TOC(heading=AGRIF,AGRIF/*, depth=1)?

AGRIF

Working group leader (and responsible for wiki pages): Laurent Debreu

Members of the working group:

• Laurent Debreu
• Sébastien Masson
• Jérôme Chanut
• Simona Flavoni
• Rachel Furner

Objectives:

Precise the needs on their application. Involved in defining priorities in workplan

Agenda:

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List of past/current/planned applications of NEMO with AGRIF (with associated publications):

1) Applications in GEOMAR-Kiel (Germany)

Agulhas current, etc). There are probably 15 papers or so (including Biastoch et al, Nature, 2008 and 2009). The best would be to ask the complete list from Arne Biastoch (if we need it in the prospective document).

2) Applications in France

• AGRIF 1/15 degree zoom in the Labrador Sea in a 1/3 degree model. PhD work of Jerome Chanut,

Chanut J., B. Barnier, W. Large, L. Debreu, T. Penduff, J.-M. Molines, and P. Mathiot, 2008 : Mesoscale eddies in the Labrador Sea and their contribution to convection and re-stratification. Journal of Physical Oceanography, 38, 1617-1643.

• AGRIF in the bay of Biscay, comparison with open boundary strategies. PhD of Sylvain Cailleau,

Cailleau S., V. Fedorenko, B. Barnier, E. Blayo, and L. Debreu, 2008: Comparison of different numerical methods used to handle the open boundary of a regional ocean circulation model of the Bay of Biscay. Ocean Modelling, 25, 1-16.

• AGRIF in the Solomon Sea, PhD work of Angelique Melet. JPO 2010 and other papers (5 in all? to be verified)

Melet A., Gourdeau L., Kessler S., Verron J. and Molines J.-M., 2010: Thermocline circulation in the Solomon Sea: a modeling study. Journal of Physical Oceanography, 40, 1302-1319.

Melet A., Verron J., Gourdeau L., and Koch-Larrouy A., 2011: Equatorward Pathways of Solomon Sea Water Masses and Their Modifications. Journal of Physical Oceanography, 41(4), 810-826.

• AGRIF in the Gulf of Mexico, PhD work of Julien Jouanno.

Jouanno J., J Sheinbaum, B. Barnier, J. M. Molines, L. Debreu, and F. Lemarié, 2008: The mesoscale variability in the Caribbean Sea. Part I: simulations with an embedded model and characteristics, Ocean Modelling, 23, 82-101.

Jouanno J., J Sheinbaum, B. Barnier, J. M. Molines, 2009: The mesoscale variability in the Caribbean Sea. Part II: energy sources. Ocean Modelling, 26 (3-4), pp. 226-239.

Jouanno J., Sheinbaum J., Barnier B., Molines J.-M., Candela J., 2012: Seasonal and interannual modulation of the eddy kinetic energy in the Caribbean Sea. Journal of Physical Oceanography, 42, 2041-2055, DOI: 10.1175/JPO-D-12-048.1.

• AGRIF in the Med Sea

Dobrinski P., Anav A., Lebeaupin Brossier C., Samson G., Stéfanon M., Bastin S., Baklouti M., Béranger K., Beuvier J., Bourdallé-Badie R., Coquart L., D'Andrea F., De Noblet-Ducoudré N., Diaz F., Dutay J.-C., Ethe C., Foujols M.-A., Khvorostyanov D., Madec G., Mancip M., Masson S., Menut L., Palmieri J., Polcher J. Turquety S., Valcke S., Viovy N., 2012: Modelling the Regional Coupled Eatrh System (MORCE):application to process and climate studies in vulnerable regions. Env. Modelling and Software, 35, 1-18 (10.1016/j.envsoft.2012.01.017)

• AGRIF in the Gulf of Guinea: PhD of Henrick Berger (LPO, Brest, december 2012).

A publication in preparation. 1/12 degree zoom in 1/4 model, H. Berger has also tried a 1/48 zoom in 1/12 model.

• AGRIF in the Subpolar gyre: ERNA model configuration (1/8 zoom in the global ORCA05 model)

1. Talandier, J. Deshayes, A-M. Treguier, X. Capet, R. Benshila, L. Debreu, R. Dussin, J-M. Molines, G. Madec: Improvements of simulated Western North Atlantic current system and impacts on AMOC, submitted to ocean modelling.

