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revision 1.44 by mlosch, Thu May 14 10:21:07 2009 UTC revision 1.50 by jmc, Fri Aug 29 17:07:41 2014 UTC
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1  % $eader: /u/gcmpack/manual/part6/part6.tex,v 1.40 2006/06/27 22:34:09 edhill Exp $  % $Header$
2  % $Name$  % $Name$
3    
4  \chapter{Physical Parameterizations - Packages I}  \chapter{Physical Parameterizations - Packages I}
# Line 8  Line 8 
8  <!-- CMIREDIR:packages: -->  <!-- CMIREDIR:packages: -->
9  \end{rawhtml}  \end{rawhtml}
10    
11  In this chapter and in the following chapter, the MITgcm ``packages'' are  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  described. While you can carry out many experiments with MITgcm by starting
13  from case studies in section \ref{sect:tutorials}, configuring  from case studies in section \ref{sec:modelExamples}, configuring
14  a brand new experiment or making major changes to an experimental configuration  a brand new experiment or making major changes to an experimental configuration
15  requires some knowledge of the {\it packages}  requires some knowledge of the {\it packages}
16  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
17  help organize and layer various code building blocks that are assembled  help organize and layer various code building blocks that are assembled
18  and selected to perform a specific experiment. Each of the specific experiments  and selected to perform a specific experiment. Each of the specific experiments
19  described in section \ref{sect:tutorials} uses a particular combination  described in section \ref{sec:modelExamples} uses a particular combination
20  of packages.  of packages.
21  Figure \ref{fig:package_organigramme} shows the full set of packages that  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  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  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  generally specialized to specific simulation types. In this layer there are
25  packages that deal with biogeochemical processes, ocean interior  packages that deal with biogeochemical processes, ocean interior
26  and boundary layer processes, atmospheric processes, sea-ice, coupled  and boundary layer processes, atmospheric processes, sea-ice, coupled
27  simulations and state estimation.  simulations and state estimation.
28  Below this layer are a set of general purpose  Below this layer are a set of general purpose
29  numerical and computational packages. The general purpose numerical packages  numerical and computational packages. The general purpose numerical packages
30  provide code for kernel numerical alogorithms  provide code for kernel numerical alogorithms
31  that apply to  that apply to
32  many different simulation types. Similarly, the general purpose computational  many different simulation types. Similarly, the general purpose computational
33  packages implement non-numerical alogorithms that provide parallelism,  packages implement non-numerical alogorithms that provide parallelism,
34  I/O and time-keeping functions that are used in many different scenarios.  I/O and time-keeping functions that are used in many different scenarios.
35    
   
36  \begin{figure}  \begin{figure}
37  %%\begin{minipage}{12cm}  %%\begin{minipage}{12cm}
38  %%\marginsize{0cm}{0cm}{0cm}{0cm}  %%\marginsize{0cm}{0cm}{0cm}{0cm}
39  %% \scalefig{0.6}  %% \scalefig{0.6}
40  %% \epsfbox{part6/organigramme_mitgcm_pkg.eps}  %% \epsfbox{s_phys_pkgs/figs/organigramme_mitgcm_pkg.eps}
41  %%\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}
42  %%\end{minipage}  %%\end{minipage}
43  \resizebox{5.5in}{!}{\includegraphics{part6/organigramme_mitgcm_pkg2.eps}}  \resizebox{5.5in}{!}{\includegraphics{s_phys_pkgs/figs/organigramme_mitgcm_pkg2.eps}}
44  \label{fig:package_organigramme}  \\
45  \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
46  simulation. Conceptually (and in terms of code organization) MITgcm consists  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  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  basic numerical and computational foundation for MITgcm simulations. This
49  layer is shown marked {\bf Foundation Code} at the bottom of the figure  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.  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  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  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  which serve as a useful way of organizing and layering the different levels of
54  functionality that make up the full MITgcm software distribution.  functionality that make up the full MITgcm software distribution.
55  The figure shows the different packages in MITgcm as boxes containing bold  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  face upper case names.  Directly above the foundation layer are two layers of
57  general purpose infrastructure software that consist of computational and  general purpose infrastructure software that consist of computational and
58  numerical packages.  These general purpose packages can be applied to both  numerical packages.  These general purpose packages can be applied to both
59  online and offline simulations and are used in many different physical  online and offline simulations and are used in many different physical
60  simulation types.  Above these layers are more specialized packages.  }  simulation types.  Above these layers are more specialized packages.  }
61    \label{fig:package_organigramme}
62  \end{figure}  \end{figure}
63    
64  The following sections describe the packages shown in  The following sections describe the packages shown in
65  figure \ref{fig:package_organiigramme}. Section \ref{sec:pkg:using}  figure \ref{fig:package_organigramme}. Section \ref{sec:pkg:using}
66  describes the general procedure for using any package in MITgcm.  describes the general procedure for using any package in MITgcm.
67  Following that sections \ref{}-\ref{}  Following that sections \ref{sec:pkg:gad}-\ref{sec:pkg:monitor}
68  layout the algorithms implemented in specific packages  layout the algorithms implemented in specific packages
69  and describe how to use the individual packages. A brief synopsis of the  and describe how to use the individual packages. A brief synopsis of the
70  function of each package is given in table \ref{tab:package_summary_tab}.  function of each package is given in table \ref{tab:package_summary_tab}.
