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

2017 ◽  
Vol 10 (4) ◽  
pp. 1423-1445 ◽  
Author(s):  
Gianpiero Cossarini ◽  
Stefano Querin ◽  
Cosimo Solidoro ◽  
Gianmaria Sannino ◽  
Paolo Lazzari ◽  
...  
Keyword(s):  
Mediterranean Sea ◽  
General Circulation Model ◽  
General Circulation ◽  
Circulation Model ◽  
Biogeochemical Model ◽  
Coupling Scheme ◽  
Integration Schemes ◽  
Wide Range ◽  
Ocean Biogeochemistry ◽  
The Mediterranean

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(107) 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 2006–2012). 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.

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

2016 ◽  
Author(s):  
Gianpiero Cossarini ◽  
Stefano Querin ◽  
Cosimo Solidoro ◽  
Gianmaria Sannino ◽  
Paolo Lazzari ◽  
...  
Keyword(s):  
General Circulation Model ◽  
General Circulation ◽  
Light Attenuation ◽  
Circulation Model ◽  
Biogeochemical Model ◽  
Coupling Scheme ◽  
Computational Performance ◽  
Wide Range ◽  
Ocean Biogeochemistry ◽  
The Mediterranean

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 three dimensional (including the non-hydrostatic term of momentum equations) and includes a finite-volume discretization and a number of additional features enabling simulations from global (O(107)m) to local scales (O(100)m). The BFM is a complex biogeochemical model that simulates the cycling of a number of constituents and nutrients within marine ecosystems. The coupler presented in this paper links the two models through an efficient scheme that manages communication and memory sharing between the models. We also test specific model options 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 2006–2012). The numerical results are consistent with the expected theoretical and observed behaviour of both the idealized system and the Mediterranean domain, thus demonstrating the applicability of the new coupled model to a wide range of ocean biogeochemistry problems.

scholarly journals A nested Atlantic-Mediterranean Sea general circulation model for operational forecasting

Ocean Science ◽  
2009 ◽  
Vol 5 (4) ◽  
pp. 461-473 ◽  
Author(s):  
P. Oddo ◽  
M. Adani ◽  
N. Pinardi ◽  
C. Fratianni ◽  
M. Tonani ◽  
...  
Keyword(s):  
Mediterranean Sea ◽  
General Circulation Model ◽  
Ocean Circulation ◽  
General Circulation ◽  
Circulation Model ◽  
Ocean Model ◽  
Global Ocean ◽  
Lateral Boundary ◽  
The Mediterranean ◽  
The Impact

Abstract. A new numerical general circulation ocean model for the Mediterranean Sea has been implemented nested within an Atlantic general circulation model within the framework of the Marine Environment and Security for the European Area project (MERSEA, Desaubies, 2006). A 4-year twin experiment was carried out from January 2004 to December 2007 with two different models to evaluate the impact on the Mediterranean Sea circulation of open lateral boundary conditions in the Atlantic Ocean. One model considers a closed lateral boundary in a large Atlantic box and the other is nested in the same box in a global ocean circulation model. Impact was observed comparing the two simulations with independent observations: ARGO for temperature and salinity profiles and tide gauges and along-track satellite observations for the sea surface height. The improvement in the nested Atlantic-Mediterranean model with respect to the closed one is particularly evident in the salinity characteristics of the Modified Atlantic Water and in the Mediterranean sea level seasonal variability.

scholarly journals A nested Atlantic-Mediterranean Sea general circulation model for operational forecasting

2009 ◽  
Vol 6 (2) ◽  
pp. 1093-1127 ◽  
Author(s):  
P. Oddo ◽  
M. Adani ◽  
N. Pinardi ◽  
C. Fratianni ◽  
M. Tonani ◽  
...  
Keyword(s):  
Mediterranean Sea ◽  
General Circulation Model ◽  
Ocean Circulation ◽  
General Circulation ◽  
Circulation Model ◽  
Ocean Model ◽  
Global Ocean ◽  
Lateral Boundary ◽  
The Mediterranean ◽  
The Impact

