darwin3 darwin:​doc/​examples/​examples.rst	Source navigation Diff markup Identifier search General search
	Version: darwin virus sigma sal Revert   Change

Warning, /doc/examples/examples.rst is written in an unsupported language. File is not indexed.

9bc4d8814d Jeff* .. _chap_modelExamples:
                 
                 MITgcm Tutorial Example Experiments
                 ***********************************
                 
                 The full MITgcm distribution comes with a set of pre-configured
                 numerical experiments.  Some of these example experiments are tests of
                 individual parts of the model code, but many are fully fledged
                 numerical simulations. Full tutorials exist for a few of the examples,
                 and are documented in sections :numref:`sec_eg_baro` -
                 :numref:`sec_eg_tank`. The other examples follow the same general
1c8cebb321 Jeff* structure as the tutorial examples, see below.  All example experiments are
9bc4d8814d Jeff* located in subdirectories under the directory :filelink:`verification`.
1c8cebb321 Jeff* A list of additional experiments (i.e, not documented as full tutorials), with brief description,
                 is provided in :numref:`subsec_add_expts_fwd` and :numref:`subsec_add_expts_adj`.
                 
                 Each example experiment directory has the following subdirectories:
                 
                 -  ``code``: contains code specific to the example. At a minimum,
                    this directory includes the following files:
                 
                    -  ``code/packages.conf``: declares the list of packages or package
                       groups to be used. If not included, the default set of packages is located
                       in :filelink:`pkg/pkg_groups`. Package groups are simply convenient
                       collections of commonly used packages which are defined in
                       :filelink:`pkg/pkg_groups` (see :ref:`using_packages`).
                       Some packages may require other packages or
                       may require their absence (that is, they are incompatible) and
                       these package dependencies are listed in :filelink:`pkg/pkg_depend`.
                 
                    -  ``code/SIZE.h``: declares the size of underlying computational grid.
                       This file is compiled instead of the MITgcm repository version :filelink:`model/inc/SIZE.h`.
                 
                    -  The ``code/`` directory may include other files and subroutines specific to the experiment,
                       i.e., containing changes from the standard repository version.
                       For example, some experiments contains CPP header options files to enable or disable
                       some parts of the code at compile time; the most common ones would be :filelink:`model/inc/CPP_OPTIONS.h`
                       for core model options  and «PKG»_OPTIONS.h for individual packages.
                 
                 -  ``input``: contains the input data files required to run the example.
                    At a minimum, the ``input`` directory contains the following files:
                 
                    -  ``input/data``: this file, written as a namelist, specifies the
                       main parameters for the experiment.
                 
                    -  ``input/data.pkg``: contains parameters relative to the packages
                       used in the experiment.
                 
                
** Warning **
Wide character in print at /usr/local/share/lxr/source line 1030, <$git> line 50.


    -  ``input/eedata``: this file contains “execution environment” data.
                       This consists of a specification of the number of
                       threads to use in :math:`x` and :math:`y`. For multi-threaded execution,these will be set to numbers greater than 1.
                 
                    - Forcing and topography file(s), as well as files describing the initial state of
                      the experiment and any other supporting data.
                      Required support files vary from experiment to experiment, depending on the setup.
                 
                 -  ``results``: this directory contains the output file ``output.txt``
                    produced by the simulation example. This file is useful for
                    comparison with your own output when you run the experiment.
                 
                 -  ``build``: this directory is initially empty and should be used to compile
                    the model and generate the executable.
                 
                 -  ``run``: this directory is initially empty and should be used to run the
                    executable. From the (empty) run directory, link files from ``input``
                    using the command ``ln -s ../input/* .``, then execute the file ``../input/prepare_run`` if it exists.
                    If you are running one of the experiment variations, i.e., using ``input.«OTHER»``,
                    first link files from ``input.«OTHER»`` (running ``../input.«OTHER»/prepare_run`` if it exists) and next link files from ``input``
                    (and run ``../input/prepare_run``). Following this procedure, file links
                    from ``input.«OTHER»`` will NOT be overwritten by identically named files in ``input``.
                 
                 .. raw:: html
                 
                    <h2> The tutorial experiments are as follows:</h2>
9bc4d8814d Jeff* 
                 .. toctree::
                    :maxdepth: 1
                 
94151a9b18 Jeff*    barotropic_gyre/barotropic_gyre.rst
1c8cebb321 Jeff* 
                 .. only:: html
                 
                    In directory :filelink:`tutorial_barotropic_gyre <verification/tutorial_barotropic_gyre>`:
                    Single layer ocean gyre (barotropic with free-surface), using a Cartesian grid. If you are new to MITgcm, start here,
                    as no prior experience with MITgcm is assumed. Introduces building and running the model, with description of model output files and
                    simple methods to load and plot model output.
                 
                 .. toctree::
                    :maxdepth: 1
                 
94151a9b18 Jeff*    baroclinic_gyre/baroclinic_gyre.rst
1c8cebb321 Jeff* 
                 .. only:: html
                 
                    In directory :filelink:`tutorial_baroclinic_gyre <verification/tutorial_baroclinic_gyre>`:
                    Ocean double-gyre using spherical coordinates (i.e., latitude-longitude coordinates) with 15 vertical layers. Second introductory tutorial, assumes you have read through
                    :ref:`sec_eg_baro`. Introduces using `NetCDF <http://www.unidata.ucar.edu/software/netcdf>`_  for model output,
                    and how to use the :ref:`diagnostics package <sub_outp_pkg_diagnostics>` to customize output and its writing frequency.
                 
b66ba975e0 Jeff* .. toctree::
                    :maxdepth: 1
                 
9c8516d9da Jeff*    reentrant_channel/reentrant_channel.rst
b66ba975e0 Jeff* 
                 .. only:: html
                 
                    In directory :filelink:`tutorial_reentrant channel <verification/tutorial_reentrant_channel>`:
fb5a9c2b45 Jeff*    Reentrant channel in the Southern Ocean with idealized topography, 49 vertical layers. Tutorial compares solution using coarse horizontal resolution,
                    with and without GM parameterization (:filelink:`pkg/gmredi`),
                    versus a high-resolution, eddy-permitting configuration. Third and final introductory tutorial,
                    assumes reader is familiar with MITgcm basics described in tutorials :ref:`sec_eg_baro` and :ref:`tutorial_baroclinic_gyre`.
                    Also introduces :filelink:`pkg/layers` and :filelink:`pkg/rbcs`.
b66ba975e0 Jeff* 
1c8cebb321 Jeff* .. toctree::
                    :maxdepth: 1
                 
d67096e55c Jeff*    advection_in_gyre/advection_in_gyre.rst
1c8cebb321 Jeff* 
                 .. only:: html
                 
                    In directory :filelink:`tutorial_advection_in_gyre <verification/tutorial_advection_in_gyre>`:
                    Short tutorial comparing the results using different advection schemes in a single-layer, ocean double-gyre.
                    Demonstrates the importance of carefully selecting an advection scheme for a specific setup.
                 
