Articles | Volume 10, issue 1
https://doi.org/10.5194/gmd-10-453-2017
© Author(s) 2017. This work is distributed under
the Creative Commons Attribution 3.0 License.
the Creative Commons Attribution 3.0 License.
https://doi.org/10.5194/gmd-10-453-2017
© Author(s) 2017. This work is distributed under
the Creative Commons Attribution 3.0 License.
the Creative Commons Attribution 3.0 License.
Model description paper
| 
01 Feb 2017
Model description paper |
| 01 Feb 2017
Bottom RedOx Model (BROM v.1.1): a coupled benthic–pelagic model for simulation of water and sediment biogeochemistry
Evgeniy V. Yakushev
CORRESPONDING AUTHOR
Norwegian Institute for Water Research (NIVA), Gaustadalléen 21,
0349 Oslo, Norway
P.P. Shirshov Institute of Oceanology RAS, Nakhimovskiy prosp. 36,
117991, Moscow, Russia
Elizaveta A. Protsenko
Norwegian Institute for Water Research (NIVA), Gaustadalléen 21,
0349 Oslo, Norway
P.P. Shirshov Institute of Oceanology RAS, Nakhimovskiy prosp. 36,
117991, Moscow, Russia
Jorn Bruggeman
Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth, PL1 3DH, UK
Philip Wallhead
Norwegian Institute for Water Research (NIVA Vest), Thormøhlensgate
53 D, 5006 Bergen, Norway
Svetlana V. Pakhomova
Norwegian Institute for Air Research (NILU), P.O. Box 100, 2027
Kjeller, Norway
P.P. Shirshov Institute of Oceanology RAS, Nakhimovskiy prosp. 36,
117991, Moscow, Russia
Norwegian University of Science and Technology (NTNU), 7491
Trondheim, Norway
Shamil Kh. Yakubov
P.P. Shirshov Institute of Oceanology RAS, Nakhimovskiy prosp. 36,
117991, Moscow, Russia
Richard G. J. Bellerby
State Key Laboratory for Estuarine and Coastal Research, East China
Normal University, Shanghai, China
Norwegian Institute for Water Research (NIVA Vest), Thormøhlensgate
53 D, 5006 Bergen, Norway
Raoul-Marie Couture
Norwegian Institute for Water Research (NIVA), Gaustadalléen 21,
0349 Oslo, Norway
University of Waterloo, Earth and Environmental Sciences, Ecohydrology
Group, 200 University Avenue West, N2L3G2, Waterloo, Canada
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Shamil Yakubov, Philip Wallhead, Elizaveta Protsenko, and Evgeniy Yakushev
Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2017-299, https://doi.org/10.5194/gmd-2017-299, 2017
Preprint withdrawn
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Aquatic biogeochemical processes can strongly interact, especially in polar regions, with processes occurring in adjacent ice and sediment layers, yet there are few modelling tools to simulate these systems in a fully coupled manner. We have developed a 1D transport model that allows simultaneous simulation of the biogeochemistry of 3 different media: ice, water, and sediments. Description of transportation processes in ice, water, and sediments for both solutes and solids was provided.
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Melt from the Greenland ice sheet and sea ice both influence light and nutrient availability in the Arctic coastal ocean. We use a 3D coupled hydrodynamic–biogeochemical model to evaluate the relative importance of these processes for timing, distribution, and magnitude of phytoplankton production in Disko Bay, west Greenland. Our study indicates that decreasing sea ice and more freshwater discharge can work synergistically and increase primary productivity of the coastal ocean around Greenland.
