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

Thu Sep 4 05:19:52 EDT 2014

Hi everyone

I just thought that I would update this thread to let you know that I have
found a solution to my persistent problem of the DIC variable diverging in
my version of the MITgcm.

Basically it was to do with sharp changes in bathymetry. Limiting the ocean
depth to 3km globally has fixed this issue which is great for now but is
clearly not a long term solution.

What is not at all clear to me however is why the DIC variable was being
affected but none of the other biogeochemical variables (alkalinity, PO4,
DOP and O2) were.

Does anyone have any ideas about why this might be?

Many thanks!

Jonny

On 29 August 2014 14:30, Jonny Williams <Jonny.Williams at bristol.ac.uk>
wrote:

> Hi again
>
> Sorry for taking up so much room in people's inboxes!
>
> I think I'm getting somewhere now. I have implemented the OBCS boundary
> conditions for the DIC variable but I am still getting the same crash
> although it does not seem to be coming from the open boundaries any more
> which is good!
>
> What I think may be happening now is that the surface fluxes are going a
> bit haywire, as (I think) indicated in the dic_tave* output files. Since
> the model I am dealing with is of such high resolution (0.1 degree) there
> are tiny gridboxes which are side-by-side of very different magnitudes and
> I think that the numerics may not be able to deal with this?
>
> For now, is there a way to turn of the surface flux of co2/dic just to
> check that the advection (etc) are behaving themselves?
>
> Thanks!
>
> Jonny
>
>
> On 29 August 2014 09:33, Jonny Williams <Jonny.Williams at bristol.ac.uk>
> wrote:
>
>> I've downloaded the whole MITgcm tree from scratch again and the
>> compilation now works with regard to the pkg/gchem/gchem_forcing_sep.F
>> changes which Jean-Michel has made so that's great!
>>
>> On the other hand the model is still crashing with the same NaNs
>> propagating out from the open boundaries and so I am going to try using the
>> OBNptrFile,OBSptrFile,OBEptrFile,OBWptrFile option.
>>
>> I am assuming that the dimensions of these files should be...
>>
>> (length of boundary) x (number of depth levels) x (number of tracers)
>>
>> and that the order of the tracers is dic, alk, po4, dop, o2
>>
>> Cheers
>>
>> Jonny
>>
>>
>>
>> On 23 August 2014 16:56, Jean-Michel Campin <jmc at ocean.mit.edu> wrote:
>>
>>> Hi Jonny,
>>>
>>> I made some changes in pkg/gchem/gchem_forcing_sep.F (CVS revision 1.36),
>>> adding a (2nd) call to OBCS_APPLY_PTRACER that I think is needed since,
>>> currently, nothing prevent pkg/dic to modify/update the ptracers fields
>>> beyond the OB lines.
>>>
>>> It has not yet been carefully tested (we will try to check this in the
>>> coming days), but if you want to give it a try (needs to get the latest
>>> MITgcm code).
>>>
>>> An other thing with OBCS that might bring some instabilities in ptracer
>>> fields
>>> is that, since you don't specify any OB values for ptracers (from your
>>> "data.obcs",
>>>  OBNptrFile,OBSptrFile,OBEptrFile,OBWptrFile are not set) you are relying
>>> on the "default ptracer option" for ptracer OBCS which is sometimes
>>> problematic.
>>> Might be usefull to try to specify these OB fields to check this aspect.
>>>
>>> Cheers,
>>> Jean-Michel
>>>
>>> On Fri, Aug 22, 2014 at 04:42:36PM +0100, Jonny Williams wrote:
>>> > Hi Jean-Michel
>>> >
>>> > Thank you very much for your email!
>>> >
>>> > In answer to your questions:
>>> >
>>> >    1. Yes, OBs are straight lines and yes, the northern/western and
>>> >    southern/western boundaries cross at wet points. The other two
>>> boundaries
