<div>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.</div>
<div> </div><div>You can confirm if the particle_type or Dark_Matter_Density field is missing by typing</div><div>>h5ls extract0062.cpu####/Grid######## where the #'s correspond to the file number which has the <font color="#006600">EnzoGrid_0056</font><br>
</div><div>From</div><div>G.S.<br></div><div class="gmail_quote">On Mon, Oct 8, 2012 at 8:23 PM, Chao Shi <span dir="ltr"><<a href="mailto:shichao116@gmail.com" target="_blank">shichao116@gmail.com</a>></span> wrote:<br>
<blockquote style="margin:0px 0px 0px 0.8ex;padding-left:1ex;border-left-color:rgb(204,204,204);border-left-width:1px;border-left-style:solid" class="gmail_quote">Hi all,<div><br></div><div>I'm trying to modify the particle_type of some particles in a hdf5 data file extract0062.cpu0000 in yt, typing the following command:</div>
<div><br></div><div><div><font color="#006600">for g in pf.h.grids:</font></div>
<div><font color="#006600"> 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</font></div>
<div><font color="#006600"> bhs = np.where(lbhs)[0] # particles that I wanted to modify</font></div>
<div><font color="#006600"> if(np.any(g['particle_type'])):</font></div><div><font color="#006600"> g['particle_type'][bhs]=9</font></div><div><font color="#006600"> f=h5py.File(g.filename)</font></div>
<div><font color="#006600"> ff = f['/Grid%08i'%<a href="http://g.id" target="_blank">g.id</a>]['particle_type']</font></div><div><font color="#006600"> ff.write_direct(g['particle_type'])</font></div>
<div><font color="#006600"> f.close()</font></div><div> </div></div><div>It spited out following error information:</div><div><br></div><div><div><font color="#006600">ReadingError Traceback (most recent call last)</font></div>
<div><font color="#006600">/home/cshi31/yt-x86_64/src/yt-hg/yt/mods.pyc in <module>()</font></div><div><font color="#006600"> 1 for g in pf.h.grids:</font></div><div><font color="#006600">----> 2 lbhs = np.logical_and(np.logical_and(g['particle_type']==1,g['particle_index']>=256**3),g['ParticleMassMsun']>1)</font></div>
<div><font color="#006600"> 3 bhs = np.where(lbhs)[0]</font></div><div><font color="#006600"> 4 if(np.any(g['particle_type'])):</font></div><div><font color="#006600"> 5 g['particle_type'][bhs]=9</font></div>
<div><font color="#006600"><br></font></div><div><font color="#006600">/home/cshi31/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.pyc in __getitem__(self, key)</font></div><div><font color="#006600"> 155 """</font></div>
<div><font color="#006600"> 156 if not self.field_data.has_key(key):</font></div><div><font color="#006600">--> 157 self.get_data(key)</font></div><div><font color="#006600"> 158 return self.field_data[key]</font></div>
<div><font color="#006600"> 159 </font></div><div><font color="#006600"><br></font></div><div><font color="#006600">/home/cshi31/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.pyc in get_data(self, field, convert)</font></div>
<div><font color="#006600"> 188 return self.field_data[field]</font></div><div><font color="#006600"> 189 try:</font></div><div><font color="#006600">--> 190 temp = self.hierarchy.io.pop(self, field)</font></div>
<div><font color="#006600"> 191 self[field] = na.multiply(temp, conv_factor, temp)</font></div><div><font color="#006600"> 192 except self.hierarchy.io._read_exception, exc:</font></div>
<div><font color="#006600"><br></font></div><div><font color="#006600">/home/cshi31/yt-x86_64/src/yt-hg/yt/utilities/io_handler.pyc in pop(self, grid, field)</font></div><div><font color="#006600"> 59 else:</font></div>
<div><font color="#006600"> 60 # We only read the one set and do not store it if it isn't pre-loaded</font></div><div><font color="#006600">---> 61 return self._read_data_set(grid, field)</font></div>
<div><font color="#006600"> 62 </font></div><div><font color="#006600"> 63 def peek(self, grid, field):</font></div><div><font color="#006600"><br></font></div><div><font color="#006600">/home/cshi31/yt-x86_64/src/yt-hg/yt/frontends/enzo/io.pyc in _read_data_set(self, grid, field)</font></div>
