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revision 1.9 by cnh, Thu Oct 25 18:36:55 2001 UTC revision 1.19 by edhill, Sat Oct 16 03:40:13 2004 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 19  Line 23 
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 in spherical
25  polar coordinates. The barotropic  polar coordinates. The barotropic
26  example experiment in section \ref{sec:eg-baro}  example experiment in section \ref{sect:eg-baro}
27  illustrated how to configure the code for a single layer  illustrated how to configure the code for a single layer
28  simulation in a Cartesian grid. In this example a similar physical problem  simulation in a Cartesian grid. In this example a similar physical problem
29  is simulated, but the code is now configured  is simulated, but the code is now configured
30  for four layers and in a spherical polar coordinate system.  for four layers and in a spherical polar coordinate system.
31    
32  \subsection{Overview}  \subsection{Overview}
33    \label{www:tutorials}
34    
35  This example experiment demonstrates using the MITgcm to simulate  This example experiment demonstrates using the MITgcm to simulate
36  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 48  domain is a sector on a sphere and the c
48  according to latitude, $\varphi$  according to latitude, $\varphi$
49    
50  \begin{equation}  \begin{equation}
51  \label{EQ:fcori}  \label{EQ:eg-fourlayer-fcori}
52  f(\varphi) = 2 \Omega \sin( \varphi )  f(\varphi) = 2 \Omega \sin( \varphi )
53  \end{equation}  \end{equation}
54    
# Line 61  f(\varphi) = 2 \Omega \sin( \varphi ) Line 66  f(\varphi) = 2 \Omega \sin( \varphi )
66  $\tau_0$ is set to $0.1N m^{-2}$.  $\tau_0$ is set to $0.1N m^{-2}$.
67  \\  \\
68    
69  Figure \ref{FIG:simulation_config}  Figure \ref{FIG:eg-fourlayer-simulation_config}
70  summarizes the configuration simulated.  summarizes the configuration simulated.
71  In contrast to the example in section \ref{sec:eg-baro}, the  In contrast to the example in section \ref{sect:eg-baro}, the
72  current experiment simulates a spherical polar domain. As indicated  current experiment simulates a spherical polar domain. As indicated
73  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
74  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 87  $\theta_{1750}=6^{\circ}$~C. The equatio
87  linear  linear
88    
89  \begin{equation}  \begin{equation}
90  \label{EQ:linear1_eos}  \label{EQ:eg-fourlayer-linear1_eos}
91  \rho = \rho_{0} ( 1 - \alpha_{\theta}\theta^{'} )  \rho = \rho_{0} ( 1 - \alpha_{\theta}\theta^{'} )
92  \end{equation}  \end{equation}
93    
94  \noindent which is implemented in the model as a density anomaly equation  \noindent which is implemented in the model as a density anomaly equation
95    
96  \begin{equation}  \begin{equation}
97  \label{EQ:linear1_eos_pert}  \label{EQ:eg-fourlayer-linear1_eos_pert}
98  \rho^{'} = -\rho_{0}\alpha_{\theta}\theta^{'}  \rho^{'} = -\rho_{0}\alpha_{\theta}\theta^{'}
99  \end{equation}  \end{equation}
100    
# Line 102  non-linear, we use $\theta$ to represent Line 107  non-linear, we use $\theta$ to represent
107  the quantity that is carried in the model core equations.  the quantity that is carried in the model core equations.
108    
109  \begin{figure}  \begin{figure}
110  \begin{center}  %% \begin{center}
111   \resizebox{7.5in}{5.5in}{  %%  \resizebox{7.5in}{5.5in}{
112     \includegraphics*[0.2in,0.7in][10.5in,10.5in]  %%    \includegraphics*[0.2in,0.7in][10.5in,10.5in]
113     {part3/case_studies/fourlayer_gyre/simulation_config.eps} }  %%    {part3/case_studies/fourlayer_gyre/simulation_config.eps} }
114  \end{center}  %% \end{center}
115    \centerline{
116      \scalefig{.95}
117      \epsfbox{part3/case_studies/fourlayer_gyre/simulation_config.eps}
118    }
119  \caption{Schematic of simulation domain and wind-stress forcing function  \caption{Schematic of simulation domain and wind-stress forcing function
120  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
121  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 123  An initial stratification is
123  imposed by setting the potential temperature, $\theta$, in each layer.  imposed by setting the potential temperature, $\theta$, in each layer.
124  The vertical spacing, $\Delta z$, is constant and equal to $500$m.  The vertical spacing, $\Delta z$, is constant and equal to $500$m.
125  }  }
126  \label{FIG:simulation_config}  \label{FIG:eg-fourlayer-simulation_config}
127  \end{figure}  \end{figure}
128    
129  \subsection{Equations solved}  \subsection{Equations solved}
130    \label{www:tutorials}
131  For this problem  For this problem
132  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
133  equations described in Marshall et. al \cite{Marshall97a} are  equations described in Marshall et. al \cite{marshall:97a} are
134  employed. The flow is three-dimensional with just temperature, $\theta$, as  employed. The flow is three-dimensional with just temperature, $\theta$, as
135  an active tracer.  The equation of state is linear.  an active tracer.  The equation of state is linear.