                 .. toctree::
                    :maxdepth: 1
                 
d67096e55c Jeff*    global_oce_latlon/global_oce_latlon.rst
1c8cebb321 Jeff* 
                 .. only:: html
                 
                    In directory :filelink:`tutorial_global_oce_latlon <verification/tutorial_global_oce_latlon>`:
                    Coarse resolution (4\ :sup:`o`\ x4\ :sup:`o`) global ocean simulation, using a spherical ocean grid with 15 vertical layers.
                    Monthly climatological forcing of of wind stress, heat and freshwater fluxes is employed, with surface restoring
                    of temperature and salinity. Simulates the large-scale ocean circulation.
                 
                 .. toctree::
                    :maxdepth: 1
                 
d67096e55c Jeff*    global_oce_in_p/global_oce_in_p.rst
1c8cebb321 Jeff* 
                 .. only:: html
                 
                    In directory :filelink:`tutorial_global_oce_in_p <verification/tutorial_global_oce_in_p>`:
                    Global ocean simulation with a similar configuration as :ref:`sec_global_oce_latlon` except pressure is used as the vertical coordinate
                
** Warning **
Wide character in print at /usr/local/share/lxr/source line 1030, <$git> line 147.


    instead of the traditional height coordinate (exploiting MITgcm's height–pressure coordinate coding isomorphism).
                    In this configuration the model does **NOT** make the  Boussinesq approximation.
                 
                 .. toctree::
                    :maxdepth: 1
                 
d67096e55c Jeff*    held_suarez_cs/held_suarez_cs.rst
1c8cebb321 Jeff* 
                 .. only:: html
                 
                    In directory :filelink:`tutorial_held_suarez_cs <verification/tutorial_held_suarez_cs>`:
                    Simulates (dry) 3-D atmosphere dynamics using Held and Suarez forcing on a (global) cubed sphere grid. The vertical coordinate
                    is a rescaled pressure coordinate (:math:`p^*`) with 20 levels; orography is flat. Radiation effects are represented by Newtonian cooling.
                 
                 .. toctree::
                    :maxdepth: 1
                 
d67096e55c Jeff*    deep_convection/deep_convection.rst
1c8cebb321 Jeff* 
                 .. only:: html
                 
                    In directory :filelink:`tutorial_deep_convection <verification/tutorial_deep_convection>`:
                    Non-uniformly surface-forced ocean deep convection in a doubly periodic box. This tutorial showcases MITgcm's non-hydrostatic
                    capability in a spatially small domain (3 km x 3 km x 1 km deep), exploring the temporal and spatial characteristics of convection
                    plumes as they might exist during a period of oceanic deep convection.
                 
                 .. toctree::
                    :maxdepth: 1
                 
d67096e55c Jeff*    plume_on_slope/plume_on_slope.rst
1c8cebb321 Jeff* 
                 .. only:: html
                 
                    In directory :filelink:`tutorial_plume_on_slope <verification/tutorial_plume_on_slope>`:
                    Non-hydrostatic simulation of a non-rotating gravity plume descending down a continental slope, forced by surface cooling. Model domain is 2-D with
                    open boundaries conditions used in a the deep-water end of the domain.
                 
                 .. toctree::
                    :maxdepth: 1
                 
d67096e55c Jeff*    global_oce_biogeo/global_oce_biogeo.rst
1c8cebb321 Jeff* 
                 .. only:: html
                 
                    In directory :filelink:`tutorial_global_oce_biogeo <verification/tutorial_global_oce_biogeo>`:
                    Global ocean simulation (similar to tutorial :ref:`sec_global_oce_latlon` except using 2.8\ :sup:`o`\ x2.8\ :sup:`o` resolution) which includes
                    a dissolved inorganic carbon biogeochemistry model. The biogeochemical model considers the coupled cycles of carbon, oxygen, phosphorus and alkalinity, which are
                    included as passive tracers. A simplified parameterization of biological production is also included.
                 
                 .. toctree::
                    :maxdepth: 1
                 
d67096e55c Jeff*    global_oce_optim/global_oce_optim.rst
1c8cebb321 Jeff* 
                 .. only:: html
                 
                    In directory :filelink:`tutorial_global_oce_optim <verification/tutorial_global_oce_optim>`:
                    This tutorial illustrates the optimization capacity of the MITgcm,
                    running the adjoint of a global ocean simulation (model setup similar to :ref:`sec_global_oce_latlon`).
                    This adjoint run optimizes a time-independent surface heat flux (i.e., the control variable) which brings
                    the model climatology closest to observed climatology, using a cost function
                    based on gridpoint error in temperature. TAF and OpenAD adjoint setups.
                 
                 .. toctree::
                    :maxdepth: 1
                 
d67096e55c Jeff*    tracer_adjsens/tracer_adjsens.rst
1c8cebb321 Jeff* 
                 .. only:: html
                 
                    In directory :filelink:`tutorial_tracer_adjsens <verification/tutorial_tracer_adjsens>`:
                    A second experiment demonstrating MITgcm's adjoint capabilities, here examining the sensitivity of surface outgassing of a passive tracer
                    as a function of tracer injection site location within the ocean interior. The global (4\ :sup:`o`\ x4\ :sup:`o`)
                    ocean setup from tutorial :ref:`sec_global_oce_latlon`
                    is again used for this tutorial. TAF and OpenAD adjoint setups.
                 
