[MITgcm-support] Forcing files in data.dic (biogeochemistry)

Mon Aug 4 06:29:03 EDT 2014

Hi there

I thought that I would update this thread since I have now found a solution
to this problem. I found the solution in this
<http://mitgcm.org/pipermail/mitgcm-support/2008-April/005351.html> thread
from the MITgcm support list archive.

Basically, the interaction of the biogeochemistry packages (DIC, GCHEM,
PTRACERS) and the OBCS boundary condition package were incompatible and
adding the following line in my data.obcs file fixed the problem...

*OBCSfixTopo=.TRUE.,*

Thanks to everyone for your help again.

Jonny

On 31 July 2014 12:00, Jonny Williams <Jonny.Williams at bristol.ac.uk> wrote:

> Hi Christoph
>
> Many thanks for your email, I really appreciate it.
>
> I am now able to run the model which is great! I am getting plausible
> values for alkalinity, PO4, DOP and O2 and these evolve through time as I
> would expect.
>
> Note that I am running with an empty *DIC_FORCING* namelist in *data.dic*.
> it seems that I need to include this namelist even though it is empty.
>
> *&DIC_FORCING*
>
> *&*
>
>
> Unfortunately, although the DIC field is being initialised correctly
> (using the values specified in *data.ptracers*), the DIC field rapidly
> becomes unphysical, giving NaNs everywhere (even over land!) after about 25
> timesteps of 24s each.
>
> The NaNs seems to 'propagate' from the corners of the domain as the
> simulation proceeds. I have attached an image of the domain after 13
> timesteps which clearly shows the unphysical nature of the output!
>
> I assume that there must be something that I am missing in my setup
> regarding DIC?
>
> Thanks again
>
> Jonny
>
>
>
>
> On 31 July 2014 11:17, Christoph Voelker <christoph.voelker at awi.de> wrote:
>
>>  Hi Jonny,
>>
>> the fractional sea-ice area, supplied via the sea-ice file (or calculated
>> in the sea-ice module) is used for reducing the air-sea gas exchange in the
>> presence of sea-ice. The simple assumption here is that sea ice is
>> impermeable, so the flux comes just from the non-covered part of the ocean
>> surface. You can certainly set all values in the file to zero; then the
>> ocean can exchange CO2 unhampered. Maybe you can even just leave the
>> filename blank, but I am not sure about that; I usually don't specify the
>> file, but I always use the sea-ice package.
>>
>> Concerning the silica file: You don't have to specify it. If you leave it
>> away, what you do is that you neglect the contribution of silicic acid to
>> the alkalinity, which in many parts of the surface ocean is small. But it
>> is not so small in the Southern Ocean, and also to some extent in the North
>> Pacific.
>> The contribution of silicic acid to alkalinity is used in the calculation
>> of the equilibrium carbonate chemistry, which is called when the model
>> calculates air-sea flux. Neglecting it will lead to a small bias in
>> equilibrium DIC values where Si is high.
>>
>>
>> Hope that helps a bit,
>> Cheers, Christoph
>>
>>
>>
>> On 7/31/14 11:45 AM, Jonny Williams wrote:
>>
>> Hi Manfredi
>>
>>  Thank you very much for your very helpful email!
>>
>>  I should clarify my model set up. Although I am using a regional model
>> which is based on an Arctic configuration I am now using it for a different
>> part of the world.
>>
>>  Also, I have the sea ice package switched off. Perhaps I need to
>> specify a sea ice file which is simply all zeros?
>>
>>  Finally do I need to supply a silica file (like sillev1.bin in the
>> tutorial model)?
>>
>>  Many thanks again
>>
>>  Jonny
>>
>>
>>
>>
>> On 30 July 2014 19:31, Manfredi Manizza <mmanizza at ucsd.edu> wrote:
>>
>>>  Hi Jonny,
>>>
>>> yes, you are correct that namelist below works fine for the verification
>>> experiment where you run the 2.8 by 2.8 global
>>> setup with dimensions 28 by 64 by 12 of input filles for sea-ice cover
>>> and for windspeed
>>>
>>> For your (coarse-res ?) Arctic set-up, you will read wind speed  via the
>>> EXF package  directly from re-analyzed products (NCEP, ECMWF, JRA-25)
>>>
>>> For the fraction of sea- ice (or sea ice cover) you will pass to the
>>> biogeochemical routine the variable that is computed
>>> by the sea-ice model that its is coupled in your run to the ocean
>>> physical model.
>>>
>>> In this case you do not have to generate any input files with specificy
