Articles | Volume 9, issue 4
Geosci. Model Dev., 9, 1523–1543, 2016
https://doi.org/10.5194/gmd-9-1523-2016
© Author(s) 2016. This work is distributed under
the Creative Commons Attribution 3.0 License.
the Creative Commons Attribution 3.0 License.
Special issue: Nucleus for European Modelling of the Ocean - NEMO
Geosci. Model Dev., 9, 1523–1543, 2016
https://doi.org/10.5194/gmd-9-1523-2016
© Author(s) 2016. This work is distributed under
the Creative Commons Attribution 3.0 License.
the Creative Commons Attribution 3.0 License.
Development and technical paper
21 Apr 2016
Development and technical paper
| 21 Apr 2016
Evaluation of an operational ocean model configuration at 1/12° spatial resolution for the Indonesian seas (NEMO2.3/INDO12) – Part 2: Biogeochemistry
Elodie Gutknecht et al.
Related authors
Elodie Gutknecht, Guillaume Reffray, Alexandre Mignot, Tomasz Dabrowski, and Marcos G. Sotillo
Ocean Sci., 15, 1489–1516, https://doi.org/10.5194/os-15-1489-2019, https://doi.org/10.5194/os-15-1489-2019, 2019
Short summary
Short summary
As part of the Copernicus Marine Environment Monitoring Service, an operational ocean forecasting system monitors the ocean dynamics and marine ecosystems of the European waters. This paper assesses the performance of the key biogeochemical variables (oxygen, nutrients, Chl a, primary production) using a 7-year pre-operational qualification simulation (2010–2016). The simulation can be used to better understand the current state, the changes and the health of European marine ecosystems.
Nicolas Metzl, Claire Lo Monaco, Coraline Leseurre, Céline Ridame, Jonathan Fin, Claude Mignon, Marion Gehlen, and Thi Tuyet Trang Chau
Biogeosciences, 19, 1451–1468, https://doi.org/10.5194/bg-19-1451-2022, https://doi.org/10.5194/bg-19-1451-2022, 2022
Short summary
Short summary
During an oceanographic cruise conducted in January 2020 in the south-western Indian Ocean, we observed very low CO2 concentrations associated with a strong phytoplankton bloom that occurred south-east of Madagascar. This biological event led to a strong regional CO2 ocean sink not previously observed.
Thi Tuyet Trang Chau, Marion Gehlen, and Frédéric Chevallier
Biogeosciences, 19, 1087–1109, https://doi.org/10.5194/bg-19-1087-2022, https://doi.org/10.5194/bg-19-1087-2022, 2022
Short summary
Short summary
Air–sea CO2 fluxes and associated uncertainty over the open ocean to coastal shelves are estimated with a new ensemble-based reconstruction of pCO2 trained on observation-based data. The regional distribution and seasonality of CO2 sources and sinks are consistent with those suggested in previous studies as well as mechanisms discussed therein. The ensemble-based uncertainty field allows identifying critical regions where improvements in pCO2 and air–sea CO2 flux estimates should be a priority.
Amanda R. Fay, Luke Gregor, Peter Landschützer, Galen A. McKinley, Nicolas Gruber, Marion Gehlen, Yosuke Iida, Goulven G. Laruelle, Christian Rödenbeck, Alizée Roobaert, and Jiye Zeng
Earth Syst. Sci. Data, 13, 4693–4710, https://doi.org/10.5194/essd-13-4693-2021, https://doi.org/10.5194/essd-13-4693-2021, 2021
Short summary
Short summary
The movement of carbon dioxide from the atmosphere to the ocean is estimated using surface ocean carbon (pCO2) measurements and an equation including variables such as temperature and wind speed; the choices of these variables lead to uncertainties. We introduce the SeaFlux ensemble which provides carbon flux maps calculated in a consistent manner, thus reducing uncertainty by using common choices for wind speed and a set definition of "global" coverage.
Anna Denvil-Sommer, Marion Gehlen, and Mathieu Vrac
Ocean Sci., 17, 1011–1030, https://doi.org/10.5194/os-17-1011-2021, https://doi.org/10.5194/os-17-1011-2021, 2021
Short summary
Short summary
In this work we explored design options for a future Atlantic-scale observational network enabling the release of carbon system estimates by combining data streams from various platforms. We used outputs of a physical–biogeochemical global ocean model at sites of real-world observations to reconstruct surface ocean pCO2 by applying a non-linear feed-forward neural network. The results provide important information for future BGC-Argo deployment, i.e. important regions and the number of floats.
Pierre Friedlingstein, Michael O'Sullivan, Matthew W. Jones, Robbie M. Andrew, Judith Hauck, Are Olsen, Glen P. Peters, Wouter Peters, Julia Pongratz, Stephen Sitch, Corinne Le Quéré, Josep G. Canadell, Philippe Ciais, Robert B. Jackson, Simone Alin, Luiz E. O. C. Aragão, Almut Arneth, Vivek Arora, Nicholas R. Bates, Meike Becker, Alice Benoit-Cattin, Henry C. Bittig, Laurent Bopp, Selma Bultan, Naveen Chandra, Frédéric Chevallier, Louise P. Chini, Wiley Evans, Liesbeth Florentie, Piers M. Forster, Thomas Gasser, Marion Gehlen, Dennis Gilfillan, Thanos Gkritzalis, Luke Gregor, Nicolas Gruber, Ian Harris, Kerstin Hartung, Vanessa Haverd, Richard A. Houghton, Tatiana Ilyina, Atul K. Jain, Emilie Joetzjer, Koji Kadono, Etsushi Kato, Vassilis Kitidis, Jan Ivar Korsbakken, Peter Landschützer, Nathalie Lefèvre, Andrew Lenton, Sebastian Lienert, Zhu Liu, Danica Lombardozzi, Gregg Marland, Nicolas Metzl, David R. Munro, Julia E. M. S. Nabel, Shin-Ichiro Nakaoka, Yosuke Niwa, Kevin O'Brien, Tsuneo Ono, Paul I. Palmer, Denis Pierrot, Benjamin Poulter, Laure Resplandy, Eddy Robertson, Christian Rödenbeck, Jörg Schwinger, Roland Séférian, Ingunn Skjelvan, Adam J. P. Smith, Adrienne J. Sutton, Toste Tanhua, Pieter P. Tans, Hanqin Tian, Bronte Tilbrook, Guido van der Werf, Nicolas Vuichard, Anthony P. Walker, Rik Wanninkhof, Andrew J. Watson, David Willis, Andrew J. Wiltshire, Wenping Yuan, Xu Yue, and Sönke Zaehle
Earth Syst. Sci. Data, 12, 3269–3340, https://doi.org/10.5194/essd-12-3269-2020, https://doi.org/10.5194/essd-12-3269-2020, 2020
Short summary
Short summary
The Global Carbon Budget 2020 describes the data sets and methodology used to quantify the emissions of carbon dioxide and their partitioning among the atmosphere, land, and ocean. These living data are updated every year to provide the highest transparency and traceability in the reporting of CO2, the key driver of climate change.
Lester Kwiatkowski, Olivier Torres, Laurent Bopp, Olivier Aumont, Matthew Chamberlain, James R. Christian, John P. Dunne, Marion Gehlen, Tatiana Ilyina, Jasmin G. John, Andrew Lenton, Hongmei Li, Nicole S. Lovenduski, James C. Orr, Julien Palmieri, Yeray Santana-Falcón, Jörg Schwinger, Roland Séférian, Charles A. Stock, Alessandro Tagliabue, Yohei Takano, Jerry Tjiputra, Katsuya Toyama, Hiroyuki Tsujino, Michio Watanabe, Akitomo Yamamoto, Andrew Yool, and Tilo Ziehn
Biogeosciences, 17, 3439–3470, https://doi.org/10.5194/bg-17-3439-2020, https://doi.org/10.5194/bg-17-3439-2020, 2020
Short summary
Short summary
We assess 21st century projections of marine biogeochemistry in the CMIP6 Earth system models. These models represent the most up-to-date understanding of climate change. The models generally project greater surface ocean warming, acidification, subsurface deoxygenation, and euphotic nitrate reductions but lesser primary production declines than the previous generation of models. This has major implications for the impact of anthropogenic climate change on marine ecosystems.
Pierre Friedlingstein, Matthew W. Jones, Michael O'Sullivan, Robbie M. Andrew, Judith Hauck, Glen P. Peters, Wouter Peters, Julia Pongratz, Stephen Sitch, Corinne Le Quéré, Dorothee C. E. Bakker, Josep G. Canadell, Philippe Ciais, Robert B. Jackson, Peter Anthoni, Leticia Barbero, Ana Bastos, Vladislav Bastrikov, Meike Becker, Laurent Bopp, Erik Buitenhuis, Naveen Chandra, Frédéric Chevallier, Louise P. Chini, Kim I. Currie, Richard A. Feely, Marion Gehlen, Dennis Gilfillan, Thanos Gkritzalis, Daniel S. Goll, Nicolas Gruber, Sören Gutekunst, Ian Harris, Vanessa Haverd, Richard A. Houghton, George Hurtt, Tatiana Ilyina, Atul K. Jain, Emilie Joetzjer, Jed O. Kaplan, Etsushi Kato, Kees Klein Goldewijk, Jan Ivar Korsbakken, Peter Landschützer, Siv K. Lauvset, Nathalie Lefèvre, Andrew Lenton, Sebastian Lienert, Danica Lombardozzi, Gregg Marland, Patrick C. McGuire, Joe R. Melton, Nicolas Metzl, David R. Munro, Julia E. M. S. Nabel, Shin-Ichiro Nakaoka, Craig Neill, Abdirahman M. Omar, Tsuneo Ono, Anna Peregon, Denis Pierrot, Benjamin Poulter, Gregor Rehder, Laure Resplandy, Eddy Robertson, Christian Rödenbeck, Roland Séférian, Jörg Schwinger, Naomi Smith, Pieter P. Tans, Hanqin Tian, Bronte Tilbrook, Francesco N. Tubiello, Guido R. van der Werf, Andrew J. Wiltshire, and Sönke Zaehle
Earth Syst. Sci. Data, 11, 1783–1838, https://doi.org/10.5194/essd-11-1783-2019, https://doi.org/10.5194/essd-11-1783-2019, 2019
Short summary
Short summary
The Global Carbon Budget 2019 describes the data sets and methodology used to quantify the emissions of carbon dioxide and their partitioning among the atmosphere, land, and ocean. These living data are updated every year to provide the highest transparency and traceability in the reporting of CO2, the key driver of climate change.
