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Vacuum in nano electrode unitcell

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wring:
I want to know the difference between nano electrode and bulk electrode,that is ,how it deals with the vacuum in nano electrode unitcell. Which requires more better hardware?

Anders Blom:
A two-probe system is periodic in the two directions perpendicular to the transport direction (which we always take as Z for simplicity). Therefore, it's easy to set up a bulk electrode cell to represent a whole metal surface, for instance. You just have to remember to make the surface unit cell large enough that the molecule in the central region does not interact with it's repeated copies.

If, on the other hand, you wish to have a 1D-type of electrode, like a nanotube, you have the opposite "problem"; you must include enough vacuum in the XY unit cell that the electrodes have no interactions with their repeated copies.

Compare the two attached figures, one for a bulk electrode ([111] 3x3 fcc Au) and one for a nanotube. Both two-probe systems are repeated 3x2 times in the transverse directions; note the unit cells!

I'm not sure I understood the question on hardware, but regarding the vacuum, obviously this adds to both the CPU and memory usage, since the real-space 3D grids can be quite large, and the Poisson equation will be heavier to solve. Usually this is, however, not a problematic constraint that limits the size of the calculation.

1D systems typically exhibit a slightly worse performance gain in parallel due to the 1x1 k-point sampling in the XY plane. On the other hand, the way ATK handles memory partitions along the transport axis, and the reduced number of neighbor atoms, typically means that you can handle a larger number of atoms in such an "elongated" configuration compared to a compact system.

jiguomin:
If the surface unit cell of electrodes are not large enough that the molecule in the central region  interacts with it's repeated copies, is the calculation resust accurate? For example , the molecule in the central region  forms bond with it's repeated copies.

Anders Blom:
When discussing "accuracy", the question is always "Compared to what?" If you experiment (envisioned or real) deals with a single molecule, then you had better simulate a single molecule, without bonds to (artificially) repeated copies. On the other hand, in many real experiments, the molecules on a metal surface can be placed rather densely.

Generally, however, you had better avoid direct formation of bonds (more specifically, basis set overlaps).

jiguomin:

--- Quote from: Anders Blom on March 30, 2011, 09:44 ---When discussing "accuracy", the question is always "Compared to what?" If you experiment (envisioned or real) deals with a single molecule, then you had better simulate a single molecule, without bonds to (artificially) repeated copies. On the other hand, in many real experiments, the molecules on a metal surface can be placed rather densely.

Generally, however, you had better avoid direct formation of bonds (more specifically, basis set overlaps).


--- End quote ---
In the model Ag(3*3)-C60-Ag(3*3) and Ag(4*4)-C60-Ag(4*4), we observed the C60 forms bonds with repeated copies in the former model but cannot be observed for the later model. Also i find that they show the different IV characteristics obviously. Iwant to know if they can be viewed as the effect of size of electrodes on the electronic transport properties or the effect of interaction between the C60 moleculers on the electronic transport properties. Thanks.

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