                 .. toctree::
                    :maxdepth: 1
                 
d67096e55c Jeff*    cfc_offline/cfc_offline.rst
1c8cebb321 Jeff* 
                 .. only:: html
                 
                    In directory :filelink:`tutorial_cfc_offline <verification/tutorial_cfc_offline>`:
                    This tutorial contains an experiment which uses MITgcm in offline mode (i.e., with prescribed ocean dynamics terms,
                    from a prior forward integration of MITgcm), simulating
                    the penetration of CFCs into the ocean interior during the last century. The model domain is global with 2.8\ :sup:`o`\ x2.8\ :sup:`o` resolution.
                 
                 .. toctree::
                    :maxdepth: 1
                 
9bc4d8814d Jeff*    rotating_tank/rotating_tank.rst
1c8cebb321 Jeff* 
                 .. only:: html
                 
d0f2385f28 Jean*    In directory :filelink:`tutorial_rotating_tank <verification/tutorial_rotating_tank>`:
1c8cebb321 Jeff*    Laboratory rotating tank simulation,
                    using a cylindrical coordinate system at laboratory scale of 46 cm diameter and 14.5 cm deep.
                    This is a typical laboratory setup for illustrating principles of geophysical fluid mechanics. An annulus of fluid is heated differentially
                    on the interior and exterior walls of the tank.
                 
                 .. _subsec_add_expts_fwd:
                 
                 Additional Example Experiments: Forward Model Setups
                 ====================================================
                 
                 For many experiments, additional information is provided in a ``README`` file located in the respective experiment's subdirectory.
                 
                 #. :filelink:`1D_ocean_ice_column <verification/1D_ocean_ice_column>` - Oceanic column with seaice on top.
                 
                 #. :filelink:`adjustment.128x64x1 <verification/adjustment.128x64x1>` - Barotropic adjustment problem on latitude-longitude
                    grid with 128x64 grid points (2.8\ :sup:`o` resolution).
                 
09461bf9e9 Jean* #. :filelink:`adjustment.cs-32x32x1 <verification/adjustment.cs-32x32x1>` -
                    Barotropic adjustment problem on cube sphere grid with 32x32 points per face
                    (roughly 2.8\ :sup:`o` resolution) with a rectangular island at the equator.
                    Note that "blank tiles" are used in the MPI test
                    (:filelink:`data.exch2.mpi <verification/adjustment.cs-32x32x1/input/data.exch2.mpi>`).
                    Also contains a non-linear free-surface, atmospheric like, barotropic
                    adjustment version (:filelink:`input.nlfs <verification/adjustment.cs-32x32x1/input.nlfs>`).
1c8cebb321 Jeff* 
                 #. :filelink:`advect_cs <verification/advect_cs>` - 2-D passive advection test on cube sphere
                    grid (32x32 grid points per face, roughly 2.8\ :sup:`o` resolution).
                 
                 #. :filelink:`advect_xy <verification/advect_xy>` - 2-D (horizontal plane) passive
                    advection test on Cartesian grid. Also contains an additional setup using Adams-Bashforth 3
                    (:filelink:`input.ab3_c4 <verification/advect_xy/input.ab3_c4>`).
                 
                 #. :filelink:`advect_xz <verification/advect_xz>` - 2-D (vertical plane) passive advection
                    test on Cartesian grid. Also contains an additional setup using non-linear free-surface
                    with divergent barotropic flow and implicit vertical advection (:filelink:`input.nlfs <verification/advect_xz/input.nlfs>`),
                    and a setup using piecewise quartic ("mono" and "weno" limiter)
                    advection schemes (:filelink:`input.pqm <verification/advect_xz/input.pqm>`).
                 
9af873c532 Hajo* #. :filelink:`aim.5l_cs <verification/aim.5l_cs>` - 5-level intermediate atmospheric physics, global
                    configuration on cube sphere grid (32x32 grid points per face,
                    roughly 2.8\ :sup:`o` resolution).
                    Also contains an additional setup with a slab-ocean and
                    thermodynamic sea ice (:filelink:`input.thSI <verification/aim.5l_cs/input.thSI>`).
                 
1c8cebb321 Jeff* #. :filelink:`aim.5l_Equatorial_Channel <verification/aim.5l_Equatorial_Channel>` - 5-level intermediate atmospheric
                    physics, 3-D equatorial channel configuration.
                 
                 #. :filelink:`aim.5l_LatLon <verification/aim.5l_LatLon>` - 5-level intermediate atmospheric physics, global
                    configuration, on latitude-longitude grid with 128x64x5 grid points
                    (2.8\ :sup:`o` resolution).
                 
7fe51dd492 Jean* #. :filelink:`atm_gray <verification/atm_gray>` - gray atmospheric physics configuration using
                    :filelink:`atm_phys <pkg/atm_phys>` package, on cube sphere grid (32x32 grid points per face)
                    with 26 pressure levels. This aquaplanet-like experiment has interactive SST with a prescribed,
                    time-invariant Q-flux.
                    Also contains a secondary setup (:filelink:`input.ape <verification/atm_gray/input.ape>`)
                    with prescribed idealized SST from Aqua-Planet Experiment
                    (APE) project (Neale and Hoskins, 2001 :cite:`neale:01`).
                 
1c8cebb321 Jeff* #. :filelink:`cfc_example <verification/cfc_example>` - Global ocean with online computation and advection
                    of CFC11 and CFC12.
                 
                 #. :filelink:`cheapAML_box <verification/cheapAML_box>` - Example using cheap atmospheric mixed layer
                    (:filelink:`cheapaml <pkg/cheapaml>`) package.
                 
                 #. :filelink:`cpl_aim+ocn <verification/cpl_aim+ocn>` - Coupled ocean-atmosphere realistic configuration
                    on cubed-sphere cs32 horizontal grid, using intermediate atmospheric
                    physics (:filelink:`pkg/aim_v23`) thermodynamic seaice (:filelink:`pkg/thsice`) and land
                    packages.
09461bf9e9 Jean*    Also contains an additional setup with seaice dynamics
838c406049 Jeff*    (:filelink:`input_cpl.icedyn  <verification/cpl_aim+ocn/input_cpl.icedyn>`,
                    :filelink:`input_atm.icedyn  <verification/cpl_aim+ocn/input_atm.icedyn>`,
                    :filelink:`input_ocn.icedyn  <verification/cpl_aim+ocn/input_ocn.icedyn>`).
1c8cebb321 Jeff* 
7fe51dd492 Jean* #. :filelink:`deep_anelastic <verification/deep_anelastic>` - Convection simulation on a giant
                    planet: relaxes both the Boussinesq approximation (anelastic) and the thin atmosphere
f1b47febb7 Jean*    approximation (deep atmosphere). Also contains an additional setup using vector-invariant
                    momentum (:filelink:`input.vecinv <verification/deep_anelastic/input.vecinv>`).
1c8cebb321 Jeff* 
838c406049 Jeff* #. :filelink:`dome <verification/dome>` - Idealized 3-D test of a density-driven bottom current
                    (Denmark Overflow Mixing and Entrainment experiment).
1c8cebb321 Jeff* 
                 #. :filelink:`exp2 <verification/exp2>` - Old version of the global ocean experiment (no GM, no
                    partial-cells). Also contains an additional setup with rigid lid
                    (:filelink:`input.rigidLid <verification/exp2/input.rigidLid>`).
                 