136  A horizontal Laplacian operator $\nabla_{h}^2$ provides viscous  A horizontal Laplacian operator $\nabla_{h}^2$ provides viscous
# Line 133  solved in this configuration, written in Line 143  solved in this configuration, written in
143  follows  follows
144    
145  \begin{eqnarray}  \begin{eqnarray}
146  \label{EQ:model_equations}  \label{EQ:eg-fourlayer-model_equations}
147  \frac{Du}{Dt} - fv +  \frac{Du}{Dt} - fv +
148    \frac{1}{\rho}\frac{\partial p^{\prime}}{\partial \lambda} -    \frac{1}{\rho}\frac{\partial p^{\prime}}{\partial \lambda} -
149    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 212  e.g. $\frac{\partial \theta}{\partial \v
212    
213    
214  \subsection{Discrete Numerical Configuration}  \subsection{Discrete Numerical Configuration}
215    \label{www:tutorials}
216    
217   The domain is discretised with   The domain is discretised with
218  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 232  y=r\varphi,~\Delta y &= &r\Delta \varphi
232    
233  The procedure for generating a set of internal grid variables from a  The procedure for generating a set of internal grid variables from a
234  spherical polar grid specification is discussed in section  spherical polar grid specification is discussed in section
235  \ref{sec:spatial_discrete_horizontal_grid}.  \ref{sect:spatial_discrete_horizontal_grid}.
236    
237  \noindent\fbox{ \begin{minipage}{5.5in}  \noindent\fbox{ \begin{minipage}{5.5in}
238  {\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 253  $\Delta x_v$, $\Delta y_u$: {\bf DXv}, {
253    
254    
255    
256  As described in \ref{sec:tracer_equations}, the time evolution of potential  As described in \ref{sect:tracer_equations}, the time evolution of potential
257  temperature,  temperature,
258  $\theta$, (equation \ref{eq:eg_fourl_theta})  $\theta$, (equation \ref{eq:eg_fourl_theta})
259  is evaluated prognostically. The centered second-order scheme with  is evaluated prognostically. The centered second-order scheme with
260  Adams-Bashforth time stepping described in section  Adams-Bashforth time stepping described in section
261  \ref{sec:tracer_equations_abII} is used to step forward the temperature  \ref{sect:tracer_equations_abII} is used to step forward the temperature
262  equation. Prognostic terms in  equation. Prognostic terms in
263  the momentum equations are solved using flux form as  the momentum equations are solved using flux form as
264  described in section \ref{sec:flux-form_momentum_eqautions}.  described in section \ref{sect:flux-form_momentum_eqautions}.
265  The pressure forces that drive the fluid motions, (  The pressure forces that drive the fluid motions, (
266  $\frac{\partial p^{'}}{\partial \lambda}$ 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
267  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 269  pressure is diagnosed explicitly by inte
269  height, $\eta$, is diagnosed using an implicit scheme. The pressure  height, $\eta$, is diagnosed using an implicit scheme. The pressure
270  field solution method is described in sections  field solution method is described in sections
271  \ref{sect:pressure-method-linear-backward} and  \ref{sect:pressure-method-linear-backward} and
272  \ref{sec:finding_the_pressure_field}.  \ref{sect:finding_the_pressure_field}.
273    
274  \subsubsection{Numerical Stability Criteria}  \subsubsection{Numerical Stability Criteria}
275    \label{www:tutorials}
276    
277  The Laplacian viscosity coefficient, $A_{h}$, is set to $400 m s^{-1}$.  The Laplacian viscosity coefficient, $A_{h}$, is set to $400 m s^{-1}$.
