/[MITgcm]/manual/s_getstarted/text/customization.tex
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revision 1.1 by cnh, Thu Oct 14 14:24:28 2004 UTC revision 1.11 by jmc, Mon Aug 30 23:09:20 2010 UTC
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1  \section[Customizing MITgcm]{Doing it yourself: customizing the code}  \section[Customizing MITgcm]{Doing it yourself: customizing the model configuration}
2    \label{sec:customize}
3    \begin{rawhtml}
4    <!-- CMIREDIR:customizing_mitgcm: -->
5    \end{rawhtml}
6    
7  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
8  easiest thing is to use and adapt the setup of the case studies  easiest thing is to use and adapt the setup of the case studies
# Line 9  part of the code (the setup relative to Line 13  part of the code (the setup relative to
13  part is covered in the parallel implementation section) and on the  part is covered in the parallel implementation section) and on the
14  variables and parameters that you are likely to change.  variables and parameters that you are likely to change.
15    
 \subsection{Configuration and setup}  
   
16  The CPP keys relative to the ``numerical model'' part of the code are  The CPP keys relative to the ``numerical model'' part of the code are
17  all defined and set in the file \textit{CPP\_OPTIONS.h }in the  all defined and set in the file \textit{CPP\_OPTIONS.h }in the
18  directory \textit{ model/inc }or in one of the \textit{code  directory \textit{ model/inc }or in one of the \textit{code
# Line 22  values can be modified in the namelist f Line 24  values can be modified in the namelist f
24  to be located in the directory where you will run the model. The  to be located in the directory where you will run the model. The
25  parameters are initialized in the routine  parameters are initialized in the routine
26  \textit{model/src/ini\_parms.F}.  Look at this routine to see in what  \textit{model/src/ini\_parms.F}.  Look at this routine to see in what
27  part of the namelist the parameters are located.  part of the namelist the parameters are located. Here is a complete list
28    of the model parameters related to the main model (namelist parameters
29    for the packages are located in the package descriptions), their meaning,
30    and their default values:
31    
32    \input{s_getstarted/text/main-parms.tex}
33    
34  In what follows the parameters are grouped into categories related to  In what follows the parameters are grouped into categories related to
35  the computational domain, the equations solved in the model, and the  the computational domain, the equations solved in the model, and the
36  simulation controls.  simulation controls.
37    
38  \subsection{Computational domain, geometry and time-discretization}  \subsection{Parameters: Computational domain, geometry and time-discretization}
39    
40  \begin{description}  \begin{description}
41  \item[dimensions] \  \item[dimensions] \
# Line 47  simulation controls. Line 54  simulation controls.
54    through the logical variables \textbf{usingCartesianGrid},    through the logical variables \textbf{usingCartesianGrid},
55    \textbf{usingSphericalPolarGrid}, and \textbf{usingCurvilinearGrid}.    \textbf{usingSphericalPolarGrid}, and \textbf{usingCurvilinearGrid}.
56    In the case of spherical and curvilinear grids, the southern    In the case of spherical and curvilinear grids, the southern
57    boundary is defined through the variable \textbf{phiMin} which    boundary is defined through the variable \textbf{ygOrigin} which
58    corresponds to the latitude of the southern most cell face (in    corresponds to the latitude of the southern most cell face (in
59    degrees). The resolution along the x and y directions is controlled    degrees). The resolution along the x and y directions is controlled
60    by the 1D arrays \textbf{delx} and \textbf{dely} (in meters in the    by the 1D arrays \textbf{delx} and \textbf{dely} (in meters in the
# Line 121  simulation controls. Line 128  simulation controls.
128  \end{description}  \end{description}
129    
130    
131  \subsection{Equation of state}  \subsection{Parameters: Equation of state}
132    
133  First, because the model equations are written in terms of  First, because the model equations are written in terms of
134  perturbations, a reference thermodynamic state needs to be specified.  perturbations, a reference thermodynamic state needs to be specified.
# Line 176  There there are also higher polynomials Line 183  There there are also higher polynomials
183  For none of these options an reference profile of temperature or  For none of these options an reference profile of temperature or
184  salinity is required.  salinity is required.
185    
186  \subsection{Momentum equations}  \subsection{Parameters: Momentum equations}
187    
188  In this section, we only focus for now on the parameters that you are  In this section, we only focus for now on the parameters that you are
189  likely to change, i.e. the ones relative to forcing and dissipation  likely to change, i.e. the ones relative to forcing and dissipation
# Line 195  variables. Line 202  variables.
202  \begin{description}  \begin{description}
203  \item[initialization] \  \item[initialization] \
204        
205    The velocity components are initialized to 0 unless the simulation    The initial horizontal velocity components can be specified from
206    is starting from a pickup file (see section on simulation control    binary files \textbf{uVelInitFile} and \textbf{vVelInitFile}.
207    parameters).    These files should contain 3D data ordered in an (x,y,r) fashion with
208      k=1 as the first vertical level (surface level).
209      If no file names are provided, the velocity is initialised to zero.
210      The initial vertical velocity is always derived from the horizontal velocity
211      using the continuity equation, even in the case of non-hydrostatic simulation
212      (see, e.g.: {\it tutorial\_deep\_convection/input/data}).
213    
214      In the case of a restart (from the end of a previous simulation),
215      the velocity field is read from a pickup file
216      (see section on simulation control parameters)
217      and the initial velocity files are ignored.
218    
219  \item[forcing] \  \item[forcing] \
220        
# Line 246  variables. Line 263  variables.
263    set to \texttt{'.FALSE.'}, free-slip boundary conditions are    set to \texttt{'.FALSE.'}, free-slip boundary conditions are
264    applied. If no-slip boundary conditions are applied at the bottom, a    applied. If no-slip boundary conditions are applied at the bottom, a
265    bottom drag can be applied as well. Two forms are available: linear    bottom drag can be applied as well. Two forms are available: linear
266    (set the variable \textbf{bottomDragLinear} in s$ ^{-1}$) and    (set the variable \textbf{bottomDragLinear} in m/s) and
267    quadratic (set the variable \textbf{bottomDragQuadratic} in    quadratic (set the variable \textbf{bottomDragQuadratic}, dimensionless).
   m$^{-1}$).  
268    
269    The Fourier and Shapiro filters are described elsewhere.    The Fourier and Shapiro filters are described elsewhere.
270    
# Line 282  variables. Line 298  variables.
298    
299  \end{description}  \end{description}
300    
301  \subsection{Tracer equations}  \subsection{Parameters: Tracer equations}
302    
303  This section covers the tracer equations i.e. the potential  This section covers the tracer equations i.e. the potential
304  temperature equation and the salinity (for the ocean) or specific  temperature equation and the salinity (for the ocean) or specific
# Line 374  for a precise definition. Line 390  for a precise definition.
390    
391  \end{description}  \end{description}
392    
393  \subsection{Simulation controls}  \subsection{Parameters: Simulation controls}
394    
395  The model ''clock'' is defined by the variable \textbf{deltaTClock}  The model ''clock'' is defined by the variable \textbf{deltaTClock}
396  (in s) which determines the IO frequencies and is used in tagging  (in s) which determines the IO frequencies and is used in tagging
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