Changeset 11735


Ignore:
Timestamp:
2019-10-18T19:50:58+02:00 (11 months ago)
Author:
nicolasmartin
Message:

Review README for test cases (a gif file mentioned to illustrate CANAL is missing)

Location:
NEMO/trunk
Files:
4 edited

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  • NEMO/trunk/cfgs/README.rst

    r11734 r11735  
    1 ************************ 
    2 Reference configurations 
    3 ************************ 
     1******************************** 
     2Run the Reference configurations 
     3******************************** 
    44 
    55.. todo:: 
  • NEMO/trunk/doc/rst/source/conf.py

    r11734 r11735  
    252252extlinks = { 
    253253   'doi'    : ('https://doi.org/%s'                                                    , 'doi:'), 
    254    'doxy'   : ('https://forge.ipsl.jussieu.fr/nemo/chrome/site/doc/NEMO/manual/html/%s',   None), 
    255    'forge'  : ('https://forge.ipsl.jussieu.fr/nemo/%s'                                 ,   None), 
    256    'gmd'    : ('https://www.geosci-model-dev.net/%s'                                   ,   None), 
    257    'github' : ('https://github.com/%s'                                                 ,   None), 
    258    'xios'   : ('https://forge.ipsl.jussieu.fr/ioserver/%s'                             ,   None), 
    259    'website': ('https://www.nemo-ocean.eu/%s'                                          ,   None), 
    260    'zenodo' : ('https://zenodo.org/publication/%s'                                     ,   None) 
     254   'doxy'   : ('https://forge.ipsl.jussieu.fr/nemo/chrome/site/doc/NEMO/manual/html/%s', None  ), 
     255   'forge'  : ('https://forge.ipsl.jussieu.fr/nemo/%s'                                 , None  ), 
     256   'gmd'    : ('https://www.geosci-model-dev.net/%s'                                   , None  ), 
     257   'github' : ('https://github.com/NEMO-ocean/%s'                                      , None  ), 
     258   'xios'   : ('https://forge.ipsl.jussieu.fr/ioserver/%s'                             , None  ), 
     259   'website': ('https://www.nemo-ocean.eu/%s'                                          , None  ), 
     260   'zenodo' : ('https://zenodo.org/publication/%s'                                     , None  ) 
    261261} 
    262262 
  • NEMO/trunk/doc/rst/source/global.rst

    r11734 r11735  
    4242.. _RST man: https://www.sphinx-doc.org/en/master/usage/restructuredtext/index.html 
    4343.. _PAPA station: http://www.pmel.noaa.gov/OCS/Papa/index-Papa.shtml 
     44.. _ISOMIP: http://staff.acecrc.org.au/~bkgalton/ISOMIP/test_cavities.pdf 
    4445 
    4546.. DOI 
  • NEMO/trunk/tests/README.rst

