/[MITgcm]/manual/s_examples/global_oce_latlon/inp_data.templ
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revision 1.1 by jmc, Thu Apr 21 20:05:12 2011 UTC revision 1.2 by mlosch, Mon May 2 10:46:28 2011 UTC
# Line 5  Line 5 
5  %\label{www:tutorials}  %\label{www:tutorials}
6    
7  This file, reproduced completely below, specifies the main parameters  This file, reproduced completely below, specifies the main parameters
8  for the experiment. The parameters that are significant for this configuration  for the experiment. The parameters that are significant for this configuration
9  are  are
10    
11  \begin{itemize}  \begin{itemize}
12    
13  \item Lines 7-10 and 11-14  \item Lines 7--8
14  \begin{verbatim} tRef= 16.0 , 15.2 , 14.5 , 13.9 , 13.3 ,  \end{verbatim}  \begin{verbatim}
15  $\cdots$ \\  tRef= 15*20.,
16    sRef= 15*35.,
17    \end{verbatim}
18    %$\cdots$
19    \\
20  set reference values for potential  set reference values for potential
21  temperature and salinity at each model level in units of $^{\circ}\mathrm{C}$ and  temperature and salinity at each model level in units of $^{\circ}\mathrm{C}$ and
22  ${\rm ppt}$. The entries are ordered from surface to depth.  ${\rm ppt}$. The entries are ordered from surface to depth.
23  Density is calculated from anomalies at each level evaluated  Density is calculated from anomalies at each level evaluated
24  with respect to the reference values set here.\\  with respect to the reference values set here.\\
25  \fbox{  \fbox{
26  \begin{minipage}{5.0in}  \begin{minipage}{5.0in}
27  {\it S/R INI\_THETA}({\it ini\_theta.F})  {\it S/R INI\_THETA}({\it ini\_theta.F}) \\
28    {\it S/R INI\_SALT}({\it ini\_salt.F})
29  \end{minipage}  \end{minipage}
30  }  }
31    
32    \item Line 9,
33  \item Line 15,  \begin{verbatim}
34  \begin{verbatim} viscAz=1.E-3, \end{verbatim}  viscAr=1.E-3,
35    \end{verbatim}
36  this line sets the vertical Laplacian dissipation coefficient to  this line sets the vertical Laplacian dissipation coefficient to
37  $1 \times 10^{-3} {\rm m^{2}s^{-1}}$. Boundary conditions  $1 \times 10^{-3} {\rm m^{2}s^{-1}}$. Boundary conditions
38  for this operator are specified later. This variable is copied into  for this operator are specified later.
 model general vertical coordinate variable {\bf viscAr}.  
39    
40  \fbox{  \fbox{
41  \begin{minipage}{5.0in}  \begin{minipage}{5.0in}
# Line 38  model general vertical coordinate variab Line 43  model general vertical coordinate variab
43  \end{minipage}  \end{minipage}
44  }  }
45    
46  \item Line 16,  \item Line 10,
47  \begin{verbatim}  \begin{verbatim}
48  viscAh=5.E5,  viscAh=5.E5,
49  \end{verbatim}  \end{verbatim}
# Line 46  this line sets the horizontal Laplacian Line 51  this line sets the horizontal Laplacian
51  $5 \times 10^{5} {\rm m^{2}s^{-1}}$. Boundary conditions  $5 \times 10^{5} {\rm m^{2}s^{-1}}$. Boundary conditions
52  for this operator are specified later.  for this operator are specified later.
53    
54  \item Lines 17,  \item Lines 11 and 13,
 \begin{verbatim}  
 no_slip_sides=.FALSE.  
 \end{verbatim}  
 this line selects a free-slip lateral boundary condition for  
 the horizontal Laplacian friction operator  
 e.g. $\frac{\partial u}{\partial y}$=0 along boundaries in $y$ and  
 $\frac{\partial v}{\partial x}$=0 along boundaries in $x$.  
   
 \item Lines 9,  
 \begin{verbatim}  
 no_slip_bottom=.TRUE.  
 \end{verbatim}  
 this line selects a no-slip boundary condition for bottom  
 boundary condition in the vertical Laplacian friction operator  
 e.g. $u=v=0$ at $z=-H$, where $H$ is the local depth of the domain.  
   
