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\chapter{Physical Parameterization and Packages} |
\chapter{Physical Parameterizations - Packages I} |
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\begin{rawhtml} |
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Within this chapter, the MITgcm ``packages'' are described. |
<!-- CMIREDIR:packages: --> |
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Initially, ``packages'' were conceived to group source code files |
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together based upon their functionality. Each package was assigned a |
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separate subdirectory (within \texttt{pkg}) and, usually, contained |
In this chapter and in the following chapter, the MITgcm ``packages'' are |
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source code for implimenting different physical parametizations. This |
described. While you can carry out many experiments with MITgcm by starting |
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was a convenient method for both segregating and rapidly including or |
from case studies in section \ref{sect:tutorials}, configuring |
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excluding parameterizations during the software build process. |
a brand new experiment or making major changes to an experimental configuration |
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requires some knowledge of the {\it packages} |
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Over time, package use has increased. The number of packages has |
that make up the full MITgcm code. Packages are used in MITgcm to |
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grown and they have evolved to contain much of the model functionality |
help organize and layer various code building blocks that are assembled |
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including momentum schemes, I/O utilities, diagnostics, ``exchange'' |
and selected to perform a specific experiment. Each of the specific experiments |
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algorithms for domain decomposition, and numerous physical |
described in section \ref{sect:tutorials} uses a particular combination |
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parameterizations. The following sections describe how to use the |
of packages. |
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existing packages and how to modify them and create new ones. |
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 |
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groupings that layer on top of each other. The top layer packages are |
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generally specialized to specific simulation types. In this layer there are |
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packages that deal with biogeochemical processes, ocean interior |
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and boundary layer processes, atmospheric processes, sea-ice, coupled |
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simulations and state estimation. |
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Below this layer are a set of general purpose |
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numerical and computational packages. The general purpose numerical packages |
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provide code for kernel numerical alogorithms |
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that apply to |
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many different simulation types. Similarly, the general purpose computational |
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packages implement non-numerical alogorithms that provide parallelism, |
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I/O and time-keeping functions that are used in many different scenarios. |
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\begin{figure} |
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\begin{minipage}{12cm} |
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\marginsize{0cm}{0cm}{0cm}{0cm} |
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%% \scalefig{0.6} |
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%% \epsfbox{part6/organigramme_mitgcm_pkg.eps} |
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\epsfig{file=part6/organigramme_mitgcm_pkg.eps, angle=-90, scale=0.85, width=17cm} |
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\end{minipage} |
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\label{fig:package_organigramme} |
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\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 |
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of several layers. At the base is a layer of core software that provides a |
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basic numerical and computational foundation for MITgcm simulations. This |
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layer is shown marked {\bf Foundation Code} at the bottom of the figure |
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and corresponds to code in the italicised subdirectories on the figure. |
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This layer is not organized into packages. All code above the foundation layer |
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is organized as packages. Much of the code in MITgcm is contained in packages |
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which serve as a useful way of organizing and layering the different levels of |
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functionality that make up the full MITgcm software distribution. |
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The figure shows the different packages in MITgcm as boxes containing bold |
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face upper case names. Directly above the foundation layer are two layers of |
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general purpose infrastructure software that consist of computational and |
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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 |
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simulation types. Above these layers are more specialized packages. } |
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\end{figure} |
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The following sections describe the packages shown in |
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figure \ref{fig:package_organiigramme}. The sections |
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layout the algorithms implemented in each package |
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and describe how to use the package. A synopsis of the function |
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of each package is given in table \ref{tab:package_summary_tab}. |
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Organizationally package code is assigned a |
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separate subdirectory in the MITgcm code distribution |
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(within the source code directory \texttt{pkg}). |
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The name of this subdirectory is used as the package name in |
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table \ref{tab:package_summary_tab}. |
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%% In this chapter the schemes for parameterizing processes that are not |
%% In this chapter the schemes for parameterizing processes that are not |
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%% represented explicitly in MITgcm are described. Some of these |
%% represented explicitly in MITgcm are described. Some of these |
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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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% Overview |
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\newpage |
\newpage |
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\input{part6/packages.tex} |
\input{part6/packages.tex} |
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% Packages Related to Hydrodynamical Kernel |
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\newpage |
\newpage |
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\input{part6/gmredi.tex} |
\section{Packages Related to Hydrodynamical Kernel} |
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\input{part6/generic_advdiff.tex} |
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\newpage |
\newpage |
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\input{part6/dic.tex} |
\input{part6/zonal_filt.tex} |
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\newpage |
\newpage |
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\input{part6/kpp.tex} |
\input{part6/exch2.tex} |
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\newpage |
\newpage |
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\input{part6/thsice.tex} |
\input{part6/gridalt.tex} |
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\newpage |
% Some Mention of Packages that are part of the main model document |
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\input{part6/bulk_force.tex} |
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% Ocean Packages |
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\newpage |
\newpage |
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\input{part6/generic_advdiff.tex} |
\section{Ocean Packages} |
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\input{part6/gmredi.tex} |
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\newpage |
\newpage |
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\input{part6/aim.tex} |
\input{part6/kpp.tex} |
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\newpage |
\newpage |
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\input{part6/land.tex} |
\input{part6/bulk_force.tex} |
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\newpage |
\newpage |
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\input{part6/aim_compon_interf.tex} |
\input{part6/exf.tex} |
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\newpage |
\newpage |
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\input{part6/aim_ocn_coupler.tex} |
\input{part6/cal.tex} |
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\section{Atmosphere Packages} |
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\newpage |
\newpage |
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\input{part6/component_communications.tex} |
\input{part6/aim.tex} |
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\newpage |
\newpage |
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\input{part6/mnc.tex} |
\input{part6/land.tex} |
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\newpage |
%% FIZHI is *** PRIVATE *** |
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\input{part6/mdsio.tex} |
%\begin{versionprivate} |
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\newpage |
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\input{part6/fizhi.tex} |
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%\end{versionprivate} |
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\section{Sea Ice Packages} |
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\newpage |
\newpage |
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\input{part6/monitor.tex} |
\input{part6/thsice.tex} |
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\newpage |
\newpage |
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\input{part6/exch2.tex} |
\input{part6/seaice.tex} |
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\section{Packages Related to Coupled Model} |
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\newpage |
\newpage |
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\input{part6/fizhi.tex} |
\input{part6/aim_compon_interf.tex} |
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\newpage |
\newpage |
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\input{part6/diagnostics.tex} |
\input{part6/aim_ocn_coupler.tex} |
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\newpage |
\newpage |
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\input{part6/rw.tex} |
\input{part6/component_communications.tex} |
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\section{Biogeochemistry Packages} |
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\newpage |
\newpage |
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\input{part6/zonal_filt.tex} |
\input{part6/gchem.tex} |
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\newpage |
\newpage |
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\input{part6/gchem.tex} |
\input{part6/dic.tex} |
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