7fe51dd492 Jean* #. :filelink:`exp4 <verification/exp4>` - Flow over a Gaussian bump in open-water or channel
                    with open boundaries. Also contains additional setups:
                 
                    - using non-linear free-surface (:filelink:`input.nlfs <verification/exp4/input.nlfs>`).
                 
                    - using Stevens (1990) :cite:`stevens:90` boundary conditions
                      (:filelink:`input.stevens <verification/exp4/input.stevens>`).
                 
                    - a simple example using float (:filelink:`flt <pkg/flt>`) package
                      (:filelink:`input.with_flt <verification/exp4/input.with_flt>`,
                      formerly :filelink:`flt_example <verification/flt_example>`).
1c8cebb321 Jeff* 
                 #. :filelink:`fizhi-cs-32x32x40 <verification/fizhi-cs-32x32x40>` - Global atmospheric simulation with realistic
                    topography, 40 vertical levels, a cubed sphere grid and the full atmospheric physics package.
                 
                 #. :filelink:`fizhi-cs-aqualev20 <verification/fizhi-cs-aqualev20>` - Global atmospheric simulation on an aqua
                    planet with full atmospheric physics. Run is perpetual March with an
7fe51dd492 Jean*    analytical SST distribution. This is the configuration used for the
                    `Aqua-Planet Experiment Project (APE) <http://www.met.reading.ac.uk/~mike/ape/>`_ ,
                    see also Neale and Hoskins (2001) :cite:`neale:01`.
1c8cebb321 Jeff* 
                 #. :filelink:`fizhi-gridalt-hs <verification/fizhi-gridalt-hs>` - Global atmospheric simulation Held-Suarez
                    (1994) :cite:`held-suar:94` forcing, with the physical forcing and the dynamical forcing
                    running on different vertical grids.
                 
                 #. :filelink:`front_relax <verification/front_relax>` - Relaxation of an 2-D (:math:`y-z`) ocean thermal front (test of
                    Gent and McWilliams scheme). Also contains additional setups:
                 
838c406049 Jeff*    - using the identical setup except with pressure as the vertical coordinate instead of height
                      (:filelink:`input.in_p <verification/front_relax/input.in_p>`)
                 
1c8cebb321 Jeff*    - using the boundary-value problem method (Ferrari et al. 2010 :cite:`ferrari:10`)
838c406049 Jeff*      (:filelink:`input.bvp <verification/front_relax/input.bvp>`)
1c8cebb321 Jeff* 
                    - with mixed-layer eddy parameterization (Ferrari and McWilliams
838c406049 Jeff*      2008 :cite:`ferrari:08`) (:filelink:`input.mxl <verification/front_relax/input.mxl>`)
1c8cebb321 Jeff* 
09461bf9e9 Jean*    - with dry-cell at the top and a sloping bottom
                      (:filelink:`input.top <verification/front_relax/input.top>`).
                 
                 #. :filelink:`global_ocean.90x40x15 <verification/global_ocean.90x40x15>` -
                    Global ocean simulation at 4\ :sup:`o`\ x4\ :sup:`o` resolution.
                    Similar to :ref:`tutorial_global_oce_latlon <sec_global_oce_latlon>`, but
                    using :math:`z^*` coordinates with quasi-non-hydrostatic and non-hydrostatic metric
                    terms. This experiment illustrates the use of :filelink:`sbo </pkg/sbo>` package.
                    Note that "blank tiles" are used in the MPI test (:filelink:`data.exch2.mpi <verification/global_ocean.90x40x15/input/data.exch2.mpi>`).
                    Also contains additional setups:
1c8cebb321 Jeff* 
                    - using :filelink:`down-slope package <pkg/down_slope>` (:filelink:`input.dwnslp <verification/global_ocean.90x40x15/input.dwnslp>`)
                 
                    - using package :filelink:`ggl90 <pkg/ggl90>` scheme (Gaspar et al. 1990 :cite:`gas-eta:90`) with parameterized tidal and wind
                      energy input into vertical mixing (:filelink:`input.idemix <verification/global_ocean.90x40x15/input.idemix>`).
                 
                 #. :filelink:`global_ocean.cs32x15 <verification/global_ocean.cs32x15>` - Global ocean experiment on the cubed
                    sphere grid. Also contains additional setups:
                 
                    - non-hydrostatic with biharmonic viscosity (:filelink:`input.viscA4 <verification/global_ocean.cs32x15/input.viscA4>`)
                 
                    - using thermodynamic sea ice and bulk force (:filelink:`input.thsice <verification/global_ocean.cs32x15/input.thsice>`)
                 
                    - using both thermodynamic (:filelink:`pkg/thsice`) and dynamic (:filelink:`pkg/seaice`) sea ice packages
                      with :filelink:`exf <pkg/exf>` package (:filelink:`input.icedyn <verification/global_ocean.cs32x15/input.icedyn>`)
                 
                    - using thermodynamic and dynamic (:filelink:`pkg/seaice`) sea ice with :filelink:`exf <pkg/exf>` package
                      package (:filelink:`input.seaice <verification/global_ocean.cs32x15/input.seaice>`).
                 
