Changes between Version 22 and Version 23 of Users/Model Interfacing/AGRIF


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Timestamp:
2018-08-31T15:11:21+02:00 (2 years ago)
Author:
nicolasmartin
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  • Users/Model Interfacing/AGRIF

    v22 v23  
    2727== Definition of the grid hierarchy 
    2828 
    29 An additional text file "AGRIF_FixedGrids.in" is required at run time. This is where the grid hierarchy is defined. An example of such a file, here taken from the VORTEX test case, is given below:  
     29An additional text file `AGRIF_FixedGrids.in` is required at run time. This is where the grid hierarchy is defined. An example of such a file, here taken from the [source:/NEMO/trunk/tests/VORTEX@10075 'VORTEX' test case], is given below:  
    3030 
    31 {{{ 
    32 1 
    33 19 38 19 38 3 3 3 
    34 0 
    35 }}} 
     31[[IncludeSource(/NEMO/trunk/tests/VORTEX/EXPREF/AGRIF_FixedGrids.in, rev=9787, line_numbers=0)]] 
    3632 
    37 The first line indicates the number of zooms (1). The second line contains the starting and ending indices in both directions on the root grid (19 38 19 38) followed by the space and time refinement factors (3 3 3). The last line is the number of child grid nested in the refined region (0). A more complex example with telescoping grids can be found below and in the cfgs/AGRIF_DEMO/EXPREF reference configuration directory (NEMO 4.0 only).  
     33The first line indicates the number of zooms (1). The second line contains the starting and ending indices in both directions on the root grid (19 38 19 38) followed by the space and time refinement factors (3 3 3). The last line is the number of child grid nested in the refined region (0). A more complex example with telescoping grids can be found below and in the [source:/NEMO/trunk/cfgs/AGRIF_DEMO@10075 'AGRIF_DEMO' reference configuration directory] (NEMO 4.0 only).  
    3834 
    3935[[span(''Add some plots here with grid staggering and positioning ?'', style=background-color:lime)]] 
     
    4440== Preprocessing 
    4541 
    46 Knowing the refinement factors and area, a pre-processing tool (utils/tools/NESTING directory) may help to create needed input files (mesh file, restart, climatological and forcing files). The key is to ensure volume matching near the child grid interface, a step done by invoking the Agrif_create_bathy.exe program. You may use the namelists provided in the utils/tools/NESTING directory as a guide. These correspond to the namelists used to create AGRIF_DEMO inputs.  
     42Knowing the refinement factors and area, a [source:/utils/tools/NESTING@10029 pre-processing tool] may help to create needed input files (mesh file, restart, climatological and forcing files). The key is to ensure volume matching near the child grid interface, a step done by invoking the Agrif_create_bathy.exe program. You may use the namelists provided in the `NESTING` directory as a guide. These correspond to the namelists used to create `AGRIF_DEMO` inputs.  
    4743 
    4844 
    4945== Namelist options 
    5046 
    51 Each child grid expects to read its own namelist so that different numerical choices can be made (these should be stored in the form 1_namelist_cfg, 2_namelist_cfg, etc... according to their rank in the grid hierarchy). Consistent time steps and number of steps with the chosen time refinement have to be provided. Specific to AGRIF is the following block: 
     47Each child grid expects to read its own namelist so that different numerical choices can be made (these should be stored in the form `1_namelist_cfg`, `2_namelist_cfg`, etc... according to their rank in the grid hierarchy). Consistent time steps and number of steps with the chosen time refinement have to be provided. Specific to AGRIF is the following block: 
    5248 
    5349[[IncludeSource(/NEMO/trunk/doc/namelists/namagrif, rev=10075, line_numbers=0, mimetype=text/x-fortran)]] 
     
