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1 % $Header: /u/gcmpack/manual/part3/case_studies/hs_atmosphere/hs_atmos.tex,v 1.9 2006/04/08 01:50:50 edhill Exp $
2 % $Name: $
3
4 \section[Held-Suarez Atmosphere MITgcm Example]{Held-Suarez forcing atmospheric simulation on a latitude-longitude grid $2.8^\circ$ resolution and on
5 a cube-sphere grid with 32 square cube faces.}
6 \label{www:tutorials}
7 \label{sect:eg-hs}
8 \begin{rawhtml}
9 <!-- CMIREDIR:eg-hs: -->
10 \end{rawhtml}
11
12 \bodytext{bgcolor="#FFFFFFFF"}
13
14 %\begin{center}
15 %{\Large \bf Using MITgcm to Simulate Global Climatological Ocean Circulation
16 %At Four Degree Resolution with Asynchronous Time Stepping}
17 %
18 %\vspace*{4mm}
19 %
20 %\vspace*{3mm}
21 %{\large May 2001}
22 %\end{center}
23
24 This example illustrates the use of the MITgcm for large scale atmospheric
25 circulation simulation. Two simulations are described
26 \begin{itemize}
27 \item global atmospheric circulation on a latitude-longitude grid and
28 \item global atmospheric circulation on a cube-sphere grid
29 \end{itemize}
30 The examples show how to use the isomorphic 'p-coordinate' scheme in
31 MITgcm to enable atmospheric simulation.
32
33
34
35 \subsection{Overview}
36 \label{www:tutorials}
37
38 This example demonstrates using the MITgcm to simulate
39 the planetary atmospheric circulation in two ways.
40 In both cases the simulation is configured with flat orography.
41 In the first case shown a $2.8^{\circ} \times 2.8^{\circ}$ spherical polar
42 horizontal grid is employed. In the second case a cube-sphere horizontal
43 grid is used that projects a cube with face size of $32 \times 32$ onto a
44 sphere.
45 Five pressure corrdinate levels are used in the vertical, ranging in thickness
46 from $100\,{\rm mb}$ at the bottom of the atmosphere to $300\,{\rm mb}$ in the middle atmosphere.
47 The total depth of the atmosphere is $1000{\rm mb}$.
48 At this resolution, the configuration can be integrated forward for many years on a
49 single processor desktop computer.
50 \\
51
52 The model is forced by relaxation to a radiative equilibrium profile
53 from Held and Suarez \cite{held-suar:94}. Initial conditions are a
54 statically stable thermal gradient and no motion. The atmosphere
55 in these experiments is dry and the only active ``physics'' are the
56 terms in the Held and Suarez \cite{held-suar:94} formula. The
57 MITgcm intermediate atmospheric physics package (see \ref{sec:pkg:aim}) and
58 MITgcm high-end physics package ( see \ref{sec:pkg:fizhi}) are turned off.
59 Altogether, this yields the following forcing
60 (from Held and Suarez \cite{held-suar:94}) that is applied to the fluid:
61
62 \begin{eqnarray}
63 \label{EQ:eg-hs-global_forcing}
64 \label{EQ:eg-hs-global_forcing_fu}
65 \vec{{\cal F}_{u}} & = & -k_{v}(p)\vec{u}
66 \\
67 \label{EQ:eg-hs-global_forcing_ft}
68 {\cal F}_{\theta} & = & -k_{T}(\phi,p)[\theta-\theta_{eq}(\phi,p)]
69 \\
70 \end{eqnarray}
71
72 \noindent where ${\vec{\cal F}_{u}}$, ${\cal F}_{\theta}$,
73 are the forcing terms in the zonal and meridional
74 momentum and in the potential temperature
75 equations respectively.
