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CH4 molecule crystal #241

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XinYu73 opened this issue Jan 3, 2024 · 0 comments
Closed

CH4 molecule crystal #241

XinYu73 opened this issue Jan 3, 2024 · 0 comments

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@XinYu73
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XinYu73 commented Jan 3, 2024

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
@XinYu73 XinYu73 changed the title CH4 molecule crytal CH4 molecule crystal Jan 3, 2024
@XinYu73 XinYu73 closed this as completed Jan 3, 2024
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