[ase-users] Vibrational analysis and symmetry constrain

[Offermans Willem]

Dear ASE friends,


To continue the discussion:

I had a look into the code.

In vibrations.py, I can find the following:

<snip>
...
p = self.atoms.positions.copy()
        for filename, a, i, disp in self.displacements():
            fd = opencew(filename)
            if fd is not None:
                self.atoms.positions[a, i] = p[a, i] + disp
                self.calculate(filename, fd)
                self.atoms.positions[a, i] = p[a, i]
…
</snip>

If I specify the inversion center, I can probably find the coordinates of a’. If there is a way to find the index number by specifying the coordinates, I can easily do
self.atoms.positions[a', i] = p[a', i] - disp (mind the apostrophe) and I would have a way to implement S2-symmetry.

Before I start coding, is there a way to generalise this?

If I have all possible symmetry operations in matrix form, such as, but not exclusive, inversion center:

-1 0 0
0 -1 0
0 0 -1

I might find all symmetry related atoms and apply the appropriate displacements.

Has anyone an idea?




Met vriendelijke groeten,
Mit freundlichen Grüßen,


Willem Offermans
Researcher Electrocatalysis SCT
VITO NV | Boeretang 200 | 2400 Mol
Phone:+32(0)14335263 Mobile:+32(0)492182073

Willem.Offermans at Vito.be<mailto:Willem.Offermans at Vito.be>

[cid:982BA063-B96A-4A1B-89AB-5A01CA9FC70D at vito.local]

On 8 Nov 2018, at 13:56, Offermans Willem via ase-users <ase-users at listserv.fysik.dtu.dk<mailto:ase-users at listserv.fysik.dtu.dk>> wrote:

Dear ASE friends,

Now I know how to specify the atoms, which have impact on the vibrational analysis, I need to deal with symmetry of the system.

My systems have S2-symmetry, i.e. there is an inversion center. How can I enforce this symmetry during the analysis? Meaning that upon displacement of an atom, the symmetry related atom will be displaced as well.



Met vriendelijke groeten,
Mit freundlichen Grüßen,


Willem Offermans
Researcher Electrocatalysis SCT
VITO NV | Boeretang 200 | 2400 Mol
Phone:+32(0)14335263 Mobile:+32(0)492182073

Willem.Offermans at Vito.be<mailto:Willem.Offermans at Vito.be>

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