Elodie Gutknecht, Guillaume Reffray, Alexandre Mignot, Tomasz Dabrowski, and Marcos G. Sotillo
Ocean Sci., 15, 1489–1516, https://doi.org/10.5194/os-15-1489-2019, https://doi.org/10.5194/os-15-1489-2019, 2019
Short summary
Short summary
As part of the Copernicus Marine Environment Monitoring Service, an operational ocean forecasting system monitors the ocean dynamics and marine ecosystems of the European waters. This paper assesses the performance of the key biogeochemical variables (oxygen, nutrients, Chl a, primary production) using a 7-year pre-operational qualification simulation (2010–2016). The simulation can be used to better understand the current state, the changes and the health of European marine ecosystems.
Jens Terhaar, James C. Orr, Marion Gehlen, Christian Ethé, and Laurent Bopp
Biogeosciences, 16, 2343–2367, https://doi.org/10.5194/bg-16-2343-2019, https://doi.org/10.5194/bg-16-2343-2019, 2019
Short summary
Short summary
A budget of anthropogenic carbon in the Arctic Ocean, the main driver of open-ocean acidification, was constructed for the first time using a high-resolution ocean model. The budget reveals that anthropogenic carbon enters the Arctic Ocean mainly by lateral transport; the air–sea flux plays a minor role. Coarser-resolution versions of the same model, typical of earth system models, store less anthropogenic carbon in the Arctic Ocean and thus underestimate ocean acidification in the Arctic Ocean.
Anna Denvil-Sommer, Marion Gehlen, Mathieu Vrac, and Carlos Mejia
Geosci. Model Dev., 12, 2091–2105, https://doi.org/10.5194/gmd-12-2091-2019, https://doi.org/10.5194/gmd-12-2091-2019, 2019
Short summary
Short summary
This work is dedicated to a new model that reconstructs the surface ocean partial pressure of carbon dioxide (pCO2) over the global ocean on a monthly 1°×1° grid. The model is based on a feed-forward neural network and represents the nonlinear relationships between pCO2 and the ocean drivers. Reconstructed pCO2 has a satisfying accuracy compared to independent observational data and shows a good agreement in seasonal and interannual variability with three existing mapping methods.
Virginie Racapé, Patricia Zunino, Herlé Mercier, Pascale Lherminier, Laurent Bopp, Fiz F. Pérèz, and Marion Gehlen
Biogeosciences, 15, 4661–4682, https://doi.org/10.5194/bg-15-4661-2018, https://doi.org/10.5194/bg-15-4661-2018, 2018
Short summary
Short summary
This study of a model–data comparison investigates the relationship between transport, air–sea flux and storage rate of Cant in the North Atlantic Subpolar Ocean over the past 53 years. It reveals the key role played by Central Water for storing Cant in the subtropical region and for supplying Cant into the deep ocean. The Cant transfer to the deep ocean occurred mainly north of the OVIDE section, and just a small fraction was exported to the subtropical gyre within the lower MOC.
Christoph Heinze, Tatiana Ilyina, and Marion Gehlen
Biogeosciences, 15, 3521–3539, https://doi.org/10.5194/bg-15-3521-2018, https://doi.org/10.5194/bg-15-3521-2018, 2018
Short summary
Short summary
The ocean becomes increasingly acidified through uptake of additional man-made CO2 from the atmosphere. This is impacting ecosystems. In order to find out whether reduced biological production of calcium carbonate shell material of biota is occurring at a large scale, we carried out a model study simulating the changes in oceanic 230Th concentrations with reduced availability of calcium carbonate particles in the water. 230Th can serve as a useful magnifying glass for acidification impacts.
Olivier Aumont, Marco van Hulten, Matthieu Roy-Barman, Jean-Claude Dutay, Christian Éthé, and Marion Gehlen
Biogeosciences, 14, 2321–2341, https://doi.org/10.5194/bg-14-2321-2017, https://doi.org/10.5194/bg-14-2321-2017, 2017
Short summary
Short summary
The marine biological carbon pump is dominated by the vertical transfer of particulate organic carbon (POC) from the surface ocean to its interior. In this study, we explore the impacts of a variable composition of this organic matter using a global ocean biogeochemical model. We show that accounting for a variable lability of POC increases POC concentrations by up to 2 orders of magnitude in the ocean's interior. Furthermore, the amount of carbon that reaches the sediments is twice as large.
Marco van Hulten, Rob Middag, Jean-Claude Dutay, Hein de Baar, Matthieu Roy-Barman, Marion Gehlen, Alessandro Tagliabue, and Andreas Sterl
Biogeosciences, 14, 1123–1152, https://doi.org/10.5194/bg-14-1123-2017, https://doi.org/10.5194/bg-14-1123-2017, 2017
Short summary
Short summary
We ran a global ocean model to understand manganese (Mn), a biologically essential element. Our model shows that (i) in the deep ocean, dissolved [Mn] is mostly homogeneous ~0.10—0.15 nM. The model reproduces this with a threshold on MnO2 of 25 pM, suggesting a minimal particle concentration is needed before aggregation and removal become efficient.
(ii) The observed distinct hydrothermal signals are produced by assuming both a strong source and a strong removal of Mn near hydrothermal vents.
Timothée Bourgeois, James C. Orr, Laure Resplandy, Jens Terhaar, Christian Ethé, Marion Gehlen, and Laurent Bopp
Biogeosciences, 13, 4167–4185, https://doi.org/10.5194/bg-13-4167-2016, https://doi.org/10.5194/bg-13-4167-2016, 2016
Short summary
Short summary
The global coastal ocean took up 0.1 Pg C yr−1 of anthropogenic carbon during 1993–2012 based on new biogeochemical simulations with an eddying 3-D global model. That is about half of the most recent estimate, an extrapolation based on surface areas. It should not be confused with the continental shelf pump, perhaps 10 times larger, which includes natural as well as anthropogenic carbon. Coastal uptake of anthropogenic carbon is limited by its offshore transport.
Roland Séférian, Marion Gehlen, Laurent Bopp, Laure Resplandy, James C. Orr, Olivier Marti, John P. Dunne, James R. Christian, Scott C. Doney, Tatiana Ilyina, Keith Lindsay, Paul R. Halloran, Christoph Heinze, Joachim Segschneider, Jerry Tjiputra, Olivier Aumont, and Anastasia Romanou
Geosci. Model Dev., 9, 1827–1851, https://doi.org/10.5194/gmd-9-1827-2016, https://doi.org/10.5194/gmd-9-1827-2016, 2016
Short summary
Short summary
This paper explores how the large diversity in spin-up protocols used for ocean biogeochemistry in CMIP5 models contributed to inter-model differences in modeled fields. We show that a link between spin-up duration and skill-score metrics emerges from both individual IPSL-CM5A-LR's results and an ensemble of CMIP5 models. Our study suggests that differences in spin-up protocols constitute a source of inter-model uncertainty which would require more attention in future intercomparison exercises.
Benoît Tranchant, Guillaume Reffray, Eric Greiner, Dwiyoga Nugroho, Ariane Koch-Larrouy, and Philippe Gaspar
Geosci. Model Dev., 9, 1037–1064, https://doi.org/10.5194/gmd-9-1037-2016, https://doi.org/10.5194/gmd-9-1037-2016, 2016
O. Aumont, C. Ethé, A. Tagliabue, L. Bopp, and M. Gehlen
Geosci. Model Dev., 8, 2465–2513, https://doi.org/10.5194/gmd-8-2465-2015, https://doi.org/10.5194/gmd-8-2465-2015, 2015
J. Martinez-Rey, L. Bopp, M. Gehlen, A. Tagliabue, and N. Gruber
Biogeosciences, 12, 4133–4148, https://doi.org/10.5194/bg-12-4133-2015, https://doi.org/10.5194/bg-12-4133-2015, 2015
T. Roy, F. Lombard, L. Bopp, and M. Gehlen
Biogeosciences, 12, 2873–2889, https://doi.org/10.5194/bg-12-2873-2015, https://doi.org/10.5194/bg-12-2873-2015, 2015
M. Gehlen, R. Séférian, D. O. B. Jones, T. Roy, R. Roth, J. Barry, L. Bopp, S. C. Doney, J. P. Dunne, C. Heinze, F. Joos, J. C. Orr, L. Resplandy, J. Segschneider, and J. Tjiputra
Biogeosciences, 11, 6955–6967, https://doi.org/10.5194/bg-11-6955-2014, https://doi.org/10.5194/bg-11-6955-2014, 2014
Short summary
Short summary
This study evaluates potential impacts of pH reductions on North Atlantic deep-sea ecosystems in response to latest IPCC scenarios.Multi-model projections of pH changes over the seafloor are analysed with reference to a critical threshold based on palaeo-oceanographic studies, contemporary observations and model results. By 2100 under the most severe IPCC CO2 scenario, pH reductions occur over ~23% of deep-sea canyons and ~8% of seamounts – including seamounts proposed as marine protected areas.
