/[MITgcm]/manual/s_phys_pkgs/text/top_section.tex
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revision 1.39 by molod, Tue Jun 27 20:47:05 2006 UTC revision 1.48 by jmc, Mon Aug 30 23:09:22 2010 UTC
# Line 10  Line 10 
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
# Line 38  I/O and time-keeping functions that are Line 38  I/O and time-keeping functions that are
38  %%\begin{minipage}{12cm}  %%\begin{minipage}{12cm}
39  %%\marginsize{0cm}{0cm}{0cm}{0cm}  %%\marginsize{0cm}{0cm}{0cm}{0cm}
40  %% \scalefig{0.6}  %% \scalefig{0.6}
41  %% \epsfbox{part6/organigramme_mitgcm_pkg.eps}  %% \epsfbox{s_phys_pkgs/figs/organigramme_mitgcm_pkg.eps}
42  %%\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}
43  %%\end{minipage}  %%\end{minipage}
44  \resizebox{5.5in}{!}{\includegraphics{part6/organigramme_mitgcm_pkg2.eps}}  \resizebox{5.5in}{!}{\includegraphics{s_phys_pkgs/figs/organigramme_mitgcm_pkg2.eps}}
45  \label{fig:package_organigramme}  \\
46  \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
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
# Line 59  general purpose infrastructure software Line 59  general purpose infrastructure software
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}.
# 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  tutorial\_offline               \ref{sect:eg-offline}  
97  tutorial\_baroclinic\_gyre      \ref{sect:eg-fourlayer}  \newpage
98  tutorial\_tracer\_adjsens       \ref{sect:eg-simple-tracer}  \input{s_phys_pkgs/text/shap_filt.tex}
99    
100  \newpage  \newpage
101  \input{part6/zonal_filt.tex}  \input{s_phys_pkgs/text/zonal_filt.tex}
 tutorial\_held\_suarez\_cs    \ref{sect:eg-hs}  
102    
103  \newpage  \newpage
104  \input{part6/exch2.tex}  \input{s_phys_pkgs/text/exch2.tex}
 tutorial\_held\_suarez\_cs   \ref{sect:eg-hs}  
105    
106  \newpage  \newpage
107  \input{part6/gridalt.tex}  \input{s_phys_pkgs/text/gridalt.tex}
 fizhi-cs-32x32x40  
108    
109  % Some Mention of Packages that are part of the main model document  % Some Mention of Packages that are part of the main model document
110    \newpage
111    \section{General purpose numerical infrastructure packages}
112    \input{s_phys_pkgs/text/obcs.tex}
113    
114    \newpage
115    \input{s_phys_pkgs/text/rbcs.tex}
116    
117    \newpage
118    \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}
 tutorial\_global\_oce\_latlon    \ref{sect:eg-global}  
 front\_relax  
 ideal\_2D\_oce  
124    
125  \newpage  \newpage
126  \input{part6/kpp.tex}  \input{s_phys_pkgs/text/kpp.tex}
 lab\_sea  
127    
128  \newpage  \newpage
129  \input{part6/bulk_force.tex}  \input{s_phys_pkgs/text/ggl90.tex}
 global\_ocean.cs32x15/input/thsice  
130    
131  \newpage  \newpage
132  \input{part6/exf.tex}  \input{s_phys_pkgs/text/opps.tex}
 global\_with\_exf  
 lab\_sea  
133    
134  \newpage  \newpage
135  \input{part6/cal.tex}  \input{s_phys_pkgs/text/bulk_force.tex}
 global\_with\_exf  
 lab\_sea  
136    
137  \newpage  \newpage
138  \input{part6/obcs.tex}  \input{s_phys_pkgs/text/exf.tex}
 exp4  
139    
 \section{Atmosphere Packages}  
140  \newpage  \newpage
141  \input{part6/aim.tex}  \input{s_phys_pkgs/text/cal.tex}
 aim.5l\_cs  
142    
143  \newpage  \newpage
144  \input{part6/land.tex}  \section{Atmosphere Packages}
145  aim.5l\_cs  \input{s_phys_pkgs/text/aim.tex}
146    
147  \newpage  \newpage
148  \input{part6/fizhi.tex}  \input{s_phys_pkgs/text/land.tex}
 fizhi-cs-aqualev20  
 fizhi-cs-32x32x40  
149    
150    \newpage
151    \input{s_phys_pkgs/text/fizhi.tex}
152    
153    \newpage
154  \section{Sea Ice Packages}  \section{Sea Ice Packages}
155    \input{s_phys_pkgs/text/thsice.tex}
156    
157  \newpage  \newpage
158  \input{part6/thsice.tex}  \input{s_phys_pkgs/text/seaice.tex}
 aim.5l\_cs/input.thsice  
 global\_ocean.cs32x15/input.thsice  
159    
160  \newpage  \newpage
161  \input{part6/seaice.tex}  \input{s_phys_pkgs/text/shelfice.tex}
 lab\_sea  
162    
 \section{Packages Related to Coupled Model}  
163  \newpage  \newpage
164  \input{part6/aim_compon_interf.tex}  \section{Packages Related to Coupled Model}
165  cpl\_aim+ocean  \input{s_phys_pkgs/text/aim_compon_interf.tex}
166    
167  \newpage  \newpage
168  \input{part6/aim_ocn_coupler.tex}  \input{s_phys_pkgs/text/atm_ocn_coupler.tex}
 cpl\_aim+ocean  
169    
170  \newpage  \newpage
171  \input{part6/component_communications.tex}  \input{s_phys_pkgs/text/component_communications.tex}
 cpl\_aim+ocean  
172    
 \section{Biogeochemistry Packages}  
173  \newpage  \newpage
174  \input{part6/gchem.tex}  \section{Biogeochemistry Packages}
175  tutorial\_global\_oce\_biogeo    \ref{sect:eg-biogeochem\_tutorial}  \input{s_phys_pkgs/text/gchem.tex}
176    
177  \newpage  \newpage
178  \input{part6/dic.tex}  \input{s_phys_pkgs/text/dic.tex}
 tutorial\_global\_oce\_biogeo    \ref{sect:eg-biogeochem\_tutorial}  
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