GOTM

General Information
Acronym of the model	GOTM
Full name of the model	General Ocean Turbulence Model
Model components	Hydrodynamics. Can be coupled to other models for Chemistry and Biology
Supported platforms	Windows, Mac, Linux
Programming Language	Fortran
Still maintained	Yes, by: Bolding & Bruggeman
Most recent version	5.2 (2019)
Model structure
Can be compiled, but executables are available
1D
Fixed grid (Eulerian)
Mass balance included
Model description
Model objective	It is a one-dimensional water column model for the most important hydrodynamic and thermodynamic processes related to vertical mixing in natural waters.
Specific application	Modelling 1-dimensional thermodynamics in a lake, modelling DOC dynamics in a lake
Background knowledge needed to run model	Knowledge of how to work with namelist files. Basic understanding of lake physics
Basic procedures	Formatting of input files, editing of XML file, using python editscenario to prepare namelist files to run the model, run the model.

Link to website/manual	Website Manual
Model characteristics
Input variables	Obligatory: Hypsograph (for lakes) Meteorlogical variables (wind speed, MSLP, air temperature, relative humidity, cloud cover) Optional: Initial temperature profile Water level Inflows Outflows Shortwave radiation
Input file format	ASCII
Output variables	potential temperature salinity potential density observed temperature observed salinity x-velocity y-velocity observed x-velocity observed y-velocity extra friction coefficient in water column drag coefficient in water column shear frequency squared shear production variance of u-fluctuations variance of v-fluctuations variance of w-fluctuations buoyancy frequency squared contribution of T-gradient to buoyancy frequency squared contribution of S-gradient to buoyancy frequency squared buoyancy (half) buoyancy variance destruction of buoyancy variance buoyancy production production of buoyancy variance extra turbulence production eddy diffusivity turbulent kinetic energy energy dissipation rate turbulence length scale turbulent diffusivity of momentum turbulent diffusivity of heat potential temperature salinity potential density observed temperature observed salinity x-velocity y-velocity observed x-velocity observed y-velocity extra friction coefficient in water column drag coefficient in water column shear frequency squared shear production variance of u-fluctuations variance of v-fluctuations variance of w-fluctuations buoyancy frequency squared contribution of T-gradient to buoyancy frequency squared contribution of S-gradient to buoyancy frequency squared buoyancy (half) buoyancy variance destruction of buoyancy variance buoyancy production production of buoyancy variance extra turbulence production eddy diffusivity turbulent kinetic energy energy dissipation rate turbulence length scale turbulent diffusivity of momentum turbulent diffusivity of heat turbulent diffusivity of salt non-local flux of u-momentum non-local flux of v-momentum non-local buoyancy flux non-local heat flux non-local salinity flux stability function for momentum diffusivity stability function for scalar diffusivity non-dimensional non-local buoyancy flux non-dimensional buoyancy time scale non-dimensional shear time scale non-dimensional buoyancy variance turbulent time scale ratio gradient Richardson number flux Richardson number surface friction velocity 10m wind (x) 10m wind (y) 2m air temperature air pressure dew point temperature saturation water vapor pressure actual water vapor presure saturation specific humidity specific humidity air density cloud cover albedo precipitation evaporation integrated precipitation integrated evaporation integrated short wave radiation integrated surface heat fluxes integrated total surface heat exchange incoming short wave radiation sensible heat flux latent heat flux long-wave back radiation net surface heat flux wind stress (x) wind stress (y) sea surface temperature observed sea surface temperature sea surface salinity sea surface elevation surface mixed layer depth bottom friction velocity bottom stress bottom mixed layer depth short-wave radiation fraction of visible light that is not shaded by overlying biogeochemistry coordinate scaling hypsograph at grid interfaces layer thickness integrated total water balance inflows over water column salt inflow temperature inflow vertical water balance advection velocity vertical water balance flux residual water balance inflows integrated inflow integrated outflow kinetic energy potential energy turbulent kinetic energy
Output file format	.netcdf or ASCII
Biogeochemical model components	O2, CO2, NO3, NH4, PO4, cyanobacteria, small phytoplankton, large phytoplankton, zooplankton, macrophtes , DOC cyanobacteria chlorophyll concentration cyanobacteria gross primary production cyanobacteria net primary production cyanobacteria concentration diatoms chlorophyll concentration diatoms gross primary production diatoms net primary production diatoms concentration dom labile dom semi-labile flagellates chlorophyll concentration flagellates gross primary production flagellates net primary production flagellates concentration selma nitrate conc in mass unit selma ammonium conc in nitrogen mass unit selma phosphate conc in phosphorus mass unit selma oxygen in O2 mass unit selma denitrification pelagic selma denitrification benthic selma sediment burial selma phosphorus burial selma oxygen surface flux (positive when into water) selma detritus selma ammonium selma nitrate selma phosphate selma oxygen selma PFe_w selma fluff selma PFe_s zooplankton concentration total_nitrogen_calculator result total_carbon_calculator result total_phosphorus_calculator result total_chlorophyll_calculator result attenuation_coefficient_of_photosynthetic_radiative_flux_calculator result total_carbon_at_interfaces_calculator result total_phosphorus_at_interfaces_calculator result
Temporal resolution	[0.001, 86400s] – integration timestep
Minimal spatial resolution	[1, 1000] levels to resolve the water column
Variables needing calibration	Wind_factor, swr_factor, g1, g2 (light attenuation), shf_factor, k_min (minimum turbulence kinetic energy)
Has successfully been used in
Climate Change Scenario	Ongoing ISIMIP work
Shallow Lake/Reservoir
Deep lake/Reservoir	Sachse et al., 2014; Kerimoglu et al., 2017
Oligotrophic water
Mesotrophic water
Eutrophic water
Ocean	Ciglenečki et al., 2015
Countries in which the model has been applied	Ireland, Sweden, Norway, Denmark, Israel
Which institutes have applied the model	Aarhus University, Denmark Dundalk Institute of Technology (DkIT), Ireland Uppsala University, Sweden NIVA, Norway
Accessibility
Open-Source, GUI, Test cases available
Available tools for pre- and post-processing	R-package (gotmtools)
Support	Google Group
Can be coupled to the following models	PCLake, ERGOM, AED
How can someone get access to this model	Github
Miscellaneous
Comments	Ice model is currently being developed. Input files are tab-delimited
Links	WET – user interface for GOTM GOTMr – package for running GOTM in R gotmtools – package for pre and post-processing FABM GOTM Google group Bolding & Bruggeman
Form was updated: 2019-07-29

