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Changeset 10605 – NEMO

Changeset 10605


Ignore:
Timestamp:
2019-01-29T19:22:27+01:00 (5 years ago)
Author:
nicolasmartin
Message:

Corrections to .rst first files

Location:
NEMO/trunk
Files:
1 added
4 edited

Legend:

Unmodified
Added
Removed

  • NEMO/trunk/README.rst

    r10602 r10605  
    5858 Component   Reference Manual      Quick start 
    5959=========== ===================== =============== 
    60  |OPA|       |NEMO manual|_        |NEMO guide|_ 
     60 |OPA|       |NEMO manual|_        |NEMO guide| 
    6161             :cite:`NEMO_manual` 
    62  |SI3|       |SI3 manual|_ 
     62 |SI3|       |SI3 manual| 
    6363             :cite:`SI3_manual` 
    64  |TOP|       |TOP manual|_ 
     64 |TOP|       |TOP manual| 
    6565             :cite:`TOP_manual` 
    6666=========== ===================== =============== 
    … …  
    9797.. |NEMO strategy| replace:: multi-year development strategy 
    9898 
    99 .. _Special Issue: http://www.geosci-model-dev.net/special_issue40.html 
     99.. _Special Issue: https://www.geosci-model-dev.net/special_issue40.html 

  • NEMO/trunk/cfgs/README.rst

    r10598 r10605  
    33************************ 
    44 
    5 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). 
    6 *The NEMO System Team is in charge only for these configurations.* 
    7  
    8 Configurations developed by external research projects or initiatives that make use of NEMO are welcome to be publicized also through the NEMO website by filling up the form `Add project <http://www.nemo-ocean.eu/projects/add>`_ 
    9  
    10 Available Configurations  
    11 ------------------------ 
     5NEMO is distributed with a set of reference configurations allowing both 
     6the user to set up his own first applications and 
     7the developer to test/validate his NEMO developments (using SETTE package). 
     8 
     9.. attention:: 
     10 
     11   Concerning the configurations, 
     12   the NEMO System Team is only in charge of the so-called reference configurations described below. 
     13 
     14.. hint:: 
     15 
     16   Configurations developed by external research projects or initiatives that 
     17   make use of NEMO are welcome to be publicized through the website by 
     18   filling up the form :website:`to add an associated project<projects/add>`. 
     19 
     20How to compile an experiment from a reference configuration 
     21=========================================================== 
     22 
     23A user who wants to compile the ORCA2_ICE_PISCES_ reference configuration using ``makenemo`` 
     24should use the following, by selecting among available architecture file or providing a user defined one: 
     25 
     26.. code-block:: console 
     27                 
     28   $ ./makenemo -r 'ORCA2_ICE_PISCES' -m 'my-fortran.fcm' -j '4' 
     29 
     30A new ``EXP00`` folder will be created within the selected reference configurations, 
     31namely ``./cfgs/ORCA2_ICE_PISCES/EXP00``, 
     32where it will be necessary to uncompress the Input & Forcing Files listed in the above table. 
     33 
     34Then it will be possible to launch the execution of the model through a runscript 
     35(opportunely adapted to the user system). 
     36    
     37List of Configurations 
     38====================== 
     39 
     40All forcing files listed below in the table are available from |NEMO archives URL|_ 
     41 
     42.. |NEMO archives URL| image:: https://www.zenodo.org/badge/DOI/10.5281/zenodo.1472245.svg 
     43.. _NEMO archives URL: https://doi.org/10.5281/zenodo.1472245 
     44 
    1245====================== ===== ===== ===== ======== ======= ================================================ 
    1346 Configuration                     Component(s)                            Input & Forcing File(s) 
    … …  
    1548 Name                   OPA   SI3   TOP   PISCES   AGRIF 
    1649====================== ===== ===== ===== ======== ======= ================================================ 
    17  AGRIF_DEMO_             X     X                     X     AGRIF_DEMO_v4.0.tar_, ORCA2_ICE_v4.0.tar_ 
    18  AMM12_                  X                                 AMM12_v4.0.tar_ 
    19  C1D_PAPA_               X                                 INPUTS_C1D_PAPA_v4.0.tar_ 
     50 AGRIF_DEMO_             X     X                     X     AGRIF_DEMO_v4.0.tar, ORCA2_ICE_v4.0.tar 
     51 AMM12_                  X                                 AMM12_v4.0.tar 
     52 C1D_PAPA_               X                                 INPUTS_C1D_PAPA_v4.0.tar 