Xiaoshuang Li, Richard Garth James Bellerby, Jianzhong Ge, Philip Wallhead, Jing Liu, and Anqiang Yang
Geosci. Model Dev., 13, 5103–5117, https://doi.org/10.5194/gmd-13-5103-2020, https://doi.org/10.5194/gmd-13-5103-2020, 2020
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We have developed an ANN model to predict pH using 11 cruise datasets from 2013 to 2017,
demonstrated its reliability using three cruise datasets during 2018 and applied it to
retrieve monthly pH for the period 2000 to 2016 on the East China Sea shelf using the
ANN model in combination with input variables from the Changjiang biology Finite-Volume
Coastal Ocean Model. This approach may be a valuable tool for understanding the seasonal
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Shamil Yakubov, Philip Wallhead, Elizaveta Protsenko, and Evgeniy Yakushev
Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2017-299, https://doi.org/10.5194/gmd-2017-299, 2017
Preprint withdrawn
Short summary
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Aquatic biogeochemical processes can strongly interact, especially in polar regions, with processes occurring in adjacent ice and sediment layers, yet there are few modelling tools to simulate these systems in a fully coupled manner. We have developed a 1D transport model that allows simultaneous simulation of the biogeochemistry of 3 different media: ice, water, and sediments. Description of transportation processes in ice, water, and sediments for both solutes and solids was provided.
Markus Schartau, Philip Wallhead, John Hemmings, Ulrike Löptien, Iris Kriest, Shubham Krishna, Ben A. Ward, Thomas Slawig, and Andreas Oschlies
Biogeosciences, 14, 1647–1701, https://doi.org/10.5194/bg-14-1647-2017, https://doi.org/10.5194/bg-14-1647-2017, 2017
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Plankton models have become an integral part in marine ecosystem and biogeochemical research. These models differ in complexity and in their number of parameters. How values are assigned to parameters is essential. An overview of major methodologies of parameter estimation is provided. Aspects of parameter identification in the literature are diverse. Individual findings could be better synthesized if notation and expertise of the different scientific communities would be reasonably merged.
Fenjuan Hu, Karsten Bolding, Jorn Bruggeman, Erik Jeppesen, Morgens R. Flindt, Luuk van Gerven, Jan H. Janse, Annette B. G. Janssen, Jan J. Kuiper, Wolf M. Mooij, and Dennis Trolle
Geosci. Model Dev., 9, 2271–2278, https://doi.org/10.5194/gmd-9-2271-2016, https://doi.org/10.5194/gmd-9-2271-2016, 2016
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We present a redesign and further development of a complex and well-known aquatic ecosystem model (PCLake) into the Framework for Aquatic Biogeochemical Models (FABM). So PCLake can run in different hydrodynamic environments, ranging from 0-D to 3-D. We introduce the methods and technical details about how the model was re-designed into a modular structure and the new features of PCLake enabled by FABM. We further present a benchmark test case to verify the new model implementation.
Momme Butenschön, James Clark, John N. Aldridge, Julian Icarus Allen, Yuri Artioli, Jeremy Blackford, Jorn Bruggeman, Pierre Cazenave, Stefano Ciavatta, Susan Kay, Gennadi Lessin, Sonja van Leeuwen, Johan van der Molen, Lee de Mora, Luca Polimene, Sevrine Sailley, Nicholas Stephens, and Ricardo Torres
Geosci. Model Dev., 9, 1293–1339, https://doi.org/10.5194/gmd-9-1293-2016, https://doi.org/10.5194/gmd-9-1293-2016, 2016
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ERSEM 15.06 is a model for marine biogeochemistry and the lower trophic levels of the marine food web. It comprises a pelagic and benthic sub-model including the microbial food web and the major biogeochemical cycles of carbon, nitrogen, phosphorus, silicate, and iron using dynamic stochiometry. Further features include modules for the carbonate system and calcification. We present full mathematical descriptions of all elements along with examples at various scales up to 3-D applications.
Jonathan Beecham, Jorn Bruggeman, John Aldridge, and Steven Mackinson
Geosci. Model Dev., 9, 947–964, https://doi.org/10.5194/gmd-9-947-2016, https://doi.org/10.5194/gmd-9-947-2016, 2016
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This paper is a description of how very different higher and lower trophic level models (Ecopath with Ecosim) and ERSEM, respectively, can be coupled together using a metadata coupling system together with a number of examples of short- and long-range projections for end to end modelling.