838c406049 Jeff*    - using pressure as vertical coordinate, with :filelink:`ggl90 <pkg/ggl90>` scheme (Gaspar et al. 1990 :cite:`gas-eta:90`)
                      and dynamic and thermodynamic seaice (:filelink:`pkg/seaice`) package and :filelink:`exf <pkg/exf>`
                      package (:filelink:`input.in_p <verification/global_ocean.cs32x15/input.in_p>`)
09461bf9e9 Jean* 
f1b47febb7 Jean* #. :filelink:`global_oce_biogeo_bling  <verification/global_oce_biogeo_bling >` - Global ocean biogeochemistry simulation,
                    based on :ref:`sub_global_oce_biogeo` but using package :filelink:`bling <pkg/bling>` instead of the :ref:`DIC <sub_pkg_dic>` package.
7fe51dd492 Jean* 
f1b47febb7 Jean* #. :filelink:`global_oce_latlon <verification/global_oce_latlon>` - Global ocean experiment
                    on a lat-lon grid, similar to :ref:`tutorial_global_oce_latlon <sec_global_oce_latlon>`
                    experiment but using the surface forcing pkg :filelink:`exf <pkg/exf>` package
                    with :filelink:`exf <pkg/exf>` interpolation (formerly
                    :filelink:`global_with_exf <verification/global_with_exf>`). Also contains additional setups:
7fe51dd492 Jean* 
                    - same as above with yearly :filelink:`exf <pkg/exf>` fields
f1b47febb7 Jean*      (:filelink:`input.yearly <verification/global_oce_latlon/input.yearly>`,
7fe51dd492 Jean*      formerly in :filelink:`global_with_exf <verification/global_with_exf>`).
                 
f1b47febb7 Jean*    - using surface forcing from a zonally averaged atmospheric energy balance model
                      with :filelink:`ebm <pkg/ebm>` package
                      (:filelink:`input.ebm <verification/global_oce_latlon/input.ebm>`,
                      formerly in :filelink:`global_ocean_ebm <verification/global_ocean_ebm>`).
1c8cebb321 Jeff* 
                 #. :filelink:`halfpipe_streamice<verification/halfpipe_streamice>` - Example using package :filelink:`streamice <pkg/streamice>`.
                 
                 #. :filelink:`hs94.128x64x5 <verification/hs94.128x64x5>` - 3-D atmosphere dynamics on lat-lon grid, using
                    Held and Suarez (1994) :cite:`held-suar:94` forcing.
                 
                 #. :filelink:`hs94.1x64x5 <verification/hs94.1x64x5>` - Zonal averaged atmosphere dynamics using Held and
                    Suarez (1994) :cite:`held-suar:94` forcing.
                 
                 #. :filelink:`hs94.cs-32x32x5 <verification/hs94.cs-32x32x5>` - 3-D atmosphere dynamics using Held and Suarez
                    (1994) :cite:`held-suar:94` forcing on the cubed sphere, similar to
                    :ref:`tutorial_held_suarez_cs <sec_held_suarez_cs>` experiment but using linear free-surface
                    and only 5 levels. Also contains an additional setup with implicit internal gravity
                    waves treatment and Adams-Bashforth 3 (:filelink:`input.impIGW <verification/hs94.cs-32x32x5/input.impIGW>`).
                 
                 #. :filelink:`ideal_2D_oce <verification/ideal_2D_oce>` - Idealized 2-D global ocean simulation on an aqua
                    planet.
                 
                 #. :filelink:`internal_wave <verification/internal_wave>` - Ocean internal wave forced by open boundary
                    conditions. Also contains an additional setup using :filelink:`pkg/kl10` (see :numref:`sub_phys_pkg_kl10`,
                    Klymak and Legg 2010 :cite:`klymaklegg10`) (:filelink:`input.kl10 <verification/internal_wave/input.kl10>`).
                 
                 #. :filelink:`inverted_barometer <verification/inverted_barometer>` - Simple test of atmospheric pressure loading with
                    radially symmetric Bessel-function geometry in a quadratic domain.
                 
                 #. :filelink:`isomip <verification/isomip>` - ISOMIP-like setup (Ice Shelf Ocean Model Intercomparison Project experiment 0)
                    including ice-shelf cavities (:filelink:`pkg/shelfice`). Also contains additional setups:
                 
                
** Warning **
Wide character in print at /usr/local/share/lxr/source line 1030, <$git> line 444.


    - with “htd” (Hellmer's thermodynamics, Hellmer 1989 :cite:`hellmer:89`) (:filelink:`input.htd <verification/isomip/input.htd>`).
                 
                    - using package :filelink:`icefront <pkg/icefront>` (:filelink:`input.icefront <verification/isomip/input.icefront>`)
                 
                    - using package :ref:`OBCS <sub_phys_pkg_obcs>` enabled to balance surface mass (freshwater and ice shelf mass flux)
                      input through open boundaries (:filelink:`input.obcs <verification/isomip/input.obcs>`).
                 
                 #. :filelink:`lab_sea <verification/lab_sea>` - Regional (2\ :sup:`o`\ x2\ :sup:`o`) Labrador Sea simulation on a lat-lon grid
                    using :filelink:`pkg/seaice`. Also contains additional setups:
                 
                
** Warning **
Wide character in print at /usr/local/share/lxr/source line 1030, <$git> line 454.


    - using the simple “free-drift” assumption for sea ice (:filelink:`input.fd <verification/lab_sea/input.fd>`)
                 
79ab3d1b9e Jean*    - using :ref:`aEVP dynamics <para_phys_pkg_seaice_EVPstar>` (instead of :ref:`LSR solver <para_phys_pkg_seaice_LSRJFNK>`)
c512e371cc drin*      and Hibler and Bryan (1987) :cite:`hibler:87` sea ice ocean stress (:filelink:`input.hb87 <verification/lab_sea/input.hb87>`)
1c8cebb321 Jeff* 
                    - using package :filelink:`salt_plume <pkg/salt_plume>` (:filelink:`input.salt_plume <verification/lab_sea/input.salt_plume>`).
                 
7fe51dd492 Jean*    - ice-free eastern subtropical North Atlantic box (:filelink:`input.natl_box <verification/lab_sea/input.natl_box>`,
                      formerly :filelink:`natl_box <verification/natl_box>`).
                 
                    - same as above with passive tracers (:filelink:`pkg/ptracers`) using package :filelink:`longstep <pkg/longstep>`
                      to speed up integration time (:filelink:`input.longstep <verification/lab_sea/input.longstep>`,
                      formerly in :filelink:`natl_box <verification/natl_box>`).
                 