76 The term $k_{v}$ in equation (\ref{EQ:eg-hs-global_forcing_fu}) applies a
77 linear frictional drag (Rayleigh damping) that is active within the
78 planetary boundary layer. It is defined so as to decay with
79 height according to
80 \begin{eqnarray}
81 \label{EQ:eg-hs-define_kv}
82 k_{v} & = & k_{f}{\rm max}(0,(p_{\rm{k}}/p^{0}_{s}-\sigma_{b})/(1-\sigma_{b}))
83 \\
84 \sigma_{b} & = & 0.7
85 \\
86 k_{f} & = & 1{\rm day}^{-1}
87 \end{eqnarray}
88
89 where $p_{\rm{k}}$ is the pressure level of the cell center for level $\rm{k}$
90 and $p^{0}_{s}$ is the pressure at the base of the atmospheric column.
91
92
93 \subsection{Discrete Numerical Configuration}
94 \label{www:tutorials}
95
96
97 The model is configured in hydrostatic form. The domain is discretised with
98 a uniform grid spacing in latitude and longitude on the sphere
99 $\Delta \phi=\Delta \lambda=4^{\circ}$, so
100 that there are ninety grid cells in the zonal and forty in the
101 meridional direction. The internal model coordinate variables
102 $x$ and $y$ are initialized according to
103 \begin{eqnarray}
104 x=r\cos(\phi),~\Delta x & = &r\cos(\Delta \phi) \\
105 y=r\lambda,~\Delta x &= &r\Delta \lambda
106 \end{eqnarray}
107
108 Arctic polar regions are not
109 included in this experiment. Meridionally the model extends from
110 $80^{\circ}{\rm S}$ to $80^{\circ}{\rm N}$.
111 Vertically the model is configured with twenty layers with the
112 following thicknesses
113 $\Delta z_{1} = 50\,{\rm m},\,
114 \Delta z_{2} = 50\,{\rm m},\,
115 \Delta z_{3} = 55\,{\rm m},\,
116 \Delta z_{4} = 60\,{\rm m},\,
117 \Delta z_{5} = 65\,{\rm m},\,
118 $
119 $
120 \Delta z_{6}~=~70\,{\rm m},\,
121 \Delta z_{7}~=~80\,{\rm m},\,
122 \Delta z_{8}~=95\,{\rm m},\,
123 \Delta z_{9}=120\,{\rm m},\,
124 \Delta z_{10}=155\,{\rm m},\,
125 $
126 $
127 \Delta z_{11}=200\,{\rm m},\,
128 \Delta z_{12}=260\,{\rm m},\,
129 \Delta z_{13}=320\,{\rm m},\,
130 \Delta z_{14}=400\,{\rm m},\,
131 \Delta z_{15}=480\,{\rm m},\,
132 $
133 $
134 \Delta z_{16}=570\,{\rm m},\,
135 \Delta z_{17}=655\,{\rm m},\,
136 \Delta z_{18}=725\,{\rm m},\,
137 \Delta z_{19}=775\,{\rm m},\,
138 \Delta z_{20}=815\,{\rm m}
139 $ (here the numeric subscript indicates the model level index number, ${\tt k}$).
140 The implicit free surface form of the pressure equation described in Marshall et. al
141 \cite{marshall:97a} is employed. A Laplacian operator, $\nabla^2$, provides viscous
142 dissipation. Thermal and haline diffusion is also represented by a Laplacian operator.
143
144 Wind-stress forcing is added to the momentum equations for both
145 the zonal flow, $u$ and the meridional flow $v$, according to equations
146 (\ref{EQ:eg-hs-global_forcing_fu}) and (\ref{EQ:eg-hs-global_forcing_fv}).
147 Thermodynamic forcing inputs are added to the equations for
148 potential temperature, $\theta$, and salinity, $S$, according to equations
149 (\ref{EQ:eg-hs-global_forcing_ft}) and (\ref{EQ:eg-hs-global_forcing_fs}).