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Geosci. Model Dev., 16, 2119–2147, https://doi.org/10.5194/gmd-16-2119-2023, https://doi.org/10.5194/gmd-16-2119-2023, 2023
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4DVarNet is a learning-based method based on traditional data assimilation (DA). This new class of algorithms can be used to provide efficient reconstructions of a dynamical system based on single observations. We provide a 4DVarNet application to sea surface height reconstructions based on nadir and future Surface Water and Ocean and Topography data. It outperforms other methods, from optimal interpolation to sophisticated DA algorithms. This work is part of on-going AI Chair Oceanix projects.
Bin Xiao, Fangli Qiao, Qi Shu, Xunqiang Yin, Guansuo Wang, and Shihong Wang
Geosci. Model Dev., 16, 1755–1777, https://doi.org/10.5194/gmd-16-1755-2023, https://doi.org/10.5194/gmd-16-1755-2023, 2023
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A new global surface-wave–tide–circulation coupled ocean model (FIO-COM32) with a resolution of 1/32° × 1/32° is developed and validated. Both the promotion of the horizontal resolution and included physical processes are shown to be important contributors to the significant improvements in FIO-COM32 simulations. It is time to merge these separated model components (surface waves, tidal currents and ocean circulation) and start a new generation of ocean model development.
Jeff Polton, James Harle, Jason Holt, Anna Katavouta, Dale Partridge, Jenny Jardine, Sarah Wakelin, Julia Rulent, Anthony Wise, Katherine Hutchinson, David Byrne, Diego Bruciaferri, Enda O'Dea, Michela De Dominicis, Pierre Mathiot, Andrew Coward, Andrew Yool, Julien Palmiéri, Gennadi Lessin, Claudia Gabriela Mayorga-Adame, Valérie Le Guennec, Alex Arnold, and Clément Rousset
Geosci. Model Dev., 16, 1481–1510, https://doi.org/10.5194/gmd-16-1481-2023, https://doi.org/10.5194/gmd-16-1481-2023, 2023
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The aim is to increase the capacity of the modelling community to respond to societally important questions that require ocean modelling. The concept of reproducibility for regional ocean modelling is developed: advocating methods for reproducible workflows and standardised methods of assessment. Then, targeting the NEMO framework, we give practical advice and worked examples, highlighting key considerations that will the expedite development cycle and upskill the user community.
Nairita Pal, Kristin N. Barton, Mark R. Petersen, Steven R. Brus, Darren Engwirda, Brian K. Arbic, Andrew F. Roberts, Joannes J. Westerink, and Damrongsak Wirasaet
Geosci. Model Dev., 16, 1297–1314, https://doi.org/10.5194/gmd-16-1297-2023, https://doi.org/10.5194/gmd-16-1297-2023, 2023
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Understanding tides is essential to accurately predict ocean currents. Over the next several decades coastal processes such as flooding and erosion will be severely impacted due to climate change. Tides affect currents along the coastal regions the most. In this paper we show the results of implementing tides in a global ocean model known as MPAS–Ocean. We also show how Antarctic ice shelf cavities affect global tides. Our work points towards future research with tide–ice interactions.
Sébastien Petton, Valérie Garnier, Matthieu Caillaud, Laurent Debreu, and Franck Dumas
Geosci. Model Dev., 16, 1191–1211, https://doi.org/10.5194/gmd-16-1191-2023, https://doi.org/10.5194/gmd-16-1191-2023, 2023
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The nesting AGRIF library is implemented in the MARS3D hydrodynamic model, a semi-implicit, free-surface numerical model which uses a time scheme as an alternating-direction implicit (ADI) algorithm. Two applications at the regional and coastal scale are introduced. We compare the two-nesting approach to the classic offline one-way approach, based on an in situ dataset. This method is an efficient means to significantly improve the physical hydrodynamics and unravel ecological challenges.
Noam S. Vogt-Vincent and Helen L. Johnson
Geosci. Model Dev., 16, 1163–1178, https://doi.org/10.5194/gmd-16-1163-2023, https://doi.org/10.5194/gmd-16-1163-2023, 2023
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Ocean currents transport things over large distances across the ocean surface. Predicting this transport is key for tackling many environmental problems, such as marine plastic pollution and coral reef resilience. However, doing this requires a good understanding ocean currents, which is currently lacking. Here, we present and validate state-of-the-art simulations for surface currents in the southwestern Indian Ocean, which will support future marine dispersal studies across this region.
