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revision 1.8 by jmc, Tue Aug 9 17:59:37 2005 UTC revision 1.12 by molod, Tue Jun 27 20:47:05 2006 UTC
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1  % $Header$  % $Header$
2  % $Name$  % $Name$
3    
4  \section{Tutorials}  \section[MITgcm Example Experiments]{Example experiments}
5  \label{sect:tutorials}  \label{sect:modelExamples}
6  \label{www:tutorials}  \begin{rawhtml}
7    <!-- CMIREDIR:modelExamples: -->
8    \end{rawhtml}
9    
10    %% a set of pre-configured numerical experiments
11    
12    The full MITgcm distribution comes with a set of pre-configured numerical experiments.
13    Some of these example experiments are tests of individual parts of the model code, but many
14    are fully fledged numerical simulations. Full tutorials exist for a few of the examples,
15    and are documented in sections \ref{sect:eg-baro} - \ref{sect:eg-tank}. The other examples
16    follow the same general structure as the tutorial examples. However, they only include brief
17    instructions in a text file called {\it README}.  The examples are located in subdirectories
18    under the directory \texttt{verification}.  Each example is briefly described below.
19    
20    \subsection{Full list of model examples}
21    
22    \begin{enumerate}
23      
24    \item \texttt{tutorial\_barotropic\_gyre}
25    
26    \item \texttt{tutorial\_barotropic\_gyre} - single layer, ocean double gyre
27      (barotropic with free-surface). This experiment is described in detail in section
28      \ref{sect:eg-baro}.
29    
30    \item \texttt{tutorial\_baroclinic\_gyre} - Four layer, ocean double gyre. This experiment
31      is described in detail in section \ref{sect:eg-fourlayer}.
32    
33    \item \texttt{tutorial\_global\_oce\_latlon} - 4x4 degree global ocean simulation with steady
34      climatological forcing. This experiment is described in detail in section \ref{sect:eg-global}.
35    
36    \item \texttt{exp4} - Flow over a Gaussian bump in open-water or channel with open boundaries.
37      
38    \item \texttt{tutorial\_deep\_convection} - Inhomogenously forced ocean convection in a
39      doubly periodic box. This experiment is described in detail in section \ref{sect:eg-bconv}.
40    
41    \item \texttt{front\_relax} - Relaxation of an ocean thermal front (test for
42    Gent/McWilliams scheme). 2D (Y-Z).
43    
44    \item \texttt{internal\_wave} - Ocean internal wave forced by open
45      boundary conditions.
46      
47    \item \texttt{natl\_box} - Eastern subtropical North Atlantic with KPP
48      scheme; 1 month integration
49      
50    \item \texttt{hs94.1x64x5} - Zonal averaged atmosphere using Held and
51      Suarez '94 forcing.
52      
53    \item \texttt{hs94.128x64x5} - 3D atmosphere dynamics using Held and
54      Suarez '94 forcing.
55      
56    \item \texttt{tutorial\_held\_suarez\_cs} - 3D atmosphere dynamics using Held and Suarez
57      (1994) forcing on the cubed sphere.  This experiment is described in detail in
58      section \ref{sect:eg-hs}.
59      
60    \item \texttt{aim.5l\_zon-ave} - Intermediate Atmospheric physics.
61      Global Zonal Mean configuration, 1x64x5 resolution.
62      
63    \item \texttt{aim.5l\_XZ\_Equatorial\_Slice} - Intermediate
64      Atmospheric physics, equatorial Slice configuration.  2D (X-Z).
65      
66    \item \texttt{aim.5l\_Equatorial\_Channel} - Intermediate Atmospheric
67      physics. 3D Equatorial Channel configuration.
68      
69    \item \texttt{aim.5l\_LatLon} - Intermediate Atmospheric physics.
70      Global configuration, on latitude longitude grid with 128x64x5 grid
71      points ($2.8^\circ$ resolution).
72      
73    \item \texttt{aim.5l_cs}
74    
75    \item \texttt{adjustment.128x64x1} Barotropic adjustment problem on
76      latitude longitude grid with 128x64 grid points ($2.8^\circ$ resolution).
