/[MITgcm]/manual/s_examples/text/model_examples.tex

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-revision 1.25 by jmc,
Tue Mar 26 13:21:28 2013 UTC
+revision 1.26 by jmc,
Fri Aug 29 17:08:21 2014 UTC
 Line 41 
 Each example is briefly described below.
    study advection of a passive tracer and CFCs.
    This experiment is described in detail in section \ref{sec:eg-offline-cfc}.
- \item \texttt{tutorial\_deep\_convection} - Inhomogenously forced
+ \item \texttt{tutorial\_deep\_convection} - Non-uniformly forced
    ocean convection in a doubly periodic box. This experiment is
    described in detail in section \ref{sec:eg-bconv}.
+ \item \texttt{tutorial\_dic\_adoffline} - Offline form of MITgcm
+   dynamics coupled to the dissolved inorganic carbon biogeochemistry model;
+   adjoint set-up.
  \item \texttt{tutorial\_global\_oce\_biogeo} - Ocean model coupled to
    the dissolved inorganic carbon biogeochemistry model. This
    experiment is described in detail in section
-Line 76 
 Each example is briefly described below.
+Line 80 
 Each example is briefly described below.
  \item \texttt{tutorial\_tracer\_adjsens} - Simple passive tracer
    experiment. Includes derivative calculation. This experiment is
-   described in detail in section \ref{sec:eg-simple-tracer-adjoint}.
+   described in detail in section \ref{sec:eg-simple-tracer-adjoint}.\\
+   Also contains an additional set-up using Secon Order Moment (SOM) advection
+   scheme ({\it input\_ad.som81/}).
+ \item \texttt{1D\_ocean\_ice\_column} - Oceanic column with seaice on top.
  \item \texttt{adjustment.128x64x1} - Barotropic adjustment problem on
    latitude longitude grid with 128x64 grid points ($2.8^\circ$ resolution).
-Line 86 
 Each example is briefly described below.
+Line 94 
 Each example is briefly described below.
    resolution).\\
    Also contains a non-linear free-surface adjustment version ({\it input.nlfs/}).
- \item \texttt{advect\_cs} Two-dimensional passive advection test on
+ \item \texttt{advect\_cs} - Two-dimensional passive advection test on
-   cube sphere grid (32x32 grid points per face, roughly $2.8^\circ$)
+   cube sphere grid (32x32 grid points per face, roughly $2.8^\circ$ resolution)
  \item \texttt{advect\_xy} - Two-dimensional (horizontal plane) passive
    advection test on Cartesian grid.\\
    Also contains an additional set-up using Adams-Bashforth 3 ({\it input.ab3\_c4/}).
  \item \texttt{advect\_xz} - Two-dimensional (vertical plane) passive
-   advection test on Cartesian grid.
+   advection test on Cartesian grid.\\
+   Also contains an additional set-up using non-linear free-surface
+    with divergent barotropic flow and implicit vertical advection ({\it input.nlfs/}).
- \item \texttt{aim.5l\_Equatorial\_Channel}
+ \item \texttt{aim.5l\_Equatorial\_Channel} -
-   - 5-levels Intermediate Atmospheric physics,
+-levels Intermediate Atmospheric physics,
 D Equatorial Channel configuration.
  \item \texttt{aim.5l\_LatLon} - 5-levels Intermediate Atmospheric physics,
-Line 107 
 Each example is briefly described below.
+Line 117 
 Each example is briefly described below.
  \item \texttt{aim.5l\_cs} - 5-levels Intermediate Atmospheric physics,
    Global configuration on cube sphere grid
    (32x32 grid points per face, roughly $2.8^\circ$).\\
-   Also contains an additional set-up with an ocean mixed layer and thermodynamics
+   Also contains an additional set-up with a slab-ocean and thermodynamic
    sea-ice ({\it input.thSI/}).
  \item \texttt{bottom\_ctrl\_5x5} - Adjoint test using the bottom
-Line 116 
 Each example is briefly described below.
