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revision 1.11 by molod, Tue Jun 27 19:08:22 2006 UTC revision 1.22 by jmc, Fri Aug 27 18:21:43 2010 UTC
# Line 9  Line 9 
9    
10  %% a set of pre-configured numerical experiments  %% a set of pre-configured numerical experiments
11    
12  The full MITgcm distribution comes with a set of pre-configured numerical experiments.  The full MITgcm distribution comes with a set of pre-configured
13  Some of these example experiments are tests of individual parts of the model code, but many  numerical experiments.  Some of these example experiments are tests of
14  are fully fledged numerical simulations. Full tutorials exist for a few of the examples,  individual parts of the model code, but many are fully fledged
15  and are documented in sections \ref{sect:eg-baro} - \ref{sect:eg-tank}. The other examples  numerical simulations. Full tutorials exist for a few of the examples,
16  follow the same general structure as the tutorial examples. However, they only include brief  and are documented in sections \ref{sect:eg-baro} -
17  instructions in a text file called {\it README}.  The examples are located in subdirectories  \ref{sect:eg-tank}. The other examples follow the same general
18  under the directory \texttt{verification}.  Each example is briefly described below.  structure as the tutorial examples. However, they only include brief
19    instructions in a text file called {\it README}.  The examples are
20    located in subdirectories under the directory \texttt{verification}.
21    Each example is briefly described below.
22    
23  \subsection{Full list of model examples}  \subsection{Full list of model examples}
24    
25  \begin{enumerate}  \begin{enumerate}
26        
27  \item \texttt{tutorial\_barotropic\_gyre} - single layer, ocean double gyre  \item \texttt{tutorial\_advection\_in\_gyre} - Test of various
28    (barotropic with free-surface). This experiment is described in detail in section    advection schemes in a single-layer double-gyre experiment.
29    \ref{sect:eg-baro}.    This experiment is described in detail in section
30      \ref{sect:eg-adv-gyre}.
31    
32    \item \texttt{tutorial\_baroclinic\_gyre} - Four layer, ocean double
33      gyre. This experiment is described in detail in section
34      \ref{sect:eg-fourlayer}.
35    
36    \item \texttt{tutorial\_barotropic\_gyre} - Single layer, ocean double
37      gyre (barotropic with free-surface).
38      This experiment is described in detail in section \ref{sect:eg-baro}.
39    
40    \item \texttt{tutorial\_cfc\_offline} - Offline form of the MITgcm to
41      study advection of a passive tracer and CFCs.
42      This experiment is described in detail in section \ref{sect:eg-offline-cfc}.
43    
44    \item \texttt{tutorial\_deep\_convection} - Inhomogenously forced
45      ocean convection in a doubly periodic box. This experiment is
46      described in detail in section \ref{sect:eg-bconv}.
47    
48    \item \texttt{tutorial\_global\_oce\_biogeo} - Ocean model coupled to
49      the dissolved inorganic carbon biogeochemistry model. This
50      experiment is described in detail in section
51      \ref{sect:eg-biogeochem_tutorial}.
52    
53    \item \texttt{tutorial\_global\_oce\_in\_p} - Global ocean simulation in
54      pressure coordinate (non-Boussinesq ocean model). Described in
55      detail in section \ref{sect:eg-globalpressure}.
56    
57    \item \texttt{tutorial\_global\_oce\_latlon} - 4x4 degree global ocean
58      simulation with steady climatological forcing. This experiment is
59      described in detail in section \ref{sect:eg-global}.
60    
61    \item \texttt{tutorial\_global\_oce\_optim} - Global ocean state
62      estimation at $4^\circ$ resolution.  This experiment is described in
63      detail in section \ref{sect:eg-global_state_estimate}.
64    
65    \item \texttt{tutorial\_held\_suarez\_cs} - 3D atmosphere dynamics
66      using Held and Suarez (1994) forcing on cubed sphere grid.  This
67      experiment is described in detail in section \ref{sect:eg-hs}.
68      
69    \item \texttt{tutorial\_offline} - Offline form of the MITgcm to study
70      advection of a passive tracer.  This experiment is described in
71      detail in section \ref{sect:eg-offline}.
72    
73    \item \texttt{tutorial\_plume\_on\_slope} - Gravity Plume on a
74      continental slope.  This experiment is described in detail in
75      section \ref{sect:eg-gravityplume}.
76    
77    \item \texttt{tutorial\_tracer\_adjsens} - Simple passive tracer
78      experiment. Includes derivative calculation. This experiment is
79      described in detail in section \ref{sect:eg-simple-tracer-adjoint}.
80    
81  \item \texttt{tutorial\_baroclinic\_gyre} - Four layer, ocean double gyre. This experiment  \item \texttt{adjustment.128x64x1} - Barotropic adjustment problem on
82    is described in detail in section \ref{sect:eg-fourlayer}.    latitude longitude grid with 128x64 grid points ($2.8^\circ$ resolution).
   
