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\section{Tutorials} |
\section[MITgcm Example Experiments]{Example experiments} |
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\label{sect:tutorials} |
\label{sect:modelExamples} |
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\label{www:tutorials} |
\begin{rawhtml} |
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<!-- CMIREDIR:modelExamples: --> |
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This is the first in a series of tutorials describing |
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example MITgcm numerical experiments. The example experiments |
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include both straightforward examples of idealized geophysical |
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fluid simulations and more involved cases encompassing |
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large scale modeling and |
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automatic differentiation. Both hydrostatic and non-hydrostatic |
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experiments are presented, as well as experiments employing |
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Cartesian, spherical-polar and cube-sphere coordinate systems. |
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These ``case study'' documents include information describing |
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the experimental configuration and detailed information on how to |
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configure the MITgcm code and input files for each experiment. |
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\input{part3/case_studies/barotropic_gyre/baro.tex} |
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\newpage |
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\input{part3/case_studies/fourlayer_gyre/fourlayer.tex} |
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\newpage |
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\input{part3/case_studies/climatalogical_ogcm/climatalogical_ogcm.tex} |
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\newpage |
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\input{part3/case_studies/ogcm_in_pressure/ogcm_in_pressure.tex} |
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\newpage |
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\input{part3/case_studies/hs_atmosphere/hs_atmos.tex} |
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\newpage |
%% a set of pre-configured numerical experiments |
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\input{part3/case_studies/doubly_periodic_convection/convection.tex} |
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\newpage |
The full MITgcm distribution comes with a set of pre-configured |
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\input{part3/case_studies/plume_on_slope/plume_on_slope.tex} |
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{sect:eg-baro} - |
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\ref{sect: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{sect: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{sect: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{sect: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{sect:eg-offline-cfc}. |
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\item \texttt{tutorial\_deep\_convection} - Inhomogenously 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{sect:eg-bconv}. |
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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{sect: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{sect: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{sect: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{sect: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{sect: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{sect: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{sect: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{sect:eg-simple-tracer-adjoint}. |
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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 $2.8^\circ$) |
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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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\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 an ocean mixed layer and thermodynamics |
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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{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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thermodynamics seaice ({\it pkg/thsice}) and land packages. |
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on cubed-sphere cs32 in a realistics 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 ridid-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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\item \texttt{exp5} - Deep convection. |
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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 an additional set-up with Mixed-Layer Eddy parameterization |
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(Ferrari \& McWilliams, 2007) ({\it input.mxl/}). |
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\item \texttt{global1x1\_tot} - ECCO-GODAE production configuration |
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version 1, 2 \& 3 |
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\item \texttt{global2x2\_tot} - ECCO production configuration version 0 |
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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, with |
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quasi-non-hydrostatics and non-hydrostatic metric terms.\\ |
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Also contains an adjoint set-up ({\it code\_ad/, input\_ad/}). |
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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 set-ups: |
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\begin{enumerate} |
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\item non-hydrostratic 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}) dynamics ({\it pkg/seaice}) sea-ice |
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and EXF package ({\it input.icedyn/}) |
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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 exf package. Similar to global\_ocean.90x40x15 |
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experiment. |
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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 an adjoint set-up ({\it code\_ad/, input\_ad/}). |
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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. 5 vertical levels.\\ |
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Also contains an additional set-up with Implicit Internal gravity waves |
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treatment ({\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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\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 an additional set-up with ({\it input.htd/}) |
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but only Martin knows what "htd" stands for. |
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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 LSR solver (instead of EVP dynamics) ({\it input.lsr/}) |
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\item using Hibler and Bryan (1987) 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 equillibrium. |
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\item \texttt{MLAdjust} - Simple tests for different viscosity formulations.\\ |
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Also contains additional set-ups: |
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\begin{enumerate} |
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\item ({\it input.0.leith/}) |
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\item ({\it input.0.leithD/}) |
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\item ({\it input.0.smag/}) |
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\item ({\it input.1.leith/}) |
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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{natl\_box\_adjoint} - Eastern subtropical North Atlantic with KPP |
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scheme; adjoint set-up. |
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\item \texttt{offline\_exf\_seaice} - oceanic surface forcing computed |
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by bulk-formulae ({\it pkg/exf}) and inposed SST (offline ocean).\\ |
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Also contains additional set-ups: |
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\begin{enumerate} |
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\item with sea-ice ({\it pkg/seaice}) thermodynamics ({\it input.seaicetd/}) |
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\item an adjoint test ({\it code\_ad/, input\_ad/}). |
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\end{enumerate} |
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\item \texttt{OpenAD} simple Adjoint experiement (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{sect:eg-tank}. |
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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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\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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\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.\\ |
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Also contains additional set-ups: |
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\begin{enumerate} |
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\item with Gaspar et al. (1990) ({\it pkg/ggl90}) scheme ({\it input.ggl90/}) |
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\item with Mellor \& Yamada (1982) level 2. ({\it pkg/my82}) scheme ({\it input.my82/}) |
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\item with Paluszkiewicz \& Romea (1997) ({\it pkg/opps}) scheme ({\it input.opps/}) |
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\item with Pacanowski \& Philander (1981) ({\it pkg/pp81}) scheme ({\it input.pp81/}) |
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\end{enumerate} |
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\end{enumerate} |
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\subsection{Directory structure of model examples} |
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Each example directory has the following subdirectories: |
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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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\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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\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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\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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\item \texttt{code/SIZE.h}: declares size of underlying |
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computational grid. The default version is located in |
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\texttt{model/inc}. |
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\end{itemize} |
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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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\item \texttt{input}: contains the input data files required to run |
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the example. At a minimum, the \texttt{input} directory contains the |
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following files: |
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\begin{itemize} |
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\item \texttt{input/data}: this file, written as a namelist, |
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specifies the main parameters for the experiment. |
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\item \texttt{input/data.pkg}: contains parameters relative to the |
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packages used in the experiment. |
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\item \texttt{input/eedata}: this file contains ``execution |
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environment'' data. At present, this consists of a specification |
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of the number of threads to use in $X$ and $Y$ under multithreaded |
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execution. |
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\end{itemize} |
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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 |
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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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\item \texttt{results}: this directory contains the output file |
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\texttt{output.txt} produced by the simulation example. This file is |
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useful for comparison with your own output when you run the |
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experiment. |
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\item \texttt{build}: this directory is where the model is compiled |
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and loaded, and where the executable resides. |
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\end{itemize} |
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Once you have chosen the example you want to run, you are ready to |
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compile the code. |
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\newpage |
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\input{part3/case_studies/carbon_outgassing_sensitivity/co2sens.tex} |
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