+Line 126 
 Each example is briefly described below.
  \item \texttt{cfc\_example} - Global ocean with online computation and
    advection of CFC11 and CFC12.
+ \item \texttt{cheapAML\_box} - Example using cheap atmospheric mixed layer
+    (cheapAML) package.
  \item \texttt{cpl\_aim+ocn} - Coupled Ocean - Atmosphere realistic
    configuration on cubed-sphere cs32 horizontal grid,
    using Intermediate Atmospheric physics ({\it pkg/aim\_v23})
-   thermodynamics seaice ({\it pkg/thsice}) and land packages.
+   thermodynamic seaice ({\it pkg/thsice}) and land packages.
-   on cubed-sphere cs32 in a realistics configuration.
+   on cubed-sphere cs32 in a realistic configuration.
  \item \texttt{cpl\_atm2d+ocn} - Coupled Ocean - Atmosphere realistic
    configuration using 2-D Atmospheric Model ({\it pkg/atm2d}).
-Line 133 
 Each example is briefly described below.
+Line 146 
 Each example is briefly described below.
  \item \texttt{exp2} - Old version of the global ocean experiment (no GM,
        no partial-cells).\\
-   Also contains an additional set-up with ridid-lid ({\it input.rigidLid/}).
+   Also contains an additional set-up with rigid-lid ({\it input.rigidLid/}).
  \item \texttt{exp4} - Flow over a Gaussian bump in open-water or
-   channel with open boundaries.
+   channel with open boundaries.\\
+   Also contains an additional set-up using non-linear free-surface ({\it input.nlfs/}).
- \item \texttt{exp5} - Deep convection.
  \item \texttt{fizhi-cs-32x32x40} - Global atmospheric simulation with
    realistic topography, 40 vertical levels, a cubed sphere grid and
-Line 156 
 Each example is briefly described below.
+Line 168 
 Each example is briefly described below.
  \item \texttt{flt\_example} - Example of using float package.
  \item \texttt{front\_relax} - Relaxation of an ocean thermal front
-   (test for Gent/McWilliams scheme). 2D (Y-Z).\\
+   (test for Gent/McWilliams scheme). 2D (y-z).\\
-   Also contains an additional set-up with Mixed-Layer Eddy parameterization
+   Also contains additional set-ups:
-   (Ferrari \& McWilliams, 2007) ({\it input.mxl/}).
+   \begin{enumerate}
+    \item using the Boundary-Value Problem method
- \item \texttt{global1x1\_tot} - ECCO-GODAE production configuration
+           (Ferrari et al., 2010) ({\it input.bvp/}).
-  version 1, 2 \& 3
+    \item with Mixed-Layer Eddy parameterization
+           (Ferrari \& McWilliams, 2007) ({\it input.mxl/}).
- \item \texttt{global2x2\_tot} - ECCO production configuration version 0
+   \end{enumerate}
- \item \texttt{global\_ocean.90x40x15} Global ocean simulation at 4x4
+ \item \texttt{global\_ocean.90x40x15} - Global ocean simulation at 4x4
-   degree resolution. Similar to tutorial\_global\_oce\_latlon, with
+   degree resolution. Similar to tutorial\_global\_oce\_latlon, but using
-   quasi-non-hydrostatics and non-hydrostatic metric terms.\\
+   $z^*$ coordinates with quasi-non-hydrostatic and non-hydrostatic metric terms.
-   Also contains an adjoint set-up ({\it code\_ad/, input\_ad/}).
+   This experiment also illustrate the use of SBO package.
+   Also contains additional set-ups:
+   \begin{enumerate}
+    \item using down-slope package ({\it pkg/down\_slope}) ({\it input.dwnslp/})
+    \item an Open-AD adjoint set-up ({\it code\_oad/, input\_oad/}).
+    \item four TAF adjoint set-ups ({\it code\_ad/}):
+    \begin{enumerate}
+      \item standard experiment ({\it input\_ad/}).
