Version 12 (modified by jchanut, 3 years ago) (diff)



    Working group leader (and responsible for wiki pages): Jérôme Chanut

    Members of the working group:

    • Rachid Benshila
    • Clément Bricaud
    • Jérôme Chanut
    • Laurent Debreu
    • Frédéric Dupont
    • Laura Gillard
    • Tim Graham
    • Sébastien Masson
    • Clark Pennelly
    • Clément Rousset


    Sustain AGRIF in NEMO and provide support to users


    • Jan-30-2014 WG meeting
    • Mar-10-2017 WG meeting

    List of NEMO-AGRIF publications in peer-reviewed journals since 2008:

    1. Biastoch, A., Böning, C. W. and Lutjeharms, J. R. E. (2008) Agulhas leakage dynamics affects decadal variability in Atlantic overturning circulation Nature, 456 . pp. 489-492.
    2. Biastoch, A., Lütjeharms, J. R. E., Böning, C. W. and Scheinert, M. (2008) Mesoscale perturbations control inter-ocean exchange south of Africa Geophysical Research Letters, 35.
    3. 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.
    4. 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.
    5. 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.
    6. 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.
    7. Biastoch, A., Beal, L., Lutjeharms, J. R. E. and Casal, T. G. D. (2009) Variability and coherence of the Agulhas Undercurrent in a High-resolution Ocean General Circulation Model Journal of Physical Oceanography, 39 . pp. 2417-2435.
    8. Biastoch, A., Böning, C. W., Schwarzkopf, F. U. and Lutjeharms, J. R. E. (2009) Increase in Agulhas leakage due to poleward shift of Southern Hemisphere westerlies Nature, 462 . pp. 495-498.
    9. Siedler, G., Rouault, M., Biastoch, A., Backeberg, B., Reason, C. J. C. and Lutjeharms, J. R. E. (2009) Modes of the southern extension of the East Madagascar Current Journal of Geophysical Research - Oceans, 114 .
    10. Van Sebille, E., van Leeuwen, P. J., Biastoch, A., Barron, C. N. and de Ruijter, W. P. M. (2009) Lagrangian validation of numerical drifter trajectories using drifting buoys: Application to the Agulhas region Ocean Modelling, 29 . pp. 269-276.
    11. Van Sebille, E., Barron, C. N., Biastoch, A., van Leeuwen, P. J., Vossepoel, F. C. and de Ruijter, W. P. M. (2009) Relating Agulhas leakage to the Agulhas Current retroflection location Ocean Science, 5 . pp. 511-521.
    12. Van Sebille, E., Biastoch, A., van Leeuwen, P. J. and de Ruijter, W. P. M. (2009) A weaker Agulhas Current leads to more Agulhas leakage Geophysical Research Letters, 36
    13. 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.
    14. Melet, A., L. Gourdeau, J. Verron (2010) Variability of the Solomon Sea from altimetry sea level data. Ocean Dynamics, 60 (4), 883-900.
    15. 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.
    16. 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.
    17. 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
    18. Melet A., J. Verron, J.M. Brankart (2012) Potential outcomes of glider data assimilation in the Solomon Sea: Control of the water mass properties and parameter estimation. Journal of Marine Systems, 94, 232-246
    19. Cronin, M. F., T. Tozuka, A. Biastoch, J. V. Durgadoo, and L. M. Beal (2013), Prevalence of strong bottom currents in the greater Agulhas system, Geophys. Res. Lett., 40, 1772–1776.
    20. Durgadoo, J. V., Loveday, B. R., Reason, C. J., Penven, P., & Biastoch, A. (2013) Agulhas leakage predominantly responds to the Southern Hemisphere westerlies. Journal of Physical Oceanography, 43(10), 2113-2131.
    21. Biastoch, A., & Böning, C. W. (2013) Anthropogenic impact on Agulhas leakage. Geophysical Research Letters, 40(6), 1138-1143.
    22. Ruehs, S., Durgadoo, J. V., Behrens, E. and Biastoch, A. (2013) Advective timescales and pathways of Agulhas leakage Geophysical Research Letters, 40 (15), 3997-4000.
    23. Scussolini, P., van Sebille, E. and Durgadoo, J. V. (2013) Paleo Agulhas rings enter the subtropical gyre during the penultimate deglaciation Climate of the Past, 9 (6), 2631-2639.
    24. Melet,A., L. Gourdeau, J. Verron, B. Djath (2013) Solomon Sea circulations and water mass modifications: response at ENSO timescales. Ocean Dynamics, 63 (1), 1-19.