    2053 GYRE_BFM_               X           X                     *none* 
    2154 GYRE_PISCES_            X           X      X              *none* 
    22  ORCA2_ICE_PISCES_       X     X     X      X              ORCA2_ICE_v4.0.tar_, INPUTS_PISCES_v4.0.tar_ 
    23  ORCA2_OFF_PISCES_                   X      X              ORCA2_OFF_v4.0.tar_, INPUTS_PISCES_v4.0.tar_ 
    24  ORCA2_OFF_TRC_                      X                     ORCA2_OFF_v4.0.tar_ 
    25  ORCA2_SAS_ICE_                X                           ORCA2_ICE_v4.0.tar_, INPUTS_SAS_v4.0.tar_ 
    26  SPITZ12_                X     X                           SPITZ12_v4.0.tar_ 
     55 ORCA2_ICE_PISCES_       X     X     X      X              ORCA2_ICE_v4.0.tar, INPUTS_PISCES_v4.0.tar 
     56 ORCA2_OFF_PISCES_                   X      X              ORCA2_OFF_v4.0.tar, INPUTS_PISCES_v4.0.tar 
     57 ORCA2_OFF_TRC_                      X                     ORCA2_OFF_v4.0.tar 
     58 ORCA2_SAS_ICE_                X                           ORCA2_ICE_v4.0.tar, INPUTS_SAS_v4.0.tar 
     59 SPITZ12_                X     X                           SPITZ12_v4.0.tar 
    2760====================== ===== ===== ===== ======== ======= ================================================ 
    28  
    29 **How to compile an experiment from a reference configuration** 
    30  
    31 A user who wants to compile the ORCA2_ICE_PISCES_ reference configuration using makenemo should use the following, by selecting among available architecture file or providing a user defined one: 
    32  
    33  
    34 .. code-block:: console 
    35                  
    36         $ ./makenemo -r 'ORCA2_ICE_PISCES' -m 'my-fortran.fcm' -j '4' 
    37  
    38 A new EXP00 folder will be created within the selected reference configurations, namely ``trunk/cfgs/ORCA2_ICE_PISCES/EXP00``, where it will be necessary to uncompress the Input & Forcing Files listed in the above table. 
    39  
    40 Then it will be possible to launch the execution of the model through a runscript (opportunely adapted to the user system). 
    4161 
    4262AGRIF_DEMO 
    4363---------- 
    4464 
    45 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 (Adaptive Grid Refinement In Fortran) in a realistic context (including the nesting of sea ice models). 
    46  
    47 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. 
    48  
    49 The 1:1 grid can be used alone as a benchmark to check that the model solution is not corrupted by grid exchanges.  
    50 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 setip instead of a split explicit free surface scheme. 
     65``AGRIF_DEMO`` is based on the ``ORCA2_ICE_PISCES`` global configuration at 2° of resolution with 
     66the inclusion of 3 online nested grids to demonstrate the overall capabilities of AGRIF in 
     67a realistic context (including the nesting of sea ice models). 
     68 
     69The configuration includes a 1:1 grid in the Pacific and two successively nested grids with 
     70odd and even refinement ratios over the Arctic ocean, 
     71with the finest grid spanning the whole Svalbard archipelago that is of 
     72particular interest to test sea ice coupling. 
     73 
     74The 1:1 grid can be used alone as a benchmark to check that 
     75the model solution is not corrupted by grid exchanges.  
     76Note that since grids interact only at the baroclinic time level, 
     77numerically exact results can not be achieved in the 1:1 case. 
     78Perfect reproducibility is obtained only by switching to a fully explicit setup instead of a split explicit free surface scheme. 
    5179 
    5280AMM12 
    5381----- 
    5482 
    55 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 `O'Dea et al., 2012 <http://www.tandfonline.com/doi/pdf/10.1080/1755876X.2012.11020128>`_). 
     83``AMM12`` stands for *Atlantic Margin Model at 12 km* that is 
     84a regional configuration covering the Northwest European Shelf domain on 
     85a regular horizontal grid of ~12 km of resolution (see :cite:`ODEA2012`). 
    5686 
    5787This configuration allows to tests several features of NEMO specifically addressed to the shelf seas.  
    58 In particular, AMM12  accounts for vertical s-coordinates system, GLS turbulence scheme, tidal lateral boundary conditions using a flather scheme (see more in BDY). 
     88In particular, ``AMM12`` accounts for vertical s-coordinates system, GLS turbulence scheme, 
     89tidal lateral boundary conditions using a flather scheme (see more in ``BDY``). 
    5990Boundaries may be completely omitted by setting ``ln_bdy = .false.`` in ``nambdy``. 