L. Bopp, L. Resplandy, J. C. Orr, S. C. Doney, J. P. Dunne, M. Gehlen, P. Halloran, C. Heinze, T. Ilyina, R. Séférian, J. Tjiputra, and M. Vichi
Biogeosciences, 10, 6225–6245, https://doi.org/10.5194/bg-10-6225-2013, https://doi.org/10.5194/bg-10-6225-2013, 2013
V. Cocco, F. Joos, M. Steinacher, T. L. Frölicher, L. Bopp, J. Dunne, M. Gehlen, C. Heinze, J. Orr, A. Oschlies, B. Schneider, J. Segschneider, and J. Tjiputra
Biogeosciences, 10, 1849–1868, https://doi.org/10.5194/bg-10-1849-2013, https://doi.org/10.5194/bg-10-1849-2013, 2013
V. Krumins, M. Gehlen, S. Arndt, P. Van Cappellen, and P. Regnier
Biogeosciences, 10, 371–398, https://doi.org/10.5194/bg-10-371-2013, https://doi.org/10.5194/bg-10-371-2013, 2013
Related subject area
Oceanography
DINCAE 2.0: multivariate convolutional neural network with error estimates to reconstruct sea surface temperature satellite and altimetry observations
RADIv1: a non-steady-state early diagenetic model for ocean sediments in Julia and MATLAB/GNU Octave
IBI-CCS: a regional high-resolution model to simulate sea level in western Europe
Empirical Lagrangian parametrization for wind-driven mixing of buoyant particles at the ocean surface
Improving ocean modeling software NEMO 4.0 benchmarking and communication efficiency
Improvements in the regional South China Sea Operational Oceanography Forecasting System (SCSOFSv2)
Reconsideration of wind stress, wind waves, and turbulence in simulating wind-driven currents of shallow lakes in the Wave and Current Coupled Model (WCCM) version 1.0
ISWFoam: a numerical model for internal solitary wave simulation in continuously stratified fluids
PyCO2SYS v1.8: marine carbonate system calculations in Python
Plume spreading test case for coastal ocean models
The interpretation of temperature and salinity variables in numerical ocean model output and the calculation of heat fluxes and heat content
S2P3-R v2.0: computationally efficient modelling of shelf seas on regional to global scales
The Lagrangian-based Floating Macroalgal Growth and Drift Model (FMGDM v1.0): application to the Yellow Sea green tide
Nemo-Nordic 2.0: operational marine forecast model for the Baltic Sea
Australian tidal currents – assessment of a barotropic model (COMPAS v1.3.0 rev6631) with an unstructured grid
Sedapp v2021: a nonlinear diffusion-based forward stratigraphic model for shallow marine environments
A discrete interaction numerical model for coagulation and fragmentation of marine detritic particulate matter (Coagfrag v.1)
Parallel computing efficiency of SWAN 40.91
Integrating CVMix into GOTM (v6.0): a consistent framework for testing, comparing, and applying ocean mixing schemes
A NEMO-based model of Sargassum distribution in the tropical Atlantic: description of the model and sensitivity analysis (NEMO-Sarg1.0)
Evaluating the physical and biogeochemical state of the global ocean component of UKESM1 in CMIP6 historical simulations
Iron and sulfur cycling in the cGENIE.muffin Earth system model (v0.9.21)
BFM17 v1.0: a reduced biogeochemical flux model for upper-ocean biophysical simulations
A mechanistic analysis of tropical Pacific dynamic sea level in GFDL-OM4 under OMIP-I and OMIP-II forcings
Comparison of ocean vertical mixing schemes in the Max Planck Institute Earth System Model (MPI-ESM1.2)
MESMO 3: Flexible phytoplankton stoichiometry and refractory dissolved organic matter
HIDRA 1.0: deep-learning-based ensemble sea level forecasting in the northern Adriatic
Towards multiscale modeling of ocean surface turbulent mixing using coupled MPAS-Ocean v6.3 and PALM v5.0
Improved representation of river runoff in Estimating the Circulation and Climate of the Ocean Version 4 (ECCOv4) simulations: implementation, evaluation, and impacts to coastal plume regions
The Regional Ice Ocean Prediction System v2: a pan-Canadian ocean analysis system using an online tidal harmonic analysis
Global storm tide modeling with ADCIRC v55: unstructured mesh design and performance
Development of a MetUM (v 11.1) and NEMO (v 3.6) coupled operational forecast model for the Maritime Continent – Part 1: Evaluation of ocean forecasts
Advanced parallel implementation of the coupled ocean–ice model FEMAO (version 2.0) with load balancing
The Meridionally Averaged Model of Eastern Boundary Upwelling Systems (MAMEBUSv1.0)
Model-driven optimization of coastal sea observatories through data assimilation in a finite element hydrodynamic model (SHYFEM v. 7_5_65)
A simplified atmospheric boundary layer model for an improved representation of air–sea interactions in eddying oceanic models: implementation and first evaluation in NEMO (4.0)
Performance of offline passive tracer advection in the Regional Ocean Modeling System (ROMS; v3.6, revision 904)
Implementation and assessment of a carbonate system model (Eco3M-CarbOx v1.1) in a highly dynamic Mediterranean coastal site (Bay of Marseille, France)
Numerical integrators for Lagrangian oceanography
Multi-grid algorithm for passive tracer transport in the NEMO ocean circulation model: a case study with the NEMO OGCM (version 3.6)
Introducing LAB60: A 1∕60° NEMO 3.6 numerical simulation of the Labrador Sea
Impact of horizontal resolution on global ocean–sea ice model simulations based on the experimental protocols of the Ocean Model Intercomparison Project phase 2 (OMIP-2)
CSIRO Environmental Modelling Suite (EMS): scientific description of the optical and biogeochemical models (vB3p0)
Constraining the response of phytoplankton to zooplankton grazing and photo-acclimation in a temperate shelf sea with a 1-D model – towards S2P3 v8.0
Doppio – a ROMS (v3.6)-based circulation model for the Mid-Atlantic Bight and Gulf of Maine: configuration and comparison to integrated coastal observing network observations
Evaluation of global ocean–sea-ice model simulations based on the experimental protocols of the Ocean Model Intercomparison Project phase 2 (OMIP-2)
Representation of the Denmark Strait overflow in a z-coordinate eddying configuration of the NEMO (v3.6) ocean model: resolution and parameter impacts
A global eddying hindcast ocean simulation with OFES2
Tracking water masses using passive-tracer transport in NEMO v3.4 with NEMOTAM: application to North Atlantic Deep Water and North Atlantic Subtropical Mode Water
Sensitivity study on the main tidal constituents of the Gulf of Tonkin by using the frequency-domain tidal solver in T-UGOm
Alexander Barth, Aida Alvera-Azcárate, Charles Troupin, and Jean-Marie Beckers
Geosci. Model Dev., 15, 2183–2196, https://doi.org/10.5194/gmd-15-2183-2022, https://doi.org/10.5194/gmd-15-2183-2022, 2022
Short summary
Short summary
Earth-observing satellites provide routine measurement of several ocean parameters. However, these datasets have a significant amount of missing data due to the presence of clouds or other limitations of the employed sensors. This paper describes a method to infer the value of the missing satellite data based on a convolutional autoencoder (a specific type of neural network architecture). The technique also provides a reliable error estimate of the interpolated value.
Olivier Sulpis, Matthew P. Humphreys, Monica M. Wilhelmus, Dustin Carroll, William M. Berelson, Dimitris Menemenlis, Jack J. Middelburg, and Jess F. Adkins
Geosci. Model Dev., 15, 2105–2131, https://doi.org/10.5194/gmd-15-2105-2022, https://doi.org/10.5194/gmd-15-2105-2022, 2022
Short summary
Short summary
A quarter of the surface of the Earth is covered by marine sediments rich in calcium carbonates, and their dissolution acts as a giant antacid tablet protecting the ocean against human-made acidification caused by massive CO2 emissions. Here, we present a new model of sediment chemistry that incorporates the latest experimental findings on calcium carbonate dissolution kinetics. This model can be used to predict how marine sediments evolve through time in response to environmental perturbations.
Alisée A. Chaigneau, Guillaume Reffray, Aurore Voldoire, and Angélique Melet
Geosci. Model Dev., 15, 2035–2062, https://doi.org/10.5194/gmd-15-2035-2022, https://doi.org/10.5194/gmd-15-2035-2022, 2022
Short summary
Short summary
Climate-change-induced sea level rise is a major threat for coastal and low-lying regions. Projections of coastal sea level changes are thus of great interest for coastal risk assessment and have significantly developed in recent years. In this paper, the objective is to provide high-resolution (6 km) projections of sea level changes in the northeastern Atlantic region bordering western Europe. For that purpose, a regional model is used to refine existing coarse global projections.
Victor Onink, Erik van Sebille, and Charlotte Laufkötter
Geosci. Model Dev., 15, 1995–2012, https://doi.org/10.5194/gmd-15-1995-2022, https://doi.org/10.5194/gmd-15-1995-2022, 2022
Short summary
Short summary
Turbulent mixing is a vital process in 3D modeling of particle transport in the ocean. However, since turbulence occurs on very short spatial scales and timescales, large-scale ocean models generally have highly simplified turbulence representations. We have developed parametrizations for the vertical turbulent transport of buoyant particles that can be easily applied in a large-scale particle tracking model. The predicted vertical concentration profiles match microplastic observations well.
Gaston Irrmann, Sébastien Masson, Éric Maisonnave, David Guibert, and Erwan Raffin
Geosci. Model Dev., 15, 1567–1582, https://doi.org/10.5194/gmd-15-1567-2022, https://doi.org/10.5194/gmd-15-1567-2022, 2022
Short summary
Short summary
To be efficient on supercomputers, software must be high-performance at computing many concurrent tasks. Communications between tasks is often necessary but time consuming, and ocean modelling software NEMO 4.0 is no exception.
In this work we describe approaches enabling fewer communications, an optimization to share the workload more equally between tasks and a new flexible configuration to assess NEMO's performance easily.
Xueming Zhu, Ziqing Zu, Shihe Ren, Miaoyin Zhang, Yunfei Zhang, Hui Wang, and Ang Li
Geosci. Model Dev., 15, 995–1015, https://doi.org/10.5194/gmd-15-995-2022, https://doi.org/10.5194/gmd-15-995-2022, 2022
Short summary
Short summary
SCSOFS has provided daily updated marine forecasting in the South China Sea for the next 5 d since 2013. Comprehensive updates have been conducted to the configurations of SCSOFS's physical model and data assimilation scheme in order to improve its forecasting skill. The three most sensitive updates are highlighted. Scientific comparison and accuracy assessment results indicate that remarkable improvements have been achieved in SCSOFSv2 with respect to the original version SCSOFSv1.
Tingfeng Wu, Boqiang Qin, Anning Huang, Yongwei Sheng, Shunxin Feng, and Céline Casenave
Geosci. Model Dev., 15, 745–769, https://doi.org/10.5194/gmd-15-745-2022, https://doi.org/10.5194/gmd-15-745-2022, 2022
Short summary
Short summary
Most hydrodynamic models were initially developed based in marine environments. They cannot be directly applied to large lakes. Based on field observations and numerical experiments of a large shallow lake, we developed a hydrodynamic model by adopting new schemes of wind stress, wind waves, and turbulence for large lakes. Our model can greatly improve the simulation of lake currents. This study will be a reminder to limnologists to prudently use ocean models to study lake hydrodynamics.