278  This value is chosen to yield a Munk layer width,  This value is chosen to yield a Munk layer width,
279    
280  \begin{eqnarray}  \begin{eqnarray}
281  \label{EQ:munk_layer}  \label{EQ:eg-fourlayer-munk_layer}
282  M_{w} = \pi ( \frac { A_{h} }{ \beta } )^{\frac{1}{3}}  M_{w} = \pi ( \frac { A_{h} }{ \beta } )^{\frac{1}{3}}
283  \end{eqnarray}  \end{eqnarray}
284    
# Line 282  time step $\delta t=1200$secs. With this Line 294  time step $\delta t=1200$secs. With this
294  parameter to the horizontal Laplacian friction  parameter to the horizontal Laplacian friction
295    
296  \begin{eqnarray}  \begin{eqnarray}
297  \label{EQ:laplacian_stability}  \label{EQ:eg-fourlayer-laplacian_stability}
298  S_{l} = 4 \frac{A_{h} \delta t}{{\Delta x}^2}  S_{l} = 4 \frac{A_{h} \delta t}{{\Delta x}^2}
299  \end{eqnarray}  \end{eqnarray}
300    
# Line 294  for stability for this term under ABII t Line 306  for stability for this term under ABII t
306  $1\times10^{-2} {\rm m}^2{\rm s}^{-1}$. The associated stability limit  $1\times10^{-2} {\rm m}^2{\rm s}^{-1}$. The associated stability limit
307    
308  \begin{eqnarray}  \begin{eqnarray}
309  \label{EQ:laplacian_stability_z}  \label{EQ:eg-fourlayer-laplacian_stability_z}
310  S_{l} = 4 \frac{A_{z} \delta t}{{\Delta z}^2}  S_{l} = 4 \frac{A_{z} \delta t}{{\Delta z}^2}
311  \end{eqnarray}  \end{eqnarray}
312    
# Line 307  and vertical ($K_{z}$) diffusion coeffic Line 319  and vertical ($K_{z}$) diffusion coeffic
319  \noindent The numerical stability for inertial oscillations  \noindent The numerical stability for inertial oscillations
320    
321  \begin{eqnarray}  \begin{eqnarray}
322  \label{EQ:inertial_stability}  \label{EQ:eg-fourlayer-inertial_stability}
323  S_{i} = f^{2} {\delta t}^2  S_{i} = f^{2} {\delta t}^2
324  \end{eqnarray}  \end{eqnarray}
325    
# Line 320  horizontal flow Line 332  horizontal flow
332  speed of $ | \vec{u} | = 2 ms^{-1}$  speed of $ | \vec{u} | = 2 ms^{-1}$
333    
334  \begin{eqnarray}  \begin{eqnarray}
335  \label{EQ:cfl_stability}  \label{EQ:eg-fourlayer-cfl_stability}
336  C_{a} = \frac{| \vec{u} | \delta t}{ \Delta x}  C_{a} = \frac{| \vec{u} | \delta t}{ \Delta x}
337  \end{eqnarray}  \end{eqnarray}
338    
# Line 332  limit of 0.5. Line 344  limit of 0.5.
344  propagating at $2~{\rm m}~{\rm s}^{-1}$  propagating at $2~{\rm m}~{\rm s}^{-1}$
345    
346  \begin{eqnarray}  \begin{eqnarray}
347  \label{EQ:igw_stability}  \label{EQ:eg-fourlayer-igw_stability}
348  S_{c} = \frac{c_{g} \delta t}{ \Delta x}  S_{c} = \frac{c_{g} \delta t}{ \Delta x}
349  \end{eqnarray}  \end{eqnarray}
350    
# Line 340  S_{c} = \frac{c_{g} \delta t}{ \Delta x} Line 352  S_{c} = \frac{c_{g} \delta t}{ \Delta x}
352  stability limit of 0.25.  stability limit of 0.25.
353        
354  \subsection{Code Configuration}  \subsection{Code Configuration}
355    \label{www:tutorials}
356  \label{SEC:eg_fourl_code_config}  \label{SEC:eg_fourl_code_config}
357    
358  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 367  directory {\it verification/exp2/}.  The
367  \item {\it code/CPP\_OPTIONS.h},  \item {\it code/CPP\_OPTIONS.h},
368  \item {\it code/SIZE.h}.  \item {\it code/SIZE.h}.
369  \end{itemize}  \end{itemize}
370  contain the code customisations and parameter settings for this  contain the code customisations and parameter settings for this
371  experiments. Below we describe the customisations  experiment. Below we describe the customisations to these files
372  to these files associated with this experiment.  associated with this experiment.
373    
374  \subsubsection{File {\it input/data}}  \subsubsection{File {\it input/data}}
375    \label{www:tutorials}
376    
377  This file, reproduced completely below, specifies the main parameters  This file, reproduced completely below, specifies the main parameters
378  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 382  are
382    
383  \item Line 4,  \item Line 4,
384  \begin{verbatim} tRef=20.,10.,8.,6., \end{verbatim}  \begin{verbatim} tRef=20.,10.,8.,6., \end{verbatim}
385  this line sets  this line sets the initial and reference values of potential
386  the initial and reference values of potential temperature at each model  temperature at each model level in units of $^{\circ}$C.  The entries
387  level in units of $^{\circ}$C.  are ordered from surface to depth. For each depth level the initial
388  The entries are ordered from surface to depth. For each  and reference profiles will be uniform in $x$ and $y$. The values
389  depth level the initial and reference profiles will be uniform in  specified here are read into the variable \varlink{tRef}{tRef} in the
390  $x$ 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}  
 }  
 }  
   
   
391    
392  \fbox{  \fbox{
393  \begin{minipage}{5.0in}    \begin{minipage}{5.0in}
394  {\it S/R INI\_THETA}      {\it S/R INI\_THETA}({\it ini\_theta.F})
395  ({\it ini\_theta.F})    \end{minipage}
 \end{minipage}  
396  }  }
397  {\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}  
 }  
   
398    
399  \item Line 6,  \item Line 6,
400  \begin{verbatim} viscAz=1.E-2, \end{verbatim}  \begin{verbatim} viscAz=1.E-2, \end{verbatim}
401  this line sets the vertical Laplacian dissipation coefficient to  this line sets the vertical Laplacian dissipation coefficient to $1
402  $1 \times 10^{-2} {\rm m^{2}s^{-1}}$. Boundary conditions  \times 10^{-2} {\rm m^{2}s^{-1}}$. Boundary conditions for this
403  for this operator are specified later.  operator are specified later.  The variable \varlink{viscAz}{viscAz}
404  The variable  is read in the routine \filelink{ini\_parms.F}{model-src-ini_parms.F}
405  {\bf  and is copied into model general vertical coordinate variable
406  \begin{rawhtml} <A href=../../../code_reference/vdb/names/ZQ.htm> \end{rawhtml}  \varlink{viscAr}{viscAr} At each time step, the viscous term
407  viscAz  contribution to the momentum equations is calculated in routine
408  \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}.  
