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

[Michael Walter]

and the missing attachment

Am Mo., 4. Nov. 2019 um 11:29 Uhr schrieb Michael Walter <
Michael.Walter at fmf.uni-freiburg.de>:

> 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
>
> > 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',
> 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
> www:
> http://www.functional-nanosystems.uni-freiburg.de/People/PDWalter/group
> publications: http://scholar.google.com/citations?user=vlmryKEAAAAJ&hl=en
>


-- 
------------------------------------------
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
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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