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revision 1.10 by adcroft, Tue Nov 13 19:01:42 2001 UTC revision 1.16 by edhill, Mon Sep 15 19:39:04 2003 UTC
# Line 1  Line 1 
1  % $Header$  % $Header$
2  % $Name$  % $Name$
3    
4  \section{Example: Four layer Baroclinic Ocean Gyre In Spherical Coordinates}  \section{Four Layer Baroclinic Ocean Gyre In Spherical Coordinates}
5  \label{sec:eg-fourlayer}  \label{www:tutorials}
6    \label{sect:eg-fourlayer}
7    
8  \bodytext{bgcolor="#FFFFFFFF"}  \bodytext{bgcolor="#FFFFFFFF"}
9    
# Line 19  Line 20 
20  This document describes an example experiment using MITgcm  This document describes an example experiment using MITgcm
21  to simulate a baroclinic ocean gyre in spherical  to simulate a baroclinic ocean gyre in spherical
22  polar coordinates. The barotropic  polar coordinates. The barotropic
23  example experiment in section \ref{sec:eg-baro}  example experiment in section \ref{sect:eg-baro}
24  illustrated how to configure the code for a single layer  illustrated how to configure the code for a single layer
25  simulation in a Cartesian grid. In this example a similar physical problem  simulation in a Cartesian grid. In this example a similar physical problem
26  is simulated, but the code is now configured  is simulated, but the code is now configured
27  for four layers and in a spherical polar coordinate system.  for four layers and in a spherical polar coordinate system.
28    
29  \subsection{Overview}  \subsection{Overview}
30    \label{www:tutorials}
31    
32  This example experiment demonstrates using the MITgcm to simulate  This example experiment demonstrates using the MITgcm to simulate
33  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 45  domain is a sector on a sphere and the c
45  according to latitude, $\varphi$  according to latitude, $\varphi$
46    
47  \begin{equation}  \begin{equation}
48  \label{EQ:fcori}  \label{EQ:eg-fourlayer-fcori}
49  f(\varphi) = 2 \Omega \sin( \varphi )  f(\varphi) = 2 \Omega \sin( \varphi )
50  \end{equation}  \end{equation}
51    
# Line 61  f(\varphi) = 2 \Omega \sin( \varphi ) Line 63  f(\varphi) = 2 \Omega \sin( \varphi )
63  $\tau_0$ is set to $0.1N m^{-2}$.  $\tau_0$ is set to $0.1N m^{-2}$.
64  \\  \\
65    
66  Figure \ref{FIG:simulation_config}  Figure \ref{FIG:eg-fourlayer-simulation_config}
67  summarizes the configuration simulated.  summarizes the configuration simulated.
68  In contrast to the example in section \ref{sec:eg-baro}, the  In contrast to the example in section \ref{sect:eg-baro}, the
69  current experiment simulates a spherical polar domain. As indicated  current experiment simulates a spherical polar domain. As indicated
70  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
71  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 84  $\theta_{1750}=6^{\circ}$~C. The equatio
84  linear  linear
85    
86  \begin{equation}  \begin{equation}
87  \label{EQ:linear1_eos}  \label{EQ:eg-fourlayer-linear1_eos}
88  \rho = \rho_{0} ( 1 - \alpha_{\theta}\theta^{'} )  \rho = \rho_{0} ( 1 - \alpha_{\theta}\theta^{'} )
89  \end{equation}  \end{equation}
90    
91  \noindent which is implemented in the model as a density anomaly equation  \noindent which is implemented in the model as a density anomaly equation
92    
93  \begin{equation}  \begin{equation}
94  \label{EQ:linear1_eos_pert}  \label{EQ:eg-fourlayer-linear1_eos_pert}
95  \rho^{'} = -\rho_{0}\alpha_{\theta}\theta^{'}  \rho^{'} = -\rho_{0}\alpha_{\theta}\theta^{'}
96  \end{equation}  \end{equation}
97    
# Line 114  An initial stratification is Line 116  An initial stratification is
116  imposed by setting the potential temperature, $\theta$, in each layer.  imposed by setting the potential temperature, $\theta$, in each layer.
117  The vertical spacing, $\Delta z$, is constant and equal to $500$m.  The vertical spacing, $\Delta z$, is constant and equal to $500$m.