 \item Line 19,  
55  \begin{verbatim}  \begin{verbatim}
56  diffKhT=1.E3,  diffKhT=0.0,
57    diffKhS=0.0,
58  \end{verbatim}  \end{verbatim}
59  this line sets the horizontal diffusion coefficient for temperature  set the horizontal diffusion coefficient for temperature and salinity
60  to $1000\,{\rm m^{2}s^{-1}}$. The boundary condition on this  to 0, since package GMREDI is used.
 operator is $\frac{\partial}{\partial x}=\frac{\partial}{\partial y}=0$ on  
 all boundaries.  
61    
62  \item Line 20,  \item Lines 12 and 14,
63  \begin{verbatim}  \begin{verbatim}
64  diffKzT=3.E-5,  diffKrT=3.E-5,
65    diffKrS=3.E-5,
66  \end{verbatim}  \end{verbatim}
67  this line sets the vertical diffusion coefficient for temperature  set the vertical diffusion coefficient for temperature and salinity
68  to $3 \times 10^{-5}\,{\rm m^{2}s^{-1}}$. The boundary  to $3 \times 10^{-5}\,{\rm m^{2}s^{-1}}$. The boundary
69  condition on this operator is $\frac{\partial}{\partial z}=0$ at both  condition on this operator is $\frac{\partial}{\partial z}=0$ at both
70  the upper and lower boundaries.  the upper and lower boundaries.
71    
72  \item Line 21,  \item Lines 15--17
73  \begin{verbatim}  \begin{verbatim}
74  diffKhS=1.E3,  rhonil=1035.,
75  \end{verbatim}  rhoConstFresh=1000.,
76  this line sets the horizontal diffusion coefficient for salinity  eosType = 'JMD95Z',
 to $1000\,{\rm m^{2}s^{-1}}$. The boundary condition on this  
 operator is $\frac{\partial}{\partial x}=\frac{\partial}{\partial y}=0$ on  
 all boundaries.  
   
 \item Line 22,  
 \begin{verbatim}  
 diffKzS=3.E-5,  
 \end{verbatim}  
 this line sets the vertical diffusion coefficient for salinity  
 to $3 \times 10^{-5}\,{\rm m^{2}s^{-1}}$. The boundary  
 condition on this operator is $\frac{\partial}{\partial z}=0$ at both  
 the upper and lower boundaries.  
   
 \item Lines 23-26  
 \begin{verbatim}  
 beta=1.E-11,  
 \end{verbatim}  
 \vspace{-5mm}$\cdots$\\  
 These settings do not apply for this experiment.  
   
 \item Line 27,  
 \begin{verbatim}  
 gravity=9.81,  
77  \end{verbatim}  \end{verbatim}
78  Sets the gravitational acceleration coefficient to $9.81{\rm m}{\rm s}^{-1}$.\\  set the reference densities for sea water and fresh water, and selects
79    the equation of state \citep{jackett95}
80  \fbox{  \fbox{
81  \begin{minipage}{5.0in}  \begin{minipage}{5.0in}
82    {\it S/R FIND\_RHO}~({\it find\_rho.F})\\
83    {\it S/R FIND\_ALPHA}~({\it find\_alpha.F}) \\
84  {\it S/R CALC\_PHI\_HYD}~({\it calc\_phi\_hyd.F})\\  {\it S/R CALC\_PHI\_HYD}~({\it calc\_phi\_hyd.F})\\
85  {\it S/R INI\_CG2D}~({\it ini\_cg2d.F})\\  {\it S/R INI\_CG2D}~({\it ini\_cg2d.F})\\
86  {\it S/R INI\_CG3D}~({\it ini\_cg3d.F})\\  {\it S/R INI\_CG3D}~({\it ini\_cg3d.F})\\
# Line 122  Sets the gravitational acceleration coef Line 90  Sets the gravitational acceleration coef
90  }  }
91    
92    
93  \item Line 28-29,  \item Lines 18--19,
 \begin{verbatim}  
 rigidLid=.FALSE.,  
 implicitFreeSurface=.TRUE.,  
 \end{verbatim}  
 Selects the barotropic pressure equation to be the implicit free surface  
 formulation.  
   