409    
410  \fbox{  \fbox{
411  \begin{minipage}{5.0in}  \begin{minipage}{5.0in}
412  {\it S/R CALC\_DIFFUSIVITY}({\it calc\_diffusivity.F})  {\it S/R CALC\_DIFFUSIVITY}({\it calc\_diffusivity.F})
413  \end{minipage}  \end{minipage}
414  }  }
 {\bf  
 \begin{rawhtml} <A href=../../../code_reference/vdb/code/53.htm> \end{rawhtml}  
 goto code  
 \begin{rawhtml} </A>\end{rawhtml}  
 }  
415    
416  \item Line 7,  \item Line 7,
417  \begin{verbatim}  \begin{verbatim}
418  viscAh=4.E2,  viscAh=4.E2,
419  \end{verbatim}  \end{verbatim}
420  this line sets the horizontal laplacian frictional dissipation coefficient to    this line sets the horizontal laplacian frictional dissipation
421  $1 \times 10^{-2} {\rm m^{2}s^{-1}}$. Boundary conditions    coefficient to $1 \times 10^{-2} {\rm m^{2}s^{-1}}$. Boundary
422  for this operator are specified later.    conditions for this operator are specified later.  The variable
423  The variable    \varlink{viscAh}{viscAh} is read in the routine
424  {\bf    \varlink{INI\_PARMS}{INI_PARMS} and applied in routines
425  \begin{rawhtml} <A href=../../../code_reference/vdb/names/SI.htm> \end{rawhtml}    \varlink{CALC\_MOM\_RHS}{CALC_MOM_RHS} and
426  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}.  
427    
428  \fbox{  \fbox{
429  \begin{minipage}{5.0in}    \begin{minipage}{5.0in}
430  {\it S/R CALC\_MOM\_RHS}({\it calc\_mom\_rhs.F})      {\it S/R CALC\_MOM\_RHS}({\it calc\_mom\_rhs.F})
431  \end{minipage}    \end{minipage}
 }  
 {\bf  
 \begin{rawhtml} <A href=../../../code_reference/vdb/code/60.htm> \end{rawhtml}  
 goto code  
 \begin{rawhtml} </A>\end{rawhtml}  
432  }  }
   
433  \fbox{  \fbox{
434  \begin{minipage}{5.0in}    \begin{minipage}{5.0in}
435  {\it S/R CALC\_GW}({\it calc\_gw.F})      {\it S/R CALC\_GW}({\it calc\_gw.F})
436  \end{minipage}    \end{minipage}
 }  
 {\bf  
 \begin{rawhtml} <A href=../../../code_reference/vdb/code/58.htm> \end{rawhtml}  
 goto code  
 \begin{rawhtml} </A>\end{rawhtml}  
437  }  }
438    
439  \item Lines 8,  \item Line 8,
440  \begin{verbatim}  \begin{verbatim}
441  no_slip_sides=.FALSE.  no_slip_sides=.FALSE.
442  \end{verbatim}  \end{verbatim}
443  this line selects a free-slip lateral boundary condition for    this line selects a free-slip lateral boundary condition for the
444  the horizontal laplacian friction operator    horizontal laplacian friction operator e.g. $\frac{\partial
445  e.g. $\frac{\partial u}{\partial y}$=0 along boundaries in $y$ and      u}{\partial y}$=0 along boundaries in $y$ and $\frac{\partial
446  $\frac{\partial v}{\partial x}$=0 along boundaries in $x$.      v}{\partial x}$=0 along boundaries in $x$.  The variable
447  The variable    \varlink{no\_slip\_sides}{no_slip_sides} is read in the routine
448  {\bf    \varlink{INI\_PARMS}{INI_PARMS} and the boundary condition is
449  \begin{rawhtml} <A href=../../../code_reference/vdb/names/UT.htm> \end{rawhtml}    evaluated in routine
450  no\_slip\_sides  
451  \begin{rawhtml} </A>\end{rawhtml}    \fbox{
452  }      \begin{minipage}{5.0in}
453  is read in the routine        {\it S/R CALC\_MOM\_RHS}({\it calc\_mom\_rhs.F})
454  {\it      \end{minipage}
455  \begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}    }
456  INI\_PARMS    \filelink{calc\_mom\_rhs.F}{calc_mom_rhs.F}
457  \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}  
 }  
   
458  \item Lines 9,  \item Lines 9,
459  \begin{verbatim}  \begin{verbatim}
460  no_slip_bottom=.TRUE.  no_slip_bottom=.TRUE.