Jingyuan Li, Qinghe Zhang, and Tongqing Chen
Geosci. Model Dev., 15, 105–127, https://doi.org/10.5194/gmd-15-105-2022, https://doi.org/10.5194/gmd-15-105-2022, 2022
Short summary
Short summary
A numerical model, ISWFoam with a modified k–ω SST model, is developed to simulate internal solitary waves (ISWs) in continuously stratified, incompressible, viscous fluids based on a fully three-dimensional (3D) Navier–Stokes equation with the finite-volume method. ISWFoam can accurately simulate the generation and evolution of ISWs, the ISW breaking phenomenon, waveform inversion of ISWs, and the interaction between ISWs and complex topography.
Matthew P. Humphreys, Ernie R. Lewis, Jonathan D. Sharp, and Denis Pierrot
Geosci. Model Dev., 15, 15–43, https://doi.org/10.5194/gmd-15-15-2022, https://doi.org/10.5194/gmd-15-15-2022, 2022
Short summary
Short summary
The ocean helps to mitigate our impact on Earth's climate by absorbing about a quarter of the carbon dioxide (CO2) released by human activities each year. However, once absorbed, chemical reactions between CO2 and water reduce seawater pH (
ocean acidification), which may have adverse effects on marine ecosystems. Our Python package, PyCO2SYS, models the chemical reactions of CO2 in seawater, allowing us to quantify the corresponding changes in pH and related chemical properties.
Vera Fofonova, Tuomas Kärnä, Knut Klingbeil, Alexey Androsov, Ivan Kuznetsov, Dmitry Sidorenko, Sergey Danilov, Hans Burchard, and Karen Helen Wiltshire
Geosci. Model Dev., 14, 6945–6975, https://doi.org/10.5194/gmd-14-6945-2021, https://doi.org/10.5194/gmd-14-6945-2021, 2021
Short summary
Short summary
We present a test case of river plume spreading to evaluate coastal ocean models. Our test case reveals the level of numerical mixing (due to parameterizations used and numerical treatment of processes in the model) and the ability of models to reproduce complex dynamics. The major result of our comparative study is that accuracy in reproducing the analytical solution depends less on the type of applied model architecture or numerical grid than it does on the type of advection scheme.
Trevor J. McDougall, Paul M. Barker, Ryan M. Holmes, Rich Pawlowicz, Stephen M. Griffies, and Paul J. Durack
Geosci. Model Dev., 14, 6445–6466, https://doi.org/10.5194/gmd-14-6445-2021, https://doi.org/10.5194/gmd-14-6445-2021, 2021
Short summary
Short summary
We show that the way that the air–sea heat flux is treated in ocean models means that the model's temperature variable should be interpreted as being Conservative Temperature, irrespective of whether the equation of state used in an ocean model is EOS-80 or TEOS-10.
Paul R. Halloran, Jennifer K. McWhorter, Beatriz Arellano Nava, Robert Marsh, and William Skirving
Geosci. Model Dev., 14, 6177–6195, https://doi.org/10.5194/gmd-14-6177-2021, https://doi.org/10.5194/gmd-14-6177-2021, 2021
Short summary
Short summary
This paper describes the latest version of a simple model for simulating coastal oceanography in response to changes in weather and climate. The latest revision of this model makes scientific improvements but focuses on improvements that allow the model to be run simply at large scales and for long periods of time to explore the implications of (for example) future climate change along large areas of coastline.
Fucang Zhou, Jianzhong Ge, Dongyan Liu, Pingxing Ding, Changsheng Chen, and Xiaodao Wei
Geosci. Model Dev., 14, 6049–6070, https://doi.org/10.5194/gmd-14-6049-2021, https://doi.org/10.5194/gmd-14-6049-2021, 2021
Short summary
Short summary
In this study, a physical–ecological model, the Floating Macroalgal Growth and Drift Model (FMGDM), was developed to determine the dynamic growth and drifting pattern of floating macroalgae. Based on Lagrangian tracking, the macroalgae bloom is jointly controlled by ocean flows, sea surface wind, temperature, irradiation, and nutrients. The FMGDM was robust in successfully reproducing the spatial and temporal dynamics of the massive green tide around the Yellow Sea.
Tuomas Kärnä, Patrik Ljungemyr, Saeed Falahat, Ida Ringgaard, Lars Axell, Vasily Korabel, Jens Murawski, Ilja Maljutenko, Anja Lindenthal, Simon Jandt-Scheelke, Svetlana Verjovkina, Ina Lorkowski, Priidik Lagemaa, Jun She, Laura Tuomi, Adam Nord, and Vibeke Huess
Geosci. Model Dev., 14, 5731–5749, https://doi.org/10.5194/gmd-14-5731-2021, https://doi.org/10.5194/gmd-14-5731-2021, 2021
Short summary
Short summary
We present Nemo-Nordic 2.0, a novel operational marine model for the Baltic Sea. The model covers the Baltic Sea and the North Sea with approximately 1 nmi resolution. We validate the model's performance against sea level, water temperature, and salinity observations, as well as sea ice charts. The skill analysis demonstrates that Nemo-Nordic 2.0 can reproduce the hydrographic features of the Baltic Sea.
David A. Griffin, Mike Herzfeld, Mark Hemer, and Darren Engwirda
Geosci. Model Dev., 14, 5561–5582, https://doi.org/10.5194/gmd-14-5561-2021, https://doi.org/10.5194/gmd-14-5561-2021, 2021
Short summary
Short summary
In support of the developing ocean renewable energy sector, and indeed all mariners, we have developed a new tidal model for Australian waters and thoroughly evaluated it using a new compilation of tide gauge and current meter data. We show that while there is certainly room for improvement, the model provides useful predictions of tidal currents for about 80 % (by area) of Australian shelf waters. So we intend to commence publishing tidal current predictions for those regions soon.
Jingzhe Li, Piyang Liu, Shuyu Sun, Zhifeng Sun, Yongzhang Zhou, Liang Gong, Jinliang Zhang, and Dongxing Du
Geosci. Model Dev., 14, 4925–4937, https://doi.org/10.5194/gmd-14-4925-2021, https://doi.org/10.5194/gmd-14-4925-2021, 2021
Short summary
Short summary
This paper introduces Sedapp, a basin fill simulation tool. Sedapp is an open-source computer code written in R language. Using this program, one can simulate the formation of sedimentary strata, especially in shallow marine environments injected by rivers. With proper parameter settings, the simulation results are very similar to the real geological bodies. Sedapp can also be used in continental fault basin environments, which may serve as a tool for oil exploration.
Gwenaëlle Gremion, Louis-Philippe Nadeau, Christiane Dufresne, Irene R. Schloss, Philippe Archambault, and Dany Dumont
Geosci. Model Dev., 14, 4535–4554, https://doi.org/10.5194/gmd-14-4535-2021, https://doi.org/10.5194/gmd-14-4535-2021, 2021
Short summary
Short summary
An accurate description of detritic organic particles is key to improving estimations of carbon export into the ocean abyss in ocean general circulation models. Yet, most parametrization are numerically impractical due to the required number of tracers needed to resolve the particle size spectrum. Here, a new parametrization that aims to minimize the tracers number while accurately describing the particles dynamics is developed and tested in a series of idealized numerical experiments.
Christo Rautenbach, Julia C. Mullarney, and Karin R. Bryan
Geosci. Model Dev., 14, 4241–4247, https://doi.org/10.5194/gmd-14-4241-2021, https://doi.org/10.5194/gmd-14-4241-2021, 2021
Short summary
Short summary
The simulation of ocean waves is important for various reasons, e.g. ship route safety and coastal vulnerability assessments. SWAN is a popular tool with which ocean waves may be predicted. Simulations using this tool can be computationally expensive. The present study thus aimed to understand which typical parallel-computing SWAN model set-up will be most effective. There thus do exist configurations where these simulations are most time-saving and effective.
Qing Li, Jorn Bruggeman, Hans Burchard, Knut Klingbeil, Lars Umlauf, and Karsten Bolding
Geosci. Model Dev., 14, 4261–4282, https://doi.org/10.5194/gmd-14-4261-2021, https://doi.org/10.5194/gmd-14-4261-2021, 2021
Short summary
Short summary
Different ocean vertical mixing schemes are usually developed in different modeling framework, making the comparison across such schemes difficult. Here, we develop a consistent framework for testing, comparing, and applying different ocean mixing schemes by integrating CVMix into GOTM, which also extends the capability of GOTM towards including the effects of ocean surface waves. A suite of test cases and toolsets for developing and evaluating ocean mixing schemes is also described.
Julien Jouanno, Rachid Benshila, Léo Berline, Antonin Soulié, Marie-Hélène Radenac, Guillaume Morvan, Frédéric Diaz, Julio Sheinbaum, Cristele Chevalier, Thierry Thibaut, Thomas Changeux, Frédéric Menard, Sarah Berthet, Olivier Aumont, Christian Ethé, Pierre Nabat, and Marc Mallet
Geosci. Model Dev., 14, 4069–4086, https://doi.org/10.5194/gmd-14-4069-2021, https://doi.org/10.5194/gmd-14-4069-2021, 2021
Short summary
Short summary
The tropical Atlantic has been facing a massive proliferation of Sargassum since 2011, with severe environmental and socioeconomic impacts. We developed a modeling framework based on the NEMO ocean model, which integrates transport by currents and waves, and physiology of Sargassum with varying internal nutrient quota, and considers stranding at the coast. Results demonstrate the ability of the model to reproduce and forecast the seasonal cycle and large-scale distribution of Sargassum biomass.
Andrew Yool, Julien Palmiéri, Colin G. Jones, Lee de Mora, Till Kuhlbrodt, Ekatarina E. Popova, A. J. George Nurser, Joel Hirschi, Adam T. Blaker, Andrew C. Coward, Edward W. Blockley, and Alistair A. Sellar
Geosci. Model Dev., 14, 3437–3472, https://doi.org/10.5194/gmd-14-3437-2021, https://doi.org/10.5194/gmd-14-3437-2021, 2021
Short summary
Short summary
The ocean plays a key role in modulating the Earth’s climate. Understanding this role is critical when using models to project future climate change. Consequently, it is necessary to evaluate their realism against the ocean's observed state. Here we validate UKESM1, a new Earth system model, focusing on the realism of its ocean physics and circulation, as well as its biological cycles and productivity. While we identify biases, generally the model performs well over a wide range of properties.