    8379 
    8480 * [[span(''Important notice concerning the change of ghost cells number:'', style=background-color:yellow)]] 
    85 The default number of ghost cells (i.e. the number of cells that serve as open boundary data provision) has been increased from 1 to 3 in NEMO 4.0. This allows to properly handle boundary conditions for numerical schemes that have a discretization order greater than 2. On the user point of view this does not change anything++ except in the definition of level 1 grids in the AGRIF_FixedGrids.in file. In order to retrieve exactly the position of a nested grid in NEMO 4.0 one has to shift indices by 2 points to the south-west. Taking the VORTEX example above for NEMO 4.0, the "old" NEMO 3.6 corresponding file would contain: 
     81The default number of ghost cells (i.e. the number of cells that serve as open boundary data provision) has been increased from 1 to 3 in NEMO 4.0. This allows to properly handle boundary conditions for numerical schemes that have a discretization order greater than 2. On the user point of view this does not change anything++ except in the definition of level 1 grids in the `AGRIF_FixedGrids.in` file. In order to retrieve exactly the position of a nested grid in NEMO 4.0 one has to shift indices by 2 points to the south-west. Taking the `VORTEX` example above for NEMO 4.0, the "old" NEMO 3.6 corresponding file would contain: 
    8682 
    87 {{{ 
    88 1 
    89 21 40 21 40 3 3 3 
    90 0 
    91 }}} 
     83[[IncludeSource(/NEMO/releases/release-3.6/NEMOGCM/CONFIG/ORCA2_LIM/EXP00/AGRIF_FixedGrids.in, rev=9594)]] 
    9284 
    9385++ Output files are now greater by 4 points in each direction. 
    9486 
    9587 
    96 === New reference configuration with AGRIF: AGRIF_DEMO  
     88=== New reference configuration with AGRIF: `AGRIF_DEMO` 
    9789 
    9890{{{#!table class='' style='width: 66%' 
     
    10597   }}} 
    10698   {{{#!td 
    107 AGRIF_DEMO is based on the [wiki:Users/ReferenceConfigurations/ORCA2_LIM3_PISCES] global 2° configuration but it includes 3 online nested grids that demonstrate the overall capabilities of AGRIF in a realistic context, including nesting sea ice models. 
     99`AGRIF_DEMO` is based on the [wiki:Users/ReferenceConfigurations/ORCA2_LIM3_PISCES ORCA2_LIM3_PISCES] global 2° configuration but it includes 3 online nested grids that demonstrate the overall capabilities of AGRIF in a realistic context, including nesting sea ice models. 
    108100 
    109101The configuration includes a 1:1 grid in the Pacific and two successively nested grids with odd and even refinement ratios over the Arctic ocean. The finest grid spanning the whole Svalbard archipelago is of particular interest to check that sea ice coupling is done properly. The 1:1 grid, used alone, is used as a benchmark to check that the solution is not corrupted by grid exchanges. 
     
    115107Corresponding AGRIF_FixedGrids.in file is given by: 
    116108 
    117 {{{ 
    118 2 
    119 42 82 49 91 1 1 1 
    120 122 153 110 143 4 4 4 
    121 0 
    122 1 
    123 38 80 71 111 3 3 3 
    124 0 
    125 }}} 
     109[[IncludeSource(/NEMO/trunk/cfgs/AGRIF_DEMO/EXPREF/AGRIF_FixedGrids.in, rev=9775, line_numbers=0)]] 
    126110 
    127111 
    128112=== New tests cases demonstrating some major features of AGRIF with NEMO: 
    129113 
    130  * tests/ICEDYN:  
     114 * `tests/ICEDYN`:  
    131115 
    132116[[span(''Clement to add an illustration here ?'', style=background-color:lime)]] 
     
    134118This is an East-west + north-south periodic channel. The configuration includes an AGRIF zoom (1:3) in the middle of the basin to test how an ice patch is advected through it but one can also test the advection schemes (Prather and Ultimate-Macho) by removing the key_agrif in the cpp keys. 
    135119 
    136  * tests/VORTEX: 
     120 * `tests/VORTEX`: 
    137121 
    138122This test case illustrates the propagation of an anticyclonic eddy over a Beta plan and a flat bottom. It is implemented here with an online refined subdomain (1:3) out of which the vortex propagates. It serves as a benchmark for quantitative estimates of nesting errors as in Debreu et al. (2012), Penven et al. (2006) or Spall and Holland (1991). The animation below (sea level anomaly in meters) illustrates with two 1:2 successively nested grids how the vortex smoothly propagates out of the refined grids.  
    139123  
    140124{{{#!imagebox 
    141 [[Image(wiki:Users/ModelInterfacing/AGRIF:VORTEX_anim.gif,width=600)]] 
     125[[Image(VORTEX_anim.gif,width=600)]] 
    142126}}} 
    143127