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1 cnh 1.7 % $Header: /u/gcmpack/manual/part3/case_studies/hs_atmosphere/hs_atmos.tex,v 1.6 2004/10/13 14:04:56 cnh Exp $
2 cnh 1.1 % $Name: $
3    
4 cnh 1.5 \section[Held-Suarez Atmosphere MITgcm Example]{Held-Suarez forcing atmospheric simulation on a latitude-longitude grid 2.8$^\circ$ resolution and on
5 cnh 1.4 a cube-sphere grid with 32 square cube faces.}
6 adcroft 1.2 \label{www:tutorials}
7 cnh 1.1 \label{sect:eg-hs}
8    
9     \bodytext{bgcolor="#FFFFFFFF"}
10    
11     %\begin{center}
12     %{\Large \bf Using MITgcm to Simulate Global Climatological Ocean Circulation
13     %At Four Degree Resolution with Asynchronous Time Stepping}
14     %
15     %\vspace*{4mm}
16     %
17     %\vspace*{3mm}
18     %{\large May 2001}
19     %\end{center}
20    
21 cnh 1.4 This example illustrates the use of the MITgcm for large scale atmospheric
22     circulation simulation. Two simulations are described
23     \begin{itemize}
24     \item global atmospheric circulation on a latitude-longitude grid and
25     \item global atmospheric circulation on a cube-sphere grid
26     \end{itemize}
27     The examples show how to use the isomorphic 'p-coordinate' scheme in
28     MITgcm to enable atmospheric simulation.
29    
30    
31 cnh 1.1
32     \subsection{Overview}
33 adcroft 1.2 \label{www:tutorials}
34 cnh 1.1
35 cnh 1.5 This example demonstrates using the MITgcm to simulate
36     the planetary atmospheric circulation in two ways.
37 cnh 1.4 In both cases the simulation is configured with flat orography.
38     In the first case shown a $2.8^{\circ} \times 2.8^{\circ}$ spherical polar
39     horizontal grid is employed. In the second case a cube-sphere horizontal
40     grid is used that projects a cube with face size of $32 \times 32$ onto a
41     sphere.
42 cnh 1.5 Five pressure corrdinate levels are used in the vertical, ranging in thickness
43 cnh 1.4 from $100\,{\rm mb}$ at the bottom of the atmosphere to $300\,{\rm mb}$ in the middle atmosphere.
44 cnh 1.5 The total depth of the atmosphere is $1000{\rm mb}$.
45     At this resolution, the configuration can be integrated forward for many years on a
46     single processor desktop computer.
47 cnh 1.1 \\
48    
49 cnh 1.5 The model is forced by relaxation to a radiative equilibrium profile
50     from Held and Suarez \cite{held-suar:94}. Initial conditions are a
51     statically stable thermal gradient and no motion. The atmosphere
52     in these experiments is dry and the only active ``physics'' are the
53     terms in the Held and Suarez \cite{held-suar:94} formula. The
54 cnh 1.6 MITgcm intermediate atmospheric physics package (see \ref{sec:pkg:aim}) and
55 cnh 1.5 MITgcm high-end physics package ( see \ref{sec:pkg:fizhi}) are turned off.
56 cnh 1.6 Altogether, this yields the following forcing
57     (from Held and Suarez \cite{held-suar:94}) that is applied to the fluid:
58 cnh 1.1
59     \begin{eqnarray}
60     \label{EQ:eg-hs-global_forcing}
61     \label{EQ:eg-hs-global_forcing_fu}
62 cnh 1.6 \vec{{\cal F}_{u}} & = & -k_{v}(p)\vec{u}
63 cnh 1.1 \\
64     \label{EQ:eg-hs-global_forcing_ft}
65 cnh 1.6 {\cal F}_{\theta} & = & -k_{T}(\phi,p)[\theta-\theta_{eq}(\phi,p)]
66 cnh 1.1 \\
67     \end{eqnarray}
68    
69 cnh 1.6 \noindent where ${\vec{\cal F}_{u}}$, ${\cal F}_{\theta}$,
70     are the forcing terms in the zonal and meridional
71     momentum and in the potential temperature
72 cnh 1.1 equations respectively.
