A problem in exporting a twin structure to .cif file

[Sunny Lin]

Hi all

I used VESTA to build a quartz Brazil law twin structure(alternating layers of right-handed quartz and left-handed quartz). Phase 1 is the right-handed quartz and phase 2 is the left-handed quartz( they have different space group). However when I exported the data into .cif file. The twin structure information is lost, only left the right-handed quartz structure. Does anyone have any idea of what's going on and how can I can keep the twin information on the .cif file?

Thank you so much

Sunny

[Philip Howie]

Dear Sunny,

The problem is that the .cif file format is not suitable for what you want to do.  It's a CRYSTALLOGRAPHIC information file, designed to represent periodic crystal structures.  If you examine the contents of a .cif file, you'll see that it contains the space group and an irreducible representation of the atomic positions, from which the rest of the structure can be generated.  In short, it behaves like just one of the two VESTA phases.

What do you intend to do with the file you create?  For representing a system like this, I would suggest a .xyz file, which simply stores the Cartesian coordinates of all the atoms.  Section 17.5.1 of the VESTA manual contains a list of alternative output file formats.

Hope that helps,

Philip

[McDermott Eamon John Gordon]

As Philip suggested, export your structure as .xyz file, which will give you cartesian coordinates for both phases. This is the important step as it will merge your two phases together.

If you need a VASP file, you could then re-import the .xyz file into VESTA, re-introduce the crystallographic information (unit cell dimensions/angles) and export as a POSCAR. Or do this by hand in a text editor.

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Eamon McDermott, M.Sc.
Institute of Materials Chemistry, TU Wien
eamon.m...@tuwien.ac.at
Office: +43 (1) 58801-165304
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On December 11, 2014 at 11:23:58 PM, Sunny Lin (sun....@gmail.com) wrote:

Hi Philip

Thank you so much for your answer. Attached is the brazil twin model I build phase 1 is the right-handed quartz and phase 2 is the left-handed quartz. I'm studying the preferential dissolution on the brazil twin and my advisor and I believe the twin boundary dissolves quickly. In order to verify that we need to use a software to calculate the energy on the twin boundary as well as the energy on right-handed quartz and left-handed quartz part. We are expecting the result shows the boundary has higher energy, so it is more unstable  which leads to a higher dissolution rate. The software we are going to use reads .vasp file. However, same thing happened when I exported the data as .vasp file that only right-handed quartz information was recorded. Do you have any idea on how to save the whole information on the .vasp file?

Thank you so much.

Sunny

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[qca...@gmail.com]

I want to ask: After I re-import the .xyz file into VESTA, how can I re-introduce the crystallographic information (unit cell dimensions/angles)? (if the cell information from this two phases are different)
Thank you very much!

Q.

Eamon McDermott於 2014年12月12日星期五 UTC+8上午9時21分18秒寫道：