mcodev31
commented
2 years ago I suspect it is because it's not quite symmetrical. The example code (which I assume you are referring to) uses the rather tight default threshold and is meant as example for integration into other software (this is a library). If you use e.g. Avogadro (it uses libmsym internally) you can see that it gives C1 with a tight threshold and Cs with normal. It also allows you to symmetrize the molecule (see below). There is also be a version of Luscus that uses libmsym where you can set all thresholds individually and generate symmetrical molecules.
Symmetrized:
9
ethanol
C 8.96061 9.67982 11.32405
C 10.04025 10.37424 12.12949
O 11.30778 10.10383 11.50844
H 9.13001 8.59331 11.29813
H 8.94613 10.05029 10.28847
H 7.97519 9.86734 11.77411
H 10.03416 10.00267 13.17270
H 9.84964 11.46473 12.15952
H 12.00577 10.53813 12.00802
9 ethanol C 8.960767 9.678596 11.324902 C 10.040371 10.373322 12.130129 O 11.307616 10.105125 11.507543 H 9.127848 8.591672 11.301701 H 8.948935 10.046791 10.288465 H 7.974955 9.869172 11.772836 H 10.035117 10.001044 13.173151 H 9.849029 11.463604 12.160981 H 12.004366 10.549272 12.000293
I want to analysis an ethanol molecular point group, This is a file with the suffix '.xyz' , it was transformed by VESTA from a ethanol crystal. When I use the program, I accept an error that is "Error Error determining point group: Point group has no primary axis for reorientation" , I don`t know how to deal with it , I wish you can help me.