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I want to use pyxtal to generate some CH4 molecular crystals, but something odd happened
from pymatgen.core import Molecule from pymatgen.symmetry.analyzer import PointGroupAnalyzer from pyxtal.molecule import pyxtal_molecule CH4 = Molecule( species=['C', 'H', 'H', 'H', 'H'], coords=np.array( [ [0.000000, 0.000000, 0.000000], [0.632633, 0.632633, 0.632633], [-0.632633, -0.632633, 0.632633], [-0.632633, 0.632633, -0.632633], [0.632633, -0.632633, -0.632633], ] ), ) pga = PointGroupAnalyzer(CH4, 0.3, eigen_tolerance=1e-3) print(pga.get_pointgroup()) hh = pyxtal_molecule(CH4) print(hh.pg)
if I run code above, I got
Td -- Pointgroup --# 4 (Cs)-- 2b site symm: 1 1a site symm: m . .
somehow point group of CH4 changed into Cs, which makes it hard to generate CH4 crystal with Space Group 215,
it seems that the issue is related to the following code in "molecule.py"
if symmetrize: pga = PointGroupAnalyzer(mol, rtol, eigen_tolerance=1e-3) mol = pga.symmetrize_molecule()["sym_mol"] pga = PointGroupAnalyzer(mol, rtol, eigen_tolerance=1e-3) self.mol_no_h = mol
The text was updated successfully, but these errors were encountered:
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I want to use pyxtal to generate some CH4 molecular crystals, but something odd happened
if I run code above, I got
somehow point group of CH4 changed into Cs, which makes it hard to generate CH4 crystal with Space Group 215,
it seems that the issue is related to the following code in "molecule.py"
The text was updated successfully, but these errors were encountered: