QuantumATK Forum
QuantumATK => General Questions and Answers => Topic started by: rw yan on October 5, 2014, 07:17
-
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.
-
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.
-
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.
-
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.