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% $Header: /u/gcmpack/manual/s_phys_pkgs/text/top_section.tex,v 1.50 2014/08/29 17:07:41 jmc Exp $ |
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% $Name: $ |
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\chapter{Physical Parameterizations - Packages I} |
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\label{chap:packagesI} |
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\begin{rawhtml} |
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<!-- CMIREDIR:packages: --> |
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\end{rawhtml} |
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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 |
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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 |
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requires some knowledge of the {\it packages} |
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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 |
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and selected to perform a specific experiment. Each of the specific experiments |
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described in section \ref{sec:modelExamples} uses a particular combination |
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of packages. |
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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{s_phys_pkgs/figs/organigramme_mitgcm_pkg.eps} |
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%%\epsfig{file=s_phys_pkgs/figs/organigramme_mitgcm_pkg.eps, angle=-90, scale=0.85, width=17cm} |
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%%\end{minipage} |
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%\resizebox{5.5in}{!}{\includegraphics{s_phys_pkgs/figs/organigramme_mitgcm_pkg2.eps}} |
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\resizebox{5.5in}{!}{\includegraphics{s_phys_pkgs/figs/mitgcm_package_organisation.eps}} |
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\\ |
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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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\label{fig:package_organigramme} |
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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_organigramme}. Section \ref{sec:pkg:using} |
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describes the general procedure for using any package in MITgcm. |
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Following that sections \ref{sec:pkg:gad}-\ref{sec:pkg:monitor} |
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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 |
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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 |
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%% represented explicitly in MITgcm are described. Some of these |
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%% processes are sub-grid scale (SGS) phenomena, other processes, such as |
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%% 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 |
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\newpage |
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\input{s_phys_pkgs/text/packages.tex} |
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% Packages Related to Hydrodynamical Kernel |
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\newpage |
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\section{Packages Related to Hydrodynamical Kernel} |
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\input{s_phys_pkgs/text/generic_advdiff.tex} |
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\newpage |
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\input{s_phys_pkgs/text/shap_filt.tex} |
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\newpage |
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\input{s_phys_pkgs/text/zonal_filt.tex} |
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\newpage |
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\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 |
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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 |
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\newpage |
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\section{Ocean Packages} |
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\input{s_phys_pkgs/text/gmredi.tex} |
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\newpage |
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\input{s_phys_pkgs/text/kpp.tex} |
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\newpage |
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\input{s_phys_pkgs/text/ggl90.tex} |
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\newpage |
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\input{s_phys_pkgs/text/opps.tex} |
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\newpage |
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\input{s_phys_pkgs/text/kl10.tex} |
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\newpage |
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\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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\newpage |
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\input{s_phys_pkgs/text/cal.tex} |
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\newpage |
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\section{Atmosphere Packages} |
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\input{s_phys_pkgs/text/aim.tex} |
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\newpage |
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\input{s_phys_pkgs/text/land.tex} |
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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} |
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\input{s_phys_pkgs/text/thsice.tex} |
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\newpage |
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\input{s_phys_pkgs/text/seaice.tex} |
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\newpage |
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\input{s_phys_pkgs/text/shelfice.tex} |
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\newpage |
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dgoldberg |
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\input{s_phys_pkgs/text/streamice.tex} |
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\newpage |
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\section{Packages Related to Coupled Model} |
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\input{s_phys_pkgs/text/aim_compon_interf.tex} |
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\newpage |
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\input{s_phys_pkgs/text/atm_ocn_coupler.tex} |
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\newpage |
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\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 |
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\input{s_phys_pkgs/text/dic.tex} |
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