I am trying to convert some cif files to .xyz file format for TEM simulation with QSTEM. All cif files obtained via Findit2009 and I followed the guideline: https://www.physics.hu-berlin.de/en/sem/software/software_convert_cfg
However, only the Li2MnO3 cif files can not be converted. I tried three Li2MnO3 and did not succeeded, while other files (such LiMn2O4 ) do not have this problem.
I doubt that whether there are some errors for those Li2MnO3 files and want to know how to solve it.
I attached the cif files and the screenshot of the converting error (the jpg.)
In order to perform this i use Vesta software (to open *.cif files and save it as *.xyz ) if you need to simulate HRTEM images by means of QSTEM you should create *.cfg file (use convert_to_CFG it's part of QSTEM software) if you need some details you can wite me
Sincerely
Hi, Prikhodko
thanks for your reply
I performed the converting procedure as follow:
1- First loading your atomic configuration into a software that can both read your format and also save it in the .xtl format (e.g. Vesta).
2- Call the program Convert2CFG (part of the QSTEM package) and open the .xtl file. This will automatically create a file with the same name but a .cfg extension and the converted structure.
the first step has no problems, while the *.xtl files I got can not be convert to a *.cfg files. The error always occur as I described, shown in the .jpg I attched in my question.
Just a hint, did you try to open the file with notepad (or similar) and check the kerning and +/- signs? (Sometimes an element with a single letter and one with two letters e.g. O and Li are not "aligned").
Hi Vigliaturo, thanks for your suggestion.
I attched two files, "1.xtl" can be sucessfully convert to *.cfg while "2.xtl". I opened them with Notepad++ and did not find the difference between them. The letters of elements seem to be aligned.
Could you have a look for me ?
Thanks a lot
Hi Prikhodko, thanks for your reply.
I load the *cfg file you provided by QSTEM, but there seems some atoms missing in this structure, as shown in the attched screenshot.
Hi, Prikhodko, Thanks for your reply.
When I choose the [100] axis, there still seem some atoms missing at the edge of this structure, as shown in the attached screenshot. I am not sure whether that affects the simulation.
Additional question: I want to know why the convert_to_CFG tool in my QSTEM can not convert this structure from *.xtl to *.cfg and what the error means.
In the website of QSTEM, there seems few learning materials for QSTEM. For example, the converting issue I met do not be mentioned in those PPT loaded from the website. Could you give some advice for learning this software ?
Thanks a lot
This edge effect is not critical... because you can see that in the left side two atomic columns are absent but in the right side you can see this two columns... it's periodic conditions... i deleted some atoms in the edge of the unit cell in your *.cif file in order to avoid overlap between atoms during supercell formation ... i suppose it's one the reason of your problem or you do something wrong ... i can not say exactly because i do not know what exactly you have done ...
Hi,
I had a question related to this thread. If we convert the files from .cif to .xtl or .xyz we lose the Debye Waller Factor for each atomic species. How do we account for that?
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