Structure model problem

[HONGBIN YANG]

Dear all,

My QSTEM simulation only give the "right" result when I use the structure model that was originally from the Example folder. If I download the .cif file and then use Vesta to get .xml file then .cfg file by conver2cfg, the simulation result would be strange. 

For example, the simulation results for silicon (110) projection is shown below: upper image--when I start with Si.cfg file (from crystallography open database), and lower image--when using Si structure model from Example folder. All the parameters used in the simulation is the same so I thought the problem should come from the structure model, but could not fix it. Can anyone help me on this? Both .cfg files and their configurations are attached.

Best,

Hongbin

[Christoph Koch]

Dear Hongbin,

 

your COD unit cell contains 17 atoms. In addition to the atoms in the unit cell, it also contains atoms with negative fractional coordinates. This makes no sense. If you delete all the atoms beyond the 8^th atom, and reduce the number of atoms in the unit cell to 8, your results will look much more similar. Remaining differences may then be due to the difference in the Debye-Waller  factor, since you are doing STEM simulations with TDS turned on.

 

With best regards,

Christoph Koch.

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[HONGBIN YANG]

Hi Professor, Koch,

Thank you for the quick response!

So far these negative values exist in every .cfg files I converted. Is there a way avoid this and what software can I use to edit the .cfg file?

Best,

Hongbin

[Christoph Koch]

Dear Hongbin,

 

When I save .xtl files with Vesta, I do not notice negative fractional coordinates. Maybe it is some setting in vesta. Do you save more than one unit cell?

 

The .cfg files can be edited  using any text editor (see http://qstem.org/?page_id=36).

 

With best regards

Christoph.