[yt-users] Slice Plot Gadget Problem

Jared Coughlin Jared.W.Coughlin.29 at nd.edu
Mon Aug 11 07:09:22 PDT 2014 

Thank you very much, I really appreciate the help!
-Jared
On Aug 11, 2014 9:44 AM, "Matthew Turk" <matthewturk at gmail.com> wrote:

> Hi Jared,
>
> I've found the bug and issued a fix, here:
>
>
> https://bitbucket.org/yt_analysis/yt/pull-request/1140/adding-check-for-no-fields-ptypes-in/diff
>
> Should go in shortly.  (I put up a projection just for fun.)
>
> -Matt
>
> On Fri, Aug 8, 2014 at 5:21 PM, Jared Coughlin
> <Jared.W.Coughlin.29 at nd.edu> wrote:
> > No problem, thank you very much for all your help, I really appreciate
> it!
> > -Jared
> >
> > On Aug 8, 2014 5:48 PM, "Nathan Goldbaum" <nathan12343 at gmail.com> wrote:
> >>
> >> Ok, I can trigger the error you're seeing locally.  I've passed this on
> to
> >> Matt who can take a closer look at what's happening and hopefully fix
> the
> >> issue you're running into.
> >>
> >> Sorry for the difficulties, hopefully we'll have this cleared up soon.
> >> Thanks also for reporting this and working with us.
> >>
> >>
> >> On Fri, Aug 8, 2014 at 12:55 PM, Jared Coughlin
> >> <Jared.W.Coughlin.29 at nd.edu> wrote:
> >>>
> >>> Hi,
> >>> I tried changing the units, and that gave the same error. I also tried
> >>> changing the center to 'c', and same thing.  I've posted the contents
> of
> >>> ds.field_list and ds.derived_field_list here:
> >>> http://paste.yt-project.org/show/5003/
> >>>
> >>> The plot of ('deposit'', 'Gas_smoothed_Density') also didn't work.  The
> >>> traceback is here: http://paste.yt-project.org/show/5004/
> >>>
> >>> The plot of ('deposit', 'all_cic') worked, however. At least, it ran
> and
> >>> produced an image without throwing any errors.  I can upload the image
> to
> >>> google drive, if you'd like?
> >>>
> >>> As for the snapshot, it's not very big, only 2.2M.  I can put that on
> >>> google drive as well.  Also, it's little endian.  I can upload the
> parameter
> >>> file and ic file, as well, if you'd like.
> >>> -Jared
> >>>
> >>>
> >>>
> >>>
> >>> On Fri, Aug 8, 2014 at 1:51 PM, Nathan Goldbaum <nathan12343 at gmail.com
> >
> >>> wrote:
> >>>>
> >>>> Hi Jared,
> >>>>
> >>>> Looking at the traceback, it seems the issue is in calculating the
> >>>> maximum gas density in the simulation.  I'm not sure why this is
> failing,
> >>>> but to see if we can create a plot at all, can you try supplying 'c'
> as the
> >>>> plot center instead of 'm'?
> >>>>
> >>>> Can you also paste the contents of 'ds.field_list' and
> >>>> 'ds.derived_field_list'?
> >>>>
> >>>> Additionally, can you create a SlicePlot of one of the following
> fields:
> >>>>
> >>>> ('deposit', 'Gas_smoothed_Density')
> >>>> ('deposit', 'all_cic')
> >>>>
> >>>> The first is another name for the SPH smoothed gas density - I'm
> >>>> checking here whether the ('gas', 'density') alias is misbehaving.
>  The
> >>>> second is the cloud-in-cell deposited density for all particles in the
> >>>> simulation - I want to make sure that deposition isn't completely
> broken for
> >>>> your dataset.
> >>>>
> >>>> Lastly, if the dataset isn't enormous and it is ok to share it, it
> would
> >>>> be helpful if you could share the actual dataset so one of us can
> reproduce
> >>>> your problem locally.  We've had a lot of success using dropbox and
> google
> >>>> drive for this purpose in the past.
> >>>>
