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revision 1.8 by cnh, Mon Oct 22 11:55:47 2001 UTC revision 1.15 by edhill, Wed Jan 28 20:50:14 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{verbatim}  \begin{verbatim}
43  news://mitgcm.org/mitgcm.support  http://mitgcm.org/htdig/
44  \end{verbatim}  \end{verbatim}
45  A mail to the email list will reach all the developers and be archived  \begin{rawhtml} </A> \end{rawhtml}
46  on the newsgroup. A users email list will be established at some time  %%% http://www.google.com/search?q=hydrostatic+site%3Amitgcm.org
47  in the future.  
48    
49    
50  \section{Obtaining the code}  \section{Obtaining the code}
51  \label{sect:obtainingCode}  \label{sect:obtainingCode}
52    
53  MITgcm can be downloaded from our system by following  MITgcm can be downloaded from our system by following
54  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
55  \begin{rawhtml} <A href=mailto:support@mitgcm.org> \end{rawhtml}  \begin{rawhtml} <A href=mailto:MITgcm-support@mitgcm.org> \end{rawhtml}
56  support@mitgcm.org  MITgcm-support@mitgcm.org
57  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}
58  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.
59  You can download the model two ways:  You can download the model two ways:
60    
61  \begin{enumerate}  \begin{enumerate}
62  \item Using CVS software. CVS is a freely available source code managment  \item Using CVS software. CVS is a freely available source code management
63  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
64  come with CVS pre-installed, otherwise good places to look for  come with CVS pre-installed, otherwise good places to look for
65  the software for a particular platform are  the software for a particular platform are
# Line 72  provides an efficient and elegant way of Line 83  provides an efficient and elegant way of
83  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
84  download a tar file.  download a tar file.
85    
86  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
87  your .cshrc or .tcshrc:  be set within your shell.  For a csh or tcsh shell, put the following
88    \begin{verbatim}
89    % setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/gcmpack
90    \end{verbatim}
91    in your .cshrc or .tcshrc file.  For bash or sh shells, put:
92  \begin{verbatim}  \begin{verbatim}
93  % setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/u0/gcmpack  % export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'
94  \end{verbatim}  \end{verbatim}
95    in your .profile or .bashrc file.
96    
97  To start using CVS, register with the MITgcm CVS server using command:  
98    To get MITgcm through CVS, first register with the MITgcm CVS server
99    using command:
100  \begin{verbatim}  \begin{verbatim}
101  % cvs login ( CVS password: cvsanon )  % cvs login ( CVS password: cvsanon )
102  \end{verbatim}  \end{verbatim}
103  You only need to do ``cvs login'' once.  You only need to do a ``cvs login'' once.
104    
105  To obtain the sources for release1 type:  To obtain the latest sources type:
106    \begin{verbatim}
107    % cvs co MITgcm
108    \end{verbatim}
109    or to get a specific release type:
110  \begin{verbatim}  \begin{verbatim}
111  % cvs co -d directory -P -r release1 MITgcmUV  % cvs co -d directory -P -r release1_beta1 MITgcm
112  \end{verbatim}  \end{verbatim}
113    The MITgcm web site contains further directions concerning the source
114    code and CVS.  It also contains a web interface to our CVS archive so
115    that one may easily view the state of files, revisions, and other
116    development milestones:
117    \begin{rawhtml} <A href=http://mitgcm.org/download target="idontexist"> \end{rawhtml}
118    \begin{verbatim}
119    http://mitgcm.org/source_code.html
120    \end{verbatim}
121    \begin{rawhtml} </A> \end{rawhtml}
122    
123    
124  This creates a directory called \textit{directory}. If \textit{directory}  The checkout process creates a directory called \textit{MITgcm}. If
125  exists this command updates your code based on the repository. Each  the directory \textit{MITgcm} exists this command updates your code
126  directory in the source tree contains a directory \textit{CVS}. This  based on the repository. Each directory in the source tree contains a
127  information is required by CVS to keep track of your file versions with  directory \textit{CVS}. This information is required by CVS to keep
128  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
129  You can also use CVS to download code updates.  More extensive  the files in \textit{CVS}!  You can also use CVS to download code
