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\section{Tutorials} |
\section[MITgcm Example Experiments]{Example experiments} |
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\label{sect:tutorials} |
\label{sec:modelExamples} |
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\label{www:tutorials} |
\begin{rawhtml} |
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<!-- CMIREDIR:modelExamples: --> |
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\end{rawhtml} |
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%% a set of pre-configured numerical experiments |
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|
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The full MITgcm distribution comes with a set of pre-configured |
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numerical experiments. Some of these example experiments are tests of |
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individual parts of the model code, but many are fully fledged |
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numerical simulations. Full tutorials exist for a few of the examples, |
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and are documented in sections \ref{sec:eg-baro} - |
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\ref{sec:eg-tank}. The other examples follow the same general |
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structure as the tutorial examples. However, they only include brief |
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instructions in a text file called {\it README}. The examples are |
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located in subdirectories under the directory \texttt{verification}. |
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Each example is briefly described below. |
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\subsection{Full list of model examples} |
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\begin{enumerate} |
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\item \texttt{tutorial\_advection\_in\_gyre} - Test of various |
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advection schemes in a single-layer double-gyre experiment. |
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This experiment is described in detail in section |
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\ref{sec:eg-adv-gyre}. |
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\item \texttt{tutorial\_baroclinic\_gyre} - Four layer, ocean double |
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gyre. This experiment is described in detail in section |
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\ref{sec:eg-fourlayer}. |
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\item \texttt{tutorial\_barotropic\_gyre} - Single layer, ocean double |
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gyre (barotropic with free-surface). |
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This experiment is described in detail in section \ref{sec:eg-baro}. |
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\item \texttt{tutorial\_cfc\_offline} - Offline form of the MITgcm to |
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study advection of a passive tracer and CFCs. |
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This experiment is described in detail in section \ref{sec:eg-offline-cfc}. |
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\item \texttt{tutorial\_deep\_convection} - Non-uniformly forced |
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ocean convection in a doubly periodic box. This experiment is |
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described in detail in section \ref{sec:eg-bconv}. |
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\item \texttt{tutorial\_dic\_adoffline} - Offline form of MITgcm |
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dynamics coupled to the dissolved inorganic carbon biogeochemistry model; |
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adjoint set-up. |
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\item \texttt{tutorial\_global\_oce\_biogeo} - Ocean model coupled to |
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the dissolved inorganic carbon biogeochemistry model. This |
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experiment is described in detail in section |
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\ref{sec:eg-biogeochem_tutorial}. |
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\item \texttt{tutorial\_global\_oce\_in\_p} - Global ocean simulation in |
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pressure coordinate (non-Boussinesq ocean model). Described in |
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detail in section \ref{sec:eg-globalpressure}. |
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\item \texttt{tutorial\_global\_oce\_latlon} - 4x4 degree global ocean |
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simulation with steady climatological forcing. This experiment is |
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described in detail in section \ref{sec:eg-global}. |
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\item \texttt{tutorial\_global\_oce\_optim} - Global ocean state |
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estimation at $4^\circ$ resolution. This experiment is described in |
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detail in section \ref{sec:eg-global_state_estimate}. |
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\item \texttt{tutorial\_held\_suarez\_cs} - 3D atmosphere dynamics |
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using Held and Suarez (1994) forcing on cubed sphere grid. This |
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experiment is described in detail in section \ref{sec:eg-hs}. |
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\item \texttt{tutorial\_offline} - Offline form of the MITgcm to study |
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advection of a passive tracer. This experiment is described in |
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detail in section \ref{sec:eg-offline}. |
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\item \texttt{tutorial\_plume\_on\_slope} - Gravity Plume on a |
