How can I bulid such two-probe system as the append files?

[zdhlover]

Hi,everyone:

    Could someone tell me how can I bulid such two-probe system as the append files?
I have been read an atricle(PRB 81, 045425(2010)), and I try many ways want to build（4,4）CNT/20-UZCNT/CNT MTJ
as in FIG. 1 of PRB 81, 045425(2010) , but I couldn't get it . Could you have some ideas to help me build a two-probe system
as 4,4）CNT/20-UZCNT/CNT MTJ?
I have been use the free CoNTub software to create a heterojunction of of cnt(4,4) and cnt(6,6).,but  I wonder what I can do next step?

ps :the append files is schematic structure of (4,4)CNT/20-UZCNT/CNT MTJ.

Many thanks!

[Anders Blom]

If you already have the structure coordinates as shown in the picture (not just image, but real coordinates), then in VNL 2010.02 you can just wrap this into a unit cell (align the tube along z first, of course) and then use the Custom Builder called "Device from bulk" to make electrodes, and you're done, essentially.

[zdhlover]

Thanks ,I understand what you mean,but ....

I have no the structure coordinates, and I only have been use the free CoNTub software to create a heterojunction of of cnt(4,4) and cnt(6,6) and delete the superfluous atoms in the cnt(6,6),and the result like the append image.

But the structure I have been build is erroneously aligned and I also don't know how can I build the right half of the  two-probe system, and how can I join these two erroneously aligned halves?

[Anders Blom]

So far so good :-)

In the Bulk Builder in VNL 2010.02, there is a command "Mirror", which if you also tick "Copy" (to add the mirrored atoms, instead of replacing the existing ones) should give you the complete central region (provided you want it symmetric), after which you can proceed with the "Device from bulk" Custom Builder, if you also get the initial unit cell size in the Z direction (looks a bit big in the picture).

Looking forward to seeing the final geometry!

[Anders Blom]

The alignment problem needs to be dealt with first... I'll get back to you on that!

Also, the system seems to be missing some atoms (there's a hole underneath, see picture), or maybe that's intentional?

[Anders Blom]

I've made some progress; I now have a Custom Builder that can align the structure, provided that it's regular enough. Then I mirrored it, and after a few manual manipulations I ended up with the structure shown in the picture. Getting closer to what you want, I hope?

However, I ran into some problems with your coordinates. Seems the structure is quite skew... When I align two obvious carbon atoms along the Z axis, you would expect most of it to be aligned properly. But there are small deviations, and in particular the first layer is not perpendicular to the Z axis.

Also the ordering of the atoms might cause problems, we should sort the coordinates in Z.

Can you check the generation of your original geometry, to see if it's possible to include more layers in the left part so that it has some part where it's a perfect (4,4) tube? It seems it starts to bend almost immediately...

[zdhlover]

Thanks， I have been uploaded the long heterojunction of of cnt(4,4) and cnt(6,6), and  could you teach me how can I sort,align, mirror and join these two erroneously aligned halves?

[Anders Blom]

I got stuck a little bit, and I'm not sure how to proceed...

First, I sorted all atom coordinates in increasing Z,Y,X. I just used Excel.

Then, I developed some scripts for aligning the geometry such that 3 atoms are in a plane. The point would be to take 3 atoms which form a "ring", so they should have the same Z coordinate, and place them in the XY plane. This worked, but the other atoms that are supposed to be part of the same "ring", do not end up with the same Z coordinates. And in general, the rest of the structure is now very slightly off axis, still.

A bit hard to explain...

The problem might be that there are too few decimals in the original coordinates.

One solution could to place a perfect ATK CNT as the end, but then the "screening part" of the junction will be non-perfect and cause scattering, so we end up with a very long system because we have to pad the system with several periods of perfect CNTs. Would be ok for the semi-empirical model though.

I attach my 2 custom builders (all this is done in VNL 2010.02), so you can play around with it a bit yourself... One aligns 2 atoms on an axis (I thought this would be enough first, and in some sense it should be, if we use the Z axis), the second aligns 3 atoms in a plane.

[zdhlover]

Thanks your untiring hard work! your work is so beautiful, and I think your method and scripts can work well for my task!

Thanks a lot !

wish you happy and good luck!

[zdhlover]

I got stuck a little bit, and I'm not sure how to proceed...

First, I sorted all atom coordinates in increasing Z,Y,X. I just used Excel.

Then, I developed some scripts for aligning the geometry such that 3 atoms are in a plane. The point would be to take 3 atoms which form a "ring", so they should have the same Z coordinate, and place them in the XY plane. This worked, but the other atoms that are supposed to be part of the same "ring", do not end up with the same Z coordinates. And in general, the rest of the structure is now very slightly off axis, still.

A bit hard to explain...

The problem might be that there are too few decimals in the original coordinates.

One solution could to place a perfect ATK CNT as the end, but then the "screening part" of the junction will be non-perfect and cause scattering, so we end up with a very long system because we have to pad the system with several periods of perfect CNTs. Would be ok for the semi-empirical model though.

I attach my 2 custom builders (all this is done in VNL 2010.02), so you can play around with it a bit yourself... One aligns 2 atoms on an axis (I thought this would be enough first, and in some sense it should be, if we use the Z axis), the second aligns 3 atoms in a plane.

I noticed that when I hovering the mouse on atom in SE windows, I found like c(3)x,y,z image,and I want to know does the number in  bracket is the list number that the atom coordinates in  the coordinates list?

[Anders Blom]

Yes, with numbering starting at 0!