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QuantumATK => General Questions and Answers => Topic started by: zdhlover on November 7, 2009, 13:44

Title: How can I bulid such two-probe system as the append files?
Post by: zdhlover on November 7, 2009, 13:44
Hi,everyone:

    Could someone tell me how can I bulid such two-probe system as the append files? May be you should notice the chiral of nanotube.
If you accomplish the structure, Could you tell me the work-flow that you do ? If you build the two-probe system in other software, could you teach me how can I import the electrode and the central region from other software into ATK/vnkl correctly?

By the way . When  we put the central region or apice of nanotube into Molecular Builder, it rotate some angle(which is complex for nanotube's chiral  ), how can I solve the problem?


Thanks a lot!
Title: Re: How can I bulid such two-probe system as the append files?
Post by: Anders Blom on November 9, 2009, 12:20
Not easy, but quite interesting! :)

I don't have a 100% ready recipe (for a good reason!), but I do have the ingredients you need.

Attached are 3 files, containing

I don't know for sure that this is the chirality you were looking for, but that's what I have, for now...

You could in principle take the (5,5) CNT from the Nanotube grower, but I think a slightly different C-C bond length was used for the definition of this system. Not different enough to be important, except that there might be a small mismatch between the radius of the tube and the cap, so it's best to use the attached one.

Now, I just dropped the periodic system on the Atomic Manipulator, and cleaved it. Then, I dropped the two caps onto it. In result, I obtained the system shown in the picture. Note that (red circles)


All that's left is now to determine a good amount of screening layers, find the exact alignment to stitch the system together, and add the carbon atoms in the center. This is the reason I didn't finish the geometry completely, because all these things affect the precise numbers to put in for the alignment (blue circles). The system will be mirror symmetric.

Perhaps we should make a full tutorial on this... For that, let me know what assumptions you make about the C chain in the middle, it seems a bit bent?

Note: the numbers in the picture do no match the input files, because I changed the right cap afterwards to be mirror of the left one.
Title: Re: How can I bulid such two-probe system as the append files?
Post by: zdhlover on November 9, 2009, 15:07
Thanks a lot. And I am very interesting in the full tutorial that you will made on this.

I am glad to tell you why I want to build such a  two-probe system ,the two-probe system that demonstrate in the the nanotube-chain-nanotube.jpg  is Model geometry of article :NANO LETTERS 2008 Vol. 8, No. 9 2900-2905

May be  the mirror symmetric of other system is also need, so I am grateful to see the full tutorial that you will made on this.

By the way , I can easily get the mirror configuration of a cap Nanotube molecular through the mirror function of the Molecular Builder in VNL.But the mirror cap nanotube molecular rotate some complex angle for it's chiral, then  I can't join the  mirror cap nanotube molecular with the electrode. How can I solve the problem?
Title: Re: How can I bulid such two-probe system as the append files?
Post by: Anders Blom on November 9, 2009, 16:10
About the last comment on the mirror, using the Molecular Builder is unfortunately not the proper way to mirror a system. It's because the MB has no sense of an overall alignment to any axis, and that's why you get the arbitrary rotation.

A much simpler way to rotate a system is the following:

Assume you have the molecule in a script, like so:

Code
from ATK.KohnSham import *

coordinates = [[  5.53619192,   9.63421974,   9.86890611],
...
               [ 10.17933558,   9.18049584,  15.10607252]]*Angstrom

elements = [Carbon, Carbon, ...]

molecule_configuration = MoleculeConfiguration(
    elements,
    coordinates
    )

(Never mind what's above, you just need any molecule in ATK/Python format.)

Now, add the following lines of code to the end of the script:

Code
import numpy
c = molecule_configuration.cartesianCoordinates()
new_coords = numpy.array([c[:,0],c[:,1],-c[:,2]]).transpose()

molecule_configuration = MoleculeConfiguration(
    molecule_configuration.elements(),
    cartesian_coordinates=new_coords
    )

and you will have the same molecule, but mirrored in the plane Z=0.

To mirror in the X=0 or Y=0 planes, just put the minus sign in the appropriate place. A similar trick can also be used to transpose the coordinate axes (i.e. to rotate 90 degrees).
Title: Re: How can I bulid such two-probe system as the append files?
Post by: zdhlover on November 10, 2009, 03:43
Thanks your beautiful method to solve the mirror symmetric problem. I also want to discuss the  rotate problem of the molecular in the Molecular Builder of VNL with you.

For example, I build a (5,5) nanotube in the Nanotube Grower of VNL,then I darg it into the Atomic Manipulator,then I cleave it into the two-probe system.After that I want to modify the middle end with saturating hydrogen atoms (may be other modification we need),so I save the two-probe system into the Equivalent bulk system  through the function of Save Equivalent Bulk in the Atomic Manipulator.Then I modify the script of the equivalent bulk system to change it into  a molecular , which allow me handle it to meet my need(for example: modify the middle end with saturating hydrogen atoms or other need  ) in the Molecular Builder of VNL. After I accomplish all in Molecular Builder of VNL,then I drag it into the Atomic Manipulator, it rotate some complex angle and I can't join it with the electrode!!So how can I do to solve the problem?
Title: Re: How can I bulid such two-probe system as the append files?
Post by: Anders Blom on November 10, 2009, 08:03
Yes, it's a problem, but it can be solved. If you send me your molecule (rotated in a bad way, after MB), I'll show you the trick ;)
Title: Re: How can I bulid such two-probe system as the append files?
Post by: zdhlover on November 10, 2009, 09:04
 ;D ;D ;D Thanks a lot, you are so kind and zealous .

