... the usual "Bohr radii vs Angstrom" problem ? On Fri, Jan 11, 2019 at 3:45 PM Laurens Siemons <[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 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 > > _______________________________________________ > users mailing list > [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
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