Sebastiaan J. van de Velde, Dominik Hülse, Christopher T. Reinhard, and Andy Ridgwell
Geosci. Model Dev., 14, 2713–2745, https://doi.org/10.5194/gmd-14-2713-2021, https://doi.org/10.5194/gmd-14-2713-2021, 2021
Short summary
Short summary
Biogeochemical interactions between iron and sulfur are central to the long-term biogeochemical evolution of Earth’s oceans. Here, we introduce an iron–sulphur cycle in a model of Earth's oceans. Our analyses show that the results of the model are robust towards parameter choices and that simulated concentrations and reactions are comparable to those observed in ancient ocean analogues (anoxic lakes). Our model represents an important step forward in the study of iron–sulfur cycling.
Katherine M. Smith, Skyler Kern, Peter E. Hamlington, Marco Zavatarelli, Nadia Pinardi, Emily F. Klee, and Kyle E. Niemeyer
Geosci. Model Dev., 14, 2419–2442, https://doi.org/10.5194/gmd-14-2419-2021, https://doi.org/10.5194/gmd-14-2419-2021, 2021
Short summary
Short summary
We present a newly developed reduced-order biogeochemical flux model that is complex and flexible enough to capture open-ocean ecosystem dynamics but reduced enough to incorporate into highly resolved numerical simulations with limited additional computational cost. The model provides improved correlations between model output and field data, indicating that significant improvements in the reproduction of real-world data can be achieved with a small number of variables.
Chia-Wei Hsu, Jianjun Yin, Stephen M. Griffies, and Raphael Dussin
Geosci. Model Dev., 14, 2471–2502, https://doi.org/10.5194/gmd-14-2471-2021, https://doi.org/10.5194/gmd-14-2471-2021, 2021
Short summary
Short summary
The new surface forcing from JRA55-do (OMIP II) significantly improved the underestimated sea level trend across the entire Pacific Ocean along 10° N in the simulation forced by CORE (OMIP I). We summarize and list out the reasons for the existing sea level biases across all studied timescales as a reference for improving the sea level simulation in the future. This study on the evaluation and improvement of ocean climate models should be of broad interest to a large modeling community.
Oliver Gutjahr, Nils Brüggemann, Helmuth Haak, Johann H. Jungclaus, Dian A. Putrasahan, Katja Lohmann, and Jin-Song von Storch
Geosci. Model Dev., 14, 2317–2349, https://doi.org/10.5194/gmd-14-2317-2021, https://doi.org/10.5194/gmd-14-2317-2021, 2021
Short summary
Short summary
We compare four ocean vertical mixing schemes in 100-year coupled simulations with the Max Planck Institute Earth System Model (MPI-ESM1.2) and analyse their model biases. Overall, the mixing schemes modify biases in the ocean interior that vary with region and variable but produce a similar global bias pattern. We therefore cannot classify any scheme as superior but conclude that the chosen mixing scheme may be important for regional biases.
Katsumi Matsumoto, Tatsuro Tanioka, and Jacob Zahn
Geosci. Model Dev., 14, 2265–2288, https://doi.org/10.5194/gmd-14-2265-2021, https://doi.org/10.5194/gmd-14-2265-2021, 2021
Short summary
Short summary
MESMO is a mathematical model that represents the essential components of the Earth, such as the global ocean, atmosphere, and sea ice. It is used to study the global climate and the global carbon cycle. We describe the third version of MESMO. A novel feature of the new version is its mathematical representations of the chemical composition of marine phytoplankton and the marine dissolved organic matter, which are both recognized as important for the global ocean carbon cycle.
Lojze Žust, Anja Fettich, Matej Kristan, and Matjaž Ličer
Geosci. Model Dev., 14, 2057–2074, https://doi.org/10.5194/gmd-14-2057-2021, https://doi.org/10.5194/gmd-14-2057-2021, 2021
Short summary
Short summary
Adriatic basin sea level modelling is a challenging problem due to the interplay between terrain, weather, tides and seiches. Current state-of-the-art numerical models (e.g. NEMO) require large computational resources to produce reliable forecasts. In this study we propose HIDRA, a novel deep learning approach for sea level modeling, which drastically reduces the numerical cost while demonstrating predictive capabilities comparable to that of the NEMO model, outperforming it in many instances.
Qing Li and Luke Van Roekel
Geosci. Model Dev., 14, 2011–2028, https://doi.org/10.5194/gmd-14-2011-2021, https://doi.org/10.5194/gmd-14-2011-2021, 2021
Short summary
Short summary
Physical processes in the ocean span multiple spatial and temporal scales. Simultaneously resolving all these in a simulation is computationally challenging. Here we develop a more efficient technique to better study the interactions across scales, particularly focusing on the ocean surface turbulent mixing, by coupling a global ocean circulation model MPAS-Ocean and a large eddy simulation model PALM. The latter is customized and ported on a GPU to further accelerate the computation.
Yang Feng, Dimitris Menemenlis, Huijie Xue, Hong Zhang, Dustin Carroll, Yan Du, and Hui Wu
Geosci. Model Dev., 14, 1801–1819, https://doi.org/10.5194/gmd-14-1801-2021, https://doi.org/10.5194/gmd-14-1801-2021, 2021
Short summary
Short summary
Simulation of coastal plume regions was improved in global ECCOv4 with a series of sensitivity tests. We find modeled SSS is closer to SMAP when using daily point-source runoff as well as increasing the resolution from coarse to intermediate. The plume characteristics, freshwater transport, and critical water properties are modified greatly. But this may not happen with a further increase to high resolution. The study will advance the seamless modeling of land–ocean–atmosphere feedback in ESMs.
Gregory C. Smith, Yimin Liu, Mounir Benkiran, Kamel Chikhar, Dorina Surcel Colan, Audrey-Anne Gauthier, Charles-Emmanuel Testut, Frederic Dupont, Ji Lei, François Roy, Jean-François Lemieux, and Fraser Davidson
Geosci. Model Dev., 14, 1445–1467, https://doi.org/10.5194/gmd-14-1445-2021, https://doi.org/10.5194/gmd-14-1445-2021, 2021
Short summary
Short summary
Canada's coastlines include diverse ocean environments. In response to the strong need to support marine activities and security, we present the first pan-Canadian operational regional ocean analysis system. A novel online tidal harmonic analysis method is introduced that uses a sliding-window approach. Innovations are compared to those from the Canadian global analysis system. Particular improvements are found near the Gulf Stream due to the higher model grid resolution.
William J. Pringle, Damrongsak Wirasaet, Keith J. Roberts, and Joannes J. Westerink
Geosci. Model Dev., 14, 1125–1145, https://doi.org/10.5194/gmd-14-1125-2021, https://doi.org/10.5194/gmd-14-1125-2021, 2021
Short summary
Short summary
We improve and test a computer model that simulates tides and storm surge over all of Earth's oceans and seas. The model varies mesh resolution (triangular element sizes) freely so that coastal areas, especially storm landfall locations, are well-described. We develop systematic tests of the resolution in order to suggest good mesh design criteria that balance computational efficiency with accuracy for both global astronomical tides and coastal storm tides under extreme weather forcing.
Bijoy Thompson, Claudio Sanchez, Boon Chong Peter Heng, Rajesh Kumar, Jianyu Liu, Xiang-Yu Huang, and Pavel Tkalich
Geosci. Model Dev., 14, 1081–1100, https://doi.org/10.5194/gmd-14-1081-2021, https://doi.org/10.5194/gmd-14-1081-2021, 2021
Short summary
Short summary
This article describes the development and ocean forecast evaluation of an atmosphere–ocean coupled prediction system for the Maritime Continent domain, which includes the eastern Indian and western Pacific oceans. The coupled system comprises regional configurations of the atmospheric model MetUM and ocean model NEMO, coupled using the OASIS3-MCT libraries. The model forecast deviation of selected fields relative to observations is within acceptable error limits of operational forecast models.
Pavel Perezhogin, Ilya Chernov, and Nikolay Iakovlev
Geosci. Model Dev., 14, 843–857, https://doi.org/10.5194/gmd-14-843-2021, https://doi.org/10.5194/gmd-14-843-2021, 2021
Short summary
Short summary
We describe the parallel implementation of the FEMAO model for an ice-covered sea with 2D Hilbert-curve domain decomposition. Load balancing is crucial because performance depends on the local depth. We propose, compare, and discuss four approaches to load balancing. The parallel library allowed us to modify the original sequential algorithm as little as possible. The performance increases almost linearly (tested with up to 996 CPU cores) for the model of the shallow White Sea.
Jordyn E. Moscoso, Andrew L. Stewart, Daniele Bianchi, and James C. McWilliams
Geosci. Model Dev., 14, 763–794, https://doi.org/10.5194/gmd-14-763-2021, https://doi.org/10.5194/gmd-14-763-2021, 2021
Short summary
Short summary
This project was created to understand the across-shore distribution of plankton in the California Current System. To complete this study, we used a quasi-2-D dynamical model coupled to an ecosystem model. This paper is a preliminary study to test and validate the model against data collected by the California Cooperative Oceanic Fisheries Investigations (CalCOFI). We show the solution of our model solution compares well to the data and discuss our model as a tool for further model development.
Christian Ferrarin, Marco Bajo, and Georg Umgiesser
Geosci. Model Dev., 14, 645–659, https://doi.org/10.5194/gmd-14-645-2021, https://doi.org/10.5194/gmd-14-645-2021, 2021
Short summary
Short summary
The problem of the optimization of ocean monitoring networks is tackled through the implementation of data assimilation techniques in a numerical model. The methodology has been applied to the tide gauge network in the Lagoon of Venice (Italy). The data assimilation methods allow identifying the minimum number of stations and their distribution that correctly represent the lagoon's dynamics. The methodology is easily exportable to other environments and can be extended to other variables.
Florian Lemarié, Guillaume Samson, Jean-Luc Redelsperger, Hervé Giordani, Théo Brivoal, and Gurvan Madec
Geosci. Model Dev., 14, 543–572, https://doi.org/10.5194/gmd-14-543-2021, https://doi.org/10.5194/gmd-14-543-2021, 2021
Short summary
Short summary
A simplified model of the atmospheric boundary layer (ABL) of intermediate complexity between a bulk parameterization and a full three-dimensional atmospheric model has been developed and integrated to the NEMO ocean model.
An objective in the derivation of such a simplified model is to reach an apt representation of ocean-only numerical simulations of some of the key processes associated with air–sea interactions at the characteristic scales of the oceanic mesoscale.
