On line biogeochemistry coarsening
Last edition: Wikinfo(changed_ts)? by Wikinfo(changed_by)?
Work in progress
Presentation
A capacity of coarsening physics to force a BGC model coupled to NEMO has been developed in NEMO_3.6, in an associated branch. 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.
This capacity is not included in the 3_6 release itself, but is available in a specific associated branch. This branch is regularly phased with the NEMO_3.6. An associated ticket to follow evolution is here.
A presentation is available here, where the methodology is presented.
What is available and working for now in this version
To be completed
Description of the successful validation tests
To be completed
What is not working yet with on line coarsening of biogeochemistry
To be completed
should include precise explanation on MPI decomposition problems too
How to set up and use on line biogeochemistry
Extract the on line biogeochemistry branch
To get the appropriate source code with the on line coarsening of biogeochemistry feature:
svn co https://forge.ipsl.jussieu.fr/nemo/browser/NEMO/branches/2018/dev_r5003_MERCATOR6_CRS
How to activate coarsening ?
To activate the coarsening, key_crs should be added to list of cpp keys. This key will only activate the coarsening of dynamics.
Some parameters are available in the namelist_cfg:
! passive tracer coarsened online simulations !----------------------------------------------------------------------- nn_factx = 3 ! Reduction factor of x-direction nn_facty = 3 ! Reduction factor of y-direction nn_msh_crs = 0 ! create (=1) a mesh file or not (=0) nn_crs_kz = 3 ! 0, volume-weighted MEAN of KZ ! 1, MAX of KZ ! 2, MIN of KZ ! 3, 10^(MEAN(LOG(KZ)) ! 4, MEDIANE of KZ ln_crs_wn = .false. ! wn coarsened (T) or computed using horizontal divergence ( F ) ! ! ln_crs_top = .true. !coarsening online for the bio / |
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Choice of operator to coarsene KZ
A 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.
Some results can be found [xxx here]
Example of xml files to output coarsened variables with XIOS
In the iodef.xml file, a "nemo" context is defined and some variable defined in file_def.xml are writted on the ocean-dynamic grid. To write variables on the coarsened grid, and in particular the passive tracers, a "nemo_crs" context should be defined in iodef.xml and the associated variable are listed in file_crs_def.xml .
Passive tracers tracers initial conditions
When initial conditions are provided in NetCDF files, the field might be:
- on the coarsened grid
- or they can be on another grid and interpolated on-the-fly . Example of namelist for PISCES :
!----------------------------------------------------------------------- &namtrc_dta ! Initialisation from data input file !----------------------------------------------------------------------- ! sn_trcdta(1) = 'DIC_REG1' , -12 , 'DIC' , .false. , .true. , 'yearly' , 'reshape_REG1toeORCA075_bilin.nc' , '' , '' sn_trcdta(2) = 'ALK_REG1' , -12 , 'ALK' , .false. , .true. , 'yearly' , 'reshape_REG1toeORCA075_bilin.nc' , '' , '' sn_trcdta(3) = 'O2_REG1' , -1 , 'O2' , .true. , .true. , 'yearly' , 'reshape_REG1toeORCA075_bilin.nc' , '' , '' sn_trcdta(5) = 'PO4_REG1' , -1 , 'PO4' , .true. , .true. , 'yearly' , 'reshape_REG1toeORCA075_bilin.nc' , '' , '' sn_trcdta(7) = 'Si_REG1' , -1 , 'Si' , .true. , .true. , 'yearly' , 'reshape_REG1toeORCA075_bilin.nc' , '' , '' sn_trcdta(10) = 'DOC_REG1' , -12 , 'DOC' , .false. , .true. , 'yearly' , 'reshape_REG1toeORCA075_bilin.nc' , '' , '' sn_trcdta(14) = 'Fe_REG1' , -12 , 'Fe' , .false. , .true. , 'yearly' , 'reshape_REG1toeORCA075_bilin.nc' , '' , '' sn_trcdta(23) = 'NO3_REG1' , -1 , 'NO3' , .true. , .true. , 'yearly' , 'reshape_REG1toeORCA075_bilin.nc' , '' , '' rn_trfac(1) = 1.0e-06 ! multiplicative factor rn_trfac(2) = 1.0e-06 ! - - - - rn_trfac(3) = 44.6e-06 ! - - - - rn_trfac(5) = 122.0e-06 ! - - - - rn_trfac(7) = 1.0e-06 ! - - - - rn_trfac(10) = 1.0e-06 ! - - - - rn_trfac(14) = 1.0e-06 ! - - - - rn_trfac(23) = 7.6e-06 ! - - - - cn_dir = './' ! root directory for the location of the data files
PISCES forcing files
They might be on the coarsened grid.
Perspectives
For the future, a few options are on the table to implement coarsening for biogeochemistry in 4.0 and future releases. Those will be discussed in Autumn 2018
Attachments (4)
- crs_wiki_1.1.pdf (350.3 KB) - added by cbricaud 8 years ago.
- iodef.xml (8.0 KB) - added by cbricaud 8 years ago.
- file_def.xml (5.5 KB) - added by cbricaud 8 years ago.
- file_crs_def.xml (5.5 KB) - added by cbricaud 8 years ago.
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