Messages

31

General Questions and Answers / Could we change the atom's shape and color in vnl 2008.10?

« on: June 8, 2010, 04:12 »

 
  Hi,everyone . May be I want to change the atom's shape and color  in vnl 2008.10 to special foucs on our view , could someone tell me how can I do that?

32

General Questions and Answers / Re: How can we achieved this in ATK?

« on: May 31, 2010, 15:35 »

Thanks a lot!
And I want to know how can we achieved that dope the junction with two electrons in ATK 2008.10?

And I also want to know how can we compute the Local density of states in the energy window as [-0.5 eV, 0.5 eV] not one energy value in atk 2008.10?

33

General Questions and Answers / How can we achieved this in ATK?

« on: May 31, 2010, 14:29 »

Hi, everyone

The junction of connections through a charge neutral 5-member ring as below, our calculations yield local spin polarization connected to the nominally unpaired pz electron on the apex C atom. In one article they say that the local spin polarization can be compensated by doping the CNTs. Experimentally, doping could be achieved either chemically with alkali atoms or by applying a back-gate voltage.To simulate this, they dope the junction with two electrons which are then compensated by an equivalent background charge spread uniformly over the whole extended molecule. And they find that doping indeed leads to additional charge around the two apex C atoms which compensates the local spin.

And my question is  how can we achieved that dope the junction with two electrons in ATK?


And I also want to know the meaning and the using method of charge in Basis set parameters of ATK.
Thanks!

34

General Questions and Answers / Re: How to calculate the projected density of each MPSH state?

« on: May 19, 2010, 14:00 »

 
hi, good everyone
I also meet the same question,I want to know when we can calculate the projected density of each MPSH state or the projected density of states of the specified atom in the bulk system or the central region?

Thanks a lot!

35

General Questions and Answers / Re: Very werid problem!

« on: May 10, 2010, 09:05 »

Do you think you can build a strange bulk structure:[[  0. ,   8.7,   0. ],
                                                                          [  8.7,   0. ,   0. ],
                                                                          [  0. ,   0. ,  11.6]]*Angstrom as the second script ?

you'd better check whether your two-probe system is correct or not at first.

36

General Questions and Answers / Re: how to build the doped single wall carbon nanotubes?

« on: April 28, 2010, 14:38 »

1). Use the Nanotube Grower to create a SWCNT you are interested in; then drag it into the Bulk Builder;
2).then you can make the supercell use the Repetition in Bulk Builder;
3).then you can choose any one of those atoms and choose the choice of Disply selected atoms only in the left panel in the Bulk Builder;
4), then you can  substitute the atom in the Basis of the Element to any element you want to

37

General Questions and Answers / Re: How can I bulid such two-probe system as the append files?

« on: April 26, 2010, 15:45 »

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?

38

Scripts, Tutorials and Applications / Re: Script for calculating the voltage drop.

« on: April 23, 2010, 16:46 »

I offer some calculation examples of voltage drop.
All calculations were done with the algorithm "ElectrodeConstraints.DensityMatrix".

As Nordland mentioned above, "ElectrodeConstraints.DensityMatrix" instead of "ElectrodeConstraints.Off" should be used when you calculate the voltage drop.
But in some cases such as "Au-DTB-Au", you might get less convergence of SCF with "ElectrodeConstraints.DensityMatrix" (More correctly, the electronic structure that seems to be strange is obtained).
Then, you had better use "ElectrodeConstraints.RealSpaceDensity" instead of "ElectrodeConstraints.DensityMatrix".

I have been build all the two-probe system as you post, but I could't get none of the beautiful pictures of voltage drop as your examples,where is my problem?
I have been notice the use of "ElectrodeConstraints.DensityMatrix" instead of "ElectrodeConstraints.Off" when I calculate the voltage drop.

The append files is my au(111) scripts and outputs,all computation performed in VNL 2008.10.

  I have been modify the scripts  that upload before because the wrong monkhorst_pack_parameters,but also the same results. And upload the modified scripts and results.

