[QE-users] Atomic distances are doubled after dynmat.x calculation

[Paolo Giannozzi]

... the usual "Bohr radii vs Angstrom" problem ?

On Fri, Jan 11, 2019 at 3:45 PM Laurens Siemons <laurenssiemons at hotmail.be>
wrote:

> Dear QE-users,
>
> I'm trying to calculate vibrational frequencies of a molecule adsorbed
> on a surface. I first run a pw.x calculation followed by a ph.x
> calculation and finally a dynmat.x calculation which generates a
> dynmat.mold and dynmat.axsf (and some other) files. When I open the
> .mold file in JMol I do not see any connectivity between the atoms, no
> bonds are shown (the same happens when I open the .axsf file in
> XCrysden). I now realize that JMol does not show any connectivity since
> all atomic distances are doubled! When I load the phonon output file in
> JMol all atomic distances are the way they need to be, so this should
> happen when running dynmat.x or when the dynamical matrix file is
> generated. Can anyone explain why this is happening?
>
> My ph.in and dynmat.in files are as followed:
>
> freq van molecule op opp
> &inputph
>   prefix = 'a101mpa4'
>   nat_todo = 11
>   amass(1) = 15.99900
>   amass(2) = 47.86700
>   amass(3) = 1.0079
>   amass(4) = 12.0107
>   amass(5) = 30.973761
>   outdir = '/scratch/antwerpen/204/vsc20442/TMP'
>   fildyn = 'a101mpa4.dynG'
>   epsil = .true.
> /
> 0.0 0.0 0.0
> 22 73 74 75 76 77 78 79 80 81 82
>
> &input
> fildyn = 'a101mpa4.dynG'
> asr = 'zero-dim'
> /
>
> Thanks in advance,
> Laurens Siemons
> PhD student, University of Antwerp
>
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-- 
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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