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

Jonny Williams Jonny.Williams at bristol.ac.uk
Mon Aug 4 07:01:23 EDT 2014 

... as often happens though, I have now uncovered a further error which
occurs when I try to restart the model using global pickup files.

Previously, when I have run without the biogeochemistry packages (DIC,
PTRACERS, GCHM) I created a symbolic link such as this...

*pickup_dic.0000012960.meta -> pickup_dic.ckptA.meta*

... to indicate that I want to use the ckptA file to restart the run from
timestep 12960. I now that I also have pickup files called

*pickup_ptracers.ckptA.meta/data *
and
*pickup_dic.ckptA.meta/data *

*... *for the DIC and PTRACERS packages.

I have created 2 further sets symbolic links thus...

*pickup_dic.0000012960.meta/data -> pickup_dic.ckptA.meta/data*
and
*pickup_ptracers.0000012960.meta/data -> pickup_ptracers.ckptA.meta/data*

Unfortunately I am getting the following error out and the model is not
running...

*forrtl: severe (64): input conversion error, unit -5, file Internal
Formatted Read*
*Image              PC                Routine            Line        Source
            *
*mitgcmuv           0000000000BAB3FE  Unknown               Unknown
 Unknown*
*mitgcmuv           0000000000BA973A  Unknown               Unknown
 Unknown*
*mitgcmuv           000000000051D78C  Unknown               Unknown
 Unknown*
*mitgcmuv           00000000005CE598  Unknown               Unknown
 Unknown*
*mitgcmuv           00000000007410B0  Unknown               Unknown
 Unknown*
*mitgcmuv           000000000070FE8E  Unknown               Unknown
 Unknown*
*mitgcmuv           0000000000735AD2  Unknown               Unknown
 Unknown*
*mitgcmuv           000000000075BCEF  Unknown               Unknown
 Unknown*
*mitgcmuv           000000000075BF19  Unknown               Unknown
 Unknown*
*mitgcmuv           00000000006A2B14  Unknown               Unknown
 Unknown*
*mitgcmuv           0000000000400F26  Unknown               Unknown
 Unknown*
*mitgcmuv           0000000000C5DBA4  Unknown               Unknown
 Unknown*
*mitgcmuv           0000000000400D8D  Unknown               Unknown
 Unknown*

Is there anything else that anyone can think of that I need to do to get
this restart to restart successfully?

Many thanks

Jonny






On 4 August 2014 11:29, Jonny Williams <Jonny.Williams at bristol.ac.uk> wrote:

> 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
>



-- 
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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