[ase-users] Problems reading XCrysDen-files in ASE-gui

[Jens Jørgen Mortensen]

Den 15-01-2013 16:21, Jakob Blomqvist skrev:
> Dear all,
>
> I will take this to the user-list too.
>
> I've tried to use ag to read xsf-files converted from Quantum Espresso 
> output files using QE's own xsf-converter script.
> There seem to be several problem illustrated with the attached 
> xsf-file QE_Au.xsf.
> The first problem is that io/xsf.py doesn't allow for symbols in it 
> but only atom number. xsf-file format, however, allows for both. 
> Another problem is that xsf.py requires that the file contains 
> BEGIN_BLOCK_DATAGRID_3D through the:
> "assert 'BEGIN_BLOCK_DATAGRID_3D' in line"
> in line #159 in ase/io/xsf.py
> but xsf-file format doesn't require it.
>
> I suggest to add some alternative section that allows for nothing 
> after the atomic positions section.
>
> Finally, If forces are included as 3 floating-point values directly 
> after the atomic positions then running ag file.xsf results in error:
>
>    File "/home/jakob/ase/ase/gui/ag.py", line 131, in main
>     run(opt, args)
>   File "/home/jakob/ase/ase/gui/ag.py", line 91, in run
>     images.read(args, string2index(opt.image_number))
>   File "/home/jakob/ase/ase/gui/images.py", line 164, in read
>     self.initialize(images, names)
>   File "/home/jakob/ase/ase/gui/images.py", line 71, in initialize
>     self.F[i] = atoms.get_forces(apply_constraint=False)
> ValueError: shape mismatch: objects cannot be broadcast to a single shape
>
> which seem to come from problems with lines #152-154 in io/xsf.py
> ###
>         if forces is not None:
>             image.set_calculator(SinglePointCalculator(None, forces, 
> None,
>                                                        None, image))
>         images.append(image)
> ###
> As they disappear if I remove these.

Thanks for reporting these bugs.  I think I have fixed them.  Could you 
try again?

Jens Jørgen

> /best
>
>
>
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