[QE-users] viewing trajectories in VMD, axsf conversion

[Tone Kokalj]

Dear Michal,

What you just reported is almost correct, with a small difference
that the script is located in scripts/ and not in bin/ subdirectory,
hence:

path-to-xcrysden/scripts/pwo2xsf.sh -r 2 -a pw_output.out > movie.axsf

A further remark: if one uses xcrysden from linux distributions (e.g.
Debian), then the "pwo2xsf.sh" script is indeed named "pwo2xsf" (here
pwo2xsf is a simple wrapper that calls pwo2xsf.sh), hence in this case:

pwo2xsf -r 2 -a pw_output.out > movie.axsf


Furthermore, it is my responsibility and fault that the pwo2xsf script
in PW/tools is obsolete: the reason is that always use xcrysden's one,
hence I forgot to update the one in PW/tools.

Best regards,
Tone
-- 
Jožef Stefan Institute, Ljubljana, Slovenia


On Thu, 2020-10-08 at 10:38 +0100, Michal Krompiec wrote:
> Hello, in case someone else struggles with generation of axsf and xsf
> files from QE outputs, I'd like to share a tip. The pwo2xsf script
> from XCRYSDEN is much more reliable than the one in PW/tools (in my
> hands, the latter just dumps the first frame and then complains about
> not being able to read ATOMIC_POSITIONS records). 
> It is used internally by XCRYSDEN but can also be utilized to save an
> axsf file.
> For example, to create an axsf file from a QE trajectory (relaxation
> or md) of a 2D slab: (-r 2 is the "reduce periodic dimension to 2"
> functionality familiar to XCRYSDEN users)
> path-to-xcrysden/bin/pwo2xsf -r 2 -a pw_output.out > movie.axsf
> Such axsf can then be opened in VMD etc.
> 
> Best regards,
> Michal Krompiec
> Merck KGaA
> 
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