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% $Name$ |
% $Name$ |
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\chapter{Physical Parameterizations - Packages I} |
\chapter{Physical Parameterizations - Packages I} |
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\label{chap:packagesI} |
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\begin{rawhtml} |
\begin{rawhtml} |
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<!-- CMIREDIR:packages: --> |
<!-- CMIREDIR:packages: --> |
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\end{rawhtml} |
\end{rawhtml} |
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In this chapter and in the following chapter, the MITgcm ``packages'' are |
In this chapter and in the following chapter, the MITgcm ``packages'' are |
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described. While you can carry out many experiments with MITgcm by starting |
described. While you can carry out many experiments with MITgcm by starting |
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from case studies in section \ref{sect:tutorials}, configuring |
from case studies in section \ref{sec:modelExamples}, configuring |
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a brand new experiment or making major changes to an experimental configuration |
a brand new experiment or making major changes to an experimental configuration |
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requires some knowledge of the {\it packages} |
requires some knowledge of the {\it packages} |
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that make up the full MITgcm code. Packages are used in MITgcm to |
that make up the full MITgcm code. Packages are used in MITgcm to |
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help organize and layer various code building blocks that are assembled |
help organize and layer various code building blocks that are assembled |
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and selected to perform a specific experiment. Each of the specific experiments |
and selected to perform a specific experiment. Each of the specific experiments |
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described in section \ref{sect:tutorials} uses a particular combination |
described in section \ref{sec:modelExamples} uses a particular combination |
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of packages. |
of packages. |
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Figure \ref{fig:package_organigramme} shows the full set of packages that |
Figure \ref{fig:package_organigramme} shows the full set of packages that |
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are available. As shown in the figure packages are classified into different |
are available. As shown in the figure packages are classified into different |
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\begin{figure} |
\begin{figure} |
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\begin{minipage}{12cm} |
%%\begin{minipage}{12cm} |
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\marginsize{0cm}{0cm}{0cm}{0cm} |
%%\marginsize{0cm}{0cm}{0cm}{0cm} |
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%% \scalefig{0.6} |
%% \scalefig{0.6} |
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%% \epsfbox{part6/organigramme_mitgcm_pkg.eps} |
%% \epsfbox{s_phys_pkgs/figs/organigramme_mitgcm_pkg.eps} |
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\epsfig{file=part6/organigramme_mitgcm_pkg.eps, angle=-90, scale=0.85, width=17cm} |
%%\epsfig{file=s_phys_pkgs/figs/organigramme_mitgcm_pkg.eps, angle=-90, scale=0.85, width=17cm} |
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\end{minipage} |
%%\end{minipage} |
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\label{fig:package_organigramme} |
\resizebox{5.5in}{!}{\includegraphics{s_phys_pkgs/figs/organigramme_mitgcm_pkg2.eps}} |
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\\ |
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\caption{ Hierarchy of code layers that are assembled to make up an MITgcm |
\caption{ Hierarchy of code layers that are assembled to make up an MITgcm |
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simulation. Conceptually (and in terms of code organization) MITgcm consists |
simulation. Conceptually (and in terms of code organization) MITgcm consists |
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of several layers. At the base is a layer of core software that provides a |
of several layers. At the base is a layer of core software that provides a |
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numerical packages. These general purpose packages can be applied to both |
numerical packages. These general purpose packages can be applied to both |
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online and offline simulations and are used in many different physical |
online and offline simulations and are used in many different physical |
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simulation types. Above these layers are more specialized packages. } |
simulation types. Above these layers are more specialized packages. } |
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\label{fig:package_organigramme} |
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\end{figure} |
\end{figure} |
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The following sections describe the packages shown in |
The following sections describe the packages shown in |
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figure \ref{fig:package_organiigramme}. The sections |
figure \ref{fig:package_organigramme}. Section \ref{sec:pkg:using} |
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layout the algorithms implemented in each package |
describes the general procedure for using any package in MITgcm. |
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and describe how to use the package. A synopsis of the function |
Following that sections \ref{sec:pkg:gad}-\ref{sec:pkg:monitor} |
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of each package is given in table \ref{tab:package_summary_tab}. |
layout the algorithms implemented in specific packages |
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and describe how to use the individual packages. A brief synopsis of the |
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function of each package is given in table \ref{tab:package_summary_tab}. |
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Organizationally package code is assigned a |
Organizationally package code is assigned a |
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separate subdirectory in the MITgcm code distribution |
separate subdirectory in the MITgcm code distribution |
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(within the source code directory \texttt{pkg}). |
(within the source code directory \texttt{pkg}). |
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%% processes are sub-grid scale (SGS) phenomena, other processes, such as |
%% processes are sub-grid scale (SGS) phenomena, other processes, such as |
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%% open-boundaries, are external to the simulation. |
%% open-boundaries, are external to the simulation. |
