A versatile marine modelling tool applied to arctic, temperate and tropical waters

Abstract

The improved understanding of complex interactions of marine ecosystem components makes the use of fully coupled hydrodynamic, biogeochemical and individual based models more and more relevant. At the same time, the increasing complexity of the models and diverse user backgrounds calls for improved user friendliness and flexibility of the model systems. We present FlexSem, a versatile and user-friendly framework for 3D hydrodynamic, biogeochemical, individual based and sediment transport modelling. The purpose of the framework is to enable natural scientists to conduct advanced 3D simulations in the marine environment, including any relevant processes. This is made possible by providing a precompiled portable framework, which still enables the user to pick any combination of models and provide user defined equation systems to be solved during the simulation. We here present the ideas behind the framework design, the implementation and documentation of the numerical solution to the Navier-Stokes equations in the hydrodynamic module, the surface heat budget model, the pelagic and benthic equation solvers and the Lagrangian movement of the agents in the agent based model. Five examples of different applications of the system are shown: 1) Hydrodynamics in the Disko Bay in west Greenland, 2) A biogeochemical pelagic and benthic model in the inner Danish waters, 3) A generic mussel farm model featuring offline physics, food levels and mussel eco-physiology, 4) Sediment transport in Clarion-Clipperton zone at the bottom of the Pacific and 5) Hydrodynamics coupled with an agent based model around Zanzibar in Tanzania. Hence we demonstrate that the model can be set up for any area with enough forcing data and used to solve a wide range of applications.

Agent-based modeling and genetics reveal the Limfjorden, Denmark, as a well-connected system for mussel larvae

“…1), where mussel density (ind. m −2 ) has been recorded on a yearly basis since 1993 (Kristensen & Hoffmann 2004). The fishable area is covered by the sampling stations, consisting of squares of 0.7 × 0.7 nautical miles, and within each square dredging is conducted at a random position and direction at >3 m depth (Kristensen & Hoffmann 2004).…”

“…m −2 ) has been recorded on a yearly basis since 1993 (Kristensen & Hoffmann 2004). The fishable area is covered by the sampling stations, consisting of squares of 0.7 × 0.7 nautical miles, and within each square dredging is conducted at a random position and direction at >3 m depth (Kristensen & Hoffmann 2004). Areas with stones and very few or no mussels, and areas protected from the fishery (some parts of Area 1, Area 4, the eastern part of Area 8, the northern part of Area 10, and Areas 16 and 17) were not sampled.…”

Sediment Transport Model Quantifies Plume Length and Light Conditions From Mussel Dredging

“…The FlexSem model system was used to describe the resuspension and transport of different size fractions of sediment particles with different sinking rates after a dredging event. FlexSem uses an unstructured computational mesh (Larsen et al, 2017(Larsen et al, , 2020. The computational mesh is made of 4,056 equilateral triangles with a characteristic length scale of 10 m covering a total area of 630 m × 630 m ( Supplementary Figure A.1).…”

“…The processes governing the dredge plume generation and transport are complex and depend on many factors, which are often site-and substrate-specific (Canal-Vergés et al, 2016). In the following study, we used the 3D FlexSem model system (Larsen et al, 2017(Larsen et al, , 2020 as a tool for predicting potential environmental impacts of mussel dredging activities supported by field data at two study sites in the Limfjorden. The aim of this study is to estimate the effects of mussel dredging causing resuspension and transport of sediment particles, and investigate how the sediment plume changes the light conditions in the water column in different scenarios.…”

Ocean Circulation Model Applications for the Estuary-Coastal-Open Sea Continuum

“…The model was applied as a standalone setup by using observed river discharges and observed sea level, water temperature and salinity as lateral boundary conditions in the North Sea and Kattegat. Pastor et al (2021) used a 3D physical model system (FlexSem; Larsen et al, 2020) coupled to an agent-based model to study dispersal and settling of mussel larvae between 17 areas in the Limfjord.…”