    r11734 r11735  
    77 
    88 
    9 The complete and up-to-date set of test cases is available on 
    10 `NEMO test cases Github repository <http://github.com/NEMO-ocean/NEMO-examples>`_. 
    11  
    12 Download it directly in the ``./tests`` root directory with 
    13  
    14 .. code-block:: console 
    15  
    16    $ git clone http://github.com/NEMO-ocean/NEMO-examples 
    17  
    189.. contents:: 
    1910   :local: 
    20  
    21 Procedure 
    22 ========= 
    23  
    24 Compile test cases 
    25 ------------------ 
    26  
    27 The compilation of the test cases is very similar to the manner the reference configurations are compiled. 
    28 If you are not familiar on how to compile NEMO, it is first recomended to read :doc:`the instructions <install>` 
    29  
    30 | 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. 
    31 | 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: 
     11   :depth: 1 
     12 
     13Installation 
     14============ 
     15 
     16Download 
     17-------- 
     18 
     19| The complete and up-to-date set of test cases is available on 
     20  :github:`NEMO test cases repository <NEMO-examples>`. 
     21| Download it directly into the :file:`./tests` root directory with 
    3222 
    3323.. code-block:: console 
    3424 
    35    $ ./makenemo -n 'WAD2' -a 'WAD' -m 'macport_osx' -j '4' 
    36  
    37 Run and analyse the test cases 
    38 ------------------------------ 
    39  
    40 There no requirement of specific input file for the test_cases presented here. The XIOS xml input files and namelist are already setup correctly. 
     25   $ git clone http://github.com/NEMO-ocean/NEMO-examples 
     26 
     27Compilation 
     28----------- 
     29 
     30The compilation of the test cases is very similar to 
     31the manner the reference configurations are compiled. 
     32If you are not familiar on how to compile NEMO, 
     33it is first recomended to read :doc:`the instructions <install>`. 
     34 
     35| As the reference configurations are compiled with ``-r`` option, 
     36  test cases can be compiled by the use of :file:`makenemo` with ``-a`` option. 
     37| Here an example to compile a copy named WAD2 of the wetting and drying test case (WAD): 
     38 
     39.. code-block:: console 
     40 
     41   $ ./makenemo -n 'WAD2' -a 'WAD' -m 'my_arch' -j '4' 
     42 
     43Run and analysis 
     44---------------- 
     45 
     46There no requirement of specific input file for the test_cases presented here. 
     47The XIOS xml input files and namelist are already setup correctly. 
    4148For detailed description and Jupyter notebook, the reader is directed on 
    42 the `NEMO test cases repository <http://github.com/NEMO-ocean/NEMO-examples>`_ 
     49the :github:`NEMO test cases repository <NEMO-examples>` 
    4350 
    4451The description below is a brief advertisement of some test cases. 
    4552 
     53List of test cases 
     54================== 
     55 
    4656ICE_AGRIF 
    47 ========= 
    48  
    49   This test case illustrates the advection of an ice patch across an East/West and North/South periodic channel 
    50   over a slab ocean (i.e. one ocean layer), and with an AGRIF zoom (1:3) in the center 
    51   The purpose of this configuration is to test the advection of the ice patch in 
    52   and across the AGRIF boundary 
    53   One can either impose ice velocities or ice-atm. stresses and let rheology define velocities 
    54   (see README for details) 
    55  
    56   .. image:: _static/ICE_AGRIF_UDIAG_43days_UM5.gif 
     57--------- 
     58 
     59.. figure:: _static/ICE_AGRIF_UDIAG_43days_UM5.gif 
     60   :width: 200px 
     61   :align: left 
     62 
     63   .. 
     64 
     65| This test case illustrates the advection of an ice patch across 
     66  an East/West and North/South periodic channel over a slab ocean (i.e. one ocean layer), 
     67  and with an AGRIF zoom (1:3) in the center. 
     68| The purpose of this configuration is to 
     69  test the advection of the ice patch in and across the AGRIF boundary. 
     70  One can either impose ice velocities or ice-atm. 
     71  Stresses and let rheology define velocities (see :file:`README` for details) 
    5772 
    5873VORTEX 
    59 ====== 
    60  
    61   This test case illustrates the propagation of an anticyclonic eddy over a Beta plan and a flat bottom. 
    62   It is implemented here with an online refined subdomain (1:3) out of which the vortex propagates. 
    63   It serves as a benchmark for quantitative estimates of nesting errors as in Debreu et al. (2012) :cite:`DEBREU2012`, 
    64   Penven et al. (2006) :cite:`PENVEN2006` or Spall and Holland (1991) :cite:`SPALL1991`. 
    65  
    66   The animation below (sea level anomaly in meters) illustrates with two 1:2 successively nested grids how 
    67   the vortex smoothly propagates out of the refined grids. 
    68  
    69   .. image:: _static/VORTEX_anim.gif 
     74------ 
     75 