REPORT OF THE WORKING GROUP MEETING (January 30, 2014)

Participants : Rachid Benshila, Daley Calvert, Julien Calandreau, Jérome Chanut, Laurent Debreu, Christian Ethe, Rachel Furner, Claire Levy, Gurvan Madec, Sébastien Masson

 

1) Discuss the update of the 3.6 version

 

History :

•       AGRIF version (and corresponding NEMO subroutines) has been updated by Julien Calandreau (INRIA) and Laurent

•       Jérome has made a lot of improvements and bug fixes in his Gilbraltar Strait configuration

•       Same for Sébastien in the Pulsation ANR project

•       Other developments in LIM, PISCES

 

Bugs that have been identified and corrected since version 3.4 :

•       zwork array (J. Chanut): a global array  « zwork » was defined in the libmpp module and (due to a bug in the AGRIF converter) this led to several problems and in particular the update step was not performed …

•       Diffusion coefficients in the corners of the sponge layern were wrong (J. Chanut)

•       Scale factors were not correctly computed in the ghost cells (where it is assumed that we are in full steps) (J. Chanut)

è same problem for OBC

•       TKE (S. Masson): near the boundaries, spatial averaging operations led to wrong Kz in the first cell inside the high resolution domain. Extrapolation is possible but does not fulfill the requirement that with, a mesh refinement factor of 1, the obtained solution of the HR grid is identical to a solution computed without a zoom. S. Masson has implemented exchanges of TKE between coarse and fine grids.

è Same problem for GLS and for OBC

•       Asselin Filter (J. Chanut) : when updating the « after » (n+1) fields, the corresponding corrections of the « now » fields linked with the Asselin filter were not done.

•       arrays out of bound in procnames in MPI (wrong declarations of AGRIF profiles in agrif_declare_variables: jpi, jpj have been replaced by ncli,nlcj)

 

Bugs  / Problems that have been identified

·      The bathymetry connection check is not complete (add a check that the coarse grid bathy have been correctly updated)

·      Reproducibility is not guaranteed (due to MPI problem) when ln_spc_dyn is set to true in namelist (which means that we take 0 as special value for dynamics in interpolations/updates).

·      Recursive updates. When more than 1 zoom level are set, the update should start from the highest resolution grid and go recursively to the root grid. Laurent implemented changes that makes this possible.

 

• Use of AGRIF for degradation online (problème de north pole, coarsening)

• Average operators with update values

• High order operators with coastlines

 

• BDY problem have been solved

 

Rachid is ready do the merge (as soon the beta version is fixed)

 

2) What are the known problems / bugs?

 

•       Number of ghost cells

o   Antartic problem (periodicity): require only one ghost cell instead of 2

o   Number of required ghost cells for high order advection schemes may be larger than 2

o   -> Remove hardcoding of the number of ghost cells, do the required modifications to the AGRIF “profiles”  (Laurent)

•       North fold problem ?

•       Timings for each grid

 

3) What are the main next developments?

 

•       Time splitting (OK for version 3.6, end of the year, Jérome)

o   only consider forward integration of the forcing mode permits to ensure volume conservation

o   (refluxing or conservative interpolation at the boundary).

o   Tells the users that we have only AGRIF working in time splitting version in the forward version of the code.

•       Parallel runs (Laurent)

•       Update of the parent grid rhs before barotropic step(s)

 

4) Version 5.0 (time and space schemes in the system).

 

 

•       Vertical grid refinement (Laurent)

o   Probably before version 5

•       Online degradation using AGRIF

•       Agrif with variable volume

o   (update of the volume, and modification of boundary conditions) (Jérome).

 

5) Nesting tools:

 

Two stages: 

a) for 3.6 version  

•       agree on all the points: bathymetry smoothing, update of coarse grids (take the maximum as default)

•       Incorporate corrections done by Jean Marc

•       The nesting tools are only essential for the creation of bathymetry:

o   Do a list available tools for 2D/3D interpolation

o   For 3.6 keep the 3D fields interpolation in nesting tools

 

b) next version

 

•       The definition of vertical coordinates should be done outside NEMO

•       Nesting tools for the s coordinates

 

5) Documentation:

•       Update of the nesting tools 3.6 documentation

•       Update of the users guide: describes what is possible or not with AGRIF.

•       Documentation for nesting in NEMO/AGRIF: starts from the notes of Sebastien, then circulate the powerpoint

•       GMD paper

 

6) Standard configuration and sanity tests

 

The standard configuration should:

•       Include more than one level of embedding (test of the recursive update starting from the finer resolution grid(s))

•       Uses time splitting

•       Include a zoom in a sea ice area (Labrador Sea, LIM3)

•       Include a zoom with PISCES

•       Zoom in Perou Chili

 

Sanitiy tests

•       Zoom with a mesh refinement of 1

•       Test constancy preservation for tracers

 

Longer visions of having AGRIF zoom in AMM

S coordinates zoom inside a z coordinate parent grid.