Pengyang Song, Dmitry Sidorenko, Patrick Scholz, Maik Thomas, and Gerrit Lohmann
Geosci. Model Dev., 16, 383–405, https://doi.org/10.5194/gmd-16-383-2023, https://doi.org/10.5194/gmd-16-383-2023, 2023
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Tides have essential effects on the ocean and climate. Most previous research applies parameterised tidal mixing to discuss their effects in models. By comparing the effect of a tidal mixing parameterisation and tidal forcing on the ocean state, we assess the advantages and disadvantages of the two methods. Our results show that tidal mixing in the North Pacific Ocean strongly affects the global thermohaline circulation. We also list some effects that are not considered in the parameterisation.
Marko Rus, Anja Fettich, Matej Kristan, and Matjaž Ličer
Geosci. Model Dev., 16, 271–288, https://doi.org/10.5194/gmd-16-271-2023, https://doi.org/10.5194/gmd-16-271-2023, 2023
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We propose a new fast and reliable deep-learning architecture HIDRA2 for sea level and storm surge modeling. HIDRA2 features new feature encoders and a fusion-regression block. We test HIDRA2 on Adriatic storm surges, which depend on an interaction between tides and seiches. We demonstrate that HIDRA2 learns to effectively mimic the timing and amplitude of Adriatic seiches. This is essential for reliable HIDRA2 predictions of total storm surge sea levels.
Joao Marcos Azevedo Correia de Souza, Sutara H. Suanda, Phellipe P. Couto, Robert O. Smith, Colette Kerry, and Moninya Roughan
Geosci. Model Dev., 16, 211–231, https://doi.org/10.5194/gmd-16-211-2023, https://doi.org/10.5194/gmd-16-211-2023, 2023
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The current paper describes the configuration and evaluation of the Moana Ocean Hindcast, a > 25-year simulation of the ocean state around New Zealand using the Regional Ocean Modeling System v3.9. This is the first open-access, long-term, continuous, realistic ocean simulation for this region and provides information for improving the understanding of the ocean processes that affect the New Zealand exclusive economic zone.
Hao Huang, Pengyang Song, Shi Qiu, Jiaqi Guo, and Xueen Chen
Geosci. Model Dev., 16, 109–133, https://doi.org/10.5194/gmd-16-109-2023, https://doi.org/10.5194/gmd-16-109-2023, 2023
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The Oceanic Regional Circulation and Tide Model (ORCTM) is developed to reproduce internal solitary wave dynamics. The three-dimensional nonlinear momentum equations are involved with the nonhydrostatic pressure obtained via solving the Poisson equation. The validation experimental results agree with the internal wave theories and observations, demonstrating that the ORCTM can successfully describe the life cycle of nonlinear internal solitary waves under different oceanic environments.
David E. Gwyther, Shane R. Keating, Colette Kerry, and Moninya Roughan
Geosci. Model Dev., 16, 157–178, https://doi.org/10.5194/gmd-16-157-2023, https://doi.org/10.5194/gmd-16-157-2023, 2023
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Ocean eddies are important for weather, climate, biology, navigation, and search and rescue. Since eddies change rapidly, models that incorporate or assimilate observations are required to produce accurate eddy timings and locations, yet the model accuracy is rarely assessed below the surface. We use a unique type of ocean model experiment to assess three-dimensional eddy structure in the East Australian Current and explore two pathways in which this subsurface structure is being degraded.
Shun Ohishi, Takemasa Miyoshi, and Misako Kachi
Geosci. Model Dev., 15, 9057–9073, https://doi.org/10.5194/gmd-15-9057-2022, https://doi.org/10.5194/gmd-15-9057-2022, 2022
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An adaptive observation error inflation (AOEI) method was proposed for atmospheric data assimilation to mitigate erroneous analysis updates caused by large observation-minus-forecast differences for satellite brightness temperature around clear- and cloudy-sky boundaries. This study implemented the AOEI with an ocean data assimilation system, leading to an improvement of analysis accuracy and dynamical balance around the frontal regions with large meridional temperature differences.