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\begin{table} |
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\caption{~} |
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\label{tab:package_summary_tab}. |
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\end{table} |
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% Overview |
% Overview |
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\newpage |
\newpage |
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\input{part6/packages.tex} |
\input{s_phys_pkgs/text/packages.tex} |
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% Packages Related to Hydrodynamical Kernel |
% Packages Related to Hydrodynamical Kernel |
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\newpage |
\newpage |
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\section{Packages Related to Hydrodynamical Kernel} |
\section{Packages Related to Hydrodynamical Kernel} |
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\input{part6/generic_advdiff.tex} |
\input{s_phys_pkgs/text/generic_advdiff.tex} |
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\newpage |
\newpage |
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\input{part6/zonal_filt.tex} |
\input{s_phys_pkgs/text/shap_filt.tex} |
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\newpage |
\newpage |
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\input{part6/exch2.tex} |
\input{s_phys_pkgs/text/zonal_filt.tex} |
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\newpage |
\newpage |
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\input{part6/gridalt.tex} |
\input{s_phys_pkgs/text/exch2.tex} |
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\newpage |
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\input{s_phys_pkgs/text/gridalt.tex} |
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% Some Mention of Packages that are part of the main model document |
% Some Mention of Packages that are part of the main model document |
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\newpage |
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\section{General purpose numerical infrastructure packages} |
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\input{s_phys_pkgs/text/obcs.tex} |
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\newpage |
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\input{s_phys_pkgs/text/rbcs.tex} |
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\newpage |
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\input{s_phys_pkgs/text/ptracers.tex} |
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% Ocean Packages |
% Ocean Packages |
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\newpage |
\newpage |
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\section{Ocean Packages} |
\section{Ocean Packages} |
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\input{part6/gmredi.tex} |
\input{s_phys_pkgs/text/gmredi.tex} |
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\newpage |
\newpage |
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\input{part6/kpp.tex} |
\input{s_phys_pkgs/text/kpp.tex} |
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\newpage |
\newpage |
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\input{part6/bulk_force.tex} |
\input{s_phys_pkgs/text/ggl90.tex} |
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\newpage |
\newpage |
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\input{part6/exf.tex} |
\input{s_phys_pkgs/text/opps.tex} |
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\newpage |
\newpage |
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\input{part6/cal.tex} |
\input{s_phys_pkgs/text/bulk_force.tex} |
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\newpage |
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\input{s_phys_pkgs/text/exf.tex} |
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\section{Atmosphere Packages} |
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\newpage |
\newpage |
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\input{part6/aim.tex} |
\input{s_phys_pkgs/text/cal.tex} |
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\newpage |
\newpage |
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\input{part6/land.tex} |
\section{Atmosphere Packages} |
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\input{s_phys_pkgs/text/aim.tex} |
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%% FIZHI is *** PRIVATE *** |
\newpage |
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%\begin{versionprivate} |
\input{s_phys_pkgs/text/land.tex} |
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\newpage |
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\input{part6/fizhi.tex} |
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%\end{versionprivate} |
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\newpage |
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\input{s_phys_pkgs/text/fizhi.tex} |
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\newpage |
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\section{Sea Ice Packages} |
\section{Sea Ice Packages} |
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\input{s_phys_pkgs/text/thsice.tex} |
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\newpage |
\newpage |
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\input{part6/thsice.tex} |
\input{s_phys_pkgs/text/seaice.tex} |
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\newpage |
\newpage |
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\input{part6/seaice.tex} |
\input{s_phys_pkgs/text/shelfice.tex} |
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\section{Packages Related to Coupled Model} |
|
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\newpage |
\newpage |
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\input{part6/aim_compon_interf.tex} |
\input{s_phys_pkgs/text/streamice.tex} |
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\newpage |
\newpage |
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\input{part6/aim_ocn_coupler.tex} |
\section{Packages Related to Coupled Model} |
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\input{s_phys_pkgs/text/aim_compon_interf.tex} |
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\newpage |
\newpage |
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\input{part6/component_communications.tex} |
\input{s_phys_pkgs/text/atm_ocn_coupler.tex} |
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\section{Biogeochemistry Packages} |
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\newpage |
\newpage |
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\input{part6/gchem.tex} |
\input{s_phys_pkgs/text/component_communications.tex} |
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\newpage |
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\section{Biogeochemistry Packages} |
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\input{s_phys_pkgs/text/gchem.tex} |
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\newpage |
\newpage |
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\input{part6/dic.tex} |
\input{s_phys_pkgs/text/dic.tex} |
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