Suggestions for Nonlinear/Biology/fennel.h

[stlaur]

Good afternoon,

I have two suggestions regarding Nonlinear/Biology/fennel.h (Rutgers trunk version):

(1) On line 516, the code splits into two cases according to surface PAR:

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            IF (PARsur(i).gt.0.0_r8) THEN

followed on line 714 by:

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            ELSE

I'll refer to those two cases as "day-time" (PAR>0) and "night-time" (PAR=0), respectively.

In the day-time case, the nitrification of NH4 depends on whether oxygen is available in the water column (or not).
On lines 686-688:

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                fac2=MAX(Bio(i,k,iOxyg),0.0_r8)     ! O2 max
                fac3=MAX(fac2/(3.0_r8+fac2),0.0_r8) ! MM for O2 dependence
                fac1=dtdays*NitriR(ng)*fac3

with `fac3' becoming zero (nitrification inhibited) if oxygen isn't available.

The night-time case, on the other hand, disregards whether oxygen is available or not.
On line 715:

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              cff3=dtdays*NitriR(ng)

I suspect there should be a Michaelis-Menten term here, like we see in the "day-time" case.

(2) On lines 703 (day-time case) and 724 (night-time case), nitrification affects the total alkalinity as:

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                Bio(i,k,iTAlk)=Bio(i,k,iTAlk)-N_Flux_Nitrifi

Here, `N_Flux_Nitrifi' is the amount of NH4 (units: millimoles of nitrogen per cubic meter) that was nitrified into NO3.
Alkalinity has units of milliequivalents per cubic meter.
Line 703 tells us that nitrification reduces alkalinity by 1 equivalent for every mole of NH4.

But when I look at the literature, I find that nitrification reduces alkalinity by *2* for every mole of NH4 nitrified.
For example, page 297 of Wolf-Gladrow et al. 2007:

"In an aerobic environment, ammonia is ultimately oxidized to nitrate. Nitrification [...] leads to a decrease of TA by 2 moles per mole of NO3 formed."

Similarly, on page 14581 of Doney et al. 2007:

"Nitrification reduces alkalinity by 2 equivalents for every mole of NH4 consumed."

So I suspect that there should be a factor "2._r8" in front of N_Flux_Nitrifi on lines 703 and 724.

Pierre

Wolf-Gladrow, D.A., R.E. Zeebe, C. Klaas, A. Kortzinger, A.G. Dickson (2007) Total alkalinity: The explicit conservative expression and its application to biogeochemical processes, Marine Chemistry, 106, 287-300, https://doi.org/10.1016/j.marchem.2007.01.006

Doney, S.C., N. Mahowald, I. Lima, R.A. Feely, F.T. Mackenzie, J.F. Lamarque, P.J. Rasch (2007) Impact of anthropogenic atmospheric nitrogen and sulfur deposition on ocean acidification and the inorganic carbon system, Proc.Natl.Acad.Sci., 104(37), 14580-14585, https://doi.org/10.1073/pnas.0702218104

[kfennel]

Hi Stlaur,

Thanks for raising these excellent points -- indeed these and other updates should be made and are, in fact, long overdue.

We're working with Hernan to get a number of updates (including PO4 as additional variable) into the trunk.

Stay tuned and have a nice weekend,
Katja