[FLASH-USERS] Loading FLASH2.5 files problem with yt

[John Zuhone]

Hi Jordi, 

The problem here is that the particle structure in the HDF5 file for versions of FLASH less than 3 is very different than versions >= 3. 

The structure in FLASH3 and later is much simpler, it’s a simple 2D real array of number of particles x number of particle attributes. But in FLASH2 it’s a compound data structure. We never got around to supporting that in yt. 

You could file an issue on the yt Github page with this error message and with the description I gave here so we don’t forget, not sure when we’d get a chance to address it. If we did address it, we’d need a copy of the file so that we could formulate the fix and test it. 

Alternatively, we could reconstruct a FLASH3-like particle structure for you, but if you have a lot of files this may not be ideal. 

Best,

John ZuHone

> On Aug 14, 2024, at 1:17 PM, Casanova, Jordi <jcasanova at regis.edu> wrote:
> 
>  
> Hello flash users!
>  
> I am using yt to analyze simulations performed with the latest version of FLASH4.7, and everything works fine. However, I would like to check out some old files performed with FLASH2.5. I am not able to load these FLASH2.5 files with yt. Below I am attaching the traceback with the error. Does anyone know what the problem might be? Thank you!
>  
>  
> yt : [INFO     ] 2024-08-14 11:03:29,105 Particle file found: test_hdf5_chk_2396
>  
>  
>     ---------------------------------------------------------------------------
>  
>     TypeError                                 Traceback (most recent call last)
>  
>     Cell In[1], line 2
>           1 import yt
>     ----> 2 ds=yt.load("/Users/novita/Desktop/test_hdf5_chk_2396")
>  
>  
>     File ~/Library/Python/3.12/lib/python/site-packages/yt/_maintenance/deprecation.py:69, in future_positional_only.<locals>.outer.<locals>.inner(*args, **kwargs)
>          60     value = kwargs[name]
>          61     issue_deprecation_warning(
>          62         f"Using the {name!r} argument as keyword (on position {no}) "
>          63         "is deprecated. "
>        (...)
>          67         **depr_kwargs,
>          68     )
>     ---> 69 return func(*args, **kwargs)
>  
>  
>     File ~/Library/Python/3.12/lib/python/site-packages/yt/loaders.py:144, in load(fn, hint, *args, **kwargs)
>         136     if missing := cls._missing_load_requirements():
>         137         warnings.warn(
>         138             f"This dataset appears to be of type {cls.__name__}, "
>         139             "but the following requirements are currently missing: "
>        (...)
>         142             stacklevel=3,
>         143         )
>     --> 144     return cls(fn, *args, **kwargs)
>         146 if len(candidates) > 1:
>         147     raise YTAmbiguousDataType(_input_fn, candidates)
>  
>  
>     File ~/Library/Python/3.12/lib/python/site-packages/yt/frontends/flash/data_structures.py:206, in FLASHDataset.__init__(self, filename, dataset_type, storage_filename, particle_filename, units_override, unit_system, default_species_fields)
>         204 # Check if the particle file has the same time
>         205 if self._particle_handle != self._handle:
>     --> 206     part_time = self._particle_handle.handle.get("real scalars")[0][1]
>         207     plot_time = self._handle.handle.get("real scalars")[0][1]
>         208     if not np.isclose(part_time, plot_time):
>  
>  
>     TypeError: 'NoneType' object is not subscriptable
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