QuantumATK Forum

QuantumATK => General Questions and Answers => Topic started by: ams_nanolab on September 24, 2013, 11:47

Title: Atoms too close
Post by: ams_nanolab on September 24, 2013, 11:47

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.

Title: Re: Atoms too close
Post by: Anders Blom on September 24, 2013, 13:30

Script?

Title: Re: Atoms too close
Post by: ams_nanolab on September 24, 2013, 13:40

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.

Title: Re: Atoms too close
Post by: Anders Blom on September 24, 2013, 16:55

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.

Title: Re: Atoms too close
Post by: ams_nanolab on September 25, 2013, 07:09

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