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

Wed Aug 27 06:51:58 EDT 2014

Thanks very much for that Jean-Michel!

Unfortunately I won't be able to try this fix out today as our computer is
undergoing maintenance, I will try tomorrow!

Thanks again

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
>
>
> _______________________________________________
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>

-- 
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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