HOWTO FABM

GETM can act as hydrodynamic host for biogechmical models integrated in the Framework for Aquatic Biogeochemical Models (FABM).

Download and Compilation

If GOTM was cloned with --recurse-submodules the FABM source code is already available for compilation. If not, it can be fetched with git submodule update --init extern/fabm -C $GOTMDIR. The compilation for the test cases include FABM after export FABM=true. Manual calls to cmake switch on FABM with the additional argument -DGETM_USE_FABM=ON.

Runtime configuration

During GETM simulations FABM is controlled by 3 configuration files. FABM is only active if gotm_fabm.yaml is present with parameter "use: True". The configuration of the BGC models in FABM needs to be provided in fabm.yaml. Example configuration files can be found here. GETM specific settings are read from getm_fabm.inp.

Additional notes

Initialization: fabm_init_method=2 initializes all state variables with constant values (provided from FABM) and afterwards overwrites only those variables with a 3D initial field which are present in fabm_init_file.

Open boundaries: Dirichlet boundary data are read from bdy_3d_bio.nc and zero-gradient conditions are applied if the file or the specific state variable is not present.

Rivers: Analogously to salinity and temperature, FABM tracer concentrations can be provided in rivers.nc. If the specific state variable is not present, dilution due to zero concentration inflow is applied.

Output: do not forget to request the FABM fields in output.yaml.