 \item \texttt{tutorial\_global\_oce\_latlon} - 4x4 degree global ocean simulation with steady  
   climatological forcing. This experiment is described in detail in section \ref{sect:eg-global}.  
   
 \item \texttt{exp4} - Flow over a Gaussian bump in open-water or channel with open boundaries.  
     
 \item \texttt{tutorial\_deep\_convection} - Inhomogenously forced ocean convection in a  
   doubly periodic box. This experiment is described in detail in section \ref{sect:eg-bconv}.  
   
 \item \texttt{front\_relax} - Relaxation of an ocean thermal front (test for  
 Gent/McWilliams scheme). 2D (Y-Z).  
   
 \item \texttt{internal\_wave} - Ocean internal wave forced by open  
   boundary conditions.  
     
 \item \texttt{natl\_box} - Eastern subtropical North Atlantic with KPP  
   scheme; 1 month integration  
     
 \item \texttt{hs94.1x64x5} - Zonal averaged atmosphere using Held and  
   Suarez '94 forcing.  
83        
84  \item \texttt{hs94.128x64x5} - 3D atmosphere dynamics using Held and  \item \texttt{adjustment.cs-32x32x1} - Barotropic adjustment problem on
85    Suarez '94 forcing.    cube sphere grid with 32x32 points per face (roughly $2.8^\circ$
86      resolution).\\
87      Also contains a non-linear free-surface adjustment version ({\it input.nlfs/}).
88        
89  \item \texttt{hs94.cs-32x32x5} - 3D atmosphere dynamics using Held and Suarez  \item \texttt{advect\_cs} Two-dimensional passive advection test on
90    (1994) forcing on the cubed sphere.  This experiment is described in detail in    cube sphere grid (32x32 grid points per face, roughly $2.8^\circ$)
   section \ref{sect:eg-hs}.  
91        
92  \item \texttt{aim.5l\_zon-ave} - Intermediate Atmospheric physics.  \item \texttt{advect\_xy} - Two-dimensional (horizontal plane) passive
93    Global Zonal Mean configuration, 1x64x5 resolution.    advection test on Cartesian grid.\\
94      Also contains an additional set-up using Adams-Bashforth 3 ({\it input.ab3\_c4/}).
95        
96  \item \texttt{aim.5l\_XZ\_Equatorial\_Slice} - Intermediate  \item \texttt{advect\_xz} - Two-dimensional (vertical plane) passive
97    Atmospheric physics, equatorial Slice configuration.  2D (X-Z).    advection test on Cartesian grid.
98        
99  \item \texttt{aim.5l\_Equatorial\_Channel} - Intermediate Atmospheric  \item \texttt{aim.5l\_Equatorial\_Channel}
100    physics. 3D Equatorial Channel configuration.    - 5-levels Intermediate Atmospheric physics,
101      3D Equatorial Channel configuration.
102        
103  \item \texttt{aim.5l\_LatLon} - Intermediate Atmospheric physics.  \item \texttt{aim.5l\_LatLon} - 5-levels Intermediate Atmospheric physics,
104    Global configuration, on latitude longitude grid with 128x64x5 grid    Global configuration, on latitude longitude grid with 128x64x5 grid
105    points ($2.8^\circ$ resolution).    points ($2.8^\circ$ resolution).
106        
107  \item \texttt{adjustment.128x64x1} Barotropic adjustment problem on  \item \texttt{aim.5l\_cs} - 5-levels Intermediate Atmospheric physics,
108    latitude longitude grid with 128x64 grid points ($2.8^\circ$ resolution).    Global configuration on cube sphere grid
109        (32x32 grid points per face, roughly $2.8^\circ$).\\
110  \item \texttt{adjustment.cs-32x32x1} Barotropic adjustment problem on    Also contains an additional set-up with an ocean mixed layer and thermodynamics
111    cube sphere grid with 32x32 points per face (roughly $2.8^\circ$    sea-ice ({\it input.thSI/}).
112    resolution).  
113      \item \texttt{bottom\_ctrl\_5x5} - Adjoint test using the bottom
114  \item \texttt{advect\_cs} Two-dimensional passive advection test on    topography as the control parameter.
115    cube sphere grid.  
116      \item \texttt{cfc\_example} - Global ocean with online computation and
117  \item \texttt{advect\_xy} Two-dimensional (horizontal plane) passive    advection of CFC11 and CFC12.
118    advection test on Cartesian grid.  
119      \item \texttt{cpl\_aim+ocn} - Coupled Ocean - Atmosphere realistic
120  \item \texttt{advect\_yz} Two-dimensional (vertical plane) passive    configuration on cubed-sphere cs32 horizontal grid,
121    advection test on Cartesian grid.    using Intermediate Atmospheric physics ({\it pkg/aim\_v23})
122      thermodynamics seaice ({\it pkg/thsice}) and land packages.
123      on cubed-sphere cs32 in a realistics configuration.