150 This produces a set of equations solved in this configuration as follows:
151
152 \begin{eqnarray}
153 \label{EQ:eg-hs-model_equations}
154 \frac{Du}{Dt} - fv +
155 \frac{1}{\rho}\frac{\partial p^{'}}{\partial x} -
156 \nabla_{h}\cdot A_{h}\nabla_{h}u -
157 \frac{\partial}{\partial z}A_{z}\frac{\partial u}{\partial z}
158 & = &
159 \begin{cases}
160 {\cal F}_u & \text{(surface)} \\
161 0 & \text{(interior)}
162 \end{cases}
163 \\
164 \frac{Dv}{Dt} + fu +
165 \frac{1}{\rho}\frac{\partial p^{'}}{\partial y} -
166 \nabla_{h}\cdot A_{h}\nabla_{h}v -
167 \frac{\partial}{\partial z}A_{z}\frac{\partial v}{\partial z}
168 & = &
169 \begin{cases}
170 {\cal F}_v & \text{(surface)} \\
171 0 & \text{(interior)}
172 \end{cases}
173 \\
174 \frac{\partial \eta}{\partial t} + \nabla_{h}\cdot \vec{u}
175 &=&
176 0
177 \\
178 \frac{D\theta}{Dt} -
179 \nabla_{h}\cdot K_{h}\nabla_{h}\theta
180 - \frac{\partial}{\partial z}\Gamma(K_{z})\frac{\partial\theta}{\partial z}
181 & = &
182 \begin{cases}
183 {\cal F}_\theta & \text{(surface)} \\
184 0 & \text{(interior)}
185 \end{cases}
186 \\
187 \frac{D s}{Dt} -
188 \nabla_{h}\cdot K_{h}\nabla_{h}s
189 - \frac{\partial}{\partial z}\Gamma(K_{z})\frac{\partial s}{\partial z}
190 & = &
191 \begin{cases}
192 {\cal F}_s & \text{(surface)} \\
193 0 & \text{(interior)}
194 \end{cases}
195 \\
196 g\rho_{0} \eta + \int^{0}_{-z}\rho^{'} dz & = & p^{'}
197 \end{eqnarray}
198
199 \noindent where $u=\frac{Dx}{Dt}=r \cos(\phi)\frac{D \lambda}{Dt}$ and
200 $v=\frac{Dy}{Dt}=r \frac{D \phi}{Dt}$
201 are the zonal and meridional components of the
202 flow vector, $\vec{u}$, on the sphere. As described in
203 MITgcm Numerical Solution Procedure \ref{chap:discretization}, the time
204 evolution of potential temperature, $\theta$, equation is solved prognostically.
205 The total pressure, $p$, is diagnosed by summing pressure due to surface
206 elevation $\eta$ and the hydrostatic pressure.
207 \\
208
209 \subsubsection{Numerical Stability Criteria}
210 \label{www:tutorials}
211
212 The Laplacian dissipation coefficient, $A_{h}$, is set to $5 \times 10^5 m s^{-1}$.
213 This value is chosen to yield a Munk layer width \cite{adcroft:95},
214 \begin{eqnarray}
215 \label{EQ:eg-hs-munk_layer}
216 M_{w} = \pi ( \frac { A_{h} }{ \beta } )^{\frac{1}{3}}
217 \end{eqnarray}
218
219 \noindent of $\approx 600$km. This is greater than the model
220 resolution in low-latitudes, $\Delta x \approx 400{\rm km}$, ensuring that the frictional
221 boundary layer is adequately resolved.
222 \\
223
224 \noindent The model is stepped forward with a
225 time step $\delta t_{\theta}=30~{\rm hours}$ for thermodynamic variables and
226 $\delta t_{v}=40~{\rm minutes}$ for momentum terms. With this time step, the stability
227 parameter to the horizontal Laplacian friction \cite{adcroft:95}
228 \begin{eqnarray}
229 \label{EQ:eg-hs-laplacian_stability}
230 S_{l} = 4 \frac{A_{h} \delta t_{v}}{{\Delta x}^2}
231 \end{eqnarray}
232
233 \noindent evaluates to 0.16 at a latitude of $\phi=80^{\circ}$, which is below the
234 0.3 upper limit for stability. The zonal grid spacing $\Delta x$ is smallest at
235 $\phi=80^{\circ}$ where $\Delta x=r\cos(\phi)\Delta \phi\approx 77{\rm km}$.
