[ase-users] Possible bug with minimum image convention

[Ask Hjorth Larsen]

Hi,
Den tir. 4. sep. 2018 kl. 14.34 skrev Tarjei Bondevik via ase-users
<ase-users at listserv.fysik.dtu.dk>:
>
> Dear ase-users,
>
>
>
> I noticed what I believe is a bug, with a very strange work-around.
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>
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> I have some code converting Lammps data files to the ase format in the following way:
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> atoms=Atoms(symbols=chem_symb_list,cell=cell_vectors)
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> atoms.set_positions(position_list)
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>
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> When trying to get_all_distances(mic=True) for atoms, the minimum image convention (mic) does not work, i.e. it behaves like its set to False.
>

You need something like Atoms(..., pbc=True) to get periodic boundary
conditions and hence any effect from using MIC.

>
>
> However, if I save atoms as a POSCAR file, and import the POSCAR file back to ase, the minimum image convention somehow works again:
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>
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> write_vasp(“tempPOSCAR”, atoms, direct=True, sort=True)
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> atoms = read("tempPOSCAR")

Probably POSCAR does not store the periodicity info at all, but the
system is assumed to be periodic if it came from a POSCAR file.

Best regards
Ask


>
>
>
>
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> Best regards,
>
> Tarjei Bondevik
>
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