461  \end{verbatim}  \end{verbatim}
462  this line selects a no-slip boundary condition for bottom    this line selects a no-slip boundary condition for bottom boundary
463  boundary condition in the vertical laplacian friction operator    condition in the vertical laplacian friction operator e.g. $u=v=0$
464  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
465  The variable    \varlink{no\_slip\_bottom}{no\_slip\_bottom} is read in the routine
466  {\bf    \filelink{INI\_PARMS}{model-src-ini_parms.F} and is applied in the
467  \begin{rawhtml} <A href=../../../code_reference/vdb/names/UK.htm> \end{rawhtml}    routine \varlink{CALC\_MOM\_RHS}{CALC_MOM_RHS}.
468  no\_slip\_bottom  
469  \begin{rawhtml} </A>\end{rawhtml}    \fbox{
470  }      \begin{minipage}{5.0in}
471  is read in the routine        {\it S/R CALC\_MOM\_RHS}({\it calc\_mom\_rhs.F})
472  {\it      \end{minipage}
473  \begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}    }
474  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}  
 }  
475    
476  \item Line 10,  \item Line 10,
477  \begin{verbatim}  \begin{verbatim}
478  diffKhT=4.E2,  diffKhT=4.E2,
479  \end{verbatim}  \end{verbatim}
480  this line sets the horizontal diffusion coefficient for temperature    this line sets the horizontal diffusion coefficient for temperature
481  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
482  operator is $\frac{\partial}{\partial x}=\frac{\partial}{\partial y}=0$ at    is $\frac{\partial}{\partial x}=\frac{\partial}{\partial y}=0$ at
483  all boundaries.    all boundaries.  The variable \varlink{diffKhT}{diffKhT} is read in
484  The variable    the routine \varlink{INI\_PARMS}{INI_PARMS} and used in routine
485  {\bf    \varlink{CALC\_GT}{CALC_GT}.
486  \begin{rawhtml} <A href=../../../code_reference/vdb/names/RC.htm> \end{rawhtml}  
487  diffKhT    \fbox{ \begin{minipage}{5.0in}
488  \begin{rawhtml} </A>\end{rawhtml}        {\it S/R CALC\_GT}({\it calc\_gt.F})
489  }      \end{minipage}
490  is read in the routine    }
491  {\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}  
 }  
492    
493  \item Line 11,  \item Line 11,
494  \begin{verbatim}  \begin{verbatim}
495  diffKzT=1.E-2,  diffKzT=1.E-2,
496  \end{verbatim}  \end{verbatim}
497  this line sets the vertical diffusion coefficient for temperature    this line sets the vertical diffusion coefficient for temperature to
498  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
499  operator is $\frac{\partial}{\partial z}$ = 0 on all boundaries.    operator is $\frac{\partial}{\partial z}$ = 0 on all boundaries.
500  The variable    The variable \varlink{diffKzT}{diffKzT} is read in the routine
501  {\bf    \varlink{INI\_PARMS}{INI_PARMS}. It is copied into model general
502  \begin{rawhtml} <A href=../../../code_reference/vdb/names/ZT.htm> \end{rawhtml}    vertical coordinate variable \varlink{diffKrT}{diffKrT} which is
503  diffKzT    used in routine \varlink{CALC\_DIFFUSIVITY}{CALC_DIFFUSIVITY}.
504  \begin{rawhtml} </A>\end{rawhtml}  
505  }    \fbox{ \begin{minipage}{5.0in}
506  is read in the routine        {\it S/R CALC\_DIFFUSIVITY}({\it calc\_diffusivity.F})
507  {\it      \end{minipage}
508  \begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}    }
509  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}  
 }  
   
   
510    
511  \item Line 13,  \item Line 13,
512  \begin{verbatim}  \begin{verbatim}
513  tAlpha=2.E-4,  tAlpha=2.E-4,
514  \end{verbatim}  \end{verbatim}
515  This line sets the thermal expansion coefficient for the fluid    This line sets the thermal expansion coefficient for the fluid to $2
516  to $2 \times 10^{-4}\,{\rm degrees}^{-1}$    \times 10^{-4}\,{\rm degrees}^{-1}$ The variable
517  The variable    \varlink{tAlpha}{tAlpha} is read in the routine
518  {\bf    \varlink{INI\_PARMS}{INI_PARMS}. The routine
519  \begin{rawhtml} <A href=../../../code_reference/vdb/names/ZV.htm> \end{rawhtml}    \varlink{FIND\_RHO}{FIND\_RHO} makes use of {\bf tAlpha}.
