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revision 1.42 by stephd, Thu Jan 17 19:31:51 2008 UTC revision 1.51 by heimbach, Wed Sep 14 02:32:11 2016 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}  \resizebox{5.5in}{!}{\includegraphics{s_phys_pkgs/figs/mitgcm_package_organisation.eps}}
45  \caption{ Hierarchy of code layers that are assembled to make up an MITgcm  \\
46    \caption{ Hierarchy of code layers that are assembled to make up an MITgcm
47  simulation. Conceptually (and in terms of code organization) MITgcm consists  simulation. Conceptually (and in terms of code organization) MITgcm consists
48  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
49  basic numerical and computational foundation for MITgcm simulations. This  basic numerical and computational foundation for MITgcm simulations. This
50  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
51  and corresponds to code in the italicised subdirectories on the figure.  and corresponds to code in the italicised subdirectories on the figure.
52  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
53  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
54  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
55  functionality that make up the full MITgcm software distribution.  functionality that make up the full MITgcm software distribution.
56  The figure shows the different packages in MITgcm as boxes containing bold  The figure shows the different packages in MITgcm as boxes containing bold
57  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
58  general purpose infrastructure software that consist of computational and  general purpose infrastructure software that consist of computational and
59  numerical packages.  These general purpose packages can be applied to both  numerical packages.  These general purpose packages can be applied to both
60  online and offline simulations and are used in many different physical  online and offline simulations and are used in many different physical
61  simulation types.  Above these layers are more specialized packages.  }  simulation types.  Above these layers are more specialized packages.  }
62    \label{fig:package_organigramme}
63  \end{figure}  \end{figure}
64    
65  The following sections describe the packages shown in  The following sections describe the packages shown in
66  figure \ref{fig:package_organiigramme}. Section \ref{sec:pkg:using}  figure \ref{fig:package_organigramme}. Section \ref{sec:pkg:using}
67  describes the general procedure for using any package in MITgcm.  describes the general procedure for using any package in MITgcm.
68  Following that sections \ref{}-\ref{}  Following that sections \ref{sec:pkg:gad}-\ref{sec:pkg:monitor}
69  layout the algorithms implemented in specific packages  layout the algorithms implemented in specific packages
70  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
71  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}.
72  Organizationally package code is assigned a  Organizationally package code is assigned a
73  separate subdirectory in the MITgcm code distribution  separate subdirectory in the MITgcm code distribution
# Line 79  table \ref{tab:package_summary_tab}. Line 80  table \ref{tab:package_summary_tab}.
80  %% processes are sub-grid scale (SGS) phenomena, other processes, such as  %% processes are sub-grid scale (SGS) phenomena, other processes, such as
81  %% open-boundaries, are external to the simulation.  %% open-boundaries, are external to the simulation.
82    
83    \begin{table}
84    \caption{~}
85    \label{tab:package_summary_tab}.
86    \end{table}
87    
88  % Overview  % Overview
89  \newpage  \newpage
90  \input{part6/packages.tex}  \input{s_phys_pkgs/text/packages.tex}
91    
92  % Packages Related to Hydrodynamical Kernel  % Packages Related to Hydrodynamical Kernel
93  \newpage  \newpage
94  \section{Packages Related to Hydrodynamical Kernel}  \section{Packages Related to Hydrodynamical Kernel}
95  \input{part6/generic_advdiff.tex}  \input{s_phys_pkgs/text/generic_advdiff.tex}
96    
97  \newpage  \newpage
98  \input{part6/zonal_filt.tex}  \input{s_phys_pkgs/text/shap_filt.tex}
99    
100  \newpage  \newpage
101  \input{part6/exch2.tex}  \input{s_phys_pkgs/text/zonal_filt.tex}
102    
103  \newpage  \newpage
104  \input{part6/gridalt.tex}  \input{s_phys_pkgs/text/exch2.tex}
105    
106  % Some Mention of Packages that are part of the main model document  \newpage
107    \input{s_phys_pkgs/text/gridalt.tex}
108    
109    % Some Mention of Packages that are part of the main model document
110    \newpage
111  \section{General purpose numerical infrastructure packages}  \section{General purpose numerical infrastructure packages}
112    \input{s_phys_pkgs/text/obcs.tex}
113    
114  \newpage  \newpage
115  \input{part6/obcs.tex}  \input{s_phys_pkgs/text/rbcs.tex}
116    
117  \newpage  \newpage
118  \input{part6/ptracers.tex}  \input{s_phys_pkgs/text/ptracers.tex}
119    
120  % Ocean Packages  % Ocean Packages
121  \newpage  \newpage
122  \section{Ocean Packages}  \section{Ocean Packages}
123  \input{part6/gmredi.tex}  \input{s_phys_pkgs/text/gmredi.tex}
124    
125  \newpage  \newpage
126  \input{part6/kpp.tex}  \input{s_phys_pkgs/text/kpp.tex}
127    
128  \newpage  \newpage
129  \input{part6/bulk_force.tex}  \input{s_phys_pkgs/text/ggl90.tex}
130    
131  \newpage  \newpage
132  \input{part6/exf.tex}  \input{s_phys_pkgs/text/opps.tex}
133    
134  \newpage  \newpage
135  \input{part6/cal.tex}  \input{s_phys_pkgs/text/kl10.tex}
136    
137    \newpage
138    \input{s_phys_pkgs/text/bulk_force.tex}
139    
140    \newpage
141    \input{s_phys_pkgs/text/exf.tex}
142    
143    \newpage
144    \input{s_phys_pkgs/text/cal.tex}
145    
 \section{Atmosphere Packages}  
146  \newpage  \newpage
147  \input{part6/aim.tex}  \section{Atmosphere Packages}
148    \input{s_phys_pkgs/text/aim.tex}
149    
150  \newpage  \newpage
151  \input{part6/land.tex}  \input{s_phys_pkgs/text/land.tex}
152    
153  \newpage  \newpage
154  \input{part6/fizhi.tex}  \input{s_phys_pkgs/text/fizhi.tex}
155    
156    \newpage
157  \section{Sea Ice Packages}  \section{Sea Ice Packages}
158    \input{s_phys_pkgs/text/thsice.tex}
159    
160  \newpage  \newpage
161  \input{part6/thsice.tex}  \input{s_phys_pkgs/text/seaice.tex}
162    
163  \newpage  \newpage
164  \input{part6/seaice.tex}  \input{s_phys_pkgs/text/shelfice.tex}
165    
 \section{Packages Related to Coupled Model}  
166  \newpage  \newpage
167  \input{part6/aim_compon_interf.tex}  \input{s_phys_pkgs/text/streamice.tex}
168    
169  \newpage  \newpage
170  \input{part6/atm_ocn_coupler.tex}  \section{Packages Related to Coupled Model}
171    \input{s_phys_pkgs/text/aim_compon_interf.tex}
172    
173  \newpage  \newpage
174  \input{part6/component_communications.tex}  \input{s_phys_pkgs/text/atm_ocn_coupler.tex}
175    
 \section{Biogeochemistry Packages}  
176  \newpage  \newpage
177  \input{part6/gchem.tex}  \input{s_phys_pkgs/text/component_communications.tex}
178    
179    \newpage
180    \section{Biogeochemistry Packages}
181    \input{s_phys_pkgs/text/gchem.tex}
182    
183  \newpage  \newpage
184  \input{part6/dic.tex}  \input{s_phys_pkgs/text/dic.tex}
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