+      \item with bottom drag as a control ({\it input\_ad.bottomdrag/}).
+      \item with kappa GM as a control ({\it input\_ad.kapgm/}).
+      \item with kappa Redi as a control ({\it input\_ad.kapredi/}).
+    \end{enumerate}
+   \end{enumerate}
  \item \texttt{global\_ocean.cs32x15} - Global ocean experiment on the
    cubed sphere grid.\\
-   Also contains additional set-ups:
+   Also contains additional forward set-ups:
    \begin{enumerate}
-    \item non-hydrostratic with biharmonic viscosity ({\it input.viscA4/})
+    \item non-hydrostatic with biharmonic viscosity ({\it input.viscA4/})
     \item using thermodynamic sea ice and bulk force ({\it input.thsice/})
-    \item using thermodynamic ({\it pkg/thsice}) dynamics ({\it pkg/seaice}) sea-ice
+    \item using thermodynamic ({\it pkg/thsice}) dynamic ({\it pkg/seaice}) sea-ice
-          and EXF package ({\it input.icedyn/})
+          and {\it exf} package ({\it input.icedyn/})
+    \item using thermodynamic - dynamic ({\it pkg/seaice}) sea-ice
+          with {\it exf} package ({\it input.seaice/})
+   \end{enumerate}
+   and few additional adjoint set-ups ({\it code\_ad/}):
+   \begin{enumerate}
+    \item standard experiment without sea-ice ({\it input\_ad/}).
+    \item using thermodynamic - dynamic sea-ice ({\it input\_ad.seaice/})
+    \item same as above without adjoint sea-ice dynamics ({\it input\_ad.seaice\_dynmix/})
+    \item using thermodynamic sea-ice from {\it thsice} package ({\it input\_ad.thsice/})
    \end{enumerate}
  \item \texttt{global\_ocean\_ebm} - Global ocean experiment on a lat-lon
-Line 186 
 Each example is briefly described below.
+Line 219 
 Each example is briefly described below.
    Also contains an adjoint set-up ({\it code\_ad/, input\_ad/}).
  \item \texttt{global\_with\_exf} - Global ocean experiment on a lat-lon
-   grid using the exf package. Similar to global\_ocean.90x40x15
+   grid using the {\it exf} package. Similar to tutorial\_global\_oce\_latlon
-   experiment.
+   experiment.\\
+   Also contains a secondary set-up with yearly {\it exf} fields ({\it input\_ad.yearly/}).
+ \item \texttt{halfpipe\_streamice} - Example using package "streamice".\\
+   Also contains adjoint set-ups using TAF ({\it code\_ad/, input\_ad/})
+    and using Open-AD ({\it code\_oad/, input\_oad/}).
  \item \texttt{hs94.128x64x5} - 3D atmosphere dynamics on lat-lon grid,
    using Held and Suarez '94 forcing.
  \item \texttt{hs94.1x64x5} - Zonal averaged atmosphere dynamics
    using Held and Suarez '94 forcing.\\
-   Also contains an adjoint set-up ({\it code\_ad/, input\_ad/}).
+   Also contains adjoint set-ups using TAF ({\it code\_ad/, input\_ad/})
+    and using Open-AD ({\it code\_oad/, input\_oad/}).
  \item \texttt{hs94.cs-32x32x5} - 3D atmosphere dynamics using Held and
-   Suarez (1994) forcing on the cubed sphere. 5 vertical levels.\\
+   Suarez (1994) forcing on the cubed sphere, similar to tutorial\_held\_suarez\_cs
+   experiment but using linear free-surface and only 5 levels.\\
    Also contains an additional set-up with Implicit Internal gravity waves
-   treatment ({\it input.impIGW/}).
+   treatment and Adams-Bashforth 3 ({\it input.impIGW/}).
  \item \texttt{ideal\_2D\_oce} - Idealized 2D global ocean simulation on
    an aqua planet.
