| 1 |
% $Header: /u/gcmpack/manual/s_examples/text/model_examples.tex,v 1.22 2010/08/27 18:21:43 jmc Exp $ |
| 2 |
% $Name: $ |
| 3 |
|
| 4 |
\section[MITgcm Example Experiments]{Example experiments} |
| 5 |
\label{sec:modelExamples} |
| 6 |
\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 |
| 13 |
numerical experiments. Some of these example experiments are tests of |
| 14 |
individual parts of the model code, but many are fully fledged |
| 15 |
numerical simulations. Full tutorials exist for a few of the examples, |
| 16 |
and are documented in sections \ref{sec:eg-baro} - |
| 17 |
\ref{sec:eg-tank}. The other examples follow the same general |
| 18 |
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} |
| 24 |
|
| 25 |
\begin{enumerate} |
| 26 |
|
| 27 |
\item \texttt{tutorial\_advection\_in\_gyre} - Test of various |
| 28 |
advection schemes in a single-layer double-gyre experiment. |
| 29 |
This experiment is described in detail in section |
| 30 |
\ref{sec: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{sec: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{sec: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{sec: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{sec: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{sec: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{sec: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{sec: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{sec: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{sec: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{sec: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{sec: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{sec:eg-simple-tracer-adjoint}. |
| 80 |
|
| 81 |
\item \texttt{adjustment.128x64x1} - Barotropic adjustment problem on |
| 82 |
latitude longitude grid with 128x64 grid points ($2.8^\circ$ resolution). |
| 83 |
|
| 84 |
\item \texttt{adjustment.cs-32x32x1} - Barotropic adjustment problem on |
| 85 |
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{advect\_cs} Two-dimensional passive advection test on |
| 90 |
cube sphere grid (32x32 grid points per face, roughly $2.8^\circ$) |
| 91 |
|
| 92 |
\item \texttt{advect\_xy} - Two-dimensional (horizontal plane) passive |
| 93 |
advection test on Cartesian grid.\\ |
| 94 |
Also contains an additional set-up using Adams-Bashforth 3 ({\it input.ab3\_c4/}). |
| 95 |
|
| 96 |
\item \texttt{advect\_xz} - Two-dimensional (vertical plane) passive |
| 97 |
advection test on Cartesian grid. |
| 98 |
|
| 99 |
\item \texttt{aim.5l\_Equatorial\_Channel} |
| 100 |
- 5-levels Intermediate Atmospheric physics, |
| 101 |
3D Equatorial Channel configuration. |
| 102 |
|
| 103 |
\item \texttt{aim.5l\_LatLon} - 5-levels Intermediate Atmospheric physics, |
| 104 |
Global configuration, on latitude longitude grid with 128x64x5 grid |
| 105 |
points ($2.8^\circ$ resolution). |
| 106 |
|
| 107 |
\item \texttt{aim.5l\_cs} - 5-levels Intermediate Atmospheric physics, |
| 108 |
Global configuration on cube sphere grid |
| 109 |
(32x32 grid points per face, roughly $2.8^\circ$).\\ |
| 110 |
Also contains an additional set-up with an ocean mixed layer and thermodynamics |
| 111 |
sea-ice ({\it input.thSI/}). |
| 112 |
|
| 113 |
\item \texttt{bottom\_ctrl\_5x5} - Adjoint test using the bottom |
| 114 |
topography as the control parameter. |
| 115 |
|
| 116 |
\item \texttt{cfc\_example} - Global ocean with online computation and |
| 117 |
advection of CFC11 and CFC12. |
| 118 |
|
| 119 |
\item \texttt{cpl\_aim+ocn} - Coupled Ocean - Atmosphere realistic |
| 120 |
configuration on cubed-sphere cs32 horizontal grid, |
| 121 |
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{hs94.1x64x5} - Zonal averaged atmosphere dynamics |
| 196 |
using Held and Suarez '94 forcing.\\ |
| 197 |
Also contains an adjoint set-up ({\it code\_ad/, input\_ad/}). |
| 198 |
|
| 199 |
\item \texttt{hs94.cs-32x32x5} - 3D atmosphere dynamics using Held and |
| 200 |
Suarez (1994) forcing on the cubed sphere. 5 vertical levels.\\ |
| 201 |
Also contains an additional set-up with Implicit Internal gravity waves |
| 202 |