118  }  }
119  \label{FIG:simulation_config}  \label{FIG:eg-fourlayer-simulation_config}
120  \end{figure}  \end{figure}
121    
122  \subsection{Equations solved}  \subsection{Equations solved}
123    \label{www:tutorials}
124  For this problem  For this problem
125  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
126  equations described in Marshall et. al \cite{marshall:97a} are  equations described in Marshall et. al \cite{marshall:97a} are
127  employed. The flow is three-dimensional with just temperature, $\theta$, as  employed. The flow is three-dimensional with just temperature, $\theta$, as
128  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 136  solved in this configuration, written in
136  follows  follows
137    
138  \begin{eqnarray}  \begin{eqnarray}
139  \label{EQ:model_equations}  \label{EQ:eg-fourlayer-model_equations}
140  \frac{Du}{Dt} - fv +  \frac{Du}{Dt} - fv +
141    \frac{1}{\rho}\frac{\partial p^{\prime}}{\partial \lambda} -    \frac{1}{\rho}\frac{\partial p^{\prime}}{\partial \lambda} -
142    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 205  e.g. $\frac{\partial \theta}{\partial \v
205    
206    
207  \subsection{Discrete Numerical Configuration}  \subsection{Discrete Numerical Configuration}
208    \label{www:tutorials}
209    
210   The domain is discretised with   The domain is discretised with
211  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 225  y=r\varphi,~\Delta y &= &r\Delta \varphi
225    
226  The procedure for generating a set of internal grid variables from a  The procedure for generating a set of internal grid variables from a
227  spherical polar grid specification is discussed in section  spherical polar grid specification is discussed in section
228  \ref{sec:spatial_discrete_horizontal_grid}.  \ref{sect:spatial_discrete_horizontal_grid}.
229    
230  \noindent\fbox{ \begin{minipage}{5.5in}  \noindent\fbox{ \begin{minipage}{5.5in}
231  {\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 246  $\Delta x_v$, $\Delta y_u$: {\bf DXv}, {
246    
247    
248    
249  As described in \ref{sec:tracer_equations}, the time evolution of potential  As described in \ref{sect:tracer_equations}, the time evolution of potential
250  temperature,  temperature,
251  $\theta$, (equation \ref{eq:eg_fourl_theta})  $\theta$, (equation \ref{eq:eg_fourl_theta})
252  is evaluated prognostically. The centered second-order scheme with  is evaluated prognostically. The centered second-order scheme with
253  Adams-Bashforth time stepping described in section  Adams-Bashforth time stepping described in section
254  \ref{sec:tracer_equations_abII} is used to step forward the temperature  \ref{sect:tracer_equations_abII} is used to step forward the temperature
255  equation. Prognostic terms in  equation. Prognostic terms in
256  the momentum equations are solved using flux form as  the momentum equations are solved using flux form as
257  described in section \ref{sec:flux-form_momentum_eqautions}.  described in section \ref{sect:flux-form_momentum_eqautions}.
258  The pressure forces that drive the fluid motions, (  The pressure forces that drive the fluid motions, (
259  $\frac{\partial p^{'}}{\partial \lambda}$ 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
260  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 262  pressure is diagnosed explicitly by inte
262  height, $\eta$, is diagnosed using an implicit scheme. The pressure  height, $\eta$, is diagnosed using an implicit scheme. The pressure
263  field solution method is described in sections  field solution method is described in sections
264  \ref{sect:pressure-method-linear-backward} and  \ref{sect:pressure-method-linear-backward} and
265  \ref{sec:finding_the_pressure_field}.  \ref{sect:finding_the_pressure_field}.
266    
267  \subsubsection{Numerical Stability Criteria}  \subsubsection{Numerical Stability Criteria}
268    \label{www:tutorials}
269    
270  The Laplacian viscosity coefficient, $A_{h}$, is set to $400 m s^{-1}$.  The Laplacian viscosity coefficient, $A_{h}$, is set to $400 m s^{-1}$.
271  This value is chosen to yield a Munk layer width,  This value is chosen to yield a Munk layer width,
272    
273  \begin{eqnarray}  \begin{eqnarray}
274  \label{EQ:munk_layer}  \label{EQ:eg-fourlayer-munk_layer}
275  M_{w} = \pi ( \frac { A_{h} }{ \beta } )^{\frac{1}{3}}  M_{w} = \pi ( \frac { A_{h} }{ \beta } )^{\frac{1}{3}}
276  \end{eqnarray}  \end{eqnarray}
277    
# Line 282  time step $\delta t=1200$secs. With this Line 287  time step $\delta t=1200$secs. With this
287  parameter to the horizontal Laplacian friction  parameter to the horizontal Laplacian friction
288    
289  \begin{eqnarray}  \begin{eqnarray}
290  \label{EQ:laplacian_stability}  \label{EQ:eg-fourlayer-laplacian_stability}
291  S_{l} = 4 \frac{A_{h} \delta t}{{\Delta x}^2}  S_{l} = 4 \frac{A_{h} \delta t}{{\Delta x}^2}
292  \end{eqnarray}  \end{eqnarray}
293    
# Line 294  for stability for this term under ABII t Line 299  for stability for this term under ABII t
299  $1\times10^{-2} {\rm m}^2{\rm s}^{-1}$. The associated stability limit  $1\times10^{-2} {\rm m}^2{\rm s}^{-1}$. The associated stability limit
300    
301  \begin{eqnarray}  \begin{eqnarray}
302  \label{EQ:laplacian_stability_z}  \label{EQ:eg-fourlayer-laplacian_stability_z}
303  S_{l} = 4 \frac{A_{z} \delta t}{{\Delta z}^2}  S_{l} = 4 \frac{A_{z} \delta t}{{\Delta z}^2}
304  \end{eqnarray}  \end{eqnarray}
305    
# Line 307  and vertical ($K_{z}$) diffusion coeffic Line 312  and vertical ($K_{z}$) diffusion coeffic
312  \noindent The numerical stability for inertial oscillations  \noindent The numerical stability for inertial oscillations
