[yt-users] Error when open hdf5 file in yt

[Geoffrey So]

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 at 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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>
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