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revision 1.7 by cnh, Sun Oct 21 04:19:40 2001 UTC revision 1.18 by edhill, Thu Jan 29 19:22:35 2004 UTC
# Line 18  you are ready to try implementing the co Line 18  you are ready to try implementing the co
18  \section{Where to find information}  \section{Where to find information}
19  \label{sect:whereToFindInfo}  \label{sect:whereToFindInfo}
20    
21  A web site is maintained for release 1 (Sealion) of MITgcm:  A web site is maintained for release 2 (``Pelican'') of MITgcm:
22    \begin{rawhtml} <A href=http://mitgcm.org/pelican/ target="idontexist"> \end{rawhtml}
23  \begin{verbatim}  \begin{verbatim}
24  http://mitgcm.org/sealion  http://mitgcm.org/pelican
25  \end{verbatim}  \end{verbatim}
26    \begin{rawhtml} </A> \end{rawhtml}
27  Here you will find an on-line version of this document, a  Here you will find an on-line version of this document, a
28  ``browsable'' copy of the code and a searchable database of the model  ``browsable'' copy of the code and a searchable database of the model
29  and site, as well as links for downloading the model and  and site, as well as links for downloading the model and
30  documentation, to data-sources and other related sites.  documentation, to data-sources, and other related sites.
31    
32  There is also a support news group for the model that you can email at  There is also a web-archived support mailing list for the model that
33  \texttt{support@mitgcm.org} or browse at:  you can email at \texttt{MITgcm-support@mitgcm.org} or browse at:
34    \begin{rawhtml} <A href=http://mitgcm.org/mailman/listinfo/mitgcm-support/ target="idontexist"> \end{rawhtml}
35    \begin{verbatim}
36    http://mitgcm.org/mailman/listinfo/mitgcm-support/
37    http://mitgcm.org/pipermail/mitgcm-support/
38    \end{verbatim}
39    \begin{rawhtml} </A> \end{rawhtml}
40    Essentially all of the MITgcm web pages can be searched using a
41    popular web crawler such as Google or through our own search facility:
42    \begin{rawhtml} <A href=http://mitgcm.org/mailman/htdig/ target="idontexist"> \end{rawhtml}
43  \begin{verbatim}  \begin{verbatim}
44  news://mitgcm.org/mitgcm.support  http://mitgcm.org/htdig/
45  \end{verbatim}  \end{verbatim}
46  A mail to the email list will reach all the developers and be archived  \begin{rawhtml} </A> \end{rawhtml}
47  on the newsgroup. A users email list will be established at some time  %%% http://www.google.com/search?q=hydrostatic+site%3Amitgcm.org
48  in the future.  
49    
50    
51  \section{Obtaining the code}  \section{Obtaining the code}
52  \label{sect:obtainingCode}  \label{sect:obtainingCode}
53    
54  MITgcm can be downloaded from our system by following  MITgcm can be downloaded from our system by following
55  the instructions below. As a courtesy we ask that you send e-mail to us at  the instructions below. As a courtesy we ask that you send e-mail to us at
56  \begin{rawhtml} <A href=mailto:support@mitgcm.org> \end{rawhtml}  \begin{rawhtml} <A href=mailto:MITgcm-support@mitgcm.org> \end{rawhtml}
57  support@mitgcm.org  MITgcm-support@mitgcm.org
58  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}
59  to enable us to keep track of who's using the model and in what application.  to enable us to keep track of who's using the model and in what application.
60  You can download the model two ways:  You can download the model two ways:
61    
62  \begin{enumerate}  \begin{enumerate}
63  \item Using CVS software. CVS is a freely available source code managment  \item Using CVS software. CVS is a freely available source code management
64  tool. To use CVS you need to have the software installed. Many systems  tool. To use CVS you need to have the software installed. Many systems
65  come with CVS pre-installed, otherwise good places to look for  come with CVS pre-installed, otherwise good places to look for
66  the software for a particular platform are  the software for a particular platform are
# Line 72  provides an efficient and elegant way of Line 84  provides an efficient and elegant way of
84  track of your changes. If CVS is not available on your machine, you can also  track of your changes. If CVS is not available on your machine, you can also
85  download a tar file.  download a tar file.
86    
87  Before you can use CVS, the following environment variable has to be set in  Before you can use CVS, the following environment variable(s) should
88  your .cshrc or .tcshrc:  be set within your shell.  For a csh or tcsh shell, put the following
89    \begin{verbatim}
90    % setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/gcmpack
91    \end{verbatim}
92    in your .cshrc or .tcshrc file.  For bash or sh shells, put:
93  \begin{verbatim}  \begin{verbatim}
94  % setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/u0/gcmpack  % export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'
95  \end{verbatim}  \end{verbatim}
96    in your .profile or .bashrc file.
97    
98    
99  To start using CVS, register with the MITgcm CVS server using command:  To get MITgcm through CVS, first register with the MITgcm CVS server
100    using command:
101  \begin{verbatim}  \begin{verbatim}
102  % cvs login ( CVS password: cvsanon )  % cvs login ( CVS password: cvsanon )
103  \end{verbatim}  \end{verbatim}
104  You only need to do ``cvs login'' once.  You only need to do a ``cvs login'' once.
105    
106  To obtain the sources for release1 type:  To obtain the latest sources type:
107    \begin{verbatim}
108    % cvs co MITgcm
109    \end{verbatim}
110    or to get a specific release type:
111  \begin{verbatim}  \begin{verbatim}
112  % cvs co -d directory -P -r release1 MITgcmUV  % cvs co -P -r checkpoint52i_post  MITgcm
113  \end{verbatim}  \end{verbatim}
114    The MITgcm web site contains further directions concerning the source
115    code and CVS.  It also contains a web interface to our CVS archive so
116    that one may easily view the state of files, revisions, and other
117    development milestones:
118    \begin{rawhtml} <A href=''http://mitgcm.org/download'' target="idontexist"> \end{rawhtml}
119    \begin{verbatim}
120    http://mitgcm.org/source_code.html
121    \end{verbatim}
122    \begin{rawhtml} </A> \end{rawhtml}
123    
124    
125  This creates a directory called \textit{directory}. If \textit{directory}  The checkout process creates a directory called \textit{MITgcm}. If
126  exists this command updates your code based on the repository. Each  the directory \textit{MITgcm} exists this command updates your code
127  directory in the source tree contains a directory \textit{CVS}. This  based on the repository. Each directory in the source tree contains a
128  information is required by CVS to keep track of your file versions with  directory \textit{CVS}. This information is required by CVS to keep
129  respect to the repository. Don't edit the files in \textit{CVS}!  track of your file versions with respect to the repository. Don't edit
130  You can also use CVS to download code updates.  More extensive  the files in \textit{CVS}!  You can also use CVS to download code
131  information on using CVS for maintaining MITgcm code can be found  updates.  More extensive information on using CVS for maintaining
132  \begin{rawhtml} <A href=http://mitgcm.org/usingcvstoget.html target="idontexist"> \end{rawhtml}  MITgcm code can be found
133    \begin{rawhtml} <A href=''http://mitgcm.org/usingcvstoget.html'' target="idontexist"> \end{rawhtml}
134  here  here
135  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}
136  .  .
# Line 106  here Line 140  here
140  \label{sect:conventionalDownload}  \label{sect:conventionalDownload}
141    
142  If you do not have CVS on your system, you can download the model as a  If you do not have CVS on your system, you can download the model as a
143  tar file from the reference web site at:  tar file from the web site at:
144  \begin{rawhtml} <A href=http://mitgcm.org/download target="idontexist"> \end{rawhtml}  \begin{rawhtml} <A href=http://mitgcm.org/download target="idontexist"> \end{rawhtml}
145  \begin{verbatim}  \begin{verbatim}
146  http://mitgcm.org/download/  http://mitgcm.org/download/
# Line 114  http://mitgcm.org/download/ Line 148  http://mitgcm.org/download/
148  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}
149  The tar file still contains CVS information which we urge you not to  The tar file still contains CVS information which we urge you not to
150  delete; even if you do not use CVS yourself the information can help  delete; even if you do not use CVS yourself the information can help
151  us if you should need to send us your copy of the code.  us if you should need to send us your copy of the code.  If a recent
152    tar file does not exist, then please contact the developers through
153    the
154    \begin{rawhtml} <A href=''mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}
155    MITgcm-support@mitgcm.org
156    \begin{rawhtml} </A> \end{rawhtml}
157    mailing list.
158    
159    \paragraph*{Upgrading from an earlier version}
160    
161    If you already have an earlier version of the code you can ``upgrade''
162    your copy instead of downloading the entire repository again. First,
163    ``cd'' (change directory) to the top of your working copy:
164    \begin{verbatim}
165    % cd MITgcm
166    \end{verbatim}
167    and then issue the cvs update command such as:
168    \begin{verbatim}
169    % cvs -q update -r checkpoint52i_post -d -P
170    \end{verbatim}
171    This will update the ``tag'' to ``checkpoint52i\_post'', add any new
172    directories (-d) and remove any empty directories (-P). The -q option
173    means be quiet which will reduce the number of messages you'll see in
174    the terminal. If you have modified the code prior to upgrading, CVS
175    will try to merge your changes with the upgrades. If there is a
176    conflict between your modifications and the upgrade, it will report
177    that file with a ``C'' in front, e.g.:
178    \begin{verbatim}
179    C model/src/ini_parms.F
180    \end{verbatim}
181    If the list of conflicts scrolled off the screen, you can re-issue the
182    cvs update command and it will report the conflicts. Conflicts are
183    indicated in the code by the delimites ``$<<<<<<<$'', ``======='' and
184    ``$>>>>>>>$''. For example,
185    {\small
186    \begin{verbatim}
187    <<<<<<< ini_parms.F
188         & bottomDragLinear,myOwnBottomDragCoefficient,
189    =======
190         & bottomDragLinear,bottomDragQuadratic,
191    >>>>>>> 1.18
192    \end{verbatim}
193    }
194    means that you added ``myOwnBottomDragCoefficient'' to a namelist at
195    the same time and place that we added ``bottomDragQuadratic''. You
196    need to resolve this conflict and in this case the line should be
197    changed to:
198    {\small
199    \begin{verbatim}
200         & bottomDragLinear,bottomDragQuadratic,myOwnBottomDragCoefficient,
201    \end{verbatim}
202    }
203    and the lines with the delimiters ($<<<<<<$,======,$>>>>>>$) be deleted.
204    Unless you are making modifications which exactly parallel
205    developments we make, these types of conflicts should be rare.
206    
207    \paragraph*{Upgrading to the current pre-release version}
208    
209    We don't make a ``release'' for every little patch and bug fix in
210    order to keep the frequency of upgrades to a minimum. However, if you
211    have run into a problem for which ``we have already fixed in the
212    latest code'' and we haven't made a ``tag'' or ``release'' since that
213    patch then you'll need to get the latest code:
214    \begin{verbatim}
215    % cvs -q update -A -d -P
216    \end{verbatim}
217    Unlike, the ``check-out'' and ``update'' procedures above, there is no
218    ``tag'' or release name. The -A tells CVS to upgrade to the
219    very latest version. As a rule, we don't recommend this since you
220    might upgrade while we are in the processes of checking in the code so
221    that you may only have part of a patch. Using this method of updating
222    also means we can't tell what version of the code you are working
223    with. So please be sure you understand what you're doing.
224    
225  \section{Model and directory structure}  \section{Model and directory structure}
226    
227  The ``numerical'' model is contained within a execution environment support  The ``numerical'' model is contained within a execution environment
228  wrapper. This wrapper is designed to provide a general framework for  support wrapper. This wrapper is designed to provide a general
229  grid-point models. MITgcmUV is a specific numerical model that uses the  framework for grid-point models. MITgcmUV is a specific numerical
230  framework. Under this structure the model is split into execution  model that uses the framework. Under this structure the model is split
231  environment support code and conventional numerical model code. The  into execution environment support code and conventional numerical
232  execution environment support code is held under the \textit{eesupp}  model code. The execution environment support code is held under the
233  directory. The grid point model code is held under the \textit{model}  \textit{eesupp} directory. The grid point model code is held under the
234  directory. Code execution actually starts in the \textit{eesupp} routines  \textit{model} directory. Code execution actually starts in the
235  and not in the \textit{model} routines. For this reason the top-level  \textit{eesupp} routines and not in the \textit{model} routines. For
236  \textit{MAIN.F} is in the \textit{eesupp/src} directory. In general,  this reason the top-level \textit{MAIN.F} is in the
237  end-users should not need to worry about this level. The top-level routine  \textit{eesupp/src} directory. In general, end-users should not need
238  for the numerical part of the code is in \textit{model/src/THE\_MODEL\_MAIN.F%  to worry about this level. The top-level routine for the numerical
239  }. Here is a brief description of the directory structure of the model under  part of the code is in \textit{model/src/THE\_MODEL\_MAIN.F}. Here is
240  the root tree (a detailed description is given in section 3: Code structure).  a brief description of the directory structure of the model under the
241    root tree (a detailed description is given in section 3: Code
242    structure).
243    
244  \begin{itemize}  \begin{itemize}
 \item \textit{bin}: this directory is initially empty. It is the default  
 directory in which to compile the code.  
245    
246    \item \textit{bin}: this directory is initially empty. It is the
247      default directory in which to compile the code.
248      
249  \item \textit{diags}: contains the code relative to time-averaged  \item \textit{diags}: contains the code relative to time-averaged
250  diagnostics. It is subdivided into two subdirectories \textit{inc} and    diagnostics. It is subdivided into two subdirectories \textit{inc}
251  \textit{src} that contain include files (*.\textit{h} files) and fortran    and \textit{src} that contain include files (*.\textit{h} files) and
252  subroutines (*.\textit{F} files), respectively.    Fortran subroutines (*.\textit{F} files), respectively.
253    
254  \item \textit{doc}: contains brief documentation notes.  \item \textit{doc}: contains brief documentation notes.
255      
256  \item \textit{eesupp}: contains the execution environment source code. Also  \item \textit{eesupp}: contains the execution environment source code.
257  subdivided into two subdirectories \textit{inc} and \textit{src}.    Also subdivided into two subdirectories \textit{inc} and
258      \textit{src}.
259  \item \textit{exe}: this directory is initially empty. It is the default    
260  directory in which to execute the code.  \item \textit{exe}: this directory is initially empty. It is the
261      default directory in which to execute the code.
262  \item \textit{model}: this directory contains the main source code. Also    
263  subdivided into two subdirectories \textit{inc} and \textit{src}.  \item \textit{model}: this directory contains the main source code.
264      Also subdivided into two subdirectories \textit{inc} and
265  \item \textit{pkg}: contains the source code for the packages. Each package    \textit{src}.
266  corresponds to a subdirectory. For example, \textit{gmredi} contains the    
267  code related to the Gent-McWilliams/Redi scheme, \textit{aim} the code  \item \textit{pkg}: contains the source code for the packages. Each
268  relative to the atmospheric intermediate physics. The packages are described    package corresponds to a subdirectory. For example, \textit{gmredi}
269  in detail in section 3.    contains the code related to the Gent-McWilliams/Redi scheme,
270      \textit{aim} the code relative to the atmospheric intermediate
271  \item \textit{tools}: this directory contains various useful tools. For    physics. The packages are described in detail in section 3.
272  example, \textit{genmake} is a script written in csh (C-shell) that should    
273  be used to generate your makefile. The directory \textit{adjoint} contains  \item \textit{tools}: this directory contains various useful tools.
274  the makefile specific to the Tangent linear and Adjoint Compiler (TAMC) that    For example, \textit{genmake2} is a script written in csh (C-shell)
275  generates the adjoint code. The latter is described in details in part V.    that should be used to generate your makefile. The directory
276      \textit{adjoint} contains the makefile specific to the Tangent
277      linear and Adjoint Compiler (TAMC) that generates the adjoint code.
278      The latter is described in details in part V.
279      
280  \item \textit{utils}: this directory contains various utilities. The  \item \textit{utils}: this directory contains various utilities. The
281  subdirectory \textit{knudsen2} contains code and a makefile that    subdirectory \textit{knudsen2} contains code and a makefile that
282  compute coefficients of the polynomial approximation to the knudsen    compute coefficients of the polynomial approximation to the knudsen
283  formula for an ocean nonlinear equation of state. The \textit{matlab}    formula for an ocean nonlinear equation of state. The
284  subdirectory contains matlab scripts for reading model output directly    \textit{matlab} subdirectory contains matlab scripts for reading
285  into matlab. \textit{scripts} contains C-shell post-processing    model output directly into matlab. \textit{scripts} contains C-shell
286  scripts for joining processor-based and tiled-based model output.    post-processing scripts for joining processor-based and tiled-based
287      model output.
288      
289    \item \textit{verification}: this directory contains the model
290      examples. See section \ref{sect:modelExamples}.
291    
 \item \textit{verification}: this directory contains the model examples. See  
 section \ref{sect:modelExamples}.  
292  \end{itemize}  \end{itemize}
293    
294  \section{Example experiments}  \section{Example experiments}
295  \label{sect:modelExamples}  \label{sect:modelExamples}
296    
297  Now that you have successfully downloaded the model code we recommend that  %% a set of twenty-four pre-configured numerical experiments
 you first try to run the examples provided with the base version. You will  
 probably want to run the example that is the closest to the configuration  
 you will use eventually. The examples are located in subdirectories under  
 the directory \textit{verification} and are briefly described below (a full  
 description is given in section 2):  
298    
299  \subsection{List of model examples}  The MITgcm distribution comes with more than a dozen pre-configured
300    numerical experiments. Some of these example experiments are tests of
301    individual parts of the model code, but many are fully fledged
302    numerical simulations. A few of the examples are used for tutorial
303    documentation in sections \ref{sect:eg-baro} - \ref{sect:eg-global}.
304    The other examples follow the same general structure as the tutorial
305    examples. However, they only include brief instructions in a text file
306    called {\it README}.  The examples are located in subdirectories under
307    the directory \textit{verification}. Each example is briefly described
308    below.
309    
310  \begin{itemize}  \subsection{Full list of model examples}
 \item \textit{exp0} - single layer, ocean double gyre (barotropic with  
 free-surface).  
311    
312  \item \textit{exp1} - 4 layers, ocean double gyre.  \begin{enumerate}
313      
314    \item \textit{exp0} - single layer, ocean double gyre (barotropic with
315      free-surface). This experiment is described in detail in section
316      \ref{sect:eg-baro}.
317    
318    \item \textit{exp1} - Four layer, ocean double gyre. This experiment
319      is described in detail in section \ref{sect:eg-baroc}.
320      
321  \item \textit{exp2} - 4x4 degree global ocean simulation with steady  \item \textit{exp2} - 4x4 degree global ocean simulation with steady
322  climatological forcing.    climatological forcing. This experiment is described in detail in
323      section \ref{sect:eg-global}.
324      
325    \item \textit{exp4} - Flow over a Gaussian bump in open-water or
326      channel with open boundaries.
327      
328    \item \textit{exp5} - Inhomogenously forced ocean convection in a
329      doubly periodic box.
330    
331  \item \textit{exp4} - flow over a Gaussian bump in open-water or channel  \item \textit{front\_relax} - Relaxation of an ocean thermal front (test for
 with open boundaries.  
   