520  tAlpha  
521  \begin{rawhtml} </A>\end{rawhtml}    \fbox{
522  }      \begin{minipage}{5.0in}
523  is read in the routine        {\it S/R FIND\_RHO}({\it find\_rho.F})
524  {\it      \end{minipage}
525  \begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}    }
526  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}  
 }  
527    
528  \item Line 18,  \item Line 18,
529  \begin{verbatim}  \begin{verbatim}
530  eosType='LINEAR'  eosType='LINEAR'
531  \end{verbatim}  \end{verbatim}
532  This line selects the linear form of the equation of state.    This line selects the linear form of the equation of state.  The
533  The variable    variable \varlink{eosType}{eosType} is read in the routine
534  {\bf    \varlink{INI\_PARMS}{INI_PARMS}. The values of {\bf eosType} sets
535  \begin{rawhtml} <A href=../../../code_reference/vdb/names/WV.htm> \end{rawhtml}    which formula in routine {\it FIND\_RHO} is used to calculate
536  eosType    density.
537  \begin{rawhtml} </A>\end{rawhtml}  
538  }    \fbox{
539  is read in the routine      \begin{minipage}{5.0in}
540  {\it        {\it S/R FIND\_RHO}({\it find\_rho.F})
541  \begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}      \end{minipage}
542  INI\_PARMS    }
543  \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}  
 }  
   
   
544    
545  \item Line 40,  \item Line 40,
546  \begin{verbatim}  \begin{verbatim}
547  usingSphericalPolarGrid=.TRUE.,  usingSphericalPolarGrid=.TRUE.,
548  \end{verbatim}  \end{verbatim}
549  This line requests that the simulation be performed in a    This line requests that the simulation be performed in a spherical
550  spherical polar coordinate system. It affects the interpretation of    polar coordinate system. It affects the interpretation of grid input
551  grid input parameters, for example {\bf delX} and {\bf delY} and    parameters, for example {\bf delX} and {\bf delY} and causes the
552  causes the grid generation routines to initialize an internal grid based    grid generation routines to initialize an internal grid based on
553  on spherical polar geometry.    spherical polar geometry.  The variable
554  The variable    \varlink{usingSphericalPolarGrid}{usingSphericalPolarGrid} is read
555  {\bf    in the routine \varlink{INI\_PARMS}{INI_PARMS}. When set to {\bf
556  \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
557  usingSphericalPolarGrid    in degrees. These values are used in the routine
558  \begin{rawhtml} </A>\end{rawhtml}  
559  }    \fbox{
560  is read in the routine      \begin{minipage}{5.0in}
561  {\it        {\it S/R INI\_SPEHRICAL\_POLAR\_GRID}({\it ini\_spherical\_polar\_grid.F})
562  \begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}      \end{minipage}
563  INI\_PARMS    }
564  \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}  
 }  
565    
566  \item Line 41,  \item Line 41,
567  \begin{verbatim}  \begin{verbatim}
568  phiMin=0.,  phiMin=0.,
569  \end{verbatim}  \end{verbatim}
570  This line sets the southern boundary of the modeled    This line sets the southern boundary of the modeled domain to
571  domain to $0^{\circ}$ latitude. This value affects both the    $0^{\circ}$ latitude. This value affects both the generation of the
572  generation of the locally orthogonal grid that the model    locally orthogonal grid that the model uses internally and affects
573  uses internally and affects the initialization of the coriolis force.    the initialization of the coriolis force.  Note - it is not required
574  Note - it is not required to set    to set a longitude boundary, since the absolute longitude does not
575  a longitude boundary, since the absolute longitude does    alter the kernel equation discretisation.  The variable
576  not alter the kernel equation discretisation.    \varlink{phiMin}{phiMin} is read in the
577  The variable    routine \varlink{INI\_PARMS}{INI_PARMS} and is used in routine
578  {\bf  
579  \begin{rawhtml} <A href=../../../code_reference/vdb/names/110.htm> \end{rawhtml}    \fbox{
580  phiMin      \begin{minipage}{5.0in}
581  \begin{rawhtml} </A>\end{rawhtml}        {\it S/R INI\_SPEHRICAL\_POLAR\_GRID}({\it ini\_spherical\_polar\_grid.F})
582  }      \end{minipage}
583  is read in the routine    }
584  {\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}  
 }  
585    
586  \item Line 42,  \item Line 42,
587  \begin{verbatim}  \begin{verbatim}
588  delX=60*1.,  delX=60*1.,
589  \end{verbatim}  \end{verbatim}
590  This line sets the horizontal grid spacing between each y-coordinate line    This line sets the horizontal grid spacing between each y-coordinate
591  in the discrete grid to $1^{\circ}$ in longitude.    line in the discrete grid to $1^{\circ}$ in longitude.  The variable
592  The variable    \varlink{delX}{delX} is read in the routine
593  {\bf    \varlink{INI\_PARMS}{INI_PARMS} and is used in routine
594  \begin{rawhtml} <A href=../../../code_reference/vdb/names/10Z.htm> \end{rawhtml}  
595  delX    \fbox{
596  \begin{rawhtml} </A>\end{rawhtml}      \begin{minipage}{5.0in}
597  }        {\it S/R INI\_SPEHRICAL\_POLAR\_GRID}({\it ini\_spherical\_polar\_grid.F})
598  is read in the routine      \end{minipage}
599  {\it    }
600  \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}  
 }  
601    
602  \item Line 43,  \item Line 43,
603  \begin{verbatim}  \begin{verbatim}
604  delY=60*1.,  delY=60*1.,
605  \end{verbatim}  \end{verbatim}
606  This line sets the horizontal grid spacing between each y-coordinate line    This line sets the horizontal grid spacing between each y-coordinate