73 cnh 1.6 The term $k_{v}$ in equation (\ref{EQ:eg-hs-global_forcing_fu}) applies a
74     linear frictional drag (Rayleigh damping) that is active within the
75     planetary boundary layer. It is defined so as to decay with
76     height according to
77     \begin{eqnarray}
78     \label{EQ:eg-hs-define_kv}
79     k_{v} & = & k_{f}{\rm max}(0,(p_{\rm{k}}/p^{0}_{s}-\sigma_{b})/(1-\sigma_{b}))
80     \\
81     \sigma_{b} & = & 0.7
82 cnh 1.1 \\
83 cnh 1.6 k_{f} & = & 1{\rm day}^{-1}
84     \end{eqnarray}
85 cnh 1.1
86 cnh 1.6 where $p_{\rm{k}}$ is the pressure level of the cell center for level $\rm{k}$
87     and $p^{0}_{s}$ is the pressure at the base of the atmospheric column.
88 cnh 1.1
89    
90     \subsection{Discrete Numerical Configuration}
91 adcroft 1.2 \label{www:tutorials}
92 cnh 1.1
93    
94     The model is configured in hydrostatic form. The domain is discretised with
95     a uniform grid spacing in latitude and longitude on the sphere
96     $\Delta \phi=\Delta \lambda=4^{\circ}$, so
97     that there are ninety grid cells in the zonal and forty in the
98     meridional direction. The internal model coordinate variables
99     $x$ and $y$ are initialized according to
100     \begin{eqnarray}
101     x=r\cos(\phi),~\Delta x & = &r\cos(\Delta \phi) \\
102     y=r\lambda,~\Delta x &= &r\Delta \lambda
103     \end{eqnarray}
104    
105     Arctic polar regions are not
106     included in this experiment. Meridionally the model extends from
107     $80^{\circ}{\rm S}$ to $80^{\circ}{\rm N}$.
108     Vertically the model is configured with twenty layers with the
109     following thicknesses
110     $\Delta z_{1} = 50\,{\rm m},\,
111     \Delta z_{2} = 50\,{\rm m},\,
112     \Delta z_{3} = 55\,{\rm m},\,
113     \Delta z_{4} = 60\,{\rm m},\,
114     \Delta z_{5} = 65\,{\rm m},\,
115     $
116     $
117     \Delta z_{6}~=~70\,{\rm m},\,
118     \Delta z_{7}~=~80\,{\rm m},\,
119     \Delta z_{8}~=95\,{\rm m},\,
120     \Delta z_{9}=120\,{\rm m},\,
121     \Delta z_{10}=155\,{\rm m},\,
122     $
123     $
124     \Delta z_{11}=200\,{\rm m},\,
125     \Delta z_{12}=260\,{\rm m},\,
126     \Delta z_{13}=320\,{\rm m},\,
127     \Delta z_{14}=400\,{\rm m},\,
128     \Delta z_{15}=480\,{\rm m},\,
129     $
130     $
131     \Delta z_{16}=570\,{\rm m},\,
132     \Delta z_{17}=655\,{\rm m},\,
133     \Delta z_{18}=725\,{\rm m},\,
134     \Delta z_{19}=775\,{\rm m},\,
135     \Delta z_{20}=815\,{\rm m}
136     $ (here the numeric subscript indicates the model level index number, ${\tt k}$).
137     The implicit free surface form of the pressure equation described in Marshall et. al
138     \cite{marshall:97a} is employed. A Laplacian operator, $\nabla^2$, provides viscous
139     dissipation. Thermal and haline diffusion is also represented by a Laplacian operator.
140    
141     Wind-stress forcing is added to the momentum equations for both
142     the zonal flow, $u$ and the meridional flow $v$, according to equations
143     (\ref{EQ:eg-hs-global_forcing_fu}) and (\ref{EQ:eg-hs-global_forcing_fv}).
144     Thermodynamic forcing inputs are added to the equations for
145     potential temperature, $\theta$, and salinity, $S$, according to equations
146     (\ref{EQ:eg-hs-global_forcing_ft}) and (\ref{EQ:eg-hs-global_forcing_fs}).
