Hi all,
I'm trying to modify the particle_type of some particles in a hdf5 data file extract0062.cpu0000 in yt, typing the following command:
for g in pf.h.grids:
lbhs = np.logical_and(np.logical_and(g['particle_type']==1,g['particle_index']>=256**3),g['ParticleMassMsun']>1) # These two lines are to pick out
bhs = np.where(lbhs)[0] # particles that I wanted to modify
if(np.any(g['particle_type'])):
g['particle_type'][bhs]=9
f=h5py.File(g.filename)
ff = f['/Grid%08i'%g.id]['particle_type'] ff.write_direct(g['particle_type'])
f.close()
It spited out following error information:
ReadingError Traceback (most recent call last)
/home/cshi31/yt-x86_64/src/yt-hg/yt/mods.pyc in <module>()
1 for g in pf.h.grids:
----> 2 lbhs = np.logical_and(np.logical_and(g['particle_type']==1,g['particle_index']>=256**3),g['ParticleMassMsun']>1)
3 bhs = np.where(lbhs)[0]
4 if(np.any(g['particle_type'])):
5 g['particle_type'][bhs]=9
/home/cshi31/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.pyc in __getitem__(self, key)
155 """
156 if not self.field_data.has_key(key):
--> 157 self.get_data(key)
158 return self.field_data[key]
159
/home/cshi31/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.pyc in get_data(self, field, convert)
188 return self.field_data[field]
189 try:
--> 190 temp = self.hierarchy.io.pop(self, field)
191 self[field] = na.multiply(temp, conv_factor, temp)
192 except self.hierarchy.io._read_exception, exc:
/home/cshi31/yt-x86_64/src/yt-hg/yt/utilities/io_handler.pyc in pop(self, grid, field)
59 else:
60 # We only read the one set and do not store it if it isn't pre-loaded
---> 61 return self._read_data_set(grid, field)
62
63 def peek(self, grid, field):
/home/cshi31/yt-x86_64/src/yt-hg/yt/frontends/enzo/io.pyc in _read_data_set(self, grid, field)
183 def _read_data_set(self, grid, field):
184 return self.modify(hdf5_light_reader.ReadData(grid.filename,
--> 185 "/Grid%08i/%s" % (grid.id, field)))
186
187 def _read_data_slice(self, grid, field, axis, coord):
ReadingError: ReadHDF5DataSet: Unable to open /home/cshi31/research/SG256-RP/extract0062
So I tried to look where the loop stopped, typed g in the command:
In [37]: g
Out[37]: EnzoGrid_0056
so it stopped at the 56th grid in that file. I tried to see what particles is contained in this grid, typing g['particle_type'],
it turned out this is what caused the problem:
In [31]: g['particle_type']
---------------------------------------------------------------------------
ReadingError Traceback (most recent call last)
/home/cshi31/yt-x86_64/src/yt-hg/yt/mods.pyc in <module>()
----> 1 g['particle_type']
/home/cshi31/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.pyc in __getitem__(self, key)
155 """
156 if not self.field_data.has_key(key):
--> 157 self.get_data(key)
158 return self.field_data[key]
159
/home/cshi31/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.pyc in get_data(self, field, convert)
188 return self.field_data[field]
189 try:
--> 190 temp = self.hierarchy.io.pop(self, field)
191 self[field] = na.multiply(temp, conv_factor, temp)
192 except self.hierarchy.io._read_exception, exc:
/home/cshi31/yt-x86_64/src/yt-hg/yt/utilities/io_handler.pyc in pop(self, grid, field)
59 else:
60 # We only read the one set and do not store it if it isn't pre-loaded
---> 61 return self._read_data_set(grid, field)
62
63 def peek(self, grid, field):
/home/cshi31/yt-x86_64/src/yt-hg/yt/frontends/enzo/io.pyc in _read_data_set(self, grid, field)
183 def _read_data_set(self, grid, field):
184 return self.modify(hdf5_light_reader.ReadData(grid.filename,
--> 185 "/Grid%08i/%s" % (grid.id, field)))
186
187 def _read_data_slice(self, grid, field, axis, coord):
ReadingError: ReadHDF5DataSet: Unable to open /home/cshi31/research/SG256-RP/extract0062.cpu0000
Can anyone help me on this? Thanks very much.
Chao