[yt-users] Deposited Particle Data
Jason Galyardt
jason.galyardt at gmail.com
Mon May 11 12:55:18 PDT 2015
Hi Matt,
I only use one species of particle: active (massive).
On a possibly related front, I've also had trouble getting yt to over-plot
particle positions on a rectangular projection (4 kpc x 24 kpc, in this
case); I can over-plot particles on a square projection just fine.
Cheers,
Jason
On Mon, May 11, 2015 at 3:51 PM, Matthew Turk <matthewturk at gmail.com> wrote:
> Hi Jason,
>
> That does look odd; the way the particle mappings are constructed may
> not be valid for your data. How many species of particles do you
> have, and of what types?
>
> -Matt
>
> On Mon, May 11, 2015 at 2:36 PM, Jason Galyardt
> <jason.galyardt at gmail.com> wrote:
> > It seems that the problem is in the evaluation of 'end', which gets set
> to
> > 0. I don't know how the ds.index._particle_indices container (which
> p_ind
> > is set to) is supposed to look, but it's got an awful lot of zeros
> packed in
> > front. In fact, of the 8017 elements, 5655 of them are exactly 0.
> >
> > Looking at line 76 with the debugger, p_ind[g2.id - g2._id_offset + 1] =
> > p_ind[1000 - 1 + 1] = p_ind[1000] = 0.
> >
> > Is this normal? Doesn't make sense to me, since there are 9000+
> particles in
> > this time step.
> >
> > Jason
> >
> > On Mon, May 11, 2015 at 1:17 PM, Nathan Goldbaum <nathan12343 at gmail.com>
> > wrote:
> >>
> >> If I had access to the dataset, I would put a breakpoint before line 76
> in
> >> your traceback here:
> >>
> >> /home/jeg/yt/yt/frontends/flash/io.pyc in _read_particle_coords(self,
> >> chunks, ptf)
> >> 74 start = p_ind[g1.id - g1._id_offset]
> >> 75 end = p_ind[g2.id - g2._id_offset + 1]
> >> ---> 76 x = np.asarray(p_fields[start:end, px],
> >> dtype="=f8")
> >> 77 y = np.asarray(p_fields[start:end, py],
> >> dtype="=f8")
> >> 78 z = np.asarray(p_fields[start:end, pz],
> >> dtype="=f8")
> >>
> >> I would try to print out start and end, as well as g1.id,
> g1._id_offset,
> >> g2.id,and g2._id_offset.
> >>
> >> This is the last frame before we leave yt and enter h5py. For some
> reason
> >> start = end here, and we'd need to look at how the dataset is being
> read in
> >> to figure out why.
> >>
> >> On Mon, May 11, 2015 at 6:38 AM, Jason Galyardt <
> jason.galyardt at gmail.com>
> >> wrote:
> >>>
> >>> Hi all,
> >>>
> >>> Per Matt's suggestion, I've tried accessing the FLASH particles via
> >>> ['all', 'particle_mass'], to no avail. The traceback can be found here:
> >>>
> >>> http://paste.yt-project.org/show/5541/
> >>>
> >>> I get the same zero-length selection exception when I use ['io',
> >>> 'particle_position_x'] or ['all', 'particle_position_x'], as Yuan
> suggests.
> >>>
> >>> To further check the input particle file format, I used the low-level
> >>> h5py interface. I was able to read both particle position and mass.
> This
> >>> script doesn't know about the grid, however.
> >>>
> >>> Any other ideas?
> >>>
> >>> Thanks,
> >>> Jason
> >>>
> >>> On Sat, May 9, 2015 at 9:59 PM, Yuan Li <bear0980 at gmail.com> wrote:
> >>>>
> >>>> I tried ['io', 'particle_position_x'] on my Flash data, and it seemed
> to
> >>>> work just fine. I use the latest yt.
> >>>>
> >>>> Yuan
> >>>>
> >>>> On Sat, May 9, 2015 at 7:51 PM, Nathan Goldbaum <
> nathan12343 at gmail.com>
> >>>> wrote:
> >>>>>
> >>>>> I'm not able to reproduce this using the Orbit dataset on
> >>>>> yt-project.org/data. Unfortunately I don't think we have any other
> flash
> >>>>> test datasets that use particles.
> >>>>>
> >>>>> It would also help to see the full error traceback you're getting.
> >>>>>
> >>>>> On Sat, May 9, 2015 at 4:32 PM, Matthew Turk <matthewturk at gmail.com>
> >>>>> wrote:
> >>>>>>
> >>>>>> Hi Jason,
> >>>>>>
> >>>>>> Don't worry about posting the data -- that's completely fine, and I
> >>>>>> think in general we should do all we can to reproduce without the
> >>>>>> dataset! I'm wondering if perhaps there's something funny about the
> >>>>>> "io" particle field. If you try "all" instead of "io", does it work
> >>>>>> any better?
> >>>>>>
> >>>>>> -Matt
> >>>>>>
> >>>>>> On Fri, May 8, 2015 at 1:01 PM, Jason Galyardt
> >>>>>> <jason.galyardt at gmail.com> wrote:
> >>>>>> > Hi all,
> >>>>>> >
> >>>>>> > Has anyone had success accessing deposited particle data generated
> >>>>>> > with
> >>>>>> > FLASH? It appears in the dataset derived field list, but when I go
> >>>>>> > to access
> >>>>>> > it (via ds.all_data()['deposit', 'io_mass']), I get an error
> >>>>>> > concerning
> >>>>>> > zero-length selection. I get the same error when I try to access
> the
> >>>>>> > 'standard' particle data (from ds.field_list), such as
> >>>>>> > ds.all_data()['io',
> >>>>>> > 'particle_mass'].
> >>>>>> >
> >>>>>> > Does this ring any bells? This very well could be user error, so
> >>>>>> > please let
> >>>>>> > me know if that seems to be the case. I've pasted a basic script
> to
> >>>>>> > reproduce the error here:
> >>>>>> >
> >>>>>> > http://paste.yt-project.org/show/5538/
> >>>>>> >
> >>>>>> > I'd rather not post the dataset publicly, but I can send you a
> link,
> >>>>>> > if
> >>>>>> > you're interested.
> >>>>>> >
> >>>>>> > Cheers,
> >>>>>> > Jason Galyardt
> >>>>>> >
> >>>>>> >
> >>>>>> >
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