124    
125    \item \texttt{cpl\_atm2d+ocn} - Coupled Ocean - Atmosphere realistic
126      configuration using 2-D Atmospheric Model ({\it pkg/atm2d}).
127    
128    \item \texttt{deep\_anelastic} - Convection simulation on a giant planet:
129      relax both the Boussinesq approximation (anelastic) and the thin atmosphere
130      approximation (deep atmosphere).
131    
132    \item \texttt{dome} - Idealized 3D test of a density-driven bottom current.
133    
134    \item \texttt{exp2} - Old version of the global ocean experiment (no GM,
135          no partial-cells).\\
136      Also contains an additional set-up with ridid-lid ({\it input.rigidLid/}).
137    
138    \item \texttt{exp4} - Flow over a Gaussian bump in open-water or
139      channel with open boundaries.
140      
141    \item \texttt{exp5} - Deep convection.
142    
143    \item \texttt{fizhi-cs-32x32x40} - Global atmospheric simulation with
144      realistic topography, 40 vertical levels, a cubed sphere grid and
145      the full atmospheric physics package.
146    
147    \item \texttt{fizhi-cs-aqualev20} - Global atmospheric simulation on an
148      aqua planet with full atmospheric physics. Run is perpetual march
149      with an analytical SST distribution.  This is the configuration for
150      the APE (Aqua Planet Experiment) participation experiment.
151    
152    \item \texttt{fizhi-gridalt-hs} - Global atmospheric simulation
153      Held-Suarez (1994) forcing, with the physical forcing and the
154      dynamical forcing running on different vertical grids.
155    
156    \item \texttt{flt\_example} - Example of using float package.
157      
158    \item \texttt{front\_relax} - Relaxation of an ocean thermal front
159      (test for Gent/McWilliams scheme). 2D (Y-Z).\\
160      Also contains an additional set-up with Mixed-Layer Eddy parameterization
161      (Ferrari \& McWilliams, 2007) ({\it input.mxl/}).
162    
163    \item \texttt{global1x1\_tot} - ECCO-GODAE production configuration
164     version 1, 2 \& 3
165    
166    \item \texttt{global2x2\_tot} - ECCO production configuration version 0
167    
168    \item \texttt{global\_ocean.90x40x15} Global ocean simulation at 4x4
169      degree resolution. Similar to tutorial\_global\_oce\_latlon, with
170      quasi-non-hydrostatics and non-hydrostatic metric terms.\\
171      Also contains an adjoint set-up ({\it code\_ad/, input\_ad/}).
172    
173    \item \texttt{global\_ocean.cs32x15} - Global ocean experiment on the
174      cubed sphere grid.\\
175      Also contains additional set-ups:
176      \begin{enumerate}
177       \item non-hydrostratic with biharmonic viscosity ({\it input.viscA4/})
178       \item using thermodynamic sea ice and bulk force ({\it input.thsice/})
179       \item using thermodynamic ({\it pkg/thsice}) dynamics ({\it pkg/seaice}) sea-ice
180             and EXF package ({\it input.icedyn/})
181      \end{enumerate}
182    
183    \item \texttt{global\_ocean\_ebm} - Global ocean experiment on a lat-lon
184      grid coupled to an atmospheric energy balance model. Similar to
185      global\_ocean.90x40x15 experiment.\\
186      Also contains an adjoint set-up ({\it code\_ad/, input\_ad/}).
187    
188    \item \texttt{global\_with\_exf} - Global ocean experiment on a lat-lon
189      grid using the exf package. Similar to global\_ocean.90x40x15
190      experiment.
191    
192    \item \texttt{hs94.128x64x5} - 3D atmosphere dynamics on lat-lon grid,
193      using Held and Suarez '94 forcing.
194        
195  \item \texttt{tutorial\_tracer\_adjsens} Simple passive tracer experiment. Includes  \item \texttt{hs94.1x64x5} - Zonal averaged atmosphere dynamics
196    derivative calculation. This experiment is described in detail in section    using Held and Suarez '94 forcing.\\
197    \ref{sect:eg-simple-tracer}.    Also contains an adjoint set-up ({\it code\_ad/, input\_ad/}).
198      
199  \item \texttt{flt\_example} Example of using float package.  \item \texttt{hs94.cs-32x32x5} - 3D atmosphere dynamics using Held and
200        Suarez (1994) forcing on the cubed sphere. 5 vertical levels.\\
201  \item \texttt{global\_ocean.90x40x15} Global circulation with GM, flux    Also contains an additional set-up with Implicit Internal gravity waves
202    boundary conditions and poles.    treatment ({\it input.impIGW/}).
   