313    
314  \begin{eqnarray}  \begin{eqnarray}
315  \label{EQ:inertial_stability}  \label{EQ:eg-fourlayer-inertial_stability}
316  S_{i} = f^{2} {\delta t}^2  S_{i} = f^{2} {\delta t}^2
317  \end{eqnarray}  \end{eqnarray}
318    
# Line 320  horizontal flow Line 325  horizontal flow
325  speed of $ | \vec{u} | = 2 ms^{-1}$  speed of $ | \vec{u} | = 2 ms^{-1}$
326    
327  \begin{eqnarray}  \begin{eqnarray}
328  \label{EQ:cfl_stability}  \label{EQ:eg-fourlayer-cfl_stability}
329  C_{a} = \frac{| \vec{u} | \delta t}{ \Delta x}  C_{a} = \frac{| \vec{u} | \delta t}{ \Delta x}
330  \end{eqnarray}  \end{eqnarray}
331    
# Line 332  limit of 0.5. Line 337  limit of 0.5.
337  propagating at $2~{\rm m}~{\rm s}^{-1}$  propagating at $2~{\rm m}~{\rm s}^{-1}$
338    
339  \begin{eqnarray}  \begin{eqnarray}
340  \label{EQ:igw_stability}  \label{EQ:eg-fourlayer-igw_stability}
341  S_{c} = \frac{c_{g} \delta t}{ \Delta x}  S_{c} = \frac{c_{g} \delta t}{ \Delta x}
342  \end{eqnarray}  \end{eqnarray}
343    
# Line 340  S_{c} = \frac{c_{g} \delta t}{ \Delta x} Line 345  S_{c} = \frac{c_{g} \delta t}{ \Delta x}
345  stability limit of 0.25.  stability limit of 0.25.
346        
347  \subsection{Code Configuration}  \subsection{Code Configuration}
348    \label{www:tutorials}
349  \label{SEC:eg_fourl_code_config}  \label{SEC:eg_fourl_code_config}
350    
351  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 360  directory {\it verification/exp2/}.  The
360  \item {\it code/CPP\_OPTIONS.h},  \item {\it code/CPP\_OPTIONS.h},
361  \item {\it code/SIZE.h}.  \item {\it code/SIZE.h}.
362  \end{itemize}  \end{itemize}
363  contain the code customisations and parameter settings for this  contain the code customisations and parameter settings for this
364  experiments. Below we describe the customisations  experiment. Below we describe the customisations to these files
365  to these files associated with this experiment.  associated with this experiment.
366    
367  \subsubsection{File {\it input/data}}  \subsubsection{File {\it input/data}}
368    \label{www:tutorials}
369    
370  This file, reproduced completely below, specifies the main parameters  This file, reproduced completely below, specifies the main parameters
371  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 375  are
375    
376  \item Line 4,  \item Line 4,
377  \begin{verbatim} tRef=20.,10.,8.,6., \end{verbatim}  \begin{verbatim} tRef=20.,10.,8.,6., \end{verbatim}
378  this line sets  this line sets the initial and reference values of potential
379  the initial and reference values of potential temperature at each model  temperature at each model level in units of $^{\circ}$C.  The entries
380  level in units of $^{\circ}$C.  are ordered from surface to depth. For each depth level the initial
381  The entries are ordered from surface to depth. For each  and reference profiles will be uniform in $x$ and $y$. The values
382  depth level the initial and reference profiles will be uniform in  specified here are read into the variable \varlink{tRef}{tRef} in the
383  $x$ 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}  
 }  
 }  
   
   
384    
385  \fbox{  \fbox{
386  \begin{minipage}{5.0in}    \begin{minipage}{5.0in}
387  {\it S/R INI\_THETA}      {\it S/R INI\_THETA}({\it ini\_theta.F})
388  ({\it ini\_theta.F})    \end{minipage}
 \end{minipage}  
 }  
 {\bf  
 \begin{rawhtml} <A href=../../../code_reference/vdb/code/98.htm> \end{rawhtml}  
 goto code  
 \begin{rawhtml} </A>\end{rawhtml}  
389  }  }
390    \filelink{ini\_theta.F}{model-src-ini_theta.F}
391    
392  \item Line 6,  \item Line 6,
393  \begin{verbatim} viscAz=1.E-2, \end{verbatim}  \begin{verbatim} viscAz=1.E-2, \end{verbatim}
394  this line sets the vertical Laplacian dissipation coefficient to  this line sets the vertical Laplacian dissipation coefficient to $1
395  $1 \times 10^{-2} {\rm m^{2}s^{-1}}$. Boundary conditions  \times 10^{-2} {\rm m^{2}s^{-1}}$. Boundary conditions for this
396  for this operator are specified later.  operator are specified later.  The variable \varlink{viscAz}{viscAz}
397  The variable  is read in the routine \filelink{ini\_parms.F}{model-src-ini_parms.F}
398  {\bf  and is copied into model general vertical coordinate variable
399  \begin{rawhtml} <A href=../../../code_reference/vdb/names/ZQ.htm> \end{rawhtml}  \varlink{viscAr}{viscAr} At each time step, the viscous term
400  viscAz  contribution to the momentum equations is calculated in routine
401  \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}.  