     76.. figure:: _static/VORTEX_anim.gif 
     77   :width: 200px 
     78   :align: right 
     79 
     80   .. 
     81 
     82This test case illustrates the propagation of an anticyclonic eddy over a Beta plan and a flat bottom. 
     83It is implemented here with an online refined subdomain (1:3) out of which the vortex propagates. 
     84It serves as a benchmark for quantitative estimates of nesting errors as in :cite:`DEBREU2012`, 
     85:cite:`PENVEN2006` or :cite:`SPALL1991`. 
     86 
     87The animation (sea level anomaly in meters) illustrates with 
     88two 1:2 successively nested grids how the vortex smoothly propagates out of the refined grids. 
    7089 
    7190ISOMIP 
    72 ====== 
    73  
    74   The purpose of this test case is to evaluate the impact of various schemes and new development with the iceshelf cavities circulation and melt. 
    75   This configuration served as initial assesment of the ice shelf module in Losh et al. (2008) :cite:`LOSCH2008` and Mathiot et al. (2017) :cite:`MATHIOT2017`. 
    76   The default setup is the one described `here <http://staff.acecrc.org.au/~bkgalton/ISOMIP/test_cavities.pdf>`_. 
    77  
    78   The figure below (meridional overturning circulation) illustrates the circulation generated after 10000 days by the ice shelf melting (ice pump). 
    79  
    80   .. image:: _static/ISOMIP_moc.png 
     91------ 
     92 
     93.. figure:: _static/ISOMIP_moc.png 
     94   :width: 200px 
     95   :align: left 
     96 
     97   .. 
     98 
     99| The purpose of this test case is to evaluate the impact of various schemes and new development with 
     100  the iceshelf cavities circulation and melt. 
     101  This configuration served as initial assesment of the ice shelf module in :cite:`LOSCH2008` and 
     102  :cite:`MATHIOT2017`. 
     103  The default setup is the one described |ISOMIP|_. 
     104| The figure (meridional overturning circulation) illustrates 
     105  the circulation generated after 10000 days by the ice shelf melting (ice pump). 
     106 
     107.. |ISOMIP| replace:: here 
    81108 
    82109LOCK_EXCHANGE 
    83 ============= 
    84  
    85   The LOCK EXCHANGE experiment is a classical fluid dynamics experiment that has been adapted 
    86   by Haidvogel and Beckmann (1999) :cite:`HAIDVOGEL1999` for testing advection schemes in ocean circulation models. 
    87   It has been used by several authors including Burchard and Bolding (2002) :cite:`BURCHARD2002` and Ilicak et al. (2012) :cite:`ILICAK2012`. 
    88   The LOCK EXCHANGE experiment can in particular illustrate the impact of different choices of numerical schemes 
    89   and/or subgrid closures on spurious interior mixing. 
    90  
    91   Below the animation of the LOCK_EXCHANGE test case using the advection scheme FCT4 (forth order) for tracer and ubs for dynamics. 
    92  
    93   .. image:: _static/LOCK-FCT4_flux_ubs.gif 
     110------------- 
     111 
     112.. figure:: _static/LOCK-FCT4_flux_ubs.gif 
     113   :width: 200px 
     114   :align: right 
     115 
     116   .. 
     117 
     118| The LOCK EXCHANGE experiment is a classical fluid dynamics experiment that has been adapted 
     119  by :cite:`HAIDVOGEL1999` for testing advection schemes in ocean circulation models. 
     120  It has been used by several authors including :cite:`BURCHARD2002` and :cite:`ILICAK2012`. 
     121  The LOCK EXCHANGE experiment can in particular illustrate 
     122  the impact of different choices of numerical schemes and/or subgrid closures on 
     123  spurious interior mixing. 
     124| Here the animation of the LOCK_EXCHANGE test case using 
     125  the advection scheme FCT4 (forth order) for tracer and ubs for dynamics. 
    94126 
    95127OVERFLOW 
    96 ======== 
    97  
    98   The OVERFLOW experiment illustrates the impact of different choices of numerical schemes 
    99   and/or subgrid closures on spurious interior mixing close to bottom topography. 
    100   The OVERFLOW experiment is adapted from the non-rotating overflow configuration described 
    101   in Haidvogel and Beckmann (1999) :cite:`HAIDVOGEL1999` and further used by Ilicak et al. (2012) :cite:`ILICAK2012`. 
    102   Here we can assess the behaviour of the second-order tracer advection scheme FCT2 and fortht-order FCT4, z-coordinate and sigma coordinate (...). 
    103  
    104   Below the animation of the OVERFLOW test case in sigma coordinate with the forth-order advection scheme FCT4. 
    105  
    106   .. image:: _static/OVF-sco_FCT4_flux_cen-ahm1000.gif 
     128-------- 
     129 
     130.. figure:: _static/OVF-sco_FCT4_flux_cen-ahm1000.gif 
     131   :width: 200px 
     132   :align: left 
     133 
     134   .. 
     135 
     136| The OVERFLOW experiment illustrates the impact of different choices of numerical schemes and/or 
     137  subgrid closures on spurious interior mixing close to bottom topography. 
     138  The OVERFLOW experiment is adapted from the non-rotating overflow configuration described in 