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continental slope. This experiment is described in detail in |
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section \ref{sec:eg-gravityplume}. |
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\item \texttt{tutorial\_tracer\_adjsens} - Simple passive tracer |
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experiment. Includes derivative calculation. This experiment is |
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described in detail in section \ref{sec:eg-simple-tracer-adjoint}.\\ |
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Also contains an additional set-up using Secon Order Moment (SOM) advection |
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scheme ({\it input\_ad.som81/}). |
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\item \texttt{1D\_ocean\_ice\_column} - Oceanic column with seaice on top. |
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\item \texttt{adjustment.128x64x1} - Barotropic adjustment problem on |
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latitude longitude grid with 128x64 grid points ($2.8^\circ$ resolution). |
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\item \texttt{adjustment.cs-32x32x1} - Barotropic adjustment problem on |
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cube sphere grid with 32x32 points per face (roughly $2.8^\circ$ |
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resolution).\\ |
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Also contains a non-linear free-surface adjustment version ({\it input.nlfs/}). |
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\item \texttt{advect\_cs} - Two-dimensional passive advection test on |
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cube sphere grid (32x32 grid points per face, roughly $2.8^\circ$ resolution) |
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\item \texttt{advect\_xy} - Two-dimensional (horizontal plane) passive |
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advection test on Cartesian grid.\\ |
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Also contains an additional set-up using Adams-Bashforth 3 ({\it input.ab3\_c4/}). |
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\item \texttt{advect\_xz} - Two-dimensional (vertical plane) passive |
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advection test on Cartesian grid.\\ |
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Also contains an additional set-up using non-linear free-surface |
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with divergent barotropic flow and implicit vertical advection ({\it input.nlfs/}). |
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\item \texttt{aim.5l\_Equatorial\_Channel} - |
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5-levels Intermediate Atmospheric physics, |
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3D Equatorial Channel configuration. |
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\item \texttt{aim.5l\_LatLon} - 5-levels Intermediate Atmospheric physics, |
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Global configuration, on latitude longitude grid with 128x64x5 grid |
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points ($2.8^\circ$ resolution). |
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\item \texttt{aim.5l\_cs} - 5-levels Intermediate Atmospheric physics, |
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Global configuration on cube sphere grid |
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(32x32 grid points per face, roughly $2.8^\circ$).\\ |
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Also contains an additional set-up with a slab-ocean and thermodynamic |
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sea-ice ({\it input.thSI/}). |
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\item \texttt{bottom\_ctrl\_5x5} - Adjoint test using the bottom |
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topography as the control parameter. |
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\item \texttt{cfc\_example} - Global ocean with online computation and |
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advection of CFC11 and CFC12. |
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\item \texttt{cheapAML\_box} - Example using cheap atmospheric mixed layer |
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(cheapAML) package. |
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\item \texttt{cpl\_aim+ocn} - Coupled Ocean - Atmosphere realistic |
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configuration on cubed-sphere cs32 horizontal grid, |
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using Intermediate Atmospheric physics ({\it pkg/aim\_v23}) |
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thermodynamic seaice ({\it pkg/thsice}) and land packages. |
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on cubed-sphere cs32 in a realistic configuration. |
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\item \texttt{cpl\_atm2d+ocn} - Coupled Ocean - Atmosphere realistic |
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configuration using 2-D Atmospheric Model ({\it pkg/atm2d}). |
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\item \texttt{deep\_anelastic} - Convection simulation on a giant planet: |
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relax both the Boussinesq approximation (anelastic) and the thin atmosphere |
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approximation (deep atmosphere). |
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\item \texttt{dome} - Idealized 3D test of a density-driven bottom current. |
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\item \texttt{exp2} - Old version of the global ocean experiment (no GM, |
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no partial-cells).\\ |
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Also contains an additional set-up with rigid-lid ({\it input.rigidLid/}). |
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\item \texttt{exp4} - Flow over a Gaussian bump in open-water or |
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channel with open boundaries.\\ |
