/[MITgcm]/manual/s_getstarted/text/getting_started.tex
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revision 1.10 by adcroft, Tue Nov 13 20:13:54 2001 UTC revision 1.13 by mlosch, Tue Dec 17 14:39:53 2002 UTC
# Line 86  You only need to do ``cvs login'' once. Line 86  You only need to do ``cvs login'' once.
86    
87  To obtain the sources for release1 type:  To obtain the sources for release1 type:
88  \begin{verbatim}  \begin{verbatim}
89  % cvs co -d directory -P -r release1 MITgcmUV  % cvs co -d directory -P -r release1_beta1 MITgcm
90  \end{verbatim}  \end{verbatim}
91    
92  This creates a directory called \textit{directory}. If \textit{directory}  This creates a directory called \textit{directory}. If \textit{directory}
# Line 116  The tar file still contains CVS informat Line 116  The tar file still contains CVS informat
116  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
117  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.
118    
119    \paragraph*{Upgrading from an earlier version}
120    
121    If you already have an earlier version of the code you can ``upgrade''
122    your copy instead of downloading the entire repository again. First,
123    ``cd'' (change directory) to the top of your working copy:
124    \begin{verbatim}
125    % cd MITgcm
126    \end{verbatim}
127    and then issue the cvs update command:
128    \begin{verbatim}
129    % cvs -q update -r release1_beta1 -d -P
130    \end{verbatim}
131    This will update the ``tag'' to ``release1\_beta1'', add any new
132    directories (-d) and remove any empty directories (-P). The -q option
133    means be quiet which will reduce the number of messages you'll see in
134    the terminal. If you have modified the code prior to upgrading, CVS
135    will try to merge your changes with the upgrades. If there is a
136    conflict between your modifications and the upgrade, it will report
137    that file with a ``C'' in front, e.g.:
138    \begin{verbatim}
139    C model/src/ini_parms.F
140    \end{verbatim}
141    If the list of conflicts scrolled off the screen, you can re-issue the
142    cvs update command and it will report the conflicts. Conflicts are
143    indicated in the code by the delimites ``<<<<<<<'', ``======='' and
144    ``>>>>>>>''. For example,
145    \begin{verbatim}
146    <<<<<<< ini_parms.F
147         & bottomDragLinear,myOwnBottomDragCoefficient,
148    =======
149         & bottomDragLinear,bottomDragQuadratic,
150    >>>>>>> 1.18
151    \end{verbatim}
152    means that you added ``myOwnBottomDragCoefficient'' to a namelist at
153    the same time and place that we added ``bottomDragQuadratic''. You
154    need to resolve this conflict and in this case the line should be
155    changed to:
156    \begin{verbatim}
157         & bottomDragLinear,bottomDragQuadratic,myOwnBottomDragCoefficient,
158    \end{verbatim}
159    and the lines with the delimiters (<<<<<<,======,>>>>>>) be deleted.
160    Unless you are making modifications which exactly parallel
161    developments we make, these types of conflicts should be rare.
162    
163    \paragraph*{Upgrading to the current pre-release version}
164    
165    We don't make a ``release'' for every little patch and bug fix in
166    order to keep the frequency of upgrades to a minimum. However, if you
167    have run into a problem for which ``we have already fixed in the
168    latest code'' and we haven't made a ``tag'' or ``release'' since that
169    patch then you'll need to get the latest code:
170    \begin{verbatim}
171    % cvs -q update -A -d -P
172    \end{verbatim}
173    Unlike, the ``check-out'' and ``update'' procedures above, there is no
174    ``tag'' or release name. The -A tells CVS to upgrade to the
175    very latest version. As a rule, we don't recommend this since you
176    might upgrade while we are in the processes of checking in the code so
177    that you may only have part of a patch. Using this method of updating
178    also means we can't tell what version of the code you are working
179    with. So please be sure you understand what you're doing.