 \item \textit{exp5} - inhomogenously forced ocean convection in a doubly  
 periodic box.  
   
 \item \textit{front\_relax} - relaxation of an ocean thermal front (test for  
332  Gent/McWilliams scheme). 2D (Y-Z).  Gent/McWilliams scheme). 2D (Y-Z).
333    
334  \item \textit{internal wave} - ocean internal wave forced by open boundary  \item \textit{internal wave} - Ocean internal wave forced by open
335  conditions.    boundary conditions.
336      
337  \item \textit{natl\_box} - eastern subtropical North Atlantic with KPP  \item \textit{natl\_box} - Eastern subtropical North Atlantic with KPP
338  scheme; 1 month integration    scheme; 1 month integration
339      
340  \item \textit{hs94.1x64x5} - zonal averaged atmosphere using Held and Suarez  \item \textit{hs94.1x64x5} - Zonal averaged atmosphere using Held and
341  '94 forcing.    Suarez '94 forcing.
342      
343  \item \textit{hs94.128x64x5} - 3D atmosphere dynamics using Held and Suarez  \item \textit{hs94.128x64x5} - 3D atmosphere dynamics using Held and
344  '94 forcing.    Suarez '94 forcing.
345      
346  \item \textit{hs94.cs-32x32x5} - 3D atmosphere dynamics using Held and  \item \textit{hs94.cs-32x32x5} - 3D atmosphere dynamics using Held and
347  Suarez '94 forcing on the cubed sphere.    Suarez '94 forcing on the cubed sphere.
348      
349  \item \textit{aim.5l\_zon-ave} - Intermediate Atmospheric physics, 5 layers  \item \textit{aim.5l\_zon-ave} - Intermediate Atmospheric physics.
350  Molteni physics package. Global Zonal Mean configuration, 1x64x5 resolution.    Global Zonal Mean configuration, 1x64x5 resolution.
351      
352  \item \textit{aim.5l\_XZ\_Equatorial\_Slice} - Intermediate Atmospheric  \item \textit{aim.5l\_XZ\_Equatorial\_Slice} - Intermediate
353  physics, 5 layers Molteni physics package. Equatorial Slice configuration.    Atmospheric physics, equatorial Slice configuration.  2D (X-Z).
354  2D (X-Z).    
   