    6091 
    61 Sample surface fluxes, river forcing and an initial restart file are included to test a realistic model run (AMM12_v4.0.tar_). 
    62  
    63 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. 
     92Sample surface fluxes, river forcing and an initial restart file are included to test a realistic model run 
     93(``AMM12_v4.0.tar``). 
     94 
     95Note that, the Baltic boundary is included within the river input file and is specified as a river source, 
     96but unlike ordinary river points the Baltic inputs also include salinity and temperature data. 
    6497 
    6598C1D_PAPA 
    6699-------- 
    67100 
    68 C1D_PAPA is a 1D configuration for the `PAPA station <http://www.pmel.noaa.gov/OCS/Papa/index-Papa.shtml>`_ located in the northern-eastern Pacific Ocean at 50.1°N, 144.9°W. See `Reffray et al. (2015) <http://www.geosci-model-dev.net/8/69/2015>`_ for the description of its physical and numerical turbulent-mixing behaviour. 
    69  
    70 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. 
     101``C1D_PAPA`` is a 1D configuration for the `PAPA station <http://www.pmel.noaa.gov/OCS/Papa/index-Papa.shtml>`_ located in the northern-eastern Pacific Ocean at 50.1°N, 144.9°W. 
     102See `Reffray et al. (2015) <http://www.geosci-model-dev.net/8/69/2015>`_ for the description of its physical and numerical turbulent-mixing behaviour. 
     103 
     104The water column setup, called NEMO1D, is activated with the inclusion of the CPP key ``key_c1d`` and 
     105has a horizontal domain of 3x3 grid points. 
    71106 
    72107This reference configuration uses 75 vertical levels grid (1m at the surface), GLS turbulence scheme with K-epsilon closure and the NCAR bulk formulae. 
    73 Data provided with INPUTS_C1D_PAPA_v4.0.tar_ file account for : 
     108Data provided with ``INPUTS_C1D_PAPA_v4.0.tar`` file account for: 
    74109 
    75110- ``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 
    … …  
    77112- ``chlorophyll_PAPASTATION.nc`` : surface chlorophyll file from Seawifs data 
    78113 
    79  
    80114GYRE_BFM 
    81115-------- 
    82116 
    83 GYRE_BFM shares the same physical setup of GYRE_PISCES_, but NEMO is coupled with the `BFM <http://www.bfm-community.eu/>`_ biogeochemical model as described in :forge:`browser/NEMO/trunk/cfgs/GYRE_BFM/README`. 
    84  
     117``GYRE_BFM`` shares the same physical setup of GYRE_PISCES_, but NEMO is coupled with the `BFM <http://www.bfm-community.eu/>`_ biogeochemical model as described in ``./cfgs/GYRE_BFM/README``. 
    85118 
    86119GYRE_PISCES 
    87120----------- 
    88121 
    89 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, which is coupled with `PISCES biogeochemical model`_. Analytical forcing for heat, freshwater and wind-stress fields are applied.   
    90  
    91 This configuration act also as demonstrator of the **USER DEFINED setup** (``ln_read_cfg = .false.``) and grid setting are handled through the ``&namusr_def`` controls in namelist_cfg: 
    92  
    93 .. code-block:: fortran 
    94  
    95   !----------------------------------------------------------------------- 
    96   &namusr_def    !   GYRE user defined namelist 
    97   !----------------------------------------------------------------------- 
    98      nn_GYRE     =     1     !  GYRE resolution [1/degrees] 
    99      ln_bench    = .false.   !  ! =T benchmark with gyre: the gridsize is kept constant 
    100      jpkglo      =    31     !  number of model levels 
    101   / 
    102  
    103 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 at :forge:`browser/NEMO/trunk/src/OCE/USR`  
    104  
    105 **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. 
    106  
    107 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:  
     122``GYRE_PISCES`` is an idealized configuration representing a Northern hemisphere double gyres system, 
     123in the Beta-plane approximation with a regular 1° horizontal resolution and 31 vertical levels, 
     124with PISCES BGC model :cite:`gmd-8-2465-2015`. 
     125Analytical forcing for heat, freshwater and wind-stress fields are applied.   
     126 
     127This configuration acts also as demonstrator of the **user defined setup** (``ln_read_cfg = .false.``) and 
     128grid setting are handled through the ``&namusr_def`` controls in ``namelist_cfg``: 
     129 
     130.. literalinclude:: ../../../cfgs/GYRE_PISCES/EXPREF/namelist_cfg 
     131   :language: fortran 
     132   :lines: 34-42 
     133 
     134Note that, the default grid size is 30x20 grid points (with ``nn_GYRE = 1``) and 
     135vertical levels are set by ``jpkglo``. 