402    
403  \fbox{  \fbox{
404  \begin{minipage}{5.0in}  \begin{minipage}{5.0in}
405  {\it S/R CALC\_DIFFUSIVITY}({\it calc\_diffusivity.F})  {\it S/R CALC\_DIFFUSIVITY}({\it calc\_diffusivity.F})
406  \end{minipage}  \end{minipage}
407  }  }
 {\bf  
 \begin{rawhtml} <A href=../../../code_reference/vdb/code/53.htm> \end{rawhtml}  
 goto code  
 \begin{rawhtml} </A>\end{rawhtml}  
 }  
408    
409  \item Line 7,  \item Line 7,
410  \begin{verbatim}  \begin{verbatim}
411  viscAh=4.E2,  viscAh=4.E2,
412  \end{verbatim}  \end{verbatim}
413  this line sets the horizontal laplacian frictional dissipation coefficient to    this line sets the horizontal laplacian frictional dissipation
414  $1 \times 10^{-2} {\rm m^{2}s^{-1}}$. Boundary conditions    coefficient to $1 \times 10^{-2} {\rm m^{2}s^{-1}}$. Boundary
415  for this operator are specified later.    conditions for this operator are specified later.  The variable
416  The variable    \varlink{viscAh}{viscAh} is read in the routine
417  {\bf    \varlink{INI\_PARMS}{INI_PARMS} and applied in routines
418  \begin{rawhtml} <A href=../../../code_reference/vdb/names/SI.htm> \end{rawhtml}    \varlink{CALC\_MOM\_RHS}{CALC_MOM_RHS} and
419  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}.  
420    
421  \fbox{  \fbox{
422  \begin{minipage}{5.0in}    \begin{minipage}{5.0in}
423  {\it S/R CALC\_MOM\_RHS}({\it calc\_mom\_rhs.F})      {\it S/R CALC\_MOM\_RHS}({\it calc\_mom\_rhs.F})
424  \end{minipage}    \end{minipage}
 }  
 {\bf  
 \begin{rawhtml} <A href=../../../code_reference/vdb/code/60.htm> \end{rawhtml}  
 goto code  
 \begin{rawhtml} </A>\end{rawhtml}  
425  }  }
   
426  \fbox{  \fbox{
427  \begin{minipage}{5.0in}    \begin{minipage}{5.0in}
428  {\it S/R CALC\_GW}({\it calc\_gw.F})      {\it S/R CALC\_GW}({\it calc\_gw.F})
429  \end{minipage}    \end{minipage}
 }  
 {\bf  
 \begin{rawhtml} <A href=../../../code_reference/vdb/code/58.htm> \end{rawhtml}  
 goto code  
 \begin{rawhtml} </A>\end{rawhtml}  
430  }  }
431    
432  \item Lines 8,  \item Line 8,
433  \begin{verbatim}  \begin{verbatim}
434  no_slip_sides=.FALSE.  no_slip_sides=.FALSE.
435  \end{verbatim}  \end{verbatim}
436  this line selects a free-slip lateral boundary condition for    this line selects a free-slip lateral boundary condition for the
437  the horizontal laplacian friction operator    horizontal laplacian friction operator e.g. $\frac{\partial
438  e.g. $\frac{\partial u}{\partial y}$=0 along boundaries in $y$ and      u}{\partial y}$=0 along boundaries in $y$ and $\frac{\partial
439  $\frac{\partial v}{\partial x}$=0 along boundaries in $x$.      v}{\partial x}$=0 along boundaries in $x$.  The variable
440  The variable    \varlink{no\_slip\_sides}{no_slip_sides} is read in the routine
441  {\bf    \varlink{INI\_PARMS}{INI_PARMS} and the boundary condition is
442  \begin{rawhtml} <A href=../../../code_reference/vdb/names/UT.htm> \end{rawhtml}    evaluated in routine
443  no\_slip\_sides  
444  \begin{rawhtml} </A>\end{rawhtml}    \fbox{
445  }      \begin{minipage}{5.0in}
446  is read in the routine        {\it S/R CALC\_MOM\_RHS}({\it calc\_mom\_rhs.F})
447  {\it      \end{minipage}
448  \begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}    }
449  INI\_PARMS    \filelink{calc\_mom\_rhs.F}{calc_mom_rhs.F}
450  \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}  
 }  
   
451  \item Lines 9,  \item Lines 9,
452  \begin{verbatim}  \begin{verbatim}
453  no_slip_bottom=.TRUE.  no_slip_bottom=.TRUE.
