Optimization of two probe system

[rw yan]

Hi,
   I am a new user of ATK and encounter problems when optimize a two probe system. The py file is attached. After optimization,the molecular structure  in center region gets twisted (the picture is attached) and the distance between S atom and Au surface is 2.26A. That is too long for S atom to adsorb in the hollow site. I just wonder whether the parameters I choose or the initial structure I set are proper. By the way, when I check the log file, I find the Fermi level of Au electrode is -0.025901eV. I want to ask what the reference energy level to this value is. The ATK version is 13.8.0.
    Thanks for your kind help. I look forward to your reply.

[Shinji Usui]

You should choose a good initial structure to get a good final optimized structure.

for example
1.  Optimize the molecule part.
2.  Make bulk like structure like [Au-bulk]-Molecule-[Au-bulk] with optimized molecule
3.  Change the Au-Molecule distance, calculate the total energy.  And  you can find the best distance between Au surfaces and S atoms.
4.  Using the lowest energy structure of 3, make 2prove structure.
5   Starting with 4 structure start the optimization of 2 probe.

 

[rw yan]

You should choose a good initial structure to get a good final optimized structure.

for example
1.  Optimize the molecule part.
2.  Make bulk like structure like [Au-bulk]-Molecule-[Au-bulk] with optimized molecule
3.  Change the Au-Molecule distance, calculate the total energy.  And  you can find the best distance between Au surfaces and S atoms.
4.  Using the lowest energy structure of 3, make 2prove structure.
5   Starting with 4 structure start the optimization of 2 probe.

 

  Thank you for your kind help. One more question, can you tell me the reference energy level to Au electrodes in the modeling system? It really confuses me. Thanks again.

[Shinji Usui]

The energy of the system depends on several factors of the system you define.
I do not think one can specify a common reference energy.