130  information on using CVS for maintaining MITgcm code can be found  updates.  More extensive information on using CVS for maintaining
131    MITgcm code can be found
132  \begin{rawhtml} <A href=http://mitgcm.org/usingcvstoget.html target="idontexist"> \end{rawhtml}  \begin{rawhtml} <A href=http://mitgcm.org/usingcvstoget.html target="idontexist"> \end{rawhtml}
133  here  here
134  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}
# Line 106  here Line 139  here
139  \label{sect:conventionalDownload}  \label{sect:conventionalDownload}
140    
141  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
142  tar file from the reference web site at:  tar file from the web site at:
143  \begin{rawhtml} <A href=http://mitgcm.org/download target="idontexist"> \end{rawhtml}  \begin{rawhtml} <A href=http://mitgcm.org/download target="idontexist"> \end{rawhtml}
144  \begin{verbatim}  \begin{verbatim}
145  http://mitgcm.org/download/  http://mitgcm.org/download/
# Line 114  http://mitgcm.org/download/ Line 147  http://mitgcm.org/download/
147  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}
148  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
149  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
150  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
151    tar file does not exist, then please contact the developers through
152    the MITgcm-support list.
153    
154    \paragraph*{Upgrading from an earlier version}
155    
156    If you already have an earlier version of the code you can ``upgrade''
157    your copy instead of downloading the entire repository again. First,
158    ``cd'' (change directory) to the top of your working copy:
159    \begin{verbatim}
160    % cd MITgcm
161    \end{verbatim}
162    and then issue the cvs update command such as:
163    \begin{verbatim}
164    % cvs -q update -r release1_beta1 -d -P
165    \end{verbatim}
166    This will update the ``tag'' to ``release1\_beta1'', add any new
167    directories (-d) and remove any empty directories (-P). The -q option
168    means be quiet which will reduce the number of messages you'll see in
169    the terminal. If you have modified the code prior to upgrading, CVS
170    will try to merge your changes with the upgrades. If there is a
171    conflict between your modifications and the upgrade, it will report
172    that file with a ``C'' in front, e.g.:
173    \begin{verbatim}
174    C model/src/ini_parms.F
175    \end{verbatim}
176    If the list of conflicts scrolled off the screen, you can re-issue the
177    cvs update command and it will report the conflicts. Conflicts are
178    indicated in the code by the delimites ``$<<<<<<<$'', ``======='' and
179    ``$>>>>>>>$''. For example,
180    \begin{verbatim}
181    <<<<<<< ini_parms.F
182         & bottomDragLinear,myOwnBottomDragCoefficient,
183    =======
184         & bottomDragLinear,bottomDragQuadratic,
185    >>>>>>> 1.18
186    \end{verbatim}
187    means that you added ``myOwnBottomDragCoefficient'' to a namelist at
188    the same time and place that we added ``bottomDragQuadratic''. You
189    need to resolve this conflict and in this case the line should be
190    changed to:
191    \begin{verbatim}
192         & bottomDragLinear,bottomDragQuadratic,myOwnBottomDragCoefficient,
193    \end{verbatim}
194    and the lines with the delimiters ($<<<<<<$,======,$>>>>>>$) be deleted.
195    Unless you are making modifications which exactly parallel
196    developments we make, these types of conflicts should be rare.
197    
198    \paragraph*{Upgrading to the current pre-release version}
199    
200    We don't make a ``release'' for every little patch and bug fix in
201    order to keep the frequency of upgrades to a minimum. However, if you
202    have run into a problem for which ``we have already fixed in the
203    latest code'' and we haven't made a ``tag'' or ``release'' since that
204    patch then you'll need to get the latest code:
205    \begin{verbatim}
206    % cvs -q update -A -d -P
207    \end{verbatim}
208    Unlike, the ``check-out'' and ``update'' procedures above, there is no
209    ``tag'' or release name. The -A tells CVS to upgrade to the
210    very latest version. As a rule, we don't recommend this since you
211    might upgrade while we are in the processes of checking in the code so
212    that you may only have part of a patch. Using this method of updating
213    also means we can't tell what version of the code you are working
214    with. So please be sure you understand what you're doing.