Kristen M. Thyng, Daijiro Kobashi, Veronica Ruiz-Xomchuk, Lixin Qu, Xu Chen, and Robert D. Hetland
Geosci. Model Dev., 14, 391–407, https://doi.org/10.5194/gmd-14-391-2021, https://doi.org/10.5194/gmd-14-391-2021, 2021
Short summary
Short summary
We modified the ROMS model to run in offline mode so that previously run fields of sea surface height and velocity fields are input to calculate tracer advection without running the full model with a larger time step; thus, it is faster. The code was tested with two advection schemes, and both are robust with over 99 % accuracy of the offline to online run after 14 simulation days. This allows for ROMS users to maximize use of new or existing output to quickly run additional tracer simulations.
Katixa Lajaunie-Salla, Frédéric Diaz, Cathy Wimart-Rousseau, Thibaut Wagener, Dominique Lefèvre, Christophe Yohia, Irène Xueref-Remy, Brian Nathan, Alexandre Armengaud, and Christel Pinazo
Geosci. Model Dev., 14, 295–321, https://doi.org/10.5194/gmd-14-295-2021, https://doi.org/10.5194/gmd-14-295-2021, 2021
Short summary
Short summary
A biogeochemical model of planktonic food webs including a carbonate balance module is applied in the Bay of Marseille (France) to represent the carbon marine cycle expected to change in the future owing to significant increases in anthropogenic emissions of CO2. The model correctly simulates the ranges and seasonal dynamics of most variables of the carbonate system (pH). This study shows that external physical forcings have an important impact on the carbonate equilibrium in this coastal area.
Tor Nordam and Rodrigo Duran
Geosci. Model Dev., 13, 5935–5957, https://doi.org/10.5194/gmd-13-5935-2020, https://doi.org/10.5194/gmd-13-5935-2020, 2020
Short summary
Short summary
In applied oceanography, a common task is to calculate the trajectory of objects floating at the sea surface or submerged in the water. We have investigated different numerical methods for doing such calculations and discuss the benefits and challenges of some common methods. We then propose a small change to some common methods that make them more efficient for this particular application. This will allow researchers to obtain more accurate answers with fewer computer resources.
Clément Bricaud, Julien Le Sommer, Gurvan Madec, Christophe Calone, Julie Deshayes, Christian Ethe, Jérôme Chanut, and Marina Levy
Geosci. Model Dev., 13, 5465–5483, https://doi.org/10.5194/gmd-13-5465-2020, https://doi.org/10.5194/gmd-13-5465-2020, 2020
Short summary
Short summary
In order to reduce the cost of ocean biogeochemical models, a multi-grid approach where ocean dynamics and tracer transport are computed with different spatial resolution has been developed in the NEMO v3.6 OGCM. Different experiments confirm that the spatial resolution of hydrodynamical fields can be coarsened without significantly affecting the resolved passive tracer fields. This approach leads to a factor of 7 reduction of the overhead associated with running a full biogeochemical model.
Clark Pennelly and Paul G. Myers
Geosci. Model Dev., 13, 4959–4975, https://doi.org/10.5194/gmd-13-4959-2020, https://doi.org/10.5194/gmd-13-4959-2020, 2020
Short summary
Short summary
A high-resolution ocean simulation was carried out within the Labrador Sea, a region that low-resolution climate simulations may misrepresent. We show that small-scale eddies and their associated transport are better resolved at higher resolution than at lower resolution. These eddies transport important properties to the interior of the Labrador Sea, impacting the stratification and reducing the convection extent so that it is far more accurate when compared to what observations suggest.
Eric P. Chassignet, Stephen G. Yeager, Baylor Fox-Kemper, Alexandra Bozec, Frederic Castruccio, Gokhan Danabasoglu, Christopher Horvat, Who M. Kim, Nikolay Koldunov, Yiwen Li, Pengfei Lin, Hailong Liu, Dmitry V. Sein, Dmitry Sidorenko, Qiang Wang, and Xiaobiao Xu
Geosci. Model Dev., 13, 4595–4637, https://doi.org/10.5194/gmd-13-4595-2020, https://doi.org/10.5194/gmd-13-4595-2020, 2020
Short summary
Short summary
This paper presents global comparisons of fundamental global climate variables from a suite of four pairs of matched low- and high-resolution ocean and sea ice simulations to assess the robustness of climate-relevant improvements in ocean simulations associated with moving from coarse (∼1°) to eddy-resolving (∼0.1°) horizontal resolutions. Despite significant improvements, greatly enhanced horizontal resolution does not deliver unambiguous bias reduction in all regions for all models.
Mark E. Baird, Karen A. Wild-Allen, John Parslow, Mathieu Mongin, Barbara Robson, Jennifer Skerratt, Farhan Rizwi, Monika Soja-Woźniak, Emlyn Jones, Mike Herzfeld, Nugzar Margvelashvili, John Andrewartha, Clothilde Langlais, Matthew P. Adams, Nagur Cherukuru, Malin Gustafsson, Scott Hadley, Peter J. Ralph, Uwe Rosebrock, Thomas Schroeder, Leonardo Laiolo, Daniel Harrison, and Andrew D. L. Steven
Geosci. Model Dev., 13, 4503–4553, https://doi.org/10.5194/gmd-13-4503-2020, https://doi.org/10.5194/gmd-13-4503-2020, 2020
Short summary
Short summary
For 20+ years, the Commonwealth Science Industry and Research Organisation (CSIRO) has been developing a biogeochemical (BGC) model for coupling with a hydrodynamic and sediment model for application in estuaries, coastal waters and shelf seas. This paper provides a full mathematical description (equations, parameters), model evaluation and access to the numerical code. The model is particularly suited to applications in shallow waters where benthic processes are critical to ecosystem function.
Angela A. Bahamondes Dominguez, Anna E. Hickman, Robert Marsh, and C. Mark Moore
Geosci. Model Dev., 13, 4019–4040, https://doi.org/10.5194/gmd-13-4019-2020, https://doi.org/10.5194/gmd-13-4019-2020, 2020
Short summary
Short summary
The central Celtic Sea has previously been studied with a 1-D model called S2P3, showing discrepancies between observations and the model results due to poor representation of some processes. Therefore, the S2P3 model was developed to include zooplankton and phytoplankton cells' adaptation to changes in irradiance. Results demonstrate that better agreement with biological observations can be achieved when the model includes these processes and is adequately constrained.
Alexander G. López, John L. Wilkin, and Julia C. Levin
Geosci. Model Dev., 13, 3709–3729, https://doi.org/10.5194/gmd-13-3709-2020, https://doi.org/10.5194/gmd-13-3709-2020, 2020
Short summary
Short summary
This article describes a regional circulation model, Doppio, for the Mid-Atlantic Bight and the Gulf of Maine. The model demonstrates useful skill in comparison to a comprehensive suite of observations. Development focused on achieving a model configuration that allows decadal-scale simulations of physical ocean circulation that can underpin studies of ecosystems and biogeochemistry. Doppio captures the temperature and salinity stratification well, along with the large-scale mean circulation.
Hiroyuki Tsujino, L. Shogo Urakawa, Stephen M. Griffies, Gokhan Danabasoglu, Alistair J. Adcroft, Arthur E. Amaral, Thomas Arsouze, Mats Bentsen, Raffaele Bernardello, Claus W. Böning, Alexandra Bozec, Eric P. Chassignet, Sergey Danilov, Raphael Dussin, Eleftheria Exarchou, Pier Giuseppe Fogli, Baylor Fox-Kemper, Chuncheng Guo, Mehmet Ilicak, Doroteaciro Iovino, Who M. Kim, Nikolay Koldunov, Vladimir Lapin, Yiwen Li, Pengfei Lin, Keith Lindsay, Hailong Liu, Matthew C. Long, Yoshiki Komuro, Simon J. Marsland, Simona Masina, Aleksi Nummelin, Jan Klaus Rieck, Yohan Ruprich-Robert, Markus Scheinert, Valentina Sicardi, Dmitry Sidorenko, Tatsuo Suzuki, Hiroaki Tatebe, Qiang Wang, Stephen G. Yeager, and Zipeng Yu
Geosci. Model Dev., 13, 3643–3708, https://doi.org/10.5194/gmd-13-3643-2020, https://doi.org/10.5194/gmd-13-3643-2020, 2020
Short summary
Short summary
The OMIP-2 framework for global ocean–sea-ice model simulations is assessed by comparing multi-model means from 11 CMIP6-class global ocean–sea-ice models calculated separately for the OMIP-1 and OMIP-2 simulations. Many features are very similar between OMIP-1 and OMIP-2 simulations, and yet key improvements in transitioning from OMIP-1 to OMIP-2 are also identified. Thus, the present assessment justifies that future ocean–sea-ice model development and analysis studies use the OMIP-2 framework.
Pedro Colombo, Bernard Barnier, Thierry Penduff, Jérôme Chanut, Julie Deshayes, Jean-Marc Molines, Julien Le Sommer, Polina Verezemskaya, Sergey Gulev, and Anne-Marie Treguier
Geosci. Model Dev., 13, 3347–3371, https://doi.org/10.5194/gmd-13-3347-2020, https://doi.org/10.5194/gmd-13-3347-2020, 2020
Short summary
Short summary
In the ocean circulation model NEMO, the representation of the overflow of dense Arctic waters through the Denmark Strait is investigated. In this
z-coordinate context, sensitivity tests show that the mixing parameterizations preferably act along the model grid slope. Thus, the representation of the overflow is more sensitive to resolution than to parameterization and is best when the numerical grid matches the local topographic slope.
Hideharu Sasaki, Shinichiro Kida, Ryo Furue, Hidenori Aiki, Nobumasa Komori, Yukio Masumoto, Toru Miyama, Masami Nonaka, Yoshikazu Sasai, and Bunmei Taguchi
Geosci. Model Dev., 13, 3319–3336, https://doi.org/10.5194/gmd-13-3319-2020, https://doi.org/10.5194/gmd-13-3319-2020, 2020
Short summary
Short summary
A quasi-global eddying ocean hindcast simulation using a new version of our model, called OFES2, was conducted to overcome several issues in its previous version. OFES2 simulated oceanic fields from 1958 to 2016 with improved global sea surface temperature and salinity, water mass properties in the Indonesian and Arabian seas, and Niño3.4 and Indian Ocean Dipole indexes. The output from OFES2 will be useful in studying various oceanic phenomena with broad spatiotemporal scales.
