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Duplicate atom generated with Structure.from_spacegroup #3721

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LindaHung-TRI opened this issue Mar 28, 2024 · 0 comments
Open

Duplicate atom generated with Structure.from_spacegroup #3721

LindaHung-TRI opened this issue Mar 28, 2024 · 0 comments
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@LindaHung-TRI
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Python version

3.10.8

Pymatgen version

2024.2.8

Operating system version

No response

Current behavior

The Ge atoms index 0 and 3 are generated almost on top of each other, just at opposite ends of the unit cell. Input is:
Structure.from_spacegroup( 154, Lattice.from_parameters(4.98502, 4.98502, 5.648, 90., 90., 120.), ('Ge', 'O'), ((0.4513, 0.0, 0.6667), (0.3969, 0.3021, 0.12)), tol=0.01)

Expected Behavior

Correct structure should only have 3 Ge atoms.

Minimal example

Structure.from_spacegroup(
    154,
    Lattice.from_parameters(4.98502, 4.98502, 5.648, 90., 90., 120.), 
    ('Ge', 'O'),
    ((0.4513, 0.0, 0.6667), (0.3969, 0.3021, 0.12)),
    tol=0.01)

Relevant files to reproduce this bug

No response

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