> >>>> Hopefully we'll be able to get to the bottom of this,
> >>>>
> >>>> Nathan
> >>>>
> >>>>
> >>>>
> >>>> On Fri, Aug 8, 2014 at 9:39 AM, Jared Coughlin
> >>>> <Jared.W.Coughlin.29 at nd.edu> wrote:
> >>>>>
> >>>>> Hi Nathan,
> >>>>> Thank you for responding! I tried what you suggested, but still no
> >>>>> luck. I'm still getting the index out of bounds error.  I've copied
> the
> >>>>> traceback to the paste bin at:
> http://paste.yt-project.org/show/5001/
> >>>>> I've included how I loaded the snapshot as well as the call to
> >>>>> yt.SlicePlot, in case that helps.  Thank you very much for all the
> help!
> >>>>> -Jared
> >>>>>
> >>>>>
> >>>>> On Thu, Aug 7, 2014 at 5:12 PM, Nathan Goldbaum <
> nathan12343 at gmail.com>
> >>>>> wrote:
> >>>>>>
> >>>>>> Hi Jared,
> >>>>>>
> >>>>>> Try instead:
> >>>>>>
> >>>>>> yt.SlicePlot(ds, 'z', ('gas', 'density'), width=(10000., 'kpc'),
> >>>>>> center ='m')
> >>>>>>
> >>>>>> (note the lower-case).
> >>>>>>
> >>>>>> ('Gas', 'Density') is a particle field, i.e. the Density values
> >>>>>> associated with each of the Gas particles in your simulation.
>  ('gas',
> >>>>>> 'density') is a mesh field - for SPH it is the smoothed gas
> density, taken
> >>>>>> from the original Gas particles.  Particle fields are unstructured,
> the
> >>>>>> field is only defined at the positions where particles exist.  Mesh
> fields
> >>>>>> are defined over the whole simulation domain.
> >>>>>>
> >>>>>> Unfortunately there's some name collision here for gadget binary
> files
> >>>>>> so I can see how this is confusing.  At the very least we should
> catch that
> >>>>>> you're trying to create a SlicePlot of a particle field and crash
> with a
> >>>>>> nicer, more understandable error.
> >>>>>>
> >>>>>> More detail on the difference between particle and mesh fields as
> well
> >>>>>> as fields in yt in general here:
> >>>>>> http://yt-project.org/docs/3.0/analyzing/fields.html
> >>>>>>
> >>>>>> Hope that helps,
> >>>>>>
> >>>>>> -Nathan
> >>>>>>
> >>>>>>
> >>>>>> On Thu, Aug 7, 2014 at 2:08 PM, Jared Coughlin
> >>>>>> <Jared.W.Coughlin.29 at nd.edu> wrote:
> >>>>>>>
> >>>>>>> Hi Nathan, I pasted the traceback here:
> >>>>>>> http://paste.yt-project.org/show/4998/
> >>>>>>> -Jared
> >>>>>>>
> >>>>>>>
> >>>>>>> On Thu, Aug 7, 2014 at 4:16 PM, Jared Coughlin
> >>>>>>> <Jared.W.Coughlin.29 at nd.edu> wrote:
> >>>>>>>>
> >>>>>>>> Hello! I have a vanilla gadget snapshot (one from the lcdm sample
> >>>>>>>> run that the code comes with) that  I was able to plot by
> following the
> >>>>>>>> instructions given here:
> >>>>>>>>
> >>>>>>>>
> http://yt-project.org/docs/3.0/cookbook/tipsy_notebook.html#tipsy-notebook
> >>>>>>>>
> >>>>>>>> I then moved on to the 'Making Smoothed Images' section of that
> page
> >>>>>>>> and tried the SlicePlot command.  However, I get the following
> error:
> >>>>>>>> IndexError: index 32767 is out of bounds for axis 0 with size
> 32767
> >>>>>>>>
> >>>>>>>> Basically, I'm not really sure what that means.  It seems like
> it's
> >>>>>>>> overstepping the bounds of an array, as, for a zero-indexed array
> of size
> >>>>>>>> 32767, index 32767 would be out of bounds by one.  I just wanted
> to see if
> >>>>>>>> anyone else has had this problem, and if so, how they fixed it?
> Thank you
> >>>>>>>> very much!
> >>>>>>>> -Jared
> >>>>>>>
> >>>>>>>
> >>>>>>>
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