source: NEMO/trunk/cfgs @ 12206

Name Size Rev Age Author Last Change
AGRIF_DEMO 12206   2 years smasson trunk: supress diatmb as it was bugged and already coded in diawri, see …
AMM12 12206   2 years smasson trunk: supress diatmb as it was bugged and already coded in diawri, see …
C1D_PAPA 12206   2 years smasson trunk: supress diatmb as it was bugged and already coded in diawri, see …
GYRE_BFM 12206   2 years smasson trunk: supress diatmb as it was bugged and already coded in diawri, see …
GYRE_PISCES 12206   2 years smasson trunk: supress diatmb as it was bugged and already coded in diawri, see …
ORCA2_ICE_PISCES 12206   2 years smasson trunk: supress diatmb as it was bugged and already coded in diawri, see …
ORCA2_OFF_PISCES 12206   2 years smasson trunk: supress diatmb as it was bugged and already coded in diawri, see …
ORCA2_OFF_TRC 12206   2 years smasson trunk: supress diatmb as it was bugged and already coded in diawri, see …
ORCA2_SAS_ICE 12206   2 years smasson trunk: supress diatmb as it was bugged and already coded in diawri, see …
SHARED 12206   2 years smasson trunk: supress diatmb as it was bugged and already coded in diawri, see …
SPITZ12 12206   2 years smasson trunk: supress diatmb as it was bugged and already coded in diawri, see …
README.rst 14.0 KB 11743   2 years nicolasmartin Review README for configuration setup
ref_cfgs.txt 217 bytes 9775   4 years clem change AGRIF config according to new implementation from Jerome
  • Property svn:ignore set to


Run the Reference configurations

.. todo::

   Lack of illustrations for ref. cfgs, and more generally in the guide.

NEMO is distributed with a set of reference configurations allowing both
the user to set up his own first applications and
the developer to test/validate his NEMO developments (using SETTE package).

.. contents::
   :depth: 1

.. attention::

   Concerning the configurations,
   the NEMO System Team is only in charge of the so-called reference configurations described below.

.. hint::

   Configurations developed by external research projects or initiatives that
   make use of NEMO are welcome to be publicized through the website by
   filling up the form :website:`to add an associated project<projects/add>`.

How to compile an experiment from a reference configuration

To compile the ORCA2_ICE_PISCES_ reference configuration using :file:`makenemo`,
one should use the following, by selecting among available architecture file or
providing a user defined one:

.. code-block:: console

   $ ./makenemo -r 'ORCA2_ICE_PISCES' -m 'my_arch' -j '4'

A new ``EXP00`` folder will be created within the selected reference configurations,
namely ``./cfgs/ORCA2_ICE_PISCES/EXP00``.
It will be necessary to uncompress the archives listed in the above table for
the given reference configuration that includes input & forcing files.

Then it will be possible to launch the execution of the model through a runscript
(opportunely adapted to the user system).

List of Configurations

All forcing files listed below in the table are available from |DOI data|_

=================== === === === === === ==================================
 Configuration       Component(s)        Archives (input & forcing files)
------------------- ------------------- ----------------------------------
 Name                O   S   T   P   A
=================== === === === === === ==================================
 AGRIF_DEMO_         X   X           X   AGRIF_DEMO_v4.0.tar,
 AMM12_              X                   AMM12_v4.0.tar
 C1D_PAPA_           X                   INPUTS_C1D_PAPA_v4.0.tar
 GYRE_BFM_           X       X           *none*
 GYRE_PISCES_        X       X   X       *none*
 ORCA2_ICE_PISCES_   X   X   X   X       ORCA2_ICE_v4.0.tar,
 ORCA2_OFF_PISCES_           X   X       ORCA2_OFF_v4.0.tar,
 ORCA2_OFF_TRC_              X           ORCA2_OFF_v4.0.tar
 ORCA2_SAS_ICE_          X               ORCA2_ICE_v4.0.tar,
 SPITZ12_            X   X               SPITZ12_v4.0.tar
=================== === === === === === ==================================

.. admonition:: Legend for component combination

   O for OCE, S for SI\ :sup:`3`, T for TOP, P for PISCES and A for AGRIF


``AGRIF_DEMO`` is based on the ``ORCA2_ICE_PISCES`` global configuration at 2° of resolution with
the inclusion of 3 online nested grids to demonstrate the overall capabilities of AGRIF in
a realistic context (including the nesting of sea ice models).

The configuration includes a 1:1 grid in the Pacific and two successively nested grids with
odd and even refinement ratios over the Arctic ocean,
with the finest grid spanning the whole Svalbard archipelago that is of
particular interest to test sea ice coupling.

.. image:: _static/AGRIF_DEMO_no_cap.jpg
   :scale: 66%
   :align: center

The 1:1 grid can be used alone as a benchmark to check that
the model solution is not corrupted by grid exchanges.
Note that since grids interact only at the baroclinic time level,
numerically exact results can not be achieved in the 1:1 case.
Perfect reproducibility is obtained only by switching to a fully explicit setup instead of
a split explicit free surface scheme.