236 \\
237
238 \noindent The vertical dissipation coefficient, $A_{z}$, is set to
239 $1\times10^{-3} {\rm m}^2{\rm s}^{-1}$. The associated stability limit
240 \begin{eqnarray}
241 \label{EQ:eg-hs-laplacian_stability_z}
242 S_{l} = 4 \frac{A_{z} \delta t_{v}}{{\Delta z}^2}
243 \end{eqnarray}
244
245 \noindent evaluates to $0.015$ for the smallest model
246 level spacing ($\Delta z_{1}=50{\rm m}$) which is again well below
247 the upper stability limit.
248 \\
249
250 The values of the horizontal ($K_{h}$) and vertical ($K_{z}$) diffusion coefficients
251 for both temperature and salinity are set to $1 \times 10^{3}~{\rm m}^{2}{\rm s}^{-1}$
252 and $3 \times 10^{-5}~{\rm m}^{2}{\rm s}^{-1}$ respectively. The stability limit
253 related to $K_{h}$ will be at $\phi=80^{\circ}$ where $\Delta x \approx 77 {\rm km}$.
254 Here the stability parameter
255 \begin{eqnarray}
256 \label{EQ:eg-hs-laplacian_stability_xtheta}
257 S_{l} = \frac{4 K_{h} \delta t_{\theta}}{{\Delta x}^2}
258 \end{eqnarray}
259 evaluates to $0.07$, well below the stability limit of $S_{l} \approx 0.5$. The
260 stability parameter related to $K_{z}$
261 \begin{eqnarray}
262 \label{EQ:eg-hs-laplacian_stability_ztheta}
263 S_{l} = \frac{4 K_{z} \delta t_{\theta}}{{\Delta z}^2}
264 \end{eqnarray}
265 evaluates to $0.005$ for $\min(\Delta z)=50{\rm m}$, well below the stability limit
266 of $S_{l} \approx 0.5$.
267 \\
268
269 \noindent The numerical stability for inertial oscillations
270 \cite{adcroft:95}
271
272 \begin{eqnarray}
273 \label{EQ:eg-hs-inertial_stability}
274 S_{i} = f^{2} {\delta t_v}^2
275 \end{eqnarray}
276
277 \noindent evaluates to $0.24$ for $f=2\omega\sin(80^{\circ})=1.43\times10^{-4}~{\rm s}^{-1}$, which is close to
278 the $S_{i} < 1$ upper limit for stability.
279 \\
280
281 \noindent The advective CFL \cite{adcroft:95} for a extreme maximum
282 horizontal flow
283 speed of $ | \vec{u} | = 2 ms^{-1}$
284
285 \begin{eqnarray}
286 \label{EQ:eg-hs-cfl_stability}
287 S_{a} = \frac{| \vec{u} | \delta t_{v}}{ \Delta x}
288 \end{eqnarray}
289
290 \noindent evaluates to $6 \times 10^{-2}$. This is well below the stability
291 limit of 0.5.
292 \\
293
294 \noindent The stability parameter for internal gravity waves propagating
295 with a maximum speed of $c_{g}=10~{\rm ms}^{-1}$
296 \cite{adcroft:95}
297
298 \begin{eqnarray}
299 \label{EQ:eg-hs-gfl_stability}
300 S_{c} = \frac{c_{g} \delta t_{v}}{ \Delta x}
301 \end{eqnarray}
302
303 \noindent evaluates to $3 \times 10^{-1}$. This is close to the linear
304 stability limit of 0.5.
