error with drag molecule configuration into costum/ molecular junction

[spin]

I want to have a two electrode system like attached figure. In molecular junction/custom, the width of central region can not be determined by user! I am making effort to put the Adamantane molecule in the central region between two electrodes system ( 2*2 and 1*1) , then compare the conductance of molecule for this two state. on the other hand I have two value of central region, 9 and 11 Ang.
Can I do it in custom?

[Anders Blom]

The Custom Builder (the one for Molecular Junction) is not intended to solve all problems It's function is to easily be able to insert the molecule between the electrodes. For further manipulations, you are relatively easily extend the unit cell by hand, in the Python code, or send the structure to the more generic Builder, where you can
1) convert it to bulk, by clicking the Bulk icon on the left
2) change the unit cell
3) convert back to device by clicking the Device button (same place)

[spin]

Dear Dr. Blom, thank you for your excellent responses. yes, I've tried the builder in VNL, in builder I can not have the molecule in central region with gold electrode in two side (device form). First we put the gold, then we define the lattice and number of repetitions for central region and afterward we can transmit it to device mode. when I put Adamantane as my molecule, the electrodes also changes from gold to Adamantane. The final device would be two electrode (Adamantane) and an ADM molecule between them!!!
I think it would be solved by python code, I haven't already written a python code but I start it and I'll come back 

Best

[Anders Blom]

I think I know what the problem is, but it's hard to explain (easy to show...). The issue is probably that your surface has only 3 gold layers, so the switching from bulk to device can't find any periodicity. But you can instruct it manually to use the same value as before. Then there should be no molecule in the electrode.

[spin]

Dear Dr. Blom
Is it possible to have an non-alternating device? in a way that atoms in electrodes be independent than central region. some times when the central region width be small, a portion of the central molecule would be appear in the electrodes!!! 

[Anders Blom]

Yes, that is inevitable, and it's crucial to understand why. In ATK, there must be a copy of the electrode inside the central region. If not, not only does the algorithm break down, but you almost certainly do not have enough screening to adiabatically go from the highly non bulk-like electronic structure around the molecule to the bulk like electrode.

See http://quantumwise.com/documents/tutorials/latest/UpgradeGuide/index.html/chap.upgrade.html#sect1.upgrade.twoprobe for some more details.

[spin]

Thank you, I got it. And how the distance between electrodes in ATK can be defined?
whether that is the C vector measure when we define the central region?

[Anders Blom]

Yes, the length of the central region in C becomes the distance over which the bias is applied, if we by this mean the distance between the electrodes. It is obviously not, however, the distance between the metal surfaces.

[spin]

In the custom/molecular junction for example we define a 2*2 electrode [Au(100)] and minimum length of 4, now; if the molecule's vertical length be more than the vertical length of electrode, the configuration of molecule would be changed. In this case, if I calculate the quantum conductance(G) of the mentioned molecule, whether the results would be correct or not?

[Anders Blom]

The surface, or rather the unit cell in the transverse plane, must be large enough that the molecule fits, otherwise you will get completely wrong results. And if the cell is only "just big enough", there may be electrostatic interactions between the repeated copies in X/Y.