``AMM12`` stands for *Atlantic Margin Model at 12 km* that is
a regional configuration covering the Northwest European Shelf domain on
a regular horizontal grid of ~12 km of resolution (see :cite:`ODEA2012`).

.. image:: _static/AMM_domain.png
   :align: center

This configuration allows to tests several features of NEMO specifically addressed to the shelf seas.
In particular, ``AMM12`` accounts for vertical s-coordinates system, GLS turbulence scheme,
tidal lateral boundary conditions using a flather scheme (see more in ``BDY``).
Boundaries may be completely omitted by setting ``ln_bdy = .false.`` in ``nambdy``.

Sample surface fluxes, river forcing and an initial restart file are included to test a realistic model run

Note that, the Baltic boundary is included within the river input file and is specified as a river source,
but unlike ordinary river points the Baltic inputs also include salinity and temperature data.


.. figure:: _static/Papa2015.jpg
   :height: 225px
   :align:  left

``C1D_PAPA`` is a 1D configuration for the `PAPA station`_ located in
the northern-eastern Pacific Ocean at 50.1°N, 144.9°W.
See :gmd:`Reffray et al. (2015) <8/69/2015>` for the description of
its physical and numerical turbulent-mixing behaviour.

| The water column setup, called NEMO1D, is activated with
  the inclusion of the CPP key ``key_c1d`` and
  has a horizontal domain of 3x3 grid points.
| This reference configuration uses 75 vertical levels grid (1m at the surface),
  GLS turbulence scheme with K-epsilon closure and the NCAR bulk formulae.

Data provided with ``INPUTS_C1D_PAPA_v4.0.tar`` file account for:

- :file:`forcing_PAPASTATION_1h_y201[0-1].nc`:
  ECMWF operational analysis atmospheric forcing rescaled to 1h
  (with long and short waves flux correction) for years 2010 and 2011
- :file:``: Initial Conditions from
  observed data and Levitus 2009 climatology
- :file:``: surface chlorophyll file from Seawifs data


``GYRE_BFM`` shares the same physical setup of GYRE_PISCES_,
but NEMO is coupled with the `BFM`_ biogeochemical model as described in ``./cfgs/GYRE_BFM/README``.


``GYRE_PISCES`` is an idealized configuration representing a Northern hemisphere double gyres system,
in the Beta-plane approximation with a regular 1° horizontal resolution and 31 vertical levels,
with PISCES BGC model :cite:`gmd-8-2465-2015`.
Analytical forcing for heat, freshwater and wind-stress fields are applied.

This configuration acts also as demonstrator of the **user defined setup**
(``ln_read_cfg = .false.``) and grid setting are handled through
the ``&namusr_def`` controls in :file:`namelist_cfg`:

.. literalinclude:: ../../../cfgs/GYRE_PISCES/EXPREF/namelist_cfg
   :language: fortran
   :lines:    35-41

Note that, the default grid size is 30x20 grid points (with ``nn_GYRE = 1``) and
vertical levels are set by ``jpkglo``.
The specific code changes can be inspected in :file:`./src/OCE/USR`.

.. rubric:: Running GYRE as a benchmark

| This simple configuration can be used as a benchmark since it is easy to increase resolution,
  with the drawback of getting results that have a very limited physical meaning.
| GYRE grid resolution can be increased at runtime by setting a different value of ``nn_GYRE``
  (integer multiplier scaling factor), as described in the following table:

=========== ============ ============ ============ ===============
``nn_GYRE``  ``jpiglo``   ``jpjglo``   ``jpkglo``   Equivalent to
=========== ============ ============ ============ ===============
 1           30           20           31           GYRE 1°
 25          750          500          101          ORCA 1/2°
 50          1500         1000         101          ORCA 1/4°
 150         4500         3000         101          ORCA 1/12°
 200         6000         4000         101          ORCA 1/16°
=========== ============ ============ ============ ===============

| Note that, it is necessary to set ``ln_bench = .true.`` in ``&namusr_def`` to
  avoid problems in the physics computation and that
  the model timestep should be adequately rescaled.
| For example if ``nn_GYRE = 150``, equivalent to an ORCA 1/12° grid,
  the timestep ``rn_rdt`` should be set to 1200 seconds
  Differently from previous versions of NEMO, the code uses by default the time-splitting scheme and
  internally computes the number of sub-steps.


``ORCA2_ICE_PISCES`` is a reference configuration for the global ocean with
a 2°x2° curvilinear horizontal mesh and 31 vertical levels,
distributed using z-coordinate system and with 10 levels in the top 100m.
ORCA is the generic name given to global ocean Mercator mesh,
(i.e. variation of meridian scale factor as cosinus of the latitude),
with two poles in the northern hemisphere so that
the ratio of anisotropy is nearly one everywhere

This configuration uses the three components

- |OCE|, the ocean dynamical core
- |ICE|, the thermodynamic-dynamic sea ice model.
- |MBG|, passive tracer transport module and PISCES BGC model :cite:`gmd-8-2465-2015`

All components share the same grid.
The model is forced with CORE-II normal year atmospheric forcing and
it uses the NCAR bulk formulae.