305
306 \subsection{Experiment Configuration}
307 \label{www:tutorials}
308 \label{SEC:eg-hs_examp_exp_config}
309
310 The model configuration for this experiment resides under the
311 directory {\it verification/hs94.128x64x5}. The experiment files
312 \begin{itemize}
313 \item {\it input/data}
314 \item {\it input/data.pkg}
315 \item {\it input/eedata},
316 \item {\it input/windx.bin},
317 \item {\it input/windy.bin},
318 \item {\it input/salt.bin},
319 \item {\it input/theta.bin},
320 \item {\it input/SSS.bin},
321 \item {\it input/SST.bin},
322 \item {\it input/topog.bin},
323 \item {\it code/CPP\_EEOPTIONS.h}
324 \item {\it code/CPP\_OPTIONS.h},
325 \item {\it code/SIZE.h}.
326 \end{itemize}
327 contain the code customizations and parameter settings for these
328 experiments. Below we describe the customizations
329 to these files associated with this experiment.
330
331 \subsubsection{File {\it input/data}}
332 \label{www:tutorials}
333
334 This file, reproduced completely below, specifies the main parameters
335 for the experiment. The parameters that are significant for this configuration
336 are
337
338 \begin{itemize}
339
340 \item Lines 7-10 and 11-14
341 \begin{verbatim} tRef= 16.0 , 15.2 , 14.5 , 13.9 , 13.3 , \end{verbatim}
342 $\cdots$ \\
343 set reference values for potential
344 temperature and salinity at each model level in units of $^{\circ}\mathrm{C}$ and
345 ${\rm ppt}$. The entries are ordered from surface to depth.
346 Density is calculated from anomalies at each level evaluated
347 with respect to the reference values set here.\\
348 \fbox{
349 \begin{minipage}{5.0in}
350 {\it S/R INI\_THETA}({\it ini\_theta.F})
351 \end{minipage}
352 }
353
354
355 \item Line 15,
356 \begin{verbatim} viscAz=1.E-3, \end{verbatim}
357 this line sets the vertical Laplacian dissipation coefficient to
358 $1 \times 10^{-3} {\rm m^{2}s^{-1}}$. Boundary conditions
359 for this operator are specified later. This variable is copied into
360 model general vertical coordinate variable {\bf viscAr}.
361
362 \fbox{
363 \begin{minipage}{5.0in}
364 {\it S/R CALC\_DIFFUSIVITY}({\it calc\_diffusivity.F})
365 \end{minipage}
366 }
367
368 \item Line 16,
369 \begin{verbatim}
370 viscAh=5.E5,
371 \end{verbatim}
372 this line sets the horizontal Laplacian frictional dissipation coefficient to
373 $5 \times 10^{5} {\rm m^{2}s^{-1}}$. Boundary conditions
374 for this operator are specified later.
375
376 \item Lines 17,
377 \begin{verbatim}
378 no_slip_sides=.FALSE.
379 \end{verbatim}
380 this line selects a free-slip lateral boundary condition for
381 the horizontal Laplacian friction operator
382 e.g. $\frac{\partial u}{\partial y}$=0 along boundaries in $y$ and
383 $\frac{\partial v}{\partial x}$=0 along boundaries in $x$.
384
385 \item Lines 9,
386 \begin{verbatim}
387 no_slip_bottom=.TRUE.
388 \end{verbatim}
389 this line selects a no-slip boundary condition for bottom
390 boundary condition in the vertical Laplacian friction operator
391 e.g. $u=v=0$ at $z=-H$, where $H$ is the local depth of the domain.
392
393 \item Line 19,
394 \begin{verbatim}
395 diffKhT=1.E3,
396 \end{verbatim}
397 this line sets the horizontal diffusion coefficient for temperature
398 to $1000\,{\rm m^{2}s^{-1}}$. The boundary condition on this
399 operator is $\frac{\partial}{\partial x}=\frac{\partial}{\partial y}=0$ on
400 all boundaries.