Reference list:
Belolipetsky, P. V., Belolipetskii, V. M., Genova, S. N., & Mooij, W. M. (2010). Numerical modeling of vertical stratification of Lake Shira in summer. Aquatic Ecology, 44(3), 561–570. https://doi.org/10.1007/s10452-010-9330-z

Bruggeman, J., & Bolding, K. (2014). A general framework for aquatic biogeochemical models. Environmental Modelling and Software, 61, 249–265. https://doi.org/10.1016/j.envsoft.2014.04.002

Burchard, H., & Baumert, H. (1995). On the performance of a mixed-layer model based on the κ-ε turbulence closure. Journal of Geophysical Research, 100, 8523–8540. https://doi.org/10.1029/94JC03229

Burchard, H., Bolding, K., Kühn, W., Meister, A., Neumann, T., & Umlauf, L. (2006). Description of a flexible and extendable physical-biogeochemical model system for the water column. Journal of Marine Systems, 61, 180–211. https://doi.org/10.1016/j.jmarsys.2005.04.011

Burchard, H., & Petersen, O. (1999). Models of turbulence in the marine environment – A comparative study of two-equation turbulence models. Journal of Marine Systems, 21(1–4), 29–53. https://doi.org/10.1016/S0924-7963(99)00004-4

Joehnk, K. D., Stepanenko, V. M., Bueche, T., Gal, G., Goyette, S., Janssen, A. B. G., … Wen, L. (2015). Integrated modelling of lakes in the climate system – a summary from ASLO Granada and more. 4th Workshop on “Parameterization of Lakes in Numerical Weather Prediction and Climate Modelling", (August). https://doi.org/10.13140/RG.2.1.2658.1924

Umlauf, L., & Burchard, H. (2003). A generic length-scale equation for geophysical turbulence models. Journal of Marine Research, 61(2), 235–265. https://doi.org/10.1357/002224003322005087

Umlauf, L., & Burchard, H. (2005). Second-order turbulence closure models for geophysical boundary layers. A review of recent work. Continental Shelf Research, 25(7–8 SPEC. ISS.), 795–827. https://doi.org/10.1016/j.csr.2004.08.004