treatment ({\it input.impIGW/}). |
| 203 |
|
| 204 |
\item \texttt{ideal\_2D\_oce} - Idealized 2D global ocean simulation on |
| 205 |
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{natl\_box} - Eastern subtropical North Atlantic with KPP |
| 242 |
scheme; 1 month integration |
| 243 |
|
| 244 |
\item \texttt{natl\_box\_adjoint} - Eastern subtropical North Atlantic with KPP |
| 245 |
scheme; adjoint set-up. |
| 246 |
|
| 247 |
\item \texttt{offline\_exf\_seaice} - oceanic surface forcing computed |
| 248 |
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{sec: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{solid-body.cs-32x32x1} Solid body rotation test for cube |
| 267 |
sphere grid. |
| 268 |
|
| 269 |
\item \texttt{tidal\_basin\_2d} 2-D vertical section (X-Z) with tidal forcing |
| 270 |
|
| 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} |
| 283 |
|
| 284 |
\subsection{Directory structure of model examples} |
| 285 |
|
| 286 |
Each example directory has the following subdirectories: |
| 287 |
|
| 288 |
\begin{itemize} |
| 289 |
\item \texttt{code}: contains the code particular to the example. At a |
| 290 |
minimum, this directory includes the following files: |
| 291 |
|
| 292 |
\begin{itemize} |
| 293 |
\item \texttt{code/packages.conf}: declares the list of packages or |
| 294 |
package groups to be used. If not included, the default version |
| 295 |
is located in \texttt{pkg/pkg\_default}. Package groups are |
| 296 |
simply convenient collections of commonly used packages which are |
| 297 |
defined in \texttt{pkg/pkg\_default}. Some packages may require |
| 298 |
other packages or may require their absence (that is, they are |
| 299 |
incompatible) and these package dependencies are listed in |
| 300 |
\texttt{pkg/pkg\_depend}. |
| 301 |
|
| 302 |
\item \texttt{code/CPP\_EEOPTIONS.h}: declares CPP keys relative to |
| 303 |
the ``execution environment'' part of the code. The default |
| 304 |
version is located in \texttt{eesupp/inc}. |
| 305 |
|
| 306 |
\item \texttt{code/CPP\_OPTIONS.h}: declares CPP keys relative to |
| 307 |
the ``numerical model'' part of the code. The default version is |
| 308 |
located in \texttt{model/inc}. |
| 309 |
|
| 310 |
\item \texttt{code/SIZE.h}: declares size of underlying |
| 311 |
computational grid. The default version is located in |
| 312 |
\texttt{model/inc}. |
| 313 |
\end{itemize} |
| 314 |
|
| 315 |
In addition, other include files and subroutines might be present in |
| 316 |
\texttt{code} depending on the particular experiment. See Section 2 |
| 317 |
for more details. |
| 318 |
|
| 319 |
\item \texttt{input}: contains the input data files required to run |
| 320 |
the example. At a minimum, the \texttt{input} directory contains the |
| 321 |
following files: |
| 322 |
|
| 323 |
\begin{itemize} |
| 324 |
\item \texttt{input/data}: this file, written as a namelist, |
| 325 |
specifies the main parameters for the experiment. |
| 326 |
|
| 327 |
\item \texttt{input/data.pkg}: contains parameters relative to the |
| 328 |
packages used in the experiment. |
| 329 |
|
| 330 |
\item \texttt{input/eedata}: this file contains ``execution |
| 331 |
environment'' data. At present, this consists of a specification |
| 332 |
of the number of threads to use in $X$ and $Y$ under multithreaded |
| 333 |
execution. |
| 334 |
\end{itemize} |
| 335 |
|
| 336 |
In addition, you will also find in this directory the forcing and |
| 337 |
topography files as well as the files describing the initial state |
| 338 |
of the experiment. This varies from experiment to experiment. See |
| 339 |
the verification directories refered to in this chapter for more details. |
| 340 |
|
| 341 |
\item \texttt{results}: this directory contains the output file |
| 342 |
\texttt{output.txt} produced by the simulation example. This file is |
| 343 |
useful for comparison with your own output when you run the |
| 344 |
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} |
| 350 |
|
| 351 |
Once you have chosen the example you want to run, you are ready to |
| 352 |
compile the code. |
| 353 |
|
Parent Directory
| 
Revision Log
| 
Revision Graph