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Overview of selected open-source and open-access software and tools
1D aquatic ecosystem model
The modularized framework runs a vertical one-dimensional aquatic ecosystem model (AEM) for water temperature, dissolved oxygen and organic carbon (dissolved and particulate as well as labile and refractory) dynamics. Production and consumption terms of the water quality dynamics (dissolved oxygen and organic carbon) are simulated using a modified Patankar Runge-Kutta scheme to ensure mass conservation and to prevent unrealistic negative values. Convective wind mixing is parameterized based on an integral energy approach.
R-package for running an ensemble of lake models using standardised input data. Lake models currently incorporated are Freshwater Lake Model (FLake), General Lake Model (GLM), General Ocean Turbulence Model (GOTM) (lake-branch), Simstrat, and MyLake. See Moore, Mesman, Ladwig, Feldbauer et al. (2021) for more information.
1D hydrodynamic lake model
R-package to run a modularized 1D integral energy model for water temperature dynamics in a lake. The mixing algorithms are based on the MINLAKE (Ford and Stefan 1980, Riley and Stefan 1988, Herb and Stefan 2004) and the MyLake (Saloranta and Andersen 2007) models. Implementations to estimate the incoming and outgoing long-wave heat fluxes were taken from Livingstone and Imboden (1989) and Goudsmit et al. (2002). The latent and sensible heat fluxes were calculated taking into account atmospheric stability using the algorithms by Verburg and Antenucci (2010). The ice algorithms from MyLake (Saloranta and Andersen 2007) were applied to simulate ice formation and melting.
R-package for interacting with the General Lake Model (GLM) in R. It includes basic functions for calculating physical derivatives and thermal properties of model output, and plotting functionality. Also includes advanced functions for model optimization. See Hipsey et al. (2019) for more information.
Two-layer food web model
R-package to run a a simple two-layer water temperature model that assumes that the lake is divided into two volumes: the epilimnion and the hypolimnion. Both layers are divided by a thermocline zone. The entrainment over the thermocline depends on a diffusion coefficient which is a function of the diffusion at neutral stability to the Richardson number. All equations and derivations are from Steven C. Chapra (2008) 'Surface Water-Quality Modeling' Waveland Press, Inc.
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