 \item \texttt{tutorial\_global\_oce\_in\_p} Global circulation in pressure  
   coordinate (non-Boussinesq ocean model). Described in detail in  
   section \ref{sect:eg-globalpressure}.  
203    
204  \item \texttt{solid-body.cs-32x32x1} Solid body rotation test for cube  \item \texttt{ideal\_2D\_oce} - Idealized 2D global ocean simulation on
205    sphere grid.    an aqua planet.
206    
207    \item \texttt{internal\_wave} - Ocean internal wave forced by open
208      boundary conditions.
209    
210    \item \texttt{inverted\_barometer} - Simple test of ocean response to
211      atmospheric pressure loading.
212    
213    \item \texttt{isomip} - ISOMIP like set-up including ice-shelf cavities
214      ({\it pkg/shelfice}).\\
215      Also contains an additional set-up with ({\it input.htd/})
216      but only Martin knows what "htd" stands for.
217    
218    \item \texttt{lab\_sea} - Regional Labrador Sea simulation on a lat-lon
219      grid using the sea ice package.\\
220      Also contains additional set-ups:
221      \begin{enumerate}
222       \item using the LSR solver (instead of EVP dynamics) ({\it input.lsr/})
223       \item using Hibler and Bryan (1987) sea-ice ocean stress ({\it input.hb87/})
224       \item using package {\it salt\_plume} ({\it input.salt\_plume/})
225      \end{enumerate}
226      and also 3 adjoint set-ups ({\it code\_ad/, input\_ad/, input\_ad.noseaicedyn/,
227      input\_ad.noseaice/}).
228    
229    \item \texttt{matrix\_example} - Test of experimental method to
230      accelerated convergence towards equillibrium.
231    
232    \item \texttt{MLAdjust} - Simple tests for different viscosity formulations.\\
233      Also contains additional set-ups:
234      \begin{enumerate}
235       \item ({\it input.0.leith/})
236       \item ({\it input.0.leithD/})
237       \item ({\it input.0.smag/})
238       \item ({\it input.1.leith/})
239      \end{enumerate}
240    
241  \item \texttt{tutorial\_plume\_on\_slope} Gravity Plume on a continental slope.  \item \texttt{natl\_box} - Eastern subtropical North Atlantic with KPP
242    This experiment is described in detail in section \ref{sect:eg-gravityplume}.    scheme; 1 month integration
243    
244  \item \texttt{tutorial\_global\_oce\_biogeo} Ocean model coupled to the dissolved  \item \texttt{natl\_box\_adjoint} - Eastern subtropical North Atlantic with KPP
245    inorganic carbon biogeochemistry model. This experiment is described in detail in section    scheme; adjoint set-up.
   \ref{sect:eg-biogeochem\_tutorial}.  
246    
247  \item \texttt{tutorial\_global\_oce\_optim} Global ocean state estimation at $4^\circ$ resolution.  \item \texttt{offline\_exf\_seaice} - oceanic surface forcing computed
248    This experiment is described in detail in section \ref{sect:eg-global\_state\_estimate}.    by bulk-formulae ({\it pkg/exf}) and inposed SST (offline ocean).\\
249      Also contains additional set-ups:
250      \begin{enumerate}
251       \item with sea-ice ({\it pkg/seaice}) thermodynamics ({\it input.seaicetd/})
252       \item an adjoint test ({\it code\_ad/, input\_ad/}).
253      \end{enumerate}
254      
255    \item \texttt{OpenAD} simple Adjoint experiement (used also to test
256      open-AD compiler)
257    
258    \item \texttt{rotating\_tank} Rotating tank simulation in cylindrical
259      coordinates.  This experiment is described in detail in section
260      \ref{sect:eg-tank}.
261    
262    \item \texttt{seaice\_obcs} similar to "lab\_sea" ({\it input.salt\_plume/})
263      experiment with only a fraction of the domain and open-boundary conditions
264      derived from "lab\_sea" experiment.
265    
266  \item \texttt{tutorial\_offline} Offline form of the MITgcm to study advection of a passive  \item \texttt{solid-body.cs-32x32x1} Solid body rotation test for cube
267    tracer.  This experiment is described in detail in section \ref{sect:eg-offline}.    sphere grid.
268    
269  \item \texttt{rotating\_tank} Rotating tank simulation in cylindrical coordinates.  \item \texttt{tidal\_basin\_2d} 2-D vertical section (X-Z) with tidal forcing
270    This experiment is described in detail in section \ref{sect:eg-tank}.  
271    \item \texttt{vermix} Simple test in a small domain (3 columns) for
272      ocean vertical mixing schemes. The standard set-up ({\it input/}) uses
273      KPP scheme.\\
274      Also contains additional set-ups:
275      \begin{enumerate}
276       \item with Gaspar et al. (1990) ({\it pkg/ggl90}) scheme ({\it input.ggl90/})
277       \item with Mellor \& Yamada (1982) level 2. ({\it pkg/my82}) scheme ({\it input.my82/})
278       \item with Paluszkiewicz \& Romea (1997) ({\it pkg/opps}) scheme ({\it input.opps/})
279       \item with Pacanowski \& Philander (1981) ({\it pkg/pp81}) scheme ({\it input.pp81/})
280      \end{enumerate}
281    
282  \end{enumerate}  \end{enumerate}
283    
# Line 173  Each example directory has the following Line 336  Each example directory has the following
336    In addition, you will also find in this directory the forcing and    In addition, you will also find in this directory the forcing and
337    topography files as well as the files describing the initial state    topography files as well as the files describing the initial state
338    of the experiment.  This varies from experiment to experiment. See    of the experiment.  This varies from experiment to experiment. See
339    section 2 for more details.    the verification directories refered to in this chapter for more details.
340    
341  \item \texttt{results}: this directory contains the output file  \item \texttt{results}: this directory contains the output file
342    \texttt{output.txt} produced by the simulation example. This file is    \texttt{output.txt} produced by the simulation example. This file is
343    useful for comparison with your own output when you run the    useful for comparison with your own output when you run the
344    experiment.    experiment.
345    
346    \item \texttt{build}: this directory is where the model is compiled
347      and loaded, and where the executable resides.
348    
349  \end{itemize}  \end{itemize}
350    
351  Once you have chosen the example you want to run, you are ready to  Once you have chosen the example you want to run, you are ready to
352  compile the code.  compile the code.
353    
   