147     This produces a set of equations solved in this configuration as follows:
148    
149     \begin{eqnarray}
150     \label{EQ:eg-hs-model_equations}
151     \frac{Du}{Dt} - fv +
152     \frac{1}{\rho}\frac{\partial p^{'}}{\partial x} -
153     \nabla_{h}\cdot A_{h}\nabla_{h}u -
154     \frac{\partial}{\partial z}A_{z}\frac{\partial u}{\partial z}
155     & = &
156     \begin{cases}
157     {\cal F}_u & \text{(surface)} \\
158     0 & \text{(interior)}
159     \end{cases}
160     \\
161     \frac{Dv}{Dt} + fu +
162     \frac{1}{\rho}\frac{\partial p^{'}}{\partial y} -
163     \nabla_{h}\cdot A_{h}\nabla_{h}v -
164     \frac{\partial}{\partial z}A_{z}\frac{\partial v}{\partial z}
165     & = &
166     \begin{cases}
167     {\cal F}_v & \text{(surface)} \\
168     0 & \text{(interior)}
169     \end{cases}
170     \\
171     \frac{\partial \eta}{\partial t} + \nabla_{h}\cdot \vec{u}
172     &=&
173     0
174     \\
175     \frac{D\theta}{Dt} -
176     \nabla_{h}\cdot K_{h}\nabla_{h}\theta
177     - \frac{\partial}{\partial z}\Gamma(K_{z})\frac{\partial\theta}{\partial z}
178     & = &
179     \begin{cases}
180     {\cal F}_\theta & \text{(surface)} \\
181     0 & \text{(interior)}
182     \end{cases}
183     \\
184     \frac{D s}{Dt} -
185     \nabla_{h}\cdot K_{h}\nabla_{h}s
186     - \frac{\partial}{\partial z}\Gamma(K_{z})\frac{\partial s}{\partial z}
187     & = &
188     \begin{cases}
189     {\cal F}_s & \text{(surface)} \\
190     0 & \text{(interior)}
191     \end{cases}
192     \\
193     g\rho_{0} \eta + \int^{0}_{-z}\rho^{'} dz & = & p^{'}
194     \end{eqnarray}
195    
196     \noindent where $u=\frac{Dx}{Dt}=r \cos(\phi)\frac{D \lambda}{Dt}$ and
197     $v=\frac{Dy}{Dt}=r \frac{D \phi}{Dt}$
198     are the zonal and meridional components of the
199     flow vector, $\vec{u}$, on the sphere. As described in
200     MITgcm Numerical Solution Procedure \ref{chap:discretization}, the time
201     evolution of potential temperature, $\theta$, equation is solved prognostically.
202     The total pressure, $p$, is diagnosed by summing pressure due to surface
203     elevation $\eta$ and the hydrostatic pressure.
204     \\
205    
206     \subsubsection{Numerical Stability Criteria}
207 adcroft 1.2 \label{www:tutorials}
208 cnh 1.1
209     The Laplacian dissipation coefficient, $A_{h}$, is set to $5 \times 10^5 m s^{-1}$.
210     This value is chosen to yield a Munk layer width \cite{adcroft:95},
211     \begin{eqnarray}
212     \label{EQ:eg-hs-munk_layer}
213     M_{w} = \pi ( \frac { A_{h} }{ \beta } )^{\frac{1}{3}}
214     \end{eqnarray}
215    
216     \noindent of $\approx 600$km. This is greater than the model
217     resolution in low-latitudes, $\Delta x \approx 400{\rm km}$, ensuring that the frictional
218     boundary layer is adequately resolved.
