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 <[email protected]<mailto:[email protected]>> 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 _______________________________________________ users mailing list [email protected]<mailto:[email protected]> https://lists.quantum-espresso.org/mailman/listinfo/users -- 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 _______________________________________________ users mailing list [email protected]<mailto:[email protected]> https://lists.quantum-espresso.org/mailman/listinfo/users
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