     139  :cite:`HAIDVOGEL1999` and further used by :cite:`ILICAK2012`. 
     140  Here we can assess the behaviour of the second-order tracer advection scheme FCT2 and 
     141  forth-order FCT4, z-coordinate and sigma coordinate (...). 
     142| Here the animation of the OVERFLOW test case in sigma coordinate with 
     143  the forth-order advection scheme FCT4. 
    107144 
    108145WAD 
    109 === 
    110  
    111   A set of simple closed basin geometries for testing the Wetting and drying capabilities. 
    112   Examples range from a closed channel with EW linear bottom slope to a parabolic EW channel with a Gaussian ridge. 
    113  
    114   Below the animation of the test case 7. This test case is a simple linear slope with a mid-depth shelf with an open boundary forced with a sinusoidally varying ssh. 
    115   This test case has been introduced to emulate a typical coastal application with a tidally forced open boundary with an adverse SSH gradient that, when released, creates a surge up the slope. 
    116   The parameters are chosen such that the surge rises above sea-level before falling back and oscillating towards an equilibrium position 
    117  
    118   .. image:: _static/wad_testcase_7.gif 
     146--- 
     147 
     148.. figure:: _static/wad_testcase_7.gif 
     149   :width: 200px 
     150   :align: right 
     151 
     152   .. 
     153 
     154| A set of simple closed basin geometries for testing the Wetting and drying capabilities. 
     155  Examples range from a closed channel with EW linear bottom slope to 
     156  a parabolic EW channel with a Gaussian ridge. 
     157| Here the animation of the test case 7. 
     158  This test case is a simple linear slope with a mid-depth shelf with 
     159  an open boundary forced with a sinusoidally varying ssh. 
     160  This test case has been introduced to emulate a typical coastal application with 
     161  a tidally forced open boundary with an adverse SSH gradient that, 
     162  when released, creates a surge up the slope. 
     163  The parameters are chosen such that 
     164  the surge rises above sea-level before falling back and oscillating towards an equilibrium position. 
    119165 
    120166CANAL 
    121 ===== 
    122  
    123   East-west periodic canal of variable size with several initial states and associated geostrophic currents (zonal jets or vortex). 
    124  
    125   .. image::_static/CANAL_image.gif 
     167----- 
     168 
     169.. figure:: _static/CANAL_image.gif 
     170   :width: 200px 
     171   :align: left 
     172 
     173   .. 
     174 
     175East-west periodic canal of variable size with several initial states and 
     176associated geostrophic currents (zonal jets or vortex). 
    126177 
    127178ICE_ADV2D 
    128 ========= 
    129  
    130   This test case illustrates the advection of an ice patch across an East/West and North/South periodic channel 
    131   over a slab ocean (i.e. one ocean layer). 
     179--------- 
     180 
     181| This test case illustrates the advection of an ice patch across 
     182  an East/West and North/South periodic channel over a slab ocean (i.e. one ocean layer). 
    132183  The configuration is similar to ICE_AGRIF, except for the AGRIF zoom. 
    133   The purpose of this configuration is to test the advection schemes available in the sea-ice code 
     184| The purpose of this configuration is to test the advection schemes available in the sea-ice code 
    134185  (for now, Prather and Ultimate-Macho from 1st to 5th order), 
    135186  especially the occurence of overshoots in ice thickness 
    136187 
    137  
    138188ICE_ADV1D 
    139 ========= 
    140  
    141   This experiment is the classical Schar & Smolarkiewicz (1996) test case :cite:`SCHAR1996`, 
    142   which has been used in :cite:`LIPSCOMB2004`, 
    143   and in which very specific shapes of ice concentration, thickness and volume converge toward the center of a basin. 
     189--------- 
     190 
     191| This experiment is the classical :cite:`SCHAR1996` test case , 
     192  which has been used in :cite:`LIPSCOMB2004`, and in which very specific shapes of ice concentration, 
     193  thickness and volume converge toward the center of a basin. 
    144194  Convergence is unidirectional (in x) while fields are homogeneous in y. 
    145   The purpose of this configuration is to test the caracteristics of advection schemes available in the sea-ice code 
     195| The purpose of this configuration is to 
     196  test the caracteristics of advection schemes available in the sea-ice code 
    146197  (for now, Prather and Ultimate-Macho from 1st to 5th order), 
    147   especially the constitency between concentration, thickness and volume, and the preservation of initial shapes. 
     198  especially the constitency between concentration, thickness and volume, 
     199  and the preservation of initial shapes. 
    148200 
    149201.. rubric:: References 
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