The Models
A collaborative project in coastal oceanography
The Models

This section provides a short overview of the different models that are used in the AMICO-BIO project.
The physical models are particular implementations of one of the following models:

The biogeochemical models are different implementations of either

ATLANTIC: At the global scale (providing the external forcing) we use the following model:
  • G1 MERCATOR (NEMO)/PISCES (schematic of PISCES after Dufour 2011) (Gehlen et al, 2007)
    gi Model
    • 1/4° global Mercator model with NEMO3.1/ORCA for the physics and NEMO3.2/PISCES for the biology.
    • 24 prognostic variables, 5 limiting nutriens, 2 phytoplankton and zooplankton species, as well as 3 compartments for detritus
    • Redfield-type model
    • variable Chl:C ratios
    • carbon and oxygen cycles
    • no feedback to the physics
    • Monod type equation without diurnal cycle
    • No sedimentary model: balance between inputs and sedimentation
    • External inputs: rivers, dust (iron, Si and P) Sedimentary iron (friction)

At the regional scale we use 2 different models:
  • R1: g2 model The Iberian-Biscay-Irish (IBI) model (NEMO) with 1/12° resolution coupled to PISCES (Dol, 2011)
    • curvilinear ORCA grid
    • extraction from global 1/12° grid
    • size: 367x634 grid points with 4.8km < dx < 8.4km
    • 5 open boundaries
    • CPU time: about 50 minutes per month
    • output: daily and hourly means

  • R2: The MANGA (MARS3D) coupled to ECOMARS3D (see schematic) (Huret et al, 2013) r2 model
    • 4km horizontal resolution
    • 30 generalised sigma levels
    • 4 limiting nutrients
    • 3 phyto- and 2 zooplankton species

MEDITERRANEAN: At the global scale (providing the external forcing) we use the following models:
  • G2: 1/12° NEMO-MED12 coupled to PISCES (Palmieri et al, in prep.) g2 model
    • 1/12° (6-8km) horizontal resolution with 567x264 grid cells
    • 50 vertical levels (1 to 450m)
    • eddy resolving
    • forcing: ARPERA atmospheric model
    • rivers: 33 rivers, Black Sea and coastal run-off

  • G3: 1/12° NEMO-MED12 coupled to ECO3M (see schematic) (Guyennon et al, in prep.) g3 model
    • 34 state variables
    • flexible stoichiometry
    • decoupled growth/C synthesis

  • G4: MARS3D-MENOR coupled to ECO3M-MED (Alekseenko et al, in revision) g4 model
    • regional model that covers the entire NW Mediterranean Sea (39.50°N–44.50°N/0.00°E–16.00°E)
    • 1.2km horizontal resolution with 1101x463 grid cells
    • 34 state variables
    • flexible stoichiometry
    • decoupled growth/C synthesis
    • forced with the Mediterranean Forecasting System (MFS) 1/16° regional model, spatially interpolated onto the 1.2km MENOR grid

At the regional scale we use 2 different models:
  • R3: The SYMPHONIE model coupled to ECO3M-S (see schematic) (Auger et al, 2011) ECO3M-S
    • curvilinear C grid with 40 sigma levels
    • 1km horizontal resolution (1/111°) with 764x556 grid cells

  • R4: The MARS3D-GULI model coupled to ECO3M-Massilia (see schematic) (Pinazo et al, 2012; Fraysse et al, 2013) R4 model
    • dx=dy=1.2km with 322x195 grid cells
    • 30 vertical sigma levels
    • carbon, nitrogen and phosphorous cycles
    • flexible stoichiometry
    • 17 state variables and 5 main compartments in the biogeochemical model: phytoplankton, heterotrophic bacteria, dissolved and particulate organic matter and dissolved inorganic matter


  • Auger P.A., Diaz F., Ulses C., Estournel C., Neveux J., Joux F., Pujo-Pay M., and Naudin J.J., 2011. Functioning of the planktonic ecosystem of the Rhone River plume (NW Mediterranean) during spring and its impact on the carbon export: a field data and 3-D modelling combined approach. Biogeosciences, 8, 3231-3261.
  • Dol M., 2011. Implémentation d'un modèle couplé online physique biogéochimie sur la façade européenne. Rapport de stage de Master 2 professionnel mention "surveillance et gestion de l'environnement", Toulouse.
  • Dufour C.O., 2011: Rôle des tourbillons de méso-échelle océanique dans la variabilité récente des flux air-mer de CO2 dans l'océan Austral. Ph.D. dissertation, University of Grenoble, France.
  • Fraysse M., C. Pinazo, V. Faure, R. Fuchs, P. Lazzari, P. Raimbault, I.L. Pairaud. 3D coupled physical-biogeochemical model development around Marseille’s coastal area (NW Mediterranean Sea): What complexity is required in coastal zone? PLoS ONE, 8 (12): e80012.
  • Huret M., Sourisseau M., Petitgas P., Struski C., Leger F., Lazure P., 2013. A multi-decadal hindcast of a physical–biogeochemical model and derived oceanographic indices in the Bay of Biscay. Journal of Marine Systems, 109-110, S77-S94.
  • Pinazo C., M. Fraysse, R. Fuchs, B. Thouvenin, I. Pairaud , P. Garreau, 2012. Modelling the Gulf of Lions coastal area with a 3D coupled physical and biogeochemical approach. 50th ECSA Conference, 3-7 June 2012, Venice, Italy