     136The specific code changes can be inspected in ``./src/OCE/USR``. 
     137 
     138**Running GYRE as a benchmark** : 
     139this simple configuration can be used as a benchmark since it is easy to increase resolution, 
     140with the drawback of getting results that have a very limited physical meaning. 
     141 
     142GYRE 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:  
    108143 
    109144=========== ========= ========== ============ =================== 
    … …  
    117152=========== ========= ========== ============ =================== 
    118153 
    119 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.  
    120  
    121 For example if ``nn_GYRE = 150``, equivalent to an ORCA 1/12° grid, the timestep should be set to 1200 seconds 
    122  
    123 .. code-block:: fortran 
    124     
    125    rn_rdt      = 1200.     !  time step for the dynamics 
    126  
    127 Differently from previous versions of NEMO, the code uses by default  the time-splitting scheme and internally computes the number of sub-steps.  
    128  
     154Note that, it is necessary to set ``ln_bench = .true.`` in ``namusr_def`` to 
     155avoid problems in the physics computation and that 
     156the model timestep should be adequately rescaled.  
     157 
     158For example if ``nn_GYRE = 150``, equivalent to an ORCA 1/12° grid, 
     159the timestep ``rn_rdt = 1200`` should be set to 1200 seconds 
     160 
     161Differently from previous versions of NEMO, 
     162the code uses by default the time-splitting scheme and 
     163internally computes the number of sub-steps.  
    129164 
    130165ORCA2_ICE_PISCES 
    131166---------------- 
    132167 
    133 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. 
    134 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 
    135  
    136 In this configuration, the ocean dynamical core  is coupled to   
    137  
    138 - **ICE**, namely SI3 (Sea Ice Integrated Initiative) a thermodynamic-dynamic sea ice model specifically designed for climate studies. 
    139 - **TOP**, passive tracer transport module and `PISCES biogeochemical model`_ 
     168``ORCA2_ICE_PISCES`` is a reference configuration for the global ocean with 
     169a 2°x2° curvilinear horizontal mesh and 31 vertical levels, 
     170distributed using z-coordinate system and with 10 levels in the top 100m. 
     171ORCA is the generic name given to global ocean Mercator mesh, 
     172(i.e. variation of meridian scale factor as cosinus of the latitude), 
     173with two poles in the northern hemisphere so that 
     174the ratio of anisotropy is nearly one everywhere 
     175 
     176this configuration uses the three components  
     177 
     178- |OPA|, the ocean dynamical core  
     179- |SI3|, the thermodynamic-dynamic sea ice model. 
     180- |TOP|, passive tracer transport module and PISCES BGC model :cite:`gmd-8-2465-2015` 
    140181 
    141182All components share the same grid. 
    142183 
    143 The model is forced with CORE-II normal year atmospheric forcing and it uses the NCAR bulk formulae. 
    144  
    145 **Ocean Physics configuration** 
     184The model is forced with CORE-II normal year atmospheric forcing and 
     185it uses the NCAR bulk formulae. 
     186 
     187In this ``ORCA2_ICE_PISCES`` configuration, 
     188AGRIF nesting can be activated that includes a nested grid in the Agulhas region. 
     189 
     190To set up this configuration, after extracting NEMO: 
     191 
     192Build your AGRIF configuration directory from ``ORCA2_ICE_PISCES``, 
     193with the ``key_agrif`` CPP key activated: 
     194 
     195.. code-block:: console 
     196                 
     197        $ ./makenemo -r 'ORCA2_ICE_PISCES' -n 'AGRIF' add_key 'key_agrif' 
     198 
     199By using the input files and namelists for ``ORCA2_ICE_PISCES``, 
     200the AGRIF test configuration is ready to run. 
     201 
     202**Ocean Physics** 
    146203 
    147204- *horizontal diffusion on momentum*: the eddy viscosity coefficient depends on the geographical position. It is taken as 40000 m^2/s, reduced in the equator regions (2000 m^2/s) excepted near the western boundaries. 
    … …  
    155212- *time step* is 5760sec (1h36') so that there is 15 time steps in one day. 
    156213 
    157  
    158  
    159 **AGRIF demonstrator** 
    160  
    161 From the ORCA2_ICE_PISCES configuration, a demonstrator using AGRIF nesting can be activated that includes a nested grid in the Agulhas region. 
