[ase-users] Possible bug with minimum image convention

[Tarjei Bondevik]

Thank you very much for your fast reply.

You were correct: by adding Atoms(..., pbc=True) the effect from MIC worked just as expected.

Best regards,
Tarjei

>-----Original Message-----
>From: Ask Hjorth Larsen [mailto:asklarsen at gmail.com]
>Sent: Tuesday, September 04, 2018 3:14 PM
>To: Tarjei Bondevik
>Cc: ase-users
>Subject: Re: [ase-users] Possible bug with minimum image convention
>
>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.
>>
>>
>>
>> I have some code converting Lammps data files to the ase format in the
>following way:
>>
>>
>>
>> atoms=Atoms(symbols=chem_symb_list,cell=cell_vectors)
>>
>> atoms.set_positions(position_list)
>>
>>
>>
>> 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:
>>
>>
>>
>> write_vasp(“tempPOSCAR”, atoms, direct=True, sort=True)
>>
>> 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
>
>
>>
>>
>>
>>
>>
>> Best regards,
>>
>> Tarjei Bondevik
>>
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