215    
216  \section{Model and directory structure}  \section{Model and directory structure}
217    
218  The ``numerical'' model is contained within a execution environment support  The ``numerical'' model is contained within a execution environment
219  wrapper. This wrapper is designed to provide a general framework for  support wrapper. This wrapper is designed to provide a general
220  grid-point models. MITgcmUV is a specific numerical model that uses the  framework for grid-point models. MITgcmUV is a specific numerical
221  framework. Under this structure the model is split into execution  model that uses the framework. Under this structure the model is split
222  environment support code and conventional numerical model code. The  into execution environment support code and conventional numerical
223  execution environment support code is held under the \textit{eesupp}  model code. The execution environment support code is held under the
224  directory. The grid point model code is held under the \textit{model}  \textit{eesupp} directory. The grid point model code is held under the
225  directory. Code execution actually starts in the \textit{eesupp} routines  \textit{model} directory. Code execution actually starts in the
226  and not in the \textit{model} routines. For this reason the top-level  \textit{eesupp} routines and not in the \textit{model} routines. For
227    this reason the top-level
228  \textit{MAIN.F} is in the \textit{eesupp/src} directory. In general,  \textit{MAIN.F} is in the \textit{eesupp/src} directory. In general,
229  end-users should not need to worry about this level. The top-level routine  end-users should not need to worry about this level. The top-level routine
230  for the numerical part of the code is in \textit{model/src/THE\_MODEL\_MAIN.F%  for the numerical part of the code is in \textit{model/src/THE\_MODEL\_MAIN.F%
# Line 139  directory in which to compile the code. Line 237  directory in which to compile the code.
237    
238  \item \textit{diags}: contains the code relative to time-averaged  \item \textit{diags}: contains the code relative to time-averaged
239  diagnostics. It is subdivided into two subdirectories \textit{inc} and  diagnostics. It is subdivided into two subdirectories \textit{inc} and
240  \textit{src} that contain include files (*.\textit{h} files) and fortran  \textit{src} that contain include files (*.\textit{h} files) and Fortran
241  subroutines (*.\textit{F} files), respectively.  subroutines (*.\textit{F} files), respectively.
242    
243  \item \textit{doc}: contains brief documentation notes.  \item \textit{doc}: contains brief documentation notes.
# Line 160  relative to the atmospheric intermediate Line 258  relative to the atmospheric intermediate
258  in detail in section 3.  in detail in section 3.
259    
260  \item \textit{tools}: this directory contains various useful tools. For  \item \textit{tools}: this directory contains various useful tools. For
261  example, \textit{genmake} is a script written in csh (C-shell) that should  example, \textit{genmake2} is a script written in csh (C-shell) that should
262  be used to generate your makefile. The directory \textit{adjoint} contains  be used to generate your makefile. The directory \textit{adjoint} contains
263  the makefile specific to the Tangent linear and Adjoint Compiler (TAMC) that  the makefile specific to the Tangent linear and Adjoint Compiler (TAMC) that
264  generates the adjoint code. The latter is described in details in part V.  generates the adjoint code. The latter is described in details in part V.