>>> >    are all dry.
>>> >    2. I have been using tracer advection scheme 77 (described here
>>> >    <
>>> http://mitgcm.org/public/r2_manual/latest/online_documents/node82.html#tab:advectionShemes_summary
>>> >)
>>> >    but I have also tried advection schemes 1 and 2 and neither of them
>>> worked.
>>> >    I don't think I am using multidimensional advection for the
>>> tracers. I
>>> >    coped the example of data.ptracers
>>> >    from verification/tutorial_global_oce_biogeo/input/data.ptracers
>>> and the
>>> >    changes I have made have been minimal except for the inclusion of
>>> the KPP
>>> >    scheme and changing the number of levels in PTRACERS_ref to 50.
>>> >    3. I've attached the relevant files.
>>> >
>>> > Please let me know if I can provide any more. Huge thanks!
>>> >
>>> > Jonny
>>> >
>>> >
>>> > On 22 August 2014 16:29, Jean-Michel Campin <jmc at ocean.mit.edu> wrote:
>>> >
>>> > > Hi Jonny,
>>> > >
>>> > > I suspect that we have a problem in the code regarding the use
>>> > > of pkg/dic with pkg/obcs.
>>> > > This combination is not currently tested (i.e., we don't have any
>>> > > verification experiment that run this case).
>>> > > The fact that setting "OBCSfixTopo=.TRUE.," was helping at lower
>>> > > resolution is not a good sign (the model is supposed to run fine
>>> > > without this flag).
>>> > >
>>> > > Will take a look at the code and get back to you.
>>> > > But to facilitate the search:
>>> > > 1) do your OB are strait lines ? and do you have wet points in a
>>> place
>>> > >   where OB cross (e.g. Northern and Eastern OB) ?
>>> > > 2) which advection scheme do you use for ptracers ? do you use
>>> > >  multi-dim advection for ptracers ?
>>> > > 3) it could help if you send us some of the relevant parameter files:
>>> > >  data.obcs data data.pkg and data.ptracers
>>> > >
>>> > > Cheers,
>>> > > Jean-Michel
>>> > >
>>> > > On Thu, Aug 21, 2014 at 12:45:39PM +0100, Jonny Williams wrote:
>>> > > > Hi everyone
>>> > > >
>>> > > > With regard to this thread, I can now successfully run my model at
>>> 1
>>> > > degree
>>> > > > resolution with all the biogeochemistry packages that I want
>>> turned on
>>> > > and
>>> > > > I can also restart the model, which is great; thanks for your help.
>>> > > >
>>> > > > I am now trying to run essentially the same model but for 0.1
>>> degree
>>> > > > resolution. Unfortunately, even using the *OBCSfixTopo=.TRUE.,
>>> *flag in
>>> > > > data.obcs I am getting unphysical values creeping in from the
>>> corners
>>> > > again
>>> > > > (see attachment in previous email).
>>> > > >
>>> > > > Does anyone have any ideas about how I can circumvent this?
>>> Notably, it
>>> > > is
>>> > > > only the DIC quantity which is going to NaNs, all the other
>>> > > biogeochemical
>>> > > > variables (alk, po4, dop, o2) carry on fine so I assume it is a
>>> problem
>>> > > > with the DIC package specifically (i.e. not GCHEM, PTRACERS)?
>>> > > >
>>> > > > Many thanks in advance for any input!
>>> > > >
>>> > > > 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
>>> > >
>>> > > > _______________________________________________
>>> > > > MITgcm-support mailing list
>>> > > > MITgcm-support at mitgcm.org
>>> > > > http://mitgcm.org/mailman/listinfo/mitgcm-support
>>> > >
>>> > >
>>> > > _______________________________________________
>>> > > 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 list
>>> > MITgcm-support at mitgcm.org
>>> > http://mitgcm.org/mailman/listinfo/mitgcm-support
>>>
>>>
>>> _______________________________________________
>>> 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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