71  Organizationally package code is assigned a  Organizationally package code is assigned a
72  separate subdirectory in the MITgcm code distribution  separate subdirectory in the MITgcm code distribution
# Line 79  table \ref{tab:package_summary_tab}. Line 79  table \ref{tab:package_summary_tab}.
79  %% processes are sub-grid scale (SGS) phenomena, other processes, such as  %% processes are sub-grid scale (SGS) phenomena, other processes, such as
80  %% open-boundaries, are external to the simulation.  %% open-boundaries, are external to the simulation.
81    
82    \begin{table}
83    \caption{~}
84    \label{tab:package_summary_tab}.
85    \end{table}
86    
87  % Overview  % Overview
88  \newpage  \newpage
89  \input{part6/packages.tex}  \input{s_phys_pkgs/text/packages.tex}
90    
91  % Packages Related to Hydrodynamical Kernel  % Packages Related to Hydrodynamical Kernel
92  \newpage  \newpage
93  \section{Packages Related to Hydrodynamical Kernel}  \section{Packages Related to Hydrodynamical Kernel}
94  \input{part6/generic_advdiff.tex}  \input{s_phys_pkgs/text/generic_advdiff.tex}
95    
96  \newpage  \newpage
97  \input{part6/zonal_filt.tex}  \input{s_phys_pkgs/text/shap_filt.tex}
98    
99  \newpage  \newpage
100  \input{part6/exch2.tex}  \input{s_phys_pkgs/text/zonal_filt.tex}
101    
102  \newpage  \newpage
103  \input{part6/gridalt.tex}  \input{s_phys_pkgs/text/exch2.tex}
   
 % Some Mention of Packages that are part of the main model document  
104    
105  \section{General purpose numerical infrastructure packages}  \newpage
106    \input{s_phys_pkgs/text/gridalt.tex}
107    
108    % Some Mention of Packages that are part of the main model document
109  \newpage  \newpage
110  \input{part6/obcs.tex}  \section{General purpose numerical infrastructure packages}
111    \input{s_phys_pkgs/text/obcs.tex}
112    
113  \newpage  \newpage
114  \input{part6/rbcs.tex}  \input{s_phys_pkgs/text/rbcs.tex}
115    
116  \newpage  \newpage
117  \input{part6/ptracers.tex}  \input{s_phys_pkgs/text/ptracers.tex}
118    
119  % Ocean Packages  % Ocean Packages
120  \newpage  \newpage
121  \section{Ocean Packages}  \section{Ocean Packages}
122  \input{part6/gmredi.tex}  \input{s_phys_pkgs/text/gmredi.tex}
123    
124  \newpage  \newpage
125  \input{part6/kpp.tex}  \input{s_phys_pkgs/text/kpp.tex}
126    
127  \newpage  \newpage
128  \input{part6/bulk_force.tex}  \input{s_phys_pkgs/text/ggl90.tex}
129    
130  \newpage  \newpage
131  \input{part6/exf.tex}  \input{s_phys_pkgs/text/opps.tex}
132    
133  \newpage  \newpage
134  \input{part6/cal.tex}  \input{s_phys_pkgs/text/kl10.tex}
135    
136    \newpage
137    \input{s_phys_pkgs/text/bulk_force.tex}
138    
139    \newpage
140    \input{s_phys_pkgs/text/exf.tex}
141    
 \section{Atmosphere Packages}  
142  \newpage  \newpage
143  \input{part6/aim.tex}  \input{s_phys_pkgs/text/cal.tex}
144    
145    \newpage
146    \section{Atmosphere Packages}
147    \input{s_phys_pkgs/text/aim.tex}
148    
149  \newpage  \newpage
150  \input{part6/land.tex}  \input{s_phys_pkgs/text/land.tex}
151    
152  \newpage  \newpage
153  \input{part6/fizhi.tex}  \input{s_phys_pkgs/text/fizhi.tex}
154    
155    \newpage
156  \section{Sea Ice Packages}  \section{Sea Ice Packages}
157    \input{s_phys_pkgs/text/thsice.tex}
158    
159  \newpage  \newpage
160  \input{part6/thsice.tex}  \input{s_phys_pkgs/text/seaice.tex}
161    
162  \newpage  \newpage
163  \input{part6/seaice.tex}  \input{s_phys_pkgs/text/shelfice.tex}
164    
165  \newpage  \newpage
166  \input{part6/shelfice.tex}  \input{s_phys_pkgs/text/streamice.tex}
167    
 \section{Packages Related to Coupled Model}  
168  \newpage  \newpage
169  \input{part6/aim_compon_interf.tex}  \section{Packages Related to Coupled Model}
170    \input{s_phys_pkgs/text/aim_compon_interf.tex}
171    
172  \newpage  \newpage
173  \input{part6/atm_ocn_coupler.tex}  \input{s_phys_pkgs/text/atm_ocn_coupler.tex}
174    
175  \newpage  \newpage
176  \input{part6/component_communications.tex}  \input{s_phys_pkgs/text/component_communications.tex}
177    
 \section{Biogeochemistry Packages}  
178  \newpage  \newpage
179  \input{part6/gchem.tex}  \section{Biogeochemistry Packages}
180    \input{s_phys_pkgs/text/gchem.tex}
181    
182  \newpage  \newpage
183  \input{part6/dic.tex}  \input{s_phys_pkgs/text/dic.tex}
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