454  \end{verbatim}  \end{verbatim}
455  this line selects a no-slip boundary condition for bottom    this line selects a no-slip boundary condition for bottom boundary
456  boundary condition in the vertical laplacian friction operator    condition in the vertical laplacian friction operator e.g. $u=v=0$
457  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
458  The variable    \varlink{no\_slip\_bottom}{no\_slip\_bottom} is read in the routine
459  {\bf    \filelink{INI\_PARMS}{model-src-ini_parms.F} and is applied in the
460  \begin{rawhtml} <A href=../../../code_reference/vdb/names/UK.htm> \end{rawhtml}    routine \varlink{CALC\_MOM\_RHS}{CALC_MOM_RHS}.
461  no\_slip\_bottom  
462  \begin{rawhtml} </A>\end{rawhtml}    \fbox{
463  }      \begin{minipage}{5.0in}
464  is read in the routine        {\it S/R CALC\_MOM\_RHS}({\it calc\_mom\_rhs.F})
465  {\it      \end{minipage}
466  \begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}    }
467  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}  
 }  
468    
469  \item Line 10,  \item Line 10,
470  \begin{verbatim}  \begin{verbatim}
471  diffKhT=4.E2,  diffKhT=4.E2,
472  \end{verbatim}  \end{verbatim}
473  this line sets the horizontal diffusion coefficient for temperature    this line sets the horizontal diffusion coefficient for temperature
474  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
475  operator is $\frac{\partial}{\partial x}=\frac{\partial}{\partial y}=0$ at    is $\frac{\partial}{\partial x}=\frac{\partial}{\partial y}=0$ at
476  all boundaries.    all boundaries.  The variable \varlink{diffKhT}{diffKhT} is read in
477  The variable    the routine \varlink{INI\_PARMS}{INI_PARMS} and used in routine
478  {\bf    \varlink{CALC\_GT}{CALC_GT}.
479  \begin{rawhtml} <A href=../../../code_reference/vdb/names/RC.htm> \end{rawhtml}  
480  diffKhT    \fbox{ \begin{minipage}{5.0in}
481  \begin{rawhtml} </A>\end{rawhtml}        {\it S/R CALC\_GT}({\it calc\_gt.F})
482  }      \end{minipage}
483  is read in the routine    }
484  {\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}  
 }  
485    
486  \item Line 11,  \item Line 11,
487  \begin{verbatim}  \begin{verbatim}
488  diffKzT=1.E-2,  diffKzT=1.E-2,
489  \end{verbatim}  \end{verbatim}
490  this line sets the vertical diffusion coefficient for temperature    this line sets the vertical diffusion coefficient for temperature to
491  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
492  operator is $\frac{\partial}{\partial z}$ = 0 on all boundaries.    operator is $\frac{\partial}{\partial z}$ = 0 on all boundaries.
493  The variable    The variable \varlink{diffKzT}{diffKzT} is read in the routine
494  {\bf    \varlink{INI\_PARMS}{INI_PARMS}. It is copied into model general
495  \begin{rawhtml} <A href=../../../code_reference/vdb/names/ZT.htm> \end{rawhtml}    vertical coordinate variable \varlink{diffKrT}{diffKrT} which is
496  diffKzT    used in routine \varlink{CALC\_DIFFUSIVITY}{CALC_DIFFUSIVITY}.
497  \begin{rawhtml} </A>\end{rawhtml}  
498  }    \fbox{ \begin{minipage}{5.0in}
499  is read in the routine        {\it S/R CALC\_DIFFUSIVITY}({\it calc\_diffusivity.F})
500  {\it      \end{minipage}
501  \begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}    }
502  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}  
 }  
   
   
503    
504  \item Line 13,  \item Line 13,
505  \begin{verbatim}  \begin{verbatim}
506  tAlpha=2.E-4,  tAlpha=2.E-4,
507  \end{verbatim}  \end{verbatim}
508  This line sets the thermal expansion coefficient for the fluid    This line sets the thermal expansion coefficient for the fluid to $2
509  to $2 \times 10^{-4}\,{\rm degrees}^{-1}$    \times 10^{-4}\,{\rm degrees}^{-1}$ The variable
510  The variable    \varlink{tAlpha}{tAlpha} is read in the routine
511  {\bf    \varlink{INI\_PARMS}{INI_PARMS}. The routine
512  \begin{rawhtml} <A href=../../../code_reference/vdb/names/ZV.htm> \end{rawhtml}    \varlink{FIND\_RHO}{FIND\_RHO} makes use of {\bf tAlpha}.
