[ase-users] Vibrational modes for a system

[Ask Hjorth Larsen]

Hi

Please attach the script.

Best regards
Ask

2016-07-24 2:25 GMT+02:00 Mark Micklich via ase-users
<ase-users at listserv.fysik.dtu.dk>:
> I can successfully use ase.vibrations to get the zero-point energy for an
> atom or a bulk slab, but it crashes if I have an adsorbed atom on a slab.
>
> I'm attempting to calculate the Delta-G for an adatom on a bulk slab, using
> the formula:
>
> Delta-E_ZPE = E(n adsorbed adatom on slab)_ZPE - E (n-1 adsorbed adatom on
> slab)_ZPE - E(adatom)_ZPE
>
>
> How can I use ase.vibrations?  I have a bulk slab with 27 atoms and 1
> adatom.  vib.get_energies() returns the error:
>
> vib_energies = vib.get_energies()
>
>
>  self.read(method, direction)
>   File "/usr/lib/python2.7/dist-packages/ase/vibrations/__init__.py", line
> 205, in read
>     H[r] = .5 * (fminus - fplus)[self.indices].ravel()
> IndexError: index 27 is out of bounds for axis 0 with size 27
>
>
> I have 28 atoms total.  27 for the bulk and 1 for the adatom.  Why is
> get_energies() only recognizing 27 atoms?
>
> Sincerely,
> Mark
>
>
> --
> Mark Micklich, M.S.
> PhD Student, Graduate Research
> Materials Science and Engineering
> Bartels Group, Computational Chemistry
> Department of Chemistry, University of California, Riverside
>
> _______________________________________________
> ase-users mailing list
> ase-users at listserv.fysik.dtu.dk
> https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users