Topics

1

General Questions and Answers / BandStructure - Extended Huckel Method

« on: May 2, 2014, 06:30 »

Good day ATK user,

I have been following this tutorial:
http://www.quantumwise.com/documents/tutorials/ATK-11.8/BasicGrapheneTutorial/index.html/chap.armchairribbon.html

At the end, they recommended to redo the calculations for different types of ribbons (armchair/zigzag) and for different widths because band gap is strongly dependent on both factors!

I have been testing upon Na-AGNR (Na ranging from 4 to 13) and indeed the band gap varied as expected. I could even recongnize the 3m, 3m+1 and 3m-1 group.

When I try to analyze the same AGNRs but repeted 15 times in the z direction, I get something strange, or at least something that I do not understand. I get too many straight and almost parallel lines (see attached 1 and 2). Also the Ef is not at the center anymore. Can you help me understanding the physical meaning of this?

btw the bandStructure is calculated using Extended Huckel method; to what extent can I trust these results? If for example, I have distorted edges or vacancies,  can I still trust the results obtained?

The attachments represent the Band Structure for a 4AGNRx15.


Many many thanks,
Luis

2

General Questions and Answers / ZGNR with withds from 4 to 9

« on: March 25, 2014, 18:48 »

I am reading a paper where the autor says that he constructed ZGNR with widhts ranging from 4 to 9 accross the ribbon. VNL is not allowing me to do that. It only allows me to create zGNR with odd number of lines accross the ribbon, for example 4, 6, 8, 10, etc.

Am I doing something wrong, or am I missunderstanding what the author on this papers is saying?

Regards,
Luis

3

General Questions and Answers / Number of bands to plot

« on: March 14, 2014, 21:25 »

Hello everyone,

Do you know guys how many bands should I plot when computing the BandStructure? When I plot all bands I get a graph that I cannot understand and I have seen some paper that they plot only a finite number of bands.

Regards,
Luis

4

General Questions and Answers / Plotting postcar from vasp with VNL

« on: March 14, 2014, 17:18 »

Hi guys,

Can you please give me some information about how to plot the POSCAR from VASP with VNL?


Regards,
Luis

5

General Questions and Answers / Tight binding - calculation

« on: February 17, 2014, 09:45 »

I was said that geometry optimization had to be carried out by DFT. Should I calculate DOS and Band Structure with tight binding? or should I continue using the same framework?

Regards,
Luis

6

General Questions and Answers / How to set the mesh grid cutoff

« on: February 14, 2014, 17:36 »

Hi guys,

Can someone explains to me what Grid Mesh cutoff is for?? VNL is giving me default values. I do not know if I should Increase or decrease it value? Or should I optimize it the same way I optimize the k-point? Does it depends on the number of atoms my nanoribbon has??

Thanks in advance for your help.

Regards,
Luis

7

General Questions and Answers / DOS and bandstructure of a ZGNR

« on: February 11, 2014, 14:33 »

Can you kindly help me understand my results for bulk zigzag Chirality? Could be that I am not reading the results properly

I analysed the DOS and Band Structure of AGNR, obtaining results quite reasonable. However, when I carried out the same analyses for ZGNR I got results that does not make any sense to me; there are many lines crossing.

I followed this tutorial (http://www.quantumwise.com/documents/tutorials/latest/GrapheneBloch/index.html/chap.bandstructure.html) and I expected to see something close to that.


This is what I did .....

(1) Relaxed a pristine 8ZGNR 12 times repeated

Calculator: DFT
k-point mesh: 1x1x9
Grid mesh cut-off: 75 Hartree
Basis set: DoubleZetaPolazired for both Hydrogen and Carbon

(2) On the border of the 8ZGNR a Stone-Wale defect was inserted

The SW defect was inserted at the middle of the ribbon along the z direction


------------------X-------------------



---------------------------------------


(3) Relaxed the nanoribbon with the defect included

I allowed to move the atoms that were at maximum 6AA around the defect.

(4) Calculated the DOS and Band structure

Calculator: DFT
k-point mesh: 1x1x21
Grid mesh cut-off: 75 Hartree
Basis set: DoubleZetaPolazired for both Hydrogen and Carbon

DOS block
k-point grid 1x1x21
Energy Zero: Fermi Level
Bands above the Fermi level: All

BandStructure block
points per segment: 200
Brillioum zone route: G, Z

As I understand, if I insert a defect on the border of a ZigZag Nanoribbon (as specified above), the bandgap should increase. In my case however, this is not happening.

I have no clue about what could the problem be. I attach the graphs of my simulations.


Regards,
Luis

8

General Questions and Answers / Geometry optimization

« on: January 14, 2014, 09:23 »

After relaxing a 8-ZGNR of approx 2.8nm long (device) with DFT I was wondering in what way could I check if my optimization is ok. I compared the initial and the final coordinates, but I do not think that is all. Can you guide me please?.