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Also contains an additional set-up using non-linear free-surface ({\it input.nlfs/}). |
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\item \texttt{fizhi-cs-32x32x40} - Global atmospheric simulation with |
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realistic topography, 40 vertical levels, a cubed sphere grid and |
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the full atmospheric physics package. |
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\item \texttt{fizhi-cs-aqualev20} - Global atmospheric simulation on an |
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aqua planet with full atmospheric physics. Run is perpetual march |
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with an analytical SST distribution. This is the configuration for |
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the APE (Aqua Planet Experiment) participation experiment. |
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\item \texttt{fizhi-gridalt-hs} - Global atmospheric simulation |
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Held-Suarez (1994) forcing, with the physical forcing and the |
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dynamical forcing running on different vertical grids. |
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\item \texttt{flt\_example} - Example of using float package. |
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\item \texttt{front\_relax} - Relaxation of an ocean thermal front |
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(test for Gent/McWilliams scheme). 2D (y-z).\\ |
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Also contains additional set-ups: |
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\begin{enumerate} |
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\item using the Boundary-Value Problem method |
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(Ferrari et al., 2010) ({\it input.bvp/}). |
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\item with Mixed-Layer Eddy parameterization |
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(Ferrari \& McWilliams, 2007) ({\it input.mxl/}). |
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\end{enumerate} |
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\item \texttt{global\_ocean.90x40x15} - Global ocean simulation at 4x4 |
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degree resolution. Similar to tutorial\_global\_oce\_latlon, but using |
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$z^*$ coordinates with quasi-non-hydrostatic and non-hydrostatic metric terms. |
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This experiment also illustrate the use of SBO package. |
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Also contains additional set-ups: |
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\begin{enumerate} |
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\item using down-slope package ({\it pkg/down\_slope}) ({\it input.dwnslp/}) |
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\item an Open-AD adjoint set-up ({\it code\_oad/, input\_oad/}). |
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\item four TAF adjoint set-ups ({\it code\_ad/}): |
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\begin{enumerate} |
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\item standard experiment ({\it input\_ad/}). |
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\item with bottom drag as a control ({\it input\_ad.bottomdrag/}). |
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\item with kappa GM as a control ({\it input\_ad.kapgm/}). |
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\item with kappa Redi as a control ({\it input\_ad.kapredi/}). |
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\end{enumerate} |
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\end{enumerate} |
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\item \texttt{global\_ocean.cs32x15} - Global ocean experiment on the |
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cubed sphere grid.\\ |
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Also contains additional forward set-ups: |
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\begin{enumerate} |
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\item non-hydrostatic with biharmonic viscosity ({\it input.viscA4/}) |
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\item using thermodynamic sea ice and bulk force ({\it input.thsice/}) |
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\item using thermodynamic ({\it pkg/thsice}) dynamic ({\it pkg/seaice}) sea-ice |
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and {\it exf} package ({\it input.icedyn/}) |
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\item using thermodynamic - dynamic ({\it pkg/seaice}) sea-ice |
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with {\it exf} package ({\it input.seaice/}) |
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\end{enumerate} |
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and few additional adjoint set-ups ({\it code\_ad/}): |
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\begin{enumerate} |
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\item standard experiment without sea-ice ({\it input\_ad/}). |
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\item using thermodynamic - dynamic sea-ice ({\it input\_ad.seaice/}) |
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\item same as above without adjoint sea-ice dynamics ({\it input\_ad.seaice\_dynmix/}) |
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\item using thermodynamic sea-ice from {\it thsice} package ({\it input\_ad.thsice/}) |
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\end{enumerate} |
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\item \texttt{global\_ocean\_ebm} - Global ocean experiment on a lat-lon |
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grid coupled to an atmospheric energy balance model. Similar to |
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global\_ocean.90x40x15 experiment.\\ |
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Also contains an adjoint set-up ({\it code\_ad/, input\_ad/}). |
