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# 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}  \item \texttt{tutorial_advection\_in\_gyre} - test of various
28      advection schemes in a single-layer double-gyre experiment.
29  \item \texttt{tutorial\_barotropic\_gyre} - single layer, ocean double gyre    This experiment is described in detail in section
30    (barotropic with free-surface). This experiment is described in detail in section    \ref{sect:eg-adv-gyre}.
31    \ref{sect:eg-baro}.  
32    \item \texttt{tutorial\_baroclinic\_gyre} - Four layer, ocean double
33  \item \texttt{tutorial\_baroclinic\_gyre} - Four layer, ocean double gyre. This experiment    gyre. This experiment is described in detail in section
34    is described in detail in section \ref{sect:eg-fourlayer}.    \ref{sect:eg-fourlayer}.
35    
36  \item \texttt{tutorial\_global\_oce\_latlon} - 4x4 degree global ocean simulation with steady  \item \texttt{tutorial\_barotropic\_gyre} - single layer, ocean double
37    climatological forcing. This experiment is described in detail in section \ref{sect:eg-global}.    gyre (barotropic with free-surface). This experiment is described in
38      detail in section \ref{sect:eg-baro}.
39  \item \texttt{exp4} - Flow over a Gaussian bump in open-water or channel with open boundaries.  
40      \item \texttt{tutorial\_cfc\_offline} Offline form of the MITgcm to
41  \item \texttt{tutorial\_deep\_convection} - Inhomogenously forced ocean convection in a    study advection of a passive tracer and CFCs.
42    doubly periodic box. This experiment is described in detail in section \ref{sect:eg-bconv}.  
43    \item \texttt{tutorial\_deep\_convection} - Inhomogenously forced
44  \item \texttt{front\_relax} - Relaxation of an ocean thermal front (test for    ocean convection in a doubly periodic box. This experiment is
45  Gent/McWilliams scheme). 2D (Y-Z).    described in detail in section \ref{sect:eg-bconv}.
46    
47  \item \texttt{internal\_wave} - Ocean internal wave forced by open  \item \texttt{tutorial\_global\_oce\_biogeo} Ocean model coupled to
48    boundary conditions.    the dissolved inorganic carbon biogeochemistry model. This
49        experiment is described in detail in section
50  \item \texttt{natl\_box} - Eastern subtropical North Atlantic with KPP    \ref{sect:eg-biogeochem_tutorial}.
51    scheme; 1 month integration  
52      \item \texttt{tutorial\_global\_oce\_in\_p} Global circulation in
53  \item \texttt{hs94.1x64x5} - Zonal averaged atmosphere using Held and    pressure coordinate (non-Boussinesq ocean model). Described in
54    Suarez '94 forcing.    detail in section \ref{sect:eg-globalpressure}.
55      
56  \item \texttt{hs94.128x64x5} - 3D atmosphere dynamics using Held and  \item \texttt{tutorial\_global\_oce\_latlon} - 4x4 degree global ocean
57    Suarez '94 forcing.    simulation with steady climatological forcing. This experiment is
58        described in detail in section \ref{sect:eg-global}.
59  \item \texttt{tutorial\_held\_suarez\_cs} - 3D atmosphere dynamics using Held and Suarez  
60    (1994) forcing on the cubed sphere.  This experiment is described in detail in  \item \texttt{tutorial\_global\_oce\_optim} Global ocean state
61    section \ref{sect:eg-hs}.    estimation at $4^\circ$ resolution.  This experiment is described in
62        detail in section \ref{sect:eg-global_state_estimate}.
63  \item \texttt{aim.5l\_zon-ave} - Intermediate Atmospheric physics.  
64    Global Zonal Mean configuration, 1x64x5 resolution.  \item \texttt{tutorial\_held\_suarez\_cs} - 3D atmosphere dynamics
65        using Held and Suarez (1994) forcing on the cubed sphere.  This
66  \item \texttt{aim.5l\_XZ\_Equatorial\_Slice} - Intermediate    experiment is described in detail in section \ref{sect:eg-hs}.
67    Atmospheric physics, equatorial Slice configuration.  2D (X-Z).    
68      \item \texttt{tutorial\_offline} Offline form of the MITgcm to study
69  \item \texttt{aim.5l\_Equatorial\_Channel} - Intermediate Atmospheric    advection of a passive tracer.  This experiment is described in
70    physics. 3D Equatorial Channel configuration.    detail in section \ref{sect:eg-offline}.
71      
72  \item \texttt{aim.5l\_LatLon} - Intermediate Atmospheric physics.  \item \texttt{tutorial\_plume\_on\_slope} Gravity Plume on a
73    Global configuration, on latitude longitude grid with 128x64x5 grid    continental slope.  This experiment is described in detail in
74    points ($2.8^\circ$ resolution).    section \ref{sect:eg-gravityplume}.
75      
76  \item \texttt{aim.5l_cs}  \item \texttt{tutorial\_tracer\_adjsens} Simple passive tracer
77      experiment. Includes derivative calculation. This experiment is
78      described in detail in section \ref{sect:eg-simple-tracer}.
79    
80  \item \texttt{adjustment.128x64x1} Barotropic adjustment problem on  \item \texttt{adjustment.128x64x1} Barotropic adjustment problem on
81    latitude longitude grid with 128x64 grid points ($2.8^\circ$ resolution).    latitude longitude grid with 128x64 grid points ($2.8^\circ$ resolution).
# Line 80  Gent/McWilliams scheme). 2D (Y-Z). Line 85  Gent/McWilliams scheme). 2D (Y-Z).
85    resolution).    resolution).
86        
87  \item \texttt{advect\_cs} Two-dimensional passive advection test on  \item \texttt{advect\_cs} Two-dimensional passive advection test on
88    cube sphere grid.    cube sphere grid (32x32 grid points per face, roughly $2.8^\circ$)
89        
90  \item \texttt{advect\_xy} Two-dimensional (horizontal plane) passive  \item \texttt{advect\_xy} Two-dimensional (horizontal plane) passive
91    advection test on Cartesian grid.    advection test on Cartesian grid.
# Line 88  Gent/McWilliams scheme). 2D (Y-Z). Line 93  Gent/McWilliams scheme). 2D (Y-Z).
93  \item \texttt{advect\_xz} Two-dimensional (vertical plane) passive  \item \texttt{advect\_xz} Two-dimensional (vertical plane) passive
94    advection test on Cartesian grid.    advection test on Cartesian grid.
95        
96  \item \texttt{tutorial\_tracer\_adjsens} Simple passive tracer experiment. Includes  \item \texttt{aim.5l\_Equatorial\_Channel}
97    derivative calculation. This experiment is described in detail in section    - 5-levels Intermediate Atmospheric physics,
98    \ref{sect:eg-simple-tracer}.    3D Equatorial Channel configuration.
   
