MITbioGeoCheMistry

Story by Helen Hill

This month we spotlight work seeking to couple the MITgcm with another open-source marine biogeochemistry tool developed and maintained by a consortium involving modelers across Europe and also South Africa.

Just as the MITgcm provides an accessible tool to model geophysical fluid dynamics, the Biogeochemical Flux Model (BFM) is widely used to model ocean biogeochemistry. In their recent paper in the journal Geoscientific Model Development, some members of the BFM development team, Gianpiero Cossarini, Cosimo Solidoro, Paolo Lazzari, together with colleagues Stefano Querin and Valeria Di Biagio (from the Instituto Nazionale di Oceanografia e di Geophysica Sperimentale – OGS, Trieste, Italy), and Gianmaria Sannino (from the Climate Modelling Laboratory, Italian National Agency for New technologies, Energy and Sustainable Economic Development, Rome, Italy) report their work developing a coupling scheme to link MITgcm and BFM models for ocean biogeochemistry simulations.

In its standard configuration, BFM solves the cycles of carbon, phosphorus, nitrogen, silica, and oxygen in the water-dissolved phase and in the plankton, detritus, and benthic compartments, parameterizing plankton dynamics by considering a number of plankton functional groups, each representing a different class of taxa. The plankton functional groups are subdivided into producers (phytoplankton), consumers (zooplankton), and decomposers (bacteria) with each of these broad functional classifications being further partitioned into functional subgroups to create a planktonic food web.

Like the MITgcm, BFM is an open-source, modular Fortran 90 numerical model. Coupling was achieved by minimally upgrading the GCHEM package in MITgcm, and developing a single additional package BFMCOUPLER specifically designed to interface with BFM. While hydrodynamic and biogeochemical models can be coupled simply by merging their codes into a single larger new combined code, the authors expect that by, in such large part, preserving the separation and modularity of the two coupled components, they can continue to leverage and benefit from continued ongoing advances in each.

The authors tested the new, coupled hydrodynamic-biogeochemical model against two case studies: an idealized experiment (a cyclonic gyre in a mid-latitude closed domain) and a realistic configuration, to test the fidelity of the coupling in the context of the interacting physics and biogeochemistry of the Adriatic-Ionian system (Mediterranean Sea).

The above figure shows a 3D rendering of the Deep Chlorophyll Maximum (DCM) in the Adriatic-Ionian Sea (averaged over July 2012). The DCM is represented as the isosurface with a chlorophyll concentration of 0.15 mgChl/m³, and is defined as the layer characterized by the highest concentration of chlorophyll in the water column (usually during the summer period). In the Mediterranean Sea, the DCM generally lies at depths ranging from 70 to 120 m depending on the depth of light penetration, the depth of the nutricline, and the mesoscale dynamics. In particular, the picture shows the uplifting and downwelling of the DCM in response to the mesoscale circulation. The deepening of the DCM from the western boundary and the Adriatic (dark blue: 50-60 m) towards the eastern boundary of the model domain (green-yellow: 80-110 m) is characteristic of increasing oligotrophication (depletion of plant nutrients) from west to east throughout the Mediterranean basin.
The video shows a 3D movie of the dense water formation and spreading in the Adriatic Sea during 2011/2012. The result provides a demonstration of a physical process that, through the action of the BFMCOUPLER a coupling scheme linking MITgcm with the BFM model for ocean biogeochemistry, drives/powers the carbon continental shelf pump (a coupled physical-biogeochemical process.) Dense water formation and spreading is the driving process of the carbon continental shelf pump that transports the atmospheric CO2 into the deep layers of the Mediterranean Sea. The movie shows the formation of the dense water on the shelf during winter and the spreading and sinking of the dense water masses in spring-summer 2012. You can also see the dense water cascading in the southern Adriatic Pit in March-April-May. Then the Carbon-rich dense water accumulates in the bottom of the southern Adriatic Sea and/or flows into the Mediterranean deep layers – Video courtesy: Gianpiero Cossarini

To find out more about this work or about BFMCOUPLER contact Gianpiero

About the Researcher:

 

Gianpiero Cossarini works as a Researcher in the Department of Oceanography of the Istituto Nazionale di Oceanografia e di Geofisica Sperimentale – OGS in Trieste, Italy. His research activities include marine biogeochemical modeling, with a focus on development of biogeochemical-transport models for marginal, coastal seas and estuaries; development and use of methodologies for data assimilation, sensitivity analysis, calibration and validation of models which he has applied variously to the Mediterranean Sea, Adriatic Sea, the Gulf of Trieste and the Venice Lagoon. When he is not hard at work modeling the biogeochemistry of the ocean he says he enjoys mountain climbing to explore the nature from another perspective.

