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1  % $Header$  % $Header$
2  % $Name$  % $Name$
3    
4  \chapter{Physical Parameterization and Packages}  \chapter{Physical Parameterizations - Packages I}
5    \label{chap:packagesI}
6    
7    \begin{rawhtml}
8    <!-- CMIREDIR:packages: -->
9    \end{rawhtml}
10    
11    In this chapter and in the following chapter, the MITgcm ``packages'' are
12    described. While you can carry out many experiments with MITgcm by starting
13    from case studies in section \ref{sec:modelExamples}, configuring
14    a brand new experiment or making major changes to an experimental configuration
15    requires some knowledge of the {\it packages}
16    that make up the full MITgcm code. Packages are used in MITgcm to
17    help organize and layer various code building blocks that are assembled
18    and selected to perform a specific experiment. Each of the specific experiments
19    described in section \ref{sec:modelExamples} uses a particular combination
20    of packages.
21    Figure \ref{fig:package_organigramme} shows the full set of packages that
22    are available. As shown in the figure packages are classified into different
23    groupings that layer on top of each other. The top layer packages are
24    generally specialized to specific simulation types. In this layer there are
25    packages that deal with biogeochemical processes, ocean interior
26    and boundary layer processes, atmospheric processes, sea-ice, coupled
27    simulations and state estimation.
28    Below this layer are a set of general purpose
29    numerical and computational packages. The general purpose numerical packages
30    provide code for kernel numerical alogorithms
31    that apply to
32    many different simulation types. Similarly, the general purpose computational
33    packages implement non-numerical alogorithms that provide parallelism,
34    I/O and time-keeping functions that are used in many different scenarios.
35    
36    \begin{figure}
37    %%\begin{minipage}{12cm}
38    %%\marginsize{0cm}{0cm}{0cm}{0cm}
39    %% \scalefig{0.6}
40    %% \epsfbox{s_phys_pkgs/figs/organigramme_mitgcm_pkg.eps}
41    %%\epsfig{file=s_phys_pkgs/figs/organigramme_mitgcm_pkg.eps, angle=-90, scale=0.85, width=17cm}
42    %%\end{minipage}
43    %\resizebox{5.5in}{!}{\includegraphics{s_phys_pkgs/figs/organigramme_mitgcm_pkg2.eps}}
44    \resizebox{5.5in}{!}{\includegraphics{s_phys_pkgs/figs/mitgcm_package_organisation.eps}}
45    \\
46    \caption{ Hierarchy of code layers that are assembled to make up an MITgcm
47    simulation. Conceptually (and in terms of code organization) MITgcm consists
48    of several layers. At the base is a layer of core software that provides a
49    basic numerical and computational foundation for MITgcm simulations. This
50    layer is shown marked {\bf Foundation Code} at the bottom of the figure
51    and corresponds to code in the italicised subdirectories on the figure.
52    This layer is not organized into packages. All code above the foundation layer
53    is organized as packages.  Much of the code in MITgcm is contained in packages
54    which serve as a useful way of organizing and layering the different levels of
55    functionality that make up the full MITgcm software distribution.
56    The figure shows the different packages in MITgcm as boxes containing bold
57    face upper case names.  Directly above the foundation layer are two layers of
58    general purpose infrastructure software that consist of computational and
59    numerical packages.  These general purpose packages can be applied to both
60    online and offline simulations and are used in many different physical
61    simulation types.  Above these layers are more specialized packages.  }
62    \label{fig:package_organigramme}
63    \end{figure}
64    
65    The following sections describe the packages shown in
66    figure \ref{fig:package_organigramme}. Section \ref{sec:pkg:using}
67    describes the general procedure for using any package in MITgcm.
68    Following that sections \ref{sec:pkg:gad}-\ref{sec:pkg:monitor}
69    layout the algorithms implemented in specific packages
70    and describe how to use the individual packages. A brief synopsis of the
71    function of each package is given in table \ref{tab:package_summary_tab}.
72    Organizationally package code is assigned a
73    separate subdirectory in the MITgcm code distribution
74    (within the source code directory \texttt{pkg}).
75    The name of this subdirectory is used as the package name in
76    table \ref{tab:package_summary_tab}.
77    
78    %% In this chapter the schemes for parameterizing processes that are not
79    %% represented explicitly in MITgcm are described.  Some of these
80    %% processes are sub-grid scale (SGS) phenomena, other processes, such as
81    %% open-boundaries, are external to the simulation.
82    
83    \begin{table}
84    \caption{~}
85    \label{tab:package_summary_tab}.
86    \end{table}
87    
88    % Overview
89    \newpage
90    \input{s_phys_pkgs/text/packages.tex}
91    
92    % Packages Related to Hydrodynamical Kernel
93    \newpage
94    \section{Packages Related to Hydrodynamical Kernel}
95    \input{s_phys_pkgs/text/generic_advdiff.tex}
96    
97    \newpage
98    \input{s_phys_pkgs/text/shap_filt.tex}
99    
100    \newpage
101    \input{s_phys_pkgs/text/zonal_filt.tex}
102    
103    \newpage
104    \input{s_phys_pkgs/text/exch2.tex}
105    
106    \newpage
107    \input{s_phys_pkgs/text/gridalt.tex}
108    
109    % Some Mention of Packages that are part of the main model document
110    \newpage
111    \section{General purpose numerical infrastructure packages}
112    \input{s_phys_pkgs/text/obcs.tex}
113    
114    \newpage
115    \input{s_phys_pkgs/text/rbcs.tex}
116    
117    \newpage
118    \input{s_phys_pkgs/text/ptracers.tex}
119    
120    % Ocean Packages
121    \newpage
122    \section{Ocean Packages}
123    \input{s_phys_pkgs/text/gmredi.tex}
124    
125    \newpage
126    \input{s_phys_pkgs/text/kpp.tex}
127    
128    \newpage
129    \input{s_phys_pkgs/text/ggl90.tex}
130    
131    \newpage
132    \input{s_phys_pkgs/text/opps.tex}
133    
134    \newpage
135    \input{s_phys_pkgs/text/kl10.tex}
136    
137    \newpage
138    \input{s_phys_pkgs/text/bulk_force.tex}
139    
140    \newpage
141    \input{s_phys_pkgs/text/exf.tex}
142    
143    \newpage
144    \input{s_phys_pkgs/text/cal.tex}
145    
146    \newpage
147    \section{Atmosphere Packages}
148    \input{s_phys_pkgs/text/aim.tex}
149    
150    \newpage
151    \input{s_phys_pkgs/text/land.tex}
152    
153    \newpage
154    \input{s_phys_pkgs/text/fizhi.tex}
155    
156    \newpage
157    \section{Sea Ice Packages}
158    \input{s_phys_pkgs/text/thsice.tex}
159    
160    \newpage
161    \input{s_phys_pkgs/text/seaice.tex}
162    
163    \newpage
164    \input{s_phys_pkgs/text/shelfice.tex}
165    
166    \newpage
167    \input{s_phys_pkgs/text/streamice.tex}
168    
169    \newpage
170    \section{Packages Related to Coupled Model}
171    \input{s_phys_pkgs/text/aim_compon_interf.tex}
172    
173    \newpage
174    \input{s_phys_pkgs/text/atm_ocn_coupler.tex}
175    
176    \newpage
177    \input{s_phys_pkgs/text/component_communications.tex}
178    
179    \newpage
180    \section{Biogeochemistry Packages}
181    \input{s_phys_pkgs/text/gchem.tex}
182    
183    \newpage
184    \input{s_phys_pkgs/text/dic.tex}
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