 \item \texttt{flt\_example} Example of using float package.  
99        
100  \item \texttt{global\_ocean.90x40x15} Global circulation with GM, flux  \item \texttt{aim.5l\_LatLon} - 5-levels Intermediate Atmospheric physics,
101    boundary conditions and poles.    Global configuration, on latitude longitude grid with 128x64x5 grid
102      points ($2.8^\circ$ resolution).
103  \item \texttt{tutorial\_global\_oce\_in\_p} Global circulation in pressure    
104    coordinate (non-Boussinesq ocean model). Described in detail in  \item \texttt{aim.5l\_cs} - 5-levels Intermediate Atmospheric physics,
105    section \ref{sect:eg-globalpressure}.    Global configuration on cube sphere grid
106      (32x32 grid points per face, roughly $2.8^\circ$).
 \item \texttt{solid-body.cs-32x32x1} Solid body rotation test for cube  
   sphere grid.  
   
 \item \texttt{tutorial\_plume\_on\_slope} Gravity Plume on a continental slope.  
   This experiment is described in detail in section \ref{sect:eg-gravityplume}.  
   
 \item \texttt{tutorial\_global\_oce\_biogeo} Ocean model coupled to the dissolved  
   inorganic carbon biogeochemistry model. This experiment is described in detail in section  
   \ref{sect:eg-biogeochem\_tutorial}.  
   
 \item \texttt{tutorial\_global\_oce\_optim} Global ocean state estimation at $4^\circ$ resolution.  
   This experiment is described in detail in section \ref{sect:eg-global\_state\_estimate}.  
   
 \item \texttt{tutorial\_offline} Offline form of the MITgcm to study advection of a passive  
   tracer.  This experiment is described in detail in section \ref{sect:eg-offline}.  
   
