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Software
Overview of selected open-source and open-access software and tools. Check out our Github repository.
1D aquatic ecosystem model
Lake-M3 is based on the philosophy to develop a modularized, easy-to-modify (that's why it's completely in Python), vertical 1D aquatic ecosystem with focus on freshwater metabolism. The model simulates water temperature, dissolved oxygen and organic carbon (dissolved and particulate as well as labile and refractory) dynamics.
Water temperature and heat transport are simulated using an eddy-diffusion approach in which the turbulent eddy diffusivity coefficients are parameterized based on the gradient Richardson number. To ensure stability, we apply the implicit Crank-Nicolson scheme for the diffusive transport. Production and consumption terms of the water quality dynamics (dissolved oxygen, phytoplankton biomass, nutrients 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. Further, the model projects growth and decay of ice and snow, as well as coupled feedback loops between organic matter and water clarity.
Scientific software
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.
tools
Scientific software
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.
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