77      
78    \item \texttt{adjustment.cs-32x32x1} Barotropic adjustment problem on
79      cube sphere grid with 32x32 points per face (roughly $2.8^\circ$
80      resolution).
81      
82    \item \texttt{advect\_cs} Two-dimensional passive advection test on
83      cube sphere grid.
84      
85    \item \texttt{advect\_xy} Two-dimensional (horizontal plane) passive
86      advection test on Cartesian grid.
87      
88    \item \texttt{advect\_xz} Two-dimensional (vertical plane) passive
89      advection test on Cartesian grid.
90      
91    \item \texttt{tutorial\_tracer\_adjsens} Simple passive tracer experiment. Includes
92      derivative calculation. This experiment is described in detail in section
93      \ref{sect:eg-simple-tracer}.
94    
95    \item \texttt{flt\_example} Example of using float package.
96      
97    \item \texttt{global\_ocean.90x40x15} Global circulation with GM, flux
98      boundary conditions and poles.
99    
100    \item \texttt{tutorial\_global\_oce\_in\_p} Global circulation in pressure
101      coordinate (non-Boussinesq ocean model). Described in detail in
102      section \ref{sect:eg-globalpressure}.
103    
104    \item \texttt{solid-body.cs-32x32x1} Solid body rotation test for cube
105      sphere grid.
106    
107    \item \texttt{tutorial\_plume\_on\_slope} Gravity Plume on a continental slope.
108      This experiment is described in detail in section \ref{sect:eg-gravityplume}.
109    
110    \item \texttt{tutorial\_global\_oce\_biogeo} Ocean model coupled to the dissolved
111      inorganic carbon biogeochemistry model. This experiment is described in detail in section
112      \ref{sect:eg-biogeochem\_tutorial}.
113    
114    \item \texttt{tutorial\_global\_oce\_optim} Global ocean state estimation at $4^\circ$ resolution.
115      This experiment is described in detail in section \ref{sect:eg-global\_state\_estimate}.
116    
117    \item \texttt{tutorial\_offline} Offline form of the MITgcm to study advection of a passive
118      tracer.  This experiment is described in detail in section \ref{sect:eg-offline}.
119    
120    \item \texttt{rotating\_tank} Rotating tank simulation in cylindrical coordinates.
121      This experiment is described in detail in section \ref{sect:eg-tank}.
122    
123    \item \texttt{MLAdjust} Simple test for different viscosity formulations.
124    
125    \item \texttt{bottom_ctrl_5x5} Adjoint test using the bottom topography as the
126      control parameter.
127    
128    \item \texttt{cfc_example} Global ocean with online computation and advection of
129    CFC11 and CFC12.
130    
131    \item \texttt{dome} Idealized 3D test of a density-driven bottom current.
132    
133    \item \texttt{exp2} Old version of the global ocean experiment.
134    
135    \item \texttt{exp5} Deep convection.
136    
137    \item \texttt{fizhi-cs-32x32x10} Global atmospheric simulation with realistic topography,
138      10 vertical levels, a cubed sphere grid and the full atmospheric physics package.
139    
140    \item \texttt{fizhi-cs-aqualev20} Global atmospheric simulation on an aqua planet with
141      full atmospheric physics. Run is perpetual march with an analytical SST distribution.
142      This is the configuration for the APE (Aqua Planet Experiment) participation experiment.
143    
144    \item \texttt{fizhi-gridalt-hs} Global atmospheric simulation Held-Suarez (1994) forcing,
145      with the physical forcing and the dynamical forcing running on different vertical grids.
146    
147    \item \texttt{global_ocean.cs32x15} Global ocean experiment on the cubed sphere grid, using
148    thermodynamic sea ice and bulk force packages.
149    
150    \item \texttt{global_ocean_ebm} Global ocean experiment on a lat-lon grid coupled to an
151    atmospheric energy balance model. Similar to global_ocean.90x40x15 experiment.
152    
153    \item \texttt{global_with_exf} Global ocean experiment on a lat-lon grid using the exf
154    package. Similar to global_ocean.90x40x15 experiment.
155    
156    \item \texttt{hs94.cs-32x32x5} 3D atmosphere dynamics using Held and Suarez
157      (1994) forcing on the cubed sphere. 5 vertical levels.
