the periodic boundry of system

[fanjiaping]

Dir sir:
      As we know, the electrode is periodic at x,y directions. And we should make the size of electrode larger than the molecule at X,Y directions to avoid the interation between the molecule and its mirror. But in some paper , the figure shows that the molecule size is larger than electrode. So I am confused by this case. Could you show me more tips on this?
      the additional figure is the case which I mentioned!

[Nordland]

You are correct in all your statements.

If the paper's simulation is carried out on the system as shown, the results are very wrong, since you will have the bucky-ball located on top of one another.

[fanjiaping]

Thank you. But if make the padding region larger enough at X,Y direction ,can we avoid the interation between the molecule and its mirror?

[nori]

But if make the padding region larger enough at X,Y direction ,can we avoid the interation between the molecule and its mirror?

Exactly, and the calculation for the system you introduced should be done so.
I guess the electrodes is actually not 3D but 1D-chain.
In molecular devices, the electron transport properties strongly depend on the electronic structure of molecules bridged between electrodes.
That's why the calculation using virtual electrodes could make some sense.
("virtual" means there is not such a electrode in real)

[fanjiaping]

　　　Thank you for your advice! Although the electron properties strongly depend on the electronic structure of molecules bridged between electrodes, we cann't exculde the influence of electrodes on whole device! However, how can we assure the sense of periodic boundry at X,Y direction if we use the virtual electrodes which have large padding region!

[nori]

we cann't exculde the influence of electrodes on whole device!

Yes, so the modeling you should do depends on what you want.
For instance, if you want to investigate a contact resistance between electrodes and molecule or the influence of electrodes against the electron transport properties more accurately, you should prepare 3D electrodes.
On the other hand, if you want to focus mainly on the intrinsic electron transport properties of molecules, using virtual electrodes may be permitted.

how can we assure the sense of periodic boundry at X,Y direction if we use the virtual electrodes which have large padding region!

In such a case, periodic boundary condition is not indispensable but only an option.
Using Neumann boundary condition gives the same result as periodic boundary condition if the cell size is enough large.

[fanjiaping]

　　　Thanks a lot! I think I understand your meaning!