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orex / supercell

The program allows you to create regular structure supercell from cif file with partial occupancy and/or substitutions.
GNU General Public License v2.0
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ERROR: Group has no unique connection. #5

Closed hlyang1992 closed 7 years ago

hlyang1992 commented 7 years ago

There is a error when deal with file below which is generated by findit. Cu2Se-41141.cif.zip

orex commented 7 years ago

It seems to be, that the file in zip archive is corrupted (not valid cif). Can you check it?

hlyang1992 commented 7 years ago

I can read the file using vesta. Then export to cif in vesta. I still get this error with the new file exported by vesta. Could you please tell me how to check it ?

orex commented 7 years ago

Just download the zip, you attached, unpack the file and check, that you can still open it with VESTA

hlyang1992 commented 7 years ago

I am very sorry for the bad file. I don't know why the file is broken. I upload the new file to google drive.good cif

orex commented 7 years ago

Now, it is good. I will return to you tomorrow.

orex commented 7 years ago

Cu1 and Cu2 sites are located close to each other (see picture).

cu2se-41141

Therefore, they can not be occupied simultaneously. Supercell program is trying to combine them to one group, but it fails, because the default value of distance within group parameter ( --tolerance) is low for the structure. To solve the problem, I can recommend you to change the default value of the parameter to 1.1. supercell -i Cu2Se-41141.cif -t 1.1

For more information, please refer to http://jcheminf.springeropen.com/articles/10.1186/s13321-016-0129-3#Sec5 and to PZT example in tutorial https://orex.github.io/supercell/doc/supercell_tutorial.pdf PZT: https://github.com/orex/supercell/tree/master/data/examples/PZT

P.S. Be careful, it is necessary to perform geometry optimization procedure for such type of compounds to achieve reliable results.

hlyang1992 commented 7 years ago

Thank you for your help..