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<p>No thats not it.<br>
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.<br>
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<div class="moz-cite-prefix">On 1/11/19 4:02 PM, Paolo Giannozzi wrote:<br>
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<div dir="ltr">... the usual "Bohr radii vs Angstrom" problem ?<br>
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<div dir="ltr">On Fri, Jan 11, 2019 at 3:45 PM Laurens Siemons <<a href="mailto:laurenssiemons@hotmail.be" moz-do-not-send="true">laurenssiemons@hotmail.be</a>> wrote:<br>
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0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
Dear QE-users,<br>
<br>
I'm trying to calculate vibrational frequencies of a molecule adsorbed <br>
on a surface. I first run a pw.x calculation followed by a ph.x <br>
calculation and finally a dynmat.x calculation which generates a <br>
dynmat.mold and dynmat.axsf (and some other) files. When I open the <br>
.mold file in JMol I do not see any connectivity between the atoms, no <br>
bonds are shown (the same happens when I open the .axsf file in <br>
XCrysden). I now realize that JMol does not show any connectivity since <br>
all atomic distances are doubled! When I load the phonon output file in <br>
JMol all atomic distances are the way they need to be, so this should <br>
happen when running dynmat.x or when the dynamical matrix file is <br>
generated. Can anyone explain why this is happening?<br>
<br>
My <a href="http://ph.in" rel="noreferrer" target="_blank" moz-do-not-send="true">
ph.in</a> and <a href="http://dynmat.in" rel="noreferrer" target="_blank" moz-do-not-send="true">
dynmat.in</a> files are as followed:<br>
<br>
freq van molecule op opp<br>
&inputph<br>
prefix = 'a101mpa4'<br>
nat_todo = 11<br>
amass(1) = 15.99900<br>
amass(2) = 47.86700<br>
amass(3) = 1.0079<br>
amass(4) = 12.0107<br>
amass(5) = 30.973761<br>
outdir = '/scratch/antwerpen/204/vsc20442/TMP'<br>
fildyn = 'a101mpa4.dynG'<br>
epsil = .true.<br>
/<br>
0.0 0.0 0.0<br>
22 73 74 75 76 77 78 79 80 81 82<br>
<br>
&input<br>
fildyn = 'a101mpa4.dynG'<br>
asr = 'zero-dim'<br>
/<br>
<br>
Thanks in advance,<br>
Laurens Siemons<br>
PhD student, University of Antwerp<br>
<br>
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-- <br>
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<div>Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,<br>
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy<br>
Phone +39-0432-558216, fax +39-0432-558222<br>
<br>
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