 \item Line 30,  
94  \begin{verbatim}  \begin{verbatim}
95  eosType='POLY3',   ivdc_kappa=100.,
96     implicitDiffusion=.TRUE.,
97  \end{verbatim}  \end{verbatim}
98  Selects the third order polynomial form of the equation of state.\\  specify an ``implicit diffusion'' scheme with increased vertical
99    diffusivity of 100~m$^2$/s in case of instable stratification.
100  \fbox{  \fbox{
101  \begin{minipage}{5.0in}  \begin{minipage}{5.0in}
 {\it S/R FIND\_RHO}~({\it find\_rho.F})\\  
 {\it S/R FIND\_ALPHA}~({\it find\_alpha.F})  
102  \end{minipage}  \end{minipage}
103  }  }
104    
105  \item Line 31,  \item \ldots
106    
107    \item Line 28,
108  \begin{verbatim}  \begin{verbatim}
109  readBinaryPrec=32,  readBinaryPrec=32,
110  \end{verbatim}  \end{verbatim}
# Line 155  use 32-bit representation for floating-p Line 117  use 32-bit representation for floating-p
117  \end{minipage}  \end{minipage}
118  }  }
119    
120  \item Line 36,  \item Line 33,
121  \begin{verbatim}  \begin{verbatim}
122  cg2dMaxIters=1000,  cg2dMaxIters=500,
123  \end{verbatim}  \end{verbatim}
124  Sets maximum number of iterations the two-dimensional, conjugate  Sets maximum number of iterations the two-dimensional, conjugate
125  gradient solver will use, {\bf irrespective of convergence  gradient solver will use, {\bf irrespective of convergence
# Line 168  criteria being met}.\\ Line 130  criteria being met}.\\
130  \end{minipage}  \end{minipage}
131  }  }
132    
133  \item Line 37,  \item Line 34,
134  \begin{verbatim}  \begin{verbatim}
135  cg2dTargetResidual=1.E-13,  cg2dTargetResidual=1.E-13,
136  \end{verbatim}  \end{verbatim}
# Line 186  maximum number of solver iterations is r Line 148  maximum number of solver iterations is r
148  \end{minipage}  \end{minipage}
149  }  }
150    
151  \item Line 42,  \item Line 39,
152  \begin{verbatim}  \begin{verbatim}
153  startTime=0,  nIter0=0,
154  \end{verbatim}  \end{verbatim}
155  Sets the starting time for the model internal time counter.  Sets the starting time for the model internal time counter.
156  When set to non-zero this option implicitly requests a  When set to non-zero this option implicitly requests a
157  checkpoint file be read for initial state.  checkpoint file be read for initial state.
158  By default the checkpoint file is named according to  By default the checkpoint file is named according to
159  the integer number of time steps in the {\bf startTime} value.  the integer number of time step value \verb+nIter0+.
160  The internal time counter works in seconds.  The internal time counter works in seconds. Alternatively,
161    \verb+startTime+ can be set.
162    
163  \item Line 43,  \item Line 40,
164  \begin{verbatim}  \begin{verbatim}
165  endTime=2808000.,  nTimesteps=20,
166  \end{verbatim}  \end{verbatim}
167  Sets the time (in seconds) at which this simulation will terminate.  Sets the time step number at which this simulation will terminate.
168  At the end of a simulation a checkpoint file is automatically  At the end of a simulation a checkpoint file is automatically
169  written so that a numerical experiment can consist of multiple  written so that a numerical experiment can consist of multiple
170  stages.  stages. Alternatively \verb+endTime+ can be set.
171    
172  \item Line 44,  \item Line 44,
173  \begin{verbatim}  \begin{verbatim}
174  #endTime=62208000000,  deltaTmom=1800.0,
 \end{verbatim}  
 A commented out setting for endTime for a 2000 year simulation.  
   
