Fine inorganics and particulate organics

[danibodc]

Ecology Fine Inorganics in Sediment, Ecology Fine Inorganics sediment (model: 'EFI_sed', sensor: '', standard: ''') Ecology Particulate Organics in Sediment, Ecology Particulate Organics sediment (model: 'EPO_sed', sensor: '', standard: ''') Ecology Fine Inorganics (model: 'EFI', sensor: '', standard: ''') Ecology Particulate Organics (model: 'EPO', sensor: '', standard: ''')

1. Please could you confirm whether the first two terms that reference 'sediment' should have matrix='wet sediment' or 'sediment' (we are assuming 'wet sediment' but please confirm.
2. Please could you confirm that the latter 2 terms (that do not reference 'sediment') should instead have matrix='water body'.
3. Please could you clarify the inorganic and organic components for these terms? We have not been able to locate the setup.txt file specified in the 'fine inorganics' description. The descriptions of the 'particulate organics' terms mention 'weight of carbon in microalgae, zooplankton, and particulate detritus' - does this mean that only carbon is included here? Should the matrix be sediment/water body as opposed to the microalgae, zooplankton, and particulate detritus?

[sharon-tickell]

I've relayed this (and the other questions posted in this batch) on to the modelling team for proper answers, but in the meantime:

For question 2, yes: anything that doesn't have the _sed suffix on the parameter name defaults to being in the water body (there's a few air, air-water interface and water-sediment interface terms, but those should all be clearly labelled as such in the description)

For question 3 - referring to that setup.txt file is rather unhelpful, isn't it! I'll see if I can dig that up for you.

[danibodc]

Ok that's great, thanks very much @sharon-tickell!

[markebaird]

Please could you confirm whether the first two terms that reference 'sediment' should have matrix='wet sediment' or >> 'sediment' (we are assuming 'wet sediment' but please confirm.

I am not sure what wet sediment means in the vocab, but the point is that particulate constituents in the sediment layers (like EFI_sed) are specified by per volume of the seabed sediment.

Please could you confirm that the latter 2 terms (that do not reference 'sediment') should instead have matrix='water body'.

Yes, as per Sharon's reply.

Please could you clarify the inorganic and organic components for these terms? We have not been able to locate the setup.txt file specified in the 'fine inorganics' description. The descriptions of the 'particulate organics' terms mention 'weight of carbon in microalgae, zooplankton, and particulate detritus' - does this mean that only carbon is included here? Should the matrix be sediment/water body as opposed to the microalgae, zooplankton, and particulate detritus?

Yes, the calculation of weight of particulate organics only includes carbon. Yes, the values are either in the water body or sediment

[danibodc]

Hi @markebaird

Many thanks for your comments.

For the particulate organics terms, which you have specified only include carbon, we are proposing to model these in terms of concentration of particulate organic carbon:

• Concentration of organic carbon {organic_C CAS 7440-44-0} {POC} per unit volume of the water body [particulate >unknown phase] by model prediction
• Concentration of organic carbon {organic_C CAS 7440-44-0} {POC} per unit volume of the wet sediment by model prediction

For the fine inorganics terms, I still have a couple of questions:

• Are these purely particulate as opposed to dissolved?
• What are the individual inorganic components being measured? The description indicates that a number are being summed: 'Sum of inorganic components (see ecology setup.txt for those specified in the code) used for TSS-dependent calculations such as phosphorus absorption'.
• Alternatively, can the inorganics be represented by any single element e.g. inorganic carbon, inorganic nitrogen, inorganic phosphorous?

[danibodc]

@markebaird

Another question regarding the following term: Ecology error (model: 'eco_error', sensor: '', standard: ''')

There is no description included - are you able to provide any insight into what this is? Does it refer to standard error?

[markebaird]

Ecology error is like a quality assurance flag. Perhaps call it a 'model diagnostic'

[markebaird]

Hi,

Thanks for you efforts in standardising our outputs / language.

Commenting on carbon organics: Could you list the variables that you are wishing to assign to vocab terms. We have a dissolved organic carbon (DOR_C) but I don't think we have a POC. But it could be obtained from adding lots of other variables together.

Also, state variables do have to be purely dissolved or purely particulate because they have different units in the sediments (concentration in porewater vs. concentration in space). For variables that sum the dissolved and particulate components (e.g. TN, total nitrogen), the dissolved component is multiplied by porosity (see https://gmd.copernicus.org/articles/13/4503/2020/gmd-13-4503-2020.html, section 10.3.2) and takes the units of per space.

In general the variables stored define the complete state of the model so that we have the information to restart it (need both NO3 and NH4). Only occasionally do we aggregate variables for convenience (DIN = NH4 + NO3).

[gwemon]

@markebaird can we clarify the per unit volume of space vs per unit volume of pore water please? In the paper you reference I read: "In the sediment, the concentration of particulates is given per unit volume of space, while the concentration of dissolved tracers is given per unit volume of porewater." What would be the equivalent of a unit of space in the real world? would it be a volume of fresh sediment that would be made of the space occupied by the porewater plus the space occupied by all the particulate constituents of the sediment?

[gwemon]

@markebaird Also, with regards to the Ecology Particulate Organics, Dani and I are discussing our options and there are advantages in going for a more specific term for your variable; something along the line of: Mass as carbon of microalgae+zooplankton+detritus per unit volume of the water body and the same for the sediment. This would mean that we are not equating EPO to POC. Would that work for you?

[markebaird]

On per unit volume of space, I just meant for 1 m2 surface area of sediment, the volume between the surface and 1 m deep would be 1 m3. So your final statement is correct. Any new particles that land on the sediment either (1) lift the water-sediment interface making a greater total volume of sediment; or (2) squeeze out porewater equivalent to their volume (Archimedes, 230 BC), or some combination of the two ...

[markebaird]

ON EPO, Yes. Thanks.