Development of BFMCOUPLER (v1.0), the coupling scheme that links the MITgcm and BFM models for ocean biogeochemistry simulations

Abstract

Abstract. In this paper, we present a coupling scheme between the Massachusetts Institute of Technology general circulation model (MITgcm) and the Biogeochemical Flux Model (BFM). The MITgcm and BFM are widely used models for geophysical fluid dynamics and for ocean biogeochemistry, respectively, and they benefit from the support of active developers and user communities. The MITgcm is a state-of-the-art general circulation model for simulating the ocean and the atmosphere. This model is fully 3-D (including the non-hydrostatic term of momentum equations) and is characterized by a finite-volume discretization and a number of additional features enabling simulations from global (O(10 7 ) m) to local scales (O(100) m). The BFM is a biogeochemical model based on plankton functional type formulations, and it simulates the cycling of a number of constituents and nutrients within marine ecosystems. The online coupling presented in this paper is based on an open-source code, and it is characterized by a modular structure. Modularity preserves the potentials of the two models, allowing for a sustainable programming effort to handle future evolutions in the two codes. We also tested specific model options and integration schemes to balance the numerical accuracy against the computational performance. The coupling scheme allows us to solve several processes that are not considered by each of the models alone, including light attenuation parameterizations along the water column, phytoplankton and detritus sinking, external inputs, and surface and bottom fluxes.Moreover, this new coupled hydrodynamic-biogeochemical model has been configured and tested against an idealized problem (a cyclonic gyre in a mid-latitude closed basin) and a realistic case study (central part of the Mediterranean Sea in [2006][2007][2008][2009][2010][2011][2012]. The numerical results consistently reproduce the interplay of hydrodynamics and biogeochemistry in both the idealized case and Mediterranean Sea experiments. The former reproduces correctly the alternation of surface bloom and deep chlorophyll maximum dynamics driven by the seasonal cycle of winter vertical mixing and summer stratification; the latter simulates the main basin-wide and mesoscale spatial features of the physical and biochemical variables in the Mediterranean, thus demonstrating the applicability of the new coupled model to a wide range of ocean biogeochemistry problems.

The Oceanographic Multipurpose Software Environment (OMUSE v1.0)

“…For example, the Earth system Modeling Framework (ESMF, Hill et al, 2004) presents an example of the integrated approach, where component modules are made to conform to a simple calling sequence and called from a single executable (which also implements the coupling algorithm). Cossarini et al (2017) provide an example of the coupling library approach. In this case the coupler consists of a wrapper around a the Biogeochemical Flux Model (BFM) code that can be called from another code (MITgcm).…”

“…In many cases, 3168 I. Pelupessy et al: OMUSE unstructured mesh models are used (Danilov, 2013;Leuttich and Westerink, 2004) in order to provide an accurate representation (Candy et al, 2014) of complex and irregular domain bounds that strongly influence local flows. An additional challenge in regional models, such as ADCIRC (Advanced 3-D Circulation) and SWAN (Simulating Waves Nearshore), is that they are not bounded entirely by a coastline and typically contain at least one boundary open to the global ocean.…”

Characterisation of extreme events waves in marine ecosystems: the case of Mediterranean Sea

“…2015) following the online scheme described in Cossarini et al (2017). The configuration in use has a horizontal resolution of 1/12°, with 75 vertical levels unevenly spaced.…”

Calibration and Validation of Environmental Controls on Planktic Foraminifera Mg/Ca Using Global Core‐Top Data

“…Conversely, accurate PSMs for the Mg/Ca of G . inflata across all timescales and other species on timescales for which Ω deep may have varied may require general circulation models with a biogeochemical module (e.g., Cossarini et al, ) capable of realistically estimating the evolution of Ω .…”

“…Our results suggest that generating accurate forward models of N. pachyderma, N. incompta, G. ruber, and G. bulloides Mg/Ca is relatively straightforward in recent millennia and can be done by combining standard general circulation model temperature fields at appropriate depth habitats and seasons with an assumed modern Ω deep value. Conversely, accurate PSMs for the Mg/Ca of G. inflata across all timescales and other species on timescales for which Ω deep may have varied may require general circulation models with a biogeochemical module (e.g., Cossarini et al, 2017) capable of realistically estimating the evolution of Ω.…”