Geometry optimization of two probe system

[sayedmesa]

Dear ATK community,

 I have preformed optimization for two-probe system where the molecule is donor-acceptor system ended by sulfur linkers ie: electrode-S-Donor-Acceptor-S-electrode.

After the optimization I found that the distance between S-atom of acceptor part and the left electrode is 2.32 ang. while the distance between S-atom of the donor part and the right electrode is 1.38 ang
I have some doubt about the last distance. Please let me know your opinion.

Thanks beforehand,
Regards,
Sayed

[Nordland]

Which version have you used ?

[sayedmesa]

I use VNL 2008.1. The initial distance in each side is 1.9 ang.  I know from literature that the normal distance between S-atom and gold electrode is between 1.9 to 2.4 ang.

Regards,
Sayed

[ipsecog]

As long as the total size of the central cell is fixed you may not get the right geometry. This must be done by hand:

• change the cell systematically (start somewhere, increase or decrease in steps)
• relax the internal geometry in each case
• pick the smallest total energy

[Anders Blom]

I can mention that in the upcoming ATK 11.2 it will be possible to automatically relax the strain of the unit cell as well, so you can optimize the two-probe geometry in one single step.