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\item \texttt{global\_with\_exf} - Global ocean experiment on a lat-lon |
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grid using the {\it exf} package. Similar to tutorial\_global\_oce\_latlon |
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experiment.\\ |
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Also contains a secondary set-up with yearly {\it exf} fields ({\it input\_ad.yearly/}). |
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\item \texttt{halfpipe\_streamice} - Example using package "streamice".\\ |
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Also contains adjoint set-ups using TAF ({\it code\_ad/, input\_ad/}) |
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and using Open-AD ({\it code\_oad/, input\_oad/}). |
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\item \texttt{hs94.128x64x5} - 3D atmosphere dynamics on lat-lon grid, |
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using Held and Suarez '94 forcing. |
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\item \texttt{hs94.1x64x5} - Zonal averaged atmosphere dynamics |
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using Held and Suarez '94 forcing.\\ |
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Also contains adjoint set-ups using TAF ({\it code\_ad/, input\_ad/}) |
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and using Open-AD ({\it code\_oad/, input\_oad/}). |
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\item \texttt{hs94.cs-32x32x5} - 3D atmosphere dynamics using Held and |
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Suarez (1994) forcing on the cubed sphere, similar to tutorial\_held\_suarez\_cs |
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experiment but using linear free-surface and only 5 levels.\\ |
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Also contains an additional set-up with Implicit Internal gravity waves |
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treatment and Adams-Bashforth 3 ({\it input.impIGW/}). |
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\item \texttt{ideal\_2D\_oce} - Idealized 2D global ocean simulation on |
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an aqua planet. |
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\item \texttt{internal\_wave} - Ocean internal wave forced by open |
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boundary conditions.\\ |
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Also contains an additional set-up using {\it pkg/kl10} (see section |
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\ref{sec:pkg:kl10}, Klymak and Legg, 2010) ({\it input.kl10/}). |
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\item \texttt{inverted\_barometer} - Simple test of ocean response to |
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atmospheric pressure loading. |
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\item \texttt{isomip} - ISOMIP like set-up including ice-shelf cavities |
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({\it pkg/shelfice}).\\ |
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Also contains additional set-ups: |
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\begin{enumerate} |
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\item with "htd" ({\it input.htd/}) |
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but only Martin knows what "htd" stands for. |
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\item using package {\it icefront} ({\it input.icefront}) |
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\end{enumerate} |
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and also adjoint set-ups using TAF ({\it code\_ad/, input\_ad/, input\_ad.htd/}) |
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or using Open-AD ({\it code\_oad/, input\_oad/}). |
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\item \texttt{lab\_sea} - Regional Labrador Sea simulation on a lat-lon |
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grid using the sea ice package.\\ |
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Also contains additional set-ups: |
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\begin{enumerate} |
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\item using the simple "free-drift" assumption for seaice ({\it input.fd/}) |
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\item using EVP dynamics (instead of LSR solver) and Hibler \& Bryan (1987) |
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sea-ice ocean stress ({\it input.hb87/}) |
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\item using package {\it salt\_plume} ({\it input.salt\_plume/}) |
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\end{enumerate} |
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and also 3 adjoint set-ups ({\it code\_ad/, input\_ad/, input\_ad.noseaicedyn/, |
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input\_ad.noseaice/}). |
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\item \texttt{matrix\_example} - Test of experimental method to |
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accelerated convergence towards equilibrium. |
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\item \texttt{MLAdjust} - Simple tests for different viscosity formulations.\\ |
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Also contains additional set-ups (see: {\it verification/MLAdjust/README}): |
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\begin{enumerate} |
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\item ({\it input.A4FlxF/}) |
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\item ({\it input.AhFlxF/}) |
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\item ({\it input.AhVrDv/}) |
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\item ({\it input.AhStTn/}) |
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\end{enumerate} |
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\item \texttt{natl\_box} - Eastern subtropical North Atlantic with KPP |
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scheme; 1 month integration |
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\item \texttt{obcs\_ctrl} - Adjoint test using Open-Boundary conditions |