219     \\
220    
221     \noindent The model is stepped forward with a
222     time step $\delta t_{\theta}=30~{\rm hours}$ for thermodynamic variables and
223     $\delta t_{v}=40~{\rm minutes}$ for momentum terms. With this time step, the stability
224     parameter to the horizontal Laplacian friction \cite{adcroft:95}
225     \begin{eqnarray}
226     \label{EQ:eg-hs-laplacian_stability}
227     S_{l} = 4 \frac{A_{h} \delta t_{v}}{{\Delta x}^2}
228     \end{eqnarray}
229    
230     \noindent evaluates to 0.16 at a latitude of $\phi=80^{\circ}$, which is below the
231     0.3 upper limit for stability. The zonal grid spacing $\Delta x$ is smallest at
232     $\phi=80^{\circ}$ where $\Delta x=r\cos(\phi)\Delta \phi\approx 77{\rm km}$.
233     \\
234    
235     \noindent The vertical dissipation coefficient, $A_{z}$, is set to
236     $1\times10^{-3} {\rm m}^2{\rm s}^{-1}$. The associated stability limit
237     \begin{eqnarray}
238     \label{EQ:eg-hs-laplacian_stability_z}
239     S_{l} = 4 \frac{A_{z} \delta t_{v}}{{\Delta z}^2}
240     \end{eqnarray}
241    
242     \noindent evaluates to $0.015$ for the smallest model
243     level spacing ($\Delta z_{1}=50{\rm m}$) which is again well below
244     the upper stability limit.
245     \\
246    
247     The values of the horizontal ($K_{h}$) and vertical ($K_{z}$) diffusion coefficients
248     for both temperature and salinity are set to $1 \times 10^{3}~{\rm m}^{2}{\rm s}^{-1}$
249     and $3 \times 10^{-5}~{\rm m}^{2}{\rm s}^{-1}$ respectively. The stability limit
250     related to $K_{h}$ will be at $\phi=80^{\circ}$ where $\Delta x \approx 77 {\rm km}$.
251     Here the stability parameter
252     \begin{eqnarray}
253     \label{EQ:eg-hs-laplacian_stability_xtheta}
254     S_{l} = \frac{4 K_{h} \delta t_{\theta}}{{\Delta x}^2}
255     \end{eqnarray}
256     evaluates to $0.07$, well below the stability limit of $S_{l} \approx 0.5$. The
257     stability parameter related to $K_{z}$
258     \begin{eqnarray}
259     \label{EQ:eg-hs-laplacian_stability_ztheta}
260     S_{l} = \frac{4 K_{z} \delta t_{\theta}}{{\Delta z}^2}
261     \end{eqnarray}
262     evaluates to $0.005$ for $\min(\Delta z)=50{\rm m}$, well below the stability limit
263     of $S_{l} \approx 0.5$.
264     \\
265    
266     \noindent The numerical stability for inertial oscillations
267     \cite{adcroft:95}
268    
269     \begin{eqnarray}
270     \label{EQ:eg-hs-inertial_stability}
271     S_{i} = f^{2} {\delta t_v}^2
272     \end{eqnarray}
273    
274     \noindent evaluates to $0.24$ for $f=2\omega\sin(80^{\circ})=1.43\times10^{-4}~{\rm s}^{-1}$, which is close to
275     the $S_{i} < 1$ upper limit for stability.
276     \\
277    
278     \noindent The advective CFL \cite{adcroft:95} for a extreme maximum
279     horizontal flow
280     speed of $ | \vec{u} | = 2 ms^{-1}$
281    
282     \begin{eqnarray}
283     \label{EQ:eg-hs-cfl_stability}
284     S_{a} = \frac{| \vec{u} | \delta t_{v}}{ \Delta x}
285     \end{eqnarray}
286    
287     \noindent evaluates to $6 \times 10^{-2}$. This is well below the stability
288     limit of 0.5.
289     \\
290    
291     \noindent The stability parameter for internal gravity waves propagating
292     with a maximum speed of $c_{g}=10~{\rm ms}^{-1}$
293     \cite{adcroft:95}
294    
295     \begin{eqnarray}
296     \label{EQ:eg-hs-gfl_stability}
297     S_{c} = \frac{c_{g} \delta t_{v}}{ \Delta x}
298     \end{eqnarray}
299    
300     \noindent evaluates to $3 \times 10^{-1}$. This is close to the linear
301     stability limit of 0.5.