The two electrodes and the screen layers you can get through cleaving a (5,5) nanotube  in the Atomic Manipulator.
The apppend files is the (5,5) nanotube molecular saturating with hydrogen atoms ,which is a part of central region I want to join with the electrodes.But it  rotated in a bad way, after MB.So 0....
By the way,The 55nanotube_Equivalent_bulk_molecular is get from the way I have been mentioned above.

I make a grateful acknowledgement for you to give me the trick, thanks a lot.

wish you best!
Title: Re: How can I bulid such two-probe system as the append files?
Post by: Anders Blom on November 10, 2009, 09:13
It seem the structure is only rotated in an inconvenient way about its own axis, i.e. we don't need to realign the axis itself?

In that case, you can quite easily rotate it about the z axis in the Atomic Manipulator. The question is, of course, by what exact angle... Can you attach the electrodes too, so we can compare?
Title: Re: How can I bulid such two-probe system as the append files?
Post by: zdhlover on November 10, 2009, 09:30
Quote from: Anders Blom on November 10, 2009, 09:13
It seem the structure is only rotated in an inconvenient way about its own axis, i.e. we don't need to realign the axis itself?

In that case, you can quite easily rotate it about the z axis in the Atomic Manipulator. The question is, of course, by what exact angle... Can you attach the electrodes too, so we can compare?
May be ,but I am not sure.may be you can drag the 55nanotube_Equivalent_bulk_molecular into the Atomic Manipulator which have a cleaving (5,5)nanotube ,then you can compare .
Th append files is only a sketch map, which is wrong of the width of the central region .


The electrodes you can get from cleaving a (5,5) nanotube in theAtomic Manipulator ,which you can adjust the width of the central region  appropriate.

And our aim is to join the molecular with two electrodes appropriateway.
Title: Re: How can I bulid such two-probe system as the append files?
Post by: Anders Blom on November 11, 2009, 01:02
I took a step back and looked at the problem from a fresh angle. The real issue here is the passivation. Now, the Molecular Builder can do it, but at the same time it messes up the alignment. So, how about we make the passivation ourselves, in a way that keeps the alignment? :)

Attached is a script which contains a quite general function that passivates a molecule. It's a bit rough, but it worked very nicely for your structure!

Basically it's a very simple "molecule in, molecule out" function; you send in the un-passivated nanotube, and get a passivated back. To satisfy your need for passivation of only one side, I also included an "exclude" filter where you can specify certain atoms that will not be passivated. The C-H bond length and the criterion for nearest neighbor (crucial to the algorithm) are easily configurable via keywords to the function.

This particular script has the molecule inside the script itself, and writes the passivated structure to a VNL file, but it is hopefully obvious how to use the function more generally.

Pictures of the un-passivated and passivated structures attached! Now, please note that the unpassivated structure I used (in the script) is actually the rotated one from the Molecular Builder, so replace it with a fresh stripped version of a nanotube segment from the Nanotube Grower before using it for real. After that, however, the passivated structure will fit right into the cleaved tube in the Atomic Manipulator!

Seems like this could be another nice new tutorial... Perhaps you can tell me a bit more about your motivation, and also how you intend to handle the vacuum gap, it was very large in your original structure. The present approach makes it much easier to passivate one segment and then make a mirror image of it for the other electrode.

Good luck!
Title: Re: How can I bulid such two-probe system as the append files?
Post by: zdhlover on November 11, 2009, 04:17
 ;D ;D ;D  you make a trick in the problem I have been mentioned, :P 
The  passivation problem I can solve in another way : I can passivate the molecular in the Molecular Builder ,then I append the hydrogen atoms in the Atomic Manipulator by hand through compare the relative coordinates of the middle end canbon atoms and the passivated hydrogen atoms in the Molecular Builder .

My aim is want to know how can we solve the bad alignment problem of the  Molecular Builder, because we may be do another operation(for example :  modify the configuration or the shape  of the central region in the Molecular Builder) not only the passivation ?

In short, may be we can solve this problem in two ways:

1,Could we constrain  it messes up the alignment in the  Molecular Builder when we do some operation in it ?

2,May be you can write a nice new tutorial  and a script which is about the alignment that we can alignment  the molecular through  the axis of arbitrary two atoms of the molecular and the arbitrary atom of the molecular  as the origin of the axis? It seems another question and a powerful function? ;D ;D ;D

All is my  crude thought, I think you are very clever and best
Title: Re: How can I bulid such two-probe system as the append files?
Post by: Anders Blom on November 11, 2009, 12:03
1. No, unfortunately you cannot right now constrain the MB not to mess up the alignment. In fact, it's kind of a feature of the instrument that it aligns the molecule according to the main moments of inertia. That might not always be what you want, however... There will be some Molecular Builder in future versions of VNL, but we have decided not to continue with exactly the same ideas, so we will redesign it quite a bit. But that is no help to you right now.

2. Aligning two atoms is, on the other hand, relatively straightforward. I believe you are already familiar with the align.py script, which is part of one of the graphene tutorials. I have attached it here for convenience, I think it does what you need.
Title: Re: How can I bulid such two-probe system as the append files?
Post by: zdhlover on November 11, 2009, 12:14
 ;D ;D Thanks a lot.
I have learned many useful trick of ATK from you ,you are so kind and earnest to help me. Thanks agin.

Whish you good luck.