Dafydd Stephenson, Simon A. Müller, and Florian Sévellec
Geosci. Model Dev., 13, 2031–2050, https://doi.org/10.5194/gmd-13-2031-2020, https://doi.org/10.5194/gmd-13-2031-2020, 2020
Short summary
Short summary
Different water types are created at the sea surface with a signature based on the local conditions of the atmosphere. They then take these conditions with them into the deeper ocean, and so their journey is an important climate process to understand. In this study, we modify and repurpose a specialised model which simulates the ocean forward and backward in time to determine where new ocean water goes, where at the surface existing water comes from, and how old it is, by tracking it as a dye.
Violaine Piton, Marine Herrmann, Florent Lyard, Patrick Marsaleix, Thomas Duhaut, Damien Allain, and Sylvain Ouillon
Geosci. Model Dev., 13, 1583–1607, https://doi.org/10.5194/gmd-13-1583-2020, https://doi.org/10.5194/gmd-13-1583-2020, 2020
Short summary
Short summary
Consequences of tidal dynamics on hydro-sedimentary processes are a recurrent issue in estuarine and coastal processes studies, and accurate tidal solutions are a prerequisite for modeling sediment transport. This study presents the implementation and optimization of a model configuration in terms of bathymetry and bottom friction and assess the influence of these parameters on tidal solutions, in a macro-tidal environment: the Gulf of Tonkin (Vietnam).
Cited articles
Allen, G. R.: Conservation hotspots of biodiversity and endemism for Indo-Pacific coral reef fishes, Aquat. Conserv., 18, 541–556, https://doi.org/10.1002/aqc.880, 2008.
Allen, G. R. and Werner, T. B.: Coral Reef Fish Assessment in the “Coral Triangle” of Southeastern Asia, Environ. Biol. Fish., 65, 209–2014, https://doi.org/10.1023/A:1020093012502, 2002.
Alongi, D. A., da Silva, M., Wasson, R. J., and Wirasantosa, S.: Sediment discharge and export of fluvial carbon and nutrients into the Arafura and Timor Seas: A regional synthesis, Mar. Geol., 343, 146–158, https://doi.org/10.1016/j.margeo.2013.07.004, 2013.
Aumont, O. and Bopp, L.: Globalizing results from ocean in situ iron fertilization studies, Global Biogeochem. Cy., 20, GB2017, https://doi.org/10.1029/2005GB002591, 2006.
Ayers, J. M., Strutton, P. G., Coles, V. J., Hood, R. R., and Matear, R. J.: Indonesian throughflow nutrient fluxes and their potential impact on Indian Ocean productivity, Geophys. Res. Lett., 41, 5060–5067, https://doi.org/10.1002/2014GL060593, 2014.
Behrenfeld, M. J. and Falkowski, P. G.: Photosynthetic rates derived from satellite-based chlorophyll concentration, Limnol. Oceanogr., 42, 1–20, 1997.
Behrenfeld, M. J., Boss, E., Siegel, D. A., and Shea, D. M.: Carbon-based ocean productivity and phytoplankton physiology from space, Global Biogeochem. Cy., 19, GB1006, https://doi.org/10.1029/2004GB002299, 2005.
Bryant, D., Burke, L., McManus, J., and Spalding, M.: Reefs at Risk: A Map-Based Indicator of Potential Threats to the World's Coral Reefs, World Resources Institute, Washington, DC, International Center for Living Aquatic Resource Management, Manila, and United Nations Environment Programme–World Conservation Monitoring Centre, Cambridge, 1998.
Buitenhuis, E. T., Vogt, M., Moriarty, R., Bednaršek, N., Doney, S. C., Leblanc, K., Le Quéré, C., Luo, Y.-W., O'Brien, C., O'Brien, T., Peloquin, J., Schiebel, R., and Swan, C.: MAREDAT: towards a world atlas of MARine Ecosystem DATa, Earth Syst. Sci. Data, 5, 227–239, https://doi.org/10.5194/essd-5-227-2013, 2013.
Cros, A., Fatan, N. A. White, A., Teoh S. J., Tan, S., Handayani, C., Huang, C., Peterson, N., Li, R. V., Siry, H. Y., Fitriana, R., Gove, J., Acoba, T., Knight, M., Acosta, R., Andrew, N., and Beare, D.: The Coral Triangle Atlas: An Integrated Online Spatial Database System for Improving Coral Reef Management, PLoS ONE, 9, e96332, https://doi.org/10.1371/journal.pone.0096332, 2014.
CSIRO: Atlas of Regional Seas, available at: http://www.marine.csiro.au/~dunn/cars2009/ (last access: 13 August 2015), 2009.
Doerffer, R. and Schiller, H: The MERIS Case 2 water algorithm, Int. J. Remote Sens., 28, 517–535, https://doi.org/10.1080/01431160600821127, 2007.
Emerson, S.: Annual net community production and the biological carbon flux in the ocean, Global Biogeochem. Cy., 28, 14–28, https://doi.org/10.1002/2013GB004680, 2014.
FAO: United Nations Food and Agricultural Organization, FAOSTAT, available at: http://faostat.fao.org/site/291/default.aspx (last access: 13 August 2015), 2007.
Ffield, A. and Gordon, A. L.: Vertical Mixing in the Indonesian Thermocline, J. Phys. Oceanogr., 22, 184–195, 1992.
Ffield, A. and Gordon, A. L.: Tidal mixing signatures in the Indonesian Seas, J. Phys. Oceanogr., 26, 1924–1937, 1996.
Foale, S., Adhuri, D., Aliño, P., Allison, E. H., Andrew, N., Cohen, P., Evans, L., Fabinyi, M., Fidelman, P., Gregory, C., Stacey, N., Tanzer, J., and Weeratunge, N.: Food security and the Coral Triangle Initiative, Mar. Policy, 38, 174–183, https://doi.org/10.1016/j.marpol.2012.05.033, 2013.
Garcia, H. E., Locarnini, R. A., Boyer, T. P., Antonov, J. I., Baranova, O. K., Zweng, M. M., and Johnson, D. R.: World Ocean Atlas 2009, Volume 3: Dissolved Oxygen, Apparent Oxygen Utilization, and Oxygen Saturation, S. Levitus, NOAA Atlas NESDIS 70, U.S. Government Printing Office, Washington, D.C., 344 pp., 2010a.
Garcia, H. E., Locarnini, R. A., Boyer, T. P., Antonov, J. I., Zweng, M. M., Baranova, O. K., and Johnson, D. R.: World Ocean Atlas 2009, Volume 4: Nutrients (phosphate, nitrate, silicate), S. Levitus, NOAA Atlas NESDIS 71, U.S. Government Printing Office, Washington, D.C., 398 pp., 2010b.
Ginsburg, R. N. (Ed.): Proceedings of the Colloquium on Global Aspects of Coral Reefs: Health, Hazards and History, Atlantic Reef Committee, 1994.
Gordon, A. L: Oceanography of the Indonesian seas and their throughflow, Oceanography, 18, 14–27, https://doi.org/10.5670/oceanog.2005.01, 2005.
Green, A. and Mous, P. J.: Delineating the Coral Triangle, its ecoregions and functional seascapes. Report on an expert workshop held in Southeast Asia Center for Marine Protected Areas, Bali, Indonesia, 30 April–2 May 2003, The Nature Conservancy, 2004.
Hendiarti, N., Siegel, H., and Ohde, T.: Investigation of different coastal processes in Indonesian waters using SeaWiFS data, Deep-Sea Res. Pt. II, 51, 85–97, https://doi.org/10.1016/j.dsr2.2003.10.003, 2004.
Hendiarti, N., Suwarso, E., Aldrian, E., Amri, K., Andiastuti, R., Sachoemar, S. I., and Wahyono, I. B.: Seasonal variation of pelagic fish catch around Java, Oceanography, 18, 112–123, https://doi.org/10.5670/oceanog.2005.12, 2005.
Henson, S. A., Sarmiento, J. L., Dunne, J. P., Bopp, L., Lima, I., Doney, S. C., John, J., and Beaulieu, C.: Detection of anthropogenic climate change in satellite records of ocean chlorophyll and productivity, Biogeosciences, 7, 621–640, https://doi.org/10.5194/bg-7-621-2010, 2010.
Hirst, A. C. and Godfrey, J. S.: The role of Indonesian ThroughFlow in a global ocean GCM, J. Phys. Oceanogr., 23, 1057–1086, 1993.
Hopley, D. and Suharsono, M.: The Status of Coral Reefs in Eastern Indonesia. Australian Institute of Marine Science, Townsville, Australia, 2000.
Jennerjahn, T. C., Ittekkot, V., Klopper, S., Adi, S., Purwo Nugroho, S., Sudiana, N., Yusmal, A., and Gaye-Haake, B.: Biogeochemistry of a tropical river affected by human activities in its catchment: Brantas River estuary and coastal waters of Madura Strait, Java, Indonesia, Estuar. Coast. Shelf S., 60, 503–514, https://doi.org/10.1016/j.ecss.2004.02.008, 2004.
Key, R. M., Kozyr, A., Sabine, C. L., Lee, K., Wanninkhof, R., Bullister, J., Feely, R. A., Millero, F., Mordy, C., and Peng, T.-H.: A global ocean carbon climatology: Results from GLODAP, Global Biogeochem. Cy., 18, GB4031, https://doi.org/10.1029/2004GB002247 2004.
Koch-Larrouy, A., Madec, G., Bouruet-Aubertot, P., Gerkema, T., Bessieres, L., and Molcard, R.: On the transformation of Pacific Water into Indonesian Throughflow Water by internal tidal mixing, Geophys. Res. Lett., 34, L04604, https://doi.org/10.1029/2006GL028405, 2007.
Koch-Larrouy, A., Morrow, R., Penduff, T., and Juza, M.: Origin and mechanism of Subantarctic Mode Water formation and transformation in the Southern Indian Ocean, Ocean Dynam., 60, 563–583, https://doi.org/10.1007/s10236-010-0276-4, 2010.
Koch-Larrouy, A., Atmadipoera, A., Van Beek, P., Madec, G., Aucan, J., Lyard, F., Grelet, J., and Souhaut, M.: Estimates of tidal mixing in the Indonesian archipelago from multidisciplinary INDOMIX in-situ data, Deep Sea Res. Pt. 1, in revision, 2016.
Lehodey, P., Senina, I., and Murtugudde, R.: A spatial ecosystem and populations dynamics model (SEAPODYM) – Modeling of tuna and tuna-like populations, Prog. Oceanogr., 78, 304–318, 2008.
