[ase-users] Converting old trajectory files does not work

[Jens Jørgen Mortensen]

Den 04/11/2019 kl. 11.29 skrev Michael Walter via ase-users:
> Dear all,
> 
> If I try to use the attached (old) trajectory file, I get
> 
> ase: error: DeprecationWarning: Please stop using old trajectory files!
> Convert to the new future-proof format like this:
> 
>      $ python -m ase.io.trajectory 64.rho_2.2-quench.final.traj
> 
> To get a full traceback, use: ase -T gui ...
> 
> That's all fine, except that python might be python2. But if I try to 
> follow the advice

Does this MR work?

https://gitlab.com/ase/ase/merge_requests/1472

Jens Jørgen

> 
>  > python -m ase.io.trajectory 64.rho_2.2-quench.final.traj
> /local_data/tmp/walt/anaconda3/lib/python3.6/runpy.py:125: 
> RuntimeWarning: 'ase.io.trajectory' found in sys.modules after import of 
> package 'ase.io <http://ase.io>', but prior to execution of 
> 'ase.io.trajectory'; this may result in unpredictable behaviour
>    warn(RuntimeWarning(msg))
> version 3
> /local_data/tmp/walt/source/ase/trunk/ase/io/pickletrajectory.py:559: 
> UserWarning: Could not unpickle constraints!
>    warnings.warn('Could not unpickle constraints!')
> self.fd= <_io.BufferedReader name='64.rho_2.2-quench.final.traj'>
> Traceback (most recent call last):
>    File "/local_data/tmp/walt/anaconda3/lib/python3.6/runpy.py", line 
> 193, in _run_module_as_main
>      "__main__", mod_spec)
>    File "/local_data/tmp/walt/anaconda3/lib/python3.6/runpy.py", line 
> 85, in _run_code
>      exec(code, run_globals)
>    File "/local_data/tmp/walt/source/ase/trunk/ase/io/trajectory.py", 
> line 440, in <module>
>      main()
>    File "/local_data/tmp/walt/source/ase/trunk/ase/io/trajectory.py", 
> line 436, in main
>      convert(name)
>    File "/local_data/tmp/walt/source/ase/trunk/ase/io/trajectory.py", 
> line 420, in convert
>      for atoms in PickleTrajectory(name, _warn=False):
>    File 
> "/local_data/tmp/walt/source/ase/trunk/ase/io/pickletrajectory.py", line 
> 355, in next
>      return self[len(self.offsets) - 1]
>    File 
> "/local_data/tmp/walt/source/ase/trunk/ase/io/pickletrajectory.py", line 
> 293, in __getitem__
>      d = pickle.load(self.fd)
> UnicodeDecodeError: 'ascii' codec can't decode byte 0xaa in position 0: 
> ordinal not in range(128)
> 
> I am not so much aware of the pickle format to fix this, so help would 
> be appreciated.
> 
> Best,
> Michael
> 
> -- 
> ------------------------------------------
> PD Dr Michael Walter
> Addresses:
> - Fraunhofer IWM, Wöhlerstrasse 11, D-79108 Freiburg i. Br., Germany
>    Tel.: +49 761 5142 296
> - FIT Freiburg Centre for Interactive Materials and Bioinspired 
> Technologies, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
>    Tel: +49 761 203 95072
> email: Michael.Walter at fmf.uni-freiburg.de 
> <mailto:Michael.Walter at fmf.uni-freiburg.de>
> www: http://www.functional-nanosystems.uni-freiburg.de/People/PDWalter/group
> publications: http://scholar.google.com/citations?user=vlmryKEAAAAJ&hl=en
> 
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