>>> dimensions becuase in the data.exf file you should have
>>> all details needed to interpolate on the fly your forcing accordingly to
>>> your Arctic domain.
>>>
>>> Debugging tip :
>>>
>>> Just make sure that in the dic package the sea-ice coverage is correctly
>>> read in order to compute the gas transfer velocity
>>> and the amount of irradiance use to compute the Net Community Production
>>> that has to be masked at the surface
>>> by the sea-ice fraction. Running 2-3 time steps with printout linese of
>>> the variables always helps
>>> to figure out that all works OK and the two parts of the code talk to
>>> each other.
>>>
>>> I hope this helps.
>>>
>>> Manfredi
>>>
>>>
>>>
>>> On 07/30/2014 07:45 AM, Jonny Williams wrote:
>>>
>>>  Hi there
>>>
>>>  I am currently trying to incorporate the GCHEM, PTRACERS and DIC
>>> packages into my setup of the MITgcm. I already have it successfully
>>> working in regional model using the OBCS and EXF forcing packages.
>>>
>>>  in the ~/MITgcm/verification/tutorial_global_oce_biogeo example, the
>>> data.dic file calls for the following files in the DIC_FORCING namelist
>>>
>>>  &DIC_FORCING
>>>   DIC_iceFile='fice.bin',
>>>   DIC_windFile='tren_speed.bin',
>>>   DIC_silicaFile='sillev1.bin',
>>>  &
>>>
>>>  What I cannot work out however is what size these files should be in
>>> my setup. From trial and error, I think the ice and wind files are monthly
>>> climatologies (longitude x latitude x 12 months) and the sillev1 file
>>> (silica data file, according to the manual
>>> <http://mitgcm.org/public/r2_manual/latest/online_documents/manual.pdf>)
>>> is of the form longitude x latitude x 15 levels.
>>>
>>>  Does anyone know what size they should be? Should they have the same
>>> number of elements as the underlying grid, or is it staggered?
>>>
>>>  This raises a more generic issue in that clearly the binary input
>>> files are not self-describing (like, say, NetCDF) and so having to
>>> reverse-engineer what size forcing and boundary condition files should is
>>> not uncommon for me.
>>>
>>>  I may well be going about this in the wrong way so any suggestions
>>> about how to avoid this situation in future would be appreciated :)
>>>
>>>  Many thanks, as always
>>>
>>>  Jonny
>>>
>>>  --
>>>  Dr Jonny Williams
>>> School of Geographical Sciences
>>> University of Bristol
>>> University Road
>>> BS8 1SS
>>>
>>>  +44 (0)117 3318352 <%2B44%20%280%29117%203318352>
>>> jonny.williams at bristol.ac.uk
>>> bit.ly/jonnywilliams
>>>
>>>
>>>  _______________________________________________
>>> MITgcm-support mailing listMITgcm-support at mitgcm.orghttp://mitgcm.org/mailman/listinfo/mitgcm-support
>>>
>>>
>>> --
>>> Dr. Manfredi Manizza
>>> Geosciences Research Division
>>> Scripps Institution of Oceanography
>>> University of California San Diego
>>> 9500 Gilman Drive La Jolla, CA 92093-0244
>>> email : mmanizza at ucsd.edu
>>> tel   : +1-858-534-7094
>>> web   : http://bluemoon.ucsd.edu/mmanizza/
>>>
>>>
>>> _______________________________________________
>>> MITgcm-support mailing list
>>> MITgcm-support at mitgcm.org
>>> http://mitgcm.org/mailman/listinfo/mitgcm-support
>>>
>>>
>>
>>
>>  --
>>  Dr Jonny Williams
>> School of Geographical Sciences
>> University of Bristol
>> University Road
>> BS8 1SS
>>
>>  +44 (0)117 3318352
>> jonny.williams at bristol.ac.uk
>> bit.ly/jonnywilliams
>>
>>
>> _______________________________________________
>> MITgcm-support mailing listMITgcm-support at mitgcm.orghttp://mitgcm.org/mailman/listinfo/mitgcm-support
>>
>>
>>
>> --
>> Christoph Voelker
>> Alfred Wegener Institute for Polar and Marine Research
>> Am Handelshafen 12
>> 27570 Bremerhaven, Germany
>> e: Christoph.Voelker at awi.de
>> t: +49 471 4831 1848
>>
>>
>> _______________________________________________
>> MITgcm-support mailing list
>> MITgcm-support at mitgcm.org
>> http://mitgcm.org/mailman/listinfo/mitgcm-support
>>
>>
>
>
> --
> Dr Jonny Williams
> School of Geographical Sciences
> University of Bristol
> University Road
> BS8 1SS
>
> +44 (0)117 3318352
> jonny.williams at bristol.ac.uk
> bit.ly/jonnywilliams
>

-- 
Dr Jonny Williams
School of Geographical Sciences
University of Bristol
University Road
BS8 1SS

+44 (0)117 3318352
jonny.williams at bristol.ac.uk
bit.ly/jonnywilliams
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