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 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 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 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 iMarNet: an ocean biogeochemistry model inter-comparison project within a common physical ocean modelling framework

2014 ◽  
Vol 11 (7) ◽  
pp. 10537-10569 ◽  
Author(s):  
L. Kwiatkowski ◽  
A. Yool ◽  
J. I. Allen ◽  
T. R. Anderson ◽  
R. Barciela ◽  
...  
Keyword(s):  
General Circulation ◽  
High Efficiency ◽  
Circulation Model ◽  
Climate Dynamics ◽  
Model Complexity ◽  
Balance Model ◽  
Marine Biota ◽  
Earth System ◽  
Wide Range ◽  
Ocean Biogeochemistry

Abstract. Ocean biogeochemistry (OBGC) models span a wide range of complexities from highly simplified, nutrient-restoring schemes, through nutrient-phytoplankton-zooplankton-detritus (NPZD) models that crudely represent the marine biota, through to models that represent a broader trophic structure by grouping organisms as plankton functional types (PFT) based on their biogeochemical role (Dynamic Green Ocean Models; DGOM) and ecosystem models which group organisms by ecological function and trait. OBGC models are now integral components of Earth System Models (ESMs), but they compete for computing resources with higher resolution dynamical setups and with other components such as atmospheric chemistry and terrestrial vegetation schemes. As such, the choice of OBGC in ESMs needs to balance model complexity and realism alongside relative computing cost. Here, we present an inter-comparison of six OBGC models that were candidates for implementation within the next UK Earth System Model (UKESM1). The models cover a large range of biological complexity (from 7 to 57 tracers) but all include representations of at least the nitrogen, carbon, alkalinity and oxygen cycles. Each OBGC model was coupled to the Nucleus for the European Modelling of the Ocean (NEMO) ocean general circulation model (GCM), and results from physically identical hindcast simulations were compared. Model skill was evaluated for biogeochemical metrics of global-scale bulk properties using conventional statistical techniques. The computing cost of each model was also measured in standardised tests run at two resource levels. No model is shown to consistently outperform or underperform all other models across all metrics. Nonetheless, the simpler models that are easier to tune are broadly closer to observations across a number of fields, and thus offer a high-efficiency option for ESMs that prioritise high resolution climate dynamics. However, simpler models provide limited insight into more complex marine biogeochemical processes and ecosystem pathways, and a parallel approach of low resolution climate dynamics and high complexity biogeochemistry is desirable in order to provide additional insights into biogeochemistry–climate interactions.

scholarly journals PLASIM–GENIE v1.0: a new intermediate complexity AOGCM

2016 ◽  
Vol 9 (9) ◽  
pp. 3347-3361 ◽  
Author(s):  
Philip B. Holden ◽  
Neil R. Edwards ◽  
Klaus Fraedrich ◽  
Edilbert Kirk ◽  
Frank Lunkeit ◽  
...  
Keyword(s):  
General Circulation Model ◽  
Ocean Circulation ◽  
General Circulation ◽  
Circulation Model ◽  
Aridity Index ◽  
Earth System Model ◽  
System Model ◽  
Earth System ◽  
Intermediate Complexity ◽  
Wide Range

Abstract. We describe the development, tuning and climate of Planet Simulator (PLASIM)–Grid-ENabled Integrated Earth system model (GENIE), a new intermediate complexity Atmosphere–Ocean General Circulation Model (AOGCM), built by coupling the Planet Simulator to the ocean, sea-ice and land-surface components of the GENIE Earth system model. PLASIM–GENIE supersedes GENIE-2, a coupling of GENIE to the Reading Intermediate General Circulation Model (IGCM). The primitive-equation atmosphere includes chaotic, three-dimensional (3-D) motion and interactive radiation and clouds, and dominates the computational load compared to the relatively simpler frictional-geostrophic ocean, which neglects momentum advection. The model is most appropriate for long-timescale or large ensemble studies where numerical efficiency is prioritised, but lack of data necessitates an internally consistent, coupled calculation of both oceanic and atmospheric fields. A 1000-year simulation with PLASIM–GENIE requires approximately 2 weeks on a single node of a 2.1 GHz AMD 6172 CPU. We demonstrate the tractability of PLASIM–GENIE ensembles by deriving a subjective tuning of the model with a 50-member ensemble of 1000-year simulations. The simulated climate is presented considering (i) global fields of seasonal surface air temperature, precipitation, wind, solar and thermal radiation, with comparisons to reanalysis data; (ii) vegetation carbon, soil moisture and aridity index; and (iii) sea surface temperature, salinity and ocean circulation. Considering its resolution, PLASIM–GENIE reproduces the main features of the climate system well and demonstrates usefulness for a wide range of applications.

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

2015 ◽  
Vol 8 (5) ◽  
pp. 1339-1356 ◽  
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 Goddard Earth Observing System-5 (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 MERRA2 reanalysis, global mesoscale simulations at 10 km resolution through 1.5 km resolution, 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 was shown to result in improvements at higher resolutions and result in AGCM simulations that exhibit seamless behavior across different resolutions and applications.

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