    162  
    163 To set up this configuration, after extracting NEMO: 
    164  
    165 Build your AGRIF configuration directory from ORCA2_ICE_PISCES, with the key_agrif CPP key activated: 
    166  
    167 .. code-block:: console 
    168                  
    169         $ ./makenemo -r 'ORCA2_ICE_PISCES' -n 'AGRIF' add_key 'key_agrif' 
    170  
    171 By using the input files and namelists for ORCA2_ICE_PISCES, the AGRIF test configuration is ready to run. 
    172  
    173  
    174214ORCA2_OFF_PISCES 
    175215---------------- 
    176216 
    177 ORCA2_OFF_PISCES  shares the same general offline configuration of ORCA2_ICE_TRC, but only PISCES model is an active component of TOP. 
     217``ORCA2_OFF_PISCES`` shares the same general offline configuration of ``ORCA2_ICE_TRC``, 
     218but only PISCES model is an active component of TOP. 
    178219 
    179220 
    … …  
    181222------------- 
    182223 
    183 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. 
    184  
    185 This enables for an offline coupling of TOP components, here specifically inorganic carbon compounds (cfc11, cfc12, sf6, c14) and water age module (age). See ``namelist_top_cfg`` to inspect the selection of each component with the dedicated logical keys. 
    186  
    187 Pre-calculated dynamical fields are provided to NEMO using the namelist ``&namdta_dyn``  in ``namelist_cfg``, in this case with a 5 days frequency (120 hours): 
     224``ORCA2_OFF_TRC`` is based on the ORCA2 global ocean configuration 
     225(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. 
     226 
     227This enables for an offline coupling of TOP components, 
     228here specifically inorganic carbon compounds (cfc11, cfc12, sf6, c14) and water age module (age). 
     229See ``namelist_top_cfg`` to inspect the selection of each component with the dedicated logical keys. 
     230 
     231Pre-calculated dynamical fields are provided to NEMO using 
     232the namelist ``&namdta_dyn``  in ``namelist_cfg``, 
     233in this case with a 5 days frequency (120 hours): 
     234 
     235.. literalinclude:: ../../../cfgs/GYRE_PISCES/EXPREF/namelist_ref 
     236   :language: fortran 
     237   :lines: 306-333 
     238 
     239Input dynamical fields for this configuration (``ORCA2_OFF_v4.0.tar``) comes from 
     240a 2000 years long climatological simulation of ORCA2_ICE using ERA40 atmospheric forcing. 
     241 
     242Note that, this configuration default uses linear free surface (``ln_linssh = .true.``) assuming that 
     243model mesh is not varying in time and 
     244it includes the bottom boundary layer parameterization (``ln_trabbl = .true.``) that 
     245requires the provision of bbl coefficients through ``sn_ubl`` and ``sn_vbl`` fields. 
     246 
     247It is also possible to activate PISCES model (see ``ORCA2_OFF_PISCES``) or 
     248a user defined set of tracers and source-sink terms with ``ln_my_trc = .true.`` 
     249(and adaptation of ``./src/TOP/MY_TRC`` routines). 
     250 
     251In addition, the offline module (OFF) allows for the provision of further fields: 
     252 
     2531. **River runoff** can be provided to TOP components by setting ``ln_dynrnf = .true.`` and 
     254   by including an input datastream similarly to the following: 
    188255 
    189256.. code-block:: fortran 
    190257 
    191   !----------------------------------------------------------------------- 
    192   &namdta_dyn    !   offline ocean input files                            (OFF_SRC only) 
    193   !----------------------------------------------------------------------- 
    194      ln_dynrnf       =  .false.    !  runoffs option enabled (T) or not (F) 
    195      ln_dynrnf_depth =  .false.    !  runoffs is spread in vertical (T) or not (F) 
    196      cn_dir      = './'      !  root directory for the ocean data location 
    197      !___________!_________________________!___________________!___________!_____________!________!___________!__________________!__________!_______________! 
    198      !           !  file name              ! frequency (hours) ! variable  ! time interp.!  clim  ! 'yearly'/ ! weights filename ! rotation ! land/sea mask ! 
    199      !           !                         !  (if <0  months)  !   name    !   (logical) !  (T/F) ! 'monthly' !                  ! pairing  !    filename   ! 