# Line 180  section \ref{sect:modelExamples}. Line 278  section \ref{sect:modelExamples}.
278  \section{Example experiments}  \section{Example experiments}
279  \label{sect:modelExamples}  \label{sect:modelExamples}
280    
281  The MITgcm distribution comes with a set of twenty-four pre-configured  %% a set of twenty-four pre-configured numerical experiments
282  numerical experiments. Some of these examples experiments are tests of  
283  individual parts of the model code, but many are fully fledged numerical  The MITgcm distribution comes with more than a dozen pre-configured
284  simulations. A few of the examples are used for tutorial documentation  numerical experiments. Some of these example experiments are tests of
285  in sections \ref{sec:eg-baro} - \ref{sec:eg-global}. The other examples  individual parts of the model code, but many are fully fledged
286  follow the same general structure as the tutorial examples. However,  numerical simulations. A few of the examples are used for tutorial
287  they only include brief instructions in a text file called {\it README}.  documentation in sections \ref{sect:eg-baro} - \ref{sect:eg-global}.
288  The examples are located in subdirectories under  The other examples follow the same general structure as the tutorial
289  the directory \textit{verification}. Each  examples. However, they only include brief instructions in a text file
290  example is briefly described below.  called {\it README}.  The examples are located in subdirectories under
291    the directory \textit{verification}. Each example is briefly described
292    below.
293    
294  \subsection{Full list of model examples}  \subsection{Full list of model examples}
295    
296  \begin{enumerate}  \begin{enumerate}
297  \item \textit{exp0} - single layer, ocean double gyre (barotropic with  \item \textit{exp0} - single layer, ocean double gyre (barotropic with
298  free-surface). This experiment is described in detail in section    free-surface). This experiment is described in detail in section
299  \ref{sec:eg-baro}.    \ref{sect:eg-baro}.
   
 \item \textit{exp1} - Four layer, ocean double gyre. This experiment is described in detail in section  
 \ref{sec:eg-baroc}.  
300    
301    \item \textit{exp1} - Four layer, ocean double gyre. This experiment
302      is described in detail in section \ref{sect:eg-baroc}.
303      
304  \item \textit{exp2} - 4x4 degree global ocean simulation with steady  \item \textit{exp2} - 4x4 degree global ocean simulation with steady
305  climatological forcing. This experiment is described in detail in section    climatological forcing. This experiment is described in detail in
306  \ref{sec:eg-global}.    section \ref{sect:eg-global}.
307      
308  \item \textit{exp4} - Flow over a Gaussian bump in open-water or channel  \item \textit{exp4} - Flow over a Gaussian bump in open-water or
309  with open boundaries.    channel with open boundaries.
310      
311  \item \textit{exp5} - Inhomogenously forced ocean convection in a doubly  \item \textit{exp5} - Inhomogenously forced ocean convection in a
312  periodic box.    doubly periodic box.
313    
314  \item \textit{front\_relax} - Relaxation of an ocean thermal front (test for  \item \textit{front\_relax} - Relaxation of an ocean thermal front (test for
315  Gent/McWilliams scheme). 2D (Y-Z).  Gent/McWilliams scheme). 2D (Y-Z).
316    
317  \item \textit{internal wave} - Ocean internal wave forced by open boundary  \item \textit{internal wave} - Ocean internal wave forced by open
318  conditions.    boundary conditions.
319      
320  \item \textit{natl\_box} - Eastern subtropical North Atlantic with KPP  \item \textit{natl\_box} - Eastern subtropical North Atlantic with KPP
321  scheme; 1 month integration    scheme; 1 month integration
322      
323  \item \textit{hs94.1x64x5} - Zonal averaged atmosphere using Held and Suarez  \item \textit{hs94.1x64x5} - Zonal averaged atmosphere using Held and
324  '94 forcing.    Suarez '94 forcing.
325      
326  \item \textit{hs94.128x64x5} - 3D atmosphere dynamics using Held and Suarez  \item \textit{hs94.128x64x5} - 3D atmosphere dynamics using Held and
327  '94 forcing.    Suarez '94 forcing.
328      
329  \item \textit{hs94.cs-32x32x5} - 3D atmosphere dynamics using Held and  \item \textit{hs94.cs-32x32x5} - 3D atmosphere dynamics using Held and
330  Suarez '94 forcing on the cubed sphere.    Suarez '94 forcing on the cubed sphere.
331      
332  \item \textit{aim.5l\_zon-ave} - Intermediate Atmospheric physics. Global  \item \textit{aim.5l\_zon-ave} - Intermediate Atmospheric physics.
