[yt-users] Using time series data from FLASH with particle files.

Nathan Goldbaum nathan12343 at gmail.com
Mon May 11 13:31:05 PDT 2015


On Mon, May 11, 2015 at 1:24 PM, Nathan Goldbaum <nathan12343 at gmail.com>
wrote:

>
>
> On Mon, May 11, 2015 at 1:19 PM, Joshua Wall <joshua.e.wall at gmail.com>
> wrote:
>
>> Dear users,
>>
>>     Since I'm already 0 for 1 today, I thought I'd also ask about this
>> error I've seen. I'm trying to get the time series of momentum density in
>> the x-dir from a simulation in FLASH where I have both the plot and
>> particle files with:
>>
>> ############################################################
>>
>> ts =
>> yt.load("/home/josh/amuse-svn/src/amuse/community/flash/SinkMomTest2/SMT_hdf5_plt_cnt_0??[!0]",
>>
>> particle_filename='/home/josh/amuse-svn/src/amuse/community/flash/SinkMomTest2/SMT_hdf5_part_0??[!0]')
>>
>> times = []
>> Mom_x = []
>> Mom_y = []
>>
>> for ds in ts:
>>
>>
>>     try:
>>         ds.add_field("total_px", function=_px, units="kg/s/m**2")
>>         ds.add_field("total_py", function=_py, units="kg/s/m**2")
>>     except:
>>         continue
>>
>>     dd = ds.all_data()
>>
>>     Mom_x.append(dd["total_px"])
>>     Mom_y.append(dd["total_py"])
>>     times.append(ds.current_time.in_units("Myr"))
>>
>> ###########################################################
>>
>> But this gives the error:
>>
>>
>> ---------------------------------------------------------------------------
>> IOError                                   Traceback (most recent call
>> last)
>> <ipython-input-3-4be7349ef199> in <module>()
>>       9 Mom_y = []
>>      10
>> ---> 11 for ds in ts:
>>      12
>>      13
>>
>> /usr/local/lib/python2.7/dist-packages/yt/data_objects/time_series.pyc in
>> __iter__(self)
>>     158         for o in self._pre_outputs:
>>     159             if isinstance(o, types.StringTypes):
>> --> 160                 ds = load(o, **self.kwargs)
>>     161                 self._setup_function(ds)
>>     162                 yield ds
>>
>> /usr/local/lib/python2.7/dist-packages/yt/convenience.pyc in load(*args,
>> **kwargs)
>>      78         if c._is_valid(*args, **kwargs): candidates.append(n)
>>      79     if len(candidates) == 1:
>> ---> 80         return output_type_registry[candidates[0]](*args,
>> **kwargs)
>>      81     if len(candidates) == 0:
>>      82         if ytcfg.get("yt", "enzo_db") != '' \
>>
>> /usr/local/lib/python2.7/dist-packages/yt/frontends/flash/data_structures.pyc
>> in __init__(self, filename, dataset_type, storage_filename,
>> particle_filename, units_override)
>>     206                 self._particle_handle =
>> HDF5FileHandler(self.particle_filename)
>>     207             except:
>> --> 208                 raise IOError(self.particle_filename)
>>     209         # These should be explicitly obtained from the file, but
>> for now that
>>     210         # will wait until a reorganization of the source tree and
>> better
>>
>> IOError:
>> /home/josh/amuse-svn/src/amuse/community/flash/SinkMomTest2/SMT_hdf5_part_0??[!0]
>>
>
> Unfortunately the FLASH frontend is gobbling the error h5py is raising
> here.
>
> A quick way to get the real error from h5py would be to replace "raise
> IOError..." on line 208 with just "raise" and then rerun the script.
>

Ah, but now that I think about it, I don't think the glob pattern should
have made it all the way down to the FLASH I/O layer.  Maybe there's a bug
in the way we set up time series for FLASH datasets that include particle
files?


>
>
>>
>> #############################################################
>>
>> Any ideas?
>>
>> Joshua Wall
>> Drexel University
>>
>> _______________________________________________
>> yt-users mailing list
>> yt-users at lists.spacepope.org
>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>
>>
>
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