On Mon, May 11, 2015 at 1:24 PM, Nathan Goldbaum
On Mon, May 11, 2015 at 1:19 PM, Joshua Wall
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
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