333  Zonal Mean configuration, 1x64x5 resolution.    Global Zonal Mean configuration, 1x64x5 resolution.
334      
335  \item \textit{aim.5l\_XZ\_Equatorial\_Slice} - Intermediate Atmospheric  \item \textit{aim.5l\_XZ\_Equatorial\_Slice} - Intermediate
336  physics, equatorial Slice configuration.    Atmospheric physics, equatorial Slice configuration.  2D (X-Z).
337  2D (X-Z).    
   
338  \item \textit{aim.5l\_Equatorial\_Channel} - Intermediate Atmospheric  \item \textit{aim.5l\_Equatorial\_Channel} - Intermediate Atmospheric
339  physics. 3D Equatorial Channel configuration.    physics. 3D Equatorial Channel configuration.
340      
341  \item \textit{aim.5l\_LatLon} - Intermediate Atmospheric physics.  \item \textit{aim.5l\_LatLon} - Intermediate Atmospheric physics.
342  Global configuration, on latitude longitude grid with 128x64x5 grid points    Global configuration, on latitude longitude grid with 128x64x5 grid
343  ($2.8^\circ{\rm degree}$ resolution).    points ($2.8^\circ{\rm degree}$ resolution).
344      
345  \item \textit{adjustment.128x64x1} Barotropic adjustment  \item \textit{adjustment.128x64x1} Barotropic adjustment problem on
346  problem on latitude longitude grid with 128x64 grid points ($2.8^\circ{\rm degree}$ resolution).    latitude longitude grid with 128x64 grid points ($2.8^\circ{\rm
347        degree}$ resolution).
348  \item \textit{adjustment.cs-32x32x1}    
349  Barotropic adjustment  \item \textit{adjustment.cs-32x32x1} Barotropic adjustment problem on
350  problem on cube sphere grid with 32x32 points per face ( roughly    cube sphere grid with 32x32 points per face ( roughly $2.8^\circ{\rm
351  $2.8^\circ{\rm degree}$ resolution).      degree}$ resolution).
352      
353  \item \textit{advect\_cs} Two-dimensional passive advection test on  \item \textit{advect\_cs} Two-dimensional passive advection test on
354  cube sphere grid.    cube sphere grid.
355      
356  \item \textit{advect\_xy} Two-dimensional (horizontal plane) passive advection  \item \textit{advect\_xy} Two-dimensional (horizontal plane) passive
357  test on cartesian grid.    advection test on Cartesian grid.
358      
359  \item \textit{advect\_yz} Two-dimensional (vertical plane) passive advection test on cartesian grid.  \item \textit{advect\_yz} Two-dimensional (vertical plane) passive
360      advection test on Cartesian grid.
361  \item \textit{carbon} Simple passive tracer experiment. Includes derivative    
362  calculation. Described in detail in section \ref{sec:eg-carbon-ad}.  \item \textit{carbon} Simple passive tracer experiment. Includes
363      derivative calculation. Described in detail in section
364      \ref{sect:eg-carbon-ad}.
365    
366  \item \textit{flt\_example} Example of using float package.  \item \textit{flt\_example} Example of using float package.
367      
368  \item \textit{global\_ocean.90x40x15} Global circulation with  \item \textit{global\_ocean.90x40x15} Global circulation with GM, flux
369  GM, flux boundary conditions and poles.    boundary conditions and poles.
370    
371  \item \textit{solid-body.cs-32x32x1} Solid body rotation test for cube sphere  \item \textit{global\_ocean\_pressure} Global circulation in pressure
372  grid.    coordinate (non-Boussinesq ocean model). Described in detail in
373      section \ref{sect:eg-globalpressure}.
374      
375    \item \textit{solid-body.cs-32x32x1} Solid body rotation test for cube
376      sphere grid.