Abstract. A new numerical general circulation ocean model for the Mediterranean Sea has been implemented nested within an Atlantic general circulation model within the framework of the Marine Environment and Security for the European Area project (MERSEA, Desaubies, 2006). A 4-year twin experiment was carried out from January 2004 to December 2007 with two different models to evaluate the impact on the Mediterranean Sea circulation of open lateral boundary conditions in the Atlantic Ocean. One model considers a closed lateral boundary in a large Atlantic box and the other is nested in the same box in a global ocean circulation model. Impact was observed comparing the two simulations with independent observations: ARGO for temperature and salinity profiles and tide gauges and along-track satellite observations for the sea surface height. The improvement in the nested Atlantic-Mediterranean model with respect to the closed one is particularly evident in the salinity characteristics of the Modified Atlantic Water and in the Mediterranean sea level seasonal variability.

Modeling the biogeochemical dynamics of the Northern Adriatic Sea with an explicit benthic-pelagic coupling

2020 ◽  
Author(s):  
Isabella Scroccaro ◽  
Marco Zavatarelli ◽  
Tomas Lovato
Keyword(s):  
Mediterranean Sea ◽  
General Circulation ◽  
Adriatic Sea ◽  
Circulation Model ◽  
Horizontal Resolution ◽  
Open Boundary ◽  
Biogeochemical Model ◽  
Northern Adriatic Sea ◽  
Northern Adriatic ◽  
The Mediterranean

<p>A high resolution three-dimensional (physical-biogeochemical) numerical model of the Northern Adriatic Sea has been implemented by coupling the European general circulation model - NEMO (Nucleus for European Modeling of the Ocean, https://www.nemo-ocean.eu/), with the marine biogeochemical model BFM (Biogeochemical Flux Model, bfm-community.eu/).</p><p>The modeling system is implemented with a horizontal resolution of about 800 m and a vertical resolution of 2 m, in z coordinates. The NEMO model is off-line nested at its open boundary with the Mediterranean Sea physical model of the Copernicus Marine Environment Monitoring Service (CMEMS, http://marine.copernicus.eu/).</p><p>The BFM component of the modeling system now includes a detailed and explicit representation of the benthic biogeochemical cycling (benthic fauna, organic matter, nutrients), as well as the dynamics of the benthic-pelagic processes.</p><p>The inclusion of the benthic dynamics in the 3D biogeochemical modeling of a shallow coastal basin, such as the Northern Adriatic Sea, represents an innovative application in the field of coastal and shelf biogeochemistry, since benthic biogeochemical processes can significantly constrain the coastal environmental dynamics.</p><p>Simulations have been performed in hindcasting mode with interannually varying physical (surface heat and water fluxes, including river runoff) and biogeochemical (river nutrient load) forcing. Results are validated against available observations from in situ and satellite platforms for sea surface temperatures, chlorophyll-a and dissolved inorganic nutrients, in order to explore the sensitivity of the pelagic environment to the inclusion of an explicit benthic dynamics and to evaluate issues related to model coupling and error/prediction limits.</p><p>The study is carried out in the framework of the European Project H2020 "ODYSSEA" (Operating a network of integrated observatory systems in the Mediterranean SEA, http://odysseaplatform.eu/), with the final goal to build an on-line forecasting modeling system of the Northern Adriatic Sea.</p>

scholarly journals Development of the GEOS-5 atmospheric general circulation model: evolution from MERRA to MERRA2

2014 ◽  
Vol 7 (6) ◽  
pp. 7575-7617 ◽  
Author(s):  
A. Molod ◽  
L. Takacs ◽  
M. Suarez ◽  
J. Bacmeister
Keyword(s):  
General Circulation Model ◽  
General Circulation ◽  
Atmospheric General Circulation Model ◽  
Weather Prediction ◽  
Circulation Model ◽  
Wave Drag ◽  
Atmospheric General Circulation ◽  
Wide Range ◽  
Simulated Climate ◽  
The Impact