180    
181  \section{Model and directory structure}  \section{Model and directory structure}
182    
183  The ``numerical'' model is contained within a execution environment support  The ``numerical'' model is contained within a execution environment
184  wrapper. This wrapper is designed to provide a general framework for  support wrapper. This wrapper is designed to provide a general
185  grid-point models. MITgcmUV is a specific numerical model that uses the  framework for grid-point models. MITgcmUV is a specific numerical
186  framework. Under this structure the model is split into execution  model that uses the framework. Under this structure the model is split
187  environment support code and conventional numerical model code. The  into execution environment support code and conventional numerical
188  execution environment support code is held under the \textit{eesupp}  model code. The execution environment support code is held under the
189  directory. The grid point model code is held under the \textit{model}  \textit{eesupp} directory. The grid point model code is held under the
190  directory. Code execution actually starts in the \textit{eesupp} routines  \textit{model} directory. Code execution actually starts in the
191  and not in the \textit{model} routines. For this reason the top-level  \textit{eesupp} routines and not in the \textit{model} routines. For
192    this reason the top-level
193  \textit{MAIN.F} is in the \textit{eesupp/src} directory. In general,  \textit{MAIN.F} is in the \textit{eesupp/src} directory. In general,
194  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
195  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 267  calculation. Described in detail in sect Line 330  calculation. Described in detail in sect
330  \item \textit{global\_ocean.90x40x15} Global circulation with  \item \textit{global\_ocean.90x40x15} Global circulation with
331  GM, flux boundary conditions and poles.  GM, flux boundary conditions and poles.
332    
333    \item \textit{global\_ocean\_pressure} Global circulation in pressure
334      coordinate (non-Boussinesq ocean model). Described in detail in
335      section \ref{sect:eg-globalpressure}.
336    
337  \item \textit{solid-body.cs-32x32x1} Solid body rotation test for cube sphere  \item \textit{solid-body.cs-32x32x1} Solid body rotation test for cube sphere
338  grid.  grid.
339    
# Line 804  here I think. To come soon...) Line 871  here I think. To come soon...)
871  \item time-discretization  \item time-discretization
872  \end{itemize}  \end{itemize}
873    
874  The time steps are set through the real variables \textbf{deltaTMom }and  The time steps are set through the real variables \textbf{deltaTMom}
875  \textbf{deltaTtracer }(in s) which represent the time step for the momentum  and \textbf{deltaTtracer} (in s) which represent the time step for the
876  and tracer equations, respectively. For synchronous integrations, simply set  momentum and tracer equations, respectively. For synchronous
877  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
878  through the variable \textbf{deltaT}). The Adams-Bashforth stabilizing  can prescribe one time step only through the variable
879  parameter is set through the variable \textbf{abEps }(dimensionless). The  \textbf{deltaT}). The Adams-Bashforth stabilizing parameter is set
880  stagger baroclinic time stepping can be activated by setting the logical  through the variable \textbf{abEps} (dimensionless). The stagger
881  variable \textbf{staggerTimeStep }to '.\texttt{TRUE}.'.  baroclinic time stepping can be activated by setting the logical
882    variable \textbf{staggerTimeStep} to '.\texttt{TRUE}.'.
883    
884  \subsection{Equation of state}  \subsection{Equation of state}
885    
886  First, because the model equations are written in terms of perturbations, a  First, because the model equations are written in terms of
887  reference thermodynamic state needs to be specified. This is done through  perturbations, a reference thermodynamic state needs to be specified.
888  the 1D arrays \textbf{tRef}\textit{\ }and \textbf{sRef}. \textbf{tRef }%  This is done through the 1D arrays \textbf{tRef} and \textbf{sRef}.
889  specifies the reference potential temperature profile (in $^{o}$C for  \textbf{tRef} specifies the reference potential temperature profile
890  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
891  k=1. Similarly, \textbf{sRef}\textit{\ }specifies the reference salinity  from the level k=1. Similarly, \textbf{sRef} specifies the reference
892  profile (in ppt) for the ocean or the reference specific humidity profile  salinity profile (in ppt) for the ocean or the reference specific
893  (in g/kg) for the atmosphere.  humidity profile (in g/kg) for the atmosphere.