355  \item \textit{aim.5l\_Equatorial\_Channel} - Intermediate Atmospheric  \item \textit{aim.5l\_Equatorial\_Channel} - Intermediate Atmospheric
356  physics, 5 layers Molteni physics package. 3D Equatorial Channel    physics. 3D Equatorial Channel configuration.
357  configuration (not completely tested).    
358    \item \textit{aim.5l\_LatLon} - Intermediate Atmospheric physics.
359  \item \textit{aim.5l\_LatLon} - Intermediate Atmospheric physics, 5 layers    Global configuration, on latitude longitude grid with 128x64x5 grid
360  Molteni physics package. Global configuration, 128x64x5 resolution.    points ($2.8^\circ{\rm degree}$ resolution).
361      
362  \item \textit{adjustment.128x64x1}  \item \textit{adjustment.128x64x1} Barotropic adjustment problem on
363      latitude longitude grid with 128x64 grid points ($2.8^\circ{\rm
364        degree}$ resolution).
365      
366    \item \textit{adjustment.cs-32x32x1} Barotropic adjustment problem on
367      cube sphere grid with 32x32 points per face ( roughly $2.8^\circ{\rm
368        degree}$ resolution).
369      
370    \item \textit{advect\_cs} Two-dimensional passive advection test on
371      cube sphere grid.
372      
373    \item \textit{advect\_xy} Two-dimensional (horizontal plane) passive
374      advection test on Cartesian grid.
375      
376    \item \textit{advect\_yz} Two-dimensional (vertical plane) passive
377      advection test on Cartesian grid.
378      
379    \item \textit{carbon} Simple passive tracer experiment. Includes
380      derivative calculation. Described in detail in section
381      \ref{sect:eg-carbon-ad}.
382    
383    \item \textit{flt\_example} Example of using float package.
384      
385    \item \textit{global\_ocean.90x40x15} Global circulation with GM, flux
386      boundary conditions and poles.
387    
388    \item \textit{global\_ocean\_pressure} Global circulation in pressure
389      coordinate (non-Boussinesq ocean model). Described in detail in
390      section \ref{sect:eg-globalpressure}.
391      
392    \item \textit{solid-body.cs-32x32x1} Solid body rotation test for cube
393      sphere grid.
394    
395  \item \textit{adjustment.cs-32x32x1}  \end{enumerate}
 \end{itemize}  
396    
397  \subsection{Directory structure of model examples}  \subsection{Directory structure of model examples}
398    
# Line 247  Each example directory has the following Line 400  Each example directory has the following
400    
401  \begin{itemize}  \begin{itemize}
402  \item \textit{code}: contains the code particular to the example. At a  \item \textit{code}: contains the code particular to the example. At a
403  minimum, this directory includes the following files:    minimum, this directory includes the following files:
   
 \begin{itemize}  
 \item \textit{code/CPP\_EEOPTIONS.h}: declares CPP keys relative to the  
 ``execution environment'' part of the code. The default version is located  
 in \textit{eesupp/inc}.  
   
 \item \textit{code/CPP\_OPTIONS.h}: declares CPP keys relative to the  
 ``numerical model'' part of the code. The default version is located in  
 \textit{model/inc}.  
404    
405  \item \textit{code/SIZE.h}: declares size of underlying computational grid.    \begin{itemize}
406  The default version is located in \textit{model/inc}.    \item \textit{code/CPP\_EEOPTIONS.h}: declares CPP keys relative to
407        the ``execution environment'' part of the code. The default
408        version is located in \textit{eesupp/inc}.
409      
410      \item \textit{code/CPP\_OPTIONS.h}: declares CPP keys relative to
411        the ``numerical model'' part of the code. The default version is
412        located in \textit{model/inc}.
413      
414      \item \textit{code/SIZE.h}: declares size of underlying
415        computational grid.  The default version is located in
416        \textit{model/inc}.
417      \end{itemize}
418      
419      In addition, other include files and subroutines might be present in
420      \textit{code} depending on the particular experiment. See Section 2
421      for more details.
422      
423    \item \textit{input}: contains the input data files required to run
424      the example. At a minimum, the \textit{input} directory contains the
425      following files:
426    
427      \begin{itemize}
428      \item \textit{input/data}: this file, written as a namelist,
429        specifies the main parameters for the experiment.
430      
431      \item \textit{input/data.pkg}: contains parameters relative to the
432        packages used in the experiment.
433      
434      \item \textit{input/eedata}: this file contains ``execution
435        environment'' data. At present, this consists of a specification
436        of the number of threads to use in $X$ and $Y$ under multithreaded
437        execution.
438      \end{itemize}
439      
440      In addition, you will also find in this directory the forcing and
441      topography files as well as the files describing the initial state
442      of the experiment.  This varies from experiment to experiment. See
443      section 2 for more details.
444    
445    \item \textit{results}: this directory contains the output file
446      \textit{output.txt} produced by the simulation example. This file is
447      useful for comparison with your own output when you run the
448      experiment.
449  \end{itemize}  \end{itemize}
450    
451  In addition, other include files and subroutines might be present in \textit{%  Once you have chosen the example you want to run, you are ready to
452  code} depending on the particular experiment. See section 2 for more details.  compile the code.
   
 \item \textit{input}: contains the input data files required to run the  
 example. At a mimimum, the \textit{input} directory contains the following  
 files:  
   
 \begin{itemize}  
 \item \textit{input/data}: this file, written as a namelist, specifies the  
 main parameters for the experiment.  
   
 \item \textit{input/data.pkg}: contains parameters relative to the packages  
 used in the experiment.  
   
 \item \textit{input/eedata}: this file contains ``execution environment''  
 data. At present, this consists of a specification of the number of threads  
 to use in $X$ and $Y$ under multithreaded execution.  
 \end{itemize}  
   
 In addition, you will also find in this directory the forcing and topography  
 files as well as the files describing the initial state of the experiment.  
 This varies from experiment to experiment. See section 2 for more details.  
   
 \item \textit{results}: this directory contains the output file \textit{%  
 output.txt} produced by the simulation example. This file is useful for  
 comparison with your own output when you run the experiment.  
 \end{itemize}  
   
