[MITgcm-support] Forcing files in data.dic (biogeochemistry)
Jonny Williams
Jonny.Williams at bristol.ac.uk
Fri Aug 29 03:10:59 EDT 2014
Thanks again for all your help.
I've started a clean download as you and Jody suggested ;) I'll let you
know how I get on!
Cheers
Jonny
On 28 August 2014 19:14, Jean-Michel Campin <jmc at ocean.mit.edu> wrote:
> Hi Jonny,
>
> OK, soon after checkpoint64o is old enough, and this explains why
> when you just update gchem_forcing_sep.F it did not work.
>
> Now, regarding the update, since you made some changes in
> ptracers_advection.F, "cvs update" will not remove it, and it's what it
> tell:
> > cvs update: conflict: ptracers_advection.F is modified but no longer in
> the
> > repository
> before trying to use your updated version of MITgcm, you need to check that
> you were able to remove any "conflict" that "cvs -n update -A" will list.
> Or, might be quicker to start from a fresh download.
>
> Cheers,
> Jean-Michel
>
> > C ptracers_advection.F
> On Thu, Aug 28, 2014 at 06:56:12PM +0100, Jonny Williams wrote:
> > Hi Jean Michel
> >
> > Thanks again
> >
> > I originally checked out the code on "2013/10/06 00:48:15"
> >
> > This was on our last supercomputer and I then copied over the whole
> MITgcm
> > folder to our new one in February. I didn't check it out again from
> scratch.
> >
> >
> > - Here is the top of the tag-index file...
> >
> >
> > START
> >
> > *$Header: /u/gcmpack/MITgcm/doc/tag-index,v 1.1928 2013/10/06 00:48:15
> jmc
> > Exp $*
> > *$Name: $*
> >
> > * Notes on tags used in MITgcmUV*
> > * ==============================*
> >
> > *o pkg/exf:*
> > * - to allow to use seaice-fraction from pkg/exf in other pkgs than
> > pkg/seaice:*
> > * rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION*
> > * and rename array obsSIce to exf_iceFraction.*
> > *o tutorial_deep_convection:*
> > * - add 1rst version of isotropic 3-D Smagorinsky code (from
> > Louis-Philippe),*
> > * for now all in this exp. code dir.*
> > * - add secondary test using Smag-3D viscosity (keep very low backgroud
> > visc for*
> > * testing) and flux-limter advection scheme for Temp. (no explicit
> > diffusion).*
> > *o eesupp/src:*
> > * - added SINGLE_DISK_IO option because reading of parameter files on*
> > * very large number of processors did not work with existing set-up*
> >
> > *checkpoint64o (2013/09/25)*
> > .
> > .
> > .
> >
> > END
> >
> >
> > - This is the output from *cvs -q -n update -A*
> >
> >
> > ggjhtw at eslogin007:~/MITgcm/pkg/ptracers> cvs -q -n update -A
> > cvs update: conflict: ptracers_advection.F is modified but no longer in
> the
> > repository
> > C ptracers_advection.F
> > cvs update: conflict: ptracers_calc_diff.F is modified but no longer in
> the
> > repository
> > C ptracers_calc_diff.F
> > cvs update: conflict: ptracers_cycle.F is modified but no longer in the
> > repository
> > C ptracers_cycle.F
> > cvs update: conflict: ptracers_dwnslp_apply.F is modified but no longer
> in
> > the repository
> > C ptracers_dwnslp_apply.F
> > cvs update: conflict: ptracers_forcing.F is modified but no longer in the
> > repository
> > C ptracers_forcing.F
> > cvs update: conflict: ptracers_implicit.F is modified but no longer in
> the
> > repository
> > C ptracers_implicit.F
> > ggjhtw at eslogin007:~/MITgcm/pkg/ptracers>
> >
> > Thanks again!!
> >
> > Jonny
> >
> >
> >
> > On 28 August 2014 18:44, Jean-Michel Campin <jmc at ocean.mit.edu> wrote:
> >
> > > Hi Jonny,
> > >
> > > Regarding question (1), it would be usefull to know
> > > when was the last time you updated your MITgcm code (full code),
> > > or if you did not before, when you downloaded it.
> > > the top of MITgcm/doc/tag_index (down to the latest "checkpoint???")
> > > is generally a good indicator.
> > > The information about gchem_forcing_sep.F is one thing, but it does not
> > > tell much about the other parts of the code.
> > >
> > > Regarding question (4): can you try:
> > > cd /home/n02/n02/ggjhtw/MITgcm/
> > > cd pkg/ptracers
> > > cvs -q -n update -A
> > > just to list (but will do nothing) how this dir compares with
> > > the latest MITgcm/pkg/ptracers code.