894    
895  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
896  \textbf{buoyancyRelation}\textit{\ }and \textbf{eosType}\textit{. }\textbf{%  variables \textbf{buoyancyRelation} and \textbf{eosType}.
897  buoyancyRelation}\textit{\ }is set to '\texttt{OCEANIC}' by default and  \textbf{buoyancyRelation} is set to '\texttt{OCEANIC}' by default and
898  needs to be set to '\texttt{ATMOSPHERIC}' for atmosphere simulations. In  needs to be set to '\texttt{ATMOSPHERIC}' for atmosphere simulations.
899  this case, \textbf{eosType}\textit{\ }must be set to '\texttt{IDEALGAS}'.  In this case, \textbf{eosType} must be set to '\texttt{IDEALGAS}'.
900  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:
901  \textbf{eosType}\textit{\ }to '\texttt{LINEAR}') and a polynomial  linear (set \textbf{eosType} to '\texttt{LINEAR}') and a polynomial
902  approximation to the full nonlinear equation ( set \textbf{eosType}\textit{\  approximation to the full nonlinear equation ( set
903  }to '\texttt{POLYNOMIAL}'). In the linear case, you need to specify the  \textbf{eosType}\textit{\ }to '\texttt{POLYNOMIAL}'). In the linear
904  thermal and haline expansion coefficients represented by the variables  case, you need to specify the thermal and haline expansion
905  \textbf{tAlpha}\textit{\ }(in K$^{-1}$) and \textbf{sBeta}\textit{\ }(in ppt$%  coefficients represented by the variables \textbf{tAlpha}\textit{\
906  ^{-1}$). For the nonlinear case, you need to generate a file of polynomial    }(in K$^{-1}$) and \textbf{sBeta} (in ppt$^{-1}$). For the nonlinear
907  coefficients called \textit{POLY3.COEFFS. }To do this, use the program  case, you need to generate a file of polynomial coefficients called
908  \textit{utils/knudsen2/knudsen2.f }under the model tree (a Makefile is  \textit{POLY3.COEFFS}. To do this, use the program
909  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
910  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
911  those of your configuration). \textit{\ }  and the values of the vertical levels in \textit{knudsen2.f} so that
912    they match those of your configuration).
913    
914    There there are also higher polynomials for the equation of state:
915    \begin{description}
916    \item['\texttt{UNESCO}':] The UNESCO equation of state formula of
917      Fofonoff and Millard \cite{fofonoff83}. This equation of state
918      assumes in-situ temperature, which is not a model variable; \emph{its use
919      is therefore discouraged, and it is only listed for completeness}.
920    \item['\texttt{JMD95Z}':] A modified UNESCO formula by Jackett and
921      McDougall \cite{jackett95}, which uses the model variable potential
922      temperature as input. The '\texttt{Z}' indicates that this equation
923      of state uses a horizontally and temporally constant pressure
924      $p_{0}=-g\rho_{0}z$.
925    \item['\texttt{JMD95P}':] A modified UNESCO formula by Jackett and
926      McDougall \cite{jackett95}, which uses the model variable potential
927      temperature as input. The '\texttt{P}' indicates that this equation
928      of state uses the actual hydrostatic pressure of the last time
929      step. Lagging the pressure in this way requires an additional pickup
930      file for restarts.
931    \item['\texttt{MDJWF}':] The new, more accurate and less expensive
932      equation of state by McDougall et~al. \cite{mcdougall03}. It also
933      requires lagging the pressure and therefore an additional pickup
934      file for restarts.
935    \end{description}
936    For none of these options an reference profile of temperature or
937    salinity is required.
938    
939  \subsection{Momentum equations}  \subsection{Momentum equations}
940    
# Line 1073  fields can be written out by setting the Line 1167  fields can be written out by setting the
1167  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
1168  integer variable w\textbf{riteBinaryPrec }(set it to \texttt{32} or \texttt{%  integer variable w\textbf{riteBinaryPrec }(set it to \texttt{32} or \texttt{%
1169  64}).  64}).
1170    
1171    %%% Local Variables:
1172    %%% mode: latex
1173    %%% TeX-master: t
1174    %%% End:
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