377    
378  \end{enumerate}  \end{enumerate}
379    
# Line 281  Each example directory has the following Line 386  Each example directory has the following
386  minimum, this directory includes the following files:  minimum, this directory includes the following files:
387    
388  \begin{itemize}  \begin{itemize}
389  \item \textit{code/CPP\_EEOPTIONS.h}: declares CPP keys relative to the  \item \textit{code/CPP\_EEOPTIONS.h}: declares CPP keys relative to
390  ``execution environment'' part of the code. The default version is located    the ``execution environment'' part of the code. The default version
391  in \textit{eesupp/inc}.    is located in \textit{eesupp/inc}.
392      
393  \item \textit{code/CPP\_OPTIONS.h}: declares CPP keys relative to the  \item \textit{code/CPP\_OPTIONS.h}: declares CPP keys relative to the
394  ``numerical model'' part of the code. The default version is located in    ``numerical model'' part of the code. The default version is located
395  \textit{model/inc}.    in \textit{model/inc}.
396      
397  \item \textit{code/SIZE.h}: declares size of underlying computational grid.  \item \textit{code/SIZE.h}: declares size of underlying computational
398  The default version is located in \textit{model/inc}.    grid.  The default version is located in \textit{model/inc}.
399  \end{itemize}  \end{itemize}
400    
401  In addition, other include files and subroutines might be present in \textit{%  In addition, other include files and subroutines might be present in
402  code} depending on the particular experiment. See section 2 for more details.  \textit{code} depending on the particular experiment. See Section 2
403    for more details.
404  \item \textit{input}: contains the input data files required to run the  
405  example. At a mimimum, the \textit{input} directory contains the following  \item \textit{input}: contains the input data files required to run
406  files:    the example. At a minimum, the \textit{input} directory contains the
407      following files:
408  \begin{itemize}  
409  \item \textit{input/data}: this file, written as a namelist, specifies the  \begin{itemize}
410  main parameters for the experiment.  \item \textit{input/data}: this file, written as a namelist, specifies
411      the main parameters for the experiment.
412  \item \textit{input/data.pkg}: contains parameters relative to the packages    
413  used in the experiment.  \item \textit{input/data.pkg}: contains parameters relative to the
414      packages used in the experiment.
415  \item \textit{input/eedata}: this file contains ``execution environment''    
416  data. At present, this consists of a specification of the number of threads  \item \textit{input/eedata}: this file contains ``execution
417  to use in $X$ and $Y$ under multithreaded execution.    environment'' data. At present, this consists of a specification of
418      the number of threads to use in $X$ and $Y$ under multithreaded
419      execution.
420  \end{itemize}  \end{itemize}
421    
422  In addition, you will also find in this directory the forcing and topography  In addition, you will also find in this directory the forcing and topography
# Line 330  the code. Line 437  the code.
437  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
438  ({\em Makefile}) that allows us to pre-process source files, specify  ({\em Makefile}) that allows us to pre-process source files, specify
439  compiler and optimization options and also figures out any file  compiler and optimization options and also figures out any file
440  dependancies. We supply a script ({\em genmake}), described in section  dependencies. We supply a script ({\em genmake}), described in section
441  \ref{sect:genmake}, that automatically creates the {\em Makefile} for  \ref{sect:genmake}, that automatically creates the {\em Makefile} for
442  you. You then need to build the dependancies and compile the code.  you. You then need to build the dependencies and compile the code.
