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

[Jens Jørgen Mortensen]

On 11/8/19 2:02 PM, Michael Walter wrote:
> Dear Jens Jorgen,
> 
> Am Mi., 6. Nov. 2019 um 12:41 Uhr schrieb Jens Jørgen Mortensen 
> <jjmo at dtu.dk <mailto:jjmo at dtu.dk>>:
> 
>     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
> 
> 
> yes, it works!
> 
> I get come warning, but I that's fine for me:
> 
> /home/mw/source/ase/upstream/ase/io/pickletrajectory.py:559: 
> UserWarning: Could not unpickle constraints!
>    warnings.warn('Could not unpickle constraints!')

Great!  The fix is in master now.

Jens Jørgen

> 
> Thanks,
> Michael
> 
> 
> 
>     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> <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>
>      > <mailto: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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>      >
> 
> 
> 
> -- 
> ------------------------------------------
> 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