 Once you have chosen the example you want to run, you are ready to compile  
 the code.  
453    
454  \section{Building the code}  \section{Building the code}
455  \label{sect:buildingCode}  \label{sect:buildingCode}
# Line 299  the code. Line 457  the code.
457  To compile the code, we use the {\em make} program. This uses a file  To compile the code, we use the {\em make} program. This uses a file
458  ({\em Makefile}) that allows us to pre-process source files, specify  ({\em Makefile}) that allows us to pre-process source files, specify
459  compiler and optimization options and also figures out any file  compiler and optimization options and also figures out any file
460  dependancies. We supply a script ({\em genmake}), described in section  dependencies. We supply a script ({\em genmake2}), described in
461  \ref{sect:genmake}, that automatically creates the {\em Makefile} for  section \ref{sect:genmake}, that automatically creates the {\em
462  you. You then need to build the dependancies and compile the code.    Makefile} for you. You then need to build the dependencies and
463    compile the code.
464    
465  As an example, let's assume that you want to build and run experiment  As an example, let's assume that you want to build and run experiment
466  \textit{verification/exp2}. The are multiple ways and places to actually  \textit{verification/exp2}. The are multiple ways and places to
467  do this but here let's build the code in  actually do this but here let's build the code in
468  \textit{verification/exp2/input}:  \textit{verification/exp2/input}:
469  \begin{verbatim}  \begin{verbatim}
470  % cd verification/exp2/input  % cd verification/exp2/input
471  \end{verbatim}  \end{verbatim}
472  First, build the {\em Makefile}:  First, build the {\em Makefile}:
473  \begin{verbatim}  \begin{verbatim}
474  % ../../../tools/genmake -mods=../code  % ../../../tools/genmake2 -mods=../code
475  \end{verbatim}  \end{verbatim}
476  The command line option tells {\em genmake} to override model source  The command line option tells {\em genmake} to override model source
477  code with any files in the directory {\em ./code/}.  code with any files in the directory {\em ./code/}.
478    
479  If there is no \textit{.genmakerc} in the \textit{input} directory, you have  On many systems, the {\em genmake2} program will be able to
480  to use the following options when invoking \textit{genmake}:  automatically recognize the hardware, find compilers and other tools
481    within the user's path (``echo \$PATH''), and then choose an
482    appropriate set of options from the files contained in the {\em
483      tools/build\_options} directory.  Under some circumstances, a user
484    may have to create a new ``optfile'' in order to specify the exact
485    combination of compiler, compiler flags, libraries, and other options
486    necessary to build a particular configuration of MITgcm.  In such
487    cases, it is generally helpful to read the existing ``optfiles'' and
488    mimic their syntax.
489    
490    Through the MITgcm-support list, the MITgcm developers are willing to
491    provide help writing or modifing ``optfiles''.  And we encourage users
492    to post new ``optfiles'' (particularly ones for new machines or
493    architectures) to the
494    \begin{rawhtml} <A href=''mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}
495    MITgcm-support@mitgcm.org
496    \begin{rawhtml} </A> \end{rawhtml}
497    list.
498    
499    To specify an optfile to {\em genmake2}, the syntax is:
500  \begin{verbatim}  \begin{verbatim}
501  % ../../../tools/genmake  -mods=../code  % ../../../tools/genmake2 -mods=../code -of /path/to/optfile
502  \end{verbatim}  \end{verbatim}
503    
504  Next, create the dependancies:  Once a {\em Makefile} has been generated, we create the dependencies:
505  \begin{verbatim}  \begin{verbatim}
506  % make depend  % make depend
507  \end{verbatim}  \end{verbatim}
508  This modifies {\em Makefile} by attaching a [long] list of files on  This modifies the {\em Makefile} by attaching a [long] list of files
509  which other files depend. The purpose of this is to reduce  upon which other files depend. The purpose of this is to reduce
510  re-compilation if and when you start to modify the code. {\tt make  re-compilation if and when you start to modify the code. The {\tt make
511  depend} also created links from the model source to this directory.    depend} command also creates links from the model source to this
512    directory.
513    
514  Now compile the code:  Next compile the code:
515  \begin{verbatim}  \begin{verbatim}
516  % make  % make
517  \end{verbatim}  \end{verbatim}
518  The {\tt make} command creates an executable called \textit{mitgcmuv}.  The {\tt make} command creates an executable called \textit{mitgcmuv}.
519    Additional make ``targets'' are defined within the makefile to aid in
520    the production of adjoint and other versions of MITgcm.
521    
522  Now you are ready to run the model. General instructions for doing so are  Now you are ready to run the model. General instructions for doing so are
523  given in section \ref{sect:runModel}. Here, we can run the model with:  given in section \ref{sect:runModel}. Here, we can run the model with:
# Line 354  executable in the {\em input} directory Line 535  executable in the {\em input} directory
535  convenience. You can also configure and compile the code in other  convenience. You can also configure and compile the code in other
536  locations, for example on a scratch disk with out having to copy the  locations, for example on a scratch disk with out having to copy the
537  entire source tree. The only requirement to do so is you have {\tt  entire source tree. The only requirement to do so is you have {\tt
538  genmake} in your path or you know the absolute path to {\tt genmake}.    genmake2} in your path or you know the absolute path to {\tt
539      genmake2}.
540    
541  The following sections outline some possible methods of organizing you  The following sections outline some possible methods of organizing
542  source and data.  your source and data.
543    
544  \subsubsection{Building from the {\em ../code directory}}  \subsubsection{Building from the {\em ../code directory}}
545    
546  This is just as simple as building in the {\em input/} directory:  This is just as simple as building in the {\em input/} directory:
547  \begin{verbatim}  \begin{verbatim}
548  % cd verification/exp2/code  % cd verification/exp2/code
549  % ../../../tools/genmake  % ../../../tools/genmake2
550  % make depend  % make depend
551  % make  % make
552  \end{verbatim}  \end{verbatim}
# Line 375  files must be in the same place. If you Line 557  files must be in the same place. If you
557  % cp ../code/mitgcmuv ./  % cp ../code/mitgcmuv ./
558  % ./mitgcmuv > output.txt  % ./mitgcmuv > output.txt
559  \end{verbatim}  \end{verbatim}
560  or if you will be making muliple runs with the same executable:  or if you will be making multiple runs with the same executable:
561  \begin{verbatim}  \begin{verbatim}
562  % cd ../  % cd ../
563  % cp -r input run1  % cp -r input run1
# Line 387  or if you will be making muliple runs wi Line 569  or if you will be making muliple runs wi
569  \subsubsection{Building from a new directory}  \subsubsection{Building from a new directory}
570    
571  Since the {\em input} directory contains input files it is often more  Since the {\em input} directory contains input files it is often more
572  useful to keep {\em input} prestine and build in a new directory  useful to keep {\em input} pristine and build in a new directory
573  within {\em verification/exp2/}:  within {\em verification/exp2/}:
574  \begin{verbatim}  \begin{verbatim}
575  % cd verification/exp2  % cd verification/exp2
576  % mkdir build  % mkdir build
577  % cd build  % cd build
578  % ../../../tools/genmake -mods=../code  % ../../../tools/genmake2 -mods=../code
579  % make depend  % make depend
580  % make  % make
581  \end{verbatim}  \end{verbatim}
# Line 415  running in a new directory each time mig Line 597  running in a new directory each time mig
597  % ./mitgcmuv > output.txt  % ./mitgcmuv > output.txt
598  \end{verbatim}  \end{verbatim}
599    
600  \subsubsection{Building from on a scratch disk}  \subsubsection{Building on a scratch disk}
601    
602  Model object files and output data can use up large amounts of disk  Model object files and output data can use up large amounts of disk
603  space so it is often the case that you will be operating on a large  space so it is often the case that you will be operating on a large
# Line 423  scratch disk. Assuming the model source Line 605  scratch disk. Assuming the model source
605  following commands will build the model in {\em /scratch/exp2-run1}:  following commands will build the model in {\em /scratch/exp2-run1}:
606  \begin{verbatim}  \begin{verbatim}
607  % cd /scratch/exp2-run1  % cd /scratch/exp2-run1
608  % ~/MITgcm/tools/genmake -rootdir=~/MITgcm -mods=~/MITgcm/verification/exp2/code  % ~/MITgcm/tools/genmake2 -rootdir=~/MITgcm \
609      -mods=~/MITgcm/verification/exp2/code
610  % make depend  % make depend
611  % make  % make
612  \end{verbatim}  \end{verbatim}
# Line 439  the one experiment: Line 622  the one experiment:
622  % cd /scratch/exp2  % cd /scratch/exp2
623  % mkdir build  % mkdir build
624  % cd build  % cd build
625  % ~/MITgcm/tools/genmake -rootdir=~/MITgcm -mods=~/MITgcm/verification/exp2/code  % ~/MITgcm/tools/genmake2 -rootdir=~/MITgcm \
626      -mods=~/MITgcm/verification/exp2/code
627  % make depend  % make depend
628  % make  % make
629  % cd ../  % cd ../
# Line 450  the one experiment: Line 634  the one experiment:
634    
635    
636    
637  \subsection{\textit{genmake}}  \subsection{Using \textit{genmake2}}
638  \label{sect:genmake}  \label{sect:genmake}
639    
640  To compile the code, use the script \textit{genmake} located in the \textit{%  To compile the code, first use the program \texttt{genmake2} (located
641  tools} directory. \textit{genmake} is a script that generates the makefile.  in the \textit{tools} directory) to generate a Makefile.
642  It has been written so that the code can be compiled on a wide diversity of  \texttt{genmake2} is a shell script written to work with all
643  machines and systems. However, if it doesn't work the first time on your  ``sh''--compatible shells including bash v1, bash v2, and Bourne.
644  platform, you might need to edit certain lines of \textit{genmake} in the  Internally, \texttt{genmake2} determines the locations of needed
645  section containing the setups for the different machines. The file is  files, the compiler, compiler options, libraries, and Unix tools.  It
646  structured like this:  relies upon a number of ``optfiles'' located in the {\em
647  \begin{verbatim}    tools/build\_options} directory.
648          .  
649          .  The purpose of the optfiles is to provide all the compilation options
650          .  for particular ``platforms'' (where ``platform'' roughly means the
651  general instructions (machine independent)  combination of the hardware and the compiler) and code configurations.
652          .  Given the combinations of possible compilers and library dependencies
653          .  ({\it eg.}  MPI and NetCDF) there may be numerous optfiles available
654          .  for a single machine.  The naming scheme for the majority of the
655      - setup machine 1  optfiles shipped with the code is
656      - setup machine 2  \begin{center}
657      - setup machine 3    {\bf OS\_HARDWARE\_COMPILER }
658      - setup machine 4  \end{center}
659         etc  where
660          .  \begin{description}
661          .  \item[OS] is the name of the operating system (generally the
662          .    lower-case output of the {\tt 'uname'} command)
663  \end{verbatim}  \item[HARDWARE] is a string that describes the CPU type and
664      corresponds to output from the  {\tt 'uname -m'} command:
665  For example, the setup corresponding to a DEC alpha machine is reproduced    \begin{description}
666  here:    \item[ia32] is for ``x86'' machines such as i386, i486, i586, i686,
667  \begin{verbatim}      and athlon
668    case OSF1+mpi:    \item[ia64] is for Intel IA64 systems (eg. Itanium, Itanium2)
669      echo "Configuring for DEC Alpha"    \item[amd64] is AMD x86\_64 systems
670      set CPP        = ( '/usr/bin/cpp -P' )    \item[ppc] is for Mac PowerPC systems
671      set DEFINES    = ( ${DEFINES}  '-DTARGET_DEC -DWORDLENGTH=1' )    \end{description}
672      set KPP        = ( 'kapf' )  \item[COMPILER] is the compiler name (generally, the name of the
673      set KPPFILES   = ( 'main.F' )    FORTRAN executable)
674      set KFLAGS1    = ( '-scan=132 -noconc -cmp=' )  \end{description}
675      set FC         = ( 'f77' )  
676      set FFLAGS     = ( '-convert big_endian -r8 -extend_source -automatic -call_shared -notransform_loops -align dcommons' )  In many cases, the default optfiles are sufficient and will result in
677      set FOPTIM     = ( '-O5 -fast -tune host -inline all' )  usable Makefiles.  However, for some machines or code configurations,
678      set NOOPTFLAGS = ( '-O0' )  new ``optfiles'' must be written. To create a new optfile, it is
679      set LIBS       = ( '-lfmpi -lmpi -lkmp_osfp10 -pthread' )  generally best to start with one of the defaults and modify it to suit
680      set NOOPTFILES = ( 'barrier.F different_multiple.F external_fields_load.F')  your needs.  Like \texttt{genmake2}, the optfiles are all written
681      set RMFILES    = ( '*.p.out' )  using a simple ``sh''--compatible syntax.  While nearly all variables
682      breaksw  used within \texttt{genmake2} may be specified in the optfiles, the
683  \end{verbatim}  critical ones that should be defined are:
684    
685  Typically, these are the lines that you might need to edit to make \textit{%  \begin{description}
686  genmake} work on your platform if it doesn't work the first time. \textit{%  \item[FC] the FORTRAN compiler (executable) to use
687  genmake} understands several options that are described here:  \item[DEFINES] the command-line DEFINE options passed to the compiler
688    \item[CPP] the C pre-processor to use
689  \begin{itemize}  \item[NOOPTFLAGS] options flags for special files that should not be
690  \item -rootdir=dir    optimized
691    \end{description}
692  indicates where the model root directory is relative to the directory where  
693  you are compiling. This option is not needed if you compile in the \textit{%  For example, the optfile for a typical Red Hat Linux machine (``ia32''
694  bin} directory (which is the default compilation directory) or within the  architecture) using the GCC (g77) compiler is
695  \textit{verification} tree.  \begin{verbatim}
696    FC=g77
697  \item -mods=dir1,dir2,...  DEFINES='-D_BYTESWAPIO -DWORDLENGTH=4'
698    CPP='cpp  -traditional -P'
699  indicates the relative or absolute paths directories where the sources  NOOPTFLAGS='-O0'
700  should take precedence over the default versions (located in \textit{model},  #  For IEEE, use the "-ffloat-store" option
701  \textit{eesupp},...). Typically, this option is used when running the  if test "x$IEEE" = x ; then
702  examples, see below.      FFLAGS='-Wimplicit -Wunused -Wuninitialized'
703        FOPTIM='-O3 -malign-double -funroll-loops'
704  \item -enable=pkg1,pkg2,...  else
705        FFLAGS='-Wimplicit -Wunused -ffloat-store'
706  enables packages source code \textit{pkg1}, \textit{pkg2},... when creating      FOPTIM='-O0 -malign-double'
707  the makefile.  fi
708    \end{verbatim}
709  \item -disable=pkg1,pkg2,...  
710    If you write an optfile for an unrepresented machine or compiler, you
711  disables packages source code \textit{pkg1}, \textit{pkg2},... when creating  are strongly encouraged to submit the optfile to the MITgcm project
712  the makefile.  for inclusion.  Please send the file to the
713    \begin{rawhtml} <A href="mail-to:MITgcm-support@mitgcm.org"> \end{rawhtml}
714  \item -platform=machine  \begin{center}
715      MITgcm-support@mitgcm.org
716  specifies the platform for which you want the makefile. In general, you  \end{center}
717  won't need this option. \textit{genmake} will select the right machine for  \begin{rawhtml} </A> \end{rawhtml}
718  you (the one you're working on!). However, this option is useful if you have  mailing list.
 a choice of several compilers on one machine and you want to use the one  
 that is not the default (ex: \texttt{pgf77} instead of \texttt{f77} under  
 Linux).  
   