    200      sn_tem      = 'dyna_grid_T'           ,       120         , 'votemper'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , '' 
    201      sn_sal      = 'dyna_grid_T'           ,       120         , 'vosaline'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , '' 
    202      sn_mld      = 'dyna_grid_T'           ,       120         , 'somixhgt'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , '' 
    203      sn_emp      = 'dyna_grid_T'           ,       120         , 'sowaflup'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , '' 
    204      sn_fmf      = 'dyna_grid_T'           ,       120         , 'iowaflup'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , '' 
    205      sn_ice      = 'dyna_grid_T'           ,       120         , 'soicecov'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , '' 
    206      sn_qsr      = 'dyna_grid_T'           ,       120         , 'soshfldo'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , '' 
    207      sn_wnd      = 'dyna_grid_T'           ,       120         , 'sowindsp'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , '' 
    208      sn_uwd      = 'dyna_grid_U'           ,       120         , 'uocetr_eff',  .true.   , .true. , 'yearly'  , ''               , ''       , '' 
    209      sn_vwd      = 'dyna_grid_V'           ,       120         , 'vocetr_eff',  .true.   , .true. , 'yearly'  , ''               , ''       , '' 
    210      sn_wwd      = 'dyna_grid_W'           ,       120         , 'wocetr_eff',  .true.   , .true. , 'yearly'  , ''               , ''       , '' 
    211      sn_avt      = 'dyna_grid_W'           ,       120         , 'voddmavs'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , '' 
    212      sn_ubl      = 'dyna_grid_U'           ,       120         , 'sobblcox'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , '' 
    213      sn_vbl      = 'dyna_grid_V'           ,       120         , 'sobblcoy'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , '' 
    214   / 
    215  
    216 Input dynamical fields for this configuration (ORCA2_OFF_v4.0.tar_) comes from a 2000 years long climatological simulation of ORCA2_ICE using ERA40 atmospheric forcing. 
    217  
    218 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. 
    219  
    220 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 :forge:`browser/NEMO/trunk/src/TOP/MY_TRC` routines). 
    221  
    222 In addition, the offline module (OFF) allows for the provision of further fields: 
    223  
    224 1. **River runoff** can be provided to TOP components by setting ``ln_dynrnf = .true.`` and by including an input datastream similarly to the following: 
     258   sn_rnf  = 'dyna_grid_T', 120, 'sorunoff' , .true., .true., 'yearly', '', '', '' 
     259 
     2602. **VVL dynamical fields**, 
     261   in the case input data were produced by a dyamical core using variable volume (``ln_linssh = .false.``) 
     262   it necessary to provide also diverce and E-P at before timestep by 
     263   including input datastreams similarly to the following 
    225264 
    226265.. code-block:: fortran 
    227266 
    228      sn_rnf      = 'dyna_grid_T'           ,       120         , 'sorunoff'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , '' 
    229  
    230 2. **VVL dynamical fields**, in the case input data were produced by a dyamical core using variable volume (``ln_linssh = .false.``) it necessary to provide also diverce and E-P at before timestep by including input datastreams similarly to the following 
    231  
    232 .. code-block:: fortran 
    233  
    234      sn_div       = 'dyna_grid_T'           ,       120         ,    'e3t'     ,  .true.   , .true. , 'yearly'  , ''               , ''       , '' 
    235      sn_empb      = 'dyna_grid_T'           ,       120         , 'sowaflupb'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , '' 
    236  
    237  
    238 More details can be found by inspecting the offline data manager at :forge:`browser/NEMO/trunk/src/OFF/dtadyn.F90` 
    239  
     267   sn_div  = 'dyna_grid_T', 120, 'e3t'      , .true., .true., 'yearly', '', '', '' 
     268   sn_empb = 'dyna_grid_T', 120, 'sowaflupb', .true., .true., 'yearly', '', '', '' 
     269 
     270 
     271More details can be found by inspecting the offline data manager in 
     272the routine ``./src/OFF/dtadyn.F90``. 
    240273 
    241274ORCA2_SAS_ICE 
    242275------------- 
    243276 
    244 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). 
    245  
    246 The standalone surface module allows surface elements such as sea-ice, iceberg drift, and surface fluxes to be run using prescribed model state fields. 
    247 It can profitably be used to compare different bulk formulae or adjust the parameters of a given bulk formula. 
     277ORCA2_SAS_ICE is a demonstrator of the Stand-Alone Surface (SAS) module and 
     278it relies on ORCA2 global ocean configuration (see ORCA2_ICE_PISCES_ for general description). 
     279 
     280The standalone surface module allows surface elements such as sea-ice, iceberg drift, and 
     281surface fluxes to be run using prescribed model state fields. 
     282It can profitably be used to compare different bulk formulae or 
     283adjust the parameters of a given bulk formula. 
    248284 
    249285More informations about SAS can be found in NEMO manual. 
    … …  
    252288------- 
    253289 
    254 SPITZ12 is a regional configuration around the Svalbard archipelago at 1/12° of horizontal resolution and 75 vertical levels. See `Rousset et al. (2015) <https://www.geosci-model-dev.net/8/2991/2015/>`_ for more details. 
