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PostPosted: Thu Apr 05, 2012 1:07 am 
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Location: CSIRO Marine and Atmospheric Research
Can someone update me on plans to parameterise a time delay of remineralisation within the BIO_SEDIMENT routine in Fennel.h? Thks.


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PostPosted: Thu Apr 12, 2012 12:59 am 
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HI- I have been working to couple the sediment transport and Fennel model within ROMS by adding a diagenetic model within the sediment bed model of ROMS. If you would like to see what we are doing, I can email you my Ocean Sciences 2012 powerpoint. email me if you would like to request it.

Other groups may be approaching the problem differently, of course.

Courtney Harris
Virginia Institute of Marine Science

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PostPosted: Fri Apr 13, 2012 12:29 pm 
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Location: Dalhousie University
Hi there,

I have included a remineralization lag in the sediments in a relatively simple way. You can see details of the parameterization and equations in the following paper:

Bianucci, L., K. L. Denman, and D. Ianson (2011), Low oxygen and high inorganic carbon on the Vancouver Island Shelf, J. Geophys. Res., 116, C07011, doi:10.1029/2010JC006720.

Hope it is useful,
Laura


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PostPosted: Mon Jun 11, 2012 7:15 pm 
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In response to some email queries; it seemed reasonable to put this on the forum as well.

To add biological reactions to the sediment bed: the main thing I’ve done is add a new variable called “bed_tracer” to the sediment model. Like the t() array, “bed_tracer(i,j,k,itrc,nstp)” is 5-d, with i,j, being horizontal grid cells, k being bed layer, itrc being an index identifying the tracer, and nstp being this time step or the previous one, etc.

The difference between bed_tracer and bed_mass type variables are that bed_tracers can have reactions, while bed_mass is conservative. Bed_mass variable influence sediment bed layers and the total thickess of the sediment bed whereas bed_tracer does not. There are two other indices that keep track of what the bed_tracers are:

1. One index stores whether this bed_tracer is associated with particles (like POM), or is dissolved in porewater.

2. The other index associates each of the bed_tracers with a variable from the t() array. So, particulate bed_tracers are associated with a sediment class in the t() array, or perhaps a detrital class from the biological part of the t() array. They are assigned the same erosive behavior as their partner. They add to and are removed from the bed via deposition and erosion. The dissolved classes of bed_tracer are associated with a dissolved constituent from the t() array – so oxygen in the sediment bed is linked to the O2 variable in the biological model. Dissolved classes of bed_tracer are added to / removed from the bed during deposition and erosion events and via diffusion across the sediment / water interface.

To deal with keeping track of the new bed_tracers, I modified the sediment bed code to handle the bed layering for bed_tracer, and added sedtr_reactions.f – a module that handles the reactions on the sediment bed of particulate and dissolved stuff.

Now I am using these reactive bed_tracers to address two problems: one is linking sediment processes (sediment.f) to the biological model (fennel.h). The other is to add radio-isotopes to the sediment bed to simulate geochronology.

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PostPosted: Sat Jun 16, 2012 12:38 pm 
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Joined: Wed Mar 31, 2010 3:29 pm
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Location: SKLEC,ECNU,Shanghai,China
Hi,guys.

Dose the Fennel BIO-module work?

I am recently run a bio-physical coupled model in a semi-closed shelf sea to simulate some species of nutrient and primary production. The model spin up on Jan 1 and end-up on Dec 30,namely a whole year. As i know,i should have to get a rational results,e.g.,with two blooms for algae,one in early spring and another in late summer,and with nutrients variation coincident. But actually i dont reach that purpose. The physical model was validated by field datasets and tells very nice. And when i coupled BIO-PHY together,it can run but doesnt give a rational result. Here attached the damn resutl for diagnosing.

At the very beginning,with the incline of the phytoplankton,NO3,NH4 and PO4 decline sharply,this seems ok to some extent.But from then on,all went beyond recognition. The nutrient species ought to increase as there exists detritus in the water column via remineralization,and also via nitrification. WHY? From the result,all the bio- state variables seem unconservation. I have run many tests by changing the initial values or the ratios,but all result in same course of variation for these variables,with slight distinction on the time that reaches the peak or trough.

Thank you for all tips and suggestions.

shou


Attachments:
File comment: each box was identified by the patch on it.X-axis stands for run time(day),Y-axis for nutrients concentrations(mmol/m3,except for temp and Chl-a).
图片1.png
图片1.png [ 25.45 KiB | Viewed 4273 times ]
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PostPosted: Sun Jun 17, 2012 11:16 am 
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Location: Dalhousie University
Hi tony1230,

I'm surprised to see PO4 as one of your model outputs. The BIO_FENNEL module does not include PO4 as state variable. Did you add this yourself?

In any event, there seems to be a problem with your PO4. PO4 has essentially disappeared in your simulation after about 100 days.

I would suggest you run the model in its original version first, before adding new functionality.

