/[MITgcm]/manual/s_phys_pkgs/text/top_section.tex
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revision 1.33 by molod, Mon Jul 18 20:45:27 2005 UTC revision 1.34 by cnh, Tue Aug 2 21:21:05 2005 UTC
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6  <!-- CMIREDIR:packages: -->  <!-- CMIREDIR:packages: -->
7  \end{rawhtml}  \end{rawhtml}
8    
9  Within this chapter, the MITgcm ``packages'' are described.  In this chapter and in the following chapter, the MITgcm ``packages'' are
10  Initially, ``packages'' were conceived to group source code files  described. While you can carry out many experiments with MITgcm by starting
11  together based upon their functionality.  Each package was assigned a  from case studies in section \ref{sect:tutorials}, configuring
12  separate subdirectory (within \texttt{pkg}) and, usually, contained  a brand new experiment or making major changes to an experimental configuration
13  source code for implimenting different physical parametizations.  This  requires some knowledge of the {\it packages}
14  was a convenient method for both segregating and rapidly including or  that make up the full MITgcm code. Packages are used in MITgcm to
15  excluding parameterizations during the software build process.  help organize and layer various code building blocks that are assembled
16    and selected to perform a specific experiment. Each of the specific experiments
17    described in section \ref{sect:tutorials} uses a particular combination
18    of packages.
19    Figure \ref{fig:package_organigramme} shows the full set of packages that
20    are available. As shown in the figure packages are classified into different
21    groupings that layer on top of each other. The top layer packages are
22    generally specialized to specific simulation types. In this layer there are
23    packages that deal with biogeochemical processes, ocean interior
24    and boundary layer processes, atmospheric processes, sea-ice, coupled
25    simulations and state estimation.
26    Below this layer are a set of general purpose
27    numerical and computational packages. The general purpose numerical packages
28    provide code for kernel numerical alogorithms
29    that apply to
30    many different simulation types. Similarly, the general purpose computational
31    packages implement non-numerical alogorithms that provide parallelism,
32    I/O and time-keeping functions that are used in many different scenarios.
33    
34  Over time, package use has increased.  The number of packages has  
35  grown and they have evolved to contain much of the model functionality  \begin{figure}
36  including momentum schemes, I/O utilities, diagnostics, ``exchange''  \begin{minipage}{12cm}
37  algorithms for domain decomposition, and numerous physical  \marginsize{0cm}{0cm}{0cm}{0cm}
38  parameterizations.  The following sections describe how to use the  %% \scalefig{0.6}
39  existing packages and how to modify them and create new ones.  %% \epsfbox{part6/organigramme_mitgcm_pkg.eps}
40    \epsfig{file=part6/organigramme_mitgcm_pkg.eps, angle=-90, scale=0.85, width=17cm}
41    \end{minipage}
42    \label{fig:package_organigramme}
43    \caption{ Hierarchy of code layers that are assembled to make up an MITgcm
44    simulation. Conceptually (and in terms of code organization) MITgcm consists
45    of several layers. At the base is a layer of core software that provides a
46    basic numerical and computational foundation for MITgcm simulations. This
47    layer is shown marked {\bf Foundation Code} at the bottom of the figure
48    and corresponds to code in the italicised subdirectories on the figure.
49    This layer is not organized into packages. All code above the foundation layer
50    is organized as packages.  Much of the code in MITgcm is contained in packages
51    which serve as a useful way of organizing and layering the different levels of
52    functionality that make up the full MITgcm software distribution.
53    The figure shows the different packages in MITgcm as boxes containing bold
54    face upper case names.  Directly above the foundation layer are two layers of
55    general purpose infrastructure software that consist of computational and
56    numerical packages.  These general purpose packages can be applied to both
57    online and offline simulations and are used in many different physical
58    simulation types.  Above these layers are more specialized packages.  }
59    \end{figure}
60    
61    The following sections describe the packages shown in
62    figure \ref{fig:package_organiigramme}. The sections
63    layout the algorithms implemented in each package
64    and describe how to use the package. A synopsis of the function
65    of each package is given in table \ref{tab:package_summary_tab}.
66    Organizationally package code is assigned a
67    separate subdirectory in the MITgcm code distribution
68    (within the source code directory \texttt{pkg}).
69    The name of this subdirectory is used as the package name in
70    table \ref{tab:package_summary_tab}.
71    
72  %% In this chapter the schemes for parameterizing processes that are not  %% In this chapter the schemes for parameterizing processes that are not
73  %% represented explicitly in MITgcm are described.  Some of these  %% represented explicitly in MITgcm are described.  Some of these

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