443    
444  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
445  \textit{verification/exp2}. The are multiple ways and places to actually  \textit{verification/exp2}. The are multiple ways and places to actually
# Line 354  to use the following options when invoki Line 461  to use the following options when invoki
461  % ../../../tools/genmake  -mods=../code  % ../../../tools/genmake  -mods=../code
462  \end{verbatim}  \end{verbatim}
463    
464  Next, create the dependancies:  Next, create the dependencies:
465  \begin{verbatim}  \begin{verbatim}
466  % make depend  % make depend
467  \end{verbatim}  \end{verbatim}
# Line 406  files must be in the same place. If you Line 513  files must be in the same place. If you
513  % cp ../code/mitgcmuv ./  % cp ../code/mitgcmuv ./
514  % ./mitgcmuv > output.txt  % ./mitgcmuv > output.txt
515  \end{verbatim}  \end{verbatim}
516  or if you will be making muliple runs with the same executable:  or if you will be making multiple runs with the same executable:
517  \begin{verbatim}  \begin{verbatim}
518  % cd ../  % cd ../
519  % cp -r input run1  % cp -r input run1
# Line 418  or if you will be making muliple runs wi Line 525  or if you will be making muliple runs wi
525  \subsubsection{Building from a new directory}  \subsubsection{Building from a new directory}
526    
527  Since the {\em input} directory contains input files it is often more  Since the {\em input} directory contains input files it is often more
528  useful to keep {\em input} prestine and build in a new directory  useful to keep {\em input} pristine and build in a new directory
529  within {\em verification/exp2/}:  within {\em verification/exp2/}:
530  \begin{verbatim}  \begin{verbatim}
531  % cd verification/exp2  % cd verification/exp2
# Line 804  here I think. To come soon...) Line 911  here I think. To come soon...)
911  \item time-discretization  \item time-discretization
912  \end{itemize}  \end{itemize}
913    
914  The time steps are set through the real variables \textbf{deltaTMom }and  The time steps are set through the real variables \textbf{deltaTMom}
915  \textbf{deltaTtracer }(in s) which represent the time step for the momentum  and \textbf{deltaTtracer} (in s) which represent the time step for the
916  and tracer equations, respectively. For synchronous integrations, simply set  momentum and tracer equations, respectively. For synchronous
917  the two variables to the same value (or you can prescribe one time step only  integrations, simply set the two variables to the same value (or you
918  through the variable \textbf{deltaT}). The Adams-Bashforth stabilizing  can prescribe one time step only through the variable
919  parameter is set through the variable \textbf{abEps }(dimensionless). The  \textbf{deltaT}). The Adams-Bashforth stabilizing parameter is set
920  stagger baroclinic time stepping can be activated by setting the logical  through the variable \textbf{abEps} (dimensionless). The stagger
921  variable \textbf{staggerTimeStep }to '.\texttt{TRUE}.'.  baroclinic time stepping can be activated by setting the logical
922    variable \textbf{staggerTimeStep} to '.\texttt{TRUE}.'.
923    
924  \subsection{Equation of state}  \subsection{Equation of state}
925    
926  First, because the model equations are written in terms of perturbations, a  First, because the model equations are written in terms of
927  reference thermodynamic state needs to be specified. This is done through  perturbations, a reference thermodynamic state needs to be specified.
928  the 1D arrays \textbf{tRef}\textit{\ }and \textbf{sRef}. \textbf{tRef }%  This is done through the 1D arrays \textbf{tRef} and \textbf{sRef}.
929  specifies the reference potential temperature profile (in $^{o}$C for  \textbf{tRef} specifies the reference potential temperature profile
930  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
931  k=1. Similarly, \textbf{sRef}\textit{\ }specifies the reference salinity  from the level k=1. Similarly, \textbf{sRef} specifies the reference
932  profile (in ppt) for the ocean or the reference specific humidity profile  salinity profile (in ppt) for the ocean or the reference specific
933  (in g/kg) for the atmosphere.  humidity profile (in g/kg) for the atmosphere.
934    
935  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
936  \textbf{buoyancyRelation}\textit{\ }and \textbf{eosType}\textit{. }\textbf{%  variables \textbf{buoyancyRelation} and \textbf{eosType}.
937  buoyancyRelation}\textit{\ }is set to '\texttt{OCEANIC}' by default and  \textbf{buoyancyRelation} is set to '\texttt{OCEANIC}' by default and
938  needs to be set to '\texttt{ATMOSPHERIC}' for atmosphere simulations. In  needs to be set to '\texttt{ATMOSPHERIC}' for atmosphere simulations.