This Month’s Featured Publication:

Other New Publications this Month

Wilton Aguiar, Mauricio M. Mata and Rodrigo Kerr (2017), On the deep convection events and Antarctic Bottom Water formation in ocean reanalysis products, Ocean Sci. Discuss., doi: 10.5194/os-2017-9

Fabrice Ardhuin, Sarah T. Gille, Dimitris Menemenlis, Cesar B. Rocha, Nicolas Rascle, Bertrand Chapron, Jonathan Gula, Jeroen Molemaker (2017), Small-scale open-ocean currents have large effects on wind-wave heights, Journal of Geophysical Research – Oceans, doi: 10.1002/2016JC012413

Adam S. Candy (2017), A consistent approach to unstructured mesh generation for geophysical models, arXiv: 1703.08491

Jordi, A., Georgas, N. & Blumberg, A. (2017), A parallel domain decomposition algorithm for coastal ocean circulation models based on integer linear programming, Ocean Dynamics, 67: 639. doi: 10.1007/s10236-017-1049-0

A.K. Jithin, A.S. Unnikrishnan, Fernando Vijayan, M.P. Subeesh, R. Fernandes, S. Khalap, S. Narayan, Y. Agarvadekar, M. Gaonkar, P. Taria, A. Kankonkara, S. Vernekar (2017), Observed tidal currents on the continental shelf off the east coast of India, Continental Shelf Research, doi: 10.1016/j.csr.2017.04.001

Vikram Khade, Jaison Kurian, Ping Chang, , Istvan Szunyogh, Kristen Thyng, Raffaele Montuoro (2017), Oceanic ensemble forecasting in the Gulf of Mexico: An application to the case of the Deep Water Horizon oil spill, Ocean Modelling, Volume 113, May 2017, Pages 171–184, doi: 10.1016/j.ocemod.2017.04.004

Brian K. Kilpatrick et al. (2017), Community Targets for JWSTs Early Release Science Program: Evaluation of WASP-63b, arXiv: 1704.07421

Kosempa, Michael (2017), Southern Ocean Transport by Combining Satellite Altimetry and Temperature/Salinity Profile Data, University of South Florida, ProQuest Dissertations Publishing, 10260614

Xinfeng Liang, Christopher G. Piecuch, Rui M. Ponte, Gael Forget, Carl Wunsch, Patrick Heimbach (2017), Change of the Global Ocean Vertical Heat Transport over 1993-2010, Journal of Climate, doi: 10.1175/JCLI-D-16-0569.1

Gustavo M. Marques, Mathew G. Wells, Laurie Padman, Tamay M. Özgökmen (2017), Flow splitting in numerical simulations of oceanic dense-water outflows, Ocean Modelling, Volume 113, May 2017, Pages 66–84, doi: 10.1016/j.ocemod.2017.03.011

Pierre Mathiot, Adrian Jenkins, Christopher Harris, Gurvan Madec (2017), Explicit and parametrised representation of under ice shelf seas in a z* coordinate ocean model, Geosci. Model Dev. Discuss., doi:10.5194/gmd-2017-37

N. J. Mayne, F. Debras, I. Baraffe, John Thuburn, David S. Amundsen, David M. Acremen, Chris Smith, Matthew K. Browning, James Manners and Nigel Wood (2017), Results from a set of three-dimensional numerical experiments of a hot Jupiter atmosphere, arXiv: 1704.00539

Jean A. Mensa, M.-L. Timmermans (2017), Characterizing the seasonal cycle of upper-ocean flows under multi-year sea ice, Ocean Modelling, Volume 113, May 2017, Pages 115–130, doi: 10.1016/j.ocemod.2017.03.009

Luke Phillipson, Ralf Toumi (2017), Impact of Data Assimilation on Ocean Current Forecasts in the Angola Basin, Ocean Modelling, doi: 10.1016/j.ocemod.2017.04.006

Rencurrel, Michael Cameron (2017), Understanding Climatic Adjustment to Variations in Tropical Ocean Heat Transport, State University of New York at Albany Dissertation, ProQuest Dissertations Publishing, 10260002,

Nataliya Stashchuk, Vasiliy Vlasenko, Phil Hosegood, W. Alex M. Nimmo-Smith (2017), Tidally induced residual current over the Malin Sea continental slope, Continental Shelf Research, Volume 139, 1 May 2017, Pages 21–34, doi: 10.1016/j.csr.2017.03.010

Tsiaras, K.P., Hoteit, I., Kalaroni, S. et al. (2017), A hybrid ensemble-OI Kalman filter for efficient data assimilation into a 3-D biogeochemical model of the Mediterranean, Ocean Dynamics, doi: 10.1007/s10236-017-1050-7

Tom Van der Stocken, Dimitris Menemenlis (2017), Modelling mangrove propagule dispersal trajectories using high-resolution estimates of ocean surface winds and currents, Biotropica, doi: 10.1111/btp.12440

Zheyu Zhou, Xiao Yu, Tian-Jian Hsu, Fengyan Shi, W. Rockwell Geyer, James T. Kirby (2017), On nonhydrostatic coastal model simulations of shear instabilities in a stratified shear flow at high Reynolds number, Journal of Geophysical Research – Oceans, doi: 10.1002/2016JC012334

Do you have news about research using MITgcm? We are looking for contributions to these pages. If you have an interesting MITgcm project (ocean, atmosphere, sea-ice, physics, biology or otherwise) that you want to tell people about, get in touch. To make a post, contact Helen