  \item \texttt{internal\_wave} - Ocean internal wave forced by open
-   boundary conditions.
+   boundary conditions.\\
+   Also contains an additional set-up using {\it pkg/kl10} (see section
+    \ref{sec:pkg:kl10}, Klymak and Legg, 2010) ({\it input.kl10/}).
  \item \texttt{inverted\_barometer} - Simple test of ocean response to
    atmospheric pressure loading.
  \item \texttt{isomip} - ISOMIP like set-up including ice-shelf cavities
    ({\it pkg/shelfice}).\\
-   Also contains an additional set-up with ({\it input.htd/})
+   Also contains additional set-ups:
-   but only Martin knows what "htd" stands for.
+   \begin{enumerate}
+    \item with "htd" ({\it input.htd/})
+           but only Martin knows what "htd" stands for.
+    \item using package {\it icefront} ({\it input.icefront})
+   \end{enumerate}
+   and also adjoint set-ups using TAF ({\it code\_ad/, input\_ad/, input\_ad.htd/})
+   or using Open-AD ({\it code\_oad/, input\_oad/}).
  \item \texttt{lab\_sea} - Regional Labrador Sea simulation on a lat-lon
    grid using the sea ice package.\\
    Also contains additional set-ups:
    \begin{enumerate}
-    \item using the LSR solver (instead of EVP dynamics) ({\it input.lsr/})
+    \item using the simple "free-drift" assumption for seaice ({\it input.fd/})
-    \item using Hibler and Bryan (1987) sea-ice ocean stress ({\it input.hb87/})
+    \item using EVP dynamics (instead of LSR solver) and Hibler \& Bryan (1987)
+          sea-ice ocean stress ({\it input.hb87/})
     \item using package {\it salt\_plume} ({\it input.salt\_plume/})
    \end{enumerate}
    and also 3 adjoint set-ups ({\it code\_ad/, input\_ad/, input\_ad.noseaicedyn/,
-   input\_ad.noseaice/}).
+    input\_ad.noseaice/}).
  \item \texttt{matrix\_example} - Test of experimental method to
-   accelerated convergence towards equillibrium.
+   accelerated convergence towards equilibrium.
  \item \texttt{MLAdjust} - Simple tests for different viscosity formulations.\\
-   Also contains additional set-ups:
+   Also contains additional set-ups (see: {\it verification/MLAdjust/README}):
    \begin{enumerate}
-    \item ({\it input.0.leith/})
+    \item ({\it input.A4FlxF/})
-    \item ({\it input.0.leithD/})
+    \item ({\it input.AhFlxF/})
-    \item ({\it input.0.smag/})
+    \item ({\it input.AhVrDv/})
-    \item ({\it input.1.leith/})
+    \item ({\it input.AhStTn/})
    \end{enumerate}
  \item \texttt{natl\_box} - Eastern subtropical North Atlantic with KPP
    scheme; 1 month integration
- \item \texttt{natl\_box\_adjoint} - Eastern subtropical North Atlantic with KPP
+ \item \texttt{obcs\_ctrl} - Adjoint test using Open-Boundary conditions
-   scheme; adjoint set-up.
+   as control parameters.
- \item \texttt{offline\_exf\_seaice} - oceanic surface forcing computed
+ \item \texttt{offline\_exf\_seaice} - Seaice on top of oceanic surface layer
-   by bulk-formulae ({\it pkg/exf}) and inposed SST (offline ocean).\\
+   in an idealized channel. Forcing is computed by bulk-formulae ({\it pkg/exf})
+   with temperature relaxation to prescribed SST (offline ocean).\\
    Also contains additional set-ups:
    \begin{enumerate}
-    \item with sea-ice ({\it pkg/seaice}) thermodynamics ({\it input.seaicetd/})
+    \item sea-ice dynamics-only using JFNK solver
-    \item an adjoint test ({\it code\_ad/, input\_ad/}).