 \item \texttt{rotating\_tank} Rotating tank simulation in cylindrical coordinates.  
   This experiment is described in detail in section \ref{sect:eg-tank}.  
   
 \item \texttt{MLAdjust} Simple test for different viscosity formulations.  
107    
108  \item \texttt{bottom_ctrl_5x5} Adjoint test using the bottom topography as the  \item \texttt{bottom\_ctrl\_5x5} Adjoint test using the bottom
109    control parameter.    topography as the control parameter.
110    
111  \item \texttt{cfc_example} Global ocean with online computation and advection of  \item \texttt{cfc\_example} Global ocean with online computation and
112  CFC11 and CFC12.    advection of CFC11 and CFC12.
113    
114  \item \texttt{dome} Idealized 3D test of a density-driven bottom current.  \item \texttt{dome} Idealized 3D test of a density-driven bottom current.
115    
116  \item \texttt{exp2} Old version of the global ocean experiment.  \item \texttt{exp2} Old version of the global ocean experiment.
117    
118    \item \texttt{exp4} - Flow over a Gaussian bump in open-water or
119      channel with open boundaries.
120      
121  \item \texttt{exp5} Deep convection.  \item \texttt{exp5} Deep convection.
122    
123  \item \texttt{fizhi-cs-32x32x10} Global atmospheric simulation with realistic topography,  \item \texttt{fizhi-cs-32x32x40} Global atmospheric simulation with
124    10 vertical levels, a cubed sphere grid and the full atmospheric physics package.    realistic topography, 10 vertical levels, a cubed sphere grid and
125      the full atmospheric physics package.
126    
127    \item \texttt{fizhi-cs-aqualev20} Global atmospheric simulation on an
128      aqua planet with full atmospheric physics. Run is perpetual march
129      with an analytical SST distribution.  This is the configuration for
130      the APE (Aqua Planet Experiment) participation experiment.
131    
132    \item \texttt{fizhi-gridalt-hs} Global atmospheric simulation
133      Held-Suarez (1994) forcing, with the physical forcing and the
134      dynamical forcing running on different vertical grids.
135    
136  \item \texttt{fizhi-cs-aqualev20} Global atmospheric simulation on an aqua planet with  \item \texttt{flt\_example} Example of using float package.
137    full atmospheric physics. Run is perpetual march with an analytical SST distribution.    
138    This is the configuration for the APE (Aqua Planet Experiment) participation experiment.  \item \texttt{front\_relax} - Relaxation of an ocean thermal front
139      (test for Gent/McWilliams scheme). 2D (Y-Z).
140    
141    \item \texttt{global\_ocean.90x40x15} Global circulation with GM, flux
142      boundary conditions and poles.
143    
144  \item \texttt{fizhi-gridalt-hs} Global atmospheric simulation Held-Suarez (1994) forcing,  \item \texttt{global\_ocean.cs32x15} Global ocean experiment on the
145    with the physical forcing and the dynamical forcing running on different vertical grids.    cubed sphere grid, using thermodynamic sea ice and bulk force
146      packages.
147    
148    \item \texttt{global\_ocean\_ebm} Global ocean experiment on a lat-lon
149      grid coupled to an atmospheric energy balance model. Similar to
150      global\_ocean.90x40x15 experiment.
151    
152  \item \texttt{global_ocean.cs32x15} Global ocean experiment on the cubed sphere grid, using  \item \texttt{global\_with\_exf} Global ocean experiment on a lat-lon
153  thermodynamic sea ice and bulk force packages.    grid using the exf package. Similar to global\_ocean.90x40x15
154      experiment.
155    
156    \item \texttt{hs94.128x64x5} - 3D atmosphere dynamics using Held and
157      Suarez '94 forcing.
158      
159    \item \texttt{hs94.1x64x5} - Zonal averaged atmosphere using Held and
160      Suarez '94 forcing.
161      
162    \item \texttt{hs94.cs-32x32x5} 3D atmosphere dynamics using Held and
163      Suarez (1994) forcing on the cubed sphere. 5 vertical levels.
164    
165  \item \texttt{global_ocean_ebm} Global ocean experiment on a lat-lon grid coupled to an  \item \texttt{ideal\_2D\_oce} Idealized 2D global ocean simulation on
166  atmospheric energy balance model. Similar to global_ocean.90x40x15 experiment.    an aqua planet.
167    
168  \item \texttt{global_with_exf} Global ocean experiment on a lat-lon grid using the exf  \item \texttt{internal\_wave} - Ocean internal wave forced by open
