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

[Laurens Siemons]

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