How to set up the parameters to "Geometric Constraints" in VNL?

[benhuzhou]

Hello
   I have met a question  about VNL, when I drag the two probe system into VNL. First, I want to optimize the geometric, but I do not konw how to set up the parameters in "Geometric constraints"? According to the VNL books, "geometric constraints" is a list of atom indices whose positions should be fixed during the optimiaztion, and the indices are integers ranging from 0 to N-1, where N is the total numbers of atoms in the atomic configuration.
  So I have two questions:
   First, Does N include the two electrode atoms?
   Second, if I have 200 atoms in the central region, and 50 atoms in the two electrode atoms, the total atoms is 250.When I fixed the electrode atoms, only optimize the central atoms,  what I need to write in "Geometric Constraints" ?
Thank you very much!

[Anders Blom]

The electrode atoms cannot be moved during a relaxation, so if all atoms in the central region will be allowed to move, you do not need to set up any constraints. However, it is often a very good idea to keep at least the first layer or two of the surface region (the part of the central region which is like the electrodes) fixed to have a better match to the electrodes, and to reduce the computation time.

[benhuzhou]

To Anders Blom:
    Thank you very much! So if I want to fix atoms in the central region, I need to know the ordinal number of atoms. By the way, the ordinal number of atoms are seperated by comma. For example, I want to fix the number of atoms (40,41,42,43,44,45), so I need to write 40,41,42,43,44,45 in "Geometric constraints". Is it right?

[Nordland]

Yes. That is the correct syntaks. The orginial index/number of the atoms can easily be found by inspecting the script - that it is the way I do it