401
402 \item Line 20,
403 \begin{verbatim}
404 diffKzT=3.E-5,
405 \end{verbatim}
406 this line sets the vertical diffusion coefficient for temperature
407 to $3 \times 10^{-5}\,{\rm m^{2}s^{-1}}$. The boundary
408 condition on this operator is $\frac{\partial}{\partial z}=0$ at both
409 the upper and lower boundaries.
410
411 \item Line 21,
412 \begin{verbatim}
413 diffKhS=1.E3,
414 \end{verbatim}
415 this line sets the horizontal diffusion coefficient for salinity
416 to $1000\,{\rm m^{2}s^{-1}}$. The boundary condition on this
417 operator is $\frac{\partial}{\partial x}=\frac{\partial}{\partial y}=0$ on
418 all boundaries.
419
420 \item Line 22,
421 \begin{verbatim}
422 diffKzS=3.E-5,
423 \end{verbatim}
424 this line sets the vertical diffusion coefficient for salinity
425 to $3 \times 10^{-5}\,{\rm m^{2}s^{-1}}$. The boundary
426 condition on this operator is $\frac{\partial}{\partial z}=0$ at both
427 the upper and lower boundaries.
428
429 \item Lines 23-26
430 \begin{verbatim}
431 beta=1.E-11,
432 \end{verbatim}
433 \vspace{-5mm}$\cdots$\\
434 These settings do not apply for this experiment.
435
436 \item Line 27,
437 \begin{verbatim}
438 gravity=9.81,
439 \end{verbatim}
440 Sets the gravitational acceleration coefficient to $9.81{\rm m}{\rm s}^{-1}$.\\
441 \fbox{
442 \begin{minipage}{5.0in}
443 {\it S/R CALC\_PHI\_HYD}~({\it calc\_phi\_hyd.F})\\
444 {\it S/R INI\_CG2D}~({\it ini\_cg2d.F})\\
445 {\it S/R INI\_CG3D}~({\it ini\_cg3d.F})\\
446 {\it S/R INI\_PARMS}~({\it ini\_parms.F})\\
447 {\it S/R SOLVE\_FOR\_PRESSURE}~({\it solve\_for\_pressure.F})
448 \end{minipage}
449 }
450
451
452 \item Line 28-29,
453 \begin{verbatim}
454 rigidLid=.FALSE.,
455 implicitFreeSurface=.TRUE.,
456 \end{verbatim}
457 Selects the barotropic pressure equation to be the implicit free surface
458 formulation.
459
460 \item Line 30,
461 \begin{verbatim}
462 eosType='POLY3',
463 \end{verbatim}
464 Selects the third order polynomial form of the equation of state.\\
465 \fbox{
466 \begin{minipage}{5.0in}
467 {\it S/R FIND\_RHO}~({\it find\_rho.F})\\
468 {\it S/R FIND\_ALPHA}~({\it find\_alpha.F})
469 \end{minipage}
470 }
471
472 \item Line 31,
473 \begin{verbatim}
474 readBinaryPrec=32,
475 \end{verbatim}
476 Sets format for reading binary input datasets holding model fields to
477 use 32-bit representation for floating-point numbers.\\
478 \fbox{
479 \begin{minipage}{5.0in}
480 {\it S/R READ\_WRITE\_FLD}~({\it read\_write\_fld.F})\\
481 {\it S/R READ\_WRITE\_REC}~({\it read\_write\_rec.F})
482 \end{minipage}
483 }
484
485 \item Line 36,
486 \begin{verbatim}
487 cg2dMaxIters=1000,
488 \end{verbatim}
489 Sets maximum number of iterations the two-dimensional, conjugate
490 gradient solver will use, {\bf irrespective of convergence
491 criteria being met}.\\
492 \fbox{
493 \begin{minipage}{5.0in}
494 {\it S/R CG2D}~({\it cg2d.F})
495 \end{minipage}
496 }
497
498 \item Line 37,
499 \begin{verbatim}
500 cg2dTargetResidual=1.E-13,
501 \end{verbatim}
502 Sets the tolerance which the two-dimensional, conjugate
503 gradient solver will use to test for convergence in equation
504 \ref{EQ:eg-hs-congrad_2d_resid} to $1 \times 10^{-13}$.