Lellouche, J.-M., Le Galloudec, O., Drévillon, M., Régnier, C., Greiner, E., Garric, G., Ferry, N., Desportes, C., Testut, C.-E., Bricaud, C., Bourdallé-Badie, R., Tranchant, B., Benkiran, M., Drillet, Y., Daudin, A., and De Nicola, C.: Evaluation of global monitoring and forecasting systems at Mercator Océan, Ocean Sci., 9, 57–81, https://doi.org/10.5194/os-9-57-2013, 2013.
Leonard, B. P.: A stable and accurate convective modelling procedure based on quadratic upstream interpolation, Comput. Method. Appl. M., 19, 59–98, 1979.
Lévy, M., Estublier, A., and Madec, G.: Choice of an Advection Scheme for Biogeochemical Models, Geophys. Res. Lett., 28, 3725–3728, 2001.
Ludwig, W., Probst, J. L., and Kempe, S.: Predicting the oceanic input of organic carbon by continental erosion, Global Biogeochem. Cy., 10, 23–41, https://doi.org/10.1029/95GB02925, 1996.
Madden, R. A. and Julian P. R.: Observations of the 40–50 day tropical oscillation – A review, Mon. Weather Rev., 122, 814–837, 1994.
Madec, G.: “NEMO ocean engine”, Note du Pole de modélisation, Institut Pierre-Simon Laplace (IPSL), France, No. 27, ISSN No. 1288-1619, 2008.
Madec, G., Delecluse, P., Imbard, M., and Lévy, C.: “OPA 8.1 Ocean General Circulation Model reference manual”, Note du Pole de modélisation, Institut Pierre-Simon Laplace (IPSL), France, No. 11, 91 pp., 1998.
Masumoto, Y.: Effects of Interannual Variability in the Eastern Indian Ocean on the Indonesian Throughflow, J. Oceanogr., 58, 175–182, 2002.
Mayorga, E., Seitzinger, S. P., Harrison, J. A., Dumont, E., Beusen, A. H. W., Bowman, A. F., Fekete, B. M., Kroeze, C., and Van Drecht, G.: Global Nutrient Export from WaterSheds 2 (NEWS 2): model development and implementation, J. Environ. Modell. Softw., 25, 837–853, 2010.
Meyers, G.: Variation of Indonesian throughflow and the El Niño-Southern Oscillation, J. Geophys. Res., 101, 12475–12482, 1996.
Milliman, J. D., Farnsworth, K. L., and Albertin, C. S.: Flux and fate of fluvial sediments leaving large islands in the East Indies, J. Sea Res., 41, 97–107, 1999.
Moore, J. K., Doney, S. C., Kleypas, J. A., Glover, D. M., and Fung, I. Y.: An intermediate complexity marine ecosystem model for the global domain, Deep-Sea Res. Pt. II, 49, 403–462, 2002.
Moore, T. S., Campbell, J. W., and Dowell, M. D: A class-based approach to characterizing and mapping the uncertainty of the MODIS ocean chlorophyll product, Remote Sens. Environ., 113, 2424–2430, 2009.
Mora, C., Chittaro, P. M., Sale, P. F., Kritzer, J. P., and Ludsin, S. A.: Patterns and processes in reef fish diversity, Nature, 421, 933–936, https://doi.org/10.1038/nature01393, 2003.
Moriarty, R. and O'Brien, T. D.: Distribution of mesozooplankton biomass in the global ocean, Earth Syst. Sci. Data, 5, 45–55, https://doi.org/10.5194/essd-5-45-2013, 2013.
Murtugudde, R., Busalacchi, A. J., and Beauchamp, J.: Seasonal-to-interannual effects of the Indonesian Throughflow on the tropical Indo-Pacific Basin, J. Geophys. Res., 103, 21425–21441, 1998.
Murtugudde, R., Signorini, S. R., Christian, J. R., Busalacchi, A. J., McClain, C. R., and Picaut, J.: Ocean color variability of the tropical Indo-Pacific basin observed by SeaWIFS during 1997–1998, J. Geophys. Res., 104, 18351–18366, 1999.
Pimentel D., Harvey, C., Resosudarmo, P., Sinclair, K., Kurz, D., McNair, M., Crist, C., Shpritz, L., Fitton, L., Saffouri, R., and Blair, R.: Environmental and Economic Costs of Soil Erosion and Conservation Benefits, Science, 267, 1117–1123, 1995.
Potemra, J. T., Lukas, R., and Mitchum, G. T.: Large-scale estimation of transport from the Pacific to the Indian Ocean, J. Geophys. Res., 102, 27795–27812, 1997.
Rixen, T., Ittekkot, V., Herunadi, B., Wetzel, P., Maier-Reimer, E., and Gaye-Haake, B.: ENSO-driven carbon see saw in the Indo-Pacific, Geophys. Res. Lett., 33, L07606, https://doi.org/10.1029/2005GL024965, 2006.
Roberts, C. M., McClean, C. J., Veron, J. E. N., Hawkins, J. P., Allen, G. R., McAllister, D. E., Mittermeier, C. G., Schueler, F. W., Spalding, M., Wells, F., Vynne, C., and Werner, T. B.: Marine Biodiversity Hotspots and Conservation Priorities for Tropical Reefs, Science, 295, 1280–1284, doi10.1126/science.1067728, 2002.
Romero, O. E., Rixen, T., and Herunadi, B.: Effects of hydrographic and climatic forcing on diatom production and export in the tropical southeastern Indian Ocean, Mar. Ecol.-Prog. Ser., 384, 69–82, https://doi.org/10.3354/meps08013, 2009.
Saji, N. H., Goswami, B. N., Vinayachandran, P. N., and Yamagata, T.: A dipole mode in the tropical Indian Ocean, Nature, 401, 360–363, 1999.
Sprintall, J. and Révelard, A.: The Indonesian throughflow response to Indo-Pacific climate variability, J. Geophys. Res.-Oceans, 119, 1161–1175, https://doi.org/10.1002/2013JC009533, 2014.
Sprintall, J., Gordon, A. L., Murtugudde, R., and Susanto, R. D.: A semi-annual Indian Ocean forced Kelvin waves observed in the Indonesian Seas, May 1997, J. Geophys. Res., 105, 17217–17230, https://doi.org/10.1029/2000JC900065, 2000.
Susanto, R. D. and Marra, J.: Effect of the 1997/98 El Niño on chlorophyll a variability along the southern coasts of Java and Sumatra, Oceanography, 18, 124–127, https://doi.org/10.5670/oceanog.2005.13, 2005.
Susanto, R. D., Gordon, A. L., Sprintall, J., and Herunadi, B.: Intraseasonal variability and tides in Makassar Strait, Geophys. Res. Lett., 27, 1499–1502, 2000.
Susanto, R. D., Gordon, A. L., and Zheng, Q.: Upwelling along the coasts of Java and Sumatra and its relation to ENSO, Geophys. Res. Lett., 28, 1599–1602, https://doi.org/10.1029/2000GL011844, 2001.
Susanto, R. D., Moore, T. S., and Marra, J.: Ocean color variability in the Indonesian Seas during the SeaWiFS era, Geochemistry Geophysics Geosystems, 7, Q05021, https://doi.org/10.1029/2005GC001009, 2006.
Tegen, I. and Fung, I.: Contribution to the Atmospheric Mineral Aerosol Load From Land-Surface Modification, J. Geophys. Res.-Atmos., 100, 18707–18726, 1995.
Tranchant, B., Reffray, G., Greiner, E., Nugroho, D., Koch-Larrouy, A., and Gaspar, P.: Evaluation of an operational ocean model configuration at 1/12° spatial resolution for the Indonesian seas (NEMO2.3/INDO12) – Part 1: Ocean physics, Geosci. Model Dev., 9, 1037–1064, https://doi.org/10.5194/gmd-9-1037-2016, 2016.
UNEP: Indonesian Seas, GIWA Regional Assessment 57, edited by: Vantier, L., Wilkinson, C., Lawrence, D., and Souter, D., University of Kalmar, Kalmar, Sweden, 2005.
UNEP: Sherman, K. and Hempel, G. (Eds.): The UNEP Large Marine Ecosystem Report: A perspective on changing conditions in LMEs of the world's Regional Seas, United Nations Environment Programme, Nairobi, Kenya, 2009.
Van Leer, B.: Towards the Ultimate Conservative Difference Scheme. IV. A New Approach to Numerical Convection, J. Comput. Phys., 23, 276–299, 1977.
Veron, J. E. E., Devantier, L. M., Turak, E., Green, A. L., Kininmonth, S., Stafford-Smith, M., and Peterson, N.: Delineating the Coral Triangle, Galaxea, J. Coral Reef Studies, 11, 91–100, 2009.
Westberry, T., Behrenfeld, M. J., Siegel, D. A., and Boss, E.: Carbon-based primary productivity modeling with vertically resolved photoacclimation, Global Biogeochem. Cy., 22, GB2024, https://doi.org/10.1029/2007GB003078, 2008.
WOA: World Ocean Atlas, available at: http://www.nodc.noaa.gov/OC5/WOA09/pr_woa09.html (last access: 13 August 2015), 2009.
WOD: World Ocean Database, available at: http://www.nodc.noaa.gov/OC5/WOD09/pr_wod09.html (last access: 13 August 2015), 2009.
Wolter, K. and Timlin, M. S.: Measuring the strength of ENSO events – how does 1997/98 rank?, Weather, 53, 315–324, 1998.
Wolter, K. and Timlin, M. S: Monitoring ENSO in COADS with a seasonally adjusted principal component index, Proc. of the 17th Climate Diagnostics Workshop, Norman, OK, OAA/NMC/CAC, NSSL, Oklahoma Clim. Survey, CIMMS and the School of Meteor., Univ. of Oklahoma, 52–57, 1993.
Zalezak, S. T.: Fully multidimensional flux-corrected transport algorithms for fluids, J. Computat. Phys., 31, 335–362, 1979.
Short summary
An operational ocean forecasting system was developed to monitor the state of the Indonesian seas in terms of circulation, biogeochemistry and fisheries (INDESO project). Here we describe the skill assessment of the physical-biogeochemical coupled model configuration. Model results reproduce the main characteristics of biogeochemical tracer distributions in space and time: phasing of chlorophyll bloom, nutrient and oxygen distributions, water mass transformation across the archipelago.
An operational ocean forecasting system was developed to monitor the state of the Indonesian...
Special issue