Diego Bruciaferri, Marina Tonani, Isabella Ascione, Fahad Al Senafi, Enda O'Dea, Helene T. Hewitt, and Andrew Saulter
Geosci. Model Dev., 15, 8705–8730, https://doi.org/10.5194/gmd-15-8705-2022, https://doi.org/10.5194/gmd-15-8705-2022, 2022
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More accurate predictions of the Gulf's ocean dynamics are needed. We investigate the impact on the predictive skills of a numerical shelf sea model of the Gulf after changing a few key aspects. Increasing the lateral and vertical resolution and optimising the vertical coordinate system to best represent the leading physical processes at stake significantly improve the accuracy of the simulated dynamics. Additional work may be needed to get real benefit from using a more realistic bathymetry.
Nieves G. Valiente, Andrew Saulter, Breogan Gomez, Christopher Bunney, Jian-Guo Li, Christine Pequignet, and Tamzin Palmer
Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2022-261, https://doi.org/10.5194/gmd-2022-261, 2022
Revised manuscript accepted for GMD
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We document the Met Office operational global and regional wave models which provide wave forecasts up to 7 days ahead. Our models present coarser resolution offshore to higher near the coastline. The increased resolution led to better skill replicating the extremes but to some overestimation during modal conditions. If currents are included, wave direction near the coast is significantly improved. New developments focus on the optimisation of the models with resolution.
Matthias Gröger, Manja Placke, H. E. Markus Meier, Florian Börgel, Sandra-Esther Brunnabend, Cyril Dutheil, Ulf Gräwe, Magnus Hieronymus, Thomas Neumann, Hagen Radtke, Semjon Schimanke, Jian Su, and Germo Väli
Geosci. Model Dev., 15, 8613–8638, https://doi.org/10.5194/gmd-15-8613-2022, https://doi.org/10.5194/gmd-15-8613-2022, 2022
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Comparisons of oceanographic climate data from different models often suffer from different model setups, forcing fields, and output of variables. This paper provides a protocol to harmonize these elements to set up multidecadal simulations for the Baltic Sea, a marginal sea in Europe. First results are shown from six different model simulations from four different model platforms. Topical studies for upwelling, marine heat waves, and stratification are also assessed.
Shun Ohishi, Tsutomu Hihara, Hidenori Aiki, Joji Ishizaka, Yasumasa Miyazawa, Misako Kachi, and Takemasa Miyoshi
Geosci. Model Dev., 15, 8395–8410, https://doi.org/10.5194/gmd-15-8395-2022, https://doi.org/10.5194/gmd-15-8395-2022, 2022
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We develop an ensemble-Kalman-filter-based regional ocean data assimilation system in which satellite and in situ observations are assimilated at a daily frequency. We find the best setting for dynamical balance and accuracy based on sensitivity experiments focused on how to inflate the ensemble spread and how to apply the analysis update to the model evolution. This study has a broader impact on more general data assimilation systems in which the initial shocks are a significant issue.
Bror Fredrik Jönsson, Christopher Follett, Jacob Bien, Stephanie Dutkiewicz, Sangwon Hyun, Gemma Kulk, Gael Forget, Christian Müller, Marie-Fanny Racault, Christopher Nigel Hill, Thomas Jackson, and Shubha Sathyendranath
EGUsphere, https://doi.org/10.5194/egusphere-2022-849, https://doi.org/10.5194/egusphere-2022-849, 2022
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While biogeochemical models and satellite-derived ocean-color data provide unprecedented information it is problematic to compare them. Here, we present a new approach based on comparing probability density distributions of model and satellite properties to assess model skills. We also introduce Earth Mover Distances as a novel and powerful metric to quantify the misfit between models and observations. We find that how 3D chlorophyll fields are aggregated can be a significant source of error.
