Atoms too close

[ams_nanolab]

Dear Sir,

I was trying to make mos2 sheets with line defects as in http://arxiv.org/abs/1304.3701 .

I am getting the following error... (screenshot attached)

How to solve this I cannot optimize the structure.

[Anders Blom]

Script?

[ams_nanolab]

I don't have the script as of now, was trying with slater-koster. However Ext-Huckel seems to work, but there's no optimize geometry option in it. Attached is the structure python file.

[Anders Blom]

There are at least 16 atoms in the structure which are placed at a distance <0.1 Å from each other (in fact, on top of each other). Check in the Builder, use the tool Select>Close Neighbors. It can be a bit hard to see them since they are sulphur atoms and the selection markers are yellow, but it seems the whole middle row is duplicated.

[ams_nanolab]

Thanks, selecting the close neighbor and deleting them helped, now the structure is fine.