Abstract. The Modern-Era Retrospective Analysis for Research and Applications-2 (MERRA2) version of the GEOS-5 Atmospheric General Circulation Model (AGCM) is currently in use in the NASA Global Modeling and Assimilation Office (GMAO) at a wide range of resolutions for a variety of applications. Details of the changes in parameterizations subsequent to the version in the original MERRA reanalysis are presented here. Results of a series of atmosphere-only sensitivity studies are shown to demonstrate changes in simulated climate associated with specific changes in physical parameterizations, and the impact of the newly implemented resolution-aware behavior on simulations at different resolutions is demonstrated. The GEOS-5 AGCM presented here is the model used as part of the GMAO's MERRA2 reanalysis, the global mesoscale "nature run", the real-time numerical weather prediction system, and for atmosphere-only, coupled ocean–atmosphere and coupled atmosphere–chemistry simulations. The seasonal mean climate of the MERRA2 version of the GEOS-5 AGCM represents a substantial improvement over the simulated climate of the MERRA version at all resolutions and for all applications. Fundamental improvements in simulated climate are associated with the increased re-evaporation of frozen precipitation and cloud condensate, resulting in a wetter atmosphere. Improvements in simulated climate are also shown to be attributable to changes in the background gravity wave drag, and to upgrades in the relationship between the ocean surface stress and the ocean roughness. The series of "resolution aware" parameters related to the moist physics were shown to result in improvements at higher resolutions, and result in AGCM simulations that exhibit seamless behavior across different resolutions and applications.

scholarly journals Population genetic structure and connectivity of the harmful dinoflagellate Alexandrium minutum in the Mediterranean Sea

2011 ◽  
Vol 279 (1726) ◽  
pp. 129-138 ◽  
Author(s):  
Silvia Casabianca ◽  
Antonella Penna ◽  
Elena Pecchioli ◽  
Antoni Jordi ◽  
Gotzon Basterretxea ◽  
...  
Keyword(s):  
Population Structure ◽  
Mediterranean Sea ◽  
Population Genetic ◽  
General Circulation ◽  
Harmful Algal Bloom ◽  
Regional Scale ◽  
Circulation Model ◽  
Alexandrium Minutum ◽  
The Mediterranean ◽  
Microalgal Species

The toxin-producing microbial species Alexandrium minutum has a wide distribution in the Mediterranean Sea and causes high biomass blooms with consequences on the environment, human health and coastal-related economic activities. Comprehension of algal genetic differences and associated connectivity is fundamental to understand the geographical scale of adaptation and dispersal pathways of harmful microalgal species. In the present study, we combine A. minutum population genetic analyses based on microsatellites with indirect connectivity ( C i ) estimations derived from a general circulation model of the Mediterranean sea. Our results show that four major clusters of genetically homogeneous groups can be identified, loosely corresponding to four regional seas: Adriatic, Ionian, Tyrrhenian and Catalan. Each of the four clusters included a small fraction of mixed and allochthonous genotypes from other Mediterranean areas, but the assignment to one of the four clusters was sufficiently robust as proved by the high ancestry coefficient values displayed by most of the individuals (>84%). The population structure of A. minutum on this scale can be explained by microalgal dispersion following the main regional circulation patterns over successive generations. We hypothesize that limited connectivity among the A. minutum populations results in low gene flow but not in the erosion of variability within the population, as indicated by the high gene diversity values. This study represents a first and new integrated approach, combining both genetic and numerical methods, to characterize and interpret the population structure of a toxic microalgal species. This approach of characterizing genetic population structure and connectivity at a regional scale holds promise for the control and management of the harmful algal bloom events in the Mediterranean Sea.

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