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1 % $Header: /u/gcmpack/manual/s_phys_pkgs/text/top_section.tex,v 1.49 2013/11/26 20:35:57 dgoldberg Exp $
2 % $Name: $
3
4 \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 \\
45 \caption{ Hierarchy of code layers that are assembled to make up an MITgcm
46 simulation. Conceptually (and in terms of code organization) MITgcm consists
47 of several layers. At the base is a layer of core software that provides a
48 basic numerical and computational foundation for MITgcm simulations. This
49 layer is shown marked {\bf Foundation Code} at the bottom of the figure
50 and corresponds to code in the italicised subdirectories on the figure.
51 This layer is not organized into packages. All code above the foundation layer
52 is organized as packages. Much of the code in MITgcm is contained in packages
53 which serve as a useful way of organizing and layering the different levels of
54 functionality that make up the full MITgcm software distribution.
55 The figure shows the different packages in MITgcm as boxes containing bold
56 face upper case names. Directly above the foundation layer are two layers of
57 general purpose infrastructure software that consist of computational and
58 numerical packages. These general purpose packages can be applied to both
59 online and offline simulations and are used in many different physical
60 simulation types. Above these layers are more specialized packages. }
61 \label{fig:package_organigramme}
62 \end{figure}
63
64 The following sections describe the packages shown in
65 figure \ref{fig:package_organigramme}. Section \ref{sec:pkg:using}
66 describes the general procedure for using any package in MITgcm.
67 Following that sections \ref{sec:pkg:gad}-\ref{sec:pkg:monitor}
68 layout the algorithms implemented in specific packages
69 and describe how to use the individual packages. A brief synopsis of the
70 function of each package is given in table \ref{tab:package_summary_tab}.
71 Organizationally package code is assigned a
72 separate subdirectory in the MITgcm code distribution
73 (within the source code directory \texttt{pkg}).
74 The name of this subdirectory is used as the package name in
75 table \ref{tab:package_summary_tab}.
76
77 %% In this chapter the schemes for parameterizing processes that are not
78 %% represented explicitly in MITgcm are described. Some of these
79 %% processes are sub-grid scale (SGS) phenomena, other processes, such as
80 %% open-boundaries, are external to the simulation.
81
82 \begin{table}
83 \caption{~}
84 \label{tab:package_summary_tab}.
85 \end{table}
86
87 % Overview
88 \newpage
89 \input{s_phys_pkgs/text/packages.tex}
90
91 % Packages Related to Hydrodynamical Kernel
92 \newpage
93 \section{Packages Related to Hydrodynamical Kernel}
94 \input{s_phys_pkgs/text/generic_advdiff.tex}
95
96 \newpage
97 \input{s_phys_pkgs/text/shap_filt.tex}
98
99 \newpage
100 \input{s_phys_pkgs/text/zonal_filt.tex}
101
102 \newpage
103 \input{s_phys_pkgs/text/exch2.tex}
104
105 \newpage
106 \input{s_phys_pkgs/text/gridalt.tex}
107
108 % Some Mention of Packages that are part of the main model document
109 \newpage
110 \section{General purpose numerical infrastructure packages}
111 \input{s_phys_pkgs/text/obcs.tex}
112
113 \newpage
114 \input{s_phys_pkgs/text/rbcs.tex}
115
116 \newpage
117 \input{s_phys_pkgs/text/ptracers.tex}
118
119 % Ocean Packages
120 \newpage
121 \section{Ocean Packages}
122 \input{s_phys_pkgs/text/gmredi.tex}
123
124 \newpage
125 \input{s_phys_pkgs/text/kpp.tex}
126
127 \newpage
128 \input{s_phys_pkgs/text/ggl90.tex}
129
130 \newpage
131 \input{s_phys_pkgs/text/opps.tex}
132
133 \newpage
134 \input{s_phys_pkgs/text/kl10.tex}
135
136 \newpage
137 \input{s_phys_pkgs/text/bulk_force.tex}
138
139 \newpage
140 \input{s_phys_pkgs/text/exf.tex}
141
142 \newpage
143 \input{s_phys_pkgs/text/cal.tex}
144
145 \newpage
146 \section{Atmosphere Packages}
147 \input{s_phys_pkgs/text/aim.tex}
148
149 \newpage
150 \input{s_phys_pkgs/text/land.tex}
151
152 \newpage
153 \input{s_phys_pkgs/text/fizhi.tex}
154
155 \newpage
156 \section{Sea Ice Packages}
157 \input{s_phys_pkgs/text/thsice.tex}
158
159 \newpage
160 \input{s_phys_pkgs/text/seaice.tex}
161
162 \newpage
163 \input{s_phys_pkgs/text/shelfice.tex}
164
165 \newpage
166 \input{s_phys_pkgs/text/streamice.tex}
167
168 \newpage
169 \section{Packages Related to Coupled Model}
170 \input{s_phys_pkgs/text/aim_compon_interf.tex}
171
172 \newpage
173 \input{s_phys_pkgs/text/atm_ocn_coupler.tex}
174
175 \newpage
176 \input{s_phys_pkgs/text/component_communications.tex}
177
178 \newpage
179 \section{Biogeochemistry Packages}
180 \input{s_phys_pkgs/text/gchem.tex}
181
182 \newpage
183 \input{s_phys_pkgs/text/dic.tex}

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