302    
303     \subsection{Experiment Configuration}
304 adcroft 1.2 \label{www:tutorials}
305 cnh 1.1 \label{SEC:eg-hs_examp_exp_config}
306    
307     The model configuration for this experiment resides under the
308 edhill 1.3 directory {\it verification/hs94.128x64x5}. The experiment files
309 cnh 1.1 \begin{itemize}
310     \item {\it input/data}
311     \item {\it input/data.pkg}
312     \item {\it input/eedata},
313     \item {\it input/windx.bin},
314     \item {\it input/windy.bin},
315     \item {\it input/salt.bin},
316     \item {\it input/theta.bin},
317     \item {\it input/SSS.bin},
318     \item {\it input/SST.bin},
319     \item {\it input/topog.bin},
320     \item {\it code/CPP\_EEOPTIONS.h}
321     \item {\it code/CPP\_OPTIONS.h},
322     \item {\it code/SIZE.h}.
323     \end{itemize}
324     contain the code customizations and parameter settings for these
325     experiments. Below we describe the customizations
326     to these files associated with this experiment.
327    
328     \subsubsection{File {\it input/data}}
329 adcroft 1.2 \label{www:tutorials}
330 cnh 1.1
331     This file, reproduced completely below, specifies the main parameters
332     for the experiment. The parameters that are significant for this configuration
333     are
334    
335     \begin{itemize}
336    
337     \item Lines 7-10 and 11-14
338     \begin{verbatim} tRef= 16.0 , 15.2 , 14.5 , 13.9 , 13.3 , \end{verbatim}
339     $\cdots$ \\
340     set reference values for potential
341     temperature and salinity at each model level in units of $^{\circ}$C and
342     ${\rm ppt}$. The entries are ordered from surface to depth.
343     Density is calculated from anomalies at each level evaluated
344     with respect to the reference values set here.\\
345     \fbox{
346     \begin{minipage}{5.0in}
347     {\it S/R INI\_THETA}({\it ini\_theta.F})
348     \end{minipage}
349     }
350    
351    
352     \item Line 15,
353     \begin{verbatim} viscAz=1.E-3, \end{verbatim}
354     this line sets the vertical Laplacian dissipation coefficient to
355     $1 \times 10^{-3} {\rm m^{2}s^{-1}}$. Boundary conditions
356     for this operator are specified later. This variable is copied into
357     model general vertical coordinate variable {\bf viscAr}.
358    
359     \fbox{
360     \begin{minipage}{5.0in}
361     {\it S/R CALC\_DIFFUSIVITY}({\it calc\_diffusivity.F})
362     \end{minipage}
363     }
364    
365     \item Line 16,
366     \begin{verbatim}
367     viscAh=5.E5,
368     \end{verbatim}
369     this line sets the horizontal Laplacian frictional dissipation coefficient to
370     $5 \times 10^{5} {\rm m^{2}s^{-1}}$. Boundary conditions
371     for this operator are specified later.
372    
373     \item Lines 17,
374     \begin{verbatim}
375     no_slip_sides=.FALSE.
376     \end{verbatim}
377     this line selects a free-slip lateral boundary condition for
378     the horizontal Laplacian friction operator
379     e.g. $\frac{\partial u}{\partial y}$=0 along boundaries in $y$ and
380     $\frac{\partial v}{\partial x}$=0 along boundaries in $x$.
381    
382     \item Lines 9,
383     \begin{verbatim}
384     no_slip_bottom=.TRUE.
385     \end{verbatim}
386     this line selects a no-slip boundary condition for bottom
387     boundary condition in the vertical Laplacian friction operator
388     e.g. $u=v=0$ at $z=-H$, where $H$ is the local depth of the domain.
389    
390     \item Line 19,
391     \begin{verbatim}
392     diffKhT=1.E3,
393     \end{verbatim}
394     this line sets the horizontal diffusion coefficient for temperature
395     to $1000\,{\rm m^{2}s^{-1}}$. The boundary condition on this
396     operator is $\frac{\partial}{\partial x}=\frac{\partial}{\partial y}=0$ on
397     all boundaries.