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as control parameters. |
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\item \texttt{offline\_exf\_seaice} - Seaice on top of oceanic surface layer |
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in an idealized channel. Forcing is computed by bulk-formulae ({\it pkg/exf}) |
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with temperature relaxation to prescribed SST (offline ocean).\\ |
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Also contains additional set-ups: |
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\begin{enumerate} |
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\item sea-ice dynamics-only using JFNK solver |
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and {\it pkg/thsice} advection ({\it input.dyn\_jfnk/}) |
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\item sea-ice dynamics-only using LSR solver |
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and {\it pkg/seaice} advection ({\it input.dyn\_lsr/}) |
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\item sea-ice thermodynamics-only using {\it pkg/seaice} ({\it input.thermo/}) |
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\item sea-ice thermodynamics-only using {\it pkg/thsice} ({\it input.thsice/}) |
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\end{enumerate} |
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and also 2 adjoint set-ups ({\it code\_ad/, input\_ad/, input\_ad.thsice/}). |
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\item \texttt{OpenAD} - Simple Adjoint experiment (used also to test |
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Open-AD compiler) |
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\item \texttt{rotating\_tank} - Rotating tank simulation in cylindrical |
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coordinates. This experiment is described in detail in section |
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\ref{sec:eg-tank}. |
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\item \texttt{seaice\_itd} - Seaice example using Ice Thickness Distribution (ITD).\\ |
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Also contains additional set-ups: |
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\begin{enumerate} |
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\item ({\it input.thermo/}) |
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\item ({\it input.lipscomb07/}) |
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\end{enumerate} |
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\item \texttt{seaice\_obcs} - Similar to "lab\_sea" ({\it input.salt\_plume/}) |
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experiment with only a fraction of the domain and open-boundary conditions |
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derived from "lab\_sea" experiment.\\ |
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Also contains additional set-ups: |
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\begin{enumerate} |
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\item ({\it input.seaiceSponge/}) |
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\item ({\it input.tides/}) |
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\end{enumerate} |
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\item \texttt{short\_surf\_wave} - Short surface wave adjusment |
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(non-hydrostatic) in homogeneous 2-D vertical section (x-z). |
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\item \texttt{so\_box\_biogeo} - Open-boundary Southern ocean box around |
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Drake passage, using same model parameters and forcing as experiment |
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"tutorial\_global\_oce\_biogeo" from which initial conditions |
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and OB conditions have been extracted. |
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\item \texttt{solid-body.cs-32x32x1} - Solid body rotation test for cube |
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sphere grid. |
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\item \texttt{tidal\_basin\_2d} - 2-D vertical section (x-z) with tidal forcing |
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(untested) |
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\item \texttt{vermix} - Simple test in a small domain (3 columns) for |
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ocean vertical mixing schemes. The standard set-up ({\it input/}) uses |
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KPP scheme \cite[]{lar-eta:94}.\\ |
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Also contains additional set-ups: |
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\begin{enumerate} |
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\item with Double Diffusion scheme from KPP ({\it input.dd/}) |
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\item with \cite{gas-eta:90} ({\it pkg/ggl90}) scheme ({\it input.ggl90/}) |
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\item with \cite{Mellor:Yamada1982} level 2. ({\it pkg/my82}) scheme ({\it input.my82/}) |
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\item with \cite{pal-rom:97} ({\it pkg/opps}) scheme ({\it input.opps/}) |
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\item with \cite{Pacanowski:Philander1981} ({\it pkg/pp81}) scheme ({\it input.pp81/}) |
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\end{enumerate} |
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|
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\end{enumerate} |
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\subsection{Directory structure of model examples} |
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|
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Each example directory has the following subdirectories: |
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|
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\begin{itemize} |
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\item \texttt{code}: contains the code particular to the example. At a |