I also  test the FFT methods,but also the same results,and I can't get nori's beautiful  image!Why?

Please notice the difference of unit between me and nori's image.
and the the final scripts that made it all work out as same that I have been send it above ,but only modify the k-point sampling  to (6,6,100).as nori said.

39

Scripts, Tutorials and Applications / Re: Script for calculating the voltage drop.

« on: April 23, 2010, 15:31 »

Thanks nori and Anders Blom，the last voltage-drop I get is same as nori's.
After my  handling, I get the beautiful image as below!

Thanks again!
Wish good luck!

40

Scripts, Tutorials and Applications / Re: Script for calculating the voltage drop.

« on: April 23, 2010, 06:00 »

I regard your voltage drop as qualitatively the same as mine.
Perhaps the quantitative difference comes from k-point sampling.
I couldn't find out the script used for the calculation in my hard disc, so that I'm not sure precise k-point sampling in my calculation.
However, it would probably not be (10,10,10) but like (6,6,100).
 

I also test the k-point sampling  like (6,6,100)and even better ,but he same results happen? And I am very interesting to know how can I get the very beautiful voltage-drop image as you.

41

Scripts, Tutorials and Applications / Re: Script for calculating the voltage drop.

« on: April 22, 2010, 10:13 »

I offer some calculation examples of voltage drop.
All calculations were done with the algorithm "ElectrodeConstraints.DensityMatrix".

As Nordland mentioned above, "ElectrodeConstraints.DensityMatrix" instead of "ElectrodeConstraints.Off" should be used when you calculate the voltage drop.
But in some cases such as "Au-DTB-Au", you might get less convergence of SCF with "ElectrodeConstraints.DensityMatrix" (More correctly, the electronic structure that seems to be strange is obtained).
Then, you had better use "ElectrodeConstraints.RealSpaceDensity" instead of "ElectrodeConstraints.DensityMatrix".

I have been build all the two-probe system as you post, but I could't get none of the beautiful pictures of voltage drop as your examples,where is my problem?
I have been notice the use of "ElectrodeConstraints.DensityMatrix" instead of "ElectrodeConstraints.Off" when I calculate the voltage drop.

The append files is my au(111) scripts and outputs,all computation performed in VNL 2008.10.

  I have been modify the scripts  that upload before because the wrong monkhorst_pack_parameters,but also the same results. And upload the modified scripts and results.

I also  test the FFT methods,but also the same results,and I can't get nori's beautiful  image!Why?

42

General Questions and Answers / Re: How can I bulid such two-probe system as the append files?

« on: April 18, 2010, 10:48 »

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!

43

General Questions and Answers / Re: what's happen when I compute the voltage drop?

« on: April 18, 2010, 04:54 »

Another possible reason is that you choose multi-grid solver.
If my memory is right, strange voltage drop is obtained with multi-grid solver of 2008.10 in some 2probe systems.

Could you try the scripts attached in this post?
With these scripts, calculations with "ElectrodeConstraints.DensityMatrix" and FFT solver are executed.

I understand what you mean.  I use your scripts compute in VNL 2008.10, and I get the result as the append files.
And I wonder are there correct?  How can we judge the image of voltage-drop and the data of the the average potential along Z axiz is correct?

44

Scripts, Tutorials and Applications / Re: Import/visualize VASP geometries in VNL 2010.02

« on: April 18, 2010, 04:07 »

 

Beautiful work, it's very useful !
 Thanks a lot !

45

General Questions and Answers / Re: what's happen when I compute the voltage drop?

« on: April 17, 2010, 17:12 »

The bug is fixed in 2008.10 so you should always use 2008.10.
Have you changed the ElectrodeConstraint?
It seems that "ElectrodeConstraints.RealSpaceDensity" is still selected in "VNL2008.10.png"...

yes, my computation  all performed with "ElectrodeConstraints.RealSpaceDensity".

and I am so sorry that I can't find the best choice you said " "ElectrodeConstraints.DensityMatrix"