398    
399     \item Line 20,
400     \begin{verbatim}
401     diffKzT=3.E-5,
402     \end{verbatim}
403     this line sets the vertical diffusion coefficient for temperature
404     to $3 \times 10^{-5}\,{\rm m^{2}s^{-1}}$. The boundary
405     condition on this operator is $\frac{\partial}{\partial z}=0$ at both
406     the upper and lower boundaries.
407    
408     \item Line 21,
409     \begin{verbatim}
410     diffKhS=1.E3,
411     \end{verbatim}
412     this line sets the horizontal diffusion coefficient for salinity
413     to $1000\,{\rm m^{2}s^{-1}}$. The boundary condition on this
414     operator is $\frac{\partial}{\partial x}=\frac{\partial}{\partial y}=0$ on
415     all boundaries.
416    
417     \item Line 22,
418     \begin{verbatim}
419     diffKzS=3.E-5,
420     \end{verbatim}
421     this line sets the vertical diffusion coefficient for salinity
422     to $3 \times 10^{-5}\,{\rm m^{2}s^{-1}}$. The boundary
423     condition on this operator is $\frac{\partial}{\partial z}=0$ at both
424     the upper and lower boundaries.
425    
426     \item Lines 23-26
427     \begin{verbatim}
428     beta=1.E-11,
429     \end{verbatim}
430     \vspace{-5mm}$\cdots$\\
431     These settings do not apply for this experiment.
432    
433     \item Line 27,
434     \begin{verbatim}
435     gravity=9.81,
436     \end{verbatim}
437     Sets the gravitational acceleration coefficient to $9.81{\rm m}{\rm s}^{-1}$.\\
438     \fbox{
439     \begin{minipage}{5.0in}
440     {\it S/R CALC\_PHI\_HYD}~({\it calc\_phi\_hyd.F})\\
441     {\it S/R INI\_CG2D}~({\it ini\_cg2d.F})\\
442     {\it S/R INI\_CG3D}~({\it ini\_cg3d.F})\\
443     {\it S/R INI\_PARMS}~({\it ini\_parms.F})\\
444     {\it S/R SOLVE\_FOR\_PRESSURE}~({\it solve\_for\_pressure.F})
445     \end{minipage}
446     }
447    
448    
449     \item Line 28-29,
450     \begin{verbatim}
451     rigidLid=.FALSE.,
452     implicitFreeSurface=.TRUE.,
453     \end{verbatim}
454     Selects the barotropic pressure equation to be the implicit free surface
455     formulation.
456    
457     \item Line 30,
458     \begin{verbatim}
459     eosType='POLY3',
460     \end{verbatim}
461     Selects the third order polynomial form of the equation of state.\\
462     \fbox{
463     \begin{minipage}{5.0in}
464     {\it S/R FIND\_RHO}~({\it find\_rho.F})\\
465     {\it S/R FIND\_ALPHA}~({\it find\_alpha.F})
466     \end{minipage}
467     }
468    
469     \item Line 31,
470     \begin{verbatim}
471     readBinaryPrec=32,
472     \end{verbatim}
473     Sets format for reading binary input datasets holding model fields to
474     use 32-bit representation for floating-point numbers.\\
475     \fbox{
476     \begin{minipage}{5.0in}
477     {\it S/R READ\_WRITE\_FLD}~({\it read\_write\_fld.F})\\
478     {\it S/R READ\_WRITE\_REC}~({\it read\_write\_rec.F})
479     \end{minipage}
480     }
481    
482     \item Line 36,
483     \begin{verbatim}
484     cg2dMaxIters=1000,
485     \end{verbatim}
486     Sets maximum number of iterations the two-dimensional, conjugate
487     gradient solver will use, {\bf irrespective of convergence
488     criteria being met}.\\
489     \fbox{
490     \begin{minipage}{5.0in}
491     {\it S/R CG2D}~({\it cg2d.F})
492     \end{minipage}
493     }
494    
495     \item Line 37,
496     \begin{verbatim}
497     cg2dTargetResidual=1.E-13,
498     \end{verbatim}
499     Sets the tolerance which the two-dimensional, conjugate
500     gradient solver will use to test for convergence in equation
501     \ref{EQ:eg-hs-congrad_2d_resid} to $1 \times 10^{-13}$.
