Configuration has atoms in (nearly) identical positions

[Hassan]

I am trying to use DFT to calculate transmission spectrum. I run into this error:

** Back Engine Exception : The configuration has atoms in (nearly) identical positions.
** Location of Exception : symmetryoperations.h:189

I don't know why, since I generated the geometry using the builder and I am quite sure the atoms are spaced nicely.

I would like to know how I can find out which atoms are overlapping since there are quite a few in my geometry (215 in the device part) and how to debug this efficiently...

The structure I am trying to simulate is attached in the file.

[Anders Blom]

To find the overlapping neighbors, open the structure in the Builder and use Select>Close Neighbors. You will find that you have a layer at the top of the structure (in Y) which is equivalent to the bottom layer. Perhaps you meant to add a bit more vacuum in Y + gate electrodes.

Also your electrodes are too short in the Z direction - see http://quantumwise.com/publications/tutorials/mini-tutorials/99. You should double them.

[Hassan]

Thank you for the prompt response! I'll fix those problems.