768  Other files relevant to this experiment are  Other files relevant to this experiment are
769  \begin{itemize}  \begin{itemize}
# Line 1029  dxF, dyF, dxG, dyG, dxC, dyC}. Line 776  dxF, dyF, dxG, dyG, dxC, dyC}.
776  \end{itemize}  \end{itemize}
777    
778  \subsection{Running The Example}  \subsection{Running The Example}
779    \label{www:tutorials}
780  \label{SEC:running_the_example}  \label{SEC:running_the_example}
781    
782  \subsubsection{Code Download}  \subsubsection{Code Download}
783    \label{www:tutorials}
784    
785   In order to run the examples you must first download the code distribution.   In order to run the examples you must first download the code distribution.
786  Instructions for downloading the code can be found in section  Instructions for downloading the code can be found in section
787  \ref{sect:obtainingCode}.  \ref{sect:obtainingCode}.
788    
789  \subsubsection{Experiment Location}  \subsubsection{Experiment Location}
790    \label{www:tutorials}
791    
792   This example experiments is located under the release sub-directory   This example experiments is located under the release sub-directory
793    
# Line 1045  Instructions for downloading the code ca Line 795  Instructions for downloading the code ca
795  {\it verification/exp2/ }  {\it verification/exp2/ }
796    
797  \subsubsection{Running the Experiment}  \subsubsection{Running the Experiment}
798    \label{www:tutorials}
799    
800   To run the experiment   To run the experiment
801    
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