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minimum, this directory includes the following files: |
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|
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\begin{itemize} |
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\item \texttt{code/packages.conf}: declares the list of packages or |
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package groups to be used. If not included, the default version |
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is located in \texttt{pkg/pkg\_default}. Package groups are |
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simply convenient collections of commonly used packages which are |
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defined in \texttt{pkg/pkg\_default}. Some packages may require |
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other packages or may require their absence (that is, they are |
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incompatible) and these package dependencies are listed in |
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\texttt{pkg/pkg\_depend}. |
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|
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|
\item \texttt{code/CPP\_EEOPTIONS.h}: declares CPP keys relative to |
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|
the ``execution environment'' part of the code. The default |
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|
version is located in \texttt{eesupp/inc}. |
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|
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|
\item \texttt{code/CPP\_OPTIONS.h}: declares CPP keys relative to |
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|
the ``numerical model'' part of the code. The default version is |
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|
located in \texttt{model/inc}. |
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|
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|
\item \texttt{code/SIZE.h}: declares size of underlying |
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|
computational grid. The default version is located in |
| 389 |
|
\texttt{model/inc}. |
| 390 |
|
\end{itemize} |
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|
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|
In addition, other include files and subroutines might be present in |
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\texttt{code} depending on the particular experiment. See Section 2 |
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|
for more details. |
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|
|
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|
\item \texttt{input}: contains the input data files required to run |
| 397 |
|
the example. At a minimum, the \texttt{input} directory contains the |
| 398 |
|
following files: |
| 399 |
|
|
| 400 |
|
\begin{itemize} |
| 401 |
|
\item \texttt{input/data}: this file, written as a namelist, |
| 402 |
|
specifies the main parameters for the experiment. |
| 403 |
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|
| 404 |
|
\item \texttt{input/data.pkg}: contains parameters relative to the |
| 405 |
|
packages used in the experiment. |
| 406 |
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|
| 407 |
|
\item \texttt{input/eedata}: this file contains ``execution |
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|
environment'' data. At present, this consists of a specification |
| 409 |
|
of the number of threads to use in $X$ and $Y$ under multi-threaded |
| 410 |
|
execution. |
| 411 |
|
\end{itemize} |
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|
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|
In addition, you will also find in this directory the forcing and |
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|
topography files as well as the files describing the initial state |
| 415 |
|
of the experiment. This varies from experiment to experiment. See |
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|
the verification directories refered to in this chapter for more details. |
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|
|
| 418 |
|
\item \texttt{results}: this directory contains the output file |
| 419 |
|
\texttt{output.txt} produced by the simulation example. This file is |
| 420 |
|
useful for comparison with your own output when you run the |
| 421 |
|
experiment. |
| 422 |
|
|
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|
\item \texttt{build}: this directory is initially empty and is used |
| 424 |
|
to compile and load the model, and to generate the executable. |
| 425 |
|
|
| 426 |
|
\item \texttt{run}: this directory is initially empty and is used |
| 427 |
|
to run the executable. |
| 428 |
|
|
| 429 |
\input{part3/case_studies/barotropic_gyre/baro.tex} |
\end{itemize} |
| 430 |
|
|
| 431 |
\newpage |
Once you have chosen the example you want to run, you are ready to |
| 432 |
\input{part3/case_studies/fourlayer_gyre/fourlayer.tex} |
compile the code. |
| 433 |
|
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|
\newpage |
|
|
\input{part3/case_studies/climatalogical_ogcm/climatalogical_ogcm.tex} |
|
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|
|
|
\newpage |
|
|
\input{part3/case_studies/ogcm_in_pressure/ogcm_in_pressure.tex} |
|
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|
|
|
\newpage |
|
|
\input{part3/case_studies/hs_atmosphere/hs_atmos.tex} |
|
|
|
|
|
\newpage |
|
|
\input{part3/case_studies/doubly_periodic_convection/convection.tex} |
|
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|
|
|
\newpage |
|
|
\input{part3/case_studies/plume_on_slope/plume_on_slope.tex} |
|
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|
|
|
\newpage |
|
|
\input{part3/case_studies/carbon_outgassing_sensitivity/co2sens.tex} |
|
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|
|
\newpage |
|
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\input{part3/case_studies/biogeochem_tutorial/biogeochem.tex} |
|
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\begin{versionprivate} |
|
|
\newpage |
|
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\input{part3/case_studies/rotating_tank/tank.tex} |
|
|
\end{versionprivate} |
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