+          and {\it pkg/thsice} advection ({\it input.dyn\_jfnk/})
+    \item sea-ice dynamics-only using LSR solver
+          and {\it pkg/seaice} advection ({\it input.dyn\_lsr/})
+    \item sea-ice thermodynamics-only using {\it pkg/seaice} ({\it input.thermo/})
+    \item sea-ice thermodynamics-only using {\it pkg/thsice} ({\it input.thsice/})
    \end{enumerate}
+   and also 2 adjoint set-ups ({\it code\_ad/, input\_ad/, input\_ad.thsice/}).
- \item \texttt{OpenAD} simple Adjoint experiement (used also to test
+ \item \texttt{OpenAD} - Simple Adjoint experiment (used also to test
-   open-AD compiler)
+   Open-AD compiler)
- \item \texttt{rotating\_tank} Rotating tank simulation in cylindrical
+ \item \texttt{rotating\_tank} - Rotating tank simulation in cylindrical
    coordinates.  This experiment is described in detail in section
    \ref{sec:eg-tank}.
- \item \texttt{seaice\_obcs} similar to "lab\_sea" ({\it input.salt\_plume/})
+ \item \texttt{seaice\_itd} - Seaice example using Ice Thickness Distribution (ITD).\\
+   Also contains additional set-ups:
+   \begin{enumerate}
+    \item ({\it input.thermo/})
+    \item ({\it input.lipscomb07/})
+   \end{enumerate}
+ \item \texttt{seaice\_obcs} - Similar to "lab\_sea" ({\it input.salt\_plume/})
    experiment with only a fraction of the domain and open-boundary conditions
-   derived from "lab\_sea" experiment.
+   derived from "lab\_sea" experiment.\\
+   Also contains additional set-ups:
+   \begin{enumerate}
+    \item ({\it input.seaiceSponge/})
+    \item ({\it input.tides/})
+   \end{enumerate}
+ \item \texttt{short\_surf\_wave} - Short surface wave adjusment
+    (non-hydrostatic) in homogeneous 2-D vertical section (x-z).
+ \item \texttt{so\_box\_biogeo} - Open-boundary Southern ocean box around
+  Drake passage, using same model parameters and forcing as experiment
+   "tutorial\_global\_oce\_biogeo" from which initial conditions
+  and OB conditions have been extracted.
- \item \texttt{solid-body.cs-32x32x1} Solid body rotation test for cube
+ \item \texttt{solid-body.cs-32x32x1} - Solid body rotation test for cube
    sphere grid.
- \item \texttt{tidal\_basin\_2d} 2-D vertical section (X-Z) with tidal forcing
+ \item \texttt{tidal\_basin\_2d} - 2-D vertical section (x-z) with tidal forcing
+  (untested)
- \item \texttt{vermix} Simple test in a small domain (3 columns) for
+ \item \texttt{vermix} - Simple test in a small domain (3 columns) for
    ocean vertical mixing schemes. The standard set-up ({\it input/}) uses
    KPP scheme \cite[]{lar-eta:94}.\\
    Also contains additional set-ups:
    \begin{enumerate}
+    \item with Double Diffusion scheme from KPP ({\it input.dd/})
     \item with \cite{gas-eta:90} ({\it pkg/ggl90}) scheme ({\it input.ggl90/})
     \item with \cite{Mellor:Yamada1982} level 2. ({\it pkg/my82}) scheme ({\it input.my82/})
     \item with \cite{pal-rom:97} ({\it pkg/opps}) scheme ({\it input.opps/})
-Line 329 
 Each example directory has the following
+Line 406 
 Each example directory has the following
    \item \texttt{input/eedata}: this file contains ``execution
      environment'' data. At present, this consists of a specification
-     of the number of threads to use in $X$ and $Y$ under multithreaded
+     of the number of threads to use in $X$ and $Y$ under multi-threaded
      execution.
    \end{itemize}

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