 \item -mpi  
   
 this is used when you want to run the model in parallel processing mode  
 under mpi (see section on parallel computation for more details).  
719    
720  \item -jam  In addition to the optfiles, \texttt{genmake2} supports a number of
721    helpful command-line options.  A complete list of these options can be
722    obtained from:
723    \begin{verbatim}
724    % genmake2 -h
725    \end{verbatim}
726    
727    The most important command-line options are:
728    \begin{description}
729      
730    \item[\texttt{--optfile=/PATH/FILENAME}] specifies the optfile that
731      should be used for a particular build.
732      
733      If no "optfile" is specified (either through the command line or the
734      MITGCM\_OPTFILE environment variable), genmake2 will try to make a
735      reasonable guess from the list provided in {\em
736        tools/build\_options}.  The method used for making this guess is
737      to first determine the combination of operating system and hardware
738      (eg. "linux\_ia32") and then find a working FORTRAN compiler within
739      the user's path.  When these three items have been identified,
740      genmake2 will try to find an optfile that has a matching name.
741      
742    \item[\texttt{--pdepend=/PATH/FILENAME}] specifies the dependency file
743      used for packages.
744      
745      If not specified, the default dependency file {\em pkg/pkg\_depend}
746      is used.  The syntax for this file is parsed on a line-by-line basis
747      where each line containes either a comment ("\#") or a simple
748      "PKGNAME1 (+|-)PKGNAME2" pairwise rule where the "+" or "-" symbol
749      specifies a "must be used with" or a "must not be used with"
750      relationship, respectively.  If no rule is specified, then it is
751      assumed that the two packages are compatible and will function
752      either with or without each other.
753      
754    \item[\texttt{--pdefault='PKG1 PKG2 PKG3 ...'}] specifies the default
755      set of packages to be used.
756      
757      If not set, the default package list will be read from {\em
758        pkg/pkg\_default}
759      
760    \item[\texttt{--adof=/path/to/file}] specifies the "adjoint" or
761      automatic differentiation options file to be used.  The file is
762      analogous to the ``optfile'' defined above but it specifies
763      information for the AD build process.
764      
765      The default file is located in {\em
766        tools/adjoint\_options/adjoint\_default} and it defines the "TAF"
767      and "TAMC" compilers.  An alternate version is also available at
768      {\em tools/adjoint\_options/adjoint\_staf} that selects the newer
769      "STAF" compiler.  As with any compilers, it is helpful to have their
770      directories listed in your {\tt \$PATH} environment variable.
771      
772    \item[\texttt{--mods='DIR1 DIR2 DIR3 ...'}] specifies a list of
773      directories containing ``modifications''.  These directories contain
774      files with names that may (or may not) exist in the main MITgcm
775      source tree but will be overridden by any identically-named sources
776      within the ``MODS'' directories.
777      
778      The order of precedence for this "name-hiding" is as follows:
779      \begin{itemize}
780      \item ``MODS'' directories (in the order given)
781      \item Packages either explicitly specified or provided by default
782        (in the order given)
783      \item Packages included due to package dependencies (in the order
784        that that package dependencies are parsed)
785      \item The "standard dirs" (which may have been specified by the
786        ``-standarddirs'' option)
787      \end{itemize}
788      
789    \item[\texttt{--make=/path/to/gmake}] Due to the poor handling of
790      soft-links and other bugs common with the \texttt{make} versions
791      provided by commercial Unix vendors, GNU \texttt{make} (sometimes
792      called \texttt{gmake}) should be preferred.  This option provides a
793      means for specifying the make executable to be used.
794    
795  this is used when you want to run the model in parallel processing mode  \end{description}
 under jam (see section on parallel computation for more details).  
 \end{itemize}  
796    
 For some of the examples, there is a file called \textit{.genmakerc} in the  
 \textit{input} directory that has the relevant \textit{genmake} options for  
 that particular example. In this way you don't need to type the options when  
 invoking \textit{genmake}.  
797    
798    
799  \section{Running the model}  \section{Running the model}
# Line 576  normally re-direct the {\em stdout} stre Line 819  normally re-direct the {\em stdout} stre
819  % ./mitgcmuv > output.txt  % ./mitgcmuv > output.txt
820  \end{verbatim}  \end{verbatim}
821    
822  For the example experiments in {\em vericication}, an example of the  For the example experiments in {\em verification}, an example of the
823  output is kept in {\em results/output.txt} for comparison. You can compare  output is kept in {\em results/output.txt} for comparison. You can compare
824  your {\em output.txt} with this one to check that the set-up works.  your {\em output.txt} with this one to check that the set-up works.
825    
# Line 665  Some examples of reading and visualizing Line 908  Some examples of reading and visualizing
908  \section{Doing it yourself: customizing the code}  \section{Doing it yourself: customizing the code}
909    
910  When you are ready to run the model in the configuration you want, the  When you are ready to run the model in the configuration you want, the
911  easiest thing is to use and adapt the setup of the case studies experiment  easiest thing is to use and adapt the setup of the case studies
912  (described previously) that is the closest to your configuration. Then, the  experiment (described previously) that is the closest to your
913  amount of setup will be minimized. In this section, we focus on the setup  configuration. Then, the amount of setup will be minimized. In this
914  relative to the ''numerical model'' part of the code (the setup relative to  section, we focus on the setup relative to the ``numerical model''
915  the ''execution environment'' part is covered in the parallel implementation  part of the code (the setup relative to the ``execution environment''
916  section) and on the variables and parameters that you are likely to change.  part is covered in the parallel implementation section) and on the
917    variables and parameters that you are likely to change.
918    
919  \subsection{Configuration and setup}  \subsection{Configuration and setup}
920    
921  The CPP keys relative to the ''numerical model'' part of the code are all  The CPP keys relative to the ``numerical model'' part of the code are
922  defined and set in the file \textit{CPP\_OPTIONS.h }in the directory \textit{%  all defined and set in the file \textit{CPP\_OPTIONS.h }in the
923  model/inc }or in one of the \textit{code }directories of the case study  directory \textit{ model/inc }or in one of the \textit{code
924  experiments under \textit{verification.} The model parameters are defined  }directories of the case study experiments under
925  and declared in the file \textit{model/inc/PARAMS.h }and their default  \textit{verification.} The model parameters are defined and declared
926  values are set in the routine \textit{model/src/set\_defaults.F. }The  in the file \textit{model/inc/PARAMS.h }and their default values are
927  default values can be modified in the namelist file \textit{data }which  set in the routine \textit{model/src/set\_defaults.F. }The default
928  needs to be located in the directory where you will run the model. The  values can be modified in the namelist file \textit{data }which needs
929  parameters are initialized in the routine \textit{model/src/ini\_parms.F}.  to be located in the directory where you will run the model. The
930  Look at this routine to see in what part of the namelist the parameters are  parameters are initialized in the routine
931  located.  \textit{model/src/ini\_parms.F}.  Look at this routine to see in what
932    part of the namelist the parameters are located.
933  In what follows the parameters are grouped into categories related to the  
934  computational domain, the equations solved in the model, and the simulation  In what follows the parameters are grouped into categories related to
935  controls.  the computational domain, the equations solved in the model, and the
936    simulation controls.
937    
938  \subsection{Computational domain, geometry and time-discretization}  \subsection{Computational domain, geometry and time-discretization}
939    
940  \begin{itemize}  \begin{description}
941  \item dimensions  \item[dimensions] \
942  \end{itemize}    
943      The number of points in the x, y, and r directions are represented
944  The number of points in the x, y,\textit{\ }and r\textit{\ }directions are    by the variables \textbf{sNx}, \textbf{sNy} and \textbf{Nr}
945  represented by the variables \textbf{sNx}\textit{, }\textbf{sNy}\textit{, }%    respectively which are declared and set in the file
946  and \textbf{Nr}\textit{\ }respectively which are declared and set in the    \textit{model/inc/SIZE.h}.  (Again, this assumes a mono-processor
947  file \textit{model/inc/SIZE.h. }(Again, this assumes a mono-processor    calculation. For multiprocessor calculations see the section on
948  calculation. For multiprocessor calculations see section on parallel    parallel implementation.)
949  implementation.)  
950    \item[grid] \
951  \begin{itemize}    
952  \item grid    Three different grids are available: cartesian, spherical polar, and
953  \end{itemize}    curvilinear (which includes the cubed sphere). The grid is set
954      through the logical variables \textbf{usingCartesianGrid},
955      \textbf{usingSphericalPolarGrid}, and \textbf{usingCurvilinearGrid}.
956      In the case of spherical and curvilinear grids, the southern
957      boundary is defined through the variable \textbf{phiMin} which
958      corresponds to the latitude of the southern most cell face (in
959      degrees). The resolution along the x and y directions is controlled
960      by the 1D arrays \textbf{delx} and \textbf{dely} (in meters in the
961      case of a cartesian grid, in degrees otherwise).  The vertical grid
962      spacing is set through the 1D array \textbf{delz} for the ocean (in
963      meters) or \textbf{delp} for the atmosphere (in Pa).  The variable
964      \textbf{Ro\_SeaLevel} represents the standard position of Sea-Level
965      in ``R'' coordinate. This is typically set to 0m for the ocean
966      (default value) and 10$^{5}$Pa for the atmosphere. For the
967      atmosphere, also set the logical variable \textbf{groundAtK1} to
968      \texttt{'.TRUE.'} which puts the first level (k=1) at the lower
969      boundary (ground).
970      
971      For the cartesian grid case, the Coriolis parameter $f$ is set
972      through the variables \textbf{f0} and \textbf{beta} which correspond
973      to the reference Coriolis parameter (in s$^{-1}$) and
974      $\frac{\partial f}{ \partial y}$(in m$^{-1}$s$^{-1}$) respectively.
975      If \textbf{beta } is set to a nonzero value, \textbf{f0} is the
976      value of $f$ at the southern edge of the domain.
977    
978    \item[topography - full and partial cells] \
979      
980      The domain bathymetry is read from a file that contains a 2D (x,y)
981      map of depths (in m) for the ocean or pressures (in Pa) for the
982      atmosphere. The file name is represented by the variable
983      \textbf{bathyFile}. The file is assumed to contain binary numbers
984      giving the depth (pressure) of the model at each grid cell, ordered
985      with the x coordinate varying fastest. The points are ordered from
986      low coordinate to high coordinate for both axes. The model code
987      applies without modification to enclosed, periodic, and double
988      periodic domains. Periodicity is assumed by default and is
989      suppressed by setting the depths to 0m for the cells at the limits
990      of the computational domain (note: not sure this is the case for the
991      atmosphere). The precision with which to read the binary data is
992      controlled by the integer variable \textbf{readBinaryPrec} which can
993      take the value \texttt{32} (single precision) or \texttt{64} (double
994      precision). See the matlab program \textit{gendata.m} in the
995      \textit{input} directories under \textit{verification} to see how
996      the bathymetry files are generated for the case study experiments.
997      
998      To use the partial cell capability, the variable \textbf{hFacMin}
999      needs to be set to a value between 0 and 1 (it is set to 1 by
1000      default) corresponding to the minimum fractional size of the cell.
1001      For example if the bottom cell is 500m thick and \textbf{hFacMin} is
1002      set to 0.1, the actual thickness of the cell (i.e. used in the code)
1003      can cover a range of discrete values 50m apart from 50m to 500m
1004      depending on the value of the bottom depth (in \textbf{bathyFile})
1005      at this point.
1006      
1007      Note that the bottom depths (or pressures) need not coincide with
1008      the models levels as deduced from \textbf{delz} or \textbf{delp}.
1009      The model will interpolate the numbers in \textbf{bathyFile} so that
1010      they match the levels obtained from \textbf{delz} or \textbf{delp}
1011      and \textbf{hFacMin}.
1012      
1013      (Note: the atmospheric case is a bit more complicated than what is
1014      written here I think. To come soon...)
1015    
1016    \item[time-discretization] \
1017      
1018      The time steps are set through the real variables \textbf{deltaTMom}
1019      and \textbf{deltaTtracer} (in s) which represent the time step for
1020      the momentum and tracer equations, respectively. For synchronous
1021      integrations, simply set the two variables to the same value (or you
1022      can prescribe one time step only through the variable
1023      \textbf{deltaT}). The Adams-Bashforth stabilizing parameter is set
1024      through the variable \textbf{abEps} (dimensionless). The stagger
1025      baroclinic time stepping can be activated by setting the logical
1026      variable \textbf{staggerTimeStep} to \texttt{'.TRUE.'}.
1027    
1028  Three different grids are available: cartesian, spherical polar, and  \end{description}
 curvilinear (including the cubed sphere). The grid is set through the  
 logical variables \textbf{usingCartesianGrid}\textit{, }\textbf{%  
 usingSphericalPolarGrid}\textit{, }and \textit{\ }\textbf{%  
 usingCurvilinearGrid}\textit{. }In the case of spherical and curvilinear  
 grids, the southern boundary is defined through the variable \textbf{phiMin}%  
 \textit{\ }which corresponds to the latitude of the southern most cell face  
 (in degrees). The resolution along the x and y directions is controlled by  
 the 1D arrays \textbf{delx}\textit{\ }and \textbf{dely}\textit{\ }(in meters  
 in the case of a cartesian grid, in degrees otherwise). The vertical grid  
 spacing is set through the 1D array \textbf{delz }for the ocean (in meters)  
 or \textbf{delp}\textit{\ }for the atmosphere (in Pa). The variable \textbf{%  
 Ro\_SeaLevel} represents the standard position of Sea-Level in ''R''  
 coordinate. This is typically set to 0m for the ocean (default value) and 10$%  
 ^{5}$Pa for the atmosphere. For the atmosphere, also set the logical  
 variable \textbf{groundAtK1} to '.\texttt{TRUE}.'. which put the first level  
 (k=1) at the lower boundary (ground).  
   
