[ase-users] getting molecule symmetry number for thermochemistry

[-]

Hi, Willem,

Here is the working example
<https://colab.research.google.com/drive/1o_0zUa5Dxe6RuTTfylTuDE1TYrAOuSh2?usp=sharing>
.

The code should look like this:



> from pymatgen.io.ase import AseAtomsAdaptor
> from pymatgen.symmetry.analyzer import PointGroupAnalyzer
>
from ase.build import molecule
>
c6h6 = molecule('C6H6')
> print (PointGroupAnalyzer(AseAtomsAdaptor.get_molecule(c6h6)).sch_symbol)
>

--
All the best,
Pavel

On Tue, 23 Mar 2021 at 15:21, Offermans Willem via ase-users <
ase-users at listserv.fysik.dtu.dk> wrote:

> 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?
>
>
>
>
>
> 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 22 Mar 2021, at 18:41, John Kitchin via ase-users <
> ase-users at listserv.fysik.dtu.dk> wrote:
>
> To (probably) answer my own question, I think Table II in this link
> https://cccbdb.nist.gov/thermo.asp
> <https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcccbdb.nist.gov%2Fthermo.asp&data=04%7C01%7C%7C908522716e5f451e2d2f08d8ed5b3d2d%7C9e2777ed82374ab992782c144d6f6da3%7C0%7C0%7C637520323419693471%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=bdDcrXhS7IKUmAb9uuMPP5eWTpPQ34B56ym6eGvJKZ4%3D&reserved=0>
> contains the information you need.  You do need to know the Point group of
> a molecule, and that can be found with pymatgen.
>
> Here is an example:
>
> from ase.build import molecule
> from pymatgen.symmetry.analyzer import PointGroupAnalyzer
>
> benzene = molecule('C6H6')
>
> PointGroupAnalyzer(Molecule(benzene.symbols,
> benzene.positions)).get_pointgroup()
>
> This yields D6h for the point group, which defines the symmetry number
> (sigma) is 12 for this molecule from Table II in that link.
>
> John
>
> -----------------------------------
> Professor John Kitchin (he/him/his)
> Doherty Hall A207F
> Department of Chemical Engineering
> Carnegie Mellon University
> Pittsburgh, PA 15213
> 412-268-7803
> @johnkitchin
> http://kitchingroup.cheme.cmu.edu
> <https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fkitchingroup.cheme.cmu.edu%2F&data=04%7C01%7C%7C908522716e5f451e2d2f08d8ed5b3d2d%7C9e2777ed82374ab992782c144d6f6da3%7C0%7C0%7C637520323419693471%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=th5L8Qq3gVKSPSJkLtE%2FhYdC27Y8uic20ihxSMNNDg8%3D&reserved=0>
>
>
>
> On Mon, Mar 22, 2021 at 12:17 PM John Kitchin <jkitchin at andrew.cmu.edu>
> wrote:
>
>> Hi everyone,
>>
>> In the ase thermochemistry module:
>>
>> https://wiki.fysik.dtu.dk/ase/_modules/ase/thermochemistry.html#IdealGasThermo
>> <https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwiki.fysik.dtu.dk%2Fase%2F_modules%2Fase%2Fthermochemistry.html%23IdealGasThermo&data=04%7C01%7C%7C908522716e5f451e2d2f08d8ed5b3d2d%7C9e2777ed82374ab992782c144d6f6da3%7C0%7C0%7C637520323419703459%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=e8b1aY%2FenqlNTup2ipXrLwENpdcR4opXp71Cd1q9STs%3D&reserved=0>
>>
>> there is a need for a symmetry number:
>>
>> symmetrynumber : integer symmetry number of the molecule. See, for
>> example, Table 10.1 and Appendix B of C. Cramer "Essentials of
>> Computational Chemistry", 2nd Ed.
>>
>> Does anyone know of a more accessible source for the symmetry number, or
>> a python library that can calculate it?
>>
>> Thanks,
>>
>> John
>>
>> -----------------------------------
>> Professor John Kitchin (he/him/his)
>> Doherty Hall A207F
>> Department of Chemical Engineering
>> Carnegie Mellon University
>> Pittsburgh, PA 15213
>> 412-268-7803
>> @johnkitchin
>> http://kitchingroup.cheme.cmu.edu
>> <https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fkitchingroup.cheme.cmu.edu%2F&data=04%7C01%7C%7C908522716e5f451e2d2f08d8ed5b3d2d%7C9e2777ed82374ab992782c144d6f6da3%7C0%7C0%7C637520323419703459%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=7EshU%2FOyavwy3gQdCTUjhstkpYLPt6jMDXTKx6CIEPs%3D&reserved=0>
>>
>> _______________________________________________
> ase-users mailing list
> ase-users at listserv.fysik.dtu.dk
> https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users
>
>
> _______________________________________________
> ase-users mailing list
> ase-users at listserv.fysik.dtu.dk
> https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://listserv.fysik.dtu.dk/pipermail/ase-users/attachments/20210323/64516296/attachment-0001.htm>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: vito.jpg
Type: image/jpeg
Size: 15232 bytes
Desc: not available
URL: <http://listserv.fysik.dtu.dk/pipermail/ase-users/attachments/20210323/64516296/attachment-0001.jpg>