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1 % $Header: /u/gcmpack/manual/part3/case_studies/climatalogical_ogcm/climatalogical_ogcm.tex,v 1.16 2008/01/15 20:04:06 jmc Exp $
2 % $Name: $
3
4 \section[Global Ocean MITgcm Example]{Global Ocean Simulation at $4^\circ$ Resolution}
5 \label{www:tutorials}
6 \label{sect:eg-global}
7 \begin{rawhtml}
8 <!-- CMIREDIR:eg-global: -->
9 \end{rawhtml}
10 \begin{center}
11 (in directory: {\it verification/tutorial\_global\_oce\_latlon/})
12 \end{center}
13
14 \bodytext{bgcolor="#FFFFFFFF"}
15
16 %\begin{center}
17 %{\Large \bf Using MITgcm to Simulate Global Climatological Ocean Circulation
18 %At Four Degree Resolution with Asynchronous Time Stepping}
19 %
20 %\vspace*{4mm}
21 %
22 %\vspace*{3mm}
23 %{\large May 2001}
24 %\end{center}
25
26
27 This example experiment demonstrates using the MITgcm to simulate
28 the planetary ocean circulation. The simulation is configured
29 with realistic geography and bathymetry on a
30 $4^{\circ} \times 4^{\circ}$ spherical polar grid.
31 The files for this experiment are in the verification directory
32 under tutorial\_global\_oce\_latlon.
33 Twenty levels are used in the vertical, ranging in thickness
34 from $50\,{\rm m}$ at the surface to $815\,{\rm m}$ at depth,
35 giving a maximum model depth of $6\,{\rm km}$.
36 At this resolution, the configuration
37 can be integrated forward for thousands of years on a single
38 processor desktop computer.
39 \\
40 \subsection{Overview}
41 \label{www:tutorials}
42
43 The model is forced with climatological wind stress data and surface
44 flux data from DaSilva \cite{DaSilva94}. Climatological data
45 from Levitus \cite{Levitus94} is used to initialize the model hydrography.
46 Levitus seasonal climatology data is also used throughout the calculation
47 to provide additional air-sea fluxes.
48 These fluxes are combined with the DaSilva climatological estimates of
49 surface heat flux and fresh water, resulting in a mixed boundary
50 condition of the style described in Haney \cite{Haney}.
51 Altogether, this yields the following forcing applied
52 in the model surface layer.
53
54 \begin{eqnarray}
55 \label{EQ:eg-global-global_forcing}
56 \label{EQ:eg-global-global_forcing_fu}
57 {\cal F}_{u} & = & \frac{\tau_{x}}{\rho_{0} \Delta z_{s}}
58 \\
59 \label{EQ:eg-global-global_forcing_fv}
60 {\cal F}_{v} & = & \frac{\tau_{y}}{\rho_{0} \Delta z_{s}}
61 \\
62 \label{EQ:eg-global-global_forcing_ft}
63 {\cal F}_{\theta} & = & - \lambda_{\theta} ( \theta - \theta^{\ast} )
64 - \frac{1}{C_{p} \rho_{0} \Delta z_{s}}{\cal Q}
65 \\
66 \label{EQ:eg-global-global_forcing_fs}
67 {\cal F}_{s} & = & - \lambda_{s} ( S - S^{\ast} )
68 + \frac{S_{0}}{\Delta z_{s}}({\cal E} - {\cal P} - {\cal R})
69 \end{eqnarray}
70
71 \noindent where ${\cal F}_{u}$, ${\cal F}_{v}$, ${\cal F}_{\theta}$,
72 ${\cal F}_{s}$ are the forcing terms in the zonal and meridional
73 momentum and in the potential temperature and salinity
74 equations respectively.
75 The term $\Delta z_{s}$ represents the top ocean layer thickness in
76 meters.
77 It is used in conjunction with a reference density, $\rho_{0}$
78 (here set to $999.8\,{\rm kg\,m^{-3}}$), a
79 reference salinity, $S_{0}$ (here set to 35~ppt),
80 and a specific heat capacity, $C_{p}$ (here set to
81 $4000~{\rm J}~^{\circ}{\rm C}^{-1}~{\rm kg}^{-1}$), to convert
82 input dataset values into time tendencies of
83 potential temperature (with units of $^{\circ}{\rm C}~{\rm s}^{-1}$),
84 salinity (with units ${\rm ppt}~s^{-1}$) and
85 velocity (with units ${\rm m}~{\rm s}^{-2}$).
