[ase-users] getting molecule symmetry number for thermochemistry

[Offermans Willem]

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 <mailto: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>
> 
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