[yt-users] An error when using yt on PLUTO 4.1

[Andrew Myers]

Hi Jun,

It looks like the ghost cell information is not getting set up properly in
the Pluto IOHandler. Could you try adding the line:

self._read_ghost_info()

to the end of the __init__ method of IOHandlerPlutoHDF5, in
yt/frontends/chombo/io.py (line 239 in the current development tip)? I
think that will solve your problem.

Best,
Andrew

On Tue, Jun 16, 2015 at 5:57 AM, 方军 <fangjun at ynu.edu.cn> wrote:

> Dear everyone,
> I recently used yt to plot the slice files for the hdf5 file from PLUTO
> 4.1.
> An error exists when ploting, i.e.,
> [('chombo', 'rho'), ('chombo', 'vx1'), ('chombo', 'vx2'), ('chombo',
> 'vx3'), ('chombo', 'prs')]
> Traceback (most recent call last):
>   File "simple_slice.py", line 18, in <module>
>     p = yt.ProjectionPlot(ds, "y", "density")
>   File
> "/home/fangjun/yt/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py",
> line 1227, in __init__
>     field_parameters = field_parameters, method = method)
>   File
> "/home/fangjun/yt/yt-x86_64/src/yt-hg/yt/data_objects/construction_data_containers.py",
> line 250, in __init__
>     self.get_data(field)
>   File
> "/home/fangjun/yt/yt-x86_64/src/yt-hg/yt/data_objects/construction_data_containers.py",
> line 295, in get_data
>     chunk_fields, "io", local_only = True)):
>   File
> "/home/fangjun/yt/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py",
> line 506, in parallel_objects
>     for obj_id, obj in oiter:
>   File
> "/home/fangjun/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
> line 592, in chunks
>     self.get_data(fields)
>   File
> "/home/fangjun/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
> line 681, in get_data
>     fluids, self, self._current_chunk)
>   File
> "/home/fangjun/yt/yt-x86_64/src/yt-hg/yt/geometry/geometry_handler.py",
> line 252, in _read_fluid_fields
>     chunk_size)
>   File "/home/fangjun/yt/yt-x86_64/src/yt-hg/yt/frontends/chombo/io.py",
> line 147, in _read_fluid_selection
>     data = self._read_data(g, fname)
>   File "/home/fangjun/yt/yt-x86_64/src/yt-hg/yt/frontends/chombo/io.py",
> line 104, in _read_data
>     shape = grid.ActiveDimensions + 2*self.ghost
>
> AttributeError: 'IOHandlerPlutoHDF5' object has no attribute 'ghost'
>
> Could you give some instructions on it?
> Best wishes,
> Jun
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