--- manual/s_examples/text/model_examples.tex 2013/03/26 13:21:28 1.25 +++ manual/s_examples/text/model_examples.tex 2014/08/29 17:08:21 1.26 @@ -1,4 +1,4 @@ -% $Header: /home/ubuntu/mnt/e9_copy/manual/s_examples/text/model_examples.tex,v 1.25 2013/03/26 13:21:28 jmc Exp $ +% $Header: /home/ubuntu/mnt/e9_copy/manual/s_examples/text/model_examples.tex,v 1.26 2014/08/29 17:08:21 jmc Exp $ % $Name: $ \section[MITgcm Example Experiments]{Example experiments} @@ -41,10 +41,14 @@ 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 @@ -76,7 +80,11 @@ \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). @@ -86,18 +94,20 @@ resolution).\\ Also contains a non-linear free-surface adjustment version ({\it input.nlfs/}). -\item \texttt{advect\_cs} Two-dimensional passive advection test on - cube sphere grid (32x32 grid points per face, roughly $2.8^\circ$) +\item \texttt{advect\_cs} - Two-dimensional passive advection test on + 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} - - 5-levels Intermediate Atmospheric physics, +\item \texttt{aim.5l\_Equatorial\_Channel} - + 5-levels Intermediate Atmospheric physics, 3D Equatorial Channel configuration. \item \texttt{aim.5l\_LatLon} - 5-levels Intermediate Atmospheric physics, @@ -107,7 +117,7 @@ \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 @@ -116,11 +126,14 @@ \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. - on cubed-sphere cs32 in a realistics configuration. + thermodynamic seaice ({\it pkg/thsice}) and land packages. + 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}). @@ -133,12 +146,11 @@ \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. - -\item \texttt{exp5} - Deep convection. + channel with open boundaries.\\ + Also contains an additional set-up using non-linear free-surface ({\it input.nlfs/}). \item \texttt{fizhi-cs-32x32x40} - Global atmospheric simulation with realistic topography, 40 vertical levels, a cubed sphere grid and @@ -156,28 +168,49 @@ \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).\\ - Also contains an additional set-up with Mixed-Layer Eddy parameterization - (Ferrari \& McWilliams, 2007) ({\it input.mxl/}). - -\item \texttt{global1x1\_tot} - ECCO-GODAE production configuration - version 1, 2 \& 3 - -\item \texttt{global2x2\_tot} - ECCO production configuration version 0 - -\item \texttt{global\_ocean.90x40x15} Global ocean simulation at 4x4 - degree resolution. Similar to tutorial\_global\_oce\_latlon, with - quasi-non-hydrostatics and non-hydrostatic metric terms.\\ - Also contains an adjoint set-up ({\it code\_ad/, input\_ad/}). + (test for Gent/McWilliams scheme). 2D (y-z).\\ + Also contains additional set-ups: + \begin{enumerate} + \item using the Boundary-Value Problem method + (Ferrari et al., 2010) ({\it input.bvp/}). + \item with Mixed-Layer Eddy parameterization + (Ferrari \& McWilliams, 2007) ({\it input.mxl/}). + \end{enumerate} + +\item \texttt{global\_ocean.90x40x15} - Global ocean simulation at 4x4 + degree resolution. Similar to tutorial\_global\_oce\_latlon, but using + $z^*$ coordinates with quasi-non-hydrostatic and non-hydrostatic metric terms. + 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 - and EXF package ({\it input.icedyn/}) + \item using thermodynamic ({\it pkg/thsice}) dynamic ({\it pkg/seaice}) sea-ice + 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 @@ -186,93 +219,137 @@ 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 - experiment. + grid using the {\it exf} package. Similar to tutorial\_global\_oce\_latlon + 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/}) - but only Martin knows what "htd" stands for. + Also contains additional set-ups: + \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 Hibler and Bryan (1987) sea-ice ocean stress ({\it input.hb87/}) + \item using the simple "free-drift" assumption for seaice ({\it input.fd/}) + \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.0.leithD/}) - \item ({\it input.0.smag/}) - \item ({\it input.1.leith/}) + \item ({\it input.A4FlxF/}) + \item ({\it input.AhFlxF/}) + \item ({\it input.AhVrDv/}) + \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 - scheme; adjoint set-up. +\item \texttt{obcs\_ctrl} - Adjoint test using Open-Boundary conditions + as control parameters. -\item \texttt{offline\_exf\_seaice} - oceanic surface forcing computed - by bulk-formulae ({\it pkg/exf}) and inposed SST (offline ocean).\\ +\item \texttt{offline\_exf\_seaice} - Seaice on top of oceanic surface layer + 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 an adjoint test ({\it code\_ad/, input\_ad/}). + \item sea-ice dynamics-only using JFNK solver + 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 - open-AD compiler) +\item \texttt{OpenAD} - Simple Adjoint experiment (used also to test + 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/}) @@ -329,7 +406,7 @@ \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}