sedimentation
Johannes Feldbauer
I am trying to implement a simple model with detritus that is being
sedimented (and later on should also be resuspended) for a lake using
GOTM as a host model. Now I have come across some questions:
I think when I first read the wiki on how to write your own
biogeochemical model in FABM the fluxes across (and I think also rate of
change of benthic variables) were declared using _SET_BOTTOM_EXCHANGE_
and I also found some of the example models are still using this. The
wiki now suggests using _ADD_BOTTOM_FLUX_() and _ADD_BOTTOM_SOURCE_, am
I understanding this correctly that this is the newer (and probably
preferred) declaration for bottom (and surface) fluxes/rates of change?
As I am developing the model for a lake I think the sedimentation flux
from pelagic to benthic variables should be depending on the fraction of
sediment area to total area of the corresponding depth (in a simple case
maybe flux = sedimentation velocity * concentration * total
area/sediment area). In this way the morphology of the basin should be
accounted for. Is there a standard variable to receive this from the
host model? Or is this done by FABM internally (or am I wrong)?
All the best,
Johannes
--
Johannes Feldbauer
Doktorand phD student
Technische Universität Dresden Technische Universitaet Dresden
Fakultät Umweltwissenschaften Faculty of Environmental Sciences
Institut für Hydrobiologie Institute of Hydrobiology
Professur für Limnologie Chair of Limnology
01062 Dresden 01062 Dresden, Germany
Tel.: +49 351 463-32684
E-Mail: johannes.feldbauer@tu-dresden.de
Jorn Bruggeman
Yes, _ADD_BOTTOM_FLUX_ and _ADD_BOTTOM_SOURCE_ are the new names for _SET_BOTTOM_EXCHANGE_ and _SET_BOTTOM_ODE_, respectively. This change was made to emphasize that these operations increment the fluxes and sources; they do not overwrite them.
As for the sedimentation flux: yes, in a lake model that flux would typically be scaled by the fraction of surface area touching the sediment, as described by a hypsograph. However, in FABM that is a detail that the host model (hydrodynamic model), not the biogeochemical model is supposed to take care of. If cells throughout the water column can [partially] touch the sediment, the host model should retrieve sediment-water fluxes for every grid cell, and itself scale those fluxes with the fraction of area that is sediment. This is the way the lake branch of GOTM does things, for instance. In this case, you wouldn’t want to apply the scaling in the biogeochemical code as well.
Cheers,
Jorn
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Karsten Bolding
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Jorn Bruggeman
Yes, it’s worth noting that FABM’s support for “bottom throughout the water column” (cells throughout the water column can be in contact with the sediment, e.g. method 2 in https://projects.au.dk/fileadmin/projects/wet/PicturesWET/Figure1.PNG) is currently limited. As long as FABM is not explicitly aware that bottom processes need to be active in every cell, it is up to the host model (e.g. GOTM-lake) to call bottom routines for every layer. That could be made to work - albeit in a very fragile manner! – with older FABM versions. However, FABM v1 and up will independently call biogeochemical routines throughout the model domain and therefore need an update to explicitly “learn” about the bottom-everywhere concept. Such an update would also noticeably increase performance in lake/hypsograph configurations. For the moment, though, we do not have the resources to work on this functionality.
But just to underline – my previous comment about not needing to scale bottom fluxes with the bottom fraction is valid for any version of FABM.
Cheers,
Jorn
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