some problems about fennel bio model

[kent]

Dear everyone :
recently I am runing ROMS coupled with Fennel bio model , But the result show many problems.
I chosed TS_MPDATA difference, but only NO3 proferm good, other variables didn't grow and all are negative and cannot change with time. U know, TS_MPDATA should result in positive numbers. I have also changed the difference method with TS_U3HADVECTION and TS_C4VADVECTION, the result may also resultd in some negative numbers, but the variables developed with time. It really confused me , So would anybody can help me?

best wishes!

[kfennel]

Are all initial concentrations for your biological variables positive?

[kent]

Thank you kfennel
Yes,the initial concentrations for my biological variables are positive.I used the WOA2009 for the NO3 initial concentration, and set the initial concentrations of the other tracers le-6, such as phytoplankton, zooplankton,NH4,Chlorophyll,LdeN,SdeN.

[wilkin]

Have you changed any of the parameter settings in bio_Fennel.in from the default values in the trunk source code?

What are your open boundary conditions on biological variables?

Have you set any biologically related CPP options, e.g. DENITRIFICATION, CARBON, etc.?

What are you showing in those plots you posted? i.e. is this a snapshot at end of month 3? Does level 22 mean the surface-most layer?

John

[kent]

Thank you John
I did not change any of parameter setting in the bio_fennel.in, and I defined every boudary as a wall. I did not set any biologically related cpp options but just defined the bio_fennel. The plots I posted are the average of the month 3 of the ROMS running with the different difference method. One is the TS_U3HADVECTION and TS_C4VADVECTION method, and the another is the TS_MPDATA. Yes, the 22 level means the surface layer. I don't know why the phytoplankton are not growing after I changed the difference method but using the same initial conditions.

[wilkin]

In an ideal world the horizontal advection scheme would make no difference whatsoever because it is only the numerical representation of how the biology variables are transported around.

If your phytoplankton are not growing that begs the question: have you specified any shortwave radiation - sunlight?

[kent]

Thank you John
I changed my initial conditions for the tracers except the NO3 and ran the model with the TS_MPDATA difference method. It performed normally at last. So maybe it's the initial conditions that resulted in the problem which I mentioned before.

[spitz]

A few things to think about
1) the initial conditions for phytoplankton might be too small (1e-6) to allow some growth the first three months (Jan, Feb, March) in the subarctic (not enough light). Since there is still grazing and mortality, after awhile the concentrations might reach values even smaller and there will be no growth.
2) In the subtropical gyre, there is not enough nitrogen to allow growth. For example, at HOT, nitrogen fixation is very important but is not in Fennel et al. (if I recall correctly).
3) The default parameters are most likely not appropriate since most likely the default parameters are representing diatom and larger copepods.
4) Since the concentrations are so small, the different advection schemes will give different results, as their associated numerical inaccuracy is different.

Hope that helps

[kent]

Thank you spitz
I still set the initial concentrations of the tracers except the NO3 1e-6 yesterday, and it performed normally with the TS_MPDATA. So I don't think the small value is the reason for the problem I met with. But I will pay attention to what you have mentioned. Thank you very much.

[alazhar]

Hi Kent,

I'm just curious, have you define SOLAR_SOURCE?
In this regards, you may also want to check your solar shortwave radiation flux (swrad) forcing to make sure you have correct photosynthetic radiation values to generate your bio growths.

-Al

[kent]

Thank you Alazhar
I have defined SOLAR_SOURCE. Meanwhile I checked my solar shortwave radiation flux (swrad) forcing, and there is nothing wrong. Now, the results of the model are being normally after changing my initial conditions. Thanks for your aopinions.

[bluemoon]

Hi kent,

I also met with the same problem while coupling bio fennel with the physical model. I want to know how you got non negative concentration of nitrate and other biological variables by changing the initial conditions.

First I tried the model with TS_U3HADVECTION and TS_C4VADVECTION as advection schemes then it results with negative concentration of biologial variables.

Second I tried with TS_MPDATA then only no3 was giving good result, rest not developing in time.

Please suggest how you changed the initial conditions as you had written in the post.


Thanking you