86 The externally supplied forcing fields used in this
87 experiment are $\tau_{x}$, $\tau_{y}$, $\theta^{\ast}$, $S^{\ast}$,
88 $\cal{Q}$ and $\cal{E}-\cal{P}-\cal{R}$. The wind stress fields ($\tau_x$, $\tau_y$)
89 have units of ${\rm N}~{\rm m}^{-2}$. The temperature forcing fields
90 ($\theta^{\ast}$ and $Q$) have units of $^{\circ}{\rm C}$ and ${\rm W}~{\rm m}^{-2}$
91 respectively. The salinity forcing fields ($S^{\ast}$ and
92 $\cal{E}-\cal{P}-\cal{R}$) have units of ${\rm ppt}$ and ${\rm m}~{\rm s}^{-1}$
93 respectively. The source files and procedures for ingesting this data into the
94 simulation are described in the experiment configuration discussion in section
95 \ref{SEC:eg-global-clim_ocn_examp_exp_config}.
96
97
98 \subsection{Discrete Numerical Configuration}
99 \label{www:tutorials}
100
101
102 The model is configured in hydrostatic form. The domain is discretised with
103 a uniform grid spacing in latitude and longitude on the sphere
104 $\Delta \phi=\Delta \lambda=4^{\circ}$, so
105 that there are ninety grid cells in the zonal and forty in the
106 meridional direction. The internal model coordinate variables
107 $x$ and $y$ are initialized according to
108 \begin{eqnarray}
109 x=r\cos(\phi),~\Delta x & = &r\cos(\Delta \phi) \\
110 y=r\lambda,~\Delta y &= &r\Delta \lambda
111 \end{eqnarray}
112
113 Arctic polar regions are not
114 included in this experiment. Meridionally the model extends from
115 $80^{\circ}{\rm S}$ to $80^{\circ}{\rm N}$.
116 Vertically the model is configured with twenty layers with the
117 following thicknesses
118 $\Delta z_{1} = 50\,{\rm m},\,
119 \Delta z_{2} = 50\,{\rm m},\,
120 \Delta z_{3} = 55\,{\rm m},\,
121 \Delta z_{4} = 60\,{\rm m},\,
122 \Delta z_{5} = 65\,{\rm m},\,
123 $
124 $
125 \Delta z_{6}~=~70\,{\rm m},\,
126 \Delta z_{7}~=~80\,{\rm m},\,
127 \Delta z_{8}~=95\,{\rm m},\,
128 \Delta z_{9}=120\,{\rm m},\,
129 \Delta z_{10}=155\,{\rm m},\,
130 $
131 $
132 \Delta z_{11}=200\,{\rm m},\,
133 \Delta z_{12}=260\,{\rm m},\,
134 \Delta z_{13}=320\,{\rm m},\,
135 \Delta z_{14}=400\,{\rm m},\,
136 \Delta z_{15}=480\,{\rm m},\,
137 $
138 $
139 \Delta z_{16}=570\,{\rm m},\,
140 \Delta z_{17}=655\,{\rm m},\,
141 \Delta z_{18}=725\,{\rm m},\,
142 \Delta z_{19}=775\,{\rm m},\,
143 \Delta z_{20}=815\,{\rm m}
144 $ (here the numeric subscript indicates the model level index number, ${\tt k}$) to
145 give a total depth, $H$, of $-5450{\rm m}$.
146 The implicit free surface form of the pressure equation described in Marshall et. al
147 \cite{marshall:97a} is employed. A Laplacian operator, $\nabla^2$, provides viscous
148 dissipation. Thermal and haline diffusion is also represented by a Laplacian operator.
149
150 Wind-stress forcing is added to the momentum equations in (\ref{EQ:eg-global-model_equations})
151 for both the zonal flow, $u$ and the meridional flow $v$, according to equations
152 (\ref{EQ:eg-global-global_forcing_fu}) and (\ref{EQ:eg-global-global_forcing_fv}).