 For the cartesian grid case, the Coriolis parameter $f$ is set through the  
 variables \textbf{f0}\textit{\ }and \textbf{beta}\textit{\ }which correspond  
 to the reference Coriolis parameter (in s$^{-1}$) and $\frac{\partial f}{%  
 \partial y}$(in m$^{-1}$s$^{-1}$) respectively. If \textbf{beta }\textit{\ }%  
 is set to a nonzero value, \textbf{f0}\textit{\ }is the value of $f$ at the  
 southern edge of the domain.  
1029    
 \begin{itemize}  
 \item topography - full and partial cells  
 \end{itemize}  
   
 The domain bathymetry is read from a file that contains a 2D (x,y) map of  
 depths (in m) for the ocean or pressures (in Pa) for the atmosphere. The  
 file name is represented by the variable \textbf{bathyFile}\textit{. }The  
 file is assumed to contain binary numbers giving the depth (pressure) of the  
 model at each grid cell, ordered with the x coordinate varying fastest. The  
 points are ordered from low coordinate to high coordinate for both axes. The  
 model code applies without modification to enclosed, periodic, and double  
 periodic domains. Periodicity is assumed by default and is suppressed by  
 setting the depths to 0m for the cells at the limits of the computational  
 domain (note: not sure this is the case for the atmosphere). The precision  
 with which to read the binary data is controlled by the integer variable  
 \textbf{readBinaryPrec }which can take the value \texttt{32} (single  
 precision) or \texttt{64} (double precision). See the matlab program \textit{%  
 gendata.m }in the \textit{input }directories under \textit{verification }to  
 see how the bathymetry files are generated for the case study experiments.  
   
 To use the partial cell capability, the variable \textbf{hFacMin}\textit{\ }%  
 needs to be set to a value between 0 and 1 (it is set to 1 by default)  
 corresponding to the minimum fractional size of the cell. For example if the  
 bottom cell is 500m thick and \textbf{hFacMin}\textit{\ }is set to 0.1, the  
 actual thickness of the cell (i.e. used in the code) can cover a range of  
 discrete values 50m apart from 50m to 500m depending on the value of the  
 bottom depth (in \textbf{bathyFile}) at this point.  
   
 Note that the bottom depths (or pressures) need not coincide with the models  
 levels as deduced from \textbf{delz}\textit{\ }or\textit{\ }\textbf{delp}%  
 \textit{. }The model will interpolate the numbers in \textbf{bathyFile}%  
 \textit{\ }so that they match the levels obtained from \textbf{delz}\textit{%  
 \ }or\textit{\ }\textbf{delp}\textit{\ }and \textbf{hFacMin}\textit{. }  
   
 (Note: the atmospheric case is a bit more complicated than what is written  
 here I think. To come soon...)  
   
 \begin{itemize}  
 \item time-discretization  
 \end{itemize}  
   
 The time steps are set through the real variables \textbf{deltaTMom }and  
 \textbf{deltaTtracer }(in s) which represent the time step for the momentum  
 and tracer equations, respectively. For synchronous integrations, simply set  
 the two variables to the same value (or you can prescribe one time step only  
 through the variable \textbf{deltaT}). The Adams-Bashforth stabilizing  
 parameter is set through the variable \textbf{abEps }(dimensionless). The  
 stagger baroclinic time stepping can be activated by setting the logical  
 variable \textbf{staggerTimeStep }to '.\texttt{TRUE}.'.  
1030    
1031  \subsection{Equation of state}  \subsection{Equation of state}
1032    
1033  First, because the model equations are written in terms of perturbations, a  First, because the model equations are written in terms of
1034  reference thermodynamic state needs to be specified. This is done through  perturbations, a reference thermodynamic state needs to be specified.
1035  the 1D arrays \textbf{tRef}\textit{\ }and \textbf{sRef}. \textbf{tRef }%  This is done through the 1D arrays \textbf{tRef} and \textbf{sRef}.
1036  specifies the reference potential temperature profile (in $^{o}$C for  \textbf{tRef} specifies the reference potential temperature profile
1037  the ocean and $^{o}$K for the atmosphere) starting from the level  (in $^{o}$C for the ocean and $^{o}$K for the atmosphere) starting
1038  k=1. Similarly, \textbf{sRef}\textit{\ }specifies the reference salinity  from the level k=1. Similarly, \textbf{sRef} specifies the reference
1039  profile (in ppt) for the ocean or the reference specific humidity profile  salinity profile (in ppt) for the ocean or the reference specific
1040  (in g/kg) for the atmosphere.  humidity profile (in g/kg) for the atmosphere.
1041    
1042  The form of the equation of state is controlled by the character variables  The form of the equation of state is controlled by the character
1043  \textbf{buoyancyRelation}\textit{\ }and \textbf{eosType}\textit{. }\textbf{%  variables \textbf{buoyancyRelation} and \textbf{eosType}.
1044  buoyancyRelation}\textit{\ }is set to '\texttt{OCEANIC}' by default and  \textbf{buoyancyRelation} is set to \texttt{'OCEANIC'} by default and
1045  needs to be set to '\texttt{ATMOSPHERIC}' for atmosphere simulations. In  needs to be set to \texttt{'ATMOSPHERIC'} for atmosphere simulations.
1046  this case, \textbf{eosType}\textit{\ }must be set to '\texttt{IDEALGAS}'.  In this case, \textbf{eosType} must be set to \texttt{'IDEALGAS'}.
1047  For the ocean, two forms of the equation of state are available: linear (set  For the ocean, two forms of the equation of state are available:
1048  \textbf{eosType}\textit{\ }to '\texttt{LINEAR}') and a polynomial  linear (set \textbf{eosType} to \texttt{'LINEAR'}) and a polynomial
1049  approximation to the full nonlinear equation ( set \textbf{eosType}\textit{\  approximation to the full nonlinear equation ( set \textbf{eosType} to
1050  }to '\texttt{POLYNOMIAL}'). In the linear case, you need to specify the  \texttt{'POLYNOMIAL'}). In the linear case, you need to specify the
1051  thermal and haline expansion coefficients represented by the variables  thermal and haline expansion coefficients represented by the variables
1052  \textbf{tAlpha}\textit{\ }(in K$^{-1}$) and \textbf{sBeta}\textit{\ }(in ppt$%  \textbf{tAlpha} (in K$^{-1}$) and \textbf{sBeta} (in ppt$^{-1}$). For
1053  ^{-1}$). For the nonlinear case, you need to generate a file of polynomial  the nonlinear case, you need to generate a file of polynomial
1054  coefficients called \textit{POLY3.COEFFS. }To do this, use the program  coefficients called \textit{POLY3.COEFFS}. To do this, use the program
1055  \textit{utils/knudsen2/knudsen2.f }under the model tree (a Makefile is  \textit{utils/knudsen2/knudsen2.f} under the model tree (a Makefile is
1056  available in the same directory and you will need to edit the number and the  available in the same directory and you will need to edit the number
1057  values of the vertical levels in \textit{knudsen2.f }so that they match  and the values of the vertical levels in \textit{knudsen2.f} so that
1058  those of your configuration). \textit{\ }  they match those of your configuration).
1059    
1060    There there are also higher polynomials for the equation of state:
1061    \begin{description}
1062    \item[\texttt{'UNESCO'}:] The UNESCO equation of state formula of
1063      Fofonoff and Millard \cite{fofonoff83}. This equation of state
1064      assumes in-situ temperature, which is not a model variable; {\em its
1065        use is therefore discouraged, and it is only listed for
1066        completeness}.
1067    \item[\texttt{'JMD95Z'}:] A modified UNESCO formula by Jackett and
1068      McDougall \cite{jackett95}, which uses the model variable potential
1069      temperature as input. The \texttt{'Z'} indicates that this equation
1070      of state uses a horizontally and temporally constant pressure
1071      $p_{0}=-g\rho_{0}z$.
1072    \item[\texttt{'JMD95P'}:] A modified UNESCO formula by Jackett and
1073      McDougall \cite{jackett95}, which uses the model variable potential
1074      temperature as input. The \texttt{'P'} indicates that this equation
1075      of state uses the actual hydrostatic pressure of the last time
1076      step. Lagging the pressure in this way requires an additional pickup
1077      file for restarts.
1078    \item[\texttt{'MDJWF'}:] The new, more accurate and less expensive
1079      equation of state by McDougall et~al. \cite{mcdougall03}. It also
1080      requires lagging the pressure and therefore an additional pickup
1081      file for restarts.
1082    \end{description}
1083    For none of these options an reference profile of temperature or
1084    salinity is required.
1085    
1086  \subsection{Momentum equations}  \subsection{Momentum equations}
1087    
1088  In this section, we only focus for now on the parameters that you are likely  In this section, we only focus for now on the parameters that you are
1089  to change, i.e. the ones relative to forcing and dissipation for example.  likely to change, i.e. the ones relative to forcing and dissipation
1090  The details relevant to the vector-invariant form of the equations and the  for example.  The details relevant to the vector-invariant form of the
1091  various advection schemes are not covered for the moment. We assume that you  equations and the various advection schemes are not covered for the
1092  use the standard form of the momentum equations (i.e. the flux-form) with  moment. We assume that you use the standard form of the momentum
1093  the default advection scheme. Also, there are a few logical variables that  equations (i.e. the flux-form) with the default advection scheme.
1094  allow you to turn on/off various terms in the momentum equation. These  Also, there are a few logical variables that allow you to turn on/off
1095  variables are called \textbf{momViscosity, momAdvection, momForcing,  various terms in the momentum equation. These variables are called
1096  useCoriolis, momPressureForcing, momStepping}\textit{, }and \textit{\ }%  \textbf{momViscosity, momAdvection, momForcing, useCoriolis,
1097  \textbf{metricTerms }and are assumed to be set to '.\texttt{TRUE}.' here.    momPressureForcing, momStepping} and \textbf{metricTerms }and are
1098  Look at the file \textit{model/inc/PARAMS.h }for a precise definition of  assumed to be set to \texttt{'.TRUE.'} here.  Look at the file
1099  these variables.  \textit{model/inc/PARAMS.h }for a precise definition of these
1100    variables.
1101    
1102    \begin{description}
1103    \item[initialization] \
1104      
1105      The velocity components are initialized to 0 unless the simulation
1106      is starting from a pickup file (see section on simulation control
1107      parameters).
1108    
1109    \item[forcing] \
1110      
1111      This section only applies to the ocean. You need to generate
1112      wind-stress data into two files \textbf{zonalWindFile} and
1113      \textbf{meridWindFile} corresponding to the zonal and meridional
1114      components of the wind stress, respectively (if you want the stress
1115      to be along the direction of only one of the model horizontal axes,
1116      you only need to generate one file). The format of the files is
1117      similar to the bathymetry file. The zonal (meridional) stress data
1118      are assumed to be in Pa and located at U-points (V-points). As for
1119      the bathymetry, the precision with which to read the binary data is
1120      controlled by the variable \textbf{readBinaryPrec}.  See the matlab
1121      program \textit{gendata.m} in the \textit{input} directories under
1122      \textit{verification} to see how simple analytical wind forcing data
1123      are generated for the case study experiments.
1124      
1125      There is also the possibility of prescribing time-dependent periodic
1126      forcing. To do this, concatenate the successive time records into a
1127      single file (for each stress component) ordered in a (x,y,t) fashion
1128      and set the following variables: \textbf{periodicExternalForcing }to
1129      \texttt{'.TRUE.'}, \textbf{externForcingPeriod }to the period (in s)
1130      of which the forcing varies (typically 1 month), and
1131      \textbf{externForcingCycle} to the repeat time (in s) of the forcing
1132      (typically 1 year -- note: \textbf{ externForcingCycle} must be a
1133      multiple of \textbf{externForcingPeriod}).  With these variables set
1134      up, the model will interpolate the forcing linearly at each
1135      iteration.
1136    
1137    \item[dissipation] \
1138      
1139      The lateral eddy viscosity coefficient is specified through the
1140      variable \textbf{viscAh} (in m$^{2}$s$^{-1}$). The vertical eddy
1141      viscosity coefficient is specified through the variable
1142      \textbf{viscAz} (in m$^{2}$s$^{-1}$) for the ocean and
1143      \textbf{viscAp} (in Pa$^{2}$s$^{-1}$) for the atmosphere.  The
1144      vertical diffusive fluxes can be computed implicitly by setting the
1145      logical variable \textbf{implicitViscosity }to \texttt{'.TRUE.'}.
1146      In addition, biharmonic mixing can be added as well through the
1147      variable \textbf{viscA4} (in m$^{4}$s$^{-1}$). On a spherical polar
1148      grid, you might also need to set the variable \textbf{cosPower}
1149      which is set to 0 by default and which represents the power of
1150      cosine of latitude to multiply viscosity. Slip or no-slip conditions
1151      at lateral and bottom boundaries are specified through the logical
1152      variables \textbf{no\_slip\_sides} and \textbf{no\_slip\_bottom}. If
1153      set to \texttt{'.FALSE.'}, free-slip boundary conditions are
1154      applied. If no-slip boundary conditions are applied at the bottom, a
1155      bottom drag can be applied as well. Two forms are available: linear
1156      (set the variable \textbf{bottomDragLinear} in s$ ^{-1}$) and
1157      quadratic (set the variable \textbf{bottomDragQuadratic} in
1158      m$^{-1}$).
1159    
1160      The Fourier and Shapiro filters are described elsewhere.
1161    
1162    \item[C-D scheme] \
1163      
1164      If you run at a sufficiently coarse resolution, you will need the
1165      C-D scheme for the computation of the Coriolis terms. The
1166      variable\textbf{\ tauCD}, which represents the C-D scheme coupling
1167      timescale (in s) needs to be set.
1168      
1169    \item[calculation of pressure/geopotential] \
1170      
1171      First, to run a non-hydrostatic ocean simulation, set the logical
1172      variable \textbf{nonHydrostatic} to \texttt{'.TRUE.'}. The pressure
1173      field is then inverted through a 3D elliptic equation. (Note: this
1174      capability is not available for the atmosphere yet.) By default, a
1175      hydrostatic simulation is assumed and a 2D elliptic equation is used
1176      to invert the pressure field. The parameters controlling the
1177      behaviour of the elliptic solvers are the variables
1178      \textbf{cg2dMaxIters} and \textbf{cg2dTargetResidual } for
1179      the 2D case and \textbf{cg3dMaxIters} and
1180      \textbf{cg3dTargetResidual} for the 3D case. You probably won't need to
1181      alter the default values (are we sure of this?).
1182      
1183      For the calculation of the surface pressure (for the ocean) or
1184      surface geopotential (for the atmosphere) you need to set the
1185      logical variables \textbf{rigidLid} and \textbf{implicitFreeSurface}
1186      (set one to \texttt{'.TRUE.'} and the other to \texttt{'.FALSE.'}
1187      depending on how you want to deal with the ocean upper or atmosphere
1188      lower boundary).
1189    
1190  \begin{itemize}  \end{description}
 \item initialization  
 \end{itemize}  
   
