s_phys_pkgs/text/top_section.tex

% $Header: /u/gcmpack/manual/part6/part6.tex,v 1.36 2005/08/11 23:58:07 heimbach Exp $
% $Name:  $

\chapter{Physical Parameterizations - Packages I}
\label{chap:packagesI}

\begin{rawhtml}
<!-- CMIREDIR:packages: -->
\end{rawhtml}

In this chapter and in the following chapter, the MITgcm ``packages'' are 
described. While you can carry out many experiments with MITgcm by starting 
from case studies in section \ref{sect:tutorials}, configuring
a brand new experiment or making major changes to an experimental configuration
requires some knowledge of the {\it packages}
that make up the full MITgcm code. Packages are used in MITgcm to
help organize and layer various code building blocks that are assembled 
and selected to perform a specific experiment. Each of the specific experiments
described in section \ref{sect:tutorials} uses a particular combination
of packages.
Figure \ref{fig:package_organigramme} shows the full set of packages that
are available. As shown in the figure packages are classified into different 
groupings that layer on top of each other. The top layer packages are 
generally specialized to specific simulation types. In this layer there are
packages that deal with biogeochemical processes, ocean interior
and boundary layer processes, atmospheric processes, sea-ice, coupled 
simulations and state estimation.
Below this layer are a set of general purpose
numerical and computational packages. The general purpose numerical packages
provide code for kernel numerical alogorithms
that apply to
many different simulation types. Similarly, the general purpose computational 
packages implement non-numerical alogorithms that provide parallelism,
I/O and time-keeping functions that are used in many different scenarios.


\begin{figure}
\begin{minipage}{12cm}
\marginsize{0cm}{0cm}{0cm}{0cm}
%% \scalefig{0.6}
%% \epsfbox{part6/organigramme_mitgcm_pkg.eps}
\epsfig{file=part6/organigramme_mitgcm_pkg.eps, angle=-90, scale=0.85, width=17cm}
\end{minipage}
\label{fig:package_organigramme}
\caption{ Hierarchy of code layers that are assembled to make up an MITgcm 
simulation. Conceptually (and in terms of code organization) MITgcm consists
of several layers. At the base is a layer of core software that provides a 
basic numerical and computational foundation for MITgcm simulations. This 
layer is shown marked {\bf Foundation Code} at the bottom of the figure
and corresponds to code in the italicised subdirectories on the figure.
This layer is not organized into packages. All code above the foundation layer
is organized as packages.  Much of the code in MITgcm is contained in packages 
which serve as a useful way of organizing and layering the different levels of 
functionality that make up the full MITgcm software distribution.
The figure shows the different packages in MITgcm as boxes containing bold 
face upper case names.  Directly above the foundation layer are two layers of 
general purpose infrastructure software that consist of computational and 
numerical packages.  These general purpose packages can be applied to both 
online and offline simulations and are used in many different physical 
simulation types.  Above these layers are more specialized packages.  }
\end{figure}

The following sections describe the packages shown in 
figure \ref{fig:package_organiigramme}. Section \ref{sec:pkg:using}
describes the general procedure for using any package in MITgcm.
Following that sections \ref{}-\ref{} 
layout the algorithms implemented in specific packages
and describe how to use the individual packages. A brief synopsis of the 
function of each package is given in table \ref{tab:package_summary_tab}.
Organizationally package code is assigned a
separate subdirectory in the MITgcm code distribution
(within the source code directory \texttt{pkg}).
The name of this subdirectory is used as the package name in
table \ref{tab:package_summary_tab}.