607  in the discrete grid to $1^{\circ}$ in latitude.    line in the discrete grid to $1^{\circ}$ in latitude.  The variable
608  The variable    \varlink{delY}{delY} is read in the routine
609  {\bf    \varlink{INI\_PARMS}{INI_PARMS} and is used in routine
610  \begin{rawhtml} <A href=../../../code_reference/vdb/names/UB.htm> \end{rawhtml}  
611  delY      \fbox{
612  \begin{rawhtml} </A>\end{rawhtml}      \begin{minipage}{5.0in}
613  }        {\it S/R INI\_SPEHRICAL\_POLAR\_GRID}({\it ini\_spherical\_polar\_grid.F})
614  is read in the routine      \end{minipage}
615  {\it    }
616  \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}  
 }  
617    
618  \item Line 44,  \item Line 44,
619  \begin{verbatim}  \begin{verbatim}
620  delZ=500.,500.,500.,500.,  delZ=500.,500.,500.,500.,
621  \end{verbatim}  \end{verbatim}
622  This line sets the vertical grid spacing between each z-coordinate line    This line sets the vertical grid spacing between each z-coordinate
623  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
624  is $2\,{\rm km}$.    depth is $2\,{\rm km}$.  The variable \varlink{delZ}{delZ} is read
625  The variable    in the routine \varlink{INI\_PARMS}{INI_PARMS}.  It is copied into
626  {\bf    the internal model coordinate variable \varlink{delR}{delR} which is
627  \begin{rawhtml} <A href=../../../code_reference/vdb/names/10W.htm> \end{rawhtml}    used in routine
628  delZ  
629  \begin{rawhtml} </A>\end{rawhtml}    \fbox{
630  }      \begin{minipage}{5.0in}
631  is read in the routine        {\it S/R INI\_VERTICAL\_GRID}({\it ini\_vertical\_grid.F})
632  {\it      \end{minipage}
633  \begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}    }
634  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}  
 }  
635    
636  \item Line 47,  \item Line 47,
637  \begin{verbatim}  \begin{verbatim}
638  bathyFile='topog.box'  bathyFile='topog.box'
639  \end{verbatim}  \end{verbatim}
640  This line specifies the name of the file from which the domain    This line specifies the name of the file from which the domain
641  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
642  depths. This file is assumed to contain 64-bit binary numbers    depths. This file is assumed to contain 64-bit binary numbers giving
643  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
644  coordinate varying fastest. The points are ordered from low coordinate    coordinate varying fastest. The points are ordered from low
645  to high coordinate for both axes. The units and orientation of the    coordinate to high coordinate for both axes. The units and
646  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
647  experiment, a depth of $0m$ indicates a solid wall and a depth    MITgcm code. In this experiment, a depth of $0m$ indicates a solid
648  of $-2000m$ indicates open ocean. The matlab program    wall and a depth of $-2000m$ indicates open ocean. The matlab
649  {\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
650  bathymetry file.    bathymetry file.  The variable \varlink{bathyFile}{bathyFile} is
651  The variable    read in the routine \varlink{INI\_PARMS}{INI_PARMS}.  The bathymetry
652  {\bf    file is read in the routine
653  \begin{rawhtml} <A href=../../../code_reference/vdb/names/179.htm> \end{rawhtml}  
654  bathyFile    \fbox{
655  \begin{rawhtml} </A>\end{rawhtml}      \begin{minipage}{5.0in}
656  }        {\it S/R INI\_DEPTHS}({\it ini\_depths.F})
657  is read in the routine      \end{minipage}
658  {\it    }
659  \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}  
 }  
   
660    
661  \item Line 50,  \item Line 50,
662  \begin{verbatim}  \begin{verbatim}
663  zonalWindFile='windx.sin_y'  zonalWindFile='windx.sin_y'
664  \end{verbatim}  \end{verbatim}
665  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
666  (zonal) surface wind stress is read. This file is also a two-dimensional    (zonal) surface wind stress is read. This file is also a
667  ($x,y$) map and is enumerated and formatted in the same manner as the    two-dimensional ($x,y$) map and is enumerated and formatted in the
668  bathymetry file. The matlab program {\it input/gendata.m} includes example    same manner as the bathymetry file. The matlab program {\it
669  code to generate a valid      input/gendata.m} includes example code to generate a valid {\bf
670  {\bf zonalWindFile}      zonalWindFile} file.  The variable
671  file.      \varlink{zonalWindFile}{zonalWindFile} is read in the routine
672  The variable    \varlink{INI\_PARMS}{INI_PARMS}.  The wind-stress file is read in
673  {\bf    the routine
674  \begin{rawhtml} <A href=../../../code_reference/vdb/names/13W.htm> \end{rawhtml}  
675  zonalWindFile    \fbox{
676  \begin{rawhtml} </A>\end{rawhtml}      \begin{minipage}{5.0in}
677  }        {\it S/R EXTERNAL\_FIELDS\_LOAD}({\it external\_fields\_load.F})
678  is read in the routine      \end{minipage}
679  {\it    }
680  \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}  
 }  
681    
682  \end{itemize}  \end{itemize}
683    
# Line 946  goto code Line 690  goto code
690  \begin{rawhtml}</PRE>\end{rawhtml}  \begin{rawhtml}</PRE>\end{rawhtml}
691    
692  \subsubsection{File {\it input/data.pkg}}  \subsubsection{File {\it input/data.pkg}}
693    \label{www:tutorials}
694    
695  This file uses standard default values and does not contain  This file uses standard default values and does not contain
696  customisations for this experiment.  customisations for this experiment.