-Katja


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PostPosted: Mon Jun 18, 2012 3:30 am 
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Location: SKLEC,ECNU,Shanghai,China
Thank you Prof. Fennel

Yes exactlly, we added the PO4 in the BIO-model. And i have run cases as you suggested that run without the PO4,but why i still got the similar results.Here attached two results with(you say the PO4 eventually vanished,but in this case,there still PO4 be left and why other states?) and without PO4(in the .png the value equal to zero) for comparing.

In these runs,for testing,i gave all the bio state variables a fixed initial value,to see whether i can get a reasonable result that can be explained in physical-biological conditions.Maybe there will be discrepancy in value but can't be in variation trend.I am so confused that i may did something wrong,but i cant figured it out.

Thanks

shou


Attachments:
File comment: Run without PO4(value=0)
图片2.png
图片2.png [ 19.16 KiB | Viewed 4220 times ]
File comment: Run with a PO4 ini value
图片3.png
图片3.png [ 19.34 KiB | Viewed 4220 times ]
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PostPosted: Mon Jun 18, 2012 9:13 am 
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Location: Marine Institute, Ireland
Hi tony1230,

You have run out of NO3 also. What happens when you significantly increase detritus remineralization rates and decrease settling velocities for phytoplankton, small and large detritus to retain more nutrients in the water column? Is it the surface layer you are showing on the plots?

Tomasz


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PostPosted: Tue Jun 19, 2012 12:44 am 
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Your plots indicate negative temperatures. -7C at day 20. That's odd.

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PostPosted: Wed Jun 20, 2012 4:53 am 
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Thank you Tomasz and Prof. Wilkin

Yes, it is odd that ROMS yielded the negative temp as reach to about -7C after few days of the run. I have took notice of that but i dont know why and how to figure it out. Some suggestion? I have check the initrial input file and no value smaller that zero exist and i used the NECP Reanalysis 2 datasets as modle's driver, say wind and radition etc..

I should have to indicate that the plots are for the surface layer and for just one point(grid cell). As the bottom results show exactly the same look, i patched the surface solo for simplicity. I have tested what Tomasz said by setting the settling velocities for LDets and SDets zeros(no deposite), but no obvious change occured(see bottom most plot, sice the phytoplankton dies out eventually,here canceled the effect of Zooplankton for test). Took the interaction between biogeochemical and physical processes into account, i run a test just with pure physical impose on it to see how the nutrients perform(see the third plot). From the variation of NO3 and NH4, both remain a relative high level with tiny variability at the beginning and at days btw 200-250(though the bio variables not took into account,but nitrification still there,i dont know the variability could be explained by this :roll: ). Here i should to point out that all the results metioned above were from Old version(V3.4) ROMS's running.

As metioned this, i have tried to use the newest ROMS to run the cases but i ran into a trouble with the temperature(see the upper most plot). Since the temp and salinity are both tracer in ROMS, why one(salinity) looks normal and another(temp) not :x ? I patch one of the nice physical results here(second plot,actually all the points for currents are nice,one for simplicity) which from a identical test as that for odd temperature. I have reported this in another post but no one reply till now :cry: !

Thank you for all suggestions and tips.

shou


Attachments:
File comment: Odd temperature perform
图片6.png
图片6.png [ 16.46 KiB | Viewed 4102 times ]
File comment: currents validation
图片7.png
图片7.png [ 18.39 KiB | Viewed 4102 times ]
File comment: with physical process only
图片5.png
图片5.png [ 16.45 KiB | Viewed 4102 times ]
File comment: No deposite for Dets
图片4.png
图片4.png [ 19.39 KiB | Viewed 4102 times ]
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PostPosted: Wed Jun 20, 2012 8:51 am 
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Location: Marine Institute, Ireland
I would sort out the temperature first before modelling biology. Check what you have in the boundary file and met forcing files (do you use bulk formulae?)


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PostPosted: Thu Jun 21, 2012 3:18 am 
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Yes Tomasz, before try to modeling biological we much simulate the temp well since it is a critical factor that influence the biological process. The 4 plots in the previous post were from two different version of ROMS run, explicit say, the upper most two plots(the temp and salt plot and the velocity plot) were produced synchronously by one test case(in this case no bio- included, using newest roms code), and the left two plots express mainly the bio-process yielded by a run in which the temp,salt and velocity were all nicely calculated.

Here are two problems. For i have been using the old version for a long time, so i wanna a fresh code because there update so many bugs or something new added. I copied my run case(input NETCDF files, *.in and *.h files) into the newest roms code, modified some cpp defines according to new cpp-file and some options in *.in file, ran the case, compared the results with observation data, and i got rational results except for temperature. Its so tricky.

I have my *.in and *.h files attached here for checking by you all. Thanks in advance.

shou


Attachments:
bohai.in [90.48 KiB]
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bohai.h [2.61 KiB]
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PostPosted: Fri Jun 22, 2012 9:04 am 
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Location: Marine Institute, Ireland
I am not sure if you are referring to the uppermost 4 plots when saying that the model performs nicely, but the temperature there drops by 10 degrees in just 1200 time steps. Are you sure it is correct? Why don't you make 2D plots/animations to see the evolution of temperature over the whole model domain?


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