Wrong number of atoms when reading from .cif file (corundum gives 46 atoms not 30)

[Chris]

Hi all,

I am trying to read a .cif file obtained from AMS, however am getting too many atoms in the unit cell. For some .cif files such as 'diaspore.cif' I am able to get the correct number of atoms (16 for AlO(OH) with 4 repeating units) after deleting the bonds added by VESTA outside of the unit cell (edit-bonds-clear all), however for others such as 'corundum'.cif' I find 46 atoms and not 30 (Al2O3 with 6 repeating units). In the past I have manually deleted the additional atoms, but is there a better method to obtain the correct number of atoms?

This appears to be a similar problem reported on a LAMMPS thread https://lammps.sandia.gov/threads/msg64260.html, however it is not clear how they managed to extract 30 atoms from the .cif file.

Regards,

Chris

[Baka Sama]

Hi.

Just reduce boundary value from 1.00 to something like 0.99 to not count "translationally" equivalent atoms.

[Chris]

Thanks! That worked perfectly.

Is there any method you would recommend for then re-centering the unit cell?

Regards,

Chris

[Prosnikov Mikhail]

What do you mean by re-centering? Any unit cell transformation is achievable through Edit -> Edit Data -> Unit Cell -> Transform..

 You can put any transformation matrix here.

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Prosnikov Mikhail, High Field Magnet Laboratory, The Netherlands

[Chris]

For example in 'offset.tif' it is clear there are now atoms missing from the image, is it possible to then automatically re-center the positions so they are all equidistant from the unit cell edge? I could do so manually, but am curious if there is an automatic method.

Thanks,

Chris

On Thursday, 25 April 2019 12:32:59 UTC+1, Baka Sama wrote:

What do you mean by re-centering? Any unit cell transformation is achievable through Edit -> Edit Data -> Unit Cell -> Transform..

 You can put any transformation matrix here.

On Thu, 25 Apr 2019 at 13:29, Chris <chris...@gmail.com> wrote:

Thanks! That worked perfectly.

Is there any method you would recommend for then re-centering the unit cell?

Regards,

Chris

On Thursday, 25 April 2019 12:10:28 UTC+1, Baka Sama wrote:

Hi.

Just reduce boundary value from 1.00 to something like 0.99 to not count "translationally" equivalent atoms.

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