505 Solver will iterate until
506 tolerance falls below this value or until the maximum number of
507 solver iterations is reached.\\
508 \fbox{
509 \begin{minipage}{5.0in}
510 {\it S/R CG2D}~({\it cg2d.F})
511 \end{minipage}
512 }
513
514 \item Line 42,
515 \begin{verbatim}
516 startTime=0,
517 \end{verbatim}
518 Sets the starting time for the model internal time counter.
519 When set to non-zero this option implicitly requests a
520 checkpoint file be read for initial state.
521 By default the checkpoint file is named according to
522 the integer number of time steps in the {\bf startTime} value.
523 The internal time counter works in seconds.
524
525 \item Line 43,
526 \begin{verbatim}
527 endTime=2808000.,
528 \end{verbatim}
529 Sets the time (in seconds) at which this simulation will terminate.
530 At the end of a simulation a checkpoint file is automatically
531 written so that a numerical experiment can consist of multiple
532 stages.
533
534 \item Line 44,
535 \begin{verbatim}
536 #endTime=62208000000,
537 \end{verbatim}
538 A commented out setting for endTime for a 2000 year simulation.
539
540 \item Line 45,
541 \begin{verbatim}
542 deltaTmom=2400.0,
543 \end{verbatim}
544 Sets the timestep $\delta t_{v}$ used in the momentum equations to
545 $20~{\rm mins}$.
546 See section \ref{SEC:mom_time_stepping}.
547
548 \fbox{
549 \begin{minipage}{5.0in}
550 {\it S/R TIMESTEP}({\it timestep.F})
551 \end{minipage}
552 }
553
554 \item Line 46,
555 \begin{verbatim}
556 tauCD=321428.,
557 \end{verbatim}
558 Sets the D-grid to C-grid coupling time scale $\tau_{CD}$ used in the momentum equations.
559 See section \ref{SEC:cd_scheme}.
560
561 \fbox{
562 \begin{minipage}{5.0in}
563 {\it S/R INI\_PARMS}({\it ini\_parms.F})\\
564 {\it S/R CALC\_MOM\_RHS}({\it calc\_mom\_rhs.F})
565 \end{minipage}
566 }
567
568 \item Line 47,
569 \begin{verbatim}
570 deltaTtracer=108000.,
571 \end{verbatim}
572 Sets the default timestep, $\delta t_{\theta}$, for tracer equations to
573 $30~{\rm hours}$.
574 See section \ref{SEC:tracer_time_stepping}.
575
576 \fbox{
577 \begin{minipage}{5.0in}
578 {\it S/R TIMESTEP\_TRACER}({\it timestep\_tracer.F})
579 \end{minipage}
580 }
581
582 \item Line 47,
583 \begin{verbatim}
584 bathyFile='topog.box'
585 \end{verbatim}
586 This line specifies the name of the file from which the domain
587 bathymetry is read. This file is a two-dimensional ($x,y$) map of
588 depths. This file is assumed to contain 64-bit binary numbers
589 giving the depth of the model at each grid cell, ordered with the x
590 coordinate varying fastest. The points are ordered from low coordinate
591 to high coordinate for both axes. The units and orientation of the
592 depths in this file are the same as used in the MITgcm code. In this
593 experiment, a depth of $0m$ indicates a solid wall and a depth
594 of $-2000m$ indicates open ocean. The matlab program
595 {\it input/gendata.m} shows an example of how to generate a
596 bathymetry file.
597
598
599 \item Line 50,
600 \begin{verbatim}
601 zonalWindFile='windx.sin_y'
602 \end{verbatim}
603 This line specifies the name of the file from which the x-direction
604 surface wind stress is read. This file is also a two-dimensional
605 ($x,y$) map and is enumerated and formatted in the same manner as the
606 bathymetry file. The matlab program {\it input/gendata.m} includes example
607 code to generate a valid
608 {\bf zonalWindFile}
609 file.