> > > and let us know what this command output is.
> > >
> > > Cheers,
> > > Jean-Michel
> > >
> > > On Thu, Aug 28, 2014 at 06:07:43PM +0100, Jonny Williams wrote:
> > > > Hi Jean-Michel
> > > >
> > > > In answer to your questions
> > > >
> > > > 1. the previous version of gchem_forcing_sep.F was "1.32
> 2013/07/04",
> > > it
> > > > is now at 1.37.
> > > > 2. no, I don't think so!
> > > > 3. yes I did clean the directory, I have a script which basically
> does
> > > > the same things as make Clean
> > > > 4. I used the instructions on that same website using "cvs update
> -d
> > > -P"
> > > > in the root ~/MITgcm directory which is from the section of the
> > > website
> > > > that you recommend. This took approximately 20 minutes or so to
> > > update the
> > > > whole directory tree. The ptracers_advection.F file is still
> present
> > > in
> > > > ~/MITgcm/pkg/ptracers
> > > >
> > > > I hope this is helpful information!
> > > >
> > > > Many thanks
> > > >
> > > > Jonny
> > > >
> > > >
> > > >
> > > > On 28 August 2014 17:40, Jean-Michel Campin <jmc at ocean.mit.edu>
> wrote:
> > > >
> > > > > Hi Jonny,
> > > > >
> > > > > 1) what was the version of the code you were working with
> > > > > (or last time you updated your MITgcm code) ?
> > > > > 2) do you have customized source file in your local "../code" dir ?
> > > > > they might need to be updated to account for the changes (updates)
> > > > > between the latest MITgcm code and the one you had before.
> > > > > 3) I don't know what is in script "New_Build_Script.txt", but
> > > > > did you clean-up your build dir (make Clean) before ?
> > > > > 4) And regarding ptracers_advection.F (where the error comes from),
> > > > > this source file has been removed (~ 8 months ago) in the latest
> > > code.
> > > > > How did you update your MITgcm code ?
> > > > > There are few tips about the use of CVS there:
> > > > > http://mitgcm.org/public/using_cvs.html
> > > > > and in particular, the section "Getting updates from the
> repository".
> > > > >
> > > > > Cheers,
> > > > > Jean-Michel
> > > > >
> > > > > On Thu, Aug 28, 2014 at 04:21:54PM +0100, Jonny Williams wrote:
> > > > > > Hi again
> > > > > >
> > > > > > Unfortunately, after updating the whole MITgcm directory tree, I
> now
> > > > > cannot
> > > > > > compile at all due to the error copied below. Does this make
> sense in
> > > > > light
> > > > > > of the changes that you've made Jean-Michel? I sent most of the
> > > output
> > > > > > from *source
> > > > > > New_Build_Script.txt *to a text file called *out*, which I have
> also
> > > > > > attached.
> > > > > >
> > > > > > Thanks!
> > > > > >
> > > > > > *ggjhtw at eslogin007:~/MITgcm/91Ma_obcs_0.1degree_bio/build>
> source
> > > > > > New_Build_Script.txt > out*
> > > > > > *ptracers_advection.f(2271): error #6404: This name does not
> have a
> > > type,
> > > > > > and must have an explicit type. [GPTR]*
> > > > > > * O gPtr(1-OLx,1-OLy,1,1,1,iTracer),*
> > > > > > *------------------------------^*
> > > > > > *compilation aborted for ptracers_advection.f (code 1)*
> > > > > > *make[1]: *** [ptracers_advection.o] Error 1*
> > > > > > *make: *** [fwd_exe_target] Error 2*
> > > > > > *ggjhtw at eslogin007:~/MITgcm/91Ma_obcs_0.1degree_bio/build>*
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > On 28 August 2014 15:50, Jonny Williams <
> > > Jonny.Williams at bristol.ac.uk>
> > > > > > wrote:
> > > > > >
> > > > > > > Hi there
> > > > > > >
> > > > > > > For your information, updating the
> pkg/gchem/gchem_forcing_sep.F
> > > file
> > > > > on
> > > > > > > its own has not worked unfortunately. I am currently updating
> the
> > > whole
> > > > > > > code tree in case there are any cross-dependencies which I have
> > > missed.
> > > > > > >
> > > > > > > I have not attempted running with
> > > > > OBNptrFile,OBSptrFile,OBEptrFile,OBWptrFile
> > > > > > > included as yet. Is clear however from the crash results that
> the
> > > > > errors
> > > > > > > are 'propagating' from the open boundaries!
> > > > > > >
> > > > > > > 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
> > > > > @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
> > > @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
> > > > >
> > > > >
> > > > > > _______________________________________________
> > > > > > 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
>
> > _______________________________________________
> > 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
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