 The velocity components are initialized to 0 unless the simulation is  
 starting from a pickup file (see section on simulation control parameters).  
   
 \begin{itemize}  
 \item forcing  
 \end{itemize}  
   
 This section only applies to the ocean. You need to generate wind-stress  
 data into two files \textbf{zonalWindFile}\textit{\ }and \textbf{%  
 meridWindFile }corresponding to the zonal and meridional components of the  
 wind stress, respectively (if you want the stress to be along the direction  
 of only one of the model horizontal axes, you only need to generate one  
 file). The format of the files is similar to the bathymetry file. The zonal  
 (meridional) stress data are assumed to be in Pa and located at U-points  
 (V-points). As for the bathymetry, the precision with which to read the  
 binary data is controlled by the variable \textbf{readBinaryPrec}.\textbf{\ }  
 See the matlab program \textit{gendata.m }in the \textit{input }directories  
 under \textit{verification }to see how simple analytical wind forcing data  
 are generated for the case study experiments.  
   
 There is also the possibility of prescribing time-dependent periodic  
 forcing. To do this, concatenate the successive time records into a single  
 file (for each stress component) ordered in a (x, y, t) fashion and set the  
 following variables: \textbf{periodicExternalForcing }to '.\texttt{TRUE}.',  
 \textbf{externForcingPeriod }to the period (in s) of which the forcing  
 varies (typically 1 month), and \textbf{externForcingCycle }to the repeat  
 time (in s) of the forcing (typically 1 year -- note: \textbf{%  
 externForcingCycle }must be a multiple of \textbf{externForcingPeriod}).  
 With these variables set up, the model will interpolate the forcing linearly  
 at each iteration.  
   
 \begin{itemize}  
 \item dissipation  
 \end{itemize}  
   
 The lateral eddy viscosity coefficient is specified through the variable  
 \textbf{viscAh}\textit{\ }(in m$^{2}$s$^{-1}$). The vertical eddy viscosity  
 coefficient is specified through the variable \textbf{viscAz }(in m$^{2}$s$%  
 ^{-1}$) for the ocean and \textbf{viscAp}\textit{\ }(in Pa$^{2}$s$^{-1}$)  
 for the atmosphere. The vertical diffusive fluxes can be computed implicitly  
 by setting the logical variable \textbf{implicitViscosity }to '.\texttt{TRUE}%  
 .'. In addition, biharmonic mixing can be added as well through the variable  
 \textbf{viscA4}\textit{\ }(in m$^{4}$s$^{-1}$). On a spherical polar grid,  
 you might also need to set the variable \textbf{cosPower} which is set to 0  
 by default and which represents the power of cosine of latitude to multiply  
 viscosity. Slip or no-slip conditions at lateral and bottom boundaries are  
 specified through the logical variables \textbf{no\_slip\_sides}\textit{\ }%  
 and \textbf{no\_slip\_bottom}. If set to '\texttt{.FALSE.}', free-slip  
 boundary conditions are applied. If no-slip boundary conditions are applied  
 at the bottom, a bottom drag can be applied as well. Two forms are  
 available: linear (set the variable \textbf{bottomDragLinear}\textit{\ }in s$%  
 ^{-1}$) and quadratic (set the variable \textbf{bottomDragQuadratic}\textit{%  
 \ }in m$^{-1}$).  
   
 The Fourier and Shapiro filters are described elsewhere.  
   
 \begin{itemize}  
 \item C-D scheme  
 \end{itemize}  
   
 If you run at a sufficiently coarse resolution, you will need the C-D scheme  
 for the computation of the Coriolis terms. The variable\textbf{\ tauCD},  
 which represents the C-D scheme coupling timescale (in s) needs to be set.  
   
 \begin{itemize}  
 \item calculation of pressure/geopotential  
 \end{itemize}  
   
 First, to run a non-hydrostatic ocean simulation, set the logical variable  
 \textbf{nonHydrostatic} to '.\texttt{TRUE}.'. The pressure field is then  
 inverted through a 3D elliptic equation. (Note: this capability is not  
 available for the atmosphere yet.) By default, a hydrostatic simulation is  
 assumed and a 2D elliptic equation is used to invert the pressure field. The  
 parameters controlling the behaviour of the elliptic solvers are the  
 variables \textbf{cg2dMaxIters}\textit{\ }and \textbf{cg2dTargetResidual }%  
 for the 2D case and \textbf{cg3dMaxIters}\textit{\ }and \textbf{%  
 cg3dTargetResidual }for the 3D case. You probably won't need to alter the  
 default values (are we sure of this?).  
   
