Changes between Version 42 and Version 43 of DevelopmentActivities/MergeOCN/Vuichard
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- 2014-02-07T09:29:35+01:00 (10 years ago)
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DevelopmentActivities/MergeOCN/Vuichard
v42 v43 25 25 1. '''fraction from passive to slow pool'''. OCN contains the version of Century published in 1993 while the ORCHIDEE is more based on the publication of 1987. The fraction towards the passive pool of the carbon flow that goes out of the slow pool is set to 0.03 in Parton 1987, instead of 0.003-0.009*clay_fraction in Parton, 1993. Soenke kept the parametrization of 1987. There is no clear motivation on the reason why. 26 26 27 > B. Guenet [[BR]] 28 27 29 == N flows in soil - Routine : nitrogen_dynamics == 28 30 … … 36 38 We keep here the original formulation of Li et al., 2000 37 39 40 > B. Guenet [[BR]] 41 38 42 2. '''Calculation of the oxygen partial pressure'''. For both the calculation of the gradient of oxygen partial pressure (d(pO2)/dz) and the change in oxygen partial pressure (d(pO2)/dt), we need dz, the depth over which one makes the calculation. It is not clear to me which depth one should use. For information, OCN used z_decomp (see [source:branches/orchidee-N/ORCHIDEE/src_stomate/stomate_soilcarbon.f90@19#L705 here]) 39 43 … … 42 46 3. '''Calculation of the oxygen partial pressure''' (2). Still in the calculation of the change in oxygen partial pressure (d(pO2)/dt) in OCN, it seems that "dz" term (z_decomp) is missing in the following equation (see [source:branches/orchidee-N/ORCHIDEE/src_stomate/stomate_soilcarbon.f90@19#L705 here]) when we compare with the reference formulation (Li et al., 2000, Eq. 4 of Table 2) 43 47 48 > B. Guenet [[BR]] 49 44 50 4. '''Conversion Respiration to O2 pressure'''. The conversion factor [source:branches/orchidee-N/ORCHIDEE/src_stomate/stomate_soilcarbon.f90@19#L699 here] used for converting the respiration term in O2 pressure accounts for the air-filled porosity (see Li et al., 2000 eq. 3 table 2). In OCN, afps_max is used instead of afps. We keep the original formulation 51 52 > B. Guenet [[BR]] 45 53 46 54 5. '''Calculation of the anaerobic balloon - anvf'''. The two constants a and b are not specified in Li et al., 2000. OCN uses a=0.85 and b=1 without mention to any publication (see [source:branches/orchidee-N/ORCHIDEE/src_stomate/stomate_soilcarbon.f90@19#L711 here]). As mention in the code of OCN these parameters have been estimated temporarily and need to be tuned. Might be good to find the values used in DNDC... 47 55 56 > B. Guenet [[BR]] 57 48 58 6. '''Ammonium adsorption'''. It is based on Li et al. 1992, JGR, Table 4 using NH4 defined as the NH4+ concentration in the soil liquid, gN kg-1 soil (p. 9774) but Zhang et al. (2000) use also the same equation but in this paper NH4+ is defined as the [NH4+] in a soil layer in kgN ha-1. In OCN, NH4 seems defined as molNH4 m-3 of water (see, [source:branches/orchidee-N/ORCHIDEE/src_stomate/stomate_soilcarbon.f90@19#L742 here]). It would be good to clarify this by checking what looks like the equation depending of the units we use. 59 60 > B. Guenet [[BR]] 49 61 50 62 7. '''Ammonium adsorption''' (2). Li et al. (1992) defines FIXNH4 as the proportion of adsorbed NH4+. One may assume that consequently the NH4+ that is not adsorbed is NH4+ x (1-FIXNH4) and that we want to consider this quantity for possible nitrification, transformation to ammonia, .... But in OCN, we do not multiply the state variable (SV) representing NH4+ by (1-FixNH4) but by (1-FixNH4/(1+FixNH4)) (see, [source:branches/orchidee-N/ORCHIDEE/src_stomate/stomate_soilcarbon.f90@19#L746 here]). This tends to assume that FixNH4 represents the ratio adsorped NH4+ to non-adsorped because FixNH4/(1+FixNH4) = (NH4adsorp/NH4non_adsorp)/((NH4non_adsorp+NH4adsorp)/NH4_non_adsorp) = NH4adsorp / NH4tot. This needs to be clarified ... 51 63 64 > B. Guenet [[BR]] 65 52 66 8. '''Nitrification rate'''. The equation for the nitrification rate comes from Schmid et al., 2001, Nutr. Cycl. Agro (eq.1) but the environmental factors used are from Zhang (2002) who used an other equation, especially for Temperature effect on nitrification. I don't know how this can be mixed together ? This seems particularly inappropriate because the default fraction of N-NH4 which is converted to N-NO3 appears equal to 2 day-1 (a factor "2" in the equation, see [source:branches/orchidee-N/ORCHIDEE/src_stomate/stomate_soilcarbon.f90@19#L805 here]). In Schmid et al., the nitrification rate at 20 ◦C and field capacity (knitrif,20) was set to 0.2 d−1 (10 times less...) 67 68 > B. Guenet [[BR]] 53 69 54 70 9. '''NO production from chemodenitrification'''. This is based on Kesik et al., 2005, Biogeosciences but Kesik et al. used NO2 concentration and not NO3 production as it is done in OCN. In parallel, there is a modification of a multiplicative constant from 300 (Kesik) to 30 (OCN). See the line in the code of OCN [source:branches/orchidee-N/ORCHIDEE/src_stomate/stomate_soilcarbon.f90@19#L809 here]. I don't know how this is reliable ? 