169  package. Similar to global_ocean.90x40x15 experiment.    boundary conditions.
170    
171  \item \texttt{hs94.cs-32x32x5} 3D atmosphere dynamics using Held and Suarez  \item \texttt{inverted\_barometer} Simple test of ocean response to
172    (1994) forcing on the cubed sphere. 5 vertical levels.    atmospheric pressure loading.
173    
174  \item \texttt{ideal_2D_oce} Idealized 2D global ocean simulation on an aqua planet.  \item \texttt{lab\_sea} Regional Labrador Sea simulation on a lat-lon
175      grid. Coupled to the sea ice model.
176    
177  \item \texttt{inverted_barometer} Simple test of ocean response to atmospheric pressure  \item \texttt{matrix\_example} Test of experimental method to
178  loading.    accelerated convergence towards equillibrium.
179    
180  \item \texttt{lab_sea} Regional Labrador Sea simulation on a lat-lon grid. Coupled to  \item \texttt{MLAdjust} Simple test for different viscosity formulations.
 the sea ice model.  
181    
182  \item \texttt{matrix_example} Test of experimental method to accelerated convergence towards  \item \texttt{natl\_box} - Eastern subtropical North Atlantic with KPP
183  equillibrium.    scheme; 1 month integration
184      
185    \item \texttt{rotating\_tank} Rotating tank simulation in cylindrical
186      coordinates.  This experiment is described in detail in section
187      \ref{sect:eg-tank}.
188    
189  \item \texttt{tutorial_cfc_offline} Offline form of the MITgcm to study advection of a passive  \item \texttt{solid-body.cs-32x32x1} Solid body rotation test for cube
190    tracer and CFCs.    sphere grid.
191    
192  \item \texttt{vermix} Simple test in a small domain (3 columns) for ocean vertical mixing schemes.  \item \texttt{vermix} Simple test in a small domain (3 columns) for
193      ocean vertical mixing schemes.
194    
195  \end{enumerate}  \end{enumerate}
196    
# Line 229  Each example directory has the following Line 249  Each example directory has the following
249    In addition, you will also find in this directory the forcing and    In addition, you will also find in this directory the forcing and
250    topography files as well as the files describing the initial state    topography files as well as the files describing the initial state
251    of the experiment.  This varies from experiment to experiment. See    of the experiment.  This varies from experiment to experiment. See
252    section 2 for more details.    the verification directories refered to in this chapter for more details.
253    
254  \item \texttt{results}: this directory contains the output file  \item \texttt{results}: this directory contains the output file
255    \texttt{output.txt} produced by the simulation example. This file is    \texttt{output.txt} produced by the simulation example. This file is
256    useful for comparison with your own output when you run the    useful for comparison with your own output when you run the
257    experiment.    experiment.
258    
259    \item \texttt{build}: this directory is where the model is compiled
260      and loaded, and where the executable resides.
261    
262  \end{itemize}  \end{itemize}
263    
264  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
# Line 248  compile the code. Line 272  compile the code.
272  \input{part3/case_studies/fourlayer_gyre/fourlayer.tex}  \input{part3/case_studies/fourlayer_gyre/fourlayer.tex}
273    
274  \newpage  \newpage
275    \input{part3/case_studies/advection_in_gyre_circulation/adv_gyre.tex}
276    
277    \newpage
278  \input{part3/case_studies/climatalogical_ogcm/climatalogical_ogcm.tex}  \input{part3/case_studies/climatalogical_ogcm/climatalogical_ogcm.tex}
279    
280  \newpage  \newpage
# Line 263  compile the code. Line 290  compile the code.
290  \input{part3/case_studies/plume_on_slope/plume_on_slope.tex}  \input{part3/case_studies/plume_on_slope/plume_on_slope.tex}
291    
292  \newpage  \newpage
 \input{part3/case_studies/carbon_outgassing_sensitivity/co2sens.tex}  
   
 \newpage  
293  \input{part3/case_studies/biogeochem_tutorial/biogeochem.tex}  \input{part3/case_studies/biogeochem_tutorial/biogeochem.tex}
294    
295  \newpage  \newpage
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