153 Thermodynamic forcing inputs are added to the equations
154 in (\ref{EQ:eg-global-model_equations}) for
155 potential temperature, $\theta$, and salinity, $S$, according to equations
156 (\ref{EQ:eg-global-global_forcing_ft}) and (\ref{EQ:eg-global-global_forcing_fs}).
157 This produces a set of equations solved in this configuration as follows:
158
159 \begin{eqnarray}
160 \label{EQ:eg-global-model_equations}
161 \frac{Du}{Dt} - fv +
162 \frac{1}{\rho}\frac{\partial p^{'}}{\partial x} -
163 \nabla_{h}\cdot A_{h}\nabla_{h}u -
164 \frac{\partial}{\partial z}A_{z}\frac{\partial u}{\partial z}
165 & = &
166 \begin{cases}
167 {\cal F}_u & \text{(surface)} \\
168 0 & \text{(interior)}
169 \end{cases}
170 \\
171 \frac{Dv}{Dt} + fu +
172 \frac{1}{\rho}\frac{\partial p^{'}}{\partial y} -
173 \nabla_{h}\cdot A_{h}\nabla_{h}v -
174 \frac{\partial}{\partial z}A_{z}\frac{\partial v}{\partial z}
175 & = &
176 \begin{cases}
177 {\cal F}_v & \text{(surface)} \\
178 0 & \text{(interior)}
179 \end{cases}
180 \\
181 \frac{\partial \eta}{\partial t} + \nabla_{h}\cdot \vec{u}
182 &=&
183 0
184 \\
185 \frac{D\theta}{Dt} -
186 \nabla_{h}\cdot K_{h}\nabla_{h}\theta
187 - \frac{\partial}{\partial z}\Gamma(K_{z})\frac{\partial\theta}{\partial z}
188 & = &
189 \begin{cases}
190 {\cal F}_\theta & \text{(surface)} \\
191 0 & \text{(interior)}
192 \end{cases}
193 \\
194 \frac{D s}{Dt} -
195 \nabla_{h}\cdot K_{h}\nabla_{h}s
196 - \frac{\partial}{\partial z}\Gamma(K_{z})\frac{\partial s}{\partial z}
197 & = &
198 \begin{cases}
199 {\cal F}_s & \text{(surface)} \\
200 0 & \text{(interior)}
201 \end{cases}
202 \\
203 g\rho_{0} \eta + \int^{0}_{-z}\rho^{'} dz & = & p^{'}
204 \end{eqnarray}
205
206 \noindent where $u=\frac{Dx}{Dt}=r \cos(\phi)\frac{D \lambda}{Dt}$ and
207 $v=\frac{Dy}{Dt}=r \frac{D \phi}{Dt}$
208 are the zonal and meridional components of the
209 flow vector, $\vec{u}$, on the sphere. As described in
210 MITgcm Numerical Solution Procedure \ref{chap:discretization}, the time
211 evolution of potential temperature, $\theta$, equation is solved prognostically.
212 The total pressure, $p$, is diagnosed by summing pressure due to surface
213 elevation $\eta$ and the hydrostatic pressure.
214 \\
215
216 \subsubsection{Numerical Stability Criteria}
217 \label{www:tutorials}
218
219 The Laplacian dissipation coefficient, $A_{h}$, is set to $5 \times 10^5 m s^{-1}$.
220 This value is chosen to yield a Munk layer width \cite{adcroft:95},
221 \begin{eqnarray}
222 \label{EQ:eg-global-munk_layer}
223 && M_{w} = \pi ( \frac { A_{h} }{ \beta } )^{\frac{1}{3}}
224 \end{eqnarray}
225
226 \noindent of $\approx 600$km. This is greater than the model
227 resolution in low-latitudes, $\Delta x \approx 400{\rm km}$, ensuring that the frictional
228 boundary layer is adequately resolved.