513  tAlpha  
514  \begin{rawhtml} </A>\end{rawhtml}    \fbox{
515  }      \begin{minipage}{5.0in}
516  is read in the routine        {\it S/R FIND\_RHO}({\it find\_rho.F})
517  {\it      \end{minipage}
518  \begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}    }
519  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}  
 }  
520    
521  \item Line 18,  \item Line 18,
522  \begin{verbatim}  \begin{verbatim}
523  eosType='LINEAR'  eosType='LINEAR'
524  \end{verbatim}  \end{verbatim}
525  This line selects the linear form of the equation of state.    This line selects the linear form of the equation of state.  The
526  The variable    variable \varlink{eosType}{eosType} is read in the routine
527  {\bf    \varlink{INI\_PARMS}{INI_PARMS}. The values of {\bf eosType} sets
528  \begin{rawhtml} <A href=../../../code_reference/vdb/names/WV.htm> \end{rawhtml}    which formula in routine {\it FIND\_RHO} is used to calculate
529  eosType    density.
530  \begin{rawhtml} </A>\end{rawhtml}  
531  }    \fbox{
532  is read in the routine      \begin{minipage}{5.0in}
533  {\it        {\it S/R FIND\_RHO}({\it find\_rho.F})
534  \begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}      \end{minipage}
535  INI\_PARMS    }
536  \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}  
 }  
   
   
537    
538  \item Line 40,  \item Line 40,
539  \begin{verbatim}  \begin{verbatim}
540  usingSphericalPolarGrid=.TRUE.,  usingSphericalPolarGrid=.TRUE.,
541  \end{verbatim}  \end{verbatim}
542  This line requests that the simulation be performed in a    This line requests that the simulation be performed in a spherical
543  spherical polar coordinate system. It affects the interpretation of    polar coordinate system. It affects the interpretation of grid input
544  grid input parameters, for example {\bf delX} and {\bf delY} and    parameters, for example {\bf delX} and {\bf delY} and causes the
545  causes the grid generation routines to initialize an internal grid based    grid generation routines to initialize an internal grid based on
546  on spherical polar geometry.    spherical polar geometry.  The variable
547  The variable    \varlink{usingSphericalPolarGrid}{usingSphericalPolarGrid} is read
548  {\bf    in the routine \varlink{INI\_PARMS}{INI_PARMS}. When set to {\bf
549  \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
550  usingSphericalPolarGrid    in degrees. These values are used in the routine
551  \begin{rawhtml} </A>\end{rawhtml}  
552  }    \fbox{
553  is read in the routine      \begin{minipage}{5.0in}
554  {\it        {\it S/R INI\_SPEHRICAL\_POLAR\_GRID}({\it ini\_spherical\_polar\_grid.F})
555  \begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}      \end{minipage}
556  INI\_PARMS    }
557  \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}  
 }  
558    
559  \item Line 41,  \item Line 41,
560  \begin{verbatim}  \begin{verbatim}
561  phiMin=0.,  phiMin=0.,
562  \end{verbatim}  \end{verbatim}
563  This line sets the southern boundary of the modeled    This line sets the southern boundary of the modeled domain to
564  domain to $0^{\circ}$ latitude. This value affects both the    $0^{\circ}$ latitude. This value affects both the generation of the
565  generation of the locally orthogonal grid that the model    locally orthogonal grid that the model uses internally and affects
566  uses internally and affects the initialization of the coriolis force.    the initialization of the coriolis force.  Note - it is not required
567  Note - it is not required to set    to set a longitude boundary, since the absolute longitude does not
568  a longitude boundary, since the absolute longitude does    alter the kernel equation discretisation.  The variable
569  not alter the kernel equation discretisation.    \varlink{phiMin}{phiMin} is read in the
570  The variable    routine \varlink{INI\_PARMS}{INI_PARMS} and is used in routine
571  {\bf  
572  \begin{rawhtml} <A href=../../../code_reference/vdb/names/110.htm> \end{rawhtml}    \fbox{
573  phiMin      \begin{minipage}{5.0in}
574  \begin{rawhtml} </A>\end{rawhtml}        {\it S/R INI\_SPEHRICAL\_POLAR\_GRID}({\it ini\_spherical\_polar\_grid.F})
575  }      \end{minipage}
576  is read in the routine    }
577  {\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}  
 }  
578    
579  \item Line 42,  \item Line 42,
580  \begin{verbatim}  \begin{verbatim}
581  delX=60*1.,  delX=60*1.,
582  \end{verbatim}  \end{verbatim}
583  This line sets the horizontal grid spacing between each y-coordinate line    This line sets the horizontal grid spacing between each y-coordinate
584  in the discrete grid to $1^{\circ}$ in longitude.    line in the discrete grid to $1^{\circ}$ in longitude.  The variable
585  The variable    \varlink{delX}{delX} is read in the routine
586  {\bf    \varlink{INI\_PARMS}{INI_PARMS} and is used in routine
587  \begin{rawhtml} <A href=../../../code_reference/vdb/names/10Z.htm> \end{rawhtml}  
588  delX    \fbox{
589  \begin{rawhtml} </A>\end{rawhtml}      \begin{minipage}{5.0in}
590  }        {\it S/R INI\_SPEHRICAL\_POLAR\_GRID}({\it ini\_spherical\_polar\_grid.F})
591  is read in the routine      \end{minipage}
592  {\it    }
593  \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}  
 }  
594    
595  \item Line 43,  \item Line 43,
596  \begin{verbatim}  \begin{verbatim}
597  delY=60*1.,  delY=60*1.,
598  \end{verbatim}  \end{verbatim}
599  This line sets the horizontal grid spacing between each y-coordinate line    This line sets the horizontal grid spacing between each y-coordinate