    25. Djath B., A., Melet, J. Verron, J. M. Molines, L. Gourdeau, L. Debreu (2014) A 1/36 degrees model of the Solomon Sea embedded into a global ocean model: on the setting up of an interactive open boundary nested model system. J. Operational Oceanography, 7(1), 34-46.
    26. Djath, B., J. Verron, A. Melet, L. Gourdeau, B. Barnier, and J.-M. Molines (2014) Multiscale dynamical analysis of a high-resolution numerical model simulation of the Solomon Sea circulation, J. Geophys. Res. Oceans, 119, 6286–6304.
    27. Talandier C., J. Deshayes, A.-M. Treguier, X. Capet, R. Benshila, L. Debreu, R. Dussin, J.-M. Molines, G. Madec (2014) Improvements of simulated Western North Atlantic current system and impacts on the AMOC. Ocean Modelling, 76, 1-19.
    28. Caley, T., Peeters, F. J. C., Biastoch, A., Rossignol, L., van Sebille, E., Durgadoo, J. V., Malaizé, B., Giraudeau, J., Arthur, K. and Zahn, R. (2014) Quantitative estimate of the paleo-Agulhas leakage Geophysical Research Letters, 41 (4). pp. 1238-1246. DOI 10.1002/2014GL059278.
    29. Duteil, O., Schwarzkopf, F. U., Böning, C. W. and Oschlies, A. (2014) Major role of the equatorial current system in setting oxygen levels in the eastern tropical Atlantic Ocean: a high-resolution model study Geophysical Research Letters, 41 . pp. 2033-2040.
    30. Gaultier, L., B. Djath, J. Verron, J.-M. Brankart, P. Brasseur, A. Melet (2014) Assessing the feasibility of the inversion of submesoscales in a high-resolution Solomon Sea model. Journal of Geophysical Research - Oceans, 119 (7), 4520–4541.
    31. Fischer, Jürgen, Karstensen, Johannes, Zantopp, Rainer J., Visbeck, Martin, Biastoch, Arne, Behrens, Erik, Böning, Claus W., Quadfasel, D., Jochumsen, K., Valdimarsson, H., Jónsson, S., Bacon, S., Holliday, N. P., Dye, S., Rhein, M. and Mertens, C. (2015) Intra-seasonal variability of the DWBC in the western subpolar North Atlantic Progress in Oceanography, 132 , 233-249.
    32. Urrego-Blanco, J., J. Sheng and F. Dupont (2016) Performance of One-Way and Two-Way Nesting Techniques Using the Shelf Circulation Modelling System for the Eastern Canadian Shelf, Atmosphere-Ocean, 54, 75-92.
    33. Deckerck, A., Y. Ourmières and A. Molcard (2016) Assessment of the coastal dynamics in a nested zoom and feedback on the boundary current: the North-Western Mediterranean Sea case. Ocean dynamics, 66(11), 1529-1542. 
    34. Müller, V., D. Kieke, P. G. Myers, C. Pennelly and C. Mertens (2017) Temperature flux carried by individual eddies across 47° N in the Atlantic Ocean. J. Geophys. Res. Oceans, 122, doi:10.1002/2016JC012175.


    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 Debreu
    • Jérome Chanut has made a lot of improvements and bug fixes in his Gilbraltar Strait configuration
    • Same for Sébastien Masson 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)

    → 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.

    → 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 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


    • AGRIF and time splitting (OK for version 3.6, end of the year, Jérome)
      • only consider forward integration of the forcing mode permits to ensure volume conservation
      • without update of the parent grid right hand side
    • Performance of parallel runs
      • allows the distribution of the processors among the fine grids

    Rachid Benshila is ready be in charge of the merge

    2) What are the known open problems ? (not to be solved for 3.6)

    • Number of ghost cells (L. Debreu)
      • Antartic problem (periodicity): require only one ghost cell instead of 2
      • Number of required ghost cells for high order advection schemes may be larger than 2
      • → 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?

    • Coupling between grids at the level of the barotropic mode (in time splitting version) (Jérome)
      • requires some modification in the organization of the step routine of NEMO
    • Vertical grid refinement (Laurent)
    • Online coarsening for tracers using AGRIF (L. Debreu, G. Madec)
    • AGRIF with variable volume

    4) 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:
      • forcings can be interpolated on the fly
      • → Do a list available tools for 3D interpolation (initialization / restart fields)
      • 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.