229 \\
230
231 \noindent The model is stepped forward with a
232 time step $\delta t_{\theta}=30~{\rm hours}$ for thermodynamic variables and
233 $\delta t_{v}=40~{\rm minutes}$ for momentum terms. With this time step, the stability
234 parameter to the horizontal Laplacian friction \cite{adcroft:95}
235 \begin{eqnarray}
236 \label{EQ:eg-global-laplacian_stability}
237 && S_{l} = 4 \frac{A_{h} \delta t_{v}}{{\Delta x}^2}
238 \end{eqnarray}
239
240 \noindent evaluates to 0.16 at a latitude of $\phi=80^{\circ}$, which is below the
241 0.3 upper limit for stability. The zonal grid spacing $\Delta x$ is smallest at
242 $\phi=80^{\circ}$ where $\Delta x=r\cos(\phi)\Delta \phi\approx 77{\rm km}$.
243 \\
244
245 \noindent The vertical dissipation coefficient, $A_{z}$, is set to
246 $1\times10^{-3} {\rm m}^2{\rm s}^{-1}$. The associated stability limit
247 \begin{eqnarray}
248 \label{EQ:eg-global-laplacian_stability_z}
249 S_{l} = 4 \frac{A_{z} \delta t_{v}}{{\Delta z}^2}
250 \end{eqnarray}
251
252 \noindent evaluates to $0.015$ for the smallest model
253 level spacing ($\Delta z_{1}=50{\rm m}$) which is again well below
254 the upper stability limit.
255 \\
256
257 The values of the horizontal ($K_{h}$) and vertical ($K_{z}$) diffusion coefficients
258 for both temperature and salinity are set to $1 \times 10^{3}~{\rm m}^{2}{\rm s}^{-1}$
259 and $3 \times 10^{-5}~{\rm m}^{2}{\rm s}^{-1}$ respectively. The stability limit
260 related to $K_{h}$ will be at $\phi=80^{\circ}$ where $\Delta x \approx 77 {\rm km}$.
261 Here the stability parameter
262 \begin{eqnarray}
263 \label{EQ:eg-global-laplacian_stability_xtheta}
264 S_{l} = \frac{4 K_{h} \delta t_{\theta}}{{\Delta x}^2}
265 \end{eqnarray}
266 evaluates to $0.07$, well below the stability limit of $S_{l} \approx 0.5$. The
267 stability parameter related to $K_{z}$
268 \begin{eqnarray}
269 \label{EQ:eg-global-laplacian_stability_ztheta}
270 S_{l} = \frac{4 K_{z} \delta t_{\theta}}{{\Delta z}^2}
271 \end{eqnarray}
272 evaluates to $0.005$ for $\min(\Delta z)=50{\rm m}$, well below the stability limit
273 of $S_{l} \approx 0.5$.
274 \\
275
276 \noindent The numerical stability for inertial oscillations
277 \cite{adcroft:95}
278
279 \begin{eqnarray}
280 \label{EQ:eg-global-inertial_stability}
281 S_{i} = f^{2} {\delta t_v}^2
282 \end{eqnarray}
283
284 \noindent evaluates to $0.24$ for $f=2\omega\sin(80^{\circ})=1.43\times10^{-4}~{\rm s}^{-1}$, which is close to
285 the $S_{i} < 1$ upper limit for stability.
286 \\
287
288 \noindent The advective CFL \cite{adcroft:95} for a extreme maximum
289 horizontal flow
290 speed of $ | \vec{u} | = 2 ms^{-1}$
291
292 \begin{eqnarray}
293 \label{EQ:eg-global-cfl_stability}
294 S_{a} = \frac{| \vec{u} | \delta t_{v}}{ \Delta x}
295 \end{eqnarray}
296
297 \noindent evaluates to $6 \times 10^{-2}$. This is well below the stability
298 limit of 0.5.
299 \\
300
301 \noindent The stability parameter for internal gravity waves propagating
302 with a maximum speed of $c_{g}=10~{\rm ms}^{-1}$
303 \cite{adcroft:95}
304
305 \begin{eqnarray}
306 \label{EQ:eg-global-gfl_stability}
307 S_{c} = \frac{c_{g} \delta t_{v}}{ \Delta x}
308 \end{eqnarray}
309
310 \noindent evaluates to $3 \times 10^{-1}$. This is close to the linear
311 stability limit of 0.5.