 \item Line 45,  
 \begin{verbatim}  
 deltaTmom=2400.0,  
175  \end{verbatim}  \end{verbatim}
176  Sets the timestep $\delta t_{v}$ used in the momentum equations to  Sets the timestep $\delta t_{v}$ used in the momentum equations to
177  $20~{\rm mins}$.  $30~{\rm mins}$.
178  %- note: Distord Physics (using different time-steps) is not described  %- note: Distord Physics (using different time-steps) is not described
179  %  in the mean time, put this section ref:  %  in the mean time, put this section ref:
180  See section \ref{sec:time_stepping}. %\ref{sec:mom_time_stepping}.  See section \ref{sec:time_stepping}. %\ref{sec:mom_time_stepping}.
# Line 228  See section \ref{sec:time_stepping}. %\r Line 185  See section \ref{sec:time_stepping}. %\r
185  \end{minipage}  \end{minipage}
186  }  }
187    
188  \item Line 46,  \item Line 45,
189  \begin{verbatim}  \begin{verbatim}
190  tauCD=321428.,  tauCD=321428.,
191  \end{verbatim}  \end{verbatim}
# Line 245  used in the momentum equations. Line 202  used in the momentum equations.
202  \end{minipage}  \end{minipage}
203  }  }
204    
205  \item Line 47,  \item Lines 46--48,
206  \begin{verbatim}  \begin{verbatim}
207  deltaTtracer=108000.,  deltaTtracer=86400.,
208  \end{verbatim}  deltaTClock = 86400.,
209  Sets the default timestep, $\delta t_{\theta}$, for tracer equations to  deltaTfreesurf= 86400.,
210  $30~{\rm hours}$.  \end{verbatim}
211  %- note: Distord Physics (using different time-steps) is not described  Sets the default timestep, $\delta t_{\theta}$, for tracer equations
212  %  in the mean time, put this section ref:  and implicit free surface equations to
213    $24~{\rm hours}$.
214    % - note: Distord Physics (using different time-steps) is not
215    % described in the mean time, put this section ref:
216  See section \ref{sec:time_stepping}. %\ref{sec:tracer_time_stepping}.  See section \ref{sec:time_stepping}. %\ref{sec:tracer_time_stepping}.
217    
218  \fbox{  \fbox{
# Line 261  See section \ref{sec:time_stepping}. %\r Line 221  See section \ref{sec:time_stepping}. %\r
221  \end{minipage}  \end{minipage}
222  }  }
223    
224  \item Line 47,  \item Line 76,
225  \begin{verbatim}  \begin{verbatim}
226  bathyFile='topog.box'  bathyFile='bathymetry.bin'
227  \end{verbatim}  \end{verbatim}
228  This line specifies the name of the file from which the domain  This line specifies the name of the file from which the domain
229  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
230  depths. This file is assumed to contain 64-bit binary numbers  depths. This file is assumed to contain 32-bit binary numbers
231  giving the depth of the model at each grid cell, ordered with the x  giving the depth of the model at each grid cell, ordered with the x
232  coordinate varying fastest. The points are ordered from low coordinate  coordinate varying fastest. The points are ordered from low coordinate
233  to high coordinate for both axes. The units and orientation of the  to high coordinate for both axes. The units and orientation of the
234  depths in this file are the same as used in the MITgcm code. In this  depths in this file are the same as used in the MITgcm code. In this
235  experiment, a depth of $0m$ indicates a solid wall and a depth  experiment, a depth of $0m$ indicates a solid wall and a depth
236  of $-2000m$ indicates open ocean. The matlab program  of $<0m$ indicates open ocean.
237  {\it input/gendata.m} shows an example of how to generate a  
 bathymetry file.  
   
   
 \item Line 50,  
 \begin{verbatim}  
 zonalWindFile='windx.sin_y'  
 \end{verbatim}  
 This line specifies the name of the file from which the x-direction  
 surface wind stress is read. This file is also a two-dimensional  
 ($x,y$) map and is enumerated and formatted in the same manner as the  
 bathymetry file. The matlab program {\it input/gendata.m} includes example  
 code to generate a valid  
 {\bf zonalWindFile}  
 file.    
238    
239    \item Line 79--80,
240    \begin{verbatim}
241    zonalWindFile='trenberth_taux.bin'
242    meridWindFile='trenberth_tauy.bin'
243    \end{verbatim}
244      These lines specify the names of the files from which the x- and y-
245      direction surface wind stress is read. These files are also
246      three-dimensional ($x,y,time$) maps and are enumerated and formatted
247      in the same manner as the bathymetry file.
248  \end{itemize}  \end{itemize}
249    
250  \noindent other lines in the file {\it input/data} are standard values  \noindent other lines in the file {\it input/data} are standard values

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