1c8cebb321 Jeff* #. :filelink:`matrix_example <verification/matrix_example>` - Test of experimental method to accelerate
                    convergence towards equilibrium.
                 
                 #. :filelink:`MLAdjust <verification/MLAdjust>` - Simple tests of different viscosity formulations
                    in a zonally reentrant, flat-bottom channel. Contains additional setups; see
                    :filelink:`verification/MLAdjust/README` for a listing of different viscosity settings in these experiments:
                 
                    - :filelink:`input.A4FlxF <verification/MLAdjust/input.A4FlxF>`
                 
                    - :filelink:`input.AhFlxF <verification/MLAdjust/input.AhFlxF>`
                 
                    - :filelink:`input.AhVrDv <verification/MLAdjust/input.AhVrDv>`
                 
                    - :filelink:`input.AhStTn <verification/MLAdjust/input.AhStTn>`
                 
                    - :filelink:`input.QGLeith <verification/MLAdjust/input.QGLeith>`
                 
                    - :filelink:`input.QGLthGM <verification/MLAdjust/input.QGLthGM>`.
                 
                 #. :filelink:`offline_exf_seaice <verification/offline_exf_seaice>` - Sea ice on top of oceanic surface layer in
                    an idealized channel. Forcing is computed by bulk-formulae
                    (:filelink:`pkg/exf`) with temperature relaxation to prescribed SST (i.e., no momentum timestepping in ocean,
                    so ocean is "offline", not to be confused with :filelink:`pkg/offline`).
                    Also contains additional setups:
                 
09461bf9e9 Jean*    - sea ice dynamics-only using :ref:`JFNK solver <para_phys_pkg_seaice_LSRJFNK>`
                      and (:filelink:`pkg/thsice`) advection
1c8cebb321 Jeff*      (:filelink:`input.dyn_jfnk <verification/offline_exf_seaice/input.dyn_jfnk>`)
                 
09461bf9e9 Jean*    - sea ice dynamics-only using :ref:`LSR solver <para_phys_pkg_seaice_LSRJFNK>`
                      and (:filelink:`pkg/seaice`) advection
1c8cebb321 Jeff*      (:filelink:`input.dyn_lsr <verification/offline_exf_seaice/input.dyn_lsr>`)
                 
09461bf9e9 Jean*    - sea ice dynamics-only using :ref:`LSR solver <para_phys_pkg_seaice_LSRJFNK>`,
                      elliptical yield curve with :ref:`non-normal flow rule <rheologies_ellnnfr>`
                      and (:filelink:`pkg/seaice`) advection
838c406049 Jeff*      (:filelink:`input.dyn_ellnnfr <verification/offline_exf_seaice/input.dyn_ellnnfr>`
                      and :filelink:`input.dyn_lsr <verification/offline_exf_seaice/input.dyn_lsr>`)
09461bf9e9 Jean* 
                    - sea ice dynamics-only using :ref:`LSR solver <para_phys_pkg_seaice_LSRJFNK>`,
                      :ref:`Mohr-Coulomb yieldcurve with elliptical plastic potential <rheologies_MCE>`
                      and (:filelink:`pkg/seaice`) advection
838c406049 Jeff*      (:filelink:`input.dyn_mce <verification/offline_exf_seaice/input.dyn_mce>` and
                      :filelink:`input.dyn_lsr <verification/offline_exf_seaice/input.dyn_lsr>`)
09461bf9e9 Jean* 
                    - sea ice dynamics-only using :ref:`Picard (KRYLOV) solver <para_phys_pkg_seaice_LSRJFNK>`,
                      :ref:`parabolic lens yieldcurve <rheologies_PL>`
                      and (:filelink:`pkg/thsice`) advection
838c406049 Jeff*      (:filelink:`input.dyn_paralens <verification/offline_exf_seaice/input.dyn_paralens>`
                      and :filelink:`input.dyn_jfnk <verification/offline_exf_seaice/input.dyn_jfnk>`)
09461bf9e9 Jean* 
                    - sea ice dynamics-only using :ref:`JFNK solver <para_phys_pkg_seaice_LSRJFNK>`, :ref:`teardrop yieldcurve <rheologies_TD>`
                      and (:filelink:`pkg/thsice`) advection
838c406049 Jeff*      (:filelink:`input.dyn_teardrop <verification/offline_exf_seaice/input.dyn_teardrop>`
                      and :filelink:`input.dyn_jfnk <verification/offline_exf_seaice/input.dyn_jfnk>`)
09461bf9e9 Jean* 
1c8cebb321 Jeff*    - sea ice thermodynamics-only using (:filelink:`pkg/seaice`) (:filelink:`input.thermo <verification/offline_exf_seaice/input.thermo>`)
                 
                    - sea ice thermodynamics-only using (:filelink:`pkg/thsice`) (:filelink:`input.thsice <verification/offline_exf_seaice/input.thsice>`).
                 
                 #. :filelink:`seaice_itd <verification/seaice_itd>` - Seaice example using ice thickness distribution (ITD); otherwise
                    very similar to :filelink:`offline_exf_seaice <verification/offline_exf_seaice>`.
                    Also contains additional setups; see
                    :filelink:`verification/seaice_itd/README` for details of these setups:
                 
                    - :filelink:`input.thermo <verification/seaice_itd/input.thermo>`
                 
                    - :filelink:`input.lipscomb07 <verification/seaice_itd/input.lipscomb07>`.
                 
                 #. :filelink:`seaice_obcs <verification/seaice_obcs>` - Similar to :filelink:`lab_sea <verification/lab_sea>`
                    (:filelink:`input.salt_plume <verification/lab_sea/input.salt_plume>`)
                    experiment with only a fraction of the domain and open boundary
                    conditions derived from :filelink:`lab_sea <verification/lab_sea>` experiment.
                    Also contains additional setups:
                 
f1b47febb7 Jean*    - with Adaptative EVP method (:filelink:`input.regDenom <verification/seaice_obcs/input.regDenom>`)
                 
1c8cebb321 Jeff*    - includes relaxation of seaice variables (:filelink:`input.seaiceSponge <verification/seaice_obcs/input.seaiceSponge>`)
                 
                    - includes tidal velocity forcing (:filelink:`input.tides <verification/seaice_obcs/input.tides>`).
                 