312
313 \subsection{Experiment Configuration}
314 \label{www:tutorials}
315 \label{SEC:eg-global-clim_ocn_examp_exp_config}
316
317 The model configuration for this experiment resides under the
318 directory {\it tutorial\_examples/global\_ocean\_circulation/}.
319 The experiment files
320
321 \begin{itemize}
322 \item {\it input/data}
323 \item {\it input/data.pkg}
324 \item {\it input/eedata},
325 \item {\it input/windx.bin},
326 \item {\it input/windy.bin},
327 \item {\it input/salt.bin},
328 \item {\it input/theta.bin},
329 \item {\it input/SSS.bin},
330 \item {\it input/SST.bin},
331 \item {\it input/topog.bin},
332 \item {\it code/CPP\_EEOPTIONS.h}
333 \item {\it code/CPP\_OPTIONS.h},
334 \item {\it code/SIZE.h}.
335 \end{itemize}
336 contain the code customizations and parameter settings for these
337 experiments. Below we describe the customizations
338 to these files associated with this experiment.
339
340 \subsubsection{Driving Datasets}
341 \label{www:tutorials}
342
343 Figures (\ref{FIG:sim_config_tclim}-\ref{FIG:sim_config_empmr}) show the
344 relaxation temperature ($\theta^{\ast}$) and salinity ($S^{\ast}$) fields,
345 the wind stress components ($\tau_x$ and $\tau_y$), the heat flux ($Q$)
346 and the net fresh water flux (${\cal E} - {\cal P} - {\cal R}$) used
347 in equations \ref{EQ:global_forcing_fu}-\ref{EQ:global_forcing_fs}. The figures
348 also indicate the lateral extent and coastline used in the experiment.
349 Figure ({\ref{FIG:model_bathymetry}) shows the depth contours of the model
350 domain.
351
352
353 \subsubsection{File {\it input/data}}
354 \label{www:tutorials}
355
356 This file, reproduced completely below, specifies the main parameters
357 for the experiment. The parameters that are significant for this configuration
358 are
359
360 \begin{itemize}
361
362 \item Lines 7-10 and 11-14
363 \begin{verbatim} tRef= 16.0 , 15.2 , 14.5 , 13.9 , 13.3 , \end{verbatim}
364 $\cdots$ \\
365 set reference values for potential
366 temperature and salinity at each model level in units of $^{\circ}\mathrm{C}$ and
367 ${\rm ppt}$. The entries are ordered from surface to depth.
368 Density is calculated from anomalies at each level evaluated
369 with respect to the reference values set here.\\
370 \fbox{
371 \begin{minipage}{5.0in}
372 {\it S/R INI\_THETA}({\it ini\_theta.F})
373 \end{minipage}
374 }
375
376
377 \item Line 15,
378 \begin{verbatim} viscAz=1.E-3, \end{verbatim}
379 this line sets the vertical Laplacian dissipation coefficient to
380 $1 \times 10^{-3} {\rm m^{2}s^{-1}}$. Boundary conditions
381 for this operator are specified later. This variable is copied into
382 model general vertical coordinate variable {\bf viscAr}.
383
384 \fbox{
385 \begin{minipage}{5.0in}
386 {\it S/R CALC\_DIFFUSIVITY}({\it calc\_diffusivity.F})
387 \end{minipage}
388 }
389
390 \item Line 16,
391 \begin{verbatim}
392 viscAh=5.E5,
393 \end{verbatim}
394 this line sets the horizontal Laplacian frictional dissipation coefficient to
395 $5 \times 10^{5} {\rm m^{2}s^{-1}}$. Boundary conditions
396 for this operator are specified later.
397
398 \item Lines 17,
399 \begin{verbatim}
400 no_slip_sides=.FALSE.
401 \end{verbatim}
402 this line selects a free-slip lateral boundary condition for
403 the horizontal Laplacian friction operator
404 e.g. $\frac{\partial u}{\partial y}$=0 along boundaries in $y$ and
405 $\frac{\partial v}{\partial x}$=0 along boundaries in $x$.
406
407 \item Lines 9,
408 \begin{verbatim}
409 no_slip_bottom=.TRUE.