600  in the discrete grid to $1^{\circ}$ in latitude.    line in the discrete grid to $1^{\circ}$ in latitude.  The variable
601  The variable    \varlink{delY}{delY} is read in the routine
602  {\bf    \varlink{INI\_PARMS}{INI_PARMS} and is used in routine
603  \begin{rawhtml} <A href=../../../code_reference/vdb/names/UB.htm> \end{rawhtml}  
604  delY      \fbox{
605  \begin{rawhtml} </A>\end{rawhtml}      \begin{minipage}{5.0in}
606  }        {\it S/R INI\_SPEHRICAL\_POLAR\_GRID}({\it ini\_spherical\_polar\_grid.F})
607  is read in the routine      \end{minipage}
608  {\it    }
609  \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}  
 }  
610    
611  \item Line 44,  \item Line 44,
612  \begin{verbatim}  \begin{verbatim}
613  delZ=500.,500.,500.,500.,  delZ=500.,500.,500.,500.,
614  \end{verbatim}  \end{verbatim}
615  This line sets the vertical grid spacing between each z-coordinate line    This line sets the vertical grid spacing between each z-coordinate
616  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
617  is $2\,{\rm km}$.    depth is $2\,{\rm km}$.  The variable \varlink{delZ}{delZ} is read
618  The variable    in the routine \varlink{INI\_PARMS}{INI_PARMS}.  It is copied into
619  {\bf    the internal model coordinate variable \varlink{delR}{delR} which is
620  \begin{rawhtml} <A href=../../../code_reference/vdb/names/10W.htm> \end{rawhtml}    used in routine
621  delZ  
622  \begin{rawhtml} </A>\end{rawhtml}    \fbox{
623  }      \begin{minipage}{5.0in}
624  is read in the routine        {\it S/R INI\_VERTICAL\_GRID}({\it ini\_vertical\_grid.F})
625  {\it      \end{minipage}
626  \begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}    }
627  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}  
 }  
628    
629  \item Line 47,  \item Line 47,
630  \begin{verbatim}  \begin{verbatim}
631  bathyFile='topog.box'  bathyFile='topog.box'
632  \end{verbatim}  \end{verbatim}
633  This line specifies the name of the file from which the domain    This line specifies the name of the file from which the domain
634  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
635  depths. This file is assumed to contain 64-bit binary numbers    depths. This file is assumed to contain 64-bit binary numbers giving
636  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
637  coordinate varying fastest. The points are ordered from low coordinate    coordinate varying fastest. The points are ordered from low
638  to high coordinate for both axes. The units and orientation of the    coordinate to high coordinate for both axes. The units and
639  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
640  experiment, a depth of $0m$ indicates a solid wall and a depth    MITgcm code. In this experiment, a depth of $0m$ indicates a solid
641  of $-2000m$ indicates open ocean. The matlab program    wall and a depth of $-2000m$ indicates open ocean. The matlab
642  {\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
643  bathymetry file.    bathymetry file.  The variable \varlink{bathyFile}{bathyFile} is
644  The variable    read in the routine \varlink{INI\_PARMS}{INI_PARMS}.  The bathymetry
645  {\bf    file is read in the routine
646  \begin{rawhtml} <A href=../../../code_reference/vdb/names/179.htm> \end{rawhtml}  
647  bathyFile    \fbox{
648  \begin{rawhtml} </A>\end{rawhtml}      \begin{minipage}{5.0in}
649  }        {\it S/R INI\_DEPTHS}({\it ini\_depths.F})
650  is read in the routine      \end{minipage}
651  {\it    }
652  \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}  
 }  
   
653    
654  \item Line 50,  \item Line 50,
655  \begin{verbatim}  \begin{verbatim}
656  zonalWindFile='windx.sin_y'  zonalWindFile='windx.sin_y'
657  \end{verbatim}  \end{verbatim}
658  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
659  (zonal) surface wind stress is read. This file is also a two-dimensional    (zonal) surface wind stress is read. This file is also a
660  ($x,y$) map and is enumerated and formatted in the same manner as the    two-dimensional ($x,y$) map and is enumerated and formatted in the
661  bathymetry file. The matlab program {\it input/gendata.m} includes example    same manner as the bathymetry file. The matlab program {\it
662  code to generate a valid      input/gendata.m} includes example code to generate a valid {\bf
663  {\bf zonalWindFile}      zonalWindFile} file.  The variable
664  file.      \varlink{zonalWindFile}{zonalWindFile} is read in the routine
665  The variable    \varlink{INI\_PARMS}{INI_PARMS}.  The wind-stress file is read in
666  {\bf    the routine
667  \begin{rawhtml} <A href=../../../code_reference/vdb/names/13W.htm> \end{rawhtml}  
668  zonalWindFile    \fbox{
669  \begin{rawhtml} </A>\end{rawhtml}      \begin{minipage}{5.0in}
670  }        {\it S/R EXTERNAL\_FIELDS\_LOAD}({\it external\_fields\_load.F})
671  is read in the routine      \end{minipage}
672  {\it    }
673  \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}  
 }  
674    
675  \end{itemize}  \end{itemize}
676    
# Line 946  goto code Line 683  goto code
683  \begin{rawhtml}</PRE>\end{rawhtml}  \begin{rawhtml}</PRE>\end{rawhtml}
684    
685  \subsubsection{File {\it input/data.pkg}}  \subsubsection{File {\it input/data.pkg}}
686    \label{www:tutorials}
687    
688  This file uses standard default values and does not contain  This file uses standard default values and does not contain
689  customisations for this experiment.  customisations for this experiment.
