[yt-users] Deposited Particle Data

[Nathan Goldbaum]

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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