939  this case, \textbf{eosType}\textit{\ }must be set to '\texttt{IDEALGAS}'.  In this case, \textbf{eosType} must be set to '\texttt{IDEALGAS}'.
940  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:
941  \textbf{eosType}\textit{\ }to '\texttt{LINEAR}') and a polynomial  linear (set \textbf{eosType} to '\texttt{LINEAR}') and a polynomial
942  approximation to the full nonlinear equation ( set \textbf{eosType}\textit{\  approximation to the full nonlinear equation ( set
943  }to '\texttt{POLYNOMIAL}'). In the linear case, you need to specify the  \textbf{eosType}\textit{\ }to '\texttt{POLYNOMIAL}'). In the linear
944  thermal and haline expansion coefficients represented by the variables  case, you need to specify the thermal and haline expansion
945  \textbf{tAlpha}\textit{\ }(in K$^{-1}$) and \textbf{sBeta}\textit{\ }(in ppt$%  coefficients represented by the variables \textbf{tAlpha}\textit{\
946  ^{-1}$). For the nonlinear case, you need to generate a file of polynomial    }(in K$^{-1}$) and \textbf{sBeta} (in ppt$^{-1}$). For the nonlinear
947  coefficients called \textit{POLY3.COEFFS. }To do this, use the program  case, you need to generate a file of polynomial coefficients called
948  \textit{utils/knudsen2/knudsen2.f }under the model tree (a Makefile is  \textit{POLY3.COEFFS}. To do this, use the program
949  available in the same directory and you will need to edit the number and the  \textit{utils/knudsen2/knudsen2.f} under the model tree (a Makefile is
950  values of the vertical levels in \textit{knudsen2.f }so that they match  available in the same directory and you will need to edit the number
951  those of your configuration). \textit{\ }  and the values of the vertical levels in \textit{knudsen2.f} so that
952    they match those of your configuration).
953    
954    There there are also higher polynomials for the equation of state:
955    \begin{description}
956    \item['\texttt{UNESCO}':] The UNESCO equation of state formula of
957      Fofonoff and Millard \cite{fofonoff83}. This equation of state
958      assumes in-situ temperature, which is not a model variable; \emph{its use
959      is therefore discouraged, and it is only listed for completeness}.
960    \item['\texttt{JMD95Z}':] A modified UNESCO formula by Jackett and
961      McDougall \cite{jackett95}, which uses the model variable potential
962      temperature as input. The '\texttt{Z}' indicates that this equation
963      of state uses a horizontally and temporally constant pressure
964      $p_{0}=-g\rho_{0}z$.
965    \item['\texttt{JMD95P}':] A modified UNESCO formula by Jackett and
966      McDougall \cite{jackett95}, which uses the model variable potential
967      temperature as input. The '\texttt{P}' indicates that this equation
968      of state uses the actual hydrostatic pressure of the last time
969      step. Lagging the pressure in this way requires an additional pickup
970      file for restarts.
971    \item['\texttt{MDJWF}':] The new, more accurate and less expensive
972      equation of state by McDougall et~al. \cite{mcdougall03}. It also
973      requires lagging the pressure and therefore an additional pickup
974      file for restarts.
975    \end{description}
976    For none of these options an reference profile of temperature or
977    salinity is required.
978    
979  \subsection{Momentum equations}  \subsection{Momentum equations}
980    
# Line 1073  fields can be written out by setting the Line 1207  fields can be written out by setting the
1207  The precision with which to write the binary data is controlled by the  The precision with which to write the binary data is controlled by the
1208  integer variable w\textbf{riteBinaryPrec }(set it to \texttt{32} or \texttt{%  integer variable w\textbf{riteBinaryPrec }(set it to \texttt{32} or \texttt{%
1209  64}).  64}).
1210    
1211    %%% Local Variables:
1212    %%% mode: latex
1213    %%% TeX-master: t
1214    %%% End:
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