Hector S. Torres, Patrice Klein, Jinbo Wang, Alexander Wineteer, Bo Qiu, Andrew F. Thompson, Lionel Renault, Ernesto Rodriguez, Dimitris Menemenlis, Andrea Molod, Christopher N. Hill, Ehud Strobach, Hong Zhang, Mar Flexas, and Dragana Perkovic-Martin
Geosci. Model Dev., 15, 8041–8058, https://doi.org/10.5194/gmd-15-8041-2022, https://doi.org/10.5194/gmd-15-8041-2022, 2022
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Wind work at the air-sea interface is the scalar product of winds and currents and is the transfer of kinetic energy between the ocean and the atmosphere. Using a new global coupled ocean-atmosphere simulation performed at kilometer resolution, we show that all scales of winds and currents impact the ocean dynamics at spatial and temporal scales. The consequential interplay of surface winds and currents in the numerical simulation motivates the need for a winds and currents satellite mission.
Manuel Aghito, Loris Calgaro, Knut-Frode Dagestad, Christian Ferrarin, Antonio Marcomini, Øyvind Breivik, and Lars Robert Hole
Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2022-212, https://doi.org/10.5194/gmd-2022-212, 2022
Revised manuscript accepted for GMD
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The newly developed ChemicalDrift model can simulate the transport and fate of chemicals in the ocean and in coastal regions. The model combines ocean physics, including transport due to currents, turbulence due to surface winds, and the sinking of particles to the sea floor, with ocean chemistry, such as the partitioning, the degradation, and the evaporation of chemicals. The model will be utilized for risk-assessment of ocean and sea floor contamination from pollutants emitted from shipping.
Qi Shu, Qiang Wang, Chuncheng Guo, Zhenya Song, Shizhu Wang, Yan He, and Fangli Qiao
Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2022-260, https://doi.org/10.5194/gmd-2022-260, 2022
Revised manuscript accepted for GMD
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Ocean models are often used for scientific studies on the Arctic Ocean. Here the Arctic Ocean simulations by state-of-the-art ocean-sea ice models participating in the OMIP were evaluated. The simulations on Arctic Ocean hydrography, freshwater content, stratification, and gateway transports were assessed and the common biases were detected. We also compared the model results with that in the previous project, and the simulations forced by different atmospheric forcing were also evaluated.
Johannes Bieser, David Amptmeijer, Ute Daewel, Joachim Kuss, Anne L. Soerensen, and Corinna Schrum
Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2021-427, https://doi.org/10.5194/gmd-2021-427, 2022
Revised manuscript accepted for GMD
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We developed a 3d model for mercury (Hg) cycling and bioaccumulation in the ocean. Hg is a major global pollutant regulated under the UN Minamata Convention. Anthropogenic Hg emission are transported globally and eventually reach the worlds Oceans. There, Hg is transformed into an even more toxic and bioaccumulative pollutant: Methylmercury (MeHg). The MERCY model is able to predict the fate of Hg in the ocean, the formation of MeHg, and its accumulation in the food web.
Zhanpeng Zhuang, Quanan Zheng, Yongzeng Yang, Zhenya Song, Yeli Yuan, Chaojie Zhou, Xinhua Zhao, Ting Zhang, and Jing Xie
Geosci. Model Dev., 15, 7221–7241, https://doi.org/10.5194/gmd-15-7221-2022, https://doi.org/10.5194/gmd-15-7221-2022, 2022
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We evaluate the impacts of surface waves and internal tides on the upper-ocean mixing in the Indian Ocean. The surface-wave-generated turbulent mixing is dominant if depth is < 30 m, while the internal-tide-induced mixing is larger than surface waves in the ocean interior from 40
to 130 m. The simulated thermal structure, mixed layer depth and surface current are all improved when the mixing schemes are jointly incorporated into the ocean model because of the strengthened vertical mixing.
Yue Xu and Xiping Yu
Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2022-187, https://doi.org/10.5194/gmd-2022-187, 2022
Revised manuscript accepted for GMD
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Accurate description of the wind energy input into ocean waves is crucial to ocean wave modeling and a physics-based consideration on the effect of wave breaking is absolutely necessary to obtain such an accurate description, particularly under extreme conditions. This study evaluates the performance of a recently improved formula, which took into account not only the effect of breaking but also the effect of air-flow separation on the leeside of steep wave crests in a reasonably consistent way.