    255  
    256 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. 
    257  
    258  
    259 .. _AGRIF_DEMO_v4.0.tar:          http://prodn.idris.fr/thredds/fileServer/ipsl_public/romr005/Online_forcing_archives/AGRIF_DEMO_v4.0.tar 
    260 .. _AMM12_v4.0.tar:               http://prodn.idris.fr/thredds/fileServer/ipsl_public/romr005/Online_forcing_archives/AMM12_v4.0.tar 
    261 .. _PISCES biogeochemical model:  http://www.geosci-model-dev.net/8/2465/2015 
    262 .. _INPUTS_PISCES_v4.0.tar:       http://prodn.idris.fr/thredds/fileServer/ipsl_public/romr005/Online_forcing_archives/INPUTS_PISCES_v4.0.tar 
    263 .. _ORCA2_OFF_v4.0.tar:           http://prodn.idris.fr/thredds/fileServer/ipsl_public/romr005/Online_forcing_archives/ORCA2_OFF_v4.0.tar 
    264 .. _ORCA2_ICE_v4.0.tar:           http://prodn.idris.fr/thredds/fileServer/ipsl_public/romr005/Online_forcing_archives/ORCA2_ICE_v4.0.tar 
    265 .. _INPUTS_SAS_v4.0.tar:          http://prodn.idris.fr/thredds/fileServer/ipsl_public/romr005/Online_forcing_archives/INPUTS_SAS_v4.0.tar 
    266 .. _INPUTS_C1D_PAPA_v4.0.tar:     http://prodn.idris.fr/thredds/fileServer/ipsl_public/romr005/Online_forcing_archives/INPUTS_C1D_PAPA_v4.0.tar 
    267 .. _SPITZ12_v4.0.tar:             http://prodn.idris.fr/thredds/fileServer/ipsl_public/romr005/Online_forcing_archives/SPITZ12_v4.0.tar 
    268  
    269 .. _COREII:                       http://prodn.idris.fr/thredds/catalog/ipsl_public/reee512/ORCA2_ONTHEFLY/FILLED_FILES/catalog.html 
    270  
     290``SPITZ12`` is a regional configuration around the Svalbard archipelago 
     291at 1/12° of horizontal resolution and 75 vertical levels. 
     292See `Rousset et al. (2015) <https://www.geosci-model-dev.net/8/2991/2015/>`_ for more details. 
     293 
     294This configuration references to year 2002, 
     295with atmospheric forcing provided every 2 hours using NCAR bulk formulae, 
     296while lateral boundary conditions for dynamical fields have 3 days time frequency. 
     297 
     298References 
     299========== 
     300 
     301.. bibliography:: configurations.bib 
     302   :all: 
     303   :style: unsrt 
     304   :labelprefix: C 
     305 
     306.. Links and substitutions 
     307 

  • NEMO/trunk/doc/rst/source/global.rst

    r10604 r10605  
    2929.. _IOIPSL: https://forge.ipsl.jussieu.fr/igcmg/browser/IOIPSL 
    3030.. _OASIS:  https://portal.enes.org/oasis 
    31 .. _XIOS:   https://forge.ipsl.jussieu.fr/ioserver 
    3231 
    3332.. NEMO 
    … …  
    3534.. _NEMO:          https://www.nemo-ocean.eu 
    3635.. _NEMO strategy: https://doi.org/10.5281/zenodo.1471663 
    37 .. _NEMO guide:    https://doi.org/10.5281/zenodo.1475325 
     36.. _NEMO guide:    :samp: https://doi.org/10.5281/zenodo.1475325 
    3837.. _NEMO manual:   https://doi.org/10.5281/zenodo.1464816 
    39 .. _SI3 manual:    https://doi.org/10.5281/zenodo.1471689 
    40 .. _TOP manual:    https://doi.org/10.5281/zenodo.1471700 
     38.. _SI3 manual:    :samp: https://doi.org/10.5281/zenodo.1471689 
     39.. _TOP manual:    :samp: https://doi.org/10.5281/zenodo.1471700 

  • NEMO/trunk/tests/README.rst

    r10554 r10605  
    33********************** 
    44 
     5The complete and up-to-date set of test cases is available on 
     6`NEMO test cases Github repository <http://github.com/NEMO-ocean/NEMO-examples>`_. 