502     Solver will iterate until
503     tolerance falls below this value or until the maximum number of
504     solver iterations is reached.\\
505     \fbox{
506     \begin{minipage}{5.0in}
507     {\it S/R CG2D}~({\it cg2d.F})
508     \end{minipage}
509     }
510    
511     \item Line 42,
512     \begin{verbatim}
513     startTime=0,
514     \end{verbatim}
515     Sets the starting time for the model internal time counter.
516     When set to non-zero this option implicitly requests a
517     checkpoint file be read for initial state.
518     By default the checkpoint file is named according to
519     the integer number of time steps in the {\bf startTime} value.
520     The internal time counter works in seconds.
521    
522     \item Line 43,
523     \begin{verbatim}
524     endTime=2808000.,
525     \end{verbatim}
526     Sets the time (in seconds) at which this simulation will terminate.
527     At the end of a simulation a checkpoint file is automatically
528     written so that a numerical experiment can consist of multiple
529     stages.
530    
531     \item Line 44,
532     \begin{verbatim}
533     #endTime=62208000000,
534     \end{verbatim}
535     A commented out setting for endTime for a 2000 year simulation.
536    
537     \item Line 45,
538     \begin{verbatim}
539     deltaTmom=2400.0,
540     \end{verbatim}
541     Sets the timestep $\delta t_{v}$ used in the momentum equations to
542     $20~{\rm mins}$.
543     See section \ref{SEC:mom_time_stepping}.
544    
545     \fbox{
546     \begin{minipage}{5.0in}
547     {\it S/R TIMESTEP}({\it timestep.F})
548     \end{minipage}
549     }
550    
551     \item Line 46,
552     \begin{verbatim}
553     tauCD=321428.,
554     \end{verbatim}
555     Sets the D-grid to C-grid coupling time scale $\tau_{CD}$ used in the momentum equations.
556     See section \ref{SEC:cd_scheme}.
557    
558     \fbox{
559     \begin{minipage}{5.0in}
560     {\it S/R INI\_PARMS}({\it ini\_parms.F})\\
561     {\it S/R CALC\_MOM\_RHS}({\it calc\_mom\_rhs.F})
562     \end{minipage}
563     }
564    
565     \item Line 47,
566     \begin{verbatim}
567     deltaTtracer=108000.,
568     \end{verbatim}
569     Sets the default timestep, $\delta t_{\theta}$, for tracer equations to
570     $30~{\rm hours}$.
571     See section \ref{SEC:tracer_time_stepping}.
572    
573     \fbox{
574     \begin{minipage}{5.0in}
575     {\it S/R TIMESTEP\_TRACER}({\it timestep\_tracer.F})
576     \end{minipage}
577     }
578    
579     \item Line 47,
580     \begin{verbatim}
581     bathyFile='topog.box'
582     \end{verbatim}
583     This line specifies the name of the file from which the domain
584     bathymetry is read. This file is a two-dimensional ($x,y$) map of
585     depths. This file is assumed to contain 64-bit binary numbers
586     giving the depth of the model at each grid cell, ordered with the x
587     coordinate varying fastest. The points are ordered from low coordinate
588     to high coordinate for both axes. The units and orientation of the
589     depths in this file are the same as used in the MITgcm code. In this
590     experiment, a depth of $0m$ indicates a solid wall and a depth
591     of $-2000m$ indicates open ocean. The matlab program
592     {\it input/gendata.m} shows an example of how to generate a
593     bathymetry file.
594    
595    
596     \item Line 50,
597     \begin{verbatim}
598     zonalWindFile='windx.sin_y'
599     \end{verbatim}
600     This line specifies the name of the file from which the x-direction
601     surface wind stress is read. This file is also a two-dimensional
602     ($x,y$) map and is enumerated and formatted in the same manner as the
603     bathymetry file. The matlab program {\it input/gendata.m} includes example
604     code to generate a valid
605     {\bf zonalWindFile}
606     file.