690    
691  \subsubsection{File {\it input/eedata}}  \subsubsection{File {\it input/eedata}}
692    \label{www:tutorials}
693    
694  This file uses standard default values and does not contain  This file uses standard default values and does not contain
695  customisations for this experiment.  customisations for this experiment.
696    
697  \subsubsection{File {\it input/windx.sin\_y}}  \subsubsection{File {\it input/windx.sin\_y}}
698    \label{www:tutorials}
699    
700  The {\it input/windx.sin\_y} file specifies a two-dimensional ($x,y$)  The {\it input/windx.sin\_y} file specifies a two-dimensional ($x,y$)
701  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 $Nm^{-2}$
702  default for MITgcm).  (the default for MITgcm).  Although $\tau_{x}$ is only a function of
703  Although $\tau_{x}$ is only a function of latitude, $y$,  latitude, $y$, in this experiment this file must still define a
704  in this experiment  complete two-dimensional map in order to be compatible with the
705  this file must still define a complete two-dimensional map in order  standard code for loading forcing fields in MITgcm (routine {\it
706  to be compatible with the standard code for loading forcing fields    EXTERNAL\_FIELDS\_LOAD}.  The included matlab program {\it
707  in MITgcm (routine {\it EXTERNAL\_FIELDS\_LOAD}.    input/gendata.m} gives a complete code for creating the {\it
708  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.  
709    
710  \subsubsection{File {\it input/topog.box}}  \subsubsection{File {\it input/topog.box}}
711    \label{www:tutorials}
712    
713    
714  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 720  The included matlab program {\it input/g
720  code for creating the {\it input/topog.box} file.  code for creating the {\it input/topog.box} file.
721    
722  \subsubsection{File {\it code/SIZE.h}}  \subsubsection{File {\it code/SIZE.h}}
723    \label{www:tutorials}
724    
725  Two lines are customized in this file for the current experiment  Two lines are customized in this file for the current experiment
726    
# Line 1006  the vertical domain extent in grid point Line 747  the vertical domain extent in grid point
747  \end{small}  \end{small}
748    
749  \subsubsection{File {\it code/CPP\_OPTIONS.h}}  \subsubsection{File {\it code/CPP\_OPTIONS.h}}
750    \label{www:tutorials}
751    
752  This file uses standard default values and does not contain  This file uses standard default values and does not contain
753  customisations for this experiment.  customisations for this experiment.
754    
755    
756  \subsubsection{File {\it code/CPP\_EEOPTIONS.h}}  \subsubsection{File {\it code/CPP\_EEOPTIONS.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  \subsubsection{Other Files }  \subsubsection{Other Files }
763    \label{www:tutorials}
764    
765  Other files relevant to this experiment are  Other files relevant to this experiment are
766  \begin{itemize}  \begin{itemize}
# Line 1029  dxF, dyF, dxG, dyG, dxC, dyC}. Line 773  dxF, dyF, dxG, dyG, dxC, dyC}.
773  \end{itemize}  \end{itemize}
774    
775  \subsection{Running The Example}  \subsection{Running The Example}
776    \label{www:tutorials}
777  \label{SEC:running_the_example}  \label{SEC:running_the_example}
778    
779  \subsubsection{Code Download}  \subsubsection{Code Download}
780    \label{www:tutorials}
781    
782   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.
783  Instructions for downloading the code can be found in section  Instructions for downloading the code can be found in section
784  \ref{sect:obtainingCode}.  \ref{sect:obtainingCode}.
785    
786  \subsubsection{Experiment Location}  \subsubsection{Experiment Location}
787    \label{www:tutorials}
788    
789   This example experiments is located under the release sub-directory   This example experiments is located under the release sub-directory
790    
# Line 1045  Instructions for downloading the code ca Line 792  Instructions for downloading the code ca
792  {\it verification/exp2/ }  {\it verification/exp2/ }
793    
794  \subsubsection{Running the Experiment}  \subsubsection{Running the Experiment}
795    \label{www:tutorials}
796    
797   To run the experiment   To run the experiment
798    
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