 \newpage  
 \input{part3/case_studies/barotropic_gyre/baro.tex}  
   
 \newpage  
 \input{part3/case_studies/fourlayer_gyre/fourlayer.tex}  
   
 \newpage  
 \input{part3/case_studies/climatalogical_ogcm/climatalogical_ogcm.tex}  
   
 \newpage  
 \input{part3/case_studies/ogcm_in_pressure/ogcm_in_pressure.tex}  
   
 \newpage  
 \input{part3/case_studies/held_suarez_cs/held_suarez_cs.tex}  
   
 \newpage  
 \input{part3/case_studies/doubly_periodic_convection/convection.tex}  
   
 \newpage  
 \input{part3/case_studies/plume_on_slope/plume_on_slope.tex}  
   
 \newpage  
 \input{part3/case_studies/carbon_outgassing_sensitivity/co2sens.tex}  
   
 \newpage  
 \input{part3/case_studies/biogeochem_tutorial/biogeochem.tex}  
   
 \newpage  
 \input{part3/case_studies/global_oce_estimation/global_oce_estimation.tex}  
   
 \newpage  
 \input{part3/case_studies/sens_airsea_tracer/doc_ad_examples.tex}  
   
 \newpage  
 \input{part3/case_studies/offline/offline_tutorial.tex}  
   
 \newpage  
 \input{part3/case_studies/rotating_tank/tank.tex}  

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