%% 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}

\newpage
\input{part6/obcs.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	edhill	1.37	% $Header: /u/gcmpack/manual/part6/part6.tex,v 1.36 2005/08/11 23:58:07 heimbach Exp $
2	adcroft	1.2	% $Name: $
3	adcroft	1.1
4	molod	1.33	\chapter{Physical Parameterizations - Packages I}
5	edhill	1.37	\label{chap:packagesI}
6
7	edhill	1.30	\begin{rawhtml}
8			<!-- CMIREDIR:packages: -->
9			\end{rawhtml}
10	cnh	1.4
11	cnh	1.34	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{sect:tutorials}, 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{sect:tutorials} 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
37			\begin{figure}
38			\begin{minipage}{12cm}
39			\marginsize{0cm}{0cm}{0cm}{0cm}
40			%% \scalefig{0.6}
41			%% \epsfbox{part6/organigramme_mitgcm_pkg.eps}
42			\epsfig{file=part6/organigramme_mitgcm_pkg.eps, angle=-90, scale=0.85, width=17cm}
43			\end{minipage}
44			\label{fig:package_organigramme}
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			\end{figure}
62
63			The following sections describe the packages shown in
64	cnh	1.35	figure \ref{fig:package_organiigramme}. Section \ref{sec:pkg:using}
65			describes the general procedure for using any package in MITgcm.
66			Following that sections \ref{}-\ref{}
67			layout the algorithms implemented in specific packages
68			and describe how to use the individual packages. A brief synopsis of the
69			function of each package is given in table \ref{tab:package_summary_tab}.
70	cnh	1.34	Organizationally package code is assigned a
71			separate subdirectory in the MITgcm code distribution
72			(within the source code directory \texttt{pkg}).
73			The name of this subdirectory is used as the package name in
74			table \ref{tab:package_summary_tab}.
75	edhill	1.25
76			%% In this chapter the schemes for parameterizing processes that are not
77			%% represented explicitly in MITgcm are described. Some of these
78			%% processes are sub-grid scale (SGS) phenomena, other processes, such as
79			%% open-boundaries, are external to the simulation.
80
81	molod	1.33	% Overview
82	edhill	1.25	\newpage
83			\input{part6/packages.tex}
84	cnh	1.4
85	molod	1.33	% Packages Related to Hydrodynamical Kernel
86	edhill	1.19	\newpage
87	molod	1.33	\section{Packages Related to Hydrodynamical Kernel}
88			\input{part6/generic_advdiff.tex}
89	edhill	1.27
90			\newpage
91	molod	1.33	\input{part6/zonal_filt.tex}
92	edhill	1.19
93			\newpage
94	molod	1.33	\input{part6/exch2.tex}
95	edhill	1.19
96			\newpage
97	molod	1.33	\input{part6/gridalt.tex}
98
99			% Some Mention of Packages that are part of the main model document
100	edhill	1.19
101	molod	1.33	% Ocean Packages
102	edhill	1.19	\newpage
103	molod	1.33	\section{Ocean Packages}
104			\input{part6/gmredi.tex}
105	edhill	1.29
106			\newpage
107	molod	1.33	\input{part6/kpp.tex}
108	edhill	1.24
109			\newpage
110	molod	1.33	\input{part6/bulk_force.tex}
111	heimbach	1.32
112			\newpage
113			\input{part6/exf.tex}
114
115			\newpage
116	molod	1.33	\input{part6/cal.tex}
117	jmc	1.20
118	heimbach	1.36	\newpage
119			\input{part6/obcs.tex}
120
121	molod	1.33	\section{Atmosphere Packages}
122	jmc	1.20	\newpage
123			\input{part6/aim.tex}
124	edhill	1.19
125			\newpage
126			\input{part6/land.tex}
127
128	molod	1.33	%% FIZHI is * PRIVATE *
129			%\begin{versionprivate}
130			\newpage
131			\input{part6/fizhi.tex}
132			%\end{versionprivate}
133	edhill	1.19
134	molod	1.33	\section{Sea Ice Packages}
135	edhill	1.19	\newpage
136	molod	1.33	\input{part6/thsice.tex}
137	edhill	1.19
138			\newpage
139	molod	1.33	\input{part6/seaice.tex}
140	edhill	1.19
141	molod	1.33	\section{Packages Related to Coupled Model}
142	edhill	1.19	\newpage
143	molod	1.33	\input{part6/aim_compon_interf.tex}
144	edhill	1.23
145			\newpage
146	molod	1.33	\input{part6/aim_ocn_coupler.tex}
147	edhill	1.19
148			\newpage
149	molod	1.33	\input{part6/component_communications.tex}
150	edhill	1.19
151	molod	1.33	\section{Biogeochemistry Packages}
152	edhill	1.19	\newpage
153	molod	1.33	\input{part6/gchem.tex}
154	cnh	1.15
155	molod	1.31	\newpage
156	molod	1.33	\input{part6/dic.tex}