Models we use

FABM

FABM is the Framework for Aquatic Biogeochemical Model.  It provides a generic, easy to use, high performance coupling layer that connects a hydrodynamic model (e.g., 1D water column, 3D world ocean) with multiple biogeochemical submodels.

FABM enables complex biogeochemical models to be developed as sets of stand-alone, process-specific modules. These can be combined at runtime to create custom-tailored models as the user requries. This approach has been adopted to implement several large ecosystem models in FABM, including ERSEM at PML. FABM has also been used in the modelling of suspended sediment and redox chemistry, it is particularly useful when coupling different models e.g. a detailed benthic redox model to ERSEM or ERSEM to a different physical model.

FABM allows ERSEM to be coupled to several hydrodynamic models, including GOTM, NEMO and ROMS. It also comes with a stand-alone box model driver.

FVCOM

The Finite Volume Community Ocean Model (FVCOM) provides 3D simulations of the ocean's physical properties (e.g. currents, stratification, salinity, temperature). The ability of FVCOM to accurately solve hydrodynamic equations coupled with the topological flexibility provided by unstructured meshes makes FVCOM ideally suited for coastal and interdisciplinary applications.  It is able to connect regional scale climate drivers with local scale responses, at scales down to a few metres.

At PML, we use this model to both investigate how changes in climate, land use and energy extraction impact the physical behaviour of the ocean as well as how those changes impact the ocean's ecosystems. We have explored how the introduction of offshore wind farms impacts the tides and stratification of the north-west European continental shelf. Similarly, how the behaviour of birds is impacted by tidal turbines in a highly energetic environment (the Orkneys) has been analysed with FVCOM outputs.

Most recently, we have been using FVCOM, in conjunction with ShellSIM and ERSEM, to investigate how changes in aquaculture practice might impact shelf seas. FVCOM is also being used at PML to investigate how microplastics accumulate in coastal seas and to try to identify possible vectors by which microplastics make their way from land and end up inside zooplankton.

Finally, FVCOM is part of the STEMM-CCS project investigating how carbon sequestration and storage might impact shelf sea ecosystems.

Related publications

• Cazenave PW, Torres R and Allen JI. 2016. Unstructured grid modelling of offshore wind farm impacts on seasonally stratified shelf seas, Progress in Oceanography, Volume 145, Pages 25–41, doi:10.1016/j.pocean.2016.04.004
• Waggitt JJ, Cazenave PW, Torres R, Williamson BJ, Scott BE. 2016. Predictable hydrodynamic conditions explain temporal variations in the density of benthic foraging seabirds in a tidal stream environment. ICES Journal of Marine Science: Journal du Conseil fsw100. Doi:10.1093/icesjms/fsw100
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• Waggitt JJ, Cazenave PW, Torres R, Williamson BJ, Scott BE. 2016. Quantifying pursuit-diving seabirds’ associations with fine-scale physical features in tidal stream environments. Journal of Applied Ecology. doi: 10.1111/1365-2664.12646
• Blackford JC, Torres R, Cazanave P, Artioli Y. 2013. Modelling Dispersion of CO₂ Plumes in Sea Water as an Aid to Monitoring and Understanding Ecological Impact, Energy Procedia, Volume 37, 2013, Pages 3379-3386, ISSN 1876-6102,
• Torres R and Uncles R. 2011. Modelling of Estuarine and Coastal Waters. In Treatise on Estuarine and Coastal Sciences. Ed. E. Wolanski and D.S. McLusky, Waltham: Ac. Press. V. 2, 395-427.

GOTM

GOTM is the abbreviation for `General Ocean Turbulence Model'. It is a one-dimensional water column model for the most important hydrodynamic and thermodynamic processes related to vertical mixing in natural waters. In addition, it has been designed such that it can easily be coupled to 3-D circulation models, and used as a module for the computation of vertical turbulent mixing. The strength of GOTM is the vast number of well-tested turbulence models that have been implemented in the code. Primarily we use GOTM as a testbest for ERSEM moel development and for sensistivity analysis, given quick runtimes of a few seconds per simulated year.

The package consists of the FORTRAN90 software, a number of idealised and realistic test cases, and a scientific documentation, all published under the GNU public license. The GOTM developers welcome contributions from the user community, see The GOTM website for details.

Related publications

• Butenschön M, Clark J, Aldridge JN, Allen JI, Artioli Y, Blackford J, Bruggeman J, Cazenave P, Ciavatta S, Kay S, Lessin G, van Leeuwen S, van der Molen J, de Mora L, Polimene L, Sailley S, Stephens N, Torres R. 2016. ERSEM 15.06: a generic model for marine biogeochemistry and the ecosystem dynamics of the lower trophic levels. Geosci. Model Dev. 9, 1293–1339. doi:10.5194/gmd-9-1293-2016  
• Burchard H, Bolding K, Kühn W, Meister A, Neumann T and Umlauf L. 2006. Description of a flexible and extendable physical–biogeochemical model system for the water column. Journal of Marine Systems, Workshop on Future Directions in Modelling Physical-Biological Interactions (WKFDPBI) 61, 180–211. doi:10.1016/j.jmarsys.2005.04.011

NEMO

The NEMO model was initially developed as a global ocean model, but has been adapted for regional and shelf seas. It is intended to be a flexible tool for studying ocean physics and its interactions with the other components of the earth climate system over a wide range of space and time scales.

The NEMO model is based on a rectangular grid. In the horizontal direction, the model uses a curvilinear orthogonal grid, often based on fractions of longitude and latitude, e.g. ¼, 1/12  degree. In the vertical direction, regular z-coordinate, or variable depth terrain following s-coordinate layers are used, or a mixture of the two. NEMO outputs a three-dimensional velocity field based on currents and tidal mixing, the sea surface height, temperature and salinity. The temperature is used to drive some of the ERSEM biological rate equations and the velocity fields to transport ERSEM model components both vertically and horizontally. 

Related publications

• Madec G. 2014: "NEMO ocean engine" (Draft edition r6039). Note du Pôle de modélisation, Institut Pierre-Simon Laplace (IPSL), France, No 27 ISSN No 1288-1619.

Particle Tracking

Particle tracking models can be used to investigate the movement and fate of various objects in the coastal or open ocean. Such models have many important applications, including tracing the likely source and fate of marine pollutants (for example, marine plastic litter); following the dispersion of larvae from fish breeding grounds; or in helping to guide search and rescue operations at sea.

We have developed a particle tracking model that uses data generated by state-of-the-art high resolution coastal ocean models. The model uses simulated properties of the marine environment, such as the speed and direction of oceanic currents, to move particles through a given model domain. Example output from the model is shown in the accompanying animation. The animation is centered on an area lying just south of Plymouth UK, and shows the path taken by virtual particles released into Plymouth Sound. The animation runs for 25 days and illustrates how time-varying forces control the movement of particles, and how shear dispersion causes particles that are initially positioned close together to separate over time.