     7 
     8Download it directly in the ``./tests`` root directory with 
     9 
     10.. code-block:: console 
     11 
     12   $ git clone http://github.com/NEMO-ocean/NEMO-examples 
     13 
    514.. contents:: 
    615   :local: 
    716 
    8 List 
    9 ==== 
     17Procedure 
     18========= 
    1019 
    11   The description below is a brief description of the test cases available in NEMO.  
     20Compile test cases 
     21------------------ 
     22 
     23The compilation of the test cases is very similar to the manner the reference configurations are compiled. 
     24If you are not familiar on how to compile NEMO, it is first recomended to read :doc:`the instructions <install>` 
     25 
     26| In the same manner as the ref. cfg are compiled with '-r' option, test cases can be compile by the use of makenemo with '-a' option. 
     27| Here an example to compile a copy named WAD2 of the wetting and drying test case (WAD) on the macport_osx architecture on 4 cores: 
     28 
     29.. code-block:: console 
     30 
     31   $ ./makenemo -n 'WAD2' -a 'WAD' -m 'macport_osx' -j '4' 
     32 
     33Run and analyse the test cases 
     34------------------------------ 
     35 
     36There no requirement of specific input file for the test_cases presented here. The XIOS xml input files and namelist are already setup correctly.  
     37For detailed description and Jupyter notebook, the reader is directed on 
     38the `NEMO test cases repository <http://github.com/NEMO-ocean/NEMO-examples>`_ 
     39 
     40The description below is a brief advertisement of some test cases. 
    1241 
    1342ICE_AGRIF 
    14 --------- 
     43========= 
    1544   
    1645  This test case illustrates the advection of an ice patch across an East/West and North/South periodic channel 
    … …  
    2453 
    2554VORTEX 
    26 ------ 
     55====== 
    2756   
    2857  This test case illustrates the propagation of an anticyclonic eddy over a Beta plan and a flat bottom. 
    … …  
    3766 
    3867ISOMIP 
    39 ------ 
     68====== 
    4069 
    4170  The purpose of this test case is to evaluate the impact of various schemes and new development with the iceshelf cavities circulation and melt. 
    … …  
    4877 
    4978LOCK_EXCHANGE 
    50 ------------- 
     79============= 
    5180 
    5281  The LOCK EXCHANGE experiment is a classical fluid dynamics experiment that has been adapted 
    … …  
    6190 
    6291OVERFLOW 
    63 -------- 
     92======== 
    6493 
    6594  The OVERFLOW experiment illustrates the impact of different choices of numerical schemes  
    … …  
    74103 
    75104WAD 
    76 --- 
     105=== 
    77106 
    78107  A set of simple closed basin geometries for testing the Wetting and drying capabilities.  
    … …  
    86115 
    87116CANAL 
    88 ----- 
     117===== 
    89118 
    90119  East-west periodic canal of variable size with several initial states and associated geostrophic currents (zonal jets or vortex). 
    … …  
    93122 
    94123ICE_ADV2D 
    95 --------- 
     124========= 
    96125   
    97126  This test case illustrates the advection of an ice patch across an East/West and North/South periodic channel 
    … …  
    104133 
    105134ICE_ADV1D 
    106 --------- 
     135========= 
    107136   
    108137  This experiment is the classical Schar & Smolarkiewicz (1996) test case :cite:`SCHAR1996`, 
    … …  
    112141  The purpose of this configuration is to test the caracteristics of advection schemes available in the sea-ice code 
    113142  (for now, Prather and Ultimate-Macho from 1st to 5th order), 
    114   especially the constitency between concentration, thickness and volume, and the preservation of initial shapes. 
    115    
    116    
    117  
    118    
    119 Compile test cases 
    120 ================== 
    121  
    122 The compilation of the test cases is very similar to the manner the reference configurations are compiled. 
    123 If you are not familiar on how to compile NEMO, it is first recomended to read :doc:`the instructions <install>` 
    124  
    125 | In the same manner as the ref. cfg are compiled with '-r' option, test cases can be compile by the use of makenemo with '-a' option. 
    126  
    127 | Here an example to compile a copy named WAD2 of the wetting and drying test case (WAD) on the macport_osx architecture on 4 cores: 
    128  
    129 .. code-block:: console 
    130   
    131    $ ./makenemo -n WAD2 -a WAD -m macport_osx -j 4 
    132  
    133 Run and analyse the test cases 
    134 ============================== 
    135  
    136 There no requirement of specific input file for the test_cases presented here. The XIOS xml input files and namelist are already setup correctly.  
    137 For detailed description and Jupyter notebook, the reader is directed on 
    138 the `NEMO test cases repository <http://github.com/NEMO-ocean/NEMO-examples>`_ 
     143  especially the constitency between concentration, thickness and volume, and the preservation of initial shapes.   
    139144 
    140145References 
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