[ase-users] trajectory/visualize issue

[Tristan Maxson]

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.

Tristan Maxson

On Sat, Mar 21, 2015 at 12:01 PM, John Kitchin <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
>
> 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
> @johnkitchin
> http://kitchingroup.cheme.cmu.edu
>
>
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