Giulia Bonino, Doroteaciro Iovino, Laurent Brodeau, and Simona Masina
Geosci. Model Dev., 15, 6873–6889, https://doi.org/10.5194/gmd-15-6873-2022, https://doi.org/10.5194/gmd-15-6873-2022, 2022
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The sea surface temperature (SST) is highly influenced by the transfer of energy driven by turbulent air–sea fluxes (TASFs). In the NEMO ocean general circulation model, TASFs are computed by means of bulk formulas. Bulk formulas require the choice of a given bulk parameterization, which influences the magnitudes of the TASFs. Our results show that parameterization-related SST differences are primarily sensitive to the wind stress differences across parameterizations.
Gustavo M. Marques, Nora Loose, Elizabeth Yankovsky, Jacob M. Steinberg, Chiung-Yin Chang, Neeraja Bhamidipati, Alistair Adcroft, Baylor Fox-Kemper, Stephen M. Griffies, Robert W. Hallberg, Malte F. Jansen, Hemant Khatri, and Laure Zanna
Geosci. Model Dev., 15, 6567–6579, https://doi.org/10.5194/gmd-15-6567-2022, https://doi.org/10.5194/gmd-15-6567-2022, 2022
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We present an idealized ocean model configuration and a set of simulations performed using varying horizontal grid spacing. While the model domain is idealized, it resembles important geometric features of the Atlantic and Southern oceans. The simulations described here serve as a framework to effectively study mesoscale eddy dynamics, to investigate the effect of mesoscale eddies on the large-scale dynamics, and to test and evaluate eddy parameterizations.
David E. Gwyther, Colette Kerry, Moninya Roughan, and Shane R. Keating
Geosci. Model Dev., 15, 6541–6565, https://doi.org/10.5194/gmd-15-6541-2022, https://doi.org/10.5194/gmd-15-6541-2022, 2022
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The ocean current flowing along the southeastern coast of Australia is called the East Australian Current (EAC). Using computer simulations, we tested how surface and subsurface observations might improve models of the EAC. Subsurface observations are particularly important for improving simulations, and if made in the correct location and time, can have impact 600 km upstream. The stability of the current affects model estimates could be capitalized upon in future observing strategies.
Giorgio Micaletto, Ivano Barletta, Silvia Mocavero, Ivan Federico, Italo Epicoco, Giorgia Verri, Giovanni Coppini, Pasquale Schiano, Giovanni Aloisio, and Nadia Pinardi
Geosci. Model Dev., 15, 6025–6046, https://doi.org/10.5194/gmd-15-6025-2022, https://doi.org/10.5194/gmd-15-6025-2022, 2022
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The full exploitation of supercomputing architectures requires a deep revision of the current climate models. This paper presents the parallelization of the three-dimensional hydrodynamic model SHYFEM (System of HydrodYnamic Finite Element Modules). Optimized numerical libraries were used to partition the model domain and solve the sparse linear system of equations in parallel. The performance assessment demonstrates a good level of scalability with a realistic configuration used as a benchmark.
Yinglong Joseph Zhang, Tomas Fernandez-MontBlanc, William Pringle, Hao-Cheng Yu, Linlin Cui, and Saeed Moghimi
Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2022-165, https://doi.org/10.5194/gmd-2022-165, 2022
Revised manuscript accepted for GMD
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Simulating global ocean from deep basin to coastal areas is a daunting task but is important for disaster mitigation efforts. We present a new 3D global ocean model on flexible mesh to study both tidal and non-tidal processes and total water prediction. We demonstrate the potential for ‘seamless’ simulation, on a single mesh, from the global ocean into a few estuaries along the US west coast. The model can serve as the backbone in a global tide-surge and compound flooding forecasting framework.