410 \end{verbatim}
411 this line selects a no-slip boundary condition for bottom
412 boundary condition in the vertical Laplacian friction operator
413 e.g. $u=v=0$ at $z=-H$, where $H$ is the local depth of the domain.
414
415 \item Line 19,
416 \begin{verbatim}
417 diffKhT=1.E3,
418 \end{verbatim}
419 this line sets the horizontal diffusion coefficient for temperature
420 to $1000\,{\rm m^{2}s^{-1}}$. The boundary condition on this
421 operator is $\frac{\partial}{\partial x}=\frac{\partial}{\partial y}=0$ on
422 all boundaries.
423
424 \item Line 20,
425 \begin{verbatim}
426 diffKzT=3.E-5,
427 \end{verbatim}
428 this line sets the vertical diffusion coefficient for temperature
429 to $3 \times 10^{-5}\,{\rm m^{2}s^{-1}}$. The boundary
430 condition on this operator is $\frac{\partial}{\partial z}=0$ at both
431 the upper and lower boundaries.
432
433 \item Line 21,
434 \begin{verbatim}
435 diffKhS=1.E3,
436 \end{verbatim}
437 this line sets the horizontal diffusion coefficient for salinity
438 to $1000\,{\rm m^{2}s^{-1}}$. The boundary condition on this
439 operator is $\frac{\partial}{\partial x}=\frac{\partial}{\partial y}=0$ on
440 all boundaries.
441
442 \item Line 22,
443 \begin{verbatim}
444 diffKzS=3.E-5,
445 \end{verbatim}
446 this line sets the vertical diffusion coefficient for salinity
447 to $3 \times 10^{-5}\,{\rm m^{2}s^{-1}}$. The boundary
448 condition on this operator is $\frac{\partial}{\partial z}=0$ at both
449 the upper and lower boundaries.
450
451 \item Lines 23-26
452 \begin{verbatim}
453 beta=1.E-11,
454 \end{verbatim}
455 \vspace{-5mm}$\cdots$\\
456 These settings do not apply for this experiment.
457
458 \item Line 27,
459 \begin{verbatim}
460 gravity=9.81,
461 \end{verbatim}
462 Sets the gravitational acceleration coefficient to $9.81{\rm m}{\rm s}^{-1}$.\\
463 \fbox{
464 \begin{minipage}{5.0in}
465 {\it S/R CALC\_PHI\_HYD}~({\it calc\_phi\_hyd.F})\\
466 {\it S/R INI\_CG2D}~({\it ini\_cg2d.F})\\
467 {\it S/R INI\_CG3D}~({\it ini\_cg3d.F})\\
468 {\it S/R INI\_PARMS}~({\it ini\_parms.F})\\
469 {\it S/R SOLVE\_FOR\_PRESSURE}~({\it solve\_for\_pressure.F})
470 \end{minipage}
471 }
472
473
474 \item Line 28-29,
475 \begin{verbatim}
476 rigidLid=.FALSE.,
477 implicitFreeSurface=.TRUE.,
478 \end{verbatim}
479 Selects the barotropic pressure equation to be the implicit free surface
480 formulation.
481
482 \item Line 30,
483 \begin{verbatim}
484 eosType='POLY3',
485 \end{verbatim}
486 Selects the third order polynomial form of the equation of state.\\
487 \fbox{
488 \begin{minipage}{5.0in}
489 {\it S/R FIND\_RHO}~({\it find\_rho.F})\\
490 {\it S/R FIND\_ALPHA}~({\it find\_alpha.F})
491 \end{minipage}
492 }
493
494 \item Line 31,
495 \begin{verbatim}
496 readBinaryPrec=32,
497 \end{verbatim}
498 Sets format for reading binary input datasets holding model fields to
499 use 32-bit representation for floating-point numbers.\\
500 \fbox{
501 \begin{minipage}{5.0in}
502 {\it S/R READ\_WRITE\_FLD}~({\it read\_write\_fld.F})\\
503 {\it S/R READ\_WRITE\_REC}~({\it read\_write\_rec.F})
504 \end{minipage}
505 }
506
507 \item Line 36,
508 \begin{verbatim}
509 cg2dMaxIters=1000,
510 \end{verbatim}
511 Sets maximum number of iterations the two-dimensional, conjugate
512 gradient solver will use, {\bf irrespective of convergence
513 criteria being met}.\\
514 \fbox{
515 \begin{minipage}{5.0in}
516 {\it S/R CG2D}~({\it cg2d.F})
517 \end{minipage}
518 }
519
520 \item Line 37,
521 \begin{verbatim}
522 cg2dTargetResidual=1.E-13,
523 \end{verbatim}
524 Sets the tolerance which the two-dimensional, conjugate
525 gradient solver will use to test for convergence in equation
526 \ref{EQ:congrad_2d_resid} to $1 \times 10^{-13}$.