 For the calculation of the surface pressure (for the ocean) or surface  
 geopotential (for the atmosphere) you need to set the logical variables  
 \textbf{rigidLid} and \textbf{implicitFreeSurface}\textit{\ }(set one to '.%  
 \texttt{TRUE}.' and the other to '.\texttt{FALSE}.' depending on how you  
 want to deal with the ocean upper or atmosphere lower boundary).  
1191    
1192  \subsection{Tracer equations}  \subsection{Tracer equations}
1193    
1194  This section covers the tracer equations i.e. the potential temperature  This section covers the tracer equations i.e. the potential
1195  equation and the salinity (for the ocean) or specific humidity (for the  temperature equation and the salinity (for the ocean) or specific
1196  atmosphere) equation. As for the momentum equations, we only describe for  humidity (for the atmosphere) equation. As for the momentum equations,
1197  now the parameters that you are likely to change. The logical variables  we only describe for now the parameters that you are likely to change.
1198  \textbf{tempDiffusion}\textit{, }\textbf{tempAdvection}\textit{, }\textbf{%  The logical variables \textbf{tempDiffusion} \textbf{tempAdvection}
1199  tempForcing}\textit{,} and \textbf{tempStepping} allow you to turn on/off  \textbf{tempForcing}, and \textbf{tempStepping} allow you to turn
1200  terms in the temperature equation (same thing for salinity or specific  on/off terms in the temperature equation (same thing for salinity or
1201  humidity with variables \textbf{saltDiffusion}\textit{, }\textbf{%  specific humidity with variables \textbf{saltDiffusion},
1202  saltAdvection}\textit{\ }etc). These variables are all assumed here to be  \textbf{saltAdvection} etc.). These variables are all assumed here to
1203  set to '.\texttt{TRUE}.'. Look at file \textit{model/inc/PARAMS.h }for a  be set to \texttt{'.TRUE.'}. Look at file \textit{model/inc/PARAMS.h}
1204  precise definition.  for a precise definition.
1205    
1206  \begin{itemize}  \begin{description}
1207  \item initialization  \item[initialization] \
1208  \end{itemize}    
1209      The initial tracer data can be contained in the binary files
1210  The initial tracer data can be contained in the binary files \textbf{%    \textbf{hydrogThetaFile} and \textbf{hydrogSaltFile}. These files
1211  hydrogThetaFile }and \textbf{hydrogSaltFile}. These files should contain 3D    should contain 3D data ordered in an (x,y,r) fashion with k=1 as the
1212  data ordered in an (x, y, r) fashion with k=1 as the first vertical level.    first vertical level.  If no file names are provided, the tracers
1213  If no file names are provided, the tracers are then initialized with the    are then initialized with the values of \textbf{tRef} and
1214  values of \textbf{tRef }and \textbf{sRef }mentioned above (in the equation    \textbf{sRef} mentioned above (in the equation of state section). In
1215  of state section). In this case, the initial tracer data are uniform in x    this case, the initial tracer data are uniform in x and y for each
1216  and y for each depth level.    depth level.
1217    
1218  \begin{itemize}  \item[forcing] \
1219  \item forcing    
1220  \end{itemize}    This part is more relevant for the ocean, the procedure for the
1221      atmosphere not being completely stabilized at the moment.
1222  This part is more relevant for the ocean, the procedure for the atmosphere    
1223  not being completely stabilized at the moment.    A combination of fluxes data and relaxation terms can be used for
1224      driving the tracer equations.  For potential temperature, heat flux
1225  A combination of fluxes data and relaxation terms can be used for driving    data (in W/m$ ^{2}$) can be stored in the 2D binary file
1226  the tracer equations. \ For potential temperature, heat flux data (in W/m$%    \textbf{surfQfile}.  Alternatively or in addition, the forcing can
1227  ^{2}$) can be stored in the 2D binary file \textbf{surfQfile}\textit{. }%    be specified through a relaxation term. The SST data to which the
1228  Alternatively or in addition, the forcing can be specified through a    model surface temperatures are restored to are supposed to be stored
1229  relaxation term. The SST data to which the model surface temperatures are    in the 2D binary file \textbf{thetaClimFile}. The corresponding
1230  restored to are supposed to be stored in the 2D binary file \textbf{%    relaxation time scale coefficient is set through the variable
1231  thetaClimFile}\textit{. }The corresponding relaxation time scale coefficient    \textbf{tauThetaClimRelax} (in s). The same procedure applies for
1232  is set through the variable \textbf{tauThetaClimRelax}\textit{\ }(in s). The    salinity with the variable names \textbf{EmPmRfile},
1233  same procedure applies for salinity with the variable names \textbf{EmPmRfile%    \textbf{saltClimFile}, and \textbf{tauSaltClimRelax} for freshwater
1234  }\textit{, }\textbf{saltClimFile}\textit{, }and \textbf{tauSaltClimRelax}%    flux (in m/s) and surface salinity (in ppt) data files and
1235  \textit{\ }for freshwater flux (in m/s) and surface salinity (in ppt) data    relaxation time scale coefficient (in s), respectively. Also for
1236  files and relaxation time scale coefficient (in s), respectively. Also for    salinity, if the CPP key \textbf{USE\_NATURAL\_BCS} is turned on,
1237  salinity, if the CPP key \textbf{USE\_NATURAL\_BCS} is turned on, natural    natural boundary conditions are applied i.e. when computing the
1238  boundary conditions are applied i.e. when computing the surface salinity    surface salinity tendency, the freshwater flux is multiplied by the
1239  tendency, the freshwater flux is multiplied by the model surface salinity    model surface salinity instead of a constant salinity value.
1240  instead of a constant salinity value.    
1241      As for the other input files, the precision with which to read the
1242  As for the other input files, the precision with which to read the data is    data is controlled by the variable \textbf{readBinaryPrec}.
1243  controlled by the variable \textbf{readBinaryPrec}. Time-dependent, periodic    Time-dependent, periodic forcing can be applied as well following
1244  forcing can be applied as well following the same procedure used for the    the same procedure used for the wind forcing data (see above).
1245  wind forcing data (see above).  
1246    \item[dissipation] \
1247      
1248      Lateral eddy diffusivities for temperature and salinity/specific
1249      humidity are specified through the variables \textbf{diffKhT} and
1250      \textbf{diffKhS} (in m$^{2}$/s). Vertical eddy diffusivities are
1251      specified through the variables \textbf{diffKzT} and
1252      \textbf{diffKzS} (in m$^{2}$/s) for the ocean and \textbf{diffKpT
1253      }and \textbf{diffKpS} (in Pa$^{2}$/s) for the atmosphere. The
1254      vertical diffusive fluxes can be computed implicitly by setting the
1255      logical variable \textbf{implicitDiffusion} to \texttt{'.TRUE.'}.
1256      In addition, biharmonic diffusivities can be specified as well
1257      through the coefficients \textbf{diffK4T} and \textbf{diffK4S} (in
1258      m$^{4}$/s). Note that the cosine power scaling (specified through
1259      \textbf{cosPower}---see the momentum equations section) is applied to
1260      the tracer diffusivities (Laplacian and biharmonic) as well. The
1261      Gent and McWilliams parameterization for oceanic tracers is
1262      described in the package section. Finally, note that tracers can be
1263      also subject to Fourier and Shapiro filtering (see the corresponding
1264      section on these filters).
1265    
1266    \item[ocean convection] \
1267      
1268      Two options are available to parameterize ocean convection: one is
1269      to use the convective adjustment scheme. In this case, you need to
1270      set the variable \textbf{cadjFreq}, which represents the frequency
1271      (in s) with which the adjustment algorithm is called, to a non-zero
1272      value (if set to a negative value by the user, the model will set it
1273      to the tracer time step). The other option is to parameterize
1274      convection with implicit vertical diffusion. To do this, set the
1275      logical variable \textbf{implicitDiffusion} to \texttt{'.TRUE.'}
1276      and the real variable \textbf{ivdc\_kappa} to a value (in m$^{2}$/s)
1277      you wish the tracer vertical diffusivities to have when mixing
1278      tracers vertically due to static instabilities. Note that
1279      \textbf{cadjFreq} and \textbf{ivdc\_kappa}can not both have non-zero
1280      value.
1281    
1282  \begin{itemize}  \end{description}
 \item dissipation  
 \end{itemize}  
   
 Lateral eddy diffusivities for temperature and salinity/specific humidity  
 are specified through the variables \textbf{diffKhT }and \textbf{diffKhS }%  
 (in m$^{2}$/s). Vertical eddy diffusivities are specified through the  
 variables \textbf{diffKzT }and \textbf{diffKzS }(in m$^{2}$/s) for the ocean  
 and \textbf{diffKpT }and \textbf{diffKpS }(in Pa$^{2}$/s) for the  
 atmosphere. The vertical diffusive fluxes can be computed implicitly by  
 setting the logical variable \textbf{implicitDiffusion }to '.\texttt{TRUE}%  
 .'. In addition, biharmonic diffusivities can be specified as well through  
 the coefficients \textbf{diffK4T }and \textbf{diffK4S }(in m$^{4}$/s). Note  
 that the cosine power scaling (specified through \textbf{cosPower }- see the  
 momentum equations section) is applied to the tracer diffusivities  
 (Laplacian and biharmonic) as well. The Gent and McWilliams parameterization  
 for oceanic tracers is described in the package section. Finally, note that  
 tracers can be also subject to Fourier and Shapiro filtering (see the  
 corresponding section on these filters).  
   
 \begin{itemize}  
 \item ocean convection  
 \end{itemize}  
   
 Two options are available to parameterize ocean convection: one is to use  
 the convective adjustment scheme. In this case, you need to set the variable  
 \textbf{cadjFreq}, which represents the frequency (in s) with which the  
 adjustment algorithm is called, to a non-zero value (if set to a negative  
 value by the user, the model will set it to the tracer time step). The other  
 option is to parameterize convection with implicit vertical diffusion. To do  
 this, set the logical variable \textbf{implicitDiffusion }to '.\texttt{TRUE}%  
 .' and the real variable \textbf{ivdc\_kappa }to a value (in m$^{2}$/s) you  
 wish the tracer vertical diffusivities to have when mixing tracers  
 vertically due to static instabilities. Note that \textbf{cadjFreq }and  
 \textbf{ivdc\_kappa }can not both have non-zero value.  
1283    
1284  \subsection{Simulation controls}  \subsection{Simulation controls}
1285    
1286  The model ''clock'' is defined by the variable \textbf{deltaTClock }(in s)  The model ''clock'' is defined by the variable \textbf{deltaTClock}
1287  which determines the IO frequencies and is used in tagging output.  (in s) which determines the IO frequencies and is used in tagging
1288  Typically, you will set it to the tracer time step for accelerated runs  output.  Typically, you will set it to the tracer time step for
1289  (otherwise it is simply set to the default time step \textbf{deltaT}).  accelerated runs (otherwise it is simply set to the default time step
1290  Frequency of checkpointing and dumping of the model state are referenced to  \textbf{deltaT}).  Frequency of checkpointing and dumping of the model
1291  this clock (see below).  state are referenced to this clock (see below).
1292    
1293  \begin{itemize}  \begin{description}
1294  \item run duration  \item[run duration] \
1295  \end{itemize}    
1296      The beginning of a simulation is set by specifying a start time (in
1297  The beginning of a simulation is set by specifying a start time (in s)    s) through the real variable \textbf{startTime} or by specifying an
1298  through the real variable \textbf{startTime }or by specifying an initial    initial iteration number through the integer variable
1299  iteration number through the integer variable \textbf{nIter0}. If these    \textbf{nIter0}. If these variables are set to nonzero values, the
1300  variables are set to nonzero values, the model will look for a ''pickup''    model will look for a ''pickup'' file \textit{pickup.0000nIter0} to
1301  file \textit{pickup.0000nIter0 }to restart the integration\textit{. }The end    restart the integration. The end of a simulation is set through the
1302  of a simulation is set through the real variable \textbf{endTime }(in s).    real variable \textbf{endTime} (in s).  Alternatively, you can
1303  Alternatively, you can specify instead the number of time steps to execute    specify instead the number of time steps to execute through the
1304  through the integer variable \textbf{nTimeSteps}.    integer variable \textbf{nTimeSteps}.
1305    
1306  \begin{itemize}  \item[frequency of output] \
1307  \item frequency of output    
1308  \end{itemize}    Real variables defining frequencies (in s) with which output files
1309      are written on disk need to be set up. \textbf{dumpFreq} controls
1310  Real variables defining frequencies (in s) with which output files are    the frequency with which the instantaneous state of the model is
1311  written on disk need to be set up. \textbf{dumpFreq }controls the frequency    saved. \textbf{chkPtFreq} and \textbf{pchkPtFreq} control the output
1312  with which the instantaneous state of the model is saved. \textbf{chkPtFreq }%    frequency of rolling and permanent checkpoint files, respectively.
1313  and \textbf{pchkPtFreq }control the output frequency of rolling and    See section 1.5.1 Output files for the definition of model state and
1314  permanent checkpoint files, respectively. See section 1.5.1 Output files for the    checkpoint files. In addition, time-averaged fields can be written
1315  definition of model state and checkpoint files. In addition, time-averaged    out by setting the variable \textbf{taveFreq} (in s).  The precision
1316  fields can be written out by setting the variable \textbf{taveFreq} (in s).    with which to write the binary data is controlled by the integer
1317  The precision with which to write the binary data is controlled by the    variable w\textbf{riteBinaryPrec} (set it to \texttt{32} or
1318  integer variable w\textbf{riteBinaryPrec }(set it to \texttt{32} or \texttt{%    \texttt{64}).
1319  64}).  
1320    \end{description}
1321    
1322    
1323    %%% Local Variables:
1324    %%% mode: latex
1325    %%% TeX-master: t
1326    %%% End:

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