Changes between Version 23 and Version 24 of Users/Model Interfacing/Biogeochemistry Coarsening


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Timestamp:
2017-05-31T21:34:53+02:00 (3 years ago)
Author:
nicolasmartin
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  • Users/Model Interfacing/Biogeochemistry Coarsening

    v23 v24  
    11= Trough grid refinement (AGRIF nesting & coarsening) 
     2 
     3[[PageOutline(2-3)]] 
    24 
    35Last edition: '''[[Wikinfo(changed_ts)]]''' by '''[[Wikinfo(changed_by)]]''' 
     
    79}}} 
    810 
    9 = Coarsening of physics for biogeochemistery model = 
     11== Coarsening of physics for biogeochemistery model 
    1012 
    11 == Presentation == 
     13=== Presentation 
    1214 
    13 A capacity of coarsening physics to force a BGC model coupled to NEMO has been developped in NEMO_3.6. This capacity allow to run 'online' a BGC model coupled to OPA-LIM with a lower resolution, to reduce the CPU coast of the BGC model, while preserving the effective resolution of the dynamics. 
     15A capacity of coarsening physics to force a BGC model coupled to NEMO has been developed in NEMO_3.6. This capacity allow to run 'online' a BGC model coupled to OPA-LIM with a lower resolution, to reduce the CPU coast of the BGC model, while preserving the effective resolution of the dynamics. 
    1416 
    15  
    16 This capacity is not included in the [browser:branches/2015/nemo_v3_6_STABLE/NEMOGCM NEMO_3.6] , but is available in a specific [browser:branches/2015/dev_r5003_MERCATOR6_CRS branch] of the 3.6 stable. This branch is regularly phazed with the NEMO_3.6. 
     17This capacity is not included in the [browser:branches/2015/nemo_v3_6_STABLE/NEMOGCM NEMO_3.6] , but is available in a specific [browser:branches/2015/dev_r5003_MERCATOR6_CRS branch] of the 3.6 stable. This branch is regularly phased with the NEMO_3.6. 
    1718An associated ticket to follow evolution is  [ticket:1426 here]. 
    1819 
    1920A presentation is available [attachment:crs_wiki_1.1.pdf​ here], where the methodology is presented. 
     21[[PdfImg(crs_wiki_1.1.pdf)]] 
    2022 
    21  
    22 == How to activate coarsening ? == 
     23=== How to activate coarsening ? 
    2324 
    2425To activate the coarsening, key_crs should be added to list of cpp keys. This key will only activate the coarsening of dynamics. 
     
    4647{{{#!td 
    4748- '''Only [[span(nn_factx, style=color: #B8860B)]] = [[span(nn_facty, style=color: #B8860B)]] = 3''' is available and the coarsening only works for grids with a T-pivot point for the north-fold lateral boundary condition( ORCA025, ORCA12,ORCA36,...). 
    48  
    4949- '''[[span(nn_msh_crs, style=color: #B8860B)]]  = 1''' : will activate the generation of the coarsened grid meshmask. 
    50  
    5150- '''[[span(nn_crs_kz, style=color: #B8860B)]]''' : is the operator to coarsen the vertical mixing coefficient.  
    52  
    5351- '''[[span(ln_crs_wn, style=color: #B8860B)]]''' : 
    5452  - when key_vvl is activated, this logical has no effect;  the coarsened vertical velocities are computed using horizontal divergence. 
     
    5957}}} 
    6058 
    61 == Choice of operator to coarsene KZ ==  
     59=== Choice of operator to coarsene KZ 
    6260 
    6361A sensiblity test has been done with an Age tracer to compare the different operators. The 3 and 4 options seems to provide the best results. 
     
    6563Some results can be found [xxx here] 
    6664 
    67 == Example of xml files to output coarsened variables with XIOS ==  
    68  
     65=== Example of xml files to output coarsened variables with XIOS 
    6966 
    7067In the [attachment:iodef.xml iodef.xml]  file, a "nemo" context is defined and some variable defined in [attachment:file_def.xml file_def.xml] are writted on the ocean-dynamic grid.   
    7168To write variables on the coarsened grid, and in particular the passive tracers, a "nemo_crs" context should be defined in  [attachment:iodef.xml iodef.xml] and the associated variable are listed in [attachment:file_crs_def.xml file_crs_def.xml ]. 
    7269 
     70=== Passive tracers tracers initial conditions 
    7371 
    74  
    75 == Passive tracers tracers initial conditions   ==  
    76  
    77 When initial conditions are provided in netcdf files, the field might be:[[BR]] 
    78  
    79  - on the coarsened grid [[BR]] 
    80  
    81  - or they can be on another grid and interpolated  [wiki:Users/SetupNewConfiguration/Weight-creator on-the-fly ]. 
     72When initial conditions are provided in NetCDF files, the field might be: 
     73 - on the coarsened grid 
     74 - or they can be on another grid and interpolated [wiki:Users/SetupNewConfiguration/Weight-creator on-the-fly ]. 
    8275   Example of namelist for PISCES : 
    8376 
    84  
    85 {{{ 
     77{{{#!f 
    8678!----------------------------------------------------------------------- 
    8779&namtrc_dta      !    Initialisation from data input file 
     
    108100}}} 
    109101 
     102=== PISCES forcing files 
    110103 
    111  
    112 == PISCES forcing files  ==  
    113104They might be on the coarsened grid.