527 Solver will iterate until
528 tolerance falls below this value or until the maximum number of
529 solver iterations is reached.\\
530 \fbox{
531 \begin{minipage}{5.0in}
532 {\it S/R CG2D}~({\it cg2d.F})
533 \end{minipage}
534 }
535
536 \item Line 42,
537 \begin{verbatim}
538 startTime=0,
539 \end{verbatim}
540 Sets the starting time for the model internal time counter.
541 When set to non-zero this option implicitly requests a
542 checkpoint file be read for initial state.
543 By default the checkpoint file is named according to
544 the integer number of time steps in the {\bf startTime} value.
545 The internal time counter works in seconds.
546
547 \item Line 43,
548 \begin{verbatim}
549 endTime=2808000.,
550 \end{verbatim}
551 Sets the time (in seconds) at which this simulation will terminate.
552 At the end of a simulation a checkpoint file is automatically
553 written so that a numerical experiment can consist of multiple
554 stages.
555
556 \item Line 44,
557 \begin{verbatim}
558 #endTime=62208000000,
559 \end{verbatim}
560 A commented out setting for endTime for a 2000 year simulation.
561
562 \item Line 45,
563 \begin{verbatim}
564 deltaTmom=2400.0,
565 \end{verbatim}
566 Sets the timestep $\delta t_{v}$ used in the momentum equations to
567 $20~{\rm mins}$.
568 See section \ref{SEC:mom_time_stepping}.
569
570 \fbox{
571 \begin{minipage}{5.0in}
572 {\it S/R TIMESTEP}({\it timestep.F})
573 \end{minipage}
574 }
575
576 \item Line 46,
577 \begin{verbatim}
578 tauCD=321428.,
579 \end{verbatim}
580 Sets the D-grid to C-grid coupling time scale $\tau_{CD}$ used in the momentum equations.
581 See section \ref{SEC:cd_scheme}.
582
583 \fbox{
584 \begin{minipage}{5.0in}
585 {\it S/R INI\_PARMS}({\it ini\_parms.F})\\
586 {\it S/R MOM\_FLUXFORM}({\it mom\_fluxform.F})
587 \end{minipage}
588 }
589
590 \item Line 47,
591 \begin{verbatim}
592 deltaTtracer=108000.,
593 \end{verbatim}
594 Sets the default timestep, $\delta t_{\theta}$, for tracer equations to
595 $30~{\rm hours}$.
596 See section \ref{SEC:tracer_time_stepping}.
597
598 \fbox{
599 \begin{minipage}{5.0in}
600 {\it S/R TIMESTEP\_TRACER}({\it timestep\_tracer.F})
601 \end{minipage}
602 }
603
604 \item Line 47,
605 \begin{verbatim}
606 bathyFile='topog.box'
607 \end{verbatim}
608 This line specifies the name of the file from which the domain
609 bathymetry is read. This file is a two-dimensional ($x,y$) map of
610 depths. This file is assumed to contain 64-bit binary numbers
611 giving the depth of the model at each grid cell, ordered with the x
612 coordinate varying fastest. The points are ordered from low coordinate
613 to high coordinate for both axes. The units and orientation of the
614 depths in this file are the same as used in the MITgcm code. In this
615 experiment, a depth of $0m$ indicates a solid wall and a depth
616 of $-2000m$ indicates open ocean. The matlab program
617 {\it input/gendata.m} shows an example of how to generate a
618 bathymetry file.