607    
608     \end{itemize}
609    
610     \noindent other lines in the file {\it input/data} are standard values
611     that are described in the MITgcm Getting Started and MITgcm Parameters
612     notes.
613    
614     \begin{small}
615     \input{part3/case_studies/climatalogical_ogcm/input/data}
616     \end{small}
617    
618     \subsubsection{File {\it input/data.pkg}}
619 adcroft 1.2 \label{www:tutorials}
620 cnh 1.1
621     This file uses standard default values and does not contain
622     customisations for this experiment.
623    
624     \subsubsection{File {\it input/eedata}}
625 adcroft 1.2 \label{www:tutorials}
626 cnh 1.1
627     This file uses standard default values and does not contain
628     customisations for this experiment.
629    
630     \subsubsection{File {\it input/windx.sin\_y}}
631 adcroft 1.2 \label{www:tutorials}
632 cnh 1.1
633     The {\it input/windx.sin\_y} file specifies a two-dimensional ($x,y$)
634     map of wind stress ,$\tau_{x}$, values. The units used are $Nm^{-2}$.
635     Although $\tau_{x}$ is only a function of $y$n in this experiment
636     this file must still define a complete two-dimensional map in order
637     to be compatible with the standard code for loading forcing fields
638     in MITgcm. The included matlab program {\it input/gendata.m} gives a complete
639     code for creating the {\it input/windx.sin\_y} file.
640    
641     \subsubsection{File {\it input/topog.box}}
642 adcroft 1.2 \label{www:tutorials}
643 cnh 1.1
644    
645     The {\it input/topog.box} file specifies a two-dimensional ($x,y$)
646     map of depth values. For this experiment values are either
647     $0m$ or $-2000\,{\rm m}$, corresponding respectively to a wall or to deep
648     ocean. The file contains a raw binary stream of data that is enumerated
649     in the same way as standard MITgcm two-dimensional, horizontal arrays.
650     The included matlab program {\it input/gendata.m} gives a complete
651     code for creating the {\it input/topog.box} file.
652    
653     \subsubsection{File {\it code/SIZE.h}}
654 adcroft 1.2 \label{www:tutorials}
655 cnh 1.1
656     Two lines are customized in this file for the current experiment
657    
658     \begin{itemize}
659    
660     \item Line 39,
661     \begin{verbatim} sNx=60, \end{verbatim} this line sets
662     the lateral domain extent in grid points for the
663     axis aligned with the x-coordinate.
664    
665     \item Line 40,
666     \begin{verbatim} sNy=60, \end{verbatim} this line sets
667     the lateral domain extent in grid points for the
668     axis aligned with the y-coordinate.
669    
670     \item Line 49,
671     \begin{verbatim} Nr=4, \end{verbatim} this line sets
672     the vertical domain extent in grid points.
673    
674     \end{itemize}
675    
676     \begin{small}
677     \input{part3/case_studies/climatalogical_ogcm/code/SIZE.h}
678     \end{small}
679    
680     \subsubsection{File {\it code/CPP\_OPTIONS.h}}
681 adcroft 1.2 \label{www:tutorials}
682 cnh 1.1
683     This file uses standard default values and does not contain
684     customisations for this experiment.
685    
686    
687     \subsubsection{File {\it code/CPP\_EEOPTIONS.h}}
688 adcroft 1.2 \label{www:tutorials}
689 cnh 1.1
690     This file uses standard default values and does not contain
691     customisations for this experiment.
692    
693     \subsubsection{Other Files }
694 adcroft 1.2 \label{www:tutorials}
695 cnh 1.1
696     Other files relevant to this experiment are
697     \begin{itemize}
698     \item {\it model/src/ini\_cori.F}. This file initializes the model
699     coriolis variables {\bf fCorU}.
700     \item {\it model/src/ini\_spherical\_polar\_grid.F}
701     \item {\it model/src/ini\_parms.F},
702     \item {\it input/windx.sin\_y},
703     \end{itemize}
704     contain the code customisations and parameter settings for this
705     experiments. Below we describe the customisations
706     to these files associated with this experiment.

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