158    
159    \item \texttt{ideal_2D_oce} Idealized 2D global ocean simulation on an aqua planet.
160    
161    \item \texttt{inverted_barometer} Simple test of ocean response to atmospheric pressure
162    loading.
163    
164    \item \texttt{lab_sea} Regional Labrador Sea simulation on a lat-lon grid. Coupled to
165    the sea ice model.
166    
167    \item \texttt{matrix_example} Test of experimental method to accelerated convergence towards
168    equillibrium.
169    
170    \item \texttt{tutorial_cfc_offline} Offline form of the MITgcm to study advection of a passive
171      tracer and CFCs.
172    
173    \item \texttt{vermix} Simple test in a small domain (3 columns) for ocean vertical mixing schemes.
174    
175    \end{enumerate}
176    
177    \subsection{Directory structure of model examples}
178    
179    Each example directory has the following subdirectories:
180    
181    \begin{itemize}
182    \item \texttt{code}: contains the code particular to the example. At a
183      minimum, this directory includes the following files:
184    
185      \begin{itemize}
186      \item \texttt{code/packages.conf}: declares the list of packages or
187        package groups to be used.  If not included, the default version
188        is located in \texttt{pkg/pkg\_default}.  Package groups are
189        simply convenient collections of commonly used packages which are
190        defined in \texttt{pkg/pkg\_default}.  Some packages may require
191        other packages or may require their absence (that is, they are
192        incompatible) and these package dependencies are listed in
193        \texttt{pkg/pkg\_depend}.
194    
195      \item \texttt{code/CPP\_EEOPTIONS.h}: declares CPP keys relative to
196        the ``execution environment'' part of the code. The default
197        version is located in \texttt{eesupp/inc}.
198      
199      \item \texttt{code/CPP\_OPTIONS.h}: declares CPP keys relative to
200        the ``numerical model'' part of the code. The default version is
201        located in \texttt{model/inc}.
202      
203      \item \texttt{code/SIZE.h}: declares size of underlying
204        computational grid.  The default version is located in
205        \texttt{model/inc}.
206      \end{itemize}
207      
208      In addition, other include files and subroutines might be present in
209      \texttt{code} depending on the particular experiment. See Section 2
210      for more details.
211      
212    \item \texttt{input}: contains the input data files required to run
213      the example. At a minimum, the \texttt{input} directory contains the
214      following files:
215    
216      \begin{itemize}
217      \item \texttt{input/data}: this file, written as a namelist,
218        specifies the main parameters for the experiment.
219      
220      \item \texttt{input/data.pkg}: contains parameters relative to the
221        packages used in the experiment.
222      
223      \item \texttt{input/eedata}: this file contains ``execution
224        environment'' data. At present, this consists of a specification
225        of the number of threads to use in $X$ and $Y$ under multithreaded
226        execution.
227      \end{itemize}
228      
229      In addition, you will also find in this directory the forcing and
230      topography files as well as the files describing the initial state
231      of the experiment.  This varies from experiment to experiment. See
232      section 2 for more details.
233    
234    \item \texttt{results}: this directory contains the output file
235      \texttt{output.txt} produced by the simulation example. This file is
236      useful for comparison with your own output when you run the
237      experiment.
238    \end{itemize}
239    
240    Once you have chosen the example you want to run, you are ready to
241    compile the code.
242    
243    
244    \newpage
245  \input{part3/case_studies/barotropic_gyre/baro.tex}  \input{part3/case_studies/barotropic_gyre/baro.tex}
246    
247  \newpage  \newpage
# Line 35  Line 271 
271  \newpage  \newpage
272  \input{part3/case_studies/global_oce_estimation/global_oce_estimation.tex}  \input{part3/case_studies/global_oce_estimation/global_oce_estimation.tex}
273    
274  \begin{versionprivate}  \newpage
275    \input{part3/case_studies/sens_airsea_tracer/doc_ad_examples.tex}
276    
277    \newpage
278    \input{part3/case_studies/offline/offline_tutorial.tex}
279    
280  \newpage  \newpage
281  \input{part3/case_studies/rotating_tank/tank.tex}  \input{part3/case_studies/rotating_tank/tank.tex}
 \end{versionprivate}  
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