Also, I unckecked "No SCF" for DFT. Is that correct?. In the tutorial online relaxation is carried out the Huckel model and they unckek it. I do not really understand why they do that.

Thanks in advance,
Luis

9

General Questions and Answers / Geometry optimization 3AGNR repeated 9 times in the z direction

« on: January 9, 2014, 01:19 »

Hello all,

I am training myself on Graphen nanoribbon. So my first goal was to optimize a 3-AGNR repeated 9 times. I kindly ask you to check if what I have done until now is Ok. You can see the pictures inside the attached document because I still do not know how to insert them within the text.

FIRST STEP: Create a basic 3-AGNR (this structure is not repeated in the z direction)

I created this nanoribbon with the help of VNL following tutorials on youtube. See figure 1.

SECOND STEP: Find the optimal k-point mesh for the 3AGNR

I found the optimal k-point mesh for the nanoribbon. In figure 2 you can see how the energy converges to -1008.39972 eV for 1x1x18 mesh configuration. I have chosen 18 even though the system seems (at least visually) to converge at 9. From 18 onward the energy does not change at all, it remains the same even to the 5th decimal point. AM I CORRECT?

THIRD STEP: optimizing the basic 3-AGN

Again, following tutorials on youtube I set ATK as shown in figure 3 for the Geometry optimization. I did not change much but the k-point configuration to 1x1x18 in the new calculator tool; the rest was left as default (ANY ADVISE HERE?). In the geometry optimization tool I only changed:

Maximum Force to 0.005 eV/A
Maximum stress to 0.005 eV/A
Maximum step size to 0.1 A

I understand that this will improve the precision of the optimization (ANY DRAWBACK ABOUT IT) The rest was left as default.

FOURTH STEP: Create an extended 3-AGNR (the basic 3-AGNR is repeated 9 times in the z direction)

 I re-inserted the just optimized 3-AGNR into the Builder tool of VNL and asked it to repeat this structure 9 times (Figure 4).

FIFTH STEP: Optimize the extended 3-AGNR

I repeated the same procedure as in THIRD STEP, only changing the k-point configuration to 1x1x2. I read that I calculate the k-points only once and then is only matter of dividing them. What I did was 18/9 = 2. However, because I am very curious about this new topic I desided to check againd the k-points configuration. I find out that it did not converge (to the 5th decimal point as for the basic 3-AGNR) at 2 but 3. CAN YOU PLEASE EXPLAIN WHY IT HAPPENS?

I want to repeat  this procedure (if everything is ok) for a longer and wider nanoribbon in which I can introduce SW defect and study different properties. I will very appreciate your suggestions or comments.


Regards,
Luis M. Vilamagua

10

General Questions and Answers / ultrafast Brenner potential accuracy

« on: December 17, 2013, 14:56 »

Guys,

Should I trust the geometry optimization carried out by the ultrafast "brenner potential" of which quantumWise enjoys?  According to this tutorial (http://www.youtube.com/watch?v=t3xJNqP4X04) Brenner potential works very well for carbon atoms (which is my case; I have a graphene nanoribbon with only one SW defect  inserted in the middle).

I tried to carry out geometry optimization as it is shown in this tutorial (http://quantumwise.com/publications/tutorials/mini-tutorials/190-reconstruction-of-the-si-100-surface-a-geometry-optimization-study-with-atk) but only leaving one atom to move at will is taking too long (half a day).

The enormous time difference of both methods is making me hesitate about using Brenner potentials.

Thanks in advance
Luis

11

General Questions and Answers / K points for monolayer graphene nanoribbons

« on: December 7, 2013, 11:06 »

Dear everyone,

I have to optimize a monolayer graphene nanoribbon (i.e. 1nm wide and 3 nm long) structure before putting defects (like SW, vacancies, dislocations, etc.) on it. I was advices to carry out the k-point mesh optimization first (the correct choice of this mesh will apparently minimize the computing time and also get precise results -- correct me if I am wrong). For doing this, I found out that I should calculate the "total energy" of the system for different meshes and then see for which mesh the energy converges.  But with 3 number I can have 1000 different conbinations. What are the values I should start with, for example, 3x3x5, 5x5x3, 1x1x1, 1x1x5??? By the way, finding the "total energy" of the system in QuantumWise means to use the "total energy" tool calculator under analysis in the script?

Any advice will be well apreciated. I am very very new with this topic.

Thank in advance,
Luis

12

General Questions and Answers / K points for graphene nanoribbon

« on: November 21, 2013, 15:07 »

Hi everyone,

I need to work with graphene nanoribbon (AGNR and ZGNR) and I was advices to optimize the primitive structure, find the adecuate K-points for it and then expand the nanoribbon.

Unfortunately, I do not know how to do this process and I think there should be a rule of thumb or papers that can allow me to get those point in an easier way. Can someone help me with this???

Thanks in advance for your help,
Luis