[ase-users] ase-users Digest, Vol 153, Issue 23

[Offermans Willem]

Dear John and ASE friends,

Thank you once more for your input.

Now it works:

<snip>
>>> from pymatgen.core import Molecule
>>> from ase.build import molecule
>>> from pymatgen.symmetry.analyzer import PointGroupAnalyzer
>>> benzene = molecule('C6H6')
>>> PointGroupAnalyzer(Molecule(benzene.symbols,benzene.positions)).get_pointgroup()
D6h
</snip>

cute :)


Met vriendelijke groeten,
Mit freundlichen Grüßen,
With kind regards,


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

Willem.Offermans at Vito.be



> On 23 Mar 2021, at 15:24, John Kitchin via ase-users <ase-users at listserv.fysik.dtu.dk> wrote:
> 
> 
>    3. Re: getting molecule symmetry number for thermochemistry
>       (Offermans Willem)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 3
> Date: Tue, 23 Mar 2021 09:20:30 +0000
> From: Offermans Willem <willem.offermans at vito.be <mailto:willem.offermans at vito.be>>
> To: ase-users <ase-users at listserv.fysik.dtu.dk <mailto:ase-users at listserv.fysik.dtu.dk>>
> Subject: Re: [ase-users] getting molecule symmetry number for
>         thermochemistry
> Message-ID: <89BCBDC8-8551-4038-AD13-F1393AC881BE at VITO.be>
> Content-Type: text/plain; charset="utf-8"
> 
> Hi John and ASE friends,
> 
> Thank you for your feedback and example. It is very much appreciated.
> 
> Unfortunately, if I try your example, I got following error:
> 
> <snip>
> from ase.build import molecule
> from pymatgen.symmetry.analyzer import PointGroupAnalyzer
> benzene = molecule('C6H6')
> PointGroupAnalyzer(molecule(benzene.symbols, benzene.positions)).get_pointgroup()
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
>   File "/home/loffermw/.conda/envs/molecularmodelling/lib/python3.9/site-packages/ase/build/molecule.py", line 40, in molecule
>     if name in extra:
> TypeError: unhashable type: ?Symbols'
> </snip>
> 
> You used: "PointGroupAnalyzer(Molecule(??. I guess the capital M is a typo. At least, I changed it to a lower m. 
> However I do not believe it is related to the above error.
> 
> Can someone help me to debug and resolve the Error?
> 
>  
> I forgot one import line in the example, here is the code that works for me.  The capital M was not a typo, it is a pymatgen object.
> 
> from pymatgen.core import Molecule
> from ase.build import molecule
> from pymatgen.symmetry.analyzer import PointGroupAnalyzer
> 
> benzene = molecule('C6H6')
> 
> PointGroupAnalyzer(Molecule(benzene.symbols,
> benzene.positions)).get_pointgroup()
> 
> This example also works:
> 
> from pymatgen.io.ase import AseAtomsAdaptor
> from ase.build import molecule
> from pymatgen.symmetry.analyzer import PointGroupAnalyzer
> 
> benzene = molecule('C6H6')
> PointGroupAnalyzer(AseAtomsAdaptor.get_molecule(benzene)).get_pointgroup()
> 
> 
> _______________________________________________
> ase-users mailing list
> ase-users at listserv.fysik.dtu.dk
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