                 #. :filelink:`shelfice_2d_remesh <verification/shelfice_2d_remesh>` - Simple experiment to test (:filelink:`pkg/shelfice`)
                    vertical remeshing code in 2-D idealized-geometry setup.
                 
                 #. :filelink:`short_surf_wave <verification/short_surf_wave>` - Short surface wave adjustment (non-hydrostatic)
                    in homogeneous 2-D vertical section (:math:`x-z`).
                 
                 #. :filelink:`so_box_biogeo <verification/so_box_biogeo>` - Open boundary Southern Ocean box around Drake
                    Passage, using same model parameters and forcing as experiment
                    :ref:`tutorial_global_oce_biogeo <sub_global_oce_biogeo>` from which initial conditions and open boundary
838c406049 Jeff*    conditions have been extracted. Also contains additional setups:
                 
                    - using the SolveSAPHE algorithm (Munhoven 2013 :cite:`munhoven:13`) to determine oceanic
                      pH (:filelink:`input.saphe <verification/so_box_biogeo/input.saphe>`)
                 
                    - using the calcite-saturation code (with 3-D pH and silica input file) with the original pH solver
                      (:filelink:`input.caSat0 <verification/so_box_biogeo/input.caSat0>`)
                 
                    - using the calcite-saturation code with the Munhoven "FAST" solver (:filelink:`input.caSat3 <verification/so_box_biogeo/input.caSat3>`)
1c8cebb321 Jeff* 
                 #. :filelink:`solid-body.cs-32x32x1 <verification/solid-body.cs-32x32x1>` - Solid body rotation test for cube sphere
                    grid.
                 
838c406049 Jeff* #. :filelink:`tutorial_deep_convection <verification/tutorial_deep_convection>` - Experiment as described
                    in :numref:`sec_deep_convection`, also contains an additional setup
                    using the Smagorinisky (1963) :cite:`smag:63` viscosity scheme
                    (:filelink:`input.smag3d <verification/tutorial_deep_convection/input.smag3d>`).
                 
                 #. :filelink:`tutorial_plume_on_slope <verification/tutorial_plume_on_slope>` - Experiment as described in
                    :numref:`tutorial_plume_on_slope`, also contains an additional setup
                    using the logarithmic law of the wall to compute the bottom drag coefficient
                    (:filelink:`input.roughBot <verification/tutorial_plume_on_slope/input.roughBot>`).
1c8cebb321 Jeff* 
                 #. :filelink:`vermix <verification/vermix>` - Simple test in a small domain (3 columns) for ocean
                    vertical mixing schemes. The standard setup (:filelink:`input <verification/vermix/input>`) uses the :ref:`KPP scheme <sub_phys_pkg_kpp>`
                    Large et al. (1994) :cite:`lar-eta:94`. Also contains additional setups:
                 
                    - with double diffusion scheme from :ref:`KPP <sub_phys_pkg_kpp>` (:filelink:`input.dd <verification/vermix/input.dd>`)
                 
                    - with package :filelink:`ggl90 <pkg/ggl90>` scheme (Gaspar et al. 1990 :cite:`gas-eta:90`) scheme
                      (:filelink:`input.ggl90 <verification/vermix/input.ggl90>`)
                 
9af873c532 Hajo*    - with :filelink:`ggl90 <pkg/ggl90>` package and parameterized Langmuir circulation effects
                      (:varlink:`useLANGMUIR` ``= .TRUE.`` in ``data.ggl90``,
                      :filelink:`input.gglLC <verification/vermix/input.gglLC>`)
                 
1c8cebb321 Jeff*    - with Mellor and Yamada (1982) :cite:`mellor:82` level 2 (:filelink:`pkg/my82`)
                      scheme (:filelink:`input.my82 <verification/vermix/input.my82>`)
                 
                    - with Paluszkiewicz and Romea (1997) :cite:`pal-rom:97` (:filelink:`pkg/opps`) scheme
                      (:filelink:`input.opps <verification/vermix/input.opps>`)
                 
                    - with Pacanowski and Philander (1981) :cite:`pacanowski:81` (:filelink:`pkg/pp81`)
                      scheme (:filelink:`input.pp81 <verification/vermix/input.pp81>`).
                 
                 .. _subsec_add_expts_adj:
                 
                 Additional Example Experiments: Adjoint Model Setups
                 ====================================================
                 
                 Unless stated otherwise, the physical setup of the adjoint run is identical to the forward run, see description above.
                 TAF adjoint setups require building with directory ``code_ad`` with input directory ``input_ad``, whereas OpenAD requires
09461bf9e9 Jean* directories ``code_oad`` and ``input_oad`` respectively.
1c8cebb321 Jeff* 
838c406049 Jeff* #. :filelink:`1D_ocean_ice_column <verification/1D_ocean_ice_column>` - Based on standard forward experiment,
                    TAF adjoint setup, uses package :filelink:`ecco <pkg/ecco>`.
1c8cebb321 Jeff* 
09461bf9e9 Jean* #. :filelink:`bottom_ctrl_5x5 <verification/bottom_ctrl_5x5>` - TAF adjoint
                    test using the bottom topography as the control parameter, uses package
                    :filelink:`ecco <pkg/ecco>` and "not self-adjoint" version of cg2d:
                    :filelink:`cg2d_nsa.F <model/src/cg2d_nsa.F>`.
                    Also contains an additional TAF adjoint setup
                    that uses default :filelink:`cg2d.F <model/src/cg2d.F>` with a hand-written
                    full (manual) adjoint routine :filelink:`cg2d_mad.F
                    <pkg/autodiff/cg2d_mad.F>` (:filelink:`input_ad.facg2d
                    <verification/bottom_ctrl_5x5/input_ad.facg2d>`)
1c8cebb321 Jeff* 
                 #. :filelink:`global_ocean.90x40x15 <verification/global_ocean.90x40x15>` - Based on standard forward experiment,
                    TAF and OpenAD adjoint setups. Also contains additional TAF adjoint setups:
                 
09461bf9e9 Jean*    - with bottom drag as a control and manual adjoint :filelink:`cg2d_mad.F
                      <pkg/autodiff/cg2d_mad.F>` (:filelink:`input_ad.bottomdrag <verification/global_ocean.90x40x15/input_ad.bottomdrag>`)
1c8cebb321 Jeff* 
                    - with :math:`\kappa_{GM}` as a control (:filelink:`input_ad.kapgm <verification/global_ocean.90x40x15/input_ad.kapgm>`)
                 
                    - with :math:`\kappa_{Redi}` as a control (:filelink:`input_ad.kapredi <verification/global_ocean.90x40x15/input_ad.kapredi>`).
                 
