Is this an Enzo sim? It is conceivable to have no particles in that grid. I've seen others encounter some grids where the hdf5 file is missing Dark_Matter_Density field because there were no DM particles in that particular grid. You can confirm if the particle_type or Dark_Matter_Density field is missing by typing

h5ls extract0062.cpu####/Grid######## where the #'s correspond to the file number which has the EnzoGrid_0056 From G.S. On Mon, Oct 8, 2012 at 8:23 PM, Chao Shi <shichao116@gmail.com> wrote:

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

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