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[IDV #GFM-139212]: IDV - Sigma coordinates in IDV

Hi Andrew-

> Yes, that's very helpful - thanks very much. We can produce GRIB data on
> pressure levels, but we would like to be able to view data on the native
> model grid to avoid losing information, especially close to the surface.
> >From your email I think now we'd be able to plot data on sigma levels
> using CF conventions.

Okay.  Let me know if you have further questions on this.

> However, our model is using a non-hydrostatic approximation, and my
> understanding is that the atmosphere_sigma_coordinate and
> atmosphere_hybrid_sigma_pressure_coordinate defined in the CF
> conventions only apply to hydrostatic models. We cannot define a simple
> relation between sigma and pressure in the same way for the
> non-hydrostatic model, but can only relate sigma to a reference
> pressure, to which the model applies perturbations as a function of time
> and space to calculate the actual pressure.

Okay.

> However, the model does provide a pressure variable at every point and
> time, and can also provide a geopotential height or height above terrain
> at each gridpoint and timestep. So is it possible for IDV to relate the
> sigma level of a variable x(t,sigma,lat,lon) in the GRIB/netCDF file to
> the height variable h(sigma,lat,lon) in order to plot x in 3D? If so,
> can this be done by supplying netCDF attributes to the variable x and
> height h as described at
> http://www.unidata.ucar.edu/software/netcdf-java/CoordinateAttributes2.html ?

Geopotential height at each point would be best since the IDV uses
the standard atmosphere to relate pressure to the vertical height
axis.

I would imagine that h would be h(t,sigma,lat,lon) (i.e., time
varying) as well?  Right now there is no way to relate the two
that I know of using the netCDF attributes.  Our netCDF expert
is away for a couple of weeks, but I will ask when he gets
back.  In the mean time, would it be possible for you to 
generate a netCDF file that has the geopotential height field
and variable as described above?  I'll see if I can figure something
out until John returns.
 
> Thanks very much for your help with this. We like what we've seen of IDV
> so far, and would very much like to be able to display our 3D fields on
> sigma levels!

Thanks for your input.

Don Murray

> On Fri, 2006-09-29 at 10:04, Unidata IDV Support wrote:
> > Hi Andrew-
> >
> > > Thanks very much for getting back to me so quickly.
> > >
> > > Attached is a sample netCDF file. Our data is produced in GRIB format
> > > (from MM5 by RIPtoGRIB), but I had to convert them to netCDF to add the
> > > 'standard_name' and 'formula_terms' attributes to the hybr level
> > > variable.
> > >
> > > I suspect that the 3D variable in this file won't display properly in
> > > IDV because the file is in NUWG conventions rather than CF.
> >
> > That's one issue.
> >
> > > When I
> > > change the global Conventions attribute to "CF-1.0", the hybr level
> > > variable shows a new attribute: ":_CoordinateTransformType =
> > > "Vertical";" in the Metadata (under Properties) when loaded into IDV,
> > > but no fields at all are displayed in the Field Selector. With
> > > Conventions = "NUWG", the CoordinateTranformType attribute is not added
> > > to the hybr level variable, but the fields appear and can be displayed
> > > (just not in 3D).
> >
> > There is no convention in NUWG for specifying a sigma formula like
> > there is in CF so the NUWG parser cannot handle the CF specification.
> > We are trying to get away from NUWG because of such limitations.
> >
> > > So do netCDF files have to be in CF convention format for sigma levels
> > > to be handled in IDV?
> >
> > Yes.
> >
> > > And if so, can you see what's wrong with the
> > > attached file? It passes the CF conventions checker.
> >
> > Which checker are you using?  The standard checker:
> >
> > http://titania.badc.rl.ac.uk/cgi-bin/cf-checker.pl
> >
> > really doesn't check to make sure that the appropriate variables
> > are contained for these dimensionless vertical coordinates.  I'm
> > not sure what it checks, but usually it seems to let bad files
> > pass.  If you are using the Unidata checker:
> >
> > http://motherlode.ucar.edu:8080/thredds/cdmValidate.html
> >
> > handles files that conform to several conventions which the
> > Common Data Model (CDM) supports.  In this case, it liked the
> > NUWG conventions.
> >
> > There are a couple of issues with the file you sent.
> >
> > - First to make it CF compliant, you need to have the convention be CF-1.0
> > - The time dimension for CF needs to be "time"
> > - The current implementation for the sigma transform needs to have
> > both the ptop and ps variables have the same units.  I'll talk
> > to the developer about that when he returns from vacation.
> > - Also ptop is a scalar variable in the CF conventions and you have
> > it defined at every point.
> > - The values for hybr are not what I would expect for sigma (1-25).
> > I would expect the range to be 0-1.
> >
> > Instead of converting to netCDF, do you have a way of producing
> > post-processed GRIB data on pressure levels?  If so, then perhaps
> > you could create those and read the GRIB directly.  There would be
> > a big memory savings as well since the IDV would not have to
> > convert from sigma to pressure on the fly.
> >
> > > Any insight you could provide would be very gratefully received!
> >
> > I'm not sure that I was very helpful, but hopefully this can
> > get you on the right track.  Thanks for trying out the IDV!
> >
> > > Thanks very much for your time,
> > >
> > > Andrew
> > >
> > > On Thu, 2006-09-28 at 01:30, Unidata IDV Support wrote:
> > > > Hello Andrew-
> > > >
> > > > > Institution: MetService of New Zealand
> > > > > Package Version: 2.0
> > > > > Operating System: os.name:Linux; os.arch:i386; 
> > > > > os.version:2.6.10-1.771_FC2smp;
> > > > > Hardware Information: java.vendor:Sun Microsystems Inc.; 
> > > > > java.version:1.5.0_06; java.home:/usr/local/AMPS/idv/jre; 
> > > > > j3d.version:1.3.1; j3d.vendor:Blackdown Java-Linux & Sun 
> > > > > Microsystems, Inc.; j3d.renderer:OpenGL;
> > > > > Inquiry: Hi,
> > > > >
> > > > > Does IDV 2.0 support sigma coordinates? I have followed the advice at 
> > > > > http://www.unidata.ucar.edu/support/help/MailArchives/idv/msg00608.html
> > > > > and 
> > > > > http://ftp.unidata.ucar.edu/support/help/MailArchives/idv/msg00606.html
> > > > >  to
> > > > > relate a hybrid sigma coordinate to vertical height, but data on 
> > > > > different sigma levels
> > > > > still appear on the 'surface' in the display window.
> > > > >
> > > > > I'd be grateful if you could let me know if relating the sigma 
> > > > > coordinate to height/pressure
> > > > > through the netCDF CF conventions (assigning the standard_name and 
> > > > > formula_terms attributes
> > > > > to the level variable) is the best method of displaying data defined 
> > > > > on sigma levels
> > > > > in IDV.
> > > >
> > > > The IDV should handle the CF atmospheric sigma coordinate.  Do you
> > > > have a sample file that we could look at to see if it's a problem
> > > > on our end or some missing attribute in the netCDF file?
> > > >
> > > > Thanks.
> > > >
> > > > Don Murray
> > > >
> > > > Ticket Details
> > > > ===================
> > > > Ticket ID: GFM-139212
> > > > Department: Support IDV
> > > > Priority: Normal
> > > > Status: Open
> > > >
> > >
> > >
> >
> >
> > Ticket Details
> > ===================
> > Ticket ID: GFM-139212
> > Department: Support IDV
> > Priority: Normal
> > Status: Open
> >
> 
> 


Ticket Details
===================
Ticket ID: GFM-139212
Department: Support IDV
Priority: Normal
Status: Open