Young-Kwang Choi, Fengyan Shi, Matt Malej, Jane M. Smith, James T. Kirby, and Stephan T. Grilli
Geosci. Model Dev., 15, 5441–5459, https://doi.org/10.5194/gmd-15-5441-2022, https://doi.org/10.5194/gmd-15-5441-2022, 2022
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The multi-grid-nesting technique is an important methodology used for modeling transoceanic tsunamis and coastal effects. In this study, we developed a two-way nesting interface in a multi-grid-nesting system for the Boussinesq wave model FUNWAVE-TVD. The interface acts as a
backboneof the nesting framework, handling data input, output, time sequencing, and internal interactions between grids at different scales.
Chen Zhao, Rupert Gladstone, Benjamin Keith Galton-Fenzi, David Gwyther, and Tore Hattermann
Geosci. Model Dev., 15, 5421–5439, https://doi.org/10.5194/gmd-15-5421-2022, https://doi.org/10.5194/gmd-15-5421-2022, 2022
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We use a coupled ice–ocean model to explore an oscillation feature found in several contributing models to MISOMIP1. The oscillation is closely related to the discretized grounding line retreat and likely strengthened by the buoyancy–melt feedback and/or melt–geometry feedback near the grounding line, and frequent ice–ocean coupling. Our model choices have a non-trivial impact on mean melt and ocean circulation strength, which might be interesting for the coupled ice–ocean community.
Benoît Pasquier, Sophia K. V. Hines, Hengdi Liang, Yingzhe Wu, Steven L. Goldstein, and Seth G. John
Geosci. Model Dev., 15, 4625–4656, https://doi.org/10.5194/gmd-15-4625-2022, https://doi.org/10.5194/gmd-15-4625-2022, 2022
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Neodymium isotopes in seawater have the potential to provide key information about ocean circulation, both today and in the past. This can shed light on the underlying drivers of global climate, which will improve our ability to predict future climate change, but uncertainties in our understanding of neodymium cycling have limited use of this tracer. We present a new model of neodymium in the modern ocean that runs extremely fast, matches observations, and is freely available for development.
Pedro Duarte, Jostein Brændshøi, Dmitry Shcherbin, Pauline Barras, Jon Albretsen, Yvonne Gusdal, Nicholas Szapiro, Andreas Martinsen, Annette Samuelsen, Keguang Wang, and Jens Boldingh Debernard
Geosci. Model Dev., 15, 4373–4392, https://doi.org/10.5194/gmd-15-4373-2022, https://doi.org/10.5194/gmd-15-4373-2022, 2022
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Sea ice models are often implemented for very large domains beyond the regions of sea ice formation, such as the whole Arctic or all of Antarctica. In this study, we implement changes in the Los Alamos Sea Ice Model, allowing it to be implemented for relatively small regions within the Arctic or Antarctica and yet considering the presence and influence of sea ice outside the represented areas. Such regional implementations are important when spatially detailed results are required.
Elias J. Hunter, Heidi L. Fuchs, John L. Wilkin, Gregory P. Gerbi, Robert J. Chant, and Jessica C. Garwood
Geosci. Model Dev., 15, 4297–4311, https://doi.org/10.5194/gmd-15-4297-2022, https://doi.org/10.5194/gmd-15-4297-2022, 2022
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ROMSPath is an offline particle tracking model tailored for use with output from Regional Ocean Modeling System (ROMS) simulations. It is an update to an established system, the Lagrangian TRANSport (LTRANS) model, including a number of improvements. These include a modification of the model coordinate system which improved accuracy and numerical efficiency, and added functionality for nested grids and Stokes drift.
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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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.
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Short summary
This paper presents a new benthic–pelagic biogeochemical model (BROM) that combines a relatively simple pelagic ecosystem model with a detailed biogeochemical model of the coupled cycles of N, P, Si, C, O, S, Mn, Fe in the water column, benthic boundary layer, and sediments, with a focus on oxygen and redox state. BROM should be of interest for the study of a range of environmental applications in addition to hypoxia, such as benthic nutrient recycling, redox biogeochemistry, and eutrophication.
This paper presents a new benthic–pelagic biogeochemical model (BROM) that combines a...