619
620
621 \item Line 50,
622 \begin{verbatim}
623 zonalWindFile='windx.sin_y'
624 \end{verbatim}
625 This line specifies the name of the file from which the x-direction
626 surface wind stress is read. This file is also a two-dimensional
627 ($x,y$) map and is enumerated and formatted in the same manner as the
628 bathymetry file. The matlab program {\it input/gendata.m} includes example
629 code to generate a valid
630 {\bf zonalWindFile}
631 file.
632
633 \end{itemize}
634
635 \noindent other lines in the file {\it input/data} are standard values
636 that are described in the MITgcm Getting Started and MITgcm Parameters
637 notes.
638
639 \begin{small}
640 \input{part3/case_studies/climatalogical_ogcm/input/data}
641 \end{small}
642
643 \subsubsection{File {\it input/data.pkg}}
644 \label{www:tutorials}
645
646 This file uses standard default values and does not contain
647 customisations for this experiment.
648
649 \subsubsection{File {\it input/eedata}}
650 \label{www:tutorials}
651
652 This file uses standard default values and does not contain
653 customisations for this experiment.
654
655 \subsubsection{File {\it input/windx.sin\_y}}
656 \label{www:tutorials}
657
658 The {\it input/windx.sin\_y} file specifies a two-dimensional ($x,y$)
659 map of wind stress ,$\tau_{x}$, values. The units used are $Nm^{-2}$.
660 Although $\tau_{x}$ is only a function of $y$n in this experiment
661 this file must still define a complete two-dimensional map in order
662 to be compatible with the standard code for loading forcing fields
663 in MITgcm. The included matlab program {\it input/gendata.m} gives a complete
664 code for creating the {\it input/windx.sin\_y} file.
665
666 \subsubsection{File {\it input/topog.box}}
667 \label{www:tutorials}
668
669
670 The {\it input/topog.box} file specifies a two-dimensional ($x,y$)
671 map of depth values. For this experiment values are either
672 $0m$ or $-2000\,{\rm m}$, corresponding respectively to a wall or to deep
673 ocean. The file contains a raw binary stream of data that is enumerated
674 in the same way as standard MITgcm two-dimensional, horizontal arrays.
675 The included matlab program {\it input/gendata.m} gives a complete
676 code for creating the {\it input/topog.box} file.
677
678 \subsubsection{File {\it code/SIZE.h}}
679 \label{www:tutorials}
680
681 Two lines are customized in this file for the current experiment
682
683 \begin{itemize}
684
685 \item Line 39,
686 \begin{verbatim} sNx=60, \end{verbatim} this line sets
687 the lateral domain extent in grid points for the
688 axis aligned with the x-coordinate.
689
690 \item Line 40,
691 \begin{verbatim} sNy=60, \end{verbatim} this line sets
692 the lateral domain extent in grid points for the
693 axis aligned with the y-coordinate.
694
695 \item Line 49,
696 \begin{verbatim} Nr=4, \end{verbatim} this line sets
697 the vertical domain extent in grid points.
698
699 \end{itemize}
700
701 \begin{small}
702 \input{part3/case_studies/climatalogical_ogcm/code/SIZE.h}
703 \end{small}
704
705 \subsubsection{File {\it code/CPP\_OPTIONS.h}}
706 \label{www:tutorials}
707
708 This file uses standard default values and does not contain
709 customisations for this experiment.
710
711
712 \subsubsection{File {\it code/CPP\_EEOPTIONS.h}}
713 \label{www:tutorials}
714
715 This file uses standard default values and does not contain
716 customisations for this experiment.
717
718 \subsubsection{Other Files }
719 \label{www:tutorials}
720
721 Other files relevant to this experiment are
722 \begin{itemize}
723 \item {\it model/src/ini\_cori.F}. This file initializes the model
724 coriolis variables {\bf fCorU}.
725 \item {\it model/src/ini\_spherical\_polar\_grid.F}
726 \item {\it model/src/ini\_parms.F},
727 \item {\it input/windx.sin\_y},
728 \end{itemize}
729 contain the code customisations and parameter settings for this
730 experiments. Below we describe the customisations
731 to these files associated with this experiment.

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