[ase-users] trajectory/visualize issue

[Jens Jørgen Mortensen]

On 03/23/2015 02:52 AM, Tristan Maxson wrote:
> I can confirm this, but I am also not sure which is the best way to 
> fix it.  Jens should probably look at this as he was the one 
> implementing the new Trajectory if I recall.

Should be fixed now.  Thanks for the feedback.

Jens Jørgen

>
> Tristan Maxson
>
> On Sat, Mar 21, 2015 at 12:01 PM, John Kitchin 
> <jkitchin at andrew.cmu.edu <mailto:jkitchin at andrew.cmu.edu>> wrote:
>
>       I made a list of atoms objects to view, and I got this error:
>     view(images)
>           File
>     "/Users/jkitchin/Dropbox/python/ase/ase/visualize/__init__.py",
>     line 49, in view
>     write(fd, atoms, format=format)
>           File
>     "/Users/jkitchin/Dropbox/python/ase/ase/io/__init__.py", line 586,
>     in write
>     write(filename, images, **kwargs)
>           File
>     "/Users/jkitchin/Dropbox/python/ase/ase/io/trajectory.py", line
>     282, in write_trajectory
>             trj = TrajectoryWriter(filename, mode='w')
>           File
>     "/Users/jkitchin/Dropbox/python/ase/ase/io/trajectory.py", line
>     65, in __init__
>     self._open(filename, mode)
>           File
>     "/Users/jkitchin/Dropbox/python/ase/ase/io/trajectory.py", line
>     71, in _open
>     self.backend = affopen(filename, mode, tag='ASE-Trajectory')
>           File "/Users/jkitchin/Dropbox/python/ase/ase/io/aff.py",
>     line 69, in affopen
>             return Writer(filename, mode, tag)
>           File "/Users/jkitchin/Dropbox/python/ase/ase/io/aff.py",
>     line 112, in __init__
>             fd = open(fd, 'wb')
>         TypeError: coercing to Unicode: need string or buffer, file found
>
>     A fix for the issue is to add this to write_trajectory in
>     ase.io.trajectory
>
>     I am not sure this is the right thing to do, since a filename
>     should be
>         passed from ase.io.write but a file descriptor is getting sent to
>         this .
>
>         if isinstance(filename, file):
>     filename = filename.name <http://filename.name/>
>
>     alternatively to edit ase.io.__init__.py around line 576
>
>     I am not sure what is best.
>
>     John
>
>     -----------------------------------
>     Professor John Kitchin
>     Doherty Hall A207F
>     Department of Chemical Engineering
>     Carnegie Mellon University
>     Pittsburgh, PA 15213
>     412-268-7803 <tel:412-268-7803>
>     @johnkitchin
>     http://kitchingroup.cheme.cmu.edu
>
>
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