610
611 \end{itemize}
612
613 \noindent other lines in the file {\it input/data} are standard values
614 that are described in the MITgcm Getting Started and MITgcm Parameters
615 notes.
616
617 \begin{small}
618 \input{part3/case_studies/climatalogical_ogcm/input/data}
619 \end{small}
620
621 \subsubsection{File {\it input/data.pkg}}
622 \label{www:tutorials}
623
624 This file uses standard default values and does not contain
625 customisations for this experiment.
626
627 \subsubsection{File {\it input/eedata}}
628 \label{www:tutorials}
629
630 This file uses standard default values and does not contain
631 customisations for this experiment.
632
633 \subsubsection{File {\it input/windx.sin\_y}}
634 \label{www:tutorials}
635
636 The {\it input/windx.sin\_y} file specifies a two-dimensional ($x,y$)
637 map of wind stress ,$\tau_{x}$, values. The units used are $Nm^{-2}$.
638 Although $\tau_{x}$ is only a function of $y$n in this experiment
639 this file must still define a complete two-dimensional map in order
640 to be compatible with the standard code for loading forcing fields
641 in MITgcm. The included matlab program {\it input/gendata.m} gives a complete
642 code for creating the {\it input/windx.sin\_y} file.
643
644 \subsubsection{File {\it input/topog.box}}
645 \label{www:tutorials}
646
647
648 The {\it input/topog.box} file specifies a two-dimensional ($x,y$)
649 map of depth values. For this experiment values are either
650 $0m$ or $-2000\,{\rm m}$, corresponding respectively to a wall or to deep
651 ocean. The file contains a raw binary stream of data that is enumerated
652 in the same way as standard MITgcm two-dimensional, horizontal arrays.
653 The included matlab program {\it input/gendata.m} gives a complete
654 code for creating the {\it input/topog.box} file.
655
656 \subsubsection{File {\it code/SIZE.h}}
657 \label{www:tutorials}
658
659 Two lines are customized in this file for the current experiment
660
661 \begin{itemize}
662
663 \item Line 39,
664 \begin{verbatim} sNx=60, \end{verbatim} this line sets
665 the lateral domain extent in grid points for the
666 axis aligned with the x-coordinate.
667
668 \item Line 40,
669 \begin{verbatim} sNy=60, \end{verbatim} this line sets
670 the lateral domain extent in grid points for the
671 axis aligned with the y-coordinate.
672
673 \item Line 49,
674 \begin{verbatim} Nr=4, \end{verbatim} this line sets
675 the vertical domain extent in grid points.
676
677 \end{itemize}
678
679 \begin{small}
680 \input{part3/case_studies/climatalogical_ogcm/code/SIZE.h}
681 \end{small}
682
683 \subsubsection{File {\it code/CPP\_OPTIONS.h}}
684 \label{www:tutorials}
685
686 This file uses standard default values and does not contain
687 customisations for this experiment.
688
689
690 \subsubsection{File {\it code/CPP\_EEOPTIONS.h}}
691 \label{www:tutorials}
692
693 This file uses standard default values and does not contain
694 customisations for this experiment.
695
696 \subsubsection{Other Files }
697 \label{www:tutorials}
698
699 Other files relevant to this experiment are
700 \begin{itemize}
701 \item {\it model/src/ini\_cori.F}. This file initializes the model
702 coriolis variables {\bf fCorU}.
703 \item {\it model/src/ini\_spherical\_polar\_grid.F}
704 \item {\it model/src/ini\_parms.F},
705 \item {\it input/windx.sin\_y},
706 \end{itemize}
707 contain the code customisations and parameter settings for this
708 experiments. Below we describe the customisations
709 to these files associated with this experiment.

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