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

[Laurens Siemons]

No thats not it.
When I load the scf.out file in XCrysden the O--H bond for example measures 1.046A and 1.9766 Bohr. When I load the .axsf file in XCrysden the same distance becomes 2.0919A and 3.9532 Bohr.

On 1/11/19 4:02 PM, Paolo Giannozzi wrote:
... the usual "Bohr radii vs Angstrom" problem ?

On Fri, Jan 11, 2019 at 3:45 PM Laurens Siemons <laurenssiemons at hotmail.be<mailto: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<http://ph.in> and dynmat.in<http://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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