697    
698  \subsubsection{File {\it input/eedata}}  \subsubsection{File {\it input/eedata}}
699    \label{www:tutorials}
700    
701  This file uses standard default values and does not contain  This file uses standard default values and does not contain
702  customisations for this experiment.  customisations for this experiment.
703    
704  \subsubsection{File {\it input/windx.sin\_y}}  \subsubsection{File {\it input/windx.sin\_y}}
705    \label{www:tutorials}
706    
707  The {\it input/windx.sin\_y} file specifies a two-dimensional ($x,y$)  The {\it input/windx.sin\_y} file specifies a two-dimensional ($x,y$)
708  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 $Nm^{-2}$
709  default for MITgcm).  (the default for MITgcm).  Although $\tau_{x}$ is only a function of
710  Although $\tau_{x}$ is only a function of latitude, $y$,  latitude, $y$, in this experiment this file must still define a
711  in this experiment  complete two-dimensional map in order to be compatible with the
712  this file must still define a complete two-dimensional map in order  standard code for loading forcing fields in MITgcm (routine {\it
713  to be compatible with the standard code for loading forcing fields    EXTERNAL\_FIELDS\_LOAD}.  The included matlab program {\it
714  in MITgcm (routine {\it EXTERNAL\_FIELDS\_LOAD}.    input/gendata.m} gives a complete code for creating the {\it
715  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.  
716    
717  \subsubsection{File {\it input/topog.box}}  \subsubsection{File {\it input/topog.box}}
718    \label{www:tutorials}
719    
720    
721  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 727  The included matlab program {\it input/g
727  code for creating the {\it input/topog.box} file.  code for creating the {\it input/topog.box} file.
728    
729  \subsubsection{File {\it code/SIZE.h}}  \subsubsection{File {\it code/SIZE.h}}
730    \label{www:tutorials}
731    
732  Two lines are customized in this file for the current experiment  Two lines are customized in this file for the current experiment
733    
# Line 1006  the vertical domain extent in grid point Line 754  the vertical domain extent in grid point
754  \end{small}  \end{small}
755    
756  \subsubsection{File {\it code/CPP\_OPTIONS.h}}  \subsubsection{File {\it code/CPP\_OPTIONS.h}}
757    \label{www:tutorials}
758    
759  This file uses standard default values and does not contain  This file uses standard default values and does not contain
760  customisations for this experiment.  customisations for this experiment.
761    
762    
763  \subsubsection{File {\it code/CPP\_EEOPTIONS.h}}  \subsubsection{File {\it code/CPP\_EEOPTIONS.h}}
764    \label{www:tutorials}
765    
766  This file uses standard default values and does not contain  This file uses standard default values and does not contain
767  customisations for this experiment.  customisations for this experiment.
768    
769  \subsubsection{Other Files }  \subsubsection{Other Files }
770    \label{www:tutorials}
771    
772  Other files relevant to this experiment are  Other files relevant to this experiment are
773  \begin{itemize}  \begin{itemize}
# Line 1029  dxF, dyF, dxG, dyG, dxC, dyC}. Line 780  dxF, dyF, dxG, dyG, dxC, dyC}.
780  \end{itemize}  \end{itemize}
781    
782  \subsection{Running The Example}  \subsection{Running The Example}
783    \label{www:tutorials}
784  \label{SEC:running_the_example}  \label{SEC:running_the_example}
785    
786  \subsubsection{Code Download}  \subsubsection{Code Download}
787    \label{www:tutorials}
788    
789   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.
790  Instructions for downloading the code can be found in section  Instructions for downloading the code can be found in section
791  \ref{sect:obtainingCode}.  \ref{sect:obtainingCode}.
792    
793  \subsubsection{Experiment Location}  \subsubsection{Experiment Location}
794    \label{www:tutorials}
795    
796   This example experiments is located under the release sub-directory   This example experiments is located under the release sub-directory
797    
# Line 1045  Instructions for downloading the code ca Line 799  Instructions for downloading the code ca
799  {\it verification/exp2/ }  {\it verification/exp2/ }
800    
801  \subsubsection{Running the Experiment}  \subsubsection{Running the Experiment}
802    \label{www:tutorials}
803    
804   To run the experiment   To run the experiment
805    
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