                 #. :filelink:`global_ocean.cs32x15 <verification/global_ocean.cs32x15>` - Based on standard forward experiment, TAF adjoint setup.
                    Also contains additional TAF adjoint setups:
                 
                    - using thermodynamic-dynamic sea ice (:filelink:`input_ad.seaice <verification/global_ocean.cs32x15/input_ad.seaice>`).
                 
                    - same as above but without adjoint sea ice dynamics
                      (:filelink:`input_ad.seaice_dynmix <verification/global_ocean.cs32x15/input_ad.seaice_dynmix>`).
                 
                    - using thermodynamic sea ice from :filelink:`pkg/thsice`
                      (:filelink:`input_ad.thsice <verification/global_ocean.cs32x15/input_ad.thsice>`).
                 
f1b47febb7 Jean* #. :filelink:`global_oce_biogeo_bling <verification/global_oce_biogeo_bling>` - Based on
                    standard forward experiment, TAF adjoint setup, uses package
                    :filelink:`ecco <pkg/ecco>` and package :filelink:`profiles <pkg/profiles>`.
                    Also contains an additional TAF adjoint setup
                    that uses package :filelink:`obsfit <pkg/obsfit>`
                    (:filelink:`input_ad.obsfit <verification/global_oce_biogeo_bling/input_ad.obsfit>`).
1c8cebb321 Jeff* 
5bc996898d Mart* #. :filelink:`global_oce_latlon <verification/global_oce_latlon>` - Simple adjoint experiment (used also to test OpenAD compiler), TAF and OpenAD adjoint setups.
9af873c532 Hajo*    Also contains additional TAF and OpenAD adjoint setups:
5bc996898d Mart* 
9af873c532 Hajo*    - using package :filelink:`ggl90 <pkg/ggl90>`
                      (:filelink:`input_ad.ggl90 <verification/global_oce_latlon/input_ad.ggl90>`,
                      :filelink:`input_oad.ggl90 <verification/global_oce_latlon/input_oad.ggl90>`).
5bc996898d Mart* 
f1b47febb7 Jean*    - using package :filelink:`kpp <pkg/kpp>`
                      (:filelink:`input_oad.kpp <verification/global_oce_latlon/input_oad.kpp>`).
5bc996898d Mart* 
f1b47febb7 Jean*    - using package :filelink:`exf <pkg/exf>`
                      (:filelink:`input_ad.w_exf <verification/global_oce_latlon/input_ad.w_exf>`,
7fe51dd492 Jean*      formerly :filelink:`global_with_exf <verification/global_with_exf>`)
1c8cebb321 Jeff* 
f1b47febb7 Jean*    - using package :filelink:`ebm <pkg/ebm>`
                      (:filelink:`input_ad.ebm <verification/global_oce_latlon/input_ad.ebm>`,
                      formerly :filelink:`global_ocean_ebm <verification/global_ocean_ebm>`)
                 
1c8cebb321 Jeff* #. :filelink:`halfpipe_streamice<verification/halfpipe_streamice>` - Based on standard forward experiment, TAF and OpenAD adjoint setups.
                 
                 #. :filelink:`hs94.1x64x5 <verification/hs94.1x64x5>` - Based on standard forward experiment, TAF and OpenAD adjoint setups.
                 
                 #. :filelink:`isomip <verification/isomip>` - Based on standard forward experiment, TAF and OpenAD adjoint setups.
                    Also contains additional TAF adjoint setup
                
** Warning **
Wide character in print at /usr/local/share/lxr/source line 1030, <$git> line 677.


    with “htd” (Hellmer's thermodynamics, Hellmer 1989 :cite:`hellmer:89`) (:filelink:`input_ad.htd <verification/isomip/input_ad.htd>`).
                 
                 #. :filelink:`lab_sea <verification/lab_sea>` - Based on standard forward experiment, TAF adjoint setup, uses
                    package :filelink:`ecco <pkg/ecco>` and :ref:`divided adjoint (DIVA) <sec_autodiff_diva>`.
                    Also contains additional TAF adjoint setups:
                 
                    - without seaice dynamics (:filelink:`input_ad.noseaicedyn <verification/lab_sea/input_ad.noseaicedyn>`).
                 
                    - without seaice altogether (:filelink:`input_ad.noseaice <verification/lab_sea/input_ad.noseaice>`).
                 
                 #. :filelink:`obcs_ctrl <verification/obcs_ctrl>` - Adjoint test using open boundary conditions as
                    control parameters, uses package :filelink:`ecco <pkg/ecco>`.
                 
                 #. :filelink:`offline_exf_seaice <verification/offline_exf_seaice>` - Based on standard forward experiment, TAF adjoint setup.
                    Also contains additional TAF adjoint setup
                    with sea ice thermodynamics-only using :filelink:`pkg/thsice` (:filelink:`input_ad.thsice <verification/offline_exf_seaice/input_ad.thsice>`).
                 
                 #. :filelink:`tutorial_dic_adjoffline <verification/tutorial_dic_adjoffline>` - TAF adjoint setup of offline form of passive tracers coupled
                    to the dissolved inorganic carbon biogeochemistry model (currently NOT documented as a tutorial experiment).
                 
                 #. :filelink:`tutorial_global_oce_biogeo <verification/tutorial_global_oce_biogeo>` - Based on forward experiment described
                    in :numref:`sub_global_oce_biogeo`, TAF and OpenAD adjoint setups.
                 
838c406049 Jeff* #. :filelink:`tutorial_tracer_adjsens <verification/tutorial_tracer_adjsens>` - Based on adjoint experiment
                    described in :numref:`sec_tracer_adj_sens`, contains an additional TAF setup using Second Order Moment (SOM)
1c8cebb321 Jeff*    advection scheme (:filelink:`input_ad.som81 <verification/tutorial_tracer_adjsens/input_ad.som81>`).

This page was automatically generated from https://github.com/darwinproject/darwin3 by the 2.3.7-MITgcm-0.1 LXR engine. The LXR team