s_phys_pkgs/text/top_section.tex

% $Header: /u/gcmpack/manual/part6/part6.tex,v 1.32 2005/07/14 21:04:52 heimbach Exp $
% $Name:  $

\chapter{Physical Parameterizations - Packages I}
\begin{rawhtml}
<!-- CMIREDIR:packages: -->
\end{rawhtml}

Within this chapter, the MITgcm ``packages'' are described.
Initially, ``packages'' were conceived to group source code files
together based upon their functionality.  Each package was assigned a
separate subdirectory (within \texttt{pkg}) and, usually, contained
source code for implimenting different physical parametizations.  This
was a convenient method for both segregating and rapidly including or
excluding parameterizations during the software build process.

Over time, package use has increased.  The number of packages has
grown and they have evolved to contain much of the model functionality
including momentum schemes, I/O utilities, diagnostics, ``exchange''
algorithms for domain decomposition, and numerous physical
parameterizations.  The following sections describe how to use the
existing packages and how to modify them and create new ones.

%% In this chapter the schemes for parameterizing processes that are not
%% represented explicitly in MITgcm are described.  Some of these
%% processes are sub-grid scale (SGS) phenomena, other processes, such as
%% open-boundaries, are external to the simulation.

% Overview
\newpage
\input{part6/packages.tex}

% Packages Related to Hydrodynamical Kernel
\newpage
\section{Packages Related to Hydrodynamical Kernel}
\input{part6/generic_advdiff.tex}

\newpage
\input{part6/zonal_filt.tex}

\newpage
\input{part6/exch2.tex}

\newpage
\input{part6/gridalt.tex}

% Some Mention of Packages that are part of the main model document

% Ocean Packages
\newpage
\section{Ocean Packages}
\input{part6/gmredi.tex}

\newpage
\input{part6/kpp.tex}

\newpage
\input{part6/bulk_force.tex}

\newpage
\input{part6/exf.tex}

\newpage
\input{part6/cal.tex}

\section{Atmosphere Packages}
\newpage
\input{part6/aim.tex}

\newpage
\input{part6/land.tex}

%% FIZHI is *** PRIVATE ***
%\begin{versionprivate}
  \newpage
  \input{part6/fizhi.tex}
%\end{versionprivate}

\section{Sea Ice Packages}
\newpage
\input{part6/thsice.tex}

\newpage
\input{part6/seaice.tex}

\section{Packages Related to Coupled Model}
\newpage
\input{part6/aim_compon_interf.tex}

\newpage
\input{part6/aim_ocn_coupler.tex}

\newpage
\input{part6/component_communications.tex}

\section{Biogeochemistry Packages}
\newpage
\input{part6/gchem.tex}

\newpage
\input{part6/dic.tex}
1	molod	1.33	% $Header: /u/gcmpack/manual/part6/part6.tex,v 1.32 2005/07/14 21:04:52 heimbach Exp $
2	adcroft	1.2	% $Name: $
3	adcroft	1.1
4	molod	1.33	\chapter{Physical Parameterizations - Packages I}
5	edhill	1.30	\begin{rawhtml}
6			<!-- CMIREDIR:packages: -->
7			\end{rawhtml}
8	cnh	1.4
9	edhill	1.25	Within this chapter, the MITgcm ``packages'' are described.
10			Initially, ``packages'' were conceived to group source code files
11			together based upon their functionality. Each package was assigned a
12			separate subdirectory (within \texttt{pkg}) and, usually, contained
13			source code for implimenting different physical parametizations. This
14			was a convenient method for both segregating and rapidly including or
15			excluding parameterizations during the software build process.
16
17	edhill	1.26	Over time, package use has increased. The number of packages has
18			grown and they have evolved to contain much of the model functionality
19	edhill	1.25	including momentum schemes, I/O utilities, diagnostics, ``exchange''
20	edhill	1.26	algorithms for domain decomposition, and numerous physical
21			parameterizations. The following sections describe how to use the
22			existing packages and how to modify them and create new ones.
23	edhill	1.25
24			%% In this chapter the schemes for parameterizing processes that are not
25			%% represented explicitly in MITgcm are described. Some of these
26			%% processes are sub-grid scale (SGS) phenomena, other processes, such as
27			%% open-boundaries, are external to the simulation.
28
29	molod	1.33	% Overview
30	edhill	1.25	\newpage
31			\input{part6/packages.tex}
32	cnh	1.4
33	molod	1.33	% Packages Related to Hydrodynamical Kernel
34	edhill	1.19	\newpage
35	molod	1.33	\section{Packages Related to Hydrodynamical Kernel}
36			\input{part6/generic_advdiff.tex}
37	edhill	1.27
38			\newpage
39	molod	1.33	\input{part6/zonal_filt.tex}
40	edhill	1.19
41			\newpage
42	molod	1.33	\input{part6/exch2.tex}
43	edhill	1.19
44			\newpage
45	molod	1.33	\input{part6/gridalt.tex}
46
47			% Some Mention of Packages that are part of the main model document
48	edhill	1.19
49	molod	1.33	% Ocean Packages
50	edhill	1.19	\newpage
51	molod	1.33	\section{Ocean Packages}
52			\input{part6/gmredi.tex}
53	edhill	1.29
54			\newpage
55	molod	1.33	\input{part6/kpp.tex}
56	edhill	1.24
57			\newpage
58	molod	1.33	\input{part6/bulk_force.tex}
59	heimbach	1.32
60			\newpage
61			\input{part6/exf.tex}
62
63			\newpage
64	molod	1.33	\input{part6/cal.tex}
65	jmc	1.20
66	molod	1.33	\section{Atmosphere Packages}
67	jmc	1.20	\newpage
68			\input{part6/aim.tex}
69	edhill	1.19
70			\newpage
71			\input{part6/land.tex}
72
73	molod	1.33	%% FIZHI is * PRIVATE *
74			%\begin{versionprivate}
75			\newpage
76			\input{part6/fizhi.tex}
77			%\end{versionprivate}
78	edhill	1.19
79	molod	1.33	\section{Sea Ice Packages}
80	edhill	1.19	\newpage
81	molod	1.33	\input{part6/thsice.tex}
82	edhill	1.19
83			\newpage
84	molod	1.33	\input{part6/seaice.tex}
85	edhill	1.19
86	molod	1.33	\section{Packages Related to Coupled Model}
87	edhill	1.19	\newpage
88	molod	1.33	\input{part6/aim_compon_interf.tex}
89	edhill	1.23
90			\newpage
91	molod	1.33	\input{part6/aim_ocn_coupler.tex}
92	edhill	1.19
93			\newpage
94	molod	1.33	\input{part6/component_communications.tex}
95	edhill	1.19
96	molod	1.33	\section{Biogeochemistry Packages}
97	edhill	1.19	\newpage
98	molod	1.33	\input{part6/gchem.tex}
99	cnh	1.15
100	molod	1.31	\newpage
101	molod	1.33	\input{part6/dic.tex}