55 71 72 > B. Guenet [[BR]] 73 56 74 10. '''NO production and N2O production'''. In OCN, NO production and N2O production are deduced from the NO3 production based on the calculation of the nitrification rate (see above). See the line in the code of OCN [source:branches/orchidee-N/ORCHIDEE/src_stomate/stomate_soilcarbon.f90@19#L812 here]. I don't know if this is correct ? 57 75 76 > B. Guenet [[BR]] 77 58 78 11. '''Relative growth rate of Nox denitrifiers'''. One uses a parameter defined as the Half Saturation of N oxydes (kgN/m3) from Table 4 of Li et al., 2000. It is set to 0.083 in Li et al. and OCN uses the value 0.087. We keep the original value. It is also not clear if the unit of this parameter are kgN per m3 of soil or per m3 of solution. In OCN, when converting from (kgN m-3) to (gN m-2) we multiply by "dpu_cste*mx_eau_eau" (see [source:branches/orchidee-N/ORCHIDEE/src_stomate/stomate_soilcarbon.f90@19#L832 here]. I don't know if this is correct. If it is per m3 of solution one should at least consider that soil is not necessary at the field capacity (ie. dpu_cste*mx_eau_eau*soilhum). 79 80 > B. Guenet [[BR]] 59 81 60 82 12. '''Relative growth rate of Nox denitrifiers (2)'''. In OCN, the term mu_nox(max) is missing in the equation that defines the relative growth rate of total denitrifiers (see eq. 2 of Table 4 of Li et al., 2000). See [source:branches/orchidee-N/ORCHIDEE/src_stomate/stomate_soilcarbon.f90@19#L845 here]. In addition, in OCN, the Relative growth rate of Nox denitrifiers is ranged between 0.0005*som(:,iactive,m,icarbon) and 0.25 * som(:,iactive,m,icarbon)). No clear justification. This is not kept so far. … … 62 84 13. '''NO3 consumption by denitrification'''. This is based on Eq. 4 Table 4 of Li et al., 2000. In OCN ([source:branches/orchidee-N/ORCHIDEE/src_stomate/stomate_soilcarbon.f90@19#L848 here]), multiplication by 0.1 of the NO3 consumption. There is no justification. This is not kept so far. 63 85 86 > B. Guenet [[BR]] 87 64 88 14. '''denitrifier bacterial population change'''. This is based on Eq. 3 of Table 4 Li et al. (2000). In OCN, there is only the denitrifier bact population change that is defined, not the population itself. And the bacterial population change is used in place of the bacterial population in the calculation of the production of NO3, NOx, N2O by denitrification. [source:branches/orchidee-N/ORCHIDEE/src_stomate/stomate_soilcarbon.f90@19#L845 here]. I don't know how it may work. 89 90 > B. Guenet [[BR]] 65 91 66 92 15. '''Vmax of nitrogen uptake by plants'''. In OCN, the same values are used both for uptake of NH4+ and NO3-. See p. 3 of the SM of Zaehle & Friend, 2010: "''As a first approximation average values for vmax, kNmin and KNmin are assumed for all PFTs (Table S1), and for both ammonium and nitrate''". However based on the two papers of Kronzucker et al. (1995, 1996), it seems that vmax should be much higher for NH4+ than for NO3- . We still use the same here for both NH4+ and NO3- as in OCN. … … 142 168 26. '''Update pools of nitrogen in the soil'''. See [source:branches/orchidee-N/ORCHIDEE/src_stomate/stomate_soilcarbon.f90@19#L995 here]. To my opinion, for a better consistency, I would recommand to consider the leaching separately when calculating the ammonium and nitrate budget. Leaching is calculated from sechiba. It might be better to remove leaching at the top of the routine especially due to the later calculation of NH4+ and NO3- concentration that will vary with the soil water content. Let's imagine that from one time step to another, the change in soil water content is only due to leaching. We don't want that the NH4+ and NO3- concentration vary from one time step to the other. The best way to avoid this is to remove first the leaching from the NH4+ and NO3- pools. This is not done yet. 143 169 170 > B. Guenet [[BR]] 171 144 172 27. '''Additional general comments'''. From my reading of the code of OCN, it appears that there are at least 3 processes/calculations for which we really need to be careful: 145 173 a. The use of the anaerobic balloon. We need to check if the fraction ''anvf'' is used in the relevant equations or not.