<div><font color="#006600"> 183 def _read_data_set(self, grid, field):</font></div><div><font color="#006600"> 184 return self.modify(hdf5_light_reader.ReadData(grid.filename,</font></div><div><font color="#006600">--> 185 "/Grid%08i/%s" % (<a href="http://grid.id" target="_blank">grid.id</a>, field)))</font></div>
<div><font color="#006600"> 186 </font></div><div><font color="#006600"> 187 def _read_data_slice(self, grid, field, axis, coord):</font></div><div><br></div><div><font color="#ff0000">ReadingError: ReadHDF5DataSet: Unable to open /home/cshi31/research/SG256-RP/extract0062</font></div>
</div><div><br></div><div><br></div><div>So I tried to look where the loop stopped, typed g in the command:</div><div><br></div><div><div><font color="#006600">In [37]: g</font></div><div><font color="#006600">Out[37]: EnzoGrid_0056</font></div>
</div><div><br></div><div>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'],</div><div>it turned out this is what caused the problem:</div>
<div><br></div><div><br></div><div><div><font color="#006600">In [31]: g['particle_type']</font></div><div><font color="#006600">---------------------------------------------------------------------------</font></div>
<div><font color="#006600">ReadingError Traceback (most recent call last)</font></div><div><font color="#006600">/home/cshi31/yt-x86_64/src/yt-hg/yt/mods.pyc in <module>()</font></div><div>
<font color="#006600">----> 1 g['particle_type']</font></div><div><font color="#006600"><br></font></div><div><font color="#006600">/home/cshi31/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.pyc in __getitem__(self, key)</font></div>
<div><font color="#006600"> 155 """</font></div><div><font color="#006600"> 156 if not self.field_data.has_key(key):</font></div><div><font color="#006600">--> 157 self.get_data(key)</font></div>
<div><font color="#006600"> 158 return self.field_data[key]</font></div><div><font color="#006600"> 159 </font></div><div><font color="#006600"><br></font></div><div><font color="#006600">/home/cshi31/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.pyc in get_data(self, field, convert)</font></div>
<div><font color="#006600"> 188 return self.field_data[field]</font></div><div><font color="#006600"> 189 try:</font></div><div><font color="#006600">--> 190 temp = self.hierarchy.io.pop(self, field)</font></div>
<div><font color="#006600"> 191 self[field] = na.multiply(temp, conv_factor, temp)</font></div><div><font color="#006600"> 192 except self.hierarchy.io._read_exception, exc:</font></div>
<div><font color="#006600"><br></font></div><div><font color="#006600">/home/cshi31/yt-x86_64/src/yt-hg/yt/utilities/io_handler.pyc in pop(self, grid, field)</font></div><div><font color="#006600"> 59 else:</font></div>
<div><font color="#006600"> 60 # We only read the one set and do not store it if it isn't pre-loaded</font></div><div><font color="#006600">---> 61 return self._read_data_set(grid, field)</font></div>
<div><font color="#006600"> 62 </font></div><div><font color="#006600"> 63 def peek(self, grid, field):</font></div><div><font color="#006600"><br></font></div><div><font color="#006600">/home/cshi31/yt-x86_64/src/yt-hg/yt/frontends/enzo/io.pyc in _read_data_set(self, grid, field)</font></div>
<div><font color="#006600"> 183 def _read_data_set(self, grid, field):</font></div><div><font color="#006600"> 184 return self.modify(hdf5_light_reader.ReadData(grid.filename,</font></div><div><font color="#006600">--> 185 "/Grid%08i/%s" % (<a href="http://grid.id" target="_blank">grid.id</a>, field)))</font></div>
<div><font color="#006600"> 186 </font></div><div><font color="#006600"> 187 def _read_data_slice(self, grid, field, axis, coord):</font></div><div><font color="#006600"><br></font></div><div><font color="#006600">ReadingError: ReadHDF5DataSet: Unable to open /home/cshi31/research/SG256-RP/extract0062.cpu0000</font></div>
</div><div><br></div><div>Can anyone help me on this? Thanks very much.</div><span class="HOEnZb"><font color="#888888"><div><br></div><div>Chao</div><div><br></div><div><br></div><div><br></div>
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<br></blockquote></div><br>