.. rubric:: Ocean Physics

:horizontal diffusion on momentum:
   the eddy viscosity coefficient depends on the geographical position.
   It is taken as 40000 m\ :sup:`2`/s, reduced in the equator regions (2000 m\ :sup:`2`/s)
   excepted near the western boundaries.
:isopycnal diffusion on tracers:
   the diffusion acts along the isopycnal surfaces (neutral surface) with
   an eddy diffusivity coefficient of 2000 m\ :sup:`2`/s.
:Eddy induced velocity parametrization:
   With a coefficient that depends on the growth rate of baroclinic instabilities
   (it usually varies from 15 m\ :sup:`2`/s to 3000 m\ :sup:`2`/s).
:lateral boundary conditions:
   Zero fluxes of heat and salt and no-slip conditions are applied through lateral solid boundaries.
:bottom boundary condition:
   Zero fluxes of heat and salt are applied through the ocean bottom.
   The Beckmann [19XX] simple bottom boundary layer parameterization is applied along
   continental slopes.
   A linear friction is applied on momentum.
   The vertical eddy viscosity and diffusivity coefficients are increased to 1 m\ :sup:`2`/s in
   case of static instability.
:time step: is 5760sec (1h36') so that there is 15 time steps in one day.


``ORCA2_OFF_PISCES`` shares the same general offline configuration of ``ORCA2_ICE_TRC``,
but only PISCES model is an active component of TOP.


| ``ORCA2_OFF_TRC`` is based on the ORCA2 global ocean configuration
  (see ORCA2_ICE_PISCES_ for general description) along with
  the tracer passive transport module (TOP),
  but dynamical fields are pre-calculated and read with specific time frequency.
| This enables for an offline coupling of TOP components,
  here specifically inorganic carbon compounds (CFC11, CFC12, SF6, C14) and water age module (age).
  See :file:`namelist_top_cfg` to inspect the selection of
  each component with the dedicated logical keys.

Pre-calculated dynamical fields are provided to NEMO using
the namelist ``&namdta_dyn``  in :file:`namelist_cfg`,
in this case with a 5 days frequency (120 hours):

.. literalinclude:: ../../namelists/namdta_dyn
   :language: fortran

Input dynamical fields for this configuration (:file:`ORCA2_OFF_v4.0.tar`) comes from
a 2000 years long climatological simulation of ORCA2_ICE using ERA40 atmospheric forcing.

| Note that,
  this configuration default uses linear free surface (``ln_linssh = .true.``) assuming that
  model mesh is not varying in time and
  it includes the bottom boundary layer parameterization (``ln_trabbl = .true.``) that
  requires the provision of BBL coefficients through ``sn_ubl`` and ``sn_vbl`` fields.
| It is also possible to activate PISCES model (see ``ORCA2_OFF_PISCES``) or
  a user defined set of tracers and source-sink terms with ``ln_my_trc = .true.``
  (and adaptation of ``./src/TOP/MY_TRC`` routines).

In addition, the offline module (OFF) allows for the provision of further fields:

1. **River runoff** can be provided to TOP components by setting ``ln_dynrnf = .true.`` and
   by including an input datastream similarly to the following:

   .. code-block:: fortran

      sn_rnf  = 'dyna_grid_T', 120, 'sorunoff' , .true., .true., 'yearly', '', '', ''

2. **VVL dynamical fields**, in the case input data were produced by a dyamical core using
   variable volume (``ln_linssh = .false.``)
   it is necessary to provide also diverce and E-P at before timestep by
   including input datastreams similarly to the following

   .. code-block:: fortran

      sn_div  = 'dyna_grid_T', 120, 'e3t'      , .true., .true., 'yearly', '', '', ''
      sn_empb = 'dyna_grid_T', 120, 'sowaflupb', .true., .true., 'yearly', '', '', ''

More details can be found by inspecting the offline data manager in
the routine :file:`./src/OFF/dtadyn.F90`.


| ORCA2_SAS_ICE is a demonstrator of the Stand-Alone Surface (SAS) module and
  it relies on ORCA2 global ocean configuration (see ORCA2_ICE_PISCES_ for general description).
| The standalone surface module allows surface elements such as sea-ice, iceberg drift, and
  surface fluxes to be run using prescribed model state fields.
  It can profitably be used to compare different bulk formulae or
  adjust the parameters of a given bulk formula.

More informations about SAS can be found in :doc:`NEMO manual <cite>`.


``SPITZ12`` is a regional configuration around the Svalbard archipelago
at 1/12° of horizontal resolution and 75 vertical levels.
See :gmd:`Rousset et al. (2015) <8/2991/2015>` for more details.

This configuration references to year 2002,
with atmospheric forcing provided every 2 hours using NCAR bulk formulae,
while lateral boundary conditions for dynamical fields have 3 days time frequency.

.. rubric:: References

.. bibliography:: cfgs.bib
   :style: unsrt
   :labelprefix: C
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